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- Committer: Package Import Robot
- Author(s): Daniel Leidert
- Date: 2014-01-18 20:07:16 UTC
- mfrom: (1.1.8)
- Revision ID: package-import@ubuntu.com-20140118200716-whsmcg7fa1eyqecq
Tags: 140117-1
New upstream release.
- files added:
- src/plproj.cpp
- files modified:
- Makefile
added
removed
src/moltools.cpp
1
/*****************************************************************************
2
TRAVIS - Trajectory Analyzer and Visualizer
3
http://www.travis-analyzer.de/
4
5
Copyright (c) 2009-2013 Martin Brehm
6
2012-2013 Martin Thomas
7
8
This file written by Martin Brehm.
9
10
This program is free software: you can redistribute it and/or modify
11
it under the terms of the GNU General Public License as published by
12
the Free Software Foundation, either version 3 of the License, or
13
(at your option) any later version.
14
15
This program is distributed in the hope that it will be useful,
16
but WITHOUT ANY WARRANTY; without even the implied warranty of
17
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18
GNU General Public License for more details.
19
20
You should have received a copy of the GNU General Public License
21
along with this program. If not, see <http://www.gnu.org/licenses/>.
22
*****************************************************************************/
23
24
#include "moltools.h"
25
#include "travis.h"
26
#include "maintools.h"
27
28
29
CAtom::CAtom()
30
{
31
m_pElement = NULL;
32
m_bExclude = false;
33
m_pMergedTo = NULL;
34
m_iIndex = -1;
35
}
36
37
38
CAtom::~CAtom()
39
{
40
}
41
42
43
CVirtualAtom::CVirtualAtom()
44
{
45
m_faWeight.SetName("CVirtualAtom::m_faWeight");
46
}
47
48
49
CVirtualAtom::~CVirtualAtom()
50
{
51
}
52
53
54
CMolecule::CMolecule()
55
{
56
m_iWannierCount = 0;
57
m_sName = NULL;
58
m_fCharge = 0;
59
m_bPseudo = false;
60
m_bChargesAssigned = false;
61
62
m_baAtomIndex.SetName("CMolecule::m_baAtomIndex");
63
m_waAtomCount.SetName("CMolecule::m_waAtomCount");
64
m_laSingleMolIndex.SetName("CMolecule::m_laSingleMolIndex");
65
m_laVirtualAtoms.SetName("CMolecule::m_laVirtualAtoms");
66
m_oaNewNumbers.SetName("CMolecule::m_oaNewNumbers");
67
m_oaRingAtomTypes.SetName("CMolecule::m_oaRingAtomTypes");
68
m_oaRingAtoms.SetName("CMolecule::m_oaRingAtoms");
69
m_oaCharges.SetName("CMolecule::m_oaCharges");
70
}
71
72
73
CMolecule::~CMolecule()
74
{
75
if (m_sName != NULL)
76
{
77
delete[] m_sName;
78
m_sName = NULL;
79
}
80
}
81
82
83
CMolAtom::CMolAtom()
84
{
85
m_oaBonds.SetName("CMolAtom::m_oaBonds");
86
}
87
88
89
CMolAtom::~CMolAtom()
90
{
91
}
92
93
94
CSingleMolecule::CSingleMolecule()
95
{
96
m_bPseudo = false;
97
98
m_oaBondGroups.SetName("CSingleMolecule::m_oaBondGroups");
99
m_oaBonds.SetName("CSingleMolecule::m_oaBonds");
100
m_oaAngleGroups.SetName("CSingleMolecule::m_oaAngleGroups");
101
m_oaAngles.SetName("CSingleMolecule::m_oaAngles");
102
m_oaRings.SetName("CSingleMolecule::m_oaRings");
103
m_laBonds.SetName("CSingleMolecule::m_laBonds");
104
m_laWannier.SetName("CSingleMolecule::m_laWannier");
105
m_oaAtomOffset.SetName("CSingleMolecule::m_oaAtomOffset");
106
m_oaMolAtoms.SetName("CSingleMolecule::m_oaMolAtoms");
107
m_baAtomIndex.SetName("CSingleMolecule::m_baAtomIndex");
108
}
109
110
111
CSingleMolecule::~CSingleMolecule()
112
{
113
}
114
115
116
CADF::CADF()
117
{
118
m_pADF = NULL;
119
m_oaVectors.SetName("CADF::m_oaVectors");
120
m_faACF.SetName("CADF::m_faACF");
121
m_faMinMaxAngle.SetName("CADF::m_faMinMaxAngle");
122
}
123
124
125
CADF::~CADF()
126
{
127
}
128
129
130
CDDF::CDDF()
131
{
132
m_bRotate = false;
133
m_oaVectors.SetName("CDDF::m_oaVectors");
134
m_faLastData.SetName("CDDF::m_faLastData");
135
m_laRotation.SetName("CDDF::m_laRotation");
136
m_faACF.SetName("CDDF::m_faACF");
137
}
138
139
140
CDDF::~CDDF()
141
{
142
}
143
144
145
CMSD::CMSD()
146
{
147
m_oaCache.SetName("CMSD::m_oaCache");
148
}
149
150
151
CMSD::~CMSD()
152
{
153
}
154
155
156
CVHDF::CVHDF()
157
{
158
m_sName = NULL;
159
m_sShortName = NULL;
160
m_pVHDF = NULL;
161
m_oaVectors.SetName("CVHDF::m_oaVectors");
162
}
163
164
165
CVHDF::~CVHDF()
166
{
167
if (m_sName != NULL)
168
{
169
delete[] m_sName;
170
m_sName = NULL;
171
}
172
if (m_sShortName != NULL)
173
{
174
delete[] m_sShortName;
175
m_sShortName = NULL;
176
}
177
if (m_pVHDF != NULL)
178
{
179
delete m_pVHDF;
180
m_pVHDF = NULL;
181
}
182
}
183
184
185
CRDF::CRDF()
186
{
187
m_fDist = NULL;
188
m_pRDF = NULL;
189
m_bProbDens = false;
190
m_faMinMaxDist.SetName("CRDF::m_faMinMaxDist");
191
m_oaVectors.SetName("CRDF::m_oaVectors");
192
m_faACF.SetName("CRDF::m_faACF");
193
}
194
195
196
CPlDF::CPlDF()
197
{
198
m_pPlDF = NULL;
199
m_oaVectors.SetName("CPlDF::m_oaVectors");
200
m_faACF.SetName("CPlDF::m_faACF");
201
}
202
203
204
CLiDF::CLiDF()
205
{
206
m_pLiDF = NULL;
207
m_oaVectors.SetName("CLiDF::m_oaVectors");
208
m_faACF.SetName("CLiDF::m_faACF");
209
}
210
211
212
CRDF::~CRDF()
213
{
214
if (m_sName != NULL)
215
{
216
delete[] m_sName;
217
m_sName = NULL;
218
}
219
if (m_sShortName != NULL)
220
{
221
delete[] m_sShortName;
222
m_sShortName = NULL;
223
}
224
if (m_fDist != NULL)
225
{
226
delete[] m_fDist;
227
m_fDist = NULL;
228
}
229
if (m_pRDF != NULL)
230
{
231
delete m_pRDF;
232
m_pRDF = NULL;
233
}
234
if (m_faData != NULL)
235
{
236
delete[] m_faData;
237
m_faData = NULL;
238
}
239
}
240
241
242
CDensDF::CDensDF()
243
{
244
m_pDensDF = NULL;
245
}
246
247
248
CDensDF::~CDensDF()
249
{
250
if (m_sName != NULL)
251
{
252
delete[] m_sName;
253
m_sName = NULL;
254
}
255
if (m_sShortName != NULL)
256
{
257
delete[] m_sShortName;
258
m_sShortName = NULL;
259
}
260
if (m_pDensDF != NULL)
261
{
262
delete m_pDensDF;
263
m_pDensDF = NULL;
264
}
265
}
266
267
268
CVDF::CVDF()
269
{
270
m_faACF.SetName("CVDF::m_faACF");
271
}
272
273
274
CVDF::~CVDF()
275
{
276
}
277
278
279
CDipDF::CDipDF()
280
{
281
m_faACF.SetName("CDipDF::m_faACF");
282
}
283
284
285
CDipDF::~CDipDF()
286
{
287
}
288
289
290
CSDF::CSDF()
291
{
292
m_pCutPlane = NULL;
293
m_fPosCounter = 0;
294
m_fAtom2PosX = 0;
295
m_fAtom3PosX = 0;
296
m_fAtom3PosY = 0;
297
}
298
299
300
CSDF::~CSDF()
301
{
302
}
303
304
305
CCDF::CCDF()
306
{
307
m_bAxisDivide = false;
308
}
309
310
311
CCDF::~CCDF()
312
{
313
}
314
315
316
CConditionSubGroup::CConditionSubGroup()
317
{
318
m_fPassed = 0;
319
m_fTotal = 0;
320
m_oaConditions.SetName("CConditionSubGroup::m_oaConditions");
321
}
322
323
324
CConditionSubGroup::~CConditionSubGroup()
325
{
326
}
327
328
329
CConditionGroup::CConditionGroup()
330
{
331
m_pTable = NULL;
332
m_bInactive = false;
333
m_fPassed = 0;
334
m_fTotal = 0;
335
m_iPassCounter = NULL;
336
m_bAlwaysTrue = NULL;
337
m_oaConditionSubGroups.SetName("CConditionGroup::m_oaConditionSubGroups");
338
}
339
340
341
CConditionGroup::~CConditionGroup()
342
{
343
}
344
345
346
bool ContainsDigit(const char *s)
347
{
348
if (strcspn(s,"0123456789") != strlen(s))
349
return true;
350
return false;
351
}
352
353
354
void ReplaceDigits(char *s)
355
{
356
char buf[32];
357
char *p, *q;
358
bool b;
359
360
p = s;
361
q = buf;
362
b = false;
363
while (*p != 0)
364
{
365
if (b)
366
{
367
switch(*p)
368
{
369
case '1': *q = 'a'; break;
370
case '2': *q = 'b'; break;
371
case '3': *q = 'c'; break;
372
case '4': *q = 'd'; break;
373
case '5': *q = 'e'; break;
374
case '6': *q = 'f'; break;
375
case '7': *q = 'g'; break;
376
case '8': *q = 'h'; break;
377
case '9': *q = 'i'; break;
378
case '0': *q = 'z'; break;
379
default: *q = *p;
380
}
381
} else
382
{
383
switch(*p)
384
{
385
case '1': b = true; *q = '_'; q++; *q = 'a'; break;
386
case '2': b = true; *q = '_'; q++; *q = 'b'; break;
387
case '3': b = true; *q = '_'; q++; *q = 'c'; break;
388
case '4': b = true; *q = '_'; q++; *q = 'd'; break;
389
case '5': b = true; *q = '_'; q++; *q = 'e'; break;
390
case '6': b = true; *q = '_'; q++; *q = 'f'; break;
391
case '7': b = true; *q = '_'; q++; *q = 'g'; break;
392
case '8': b = true; *q = '_'; q++; *q = 'h'; break;
393
case '9': b = true; *q = '_'; q++; *q = 'i'; break;
394
case '0': b = true; *q = '_'; q++; *q = 'z'; break;
395
default: *q = *p;
396
}
397
}
398
p++;
399
q++;
400
}
401
*q = 0;
402
strcpy(s,buf);
403
}
404
405
406
void xAddAtom(const char *s)
407
{
408
BTIN;
409
int z;
410
CAtom *a;
411
char buf[64];
412
413
if (g_oaAtoms.GetSize() >= 254)
414
{
415
eprintf("More than 254 different atom types not supported.\n");
416
return;
417
}
418
419
strcpy(buf,s);
420
ReplaceDigits(buf);
421
422
// printf("AddAtom: \"%s\".\n",s);
423
for (z=0;z<g_oaAtoms.GetSize();z++)
424
{
425
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName)==0)
426
{
427
((CAtom*)g_oaAtoms[z])->m_iCount++;
428
BTOUT;
429
return;
430
}
431
}
432
if (ContainsDigit(s))
433
eprintf("Digits in element labels not allowed. Renaming %s to %s.\n",s,buf);
434
435
try { a = new CAtom(); } catch(...) { a = NULL; }
436
if (a == NULL) NewException((double)sizeof(CAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
437
438
a->m_iIndex = g_oaAtoms.GetSize();
439
strcpy(a->m_sName,buf);
440
if (islower(a->m_sName[0]))
441
a->m_sName[0] = toupper(a->m_sName[0]);
442
if (strlen(a->m_sName) > 1)
443
if (isupper(a->m_sName[1]))
444
a->m_sName[1] = tolower(a->m_sName[1]);
445
a->m_iCount = 1;
446
/* if (s[0] != '#')
447
{*/
448
a->m_pElement = FindElement(buf,false);
449
if (a->m_pElement == NULL)
450
{
451
try { a->m_pElement = new CElement(); } catch(...) { a->m_pElement = NULL; }
452
if (a->m_pElement == NULL) NewException((double)sizeof(CElement),__FILE__,__LINE__,__PRETTY_FUNCTION__);
453
454
try { a->m_pElement->m_sLabel = new char[strlen(a->m_sName)+1]; } catch(...) { a->m_pElement->m_sLabel = NULL; }
455
if (a->m_pElement->m_sLabel == NULL) NewException((double)(strlen(a->m_sName)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
456
457
strcpy(a->m_pElement->m_sLabel,a->m_sName);
458
}
459
/* a->m_fMass = AtomMass(s);
460
a->m_fRadius = AtomRadius(s);
461
a->m_iOrd = AtomOrd(s);*/
462
// a->m_fVDWRadius = AtomVDWRadius(s);
463
/* } else
464
{
465
a->m_fMass = 0.0f;
466
a->m_fRadius = 0.0f;
467
a->m_iOrd = 0;
468
// a->m_fVDWRadius = 0.0f;
469
}*/
470
g_oaAtoms.Add(a);
471
// g_pAtoms[g_iElementCount].Offset = offset;
472
// printf("Fuege Atom %s an Stelle %d neu hinzu. Der Offset ist %d.\n",s,g_iAtomCount,offset);
473
// g_iElementCount++;
474
BTOUT;
475
}
476
477
478
void CSingleMolecule::Dump()
479
{
480
BTIN;
481
int z, z2;
482
mprintf("### Single Molecule Dump ###\n");
483
mprintf("%d Elemente.\n",m_baAtomIndex.GetSize());
484
for (z=0;z<m_baAtomIndex.GetSize();z++)
485
{
486
mprintf(" * Element %d: %s. %d Vertreter *\n Atome ",z+1,((CAtom*)g_oaAtoms[m_baAtomIndex[z]])->m_sName,((CxIntArray*)m_oaAtomOffset[z])->GetSize());
487
for (z2=0;z2<((CxIntArray*)m_oaAtomOffset[z])->GetSize();z2++)
488
{
489
mprintf("%d",((CxIntArray*)m_oaAtomOffset[z])->GetAt(z2));
490
if (z2 < ((CxIntArray*)m_oaAtomOffset[z])->GetSize()-1)
491
mprintf(", ");
492
}
493
mprintf("\n");
494
}
495
BTOUT;
496
}
497
498
499
void CMolecule::Dump()
500
{
501
BTIN;
502
int z;
503
mprintf("### Molecule Type Dump ###\n");
504
mprintf("%d Elemente.\n",m_baAtomIndex.GetSize());
505
for (z=0;z<m_baAtomIndex.GetSize();z++)
506
mprintf(" * Element %d: %s. %d Vertreter *\n",z+1,((CAtom*)g_oaAtoms[m_baAtomIndex[z]])->m_sName,m_waAtomCount[z]);
507
BTOUT;
508
}
509
510
511
void CADF::BuildName()
512
{
513
BTIN;
514
int z, z2;
515
char tmp[256];
516
CAtomGroup *ag;
517
518
tmp[0] = 0;
519
if (m_iDeriv != 0)
520
sprintf(tmp,"deriv%d_",m_iDeriv);
521
for (z2=0;z2<m_oaVectors.GetSize()/6;z2++)
522
{
523
for (z=0;z<2;z++)
524
{
525
strcat(tmp,"[");
526
if (m_iVecType[z] == 0) // Position
527
{
528
if (m_bOrtho[z])
529
{
530
/* if (m_bSameFoot && (z == 1))
531
ag = (CAtomGroup*)m_oaVectors[z2*6];
532
else */ag = (CAtomGroup*)m_oaVectors[z2*6+z*3];
533
strcat(tmp,ag->m_sName);
534
if (m_iRefOrSec[z][0])
535
strcat(tmp,"o_");
536
else strcat(tmp,"r_");
537
strcat(tmp,((CAtomGroup*)m_oaVectors[z2*6+z*3+1])->m_sName);
538
if (m_iRefOrSec[z][1])
539
strcat(tmp,"o_");
540
else strcat(tmp,"r_");
541
strcat(tmp,((CAtomGroup*)m_oaVectors[z2*6+z*3+2])->m_sName);
542
if (m_iRefOrSec[z][2])
543
strcat(tmp,"o");
544
else strcat(tmp,"r");
545
} else
546
{
547
/* if (m_bSameFoot && (z == 1))
548
ag = (CAtomGroup*)m_oaVectors[z2*6];
549
else */ag = (CAtomGroup*)m_oaVectors[z2*6+z*3];
550
strcat(tmp,ag->m_sName);
551
if (m_iRefOrSec[z][0])
552
strcat(tmp,"o_");
553
else strcat(tmp,"r_");
554
strcat(tmp,((CAtomGroup*)m_oaVectors[z2*6+z*3+1])->m_sName);
555
if (m_iRefOrSec[z][1])
556
strcat(tmp,"o");
557
else strcat(tmp,"r");
558
}
559
} else if (m_iVecType[z] == 1) // Dipol
560
{
561
strcat(tmp,"dip_");
562
strcat(tmp,(m_iRefOrSec[z][0]!=0)?((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName:((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
563
} else if (m_iVecType[z] == 2) // Geschwindigkeit
564
{
565
strcat(tmp,"vel_");
566
strcat(tmp,((CAtomGroup*)m_oaVectors[z*3])->m_sName);
567
} else if (m_iVecType[z] == 3) // Kraft
568
{
569
strcat(tmp,"frc_");
570
strcat(tmp,((CAtomGroup*)m_oaVectors[z*3])->m_sName);
571
}
572
if (z == 0)
573
strcat(tmp,"]-");
574
else strcat(tmp,"]");
575
}
576
if (z2<(m_oaVectors.GetSize()/6)-1)
577
strcat(tmp,"_");
578
}
579
580
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
581
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
582
583
strcpy(m_sShortName,tmp);
584
if (m_iShowMol != -1)
585
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
586
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
587
strcat(tmp,m_sShortName);
588
589
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
590
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
591
592
strcpy(m_sName,tmp);
593
BTOUT;
594
}
595
596
597
void CPlDF::BuildName()
598
{
599
BTIN;
600
char tmp[256];
601
CAtomGroup *ag;
602
603
tmp[0] = 0;
604
605
strcat(tmp,"[");
606
if (m_bNormal)
607
{
608
ag = (CAtomGroup*)m_oaVectors[0];
609
strcat(tmp,ag->m_sName);
610
if (m_iRefOrSec[0])
611
strcat(tmp,"o_");
612
else strcat(tmp,"r_");
613
strcat(tmp,((CAtomGroup*)m_oaVectors[1])->m_sName);
614
if (m_iRefOrSec[1])
615
strcat(tmp,"o");
616
else strcat(tmp,"r");
617
} else
618
{
619
ag = (CAtomGroup*)m_oaVectors[0];
620
strcat(tmp,ag->m_sName);
621
if (m_iRefOrSec[0])
622
strcat(tmp,"o_");
623
else strcat(tmp,"r_");
624
strcat(tmp,((CAtomGroup*)m_oaVectors[1])->m_sName);
625
if (m_iRefOrSec[1])
626
strcat(tmp,"o_");
627
else strcat(tmp,"r_");
628
strcat(tmp,((CAtomGroup*)m_oaVectors[2])->m_sName);
629
if (m_iRefOrSec[2])
630
strcat(tmp,"o");
631
else strcat(tmp,"r");
632
}
633
strcat(tmp,"]_");
634
strcat(tmp,((CAtomGroup*)m_oaVectors[3])->m_sName);
635
if (m_iRefOrSec[3])
636
strcat(tmp,"o");
637
else strcat(tmp,"r");
638
639
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
640
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
641
642
strcpy(m_sShortName,tmp);
643
if (m_iShowMol != -1)
644
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
645
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
646
strcat(tmp,m_sShortName);
647
648
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
649
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
650
651
strcpy(m_sName,tmp);
652
BTOUT;
653
}
654
655
656
void CLiDF::BuildName()
657
{
658
BTIN;
659
char tmp[256];
660
CAtomGroup *ag;
661
662
tmp[0] = 0;
663
664
strcat(tmp,"[");
665
if (m_bNormal)
666
{
667
ag = (CAtomGroup*)m_oaVectors[0];
668
strcat(tmp,ag->m_sName);
669
if (m_iRefOrSec[0])
670
strcat(tmp,"o_");
671
else strcat(tmp,"r_");
672
strcat(tmp,((CAtomGroup*)m_oaVectors[1])->m_sName);
673
if (m_iRefOrSec[1])
674
strcat(tmp,"o_");
675
else strcat(tmp,"r_");
676
strcat(tmp,((CAtomGroup*)m_oaVectors[2])->m_sName);
677
if (m_iRefOrSec[2])
678
strcat(tmp,"o");
679
else strcat(tmp,"r");
680
} else
681
{
682
ag = (CAtomGroup*)m_oaVectors[0];
683
strcat(tmp,ag->m_sName);
684
if (m_iRefOrSec[0])
685
strcat(tmp,"o_");
686
else strcat(tmp,"r_");
687
strcat(tmp,((CAtomGroup*)m_oaVectors[1])->m_sName);
688
if (m_iRefOrSec[1])
689
strcat(tmp,"o");
690
else strcat(tmp,"r");
691
}
692
strcat(tmp,"]_");
693
strcat(tmp,((CAtomGroup*)m_oaVectors[3])->m_sName);
694
if (m_iRefOrSec[3])
695
strcat(tmp,"o");
696
else strcat(tmp,"r");
697
698
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
699
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
700
701
strcpy(m_sShortName,tmp);
702
if (m_iShowMol != -1)
703
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
704
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
705
strcat(tmp,m_sShortName);
706
707
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
708
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
709
710
strcpy(m_sName,tmp);
711
BTOUT;
712
}
713
714
715
void CDDF::BuildName()
716
{
717
BTIN;
718
int z;
719
char tmp[256];
720
CAtomGroup *ag;
721
722
tmp[0] = 0;
723
if (m_iDeriv != 0)
724
sprintf(tmp,"deriv%d_",m_iDeriv);
725
for (z=0;z<3;z++)
726
{
727
strcat(tmp,"[");
728
if (m_bOrtho[z])
729
{
730
ag = (CAtomGroup*)m_oaVectors[z*3];
731
strcat(tmp,ag->m_sName);
732
if (m_iRefOrSec[z][0])
733
strcat(tmp,"o_");
734
else strcat(tmp,"r_");
735
strcat(tmp,((CAtomGroup*)m_oaVectors[z*3+1])->m_sName);
736
if (m_iRefOrSec[z][1])
737
strcat(tmp,"o_");
738
else strcat(tmp,"r_");
739
strcat(tmp,((CAtomGroup*)m_oaVectors[z*3+2])->m_sName);
740
if (m_iRefOrSec[z][2])
741
strcat(tmp,"o");
742
else strcat(tmp,"r");
743
} else
744
{
745
ag = (CAtomGroup*)m_oaVectors[z*3];
746
strcat(tmp,ag->m_sName);
747
if (m_iRefOrSec[z][0])
748
strcat(tmp,"o_");
749
else strcat(tmp,"r_");
750
strcat(tmp,((CAtomGroup*)m_oaVectors[z*3+1])->m_sName);
751
if (m_iRefOrSec[z][1])
752
strcat(tmp,"o");
753
else strcat(tmp,"r");
754
}
755
if (z < 2)
756
strcat(tmp,"]-");
757
else strcat(tmp,"]");
758
}
759
760
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
761
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
762
763
strcpy(m_sShortName,tmp);
764
if (m_iShowMol != -1)
765
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
766
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
767
strcat(tmp,m_sShortName);
768
769
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
770
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
771
772
strcpy(m_sName,tmp);
773
BTOUT;
774
}
775
776
777
void CDipDF::BuildName()
778
{
779
BTIN;
780
char tmp[256];
781
782
tmp[0] = 0;
783
if (m_iDeriv != 0)
784
sprintf(tmp,"deriv%d_",m_iDeriv);
785
if (m_iRefOrSec)
786
sprintf(tmp,"%s",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
787
else sprintf(tmp,"%s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
788
789
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
790
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
791
792
strcpy(m_sName,tmp);
793
794
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
795
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
796
797
strcpy(m_sShortName,tmp);
798
BTOUT;
799
}
800
801
802
void CADF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
803
{
804
BXIN;
805
int z, z1t, z1a, z2t, z2a, z3t, z3a, z4t, z4a, z5t, z5a, z6t, z6a;
806
CAtomGroup *g1, *g2, *g3, *g4, *g5, *g6;
807
CxIntArray *a1, *a2, *a3, *a4, *a5, *a6;
808
809
vec->RemoveAll_KeepSize();
810
for (z=0;z<m_oaVectors.GetSize()/6;z++)
811
{
812
if (m_bOrtho[0])
813
{
814
g1 = (CAtomGroup*)m_oaVectors[z*6];
815
g2 = (CAtomGroup*)m_oaVectors[z*6+1];
816
g3 = (CAtomGroup*)m_oaVectors[z*6+2];
817
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
818
{
819
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
820
for (z1a=0;z1a<a1->GetSize();z1a++)
821
{
822
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
823
{
824
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
825
for (z2a=0;z2a<a2->GetSize();z2a++)
826
{
827
for (z3t=0;z3t<g3->m_baAtomType.GetSize();z3t++)
828
{
829
a3 = (CxIntArray*)g3->m_oaAtoms[z3t];
830
for (z3a=0;z3a<a3->GetSize();z3a++)
831
{
832
if (m_bOrtho[1])
833
{
834
/* if (m_bSameFoot)
835
g4 = g1;
836
else */g4 = (CAtomGroup*)m_oaVectors[z*6+3];
837
g5 = (CAtomGroup*)m_oaVectors[z*6+4];
838
g6 = (CAtomGroup*)m_oaVectors[z*6+5];
839
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
840
{
841
/* if (m_bSameFoot && (z4t != z1t))
842
continue;*/
843
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
844
for (z4a=0;z4a<a4->GetSize();z4a++)
845
{
846
/* if (m_bSameFoot && (z4a != z1a))
847
continue;*/
848
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
849
{
850
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
851
for (z5a=0;z5a<a5->GetSize();z5a++)
852
{
853
for (z6t=0;z6t<g6->m_baAtomType.GetSize();z6t++)
854
{
855
a6 = (CxIntArray*)g6->m_oaAtoms[z6t];
856
for (z6a=0;z6a<a6->GetSize();z6a++)
857
{
858
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
859
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
860
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
861
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
862
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
863
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
864
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
865
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
866
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
867
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
868
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
869
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
870
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
871
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
872
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
873
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
874
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
875
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
876
}
877
}
878
}
879
}
880
}
881
}
882
} else
883
{
884
/* if (m_bSameFoot)
885
g4 = g1;
886
else */g4 = (CAtomGroup*)m_oaVectors[z*6+3];
887
g5 = (CAtomGroup*)m_oaVectors[z*6+4];
888
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
889
{
890
/* if (m_bSameFoot && (z4t != z1t))
891
continue;*/
892
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
893
for (z4a=0;z4a<a4->GetSize();z4a++)
894
{
895
/* if (m_bSameFoot && (z4a != z1a))
896
continue;*/
897
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
898
{
899
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
900
for (z5a=0;z5a<a5->GetSize();z5a++)
901
{
902
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
903
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
904
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
905
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
906
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
907
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
908
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
909
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
910
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
911
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
912
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
913
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
914
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
915
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
916
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
917
vec->Add(0);
918
}
919
}
920
}
921
}
922
} // END IF NOT ORTHO[1]
923
}
924
}
925
}
926
}
927
}
928
}
929
} else
930
{
931
g1 = (CAtomGroup*)m_oaVectors[z*6];
932
g2 = (CAtomGroup*)m_oaVectors[z*6+1];
933
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
934
{
935
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
936
for (z1a=0;z1a<a1->GetSize();z1a++)
937
{
938
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
939
{
940
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
941
for (z2a=0;z2a<a2->GetSize();z2a++)
942
{
943
if (m_bOrtho[1])
944
{
945
/* if (m_bSameFoot)
946
g4 = g1;
947
else */g4 = (CAtomGroup*)m_oaVectors[z*6+3];
948
g5 = (CAtomGroup*)m_oaVectors[z*6+4];
949
g6 = (CAtomGroup*)m_oaVectors[z*6+5];
950
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
951
{
952
/* if (m_bSameFoot && (z4t != z1t))
953
continue;*/
954
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
955
for (z4a=0;z4a<a4->GetSize();z4a++)
956
{
957
/* if (m_bSameFoot && (z4a != z1a))
958
continue;*/
959
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
960
{
961
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
962
for (z5a=0;z5a<a5->GetSize();z5a++)
963
{
964
for (z6t=0;z6t<g6->m_baAtomType.GetSize();z6t++)
965
{
966
a6 = (CxIntArray*)g6->m_oaAtoms[z6t];
967
for (z6a=0;z6a<a6->GetSize();z6a++)
968
{
969
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
970
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
971
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
972
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
973
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
974
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
975
vec->Add(0);
976
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
977
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
978
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
979
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
980
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
981
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
982
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
983
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
984
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
985
}
986
}
987
}
988
}
989
}
990
}
991
} else
992
{
993
/* if (m_bSameFoot)
994
g4 = g1;
995
else */g4 = (CAtomGroup*)m_oaVectors[z*6+3];
996
g5 = (CAtomGroup*)m_oaVectors[z*6+4];
997
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
998
{
999
/* if (m_bSameFoot && (z4t != z1t))
1000
continue;*/
1001
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1002
for (z4a=0;z4a<a4->GetSize();z4a++)
1003
{
1004
/* if (m_bSameFoot && (z4a != z1a))
1005
continue;*/
1006
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
1007
{
1008
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
1009
for (z5a=0;z5a<a5->GetSize();z5a++)
1010
{
1011
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1012
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1013
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1014
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1015
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1016
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1017
vec->Add(0);
1018
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1019
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1020
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1021
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1022
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1023
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1024
vec->Add(0);
1025
}
1026
}
1027
}
1028
}
1029
} // END IF NOT ORTHO[1]
1030
}
1031
}
1032
}
1033
}
1034
}
1035
}
1036
BXOUT;
1037
}
1038
1039
1040
/* Mega abartig !!!! */
1041
void CDDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
1042
{
1043
BXIN;
1044
int z, z1t, z1a, z2t, z2a, z3t, z3a, z4t, z4a, z5t, z5a, z6t, z6a, z7t, z7a, z8t, z8a, z9t, z9a;
1045
CAtomGroup *g1, *g2, *g3, *g4, *g5, *g6, *g7, *g8, *g9;
1046
CxIntArray *a1, *a2, *a3, *a4, *a5, *a6, *a7, *a8, *a9;
1047
1048
vec->RemoveAll_KeepSize();
1049
for (z=0;z<m_oaVectors.GetSize()/9;z++)
1050
{
1051
if (m_bOrtho[0])
1052
{
1053
g1 = (CAtomGroup*)m_oaVectors[z*9];
1054
g2 = (CAtomGroup*)m_oaVectors[z*9+1];
1055
g3 = (CAtomGroup*)m_oaVectors[z*9+2];
1056
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1057
{
1058
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1059
for (z1a=0;z1a<a1->GetSize();z1a++)
1060
{
1061
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1062
{
1063
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1064
for (z2a=0;z2a<a2->GetSize();z2a++)
1065
{
1066
for (z3t=0;z3t<g3->m_baAtomType.GetSize();z3t++)
1067
{
1068
a3 = (CxIntArray*)g3->m_oaAtoms[z3t];
1069
for (z3a=0;z3a<a3->GetSize();z3a++)
1070
{
1071
if (m_bOrtho[1])
1072
{
1073
g4 = (CAtomGroup*)m_oaVectors[z*9+3];
1074
g5 = (CAtomGroup*)m_oaVectors[z*9+4];
1075
g6 = (CAtomGroup*)m_oaVectors[z*9+5];
1076
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1077
{
1078
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1079
for (z4a=0;z4a<a4->GetSize();z4a++)
1080
{
1081
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
1082
{
1083
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
1084
for (z5a=0;z5a<a5->GetSize();z5a++)
1085
{
1086
for (z6t=0;z6t<g6->m_baAtomType.GetSize();z6t++)
1087
{
1088
a6 = (CxIntArray*)g6->m_oaAtoms[z6t];
1089
for (z6a=0;z6a<a6->GetSize();z6a++)
1090
{
1091
if (m_bOrtho[2])
1092
{
1093
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1094
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1095
g9 = (CAtomGroup*)m_oaVectors[z*9+8];
1096
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1097
{
1098
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1099
for (z7a=0;z7a<a7->GetSize();z7a++)
1100
{
1101
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1102
{
1103
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1104
for (z8a=0;z8a<a8->GetSize();z8a++)
1105
{
1106
for (z9t=0;z9t<g9->m_baAtomType.GetSize();z9t++)
1107
{
1108
a9 = (CxIntArray*)g9->m_oaAtoms[z9t];
1109
for (z9a=0;z9a<a9->GetSize();z9a++)
1110
{
1111
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1112
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1113
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1114
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1115
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1116
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1117
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
1118
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1119
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1120
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1121
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1122
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1123
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1124
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1125
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1126
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
1127
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1128
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1129
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1130
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1131
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1132
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1133
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1134
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1135
if ((!m_iRefOrSec[2][2]) || (obs == NULL))
1136
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1137
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1138
}
1139
}
1140
}
1141
}
1142
}
1143
}
1144
} else // IF NOT ORTHO[2]
1145
{
1146
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1147
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1148
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1149
{
1150
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1151
for (z7a=0;z7a<a7->GetSize();z7a++)
1152
{
1153
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1154
{
1155
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1156
for (z8a=0;z8a<a8->GetSize();z8a++)
1157
{
1158
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1159
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1160
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1161
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1162
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1163
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1164
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
1165
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1166
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1167
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1168
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1169
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1170
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1171
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1172
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1173
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
1174
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1175
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1176
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1177
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1178
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1179
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1180
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1181
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1182
vec->Add(0);
1183
}
1184
}
1185
}
1186
}
1187
} // END IF NOT ORTHO[2]
1188
}
1189
}
1190
}
1191
}
1192
}
1193
}
1194
} else // IF NOT ORTHO[1]
1195
{
1196
g4 = (CAtomGroup*)m_oaVectors[z*9+3];
1197
g5 = (CAtomGroup*)m_oaVectors[z*9+4];
1198
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1199
{
1200
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1201
for (z4a=0;z4a<a4->GetSize();z4a++)
1202
{
1203
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
1204
{
1205
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
1206
for (z5a=0;z5a<a5->GetSize();z5a++)
1207
{
1208
if (m_bOrtho[2])
1209
{
1210
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1211
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1212
g9 = (CAtomGroup*)m_oaVectors[z*9+8];
1213
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1214
{
1215
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1216
for (z7a=0;z7a<a7->GetSize();z7a++)
1217
{
1218
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1219
{
1220
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1221
for (z8a=0;z8a<a8->GetSize();z8a++)
1222
{
1223
for (z9t=0;z9t<g9->m_baAtomType.GetSize();z9t++)
1224
{
1225
a9 = (CxIntArray*)g9->m_oaAtoms[z9t];
1226
for (z9a=0;z9a<a9->GetSize();z9a++)
1227
{
1228
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1229
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1230
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1231
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1232
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1233
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1234
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
1235
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1236
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1237
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1238
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1239
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1240
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1241
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1242
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1243
vec->Add(0);
1244
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1245
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1246
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1247
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1248
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1249
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1250
if ((!m_iRefOrSec[2][2]) || (obs == NULL))
1251
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1252
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1253
}
1254
}
1255
}
1256
}
1257
}
1258
}
1259
} else // IF NOT ORTHO[2]
1260
{
1261
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1262
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1263
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1264
{
1265
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1266
for (z7a=0;z7a<a7->GetSize();z7a++)
1267
{
1268
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1269
{
1270
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1271
for (z8a=0;z8a<a8->GetSize();z8a++)
1272
{
1273
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1274
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1275
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1276
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1277
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1278
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1279
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
1280
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1281
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1282
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1283
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1284
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1285
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1286
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1287
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1288
vec->Add(0);
1289
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1290
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1291
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1292
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1293
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1294
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1295
vec->Add(0);
1296
}
1297
}
1298
}
1299
}
1300
} // END IF NOT ORTHO[2]
1301
}
1302
}
1303
}
1304
}
1305
} // END IF NOT ORTHO[1]
1306
}
1307
}
1308
}
1309
}
1310
}
1311
}
1312
} else // IF NOT ORTHO[0]
1313
{
1314
g1 = (CAtomGroup*)m_oaVectors[z*9];
1315
g2 = (CAtomGroup*)m_oaVectors[z*9+1];
1316
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1317
{
1318
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1319
for (z1a=0;z1a<a1->GetSize();z1a++)
1320
{
1321
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1322
{
1323
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1324
for (z2a=0;z2a<a2->GetSize();z2a++)
1325
{
1326
if (m_bOrtho[1])
1327
{
1328
g4 = (CAtomGroup*)m_oaVectors[z*9+3];
1329
g5 = (CAtomGroup*)m_oaVectors[z*9+4];
1330
g6 = (CAtomGroup*)m_oaVectors[z*9+5];
1331
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1332
{
1333
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1334
for (z4a=0;z4a<a4->GetSize();z4a++)
1335
{
1336
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
1337
{
1338
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
1339
for (z5a=0;z5a<a5->GetSize();z5a++)
1340
{
1341
for (z6t=0;z6t<g6->m_baAtomType.GetSize();z6t++)
1342
{
1343
a6 = (CxIntArray*)g6->m_oaAtoms[z6t];
1344
for (z6a=0;z6a<a6->GetSize();z6a++)
1345
{
1346
if (m_bOrtho[2])
1347
{
1348
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1349
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1350
g9 = (CAtomGroup*)m_oaVectors[z*9+8];
1351
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1352
{
1353
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1354
for (z7a=0;z7a<a7->GetSize();z7a++)
1355
{
1356
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1357
{
1358
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1359
for (z8a=0;z8a<a8->GetSize();z8a++)
1360
{
1361
for (z9t=0;z9t<g9->m_baAtomType.GetSize();z9t++)
1362
{
1363
a9 = (CxIntArray*)g9->m_oaAtoms[z9t];
1364
for (z9a=0;z9a<a9->GetSize();z9a++)
1365
{
1366
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1367
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1368
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1369
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1370
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1371
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1372
vec->Add(0);
1373
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1374
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1375
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1376
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1377
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1378
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1379
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
1380
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1381
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1382
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1383
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1384
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1385
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1386
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1387
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1388
if ((!m_iRefOrSec[2][2]) || (obs == NULL))
1389
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1390
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1391
}
1392
}
1393
}
1394
}
1395
}
1396
}
1397
} else // IF NOT ORTHO[2]
1398
{
1399
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1400
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1401
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1402
{
1403
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1404
for (z7a=0;z7a<a7->GetSize();z7a++)
1405
{
1406
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1407
{
1408
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1409
for (z8a=0;z8a<a8->GetSize();z8a++)
1410
{
1411
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1412
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1413
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1414
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1415
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1416
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1417
vec->Add(0);
1418
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1419
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1420
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1421
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1422
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1423
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1424
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
1425
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1426
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1427
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1428
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1429
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1430
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1431
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1432
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1433
vec->Add(0);
1434
}
1435
}
1436
}
1437
}
1438
} // END IF NOT ORTHO[2]
1439
}
1440
}
1441
}
1442
}
1443
}
1444
}
1445
} else // IF NOT ORTHO[1]
1446
{
1447
g4 = (CAtomGroup*)m_oaVectors[z*9+3];
1448
g5 = (CAtomGroup*)m_oaVectors[z*9+4];
1449
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1450
{
1451
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1452
for (z4a=0;z4a<a4->GetSize();z4a++)
1453
{
1454
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
1455
{
1456
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
1457
for (z5a=0;z5a<a5->GetSize();z5a++)
1458
{
1459
if (m_bOrtho[2])
1460
{
1461
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1462
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1463
g9 = (CAtomGroup*)m_oaVectors[z*9+8];
1464
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1465
{
1466
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1467
for (z7a=0;z7a<a7->GetSize();z7a++)
1468
{
1469
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1470
{
1471
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1472
for (z8a=0;z8a<a8->GetSize();z8a++)
1473
{
1474
for (z9t=0;z9t<g9->m_baAtomType.GetSize();z9t++)
1475
{
1476
a9 = (CxIntArray*)g9->m_oaAtoms[z9t];
1477
for (z9a=0;z9a<a9->GetSize();z9a++)
1478
{
1479
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1480
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1481
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1482
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1483
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1484
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1485
vec->Add(0);
1486
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1487
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1488
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1489
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1490
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1491
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1492
vec->Add(0);
1493
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1494
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1495
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1496
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1497
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1498
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1499
if ((!m_iRefOrSec[2][2]) || (obs == NULL))
1500
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1501
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1502
}
1503
}
1504
}
1505
}
1506
}
1507
}
1508
} else // IF NOT ORTHO[2]
1509
{
1510
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1511
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1512
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1513
{
1514
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1515
for (z7a=0;z7a<a7->GetSize();z7a++)
1516
{
1517
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1518
{
1519
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1520
for (z8a=0;z8a<a8->GetSize();z8a++)
1521
{
1522
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1523
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1524
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1525
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1526
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1527
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1528
vec->Add(0);
1529
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1530
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1531
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1532
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1533
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1534
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1535
vec->Add(0);
1536
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1537
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1538
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1539
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1540
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1541
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1542
vec->Add(0);
1543
}
1544
}
1545
}
1546
}
1547
} // END IF NOT ORTHO[2]
1548
}
1549
}
1550
}
1551
}
1552
} // END IF NOT ORTHO[1]
1553
}
1554
}
1555
}
1556
}
1557
} // END IF NOT ORTHO[0]
1558
} // END FOR ALL SETS
1559
BXOUT;
1560
}
1561
1562
1563
void CPlDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
1564
{
1565
BXIN;
1566
int z, z1t, z1a, z2t, z2a, z3t, z3a, z4t, z4a;
1567
CAtomGroup *g1, *g2, *g3, *g4;
1568
CxIntArray *a1, *a2, *a3, *a4;
1569
1570
vec->RemoveAll_KeepSize();
1571
for (z=0;z<m_oaVectors.GetSize()/4;z++)
1572
{
1573
if (m_bNormal)
1574
{
1575
g1 = (CAtomGroup*)m_oaVectors[z*4];
1576
g2 = (CAtomGroup*)m_oaVectors[z*4+1];
1577
g4 = (CAtomGroup*)m_oaVectors[z*4+3];
1578
1579
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1580
{
1581
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1582
for (z1a=0;z1a<a1->GetSize();z1a++)
1583
{
1584
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1585
{
1586
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1587
for (z2a=0;z2a<a2->GetSize();z2a++)
1588
{
1589
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1590
{
1591
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1592
for (z4a=0;z4a<a4->GetSize();z4a++)
1593
{
1594
if ((!m_iRefOrSec[0]) || (obs == NULL))
1595
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1596
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1597
if ((!m_iRefOrSec[1]) || (obs == NULL))
1598
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1599
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1600
vec->Add(0);
1601
if ((!m_iRefOrSec[3]) || (obs == NULL))
1602
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1603
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1604
}
1605
}
1606
}
1607
}
1608
}
1609
}
1610
} else // IF NOT NORMAL
1611
{
1612
g1 = (CAtomGroup*)m_oaVectors[z*4];
1613
g2 = (CAtomGroup*)m_oaVectors[z*4+1];
1614
g3 = (CAtomGroup*)m_oaVectors[z*4+2];
1615
g4 = (CAtomGroup*)m_oaVectors[z*4+3];
1616
1617
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1618
{
1619
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1620
for (z1a=0;z1a<a1->GetSize();z1a++)
1621
{
1622
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1623
{
1624
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1625
for (z2a=0;z2a<a2->GetSize();z2a++)
1626
{
1627
for (z3t=0;z3t<g3->m_baAtomType.GetSize();z3t++)
1628
{
1629
a3 = (CxIntArray*)g3->m_oaAtoms[z3t];
1630
for (z3a=0;z3a<a3->GetSize();z3a++)
1631
{
1632
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1633
{
1634
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1635
for (z4a=0;z4a<a4->GetSize();z4a++)
1636
{
1637
if ((!m_iRefOrSec[0]) || (obs == NULL))
1638
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1639
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1640
if ((!m_iRefOrSec[1]) || (obs == NULL))
1641
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1642
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1643
if ((!m_iRefOrSec[2]) || (obs == NULL))
1644
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1645
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1646
if ((!m_iRefOrSec[3]) || (obs == NULL))
1647
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1648
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1649
}
1650
}
1651
}
1652
}
1653
}
1654
}
1655
}
1656
}
1657
}
1658
} // END FOR ALL SETS
1659
BXOUT;
1660
}
1661
1662
1663
void CLiDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
1664
{
1665
BXIN;
1666
int z, z1t, z1a, z2t, z2a, z3t, z3a, z4t, z4a;
1667
CAtomGroup *g1, *g2, *g3, *g4;
1668
CxIntArray *a1, *a2, *a3, *a4;
1669
1670
vec->RemoveAll_KeepSize();
1671
for (z=0;z<m_oaVectors.GetSize()/4;z++)
1672
{
1673
if (m_bNormal)
1674
{
1675
g1 = (CAtomGroup*)m_oaVectors[z*4];
1676
g2 = (CAtomGroup*)m_oaVectors[z*4+1];
1677
g3 = (CAtomGroup*)m_oaVectors[z*4+2];
1678
g4 = (CAtomGroup*)m_oaVectors[z*4+3];
1679
1680
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1681
{
1682
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1683
for (z1a=0;z1a<a1->GetSize();z1a++)
1684
{
1685
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1686
{
1687
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1688
for (z2a=0;z2a<a2->GetSize();z2a++)
1689
{
1690
for (z3t=0;z3t<g3->m_baAtomType.GetSize();z3t++)
1691
{
1692
a3 = (CxIntArray*)g3->m_oaAtoms[z3t];
1693
for (z3a=0;z3a<a3->GetSize();z3a++)
1694
{
1695
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1696
{
1697
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1698
for (z4a=0;z4a<a4->GetSize();z4a++)
1699
{
1700
if ((!m_iRefOrSec[0]) || (obs == NULL))
1701
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1702
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1703
if ((!m_iRefOrSec[1]) || (obs == NULL))
1704
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1705
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1706
if ((!m_iRefOrSec[2]) || (obs == NULL))
1707
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1708
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1709
if ((!m_iRefOrSec[3]) || (obs == NULL))
1710
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1711
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1712
}
1713
}
1714
}
1715
}
1716
}
1717
}
1718
}
1719
}
1720
} else // If not Normal
1721
{
1722
g1 = (CAtomGroup*)m_oaVectors[z*4];
1723
g2 = (CAtomGroup*)m_oaVectors[z*4+1];
1724
g4 = (CAtomGroup*)m_oaVectors[z*4+3];
1725
1726
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1727
{
1728
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1729
for (z1a=0;z1a<a1->GetSize();z1a++)
1730
{
1731
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1732
{
1733
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1734
for (z2a=0;z2a<a2->GetSize();z2a++)
1735
{
1736
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1737
{
1738
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1739
for (z4a=0;z4a<a4->GetSize();z4a++)
1740
{
1741
if ((!m_iRefOrSec[0]) || (obs == NULL))
1742
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1743
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1744
if ((!m_iRefOrSec[1]) || (obs == NULL))
1745
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1746
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1747
vec->Add(0);
1748
if ((!m_iRefOrSec[3]) || (obs == NULL))
1749
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1750
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1751
}
1752
}
1753
}
1754
}
1755
}
1756
}
1757
}
1758
