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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/timestep.cpp
1
/*****************************************************************************
2
TRAVIS - Trajectory Analyzer and Visualizer
3
http://www.travis-analyzer.de/
4
5
Copyright (c) 2009-2013 Martin Brehm
6
2012-2013 Martin Thomas
7
8
This file written by Martin Brehm.
9
10
This program is free software: you can redistribute it and/or modify
11
it under the terms of the GNU General Public License as published by
12
the Free Software Foundation, either version 3 of the License, or
13
(at your option) any later version.
14
15
This program is distributed in the hope that it will be useful,
16
but WITHOUT ANY WARRANTY; without even the implied warranty of
17
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18
GNU General Public License for more details.
19
20
You should have received a copy of the GNU General Public License
21
along with this program. If not, see <http://www.gnu.org/licenses/>.
22
*****************************************************************************/
23
24
#include "timestep.h"
25
#include "travis.h"
26
27
28
void CTimeStep::CalcCenters()
29
{
30
BTIN;
31
int z, z2, z3, z4, c;
32
CxVector3 tv;
33
CMolecule *m;
34
CVirtualAtom *v;
35
CSingleMolecule *sm;
36
37
tv = 0;
38
39
// mprintf("** CalcCenters **");
40
41
if (m_vaCoords.GetSize() < g_iGesVirtAtomCount)
42
m_vaCoords.SetSize(g_iGesVirtAtomCount);
43
44
// mprintf("CalcCenters(): Size is now %d.\n",m_vaCoords.GetSize());
45
46
if (g_bUseVelocities)
47
if (m_vaVelocities.GetSize() < g_iGesVirtAtomCount)
48
m_vaVelocities.SetSize(g_iGesVirtAtomCount);
49
50
if (g_bUseForces)
51
if (m_vaForces.GetSize() < g_iGesVirtAtomCount)
52
m_vaForces.SetSize(g_iGesVirtAtomCount);
53
54
for (z=0;z<g_oaVirtualAtoms.GetSize();z++)
55
{
56
v = (CVirtualAtom*)g_oaVirtualAtoms[z];
57
m = (CMolecule*)g_oaMolecules[v->m_iMolecule];
58
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
59
{
60
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
61
if (v->m_iMode == 0) // Mittel aus Atompositionen
62
{
63
tv = 0;
64
c = 0;
65
for (z3=0;z3<v->m_oCenterAtoms.m_baAtomType.GetSize();z3++)
66
{
67
for (z4=0;z4<((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetSize();z4++)
68
{
69
// mprintf("{%d:(%G|%G|%G) }\n",((CxIntArray*)sm->m_oaAtomOffset[v->m_oCenterAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetAt(z4)),m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_oCenterAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetAt(z4))][0],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_oCenterAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetAt(z4))][1],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_oCenterAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetAt(z4))][2]);
70
tv += m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_oCenterAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetAt(z4))] * v->m_faWeight[c];
71
c++;
72
}
73
}
74
tv /= v->m_fGesWeight;
75
} else if (v->m_iMode == 1) // Abstand, Winkel, Dihedralwinkel
76
{
77
tv = PointFromRAD(m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_iAtomType[0]])->GetAt(v->m_iAtom[0])],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_iAtomType[1]])->GetAt(v->m_iAtom[1])],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_iAtomType[2]])->GetAt(v->m_iAtom[2])],v->m_fValues[0],v->m_fValues[1],v->m_fValues[2]);
78
} else if (v->m_iMode == 2) // Dipolvektor
79
{
80
if (!g_bDipole)
81
{
82
eprintf("Cannot use dipole vectors.\n");
83
BTOUT;
84
return;
85
}
86
tv = sm->m_vDipole + m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[sm->m_baAtomIndex.GetSize()-1])->GetAt(0)];
87
} else if (v->m_iMode == 3) // Geschwindigkeitsvektor
88
{
89
} else if (v->m_iMode == 4) // Kraftvektor
90
{
91
}
92
// mprintf("%d:(%G|%G|%G), ",((CxIntArray*)sm->m_oaAtomOffset[sm->m_baAtomIndex.GetSize()-1])->GetAt(v->m_iMolVirtAtom),tv[0],tv[1],tv[2]);
93
m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[sm->m_baAtomIndex.GetSize()-1])->GetAt(v->m_iMolVirtAtom)] = tv;
94
}
95
}
96
BTOUT;
97
}
98
99
100
bool CTimeStep::BondRange(int i1, int i2, double *f)
101
{
102
BTIN;
103
int a, b;
104
double d;
105
double x, y, z;
106
107
if (g_iScanMolStep == -1)
108
return false;
109
110
x = m_vaCoords[i1][0] - m_vaCoords[i2][0];
111
y = m_vaCoords[i1][1] - m_vaCoords[i2][1];
112
z = m_vaCoords[i1][2] - m_vaCoords[i2][2];
113
114
if (g_bPeriodic)
115
{
116
if (g_bPeriodicX)
117
{
118
while (x < -g_fBoxX/2)
119
x += g_fBoxX;
120
while (x > g_fBoxX/2)
121
x -= g_fBoxX;
122
}
123
124
if (g_bPeriodicY)
125
{
126
while (y < -g_fBoxY/2)
127
y += g_fBoxY;
128
while (y > g_fBoxY/2)
129
y -= g_fBoxY;
130
}
131
132
if (g_bPeriodicZ)
133
{
134
while (z < -g_fBoxZ/2)
135
z += g_fBoxZ;
136
while (z > g_fBoxZ/2)
137
z -= g_fBoxZ;
138
}
139
}
140
141
d = (float)sqrt(x*x+y*y+z*z);
142
143
if (f != NULL)
144
*f = d;
145
146
a = g_baAtomIndex[i1];
147
b = g_baAtomIndex[i2];
148
149
if ((a >= g_oaAtoms.GetSize()) || (b >= g_oaAtoms.GetSize()))
150
{
151
BTOUT;
152
return false;
153
}
154
155
if (((CAtom*)g_oaAtoms[a])->m_pElement->m_fRadius == 0)
156
{
157
BTOUT;
158
return false;
159
}
160
161
if (((CAtom*)g_oaAtoms[b])->m_pElement->m_fRadius == 0)
162
{
163
BTOUT;
164
return false;
165
}
166
167
if (d < (((CAtom*)g_oaAtoms[a])->m_pElement->m_fRadius+((CAtom*)g_oaAtoms[b])->m_pElement->m_fRadius)*g_fBondFactor)
168
{
169
// printf(" \"%s\" br=%f, \"%s\" br=%f Hat Nachbarn %s%d im Abstand von %.3f.\n",m_pLabels[i1],c1,m_pLabels[i2],c2,m_pLabels[i2],i2+1,d);
170
BTOUT;
171
return true;
172
} else
173
{
174
BTOUT;
175
return false;
176
}
177
}
178
179
180
bool CTimeStep::MirrorBond(int i1, int i2)
181
{
182
BTIN;
183
bool changed;
184
185
changed = false;
186
187
if (g_bPeriodicX)
188
{
189
while (m_vaCoords[i1][0]-m_vaCoords[i2][0] > g_fBoxX/2)
190
{
191
m_vaCoords[i2][0] += g_fBoxX;
192
changed = true;
193
}
194
while (m_vaCoords[i2][0]-m_vaCoords[i1][0] > g_fBoxX/2)
195
{
196
m_vaCoords[i2][0] -= g_fBoxX;
197
changed = true;
198
}
199
}
200
201
if (g_bPeriodicY)
202
{
203
while (m_vaCoords[i1][1]-m_vaCoords[i2][1] > g_fBoxY/2)
204
{
205
m_vaCoords[i2][1] += g_fBoxY;
206
changed = true;
207
}
208
while (m_vaCoords[i2][1]-m_vaCoords[i1][1] > g_fBoxY/2)
209
{
210
m_vaCoords[i2][1] -= g_fBoxY;
211
changed = true;
212
}
213
}
214
215
if (g_bPeriodicZ)
216
{
217
while (m_vaCoords[i1][2]-m_vaCoords[i2][2] > g_fBoxZ/2)
218
{
219
m_vaCoords[i2][2] += g_fBoxZ;
220
changed = true;
221
}
222
while (m_vaCoords[i2][2]-m_vaCoords[i1][2] > g_fBoxZ/2)
223
{
224
m_vaCoords[i2][2] -= g_fBoxZ;
225
changed = true;
226
}
227
}
228
229
if (changed)
230
{
231
BTOUT;
232
return true;
233
}
234
BTOUT;
235
return false;
236
}
237
238
239
void CTimeStep::RECURSION_ScanMolecules(int i, CxByteArray *ta, CSingleMolecule *sm, int depth, int *stack, unsigned long bmask, bool w)
240
{
241
BTIN;
242
int z, z2;
243
int nblist[64], nbs;
244
double f;
245
CxIntArray *wa;
246
CMolAtom *ma;
247
// mprintf(" Rekursion fuer Atom %d.\n",i+1);
248
249
// mprintf("Depth=%d, i=%d.\n",depth,i);
250
if (g_bVerbose)
251
{
252
mprintf(" ");
253
for (z=1;z<depth;z++)
254
{
255
if ((bmask & (int)pow(2.0,z)) != 0)
256
mprintf(WHITE,"| ");
257
else mprintf(" ");
258
}
259
if (depth != 0)
260
{
261
if (w)
262
mprintf(WHITE,"|--");
263
else mprintf(WHITE,"`--");
264
}
265
mprintf(CYAN,"%s",((CAtom*)g_oaAtoms[g_baAtomIndex[i]])->m_sName);
266
mprintf("(%d)",i+1);
267
}
268
269
stack[depth] = i;
270
g_laAtomSMIndex[i] = (unsigned long)g_oaSingleMolecules.GetSize()-1;
271
(*ta)[i] = 1;
272
// mprintf(" sm->m_baAtomIndex.GetSize()=%d\n",sm->m_baAtomIndex.GetSize());
273
for (z=0;z<sm->m_baAtomIndex.GetSize();z++)
274
{
275
if (sm->m_baAtomIndex[z] == g_baAtomIndex[i])
276
{
277
try { ma = new CMolAtom(); } catch(...) { ma = NULL; }
278
if (ma == NULL) NewException((double)sizeof(CMolAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
279
280
ma->m_iOffset = i;
281
ma->m_iType = z;
282
sm->m_oaMolAtoms.Add(ma);
283
goto _ok;
284
}
285
}
286
287
try { ma = new CMolAtom(); } catch(...) { ma = NULL; }
288
if (ma == NULL) NewException((double)sizeof(CMolAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
289
290
ma->m_iOffset = i;
291
ma->m_iType = sm->m_baAtomIndex.GetSize();
292
ma->m_iNumber = 0;
293
sm->m_oaMolAtoms.Add(ma);
294
295
sm->m_baAtomIndex.Add(g_baAtomIndex[i]);
296
_ok:
297
m_iConnectedAtoms++;
298
299
if (!g_bVerbose)
300
if ((m_iConnectedAtoms % m_iGesAtomModulo)==0)
301
mprintf(WHITE,"#");
302
303
nbs = 0;
304
for (z=0;z<(long)m_iGesAtomCount;z++) // Schon mal alle Nachbarn raussuchen
305
{
306
if (z == i)
307
continue;
308
if (((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_bExclude)
309
continue;
310
if (BondRange(i,z,&f))
311
{
312
if ((*ta)[z] != 0)
313
{
314
if ((depth > 0) && (z != stack[depth-1]))
315
{
316
if (sm->m_oaRings.GetSize() < 100)
317
{
318
if (g_bVerbose)
319
{
320
mprintf(GREEN," <-- Ring closure: ");
321
mprintf("%s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[stack[depth]]])->m_sName,stack[depth]+1);
322
}
323
324
try { wa = new CxIntArray("CTimeStep::RECURSION_ScanMolecules():wa"); } catch(...) { wa = NULL; }
325
if (wa == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
326
327
sm->m_oaRings.Add(wa);
328
wa->Add(stack[depth]);
329
z2 = depth-1;
330
while ((stack[z2] != z) && (z2 >= 0))
331
{
332
wa->Add(stack[z2]);
333
if (g_bVerbose)
334
mprintf(" - %s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[stack[z2]]])->m_sName,stack[z2]+1);
335
z2--;
336
}
337
wa->Add(z);
338
if (g_bVerbose)
339
mprintf(" - %s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_sName,z+1);
340
} else if (!m_bAbortRing)
341
{
342
m_bAbortRing = true;
343
eprintf("\n### More than 100 rings, aborting ring system scan for molecule %d.",sm->m_iIndex+1);
344
}
345
}
346
continue;
347
}
348
/* for (z2=0;z2<g_waBondBlackList.GetSize();z2+=2)
349
if (((g_waBondBlackList[z2] == i) && (g_waBondBlackList[z2+1] == z)) ||
350
((g_waBondBlackList[z2] == z) && (g_waBondBlackList[z2+1] == i)))
351
{
352
if (g_bVerbose)
353
{
354
mprintf("\n ");
355
for (z2=1;z2<depth+1;z2++)
356
{
357
if ((bmask & (int)pow(2,z2)) != 0)
358
mprintf(WHITE,"| ");
359
else mprintf(" ");
360
}
361
if (z+1 < nbs)
362
mprintf(WHITE,"|--");
363
else mprintf("`--");
364
mprintf("%s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_sName,z+1);
365
mprintf(GREEN," <-- This bond has been broken, skipping.\n");
366
}
367
g_iBondBlackListUsed++;
368
goto _nextnb;
369
}*/
370
if (f < 50.0f)
371
{
372
if (g_iCloseAtomCounter < 25)
373
eprintf("\n### The atoms %s(%d) and %s(%d) are VERY close to each other. (Distance=%.4f pm)",((CAtom*)g_oaAtoms[g_baAtomIndex[i]])->m_sName,i+1,((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_sName,z+1,f);
374
else if (g_iCloseAtomCounter == 25)
375
eprintf("\n### Suppressing further \"atoms close to each other\" warnings.");
376
377
g_iCloseAtomCounter++;
378
}
379
nblist[nbs] = z;
380
nbs++;
381
if (nbs >= MAX_BONDS)
382
{
383
eprintf("\n### Atom %s(%d) has more than %d bonds. Ignoring further bonds (defined via MAX_BONDS in config.h).",((CAtom*)g_oaAtoms[g_baAtomIndex[i]])->m_sName,i+1,MAX_BONDS);
384
goto _nbdone;
385
}
386
}
387
}
388
_nbdone:
389
if (g_bVerbose)
390
mprintf("\n");
391
for (z=0;z<nbs;z++) // Fuer das aktuelle Atom z2 alle Nachbarn durchgehen
392
{
393
for (z2=0;z2<g_laBondBlackList.GetSize();z2+=2)
394
{
395
if (((g_laBondBlackList[z2] == i) && (g_laBondBlackList[z2+1] == nblist[z])) ||
396
((g_laBondBlackList[z2] == nblist[z]) && (g_laBondBlackList[z2+1] == i)))
397
{
398
if (g_bVerbose)
399
{
400
mprintf(" ");
401
for (z2=1;z2<depth+1;z2++)
402
{
403
if ((bmask & (int)pow(2.0,z2)) != 0)
404
mprintf(WHITE,"| ");
405
else mprintf(" ");
406
}
407
if (z+1 < nbs)
408
mprintf(WHITE,"|--");
409
else mprintf(WHITE,"`--");
410
mprintf(CYAN,"%s",((CAtom*)g_oaAtoms[g_baAtomIndex[nblist[z]]])->m_sName);
411
mprintf("(%d)",nblist[z]+1);
412
mprintf(GREEN," <-- This bond shall be broken, skipping.\n");
413
}
414
g_iBondBlackListUsed++;
415
goto _nextnb;
416
}
417
}
418
419
sm->m_laBonds.Add(i);
420
sm->m_laBonds.Add(nblist[z]);
421
422
if ((*ta)[nblist[z]] == 0) // Der Nachbar ist noch immer frei
423
{
424
if (z+1 == nbs)
425
bmask -= (int)pow(2.0,depth+1);
426
RECURSION_ScanMolecules(nblist[z],ta,sm,depth+1,stack,bmask,(z+1==nbs)?false:true);
427
} else // Ringschluss
428
{
429
if (g_bVerbose)
430
{
431
mprintf(" ");
432
for (z2=1;z2<depth+1;z2++)
433
{
434
if ((bmask & (int)pow(2.0,z2)) != 0)
435
mprintf(WHITE,"| ");
436
else mprintf(" ");
437
}
438
if (z+1 < nbs)
439
mprintf(WHITE,"|--");
440
else mprintf(WHITE,"`--");
441
mprintf(CYAN,"%s",((CAtom*)g_oaAtoms[g_baAtomIndex[nblist[z]]])->m_sName);
442
mprintf("(%d)",nblist[z]+1);
443
mprintf(GREEN," <-- Ring closure\n");
444
}
445
}
446
_nextnb:;
447
}
448
BTOUT;
449
}
450
451
452
void CTimeStep::BuildAtomIndex()
453
{
454
BTIN;
455
int z, z2;
456
CAtom *at;
457
char buf[64];
458
459
g_baAtomIndex.SetSize(m_iGesAtomCount);
460
for (z=0;z<(long)m_iGesAtomCount;z++)
461
{
462
strcpy(buf,(char*)m_paLabels[z]);
463
ReplaceDigits(buf);
464
for (z2=0;z2<g_oaAtoms.GetSize();z2++)
465
{
466
if (mystricmp(buf,((CAtom*)g_oaAtoms[z2])->m_sName)==0)
467
{
468
at = (CAtom*)g_oaAtoms[z2];
469
// mprintf("Atom %d: Type %d (%s).\n",z,z2,at->m_sName);
470
while (at->m_pMergedTo != NULL)
471
{
472
at = at->m_pMergedTo;
473
// mprintf(" ...was merged to %s.\n",at->m_sName);
474
}
475
// mprintf(" Index is %d.\n",at->m_iIndex);
476
g_baAtomIndex[z] = (unsigned char)at->m_iIndex;
477
goto _e;
478
}
479
}
480
g_baAtomIndex[z] = 255;
481
eprintf("Error: CTimeStep::BuildAtomIndex(): Atom type \"%s\" not known.\n",buf);
482
_e:;
483
}
484
BTOUT;
485
}
486
487
488
bool CTimeStep::ScanMolecules()
489
{
490
BTIN;
491
int z, z2, z3, z4, z5, i, i2, ti, ti2, i1;
492
CxByteArray ta;
493
CSingleMolecule *sm, *sm2;
494
CxIntArray *wa, *waz2, *waz3, *waneu;
495
CMolecule *m;
496
CMolAtom *ma, *ma2, *ma3;
497
CMolBond *bond, *bond2;
498
CMolBondGroup *bg;
499
CMolAngle *angle, *angle2;
500
CMolAngleGroup *ag;
501
CAtom *at;
502
float f;
503
bool b;
504
double tfs;
505
int *stack;
506
507
BuildAtomIndex();
508
// CalcRadii();
509
510
try { stack = new int[g_iGesAtomCount]; } catch(...) { stack = NULL; }
511
if (stack == NULL) NewException((double)g_iGesAtomCount*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);
512
513
b = false;
514
for (z=0;z<g_oaAtoms.GetSize();z++)
515
{
516
if (z == g_iVirtAtomType)
517
continue;
518
at = (CAtom*)g_oaAtoms[z];
519
if (at->m_pMergedTo != NULL)
520
continue;
521
if (at->m_pElement->m_fRadius == 0)
522
{
523
if (!b)
524
{
525
b = true;
526
mprintf("\n");
527
}
528
at->m_bExclude = AskYesNo(" Atom type \"%s\" has bond radius 0. Exclude it from the system (y/n)? [yes] ",true,at->m_sName);
529
// if (!at->m_bExclude)
530
// at->m_pElement->m_fRadius = AskFloat_ND(" Please enter covalent bond radius for %s (in pm): ",at->m_sName);
531
}
532
}
533
534
ta.SetSize(g_iGesAtomCount);
535
g_laAtomSMIndex.SetSize(g_iGesAtomCount);
536
for (z=0;z<g_iGesAtomCount;z++)
537
{
538
ta[z] = 0;
539
g_laAtomSMIndex[z] = -1;
540
}
541
g_iBondBlackListUsed = 0;
542
g_oaSingleMolecules.RemoveAll();
543
g_oaMolecules.RemoveAll();
544
m_iConnectedAtoms = 0;
545
m_iGesAtomModulo = (m_iGesAtomCount / 60)+1;
546
if (g_iScanMolStep == -1)
547
{
548
mprintf(WHITE,"\n Skipping molecule recognition, using atoms as molecules...\n\n");
549
for (z=0;z<(long)m_iGesAtomCount;z++)
550
{
551
if (((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_bExclude)
552
continue;
553
554
try { sm = new CSingleMolecule(); } catch(...) { sm = NULL; }
555
if (sm == NULL) NewException((double)sizeof(CSingleMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
556
557
sm->m_iIndex = g_oaSingleMolecules.GetSize();
558
559
g_oaSingleMolecules.Add(sm);
560
561
g_laAtomSMIndex[z] = (unsigned long)g_oaSingleMolecules.GetSize()-1;
562
563
try { ma = new CMolAtom(); } catch(...) { ma = NULL; }
564
if (ma == NULL) NewException((double)sizeof(CMolAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
565
566
ma->m_iOffset = z;
567
ma->m_iType = sm->m_baAtomIndex.GetSize();
568
ma->m_iNumber = 0;
569
sm->m_oaMolAtoms.Add(ma);
570
sm->m_baAtomIndex.Add(g_baAtomIndex[z]);
571
}
572
mprintf(" %d molecules found.\n\n",g_oaSingleMolecules.GetSize());
573
} else
574
{
575
if (g_bVerbose)
576
{
577
mprintf(WHITE,"\n Molecule recognition...\n\n");
578
mprintf(WHITE,">>> Output of the molecule tree >>>\n");
579
} else mprintf("\n Molecule recognition [");
580
// fflush(stdout);
581
for (z=0;z<(long)m_iGesAtomCount;z++)
582
{
583
if (ta[z] != 0) // Dieses Atom wurde bereits in irgendein Molekuel eingebaut
584
{
585
// mprintf("> Atom %d: Schon vergeben.\n",z+1);
586
continue;
587
}
588
// mprintf("# Atom %d: Starte Rekursion.\n",z+1);
589
590
if (((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_bExclude)
591
continue;
592
593
try { sm = new CSingleMolecule(); } catch(...) { sm = NULL; }
594
if (sm == NULL) NewException((double)sizeof(CSingleMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
595
596
sm->m_iIndex = g_oaSingleMolecules.GetSize();
597
598
g_oaSingleMolecules.Add(sm);
599
600
// sm->m_iAtomGes = 0;
601
/* for (z2=0;z2<16;z2++)
602
sm->m_iAtomCount[z2] = 0;
603
sm->m_iElements = 0;*/
604
if (g_bVerbose)
605
mprintf(YELLOW,"\nThe next molecule starts with %s(%d):\n",m_paLabels[z],z+1);
606
607
m_bAbortRing = false;
608
609
RECURSION_ScanMolecules(z,&ta,sm,0,stack,0xFFFFFFFF,true);
610
611
// printf("%d Atome in diesem Molekuel.\n",g_pSingleMolecules[g_oaSingleMolecules.GetSize()].AtomGes);
612
613
// g_oaSingleMolecules.GetSize()++;
614
}
615
if (g_bVerbose)
616
{
617
mprintf(WHITE,"\n<<< Output of the molecule tree <<<\n\n");
618
mprintf("%d molecules found.\n\n",g_oaSingleMolecules.GetSize());
619
} else mprintf("]\n\n %d molecules found.\n\n",g_oaSingleMolecules.GetSize());
620
}
621
622
if (g_iCloseAtomCounter != 0)
623
{
624
mprintf(RED,"\n*** Warning: ");
625
mprintf("Some of the atoms were found to be very close to each other (distance < 50 pm).\n");
626
mprintf(" This usually indicates a problem, e.g. an incorrect cell vector.\n\n");
627
if (!AskYesNo(" Continue with molecule recognition anyways (y/n)? [yes] ",true))
628
return false;
629
mprintf("\n");
630
}
631
632
mprintf(" Sorting atom types...\n");
633
SortSingleMolAtomTypes();
634
635
delete[] stack;
636
637
/* mprintf("\n");
638
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
639
{
640
mprintf("%d ",z+1);
641
((CSingleMolecule*)g_oaSingleMolecules[z])->Dump();
642
}
643
644
mprintf("$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n");*/
645
646
/* mprintf("\n");
647
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
648
{
649
mprintf("%d ",z+1);
650
((CSingleMolecule*)g_oaSingleMolecules[z])->Dump();
651
}
652
mprintf("$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n");*/
653
if (g_iBondBlackListUsed != 0)
654
mprintf(" %d bonds have been broken.\n",g_iBondBlackListUsed);
655
656
/* if (g_oaSingleMolecules.GetSize() >= 4096)
657
{
658
mprintf("\n>>> Mehr als 4096 Molekuele! Dies wird nicht unterstuetzt. <<<\n\n");
659
// g_oaSingleMolecules.GetSize() = 4096;
660
}*/
661
662
mprintf(" Setting up bond lists...\n");
663
// Die Bindungen in m_oaMolAtoms aufbauen
664
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
665
{
666
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
667
for (z2=0;z2<sm->m_laBonds.GetSize()/2;z2++)
668
{
669
i = sm->m_laBonds[z2*2];
670
i2 = sm->m_laBonds[z2*2+1];
671
ti = -1;
672
for (z3=0;z3<sm->m_oaMolAtoms.GetSize();z3++)
673
{
674
if (((CMolAtom*)sm->m_oaMolAtoms[z3])->m_iOffset == i)
675
{
676
ti = z3;
677
break;
678
}
679
}
680
if (ti == -1)
681
{
682
eprintf("CTimeStep::ScanMolecules(): Atom 1 of bond (%d) not found.\n",i);
683
return false;
684
}
685
ti2 = -1;
686
for (z3=0;z3<sm->m_oaMolAtoms.GetSize();z3++)
687
{
688
if (((CMolAtom*)sm->m_oaMolAtoms[z3])->m_iOffset == i2)
689
{
690
ti2 = z3;
691
break;
692
}
693
}
694
if (ti2 == -1)
695
{
696
eprintf("CTimeStep::ScanMolecules(): Atom 2 of bond (%d) not found.\n",i2);
697
return false;
698
}
699
((CMolAtom*)sm->m_oaMolAtoms[ti])->m_oaBonds.Add((CMolAtom*)sm->m_oaMolAtoms[ti2]);
700
((CMolAtom*)sm->m_oaMolAtoms[ti2])->m_oaBonds.Add((CMolAtom*)sm->m_oaMolAtoms[ti]);
701
}
702
}
703
704
// Die AtomCodes berechnen
705
mprintf(" Building atom codes...\n");
706
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
707
{
708
// mprintf("Molecule %d: ",z+1);
709
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
710
if (g_bVerbose)
711
mprintf(YELLOW,"\n*** Singlemolecule %d ***\n\n",z+1);
712
sm->BuildAtomCodes();
713
}
714
715
mprintf(" Creating topological atom order...\n");
716
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
717
{
718
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
719
for (z2=0;z2<sm->m_baAtomIndex.GetSize();z2++)
720
{
721
try { wa = new CxIntArray("CTimeStep::ScanMolecules():wa"); } catch(...) { wa = NULL; }
722
if (wa == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
723
724
sm->m_oaAtomOffset.Add(wa);
725
for (z3=0;z3<sm->m_oaMolAtoms.GetSize();z3++)
726
{
727
ma = (CMolAtom*)sm->m_oaMolAtoms[z3];
728
if (ma->m_iType != z2)
729
continue;
730
ma->m_iNumber = wa->GetSize();
731
wa->Add(ma->m_iOffset);
732
}
733
}
734
}
735
736
mprintf(" Creating bond list...\n");
737
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
738
{
739
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
740
// mprintf("%d:\n",z+1);
741
for (z2=0;z2<sm->m_oaMolAtoms.GetSize();z2++)
742
{
743
ma = (CMolAtom*)sm->m_oaMolAtoms[z2];
744
for (z3=0;z3<ma->m_oaBonds.GetSize();z3++)
745
{
746
ma2 = (CMolAtom*)ma->m_oaBonds[z3];
747
if (ma2->m_iMolAtomNumber < z2 /* == ma->m_iMolAtomNumber*/)
748
continue;
749
750
// mprintf(" %s%2d <--> %s%2d\n",((CAtom*)g_oaAtoms[sm->m_baAtomIndex[ma->m_iType]])->m_sName,ma->m_iNumber+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[ma2->m_iType]])->m_sName,ma2->m_iNumber+1);
751
752
try { bond = new CMolBond(); } catch(...) { bond = NULL; }
753
if (bond == NULL) NewException((double)sizeof(CMolBond),__FILE__,__LINE__,__PRETTY_FUNCTION__);
754
755
bond->m_iAtom[0] = ma->m_iNumber;
756
bond->m_iAtom[1] = ma2->m_iNumber;
757
bond->m_iAtomType[0] = ma->m_iType;
758
bond->m_iAtomType[1] = ma2->m_iType;
759
bond->m_iMolAtom[0] = z2;
760
bond->m_iMolAtom[1] = ma2->m_iMolAtomNumber;
761
bond->m_iAtomOffset[0] = ma->m_iOffset;
762
bond->m_iAtomOffset[1] = ma2->m_iOffset;
763
sm->m_oaBonds.Add(bond);
764
}
765
}
766
/* if (z == 0)
767
mprintf(" %d Bonds added.\n",oatemp.GetSize());*/
768
for (z2=0;z2<sm->m_oaBonds.GetSize();z2++)
769
{
770
bond = (CMolBond*)sm->m_oaBonds[z2];
771
for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)
772
{
773
bg = (CMolBondGroup*)sm->m_oaBondGroups[z3];
774
for (z4=0;z4<bg->m_oaBonds.GetSize();z4++)
775
{
776
bond2 = (CMolBond*)bg->m_oaBonds[z4];
777
if (((((CMolAtom*)sm->m_oaMolAtoms[bond->m_iMolAtom[0]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[bond2->m_iMolAtom[0]])->m_fAtomCode) &&
778
(((CMolAtom*)sm->m_oaMolAtoms[bond->m_iMolAtom[1]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[bond2->m_iMolAtom[1]])->m_fAtomCode)) ||
779
((((CMolAtom*)sm->m_oaMolAtoms[bond->m_iMolAtom[0]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[bond2->m_iMolAtom[1]])->m_fAtomCode) &&
780
(((CMolAtom*)sm->m_oaMolAtoms[bond->m_iMolAtom[1]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[bond2->m_iMolAtom[0]])->m_fAtomCode)))
781
{
782
bg->m_oaBonds.Add(bond);
783
goto _bonddone;
784
}
785
}
786
}
787
788
try { bg = new CMolBondGroup(); } catch(...) { bg = NULL; }
789
if (bg == NULL) NewException((double)sizeof(CMolBondGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
790
791
bg->m_oaBonds.Add(bond);
792
sm->m_oaBondGroups.Add(bg);
793
_bonddone:;
794
}
795
/* if (z == 0)
796
{
797
mprintf(" %d Bond groups found:\n",sm->m_oaBondGroups.GetSize());
798
for (z2=0;z2<sm->m_oaBondGroups.GetSize();z2++)
799
{
800
mprintf(" - ");
801
bg = (CMolBondGroup*)sm->m_oaBondGroups[z2];
802
for (z3=0;z3<bg->m_oaBonds.GetSize();z3++)
803
{
804
bond = (CMolBond*)bg->m_oaBonds[z3];
805
mprintf("%s%2d <--> %s%2d",((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[0]]])->m_sName,bond->m_iAtom[0]+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[1]]])->m_sName,bond->m_iAtom[1]+1);
806
if (z3 < bg->m_oaBonds.GetSize()-1)
807
mprintf(", ");
808
}
809
mprintf("\n");
810
}
811
}*/
812
}
813
814
mprintf(" Creating angle list...\n");
815
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
816
{
817
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
818
// mprintf("%d:\n",z+1);
819
for (z2=0;z2<sm->m_oaMolAtoms.GetSize();z2++)
820
{
821
ma = (CMolAtom*)sm->m_oaMolAtoms[z2];
822
for (z3=0;z3<ma->m_oaBonds.GetSize();z3++)
823
{
824
ma2 = (CMolAtom*)ma->m_oaBonds[z3];
825
for (z4=z3+1;z4<ma->m_oaBonds.GetSize();z4++)
826
{
827
ma3 = (CMolAtom*)ma->m_oaBonds[z4];
828
// mprintf(" (%s%2d, %s%2d, %s%2d)\n",((CAtom*)g_oaAtoms[sm->m_baAtomIndex[ma2->m_iType]])->m_sName,ma2->m_iNumber+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[ma->m_iType]])->m_sName,ma->m_iNumber+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[ma3->m_iType]])->m_sName,ma3->m_iNumber+1);
829
830
try { angle = new CMolAngle(); } catch(...) { angle = NULL; }
831
if (angle == NULL) NewException((double)sizeof(CMolAngle),__FILE__,__LINE__,__PRETTY_FUNCTION__);
832
833
angle->m_iAtom[0] = ma2->m_iNumber;
834
angle->m_iAtom[1] = ma->m_iNumber;
835
angle->m_iAtom[2] = ma3->m_iNumber;
836
angle->m_iAtomType[0] = ma2->m_iType;
837
angle->m_iAtomType[1] = ma->m_iType;
838
angle->m_iAtomType[2] = ma3->m_iType;
839
angle->m_iMolAtom[0] = ma2->m_iMolAtomNumber;
840
angle->m_iMolAtom[1] = z2;
841
angle->m_iMolAtom[2] = ma3->m_iMolAtomNumber;
842
angle->m_iAtomOffset[0] = ma2->m_iOffset;
843
angle->m_iAtomOffset[1] = ma->m_iOffset;
844
angle->m_iAtomOffset[2] = ma3->m_iOffset;
845
sm->m_oaAngles.Add(angle);
846
}
847
}
848
}
849
/* if (z == 0)
850
mprintf(" %d Angles added.\n",oatemp.GetSize());*/
