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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/gather.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
25
#include "travis.h"
26
#include "tools.h"
27
#include "database.h"
28
#include "statistics.h"
29
#include "maintools.h"
30
#include "dacf.h"
31
#include "interface.h"
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
25
#include "travis.h"
26
#include "tools.h"
27
#include "database.h"
28
#include "statistics.h"
29
#include "maintools.h"
30
#include "dacf.h"
31
#include "interface.h"
32
32
#include "structurefactor.h"
33
34
35
bool GatherInfos()
36
{
37
BTIN;
38
char buf[4096], buf2[256];
39
float tf, tf2;
40
FILE *a;
41
bool tb=false, tb2;
42
int z, z0, z2, z3, z4, z5, z6, z7;
43
int ti, ti2, ti3;
44
unsigned char ty, rty, atom;
45
unsigned char ty2, rty2, atom2;
46
CVirtualAtom *va;
47
CObservation *o;
48
CMolecule *mol;
49
CSingleMolecule *sm, *sm2;
50
CAtomGroup *ag;
51
CxWordArray tempwa;
52
CMolecule *m, *m2;
53
CAtom *at;
54
CElement *el;
55
CxIntArray *pia, ia;
56
57
g_bKeepUnfoldedCoords = false;
58
g_iDoubleBoxFactor = 1;
59
g_bBondACF = false;
60
g_bCombined = false;
61
g_bRefEnvFix = false;
62
g_bTimeDiff = false;
63
g_bRemoveCOM = false;
64
g_bSaveCoordsUnchanged = false;
65
g_bSDFUniform = false;
66
a = NULL;
67
ti2 = -1;
68
69
mprintf(YELLOW,"\n*** Interactive query of settings ***\n\n");
70
// SAVEPOS;
71
72
ti = 0;
73
if (g_bUnknownElements)
74
{
75
tb2 = false;
76
_unkstart:
77
tb = false;
78
mprintf(WHITE,"Unrecognized atom types: ");
79
for (z=0;z<g_oaAtoms.GetSize();z++)
80
{
81
if (z == g_iVirtAtomType)
82
continue;
83
84
at = (CAtom*)g_oaAtoms[z];
85
while (at->m_pMergedTo != NULL)
86
{
87
// mprintf("%s merged to %s\n",at->m_sName,at->m_pMergedTo->m_sName);
88
at = at->m_pMergedTo;
89
}
90
if (at->m_pElement->m_fRadius != 0)
91
continue;
92
if (tb)
93
mprintf(", ");
94
tb = true;
95
mprintf("%s",at->m_sName);
96
ti++;
97
ti2 = z;
98
}
99
mprintf("\n\n");
100
101
if ((ti == 1) && (mystricmp("X",((CAtom*)g_oaAtoms[ti2])->m_sName) == 0))
102
{ // Only Wannier centers unrecognized.
103
mprintf(" Possibly, atom type \"X\" are Wannier centers. If so, do not assign data to them.\n\n");
104
tb2 = false;
105
} else tb2 = true;
106
107
tb = false;
108
if (AskYesNo(" Do you want to assign atom data to them (y/n)? [%s] ",tb2,tb2?"yes":"no"))
109
{
110
if (tb2)
111
{
112
if (AskYesNo(" Automatically rename all atoms to corresponding elements (y/n)? [yes] ",true))
113
{
114
mprintf("\n");
115
tb2 = true;
116
tb = false;
117
for (z=0;z<g_oaAtoms.GetSize();z++)
118
{
119
if (z == g_iVirtAtomType)
120
continue;
121
122
at = (CAtom*)g_oaAtoms[z];
123
if (at->m_pElement->m_fRadius != 0)
124
continue;
125
126
buf2[0] = at->m_sName[0];
127
buf2[1] = at->m_sName[1];
128
buf2[2] = 0;
129
el = FindElement(buf2,true);
130
if (el != NULL)
131
{
132
if (el->m_fRadius == 0)
133
goto _unkX2;
134
} else
135
{
136
_unkX2:
137
buf2[1] = 0;
138
el = FindElement(buf2,true);
139
if (el != NULL)
140
{
141
if (el->m_fRadius == 0)
142
goto _unkX3;
143
} else
144
{
145
_unkX3:
146
strcpy(buf2,at->m_sName);
147
}
148
}
149
if (el == NULL)
150
{
151
mprintf(" - Skipping %s... (have no guess for atom type)\n",at->m_sName);
152
tb = true;
153
continue;
154
}
155
156
xAddAtom(buf2);
157
158
mprintf(" - Renaming %s to %s...\n",at->m_sName,buf2);
159
for (z2=0;z2<g_oaAtoms.GetSize();z2++)
160
{
161
if (((CAtom*)g_oaAtoms[z2])->m_pElement == el)
162
{
163
at = (CAtom*)g_oaAtoms[z2];
164
el = at->m_pElement;
165
goto _unkX1;
166
}
167
}
168
eprintf(" Strange error ^^\n");
169
_unkX1:;
170
for (z2=0;z2<(int)g_TimeStep.m_iGesAtomCount;z2++)
171
{
172
strcpy(buf,(char*)g_TimeStep.m_paLabels[z2]);
173
ReplaceDigits(buf);
174
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName) == 0)
175
{
176
at->m_iCount++;
177
((CAtom*)g_oaAtoms[z])->m_iCount--;
178
}
179
}
180
// mprintf("\nmerging %s to %s.\n",((CAtom*)g_oaAtoms[z])->m_sName,at->m_sName);
181
((CAtom*)g_oaAtoms[z])->m_pMergedTo = at;
182
}
183
if (tb)
184
{
185
mprintf("\n");
186
goto _unkstart;
187
}
188
tb = false;
189
goto _unkdone;
190
}
191
}
192
ti = g_oaAtoms.GetSize();
193
for (z=0;z<ti;z++)
194
{
195
if (z == g_iVirtAtomType)
196
continue;
197
198
at = (CAtom*)g_oaAtoms[z];
199
200
while (at->m_pMergedTo != NULL)
201
{
202
// mprintf("%s merged to %s\n",at->m_sName,at->m_pMergedTo->m_sName);
203
at = at->m_pMergedTo;
204
}
205
206
if (at->m_pElement->m_fRadius != 0)
207
continue;
208
mprintf(WHITE,"\n * Element %s\n\n",at->m_sName);
209
210
buf2[0] = at->m_sName[0];
211
buf2[1] = at->m_sName[1];
212
buf2[2] = 0;
213
el = FindElement(buf2,true);
214
if (el != NULL)
215
{
216
if (el->m_fRadius == 0)
217
goto _unk2;
218
} else
219
{
220
_unk2:
221
buf2[1] = 0;
222
el = FindElement(buf2,true);
223
if (el != NULL)
224
{
225
if (el->m_fRadius == 0)
226
goto _unk3;
227
} else
228
{
229
_unk3:
230
strcpy(buf2,at->m_sName);
231
}
232
}
233
234
if (AskYesNo(" Do you want to rename this element (y/n)? [yes] ",true))
235
{
236
_unk5:
237
AskString(" Enter new name for %s: [%s] ",buf,buf2,at->m_sName,buf2);
238
if (strlen(buf) > 7)
239
{
240
eprintf("Atom labels may have maximum length of 7 characters.\n");
241
goto _unk5;
242
}
243
if (ContainsDigit(buf))
244
{
245
eprintf("Digits in element labels not allowed.\n");
246
goto _unk5;
247
}
248
el = FindElement(buf,true);
249
if (el != NULL)
250
{
251
xAddAtom(buf);
252
if (AskYesNo(" Element %s is known. Merge %s atoms into %s (y/n)? [yes] ",true,buf,at->m_sName,buf))
253
{
254
for (z2=0;z2<g_oaAtoms.GetSize();z2++)
255
{
256
if (((CAtom*)g_oaAtoms[z2])->m_pElement == el)
257
{
258
at = (CAtom*)g_oaAtoms[z2];
259
el = at->m_pElement;
260
goto _unk1;
261
}
262
}
263
eprintf(" Strange error ^^\n");
264
_unk1:;
265
}
266
} else
267
{
268
mprintf(" Adding element %s...",buf);
269
270
try { at = new CAtom(); } catch(...) { at = NULL; }
271
if (at == NULL) NewException((double)sizeof(CAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
272
273
at->m_iIndex = g_oaAtoms.GetSize();
274
g_oaAtoms.Add(at);
275
276
try { at->m_pElement = new CElement(); } catch(...) { at->m_pElement = NULL; }
277
if (at->m_pElement == NULL) NewException((double)sizeof(CElement),__FILE__,__LINE__,__PRETTY_FUNCTION__);
278
279
el = at->m_pElement;
280
sprintf(at->m_sName,"%s",buf);
281
}
282
for (z2=0;z2<(int)g_TimeStep.m_iGesAtomCount;z2++)
283
{
284
strcpy(buf,(char*)g_TimeStep.m_paLabels[z2]);
285
ReplaceDigits(buf);
286
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName) == 0)
287
{
288
at->m_iCount++;
289
((CAtom*)g_oaAtoms[z])->m_iCount--;
290
}
291
}
292
((CAtom*)g_oaAtoms[z])->m_pMergedTo = at;
293
if (el->m_fRadius != 0)
294
continue;
295
} // END IF RENAME
296
297
if (AskYesNo(" Do you want to copy the atom parameters from another element (y/n)? [yes] ",true))
298
{
299
_unk4:
300
AskString(" Copy atom parameters from which element? [%s] ",buf,buf2,buf2);
301
el = FindElement(buf,true);
302
if (el == NULL)
303
{
304
eprintf("This element is not defined.\n");
305
goto _unk4;
306
}
307
if (el->m_fRadius == 0)
308
{
309
if (!AskYesNo(" This element has a radius of 0 (will form no bonds). Use it anyway (y/n)? [yes] ",true))
310
goto _unk4;
311
}
312
313
mprintf(WHITE,"\n A covalent radius of 0 pm hinders atoms of this kind from forming any bonds.\n\n");
314
315
at->m_pElement->m_fRadius = AskFloat(" Please enter covalent radius in pm: [%.2f] ",el->m_fRadius,el->m_fRadius);
316
at->m_pElement->m_fMass = AskFloat(" Please enter atom mass in u: [%.2f] ",el->m_fMass,el->m_fMass);
317
318
if (!tb && (fabs(at->m_pElement->m_fMass-el->m_fMass) < 0.01))
319
{
320
tb = true;
321
mprintf(RED,"\n Warning: ");
322
mprintf("Elements %s and %s keep their different labels, but will have\n",at->m_sName,buf);
323
mprintf(" the same mass and therefore also the same atom codes. They will not\n");
324
mprintf(" be distinguished in the molecule recognition!\n");
325
}
326
// mprintf(" Using mass=%.2fu, radius=%.2fpm, ord. number=%d.\n",at->m_pElement->m_fMass,el->m_fRadius,el->m_iOrd);
327
// at->m_pElement->CopyData(el);
328
} else
329
{
330
el = FindElement(buf2,true);
331
mprintf(WHITE,"\n A covalent radius of 0 pm hinders atoms of this kind from forming any bonds.\n\n");
332
if (el != NULL)
333
{
334
mprintf(" (Default values are for %s)\n\n",buf2);
335
at->m_pElement->m_fRadius = AskFloat(" Please enter covalent radius in pm: [%.2f] ",el->m_fRadius,el->m_fRadius);
336
at->m_pElement->m_fMass = AskFloat(" Please enter atom mass in u: [%.2f] ",el->m_fMass,el->m_fMass);
337
} else
338
{
339
at->m_pElement->m_fRadius = AskFloat(" Please enter covalent radius in pm: [100] ",100);
340
at->m_pElement->m_fMass = AskFloat_ND(" Please enter atom mass in u: ");
341
}
342
}
343
}
344
_unkdone:
345
mprintf("\n");
346
mprintf(WHITE,"%d atoms in the system: ",g_iGesAtomCount);
347
348
for (z=0;z<g_oaAtoms.GetSize();z++)
349
{
350
if (z == g_iVirtAtomType)
351
continue;
352
if (((CAtom*)g_oaAtoms[z])->m_pMergedTo != NULL)
353
continue;
354
mprintf("%dx %s",((CAtom*)g_oaAtoms[z])->m_iCount,((CAtom*)g_oaAtoms[z])->m_sName);
355
if (((CAtom*)g_oaAtoms[z])->m_pMergedTo != NULL)
356
mprintf(" (merged to %s)",((CAtom*)g_oaAtoms[z])->m_pMergedTo->m_sName);
357
if (z < (int)g_oaAtoms.GetSize()-1)
358
if (z+1 != g_iVirtAtomType)
359
mprintf(", ");
360
}
361
mprintf("\n");
362
} // END IF CHANGE UNKNOWN
363
mprintf("\n");
364
} // END IF UNKNOWN
365
366
ia.RemoveAll();
367
tb2 = false;
368
for (z=0;z<g_oaAtoms.GetSize();z++)
369
{
370
tb = false;
371
for (z3=0;z3<ia.GetSize();z3++)
372
{
373
if (z == ia[z3])
374
goto _next;
375
}
376
if (((CAtom*)g_oaAtoms[z])->m_pMergedTo != NULL)
377
continue;
378
if (z == g_iVirtAtomType)
379
continue;
380
for (z2=z+1;z2<g_oaAtoms.GetSize();z2++)
381
{
382
if (((CAtom*)g_oaAtoms[z2])->m_pMergedTo != NULL)
383
continue;
384
if (z2 == g_iVirtAtomType)
385
continue;
386
if (fabs(((CAtom*)g_oaAtoms[z])->m_pElement->m_fMass - ((CAtom*)g_oaAtoms[z2])->m_pElement->m_fMass) < 0.01)
387
{
388
if (!tb)
389
{
390
tb = true;
391
tb2 = true;
392
mprintf(RED,"\n Warning: ");
393
mprintf("The following atoms have the same mass and will therefore not be\n");
394
mprintf(" distinguished in the molecule recognition:\n\n");
395
mprintf(WHITE," Mass=%.2f: %s, %s",((CAtom*)g_oaAtoms[z])->m_pElement->m_fMass,((CAtom*)g_oaAtoms[z])->m_sName,((CAtom*)g_oaAtoms[z2])->m_sName);
396
ia.Add(z);
397
ia.Add(z2);
398
} else
399
{
400
mprintf(WHITE,", %s",((CAtom*)g_oaAtoms[z2])->m_sName);
401
}
402
}
403
}
404
if (tb)
405
mprintf("\n");
406
_next:;
407
}
408
if (tb2)
409
mprintf("\n");
410
411
mprintf(" The advanced mode includes some options which are quite powerful,\n yet possibly weird or seldomly required. ");
412
mprintf("This includes support for\n NPT ensemble, non-periodic systems, user-definded virtual atoms, pseudomolecules, ...\n\n");
413
414
g_bAdvanced1 = AskYesNo(" Use the advanced mode up to the function selection menu (y/n)? [no] ",false);
415
416
mprintf("\n");
417
418
if (g_bAdvanced1)
419
{
420
do
421
{
422
mprintf(" Use periodic boundary conditions (0=no, x, y, z, xy, xz, xyz)? [xyz] ");
423
inpprintf("! Use periodic boundary conditions (0=no, x, y, z, xy, xz, xyz)? [xyz]\n");
424
myget(buf);
425
} while (!ParsePeriodic(buf));
426
427
if (!g_bPeriodic)
428
{
429
/* if (AskYesNo(" Enter Box Size anyways (e.g. fo RDFs) (yes/no)? [yes] ",true))
430
{
431
goto _askbox;
432
} else
433
{
434
g_fBoxX = GuessBoxSize();
435
g_fBoxY = GuessBoxSize();
436
g_fBoxZ = GuessBoxSize();
437
mprintf("\nGuessed box size (for density 1.0 g/cm^3) is %.2f x %.2f x %.2f pm.\n\n",g_fBoxX,g_fBoxX,g_fBoxX);
438
}*/
439
// g_fBoxX = (g_TimeStep.m_vMax[0]-g_TimeStep.m_vMin[0])*10.0;
440
// g_fBoxY = (g_TimeStep.m_vMax[1]-g_TimeStep.m_vMin[1])*10.0;
441
// g_fBoxZ = (g_TimeStep.m_vMax[2]-g_TimeStep.m_vMin[2])*10.0;
442
// mprintf("\n Using cell vector of %.2f x %.2f x %.2f pm to \"fake\" non-periodic box.\n\n",g_fBoxX,g_fBoxY,g_fBoxZ);
443
}
444
} else
445
ParsePeriodic("xyz");
446
447
if (g_bPeriodic)
448
{
449
tf = GuessBoxSize();
450
mprintf(" A cell vector of %.2f pm would result in a density of 1.0 g/cm^3.\n\n",tf);
451
if (g_bAdvanced1)
452
{
453
g_bNPT = AskYesNo(" Use time-dependent cell vector (NPT ensemble) (y/n)? [no] ",false);
454
mprintf("\n");
455
} else g_bNPT = false;
456
457
if (g_bNPT)
458
{
459
if (g_fBoxX != 0)
460
{
461
mprintf(" Your PDB file contains cell vector information.\n\n");
462
} else
463
{
464
mprintf(" The trajectory does not contain cell vector information.\n");
465
mprintf(" (supported: PDB file with \"CRYST1\" section, like written by GROMACS trjconv)\n");
466
mprintf(" You have to supply a plain text file which contains the cell vectors for each step.\n");
467
mprintf(" It should contain three space-separated floating point numbers (X, Y, Z vector) per line.\n");
468
mprintf(" These numbers need to be IN ANGSTROM! (1 angstrom = 100 pm)\n\n");
469
_nptfileagain:
470
AskString_ND(" Please enter cell vector text file name: ",g_sNPTFile);
471
if (!FileExist(g_sNPTFile))
472
{
473
eprintf("Could not open file \"%s\" for reading.\n",g_sNPTFile);
474
goto _nptfileagain;
475
}
476
g_fNPTFile = fopen(g_sNPTFile,"rt");
477
g_TimeStep.ReadCellVector(g_fNPTFile);
478
fclose(g_fNPTFile);
479
mprintf("\n");
480
}
481
mprintf(" The initial cell vector is ( %.2f pm | %.2f pm | %.2f pm ).\n",g_fBoxX,g_fBoxY,g_fBoxZ);
482
mprintf(" The initial box density is %.6f g/cm^3.\n\n",tf*tf*tf/g_fBoxX/g_fBoxY/g_fBoxZ);
483
} else
484
{
485
if (g_fBoxX != 0)
486
{
487
mprintf(" Cell vector found in trajectory file:\n");
488
mprintf(" X = %.2f pm, Y = %.2f pm, Z = %.2f pm\n\n",g_fBoxX,g_fBoxY,g_fBoxZ);
489
if (AskYesNo(" Use these values (y/n)? [yes] ",true))
490
goto _celldone;
491
}
492
_askbox:
493
if (!AskYesNo(" Are the 3 cell vectors of the same size (yes/no)? [yes] ",true))
494
{
495
if (g_bPeriodicX)
496
g_fBoxX = AskFloat_ND(" Enter length of X cell vector in pm: ");
497
if (g_bPeriodicY)
498
g_fBoxY = AskFloat_ND(" Enter length of Y cell vector in pm: ");
499
if (g_bPeriodicZ)
500
g_fBoxZ = AskFloat_ND(" Enter length of Z cell vector in pm: ");
501
} else
502
{
503
g_fBoxX = AskFloat_ND(" Enter length of cell vector in pm: ");
504
g_fBoxY = g_fBoxX;
505
g_fBoxZ = g_fBoxX;
506
}
507
if ((g_fBoxX <= 0) || (g_fBoxY <= 0) || (g_fBoxZ <= 0))
508
{
509
eprintf("Cell vector of length <= 0 is not allowed.\n");
510
goto _askbox;
511
}
512
_celldone:
513
if (g_bPeriodicX && g_bPeriodicY && g_bPeriodicZ)
514
{
515
mprintf("\n The box size is %.2f x %.2f x %.2f pm.\n",g_fBoxX,g_fBoxY,g_fBoxZ);
516
mprintf(" The overall box density is %.6f g/cm^3.\n",tf*tf*tf/g_fBoxX/g_fBoxY/g_fBoxZ);
517
if (tf*tf*tf/g_fBoxX/g_fBoxY/g_fBoxZ > 15.0f)
518
{
519
mprintf("\n");
520
if (!AskYesNo(" The density of your box seems to be very high. Continue (y) or change input (n)? [n] ",false))
521
{
522
mprintf("\n");
523
goto _askbox;
524
}
525
mprintf("\n");
526
}
527
}
528
}
529
530
if (g_bAdvanced1 && g_bPeriodic)
531
{
532
mprintf("\n");
533
if (AskYesNo(" Should the periodic box be multiplied (y/n)? [no] ",false))
534
{
535
mprintf("\n");
536
g_bDoubleBox = true;
537
538
if (g_bPeriodicX)
539
g_iDoubleBoxX = AskUnsignedInteger(" Replicate the box n times in x direction: [2] ",2);
540
else g_iDoubleBoxX = 1;
541
542
if (g_bPeriodicY)
543
g_iDoubleBoxY = AskUnsignedInteger(" Replicate the box n times in y direction: [2] ",2);
544
else g_iDoubleBoxY = 1;
545
546
if (g_bPeriodicZ)
547
g_iDoubleBoxZ = AskUnsignedInteger(" Replicate the box n times in z direction: [2] ",2);
548
else g_iDoubleBoxZ = 1;
549
550
g_iDoubleBoxFactor = g_iDoubleBoxX * g_iDoubleBoxY * g_iDoubleBoxZ;
551
g_fBoxX *= g_iDoubleBoxX;
552
g_fBoxY *= g_iDoubleBoxY;
553
g_fBoxZ *= g_iDoubleBoxZ;
554
g_iGesAtomCount *= g_iDoubleBoxFactor;
555
g_iGesVirtAtomCount *= g_iDoubleBoxFactor;
556
} else g_bDoubleBox = false;
557
} else g_bDoubleBox = false;
558
} else g_bDoubleBox = false;
559
560
try { g_pUniteTemp = new bool[g_iGesAtomCount]; } catch(...) { g_pUniteTemp = NULL; }
561
if (g_pUniteTemp == NULL) NewException((double)g_iGesAtomCount*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
562
563
if (!g_bPeriodic)
564
g_bNPT = false;
565
566
if (g_bPeriodic)
567
{
568
g_fMinPeriodic = 1e30f;
569
if (g_bPeriodicX)
570
if (g_fMinPeriodic > g_fBoxX)
571
g_fMinPeriodic = g_fBoxX;
572
if (g_bPeriodicY)
573
if (g_fMinPeriodic > g_fBoxY)
574
g_fMinPeriodic = g_fBoxY;
575
if (g_bPeriodicZ)
576
if (g_fMinPeriodic > g_fBoxZ)
577
g_fMinPeriodic = g_fBoxZ;
578
}
579
580
// SAVEPOS;
581
_molbegin:
582
if (!g_bStreamInput)
583
{
584
if (g_bAdvanced1)
585
{
586
mprintf("\n");
587
g_iScanMolStep = AskInteger(" Execute molecule recognition for which time step (-1 = disable)? [0] ",0);
588
} else g_iScanMolStep = 0;
589
590
a = fopen(g_sInputTraj,"rb");
591
if ((g_bNPT) && (g_sNPTFile[0] != 0))
592
g_fNPTFile = fopen(g_sNPTFile,"rt");
593
if (g_iScanMolStep > 0)
594
{
595
mprintf(" Fast-forwarding to step %d...\n",g_iScanMolStep);
596
mprintf(WHITE," [");
597
for (z=0;z<g_iScanMolStep;z++)
598
{
599
if ((g_bNPT) && (g_sNPTFile[0] != 0))
600
fgets(buf,256,g_fNPTFile);
601
if (fmod(z,g_iScanMolStep/60.0) < 1.0)
602
mprintf(WHITE,"#");
603
if (!g_TimeStep.SkipTimestep(a))
604
{
605
eprintf("Error.\n",g_iScanMolStep);
606
goto _skipfail;
607
}
608
}
609
mprintf(WHITE,"]\n");
610
g_iFastForwardPos = ftell(a);
611
mprintf(" Step %d begins at offset %lu (%.1f MB).\n\n",g_iScanMolStep+1,g_iFastForwardPos,g_iFastForwardPos/1024.0/1024.0);
612
}
613
_skipfail:;
614
g_TimeStep.ReadTimestep(a,true);
615
if (g_bNPT)
616
{
617
if (g_sNPTFile[0] != 0)
618
g_TimeStep.ReadCellVector(g_fNPTFile);
619
mprintf("\n NPT: Using a cell vector of ( %.2f pm | %.2f pm | %.2f pm ) for molecule recognition.\n",g_fBoxX,g_fBoxY,g_fBoxZ);
620
}
621
} else
622
{
623
g_iScanMolStep = 0;
624
mprintf("\n Stream input: Executing molecule recognition from first timestep...\n");
625
}
626
627
g_iCloseAtomCounter = 0;
628
629
if (!g_TimeStep.ScanMolecules())
630
return false;
631
632
if (!g_bStreamInput)
633
{
634
fclose(a);
635
if (g_sNPTFile[0] != 0)
636
fclose(g_fNPTFile);
637
}
638
639
if (g_bPeriodic)
640
{
641
mprintf("\n Uniting molecules which have been broken by wrapping...\n");
642
g_TimeStep.UniteMolecules(true);
643
}
644
645
mprintf(YELLOW,"\n*** The following %d kind%s of molecules ha%s been recognized:\n",g_oaMolecules.GetSize(),(g_oaMolecules.GetSize()>1)?"s":"",(g_oaMolecules.GetSize()>1)?"ve":"s");
646
mprintf(" (ordered by molecular mass)\n\n");
647
for (z=0;z<g_oaMolecules.GetSize();z++)
648
{
649
mprintf(WHITE," - Molecule %d: %s ",z+1,((CMolecule*)g_oaMolecules[z])->m_sName);
650
mprintf("(%d piece%s, %.2f g/mol)\n",((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize(),(((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize()>1)?"s":"",((CMolecule*)g_oaMolecules[z])->m_fMass);
651
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
652
mprintf(" (%d noneq. atom%s, %d noneq. bond%s, %d noneq. angle%s)\n",sm->m_iAtomClasses,(sm->m_iAtomClasses==1)?"":"s",sm->m_oaBondGroups.GetSize(),(sm->m_oaBondGroups.GetSize()==1)?"":"s",sm->m_oaAngleGroups.GetSize(),(sm->m_oaAngleGroups.GetSize()==1)?"":"s");
653
if (((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms.GetSize() != 0)
654
{
655
if (((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms.GetSize() == 1)
656
mprintf(WHITE," Detected %d ring:\n",((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms.GetSize());
657
else mprintf(WHITE," Detected %d rings:\n",((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms.GetSize());
658
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms.GetSize();z2++)
659
{
660
mprintf(WHITE," %2d.) %2d-ring: ",z2+1,((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize());
661
if (((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize() > 20)
662
{
663
for (z3=0;z3<5;z3++)
664
{
665
mprintf("%s%d",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[z])->m_baAtomIndex[((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetAt(z3)+1);
666
if (z3+1 < ((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize())
667
mprintf(" - ");
668
}
669
mprintf(RED,"...");
670
mprintf(" - ");
671
for (z3=((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize()-5;z3<((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize();z3++)
672
{
673
mprintf("%s%d",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[z])->m_baAtomIndex[((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetAt(z3)+1);
674
if (z3+1 < ((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize())
675
mprintf(" - ");
676
}
677
} else
678
{
679
for (z3=0;z3<((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize();z3++)
680
{
681
mprintf("%s%d",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[z])->m_baAtomIndex[((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetAt(z3)+1);
682
if (z3+1 < ((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize())
683
mprintf(" - ");
684
}
685
}
686
mprintf("\n");
687
if (z2 >= 9)
688
{
689
mprintf(RED,"\n Showing only the first 10 rings.\n");
690
break;
691
}
692
}
693
}
694
695
mprintf("\n");
696
}
697
698
if (g_oaMolecules.GetSize() == 0)
699
{
700
eprintf("You don't have any atom/molecule in your simulation. This is probably not what you wanted.\n");
701
eprintf("Stopping execution.\n");
702
return false;
703
}
704
705
/* if (g_bVerbose)
706
{
707
mprintf(WHITE,">>> Output of the molecule tree >>>\n");
708
g_TimeStep.PrintMegaTree();
709
mprintf(WHITE,"<<< Output of the molecule tree <<<\n\n");
710
}*/
711
712
_matrixagain:
713
714
mprintf("\n");
715
if (!AskYesNo(" Accept these molecules (y) or change something (n)? [yes] ",true))
716
{
717
tb = false;
718
mprintf("\n");
719
mprintf(" If you want some atom types to form no bonds at all, assign covalent radius 0 to them.\n");
720
_modagain:
721
mprintf(YELLOW,"\n *** Modify Molecules ***\n\n");
722
mprintf(" Your choices:\n\n");
723
724
mprintf(" 1.) Change covalent atom radii used for bond recognition\n");
725
mprintf(" 2.) Break specific bonds\n");
726
mprintf(" 3.) Rename elements\n");
727
728
mprintf("\n");
729
switch(AskRangeInteger(" Please select: [done] ",1,3,0))
730
{
731
case 1:
732
mprintf("\n These values have been used (covalent radii from literature multiplied with %.2f):\n\n",g_fBondFactor);
733
for (z=0;z<g_oaAtoms.GetSize()-1;z++)
734
mprintf(" - %-2s %5.1f pm\n",((CAtom*)g_oaAtoms[z])->m_sName,((CAtom*)g_oaAtoms[z])->m_pElement->m_fRadius*g_fBondFactor);
735
mprintf("\n");
736
_arnew:
737
AskString(" Which radius do you want to change (RETURN=done)? ",buf,"");
738
if (strlen(buf) == 0)
739
goto _ardone;
740
for (z=0;z<g_oaAtoms.GetSize()-1;z++)
741
{
742
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName) == 0)
743
{
744
((CAtom*)g_oaAtoms[z])->m_pElement->m_fRadius = AskFloat(" Please enter new bond radius for %s in pm: [%.1f] ",((CAtom*)g_oaAtoms[z])->m_pElement->m_fRadius*g_fBondFactor,((CAtom*)g_oaAtoms[z])->m_sName,((CAtom*)g_oaAtoms[z])->m_pElement->m_fRadius*g_fBondFactor) / g_fBondFactor;
745
if (((CAtom*)g_oaAtoms[z])->m_pElement->m_fRadius == 0)
746
mprintf("\n Atom %s will form no bonds now.\n\n",((CAtom*)g_oaAtoms[z])->m_sName);
747
mprintf("\n");
748
tb = true;
749
goto _arnew;
750
}
751
}
752
eprintf(" Atom \"%s\" is not in the system.\n\n",buf);
753
goto _arnew;
754
_ardone:
755
mprintf("\n");
756
break;
757
758
case 2:
759
_breakagain:
760
mprintf("\n");
761
if (g_oaMolecules.GetSize() > 1)
762
{
763
_breakmol: ti = AskUnsignedInteger_ND(" Break bonds in which molecule (1-%d)? ",g_oaMolecules.GetSize())-1;
764
if ((ti < 0) || (ti >= (int)g_oaMolecules.GetSize()))
765
{
766
eprintf("Wrong Input.\n\n");
767
goto _breakmol;
768
}
769
} else ti = 0;
770
mol = (CMolecule*)g_oaMolecules[ti];
771
tb = true;
772
if (AskYesNo(" Break all bonds within this molecule (y/n)? [no] ",false))
773
{
774
for (z=0;z<mol->m_laSingleMolIndex.GetSize();z++)
775
{
776
sm = (CSingleMolecule*)g_oaSingleMolecules[mol->m_laSingleMolIndex[z]];
777
g_laBondBlackList.Append(&sm->m_laBonds);
778
}
779
} else
780
{
781
_breaka1: AskString_ND(" Enter 1st atom of the bond to break (e.g. O2): ",buf);
782
if (!ParseAtom(buf,ti,ty,rty,atom))
783
goto _breaka1;
784
_breaka2: AskString_ND(" Enter 2nd atom of the bond to break (e.g. O2): ",buf);
785
if (!ParseAtom(buf,ti,ty2,rty2,atom2))
786
goto _breaka2;
787
for (z=0;z<mol->m_laSingleMolIndex.GetSize();z++)
788
{
789
sm = (CSingleMolecule*)g_oaSingleMolecules[mol->m_laSingleMolIndex[z]];
790
g_laBondBlackList.Add(((CxIntArray*)sm->m_oaAtomOffset[ty])->GetAt(atom));
791
g_laBondBlackList.Add(((CxIntArray*)sm->m_oaAtomOffset[ty2])->GetAt(atom2));
792
}
793
}
794
if (AskYesNo("\n Break another bond (y/n)? [no] ",false))
795
goto _breakagain;
796
mprintf("\n");
797
break;
798
799
case 3:
800
/*********************************************************************************************************************/
801
_rennew:
802
mprintf("\n The system contains the following atoms:\n\n ");
803
tb2 = false;
804
for (z=0;z<g_oaAtoms.GetSize();z++)
805
{
806
if (z == g_iVirtAtomType)
807
continue;
808
if (((CAtom*)g_oaAtoms[z])->m_pMergedTo != NULL)
809
continue;
810
if (tb2)
811
mprintf(", ");
812
tb2 = true;
813
mprintf("%dx %s",((CAtom*)g_oaAtoms[z])->m_iCount,((CAtom*)g_oaAtoms[z])->m_sName);
814
}
815
mprintf("\n\n");
816
817
_renerr:
818
AskString(" Which element to rename: [done] ",buf,"");
819
820
if (strlen(buf) == 0)
821
goto _rendone;
822
823
for (z=0;z<g_oaAtoms.GetSize();z++)
824
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName) == 0)
825
goto _renfound;
826
eprintf("\n Atom \"%s\" not in the system.\n\n",buf);
827
goto _renerr;
828
_renfound:
829
tb = true;
830
at = (CAtom*)g_oaAtoms[z];
831
832
AskString_ND(" Enter new name for %s: ",buf2,buf);
833
if (strlen(buf2) > 7)
834
{
835
eprintf("\n Atom labels may have maximum length of 7 characters.\n\n");
836
goto _renfound;
837
}
838
if (ContainsDigit(buf2))
839
{
840
eprintf("\n Digits in element labels not allowed.\n\n");
841
goto _renfound;
842
}
843
el = FindElement(buf2,true);
844
if (el != NULL)
845
{
846
xAddAtom(buf2);
847
if (AskYesNo(" Element %s is known. Merge %s atoms into %s (y/n)? [yes] ",true,buf2,buf,buf2))
848
{
849
for (z2=0;z2<g_oaAtoms.GetSize();z2++)
850
{
851
if (((CAtom*)g_oaAtoms[z2])->m_pElement == el)
852
{
853
at = (CAtom*)g_oaAtoms[z2];
854
at->m_iCount--;
855
el = at->m_pElement;
856
goto _ren1;
857
}
858
}
859
eprintf("\n Strange error ^^\n");
860
_ren1:;
861
}
862
} else
863
{
864
mprintf("\n Adding element %s...\n\n",buf2);
865
866
try { at = new CAtom(); } catch(...) { at = NULL; }
867
if (at == NULL) NewException((double)sizeof(CAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
868
869
at->m_iIndex = g_oaAtoms.GetSize();
870
g_oaAtoms.Add(at);
871
at->m_iCount = 0;
872
873
try { at->m_pElement = new CElement(); } catch(...) { at->m_pElement = NULL; }
874
if (at->m_pElement == NULL) NewException((double)sizeof(CElement),__FILE__,__LINE__,__PRETTY_FUNCTION__);
875
876
at->m_pElement->m_fRadius = AskFloat(" Please enter covalent radius in pm: [100.0] ",100.0f);
877
at->m_pElement->m_fMass = AskFloat(" Please enter atom mass in u: [0] ",0);
878
sprintf(at->m_sName,"%s",buf2);
879
}
880
for (z2=0;z2<(int)g_TimeStep.m_iGesAtomCount;z2++)
881
{
882
strcpy(buf,(char*)g_TimeStep.m_paLabels[z2]);
883
ReplaceDigits(buf);
884
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName) == 0)
885
{
886
at->m_iCount++;
887
((CAtom*)g_oaAtoms[z])->m_iCount--;
888
}
889
}
890
((CAtom*)g_oaAtoms[z])->m_pMergedTo = at;
891
mprintf("\n");
892
goto _rennew;
893
_rendone:;
894
mprintf("\n The system contains the following atoms:\n\n ");
895
tb2 = false;
896
for (z=0;z<g_oaAtoms.GetSize();z++)
897
{
898
if (z == g_iVirtAtomType)
899
continue;
900
if (((CAtom*)g_oaAtoms[z])->m_pMergedTo != NULL)
901
continue;
902
if (tb2)
903
mprintf(", ");
904
tb2 = true;
905
mprintf("%dx %s",((CAtom*)g_oaAtoms[z])->m_iCount,((CAtom*)g_oaAtoms[z])->m_sName);
906
}
907
mprintf("\n");
908
/*********************************************************************************************************************/
909
break;
910
911
default:
912
goto _fin;
913
}
914
goto _modagain;
915
_fin:
916
if (tb)
917
{
918
mprintf(WHITE,"\n Going back to molecule recognition with changed settings.\n\n");
919
goto _molbegin;
920
} else
921
mprintf(WHITE,"\n Nothing was changed, not repeating molecule recognition.\n\n");
922
}
923
924
if (g_bAdvanced1)
925
{
926
g_bMegaMat = !AskYesNo(" Show bond matrices only for first representant of each molecule type (y/n)? [yes] ",true);
927
g_bMatOnlyBind = AskYesNo(" Show only bonds in the bond matrices (y/n)? [yes] ",true);
928
} else
929
{
930
g_bMegaMat = false;
931
g_bMatOnlyBind = true;
932
}
933
934
mprintf(WHITE,"\nOutput of bond matrices:\n");
935
g_TimeStep.PrintMatrix(!g_bMegaMat,g_bMatOnlyBind);
936
937
mprintf("\n");
938
mprintf(" You can create images of the structural formulas with the atom labels for easier\n");
939
mprintf(" identification of the atoms (requires installed GraphViz package - see www.graphviz.org).\n\n");
940
941
if (AskYesNo(" Create images of the structural formulas (y/n)? [no] ",false))
942
{
943
if (g_bAdvanced1)
944
ti = AskUnsignedInteger(" How many iterations to perform for formula optimization? [10] ",10);
945
else ti = 10;
946
RenderStructFormulas(ti);
947
}
948
949
mprintf(WHITE,"\n The atoms are currently ordered by topological priority.\n");
950
951
if (g_bAdvanced1)
952
{
953
mprintf("\n");
954
955
// This block written @ Ballmer peak ;-P Try it out yourself.