} // END FOR ALL SETS
1759
BXOUT;
1760
}
1761
1762
1763
void CRDF::BuildName()
1764
{
1765
BTIN;
1766
int z;
1767
char tmp[256];
1768
1769
tmp[0] = 0;
1770
if (m_iDeriv != 0)
1771
sprintf(tmp,"deriv%d_",m_iDeriv);
1772
for (z=0;z<m_oaVectors.GetSize()/2;z++)
1773
{
1774
strcat(tmp,"[");
1775
1776
strcat(tmp,((CAtomGroup*)m_oaVectors[z*2])->m_sName);
1777
if (m_iRefOrSec[0])
1778
strcat(tmp,"o_");
1779
else strcat(tmp,"r_");
1780
strcat(tmp,((CAtomGroup*)m_oaVectors[z*2+1])->m_sName);
1781
if (m_iRefOrSec[1])
1782
strcat(tmp,"o");
1783
else strcat(tmp,"r");
1784
1785
if (z < (m_oaVectors.GetSize()/2)-1)
1786
strcat(tmp,"],");
1787
else strcat(tmp,"]");
1788
}
1789
1790
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
1791
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1792
1793
strcpy(m_sShortName,tmp);
1794
if (m_iShowMol != -1)
1795
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1796
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
1797
strcat(tmp,m_sShortName);
1798
1799
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
1800
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1801
1802
strcpy(m_sName,tmp);
1803
1804
BTOUT;
1805
}
1806
1807
1808
void CDensDF::BuildName()
1809
{
1810
BTIN;
1811
char tmp[256];
1812
int z;
1813
1814
sprintf(tmp,"%s_%s%d_%s",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,((CAtom*)g_oaAtoms[m_iCenterAtomRealType])->m_sName,m_iCenterAtom+1,(m_bDensityMass?"mass":"particle"));
1815
1816
for (z=0;z<g_oaMolecules.GetSize();z++)
1817
{
1818
if (!m_pDensityMolSelect[z])
1819
continue;
1820
strcat(tmp,"_");
1821
strcat(tmp,((CMolecule*)g_oaMolecules[z])->m_sName);
1822
if (!m_pDensityMolAG[z]->m_bAllAtoms)
1823
{
1824
strcat(tmp,"_");
1825
strcat(tmp,m_pDensityMolAG[z]->m_sName);
1826
}
1827
}
1828
1829
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
1830
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1831
1832
strcpy(m_sName,tmp);
1833
BTOUT;
1834
}
1835
1836
1837
void CVHDF::BuildName()
1838
{
1839
BTIN;
1840
int z;
1841
char tmp[256];
1842
1843
tmp[0] = 0;
1844
for (z=0;z<m_oaVectors.GetSize()/2;z++)
1845
{
1846
strcat(tmp,"[");
1847
1848
strcat(tmp,((CAtomGroup*)m_oaVectors[z*2])->m_sName);
1849
if (m_iRefOrSec[0])
1850
strcat(tmp,"o_");
1851
else strcat(tmp,"r_");
1852
strcat(tmp,((CAtomGroup*)m_oaVectors[z*2+1])->m_sName);
1853
if (m_iRefOrSec[1])
1854
strcat(tmp,"o");
1855
else strcat(tmp,"r");
1856
1857
if (z < (m_oaVectors.GetSize()/2)-1)
1858
strcat(tmp,"],");
1859
else strcat(tmp,"]");
1860
}
1861
1862
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
1863
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1864
1865
strcpy(m_sShortName,tmp);
1866
if (m_iShowMol != -1)
1867
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1868
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
1869
strcat(tmp,m_sShortName);
1870
1871
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
1872
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1873
1874
strcpy(m_sName,tmp);
1875
BTOUT;
1876
}
1877
1878
1879
void CRDF::Parse()
1880
{
1881
BTIN;
1882
char buf[256];
1883
int ti;
1884
CAtomGroup *ag;
1885
1886
try { m_pRDF = new CDF(); } catch(...) { m_pRDF = NULL; }
1887
if (m_pRDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1888
1889
m_iShowAtomGes = 0;
1890
m_iRefAtomGes = 0;
1891
m_iCombinations = 0;
1892
mprintf(WHITE,"\n>>> Radial Distribution Function >>>\n\n");
1893
/* if (m_bSelf)
1894
{
1895
m_iRefOrSec[0] = 0;
1896
m_iRefOrSec[1] = 0;
1897
} else
1898
{
1899
m_iRefOrSec[0] = 0;
1900
m_iRefOrSec[1] = 1;
1901
}*/
1902
if (m_iShowMol != -1)
1903
m_iRefOrSec[0] = AskRangeInteger(" Take reference atom(s) from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1904
else m_iRefOrSec[0] = 0; // Kein OM: Nimm alles aus RM
1905
if (m_iShowMol != -1)
1906
m_iRefOrSec[1] = AskRangeInteger(" Take observed atom(s) from RM %s (0) or from OM %s (1)? [1] ",0,1,1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1907
else m_iRefOrSec[1] = 0; // Kein OM: Nimm alles aus RM
1908
1909
_rdfnewset:
1910
mprintf("\n");
1911
1912
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1913
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1914
1915
_rdfatom1:
1916
// 1 reales + 2 virtuelle = 3 gesamt
1917
if (((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol])->m_iAtomGes == 3)
1918
{
1919
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol])->m_sName);
1920
ag->Reset();
1921
ag->m_pMolecule = (CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol];
1922
ag->AddAtom(0,0,false);
1923
ag->SortAtoms();
1924
ag->BuildName();
1925
} else
1926
{
1927
if (m_iRefOrSec[0])
1928
{
1929
mprintf(" Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1930
inpprintf("! Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1931
} else
1932
{
1933
mprintf(" Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
1934
inpprintf("! Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
1935
}
1936
myget(buf);
1937
if (strlen(buf) == 0)
1938
{
1939
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol],"#2"))
1940
{
1941
eprintf("Weird error.\n");
1942
goto _rdfatom1;
1943
}
1944
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol],buf))
1945
goto _rdfatom1;
1946
}
1947
m_oaVectors.Add(ag);
1948
m_iRefAtomGes += ag->m_iAtomGes;
1949
ti = ag->m_iAtomGes;
1950
1951
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1952
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1953
1954
_rdfatom2:
1955
if (((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol])->m_iAtomGes == 3)
1956
{
1957
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol])->m_sName);
1958
ag->Reset();
1959
ag->m_pMolecule = (CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol];
1960
ag->AddAtom(0,0,false);
1961
ag->SortAtoms();
1962
ag->BuildName();
1963
} else
1964
{
1965
if (m_iRefOrSec[1])
1966
{
1967
mprintf(" Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1968
inpprintf("! Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1969
} else
1970
{
1971
mprintf(" Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
1972
inpprintf("! Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
1973
}
1974
myget(buf);
1975
1976
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1977
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1978
1979
if (strlen(buf) == 0)
1980
{
1981
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol],"#2"))
1982
{
1983
eprintf("Weird error.\n");
1984
goto _rdfatom2;
1985
}
1986
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol],buf))
1987
goto _rdfatom2;
1988
}
1989
m_oaVectors.Add(ag);
1990
m_iShowAtomGes += ag->m_iAtomGes;
1991
m_iCombinations += ti * ag->m_iAtomGes;
1992
1993
if (g_bAdvanced2)
1994
if (AskYesNo(" Add another set of atoms to this (!) RDF (y/n)? [no] ",false))
1995
goto _rdfnewset;
1996
1997
mprintf(" This yields in %d combinations.\n\n",m_iCombinations);
1998
1999
ParseDeriv();
2000
2001
switch(m_iDeriv)
2002
{
2003
case 0:
2004
m_fMinDist = AskFloat(" Enter the minimal radius of this RDF in pm: [0] ",0.0f);
2005
m_fMaxDist = AskFloat(" Enter the maximal radius of this RDF in pm: [%d.0] ",(float)HalfBox(),HalfBox());
2006
break;
2007
case 1:
2008
if (m_bDerivAbs)
2009
m_fMinDist = AskFloat(" Enter the minimal value of this d1-RDF in pm/ps: [0] ",0.0f);
2010
else m_fMinDist = AskFloat(" Enter the minimal value of this d1-RDF in pm/ps: [-10.0] ",-10.0f);
2011
m_fMaxDist = AskFloat(" Enter the maximal value of this d1-RDF in pm/ps: [10.0] ",10.0f);
2012
break;
2013
case 2:
2014
if (m_bDerivAbs)
2015
m_fMinDist = AskFloat(" Enter the minimal value of this d2-RDF in pm/ps^2: [0] ",0.0f);
2016
else m_fMinDist = AskFloat(" Enter the minimal value of this d2-RDF in pm/ps^2: [-10.0] ",-10.0f);
2017
m_fMaxDist = AskFloat(" Enter the maximal value of this d2-RDF in pm/ps^2: [10.0] ",10.0f);
2018
break;
2019
}
2020
m_bAdaptive = false/*AskYesNo(" Enter binning resolution (n) or use adaptive binnig (y)? [no] ",false)*/;
2021
if (!m_bAdaptive)
2022
m_iResolution = AskUnsignedInteger(" Enter the resolution (bin count) for this RDF: [300] ",/*(int)((m_fMaxDist-m_fMinDist)/10.0f),(int)((m_fMaxDist-m_fMinDist)/10.0f)*/300);
2023
else m_iResolution = 65536;
2024
2025
if (g_bAdvanced2)
2026
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
2027
else m_iHistogramRes = 0;
2028
2029
if (m_iDeriv == 0)
2030
{
2031
if (m_iShowMol != -1)
2032
m_bRadialCorrect = AskYesNo(" Correct radial distribution for this RDF (y/n)? [yes] ",true);
2033
else m_bRadialCorrect = AskYesNo(" Correct radial distribution for this RDF (y/n)? [no] ",false);
2034
} else m_bRadialCorrect = false;
2035
2036
if (g_bAdvanced2 && m_bRadialCorrect)
2037
m_bProbDens = AskYesNo(" Compute occurence in nm^(-3) (y) or rel. to uniform density (n)? [no] ",false);
2038
else m_bProbDens = false;
2039
2040
if (g_bBetaFeatures)
2041
m_bCalcSD = AskYesNo(" Calculate standard deviation for this RDF (y/n)? [no] ",false);
2042
else m_bCalcSD = false;
2043
2044
if (m_bCalcSD)
2045
{
2046
m_iSDBlocks = AskUnsignedInteger(" How many different block lenghts to use? [100] ",100);
2047
m_iSDBlockMin = AskUnsignedInteger(" Enter minimal block length in time steps: [1] ",1);
2048
if (g_iTrajSteps != -1)
2049
m_iSDBlockMax = AskUnsignedInteger(" Enter maximal block length in time steps: [%d] ",g_iTrajSteps/10,g_iTrajSteps/10);
2050
else m_iSDBlockMax = AskUnsignedInteger(" Enter maximal block length in time steps: [1000] ",1000);
2051
m_bSDVerbose = AskYesNo(" Write out correlation length extrapolation fit data for each bin (y/n)? [no] ",false);
2052
m_fSDTimesSigma = AskFloat(" Use which factor of sigma for confidence range? [3.0] ",3.0);
2053
mprintf("\n %.2f sigma leads to a confidence level of %.5f%c.\n",m_fSDTimesSigma,2.0*NormalDistIntegral(m_fSDTimesSigma)-1.0,'%');
2054
}
2055
2056
BuildName();
2057
mprintf(WHITE,"\n<<< End of Radial Distribution Function <<<\n\n");
2058
BTOUT;
2059
}
2060
2061
2062
void CDensDF::Parse()
2063
{
2064
BTIN;
2065
char buf[256];
2066
int z;
2067
CMolecule *m;
2068
2069
try { m_pDensDF = new CDF(); } catch(...) { m_pDensDF = NULL; }
2070
if (m_pDensDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2071
2072
mprintf(WHITE,"\n>>> Density Distribution Function >>>\n\n");
2073
2074
m_bDensityMass = AskYesNo(" Observe mass density (y) or particle density (n)? [yes] ",true);
2075
2076
mprintf("\n Choose a reference atom around which the density will be analyzed.\n\n");
2077
2078
// 1 reales + 2 virtuelle = 3 gesamt
2079
if (((CMolecule*)g_oaMolecules[m_iShowMol])->m_iAtomGesNoVirt == 1)
2080
{
2081
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2082
if (!ParseAtom("#2",m_iShowMol,m_iCenterAtomType,m_iCenterAtomRealType,m_iCenterAtom))
2083
{
2084
eprintf("Weird error.\n");
2085
abort();
2086
}
2087
} else
2088
{
2089
_densatom1:
2090
mprintf(" Which atom to take from OM %s (e.g. C1)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2091
inpprintf("! Which atom to take from OM %s (e.g. C1)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2092
myget(buf);
2093
if (strlen(buf) == 0)
2094
{
2095
if (!ParseAtom("#2",m_iShowMol,m_iCenterAtomType,m_iCenterAtomRealType,m_iCenterAtom))
2096
{
2097
eprintf("Weird error.\n");
2098
abort();
2099
}
2100
} else if (!ParseAtom(buf,m_iShowMol,m_iCenterAtomType,m_iCenterAtomRealType,m_iCenterAtom))
2101
goto _densatom1;
2102
}
2103
2104
try { m_pDensityMolSelect = new bool[g_oaMolecules.GetSize()]; } catch(...) { m_pDensityMolSelect = NULL; }
2105
if (m_pDensityMolSelect == NULL) NewException((double)g_oaMolecules.GetSize()*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2106
2107
try { m_pDensityMolAG = new CAtomGroup*[g_oaMolecules.GetSize()]; } catch(...) { m_pDensityMolAG = NULL; }
2108
if (m_pDensityMolAG == NULL) NewException((double)g_oaMolecules.GetSize()*sizeof(CAtomGroup*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2109
2110
mprintf("\n Please choose the atoms to observe:\n\n");
2111
2112
for (z=0;z<g_oaMolecules.GetSize();z++)
2113
{
2114
m = (CMolecule*)g_oaMolecules[z];
2115
m_pDensityMolSelect[z] = AskYesNo(" Consider contributions from %s (y/n)? [%s] ",!m->m_bPseudo,((CMolecule*)g_oaMolecules[z])->m_sName,m->m_bPseudo?"no":"yes");
2116
if (m_pDensityMolSelect[z])
2117
{
2118
try { m_pDensityMolAG[z] = new CAtomGroup(); } catch(...) { m_pDensityMolAG[z] = NULL; }
2119
if (m_pDensityMolAG[z] == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2120
_densatom2:
2121
AskString(" Which atoms from %s to observe (e.g. C1-3,C6,N)? [all] ",buf,"",m->m_sName);
2122
if (strlen(buf) == 0)
2123
{
2124
m_pDensityMolAG[z]->AddAllAtoms(m,false);
2125
} else if (!m_pDensityMolAG[z]->ParseAtoms(m,buf))
2126
goto _densatom2;
2127
}
2128
}
2129
2130
mprintf("\n");
2131
2132
m_fMinDist = AskFloat(" Enter the minimal radius of this Density DF in pm: [0] ",0.0f);
2133
m_fMaxDist = AskFloat(" Enter the maximal radius of this Density DF in pm: [%d.0] ",(float)HalfBox(),HalfBox());
2134
2135
m_iResolution = AskUnsignedInteger(" Enter the resolution (bin count) for this Density DF: [300] ",300);
2136
2137
if (g_bAdvanced2)
2138
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
2139
else m_iHistogramRes = 0;
2140
2141
BuildName();
2142
mprintf(WHITE,"\n<<< End of Density Distribution Function <<<\n\n");
2143
BTOUT;
2144
}
2145
2146
2147
void CRDF::ParseCondition(int rm, CNbSearch *n, bool nbana)
2148
{
2149
BTIN;
2150
char buf[256];
2151
int ti;
2152
CAtomGroup *ag;
2153
2154
try { m_pRDF = new CDF(); } catch(...) { m_pRDF = NULL; }
2155
if (m_pRDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2156
2157
m_iShowAtomGes = 0;
2158
m_iRefAtomGes = 0;
2159
m_iCombinations = 0;
2160
m_iRefOrSec[0] = 0;
2161
m_iRefOrSec[1] = 1;
2162
mprintf(WHITE,"\n>>> Distance Condition >>>\n");
2163
2164
_rdfnewset:
2165
mprintf("\n");
2166
2167
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2168
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2169
2170
_rdfatom1:
2171
if (((CMolecule*)g_oaMolecules[rm])->m_iAtomGes == 3)
2172
{
2173
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[rm])->m_sName);
2174
ag->Reset();
2175
ag->m_pMolecule = (CMolecule*)g_oaMolecules[rm];
2176
ag->AddAtom(0,0,false);
2177
ag->SortAtoms();
2178
ag->BuildName();
2179
} else
2180
{
2181
mprintf(" Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[rm])->m_sName);
2182
inpprintf("! Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[rm])->m_sName);
2183
myget(buf);
2184
if (strlen(buf) == 0)
2185
{
2186
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[rm],"#2"))
2187
{
2188
eprintf("Weird error.\n");
2189
goto _rdfatom1;
2190
}
2191
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[rm],buf))
2192
goto _rdfatom1;
2193
}
2194
m_oaVectors.Add(ag);
2195
m_iRefAtomGes += ag->m_iAtomGes;
2196
ti = ag->m_iAtomGes;
2197
2198
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2199
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2200
2201
_rdfatom2:
2202
if (((CMolecule*)g_oaMolecules[m_iShowMol])->m_iAtomGes == 3)
2203
{
2204
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2205
ag->Reset();
2206
ag->m_pMolecule = (CMolecule*)g_oaMolecules[m_iShowMol];
2207
ag->AddAtom(0,0,false);
2208
ag->SortAtoms();
2209
ag->BuildName();
2210
} else
2211
{
2212
mprintf(" Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2213
inpprintf("! Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2214
myget(buf);
2215
2216
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2217
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2218
2219
if (strlen(buf) == 0)
2220
{
2221
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],"#2"))
2222
{
2223
eprintf("Weird error.\n");
2224
goto _rdfatom2;
2225
}
2226
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],buf))
2227
goto _rdfatom2;
2228
}
2229
m_oaVectors.Add(ag);
2230
m_iShowAtomGes += ag->m_iAtomGes;
2231
m_iCombinations += ti * ag->m_iAtomGes;
2232
2233
if (AskYesNo(" Enter another set of atoms for this condition (y/n)? [no] ",false))
2234
goto _rdfnewset;
2235
2236
if (!nbana)
2237
{
2238
if (AskUnsignedInteger("\n Enter min./max. distance (0) or min./max. nearest neighbor count (1)? [0] ",0)==0)
2239
{
2240
g_bEnvDisableSortNb = true;
2241
2242
do {
2243
m_faMinMaxDist.Add(AskFloat(" Enter the minimal distance in pm: [0] ",0.0f));
2244
m_faMinMaxDist.Add(AskFloat(" Enter the maximal distance in pm: [400] ",400.0f));
2245
} while (AskYesNo(" Enter another distance interval (y/n)? [no] ",false));
2246
n->m_iNbCountMin = -1;
2247
n->m_iNbCountMax = -1;
2248
} else
2249
{
2250
n->m_iNbCountMin = AskRangeInteger(" Use next neighbors from the n-th on? [1] ",0,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),1)-1;
2251
n->m_iNbCountMax = AskRangeInteger(" Use next neighbors up to the n-th? [%d] ",n->m_iNbCountMin+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),n->m_iNbCountMin+1,n->m_iNbCountMin+1)-1;
2252
// m_faMinMaxDist.Add(0);
2253
// m_faMinMaxDist.Add(9E20f);
2254
}
2255
} else
2256
{
2257
m_faMinMaxDist.Add(0);
2258
m_faMinMaxDist.Add(1.0e30f);
2259
n->m_iNbCountMin = -2;
2260
n->m_iNbCountMax = -2;
2261
}
2262
mprintf(WHITE,"\n<<< End of Distance Condition <<<\n\n");
2263
BTOUT;
2264
}
2265
2266
2267
void CRDF::ParseConditionGrid(int rm, CNbSearch *n, int gridmode)
2268
{
2269
BTIN;
2270
char buf[256];
2271
int ti;
2272
CAtomGroup *ag;
2273
2274
try { m_pRDF = new CDF(); } catch(...) { m_pRDF = NULL; }
2275
if (m_pRDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2276
2277
m_iShowAtomGes = 0;
2278
m_iRefAtomGes = 0;
2279
m_iCombinations = 0;
2280
m_iRefOrSec[0] = 0;
2281
m_iRefOrSec[1] = 1;
2282
mprintf(WHITE,"\n>>> Distance Condition >>>\n");
2283
2284
_rdfnewset:
2285
mprintf("\n");
2286
2287
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2288
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2289
2290
_rdfatom1:
2291
if (((CMolecule*)g_oaMolecules[rm])->m_iAtomGes == 3)
2292
{
2293
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[rm])->m_sName);
2294
ag->Reset();
2295
ag->m_pMolecule = (CMolecule*)g_oaMolecules[rm];
2296
ag->AddAtom(0,0,false);
2297
ag->SortAtoms();
2298
ag->BuildName();
2299
} else
2300
{
2301
mprintf(" Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[rm])->m_sName);
2302
inpprintf("! Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[rm])->m_sName);
2303
myget(buf);
2304
if (strlen(buf) == 0)
2305
{
2306
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[rm],"#2"))
2307
{
2308
eprintf("Weird error.\n");
2309
goto _rdfatom1;
2310
}
2311
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[rm],buf))
2312
goto _rdfatom1;
2313
}
2314
m_oaVectors.Add(ag);
2315
m_iRefAtomGes += ag->m_iAtomGes;
2316
ti = ag->m_iAtomGes;
2317
2318
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2319
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2320
2321
_rdfatom2:
2322
if (((CMolecule*)g_oaMolecules[m_iShowMol])->m_iAtomGes == 3)
2323
{
2324
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2325
ag->Reset();
2326
ag->m_pMolecule = (CMolecule*)g_oaMolecules[m_iShowMol];
2327
ag->AddAtom(0,0,false);
2328
ag->SortAtoms();
2329
ag->BuildName();
2330
} else
2331
{
2332
mprintf(" Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2333
inpprintf("! Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2334
myget(buf);
2335
2336
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2337
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2338
2339
if (strlen(buf) == 0)
2340
{
2341
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],"#2"))
2342
{
2343
eprintf("Weird error.\n");
2344
goto _rdfatom2;
2345
}
2346
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],buf))
2347
goto _rdfatom2;
2348
}
2349
m_oaVectors.Add(ag);
2350
m_iShowAtomGes += ag->m_iAtomGes;
2351
m_iCombinations += ti * ag->m_iAtomGes;
2352
2353
if (AskYesNo(" Enter another set of atoms (y/n)? [no] ",false))
2354
goto _rdfnewset;
2355
2356
if (gridmode == 6)
2357
{
2358
if (AskUnsignedInteger("\n Enter min./max. distance (0) or min./max. nearest neighbor count (1)? [0] ",0)==0)
2359
{
2360
m_faMinMaxDist.Add(AskFloat(" Enter the minimal distance in pm: [0] ",0.0f));
2361
m_faMinMaxDist.Add(AskFloat(" Enter the maximal distance in pm: [400] ",400.0f));
2362
n->m_iNbCountMin = -1;
2363
n->m_iNbCountMax = -1;
2364
} else
2365
{
2366
n->m_iNbCountMin = AskRangeInteger(" Use next neighbors from the n-th on? [1] ",0,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),1)-1;
2367
n->m_iNbCountMax = AskRangeInteger(" Use next neighbors up to the n-th? [%d] ",n->m_iNbCountMin+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),n->m_iNbCountMin+1,n->m_iNbCountMin+1)-1;
2368
// m_faMinMaxDist.Add(0);
2369
// m_faMinMaxDist.Add(9E20f);
2370
}
2371
} else if ((gridmode == 4) || (gridmode == 5))
2372
{
2373
n->m_iNbCountMin = 0;
2374
n->m_iNbCountMax = 0;
2375
// m_faMinMaxDist.Add(0);
2376
// m_faMinMaxDist.Add(9E20f);
2377
} else if (gridmode == 2)
2378
{
2379
m_faMinMaxDist.Add(AskFloat(" Enter the minimal distance in pm: [0] ",0.0f));
2380
m_faMinMaxDist.Add(AskFloat(" Enter the maximal distance in pm: [400] ",400.0f));
2381
n->m_iNbCountMin = -1;
2382
n->m_iNbCountMax = -1;
2383
} else
2384
{
2385
m_faMinMaxDist.Add(0.0f);
2386
m_faMinMaxDist.Add(400.0f);
2387
n->m_iNbCountMin = -1;
2388
n->m_iNbCountMax = -1;
2389
}
2390
mprintf(WHITE,"\n<<< End of Distance Condition <<<\n\n");
2391
BTOUT;
2392
}
2393
2394
2395
void CRDF::ParseCondition_OnlyValues(CNbSearch *n)
2396
{
2397
BTIN;
2398
int z;
2399
2400
mprintf(" Distance condition between ");
2401
for (z=0;z<m_oaVectors.GetSize()/2;z++)
2402
{
2403
mprintf("%s and %s",((CAtomGroup*)m_oaVectors[z*2])->m_sName,((CAtomGroup*)m_oaVectors[z*2+1])->m_sName);
2404
if (z < (m_oaVectors.GetSize()/2)-1)
2405
mprintf(", ");
2406
}
2407
mprintf("\n");
2408
if (n->m_iNbCountMin == -1)
2409
{
2410
for (z=0;z<m_faMinMaxDist.GetSize()/2;z++)
2411
{
2412
mprintf(" Interval %d:\n",z+1,m_faMinMaxDist.GetSize()/2);
2413
m_faMinMaxDist[z*2] = AskFloat(" Enter the minimal distance in pm: [0] ",0.0f);
2414
m_faMinMaxDist[z*2+1] = AskFloat(" Enter the maximal distance in pm: [400] ",400.0f);
2415
}
2416
} else
2417
{
2418
n->m_iNbCountMin = AskRangeInteger(" Use next neighbors from the n-th on? [1] ",0,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),1)-1;
2419
n->m_iNbCountMax = AskRangeInteger(" Use next neighbors up to the n-th? [%d] ",n->m_iNbCountMin+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),n->m_iNbCountMin+1,n->m_iNbCountMin+1)-1;
2420
}
2421
2422
BTOUT;
2423
}
2424
2425
2426
void CVHDF::Parse()
2427
{
2428
BTIN;
2429
char buf[256];
2430
int ti;
2431
CAtomGroup *ag;
2432
2433
try { m_pVHDF = new C2DF(); } catch(...) { m_pVHDF = NULL; }
2434
if (m_pVHDF == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2435
2436
m_iShowAtomGes = 0;
2437
m_iRefAtomGes = 0;
2438
m_iCombinations = 0;
2439
mprintf(WHITE,"\n>>> Van Hove Correlation Function >>>\n\n");
2440
if (m_iShowMol != -1)
2441
{
2442
m_iRefOrSec[0] = AskRangeInteger(" Take (fixed) reference atom(s) from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2443
m_iRefOrSec[1] = AskRangeInteger(" Take (moving) observed atom(s) from RM %s (0) or from OM %s (1)? [1] ",0,1,1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2444
} else // Kein OM: Nimm alles aus RM
2445
{
2446
m_iRefOrSec[0] = 0;
2447
m_iRefOrSec[1] = 0;
2448
}
2449
_rdfnewset:
2450
mprintf("\n");
2451
2452
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2453
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2454
2455
_rdfatom1:
2456
if (m_iRefOrSec[0])
2457
{
2458
mprintf(" Which (fixed) reference atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2459
inpprintf("! Which (fixed) reference atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2460
} else
2461
{
2462
mprintf(" Which (fixed) reference atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2463
inpprintf("! Which (fixed) reference atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2464
}
2465
myget(buf);
2466
if (strlen(buf) == 0)
2467
{
2468
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol],"#2"))
2469
goto _rdfatom1;
2470
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol],buf))
2471
goto _rdfatom1;
2472
m_oaVectors.Add(ag);
2473
m_iRefAtomGes += ag->m_iAtomGes;
2474
ti = ag->m_iAtomGes;
2475
2476
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2477
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2478
2479
_rdfatom2:
2480
if (m_iRefOrSec[1])
2481
{
2482
mprintf(" Which (moving) observed atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2483
inpprintf("! Which (moving) observed atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2484
} else
2485
{
2486
mprintf(" Which (moving) observed atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2487
inpprintf("! Which (moving) observed atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2488
}
2489
myget(buf);
2490
2491
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2492
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2493
2494
if (strlen(buf) == 0)
2495
{
2496
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol],"#2"))
2497
goto _rdfatom2;
2498
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol],buf))
2499
goto _rdfatom2;
2500
m_oaVectors.Add(ag);
2501
m_iShowAtomGes += ag->m_iAtomGes;
2502
m_iCombinations += ti * ag->m_iAtomGes;
2503
2504
if (g_bAdvanced2)
2505
if (AskYesNo(" Enter another set of atoms (y/n)? [no] ",false))
2506
goto _rdfnewset;
2507
2508
m_fMinDist = 0; //AskFloat(" Enter the minimal radius of this VHCF in pm: [0] ",0.0f);
2509
m_fMaxDist = AskFloat(" Enter the radius of this VHCF in pm: [%d.0] ",(float)HalfBox(),HalfBox());
2510
m_iResolution = AskUnsignedInteger(" Enter the radial resolution of this VHCF: [100] ",100);
2511
m_bRadialCorrect = AskYesNo(" Correct radial distribution for this VHCF (y/n)? [%s] ",!m_bSelf,m_bSelf?"no":"yes");
2512
2513
_depth:
2514
if (g_iTrajSteps != -1)
2515
m_iDepth = AskUnsignedInteger(" Enter the temporal resolution (time depth) of this VHCF (in time steps): [%d] ",int(g_iTrajSteps*0.75),int(g_iTrajSteps*0.75));
2516
else m_iDepth = AskUnsignedInteger(" Enter the temporal resolution (time depth) of this VHCF (in time steps): [5000] ",5000);
2517
2518
mprintf("\n This will occupy %s of RAM.\n",FormatBytes((double)m_iDepth*g_iGesVirtAtomCount*3.0*sizeof(float)));
2519
if (m_iDepth*g_iGesVirtAtomCount*3.0*sizeof(float)/1024.0f/1024.0f >= 1000.0f)
2520
if (!AskYesNo(" Make sure that enough free RAM is available. Continue (y/n)? [yes] ",true))
2521
goto _depth;
2522
mprintf("\n");
2523
2524
_resagain:
2525
m_iStride = AskUnsignedInteger(" Take each n-th time step for the temporal axis? [%d] ",max(1,m_iDepth/100),max(1,m_iDepth/100));
2526
2527
mprintf("\n This results in a plot resolution of %d on the temporal axis.\n",m_iDepth/m_iStride);
2528
2529
if (m_iDepth/m_iStride > 200)
2530
{
2531
mprintf("\n");
2532
if (!AskYesNo(" The resolution seems quite high, the plot will take much time to render. Contiune (y/n)? [yes] ",true))
2533
goto _resagain;
2534
}
2535
2536
if (g_bAdvanced2)
2537
{
2538
mprintf("\n");
2539
m_bSwapAxes = AskYesNo(" Put distance on X axis and time on Y axis (y) or swap axes (n)? [yes] ",true);
2540
m_iGraceBunchTime = AskUnsignedInteger(" How many time graphs do you want do draw in the distance grace stack (0=disable)? [10] ",10);
2541
m_iGraceBunchDist = AskUnsignedInteger(" How many distance graphs do you want do draw in the time grace stack (0=disable)? [10] ",10);
2542
} else
2543
{
2544
m_bSwapAxes = true;
2545
m_iGraceBunchTime = 0;
2546
m_iGraceBunchDist = 0;
2547
}
2548
2549
BuildName();
2550
mprintf(WHITE,"\n<<< End of Van Hove Correlation Function <<<\n\n");
2551
BTOUT;
2552
}
2553
2554
2555
void CADF::Parse()
2556
{
2557
BTIN;
2558
char buf[256];
2559
int z, z2, ti;
2560
CAtomGroup *ag;
2561
float tf;
2562
2563
try { m_pADF = new CDF(); } catch(...) { m_pADF = NULL; }
2564
if (m_pADF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2565
2566
mprintf(WHITE,"\n>>> Angular Distribution Function >>>\n\n");
2567
for (z=0;z<2;z++)
2568
{
2569
m_iVecType[z] = AskRangeInteger(" Should the %d. vector depict position (1), dipole (2), velocity (3) or force (4)? [1] ",1,4,1,z+1) - 1;
2570
if (m_iVecType[z] == 1)
2571
{
2572
g_bDipole = true;
2573
ParseDipole();
2574
}
2575
}
2576
z2 = 0;
2577
m_iCombinations = 0;
2578
do {
2579
ti = 1;
2580
if (z2 != 0)
2581
mprintf("\n %d. set of vectors\n\n",z2+1);
2582
for (z=0;z<2;z++)
2583
{
2584
if (m_iVecType[z] == 0) // Position
2585
{
2586
/* if (z2 == 0)
2587
if ((z == 1) && (m_iVecType[0] == 0) && (m_iVecType[1] == 0))
2588
m_bSameFoot = AskYesNo(" Should the base points of the 1st and 2nd vectors always be equal (y/n)? [no] ",false);
2589
else m_bSameFoot = false;*/
2590
2591
if (z2 == 0)
2592
m_bOrtho[z] = (AskRangeInteger("\n Should the %d. vector connect 2 points (0) or stand perpendicular to 3 points (1)? [0] ",0,1,0,z+1) != 0);
2593
2594
mprintf("\n");
2595
if (m_bOrtho[z])
2596
{
2597
/* if (m_bSameFoot && (z == 1))
2598
{
2599
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
2600
m_oaVectors.Add(NULL);
2601
} else*/
2602
{
2603
_ax1: if (z2 == 0)
2604
{
2605
if (m_iShowMol != -1)
2606
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) at the base point from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2607
else m_iRefOrSec[z][0] = 0;
2608
}
2609
mprintf(" Please enter the atom(s) at the base point (e.g. C7): ");
2610
inpprintf("! Please enter the atom(s) at the base point (e.g. C7):\n");
2611
myget(buf);
2612
2613
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2614
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2615
2616
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2617
{
2618
eprintf("Wrong input.\n");
2619
inpprintf("! Wrong input.\n");
2620
delete ag;
2621
goto _ax1;
2622
}
2623
m_oaVectors.Add(ag);
2624
ti *= ag->m_iAtomGes;
2625
}
2626
_ax2: if (z2 == 0)
2627
{
2628
if (m_iShowMol != -1)
2629
m_iRefOrSec[z][1] = AskRangeInteger(" Take 2nd atom(s) of normal plane from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2630
else m_iRefOrSec[z][1] = 0;
2631
}
2632
mprintf(" Please enter the 2nd atom(s) of the normal plane (e.g. C7): ");
2633
inpprintf("! Please enter the 2nd atom(s) of the normal plane (e.g. C7):\n");
2634
myget(buf);
2635
2636
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2637
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2638
2639
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2640
{
2641
eprintf("Wrong input.\n");
2642
inpprintf("! Wrong input.\n");
2643
delete ag;
2644
goto _ax2;
2645
}
2646
m_oaVectors.Add(ag);
2647
ti *= ag->m_iAtomGes;
2648
_ax3: if (z2 == 0)
2649
{
2650
if (m_iShowMol != -1)
2651
m_iRefOrSec[z][2] = AskRangeInteger(" Take 3rd atom(s) of normal plane from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2652
else m_iRefOrSec[z][2] = 0;
2653
}
2654
mprintf(" Please enter the 3rd atom(s) of the normal plane (e.g. C7): ");
2655
inpprintf("! Please enter the 3rd atom(s) of the normal plane (e.g. C7):\n");
2656
myget(buf);
2657
2658
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2659
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2660
2661
if (!ag->ParseAtoms((!m_iRefOrSec[z][2])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2662
{
2663
eprintf("Wrong input.\n");
2664
inpprintf("! Wrong input.\n");
2665
delete ag;
2666
goto _ax3;
2667
}
2668
m_oaVectors.Add(ag);
2669
ti *= ag->m_iAtomGes;
2670
} else // IF ORTHO
2671
{
2672
/* if (m_bSameFoot && (z == 1))
2673
{
2674
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
2675
m_oaVectors.Add(NULL);
2676
} else*/
2677
{
2678
_ax4: if (z2 == 0)
2679
{
2680
if (m_iShowMol != -1)
2681
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) at the base point from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2682
else m_iRefOrSec[z][0] = 0;
2683
}
2684
mprintf(" Please enter the atom(s) at the base point (e.g. C7): ");
2685
inpprintf("! Please enter the atom(s) at the base point (e.g. C7):\n");
2686
myget(buf);
2687
2688
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2689
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2690
2691
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2692
{
2693
eprintf("Wrong input.\n");
2694
inpprintf("! Wrong input.\n");
2695
delete ag;
2696
goto _ax4;
2697
}
2698
m_oaVectors.Add(ag);
2699
ti *= ag->m_iAtomGes;
2700
} // END IF NOT SAMEFOOT
2701
_ax5: if (z2 == 0)
2702
{
2703
if (m_iShowMol != -1)
2704
m_iRefOrSec[z][1] = AskRangeInteger(" Take atom(s) at the tip point from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2705
else m_iRefOrSec[z][1] = 0;
2706
}
2707
mprintf(" Please enter the atom(s) at the tip point (e.g. C7): ");
2708
inpprintf("! Please enter the atom(s) at the tip point (e.g. C7):\n");
2709
myget(buf);
2710
2711
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2712
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2713
2714
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2715
{
2716
eprintf("Wrong input.\n");
2717
inpprintf("! Wrong input.\n");
2718
delete ag;
2719
goto _ax5;
2720
}
2721
m_oaVectors.Add(ag);
2722
ti *= ag->m_iAtomGes;
2723
m_oaVectors.Add(NULL);
2724
} // END IF NOT ORTHO
2725
} else if (m_iVecType[z] == 1) // Dipol
2726
{
2727
if (m_iShowMol != -1)
2728
m_iRefOrSec[z][0] = AskRangeInteger(" Take dipole vector from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2729
else m_iRefOrSec[z][0] = 0;
2730
} else if (m_iVecType[z] == 2) // Geschwindigkeit
2731
{
2732
_ax6: if (m_iShowMol != -1)
2733
m_iRefOrSec[z][0] = AskRangeInteger(" Take velocity vector from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2734
else m_iRefOrSec[z][0] = 0;
2735
mprintf(" Velocity vector of which atoms to use (e.g. C7)? [#2] ");
2736
inpprintf("! Velocity vector of which atoms to use (e.g. C7)? [#2]\n");
2737
myget(buf);
2738
2739
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2740
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2741
2742
if (strlen(buf)==0)
2743
{
2744
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],"#2"))
2745
{
2746
eprintf("Weird error.\n");
2747
inpprintf("! Weird error.\n");
2748
abort();
2749
}
2750
} else if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2751
{
2752
eprintf("Wrong input.\n");
2753
inpprintf("! Wrong input.\n");
2754
delete ag;
2755
goto _ax6;
2756
}
2757
m_oaVectors.Add(ag);
2758
ti *= ag->m_iAtomGes;
2759
} else if (m_iVecType[z] == 3) // Kraft
2760
{
2761
_ax7: if (m_iShowMol != -1)
2762
m_iRefOrSec[z][0] = AskRangeInteger(" Take force vektor from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2763
else m_iRefOrSec[z][0] = 0;
2764
mprintf(" Force vector of which atoms to use (e.g. C7)? [#2] ");
2765
inpprintf("! Force vector of which atoms to use (e.g. C7)? [#2]\n");
2766
myget(buf);
2767
2768
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2769
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2770
2771
if (strlen(buf)==0)
2772
{
2773
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],"#2"))
2774
{
2775
eprintf("Weird Error.\n");
2776
inpprintf("! Weird Error.\n");
2777
abort();
2778
}
2779
} else if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2780
{
2781
eprintf("Wrong input.\n");
2782
inpprintf("! Wrong input.\n");
2783
delete ag;
2784
goto _ax7;
2785
}
2786
m_oaVectors.Add(ag);
2787
ti *= ag->m_iAtomGes;
2788
}
2789
} // END FOR 0..1
2790
z2++;
2791
m_iCombinations += ti;
2792
} while (g_bAdvanced2?AskYesNo("\n Add another set of vectors to this (!) ADF (y/n)? [no] ",false):false);
2793
2794
ParseDeriv();
2795
2796
switch(m_iDeriv)
2797
{
2798
case 0:
2799
m_fMinAngle = AskFloat("\n Enter minimal angle between the vectors: [0 deg] ",0.0f);
2800
m_fMaxAngle = AskFloat(" Enter maximal angle between the vectors: [180 deg] ",180.0f);
2801
break;
2802
case 1:
2803
if (m_bDerivAbs)
2804
m_fMinAngle = AskFloat(" Enter the minimal value of this d1-ADF in deg/ps: [0] ",0.0f);
2805
else m_fMinAngle = AskFloat(" Enter the minimal value of this d1-ADF in deg/ps: [-10.0] ",-10.0f);
2806
m_fMaxAngle = AskFloat(" Enter the maximal value of this d1-ADF in deg/ps: [10.0] ",10.0f);
2807
break;
2808
case 2:
2809
if (m_bDerivAbs)
2810
m_fMinAngle = AskFloat(" Enter the minimal value of this d2-ADF in deg/ps^2: [0] ",0.0f);
2811
else m_fMinAngle = AskFloat(" Enter the minimal value of this d2-ADF in deg/ps^2: [-10.0] ",-10.0f);
2812
m_fMaxAngle = AskFloat(" Enter the maximal value of this d2-ADF in deg/ps^2: [10.0] ",10.0f);
2813
break;
2814
}
2815
2816
/* if (m_fMaxAngle <= 90.0f)
2817
m_bFoldAngle = AskYesNo(" Should angles > 90 deg be \"mirrored\" (180 deg = 0 deg) (y/n)? [yes] ",true);
2818
else*/ m_bFoldAngle = false;
2819
m_bCosine = (AskRangeInteger(" Plot ADF against angle (0) or against cosine (1)? [0] ",0,1,0)!=0);
2820
if (m_bCosine)
2821
{
2822
m_fMinAngle = (float)cos(m_fMinAngle/180.0*Pi);
2823
m_fMaxAngle = (float)cos(m_fMaxAngle/180.0*Pi);
2824
if (m_fMinAngle > m_fMaxAngle)
2825
{
2826
tf = m_fMinAngle;
2827
m_fMinAngle = m_fMaxAngle;
2828
m_fMaxAngle = tf;
2829
}
2830
mprintf(" The data range is %.2f to %.2f.\n",m_fMinAngle,m_fMaxAngle);
2831
}
2832
if (!m_bCosine)
2833
m_bMirror = AskYesNo(" Force this ADF to be mirror-symmetric to the 90 deg line (y/n)? [no] ",false);
2834
else m_bMirror = false;
2835
m_iResolution = AskUnsignedInteger(" Please enter the resolution (bin count) for this ADF: [100] ",100);
2836
2837
if (g_bAdvanced2)
2838
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
2839
m_iHistogramRes = 0;
2840
2841
if (m_iShowMol != -1)
2842
m_bStat = AskYesNo(" Apply cone correction (y/n)? [%c] ",!m_bCosine,(!m_bCosine)?'y':'n');
2843
else m_bStat = 0;
2844
/* mprintf("\n Save temporal development of this ADF (0=nein, 1=ja)? [0] ");
2845
myget(buf);
2846
m_bSaveAngle = (atoi(buf)!=0);*/
2847
BuildName();
2848
mprintf(WHITE,"\n<<< End of Angular Distribution Function <<<\n\n");
2849
BTOUT;
2850
}
2851
2852
2853
void CDDF::Parse()
2854
{
2855
BTIN;
2856
char buf[256];
2857
CAtomGroup *ag;
2858
int z0, z, z2, i;
2859
float tf;
2860
2861
try { m_pDDF = new CDF(); } catch(...) { m_pDDF = NULL; }
2862
if (m_pDDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2863
2864
mprintf(WHITE,"\n>>> Dihedral Distribution Function >>>\n\n");
2865
m_bClassical = AskYesNo(" Use \"simple\" (y) (4 atoms) or \"generalized\" (n) (3 vectors) Dihedrals? [yes] ",true);
2866
2867
m_iCombinations = 1;
2868
if (m_bClassical)
2869
{
2870
m_bOrtho[0] = false;
2871
m_bOrtho[1] = false;
2872
m_bOrtho[2] = false;
2873
z0 = m_oaVectors.GetSize();
2874
for (z=0;z<3;z++)
2875
{
2876
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2877
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2878
2879
m_oaVectors.Add(ag);
2880
2881
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2882
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2883
2884
m_oaVectors.Add(ag);
2885
m_oaVectors.Add(NULL);
2886
}
2887
for (z=0;z<4;z++)
2888
{
2889
_bx: if (m_iShowMol != -1)
2890
i = AskRangeInteger(" Take the %d. atom from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2891
else i = 0;
2892
switch(z)
2893
{
2894
case 0:
2895
m_iRefOrSec[0][1] = i;
2896
break;
2897
case 1:
2898
m_iRefOrSec[0][0] = i;
2899
m_iRefOrSec[2][0] = i;
2900
break;
2901
case 2:
2902
m_iRefOrSec[2][1] = i;
2903
m_iRefOrSec[1][0] = i;
2904
break;
2905
case 3:
2906
m_iRefOrSec[1][1] = i;
2907
break;
2908
}
2909
mprintf(" Enter the %d. atom(s) (e.g. C7): ",z+1);
2910
inpprintf("! Enter the %d. atom(s) (e.g. C7):\n",z+1);
2911
myget(buf);
2912
switch(z)
2913
{
2914
case 0:
2915
if (!((CAtomGroup*)m_oaVectors[z0+0*3+1])->ParseAtoms((!m_iRefOrSec[0][1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2916
{
2917
eprintf("Wrong input.\n");
2918
inpprintf("! Wrong input.\n");
2919
goto _bx;
2920
}
2921
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+0*3+1])->m_iAtomGes;
2922
break;
2923
case 1:
2924
if (!((CAtomGroup*)m_oaVectors[z0+0*3+0])->ParseAtoms((!m_iRefOrSec[0][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2925
{
2926
eprintf("Wrong input.\n");
2927
inpprintf("! Wrong input.\n");
2928
goto _bx;
2929
}
2930
if (!((CAtomGroup*)m_oaVectors[z0+2*3+0])->ParseAtoms((!m_iRefOrSec[2][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2931
{
2932
eprintf("Wrong input.\n");
2933
inpprintf("! Wrong input.\n");
2934
goto _bx;
2935
}
2936
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+0*3+0])->m_iAtomGes;
2937
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+0*3+0])->m_iAtomGes;
2938
break;
2939
case 2:
2940
if (!((CAtomGroup*)m_oaVectors[z0+2*3+1])->ParseAtoms((!m_iRefOrSec[2][1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2941
{
2942
eprintf("Wrong input.\n");
2943
inpprintf("! Wrong input.\n");
2944
goto _bx;
2945
}
2946
if (!((CAtomGroup*)m_oaVectors[z0+1*3+0])->ParseAtoms((!m_iRefOrSec[1][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2947
{
2948
eprintf("Wrong input.\n");
2949
inpprintf("! Wrong input.\n");
2950
goto _bx;
2951
}
2952
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+2*3+1])->m_iAtomGes;
2953
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+2*3+1])->m_iAtomGes;
2954
break;
2955
case 3:
2956
if (!((CAtomGroup*)m_oaVectors[z0+1*3+1])->ParseAtoms((!m_iRefOrSec[1][1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2957
{
2958
eprintf("Wrong input.\n");
2959
inpprintf("! Wrong input.\n");
2960
goto _bx;
2961
}
2962
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+1*3+1])->m_iAtomGes;
2963
break;
2964
}
2965
}
2966
} else // NONCLASSIC
2967
{
2968
mprintf("\nYou now have to define 3 vectors:\n");
2969
mprintf("The 1st and 2nd vector are projected onto the normal plane of the 3rd vector.\n");
2970
mprintf("The angle between the two projected vectors in the plane is evaluated.\n");
2971
for (z=0;z<3;z++)
2972
{
2973
mprintf(WHITE,"\n * Vector %d\n",z+1);
2974
m_bOrtho[z] = (AskRangeInteger(" Shall the %d. vector connect 2 points (0) or be orthogonal to a plane (1)? [0] ",0,1,0,z+1) != 0);
2975
if (m_bOrtho[z])
2976
{
2977
for (z2=0;z2<3;z2++)
2978
{
2979
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2980
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2981
2982
_by: if (m_iShowMol != -1)
2983
m_iRefOrSec[z][z2] = AskRangeInteger(" Take the %d. atom(s) of the plane from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z2+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2984
else m_iRefOrSec[z][z2] = 0;
2985
mprintf(" Please enter the %d. atom(s) (e.g. C7): ",z2+1);
2986
inpprintf("! Please enter the %d. atom(s) (e.g. C7):\n",z2+1);
2987
myget(buf);
2988
if (!ag->ParseAtoms((!m_iRefOrSec[z][z2])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2989
{
2990
eprintf("Wrong input.\n");
2991
inpprintf("! Wrong input.\n");
2992
goto _by;
2993
}
2994
m_iCombinations *= ag->m_iAtomGes;
2995
m_oaVectors.Add(ag);
2996
}
2997
} else // Ortho
2998
{
2999
for (z2=0;z2<2;z2++)
3000
{
3001
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3002
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3003
3004
_bz: if (m_iShowMol != -1)
3005
m_iRefOrSec[z][z2] = AskRangeInteger(" Take the %d. atom(s) of the vector from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z2+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3006
else m_iRefOrSec[z][z2] = 0;
3007
mprintf(" Please enter the %d. atom(s) (e.g. C7): ",z2+1);
3008
inpprintf("! Please enter the %d. atom(s) (e.g. C7):\n",z2+1);
3009
myget(buf);
3010
if (!ag->ParseAtoms((!m_iRefOrSec[z][z2])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3011
{
3012
eprintf("Wrong input.\n");
3013
inpprintf("! Wrong input.\n");
3014
goto _bz;
3015
}
3016
m_iCombinations *= ag->m_iAtomGes;
3017
m_oaVectors.Add(ag);
3018
}
3019
m_oaVectors.Add(NULL);
3020
} // ENDIF ORTHO
3021
} // END FOR
3022
} // END IF NONCLASSIC
3023
3024
/* mprintf("\n");
3025
mprintf(" The \"classical\" dihedral angle is defined for a range of 0 ... 180 deg.\n\n");
3026
m_bAbs = !AskYesNo(" Do you want to extend the range to -180 ... +180 deg (y/n)? [no] ",false);*/
3027
3028
mprintf("\n");
3029
mprintf(" Per default, the dihedral angle is defined in a range of -180 ... 180 deg.\n\n");
3030
m_bPositive = AskYesNo(" Use range of 0 ... 360 deg instead (e.g. -90 deg becomes 270 deg, ...) (y/n)? [no] ",false);
3031
m_bAbs = false;
3032
mprintf("\n");
3033
3034
ParseDeriv();
3035
3036
switch(m_iDeriv)
3037
{
3038
case 0:
3039
if (m_bPositive)
3040
{
3041
m_fMinAngle = AskFloat("\n Enter minimal dihedral angle to observe: [0 deg] ",0);
3042
m_fMaxAngle = AskFloat(" Enter maximal dihedral angle to observe: [360 deg] ",360.0f);
1
/*****************************************************************************
2
TRAVIS - Trajectory Analyzer and Visualizer
3
http://www.travis-analyzer.de/
4
5
Copyright (c) 2009-2014 Martin Brehm
6
2012-2014 Martin Thomas
7
8
This file written by Martin Brehm.
9
10
This program is free software: you can redistribute it and/or modify
11
it under the terms of the GNU General Public License as published by
12
the Free Software Foundation, either version 3 of the License, or
13
(at your option) any later version.
14
15
This program is distributed in the hope that it will be useful,
16
but WITHOUT ANY WARRANTY; without even the implied warranty of
17
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18
GNU General Public License for more details.
19
20
You should have received a copy of the GNU General Public License
21
along with this program. If not, see <http://www.gnu.org/licenses/>.
22
*****************************************************************************/
23
24
#include "moltools.h"
25
#include "travis.h"
26
#include "maintools.h"
27
#include "plproj.h"
28
29
30
31
CAtom::CAtom()
32
{
33
m_pElement = NULL;
34
m_bExclude = false;
35
m_pMergedTo = NULL;
36
m_iIndex = -1;
37
}
38
39
40
CAtom::~CAtom()
41
{
42
}
43
44
45
CVirtualAtom::CVirtualAtom()
46
{
47
m_faWeight.SetName("CVirtualAtom::m_faWeight");
48
}
49
50
51
CVirtualAtom::~CVirtualAtom()
52
{
53
}
54
55
56
CMolecule::CMolecule()
57
{
58
m_iWannierCount = 0;
59
m_sName = NULL;
60
m_fCharge = 0;
61
m_bPseudo = false;
62
m_bChargesAssigned = false;
63
64
m_baAtomIndex.SetName("CMolecule::m_baAtomIndex");
65
m_waAtomCount.SetName("CMolecule::m_waAtomCount");
66
m_laSingleMolIndex.SetName("CMolecule::m_laSingleMolIndex");
67
m_laVirtualAtoms.SetName("CMolecule::m_laVirtualAtoms");
68
m_oaNewNumbers.SetName("CMolecule::m_oaNewNumbers");
69
m_oaRingAtomTypes.SetName("CMolecule::m_oaRingAtomTypes");
70
m_oaRingAtoms.SetName("CMolecule::m_oaRingAtoms");
71
m_oaCharges.SetName("CMolecule::m_oaCharges");
72
}
73
74
75
CMolecule::~CMolecule()
76
{
77
if (m_sName != NULL)
78
{
79
delete[] m_sName;
80
m_sName = NULL;
81
}
82
}
83
84
85
CMolAtom::CMolAtom()
86
{
87
m_oaBonds.SetName("CMolAtom::m_oaBonds");
88
}
89
90
91
CMolAtom::~CMolAtom()
92
{
93
}
94
95
96
CSingleMolecule::CSingleMolecule()
97
{
98
m_bPseudo = false;
99
100
m_oaBondGroups.SetName("CSingleMolecule::m_oaBondGroups");
101
m_oaBonds.SetName("CSingleMolecule::m_oaBonds");
102
m_oaAngleGroups.SetName("CSingleMolecule::m_oaAngleGroups");
103
m_oaAngles.SetName("CSingleMolecule::m_oaAngles");
104
m_oaRings.SetName("CSingleMolecule::m_oaRings");
105
m_laBonds.SetName("CSingleMolecule::m_laBonds");
106
m_laWannier.SetName("CSingleMolecule::m_laWannier");
107
m_oaAtomOffset.SetName("CSingleMolecule::m_oaAtomOffset");
108
m_oaMolAtoms.SetName("CSingleMolecule::m_oaMolAtoms");
109
m_baAtomIndex.SetName("CSingleMolecule::m_baAtomIndex");
110
}
111
112
113
CSingleMolecule::~CSingleMolecule()
114
{
115
}
116
117
118
CADF::CADF()
119
{
120
m_pADF = NULL;
121
m_oaVectors.SetName("CADF::m_oaVectors");
122
m_faACF.SetName("CADF::m_faACF");
123
m_faMinMaxAngle.SetName("CADF::m_faMinMaxAngle");
124
}
125
126
127
CADF::~CADF()
128
{
129
}
130
131
132
CDDF::CDDF()
133
{
134
m_bRotate = false;
135
m_oaVectors.SetName("CDDF::m_oaVectors");
136
m_faLastData.SetName("CDDF::m_faLastData");
137
m_laRotation.SetName("CDDF::m_laRotation");
138
m_faACF.SetName("CDDF::m_faACF");
139
}
140
141
142
CDDF::~CDDF()
143
{
144
}
145
146
147
CMSD::CMSD()
148
{
149
m_oaCache.SetName("CMSD::m_oaCache");
150
}
151
152
153
CMSD::~CMSD()
154
{
155
}
156
157
158
CVHDF::CVHDF()
159
{
160
m_sName = NULL;
161
m_sShortName = NULL;
162
m_pVHDF = NULL;
163
m_oaVectors.SetName("CVHDF::m_oaVectors");
164
}
165
166
167
CVHDF::~CVHDF()
168
{
169
if (m_sName != NULL)
170
{
171
delete[] m_sName;
172
m_sName = NULL;
173
}
174
if (m_sShortName != NULL)
175
{
176
delete[] m_sShortName;
177
m_sShortName = NULL;
178
}
179
if (m_pVHDF != NULL)
180
{
181
delete m_pVHDF;
182
m_pVHDF = NULL;
183
}
184
}
185
186
187
CRDF::CRDF()
188
{
189
m_fDist = NULL;
190
m_pRDF = NULL;
191
m_bProbDens = false;
192
m_faMinMaxDist.SetName("CRDF::m_faMinMaxDist");
193
m_oaVectors.SetName("CRDF::m_oaVectors");
194
m_faACF.SetName("CRDF::m_faACF");
195
}
196
197
198
CPlDF::CPlDF()
199
{
200
m_pPlDF = NULL;
201
m_oaVectors.SetName("CPlDF::m_oaVectors");
202
m_faACF.SetName("CPlDF::m_faACF");
203
}
204
205
206
CLiDF::CLiDF()
207
{
208
m_pLiDF = NULL;
209
m_oaVectors.SetName("CLiDF::m_oaVectors");
210
m_faACF.SetName("CLiDF::m_faACF");
211
}
212
213
214
CRDF::~CRDF()
215
{
216
if (m_sName != NULL)
217
{
218
delete[] m_sName;
219
m_sName = NULL;
220
}
221
if (m_sShortName != NULL)
222
{
223
delete[] m_sShortName;
224
m_sShortName = NULL;
225
}
226
if (m_fDist != NULL)
227
{
228
delete[] m_fDist;
229
m_fDist = NULL;
230
}
231
if (m_pRDF != NULL)
232
{
233
delete m_pRDF;
234
m_pRDF = NULL;
235
}
236
if (m_faData != NULL)
237
{
238
delete[] m_faData;
239
m_faData = NULL;
240
}
241
}
242
243
244
CDensDF::CDensDF()
245
{
246
m_pDensDF = NULL;
247
}
248
249
250
CDensDF::~CDensDF()
251
{
252
if (m_sName != NULL)
253
{
254
delete[] m_sName;
255
m_sName = NULL;
256
}
257
if (m_sShortName != NULL)
258
{
259
delete[] m_sShortName;
260
m_sShortName = NULL;
261
}
262
if (m_pDensDF != NULL)
263
{
264
delete m_pDensDF;
265
m_pDensDF = NULL;
266
}
267
}
268
269
270
CVDF::CVDF()
271
{
272
m_faACF.SetName("CVDF::m_faACF");
273
}
274
275
276
CVDF::~CVDF()
277
{
278
}
279
280
281
CDipDF::CDipDF()
282
{
283
m_faACF.SetName("CDipDF::m_faACF");
284
}
285
286
287
CDipDF::~CDipDF()
288
{
289
}
290
291
292
CSDF::CSDF()
293
{
294
m_pCutPlane = NULL;
295
m_fPosCounter = 0;
296
m_fAtom2PosX = 0;
297
m_fAtom3PosX = 0;
298
m_fAtom3PosY = 0;
299
}
300
301
302
CSDF::~CSDF()
303
{
304
}
305
306
307
CCDF::CCDF()
308
{
309
m_bAxisDivide = false;
310
}
311
312
313
CCDF::~CCDF()
314
{
315
}
316
317
318
CConditionSubGroup::CConditionSubGroup()
319
{
320
m_fPassed = 0;
321
m_fTotal = 0;
322
m_oaConditions.SetName("CConditionSubGroup::m_oaConditions");
323
}
324
325
326
CConditionSubGroup::~CConditionSubGroup()
327
{
328
}
329
330
331
CConditionGroup::CConditionGroup()
332
{
333
m_pTable = NULL;
334
m_bInactive = false;
335
m_fPassed = 0;
336
m_fTotal = 0;
337
m_iPassCounter = NULL;
338
m_bAlwaysTrue = NULL;
339
m_oaConditionSubGroups.SetName("CConditionGroup::m_oaConditionSubGroups");
340
}
341
342
343
CConditionGroup::~CConditionGroup()
344
{
345
}
346
347
348
bool ContainsDigit(const char *s)
349
{
350
if (strcspn(s,"0123456789") != strlen(s))
351
return true;
352
return false;
353
}
354
355
356
void ReplaceDigits(char *s)
357
{
358
char buf[32];
359
char *p, *q;
360
bool b;
361
362
p = s;
363
q = buf;
364
b = false;
365
while (*p != 0)
366
{
367
if (b)
368
{
369
switch(*p)
370
{
371
case '1': *q = 'a'; break;
372
case '2': *q = 'b'; break;
373
case '3': *q = 'c'; break;
374
case '4': *q = 'd'; break;
375
case '5': *q = 'e'; break;
376
case '6': *q = 'f'; break;
377
case '7': *q = 'g'; break;
378
case '8': *q = 'h'; break;
379
case '9': *q = 'i'; break;
380
case '0': *q = 'z'; break;
381
default: *q = *p;
382
}
383
} else
384
{
385
switch(*p)
386
{
387
case '1': b = true; *q = '_'; q++; *q = 'a'; break;
388
case '2': b = true; *q = '_'; q++; *q = 'b'; break;
389
case '3': b = true; *q = '_'; q++; *q = 'c'; break;
390
case '4': b = true; *q = '_'; q++; *q = 'd'; break;
391
case '5': b = true; *q = '_'; q++; *q = 'e'; break;
392
case '6': b = true; *q = '_'; q++; *q = 'f'; break;
393
case '7': b = true; *q = '_'; q++; *q = 'g'; break;
394
case '8': b = true; *q = '_'; q++; *q = 'h'; break;
395
case '9': b = true; *q = '_'; q++; *q = 'i'; break;
396
case '0': b = true; *q = '_'; q++; *q = 'z'; break;
397
default: *q = *p;
398
}
399
}
400
p++;
401
q++;
402
}
403
*q = 0;
404
strcpy(s,buf);
405
}
406
407
408
void xAddAtom(const char *s)
409
{
410
BTIN;
411
int z;
412
CAtom *a;
413
char buf[64];
414
415
if (g_oaAtoms.GetSize() >= 254)
416
{
417
eprintf("More than 254 different atom types not supported.\n");
418
return;
419
}
420
421
strcpy(buf,s);
422
ReplaceDigits(buf);
423
424
// printf("AddAtom: \"%s\".\n",s);
425
for (z=0;z<g_oaAtoms.GetSize();z++)
426
{
427
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName)==0)
428
{
429
((CAtom*)g_oaAtoms[z])->m_iCount++;
430
BTOUT;
431
return;
432
}
433
}
434
if (ContainsDigit(s))
435
eprintf("Digits in element labels not allowed. Renaming %s to %s.\n",s,buf);
436
437