851
if (sm->m_oaAngles.GetSize() > 1000)
852
mprintf(WHITE," [");
853
tfs = sm->m_oaAngles.GetSize() / 50.0;
854
for (z2=0;z2<sm->m_oaAngles.GetSize();z2++)
855
{
856
if (sm->m_oaAngles.GetSize() > 1000)
857
if (fmod(z2,tfs) < 1)
858
mprintf(WHITE,"#");
859
angle = (CMolAngle*)sm->m_oaAngles[z2];
860
for (z3=0;z3<sm->m_oaAngleGroups.GetSize();z3++)
861
{
862
ag = (CMolAngleGroup*)sm->m_oaAngleGroups[z3];
863
for (z4=0;z4<ag->m_oaAngles.GetSize();z4++)
864
{
865
angle2 = (CMolAngle*)ag->m_oaAngles[z4];
866
if (( ((CMolAtom*)sm->m_oaMolAtoms[angle->m_iMolAtom[1]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[angle2->m_iMolAtom[1]])->m_fAtomCode) &&
867
(((( ((CMolAtom*)sm->m_oaMolAtoms[angle->m_iMolAtom[0]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[angle2->m_iMolAtom[0]])->m_fAtomCode) &&
868
( ((CMolAtom*)sm->m_oaMolAtoms[angle->m_iMolAtom[2]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[angle2->m_iMolAtom[2]])->m_fAtomCode))) ||
869
(( ((CMolAtom*)sm->m_oaMolAtoms[angle->m_iMolAtom[0]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[angle2->m_iMolAtom[2]])->m_fAtomCode) &&
870
( ((CMolAtom*)sm->m_oaMolAtoms[angle->m_iMolAtom[2]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[angle2->m_iMolAtom[0]])->m_fAtomCode))))
871
{
872
ag->m_oaAngles.Add(angle);
873
goto _angledone;
874
}
875
}
876
}
877
878
try { ag = new CMolAngleGroup(); } catch(...) { ag = NULL; }
879
if (ag == NULL) NewException((double)sizeof(CMolAngleGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
880
881
ag->m_oaAngles.Add(angle);
882
sm->m_oaAngleGroups.Add(ag);
883
_angledone:;
884
}
885
if (sm->m_oaAngles.GetSize() > 1000)
886
mprintf(WHITE,"]\n");
887
/* if (z == 0)
888
{
889
mprintf(" %d Angle groups found:\n",sm->m_oaAngleGroups.GetSize());
890
for (z2=0;z2<sm->m_oaAngleGroups.GetSize();z2++)
891
{
892
mprintf(" - ");
893
ag = (CMolAngleGroup*)sm->m_oaAngleGroups[z2];
894
for (z3=0;z3<ag->m_oaAngles.GetSize();z3++)
895
{
896
angle = (CMolAngle*)ag->m_oaAngles[z3];
897
mprintf(" (%s%2d, %s%2d, %s%2d)",((CAtom*)g_oaAtoms[sm->m_baAtomIndex[angle->m_iAtomType[0]]])->m_sName,angle->m_iAtom[0]+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[angle->m_iAtomType[1]]])->m_sName,angle->m_iAtom[1]+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[angle->m_iAtomType[2]]])->m_sName,angle->m_iAtom[2]+1);
898
if (z3 < ag->m_oaAngles.GetSize()-1)
899
mprintf(", ");
900
}
901
mprintf("\n");
902
}
903
}*/
904
}
905
906
mprintf(" Grouping together equivalent molecules...\n");
907
for (z=0;z<g_oaSingleMolecules.GetSize();z++) // Alle Molekuelvertreter durchgehen
908
{
909
// mprintf("Pruefe SM %d...\n",z+1);
910
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
911
for (z2=0;z2<g_oaMolecules.GetSize();z2++) // Alle schon vorhandenen Molekueltemplates durchgehen
912
{
913
m = (CMolecule*)g_oaMolecules[z2];
914
sm2 = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];
915
/* if (m->m_baAtomIndex.GetSize() != sm->m_baAtomIndex.GetSize())
916
goto _cont; // Nich die Gleiche Anzahl verschiedener Elemente -> Keine Uebereinstimmung
917
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
918
{
919
if (m->m_baAtomIndex[z3] != sm->m_baAtomIndex[z3])
920
goto _cont; // Elemente an Position z3 unterscheiden sich -> keine Uebereinstimmung
921
if (m->m_waAtomCount[z3] != ((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize())
922
goto _cont; // Anzahl an Atomen dieser Elementsorte unterscheidet sich -> Keine Uebereinstimmung*/
923
// mprintf(" Stimmt mit M%d ueberein.\n",z2);
924
// ((CMolecule*)g_oaMolecules[z2])->Count++;
925
// g_pSingleMolecules[z].m_iMoleculeOffset = z2;
926
// }
927
if (sm->m_oaMolAtoms.GetSize() != sm2->m_oaMolAtoms.GetSize())
928
goto _cont;
929
for (z3=0;z3<sm->m_oaMolAtoms.GetSize();z3++)
930
if (((CMolAtom*)sm->m_oaMolAtoms[z3])->m_fAtomCode != ((CMolAtom*)sm2->m_oaMolAtoms[z3])->m_fAtomCode)
931
goto _cont;
932
sm->m_iMolSMIndex = m->m_laSingleMolIndex.GetSize();
933
m->m_laSingleMolIndex.Add(z);
934
// sm->m_iMolType = z2;
935
goto _fert;
936
_cont:;
937
}
938
939
try { m = new CMolecule(); } catch(...) { m = NULL; }
940
if (m == NULL) NewException((double)sizeof(CMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
941
942
g_oaMolecules.Add(m);
943
// m->Count = 1; // Neues Molekueltemplate hinzufuegen
944
// m->Elements = ((CSingleMolecule*)g_oaSingleMolecules[z])->m_iElements;
945
m->m_iAtomGes = 0;
946
f = 0;
947
for (z2=0;z2<sm->m_oaAtomOffset.GetSize();z2++)
948
{
949
m->m_iAtomGes += ((CxIntArray*)sm->m_oaAtomOffset[z2])->GetSize();
950
f += ((CAtom*)g_oaAtoms[sm->m_baAtomIndex[z2]])->m_pElement->m_fMass * ((CxIntArray*)sm->m_oaAtomOffset[z2])->GetSize();
951
}
952
m->m_iAtomGesNoVirt = m->m_iAtomGes;
953
m->m_fMass = f;
954
((CSingleMolecule*)g_oaSingleMolecules[z])->m_iMolType = g_oaMolecules.GetSize()-1;
955
for (z2=0;z2<((CSingleMolecule*)g_oaSingleMolecules[z])->m_baAtomIndex.GetSize();z2++)
956
{
957
m->m_baAtomIndex.Add(((CSingleMolecule*)g_oaSingleMolecules[z])->m_baAtomIndex[z2]);
958
m->m_waAtomCount.Add(((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[z])->m_oaAtomOffset[z2])->GetSize());
959
// m->AtomCount[z2] = ((CSingleMolecule*)g_oaSingleMolecules[z])->m_iAtomCount[z2];
960
}
961
sm->m_iMolSMIndex = m->m_laSingleMolIndex.GetSize();
962
m->m_laSingleMolIndex.Add(z);
963
// g_pSingleMolecules[z].m_iMoleculeOffset = g_oaMolecules.GetSize();
964
m->BuildName();
965
966
// Standardmaessig geom. Zentrum als Dipolzentrum
967
m->m_iDipoleCenterType = m->m_baAtomIndex.GetSize();
968
m->m_iDipoleCenterIndex = 0;
969
970
// mprintf("### Erzeuge neues Molekuel %d \"%s\".\n",g_oaMolecules.GetSize(),m->Name);
971
// g_oaMolecules.GetSize()++;
972
_fert:;
973
}
974
mprintf(" Found %d unique molecule types.\n",g_oaMolecules.GetSize());
975
976
// Sort by molecular mass
977
mprintf(" Sorting molecule types by molecular mass...\n");
978
for (z=0;z<g_oaMolecules.GetSize();z++)
979
{
980
// mprintf("@ z=%d\n",z);
981
f = -1.0f;
982
z3 = -1;
983
for (z2=z;z2<g_oaMolecules.GetSize();z2++)
984
{
985
// mprintf("@ z2=%d\n",z2);
986
if (((CMolecule*)g_oaMolecules[z2])->m_fMass > f)
987
{
988
// mprintf("@ %f > %f --> z3 = %d\n",((CMolecule*)g_oaMolecules[z2])->m_fMass,f,z2);
989
f = ((CMolecule*)g_oaMolecules[z2])->m_fMass;
990
z3 = z2;
991
}
992
}
993
if (z3 == -1)
994
abort();
995
if (f > 0)
996
{
997
// mprintf("@ Swapping %d with %d.\n",z,z3);
998
m = (CMolecule*)g_oaMolecules[z3];
999
g_oaMolecules[z3] = g_oaMolecules[z];
1000
g_oaMolecules[z] = m;
1001
}
1002
}
1003
1004
for (z=0;z<g_oaMolecules.GetSize();z++)
1005
{
1006
((CMolecule*)g_oaMolecules[z])->m_iIndex = z;
1007
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)
1008
((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[z2]])->m_iMolType = z;
1009
}
1010
1011
1012
/* for (z=0;z<g_oaMolecules.GetSize();z++)
1013
{
1014
m = (CMolecule*)g_oaMolecules[z];
1015
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
1016
mprintf("Molecule %d Ring systems:\n",z+1);
1017
for (z2=0;z2<sm->m_oaRings.GetSize();z2++)
1018
{
1019
wa = (CxIntArray*)sm->m_oaRings[z2];
1020
mprintf(" - Ring %d: ",z2+1);
1021
for (z3=0;z3<wa->GetSize();z3++)
1022
{
1023
mprintf("%d",(*wa)[z3]);
1024
if (z3+1 < wa->GetSize())
1025
mprintf(", ");
1026
}
1027
mprintf("\n");
1028
}
1029
mprintf("\n");
1030
}*/
1031
1032
ti = 0;
1033
for (z=0;z<g_oaMolecules.GetSize();z++)
1034
{
1035
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
1036
ti += sm->m_oaRings.GetSize();
1037
}
1038
1039
mprintf(" Found %d rings.\n",ti);
1040
if (ti != 0)
1041
{
1042
mprintf(" Refining ring systems...\n");
1043
1044
try { wa = new CxIntArray("CTimeStep::ScanMolecules():wa"); } catch(...) { wa = NULL; }
1045
if (wa == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1046
1047
// Process ring systems
1048
for (z=0;z<g_oaMolecules.GetSize();z++)
1049
{
1050
m = (CMolecule*)g_oaMolecules[z];
1051
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
1052
if (sm->m_oaRings.GetSize() > 100)
1053
{
1054
eprintf(" More than 100 rings in molecule %d, skipping refinement. Ring system may be improper.\n",z+1);
1055
continue;
1056
}
1057
ti2 = 0;
1058
_again:
1059
ti2++;
1060
if (ti2 > 1000)
1061
{
1062
eprintf(" Too many iterations in molecule %d, aborting refinement. Ring system may be improper.\n",z+1);
1063
continue;
1064
}
1065
// mprintf("### again\n");
1066
for (z2=0;z2<sm->m_oaRings.GetSize();z2++)
1067
{
1068
waz2 = (CxIntArray*)sm->m_oaRings[z2];
1069
for (z3=z2+1;z3<sm->m_oaRings.GetSize();z3++)
1070
{
1071
waz3 = (CxIntArray*)sm->m_oaRings[z3];
1072
1073
// mprintf("*A* Checking if %d(%d) contains %d(%d)...\n",z2+1,waz2->GetSize(),z3+1,waz3->GetSize());
1074
// Check if waz2 contains waz3
1075
wa->SetSize(waz2->GetSize());
1076
for (z4=0;z4<waz2->GetSize();z4++)
1077
(*wa)[z4] = 0;
1078
for (z4=0;z4<waz3->GetSize();z4++)
1079
{
1080
for (z5=0;z5<waz2->GetSize();z5++)
1081
{
1082
if ((*waz3)[z4] == (*waz2)[z5])
1083
{
1084
(*wa)[z5] = 1;
1085
goto _found2;
1086
}
1087
}
1088
goto _notfound2;
1089
_found2:;
1090
}
1091
// mprintf(" Yes!\n");
1092
1093
try { waneu = new CxIntArray("CTimeStep::ScanMolecules():waneu"); } catch(...) { waneu = NULL; }
1094
if (waneu == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1095
1096
for (z4=0;z4<waz2->GetSize();z4++)
1097
{
1098
if (z4 == 0)
1099
{
1100
if (((*wa)[z4] == 0) || ((*wa)[z4+1] == 0) || ((*wa)[waz2->GetSize()-1] == 0))
1101
waneu->Add((*waz2)[z4]);
1102
} else if (z4 == waz2->GetSize()-1)
1103
{
1104
if (((*wa)[z4] == 0) || ((*wa)[z4-1] == 0) || ((*wa)[0] == 0))
1105
waneu->Add((*waz2)[z4]);
1106
} else
1107
{
1108
if (((*wa)[z4] == 0) || ((*wa)[z4+1] == 0) || ((*wa)[z4-1] == 0))
1109
waneu->Add((*waz2)[z4]);
1110
}
1111
}
1112
// mprintf(" Took %d from %d atoms from waz2.\n",waneu->GetSize(),waz2->GetSize());
1113
i1 = waz2->GetSize();
1114
delete waz2;
1115
sm->m_oaRings[z2] = waneu;
1116
if (waneu->GetSize() != i1)
1117
goto _again;
1118
_notfound2:
1119
1120
// mprintf("*B* Checking if %d contains %d...\n",z3+1,z2+1);
1121
// Check if waz3 contains waz2
1122
wa->SetSize(waz3->GetSize());
1123
for (z4=0;z4<waz3->GetSize();z4++)
1124
(*wa)[z4] = 0;
1125
for (z4=0;z4<waz2->GetSize();z4++)
1126
{
1127
for (z5=0;z5<waz3->GetSize();z5++)
1128
{
1129
if ((*waz2)[z4] == (*waz3)[z5])
1130
{
1131
(*wa)[z5] = 1;
1132
goto _found3;
1133
}
1134
}
1135
goto _notfound3;
1136
_found3:;
1137
}
1138
// mprintf(" Yes!\n");
1139
1140
try { waneu = new CxIntArray("CTimeStep::ScanMolecules():waneu"); } catch(...) { waneu = NULL; }
1141
if (waneu == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1142
1143
for (z4=0;z4<waz3->GetSize();z4++)
1144
{
1145
if (z4 == 0)
1146
{
1147
if (((*wa)[z4] == 0) || ((*wa)[z4+1] == 0) || ((*wa)[waz3->GetSize()-1] == 0))
1148
waneu->Add((*waz3)[z4]);
1149
} else if (z4 == waz3->GetSize()-1)
1150
{
1151
if (((*wa)[z4] == 0) || ((*wa)[z4-1] == 0) || ((*wa)[0] == 0))
1152
waneu->Add((*waz3)[z4]);
1153
} else
1154
{
1155
if (((*wa)[z4] == 0) || ((*wa)[z4+1] == 0) || ((*wa)[z4-1] == 0))
1156
waneu->Add((*waz3)[z4]);
1157
}
1158
}
1159
// mprintf(" Took %d from %d atoms from waz3.\n",waneu->GetSize(),waz3->GetSize());
1160
i1 = waz3->GetSize();
1161
delete waz3;
1162
sm->m_oaRings[z3] = waneu;
1163
if (waneu->GetSize() != i1)
1164
goto _again;
1165
_notfound3:;
1166
}
1167
}
1168
}
1169
delete wa;
1170
1171
mprintf(" Assigning ring systems to molecule types...\n");
1172
for (z=0;z<g_oaMolecules.GetSize();z++)
1173
{
1174
m = (CMolecule*)g_oaMolecules[z];
1175
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
1176
for (z2=0;z2<sm->m_oaRings.GetSize();z2++)
1177
{
1178
wa = (CxIntArray*)sm->m_oaRings[z2];
1179
1180
try { waz2 = new CxIntArray("CTimeStep::ScanMolecules():waz2"); } catch(...) { waz2 = NULL; }
1181
if (waz2 == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1182
1183
try { waz3 = new CxIntArray("CTimeStep::ScanMolecules():waz3"); } catch(...) { waz3 = NULL; }
1184
if (waz3 == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1185
1186
m->m_oaRingAtomTypes.Add(waz2);
1187
m->m_oaRingAtoms.Add(waz3);
1188
for (z3=0;z3<wa->GetSize();z3++)
1189
{
1190
for (z4=0;z4<sm->m_baAtomIndex.GetSize();z4++)
1191
{
1192
for (z5=0;z5<((CxIntArray*)sm->m_oaAtomOffset[z4])->GetSize();z5++)
1193
{
1194
if (((CxIntArray*)sm->m_oaAtomOffset[z4])->GetAt(z5) == wa->GetAt(z3))
1195
{
1196
waz2->Add(z4);
1197
waz3->Add(z5);
1198
goto _done;
1199
}
1200
}
1201
}
1202
_done:;
1203
}
1204
}
1205
}
1206
1207
mprintf(" Sorting rings by size...\n");
1208
for (z=0;z<g_oaMolecules.GetSize();z++)
1209
{
1210
m = (CMolecule*)g_oaMolecules[z];
1211
1212
for (z2=0;z2<m->m_oaRingAtoms.GetSize();z2++)
1213
{
1214
i1 = 0;
1215
ti = -1;
1216
for (z3=z2;z3<m->m_oaRingAtoms.GetSize();z3++)
1217
{
1218
if (((CxIntArray*)m->m_oaRingAtoms[z3])->GetSize() > i1)
1219
{
1220
i1 = ((CxIntArray*)m->m_oaRingAtoms[z3])->GetSize();
1221
ti = z3;
1222
}
1223
}
1224
if ((ti != -1) && (ti != z2))
1225
{
1226
wa = (CxIntArray*)m->m_oaRingAtoms[z2];
1227
m->m_oaRingAtoms[z2] = m->m_oaRingAtoms[ti];
1228
m->m_oaRingAtoms[ti] = wa;
1229
wa = (CxIntArray*)m->m_oaRingAtomTypes[z2];
1230
m->m_oaRingAtomTypes[z2] = m->m_oaRingAtomTypes[ti];
1231
m->m_oaRingAtomTypes[ti] = wa;
1232
}
1233
}
1234
}
1235
}
1236
1237
/* for (z=0;z<g_oaMolecules.GetSize();z++)
1238
{
1239
m = (CMolecule*)g_oaMolecules[z];
1240
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
1241
mprintf("Molecule %d Ring systems:\n",z+1);
1242
for (z2=0;z2<sm->m_oaRings.GetSize();z2++)
1243
{
1244
wa = (CxIntArray*)sm->m_oaRings[z2];
1245
mprintf(" - Ring %d: ",z2+1);
1246
for (z3=0;z3<wa->GetSize();z3++)
1247
{
1248
mprintf("%d",(*wa)[z3]);
1249
if (z3+1 < wa->GetSize())
1250
mprintf(", ");
1251
}
1252
mprintf("\n");
1253
}
1254
mprintf("\n");
1255
}*/
1256
1257
/* mprintf("\n%d Molekuelsorten gefunden.\n",g_oaMolecules.GetSize());
1258
for (z=0;z<g_oaMolecules.GetSize();z++)
1259
mprintf("Molekuel \"%s\": %d Atome gesamt, %d mal in der Simulation.\n",g_pMolecules[z].Name,g_pMolecules[z].AtomGes,g_pMolecules[z].Count);
1260
*/
1261
/* mprintf("\n");
1262
for (z=0;z<g_oaMolecules.GetSize();z++)
1263
{
1264
mprintf("%d ",z+1);
1265
((CMolecule*)g_oaMolecules[z])->Dump();
1266
}*/
1267
mprintf(" Molecule recognition finished.\n");
1268
BTOUT;
1269
return true;
1270
}
1271
1272
1273
void CTimeStep::RECURSION_MegaTree(int i, char *ta, int depth, unsigned long bmask, bool w, int *stack)
1274
{
1275
BTIN;
1276
int z, z2;
1277
int nblist[20], nbs;
1278
1279
stack[depth] = i;
1280
ta[i] = 1;
1281
for (z=1;z<depth;z++)
1282
{
1283
if ((bmask & (int)pow(2.0,z)) != 0)
1284
mprintf(WHITE,"| ");
1285
else mprintf(" ");
1286
}
1287
if (depth != 0)
1288
{
1289
if (w)
1290
mprintf(WHITE,"|--");
1291
else mprintf(WHITE,"`--");
1292
}
1293
mprintf("%s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[i]])->m_sName,i+1);
1294
nbs = 0;
1295
for (z=0;z<(long)m_iGesAtomCount;z++) // Schon mal alle Nachbarn raussuchen
1296
{
1297
if (z == i)
1298
continue;
1299
if (BondRange(i,z,NULL))
1300
{
1301
if (ta[z] != 0)
1302
{
1303
if ((depth > 0) && (z != stack[depth-1]))
1304
{
1305
mprintf(GREEN," <-- Ring closure: ");
1306
mprintf("%s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[stack[depth]]])->m_sName,stack[depth]+1);
1307
z2 = depth-1;
1308
while ((stack[z2] != z) && (z2 >= 0))
1309
{
1310
mprintf(" - %s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[stack[z2]]])->m_sName,stack[z2]+1);
1311
z2--;
1312
}
1313
mprintf(" - %s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_sName,z+1);
1314
// mprintf("Ringschluss! [d-1=%d,d=%d,i=%d] %s(%d)\n",stack[depth-1]+1,stack[depth]+1,i+1,((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_sName,z+1);
1315
}
1316
continue;
1317
}
1318
nblist[nbs] = z;
1319
nbs++;
1320
}
1321
}
1322
mprintf("\n");
1323
for (z=0;z<nbs;z++) // Fuer das aktuelle Atom z2 alle Nachbarn finden
1324
{
1325
if (ta[nblist[z]] != 0) // Der Nachbar wurde uns weggeschnappt -> Ringschluss
1326
{
1327
for (z2=1;z2<depth+1;z2++)
1328
{
1329
if ((bmask & (int)pow(2.0,z2)) != 0)
1330
mprintf(WHITE,"| ");
1331
else mprintf(" ");
1332
}
1333
if (z+1 < nbs)
1334
mprintf(WHITE,"|--");
1335
else mprintf("`--");
1336
mprintf("%s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[nblist[z]]])->m_sName,nblist[z]+1);
1337
mprintf(GREEN," <-- Ring closure\n");
1338
} else
1339
{
1340
if (z+1 == nbs)
1341
bmask -= (int)pow(2.0,depth+1);
1342
RECURSION_MegaTree(nblist[z],ta,/*sm,*/depth+1,bmask,(z+1==nbs)?false:true,stack);
1343
}
1344
}
1345
BTOUT;
1346
}
1347
1348
1349
void CTimeStep::PrintMegaTree()
1350
{
1351
BTIN;
1352
int z;
1353
char ta[16384];
1354
int stack[16384];
1355
1356
for (z=0;z<16384;z++)
1357
ta[z] = 0;
1358
for (z=0;z<(long)m_iGesAtomCount;z++)
1359
{
1360
if (ta[z] != 0) // Dieses Atom wurde bereits in irgendein Molekuel eingebaut
1361
continue;
1362
mprintf(YELLOW,"\nThe next molecule starts with %s(%d):\n",m_paLabels[z],z+1);
1363
RECURSION_MegaTree(z,ta,0,0xFFFFFFFF,true,stack);
1364
}
1365
mprintf("\n");
1366
BTOUT;
1367
}
1368
1369
1370
void CTimeStep::PrintMatrix(bool onlyfirst, bool onlybind)
1371
{
1372
BTIN;
1373
int z, z2, z3, z4, z5, z6, z7, z8, ti, ti2;
1374
float tf;
1375
bool b, c, noh;
1376
CxVector3 vec1, vec2;
1377
CSingleMolecule *sm;
1378
CMolecule *m;
1379
CMolAtom *ma, *ma0;
1380
CxIntArray *wa, *wat;
1381
1382
for (z=0;z<g_oaMolecules.GetSize();z++)
1383
{
1384
m = (CMolecule*)g_oaMolecules[z];
1385
for (z6=0;z6<(onlyfirst?1:m->m_laSingleMolIndex.GetSize());z6++)
1386
{
1387
mprintf(YELLOW,"\n*** Molecule %d: %s; Representant %d; Distances in pm ***\n",z+1,m->m_sName,z6+1);
1388
if ((m->m_baAtomIndex.GetSize() == 1) && (m->m_waAtomCount[0] == 1))
1389
{
1390
mprintf("[only 1 Atom]\n");
1391
continue;
1392
}
1393
if (m->m_iAtomGes > 200)
1394
{
1395
mprintf(WHITE,"\n This molecule has > 200 atoms. Output would flood the screen. Skipping.\n");
1396
continue;
1397
}
1398
noh = false;
1399
_matagain:
1400
if (m->m_oaRingAtoms.GetSize() != 0)
1401
mprintf(GREEN," (ring bonds are shown in green)\n");
1402
mprintf("\n");
1403
mprintf(" ");
1404
for (z2=0;z2<m->m_baAtomIndex.GetSize();z2++)
1405
{
1406
if (noh) // Skip H atoms
1407
if (mystricmp(((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,"H") == 0)
1408
continue;
1409
for (z3=0;z3<m->m_waAtomCount[z2];z3++)
1410
{
1411
if (((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName[1] == 0)
1412
mprintf(" ");
1413
mprintf(WHITE,"%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,z3+1);
1414
if (z3+1 < 10)
1415
mprintf(" ");
1416
}
1417
}
1418
mprintf("\n");
1419
for (z2=0;z2<m->m_baAtomIndex.GetSize();z2++)
1420
{
1421
if (noh) // Skip H atoms
1422
if (mystricmp(((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,"H") == 0)
1423
continue;
1424
for (z3=0;z3<m->m_waAtomCount[z2];z3++)
1425
{
1426
mprintf(WHITE,"%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,z3+1);
1427
if (((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName[1] == 0)
1428
mprintf(" ");
1429
if (z3+1 < 10)
1430
mprintf(" ");
1431
for (z4=0;z4<m->m_baAtomIndex.GetSize();z4++)
1432
{
1433
if (noh) // Skip H atoms
1434
if (mystricmp(((CAtom*)g_oaAtoms[m->m_baAtomIndex[z4]])->m_sName,"H") == 0)
1435
continue;
1436
for (z5=0;z5<m->m_waAtomCount[z4];z5++)
1437
{
1438
if ((z2 == z4) && (z3 == z5))
1439
{
1440
mprintf(BLUE,"*** ");
1441
continue;
1442
}
1443
ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z6]])->m_oaAtomOffset[z2])->GetAt(z3);
1444
vec1 = g_TimeStep.m_vaCoords[ti];
1445
ti2 = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z6]])->m_oaAtomOffset[z4])->GetAt(z5);
1446
vec2 = g_TimeStep.m_vaCoords[ti2];
1447
vec1 -= vec2;
1448
tf = vec1.GetLength();
1449
if ((g_TimeStep.BondRange(ti,ti2,NULL)) || (!onlybind))
1450
{
1451
for (z8=0;z8<m->m_oaRingAtomTypes.GetSize();z8++)
1452
{
1453
wat = (CxIntArray*)m->m_oaRingAtomTypes[z8];
1454
wa = (CxIntArray*)m->m_oaRingAtoms[z8];
1455
for (z7=0;z7<wa->GetSize();z7++)
1456
{
1457
if (((*wat)[z7] == z2) && ((*wa)[z7] == z3))
1458
{
1459
if (z7 == 0)
1460
{
1461
if (((*wat)[z7+1] == z4) && ((*wa)[z7+1] == z5))
1462
goto _green;
1463
if (((*wat)[wa->GetSize()-1] == z4) && ((*wa)[wa->GetSize()-1] == z5))
1464
goto _green;
1465
} else if (z7 == wa->GetSize()-1)
1466
{
1467
if (((*wat)[0] == z4) && ((*wa)[0] == z5))
1468
goto _green;
1469
if (((*wat)[z7-1] == z4) && ((*wa)[z7-1] == z5))
1470
goto _green;
1471
} else
1472
{
1473
if (((*wat)[z7+1] == z4) && ((*wa)[z7+1] == z5))
1474
goto _green;
1475
if (((*wat)[z7-1] == z4) && ((*wa)[z7-1] == z5))
1476
goto _green;
1477
}
1478
}
1479
}
1480
}
1481
mprintf("%3.0f ",tf);
1482
continue;
1483
_green:
1484
mprintf(GREEN,"%3.0f ",tf);
1485
} else mprintf(" - ");
1486
}
1487
}
1488
mprintf("\n");
1489
}
1490
}
1491
if ((!noh) && (m->m_iAtomGes > 30))
1492
{
1493
mprintf(WHITE,"\n This was a very large molecule.\n Printing the matrix again without H atoms.\n");
1494
noh = true;
1495
goto _matagain;
1496
}
1497
// if (((!onlyfirst) && ((z2 < ((CMolecule*)g_oaMolecules[z])->Elements-1) || (g_oaMolecules.GetSize()-1))) || (z < g_oaMolecules.GetSize()-1))
1498
// mprintf(">>>");
1499
}
1500
1501
if (m->m_oaRingAtoms.GetSize() != 0)
1502
{
1503
mprintf("\n");
1504
for (z2=0;z2<m->m_oaRingAtoms.GetSize();z2++)
1505
{
1506
mprintf(" %d-ring: ",((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize());
1507
if (((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize() > 20)
1508
{
1509
for (z3=0;z3<5;z3++)
1510
{
1511
mprintf("%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[((CxIntArray*)m->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)m->m_oaRingAtoms[z2])->GetAt(z3)+1);
1512
if (z3+1 < ((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize())
1513
mprintf(" - ");
1514
}
1515
mprintf(RED,"...");
1516
mprintf(" - ");
1517
for (z3=((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize()-5;z3<((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize();z3++)
1518
{
1519
mprintf("%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[((CxIntArray*)m->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)m->m_oaRingAtoms[z2])->GetAt(z3)+1);
1520
if (z3+1 < ((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize())
1521
mprintf(" - ");
1522
}
1523
} else
1524
{
1525
for (z3=0;z3<((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize();z3++)
1526
{
1527
mprintf("%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[((CxIntArray*)m->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)m->m_oaRingAtoms[z2])->GetAt(z3)+1);
1528
if (z3+1 < ((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize())
1529
mprintf(" - ");
1530
}
1531
}
1532
mprintf("\n");
1533
if (z2 >= 99)
1534
{
1535
mprintf(RED,"\n Only showing the first 100 rings.\n");
1536
break;
1537
}
1538
}
1539
}
1540
1541
c = false;
1542
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];
1543
for (z2=0;z2<m->m_baAtomIndex.GetSize();z2++)
1544
{
1545
b = false;
1546
ma = NULL;
1547
for (z3=0;z3<sm->m_oaMolAtoms.GetSize();z3++)
1548
{
1549
if (((CMolAtom*)sm->m_oaMolAtoms[z3])->m_iType != z2)
1550
continue;
1551
ma0 = ma;
1552
ma = (CMolAtom*)sm->m_oaMolAtoms[z3];
1553
if (ma0 == NULL)
1554
continue;
1555
z4 = ma0->m_iNumber;
1556
if (ma->m_fAtomCode == ma0->m_fAtomCode)
1557
{
1558
if (b)
1559
{
1560
mprintf(", %s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,ma->m_iNumber+1);
1561
} else
1562
{
1563
if (!c)
1564
{
1565
c = true;
1566
mprintf("\n");
1567
}
1568
mprintf(" Atoms %s%d, %s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,z4+1,((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,ma->m_iNumber+1);
1569
b = true;
1570
}
1571
} else if (b)
1572
{
1573
mprintf(" are equivalent.\n");
1574
b = false;
1575
}
1576
}
1577
if (b)
1578
mprintf(" are equivalent.\n");
1579
}
1580
} // Tabelle Ende
1581
BTOUT;
1582
}
1583
1584
1585
void CTimeStep::Transform(const CxMatrix3 &mat)
1586
{
1587
BTIN;
1588
int z;
1589
// CxVector3 v;
1590
1591
for (z=0;z<g_iGesVirtAtomCount;z++)
1592
{
1593
// if (z < g_iGesAtomCount)
1594
// mprintf("@ %2d: ( %g | %g | %g ) --> ",z,m_vaCoords[z][0],m_vaCoords[z][1],m_vaCoords[z][2]);
1595
m_vaCoords[z] = mat * m_vaCoords[z];
1596
// if (z < g_iGesAtomCount)
1597
// mprintf("( %g | %g | %g )\n",m_vaCoords[z][0],m_vaCoords[z][1],m_vaCoords[z][2]);
1598
}
1599
1600
if (g_bUseVelocities)
1601
for (z=0;z<g_iGesVirtAtomCount;z++)
1602
m_vaVelocities[z] = mat * m_vaVelocities[z];
1603
1604
if (g_bUseForces)
1605
for (z=0;z<g_iGesVirtAtomCount;z++)
1606
m_vaForces[z] = mat * m_vaForces[z];
1607
BTOUT;
1608
}
1609
1610
1611
void CTimeStep::Transform(const CxDMatrix3 &mat)
1612
{
1613
BTIN;
1614
int z;
1615
1616
for (z=0;z<g_iGesVirtAtomCount;z++)
1617
m_vaCoords[z] = mat * m_vaCoords[z];
1618
1619
if (g_bUseVelocities)
1620
for (z=0;z<g_iGesVirtAtomCount;z++)
1621
m_vaVelocities[z] = mat * m_vaVelocities[z];
1622
1623
if (g_bUseForces)
1624
for (z=0;z<g_iGesVirtAtomCount;z++)
1625
m_vaForces[z] = mat * m_vaForces[z];
1626
BTOUT;
1627
}
1628
1629
1630
void CTimeStep::Transform(const CxQuaternion &q)
1631
{
1632
BTIN;
1633
int z;
1634
1635
for (z=0;z<g_iGesVirtAtomCount;z++)
1636
m_vaCoords[z] = q.Transform(m_vaCoords[z]);
1637
1638
if (g_bUseVelocities)
1639
for (z=0;z<g_iGesVirtAtomCount;z++)
1640
m_vaVelocities[z] = q.Transform(m_vaVelocities[z]);
1641
1642
if (g_bUseForces)
1643
for (z=0;z<g_iGesVirtAtomCount;z++)
1644
m_vaForces[z] = q.Transform(m_vaForces[z]);
1645
BTOUT;
1646
}
1647
1648
1649
void CTimeStep::SubVelocities(const CxVector3 &vec)
1650
{
1651
BTIN;
1652
int z;
1653
1654
for (z=0;z<g_iGesVirtAtomCount;z++)
1655
m_vaVelocities[z] -= vec;
1656
BTOUT;
1657
}
1658
1659
1660
void CTimeStep::FoldMolecules()
1661
{
1662
BTIN;
1663
int z, z2, z3, z4;
1664
CxVector3 v, vc;
1665
CMolecule *m;
1666
CSingleMolecule *sm;
1667
1668
if (!g_bPeriodic)
1669
return;
1670
1671
// mprintf("*** Fold ***\n");
1672
1673
for (z=0;z<g_oaMolecules.GetSize();z++)
1674
{
1675
m = (CMolecule*)g_oaMolecules[z];
1676
if (m->m_bPseudo)
1677
continue;
1678
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1679
{
1680
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
1681
1682