956
if (AskYesNo(" Change the atom ordering in some molecule (y/n)? [no] ",false))
957
{
958
if (AskYesNo(" Order atoms like in the input file instead (y/n)? [no] ",false))
959
{
960
ReorderLikeInput(); // Crazy shit!! (Ballmer Peak)
961
} else
962
{
963
_reordernext:
964
sprintf(buf," Change atom ordering in which of the molecules (");
965
for (z=0;z<g_oaMolecules.GetSize();z++)
966
{
967
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
968
strcat(buf,buf2);
969
if (z < g_oaMolecules.GetSize()-1)
970
strcat(buf,", ");
971
}
972
strcat(buf,")? ");
973
ti = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize())-1;
974
mol = (CMolecule*)g_oaMolecules[ti];
975
mol->m_oaNewNumbers.SetSize(mol->m_baAtomIndex.GetSize());
976
for (z=0;z<mol->m_baAtomIndex.GetSize();z++)
977
{
978
mprintf("* Atom type %s\n",((CAtom*)g_oaAtoms[mol->m_baAtomIndex[z]])->m_sName);
979
if (mol->m_oaNewNumbers[z] != NULL)
980
delete mol->m_oaNewNumbers[z];
981
982
try { mol->m_oaNewNumbers[z] = new CxIntArray("gather():mol->m_oaNewNumbers[z]"); } catch(...) { mol->m_oaNewNumbers[z] = NULL; }
983
if (mol->m_oaNewNumbers[z] == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
984
985
for (z2=0;z2<mol->m_waAtomCount[z];z2++)
986
{
987
_renumberagain:
988
ti2 = AskRangeInteger(" Which number should %s%d bear? [%d] ",1,mol->m_waAtomCount[z],z2+1,((CAtom*)g_oaAtoms[mol->m_baAtomIndex[z]])->m_sName,z2+1,z2+1);
989
for (z3=0;z3<z2;z3++)
990
if (((CxIntArray*)mol->m_oaNewNumbers[z])->GetAt(z3) == ti2-1)
991
{
992
eprintf("This number already was chosen for %s%d!\n",((CAtom*)g_oaAtoms[mol->m_baAtomIndex[z]])->m_sName,z3+1);
993
goto _renumberagain;
994
}
995
(*((CxIntArray*)mol->m_oaNewNumbers[z])).Add(ti2-1);
996
}
997
}
998
mprintf("\n Reordering atoms...");
999
ReorderAtoms(ti);
1000
mprintf("Done.\n\n");
1001
if (AskYesNo(" Change atom ordering of another molecule (y/n)? [no] ",false))
1002
goto _reordernext;
1003
goto _matrixagain;
1004
} // End "this block"
1005
1006
mprintf(WHITE,"\n Going back to molecule recognition with changed settings.\n\n");
1007
goto _molbegin;
1008
} // END IF REORDER
1009
} // END IF ADVANCED
1010
1011
mprintf(WHITE,"\n Defining virtual atom #1 as molecular Center of Geometry:\n");
1012
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1013
{
1014
mprintf(" - %s...\n",((CMolecule*)g_oaMolecules[z0])->m_sName);
1015
va = AddVirtualAtom(z0);
1016
va->m_iMode = 0;
1017
va->m_oCenterAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],false);
1018
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1019
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1020
va->m_faWeight[z] = 1.0f;
1021
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1022
}
1023
1024
mprintf(WHITE,"\n Defining virtual atom #2 as molecular Center of Mass:\n");
1025
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1026
{
1027
mprintf(" - %s...\n",((CMolecule*)g_oaMolecules[z0])->m_sName);
1028
va = AddVirtualAtom(z0);
1029
va->m_iMode = 0;
1030
va->m_oCenterAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],false);
1031
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1032
z3 = 0;
1033
tf2 = 0;
1034
for (z=0;z<va->m_oCenterAtoms.m_baAtomType.GetSize();z++)
1035
{
1036
tf = ((CAtom*)g_oaAtoms[va->m_oCenterAtoms.m_baRealAtomType[z]])->m_pElement->m_fMass;
1037
for (z2=0;z2<((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z])->GetSize();z2++)
1038
{
1039
va->m_faWeight[z3] = tf;
1040
tf2 += tf;
1041
z3++;
1042
}
1043
}
1044
va->m_fGesWeight = tf2;
1045
if (va->m_fGesWeight == 0)
1046
{
1047
eprintf(" Molecule %s has total mass of zero. Defining #2 as Center of Geometry.\n",((CMolecule*)g_oaMolecules[z0])->m_sName);
1048
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1049
va->m_faWeight[z] = 1.0f;
1050
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1051
}
1052
}
1053
1054
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1055
{
1056
m = (CMolecule*)g_oaMolecules[z0];
1057
if (m->m_oaRingAtoms.GetSize() != 0)
1058
{
1059
mprintf(WHITE,"\n Defining ring centers in %s:\n",m->m_sName);
1060
for (z=0;z<m->m_oaRingAtoms.GetSize();z++)
1061
{
1062
mprintf(" - Defining #%d as Center of Ring %d: ",z+3,z+1);
1063
for (z3=0;z3<((CxIntArray*)m->m_oaRingAtoms[z])->GetSize();z3++)
1064
{
1065
mprintf("%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[((CxIntArray*)m->m_oaRingAtomTypes[z])->GetAt(z3)]])->m_sName,((CxIntArray*)m->m_oaRingAtoms[z])->GetAt(z3)+1);
1066
if (z3+1 < ((CxIntArray*)m->m_oaRingAtoms[z])->GetSize())
1067
mprintf(" - ");
1068
}
1069
mprintf("\n");
1070
va = AddVirtualAtom(z0);
1071
va->m_iMode = 0;
1072
va->m_oCenterAtoms.m_pMolecule = m;
1073
for (z3=0;z3<((CxIntArray*)m->m_oaRingAtoms[z])->GetSize();z3++)
1074
va->m_oCenterAtoms.AddAtom(((CxIntArray*)m->m_oaRingAtomTypes[z])->GetAt(z3),((CxIntArray*)m->m_oaRingAtoms[z])->GetAt(z3),false);
1075
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1076
for (z3=0;z3<va->m_oCenterAtoms.m_iAtomGes;z3++)
1077
va->m_faWeight[z3] = 1.0f;
1078
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1079
}
1080
}
1081
}
1082
1083
if (g_bAdvanced1)
1084
{
1085
mprintf("\n");
1086
if (AskYesNo("\n Define additional virtual atoms (y/n)? [no] ",false))
1087
{
1088
_vabeg:
1089
sprintf(buf," To which molecule shall the virtual atom belong (");
1090
for (z=0;z<g_oaMolecules.GetSize();z++)
1091
{
1092
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
1093
strcat(buf,buf2);
1094
if (z < g_oaMolecules.GetSize()-1)
1095
strcat(buf,", ");
1096
}
1097
strcat(buf,")? ");
1098
1099
z = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize());
1100
va = AddVirtualAtom(z-1);
1101
mprintf(WHITE,"\n*** Defining virtual atom #%d in %s\n",va->m_iMolVirtAtom+1,((CMolecule*)g_oaMolecules[va->m_iMolecule])->m_sName);
1102
va->m_iMode = AskRangeInteger(" Define v.a. as center (0) or through distance/angle/dihedral (1)? [center] ",0,1,0);
1103
if (va->m_iMode == 0)
1104
{
1105
_vaatoms:
1106
mprintf(" Which atoms to use for center (e.g. \"C1,C3-5,H\")? [all] ");
1107
inpprintf("! Which atoms to use for center (e.g. \"C1,C3-5,H\")? [all]\n");
1108
myget(buf);
1109
if (strlen(buf)==0)
1110
va->m_oCenterAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],false);
1111
else if (!va->m_oCenterAtoms.ParseAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],buf))
1112
goto _vaatoms;
1113
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1114
_vaweight:
1115
mprintf(" How shall these atoms be weightened (RETURN=equal, *=mass, #=manually)? [equal] ");
1116
inpprintf("! How shall these atoms be weightened (RETURN=equal, *=mass, #=manually)? [equal]\n");
1117
myget(buf);
1118
if (strlen(buf)==0)
1119
{
1120
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1121
va->m_faWeight[z] = 1.0f;
1122
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1123
} else if (buf[0] == '*')
1124
{
1125
z3 = 0;
1126
tf2 = 0;
1127
for (z=0;z<va->m_oCenterAtoms.m_baAtomType.GetSize();z++)
1128
{
1129
tf = ((CAtom*)g_oaAtoms[va->m_oCenterAtoms.m_baRealAtomType[z]])->m_pElement->m_fMass;
1130
for (z2=0;z2<((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z])->GetSize();z2++)
1131
{
1132
va->m_faWeight[z3] = tf;
1133
tf2 += tf;
1134
z3++;
1135
}
1136
}
1137
va->m_fGesWeight = tf2;
1138
if (va->m_fGesWeight == 0)
1139
{
1140
eprintf("\n Molecule has total mass of zero. Weighting atoms equally.\n\n");
1141
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1142
va->m_faWeight[z] = 1.0f;
1143
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1144
}
1145
} else if (buf[0] == '#')
1146
{
1147
_vawagain:
1148
z3 = 0;
1149
tf2 = 0;
1150
mprintf("\n");
1151
for (z=0;z<va->m_oCenterAtoms.m_baAtomType.GetSize();z++)
1152
{
1153
for (z2=0;z2<((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z])->GetSize();z2++)
1154
{
1155
tf = AskFloat(" Enter the weight for %s%d: [1] ",1.0f,((CAtom*)g_oaAtoms[va->m_oCenterAtoms.m_baRealAtomType[z]])->m_pElement->m_sLabel, ((CxIntArray *)va->m_oCenterAtoms.m_oaAtoms[z])->GetAt(z2)+1);
1156
va->m_faWeight[z3] = tf;
1157
tf2 += tf;
1158
z3++;
1159
}
1160
}
1161
mprintf(" The sum of weights is %.4f.\n\n",tf2);
1162
va->m_fGesWeight = tf2;
1163
if (va->m_fGesWeight == 0)
1164
{
1165
eprintf("Sum of weights may not be zero. Enter the weights again.\n\n");
1166
goto _vawagain;
1167
}
1168
} else
1169
{
1170
eprintf("Wrong input.\n");
1171
inpprintf("! Wrong input.\n");
1172
goto _vaweight;
1173
}
1174
} else
1175
{
1176
_vabond:
1177
mprintf(" Enter 2nd atom for distance #%d- (e.g. C2): ",va->m_iMolVirtAtom+1);
1178
inpprintf("! Enter 2nd atom for distance #%d- (e.g. C2):\n",va->m_iMolVirtAtom+1);
1179
myget(buf);
1180
if (!ParseAtom(buf,va->m_iMolecule,va->m_iAtomType[0],va->m_iRealAtomType[0],va->m_iAtom[0]))
1181
goto _vabond;
1182
if ((va->m_iRealAtomType[0] == g_iVirtAtomType) && (va->m_iAtom[0] == va->m_iMolVirtAtom))
1183
{
1184
eprintf("This atom was already chosen.\n");
1185
goto _vabond;
1186
}
1187
_vaangle:
1188
mprintf(" Enter 3rd atom for angle #%d-%s%d- (e.g. C2)? ",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1);
1189
inpprintf("! Enter 3rd atom for angle #%d-%s%d- (e.g. C2)?\n",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1);
1190
myget(buf);
1191
if (!ParseAtom(buf,va->m_iMolecule,va->m_iAtomType[1],va->m_iRealAtomType[1],va->m_iAtom[1]))
1192
goto _vaangle;
1193
if (((va->m_iRealAtomType[1] == g_iVirtAtomType) && (va->m_iAtom[1] == va->m_iMolVirtAtom)) || ((va->m_iRealAtomType[1] == va->m_iRealAtomType[0]) && (va->m_iAtom[1] == va->m_iAtom[0])))
1194
{
1195
eprintf("This atom was already chosen.\n");
1196
goto _vaangle;
1197
}
1198
_vadihedral:
1199
mprintf(" Enter 4th atom for dihedral #%d-%s%d-%s%d- (e.g. C2)? ",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1);
1200
inpprintf("! Enter 4th atom for dihedral #%d-%s%d-%s%d- (e.g. C2)?\n",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1);
1201
myget(buf);
1202
if (!ParseAtom(buf,va->m_iMolecule,va->m_iAtomType[2],va->m_iRealAtomType[2],va->m_iAtom[2]))
1203
goto _vadihedral;
1204
if (((va->m_iRealAtomType[2] == g_iVirtAtomType) && (va->m_iAtom[2] == va->m_iMolVirtAtom)) || ((va->m_iRealAtomType[2] == va->m_iRealAtomType[0]) && (va->m_iAtom[2] == va->m_iAtom[0])) || ((va->m_iRealAtomType[2] == va->m_iRealAtomType[1]) && (va->m_iAtom[2] == va->m_iAtom[1])))
1205
{
1206
eprintf("This atom was already chosen.\n");
1207
goto _vadihedral;
1208
}
1209
1210
va->m_fValues[0] = AskFloat_ND(" Enter distance #%d-%s%d in pm: ",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1);
1211
va->m_fValues[1] = AskFloat_ND(" Enter angle #%d-%s%d-%s%d in degree: ",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1) * (float)Pi / 180.0f;
1212
va->m_fValues[2] = AskFloat_ND(" Enter dihedral #%d-%s%d-%s%d-%s%d in degree: ",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[2]])->m_sName,va->m_iAtom[2]+1) * (float)Pi / 180.0f;
1213
}
1214
1215
if (AskYesNo("\n Define further virtual atoms (y/n)? [no] ",false))
1216
goto _vabeg;
1217
}
1218
1219
mprintf("\n");
1220
if (AskYesNo(" Do you want to define pseudo-molecules (y/n)? [no] ",false))
1221
{
1222
tb2 = false;
1223
ti = 0;
1224
mprintf("\n If you need the center of mass or center of geometry of the whole system, you should\n");
1225
mprintf(" define a pseudo-molecule over the whole system, and use its atoms #1 and #2.\n\n");
1226
if (AskYesNo(" Define a pseudo-molecule over the whole system (y/n)? [yes] ",true))
1227
{
1228
ti++;
1229
/************************************************************************/
1230
mprintf("\n");
1231
try { m2 = new CMolecule(); } catch(...) { m2 = NULL; }
1232
if (m2 == NULL) NewException((double)sizeof(CMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1233
1234
try { sm2 = new CSingleMolecule(); } catch(...) { sm2 = NULL; }
1235
if (sm2 == NULL) NewException((double)sizeof(CSingleMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1236
1237
m2->m_bPseudo = true;
1238
sm2->m_bPseudo = true;
1239
m2->m_iIndex = g_oaMolecules.GetSize();
1240
sm2->m_iMolType = g_oaMolecules.GetSize();
1241
sm2->m_iMolSMIndex = 0;
1242
m2->m_laSingleMolIndex.Add(g_oaSingleMolecules.GetSize());
1243
g_oaMolecules.Add(m2);
1244
g_oaSingleMolecules.Add(sm2);
1245
1246
mprintf(WHITE," >>> Pseudo-molecule %d (= molecule %d) >>>\n\n",ti,g_oaMolecules.GetSize());
1247
mprintf(" Adding all atoms from all molecules...\n");
1248
1249
for (z=0;z<g_oaMolecules.GetSize();z++)
1250
{
1251
m = (CMolecule*)g_oaMolecules[z];
1252
if (m->m_bPseudo)
1253
continue;
1254
1255
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1256
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1257
1258
ag->AddAllAtoms(m,false);
1259
1260
ia.RemoveAll();
1261
1262
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1263
ia.Add(z2);
1264
1265
for (z2=0;z2<ag->m_baAtomType.GetSize();z2++)
1266
{
1267
m2->m_iAtomGes += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1268
1269
for (z4=0;z4<m2->m_baAtomIndex.GetSize();z4++)
1270
{
1271
if (m2->m_baAtomIndex[z4] == ag->m_baRealAtomType[z2])
1272
{
1273
m2->m_waAtomCount[z4] += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1274
pia = (CxIntArray*)sm2->m_oaAtomOffset[z4];
1275
goto _pmafound;
1276
}
1277
}
1278
1279
m2->m_baAtomIndex.Add(ag->m_baRealAtomType[z2]);
1280
sm2->m_baAtomIndex.Add(ag->m_baRealAtomType[z2]);
1281
m2->m_waAtomCount.Add(((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize());
1282
1283
try { pia = new CxIntArray("gather():pia"); } catch(...) { pia = NULL; }
1284
if (pia == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1285
1286
sm2->m_oaAtomOffset.Add(pia);
1287
_pmafound:
1288
for (z4=0;z4<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z4++)
1289
{
1290
for (z5=0;z5<ia.GetSize();z5++)
1291
{
1292
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[ia[z5]]];
1293
for (z6=0;z6<sm2->m_oaAtomOffset.GetSize();z6++)
1294
{
1295
for (z7=0;z7<((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetSize();z7++)
1296
{
1297
if (((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetAt(z7) == ((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)))
1298
{
1299
eprintf("Weird error: Atom %s%d from %s[%d] is already in the pseudo-molecule; skipping.\n",((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)+1,m->m_sName,ia[z5]+1);
1300
m2->m_waAtomCount[m2->m_waAtomCount.GetSize()-1]--;
1301
abort();
1302
}
1303
}
1304
}
1305
pia->Add(((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)));
1306
}
1307
}
1308
}
1309
delete ag;
1310
}
1311
mprintf("\n");
1312
/********************************************************************************/
1313
goto _nopseudomol;
1314
}
1315
_pseudomolnext:
1316
ti++;
1317
1318
if (!tb2)
1319
{
1320
tb2 = true;
1321
mprintf("\n You may define custom element labels. This enables keeping apart\n atoms of the same type from different molecules/positions.\n\n");
1322
tb = AskYesNo(" Keep the standard element labels (y) or define custom labels (n)? [yes] ",true);
1323
mprintf("\n");
1324
}
1325
1326
try { m2 = new CMolecule(); } catch(...) { m2 = NULL; }
1327
if (m2 == NULL) NewException((double)sizeof(CMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1328
1329
try { sm2 = new CSingleMolecule(); } catch(...) { sm2 = NULL; }
1330
if (sm2 == NULL) NewException((double)sizeof(CSingleMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1331
1332
m2->m_bPseudo = true;
1333
sm2->m_bPseudo = true;
1334
m2->m_iIndex = g_oaMolecules.GetSize();
1335
sm2->m_iMolType = g_oaMolecules.GetSize();
1336
sm2->m_iMolSMIndex = 0;
1337
m2->m_laSingleMolIndex.Add(g_oaSingleMolecules.GetSize());
1338
g_oaMolecules.Add(m2);
1339
g_oaSingleMolecules.Add(sm2);
1340
1341
mprintf(WHITE," >>> Pseudo-molecule %d (= molecule %d) >>>\n\n",ti,g_oaMolecules.GetSize());
1342
/* if (ti == 1)
1343
mprintf(WHITE," You may define custom element labels. This enables keeping apart\n atoms of the same type from different molecules/positions.\n\n");
1344
tb = AskYesNo(" Keep the standard element labels (y) or define custom labels (n)? [yes] ",true);
1345
mprintf("\n");
1346
*/
1347
for (z=0;z<g_oaMolecules.GetSize();z++)
1348
{
1349
m = (CMolecule*)g_oaMolecules[z];
1350
if (m->m_bPseudo)
1351
continue;
1352
if (AskYesNo(" Use atoms from molecule %d (%s) (y/n)? [no] ",false,z+1,m->m_sName))
1353
{
1354
mprintf("\n");
1355
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1356
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1357
1358
if (AskYesNo(" Use all atoms (y) from %s or only certain atoms (n)? [no] ",false,m->m_sName))
1359
{
1360
ag->AddAllAtoms(m,false);
1361
} else
1362
{
1363
_pseudomolp1:
1364
AskString_ND(" Please enter atoms from %s to use (e.g. C1-3,H,O4): ",buf,m->m_sName);
1365
if (!ag->ParseAtoms(m,buf))
1366
goto _pseudomolp1;
1367
}
1368
ia.RemoveAll();
1369
if (m->m_laSingleMolIndex.GetSize() > 1)
1370
{
1371
if (!AskYesNo(" Add selected atoms from all %s molecules (y), or only from certain molecules (n)? [yes] ",true,m->m_sName))
1372
{
1373
_pseudomolil:
1374
AskString_ND(" Enter the %s molecules to use (range 1-%d, e.g. 1,3-6,8): ",buf,m->m_sName,m->m_laSingleMolIndex.GetSize());
1375
ia.RemoveAll();
1376
if (!ParseIntList(buf,&ia))
1377
goto _pseudomolil;
1378
for (z2=0;z2<ia.GetSize();z2++)
1379
{
1380
if ((ia[z2] < 1) || (ia[z2] > m->m_laSingleMolIndex.GetSize()))
1381
{
1382
eprintf("Invalid number: %d (should be between 1 and %d).\n",ia[z2],m->m_laSingleMolIndex.GetSize());
1383
goto _pseudomolil;
1384
}
1385
ia[z2]--;
1386
}
1387
} else
1388
{
1389
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1390
ia.Add(z2);
1391
}
1392
} else ia.Add(0);
1393
1394
if (!tb) // Custom Labels
1395
{
1396
for (z2=0;z2<ag->m_baAtomType.GetSize();z2++)
1397
{
1398
_pmlagain:
1399
AskString(" How should %s from %s be labeled? [%s] ",buf,((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,m->m_sName,((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName);
1400
if (ContainsDigit(buf))
1401
{
1402
eprintf("Digits in element labels not allowed.\n");
1403
goto _pmlagain;
1404
}
1405
for (z3=0;z3<g_oaAtoms.GetSize();z3++)
1406
{
1407
if (mystricmp(buf,((CAtom*)g_oaAtoms[z3])->m_sName) == 0)
1408
{
1409
ti2 = z3;
1410
goto _pseudomold1;
1411
}
1412
}
1413
if (strlen(buf) > 7)
1414
{
1415
mprintf(" Element labels may only have up to 7 characters; truncating.\n");
1416
buf[7] = 0;
1417
}
1418
mprintf(" Adding new element label \"%s\"...\n",buf);
1419
1420
try { at = new CAtom(); } catch(...) { at = NULL; }
1421
if (at == NULL) NewException((double)sizeof(CAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1422
1423
at->m_iIndex = g_oaAtoms.GetSize();
1424
at->m_pElement = ((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_pElement;
1425
memcpy(at->m_sName,buf,8);
1426
at->m_iCount = ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1427
ti2 = g_oaAtoms.GetSize();
1428
g_oaAtoms.Add(at);
1429
_pseudomold1:
1430
m2->m_iAtomGes += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1431
for (z3=0;z3<m2->m_baAtomIndex.GetSize();z3++)
1432
{
1433
if (m2->m_baAtomIndex[z3] == ti2)
1434
{
1435
m2->m_waAtomCount[z3] += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1436
for (z4=0;z4<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z4++)
1437
{
1438
for (z5=0;z5<ia.GetSize();z5++)
1439
{
1440
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[ia[z5]]];
1441
for (z6=0;z6<sm2->m_oaAtomOffset.GetSize();z6++)
1442
{
1443
for (z7=0;z7<((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetSize();z7++)
1444
{
1445
if (((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetAt(z7) == ((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)))
1446
{
1447
eprintf("Atom %s%d from %s[%d] is already in the pseudo-molecule; skipping.\n",((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)+1,m->m_sName,ia[z5]+1);
1448
m2->m_waAtomCount[z3]--;
1449
goto _pseudomolsk1;
1450
}
1451
}
1452
}
1453
// mprintf("Molecule %d, SM %d, Type %d, Atom %d: Line %d.\n",z,ia[z5],((CxIntArray*)sm->m_oaAtomOffset[z2])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)));
1454
((CxIntArray*)sm2->m_oaAtomOffset[z3])->Add(((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)));
1455
_pseudomolsk1:;
1456
}
1457
}
1458
goto _pseudomold2;
1459
}
1460
}
1461
m2->m_baAtomIndex.Add(ti2);
1462
sm2->m_baAtomIndex.Add(ti2);
1463
m2->m_waAtomCount.Add(((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize());
1464
1465
try { pia = new CxIntArray("gather():pia"); } catch(...) { pia = NULL; }
1466
if (pia == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1467
1468
sm2->m_oaAtomOffset.Add(pia);
1469
for (z4=0;z4<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z4++)
1470
{
1471
for (z5=0;z5<ia.GetSize();z5++)
1472
{
1473
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[ia[z5]]];
1474
for (z6=0;z6<sm2->m_oaAtomOffset.GetSize();z6++)
1475
{
1476
for (z7=0;z7<((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetSize();z7++)
1477
{
1478
if (((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetAt(z7) == ((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)))
1479
{
1480
eprintf("Atom %s%d from %s[%d] is already in the pseudo-molecule; skipping.\n",((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)+1,m->m_sName,ia[z5]+1);
1481
m2->m_waAtomCount[m2->m_waAtomCount.GetSize()-1]--;
1482
goto _pseudomolsk2;
1483
}
1484
}
1485
}
1486
pia->Add(((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)));
1487
_pseudomolsk2:;
1488
}
1489
}
1490
_pseudomold2:;
1491
}
1492
} else // If not custom labels
1493
{
1494
for (z2=0;z2<ag->m_baAtomType.GetSize();z2++)
1495
{
1496
for (z4=0;z4<m2->m_baAtomIndex.GetSize();z4++)
1497
{
1498
if (m2->m_baAtomIndex[z4] == ag->m_baRealAtomType[z2])
1499
{
1500
m2->m_waAtomCount[z4] += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1501
pia = (CxIntArray*)sm2->m_oaAtomOffset[z4];
1502
goto _pmafound2;
1503
}
1504
}
1505
1506
m2->m_iAtomGes += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1507
m2->m_baAtomIndex.Add(ag->m_baRealAtomType[z2]);
1508
sm2->m_baAtomIndex.Add(ag->m_baRealAtomType[z2]);
1509
m2->m_waAtomCount.Add(((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize());
1510
1511
try { pia = new CxIntArray("gather():pia"); } catch(...) { pia = NULL; }
1512
if (pia == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1513
1514
sm2->m_oaAtomOffset.Add(pia);
1515
_pmafound2:
1516
for (z4=0;z4<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z4++)
1517
{
1518
for (z5=0;z5<ia.GetSize();z5++)
1519
{
1520
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[ia[z5]]];
1521
for (z6=0;z6<sm2->m_oaAtomOffset.GetSize();z6++)
1522
{
1523
for (z7=0;z7<((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetSize();z7++)
1524
{
1525
if (((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetAt(z7) == ((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)))
1526
{
1527
eprintf("Atom %s%d from %s[%d] is already in the pseudo-molecule; skipping.\n",((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)+1,m->m_sName,ia[z5]+1);
1528
m2->m_waAtomCount[m2->m_waAtomCount.GetSize()-1]--;
1529
goto _pseudomolsk3;
1530
}
1531
}
1532
}
1533
pia->Add(((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)));
1534
_pseudomolsk3:;
1535
}
1536
}
1537
}
1538
}
1539
delete ag;
1540
if (AskYesNo(" Use another set of atoms from %s (y/n)? [no] ",false,m->m_sName))
1541
{
1542
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1543
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1544
1545
goto _pseudomolp1;
1546
}
1547
}
1548
mprintf("\n");
1549
}
1550
_nopseudomol:
1551
m2->BuildName();
1552
mprintf(WHITE," <<< Pseudo-molecule %d (= molecule %d) defined as %s <<<\n\n",ti,g_oaMolecules.GetSize(),m2->m_sName);
1553
if (AskYesNo(" Define another pseudo-molecule (y/n)? [no] ",false))
1554
goto _pseudomolnext;
1555
mprintf(WHITE,"\n The following pseudo-molecules have been defined:\n");
1556
mprintf(" (note: pseudo-molecules start with a $ sign)\n\n");
1557
ti = 0;
1558
for (z=0;z<g_oaMolecules.GetSize();z++)
1559
{
1560
m = (CMolecule*)g_oaMolecules[z];
1561
if (m->m_bPseudo)
1562
{
1563
ti++;
1564
mprintf(" %d.) Molecule %d - %s\n",ti,z+1,m->m_sName);
1565
}
1566
}
1567
mprintf(WHITE,"\n Defining virtual atom #1 as molecular Center of Geometry:\n");
1568
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1569
{
1570
m = (CMolecule*)g_oaMolecules[z0];
1571
if (!m->m_bPseudo)
1572
continue;
1573
mprintf(" - %s...\n",m->m_sName);
1574
va = AddVirtualAtom(z0);
1575
va->m_iMode = 0;
1576
va->m_oCenterAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],false);
1577
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1578
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1579
va->m_faWeight[z] = 1.0f;
1580
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1581
}
1582
1583
mprintf(WHITE,"\n Defining virtual atom #2 as molecular Center of Mass:\n");
1584
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1585
{
1586
m = (CMolecule*)g_oaMolecules[z0];
1587
if (!m->m_bPseudo)
1588
continue;
1589
mprintf(" - %s...\n",m->m_sName);
1590
va = AddVirtualAtom(z0);
1591
va->m_iMode = 0;
1592
va->m_oCenterAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],false);
1593
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1594
z3 = 0;
1595
tf2 = 0;
1596
for (z=0;z<va->m_oCenterAtoms.m_baAtomType.GetSize();z++)
1597
{
1598
tf = ((CAtom*)g_oaAtoms[va->m_oCenterAtoms.m_baRealAtomType[z]])->m_pElement->m_fMass;
1599
for (z2=0;z2<((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z])->GetSize();z2++)
1600
{
1601
va->m_faWeight[z3] = tf;
1602
tf2 += tf;
1603
z3++;
1604
}
1605
}
1606
va->m_fGesWeight = tf2;
1607
if (va->m_fGesWeight == 0)
1608
{
1609
eprintf(" Molecule %s has total mass of zero. Defining #2 as Center of Geometry.\n",m->m_sName);
1610
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1611
va->m_faWeight[z] = 1.0f;
1612
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1613
}
1614
}
1615
}
1616
}
1617
1618
mprintf(GREEN,"\n>>> %d virtual atoms have been defined: >>>\n",g_oaVirtualAtoms.GetSize());
1619
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1620
{
1621
for (z=0;z<((CMolecule*)g_oaMolecules[z0])->m_laVirtualAtoms.GetSize();z++)
1622
{
1623
va = (CVirtualAtom*)g_oaVirtualAtoms[((CMolecule*)g_oaMolecules[z0])->m_laVirtualAtoms[z]];
1624
if (va->m_iMolVirtAtom < 2)
1625
{
1626
mprintf(WHITE,"\n #%d in %s: %s.",va->m_iMolVirtAtom+1,((CMolecule*)g_oaMolecules[va->m_iMolecule])->m_sName,(va->m_iMolVirtAtom==0)?"Center of Geometry":"Center of Mass");
1627
if (va->m_iMolVirtAtom == 1)
1628
mprintf("\n");
1629
continue;
1630
}
1631
mprintf(WHITE,"\n #%d in %s - defined through %s\n",va->m_iMolVirtAtom+1,((CMolecule*)g_oaMolecules[va->m_iMolecule])->m_sName,(va->m_iMode==0)?"center:":"distance/angle/dihedral:");
1632
if (va->m_iMode == 0)
1633
{
1634
if (!((CMolecule*)g_oaMolecules[z0])->m_bPseudo || (z > 1))
1635
{
1636
z4 = 0;
1637
for (z2=0;z2<va->m_oCenterAtoms.m_baAtomType.GetSize();z2++)
1638
{
1639
for (z3=0;z3<((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z2])->GetSize();z3++)
1640
{
1641
mprintf(" - %2s%-3d Weight %.2f%c\n",((CAtom*)g_oaAtoms[va->m_oCenterAtoms.m_baRealAtomType[z2]])->m_sName,((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z2])->GetAt(z3)+1,va->m_faWeight[z4]/va->m_fGesWeight*100.0f,'%');
1642
z4++;
1643
}
1644
}
1645
} else mprintf(" (pseudo-molecule, skipping atoms)\n");
1646
} else
1647
{
1648
mprintf(" - Distance #%d-%s%d = %.2f pm\n",z+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,va->m_fValues[0]);
1649
mprintf(" - Angle #%d-%s%d-%s%d = %.2f degree\n",z+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1,va->m_fValues[1]*180.0/Pi);
1650
mprintf(" - Dihedral #%d-%s%d-%s%d-%s%d = %.2f degree\n",z+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[2]])->m_sName,va->m_iAtom[2]+1,va->m_fValues[2]*180.0/Pi);
1651
}
1652
}
1653
}
1654
mprintf(GREEN,"\n<<< End of virtual atoms <<<\n\n");
1655
1656
if (g_bPeriodic)
1657
g_TimeStep.UniteMolecules(false);
1658
1659
g_TimeStep.CalcCenters();
1660
g_bFoldAtomwise = false;
1661
1662
if (g_bPeriodic)
1663
g_TimeStep.FoldMolecules();
1664
1665
BuildAtomIndices();
1666
1667
// g_TimeStep.WritePOV("step.pov");
1668
1669
mprintf(WHITE,"\n>>> List of functions <<<\n\n");
1670
DumpAnalyses();
1671
1672
mprintf(" (You may specify multiple analyses at once, but\n");
1673
mprintf(" the safe way is to perform only one kind of analysis at a time.)\n");
1674
_fncinput:
1675
inpprintf("! Which functions to compute (comma separated)?\n");
1676
mprintf("\n Which functions to compute (comma separated)? ");
1677
myget(buf);
1678
mprintf("\n");
1679
if (!ParseFunctions(buf))
1680
{
1681
eprintf("Wrong input.\n");
1682
inpprintf("! Wrong input.\n");
1683
goto _fncinput;
1684
}
1685
mprintf("\n");
1686
1687
if (g_bRegionAnalysis)
1688
{
1689
if (!(g_bRDF || g_bSDF || g_bADF || g_bDDF || g_bCDF || g_bRevSDF || g_bDens))
1690
{
1691
eprintf(" Region-specific analysis needs to be applied to some static analysis.\n\n");
1692
return false;
1693
}
1694
g_iaSMRegion.SetSize(g_oaSingleMolecules.GetSize());
1695
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
1696
g_iaSMRegion[z] = (rand()%2)+1;
1697
}
1698
1699
if (g_bVoro || g_bVoid || g_bSaveJustTraj || g_bSaveRefEnv || g_bCutCluster)
1700
g_bNeedMoleculeWrap = true;
1701
1702
if (g_bNPT && (g_bACF || g_bMSD))
1703
{
1704
mprintf(RED," Warning: ");
1705
mprintf("When a variable cell vector is used, dynamical analyses (like spectra or MSDs)\n");
1706
mprintf(" will give erroneous results.\n\n");
1707
}
1708
1709
mprintf(WHITE," The advanced mode includes some options which are quite powerful,\n yet possibly weird or seldomly required.\n\n");
1710
1711
g_bAdvanced2 = AskYesNo(" Use the advanced mode for the main part (y/n)? [no] ",false);
1712
mprintf("\n");
1713
1714
if (g_bThermo || g_bVDF || g_bRaman || g_bCombined || g_bBondACF || g_bVHDF || g_bACF || g_bUseVelocities || g_bUseForces || g_bMSD || g_bAggregation || g_bDLDisp || g_bDLDF || g_bDACF || g_bRDyn || g_bIRSpec || g_bIRSpec || g_bTimeDiff || g_bDeriv)
1715
{
1716
g_fTimestepLength = AskFloat(" Enter the length of one trajectory time step in fs: [0.5] ",0.5f);
1717
mprintf("\n");
1718
}
1719
1720
/*********** Interface ***************/
1721
if (!Interface_BeforeAnalysis())
1722
return false;
1723
1724
if (g_bCDF)
1725
{
1726
mprintf(YELLOW,"*** Combined Distribution Function\n\n");
1727
g_iCDFChannels = AskUnsignedInteger(" How many channels should the Combined Distribution Function have? [2] ",2);
1728
1729
try { g_iObsChannel = new int[g_iCDFChannels]; } catch(...) { g_iObsChannel = NULL; }
1730
if (g_iObsChannel == NULL) NewException((double)g_iCDFChannels*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1731
1732
mprintf(" Choose from these functions: rdf, adf, ddf, dip, vdf");
1733
if (g_bBetaFeatures)
1734
mprintf(", pldf, lidf");
1735
mprintf("\n");
1736
for (z=0;z<g_iCDFChannels;z++)
1737
{
1738
_entertype:
1739
AskString_ND(" Channel %d: Enter function type (e.g. rdf): ",buf,z+1);
1740
if (mystricmp(buf,"rdf")==0)
1741
{
1742
g_iObsChannel[z] = 0;
1743
g_bRDF = true;
1744
} else if (mystricmp(buf,"adf")==0)
1745
{
1746
g_iObsChannel[z] = 1;
1747
g_bADF = true;
1748
} else if (mystricmp(buf,"ddf")==0)
1749
{
1750
g_iObsChannel[z] = 2;
1751
g_bDDF = true;
1752
} else if (mystricmp(buf,"dip")==0)
1753
{
1754
g_iObsChannel[z] = 3;
1755
g_bDipDF = true;
1756
} else if (mystricmp(buf,"vdf")==0)
1757
{
1758
g_iObsChannel[z] = 4;
1759
g_bVDF = true;
1760
} else if ((mystricmp(buf,"pldf")==0) && g_bBetaFeatures)
1761
{
1762
g_iObsChannel[z] = 5;
1763
g_bPlDF = true;
1764
} else if ((mystricmp(buf,"lidf")==0) && g_bBetaFeatures)
1765
{
1766
g_iObsChannel[z] = 6;
1767
g_bLiDF = true;
1768
} else
1769
{
1770
eprintf("Wrong input.\n");
1771
inpprintf("! Wrong input.\n");
1772
goto _entertype;
1773
}
1774
}
1775
} else g_iCDFChannels = 1;
1776
1777
if (g_bDipDF || g_bDipole)
1778
ParseDipole();
1779
1780
if (g_bVoro)
1781
{
1782
try { g_pVoroWrapper = new CVoroWrapper(); } catch(...) { g_pVoroWrapper = NULL; }
1783
if (g_pVoroWrapper == NULL) NewException((double)sizeof(CVoroWrapper),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1784
1785
g_pVoroWrapper->Parse();
1786
}
1787
1788
/* if (g_bSFac)
1789
{
1790
try { g_pSFac = new CStructureFactor(); } catch(...) { g_pSFac = NULL; }
1791
if (g_pSFac == NULL) NewException((double)sizeof(CStructureFactor),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1792
1793
g_pSFac->Parse();
1794
}*/
1795
1796
if (g_bResp)
1797
{
1798
try { g_pResp = new CResp(); } catch(...) { g_pResp = NULL; }
1799
if (g_pResp == NULL) NewException((double)sizeof(CResp),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1800
1801
g_pResp->m_pTimeStep = &g_TimeStep;
1802
g_pResp->ParseResp();
1803
1804
if (!g_bFFGen)
1805
return true;
1806
}
1807
1808
if (g_bFFGen)
1809
{
1810
try { g_pFFGen = new CFFGen(); } catch(...) { g_pFFGen = NULL; }
1811
if (g_pFFGen == NULL) NewException((double)sizeof(CFFGen),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1812
1813
g_pFFGen->Parse(&g_TimeStep);
1814
1815
return true;
1816
}
1817
1818
if (g_bVoid)
1819
{
1820
try { g_pVoroWrapper = new CVoroWrapper(); } catch(...) { g_pVoroWrapper = NULL; }
1821
if (g_pVoroWrapper == NULL) NewException((double)sizeof(CVoroWrapper),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1822
1823
try { g_pVoroAnalysis = new CVoroAnalysis(); } catch(...) { g_pVoroAnalysis = NULL; }
1824
if (g_pVoroAnalysis == NULL) NewException((double)sizeof(CVoroAnalysis),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1825
1826
g_pVoroAnalysis->Parse();
1827
}
1828
1829
if (g_bAggregation)
1830
{
1831
mprintf(WHITE,">>> Selection of Aggregation Functions >>>\n\n");
1832
1833
g_bDACF = AskYesNo(" Compute Dimer Existence Autocorrelation Functions (DACFs) (y/n)? [yes] ",true);
1834
g_bDLDF = AskYesNo(" Compute Dimer Lifetime Distribution Functions (DLDFs) (y/n)? [yes] ",true);
1835
g_bDDisp = AskYesNo(" Compute Dimer Displacement Functions / Pair Diffusion (y/n)? [no] ",false);
1836
if (g_bDDisp)
1837
{
1838
g_bPairMSD = AskYesNo(" Compute Pair Mean Square Displacement (Pair Diffusion) (y/n)? [yes] ",true);
1839
g_bDLDisp = AskYesNo(" Compute combined Dimer Lifetime/Displacement Function (DLDisp) (y/n)? [yes] ",true);
1840
} else
1841
{
1842
g_bDLDisp = false;
1843
g_bPairMSD = false;
1844
}
1845
1846
mprintf(WHITE,"\n<<< Selection of Aggregation Functions <<<\n\n");
1847
}
1848
1849
if (g_bNbExchange)
1850
{
1851
mprintf(WHITE,">>> Selection of Neighborhood Exchange Functions >>>\n\n");
1852
mprintf(WHITE,"\n<<< Selection of Neighborhood Exchange Functions <<<\n\n");
1853
}
1854
1855
if (g_bAdvanced2)
1856
{
1857
if (g_bRDyn || g_bIRSpec)
1858
g_bRDynCacheMode = AskYesNo(" Use RDyn cached mode (do this unless there are problems) (y/n)? [yes] ",true);
1859
1860
if (g_bMSD)
1861
g_bMSDCacheMode = AskYesNo(" Use MSD cached mode (do this unless there are problems) (y/n)? [yes] ",true);
1862
} else
1863
{
1864
g_bRDynCacheMode = true;
1865
g_bMSDCacheMode = true;
1866
}
1867
1868
if (g_bClusterAnalysis)
1869
{
1870
try { g_pClusterAnalysis = new CClusterAnalysis(); } catch(...) { g_pClusterAnalysis = NULL; }
1871
if (g_pClusterAnalysis == NULL) NewException((double)sizeof(CClusterAnalysis),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1872
1873
g_pClusterAnalysis->Parse();
1874
}
1875
1876
if (g_bMicroHet)
1877
{
1878
try { g_pMicroHet = new CMicroHet(); } catch(...) { g_pMicroHet = NULL; }
1879
if (g_pMicroHet == NULL) NewException((double)sizeof(CMicroHet),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1880
1881
g_pMicroHet->Parse();
1882
}
1883
1884
if (g_bThermo)
1885
{
1886
try { g_pThermoAnalysis = new CThermoAnalysis(); } catch(...) { g_pThermoAnalysis = NULL; }
1887
if (g_pThermoAnalysis == NULL) NewException((double)sizeof(CThermoAnalysis),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1888
1889
g_pThermoAnalysis->Parse();
1890
}
1891
1892
if (g_bFESA)
1893
{
1894
try { g_pFESA = new CFESAnalysis(); } catch(...) { g_pFESA = NULL; }
1895
if (g_pFESA == NULL) NewException((double)sizeof(CFESAnalysis),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1896
1897
g_pFESA->Parse();
1898
}
1899
1900
if (g_bACF)
1901
{
1902
// mprintf(YELLOW,">>> Select Autocorrelation Functions >>>\n\n");
1903
1904
if (!g_bPowerSpec)
1905
g_bVACF = AskYesNo(" Calculate velocity autocorrelation function / power spectra (y/n)? [yes] ",true);
1906
else g_bVACF = true;
1907
1908
if (g_bVACF)
1909
g_bUseVelocities = true;
1910
1911
/* if (g_bBetaFeatures)
1912
g_bBondACF = AskYesNo(" Calculate bond vibration spectra (y/n)? [no] ",false);
1913
else*/ g_bBondACF = false;
1914
1915
/* g_bDipACF = AskYesNo(" Calculate dipole autocorrelation function / IR spectra (y/n)? [no] ",false);
1916
if (g_bDipACF)
1917
g_bDipole = true;*/
1918
1919
// mprintf(YELLOW,"\n<<< End of Select Autocorrelation Functions <<<\n\n");
1920
}
1921
1922
if (g_bBondACF)
1923
{
1924
mprintf(WHITE,">>> Bond vibration spectra >>>\n\n");
1925
if (g_iTrajSteps != -1)
1926
g_iBondACFDepth = AskUnsignedInteger(" Enter bond ACF depth in time steps: [%d] ",g_iTrajSteps/2,g_iTrajSteps/2);
1927
else g_iBondACFDepth = AskUnsignedInteger(" Enter bond ACF depth in time steps: [%d] ",4096,4096);
1928
ti = CalcFFTSize(g_iBondACFDepth,false);
1929
if (g_iBondACFDepth != ti)
1930
{
1931
mprintf(WHITE,"\n The next \"fast\" size for FFT is %d. Using this instead of %d as size.\n",ti,g_iBondACFDepth);
1932
g_iBondACFDepth = ti;
1933
}
1934
g_bBondACFNormalize = AskYesNo(" Normalize all bond ACFs (removes intensity info for the peaks) (y/n)? [no] ",false);
1935
g_bBondACFSymmetrize = AskYesNo(" Symmetrize all bond ACFs (y/n)? [no] ",false);
1936
g_bBondACFWindow = AskYesNo(" Apply window function to bond ACFs (y/n)? [yes] ",true);
1937
g_bBondACFDebug = AskYesNo(" Write out bond ACF debug data (y/n)? [no] ",false);
1938
mprintf(WHITE,"\n<<< End of Bond vibration spectra <<<\n\n");
1939
}
1940
1941
if (g_bRDyn || g_bIRSpec || g_bBondACF || g_bVACF)
1942
{
1943
if (g_bAdvanced2)
1944
g_bACFFFT = AskYesNo(" Use fourier transform for autocorrelation (much faster) (y/n)? [yes] ",true);
1945
else g_bACFFFT = true;
1946
} else g_bACFFFT = true;
1947
1948
if (g_bCDF || g_bDipDF || g_bRDF || g_bVHDF || g_bSDF || g_bPlDF || g_bLiDF || g_bVoidSDF || g_bRevSDF || g_bADF || g_bDDF || g_bSaveRefEnv || g_bCutCluster || g_bCond || g_bNbAnalysis)
1949
{
1950
if (g_oaMolecules.GetSize() > 1)
1951
{
1952
sprintf(buf,"\n Which of the molecules should be the reference molecule (");
1953
for (z=0;z<g_oaMolecules.GetSize();z++)
1954
{
1955
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
1956
strcat(buf,buf2);
1957
if (z < g_oaMolecules.GetSize()-1)
1958
strcat(buf,", ");
1959
}
1960
strcat(buf,")? ");
1961
g_iFixMol = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize()) - 1;
1962
} else g_iFixMol = 0;
1963
mprintf(WHITE,"\n %s is the reference molecule.\n\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
1964
} else g_iFixMol = -1;
1965
1966
if (g_bSaveRefEnv)
1967
{
1968
mprintf(YELLOW,">>> Save environment of the reference molecule >>>\n\n");
1969
g_bSaveRefWithEnv = AskYesNo(" Save the reference molecule itself (y/n)? [yes] ",true);
1970
g_bRefEnvCenter = AskYesNo(" Center the reference molecule in the box (y/n)? [yes] ",true);
1971
if (g_bRefEnvCenter)
1972
{
1973
mprintf("\n The first reference atom will be put into the middle of the box.\n\n");
1974
g_bRefEnvFix = AskYesNo(" Fix rotational freedom of the reference molecule (y/n)? [no] ",false);
1975
if (g_bRefEnvFix)
1976
{
1977
mprintf("\n The 2nd reference atom will be put onto the positive X axis,\n");
1978
mprintf(" and the 3rd reference atom into the X-Y plane with positive Y values.\n\n");
1979
}
1980
mprintf(WHITE," You will be asked for the reference atom(s) lateron.\n\n");
1981
}
1982
if (((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() > 1)
1983
g_iSaveRefMol = AskRangeInteger(" Which representative of the reference molecules to use (1-%d)? [1] ",1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize(),1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()) - 1;
1984
else g_iSaveRefMol = 0;
1985
mprintf(WHITE,"\nPlease choose mode for neighborhood detection:\n\n");
1986
inpprintf("! Please choose mode for neighborhood detection:\n");
1987
mprintf(" 1.) Search neighbors once in the beginning and always show those.\n");
1988
mprintf(" 2.) Search neighbors in every step and show the current neighbors.\n");
1989
mprintf(" (Warning: Neighbor count differs from step to step - be aware.\n");
1990
mprintf(" 3.) Find the frequentiest neighbors over all steps and always show those.\n\n");
1991
mprintf(WHITE," Please note: ");
1992
mprintf("Programs such as VMD cannot handle variable atom count \n");
1993
mprintf(" along a trajectory and will therefore not work properly with mode 2!\n\n");
1994
g_iNbhMode = AskRangeInteger(" Choice (1-3): [3] ",1,3,3);
1995
mprintf(YELLOW,"\n<<< End of Save environment of the reference molecule <<<\n\n");
1996
}
1997
1998
if (g_bCutCluster)
1999
{
2000
mprintf(WHITE,">>> Cut clusters >>>\n\n");
2001
g_bSaveRefWithEnv = AskYesNo(" Show reference molecule itself (y/n)? [yes] ",true);
2002
g_bRefEnvCenter = AskYesNo(" Center reference molecule in the box (y/n)? [yes] ",true);
2003
if (g_bRefEnvCenter)
2004
g_bRefEnvFix = AskYesNo(" Fix rotational freedom of the reference molecule (y/n)? [no] ",false);
2005
_clustercount:
2006
g_iClusterCount = AskUnsignedInteger(" How many clusters to create? [100] ",100);
2007
g_iClusterSteps = AskUnsignedInteger(" How many time steps to use for cluster creation? [%d] ",g_iTrajSteps,g_iTrajSteps);
2008
mprintf("\nCreating cluster distribution...");
2009
for (z=0;z<g_iClusterCount;z++)
2010
{
2011
if (fmod(z,g_iClusterCount/25.0) < 1.0)
2012
mprintf(".");
2013
z3=0;
2014
_clustagain:
2015
z3++;
2016
if (z3 > 500)
2017
{
2018
eprintf("Error: Too few molecules / time steps for requested cluster count.\n");
2019
goto _clustercount;
2020
}
2021
ti = ((((unsigned long)rand()%16384)+rand()*16384) % g_iClusterSteps) + 1;
2022
ti2 = rand()%((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize();
2023
for (z2=0;z2<g_iaClusterSteps.GetSize();z2++)
2024
if ((g_iaClusterSteps[z2] == ti) && (g_iaClusterMol[z2] == ti2))
2025
goto _clustagain;
2026
g_iaClusterSteps.Add(ti);
2027
g_iaClusterMol.Add(ti2);
2028
}
2029
mprintf("Done.\n");
2030
mprintf("Sorting cluster distribution...");
2031
for (z=0;z<g_iClusterCount-1;z++)
2032
{
2033
if (fmod(z,(g_iClusterCount-1)/25.0) < 1.0)
2034
mprintf(".");
2035
ti = 99999999;
2036
ti2 = 99999999;
2037
ti3 = -1;
2038
for (z2=z;z2<g_iClusterCount;z2++)
2039
{
2040
if (g_iaClusterSteps[z2] < ti)
2041
{
2042
ti = g_iaClusterSteps[z2];
2043
ti2 = g_iaClusterMol[z2];
2044
ti3 = z2;
2045
} else if (g_iaClusterSteps[z2] == ti)
2046
{
2047
if (g_iaClusterMol[z2] < ti2)
2048
{
2049
ti2 = g_iaClusterMol[z2];
2050
ti3 = z2;
2051
}
2052
}
2053
}
2054
if (ti3 == -1)
2055
abort();
2056
ti = g_iaClusterSteps[z];
2057
g_iaClusterSteps[z] = g_iaClusterSteps[ti3];
2058
g_iaClusterSteps[ti3] = ti;
2059
ti = g_iaClusterMol[z];
2060
g_iaClusterMol[z] = g_iaClusterMol[ti3];
2061
g_iaClusterMol[ti3] = ti;
2062
}
2063
mprintf("Done.\n\n");
2064
mprintf("Writing cluster selection to \"cluster.csv\"...");
2065
a = OpenFileWrite("cluster.csv",true);
2066
mfprintf(a,"# Cluster; Timestep; Ref. Mol.\n");
2067
2068
for (z=0;z<g_iClusterCount;z++)
2069
mfprintf(a,"%d; %d; %d\n",z+1,g_iaClusterSteps[z],g_iaClusterMol[z]+1);
2070
2071
fclose(a);
2072
mprintf("Done.\n\n");
2073
mprintf(WHITE,"<<< End of Cut clusters <<<\n\n");
2074
}
2075
2076
if (g_bSDF || g_bVoidSDF || g_bAvg || ((g_bSaveRefEnv || g_bCutCluster) && g_bRefEnvFix)) // Nur fuer SDFs: Welche zwei weiteren Atome fixieren?
2077
{
2078
g_iRefSystemDim = 3;
2079
_ref3again:
2080
mprintf(" Please enter three reference atoms (e.g. C1,H2,O1): ");
2081
inpprintf("! Please enter three reference atoms (e.g. C1,H2,O1):\n");
2082
myget(buf);
2083
if (!ParseRefSystem(g_iFixMol,buf,3))
2084
goto _ref3again;
2085
for (z=1;z<3;z++)
2086
{
2087
for (z2=0;z2<z;z2++)
2088
{
2089
if ((g_iFixAtomType[z] == g_iFixAtomType[z2]) && (g_iFixAtom[z] == g_iFixAtom[z2]))
2090
{
2091
eprintf("Please enter three different atoms.\n\n");
2092
inpprintf("! Please enter three different atoms.\n");
2093
goto _ref3again;
2094
}
2095
}
2096
}
2097
mprintf("\n");
2098
mprintf(WHITE,"Reference plane: Fixing in %s the %d. %s-, the %d. %s- and the %d. %s atom.\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[1]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName,g_iFixAtom[2]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_sName);
2099
mprintf("\n");
2100
} else if (g_bRevSDF)
2101
{
2102
g_iRefSystemDim = 2;
2103
_ref2again:
2104
mprintf(" Please enter two reference atoms (e.g. C1,H3): ");
2105
inpprintf("! Please enter two reference atoms (e.g. C1,H3):\n");
2106
myget(buf);
2107
if (!ParseRefSystem(g_iFixMol,buf,2))
2108
goto _ref2again;
2109
if ((g_iFixAtomType[0] == g_iFixAtomType[1]) && (g_iFixAtom[0] == g_iFixAtom[1]))
2110
{
2111
eprintf("Please enter two different atoms.\n\n");
2112
inpprintf("! Please enter two different atoms.\n");
2113
goto _ref2again;
2114
}
2115
mprintf("\n");
2116
mprintf(WHITE,"Reference axis: Fixing in %s the %d. %s and the %d. %s atom.\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[1]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName);
2117
mprintf("\n");
2118
} else if (g_bVHDF || g_bRDF || g_bADF || g_bPlDF || g_bLiDF || g_bDDF || g_bSaveRefEnv || g_bSaveRefEnv || g_bCutCluster) // Fuer Verteilungsfunktion: Welches Atom im Ursprung
2119
{
2120
g_iRefSystemDim = 1;
2121
if (g_bAdvanced2)
2122
{
2123
_ref1again:
2124
mprintf(" Please enter the atom to put into the box center (e.g. C3): [center of mass] ");
2125
inpprintf("! Please enter the atom to put into the box center (e.g. C3): [center of mass]\n");
2126
myget(buf);
2127
if (strlen(buf)==0)
2128
{
2129
if (!ParseRefSystem(g_iFixMol,"#2",1))
2130
{
2131
eprintf("Weird error.\n");
2132
inpprintf("! Weird error.\n");
2133
abort();
2134
}
2135
} else if (!ParseRefSystem(g_iFixMol,buf,1))
2136
goto _ref1again;
2137
mprintf("\n");
2138
mprintf(WHITE,"Reference atom: Fixing in %s the %d. %s atom.\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName);
2139
mprintf("\n");
2140
} else
2141
{
2142
if (!ParseRefSystem(g_iFixMol,"#2",1))
2143
{
2144
eprintf("Weird error.\n");
2145
inpprintf("! Weird error.\n");
2146
abort();
2147
}
2148
}
2149
} else if (g_iFixMol != -1)
2150
{
2151
g_iRefSystemDim = 1;
2152
if (!ParseRefSystem(g_iFixMol,"#2",1))
2153
{
2154
eprintf("Weird error.\n");
2155
abort();
2156
}
2157
mprintf(" Reference atom: Fixing in %s the %d. %s atom.\n\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName);
2158
}
2159
2160
if (g_bSaveRefEnv || g_bCutCluster)
2161
{
2162
mprintf(WHITE,">>> Neighborhood Definition >>>\n\n");
2163
2164
try { g_pNbSet = new CNbSet(); } catch(...) { g_pNbSet = NULL; }
2165
if (g_pNbSet == NULL) NewException((double)sizeof(CNbSet),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2166
2167
g_pNbSet->Parse(g_iFixMol);
2168
mprintf(WHITE,"\n<<< End of Neighborhood Definition <<<\n\n");
2169
2170
if (g_bSaveRefEnv)
2171
{
2172
if (AskYesNo(" Create a temporal development overlay (TDO) plot (y/n)? [no] ",false))
2173
{
2174
g_bTDO = true;
2175
g_laTDOSteps.RemoveAll();
2176
if (AskYesNo(" Use equidistant intervals (y) or specify each point (n) (y/n)? [yes] ",true))
2177
{
2178
g_bTDOEqui = true;
2179
g_iTDOCount = AskUnsignedInteger(" Enter the overlay count: [5] ",5);
2180
g_iTDOStart = AskUnsignedInteger(" Enter the starting timestep: [0] ",0);
2181
g_iTDOStride = AskUnsignedInteger(" Enter the overlay distance in steps: [1000] ",1000);
2182
for (z=0;z<g_iTDOCount;z++)
2183
g_laTDOSteps.Add(g_iTDOStart+z*g_iTDOStride);
2184
} else
2185
{
2186
g_bTDOEqui = false;
2187
while (true)
2188
{
2189
ti = AskUnsignedInteger(" Enter timestep for %dth overlay: [done] ",999999,g_laTDOSteps.GetSize()+1);
2190
if (ti == 999999)
2191
break;
2192
g_laTDOSteps.Add(ti);
2193
}
2194
}
2195
g_fTDOBleaching = AskRangeFloat(" Enter the TDO bleaching grade (0-1): [0.8] ",0.0f,1.0f,0.8f);
2196
} else g_bTDO = false;
2197
}
2198
}
2199
2200
if (g_bAggregation || g_bNbAnalysis || g_bPlDF || g_bLiDF || g_bRDyn || g_bIRSpec || g_bDipDF || g_bMSD || g_bADF || g_bDDF || g_bVACF || g_bDipACF || g_bRevSDF || g_bSDF || g_bVHDF || g_bRDF || g_bDens || g_bVDF || g_bFDF || g_bCond) // Fuer Verteilungsfunktion: Welches Atom beobachten?