try { a = new CAtom(); } catch(...) { a = NULL; }
438
if (a == NULL) NewException((double)sizeof(CAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
439
440
a->m_iIndex = g_oaAtoms.GetSize();
441
strcpy(a->m_sName,buf);
442
if (islower(a->m_sName[0]))
443
a->m_sName[0] = toupper(a->m_sName[0]);
444
if (strlen(a->m_sName) > 1)
445
if (isupper(a->m_sName[1]))
446
a->m_sName[1] = tolower(a->m_sName[1]);
447
a->m_iCount = 1;
448
/* if (s[0] != '#')
449
{*/
450
a->m_pElement = FindElement(buf,false);
451
if (a->m_pElement == NULL)
452
{
453
try { a->m_pElement = new CElement(); } catch(...) { a->m_pElement = NULL; }
454
if (a->m_pElement == NULL) NewException((double)sizeof(CElement),__FILE__,__LINE__,__PRETTY_FUNCTION__);
455
456
try { a->m_pElement->m_sLabel = new char[strlen(a->m_sName)+1]; } catch(...) { a->m_pElement->m_sLabel = NULL; }
457
if (a->m_pElement->m_sLabel == NULL) NewException((double)(strlen(a->m_sName)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
458
459
strcpy(a->m_pElement->m_sLabel,a->m_sName);
460
}
461
/* a->m_fMass = AtomMass(s);
462
a->m_fRadius = AtomRadius(s);
463
a->m_iOrd = AtomOrd(s);*/
464
// a->m_fVDWRadius = AtomVDWRadius(s);
465
/* } else
466
{
467
a->m_fMass = 0.0f;
468
a->m_fRadius = 0.0f;
469
a->m_iOrd = 0;
470
// a->m_fVDWRadius = 0.0f;
471
}*/
472
g_oaAtoms.Add(a);
473
// g_pAtoms[g_iElementCount].Offset = offset;
474
// printf("Fuege Atom %s an Stelle %d neu hinzu. Der Offset ist %d.\n",s,g_iAtomCount,offset);
475
// g_iElementCount++;
476
BTOUT;
477
}
478
479
480
void CSingleMolecule::Dump()
481
{
482
BTIN;
483
int z, z2;
484
mprintf("### Single Molecule Dump ###\n");
485
mprintf("%d Elemente.\n",m_baAtomIndex.GetSize());
486
for (z=0;z<m_baAtomIndex.GetSize();z++)
487
{
488
mprintf(" * Element %d: %s. %d Vertreter *\n Atome ",z+1,((CAtom*)g_oaAtoms[m_baAtomIndex[z]])->m_sName,((CxIntArray*)m_oaAtomOffset[z])->GetSize());
489
for (z2=0;z2<((CxIntArray*)m_oaAtomOffset[z])->GetSize();z2++)
490
{
491
mprintf("%d",((CxIntArray*)m_oaAtomOffset[z])->GetAt(z2));
492
if (z2 < ((CxIntArray*)m_oaAtomOffset[z])->GetSize()-1)
493
mprintf(", ");
494
}
495
mprintf("\n");
496
}
497
BTOUT;
498
}
499
500
501
void CMolecule::Dump()
502
{
503
BTIN;
504
int z;
505
mprintf("### Molecule Type Dump ###\n");
506
mprintf("%d Elemente.\n",m_baAtomIndex.GetSize());
507
for (z=0;z<m_baAtomIndex.GetSize();z++)
508
mprintf(" * Element %d: %s. %d Vertreter *\n",z+1,((CAtom*)g_oaAtoms[m_baAtomIndex[z]])->m_sName,m_waAtomCount[z]);
509
BTOUT;
510
}
511
512
513
void CADF::BuildName()
514
{
515
BTIN;
516
int z, z2;
517
char tmp[256];
518
CAtomGroup *ag;
519
520
tmp[0] = 0;
521
if (m_iDeriv != 0)
522
sprintf(tmp,"deriv%d_",m_iDeriv);
523
for (z2=0;z2<m_oaVectors.GetSize()/6;z2++)
524
{
525
for (z=0;z<2;z++)
526
{
527
strcat(tmp,"[");
528
if (m_iVecType[z] == 0) // Position
529
{
530
if (m_bOrtho[z])
531
{
532
/* if (m_bSameFoot && (z == 1))
533
ag = (CAtomGroup*)m_oaVectors[z2*6];
534
else */ag = (CAtomGroup*)m_oaVectors[z2*6+z*3];
535
strcat(tmp,ag->m_sName);
536
if (m_iRefOrSec[z][0])
537
strcat(tmp,"o_");
538
else strcat(tmp,"r_");
539
strcat(tmp,((CAtomGroup*)m_oaVectors[z2*6+z*3+1])->m_sName);
540
if (m_iRefOrSec[z][1])
541
strcat(tmp,"o_");
542
else strcat(tmp,"r_");
543
strcat(tmp,((CAtomGroup*)m_oaVectors[z2*6+z*3+2])->m_sName);
544
if (m_iRefOrSec[z][2])
545
strcat(tmp,"o");
546
else strcat(tmp,"r");
547
} else
548
{
549
/* if (m_bSameFoot && (z == 1))
550
ag = (CAtomGroup*)m_oaVectors[z2*6];
551
else */ag = (CAtomGroup*)m_oaVectors[z2*6+z*3];
552
strcat(tmp,ag->m_sName);
553
if (m_iRefOrSec[z][0])
554
strcat(tmp,"o_");
555
else strcat(tmp,"r_");
556
strcat(tmp,((CAtomGroup*)m_oaVectors[z2*6+z*3+1])->m_sName);
557
if (m_iRefOrSec[z][1])
558
strcat(tmp,"o");
559
else strcat(tmp,"r");
560
}
561
} else if (m_iVecType[z] == 1) // Dipol
562
{
563
strcat(tmp,"dip_");
564
strcat(tmp,(m_iRefOrSec[z][0]!=0)?((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName:((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
565
} else if (m_iVecType[z] == 2) // Geschwindigkeit
566
{
567
strcat(tmp,"vel_");
568
strcat(tmp,((CAtomGroup*)m_oaVectors[z*3])->m_sName);
569
} else if (m_iVecType[z] == 3) // Kraft
570
{
571
strcat(tmp,"frc_");
572
strcat(tmp,((CAtomGroup*)m_oaVectors[z*3])->m_sName);
573
}
574
if (z == 0)
575
strcat(tmp,"]-");
576
else strcat(tmp,"]");
577
}
578
if (z2<(m_oaVectors.GetSize()/6)-1)
579
strcat(tmp,"_");
580
}
581
582
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
583
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
584
585
strcpy(m_sShortName,tmp);
586
if (m_iShowMol != -1)
587
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
588
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
589
strcat(tmp,m_sShortName);
590
591
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
592
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
593
594
strcpy(m_sName,tmp);
595
BTOUT;
596
}
597
598
599
void CPlDF::BuildName()
600
{
601
BTIN;
602
char tmp[256];
603
CAtomGroup *ag;
604
605
tmp[0] = 0;
606
607
strcat(tmp,"[");
608
if (m_bNormal)
609
{
610
ag = (CAtomGroup*)m_oaVectors[0];
611
strcat(tmp,ag->m_sName);
612
if (m_iRefOrSec[0])
613
strcat(tmp,"o_");
614
else strcat(tmp,"r_");
615
strcat(tmp,((CAtomGroup*)m_oaVectors[1])->m_sName);
616
if (m_iRefOrSec[1])
617
strcat(tmp,"o");
618
else strcat(tmp,"r");
619
} else
620
{
621
ag = (CAtomGroup*)m_oaVectors[0];
622
strcat(tmp,ag->m_sName);
623
if (m_iRefOrSec[0])
624
strcat(tmp,"o_");
625
else strcat(tmp,"r_");
626
strcat(tmp,((CAtomGroup*)m_oaVectors[1])->m_sName);
627
if (m_iRefOrSec[1])
628
strcat(tmp,"o_");
629
else strcat(tmp,"r_");
630
strcat(tmp,((CAtomGroup*)m_oaVectors[2])->m_sName);
631
if (m_iRefOrSec[2])
632
strcat(tmp,"o");
633
else strcat(tmp,"r");
634
}
635
strcat(tmp,"]_");
636
strcat(tmp,((CAtomGroup*)m_oaVectors[3])->m_sName);
637
if (m_iRefOrSec[3])
638
strcat(tmp,"o");
639
else strcat(tmp,"r");
640
641
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
642
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
643
644
strcpy(m_sShortName,tmp);
645
if (m_iShowMol != -1)
646
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
647
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
648
strcat(tmp,m_sShortName);
649
650
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
651
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
652
653
strcpy(m_sName,tmp);
654
BTOUT;
655
}
656
657
658
void CLiDF::BuildName()
659
{
660
BTIN;
661
char tmp[256];
662
CAtomGroup *ag;
663
664
tmp[0] = 0;
665
666
strcat(tmp,"[");
667
if (m_bNormal)
668
{
669
ag = (CAtomGroup*)m_oaVectors[0];
670
strcat(tmp,ag->m_sName);
671
if (m_iRefOrSec[0])
672
strcat(tmp,"o_");
673
else strcat(tmp,"r_");
674
strcat(tmp,((CAtomGroup*)m_oaVectors[1])->m_sName);
675
if (m_iRefOrSec[1])
676
strcat(tmp,"o_");
677
else strcat(tmp,"r_");
678
strcat(tmp,((CAtomGroup*)m_oaVectors[2])->m_sName);
679
if (m_iRefOrSec[2])
680
strcat(tmp,"o");
681
else strcat(tmp,"r");
682
} else
683
{
684
ag = (CAtomGroup*)m_oaVectors[0];
685
strcat(tmp,ag->m_sName);
686
if (m_iRefOrSec[0])
687
strcat(tmp,"o_");
688
else strcat(tmp,"r_");
689
strcat(tmp,((CAtomGroup*)m_oaVectors[1])->m_sName);
690
if (m_iRefOrSec[1])
691
strcat(tmp,"o");
692
else strcat(tmp,"r");
693
}
694
strcat(tmp,"]_");
695
strcat(tmp,((CAtomGroup*)m_oaVectors[3])->m_sName);
696
if (m_iRefOrSec[3])
697
strcat(tmp,"o");
698
else strcat(tmp,"r");
699
700
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
701
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
702
703
strcpy(m_sShortName,tmp);
704
if (m_iShowMol != -1)
705
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
706
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
707
strcat(tmp,m_sShortName);
708
709
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
710
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
711
712
strcpy(m_sName,tmp);
713
BTOUT;
714
}
715
716
717
void CDDF::BuildName()
718
{
719
BTIN;
720
int z;
721
char tmp[256];
722
CAtomGroup *ag;
723
724
tmp[0] = 0;
725
if (m_iDeriv != 0)
726
sprintf(tmp,"deriv%d_",m_iDeriv);
727
for (z=0;z<3;z++)
728
{
729
strcat(tmp,"[");
730
if (m_bOrtho[z])
731
{
732
ag = (CAtomGroup*)m_oaVectors[z*3];
733
strcat(tmp,ag->m_sName);
734
if (m_iRefOrSec[z][0])
735
strcat(tmp,"o_");
736
else strcat(tmp,"r_");
737
strcat(tmp,((CAtomGroup*)m_oaVectors[z*3+1])->m_sName);
738
if (m_iRefOrSec[z][1])
739
strcat(tmp,"o_");
740
else strcat(tmp,"r_");
741
strcat(tmp,((CAtomGroup*)m_oaVectors[z*3+2])->m_sName);
742
if (m_iRefOrSec[z][2])
743
strcat(tmp,"o");
744
else strcat(tmp,"r");
745
} else
746
{
747
ag = (CAtomGroup*)m_oaVectors[z*3];
748
strcat(tmp,ag->m_sName);
749
if (m_iRefOrSec[z][0])
750
strcat(tmp,"o_");
751
else strcat(tmp,"r_");
752
strcat(tmp,((CAtomGroup*)m_oaVectors[z*3+1])->m_sName);
753
if (m_iRefOrSec[z][1])
754
strcat(tmp,"o");
755
else strcat(tmp,"r");
756
}
757
if (z < 2)
758
strcat(tmp,"]-");
759
else strcat(tmp,"]");
760
}
761
762
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
763
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
764
765
strcpy(m_sShortName,tmp);
766
if (m_iShowMol != -1)
767
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
768
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
769
strcat(tmp,m_sShortName);
770
771
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
772
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
773
774
strcpy(m_sName,tmp);
775
BTOUT;
776
}
777
778
779
void CDipDF::BuildName()
780
{
781
BTIN;
782
char tmp[256];
783
784
tmp[0] = 0;
785
if (m_iDeriv != 0)
786
sprintf(tmp,"deriv%d_",m_iDeriv);
787
if (m_iRefOrSec)
788
sprintf(tmp,"%s",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
789
else sprintf(tmp,"%s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
790
791
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
792
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
793
794
strcpy(m_sName,tmp);
795
796
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
797
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
798
799
strcpy(m_sShortName,tmp);
800
BTOUT;
801
}
802
803
804
void CADF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
805
{
806
BXIN;
807
int z, z1t, z1a, z2t, z2a, z3t, z3a, z4t, z4a, z5t, z5a, z6t, z6a;
808
CAtomGroup *g1, *g2, *g3, *g4, *g5, *g6;
809
CxIntArray *a1, *a2, *a3, *a4, *a5, *a6;
810
811
vec->RemoveAll_KeepSize();
812
for (z=0;z<m_oaVectors.GetSize()/6;z++)
813
{
814
if (m_bOrtho[0])
815
{
816
g1 = (CAtomGroup*)m_oaVectors[z*6];
817
g2 = (CAtomGroup*)m_oaVectors[z*6+1];
818
g3 = (CAtomGroup*)m_oaVectors[z*6+2];
819
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
820
{
821
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
822
for (z1a=0;z1a<a1->GetSize();z1a++)
823
{
824
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
825
{
826
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
827
for (z2a=0;z2a<a2->GetSize();z2a++)
828
{
829
for (z3t=0;z3t<g3->m_baAtomType.GetSize();z3t++)
830
{
831
a3 = (CxIntArray*)g3->m_oaAtoms[z3t];
832
for (z3a=0;z3a<a3->GetSize();z3a++)
833
{
834
if (m_bOrtho[1])
835
{
836
/* if (m_bSameFoot)
837
g4 = g1;
838
else */g4 = (CAtomGroup*)m_oaVectors[z*6+3];
839
g5 = (CAtomGroup*)m_oaVectors[z*6+4];
840
g6 = (CAtomGroup*)m_oaVectors[z*6+5];
841
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
842
{
843
/* if (m_bSameFoot && (z4t != z1t))
844
continue;*/
845
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
846
for (z4a=0;z4a<a4->GetSize();z4a++)
847
{
848
/* if (m_bSameFoot && (z4a != z1a))
849
continue;*/
850
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
851
{
852
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
853
for (z5a=0;z5a<a5->GetSize();z5a++)
854
{
855
for (z6t=0;z6t<g6->m_baAtomType.GetSize();z6t++)
856
{
857
a6 = (CxIntArray*)g6->m_oaAtoms[z6t];
858
for (z6a=0;z6a<a6->GetSize();z6a++)
859
{
860
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
861
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
862
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
863
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
864
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
865
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
866
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
867
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
868
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
869
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
870
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
871
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
872
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
873
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
874
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
875
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
876
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
877
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
878
}
879
}
880
}
881
}
882
}
883
}
884
} else
885
{
886
/* if (m_bSameFoot)
887
g4 = g1;
888
else */g4 = (CAtomGroup*)m_oaVectors[z*6+3];
889
g5 = (CAtomGroup*)m_oaVectors[z*6+4];
890
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
891
{
892
/* if (m_bSameFoot && (z4t != z1t))
893
continue;*/
894
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
895
for (z4a=0;z4a<a4->GetSize();z4a++)
896
{
897
/* if (m_bSameFoot && (z4a != z1a))
898
continue;*/
899
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
900
{
901
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
902
for (z5a=0;z5a<a5->GetSize();z5a++)
903
{
904
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
905
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
906
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
907
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
908
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
909
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
910
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
911
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
912
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
913
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
914
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
915
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
916
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
917
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
918
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
919
vec->Add(0);
920
}
921
}
922
}
923
}
924
} // END IF NOT ORTHO[1]
925
}
926
}
927
}
928
}
929
}
930
}
931
} else
932
{
933
g1 = (CAtomGroup*)m_oaVectors[z*6];
934
g2 = (CAtomGroup*)m_oaVectors[z*6+1];
935
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
936
{
937
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
938
for (z1a=0;z1a<a1->GetSize();z1a++)
939
{
940
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
941
{
942
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
943
for (z2a=0;z2a<a2->GetSize();z2a++)
944
{
945
if (m_bOrtho[1])
946
{
947
/* if (m_bSameFoot)
948
g4 = g1;
949
else */g4 = (CAtomGroup*)m_oaVectors[z*6+3];
950
g5 = (CAtomGroup*)m_oaVectors[z*6+4];
951
g6 = (CAtomGroup*)m_oaVectors[z*6+5];
952
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
953
{
954
/* if (m_bSameFoot && (z4t != z1t))
955
continue;*/
956
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
957
for (z4a=0;z4a<a4->GetSize();z4a++)
958
{
959
/* if (m_bSameFoot && (z4a != z1a))
960
continue;*/
961
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
962
{
963
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
964
for (z5a=0;z5a<a5->GetSize();z5a++)
965
{
966
for (z6t=0;z6t<g6->m_baAtomType.GetSize();z6t++)
967
{
968
a6 = (CxIntArray*)g6->m_oaAtoms[z6t];
969
for (z6a=0;z6a<a6->GetSize();z6a++)
970
{
971
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
972
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
973
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
974
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
975
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
976
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
977
vec->Add(0);
978
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
979
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
980
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
981
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
982
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
983
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
984
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
985
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
986
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
987
}
988
}
989
}
990
}
991
}
992
}
993
} else
994
{
995
/* if (m_bSameFoot)
996
g4 = g1;
997
else */g4 = (CAtomGroup*)m_oaVectors[z*6+3];
998
g5 = (CAtomGroup*)m_oaVectors[z*6+4];
999
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1000
{
1001
/* if (m_bSameFoot && (z4t != z1t))
1002
continue;*/
1003
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1004
for (z4a=0;z4a<a4->GetSize();z4a++)
1005
{
1006
/* if (m_bSameFoot && (z4a != z1a))
1007
continue;*/
1008
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
1009
{
1010
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
1011
for (z5a=0;z5a<a5->GetSize();z5a++)
1012
{
1013
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1014
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1015
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1016
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1017
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1018
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1019
vec->Add(0);
1020
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1021
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1022
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1023
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1024
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1025
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1026
vec->Add(0);
1027
}
1028
}
1029
}
1030
}
1031
} // END IF NOT ORTHO[1]
1032
}
1033
}
1034
}
1035
}
1036
}
1037
}
1038
BXOUT;
1039
}
1040
1041
1042
/* Mega abartig !!!! */
1043
void CDDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
1044
{
1045
BXIN;
1046
int z, z1t, z1a, z2t, z2a, z3t, z3a, z4t, z4a, z5t, z5a, z6t, z6a, z7t, z7a, z8t, z8a, z9t, z9a;
1047
CAtomGroup *g1, *g2, *g3, *g4, *g5, *g6, *g7, *g8, *g9;
1048
CxIntArray *a1, *a2, *a3, *a4, *a5, *a6, *a7, *a8, *a9;
1049
1050
vec->RemoveAll_KeepSize();
1051
for (z=0;z<m_oaVectors.GetSize()/9;z++)
1052
{
1053
if (m_bOrtho[0])
1054
{
1055
g1 = (CAtomGroup*)m_oaVectors[z*9];
1056
g2 = (CAtomGroup*)m_oaVectors[z*9+1];
1057
g3 = (CAtomGroup*)m_oaVectors[z*9+2];
1058
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1059
{
1060
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1061
for (z1a=0;z1a<a1->GetSize();z1a++)
1062
{
1063
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1064
{
1065
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1066
for (z2a=0;z2a<a2->GetSize();z2a++)
1067
{
1068
for (z3t=0;z3t<g3->m_baAtomType.GetSize();z3t++)
1069
{
1070
a3 = (CxIntArray*)g3->m_oaAtoms[z3t];
1071
for (z3a=0;z3a<a3->GetSize();z3a++)
1072
{
1073
if (m_bOrtho[1])
1074
{
1075
g4 = (CAtomGroup*)m_oaVectors[z*9+3];
1076
g5 = (CAtomGroup*)m_oaVectors[z*9+4];
1077
g6 = (CAtomGroup*)m_oaVectors[z*9+5];
1078
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1079
{
1080
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1081
for (z4a=0;z4a<a4->GetSize();z4a++)
1082
{
1083
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
1084
{
1085
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
1086
for (z5a=0;z5a<a5->GetSize();z5a++)
1087
{
1088
for (z6t=0;z6t<g6->m_baAtomType.GetSize();z6t++)
1089
{
1090
a6 = (CxIntArray*)g6->m_oaAtoms[z6t];
1091
for (z6a=0;z6a<a6->GetSize();z6a++)
1092
{
1093
if (m_bOrtho[2])
1094
{
1095
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1096
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1097
g9 = (CAtomGroup*)m_oaVectors[z*9+8];
1098
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1099
{
1100
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1101
for (z7a=0;z7a<a7->GetSize();z7a++)
1102
{
1103
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1104
{
1105
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1106
for (z8a=0;z8a<a8->GetSize();z8a++)
1107
{
1108
for (z9t=0;z9t<g9->m_baAtomType.GetSize();z9t++)
1109
{
1110
a9 = (CxIntArray*)g9->m_oaAtoms[z9t];
1111
for (z9a=0;z9a<a9->GetSize();z9a++)
1112
{
1113
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1114
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1115
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1116
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1117
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1118
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1119
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
1120
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1121
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1122
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1123
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1124
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1125
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1126
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1127
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1128
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
1129
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1130
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1131
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1132
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1133
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1134
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1135
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1136
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1137
if ((!m_iRefOrSec[2][2]) || (obs == NULL))
1138
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1139
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1140
}
1141
}
1142
}
1143
}
1144
}
1145
}
1146
} else // IF NOT ORTHO[2]
1147
{
1148
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1149
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1150
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1151
{
1152
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1153
for (z7a=0;z7a<a7->GetSize();z7a++)
1154
{
1155
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1156
{
1157
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1158
for (z8a=0;z8a<a8->GetSize();z8a++)
1159
{
1160
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1161
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1162
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1163
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1164
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1165
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1166
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
1167
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1168
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1169
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1170
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1171
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1172
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1173
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1174
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1175
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
1176
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1177
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1178
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1179
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1180
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1181
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1182
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1183
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1184
vec->Add(0);
1185
}
1186
}
1187
}
1188
}
1189
} // END IF NOT ORTHO[2]
1190
}
1191
}
1192
}
1193
}
1194
}
1195
}
1196
} else // IF NOT ORTHO[1]
1197
{
1198
g4 = (CAtomGroup*)m_oaVectors[z*9+3];
1199
g5 = (CAtomGroup*)m_oaVectors[z*9+4];
1200
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1201
{
1202
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1203
for (z4a=0;z4a<a4->GetSize();z4a++)
1204
{
1205
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
1206
{
1207
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
1208
for (z5a=0;z5a<a5->GetSize();z5a++)
1209
{
1210
if (m_bOrtho[2])
1211
{
1212
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1213
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1214
g9 = (CAtomGroup*)m_oaVectors[z*9+8];
1215
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1216
{
1217
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1218
for (z7a=0;z7a<a7->GetSize();z7a++)
1219
{
1220
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1221
{
1222
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1223
for (z8a=0;z8a<a8->GetSize();z8a++)
1224
{
1225
for (z9t=0;z9t<g9->m_baAtomType.GetSize();z9t++)
1226
{
1227
a9 = (CxIntArray*)g9->m_oaAtoms[z9t];
1228
for (z9a=0;z9a<a9->GetSize();z9a++)
1229
{
1230
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1231
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1232
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1233
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1234
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1235
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1236
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
1237
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1238
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1239
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1240
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1241
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1242
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1243
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1244
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1245
vec->Add(0);
1246
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1247
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1248
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1249
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1250
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1251
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1252
if ((!m_iRefOrSec[2][2]) || (obs == NULL))
1253
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1254
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1255
}
1256
}
1257
}
1258
}
1259
}
1260
}
1261
} else // IF NOT ORTHO[2]
1262
{
1263
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1264
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1265
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1266
{
1267
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1268
for (z7a=0;z7a<a7->GetSize();z7a++)
1269
{
1270
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1271
{
1272
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1273
for (z8a=0;z8a<a8->GetSize();z8a++)
1274
{
1275
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1276
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1277
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1278
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1279
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1280
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1281
if ((!m_iRefOrSec[0][2]) || (obs == NULL))
1282
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1283
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1284
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1285
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1286
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1287
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1288
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1289
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1290
vec->Add(0);
1291
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1292
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1293
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1294
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1295
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1296
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1297
vec->Add(0);
1298
}
1299
}
1300
}
1301
}
1302
} // END IF NOT ORTHO[2]
1303
}
1304
}
1305
}
1306
}
1307
} // END IF NOT ORTHO[1]
1308
}
1309
}
1310
}
1311
}
1312
}
1313
}
1314
} else // IF NOT ORTHO[0]
1315
{
1316
g1 = (CAtomGroup*)m_oaVectors[z*9];
1317
g2 = (CAtomGroup*)m_oaVectors[z*9+1];
1318
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1319
{
1320
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1321
for (z1a=0;z1a<a1->GetSize();z1a++)
1322
{
1323
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1324
{
1325
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1326
for (z2a=0;z2a<a2->GetSize();z2a++)
1327
{
1328
if (m_bOrtho[1])
1329
{
1330
g4 = (CAtomGroup*)m_oaVectors[z*9+3];
1331
g5 = (CAtomGroup*)m_oaVectors[z*9+4];
1332
g6 = (CAtomGroup*)m_oaVectors[z*9+5];
1333
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1334
{
1335
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1336
for (z4a=0;z4a<a4->GetSize();z4a++)
1337
{
1338
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
1339
{
1340
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
1341
for (z5a=0;z5a<a5->GetSize();z5a++)
1342
{
1343
for (z6t=0;z6t<g6->m_baAtomType.GetSize();z6t++)
1344
{
1345
a6 = (CxIntArray*)g6->m_oaAtoms[z6t];
1346
for (z6a=0;z6a<a6->GetSize();z6a++)
1347
{
1348
if (m_bOrtho[2])
1349
{
1350
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1351
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1352
g9 = (CAtomGroup*)m_oaVectors[z*9+8];
1353
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1354
{
1355
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1356
for (z7a=0;z7a<a7->GetSize();z7a++)
1357
{
1358
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1359
{
1360
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1361
for (z8a=0;z8a<a8->GetSize();z8a++)
1362
{
1363
for (z9t=0;z9t<g9->m_baAtomType.GetSize();z9t++)
1364
{
1365
a9 = (CxIntArray*)g9->m_oaAtoms[z9t];
1366
for (z9a=0;z9a<a9->GetSize();z9a++)
1367
{
1368
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1369
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1370
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1371
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1372
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1373
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1374
vec->Add(0);
1375
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1376
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1377
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1378
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1379
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1380
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1381
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
1382
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1383
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1384
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1385
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1386
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1387
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1388
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1389
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1390
if ((!m_iRefOrSec[2][2]) || (obs == NULL))
1391
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1392
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1393
}
1394
}
1395
}
1396
}
1397
}
1398
}
1399
} else // IF NOT ORTHO[2]
1400
{
1401
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1402
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1403
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1404
{
1405
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1406
for (z7a=0;z7a<a7->GetSize();z7a++)
1407
{
1408
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1409
{
1410
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1411
for (z8a=0;z8a<a8->GetSize();z8a++)
1412
{
1413
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1414
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1415
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1416
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1417
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1418
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1419
vec->Add(0);
1420
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1421
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1422
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1423
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1424
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1425
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1426
if ((!m_iRefOrSec[1][2]) || (obs == NULL))
1427
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1428
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g6->m_baAtomType[z6t]])->GetAt(a6->GetAt(z6a)));
1429
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1430
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1431
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1432
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1433
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1434
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1435
vec->Add(0);
1436
}
1437
}
1438
}
1439
}
1440
} // END IF NOT ORTHO[2]
1441
}
1442
}
1443
}
1444
}
1445
}
1446
}
1447
} else // IF NOT ORTHO[1]
1448
{
1449
g4 = (CAtomGroup*)m_oaVectors[z*9+3];
1450
g5 = (CAtomGroup*)m_oaVectors[z*9+4];
1451
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1452
{
1453
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1454
for (z4a=0;z4a<a4->GetSize();z4a++)
1455
{
1456
for (z5t=0;z5t<g5->m_baAtomType.GetSize();z5t++)
1457
{
1458
a5 = (CxIntArray*)g5->m_oaAtoms[z5t];
1459
for (z5a=0;z5a<a5->GetSize();z5a++)
1460
{
1461
if (m_bOrtho[2])
1462
{
1463
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1464
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1465
g9 = (CAtomGroup*)m_oaVectors[z*9+8];
1466
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1467
{
1468
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1469
for (z7a=0;z7a<a7->GetSize();z7a++)
1470
{
1471
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1472
{
1473
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1474
for (z8a=0;z8a<a8->GetSize();z8a++)
1475
{
1476
for (z9t=0;z9t<g9->m_baAtomType.GetSize();z9t++)
1477
{
1478
a9 = (CxIntArray*)g9->m_oaAtoms[z9t];
1479
for (z9a=0;z9a<a9->GetSize();z9a++)
1480
{
1481
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1482
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1483
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1484
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1485
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1486
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1487
vec->Add(0);
1488
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1489
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1490
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1491
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1492
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1493
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1494
vec->Add(0);
1495
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1496
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1497
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1498
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1499
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1500
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1501
if ((!m_iRefOrSec[2][2]) || (obs == NULL))
1502
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1503
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g9->m_baAtomType[z9t]])->GetAt(a9->GetAt(z9a)));
1504
}
1505
}
1506
}
1507
}
1508
}
1509
}
1510
} else // IF NOT ORTHO[2]
1511
{
1512
g7 = (CAtomGroup*)m_oaVectors[z*9+6];
1513
g8 = (CAtomGroup*)m_oaVectors[z*9+7];
1514
for (z7t=0;z7t<g7->m_baAtomType.GetSize();z7t++)
1515
{
1516
a7 = (CxIntArray*)g7->m_oaAtoms[z7t];
1517
for (z7a=0;z7a<a7->GetSize();z7a++)
1518
{
1519
for (z8t=0;z8t<g8->m_baAtomType.GetSize();z8t++)
1520
{
1521
a8 = (CxIntArray*)g8->m_oaAtoms[z8t];
1522
for (z8a=0;z8a<a8->GetSize();z8a++)
1523
{
1524
if ((!m_iRefOrSec[0][0]) || (obs == NULL))
1525
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1526
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1527
if ((!m_iRefOrSec[0][1]) || (obs == NULL))
1528
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1529
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1530
vec->Add(0);
1531
if ((!m_iRefOrSec[1][0]) || (obs == NULL))
1532
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1533
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1534
if ((!m_iRefOrSec[1][1]) || (obs == NULL))
1535
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1536
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g5->m_baAtomType[z5t]])->GetAt(a5->GetAt(z5a)));
1537
vec->Add(0);
1538
if ((!m_iRefOrSec[2][0]) || (obs == NULL))
1539
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1540
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g7->m_baAtomType[z7t]])->GetAt(a7->GetAt(z7a)));
1541
if ((!m_iRefOrSec[2][1]) || (obs == NULL))
1542
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1543
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g8->m_baAtomType[z8t]])->GetAt(a8->GetAt(z8a)));
1544
vec->Add(0);
1545
}
1546
}
1547
}
1548
}
1549
} // END IF NOT ORTHO[2]
1550
}
1551
}
1552
}
1553
}
1554
} // END IF NOT ORTHO[1]
1555
}
1556
}
1557
}
1558
}
1559
} // END IF NOT ORTHO[0]
1560
} // END FOR ALL SETS
1561
BXOUT;
1562
}
1563
1564
1565
void CPlDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
1566
{
1567
BXIN;
1568
int z, z1t, z1a, z2t, z2a, z3t, z3a, z4t, z4a;
1569
CAtomGroup *g1, *g2, *g3, *g4;
1570
CxIntArray *a1, *a2, *a3, *a4;
1571
1572
vec->RemoveAll_KeepSize();
1573
for (z=0;z<m_oaVectors.GetSize()/4;z++)
1574
{
1575
if (m_bNormal)
1576
{
1577
g1 = (CAtomGroup*)m_oaVectors[z*4];
1578
g2 = (CAtomGroup*)m_oaVectors[z*4+1];
1579
g4 = (CAtomGroup*)m_oaVectors[z*4+3];
1580
1581
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1582
{
1583
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1584
for (z1a=0;z1a<a1->GetSize();z1a++)
1585
{
1586
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1587
{
1588
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1589
for (z2a=0;z2a<a2->GetSize();z2a++)
1590
{
1591
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1592
{
1593
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1594
for (z4a=0;z4a<a4->GetSize();z4a++)
1595
{
1596
if ((!m_iRefOrSec[0]) || (obs == NULL))
1597
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1598
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1599
if ((!m_iRefOrSec[1]) || (obs == NULL))
1600
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1601
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1602
vec->Add(0);
1603
if ((!m_iRefOrSec[3]) || (obs == NULL))
1604
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1605
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1606
}
1607
}
1608
}
1609
}
1610
}
1611
}
1612
} else // IF NOT NORMAL
1613
{
1614
g1 = (CAtomGroup*)m_oaVectors[z*4];
1615
g2 = (CAtomGroup*)m_oaVectors[z*4+1];
1616
g3 = (CAtomGroup*)m_oaVectors[z*4+2];
1617
g4 = (CAtomGroup*)m_oaVectors[z*4+3];
1618
1619
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1620
{
1621
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1622
for (z1a=0;z1a<a1->GetSize();z1a++)
1623
{
1624
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1625
{
1626
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1627
for (z2a=0;z2a<a2->GetSize();z2a++)
1628
{
1629
for (z3t=0;z3t<g3->m_baAtomType.GetSize();z3t++)
1630
{
1631
a3 = (CxIntArray*)g3->m_oaAtoms[z3t];
1632
for (z3a=0;z3a<a3->GetSize();z3a++)
1633
{
1634
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1635
{
1636
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1637
for (z4a=0;z4a<a4->GetSize();z4a++)
1638
{
1639
if ((!m_iRefOrSec[0]) || (obs == NULL))
1640
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1641
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1642
if ((!m_iRefOrSec[1]) || (obs == NULL))
1643
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1644
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1645
if ((!m_iRefOrSec[2]) || (obs == NULL))
1646
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1647
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1648
if ((!m_iRefOrSec[3]) || (obs == NULL))
1649
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1650
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1651
}
1652
}
1653
}
1654
}
1655
}
1656
}
1657
}
1658
}
1659
}
1660
} // END FOR ALL SETS
1661
BXOUT;
1662
}
1663
1664
1665
void CLiDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
1666
{
1667
BXIN;
1668
int z, z1t, z1a, z2t, z2a, z3t, z3a, z4t, z4a;
1669
CAtomGroup *g1, *g2, *g3, *g4;
1670
CxIntArray *a1, *a2, *a3, *a4;
1671
1672
vec->RemoveAll_KeepSize();
1673
for (z=0;z<m_oaVectors.GetSize()/4;z++)
1674
{
1675
if (m_bNormal)
1676
{
1677
g1 = (CAtomGroup*)m_oaVectors[z*4];
1678
g2 = (CAtomGroup*)m_oaVectors[z*4+1];
1679
g3 = (CAtomGroup*)m_oaVectors[z*4+2];
1680
g4 = (CAtomGroup*)m_oaVectors[z*4+3];
1681
1682
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1683
{
1684
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1685
for (z1a=0;z1a<a1->GetSize();z1a++)
1686
{
1687
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1688
{
1689
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1690
for (z2a=0;z2a<a2->GetSize();z2a++)
1691
{
1692
for (z3t=0;z3t<g3->m_baAtomType.GetSize();z3t++)
1693
{
1694
a3 = (CxIntArray*)g3->m_oaAtoms[z3t];
1695
for (z3a=0;z3a<a3->GetSize();z3a++)
1696
{
1697
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1698
{
1699
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1700
for (z4a=0;z4a<a4->GetSize();z4a++)
1701
{
1702
if ((!m_iRefOrSec[0]) || (obs == NULL))
1703
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1704
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1705
if ((!m_iRefOrSec[1]) || (obs == NULL))
1706
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1707
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1708
if ((!m_iRefOrSec[2]) || (obs == NULL))
1709
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1710
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g3->m_baAtomType[z3t]])->GetAt(a3->GetAt(z3a)));
1711
if ((!m_iRefOrSec[3]) || (obs == NULL))
1712
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1713
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1714
}
1715
}
1716
}
1717
}
1718
}
1719
}
1720
}
1721
}
1722
} else // If not Normal
1723
{
1724
g1 = (CAtomGroup*)m_oaVectors[z*4];
1725
g2 = (CAtomGroup*)m_oaVectors[z*4+1];
1726
g4 = (CAtomGroup*)m_oaVectors[z*4+3];
1727
1728
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
1729
{
1730
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
1731
for (z1a=0;z1a<a1->GetSize();z1a++)
1732
{
1733
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
1734
{
1735
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
1736
for (z2a=0;z2a<a2->GetSize();z2a++)
1737
{
1738
for (z4t=0;z4t<g4->m_baAtomType.GetSize();z4t++)
1739
{
1740
a4 = (CxIntArray*)g4->m_oaAtoms[z4t];
1741
for (z4a=0;z4a<a4->GetSize();z4a++)
1742
{
1743
if ((!m_iRefOrSec[0]) || (obs == NULL))
1744
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1745
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
1746
if ((!m_iRefOrSec[1]) || (obs == NULL))
1747
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1748
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
1749
vec->Add(0);
1750
if ((!m_iRefOrSec[3]) || (obs == NULL))
1751
vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1752
else vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g4->m_baAtomType[z4t]])->GetAt(a4->GetAt(z4a)));
1753
}
1754
}
1755
}
1756
}
1757
}
1758
}
1759
}
1760
} // END FOR ALL SETS
1761
BXOUT;
1762
}
1763
1764
1765
void CRDF::BuildName()
1766
{
1767
BTIN;
1768
int z;
1769
char tmp[256];
1770
1771
tmp[0] = 0;
1772
if (m_iDeriv != 0)
1773
sprintf(tmp,"deriv%d_",m_iDeriv);
1774
for (z=0;z<m_oaVectors.GetSize()/2;z++)
1775
{
1776
strcat(tmp,"[");
1777
1778
strcat(tmp,((CAtomGroup*)m_oaVectors[z*2])->m_sName);
1779
if (m_iRefOrSec[0])
1780
strcat(tmp,"o_");
1781
else strcat(tmp,"r_");
1782
strcat(tmp,((CAtomGroup*)m_oaVectors[z*2+1])->m_sName);
1783
if (m_iRefOrSec[1])
1784
strcat(tmp,"o");
1785
else strcat(tmp,"r");
1786
1787
if (z < (m_oaVectors.GetSize()/2)-1)
1788
strcat(tmp,"],");
1789
else strcat(tmp,"]");
1790
}
1791
1792
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
1793
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1794
1795
strcpy(m_sShortName,tmp);
1796
if (m_iShowMol != -1)
1797
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1798
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
1799
strcat(tmp,m_sShortName);
1800
1801
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
1802
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1803
1804
strcpy(m_sName,tmp);
1805
1806
BTOUT;
1807
}
1808
1809
1810
void CDensDF::BuildName()
1811
{
1812
BTIN;
1813
char tmp[256];
1814
int z;
1815
1816
sprintf(tmp,"%s_%s%d_%s",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,((CAtom*)g_oaAtoms[m_iCenterAtomRealType])->m_sName,m_iCenterAtom+1,(m_bDensityMass?"mass":"particle"));
1817
1818
for (z=0;z<g_oaMolecules.GetSize();z++)
1819
{
1820
if (!m_pDensityMolSelect[z])
1821
continue;
1822
strcat(tmp,"_");
1823
strcat(tmp,((CMolecule*)g_oaMolecules[z])->m_sName);
1824
if (!m_pDensityMolAG[z]->m_bAllAtoms)
1825
{
1826
strcat(tmp,"_");
1827
strcat(tmp,m_pDensityMolAG[z]->m_sName);
1828
}
1829
}
1830
1831
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
1832
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1833
1834
strcpy(m_sName,tmp);
1835
BTOUT;
1836
}
1837
1838
1839
void CVHDF::BuildName()
1840
{
1841
BTIN;
1842
int z;
1843
char tmp[256];
1844
1845
tmp[0] = 0;
1846
for (z=0;z<m_oaVectors.GetSize()/2;z++)
1847
{
1848
strcat(tmp,"[");
1849
1850
strcat(tmp,((CAtomGroup*)m_oaVectors[z*2])->m_sName);
1851
if (m_iRefOrSec[0])
1852
strcat(tmp,"o_");
1853
else strcat(tmp,"r_");
1854
strcat(tmp,((CAtomGroup*)m_oaVectors[z*2+1])->m_sName);
1855
if (m_iRefOrSec[1])
1856
strcat(tmp,"o");
1857
else strcat(tmp,"r");
1858
1859
if (z < (m_oaVectors.GetSize()/2)-1)
1860
strcat(tmp,"],");
1861
else strcat(tmp,"]");
1862
}
1863
1864
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
1865
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1866
1867
strcpy(m_sShortName,tmp);
1868
if (m_iShowMol != -1)
1869
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1870
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
1871
strcat(tmp,m_sShortName);
1872
1873
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
1874
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1875
1876
strcpy(m_sName,tmp);
1877
BTOUT;
1878
}
1879
1880
1881
void CRDF::Parse()
1882
{
1883
BTIN;
1884
char buf[256];
1885
int ti;
1886
CAtomGroup *ag;
1887
1888
try { m_pRDF = new CDF(); } catch(...) { m_pRDF = NULL; }
1889
if (m_pRDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1890
1891
m_iShowAtomGes = 0;
1892
m_iRefAtomGes = 0;
1893
m_iCombinations = 0;
1894
mprintf(WHITE,"\n>>> Radial Distribution Function >>>\n\n");
1895
/* if (m_bSelf)
1896
{
1897
m_iRefOrSec[0] = 0;
1898
m_iRefOrSec[1] = 0;
1899
} else
1900
{
1901
m_iRefOrSec[0] = 0;
1902
m_iRefOrSec[1] = 1;
1903
}*/
1904
if (m_iShowMol != -1)
1905
m_iRefOrSec[0] = AskRangeInteger(" Take reference atom(s) from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1906
else m_iRefOrSec[0] = 0; // Kein OM: Nimm alles aus RM
1907
if (m_iShowMol != -1)
1908
m_iRefOrSec[1] = AskRangeInteger(" Take observed atom(s) from RM %s (0) or from OM %s (1)? [1] ",0,1,1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1909
else m_iRefOrSec[1] = 0; // Kein OM: Nimm alles aus RM
1910
1911
_rdfnewset:
1912
mprintf("\n");
1913
1914
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1915
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1916
1917
_rdfatom1:
1918
// 1 reales + 2 virtuelle = 3 gesamt
1919
if (((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol])->m_iAtomGes == 3)
1920
{
1921
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol])->m_sName);
1922
ag->Reset();
1923
ag->m_pMolecule = (CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol];
1924
ag->AddAtom(0,0,false);
1925
ag->SortAtoms();
1926
ag->BuildName();
1927
} else
1928
{
1929
if (m_iRefOrSec[0])
1930
{
1931
mprintf(" Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1932
inpprintf("! Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1933
} else
1934
{
1935
mprintf(" Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
1936
inpprintf("! Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
1937
}
1938
myget(buf);
1939
if (strlen(buf) == 0)
1940
{
1941
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol],"#2"))
1942
{
1943
eprintf("Weird error.\n");
1944
goto _rdfatom1;
1945
}
1946
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol],buf))
1947
goto _rdfatom1;
1948
}
1949
m_oaVectors.Add(ag);
1950
m_iRefAtomGes += ag->m_iAtomGes;
1951
ti = ag->m_iAtomGes;
1952
1953
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1954
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1955
1956
_rdfatom2:
1957
if (((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol])->m_iAtomGes == 3)
1958
{
1959
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol])->m_sName);
1960
ag->Reset();
1961
ag->m_pMolecule = (CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol];
1962
ag->AddAtom(0,0,false);
1963
ag->SortAtoms();
1964
ag->BuildName();
1965
} else
1966
{
1967
if (m_iRefOrSec[1])
1968
{
1969
mprintf(" Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1970
inpprintf("! Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
1971
} else
1972
{
1973
mprintf(" Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
1974
inpprintf("! Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
1975
}
1976
myget(buf);
1977
1978
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1979
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1980
1981
if (strlen(buf) == 0)
1982
{
1983
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol],"#2"))
1984
{
1985
eprintf("Weird error.\n");
1986
goto _rdfatom2;
1987
}
1988
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol],buf))
1989
goto _rdfatom2;
1990
}
1991
m_oaVectors.Add(ag);
1992
m_iShowAtomGes += ag->m_iAtomGes;
1993
m_iCombinations += ti * ag->m_iAtomGes;
1994
1995
if (g_bAdvanced2)
1996
if (AskYesNo(" Add another set of atoms to this (!) RDF (y/n)? [no] ",false))
1997
goto _rdfnewset;
1998
1999
mprintf(" This yields in %d combinations.\n\n",m_iCombinations);
2000
2001
ParseDeriv();
2002
2003
switch(m_iDeriv)
2004
{
2005
case 0:
2006
m_fMinDist = AskFloat(" Enter the minimal radius of this RDF in pm: [0] ",0.0f);
2007
m_fMaxDist = AskFloat(" Enter the maximal radius of this RDF in pm: [%d.0] ",(float)HalfBox(),HalfBox());
2008
break;
2009
case 1:
2010
if (m_bDerivAbs)
2011
m_fMinDist = AskFloat(" Enter the minimal value of this d1-RDF in pm/ps: [0] ",0.0f);
2012
else m_fMinDist = AskFloat(" Enter the minimal value of this d1-RDF in pm/ps: [-10.0] ",-10.0f);
2013
m_fMaxDist = AskFloat(" Enter the maximal value of this d1-RDF in pm/ps: [10.0] ",10.0f);
2014
break;
2015
case 2:
2016
if (m_bDerivAbs)
2017
m_fMinDist = AskFloat(" Enter the minimal value of this d2-RDF in pm/ps^2: [0] ",0.0f);
2018
else m_fMinDist = AskFloat(" Enter the minimal value of this d2-RDF in pm/ps^2: [-10.0] ",-10.0f);
2019
m_fMaxDist = AskFloat(" Enter the maximal value of this d2-RDF in pm/ps^2: [10.0] ",10.0f);
2020
break;
2021
}
2022
m_bAdaptive = false/*AskYesNo(" Enter binning resolution (n) or use adaptive binnig (y)? [no] ",false)*/;
2023
if (!m_bAdaptive)
2024
m_iResolution = AskUnsignedInteger(" Enter the resolution (bin count) for this RDF: [300] ",/*(int)((m_fMaxDist-m_fMinDist)/10.0f),(int)((m_fMaxDist-m_fMinDist)/10.0f)*/300);
2025
else m_iResolution = 65536;
2026
2027
if (g_bAdvanced2)
2028
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
2029
else m_iHistogramRes = 0;
2030
2031
if (m_iDeriv == 0)
2032
{
2033
if (m_iShowMol != -1)
2034
m_bRadialCorrect = AskYesNo(" Correct radial distribution for this RDF (y/n)? [yes] ",true);
2035
else m_bRadialCorrect = AskYesNo(" Correct radial distribution for this RDF (y/n)? [no] ",false);
2036
} else m_bRadialCorrect = false;
2037
2038
if (g_bAdvanced2 && m_bRadialCorrect)
2039