// mprintf("\n%d, %d",m->m_baAtomIndex.GetSize(),((CxIntArray*)sm->m_oaAtomOffset[m->m_baAtomIndex.GetSize()-1])->GetAt(1));
1683
1684
// Massenzentrum
1685
v = m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[m->m_baAtomIndex.GetSize()-1])->GetAt(1)];
1686
1687
/* mprintf(" .Mol ");
1688
v.Dump();
1689
mprintf("\n");
1690
1691
*/ vc = CxVector3(0,0,0);
1692
1693
if (g_bPeriodicX)
1694
{
1695
while (v[0] < -g_fBoxX/2) { v[0] += g_fBoxX; vc[0] += g_fBoxX; }
1696
while (v[0] >= g_fBoxX/2) { v[0] -= g_fBoxX; vc[0] -= g_fBoxX; }
1697
}
1698
if (g_bPeriodicY)
1699
{
1700
while (v[1] < -g_fBoxY/2) { v[1] += g_fBoxY; vc[1] += g_fBoxY; }
1701
while (v[1] >= g_fBoxY/2) { v[1] -= g_fBoxY; vc[1] -= g_fBoxY; }
1702
}
1703
if (g_bPeriodicZ)
1704
{
1705
while (v[2] < -g_fBoxZ/2) { v[2] += g_fBoxZ; vc[2] += g_fBoxZ; }
1706
while (v[2] >= g_fBoxZ/2) { v[2] -= g_fBoxZ; vc[2] -= g_fBoxZ; }
1707
}
1708
1709
if ((vc[0] == 0) && (vc[1] == 0) && (vc[2] == 0))
1710
continue;
1711
1712
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
1713
for (z4=0;z4<m->m_waAtomCount[z3];z4++)
1714
m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)] += vc;
1715
1716
if (g_bWannier)
1717
for (z3=0;z3<sm->m_laWannier.GetSize();z3++)
1718
m_vaCoords[sm->m_laWannier[z3]] += vc;
1719
}
1720
}
1721
// mprintf(" Fold Done\n");
1722
BTOUT;
1723
}
1724
1725
1726
void CTimeStep::FoldAtoms()
1727
{
1728
BTIN;
1729
int z;
1730
1731
if (!g_bPeriodic)
1732
return;
1733
1734
for (z=0;z<g_iGesVirtAtomCount;z++)
1735
{
1736
if (g_bPeriodicX)
1737
{
1738
while (m_vaCoords[z][0] < -g_fBoxX/2) m_vaCoords[z][0] += g_fBoxX;
1739
while (m_vaCoords[z][0] >= g_fBoxX/2) m_vaCoords[z][0] -= g_fBoxX;
1740
}
1741
1742
if (g_bPeriodicY)
1743
{
1744
while (m_vaCoords[z][1] < -g_fBoxY/2) m_vaCoords[z][1] += g_fBoxY;
1745
while (m_vaCoords[z][1] >= g_fBoxY/2) m_vaCoords[z][1] -= g_fBoxY;
1746
}
1747
1748
if (g_bPeriodicZ)
1749
{
1750
while (m_vaCoords[z][2] < -g_fBoxZ/2) m_vaCoords[z][2] += g_fBoxZ;
1751
while (m_vaCoords[z][2] >= g_fBoxZ/2) m_vaCoords[z][2] -= g_fBoxZ;
1752
}
1753
}
1754
BTOUT;
1755
}
1756
1757
1758
void CTimeStep::CenterPos(const CxVector3 &vec)
1759
{
1760
BTIN;
1761
int z/*, z2, z3, z4*/;
1762
1763
/* for (z=0;z<g_oaMolecules.GetSize();z++)
1764
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->Count;z2++)
1765
for (z3=0;z3<((CMolecule*)g_oaMolecules[z])->Elements;z3++)
1766
for (z4=0;z4<((CMolecule*)g_oaMolecules[z])->AtomCount[z3];z4++)
1767
m_vaCoords[((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->SingleMolIndex[z2]])->m_iAtomOffset[z3][z4]] -= vec;*/
1768
1769
for (z=0;z<g_iGesVirtAtomCount;z++)
1770
m_vaCoords[z] -= vec;
1771
BTOUT;
1772
}
1773
1774
1775
void CTimeStep::AddAtoms()
1776
{
1777
BTIN;
1778
char *q;
1779
int z;
1780
// bool labeledatoms;
1781
1782
// labeledatoms = false;
1783
for (z=0;z<(long)m_iGesAtomCount;z++)
1784
{
1785
q = (char*)m_paLabels[z];
1786
q+=strlen(q)-1;
1787
/* while ((*q >= '0') && (*q <= '9'))
1788
{
1789
if (!labeledatoms)
1790
{
1791
mprintf(">>>\n>>> The atoms in the input file are numbered.\n>>> Ignoring this, using own numbers ;-)\n>>>\n");
1792
labeledatoms = true;
1793
}
1794
*q = 0;
1795
q--;
1796
}*/
1797
// printf("AddAtoms: \"%s\"\n",q);
1798
xAddAtom((char*)m_paLabels[z]);
1799
}
1800
BTOUT;
1801
}
1802
1803
1804
void CTimeStep::WriteTimestep(FILE *a)
1805
{
1806
BTIN;
1807
int z, z2, z3, z4, z0;
1808
CMolecule *m;
1809
CSingleMolecule *sm;
1810
1811
if (g_bSaveVirtAtoms)
1812
mfprintf(a," %d\n",g_iGesVirtAtomCount);
1813
else mfprintf(a," %d\n",g_iGesAtomCount);
1814
if (m_pComment != NULL)
1815
mfprintf(a,"%s\n",m_pComment);
1816
else mfprintf(a,"\n");
1817
1818
if (g_bWriteAtomwise)
1819
{
1820
for (z0=0;z0<g_oaAtoms.GetSize();z0++)
1821
{
1822
for (z=0;z<g_oaMolecules.GetSize();z++)
1823
{
1824
m = (CMolecule*)g_oaMolecules[z];
1825
if (m->m_bPseudo)
1826
continue;
1827
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
1828
{
1829
if (m->m_baAtomIndex[z3] != z0)
1830
continue;
1831
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
1832
continue;
1833
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1834
{
1835
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
1836
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
1837
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
1838
}
1839
}
1840
}
1841
}
1842
} else
1843
{
1844
for (z=0;z<g_oaMolecules.GetSize();z++)
1845
{
1846
m = (CMolecule*)g_oaMolecules[z];
1847
if (m->m_bPseudo)
1848
continue;
1849
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1850
{
1851
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
1852
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
1853
{
1854
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
1855
continue;
1856
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
1857
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
1858
}
1859
}
1860
}
1861
}
1862
1863
BTOUT;
1864
}
1865
1866
1867
void CTimeStep::WriteTimestepNb(FILE *a, CNbSet *nbs, int singlemol)
1868
{
1869
BTIN;
1870
int z, z2, z3, z4, z0, n, ti;
1871
CMolecule *m;
1872
CSingleMolecule *sm;
1873
CConditionGroup *cg;
1874
CConditionSubGroup *cs;
1875
CNbSearch *nb;
1876
1877
n = 0;
1878
1879
for (z=0;z<g_oaMolecules.GetSize();z++)
1880
{
1881
if (nbs->m_oaConditionGroups[z] == NULL)
1882
continue;
1883
m = (CMolecule*)g_oaMolecules[z];
1884
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1885
{
1886
if (((CConditionGroup*)nbs->m_oaConditionGroups[z])->Contains(z2))
1887
{
1888
n += m->m_iAtomGes;
1889
if (!g_bSaveVirtAtoms)
1890
n -= m->m_laVirtualAtoms.GetSize();
1891
}
1892
}
1893
}
1894
1895
mfprintf(a," %d\n",n);
1896
1897
mfprintf(a,"# Step %d",((int)g_iSteps));
1898
1899
if (singlemol >= 0)
1900
{
1901
sm = (CSingleMolecule*)g_oaSingleMolecules[singlemol];
1902
m = (CMolecule*)g_oaMolecules[sm->m_iMolType];
1903
if (!g_bSaveVirtAtoms)
1904
{
1905
if (g_bWriteAtomwise)
1906
mfprintf(a,", RM=%s[%d]",m->m_sName,sm->m_iMolSMIndex+1);
1907
else mfprintf(a,", RM=%s[%d] (%d atoms)",m->m_sName,sm->m_iMolSMIndex+1,m->m_iAtomGes-m->m_laVirtualAtoms.GetSize());
1908
} else
1909
{
1910
if (g_bWriteAtomwise)
1911
mfprintf(a,", RM=%s[%d]",m->m_sName,sm->m_iMolSMIndex+1);
1912
else mfprintf(a,", RM=%s[%d] (%d atoms)",m->m_sName,sm->m_iMolSMIndex+1,m->m_iAtomGes);
1913
}
1914
}
1915
1916
if (g_bEnvWriteDetailedInfo)
1917
{
1918
for (z=0;z<g_oaMolecules.GetSize();z++)
1919
{
1920
if (nbs->m_oaConditionGroups[z] == NULL)
1921
continue;
1922
m = (CMolecule*)g_oaMolecules[z];
1923
1924
cg = (CConditionGroup*)nbs->m_oaConditionGroups[z];
1925
1926
if (g_bEnvSortNb)
1927
{
1928
nb = NULL;
1929
if (cg->m_oaConditionSubGroups.GetSize() == 1)
1930
{
1931
cs = (CConditionSubGroup*)cg->m_oaConditionSubGroups[0];
1932
if (cs->m_oaConditions.GetSize() == 1)
1933
nb = (CNbSearch*)cs->m_oaConditions[0];
1934
}
1935
if (nb == NULL)
1936
goto _nosortinfo;
1937
1938
if (nb->m_iNbCountMin <= -1)
1939
goto _nosortinfo;
1940
1941
for (z2=nb->m_iNbCountMin;z2<=nb->m_iNbCountMax;z2++)
1942
{
1943
ti = nb->m_pNbSort[z2].m_iOM;
1944
if (!g_bSaveVirtAtoms)
1945
{
1946
if (m->m_laSingleMolIndex[ti] != singlemol)
1947
{
1948
if (g_bWriteAtomwise)
1949
mfprintf(a,", %s[%d] d=%.3fpm",m->m_sName,z2+1,nb->m_pNbSort[z2].m_fMinDist);
1950
else mfprintf(a,", %s[%d] d=%.3fpm (%d atoms)",m->m_sName,ti+1,nb->m_pNbSort[z2].m_fMinDist,m->m_iAtomGes-m->m_laVirtualAtoms.GetSize());
1951
}
1952
} else
1953
{
1954
if (m->m_laSingleMolIndex[ti] != singlemol)
1955
{
1956
if (g_bWriteAtomwise)
1957
mfprintf(a,", %s[%d] d=%.3fpm",m->m_sName,z2+1,nb->m_pNbSort[z2].m_fMinDist);
1958
else mfprintf(a,", %s[%d] d=%.3fpm (%d atoms)",m->m_sName,ti+1,nb->m_pNbSort[z2].m_fMinDist,m->m_iAtomGes);
1959
}
1960
}
1961
}
1962
} else
1963
{
1964
_nosortinfo:
1965
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1966
{
1967
if (cg->Contains(z2))
1968
{
1969
if (!g_bSaveVirtAtoms)
1970
{
1971
if (m->m_laSingleMolIndex[z2] != singlemol)
1972
{
1973
if (g_bWriteAtomwise)
1974
mfprintf(a,", %s[%d]",m->m_sName,z2+1);
1975
else mfprintf(a,", %s[%d] (%d atoms)",m->m_sName,z2+1,m->m_iAtomGes-m->m_laVirtualAtoms.GetSize());
1976
}
1977
} else
1978
{
1979
if (m->m_laSingleMolIndex[z2] != singlemol)
1980
{
1981
if (g_bWriteAtomwise)
1982
mfprintf(a,", %s[%d]",m->m_sName,z2+1);
1983
else mfprintf(a,", %s[%d] (%d atoms)",m->m_sName,z2+1,m->m_iAtomGes);
1984
}
1985
}
1986
}
1987
}
1988
}
1989
}
1990
}
1991
1992
mfprintf(a,"\n");
1993
1994
if (g_bWriteAtomwise)
1995
{
1996
for (z0=0;z0<g_oaAtoms.GetSize();z0++)
1997
{
1998
for (z=0;z<g_oaMolecules.GetSize();z++)
1999
{
2000
if (nbs->m_oaConditionGroups[z] == NULL)
2001
continue;
2002
m = (CMolecule*)g_oaMolecules[z];
2003
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2004
{
2005
if (m->m_baAtomIndex[z3] != z0)
2006
continue;
2007
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
2008
continue;
2009
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
2010
{
2011
if (((CConditionGroup*)nbs->m_oaConditionGroups[z])->Contains(z2))
2012
{
2013
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
2014
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
2015
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
2016
}
2017
}
2018
}
2019
}
2020
}
2021
} else
2022
{
2023
if (singlemol >= 0)
2024
{
2025
sm = (CSingleMolecule*)g_oaSingleMolecules[singlemol];
2026
m = (CMolecule*)g_oaMolecules[sm->m_iMolType];
2027
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2028
{
2029
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
2030
continue;
2031
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
2032
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
2033
}
2034
}
2035
2036
for (z=0;z<g_oaMolecules.GetSize();z++)
2037
{
2038
if (nbs->m_oaConditionGroups[z] == NULL)
2039
continue;
2040
m = (CMolecule*)g_oaMolecules[z];
2041
cg = (CConditionGroup*)nbs->m_oaConditionGroups[z];
2042
2043
if (g_bEnvSortNb)
2044
{
2045
nb = NULL;
2046
if (cg->m_oaConditionSubGroups.GetSize() == 1)
2047
{
2048
cs = (CConditionSubGroup*)cg->m_oaConditionSubGroups[0];
2049
if (cs->m_oaConditions.GetSize() == 1)
2050
nb = (CNbSearch*)cs->m_oaConditions[0];
2051
}
2052
if (nb == NULL)
2053
goto _nosort;
2054
2055
if (nb->m_iNbCountMin <= -1)
2056
goto _nosort;
2057
2058
for (z2=nb->m_iNbCountMin;z2<=nb->m_iNbCountMax;z2++)
2059
{
2060
ti = nb->m_pNbSort[z2].m_iOM;
2061
2062
if (m->m_laSingleMolIndex[ti] == singlemol)
2063
continue;
2064
2065
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[ti]];
2066
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2067
{
2068
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
2069
continue;
2070
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
2071
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
2072
}
2073
}
2074
} else
2075
{
2076
_nosort:
2077
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
2078
{
2079
if (((CConditionGroup*)nbs->m_oaConditionGroups[z])->Contains(z2))
2080
{
2081
if (m->m_laSingleMolIndex[z2] == singlemol)
2082
continue;
2083
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
2084
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2085
{
2086
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
2087
continue;
2088
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
2089
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
2090
}
2091
}
2092
}
2093
}
2094
}
2095
}
2096
2097
BTOUT;
2098
}
2099
2100
2101
/*void CTimeStep::WriteTimestepNb(int refmol, FILE *a)
2102
{
2103
BTIN;
2104
int z, c, z2, z3, z4, z0;
2105
int ti;
2106
CMolecule *m, *m2;
2107
2108
m = (CMolecule*)g_oaMolecules[g_iFixMol];
2109
2110
c = 0;
2111
if (g_bRefEnvVirt)
2112
{
2113
for (z=0;z<g_oaMolecules.GetSize();z++)
2114
c += g_pNbAll->m_waScanNeighborCount[z]*((CMolecule*)g_oaMolecules[z])->m_iAtomGes;
2115
if (g_bSaveRefWithEnv)
2116
c += m->m_iAtomGes;
2117
} else
2118
{
2119
for (z=0;z<g_oaMolecules.GetSize();z++)
2120
c += g_pNbAll->m_waScanNeighborCount[z]*(((CMolecule*)g_oaMolecules[z])->m_iAtomGes-((CMolecule*)g_oaMolecules[z])->m_waVirtualAtoms.GetSize());
2121
if (g_bSaveRefWithEnv)
2122
c += m->m_iAtomGes - m->m_waVirtualAtoms.GetSize();
2123
}
2124
2125
mfprintf(a," %d\n\n",c);
2126
2127
if (g_bRefEnvAtomwise)
2128
{
2129
for (z0=0;z0<g_oaAtoms.GetSize();z0++)
2130
{
2131
if (g_bSaveRefWithEnv)
2132
{
2133
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2134
{
2135
if (m->m_baAtomIndex[z3] != z0)
2136
continue;
2137
if (!g_bRefEnvVirt)
2138
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
2139
continue;
2140
for (z4=0;z4<m->m_waAtomCount[z3];z4++)
2141
{
2142
ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[refmol]])->m_oaAtomOffset[z3])->GetAt(z4);
2143
mfprintf(a," %s %f %f %f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0f,m_vaCoords[ti][1]/100.0f,m_vaCoords[ti][2]/100.0f);
2144
}
2145
}
2146
}
2147
for (z=0;z<g_oaMolecules.GetSize();z++)
2148
{
2149
m2 = (CMolecule*)g_oaMolecules[z];
2150
for (z2=0;z2<g_pNbAll->m_waScanNeighborCount[z];z2++)
2151
{
2152
for (z3=0;z3<m2->m_baAtomIndex.GetSize();z3++)
2153
{
2154
if (m2->m_baAtomIndex[z3] != z0)
2155
continue;
2156
if (!g_bRefEnvVirt)
2157
if (m2->m_baAtomIndex[z3] == g_iVirtAtomType)
2158
continue;
2159
for (z4=0;z4<m2->m_waAtomCount[z3];z4++)
2160
{
2161
ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[((CxIntArray*)g_pNbAll->m_oaScanNeighbors[z])->GetAt(z2)]])->m_oaAtomOffset[z3])->GetAt(z4);
2162
mfprintf(a," %s %f %f %f\n",((CAtom*)g_oaAtoms[m2->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0f,m_vaCoords[ti][1]/100.0f,m_vaCoords[ti][2]/100.0f);
2163
}
2164
}
2165
}
2166
}
2167
}
2168
} else
2169
{
2170
if (g_bSaveRefWithEnv)
2171
{
2172
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2173
{
2174
if (!g_bRefEnvVirt)
2175
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
2176
continue;
2177
for (z4=0;z4<m->m_waAtomCount[z3];z4++)
2178
{
2179
ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[refmol]])->m_oaAtomOffset[z3])->GetAt(z4);
2180
mfprintf(a," %s %f %f %f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0,m_vaCoords[ti][1]/100.0,m_vaCoords[ti][2]/100.0);
2181
}
2182
}
2183
}
2184
for (z=0;z<g_oaMolecules.GetSize();z++)
2185
{
2186
m2 = (CMolecule*)g_oaMolecules[z];
2187
for (z2=0;z2<g_pNbAll->m_waScanNeighborCount[z];z2++)
2188
{
2189
for (z3=0;z3<m2->m_baAtomIndex.GetSize();z3++)
2190
{
2191
if (!g_bRefEnvVirt)
2192
if (m2->m_baAtomIndex[z3] == g_iVirtAtomType)
2193
continue;
2194
for (z4=0;z4<m2->m_waAtomCount[z3];z4++)
2195
{
2196
ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[((CxIntArray*)g_pNbAll->m_oaScanNeighbors[z])->GetAt(z2)]])->m_oaAtomOffset[z3])->GetAt(z4);
2197
mfprintf(a," %s %f %f %f\n",((CAtom*)g_oaAtoms[m2->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0,m_vaCoords[ti][1]/100.0,m_vaCoords[ti][2]/100.0);
2198
}
2199
}
2200
}
2201
}
2202
}
2203
BTOUT;
2204
}*/
2205
2206
2207
/*float CTimeStep::MolDist(CSingleMolecule *ref, CSingleMolecule *sm2, CNbSearch *nb)
2208
{
2209
BXIN;
2210
int z3, z4;
2211
float d;
2212
CxVector3 vec;
2213
2214
d = 99999.0f;
2215
for (z3=0;z3<nb->m_waRefElements.GetSize();z3++)
2216
for (z4=0;z4<((CxIntArray*)nb->m_oaNbElements[sm2->m_iMolType])->GetSize();z4++)
2217
{
2218
vec = m_vaCoords[((CxIntArray*)ref->m_oaAtomOffset[nb->m_waRefElements[z3]])->GetAt(nb->m_waRefAtoms[z3])] - m_vaCoords[((CxIntArray*)sm2->m_oaAtomOffset[((CxIntArray*)nb->m_oaNbElements[sm2->m_iMolType])->GetAt(z4)])->GetAt(((CxIntArray*)nb->m_oaNbAtoms[sm2->m_iMolType])->GetAt(z4))];
2219
if (g_bFold)
2220
{
2221
while (vec[0] >= g_fBoxX/2) vec[0] -= g_fBoxX;
2222
while (vec[0] < -g_fBoxX/2) vec[0] += g_fBoxX;
2223
while (vec[1] >= g_fBoxY/2) vec[1] -= g_fBoxY;
2224
while (vec[1] < -g_fBoxY/2) vec[1] += g_fBoxY;
2225
while (vec[2] >= g_fBoxZ/2) vec[2] -= g_fBoxZ;
2226
while (vec[2] < -g_fBoxZ/2) vec[2] += g_fBoxZ;
2227
}
2228
if (vec.GetLength() < d)
2229
d = vec.GetLength();
2230
}
2231
BXOUT;
2232
if (d < 90000.0f)
2233
return d;
2234
else return -1.0f;
2235
}*/
2236
2237
2238
/*void CTimeStep::ScanNeighborhood(int fixmol, int refmol, CNbSearch *nb, CNbSearch *prev)
2239
{
2240
BTIN;
2241
float *del, d;
2242
int *best, b;
2243
int z, z2, z3, c;
2244
CMolecule *m, *m2;
2245
CSingleMolecule *sm, *sm2;
2246
CxVector3 vec;
2247
2248
m = (CMolecule*)g_oaMolecules[fixmol];
2249
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[refmol]];
2250
del = new float[g_oaSingleMolecules.GetSize()];
2251
best = new int[g_oaSingleMolecules.GetSize()];
2252
2253
// printf("Suche Nachbarschaft von Molekuel %d...\n",refmol+1);
2254
2255
for (z=0;z<g_oaMolecules.GetSize();z++)
2256
{
2257
if (((!nb->m_bDistMode) && (nb->m_waMolCount[z] == 0)) || (nb->m_bDistMode && (nb->m_faMolDist[z] == 0)))
2258
{
2259
nb->m_waScanNeighborCount[z] = 0;
2260
continue;
2261
}
2262
m2 = (CMolecule*)g_oaMolecules[z];
2263
// printf("*** Molekuel %d: %s\n",z+1,m2->Name);
2264
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)
2265
{
2266
del[z2] = 99999.0f;
2267
if ((z == fixmol) && (z2 == refmol))
2268
continue;
2269
if (prev != NULL)
2270
if (!prev->Contains(z,z2))
2271
continue;
2272
// printf(" - Vertreter %d\n",z2+1);
2273
sm2 = (CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[z2]];
2274
del[z2] = MolDist(sm,sm2,nb);
2275
// printf(" - Finaler Abstand: %f\n",del[z2]);
2276
}
2277
if (nb->m_bDistMode)
2278
{
2279
// printf("**DistMode**\n");
2280
// mprintf("Die Nachbarn: ");
2281
c = 0;
2282
for (z3=0;z3<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z3++)
2283
if ((del[z3] <= nb->m_faMolDist[z]) && (del[z3] >= nb->m_faMolMinDist[z]))
2284
{
2285
// mprintf("%d (%f), ",z3+1,del[z3]);
2286
best[c] = z3;
2287
c++;
2288
}
2289
// mprintf("\n");
2290
// printf(" # Die naechsten Nachbarn: ");
2291
for (z2=0;z2<c;z2++)
2292
{
2293
// printf("%d, ",best[z2]+1);
2294
nb->m_iNeighbourCount++;
2295
for (z3=0;z3<nb->m_waScanNeighborCount[z];z3++)
2296
if (((CxIntArray*)nb->m_oaScanNeighbors[z])->GetAt(z3) == best[z2])
2297
{
2298
((CxIntArray*)nb->m_oaScanNeighborHits[z])->GetAt(z3)++;
2299
goto _enddist;
2300
}
2301
((CxIntArray*)nb->m_oaScanNeighbors[z])->Add(best[z2]);
2302
((CxIntArray*)nb->m_oaScanNeighborHits[z])->Add(1);
2303
nb->m_waScanNeighborCount[z]++;
2304
_enddist:;
2305
}
2306
// printf("\n");
2307
} else
2308
{
2309
// printf("**CountMode**\n");
2310
for (z2=0;z2<nb->m_waMolCount[z];z2++)
2311
{
2312
d = 999999.0f;
2313
b = -1;
2314
for (z3=0;z3<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z3++)
2315
{
2316
if (del[z3] < d)
2317
{
2318
d = del[z3];
2319
b = z3;
2320
}
2321
}
2322
best[z2] = b;
2323
del[b] = 1000000.0f;
2324
}
2325
// printf(" # Die naechsten Nachbarn: ");
2326
for (z2=nb->m_waMolCountMin[z]-1;z2<nb->m_waMolCount[z];z2++)
2327
{
2328
// printf("%d, ",best[z2]);
2329
nb->m_iNeighbourCount++;
2330
for (z3=0;z3<nb->m_waScanNeighborCount[z];z3++)
2331
if (((CxIntArray*)nb->m_oaScanNeighbors[z])->GetAt(z3) == best[z2])
2332
{
2333
((CxIntArray*)nb->m_oaScanNeighborHits[z])->GetAt(z3)++;
2334
goto _end;
2335
}
2336
((CxIntArray*)nb->m_oaScanNeighbors[z])->Add(best[z2]);
2337
((CxIntArray*)nb->m_oaScanNeighborHits[z])->Add(1);
2338
nb->m_waScanNeighborCount[z]++;
2339
_end:;
2340
}
2341
// printf("\n");
2342
}
2343
}
2344
delete del;
2345
delete best;
2346
BTOUT;
2347
}*/
2348
2349
2350
/*void CTimeStep::ScanAngle(int fixmol, int refmol, CCondition *co, CNbSearch *prev)
2351
{
2352
BTIN;
2353
int z2, z3, z4;
2354
float tf;
2355
CMolecule *m, *m2;
2356
CSingleMolecule *sm, *sm2;
2357
CxVector3 vec0, vec1, vec2, vec3, vec4, vec5;
2358
CxIntArray tempwa;
2359
CNbSearch *nb;
2360
2361
// mprintf("*** ScanAngle ***\n");
2362
// mprintf(" FixMol = %d, RefMol = %d\n",fixmol,refmol);
2363
m = (CMolecule*)g_oaMolecules[fixmol];
2364
// mprintf(" m->m_laSingleMolIndex[refmol] = %d\n",m->m_laSingleMolIndex[refmol]);
2365
2366
nb = co->m_pTempNbS;
2367
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[refmol]];
2368
2369
// printf("Suche Nachbarschaft von Molekuel %d...\n",refmol+1);
2370
2371
// mprintf(" SecondMol = %d\n",co->m_iSecondMol);
2372
m2 = (CMolecule*)g_oaMolecules[co->m_iSecondMol];
2373
2374
// printf("*** Molekuel %d: %s\n",z+1,m2->Name);
2375
for (z2=0;z2<m2->m_laSingleMolIndex.GetSize();z2++)
2376
{
2377
if ((co->m_iSecondMol == fixmol) && (z2 == refmol))
2378
continue;
2379
if (prev != NULL)
2380
if (!prev->Contains(co->m_iSecondMol,z2))
2381
continue;
2382
// printf(" - Vertreter %d\n",z2+1);
2383
sm2 = (CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[z2]];
2384
2385
co->m_pADF->BuildAtomList(sm,sm2,NULL,&tempwa);
2386
2387
for (z4=0;z4<tempwa.GetSize();z4+=6)
2388
{
2389
if (co->m_pADF->m_bOrtho[0])
2390
{
2391
vec0 = m_vaCoords[tempwa[z4]];
2392
vec2 = m_vaCoords[tempwa[z4+1]];
2393
vec3 = m_vaCoords[tempwa[z4+2]];
2394
vec1 = CrossP(vec2-vec0,vec3-vec0);
2395
} else
2396
{
2397
vec0 = m_vaCoords[tempwa[z4]];
2398
vec2 = m_vaCoords[tempwa[z4+1]];
2399
vec1 = vec2-vec0;
2400
}
2401
if (co->m_pADF->m_bOrtho[1])
2402
{
2403
vec4 = m_vaCoords[tempwa[z4+3]];
2404
vec3 = m_vaCoords[tempwa[z4+4]];
2405
vec5 = m_vaCoords[tempwa[z4+5]];
2406
vec2 = CrossP(vec3-vec4,vec5-vec4);
2407
} else
2408
{
2409
vec4 = m_vaCoords[tempwa[z4+3]];
2410
vec3 = m_vaCoords[tempwa[z4+4]];
2411
vec2 = vec3-vec4;
2412
}
2413
2414
tf = Angle_Deg(vec1,vec2);
2415
2416
if ((tf >= co->m_pADF->m_fMinAngle) && (tf <= co->m_pADF->m_fMaxAngle))
2417
{
2418
nb->m_iNeighbourCount++;
2419
for (z3=0;z3<nb->m_waScanNeighborCount[co->m_iSecondMol];z3++)
2420
if (((CxIntArray*)nb->m_oaScanNeighbors[co->m_iSecondMol])->GetAt(z3) == z2)
2421
{
2422
((CxIntArray*)nb->m_oaScanNeighborHits[co->m_iSecondMol])->GetAt(z3)++;
2423
goto _endang;
2424
}
2425
((CxIntArray*)nb->m_oaScanNeighbors[co->m_iSecondMol])->Add(z2);
2426
((CxIntArray*)nb->m_oaScanNeighborHits[co->m_iSecondMol])->Add(1);
2427
nb->m_waScanNeighborCount[co->m_iSecondMol]++;
2428
_endang:; break;
2429
}
2430
}
2431
}
2432
BTOUT;
2433
}*/
2434
2435
/*void CTimeStep::GatherNbDiagram(int refmol, CNbSearch *nb)
2436
{
2437
BTIN;
2438
float *del, d;
2439
int *best, b;
2440
bool *done;
2441
int z, z2, z3, z4, c, z0;
2442
CMolecule *m, *m2;
2443
CSingleMolecule *sm, *sm2;
2444
CxVector3 vec;
2445
// FILE *a;
2446
2447
m = (CMolecule*)g_oaMolecules[g_iFixMol];
2448
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[refmol]];
2449
del = new float[g_oaSingleMolecules.GetSize()];
2450
best = new int[g_oaSingleMolecules.GetSize()];
2451
done = new bool[g_oaSingleMolecules.GetSize()];
2452
2453
// printf("Suche Nachbarschaft von Molekuel %d...\n",refmol+1);
2454
2455
for (z=0;z<g_oaMolecules.GetSize();z++)
2456
{
2457
if (nb->m_bDistMode && (nb->m_faMolDist[z] == 0))
2458
{
2459
nb->m_waScanNeighborCount[z] = 0;
2460
continue;
2461
}
2462
m2 = (CMolecule*)g_oaMolecules[z];
2463
// printf("*** Molekuel %d: %s\n",z+1,m2->Name);
2464
// for (z2=0;z2<=((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)
2465
// del[z2] = 99999.0f;
2466
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)
2467
{
2468
del[z2] = 99999.0f;
2469
if ((z == g_iFixMol) && (z2 == refmol))
2470
continue;
2471
// printf(" - Vertreter %d\n",z2+1);
2472
sm2 = (CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[z2]];
2473
for (z3=0;z3<nb->m_waRefElements.GetSize();z3++)
2474
for (z4=0;z4<((CxIntArray*)nb->m_oaNbElements[z])->GetSize();z4++)
2475
{
2476
vec = m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[nb->m_waRefElements[z3]])->GetAt(nb->m_waRefAtoms[z3])] - m_vaCoords[((CxIntArray*)sm2->m_oaAtomOffset[((CxIntArray*)nb->m_oaNbElements[z])->GetAt(z4)])->GetAt(((CxIntArray*)nb->m_oaNbAtoms[z])->GetAt(z4))];
2477
if (g_bFold)
2478
{
2479
while (vec[0] >= g_fBoxX/2) vec[0] -= g_fBoxX;
2480
while (vec[0] < -g_fBoxX/2) vec[0] += g_fBoxX;
2481
while (vec[1] >= g_fBoxY/2) vec[1] -= g_fBoxY;
2482
while (vec[1] < -g_fBoxY/2) vec[1] += g_fBoxY;
2483
while (vec[2] >= g_fBoxZ/2) vec[2] -= g_fBoxZ;
2484
while (vec[2] < -g_fBoxZ/2) vec[2] += g_fBoxZ;
2485
}
2486
d = vec.GetLength();
2487
// printf(" = m1 %d (%d|%d); m2 %d (%d|%d); Dist = %f\n",z3+1,m->m_waNbElements[z3]+1,m->m_waNbAtoms[z3]+1,z4+1,m2->m_waNbElements[z4]+1,m2->m_waNbAtoms[z4]+1,d);
2488
if (d < del[z2])
2489
del[z2] = d;
2490
}
2491
// printf(" - Finaler Abstand: %f\n",del[z2]);
2492
}
2493
2494
for (z0=0;z0<nb->m_pAF->m_iResolution;z0++)
2495
{
2496
c = 0;
2497
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)
2498
done[z2] = false;
2499
while (true)
2500
{
2501
d = 999999.0f;
2502
b = -1;
2503
for (z3=0;z3<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z3++)
2504
{
2505
if (done[z3])
2506
continue;
2507
if (del[z3] < d)
2508
{
2509
d = del[z3];
2510
b = z3;
2511
}
2512
}
2513
if (d > nb->m_pAF->m_fMaxVal*z0/nb->m_pAF->m_iResolution)
2514
break;
2515
best[c] = b;
2516
done[b] = true;
2517
c++;
2518
// if (c >= ((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize())
2519
// break;
2520
}
2521
nb->m_pAF->AddToBin(nb->m_pAF->m_fMaxVal*z0/nb->m_pAF->m_iResolution,(float)c);
2522
// if (g_iSteps == 1)
2523
// mfprintf(a,"%f;%f\n",nb->m_pAF->m_fMaxVal*z0/nb->m_pAF->m_iResolution,(float)c);
2524
}
2525
// if (g_iSteps == 1)
2526
// fclose(a);
2527
}
2528
delete del;
2529
delete best;
2530
BTOUT;
2531
}*/
2532
2533
2534
int CTimeStep::REC_UniteMolecules(CSingleMolecule *sm, int i0, int depth)
2535
{
2536
int z, z2, n;
2537
CMolAtom *m;
2538
2539
n = 0;
2540
m = (CMolAtom*)sm->m_oaMolAtoms[i0];
2541
2542
/* if (g_bVerbose)
2543
{
2544
mprintf("# ");
2545
for (z2=0;z2<depth;z2++)
2546
mprintf(". ");
2547
mprintf(">>> REC_UniteMolecules MolAtom=%d, Offset=%d.\n",i0,m->m_iOffset);
2548
}*/
2549
2550
g_pUniteTemp[m->m_iOffset] = true;
2551
2552
for (z=0;z<m->m_oaBonds.GetSize();z++)
2553
{
2554
if (!g_pUniteTemp[((CMolAtom*)m->m_oaBonds[z])->m_iOffset])
2555
{
2556
if (MirrorBond(m->m_iOffset,((CMolAtom*)m->m_oaBonds[z])->m_iOffset))
2557
{
2558
if (g_bVerbose)
2559
{
2560
mprintf("# ");
2561
for (z2=0;z2<depth;z2++)
2562
mprintf(". ");
2563
mprintf(" Bond %s(%d) <--> %s(%d) unwrapped.\n",((CAtom*)g_oaAtoms[g_baAtomIndex[m->m_iOffset]])->m_sName,m->m_iOffset+1,((CAtom*)g_oaAtoms[g_baAtomIndex[((CMolAtom*)m->m_oaBonds[z])->m_iOffset]])->m_sName,((CMolAtom*)m->m_oaBonds[z])->m_iOffset+1);
2564
}
2565
n++;