2201
{
2202
if (g_bVACF)
2203
{
2204
if (g_bAdvanced2)
2205
g_bVACFCacheMode = AskYesNo(" Use VACF cached mode (do this unless there are problems) (y/n)? [yes] ",true);
2206
else g_bVACFCacheMode = true;
2207
2208
if (g_bPowerSpec)
2209
{
2210
g_bGlobalVACF = AskYesNo(" Compute power spectrum of whole system (y/n)? [yes] ",true);
2211
2212
if (g_bGlobalVACF)
2213
if (!AskYesNo(" Compute also power spectra for certain atoms/molecules (y/n)? [no] ",false))
2214
goto _endobs;
2215
} else
2216
{
2217
g_bGlobalVACF = AskYesNo(" Compute global velocity ACF of whole system (y/n)? [yes] ",true);
2218
2219
if (g_bGlobalVACF)
2220
if (!AskYesNo(" Compute also velocity ACFs for certain atoms/molecules (y/n)? [no] ",false))
2221
goto _endobs;
2222
}
2223
}
2224
2225
if (g_bIRSpec)
2226
{
2227
g_bGlobalIR = AskYesNo(" Compute IR spectrum of whole system (y/n)? [yes] ",true);
2228
if (g_bGlobalIR)
2229
if (!AskYesNo(" Compute also IR spectra for certain molecule types (y/n)? [no] ",false))
2230
goto _endobs;
2231
}
2232
2233
/* if (g_bDipACF)
2234
{
2235
g_bGlobalDipACF = AskYesNo(" Create global dipole ACF of all atoms (y/n)? [yes] ",true);
2236
}*/
2237
_nextsdf:
2238
mprintf(YELLOW,"\n>>> Observation %d >>>\n\n",g_oaObserv.GetSize()+1);
2239
2240
try { o = new CObservation(); } catch(...) { o = NULL; }
2241
if (o == NULL) NewException((double)sizeof(CObservation),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2242
2243
o->m_pConditions = NULL;
2244
g_oaObserv.Add(o);
2245
o->m_bTimeDev = false;
2246
if (g_bAggregation || g_bNbExchange)
2247
{
2248
o->m_bSelf = false;
2249
o->m_bOthers = false;
2250
} else if (g_bNbAnalysis)
2251
{
2252
o->m_bSelf = false;
2253
o->m_bOthers = true;
2254
mprintf(" Performing this observation intermolecular.\n\n");
2255
} else if (g_iFixMol != -1)
2256
{
2257
if (AskRangeInteger(" Perform this observation intramolecular (within the reference molecule) (0) or intermolecular (1)? [1] ",0,1,1) == 1)
2258
{
2259
o->m_bSelf = false;
2260
o->m_bOthers = true;
2261
} else
2262
{
2263
o->m_bSelf = true;
2264
o->m_bOthers = false;
2265
}
2266
mprintf("\n");
2267
} else
2268
{
2269
o->m_bSelf = false;
2270
o->m_bOthers = true;
2271
}
2272
if (o->m_bOthers)
2273
{
2274
if (g_bCDF)
2275
{
2276
mprintf(WHITE," Please note: ");
2277
mprintf("Although you specified this observation to be intermolecular, you may of course\n");
2278
mprintf(" choose atoms from RM only (or OM only), which will yield an intramolecular quantity.\n\n");
2279
}
2280
if (g_bCDF)
2281
o->m_bSecondShowMol = AskYesNo(" CDF: Perform a three-body analysis (y) or observe one molecule at a time (n)? [no] ",false);
2282
else o->m_bSecondShowMol = false;
2283
if (o->m_bSecondShowMol)
2284
{
2285
mprintf(WHITE,"\n You have to select two observed molecules (OMs):\n");
2286
mprintf(" The first CDF channel observes the 1st OM, the second channel observes the 2nd OM.\n\n");
2287
}
2288
if (g_oaMolecules.GetSize() > 1)
2289
{
2290
_obsmolagain:
2291
if (o->m_bSecondShowMol)
2292
sprintf(buf," Which 1st molecule should be observed (");
2293
else sprintf(buf," Which molecule should be observed (");
2294
for (z=0;z<g_oaMolecules.GetSize();z++)
2295
{
2296
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
2297
strcat(buf,buf2);
2298
if (z < g_oaMolecules.GetSize()-1)
2299
strcat(buf,", ");
2300
}
2301
strcat(buf,")? ");
2302
o->m_iShowMol = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize()) - 1;
2303
if ((((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize() == 1) && (o->m_iShowMol == g_iFixMol))
2304
{
2305
eprintf("Error: There is only 1 molecule of %s.\n--> Intermolecular observation between %s and %s not possible.\n\n",((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName);
2306
goto _obsmolagain;
2307
}
2308
} else
2309
{
2310
mprintf(" Only one molecule type, choosing %s as observed molecule (OM).\n",((CMolecule*)g_oaMolecules[0])->m_sName);
2311
o->m_iShowMol = 0;
2312
}
2313
o->m_iShowMolCount = ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();
2314
if (o->m_bSecondShowMol)
2315
{
2316
if (g_oaMolecules.GetSize() > 1)
2317
{
2318
_obsmol2again:
2319
sprintf(buf," Which 2nd molecule should be observed (");
2320
for (z=0;z<g_oaMolecules.GetSize();z++)
2321
{
2322
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
2323
strcat(buf,buf2);
2324
if (z < g_oaMolecules.GetSize()-1)
2325
strcat(buf,", ");
2326
}
2327
strcat(buf,")? ");
2328
o->m_iShowMol2 = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize()) - 1;
2329
if ((((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex.GetSize() == 1) && (o->m_iShowMol2 == g_iFixMol))
2330
{
2331
eprintf("Error: There is only 1 molecule of %s.\n --> Intermolecular observation between %s and %s not possible.\n\n",((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName);
2332
goto _obsmol2again;
2333
}
2334
} else o->m_iShowMol2 = 0;
2335
o->m_iShowMol2Count = ((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex.GetSize();
2336
if (o->m_iShowMol == o->m_iShowMol2)
2337
o->m_bExclude1eq2 = AskYesNo(" Exclude the case \"1st OM = 2nd OM\" (y/n)? [yes] ",true);
2338
else o->m_bExclude1eq2 = false;
2339
}
2340
} else
2341
{
2342
o->m_iShowMol = -1;
2343
o->m_iShowMol2 = -1;
2344
o->m_bSecondShowMol = false;
2345
o->m_iShowMolCount = 1;
2346
}
2347
2348
buf[0] = 0;
2349
if ((o->m_bSecondShowMol) && (o->m_iShowMol != o->m_iShowMol2))
2350
sprintf(buf," of %s / %s / %s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName);
2351
else if ((o->m_iShowMol != -1) && (g_iFixMol != -1))
2352
sprintf(buf," of %s / %s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName);
2353
else if (g_iFixMol != -1) sprintf(buf," of %s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2354
2355
if (g_iFixMol != -1)
2356
{
2357
if (g_bAdvanced2)
2358
{
2359
if (AskYesNo(" Observe only certain molecules%s (y/n)? [no] ",false,buf))
2360
{
2361
o->m_bObsCertain = true;
2362
if (!g_bCDF && (g_bRDF || g_bADF || g_bDDF || g_bDipDF))
2363
o->m_bDecompDist = AskYesNo(" Decompose distribution functions into contributions from molecules (y/n)? [yes] ",true);
2364
2365
if (((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() > 1)
2366
{
2367
mprintf(" Which %s molecules (RM) to take into account (e.g. 1,3-7)? [all] ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2368
inpprintf("! Which %s molecules (RM) to take into account (e.g. 1,3-7)? [all]\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2369
myget(buf);
2370
if (strlen(buf)==0)
2371
{
2372
for (z=0;z<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
2373
o->m_waObsRefList.Add(z);
2374
} else
2375
{
2376
ParseIntList(buf,&o->m_waObsRefList);
2377
for (z=0;z<o->m_waObsRefList.GetSize();z++)
2378
o->m_waObsRefList[z]--;
2379
}
2380
} else o->m_waObsRefList.Add(0);
2381
2382
// mprintf("RefList[0] = %d\n",o->m_waObsRefList[0]);
2383
2384
if (o->m_iShowMol != -1)
2385
{
2386
if (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize() > 1)
2387
{
2388
mprintf(" Which %s molecules (OM) to take into account (e.g. 1,3-7)? [all] ",((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName);
2389
inpprintf("! Which %s molecules (OM) to take into account (e.g. 1,3-7)? [all]\n",((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName);
2390
myget(buf);
2391
if (strlen(buf)==0)
2392
{
2393
for (z=0;z<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
2394
o->m_waObsShowList.Add(z);
2395
} else
2396
{
2397
ParseIntList(buf,&o->m_waObsShowList);
2398
for (z=0;z<o->m_waObsShowList.GetSize();z++)
2399
o->m_waObsShowList[z]--;
2400
}
2401
} else o->m_waObsShowList.Add(0);
2402
} else o->m_waObsShowList.Add(0); // Dummy
2403
2404
if (o->m_bSecondShowMol)
2405
{
2406
if (o->m_iShowMol2 != -1)
2407
{
2408
if (((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex.GetSize() > 1)
2409
{
2410
mprintf(" Which %s molecules (2nd OM) to take into account (e.g. 1,3-7)? [all] ",((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName);
2411
inpprintf("! Which %s molecules (2nd OM) to take into account (e.g. 1,3-7)? [all]\n",((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName);
2412
myget(buf);
2413
if (strlen(buf)==0)
2414
{
2415
for (z=0;z<((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex.GetSize();z++)
2416
o->m_waObsShow2List.Add(z);
2417
} else
2418
{
2419
ParseIntList(buf,&o->m_waObsShow2List);
2420
for (z=0;z<o->m_waObsShow2List.GetSize();z++)
2421
o->m_waObsShow2List[z]--;
2422
}
2423
} else o->m_waObsShow2List.Add(0);
2424
} else o->m_waObsShow2List.Add(0); // Dummy
2425
}
2426
} else // if not onlysome
2427
{
2428
o->m_bObsCertain = false;
2429
o->m_bDecompDist = false;
2430
}
2431
} else // if not advanced
2432
{
2433
o->m_bObsCertain = false;
2434
o->m_bDecompDist = false;
2435
}
2436
} else
2437
{
2438
o->m_bObsCertain = false;
2439
o->m_bDecompDist = false;
2440
}
2441
2442
o->m_bDecompType = false;
2443
2444
if ((!o->m_bObsCertain) && (!g_bCDF) && g_bAdvanced2 && (g_bRDF || g_bADF || g_bDDF || g_bDipDF))
2445
{
2446
if (AskYesNo(" Decompose this observation into contributions from different elements (y/n)? [no] ",false))
2447
{
2448
o->m_bDecompType = true;
2449
}
2450
}
2451
2452
if (g_bRegionAnalysis)
2453
{
2454
AskString(" Take reference molecules from which regions? [all] ",buf,"0");
2455
ParseIntList(buf,&o->m_iaRMRegions);
2456
// for (z6=0;z6<o->m_iaRMRegions.GetSize();z6++)
2457
// if (o->m_iaRMRegions[z6] != 0)
2458
// o->m_iaRMRegions[z6]--;
2459
2460
if (o->m_bOthers)
2461
{
2462
if (o->m_bSecondShowMol)
2463
{
2464
AskString(" Take 1st observed molecules from which regions? [all] ",buf,"0");
2465
ParseIntList(buf,&o->m_iaOM1Regions);
2466
// for (z6=0;z6<o->m_iaOM1Regions.GetSize();z6++)
2467
// if (o->m_iaOM1Regions[z6] != 0)
2468
// o->m_iaOM1Regions[z6]--;
2469
AskString(" Take 2nd observed molecules from which regions? [all] ",buf,"0");
2470
ParseIntList(buf,&o->m_iaOM2Regions);
2471
// for (z6=0;z6<o->m_iaOM2Regions.GetSize();z6++)
2472
// if (o->m_iaOM2Regions[z6] != 0)
2473
// o->m_iaOM2Regions[z6]--;
2474
} else
2475
{
2476
AskString(" Take observed molecules from which regions? [all] ",buf,"0");
2477
ParseIntList(buf,&o->m_iaOM1Regions);
2478
// for (z6=0;z6<o->m_iaOM1Regions.GetSize();z6++)
2479
// if (o->m_iaOM1Regions[z6] != 0)
2480
// o->m_iaOM1Regions[z6]--;
2481
}
2482
}
2483
}
2484
2485
if (g_bAggregation || g_bNbExchange)
2486
{
2487
try { o->m_pDACF = new CDACF(); } catch(...) { o->m_pDACF = NULL; }
2488
if (o->m_pDACF == NULL) NewException((double)sizeof(CDACF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2489
2490
o->m_pDACF->Parse();
2491
}
2492
2493
if (g_bRDyn)
2494
{
2495
try { o->m_pRDyn = new CReorDyn(); } catch(...) { o->m_pRDyn = NULL; }
2496
if (o->m_pRDyn == NULL) NewException((double)sizeof(CReorDyn),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2497
2498
o->m_pRDyn->m_iShowMol = o->m_iShowMol;
2499
o->m_pRDyn->Parse();
2500
}
2501
2502
if (g_bIRSpec)
2503
{
2504
try { o->m_pIRSpec = new CReorDyn(); } catch(...) { o->m_pIRSpec = NULL; }
2505
if (o->m_pIRSpec == NULL) NewException((double)sizeof(CReorDyn),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2506
2507
o->m_pIRSpec->m_iShowMol = o->m_iShowMol;
2508
o->m_pIRSpec->ParseSpec();
2509
}
2510
2511
if (g_bDens)
2512
{
2513
try { o->m_pDensityDF = new CDensDF(); } catch(...) { o->m_pDensityDF = NULL; }
2514
if (o->m_pDensityDF == NULL) NewException((double)sizeof(CDensDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2515
2516
o->m_pDensityDF->m_iShowMol = o->m_iShowMol;
2517
o->m_pDensityDF->Parse();
2518
}
2519
2520
if (g_bSDF)
2521
{
2522
try { o->m_pSDF = new CSDF(); } catch(...) { o->m_pSDF = NULL; }
2523
if (o->m_pSDF == NULL) NewException((double)sizeof(CSDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
33
#include "plproj.h"
34
35
36
bool GatherInfos()
37
{
38
BTIN;
39
char buf[4096], buf2[256];
40
float tf, tf2;
41
FILE *a;
42
bool tb=false, tb2;
43
int z, z0, z2, z3, z4, z5, z6, z7;
44
int ti, ti2, ti3;
45
unsigned char ty, rty, atom;
46
unsigned char ty2, rty2, atom2;
47
CVirtualAtom *va;
48
CObservation *o;
49
CMolecule *mol;
50
CSingleMolecule *sm, *sm2;
51
CAtomGroup *ag;
52
CxWordArray tempwa;
53
CMolecule *m, *m2;
54
CAtom *at;
55
CElement *el;
56
CxIntArray *pia, ia;
57
58
g_bKeepUnfoldedCoords = false;
59
g_iDoubleBoxFactor = 1;
60
g_bBondACF = false;
61
g_bCombined = false;
62
g_bRefEnvFix = false;
63
g_bTimeDiff = false;
64
g_bRemoveCOM = false;
65
g_bSaveCoordsUnchanged = false;
66
g_bSDFUniform = false;
67
a = NULL;
68
ti2 = -1;
69
70
mprintf(YELLOW,"\n*** Interactive query of settings ***\n\n");
71
// SAVEPOS;
72
73
ti = 0;
74
if (g_bUnknownElements)
75
{
76
tb2 = false;
77
_unkstart:
78
tb = false;
79
mprintf(WHITE,"Unrecognized atom types: ");
80
for (z=0;z<g_oaAtoms.GetSize();z++)
81
{
82
if (z == g_iVirtAtomType)
83
continue;
84
85
at = (CAtom*)g_oaAtoms[z];
86
while (at->m_pMergedTo != NULL)
87
{
88
// mprintf("%s merged to %s\n",at->m_sName,at->m_pMergedTo->m_sName);
89
at = at->m_pMergedTo;
90
}
91
if (at->m_pElement->m_fRadius != 0)
92
continue;
93
if (tb)
94
mprintf(", ");
95
tb = true;
96
mprintf("%s",at->m_sName);
97
ti++;
98
ti2 = z;
99
}
100
mprintf("\n\n");
101
102
if ((ti == 1) && (mystricmp("X",((CAtom*)g_oaAtoms[ti2])->m_sName) == 0))
103
{ // Only Wannier centers unrecognized.
104
mprintf(" Possibly, atom type \"X\" are Wannier centers. If so, do not assign data to them.\n\n");
105
tb2 = false;
106
} else tb2 = true;
107
108
tb = false;
109
if (AskYesNo(" Do you want to assign atom data to them (y/n)? [%s] ",tb2,tb2?"yes":"no"))
110
{
111
if (tb2)
112
{
113
if (AskYesNo(" Automatically rename all atoms to corresponding elements (y/n)? [yes] ",true))
114
{
115
mprintf("\n");
116
tb2 = true;
117
tb = false;
118
for (z=0;z<g_oaAtoms.GetSize();z++)
119
{
120
if (z == g_iVirtAtomType)
121
continue;
122
123
at = (CAtom*)g_oaAtoms[z];
124
if (at->m_pElement->m_fRadius != 0)
125
continue;
126
127
buf2[0] = at->m_sName[0];
128
buf2[1] = at->m_sName[1];
129
buf2[2] = 0;
130
el = FindElement(buf2,true);
131
if (el != NULL)
132
{
133
if (el->m_fRadius == 0)
134
goto _unkX2;
135
} else
136
{
137
_unkX2:
138
buf2[1] = 0;
139
el = FindElement(buf2,true);
140
if (el != NULL)
141
{
142
if (el->m_fRadius == 0)
143
goto _unkX3;
144
} else
145
{
146
_unkX3:
147
strcpy(buf2,at->m_sName);
148
}
149
}
150
if (el == NULL)
151
{
152
mprintf(" - Skipping %s... (have no guess for atom type)\n",at->m_sName);
153
tb = true;
154
continue;
155
}
156
157
xAddAtom(buf2);
158
159
mprintf(" - Renaming %s to %s...\n",at->m_sName,buf2);
160
for (z2=0;z2<g_oaAtoms.GetSize();z2++)
161
{
162
if (((CAtom*)g_oaAtoms[z2])->m_pElement == el)
163
{
164
at = (CAtom*)g_oaAtoms[z2];
165
el = at->m_pElement;
166
goto _unkX1;
167
}
168
}
169
eprintf(" Strange error ^^\n");
170
_unkX1:;
171
for (z2=0;z2<(int)g_TimeStep.m_iGesAtomCount;z2++)
172
{
173
strcpy(buf,(char*)g_TimeStep.m_paLabels[z2]);
174
ReplaceDigits(buf);
175
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName) == 0)
176
{
177
at->m_iCount++;
178
((CAtom*)g_oaAtoms[z])->m_iCount--;
179
}
180
}
181
// mprintf("\nmerging %s to %s.\n",((CAtom*)g_oaAtoms[z])->m_sName,at->m_sName);
182
((CAtom*)g_oaAtoms[z])->m_pMergedTo = at;
183
}
184
if (tb)
185
{
186
mprintf("\n");
187
goto _unkstart;
188
}
189
tb = false;
190
goto _unkdone;
191
}
192
}
193
ti = g_oaAtoms.GetSize();
194
for (z=0;z<ti;z++)
195
{
196
if (z == g_iVirtAtomType)
197
continue;
198
199
at = (CAtom*)g_oaAtoms[z];
200
201
while (at->m_pMergedTo != NULL)
202
{
203
// mprintf("%s merged to %s\n",at->m_sName,at->m_pMergedTo->m_sName);
204
at = at->m_pMergedTo;
205
}
206
207
if (at->m_pElement->m_fRadius != 0)
208
continue;
209
mprintf(WHITE,"\n * Element %s\n\n",at->m_sName);
210
211
buf2[0] = at->m_sName[0];
212
buf2[1] = at->m_sName[1];
213
buf2[2] = 0;
214
el = FindElement(buf2,true);
215
if (el != NULL)
216
{
217
if (el->m_fRadius == 0)
218
goto _unk2;
219
} else
220
{
221
_unk2:
222
buf2[1] = 0;
223
el = FindElement(buf2,true);
224
if (el != NULL)
225
{
226
if (el->m_fRadius == 0)
227
goto _unk3;
228
} else
229
{
230
_unk3:
231
strcpy(buf2,at->m_sName);
232
}
233
}
234
235
if (AskYesNo(" Do you want to rename this element (y/n)? [yes] ",true))
236
{
237
_unk5:
238
AskString(" Enter new name for %s: [%s] ",buf,buf2,at->m_sName,buf2);
239
if (strlen(buf) > 7)
240
{
241
eprintf("Atom labels may have maximum length of 7 characters.\n");
242
goto _unk5;
243
}
244
if (ContainsDigit(buf))
245
{
246
eprintf("Digits in element labels not allowed.\n");
247
goto _unk5;
248
}
249
el = FindElement(buf,true);
250
if (el != NULL)
251
{
252
xAddAtom(buf);
253
if (AskYesNo(" Element %s is known. Merge %s atoms into %s (y/n)? [yes] ",true,buf,at->m_sName,buf))
254
{
255
for (z2=0;z2<g_oaAtoms.GetSize();z2++)
256
{
257
if (((CAtom*)g_oaAtoms[z2])->m_pElement == el)
258
{
259
at = (CAtom*)g_oaAtoms[z2];
260
el = at->m_pElement;
261
goto _unk1;
262
}
263
}
264
eprintf(" Strange error ^^\n");
265
_unk1:;
266
}
267
} else
268
{
269
mprintf(" Adding element %s...",buf);
270
271
try { at = new CAtom(); } catch(...) { at = NULL; }
272
if (at == NULL) NewException((double)sizeof(CAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
273
274
at->m_iIndex = g_oaAtoms.GetSize();
275
g_oaAtoms.Add(at);
276
277
try { at->m_pElement = new CElement(); } catch(...) { at->m_pElement = NULL; }
278
if (at->m_pElement == NULL) NewException((double)sizeof(CElement),__FILE__,__LINE__,__PRETTY_FUNCTION__);
279
280
el = at->m_pElement;
281
sprintf(at->m_sName,"%s",buf);
282
}
283
for (z2=0;z2<(int)g_TimeStep.m_iGesAtomCount;z2++)
284
{
285
strcpy(buf,(char*)g_TimeStep.m_paLabels[z2]);
286
ReplaceDigits(buf);
287
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName) == 0)
288
{
289
at->m_iCount++;
290
((CAtom*)g_oaAtoms[z])->m_iCount--;
291
}
292
}
293
((CAtom*)g_oaAtoms[z])->m_pMergedTo = at;
294
if (el->m_fRadius != 0)
295
continue;
296
} // END IF RENAME
297
298
if (AskYesNo(" Do you want to copy the atom parameters from another element (y/n)? [yes] ",true))
299
{
300
_unk4:
301
AskString(" Copy atom parameters from which element? [%s] ",buf,buf2,buf2);
302
el = FindElement(buf,true);
303
if (el == NULL)
304
{
305
eprintf("This element is not defined.\n");
306
goto _unk4;
307
}
308
if (el->m_fRadius == 0)
309
{
310
if (!AskYesNo(" This element has a radius of 0 (will form no bonds). Use it anyway (y/n)? [yes] ",true))
311
goto _unk4;
312
}
313
314
mprintf(WHITE,"\n A covalent radius of 0 pm hinders atoms of this kind from forming any bonds.\n\n");
315
316
at->m_pElement->m_fRadius = AskFloat(" Please enter covalent radius in pm: [%.2f] ",el->m_fRadius,el->m_fRadius);
317
at->m_pElement->m_fMass = AskFloat(" Please enter atom mass in u: [%.2f] ",el->m_fMass,el->m_fMass);
318
319
if (!tb && (fabs(at->m_pElement->m_fMass-el->m_fMass) < 0.01))
320
{
321
tb = true;
322
mprintf(RED,"\n Warning: ");
323
mprintf("Elements %s and %s keep their different labels, but will have\n",at->m_sName,buf);
324
mprintf(" the same mass and therefore also the same atom codes. They will not\n");
325
mprintf(" be distinguished in the molecule recognition!\n");
326
}
327
// mprintf(" Using mass=%.2fu, radius=%.2fpm, ord. number=%d.\n",at->m_pElement->m_fMass,el->m_fRadius,el->m_iOrd);
328
// at->m_pElement->CopyData(el);
329
} else
330
{
331
el = FindElement(buf2,true);
332
mprintf(WHITE,"\n A covalent radius of 0 pm hinders atoms of this kind from forming any bonds.\n\n");
333
if (el != NULL)
334
{
335
mprintf(" (Default values are for %s)\n\n",buf2);
336
at->m_pElement->m_fRadius = AskFloat(" Please enter covalent radius in pm: [%.2f] ",el->m_fRadius,el->m_fRadius);
337
at->m_pElement->m_fMass = AskFloat(" Please enter atom mass in u: [%.2f] ",el->m_fMass,el->m_fMass);
338
} else
339
{
340
at->m_pElement->m_fRadius = AskFloat(" Please enter covalent radius in pm: [100] ",100);
341
at->m_pElement->m_fMass = AskFloat_ND(" Please enter atom mass in u: ");
342
}
343
}
344
}
345
_unkdone:
346
mprintf("\n");
347
mprintf(WHITE,"%d atoms in the system: ",g_iGesAtomCount);
348
349
for (z=0;z<g_oaAtoms.GetSize();z++)
350
{
351
if (z == g_iVirtAtomType)
352
continue;
353
if (((CAtom*)g_oaAtoms[z])->m_pMergedTo != NULL)
354
continue;
355
mprintf("%dx %s",((CAtom*)g_oaAtoms[z])->m_iCount,((CAtom*)g_oaAtoms[z])->m_sName);
356
if (((CAtom*)g_oaAtoms[z])->m_pMergedTo != NULL)
357
mprintf(" (merged to %s)",((CAtom*)g_oaAtoms[z])->m_pMergedTo->m_sName);
358
if (z < (int)g_oaAtoms.GetSize()-1)
359
if (z+1 != g_iVirtAtomType)
360
mprintf(", ");
361
}
362
mprintf("\n");
363
} // END IF CHANGE UNKNOWN
364
mprintf("\n");
365
} // END IF UNKNOWN
366
367
ia.RemoveAll();
368
tb2 = false;
369
for (z=0;z<g_oaAtoms.GetSize();z++)
370
{
371
tb = false;
372
for (z3=0;z3<ia.GetSize();z3++)
373
{
374
if (z == ia[z3])
375
goto _next;
376
}
377
if (((CAtom*)g_oaAtoms[z])->m_pMergedTo != NULL)
378
continue;
379
if (z == g_iVirtAtomType)
380
continue;
381
for (z2=z+1;z2<g_oaAtoms.GetSize();z2++)
382
{
383
if (((CAtom*)g_oaAtoms[z2])->m_pMergedTo != NULL)
384
continue;
385
if (z2 == g_iVirtAtomType)
386
continue;
387
if (fabs(((CAtom*)g_oaAtoms[z])->m_pElement->m_fMass - ((CAtom*)g_oaAtoms[z2])->m_pElement->m_fMass) < 0.01)
388
{
389
if (!tb)
390
{
391
tb = true;
392
tb2 = true;
393
mprintf(RED,"\n Warning: ");
394
mprintf("The following atoms have the same mass and will therefore not be\n");
395
mprintf(" distinguished in the molecule recognition:\n\n");
396
mprintf(WHITE," Mass=%.2f: %s, %s",((CAtom*)g_oaAtoms[z])->m_pElement->m_fMass,((CAtom*)g_oaAtoms[z])->m_sName,((CAtom*)g_oaAtoms[z2])->m_sName);
397
ia.Add(z);
398
ia.Add(z2);
399
} else
400
{
401
mprintf(WHITE,", %s",((CAtom*)g_oaAtoms[z2])->m_sName);
402
}
403
}
404
}
405
if (tb)
406
mprintf("\n");
407
_next:;
408
}
409
if (tb2)
410
mprintf("\n");
411
412
mprintf(" The advanced mode includes some options which are quite powerful,\n yet possibly weird or seldomly required. ");
413
mprintf("This includes support for\n NPT ensemble, non-periodic systems, user-definded virtual atoms, pseudomolecules, ...\n\n");
414
415
g_bAdvanced1 = AskYesNo(" Use the advanced mode up to the function selection menu (y/n)? [no] ",false);
416
417
mprintf("\n");
418
419
if (g_bAdvanced1)
420
{
421
do
422
{
423
mprintf(" Use periodic boundary conditions (0=no, x, y, z, xy, xz, xyz)? [xyz] ");
424
inpprintf("! Use periodic boundary conditions (0=no, x, y, z, xy, xz, xyz)? [xyz]\n");
425
myget(buf);
426
} while (!ParsePeriodic(buf));
427
428
if (!g_bPeriodic)
429
{
430
/* if (AskYesNo(" Enter Box Size anyways (e.g. fo RDFs) (yes/no)? [yes] ",true))
431
{
432
goto _askbox;
433
} else
434
{
435
g_fBoxX = GuessBoxSize();
436
g_fBoxY = GuessBoxSize();
437
g_fBoxZ = GuessBoxSize();
438
mprintf("\nGuessed box size (for density 1.0 g/cm^3) is %.2f x %.2f x %.2f pm.\n\n",g_fBoxX,g_fBoxX,g_fBoxX);
439
}*/
440
// g_fBoxX = (g_TimeStep.m_vMax[0]-g_TimeStep.m_vMin[0])*10.0;
441
// g_fBoxY = (g_TimeStep.m_vMax[1]-g_TimeStep.m_vMin[1])*10.0;
442
// g_fBoxZ = (g_TimeStep.m_vMax[2]-g_TimeStep.m_vMin[2])*10.0;
443
// mprintf("\n Using cell vector of %.2f x %.2f x %.2f pm to \"fake\" non-periodic box.\n\n",g_fBoxX,g_fBoxY,g_fBoxZ);
444
}
445
} else
446
ParsePeriodic("xyz");
447
448
if (g_bPeriodic)
449
{
450
tf = GuessBoxSize();
451
mprintf(" A cell vector of %.2f pm would result in a density of 1.0 g/cm^3.\n\n",tf);
452
if (g_bAdvanced1)
453
{
454
g_bNPT = AskYesNo(" Use time-dependent cell vector (NPT ensemble) (y/n)? [no] ",false);
455
mprintf("\n");
456
} else g_bNPT = false;
457
458
if (g_bNPT)
459
{
460
if (g_fBoxX != 0)
461
{
462
mprintf(" Your PDB file contains cell vector information.\n\n");
463
} else
464
{
465
mprintf(" The trajectory does not contain cell vector information.\n");
466
mprintf(" (supported: PDB file with \"CRYST1\" section, like written by GROMACS trjconv)\n");
467
mprintf(" You have to supply a plain text file which contains the cell vectors for each step.\n");
468
mprintf(" It should contain three space-separated floating point numbers (X, Y, Z vector) per line.\n");
469
mprintf(" These numbers need to be IN ANGSTROM! (1 angstrom = 100 pm)\n\n");
470
_nptfileagain:
471
AskString_ND(" Please enter cell vector text file name: ",g_sNPTFile);
472
if (!FileExist(g_sNPTFile))
473
{
474
eprintf("Could not open file \"%s\" for reading.\n",g_sNPTFile);
475
goto _nptfileagain;
476
}
477
g_fNPTFile = fopen(g_sNPTFile,"rt");
478
g_TimeStep.ReadCellVector(g_fNPTFile);
479
fclose(g_fNPTFile);
480
mprintf("\n");
481
}
482
mprintf(" The initial cell vector is ( %.2f pm | %.2f pm | %.2f pm ).\n",g_fBoxX,g_fBoxY,g_fBoxZ);
483
mprintf(" The initial box density is %.6f g/cm^3.\n\n",tf*tf*tf/g_fBoxX/g_fBoxY/g_fBoxZ);
484
} else
485
{
486
if (g_fBoxX != 0)
487
{
488
mprintf(" Cell vector found in trajectory file:\n");
489
mprintf(" X = %.2f pm, Y = %.2f pm, Z = %.2f pm\n\n",g_fBoxX,g_fBoxY,g_fBoxZ);
490
if (AskYesNo(" Use these values (y/n)? [yes] ",true))
491
goto _celldone;
492
}
493
_askbox:
494
if (!AskYesNo(" Are the 3 cell vectors of the same size (yes/no)? [yes] ",true))
495
{
496
if (g_bPeriodicX)
497
g_fBoxX = AskFloat_ND(" Enter length of X cell vector in pm: ");
498
if (g_bPeriodicY)
499
g_fBoxY = AskFloat_ND(" Enter length of Y cell vector in pm: ");
500
if (g_bPeriodicZ)
501
g_fBoxZ = AskFloat_ND(" Enter length of Z cell vector in pm: ");
502
} else
503
{
504
g_fBoxX = AskFloat_ND(" Enter length of cell vector in pm: ");
505
g_fBoxY = g_fBoxX;
506
g_fBoxZ = g_fBoxX;
507
}
508
if ((g_fBoxX <= 0) || (g_fBoxY <= 0) || (g_fBoxZ <= 0))
509
{
510
eprintf("Cell vector of length <= 0 is not allowed.\n");
511
goto _askbox;
512
}
513
_celldone:
514
if (g_bPeriodicX && g_bPeriodicY && g_bPeriodicZ)
515
{
516
mprintf("\n The box size is %.2f x %.2f x %.2f pm.\n",g_fBoxX,g_fBoxY,g_fBoxZ);
517
mprintf(" The overall box density is %.6f g/cm^3.\n",tf*tf*tf/g_fBoxX/g_fBoxY/g_fBoxZ);
518
if (tf*tf*tf/g_fBoxX/g_fBoxY/g_fBoxZ > 15.0f)
519
{
520
mprintf("\n");
521
if (!AskYesNo(" The density of your box seems to be very high. Continue (y) or change input (n)? [n] ",false))
522
{
523
mprintf("\n");
524
goto _askbox;
525
}
526
mprintf("\n");
527
}
528
}
529
}
530
531
if (g_bAdvanced1 && g_bPeriodic)
532
{
533
mprintf("\n");
534
if (AskYesNo(" Should the periodic box be multiplied (y/n)? [no] ",false))
535
{
536
mprintf("\n");
537
g_bDoubleBox = true;
538
539
if (g_bPeriodicX)
540
g_iDoubleBoxX = AskUnsignedInteger(" Replicate the box n times in x direction: [2] ",2);
541
else g_iDoubleBoxX = 1;
542
543
if (g_bPeriodicY)
544
g_iDoubleBoxY = AskUnsignedInteger(" Replicate the box n times in y direction: [2] ",2);
545
else g_iDoubleBoxY = 1;
546
547
if (g_bPeriodicZ)
548
g_iDoubleBoxZ = AskUnsignedInteger(" Replicate the box n times in z direction: [2] ",2);
549
else g_iDoubleBoxZ = 1;
550
551
g_iDoubleBoxFactor = g_iDoubleBoxX * g_iDoubleBoxY * g_iDoubleBoxZ;
552
g_fBoxX *= g_iDoubleBoxX;
553
g_fBoxY *= g_iDoubleBoxY;
554
g_fBoxZ *= g_iDoubleBoxZ;
555
g_iGesAtomCount *= g_iDoubleBoxFactor;
556
g_iGesVirtAtomCount *= g_iDoubleBoxFactor;
557
} else g_bDoubleBox = false;
558
} else g_bDoubleBox = false;
559
} else g_bDoubleBox = false;
560
561
try { g_pUniteTemp = new bool[g_iGesAtomCount]; } catch(...) { g_pUniteTemp = NULL; }
562
if (g_pUniteTemp == NULL) NewException((double)g_iGesAtomCount*sizeof(bool),__FILE__,__LINE__,__PRETTY_FUNCTION__);
563
564
if (!g_bPeriodic)
565
g_bNPT = false;
566
567
if (g_bPeriodic)
568
{
569
g_fMinPeriodic = 1e30f;
570
if (g_bPeriodicX)
571
if (g_fMinPeriodic > g_fBoxX)
572
g_fMinPeriodic = g_fBoxX;
573
if (g_bPeriodicY)
574
if (g_fMinPeriodic > g_fBoxY)
575
g_fMinPeriodic = g_fBoxY;
576
if (g_bPeriodicZ)
577
if (g_fMinPeriodic > g_fBoxZ)
578
g_fMinPeriodic = g_fBoxZ;
579
}
580
581
// SAVEPOS;
582
_molbegin:
583
if (!g_bStreamInput)
584
{
585
if (g_bAdvanced1)
586
{
587
mprintf("\n");
588
g_iScanMolStep = AskInteger(" Execute molecule recognition for which time step (-1 = disable)? [0] ",0);
589
} else g_iScanMolStep = 0;
590
591
a = fopen(g_sInputTraj,"rb");
592
if ((g_bNPT) && (g_sNPTFile[0] != 0))
593
g_fNPTFile = fopen(g_sNPTFile,"rt");
594
if (g_iScanMolStep > 0)
595
{
596
mprintf(" Fast-forwarding to step %d...\n",g_iScanMolStep);
597
mprintf(WHITE," [");
598
for (z=0;z<g_iScanMolStep;z++)
599
{
600
if ((g_bNPT) && (g_sNPTFile[0] != 0))
601
fgets(buf,256,g_fNPTFile);
602
if (fmod(z,g_iScanMolStep/60.0) < 1.0)
603
mprintf(WHITE,"#");
604
if (!g_TimeStep.SkipTimestep(a))
605
{
606
eprintf("Error.\n",g_iScanMolStep);
607
goto _skipfail;
608
}
609
}
610
mprintf(WHITE,"]\n");
611
g_iFastForwardPos = ftell(a);
612
mprintf(" Step %d begins at offset %lu (%.1f MB).\n\n",g_iScanMolStep+1,g_iFastForwardPos,g_iFastForwardPos/1024.0/1024.0);
613
}
614
_skipfail:;
615
g_TimeStep.ReadTimestep(a,true);
616
if (g_bNPT)
617
{
618
if (g_sNPTFile[0] != 0)
619
g_TimeStep.ReadCellVector(g_fNPTFile);
620
mprintf("\n NPT: Using a cell vector of ( %.2f pm | %.2f pm | %.2f pm ) for molecule recognition.\n",g_fBoxX,g_fBoxY,g_fBoxZ);
621
}
622
} else
623
{
624
g_iScanMolStep = 0;
625
mprintf("\n Stream input: Executing molecule recognition from first timestep...\n");
626
}
627
628
g_iCloseAtomCounter = 0;
629
630
if (!g_TimeStep.ScanMolecules())
631
return false;
632
633
if (!g_bStreamInput)
634
{
635
fclose(a);
636
if (g_sNPTFile[0] != 0)
637
fclose(g_fNPTFile);
638
}
639
640
if (g_bPeriodic)
641
{
642
mprintf("\n Uniting molecules which have been broken by wrapping...\n");
643
g_TimeStep.UniteMolecules(true);
644
}
645
646
mprintf(YELLOW,"\n*** The following %d kind%s of molecules ha%s been recognized:\n",g_oaMolecules.GetSize(),(g_oaMolecules.GetSize()>1)?"s":"",(g_oaMolecules.GetSize()>1)?"ve":"s");
647
mprintf(" (ordered by molecular mass)\n\n");
648
for (z=0;z<g_oaMolecules.GetSize();z++)
649
{
650
mprintf(WHITE," - Molecule %d: %s ",z+1,((CMolecule*)g_oaMolecules[z])->m_sName);
651
mprintf("(%d piece%s, %.2f g/mol)\n",((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize(),(((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize()>1)?"s":"",((CMolecule*)g_oaMolecules[z])->m_fMass);
652
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
653
mprintf(" (%d noneq. atom%s, %d noneq. bond%s, %d noneq. angle%s)\n",sm->m_iAtomClasses,(sm->m_iAtomClasses==1)?"":"s",sm->m_oaBondGroups.GetSize(),(sm->m_oaBondGroups.GetSize()==1)?"":"s",sm->m_oaAngleGroups.GetSize(),(sm->m_oaAngleGroups.GetSize()==1)?"":"s");
654
if (((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms.GetSize() != 0)
655
{
656
if (((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms.GetSize() == 1)
657
mprintf(WHITE," Detected %d ring:\n",((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms.GetSize());
658
else mprintf(WHITE," Detected %d rings:\n",((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms.GetSize());
659
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms.GetSize();z2++)
660
{
661
mprintf(WHITE," %2d.) %2d-ring: ",z2+1,((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize());
662
if (((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize() > 20)
663
{
664
for (z3=0;z3<5;z3++)
665
{
666
mprintf("%s%d",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[z])->m_baAtomIndex[((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetAt(z3)+1);
667
if (z3+1 < ((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize())
668
mprintf(" - ");
669
}
670
mprintf(RED,"...");
671
mprintf(" - ");
672
for (z3=((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize()-5;z3<((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize();z3++)
673
{
674
mprintf("%s%d",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[z])->m_baAtomIndex[((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetAt(z3)+1);
675
if (z3+1 < ((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize())
676
mprintf(" - ");
677
}
678
} else
679
{
680
for (z3=0;z3<((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize();z3++)
681
{
682
mprintf("%s%d",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[z])->m_baAtomIndex[((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetAt(z3)+1);
683
if (z3+1 < ((CxIntArray*)((CMolecule*)g_oaMolecules[z])->m_oaRingAtoms[z2])->GetSize())
684
mprintf(" - ");
685
}
686
}
687
mprintf("\n");
688
if (z2 >= 9)
689
{
690
mprintf(RED,"\n Showing only the first 10 rings.\n");
691
break;
692
}
693
}
694
}
695
696
mprintf("\n");
697
}
698
699
if (g_oaMolecules.GetSize() == 0)
700
{
701
eprintf("You don't have any atom/molecule in your simulation. This is probably not what you wanted.\n");
702
eprintf("Stopping execution.\n");
703
return false;
704
}
705
706
/* if (g_bVerbose)
707
{
708
mprintf(WHITE,">>> Output of the molecule tree >>>\n");
709
g_TimeStep.PrintMegaTree();
710
mprintf(WHITE,"<<< Output of the molecule tree <<<\n\n");
711
}*/
712
713
_matrixagain:
714
715
mprintf("\n");
716
if (!AskYesNo(" Accept these molecules (y) or change something (n)? [yes] ",true))
717
{
718
tb = false;
719
mprintf("\n");
720
mprintf(" If you want some atom types to form no bonds at all, assign covalent radius 0 to them.\n");
721
_modagain:
722
mprintf(YELLOW,"\n *** Modify Molecules ***\n\n");
723
mprintf(" Your choices:\n\n");
724
725
mprintf(" 1.) Change covalent atom radii used for bond recognition\n");
726
mprintf(" 2.) Break specific bonds\n");
727
mprintf(" 3.) Rename elements\n");
728
729
mprintf("\n");
730
switch(AskRangeInteger(" Please select: [done] ",1,3,0))
731
{
732
case 1:
733
mprintf("\n These values have been used (covalent radii from literature multiplied with %.2f):\n\n",g_fBondFactor);
734
for (z=0;z<g_oaAtoms.GetSize()-1;z++)
735
mprintf(" - %-2s %5.1f pm\n",((CAtom*)g_oaAtoms[z])->m_sName,((CAtom*)g_oaAtoms[z])->m_pElement->m_fRadius*g_fBondFactor);
736
mprintf("\n");
737
_arnew:
738
AskString(" Which radius do you want to change (RETURN=done)? ",buf,"");
739
if (strlen(buf) == 0)
740
goto _ardone;
741
for (z=0;z<g_oaAtoms.GetSize()-1;z++)
742
{
743
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName) == 0)
744
{
745
((CAtom*)g_oaAtoms[z])->m_pElement->m_fRadius = AskFloat(" Please enter new bond radius for %s in pm: [%.1f] ",((CAtom*)g_oaAtoms[z])->m_pElement->m_fRadius*g_fBondFactor,((CAtom*)g_oaAtoms[z])->m_sName,((CAtom*)g_oaAtoms[z])->m_pElement->m_fRadius*g_fBondFactor) / g_fBondFactor;
746
if (((CAtom*)g_oaAtoms[z])->m_pElement->m_fRadius == 0)
747
mprintf("\n Atom %s will form no bonds now.\n\n",((CAtom*)g_oaAtoms[z])->m_sName);
748
mprintf("\n");
749
tb = true;
750
goto _arnew;
751
}
752
}
753
eprintf(" Atom \"%s\" is not in the system.\n\n",buf);
754
goto _arnew;
755
_ardone:
756
mprintf("\n");
757
break;
758
759
case 2:
760
_breakagain:
761
mprintf("\n");
762
if (g_oaMolecules.GetSize() > 1)
763
{
764
_breakmol: ti = AskUnsignedInteger_ND(" Break bonds in which molecule (1-%d)? ",g_oaMolecules.GetSize())-1;
765
if ((ti < 0) || (ti >= (int)g_oaMolecules.GetSize()))
766
{
767
eprintf("Wrong Input.\n\n");
768
goto _breakmol;
769
}
770
} else ti = 0;
771
mol = (CMolecule*)g_oaMolecules[ti];
772
tb = true;
773
if (AskYesNo(" Break all bonds within this molecule (y/n)? [no] ",false))
774
{
775
for (z=0;z<mol->m_laSingleMolIndex.GetSize();z++)
776
{
777
sm = (CSingleMolecule*)g_oaSingleMolecules[mol->m_laSingleMolIndex[z]];
778
g_laBondBlackList.Append(&sm->m_laBonds);
779
}
780
} else
781
{
782
_breaka1: AskString_ND(" Enter 1st atom of the bond to break (e.g. O2): ",buf);
783
if (!ParseAtom(buf,ti,ty,rty,atom))
784
goto _breaka1;
785
_breaka2: AskString_ND(" Enter 2nd atom of the bond to break (e.g. O2): ",buf);
786
if (!ParseAtom(buf,ti,ty2,rty2,atom2))
787
goto _breaka2;
788
for (z=0;z<mol->m_laSingleMolIndex.GetSize();z++)
789
{
790
sm = (CSingleMolecule*)g_oaSingleMolecules[mol->m_laSingleMolIndex[z]];
791
g_laBondBlackList.Add(((CxIntArray*)sm->m_oaAtomOffset[ty])->GetAt(atom));
792
g_laBondBlackList.Add(((CxIntArray*)sm->m_oaAtomOffset[ty2])->GetAt(atom2));
793
}
794
}
795
if (AskYesNo("\n Break another bond (y/n)? [no] ",false))
796
goto _breakagain;
797
mprintf("\n");
798
break;
799
800
case 3:
801
/*********************************************************************************************************************/
802
_rennew:
803
mprintf("\n The system contains the following atoms:\n\n ");
804
tb2 = false;
805
for (z=0;z<g_oaAtoms.GetSize();z++)
806
{
807
if (z == g_iVirtAtomType)
808
continue;
809
if (((CAtom*)g_oaAtoms[z])->m_pMergedTo != NULL)
810
continue;
811
if (tb2)
812
mprintf(", ");
813
tb2 = true;
814
mprintf("%dx %s",((CAtom*)g_oaAtoms[z])->m_iCount,((CAtom*)g_oaAtoms[z])->m_sName);
815
}
816
mprintf("\n\n");
817
818
_renerr:
819
AskString(" Which element to rename: [done] ",buf,"");
820
821
if (strlen(buf) == 0)
822
goto _rendone;
823
824
for (z=0;z<g_oaAtoms.GetSize();z++)
825
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName) == 0)
826
goto _renfound;
827
eprintf("\n Atom \"%s\" not in the system.\n\n",buf);
828
goto _renerr;
829
_renfound:
830
tb = true;
831
at = (CAtom*)g_oaAtoms[z];
832
833
AskString_ND(" Enter new name for %s: ",buf2,buf);
834
if (strlen(buf2) > 7)
835
{
836
eprintf("\n Atom labels may have maximum length of 7 characters.\n\n");
837
goto _renfound;
838
}
839
if (ContainsDigit(buf2))
840
{
841
eprintf("\n Digits in element labels not allowed.\n\n");
842
goto _renfound;
843
}
844
el = FindElement(buf2,true);
845
if (el != NULL)
846
{
847
xAddAtom(buf2);
848
if (AskYesNo(" Element %s is known. Merge %s atoms into %s (y/n)? [yes] ",true,buf2,buf,buf2))
849
{
850
for (z2=0;z2<g_oaAtoms.GetSize();z2++)
851
{
852
if (((CAtom*)g_oaAtoms[z2])->m_pElement == el)
853
{
854
at = (CAtom*)g_oaAtoms[z2];
855
at->m_iCount--;
856
el = at->m_pElement;
857
goto _ren1;
858
}
859
}
860
eprintf("\n Strange error ^^\n");
861
_ren1:;
862
}
863
} else
864
{
865
mprintf("\n Adding element %s...\n\n",buf2);
866
867
try { at = new CAtom(); } catch(...) { at = NULL; }
868
if (at == NULL) NewException((double)sizeof(CAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
869
870
at->m_iIndex = g_oaAtoms.GetSize();
871
g_oaAtoms.Add(at);
872
at->m_iCount = 0;
873
874
try { at->m_pElement = new CElement(); } catch(...) { at->m_pElement = NULL; }
875
if (at->m_pElement == NULL) NewException((double)sizeof(CElement),__FILE__,__LINE__,__PRETTY_FUNCTION__);
876
877
at->m_pElement->m_fRadius = AskFloat(" Please enter covalent radius in pm: [100.0] ",100.0f);
878
at->m_pElement->m_fMass = AskFloat(" Please enter atom mass in u: [0] ",0);
879
sprintf(at->m_sName,"%s",buf2);
880
}
881
for (z2=0;z2<(int)g_TimeStep.m_iGesAtomCount;z2++)
882
{
883
strcpy(buf,(char*)g_TimeStep.m_paLabels[z2]);
884
ReplaceDigits(buf);
885
if (mystricmp(buf,((CAtom*)g_oaAtoms[z])->m_sName) == 0)
886
{
887
at->m_iCount++;
888
((CAtom*)g_oaAtoms[z])->m_iCount--;
889
}
890
}
891
((CAtom*)g_oaAtoms[z])->m_pMergedTo = at;
892
mprintf("\n");
893
goto _rennew;
894
_rendone:;
895
mprintf("\n The system contains the following atoms:\n\n ");
896
tb2 = false;
897
for (z=0;z<g_oaAtoms.GetSize();z++)
898
{
899
if (z == g_iVirtAtomType)
900
continue;
901
if (((CAtom*)g_oaAtoms[z])->m_pMergedTo != NULL)
902
continue;
903
if (tb2)
904
mprintf(", ");
905
tb2 = true;
906
mprintf("%dx %s",((CAtom*)g_oaAtoms[z])->m_iCount,((CAtom*)g_oaAtoms[z])->m_sName);
907
}
908
mprintf("\n");
909
/*********************************************************************************************************************/
910
break;
911
912
default:
913
goto _fin;
914
}
915
goto _modagain;
916
_fin:
917
if (tb)
918
{
919
mprintf(WHITE,"\n Going back to molecule recognition with changed settings.\n\n");
920
goto _molbegin;
921
} else
922
mprintf(WHITE,"\n Nothing was changed, not repeating molecule recognition.\n\n");
923
}
924
925
if (g_bAdvanced1)
926
{
927
g_bMegaMat = !AskYesNo(" Show bond matrices only for first representant of each molecule type (y/n)? [yes] ",true);
928
g_bMatOnlyBind = AskYesNo(" Show only bonds in the bond matrices (y/n)? [yes] ",true);
929
} else
930
{
931
g_bMegaMat = false;
932
g_bMatOnlyBind = true;
933
}
934
935
mprintf(WHITE,"\nOutput of bond matrices:\n");
936
g_TimeStep.PrintMatrix(!g_bMegaMat,g_bMatOnlyBind);
937
938
mprintf("\n");
939
mprintf(" You can create images of the structural formulas with the atom labels for easier\n");
940
mprintf(" identification of the atoms (requires installed GraphViz package - see www.graphviz.org).\n\n");
941
942
if (AskYesNo(" Create images of the structural formulas (y/n)? [no] ",false))
943
{
944
if (g_bAdvanced1)
945
ti = AskUnsignedInteger(" How many iterations to perform for formula optimization? [10] ",10);
946
else ti = 10;
947
RenderStructFormulas(ti);
948
}
949
950
mprintf(WHITE,"\n The atoms are currently ordered by topological priority.\n");
951
952
if (g_bAdvanced1)
953
{
954
mprintf("\n");
955
956
// This block written @ Ballmer peak ;-P Try it out yourself.