m_bProbDens = AskYesNo(" Compute occurence in nm^(-3) (y) or rel. to uniform density (n)? [no] ",false);
2040
else m_bProbDens = false;
2041
2042
if (g_bBetaFeatures)
2043
{
2044
m_bLongMode = AskYesNo(" Use correction trick for longer RDFs (y/n)? [no] ",false);
2045
m_bCalcSD = AskYesNo(" Calculate standard deviation for this RDF (y/n)? [no] ",false);
2046
} else
2047
{
2048
m_bCalcSD = false;
2049
m_bLongMode = false;
2050
}
2051
2052
if (m_bCalcSD)
2053
{
2054
m_iSDBlocks = AskUnsignedInteger(" How many different block lenghts to use? [100] ",100);
2055
m_iSDBlockMin = AskUnsignedInteger(" Enter minimal block length in time steps: [1] ",1);
2056
if (g_iTrajSteps != -1)
2057
m_iSDBlockMax = AskUnsignedInteger(" Enter maximal block length in time steps: [%d] ",g_iTrajSteps/10,g_iTrajSteps/10);
2058
else m_iSDBlockMax = AskUnsignedInteger(" Enter maximal block length in time steps: [1000] ",1000);
2059
m_bSDVerbose = AskYesNo(" Write out correlation length extrapolation fit data for each bin (y/n)? [no] ",false);
2060
m_fSDTimesSigma = AskFloat(" Use which factor of sigma for confidence range? [3.0] ",3.0);
2061
mprintf("\n %.2f sigma leads to a confidence level of %.5f%c.\n",m_fSDTimesSigma,2.0*NormalDistIntegral(m_fSDTimesSigma)-1.0,'%');
2062
}
2063
2064
BuildName();
2065
mprintf(WHITE,"\n<<< End of Radial Distribution Function <<<\n\n");
2066
BTOUT;
2067
}
2068
2069
2070
void CDensDF::Parse()
2071
{
2072
BTIN;
2073
char buf[256];
2074
int z;
2075
CMolecule *m;
2076
2077
try { m_pDensDF = new CDF(); } catch(...) { m_pDensDF = NULL; }
2078
if (m_pDensDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2079
2080
mprintf(WHITE,"\n>>> Density Distribution Function >>>\n\n");
2081
2082
m_bDensityMass = AskYesNo(" Observe mass density (y) or particle density (n)? [yes] ",true);
2083
2084
mprintf("\n Choose a reference atom around which the density will be analyzed.\n\n");
2085
2086
// 1 reales + 2 virtuelle = 3 gesamt
2087
if (((CMolecule*)g_oaMolecules[m_iShowMol])->m_iAtomGesNoVirt == 1)
2088
{
2089
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2090
if (!ParseAtom("#2",m_iShowMol,m_iCenterAtomType,m_iCenterAtomRealType,m_iCenterAtom))
2091
{
2092
eprintf("Weird error.\n");
2093
abort();
2094
}
2095
} else
2096
{
2097
_densatom1:
2098
mprintf(" Which atom to take from OM %s (e.g. C1)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2099
inpprintf("! Which atom to take from OM %s (e.g. C1)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2100
myget(buf);
2101
if (strlen(buf) == 0)
2102
{
2103
if (!ParseAtom("#2",m_iShowMol,m_iCenterAtomType,m_iCenterAtomRealType,m_iCenterAtom))
2104
{
2105
eprintf("Weird error.\n");
2106
abort();
2107
}
2108
} else if (!ParseAtom(buf,m_iShowMol,m_iCenterAtomType,m_iCenterAtomRealType,m_iCenterAtom))
2109
goto _densatom1;
2110
}
2111
2112
try { m_pDensityMolSelect = new bool[g_oaMolecules.GetSize()]; } catch(...) { m_pDensityMolSelect = NULL; }
2113
if (m_pDensityMolSelect == NULL) NewException((double)g_oaMolecules.GetSize()*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2114
2115
try { m_pDensityMolAG = new CAtomGroup*[g_oaMolecules.GetSize()]; } catch(...) { m_pDensityMolAG = NULL; }
2116
if (m_pDensityMolAG == NULL) NewException((double)g_oaMolecules.GetSize()*sizeof(CAtomGroup*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2117
2118
mprintf("\n Please choose the atoms to observe:\n\n");
2119
2120
for (z=0;z<g_oaMolecules.GetSize();z++)
2121
{
2122
m = (CMolecule*)g_oaMolecules[z];
2123
m_pDensityMolSelect[z] = AskYesNo(" Consider contributions from %s (y/n)? [%s] ",!m->m_bPseudo,((CMolecule*)g_oaMolecules[z])->m_sName,m->m_bPseudo?"no":"yes");
2124
if (m_pDensityMolSelect[z])
2125
{
2126
try { m_pDensityMolAG[z] = new CAtomGroup(); } catch(...) { m_pDensityMolAG[z] = NULL; }
2127
if (m_pDensityMolAG[z] == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2128
_densatom2:
2129
AskString(" Which atoms from %s to observe (e.g. C1-3,C6,N)? [all] ",buf,"",m->m_sName);
2130
if (strlen(buf) == 0)
2131
{
2132
m_pDensityMolAG[z]->AddAllAtoms(m,false);
2133
} else if (!m_pDensityMolAG[z]->ParseAtoms(m,buf))
2134
goto _densatom2;
2135
}
2136
}
2137
2138
mprintf("\n");
2139
2140
m_fMinDist = AskFloat(" Enter the minimal radius of this Density DF in pm: [0] ",0.0f);
2141
m_fMaxDist = AskFloat(" Enter the maximal radius of this Density DF in pm: [%d.0] ",(float)HalfBox(),HalfBox());
2142
2143
m_iResolution = AskUnsignedInteger(" Enter the resolution (bin count) for this Density DF: [300] ",300);
2144
2145
if (g_bAdvanced2)
2146
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
2147
else m_iHistogramRes = 0;
2148
2149
BuildName();
2150
mprintf(WHITE,"\n<<< End of Density Distribution Function <<<\n\n");
2151
BTOUT;
2152
}
2153
2154
2155
void CRDF::ParseCondition(int rm, CNbSearch *n, bool nbana)
2156
{
2157
BTIN;
2158
char buf[256];
2159
int ti;
2160
CAtomGroup *ag;
2161
2162
try { m_pRDF = new CDF(); } catch(...) { m_pRDF = NULL; }
2163
if (m_pRDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2164
2165
m_iShowAtomGes = 0;
2166
m_iRefAtomGes = 0;
2167
m_iCombinations = 0;
2168
m_iRefOrSec[0] = 0;
2169
m_iRefOrSec[1] = 1;
2170
mprintf(WHITE,"\n>>> Distance Condition >>>\n");
2171
2172
_rdfnewset:
2173
mprintf("\n");
2174
2175
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2176
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2177
2178
_rdfatom1:
2179
if (((CMolecule*)g_oaMolecules[rm])->m_iAtomGes == 3)
2180
{
2181
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[rm])->m_sName);
2182
ag->Reset();
2183
ag->m_pMolecule = (CMolecule*)g_oaMolecules[rm];
2184
ag->AddAtom(0,0,false);
2185
ag->SortAtoms();
2186
ag->BuildName();
2187
} else
2188
{
2189
mprintf(" Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[rm])->m_sName);
2190
inpprintf("! Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[rm])->m_sName);
2191
myget(buf);
2192
if (strlen(buf) == 0)
2193
{
2194
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[rm],"#2"))
2195
{
2196
eprintf("Weird error.\n");
2197
goto _rdfatom1;
2198
}
2199
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[rm],buf))
2200
goto _rdfatom1;
2201
}
2202
m_oaVectors.Add(ag);
2203
m_iRefAtomGes += ag->m_iAtomGes;
2204
ti = ag->m_iAtomGes;
2205
2206
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2207
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2208
2209
_rdfatom2:
2210
if (((CMolecule*)g_oaMolecules[m_iShowMol])->m_iAtomGes == 3)
2211
{
2212
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2213
ag->Reset();
2214
ag->m_pMolecule = (CMolecule*)g_oaMolecules[m_iShowMol];
2215
ag->AddAtom(0,0,false);
2216
ag->SortAtoms();
2217
ag->BuildName();
2218
} else
2219
{
2220
mprintf(" Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2221
inpprintf("! Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2222
myget(buf);
2223
2224
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2225
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2226
2227
if (strlen(buf) == 0)
2228
{
2229
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],"#2"))
2230
{
2231
eprintf("Weird error.\n");
2232
goto _rdfatom2;
2233
}
2234
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],buf))
2235
goto _rdfatom2;
2236
}
2237
m_oaVectors.Add(ag);
2238
m_iShowAtomGes += ag->m_iAtomGes;
2239
m_iCombinations += ti * ag->m_iAtomGes;
2240
2241
if (AskYesNo(" Enter another set of atoms for this condition (y/n)? [no] ",false))
2242
goto _rdfnewset;
2243
2244
if (!nbana)
2245
{
2246
if (AskUnsignedInteger("\n Enter min./max. distance (0) or min./max. nearest neighbor count (1)? [0] ",0)==0)
2247
{
2248
g_bEnvDisableSortNb = true;
2249
2250
do {
2251
m_faMinMaxDist.Add(AskFloat(" Enter the minimal distance in pm: [0] ",0.0f));
2252
m_faMinMaxDist.Add(AskFloat(" Enter the maximal distance in pm: [400] ",400.0f));
2253
} while (AskYesNo(" Enter another distance interval (y/n)? [no] ",false));
2254
n->m_iNbCountMin = -1;
2255
n->m_iNbCountMax = -1;
2256
} else
2257
{
2258
n->m_iNbCountMin = AskRangeInteger(" Use next neighbors from the n-th on? [1] ",0,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),1)-1;
2259
n->m_iNbCountMax = AskRangeInteger(" Use next neighbors up to the n-th? [%d] ",n->m_iNbCountMin+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),n->m_iNbCountMin+1,n->m_iNbCountMin+1)-1;
2260
// m_faMinMaxDist.Add(0);
2261
// m_faMinMaxDist.Add(9E20f);
2262
}
2263
} else
2264
{
2265
m_faMinMaxDist.Add(0);
2266
m_faMinMaxDist.Add(1.0e30f);
2267
n->m_iNbCountMin = -2;
2268
n->m_iNbCountMax = -2;
2269
}
2270
mprintf(WHITE,"\n<<< End of Distance Condition <<<\n\n");
2271
BTOUT;
2272
}
2273
2274
2275
void CRDF::ParseConditionGrid(int rm, CNbSearch *n, int gridmode)
2276
{
2277
BTIN;
2278
char buf[256];
2279
int ti;
2280
CAtomGroup *ag;
2281
2282
try { m_pRDF = new CDF(); } catch(...) { m_pRDF = NULL; }
2283
if (m_pRDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2284
2285
m_iShowAtomGes = 0;
2286
m_iRefAtomGes = 0;
2287
m_iCombinations = 0;
2288
m_iRefOrSec[0] = 0;
2289
m_iRefOrSec[1] = 1;
2290
mprintf(WHITE,"\n>>> Distance Condition >>>\n");
2291
2292
_rdfnewset:
2293
mprintf("\n");
2294
2295
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2296
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2297
2298
_rdfatom1:
2299
if (((CMolecule*)g_oaMolecules[rm])->m_iAtomGes == 3)
2300
{
2301
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[rm])->m_sName);
2302
ag->Reset();
2303
ag->m_pMolecule = (CMolecule*)g_oaMolecules[rm];
2304
ag->AddAtom(0,0,false);
2305
ag->SortAtoms();
2306
ag->BuildName();
2307
} else
2308
{
2309
mprintf(" Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[rm])->m_sName);
2310
inpprintf("! Which atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[rm])->m_sName);
2311
myget(buf);
2312
if (strlen(buf) == 0)
2313
{
2314
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[rm],"#2"))
2315
{
2316
eprintf("Weird error.\n");
2317
goto _rdfatom1;
2318
}
2319
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[rm],buf))
2320
goto _rdfatom1;
2321
}
2322
m_oaVectors.Add(ag);
2323
m_iRefAtomGes += ag->m_iAtomGes;
2324
ti = ag->m_iAtomGes;
2325
2326
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2327
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2328
2329
_rdfatom2:
2330
if (((CMolecule*)g_oaMolecules[m_iShowMol])->m_iAtomGes == 3)
2331
{
2332
mprintf(" %s is only one atom, there is no choice.\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2333
ag->Reset();
2334
ag->m_pMolecule = (CMolecule*)g_oaMolecules[m_iShowMol];
2335
ag->AddAtom(0,0,false);
2336
ag->SortAtoms();
2337
ag->BuildName();
2338
} else
2339
{
2340
mprintf(" Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2341
inpprintf("! Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2342
myget(buf);
2343
2344
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2345
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2346
2347
if (strlen(buf) == 0)
2348
{
2349
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],"#2"))
2350
{
2351
eprintf("Weird error.\n");
2352
goto _rdfatom2;
2353
}
2354
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],buf))
2355
goto _rdfatom2;
2356
}
2357
m_oaVectors.Add(ag);
2358
m_iShowAtomGes += ag->m_iAtomGes;
2359
m_iCombinations += ti * ag->m_iAtomGes;
2360
2361
if (AskYesNo(" Enter another set of atoms (y/n)? [no] ",false))
2362
goto _rdfnewset;
2363
2364
if (gridmode == 6)
2365
{
2366
if (AskUnsignedInteger("\n Enter min./max. distance (0) or min./max. nearest neighbor count (1)? [0] ",0)==0)
2367
{
2368
m_faMinMaxDist.Add(AskFloat(" Enter the minimal distance in pm: [0] ",0.0f));
2369
m_faMinMaxDist.Add(AskFloat(" Enter the maximal distance in pm: [400] ",400.0f));
2370
n->m_iNbCountMin = -1;
2371
n->m_iNbCountMax = -1;
2372
} else
2373
{
2374
n->m_iNbCountMin = AskRangeInteger(" Use next neighbors from the n-th on? [1] ",0,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),1)-1;
2375
n->m_iNbCountMax = AskRangeInteger(" Use next neighbors up to the n-th? [%d] ",n->m_iNbCountMin+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),n->m_iNbCountMin+1,n->m_iNbCountMin+1)-1;
2376
// m_faMinMaxDist.Add(0);
2377
// m_faMinMaxDist.Add(9E20f);
2378
}
2379
} else if ((gridmode == 4) || (gridmode == 5))
2380
{
2381
n->m_iNbCountMin = 0;
2382
n->m_iNbCountMax = 0;
2383
// m_faMinMaxDist.Add(0);
2384
// m_faMinMaxDist.Add(9E20f);
2385
} else if (gridmode == 2)
2386
{
2387
m_faMinMaxDist.Add(AskFloat(" Enter the minimal distance in pm: [0] ",0.0f));
2388
m_faMinMaxDist.Add(AskFloat(" Enter the maximal distance in pm: [400] ",400.0f));
2389
n->m_iNbCountMin = -1;
2390
n->m_iNbCountMax = -1;
2391
} else
2392
{
2393
m_faMinMaxDist.Add(0.0f);
2394
m_faMinMaxDist.Add(400.0f);
2395
n->m_iNbCountMin = -1;
2396
n->m_iNbCountMax = -1;
2397
}
2398
mprintf(WHITE,"\n<<< End of Distance Condition <<<\n\n");
2399
BTOUT;
2400
}
2401
2402
2403
void CRDF::ParseCondition_OnlyValues(CNbSearch *n)
2404
{
2405
BTIN;
2406
int z;
2407
2408
mprintf(" Distance condition between ");
2409
for (z=0;z<m_oaVectors.GetSize()/2;z++)
2410
{
2411
mprintf("%s and %s",((CAtomGroup*)m_oaVectors[z*2])->m_sName,((CAtomGroup*)m_oaVectors[z*2+1])->m_sName);
2412
if (z < (m_oaVectors.GetSize()/2)-1)
2413
mprintf(", ");
2414
}
2415
mprintf("\n");
2416
if (n->m_iNbCountMin == -1)
2417
{
2418
for (z=0;z<m_faMinMaxDist.GetSize()/2;z++)
2419
{
2420
mprintf(" Interval %d:\n",z+1,m_faMinMaxDist.GetSize()/2);
2421
m_faMinMaxDist[z*2] = AskFloat(" Enter the minimal distance in pm: [0] ",0.0f);
2422
m_faMinMaxDist[z*2+1] = AskFloat(" Enter the maximal distance in pm: [400] ",400.0f);
2423
}
2424
} else
2425
{
2426
n->m_iNbCountMin = AskRangeInteger(" Use next neighbors from the n-th on? [1] ",0,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),1)-1;
2427
n->m_iNbCountMax = AskRangeInteger(" Use next neighbors up to the n-th? [%d] ",n->m_iNbCountMin+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize(),n->m_iNbCountMin+1,n->m_iNbCountMin+1)-1;
2428
}
2429
2430
BTOUT;
2431
}
2432
2433
2434
void CVHDF::Parse()
2435
{
2436
BTIN;
2437
char buf[256];
2438
int ti;
2439
CAtomGroup *ag;
2440
2441
try { m_pVHDF = new C2DF(); } catch(...) { m_pVHDF = NULL; }
2442
if (m_pVHDF == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2443
2444
m_iShowAtomGes = 0;
2445
m_iRefAtomGes = 0;
2446
m_iCombinations = 0;
2447
mprintf(WHITE,"\n>>> Van Hove Correlation Function >>>\n\n");
2448
if (m_iShowMol != -1)
2449
{
2450
m_iRefOrSec[0] = AskRangeInteger(" Take (fixed) reference atom(s) from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2451
m_iRefOrSec[1] = AskRangeInteger(" Take (moving) observed atom(s) from RM %s (0) or from OM %s (1)? [1] ",0,1,1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2452
} else // Kein OM: Nimm alles aus RM
2453
{
2454
m_iRefOrSec[0] = 0;
2455
m_iRefOrSec[1] = 0;
2456
}
2457
_rdfnewset:
2458
mprintf("\n");
2459
2460
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2461
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2462
2463
_rdfatom1:
2464
if (m_iRefOrSec[0])
2465
{
2466
mprintf(" Which (fixed) reference atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2467
inpprintf("! Which (fixed) reference atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2468
} else
2469
{
2470
mprintf(" Which (fixed) reference atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2471
inpprintf("! Which (fixed) reference atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2472
}
2473
myget(buf);
2474
if (strlen(buf) == 0)
2475
{
2476
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol],"#2"))
2477
goto _rdfatom1;
2478
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[0])?m_iShowMol:g_iFixMol],buf))
2479
goto _rdfatom1;
2480
m_oaVectors.Add(ag);
2481
m_iRefAtomGes += ag->m_iAtomGes;
2482
ti = ag->m_iAtomGes;
2483
2484
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2485
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2486
2487
_rdfatom2:
2488
if (m_iRefOrSec[1])
2489
{
2490
mprintf(" Which (moving) observed atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2491
inpprintf("! Which (moving) observed atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2492
} else
2493
{
2494
mprintf(" Which (moving) observed atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2495
inpprintf("! Which (moving) observed atom(s) to take from RM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2496
}
2497
myget(buf);
2498
2499
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2500
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2501
2502
if (strlen(buf) == 0)
2503
{
2504
if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol],"#2"))
2505
goto _rdfatom2;
2506
} else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec[1])?m_iShowMol:g_iFixMol],buf))
2507
goto _rdfatom2;
2508
m_oaVectors.Add(ag);
2509
m_iShowAtomGes += ag->m_iAtomGes;
2510
m_iCombinations += ti * ag->m_iAtomGes;
2511
2512
if (g_bAdvanced2)
2513
if (AskYesNo(" Enter another set of atoms (y/n)? [no] ",false))
2514
goto _rdfnewset;
2515
2516
m_fMinDist = 0; //AskFloat(" Enter the minimal radius of this VHCF in pm: [0] ",0.0f);
2517
m_fMaxDist = AskFloat(" Enter the radius of this VHCF in pm: [%d.0] ",(float)HalfBox(),HalfBox());
2518
m_iResolution = AskUnsignedInteger(" Enter the radial resolution of this VHCF: [100] ",100);
2519
m_bRadialCorrect = AskYesNo(" Correct radial distribution for this VHCF (y/n)? [%s] ",!m_bSelf,m_bSelf?"no":"yes");
2520
2521
_depth:
2522
if (g_iTrajSteps != -1)
2523
m_iDepth = AskUnsignedInteger(" Enter the temporal resolution (time depth) of this VHCF (in time steps): [%d] ",int(g_iTrajSteps*0.75),int(g_iTrajSteps*0.75));
2524
else m_iDepth = AskUnsignedInteger(" Enter the temporal resolution (time depth) of this VHCF (in time steps): [5000] ",5000);
2525
2526
mprintf("\n This will occupy %s of RAM.\n",FormatBytes((double)m_iDepth*g_iGesVirtAtomCount*3.0*sizeof(float)));
2527
if (m_iDepth*g_iGesVirtAtomCount*3.0*sizeof(float)/1024.0f/1024.0f >= 1000.0f)
2528
if (!AskYesNo(" Make sure that enough free RAM is available. Continue (y/n)? [yes] ",true))
2529
goto _depth;
2530
mprintf("\n");
2531
2532
_resagain:
2533
m_iStride = AskUnsignedInteger(" Take each n-th time step for the temporal axis? [%d] ",max(1,m_iDepth/100),max(1,m_iDepth/100));
2534
2535
mprintf("\n This results in a plot resolution of %d on the temporal axis.\n",m_iDepth/m_iStride);
2536
2537
if (m_iDepth/m_iStride > 200)
2538
{
2539
mprintf("\n");
2540
if (!AskYesNo(" The resolution seems quite high, the plot will take much time to render. Contiune (y/n)? [yes] ",true))
2541
goto _resagain;
2542
}
2543
2544
if (g_bAdvanced2)
2545
{
2546
mprintf("\n");
2547
m_bSwapAxes = AskYesNo(" Put distance on X axis and time on Y axis (y) or swap axes (n)? [yes] ",true);
2548
m_iGraceBunchTime = AskUnsignedInteger(" How many time graphs do you want do draw in the distance grace stack (0=disable)? [10] ",10);
2549
m_iGraceBunchDist = AskUnsignedInteger(" How many distance graphs do you want do draw in the time grace stack (0=disable)? [10] ",10);
2550
} else
2551
{
2552
m_bSwapAxes = true;
2553
m_iGraceBunchTime = 0;
2554
m_iGraceBunchDist = 0;
2555
}
2556
2557
BuildName();
2558
mprintf(WHITE,"\n<<< End of Van Hove Correlation Function <<<\n\n");
2559
BTOUT;
2560
}
2561
2562
2563
void CADF::Parse()
2564
{
2565
BTIN;
2566
char buf[256];
2567
int z, z2, ti;
2568
CAtomGroup *ag;
2569
float tf;
2570
2571
try { m_pADF = new CDF(); } catch(...) { m_pADF = NULL; }
2572
if (m_pADF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2573
2574
mprintf(WHITE,"\n>>> Angular Distribution Function >>>\n\n");
2575
for (z=0;z<2;z++)
2576
{
2577
m_iVecType[z] = AskRangeInteger(" Should the %d. vector depict position (1), dipole (2), velocity (3) or force (4)? [1] ",1,4,1,z+1) - 1;
2578
if (m_iVecType[z] == 1)
2579
{
2580
g_bDipole = true;
2581
ParseDipole();
2582
}
2583
}
2584
z2 = 0;
2585
m_iCombinations = 0;
2586
do {
2587
ti = 1;
2588
if (z2 != 0)
2589
mprintf("\n %d. set of vectors\n\n",z2+1);
2590
for (z=0;z<2;z++)
2591
{
2592
if (m_iVecType[z] == 0) // Position
2593
{
2594
/* if (z2 == 0)
2595
if ((z == 1) && (m_iVecType[0] == 0) && (m_iVecType[1] == 0))
2596
m_bSameFoot = AskYesNo(" Should the base points of the 1st and 2nd vectors always be equal (y/n)? [no] ",false);
2597
else m_bSameFoot = false;*/
2598
2599
if (z2 == 0)
2600
m_bOrtho[z] = (AskRangeInteger("\n Should the %d. vector connect 2 points (0) or stand perpendicular to 3 points (1)? [0] ",0,1,0,z+1) != 0);
2601
2602
mprintf("\n");
2603
if (m_bOrtho[z])
2604
{
2605
/* if (m_bSameFoot && (z == 1))
2606
{
2607
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
2608
m_oaVectors.Add(NULL);
2609
} else*/
2610
{
2611
_ax1: if (z2 == 0)
2612
{
2613
if (m_iShowMol != -1)
2614
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) at the base point from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2615
else m_iRefOrSec[z][0] = 0;
2616
}
2617
mprintf(" Please enter the atom(s) at the base point (e.g. C7): ");
2618
inpprintf("! Please enter the atom(s) at the base point (e.g. C7):\n");
2619
myget(buf);
2620
2621
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2622
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2623
2624
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2625
{
2626
eprintf("Wrong input.\n");
2627
inpprintf("! Wrong input.\n");
2628
delete ag;
2629
goto _ax1;
2630
}
2631
m_oaVectors.Add(ag);
2632
ti *= ag->m_iAtomGes;
2633
}
2634
_ax2: if (z2 == 0)
2635
{
2636
if (m_iShowMol != -1)
2637
m_iRefOrSec[z][1] = AskRangeInteger(" Take 2nd atom(s) of normal plane from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2638
else m_iRefOrSec[z][1] = 0;
2639
}
2640
mprintf(" Please enter the 2nd atom(s) of the normal plane (e.g. C7): ");
2641
inpprintf("! Please enter the 2nd atom(s) of the normal plane (e.g. C7):\n");
2642
myget(buf);
2643
2644
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2645
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2646
2647
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2648
{
2649
eprintf("Wrong input.\n");
2650
inpprintf("! Wrong input.\n");
2651
delete ag;
2652
goto _ax2;
2653
}
2654
m_oaVectors.Add(ag);
2655
ti *= ag->m_iAtomGes;
2656
_ax3: if (z2 == 0)
2657
{
2658
if (m_iShowMol != -1)
2659
m_iRefOrSec[z][2] = AskRangeInteger(" Take 3rd atom(s) of normal plane from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2660
else m_iRefOrSec[z][2] = 0;
2661
}
2662
mprintf(" Please enter the 3rd atom(s) of the normal plane (e.g. C7): ");
2663
inpprintf("! Please enter the 3rd atom(s) of the normal plane (e.g. C7):\n");
2664
myget(buf);
2665
2666
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2667
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2668
2669
if (!ag->ParseAtoms((!m_iRefOrSec[z][2])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2670
{
2671
eprintf("Wrong input.\n");
2672
inpprintf("! Wrong input.\n");
2673
delete ag;
2674
goto _ax3;
2675
}
2676
m_oaVectors.Add(ag);
2677
ti *= ag->m_iAtomGes;
2678
} else // IF ORTHO
2679
{
2680
/* if (m_bSameFoot && (z == 1))
2681
{
2682
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
2683
m_oaVectors.Add(NULL);
2684
} else*/
2685
{
2686
_ax4: if (z2 == 0)
2687
{
2688
if (m_iShowMol != -1)
2689
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) at the base point from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2690
else m_iRefOrSec[z][0] = 0;
2691
}
2692
mprintf(" Please enter the atom(s) at the base point (e.g. C7): ");
2693
inpprintf("! Please enter the atom(s) at the base point (e.g. C7):\n");
2694
myget(buf);
2695
2696
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2697
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2698
2699
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2700
{
2701
eprintf("Wrong input.\n");
2702
inpprintf("! Wrong input.\n");
2703
delete ag;
2704
goto _ax4;
2705
}
2706
m_oaVectors.Add(ag);
2707
ti *= ag->m_iAtomGes;
2708
} // END IF NOT SAMEFOOT
2709
_ax5: if (z2 == 0)
2710
{
2711
if (m_iShowMol != -1)
2712
m_iRefOrSec[z][1] = AskRangeInteger(" Take atom(s) at the tip point from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2713
else m_iRefOrSec[z][1] = 0;
2714
}
2715
mprintf(" Please enter the atom(s) at the tip point (e.g. C7): ");
2716
inpprintf("! Please enter the atom(s) at the tip point (e.g. C7):\n");
2717
myget(buf);
2718
2719
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2720
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2721
2722
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2723
{
2724
eprintf("Wrong input.\n");
2725
inpprintf("! Wrong input.\n");
2726
delete ag;
2727
goto _ax5;
2728
}
2729
m_oaVectors.Add(ag);
2730
ti *= ag->m_iAtomGes;
2731
m_oaVectors.Add(NULL);
2732
} // END IF NOT ORTHO
2733
} else if (m_iVecType[z] == 1) // Dipol
2734
{
2735
if (m_iShowMol != -1)
2736
m_iRefOrSec[z][0] = AskRangeInteger(" Take dipole vector from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2737
else m_iRefOrSec[z][0] = 0;
2738
} else if (m_iVecType[z] == 2) // Geschwindigkeit
2739
{
2740
_ax6: if (m_iShowMol != -1)
2741
m_iRefOrSec[z][0] = AskRangeInteger(" Take velocity vector from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2742
else m_iRefOrSec[z][0] = 0;
2743
mprintf(" Velocity vector of which atoms to use (e.g. C7)? [#2] ");
2744
inpprintf("! Velocity vector of which atoms to use (e.g. C7)? [#2]\n");
2745
myget(buf);
2746
2747
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2748
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2749
2750
if (strlen(buf)==0)
2751
{
2752
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],"#2"))
2753
{
2754
eprintf("Weird error.\n");
2755
inpprintf("! Weird error.\n");
2756
abort();
2757
}
2758
} else if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2759
{
2760
eprintf("Wrong input.\n");
2761
inpprintf("! Wrong input.\n");
2762
delete ag;
2763
goto _ax6;
2764
}
2765
m_oaVectors.Add(ag);
2766
ti *= ag->m_iAtomGes;
2767
} else if (m_iVecType[z] == 3) // Kraft
2768
{
2769
_ax7: if (m_iShowMol != -1)
2770
m_iRefOrSec[z][0] = AskRangeInteger(" Take force vektor from RM %s (0) or from OM %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
2771
else m_iRefOrSec[z][0] = 0;
2772
mprintf(" Force vector of which atoms to use (e.g. C7)? [#2] ");
2773
inpprintf("! Force vector of which atoms to use (e.g. C7)? [#2]\n");
2774
myget(buf);
2775
2776
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2777
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2778
2779
if (strlen(buf)==0)
2780
{
2781
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],"#2"))
2782
{
2783
eprintf("Weird Error.\n");
2784
inpprintf("! Weird Error.\n");
2785
abort();
2786
}
2787
} else if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2788
{
2789
eprintf("Wrong input.\n");
2790
inpprintf("! Wrong input.\n");
2791
delete ag;
2792
goto _ax7;
2793
}
2794
m_oaVectors.Add(ag);
2795
ti *= ag->m_iAtomGes;
2796
}
2797
} // END FOR 0..1
2798
z2++;
2799
m_iCombinations += ti;
2800
} while (g_bAdvanced2?AskYesNo("\n Add another set of vectors to this (!) ADF (y/n)? [no] ",false):false);
2801
2802
ParseDeriv();
2803
2804
switch(m_iDeriv)
2805
{
2806
case 0:
2807
mprintf("\n");
2808
_anglowag:
2809
m_fMinAngle = AskFloat(" Enter minimal angle between the vectors: [0 deg] ",0.0f);
2810
if (m_fMinAngle < 0)
2811
{
2812
eprintf(" Angles < 0 degree are not defined.\n");
2813
goto _anglowag;
2814
}
2815
m_fMaxAngle = AskFloat(" Enter maximal angle between the vectors: [180 deg] ",180.0f);
2816
break;
2817
case 1:
2818
if (m_bDerivAbs)
2819
m_fMinAngle = AskFloat(" Enter the minimal value of this d1-ADF in deg/ps: [0] ",0.0f);
2820
else m_fMinAngle = AskFloat(" Enter the minimal value of this d1-ADF in deg/ps: [-10.0] ",-10.0f);
2821
m_fMaxAngle = AskFloat(" Enter the maximal value of this d1-ADF in deg/ps: [10.0] ",10.0f);
2822
break;
2823
case 2:
2824
if (m_bDerivAbs)
2825
m_fMinAngle = AskFloat(" Enter the minimal value of this d2-ADF in deg/ps^2: [0] ",0.0f);
2826
else m_fMinAngle = AskFloat(" Enter the minimal value of this d2-ADF in deg/ps^2: [-10.0] ",-10.0f);
2827
m_fMaxAngle = AskFloat(" Enter the maximal value of this d2-ADF in deg/ps^2: [10.0] ",10.0f);
2828
break;
2829
}
2830
2831
/* if (m_fMaxAngle <= 90.0f)
2832
m_bFoldAngle = AskYesNo(" Should angles > 90 deg be \"mirrored\" (180 deg = 0 deg) (y/n)? [yes] ",true);
2833
else*/ m_bFoldAngle = false;
2834
m_bCosine = (AskRangeInteger(" Plot ADF against angle (0) or against cosine (1)? [0] ",0,1,0)!=0);
2835
if (m_bCosine)
2836
{
2837
m_fMinAngle = (float)cos(m_fMinAngle/180.0*Pi);
2838
m_fMaxAngle = (float)cos(m_fMaxAngle/180.0*Pi);
2839
if (m_fMinAngle > m_fMaxAngle)
2840
{
2841
tf = m_fMinAngle;
2842
m_fMinAngle = m_fMaxAngle;
2843
m_fMaxAngle = tf;
2844
}
2845
mprintf(" The data range is %.2f to %.2f.\n",m_fMinAngle,m_fMaxAngle);
2846
}
2847
if (!m_bCosine)
2848
m_bMirror = AskYesNo(" Force this ADF to be mirror-symmetric to the 90 deg line (y/n)? [no] ",false);
2849
else m_bMirror = false;
2850
m_iResolution = AskUnsignedInteger(" Please enter the resolution (bin count) for this ADF: [100] ",100);
2851
2852
if (g_bAdvanced2)
2853
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
2854
else m_iHistogramRes = 0;
2855
2856
if (m_iShowMol != -1)
2857
m_bStat = AskYesNo(" Apply cone correction (y/n)? [%c] ",!m_bCosine,(!m_bCosine)?'y':'n');
2858
else m_bStat = 0;
2859
/* mprintf("\n Save temporal development of this ADF (0=nein, 1=ja)? [0] ");
2860
myget(buf);
2861
m_bSaveAngle = (atoi(buf)!=0);*/
2862
BuildName();
2863
mprintf(WHITE,"\n<<< End of Angular Distribution Function <<<\n\n");
2864
BTOUT;
2865
}
2866
2867
2868
void CDDF::Parse()
2869
{
2870
BTIN;
2871
char buf[256];
2872
CAtomGroup *ag;
2873
int z0, z, z2, i;
2874
float tf;
2875
2876
try { m_pDDF = new CDF(); } catch(...) { m_pDDF = NULL; }
2877
if (m_pDDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2878
2879
mprintf(WHITE,"\n>>> Dihedral Distribution Function >>>\n\n");
2880
m_bClassical = AskYesNo(" Use \"simple\" (y) (4 atoms) or \"generalized\" (n) (3 vectors) Dihedrals? [yes] ",true);
2881
2882
m_iCombinations = 1;
2883
if (m_bClassical)
2884
{
2885
m_bOrtho[0] = false;
2886
m_bOrtho[1] = false;
2887
m_bOrtho[2] = false;
2888
z0 = m_oaVectors.GetSize();
2889
for (z=0;z<3;z++)
2890
{
2891
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2892
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2893
2894
m_oaVectors.Add(ag);
2895
2896
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2897
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2898
2899
m_oaVectors.Add(ag);
2900
m_oaVectors.Add(NULL);
2901
}
2902
for (z=0;z<4;z++)
2903
{
2904
_bx: if (m_iShowMol != -1)
2905
i = AskRangeInteger(" Take the %d. atom from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2906
else i = 0;
2907
switch(z)
2908
{
2909
case 0:
2910
m_iRefOrSec[0][1] = i;
2911
break;
2912
case 1:
2913
m_iRefOrSec[0][0] = i;
2914
m_iRefOrSec[2][0] = i;
2915
break;
2916
case 2:
2917
m_iRefOrSec[2][1] = i;
2918
m_iRefOrSec[1][0] = i;
2919
break;
2920
case 3:
2921
m_iRefOrSec[1][1] = i;
2922
break;
2923
}
2924
mprintf(" Enter the %d. atom(s) (e.g. C7): ",z+1);
2925
inpprintf("! Enter the %d. atom(s) (e.g. C7):\n",z+1);
2926
myget(buf);
2927
switch(z)
2928
{
2929
case 0:
2930
if (!((CAtomGroup*)m_oaVectors[z0+0*3+1])->ParseAtoms((!m_iRefOrSec[0][1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2931
{
2932
eprintf("Wrong input.\n");
2933
inpprintf("! Wrong input.\n");
2934
goto _bx;
2935
}
2936
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+0*3+1])->m_iAtomGes;
2937
break;
2938
case 1:
2939
if (!((CAtomGroup*)m_oaVectors[z0+0*3+0])->ParseAtoms((!m_iRefOrSec[0][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2940
{
2941
eprintf("Wrong input.\n");
2942
inpprintf("! Wrong input.\n");
2943
goto _bx;
2944
}
2945
if (!((CAtomGroup*)m_oaVectors[z0+2*3+0])->ParseAtoms((!m_iRefOrSec[2][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2946
{
2947
eprintf("Wrong input.\n");
2948
inpprintf("! Wrong input.\n");
2949
goto _bx;
2950
}
2951
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+0*3+0])->m_iAtomGes;
2952
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+0*3+0])->m_iAtomGes;
2953
break;
2954
case 2:
2955
if (!((CAtomGroup*)m_oaVectors[z0+2*3+1])->ParseAtoms((!m_iRefOrSec[2][1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2956
{
2957
eprintf("Wrong input.\n");
2958
inpprintf("! Wrong input.\n");
2959
goto _bx;
2960
}
2961
if (!((CAtomGroup*)m_oaVectors[z0+1*3+0])->ParseAtoms((!m_iRefOrSec[1][0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2962
{
2963
eprintf("Wrong input.\n");
2964
inpprintf("! Wrong input.\n");
2965
goto _bx;
2966
}
2967
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+2*3+1])->m_iAtomGes;
2968
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+2*3+1])->m_iAtomGes;
2969
break;
2970
case 3:
2971
if (!((CAtomGroup*)m_oaVectors[z0+1*3+1])->ParseAtoms((!m_iRefOrSec[1][1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
2972
{
2973
eprintf("Wrong input.\n");
2974
inpprintf("! Wrong input.\n");
2975
goto _bx;
2976
}
2977
m_iCombinations *= ((CAtomGroup*)m_oaVectors[z0+1*3+1])->m_iAtomGes;
2978
break;
2979
}
2980
}
2981
} else // NONCLASSIC
2982
{
2983
mprintf("\nYou now have to define 3 vectors:\n");
2984
mprintf("The 1st and 2nd vector are projected onto the normal plane of the 3rd vector.\n");
2985
mprintf("The angle between the two projected vectors in the plane is evaluated.\n");
2986
for (z=0;z<3;z++)
2987
{
2988
mprintf(WHITE,"\n * Vector %d\n",z+1);
2989
m_bOrtho[z] = (AskRangeInteger(" Shall the %d. vector connect 2 points (0) or be orthogonal to a plane (1)? [0] ",0,1,0,z+1) != 0);
2990
if (m_bOrtho[z])
2991
{
2992
for (z2=0;z2<3;z2++)
2993
{
2994
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
2995
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2996
2997
_by: if (m_iShowMol != -1)
2998
m_iRefOrSec[z][z2] = AskRangeInteger(" Take the %d. atom(s) of the plane from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z2+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
2999
else m_iRefOrSec[z][z2] = 0;
3000
mprintf(" Please enter the %d. atom(s) (e.g. C7): ",z2+1);
3001
inpprintf("! Please enter the %d. atom(s) (e.g. C7):\n",z2+1);
3002
myget(buf);
3003
if (!ag->ParseAtoms((!m_iRefOrSec[z][z2])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3004
{
3005
eprintf("Wrong input.\n");
3006
inpprintf("! Wrong input.\n");
3007
goto _by;
3008
}
3009
m_iCombinations *= ag->m_iAtomGes;
3010
m_oaVectors.Add(ag);
3011
}
3012
} else // Ortho
3013
{
3014
for (z2=0;z2<2;z2++)
3015
{
3016
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3017
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3018
3019
_bz: if (m_iShowMol != -1)
3020
m_iRefOrSec[z][z2] = AskRangeInteger(" Take the %d. atom(s) of the vector from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z2+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3021
else m_iRefOrSec[z][z2] = 0;
3022
mprintf(" Please enter the %d. atom(s) (e.g. C7): ",z2+1);
3023
inpprintf("! Please enter the %d. atom(s) (e.g. C7):\n",z2+1);
3024
myget(buf);
3025
if (!ag->ParseAtoms((!m_iRefOrSec[z][z2])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3026
{
3027
eprintf("Wrong input.\n");
3028
inpprintf("! Wrong input.\n");
3029
goto _bz;
3030
}
3031
m_iCombinations *= ag->m_iAtomGes;
3032
m_oaVectors.Add(ag);
3033
}
3034
m_oaVectors.Add(NULL);
3035
} // ENDIF ORTHO
3036
} // END FOR
3037
} // END IF NONCLASSIC
3038
3039
/* mprintf("\n");
3040
mprintf(" The \"classical\" dihedral angle is defined for a range of 0 ... 180 deg.\n\n");
3041
m_bAbs = !AskYesNo(" Do you want to extend the range to -180 ... +180 deg (y/n)? [no] ",false);*/
3042
3043
mprintf("\n");
3044
mprintf(" Per default, the dihedral angle is defined in a range of -180 ... 180 deg.\n\n");
3045
m_bPositive = AskYesNo(" Use range of 0 ... 360 deg instead (e.g. -90 deg becomes 270 deg, ...) (y/n)? [no] ",false);
3046
m_bAbs = false;
3047
mprintf("\n");
3048
3049
ParseDeriv();
3050
3051
switch(m_iDeriv)
3052
{
3053
case 0:
3054
if (m_bPositive)
3055
{
3056
m_fMinAngle = AskFloat("\n Enter minimal dihedral angle to observe: [0 deg] ",0);
3057
m_fMaxAngle = AskFloat(" Enter maximal dihedral angle to observe: [360 deg] ",360.0f);
3058
} else
3059
{
3060
m_fMinAngle = AskFloat("\n Enter minimal dihedral angle to observe: [-180 deg] ",-180.0f);
3061
m_fMaxAngle = AskFloat(" Enter maximal dihedral angle to observe: [180 deg] ",180.0f);
3062
}
3063
break;
3064
case 1:
3065
if (m_bDerivAbs)
3066
m_fMinAngle = AskFloat(" Enter the minimal value of this d1-DDF in deg/ps: [0] ",0.0f);
3067
else m_fMinAngle = AskFloat(" Enter the minimal value of this d1-DDF in deg/ps: [-10.0] ",-10.0f);
3068
m_fMaxAngle = AskFloat(" Enter the maximal value of this d1-DDF in deg/ps: [10.0] ",10.0f);
3069
break;
3070
case 2:
3071
if (m_bDerivAbs)
3072
m_fMinAngle = AskFloat(" Enter the minimal value of this d2-DDF in deg/ps^2: [0] ",0.0f);
3073
else m_fMinAngle = AskFloat(" Enter the minimal value of this d2-DDF in deg/ps^2: [-10.0] ",-10.0f);
3074
m_fMaxAngle = AskFloat(" Enter the maximal value of this d2-DDF in deg/ps^2: [10.0] ",10.0f);
3075
break;
3076
}
3077
3078
if (m_iDeriv == 0)
3079
{
3080
m_bCosine = (AskRangeInteger(" Plot DDF against angle (0) or against cosine (1)? [0] ",0,1,0) != 0);
3081
if (m_bCosine)
3082
{
3083
if ((m_fMinAngle <= 0) && (m_fMaxAngle >= 0))
3084
{
3085
if (fabsf(m_fMinAngle) > fabsf(m_fMaxAngle))
3086
m_fMinAngle = cosf(fabsf(m_fMinAngle));
3087
else m_fMinAngle = cosf(fabsf(m_fMaxAngle));
3088
m_fMaxAngle = 1.0f;
3043
3089
} else
3044
{
3045
m_fMinAngle = AskFloat("\n Enter minimal dihedral angle to observe: [-180 deg] ",-180.0f);
3046
m_fMaxAngle = AskFloat(" Enter maximal dihedral angle to observe: [180 deg] ",180.0f);
3047
}
3048
break;
3049
case 1:
3050
if (m_bDerivAbs)
3051
m_fMinAngle = AskFloat(" Enter the minimal value of this d1-DDF in deg/ps: [0] ",0.0f);
3052
else m_fMinAngle = AskFloat(" Enter the minimal value of this d1-DDF in deg/ps: [-10.0] ",-10.0f);
3053
m_fMaxAngle = AskFloat(" Enter the maximal value of this d1-DDF in deg/ps: [10.0] ",10.0f);
3054
break;
3055
case 2:
3056
if (m_bDerivAbs)
3057
m_fMinAngle = AskFloat(" Enter the minimal value of this d2-DDF in deg/ps^2: [0] ",0.0f);
3058
else m_fMinAngle = AskFloat(" Enter the minimal value of this d2-DDF in deg/ps^2: [-10.0] ",-10.0f);
3059
m_fMaxAngle = AskFloat(" Enter the maximal value of this d2-DDF in deg/ps^2: [10.0] ",10.0f);
3060
break;
3061
}
3062
3063
if (m_iDeriv == 0)
3064
{
3065
m_bCosine = (AskRangeInteger(" Plot DDF against angle (0) or against cosine (1)? [0] ",0,1,0) != 0);
3066
if (m_bCosine)
3067
{
3068
m_fMinAngle = (float)cos(m_fMinAngle/180.0*Pi);
3069
m_fMaxAngle = (float)cos(m_fMaxAngle/180.0*Pi);
3070
if (m_fMinAngle > m_fMaxAngle)
3071
{
3072
tf = m_fMinAngle;
3073
m_fMinAngle = m_fMaxAngle;
3074
m_fMaxAngle = tf;
3075
}
3076
m_bAbs = false;
3077
m_bSymm = false;
3078
mprintf("\n The data range is %.2f to %.2f.\n\n",m_fMinAngle,m_fMaxAngle);
3079
} else
3080
{
3081
/* m_bAbs = AskYesNo(" Use absolute angle values (y) or signed values (n)? [yes] ",true);
3082
if (!m_bAbs)
3083
{
3084
m_fMinAngle = -m_fMaxAngle;
3085
mprintf("\n The data range is %.2f to %.2f.\n\n",m_fMinAngle,m_fMaxAngle);
3086
m_bSymm = AskYesNo(" Force this DDF to be symmetrical to the 0 degree line (y/n)? [no] ",false);
3087
} else m_bSymm = false;*/
3088
// if (!m_bAbs)
3089
// {
3090
// m_fMinAngle = -m_fMaxAngle;
3091
mprintf("\n The data range is %.2f to %.2f.\n\n",m_fMinAngle,m_fMaxAngle);
3092
if (!m_bPositive)
3093
m_bSymm = AskYesNo(" Add also bin entries for inverse angles (force symmetry) (y/n)? [no] ",false);
3094
else m_bSymm = false;
3095
// } else m_bSymm = false;
3096
}
3097
} else
3098
{
3099
m_bCosine = false;
3100
m_bAbs = false;
3101
m_bSymm = false;
3102
}
3103
m_iResolution = AskUnsignedInteger(" Please enter binning resolution for this DDF: [100] ",100);
3104
3105
if (g_bAdvanced2)
3106
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3107
else m_iHistogramRes = 0;
3108
3109
/* mprintf("\n Save temporal Development of Dihedrals (0=no, 1=yes)? [0] ");
3110
myget(buf);
3111
m_bSaveAngle = atoi(buf)!=0;*/
3112
BuildName();
3113
mprintf(WHITE,"\n<<< End of Dihedral Distribution Function <<<\n\n");
3114
BTOUT;
3115
}
3116
3117
3118
void CPlDF::Parse()
3119
{
3120
BTIN;
3121
char buf[256];
3122
CAtomGroup *ag;
3123
int z;
3124
3125
try { m_pPlDF = new CDF(); } catch(...) { m_pPlDF = NULL; }
3126
if (m_pPlDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3127
3128
mprintf(WHITE,"\n>>> Plane Distance Distribution Function >>>\n\n");
3129
3130
m_bNormal = !AskYesNo(" Define plane via 3 atoms (y) or as normal plane of a vector (n) (y/n)? [yes] ",true);
3131
3132
m_iCombinations = 1;
3133
if (m_bNormal)
3134
{
3135
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3136
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3137
_b2:
3138
if (m_iShowMol != -1)
3139
m_iRefOrSec[0] = AskRangeInteger(" Take the base atom of the vector/plane from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3140
else m_iRefOrSec[0] = 0;
3141
mprintf(" Please enter the base atom (e.g. C7): ");
3142
inpprintf("! Please enter the base atom (e.g. C7):\n");
3143
myget(buf);
3144
if (!ag->ParseAtoms((!m_iRefOrSec[0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3145
{
3146
eprintf("Wrong input.\n");
3147
inpprintf("! Wrong input.\n");
3148
goto _b2;
3149
}
3150
m_iCombinations *= ag->m_iAtomGes;
3151
m_oaVectors.Add(ag);
3152
3153
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3154
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3155
_b3:
3156
if (m_iShowMol != -1)
3157
m_iRefOrSec[1] = AskRangeInteger(" Take the atom at the tip of the vector from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3158
else m_iRefOrSec[1] = 0;
3159
mprintf(" Please enter the tip atom (e.g. C7): ");
3160
inpprintf("! Please enter the tip atom (e.g. C7):\n");
3161
myget(buf);
3162
if (!ag->ParseAtoms((!m_iRefOrSec[1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3163
{
3164
eprintf("Wrong input.\n");
3165
inpprintf("! Wrong input.\n");
3166
goto _b3;
3167
}
3168
m_iCombinations *= ag->m_iAtomGes;
3169
m_oaVectors.Add(ag);
3170
m_oaVectors.Add(NULL); // Dummy placeholder
3171
} else
3172
{
3173
for (z=0;z<3;z++)
3174
{
3175
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3176
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3177
_b1:
3178
if (m_iShowMol != -1)
3179
m_iRefOrSec[z] = AskRangeInteger(" Take the %d. atom(s) of the plane from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3180
else m_iRefOrSec[z] = 0;
3181
mprintf(" Please enter the %d. atom (e.g. C7): ",z+1);
3182
inpprintf("! Please enter the %d. atom (e.g. C7):\n",z+1);
3183
myget(buf);
3184
if (!ag->ParseAtoms((!m_iRefOrSec[z])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3185
{
3186
eprintf("Wrong input.\n");
3187
inpprintf("! Wrong input.\n");
3188
goto _b1;
3189
}
3190
m_iCombinations *= ag->m_iAtomGes;
3191
m_oaVectors.Add(ag);
3192
}
3193
}
3194
mprintf(" Plane defined.\n\n");
3195
3196
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3197
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3198
_b4:
3199
if (m_iShowMol != -1)
3200
m_iRefOrSec[3] = AskRangeInteger(" Take the atom(s) to observe from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3201
else m_iRefOrSec[3] = 0;
3202
mprintf(" Please enter the atom(s) to observe (e.g. C7): ");
3203
inpprintf("! Please enter the atom(s) to observe (e.g. C7):\n");
3204
myget(buf);
3205
if (!ag->ParseAtoms((!m_iRefOrSec[3])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3206
{
3207
eprintf("Wrong input.\n");
3208
inpprintf("! Wrong input.\n");
3209
goto _b4;
3210
}
3211
m_iCombinations *= ag->m_iAtomGes;
3212
m_oaVectors.Add(ag);
3213
3214
m_fMinDist = AskFloat(" Enter the minimal distance to observe (in pm): [-%d.0] ",(float)-HalfBox(),HalfBox());
3215
m_fMaxDist = AskFloat(" Enter the maximal distance to observe (in pm): [%d.0] ",(float)HalfBox(),HalfBox());
3216
3217
m_iResolution = AskUnsignedInteger(" Please enter binning resolution for this PlDF: [100] ",100);
3218
3219
if (g_bAdvanced2)
3220
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3221
else m_iHistogramRes = 0;
3222
3223
BuildName();
3224
mprintf(WHITE,"\n<<< End of Plane Distance Distribution Function <<<\n\n");
3225
BTOUT;
3226
}
3227
3228
3229
void CLiDF::Parse()
3230
{
3231
BTIN;
3232
char buf[256];
3233
CAtomGroup *ag;
3234
int z;
3235
3236
try { m_pLiDF = new CDF(); } catch(...) { m_pLiDF = NULL; }
3237
if (m_pLiDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3238
3239
mprintf(WHITE,"\n>>> Line Distance Distribution Function >>>\n\n");
3240
3241
m_bNormal = !AskYesNo(" Define line via 2 atoms (y) or as normal vector of a plane (n) (y/n)? [yes] ",true);
3242
3243
m_iCombinations = 1;
3244
if (m_bNormal)
3245
{
3246
mprintf("\n The line will pass through the 1st point of the plane.\n\n");
3247
for (z=0;z<3;z++)
3248
{
3249
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3250
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3251
_b3:
3252
if (m_iShowMol != -1)
3253
m_iRefOrSec[z] = AskRangeInteger(" Take the %d. atom(s) of the plane from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3254
else m_iRefOrSec[z] = 0;
3255
mprintf(" Please enter the %d. atom (e.g. C7): ",z+1);
3256
inpprintf("! Please enter the %d. atom (e.g. C7):\n",z+1);
3257
myget(buf);
3258
if (!ag->ParseAtoms((!m_iRefOrSec[z])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3259
{
3260
eprintf("Wrong input.\n");
3261
inpprintf("! Wrong input.\n");
3262
goto _b3;
3263
}
3264
m_iCombinations *= ag->m_iAtomGes;
3265
m_oaVectors.Add(ag);
3266
}
3267
} else
3268
{
3269
for (z=0;z<2;z++)
3270
{
3271
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3272
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3273
_b1:
3274
if (m_iShowMol != -1)
3275
m_iRefOrSec[z] = AskRangeInteger(" Take the %d. atom(s) of the line from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3276
else m_iRefOrSec[z] = 0;
3277
mprintf(" Please enter the %d. atom (e.g. C7): ",z+1);
3278
inpprintf("! Please enter the %d. atom (e.g. C7):\n",z+1);
3279
myget(buf);
3280
if (!ag->ParseAtoms((!m_iRefOrSec[z])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3281
{
3282
eprintf("Wrong input.\n");
3283
inpprintf("! Wrong input.\n");
3284
goto _b1;
3285
}
3286
m_iCombinations *= ag->m_iAtomGes;
3287
m_oaVectors.Add(ag);
3288
}
3289
m_oaVectors.Add(NULL);
3290
}
3291
3292
mprintf(" Line defined.\n\n");
3293
3294
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3295
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3296
_b2:
3297
if (m_iShowMol != -1)
3298
m_iRefOrSec[3] = AskRangeInteger(" Take the atom(s) to observe from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3299
else m_iRefOrSec[3] = 0;
3300
mprintf(" Please enter the atom(s) to observe (e.g. C7): ");
3301
inpprintf("! Please enter the atom(s) to observe (e.g. C7):\n");
3302
myget(buf);
3303
if (!ag->ParseAtoms((!m_iRefOrSec[3])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3304
{
3305
eprintf("Wrong input.\n");
3306
inpprintf("! Wrong input.\n");
3307
goto _b2;
3308
}
3309
m_iCombinations *= ag->m_iAtomGes;
3310
m_oaVectors.Add(ag);
3311
3312
m_fMinDist = AskFloat(" Enter the minimal distance to observe (in pm): [0] ",0.0f);
3313
m_fMaxDist = AskFloat(" Enter the maximal distance to observe (in pm): [%d.0] ",(float)HalfBox(),HalfBox());
3314
3315
m_iResolution = AskUnsignedInteger(" Please enter binning resolution for this LiDF: [100] ",100);
3316
3317
if (g_bAdvanced2)
3318
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3319
else m_iHistogramRes = 0;
3320
3321
if (m_iShowMol != -1)
3322
m_bRadialCorrect = AskYesNo(" Correct radial distribution for this LiDF (y/n)? [yes] ",true);
3323
else m_bRadialCorrect = AskYesNo(" Correct radial distribution for this LiDF (y/n)? [no] ",false);
3324
3325
BuildName();
3326
mprintf(WHITE,"\n<<< End of Line Distance Distribution Function <<<\n\n");
3327
BTOUT;
3328
}
3329
3330
3331
void CDipDF::Parse()
3332
{
3333
BTIN;
3334
float tf;
3335
double td, td2, td3;
3336
CMolecule *m;
3337
CSingleMolecule *sm;
3338
int z;
3339
3340
g_bDipole = true;
3341
3342
try { m_pDipoleDF = new CDF(); } catch(...) { m_pDipoleDF = NULL; }
3343
if (m_pDipoleDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3344
3345
mprintf(WHITE,"\n>>> Dipole Distribution Function >>>\n\n");
3346
if (m_iShowMol != -1)
3347
m_iRefOrSec = AskRangeInteger(" Observe dipole moment from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3348
else m_iRefOrSec = 0;
3349
3350
ParseDeriv();
3351
3352
if (m_iRefOrSec != 0)
3353
m = (CMolecule*)g_oaMolecules[m_iShowMol];
3354
else m = (CMolecule*)g_oaMolecules[g_iFixMol];
3355
3356
td = 0;
3357
td2 = 1.0e10;
3358
td3 = 0;
3359
for (z=0;z<m->m_laSingleMolIndex.GetSize();z++)
3360
{
3361
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z]];
3362
tf = sm->m_vDipole.GetLength();
3363
if (tf > td)
3364
td = tf;
3365
if (tf < td2)
3366
td2 = tf;
3367
td3 += tf;
3368
}
3369
td3 /= (double)m->m_laSingleMolIndex.GetSize();
3370
3371
mprintf("\n Dipole moment of %s (1st step): Min. %.3f, Max. %.3f, Avg. %.3f Debye.\n\n",m->m_sName,td2,td,td3);
3372
3373
switch(m_iDeriv)
3374
{
3375
case 0:
3376
m_fDipoleMin = AskFloat(" Enter the lower bound for dipole values (in Debye): [0] ",0.0f);
3377
m_fDipoleMax = AskFloat(" Enter the upper bound for dipole values (in Debye): [%d] ",float(int(td*2.0)),int(td*2.0));
3378
break;
3379
case 1:
3380
if (m_bDerivAbs)
3381
m_fDipoleMin = AskFloat(" Enter the minimal value of this d1-DDF in Debye/ps: [0] ",0.0f);
3382
else m_fDipoleMin = AskFloat(" Enter the minimal value of this d1-DDF in Debye/ps: [-10.0] ",-10.0f);
3383
m_fDipoleMax = AskFloat(" Enter the maximal value of this d1-DDF in Debye/ps: [10.0] ",10.0f);
3384
break;
3385
case 2:
3386
if (m_bDerivAbs)
3387
m_fDipoleMin = AskFloat(" Enter the minimal value of this d2-DDF in Debye/ps^2: [0] ",0.0f);
3388
else m_fDipoleMin = AskFloat(" Enter the minimal value of this d2-DDF in Debye/ps^2: [-10.0] ",-10.0f);
3389
m_fDipoleMax = AskFloat(" Enter the maximal value of this d2-DDF in Debye/ps^2: [10.0] ",10.0f);
3390
break;
3391
}
3392
3393
m_iResolution = AskUnsignedInteger(" Enter binning resolution for the Dipole DF: [%d] ",int((m_fDipoleMax-m_fDipoleMin)*10.0),int((m_fDipoleMax-m_fDipoleMin)*10.0));
3394
3395
if (g_bAdvanced2)
3396
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3397
else m_iHistogramRes = 0;
3398
3399
BuildName();
3400
mprintf(WHITE,"\n<<< End of Dipole Distribution Function <<<\n\n");
3401
BTOUT;
3402
}
3403
3404
3405
void CSDF::Parse(bool voro)
3406
{
3407
BTIN;
3408
int ti;
3409
char buf[256];
3410
3411
m_iShowAtomGes = 0;
3412
3413
try { m_pSDF = new C3DF(); } catch(...) { m_pSDF = NULL; }
3414
if (m_pSDF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3415
3416
mprintf(WHITE,"\n>>> Spatial Distribution Function >>>\n\n");
3417
_sdfatoms:
3418
if (!voro)
3419
{
3420
if (m_bIntra)
3421
{
3422
mprintf(" Observing atoms in reference molecule %s.\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
3423
m_iRefOrSec = 0;
3424
} else
3425
{
3426
mprintf(" Observing atoms in observed molecule %s.\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3427
m_iRefOrSec = 1;
3428
}
3429
/* if (m_iShowMol != -1)
3430
m_iRefOrSec = AskRangeInteger(" Observe atoms in RM %s (0) or in OM %s (1)? [1] ",0,1,1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3431
else m_iRefOrSec = 0;*/
3432
mprintf(" Which atoms to observe (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ");
3433
inpprintf("! Which atoms to observe (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n");
3434
myget(buf);
3435
if (strlen(buf) == 0)
3436
{
3437
if (!m_oAtoms.ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec==0)?g_iFixMol:m_iShowMol],"#2"))
3438
{
3439
eprintf("Strange error ^^\n");
3440
inpprintf("! Strange error ^\n");
3441
goto _sdfatoms;
3442
}
3443
} else
3444
{
3445
if (!m_oAtoms.ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec==0)?g_iFixMol:m_iShowMol],buf))
3446
{
3447
eprintf("Wrong input.\n");
3448
inpprintf("! Wrong input.\n");
3449
goto _sdfatoms;
3450
}
3451
}
3452
3453
m_iShowAtomGes += m_oAtoms.m_iAtomGes;
3454
m_fParticleDensity = m_oAtoms.m_iAtomGes * ((CMolecule*)g_oaMolecules[(m_iRefOrSec==0)?g_iFixMol:m_iShowMol])->m_laSingleMolIndex.GetSize() / g_fBoxX / g_fBoxY / g_fBoxZ * 1E9f;
3455
}
3456
3457
m_fRadius = AskFloat(" Please enter radius of this SDF in pm: [%d.0] ",(float)HalfBox(),HalfBox());
3458
_sdfresagain:
3459
ti = g_pDatabase->GetInt("/PLOT3D/DEFAULTS/BIN_RES");
3460
m_iResolution = AskUnsignedInteger(" Please enter binning resolution of this SDF per dimension: [%d] ",ti,ti);
3461
3462
if (m_iResolution > 300)
3463
{
3464
eprintf("\nWarning: ");
3465