2566
}
2567
n += REC_UniteMolecules(sm,((CMolAtom*)m->m_oaBonds[z])->m_iMolAtomNumber,depth+1);
2568
}
2569
}
2570
/* if (g_bVerbose)
2571
{
2572
mprintf("# ");
2573
for (z2=0;z2<depth;z2++)
2574
mprintf(". ");
2575
mprintf("<<< REC_UniteMolecules MolAtom=%d, Offset=%d.\n",i0,m->m_iOffset);
2576
}*/
2577
return n;
2578
}
2579
2580
2581
void CTimeStep::UniteMolecules(bool verbose)
2582
{
2583
BTIN;
2584
int z, z2, n;
2585
CMolecule *m;
2586
CSingleMolecule *sm;
2587
2588
for (z=0;z<g_iGesAtomCount;z++)
2589
g_pUniteTemp[z] = false;
2590
for (z=0;z<g_oaMolecules.GetSize();z++)
2591
{
2592
m = (CMolecule*)g_oaMolecules[z];
2593
if (m->m_bPseudo)
2594
continue;
2595
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
2596
{
2597
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
2598
2599
// if (g_bVerbose)
2600
// mprintf(" # UniteMolecules molecule %s (%d)\n",m->m_sName,z2+1);
2601
2602
n = REC_UniteMolecules(sm,0,0);
2603
2604
if ((n != 0) && verbose)
2605
mprintf(" - Molecule %s[%d] united, %d bonds unwrapped.\n",m->m_sName,z2+1,n);
2606
2607
if ((n != 0) && (!verbose) && g_bVerbose)
2608
mprintf("\n # UniteMolecules: Molecule %s[%d] united, %d bonds unwrapped.",m->m_sName,z2+1,n);
2609
2610
}
2611
}
2612
BTOUT;
2613
}
2614
2615
2616
bool CTimeStep::ReadTimestep(FILE *a, bool needinfo)
2617
{
2618
BTIN;
2619
switch(g_iTrajFormat)
2620
{
2621
case 0:
2622
if (!ReadXYZ(a,needinfo,&m_vaCoords))
2623
return false;
2624
break;
2625
2626
case 1:
2627
if (!ReadPDB(a,needinfo,&m_vaCoords))
2628
return false;
2629
break;
2630
2631
case 2:
2632
if (!ReadMol2(a,needinfo))
2633
return false;
2634
break;
2635
2636
case 3:
2637
if (!ReadLAMMPS(a,needinfo))
2638
return false;
2639
break;
2640
2641
case 4:
2642
if (!ReadDLPOLY(a,needinfo))
2643
return false;
2644
break;
2645
}
2646
if (g_bDoubleBox)
2647
DoubleBox();
2648
BTOUT;
2649
return true;
2650
}
2651
2652
2653
bool CTimeStep::SkipTimestep(FILE *a)
2654
{
2655
BTIN;
2656
switch(g_iTrajFormat)
2657
{
2658
case 0:
2659
if (!SkipXYZ(a))
2660
return false;
2661
break;
2662
2663
case 1:
2664
if (!SkipPDB(a))
2665
return false;
2666
break;
2667
2668
case 2:
2669
if (!SkipMol2(a))
2670
return false;
2671
break;
2672
2673
case 3:
2674
if (!SkipLAMMPS(a))
2675
return false;
2676
break;
2677
2678
case 4:
2679
if (!SkipDLPOLY(a))
2680
return false;
2681
break;
2682
}
2683
BTOUT;
2684
return true;
2685
}
2686
2687
2688
bool CTimeStep::ReadTimestepVel(FILE *a)
2689
{
2690
BTIN;
2691
char buf[256], *p, *q;
2692
int z, tc;
2693
2694
buf[0] = 0;
2695
fgets(buf,256,a);
2696
if (feof(a))
2697
{
2698
BTOUT;
2699
return false;
2700
}
2701
if (strlen(buf) > 0)
2702
buf[strlen(buf)-1] = 0;
2703
tc = atoi(buf);
2704
if (tc == 0)
2705
{
2706
BTOUT;
2707
return false;
2708
}
2709
m_vaVelocities.SetSize(tc);
2710
buf[0] = 0;
2711
fgets(buf,256,a); // Zeitschritt - egal hier
2712
if (strlen(buf) > 0)
2713
buf[strlen(buf)-1] = 0;
2714
for (z=0;z<tc;z++) // den ersten Zeitschritt einlesen
2715
{
2716
buf[0] = 0;
2717
fgets(buf,256,a);
2718
if (feof(a))
2719
{
2720
BTOUT;
2721
return false;
2722
}
2723
if (strlen(buf) > 0)
2724
buf[strlen(buf)-1] = 0;
2725
q = buf;
2726
while (*q == ' ')
2727
q++;
2728
p = strchr(q,' ');
2729
if (p == NULL)
2730
{
2731
eprintf("CTimeStep::ReadTimestepVel(): Error 1. %d, \"%s\"\n",z+1,buf);
2732
continue;
2733
}
2734
while (isdigit(*(p-1)) && (p > buf))
2735
p--;
2736
if (p == buf)
2737
{
2738
eprintf("CTimeStep::ReadTimestepVel(): No Atom laben found. %d, \"%s\"\n",z+1,buf);
2739
continue;
2740
}
2741
*p = 0;
2742
p++;
2743
q = strchr(p,' ');
2744
if (q == NULL)
2745
{
2746
eprintf("CTimeStep::ReadTimestepVel(): Error 2. %d, \"%s\"\n",z+1,p);
2747
continue;
2748
}
2749
while (*q == ' ')
2750
q++;
2751
p = strchr(q,' ');
2752
if (p == NULL)
2753
{
2754
eprintf("CTimeStep::ReadTimestepVel(): Error 3. %d, \"%s\"\n",z+1,q);
2755
continue;
2756
}
2757
*p = 0;
2758
m_vaVelocities[z][0] = (float)atof(q);
2759
q = p+1;
2760
while (*q == ' ')
2761
q++;
2762
p = strchr(q,' ');
2763
if (p == NULL)
2764
{
2765
eprintf("CTimeStep::ReadTimestepVel(): Error 4. %d, \"%s\"\n",z+1,q);
2766
continue;
2767
}
2768
*p = 0;
2769
m_vaVelocities[z][1] = (float)atof(q);
2770
q = p+1;
2771
while (*q == ' ')
2772
q++;
2773
p = strchr(q,' ');
2774
if (p != NULL)
2775
*p = 0;
2776
m_vaVelocities[z][2] = (float)atof(q);
2777
}
2778
if (g_bDoubleBox)
2779
DoubleBoxVelocity();
2780
BTOUT;
2781
return true;
2782
}
2783
2784
2785
bool CTimeStep::ReadTimestepForce(FILE *a)
2786
{
2787
BTIN;
2788
char buf[256], *p, *q;
2789
int z, tc;
2790
2791
buf[0] = 0;
2792
fgets(buf,256,a);
2793
if (feof(a))
2794
{
2795
BTOUT;
2796
return false;
2797
}
2798
if (strlen(buf) > 0)
2799
buf[strlen(buf)-1] = 0;
2800
tc = atoi(buf);
2801
if (tc == 0)
2802
{
2803
BTOUT;
2804
return false;
2805
}
2806
m_vaForces.SetSize(tc);
2807
buf[0] = 0;
2808
fgets(buf,256,a); // Zeitschritt - egal hier
2809
if (strlen(buf) > 0)
2810
buf[strlen(buf)-1] = 0;
2811
for (z=0;z<tc;z++) // den ersten Zeitschritt einlesen
2812
{
2813
buf[0] = 0;
2814
fgets(buf,256,a);
2815
if (feof(a))
2816
{
2817
BTOUT;
2818
return false;
2819
}
2820
if (strlen(buf) > 0)
2821
buf[strlen(buf)-1] = 0;
2822
q = buf;
2823
while (*q == ' ')
2824
q++;
2825
p = strchr(q,' ');
2826
if (p == NULL)
2827
{
2828
eprintf("CTimeStep::ReadTimestepForce(): Error 1. %d, \"%s\"\n",z+1,buf);
2829
continue;
2830
}
2831
while (isdigit(*(p-1)) && (p > buf))
2832
p--;
2833
if (p == buf)
2834
{
2835
eprintf("CTimeStep::ReadTimestepForce(): No Atom laben found. %d, \"%s\"\n",z+1,buf);
2836
continue;
2837
}
2838
*p = 0;
2839
p++;
2840
q = strchr(p,' ');
2841
if (q == NULL)
2842
{
2843
eprintf("CTimeStep::ReadTimestepForce(): Error 2. %d, \"%s\"\n",z+1,p);
2844
continue;
2845
}
2846
while (*q == ' ')
2847
q++;
2848
p = strchr(q,' ');
2849
if (p == NULL)
2850
{
2851
eprintf("CTimeStep::ReadTimestepForce(): Error 3. %d, \"%s\"\n",z+1,q);
2852
continue;
2853
}
2854
*p = 0;
2855
m_vaForces[z][0] = (float)atof(q);
2856
q = p+1;
2857
while (*q == ' ')
2858
q++;
2859
p = strchr(q,' ');
2860
if (p == NULL)
2861
{
2862
eprintf("CTimeStep::ReadTimestepForce(): Error 4. %d, \"%s\"\n",z+1,q);
2863
continue;
2864
}
2865
*p = 0;
2866
m_vaForces[z][1] = (float)atof(q);
2867
q = p+1;
2868
while (*q == ' ')
2869
q++;
2870
p = strchr(q,' ');
2871
if (p != NULL)
2872
*p = 0;
2873
m_vaForces[z][2] = (float)atof(q);
2874
}
2875
if (g_bDoubleBox)
2876
DoubleBoxForce();
2877
BTOUT;
2878
return true;
2879
}
2880
2881
2882
bool CTimeStep::SkipXYZ(FILE *a)
2883
{
2884
BTIN;
2885
char buf[256];
2886
int z, tc;
2887
2888
// mprintf("*** Skip Anfang ***\n");
2889
buf[0] = 0;
2890
fgets_bin(buf,256,a);
2891
if (feof(a))
2892
{
2893
BTOUT;
2894
return false;
2895
}
2896
if (strlen(buf)==0)
2897
{
2898
BTOUT;
2899
return false;
2900
}
2901
buf[strlen(buf)-1] = 0;
2902
tc = atoi(buf);
2903
// mprintf("SkipA: \"%s\".\n",buf);
2904
if (tc == 0)
2905
{
2906
BTOUT;
2907
return false;
2908
}
2909
// buf[0] = 0;
2910
fgets_bin(buf,256,a); // Zeitschritt - egal hier
2911
// mprintf("SkipB: \"%s\".\n",buf);
2912
for (z=0;z<tc;z++) // den ersten Zeitschritt einlesen
2913
{
2914
// buf[0] = 0;
2915
fgets_bin(buf,256,a);
2916
// mprintf("SkipC%d: \"%s\".\n",z,buf);
2917
if (feof(a))
2918
{
2919
BTOUT;
2920
return false;
2921
}
2922
}
2923
// mprintf("*** Skip Ende ***\n");
2924
BTOUT;
2925
return true;
2926
}
2927
2928
2929
void CTimeStep::CopyFrom(CTimeStep *t)
2930
{
2931
BTIN;
2932
int z;
2933
char *p;
2934
CxVector3 v;
2935
2936
m_iGesAtomCount = t->m_iGesAtomCount;
2937
m_vaCoords.CopyFrom(&t->m_vaCoords);
2938
if (g_bKeepUnfoldedCoords)
2939
m_vaCoords_Unfolded.CopyFrom(&t->m_vaCoords_Unfolded);
2940
m_vaForces.CopyFrom(&t->m_vaForces);
2941
m_vaVelocities.CopyFrom(&t->m_vaVelocities);
2942
if (t->m_paLabels.GetSize() != 0)
2943
{
2944
for (z=0;z<m_paLabels.GetSize();z++)
2945
delete[] (char*)m_paLabels[z];
2946
m_paLabels.RemoveAll();
2947
for (z=0;z<t->m_paLabels.GetSize();z++)
2948
{
2949
try { p = new char[strlen((char*)t->m_paLabels[z])+1]; } catch(...) { p = NULL; }
2950
if (p == NULL) NewException((double)(strlen((char*)t->m_paLabels[z])+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2951
2952
strcpy(p,(char*)t->m_paLabels[z]);
2953
m_paLabels.Add(p);
2954
}
2955
}
2956
if (t->m_pComment != NULL)
2957
{
2958
if (m_pComment == NULL)
2959
{
2960
try { m_pComment = new char[256]; } catch(...) { m_pComment = NULL; }
2961
if (m_pComment == NULL) NewException((double)256*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2962
}
2963
strcpy(m_pComment,t->m_pComment);
2964
}
2965
BTOUT;
2966
}
2967
2968
2969
long CTimeStep::ExtractNumber(int i)
2970
{
2971
BXIN;
2972
char *p, *q, buf[20];
2973
int z;
2974
long l;
2975
2976
if (m_pComment == NULL)
2977
return -1;
2978
p = m_pComment;
2979
for (z=0;z<i;z++)
2980
{
2981
while ((!isdigit(*p)) && (*p != 0))
2982
p++;
2983
if (*p == 0)
2984
{
2985
BXOUT;
2986
return -1;
2987
}
2988
q = p+1;
2989
while ((isdigit(*q)) && (*q != 0))
2990
q++;
2991
if (*q == 0)
2992
{
2993
BXOUT;
2994
return -1;
2995
}
2996
p = q+1;
2997
}
2998
while ((!isdigit(*p)) && (*p != 0))
2999
p++;
3000
if (*p == 0)
3001
{
3002
BXOUT;
3003
return -1;
3004
}
3005
q = p;
3006
while ((isdigit(*q)) && (*q != 0))
3007
q++;
3008
if (q == p)
3009
{
3010
BXOUT;
3011
return -1;
3012
}
3013
memcpy(buf,p,q-p);
3014
buf[q-p] = 0;
3015
l = atoi(buf);
3016
BXOUT;
3017
return l;
3018
}
3019
3020
3021
int CTimeStep::GetCommentNumberCount()
3022
{
3023
BXIN;
3024
char *p, *q;
3025
int z;
3026
3027
if (m_pComment == NULL)
3028
return 0;
3029
p = m_pComment;
3030
z = 0;
3031
while (true)
3032
{
3033
while ((!isdigit(*p)) && (*p != 0))
3034
p++;
3035
if (*p == 0)
3036
{
3037
// mprintf("GetCommentNumberCount 1: %d (p=\"%s\", q=\"%s\")\n",z,p,q);
3038
BXOUT;
3039
return z;
3040
}
3041
q = p;
3042
while ((isdigit(*q)) && (*q != 0))
3043
q++;
3044
if (q == p)
3045
{
3046
// mprintf("GetCommentNumberCount 2: %d (p=\"%s\", q=\"%s\")\n",z,p,q);
3047
BXOUT;
3048
return z;
3049
}
3050
z++;
3051
if (*q == 0)
3052
{
3053
// mprintf("GetCommentNumberCount 3: %d (p=\"%s\", q=\"%s\")\n",z,p,q);
3054
BXOUT;
3055
return z;
3056
}
3057
p = q+1;
3058
}
3059
return 0; // Never happens
3060
}
3061
3062
3063
bool CTimeStep::ScanWannier(bool verbose)
3064
{
3065
BTIN;
3066
int z, z2, z3;
3067
float td, d, dx, dy, dz;
3068
CMolecule *m;
3069
3070
if (g_bVerbose)
3071
{
3072
mprintf(WHITE,"\n*** ScanWannier ***\n\n");
3073
verbose = true;
3074
}
3075
3076
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
3077
((CSingleMolecule*)g_oaSingleMolecules[z])->m_laWannier.RemoveAll_KeepSize();
3078
3079
for (z=0;z<g_iGesAtomCount;z++)
3080
{
3081
if (g_baAtomIndex[z] != g_iWannierAtomType)
3082
continue;
3083
d = 9999.0f;
3084
z3 = -1;
3085
for (z2=0;z2<g_iGesAtomCount;z2++)
3086
{
3087
if (g_baAtomIndex[z2] == g_iWannierAtomType)
3088
continue;
3089
dx = m_vaCoords[z][0]-m_vaCoords[z2][0];
3090
dy = m_vaCoords[z][1]-m_vaCoords[z2][1];
3091
dz = m_vaCoords[z][2]-m_vaCoords[z2][2];
3092
if (g_bPeriodicX)
3093
{
3094
while (dx > g_fBoxX/2.0f) dx -= g_fBoxX;
3095
while (dx < -g_fBoxX/2.0f) dx += g_fBoxX;
3096
}
3097
if (g_bPeriodicY)
3098
{
3099
while (dy > g_fBoxY/2.0f) dy -= g_fBoxY;
3100
while (dy < -g_fBoxY/2.0f) dy += g_fBoxY;
3101
}
3102
if (g_bPeriodicZ)
3103
{
3104
while (dz > g_fBoxZ/2.0f) dz -= g_fBoxZ;
3105
while (dz < -g_fBoxZ/2.0f) dz += g_fBoxZ;
3106
}
3107
td = (float)sqrt(dx*dx+dy*dy+dz*dz);
3108
if (td < d)
3109
{
3110
d = td;
3111
z3 = z2;
3112
}
3113
}
3114
if (z3 == -1)
3115
abort();
3116
if (g_bPeriodicX)
3117
{
3118
while (m_vaCoords[z][0]-m_vaCoords[z3][0] > g_fBoxX/2.0f) m_vaCoords[z][0] -= g_fBoxX;
3119
while (m_vaCoords[z][0]-m_vaCoords[z3][0] < -g_fBoxX/2.0f) m_vaCoords[z][0] += g_fBoxX;
3120
}
3121
if (g_bPeriodicY)
3122
{
3123
while (m_vaCoords[z][1]-m_vaCoords[z3][1] > g_fBoxY/2.0f) m_vaCoords[z][1] -= g_fBoxY;
3124
while (m_vaCoords[z][1]-m_vaCoords[z3][1] < -g_fBoxY/2.0f) m_vaCoords[z][1] += g_fBoxY;
3125
}
3126
if (g_bPeriodicZ)
3127
{
3128
while (m_vaCoords[z][2]-m_vaCoords[z3][2] > g_fBoxZ/2.0f) m_vaCoords[z][2] -= g_fBoxZ;
3129
while (m_vaCoords[z][2]-m_vaCoords[z3][2] < -g_fBoxZ/2.0f) m_vaCoords[z][2] += g_fBoxZ;
3130
}
3131
z2 = g_laAtomSMIndex[z3];
3132
if (d > 100.0)
3133
{
3134
eprintf("Step %d: Wannier center at offset %d too far away from any atom (closest atom is %s[%d] %s%d, %.0f pm).\n",g_iSteps,z+1,((CMolecule*)g_oaMolecules[((CSingleMolecule*)g_oaSingleMolecules[z2])->m_iMolType])->m_sName,((CSingleMolecule*)g_oaSingleMolecules[z2])->m_iMolSMIndex+1,((CAtom*)g_oaAtoms[g_waAtomRealElement[z3]])->m_sName,g_waAtomMolNumber[z3]+1,d);
3135
} else if (verbose)
3136
mprintf(" - Wannier center %d belongs to %s[%d] %s%d (%.0f pm).\n",z+1,((CMolecule*)g_oaMolecules[((CSingleMolecule*)g_oaSingleMolecules[z2])->m_iMolType])->m_sName,((CSingleMolecule*)g_oaSingleMolecules[z2])->m_iMolSMIndex+1,((CAtom*)g_oaAtoms[g_waAtomRealElement[z3]])->m_sName,g_waAtomMolNumber[z3]+1,d);
3137
/* if (z2 == -1)
3138
{
3139
eprintf("Wannier center %d: Atom %d does not belong to any molecule.\n",z+1,z3+1);
3140
continue;
3141
}*/
3142
// mprintf("Wannier Center %d hat Abstand %.2f zu Atom %d in SM %d.\n",z+1,d,z3+1,z2+1);
3143
((CSingleMolecule*)g_oaSingleMolecules[z2])->m_laWannier.Add(z);
3144
}
3145
if (verbose)
3146
mprintf("\n\n");
3147
for (z=0;z<g_oaMolecules.GetSize();z++)
3148
{
3149
m = (CMolecule*)g_oaMolecules[z];
3150
if (m->m_iWannierCount == 0)
3151
{
3152
m->m_iWannierCount = ((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]])->m_laWannier.GetSize();
3153
td = 0;
3154
for (z2=0;z2<m->m_baAtomIndex.GetSize();z2++)
3155
{
3156
if (m->m_baAtomIndex[z2] == g_iWannierAtomType)
3157
continue;
3158
if (m->m_baAtomIndex[z2] == g_iVirtAtomType)
3159
continue;
3160
td += ((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_fCharge * m->m_waAtomCount[z2];
3161
}
3162
m->m_fCharge = td-m->m_iWannierCount*g_fWannierCharge;
3163
mprintf(" - Molecule %s contains %d wannier centers. Total charge is %.2f - %.2f = %.2f\n",m->m_sName,m->m_iWannierCount,td,m->m_iWannierCount*g_fWannierCharge,m->m_fCharge);
3164
if (m->m_fCharge > 5.0)
3165
{
3166
eprintf("\n This molecular charge seems to be too high.\n\n");
3167
if (!AskYesNo(" Do you want to continue (y/n)? [yes] ",true))
3168
return false;
3169
}
3170
}
3171
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
3172
{
3173
if (m->m_iWannierCount != ((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]])->m_laWannier.GetSize())
3174
eprintf("Step %d: Molecule %s[%d] contains %d instead of %d wannier centers.\n",g_iSteps,m->m_sName,z2+1,((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]])->m_laWannier.GetSize(),m->m_iWannierCount);
3175
}
3176
}
3177
BTOUT;
3178
return true;
3179
}
3180
3181
3182
void CTimeStep::CalcDipoles()
3183
{
3184
BTIN;
3185
int z, z2, z3, z4;
3186
CMolecule *m;
3187
CSingleMolecule *sm;
3188
CAtom *a;
3189
CxVector3 dc;
3190
3191
// mprintf("\n*** CalcDipoles ***");
3192
3193
for (z=0;z<g_oaMolecules.GetSize();z++)
3194
{
3195
m = (CMolecule*)g_oaMolecules[z];
3196
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
3197
{
3198
if (g_bVerbose)
3199
mprintf("\nCalcDipoles %s (%d):\n",m->m_sName,z2+1);
3200
3201
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
3202
3203
sm->m_vDipole = CxVector3(0,0,0);
3204
3205
if ((!g_bWannier) && (!m->m_bChargesAssigned))
3206
continue;
3207
3208
if (g_bDipoleRefFixed)
3209
dc = CxVector3(0,0,0);
3210
else dc = m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[m->m_iDipoleCenterType])->GetAt(m->m_iDipoleCenterIndex)];
3211
3212
if (g_bVerbose)
3213
mprintf(" Ref. point is ( %f | %f | %f )\n",dc[0],dc[1],dc[2]);
3214
3215
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
3216
{
3217
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
3218
continue;
3219
3220
if (g_bWannier)
3221
if (m->m_baAtomIndex[z3] == g_iWannierAtomType)
3222
continue;
3223
3224
a = (CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]];
3225
for (z4=0;z4<m->m_waAtomCount[z3];z4++)
3226
{
3227
// mprintf(" %s%d %.2f x ",a->m_sName,z4+1,a->m_fCharge);
3228
// (m_vaCoords[sm->m_iAtomOffset[z3][z4]]-m_vaCoords[sm->m_iAtomOffset[m->Elements-1][0]]).Dump();
3229
// mprintf("\n");
3230
// mprintf(" %s%d %.2f (%d)\n",a->m_sName,z4+1,a->m_fCharge,((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4));
3231
3232
if (g_bWannier)
3233
{
3234
sm->m_vDipole += a->m_fCharge * (m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)] - dc);
3235
3236
if (g_bVerbose)
3237
mprintf(" %.2f: ( %f | %f | %f )\n",a->m_fCharge,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]);
3238
} else
3239
{
3240
if (g_bReadChargesFrom4thXYZ)
3241
{
3242
// mprintf("Moep. z3=%d, z4=%d, c=%f.\n",z3,z4,m_faCharge[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)]);
3243
sm->m_vDipole += m_faCharge[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)] * (m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)] - dc);
3244
if (g_bVerbose)
3245
mprintf(" %.2f: ( %f | %f | %f )\n",m_faCharge[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]);
3246
} else
3247
{
3248
sm->m_vDipole += ((CxFloatArray*)m->m_oaCharges[z3])->GetAt(z4) * (m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)] - dc);
3249
if (g_bVerbose)
3250
mprintf(" %.2f: ( %f | %f | %f )\n",((CxFloatArray*)m->m_oaCharges[z3])->GetAt(z4),m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]);
3251
}
3252
}
3253
}
3254
}
3255
for (z3=0;z3<sm->m_laWannier.GetSize();z3++)
3256
{
3257
// mprintf(" - %.2f x ",g_fWannierCharge);
3258
// (m_vaCoords[sm->m_waWannier[z3]] - m_vaCoords[sm->m_iAtomOffset[m->Elements-1][0]]).Dump();
3259
// mprintf("\n");
3260
sm->m_vDipole -= g_fWannierCharge * (m_vaCoords[sm->m_laWannier[z3]] - dc);
3261
3262
if (g_bVerbose)
3263
mprintf(" %.2f: ( %f | %f | %f )\n",-g_fWannierCharge,m_vaCoords[sm->m_laWannier[z3]][0],m_vaCoords[sm->m_laWannier[z3]][1],m_vaCoords[sm->m_laWannier[z3]][2]);
3264
}
3265
// mprintf(" = ");
3266
// sm->m_vDipole.Dump();
3267
// mprintf("\n");
3268
sm->m_vDipole *= 0.048008f; // Conversion e*pm --> Debye
3269
3270
if (g_bVerbose)
3271
mprintf(" Result: %f.\n",sm->m_vDipole.GetLength());
3272
3273
// mprintf("Molecule %s - Dipole %.3f\n",m->Name,sm->m_vDipole.GetLength());
3274
}
3275
}
3276
BTOUT;
3277
}
3278
3279
3280
void CTimeStep::DoubleBox()
3281
{
3282
int px, py, pz, z;
3283
char *p;
3284
3285
if (m_vaCoords.GetSize() < g_iGesAtomCount)
3286
m_vaCoords.SetSize(g_iGesAtomCount);
3287
3288
if (m_paLabels.GetSize() != 0)
3289
m_paLabels.SetSize(g_iGesAtomCount);
3290
3291
for (pz=0;pz<g_iDoubleBoxZ;pz++)
3292
{
3293
for (py=0;py<g_iDoubleBoxY;py++)
3294
{
3295
for (px=0;px<g_iDoubleBoxX;px++)
3296
{
3297
if ((px == 0) && (py == 0) && (pz == 0))
3298
continue;
3299
for (z=0;z<g_iGesAtomCount/g_iDoubleBoxFactor;z++)
3300
{
3301
m_vaCoords[(pz*g_iDoubleBoxX*g_iDoubleBoxY+py*g_iDoubleBoxX+px)*g_iGesAtomCount/g_iDoubleBoxFactor+z] = m_vaCoords[z] + CxVector3(px*g_fBoxX/g_iDoubleBoxX,py*g_fBoxY/g_iDoubleBoxY,pz*g_fBoxZ/g_iDoubleBoxZ);
3302
if (m_paLabels.GetSize() != 0)
3303
{
3304
try { p = new char[strlen((char*)m_paLabels[z])+1]; } catch(...) { p = NULL; }
3305
if (p == NULL) NewException((double)(strlen((char*)m_paLabels[z])+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3306
3307
strcpy(p,(char*)m_paLabels[z]);
3308
m_paLabels[(pz*g_iDoubleBoxX*g_iDoubleBoxY+py*g_iDoubleBoxX+px)*g_iGesAtomCount/g_iDoubleBoxFactor+z] = p;
3309
}
3310
}
3311
}
3312
}
3313
}
3314
m_iGesAtomCount = g_iGesAtomCount;
3315
}
3316
3317
3318
void CTimeStep::DoubleBoxVelocity()
3319
{
3320
int px, py, pz, z;
3321
3322
if (m_vaVelocities.GetSize() < g_iGesAtomCount)
3323
m_vaVelocities.SetSize(g_iGesAtomCount);
3324
3325
for (pz=0;pz<g_iDoubleBoxZ;pz++)
3326
{
3327
for (py=0;py<g_iDoubleBoxY;py++)
3328
{
3329
for (px=0;px<g_iDoubleBoxX;px++)
3330
{
3331
if ((px == 0) && (py == 0) && (pz == 0))
3332
continue;
3333
for (z=0;z<g_iGesAtomCount/g_iDoubleBoxFactor;z++)
3334
m_vaVelocities[(pz*g_iDoubleBoxX*g_iDoubleBoxY+py*g_iDoubleBoxX+px)*g_iGesAtomCount/g_iDoubleBoxFactor+z] = m_vaVelocities[z];
3335
}
3336
}
3337
}
3338
}
3339
3340
3341
void CTimeStep::DoubleBoxForce()
3342
{
3343
int px, py, pz, z;
3344
3345
if (m_vaForces.GetSize() < g_iGesAtomCount)
3346
m_vaForces.SetSize(g_iGesAtomCount);
3347
3348
for (pz=0;pz<g_iDoubleBoxZ;pz++)
3349
{
3350
for (py=0;py<g_iDoubleBoxY;py++)
3351
{
3352
for (px=0;px<g_iDoubleBoxX;px++)
3353
{
3354
if ((px == 0) && (py == 0) && (pz == 0))
3355
continue;
3356
for (z=0;z<g_iGesAtomCount/g_iDoubleBoxFactor;z++)
3357
m_vaForces[(pz*g_iDoubleBoxX*g_iDoubleBoxY+py*g_iDoubleBoxX+px)*g_iGesAtomCount/g_iDoubleBoxFactor+z] = m_vaForces[z];
3358
}
3359
}
3360
}
3361
}
3362
3363
3364
bool CTimeStep::ReadXYZ(FILE *a, bool needinfo, CxVec3Array *v)
3365
{
3366
BTIN;
3367
char buf[256], obuf[256], *p, *q, *r;
3368
int z, /*i,*/ j;
3369
const char *separators = " ,;\"'\t";
3370
3371
// mprintf("*** Read Anfang.\n");
3372
j = 0;
3373
// m_iSizeBytes = 0;
3374
_readagain:
3375
buf[0] = 0;
3376
fgets_bin(buf,256,a);
3377
// m_iSizeBytes += strlen(buf);
3378
if (strlen(buf) > 0)
3379
buf[strlen(buf)-1] = 0;
3380
// mprintf("Read1: \"%s\".\n",buf);
3381
goto _firsttry;
3382
_again:
3383
eprintf("\nTrajectory file seems to be damaged. Searching for next time step...");
3384
_firsttry:
3385
if (feof(a))
3386
{
3387
// mprintf("CTimeStep::ReadTimestep(): Unexpected End of File (1).\n");
3388
BTOUT;
3389
return false;
3390
}
3391
if (strchr(buf,'.') != NULL)
3392
{
3393
if (j < 10)
3394
eprintf("x",j,buf);
3395
// mprintf("x: %d - \"%s\"\n",j,buf);
3396
j++;
3397
goto _readagain;
3398
}
3399
m_iGesAtomCount = atoi(buf);
3400
if (m_iGesAtomCount == 0)
3401
{
3402
eprintf("\nCTimeStep::ReadXYZ(): Error - atom count = 0. \"%s\"",buf);
3403
goto _readagain;
3404
}
3405
if (m_pComment == NULL)
3406
{
3407
try { m_pComment = new char[128]; } catch(...) { m_pComment = NULL; }
3408
if (m_pComment == NULL) NewException((double)128*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3409
}
3410
if (needinfo)
3411
{
3412
for (z=0;z<m_paLabels.GetSize();z++)
3413
delete[] (char*)m_paLabels[z];
3414
m_paLabels.RemoveAll();
3415
if (g_bDoubleBox)
3416
m_paLabels.SetSize(m_iGesAtomCount*g_iDoubleBoxFactor);
3417
else m_paLabels.SetSize(m_iGesAtomCount);
3418
}
3419
if (v->GetSize() < (long)m_iGesAtomCount)
3420
v->SetSize(m_iGesAtomCount);
3421
3422
if (g_bKeepOriginalCoords)
3423
{
3424
if (m_vaCoords_Original.GetSize() < (long)m_iGesAtomCount)
3425
m_vaCoords_Original.SetSize(m_iGesAtomCount);
3426
}
3427
3428
m_pComment[0] = 0;
3429
fgets_bin(m_pComment,128,a); // Zeitschritt - egal hier
3430
// if (strlen(m_pComment) > 0)
3431
// m_pComment[strlen(m_pComment)-1] = 0;
3432
3433
p = m_pComment;
3434
while (*p != 0)
3435
{
3436
if ((*p == 10) || (*p == 13))
3437
*p = 0;
3438
p++;
3439
}
3440
// mprintf("Comment: \"%s\".\n",m_pComment);
3441
// m_iSizeBytes += strlen(m_pComment);
3442
3443
if (g_bReadChargesFrom4thXYZ)
3444
m_faCharge.SetSize(m_iGesAtomCount);
3445
3446
for (z=0;z<(long)m_iGesAtomCount;z++) // den ersten Zeitschritt einlesen
3447
{
3448
buf[0] = 0;
3449
fgets_bin(buf,256,a);
3450
if (feof(a))
3451
{
3452
eprintf("\nCTimeStep::ReadXYZ(): Unexpected end of file (2). \"%s\"\n",buf);
3453
BTOUT;
3454
return false;
3455
}
3456
// m_iSizeBytes += strlen(buf);
3457
buf[strlen(buf)-1] = 0;
3458
// mprintf(" %d: \"%s\".\n",z,buf);
3459
strcpy(obuf,buf);
3460
// i = 0;
3461
3462
p = &buf[0];
3463
while (strchr(separators,*p) != NULL)
3464
p++;
3465
q = p+1;
3466
while ((strchr(separators,*q) == NULL) && (*q != 0))
3467
q++;
3468
if (*q == 0)
3469
{
3470
eprintf("\nCTimeStep::ReadXYZ(): %d: Incomplete line (1): \"%s\"\n",z+1,obuf);
3471
BTOUT;
3472
return false;
3473
}
3474
*q = 0;
3475
3476
if (needinfo)
3477
{
3478
if (strlen(p) > 7)
3479
{
3480
eprintf("\nCTimeStep::ReadXYZ(): \"%s\" - Maximum length of atom labels is 7 chars; truncating.\n",p);
3481
p[7] = 0;
3482
}
3483
3484
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
3485
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3486
3487
strcpy(r,p);
3488
m_paLabels[z] = r;
3489
}
3490
3491
q++;
3492
while (strchr(separators,*q) != NULL)
3493
q++;
3494
p = q;
3495
while ((strchr(separators,*p) == NULL) && (*p != 0))
3496
p++;
3497
if (*p == 0)
3498
{
3499
eprintf("\nCTimeStep::ReadXYZ(): %d: Incomplete line (2): \"%s\"",z+1,obuf);
3500
goto _again;
3501
}
3502
*p = 0;
3503
(*v)[z][0] = (float)atof(q) * 100.0f;
3504
3505
if (g_bKeepOriginalCoords)
3506
m_vaCoords_Original[z][0] = (double)atof(q) * 100.0;
3507
3508
q = p+1;
3509
while (strchr(separators,*q) != NULL)
3510
q++;
3511
p = q;
3512
while ((strchr(separators,*p) == NULL) && (*p != 0))
3513
p++;
3514
if (*p == 0)
3515
{
3516
eprintf("\nCTimeStep::ReadXYZ(): %d: Incomplete line (3) \"%s\"",z+1,obuf);
3517
goto _again;
3518
}
3519
*p = 0;
3520
(*v)[z][1] = (float)atof(q) * 100.0f;
3521
3522
if (g_bKeepOriginalCoords)
3523
m_vaCoords_Original[z][1] = (double)atof(q) * 100.0;
3524
3525
q = p+1;
3526
while (strchr(separators,*q) != NULL)
3527
q++;
3528
p = q;
3529
while ((strchr(separators,*p) == NULL) && (*p != 0))
3530
p++;
3531
if (g_bReadChargesFrom4thXYZ)
3532
{
3533
if (*p == 0)
3534
{
3535
eprintf("\nCTimeStep::ReadXYZ(): %d: Incomplete line (4) \"%s\"",z+1,obuf);
3536
goto _again;
3537
}
3538
*p = 0;
3539
} else
3540
{
3541
if (*p != 0)
3542
*p = 0;
3543
}
3544
(*v)[z][2] = (float)atof(q) * 100.0f;
3545
3546
if (g_bKeepOriginalCoords)
3547
m_vaCoords_Original[z][2] = (double)atof(q) * 100.0;
3548
3549
if (g_bReadChargesFrom4thXYZ)
3550
{
3551
q = p+1;
3552
while (strchr(separators,*q) != NULL)
3553
q++;
3554
p = q;
3555
while ((strchr(separators,*p) == NULL) && (*p != 0))
3556
p++;
3557
if (*p != 0)
3558
*p = 0;
3559
m_faCharge[z] = (float)atof(q);
3560
} else if (needinfo && (z==0))
3561
{
3562
if (*p == 0)
3563
goto _no4;
3564
q = p+1;
3565
if (*q == 0)
3566
goto _no4;
3567
while (strchr(separators,*q) != NULL)
3568
q++;
3569
p = q;
3570
while ((strchr(separators,*p) == NULL) && (*p != 0))
3571
p++;
3572
if ((p-q) > 3)
3573
{
3574
for (;q<p;q++)
3575
if (!(((*q >= '0') && (*q <= '9')) || (*q == '-') || (*q == '.')))