957
if (AskYesNo(" Change the atom ordering in some molecule (y/n)? [no] ",false))
958
{
959
if (AskYesNo(" Order atoms like in the input file instead (y/n)? [no] ",false))
960
{
961
ReorderLikeInput(); // Crazy shit!! (Ballmer Peak)
962
} else
963
{
964
_reordernext:
965
sprintf(buf," Change atom ordering in which of the molecules (");
966
for (z=0;z<g_oaMolecules.GetSize();z++)
967
{
968
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
969
strcat(buf,buf2);
970
if (z < g_oaMolecules.GetSize()-1)
971
strcat(buf,", ");
972
}
973
strcat(buf,")? ");
974
ti = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize())-1;
975
mol = (CMolecule*)g_oaMolecules[ti];
976
mol->m_oaNewNumbers.SetSize(mol->m_baAtomIndex.GetSize());
977
for (z=0;z<mol->m_baAtomIndex.GetSize();z++)
978
{
979
mprintf("* Atom type %s\n",((CAtom*)g_oaAtoms[mol->m_baAtomIndex[z]])->m_sName);
980
if (mol->m_oaNewNumbers[z] != NULL)
981
delete mol->m_oaNewNumbers[z];
982
983
try { mol->m_oaNewNumbers[z] = new CxIntArray("gather():mol->m_oaNewNumbers[z]"); } catch(...) { mol->m_oaNewNumbers[z] = NULL; }
984
if (mol->m_oaNewNumbers[z] == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
985
986
for (z2=0;z2<mol->m_waAtomCount[z];z2++)
987
{
988
_renumberagain:
989
ti2 = AskRangeInteger(" Which number should %s%d bear? [%d] ",1,mol->m_waAtomCount[z],z2+1,((CAtom*)g_oaAtoms[mol->m_baAtomIndex[z]])->m_sName,z2+1,z2+1);
990
for (z3=0;z3<z2;z3++)
991
if (((CxIntArray*)mol->m_oaNewNumbers[z])->GetAt(z3) == ti2-1)
992
{
993
eprintf("This number already was chosen for %s%d!\n",((CAtom*)g_oaAtoms[mol->m_baAtomIndex[z]])->m_sName,z3+1);
994
goto _renumberagain;
995
}
996
(*((CxIntArray*)mol->m_oaNewNumbers[z])).Add(ti2-1);
997
}
998
}
999
mprintf("\n Reordering atoms...");
1000
ReorderAtoms(ti);
1001
mprintf("Done.\n\n");
1002
if (AskYesNo(" Change atom ordering of another molecule (y/n)? [no] ",false))
1003
goto _reordernext;
1004
goto _matrixagain;
1005
} // End "this block"
1006
1007
mprintf(WHITE,"\n Going back to molecule recognition with changed settings.\n\n");
1008
goto _molbegin;
1009
} // END IF REORDER
1010
} // END IF ADVANCED
1011
1012
mprintf(WHITE,"\n Defining virtual atom #1 as molecular Center of Geometry:\n");
1013
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1014
{
1015
mprintf(" - %s...\n",((CMolecule*)g_oaMolecules[z0])->m_sName);
1016
va = AddVirtualAtom(z0);
1017
va->m_iMode = 0;
1018
va->m_oCenterAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],false);
1019
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1020
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1021
va->m_faWeight[z] = 1.0f;
1022
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1023
}
1024
1025
mprintf(WHITE,"\n Defining virtual atom #2 as molecular Center of Mass:\n");
1026
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1027
{
1028
mprintf(" - %s...\n",((CMolecule*)g_oaMolecules[z0])->m_sName);
1029
va = AddVirtualAtom(z0);
1030
va->m_iMode = 0;
1031
va->m_oCenterAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],false);
1032
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1033
z3 = 0;
1034
tf2 = 0;
1035
for (z=0;z<va->m_oCenterAtoms.m_baAtomType.GetSize();z++)
1036
{
1037
tf = ((CAtom*)g_oaAtoms[va->m_oCenterAtoms.m_baRealAtomType[z]])->m_pElement->m_fMass;
1038
for (z2=0;z2<((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z])->GetSize();z2++)
1039
{
1040
va->m_faWeight[z3] = tf;
1041
tf2 += tf;
1042
z3++;
1043
}
1044
}
1045
va->m_fGesWeight = tf2;
1046
if (va->m_fGesWeight == 0)
1047
{
1048
eprintf(" Molecule %s has total mass of zero. Defining #2 as Center of Geometry.\n",((CMolecule*)g_oaMolecules[z0])->m_sName);
1049
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1050
va->m_faWeight[z] = 1.0f;
1051
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1052
}
1053
}
1054
1055
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1056
{
1057
m = (CMolecule*)g_oaMolecules[z0];
1058
if (m->m_oaRingAtoms.GetSize() != 0)
1059
{
1060
mprintf(WHITE,"\n Defining ring centers in %s:\n",m->m_sName);
1061
for (z=0;z<m->m_oaRingAtoms.GetSize();z++)
1062
{
1063
mprintf(" - Defining #%d as Center of Ring %d: ",z+3,z+1);
1064
for (z3=0;z3<((CxIntArray*)m->m_oaRingAtoms[z])->GetSize();z3++)
1065
{
1066
mprintf("%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[((CxIntArray*)m->m_oaRingAtomTypes[z])->GetAt(z3)]])->m_sName,((CxIntArray*)m->m_oaRingAtoms[z])->GetAt(z3)+1);
1067
if (z3+1 < ((CxIntArray*)m->m_oaRingAtoms[z])->GetSize())
1068
mprintf(" - ");
1069
}
1070
mprintf("\n");
1071
va = AddVirtualAtom(z0);
1072
va->m_iMode = 0;
1073
va->m_oCenterAtoms.m_pMolecule = m;
1074
for (z3=0;z3<((CxIntArray*)m->m_oaRingAtoms[z])->GetSize();z3++)
1075
va->m_oCenterAtoms.AddAtom(((CxIntArray*)m->m_oaRingAtomTypes[z])->GetAt(z3),((CxIntArray*)m->m_oaRingAtoms[z])->GetAt(z3),false);
1076
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1077
for (z3=0;z3<va->m_oCenterAtoms.m_iAtomGes;z3++)
1078
va->m_faWeight[z3] = 1.0f;
1079
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1080
}
1081
}
1082
}
1083
1084
if (g_bAdvanced1)
1085
{
1086
mprintf("\n");
1087
if (AskYesNo("\n Define additional virtual atoms (y/n)? [no] ",false))
1088
{
1089
_vabeg:
1090
sprintf(buf," To which molecule shall the virtual atom belong (");
1091
for (z=0;z<g_oaMolecules.GetSize();z++)
1092
{
1093
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
1094
strcat(buf,buf2);
1095
if (z < g_oaMolecules.GetSize()-1)
1096
strcat(buf,", ");
1097
}
1098
strcat(buf,")? ");
1099
1100
z = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize());
1101
va = AddVirtualAtom(z-1);
1102
mprintf(WHITE,"\n*** Defining virtual atom #%d in %s\n",va->m_iMolVirtAtom+1,((CMolecule*)g_oaMolecules[va->m_iMolecule])->m_sName);
1103
va->m_iMode = AskRangeInteger(" Define v.a. as center (0) or through distance/angle/dihedral (1)? [center] ",0,1,0);
1104
if (va->m_iMode == 0)
1105
{
1106
_vaatoms:
1107
mprintf(" Which atoms to use for center (e.g. \"C1,C3-5,H\")? [all] ");
1108
inpprintf("! Which atoms to use for center (e.g. \"C1,C3-5,H\")? [all]\n");
1109
myget(buf);
1110
if (strlen(buf)==0)
1111
va->m_oCenterAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],false);
1112
else if (!va->m_oCenterAtoms.ParseAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],buf))
1113
goto _vaatoms;
1114
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1115
_vaweight:
1116
mprintf(" How shall these atoms be weightened (RETURN=equal, *=mass, #=manually)? [equal] ");
1117
inpprintf("! How shall these atoms be weightened (RETURN=equal, *=mass, #=manually)? [equal]\n");
1118
myget(buf);
1119
if (strlen(buf)==0)
1120
{
1121
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1122
va->m_faWeight[z] = 1.0f;
1123
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1124
} else if (buf[0] == '*')
1125
{
1126
z3 = 0;
1127
tf2 = 0;
1128
for (z=0;z<va->m_oCenterAtoms.m_baAtomType.GetSize();z++)
1129
{
1130
tf = ((CAtom*)g_oaAtoms[va->m_oCenterAtoms.m_baRealAtomType[z]])->m_pElement->m_fMass;
1131
for (z2=0;z2<((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z])->GetSize();z2++)
1132
{
1133
va->m_faWeight[z3] = tf;
1134
tf2 += tf;
1135
z3++;
1136
}
1137
}
1138
va->m_fGesWeight = tf2;
1139
if (va->m_fGesWeight == 0)
1140
{
1141
eprintf("\n Molecule has total mass of zero. Weighting atoms equally.\n\n");
1142
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1143
va->m_faWeight[z] = 1.0f;
1144
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1145
}
1146
} else if (buf[0] == '#')
1147
{
1148
_vawagain:
1149
z3 = 0;
1150
tf2 = 0;
1151
mprintf("\n");
1152
for (z=0;z<va->m_oCenterAtoms.m_baAtomType.GetSize();z++)
1153
{
1154
for (z2=0;z2<((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z])->GetSize();z2++)
1155
{
1156
tf = AskFloat(" Enter the weight for %s%d: [1] ",1.0f,((CAtom*)g_oaAtoms[va->m_oCenterAtoms.m_baRealAtomType[z]])->m_pElement->m_sLabel, ((CxIntArray *)va->m_oCenterAtoms.m_oaAtoms[z])->GetAt(z2)+1);
1157
va->m_faWeight[z3] = tf;
1158
tf2 += tf;
1159
z3++;
1160
}
1161
}
1162
mprintf(" The sum of weights is %.4f.\n\n",tf2);
1163
va->m_fGesWeight = tf2;
1164
if (va->m_fGesWeight == 0)
1165
{
1166
eprintf("Sum of weights may not be zero. Enter the weights again.\n\n");
1167
goto _vawagain;
1168
}
1169
} else
1170
{
1171
eprintf("Wrong input.\n");
1172
inpprintf("! Wrong input.\n");
1173
goto _vaweight;
1174
}
1175
} else
1176
{
1177
_vabond:
1178
mprintf(" Enter 2nd atom for distance #%d- (e.g. C2): ",va->m_iMolVirtAtom+1);
1179
inpprintf("! Enter 2nd atom for distance #%d- (e.g. C2):\n",va->m_iMolVirtAtom+1);
1180
myget(buf);
1181
if (!ParseAtom(buf,va->m_iMolecule,va->m_iAtomType[0],va->m_iRealAtomType[0],va->m_iAtom[0]))
1182
goto _vabond;
1183
if ((va->m_iRealAtomType[0] == g_iVirtAtomType) && (va->m_iAtom[0] == va->m_iMolVirtAtom))
1184
{
1185
eprintf("This atom was already chosen.\n");
1186
goto _vabond;
1187
}
1188
_vaangle:
1189
mprintf(" Enter 3rd atom for angle #%d-%s%d- (e.g. C2)? ",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1);
1190
inpprintf("! Enter 3rd atom for angle #%d-%s%d- (e.g. C2)?\n",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1);
1191
myget(buf);
1192
if (!ParseAtom(buf,va->m_iMolecule,va->m_iAtomType[1],va->m_iRealAtomType[1],va->m_iAtom[1]))
1193
goto _vaangle;
1194
if (((va->m_iRealAtomType[1] == g_iVirtAtomType) && (va->m_iAtom[1] == va->m_iMolVirtAtom)) || ((va->m_iRealAtomType[1] == va->m_iRealAtomType[0]) && (va->m_iAtom[1] == va->m_iAtom[0])))
1195
{
1196
eprintf("This atom was already chosen.\n");
1197
goto _vaangle;
1198
}
1199
_vadihedral:
1200
mprintf(" Enter 4th atom for dihedral #%d-%s%d-%s%d- (e.g. C2)? ",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1);
1201
inpprintf("! Enter 4th atom for dihedral #%d-%s%d-%s%d- (e.g. C2)?\n",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1);
1202
myget(buf);
1203
if (!ParseAtom(buf,va->m_iMolecule,va->m_iAtomType[2],va->m_iRealAtomType[2],va->m_iAtom[2]))
1204
goto _vadihedral;
1205
if (((va->m_iRealAtomType[2] == g_iVirtAtomType) && (va->m_iAtom[2] == va->m_iMolVirtAtom)) || ((va->m_iRealAtomType[2] == va->m_iRealAtomType[0]) && (va->m_iAtom[2] == va->m_iAtom[0])) || ((va->m_iRealAtomType[2] == va->m_iRealAtomType[1]) && (va->m_iAtom[2] == va->m_iAtom[1])))
1206
{
1207
eprintf("This atom was already chosen.\n");
1208
goto _vadihedral;
1209
}
1210
1211
va->m_fValues[0] = AskFloat_ND(" Enter distance #%d-%s%d in pm: ",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1);
1212
va->m_fValues[1] = AskFloat_ND(" Enter angle #%d-%s%d-%s%d in degree: ",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1) * (float)Pi / 180.0f;
1213
va->m_fValues[2] = AskFloat_ND(" Enter dihedral #%d-%s%d-%s%d-%s%d in degree: ",va->m_iMolVirtAtom+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[2]])->m_sName,va->m_iAtom[2]+1) * (float)Pi / 180.0f;
1214
}
1215
1216
if (AskYesNo("\n Define further virtual atoms (y/n)? [no] ",false))
1217
goto _vabeg;
1218
}
1219
1220
mprintf("\n");
1221
if (AskYesNo(" Do you want to define pseudo-molecules (y/n)? [no] ",false))
1222
{
1223
tb2 = false;
1224
ti = 0;
1225
mprintf("\n If you need the center of mass or center of geometry of the whole system, you should\n");
1226
mprintf(" define a pseudo-molecule over the whole system, and use its atoms #1 and #2.\n\n");
1227
if (AskYesNo(" Define a pseudo-molecule over the whole system (y/n)? [yes] ",true))
1228
{
1229
ti++;
1230
/************************************************************************/
1231
mprintf("\n");
1232
try { m2 = new CMolecule(); } catch(...) { m2 = NULL; }
1233
if (m2 == NULL) NewException((double)sizeof(CMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1234
1235
try { sm2 = new CSingleMolecule(); } catch(...) { sm2 = NULL; }
1236
if (sm2 == NULL) NewException((double)sizeof(CSingleMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1237
1238
m2->m_bPseudo = true;
1239
sm2->m_bPseudo = true;
1240
m2->m_iIndex = g_oaMolecules.GetSize();
1241
sm2->m_iMolType = g_oaMolecules.GetSize();
1242
sm2->m_iMolSMIndex = 0;
1243
m2->m_laSingleMolIndex.Add(g_oaSingleMolecules.GetSize());
1244
g_oaMolecules.Add(m2);
1245
g_oaSingleMolecules.Add(sm2);
1246
1247
mprintf(WHITE," >>> Pseudo-molecule %d (= molecule %d) >>>\n\n",ti,g_oaMolecules.GetSize());
1248
mprintf(" Adding all atoms from all molecules...\n");
1249
1250
for (z=0;z<g_oaMolecules.GetSize();z++)
1251
{
1252
m = (CMolecule*)g_oaMolecules[z];
1253
if (m->m_bPseudo)
1254
continue;
1255
1256
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1257
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1258
1259
ag->AddAllAtoms(m,false);
1260
1261
ia.RemoveAll();
1262
1263
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1264
ia.Add(z2);
1265
1266
for (z2=0;z2<ag->m_baAtomType.GetSize();z2++)
1267
{
1268
m2->m_iAtomGes += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1269
1270
for (z4=0;z4<m2->m_baAtomIndex.GetSize();z4++)
1271
{
1272
if (m2->m_baAtomIndex[z4] == ag->m_baRealAtomType[z2])
1273
{
1274
m2->m_waAtomCount[z4] += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1275
pia = (CxIntArray*)sm2->m_oaAtomOffset[z4];
1276
goto _pmafound;
1277
}
1278
}
1279
1280
m2->m_baAtomIndex.Add(ag->m_baRealAtomType[z2]);
1281
sm2->m_baAtomIndex.Add(ag->m_baRealAtomType[z2]);
1282
m2->m_waAtomCount.Add(((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize());
1283
1284
try { pia = new CxIntArray("gather():pia"); } catch(...) { pia = NULL; }
1285
if (pia == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1286
1287
sm2->m_oaAtomOffset.Add(pia);
1288
_pmafound:
1289
for (z4=0;z4<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z4++)
1290
{
1291
for (z5=0;z5<ia.GetSize();z5++)
1292
{
1293
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[ia[z5]]];
1294
for (z6=0;z6<sm2->m_oaAtomOffset.GetSize();z6++)
1295
{
1296
for (z7=0;z7<((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetSize();z7++)
1297
{
1298
if (((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetAt(z7) == ((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)))
1299
{
1300
eprintf("Weird error: Atom %s%d from %s[%d] is already in the pseudo-molecule; skipping.\n",((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)+1,m->m_sName,ia[z5]+1);
1301
m2->m_waAtomCount[m2->m_waAtomCount.GetSize()-1]--;
1302
abort();
1303
}
1304
}
1305
}
1306
pia->Add(((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)));
1307
}
1308
}
1309
}
1310
delete ag;
1311
}
1312
mprintf("\n");
1313
/********************************************************************************/
1314
goto _nopseudomol;
1315
}
1316
_pseudomolnext:
1317
ti++;
1318
1319
if (!tb2)
1320
{
1321
tb2 = true;
1322
mprintf("\n You may define custom element labels. This enables keeping apart\n atoms of the same type from different molecules/positions.\n\n");
1323
tb = AskYesNo(" Keep the standard element labels (y) or define custom labels (n)? [yes] ",true);
1324
mprintf("\n");
1325
}
1326
1327
try { m2 = new CMolecule(); } catch(...) { m2 = NULL; }
1328
if (m2 == NULL) NewException((double)sizeof(CMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1329
1330
try { sm2 = new CSingleMolecule(); } catch(...) { sm2 = NULL; }
1331
if (sm2 == NULL) NewException((double)sizeof(CSingleMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1332
1333
m2->m_bPseudo = true;
1334
sm2->m_bPseudo = true;
1335
m2->m_iIndex = g_oaMolecules.GetSize();
1336
sm2->m_iMolType = g_oaMolecules.GetSize();
1337
sm2->m_iMolSMIndex = 0;
1338
m2->m_laSingleMolIndex.Add(g_oaSingleMolecules.GetSize());
1339
g_oaMolecules.Add(m2);
1340
g_oaSingleMolecules.Add(sm2);
1341
1342
mprintf(WHITE," >>> Pseudo-molecule %d (= molecule %d) >>>\n\n",ti,g_oaMolecules.GetSize());
1343
/* if (ti == 1)
1344
mprintf(WHITE," You may define custom element labels. This enables keeping apart\n atoms of the same type from different molecules/positions.\n\n");
1345
tb = AskYesNo(" Keep the standard element labels (y) or define custom labels (n)? [yes] ",true);
1346
mprintf("\n");
1347
*/
1348
for (z=0;z<g_oaMolecules.GetSize();z++)
1349
{
1350
m = (CMolecule*)g_oaMolecules[z];
1351
if (m->m_bPseudo)
1352
continue;
1353
if (AskYesNo(" Use atoms from molecule %d (%s) (y/n)? [no] ",false,z+1,m->m_sName))
1354
{
1355
mprintf("\n");
1356
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1357
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1358
1359
if (AskYesNo(" Use all atoms (y) from %s or only certain atoms (n)? [no] ",false,m->m_sName))
1360
{
1361
ag->AddAllAtoms(m,false);
1362
} else
1363
{
1364
_pseudomolp1:
1365
AskString_ND(" Please enter atoms from %s to use (e.g. C1-3,H,O4): ",buf,m->m_sName);
1366
if (!ag->ParseAtoms(m,buf))
1367
goto _pseudomolp1;
1368
}
1369
ia.RemoveAll();
1370
if (m->m_laSingleMolIndex.GetSize() > 1)
1371
{
1372
if (!AskYesNo(" Add selected atoms from all %s molecules (y), or only from certain molecules (n)? [yes] ",true,m->m_sName))
1373
{
1374
_pseudomolil:
1375
AskString_ND(" Enter the %s molecules to use (range 1-%d, e.g. 1,3-6,8): ",buf,m->m_sName,m->m_laSingleMolIndex.GetSize());
1376
ia.RemoveAll();
1377
if (!ParseIntList(buf,&ia))
1378
goto _pseudomolil;
1379
for (z2=0;z2<ia.GetSize();z2++)
1380
{
1381
if ((ia[z2] < 1) || (ia[z2] > m->m_laSingleMolIndex.GetSize()))
1382
{
1383
eprintf("Invalid number: %d (should be between 1 and %d).\n",ia[z2],m->m_laSingleMolIndex.GetSize());
1384
goto _pseudomolil;
1385
}
1386
ia[z2]--;
1387
}
1388
} else
1389
{
1390
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1391
ia.Add(z2);
1392
}
1393
} else ia.Add(0);
1394
1395
if (!tb) // Custom Labels
1396
{
1397
for (z2=0;z2<ag->m_baAtomType.GetSize();z2++)
1398
{
1399
_pmlagain:
1400
AskString(" How should %s from %s be labeled? [%s] ",buf,((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,m->m_sName,((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName);
1401
if (ContainsDigit(buf))
1402
{
1403
eprintf("Digits in element labels not allowed.\n");
1404
goto _pmlagain;
1405
}
1406
for (z3=0;z3<g_oaAtoms.GetSize();z3++)
1407
{
1408
if (mystricmp(buf,((CAtom*)g_oaAtoms[z3])->m_sName) == 0)
1409
{
1410
ti2 = z3;
1411
goto _pseudomold1;
1412
}
1413
}
1414
if (strlen(buf) > 7)
1415
{
1416
mprintf(" Element labels may only have up to 7 characters; truncating.\n");
1417
buf[7] = 0;
1418
}
1419
mprintf(" Adding new element label \"%s\"...\n",buf);
1420
1421
try { at = new CAtom(); } catch(...) { at = NULL; }
1422
if (at == NULL) NewException((double)sizeof(CAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1423
1424
at->m_iIndex = g_oaAtoms.GetSize();
1425
at->m_pElement = ((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_pElement;
1426
memcpy(at->m_sName,buf,8);
1427
at->m_iCount = ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1428
ti2 = g_oaAtoms.GetSize();
1429
g_oaAtoms.Add(at);
1430
_pseudomold1:
1431
m2->m_iAtomGes += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1432
for (z3=0;z3<m2->m_baAtomIndex.GetSize();z3++)
1433
{
1434
if (m2->m_baAtomIndex[z3] == ti2)
1435
{
1436
m2->m_waAtomCount[z3] += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1437
for (z4=0;z4<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z4++)
1438
{
1439
for (z5=0;z5<ia.GetSize();z5++)
1440
{
1441
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[ia[z5]]];
1442
for (z6=0;z6<sm2->m_oaAtomOffset.GetSize();z6++)
1443
{
1444
for (z7=0;z7<((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetSize();z7++)
1445
{
1446
if (((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetAt(z7) == ((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)))
1447
{
1448
eprintf("Atom %s%d from %s[%d] is already in the pseudo-molecule; skipping.\n",((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)+1,m->m_sName,ia[z5]+1);
1449
m2->m_waAtomCount[z3]--;
1450
goto _pseudomolsk1;
1451
}
1452
}
1453
}
1454
// mprintf("Molecule %d, SM %d, Type %d, Atom %d: Line %d.\n",z,ia[z5],((CxIntArray*)sm->m_oaAtomOffset[z2])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)));
1455
((CxIntArray*)sm2->m_oaAtomOffset[z3])->Add(((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)));
1456
_pseudomolsk1:;
1457
}
1458
}
1459
goto _pseudomold2;
1460
}
1461
}
1462
m2->m_baAtomIndex.Add(ti2);
1463
sm2->m_baAtomIndex.Add(ti2);
1464
m2->m_waAtomCount.Add(((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize());
1465
1466
try { pia = new CxIntArray("gather():pia"); } catch(...) { pia = NULL; }
1467
if (pia == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1468
1469
sm2->m_oaAtomOffset.Add(pia);
1470
for (z4=0;z4<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z4++)
1471
{
1472
for (z5=0;z5<ia.GetSize();z5++)
1473
{
1474
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[ia[z5]]];
1475
for (z6=0;z6<sm2->m_oaAtomOffset.GetSize();z6++)
1476
{
1477
for (z7=0;z7<((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetSize();z7++)
1478
{
1479
if (((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetAt(z7) == ((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)))
1480
{
1481
eprintf("Atom %s%d from %s[%d] is already in the pseudo-molecule; skipping.\n",((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)+1,m->m_sName,ia[z5]+1);
1482
m2->m_waAtomCount[m2->m_waAtomCount.GetSize()-1]--;
1483
goto _pseudomolsk2;
1484
}
1485
}
1486
}
1487
pia->Add(((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)));
1488
_pseudomolsk2:;
1489
}
1490
}
1491
_pseudomold2:;
1492
}
1493
} else // If not custom labels
1494
{
1495
for (z2=0;z2<ag->m_baAtomType.GetSize();z2++)
1496
{
1497
for (z4=0;z4<m2->m_baAtomIndex.GetSize();z4++)
1498
{
1499
if (m2->m_baAtomIndex[z4] == ag->m_baRealAtomType[z2])
1500
{
1501
m2->m_waAtomCount[z4] += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1502
pia = (CxIntArray*)sm2->m_oaAtomOffset[z4];
1503
goto _pmafound2;
1504
}
1505
}
1506
1507
m2->m_iAtomGes += ((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize();
1508
m2->m_baAtomIndex.Add(ag->m_baRealAtomType[z2]);
1509
sm2->m_baAtomIndex.Add(ag->m_baRealAtomType[z2]);
1510
m2->m_waAtomCount.Add(((CxIntArray*)ag->m_oaAtoms[z2])->GetSize() * ia.GetSize());
1511
1512
try { pia = new CxIntArray("gather():pia"); } catch(...) { pia = NULL; }
1513
if (pia == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1514
1515
sm2->m_oaAtomOffset.Add(pia);
1516
_pmafound2:
1517
for (z4=0;z4<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z4++)
1518
{
1519
for (z5=0;z5<ia.GetSize();z5++)
1520
{
1521
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[ia[z5]]];
1522
for (z6=0;z6<sm2->m_oaAtomOffset.GetSize();z6++)
1523
{
1524
for (z7=0;z7<((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetSize();z7++)
1525
{
1526
if (((CxIntArray*)sm2->m_oaAtomOffset[z6])->GetAt(z7) == ((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)))
1527
{
1528
eprintf("Atom %s%d from %s[%d] is already in the pseudo-molecule; skipping.\n",((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z2]])->m_sName,((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)+1,m->m_sName,ia[z5]+1);
1529
m2->m_waAtomCount[m2->m_waAtomCount.GetSize()-1]--;
1530
goto _pseudomolsk3;
1531
}
1532
}
1533
}
1534
pia->Add(((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z4)));
1535
_pseudomolsk3:;
1536
}
1537
}
1538
}
1539
}
1540
delete ag;
1541
if (AskYesNo(" Use another set of atoms from %s (y/n)? [no] ",false,m->m_sName))
1542
{
1543
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
1544
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1545
1546
goto _pseudomolp1;
1547
}
1548
}
1549
mprintf("\n");
1550
}
1551
_nopseudomol:
1552
m2->BuildName();
1553
mprintf(WHITE," <<< Pseudo-molecule %d (= molecule %d) defined as %s <<<\n\n",ti,g_oaMolecules.GetSize(),m2->m_sName);
1554
if (AskYesNo(" Define another pseudo-molecule (y/n)? [no] ",false))
1555
goto _pseudomolnext;
1556
mprintf(WHITE,"\n The following pseudo-molecules have been defined:\n");
1557
mprintf(" (note: pseudo-molecules start with a $ sign)\n\n");
1558
ti = 0;
1559
for (z=0;z<g_oaMolecules.GetSize();z++)
1560
{
1561
m = (CMolecule*)g_oaMolecules[z];
1562
if (m->m_bPseudo)
1563
{
1564
ti++;
1565
mprintf(" %d.) Molecule %d - %s\n",ti,z+1,m->m_sName);
1566
}
1567
}
1568
mprintf(WHITE,"\n Defining virtual atom #1 as molecular Center of Geometry:\n");
1569
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1570
{
1571
m = (CMolecule*)g_oaMolecules[z0];
1572
if (!m->m_bPseudo)
1573
continue;
1574
mprintf(" - %s...\n",m->m_sName);
1575
va = AddVirtualAtom(z0);
1576
va->m_iMode = 0;
1577
va->m_oCenterAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],false);
1578
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1579
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1580
va->m_faWeight[z] = 1.0f;
1581
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1582
}
1583
1584
mprintf(WHITE,"\n Defining virtual atom #2 as molecular Center of Mass:\n");
1585
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1586
{
1587
m = (CMolecule*)g_oaMolecules[z0];
1588
if (!m->m_bPseudo)
1589
continue;
1590
mprintf(" - %s...\n",m->m_sName);
1591
va = AddVirtualAtom(z0);
1592
va->m_iMode = 0;
1593
va->m_oCenterAtoms.AddAllAtoms((CMolecule*)g_oaMolecules[va->m_iMolecule],false);
1594
va->m_faWeight.SetSize(va->m_oCenterAtoms.m_iAtomGes);
1595
z3 = 0;
1596
tf2 = 0;
1597
for (z=0;z<va->m_oCenterAtoms.m_baAtomType.GetSize();z++)
1598
{
1599
tf = ((CAtom*)g_oaAtoms[va->m_oCenterAtoms.m_baRealAtomType[z]])->m_pElement->m_fMass;
1600
for (z2=0;z2<((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z])->GetSize();z2++)
1601
{
1602
va->m_faWeight[z3] = tf;
1603
tf2 += tf;
1604
z3++;
1605
}
1606
}
1607
va->m_fGesWeight = tf2;
1608
if (va->m_fGesWeight == 0)
1609
{
1610
eprintf(" Molecule %s has total mass of zero. Defining #2 as Center of Geometry.\n",m->m_sName);
1611
for (z=0;z<va->m_oCenterAtoms.m_iAtomGes;z++)
1612
va->m_faWeight[z] = 1.0f;
1613
va->m_fGesWeight = (float)va->m_oCenterAtoms.m_iAtomGes;
1614
}
1615
}
1616
}
1617
}
1618
1619
mprintf(GREEN,"\n>>> %d virtual atoms have been defined: >>>\n",g_oaVirtualAtoms.GetSize());
1620
for (z0=0;z0<g_oaMolecules.GetSize();z0++)
1621
{
1622
for (z=0;z<((CMolecule*)g_oaMolecules[z0])->m_laVirtualAtoms.GetSize();z++)
1623
{
1624
va = (CVirtualAtom*)g_oaVirtualAtoms[((CMolecule*)g_oaMolecules[z0])->m_laVirtualAtoms[z]];
1625
if (va->m_iMolVirtAtom < 2)
1626
{
1627
mprintf(WHITE,"\n #%d in %s: %s.",va->m_iMolVirtAtom+1,((CMolecule*)g_oaMolecules[va->m_iMolecule])->m_sName,(va->m_iMolVirtAtom==0)?"Center of Geometry":"Center of Mass");
1628
if (va->m_iMolVirtAtom == 1)
1629
mprintf("\n");
1630
continue;
1631
}
1632
mprintf(WHITE,"\n #%d in %s - defined through %s\n",va->m_iMolVirtAtom+1,((CMolecule*)g_oaMolecules[va->m_iMolecule])->m_sName,(va->m_iMode==0)?"center:":"distance/angle/dihedral:");
1633
if (va->m_iMode == 0)
1634
{
1635
if (!((CMolecule*)g_oaMolecules[z0])->m_bPseudo || (z > 1))
1636
{
1637
z4 = 0;
1638
for (z2=0;z2<va->m_oCenterAtoms.m_baAtomType.GetSize();z2++)
1639
{
1640
for (z3=0;z3<((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z2])->GetSize();z3++)
1641
{
1642
mprintf(" - %2s%-3d Weight %.2f%c\n",((CAtom*)g_oaAtoms[va->m_oCenterAtoms.m_baRealAtomType[z2]])->m_sName,((CxIntArray*)va->m_oCenterAtoms.m_oaAtoms[z2])->GetAt(z3)+1,va->m_faWeight[z4]/va->m_fGesWeight*100.0f,'%');
1643
z4++;
1644
}
1645
}
1646
} else mprintf(" (pseudo-molecule, skipping atoms)\n");
1647
} else
1648
{
1649
mprintf(" - Distance #%d-%s%d = %.2f pm\n",z+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,va->m_fValues[0]);
1650
mprintf(" - Angle #%d-%s%d-%s%d = %.2f degree\n",z+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1,va->m_fValues[1]*180.0/Pi);
1651
mprintf(" - Dihedral #%d-%s%d-%s%d-%s%d = %.2f degree\n",z+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[0]])->m_sName,va->m_iAtom[0]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[1]])->m_sName,va->m_iAtom[1]+1,((CAtom*)g_oaAtoms[va->m_iRealAtomType[2]])->m_sName,va->m_iAtom[2]+1,va->m_fValues[2]*180.0/Pi);
1652
}
1653
}
1654
}
1655
mprintf(GREEN,"\n<<< End of virtual atoms <<<\n\n");
1656
1657
if (g_bPeriodic)
1658
g_TimeStep.UniteMolecules(false);
1659
1660
g_TimeStep.CalcCenters();
1661
g_bFoldAtomwise = false;
1662
1663
if (g_bPeriodic)
1664
g_TimeStep.FoldMolecules();
1665
1666
BuildAtomIndices();
1667
1668
// g_TimeStep.WritePOV("step.pov");
1669
1670
mprintf(WHITE,"\n>>> List of functions <<<\n\n");
1671
DumpAnalyses();
1672
1673
mprintf(" (You may specify multiple analyses at once, but\n");
1674
mprintf(" the safe way is to perform only one kind of analysis at a time.)\n");
1675
_fncinput:
1676
inpprintf("! Which functions to compute (comma separated)?\n");
1677
mprintf("\n Which functions to compute (comma separated)? ");
1678
myget(buf);
1679
mprintf("\n");
1680
if (!ParseFunctions(buf))
1681
{
1682
eprintf("Wrong input.\n");
1683
inpprintf("! Wrong input.\n");
1684
goto _fncinput;
1685
}
1686
mprintf("\n");
1687
1688
if (g_bRegionAnalysis)
1689
{
1690
if (!(g_bRDF || g_bSDF || g_bADF || g_bDDF || g_bCDF || g_bRevSDF || g_bDens))
1691
{
1692
eprintf(" Region-specific analysis needs to be applied to some static analysis.\n\n");
1693
return false;
1694
}
1695
g_iaSMRegion.SetSize(g_oaSingleMolecules.GetSize());
1696
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
1697
g_iaSMRegion[z] = (rand()%2)+1;
1698
}
1699
1700
if (g_bVoro || g_bVoid || g_bSaveJustTraj || g_bSaveRefEnv || g_bCutCluster)
1701
g_bNeedMoleculeWrap = true;
1702
1703
if (g_bNPT && (g_bACF || g_bMSD))
1704
{
1705
mprintf(RED," Warning: ");
1706
mprintf("When a variable cell vector is used, dynamical analyses (like spectra or MSDs)\n");
1707
mprintf(" will give erroneous results.\n\n");
1708
}
1709
1710
mprintf(WHITE," The advanced mode includes some options which are quite powerful,\n yet possibly weird or seldomly required.\n\n");
1711
1712
g_bAdvanced2 = AskYesNo(" Use the advanced mode for the main part (y/n)? [no] ",false);
1713
mprintf("\n");
1714
1715
if (g_bThermo || g_bVDF || g_bRaman || g_bCombined || g_bBondACF || g_bVHDF || g_bACF || g_bUseVelocities || g_bUseForces || g_bMSD || g_bAggregation || g_bDLDisp || g_bDLDF || g_bDACF || g_bRDyn || g_bIRSpec || g_bIRSpec || g_bTimeDiff || g_bDeriv)
1716
{
1717
g_fTimestepLength = AskFloat(" Enter the length of one trajectory time step in fs: [0.5] ",0.5f);
1718
mprintf("\n");
1719
}
1720
1721
/*********** Interface ***************/
1722
if (!Interface_BeforeAnalysis())
1723
return false;
1724
1725
if (g_bCDF)
1726
{
1727
mprintf(YELLOW,"*** Combined Distribution Function\n\n");
1728
g_iCDFChannels = AskUnsignedInteger(" How many channels should the Combined Distribution Function have? [2] ",2);
1729
1730
try { g_iObsChannel = new int[g_iCDFChannels]; } catch(...) { g_iObsChannel = NULL; }
1731
if (g_iObsChannel == NULL) NewException((double)g_iCDFChannels*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1732
1733
mprintf(" Choose from these functions: rdf, adf, ddf, dip, vdf");
1734
if (g_bBetaFeatures)
1735
mprintf(", pldf, lidf");
1736
mprintf("\n");
1737
for (z=0;z<g_iCDFChannels;z++)
1738
{
1739
_entertype:
1740
AskString_ND(" Channel %d: Enter function type (e.g. rdf): ",buf,z+1);
1741
if (mystricmp(buf,"rdf")==0)
1742
{
1743
g_iObsChannel[z] = 0;
1744
g_bRDF = true;
1745
} else if (mystricmp(buf,"adf")==0)
1746
{
1747
g_iObsChannel[z] = 1;
1748
g_bADF = true;
1749
} else if (mystricmp(buf,"ddf")==0)
1750
{
1751
g_iObsChannel[z] = 2;
1752
g_bDDF = true;
1753
} else if (mystricmp(buf,"dip")==0)
1754
{
1755
g_iObsChannel[z] = 3;
1756
g_bDipDF = true;
1757
} else if (mystricmp(buf,"vdf")==0)
1758
{
1759
g_iObsChannel[z] = 4;
1760
g_bVDF = true;
1761
} else if ((mystricmp(buf,"pldf")==0) && g_bBetaFeatures)
1762
{
1763
g_iObsChannel[z] = 5;
1764
g_bPlDF = true;
1765
} else if ((mystricmp(buf,"lidf")==0) && g_bBetaFeatures)
1766
{
1767
g_iObsChannel[z] = 6;
1768
g_bLiDF = true;
1769
} else
1770
{
1771
eprintf("Wrong input.\n");
1772
inpprintf("! Wrong input.\n");
1773
goto _entertype;
1774
}
1775
}
1776
} else g_iCDFChannels = 1;
1777
1778
if (g_bDipDF || g_bDipole)
1779
ParseDipole();
1780
1781
if (g_bVoro)
1782
{
1783
try { g_pVoroWrapper = new CVoroWrapper(); } catch(...) { g_pVoroWrapper = NULL; }
1784
if (g_pVoroWrapper == NULL) NewException((double)sizeof(CVoroWrapper),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1785
1786
g_pVoroWrapper->Parse();
1787
}
1788
1789
/* if (g_bSFac)
1790
{
1791
try { g_pSFac = new CStructureFactor(); } catch(...) { g_pSFac = NULL; }
1792
if (g_pSFac == NULL) NewException((double)sizeof(CStructureFactor),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1793
1794
g_pSFac->Parse();
1795
}*/
1796
1797
if (g_bResp)
1798
{
1799
try { g_pResp = new CResp(); } catch(...) { g_pResp = NULL; }
1800
if (g_pResp == NULL) NewException((double)sizeof(CResp),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1801
1802
g_pResp->m_pTimeStep = &g_TimeStep;
1803
g_pResp->ParseResp();
1804
1805
if (!g_bFFGen)
1806
return true;
1807
}
1808
1809
if (g_bFFGen)
1810
{
1811
try { g_pFFGen = new CFFGen(); } catch(...) { g_pFFGen = NULL; }
1812
if (g_pFFGen == NULL) NewException((double)sizeof(CFFGen),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1813
1814
g_pFFGen->Parse(&g_TimeStep);
1815
1816
return true;
1817
}
1818
1819
if (g_bVoid)
1820
{
1821
try { g_pVoroWrapper = new CVoroWrapper(); } catch(...) { g_pVoroWrapper = NULL; }
1822
if (g_pVoroWrapper == NULL) NewException((double)sizeof(CVoroWrapper),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1823
1824
try { g_pVoroAnalysis = new CVoroAnalysis(); } catch(...) { g_pVoroAnalysis = NULL; }
1825
if (g_pVoroAnalysis == NULL) NewException((double)sizeof(CVoroAnalysis),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1826
1827
g_pVoroAnalysis->Parse();
1828
}
1829
1830
if (g_bAggregation)
1831
{
1832
mprintf(WHITE,">>> Selection of Aggregation Functions >>>\n\n");
1833
1834
g_bDACF = AskYesNo(" Compute Dimer Existence Autocorrelation Functions (DACFs) (y/n)? [yes] ",true);
1835
g_bDLDF = AskYesNo(" Compute Dimer Lifetime Distribution Functions (DLDFs) (y/n)? [yes] ",true);
1836
g_bDDisp = AskYesNo(" Compute Dimer Displacement Functions / Pair Diffusion (y/n)? [no] ",false);
1837
if (g_bDDisp)
1838
{
1839
g_bPairMSD = AskYesNo(" Compute Pair Mean Square Displacement (Pair Diffusion) (y/n)? [yes] ",true);
1840
g_bDLDisp = AskYesNo(" Compute combined Dimer Lifetime/Displacement Function (DLDisp) (y/n)? [yes] ",true);
1841
} else
1842
{
1843
g_bDLDisp = false;
1844
g_bPairMSD = false;
1845
}
1846
1847
mprintf(WHITE,"\n<<< Selection of Aggregation Functions <<<\n\n");
1848
}
1849
1850
if (g_bNbExchange)
1851
{
1852
mprintf(WHITE,">>> Selection of Neighborhood Exchange Functions >>>\n\n");
1853
mprintf(WHITE,"\n<<< Selection of Neighborhood Exchange Functions <<<\n\n");
1854
}
1855
1856
if (g_bAdvanced2)
1857
{
1858
if (g_bRDyn || g_bIRSpec)
1859
g_bRDynCacheMode = AskYesNo(" Use RDyn cached mode (do this unless there are problems) (y/n)? [yes] ",true);
1860
1861
if (g_bMSD)
1862
g_bMSDCacheMode = AskYesNo(" Use MSD cached mode (do this unless there are problems) (y/n)? [yes] ",true);
1863
} else
1864
{
1865
g_bRDynCacheMode = true;
1866
g_bMSDCacheMode = true;
1867
}
1868
1869
if (g_bClusterAnalysis)
1870
{
1871
try { g_pClusterAnalysis = new CClusterAnalysis(); } catch(...) { g_pClusterAnalysis = NULL; }
1872
if (g_pClusterAnalysis == NULL) NewException((double)sizeof(CClusterAnalysis),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1873
1874
g_pClusterAnalysis->Parse();
1875
}
1876
1877
if (g_bMicroHet)
1878
{
1879
try { g_pMicroHet = new CMicroHet(); } catch(...) { g_pMicroHet = NULL; }
1880
if (g_pMicroHet == NULL) NewException((double)sizeof(CMicroHet),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1881
1882
g_pMicroHet->Parse();
1883
}
1884
1885
if (g_bThermo)
1886
{
1887
try { g_pThermoAnalysis = new CThermoAnalysis(); } catch(...) { g_pThermoAnalysis = NULL; }
1888
if (g_pThermoAnalysis == NULL) NewException((double)sizeof(CThermoAnalysis),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1889
1890
g_pThermoAnalysis->Parse();
1891
}
1892
1893
if (g_bFESA)
1894
{
1895
try { g_pFESA = new CFESAnalysis(); } catch(...) { g_pFESA = NULL; }
1896
if (g_pFESA == NULL) NewException((double)sizeof(CFESAnalysis),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1897
1898
g_pFESA->Parse();
1899
}
1900
1901
if (g_bACF)
1902
{
1903
// mprintf(YELLOW,">>> Select Autocorrelation Functions >>>\n\n");
1904
1905
if (!g_bPowerSpec)
1906
g_bVACF = AskYesNo(" Calculate velocity autocorrelation function / power spectra (y/n)? [yes] ",true);
1907
else g_bVACF = true;
1908
1909
if (g_bVACF)
1910
g_bUseVelocities = true;
1911
1912
/* if (g_bBetaFeatures)
1913
g_bBondACF = AskYesNo(" Calculate bond vibration spectra (y/n)? [no] ",false);
1914
else*/ g_bBondACF = false;
1915
1916
/* g_bDipACF = AskYesNo(" Calculate dipole autocorrelation function / IR spectra (y/n)? [no] ",false);
1917
if (g_bDipACF)
1918
g_bDipole = true;*/
1919
1920
// mprintf(YELLOW,"\n<<< End of Select Autocorrelation Functions <<<\n\n");
1921
}
1922
1923
if (g_bBondACF)
1924
{
1925
mprintf(WHITE,">>> Bond vibration spectra >>>\n\n");
1926
if (g_iTrajSteps != -1)
1927
g_iBondACFDepth = AskUnsignedInteger(" Enter bond ACF depth in time steps: [%d] ",g_iTrajSteps/2,g_iTrajSteps/2);
1928
else g_iBondACFDepth = AskUnsignedInteger(" Enter bond ACF depth in time steps: [%d] ",4096,4096);
1929
ti = CalcFFTSize(g_iBondACFDepth,false);
1930
if (g_iBondACFDepth != ti)
1931
{
1932
mprintf(WHITE,"\n The next \"fast\" size for FFT is %d. Using this instead of %d as size.\n",ti,g_iBondACFDepth);
1933
g_iBondACFDepth = ti;
1934
}
1935
g_bBondACFNormalize = AskYesNo(" Normalize all bond ACFs (removes intensity info for the peaks) (y/n)? [no] ",false);
1936
g_bBondACFSymmetrize = AskYesNo(" Symmetrize all bond ACFs (y/n)? [no] ",false);
1937
g_bBondACFWindow = AskYesNo(" Apply window function to bond ACFs (y/n)? [yes] ",true);
1938
g_bBondACFDebug = AskYesNo(" Write out bond ACF debug data (y/n)? [no] ",false);
1939
mprintf(WHITE,"\n<<< End of Bond vibration spectra <<<\n\n");
1940
}
1941
1942
if (g_bRDyn || g_bIRSpec || g_bBondACF || g_bVACF)
1943
{
1944
if (g_bAdvanced2)
1945
g_bACFFFT = AskYesNo(" Use fourier transform for autocorrelation (much faster) (y/n)? [yes] ",true);
1946
else g_bACFFFT = true;
1947
} else g_bACFFFT = true;
1948
1949
if (g_bCDF || g_bPlProj || g_bDipDF || g_bRDF || g_bVHDF || g_bSDF || g_bPlDF || g_bLiDF || g_bVoidSDF || g_bRevSDF || g_bADF || g_bDDF || g_bSaveRefEnv || g_bCutCluster || g_bCond || g_bNbAnalysis)
1950
{
1951
if (g_oaMolecules.GetSize() > 1)
1952
{
1953
sprintf(buf,"\n Which of the molecules should be the reference molecule (");
1954
for (z=0;z<g_oaMolecules.GetSize();z++)
1955
{
1956
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
1957
strcat(buf,buf2);
1958
if (z < g_oaMolecules.GetSize()-1)
1959
strcat(buf,", ");
1960
}
1961
strcat(buf,")? ");
1962
g_iFixMol = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize()) - 1;
1963
} else g_iFixMol = 0;
1964
mprintf(WHITE,"\n %s is the reference molecule.\n\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
1965
} else g_iFixMol = -1;
1966
1967
if (g_bSaveRefEnv)
1968
{
1969
mprintf(YELLOW,">>> Save environment of the reference molecule >>>\n\n");
1970
g_bSaveRefWithEnv = AskYesNo(" Save the reference molecule itself (y/n)? [yes] ",true);
1971
g_bRefEnvCenter = AskYesNo(" Center the reference molecule in the box (y/n)? [yes] ",true);
1972
if (g_bRefEnvCenter)
1973
{
1974
mprintf("\n The first reference atom will be put into the middle of the box.\n\n");
1975
g_bRefEnvFix = AskYesNo(" Fix rotational freedom of the reference molecule (y/n)? [no] ",false);
1976
if (g_bRefEnvFix)
1977
{
1978
mprintf("\n The 2nd reference atom will be put onto the positive X axis,\n");
1979
mprintf(" and the 3rd reference atom into the X-Y plane with positive Y values.\n\n");
1980
}
1981
mprintf(WHITE," You will be asked for the reference atom(s) lateron.\n\n");
1982
}
1983
if (((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() > 1)
1984
g_iSaveRefMol = AskRangeInteger(" Which representative of the reference molecules to use (1-%d)? [1] ",1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize(),1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()) - 1;
1985
else g_iSaveRefMol = 0;
1986
mprintf(WHITE,"\nPlease choose mode for neighborhood detection:\n\n");
1987
inpprintf("! Please choose mode for neighborhood detection:\n");
1988
mprintf(" 1.) Search neighbors once in the beginning and always show those.\n");
1989
mprintf(" 2.) Search neighbors in every step and show the current neighbors.\n");
1990
mprintf(" (Warning: Neighbor count differs from step to step - be aware.\n");
1991
mprintf(" 3.) Find the frequentiest neighbors over all steps and always show those.\n\n");
1992
mprintf(WHITE," Please note: ");
1993
mprintf("Programs such as VMD cannot handle variable atom count \n");
1994
mprintf(" along a trajectory and will therefore not work properly with mode 2!\n\n");
1995
g_iNbhMode = AskRangeInteger(" Choice (1-3): [3] ",1,3,3);
1996
mprintf(YELLOW,"\n<<< End of Save environment of the reference molecule <<<\n\n");
1997
}
1998
1999
if (g_bCutCluster)
2000
{
2001
mprintf(WHITE,">>> Cut clusters >>>\n\n");
2002
g_bSaveRefWithEnv = AskYesNo(" Show reference molecule itself (y/n)? [yes] ",true);
2003
g_bRefEnvCenter = AskYesNo(" Center reference molecule in the box (y/n)? [yes] ",true);
2004
if (g_bRefEnvCenter)
2005
g_bRefEnvFix = AskYesNo(" Fix rotational freedom of the reference molecule (y/n)? [no] ",false);
2006
_clustercount:
2007
g_iClusterCount = AskUnsignedInteger(" How many clusters to create? [100] ",100);
2008
g_iClusterSteps = AskUnsignedInteger(" How many time steps to use for cluster creation? [%d] ",g_iTrajSteps,g_iTrajSteps);
2009
mprintf("\nCreating cluster distribution...");
2010
for (z=0;z<g_iClusterCount;z++)
2011
{
2012
if (fmod(z,g_iClusterCount/25.0) < 1.0)
2013
mprintf(".");
2014
z3=0;
2015
_clustagain:
2016
z3++;
2017
if (z3 > 500)
2018
{
2019
eprintf("Error: Too few molecules / time steps for requested cluster count.\n");
2020
goto _clustercount;
2021
}
2022
ti = ((((unsigned long)rand()%16384)+rand()*16384) % g_iClusterSteps) + 1;
2023
ti2 = rand()%((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize();
2024
for (z2=0;z2<g_iaClusterSteps.GetSize();z2++)
2025
if ((g_iaClusterSteps[z2] == ti) && (g_iaClusterMol[z2] == ti2))
2026
goto _clustagain;
2027
g_iaClusterSteps.Add(ti);
2028
g_iaClusterMol.Add(ti2);
2029
}
2030
mprintf("Done.\n");
2031
mprintf("Sorting cluster distribution...");
2032
for (z=0;z<g_iClusterCount-1;z++)
2033
{
2034
if (fmod(z,(g_iClusterCount-1)/25.0) < 1.0)
2035
mprintf(".");
2036
ti = 99999999;
2037
ti2 = 99999999;
2038
ti3 = -1;
2039
for (z2=z;z2<g_iClusterCount;z2++)
2040
{
2041
if (g_iaClusterSteps[z2] < ti)
2042
{
2043
ti = g_iaClusterSteps[z2];
2044
ti2 = g_iaClusterMol[z2];
2045
ti3 = z2;
2046
} else if (g_iaClusterSteps[z2] == ti)
2047
{
2048
if (g_iaClusterMol[z2] < ti2)
2049
{
2050
ti2 = g_iaClusterMol[z2];
2051
ti3 = z2;
2052
}
2053
}
2054
}
2055
if (ti3 == -1)
2056
abort();
2057
ti = g_iaClusterSteps[z];
2058
g_iaClusterSteps[z] = g_iaClusterSteps[ti3];
2059
g_iaClusterSteps[ti3] = ti;
2060
ti = g_iaClusterMol[z];
2061
g_iaClusterMol[z] = g_iaClusterMol[ti3];
2062
g_iaClusterMol[ti3] = ti;
2063
}
2064
mprintf("Done.\n\n");
2065
mprintf("Writing cluster selection to \"cluster.csv\"...");
2066
a = OpenFileWrite("cluster.csv",true);
2067
mfprintf(a,"# Cluster; Timestep; Ref. Mol.\n");
2068
2069
for (z=0;z<g_iClusterCount;z++)
2070
mfprintf(a,"%d; %d; %d\n",z+1,g_iaClusterSteps[z],g_iaClusterMol[z]+1);
2071
2072
fclose(a);
2073
mprintf("Done.\n\n");
2074
mprintf(WHITE,"<<< End of Cut clusters <<<\n\n");
2075
}
2076
2077
if (g_bSDF || g_bPlProj || g_bVoidSDF || g_bAvg || ((g_bSaveRefEnv || g_bCutCluster) && g_bRefEnvFix)) // Nur fuer SDFs: Welche zwei weiteren Atome fixieren?