mprintf("This large resolution will consume much RAM (%s)\n",FormatBytes(pow((double)m_iResolution,3)*sizeof(double)));
3466
mprintf(" and result in very large SDF output files.\n\n");
3467
if (!AskYesNo(" Use this resolution (y/n)? [no] ",false))
3468
goto _sdfresagain;
3469
}
3470
3471
if (g_bAdvanced2)
3472
{
3473
m_bVdWSpheres = false; //AskYesNo(" Process atoms as VdW spheres rather than points (y/n)? [no] ",false);
3474
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3475
m_bClipPlane = AskYesNo(" Use a clipping plane for this SDF (y/n)? [no] ",false);
3476
if (m_bClipPlane)
3477
{
3478
_cut: mprintf(" Should the clipping plane stand perpendicular to the X, Y or Z axis (x/y/z)? [x] ");
3479
inpprintf("! Should the clipping plane stand perpendicular to the X, Y or Z axis (x/y/z)? [x]\n");
3480
myget(buf);
3481
switch(tolower(buf[0]))
3482
{
3483
case 0:
3484
case 'x':
3485
m_iClipDirection = 0;
3486
break;
3487
case 'y':
3488
m_iClipDirection = 1;
3489
break;
3490
case 'z':
3491
m_iClipDirection = 2;
3492
break;
3493
default:
3494
eprintf(" Wrong input! Please enter 'x', 'y' or 'z'.\n");
3495
inpprintf("! Wrong input! Please enter 'x', 'y' or 'z'.\n");
3496
goto _cut;
3497
}
3498
m_fClipValue = AskFloat(" Please enter distance of clipping plane from origin (in pm): [0] ",0.0f);
3499
}
3500
m_bInvert = AskYesNo(" Should this SDF be inverted (y/n)? [no] ",false);
3501
m_bSDFMirrorXY = AskYesNo(" Force this SDF to be symmetrical to the XY plane (y/n)? [no] ",false);
3502
m_bSDFMirrorBisect = AskYesNo(" Force this SDF to be symmetrical to the angle bisector (y/n)? [no] ",false);
3503
m_bCutPlane = AskYesNo(" Add a particle density cut plane to this SDF (y/n)? [no] ",false);
3504
if (m_bCutPlane)
3505
{
3506
m_iCutPlaneResolution = AskUnsignedInteger(" Enter the binning resolution for the cut plane per dimension: [100] ",100);
3507
m_bCutPlaneShowAtoms = AskYesNo(" Show reference atoms in Pseudo SDF plot (y/n)? [yes] ",true);
3508
}
3509
} else
3510
{
3511
m_bVdWSpheres = false;
3090
{
3091
m_fMinAngle = cosf(m_fMinAngle/180.0f*Pi);
3092
m_fMaxAngle = cosf(m_fMaxAngle/180.0f*Pi);
3093
}
3094
if (m_fMinAngle > m_fMaxAngle)
3095
{
3096
tf = m_fMinAngle;
3097
m_fMinAngle = m_fMaxAngle;
3098
m_fMaxAngle = tf;
3099
}
3100
m_bAbs = false;
3101
m_bSymm = false;
3102
mprintf("\n The data range is %.2f to %.2f.\n\n",m_fMinAngle,m_fMaxAngle);
3103
} else
3104
{
3105
/* m_bAbs = AskYesNo(" Use absolute angle values (y) or signed values (n)? [yes] ",true);
3106
if (!m_bAbs)
3107
{
3108
m_fMinAngle = -m_fMaxAngle;
3109
mprintf("\n The data range is %.2f to %.2f.\n\n",m_fMinAngle,m_fMaxAngle);
3110
m_bSymm = AskYesNo(" Force this DDF to be symmetrical to the 0 degree line (y/n)? [no] ",false);
3111
} else m_bSymm = false;*/
3112
// if (!m_bAbs)
3113
// {
3114
// m_fMinAngle = -m_fMaxAngle;
3115
mprintf("\n The data range is %.2f to %.2f.\n\n",m_fMinAngle,m_fMaxAngle);
3116
if (!m_bPositive)
3117
m_bSymm = AskYesNo(" Add also bin entries for inverse angles (force symmetry) (y/n)? [no] ",false);
3118
else m_bSymm = false;
3119
// } else m_bSymm = false;
3120
}
3121
} else
3122
{
3123
m_bCosine = false;
3124
m_bAbs = false;
3125
m_bSymm = false;
3126
}
3127
m_iResolution = AskUnsignedInteger(" Please enter binning resolution for this DDF: [100] ",100);
3128
3129
if (g_bAdvanced2)
3130
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3131
else m_iHistogramRes = 0;
3132
3133
/* mprintf("\n Save temporal Development of Dihedrals (0=no, 1=yes)? [0] ");
3134
myget(buf);
3135
m_bSaveAngle = atoi(buf)!=0;*/
3136
BuildName();
3137
mprintf(WHITE,"\n<<< End of Dihedral Distribution Function <<<\n\n");
3138
BTOUT;
3139
}
3140
3141
3142
void CPlDF::Parse()
3143
{
3144
BTIN;
3145
char buf[256];
3146
CAtomGroup *ag;
3147
int z;
3148
3149
try { m_pPlDF = new CDF(); } catch(...) { m_pPlDF = NULL; }
3150
if (m_pPlDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3151
3152
mprintf(WHITE,"\n>>> Plane Distance Distribution Function >>>\n\n");
3153
3154
m_bNormal = !AskYesNo(" Define plane via 3 atoms (y) or as normal plane of a vector (n) (y/n)? [yes] ",true);
3155
3156
m_iCombinations = 1;
3157
if (m_bNormal)
3158
{
3159
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3160
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3161
_b2:
3162
if (m_iShowMol != -1)
3163
m_iRefOrSec[0] = AskRangeInteger(" Take the base atom of the vector/plane from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3164
else m_iRefOrSec[0] = 0;
3165
mprintf(" Please enter the base atom (e.g. C7): ");
3166
inpprintf("! Please enter the base atom (e.g. C7):\n");
3167
myget(buf);
3168
if (!ag->ParseAtoms((!m_iRefOrSec[0])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3169
{
3170
eprintf("Wrong input.\n");
3171
inpprintf("! Wrong input.\n");
3172
goto _b2;
3173
}
3174
m_iCombinations *= ag->m_iAtomGes;
3175
m_oaVectors.Add(ag);
3176
3177
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3178
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3179
_b3:
3180
if (m_iShowMol != -1)
3181
m_iRefOrSec[1] = AskRangeInteger(" Take the atom at the tip of the vector from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3182
else m_iRefOrSec[1] = 0;
3183
mprintf(" Please enter the tip atom (e.g. C7): ");
3184
inpprintf("! Please enter the tip atom (e.g. C7):\n");
3185
myget(buf);
3186
if (!ag->ParseAtoms((!m_iRefOrSec[1])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3187
{
3188
eprintf("Wrong input.\n");
3189
inpprintf("! Wrong input.\n");
3190
goto _b3;
3191
}
3192
m_iCombinations *= ag->m_iAtomGes;
3193
m_oaVectors.Add(ag);
3194
m_oaVectors.Add(NULL); // Dummy placeholder
3195
} else
3196
{
3197
for (z=0;z<3;z++)
3198
{
3199
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3200
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3201
_b1:
3202
if (m_iShowMol != -1)
3203
m_iRefOrSec[z] = AskRangeInteger(" Take the %d. atom(s) of the plane from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3204
else m_iRefOrSec[z] = 0;
3205
mprintf(" Please enter the %d. atom (e.g. C7): ",z+1);
3206
inpprintf("! Please enter the %d. atom (e.g. C7):\n",z+1);
3207
myget(buf);
3208
if (!ag->ParseAtoms((!m_iRefOrSec[z])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3209
{
3210
eprintf("Wrong input.\n");
3211
inpprintf("! Wrong input.\n");
3212
goto _b1;
3213
}
3214
m_iCombinations *= ag->m_iAtomGes;
3215
m_oaVectors.Add(ag);
3216
}
3217
}
3218
mprintf(" Plane defined.\n\n");
3219
3220
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3221
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3222
_b4:
3223
if (m_iShowMol != -1)
3224
m_iRefOrSec[3] = AskRangeInteger(" Take the atom(s) to observe from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3225
else m_iRefOrSec[3] = 0;
3226
mprintf(" Please enter the atom(s) to observe (e.g. C7): ");
3227
inpprintf("! Please enter the atom(s) to observe (e.g. C7):\n");
3228
myget(buf);
3229
if (!ag->ParseAtoms((!m_iRefOrSec[3])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3230
{
3231
eprintf("Wrong input.\n");
3232
inpprintf("! Wrong input.\n");
3233
goto _b4;
3234
}
3235
m_iCombinations *= ag->m_iAtomGes;
3236
m_oaVectors.Add(ag);
3237
3238
m_fMinDist = AskFloat(" Enter the minimal distance to observe (in pm): [-%d.0] ",(float)-HalfBox(),HalfBox());
3239
m_fMaxDist = AskFloat(" Enter the maximal distance to observe (in pm): [%d.0] ",(float)HalfBox(),HalfBox());
3240
3241
m_iResolution = AskUnsignedInteger(" Please enter binning resolution for this PlDF: [100] ",100);
3242
3243
if (g_bAdvanced2)
3244
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3245
else m_iHistogramRes = 0;
3246
3247
BuildName();
3248
mprintf(WHITE,"\n<<< End of Plane Distance Distribution Function <<<\n\n");
3249
BTOUT;
3250
}
3251
3252
3253
void CLiDF::Parse()
3254
{
3255
BTIN;
3256
char buf[256];
3257
CAtomGroup *ag;
3258
int z;
3259
3260
try { m_pLiDF = new CDF(); } catch(...) { m_pLiDF = NULL; }
3261
if (m_pLiDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3262
3263
mprintf(WHITE,"\n>>> Line Distance Distribution Function >>>\n\n");
3264
3265
m_bNormal = !AskYesNo(" Define line via 2 atoms (y) or as normal vector of a plane (n) (y/n)? [yes] ",true);
3266
3267
m_iCombinations = 1;
3268
if (m_bNormal)
3269
{
3270
mprintf("\n The line will pass through the 1st point of the plane.\n\n");
3271
for (z=0;z<3;z++)
3272
{
3273
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3274
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3275
_b3:
3276
if (m_iShowMol != -1)
3277
m_iRefOrSec[z] = AskRangeInteger(" Take the %d. atom(s) of the plane from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3278
else m_iRefOrSec[z] = 0;
3279
mprintf(" Please enter the %d. atom (e.g. C7): ",z+1);
3280
inpprintf("! Please enter the %d. atom (e.g. C7):\n",z+1);
3281
myget(buf);
3282
if (!ag->ParseAtoms((!m_iRefOrSec[z])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3283
{
3284
eprintf("Wrong input.\n");
3285
inpprintf("! Wrong input.\n");
3286
goto _b3;
3287
}
3288
m_iCombinations *= ag->m_iAtomGes;
3289
m_oaVectors.Add(ag);
3290
}
3291
} else
3292
{
3293
for (z=0;z<2;z++)
3294
{
3295
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3296
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3297
_b1:
3298
if (m_iShowMol != -1)
3299
m_iRefOrSec[z] = AskRangeInteger(" Take the %d. atom(s) of the line from RM %s (0) or from OM %s (1)? [0] ",0,1,0,z+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3300
else m_iRefOrSec[z] = 0;
3301
mprintf(" Please enter the %d. atom (e.g. C7): ",z+1);
3302
inpprintf("! Please enter the %d. atom (e.g. C7):\n",z+1);
3303
myget(buf);
3304
if (!ag->ParseAtoms((!m_iRefOrSec[z])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3305
{
3306
eprintf("Wrong input.\n");
3307
inpprintf("! Wrong input.\n");
3308
goto _b1;
3309
}
3310
m_iCombinations *= ag->m_iAtomGes;
3311
m_oaVectors.Add(ag);
3312
}
3313
m_oaVectors.Add(NULL);
3314
}
3315
3316
mprintf(" Line defined.\n\n");
3317
3318
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3319
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3320
_b2:
3321
if (m_iShowMol != -1)
3322
m_iRefOrSec[3] = AskRangeInteger(" Take the atom(s) to observe from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3323
else m_iRefOrSec[3] = 0;
3324
mprintf(" Please enter the atom(s) to observe (e.g. C7): ");
3325
inpprintf("! Please enter the atom(s) to observe (e.g. C7):\n");
3326
myget(buf);
3327
if (!ag->ParseAtoms((!m_iRefOrSec[3])?(CMolecule*)g_oaMolecules[g_iFixMol]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
3328
{
3329
eprintf("Wrong input.\n");
3330
inpprintf("! Wrong input.\n");
3331
goto _b2;
3332
}
3333
m_iCombinations *= ag->m_iAtomGes;
3334
m_oaVectors.Add(ag);
3335
3336
m_fMinDist = AskFloat(" Enter the minimal distance to observe (in pm): [0] ",0.0f);
3337
m_fMaxDist = AskFloat(" Enter the maximal distance to observe (in pm): [%d.0] ",(float)HalfBox(),HalfBox());
3338
3339
m_iResolution = AskUnsignedInteger(" Please enter binning resolution for this LiDF: [100] ",100);
3340
3341
if (g_bAdvanced2)
3342
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3343
else m_iHistogramRes = 0;
3344
3345
if (m_iShowMol != -1)
3346
m_bRadialCorrect = AskYesNo(" Correct radial distribution for this LiDF (y/n)? [yes] ",true);
3347
else m_bRadialCorrect = AskYesNo(" Correct radial distribution for this LiDF (y/n)? [no] ",false);
3348
3349
BuildName();
3350
mprintf(WHITE,"\n<<< End of Line Distance Distribution Function <<<\n\n");
3351
BTOUT;
3352
}
3353
3354
3355
void CDipDF::Parse()
3356
{
3357
BTIN;
3358
float tf;
3359
double td, td2, td3;
3360
CMolecule *m;
3361
CSingleMolecule *sm;
3362
int z;
3363
3364
g_bDipole = true;
3365
3366
try { m_pDipoleDF = new CDF(); } catch(...) { m_pDipoleDF = NULL; }
3367
if (m_pDipoleDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3368
3369
mprintf(WHITE,"\n>>> Dipole Distribution Function >>>\n\n");
3370
if (m_iShowMol != -1)
3371
m_iRefOrSec = AskRangeInteger(" Observe dipole moment from RM %s (0) or from OM %s (1)? [0] ",0,1,0,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3372
else m_iRefOrSec = 0;
3373
3374
ParseDeriv();
3375
3376
if (m_iRefOrSec != 0)
3377
m = (CMolecule*)g_oaMolecules[m_iShowMol];
3378
else m = (CMolecule*)g_oaMolecules[g_iFixMol];
3379
3380
td = 0;
3381
td2 = 1.0e10;
3382
td3 = 0;
3383
for (z=0;z<m->m_laSingleMolIndex.GetSize();z++)
3384
{
3385
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z]];
3386
tf = sm->m_vDipole.GetLength();
3387
if (tf > td)
3388
td = tf;
3389
if (tf < td2)
3390
td2 = tf;
3391
td3 += tf;
3392
}
3393
td3 /= (double)m->m_laSingleMolIndex.GetSize();
3394
3395
mprintf("\n Dipole moment of %s (1st step): Min. %.3f, Max. %.3f, Avg. %.3f Debye.\n\n",m->m_sName,td2,td,td3);
3396
3397
switch(m_iDeriv)
3398
{
3399
case 0:
3400
m_fDipoleMin = AskFloat(" Enter the lower bound for dipole values (in Debye): [0] ",0.0f);
3401
m_fDipoleMax = AskFloat(" Enter the upper bound for dipole values (in Debye): [%d] ",float(int(td*2.0)),int(td*2.0));
3402
break;
3403
case 1:
3404
if (m_bDerivAbs)
3405
m_fDipoleMin = AskFloat(" Enter the minimal value of this d1-DDF in Debye/ps: [0] ",0.0f);
3406
else m_fDipoleMin = AskFloat(" Enter the minimal value of this d1-DDF in Debye/ps: [-10.0] ",-10.0f);
3407
m_fDipoleMax = AskFloat(" Enter the maximal value of this d1-DDF in Debye/ps: [10.0] ",10.0f);
3408
break;
3409
case 2:
3410
if (m_bDerivAbs)
3411
m_fDipoleMin = AskFloat(" Enter the minimal value of this d2-DDF in Debye/ps^2: [0] ",0.0f);
3412
else m_fDipoleMin = AskFloat(" Enter the minimal value of this d2-DDF in Debye/ps^2: [-10.0] ",-10.0f);
3413
m_fDipoleMax = AskFloat(" Enter the maximal value of this d2-DDF in Debye/ps^2: [10.0] ",10.0f);
3414
break;
3415
}
3416
3417
m_iResolution = AskUnsignedInteger(" Enter binning resolution for the Dipole DF: [%d] ",int((m_fDipoleMax-m_fDipoleMin)*10.0),int((m_fDipoleMax-m_fDipoleMin)*10.0));
3418
3419
if (g_bAdvanced2)
3420
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3421
else m_iHistogramRes = 0;
3422
3423
BuildName();
3424
mprintf(WHITE,"\n<<< End of Dipole Distribution Function <<<\n\n");
3425
BTOUT;
3426
}
3427
3428
3429
void CSDF::Parse(bool voro)
3430
{
3431
BTIN;
3432
int ti;
3433
char buf[256];
3434
3435
m_iShowAtomGes = 0;
3436
3437
try { m_pSDF = new C3DF(); } catch(...) { m_pSDF = NULL; }
3438
if (m_pSDF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3439
3440
mprintf(WHITE,"\n>>> Spatial Distribution Function >>>\n\n");
3441
_sdfatoms:
3442
if (!voro)
3443
{
3444
if (m_bIntra)
3445
{
3446
mprintf(" Observing atoms in reference molecule %s.\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
3447
m_iRefOrSec = 0;
3448
} else
3449
{
3450
mprintf(" Observing atoms in observed molecule %s.\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3451
m_iRefOrSec = 1;
3452
}
3453
/* if (m_iShowMol != -1)
3454
m_iRefOrSec = AskRangeInteger(" Observe atoms in RM %s (0) or in OM %s (1)? [1] ",0,1,1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3455
else m_iRefOrSec = 0;*/
3456
mprintf(" Which atoms to observe (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ");
3457
inpprintf("! Which atoms to observe (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n");
3458
myget(buf);
3459
if (strlen(buf) == 0)
3460
{
3461
if (!m_oAtoms.ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec==0)?g_iFixMol:m_iShowMol],"#2"))
3462
{
3463
eprintf("Strange error ^^\n");
3464
inpprintf("! Strange error ^\n");
3465
goto _sdfatoms;
3466
}
3467
} else
3468
{
3469
if (!m_oAtoms.ParseAtoms((CMolecule*)g_oaMolecules[(m_iRefOrSec==0)?g_iFixMol:m_iShowMol],buf))
3470
{
3471
eprintf("Wrong input.\n");
3472
inpprintf("! Wrong input.\n");
3473
goto _sdfatoms;
3474
}
3475
}
3476
3477
m_iShowAtomGes += m_oAtoms.m_iAtomGes;
3478
m_fParticleDensity = m_oAtoms.m_iAtomGes * ((CMolecule*)g_oaMolecules[(m_iRefOrSec==0)?g_iFixMol:m_iShowMol])->m_laSingleMolIndex.GetSize() / g_fBoxX / g_fBoxY / g_fBoxZ * 1E9f;
3479
}
3480
3481
m_fRadius = AskFloat(" Please enter radius of this SDF in pm: [%d.0] ",(float)HalfBox(),HalfBox());
3482
_sdfresagain:
3483
ti = g_pDatabase->GetInt("/PLOT3D/DEFAULTS/BIN_RES");
3484
m_iResolution = AskUnsignedInteger(" Please enter binning resolution of this SDF per dimension: [%d] ",ti,ti);
3485
3486
if (m_iResolution > 300)
3487
{
3488
eprintf("\nWarning: ");
3489
mprintf("This large resolution will consume much RAM (%s)\n",FormatBytes(pow((double)m_iResolution,3)*sizeof(double)));
3490
mprintf(" and result in very large SDF output files.\n\n");
3491
if (!AskYesNo(" Use this resolution (y/n)? [no] ",false))
3492
goto _sdfresagain;
3493
}
3494
3495
if (g_bAdvanced2)
3496
{
3497
m_bVdWSpheres = false; //AskYesNo(" Process atoms as VdW spheres rather than points (y/n)? [no] ",false);
3498
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3499
m_bClipPlane = AskYesNo(" Use a clipping plane for this SDF (y/n)? [no] ",false);
3500
if (m_bClipPlane)
3501
{
3502
_cut: mprintf(" Should the clipping plane stand perpendicular to the X, Y or Z axis (x/y/z)? [x] ");
3503
inpprintf("! Should the clipping plane stand perpendicular to the X, Y or Z axis (x/y/z)? [x]\n");
3504
myget(buf);
3505
switch(tolower(buf[0]))
3506
{
3507
case 0:
3508
case 'x':
3509
m_iClipDirection = 0;
3510
break;
3511
case 'y':
3512
m_iClipDirection = 1;
3513
break;
3514
case 'z':
3515
m_iClipDirection = 2;
3516
break;
3517
default:
3518
eprintf(" Wrong input! Please enter 'x', 'y' or 'z'.\n");
3519
inpprintf("! Wrong input! Please enter 'x', 'y' or 'z'.\n");
3520
goto _cut;
3521
}
3522
m_fClipValue = AskFloat(" Please enter distance of clipping plane from origin (in pm): [0] ",0.0f);
3523
}
3524
m_bInvert = AskYesNo(" Should this SDF be inverted (y/n)? [no] ",false);
3525
m_bSDFMirrorXY = AskYesNo(" Force this SDF to be symmetrical to the XY plane (y/n)? [no] ",false);
3526
m_bSDFMirrorBisect = AskYesNo(" Force this SDF to be symmetrical to the angle bisector (y/n)? [no] ",false);
3527
m_bCutPlane = AskYesNo(" Add a particle density cut plane to this SDF (y/n)? [no] ",false);
3528
if (m_bCutPlane)
3529
{
3530
m_iCutPlaneResolution = AskUnsignedInteger(" Enter the binning resolution for the cut plane per dimension: [100] ",100);
3531
m_bCutPlaneShowAtoms = AskYesNo(" Show reference atoms in Pseudo SDF plot (y/n)? [yes] ",true);
3532
}
3533
} else
3534
{
3535
m_bVdWSpheres = false;
3536
m_bClipPlane = false;
3537
m_bInvert = false;
3538
m_bSDFMirrorXY = false;
3539
m_bSDFMirrorBisect = false;
3540
m_bCutPlane = false;
3512
3541
m_iHistogramRes = 0;
3513
m_bClipPlane = false;
3514
m_bInvert = false;
3515
m_bSDFMirrorXY = false;
3516
m_bSDFMirrorBisect = false;
3517
m_bCutPlane = false;
3518
}
3519
3520
if (!voro)
3521
BuildName();
3522
3523
mprintf(WHITE,"\n<<< End of Spatial Distribution Function <<<\n\n");
3524
BTOUT;
3525
}
3526
3527
3528
void CVDF::Parse()
3529
{
3530
BTIN;
3531
char buf[256];
3532
3533
m_iShowAtomGes = 0;
3534
3535
try { m_pVDF = new CDF(); } catch(...) { m_pVDF = NULL; }
3536
if (m_pVDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3537
3538
mprintf(WHITE,"\n>>> Velocity Distribution Function >>>\n\n");
3539
_atoms:
3540
if (g_iFixMol == -1)
3541
{
3542
mprintf(" Observing atoms from OM %s.\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3543
m_iRefOrSec = 1;
3544
} else if (m_iShowMol == -1)
3545
{
3546
mprintf(" Observing atoms from RM %s.\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
3547
m_iRefOrSec = 0;
3548
} else m_iRefOrSec = AskRangeInteger(" Observe atoms in RM %s (0) or in OM %s (1)? [1]",0,1,1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3549
3550
mprintf(" Which atoms to observe (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ");
3551
inpprintf("! Which atoms to observe (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n");
3552
myget(buf);
3553
if (strlen(buf) == 0)
3554
{
3555
m_oAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[m_iRefOrSec?m_iShowMol:g_iFixMol],false);
3556
if (!m_oAtoms.ParseAtoms((CMolecule*)g_oaMolecules[m_iRefOrSec?m_iShowMol:g_iFixMol],"#2"))
3557
{
3558
eprintf("Strange error ^^\n");
3559
inpprintf("! Strange error ^^\n");
3560
goto _atoms;
3561
}
3562
} else
3563
{
3564
if (!m_oAtoms.ParseAtoms((CMolecule*)g_oaMolecules[m_iRefOrSec?m_iShowMol:g_iFixMol],buf))
3565
{
3566
eprintf("Wrong input.\n");
3567
inpprintf("! Wrong input.\n");
3568
goto _atoms;
3569
}
3570
}
3571
m_iCombinations = m_oAtoms.m_iAtomGes;
3572
m_iShowAtomGes += m_oAtoms.m_iAtomGes;
3573
// m_fParticleDensity = m_oAtoms.m_iAtomGes * ((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize() / g_fBoxX / g_fBoxY / g_fBoxZ;
3574
3575
ParseDeriv();
3576
3577
switch(m_iDeriv)
3578
{
3579
case 0:
3580
/* if (AskYesNo(" Scan for velocity range (y) or enter range manually (n)? [no] ",false))
3581
{
3582
m_bScanRange = true;
3583
g_bScanVelocities = true;
3584
} else*/
3585
{
3586
m_bScanRange = false;
3587
m_fMinSpeed = 0; //AskFloat(" Please enter the minimal velocity: [0.0 pm/fs] ",0.0f);
3588
m_fMaxSpeed = AskFloat(" Please enter the maximal velocity: [10000.0 pm/ps] ",10000.0f);
3589
}
3590
break;
3591
case 1:
3592
if (m_bDerivAbs)
3593
m_fMinSpeed = AskFloat(" Enter the minimal value of this d1-VDF in pm/ps^2: [0] ",0.0f);
3594
else m_fMinSpeed = AskFloat(" Enter the minimal value of this d1-VDF in pm/ps^2: [-10.0] ",-10.0f);
3595
m_fMaxSpeed = AskFloat(" Enter the maximal value of this d1-VDF in pm/ps^2: [10.0] ",10.0f);
3596
break;
3597
case 2:
3598
if (m_bDerivAbs)
3599
m_fMinSpeed = AskFloat(" Enter the minimal value of this d2-VDF in pm/ps^3: [0] ",0.0f);
3600
else m_fMinSpeed = AskFloat(" Enter the minimal value of this d2-VDF in pm/ps^3: [-10.0] ",-10.0f);
3601
m_fMaxSpeed = AskFloat(" Enter the maximal value of this d2-VDF in pm/ps^3: [10.0] ",10.0f);
3602
break;
3603
}
3604
3542
}
3543
3544
if (!voro)
3545
BuildName();
3546
3547
mprintf(WHITE,"\n<<< End of Spatial Distribution Function <<<\n\n");
3548
BTOUT;
3549
}
3550
3551
3552
void CVDF::Parse()
3553
{
3554
BTIN;
3555
char buf[256];
3556
3557
m_iShowAtomGes = 0;
3558
3559
try { m_pVDF = new CDF(); } catch(...) { m_pVDF = NULL; }
3560
if (m_pVDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3561
3562
mprintf(WHITE,"\n>>> Velocity Distribution Function >>>\n\n");
3563
_atoms:
3564
if (g_iFixMol == -1)
3565
{
3566
mprintf(" Observing atoms from OM %s.\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3567
m_iRefOrSec = 1;
3568
} else if (m_iShowMol == -1)
3569
{
3570
mprintf(" Observing atoms from RM %s.\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
3571
m_iRefOrSec = 0;
3572
} else m_iRefOrSec = AskRangeInteger(" Observe atoms in RM %s (0) or in OM %s (1)? [1]",0,1,1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3573
3574
mprintf(" Which atoms to observe (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ");
3575
inpprintf("! Which atoms to observe (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n");
3576
myget(buf);
3577
if (strlen(buf) == 0)
3578
{
3579
m_oAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[m_iRefOrSec?m_iShowMol:g_iFixMol],false);
3580
if (!m_oAtoms.ParseAtoms((CMolecule*)g_oaMolecules[m_iRefOrSec?m_iShowMol:g_iFixMol],"#2"))
3581
{
3582
eprintf("Strange error ^^\n");
3583
inpprintf("! Strange error ^^\n");
3584
goto _atoms;
3585
}
3586
} else
3587
{
3588
if (!m_oAtoms.ParseAtoms((CMolecule*)g_oaMolecules[m_iRefOrSec?m_iShowMol:g_iFixMol],buf))
3589
{
3590
eprintf("Wrong input.\n");
3591
inpprintf("! Wrong input.\n");
3592
goto _atoms;
3593
}
3594
}
3595
m_iCombinations = m_oAtoms.m_iAtomGes;
3596
m_iShowAtomGes += m_oAtoms.m_iAtomGes;
3597
// m_fParticleDensity = m_oAtoms.m_iAtomGes * ((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize() / g_fBoxX / g_fBoxY / g_fBoxZ;
3598
3599
ParseDeriv();
3600
3601
switch(m_iDeriv)
3602
{
3603
case 0:
3604
/* if (AskYesNo(" Scan for velocity range (y) or enter range manually (n)? [no] ",false))
3605
{
3606
m_bScanRange = true;
3607
g_bScanVelocities = true;
3608
} else*/
3609
{
3610
m_bScanRange = false;
3611
m_fMinSpeed = 0; //AskFloat(" Please enter the minimal velocity: [0.0 pm/fs] ",0.0f);
3612
m_fMaxSpeed = AskFloat(" Please enter the maximal velocity: [10000.0 pm/ps] ",10000.0f);
3613
}
3614
break;
3615
case 1:
3616
if (m_bDerivAbs)
3617
m_fMinSpeed = AskFloat(" Enter the minimal value of this d1-VDF in pm/ps^2: [0] ",0.0f);
3618
else m_fMinSpeed = AskFloat(" Enter the minimal value of this d1-VDF in pm/ps^2: [-10.0] ",-10.0f);
3619
m_fMaxSpeed = AskFloat(" Enter the maximal value of this d1-VDF in pm/ps^2: [10.0] ",10.0f);
3620
break;
3621
case 2:
3622
if (m_bDerivAbs)
3623
m_fMinSpeed = AskFloat(" Enter the minimal value of this d2-VDF in pm/ps^3: [0] ",0.0f);
3624
else m_fMinSpeed = AskFloat(" Enter the minimal value of this d2-VDF in pm/ps^3: [-10.0] ",-10.0f);
3625
m_fMaxSpeed = AskFloat(" Enter the maximal value of this d2-VDF in pm/ps^3: [10.0] ",10.0f);
3626
break;
3627
}
3628
3605
3629
m_iResolution = AskInteger(" Please enter the binning resolution for this VDF: [300] ",300);
3606
if (g_bAdvanced2)
3607
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3608
else m_iHistogramRes = 0;
3609
/* mprintf(" Save temporal Development of Velocity (0=no, 1=yes)? [0] ");
3610
myget(buf);
3611
m_bSaveSpeed = atoi(buf)!=0;*/
3612
BuildName();
3613
mprintf(WHITE,"\n<<< End of Velocity Distribution Function <<<\n\n");
3614
BTOUT;
3615
}
3616
3617
3618
void CSDF::BuildName()
3619
{
3620
BTIN;
3621
char tmp[256];
3622
3623
tmp[0] = 0;
3624
3625
if (m_iRefOrSec)
3626
sprintf(tmp,"%s_%s%d%s%d%s%d_%s_%s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName,g_iFixAtom[1]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_sName,g_iFixAtom[2]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,m_oAtoms.m_sName);
3627
else sprintf(tmp,"%s_%s%d%s%d%s%d_%s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName,g_iFixAtom[1]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_sName,g_iFixAtom[2]+1,m_oAtoms.m_sName);
3628
3629
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
3630
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3631
3632
strcpy(m_sName,tmp);
3633
BTOUT;
3634
}
3635
3636
3637
void CVDF::BuildName()
3638
{
3639
BTIN;
3640
char tmp[256];
3641
3642
if (m_iDeriv != 0)
3643
sprintf(tmp,"deriv%d_%s",m_iDeriv,m_oAtoms.m_sName);
3644
else sprintf(tmp,"%s",m_oAtoms.m_sName);
3645
3646
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
3647
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3648
3649
strcpy(m_sShortName,m_oAtoms.m_sName);
3650
if (g_iFixMol == -1)
3651
{
3652
sprintf(tmp,"%s_",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3653
} else if (m_iRefOrSec)
3654
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3655
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
3656
strcat(tmp,m_sShortName);
3657
3658
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
3659
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3660
3661
strcpy(m_sName,tmp);
3662
BTOUT;
3663
}
3664
3665
3666
void CSDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
3667
{
3668
BXIN;
3669
int z1t, z1a;
3670
CxIntArray *a1;
3671
3672
vec->RemoveAll_KeepSize();
3673
for (z1t=0;z1t<m_oAtoms.m_baAtomType.GetSize();z1t++)
3674
{
3675
// mprintf("(a) BuildAtomList z1t=%d, WA=%X\n",z1t,m_oAtoms.m_oaAtoms[z1t]);
3676
a1 = (CxIntArray*)m_oAtoms.m_oaAtoms[z1t];
3677
// mprintf("(b) BuildAtomList wa.GetSize()=%d\n",a1->GetSize());
3678
for (z1a=0;z1a<a1->GetSize();z1a++)
3679
if (m_iRefOrSec)
3680
{
3681
// mprintf("(c) BuildAtomList z1t=%d, z1a=%d, Type=%d, WA=%X\n",z1t,z1a,m_oAtoms.m_baAtomType[z1t],obs->m_oaAtomOffset[m_oAtoms.m_baAtomType[z1t]]);
3682
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[m_oAtoms.m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3683
} else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[m_oAtoms.m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3684
}
3685
BXOUT;
3686
}
3687
3688
3689
void CVDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
3690
{
3691
BXIN;
3692
int z1t, z1a;
3693
CxIntArray *a1;
3694
3695
vec->RemoveAll_KeepSize();
3696
for (z1t=0;z1t<m_oAtoms.m_baAtomType.GetSize();z1t++)
3697
{
3698
a1 = (CxIntArray*)m_oAtoms.m_oaAtoms[z1t];
3699
for (z1a=0;z1a<a1->GetSize();z1a++)
3700
if (m_iRefOrSec)
3701
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[m_oAtoms.m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3702
else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[m_oAtoms.m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3703
}
3704
BXOUT;
3705
}
3706
3707
3708
void CRDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
3709
{
3710
BXIN;
3711
int z, z1t, z1a, z2t, z2a;
3712
CAtomGroup *g1, *g2;
3713
CxIntArray *a1, *a2;
3714
3715
vec->RemoveAll_KeepSize();
3716
for (z=0;z<m_oaVectors.GetSize()/2;z++)
3717
{
3718
g1 = (CAtomGroup*)m_oaVectors[z*2];
3719
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
3720
{
3721
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
3722
for (z1a=0;z1a<a1->GetSize();z1a++)
3723
{
3724
g2 = (CAtomGroup*)m_oaVectors[z*2+1];
3725
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
3726
{
3727
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
3728
for (z2a=0;z2a<a2->GetSize();z2a++)
3729
{
3730
if (m_iRefOrSec[0])
3731
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3732
else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3733
if (m_iRefOrSec[1])
3734
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
3735
else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
3736
// mprintf("Vector z=%d, z1t=%d, z1a=%d, z2t=%d, z2a=%d.\n",z,z1t,z1a,z2t,z2a);
3737
}
3738
}
3739
}
3740
}
3741
}
3742
BXOUT;
3743
}
3744
3745
3746
void CVHDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
3747
{
3748
BXIN;
3749
int z, z1t, z1a, z2t, z2a;
3750
CAtomGroup *g1, *g2;
3751
CxIntArray *a1, *a2;
3752
3753
vec->RemoveAll_KeepSize();
3754
for (z=0;z<m_oaVectors.GetSize()/2;z++)
3755
{
3756
g1 = (CAtomGroup*)m_oaVectors[z*2];
3757
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
3758
{
3759
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
3760
for (z1a=0;z1a<a1->GetSize();z1a++)
3761
{
3762
g2 = (CAtomGroup*)m_oaVectors[z*2+1];
3763
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
3764
{
3765
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
3766
for (z2a=0;z2a<a2->GetSize();z2a++)
3767
{
3768
if (m_iRefOrSec[0])
3769
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3770
else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3771
if (m_iRefOrSec[1])
3772
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
3773
else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
3774
}
3775
}
3776
}
3777
}
3778
}
3779
BXOUT;
3780
}
3781
3782
3783
/*int FindAtom(char *s)
3784
{
3785
BTIN;
3786
int z;
3787
for (z=0;z<g_oaAtoms.GetSize();z++)
3788
if (mystricmp(s,((CAtom*)g_oaAtoms[z])->m_sName)==0)
3789
{
3790
BTOUT;
3791
return z;
3792
}
3793
BTOUT;
3794
return -1;
3795
}*/
3796
3797
3798
int CMolecule::FindAtomInMol(const char *s)
3799
{
3800
BTIN;
3801
int z;
3802
for (z=0;z<m_baAtomIndex.GetSize();z++)
3803
if (mystricmp(s,((CAtom*)g_oaAtoms[m_baAtomIndex[z]])->m_sName)==0)
3804
{
3805
BTOUT;
3806
return z;
3807
}
3808
BTOUT;
3809
return -1;
3810
}
3811
3812
3813
void CMolecule::BuildName()
3814
{
3815
BTIN;
3816
int z, z2;
3817
char buf[16], buf2[256];
3818
3819
if (m_bPseudo)
3820
{
3821
buf2[0] = '$';
3822
buf2[1] = 0;
3823
} else buf2[0] = 0;
3824
for (z=0;z<g_oaAtoms.GetSize();z++)
3825
{
3826
for (z2=0;z2<m_baAtomIndex.GetSize();z2++)
3827
{
3828
if (m_baAtomIndex[z2] != z)
3829
continue;
3830
if (m_waAtomCount[z2] > 1)
3831
sprintf(buf,"%s%d",((CAtom*)g_oaAtoms[z])->m_sName,m_waAtomCount[z2]);
3832
else sprintf(buf,"%s",((CAtom*)g_oaAtoms[z])->m_sName);
3833
strcat(buf2,buf);
3834
}
3835
}
3836
3837
try { m_sName = new char[strlen(buf2)+1]; } catch(...) { m_sName = NULL; }
3838
if (m_sName == NULL) NewException((double)(strlen(buf2)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3839
3840
strcpy(m_sName,buf2);
3841
BTOUT;
3842
}
3843
3844
3845
bool CConditionGroup::Contains(int mol)
3846
{
3847
BXIN;
3848
int z;
3849
3850
if (m_bInactive)
3851
return m_bAlwaysTrue[mol];
3852
3853
if (m_bInvertCondition)
3854
{
3855
if (m_bAlwaysTrue[mol])
3856
{
3857
BXOUT;
3858
return false;
3859
}
3860
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
3861
{
3862
if (((CConditionSubGroup*)m_oaConditionSubGroups[z])->Contains(mol))
3863
{
3864
BXOUT;
3865
return false;
3866
}
3867
}
3868
BXOUT;
3869
return true;
3870
} else
3871
{
3872
if (m_bAlwaysTrue[mol])
3873
{
3874
BXOUT;
3875
return true;
3876
}
3877
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
3878
{
3879
if (((CConditionSubGroup*)m_oaConditionSubGroups[z])->Contains(mol))
3880
{
3881
BXOUT;
3882
return true;
3883
}
3884
}
3885
BXOUT;
3886
return false;
3887
}
3888
}
3889
3890
3891
void CConditionGroup::MarkPassedAtoms(int om, bool passed)
3892
{
3893
BXIN;
3894
int z;
3895
// int ti;
3896
3897
// mprintf("######## OM %d ##########\n",om+1);
3898
3899
for (z=0;z<g_iGesVirtAtomCount;z++)
3900
g_baAtomPassedCondition[z] = 110; // 110 heisst: Atom kommt nicht in einer Condition vor
3901
3902
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
3903
((CConditionSubGroup*)m_oaConditionSubGroups[z])->MarkPassedAtoms(om);
3904
3905
// for (z=0;z<g_iGesVirtAtomCount;z++)
3906
// mprintf("\nAtom %d: %d.",z+1,g_baAtomPassedCondition[z]);
3907
3908
// ti = 0;
3909
if (m_bInvertCondition)
3910
{
3911
for (z=0;z<g_iGesVirtAtomCount;z++)
3912
{
3913
if (g_baAtomPassedCondition[z] != 100) // Entweder Condition nicht bestanden oder Atom kam gar nicht darin vor
3914
{
3915
// ti++;
3916
g_baAtomPassedCondition[z] = 1;
3917
// mprintf("%d: Ok\n",z+1);
3918
// mprintf("\n %d --> Wird genommen.",z+1);
3919
} else // Condition bestanden
3920
{
3921
// mprintf("Atom %s%d nicht bestanden (%d).\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_sName,g_waAtomMolNumber[z]+1,g_baAtomPassedCondition[z]);
3922
// mprintf("\n%d erfuellt --> durchgefallen",z+1);
3923
g_baAtomPassedCondition[z] = 0;
3924
}
3925
}
3926
} else
3927
{
3928
for (z=0;z<g_iGesVirtAtomCount;z++)
3929
{
3930
if (passed)
3931
{
3932
if (g_baAtomPassedCondition[z] >= 100) // Entweder Condition bestanden oder Atom kam gar nicht darin vor
3933
{
3934
// ti++;
3935
g_baAtomPassedCondition[z] = 1;
3936
} else // Condition nicht bestanden
3937
{
3938
// mprintf("Atom %s%d nicht bestanden (%d).\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_sName,g_waAtomMolNumber[z]+1,g_baAtomPassedCondition[z]);
3939
g_baAtomPassedCondition[z] = 0;
3940
}
3941
} else
3942
{
3943
if (g_baAtomPassedCondition[z] == 100) // Condition bestanden
3944
{
3945
// ti++;
3946
// mprintf("### Atom %s[%d] %s%d bestanden (%d).\n",((CMolecule*)g_oaMolecules[g_waAtomMolIndex[z]])->m_sName,g_laAtomSMLocalIndex[z]+1,((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_sName,g_waAtomMolNumber[z]+1,g_baAtomPassedCondition[z]);
3947
g_baAtomPassedCondition[z] = 0;
3948
} else // Entweder Condition nicht bestanden oder Atom kam gar nicht darin vor
3949
{
3950
// mprintf("--- Atom %s[%d] %s%d nicht bestanden (%d).\n",((CMolecule*)g_oaMolecules[g_waAtomMolIndex[z]])->m_sName,g_laAtomSMLocalIndex[z]+1,((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_sName,g_waAtomMolNumber[z]+1,g_baAtomPassedCondition[z]);
3951
g_baAtomPassedCondition[z] = 1;
3952
}
3953
}
3954
}
3955
}
3956
// mprintf("\nMarked %d / %d atoms as enabled.",ti,g_iGesVirtAtomCount);
3957
3958
BXOUT;
3959
}
3960
3961
3962
void CConditionGroup::ScanNeighborhoodAllOM(CTimeStep *t, CSingleMolecule *rm)
3963
{
3964
BXIN;
3965
int z, z2, t1, t2, i;
3966
3967
if (m_bInactive)
3968
return;
3969
3970
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
3971
((CConditionSubGroup*)m_oaConditionSubGroups[z])->ScanNeighborhoodAllOM(t,rm);
3972
3973
if (m_oaConditionSubGroups.GetSize() == 2)
3974
{
3975
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
3976
{
3977
t1 = 0;
3978
t2 = 0;
3979
for (z2=0;z2<((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_oaConditions.GetSize();z2++)
3980
t1 += ((CNbSearch*)((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_oaConditions[z2])->m_iCombPassCount[z];
3981
for (z2=0;z2<((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_oaConditions.GetSize();z2++)
3982
t2 += ((CNbSearch*)((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_oaConditions[z2])->m_iCombPassCount[z];
3983
m_pTable[t1*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+t2]++;
3984
m_fTableGes++;
3985
}
3986
}
3987
3988
i = 0;
3989
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
3990
{
3991
m_fTotal++;
3992
if (m_bInvertCondition)
3993
{
3994
for (z2=0;z2<m_oaConditionSubGroups.GetSize();z2++)
3995
if (((CConditionSubGroup*)m_oaConditionSubGroups[z2])->Contains(z))
3996
goto _nopass;
3997
m_fPassed++;
3998
m_iPassCounter[z]++;
3999
m_bAnyPassed = true;
4000
} else
4001
{
4002
for (z2=0;z2<m_oaConditionSubGroups.GetSize();z2++)
4003
{
4004
if (((CConditionSubGroup*)m_oaConditionSubGroups[z2])->Contains(z))
4005
{
4006
// mprintf("passed[%d]++\n",z);
4007
m_fPassed++;
4008
m_iPassCounter[z]++;
4009
m_bAnyPassed = true;
4010
i++;
4011
goto _nopass;
4012
}
4013
}
4014
}
4015
_nopass:;
4016
}
4017
m_pHistogram[i]++;
4018
m_iHistoGes++;
4019
4020
BXOUT;
4021
}
4022
4023
4024
void CConditionGroup::PreScanNeighborhoodAllOM(CTimeStep *t, CSingleMolecule *rm)
4025
{
4026
BXIN;
4027
int z;
4028
4029
if (m_bInactive)
4030
return;
4031
4032
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
4033
((CConditionSubGroup*)m_oaConditionSubGroups[z])->PreScanNeighborhoodAllOM(t,rm);
4034
4035
BXOUT;
4036
}
4037
4038
4039
void CConditionGroup::Parse(int rm, int sm)
4040
{
4041
BTIN;
4042
CConditionSubGroup *sg;
4043
int z;
4044
4045
m_iShowMol = sm;
4046
m_iRefMol = rm;
4047
4048
try { m_bAlwaysTrue = new bool[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_bAlwaysTrue = NULL; }
4049
if (m_bAlwaysTrue == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4050
4051
try { m_iPassCounter = new long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iPassCounter = NULL; }
4052
if (m_iPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4053
4054
try { m_iOMPassCounter = new long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iOMPassCounter = NULL; }
4055
if (m_iOMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4056
4057
for (z=0;z<((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize();z++)
4058
{
4059
m_bAlwaysTrue[z] = false;
4060
m_iPassCounter[z] = 0;
4061
m_iOMPassCounter[z] = 0;
4062
}
4063
4064
try { m_iRMPassCounter = new long[((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iRMPassCounter = NULL; }
4065
if (m_iRMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4066
4067
for (z=0;z<((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize();z++)
4068
m_iRMPassCounter[z] = 0;
4069
4070
mprintf("Different sets of conditions are connected with OR (at least one of them has to be fulfilled).\n");
4071
mprintf("Different conditions within one set are connected with AND (have to be fulfilled at the same time).\n");
4072
mprintf("If you create 1 or 2 sets of conditions, a table with subcondition count populations will be printed.\n\n");
4073
_newset:
4074
mprintf(YELLOW,">>> %d. set of conditions >>>\n",m_oaConditionSubGroups.GetSize()+1);
4075
4076
try { sg = new CConditionSubGroup(); } catch(...) { sg = NULL; }
4077
if (sg == NULL) NewException((double)sizeof(CConditionSubGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4078
4079
sg->m_iShowMol = m_iShowMol;
4080
sg->m_iNumber = m_oaConditionSubGroups.GetSize();
4081
m_oaConditionSubGroups.Add(sg);
4082
sg->Parse(rm,sm);
4083
mprintf(YELLOW,"\n<<< End of %d. set of conditions <<<\n\n",m_oaConditionSubGroups.GetSize());
4084
if (AskYesNo(" Enter an additional set of conditions (y/n)? [no] ",false))
4085
goto _newset;
4086
4087
m_bInvertCondition = AskYesNo(" Invert this condition (only add bin entries if failed) (y/n)? [no] ",false);
4088
4089
if (m_oaConditionSubGroups.GetSize() == 2)
4090
{
4091
m_fTableGes = 0;
4092
4093
try { m_pTable = new double[(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)]; } catch(...) { m_pTable = NULL; }
4094
if (m_pTable == NULL) NewException((double)(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4095
4096
for (z=0;z<(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1);z++)
4097
m_pTable[z] = 0;
4098
}
4099
4100
/* m_bNeedNbCountMode = false;
4101
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
4102
{
4103
sg = (CConditionSubGroup*)m_oaConditionSubGroups[z];
4104
for (z2=0;z2<sg->m_oaConditions.GetSize();z2++)
4105
if (((CNbSearch*)sg->m_oaConditions[z2])->m_iNbCountMin != -1)
4106
m_bNeedNbCountMode = true;
4107
}*/
4108
m_iHistoGes = 0;
4109
4110
try {m_pHistogram = new unsigned long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1]; } catch(...) { m_pHistogram = NULL; }
4111
if (m_pHistogram == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1*sizeof(unsigned long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4112
4113
for (z=0;z<((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1;z++)
4114
m_pHistogram[z] = 0;
4115
BTOUT;
4116
}
4117
4118
4119
void CConditionGroup::PrintData()
4120
{
4121
int z;
4122
4123
mprintf(GREEN,"\n>>> Condition Data >>>\n\n");
4124
mprintf(" %.0f of %.0f molecules passed the conditions (%.2f percent).\n",m_fPassed,m_fTotal,ZeroDivide(m_fPassed,m_fTotal)*100.0f);
4125
if (m_fPassed == 0)
4126
{
4127
mprintf(YELLOW,"\n No molecules at all passed the condition.\n");
4128
mprintf(" This is probably not what you wanted.\n");
4129
} else
4130
{
4131
mprintf(YELLOW,"\nList of reference molecules (%s) that passed the conditions:\n\n",((CMolecule*)g_oaMolecules[m_iRefMol])->m_sName);
4132
for (z=0;z<((CMolecule*)g_oaMolecules[m_iRefMol])->m_laSingleMolIndex.GetSize();z++)
4133
if (m_iRMPassCounter[z] > 0)
4134
mprintf(" - %2d: %10.4f percent of the time (%d hits)\n",z+1,((double)m_iRMPassCounter[z])/g_iSteps*100.0,m_iRMPassCounter[z]);
4135
4136
mprintf(YELLOW,"\nList of observed molecules (%s) that passed the conditions:\n\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
4137
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
4138
if (m_iOMPassCounter[z] > 0)
4139
mprintf(" - %2d: %10.4f percent of the time (%d hits)\n",z+1,((double)m_iOMPassCounter[z])/g_iSteps*100.0,m_iOMPassCounter[z]);
4140
}
4141
mprintf(YELLOW,"\nNeighbor count histogram:\n\n");
4142
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1;z++)
4143
if (m_pHistogram[z] != 0)
4144
mprintf(" - %d Neighbors: %8.4f percent of the time (%d hits).\n",z,((double)m_pHistogram[z])/m_iHistoGes*100.0,m_pHistogram[z]);
4145
mprintf(YELLOW,"\nListing for all sets of conditions:\n");
4146
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
4147
((CConditionSubGroup*)m_oaConditionSubGroups[z])->PrintData();
4148
mprintf(GREEN,"\n<<< End of Condition Data <<<\n\n");
4149
}
4150
4151
4152
void CConditionGroup::PrintData(char *s)
4153
{
4154
int z;
4155
FILE *a;
4156
4157
mprintf(GREEN,"\n>>> Condition Data >>>\n\n");
4158
mprintf(" %.0f of %.0f molecules passed the conditions (%.2f percent).\n",m_fPassed,m_fTotal,ZeroDivide(m_fPassed,m_fTotal)*100.0f);
4159
if (m_fPassed == 0)
4160
{
4161
mprintf("\n No molecules at all passed the condition.\n");
4162
mprintf(" This is probably not what you wanted.\n");
4163
}
4164
mprintf("\nNeighbor count histogram:\n\n");
4165
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1;z++)
4166
if (m_pHistogram[z] != 0)
4167
mprintf(" - %d Neighbors: %8.4f percent of the time (%d hits).\n",z,((double)m_pHistogram[z])/m_iHistoGes*100.0,m_pHistogram[z]);
4168
mprintf("\n Saving detailed condition data as \"%s\"...\n",s);
4169
4170
a = OpenFileWrite(s,true);
4171
4172
mfprintf(a,"\n>>> Condition Data >>>\n\n");
4173
mfprintf(a," %.0f of %.0f molecules passed the conditions (%.2f percent).\n",m_fPassed,m_fTotal,ZeroDivide(m_fPassed,m_fTotal)*100.0f);
4174
if (m_fPassed == 0)
4175
{
4176
mfprintf(a,"\n No molecules at all passed the condition.\n");
4177
mfprintf(a," This is probably not what you wanted.\n");
4178
} else
4179
{
4180
mfprintf(a,"\nList of reference molecules (%s) that passed the conditions:\n\n",((CMolecule*)g_oaMolecules[m_iRefMol])->m_sName);
4181
for (z=0;z<((CMolecule*)g_oaMolecules[m_iRefMol])->m_laSingleMolIndex.GetSize();z++)
4182
if (m_iRMPassCounter[z] > 0)
4183
mfprintf(a," - %2d: %10.4f percent of the time (%lu hits)\n",z+1,((double)m_iRMPassCounter[z])/g_iSteps*100.0,m_iRMPassCounter[z]);
4184
4185
mfprintf(a,"\nList of observed molecules (%s) that passed the conditions:\n\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
4186
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
4187
if (m_iOMPassCounter[z] > 0)
4188
mfprintf(a," - %2d: %10.4f percent of the time (%lu hits)\n",z+1,((double)m_iOMPassCounter[z])/g_iSteps*100.0,m_iOMPassCounter[z]);
4189
}
4190
mfprintf(a,"\nNeighbor count histogram:\n\n");
4191
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1;z++)
4192
if (m_pHistogram[z] != 0)
4193
mfprintf(a," - %d Neighbors: %8.4f percent of the time (%lu hits).\n",z,((double)m_pHistogram[z])/m_iHistoGes*100.0,m_pHistogram[z]);
4194
mfprintf(a,"\nListing for all sets of conditions:\n");
4195
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
4196
((CConditionSubGroup*)m_oaConditionSubGroups[z])->PrintData(a);
4197
mfprintf(a,"\n<<< End of Condition Data <<<\n\n");
4198
4199
fclose(a);
4200
mprintf(GREEN,"\n<<< End of Condition Data <<<\n\n");
4201
}
4202
4203
4204
bool CConditionSubGroup::Contains(int mol)
4205
{
4206
BXIN;
4207
int z;
4208
4209
for (z=0;z<m_oaConditions.GetSize();z++)
4210
{
4211
if (!((CNbSearch*)m_oaConditions[z])->m_bPassed[mol])
4212
{
4213
BXOUT;
4214
return false;
4215
}
4216
}
4217
BXOUT;
4218
return true;
4219
}
4220
4221
4222
void CConditionSubGroup::MarkPassedAtoms(int om)
4223
{
4224
int z, z2;
4225
4226
for (z=0;z<g_iGesVirtAtomCount;z++)
4227
m_bTempPassed[z] = false;
4228
4229
for (z=0;z<m_oaConditions.GetSize();z++)
4230
{
4231
for (z2=0;z2<g_iGesVirtAtomCount;z2++)
4232
if (g_baAtomPassedCondition[z2] < 100)
4233
g_baAtomPassedCondition[z2] = 0;
4234
4235
((CNbSearch*)m_oaConditions[z])->MarkPassedAtoms(om);
4236
4237
for (z2=0;z2<g_iGesVirtAtomCount;z2++)
4238
if (g_baAtomPassedCondition[z2] == 1)
4239
m_bTempPassed[z2] = true;
4240
}
4241
4242
for (z=0;z<g_iGesVirtAtomCount;z++)
4243
if (m_bTempPassed[z])
4244
g_baAtomPassedCondition[z] = 100;
4245
}
4246
4247
4248
void CConditionSubGroup::ScanNeighborhoodAllOM(CTimeStep *t, CSingleMolecule *rm)
4249
{
4250
int z, z2;
4251
4252
for (z=0;z<m_oaConditions.GetSize();z++)
4253
((CNbSearch*)m_oaConditions[z])->ScanAllOM(rm,t);
4254
4255
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
4256
{
4257
m_fTotal++;
4258
for (z2=0;z2<m_oaConditions.GetSize();z2++)
4259
if (!((CNbSearch*)m_oaConditions[z2])->m_bPassed[z])
4260
goto _nopass;
4261
m_fPassed++;
4262
_nopass:;
4263
}
4264
}
4265
4266
4267
void CConditionSubGroup::PreScanNeighborhoodAllOM(CTimeStep *t, CSingleMolecule *rm)
4268
{
4269
int z;
4270
4271
for (z=0;z<m_oaConditions.GetSize();z++)
4272
((CNbSearch*)m_oaConditions[z])->PreScanAllOM(rm,t);
4273
}
4274
4275
4276
void CConditionSubGroup::Parse(int rm, int sm)
4277
{
4278
BTIN;
4279
CNbSearch *n;
4280
4281
m_iCombinations = 0;
4282
do
4283
{
4284
try { n = new CNbSearch(); } catch(...) { n = NULL; }
4285
if (n == NULL) NewException((double)sizeof(CNbSearch),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4286
4287
n->m_iNumber = m_oaConditions.GetSize();
4288
m_oaConditions.Add(n);
4289
n->Parse(rm,sm,false);
4290
m_iCombinations += n->m_iCombinationsEnabled;
4291
} while (AskYesNo(" Add another condition to this set of conditions (y/n)? [no] ",false));
4292
4293
try { m_bTempPassed = new bool[g_iGesVirtAtomCount]; } catch(...) { m_bTempPassed = NULL; }
4294
if (m_bTempPassed == NULL) NewException((double)g_iGesVirtAtomCount*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4295
4296
BTOUT;
4297
}
4298
4299
4300
void CADF::ParseCondition(int rm, bool nocrit)
4301
{
4302
BTIN;
4303
char buf[256];
4304
int z, z2, ti;
4305
CAtomGroup *ag;
4306
4307
mprintf(WHITE,"\n>>> Angular Condition >>>\n");
4308
for (z=0;z<2;z++)
4309
m_iVecType[z] = 0;
4310
z2 = 0;
4311
m_iCombinations = 0;
4312
do {
4313
ti = 1;
4314
if (z2 != 0)
4315
mprintf("\n %d. set of vectors\n\n",z2+1);
4316
for (z=0;z<2;z++)
4317
{
4318
/* if (z == 1)
4319
m_bSameFoot = AskYesNo(" Should the base points of the 1st and 2nd vectors always be equal (y/n)? [no] ",false);
4320
else m_bSameFoot = false;*/
4321
m_bOrtho[z] = (AskRangeInteger("\n Should the %d. vector connect two points (0) or stand perpendicular on 3 points (1)? [0] ",0,1,0,z+1) != 0);
4322
mprintf("\n");
4323
if (m_bOrtho[z])
4324
{
4325
/* if (m_bSameFoot && (z == 1))
4326
{
4327
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
4328
m_oaVectors.Add(NULL);
4329
} else*/
4330
{
4331
_ax1: if (m_iShowMol != -1)
4332
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) in base point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4333
else m_iRefOrSec[z][0] = 0;
4334
mprintf(" Enter atom(s) in the base point (e.g. C7): ");
4335
inpprintf("! Enter atom(s) in the base point (e.g. C7):\n");
4336
myget(buf);
4337
4338
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4339
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4340
4341
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4342
{
4343
eprintf("Wrong input.\n");
4344
inpprintf("! Wrong input.\n");
4345
delete ag;
4346
goto _ax1;
4347
}
4348
m_oaVectors.Add(ag);
4349
ti *= ag->m_iAtomGes;
4350
}
4351
_ax2: if (m_iShowMol != -1)
4352
m_iRefOrSec[z][1] = AskRangeInteger(" Take 2nd atom(s) of normal plane from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4353
else m_iRefOrSec[z][1] = 0;
4354
mprintf(" Enter 2nd atom(s) of normal plane (e.g. C7): ");
4355
inpprintf("! Enter 2nd atom(s) of normal plane (e.g. C7):\n");
4356
myget(buf);
4357
4358
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4359
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4360
4361
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4362
{
4363
eprintf("Wrong input.\n");
4364
inpprintf("! Wrong input.\n");
4365
delete ag;
4366
goto _ax2;
4367
}
4368
m_oaVectors.Add(ag);
4369
ti *= ag->m_iAtomGes;
4370
_ax3: if (m_iShowMol != -1)
4371
m_iRefOrSec[z][2] = AskRangeInteger(" Take 3rd atom(s) of normal plane from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4372
else m_iRefOrSec[z][2] = 0;
4373
mprintf(" Enter 3rd atom(s) of normal plane (e.g. C7): ");
4374
inpprintf("! Enter 3rd atom(s) of normal plane (e.g. C7):\n");
4375
myget(buf);
4376
4377
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4378
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4379
4380
if (!ag->ParseAtoms((!m_iRefOrSec[z][2])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4381
{
4382
eprintf("Wrong input.\n");
4383
inpprintf("! Wrong input.\n");
4384
delete ag;
4385
goto _ax3;
4386
}
4387
m_oaVectors.Add(ag);
4388
ti *= ag->m_iAtomGes;
4389
} else // IF NOT ORTHO
4390
{
4391
/* if (m_bSameFoot && (z == 1))
4392
{
4393
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
4394
m_oaVectors.Add(NULL);
4395
} else*/
4396
{
4397
_ax4: if (m_iShowMol != -1)
4398
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) in base point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4399
else m_iRefOrSec[z][0] = 0;
4400
mprintf(" Enter atom(s) in the base point (e.g. C7): ");
4401
inpprintf("! Enter atom(s) in the base point (e.g. C7):\n");
4402
myget(buf);
4403
4404
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4405
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4406
4407
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4408
{
4409
eprintf("Wrong input.\n");
4410
inpprintf("! Wrong input.\n");
4411
delete ag;
4412
goto _ax4;
4413
}
4414
m_oaVectors.Add(ag);
4415
ti *= ag->m_iAtomGes;
4416
} // END IF NOT SAMEFOOT
4417
_ax5: if (m_iShowMol != -1)
4418
m_iRefOrSec[z][1] = AskRangeInteger(" Take atom(s) in tip point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4419
else m_iRefOrSec[z][1] = 0;
4420
mprintf(" Enter atom(s) in the tip point (e.g. C7): ");
4421
inpprintf("! Enter atom(s) in the tip point (e.g. C7):\n");
4422
myget(buf);
4423
4424
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4425
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4426
4427
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4428
{
4429
eprintf("Wrong input.\n");
4430
inpprintf("! Wrong input.\n");
4431
delete ag;
4432
goto _ax5;
4433
}
4434
m_oaVectors.Add(ag);
4435
ti *= ag->m_iAtomGes;
4436
m_oaVectors.Add(NULL);
4437
} // END IF NOT ORTHO
4438
} // END FOR 0..1
4439
m_iCombinations += ti;
4440
z2++;
4441
} while (AskYesNo("\n Enter another set of vectors (y/n)? [no] ",false));
4442
if (!nocrit)
4443
{
4444
do {
4445
m_faMinMaxAngle.Add(AskFloat(" Enter minimal angle between the vectors in degree: [0.0] ",0.0f));