3576
goto _no4;
3577
g_bXYZ4thCol = true;
3578
_no4:;
3579
}
3580
}
3581
3582
/* q = strchr(buf,'.');
3583
if (q != NULL)
3584
{
3585
i++;
3586
q = strchr(q+1,'.');
3587
}
3588
if (q != NULL)
3589
{
3590
i++;
3591
q = strchr(q+1,'.');
3592
}
3593
if (q==NULL)
3594
{
3595
eprintf("\nCTimeStep::ReadXYZ(): Error - only %d/3 dots. %d, \"%s\"",i,z+1,buf);
3596
goto _again;
3597
}
3598
q = buf;
3599
while (*q == ' ')
3600
q++;
3601
p = strchr(q,' ');
3602
if (p == NULL)
3603
{
3604
eprintf("\nCTimeStep::ReadXYZ(): Error 1. %d, \"%s\"",z+1,buf);
3605
goto _again;
3606
}
3607
while (isdigit(*(p-1)) && (p > buf))
3608
p--;
3609
if (p == buf)
3610
{
3611
eprintf("\nCTimeStep::ReadXYZ(): No Atom label found. %d, \"%s\"",z+1,buf);
3612
goto _again;
3613
}
3614
*p = 0;
3615
if (needinfo)
3616
{
3617
r = new char[strlen(q)+1];
3618
strcpy(r,q);
3619
m_paLabels[z] = r;
3620
}
3621
q = p+1;
3622
while (*q == ' ')
3623
q++;
3624
p = strchr(q,' ');
3625
if (p == NULL)
3626
{
3627
eprintf("\nCTimeStep::ReadXYZ(): Error 3. %d, \"%s\"",z+1,q);
3628
goto _again;
3629
}
3630
*p = 0;
3631
(*v)[z][0] = (float)atof(q) * 100.0f;
3632
q = p+1;
3633
while (*q == ' ')
3634
q++;
3635
p = strchr(q,' ');
3636
if (p == NULL)
3637
{
3638
eprintf("\nCTimeStep::ReadXYZ(): Error 4. %d, \"%s\"",z+1,q);
3639
goto _again;
3640
}
3641
*p = 0;
3642
(*v)[z][1] = (float)atof(q) * 100.0f;
3643
q = p+1;
3644
while (*q == ' ')
3645
q++;
3646
p = strchr(q,' ');
3647
if (p != NULL)
3648
*p = 0;
3649
(*v)[z][2] = (float)atof(q) * 100.0f;*/
3650
3651
3652
}
3653
// mprintf("*** Read Ende.\n");
3654
BTOUT;
3655
return true;
3656
}
3657
3658
3659
bool CTimeStep::ReadPDB(FILE *a, bool needinfo, CxVec3Array *v)
3660
{
3661
int i;
3662
static char buf[256], obuf[256], buf2[64];
3663
char *p, *q, *r;
3664
float x, y, z;
3665
bool b;
3666
3667
v->RemoveAll_KeepSize();
3668
for (i=0;i<m_paLabels.GetSize();i++)
3669
delete[] (char*)m_paLabels[i];
3670
m_paLabels.RemoveAll();
3671
while (true)
3672
{
3673
fgets_bin(buf,256,a);
3674
if (feof(a))
3675
return false;
3676
if (strlen(buf) == 0)
3677
continue;
3678
buf[strlen(buf)-1] = 0;
3679
strcpy(obuf,buf);
3680
if (g_bNPT)
3681
{
3682
if (strstr(buf,"CRYST1") != 0) // Boxlaenge
3683
{
3684
// mprintf(GREY,"\"%s\".\n",buf);
3685
p = &buf[6];
3686
while (*p == ' ')
3687
p++;
3688
q = p;
3689
while ((*q != ' ') && (*q != 0))
3690
q++;
3691
if (*q == 0)
3692
{
3693
eprintf("Error 5 reading PDB line: \"%s\".\n",obuf);
3694
return false;
3695
}
3696
*q = 0;
3697
g_fBoxX = (float)(atof(p)*100.0);
3698
p = q+1;
3699
3700
while (*p == ' ')
3701
p++;
3702
q = p;
3703
while ((*q != ' ') && (*q != 0))
3704
q++;
3705
if (*q == 0)
3706
{
3707
eprintf("Error 6 reading PDB line: \"%s\".\n",obuf);
3708
return false;
3709
}
3710
*q = 0;
3711
g_fBoxY = (float)(atof(p)*100.0);
3712
p = q+1;
3713
3714
while (*p == ' ')
3715
p++;
3716
q = p;
3717
while ((*q != ' ') && (*q != 0))
3718
q++;
3719
if (*q != 0)
3720
*q = 0;
3721
g_fBoxZ = (float)(atof(p)*100.0);
3722
// mprintf(GREY,"--> %f %f %f\n",g_fBoxX,g_fBoxY,g_fBoxZ);
3723
}
3724
}
3725
3726
if (strstr(buf,"END") == buf)
3727
break;
3728
3729
if ((strstr(buf,"ATOM")==0) && (strstr(buf,"HETATM")==0))
3730
continue;
3731
3732
p = &buf[7];
3733
while (!(isalpha(*p) || (*p == '_')) && (*p != 0))
3734
p++;
3735
if (*p == 0)
3736
{
3737
eprintf("Error 4 reading PDB line: \"%s\".\n",obuf);
3738
return false;
3739
}
3740
q = p;
3741
while (isalpha(*q) || (*q == '_'))
3742
q++;
3743
if (needinfo)
3744
{
3745
*q = 0;
3746
if (strlen(p) > 7)
3747
{
3748
eprintf("\nCTimeStep::ReadPDB(): \"%s\" - maximum length for atom labels is 7 chars; truncating.\n",p);
3749
p[7] = 0;
3750
}
3751
3752
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
3753
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3754
3755
strcpy(r,p);
3756
m_paLabels.Add(r);
3757
}
3758
p = q+1;
3759
3760
while ((*p != '.') && (*p != 0))
3761
p++;
3762
3763
while (*p != ' ')
3764
p--;
3765
3766
p++;
3767
3768
q = p;
3769
b = false;
3770
while (*q != 0)
3771
{
3772
if (b)
3773
{
3774
if ((*q == ' ') || (*q == '-'))
3775
break;
3776
}
3777
if (*q == 0)
3778
break;
3779
if ((*q == '-') || (*q == '.') || ((*q >= '0') && (*q <= '9')))
3780
b = true;
3781
q++;
3782
}
3783
// q = strchr(p,' ');
3784
if (*q == 0)
3785
{
3786
eprintf("\nCTimeStep::ReadPDB(): Error 1. \"%s\".",obuf);
3787
return false;
3788
}
3789
memcpy(buf2,p,q-p);
3790
buf2[q-p] = 0;
3791
x = (float)atof(buf2) * 100.0f;
3792
// mprintf("\n \"%s\".",buf2);
3793
3794
p = q;
3795
b = false;
3796
while (*q != 0)
3797
{
3798
if (b)
3799
{
3800
if ((*q == ' ') || (*q == '-'))
3801
break;
3802
}
3803
if (*q == 0)
3804
break;
3805
if ((*q == '-') || (*q == '.') || ((*q >= '0') && (*q <= '9')))
3806
b = true;
3807
q++;
3808
}
3809
// q = strchr(p,' ');
3810
if (*q == 0)
3811
{
3812
eprintf("\nCTimeStep::ReadPDB(): Error 2. \"%s\".",obuf);
3813
return false;
3814
}
3815
memcpy(buf2,p,q-p);
3816
buf2[q-p] = 0;
3817
y = (float)atof(buf2) * 100.0f;
3818
// mprintf("\n \"%s\".",buf2);
3819
3820
z = (float)atof(q) * 100.0f;
3821
// mprintf("\n \"%s\".",q);
3822
3823
// mprintf("\n%f, %f, %f",x,y,z);
3824
3825
m_vaCoords.Add(CxVector3(x,y,z));
3826
}
3827
m_iGesAtomCount = m_vaCoords.GetSize();
3828
3829
return true;
3830
}
3831
3832
3833
bool CTimeStep::SkipPDB(FILE *a)
3834
{
3835
char buf[256];
3836
// bool b;
3837
3838
while (true)
3839
{
3840
fgets_bin(buf,256,a);
3841
if (feof(a))
3842
return false;
3843
if (strlen(buf) == 0)
3844
continue;
3845
buf[strlen(buf)-1] = 0;
3846
if (strstr(buf,"END") == buf)
3847
break;
3848
}
3849
return true;
3850
}
3851
3852
3853
bool CTimeStep::ReadLAMMPS(FILE *a, bool needinfo)
3854
{
3855
int i;
3856
char buf[256], obuf[256], *p, *q, *r;
3857
float x, y, z;
3858
3859
m_vaCoords.RemoveAll_KeepSize();
3860
for (i=0;i<m_paLabels.GetSize();i++)
3861
delete[] (char*)m_paLabels[i];
3862
m_paLabels.RemoveAll();
3863
m_iGesAtomCount = 0;
3864
while (true)
3865
{
3866
fgets_bin(buf,256,a);
3867
if (feof(a))
3868
return false;
3869
if (strlen(buf) == 0)
3870
continue;
3871
buf[strlen(buf)-1] = 0;
3872
strcpy(obuf,buf);
3873
if (g_bNPT)
3874
{
3875
if (strstr(buf,"ITEM: BOX BOUNDS") != 0) // Boxlaenge
3876
{
3877
for (i=0;i<3;i++)
3878
{
3879
fgets_bin(buf,256,a);
3880
if (feof(a))
3881
return false;
3882
3883
p = &buf[0];
3884
while (strchr(" ",*p) != NULL)
3885
p++;
3886
q = p+1;
3887
while ((strchr(" ",*q) == NULL) && (*q != 0))
3888
q++;
3889
if (*q == 0)
3890
{
3891
eprintf("\nCTimeStep::ReadLAMMPS(): Incomplete line: \"%s\"\n",obuf);
3892
return false;
3893
}
3894
*q = 0;
3895
x = atof(p);
3896
3897
p = q+1;
3898
while (strchr(" ",*p) != NULL)
3899
p++;
3900
3901
y = atof(p);
3902
3903
switch(i)
3904
{
3905
case 0: g_fBoxX = (y-x)*100.0f; break;
3906
case 1: g_fBoxY = (y-x)*100.0f; break;
3907
case 2: g_fBoxZ = (y-x)*100.0f; break;
3908
}
3909
}
3910
}
3911
}
3912
if (strstr(buf,"ITEM: NUMBER OF ATOMS") != 0)
3913
{
3914
fgets_bin(buf,256,a);
3915
if (feof(a))
3916
return false;
3917
buf[strlen(buf)-1] = 0;
3918
m_iGesAtomCount = atoi(buf);
3919
continue;
3920
}
3921
if (strstr(buf,"ITEM: ATOMS") != 0)
3922
{
3923
if (strstr(buf,"ITEM: ATOMS element xu yu zu") == 0)
3924
{
3925
eprintf("CTimeStep::ReadLAMMPS(): Wrong LAMMPS dump style: \"%s\".\n",buf);
3926
eprintf("You need to use \"dump custom element xu yu zu\".\n");
3927
return false;
3928
}
3929
3930
if (m_iGesAtomCount == 0)
3931
{
3932
eprintf("CTimeStep::ReadLAMMPS(): \"ITEM: ATOMS\" before \"ITEM: NUMBER OF ATOMS\".\n");
3933
return false;
3934
}
3935
3936
if (needinfo)
3937
{
3938
if (g_bDoubleBox)
3939
m_paLabels.SetSize(m_iGesAtomCount*g_iDoubleBoxFactor);
3940
else m_paLabels.SetSize(m_iGesAtomCount);
3941
}
3942
3943
for (i=0;i<(int)m_iGesAtomCount;i++)
3944
{
3945
fgets_bin(buf,256,a);
3946
if (feof(a))
3947
return false;
3948
3949
p = &buf[0];
3950
while (strchr(" ",*p) != NULL)
3951
p++;
3952
q = p+1;
3953
while ((strchr(" ",*q) == NULL) && (*q != 0))
3954
q++;
3955
if (*q == 0)
3956
{
3957
eprintf("\nCTimeStep::ReadLAMMPS(): %d: Incomplete line (1): \"%s\"\n",i+1,obuf);
3958
BTOUT;
3959
return false;
3960
}
3961
*q = 0;
3962
3963
if (needinfo)
3964
{
3965
if (strlen(p) > 7)
3966
{
3967
eprintf("\nCTimeStep::ReadLAMMPS(): \"%s\" - maximum length for atom labels is 7 chars; truncating.\n",p);
3968
p[7] = 0;
3969
}
3970
3971
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
3972
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3973
3974
strcpy(r,p);
3975
m_paLabels[i] = r;
3976
}
3977
3978
q++;
3979
while (strchr(" ",*q) != NULL)
3980
q++;
3981
p = q;
3982
while ((strchr(" ",*p) == NULL) && (*p != 0))
3983
p++;
3984
if (*p == 0)
3985
{
3986
eprintf("\nCTimeStep::ReadLAMMPS(): %d: Incomplete line (2): \"%s\"",i+1,obuf);
3987
return false;
3988
}
3989
*p = 0;
3990
x = (float)atof(q) * 100.0f;
3991
q = p+1;
3992
while (strchr(" ",*q) != NULL)
3993
q++;
3994
p = q;
3995
while ((strchr(" ",*p) == NULL) && (*p != 0))
3996
p++;
3997
if (*p == 0)
3998
{
3999
eprintf("\nCTimeStep::ReadLAMMPS(): %d: Incomplete line (3) \"%s\"",i+1,obuf);
4000
return false;
4001
}
4002
*p = 0;
4003
y = (float)atof(q) * 100.0f;
4004
q = p+1;
4005
while (strchr(" ",*q) != NULL)
4006
q++;
4007
p = q;
4008
while ((strchr(" ",*p) == NULL) && (*p != 0))
4009
p++;
4010
if (*p != 0)
4011
*p = 0;
4012
z = (float)atof(q) * 100.0f;
4013
4014
m_vaCoords.Add(CxVector3(x,y,z));
4015
}
4016
break;
4017
}
4018
}
4019
return true;
4020
}
4021
4022
4023
bool CTimeStep::SkipLAMMPS(FILE *a)
4024
{
4025
int i, j;
4026
char buf[256];
4027
4028
j = 0;
4029
while (true)
4030
{
4031
fgets_bin(buf,256,a);
4032
if (feof(a))
4033
return false;
4034
if (strlen(buf) == 0)
4035
continue;
4036
buf[strlen(buf)-1] = 0;
4037
if (strstr(buf,"ITEM: NUMBER OF ATOMS") != 0)
4038
{
4039
fgets_bin(buf,256,a);
4040
if (feof(a))
4041
return false;
4042
buf[strlen(buf)-1] = 0;
4043
j = atoi(buf);
4044
continue;
4045
}
4046
if (strstr(buf,"ITEM: ATOMS") != 0)
4047
{
4048
if (j == 0)
4049
{
4050
eprintf("CTimeStep::SkipLAMMPS(): \"ITEM: ATOMS\" before \"ITEM: NUMBER OF ATOMS\".\n");
4051
return false;
4052
}
4053
for (i=0;i<j;i++)
4054
{
4055
fgets_bin(buf,256,a);
4056
if (feof(a))
4057
return false;
4058
}
4059
break;
4060
}
4061
}
4062
return true;
4063
}
4064
4065
4066
bool CTimeStep::ReadDLPOLY(FILE *a, bool needinfo)
4067
{
4068
int i;
4069
char buf[256], obuf[256], *p, *q, *r;
4070
float x, y, z;
4071
4072
m_vaCoords.RemoveAll_KeepSize();
4073
for (i=0;i<m_paLabels.GetSize();i++)
4074
delete[] (char*)m_paLabels[i];
4075
m_paLabels.RemoveAll();
4076
m_iGesAtomCount = 0;
4077
while (true)
4078
{
4079
fgets_bin(buf,256,a);
4080
if (feof(a))
4081
return false;
4082
if (strlen(buf) == 0)
4083
continue;
4084
buf[strlen(buf)-1] = 0;
4085
strcpy(obuf,buf);
4086
4087
if (strstr(buf,"timestep") != 0)
4088
{
4089
p = &buf[0];
4090
while (*p == ' ')
4091
p++;
4092
q = p;
4093
while ((*q != ' ') && (*q != 0))
4094
q++;
4095
if (*q == 0)
4096
{
4097
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line A: \"%s\"\n",obuf);
4098
return false;
4099
}
4100
*q = 0;
4101
p=q+1;
4102
4103
while (*p == ' ')
4104
p++;
4105
q = p;
4106
while ((*q != ' ') && (*q != 0))
4107
q++;
4108
if (*q == 0)
4109
{
4110
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line B: \"%s\"\n",obuf);
4111
return false;
4112
}
4113
*q = 0;
4114
p=q+1;
4115
4116
while (*p == ' ')
4117
p++;
4118
q = p;
4119
while ((*q != ' ') && (*q != 0))
4120
q++;
4121
if (*q == 0)
4122
{
4123
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line C: \"%s\"\n",obuf);
4124
return false;
4125
}
4126
*q = 0;
4127
m_iGesAtomCount = atoi(p);
4128
4129
if (g_bNPT)
4130
{
4131
for (i=0;i<3;i++)
4132
{
4133
fgets_bin(buf,256,a);
4134
if (feof(a))
4135
return false;
4136
4137
p = &buf[0];
4138
4139
while (*p == ' ')
4140
p++;
4141
q = p;
4142
while ((*q != ' ') && (*q != 0))
4143
q++;
4144
if (*q == 0)
4145
{
4146
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line D: \"%s\"\n",obuf);
4147
return false;
4148
}
4149
*q = 0;
4150
x = atof(p);
4151
p = q+1;
4152
4153
while (*p == ' ')
4154
p++;
4155
q = p;
4156
while ((*q != ' ') && (*q != 0))
4157
q++;
4158
if (*q == 0)
4159
{
4160
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line E: \"%s\"\n",obuf);
4161
return false;
4162
}
4163
*q = 0;
4164
y = atof(p);
4165
p = q+1;
4166
4167
while (*p == ' ')
4168
p++;
4169
q = p;
4170
while ((*q != ' ') && (*q != 0))
4171
q++;
4172
*q = 0;
4173
z = atof(p);
4174
4175
switch(i)
4176
{
4177
case 0:
4178
if ((y != 0) || (z != 0))
4179
{
4180
eprintf("\nCTimeStep::ReadDLPOLY(): X: Only orthorhombic cells are supported.\n");
4181
return false;
4182
}
4183
g_fBoxX = x*100.0f;
4184
break;
4185
4186
case 1:
4187
if ((x != 0) || (z != 0))
4188
{
4189
eprintf("\nCTimeStep::ReadDLPOLY(): Y: Only orthorhombic cells are supported.\n");
4190
return false;
4191
}
4192
g_fBoxY = y*100.0f;
4193
break;
4194
4195
case 2:
4196
if ((x != 0) || (y != 0))
4197
{
4198
eprintf("\nCTimeStep::ReadDLPOLY(): Z: Only orthorhombic cells are supported.\n");
4199
return false;
4200
}
4201
g_fBoxZ = z*100.0f;
4202
break;
4203
4204
}
4205
}
4206
} else
4207
{
4208
fgets_bin(buf,256,a);
4209
fgets_bin(buf,256,a);
4210
fgets_bin(buf,256,a);
4211
}
4212
4213
if (m_iGesAtomCount == 0)
4214
{
4215
eprintf("CTimeStep::ReadDLPOLY(): Error: Atom count is 0.\n");
4216
return false;
4217
}
4218
4219
if (needinfo)
4220
{
4221
if (g_bDoubleBox)
4222
m_paLabels.SetSize(m_iGesAtomCount*g_iDoubleBoxFactor);
4223
else m_paLabels.SetSize(m_iGesAtomCount);
4224
}
4225
4226
for (i=0;i<(int)m_iGesAtomCount;i++)
4227
{
4228
_readagain:
4229
fgets_bin(buf,256,a);
4230
if (feof(a))
4231
return false;
4232
4233
p = &buf[0];
4234
while (*p == ' ')
4235
p++;
4236
q = p;
4237
4238
// Numer at beginning of line: Likely velocities. Skip that line
4239
if ((*p == '-') || (*p == '.') || ((*p >= '0') && (*p <= '9')))
4240
goto _readagain;
4241
4242
while ((*q != ' ') && (*q != 0))
4243
q++;
4244
if (*q == 0)
4245
{
4246
eprintf("\nCTimeStep::ReadDLPOLY(): %d: Incomplete line F: \"%s\"\n",i+1,obuf);
4247
return false;
4248
}
4249
*q = 0;
4250
4251
if (needinfo)
4252
{
4253
if (strlen(p) > 7)
4254
{
4255
eprintf("\nCTimeStep::ReadDLPOLY(): \"%s\" - maximum length for atom labels is 7 chars; truncating.\n",p);
4256
p[7] = 0;
4257
}
4258
4259
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
4260
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4261
4262
strcpy(r,p);
4263
m_paLabels[i] = r;
4264
}
4265
4266
fgets_bin(buf,256,a);
4267
if (feof(a))
4268
return false;
4269
4270
p = &buf[0];
4271
4272
while (*p == ' ')
4273
p++;
4274
q = p;
4275
while ((*q != ' ') && (*q != 0))
4276
q++;
4277
if (*q == 0)
4278
{
4279
eprintf("\nCTimeStep::ReadDLPOLY(): %d: Incomplete line G: \"%s\"\n",i+1,obuf);
4280
return false;
4281
}
4282
*q = 0;
4283
x = atof(p)*100.0f;
4284
p = q+1;
4285
4286
while (*p == ' ')
4287
p++;
4288
q = p;
4289
while ((*q != ' ') && (*q != 0))
4290
q++;
4291
if (*q == 0)
4292
{
4293
eprintf("\nCTimeStep::ReadDLPOLY(): %d: Incomplete line H: \"%s\"\n",i+1,obuf);
4294
return false;
4295
}
4296
*q = 0;
4297
y = atof(p)*100.0f;
4298
p = q+1;
4299
4300
while (*p == ' ')
4301
p++;
4302
q = p;
4303
while ((*q != ' ') && (*q != 0))
4304
q++;
4305
*q = 0;
4306
z = atof(p)*100.0f;
4307
4308
m_vaCoords.Add(CxVector3(x,y,z));
4309
}
4310
break;
4311
}
4312
}
4313
return true;
4314
}
4315
4316
4317
bool CTimeStep::SkipDLPOLY(FILE *a)
4318
{
4319
int i, j;
4320
char buf[256], obuf[256], *p, *q;
4321
4322
while (true)
4323
{
4324
fgets_bin(buf,256,a);
4325
if (feof(a))
4326
return false;
4327
if (strlen(buf) == 0)
4328
continue;
4329
buf[strlen(buf)-1] = 0;
4330
strcpy(obuf,buf);
4331
4332
if (strstr(buf,"timestep") != 0)
4333
{
4334
p = &buf[0];
4335
while (*p == ' ')
4336
p++;
4337
q = p;
4338
while ((*q != ' ') && (*q != 0))
4339
q++;
4340
if (*q == 0)
4341
{
4342
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line A: \"%s\"\n",obuf);
4343
return false;
4344
}
4345
*q = 0;
4346
p=q+1;
4347
4348
while (*p == ' ')
4349
p++;
4350
q = p;
4351
while ((*q != ' ') && (*q != 0))
4352
q++;
4353
if (*q == 0)
4354
{
4355
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line B: \"%s\"\n",obuf);
4356
return false;
4357
}
4358
*q = 0;
4359
p=q+1;
4360
4361
while (*p == ' ')
4362
p++;
4363
q = p;
4364
while ((*q != ' ') && (*q != 0))
4365
q++;
4366
if (*q == 0)
4367
{
4368
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line C: \"%s\"\n",obuf);
4369
return false;
4370
}
4371
*q = 0;
4372
j = atoi(p);
4373
4374
fgets_bin(buf,256,a);
4375
fgets_bin(buf,256,a);
4376
fgets_bin(buf,256,a);
4377
4378
if (j == 0)
4379
{
4380
eprintf("CTimeStep::ReadDLPOLY(): Error: Atom count is 0.\n");
4381
return false;
4382
}
4383
4384
for (i=0;i<j;i++)
4385
{
4386
fgets_bin(buf,256,a);
4387
fgets_bin(buf,256,a);
4388
if (feof(a))
4389
return false;
4390
}
4391
break;
4392
}
4393
}
4394
return true;
4395
}
4396
4397
4398
bool CTimeStep::ReadMol2(FILE *a, bool needinfo)
4399
{
4400
int i;
4401
char buf[256], obuf[256], *p, *q, *r;
4402
float x, y, z;
4403
4404
fgets_bin(buf,256,a);
4405
fgets_bin(buf,256,a);
4406
fgets_bin(buf,256,a);
4407
p = buf;
4408
while (*p == ' ')
4409
p++;
4410
q = p;
4411
while ((*q != ' ') && (*q != 0))
4412
q++;
4413
*q = 0;
4414
m_iGesAtomCount = atoi(p);
4415
4416
if (needinfo)
4417
{
4418
m_vaCoords.RemoveAll_KeepSize();
4419
for (i=0;i<m_paLabels.GetSize();i++)
4420
delete[] (char*)m_paLabels[i];
4421
m_paLabels.RemoveAll();
4422
m_paLabels.SetSize(m_iGesAtomCount);
4423
for (i=0;i<m_paMol2Types.GetSize();i++)
4424
delete[] (char*)m_paMol2Types[i];
4425
m_paMol2Types.RemoveAll();
4426
m_paMol2Types.SetSize(m_iGesAtomCount);
4427
}
4428
fgets_bin(buf,256,a);
4429
fgets_bin(buf,256,a);
4430
fgets_bin(buf,256,a);
4431
fgets_bin(buf,256,a);
4432
fgets_bin(buf,256,a);
4433
4434
for (i=0;i<(long)m_iGesAtomCount;i++)
4435
{
4436
fgets_bin(buf,256,a);
4437
if (feof(a))
4438
return false;
4439
buf[strlen(buf)-1] = 0;
4440
strcpy(obuf,buf);
4441
// mprintf(" \"%s\"\n",buf);
4442
p = buf;
4443
while (*p == ' ')
4444
p++;
4445
while ((*p != ' ') && (*p != 0))
4446
p++;
4447
while (*p == ' ')
4448
p++;
4449
q = p;
4450
while (isalpha(*q) || (*q == '_'))
4451
q++;
4452
if (needinfo)
4453
{
4454
*q = 0;
4455
if (strlen(p) > 7)
4456
{
4457
eprintf("\nCTimeStep::ReadMol2(): \"%s\" - maximum length for atom labels is 7 chars; truncating.\n",p);
4458
p[7] = 0;
4459
}
4460
4461
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
4462
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4463
4464
strcpy(r,p);
4465
m_paLabels[i] = r;
4466
}
4467
p = q+1;
4468
while ((*p != ' ') && (*p != 0))
4469
p++;
4470
while (*p == ' ')
4471
p++;
4472
4473
q = strchr(p,' ');
4474
if (q == NULL)
4475
{
4476
eprintf("\nCTimeStep::ReadMol2(): Error 1. %d. \"%s\".",i+1,obuf);
4477
return false;
4478
}
4479
*q = 0;
4480
x = (float)atof(p) * 100.0f;
4481
p = q+1;
4482
while (*p == ' ')
4483
p++;
4484
4485
q = strchr(p,' ');
4486
if (q == NULL)
4487
{
4488
eprintf("\nCTimeStep::ReadMol2(): Error 2. %d. \"%s\".",i+1,obuf);
4489
return false;
4490
}
4491
*q = 0;
4492
y = (float)atof(p) * 100.0f;
4493
p = q+1;
4494
while (*p == ' ')
4495
p++;
4496
4497
q = strchr(p,' ');
4498
if (q == NULL)
4499
{
4500
eprintf("\nCTimeStep::ReadMol2(): Error 3. %d. \"%s\".",i+1,obuf);
4501
return false;
4502
}
4503
*q = 0;
4504
z = (float)atof(p) * 100.0f;
4505
m_vaCoords.Add(CxVector3(x,y,z));
4506
4507
p = q+1;
4508
while (*p == ' ')
4509
p++;
4510
q = p;
4511
while ((*q != ' ') && (*q != 0))
4512
q++;
4513
if (needinfo)
4514
{
4515
*q = 0;
4516
4517
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
4518
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4519
4520
strcpy(r,p);
4521
m_paMol2Types[i] = r;
4522
}
4523
/* mprintf(" X=%f, Y=%f, Z=%f",x,y,z);
4524
if (needinfo)
4525
mprintf(", A=%s, B=%s",(char*)m_paLabels[i],(char*)m_paMol2Types[i]);
4526
mprintf("\n");*/
4527
}
4528
m_iGesAtomCount = m_vaCoords.GetSize();
4529
4530
return true;
4531
}
4532
4533
4534
bool CTimeStep::SkipMol2(FILE *a)
4535
{
4536
int i;
4537
char buf[256];
4538
4539
fgets_bin(buf,256,a);
4540
fgets_bin(buf,256,a);
4541
fgets_bin(buf,256,a);
4542
fgets_bin(buf,256,a);
4543
fgets_bin(buf,256,a);
4544
fgets_bin(buf,256,a);
4545
fgets_bin(buf,256,a);
4546
fgets_bin(buf,256,a);
4547
4548
for (i=0;i<(long)m_iGesAtomCount;i++)
4549
{
4550
fgets_bin(buf,256,a);
4551
if (feof(a))
4552
return false;
4553
}
4554
4555
return true;
4556
}
4557
4558
4559
void CTimeStep::CalcMinMax()
4560
{
4561
int z;
4562
4563
m_vMin[0] = 1E20f;
4564
m_vMin[1] = 1E20f;
4565
m_vMin[2] = 1E20f;
4566
m_vMax[0] = -1E20f;
4567
m_vMax[1] = -1E20f;
4568
m_vMax[2] = -1E20f;
4569
4570
for (z=0;z<(long)m_iGesAtomCount;z++)
4571
{
4572
if (m_vMin[0] > m_vaCoords[z][0])
4573
m_vMin[0] = m_vaCoords[z][0];
4574
if (m_vMin[1] > m_vaCoords[z][1])
4575
m_vMin[1] = m_vaCoords[z][1];
4576
if (m_vMin[2] > m_vaCoords[z][2])
4577
m_vMin[2] = m_vaCoords[z][2];
4578
if (m_vMax[0] < m_vaCoords[z][0])
4579
m_vMax[0] = m_vaCoords[z][0];
4580
if (m_vMax[1] < m_vaCoords[z][1])
4581
m_vMax[1] = m_vaCoords[z][1];
4582
if (m_vMax[2] < m_vaCoords[z][2])
4583
m_vMax[2] = m_vaCoords[z][2];
4584
}
4585
}
4586
4587
4588
void CTimeStep::WriteMol2(FILE *a)
4589
{
4590
int z, z2, z3, z4, ti, c, mc;
4591
CMolecule *m;
4592
CSingleMolecule *sm;
4593
int bonds;
4594
int *tpi;
4595
char *cc;
4596
4597
bonds = 0;
4598
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
4599
bonds += ((CSingleMolecule*)g_oaSingleMolecules[z])->m_oaBonds.GetSize();
4600
4601
try { tpi = new int[g_iGesAtomCount]; } catch(...) { tpi = NULL; }
4602
if (tpi == NULL) NewException((double)g_iGesAtomCount*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4603
4604
mfprintf(a," @<TRIPOS>MOLECULE\n");
4605
mfprintf(a,"MOL\n");
4606
mfprintf(a," %d %d %d 0 0\n",g_iGesAtomCount,bonds,g_oaSingleMolecules.GetSize());
4607
mfprintf(a," SMALL\n");
4608
mfprintf(a,"resp\n\n\n");
4609
mfprintf(a," @<TRIPOS>ATOM\n");
4610
c = 0;
4611
mc = 0;
4612
if (m_faCharge.GetSize() != g_iGesAtomCount)
4613
{
4614
m_faCharge.SetSize(g_iGesAtomCount);
4615
for (z=0;z<g_iGesAtomCount;z++)
4616
m_faCharge[z] = 0;
4617
}
4618
for (z=0;z<g_oaMolecules.GetSize();z++)
4619
{
4620
m = (CMolecule*)g_oaMolecules[z];
4621
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
4622
{
4623
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
4624
mc++;
4625
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
4626
{
4627
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
4628
continue;
4629
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
4630
{
4631
ti = ((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4);
4632
if (m_paMol2Types.GetSize() != 0)
4633
cc = (char*)m_paMol2Types[ti];
4634
else cc = ((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName;
4635
tpi[ti] = c++;
4636
mfprintf(a," %6d %2s % 11.4f % 11.4f % 11.4f %2s %4d MOL % 8.4f\n",c,((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0,m_vaCoords[ti][1]/100.0,m_vaCoords[ti][2]/100.0,cc,mc,m_faCharge[ti]);
4637
}
4638
}
4639
}
4640
}
4641
mfprintf(a," @<TRIPOS>BOND\n");
4642
c = 0;
4643
for (z=0;z<g_oaMolecules.GetSize();z++)
4644
{
4645
m = (CMolecule*)g_oaMolecules[z];
4646
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
4647
{
4648
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
4649
for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)
4650
mfprintf(a," %6d %6d %6d 1\n",++c,tpi[((CMolBond*)sm->m_oaBonds[z3])->m_iAtomOffset[0]]+1,tpi[((CMolBond*)sm->m_oaBonds[z3])->m_iAtomOffset[1]]+1);
4651
}
4652
}
4653
mfprintf(a," @<TRIPOS>SUBSTRUCTURE\n");
4654
c = 0;
4655
for (z=0;z<g_oaMolecules.GetSize();z++)
4656
{
4657
m = (CMolecule*)g_oaMolecules[z];