2078
{
2079
g_iRefSystemDim = 3;
2080
_ref3again:
2081
mprintf(WHITE," You have to choose three reference atoms from the reference molecule %s:\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2082
mprintf(" The first reference atom will be put into the center.\n");
2083
mprintf(" The 2nd reference atom will be put onto the positive X axis.\n");
2084
mprintf(" The 3rd reference atom will be put into the X-Y plane with positive Y values.\n\n");
2085
mprintf(" Please enter three comma-separated reference atoms (e.g. \"C1,H2,O1\"): ");
2086
inpprintf("! Please enter three comma-separated reference atoms (e.g. \"C1,H2,O1\"):\n");
2087
myget(buf);
2088
if (!ParseRefSystem(g_iFixMol,buf,3))
2089
goto _ref3again;
2090
for (z=1;z<3;z++)
2091
{
2092
for (z2=0;z2<z;z2++)
2093
{
2094
if ((g_iFixAtomType[z] == g_iFixAtomType[z2]) && (g_iFixAtom[z] == g_iFixAtom[z2]))
2095
{
2096
eprintf("Please enter three pairwise different atoms.\n\n");
2097
inpprintf("! Please enter three pairwise different atoms.\n");
2098
goto _ref3again;
2099
}
2100
}
2101
}
2102
mprintf("\n");
2103
mprintf(WHITE," Reference plane: Fixing in %s the %d. %s-, the %d. %s- and the %d. %s atom.\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[1]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName,g_iFixAtom[2]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_sName);
2104
mprintf("\n");
2105
} else if (g_bRevSDF)
2106
{
2107
g_iRefSystemDim = 2;
2108
_ref2again:
2109
mprintf(" Please enter two reference atoms (e.g. C1,H3): ");
2110
inpprintf("! Please enter two reference atoms (e.g. C1,H3):\n");
2111
myget(buf);
2112
if (!ParseRefSystem(g_iFixMol,buf,2))
2113
goto _ref2again;
2114
if ((g_iFixAtomType[0] == g_iFixAtomType[1]) && (g_iFixAtom[0] == g_iFixAtom[1]))
2115
{
2116
eprintf("Please enter two different atoms.\n\n");
2117
inpprintf("! Please enter two different atoms.\n");
2118
goto _ref2again;
2119
}
2120
mprintf("\n");
2121
mprintf(WHITE,"Reference axis: Fixing in %s the %d. %s and the %d. %s atom.\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[1]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName);
2122
mprintf("\n");
2123
} else if (g_bVHDF || g_bRDF || g_bADF || g_bPlDF || g_bLiDF || g_bDDF || g_bSaveRefEnv || g_bSaveRefEnv || g_bCutCluster) // Fuer Verteilungsfunktion: Welches Atom im Ursprung
2124
{
2125
g_iRefSystemDim = 1;
2126
if (g_bAdvanced2)
2127
{
2128
_ref1again:
2129
mprintf(" Please enter the atom to put into the box center (e.g. C3): [center of mass] ");
2130
inpprintf("! Please enter the atom to put into the box center (e.g. C3): [center of mass]\n");
2131
myget(buf);
2132
if (strlen(buf)==0)
2133
{
2134
if (!ParseRefSystem(g_iFixMol,"#2",1))
2135
{
2136
eprintf("Weird error.\n");
2137
inpprintf("! Weird error.\n");
2138
abort();
2139
}
2140
} else if (!ParseRefSystem(g_iFixMol,buf,1))
2141
goto _ref1again;
2142
mprintf("\n");
2143
mprintf(WHITE,"Reference atom: Fixing in %s the %d. %s atom.\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName);
2144
mprintf("\n");
2145
} else
2146
{
2147
if (!ParseRefSystem(g_iFixMol,"#2",1))
2148
{
2149
eprintf("Weird error.\n");
2150
inpprintf("! Weird error.\n");
2151
abort();
2152
}
2153
}
2154
} else if (g_iFixMol != -1)
2155
{
2156
g_iRefSystemDim = 1;
2157
if (!ParseRefSystem(g_iFixMol,"#2",1))
2158
{
2159
eprintf("Weird error.\n");
2160
abort();
2161
}
2162
mprintf(" Reference atom: Fixing in %s the %d. %s atom.\n\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName);
2163
}
2164
2165
if (g_bSaveRefEnv || g_bCutCluster)
2166
{
2167
mprintf(WHITE,">>> Neighborhood Definition >>>\n\n");
2168
2169
try { g_pNbSet = new CNbSet(); } catch(...) { g_pNbSet = NULL; }
2170
if (g_pNbSet == NULL) NewException((double)sizeof(CNbSet),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2171
2172
g_pNbSet->Parse(g_iFixMol);
2173
mprintf(WHITE,"\n<<< End of Neighborhood Definition <<<\n\n");
2174
2175
if (g_bSaveRefEnv)
2176
{
2177
if (AskYesNo(" Create a temporal development overlay (TDO) plot (y/n)? [no] ",false))
2178
{
2179
g_bTDO = true;
2180
g_laTDOSteps.RemoveAll();
2181
if (AskYesNo(" Use equidistant intervals (y) or specify each point (n) (y/n)? [yes] ",true))
2182
{
2183
g_bTDOEqui = true;
2184
g_iTDOCount = AskUnsignedInteger(" Enter the overlay count: [5] ",5);
2185
g_iTDOStart = AskUnsignedInteger(" Enter the starting timestep: [0] ",0);
2186
g_iTDOStride = AskUnsignedInteger(" Enter the overlay distance in steps: [1000] ",1000);
2187
for (z=0;z<g_iTDOCount;z++)
2188
g_laTDOSteps.Add(g_iTDOStart+z*g_iTDOStride);
2189
} else
2190
{
2191
g_bTDOEqui = false;
2192
while (true)
2193
{
2194
ti = AskUnsignedInteger(" Enter timestep for %dth overlay: [done] ",999999,g_laTDOSteps.GetSize()+1);
2195
if (ti == 999999)
2196
break;
2197
g_laTDOSteps.Add(ti);
2198
}
2199
}
2200
g_fTDOBleaching = AskRangeFloat(" Enter the TDO bleaching grade (0-1): [0.8] ",0.0f,1.0f,0.8f);
2201
} else g_bTDO = false;
2202
}
2203
}
2204
2205
if (g_bPlProj || g_bAggregation || g_bNbAnalysis || g_bPlDF || g_bLiDF || g_bRDyn || g_bIRSpec || g_bDipDF || g_bMSD || g_bADF || g_bDDF || g_bVACF || g_bDipACF || g_bRevSDF || g_bSDF || g_bVHDF || g_bRDF || g_bDens || g_bVDF || g_bFDF || g_bCond) // Fuer Verteilungsfunktion: Welches Atom beobachten?
2206
{
2207
if (g_bVACF)
2208
{
2209
if (g_bAdvanced2)
2210
g_bVACFCacheMode = AskYesNo(" Use VACF cached mode (do this unless there are problems) (y/n)? [yes] ",true);
2211
else g_bVACFCacheMode = true;
2212
2213
if (g_bPowerSpec)
2214
{
2215
g_bGlobalVACF = AskYesNo(" Compute power spectrum of whole system (y/n)? [yes] ",true);
2216
2217
if (g_bGlobalVACF)
2218
if (!AskYesNo(" Compute also power spectra for certain atoms/molecules (y/n)? [no] ",false))
2219
goto _endobs;
2220
} else
2221
{
2222
g_bGlobalVACF = AskYesNo(" Compute global velocity ACF of whole system (y/n)? [yes] ",true);
2223
2224
if (g_bGlobalVACF)
2225
if (!AskYesNo(" Compute also velocity ACFs for certain atoms/molecules (y/n)? [no] ",false))
2226
goto _endobs;
2227
}
2228
}
2229
2230
if (g_bIRSpec)
2231
{
2232
g_bGlobalIR = AskYesNo(" Compute IR spectrum of whole system (y/n)? [yes] ",true);
2233
if (g_bGlobalIR)
2234
if (!AskYesNo(" Compute also IR spectra for certain molecule types (y/n)? [no] ",false))
2235
goto _endobs;
2236
}
2237
2238
/* if (g_bDipACF)
2239
{
2240
g_bGlobalDipACF = AskYesNo(" Create global dipole ACF of all atoms (y/n)? [yes] ",true);
2241
}*/
2242
_nextsdf:
2243
mprintf(YELLOW,"\n>>> Observation %d >>>\n\n",g_oaObserv.GetSize()+1);
2244
2245
try { o = new CObservation(); } catch(...) { o = NULL; }
2246
if (o == NULL) NewException((double)sizeof(CObservation),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2247
2248
o->m_pConditions = NULL;
2249
g_oaObserv.Add(o);
2250
o->m_bTimeDev = false;
2251
if (g_bAggregation || g_bNbExchange)
2252
{
2253
o->m_bSelf = false;
2254
o->m_bOthers = false;
2255
} else if (g_bNbAnalysis)
2256
{
2257
o->m_bSelf = false;
2258
o->m_bOthers = true;
2259
mprintf(" Performing this observation intermolecular.\n\n");
2260
} else if (g_iFixMol != -1)
2261
{
2262
if (AskRangeInteger(" Perform this observation intramolecular (within the reference molecule) (0) or intermolecular (1)? [1] ",0,1,1) == 1)
2263
{
2264
o->m_bSelf = false;
2265
o->m_bOthers = true;
2266
} else
2267
{
2268
o->m_bSelf = true;
2269
o->m_bOthers = false;
2270
}
2271
mprintf("\n");
2272
} else
2273
{
2274
o->m_bSelf = false;
2275
o->m_bOthers = true;
2276
}
2277
if (o->m_bOthers)
2278
{
2279
if (g_bCDF)
2280
{
2281
mprintf(WHITE," Please note: ");
2282
mprintf("Although you specified this observation to be intermolecular, you may of course\n");
2283
mprintf(" choose atoms from RM only (or OM only), which will yield an intramolecular quantity.\n\n");
2284
}
2285
if (g_bCDF)
2286
o->m_bSecondShowMol = AskYesNo(" CDF: Perform a three-body analysis (y) or observe one molecule at a time (n)? [no] ",false);
2287
else o->m_bSecondShowMol = false;
2288
if (o->m_bSecondShowMol)
2289
{
2290
mprintf(WHITE,"\n You have to select two observed molecules (OMs):\n");
2291
mprintf(" The first CDF channel observes the 1st OM, the second channel observes the 2nd OM.\n\n");
2292
}
2293
if (g_oaMolecules.GetSize() > 1)
2294
{
2295
_obsmolagain:
2296
if (o->m_bSecondShowMol)
2297
sprintf(buf," Which 1st molecule should be observed (");
2298
else sprintf(buf," Which molecule should be observed (");
2299
for (z=0;z<g_oaMolecules.GetSize();z++)
2300
{
2301
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
2302
strcat(buf,buf2);
2303
if (z < g_oaMolecules.GetSize()-1)
2304
strcat(buf,", ");
2305
}
2306
strcat(buf,")? ");
2307
o->m_iShowMol = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize()) - 1;
2308
if ((((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize() == 1) && (o->m_iShowMol == g_iFixMol))
2309
{
2310
eprintf("Error: There is only 1 molecule of %s.\n--> Intermolecular observation between %s and %s not possible.\n\n",((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName);
2311
goto _obsmolagain;
2312
}
2313
} else
2314
{
2315
mprintf(" Only one molecule type, choosing %s as observed molecule (OM).\n",((CMolecule*)g_oaMolecules[0])->m_sName);
2316
o->m_iShowMol = 0;
2317
}
2318
o->m_iShowMolCount = ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();
2319
if (o->m_bSecondShowMol)
2320
{
2321
if (g_oaMolecules.GetSize() > 1)
2322
{
2323
_obsmol2again:
2324
sprintf(buf," Which 2nd molecule should be observed (");
2325
for (z=0;z<g_oaMolecules.GetSize();z++)
2326
{
2327
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
2328
strcat(buf,buf2);
2329
if (z < g_oaMolecules.GetSize()-1)
2330
strcat(buf,", ");
2331
}
2332
strcat(buf,")? ");
2333
o->m_iShowMol2 = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize()) - 1;
2334
if ((((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex.GetSize() == 1) && (o->m_iShowMol2 == g_iFixMol))
2335
{
2336
eprintf("Error: There is only 1 molecule of %s.\n --> Intermolecular observation between %s and %s not possible.\n\n",((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName);
2337
goto _obsmol2again;
2338
}
2339
} else o->m_iShowMol2 = 0;
2340
o->m_iShowMol2Count = ((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex.GetSize();
2341
if (o->m_iShowMol == o->m_iShowMol2)
2342
o->m_bExclude1eq2 = AskYesNo(" Exclude the case \"1st OM = 2nd OM\" (y/n)? [yes] ",true);
2343
else o->m_bExclude1eq2 = false;
2344
}
2345
} else
2346
{
2347
o->m_iShowMol = -1;
2348
o->m_iShowMol2 = -1;
2349
o->m_bSecondShowMol = false;
2350
o->m_iShowMolCount = 1;
2351
}
2352
2353
buf[0] = 0;
2354
if ((o->m_bSecondShowMol) && (o->m_iShowMol != o->m_iShowMol2))
2355
sprintf(buf," of %s / %s / %s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName);
2356
else if ((o->m_iShowMol != -1) && (g_iFixMol != -1))
2357
sprintf(buf," of %s / %s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName);
2358
else if (g_iFixMol != -1) sprintf(buf," of %s",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2359
2360
if (g_iFixMol != -1)
2361
{
2362
if (g_bAdvanced2)
2363
{
2364
if (AskYesNo(" Observe only certain molecules%s (y/n)? [no] ",false,buf))
2365
{
2366
o->m_bObsCertain = true;
2367
if (!g_bCDF && (g_bRDF || g_bADF || g_bDDF || g_bDipDF))
2368
o->m_bDecompDist = AskYesNo(" Decompose distribution functions into contributions from molecules (y/n)? [yes] ",true);
2369
2370
if (((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() > 1)
2371
{
2372
mprintf(" Which %s molecules (RM) to take into account (e.g. 1,3-7)? [all] ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2373
inpprintf("! Which %s molecules (RM) to take into account (e.g. 1,3-7)? [all]\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);
2374
myget(buf);
2375
if (strlen(buf)==0)
2376
{
2377
for (z=0;z<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
2378
o->m_waObsRefList.Add(z);
2379
} else
2380
{
2381
ParseIntList(buf,&o->m_waObsRefList);
2382
for (z=0;z<o->m_waObsRefList.GetSize();z++)
2383
o->m_waObsRefList[z]--;
2384
}
2385
} else o->m_waObsRefList.Add(0);
2386
2387
// mprintf("RefList[0] = %d\n",o->m_waObsRefList[0]);
2388
2389
if (o->m_iShowMol != -1)
2390
{
2391
if (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize() > 1)
2392
{
2393
mprintf(" Which %s molecules (OM) to take into account (e.g. 1,3-7)? [all] ",((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName);
2394
inpprintf("! Which %s molecules (OM) to take into account (e.g. 1,3-7)? [all]\n",((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName);
2395
myget(buf);
2396
if (strlen(buf)==0)
2397
{
2398
for (z=0;z<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
2399
o->m_waObsShowList.Add(z);
2400
} else
2401
{
2402
ParseIntList(buf,&o->m_waObsShowList);
2403
for (z=0;z<o->m_waObsShowList.GetSize();z++)
2404
o->m_waObsShowList[z]--;
2405
}
2406
} else o->m_waObsShowList.Add(0);
2407
} else o->m_waObsShowList.Add(0); // Dummy
2408
2409
if (o->m_bSecondShowMol)
2410
{
2411
if (o->m_iShowMol2 != -1)
2412
{
2413
if (((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex.GetSize() > 1)
2414
{
2415
mprintf(" Which %s molecules (2nd OM) to take into account (e.g. 1,3-7)? [all] ",((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName);
2416
inpprintf("! Which %s molecules (2nd OM) to take into account (e.g. 1,3-7)? [all]\n",((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_sName);
2417
myget(buf);
2418
if (strlen(buf)==0)
2419
{
2420
for (z=0;z<((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex.GetSize();z++)
2421
o->m_waObsShow2List.Add(z);
2422
} else
2423
{
2424
ParseIntList(buf,&o->m_waObsShow2List);
2425
for (z=0;z<o->m_waObsShow2List.GetSize();z++)
2426
o->m_waObsShow2List[z]--;
2427
}
2428
} else o->m_waObsShow2List.Add(0);
2429
} else o->m_waObsShow2List.Add(0); // Dummy
2430
}
2431
} else // if not onlysome
2432
{
2433
o->m_bObsCertain = false;
2434
o->m_bDecompDist = false;
2435
}
2436
} else // if not advanced
2437
{
2438
o->m_bObsCertain = false;
2439
o->m_bDecompDist = false;
2440
}
2441
} else
2442
{
2443
o->m_bObsCertain = false;
2444
o->m_bDecompDist = false;
2445
}
2446
2447
o->m_bDecompType = false;
2448
2449
if ((!o->m_bObsCertain) && (!g_bCDF) && g_bAdvanced2 && (g_bRDF || g_bADF || g_bDDF || g_bDipDF))
2450
{
2451
if (AskYesNo(" Decompose this observation into contributions from different elements (y/n)? [no] ",false))
2452
{
2453
o->m_bDecompType = true;
2454
}
2455
}
2456
2457
if (g_bRegionAnalysis)
2458
{
2459
AskString(" Take reference molecules from which regions? [all] ",buf,"0");
2460
ParseIntList(buf,&o->m_iaRMRegions);
2461
// for (z6=0;z6<o->m_iaRMRegions.GetSize();z6++)
2462
// if (o->m_iaRMRegions[z6] != 0)
2463
// o->m_iaRMRegions[z6]--;
2464
2465
if (o->m_bOthers)
2466
{
2467
if (o->m_bSecondShowMol)
2468
{
2469
AskString(" Take 1st observed molecules from which regions? [all] ",buf,"0");
2470
ParseIntList(buf,&o->m_iaOM1Regions);
2471
// for (z6=0;z6<o->m_iaOM1Regions.GetSize();z6++)
2472
// if (o->m_iaOM1Regions[z6] != 0)
2473
// o->m_iaOM1Regions[z6]--;
2474
AskString(" Take 2nd observed molecules from which regions? [all] ",buf,"0");
2475
ParseIntList(buf,&o->m_iaOM2Regions);
2476
// for (z6=0;z6<o->m_iaOM2Regions.GetSize();z6++)
2477
// if (o->m_iaOM2Regions[z6] != 0)
2478
// o->m_iaOM2Regions[z6]--;
2479
} else
2480
{
2481
AskString(" Take observed molecules from which regions? [all] ",buf,"0");
2482
ParseIntList(buf,&o->m_iaOM1Regions);
2483
// for (z6=0;z6<o->m_iaOM1Regions.GetSize();z6++)
2484
// if (o->m_iaOM1Regions[z6] != 0)
2485
// o->m_iaOM1Regions[z6]--;
2486
}
2487
}
2488
}
2489
2490
if (g_bAggregation || g_bNbExchange)
2491
{
2492
try { o->m_pDACF = new CDACF(); } catch(...) { o->m_pDACF = NULL; }
2493
if (o->m_pDACF == NULL) NewException((double)sizeof(CDACF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2494
2495
o->m_pDACF->Parse();
2496
}
2497
2498
if (g_bRDyn)
2499
{
2500
try { o->m_pRDyn = new CReorDyn(); } catch(...) { o->m_pRDyn = NULL; }
2501
if (o->m_pRDyn == NULL) NewException((double)sizeof(CReorDyn),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2502
2503
o->m_pRDyn->m_iShowMol = o->m_iShowMol;
2504
o->m_pRDyn->Parse();
2505
}
2506
2507
if (g_bIRSpec)
2508
{
2509
try { o->m_pIRSpec = new CReorDyn(); } catch(...) { o->m_pIRSpec = NULL; }
2510
if (o->m_pIRSpec == NULL) NewException((double)sizeof(CReorDyn),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2511
2512
o->m_pIRSpec->m_iShowMol = o->m_iShowMol;
2513
o->m_pIRSpec->ParseSpec();
2514
}
2515
2516
if (g_bDens)
2517
{
2518
try { o->m_pDensityDF = new CDensDF(); } catch(...) { o->m_pDensityDF = NULL; }
2519
if (o->m_pDensityDF == NULL) NewException((double)sizeof(CDensDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2520
2521
o->m_pDensityDF->m_iShowMol = o->m_iShowMol;
2522
o->m_pDensityDF->Parse();
2523
}
2524
2525
if (g_bSDF)
2526
{
2527
try { o->m_pSDF = new CSDF(); } catch(...) { o->m_pSDF = NULL; }
2528
if (o->m_pSDF == NULL) NewException((double)sizeof(CSDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2529
2530
o->m_pSDF->m_bIntra = o->m_bSelf;
2531
o->m_pSDF->m_iShowMol = o->m_iShowMol;
2532
o->m_pSDF->Parse(false);
2533
}
2534
2535
if (g_bPlProj)
2536
{
2537
try { o->m_pPlProj = new CPlProj(); } catch(...) { o->m_pPlProj = NULL; }
2538
if (o->m_pPlProj == NULL) NewException((double)sizeof(CPlProj),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2524
2539
2525
o->m_pSDF->m_bIntra = o->m_bSelf;
2526
o->m_pSDF->m_iShowMol = o->m_iShowMol;
2527
o->m_pSDF->Parse(false);
2528
}
2529
2530
if (g_bRevSDF)
2531
{
2532
try { o->m_pRevSDF = new CRevSDF(); } catch(...) { o->m_pRevSDF = NULL; }
2533
if (o->m_pRevSDF == NULL) NewException((double)sizeof(CRevSDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2534
2535
o->m_pRevSDF->m_bIntra = o->m_bSelf;
2536
o->m_pRevSDF->m_iShowMol = o->m_iShowMol;
2537
o->m_pRevSDF->Parse();
2538
}
2539
2540
if (g_bNbAnalysis)
2541
{
2542
try { o->m_pNbAnalysis = new CNbAnalysis(); } catch(...) { o->m_pNbAnalysis = NULL; }
2543
if (o->m_pNbAnalysis == NULL) NewException((double)sizeof(CNbAnalysis),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2544
2545
o->m_pNbAnalysis->m_iShowMol = o->m_iShowMol;
2546
o->m_pNbAnalysis->Parse();
2547
}
2548
2549
try { o->m_pRDF = new CRDF*[g_iCDFChannels]; } catch(...) { o->m_pRDF = NULL; }
2550
if (o->m_pRDF == NULL) NewException((double)g_iCDFChannels*sizeof(CRDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2551
2552
try { o->m_pADF = new CADF*[g_iCDFChannels]; } catch(...) { o->m_pADF = NULL; }
2553
if (o->m_pADF == NULL) NewException((double)g_iCDFChannels*sizeof(CADF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2554
2555
try { o->m_pDDF = new CDDF*[g_iCDFChannels]; } catch(...) { o->m_pDDF = NULL; }
2556
if (o->m_pDDF == NULL) NewException((double)g_iCDFChannels*sizeof(CDDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2557
2558
try { o->m_pDipDF = new CDipDF*[g_iCDFChannels]; } catch(...) { o->m_pDipDF = NULL; }
2559
if (o->m_pDipDF == NULL) NewException((double)g_iCDFChannels*sizeof(CDipDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2560
2561
try { o->m_pVDF = new CVDF*[g_iCDFChannels]; } catch(...) { o->m_pVDF = NULL; }
2562
if (o->m_pVDF == NULL) NewException((double)g_iCDFChannels*sizeof(CVDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2563
2564
try { o->m_pPlDF = new CPlDF*[g_iCDFChannels]; } catch(...) { o->m_pPlDF = NULL; }
2565
if (o->m_pPlDF == NULL) NewException((double)g_iCDFChannels*sizeof(CVDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2566
2567
try { o->m_pLiDF = new CLiDF*[g_iCDFChannels]; } catch(...) { o->m_pLiDF = NULL; }
2568
if (o->m_pLiDF == NULL) NewException((double)g_iCDFChannels*sizeof(CVDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2569
2570
for (z=0;z<g_iCDFChannels;z++)
2571
{
2572
o->m_pRDF[z] = NULL;
2573
o->m_pADF[z] = NULL;
2574
o->m_pDDF[z] = NULL;
2575
o->m_pDipDF[z] = NULL;
2576
o->m_pVDF[z] = NULL;
2577
o->m_pPlDF[z] = NULL;
2578
o->m_pLiDF[z] = NULL;
2579
}
2580
2581
if (g_bCDF)
2582
{
2583
try { o->m_pCDF = new CCDF(); } catch(...) { o->m_pCDF = NULL; }
2584
if (o->m_pCDF == NULL) NewException((double)sizeof(CCDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2585
2586
try { o->m_pCDF->m_iCombinations = new int[g_iCDFChannels]; } catch(...) { o->m_pCDF->m_iCombinations = NULL; }
2587
if (o->m_pCDF->m_iCombinations == NULL) NewException((double)g_iCDFChannels*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2588
2589
mprintf(BLUE,"\n>>> Combined Distribution Function >>>\n");
2590
// o->m_pCDF->m_bChannelAll = new bool[g_iCDFChannels];
2591
o->m_pCDF->m_iCombinationProd = 1;
2592
for (z=0;z<g_iCDFChannels;z++)
2540
o->m_pPlProj->m_bIntra = o->m_bSelf;
2541
o->m_pPlProj->m_iShowMol = o->m_iShowMol;
2542
o->m_pPlProj->Parse();
2543
}
2544
2545
if (g_bRevSDF)
2546
{
2547
try { o->m_pRevSDF = new CRevSDF(); } catch(...) { o->m_pRevSDF = NULL; }
2548
if (o->m_pRevSDF == NULL) NewException((double)sizeof(CRevSDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2549
2550
o->m_pRevSDF->m_bIntra = o->m_bSelf;
2551
o->m_pRevSDF->m_iShowMol = o->m_iShowMol;
2552
o->m_pRevSDF->Parse();
2553
}
2554
2555
if (g_bNbAnalysis)
2556
{
2557
try { o->m_pNbAnalysis = new CNbAnalysis(); } catch(...) { o->m_pNbAnalysis = NULL; }
2558
if (o->m_pNbAnalysis == NULL) NewException((double)sizeof(CNbAnalysis),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2559
2560
o->m_pNbAnalysis->m_iShowMol = o->m_iShowMol;
2561
o->m_pNbAnalysis->Parse();
2562
}
2563
2564
try { o->m_pRDF = new CRDF*[g_iCDFChannels]; } catch(...) { o->m_pRDF = NULL; }
2565
if (o->m_pRDF == NULL) NewException((double)g_iCDFChannels*sizeof(CRDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2566
2567
try { o->m_pADF = new CADF*[g_iCDFChannels]; } catch(...) { o->m_pADF = NULL; }
2568
if (o->m_pADF == NULL) NewException((double)g_iCDFChannels*sizeof(CADF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2569
2570
try { o->m_pDDF = new CDDF*[g_iCDFChannels]; } catch(...) { o->m_pDDF = NULL; }
2571
if (o->m_pDDF == NULL) NewException((double)g_iCDFChannels*sizeof(CDDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2572
2573
try { o->m_pDipDF = new CDipDF*[g_iCDFChannels]; } catch(...) { o->m_pDipDF = NULL; }
2574
if (o->m_pDipDF == NULL) NewException((double)g_iCDFChannels*sizeof(CDipDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2575
2576
try { o->m_pVDF = new CVDF*[g_iCDFChannels]; } catch(...) { o->m_pVDF = NULL; }
2577
if (o->m_pVDF == NULL) NewException((double)g_iCDFChannels*sizeof(CVDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2578
2579
try { o->m_pPlDF = new CPlDF*[g_iCDFChannels]; } catch(...) { o->m_pPlDF = NULL; }
2580
if (o->m_pPlDF == NULL) NewException((double)g_iCDFChannels*sizeof(CVDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2581
2582
try { o->m_pLiDF = new CLiDF*[g_iCDFChannels]; } catch(...) { o->m_pLiDF = NULL; }
2583
if (o->m_pLiDF == NULL) NewException((double)g_iCDFChannels*sizeof(CVDF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2584
2585
for (z=0;z<g_iCDFChannels;z++)
2586
{
2587
o->m_pRDF[z] = NULL;
2588
o->m_pADF[z] = NULL;
2589
o->m_pDDF[z] = NULL;
2590
o->m_pDipDF[z] = NULL;
2591
o->m_pVDF[z] = NULL;
2592
o->m_pPlDF[z] = NULL;
2593
o->m_pLiDF[z] = NULL;
2594
}
2595
2596
if (g_bCDF)
2597
{
2598
try { o->m_pCDF = new CCDF(); } catch(...) { o->m_pCDF = NULL; }
2599
if (o->m_pCDF == NULL) NewException((double)sizeof(CCDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2600
2601
try { o->m_pCDF->m_iCombinations = new int[g_iCDFChannels]; } catch(...) { o->m_pCDF->m_iCombinations = NULL; }
2602
if (o->m_pCDF->m_iCombinations == NULL) NewException((double)g_iCDFChannels*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2603
2604
mprintf(BLUE,"\n>>> Combined Distribution Function >>>\n");
2605
// o->m_pCDF->m_bChannelAll = new bool[g_iCDFChannels];
2606
o->m_pCDF->m_iCombinationProd = 1;
2607
for (z=0;z<g_iCDFChannels;z++)
2608
{
2609
mprintf(BLUE,"\n### Channel %d ###\n",z+1);
2610
switch(g_iObsChannel[z])
2611
{
2612
case 0:
2613
try { o->m_pRDF[z] = new CRDF(); } catch(...) { o->m_pRDF[z] = NULL; }
2614
if (o->m_pRDF[z] == NULL) NewException((double)sizeof(CRDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2615
2616
if (o->m_bSecondShowMol && (z == 1))
2617
o->m_pRDF[z]->m_iShowMol = o->m_iShowMol2;
2618
else o->m_pRDF[z]->m_iShowMol = o->m_iShowMol;
2619
o->m_pRDF[z]->Parse();
2620
o->m_pCDF->m_iCombinations[z] = o->m_pRDF[z]->m_iCombinations;
2621
o->m_pCDF->m_iCombinationProd *= o->m_pRDF[z]->m_iCombinations;
2622
/* if (o->m_pRDF[z]->m_bSaveDist)
2623
o->m_bTimeDev = true;*/
2624
break;
2625
2626
case 1:
2627
try { o->m_pADF[z] = new CADF(); } catch(...) { o->m_pADF[z] = NULL; }
2628
if (o->m_pADF[z] == NULL) NewException((double)sizeof(CADF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2629
2630
if (o->m_bSecondShowMol && (z == 1))
2631
o->m_pADF[z]->m_iShowMol = o->m_iShowMol2;
2632
else o->m_pADF[z]->m_iShowMol = o->m_iShowMol;
2633
o->m_pADF[z]->Parse();
2634
o->m_pCDF->m_iCombinations[z] = o->m_pADF[z]->m_iCombinations;
2635
o->m_pCDF->m_iCombinationProd *= o->m_pADF[z]->m_iCombinations;
2636
/* if (o->m_pADF[z]->m_bSaveAngle)
2637
o->m_bTimeDev = true;*/
2638
break;
2639
2640
case 2:
2641
try { o->m_pDDF[z] = new CDDF(); } catch(...) { o->m_pDDF[z] = NULL; }
2642
if (o->m_pDDF[z] == NULL) NewException((double)sizeof(CDDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2643
2644
if (o->m_bSecondShowMol && (z == 1))
2645
o->m_pDDF[z]->m_iShowMol = o->m_iShowMol2;
2646
else o->m_pDDF[z]->m_iShowMol = o->m_iShowMol;
2647
o->m_pDDF[z]->Parse();
2648
o->m_pCDF->m_iCombinations[z] = o->m_pDDF[z]->m_iCombinations;
2649
o->m_pCDF->m_iCombinationProd *= o->m_pDDF[z]->m_iCombinations;
2650
/* if (o->m_pDDF[z]->m_bSaveAngle)
2651
o->m_bTimeDev = true;*/
2652
break;
2653
2654
case 3:
2655
try { o->m_pDipDF[z] = new CDipDF(); } catch(...) { o->m_pDipDF[z] = NULL; }
2656
if (o->m_pDipDF[z] == NULL) NewException((double)sizeof(CDipDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2657
2658
if (o->m_bSecondShowMol && (z == 1))
2659
o->m_pDipDF[z]->m_iShowMol = o->m_iShowMol2;
2660
else o->m_pDipDF[z]->m_iShowMol = o->m_iShowMol;
2661
o->m_pDipDF[z]->m_iCombinations = 1;
2662
o->m_pDipDF[z]->Parse();
2663
o->m_pCDF->m_iCombinations[z] = 1;
2664
/* if (o->m_pDipDF[z]->m_bSaveDipole)
2665
o->m_bTimeDev = true;*/
2666
break;
2667
2668
case 4:
2669
try { o->m_pVDF[z] = new CVDF(); } catch(...) { o->m_pVDF[z] = NULL; }
2670
if (o->m_pVDF[z] == NULL) NewException((double)sizeof(CVDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2671
2672
if (o->m_bSecondShowMol && (z == 1))
2673
o->m_pVDF[z]->m_iShowMol = o->m_iShowMol2;
2674
else o->m_pVDF[z]->m_iShowMol = o->m_iShowMol;
2675
o->m_pVDF[z]->Parse();
2676
o->m_pCDF->m_iCombinations[z] = o->m_pVDF[z]->m_iCombinations;
2677
o->m_pCDF->m_iCombinationProd *= o->m_pVDF[z]->m_iCombinations;
2678
g_bUseVelocities = true;
2679
/* if (o->m_pVDF[z]->m_bSaveSpeed)
2680
o->m_bTimeDev = true;*/
2681
break;
2682
2683
case 5:
2684
try { o->m_pPlDF[z] = new CPlDF(); } catch(...) { o->m_pPlDF[z] = NULL; }
2685
if (o->m_pPlDF[z] == NULL) NewException((double)sizeof(CPlDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2686
2687
if (o->m_bSecondShowMol && (z == 1))
2688
o->m_pPlDF[z]->m_iShowMol = o->m_iShowMol2;
2689
else o->m_pPlDF[z]->m_iShowMol = o->m_iShowMol;
2690
o->m_pPlDF[z]->Parse();
2691
o->m_pCDF->m_iCombinations[z] = o->m_pPlDF[z]->m_iCombinations;
2692
o->m_pCDF->m_iCombinationProd *= o->m_pPlDF[z]->m_iCombinations;
2693
break;
2694
2695
case 6:
2696
try { o->m_pLiDF[z] = new CLiDF(); } catch(...) { o->m_pLiDF[z] = NULL; }
2697
if (o->m_pLiDF[z] == NULL) NewException((double)sizeof(CLiDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2698
2699
if (o->m_bSecondShowMol && (z == 1))
2700
o->m_pLiDF[z]->m_iShowMol = o->m_iShowMol2;
2701
else o->m_pLiDF[z]->m_iShowMol = o->m_iShowMol;
2702
o->m_pLiDF[z]->Parse();
2703
o->m_pCDF->m_iCombinations[z] = o->m_pLiDF[z]->m_iCombinations;
2704
o->m_pCDF->m_iCombinationProd *= o->m_pLiDF[z]->m_iCombinations;
2705
break;
2706
}
2707
/* if (z != 0)
2708
o->m_pCDF->m_bChannelAll[z] = AskYesNo(" Should this CDF Channel observe all OMs (y) or only the current one (n)? [no] ",false);
2709
else o->m_pCDF->m_bChannelAll[z] = false;*/
2710
}
2711
/* mprintf(" Write out temporal development for this CDF (1=yes,0=no)? [no] ");
2712
myget(buf);
2713
o->m_pCDF->m_bTimeDev = (atoi(buf)!=0);
2714
if (o->m_pCDF->m_bTimeDev)
2715
o->m_bTimeDev = true;*/
2716
2717
mprintf("\n");
2718
2719
try { o->m_pCDF->m_iResolution = new int[g_iCDFChannels]; } catch(...) { o->m_pCDF->m_iResolution = NULL; }
2720
if (o->m_pCDF->m_iResolution == NULL) NewException((double)g_iCDFChannels*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2721
2722
for (z=0;z<g_iCDFChannels;z++)
2723
{
2724
switch(g_iObsChannel[z])
2725
{
2726
case 0: sprintf(buf,"RDF"); break;
2727
case 1: sprintf(buf,"ADF"); break;
2728
case 2: sprintf(buf,"DDF"); break;
2729
case 3: sprintf(buf,"DipDF"); break;
2730
case 4: sprintf(buf,"VDF"); break;
2731
case 5: sprintf(buf,"PlDF"); break;
2732
case 6: sprintf(buf,"LiDF"); break;
2733
}
2734
o->m_pCDF->m_iResolution[z] = AskUnsignedInteger(" Please enter the resolution (bin count) for CDF channel %d (%s): [100] ",100,z+1,buf);
2735
}
2736
2737
if (g_bAdvanced2)
2738
o->m_pCDF->m_iHistogramRes = AskUnsignedInteger(" Please enter CDF histogram resolution (0=no histogram): [5000] ",5000);
2739
else o->m_pCDF->m_iHistogramRes = 0;
2740
2741
if (g_iCDFChannels == 2)
2742
{
2743
try { o->m_pCDF->m_pCombineList = new char[o->m_pCDF->m_iCombinationProd]; } catch(...) { o->m_pCDF->m_pCombineList = NULL; }
2744
if (o->m_pCDF->m_pCombineList == NULL) NewException((double)o->m_pCDF->m_iCombinationProd*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2745
2746
if ((o->m_pCDF->m_iCombinations[0] > 1) && (o->m_pCDF->m_iCombinations[1] > 1))
2747
{
2748
mprintf("\n");
2749
for (z=0;z<g_iCDFChannels;z++)
2750
{
2751
mprintf(WHITE,"CDF channel %d has the following %d observations:\n",z+1,o->m_pCDF->m_iCombinations[z]);
2752
o->ListCDFObservations(z);
2753
mprintf("\n");
2754
}
2755
if (o->m_pCDF->m_iCombinations[0] == o->m_pCDF->m_iCombinations[1])
2756
{
2757
if (AskYesNo(" Combine n-th with n-th observation? (y/n) [yes] ",true))
2758
{
2759
for (z=0;z<o->m_pCDF->m_iCombinations[0];z++)
2760
for (z2=0;z2<o->m_pCDF->m_iCombinations[1];z2++)
2761
o->m_pCDF->m_pCombineList[z*o->m_pCDF->m_iCombinations[1]+z2] = (z==z2)?1:0;
2762
goto _combdone;
2763
} goto _askcomball;
2764
} else
2765
{
2766
_askcomball:
2767
if (!AskYesNo(" Combine each with each observation (y), or use only some combinations (n)? [yes] ",true))
2768
{
2769
for (z=0;z<o->m_pCDF->m_iCombinations[0];z++)
2770
for (z2=0;z2<o->m_pCDF->m_iCombinations[1];z2++)
2771
o->m_pCDF->m_pCombineList[z*o->m_pCDF->m_iCombinations[1]+z2] = 0;
2772
2773
mprintf("\n Please enter all the combinations you want to observe.\n");
2774
mprintf(" Enter each combination as a comma-separated %d-tuple (e.g. ",g_iCDFChannels);
2775
for (z=0;z<g_iCDFChannels;z++)
2776
{
2777
mprintf("%d",z+1);
2778
if (z+1 < g_iCDFChannels)
2779
mprintf(",");
2780
}
2781
mprintf(").\n\n");
2782
_nextcomb:
2783
AskString(" Enter combination (return=finished): ",buf,"");
2784
if (strlen(buf)==0)
2785
goto _combdone;
2786
tempwa.RemoveAll_KeepSize();
2787
ParseIntList(buf,&tempwa);
2788
if (tempwa.GetSize() != g_iCDFChannels)
2789
{
2790
eprintf(" Wrong input, %d instead of %d values.\n",tempwa.GetSize(),g_iCDFChannels);
2791
goto _nextcomb;
2792
}
2793
for (z=0;z<g_iCDFChannels;z++)
2794
{
2795
if ((tempwa[z] < 1) || (tempwa[z] > o->m_pCDF->m_iCombinations[z]))
2796
{
2797
eprintf(" Wrong input, channel %d has only %d observations (%d requested).\n",z+1,o->m_pCDF->m_iCombinations[z],tempwa[z]);
2798
goto _nextcomb;
2799
}
2800
tempwa[z]--;
2801
}
2802
if (o->m_pCDF->m_pCombineList[tempwa[0]*o->m_pCDF->m_iCombinations[1]+tempwa[1]] == 1)
2803
{
2804
eprintf(" This combination has already been added.\n");
2805
goto _nextcomb;
2806
}
2807
o->m_pCDF->m_pCombineList[tempwa[0]*o->m_pCDF->m_iCombinations[1]+tempwa[1]] = 1;
2808
goto _nextcomb;
2809
} else goto _combineall;
2810
_combdone:;
2811
}
2812
} else
2813
{
2814
_combineall:
2815
for (z=0;z<o->m_pCDF->m_iCombinationProd;z++)
2816
o->m_pCDF->m_pCombineList[z] = 1;
2817
}
2818
2819
o->m_pCDF->m_iCombinationsEnabled = 0;
2820
for (z=0;z<o->m_pCDF->m_iCombinationProd;z++)
2821
if (o->m_pCDF->m_pCombineList[z] != 0)
2822
o->m_pCDF->m_iCombinationsEnabled++;
2823
2824
if (o->m_pCDF->m_iCombinationsEnabled == 1)
2825
{
2826
mprintf(WHITE,"\n Using 1 combination for each RM-OM pair.\n\n");
2827
} else
2828
{
2829
mprintf(WHITE,"\n Using %d combinations for each RM-OM pair:\n\n",o->m_pCDF->m_iCombinationsEnabled);
2830
z3 = 0;
2831
for (z=0;z<o->m_pCDF->m_iCombinations[0];z++)
2832
{
2833
for (z2=0;z2<o->m_pCDF->m_iCombinations[1];z2++)
2834
{
2835
if (o->m_pCDF->m_pCombineList[z*o->m_pCDF->m_iCombinations[1]+z2] == 1)
2836
{
2837
mprintf(" %2d.) %2d - %2d\n",z3+1,z+1,z2+1);
2838
z3++;
2839
}
2840
}
2841
}
2842
mprintf("\n");
2843
}
2844
2845
if (g_bAdvanced2)
2846
{
2847
o->m_pCDF->m_bAxisDivide = AskYesNo(" Write out +/- correlation plot for this CDF (y/n)? [no] ",false);
2848
2849
if (o->m_pCDF->m_bAxisDivide)
2850
o->m_pCDF->m_bAxisDivideAll = AskYesNo(" Also write tensor product and axis projection quotients (y/n)? [no] ",false);
2851
} else
2852
{
2853
o->m_pCDF->m_bAxisDivide = false;
2854
o->m_pCDF->m_bAxisDivideAll = false;
2855
}
2856
2857
if (g_bAdvanced2)
2858
{
2859
o->m_pCDF->m_bGraceBunch = AskYesNo(" Write out grace stack (multiple 2D plots) for this CDF (y/n)? [no] ",false);
2860
if (o->m_pCDF->m_bGraceBunch)