4446
m_faMinMaxAngle.Add(AskFloat(" Enter maximal angle between the vectors in degree: [180.0] ",180.0f));
4447
} while (AskYesNo(" Enter another angle interval (y/n)? [no] ",false));
4448
} else
4449
{
4450
m_faMinMaxAngle.Add(0.0f);
4451
m_faMinMaxAngle.Add(180.0f);
4452
}
4453
mprintf(WHITE,"\n<<< End of Angular Condition <<<\n\n");
4454
BTOUT;
4455
}
4456
4457
4458
void CADF::ParseConditionGrid(int rm, int gridmode)
4459
{
4460
BTIN;
4461
char buf[256];
4462
int z, z2, ti;
4463
CAtomGroup *ag;
4464
4465
mprintf(WHITE,"\n>>> Angular Condition >>>\n");
4466
for (z=0;z<2;z++)
4467
m_iVecType[z] = 0;
4468
z2 = 0;
4469
m_iCombinations = 0;
4470
do {
4471
ti = 1;
4472
if (z2 != 0)
4473
mprintf("\n %d. set of vectors\n\n",z2+1);
4474
for (z=0;z<2;z++)
4475
{
4476
/* if (z == 1)
4477
m_bSameFoot = AskYesNo(" Should the base points of the 1st and 2nd vectors always be equal (y/n)? [no] ",false);
4478
else m_bSameFoot = false;*/
4479
m_bOrtho[z] = (AskRangeInteger("\n Should the %d. vector connect two points (0) or stand perpendicular on 3 points (1)? [0] ",0,1,0,z+1) != 0);
4480
mprintf("\n");
4481
if (m_bOrtho[z])
4482
{
4483
/* if (m_bSameFoot && (z == 1))
4484
{
4485
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
4486
m_oaVectors.Add(NULL);
4487
} else*/
4488
{
4489
_ax1: if (m_iShowMol != -1)
4490
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) in base point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4491
else m_iRefOrSec[z][0] = 0;
4492
mprintf(" Enter atom(s) in the base point (e.g. C7): ");
4493
inpprintf("! Enter atom(s) in the base point (e.g. C7):\n");
4494
myget(buf);
4495
4496
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4497
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4498
4499
m_oaVectors.Add(ag);
4500
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4501
{
4502
eprintf("Wrong input.\n");
4503
inpprintf("! Wrong input.\n");
4504
goto _ax1;
4505
}
4506
ti *= ag->m_iAtomGes;
4507
}
4508
_ax2: if (m_iShowMol != -1)
4509
m_iRefOrSec[z][1] = AskRangeInteger(" Take 2nd atom(s) of normal plane from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4510
else m_iRefOrSec[z][1] = 0;
4511
mprintf(" Enter 2nd atom(s) of normal plane (e.g. C7): ");
4512
inpprintf("! Enter 2nd atom(s) of normal plane (e.g. C7):\n");
4513
myget(buf);
4514
4515
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4516
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4517
4518
m_oaVectors.Add(ag);
4519
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4520
{
4521
eprintf("Wrong input.\n");
4522
inpprintf("! Wrong input.\n");
4523
goto _ax2;
4524
}
4525
ti *= ag->m_iAtomGes;
4526
_ax3: if (m_iShowMol != -1)
4527
m_iRefOrSec[z][2] = AskRangeInteger(" Take 3rd atom(s) of normal plane from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4528
else m_iRefOrSec[z][2] = 0;
4529
mprintf(" Enter 3rd atom(s) of normal plane (e.g. C7): ");
4530
inpprintf("! Enter 3rd atom(s) of normal plane (e.g. C7):\n");
4531
myget(buf);
4532
4533
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4534
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4535
4536
m_oaVectors.Add(ag);
4537
if (!ag->ParseAtoms((!m_iRefOrSec[z][2])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4538
{
4539
eprintf("Wrong input.\n");
4540
inpprintf("! Wrong input.\n");
4541
goto _ax3;
4542
}
4543
ti *= ag->m_iAtomGes;
4544
} else // IF NOT ORTHO
4545
{
4546
/* if (m_bSameFoot && (z == 1))
4547
{
4548
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
4549
m_oaVectors.Add(NULL);
4550
} else*/
4551
{
4552
_ax4: if (m_iShowMol != -1)
4553
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) in base point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4554
else m_iRefOrSec[z][0] = 0;
4555
mprintf(" Enter atom(s) in the base point (e.g. C7): ");
4556
inpprintf("! Enter atom(s) in the base point (e.g. C7):\n");
4557
myget(buf);
4558
4559
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4560
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4561
4562
m_oaVectors.Add(ag);
4563
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4564
{
4565
eprintf("Wrong input.\n");
4566
inpprintf("! Wrong input.\n");
4567
goto _ax4;
4568
}
4569
ti *= ag->m_iAtomGes;
4570
} // END IF NOT SAMEFOOT
4571
_ax5: if (m_iShowMol != -1)
4572
m_iRefOrSec[z][1] = AskRangeInteger(" Take atom(s) in tip point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4573
else m_iRefOrSec[z][1] = 0;
4574
mprintf(" Enter atom(s) in the tip point (e.g. C7): ");
4575
inpprintf("! Enter atom(s) in the tip point (e.g. C7):\n");
4576
myget(buf);
4577
4578
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4579
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4580
4581
m_oaVectors.Add(ag);
4582
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4583
{
4584
eprintf("Wrong input.\n");
4585
inpprintf("! Wrong input.\n");
4586
goto _ax5;
4587
}
4588
ti *= ag->m_iAtomGes;
4589
m_oaVectors.Add(NULL);
4590
} // END IF NOT ORTHO
4591
} // END FOR 0..1
4592
m_iCombinations += ti;
4593
z2++;
4594
} while (AskYesNo("\n Enter another set of vectors (y/n)? [no] ",false));
4595
if ((gridmode == 1) || (gridmode == 6))
4596
{
4597
m_faMinMaxAngle.Add(AskFloat(" Enter minimal angle between the vectors in degree: [0.0] ",0.0f));
4598
m_faMinMaxAngle.Add(AskFloat(" Enter maximal angle between the vectors in degree: [180.0] ",180.0f));
4599
} else
4600
{
4601
m_faMinMaxAngle.Add(0.0f);
4602
m_faMinMaxAngle.Add(180.0f);
4603
}
4604
mprintf(WHITE,"\n<<< End of Angular Condition <<<\n\n");
4605
BTOUT;
4606
}
4607
4608
4609
void CADF::ParseCondition_OnlyValues()
4610
{
4611
BTIN;
4612
int z;
4613
4614
mprintf(" Angular condition between vectors:\n");
4615
for (z=0;z<m_oaVectors.GetSize()/6;z++)
4616
{
4617
mprintf(" ");
4618
if (m_oaVectors[z*6+2] != NULL)
4619
mprintf("normal(%s, %s, %s)",((CAtomGroup*)m_oaVectors[z*6])->m_sName,((CAtomGroup*)m_oaVectors[z*6+1])->m_sName,((CAtomGroup*)m_oaVectors[z*6+2])->m_sName);
4620
else mprintf("(%s --> %s)",((CAtomGroup*)m_oaVectors[z*6])->m_sName,((CAtomGroup*)m_oaVectors[z*6+1])->m_sName);
4621
mprintf(" and ");
4622
if (m_oaVectors[z*6+5] != NULL)
4623
mprintf("normal(%s, %s, %s)",((CAtomGroup*)m_oaVectors[z*6+3])->m_sName,((CAtomGroup*)m_oaVectors[z*6+4])->m_sName,((CAtomGroup*)m_oaVectors[z*6+5])->m_sName);
4624
else mprintf("(%s --> %s)",((CAtomGroup*)m_oaVectors[z*6+3])->m_sName,((CAtomGroup*)m_oaVectors[z*6+4])->m_sName);
4625
mprintf("\n");
4626
}
4627
for (z=0;z<m_faMinMaxAngle.GetSize()/2;z++)
4628
{
4629
mprintf(" Interval %d:\n",z+1,m_faMinMaxAngle.GetSize()/2);
4630
m_faMinMaxAngle[z*2] = AskFloat(" Enter minimal angle between the vectors in degree: [0.0] ",0.0f);
4631
m_faMinMaxAngle[z*2+1] = AskFloat(" Enter maximal angle between the vectors in degree: [180.0] ",180.0f);
4632
}
4633
// mprintf(WHITE,"\n<<< End of Angular Condition <<<\n\n");
4634
BTOUT;
4635
}
4636
4637
4638
CObservation::CObservation()
4639
{
4640
m_pConditions = NULL;
4641
m_pConditionsOM2 = NULL;
4642
m_pMSD = NULL;
4643
m_pSDF = NULL;
4644
m_pCDF = NULL;
4645
m_pVACF = NULL;
4646
m_pDipACF = NULL;
4647
m_pADF = NULL;
4648
m_pDDF = NULL;
4649
m_pRDF = NULL;
4650
m_pDipDF = NULL;
3630
3631
if (g_bAdvanced2)
3632
m_iHistogramRes = AskUnsignedInteger(" Please enter histogram resolution (0=no histogram): [5000] ",5000);
3633
else m_iHistogramRes = 0;
3634
3635
/* mprintf(" Save temporal Development of Velocity (0=no, 1=yes)? [0] ");
3636
myget(buf);
3637
m_bSaveSpeed = atoi(buf)!=0;*/
3638
BuildName();
3639
mprintf(WHITE,"\n<<< End of Velocity Distribution Function <<<\n\n");
3640
BTOUT;
3641
}
3642
3643
3644
void CSDF::BuildName()
3645
{
3646
BTIN;
3647
char tmp[256];
3648
3649
tmp[0] = 0;
3650
3651
if (m_iRefOrSec)
3652
sprintf(tmp,"%s_%s%d%s%d%s%d_%s_%s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName,g_iFixAtom[1]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_sName,g_iFixAtom[2]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,m_oAtoms.m_sName);
3653
else sprintf(tmp,"%s_%s%d%s%d%s%d_%s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName,g_iFixAtom[1]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_sName,g_iFixAtom[2]+1,m_oAtoms.m_sName);
3654
3655
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
3656
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3657
3658
strcpy(m_sName,tmp);
3659
BTOUT;
3660
}
3661
3662
3663
void CVDF::BuildName()
3664
{
3665
BTIN;
3666
char tmp[256];
3667
3668
if (m_iDeriv != 0)
3669
sprintf(tmp,"deriv%d_%s",m_iDeriv,m_oAtoms.m_sName);
3670
else sprintf(tmp,"%s",m_oAtoms.m_sName);
3671
3672
try { m_sShortName = new char[strlen(tmp)+1]; } catch(...) { m_sShortName = NULL; }
3673
if (m_sShortName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3674
3675
strcpy(m_sShortName,m_oAtoms.m_sName);
3676
if (g_iFixMol == -1)
3677
{
3678
sprintf(tmp,"%s_",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3679
} else if (m_iRefOrSec)
3680
sprintf(tmp,"%s_%s%d_%s_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
3681
else sprintf(tmp,"%s_%s%d_",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1);
3682
strcat(tmp,m_sShortName);
3683
3684
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
3685
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3686
3687
strcpy(m_sName,tmp);
3688
BTOUT;
3689
}
3690
3691
3692
void CSDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
3693
{
3694
BXIN;
3695
int z1t, z1a;
3696
CxIntArray *a1;
3697
3698
vec->RemoveAll_KeepSize();
3699
for (z1t=0;z1t<m_oAtoms.m_baAtomType.GetSize();z1t++)
3700
{
3701
// mprintf("(a) BuildAtomList z1t=%d, WA=%X\n",z1t,m_oAtoms.m_oaAtoms[z1t]);
3702
a1 = (CxIntArray*)m_oAtoms.m_oaAtoms[z1t];
3703
// mprintf("(b) BuildAtomList wa.GetSize()=%d\n",a1->GetSize());
3704
for (z1a=0;z1a<a1->GetSize();z1a++)
3705
if (m_iRefOrSec)
3706
{
3707
// mprintf("(c) BuildAtomList z1t=%d, z1a=%d, Type=%d, WA=%X\n",z1t,z1a,m_oAtoms.m_baAtomType[z1t],obs->m_oaAtomOffset[m_oAtoms.m_baAtomType[z1t]]);
3708
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[m_oAtoms.m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3709
} else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[m_oAtoms.m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3710
}
3711
BXOUT;
3712
}
3713
3714
3715
void CVDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
3716
{
3717
BXIN;
3718
int z1t, z1a;
3719
CxIntArray *a1;
3720
3721
vec->RemoveAll_KeepSize();
3722
for (z1t=0;z1t<m_oAtoms.m_baAtomType.GetSize();z1t++)
3723
{
3724
a1 = (CxIntArray*)m_oAtoms.m_oaAtoms[z1t];
3725
for (z1a=0;z1a<a1->GetSize();z1a++)
3726
if (m_iRefOrSec)
3727
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[m_oAtoms.m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3728
else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[m_oAtoms.m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3729
}
3730
BXOUT;
3731
}
3732
3733
3734
void CRDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
3735
{
3736
BXIN;
3737
int z, z1t, z1a, z2t, z2a;
3738
CAtomGroup *g1, *g2;
3739
CxIntArray *a1, *a2;
3740
3741
vec->RemoveAll_KeepSize();
3742
for (z=0;z<m_oaVectors.GetSize()/2;z++)
3743
{
3744
g1 = (CAtomGroup*)m_oaVectors[z*2];
3745
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
3746
{
3747
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
3748
for (z1a=0;z1a<a1->GetSize();z1a++)
3749
{
3750
g2 = (CAtomGroup*)m_oaVectors[z*2+1];
3751
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
3752
{
3753
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
3754
for (z2a=0;z2a<a2->GetSize();z2a++)
3755
{
3756
if (m_iRefOrSec[0])
3757
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3758
else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3759
if (m_iRefOrSec[1])
3760
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
3761
else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
3762
// mprintf("Vector z=%d, z1t=%d, z1a=%d, z2t=%d, z2a=%d.\n",z,z1t,z1a,z2t,z2a);
3763
}
3764
}
3765
}
3766
}
3767
}
3768
BXOUT;
3769
}
3770
3771
3772
void CVHDF::BuildAtomList(CSingleMolecule *ref, CSingleMolecule *obs, CxIntArray *vec)
3773
{
3774
BXIN;
3775
int z, z1t, z1a, z2t, z2a;
3776
CAtomGroup *g1, *g2;
3777
CxIntArray *a1, *a2;
3778
3779
vec->RemoveAll_KeepSize();
3780
for (z=0;z<m_oaVectors.GetSize()/2;z++)
3781
{
3782
g1 = (CAtomGroup*)m_oaVectors[z*2];
3783
for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)
3784
{
3785
a1 = (CxIntArray*)g1->m_oaAtoms[z1t];
3786
for (z1a=0;z1a<a1->GetSize();z1a++)
3787
{
3788
g2 = (CAtomGroup*)m_oaVectors[z*2+1];
3789
for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)
3790
{
3791
a2 = (CxIntArray*)g2->m_oaAtoms[z2t];
3792
for (z2a=0;z2a<a2->GetSize();z2a++)
3793
{
3794
if (m_iRefOrSec[0])
3795
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3796
else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));
3797
if (m_iRefOrSec[1])
3798
vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
3799
else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));
3800
}
3801
}
3802
}
3803
}
3804
}
3805
BXOUT;
3806
}
3807
3808
3809
/*int FindAtom(char *s)
3810
{
3811
BTIN;
3812
int z;
3813
for (z=0;z<g_oaAtoms.GetSize();z++)
3814
if (mystricmp(s,((CAtom*)g_oaAtoms[z])->m_sName)==0)
3815
{
3816
BTOUT;
3817
return z;
3818
}
3819
BTOUT;
3820
return -1;
3821
}*/
3822
3823
3824
int CMolecule::FindAtomInMol(const char *s)
3825
{
3826
BTIN;
3827
int z;
3828
for (z=0;z<m_baAtomIndex.GetSize();z++)
3829
if (mystricmp(s,((CAtom*)g_oaAtoms[m_baAtomIndex[z]])->m_sName)==0)
3830
{
3831
BTOUT;
3832
return z;
3833
}
3834
BTOUT;
3835
return -1;
3836
}
3837
3838
3839
void CMolecule::BuildName()
3840
{
3841
BTIN;
3842
int z, z2;
3843
char buf[16], buf2[256];
3844
3845
if (m_bPseudo)
3846
{
3847
buf2[0] = '$';
3848
buf2[1] = 0;
3849
} else buf2[0] = 0;
3850
for (z=0;z<g_oaAtoms.GetSize();z++)
3851
{
3852
for (z2=0;z2<m_baAtomIndex.GetSize();z2++)
3853
{
3854
if (m_baAtomIndex[z2] != z)
3855
continue;
3856
if (m_waAtomCount[z2] > 1)
3857
sprintf(buf,"%s%d",((CAtom*)g_oaAtoms[z])->m_sName,m_waAtomCount[z2]);
3858
else sprintf(buf,"%s",((CAtom*)g_oaAtoms[z])->m_sName);
3859
strcat(buf2,buf);
3860
}
3861
}
3862
3863
try { m_sName = new char[strlen(buf2)+1]; } catch(...) { m_sName = NULL; }
3864
if (m_sName == NULL) NewException((double)(strlen(buf2)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3865
3866
strcpy(m_sName,buf2);
3867
BTOUT;
3868
}
3869
3870
3871
bool CConditionGroup::Contains(int mol)
3872
{
3873
BXIN;
3874
int z;
3875
3876
if (m_bInactive)
3877
return m_bAlwaysTrue[mol];
3878
3879
if (m_bInvertCondition)
3880
{
3881
if (m_bAlwaysTrue[mol])
3882
{
3883
BXOUT;
3884
return false;
3885
}
3886
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
3887
{
3888
if (((CConditionSubGroup*)m_oaConditionSubGroups[z])->Contains(mol))
3889
{
3890
BXOUT;
3891
return false;
3892
}
3893
}
3894
BXOUT;
3895
return true;
3896
} else
3897
{
3898
if (m_bAlwaysTrue[mol])
3899
{
3900
BXOUT;
3901
return true;
3902
}
3903
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
3904
{
3905
if (((CConditionSubGroup*)m_oaConditionSubGroups[z])->Contains(mol))
3906
{
3907
BXOUT;
3908
return true;
3909
}
3910
}
3911
BXOUT;
3912
return false;
3913
}
3914
}
3915
3916
3917
void CConditionGroup::MarkPassedAtoms(int om, bool passed)
3918
{
3919
BXIN;
3920
int z;
3921
// int ti;
3922
3923
// mprintf("######## OM %d ##########\n",om+1);
3924
3925
for (z=0;z<g_iGesVirtAtomCount;z++)
3926
g_baAtomPassedCondition[z] = 110; // 110 heisst: Atom kommt nicht in einer Condition vor
3927
3928
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
3929
((CConditionSubGroup*)m_oaConditionSubGroups[z])->MarkPassedAtoms(om);
3930
3931
// for (z=0;z<g_iGesVirtAtomCount;z++)
3932
// mprintf("\nAtom %d: %d.",z+1,g_baAtomPassedCondition[z]);
3933
3934
// ti = 0;
3935
if (m_bInvertCondition)
3936
{
3937
for (z=0;z<g_iGesVirtAtomCount;z++)
3938
{
3939
if (g_baAtomPassedCondition[z] != 100) // Entweder Condition nicht bestanden oder Atom kam gar nicht darin vor
3940
{
3941
// ti++;
3942
g_baAtomPassedCondition[z] = 1;
3943
// mprintf("%d: Ok\n",z+1);
3944
// mprintf("\n %d --> Wird genommen.",z+1);
3945
} else // Condition bestanden
3946
{
3947
// mprintf("Atom %s%d nicht bestanden (%d).\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_sName,g_waAtomMolNumber[z]+1,g_baAtomPassedCondition[z]);
3948
// mprintf("\n%d erfuellt --> durchgefallen",z+1);
3949
g_baAtomPassedCondition[z] = 0;
3950
}
3951
}
3952
} else
3953
{
3954
for (z=0;z<g_iGesVirtAtomCount;z++)
3955
{
3956
if (passed)
3957
{
3958
if (g_baAtomPassedCondition[z] >= 100) // Entweder Condition bestanden oder Atom kam gar nicht darin vor
3959
{
3960
// ti++;
3961
g_baAtomPassedCondition[z] = 1;
3962
} else // Condition nicht bestanden
3963
{
3964
// mprintf("Atom %s%d nicht bestanden (%d).\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_sName,g_waAtomMolNumber[z]+1,g_baAtomPassedCondition[z]);
3965
g_baAtomPassedCondition[z] = 0;
3966
}
3967
} else
3968
{
3969
if (g_baAtomPassedCondition[z] == 100) // Condition bestanden
3970
{
3971
// ti++;
3972
// mprintf("### Atom %s[%d] %s%d bestanden (%d).\n",((CMolecule*)g_oaMolecules[g_waAtomMolIndex[z]])->m_sName,g_laAtomSMLocalIndex[z]+1,((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_sName,g_waAtomMolNumber[z]+1,g_baAtomPassedCondition[z]);
3973
g_baAtomPassedCondition[z] = 0;
3974
} else // Entweder Condition nicht bestanden oder Atom kam gar nicht darin vor
3975
{
3976
// mprintf("--- Atom %s[%d] %s%d nicht bestanden (%d).\n",((CMolecule*)g_oaMolecules[g_waAtomMolIndex[z]])->m_sName,g_laAtomSMLocalIndex[z]+1,((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_sName,g_waAtomMolNumber[z]+1,g_baAtomPassedCondition[z]);
3977
g_baAtomPassedCondition[z] = 1;
3978
}
3979
}
3980
}
3981
}
3982
// mprintf("\nMarked %d / %d atoms as enabled.",ti,g_iGesVirtAtomCount);
3983
3984
BXOUT;
3985
}
3986
3987
3988
void CConditionGroup::ScanNeighborhoodAllOM(CTimeStep *t, CSingleMolecule *rm)
3989
{
3990
BXIN;
3991
int z, z2, t1, t2, i;
3992
3993
if (m_bInactive)
3994
return;
3995
3996
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
3997
((CConditionSubGroup*)m_oaConditionSubGroups[z])->ScanNeighborhoodAllOM(t,rm);
3998
3999
if (m_oaConditionSubGroups.GetSize() == 2)
4000
{
4001
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
4002
{
4003
t1 = 0;
4004
t2 = 0;
4005
for (z2=0;z2<((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_oaConditions.GetSize();z2++)
4006
t1 += ((CNbSearch*)((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_oaConditions[z2])->m_iCombPassCount[z];
4007
for (z2=0;z2<((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_oaConditions.GetSize();z2++)
4008
t2 += ((CNbSearch*)((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_oaConditions[z2])->m_iCombPassCount[z];
4009
m_pTable[t1*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+t2]++;
4010
m_fTableGes++;
4011
}
4012
}
4013
4014
i = 0;
4015
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
4016
{
4017
m_fTotal++;
4018
if (m_bInvertCondition)
4019
{
4020
for (z2=0;z2<m_oaConditionSubGroups.GetSize();z2++)
4021
if (((CConditionSubGroup*)m_oaConditionSubGroups[z2])->Contains(z))
4022
goto _nopass;
4023
m_fPassed++;
4024
m_iPassCounter[z]++;
4025
m_bAnyPassed = true;
4026
} else
4027
{
4028
for (z2=0;z2<m_oaConditionSubGroups.GetSize();z2++)
4029
{
4030
if (((CConditionSubGroup*)m_oaConditionSubGroups[z2])->Contains(z))
4031
{
4032
// mprintf("passed[%d]++\n",z);
4033
m_fPassed++;
4034
m_iPassCounter[z]++;
4035
m_bAnyPassed = true;
4036
i++;
4037
goto _nopass;
4038
}
4039
}
4040
}
4041
_nopass:;
4042
}
4043
m_pHistogram[i]++;
4044
m_iHistoGes++;
4045
4046
BXOUT;
4047
}
4048
4049
4050
void CConditionGroup::PreScanNeighborhoodAllOM(CTimeStep *t, CSingleMolecule *rm)
4051
{
4052
BXIN;
4053
int z;
4054
4055
if (m_bInactive)
4056
return;
4057
4058
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
4059
((CConditionSubGroup*)m_oaConditionSubGroups[z])->PreScanNeighborhoodAllOM(t,rm);
4060
4061
BXOUT;
4062
}
4063
4064
4065
void CConditionGroup::Parse(int rm, int sm)
4066
{
4067
BTIN;
4068
CConditionSubGroup *sg;
4069
int z;
4070
4071
m_iShowMol = sm;
4072
m_iRefMol = rm;
4073
4074
try { m_bAlwaysTrue = new bool[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_bAlwaysTrue = NULL; }
4075
if (m_bAlwaysTrue == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4076
4077
try { m_iPassCounter = new long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iPassCounter = NULL; }
4078
if (m_iPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4079
4080
try { m_iOMPassCounter = new long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iOMPassCounter = NULL; }
4081
if (m_iOMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4082
4083
for (z=0;z<((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize();z++)
4084
{
4085
m_bAlwaysTrue[z] = false;
4086
m_iPassCounter[z] = 0;
4087
m_iOMPassCounter[z] = 0;
4088
}
4089
4090
try { m_iRMPassCounter = new long[((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iRMPassCounter = NULL; }
4091
if (m_iRMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4092
4093
for (z=0;z<((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize();z++)
4094
m_iRMPassCounter[z] = 0;
4095
4096
mprintf("Different sets of conditions are connected with OR (at least one of them has to be fulfilled).\n");
4097
mprintf("Different conditions within one set are connected with AND (have to be fulfilled at the same time).\n");
4098
mprintf("If you create 1 or 2 sets of conditions, a table with subcondition count populations will be printed.\n\n");
4099
_newset:
4100
mprintf(YELLOW,">>> %d. set of conditions >>>\n",m_oaConditionSubGroups.GetSize()+1);
4101
4102
try { sg = new CConditionSubGroup(); } catch(...) { sg = NULL; }
4103
if (sg == NULL) NewException((double)sizeof(CConditionSubGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4104
4105
sg->m_iShowMol = m_iShowMol;
4106
sg->m_iNumber = m_oaConditionSubGroups.GetSize();
4107
m_oaConditionSubGroups.Add(sg);
4108
sg->Parse(rm,sm);
4109
mprintf(YELLOW,"\n<<< End of %d. set of conditions <<<\n\n",m_oaConditionSubGroups.GetSize());
4110
if (AskYesNo(" Enter an additional set of conditions (y/n)? [no] ",false))
4111
goto _newset;
4112
4113
m_bInvertCondition = AskYesNo(" Invert this condition (only add bin entries if failed) (y/n)? [no] ",false);
4114
4115
if (m_oaConditionSubGroups.GetSize() == 2)
4116
{
4117
m_fTableGes = 0;
4118
4119
try { m_pTable = new double[(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)]; } catch(...) { m_pTable = NULL; }
4120
if (m_pTable == NULL) NewException((double)(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4121
4122
for (z=0;z<(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1);z++)
4123
m_pTable[z] = 0;
4124
}
4125
4126
/* m_bNeedNbCountMode = false;
4127
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
4128
{
4129
sg = (CConditionSubGroup*)m_oaConditionSubGroups[z];
4130
for (z2=0;z2<sg->m_oaConditions.GetSize();z2++)
4131
if (((CNbSearch*)sg->m_oaConditions[z2])->m_iNbCountMin != -1)
4132
m_bNeedNbCountMode = true;
4133
}*/
4134
m_iHistoGes = 0;
4135
4136
try {m_pHistogram = new unsigned long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1]; } catch(...) { m_pHistogram = NULL; }
4137
if (m_pHistogram == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1*sizeof(unsigned long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4138
4139
for (z=0;z<((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1;z++)
4140
m_pHistogram[z] = 0;
4141
BTOUT;
4142
}
4143
4144
4145
void CConditionGroup::PrintData()
4146
{
4147
int z;
4148
4149
mprintf(GREEN,"\n>>> Condition Data >>>\n\n");
4150
mprintf(" %.0f of %.0f molecules passed the conditions (%.2f percent).\n",m_fPassed,m_fTotal,ZeroDivide(m_fPassed,m_fTotal)*100.0f);
4151
if (m_fPassed == 0)
4152
{
4153
mprintf(YELLOW,"\n No molecules at all passed the condition.\n");
4154
mprintf(" This is probably not what you wanted.\n");
4155
} else
4156
{
4157
mprintf(YELLOW,"\nList of reference molecules (%s) that passed the conditions:\n\n",((CMolecule*)g_oaMolecules[m_iRefMol])->m_sName);
4158
for (z=0;z<((CMolecule*)g_oaMolecules[m_iRefMol])->m_laSingleMolIndex.GetSize();z++)
4159
if (m_iRMPassCounter[z] > 0)
4160
mprintf(" - %2d: %10.4f percent of the time (%d hits)\n",z+1,((double)m_iRMPassCounter[z])/g_iSteps*100.0,m_iRMPassCounter[z]);
4161
4162
mprintf(YELLOW,"\nList of observed molecules (%s) that passed the conditions:\n\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
4163
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
4164
if (m_iOMPassCounter[z] > 0)
4165
mprintf(" - %2d: %10.4f percent of the time (%d hits)\n",z+1,((double)m_iOMPassCounter[z])/g_iSteps*100.0,m_iOMPassCounter[z]);
4166
}
4167
mprintf(YELLOW,"\nNeighbor count histogram:\n\n");
4168
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1;z++)
4169
if (m_pHistogram[z] != 0)
4170
mprintf(" - %d Neighbors: %8.4f percent of the time (%d hits).\n",z,((double)m_pHistogram[z])/m_iHistoGes*100.0,m_pHistogram[z]);
4171
mprintf(YELLOW,"\nListing for all sets of conditions:\n");
4172
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
4173
((CConditionSubGroup*)m_oaConditionSubGroups[z])->PrintData();
4174
mprintf(GREEN,"\n<<< End of Condition Data <<<\n\n");
4175
}
4176
4177
4178
void CConditionGroup::PrintData(char *s)
4179
{
4180
int z;
4181
FILE *a;
4182
4183
mprintf(GREEN,"\n>>> Condition Data >>>\n\n");
4184
mprintf(" %.0f of %.0f molecules passed the conditions (%.2f percent).\n",m_fPassed,m_fTotal,ZeroDivide(m_fPassed,m_fTotal)*100.0f);
4185
if (m_fPassed == 0)
4186
{
4187
mprintf("\n No molecules at all passed the condition.\n");
4188
mprintf(" This is probably not what you wanted.\n");
4189
}
4190
mprintf("\nNeighbor count histogram:\n\n");
4191
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1;z++)
4192
if (m_pHistogram[z] != 0)
4193
mprintf(" - %d Neighbors: %8.4f percent of the time (%d hits).\n",z,((double)m_pHistogram[z])/m_iHistoGes*100.0,m_pHistogram[z]);
4194
mprintf("\n Saving detailed condition data as \"%s\"...\n",s);
4195
4196
a = OpenFileWrite(s,true);
4197
4198
mfprintf(a,"\n>>> Condition Data >>>\n\n");
4199
mfprintf(a," %.0f of %.0f molecules passed the conditions (%.2f percent).\n",m_fPassed,m_fTotal,ZeroDivide(m_fPassed,m_fTotal)*100.0f);
4200
if (m_fPassed == 0)
4201
{
4202
mfprintf(a,"\n No molecules at all passed the condition.\n");
4203
mfprintf(a," This is probably not what you wanted.\n");
4204
} else
4205
{
4206
mfprintf(a,"\nList of reference molecules (%s) that passed the conditions:\n\n",((CMolecule*)g_oaMolecules[m_iRefMol])->m_sName);
4207
for (z=0;z<((CMolecule*)g_oaMolecules[m_iRefMol])->m_laSingleMolIndex.GetSize();z++)
4208
if (m_iRMPassCounter[z] > 0)
4209
mfprintf(a," - %2d: %10.4f percent of the time (%lu hits)\n",z+1,((double)m_iRMPassCounter[z])/g_iSteps*100.0,m_iRMPassCounter[z]);
4210
4211
mfprintf(a,"\nList of observed molecules (%s) that passed the conditions:\n\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
4212
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
4213
if (m_iOMPassCounter[z] > 0)
4214
mfprintf(a," - %2d: %10.4f percent of the time (%lu hits)\n",z+1,((double)m_iOMPassCounter[z])/g_iSteps*100.0,m_iOMPassCounter[z]);
4215
}
4216
mfprintf(a,"\nNeighbor count histogram:\n\n");
4217
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1;z++)
4218
if (m_pHistogram[z] != 0)
4219
mfprintf(a," - %d Neighbors: %8.4f percent of the time (%lu hits).\n",z,((double)m_pHistogram[z])/m_iHistoGes*100.0,m_pHistogram[z]);
4220
mfprintf(a,"\nListing for all sets of conditions:\n");
4221
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
4222
((CConditionSubGroup*)m_oaConditionSubGroups[z])->PrintData(a);
4223
mfprintf(a,"\n<<< End of Condition Data <<<\n\n");
4224
4225
fclose(a);
4226
mprintf(GREEN,"\n<<< End of Condition Data <<<\n\n");
4227
}
4228
4229
4230
bool CConditionSubGroup::Contains(int mol)
4231
{
4232
BXIN;
4233
int z;
4234
4235
for (z=0;z<m_oaConditions.GetSize();z++)
4236
{
4237
if (!((CNbSearch*)m_oaConditions[z])->m_bPassed[mol])
4238
{
4239
BXOUT;
4240
return false;
4241
}
4242
}
4243
BXOUT;
4244
return true;
4245
}
4246
4247
4248
void CConditionSubGroup::MarkPassedAtoms(int om)
4249
{
4250
int z, z2;
4251
4252
for (z=0;z<g_iGesVirtAtomCount;z++)
4253
m_bTempPassed[z] = false;
4254
4255
for (z=0;z<m_oaConditions.GetSize();z++)
4256
{
4257
for (z2=0;z2<g_iGesVirtAtomCount;z2++)
4258
if (g_baAtomPassedCondition[z2] < 100)
4259
g_baAtomPassedCondition[z2] = 0;
4260
4261
((CNbSearch*)m_oaConditions[z])->MarkPassedAtoms(om);
4262
4263
for (z2=0;z2<g_iGesVirtAtomCount;z2++)
4264
if (g_baAtomPassedCondition[z2] == 1)
4265
m_bTempPassed[z2] = true;
4266
}
4267
4268
for (z=0;z<g_iGesVirtAtomCount;z++)
4269
if (m_bTempPassed[z])
4270
g_baAtomPassedCondition[z] = 100;
4271
}
4272
4273
4274
void CConditionSubGroup::ScanNeighborhoodAllOM(CTimeStep *t, CSingleMolecule *rm)
4275
{
4276
int z, z2;
4277
4278
for (z=0;z<m_oaConditions.GetSize();z++)
4279
((CNbSearch*)m_oaConditions[z])->ScanAllOM(rm,t);
4280
4281
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
4282
{
4283
m_fTotal++;
4284
for (z2=0;z2<m_oaConditions.GetSize();z2++)
4285
if (!((CNbSearch*)m_oaConditions[z2])->m_bPassed[z])
4286
goto _nopass;
4287
m_fPassed++;
4288
_nopass:;
4289
}
4290
}
4291
4292
4293
void CConditionSubGroup::PreScanNeighborhoodAllOM(CTimeStep *t, CSingleMolecule *rm)
4294
{
4295
int z;
4296
4297
for (z=0;z<m_oaConditions.GetSize();z++)
4298
((CNbSearch*)m_oaConditions[z])->PreScanAllOM(rm,t);
4299
}
4300
4301
4302
void CConditionSubGroup::Parse(int rm, int sm)
4303
{
4304
BTIN;
4305
CNbSearch *n;
4306
4307
m_iCombinations = 0;
4308
do
4309
{
4310
try { n = new CNbSearch(); } catch(...) { n = NULL; }
4311
if (n == NULL) NewException((double)sizeof(CNbSearch),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4312
4313
n->m_iNumber = m_oaConditions.GetSize();
4314
m_oaConditions.Add(n);
4315
n->Parse(rm,sm,false);
4316
m_iCombinations += n->m_iCombinationsEnabled;
4317
} while (AskYesNo(" Add another condition to this set of conditions (y/n)? [no] ",false));
4318
4319
try { m_bTempPassed = new bool[g_iGesVirtAtomCount]; } catch(...) { m_bTempPassed = NULL; }
4320
if (m_bTempPassed == NULL) NewException((double)g_iGesVirtAtomCount*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4321
4322
BTOUT;
4323
}
4324
4325
4326
void CADF::ParseCondition(int rm, bool nocrit)
4327
{
4328
BTIN;
4329
char buf[256];
4330
int z, z2, ti;
4331
CAtomGroup *ag;
4332
4333
mprintf(WHITE,"\n>>> Angular Condition >>>\n");
4334
for (z=0;z<2;z++)
4335
m_iVecType[z] = 0;
4336
z2 = 0;
4337
m_iCombinations = 0;
4338
do {
4339
ti = 1;
4340
if (z2 != 0)
4341
mprintf("\n %d. set of vectors\n\n",z2+1);
4342
for (z=0;z<2;z++)
4343
{
4344
/* if (z == 1)
4345
m_bSameFoot = AskYesNo(" Should the base points of the 1st and 2nd vectors always be equal (y/n)? [no] ",false);
4346
else m_bSameFoot = false;*/
4347
m_bOrtho[z] = (AskRangeInteger("\n Should the %d. vector connect two points (0) or stand perpendicular on 3 points (1)? [0] ",0,1,0,z+1) != 0);
4348
mprintf("\n");
4349
if (m_bOrtho[z])
4350
{
4351
/* if (m_bSameFoot && (z == 1))
4352
{
4353
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
4354
m_oaVectors.Add(NULL);
4355
} else*/
4356
{
4357
_ax1: if (m_iShowMol != -1)
4358
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) in base point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4359
else m_iRefOrSec[z][0] = 0;
4360
mprintf(" Enter atom(s) in the base point (e.g. C7): ");
4361
inpprintf("! Enter atom(s) in the base point (e.g. C7):\n");
4362
myget(buf);
4363
4364
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4365
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4366
4367
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4368
{
4369
eprintf("Wrong input.\n");
4370
inpprintf("! Wrong input.\n");
4371
delete ag;
4372
goto _ax1;
4373
}
4374
m_oaVectors.Add(ag);
4375
ti *= ag->m_iAtomGes;
4376
}
4377
_ax2: if (m_iShowMol != -1)
4378
m_iRefOrSec[z][1] = AskRangeInteger(" Take 2nd atom(s) of normal plane from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4379
else m_iRefOrSec[z][1] = 0;
4380
mprintf(" Enter 2nd atom(s) of normal plane (e.g. C7): ");
4381
inpprintf("! Enter 2nd atom(s) of normal plane (e.g. C7):\n");
4382
myget(buf);
4383
4384
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4385
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4386
4387
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4388
{
4389
eprintf("Wrong input.\n");
4390
inpprintf("! Wrong input.\n");
4391
delete ag;
4392
goto _ax2;
4393
}
4394
m_oaVectors.Add(ag);
4395
ti *= ag->m_iAtomGes;
4396
_ax3: if (m_iShowMol != -1)
4397
m_iRefOrSec[z][2] = AskRangeInteger(" Take 3rd atom(s) of normal plane from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4398
else m_iRefOrSec[z][2] = 0;
4399
mprintf(" Enter 3rd atom(s) of normal plane (e.g. C7): ");
4400
inpprintf("! Enter 3rd atom(s) of normal plane (e.g. C7):\n");
4401
myget(buf);
4402
4403
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4404
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4405
4406
if (!ag->ParseAtoms((!m_iRefOrSec[z][2])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4407
{
4408
eprintf("Wrong input.\n");
4409
inpprintf("! Wrong input.\n");
4410
delete ag;
4411
goto _ax3;
4412
}
4413
m_oaVectors.Add(ag);
4414
ti *= ag->m_iAtomGes;
4415
} else // IF NOT ORTHO
4416
{
4417
/* if (m_bSameFoot && (z == 1))
4418
{
4419
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
4420
m_oaVectors.Add(NULL);
4421
} else*/
4422
{
4423
_ax4: if (m_iShowMol != -1)
4424
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) in base point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4425
else m_iRefOrSec[z][0] = 0;
4426
mprintf(" Enter atom(s) in the base point (e.g. C7): ");
4427
inpprintf("! Enter atom(s) in the base point (e.g. C7):\n");
4428
myget(buf);
4429
4430
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4431
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4432
4433
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4434
{
4435
eprintf("Wrong input.\n");
4436
inpprintf("! Wrong input.\n");
4437
delete ag;
4438
goto _ax4;
4439
}
4440
m_oaVectors.Add(ag);
4441
ti *= ag->m_iAtomGes;
4442
} // END IF NOT SAMEFOOT
4443
_ax5: if (m_iShowMol != -1)
4444
m_iRefOrSec[z][1] = AskRangeInteger(" Take atom(s) in tip point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4445
else m_iRefOrSec[z][1] = 0;
4446
mprintf(" Enter atom(s) in the tip point (e.g. C7): ");
4447
inpprintf("! Enter atom(s) in the tip point (e.g. C7):\n");
4448
myget(buf);
4449
4450
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4451
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4452
4453
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4454
{
4455
eprintf("Wrong input.\n");
4456
inpprintf("! Wrong input.\n");
4457
delete ag;
4458
goto _ax5;
4459
}
4460
m_oaVectors.Add(ag);
4461
ti *= ag->m_iAtomGes;
4462
m_oaVectors.Add(NULL);
4463
} // END IF NOT ORTHO
4464
} // END FOR 0..1
4465
m_iCombinations += ti;
4466
z2++;
4467
} while (AskYesNo("\n Enter another set of vectors (y/n)? [no] ",false));
4468
if (!nocrit)
4469
{
4470
do {
4471
m_faMinMaxAngle.Add(AskFloat(" Enter minimal angle between the vectors in degree: [0.0] ",0.0f));
4472
m_faMinMaxAngle.Add(AskFloat(" Enter maximal angle between the vectors in degree: [180.0] ",180.0f));
4473
} while (AskYesNo(" Enter another angle interval (y/n)? [no] ",false));
4474
} else
4475
{
4476
m_faMinMaxAngle.Add(0.0f);
4477
m_faMinMaxAngle.Add(180.0f);
4478
}
4479
mprintf(WHITE,"\n<<< End of Angular Condition <<<\n\n");
4480
BTOUT;
4481
}
4482
4483
4484
void CADF::ParseConditionGrid(int rm, int gridmode)
4485
{
4486
BTIN;
4487
char buf[256];
4488
int z, z2, ti;
4489
CAtomGroup *ag;
4490
4491
mprintf(WHITE,"\n>>> Angular Condition >>>\n");
4492
for (z=0;z<2;z++)
4493
m_iVecType[z] = 0;
4494
z2 = 0;
4495
m_iCombinations = 0;
4496
do {
4497
ti = 1;
4498
if (z2 != 0)
4499
mprintf("\n %d. set of vectors\n\n",z2+1);
4500
for (z=0;z<2;z++)
4501
{
4502
/* if (z == 1)
4503
m_bSameFoot = AskYesNo(" Should the base points of the 1st and 2nd vectors always be equal (y/n)? [no] ",false);
4504
else m_bSameFoot = false;*/
4505
m_bOrtho[z] = (AskRangeInteger("\n Should the %d. vector connect two points (0) or stand perpendicular on 3 points (1)? [0] ",0,1,0,z+1) != 0);
4506
mprintf("\n");
4507
if (m_bOrtho[z])
4508
{
4509
/* if (m_bSameFoot && (z == 1))
4510
{
4511
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
4512
m_oaVectors.Add(NULL);
4513
} else*/
4514
{
4515
_ax1: if (m_iShowMol != -1)
4516
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) in base point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4517
else m_iRefOrSec[z][0] = 0;
4518
mprintf(" Enter atom(s) in the base point (e.g. C7): ");
4519
inpprintf("! Enter atom(s) in the base point (e.g. C7):\n");
4520
myget(buf);
4521
4522
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4523
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4524
4525
m_oaVectors.Add(ag);
4526
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4527
{
4528
eprintf("Wrong input.\n");
4529
inpprintf("! Wrong input.\n");
4530
goto _ax1;
4531
}
4532
ti *= ag->m_iAtomGes;
4533
}
4534
_ax2: if (m_iShowMol != -1)
4535
m_iRefOrSec[z][1] = AskRangeInteger(" Take 2nd atom(s) of normal plane from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4536
else m_iRefOrSec[z][1] = 0;
4537
mprintf(" Enter 2nd atom(s) of normal plane (e.g. C7): ");
4538
inpprintf("! Enter 2nd atom(s) of normal plane (e.g. C7):\n");
4539
myget(buf);
4540
4541
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4542
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4543
4544
m_oaVectors.Add(ag);
4545
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4546
{
4547
eprintf("Wrong input.\n");
4548
inpprintf("! Wrong input.\n");
4549
goto _ax2;
4550
}
4551
ti *= ag->m_iAtomGes;
4552
_ax3: if (m_iShowMol != -1)
4553
m_iRefOrSec[z][2] = AskRangeInteger(" Take 3rd atom(s) of normal plane from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4554
else m_iRefOrSec[z][2] = 0;
4555
mprintf(" Enter 3rd atom(s) of normal plane (e.g. C7): ");
4556
inpprintf("! Enter 3rd atom(s) of normal plane (e.g. C7):\n");
4557
myget(buf);
4558
4559
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4560
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4561
4562
m_oaVectors.Add(ag);
4563
if (!ag->ParseAtoms((!m_iRefOrSec[z][2])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4564
{
4565
eprintf("Wrong input.\n");
4566
inpprintf("! Wrong input.\n");
4567
goto _ax3;
4568
}
4569
ti *= ag->m_iAtomGes;
4570
} else // IF NOT ORTHO
4571
{
4572
/* if (m_bSameFoot && (z == 1))
4573
{
4574
m_iRefOrSec[1][0] = m_iRefOrSec[0][0];
4575
m_oaVectors.Add(NULL);
4576
} else*/
4577
{
4578
_ax4: if (m_iShowMol != -1)
4579
m_iRefOrSec[z][0] = AskRangeInteger(" Take atom(s) in base point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4580
else m_iRefOrSec[z][0] = 0;
4581
mprintf(" Enter atom(s) in the base point (e.g. C7): ");
4582
inpprintf("! Enter atom(s) in the base point (e.g. C7):\n");
4583
myget(buf);
4584
4585
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4586
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4587
4588
m_oaVectors.Add(ag);
4589
if (!ag->ParseAtoms((!m_iRefOrSec[z][0])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4590
{
4591
eprintf("Wrong input.\n");
4592
inpprintf("! Wrong input.\n");
4593
goto _ax4;
4594
}
4595
ti *= ag->m_iAtomGes;
4596
} // END IF NOT SAMEFOOT
4597
_ax5: if (m_iShowMol != -1)
4598
m_iRefOrSec[z][1] = AskRangeInteger(" Take atom(s) in tip point from 1st mol. %s (0) or from 2nd mol. %s (1)? [%d] ",0,1,z,((CMolecule*)g_oaMolecules[rm])->m_sName,((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,z);
4599
else m_iRefOrSec[z][1] = 0;
4600
mprintf(" Enter atom(s) in the tip point (e.g. C7): ");
4601
inpprintf("! Enter atom(s) in the tip point (e.g. C7):\n");
4602
myget(buf);
4603
4604
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
4605
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4606
4607
m_oaVectors.Add(ag);
4608
if (!ag->ParseAtoms((!m_iRefOrSec[z][1])?(CMolecule*)g_oaMolecules[rm]:(CMolecule*)g_oaMolecules[m_iShowMol],buf))
4609
{
4610
eprintf("Wrong input.\n");
4611
inpprintf("! Wrong input.\n");
4612
goto _ax5;
4613
}
4614
ti *= ag->m_iAtomGes;
4615
m_oaVectors.Add(NULL);
4616
} // END IF NOT ORTHO
4617
} // END FOR 0..1
4618
m_iCombinations += ti;
4619
z2++;
4620
} while (AskYesNo("\n Enter another set of vectors (y/n)? [no] ",false));
4621
if ((gridmode == 1) || (gridmode == 6))
4622
{
4623
m_faMinMaxAngle.Add(AskFloat(" Enter minimal angle between the vectors in degree: [0.0] ",0.0f));
4624
m_faMinMaxAngle.Add(AskFloat(" Enter maximal angle between the vectors in degree: [180.0] ",180.0f));
4625
} else
4626
{
4627
m_faMinMaxAngle.Add(0.0f);
4628
m_faMinMaxAngle.Add(180.0f);
4629
}
4630
mprintf(WHITE,"\n<<< End of Angular Condition <<<\n\n");
4631
BTOUT;
4632
}
4633
4634
4635
void CADF::ParseCondition_OnlyValues()
4636
{
4637
BTIN;
4638
int z;
4639
4640
mprintf(" Angular condition between vectors:\n");
4641
for (z=0;z<m_oaVectors.GetSize()/6;z++)
4642
{
4643
mprintf(" ");
4644
if (m_oaVectors[z*6+2] != NULL)
4645
mprintf("normal(%s, %s, %s)",((CAtomGroup*)m_oaVectors[z*6])->m_sName,((CAtomGroup*)m_oaVectors[z*6+1])->m_sName,((CAtomGroup*)m_oaVectors[z*6+2])->m_sName);
4646
else mprintf("(%s --> %s)",((CAtomGroup*)m_oaVectors[z*6])->m_sName,((CAtomGroup*)m_oaVectors[z*6+1])->m_sName);
4647
mprintf(" and ");
4648
if (m_oaVectors[z*6+5] != NULL)
4649
mprintf("normal(%s, %s, %s)",((CAtomGroup*)m_oaVectors[z*6+3])->m_sName,((CAtomGroup*)m_oaVectors[z*6+4])->m_sName,((CAtomGroup*)m_oaVectors[z*6+5])->m_sName);
4650
else mprintf("(%s --> %s)",((CAtomGroup*)m_oaVectors[z*6+3])->m_sName,((CAtomGroup*)m_oaVectors[z*6+4])->m_sName);
4651
mprintf("\n");
4652
}
4653
for (z=0;z<m_faMinMaxAngle.GetSize()/2;z++)
4654
{
4655
mprintf(" Interval %d:\n",z+1,m_faMinMaxAngle.GetSize()/2);
4656
m_faMinMaxAngle[z*2] = AskFloat(" Enter minimal angle between the vectors in degree: [0.0] ",0.0f);
4657
m_faMinMaxAngle[z*2+1] = AskFloat(" Enter maximal angle between the vectors in degree: [180.0] ",180.0f);
4658
}
4659
// mprintf(WHITE,"\n<<< End of Angular Condition <<<\n\n");
4660
BTOUT;
4661
}
4662
4663
4664
CObservation::CObservation()
4665
{
4666
m_pConditions = NULL;
4667
m_pConditionsOM2 = NULL;
4668
m_pMSD = NULL;
4669
m_pSDF = NULL;
4670
m_pCDF = NULL;
4671
m_pVACF = NULL;
4672
m_pDipACF = NULL;
4673
m_pADF = NULL;
4674
m_pDDF = NULL;
4675
m_pRDF = NULL;
4676
m_pDipDF = NULL;
4651
4677
m_pVDF = NULL;
4652
m_bBinOnlyPassedAtoms = false;
4653
m_bBinOnlyNotPassedAtoms = false;
4654
4655
m_waSaveRefList.SetName("CObservation::m_waSaveRefList");
4656
m_waSaveShowList.SetName("CObservation::m_waSaveShowList");
4657
m_waObsRefList.SetName("CObservation::m_waObsRefList");
4658
m_waObsShowList.SetName("CObservation::m_waObsShowList");
4659
m_waObsShow2List.SetName("CObservation::m_waObsShow2List");
4660
m_waDecompTypeRefOffs.SetName("CObservation::m_waDecompTypeRefOffs");
4661
m_waDecompTypeObsOffs.SetName("CObservation::m_waDecompTypeObsOffs");
4662
m_waDecompTypeRefList.SetName("CObservation::m_waDecompTypeRefList");
4663
m_waDecompTypeObsList.SetName("CObservation::m_waDecompTypeObsList");
4664
m_iaRMRegions.SetName("CObservation::m_iaRMRegions");
4665
m_iaOM1Regions.SetName("CObservation::m_iaOM1Regions");
4666
m_iaOM2Regions.SetName("CObservation::m_iaOM2Regions");
4667
}
4668
4669
4670
CObservation::~CObservation()
4671
{
4672
int z;
4673
4674
if (m_pConditions != NULL)
4675
{
4676
delete m_pConditions;
4677
m_pConditions = NULL;
4678
}
4679
if (m_pMSD != NULL)
4680
{
4681
delete m_pMSD;
4682
m_pMSD = NULL;
4683
}
4684
if (m_pSDF != NULL)
4685
{
4686
delete m_pSDF;
4687
m_pSDF = NULL;
4688
}
4689
if (m_pCDF != NULL)
4690
{
4691
delete m_pCDF;
4692
m_pCDF = NULL;
4693
}
4694
if (m_pVACF != NULL)
4695
{
4696
delete m_pVACF;
4697
m_pVACF = NULL;
4698
}
4699
if (m_pDipACF != NULL)
4700
{
4701
delete m_pDipACF;
4702
m_pDipACF = NULL;
4703
}
4704
4705
if (m_pRDF != NULL)
4706
{
4707
for (z=0;z<g_iCDFChannels;z++)
4708
{
4709
if (m_pRDF[z] != NULL)
4710
{
4711
delete m_pRDF[z];
4712
m_pRDF[z] = NULL;
4713
}
4714
}
4715
delete[] m_pRDF;
4716
m_pRDF = NULL;
4717
}
4718
if (m_pADF != NULL)
4719
{
4720
for (z=0;z<g_iCDFChannels;z++)
4721
{
4722
if (m_pADF[z] != NULL)
4723
{
4724
delete m_pADF[z];
4725
m_pADF[z] = NULL;
4726
}
4727
}
4728
delete[] m_pADF;
4729
m_pADF = NULL;
4730
}
4731
if (m_pDDF != NULL)
4732
{
4733
for (z=0;z<g_iCDFChannels;z++)
4734
{
4735
if (m_pDDF[z] != NULL)
4736
{
4737
delete m_pDDF[z];
4738
m_pDDF[z] = NULL;
4739
}
4740
}
4741
delete[] m_pDDF;
4742
m_pDDF = NULL;
4743
}
4744
if (m_pDipDF != NULL)
4745
{
4746
for (z=0;z<g_iCDFChannels;z++)
4747
{
4748
if (m_pDipDF[z] != NULL)
4749
{
4750
delete m_pDipDF[z];
4751
m_pDipDF[z] = NULL;
4752
}
4753
}
4754
delete[] m_pDipDF;
4755
m_pDipDF = NULL;
4756
}
4757
if (m_pVDF != NULL)
4758
{
4759
for (z=0;z<g_iCDFChannels;z++)
4760
{
4761
if (m_pVDF[z] != NULL)
4762
{
4763
delete m_pVDF[z];
4764
m_pVDF[z] = NULL;
4765
}
4766
}
4767
delete[] m_pVDF;
4768
m_pVDF = NULL;
4769
}
4770
}
4771
4772
4773
void CSingleMolecule::BuildAtomCodes()
4774
{
4775
int z, z2, c1, c2, i;
4776
double ac;
4777
CMolAtom *ma;
4778
4779
// Die Anfangswerte der AtomCodes: [Ordnungszahl] * 10.0 + [Zahl der Nicht-Wasserstoff-Bindungen]
4780
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4781
{
4782
ma = (CMolAtom*)m_oaMolAtoms[z];
4783
ma->m_fAtomCode = 10.0 * ((CAtom*)g_oaAtoms[m_baAtomIndex[ma->m_iType]])->m_pElement->m_fMass;
4784
4785
i = 0;
4786
for (z2=0;z2<ma->m_oaBonds.GetSize();z2++)
4787
{
4788
// Alle Wasserstoff-Atome ueberspringen
4789
if (((CAtom*)g_oaAtoms[m_baAtomIndex[((CMolAtom*)ma->m_oaBonds[z2])->m_iType]])->m_pElement->m_fMass < 4.5)
4790
continue;
4791
ma->m_fAtomCode++;
4792
i++;
4793
}
4794
4795
if (g_bVerbose)
4796
mprintf(" Atom %d (%s%d): 10.0 * %.2f + %d = %.2f\n",z+1,((CAtom*)g_oaAtoms[m_baAtomIndex[ma->m_iType]])->m_sName,ma->m_iOffset+1,((CAtom*)g_oaAtoms[m_baAtomIndex[ma->m_iType]])->m_pElement->m_fMass,i,ma->m_fAtomCode);
4797
}
4798
4799
i = 0;
4800
do {
4801
c1 = CountDifferentAtomCodes();
4802
4803
if (g_bVerbose)
4804
mprintf(WHITE,"\n Cycle %d: %d different atom codes exist.\n\n",i+1,c1);
4805
4806
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4807
{
4808
ma = (CMolAtom*)m_oaMolAtoms[z];
4809
ma->m_fTempAtomCode = ma->m_fAtomCode * 5.0;
4810
4811
for (z2=0;z2<ma->m_oaBonds.GetSize();z2++)
4812
ma->m_fTempAtomCode += ((CMolAtom*)ma->m_oaBonds[z2])->m_fAtomCode;
4813
}
4814
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4815
{
4816
ma = (CMolAtom*)m_oaMolAtoms[z];
4817
ma->m_fAtomCode = ma->m_fTempAtomCode;
4818
4819
if (g_bVerbose)
4820
mprintf(" Atom %d (%s%d): %.2f\n",z+1,((CAtom*)g_oaAtoms[m_baAtomIndex[ma->m_iType]])->m_sName,ma->m_iOffset+1,ma->m_fAtomCode);
4821
}
4822
c2 = CountDifferentAtomCodes();
4823
i++;
4824
// mprintf("Iteration %d: %d classes before, %d classes after.\n",i,c1,c2);
4825
} while (c1 != c2);
4826
4827
if (g_bVerbose)
4828
mprintf(WHITE,"\nSorting...\n");
4829
4830
m_iAtomClasses = c2;
4831
// mprintf("Finished.\n");
4832
// mprintf("%d Iterations, %d atom classes found.\n",i,c2);
4833
// mprintf("Sorting Atom Codes...");
4834
4835
// Sortieren mittels StackSort
4836
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4837
{
4838
ac = -1;
4839
i = -1;
4840
for (z2=z;z2<m_oaMolAtoms.GetSize();z2++)
4841
{
4842
if (((CMolAtom*)m_oaMolAtoms[z2])->m_fAtomCode > ac)
4843
{
4844
ac = ((CMolAtom*)m_oaMolAtoms[z2])->m_fAtomCode;
4845
i = z2;
4846
}
4847
}
4848
if (i != -1)
4849
{
4850
ma = (CMolAtom*)m_oaMolAtoms[z];
4851
m_oaMolAtoms[z] = m_oaMolAtoms[i];
4852
m_oaMolAtoms[i] = ma;
4853
((CMolAtom*)m_oaMolAtoms[z])->m_iMolAtomNumber = z;
4854
} else
4855
{
4856
eprintf("CSingleMolecule::BuildAtomCodes(): Weird error.\n");
4857
return;
4858
}
4859
}
4860
4861
if (g_bVerbose)
4862
{
4863
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4864
{
4865
ma = (CMolAtom*)m_oaMolAtoms[z];
4866
mprintf(" Atom %d (%s%d): %.2f\n",z+1,((CAtom*)g_oaAtoms[m_baAtomIndex[ma->m_iType]])->m_sName,ma->m_iOffset+1,ma->m_fAtomCode);
4867
}
4868
mprintf(WHITE,"Finished.\n\n");
4869
}
4870
// mprintf("Finished.\n");
4871
}
4872
4873
4874
int CSingleMolecule::CountDifferentAtomCodes()
4875
{
4876
int z, z2, i;
4877
double *d;
4878
4879
try { d = new double[m_oaMolAtoms.GetSize()]; } catch(...) { d = NULL; }
4880
if (d == NULL) NewException((double)m_oaMolAtoms.GetSize()*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4881
4882
i = 0;
4883
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4884
{
4885
for (z2=0;z2<i;z2++)
4886
if (d[z2] == ((CMolAtom*)m_oaMolAtoms[z])->m_fAtomCode)
4887
goto _next;
4888
d[i] = ((CMolAtom*)m_oaMolAtoms[z])->m_fAtomCode;
4889
i++;
4890
_next:;
4891
}
4892
delete[] d;
4893
return i;
4894
}
4895
4896
4897
void CMSD::Parse()
4898
{
4899
char buf[256];
4900
int ti;
4901
// float tf;
4902
4903
BTIN;
4904
4905
try { m_pMSD = new CAF(); } catch(...) { m_pMSD = NULL; }
4906
if (m_pMSD == NULL) NewException((double)sizeof(CAF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4907
4908
mprintf(WHITE,"\n*** Mean Square Displacement\n\n");
4909
4910
try { m_pAtomGroup = new CAtomGroup(); } catch(...) { m_pAtomGroup = NULL; }
4911
if (m_pAtomGroup == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4912
4913
_rdfatom1:
4914
mprintf(" Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
4915
inpprintf("! Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
4916
myget(buf);
4917
if (strlen(buf) == 0)
4918
{
4919
if (!m_pAtomGroup->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],"#2"))
4920
{
4921
eprintf("Weird error.\n");
4922
inpprintf("! Weird error.\n");
4923
goto _rdfatom1;
4924
}
4925
} else if (!m_pAtomGroup->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],buf))
4926
{
4927
eprintf("Wrong input.\n");
4928
inpprintf("! Wrong input.\n");
4929
goto _rdfatom1;
4930
}
4931
4932
//_depth:
4933
if (g_iTrajSteps != -1)
4934
m_iResolution = AskUnsignedInteger(" Enter the resolution (=depth) for this MSD (in time steps): [%d] ",int(g_iTrajSteps*0.75),int(g_iTrajSteps*0.75));
4935
else m_iResolution = AskUnsignedInteger(" Enter the resolution (=depth) for this MSD (in time steps): [10000] ",10000);
4936
4937
m_iShowAtoms = m_pAtomGroup->m_iAtomGes;
4938
4939
/* if (g_iTrajSteps != -1)
4940
{
4941
if (g_bMSDCacheMode)
4942
{
4943
tf = g_iTrajSteps*m_pAtomGroup->m_iAtomGes*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*3.0f*sizeof(float)/1024.0f/1024.0f;
4944
if (tf >= 10.0f)
4945
if (!AskYesNo(" This will occupy %.0f MB RAM (once, not for every MSD!). Continue (y/n)? [yes] ",true,tf))
4946
goto _depth;
4947
} else
4948
{
4949
tf = m_iResolution*g_iGesVirtAtomCount*12.0f*sizeof(double)/1024.0f/1024.0f;
4950
if (tf >= 10.0f)
4951
if (!AskYesNo(" This will occupy %.0f MB RAM (once, not for every MSD!). Continue (y/n)? [yes] ",true,tf))
4952
goto _depth;
4953
}
4954
}*/
4955
/* if (m_iResolution > g_iMaxMSDDepth)
4956
g_iMaxMSDDepth = m_iReolution;*/
4957
4958
ti = m_iResolution / 1000;
4959
if (ti < 1)
4960
ti = 1;
4961
m_iStride = AskUnsignedInteger(" Take every n-th step for the time axis of the MSD: [%d] ",ti,ti);
4962
m_iStride2 = AskUnsignedInteger(" Shift correlation window n time steps at once: [%d] ",m_iStride,m_iStride);
4963
4964
if (g_bAdvanced2)
4965
{
4966
m_bSplit = AskYesNo(" Decompose this MSD into contributions from each individual molecule (y/n)? [no] ",false);
4967
if (AskYesNo(" Take into account only certain dimensions for displacement (y/n)? [no] ",false))
4968
{
4969
m_bTakeX = AskYesNo(" Take into account contributions along X axis (y/n)? [yes] ",true);
4970
m_bTakeY = AskYesNo(" Take into account contributions along X axis (y/n)? [yes] ",true);
4971
m_bTakeZ = AskYesNo(" Take into account contributions along X axis (y/n)? [yes] ",true);
4972
} else
4973
{
4974
m_bTakeX = true;
4975
m_bTakeY = true;
4976
m_bTakeZ = true;
4977
}
4978
} else
4979
{
4980
m_bSplit = false;
4981
m_bTakeX = true;
4982
m_bTakeY = true;
4983
m_bTakeZ = true;
4984
}
4985
4986
BuildName();
4987
BTOUT;
4988
}
4989
4990
4991
void CMSD::BuildName()
4992
{
4993
BTIN;
4994
char tmp[256];
4995
4996
sprintf(tmp,"%s_%s",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,m_pAtomGroup->m_sName);
4997
4998
if ((!m_bTakeX) || (!m_bTakeY) || (!m_bTakeZ))
4999
{
5000
strcat(tmp,"_");
5001
if (m_bTakeX)
5002
strcat(tmp,"X");
5003
if (m_bTakeY)
5004
strcat(tmp,"Y");
5005
if (m_bTakeZ)
5006
strcat(tmp,"Z");
5007
}
5008
5009
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
5010
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5011
5012
strcpy(m_sName,tmp);
5013
BTOUT;
5014
}
5015
5016
5017
void CVHDF::CorrectCount()
5018
{
5019