4658
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
4659
{
4660
mfprintf(a," %4d MOL %4d TEMP 0 **** **** 0 ROOT\n",c+1,c+1);
4661
c++;
4662
}
4663
}
4664
delete[] tpi;
4665
}
4666
4667
4668
void CTimeStep::ReadCellVector(FILE *a)
4669
{
4670
char buf[256], obuf[256];
4671
char *p, *q;
4672
float tf;
4673
4674
fgets(buf,256,a);
4675
if (feof(a))
4676
{
4677
eprintf("\nReadCellVector: End of file.\n");
4678
eprintf("Your cell vector text file is too short.\n");
4679
return;
4680
}
4681
if (strlen(buf) == 0)
4682
{
4683
eprintf("\nReadCellVector: Empty line.\n");
4684
return;
4685
}
4686
buf[strlen(buf)-1] = 0;
4687
strcpy(obuf,buf);
4688
// mprintf(GREY,"\nReadCellVector: \"%s\".\n",buf);
4689
p = buf;
4690
while ((!isnumeric(*p)) && (*p != 0))
4691
p++;
4692
if (*p == 0)
4693
{
4694
eprintf("\nReadCellVector: Incomplete line (1) \"%s\".\n",obuf);
4695
return;
4696
}
4697
q = p;
4698
while (isnumeric(*q))
4699
q++;
4700
if (*q == 0)
4701
{
4702
eprintf("\nReadCellVector: Incomplete line (2) \"%s\".\n",obuf);
4703
return;
4704
}
4705
*q = 0;
4706
tf = (float)(atof(p)*100.0);
4707
if (tf <= 0)
4708
{
4709
eprintf("\nReadCellVector: Cell vectors need to be > 0 (X) \"%s\".\n",obuf);
4710
return;
4711
}
4712
g_fBoxX = tf;
4713
4714
p = q+1;
4715
while ((!isnumeric(*p)) && (*p != 0))
4716
p++;
4717
if (*p == 0)
4718
{
4719
eprintf("\nReadCellVector: Incomplete line (3) \"%s\".\n",obuf);
4720
return;
4721
}
4722
q = p;
4723
while (isnumeric(*q))
4724
q++;
4725
if (*q == 0)
4726
{
4727
eprintf("\nReadCellVector: Incomplete line (4) \"%s\".\n",obuf);
4728
return;
4729
}
4730
*q = 0;
4731
tf = (float)(atof(p)*100.0);
4732
if (tf <= 0)
4733
{
4734
eprintf("\nReadCellVector: Cell vectors need to be > 0 (Y) \"%s\".\n",obuf);
4735
return;
4736
}
4737
g_fBoxY = tf;
4738
p = q+1;
4739
4740
while ((!isnumeric(*p)) && (*p != 0))
4741
p++;
4742
if (*p == 0)
4743
{
4744
eprintf("\nReadCellVector: Incomplete line (5) \"%s\".\n",obuf);
4745
return;
4746
}
4747
q = p;
4748
while (isnumeric(*q))
4749
q++;
4750
if (*q != 0)
4751
*q = 0;
4752
tf = (float)(atof(p)*100.0);
4753
if (tf <= 0)
4754
{
4755
eprintf("\nReadCellVector: Cell vectors need to be > 0 (Z) \"%s\".\n",obuf);
4756
return;
4757
}
4758
g_fBoxZ = tf;
4759
4760
// mprintf(GREY," --> %f %f %f\n",g_fBoxX,g_fBoxY,g_fBoxZ);
4761
}
4762
4763
4764
void CTimeStep::CenterCOM()
4765
{
4766
CxVector3 vc;
4767
double m;
4768
int z;
4769
4770
vc = CxVector3(0,0,0);
4771
m = 0;
4772
for (z=0;z<g_iGesAtomCount;z++)
4773
{
4774
if (g_bWannier)
4775
if (g_baAtomIndex[z] == g_iWannierAtomType)
4776
continue;
4777
vc += m_vaCoords[z] * ((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_pElement->m_fMass;
4778
m += ((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_pElement->m_fMass;
4779
}
4780
vc /= m;
4781
for (z=0;z<g_iGesAtomCount;z++)
4782
m_vaCoords[z] -= vc;
4783
}
4784
4785
4786
float CTimeStep::FoldedDistance(int i1, int i2)
4787
{
4788
CxVector3 t;
4789
4790
t = m_vaCoords[i2]-m_vaCoords[i1];
4791
4792
if (g_bPeriodicX)
4793
{
4794
while (t[0] < -g_fBoxX/2) t[0] += g_fBoxX;
4795
while (t[0] >= g_fBoxX/2) t[0] -= g_fBoxX;
4796
}
4797
4798
if (g_bPeriodicY)
4799
{
4800
while (t[1] < -g_fBoxY/2) t[1] += g_fBoxY;
4801
while (t[1] >= g_fBoxY/2) t[1] -= g_fBoxY;
4802
}
4803
4804
if (g_bPeriodicZ)
4805
{
4806
while (t[2] < -g_fBoxZ/2) t[2] += g_fBoxZ;
4807
while (t[2] >= g_fBoxZ/2) t[2] -= g_fBoxZ;
4808
}
4809
4810
return t.GetLength();
4811
}
4812
4813
4814
void CTimeStep::FoldAtomsPositive()
4815
{
4816
BTIN;
4817
int z;
4818
4819
if (!g_bPeriodic)
4820
return;
4821
4822
for (z=0;z<g_iGesVirtAtomCount;z++)
4823
{
4824
if (g_bPeriodicX)
4825
{
4826
while (m_vaCoords[z][0] < 0) m_vaCoords[z][0] += g_fBoxX;
4827
while (m_vaCoords[z][0] >= g_fBoxX) m_vaCoords[z][0] -= g_fBoxX;
4828
}
4829
4830
if (g_bPeriodicX)
4831
{
4832
while (m_vaCoords[z][1] < 0) m_vaCoords[z][1] += g_fBoxY;
4833
while (m_vaCoords[z][1] >= g_fBoxY) m_vaCoords[z][1] -= g_fBoxY;
4834
}
4835
4836
if (g_bPeriodicX)
4837
{
4838
while (m_vaCoords[z][2] < 0) m_vaCoords[z][2] += g_fBoxZ;
4839
while (m_vaCoords[z][2] >= g_fBoxZ) m_vaCoords[z][2] -= g_fBoxZ;
4840
}
4841
}
4842
BTOUT;
4843
}
4844
4845
4846
void CTimeStep::WritePOV(const char *s)
4847
{
4848
FILE *b;
4849
CMolecule *m;
4850
CSingleMolecule *sm;
4851
CElement *el, *el2;
4852
int z, z2, z3, z4, o, o2;
4853
CxVector3 vec1, vec2, vec3, vec1b, vec2b, vec3b, vecA, vecB, vecC, vecD;
4854
CMolBond *mb;
4855
CxVector3 cam;
4856
// float cr, cg, cb;
4857
4858
b = OpenFileWrite(s,true);
4859
4860
mfprintf(b,"// Written by TRAVIS\n");
4861
mfprintf(b,"// See http://www.travis-analyzer.de\n\n");
4862
mfprintf(b,"#version 3.6;\n");
4863
mfprintf(b,"\n");
4864
4865
mfprintf(b,"/**** Atoms ****/\n");
4866
4867
mfprintf(b,"#declare atom_draw = true;\n");
4868
mfprintf(b,"#declare atom_r = 0.65;\n");
4869
mfprintf(b,"#declare atom_specular = 0.7;\n");
4870
mfprintf(b,"#declare atom_reflect = 0;\n");
4871
mfprintf(b,"#declare atom_ambient = 0.2;\n");
4872
mfprintf(b,"#declare atom_diffuse = 0.7;\n");
4873
mfprintf(b,"//#declare atom_color = < 1.0, 1.0, 1.0, 0, 0 >;\n");
4874
mfprintf(b,"//#declare atom_trans = 0.7;\n");
4875
4876
mfprintf(b,"\n");
4877
4878
mfprintf(b,"#declare atom_draw_halo1 = true;\n");
4879
mfprintf(b,"#declare atom_r_halo1 = 0.008;\n");
4880
mfprintf(b,"#declare atom_d_halo1 = 0.0125;\n");
4881
mfprintf(b,"#declare atom_color_halo1 = < 0, 0, 0, 0, 0 >;\n");
4882
mfprintf(b,"#declare atom_specular_halo1 = 0;\n");
4883
mfprintf(b,"#declare atom_reflect_halo1 = 0;\n");
4884
mfprintf(b,"#declare atom_ambient_halo1 = 1.0;\n");
4885
mfprintf(b,"#declare atom_diffuse_halo1 = 0;\n");
4886
4887
mfprintf(b,"\n");
4888
4889
mfprintf(b,"#declare atom_draw_halo2 = true;\n");
4890
mfprintf(b,"#declare atom_r_halo2 = 0.003;\n");
4891
mfprintf(b,"#declare atom_d_halo2 = 0.01875;\n");
4892
mfprintf(b,"#declare atom_color_halo2 = < 1, 1, 1, 0, 0 >;\n");
4893
mfprintf(b,"#declare atom_specular_halo2 = 0;\n");
4894
mfprintf(b,"#declare atom_reflect_halo2 = 0;\n");
4895
mfprintf(b,"#declare atom_ambient_halo2 = 1.0;\n");
4896
mfprintf(b,"#declare atom_diffuse_halo2 = 0;\n");
4897
4898
mfprintf(b,"\n");
4899
4900
mfprintf(b,"#declare atom_draw_halo3 = true;\n");
4901
mfprintf(b,"#declare atom_r_halo3 = 0.003;\n");
4902
mfprintf(b,"#declare atom_d_halo3 = 0.025;\n");
4903
mfprintf(b,"#declare atom_color_halo3 = < 1, 1, 1, 0, 0.5 >;\n");
4904
mfprintf(b,"#declare atom_specular_halo3 = 0;\n");
4905
mfprintf(b,"#declare atom_reflect_halo3 = 0;\n");
4906
mfprintf(b,"#declare atom_ambient_halo3 = 1.0;\n");
4907
mfprintf(b,"#declare atom_diffuse_halo3 = 0;\n");
4908
4909
mfprintf(b,"\n");
4910
4911
mfprintf(b,"/**** Bonds ****/\n");
4912
4913
mfprintf(b,"#declare bond_draw = true;\n");
4914
mfprintf(b,"#declare bond_r = 0.015;\n");
4915
mfprintf(b,"#declare bond_specular = 0.7;\n");
4916
mfprintf(b,"#declare bond_reflect = 0;\n");
4917
mfprintf(b,"#declare bond_ambient = 0.2;\n");
4918
mfprintf(b,"#declare bond_diffuse = 0.7;\n");
4919
4920
mfprintf(b,"\n");
4921
4922
mfprintf(b,"#declare bond_draw_halo1 = true;\n");
4923
mfprintf(b,"#declare bond_r_halo1 = 0.008;\n");
4924
mfprintf(b,"#declare bond_d_halo1 = 0;\n");
4925
mfprintf(b,"#declare bond_color_halo1 = < 0, 0, 0, 0, 0 >;\n");
4926
mfprintf(b,"#declare bond_specular_halo1 = 0;\n");
4927
mfprintf(b,"#declare bond_reflect_halo1 = 0;\n");
4928
mfprintf(b,"#declare bond_ambient_halo1 = 1.0;\n");
4929
mfprintf(b,"#declare bond_diffuse_halo1 = 0;\n");
4930
4931
mfprintf(b,"\n");
4932
4933
mfprintf(b,"#declare bond_draw_halo2 = true;\n");
4934
mfprintf(b,"#declare bond_r_halo2 = 0.003;\n");
4935
mfprintf(b,"#declare bond_d_halo2 = 0.0286;\n");
4936
mfprintf(b,"#declare bond_color_halo2 = < 1, 1, 1, 0, 0 >;\n");
4937
mfprintf(b,"#declare bond_specular_halo2 = 0;\n");
4938
mfprintf(b,"#declare bond_reflect_halo2 = 0;\n");
4939
mfprintf(b,"#declare bond_ambient_halo2 = 1.0;\n");
4940
mfprintf(b,"#declare bond_diffuse_halo2 = 0;\n");
4941
4942
mfprintf(b,"\n");
4943
4944
mfprintf(b,"#declare bond_draw_halo3 = true;\n");
4945
mfprintf(b,"#declare bond_r_halo3 = 0.003;\n");
4946
mfprintf(b,"#declare bond_d_halo3 = 0.0333;\n");
4947
mfprintf(b,"#declare bond_color_halo3 = < 1, 1, 1, 0, 0.5 >;\n");
4948
mfprintf(b,"#declare bond_specular_halo3 = 0;\n");
4949
mfprintf(b,"#declare bond_reflect_halo3 = 0;\n");
4950
mfprintf(b,"#declare bond_ambient_halo3 = 1.0;\n");
4951
mfprintf(b,"#declare bond_diffuse_halo3 = 0;\n");
4952
4953
mfprintf(b,"\n");
4954
4955
mfprintf(b,"#declare bond_draw_stub = true;\n");
4956
mfprintf(b,"#declare bond_r_stub = 0.004;\n");
4957
mfprintf(b,"#declare bond_l_stub = 0.004;\n");
4958
mfprintf(b,"#declare bond_color_stub = < 0, 0, 0, 0, 0 >;\n");
4959
mfprintf(b,"#declare bond_specular_stub = 0;\n");
4960
mfprintf(b,"#declare bond_reflect_stub = 0;\n");
4961
mfprintf(b,"#declare bond_ambient_stub = 1.0;\n");
4962
mfprintf(b,"#declare bond_diffuse_stub = 0;\n");
4963
4964
mfprintf(b,"\n");
4965
4966
mfprintf(b,"/**** Element Colors ****/\n");
4967
for (z=0;z<g_oaAtoms.GetSize();z++)
4968
{
4969
if (z == g_iVirtAtomType)
4970
continue;
4971
el = ((CAtom*)g_oaAtoms[z])->m_pElement;
4972
mfprintf(b,"#declare elem_%s_col = < %f, %f, %f, 0, 0 >;\n",el->m_sLabel,el->m_iColorR/255.0,el->m_iColorG/255.0,el->m_iColorB/255.0);
4973
}
4974
4975
mfprintf(b,"\n/**** Element Radii ****/\n");
4976
for (z=0;z<g_oaAtoms.GetSize();z++)
4977
{
4978
if (z == g_iVirtAtomType)
4979
continue;
4980
el = ((CAtom*)g_oaAtoms[z])->m_pElement;
4981
mfprintf(b,"#declare elem_%s_r = %f;\n",el->m_sLabel,el->m_fRadius/1000.0);
4982
}
4983
mfprintf(b,"\n");
4984
4985
cam[0] = 0;
4986
cam[1] = 0;
4987
cam[2] = 40.0;
4988
4989
mfprintf(b,"global_settings {\n");
4990
mfprintf(b," assumed_gamma 1\n");
4991
mfprintf(b,"/* radiosity {\n");
4992
mfprintf(b," pretrace_start 0.08\n");
4993
mfprintf(b," pretrace_end 0.04\n");
4994
mfprintf(b," count 100\n\n");
4995
mfprintf(b," nearest_count 5\n");
4996
mfprintf(b," error_bound 0.4\n");
4997
mfprintf(b," recursion_limit 1\n\n");
4998
mfprintf(b," low_error_factor .5\n");
4999
mfprintf(b," gray_threshold 0.0\n");
5000
mfprintf(b," minimum_reuse 0.015\n");
5001
mfprintf(b," brightness 1\n\n");
5002
mfprintf(b," adc_bailout 0.01/2\n");
5003
mfprintf(b," }*/\n");
5004
mfprintf(b,"}\n");
5005
5006
mfprintf(b,"\ncamera {\n");
5007
mfprintf(b," location <%f, %f, %f>\n",cam[0],cam[1],cam[2]);
5008
mfprintf(b," sky y\n");
5009
mfprintf(b," right -0.06*x*image_width/image_height\n");
5010
mfprintf(b," up 0.06*y\n");
5011
mfprintf(b," look_at <0, 0, 0>\n");
5012
mfprintf(b,"}\n");
5013
mfprintf(b,"\n");
5014
5015
mfprintf(b,"// Solid background\n");
5016
mfprintf(b,"background { rgb < 0.15, 0.1, 0.3 > }\n");
5017
mfprintf(b,"\n");
5018
5019
mfprintf(b,"// Gradient background\n");
5020
mfprintf(b,"sky_sphere {\n");
5021
mfprintf(b," pigment {\n");
5022
mfprintf(b," gradient y\n");
5023
mfprintf(b," color_map {\n");
5024
mfprintf(b," [ 0 color rgb < 0.05, 0.05, 0.05 > ]\n");
5025
mfprintf(b," [ 1 color rgb < 0.20, 0.16, 0.50 > ]\n");
5026
mfprintf(b," }\n");
5027
mfprintf(b," scale 0.1\n");
5028
mfprintf(b," translate -0.05\n");
5029
mfprintf(b," }\n");
5030
mfprintf(b,"}\n\n");
5031
5032
mfprintf(b,"/**** Invisible, only for Radiosity ****/\n");
5033
mfprintf(b,"sphere {\n");
5034
mfprintf(b," <0, 0, 0>, 1\n");
5035
mfprintf(b," texture {\n");
5036
mfprintf(b," pigment {color rgb < 1.0, 1.0, 1.0 > }\n");
5037
mfprintf(b," finish { diffuse 0 ambient 1 }\n");
5038
mfprintf(b," }\n");
5039
mfprintf(b," hollow on\n");
5040
mfprintf(b," no_shadow\n");
5041
mfprintf(b," no_image\n");
5042
mfprintf(b," scale 30000\n");
5043
mfprintf(b,"}\n\n");
5044
5045
mfprintf(b,"light_source { < -8, 20, 20 > color rgb 0.8 }\n");
5046
mfprintf(b,"//light_source { < 25, 12, 20 > color rgb 0.5 }\n\n");
5047
5048
mfprintf(b,"#macro m_atom_color(col)\n");
5049
mfprintf(b," #ifdef(atom_color)\n");
5050
mfprintf(b," atom_color\n");
5051
mfprintf(b," #else #if (defined(atom_trans))\n");
5052
mfprintf(b," col + < 0, 0, 0, 0, atom_trans >\n");
5053
mfprintf(b," #else\n");
5054
mfprintf(b," col\n");
5055
mfprintf(b," #end #end\n");
5056
mfprintf(b,"#end\n");
5057
5058
mfprintf(b,"\nunion {\n");
5059
5060
for (z=0;z<g_oaMolecules.GetSize();z++)
5061
{
5062
m = (CMolecule*)g_oaMolecules[z];
5063
5064
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
5065
{
5066
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
5067
5068
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
5069
{
5070
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
5071
continue;
5072
5073
el = ((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_pElement;
5074
5075
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
5076
{
5077
o = ((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4);
5078
vec1 = m_vaCoords[o];
5079
vec1 /= 1000.0;
5080
5081
mfprintf(b,"#if (atom_draw)\n");
5082
mfprintf(b," sphere { <%g, %g, %g>, elem_%s_r*atom_r\n",vec1[0],vec1[1],vec1[2],el->m_sLabel);
5083
mfprintf(b," pigment { rgbft m_atom_color(elem_%s_col) } finish { reflection atom_reflect specular atom_specular ambient atom_ambient diffuse atom_diffuse } }\n",el->m_sLabel);
5084
mfprintf(b,"#end\n");
5085
5086
vec2 = cam - vec1;
5087
vec2.Normalize();
5088
5089
// if (shadow)
5090
{
5091
mfprintf(b,"#if (atom_draw_halo1)\n");
5092
mfprintf(b," disc { < %g - (%g) * atom_d_halo1, %g - (%g) * atom_d_halo1, %g - (%g) * atom_d_halo1 >,\n",vec1[0],vec2[0],vec1[1],vec2[1],vec1[2],vec2[2]);
5093
mfprintf(b," < %g, %g, %g >, (elem_%s_r * atom_r) + atom_r_halo1, elem_%s_r * atom_r\n",vec2[0],vec2[1],vec2[2],el->m_sLabel,el->m_sLabel);
5094
mfprintf(b," pigment { rgbft atom_color_halo1 } finish { reflection atom_reflect_halo1 specular atom_specular_halo1 ambient atom_ambient_halo1 diffuse atom_diffuse_halo1 } no_reflection no_radiosity }\n");
5095
mfprintf(b,"#end\n");
5096
}
5097
5098
// if (halo)
5099
{
5100
mfprintf(b,"#if (atom_draw_halo2)\n");
5101
mfprintf(b," disc { < %g - (%g) * atom_d_halo2, %g - (%g) * atom_d_halo2, %g - (%g) * atom_d_halo2 >,\n",vec1[0],vec2[0],vec1[1],vec2[1],vec1[2],vec2[2]);
5102
mfprintf(b," < %g, %g, %g >, (elem_%s_r * atom_r) + atom_r_halo1 + atom_r_halo2, elem_%s_r * atom_r\n",vec2[0],vec2[1],vec2[2],el->m_sLabel,el->m_sLabel);
5103
mfprintf(b," pigment { rgbft atom_color_halo2 } finish { reflection atom_reflect_halo2 specular atom_specular_halo2 ambient atom_ambient_halo2 diffuse atom_diffuse_halo2 } no_reflection no_radiosity }\n");
5104
mfprintf(b,"#end\n");
5105
5106
mfprintf(b,"#if (atom_draw_halo3)\n");
5107
mfprintf(b," disc { < %g - (%g) * atom_d_halo3, %g - (%g) * atom_d_halo3, %g - (%g) * atom_d_halo3 >,\n",vec1[0],vec2[0],vec1[1],vec2[1],vec1[2],vec2[2]);
5108
mfprintf(b," < %g, %g, %g >, (elem_%s_r * atom_r) + atom_r_halo1 + atom_r_halo2 + atom_r_halo3, elem_%s_r * atom_r\n",vec2[0],vec2[1],vec2[2],el->m_sLabel,el->m_sLabel);
5109
mfprintf(b," pigment { rgbft atom_color_halo3 } finish { reflection atom_reflect_halo3 specular atom_specular_halo3 ambient atom_ambient_halo3 diffuse atom_diffuse_halo3 } no_reflection no_radiosity }\n");
5110
mfprintf(b,"#end\n");
5111
}
5112
}
5113
}
5114
5115
for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)
5116
{
5117
mb = (CMolBond*)sm->m_oaBonds[z3];
5118
o = mb->m_iAtomOffset[0];
5119
o2 = mb->m_iAtomOffset[1];
5120
5121
el = ((CAtom*)g_oaAtoms[g_waAtomRealElement[o]])->m_pElement;
5122
el2 = ((CAtom*)g_oaAtoms[g_waAtomRealElement[o2]])->m_pElement;
5123
5124
vec1 = m_vaCoords[o];
5125
vec1 /= 1000.0;
5126
5127
vec2 = m_vaCoords[o2];
5128
vec2 /= 1000.0;
5129
5130
if ((vec1-vec2).GetLength() > 0.3)
5131
continue;
5132
5133
vec3 = (vec1/el->m_fRadius + vec2/el2->m_fRadius) / (1.0/el->m_fRadius+1.0/el2->m_fRadius);
5134
5135
vec3b = vec2 - vec1;
5136
vec3b.Normalize();
5137
5138
mfprintf(b,"#local vec1c = < %g + (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ),\n",vec1[0],vec3b[0],el->m_sLabel,el->m_sLabel,el->m_sLabel,el->m_sLabel);
5139
mfprintf(b," %g + (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ),\n",vec1[1],vec3b[1],el->m_sLabel,el->m_sLabel,el->m_sLabel,el->m_sLabel);
5140
mfprintf(b," %g + (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ) >;\n",vec1[2],vec3b[2],el->m_sLabel,el->m_sLabel,el->m_sLabel,el->m_sLabel);
5141
mfprintf(b,"#local vec2c = < %g - (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ),\n",vec2[0],vec3b[0],el2->m_sLabel,el2->m_sLabel,el2->m_sLabel,el2->m_sLabel);
5142
mfprintf(b," %g - (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ),\n",vec2[1],vec3b[1],el2->m_sLabel,el2->m_sLabel,el2->m_sLabel,el2->m_sLabel);
5143
mfprintf(b," %g - (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ) >;\n",vec2[2],vec3b[2],el2->m_sLabel,el2->m_sLabel,el2->m_sLabel,el2->m_sLabel);
5144
5145
mfprintf(b,"#if (bond_draw)\n");
5146
mfprintf(b," cylinder { < %g, %g, %g >, vec1c, bond_r open\n",vec3[0],vec3[1],vec3[2]);
5147
mfprintf(b," pigment { rgbft m_atom_color(elem_%s_col) } finish { reflection bond_reflect specular bond_specular ambient bond_ambient diffuse bond_diffuse } }\n",el->m_sLabel);
5148
mfprintf(b," cylinder { < %g, %g, %g >, vec2c, bond_r open\n",vec3[0],vec3[1],vec3[2]);
5149
mfprintf(b," pigment { rgbft m_atom_color(elem_%s_col) } finish { reflection bond_reflect specular bond_specular ambient bond_ambient diffuse bond_diffuse } }\n",el2->m_sLabel);
5150
mfprintf(b,"#end\n");
5151
5152
vec3 = cam - (vec1 + vec2) / 2.0;
5153
vec3.Normalize();
5154
5155
vec2b = vec2-vec1;
5156
vec1b = CrossP(vec3,vec2b);
5157
vec1b.Normalize();
5158
5159
mfprintf(b,"#local vec3 = < %g, %g, %g >;\n",vec3[0],vec3[1],vec3[2]);
5160
mfprintf(b,"#local vec1b = < %g, %g, %g >;\n",vec1b[0],vec1b[1],vec1b[2]);
5161
5162
// if (shadow)
5163
{
5164
mfprintf(b,"#if (bond_draw_halo1)\n");
5165
mfprintf(b," #local vecA = vec1c + vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo1;\n");
5166
mfprintf(b," #local vecB = vec2c + vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo1;\n");
5167
mfprintf(b," #local vecC = vec2c + vec1b * (bond_r) - vec3 * bond_d_halo1;\n");
5168
mfprintf(b," #local vecD = vec1c + vec1b * (bond_r) - vec3 * bond_d_halo1;\n");
5169
mfprintf(b," triangle { vecA, vecB, vecC\n");
5170
mfprintf(b," pigment { rgbft bond_color_halo1 } finish { reflection bond_reflect_halo1 specular bond_specular_halo1 ambient bond_ambient_halo1 diffuse bond_diffuse_halo1 } no_reflection no_radiosity }\n");
5171
mfprintf(b," triangle { vecA, vecD, vecC\n");
5172
mfprintf(b," pigment { rgbft bond_color_halo1 } finish { reflection bond_reflect_halo1 specular bond_specular_halo1 ambient bond_ambient_halo1 diffuse bond_diffuse_halo1 } no_reflection no_radiosity }\n");
5173
mfprintf(b," #local vecA = vec1c - vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo1;\n");
5174
mfprintf(b," #local vecB = vec2c - vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo1;\n");
5175
mfprintf(b," #local vecC = vec2c - vec1b * (bond_r) - vec3 * bond_d_halo1;\n");
5176
mfprintf(b," #local vecD = vec1c - vec1b * (bond_r) - vec3 * bond_d_halo1;\n");
5177
mfprintf(b," triangle { vecA, vecB, vecC\n");
5178
mfprintf(b," pigment { rgbft bond_color_halo1 } finish { reflection bond_reflect_halo1 specular bond_specular_halo1 ambient bond_ambient_halo1 diffuse bond_diffuse_halo1 } no_reflection no_radiosity }\n");
5179
mfprintf(b," triangle { vecA, vecD, vecC\n");
5180
mfprintf(b," pigment { rgbft bond_color_halo1 } finish { reflection bond_reflect_halo1 specular bond_specular_halo1 ambient bond_ambient_halo1 diffuse bond_diffuse_halo1 } no_reflection no_radiosity }\n");
5181
mfprintf(b,"#end\n");
5182
}
5183
5184
// if (halo)
5185
{
5186
mfprintf(b,"#if (bond_draw_halo2)\n");
5187
mfprintf(b," #local vecA = vec1c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5188
mfprintf(b," #local vecB = vec2c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5189
mfprintf(b," #local vecC = vec2c + vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo2;\n");
5190
mfprintf(b," #local vecD = vec1c + vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo2;\n");
5191
mfprintf(b," triangle { vecA, vecB, vecC\n");
5192
mfprintf(b," pigment { rgbft bond_color_halo2 } finish { reflection bond_reflect_halo2 specular bond_specular_halo2 ambient bond_ambient_halo2 diffuse bond_diffuse_halo2 } no_reflection no_radiosity }\n");
5193
mfprintf(b," triangle { vecA, vecD, vecC\n");
5194
mfprintf(b," pigment { rgbft bond_color_halo2 } finish { reflection bond_reflect_halo2 specular bond_specular_halo2 ambient bond_ambient_halo2 diffuse bond_diffuse_halo2 } no_reflection no_radiosity }\n");
5195
mfprintf(b," #local vecA = vec1c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5196
mfprintf(b," #local vecB = vec2c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5197
mfprintf(b," #local vecC = vec2c - vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo2;\n");
5198
mfprintf(b," #local vecD = vec1c - vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo2;\n");
5199
mfprintf(b," triangle { vecA, vecB, vecC\n");
5200
mfprintf(b," pigment { rgbft bond_color_halo2 } finish { reflection bond_reflect_halo2 specular bond_specular_halo2 ambient bond_ambient_halo2 diffuse bond_diffuse_halo2 } no_reflection no_radiosity }\n");
5201
mfprintf(b," triangle { vecA, vecD, vecC\n");
5202
mfprintf(b," pigment { rgbft bond_color_halo2 } finish { reflection bond_reflect_halo2 specular bond_specular_halo2 ambient bond_ambient_halo2 diffuse bond_diffuse_halo2 } no_reflection no_radiosity }\n");
5203
mfprintf(b,"#end\n");
5204
5205
mfprintf(b,"#if (bond_draw_halo3)\n");
5206
mfprintf(b," #local vecA = vec1c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2 + bond_r_halo3) - vec3 * bond_d_halo2;\n");
5207
mfprintf(b," #local vecB = vec2c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2 + bond_r_halo3) - vec3 * bond_d_halo2;\n");
5208
mfprintf(b," #local vecC = vec2c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5209
mfprintf(b," #local vecD = vec1c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5210
mfprintf(b," triangle { vecA, vecB, vecC\n");
5211
mfprintf(b," pigment { rgbft bond_color_halo3 } finish { reflection bond_reflect_halo3 specular bond_specular_halo3 ambient bond_ambient_halo3 diffuse bond_diffuse_halo3 } no_reflection no_radiosity }\n");
5212
mfprintf(b," triangle { vecA, vecD, vecC\n");
5213
mfprintf(b," pigment { rgbft bond_color_halo3 } finish { reflection bond_reflect_halo3 specular bond_specular_halo3 ambient bond_ambient_halo3 diffuse bond_diffuse_halo3 } no_reflection no_radiosity }\n");
5214
mfprintf(b," #local vecA = vec1c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2 + bond_r_halo3) - vec3 * bond_d_halo2;\n");
5215
mfprintf(b," #local vecB = vec2c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2 + bond_r_halo3) - vec3 * bond_d_halo2;\n");
5216
mfprintf(b," #local vecC = vec2c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5217
mfprintf(b," #local vecD = vec1c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5218
mfprintf(b," triangle { vecA, vecB, vecC\n");
5219
mfprintf(b," pigment { rgbft bond_color_halo3 } finish { reflection bond_reflect_halo3 specular bond_specular_halo3 ambient bond_ambient_halo3 diffuse bond_diffuse_halo3 } no_reflection no_radiosity }\n");
5220
mfprintf(b," triangle { vecA, vecD, vecC\n");
5221
mfprintf(b," pigment { rgbft bond_color_halo3 } finish { reflection bond_reflect_halo3 specular bond_specular_halo3 ambient bond_ambient_halo3 diffuse bond_diffuse_halo3 } no_reflection no_radiosity }\n");
5222
mfprintf(b,"#end\n");
5223
}
5224
5225
// if (shadow)
5226
{
5227
vec3 = vec2 - vec1;
5228
vec3.Normalize();