2861
{
2862
o->m_pCDF->m_iGraceBunchC1 = AskUnsignedInteger(" How many graphs do you want do draw in the channel 1 grace stack (0=disable)? [10] ",10);
2863
o->m_pCDF->m_iGraceBunchC2 = AskUnsignedInteger(" How many graphs do you want do draw in the channel 2 grace stack (0=disable)? [10] ",10);
2864
}
2865
} else o->m_pCDF->m_bGraceBunch = false;
2866
}
2867
2868
if (g_iCDFChannels == 3)
2869
{
2870
mprintf("\n");
2871
2872
try { o->m_pCDF->m_pCombineList = new char[o->m_pCDF->m_iCombinationProd]; } catch(...) { o->m_pCDF->m_pCombineList = NULL; }
2873
if (o->m_pCDF->m_pCombineList == NULL) NewException((double)o->m_pCDF->m_iCombinationProd*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2874
2875
if ((o->m_pCDF->m_iCombinations[0] > 1) || (o->m_pCDF->m_iCombinations[1] > 1) || (o->m_pCDF->m_iCombinations[2] > 1))
2876
{
2877
for (z=0;z<g_iCDFChannels;z++)
2878
{
2879
mprintf(WHITE,"CDF channel %d has the following %d observations:\n",z+1,o->m_pCDF->m_iCombinations[z]);
2880
o->ListCDFObservations(z);
2881
mprintf("\n");
2882
}
2883
if (!AskYesNo(" Combine each with each observation (y), or use only some combinations (n)? [yes] ",true))
2884
{
2885
for (z=0;z<o->m_pCDF->m_iCombinations[0];z++)
2886
for (z2=0;z2<o->m_pCDF->m_iCombinations[1];z2++)
2887
for (z3=0;z3<o->m_pCDF->m_iCombinations[2];z3++)
2888
o->m_pCDF->m_pCombineList[z*o->m_pCDF->m_iCombinations[1]*o->m_pCDF->m_iCombinations[2]+z2*o->m_pCDF->m_iCombinations[2]+z3] = 0;
2889
2890
mprintf("\n Please enter all the combinations you want to observe.\n");
2891
mprintf(" Enter each combination as a comma-separated %d-tuple (e.g. ",g_iCDFChannels);
2892
for (z=0;z<g_iCDFChannels;z++)
2893
{
2894
mprintf("%d",z+1);
2895
if (z+1 < g_iCDFChannels)
2896
mprintf(",");
2897
}
2898
mprintf(").\n\n");
2899
_3nextcomb:
2900
AskString(" Enter combination (return=finished): ",buf,"");
2901
if (strlen(buf)==0)
2902
goto _3combdone;
2903
tempwa.RemoveAll_KeepSize();
2904
ParseIntList(buf,&tempwa);
2905
if (tempwa.GetSize() != g_iCDFChannels)
2906
{
2907
eprintf(" Wrong input, %d instead of %d values.\n",tempwa.GetSize(),g_iCDFChannels);
2908
goto _3nextcomb;
2909
}
2910
for (z=0;z<g_iCDFChannels;z++)
2911
{
2912
if ((tempwa[z] < 1) || (tempwa[z] > o->m_pCDF->m_iCombinations[z]))
2913
{
2914
eprintf(" Wrong input, channel %d has only %d observations (%d requested).\n",z+1,o->m_pCDF->m_iCombinations[z],tempwa[z]);
2915
goto _3nextcomb;
2916
}
2917
tempwa[z]--;
2918
}
2919
if (o->m_pCDF->m_pCombineList[tempwa[0]*o->m_pCDF->m_iCombinations[1]*o->m_pCDF->m_iCombinations[2]+tempwa[1]*o->m_pCDF->m_iCombinations[2]+tempwa[2]] == 1)
2920
{
2921
eprintf(" This combination has already been added.\n");
2922
goto _3nextcomb;
2923
}
2924
o->m_pCDF->m_pCombineList[tempwa[0]*o->m_pCDF->m_iCombinations[1]*o->m_pCDF->m_iCombinations[2]+tempwa[1]*o->m_pCDF->m_iCombinations[2]+tempwa[2]] = 1;
2925
goto _3nextcomb;
2926
} else goto _3combineall;
2927
} else
2928
{
2929
_3combineall:
2930
for (z=0;z<o->m_pCDF->m_iCombinationProd;z++)
2931
o->m_pCDF->m_pCombineList[z] = 1;
2932
}
2933
_3combdone:
2934
o->m_pCDF->m_iCombinationsEnabled = 0;
2935
for (z=0;z<o->m_pCDF->m_iCombinationProd;z++)
2936
if (o->m_pCDF->m_pCombineList[z] != 0)
2937
o->m_pCDF->m_iCombinationsEnabled++;
2938
2939
if (o->m_pCDF->m_iCombinationsEnabled == 1)
2940
{
2941
mprintf(WHITE,"\n Using 1 combination for each RM-OM pair.\n\n");
2942
} else
2943
{
2944
mprintf(WHITE,"\n Using %d combinations for each RM-OM pair:\n\n",o->m_pCDF->m_iCombinationsEnabled);
2945
z4 = 0;
2946
for (z=0;z<o->m_pCDF->m_iCombinations[0];z++)
2947
for (z2=0;z2<o->m_pCDF->m_iCombinations[1];z2++)
2948
for (z3=0;z3<o->m_pCDF->m_iCombinations[2];z3++)
2949
if (o->m_pCDF->m_pCombineList[z*o->m_pCDF->m_iCombinations[1]*o->m_pCDF->m_iCombinations[2]+z2*o->m_pCDF->m_iCombinations[2]+z3] == 1)
2950
{
2951
mprintf(" %2d.) %2d - %2d - %2d\n",z4+1,z+1,z2+1,z3+1);
2952
z4++;
2953
}
2954
mprintf("\n");
2955
}
2956
2957
if (g_bAdvanced2)
2958
{
2959
o->m_pCDF->m_b3DSlices = AskYesNo(" Write out 2D slices for this CDF (y/n)? [no] ",false);
2960
2961
if (o->m_pCDF->m_b3DSlices)
2962
for (z=0;z<3;z++)
2963
o->m_pCDF->m_i3DSliceIntervals[z] = AskUnsignedInteger(" How many slice intervals to create along channel %d axis (0=skip)? [0] ",0,z+1);
2964
} else o->m_pCDF->m_b3DSlices = false;
2965
} // end if channels == 3
2966
2967
2968
if (g_bAdvanced2)
2969
{
2970
o->m_pCDF->m_bDumpDat = AskYesNo(" Write out input tuples (very large!) for this CDF (y/n)? [no] ",false);
2971
if ((g_iCDFChannels == 2) && (g_iObsChannel[0] == 0) && (g_iObsChannel[1] == 1))
2972
o->m_pCDF->m_iNormalize = AskRangeInteger(" Normalize uniformly (3), data range (2), integral (1), or do not normalize (0)? [1] ",0,3,1);
2973
else o->m_pCDF->m_iNormalize = AskRangeInteger(" Normalize data range (2), integral (1), or do not normalize (0)? [1] ",0,2,1);
2974
if (o->m_pCDF->m_iNormalize == 1)
2975
o->m_pCDF->m_fNormValue = AskFloat(" Set CDF integral to which value? [1000000] ",1000000.0f);
2976
if (o->m_pCDF->m_iNormalize == 2)
2977
o->m_pCDF->m_fNormValue = AskFloat(" Set maximum entry to which value? [100] ",100.0f);
2978
} else
2979
{
2980
o->m_pCDF->m_bDumpDat = false;
2981
o->m_pCDF->m_iNormalize = 1;
2982
o->m_pCDF->m_fNormValue = 1000000.0f;
2983
}
2984
2985
mprintf(BLUE,"\n<<< End of Combined Distribution Function <<<\n\n");
2986
} else
2987
{
2988
if (g_bRDF)
2989
{
2990
try { o->m_pRDF[0] = new CRDF(); } catch(...) { o->m_pRDF[0] = NULL; }
2991
if (o->m_pRDF[0] == NULL) NewException((double)sizeof(CRDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2992
2993
o->m_pRDF[0]->m_iShowMol = o->m_iShowMol;
2994
o->m_pRDF[0]->Parse();
2995
o->m_pRDF[0]->m_bSelf = o->m_bSelf;
2996
}
2997
if (g_bPlDF)
2998
{
2999
try { o->m_pPlDF[0] = new CPlDF(); } catch(...) { o->m_pPlDF[0] = NULL; }
3000
if (o->m_pPlDF[0] == NULL) NewException((double)sizeof(CPlDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3001
3002
o->m_pPlDF[0]->m_iShowMol = o->m_iShowMol;
3003
o->m_pPlDF[0]->Parse();
3004
o->m_pPlDF[0]->m_bSelf = o->m_bSelf;
3005
}
3006
if (g_bLiDF)
3007
{
3008
try { o->m_pLiDF[0] = new CLiDF(); } catch(...) { o->m_pLiDF[0] = NULL; }
3009
if (o->m_pLiDF[0] == NULL) NewException((double)sizeof(CLiDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3010
3011
o->m_pLiDF[0]->m_iShowMol = o->m_iShowMol;
3012
o->m_pLiDF[0]->Parse();
3013
o->m_pLiDF[0]->m_bSelf = o->m_bSelf;
3014
}
3015
if (g_bVHDF)
3016
{
3017
try { o->m_pVHDF = new CVHDF(); } catch(...) { o->m_pVHDF = NULL; }
3018
if (o->m_pVHDF == NULL) NewException((double)sizeof(CVHDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3019
3020
o->m_pVHDF->m_iShowMol = o->m_iShowMol;
3021
o->m_pVHDF->m_bSelf = o->m_bSelf;
3022
o->m_pVHDF->Parse();
3023
}
3024
if (g_bADF)
3025
{
3026
try { o->m_pADF[0] = new CADF(); } catch(...) { o->m_pADF[0] = NULL; }
3027
if (o->m_pADF[0] == NULL) NewException((double)sizeof(CADF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3028
3029
o->m_pADF[0]->m_iShowMol = o->m_iShowMol;
3030
o->m_pADF[0]->m_bSelf = o->m_bSelf;
3031
o->m_pADF[0]->Parse();
3032
}
3033
if (g_bDDF)
3034
{
3035
try { o->m_pDDF[0] = new CDDF(); } catch(...) { o->m_pDDF[0] = NULL; }
3036
if (o->m_pDDF[0] == NULL) NewException((double)sizeof(CDDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3037
3038
o->m_pDDF[0]->m_iShowMol = o->m_iShowMol;
3039
o->m_pDDF[0]->m_bSelf = o->m_bSelf;
3040
o->m_pDDF[0]->Parse();
3041
}
3042
if (g_bDipDF)
3043
{
3044
try { o->m_pDipDF[0] = new CDipDF(); } catch(...) { o->m_pDipDF[0] = NULL; }
3045
if (o->m_pDipDF[0] == NULL) NewException((double)sizeof(CDipDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3046
3047
o->m_pDipDF[0]->m_iShowMol = o->m_iShowMol;
3048
o->m_pDipDF[0]->m_bSelf = o->m_bSelf;
3049
o->m_pDipDF[0]->Parse();
3050
}
3051
if (g_bVDF)
3052
{
3053
try { o->m_pVDF[0] = new CVDF(); } catch(...) { o->m_pVDF[0] = NULL; }
3054
if (o->m_pVDF[0] == NULL) NewException((double)sizeof(CVDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3055
3056
o->m_pVDF[0]->m_iShowMol = o->m_iShowMol;
3057
o->m_pVDF[0]->m_bSelf = true;
3058
o->m_pVDF[0]->Parse();
3059
g_bUseVelocities = true;
3060
}
3061
if (g_bMSD)
3062
{
3063
try { o->m_pMSD = new CMSD(); } catch(...) { o->m_pMSD = NULL; }
3064
if (o->m_pMSD == NULL) NewException((double)sizeof(CMSD),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3065
3066
o->m_pMSD->m_iShowMol = o->m_iShowMol;
3067
o->m_pMSD->Parse();
3068
}
3069
}
3070
3071
if ((g_bCDF && (g_iCDFChannels == 2)) || g_bRDF || g_bADF || g_bVDF || g_bDDF || g_bDipDF)
3072
{
3073
if (!o->m_bSecondShowMol)
3074
{
3075
if (AskYesNo(" Save temporal development for this observation (y/n)? [no] ",false))
3076
{
3077
mprintf(WHITE,"\n>>> Save temporal development >>>\n\n");
3078
o->m_bTimeDev = true;
3079
3080
if (g_fTimestepLength == 0)
3081
{
3082
g_fTimestepLength = AskFloat(" Enter the length of one trajectory time step in fs: [0.5] ",0.5f);
3083
mprintf("\n");
3084
}
3085
3086
if (g_bDDF && (!g_bCDF))
3087
{
3088
if ((o->m_pDDF[0]->m_iDeriv == 0) && (!o->m_pDDF[0]->m_bCosine) && (!o->m_pDDF[0]->m_bAbs) && (!o->m_pDDF[0]->m_bPositive))
3089
{
3090
mprintf("\n You can include full rotations into the DDF's temporal development.\n");
3091
mprintf(" This means, if a dihedral makes a full rotation, the value will be 360 deg insteat of 0 deg.\n");
3092
mprintf(" You may count the number of full rotations during simulation in this way.\n\n");
3093
o->m_pDDF[0]->m_bRotate = AskYesNo(" Include full rotations into the DDF's temporal development (y/n)? [no] ",false);
3094
} else o->m_pDDF[0]->m_bRotate = false;
3095
if (o->m_pDDF[0]->m_bRotate)
3096
{
3097
mprintf(WHITE,"\n Warning: ");
3098
mprintf("This only works if your trajectory time step is small enough to ensure\n");
3099
mprintf(" that the dihedral is never changing more than 180 deg within one step!\n\n");
3100
}
3101
}
3102
if (g_bRDF || g_bADF || g_bVDF || g_bDDF || g_bDipDF)
3103
{
3104
if (AskYesNo(" Create combined development/histogram-plots for 2D analyses (y/n)? [yes] ",true))
3105
{
3106
g_bCombined = true;
3107
o->m_bCombinedPlot = true;
3108
if (AskYesNo(" Use grey tones for combined plot (y) or standard colors (n)? [no] ",false))
3109
{
3110
o->m_bCombinedGreyMode = true;
3111
o->m_iCombinedGreyMin = AskRangeInteger(" Darkest shade of grey to use (0=black, 255=white)? [128] ",0,255,128);
3112
o->m_iCombinedGreyMax = AskRangeInteger(" Lightest shade of grey to use (0=black, 255=white)? [224] ",o->m_iCombinedGreyMin,255,224);
3113
o->m_iCombinedGreyShades = AskUnsignedInteger(" How many different shades of grey to use? [4] ",4);
3114
} else o->m_bCombinedGreyMode = false;
3115
} else o->m_bCombinedPlot = false;
3116
} else o->m_bCombinedPlot = false;
3117
3118
if (((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() > 1)
3119
{
3120
mprintf(" Save development for which rep. of the reference molecule (e.g. 1,3-7)? [1] ");
3121
inpprintf("! Save development for which rep. of the reference molecule (e.g. 1,3-7)? [1]\n");
3122
myget(buf);
3123
if (strlen(buf)==0)
3124
o->m_waSaveRefList.Add(0);
3125
else {
3126
ParseIntList(buf,&o->m_waSaveRefList);
3127
for (z=0;z<o->m_waSaveRefList.GetSize();z++)
3128
o->m_waSaveRefList[z]--;
3129
}
3130
} else o->m_waSaveRefList.Add(0);
3131
if (o->m_iShowMol != -1)
3132
{
3133
if (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize() > 1)
3134
{
3135
mprintf(" Save development for which rep. of the observed molecule (e.g. 1,3-7)? [all] ");
3136
inpprintf("! Save development for which rep. of the observed molecule (e.g. 1,3-7)? [all]\n");
3137
myget(buf);
3138
if (strlen(buf)==0)
3139
{
3140
for (z=0;z<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
3141
o->m_waSaveShowList.Add(z);
3142
} else
3143
{
3144
ParseIntList(buf,&o->m_waSaveShowList);
3145
for (z=0;z<o->m_waSaveShowList.GetSize();z++)
3146
o->m_waSaveShowList[z]--;
3147
}
3148
} else o->m_waSaveShowList.Add(0);
3149
} else o->m_waSaveShowList.Add(0); // Dummy
3150
if ((o->m_waSaveRefList.GetSize() > 1) && (o->m_bOthers))
3151
o->m_bSaveSeparateFiles = AskYesNo(" Developments for different ref. molecules to same (n) or different (y) files? [yes] ",true);
3152
else o->m_bSaveSeparateFiles = false;
3153
if ((g_bCDF) && (g_iCDFChannels == 2))
3154
{
3155
if (AskYesNo(" Generate time development animation (TDO) for CDF (y/n)? [no] ",false))
3156
{
3157
o->m_pCDF->m_bTDAnimation = true;
3158
o->m_pCDF->m_iTDASteps = AskUnsignedInteger(" How many steps should the animation have? [1000] ",1000);
3159
o->m_pCDF->m_iTDAStride = AskUnsignedInteger(" Enter distance between the frames in timesteps: [100] ",50);
3160
o->m_pCDF->m_iTDATail = AskUnsignedInteger(" Enter length of the tail in timesteps: [100] ",100);
3161
o->m_pCDF->m_bTDATrace = AskYesNo(" Show trace (y/n)? [yes] ",true);
3162
o->m_pCDF->m_iTDAResX = AskUnsignedInteger(" Enter width (in pixel) of the TDA images: [640] ",640);
3163
o->m_pCDF->m_iTDAResY = AskUnsignedInteger(" Enter height (in pixel) of the TDA images: [480] ",480);
3164
} else o->m_pCDF->m_bTDAnimation = false;
3165
}
3166
mprintf("\n Saving temporal development for reference molecules ");
3167
for (z=0;z<o->m_waSaveRefList.GetSize();z++)
3168
{
3169
if (z < (int)o->m_waSaveRefList.GetSize()-1)
3170
{
3171
mprintf("%d, ",o->m_waSaveRefList[z]+1);
3172
if (((z+1) % 16) == 0)
3173
mprintf("\n ");
3174
} else mprintf("%d",o->m_waSaveRefList[z]+1);
3175
}
3176
if (o->m_bOthers)
3177
{
3178
mprintf("\n and for observed molecules ");
3179
for (z=0;z<o->m_waSaveShowList.GetSize();z++)
3180
{
3181
if (z < (int)o->m_waSaveShowList.GetSize()-1)
3182
{
3183
mprintf("%d, ",o->m_waSaveShowList[z]+1);
3184
if (((z+1) % 16) == 0)
3185
mprintf("\n ");
3186
} else mprintf("%d",o->m_waSaveShowList[z]+1);
3187
}
3188
}
3189
mprintf(".\n");
3190
mprintf(WHITE,"\n<<< End of Save temporal development <<<\n\n");
3191
} else o->m_bTimeDev = false;
3192
3193
if (g_bAdvanced2)
3194
{
3195
if (AskYesNo(" Create a temporal difference plot for this observation (y/n)? [no] ",false))
3196
{
3197
o->m_bTimeDiff = true;
3198
g_bTimeDiff = true;
3199
o->m_iTimeDiffDepth = AskUnsignedInteger(" Enter temporal depth of this plot in time steps: [1000] ",1000);
3200
o->m_b3DTimeDiff = AskYesNo(" Create also 3D temporal difference plots (y/n)? [yes] ",true);
3201
if (o->m_b3DTimeDiff)
3202
{
3203
tf = 0;
3204
tf2 = 0;
3205
if (g_bRDF)
3206
{
3207
tf = o->m_pRDF[0]->m_fMinDist;
3208
tf2 = o->m_pRDF[0]->m_fMaxDist;
3209
}
3210
if (g_bADF)
3211
{
3212
tf = o->m_pADF[0]->m_fMinAngle;
3213
tf2 = o->m_pADF[0]->m_fMaxAngle;
3214
}
3215
if (g_bDDF)
3216
{
3217
tf = o->m_pDDF[0]->m_fMinAngle;
3218
tf2 = o->m_pDDF[0]->m_fMaxAngle;
3219
}
3220
if (g_bVDF)
3221
{
3222
tf = o->m_pVDF[0]->m_fMinSpeed;
3223
tf2 = o->m_pVDF[0]->m_fMaxSpeed;
3224
}
3225
if (g_bDipDF)
3226
{
3227
tf = o->m_pDipDF[0]->m_fDipoleMin;
3228
tf2 = o->m_pDipDF[0]->m_fDipoleMax;
3229
}
3230
o->m_iTimeDiffStride3D = AskUnsignedInteger(" Take every n-th time step for the tau axis: [%d] ",o->m_iTimeDiffDepth/100,o->m_iTimeDiffDepth/100);
3231
o->m_fTimeDiffMinVal3D = AskFloat(" Enter min. value for the starting point: [%.2f] ",tf,tf);
3232
o->m_fTimeDiffMaxVal3D = AskFloat(" Enter max. value for the starting point: [%.2f] ",tf2,tf2);
3233
o->m_iTimeDiffRes3D = AskUnsignedInteger(" Enter binning resolution for the starting value: [100] ",100);
3234
mprintf("\n Temporal before/after 3D plot:\n");
3235
o->m_iTimeDiffDistSteps= AskUnsignedInteger(" Every how many time steps create a 2D slice (0 to disable): [0] ",0);
3236
o->m_fTimeDiffDistMinValX = AskFloat(" Enter min. value for the starting point: [%.2f] ",tf,tf);
3237
o->m_fTimeDiffDistMaxValX = AskFloat(" Enter max. value for the starting point: [%.2f] ",tf2,tf2);
3238
o->m_iTimeDiffDistResX = AskUnsignedInteger(" Enter binning resolution for the X axis: [100] ",100);
3239
o->m_fTimeDiffDistMinValY = AskFloat(" Enter min. value for the end point: [%.2f] ",tf,tf);
3240
o->m_fTimeDiffDistMaxValY = AskFloat(" Enter max. value for the end point: [%.2f] ",tf2,tf2);
3241
o->m_iTimeDiffDistResY = AskUnsignedInteger(" Enter binning resolution for the Y axis: [100] ",100);
3242
}
3243
mprintf("\n");
3244
} else o->m_bTimeDiff = false;
3245
} else o->m_bTimeDiff = false;
3246
} else
3247
{
3248
o->m_bTimeDev = false;
3249
o->m_bTimeDiff = false;
3250
}
3251
} else
3252
{
3253
o->m_bTimeDev = false;
3254
o->m_bTimeDiff = false;
3255
}
3256
3257
if ((g_iFixMol != -1) && (o->m_iShowMol != -1) && (g_bRDyn || g_bDipDF || g_bMSD || g_bADF || g_bPlDF || g_bLiDF || g_bDDF || g_bVACF || g_bDipACF ||g_bRevSDF || g_bSDF || g_bPlProj || g_bVHDF || g_bRDF || g_bVDF || g_bFDF || g_bCond))
3258
{
3259
if (g_bCond)
3260
goto _askcond;
3261
if (AskYesNo(" Add a condition to this observation (y/n)? [no] ",false))
3262
{
3263
_askcond:
3264
mprintf(GREEN,"\n>>> Condition input >>>\n\n");
3265
// mprintf("You may enter several sets of conditions. They are connected with \"or\",\nonly one of them needs to apply to take a configuration into account.\n\n");
3266
// mprintf("In each set of conditions, you may enter several conditions. They are connected\nwith \"and\", all of them have to apply to make this set of conditions apply.\n");
3267
3268
if (o->m_bSecondShowMol)
3269
{
3270
if (!AskYesNo(" Add a condition between RM and 1st OM (y/n)? [yes] ",true))
3271
goto _no1stcond;
3272
mprintf(WHITE,"\n *** Input of Condition between RM and 1st OM ***\n\n");
3273
}
3274
3275
try { o->m_pConditions = new CConditionGroup(); } catch(...) { o->m_pConditions = NULL; }
3276
if (o->m_pConditions == NULL) NewException((double)sizeof(CConditionGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3277
3278
o->m_pConditions->m_iShowMol = o->m_iShowMol;
3279
o->m_pConditions->Parse(g_iFixMol,o->m_iShowMol);
3280
_no1stcond:
3281
3282
if (o->m_bSecondShowMol)
3283
{
3284
mprintf("\n");
3285
if (!AskYesNo(" Add a condition between RM and 2nd OM (y/n)? [yes] ",true))
3286
goto _no2ndcond;
3287
mprintf(WHITE,"\n *** Input of Condition between RM and 2nd OM ***\n\n");
3288
3289
try { o->m_pConditionsOM2 = new CConditionGroup(); } catch(...) { o->m_pConditionsOM2 = NULL; }
3290
if (o->m_pConditionsOM2 == NULL) NewException((double)sizeof(CConditionGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3291
3292
o->m_pConditionsOM2->m_iShowMol = o->m_iShowMol2;
3293
o->m_pConditionsOM2->Parse(g_iFixMol,o->m_iShowMol2);
3294
_no2ndcond:;
3295
}
3296
3297
if (o->m_pConditions != NULL)
3298
{
3299
if (o->m_pConditions->m_bInvertCondition)
3300
{
3301
o->m_bBinOnlyNotPassedAtoms = false;
3302
o->m_bBinOnlyPassedAtoms = false;
3303
goto _nobinonly;
3304
}
3305
}
3306
3307
if (o->m_pConditionsOM2 != NULL)
3308
{
3309
if (o->m_pConditionsOM2->m_bInvertCondition)
3310
{
3311
o->m_bBinOnlyNotPassedAtoms = false;
3312
o->m_bBinOnlyPassedAtoms = false;
3313
goto _nobinonly;
3314
}
3315
}
3316
3317
mprintf("\n Normally, TRAVIS evaluates the condition for each RM-OM pair. If the condition\n");
3318
mprintf(" is fulfilled, all atoms from this pair are evaluated. The following question\n");
3319
mprintf(" enables to take into account only exactly the atoms which fulfilled the condition.\n\n");
3320
3321
mprintf(" If you have a distance condition with \"nearest neighbor mode\", only the atom\n");
3322
mprintf(" from the OM that is closest to the RM will be taken into account.\n\n");
3323
3324
o->m_bBinOnlyPassedAtoms = AskYesNo(" Add only atoms to the bin that passed the condition(s) (y/n)? [no] ",false);
3325
/* if (!o->m_bBinOnlyPassedAtoms)
3326
o->m_bBinOnlyNotPassedAtoms = AskYesNo(" Add only atoms to the bin that did NOT pass the condition(s) (y/n)? [no] ",false);
3327
else*/ o->m_bBinOnlyNotPassedAtoms = false;
3328
_nobinonly:
3329
3330
g_bSaveCondSnapshot = AskYesNo(" Save a snapshot every time the conditions are fulfilled (y/n)? [no] ",false);
3331
3332
if (g_bSaveCondSnapshot)
3333
g_bNeedMoleculeWrap = true;
3334
3335
if (g_bSaveCondSnapshot)
3336
{
3337
g_bSaveCondWholeBox = AskYesNo(" Save the whole box (y) or only the RM/OM pair (n)? [no] ",false);
3338
if (g_bSaveCondWholeBox)
3339
mprintf("\n The RM that fulfills the condition will be centered (coordinates 0|0|0).\n");
3340
}
3341
3342
mprintf(GREEN,"\n<<< End of Condition input <<<\n\n");
3343
}
3344
}
3345
3346
if (g_bVACF)
3347
{
3348
mprintf(WHITE,"\n>>> Velocity autocorrelation function >>>\n\n");
3349
3350
try { o->m_pVACF = new CACF(); } catch(...) { o->m_pVACF = NULL; }
3351
if (o->m_pVACF == NULL) NewException((double)sizeof(CACF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3352
3353
o->m_pVACF->m_iShowMol = o->m_iShowMol;
3354
o->m_pVACF->Parse();
3355
mprintf(WHITE,"\n<< End of Velocity autocorrelation function <<<\n\n");
3356
}
3357
3358
/* if (g_bDipACF)
3359
{
3360
mprintf(WHITE,"\n>>> Dipole moment autocorrelation function >>>\n\n");
3361
3362
try { o->m_pDipACF = new CACF(); } catch(...) { o->m_pDipACF = NULL; }
3363
if (o->m_pDipACF == NULL) NewException((double)sizeof(CACF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3364
3365
o->m_pDipACF->Parse();
3366
mprintf(WHITE,"\n<<< End of Dipole moment autocorrelation function <<<\n\n");
3367
}*/
3368
3369
if (g_bUseVelocities)
3370
{
3371
if (g_iFixMol != -1)
3372
o->m_bVelocityRelToRef = (AskRangeInteger(" Use absolute velocities (0) or relative to the reference molecule (1)? [0] ",0,1,0) != 0);
3373
else o->m_bVelocityRelToRef = false;
3374
}
3375
3376
mprintf(YELLOW,"\n<<< End of Observation %d <<<\n",g_oaObserv.GetSize());
3377
3378
if (AskYesNo("\n Add another observation (y/n)? [no] ",false))
3379
goto _nextsdf;
3380
mprintf("\n");
3381
3382
mprintf(WHITE,">>> Observation List >>>\n\n");
3383
for (z2=0;z2<g_oaObserv.GetSize();z2++)
3384
{
3385
mprintf(YELLOW," *** Observation %d\n",z2+1);
3386
o = (CObservation*)g_oaObserv[z2];
3387
3388
if (g_bCond)
3389
mprintf(" - Condition between %s and %s\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName);
3390
3391
if (g_bAggregation)
3392
{
3393
mprintf(" - Aggregation functions - %d value sets:\n",o->m_pDACF->m_oaSubDACFs.GetSize());
3394
for (z3=0;z3<o->m_pDACF->m_oaSubDACFs.GetSize();z3++)
3395
mprintf(" > %s\n",((CDACFSub*)o->m_pDACF->m_oaSubDACFs[z3])->m_sName);
3396
}
3397
3398
if (g_bNbExchange)
3399
{
3400
mprintf(" - Neighborhood exchange functions:\n");
3401
for (z3=0;z3<o->m_pDACF->m_oaSubDACFs.GetSize();z3++)
3402
mprintf(" > %s\n",((CDACFSub*)o->m_pDACF->m_oaSubDACFs[z3])->m_sName);
3403
}
3404
3405
if (g_bRDyn)
3406
mprintf(" - Reorientation Dynamics: %s\n",o->m_pRDyn->m_sName);
3407
3408
if (g_bIRSpec)
3409
mprintf(" - IR Spectrum: %s\n",o->m_pIRSpec->m_sName);
3410
3411
if (g_bDens)
3412
mprintf(" - Density DF: %s\n",o->m_pDensityDF->m_sName);
3413
3414
if (g_bSDF)
3415
mprintf(" - SDF: %s\n",o->m_pSDF->m_sName);
3416
3417
if (g_bPlProj)
3418
mprintf(" - Plane Projection DF: %s\n",o->m_pPlProj->m_sName);
3419
3420
if (g_bRevSDF)
3421
mprintf(" - Pseudo SDF: %s\n",o->m_pRevSDF->m_sName);
3422
3423
if (g_bNbAnalysis)
3424
mprintf(" - Neighborhood Analysis: %s\n",o->m_pNbAnalysis->m_sName);
3425
3426
if (g_bVACF)
3427
mprintf(" - VACF: %s\n",o->m_pVACF->m_sName);
3428
3429
if (g_bMSD)
3430
mprintf(" - MSD: %s\n",o->m_pMSD->m_sName);
3431
3432
if (g_bVHDF)
3433
mprintf(" - VHDF: %s\n",o->m_pVHDF->m_sName);
3434
3435
if (g_bCDF)
3436
{
3437
mprintf(" - Combined Distribution Function:\n");
3438
for (z3=0;z3<g_iCDFChannels;z3++)
3439
{
3440
if (o->m_pRDF[z3] != NULL)
3441
mprintf(" - Channel %d: RDF: %s\n",z3+1,o->m_pRDF[z3]->m_sName);
3442
if (o->m_pADF[z3] != NULL)
3443
mprintf(" - Channel %d: ADF: %s\n",z3+1,o->m_pADF[z3]->m_sName);
3444
if (o->m_pDDF[z3] != NULL)
3445
mprintf(" - Channel %d: DDF: %s\n",z3+1,o->m_pDDF[z3]->m_sName);
3446
if (o->m_pDipDF[z3] != NULL)
3447
mprintf(" - Channel %d: DipDF: %s\n",z3+1,o->m_pDipDF[z3]->m_sName);
3448
if (o->m_pVDF[z3] != NULL)
3449
mprintf(" - Channel %d: VDF: %s\n",z3+1,o->m_pVDF[z3]->m_sName);
3450
if (o->m_pPlDF[z3] != NULL)
3451
mprintf(" - Channel %d: PlDF: %s\n",z3+1,o->m_pPlDF[z3]->m_sName);
3452
if (o->m_pLiDF[z3] != NULL)
3453
mprintf(" - Channel %d: LiDF: %s\n",z3+1,o->m_pLiDF[z3]->m_sName);
3454
}
3455
} else
3456
{
3457
if (g_bRDF)
3458
mprintf(" - RDF: %s\n",o->m_pRDF[0]->m_sName);
3459
if (g_bDipDF)
3460
mprintf(" - DipDF: %s\n",o->m_pDipDF[0]->m_sName);
3461
if (g_bADF)
3462
mprintf(" - ADF: %s\n",o->m_pADF[0]->m_sName);
3463
if (g_bDDF)
3464
mprintf(" - DDF: %s\n",o->m_pDDF[0]->m_sName);
3465
if (g_bVDF)
3466
mprintf(" - VDF: %s\n",o->m_pVDF[0]->m_sName);
3467
if (g_bPlDF)
3468
mprintf(" - PlDF: %s\n",o->m_pPlDF[0]->m_sName);
3469
if (g_bLiDF)
3470
mprintf(" - LiDF: %s\n",o->m_pLiDF[0]->m_sName);
3471
}
3472
}
3473
mprintf(WHITE,"\n<<< End of Observation List <<<\n\n");
3474
}
3475
_endobs:
3476
3477
if (g_bVACF && g_bGlobalVACF)
3478
{
3479
try { g_pGlobalVACF = new CACF(); } catch(...) { g_pGlobalVACF = NULL; }
3480
if (g_pGlobalVACF == NULL) NewException((double)sizeof(CACF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3481
3482
mprintf(WHITE,"\n>>> Global velocity autocorrelation function >>>\n\n");
3483
g_pGlobalVACF->Parse();
3484
mprintf(WHITE,"\n<<< End of global velocity autocorrelation function <<<\n\n");
3485
}
3486
3487
if (g_bIRSpec && g_bGlobalIR)
3488
{
3489
try { g_pGlobalIR = new CReorDyn(); } catch(...) { g_pGlobalIR = NULL; }
3490
if (g_pGlobalIR == NULL) NewException((double)sizeof(CReorDyn),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3491
3492
mprintf(WHITE,"\n*** Definition of system-wide IR spectrum ***\n\n");
3493
g_pGlobalIR->ParseSpec();
3494
}
3495
3496
if (g_bSDF || g_bVoidSDF || g_bCreateRevSDF)
3497
{
3498
g_iSDFSmoothGrade = AskInteger(" Up to which degree should the SDFs be smoothened (0=not at all)? [3] ",3);
3499
3500
if (g_bSDF)
3501
{
3502
_sdf_norm_again:
3503
g_bSDFUniform = AskYesNo(" Calculate SDF values in nm^-3 (n) or relative to uniform density (y)? [no] ",false);
3504
if (g_bSDFUniform && ((!g_bPeriodicX) || (!g_bPeriodicY) || (!g_bPeriodicZ)))
3505
{
3506
eprintf("\n Error: Uniform particle density is only defined for XYZ-periodic systems.\n\n");
3507
goto _sdf_norm_again;
3508
}
3509
}
3510
// g_iSDFScale = AskRangeInteger(" SDF values in ppm (1), pm^-3 (2), nm^-3 (3) or rel. to uniform density (4)? [4] ",1,4,4) - 1;
3511
// g_iSDFScale = 2; // nm^-3
3512
} else if (g_bCDF && (g_iCDFChannels == 3))
3513
g_iSDFSmoothGrade = AskInteger(" Up to which degree should the 3D CDFs be smoothened (0=not at all)? [3] ",3);
3514
3515
// if (g_bVDF || g_bSVDF)
3516
// g_bSaveVelForce = AskYesNo(" Save maximum/averaged velocity time development (y/n)? [yes] ",true);
3517
3518
// if (g_bVDF || g_bFDF)
3519
// {
3520
// g_fVelPercentage = AskFloat(" Which percentage of all velocities/forces to take into account? [95] ",95.0f);
3521
// g_fForcePercentage = g_fVelPercentage;
3522
// }
3523
g_bSaveVelForce = false;
3524
3525
if ((g_bSDF && g_bAdvanced2) || g_bSaveRefEnv || g_bCutCluster || g_bSaveJustTraj)
3526
{
3527
mprintf(WHITE,"\n>>> Coordinate output options >>>\n\n");
3528
3529
if ((g_bSDF && g_bAdvanced2) || g_bSaveRefEnv || g_bCutCluster)
3530
{
3531
if (g_bAdvanced2)
3532
g_bWriteAtomwise = (AskRangeInteger(" Sort output coordinates by molecules (0) or by element types (1)? [molecules] ",0,1,0)!=0);
3533
else g_bWriteAtomwise = false;
3534
}
3535
3536
g_bSaveVirtAtoms = AskYesNo(" Save also virtual atoms (y/n)? [no] ",false);
3537
3538
if (g_bSaveVirtAtoms)
3539
{
3540
if (AskYesNo(" Ref.Env.: Use alias names (instead of #) for virtual atoms (y/n)? [no] ",false))
3541
{
3542
for (z2=0;z2<g_oaMolecules.GetSize();z2++)
3543
{
3544
CMolecule *m = (CMolecule*)g_oaMolecules[z2];
3545
for (z=0;z<m->m_baAtomIndex.GetSize();z++)
3546
{
3547
if (m->m_baAtomIndex[z] != g_iVirtAtomType)
3548
continue;
3549
for (z3=0;z3<m->m_waAtomCount[z];z3++)
3550
{
3551
mprintf(" How to name atom #%d in %s? [#%d] ",z3+1,m->m_sName,z3+1);
3552
inpprintf("! How to name atom #%d in %s? [#%d]\n",z3+1,m->m_sName,z3+1);
3553
myget(buf);
3554
if (strlen(buf) != 0)
3555
strcpy(((CVirtualAtom*)g_oaVirtualAtoms[m->m_laVirtualAtoms[z3]])->m_sLabel,buf);
3556
}
3557
}
3558
}
3559
}
3560
}
3561
3562
if (g_bSaveRefEnv || g_bCutCluster)
3563
g_bEnvWriteDetailedInfo = AskYesNo(" Write detailed (long) comment lines into output xyz file (y/n)? [yes] ",true);
3564
else g_bEnvWriteDetailedInfo = false;
3565
3566
if ((g_bSaveRefEnv || g_bCutCluster) && !g_bEnvDisableSortNb)
3567
g_bEnvSortNb = AskYesNo(" Sort molecules according to distance from reference molecule (y/n)? [yes] ",true);
3568
else g_bEnvSortNb = false;
3569
3570
mprintf(WHITE,"\n<<< End of Coordinate output options <<<\n\n");
3571
} else
3572
{
3573
g_bWriteAtomwise = false;
3574
g_bSaveVirtAtoms = false;
3575
}
3576
3577
if (g_bSaveRefEnv || g_bCutCluster)
3578
g_bCenterZero = AskYesNo(" Put the center of the system to (0|0|0) (y) or to (x/2|y/2|z/2) (n)? [yes] ",true);
3579
3580
g_bMiddleAvg = false;
3581
g_iSwapAtoms = 0;
3582
3583
if (g_bSaveJustTraj)
3584
{
3585
mprintf(WHITE,"\n>>> Process Trajectory >>>\n\n");
3586
3587
if (g_bAdvanced2)
3588
g_bSaveTrajNoRot = AskYesNo(" Remove angular momentum from trajectory (y/n)? [no] ",false);
3589
else g_bSaveTrajNoRot = false;
3590
3591
if (g_bSaveTrajNoRot)
3592
{
3593
mprintf("\n This centers the mass center of the system. All atoms of the system are saved.\n\n");
3594
g_bSaveCoordsUnchanged = false;
3595
g_bSaveJustCenter = false;
3596
if(AskYesNo(" Put the center of the system to (0|0|0) (y) or to (x/2|y/2|z/2) (n)? [yes] ",true))
3597
g_bCenterZero = true;
3598
else g_bCenterZero = false;
3599
goto _norot;
3600
} else
3601
{
3602
switch(AskRangeInteger(" Put the center of the system to (0|0|0) (0), to (x/2|y/2|z/2) (1), or leave coords unchanged (2)? [1] ",0,2,1))
3603
{
3604
case 0:
3605
g_bCenterZero = true;
3606
g_bSaveCoordsUnchanged = false;
3607
break;
3608
case 1:
3609
g_bCenterZero = false;
3610
g_bSaveCoordsUnchanged = false;
3611
break;
3612
case 2:
3613
g_bSaveCoordsUnchanged = true;
3614
break;
3615
}
3616
3617
if (!g_bSaveCoordsUnchanged)
3618
g_bSaveJustCenter = AskYesNo("\n Put a specific atom into the box center (y/n)? [no] ",false);
3619
else g_bSaveJustCenter = false;
3620
}
3621
3622
if (g_bSaveJustCenter)
3623
{
3624
if (g_oaMolecules.GetSize() > 1)
3625
{
3626
sprintf(buf," Choose center atom from which of the molecules (");
3627
for (z=0;z<g_oaMolecules.GetSize();z++)
3628
{
3629
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
3630
strcat(buf,buf2);
3631
if (z < g_oaMolecules.GetSize()-1)
3632
strcat(buf,", ");
3633
}
3634
strcat(buf,")? ");
3635
g_iSaveJustMol = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize()) - 1;
3636
} else
3637
{
3638
g_iSaveJustMol = 0;
3639
mprintf(" Choosing center atom from %s.\n",((CMolecule*)g_oaMolecules[0])->m_sName);
3640
}
3641
if (((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_laSingleMolIndex.GetSize() > 1)
3642
g_iSaveJustSM = AskRangeInteger(" Take which representant from %s (1-%d)? [1] ",1,((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_laSingleMolIndex.GetSize(),1,((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_sName,((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_laSingleMolIndex.GetSize()) - 1;
3643
else g_iSaveJustSM = 0;
3644
_proccenter:
3645
AskString(" Which atom from %s %d to put into the box center? [#2] ",buf,"#2",((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_sName,g_iSaveJustSM+1);
3646
if (!ParseAtom(buf,g_iSaveJustMol,g_iSaveJustAtomType,g_iSaveJustRealAtomType,g_iSaveJustAtom))
3647
goto _proccenter;
3648
}
3649
g_iSaveGesAtoms = 0;
3650
if (!AskYesNo(" Save all atoms in the system (y/n)? [yes] ",true))
3651
{
3652
mprintf("\n");
3653
for (z=0;z<g_oaMolecules.GetSize();z++)
3654
{
3655
if (AskYesNo(" Save (some/all) atoms from molecule %s (y/n)? [yes] ",true,((CMolecule*)g_oaMolecules[z])->m_sName))
3656
{
3657
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3658
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3659
3660
g_oaSaveMolecules.Add(ag);
3661
_savejust1: mprintf(" Which atoms to save from %s (e.g. \"C1,C3-5,H\")? [all] ",((CMolecule*)g_oaMolecules[z])->m_sName);
3662
inpprintf("! Which atoms to save from %s (e.g. \"C1,C3-5,H\")? [all]\n",((CMolecule*)g_oaMolecules[z])->m_sName);
3663
myget(buf);
3664
if (strlen(buf)==0)
3665
ag->AddAllAtoms((CMolecule*)g_oaMolecules[z],g_bSaveVirtAtoms);
3666
else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[z],buf))
3667
goto _savejust1;
3668
g_iSaveGesAtoms += ag->m_iAtomGes * ((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();
3669
}
3670
}
3671
} else
3672
{
3673
_norot:
3674
for (z=0;z<g_oaMolecules.GetSize();z++)
3675
{
3676
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3677
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3678
3679
g_oaSaveMolecules.Add(ag);
3680
ag->AddAllAtoms((CMolecule*)g_oaMolecules[z],g_bSaveVirtAtoms);
3681
g_iSaveGesAtoms += ag->m_iAtomGes * ((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();
3682
}
3683
}
3684
3685
if (g_bUnknownElements)
3686
{
3687
g_bUnwrapWannier = AskYesNo(" Write out Wannier centers together with trajectory (y/n)? [no] ",false);
3688
3689
if (g_bUnwrapWannier)
3690
ParseDipole();
3691
3692
} else g_bUnwrapWannier = false;
3693
3694
if ((!g_bSaveCoordsUnchanged) && (!g_bSaveTrajNoRot))
3695
g_bUnwrap = AskYesNo(" Try to unwrap the trajectory (y/n)? [no] ",false);
3696
else g_bUnwrap = false;
3697
3698
if (g_bUnwrap)
3699
mprintf("\n Attention! This feature only works if the time step\n in the trajectory is quite small. One particle may never\n move further than half of the box length in one time step!\n");
3700
3701
mprintf("\nSaving %d atoms per step:\n",g_iSaveGesAtoms);
3702
for (z2=0;z2<g_oaSaveMolecules.GetSize();z2++)
3703
{
3704