int x, y;
5020
5021
for (y=0;y<m_iResolution;y++)
5022
for (x=0;x<m_iDepth/m_iStride;x++)
5023
if (m_pCount[x] != 0)
5024
m_pVHDF->m_pBin[y*m_iDepth/m_iStride+x] /= m_pCount[x];
5025
}
5026
5027
5028
void CConditionSubGroup::PrintData()
5029
{
5030
int z;
5031
double d;
5032
5033
mprintf(GREEN,"\n*** Data for %d. set of conditions ***\n\n",m_iNumber+1);
5034
mprintf(" %.0f of %.0f molecules passed this set of conditions (%.4f percent).\n",m_fPassed,m_fTotal,ZeroDivide(m_fPassed,m_fTotal)*100.0f);
5035
d = 1.0;
5036
for (z=0;z<m_oaConditions.GetSize();z++)
5037
{
5038
mprintf(" - Condition %d: %.0f of %.0f molecules passed (%.4f percent).\n",z+1,((CNbSearch*)m_oaConditions[z])->m_fMoleculesPassed,((CNbSearch*)m_oaConditions[z])->m_fMoleculesTotal,ZeroDivide(((CNbSearch*)m_oaConditions[z])->m_fMoleculesPassed,((CNbSearch*)m_oaConditions[z])->m_fMoleculesTotal)*100.0);
5039
d *= ZeroDivide(((CNbSearch*)m_oaConditions[z])->m_fMoleculesPassed,((CNbSearch*)m_oaConditions[z])->m_fMoleculesTotal);
5040
}
5041
mprintf("\n");
5042
if (m_oaConditions.GetSize() > 1)
5043
{
5044
mprintf(" The product of the condition probabilities is %.4f percent.\n",d*100.0);
5045
mprintf(" If the conditions would be uncorrelated, this would be also the probability for the set.\n");
5046
mprintf(" Therefore, the conditions are %s correlated for %.4f percent.\n\n",(d<ZeroDivide(m_fPassed,m_fTotal))?"positively":"negatively",(d<ZeroDivide(m_fPassed,m_fTotal))?(ZeroDivide(ZeroDivide(m_fPassed,m_fTotal),d)-1.0)*100.0:(ZeroDivide(d,ZeroDivide(m_fPassed,m_fTotal))-1.0)*100.0);
5047
}
5048
5049
for (z=0;z<m_oaConditions.GetSize();z++)
5050
((CNbSearch*)m_oaConditions[z])->PrintTable();
5051
}
5052
5053
5054
void CConditionSubGroup::PrintData(FILE *a)
5055
{
5056
int z;
5057
5058
mfprintf(a,"\n*** Data for %d. set of conditions ***\n\n",m_iNumber+1);
5059
mfprintf(a," %.0f of %.0f molecules passed this set of conditions (%.4f percent).\n",m_fPassed,m_fTotal,ZeroDivide(m_fPassed,m_fTotal)*100.0f);
5060
for (z=0;z<m_oaConditions.GetSize();z++)
5061
((CNbSearch*)m_oaConditions[z])->PrintTable(a);
5062
}
5063
5064
5065
void CConditionSubGroup::PrintSingle(int om)
5066
{
5067
int z;
5068
5069
for (z=0;z<m_oaConditions.GetSize();z++)
5070
((CNbSearch*)m_oaConditions[z])->PrintSingle(om);
5071
}
5072
5073
5074
void CConditionGroup::PrintSingle(int om)
5075
{
5076
int z;
5077
5078
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
5079
((CConditionSubGroup*)m_oaConditionSubGroups[z])->PrintSingle(om);
5080
}
5081
5082
5083
void CConditionGroup::PrintTable()
5084
{
5085
int z, z2;
5086
double tf1, tf2, tf3;
5087
5088
mprintf(WHITE,"*** Condition Table ***\n\n");
5089
mprintf(" The rows indicate how many subconditions of condition 1 are fulfilled.\n");
5090
mprintf(" The columns indicate how many subconditions of condition 2 are fulfilled.\n\n");
5091
5092
mprintf(" ");
5093
for (z=0;z<((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1;z++)
5094
mprintf("| %4d ",z);
5095
mprintf("\n");
5096
mprintf("-----");
5097
for (z=0;z<((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1;z++)
5098
mprintf("|---------",z);
5099
mprintf("\n");
5100
tf1 = 0;
5101
tf2 = 0;
5102
tf3 = 0;
5103
for (z=0;z<((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1;z++)
5104
{
5105
mprintf(" %3d ",z);
5106
for (z2=0;z2<((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1;z2++)
5107
{
5108
if ((z > 0) && (z2 == 0))
5109
tf1 += m_pTable[z*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+z2];
5110
if ((z == 0) && (z2 > 0))
5111
tf2 += m_pTable[z*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+z2];
5112
if ((z > 0) && (z2 > 0))
5113
tf3 += m_pTable[z*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+z2];
5114
mprintf("| %7.3f ",m_pTable[z*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+z2]/m_fTableGes*100.0);
5115
}
5116
mprintf("\n");
5117
}
5118
mprintf("\n");
5119
mprintf(" A RM/OM pair fulfills no condition: %7.3f percent of the time.\n",m_pTable[0]/m_fTableGes*100.0);
5120
mprintf(" A RM/OM pair fulfills only condition 1: %7.3f percent of the time.\n",tf1/m_fTableGes*100.0);
5121
mprintf(" A RM/OM pair fulfills only condition 2: %7.3f percent of the time.\n",tf2/m_fTableGes*100.0);
5122
mprintf(" A RM/OM pair fulfills both conditions: %7.3f percent of the time.\n",tf3/m_fTableGes*100.0);
5123
mprintf(" Total: %7.3f percent of the time.\n",100.0);
5124
mprintf("\n");
5125
mprintf(WHITE,"*** Condition Table End ***\n\n");
5126
}
5127
5128
5129
void CObservation::ListCDFObservations(int z)
5130
{
5131
int z2, ti, ti2, ti3;
5132
CxIntArray tempwa;
5133
5134
switch(g_iObsChannel[z])
5135
{
5136
case 0: // RDF
5137
if (m_bOthers)
5138
{
5139
if (m_bSecondShowMol && (z == 1))
5140
m_pRDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol2])->m_laSingleMolIndex[0]],&tempwa);
5141
else m_pRDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex[0]],&tempwa);
5142
} else m_pRDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],&tempwa);
5143
for (z2=0;z2<tempwa.GetSize()/2;z2++)
5144
{
5145
ti = tempwa[z2*2];
5146
ti2 = tempwa[z2*2+1];
5147
mprintf(" * %2d.) Distance %s%d (%s) <--> %s%d (%s)\n",z2+1,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5148
}
5149
break;
5150
5151
case 1: // ADF
5152
if (m_bOthers)
5153
{
5154
if (m_bSecondShowMol && (z == 1))
5155
m_pADF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol2])->m_laSingleMolIndex[0]],&tempwa);
5156
else m_pADF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex[0]],&tempwa);
5157
} else m_pADF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],&tempwa);
5158
for (z2=0;z2<tempwa.GetSize()/6;z2++)
5159
{
5160
mprintf(" * %2d.) Angle ",z2+1);
5161
if (m_pADF[z]->m_bOrtho[0])
5162
{
5163
ti = tempwa[z2*6];
5164
ti2 = tempwa[z2*6+1];
5165
ti3 = tempwa[z2*6+2];
5166
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)] to ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5167
} else
5168
{
5169
ti = tempwa[z2*6];
5170
ti2 = tempwa[z2*6+1];
5171
mprintf("[%s%d (%s) --> %s%d (%s)] to ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5172
}
5173
if (m_pADF[z]->m_bOrtho[1])
5174
{
5175
ti = tempwa[z2*6+3];
5176
ti2 = tempwa[z2*6+4];
5177
ti3 = tempwa[z2*6+5];
5178
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)]\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5179
} else
5180
{
5181
ti = tempwa[z2*6+3];
5182
ti2 = tempwa[z2*6+4];
5183
mprintf("[%s%d (%s) --> %s%d (%s)]\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5184
}
5185
}
5186
break;
5187
5188
case 2: // DDF
5189
if (m_bOthers)
5190
{
5191
if (m_bSecondShowMol && (z == 1))
5192
m_pDDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol2])->m_laSingleMolIndex[0]],&tempwa);
5193
else m_pDDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex[0]],&tempwa);
5194
} else m_pDDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],&tempwa);
5195
for (z2=0;z2<tempwa.GetSize()/9;z2++)
5196
{
5197
mprintf(" * %2d.) Dihedral Angle ",z2+1);
5198
if (m_pDDF[z]->m_bOrtho[0])
5199
{
5200
ti = tempwa[z2*9];
5201
ti2 = tempwa[z2*9+1];
5202
ti3 = tempwa[z2*9+2];
5203
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5204
} else
5205
{
5206
ti = tempwa[z2*9];
5207
ti2 = tempwa[z2*9+1];
5208
mprintf("[%s%d (%s) --> %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5209
}
5210
if (m_pDDF[z]->m_bOrtho[1])
5211
{
5212
ti = tempwa[z2*9+3];
5213
ti2 = tempwa[z2*9+4];
5214
ti3 = tempwa[z2*9+5];
5215
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5216
} else
5217
{
5218
ti = tempwa[z2*9+3];
5219
ti2 = tempwa[z2*9+4];
5220
mprintf("[%s%d (%s) --> %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5221
}
5222
if (m_pDDF[z]->m_bOrtho[2])
5223
{
5224
ti = tempwa[z2*9+6];
5225
ti2 = tempwa[z2*9+7];
5226
ti3 = tempwa[z2*9+8];
5227
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)]\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5228
} else
5229
{
5230
ti = tempwa[z2*9+6];
5231
ti2 = tempwa[z2*9+7];
5232
mprintf("[%s%d (%s) --> %s%d (%s)]\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5233
}
5234
}
5235
break;
5236
5237
case 3:
5238
eprintf("(not implemented)\n");
5239
break;
5240
5241
case 4:
5242
eprintf("(not implemented)\n");
5243
break;
5244
5245
case 5: // PlDF
5246
if (m_bOthers)
5247
{
5248
if (m_bSecondShowMol && (z == 1))
5249
m_pPlDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol2])->m_laSingleMolIndex[0]],&tempwa);
5250
else m_pPlDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex[0]],&tempwa);
5251
} else m_pPlDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],&tempwa);
5252
for (z2=0;z2<tempwa.GetSize()/4;z2++)
5253
{
5254
mprintf(" * %2d.) Distance from Plane ",z2+1);
5255
if (m_pPlDF[z]->m_bNormal)
5256
{
5257
ti = tempwa[z2*4];
5258
ti2 = tempwa[z2*4+1];
5259
mprintf("[%s%d (%s) --> %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5260
} else
5261
{
5262
ti = tempwa[z2*4];
5263
ti2 = tempwa[z2*4+1];
5264
ti3 = tempwa[z2*4+2];
5265
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5266
}
5267
ti = tempwa[z2*4+3];
5268
mprintf("%s%d (%s)\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName);
5269
}
5270
break;
5271
5272
case 6: // LiDF
5273
if (m_bOthers)
5274
{
5275
if (m_bSecondShowMol && (z == 1))
5276
m_pLiDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol2])->m_laSingleMolIndex[0]],&tempwa);
5277
else m_pLiDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex[0]],&tempwa);
5278
} else m_pLiDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],&tempwa);
5279
for (z2=0;z2<tempwa.GetSize()/4;z2++)
5280
{
5281
mprintf(" * %2d.) Distance from Plane ",z2+1);
5282
if (m_pLiDF[z]->m_bNormal)
5283
{
5284
ti = tempwa[z2*4];
5285
ti2 = tempwa[z2*4+1];
5286
ti3 = tempwa[z2*4+2];
5287
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5288
} else
5289
{
5290
ti = tempwa[z2*4];
5291
ti2 = tempwa[z2*4+1];
5292
mprintf("[%s%d (%s) --> %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5293
}
5294
ti = tempwa[z2*4+3];
5295
mprintf("%s%d (%s)\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName);
5296
}
5297
break;
5298
}
5299
}
5300
5301
5302
void CSDF::CreateCutPlane()
5303
{
5304
int x, y;
5305
CxVector3 vec;
5306
5307
try { m_pCutPlane = new C2DF(); } catch(...) { m_pCutPlane = NULL; }
5308
if (m_pCutPlane == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5309
5310
m_pCutPlane->m_fMinVal[0] = -m_fRadius;
5311
m_pCutPlane->m_fMinVal[1] = -m_fRadius;
5312
m_pCutPlane->m_fMaxVal[0] = m_fRadius;
5313
m_pCutPlane->m_fMaxVal[1] = m_fRadius;
5314
m_pCutPlane->m_iRes[0] = m_iCutPlaneResolution;
5315
m_pCutPlane->m_iRes[1] = m_iCutPlaneResolution;
5316
m_pCutPlane->SetLabelX("X [pm]");
5317
m_pCutPlane->SetLabelY("Y [pm]");
5318
m_pCutPlane->Create();
5319
5320
vec[2] = 0;
5321
for (y=0;y<m_iCutPlaneResolution;y++)
5322
{
5323
vec[1] = (float)(((y+0.5)/m_pCutPlane->m_iRes[1])*(m_pCutPlane->m_fMaxVal[1]-m_pCutPlane->m_fMinVal[1])+m_pCutPlane->m_fMinVal[1]);
5324
for (x=0;x<m_iCutPlaneResolution;x++)
5325
{
5326
vec[0] = (float)(((x+0.5)/m_pCutPlane->m_iRes[0])*(m_pCutPlane->m_fMaxVal[0]-m_pCutPlane->m_fMinVal[0])+m_pCutPlane->m_fMinVal[0]);
5327
m_pCutPlane->AddToBin(x,y,m_pSDF->GetValue(vec));
5328
}
5329
}
5330
if (m_bCutPlaneShowAtoms)
5331
{
5332
m_pCutPlane->AddCircle(0,0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_fRadius*0.75,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorR/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorG/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorB/255.0);
5333
m_pCutPlane->AddCircle(m_fAtom2PosX / m_fPosCounter,0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_fRadius*0.75,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorR/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorG/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorB/255.0);
5334
m_pCutPlane->AddCircle(m_fAtom3PosX / m_fPosCounter,m_fAtom3PosY / m_fPosCounter,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_pElement->m_fRadius*0.75,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_pElement->m_iColorR/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_pElement->m_iColorG/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_pElement->m_iColorB/255.0);
5335
}
5336
}
5337
5338
5339
void CConditionGroup::Reset()
5340
{
5341
int z;
5342
5343
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
5344
((CConditionSubGroup*)m_oaConditionSubGroups[z])->Reset();
5345
5346
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5347
m_iPassCounter[z] = 0;
5348
}
5349
5350
5351
void CConditionSubGroup::Reset()
5352
{
5353
int z;
5354
5355
for (z=0;z<m_oaConditions.GetSize();z++)
5356
((CNbSearch*)m_oaConditions[z])->Reset();
5357
}
5358
5359
5360
void CRDF::CopyFrom(CRDF *p)
5361
{
5362
int z;
5363
CAtomGroup *ag;
5364
5365
m_bAdaptive = p->m_bAdaptive;
5366
m_bRadialCorrect = p->m_bRadialCorrect;
5367
m_bSelf = p->m_bSelf;
5368
m_fMinDist = p->m_fMinDist;
5369
m_fMaxDist = p->m_fMaxDist;
5370
m_iCombinations = p->m_iCombinations;
5371
m_iHistogramRes = p->m_iHistogramRes;
5372
m_iRefAtomGes = p->m_iRefAtomGes;
5373
m_iRefOrSec[0] = p->m_iRefOrSec[0];
5374
m_iRefOrSec[1] = p->m_iRefOrSec[1];
5375
m_iResolution = p->m_iResolution;
5376
m_iShowAtomGes = p->m_iShowAtomGes;
5377
m_iShowMol = p->m_iShowMol;
5378
5379
if (p->m_sName != NULL)
5380
{
5381
try { m_sName = new char[strlen(p->m_sName)+1]; } catch(...) { m_sName = NULL; }
5382
if (m_sName == NULL) NewException((double)(strlen(p->m_sName)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5383
5384
strcpy(m_sName,p->m_sName);
5385
} else m_sName = NULL;
5386
5387
if (p->m_sShortName != NULL)
5388
{
5389
try { m_sShortName = new char[strlen(p->m_sShortName)+1]; } catch(...) { m_sShortName = NULL; }
5390
if (m_sShortName == NULL) NewException((double)(strlen(p->m_sShortName)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5391
5392
strcpy(m_sShortName,p->m_sShortName);
5393
} else m_sShortName = NULL;
5394
5395
if (p->m_baDataEnabled != NULL)
5396
{
5397
try { m_baDataEnabled = new CxByteArray[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_baDataEnabled = NULL; }
5398
if (m_baDataEnabled == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5399
5400
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5401
m_baDataEnabled[z].CopyFrom(&p->m_baDataEnabled[z]);
5402
}
5403
5404
if (p->m_faData != NULL)
5405
{
5406
try { m_faData = new CxDoubleArray[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_faData = NULL; }
5407
if (m_faData == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5408
5409
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5410
m_faData[z].CopyFrom(&p->m_faData[z]);
5411
}
5412
5413
for (z=0;z<p->m_oaVectors.GetSize();z++)
5414
{
5415
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
5416
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5417
5418
ag->CopyFrom((CAtomGroup*)p->m_oaVectors[z]);
5419
m_oaVectors.Add(ag);
5420
}
5421
5422
m_faMinMaxDist.CopyFrom(&p->m_faMinMaxDist);
5423
5424
if (p->m_pRDF != NULL)
5425
{
5426
try { m_pRDF = new CDF(); } catch(...) { m_pRDF = NULL; }
5427
if (m_pRDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5428
5429
m_pRDF->CopyFrom(p->m_pRDF);
5430
}
5431
}
5432
5433
5434
void CADF::CopyFrom(CADF *p)
5435
{
5436
int z, z2;
5437
CAtomGroup *ag;
5438
5439
m_bCosine = p->m_bCosine;
5440
m_bFoldAngle = p->m_bFoldAngle;
5441
m_bMirror = p->m_bMirror;
5442
m_bOrtho[0] = p->m_bOrtho[0];
5443
m_bOrtho[1] = p->m_bOrtho[1];
5444
m_iVecType[0] = p->m_iVecType[0];
5445
m_iVecType[1] = p->m_iVecType[1];
5446
m_bSelf = p->m_bSelf;
5447
m_bStat = p->m_bStat;
5448
m_fMinAngle = p->m_fMinAngle;
5449
m_fMaxAngle = p->m_fMaxAngle;
5450
m_iCombinations = p->m_iCombinations;
5451
m_iHistogramRes = p->m_iHistogramRes;
5452
for (z=0;z<2;z++)
5453
for (z2=0;z2<3;z2++)
5454
m_iRefOrSec[z][z2] = p->m_iRefOrSec[z][z2];
5455
m_iResolution = p->m_iResolution;
5456
m_iShowMol = p->m_iShowMol;
5457
5458
if (p->m_sName != NULL)
5459
{
5460
try { m_sName = new char[strlen(p->m_sName)+1]; } catch(...) { m_sName = NULL; }
5461
if (m_sName == NULL) NewException((double)(strlen(p->m_sName)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5462
5463
strcpy(m_sName,p->m_sName);
5464
} else m_sName = NULL;
5465
5466
if (p->m_sShortName != NULL)
5467
{
5468
try { m_sShortName = new char[strlen(p->m_sShortName)+1]; } catch(...) { m_sShortName = NULL; }
5469
if (m_sShortName == NULL) NewException((double)(strlen(p->m_sShortName)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5470
5471
strcpy(m_sShortName,p->m_sShortName);
5472
} else m_sShortName = NULL;
5473
5474
if (p->m_baDataEnabled != NULL)
5475
{
5476
try { m_baDataEnabled = new CxByteArray[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_baDataEnabled = NULL; }
5477
if (m_baDataEnabled == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5478
5479
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5480
m_baDataEnabled[z].CopyFrom(&p->m_baDataEnabled[z]);
5481
}
5482
5483
if (p->m_faData != NULL)
5484
{
5485
try { m_faData = new CxDoubleArray[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_faData = NULL; }
5486
if (m_faData == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5487
5488
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5489
m_faData[z].CopyFrom(&p->m_faData[z]);
5490
}
5491
5492
for (z=0;z<p->m_oaVectors.GetSize();z++)
5493
{
5494
if (p->m_oaVectors[z] != NULL)
5495
{
5496
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
5497
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5498
5499
ag->CopyFrom((CAtomGroup*)p->m_oaVectors[z]);
5500
m_oaVectors.Add(ag);
5501
} else m_oaVectors.Add(NULL);
5502
}
5503
5504
m_faMinMaxAngle.CopyFrom(&p->m_faMinMaxAngle);
5505
5506
if (p->m_pADF != NULL)
5507
{
5508
try { m_pADF = new CDF(); } catch(...) { m_pADF = NULL; }
5509
if (m_pADF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5510
5511
m_pADF->CopyFrom(p->m_pADF);
5512
}
5513
}
5514
5515
5516
void CConditionSubGroup::CopyFrom(CConditionSubGroup *p)
5517
{
5518
int z;
5519
CNbSearch *nb;
5520
5521
m_fPassed = p->m_fPassed;
5522
m_fTotal = p->m_fTotal;
5523
m_iCombinations = p->m_iCombinations;
5524
m_iNumber = p->m_iNumber;
5525
m_iShowMol = p->m_iShowMol;
5526
if (p->m_bTempPassed != NULL)
5527
{
5528
try { m_bTempPassed = new bool[g_iGesVirtAtomCount]; } catch(...) { m_bTempPassed = NULL; }
5529
if (m_bTempPassed == NULL) NewException((double)g_iGesVirtAtomCount*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5530
5531
memcpy(m_bTempPassed,p->m_bTempPassed,sizeof(bool)*g_iGesVirtAtomCount);
5532
}
5533
for (z=0;z<p->m_oaConditions.GetSize();z++)
5534
{
5535
try { nb = new CNbSearch(); } catch(...) { nb = NULL; }
5536
if (nb == NULL) NewException((double)sizeof(CNbSearch),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5537
5538
nb->CopyFrom((CNbSearch*)p->m_oaConditions[z]);
5539
m_oaConditions.Add(nb);
5540
}
5541
}
5542
5543
5544
void CConditionGroup::CopyFrom(CConditionGroup *p)
5545
{
5546
int z;
5547
CConditionSubGroup *sg;
5548
5549
m_bInactive = p->m_bInactive;
5550
m_iShowMol = p->m_iShowMol;
5551
m_iRefMol = p->m_iRefMol;
5552
m_iHistoGes = p->m_iHistoGes;
5553
m_bAnyPassed = p->m_bAnyPassed;
5554
m_fTableGes = p->m_fTableGes;
5555
m_fPassed = p->m_fPassed;
5556
m_fTotal = p->m_fTotal;
5557
m_bInvertCondition = p->m_bInvertCondition;
5558
5559
if (p->m_bAlwaysTrue != NULL)
5560
{
5561
try { m_bAlwaysTrue = new bool[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_bAlwaysTrue = NULL; }
5562
if (m_bAlwaysTrue == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5563
5564
memcpy(m_bAlwaysTrue,p->m_bAlwaysTrue,sizeof(bool)*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize());
5565
}
5566
if (p->m_iPassCounter != NULL)
5567
{
5568
try { m_iPassCounter = new long[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iPassCounter = NULL; }
5569
if (m_iPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5570
5571
memcpy(m_iPassCounter,p->m_iPassCounter,sizeof(long)*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize());
5572
}
5573
if (p->m_iOMPassCounter != NULL)
5574
{
5575
try { m_iOMPassCounter = new long[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iOMPassCounter = NULL; }
5576
if (m_iOMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5577
5578
memcpy(m_iOMPassCounter,p->m_iOMPassCounter,sizeof(long)*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize());
5579
}
5580
if (p->m_iRMPassCounter != NULL)
5581
{
5582
try { m_iRMPassCounter = new long[((CMolecule*)g_oaMolecules[m_iRefMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iRMPassCounter = NULL; }
5583
if (m_iRMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iRefMol])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5584
5585
memcpy(m_iRMPassCounter,p->m_iRMPassCounter,sizeof(long)*((CMolecule*)g_oaMolecules[m_iRefMol])->m_laSingleMolIndex.GetSize());
5586
}
5587
for (z=0;z<p->m_oaConditionSubGroups.GetSize();z++)
5588
{
5589
try { sg = new CConditionSubGroup(); } catch(...) { sg = NULL; }
5590
if (sg == NULL) NewException((double)sizeof(CConditionSubGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5591
5592
sg->CopyFrom((CConditionSubGroup*)p->m_oaConditionSubGroups[z]);
5593
m_oaConditionSubGroups.Add(sg);
5594
}
5595
5596
if (p->m_pTable != NULL)
5597
{
5598
try { m_pTable = new double[(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)]; } catch(...) { m_pTable = NULL; }
5599
if (m_pTable == NULL) NewException((double)(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5600
5601
memcpy(m_pTable,p->m_pTable,sizeof(double)*(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1));
5602
}
5603
5604
if (p->m_pHistogram != NULL)
5605
{
5606
try { m_pHistogram = new unsigned long[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1]; } catch(...) { m_pHistogram = NULL; }
5607
if (m_pHistogram == NULL) NewException((double)(((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1)*sizeof(unsigned long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5608
5609
memcpy(m_pHistogram,p->m_pHistogram,sizeof(unsigned long)*(((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1));
5610
}
5611
}
5612
5613
5614
void CConditionGroup::Parse_OnlyValues()
5615
{
5616
BTIN;
5617
int z;
5618
5619
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
5620
{
5621
mprintf(YELLOW,">>> %d. set of conditions >>>\n\n",z+1);
5622
((CConditionSubGroup*)m_oaConditionSubGroups[z])->Parse_OnlyValues();
5623
mprintf(YELLOW,"<<< End of %d. set of conditions <<<\n\n",z+1);
5624
}
5625
}
5626
5627
5628
void CConditionSubGroup::Parse_OnlyValues()
5629
{
5630
BTIN;
5631
int z;
5632
5633
for (z=0;z<m_oaConditions.GetSize();z++)
5634
{
5635
mprintf(YELLOW," >>> %d. condition within this set >>>\n\n",z+1);
5636
((CNbSearch*)m_oaConditions[z])->Parse_OnlyValues();
5637
mprintf(YELLOW,"\n <<< End of %d. condition <<<\n\n",z+1);
5638
}
5639
BTOUT;
5640
}
5641
5642
5643
void CConditionGroup::CopyResults(CConditionGroup *p)
5644
{
5645
int z;
5646
5647
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
5648
((CConditionSubGroup*)m_oaConditionSubGroups[z])->CopyResults((CConditionSubGroup*)p->m_oaConditionSubGroups[z]);
5649
}
5650
5651
5652
void CConditionSubGroup::CopyResults(CConditionSubGroup *p)
5653
{
5654
int z;
5655
5656
for (z=0;z<m_oaConditions.GetSize();z++)
5657
((CNbSearch*)m_oaConditions[z])->CopyResults((CNbSearch*)p->m_oaConditions[z]);
5658
}
5659
5660
5661
void CConditionGroup::ReScan(CSingleMolecule *rm)
5662
{
5663
BXIN;
5664
int z, z2, t1, t2, i;
5665
5666
if (m_bInactive)
5667
return;
5668
5669
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
5670
((CConditionSubGroup*)m_oaConditionSubGroups[z])->ReScan(rm);
5671
5672
if (m_oaConditionSubGroups.GetSize() == 2)
5673
{
5674
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5675
{
5676
t1 = 0;
5677
t2 = 0;
5678
for (z2=0;z2<((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_oaConditions.GetSize();z2++)
5679
t1 += ((CNbSearch*)((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_oaConditions[z2])->m_iCombPassCount[z];
5680
for (z2=0;z2<((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_oaConditions.GetSize();z2++)
5681
t2 += ((CNbSearch*)((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_oaConditions[z2])->m_iCombPassCount[z];
5682
m_pTable[t1*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+t2]++;
5683
m_fTableGes++;
5684
}
5685
}
5686
5687
i = 0;
5688
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5689
{
5690
m_fTotal++;
5691
if (m_bInvertCondition)
5692
{
5693
for (z2=0;z2<m_oaConditionSubGroups.GetSize();z2++)
5694
if (((CConditionSubGroup*)m_oaConditionSubGroups[z2])->Contains(z))
5695
goto _nopass;
5696
m_fPassed++;
5697
m_iPassCounter[z]++;
5698
m_bAnyPassed = true;
5699
} else
5700
{
5701
for (z2=0;z2<m_oaConditionSubGroups.GetSize();z2++)
5702
if (((CConditionSubGroup*)m_oaConditionSubGroups[z2])->Contains(z))
5703
{
5704
// mprintf("passed[%d]++\n",z);
5705
m_fPassed++;
5706
m_iPassCounter[z]++;
5707
m_bAnyPassed = true;
5708
i++;
5709
goto _nopass;
5710
}
5711
}
5712
_nopass:;
5713
}
5714
m_pHistogram[i]++;
5715
m_iHistoGes++;
5716
5717
BXOUT;
5718
}
5719
5720
5721
void CConditionSubGroup::ReScan(CSingleMolecule *rm)
5722
{
5723
int z, z2;
5724
5725
for (z=0;z<m_oaConditions.GetSize();z++)
5726
((CNbSearch*)m_oaConditions[z])->ReScan(rm);
5727
5728
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5729
{
5730
m_fTotal++;
5731
for (z2=0;z2<m_oaConditions.GetSize();z2++)
5732
if (!((CNbSearch*)m_oaConditions[z2])->m_bPassed[z])
5733
goto _nopass;
5734
m_fPassed++;
5735
_nopass:;
5736
}
5737
}
5738
5739
5740
CNbSearch* CConditionGroup::AddSingleCondition(int rm, int sm, int gridmode)
5741
{
5742
BTIN;
5743
CConditionSubGroup *sg;
5744
int z;
5745
5746
m_iShowMol = sm;
5747
m_iRefMol = rm;
5748
5749
try { m_bAlwaysTrue = new bool[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_bAlwaysTrue = NULL; }
5750
if (m_bAlwaysTrue == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5751
5752
try { m_iPassCounter = new long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iPassCounter = NULL; }
5753
if (m_iPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5754
5755
try { m_iOMPassCounter = new long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iOMPassCounter = NULL; }
5756
if (m_iOMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5757
5758
for (z=0;z<((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize();z++)
5759
{
5760
m_bAlwaysTrue[z] = false;
5761
m_iPassCounter[z] = 0;
5762
m_iOMPassCounter[z] = 0;
5763
}
5764
5765
try { m_iRMPassCounter = new long[((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iRMPassCounter = NULL; }
5766
if (m_iRMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5767
5768
for (z=0;z<((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize();z++)
5769
m_iRMPassCounter[z] = 0;
5770
5771
try { sg = new CConditionSubGroup(); } catch(...) { sg = NULL; }
5772
if (sg == NULL) NewException((double)sizeof(CConditionSubGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5773
5774
sg->m_iShowMol = m_iShowMol;
5775
sg->m_iNumber = m_oaConditionSubGroups.GetSize();
5776
m_oaConditionSubGroups.Add(sg);
5777
5778
m_bInvertCondition = false;
5779
5780
m_iHistoGes = 0;
5781
5782
try { m_pHistogram = new unsigned long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1]; } catch(...) { m_pHistogram = NULL; }
5783
if (m_pHistogram == NULL) NewException((double)(((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1)*sizeof(unsigned long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5784
5785
for (z=0;z<((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1;z++)
5786
m_pHistogram[z] = 0;
5787
5788
BTOUT;
5789
return sg->AddSingleCondition(rm,sm,gridmode);
5790
}
5791
5792
5793
CNbSearch* CConditionSubGroup::AddSingleCondition(int rm, int sm, int gridmode)
5794
{
5795
BTIN;
5796
CNbSearch *n;
5797
5798
m_iCombinations = 0;
5799
5800
try { n = new CNbSearch(); } catch(...) { n = NULL; }
5801
if (n == NULL) NewException((double)sizeof(CNbSearch),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5802
5803
n->m_iNumber = m_oaConditions.GetSize();
5804
m_oaConditions.Add(n);
5805
n->ParseGrid(rm,sm,gridmode);
5806
m_iCombinations += n->m_iCombinationsEnabled;
5807
5808
try { m_bTempPassed = new bool[g_iGesVirtAtomCount]; } catch(...) { m_bTempPassed = NULL; }
5809
if (m_bTempPassed == NULL) NewException((double)g_iGesVirtAtomCount*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5810
5811
BTOUT;
5812
return n;
5813
}
5814
5815
5816
void CObservation::BuildTimeDiff(CDF *df, bool ddf)
5817
{
5818
int z, z2, z3, z4, i;
5819
CxFloatArray *ptfa;
5820
double tf, tfa, tfsq, tfs, tf0;
5821
char buf[256];
5822
5823
try { df->m_pTimeDiff = new CDF(); } catch(...) { df->m_pTimeDiff = NULL; }
5824
if (df->m_pTimeDiff == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5825
5826
df->m_pTimeDiff->m_iResolution = m_iTimeDiffDepth;
5827
df->m_pTimeDiff->m_fMinVal = 0;
5828
df->m_pTimeDiff->m_fMaxVal = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5829
df->m_pTimeDiff->Create();
5830
df->m_pTimeDiff->SetLabelX("Tau [ps]");
5831
sprintf(buf,"Delta ");
5832
strcat(buf,df->m_sLabelX);
5833
df->m_pTimeDiff->SetLabelY(buf);
5834
5835
try { df->m_pTimeDiffAbs = new CDF(); } catch(...) { df->m_pTimeDiffAbs = NULL; }
5836
if (df->m_pTimeDiffAbs == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5837
5838
df->m_pTimeDiffAbs->m_iResolution = m_iTimeDiffDepth;
5839
df->m_pTimeDiffAbs->m_fMinVal = 0;
5840
df->m_pTimeDiffAbs->m_fMaxVal = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5841
df->m_pTimeDiffAbs->Create();
5842
df->m_pTimeDiffAbs->SetLabelX("Tau [ps]");
5843
df->m_pTimeDiffAbs->SetLabelY(buf);
5844
5845
sprintf(buf,"Delta Square ");
5846
strcat(buf,df->m_sLabelX);
5847
5848
try { df->m_pTimeDiffSqr = new CDF(); } catch(...) { df->m_pTimeDiffSqr = NULL; }
5849
if (df->m_pTimeDiffSqr == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5850
5851
df->m_pTimeDiffSqr->m_iResolution = m_iTimeDiffDepth;
5852
df->m_pTimeDiffSqr->m_fMinVal = 0;
5853
df->m_pTimeDiffSqr->m_fMaxVal = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5854
df->m_pTimeDiffSqr->Create();
5855
df->m_pTimeDiffSqr->SetLabelX("Tau [ps]");
5856
df->m_pTimeDiffSqr->SetLabelY(buf);
5857
5858
if (m_b3DTimeDiff)
5859
{
5860
sprintf(buf,"Delta ");
5861
strcat(buf,df->m_sLabelX);
5862
5863
try { df->m_p3DTimeDiff = new C2DF(); } catch(...) { df->m_p3DTimeDiff = NULL; }
5864
if (df->m_p3DTimeDiff == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5865
5866
df->m_p3DTimeDiff->m_iRes[0] = m_iTimeDiffDepth/m_iTimeDiffStride3D;
5867
df->m_p3DTimeDiff->m_iRes[1] = m_iTimeDiffRes3D;
5868
df->m_p3DTimeDiff->m_fMinVal[0] = 0;
5869
df->m_p3DTimeDiff->m_fMaxVal[0] = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5870
df->m_p3DTimeDiff->m_fMinVal[1] = m_fTimeDiffMinVal3D;
5871
df->m_p3DTimeDiff->m_fMaxVal[1] = m_fTimeDiffMaxVal3D;
5872
df->m_p3DTimeDiff->Create();
5873
df->m_p3DTimeDiff->SetLabelX("Tau [ps]");
5874
df->m_p3DTimeDiff->SetLabelY(df->m_sLabelX);
5875
df->m_p3DTimeDiff->SetLabelZ(buf);
5876
5877
try { df->m_p3DTimeDiffAbs = new C2DF(); } catch(...) { df->m_p3DTimeDiffAbs = NULL; }
5878
if (df->m_p3DTimeDiffAbs == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5879
5880
df->m_p3DTimeDiffAbs->m_iRes[0] = m_iTimeDiffDepth/m_iTimeDiffStride3D;
5881
df->m_p3DTimeDiffAbs->m_iRes[1] = m_iTimeDiffRes3D;
5882
df->m_p3DTimeDiffAbs->m_fMinVal[0] = 0;
5883
df->m_p3DTimeDiffAbs->m_fMaxVal[0] = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5884
df->m_p3DTimeDiffAbs->m_fMinVal[1] = m_fTimeDiffMinVal3D;
5885
df->m_p3DTimeDiffAbs->m_fMaxVal[1] = m_fTimeDiffMaxVal3D;
5886
df->m_p3DTimeDiffAbs->Create();
5887
df->m_p3DTimeDiffAbs->SetLabelX("Tau [ps]");
5888
df->m_p3DTimeDiffAbs->SetLabelY(df->m_sLabelX);
5889
df->m_p3DTimeDiffAbs->SetLabelZ(buf);
5890
5891
if (m_iTimeDiffDistSteps != 0)
5892
{
5893
try { df->m_pTimeDiffDistPairs = new C2DF*[m_iTimeDiffDepth/m_iTimeDiffStride3D/m_iTimeDiffDistSteps]; } catch(...) { df->m_pTimeDiffDistPairs = NULL; }
5894
if (df->m_pTimeDiffDistPairs == NULL) NewException((double)m_iTimeDiffDepth/m_iTimeDiffStride3D/m_iTimeDiffDistSteps*sizeof(C2DF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5895
5896
for (z=0;z<m_iTimeDiffDepth/m_iTimeDiffStride3D/m_iTimeDiffDistSteps;z++)
5897
{
5898
try { df->m_pTimeDiffDistPairs[z] = new C2DF(); } catch(...) { df->m_pTimeDiffDistPairs[z] = NULL; }
5899
if (df->m_pTimeDiffDistPairs[z] == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5900
5901
df->m_pTimeDiffDistPairs[z]->m_iRes[0] = m_iTimeDiffDistResX;
5902
df->m_pTimeDiffDistPairs[z]->m_iRes[1] = m_iTimeDiffDistResY;
5903
df->m_pTimeDiffDistPairs[z]->m_fMinVal[0] = m_fTimeDiffDistMinValX;
5904
df->m_pTimeDiffDistPairs[z]->m_fMaxVal[0] = m_fTimeDiffDistMaxValX;
5905
df->m_pTimeDiffDistPairs[z]->m_fMinVal[1] = m_fTimeDiffDistMinValY;
5906
df->m_pTimeDiffDistPairs[z]->m_fMaxVal[1] = m_fTimeDiffDistMaxValY;
5907
df->m_pTimeDiffDistPairs[z]->Create();
5908
df->m_pTimeDiffDistPairs[z]->SetLabelX(df->m_sLabelX);
5909
df->m_pTimeDiffDistPairs[z]->SetLabelY(df->m_sLabelX);
5910
}
5911
}
5912
5913
try { df->m_pTimeDiffDist3DF = new C3DF(); } catch(...) { df->m_pTimeDiffDist3DF = NULL; }
5914
if (df->m_pTimeDiffDist3DF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5915
5916
df->m_pTimeDiffDist3DF->m_iRes[0] = m_iTimeDiffDistResX;
5917
df->m_pTimeDiffDist3DF->m_iRes[1] = m_iTimeDiffDistResY;
5918
df->m_pTimeDiffDist3DF->m_iRes[2] = m_iTimeDiffDepth/m_iTimeDiffStride3D;
5919
df->m_pTimeDiffDist3DF->m_fMinVal[0] = m_fTimeDiffDistMinValX;
5920
df->m_pTimeDiffDist3DF->m_fMaxVal[0] = m_fTimeDiffDistMaxValX;
5921
df->m_pTimeDiffDist3DF->m_fMinVal[1] = m_fTimeDiffDistMinValY;
5922
df->m_pTimeDiffDist3DF->m_fMaxVal[1] = m_fTimeDiffDistMaxValY;
5923
df->m_pTimeDiffDist3DF->m_fMinVal[2] = 0;
5924
df->m_pTimeDiffDist3DF->m_fMaxVal[2] = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5925
df->m_pTimeDiffDist3DF->Create();
5926
df->m_pTimeDiffDist3DF->SetLabelX(df->m_sLabelX);
5927
df->m_pTimeDiffDist3DF->SetLabelY(df->m_sLabelX);
5928
5929
sprintf(buf,"Delta Square ");
5930
strcat(buf,df->m_sLabelX);
5931
5932
try { df->m_p3DTimeDiffSqr = new C2DF(); } catch(...) { df->m_p3DTimeDiffSqr = NULL; }
5933
if (df->m_p3DTimeDiffSqr == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5934
5935
df->m_p3DTimeDiffSqr->m_iRes[0] = m_iTimeDiffDepth/m_iTimeDiffStride3D;
5936
df->m_p3DTimeDiffSqr->m_iRes[1] = m_iTimeDiffRes3D;
5937
df->m_p3DTimeDiffSqr->m_fMinVal[0] = 0;
5938
df->m_p3DTimeDiffSqr->m_fMaxVal[0] = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5939
df->m_p3DTimeDiffSqr->m_fMinVal[1] = m_fTimeDiffMinVal3D;
5940
df->m_p3DTimeDiffSqr->m_fMaxVal[1] = m_fTimeDiffMaxVal3D;
5941
df->m_p3DTimeDiffSqr->Create();
5942
df->m_p3DTimeDiffSqr->SetLabelX("Tau [ps]");
5943
df->m_p3DTimeDiffSqr->SetLabelY(df->m_sLabelX);
5944
df->m_p3DTimeDiffSqr->SetLabelZ(buf);
5945
5946
try { df->m_p3DTimeDiffT = new C2DF(); } catch(...) { df->m_p3DTimeDiffT = NULL; }
5947
if (df->m_p3DTimeDiffT == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5948
5949
df->m_p3DTimeDiffT->m_iRes[0] = m_iTimeDiffDepth/m_iTimeDiffStride3D;
5950
df->m_p3DTimeDiffT->m_iRes[1] = m_iTimeDiffRes3D;
5951
df->m_p3DTimeDiffT->m_fMinVal[0] = 0;
5952
df->m_p3DTimeDiffT->m_fMaxVal[0] = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5953
df->m_p3DTimeDiffT->m_fMinVal[1] = m_fTimeDiffMinVal3D;
5954
df->m_p3DTimeDiffT->m_fMaxVal[1] = m_fTimeDiffMaxVal3D;
5955
df->m_p3DTimeDiffT->Create();
5956
}
5957
5958
for (z2=0;z2<df->m_oaTimeDiffBuf.GetSize();z2++)
5959
{
5960
mprintf(" %4d/%d 2D [",z2+1,df->m_oaTimeDiffBuf.GetSize());
5961
ptfa = (CxFloatArray*)df->m_oaTimeDiffBuf[z2];
5962
tfs = m_iTimeDiffDepth/50.0;
5963
for (z3=0;z3<m_iTimeDiffDepth;z3++) // Das ist das Tau
5964
{
5965
if (fmod(z3,tfs) < 1.0)
5966
mprintf(WHITE,"#");
5967
tf = 0;
5968
tfa = 0;
5969
tfsq = 0;
5970
for (z4=0;z4<(int)ptfa->GetSize()-z3-1;z4++) // Das ist der Startpunkt
5971
{
5972
tf0 = (*ptfa)[z3+z4]-(*ptfa)[z4];
5973
if (ddf)
5974
{
5975
if (tf0 > 180.0)
5976
tf0 -= 360.0;
5977
if (tf0 <= -180.0)
5978
tf0 += 360.0;
5979
}
5980
tfa += fabs(tf0);
5981
tf += tf0;
5982
tfsq += tf0 * tf0;
5983
}
5984
df->m_pTimeDiff->AddToBin_Int(z3,tf/(ptfa->GetSize()-z3-1));
5985
df->m_pTimeDiffAbs->AddToBin_Int(z3,tfa/(ptfa->GetSize()-z3-1));
5986
df->m_pTimeDiffSqr->AddToBin_Int(z3,tfsq/(ptfa->GetSize()-z3-1));
5987
5988
df->m_pTimeDiff->m_fBinEntries += ptfa->GetSize()-z3-2;
5989
df->m_pTimeDiffAbs->m_fBinEntries += ptfa->GetSize()-z3-2;
5990
df->m_pTimeDiffSqr->m_fBinEntries += ptfa->GetSize()-z3-2;
5991
}
5992
mprintf("]\n");
5993
if (m_b3DTimeDiff)
5994
{
5995
mprintf(" %4d/%d 3D [",z2+1,df->m_oaTimeDiffBuf.GetSize());
5996
tfs = m_iTimeDiffDepth/50.0;
5997
for (z3=0;z3<m_iTimeDiffDepth;z3+=m_iTimeDiffStride3D) // Das ist das Tau
5998
{
5999
if (fmod(z3,tfs) < 1.0)
6000
mprintf(WHITE,"#");
6001
i = z3/m_iTimeDiffStride3D;
6002
for (z4=0;z4<(int)ptfa->GetSize()-z3-1;z4++) // Das ist der Startpunkt
6003
{
6004
tf0 = (*ptfa)[z3+z4]-(*ptfa)[z4];
6005
if (ddf)
6006
{
6007
if (tf0 > 180.0)
6008
tf0 -= 360.0;
6009
if (tf0 <= -180.0)
6010
tf0 += 360.0;
6011
}
6012
df->m_p3DTimeDiff->AddToBin_IntX(i,(*ptfa)[z4],tf0);
6013
df->m_p3DTimeDiffAbs->AddToBin_IntX(i,(*ptfa)[z4],fabs(tf0));
6014
df->m_p3DTimeDiffSqr->AddToBin_IntX(i,(*ptfa)[z4],tf0*tf0);
6015
df->m_p3DTimeDiffT->AddToBin_IntX(i,(*ptfa)[z4],1.0);
6016
df->m_pTimeDiffDist3DF->AddToBin_IntZ((*ptfa)[z4],(*ptfa)[z3+z4],i);
6017
if (m_iTimeDiffDistSteps != 0)
6018
if ((i % m_iTimeDiffDistSteps) == 0)
6019
df->m_pTimeDiffDistPairs[i/m_iTimeDiffDistSteps]->AddToBin((*ptfa)[z4],(*ptfa)[z3+z4]);
6020
}
6021
}
6022
mprintf("]\n");
6023
}
6024
}
6025
for (z3=0;z3<m_iTimeDiffDepth;z3++) // Das ist das Tau
6026
{
6027
df->m_pTimeDiff->m_pBin[z3] /= df->m_oaTimeDiffBuf.GetSize();
6028
df->m_pTimeDiffAbs->m_pBin[z3] /= df->m_oaTimeDiffBuf.GetSize();
6029
df->m_pTimeDiffSqr->m_pBin[z3] /= df->m_oaTimeDiffBuf.GetSize();
6030
}
6031
if (m_b3DTimeDiff)
6032
{
6033
for (z2=0;z2<df->m_p3DTimeDiff->m_iRes[0]*df->m_p3DTimeDiff->m_iRes[1];z2++)
6034
{
6035
if (df->m_p3DTimeDiffT->m_pBin[z2] != 0)
6036
{
6037
df->m_p3DTimeDiff->m_pBin[z2] /= df->m_p3DTimeDiffT->m_pBin[z2];
6038
df->m_p3DTimeDiffAbs->m_pBin[z2] /= df->m_p3DTimeDiffT->m_pBin[z2];
6039
df->m_p3DTimeDiffSqr->m_pBin[z2] /= df->m_p3DTimeDiffT->m_pBin[z2];
6040
}
6041
}
6042
if (m_iTimeDiffDistSteps != 0)
6043
for (z=0;z<m_iTimeDiffDepth/m_iTimeDiffStride3D/m_iTimeDiffDistSteps;z++)
6044
df->m_pTimeDiffDistPairs[z]->NormalizeBinIntegral(1000000.0);
6045
}
6046
}
6047
6048
6049
void CObservation::WriteTimeDiff(CDF *df, const char *anaup, const char *analow, const char *name, const char *multibuf, bool ddf)
6050
{
6051
char buf[256];
6052
int z, z2;
6053
C3DF *temp3DF;
6054
6055
mprintf(" Creating temporal difference plot...\n");
6056
BuildTimeDiff(df,ddf);
6057
mprintf(" (%.0f bin entries)\n",df->m_pTimeDiff->m_fBinEntries);
6058
sprintf(buf,"%s_timediff_%s%s.csv",analow,name,multibuf);
6059
mprintf(" Saving %s temporal difference plot as \"%s\"...\n",anaup,buf);
6060
df->m_pTimeDiff->Write("",buf,"",true);
6061
sprintf(buf,"%s_timediff_%s%s.agr",analow,name,multibuf);
6062
mprintf(" Saving %s temporal difference plot AGR file as \"%s\"...\n",anaup,buf);
6063
df->m_pTimeDiff->WriteAgr("",buf,"",name,false);
6064
6065
sprintf(buf,"%s_timediff_%s%s_abs.csv",analow,name,multibuf);
6066
mprintf(" Saving %s absolute temporal difference plot as \"%s\"...\n",anaup,buf);
6067
df->m_pTimeDiffAbs->Write("",buf,"",true);
6068
sprintf(buf,"%s_timediff_%s%s_abs.agr",analow,name,multibuf);
6069
mprintf(" Saving %s absolute temporal difference plot AGR file as \"%s\"...\n",anaup,buf);
6070
df->m_pTimeDiffAbs->WriteAgr("",buf,"",name,false);
6071
6072
sprintf(buf,"%s_timediff_%s%s_sqr.csv",analow,name,multibuf);
6073
mprintf(" Saving %s squared temporal difference plot as \"%s\"...\n",anaup,buf);
6074
df->m_pTimeDiffSqr->Write("",buf,"",true);
6075
sprintf(buf,"%s_timediff_%s%s_sqr.agr",analow,name,multibuf);
6076
mprintf(" Saving %s squared temporal difference plot AGR file as \"%s\"...\n",anaup,buf);
6077
df->m_pTimeDiffSqr->WriteAgr("",buf,"",name,false);
6078
6079
if (m_b3DTimeDiff)
6080
{
6081
mprintf(" Writing temporal 3D difference plot...\n");
6082
mprintf(" (%.0f bin entries)\n",df->m_p3DTimeDiff->m_fBinEntries);
6083
sprintf(buf,"%s_timediff_%s%s_triples.csv",analow,name,multibuf);
6084
mprintf(" Saving %s temporal difference plot triples as \"%s\"...\n",anaup,buf);
6085
df->m_p3DTimeDiff->Write("",buf,"");
6086
sprintf(buf,"%s_timediff_%s%s_matrix.csv",analow,name,multibuf);
6087
mprintf(" Saving %s temporal difference plot matrix as \"%s\"...\n",anaup,buf);
6088
df->m_p3DTimeDiff->WriteCSV("",buf,"");
6089
sprintf(buf,"%s_timediff_%s%s.nb",analow,name,multibuf);
6090
mprintf(" Saving %s temporal difference plot Mathematica Notebook as \"%s\"...\n",anaup,buf);
6091
df->m_p3DTimeDiff->WriteMathematicaNb("",buf,"",false);
6092
sprintf(buf,"%s_timediff_%s%s",analow,name,multibuf);
6093
mprintf(" Saving %s temporal difference plot Gnuplot Input as \"%s.gp\"...\n",anaup,buf);
6094
df->m_p3DTimeDiff->WriteGnuplotInput("",buf,"",false);
6095
6096
sprintf(buf,"%s_timediff_%s%s_triples_abs.csv",analow,name,multibuf);
6097
mprintf(" Saving %s absolute temporal difference plot triples as \"%s\"...\n",anaup,buf);
6098
df->m_p3DTimeDiffAbs->Write("",buf,"");
6099
sprintf(buf,"%s_timediff_%s%s_matrix_abs.csv",analow,name,multibuf);
6100
mprintf(" Saving %s absolute temporal difference plot matrix as \"%s\"...\n",anaup,buf);
6101
df->m_p3DTimeDiffAbs->WriteCSV("",buf,"");
6102
sprintf(buf,"%s_timediff_%s%s_abs.nb",analow,name,multibuf);
6103
mprintf(" Saving %s absolute temporal difference plot Mathematica Notebook as \"%s\"...\n",anaup,buf);
6104
df->m_p3DTimeDiffAbs->WriteMathematicaNb("",buf,"",false);
6105
sprintf(buf,"%s_timediff_%s%s_abs",analow,name,multibuf);
6106
mprintf(" Saving %s absolute temporal difference plot Gnuplot Input as \"%s.gp\"...\n",anaup,buf);
6107
df->m_p3DTimeDiffAbs->WriteGnuplotInput("",buf,"",false);
6108
6109
sprintf(buf,"%s_timediff_%s%s_triples_sqr.csv",analow,name,multibuf);
6110
mprintf(" Saving %s squared temporal difference plot triples as \"%s\"...\n",anaup,buf);
6111
df->m_p3DTimeDiffSqr->Write("",buf,"");
6112
sprintf(buf,"%s_timediff_%s%s_matrix_sqr.csv",analow,name,multibuf);
6113
mprintf(" Saving %s squared temporal difference plot matrix as \"%s\"...\n",anaup,buf);
6114
df->m_p3DTimeDiffSqr->WriteCSV("",buf,"");
6115
sprintf(buf,"%s_timediff_%s%s_sqr.nb",analow,name,multibuf);
6116
mprintf(" Saving %s squared temporal difference plot Mathematica Notebook as \"%s\"...\n",anaup,buf);
6117
df->m_p3DTimeDiffSqr->WriteMathematicaNb("",buf,"",false);
6118
sprintf(buf,"%s_timediff_%s%s_sqr",analow,name,multibuf);
6119
mprintf(" Saving %s squared temporal difference plot Gnuplot Input as \"%s.gp\"...\n",anaup,buf);
6120
df->m_p3DTimeDiffSqr->WriteGnuplotInput("",buf,"",false);
6121
6122
if (m_iTimeDiffDistSteps != 0)
6123
{
6124
for (z=0;z<m_iTimeDiffDepth/m_iTimeDiffStride3D/m_iTimeDiffDistSteps;z++)
6125
{
6126
sprintf(buf,"%s_timediff_beforeafter_%s%s_tau%.3f_triples.csv",analow,name,multibuf,z*m_iTimeDiffStride3D*m_iTimeDiffDistSteps*g_fTimestepLength/1000.0);
6127
mprintf(" Saving %s before/after plot triples as \"%s\"...\n",anaup,buf);
6128
df->m_pTimeDiffDistPairs[z]->Write("",buf,"");
6129
sprintf(buf,"%s_timediff_beforeafter_%s%s_tau%.3f_matrix.csv",analow,name,multibuf,z*m_iTimeDiffStride3D*m_iTimeDiffDistSteps*g_fTimestepLength/1000.0);
6130
mprintf(" Saving %s before/after plot matrix as \"%s\"...\n",anaup,buf);
6131
df->m_pTimeDiffDistPairs[z]->WriteCSV("",buf,"");
6132
sprintf(buf,"%s_timediff_beforeafter_%s%s_tau%.3f.nb",analow,name,multibuf,z*m_iTimeDiffStride3D*m_iTimeDiffDistSteps*g_fTimestepLength/1000.0);
6133
mprintf(" Saving %s before/after plot Mathematica Notebook as \"%s\"...\n",anaup,buf);
6134
df->m_pTimeDiffDistPairs[z]->WriteMathematicaNb("",buf,"",false);
6135
sprintf(buf,"%s_timediff_beforeafter_%s%s_tau%.3f",analow,name,multibuf,z*m_iTimeDiffStride3D*m_iTimeDiffDistSteps*g_fTimestepLength/1000.0);
6136
mprintf(" Saving %s before/after plot Gnuplot Input as \"%s.gp\"...\n",anaup,buf);
6137
df->m_pTimeDiffDistPairs[z]->WriteGnuplotInput("",buf,"",false);
6138
}
6139
}
6140
for (z2=0;z2<=3;z2++)
6141
{
6142
try { temp3DF = new C3DF(); } catch(...) { temp3DF = NULL; }
6143
if (temp3DF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
6144
6145
temp3DF->CopyFrom(df->m_pTimeDiffDist3DF);
6146
if (z2 != 0)
6147
{
6148
temp3DF->Smooth(z2);
6149
sprintf(buf,".s%d%s.plt",z2,multibuf);
6150
} else sprintf(buf,"%s.plt",multibuf);
6151
mprintf(" Saving 3D Plot as \"%s%s\"...\n",name,buf);
6152
temp3DF->WritePLT("",name,buf,false);
6153
6154
if (z2 != 0)
6155
sprintf(buf,".s%d%s.cube",z2,multibuf);
6156
else sprintf(buf,"%s.cube",multibuf);
6157
mprintf(" Saving 3D Plot as \"%s%s\"...\n",name,buf);
6158
temp3DF->WriteCube("",name,buf,false);
6159
}
6160
}
6161
}
6162
6163
6164
void CObservation::CreateTimeDiff(CDF *df, int comb)
6165
{
6166
int z2;
6167
CxFloatArray *ptfa;
6168
6169
if (m_bSelf)
6170
{
6171
for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()*comb;z2++)
6172
{
6173
try { ptfa = new CxFloatArray("CObservation::CreateTimeDiff():ptfa"); } catch(...) { ptfa = NULL; }
6174
if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
6175
6176
if (g_iTrajSteps != -1)
6177
{
6178
ptfa->SetMaxSize((long)(g_iTrajSteps*1.1));
6179
ptfa->SetGrow((long)(g_iTrajSteps*0.1));
6180
} else ptfa->SetGrow(1000);
6181
df->m_oaTimeDiffBuf.Add(ptfa);
6182
}
6183
} else
6184
{
6185
for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*comb;z2++)
6186
{
6187
try { ptfa = new CxFloatArray("CObservation::CreateTimeDiff():ptfa"); } catch(...) { ptfa = NULL; }
6188
if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
6189
6190
if (g_iTrajSteps != -1)
6191
{
6192
ptfa->SetMaxSize((long)(g_iTrajSteps*1.1));
6193
ptfa->SetGrow((long)(g_iTrajSteps*0.1));
6194
} else ptfa->SetGrow(1000);
6195
df->m_oaTimeDiffBuf.Add(ptfa);
6196
}
6197
}
6198
}
6199
6200
6201
void CMSD::WriteSplit(const char *s)
6202
{
6203
FILE *a;
6204
int z, z2, z3;
6205
CAF *af;
6206
6207
a = OpenFileWrite(s,true);
6208
mfprintf(a,"# tau [ps]; Total MSD [pm^2]");
6209
6210
for (z=0;z<m_pAtomGroup->m_oaAtoms.GetSize();z++)
6211
for (z2=0;z2<((CxIntArray*)m_pAtomGroup->m_oaAtoms[z])->GetSize();z2++)
6212
for (z3=0;z3<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z3++)
6213
{
6214
if (m_pAtomGroup->m_baRealAtomType[z] == g_iVirtAtomType)
6215
mfprintf(a,"; Mol. %d #%d",z3+1,((CxIntArray*)m_pAtomGroup->m_oaAtoms[z])->GetAt(z2)+1);
6216
else mfprintf(a,"; Mol. %d %s%d",z3+1,((CAtom*)g_oaAtoms[m_pAtomGroup->m_baRealAtomType[z]])->m_sName,((CxIntArray*)m_pAtomGroup->m_oaAtoms[z])->GetAt(z2)+1);
6217
}
6218
mfprintf(a,"\n");
6219
6220
for (z=0;z<m_pMSD->m_iResolution;z++)
6221
{
6222
mfprintf(a,"%f; %f",m_pMSD->m_fMinVal+z*(m_pMSD->m_fMaxVal-m_pMSD->m_fMinVal)/m_pMSD->m_iResolution,m_pMSD->m_pBin[z]);
6223
6224
for (z2=0;z2<m_pAtomGroup->m_iAtomGes;z2++)
6225
for (z3=0;z3<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z3++)
6226
{
6227
af = m_pSplitMSD[z2*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+z3];
6228
mfprintf(a,"; %f",af->m_pBin[z]);
6229
}
6230
mfprintf(a,"\n");
6231
}
6232
6233
fclose(a);
6234
}
4678
m_pPlProj = NULL;
4679
m_bBinOnlyPassedAtoms = false;
4680
m_bBinOnlyNotPassedAtoms = false;
4681
4682
m_waSaveRefList.SetName("CObservation::m_waSaveRefList");
4683
m_waSaveShowList.SetName("CObservation::m_waSaveShowList");
4684
m_waObsRefList.SetName("CObservation::m_waObsRefList");
4685
m_waObsShowList.SetName("CObservation::m_waObsShowList");
4686
m_waObsShow2List.SetName("CObservation::m_waObsShow2List");
4687
m_waDecompTypeRefOffs.SetName("CObservation::m_waDecompTypeRefOffs");
4688
m_waDecompTypeObsOffs.SetName("CObservation::m_waDecompTypeObsOffs");
4689
m_waDecompTypeRefList.SetName("CObservation::m_waDecompTypeRefList");
4690
m_waDecompTypeObsList.SetName("CObservation::m_waDecompTypeObsList");
4691
m_iaRMRegions.SetName("CObservation::m_iaRMRegions");
4692
m_iaOM1Regions.SetName("CObservation::m_iaOM1Regions");
4693
m_iaOM2Regions.SetName("CObservation::m_iaOM2Regions");
4694
}
4695
4696
4697
CObservation::~CObservation()
4698
{
4699
int z;
4700
4701
if (m_pConditions != NULL)
4702
{
4703
delete m_pConditions;
4704
m_pConditions = NULL;
4705
}
4706
if (m_pMSD != NULL)
4707
{
4708
delete m_pMSD;
4709
m_pMSD = NULL;
4710
}
4711
if (m_pSDF != NULL)
4712
{
4713
delete m_pSDF;
4714
m_pSDF = NULL;
4715
}
4716
if (m_pCDF != NULL)
4717
{
4718
delete m_pCDF;
4719
m_pCDF = NULL;
4720
}
4721
if (m_pVACF != NULL)
4722
{
4723
delete m_pVACF;
4724
m_pVACF = NULL;
4725
}
4726
if (m_pDipACF != NULL)
4727
{
4728
delete m_pDipACF;
4729
m_pDipACF = NULL;
4730
}
4731
4732
if (m_pRDF != NULL)
4733
{
4734
for (z=0;z<g_iCDFChannels;z++)
4735
{
4736
if (m_pRDF[z] != NULL)
4737
{
4738
delete m_pRDF[z];
4739
m_pRDF[z] = NULL;
4740
}
4741
}
4742
delete[] m_pRDF;
4743
m_pRDF = NULL;
4744
}
4745
if (m_pADF != NULL)
4746
{
4747
for (z=0;z<g_iCDFChannels;z++)
4748
{
4749
if (m_pADF[z] != NULL)
4750
{
4751
delete m_pADF[z];
4752
m_pADF[z] = NULL;
4753
}
4754
}
4755
delete[] m_pADF;
4756
m_pADF = NULL;
4757
}
4758
if (m_pDDF != NULL)
4759
{
4760
for (z=0;z<g_iCDFChannels;z++)
4761
{
4762
if (m_pDDF[z] != NULL)
4763
{
4764
delete m_pDDF[z];
4765
m_pDDF[z] = NULL;
4766
}
4767
}
4768
delete[] m_pDDF;
4769
m_pDDF = NULL;
4770
}
4771
if (m_pDipDF != NULL)
4772
{
4773
for (z=0;z<g_iCDFChannels;z++)
4774
{
4775
if (m_pDipDF[z] != NULL)
4776
{
4777
delete m_pDipDF[z];
4778
m_pDipDF[z] = NULL;
4779
}
4780
}
4781
delete[] m_pDipDF;
4782
m_pDipDF = NULL;
4783
}
4784
if (m_pVDF != NULL)
4785
{
4786
for (z=0;z<g_iCDFChannels;z++)
4787
{
4788
if (m_pVDF[z] != NULL)
4789
{
4790
delete m_pVDF[z];
4791
m_pVDF[z] = NULL;
4792
}
4793
}
4794
delete[] m_pVDF;
4795
m_pVDF = NULL;
4796
}
4797
}
4798
4799
4800
void CSingleMolecule::BuildAtomCodes()
4801
{
4802
int z, z2, c1, c2, i;
4803
double ac;
4804
CMolAtom *ma;
4805
4806
// Die Anfangswerte der AtomCodes: [Ordnungszahl] * 10.0 + [Zahl der Nicht-Wasserstoff-Bindungen]
4807
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4808
{
4809
ma = (CMolAtom*)m_oaMolAtoms[z];
4810
ma->m_fAtomCode = 10.0 * ((CAtom*)g_oaAtoms[m_baAtomIndex[ma->m_iType]])->m_pElement->m_fMass;
4811
4812
i = 0;
4813
for (z2=0;z2<ma->m_oaBonds.GetSize();z2++)
4814
{
4815
// Alle Wasserstoff-Atome ueberspringen
4816
if (((CAtom*)g_oaAtoms[m_baAtomIndex[((CMolAtom*)ma->m_oaBonds[z2])->m_iType]])->m_pElement->m_fMass < 4.5)
4817
continue;
4818
ma->m_fAtomCode++;
4819
i++;
4820
}
4821
4822
if (g_bVerbose)
4823
mprintf(" Atom %d (%s%d): 10.0 * %.2f + %d = %.2f\n",z+1,((CAtom*)g_oaAtoms[m_baAtomIndex[ma->m_iType]])->m_sName,ma->m_iOffset+1,((CAtom*)g_oaAtoms[m_baAtomIndex[ma->m_iType]])->m_pElement->m_fMass,i,ma->m_fAtomCode);
4824
}
4825
4826
i = 0;
4827
do {
4828
c1 = CountDifferentAtomCodes();
4829
4830
if (g_bVerbose)
4831
mprintf(WHITE,"\n Cycle %d: %d different atom codes exist.\n\n",i+1,c1);
4832
4833
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4834
{
4835
ma = (CMolAtom*)m_oaMolAtoms[z];
4836
ma->m_fTempAtomCode = ma->m_fAtomCode * 5.0;
4837
4838
for (z2=0;z2<ma->m_oaBonds.GetSize();z2++)
4839
ma->m_fTempAtomCode += ((CMolAtom*)ma->m_oaBonds[z2])->m_fAtomCode;
4840
}
4841
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4842
{
4843
ma = (CMolAtom*)m_oaMolAtoms[z];
4844
ma->m_fAtomCode = ma->m_fTempAtomCode;
4845
4846
if (g_bVerbose)
4847
mprintf(" Atom %d (%s%d): %.2f\n",z+1,((CAtom*)g_oaAtoms[m_baAtomIndex[ma->m_iType]])->m_sName,ma->m_iOffset+1,ma->m_fAtomCode);
4848
}
4849
c2 = CountDifferentAtomCodes();
4850
i++;
4851
// mprintf("Iteration %d: %d classes before, %d classes after.\n",i,c1,c2);
4852
} while (c1 != c2);
4853
4854
if (g_bVerbose)
4855
mprintf(WHITE,"\nSorting...\n");
4856
4857
m_iAtomClasses = c2;
4858
// mprintf("Finished.\n");
4859
// mprintf("%d Iterations, %d atom classes found.\n",i,c2);
4860
// mprintf("Sorting Atom Codes...");
4861
4862
// Sortieren mittels StackSort
4863
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4864
{
4865
ac = -1;
4866
i = -1;
4867
for (z2=z;z2<m_oaMolAtoms.GetSize();z2++)
4868
{
4869
if (((CMolAtom*)m_oaMolAtoms[z2])->m_fAtomCode > ac)
4870
{
4871
ac = ((CMolAtom*)m_oaMolAtoms[z2])->m_fAtomCode;
4872
i = z2;
4873
}
4874
}
4875
if (i != -1)
4876
{
4877
ma = (CMolAtom*)m_oaMolAtoms[z];
4878
m_oaMolAtoms[z] = m_oaMolAtoms[i];
4879
m_oaMolAtoms[i] = ma;
4880
((CMolAtom*)m_oaMolAtoms[z])->m_iMolAtomNumber = z;
4881
} else
4882
{
4883
eprintf("CSingleMolecule::BuildAtomCodes(): Weird error.\n");
4884
return;
4885
}
4886
}
4887
4888
if (g_bVerbose)
4889
{
4890
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4891
{
4892
ma = (CMolAtom*)m_oaMolAtoms[z];
4893