5229
5230
mfprintf(b,"#if (bond_draw_stub)\n");
5231
mfprintf(b," #local vec3 = < %g, %g, %g >;\n",vec3[0],vec3[1],vec3[2]);
5232
mfprintf(b," difference {\n");
5233
mfprintf(b," cylinder { vec1c, vec1c + vec3 * bond_l_stub, bond_r + bond_r_stub }\n");
5234
mfprintf(b," cylinder { vec1c - vec3 * (bond_l_stub+0.001), vec1c + vec3 * (bond_l_stub+0.001), bond_r }\n");
5235
mfprintf(b," pigment { rgbft bond_color_stub } finish { reflection bond_reflect_stub specular bond_specular_stub ambient bond_ambient_stub diffuse bond_diffuse_stub } }\n");
5236
mfprintf(b," difference {\n");
5237
mfprintf(b," cylinder { vec2c, vec2c - vec3 * bond_l_stub, bond_r + bond_r_stub }\n");
5238
mfprintf(b," cylinder { vec2c + vec3 * (bond_l_stub+0.001), vec2c - vec3 * (bond_l_stub+0.001), bond_r }\n");
5239
mfprintf(b," pigment { rgbft bond_color_stub } finish { reflection bond_reflect_stub specular bond_specular_stub ambient bond_ambient_stub diffuse bond_diffuse_stub } }\n");
5240
mfprintf(b,"#end\n");
5241
}
5242
}
5243
}
5244
}
5245
5246
mfprintf(b,"\n no_shadow\n}\n\n");
5247
5248
fclose(b);
5249
}
5250
5251
5252
void CTimeStep::DumpDipoles()
5253
{
5254
int z, z2, z3, z4, ti;
5255
CMolecule *m;
5256
CSingleMolecule *sm;
5257
CxVector3 dc;
5258
5259
if (!(g_bDipole && g_bDumpDipoleVector))
5260
return;
5261
5262
fprintf(g_fDumpDipole,"%lu",g_iSteps);
5263
for (z=0;z<g_oaMolecules.GetSize();z++)
5264
{
5265
if (g_oaDumpDipoleVector[z] == NULL)
5266
continue;
5267
m = (CMolecule*)g_oaMolecules[z];
5268
for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)
5269
{
5270
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[((CxIntArray*)g_oaDumpDipoleVector[z])->GetAt(z2)]];
5271
fprintf(g_fDumpDipole,"; %10G; %10G; %10G",sm->m_vDipole[0],sm->m_vDipole[1],sm->m_vDipole[2]);
5272
if (g_bDumpDipoleAbs)
5273
fprintf(g_fDumpDipole,"; %10G",sm->m_vDipole.GetLength());
5274
}
5275
}
5276
fprintf(g_fDumpDipole,"\n");
5277
5278
if (g_bDumpDipoleXYZ)
5279
{
5280
fprintf(g_fDumpDipoleXYZ,"%d\n\n",g_iDumpDipoleXYZAtoms);
5281
for (z=0;z<g_oaMolecules.GetSize();z++)
5282
{
5283
if (g_oaDumpDipoleVector[z] == NULL)
5284
continue;
5285
m = (CMolecule*)g_oaMolecules[z];
5286
for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)
5287
{
5288
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[((CxIntArray*)g_oaDumpDipoleVector[z])->GetAt(z2)]];
5289
5290
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
5291
{
5292
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
5293
continue;
5294
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
5295
{
5296
ti = ((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4);
5297
fprintf(g_fDumpDipoleXYZ,"%s %12f %12f %12f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0,m_vaCoords[ti][1]/100.0,m_vaCoords[ti][2]/100.0);
5298
}
5299
}
5300
}
5301
}
5302
5303
for (z=0;z<g_oaMolecules.GetSize();z++)
5304
{
5305
if (g_oaDumpDipoleVector[z] == NULL)
5306
continue;
5307
m = (CMolecule*)g_oaMolecules[z];
5308
for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)
5309
{
5310
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[((CxIntArray*)g_oaDumpDipoleVector[z])->GetAt(z2)]];
5311
dc = m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[m->m_iDipoleCenterType])->GetAt(m->m_iDipoleCenterIndex)];
5312
fprintf(g_fDumpDipoleXYZ,"B %12f %12f %12f\n",dc[0]/100.0,dc[1]/100.0,dc[2]/100.0);
5313
fprintf(g_fDumpDipoleXYZ,"B %12f %12f %12f\n",dc[0]/100.0+sm->m_vDipole[0]*g_fDumpDipoleScale,dc[1]/100.0+sm->m_vDipole[1]*g_fDumpDipoleScale,dc[2]/100.0+sm->m_vDipole[2]*g_fDumpDipoleScale);
5314
}
5315
}
5316
}
5317
}
5318
5319
5320
CTimeStep::CTimeStep()
5321
{
5322
m_pComment = NULL;
5323
5324
m_vaCoords.SetName("CTimeStep::m_vaCoords");
5325
m_vaCoords_Unfolded.SetName("CTimeStep::m_vaCoords_Unfolded");
5326
m_vaCoords_Original.SetName("CTimeStep::m_vaCoords_Original");
5327
m_vaVelocities.SetName("CTimeStep::m_vaVelocities");
5328
m_vaForces.SetName("CTimeStep::m_vaForces");
5329
m_paLabels.SetName("CTimeStep::m_paLabels");
5330
m_paMol2Types.SetName("CTimeStep::m_paMol2Types");
5331
m_faCharge.SetName("CTimeStep::m_faCharge");
5332
}
5333
5334
5335
CTimeStep::~CTimeStep()
5336
{
5337
/* if (m_pLabels != NULL)
5338
delete[] m_pLabels;*/
5339
if (m_pComment != NULL)
5340
delete[] m_pComment;
5341
}
5342
1
/*****************************************************************************
2
TRAVIS - Trajectory Analyzer and Visualizer
3
http://www.travis-analyzer.de/
4
5
Copyright (c) 2009-2014 Martin Brehm
6
2012-2014 Martin Thomas
7
8
This file written by Martin Brehm.
9
10
This program is free software: you can redistribute it and/or modify
11
it under the terms of the GNU General Public License as published by
12
the Free Software Foundation, either version 3 of the License, or
13
(at your option) any later version.
14
15
This program is distributed in the hope that it will be useful,
16
but WITHOUT ANY WARRANTY; without even the implied warranty of
17
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18
GNU General Public License for more details.
19
20
You should have received a copy of the GNU General Public License
21
along with this program. If not, see <http://www.gnu.org/licenses/>.
22
*****************************************************************************/
23
24
#include "timestep.h"
25
#include "travis.h"
26
27
28
void CTimeStep::CalcCenters()
29
{
30
BTIN;
31
int z, z2, z3, z4, c;
32
CxVector3 tv;
33
CMolecule *m;
34
CVirtualAtom *v;
35
CSingleMolecule *sm;
36
37
tv = 0;
38
39
// mprintf("** CalcCenters **");
40
41
if (m_vaCoords.GetSize() < g_iGesVirtAtomCount)
42
m_vaCoords.SetSize(g_iGesVirtAtomCount);
43
44
// mprintf("CalcCenters(): Size is now %d.\n",m_vaCoords.GetSize());
45
46
if (g_bUseVelocities)
47
if (m_vaVelocities.GetSize() < g_iGesVirtAtomCount)
48
m_vaVelocities.SetSize(g_iGesVirtAtomCount);
49
50
if (g_bUseForces)
51
if (m_vaForces.GetSize() < g_iGesVirtAtomCount)
52
m_vaForces.SetSize(g_iGesVirtAtomCount);
53
54
for (z=0;z<g_oaVirtualAtoms.GetSize();z++)
55
{
56
v = (CVirtualAtom*)g_oaVirtualAtoms[z];
57
m = (CMolecule*)g_oaMolecules[v->m_iMolecule];
58
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
59
{
60
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
61
if (v->m_iMode == 0) // Mittel aus Atompositionen
62
{
63
tv = 0;
64
c = 0;
65
for (z3=0;z3<v->m_oCenterAtoms.m_baAtomType.GetSize();z3++)
66
{
67
for (z4=0;z4<((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetSize();z4++)
68
{
69
// mprintf("{%d:(%G|%G|%G) }\n",((CxIntArray*)sm->m_oaAtomOffset[v->m_oCenterAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetAt(z4)),m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_oCenterAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetAt(z4))][0],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_oCenterAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetAt(z4))][1],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_oCenterAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetAt(z4))][2]);
70
tv += m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_oCenterAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)v->m_oCenterAtoms.m_oaAtoms[z3])->GetAt(z4))] * v->m_faWeight[c];
71
c++;
72
}
73
}
74
tv /= v->m_fGesWeight;
75
} else if (v->m_iMode == 1) // Abstand, Winkel, Dihedralwinkel
76
{
77
tv = PointFromRAD(m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_iAtomType[0]])->GetAt(v->m_iAtom[0])],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_iAtomType[1]])->GetAt(v->m_iAtom[1])],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[v->m_iAtomType[2]])->GetAt(v->m_iAtom[2])],v->m_fValues[0],v->m_fValues[1],v->m_fValues[2]);
78
} else if (v->m_iMode == 2) // Dipolvektor
79
{
80
if (!g_bDipole)
81
{
82
eprintf("Cannot use dipole vectors.\n");
83
BTOUT;
84
return;
85
}
86
tv = sm->m_vDipole + m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[sm->m_baAtomIndex.GetSize()-1])->GetAt(0)];
87
} else if (v->m_iMode == 3) // Geschwindigkeitsvektor
88
{
89
} else if (v->m_iMode == 4) // Kraftvektor
90
{
91
}
92
// mprintf("%d:(%G|%G|%G), ",((CxIntArray*)sm->m_oaAtomOffset[sm->m_baAtomIndex.GetSize()-1])->GetAt(v->m_iMolVirtAtom),tv[0],tv[1],tv[2]);
93
m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[sm->m_baAtomIndex.GetSize()-1])->GetAt(v->m_iMolVirtAtom)] = tv;
94
}
95
}
96
BTOUT;
97
}
98
99
100
bool CTimeStep::BondRange(int i1, int i2, double *f)
101
{
102
BTIN;
103
int a, b;
104
double d;
105
double x, y, z;
106
107
if (g_iScanMolStep == -1)
108
return false;
109
110
x = m_vaCoords[i1][0] - m_vaCoords[i2][0];
111
y = m_vaCoords[i1][1] - m_vaCoords[i2][1];
112
z = m_vaCoords[i1][2] - m_vaCoords[i2][2];
113
114
if (g_bPeriodic)
115
{
116
if (g_bPeriodicX)
117
{
118
while (x < -g_fBoxX/2)
119
x += g_fBoxX;
120
while (x > g_fBoxX/2)
121
x -= g_fBoxX;
122
}
123
124
if (g_bPeriodicY)
125
{
126
while (y < -g_fBoxY/2)
127
y += g_fBoxY;
128
while (y > g_fBoxY/2)
129
y -= g_fBoxY;
130
}
131
132
if (g_bPeriodicZ)
133
{
134
while (z < -g_fBoxZ/2)
135
z += g_fBoxZ;
136
while (z > g_fBoxZ/2)
137
z -= g_fBoxZ;
138
}
139
}
140
141
d = (float)sqrt(x*x+y*y+z*z);
142
143
if (f != NULL)
144
*f = d;
145
146
a = g_baAtomIndex[i1];
147
b = g_baAtomIndex[i2];
148
149
if ((a >= g_oaAtoms.GetSize()) || (b >= g_oaAtoms.GetSize()))
150
{
151
BTOUT;
152
return false;
153
}
154
155
if (((CAtom*)g_oaAtoms[a])->m_pElement->m_fRadius == 0)
156
{
157
BTOUT;
158
return false;
159
}
160
161
if (((CAtom*)g_oaAtoms[b])->m_pElement->m_fRadius == 0)
162
{
163
BTOUT;
164
return false;
165
}
166
167
if (d < (((CAtom*)g_oaAtoms[a])->m_pElement->m_fRadius+((CAtom*)g_oaAtoms[b])->m_pElement->m_fRadius)*g_fBondFactor)
168
{
169
// printf(" \"%s\" br=%f, \"%s\" br=%f Hat Nachbarn %s%d im Abstand von %.3f.\n",m_pLabels[i1],c1,m_pLabels[i2],c2,m_pLabels[i2],i2+1,d);
170
BTOUT;
171
return true;
172
} else
173
{
174
BTOUT;
175
return false;
176
}
177
}
178
179
180
bool CTimeStep::MirrorBond(int i1, int i2)
181
{
182
BTIN;
183
bool changed;
184
185
changed = false;
186
187
if (g_bPeriodicX)
188
{
189
while (m_vaCoords[i1][0]-m_vaCoords[i2][0] > g_fBoxX/2)
190
{
191
m_vaCoords[i2][0] += g_fBoxX;
192
changed = true;
193
}
194
while (m_vaCoords[i2][0]-m_vaCoords[i1][0] > g_fBoxX/2)
195
{
196
m_vaCoords[i2][0] -= g_fBoxX;
197
changed = true;
198
}
199
}
200
201
if (g_bPeriodicY)
202
{
203
while (m_vaCoords[i1][1]-m_vaCoords[i2][1] > g_fBoxY/2)
204
{
205
m_vaCoords[i2][1] += g_fBoxY;
206
changed = true;
207
}
208
while (m_vaCoords[i2][1]-m_vaCoords[i1][1] > g_fBoxY/2)
209
{
210
m_vaCoords[i2][1] -= g_fBoxY;
211
changed = true;
212
}
213
}
214
215
if (g_bPeriodicZ)
216
{
217
while (m_vaCoords[i1][2]-m_vaCoords[i2][2] > g_fBoxZ/2)
218
{
219
m_vaCoords[i2][2] += g_fBoxZ;
220
changed = true;
221
}
222
while (m_vaCoords[i2][2]-m_vaCoords[i1][2] > g_fBoxZ/2)
223
{
224
m_vaCoords[i2][2] -= g_fBoxZ;
225
changed = true;
226
}
227
}
228
229
if (changed)
230
{
231
BTOUT;
232
return true;
233
}
234
BTOUT;
235
return false;
236
}
237
238
239
void CTimeStep::RECURSION_ScanMolecules(int i, CxByteArray *ta, CSingleMolecule *sm, int depth, int *stack, unsigned long bmask, bool w)
240
{
241
BTIN;
242
int z, z2;
243
int nblist[64], nbs;
244
double f;
245
CxIntArray *wa;
246
CMolAtom *ma;
247
// mprintf(" Rekursion fuer Atom %d.\n",i+1);
248
249
// mprintf("Depth=%d, i=%d.\n",depth,i);
250
if (g_bVerbose)
251
{
252
mprintf(" ");
253
for (z=1;z<depth;z++)
254
{
255
if ((bmask & (int)pow(2.0,z)) != 0)
256
mprintf(WHITE,"| ");
257
else mprintf(" ");
258
}
259
if (depth != 0)
260
{
261
if (w)
262
mprintf(WHITE,"|--");
263
else mprintf(WHITE,"`--");
264
}
265
mprintf(CYAN,"%s",((CAtom*)g_oaAtoms[g_baAtomIndex[i]])->m_sName);
266
mprintf("(%d)",i+1);
267
}
268
269
stack[depth] = i;
270
g_laAtomSMIndex[i] = (unsigned long)g_oaSingleMolecules.GetSize()-1;
271
(*ta)[i] = 1;
272
// mprintf(" sm->m_baAtomIndex.GetSize()=%d\n",sm->m_baAtomIndex.GetSize());
273
for (z=0;z<sm->m_baAtomIndex.GetSize();z++)
274
{
275
if (sm->m_baAtomIndex[z] == g_baAtomIndex[i])
276
{
277
try { ma = new CMolAtom(); } catch(...) { ma = NULL; }
278
if (ma == NULL) NewException((double)sizeof(CMolAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
279
280
ma->m_iOffset = i;
281
ma->m_iType = z;
282
sm->m_oaMolAtoms.Add(ma);
283
goto _ok;
284
}
285
}
286
287
try { ma = new CMolAtom(); } catch(...) { ma = NULL; }
288
if (ma == NULL) NewException((double)sizeof(CMolAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
289
290
ma->m_iOffset = i;
291
ma->m_iType = sm->m_baAtomIndex.GetSize();
292
ma->m_iNumber = 0;
293
sm->m_oaMolAtoms.Add(ma);
294
295
sm->m_baAtomIndex.Add(g_baAtomIndex[i]);
296
_ok:
297
m_iConnectedAtoms++;
298
299
if (!g_bVerbose)
300
if ((m_iConnectedAtoms % m_iGesAtomModulo)==0)
301
mprintf(WHITE,"#");
302
303
nbs = 0;
304
for (z=0;z<(long)m_iGesAtomCount;z++) // Schon mal alle Nachbarn raussuchen
305
{
306
if (z == i)
307
continue;
308
if (((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_bExclude)
309
continue;
310
if (BondRange(i,z,&f))
311
{
312
if ((*ta)[z] != 0)
313
{
314
if ((depth > 0) && (z != stack[depth-1]))
315
{
316
if (sm->m_oaRings.GetSize() < 100)
317
{
318
if (g_bVerbose)
319
{
320
mprintf(GREEN," <-- Ring closure: ");
321
mprintf("%s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[stack[depth]]])->m_sName,stack[depth]+1);
322
}
323
324
try { wa = new CxIntArray("CTimeStep::RECURSION_ScanMolecules():wa"); } catch(...) { wa = NULL; }
325
if (wa == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
326
327
sm->m_oaRings.Add(wa);
328
wa->Add(stack[depth]);
329
z2 = depth-1;
330
while ((stack[z2] != z) && (z2 >= 0))
331
{
332
wa->Add(stack[z2]);
333
if (g_bVerbose)
334
mprintf(" - %s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[stack[z2]]])->m_sName,stack[z2]+1);
335
z2--;
336
}
337
wa->Add(z);
338
if (g_bVerbose)
339
mprintf(" - %s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_sName,z+1);
340
} else if (!m_bAbortRing)
341
{
342
m_bAbortRing = true;
343
eprintf("\n### More than 100 rings, aborting ring system scan for molecule %d.",sm->m_iIndex+1);
344
}
345
}
346
continue;
347
}
348
/* for (z2=0;z2<g_waBondBlackList.GetSize();z2+=2)
349
if (((g_waBondBlackList[z2] == i) && (g_waBondBlackList[z2+1] == z)) ||
350
((g_waBondBlackList[z2] == z) && (g_waBondBlackList[z2+1] == i)))
351
{
352
if (g_bVerbose)
353
{
354
mprintf("\n ");
355
for (z2=1;z2<depth+1;z2++)
356
{
357
if ((bmask & (int)pow(2,z2)) != 0)
358
mprintf(WHITE,"| ");
359
else mprintf(" ");
360
}
361
if (z+1 < nbs)
362
mprintf(WHITE,"|--");
363
else mprintf("`--");
364
mprintf("%s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_sName,z+1);
365
mprintf(GREEN," <-- This bond has been broken, skipping.\n");
366
}
367
g_iBondBlackListUsed++;
368
goto _nextnb;
369
}*/
370
if (f < 50.0f)
371
{
372
if (g_iCloseAtomCounter < 25)
373
eprintf("\n### The atoms %s(%d) and %s(%d) are VERY close to each other. (Distance=%.4f pm)",((CAtom*)g_oaAtoms[g_baAtomIndex[i]])->m_sName,i+1,((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_sName,z+1,f);
374
else if (g_iCloseAtomCounter == 25)
375
eprintf("\n### Suppressing further \"atoms close to each other\" warnings.");
376
377
g_iCloseAtomCounter++;
378
}
379
nblist[nbs] = z;
380
nbs++;
381
if (nbs >= MAX_BONDS)
382
{
383
eprintf("\n### Atom %s(%d) has more than %d bonds. Ignoring further bonds (defined via MAX_BONDS in config.h).",((CAtom*)g_oaAtoms[g_baAtomIndex[i]])->m_sName,i+1,MAX_BONDS);
384
goto _nbdone;
385
}
386
}
387
}
388
_nbdone:
389
if (g_bVerbose)
390
mprintf("\n");
391
for (z=0;z<nbs;z++) // Fuer das aktuelle Atom z2 alle Nachbarn durchgehen
392
{
393
for (z2=0;z2<g_laBondBlackList.GetSize();z2+=2)
394
{
395
if (((g_laBondBlackList[z2] == i) && (g_laBondBlackList[z2+1] == nblist[z])) ||
396
((g_laBondBlackList[z2] == nblist[z]) && (g_laBondBlackList[z2+1] == i)))
397
{
398
if (g_bVerbose)
399
{
400
mprintf(" ");
401
for (z2=1;z2<depth+1;z2++)
402
{
403
if ((bmask & (int)pow(2.0,z2)) != 0)
404
mprintf(WHITE,"| ");
405
else mprintf(" ");
406
}
407
if (z+1 < nbs)
408
mprintf(WHITE,"|--");
409
else mprintf(WHITE,"`--");
410
mprintf(CYAN,"%s",((CAtom*)g_oaAtoms[g_baAtomIndex[nblist[z]]])->m_sName);
411
mprintf("(%d)",nblist[z]+1);
412
mprintf(GREEN," <-- This bond shall be broken, skipping.\n");
413
}
414
g_iBondBlackListUsed++;
415
goto _nextnb;
416
}
417
}
418
419
sm->m_laBonds.Add(i);
420
sm->m_laBonds.Add(nblist[z]);
421
422
if ((*ta)[nblist[z]] == 0) // Der Nachbar ist noch immer frei
423
{
424
if (z+1 == nbs)
425
bmask -= (int)pow(2.0,depth+1);
426
RECURSION_ScanMolecules(nblist[z],ta,sm,depth+1,stack,bmask,(z+1==nbs)?false:true);
427
} else // Ringschluss
428
{
429
if (g_bVerbose)
430
{
431
mprintf(" ");
432
for (z2=1;z2<depth+1;z2++)
433
{
434
if ((bmask & (int)pow(2.0,z2)) != 0)
435
mprintf(WHITE,"| ");
436
else mprintf(" ");
437
}
438
if (z+1 < nbs)
439
mprintf(WHITE,"|--");
440
else mprintf(WHITE,"`--");
441
mprintf(CYAN,"%s",((CAtom*)g_oaAtoms[g_baAtomIndex[nblist[z]]])->m_sName);
442
mprintf("(%d)",nblist[z]+1);
443
mprintf(GREEN," <-- Ring closure\n");
444
}
445
}
446
_nextnb:;
447
}
448
BTOUT;
449
}
450
451
452
void CTimeStep::BuildAtomIndex()
453
{
454
BTIN;
455
int z, z2;
456
CAtom *at;
457
char buf[64];
458
459
g_baAtomIndex.SetSize(m_iGesAtomCount);
460
for (z=0;z<(long)m_iGesAtomCount;z++)
461
{
462
strcpy(buf,(char*)m_paLabels[z]);
463
ReplaceDigits(buf);
464
for (z2=0;z2<g_oaAtoms.GetSize();z2++)
465
{
466
if (mystricmp(buf,((CAtom*)g_oaAtoms[z2])->m_sName)==0)
467
{
468
at = (CAtom*)g_oaAtoms[z2];
469
// mprintf("Atom %d: Type %d (%s).\n",z,z2,at->m_sName);
470
while (at->m_pMergedTo != NULL)
471
{
472
at = at->m_pMergedTo;
473
// mprintf(" ...was merged to %s.\n",at->m_sName);
474
}
475
// mprintf(" Index is %d.\n",at->m_iIndex);
476
g_baAtomIndex[z] = (unsigned char)at->m_iIndex;
477
goto _e;
478
}
479
}
480
g_baAtomIndex[z] = 255;
481
eprintf("Error: CTimeStep::BuildAtomIndex(): Atom type \"%s\" not known.\n",buf);
482
_e:;
483
}
484
BTOUT;
485
}
486
487
488
bool CTimeStep::ScanMolecules()
489
{
490
BTIN;
491
int z, z2, z3, z4, z5, i, i2, ti, ti2, i1;
492
CxByteArray ta;
493
CSingleMolecule *sm, *sm2;
494
CxIntArray *wa, *waz2, *waz3, *waneu;
495
CMolecule *m;
496
CMolAtom *ma, *ma2, *ma3;
497
CMolBond *bond, *bond2;
498
CMolBondGroup *bg;
499
CMolAngle *angle, *angle2;
500
CMolAngleGroup *ag;
501
CAtom *at;
502
float f;
503
bool b;
504
double tfs;
505
int *stack;
506
507
BuildAtomIndex();
508
// CalcRadii();
509
510
try { stack = new int[g_iGesAtomCount]; } catch(...) { stack = NULL; }
511
if (stack == NULL) NewException((double)g_iGesAtomCount*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);
512
513
b = false;
514
for (z=0;z<g_oaAtoms.GetSize();z++)
515
{
516
if (z == g_iVirtAtomType)
517
continue;
518
at = (CAtom*)g_oaAtoms[z];
519
if (at->m_pMergedTo != NULL)
520
continue;
521
if (at->m_pElement->m_fRadius == 0)
522
{
523
if (!b)
524
{
525
b = true;
526
mprintf("\n");
527
}
528
at->m_bExclude = AskYesNo(" Atom type \"%s\" has bond radius 0. Exclude it from the system (y/n)? [yes] ",true,at->m_sName);
529
// if (!at->m_bExclude)
530
// at->m_pElement->m_fRadius = AskFloat_ND(" Please enter covalent bond radius for %s (in pm): ",at->m_sName);
531
}
532
}
533
534
ta.SetSize(g_iGesAtomCount);
535
g_laAtomSMIndex.SetSize(g_iGesAtomCount);
536
for (z=0;z<g_iGesAtomCount;z++)
537
{
538
ta[z] = 0;
539
g_laAtomSMIndex[z] = -1;
540
}
541
g_iBondBlackListUsed = 0;
542
g_oaSingleMolecules.RemoveAll();
543
g_oaMolecules.RemoveAll();
544
m_iConnectedAtoms = 0;
545
m_iGesAtomModulo = (m_iGesAtomCount / 60)+1;
546
if (g_iScanMolStep == -1)
547
{
548
mprintf(WHITE,"\n Skipping molecule recognition, using atoms as molecules...\n\n");
549
for (z=0;z<(long)m_iGesAtomCount;z++)
550
{
551
if (((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_bExclude)
552
continue;
553
554
try { sm = new CSingleMolecule(); } catch(...) { sm = NULL; }
555
if (sm == NULL) NewException((double)sizeof(CSingleMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
556
557
sm->m_iIndex = g_oaSingleMolecules.GetSize();
558
559
g_oaSingleMolecules.Add(sm);
560
561
g_laAtomSMIndex[z] = (unsigned long)g_oaSingleMolecules.GetSize()-1;
562
563
try { ma = new CMolAtom(); } catch(...) { ma = NULL; }
564
if (ma == NULL) NewException((double)sizeof(CMolAtom),__FILE__,__LINE__,__PRETTY_FUNCTION__);
565
566
ma->m_iOffset = z;
567
ma->m_iType = sm->m_baAtomIndex.GetSize();
568
ma->m_iNumber = 0;
569
sm->m_oaMolAtoms.Add(ma);
570
sm->m_baAtomIndex.Add(g_baAtomIndex[z]);
571
}
572
mprintf(" %d molecules found.\n\n",g_oaSingleMolecules.GetSize());
573
} else
574
{
575
if (g_bVerbose)
576
{
577
mprintf(WHITE,"\n Molecule recognition...\n\n");
578
mprintf(WHITE,">>> Output of the molecule tree >>>\n");
579
} else mprintf("\n Molecule recognition [");
580
// fflush(stdout);
581
for (z=0;z<(long)m_iGesAtomCount;z++)
582
{
583
if (ta[z] != 0) // Dieses Atom wurde bereits in irgendein Molekuel eingebaut
584
{
585
// mprintf("> Atom %d: Schon vergeben.\n",z+1);
586
continue;
587
}
588
// mprintf("# Atom %d: Starte Rekursion.\n",z+1);
589
590
if (((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_bExclude)
591
continue;
592
593
try { sm = new CSingleMolecule(); } catch(...) { sm = NULL; }
594
if (sm == NULL) NewException((double)sizeof(CSingleMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
595
596
sm->m_iIndex = g_oaSingleMolecules.GetSize();
597
598
g_oaSingleMolecules.Add(sm);
599
600
// sm->m_iAtomGes = 0;
601
/* for (z2=0;z2<16;z2++)
602
sm->m_iAtomCount[z2] = 0;
603
sm->m_iElements = 0;*/
604
if (g_bVerbose)
605
mprintf(YELLOW,"\nThe next molecule starts with %s(%d):\n",m_paLabels[z],z+1);
606
607
m_bAbortRing = false;
608
609
RECURSION_ScanMolecules(z,&ta,sm,0,stack,0xFFFFFFFF,true);
610
611
// printf("%d Atome in diesem Molekuel.\n",g_pSingleMolecules[g_oaSingleMolecules.GetSize()].AtomGes);
612
613
// g_oaSingleMolecules.GetSize()++;
614
}
615
if (g_bVerbose)
616
{
617
mprintf(WHITE,"\n<<< Output of the molecule tree <<<\n\n");
618
mprintf("%d molecules found.\n\n",g_oaSingleMolecules.GetSize());
619
} else mprintf("]\n\n %d molecules found.\n\n",g_oaSingleMolecules.GetSize());
620
}
621
622
if (g_iCloseAtomCounter != 0)
623
{
624
mprintf(RED,"\n*** Warning: ");
625
mprintf("Some of the atoms were found to be very close to each other (distance < 50 pm).\n");
626
mprintf(" This usually indicates a problem, e.g. an incorrect cell vector.\n\n");
627
if (!AskYesNo(" Continue with molecule recognition anyways (y/n)? [yes] ",true))
628
return false;
629
mprintf("\n");
630
}
631
632
mprintf(" Sorting atom types...\n");
633
SortSingleMolAtomTypes();
634
635
delete[] stack;
636
637
/* mprintf("\n");
638
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
639
{
640
mprintf("%d ",z+1);
641
((CSingleMolecule*)g_oaSingleMolecules[z])->Dump();
642
}
643
644
mprintf("$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n");*/
645
646
/* mprintf("\n");
647
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
648
{
649
mprintf("%d ",z+1);
650
((CSingleMolecule*)g_oaSingleMolecules[z])->Dump();
651
}
652
mprintf("$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n");*/
653
if (g_iBondBlackListUsed != 0)
654
mprintf(" %d bonds have been broken.\n",g_iBondBlackListUsed);
655
656
/* if (g_oaSingleMolecules.GetSize() >= 4096)
657
{
658
mprintf("\n>>> Mehr als 4096 Molekuele! Dies wird nicht unterstuetzt. <<<\n\n");
659
// g_oaSingleMolecules.GetSize() = 4096;
660
}*/
661
662
mprintf(" Setting up bond lists...\n");
663
// Die Bindungen in m_oaMolAtoms aufbauen
664
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
665
{
666