ag = (CAtomGroup*)g_oaSaveMolecules[z2];
3705
mprintf(" - In %s: ",ag->m_pMolecule->m_sName);
3706
for (z=0;z<ag->m_baAtomType.GetSize();z++)
3707
{
3708
for (z3=0;z3<((CxIntArray*)ag->m_oaAtoms[z])->GetSize();z3++)
3709
{
3710
mprintf("%s%d",((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z]])->m_sName,((CxIntArray*)ag->m_oaAtoms[z])->GetAt(z3)+1);
3711
if (z3 < ((CxIntArray*)ag->m_oaAtoms[z])->GetSize()-1)
3712
mprintf(", ");
3713
}
3714
if (z+1 < ag->m_baAtomType.GetSize())
3715
mprintf(", ");
3716
}
3717
mprintf("\n");
3718
}
3719
// g_bTrajAtomwise = (AskRangeInteger("\n Save trajectory ordered molecule-wise (0) or atom-wise (1)? [0] ",0,1,0)!=0);
3720
3721
mprintf("\n");
3722
3723
if (g_bAdvanced2)
3724
{
3725
if ((int)g_iSaveGesAtoms == g_iGesAtomCount)
2593
3726
{
2594
mprintf(BLUE,"\n### Channel %d ###\n",z+1);
2595
switch(g_iObsChannel[z])
3727
switch(AskRangeInteger(" Sort output coordinates by molecules (0), element types (1), or input file order (2)? [0] ",0,2,0))
2596
3728
{
2597
3729
case 0:
2598
try { o->m_pRDF[z] = new CRDF(); } catch(...) { o->m_pRDF[z] = NULL; }
2599
if (o->m_pRDF[z] == NULL) NewException((double)sizeof(CRDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2600
2601
if (o->m_bSecondShowMol && (z == 1))
2602
o->m_pRDF[z]->m_iShowMol = o->m_iShowMol2;
2603
else o->m_pRDF[z]->m_iShowMol = o->m_iShowMol;
2604
o->m_pRDF[z]->Parse();
2605
o->m_pCDF->m_iCombinations[z] = o->m_pRDF[z]->m_iCombinations;
2606
o->m_pCDF->m_iCombinationProd *= o->m_pRDF[z]->m_iCombinations;
2607
/* if (o->m_pRDF[z]->m_bSaveDist)
2608
o->m_bTimeDev = true;*/
3730
g_bWriteAtomwise = false;
3731
g_bWriteInputOrder = false;
2609
3732
break;
2610
2611
3733
case 1:
2612
try { o->m_pADF[z] = new CADF(); } catch(...) { o->m_pADF[z] = NULL; }
2613
if (o->m_pADF[z] == NULL) NewException((double)sizeof(CADF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2614
2615
if (o->m_bSecondShowMol && (z == 1))
2616
o->m_pADF[z]->m_iShowMol = o->m_iShowMol2;
2617
else o->m_pADF[z]->m_iShowMol = o->m_iShowMol;
2618
o->m_pADF[z]->Parse();
2619
o->m_pCDF->m_iCombinations[z] = o->m_pADF[z]->m_iCombinations;
2620
o->m_pCDF->m_iCombinationProd *= o->m_pADF[z]->m_iCombinations;
2621
/* if (o->m_pADF[z]->m_bSaveAngle)
2622
o->m_bTimeDev = true;*/
3734
g_bWriteAtomwise = true;
3735
g_bWriteInputOrder = false;
2623
3736
break;
2624
2625
3737
case 2:
2626
try { o->m_pDDF[z] = new CDDF(); } catch(...) { o->m_pDDF[z] = NULL; }
2627
if (o->m_pDDF[z] == NULL) NewException((double)sizeof(CDDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2628
2629
if (o->m_bSecondShowMol && (z == 1))
2630
o->m_pDDF[z]->m_iShowMol = o->m_iShowMol2;
2631
else o->m_pDDF[z]->m_iShowMol = o->m_iShowMol;
2632
o->m_pDDF[z]->Parse();
2633
o->m_pCDF->m_iCombinations[z] = o->m_pDDF[z]->m_iCombinations;
2634
o->m_pCDF->m_iCombinationProd *= o->m_pDDF[z]->m_iCombinations;
2635
/* if (o->m_pDDF[z]->m_bSaveAngle)
2636
o->m_bTimeDev = true;*/
2637
break;
2638
2639
case 3:
2640
try { o->m_pDipDF[z] = new CDipDF(); } catch(...) { o->m_pDipDF[z] = NULL; }
2641
if (o->m_pDipDF[z] == NULL) NewException((double)sizeof(CDipDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2642
2643
if (o->m_bSecondShowMol && (z == 1))
2644
o->m_pDipDF[z]->m_iShowMol = o->m_iShowMol2;
2645
else o->m_pDipDF[z]->m_iShowMol = o->m_iShowMol;
2646
o->m_pDipDF[z]->m_iCombinations = 1;
2647
o->m_pDipDF[z]->Parse();
2648
o->m_pCDF->m_iCombinations[z] = 1;
2649
/* if (o->m_pDipDF[z]->m_bSaveDipole)
2650
o->m_bTimeDev = true;*/
2651
break;
2652
2653
case 4:
2654
try { o->m_pVDF[z] = new CVDF(); } catch(...) { o->m_pVDF[z] = NULL; }
2655
if (o->m_pVDF[z] == NULL) NewException((double)sizeof(CVDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2656
2657
if (o->m_bSecondShowMol && (z == 1))
2658
o->m_pVDF[z]->m_iShowMol = o->m_iShowMol2;
2659
else o->m_pVDF[z]->m_iShowMol = o->m_iShowMol;
2660
o->m_pVDF[z]->Parse();
2661
o->m_pCDF->m_iCombinations[z] = o->m_pVDF[z]->m_iCombinations;
2662
o->m_pCDF->m_iCombinationProd *= o->m_pVDF[z]->m_iCombinations;
2663
g_bUseVelocities = true;
2664
/* if (o->m_pVDF[z]->m_bSaveSpeed)
2665
o->m_bTimeDev = true;*/
2666
break;
2667
2668
case 5:
2669
try { o->m_pPlDF[z] = new CPlDF(); } catch(...) { o->m_pPlDF[z] = NULL; }
2670
if (o->m_pPlDF[z] == NULL) NewException((double)sizeof(CPlDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2671
2672
if (o->m_bSecondShowMol && (z == 1))
2673
o->m_pPlDF[z]->m_iShowMol = o->m_iShowMol2;
2674
else o->m_pPlDF[z]->m_iShowMol = o->m_iShowMol;
2675
o->m_pPlDF[z]->Parse();
2676
o->m_pCDF->m_iCombinations[z] = o->m_pPlDF[z]->m_iCombinations;
2677
o->m_pCDF->m_iCombinationProd *= o->m_pPlDF[z]->m_iCombinations;
2678
break;
2679
2680
case 6:
2681
try { o->m_pLiDF[z] = new CLiDF(); } catch(...) { o->m_pLiDF[z] = NULL; }
2682
if (o->m_pLiDF[z] == NULL) NewException((double)sizeof(CLiDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2683
2684
if (o->m_bSecondShowMol && (z == 1))
2685
o->m_pLiDF[z]->m_iShowMol = o->m_iShowMol2;
2686
else o->m_pLiDF[z]->m_iShowMol = o->m_iShowMol;
2687
o->m_pLiDF[z]->Parse();
2688
o->m_pCDF->m_iCombinations[z] = o->m_pLiDF[z]->m_iCombinations;
2689
o->m_pCDF->m_iCombinationProd *= o->m_pLiDF[z]->m_iCombinations;
2690
break;
2691
}
2692
/* if (z != 0)
2693
o->m_pCDF->m_bChannelAll[z] = AskYesNo(" Should this CDF Channel observe all OMs (y) or only the current one (n)? [no] ",false);
2694
else o->m_pCDF->m_bChannelAll[z] = false;*/
2695
}
2696
/* mprintf(" Write out temporal development for this CDF (1=yes,0=no)? [no] ");
2697
myget(buf);
2698
o->m_pCDF->m_bTimeDev = (atoi(buf)!=0);
2699
if (o->m_pCDF->m_bTimeDev)
2700
o->m_bTimeDev = true;*/
2701
2702
mprintf("\n");
2703
2704
try { o->m_pCDF->m_iResolution = new int[g_iCDFChannels]; } catch(...) { o->m_pCDF->m_iResolution = NULL; }
2705
if (o->m_pCDF->m_iResolution == NULL) NewException((double)g_iCDFChannels*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2706
2707
for (z=0;z<g_iCDFChannels;z++)
2708
{
2709
switch(g_iObsChannel[z])
2710
{
2711
case 0: sprintf(buf,"RDF"); break;
2712
case 1: sprintf(buf,"ADF"); break;
2713
case 2: sprintf(buf,"DDF"); break;
2714
case 3: sprintf(buf,"DipDF"); break;
2715
case 4: sprintf(buf,"VDF"); break;
2716
case 5: sprintf(buf,"PlDF"); break;
2717
case 6: sprintf(buf,"LiDF"); break;
2718
}
2719
o->m_pCDF->m_iResolution[z] = AskUnsignedInteger(" Please enter the resolution (bin count) for CDF channel %d (%s): [100] ",100,z+1,buf);
2720
}
2721
2722
if (g_bAdvanced2)
2723
o->m_pCDF->m_iHistogramRes = AskUnsignedInteger(" Please enter CDF histogram resolution (0=no histogram): [5000] ",5000);
2724
else o->m_pCDF->m_iHistogramRes = 0;
2725
2726
if (g_iCDFChannels == 2)
2727
{
2728
try { o->m_pCDF->m_pCombineList = new char[o->m_pCDF->m_iCombinationProd]; } catch(...) { o->m_pCDF->m_pCombineList = NULL; }
2729
if (o->m_pCDF->m_pCombineList == NULL) NewException((double)o->m_pCDF->m_iCombinationProd*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2730
2731
if ((o->m_pCDF->m_iCombinations[0] > 1) && (o->m_pCDF->m_iCombinations[1] > 1))
2732
{
2733
mprintf("\n");
2734
for (z=0;z<g_iCDFChannels;z++)
2735
{
2736
mprintf(WHITE,"CDF channel %d has the following %d observations:\n",z+1,o->m_pCDF->m_iCombinations[z]);
2737
o->ListCDFObservations(z);
2738
mprintf("\n");
2739
}
2740
if (o->m_pCDF->m_iCombinations[0] == o->m_pCDF->m_iCombinations[1])
2741
{
2742
if (AskYesNo(" Combine n-th with n-th observation? (y/n) [yes] ",true))
2743
{
2744
for (z=0;z<o->m_pCDF->m_iCombinations[0];z++)
2745
for (z2=0;z2<o->m_pCDF->m_iCombinations[1];z2++)
2746
o->m_pCDF->m_pCombineList[z*o->m_pCDF->m_iCombinations[1]+z2] = (z==z2)?1:0;
2747
goto _combdone;
2748
} goto _askcomball;
2749
} else
2750
{
2751
_askcomball:
2752
if (!AskYesNo(" Combine each with each observation (y), or use only some combinations (n)? [yes] ",true))
2753
{
2754
for (z=0;z<o->m_pCDF->m_iCombinations[0];z++)
2755
for (z2=0;z2<o->m_pCDF->m_iCombinations[1];z2++)
2756
o->m_pCDF->m_pCombineList[z*o->m_pCDF->m_iCombinations[1]+z2] = 0;
2757
2758
mprintf("\n Please enter all the combinations you want to observe.\n");
2759
mprintf(" Enter each combination as a comma-separated %d-tuple (e.g. ",g_iCDFChannels);
2760
for (z=0;z<g_iCDFChannels;z++)
2761
{
2762
mprintf("%d",z+1);
2763
if (z+1 < g_iCDFChannels)
2764
mprintf(",");
2765
}
2766
mprintf(").\n\n");
2767
_nextcomb:
2768
AskString(" Enter combination (return=finished): ",buf,"");
2769
if (strlen(buf)==0)
2770
goto _combdone;
2771
tempwa.RemoveAll_KeepSize();
2772
ParseIntList(buf,&tempwa);
2773
if (tempwa.GetSize() != g_iCDFChannels)
2774
{
2775
eprintf(" Wrong input, %d instead of %d values.\n",tempwa.GetSize(),g_iCDFChannels);
2776
goto _nextcomb;
2777
}
2778
for (z=0;z<g_iCDFChannels;z++)
2779
{
2780
if ((tempwa[z] < 1) || (tempwa[z] > o->m_pCDF->m_iCombinations[z]))
2781
{
2782
eprintf(" Wrong input, channel %d has only %d observations (%d requested).\n",z+1,o->m_pCDF->m_iCombinations[z],tempwa[z]);
2783
goto _nextcomb;
2784
}
2785
tempwa[z]--;
2786
}
2787
if (o->m_pCDF->m_pCombineList[tempwa[0]*o->m_pCDF->m_iCombinations[1]+tempwa[1]] == 1)
2788
{
2789
eprintf(" This combination has already been added.\n");
2790
goto _nextcomb;
2791
}
2792
o->m_pCDF->m_pCombineList[tempwa[0]*o->m_pCDF->m_iCombinations[1]+tempwa[1]] = 1;
2793
goto _nextcomb;
2794
} else goto _combineall;
2795
_combdone:;
2796
}
2797
} else
2798
{
2799
_combineall:
2800
for (z=0;z<o->m_pCDF->m_iCombinationProd;z++)
2801
o->m_pCDF->m_pCombineList[z] = 1;
2802
}
2803
2804
o->m_pCDF->m_iCombinationsEnabled = 0;
2805
for (z=0;z<o->m_pCDF->m_iCombinationProd;z++)
2806
if (o->m_pCDF->m_pCombineList[z] != 0)
2807
o->m_pCDF->m_iCombinationsEnabled++;
2808
2809
if (o->m_pCDF->m_iCombinationsEnabled == 1)
2810
{
2811
mprintf(WHITE,"\n Using 1 combination for each RM-OM pair.\n\n");
2812
} else
2813
{
2814
mprintf(WHITE,"\n Using %d combinations for each RM-OM pair:\n\n",o->m_pCDF->m_iCombinationsEnabled);
2815
z3 = 0;
2816
for (z=0;z<o->m_pCDF->m_iCombinations[0];z++)
2817
{
2818
for (z2=0;z2<o->m_pCDF->m_iCombinations[1];z2++)
2819
{
2820
if (o->m_pCDF->m_pCombineList[z*o->m_pCDF->m_iCombinations[1]+z2] == 1)
2821
{
2822
mprintf(" %2d.) %2d - %2d\n",z3+1,z+1,z2+1);
2823
z3++;
2824
}
2825
}
2826
}
2827
mprintf("\n");
2828
}
2829
2830
if (g_bAdvanced2)
2831
{
2832
o->m_pCDF->m_bAxisDivide = AskYesNo(" Write out +/- correlation plot for this CDF (y/n)? [no] ",false);
2833
2834
if (o->m_pCDF->m_bAxisDivide)
2835
o->m_pCDF->m_bAxisDivideAll = AskYesNo(" Also write tensor product and axis projection quotients (y/n)? [no] ",false);
2836
} else
2837
{
2838
o->m_pCDF->m_bAxisDivide = false;
2839
o->m_pCDF->m_bAxisDivideAll = false;
2840
}
2841
2842
if (g_bAdvanced2)
2843
{
2844
o->m_pCDF->m_bGraceBunch = AskYesNo(" Write out grace stack (multiple 2D plots) for this CDF (y/n)? [no] ",false);
2845
if (o->m_pCDF->m_bGraceBunch)
2846
{
2847
o->m_pCDF->m_iGraceBunchC1 = AskUnsignedInteger(" How many graphs do you want do draw in the channel 1 grace stack (0=disable)? [10] ",10);
2848
o->m_pCDF->m_iGraceBunchC2 = AskUnsignedInteger(" How many graphs do you want do draw in the channel 2 grace stack (0=disable)? [10] ",10);
2849
}
2850
} else o->m_pCDF->m_bGraceBunch = false;
2851
}
2852
2853
if (g_iCDFChannels == 3)
2854
{
2855
mprintf("\n");
2856
2857
try { o->m_pCDF->m_pCombineList = new char[o->m_pCDF->m_iCombinationProd]; } catch(...) { o->m_pCDF->m_pCombineList = NULL; }
2858
if (o->m_pCDF->m_pCombineList == NULL) NewException((double)o->m_pCDF->m_iCombinationProd*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2859
2860
if ((o->m_pCDF->m_iCombinations[0] > 1) || (o->m_pCDF->m_iCombinations[1] > 1) || (o->m_pCDF->m_iCombinations[2] > 1))
2861
{
2862
for (z=0;z<g_iCDFChannels;z++)
2863
{
2864
mprintf(WHITE,"CDF channel %d has the following %d observations:\n",z+1,o->m_pCDF->m_iCombinations[z]);
2865
o->ListCDFObservations(z);
2866
mprintf("\n");
2867
}
2868
if (!AskYesNo(" Combine each with each observation (y), or use only some combinations (n)? [yes] ",true))
2869
{
2870
for (z=0;z<o->m_pCDF->m_iCombinations[0];z++)
2871
for (z2=0;z2<o->m_pCDF->m_iCombinations[1];z2++)
2872
for (z3=0;z3<o->m_pCDF->m_iCombinations[2];z3++)
2873
o->m_pCDF->m_pCombineList[z*o->m_pCDF->m_iCombinations[1]*o->m_pCDF->m_iCombinations[2]+z2*o->m_pCDF->m_iCombinations[2]+z3] = 0;
2874
2875
mprintf("\n Please enter all the combinations you want to observe.\n");
2876
mprintf(" Enter each combination as a comma-separated %d-tuple (e.g. ",g_iCDFChannels);
2877
for (z=0;z<g_iCDFChannels;z++)
2878
{
2879
mprintf("%d",z+1);
2880
if (z+1 < g_iCDFChannels)
2881
mprintf(",");
2882
}
2883
mprintf(").\n\n");
2884
_3nextcomb:
2885
AskString(" Enter combination (return=finished): ",buf,"");
2886
if (strlen(buf)==0)
2887
goto _3combdone;
2888
tempwa.RemoveAll_KeepSize();
2889
ParseIntList(buf,&tempwa);
2890
if (tempwa.GetSize() != g_iCDFChannels)
2891
{
2892
eprintf(" Wrong input, %d instead of %d values.\n",tempwa.GetSize(),g_iCDFChannels);
2893
goto _3nextcomb;
2894
}
2895
for (z=0;z<g_iCDFChannels;z++)
2896
{
2897
if ((tempwa[z] < 1) || (tempwa[z] > o->m_pCDF->m_iCombinations[z]))
2898
{
2899
eprintf(" Wrong input, channel %d has only %d observations (%d requested).\n",z+1,o->m_pCDF->m_iCombinations[z],tempwa[z]);
2900
goto _3nextcomb;
2901
}
2902
tempwa[z]--;
2903
}
2904
if (o->m_pCDF->m_pCombineList[tempwa[0]*o->m_pCDF->m_iCombinations[1]*o->m_pCDF->m_iCombinations[2]+tempwa[1]*o->m_pCDF->m_iCombinations[2]+tempwa[2]] == 1)
2905
{
2906
eprintf(" This combination has already been added.\n");
2907
goto _3nextcomb;
2908
}
2909
o->m_pCDF->m_pCombineList[tempwa[0]*o->m_pCDF->m_iCombinations[1]*o->m_pCDF->m_iCombinations[2]+tempwa[1]*o->m_pCDF->m_iCombinations[2]+tempwa[2]] = 1;
2910
goto _3nextcomb;
2911
} else goto _3combineall;
2912
} else
2913
{
2914
_3combineall:
2915
for (z=0;z<o->m_pCDF->m_iCombinationProd;z++)
2916
o->m_pCDF->m_pCombineList[z] = 1;
2917
}
2918
_3combdone:
2919
o->m_pCDF->m_iCombinationsEnabled = 0;
2920
for (z=0;z<o->m_pCDF->m_iCombinationProd;z++)
2921
if (o->m_pCDF->m_pCombineList[z] != 0)
2922
o->m_pCDF->m_iCombinationsEnabled++;
2923
2924
if (o->m_pCDF->m_iCombinationsEnabled == 1)
2925
{
2926
mprintf(WHITE,"\n Using 1 combination for each RM-OM pair.\n\n");
2927
} else
2928
{
2929
mprintf(WHITE,"\n Using %d combinations for each RM-OM pair:\n\n",o->m_pCDF->m_iCombinationsEnabled);
2930
z4 = 0;
2931
for (z=0;z<o->m_pCDF->m_iCombinations[0];z++)
2932
for (z2=0;z2<o->m_pCDF->m_iCombinations[1];z2++)
2933
for (z3=0;z3<o->m_pCDF->m_iCombinations[2];z3++)
2934
if (o->m_pCDF->m_pCombineList[z*o->m_pCDF->m_iCombinations[1]*o->m_pCDF->m_iCombinations[2]+z2*o->m_pCDF->m_iCombinations[2]+z3] == 1)
2935
{
2936
mprintf(" %2d.) %2d - %2d - %2d\n",z4+1,z+1,z2+1,z3+1);
2937
z4++;
2938
}
2939
mprintf("\n");
2940
}
2941
2942
if (g_bAdvanced2)
2943
{
2944
o->m_pCDF->m_b3DSlices = AskYesNo(" Write out 2D slices for this CDF (y/n)? [no] ",false);
2945
2946
if (o->m_pCDF->m_b3DSlices)
2947
for (z=0;z<3;z++)
2948
o->m_pCDF->m_i3DSliceIntervals[z] = AskUnsignedInteger(" How many slice intervals to create along channel %d axis (0=skip)? [0] ",0,z+1);
2949
} else o->m_pCDF->m_b3DSlices = false;
2950
} // end if channels == 3
2951
2952
2953
if (g_bAdvanced2)
2954
{
2955
o->m_pCDF->m_bDumpDat = AskYesNo(" Write out input tuples (very large!) for this CDF (y/n)? [no] ",false);
2956
if ((g_iCDFChannels == 2) && (g_iObsChannel[0] == 0) && (g_iObsChannel[1] == 1))
2957
o->m_pCDF->m_iNormalize = AskRangeInteger(" Normalize uniformly (3), data range (2), integral (1), or do not normalize (0)? [1] ",0,3,1);
2958
else o->m_pCDF->m_iNormalize = AskRangeInteger(" Normalize data range (2), integral (1), or do not normalize (0)? [1] ",0,2,1);
2959
if (o->m_pCDF->m_iNormalize == 1)
2960
o->m_pCDF->m_fNormValue = AskFloat(" Set CDF integral to which value? [1000000] ",1000000.0f);
2961
if (o->m_pCDF->m_iNormalize == 2)
2962
o->m_pCDF->m_fNormValue = AskFloat(" Set maximum entry to which value? [100] ",100.0f);
2963
} else
2964
{
2965
o->m_pCDF->m_bDumpDat = false;
2966
o->m_pCDF->m_iNormalize = 1;
2967
o->m_pCDF->m_fNormValue = 1000000.0f;
2968
}
2969
2970
mprintf(BLUE,"\n<<< End of Combined Distribution Function <<<\n\n");
2971
} else
2972
{
2973
if (g_bRDF)
2974
{
2975
try { o->m_pRDF[0] = new CRDF(); } catch(...) { o->m_pRDF[0] = NULL; }
2976
if (o->m_pRDF[0] == NULL) NewException((double)sizeof(CRDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2977
2978
o->m_pRDF[0]->m_iShowMol = o->m_iShowMol;
2979
o->m_pRDF[0]->Parse();
2980
o->m_pRDF[0]->m_bSelf = o->m_bSelf;
2981
}
2982
if (g_bPlDF)
2983
{
2984
try { o->m_pPlDF[0] = new CPlDF(); } catch(...) { o->m_pPlDF[0] = NULL; }
2985
if (o->m_pPlDF[0] == NULL) NewException((double)sizeof(CPlDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2986
2987
o->m_pPlDF[0]->m_iShowMol = o->m_iShowMol;
2988
o->m_pPlDF[0]->Parse();
2989
o->m_pPlDF[0]->m_bSelf = o->m_bSelf;
2990
}
2991
if (g_bLiDF)
2992
{
2993
try { o->m_pLiDF[0] = new CLiDF(); } catch(...) { o->m_pLiDF[0] = NULL; }
2994
if (o->m_pLiDF[0] == NULL) NewException((double)sizeof(CLiDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2995
2996
o->m_pLiDF[0]->m_iShowMol = o->m_iShowMol;
2997
o->m_pLiDF[0]->Parse();
2998
o->m_pLiDF[0]->m_bSelf = o->m_bSelf;
2999
}
3000
if (g_bVHDF)
3001
{
3002
try { o->m_pVHDF = new CVHDF(); } catch(...) { o->m_pVHDF = NULL; }
3003
if (o->m_pVHDF == NULL) NewException((double)sizeof(CVHDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3004
3005
o->m_pVHDF->m_iShowMol = o->m_iShowMol;
3006
o->m_pVHDF->m_bSelf = o->m_bSelf;
3007
o->m_pVHDF->Parse();
3008
}
3009
if (g_bADF)
3010
{
3011
try { o->m_pADF[0] = new CADF(); } catch(...) { o->m_pADF[0] = NULL; }
3012
if (o->m_pADF[0] == NULL) NewException((double)sizeof(CADF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3013
3014
o->m_pADF[0]->m_iShowMol = o->m_iShowMol;
3015
o->m_pADF[0]->m_bSelf = o->m_bSelf;
3016
o->m_pADF[0]->Parse();
3017
}
3018
if (g_bDDF)
3019
{
3020
try { o->m_pDDF[0] = new CDDF(); } catch(...) { o->m_pDDF[0] = NULL; }
3021
if (o->m_pDDF[0] == NULL) NewException((double)sizeof(CDDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3022
3023
o->m_pDDF[0]->m_iShowMol = o->m_iShowMol;
3024
o->m_pDDF[0]->m_bSelf = o->m_bSelf;
3025
o->m_pDDF[0]->Parse();
3026
}
3027
if (g_bDipDF)
3028
{
3029
try { o->m_pDipDF[0] = new CDipDF(); } catch(...) { o->m_pDipDF[0] = NULL; }
3030
if (o->m_pDipDF[0] == NULL) NewException((double)sizeof(CDipDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3031
3032
o->m_pDipDF[0]->m_iShowMol = o->m_iShowMol;
3033
o->m_pDipDF[0]->m_bSelf = o->m_bSelf;
3034
o->m_pDipDF[0]->Parse();
3035
}
3036
if (g_bVDF)
3037
{
3038
try { o->m_pVDF[0] = new CVDF(); } catch(...) { o->m_pVDF[0] = NULL; }
3039
if (o->m_pVDF[0] == NULL) NewException((double)sizeof(CVDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3040
3041
o->m_pVDF[0]->m_iShowMol = o->m_iShowMol;
3042
o->m_pVDF[0]->m_bSelf = true;
3043
o->m_pVDF[0]->Parse();
3044
g_bUseVelocities = true;
3045
}
3046
if (g_bMSD)
3047
{
3048
try { o->m_pMSD = new CMSD(); } catch(...) { o->m_pMSD = NULL; }
3049
if (o->m_pMSD == NULL) NewException((double)sizeof(CMSD),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3050
3051
o->m_pMSD->m_iShowMol = o->m_iShowMol;
3052
o->m_pMSD->Parse();
3053
}
3054
}
3055
3056
if ((g_bCDF && (g_iCDFChannels == 2)) || g_bRDF || g_bADF || g_bVDF || g_bDDF || g_bDipDF)
3057
{
3058
if (!o->m_bSecondShowMol)
3059
{
3060
if (AskYesNo(" Save temporal development for this observation (y/n)? [no] ",false))
3061
{
3062
mprintf(WHITE,"\n>>> Save temporal development >>>\n\n");
3063
o->m_bTimeDev = true;
3064
3065
if (g_fTimestepLength == 0)
3066
{
3067
g_fTimestepLength = AskFloat(" Enter the length of one trajectory time step in fs: [0.5] ",0.5f);
3068
mprintf("\n");
3069
}
3070
3071
if (g_bDDF && (!g_bCDF))
3072
{
3073
if ((o->m_pDDF[0]->m_iDeriv == 0) && (!o->m_pDDF[0]->m_bCosine) && (!o->m_pDDF[0]->m_bAbs) && (!o->m_pDDF[0]->m_bPositive))
3074
{
3075
mprintf("\n You can include full rotations into the DDF's temporal development.\n");
3076
mprintf(" This means, if a dihedral makes a full rotation, the value will be 360 deg insteat of 0 deg.\n");
3077
mprintf(" You may count the number of full rotations during simulation in this way.\n\n");
3078
o->m_pDDF[0]->m_bRotate = AskYesNo(" Include full rotations into the DDF's temporal development (y/n)? [no] ",false);
3079
} else o->m_pDDF[0]->m_bRotate = false;
3080
if (o->m_pDDF[0]->m_bRotate)
3081
{
3082
mprintf(WHITE,"\n Warning: ");
3083
mprintf("This only works if your trajectory time step is small enough to ensure\n");
3084
mprintf(" that the dihedral is never changing more than 180 deg within one step!\n\n");
3085
}
3086
}
3087
if (g_bRDF || g_bADF || g_bVDF || g_bDDF || g_bDipDF)
3088
{
3089
if (AskYesNo(" Create combined development/histogram-plots for 2D analyses (y/n)? [yes] ",true))
3090
{
3091
g_bCombined = true;
3092
o->m_bCombinedPlot = true;
3093
if (AskYesNo(" Use grey tones for combined plot (y) or standard colors (n)? [no] ",false))
3094
{
3095
o->m_bCombinedGreyMode = true;
3096
o->m_iCombinedGreyMin = AskRangeInteger(" Darkest shade of grey to use (0=black, 255=white)? [128] ",0,255,128);
3097
o->m_iCombinedGreyMax = AskRangeInteger(" Lightest shade of grey to use (0=black, 255=white)? [224] ",o->m_iCombinedGreyMin,255,224);
3098
o->m_iCombinedGreyShades = AskUnsignedInteger(" How many different shades of grey to use? [4] ",4);
3099
} else o->m_bCombinedGreyMode = false;
3100
} else o->m_bCombinedPlot = false;
3101
} else o->m_bCombinedPlot = false;
3102
3103
if (((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() > 1)
3104
{
3105
mprintf(" Save development for which rep. of the reference molecule (e.g. 1,3-7)? [1] ");
3106
inpprintf("! Save development for which rep. of the reference molecule (e.g. 1,3-7)? [1]\n");
3107
myget(buf);
3108
if (strlen(buf)==0)
3109
o->m_waSaveRefList.Add(0);
3110
else {
3111
ParseIntList(buf,&o->m_waSaveRefList);
3112
for (z=0;z<o->m_waSaveRefList.GetSize();z++)
3113
o->m_waSaveRefList[z]--;
3114
}
3115
} else o->m_waSaveRefList.Add(0);
3116
if (o->m_iShowMol != -1)
3117
{
3118
if (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize() > 1)
3119
{
3120
mprintf(" Save development for which rep. of the observed molecule (e.g. 1,3-7)? [all] ");
3121
inpprintf("! Save development for which rep. of the observed molecule (e.g. 1,3-7)? [all]\n");
3122
myget(buf);
3123
if (strlen(buf)==0)
3124
{
3125
for (z=0;z<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z++)
3126
o->m_waSaveShowList.Add(z);
3127
} else
3128
{
3129
ParseIntList(buf,&o->m_waSaveShowList);
3130
for (z=0;z<o->m_waSaveShowList.GetSize();z++)
3131
o->m_waSaveShowList[z]--;
3132
}
3133
} else o->m_waSaveShowList.Add(0);
3134
} else o->m_waSaveShowList.Add(0); // Dummy
3135
if ((o->m_waSaveRefList.GetSize() > 1) && (o->m_bOthers))
3136
o->m_bSaveSeparateFiles = AskYesNo(" Developments for different ref. molecules to same (n) or different (y) files? [yes] ",true);
3137
else o->m_bSaveSeparateFiles = false;
3138
if ((g_bCDF) && (g_iCDFChannels == 2))
3139
{
3140
if (AskYesNo(" Generate time development animation (TDO) for CDF (y/n)? [no] ",false))
3141
{
3142
o->m_pCDF->m_bTDAnimation = true;
3143
o->m_pCDF->m_iTDASteps = AskUnsignedInteger(" How many steps should the animation have? [1000] ",1000);
3144
o->m_pCDF->m_iTDAStride = AskUnsignedInteger(" Enter distance between the frames in timesteps: [100] ",50);
3145
o->m_pCDF->m_iTDATail = AskUnsignedInteger(" Enter length of the tail in timesteps: [100] ",100);
3146
o->m_pCDF->m_bTDATrace = AskYesNo(" Show trace (y/n)? [yes] ",true);
3147
o->m_pCDF->m_iTDAResX = AskUnsignedInteger(" Enter width (in pixel) of the TDA images: [640] ",640);
3148
o->m_pCDF->m_iTDAResY = AskUnsignedInteger(" Enter height (in pixel) of the TDA images: [480] ",480);
3149
} else o->m_pCDF->m_bTDAnimation = false;
3150
}
3151
mprintf("\n Saving temporal development for reference molecules ");
3152
for (z=0;z<o->m_waSaveRefList.GetSize();z++)
3153
{
3154
if (z < (int)o->m_waSaveRefList.GetSize()-1)
3155
{
3156
mprintf("%d, ",o->m_waSaveRefList[z]+1);
3157
if (((z+1) % 16) == 0)
3158
mprintf("\n ");
3159
} else mprintf("%d",o->m_waSaveRefList[z]+1);
3160
}
3161
if (o->m_bOthers)
3162
{
3163
mprintf("\n and for observed molecules ");
3164
for (z=0;z<o->m_waSaveShowList.GetSize();z++)
3165
{
3166
if (z < (int)o->m_waSaveShowList.GetSize()-1)
3167
{
3168
mprintf("%d, ",o->m_waSaveShowList[z]+1);
3169
if (((z+1) % 16) == 0)
3170
mprintf("\n ");
3171
} else mprintf("%d",o->m_waSaveShowList[z]+1);
3172
}
3173
}
3174
mprintf(".\n");
3175
mprintf(WHITE,"\n<<< End of Save temporal development <<<\n\n");
3176
} else o->m_bTimeDev = false;
3177
3178
if (g_bAdvanced2)
3179
{
3180
if (AskYesNo(" Create a temporal difference plot for this observation (y/n)? [no] ",false))
3181
{
3182
o->m_bTimeDiff = true;
3183
g_bTimeDiff = true;
3184
o->m_iTimeDiffDepth = AskUnsignedInteger(" Enter temporal depth of this plot in time steps: [1000] ",1000);
3185
o->m_b3DTimeDiff = AskYesNo(" Create also 3D temporal difference plots (y/n)? [yes] ",true);
3186
if (o->m_b3DTimeDiff)
3187
{
3188
tf = 0;
3189
tf2 = 0;
3190
if (g_bRDF)
3191
{
3192
tf = o->m_pRDF[0]->m_fMinDist;
3193
tf2 = o->m_pRDF[0]->m_fMaxDist;
3194
}
3195
if (g_bADF)
3196
{
3197
tf = o->m_pADF[0]->m_fMinAngle;
3198
tf2 = o->m_pADF[0]->m_fMaxAngle;
3199
}
3200
if (g_bDDF)
3201
{
3202
tf = o->m_pDDF[0]->m_fMinAngle;
3203
tf2 = o->m_pDDF[0]->m_fMaxAngle;
3204
}
3205
if (g_bVDF)
3206
{
3207
tf = o->m_pVDF[0]->m_fMinSpeed;
3208
tf2 = o->m_pVDF[0]->m_fMaxSpeed;
3209
}
3210
if (g_bDipDF)
3211
{
3212
tf = o->m_pDipDF[0]->m_fDipoleMin;
3213
tf2 = o->m_pDipDF[0]->m_fDipoleMax;
3214
}
3215
o->m_iTimeDiffStride3D = AskUnsignedInteger(" Take every n-th time step for the tau axis: [%d] ",o->m_iTimeDiffDepth/100,o->m_iTimeDiffDepth/100);
3216
o->m_fTimeDiffMinVal3D = AskFloat(" Enter min. value for the starting point: [%.2f] ",tf,tf);
3217
o->m_fTimeDiffMaxVal3D = AskFloat(" Enter max. value for the starting point: [%.2f] ",tf2,tf2);
3218
o->m_iTimeDiffRes3D = AskUnsignedInteger(" Enter binning resolution for the starting value: [100] ",100);
3219
mprintf("\n Temporal before/after 3D plot:\n");
3220
o->m_iTimeDiffDistSteps= AskUnsignedInteger(" Every how many time steps create a 2D slice (0 to disable): [0] ",0);
3221
o->m_fTimeDiffDistMinValX = AskFloat(" Enter min. value for the starting point: [%.2f] ",tf,tf);
3222
o->m_fTimeDiffDistMaxValX = AskFloat(" Enter max. value for the starting point: [%.2f] ",tf2,tf2);
3223
o->m_iTimeDiffDistResX = AskUnsignedInteger(" Enter binning resolution for the X axis: [100] ",100);
3224
o->m_fTimeDiffDistMinValY = AskFloat(" Enter min. value for the end point: [%.2f] ",tf,tf);
3225
o->m_fTimeDiffDistMaxValY = AskFloat(" Enter max. value for the end point: [%.2f] ",tf2,tf2);
3226
o->m_iTimeDiffDistResY = AskUnsignedInteger(" Enter binning resolution for the Y axis: [100] ",100);
3227
}
3228
mprintf("\n");
3229
} else o->m_bTimeDiff = false;
3230
} else o->m_bTimeDiff = false;
3231
} else
3232
{
3233
o->m_bTimeDev = false;
3234
o->m_bTimeDiff = false;
3235
}
3236
} else
3237
{
3238
o->m_bTimeDev = false;
3239
o->m_bTimeDiff = false;
3240
}
3241
3242
if ((g_iFixMol != -1) && (o->m_iShowMol != -1) && (g_bRDyn || g_bDipDF || g_bMSD || g_bADF || g_bPlDF || g_bLiDF || g_bDDF || g_bVACF || g_bDipACF ||g_bRevSDF || g_bSDF || g_bVHDF || g_bRDF || g_bVDF || g_bFDF || g_bCond))
3243
{
3244
if (g_bCond)
3245
goto _askcond;
3246
if (AskYesNo(" Add a condition to this observation (y/n)? [no] ",false))
3247
{
3248
_askcond:
3249
mprintf(GREEN,"\n>>> Condition input >>>\n\n");
3250
// mprintf("You may enter several sets of conditions. They are connected with \"or\",\nonly one of them needs to apply to take a configuration into account.\n\n");
3251
// mprintf("In each set of conditions, you may enter several conditions. They are connected\nwith \"and\", all of them have to apply to make this set of conditions apply.\n");
3252
3253
if (o->m_bSecondShowMol)
3254
{
3255
if (!AskYesNo(" Add a condition between RM and 1st OM (y/n)? [yes] ",true))
3256
goto _no1stcond;
3257
mprintf(WHITE,"\n *** Input of Condition between RM and 1st OM ***\n\n");
3258
}
3259
3260
try { o->m_pConditions = new CConditionGroup(); } catch(...) { o->m_pConditions = NULL; }
3261
if (o->m_pConditions == NULL) NewException((double)sizeof(CConditionGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3262
3263
o->m_pConditions->m_iShowMol = o->m_iShowMol;
3264
o->m_pConditions->Parse(g_iFixMol,o->m_iShowMol);
3265
_no1stcond:
3266
3267
if (o->m_bSecondShowMol)
3268
{
3269
mprintf("\n");
3270
if (!AskYesNo(" Add a condition between RM and 2nd OM (y/n)? [yes] ",true))
3271
goto _no2ndcond;
3272
mprintf(WHITE,"\n *** Input of Condition between RM and 2nd OM ***\n\n");
3273
3274
try { o->m_pConditionsOM2 = new CConditionGroup(); } catch(...) { o->m_pConditionsOM2 = NULL; }
3275
if (o->m_pConditionsOM2 == NULL) NewException((double)sizeof(CConditionGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3276
3277
o->m_pConditionsOM2->m_iShowMol = o->m_iShowMol2;
3278
o->m_pConditionsOM2->Parse(g_iFixMol,o->m_iShowMol2);
3279
_no2ndcond:;
3280
}
3281
3282
if (o->m_pConditions != NULL)
3283
{
3284
if (o->m_pConditions->m_bInvertCondition)
3285
{
3286
o->m_bBinOnlyNotPassedAtoms = false;
3287
o->m_bBinOnlyPassedAtoms = false;
3288
goto _nobinonly;
3289
}
3290
}
3291
3292
if (o->m_pConditionsOM2 != NULL)
3293
{
3294
if (o->m_pConditionsOM2->m_bInvertCondition)
3295
{
3296
o->m_bBinOnlyNotPassedAtoms = false;
3297
o->m_bBinOnlyPassedAtoms = false;
3298
goto _nobinonly;
3299
}
3300
}
3301
3302
mprintf("\n Normally, TRAVIS evaluates the condition for each RM-OM pair. If the condition\n");
3303
mprintf(" is fulfilled, all atoms from this pair are evaluated. The following question\n");
3304
mprintf(" enables to take into account only exactly the atoms which fulfilled the condition.\n\n");
3305
3306
mprintf(" If you have a distance condition with \"nearest neighbor mode\", only the atom\n");
3307
mprintf(" from the OM that is closest to the RM will be taken into account.\n\n");
3308
3309
o->m_bBinOnlyPassedAtoms = AskYesNo(" Add only atoms to the bin that passed the condition(s) (y/n)? [no] ",false);
3310
/* if (!o->m_bBinOnlyPassedAtoms)
3311
o->m_bBinOnlyNotPassedAtoms = AskYesNo(" Add only atoms to the bin that did NOT pass the condition(s) (y/n)? [no] ",false);
3312
else*/ o->m_bBinOnlyNotPassedAtoms = false;
3313
_nobinonly:
3314
3315
g_bSaveCondSnapshot = AskYesNo(" Save a snapshot every time the conditions are fulfilled (y/n)? [no] ",false);
3316
3317
if (g_bSaveCondSnapshot)
3318
g_bNeedMoleculeWrap = true;
3319
3320
if (g_bSaveCondSnapshot)
3321
{
3322
g_bSaveCondWholeBox = AskYesNo(" Save the whole box (y) or only the RM/OM pair (n)? [no] ",false);
3323
if (g_bSaveCondWholeBox)
3324
mprintf("\n The RM that fulfills the condition will be centered (coordinates 0|0|0).\n");
3325
}
3326
3327
mprintf(GREEN,"\n<<< End of Condition input <<<\n\n");
3328
}
3329
}
3330
3331
if (g_bVACF)
3332
{
3333
mprintf(WHITE,"\n>>> Velocity autocorrelation function >>>\n\n");
3334
3335
try { o->m_pVACF = new CACF(); } catch(...) { o->m_pVACF = NULL; }
3336
if (o->m_pVACF == NULL) NewException((double)sizeof(CACF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3337
3338
o->m_pVACF->m_iShowMol = o->m_iShowMol;
3339
o->m_pVACF->Parse();
3340
mprintf(WHITE,"\n<< End of Velocity autocorrelation function <<<\n\n");
3341
}
3342
3343
/* if (g_bDipACF)
3344
{
3345
mprintf(WHITE,"\n>>> Dipole moment autocorrelation function >>>\n\n");
3346
3347
try { o->m_pDipACF = new CACF(); } catch(...) { o->m_pDipACF = NULL; }
3348
if (o->m_pDipACF == NULL) NewException((double)sizeof(CACF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3349
3350
o->m_pDipACF->Parse();
3351
mprintf(WHITE,"\n<<< End of Dipole moment autocorrelation function <<<\n\n");
3352
}*/
3353
3354
if (g_bUseVelocities)
3355
{
3356
if (g_iFixMol != -1)
3357
o->m_bVelocityRelToRef = (AskRangeInteger(" Use absolute velocities (0) or relative to the reference molecule (1)? [0] ",0,1,0) != 0);
3358
else o->m_bVelocityRelToRef = false;
3359
}
3360
3361
mprintf(YELLOW,"\n<<< End of Observation %d <<<\n",g_oaObserv.GetSize());
3362
3363
if (AskYesNo("\n Add another observation (y/n)? [no] ",false))
3364
goto _nextsdf;
3365
mprintf("\n");
3366
3367
mprintf(WHITE,">>> Observation List >>>\n\n");
3368
for (z2=0;z2<g_oaObserv.GetSize();z2++)
3369
{
3370
mprintf(YELLOW," *** Observation %d\n",z2+1);
3371
o = (CObservation*)g_oaObserv[z2];
3372
3373
if (g_bCond)
3374
mprintf(" - Condition between %s and %s\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName);
3375
3376
if (g_bAggregation)
3377
{
3378
mprintf(" - Aggregation functions - %d value sets:\n",o->m_pDACF->m_oaSubDACFs.GetSize());
3379
for (z3=0;z3<o->m_pDACF->m_oaSubDACFs.GetSize();z3++)
3380
mprintf(" > %s\n",((CDACFSub*)o->m_pDACF->m_oaSubDACFs[z3])->m_sName);
3381
}
3382
3383
if (g_bNbExchange)
3384
{
3385
mprintf(" - Neighborhood exchange functions:\n");
3386
for (z3=0;z3<o->m_pDACF->m_oaSubDACFs.GetSize();z3++)
3387
mprintf(" > %s\n",((CDACFSub*)o->m_pDACF->m_oaSubDACFs[z3])->m_sName);
3388
}
3389
3390
if (g_bRDyn)
3391
mprintf(" - Reorientation Dynamics: %s\n",o->m_pRDyn->m_sName);
3392
3393
if (g_bIRSpec)
3394
mprintf(" - IR Spectrum: %s\n",o->m_pIRSpec->m_sName);
3395
3396
if (g_bDens)
3397
mprintf(" - Density DF: %s\n",o->m_pDensityDF->m_sName);
3398
3399
if (g_bSDF)
3400
mprintf(" - SDF: %s\n",o->m_pSDF->m_sName);
3401
3402
if (g_bRevSDF)
3403
mprintf(" - Pseudo SDF: %s\n",o->m_pRevSDF->m_sName);
3404
3405
if (g_bNbAnalysis)
3406