mprintf(" Atom %d (%s%d): %.2f\n",z+1,((CAtom*)g_oaAtoms[m_baAtomIndex[ma->m_iType]])->m_sName,ma->m_iOffset+1,ma->m_fAtomCode);
4894
}
4895
mprintf(WHITE,"Finished.\n\n");
4896
}
4897
// mprintf("Finished.\n");
4898
}
4899
4900
4901
int CSingleMolecule::CountDifferentAtomCodes()
4902
{
4903
int z, z2, i;
4904
double *d;
4905
4906
try { d = new double[m_oaMolAtoms.GetSize()]; } catch(...) { d = NULL; }
4907
if (d == NULL) NewException((double)m_oaMolAtoms.GetSize()*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4908
4909
i = 0;
4910
for (z=0;z<m_oaMolAtoms.GetSize();z++)
4911
{
4912
for (z2=0;z2<i;z2++)
4913
if (d[z2] == ((CMolAtom*)m_oaMolAtoms[z])->m_fAtomCode)
4914
goto _next;
4915
d[i] = ((CMolAtom*)m_oaMolAtoms[z])->m_fAtomCode;
4916
i++;
4917
_next:;
4918
}
4919
delete[] d;
4920
return i;
4921
}
4922
4923
4924
void CMSD::Parse()
4925
{
4926
char buf[256];
4927
int ti;
4928
// float tf;
4929
4930
BTIN;
4931
4932
try { m_pMSD = new CAF(); } catch(...) { m_pMSD = NULL; }
4933
if (m_pMSD == NULL) NewException((double)sizeof(CAF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4934
4935
mprintf(WHITE,"\n*** Mean Square Displacement\n\n");
4936
4937
try { m_pAtomGroup = new CAtomGroup(); } catch(...) { m_pAtomGroup = NULL; }
4938
if (m_pAtomGroup == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4939
4940
_rdfatom1:
4941
mprintf(" Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2] ",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
4942
inpprintf("! Which atom(s) to take from OM %s (e.g. \"C1,C3-5,H\", \"*\"=all)? [#2]\n",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName);
4943
myget(buf);
4944
if (strlen(buf) == 0)
4945
{
4946
if (!m_pAtomGroup->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],"#2"))
4947
{
4948
eprintf("Weird error.\n");
4949
inpprintf("! Weird error.\n");
4950
goto _rdfatom1;
4951
}
4952
} else if (!m_pAtomGroup->ParseAtoms((CMolecule*)g_oaMolecules[m_iShowMol],buf))
4953
{
4954
eprintf("Wrong input.\n");
4955
inpprintf("! Wrong input.\n");
4956
goto _rdfatom1;
4957
}
4958
4959
//_depth:
4960
if (g_iTrajSteps != -1)
4961
m_iResolution = AskUnsignedInteger(" Enter the resolution (=depth) for this MSD (in time steps): [%d] ",int(g_iTrajSteps*0.75),int(g_iTrajSteps*0.75));
4962
else m_iResolution = AskUnsignedInteger(" Enter the resolution (=depth) for this MSD (in time steps): [10000] ",10000);
4963
4964
m_iShowAtoms = m_pAtomGroup->m_iAtomGes;
4965
4966
/* if (g_iTrajSteps != -1)
4967
{
4968
if (g_bMSDCacheMode)
4969
{
4970
tf = g_iTrajSteps*m_pAtomGroup->m_iAtomGes*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*3.0f*sizeof(float)/1024.0f/1024.0f;
4971
if (tf >= 10.0f)
4972
if (!AskYesNo(" This will occupy %.0f MB RAM (once, not for every MSD!). Continue (y/n)? [yes] ",true,tf))
4973
goto _depth;
4974
} else
4975
{
4976
tf = m_iResolution*g_iGesVirtAtomCount*12.0f*sizeof(double)/1024.0f/1024.0f;
4977
if (tf >= 10.0f)
4978
if (!AskYesNo(" This will occupy %.0f MB RAM (once, not for every MSD!). Continue (y/n)? [yes] ",true,tf))
4979
goto _depth;
4980
}
4981
}*/
4982
/* if (m_iResolution > g_iMaxMSDDepth)
4983
g_iMaxMSDDepth = m_iReolution;*/
4984
4985
ti = m_iResolution / 1000;
4986
if (ti < 1)
4987
ti = 1;
4988
m_iStride = AskUnsignedInteger(" Take every n-th step for the time axis of the MSD: [%d] ",ti,ti);
4989
m_iStride2 = AskUnsignedInteger(" Shift correlation window n time steps at once: [%d] ",m_iStride,m_iStride);
4990
4991
if (g_bAdvanced2)
4992
{
4993
m_bSplit = AskYesNo(" Decompose this MSD into contributions from each individual molecule (y/n)? [no] ",false);
4994
if (AskYesNo(" Take into account only certain dimensions for displacement (y/n)? [no] ",false))
4995
{
4996
m_bTakeX = AskYesNo(" Take into account contributions along X axis (y/n)? [yes] ",true);
4997
m_bTakeY = AskYesNo(" Take into account contributions along X axis (y/n)? [yes] ",true);
4998
m_bTakeZ = AskYesNo(" Take into account contributions along X axis (y/n)? [yes] ",true);
4999
} else
5000
{
5001
m_bTakeX = true;
5002
m_bTakeY = true;
5003
m_bTakeZ = true;
5004
}
5005
} else
5006
{
5007
m_bSplit = false;
5008
m_bTakeX = true;
5009
m_bTakeY = true;
5010
m_bTakeZ = true;
5011
}
5012
5013
BuildName();
5014
BTOUT;
5015
}
5016
5017
5018
void CMSD::BuildName()
5019
{
5020
BTIN;
5021
char tmp[256];
5022
5023
sprintf(tmp,"%s_%s",((CMolecule*)g_oaMolecules[m_iShowMol])->m_sName,m_pAtomGroup->m_sName);
5024
5025
if ((!m_bTakeX) || (!m_bTakeY) || (!m_bTakeZ))
5026
{
5027
strcat(tmp,"_");
5028
if (m_bTakeX)
5029
strcat(tmp,"X");
5030
if (m_bTakeY)
5031
strcat(tmp,"Y");
5032
if (m_bTakeZ)
5033
strcat(tmp,"Z");
5034
}
5035
5036
try { m_sName = new char[strlen(tmp)+1]; } catch(...) { m_sName = NULL; }
5037
if (m_sName == NULL) NewException((double)(strlen(tmp)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5038
5039
strcpy(m_sName,tmp);
5040
BTOUT;
5041
}
5042
5043
5044
void CVHDF::CorrectCount()
5045
{
5046
int x, y;
5047
5048
for (y=0;y<m_iResolution;y++)
5049
for (x=0;x<m_iDepth/m_iStride;x++)
5050
if (m_pCount[x] != 0)
5051
m_pVHDF->m_pBin[y*m_iDepth/m_iStride+x] /= m_pCount[x];
5052
}
5053
5054
5055
void CConditionSubGroup::PrintData()
5056
{
5057
int z;
5058
double d;
5059
5060
mprintf(GREEN,"\n*** Data for %d. set of conditions ***\n\n",m_iNumber+1);
5061
mprintf(" %.0f of %.0f molecules passed this set of conditions (%.4f percent).\n",m_fPassed,m_fTotal,ZeroDivide(m_fPassed,m_fTotal)*100.0f);
5062
d = 1.0;
5063
for (z=0;z<m_oaConditions.GetSize();z++)
5064
{
5065
mprintf(" - Condition %d: %.0f of %.0f molecules passed (%.4f percent).\n",z+1,((CNbSearch*)m_oaConditions[z])->m_fMoleculesPassed,((CNbSearch*)m_oaConditions[z])->m_fMoleculesTotal,ZeroDivide(((CNbSearch*)m_oaConditions[z])->m_fMoleculesPassed,((CNbSearch*)m_oaConditions[z])->m_fMoleculesTotal)*100.0);
5066
d *= ZeroDivide(((CNbSearch*)m_oaConditions[z])->m_fMoleculesPassed,((CNbSearch*)m_oaConditions[z])->m_fMoleculesTotal);
5067
}
5068
mprintf("\n");
5069
if (m_oaConditions.GetSize() > 1)
5070
{
5071
mprintf(" The product of the condition probabilities is %.4f percent.\n",d*100.0);
5072
mprintf(" If the conditions would be uncorrelated, this would be also the probability for the set.\n");
5073
mprintf(" Therefore, the conditions are %s correlated for %.4f percent.\n\n",(d<ZeroDivide(m_fPassed,m_fTotal))?"positively":"negatively",(d<ZeroDivide(m_fPassed,m_fTotal))?(ZeroDivide(ZeroDivide(m_fPassed,m_fTotal),d)-1.0)*100.0:(ZeroDivide(d,ZeroDivide(m_fPassed,m_fTotal))-1.0)*100.0);
5074
}
5075
5076
for (z=0;z<m_oaConditions.GetSize();z++)
5077
((CNbSearch*)m_oaConditions[z])->PrintTable();
5078
}
5079
5080
5081
void CConditionSubGroup::PrintData(FILE *a)
5082
{
5083
int z;
5084
5085
mfprintf(a,"\n*** Data for %d. set of conditions ***\n\n",m_iNumber+1);
5086
mfprintf(a," %.0f of %.0f molecules passed this set of conditions (%.4f percent).\n",m_fPassed,m_fTotal,ZeroDivide(m_fPassed,m_fTotal)*100.0f);
5087
for (z=0;z<m_oaConditions.GetSize();z++)
5088
((CNbSearch*)m_oaConditions[z])->PrintTable(a);
5089
}
5090
5091
5092
void CConditionSubGroup::PrintSingle(int om)
5093
{
5094
int z;
5095
5096
for (z=0;z<m_oaConditions.GetSize();z++)
5097
((CNbSearch*)m_oaConditions[z])->PrintSingle(om);
5098
}
5099
5100
5101
void CConditionGroup::PrintSingle(int om)
5102
{
5103
int z;
5104
5105
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
5106
((CConditionSubGroup*)m_oaConditionSubGroups[z])->PrintSingle(om);
5107
}
5108
5109
5110
void CConditionGroup::PrintTable()
5111
{
5112
int z, z2;
5113
double tf1, tf2, tf3;
5114
5115
mprintf(WHITE,"*** Condition Table ***\n\n");
5116
mprintf(" The rows indicate how many subconditions of condition 1 are fulfilled.\n");
5117
mprintf(" The columns indicate how many subconditions of condition 2 are fulfilled.\n\n");
5118
5119
mprintf(" ");
5120
for (z=0;z<((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1;z++)
5121
mprintf("| %4d ",z);
5122
mprintf("\n");
5123
mprintf("-----");
5124
for (z=0;z<((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1;z++)
5125
mprintf("|---------",z);
5126
mprintf("\n");
5127
tf1 = 0;
5128
tf2 = 0;
5129
tf3 = 0;
5130
for (z=0;z<((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1;z++)
5131
{
5132
mprintf(" %3d ",z);
5133
for (z2=0;z2<((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1;z2++)
5134
{
5135
if ((z > 0) && (z2 == 0))
5136
tf1 += m_pTable[z*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+z2];
5137
if ((z == 0) && (z2 > 0))
5138
tf2 += m_pTable[z*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+z2];
5139
if ((z > 0) && (z2 > 0))
5140
tf3 += m_pTable[z*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+z2];
5141
mprintf("| %7.3f ",m_pTable[z*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+z2]/m_fTableGes*100.0);
5142
}
5143
mprintf("\n");
5144
}
5145
mprintf("\n");
5146
mprintf(" A RM/OM pair fulfills no condition: %7.3f percent of the time.\n",m_pTable[0]/m_fTableGes*100.0);
5147
mprintf(" A RM/OM pair fulfills only condition 1: %7.3f percent of the time.\n",tf1/m_fTableGes*100.0);
5148
mprintf(" A RM/OM pair fulfills only condition 2: %7.3f percent of the time.\n",tf2/m_fTableGes*100.0);
5149
mprintf(" A RM/OM pair fulfills both conditions: %7.3f percent of the time.\n",tf3/m_fTableGes*100.0);
5150
mprintf(" Total: %7.3f percent of the time.\n",100.0);
5151
mprintf("\n");
5152
mprintf(WHITE,"*** Condition Table End ***\n\n");
5153
}
5154
5155
5156
void CObservation::ListCDFObservations(int z)
5157
{
5158
int z2, ti, ti2, ti3;
5159
CxIntArray tempwa;
5160
5161
switch(g_iObsChannel[z])
5162
{
5163
case 0: // RDF
5164
if (m_bOthers)
5165
{
5166
if (m_bSecondShowMol && (z == 1))
5167
m_pRDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol2])->m_laSingleMolIndex[0]],&tempwa);
5168
else m_pRDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex[0]],&tempwa);
5169
} else m_pRDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],&tempwa);
5170
for (z2=0;z2<tempwa.GetSize()/2;z2++)
5171
{
5172
ti = tempwa[z2*2];
5173
ti2 = tempwa[z2*2+1];
5174
mprintf(" * %2d.) Distance %s%d (%s) <--> %s%d (%s)\n",z2+1,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5175
}
5176
break;
5177
5178
case 1: // ADF
5179
if (m_bOthers)
5180
{
5181
if (m_bSecondShowMol && (z == 1))
5182
m_pADF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol2])->m_laSingleMolIndex[0]],&tempwa);
5183
else m_pADF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex[0]],&tempwa);
5184
} else m_pADF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],&tempwa);
5185
for (z2=0;z2<tempwa.GetSize()/6;z2++)
5186
{
5187
mprintf(" * %2d.) Angle ",z2+1);
5188
if (m_pADF[z]->m_bOrtho[0])
5189
{
5190
ti = tempwa[z2*6];
5191
ti2 = tempwa[z2*6+1];
5192
ti3 = tempwa[z2*6+2];
5193
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)] to ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5194
} else
5195
{
5196
ti = tempwa[z2*6];
5197
ti2 = tempwa[z2*6+1];
5198
mprintf("[%s%d (%s) --> %s%d (%s)] to ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5199
}
5200
if (m_pADF[z]->m_bOrtho[1])
5201
{
5202
ti = tempwa[z2*6+3];
5203
ti2 = tempwa[z2*6+4];
5204
ti3 = tempwa[z2*6+5];
5205
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)]\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5206
} else
5207
{
5208
ti = tempwa[z2*6+3];
5209
ti2 = tempwa[z2*6+4];
5210
mprintf("[%s%d (%s) --> %s%d (%s)]\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5211
}
5212
}
5213
break;
5214
5215
case 2: // DDF
5216
if (m_bOthers)
5217
{
5218
if (m_bSecondShowMol && (z == 1))
5219
m_pDDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol2])->m_laSingleMolIndex[0]],&tempwa);
5220
else m_pDDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex[0]],&tempwa);
5221
} else m_pDDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],&tempwa);
5222
for (z2=0;z2<tempwa.GetSize()/9;z2++)
5223
{
5224
mprintf(" * %2d.) Dihedral Angle ",z2+1);
5225
if (m_pDDF[z]->m_bOrtho[0])
5226
{
5227
ti = tempwa[z2*9];
5228
ti2 = tempwa[z2*9+1];
5229
ti3 = tempwa[z2*9+2];
5230
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5231
} else
5232
{
5233
ti = tempwa[z2*9];
5234
ti2 = tempwa[z2*9+1];
5235
mprintf("[%s%d (%s) --> %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5236
}
5237
if (m_pDDF[z]->m_bOrtho[1])
5238
{
5239
ti = tempwa[z2*9+3];
5240
ti2 = tempwa[z2*9+4];
5241
ti3 = tempwa[z2*9+5];
5242
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5243
} else
5244
{
5245
ti = tempwa[z2*9+3];
5246
ti2 = tempwa[z2*9+4];
5247
mprintf("[%s%d (%s) --> %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5248
}
5249
if (m_pDDF[z]->m_bOrtho[2])
5250
{
5251
ti = tempwa[z2*9+6];
5252
ti2 = tempwa[z2*9+7];
5253
ti3 = tempwa[z2*9+8];
5254
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)]\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5255
} else
5256
{
5257
ti = tempwa[z2*9+6];
5258
ti2 = tempwa[z2*9+7];
5259
mprintf("[%s%d (%s) --> %s%d (%s)]\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5260
}
5261
}
5262
break;
5263
5264
case 3:
5265
eprintf("(not implemented)\n");
5266
break;
5267
5268
case 4:
5269
eprintf("(not implemented)\n");
5270
break;
5271
5272
case 5: // PlDF
5273
if (m_bOthers)
5274
{
5275
if (m_bSecondShowMol && (z == 1))
5276
m_pPlDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol2])->m_laSingleMolIndex[0]],&tempwa);
5277
else m_pPlDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex[0]],&tempwa);
5278
} else m_pPlDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],&tempwa);
5279
for (z2=0;z2<tempwa.GetSize()/4;z2++)
5280
{
5281
mprintf(" * %2d.) Distance from Plane ",z2+1);
5282
if (m_pPlDF[z]->m_bNormal)
5283
{
5284
ti = tempwa[z2*4];
5285
ti2 = tempwa[z2*4+1];
5286
mprintf("[%s%d (%s) --> %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5287
} else
5288
{
5289
ti = tempwa[z2*4];
5290
ti2 = tempwa[z2*4+1];
5291
ti3 = tempwa[z2*4+2];
5292
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5293
}
5294
ti = tempwa[z2*4+3];
5295
mprintf("%s%d (%s)\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName);
5296
}
5297
break;
5298
5299
case 6: // LiDF
5300
if (m_bOthers)
5301
{
5302
if (m_bSecondShowMol && (z == 1))
5303
m_pLiDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol2])->m_laSingleMolIndex[0]],&tempwa);
5304
else m_pLiDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex[0]],&tempwa);
5305
} else m_pLiDF[z]->BuildAtomList((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],(CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]],&tempwa);
5306
for (z2=0;z2<tempwa.GetSize()/4;z2++)
5307
{
5308
mprintf(" * %2d.) Distance from Plane ",z2+1);
5309
if (m_pLiDF[z]->m_bNormal)
5310
{
5311
ti = tempwa[z2*4];
5312
ti2 = tempwa[z2*4+1];
5313
ti3 = tempwa[z2*4+2];
5314
mprintf("[%s%d (%s), %s%d (%s), %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti3]])->m_sName,g_waAtomMolNumber[ti3]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti3]])->m_sName);
5315
} else
5316
{
5317
ti = tempwa[z2*4];
5318
ti2 = tempwa[z2*4+1];
5319
mprintf("[%s%d (%s) --> %s%d (%s)] - ",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti2]])->m_sName,g_waAtomMolNumber[ti2]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti2]])->m_sName);
5320
}
5321
ti = tempwa[z2*4+3];
5322
mprintf("%s%d (%s)\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName);
5323
}
5324
break;
5325
}
5326
}
5327
5328
5329
void CSDF::CreateCutPlane()
5330
{
5331
int x, y;
5332
CxVector3 vec;
5333
5334
try { m_pCutPlane = new C2DF(); } catch(...) { m_pCutPlane = NULL; }
5335
if (m_pCutPlane == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5336
5337
m_pCutPlane->m_fMinVal[0] = -m_fRadius;
5338
m_pCutPlane->m_fMinVal[1] = -m_fRadius;
5339
m_pCutPlane->m_fMaxVal[0] = m_fRadius;
5340
m_pCutPlane->m_fMaxVal[1] = m_fRadius;
5341
m_pCutPlane->m_iRes[0] = m_iCutPlaneResolution;
5342
m_pCutPlane->m_iRes[1] = m_iCutPlaneResolution;
5343
m_pCutPlane->SetLabelX("X [pm]");
5344
m_pCutPlane->SetLabelY("Y [pm]");
5345
m_pCutPlane->Create();
5346
5347
vec[2] = 0;
5348
for (y=0;y<m_iCutPlaneResolution;y++)
5349
{
5350
vec[1] = (float)(((y+0.5)/m_pCutPlane->m_iRes[1])*(m_pCutPlane->m_fMaxVal[1]-m_pCutPlane->m_fMinVal[1])+m_pCutPlane->m_fMinVal[1]);
5351
for (x=0;x<m_iCutPlaneResolution;x++)
5352
{
5353
vec[0] = (float)(((x+0.5)/m_pCutPlane->m_iRes[0])*(m_pCutPlane->m_fMaxVal[0]-m_pCutPlane->m_fMinVal[0])+m_pCutPlane->m_fMinVal[0]);
5354
m_pCutPlane->AddToBin(x,y,m_pSDF->GetValue(vec));
5355
}
5356
}
5357
if (m_bCutPlaneShowAtoms)
5358
{
5359
m_pCutPlane->AddCircle(0,0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_fRadius*0.75,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorR/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorG/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorB/255.0);
5360
m_pCutPlane->AddCircle(m_fAtom2PosX / m_fPosCounter,0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_fRadius*0.75,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorR/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorG/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorB/255.0);
5361
m_pCutPlane->AddCircle(m_fAtom3PosX / m_fPosCounter,m_fAtom3PosY / m_fPosCounter,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_pElement->m_fRadius*0.75,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_pElement->m_iColorR/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_pElement->m_iColorG/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_pElement->m_iColorB/255.0);
5362
}
5363
}
5364
5365
5366
void CConditionGroup::Reset()
5367
{
5368
int z;
5369
5370
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
5371
((CConditionSubGroup*)m_oaConditionSubGroups[z])->Reset();
5372
5373
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5374
m_iPassCounter[z] = 0;
5375
}
5376
5377
5378
void CConditionSubGroup::Reset()
5379
{
5380
int z;
5381
5382
for (z=0;z<m_oaConditions.GetSize();z++)
5383
((CNbSearch*)m_oaConditions[z])->Reset();
5384
}
5385
5386
5387
void CRDF::CopyFrom(CRDF *p)
5388
{
5389
int z;
5390
CAtomGroup *ag;
5391
5392
m_bAdaptive = p->m_bAdaptive;
5393
m_bRadialCorrect = p->m_bRadialCorrect;
5394
m_bSelf = p->m_bSelf;
5395
m_fMinDist = p->m_fMinDist;
5396
m_fMaxDist = p->m_fMaxDist;
5397
m_iCombinations = p->m_iCombinations;
5398
m_iHistogramRes = p->m_iHistogramRes;
5399
m_iRefAtomGes = p->m_iRefAtomGes;
5400
m_iRefOrSec[0] = p->m_iRefOrSec[0];
5401
m_iRefOrSec[1] = p->m_iRefOrSec[1];
5402
m_iResolution = p->m_iResolution;
5403
m_iShowAtomGes = p->m_iShowAtomGes;
5404
m_iShowMol = p->m_iShowMol;
5405
5406
if (p->m_sName != NULL)
5407
{
5408
try { m_sName = new char[strlen(p->m_sName)+1]; } catch(...) { m_sName = NULL; }
5409
if (m_sName == NULL) NewException((double)(strlen(p->m_sName)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5410
5411
strcpy(m_sName,p->m_sName);
5412
} else m_sName = NULL;
5413
5414
if (p->m_sShortName != NULL)
5415
{
5416
try { m_sShortName = new char[strlen(p->m_sShortName)+1]; } catch(...) { m_sShortName = NULL; }
5417
if (m_sShortName == NULL) NewException((double)(strlen(p->m_sShortName)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5418
5419
strcpy(m_sShortName,p->m_sShortName);
5420
} else m_sShortName = NULL;
5421
5422
if (p->m_baDataEnabled != NULL)
5423
{
5424
try { m_baDataEnabled = new CxByteArray[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_baDataEnabled = NULL; }
5425
if (m_baDataEnabled == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5426
5427
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5428
m_baDataEnabled[z].CopyFrom(&p->m_baDataEnabled[z]);
5429
}
5430
5431
if (p->m_faData != NULL)
5432
{
5433
try { m_faData = new CxDoubleArray[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_faData = NULL; }
5434
if (m_faData == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5435
5436
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5437
m_faData[z].CopyFrom(&p->m_faData[z]);
5438
}
5439
5440
for (z=0;z<p->m_oaVectors.GetSize();z++)
5441
{
5442
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
5443
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5444
5445
ag->CopyFrom((CAtomGroup*)p->m_oaVectors[z]);
5446
m_oaVectors.Add(ag);
5447
}
5448
5449
m_faMinMaxDist.CopyFrom(&p->m_faMinMaxDist);
5450
5451
if (p->m_pRDF != NULL)
5452
{
5453
try { m_pRDF = new CDF(); } catch(...) { m_pRDF = NULL; }
5454
if (m_pRDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5455
5456
m_pRDF->CopyFrom(p->m_pRDF);
5457
}
5458
}
5459
5460
5461
void CADF::CopyFrom(CADF *p)
5462
{
5463
int z, z2;
5464
CAtomGroup *ag;
5465
5466
m_bCosine = p->m_bCosine;
5467
m_bFoldAngle = p->m_bFoldAngle;
5468
m_bMirror = p->m_bMirror;
5469
m_bOrtho[0] = p->m_bOrtho[0];
5470
m_bOrtho[1] = p->m_bOrtho[1];
5471
m_iVecType[0] = p->m_iVecType[0];
5472
m_iVecType[1] = p->m_iVecType[1];
5473
m_bSelf = p->m_bSelf;
5474
m_bStat = p->m_bStat;
5475
m_fMinAngle = p->m_fMinAngle;
5476
m_fMaxAngle = p->m_fMaxAngle;
5477
m_iCombinations = p->m_iCombinations;
5478
m_iHistogramRes = p->m_iHistogramRes;
5479
for (z=0;z<2;z++)
5480
for (z2=0;z2<3;z2++)
5481
m_iRefOrSec[z][z2] = p->m_iRefOrSec[z][z2];
5482
m_iResolution = p->m_iResolution;
5483
m_iShowMol = p->m_iShowMol;
5484
5485
if (p->m_sName != NULL)
5486
{
5487
try { m_sName = new char[strlen(p->m_sName)+1]; } catch(...) { m_sName = NULL; }
5488
if (m_sName == NULL) NewException((double)(strlen(p->m_sName)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5489
5490
strcpy(m_sName,p->m_sName);
5491
} else m_sName = NULL;
5492
5493
if (p->m_sShortName != NULL)
5494
{
5495
try { m_sShortName = new char[strlen(p->m_sShortName)+1]; } catch(...) { m_sShortName = NULL; }
5496
if (m_sShortName == NULL) NewException((double)(strlen(p->m_sShortName)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5497
5498
strcpy(m_sShortName,p->m_sShortName);
5499
} else m_sShortName = NULL;
5500
5501
if (p->m_baDataEnabled != NULL)
5502
{
5503
try { m_baDataEnabled = new CxByteArray[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_baDataEnabled = NULL; }
5504
if (m_baDataEnabled == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5505
5506
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5507
m_baDataEnabled[z].CopyFrom(&p->m_baDataEnabled[z]);
5508
}
5509
5510
if (p->m_faData != NULL)
5511
{
5512
try { m_faData = new CxDoubleArray[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_faData = NULL; }
5513
if (m_faData == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5514
5515
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5516
m_faData[z].CopyFrom(&p->m_faData[z]);
5517
}
5518
5519
for (z=0;z<p->m_oaVectors.GetSize();z++)
5520
{
5521
if (p->m_oaVectors[z] != NULL)
5522
{
5523
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
5524
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5525
5526
ag->CopyFrom((CAtomGroup*)p->m_oaVectors[z]);
5527
m_oaVectors.Add(ag);
5528
} else m_oaVectors.Add(NULL);
5529
}
5530
5531
m_faMinMaxAngle.CopyFrom(&p->m_faMinMaxAngle);
5532
5533
if (p->m_pADF != NULL)
5534
{
5535
try { m_pADF = new CDF(); } catch(...) { m_pADF = NULL; }
5536
if (m_pADF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5537
5538
m_pADF->CopyFrom(p->m_pADF);
5539
}
5540
}
5541
5542
5543
void CConditionSubGroup::CopyFrom(CConditionSubGroup *p)
5544
{
5545
int z;
5546
CNbSearch *nb;
5547
5548
m_fPassed = p->m_fPassed;
5549
m_fTotal = p->m_fTotal;
5550
m_iCombinations = p->m_iCombinations;
5551
m_iNumber = p->m_iNumber;
5552
m_iShowMol = p->m_iShowMol;
5553
if (p->m_bTempPassed != NULL)
5554
{
5555
try { m_bTempPassed = new bool[g_iGesVirtAtomCount]; } catch(...) { m_bTempPassed = NULL; }
5556
if (m_bTempPassed == NULL) NewException((double)g_iGesVirtAtomCount*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5557
5558
memcpy(m_bTempPassed,p->m_bTempPassed,sizeof(bool)*g_iGesVirtAtomCount);
5559
}
5560
for (z=0;z<p->m_oaConditions.GetSize();z++)
5561
{
5562
try { nb = new CNbSearch(); } catch(...) { nb = NULL; }
5563
if (nb == NULL) NewException((double)sizeof(CNbSearch),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5564
5565
nb->CopyFrom((CNbSearch*)p->m_oaConditions[z]);
5566
m_oaConditions.Add(nb);
5567
}
5568
}
5569
5570
5571
void CConditionGroup::CopyFrom(CConditionGroup *p)
5572
{
5573
int z;
5574
CConditionSubGroup *sg;
5575
5576
m_bInactive = p->m_bInactive;
5577
m_iShowMol = p->m_iShowMol;
5578
m_iRefMol = p->m_iRefMol;
5579
m_iHistoGes = p->m_iHistoGes;
5580
m_bAnyPassed = p->m_bAnyPassed;
5581
m_fTableGes = p->m_fTableGes;
5582
m_fPassed = p->m_fPassed;
5583
m_fTotal = p->m_fTotal;
5584
m_bInvertCondition = p->m_bInvertCondition;
5585
5586
if (p->m_bAlwaysTrue != NULL)
5587
{
5588
try { m_bAlwaysTrue = new bool[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_bAlwaysTrue = NULL; }
5589
if (m_bAlwaysTrue == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5590
5591
memcpy(m_bAlwaysTrue,p->m_bAlwaysTrue,sizeof(bool)*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize());
5592
}
5593
if (p->m_iPassCounter != NULL)
5594
{
5595
try { m_iPassCounter = new long[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iPassCounter = NULL; }
5596
if (m_iPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5597
5598
memcpy(m_iPassCounter,p->m_iPassCounter,sizeof(long)*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize());
5599
}
5600
if (p->m_iOMPassCounter != NULL)
5601
{
5602
try { m_iOMPassCounter = new long[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iOMPassCounter = NULL; }
5603
if (m_iOMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5604
5605
memcpy(m_iOMPassCounter,p->m_iOMPassCounter,sizeof(long)*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize());
5606
}
5607
if (p->m_iRMPassCounter != NULL)
5608
{
5609
try { m_iRMPassCounter = new long[((CMolecule*)g_oaMolecules[m_iRefMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iRMPassCounter = NULL; }
5610
if (m_iRMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[m_iRefMol])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5611
5612
memcpy(m_iRMPassCounter,p->m_iRMPassCounter,sizeof(long)*((CMolecule*)g_oaMolecules[m_iRefMol])->m_laSingleMolIndex.GetSize());
5613
}
5614
for (z=0;z<p->m_oaConditionSubGroups.GetSize();z++)
5615
{
5616
try { sg = new CConditionSubGroup(); } catch(...) { sg = NULL; }
5617
if (sg == NULL) NewException((double)sizeof(CConditionSubGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5618
5619
sg->CopyFrom((CConditionSubGroup*)p->m_oaConditionSubGroups[z]);
5620
m_oaConditionSubGroups.Add(sg);
5621
}
5622
5623
if (p->m_pTable != NULL)
5624
{
5625
try { m_pTable = new double[(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)]; } catch(...) { m_pTable = NULL; }
5626
if (m_pTable == NULL) NewException((double)(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5627
5628
memcpy(m_pTable,p->m_pTable,sizeof(double)*(((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_iCombinations+1) * (((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1));
5629
}
5630
5631
if (p->m_pHistogram != NULL)
5632
{
5633
try { m_pHistogram = new unsigned long[((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1]; } catch(...) { m_pHistogram = NULL; }
5634
if (m_pHistogram == NULL) NewException((double)(((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1)*sizeof(unsigned long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5635
5636
memcpy(m_pHistogram,p->m_pHistogram,sizeof(unsigned long)*(((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+1));
5637
}
5638
}
5639
5640
5641
void CConditionGroup::Parse_OnlyValues()
5642
{
5643
BTIN;
5644
int z;
5645
5646
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
5647
{
5648
mprintf(YELLOW,">>> %d. set of conditions >>>\n\n",z+1);
5649
((CConditionSubGroup*)m_oaConditionSubGroups[z])->Parse_OnlyValues();
5650
mprintf(YELLOW,"<<< End of %d. set of conditions <<<\n\n",z+1);
5651
}
5652
}
5653
5654
5655
void CConditionSubGroup::Parse_OnlyValues()
5656
{
5657
BTIN;
5658
int z;
5659
5660
for (z=0;z<m_oaConditions.GetSize();z++)
5661
{
5662
mprintf(YELLOW," >>> %d. condition within this set >>>\n\n",z+1);
5663
((CNbSearch*)m_oaConditions[z])->Parse_OnlyValues();
5664
mprintf(YELLOW,"\n <<< End of %d. condition <<<\n\n",z+1);
5665
}
5666
BTOUT;
5667
}
5668
5669
5670
void CConditionGroup::CopyResults(CConditionGroup *p)
5671
{
5672
int z;
5673
5674
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
5675
((CConditionSubGroup*)m_oaConditionSubGroups[z])->CopyResults((CConditionSubGroup*)p->m_oaConditionSubGroups[z]);
5676
}
5677
5678
5679
void CConditionSubGroup::CopyResults(CConditionSubGroup *p)
5680
{
5681
int z;
5682
5683
for (z=0;z<m_oaConditions.GetSize();z++)
5684
((CNbSearch*)m_oaConditions[z])->CopyResults((CNbSearch*)p->m_oaConditions[z]);
5685
}
5686
5687
5688
void CConditionGroup::ReScan(CSingleMolecule *rm)
5689
{
5690
BXIN;
5691
int z, z2, t1, t2, i;
5692
5693
if (m_bInactive)
5694
return;
5695
5696
for (z=0;z<m_oaConditionSubGroups.GetSize();z++)
5697
((CConditionSubGroup*)m_oaConditionSubGroups[z])->ReScan(rm);
5698
5699
if (m_oaConditionSubGroups.GetSize() == 2)
5700
{
5701
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5702
{
5703
t1 = 0;
5704
t2 = 0;
5705
for (z2=0;z2<((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_oaConditions.GetSize();z2++)
5706
t1 += ((CNbSearch*)((CConditionSubGroup*)m_oaConditionSubGroups[0])->m_oaConditions[z2])->m_iCombPassCount[z];
5707
for (z2=0;z2<((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_oaConditions.GetSize();z2++)
5708
t2 += ((CNbSearch*)((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_oaConditions[z2])->m_iCombPassCount[z];
5709
m_pTable[t1*(((CConditionSubGroup*)m_oaConditionSubGroups[1])->m_iCombinations+1)+t2]++;
5710
m_fTableGes++;
5711
}
5712
}
5713
5714
i = 0;
5715
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5716
{
5717
m_fTotal++;
5718
if (m_bInvertCondition)
5719
{
5720
for (z2=0;z2<m_oaConditionSubGroups.GetSize();z2++)
5721
if (((CConditionSubGroup*)m_oaConditionSubGroups[z2])->Contains(z))
5722
goto _nopass;
5723
m_fPassed++;
5724
m_iPassCounter[z]++;
5725
m_bAnyPassed = true;
5726
} else
5727
{
5728
for (z2=0;z2<m_oaConditionSubGroups.GetSize();z2++)
5729
if (((CConditionSubGroup*)m_oaConditionSubGroups[z2])->Contains(z))
5730
{
5731
// mprintf("passed[%d]++\n",z);
5732
m_fPassed++;
5733
m_iPassCounter[z]++;
5734
m_bAnyPassed = true;
5735
i++;
5736
goto _nopass;
5737
}
5738
}
5739
_nopass:;
5740
}
5741
m_pHistogram[i]++;
5742
m_iHistoGes++;
5743
5744
BXOUT;
5745
}
5746
5747
5748
void CConditionSubGroup::ReScan(CSingleMolecule *rm)
5749
{
5750
int z, z2;
5751
5752
for (z=0;z<m_oaConditions.GetSize();z++)
5753
((CNbSearch*)m_oaConditions[z])->ReScan(rm);
5754
5755
for (z=0;z<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
5756
{
5757
m_fTotal++;
5758
for (z2=0;z2<m_oaConditions.GetSize();z2++)
5759
if (!((CNbSearch*)m_oaConditions[z2])->m_bPassed[z])
5760
goto _nopass;
5761
m_fPassed++;
5762
_nopass:;
5763
}
5764
}
5765
5766
5767
CNbSearch* CConditionGroup::AddSingleCondition(int rm, int sm, int gridmode)
5768
{
5769
BTIN;
5770
CConditionSubGroup *sg;
5771
int z;
5772
5773
m_iShowMol = sm;
5774
m_iRefMol = rm;
5775
5776
try { m_bAlwaysTrue = new bool[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_bAlwaysTrue = NULL; }
5777
if (m_bAlwaysTrue == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5778
5779
try { m_iPassCounter = new long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iPassCounter = NULL; }
5780
if (m_iPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5781
5782
try { m_iOMPassCounter = new long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iOMPassCounter = NULL; }
5783
if (m_iOMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5784
5785
for (z=0;z<((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize();z++)
5786
{
5787
m_bAlwaysTrue[z] = false;
5788
m_iPassCounter[z] = 0;
5789
m_iOMPassCounter[z] = 0;
5790
}
5791
5792
try { m_iRMPassCounter = new long[((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize()]; } catch(...) { m_iRMPassCounter = NULL; }
5793
if (m_iRMPassCounter == NULL) NewException((double)((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize()*sizeof(long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5794
5795
for (z=0;z<((CMolecule*)g_oaMolecules[rm])->m_laSingleMolIndex.GetSize();z++)
5796
m_iRMPassCounter[z] = 0;
5797
5798
try { sg = new CConditionSubGroup(); } catch(...) { sg = NULL; }
5799
if (sg == NULL) NewException((double)sizeof(CConditionSubGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5800
5801
sg->m_iShowMol = m_iShowMol;
5802
sg->m_iNumber = m_oaConditionSubGroups.GetSize();
5803
m_oaConditionSubGroups.Add(sg);
5804
5805
m_bInvertCondition = false;
5806
5807
m_iHistoGes = 0;
5808
5809
try { m_pHistogram = new unsigned long[((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1]; } catch(...) { m_pHistogram = NULL; }
5810
if (m_pHistogram == NULL) NewException((double)(((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1)*sizeof(unsigned long),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5811
5812
for (z=0;z<((CMolecule*)g_oaMolecules[sm])->m_laSingleMolIndex.GetSize()+1;z++)
5813
m_pHistogram[z] = 0;
5814
5815
BTOUT;
5816
return sg->AddSingleCondition(rm,sm,gridmode);
5817
}
5818
5819
5820
CNbSearch* CConditionSubGroup::AddSingleCondition(int rm, int sm, int gridmode)
5821
{
5822
BTIN;
5823
CNbSearch *n;
5824
5825
m_iCombinations = 0;
5826
5827
try { n = new CNbSearch(); } catch(...) { n = NULL; }
5828
if (n == NULL) NewException((double)sizeof(CNbSearch),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5829
5830
n->m_iNumber = m_oaConditions.GetSize();
5831
m_oaConditions.Add(n);
5832
n->ParseGrid(rm,sm,gridmode);
5833
m_iCombinations += n->m_iCombinationsEnabled;
5834
5835
try { m_bTempPassed = new bool[g_iGesVirtAtomCount]; } catch(...) { m_bTempPassed = NULL; }
5836
if (m_bTempPassed == NULL) NewException((double)g_iGesVirtAtomCount*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5837
5838
BTOUT;
5839
return n;
5840
}
5841
5842
5843
void CObservation::BuildTimeDiff(CDF *df, bool ddf)
5844
{
5845
int z, z2, z3, z4, i;
5846
CxFloatArray *ptfa;
5847
double tf, tfa, tfsq, tfs, tf0;
5848
char buf[256];
5849
5850
try { df->m_pTimeDiff = new CDF(); } catch(...) { df->m_pTimeDiff = NULL; }
5851
if (df->m_pTimeDiff == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5852
5853
df->m_pTimeDiff->m_iResolution = m_iTimeDiffDepth;
5854
df->m_pTimeDiff->m_fMinVal = 0;
5855
df->m_pTimeDiff->m_fMaxVal = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5856
df->m_pTimeDiff->Create();
5857
df->m_pTimeDiff->SetLabelX("Tau [ps]");
5858
sprintf(buf,"Delta ");
5859
strcat(buf,df->m_sLabelX);
5860
df->m_pTimeDiff->SetLabelY(buf);
5861
5862
try { df->m_pTimeDiffAbs = new CDF(); } catch(...) { df->m_pTimeDiffAbs = NULL; }
5863
if (df->m_pTimeDiffAbs == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5864
5865
df->m_pTimeDiffAbs->m_iResolution = m_iTimeDiffDepth;
5866
df->m_pTimeDiffAbs->m_fMinVal = 0;
5867
df->m_pTimeDiffAbs->m_fMaxVal = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5868
df->m_pTimeDiffAbs->Create();
5869
df->m_pTimeDiffAbs->SetLabelX("Tau [ps]");
5870
df->m_pTimeDiffAbs->SetLabelY(buf);
5871
5872
sprintf(buf,"Delta Square ");
5873
strcat(buf,df->m_sLabelX);
5874
5875
try { df->m_pTimeDiffSqr = new CDF(); } catch(...) { df->m_pTimeDiffSqr = NULL; }
5876
if (df->m_pTimeDiffSqr == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5877
5878
df->m_pTimeDiffSqr->m_iResolution = m_iTimeDiffDepth;
5879
df->m_pTimeDiffSqr->m_fMinVal = 0;
5880
df->m_pTimeDiffSqr->m_fMaxVal = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5881
df->m_pTimeDiffSqr->Create();
5882
df->m_pTimeDiffSqr->SetLabelX("Tau [ps]");
5883
df->m_pTimeDiffSqr->SetLabelY(buf);
5884
5885
if (m_b3DTimeDiff)
5886
{
5887
sprintf(buf,"Delta ");
5888
strcat(buf,df->m_sLabelX);
5889
5890
try { df->m_p3DTimeDiff = new C2DF(); } catch(...) { df->m_p3DTimeDiff = NULL; }
5891
if (df->m_p3DTimeDiff == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5892
5893
df->m_p3DTimeDiff->m_iRes[0] = m_iTimeDiffDepth/m_iTimeDiffStride3D;
5894
df->m_p3DTimeDiff->m_iRes[1] = m_iTimeDiffRes3D;
5895
df->m_p3DTimeDiff->m_fMinVal[0] = 0;
5896
df->m_p3DTimeDiff->m_fMaxVal[0] = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5897
df->m_p3DTimeDiff->m_fMinVal[1] = m_fTimeDiffMinVal3D;
5898
df->m_p3DTimeDiff->m_fMaxVal[1] = m_fTimeDiffMaxVal3D;
5899
df->m_p3DTimeDiff->Create();
5900
df->m_p3DTimeDiff->SetLabelX("Tau [ps]");
5901
df->m_p3DTimeDiff->SetLabelY(df->m_sLabelX);
5902
df->m_p3DTimeDiff->SetLabelZ(buf);
5903
5904
try { df->m_p3DTimeDiffAbs = new C2DF(); } catch(...) { df->m_p3DTimeDiffAbs = NULL; }
5905
if (df->m_p3DTimeDiffAbs == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5906
5907
df->m_p3DTimeDiffAbs->m_iRes[0] = m_iTimeDiffDepth/m_iTimeDiffStride3D;
5908
df->m_p3DTimeDiffAbs->m_iRes[1] = m_iTimeDiffRes3D;
5909
df->m_p3DTimeDiffAbs->m_fMinVal[0] = 0;
5910
df->m_p3DTimeDiffAbs->m_fMaxVal[0] = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5911
df->m_p3DTimeDiffAbs->m_fMinVal[1] = m_fTimeDiffMinVal3D;
5912
df->m_p3DTimeDiffAbs->m_fMaxVal[1] = m_fTimeDiffMaxVal3D;
5913
df->m_p3DTimeDiffAbs->Create();
5914
df->m_p3DTimeDiffAbs->SetLabelX("Tau [ps]");
5915
df->m_p3DTimeDiffAbs->SetLabelY(df->m_sLabelX);
5916
df->m_p3DTimeDiffAbs->SetLabelZ(buf);
5917
5918
if (m_iTimeDiffDistSteps != 0)
5919
{
5920
try { df->m_pTimeDiffDistPairs = new C2DF*[m_iTimeDiffDepth/m_iTimeDiffStride3D/m_iTimeDiffDistSteps]; } catch(...) { df->m_pTimeDiffDistPairs = NULL; }
5921
if (df->m_pTimeDiffDistPairs == NULL) NewException((double)m_iTimeDiffDepth/m_iTimeDiffStride3D/m_iTimeDiffDistSteps*sizeof(C2DF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5922
5923
for (z=0;z<m_iTimeDiffDepth/m_iTimeDiffStride3D/m_iTimeDiffDistSteps;z++)
5924
{
5925
try { df->m_pTimeDiffDistPairs[z] = new C2DF(); } catch(...) { df->m_pTimeDiffDistPairs[z] = NULL; }
5926
if (df->m_pTimeDiffDistPairs[z] == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5927
5928
df->m_pTimeDiffDistPairs[z]->m_iRes[0] = m_iTimeDiffDistResX;
5929
df->m_pTimeDiffDistPairs[z]->m_iRes[1] = m_iTimeDiffDistResY;
5930
df->m_pTimeDiffDistPairs[z]->m_fMinVal[0] = m_fTimeDiffDistMinValX;
5931
df->m_pTimeDiffDistPairs[z]->m_fMaxVal[0] = m_fTimeDiffDistMaxValX;
5932
df->m_pTimeDiffDistPairs[z]->m_fMinVal[1] = m_fTimeDiffDistMinValY;
5933
df->m_pTimeDiffDistPairs[z]->m_fMaxVal[1] = m_fTimeDiffDistMaxValY;
5934
df->m_pTimeDiffDistPairs[z]->Create();
5935
df->m_pTimeDiffDistPairs[z]->SetLabelX(df->m_sLabelX);
5936
df->m_pTimeDiffDistPairs[z]->SetLabelY(df->m_sLabelX);
5937
}
5938
}
5939
5940
try { df->m_pTimeDiffDist3DF = new C3DF(); } catch(...) { df->m_pTimeDiffDist3DF = NULL; }
5941
if (df->m_pTimeDiffDist3DF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5942
5943
df->m_pTimeDiffDist3DF->m_iRes[0] = m_iTimeDiffDistResX;
5944
df->m_pTimeDiffDist3DF->m_iRes[1] = m_iTimeDiffDistResY;
5945
df->m_pTimeDiffDist3DF->m_iRes[2] = m_iTimeDiffDepth/m_iTimeDiffStride3D;
5946
df->m_pTimeDiffDist3DF->m_fMinVal[0] = m_fTimeDiffDistMinValX;
5947
df->m_pTimeDiffDist3DF->m_fMaxVal[0] = m_fTimeDiffDistMaxValX;
5948
df->m_pTimeDiffDist3DF->m_fMinVal[1] = m_fTimeDiffDistMinValY;
5949
df->m_pTimeDiffDist3DF->m_fMaxVal[1] = m_fTimeDiffDistMaxValY;
5950
df->m_pTimeDiffDist3DF->m_fMinVal[2] = 0;
5951
df->m_pTimeDiffDist3DF->m_fMaxVal[2] = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5952
df->m_pTimeDiffDist3DF->Create();
5953
df->m_pTimeDiffDist3DF->SetLabelX(df->m_sLabelX);
5954
df->m_pTimeDiffDist3DF->SetLabelY(df->m_sLabelX);
5955
5956
sprintf(buf,"Delta Square ");
5957
strcat(buf,df->m_sLabelX);
5958
5959
try { df->m_p3DTimeDiffSqr = new C2DF(); } catch(...) { df->m_p3DTimeDiffSqr = NULL; }
5960
if (df->m_p3DTimeDiffSqr == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5961
5962
df->m_p3DTimeDiffSqr->m_iRes[0] = m_iTimeDiffDepth/m_iTimeDiffStride3D;
5963
df->m_p3DTimeDiffSqr->m_iRes[1] = m_iTimeDiffRes3D;
5964
df->m_p3DTimeDiffSqr->m_fMinVal[0] = 0;
5965
df->m_p3DTimeDiffSqr->m_fMaxVal[0] = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5966
df->m_p3DTimeDiffSqr->m_fMinVal[1] = m_fTimeDiffMinVal3D;
5967
df->m_p3DTimeDiffSqr->m_fMaxVal[1] = m_fTimeDiffMaxVal3D;
5968
df->m_p3DTimeDiffSqr->Create();
5969
df->m_p3DTimeDiffSqr->SetLabelX("Tau [ps]");
5970
df->m_p3DTimeDiffSqr->SetLabelY(df->m_sLabelX);
5971
df->m_p3DTimeDiffSqr->SetLabelZ(buf);
5972
5973
try { df->m_p3DTimeDiffT = new C2DF(); } catch(...) { df->m_p3DTimeDiffT = NULL; }
5974
if (df->m_p3DTimeDiffT == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
5975
5976
df->m_p3DTimeDiffT->m_iRes[0] = m_iTimeDiffDepth/m_iTimeDiffStride3D;
5977
df->m_p3DTimeDiffT->m_iRes[1] = m_iTimeDiffRes3D;
5978
df->m_p3DTimeDiffT->m_fMinVal[0] = 0;
5979
df->m_p3DTimeDiffT->m_fMaxVal[0] = m_iTimeDiffDepth * g_fTimestepLength / 1000.0;
5980
df->m_p3DTimeDiffT->m_fMinVal[1] = m_fTimeDiffMinVal3D;
5981
df->m_p3DTimeDiffT->m_fMaxVal[1] = m_fTimeDiffMaxVal3D;
5982
df->m_p3DTimeDiffT->Create();
5983
}
5984
5985
for (z2=0;z2<df->m_oaTimeDiffBuf.GetSize();z2++)
5986
{
5987
mprintf(" %4d/%d 2D [",z2+1,df->m_oaTimeDiffBuf.GetSize());
5988
ptfa = (CxFloatArray*)df->m_oaTimeDiffBuf[z2];
5989
tfs = m_iTimeDiffDepth/50.0;
5990
for (z3=0;z3<m_iTimeDiffDepth;z3++) // Das ist das Tau
5991
{
5992
if (fmod(z3,tfs) < 1.0)
5993
mprintf(WHITE,"#");
5994
tf = 0;
5995
tfa = 0;
5996
tfsq = 0;
5997
for (z4=0;z4<(int)ptfa->GetSize()-z3-1;z4++) // Das ist der Startpunkt
5998
{
5999
tf0 = (*ptfa)[z3+z4]-(*ptfa)[z4];
6000
if (ddf)
6001
{
6002
if (tf0 > 180.0)
6003
tf0 -= 360.0;
6004
if (tf0 <= -180.0)
6005
tf0 += 360.0;
6006
}
6007
tfa += fabs(tf0);
6008
tf += tf0;
6009
tfsq += tf0 * tf0;
6010
}
6011
df->m_pTimeDiff->AddToBin_Int(z3,tf/(ptfa->GetSize()-z3-1));
6012
df->m_pTimeDiffAbs->AddToBin_Int(z3,tfa/(ptfa->GetSize()-z3-1));
6013
df->m_pTimeDiffSqr->AddToBin_Int(z3,tfsq/(ptfa->GetSize()-z3-1));
6014
6015
df->m_pTimeDiff->m_fBinEntries += ptfa->GetSize()-z3-2;
6016
df->m_pTimeDiffAbs->m_fBinEntries += ptfa->GetSize()-z3-2;
6017
df->m_pTimeDiffSqr->m_fBinEntries += ptfa->GetSize()-z3-2;
6018
}
6019
mprintf("]\n");
6020
if (m_b3DTimeDiff)
6021
{
6022
mprintf(" %4d/%d 3D [",z2+1,df->m_oaTimeDiffBuf.GetSize());
6023
tfs = m_iTimeDiffDepth/50.0;
6024
for (z3=0;z3<m_iTimeDiffDepth;z3+=m_iTimeDiffStride3D) // Das ist das Tau
6025
{
6026
if (fmod(z3,tfs) < 1.0)
6027
mprintf(WHITE,"#");
6028
i = z3/m_iTimeDiffStride3D;
6029
for (z4=0;z4<(int)ptfa->GetSize()-z3-1;z4++) // Das ist der Startpunkt
6030
{
6031
tf0 = (*ptfa)[z3+z4]-(*ptfa)[z4];
6032
if (ddf)
6033
{
6034
if (tf0 > 180.0)
6035
tf0 -= 360.0;
6036
if (tf0 <= -180.0)
6037
tf0 += 360.0;
6038
}
6039
df->m_p3DTimeDiff->AddToBin_IntX(i,(*ptfa)[z4],tf0);
6040
df->m_p3DTimeDiffAbs->AddToBin_IntX(i,(*ptfa)[z4],fabs(tf0));
6041
df->m_p3DTimeDiffSqr->AddToBin_IntX(i,(*ptfa)[z4],tf0*tf0);
6042
df->m_p3DTimeDiffT->AddToBin_IntX(i,(*ptfa)[z4],1.0);
6043
df->m_pTimeDiffDist3DF->AddToBin_IntZ((*ptfa)[z4],(*ptfa)[z3+z4],i);
6044
if (m_iTimeDiffDistSteps != 0)
6045
if ((i % m_iTimeDiffDistSteps) == 0)
6046
df->m_pTimeDiffDistPairs[i/m_iTimeDiffDistSteps]->AddToBin((*ptfa)[z4],(*ptfa)[z3+z4]);
6047
}
6048
}
6049
mprintf("]\n");
6050
}
6051
}
6052
for (z3=0;z3<m_iTimeDiffDepth;z3++) // Das ist das Tau
6053
{
6054
df->m_pTimeDiff->m_pBin[z3] /= df->m_oaTimeDiffBuf.GetSize();
6055
df->m_pTimeDiffAbs->m_pBin[z3] /= df->m_oaTimeDiffBuf.GetSize();
6056
df->m_pTimeDiffSqr->m_pBin[z3] /= df->m_oaTimeDiffBuf.GetSize();
6057
}
6058
if (m_b3DTimeDiff)
6059
{
6060
for (z2=0;z2<df->m_p3DTimeDiff->m_iRes[0]*df->m_p3DTimeDiff->m_iRes[1];z2++)
6061
{
6062
if (df->m_p3DTimeDiffT->m_pBin[z2] != 0)
6063
{
6064
df->m_p3DTimeDiff->m_pBin[z2] /= df->m_p3DTimeDiffT->m_pBin[z2];
6065
df->m_p3DTimeDiffAbs->m_pBin[z2] /= df->m_p3DTimeDiffT->m_pBin[z2];
6066
df->m_p3DTimeDiffSqr->m_pBin[z2] /= df->m_p3DTimeDiffT->m_pBin[z2];
6067
}
6068
}
6069
if (m_iTimeDiffDistSteps != 0)
6070
for (z=0;z<m_iTimeDiffDepth/m_iTimeDiffStride3D/m_iTimeDiffDistSteps;z++)
6071
df->m_pTimeDiffDistPairs[z]->NormalizeBinIntegral(1000000.0);
6072
}
6073
}
6074
6075
6076
void CObservation::WriteTimeDiff(CDF *df, const char *anaup, const char *analow, const char *name, const char *multibuf, bool ddf)
6077
{
6078
char buf[256];
6079
int z, z2;
6080
C3DF *temp3DF;
6081
6082
mprintf(" Creating temporal difference plot...\n");
6083
BuildTimeDiff(df,ddf);
6084
mprintf(" (%.0f bin entries)\n",df->m_pTimeDiff->m_fBinEntries);
6085
sprintf(buf,"%s_timediff_%s%s.csv",analow,name,multibuf);
6086
mprintf(" Saving %s temporal difference plot as \"%s\"...\n",anaup,buf);
6087
df->m_pTimeDiff->Write("",buf,"",true);
6088
sprintf(buf,"%s_timediff_%s%s.agr",analow,name,multibuf);
6089
mprintf(" Saving %s temporal difference plot AGR file as \"%s\"...\n",anaup,buf);
6090
df->m_pTimeDiff->WriteAgr("",buf,"",name,false);
6091
6092
sprintf(buf,"%s_timediff_%s%s_abs.csv",analow,name,multibuf);
6093
mprintf(" Saving %s absolute temporal difference plot as \"%s\"...\n",anaup,buf);
6094
df->m_pTimeDiffAbs->Write("",buf,"",true);
6095
sprintf(buf,"%s_timediff_%s%s_abs.agr",analow,name,multibuf);
6096
mprintf(" Saving %s absolute temporal difference plot AGR file as \"%s\"...\n",anaup,buf);
6097
df->m_pTimeDiffAbs->WriteAgr("",buf,"",name,false);
6098
6099
sprintf(buf,"%s_timediff_%s%s_sqr.csv",analow,name,multibuf);
6100
mprintf(" Saving %s squared temporal difference plot as \"%s\"...\n",anaup,buf);
6101
df->m_pTimeDiffSqr->Write("",buf,"",true);
6102
sprintf(buf,"%s_timediff_%s%s_sqr.agr",analow,name,multibuf);
6103
mprintf(" Saving %s squared temporal difference plot AGR file as \"%s\"...\n",anaup,buf);
6104
df->m_pTimeDiffSqr->WriteAgr("",buf,"",name,false);
6105
6106
if (m_b3DTimeDiff)
6107
{
6108
mprintf(" Writing temporal 3D difference plot...\n");
6109
mprintf(" (%.0f bin entries)\n",df->m_p3DTimeDiff->m_fBinEntries);
6110
sprintf(buf,"%s_timediff_%s%s_triples.csv",analow,name,multibuf);
6111
mprintf(" Saving %s temporal difference plot triples as \"%s\"...\n",anaup,buf);
6112
df->m_p3DTimeDiff->Write("",buf,"");
6113
sprintf(buf,"%s_timediff_%s%s_matrix.csv",analow,name,multibuf);
6114
mprintf(" Saving %s temporal difference plot matrix as \"%s\"...\n",anaup,buf);
6115
df->m_p3DTimeDiff->WriteCSV("",buf,"");
6116
sprintf(buf,"%s_timediff_%s%s.nb",analow,name,multibuf);
6117
mprintf(" Saving %s temporal difference plot Mathematica Notebook as \"%s\"...\n",anaup,buf);
6118
df->m_p3DTimeDiff->WriteMathematicaNb("",buf,"",false);
6119
sprintf(buf,"%s_timediff_%s%s",analow,name,multibuf);
6120
mprintf(" Saving %s temporal difference plot Gnuplot Input as \"%s.gp\"...\n",anaup,buf);
6121
df->m_p3DTimeDiff->WriteGnuplotInput("",buf,"",false);
6122
6123
sprintf(buf,"%s_timediff_%s%s_triples_abs.csv",analow,name,multibuf);
6124
mprintf(" Saving %s absolute temporal difference plot triples as \"%s\"...\n",anaup,buf);
6125
df->m_p3DTimeDiffAbs->Write("",buf,"");
6126
sprintf(buf,"%s_timediff_%s%s_matrix_abs.csv",analow,name,multibuf);
6127
mprintf(" Saving %s absolute temporal difference plot matrix as \"%s\"...\n",anaup,buf);
6128
df->m_p3DTimeDiffAbs->WriteCSV("",buf,"");
6129
sprintf(buf,"%s_timediff_%s%s_abs.nb",analow,name,multibuf);
6130
mprintf(" Saving %s absolute temporal difference plot Mathematica Notebook as \"%s\"...\n",anaup,buf);
6131
df->m_p3DTimeDiffAbs->WriteMathematicaNb("",buf,"",false);
6132
sprintf(buf,"%s_timediff_%s%s_abs",analow,name,multibuf);
6133
mprintf(" Saving %s absolute temporal difference plot Gnuplot Input as \"%s.gp\"...\n",anaup,buf);
6134
df->m_p3DTimeDiffAbs->WriteGnuplotInput("",buf,"",false);
6135
6136
sprintf(buf,"%s_timediff_%s%s_triples_sqr.csv",analow,name,multibuf);
6137
mprintf(" Saving %s squared temporal difference plot triples as \"%s\"...\n",anaup,buf);
6138
df->m_p3DTimeDiffSqr->Write("",buf,"");
6139
sprintf(buf,"%s_timediff_%s%s_matrix_sqr.csv",analow,name,multibuf);
6140
mprintf(" Saving %s squared temporal difference plot matrix as \"%s\"...\n",anaup,buf);
6141
df->m_p3DTimeDiffSqr->WriteCSV("",buf,"");
6142
sprintf(buf,"%s_timediff_%s%s_sqr.nb",analow,name,multibuf);
6143
mprintf(" Saving %s squared temporal difference plot Mathematica Notebook as \"%s\"...\n",anaup,buf);
6144
df->m_p3DTimeDiffSqr->WriteMathematicaNb("",buf,"",false);
6145
sprintf(buf,"%s_timediff_%s%s_sqr",analow,name,multibuf);
6146
mprintf(" Saving %s squared temporal difference plot Gnuplot Input as \"%s.gp\"...\n",anaup,buf);
6147
df->m_p3DTimeDiffSqr->WriteGnuplotInput("",buf,"",false);
6148
6149
if (m_iTimeDiffDistSteps != 0)
6150
{
6151
for (z=0;z<m_iTimeDiffDepth/m_iTimeDiffStride3D/m_iTimeDiffDistSteps;z++)
6152
{
6153
sprintf(buf,"%s_timediff_beforeafter_%s%s_tau%.3f_triples.csv",analow,name,multibuf,z*m_iTimeDiffStride3D*m_iTimeDiffDistSteps*g_fTimestepLength/1000.0);
6154
mprintf(" Saving %s before/after plot triples as \"%s\"...\n",anaup,buf);
6155
df->m_pTimeDiffDistPairs[z]->Write("",buf,"");
6156
sprintf(buf,"%s_timediff_beforeafter_%s%s_tau%.3f_matrix.csv",analow,name,multibuf,z*m_iTimeDiffStride3D*m_iTimeDiffDistSteps*g_fTimestepLength/1000.0);
6157
mprintf(" Saving %s before/after plot matrix as \"%s\"...\n",anaup,buf);
6158
df->m_pTimeDiffDistPairs[z]->WriteCSV("",buf,"");
6159
sprintf(buf,"%s_timediff_beforeafter_%s%s_tau%.3f.nb",analow,name,multibuf,z*m_iTimeDiffStride3D*m_iTimeDiffDistSteps*g_fTimestepLength/1000.0);
6160
mprintf(" Saving %s before/after plot Mathematica Notebook as \"%s\"...\n",anaup,buf);
6161
df->m_pTimeDiffDistPairs[z]->WriteMathematicaNb("",buf,"",false);
6162
sprintf(buf,"%s_timediff_beforeafter_%s%s_tau%.3f",analow,name,multibuf,z*m_iTimeDiffStride3D*m_iTimeDiffDistSteps*g_fTimestepLength/1000.0);
6163
mprintf(" Saving %s before/after plot Gnuplot Input as \"%s.gp\"...\n",anaup,buf);
6164
df->m_pTimeDiffDistPairs[z]->WriteGnuplotInput("",buf,"",false);
6165
}
6166
}
6167
for (z2=0;z2<=3;z2++)
6168
{
6169
try { temp3DF = new C3DF(); } catch(...) { temp3DF = NULL; }
6170
if (temp3DF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
6171
6172
temp3DF->CopyFrom(df->m_pTimeDiffDist3DF);
6173
if (z2 != 0)
6174
{
6175
temp3DF->Smooth(z2);
6176
sprintf(buf,".s%d%s.plt",z2,multibuf);
6177
} else sprintf(buf,"%s.plt",multibuf);
6178
mprintf(" Saving 3D Plot as \"%s%s\"...\n",name,buf);
6179
temp3DF->WritePLT("",name,buf,false);
6180
6181
if (z2 != 0)
6182
sprintf(buf,".s%d%s.cube",z2,multibuf);
6183
else sprintf(buf,"%s.cube",multibuf);
6184
mprintf(" Saving 3D Plot as \"%s%s\"...\n",name,buf);
6185
temp3DF->WriteCube("",name,buf,false);
6186
}
6187
}
6188
}
6189
6190
6191
void CObservation::CreateTimeDiff(CDF *df, int comb)
6192
{
6193
int z2;
6194
CxFloatArray *ptfa;
6195
6196
if (m_bSelf)
6197
{
6198
for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()*comb;z2++)
6199
{
6200
try { ptfa = new CxFloatArray("CObservation::CreateTimeDiff():ptfa"); } catch(...) { ptfa = NULL; }
6201
if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
6202
6203
if (g_iTrajSteps != -1)
6204
{
6205
ptfa->SetMaxSize((long)(g_iTrajSteps*1.1));
6206
ptfa->SetGrow((long)(g_iTrajSteps*0.1));
6207
} else ptfa->SetGrow(1000);
6208
df->m_oaTimeDiffBuf.Add(ptfa);
6209
}
6210
} else
6211
{
6212
for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()*comb;z2++)
6213
{
6214
try { ptfa = new CxFloatArray("CObservation::CreateTimeDiff():ptfa"); } catch(...) { ptfa = NULL; }
6215
if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
6216
6217
if (g_iTrajSteps != -1)
6218
{
6219
ptfa->SetMaxSize((long)(g_iTrajSteps*1.1));
6220
ptfa->SetGrow((long)(g_iTrajSteps*0.1));
6221
} else ptfa->SetGrow(1000);
6222
df->m_oaTimeDiffBuf.Add(ptfa);
6223
}
6224
}
6225
}
6226
6227
6228
void CMSD::WriteSplit(const char *s)
6229
{
6230
FILE *a;
6231
int z, z2, z3;
6232
CAF *af;
6233
6234
a = OpenFileWrite(s,true);
6235
mfprintf(a,"# tau [ps]; Total MSD [pm^2]");
6236
6237
for (z=0;z<m_pAtomGroup->m_oaAtoms.GetSize();z++)
6238
for (z2=0;z2<((CxIntArray*)m_pAtomGroup->m_oaAtoms[z])->GetSize();z2++)
6239
for (z3=0;z3<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z3++)
6240
{
6241
if (m_pAtomGroup->m_baRealAtomType[z] == g_iVirtAtomType)
6242
mfprintf(a,"; Mol. %d #%d",z3+1,((CxIntArray*)m_pAtomGroup->m_oaAtoms[z])->GetAt(z2)+1);
6243
else mfprintf(a,"; Mol. %d %s%d",z3+1,((CAtom*)g_oaAtoms[m_pAtomGroup->m_baRealAtomType[z]])->m_sName,((CxIntArray*)m_pAtomGroup->m_oaAtoms[z])->GetAt(z2)+1);
6244
}
6245
mfprintf(a,"\n");
6246
6247
for (z=0;z<m_pMSD->m_iResolution;z++)
6248
{
6249
mfprintf(a,"%f; %f",m_pMSD->m_fMinVal+z*(m_pMSD->m_fMaxVal-m_pMSD->m_fMinVal)/m_pMSD->m_iResolution,m_pMSD->m_pBin[z]);
6250
6251
for (z2=0;z2<m_pAtomGroup->m_iAtomGes;z2++)
6252
for (z3=0;z3<((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize();z3++)
6253
{
6254
af = m_pSplitMSD[z2*((CMolecule*)g_oaMolecules[m_iShowMol])->m_laSingleMolIndex.GetSize()+z3];
6255
mfprintf(a,"; %f",af->m_pBin[z]);
6256
}
6257
mfprintf(a,"\n");
6258
}
6259
6260
fclose(a);
6261
}
Loggerhead is a web-based interface for Breezy
Version: 2.0.1