mprintf(" - Neighborhood Analysis: %s\n",o->m_pNbAnalysis->m_sName);
3407
3408
if (g_bVACF)
3409
mprintf(" - VACF: %s\n",o->m_pVACF->m_sName);
3410
3411
if (g_bMSD)
3412
mprintf(" - MSD: %s\n",o->m_pMSD->m_sName);
3413
3414
if (g_bVHDF)
3415
mprintf(" - VHDF: %s\n",o->m_pVHDF->m_sName);
3416
3417
if (g_bCDF)
3418
{
3419
mprintf(" - Combined Distribution Function:\n");
3420
for (z3=0;z3<g_iCDFChannels;z3++)
3421
{
3422
if (o->m_pRDF[z3] != NULL)
3423
mprintf(" - Channel %d: RDF: %s\n",z3+1,o->m_pRDF[z3]->m_sName);
3424
if (o->m_pADF[z3] != NULL)
3425
mprintf(" - Channel %d: ADF: %s\n",z3+1,o->m_pADF[z3]->m_sName);
3426
if (o->m_pDDF[z3] != NULL)
3427
mprintf(" - Channel %d: DDF: %s\n",z3+1,o->m_pDDF[z3]->m_sName);
3428
if (o->m_pDipDF[z3] != NULL)
3429
mprintf(" - Channel %d: DipDF: %s\n",z3+1,o->m_pDipDF[z3]->m_sName);
3430
if (o->m_pVDF[z3] != NULL)
3431
mprintf(" - Channel %d: VDF: %s\n",z3+1,o->m_pVDF[z3]->m_sName);
3432
if (o->m_pPlDF[z3] != NULL)
3433
mprintf(" - Channel %d: PlDF: %s\n",z3+1,o->m_pPlDF[z3]->m_sName);
3434
if (o->m_pLiDF[z3] != NULL)
3435
mprintf(" - Channel %d: LiDF: %s\n",z3+1,o->m_pLiDF[z3]->m_sName);
3436
}
3437
} else
3438
{
3439
if (g_bRDF)
3440
mprintf(" - RDF: %s\n",o->m_pRDF[0]->m_sName);
3441
if (g_bDipDF)
3442
mprintf(" - DipDF: %s\n",o->m_pDipDF[0]->m_sName);
3443
if (g_bADF)
3444
mprintf(" - ADF: %s\n",o->m_pADF[0]->m_sName);
3445
if (g_bDDF)
3446
mprintf(" - DDF: %s\n",o->m_pDDF[0]->m_sName);
3447
if (g_bVDF)
3448
mprintf(" - VDF: %s\n",o->m_pVDF[0]->m_sName);
3449
if (g_bPlDF)
3450
mprintf(" - PlDF: %s\n",o->m_pPlDF[0]->m_sName);
3451
if (g_bLiDF)
3452
mprintf(" - LiDF: %s\n",o->m_pLiDF[0]->m_sName);
3453
}
3454
}
3455
mprintf(WHITE,"\n<<< End of Observation List <<<\n\n");
3456
}
3457
_endobs:
3458
3459
if (g_bVACF && g_bGlobalVACF)
3460
{
3461
try { g_pGlobalVACF = new CACF(); } catch(...) { g_pGlobalVACF = NULL; }
3462
if (g_pGlobalVACF == NULL) NewException((double)sizeof(CACF),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3463
3464
mprintf(WHITE,"\n>>> Global velocity autocorrelation function >>>\n\n");
3465
g_pGlobalVACF->Parse();
3466
mprintf(WHITE,"\n<<< End of global velocity autocorrelation function <<<\n\n");
3467
}
3468
3469
if (g_bIRSpec && g_bGlobalIR)
3470
{
3471
try { g_pGlobalIR = new CReorDyn(); } catch(...) { g_pGlobalIR = NULL; }
3472
if (g_pGlobalIR == NULL) NewException((double)sizeof(CReorDyn),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3473
3474
mprintf(WHITE,"\n*** Definition of system-wide IR spectrum ***\n\n");
3475
g_pGlobalIR->ParseSpec();
3476
}
3477
3478
if (g_bSDF || g_bVoidSDF || g_bCreateRevSDF)
3479
{
3480
g_iSDFSmoothGrade = AskInteger(" Up to which degree should the SDFs be smoothened (0=not at all)? [3] ",3);
3481
3482
if (g_bSDF)
3483
{
3484
_sdf_norm_again:
3485
g_bSDFUniform = AskYesNo(" Calculate SDF values in nm^-3 (n) or relative to uniform density (y)? [no] ",false);
3486
if (g_bSDFUniform && ((!g_bPeriodicX) || (!g_bPeriodicY) || (!g_bPeriodicZ)))
3487
{
3488
eprintf("\n Error: Uniform particle density is only defined for XYZ-periodic systems.\n\n");
3489
goto _sdf_norm_again;
3490
}
3491
}
3492
// g_iSDFScale = AskRangeInteger(" SDF values in ppm (1), pm^-3 (2), nm^-3 (3) or rel. to uniform density (4)? [4] ",1,4,4) - 1;
3493
// g_iSDFScale = 2; // nm^-3
3494
} else if (g_bCDF && (g_iCDFChannels == 3))
3495
g_iSDFSmoothGrade = AskInteger(" Up to which degree should the 3D CDFs be smoothened (0=not at all)? [3] ",3);
3496
3497
// if (g_bVDF || g_bSVDF)
3498
// g_bSaveVelForce = AskYesNo(" Save maximum/averaged velocity time development (y/n)? [yes] ",true);
3499
3500
// if (g_bVDF || g_bFDF)
3501
// {
3502
// g_fVelPercentage = AskFloat(" Which percentage of all velocities/forces to take into account? [95] ",95.0f);
3503
// g_fForcePercentage = g_fVelPercentage;
3504
// }
3505
g_bSaveVelForce = false;
3506
3507
if ((g_bSDF && g_bAdvanced2) || g_bSaveRefEnv || g_bCutCluster || g_bSaveJustTraj)
3508
{
3509
mprintf(WHITE,"\n>>> Coordinate output options >>>\n\n");
3510
3511
if (g_bAdvanced2)
3512
g_bWriteAtomwise = (AskRangeInteger(" Sort output coordinates after molecules (0) or after elements (1)? [molecules] ",0,1,0)!=0);
3513
else g_bWriteAtomwise = false;
3514
3515
g_bSaveVirtAtoms = AskYesNo(" Save also virtual atoms (y/n)? [no] ",false);
3516
3517
if (g_bSaveVirtAtoms)
3518
{
3519
if (AskYesNo(" Ref.Env.: Use alias names (instead of #) for virtual atoms (y/n)? [no] ",false))
3520
{
3521
for (z2=0;z2<g_oaMolecules.GetSize();z2++)
3522
{
3523
CMolecule *m = (CMolecule*)g_oaMolecules[z2];
3524
for (z=0;z<m->m_baAtomIndex.GetSize();z++)
3525
{
3526
if (m->m_baAtomIndex[z] != g_iVirtAtomType)
3527
continue;
3528
for (z3=0;z3<m->m_waAtomCount[z];z3++)
3529
{
3530
mprintf(" How to name atom #%d in %s? [#%d] ",z3+1,m->m_sName,z3+1);
3531
inpprintf("! How to name atom #%d in %s? [#%d]\n",z3+1,m->m_sName,z3+1);
3532
myget(buf);
3533
if (strlen(buf) != 0)
3534
strcpy(((CVirtualAtom*)g_oaVirtualAtoms[m->m_laVirtualAtoms[z3]])->m_sLabel,buf);
3535
}
3536
}
3537
}
3538
}
3539
}
3540
3541
if (g_bSaveRefEnv || g_bCutCluster)
3542
g_bEnvWriteDetailedInfo = AskYesNo(" Write detailed (long) comment lines into output xyz file (y/n)? [yes] ",true);
3543
else g_bEnvWriteDetailedInfo = false;
3544
3545
if ((g_bSaveRefEnv || g_bCutCluster) && !g_bEnvDisableSortNb)
3546
g_bEnvSortNb = AskYesNo(" Sort molecules according to distance from reference molecule (y/n)? [yes] ",true);
3547
else g_bEnvSortNb = false;
3548
3549
mprintf(WHITE,"\n<<< End of Coordinate output options <<<\n\n");
3550
} else
3551
{
3552
g_bWriteAtomwise = false;
3553
g_bSaveVirtAtoms = false;
3554
}
3555
3556
if (g_bSaveRefEnv || g_bCutCluster)
3557
g_bCenterZero = AskYesNo(" Put the center of the system to (0|0|0) (y) or to (x/2|y/2|z/2) (n)? [yes] ",true);
3558
3559
g_bMiddleAvg = false;
3560
g_iSwapAtoms = 0;
3561
3562
if (g_bSaveJustTraj)
3563
{
3564
mprintf(WHITE,"\n>>> Process Trajectory >>>\n\n");
3565
3566
if (g_bAdvanced2)
3567
g_bSaveTrajNoRot = AskYesNo(" Remove angular momentum from trajectory (y/n)? [no] ",false);
3568
else g_bSaveTrajNoRot = false;
3569
3570
if (g_bSaveTrajNoRot)
3571
{
3572
mprintf("\n This centers the mass center of the system. All atoms of the system are saved.\n\n");
3573
g_bSaveCoordsUnchanged = false;
3574
g_bSaveJustCenter = false;
3575
if(AskYesNo(" Put the center of the system to (0|0|0) (y) or to (x/2|y/2|z/2) (n)? [yes] ",true))
3576
g_bCenterZero = true;
3577
else g_bCenterZero = false;
3578
goto _norot;
3579
} else
3580
{
3581
switch(AskRangeInteger(" Put the center of the system to (0|0|0) (0), to (x/2|y/2|z/2) (1), or leave coords unchanged (2)? [1] ",0,2,1))
3582
{
3583
case 0:
3584
g_bCenterZero = true;
3585
g_bSaveCoordsUnchanged = false;
3586
break;
3587
case 1:
3588
g_bCenterZero = false;
3589
g_bSaveCoordsUnchanged = false;
3590
break;
3591
case 2:
3592
g_bSaveCoordsUnchanged = true;
3593
break;
3594
}
3595
3596
if (!g_bSaveCoordsUnchanged)
3597
g_bSaveJustCenter = AskYesNo("\n Put a specific atom into the box center (y/n)? [no] ",false);
3598
else g_bSaveJustCenter = false;
3599
}
3600
3601
if (g_bSaveJustCenter)
3602
{
3603
if (g_oaMolecules.GetSize() > 1)
3604
{
3605
sprintf(buf," Choose center atom from which of the molecules (");
3606
for (z=0;z<g_oaMolecules.GetSize();z++)
3607
{
3608
sprintf(buf2,"%s=%d",((CMolecule*)g_oaMolecules[z])->m_sName,z+1);
3609
strcat(buf,buf2);
3610
if (z < g_oaMolecules.GetSize()-1)
3611
strcat(buf,", ");
3612
}
3613
strcat(buf,")? ");
3614
g_iSaveJustMol = AskRangeInteger_ND(buf,1,g_oaMolecules.GetSize()) - 1;
3615
} else
3616
{
3617
g_iSaveJustMol = 0;
3618
mprintf(" Choosing center atom from %s.\n",((CMolecule*)g_oaMolecules[0])->m_sName);
3619
}
3620
if (((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_laSingleMolIndex.GetSize() > 1)
3621
g_iSaveJustSM = AskRangeInteger(" Take which representant from %s (1-%d)? [1] ",1,((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_laSingleMolIndex.GetSize(),1,((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_sName,((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_laSingleMolIndex.GetSize()) - 1;
3622
else g_iSaveJustSM = 0;
3623
_proccenter:
3624
AskString(" Which atom from %s %d to put into the box center? [#2] ",buf,"#2",((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_sName,g_iSaveJustSM+1);
3625
if (!ParseAtom(buf,g_iSaveJustMol,g_iSaveJustAtomType,g_iSaveJustRealAtomType,g_iSaveJustAtom))
3626
goto _proccenter;
3627
}
3628
g_iSaveGesAtoms = 0;
3629
if (!AskYesNo(" Save all atoms in the system (y/n)? [yes] ",true))
3630
{
3631
mprintf("\n");
3632
for (z=0;z<g_oaMolecules.GetSize();z++)
3633
{
3634
if (AskYesNo(" Save (some/all) atoms from molecule %s (y/n)? [yes] ",true,((CMolecule*)g_oaMolecules[z])->m_sName))
3635
{
3636
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3637
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3638
3639
g_oaSaveMolecules.Add(ag);
3640
_savejust1: mprintf(" Which atoms to save from %s (e.g. \"C1,C3-5,H\")? [all] ",((CMolecule*)g_oaMolecules[z])->m_sName);
3641
inpprintf("! Which atoms to save from %s (e.g. \"C1,C3-5,H\")? [all]\n",((CMolecule*)g_oaMolecules[z])->m_sName);
3642
myget(buf);
3643
if (strlen(buf)==0)
3644
ag->AddAllAtoms((CMolecule*)g_oaMolecules[z],g_bSaveVirtAtoms);
3645
else if (!ag->ParseAtoms((CMolecule*)g_oaMolecules[z],buf))
3646
goto _savejust1;
3647
g_iSaveGesAtoms += ag->m_iAtomGes * ((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();
3648
}
3649
}
3650
} else
3651
{
3652
_norot:
3653
for (z=0;z<g_oaMolecules.GetSize();z++)
3654
{
3655
try { ag = new CAtomGroup(); } catch(...) { ag = NULL; }
3656
if (ag == NULL) NewException((double)sizeof(CAtomGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3657
3658
g_oaSaveMolecules.Add(ag);
3659
ag->AddAllAtoms((CMolecule*)g_oaMolecules[z],g_bSaveVirtAtoms);
3660
g_iSaveGesAtoms += ag->m_iAtomGes * ((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();
3661
}
3662
}
3663
3664
if (g_bUnknownElements)
3665
{
3666
g_bUnwrapWannier = AskYesNo(" Write out Wannier centers together with trajectory (y/n)? [no] ",false);
3667
3668
if (g_bUnwrapWannier)
3669
ParseDipole();
3670
3671
} else g_bUnwrapWannier = false;
3672
3673
if ((!g_bSaveCoordsUnchanged) && (!g_bSaveTrajNoRot))
3674
g_bUnwrap = AskYesNo(" Try to unwrap the trajectory (y/n)? [no] ",false);
3675
else g_bUnwrap = false;
3676
3677
if (g_bUnwrap)
3678
mprintf("\n Attention! This feature only works if the time step\n in the trajectory is quite small. One particle may never\n move further than half of the box length in one time step!\n");
3679
3680
mprintf("\nSaving %d atoms per step:\n",g_iSaveGesAtoms);
3681
for (z2=0;z2<g_oaSaveMolecules.GetSize();z2++)
3682
{
3683
ag = (CAtomGroup*)g_oaSaveMolecules[z2];
3684
mprintf(" - In %s: ",ag->m_pMolecule->m_sName);
3685
for (z=0;z<ag->m_baAtomType.GetSize();z++)
3686
{
3687
for (z3=0;z3<((CxIntArray*)ag->m_oaAtoms[z])->GetSize();z3++)
3688
{
3689
mprintf("%s%d",((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z]])->m_sName,((CxIntArray*)ag->m_oaAtoms[z])->GetAt(z3)+1);
3690
if (z3 < ((CxIntArray*)ag->m_oaAtoms[z])->GetSize()-1)
3691
mprintf(", ");
3692
}
3693
if (z+1 < ag->m_baAtomType.GetSize())
3694
mprintf(", ");
3695
}
3696
mprintf("\n");
3697
}
3698
// g_bTrajAtomwise = (AskRangeInteger("\n Save trajectory ordered molecule-wise (0) or atom-wise (1)? [0] ",0,1,0)!=0);
3699
mprintf(WHITE,"\n<<<< End of Process Trajectory <<<\n\n");
3700
} else g_bUnwrap = false;
3701
3702
if (g_bUnwrap)
3703
{
3704
g_vaUnwrapArray.SetSize(g_oaSingleMolecules.GetSize());
3705
for (z=0;z<g_vaUnwrapArray.GetSize();z++)
3706
g_vaUnwrapArray[z] = 0;
3707
}
3708
3709
if (g_bReact)
3710
{
3711
try { g_pReact = new CReact(); } catch(...) { g_pReact = NULL; }
3712
if (g_pReact == NULL) NewException((double)sizeof(CReact),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3713
3714
g_pReact->Parse();
3715
g_bFold = false;
3716
// g_bSilentProgress = true;
3717
}
3718
3719
g_iBinning = 2;
3720
3721
if (g_bPeriodic && (g_bSDF || g_bSaveRefEnv || g_bCutCluster || g_bRevSDF) && (!g_bUnwrap))
3722
{
3723
g_bFold = true;
3724
mprintf("\n Wrapping molecules into the box.\n");
3725
} else if (g_bSaveJustTraj && !g_bSaveTrajNoRot && !g_bUnwrap)
3726
{
3727
if (g_bPeriodic && (!g_bUnwrap) && (!g_bSaveCoordsUnchanged))
3728
{
3729
g_bFold = AskYesNo("\n Wrap the molecules into the box (y/n)? [yes] ",true);
3730
} else
3731
{
3732
mprintf("\n Not wrapping molecules into the box.\n");
3733
g_bFold = false;
3734
}
3735
} else
3736
{
3737
g_bFold = false;
3738
mprintf("\n Not wrapping molecules into the box.\n");
3739
}
3740
3738
g_bWriteAtomwise = false;
3739
g_bWriteInputOrder = true;
3740
break;
3741
default:
3742
eprintf("Should never happen ^^\n");
3743
abort();
3744
}
3745
} else
3746
{
3747
g_bWriteAtomwise = (AskRangeInteger(" Sort output coordinates by molecules (0) or by element types (1)? [0] ",0,1,0)!=0);
3748
g_bWriteInputOrder = false;
3749
}
3750
} else
3751
{
3752
g_bWriteAtomwise = false;
3753
g_bWriteInputOrder = false;
3754
}
3755
3756
mprintf(WHITE,"\n<<<< End of Process Trajectory <<<\n\n");
3757
} else g_bUnwrap = false;
3758
3759
if (g_bUnwrap)
3760
{
3761
g_vaUnwrapArray.SetSize(g_oaSingleMolecules.GetSize());
3762
for (z=0;z<g_vaUnwrapArray.GetSize();z++)
3763
g_vaUnwrapArray[z] = 0;
3764
}
3765
3766
if (g_bReact)
3767
{
3768
try { g_pReact = new CReact(); } catch(...) { g_pReact = NULL; }
3769
if (g_pReact == NULL) NewException((double)sizeof(CReact),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3770
3771
g_pReact->Parse();
3772
g_bFold = false;
3773
// g_bSilentProgress = true;
3774
}
3775
3776
g_iBinning = 2;
3777
3778
if (g_bPeriodic && (g_bSDF || g_bPlProj || g_bSaveRefEnv || g_bCutCluster || g_bRevSDF) && (!g_bUnwrap))
3779
{
3780
g_bFold = true;
3781
// mprintf("\n Wrapping molecules into the box.\n");
3782
} else if (g_bSaveJustTraj && !g_bSaveTrajNoRot && !g_bUnwrap)
3783
{
3784
if (g_bPeriodic && (!g_bUnwrap) && (!g_bSaveCoordsUnchanged))
3785
{
3786
g_bFold = AskYesNo("\n Wrap the molecules into the box (y/n)? [yes] ",true);
3787
} else
3788
{
3789
// mprintf("\n Not wrapping molecules into the box.\n");
3790
g_bFold = false;
3791
}
3792
} else
3793
{
3794
g_bFold = false;
3795
// mprintf("\n Not wrapping molecules into the box.\n");
3796
}
3797
3741
3798
if (g_bAdvanced2 && g_bFold)
3742
g_bFoldAtomwise = (AskRangeInteger(" Wrap molecule-wise (0) or atom-wise (1)? [0] ",0,1,0)!=0);
3743
else g_bFoldAtomwise = false;
3744
3745
if (g_bMSD || g_bPairMSD || g_bSaveJustTraj || g_bACF || (g_bIRSpec && g_bDipoleRefFixed) || g_bVHDF/* || g_bThermo*/)
3746
{
3747
if (g_bUnwrap)
3748
g_bRemoveCOM = AskYesNo(" Remove center of mass movement of the MD box (y/n)? [no] ",false);
3749
else g_bRemoveCOM = AskYesNo(" Remove center of mass movement of the MD box (y/n)? [yes] ",true);
3750
} else g_bRemoveCOM = false;
3751
3752
if (g_bUseVelocities && (g_fTimestepLength > 1.0))
3753
{
3754
mprintf(RED,"\n Warning: ");
3755
mprintf("Atom velocities are obtained from positions by numerical differentiation.\n");
3756
mprintf(" This is only reliable for trajectory timestep distances <= approx. 1 fs.\n");
3757
mprintf(" Your timestep distance is %.2f fs, which is larger than 1 fs.\n\n",g_fTimestepLength);
3758
3759
if (!AskYesNo(" Proceed anyway (y/n)? [yes] ",true))
3760
return false;
3761
}
3762
3763
if (g_TimeStep.GetCommentNumberCount() > 0)
3764
{
3765
g_bSkipDoubleSteps = AskYesNo(" Skip repeated time steps (y/n)? [no] ",false);
3766
if (g_bSkipDoubleSteps)
3767
{
3768
mprintf("\n");
3769
mprintf(" The comment line is \"%s\".\n",g_TimeStep.m_pComment);
3770
if (g_TimeStep.GetCommentNumberCount() > 1)
3771
{
3772
if (!AskYesNo(" Does this line contain the time step number (y/n)? [yes] ",true))
3773
g_bSkipDoubleSteps = false;
3774
if (g_bSkipDoubleSteps)
3775
{
3776
sprintf(buf," Choose the time step number: ");
3777
for (z=0;z<g_TimeStep.GetCommentNumberCount();z++)
3778
if (z < g_TimeStep.GetCommentNumberCount()-1)
3779
{
3780
sprintf(buf2,"%ld (%d), ",g_TimeStep.ExtractNumber(z),z+1);
3781
strcat(buf,buf2);
3782
} else
3783
{
3784
sprintf(buf2,"%ld (%d)",g_TimeStep.ExtractNumber(z),z+1);
3785
strcat(buf,buf2);
3786
}
3787
strcat(buf," [1] ");
3788
g_iNumberPos = AskRangeInteger(buf,1,g_TimeStep.GetCommentNumberCount(),1) - 1;
3789
} else
3790
{
3791
if (!AskYesNo(" Is %d the time step number of the first time step (y/n)? [yes] ",true,g_TimeStep.ExtractNumber(0)))
3792
g_bSkipDoubleSteps = false;
3793
}
3794
if (!g_bSkipDoubleSteps)
3795
mprintf(" NOT skipping repeated time steps.\n");
3796
}
3797
mprintf("\n");
3798
}
3799
}
3800
3801
if (g_bAdvanced2)
3802
{
3803
if (AskYesNo(" Perform a multi-interval analysis (y/n)? [no] ",false))
3804
{
3805
g_bMultiInterval = true;
3806
if (AskYesNo(" Use equidistant intervals (y) or enter data manually (n)? [yes] ",true))
3807
{
3808
g_iMultiIntervalBegin = AskUnsignedInteger(" In which time step to start processing the trajectory? [1] ",1) - 1;
3809
if (g_iMultiIntervalBegin == -1)
3810
g_iMultiIntervalBegin = 0;
3811
ti = AskUnsignedInteger(" How many intervals to create? [5] ",5);
3812
if (g_iTrajSteps != -1)
3813
{
3814
g_iMultiIntervalStride = AskUnsignedInteger(" Start a new interval each n-th step? [%d] ",g_iTrajSteps/ti,g_iTrajSteps/ti);
3815
g_iMultiIntervalLength = AskUnsignedInteger(" Enter the length in steps of one interval: [%d] ",g_iTrajSteps/ti,g_iTrajSteps/ti);
3816
} else
3817
{
3818
g_iMultiIntervalStride = AskUnsignedInteger(" Start a new interval each n-th step? [%d] ",10000/ti,10000/ti);
3819
g_iMultiIntervalLength = AskUnsignedInteger(" Enter the length in steps of one interval: [%d] ",10000/ti,10000/ti);
3820
}
3821
for (z=0;z<ti;z++)
3822
{
3823
g_laMultiIntervalStart.Add(g_iMultiIntervalBegin+z*g_iMultiIntervalStride);
3824
g_laMultiIntervalEnd.Add(g_iMultiIntervalBegin+z*g_iMultiIntervalStride+g_iMultiIntervalLength);
3825
}
3826
} else
3827
{
3828
_intervalagain:
3829
ti = AskInteger(" Enter starting time step of %d. interval: [quit] ",-1,g_laMultiIntervalStart.GetSize()+1);
3830
if (ti == 0)
3831
{
3832
eprintf("Please enter a number >= 1.\n");
3833
goto _intervalagain;
3834
}
3835
if (ti != -1)
3836
{
3837
g_laMultiIntervalStart.Add(ti-1);
3838
g_laMultiIntervalEnd.Add(AskUnsignedInteger_ND(" Enter ending time step of %d. interval: ",g_laMultiIntervalStart.GetSize())-1);
3839
goto _intervalagain;
3840
}
3841
}
3842
mprintf(WHITE,"\n* %d Intervals have been defined:\n",g_laMultiIntervalStart.GetSize());
3843
for (z=0;z<g_laMultiIntervalStart.GetSize();z++)
3844
mprintf(" - Interval %2d: Steps %6d - %6d.\n",z+1,g_laMultiIntervalStart[z]+1,g_laMultiIntervalEnd[z]+1);
3845
mprintf("\n");
3846
} else goto _nomulti;
3847
} else
3848
{
3849
_nomulti:
3850
g_iBeginStep = AskUnsignedInteger(" In which time step to start processing the trajectory? [1] ",1) - 1;
3851
if (g_iBeginStep == -1)
3852
g_iBeginStep = 0;
3853
g_iMaxStep = AskUnsignedInteger(" How many time steps to use (from this position on)? [all] ",0);
3854
if (g_iMaxStep == 0)
3855
g_iMaxStep = -1; // Alle verwenden
3856
}
3857
g_iStride = AskUnsignedInteger(" Use every n-th time step from the trajectory? [1] ",1);
3858
3859
if (g_iTrajSteps != -1)
3860
{
3861
if (g_iMaxStep == -1)
3862
mprintf(YELLOW,"\n Using %d time steps: Every %d%s within range %d - approx. %d.\n",(g_iTrajSteps-g_iBeginStep)/g_iStride,g_iStride,(g_iStride==1)?"st":"th",g_iBeginStep+1,g_iTrajSteps);
3863
else mprintf(YELLOW,"\n Using %d time steps: Every %d%s within range %d - %d.\n",g_iMaxStep/g_iStride,g_iStride,(g_iStride==1)?"st":"th",g_iBeginStep+1,g_iBeginStep+g_iMaxStep);
3864
} else if (g_iMaxStep != -1)
3865
mprintf(YELLOW,"\n Using %d time steps: Every %d%s within range %d - %d.\n",g_iMaxStep/g_iStride,g_iStride,(g_iStride==1)?"st":"th",g_iBeginStep+1,g_iBeginStep+g_iMaxStep);
3866
else mprintf(YELLOW,"\n Using every %d%s time step beginning from step %d.\n",g_iStride,(g_iStride==1)?"st":"th",g_iBeginStep+1);
3867
3868
ti = -1;
3869
if (g_iTrajSteps != -1)
3870
{
3871
if (g_iMaxStep == -1)
3872
ti = (g_iTrajSteps-g_iBeginStep)/g_iStride;
3873
else ti = g_iMaxStep/g_iStride;
3874
} else if (g_iMaxStep != -1)
3875
ti = g_iMaxStep/g_iStride;
3876
3877
if (ti >= 0)
3878
{
3879
if (g_bMSD)
3880
{
3881
for (z=0;z<g_oaObserv.GetSize();z++)
3882
{
3883
o = (CObservation*)g_oaObserv[z];
3884
if (o->m_pMSD->m_iResolution > ti)
3885
{
3886
eprintf("\n MSD resolution of %d requires at least %d time steps, but using only %d steps.\n This will lead to erroneous results!\n\n",o->m_pMSD->m_iResolution,o->m_pMSD->m_iResolution,ti);
3887
if (!AskYesNo(" Continue anyway (y/n)? [yes] ",true))
3888
return false;
3889
goto _lessstepdone;
3890
}
3891
}
3892
}
3893
if (g_bRDyn)
3894
{
3895
for (z=0;z<g_oaObserv.GetSize();z++)
3896
{
3897
o = (CObservation*)g_oaObserv[z];
3898
if (o->m_pRDyn->m_iDepth*o->m_pRDyn->m_iStride > ti)
3899
{
3900
eprintf("\n Reorientation dynamics resolution of %d requires at least %d time steps, but using only %d steps.\n This will lead to erroneous results!\n\n",o->m_pRDyn->m_iDepth*o->m_pRDyn->m_iStride,o->m_pRDyn->m_iDepth*o->m_pRDyn->m_iStride,ti);
3901
if (!AskYesNo(" Continue anyway (y/n)? [yes] ",true))
3902
return false;
3903
goto _lessstepdone;
3904
}
3905
}
3906
}
3907
if (g_bIRSpec)
3908
{
3909
for (z=0;z<g_oaObserv.GetSize();z++)
3910
{
3911
o = (CObservation*)g_oaObserv[z];
3912
if (o->m_pIRSpec->m_iDepth*o->m_pIRSpec->m_iStride > ti)
3913
{
3914
eprintf("\n IR spectrum resolution of %d requires at least %d time steps, but using only %d steps.\n This will lead to erroneous results!\n\n",o->m_pIRSpec->m_iDepth*o->m_pIRSpec->m_iStride,o->m_pIRSpec->m_iDepth*o->m_pIRSpec->m_iStride,ti);
3915
if (!AskYesNo(" Continue anyway (y/n)? [yes] ",true))
3916
return false;
3917
goto _lessstepdone;
3918
}
3919
}
3920
}
3921
}
3922
_lessstepdone:
3923
3924
if (g_bScanVelocities)
3925
{
3926
mprintf(WHITE,"\n>>> Velocity Pre-Analysis >>>\n\n");
3927
g_iScanVelStart = AskUnsignedInteger(" Start in which time step for velocity pre-analysis? [0] ",0);
3928
g_iScanVelSteps = AskUnsignedInteger(" Use how many time steps from this point on for vel. pre-analysis? [all] ",0);
3929
g_iScanVelStride = AskUnsignedInteger(" Use every n-th step for velocity pre-analysis? [10] ",10);
3930
mprintf(WHITE,"\n<<< End of Velocity Pre-Analysis <<<\n");
3931
}
3932
3933
if (g_bSaveRefEnv && (g_iNbhMode == 3))
3934
{
3935
mprintf(WHITE,"\n>>> Neighborhood Pre-Analysis >>>\n\n");
3936
g_iScanNbhStart = AskUnsignedInteger(" Start in which time step for neighborhood analysis? [0] ",0);
3937
g_iScanNbhSteps = AskUnsignedInteger(" Use how many time steps from this point on for nbh analysis? [all] ",0);
3938
g_iScanNbhStride = AskUnsignedInteger(" Use every n-th step for the neighborhood analysis? [10] ",10);
3939
mprintf(WHITE,"\n<<< End of Neighborhood Pre-Analysis <<<\n");
3940
}
3941
3942
mprintf(WHITE,"\n########## All information collected ##########\n\n");
3943
BTOUT;
3944
return true;
3945
}
3946
3947
3799
{
3800
if (g_bSDF || g_bPlProj)
3801
g_bFoldAtomwise = (AskRangeInteger(" Wrap molecule-wise (0) or atom-wise (1)? [1] ",0,1,1)!=0);
3802
else
3803
g_bFoldAtomwise = (AskRangeInteger(" Wrap molecule-wise (0) or atom-wise (1)? [0] ",0,1,0)!=0);
3804
} else
3805
{
3806
if (g_bSDF || g_bPlProj)
3807
g_bFoldAtomwise = true;
3808
else
3809
g_bFoldAtomwise = false;
3810
}
3811
3812
if (g_bFold)
3813
{
3814
if (g_bFoldAtomwise)
3815
mprintf("\n Wrapping molecules into the box (atom-wise).\n\n");
3816
else mprintf("\n Wrapping molecules into the box (molecule-wise).\n\n");
3817
} else mprintf("\n Not wrapping molecules into the box.\n\n");
3818
3819
if (g_bMSD || g_bPairMSD || g_bSaveJustTraj || g_bACF || (g_bIRSpec && g_bDipoleRefFixed) || g_bVHDF/* || g_bThermo*/)
3820
{
3821
if (g_bUnwrap)
3822
g_bRemoveCOM = AskYesNo(" Remove center of mass movement of the box (y/n)? [no] ",false);
3823
else g_bRemoveCOM = AskYesNo(" Remove center of mass movement of the box (y/n)? [yes] ",true);
3824
mprintf("\n");
3825
} else
3826
{
3827
mprintf(" Not removing center of mass movement of the box.\n\n");
3828
g_bRemoveCOM = false;
3829
}
3830
3831
if (g_bUseVelocities && (g_fTimestepLength > 1.0))
3832
{
3833
mprintf(RED," Warning: ");
3834
mprintf("Atom velocities are obtained from positions by numerical differentiation.\n");
3835
mprintf(" This is only reliable for trajectory timestep distances <= approx. 1 fs.\n");
3836
mprintf(" Your timestep distance is %.2f fs, which is larger than 1 fs.\n\n",g_fTimestepLength);
3837
3838
if (!AskYesNo(" Proceed anyway (y/n)? [yes] ",true))
3839
return false;
3840
}
3841
3842
if (g_TimeStep.GetCommentNumberCount() > 0)
3843
{
3844
g_bSkipDoubleSteps = AskYesNo(" Skip repeated time steps (y/n)? [no] ",false);
3845
if (g_bSkipDoubleSteps)
3846
{
3847
mprintf("\n");
3848
mprintf(" The comment line is \"%s\".\n",g_TimeStep.m_pComment);
3849
if (g_TimeStep.GetCommentNumberCount() > 1)
3850
{
3851
if (!AskYesNo(" Does this line contain the time step number (y/n)? [yes] ",true))
3852
g_bSkipDoubleSteps = false;
3853
if (g_bSkipDoubleSteps)
3854
{
3855
sprintf(buf," Choose the time step number: ");
3856
for (z=0;z<g_TimeStep.GetCommentNumberCount();z++)
3857
if (z < g_TimeStep.GetCommentNumberCount()-1)
3858
{
3859
sprintf(buf2,"%ld (%d), ",g_TimeStep.ExtractNumber(z),z+1);
3860
strcat(buf,buf2);
3861
} else
3862
{
3863
sprintf(buf2,"%ld (%d)",g_TimeStep.ExtractNumber(z),z+1);
3864
strcat(buf,buf2);
3865
}
3866
strcat(buf," [1] ");
3867
g_iNumberPos = AskRangeInteger(buf,1,g_TimeStep.GetCommentNumberCount(),1) - 1;
3868
} else
3869
{
3870
if (!AskYesNo(" Is %d the time step number of the first time step (y/n)? [yes] ",true,g_TimeStep.ExtractNumber(0)))
3871
g_bSkipDoubleSteps = false;
3872
}
3873
if (!g_bSkipDoubleSteps)
3874
mprintf(" NOT skipping repeated time steps.\n");
3875
}
3876
mprintf("\n");
3877
}
3878
}
3879
3880
if (g_bAdvanced2)
3881
{
3882
if (AskYesNo(" Perform a multi-interval analysis (y/n)? [no] ",false))
3883
{
3884
g_bMultiInterval = true;
3885
if (AskYesNo(" Use equidistant intervals (y) or enter data manually (n)? [yes] ",true))
3886
{
3887
g_iMultiIntervalBegin = AskUnsignedInteger(" In which time step to start processing the trajectory? [1] ",1) - 1;
3888
if (g_iMultiIntervalBegin == -1)
3889
g_iMultiIntervalBegin = 0;
3890
ti = AskUnsignedInteger(" How many intervals to create? [5] ",5);
3891
if (g_iTrajSteps != -1)
3892
{
3893
g_iMultiIntervalStride = AskUnsignedInteger(" Start a new interval each n-th step? [%d] ",g_iTrajSteps/ti,g_iTrajSteps/ti);
3894
g_iMultiIntervalLength = AskUnsignedInteger(" Enter the length in steps of one interval: [%d] ",g_iTrajSteps/ti,g_iTrajSteps/ti);
3895
} else
3896
{
3897
g_iMultiIntervalStride = AskUnsignedInteger(" Start a new interval each n-th step? [%d] ",10000/ti,10000/ti);
3898
g_iMultiIntervalLength = AskUnsignedInteger(" Enter the length in steps of one interval: [%d] ",10000/ti,10000/ti);
3899
}
3900
for (z=0;z<ti;z++)
3901
{
3902
g_laMultiIntervalStart.Add(g_iMultiIntervalBegin+z*g_iMultiIntervalStride);
3903
g_laMultiIntervalEnd.Add(g_iMultiIntervalBegin+z*g_iMultiIntervalStride+g_iMultiIntervalLength);
3904
}
3905
} else
3906
{
3907
_intervalagain:
3908
ti = AskInteger(" Enter starting time step of %d. interval: [quit] ",-1,g_laMultiIntervalStart.GetSize()+1);
3909
if (ti == 0)
3910
{
3911
eprintf("Please enter a number >= 1.\n");
3912
goto _intervalagain;
3913
}
3914
if (ti != -1)
3915
{
3916
g_laMultiIntervalStart.Add(ti-1);
3917
g_laMultiIntervalEnd.Add(AskUnsignedInteger_ND(" Enter ending time step of %d. interval: ",g_laMultiIntervalStart.GetSize())-1);
3918
goto _intervalagain;
3919
}
3920
}
3921
mprintf(WHITE,"\n* %d Intervals have been defined:\n",g_laMultiIntervalStart.GetSize());
3922
for (z=0;z<g_laMultiIntervalStart.GetSize();z++)
3923
mprintf(" - Interval %2d: Steps %6d - %6d.\n",z+1,g_laMultiIntervalStart[z]+1,g_laMultiIntervalEnd[z]+1);
3924
mprintf("\n");
3925
} else goto _nomulti;
3926
} else
3927
{
3928
_nomulti:
3929
g_iBeginStep = AskUnsignedInteger(" In which time step to start processing the trajectory? [1] ",1) - 1;
3930
if (g_iBeginStep == -1)
3931
g_iBeginStep = 0;
3932
g_iMaxStep = AskUnsignedInteger(" How many time steps to use (from this position on)? [all] ",0);
3933
if (g_iMaxStep == 0)
3934
g_iMaxStep = -1; // Alle verwenden
3935
}
3936
g_iStride = AskUnsignedInteger(" Use every n-th time step from the trajectory? [1] ",1);
3937
3938
if (g_iTrajSteps != -1)
3939
{
3940
if (g_iMaxStep == -1)
3941
mprintf(YELLOW,"\n Using %d time steps: Every %d%s within range %d - approx. %d.\n",(g_iTrajSteps-g_iBeginStep)/g_iStride,g_iStride,(g_iStride==1)?"st":"th",g_iBeginStep+1,g_iTrajSteps);
3942
else mprintf(YELLOW,"\n Using %d time steps: Every %d%s within range %d - %d.\n",g_iMaxStep/g_iStride,g_iStride,(g_iStride==1)?"st":"th",g_iBeginStep+1,g_iBeginStep+g_iMaxStep);
3943
} else if (g_iMaxStep != -1)
3944
mprintf(YELLOW,"\n Using %d time steps: Every %d%s within range %d - %d.\n",g_iMaxStep/g_iStride,g_iStride,(g_iStride==1)?"st":"th",g_iBeginStep+1,g_iBeginStep+g_iMaxStep);
3945
else mprintf(YELLOW,"\n Using every %d%s time step beginning from step %d.\n",g_iStride,(g_iStride==1)?"st":"th",g_iBeginStep+1);
3946
3947
ti = -1;
3948
if (g_iTrajSteps != -1)
3949
{
3950
if (g_iMaxStep == -1)
3951
ti = (g_iTrajSteps-g_iBeginStep)/g_iStride;
3952
else ti = g_iMaxStep/g_iStride;
3953
} else if (g_iMaxStep != -1)
3954
ti = g_iMaxStep/g_iStride;
3955
3956
if (ti >= 0)
3957
{
3958
if (g_bMSD)
3959
{
3960
for (z=0;z<g_oaObserv.GetSize();z++)
3961
{
3962
o = (CObservation*)g_oaObserv[z];
3963
if (o->m_pMSD->m_iResolution > ti)
3964
{
3965
eprintf("\n MSD resolution of %d requires at least %d time steps, but using only %d steps.\n This will lead to erroneous results!\n\n",o->m_pMSD->m_iResolution,o->m_pMSD->m_iResolution,ti);
3966
if (!AskYesNo(" Continue anyway (y/n)? [yes] ",true))
3967
return false;
3968
goto _lessstepdone;
3969
}
3970
}
3971
}
3972
if (g_bRDyn)
3973
{
3974
for (z=0;z<g_oaObserv.GetSize();z++)
3975
{
3976
o = (CObservation*)g_oaObserv[z];
3977
if (o->m_pRDyn->m_iDepth*o->m_pRDyn->m_iStride > ti)
3978
{
3979
eprintf("\n Reorientation dynamics resolution of %d requires at least %d time steps, but using only %d steps.\n This will lead to erroneous results!\n\n",o->m_pRDyn->m_iDepth*o->m_pRDyn->m_iStride,o->m_pRDyn->m_iDepth*o->m_pRDyn->m_iStride,ti);
3980
if (!AskYesNo(" Continue anyway (y/n)? [yes] ",true))
3981
return false;
3982
goto _lessstepdone;
3983
}
3984
}
3985
}
3986
if (g_bIRSpec)
3987
{
3988
for (z=0;z<g_oaObserv.GetSize();z++)
3989
{
3990
o = (CObservation*)g_oaObserv[z];
3991
if (o->m_pIRSpec->m_iDepth*o->m_pIRSpec->m_iStride > ti)
3992
{
3993
eprintf("\n IR spectrum resolution of %d requires at least %d time steps, but using only %d steps.\n This will lead to erroneous results!\n\n",o->m_pIRSpec->m_iDepth*o->m_pIRSpec->m_iStride,o->m_pIRSpec->m_iDepth*o->m_pIRSpec->m_iStride,ti);
3994
if (!AskYesNo(" Continue anyway (y/n)? [yes] ",true))
3995
return false;
3996
goto _lessstepdone;
3997
}
3998
}
3999
}
4000
}
4001
_lessstepdone:
4002
4003
if (g_bScanVelocities)
4004
{
4005
mprintf(WHITE,"\n>>> Velocity Pre-Analysis >>>\n\n");
4006
g_iScanVelStart = AskUnsignedInteger(" Start in which time step for velocity pre-analysis? [0] ",0);
4007
g_iScanVelSteps = AskUnsignedInteger(" Use how many time steps from this point on for vel. pre-analysis? [all] ",0);
4008
g_iScanVelStride = AskUnsignedInteger(" Use every n-th step for velocity pre-analysis? [10] ",10);
4009
mprintf(WHITE,"\n<<< End of Velocity Pre-Analysis <<<\n");
4010
}
4011
4012
if (g_bSaveRefEnv && (g_iNbhMode == 3))
4013
{
4014
mprintf(WHITE,"\n>>> Neighborhood Pre-Analysis >>>\n\n");
4015
g_iScanNbhStart = AskUnsignedInteger(" Start in which time step for neighborhood analysis? [0] ",0);
4016
g_iScanNbhSteps = AskUnsignedInteger(" Use how many time steps from this point on for nbh analysis? [all] ",0);
4017
g_iScanNbhStride = AskUnsignedInteger(" Use every n-th step for the neighborhood analysis? [10] ",10);
4018
mprintf(WHITE,"\n<<< End of Neighborhood Pre-Analysis <<<\n");
4019
}
4020
4021
mprintf(WHITE,"\n########## All information collected ##########\n\n");
4022
BTOUT;
4023
return true;
4024
}
4025
4026
4027
4028
/* a = fopen("struct.xyz","wt");
4029
mfprintf(a,"%d\n\n",g_iGesAtomCount*20);
4030
4031
FILE *b;
4032
for (z=0;z<20;z++)
4033
{
4034
g_pTempTimestep = new CTimeStep();
4035
g_pTempTimestep->CopyFrom(&g_TimeStep);
4036
g_pTempTimestep->CenterCOM();
4037
CxMatrix3 ma;
4038
CxVector3 vec1;
4039
vec1[0] = ((rand()%20001)-10000)/10000.0;
4040
vec1[1] = ((rand()%20001)-10000)/10000.0;
4041
vec1[2] = ((rand()%20001)-10000)/10000.0;
4042
vec1.Normalize();
4043
tf = (rand()%10000)/10000.0*2.0*Pi;
4044
ma.RotMat(vec1,tf);
4045
g_pTempTimestep->Transform(ma);
4046
4047
vec1[0] = (rand()%20000)/10.0;
4048
vec1[1] = (rand()%20000)/10.0;
4049
vec1[2] = (rand()%20000)/10.0;
4050
4051
for (z2=0;z2<g_iGesAtomCount;z2++)
4052
g_pTempTimestep->m_vaCoords[z2] += vec1;
4053
4054
sprintf(buf,"coord_%02d.xyz",z+1);
4055
b = fopen(buf,"wt");
4056
// mfprintf(b,"%d\n\n",g_iGesAtomCount);
4057
for (z2=0;z2<g_iGesAtomCount;z2++)
4058
{
4059
mfprintf(a,"%s %f %f %f\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[z2]])->m_sName,g_pTempTimestep->m_vaCoords[z2][0]/100.0,g_pTempTimestep->m_vaCoords[z2][1]/100.0,g_pTempTimestep->m_vaCoords[z2][2]/100.0);
4060
mfprintf(b,"%s %f %f %f\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[z2]])->m_sName,g_pTempTimestep->m_vaCoords[z2][0]/100.0,g_pTempTimestep->m_vaCoords[z2][1]/100.0,g_pTempTimestep->m_vaCoords[z2][2]/100.0);
4061
}
4062
fclose(b);
4063
}
4064
fclose(a);*/
Loggerhead is a web-based interface for Breezy
Version: 2.0.1