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
667
for (z2=0;z2<sm->m_laBonds.GetSize()/2;z2++)
668
{
669
i = sm->m_laBonds[z2*2];
670
i2 = sm->m_laBonds[z2*2+1];
671
ti = -1;
672
for (z3=0;z3<sm->m_oaMolAtoms.GetSize();z3++)
673
{
674
if (((CMolAtom*)sm->m_oaMolAtoms[z3])->m_iOffset == i)
675
{
676
ti = z3;
677
break;
678
}
679
}
680
if (ti == -1)
681
{
682
eprintf("CTimeStep::ScanMolecules(): Atom 1 of bond (%d) not found.\n",i);
683
return false;
684
}
685
ti2 = -1;
686
for (z3=0;z3<sm->m_oaMolAtoms.GetSize();z3++)
687
{
688
if (((CMolAtom*)sm->m_oaMolAtoms[z3])->m_iOffset == i2)
689
{
690
ti2 = z3;
691
break;
692
}
693
}
694
if (ti2 == -1)
695
{
696
eprintf("CTimeStep::ScanMolecules(): Atom 2 of bond (%d) not found.\n",i2);
697
return false;
698
}
699
((CMolAtom*)sm->m_oaMolAtoms[ti])->m_oaBonds.Add((CMolAtom*)sm->m_oaMolAtoms[ti2]);
700
((CMolAtom*)sm->m_oaMolAtoms[ti2])->m_oaBonds.Add((CMolAtom*)sm->m_oaMolAtoms[ti]);
701
}
702
}
703
704
// Die AtomCodes berechnen
705
mprintf(" Building atom codes...\n");
706
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
707
{
708
// mprintf("Molecule %d: ",z+1);
709
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
710
if (g_bVerbose)
711
mprintf(YELLOW,"\n*** Singlemolecule %d ***\n\n",z+1);
712
sm->BuildAtomCodes();
713
}
714
715
mprintf(" Creating topological atom order...\n");
716
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
717
{
718
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
719
for (z2=0;z2<sm->m_baAtomIndex.GetSize();z2++)
720
{
721
try { wa = new CxIntArray("CTimeStep::ScanMolecules():wa"); } catch(...) { wa = NULL; }
722
if (wa == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
723
724
sm->m_oaAtomOffset.Add(wa);
725
for (z3=0;z3<sm->m_oaMolAtoms.GetSize();z3++)
726
{
727
ma = (CMolAtom*)sm->m_oaMolAtoms[z3];
728
if (ma->m_iType != z2)
729
continue;
730
ma->m_iNumber = wa->GetSize();
731
wa->Add(ma->m_iOffset);
732
}
733
}
734
}
735
736
mprintf(" Creating bond list...\n");
737
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
738
{
739
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
740
// mprintf("%d:\n",z+1);
741
for (z2=0;z2<sm->m_oaMolAtoms.GetSize();z2++)
742
{
743
ma = (CMolAtom*)sm->m_oaMolAtoms[z2];
744
for (z3=0;z3<ma->m_oaBonds.GetSize();z3++)
745
{
746
ma2 = (CMolAtom*)ma->m_oaBonds[z3];
747
if (ma2->m_iMolAtomNumber < z2 /* == ma->m_iMolAtomNumber*/)
748
continue;
749
750
// mprintf(" %s%2d <--> %s%2d\n",((CAtom*)g_oaAtoms[sm->m_baAtomIndex[ma->m_iType]])->m_sName,ma->m_iNumber+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[ma2->m_iType]])->m_sName,ma2->m_iNumber+1);
751
752
try { bond = new CMolBond(); } catch(...) { bond = NULL; }
753
if (bond == NULL) NewException((double)sizeof(CMolBond),__FILE__,__LINE__,__PRETTY_FUNCTION__);
754
755
bond->m_iAtom[0] = ma->m_iNumber;
756
bond->m_iAtom[1] = ma2->m_iNumber;
757
bond->m_iAtomType[0] = ma->m_iType;
758
bond->m_iAtomType[1] = ma2->m_iType;
759
bond->m_iMolAtom[0] = z2;
760
bond->m_iMolAtom[1] = ma2->m_iMolAtomNumber;
761
bond->m_iAtomOffset[0] = ma->m_iOffset;
762
bond->m_iAtomOffset[1] = ma2->m_iOffset;
763
sm->m_oaBonds.Add(bond);
764
}
765
}
766
/* if (z == 0)
767
mprintf(" %d Bonds added.\n",oatemp.GetSize());*/
768
for (z2=0;z2<sm->m_oaBonds.GetSize();z2++)
769
{
770
bond = (CMolBond*)sm->m_oaBonds[z2];
771
for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)
772
{
773
bg = (CMolBondGroup*)sm->m_oaBondGroups[z3];
774
for (z4=0;z4<bg->m_oaBonds.GetSize();z4++)
775
{
776
bond2 = (CMolBond*)bg->m_oaBonds[z4];
777
if (((((CMolAtom*)sm->m_oaMolAtoms[bond->m_iMolAtom[0]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[bond2->m_iMolAtom[0]])->m_fAtomCode) &&
778
(((CMolAtom*)sm->m_oaMolAtoms[bond->m_iMolAtom[1]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[bond2->m_iMolAtom[1]])->m_fAtomCode)) ||
779
((((CMolAtom*)sm->m_oaMolAtoms[bond->m_iMolAtom[0]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[bond2->m_iMolAtom[1]])->m_fAtomCode) &&
780
(((CMolAtom*)sm->m_oaMolAtoms[bond->m_iMolAtom[1]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[bond2->m_iMolAtom[0]])->m_fAtomCode)))
781
{
782
bg->m_oaBonds.Add(bond);
783
goto _bonddone;
784
}
785
}
786
}
787
788
try { bg = new CMolBondGroup(); } catch(...) { bg = NULL; }
789
if (bg == NULL) NewException((double)sizeof(CMolBondGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
790
791
bg->m_oaBonds.Add(bond);
792
sm->m_oaBondGroups.Add(bg);
793
_bonddone:;
794
}
795
/* if (z == 0)
796
{
797
mprintf(" %d Bond groups found:\n",sm->m_oaBondGroups.GetSize());
798
for (z2=0;z2<sm->m_oaBondGroups.GetSize();z2++)
799
{
800
mprintf(" - ");
801
bg = (CMolBondGroup*)sm->m_oaBondGroups[z2];
802
for (z3=0;z3<bg->m_oaBonds.GetSize();z3++)
803
{
804
bond = (CMolBond*)bg->m_oaBonds[z3];
805
mprintf("%s%2d <--> %s%2d",((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[0]]])->m_sName,bond->m_iAtom[0]+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[1]]])->m_sName,bond->m_iAtom[1]+1);
806
if (z3 < bg->m_oaBonds.GetSize()-1)
807
mprintf(", ");
808
}
809
mprintf("\n");
810
}
811
}*/
812
}
813
814
mprintf(" Creating angle list...\n");
815
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
816
{
817
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
818
// mprintf("%d:\n",z+1);
819
for (z2=0;z2<sm->m_oaMolAtoms.GetSize();z2++)
820
{
821
ma = (CMolAtom*)sm->m_oaMolAtoms[z2];
822
for (z3=0;z3<ma->m_oaBonds.GetSize();z3++)
823
{
824
ma2 = (CMolAtom*)ma->m_oaBonds[z3];
825
for (z4=z3+1;z4<ma->m_oaBonds.GetSize();z4++)
826
{
827
ma3 = (CMolAtom*)ma->m_oaBonds[z4];
828
// mprintf(" (%s%2d, %s%2d, %s%2d)\n",((CAtom*)g_oaAtoms[sm->m_baAtomIndex[ma2->m_iType]])->m_sName,ma2->m_iNumber+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[ma->m_iType]])->m_sName,ma->m_iNumber+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[ma3->m_iType]])->m_sName,ma3->m_iNumber+1);
829
830
try { angle = new CMolAngle(); } catch(...) { angle = NULL; }
831
if (angle == NULL) NewException((double)sizeof(CMolAngle),__FILE__,__LINE__,__PRETTY_FUNCTION__);
832
833
angle->m_iAtom[0] = ma2->m_iNumber;
834
angle->m_iAtom[1] = ma->m_iNumber;
835
angle->m_iAtom[2] = ma3->m_iNumber;
836
angle->m_iAtomType[0] = ma2->m_iType;
837
angle->m_iAtomType[1] = ma->m_iType;
838
angle->m_iAtomType[2] = ma3->m_iType;
839
angle->m_iMolAtom[0] = ma2->m_iMolAtomNumber;
840
angle->m_iMolAtom[1] = z2;
841
angle->m_iMolAtom[2] = ma3->m_iMolAtomNumber;
842
angle->m_iAtomOffset[0] = ma2->m_iOffset;
843
angle->m_iAtomOffset[1] = ma->m_iOffset;
844
angle->m_iAtomOffset[2] = ma3->m_iOffset;
845
sm->m_oaAngles.Add(angle);
846
}
847
}
848
}
849
/* if (z == 0)
850
mprintf(" %d Angles added.\n",oatemp.GetSize());*/
851
if (sm->m_oaAngles.GetSize() > 1000)
852
mprintf(WHITE," [");
853
tfs = sm->m_oaAngles.GetSize() / 50.0;
854
for (z2=0;z2<sm->m_oaAngles.GetSize();z2++)
855
{
856
if (sm->m_oaAngles.GetSize() > 1000)
857
if (fmod(z2,tfs) < 1)
858
mprintf(WHITE,"#");
859
angle = (CMolAngle*)sm->m_oaAngles[z2];
860
for (z3=0;z3<sm->m_oaAngleGroups.GetSize();z3++)
861
{
862
ag = (CMolAngleGroup*)sm->m_oaAngleGroups[z3];
863
for (z4=0;z4<ag->m_oaAngles.GetSize();z4++)
864
{
865
angle2 = (CMolAngle*)ag->m_oaAngles[z4];
866
if (( ((CMolAtom*)sm->m_oaMolAtoms[angle->m_iMolAtom[1]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[angle2->m_iMolAtom[1]])->m_fAtomCode) &&
867
(((( ((CMolAtom*)sm->m_oaMolAtoms[angle->m_iMolAtom[0]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[angle2->m_iMolAtom[0]])->m_fAtomCode) &&
868
( ((CMolAtom*)sm->m_oaMolAtoms[angle->m_iMolAtom[2]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[angle2->m_iMolAtom[2]])->m_fAtomCode))) ||
869
(( ((CMolAtom*)sm->m_oaMolAtoms[angle->m_iMolAtom[0]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[angle2->m_iMolAtom[2]])->m_fAtomCode) &&
870
( ((CMolAtom*)sm->m_oaMolAtoms[angle->m_iMolAtom[2]])->m_fAtomCode == ((CMolAtom*)sm->m_oaMolAtoms[angle2->m_iMolAtom[0]])->m_fAtomCode))))
871
{
872
ag->m_oaAngles.Add(angle);
873
goto _angledone;
874
}
875
}
876
}
877
878
try { ag = new CMolAngleGroup(); } catch(...) { ag = NULL; }
879
if (ag == NULL) NewException((double)sizeof(CMolAngleGroup),__FILE__,__LINE__,__PRETTY_FUNCTION__);
880
881
ag->m_oaAngles.Add(angle);
882
sm->m_oaAngleGroups.Add(ag);
883
_angledone:;
884
}
885
if (sm->m_oaAngles.GetSize() > 1000)
886
mprintf(WHITE,"]\n");
887
/* if (z == 0)
888
{
889
mprintf(" %d Angle groups found:\n",sm->m_oaAngleGroups.GetSize());
890
for (z2=0;z2<sm->m_oaAngleGroups.GetSize();z2++)
891
{
892
mprintf(" - ");
893
ag = (CMolAngleGroup*)sm->m_oaAngleGroups[z2];
894
for (z3=0;z3<ag->m_oaAngles.GetSize();z3++)
895
{
896
angle = (CMolAngle*)ag->m_oaAngles[z3];
897
mprintf(" (%s%2d, %s%2d, %s%2d)",((CAtom*)g_oaAtoms[sm->m_baAtomIndex[angle->m_iAtomType[0]]])->m_sName,angle->m_iAtom[0]+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[angle->m_iAtomType[1]]])->m_sName,angle->m_iAtom[1]+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[angle->m_iAtomType[2]]])->m_sName,angle->m_iAtom[2]+1);
898
if (z3 < ag->m_oaAngles.GetSize()-1)
899
mprintf(", ");
900
}
901
mprintf("\n");
902
}
903
}*/
904
}
905
906
mprintf(" Grouping together equivalent molecules...\n");
907
for (z=0;z<g_oaSingleMolecules.GetSize();z++) // Alle Molekuelvertreter durchgehen
908
{
909
// mprintf("Pruefe SM %d...\n",z+1);
910
sm = (CSingleMolecule*)g_oaSingleMolecules[z];
911
for (z2=0;z2<g_oaMolecules.GetSize();z2++) // Alle schon vorhandenen Molekueltemplates durchgehen
912
{
913
m = (CMolecule*)g_oaMolecules[z2];
914
sm2 = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];
915
/* if (m->m_baAtomIndex.GetSize() != sm->m_baAtomIndex.GetSize())
916
goto _cont; // Nich die Gleiche Anzahl verschiedener Elemente -> Keine Uebereinstimmung
917
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
918
{
919
if (m->m_baAtomIndex[z3] != sm->m_baAtomIndex[z3])
920
goto _cont; // Elemente an Position z3 unterscheiden sich -> keine Uebereinstimmung
921
if (m->m_waAtomCount[z3] != ((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize())
922
goto _cont; // Anzahl an Atomen dieser Elementsorte unterscheidet sich -> Keine Uebereinstimmung*/
923
// mprintf(" Stimmt mit M%d ueberein.\n",z2);
924
// ((CMolecule*)g_oaMolecules[z2])->Count++;
925
// g_pSingleMolecules[z].m_iMoleculeOffset = z2;
926
// }
927
if (sm->m_oaMolAtoms.GetSize() != sm2->m_oaMolAtoms.GetSize())
928
goto _cont;
929
for (z3=0;z3<sm->m_oaMolAtoms.GetSize();z3++)
930
if (((CMolAtom*)sm->m_oaMolAtoms[z3])->m_fAtomCode != ((CMolAtom*)sm2->m_oaMolAtoms[z3])->m_fAtomCode)
931
goto _cont;
932
sm->m_iMolSMIndex = m->m_laSingleMolIndex.GetSize();
933
m->m_laSingleMolIndex.Add(z);
934
// sm->m_iMolType = z2;
935
goto _fert;
936
_cont:;
937
}
938
939
try { m = new CMolecule(); } catch(...) { m = NULL; }
940
if (m == NULL) NewException((double)sizeof(CMolecule),__FILE__,__LINE__,__PRETTY_FUNCTION__);
941
942
g_oaMolecules.Add(m);
943
// m->Count = 1; // Neues Molekueltemplate hinzufuegen
944
// m->Elements = ((CSingleMolecule*)g_oaSingleMolecules[z])->m_iElements;
945
m->m_iAtomGes = 0;
946
f = 0;
947
for (z2=0;z2<sm->m_oaAtomOffset.GetSize();z2++)
948
{
949
m->m_iAtomGes += ((CxIntArray*)sm->m_oaAtomOffset[z2])->GetSize();
950
f += ((CAtom*)g_oaAtoms[sm->m_baAtomIndex[z2]])->m_pElement->m_fMass * ((CxIntArray*)sm->m_oaAtomOffset[z2])->GetSize();
951
}
952
m->m_iAtomGesNoVirt = m->m_iAtomGes;
953
m->m_fMass = f;
954
((CSingleMolecule*)g_oaSingleMolecules[z])->m_iMolType = g_oaMolecules.GetSize()-1;
955
for (z2=0;z2<((CSingleMolecule*)g_oaSingleMolecules[z])->m_baAtomIndex.GetSize();z2++)
956
{
957
m->m_baAtomIndex.Add(((CSingleMolecule*)g_oaSingleMolecules[z])->m_baAtomIndex[z2]);
958
m->m_waAtomCount.Add(((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[z])->m_oaAtomOffset[z2])->GetSize());
959
// m->AtomCount[z2] = ((CSingleMolecule*)g_oaSingleMolecules[z])->m_iAtomCount[z2];
960
}
961
sm->m_iMolSMIndex = m->m_laSingleMolIndex.GetSize();
962
m->m_laSingleMolIndex.Add(z);
963
// g_pSingleMolecules[z].m_iMoleculeOffset = g_oaMolecules.GetSize();
964
m->BuildName();
965
966
// Standardmaessig geom. Zentrum als Dipolzentrum
967
m->m_iDipoleCenterType = m->m_baAtomIndex.GetSize();
968
m->m_iDipoleCenterIndex = 0;
969
970
// mprintf("### Erzeuge neues Molekuel %d \"%s\".\n",g_oaMolecules.GetSize(),m->Name);
971
// g_oaMolecules.GetSize()++;
972
_fert:;
973
}
974
mprintf(" Found %d unique molecule types.\n",g_oaMolecules.GetSize());
975
976
// Sort by molecular mass
977
mprintf(" Sorting molecule types by molecular mass...\n");
978
for (z=0;z<g_oaMolecules.GetSize();z++)
979
{
980
// mprintf("@ z=%d\n",z);
981
f = -1.0f;
982
z3 = -1;
983
for (z2=z;z2<g_oaMolecules.GetSize();z2++)
984
{
985
// mprintf("@ z2=%d\n",z2);
986
if (((CMolecule*)g_oaMolecules[z2])->m_fMass > f)
987
{
988
// mprintf("@ %f > %f --> z3 = %d\n",((CMolecule*)g_oaMolecules[z2])->m_fMass,f,z2);
989
f = ((CMolecule*)g_oaMolecules[z2])->m_fMass;
990
z3 = z2;
991
}
992
}
993
if (z3 == -1)
994
abort();
995
if (f > 0)
996
{
997
// mprintf("@ Swapping %d with %d.\n",z,z3);
998
m = (CMolecule*)g_oaMolecules[z3];
999
g_oaMolecules[z3] = g_oaMolecules[z];
1000
g_oaMolecules[z] = m;
1001
}
1002
}
1003
1004
for (z=0;z<g_oaMolecules.GetSize();z++)
1005
{
1006
((CMolecule*)g_oaMolecules[z])->m_iIndex = z;
1007
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)
1008
((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[z2]])->m_iMolType = z;
1009
}
1010
1011
1012
/* for (z=0;z<g_oaMolecules.GetSize();z++)
1013
{
1014
m = (CMolecule*)g_oaMolecules[z];
1015
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
1016
mprintf("Molecule %d Ring systems:\n",z+1);
1017
for (z2=0;z2<sm->m_oaRings.GetSize();z2++)
1018
{
1019
wa = (CxIntArray*)sm->m_oaRings[z2];
1020
mprintf(" - Ring %d: ",z2+1);
1021
for (z3=0;z3<wa->GetSize();z3++)
1022
{
1023
mprintf("%d",(*wa)[z3]);
1024
if (z3+1 < wa->GetSize())
1025
mprintf(", ");
1026
}
1027
mprintf("\n");
1028
}
1029
mprintf("\n");
1030
}*/
1031
1032
ti = 0;
1033
for (z=0;z<g_oaMolecules.GetSize();z++)
1034
{
1035
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
1036
ti += sm->m_oaRings.GetSize();
1037
}
1038
1039
mprintf(" Found %d rings.\n",ti);
1040
if (ti != 0)
1041
{
1042
mprintf(" Refining ring systems...\n");
1043
1044
try { wa = new CxIntArray("CTimeStep::ScanMolecules():wa"); } catch(...) { wa = NULL; }
1045
if (wa == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1046
1047
// Process ring systems
1048
for (z=0;z<g_oaMolecules.GetSize();z++)
1049
{
1050
m = (CMolecule*)g_oaMolecules[z];
1051
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
1052
if (sm->m_oaRings.GetSize() > 100)
1053
{
1054
eprintf(" More than 100 rings in molecule %d, skipping refinement. Ring system may be improper.\n",z+1);
1055
continue;
1056
}
1057
ti2 = 0;
1058
_again:
1059
ti2++;
1060
if (ti2 > 1000)
1061
{
1062
eprintf(" Too many iterations in molecule %d, aborting refinement. Ring system may be improper.\n",z+1);
1063
continue;
1064
}
1065
// mprintf("### again\n");
1066
for (z2=0;z2<sm->m_oaRings.GetSize();z2++)
1067
{
1068
waz2 = (CxIntArray*)sm->m_oaRings[z2];
1069
for (z3=z2+1;z3<sm->m_oaRings.GetSize();z3++)
1070
{
1071
waz3 = (CxIntArray*)sm->m_oaRings[z3];
1072
1073
// mprintf("*A* Checking if %d(%d) contains %d(%d)...\n",z2+1,waz2->GetSize(),z3+1,waz3->GetSize());
1074
// Check if waz2 contains waz3
1075
wa->SetSize(waz2->GetSize());
1076
for (z4=0;z4<waz2->GetSize();z4++)
1077
(*wa)[z4] = 0;
1078
for (z4=0;z4<waz3->GetSize();z4++)
1079
{
1080
for (z5=0;z5<waz2->GetSize();z5++)
1081
{
1082
if ((*waz3)[z4] == (*waz2)[z5])
1083
{
1084
(*wa)[z5] = 1;
1085
goto _found2;
1086
}
1087
}
1088
goto _notfound2;
1089
_found2:;
1090
}
1091
// mprintf(" Yes!\n");
1092
1093
try { waneu = new CxIntArray("CTimeStep::ScanMolecules():waneu"); } catch(...) { waneu = NULL; }
1094
if (waneu == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1095
1096
for (z4=0;z4<waz2->GetSize();z4++)
1097
{
1098
if (z4 == 0)
1099
{
1100
if (((*wa)[z4] == 0) || ((*wa)[z4+1] == 0) || ((*wa)[waz2->GetSize()-1] == 0))
1101
waneu->Add((*waz2)[z4]);
1102
} else if (z4 == waz2->GetSize()-1)
1103
{
1104
if (((*wa)[z4] == 0) || ((*wa)[z4-1] == 0) || ((*wa)[0] == 0))
1105
waneu->Add((*waz2)[z4]);
1106
} else
1107
{
1108
if (((*wa)[z4] == 0) || ((*wa)[z4+1] == 0) || ((*wa)[z4-1] == 0))
1109
waneu->Add((*waz2)[z4]);
1110
}
1111
}
1112
// mprintf(" Took %d from %d atoms from waz2.\n",waneu->GetSize(),waz2->GetSize());
1113
i1 = waz2->GetSize();
1114
delete waz2;
1115
sm->m_oaRings[z2] = waneu;
1116
if (waneu->GetSize() != i1)
1117
goto _again;
1118
_notfound2:
1119
1120
// mprintf("*B* Checking if %d contains %d...\n",z3+1,z2+1);
1121
// Check if waz3 contains waz2
1122
wa->SetSize(waz3->GetSize());
1123
for (z4=0;z4<waz3->GetSize();z4++)
1124
(*wa)[z4] = 0;
1125
for (z4=0;z4<waz2->GetSize();z4++)
1126
{
1127
for (z5=0;z5<waz3->GetSize();z5++)
1128
{
1129
if ((*waz2)[z4] == (*waz3)[z5])
1130
{
1131
(*wa)[z5] = 1;
1132
goto _found3;
1133
}
1134
}
1135
goto _notfound3;
1136
_found3:;
1137
}
1138
// mprintf(" Yes!\n");
1139
1140
try { waneu = new CxIntArray("CTimeStep::ScanMolecules():waneu"); } catch(...) { waneu = NULL; }
1141
if (waneu == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1142
1143
for (z4=0;z4<waz3->GetSize();z4++)
1144
{
1145
if (z4 == 0)
1146
{
1147
if (((*wa)[z4] == 0) || ((*wa)[z4+1] == 0) || ((*wa)[waz3->GetSize()-1] == 0))
1148
waneu->Add((*waz3)[z4]);
1149
} else if (z4 == waz3->GetSize()-1)
1150
{
1151
if (((*wa)[z4] == 0) || ((*wa)[z4-1] == 0) || ((*wa)[0] == 0))
1152
waneu->Add((*waz3)[z4]);
1153
} else
1154
{
1155
if (((*wa)[z4] == 0) || ((*wa)[z4+1] == 0) || ((*wa)[z4-1] == 0))
1156
waneu->Add((*waz3)[z4]);
1157
}
1158
}
1159
// mprintf(" Took %d from %d atoms from waz3.\n",waneu->GetSize(),waz3->GetSize());
1160
i1 = waz3->GetSize();
1161
delete waz3;
1162
sm->m_oaRings[z3] = waneu;
1163
if (waneu->GetSize() != i1)
1164
goto _again;
1165
_notfound3:;
1166
}
1167
}
1168
}
1169
delete wa;
1170
1171
mprintf(" Assigning ring systems to molecule types...\n");
1172
for (z=0;z<g_oaMolecules.GetSize();z++)
1173
{
1174
m = (CMolecule*)g_oaMolecules[z];
1175
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
1176
for (z2=0;z2<sm->m_oaRings.GetSize();z2++)
1177
{
1178
wa = (CxIntArray*)sm->m_oaRings[z2];
1179
1180
try { waz2 = new CxIntArray("CTimeStep::ScanMolecules():waz2"); } catch(...) { waz2 = NULL; }
1181
if (waz2 == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1182
1183
try { waz3 = new CxIntArray("CTimeStep::ScanMolecules():waz3"); } catch(...) { waz3 = NULL; }
1184
if (waz3 == NULL) NewException((double)sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);
1185
1186
m->m_oaRingAtomTypes.Add(waz2);
1187
m->m_oaRingAtoms.Add(waz3);
1188
for (z3=0;z3<wa->GetSize();z3++)
1189
{
1190
for (z4=0;z4<sm->m_baAtomIndex.GetSize();z4++)
1191
{
1192
for (z5=0;z5<((CxIntArray*)sm->m_oaAtomOffset[z4])->GetSize();z5++)
1193
{
1194
if (((CxIntArray*)sm->m_oaAtomOffset[z4])->GetAt(z5) == wa->GetAt(z3))
1195
{
1196
waz2->Add(z4);
1197
waz3->Add(z5);
1198
goto _done;
1199
}
1200
}
1201
}
1202
_done:;
1203
}
1204
}
1205
}
1206
1207
mprintf(" Sorting rings by size...\n");
1208
for (z=0;z<g_oaMolecules.GetSize();z++)
1209
{
1210
m = (CMolecule*)g_oaMolecules[z];
1211
1212
for (z2=0;z2<m->m_oaRingAtoms.GetSize();z2++)
1213
{
1214
i1 = 0;
1215
ti = -1;
1216
for (z3=z2;z3<m->m_oaRingAtoms.GetSize();z3++)
1217
{
1218
if (((CxIntArray*)m->m_oaRingAtoms[z3])->GetSize() > i1)
1219
{
1220
i1 = ((CxIntArray*)m->m_oaRingAtoms[z3])->GetSize();
1221
ti = z3;
1222
}
1223
}
1224
if ((ti != -1) && (ti != z2))
1225
{
1226
wa = (CxIntArray*)m->m_oaRingAtoms[z2];
1227
m->m_oaRingAtoms[z2] = m->m_oaRingAtoms[ti];
1228
m->m_oaRingAtoms[ti] = wa;
1229
wa = (CxIntArray*)m->m_oaRingAtomTypes[z2];
1230
m->m_oaRingAtomTypes[z2] = m->m_oaRingAtomTypes[ti];
1231
m->m_oaRingAtomTypes[ti] = wa;
1232
}
1233
}
1234
}
1235
}
1236
1237
/* for (z=0;z<g_oaMolecules.GetSize();z++)
1238
{
1239
m = (CMolecule*)g_oaMolecules[z];
1240
sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex[0]];
1241
mprintf("Molecule %d Ring systems:\n",z+1);
1242
for (z2=0;z2<sm->m_oaRings.GetSize();z2++)
1243
{
1244
wa = (CxIntArray*)sm->m_oaRings[z2];
1245
mprintf(" - Ring %d: ",z2+1);
1246
for (z3=0;z3<wa->GetSize();z3++)
1247
{
1248
mprintf("%d",(*wa)[z3]);
1249
if (z3+1 < wa->GetSize())
1250
mprintf(", ");
1251
}
1252
mprintf("\n");
1253
}
1254
mprintf("\n");
1255
}*/
1256
1257
/* mprintf("\n%d Molekuelsorten gefunden.\n",g_oaMolecules.GetSize());
1258
for (z=0;z<g_oaMolecules.GetSize();z++)
1259
mprintf("Molekuel \"%s\": %d Atome gesamt, %d mal in der Simulation.\n",g_pMolecules[z].Name,g_pMolecules[z].AtomGes,g_pMolecules[z].Count);
1260
*/
1261
/* mprintf("\n");
1262
for (z=0;z<g_oaMolecules.GetSize();z++)
1263
{
1264
mprintf("%d ",z+1);
1265
((CMolecule*)g_oaMolecules[z])->Dump();
1266
}*/
1267
mprintf(" Molecule recognition finished.\n");
1268
BTOUT;
1269
return true;
1270
}
1271
1272
1273
void CTimeStep::RECURSION_MegaTree(int i, char *ta, int depth, unsigned long bmask, bool w, int *stack)
1274
{
1275
BTIN;
1276
int z, z2;
1277
int nblist[20], nbs;
1278
1279
stack[depth] = i;
1280
ta[i] = 1;
1281
for (z=1;z<depth;z++)
1282
{
1283
if ((bmask & (int)pow(2.0,z)) != 0)
1284
mprintf(WHITE,"| ");
1285
else mprintf(" ");
1286
}
1287
if (depth != 0)
1288
{
1289
if (w)
1290
mprintf(WHITE,"|--");
1291
else mprintf(WHITE,"`--");
1292
}
1293
mprintf("%s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[i]])->m_sName,i+1);
1294
nbs = 0;
1295
for (z=0;z<(long)m_iGesAtomCount;z++) // Schon mal alle Nachbarn raussuchen
1296
{
1297
if (z == i)
1298
continue;
1299
if (BondRange(i,z,NULL))
1300
{
1301
if (ta[z] != 0)
1302
{
1303
if ((depth > 0) && (z != stack[depth-1]))
1304
{
1305
mprintf(GREEN," <-- Ring closure: ");
1306
mprintf("%s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[stack[depth]]])->m_sName,stack[depth]+1);
1307
z2 = depth-1;
1308
while ((stack[z2] != z) && (z2 >= 0))
1309
{
1310
mprintf(" - %s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[stack[z2]]])->m_sName,stack[z2]+1);
1311
z2--;
1312
}
1313
mprintf(" - %s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_sName,z+1);
1314
// mprintf("Ringschluss! [d-1=%d,d=%d,i=%d] %s(%d)\n",stack[depth-1]+1,stack[depth]+1,i+1,((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_sName,z+1);
1315
}
1316
continue;
1317
}
1318
nblist[nbs] = z;
1319
nbs++;
1320
}
1321
}
1322
mprintf("\n");
1323
for (z=0;z<nbs;z++) // Fuer das aktuelle Atom z2 alle Nachbarn finden
1324
{
1325
if (ta[nblist[z]] != 0) // Der Nachbar wurde uns weggeschnappt -> Ringschluss
1326
{
1327
for (z2=1;z2<depth+1;z2++)
1328
{
1329
if ((bmask & (int)pow(2.0,z2)) != 0)
1330
mprintf(WHITE,"| ");
1331
else mprintf(" ");
1332
}
1333
if (z+1 < nbs)
1334
mprintf(WHITE,"|--");
1335
else mprintf("`--");
1336
mprintf("%s(%d)",((CAtom*)g_oaAtoms[g_baAtomIndex[nblist[z]]])->m_sName,nblist[z]+1);
1337
mprintf(GREEN," <-- Ring closure\n");
1338
} else
1339
{
1340
if (z+1 == nbs)
1341
bmask -= (int)pow(2.0,depth+1);
1342
RECURSION_MegaTree(nblist[z],ta,/*sm,*/depth+1,bmask,(z+1==nbs)?false:true,stack);
1343
}
1344
}
1345
BTOUT;
1346
}
1347
1348
1349
void CTimeStep::PrintMegaTree()
1350
{
1351
BTIN;
1352
int z;
1353
char ta[16384];
1354
int stack[16384];
1355
1356
for (z=0;z<16384;z++)
1357
ta[z] = 0;
1358
for (z=0;z<(long)m_iGesAtomCount;z++)
1359
{
1360
if (ta[z] != 0) // Dieses Atom wurde bereits in irgendein Molekuel eingebaut
1361
continue;
1362
mprintf(YELLOW,"\nThe next molecule starts with %s(%d):\n",m_paLabels[z],z+1);
1363
RECURSION_MegaTree(z,ta,0,0xFFFFFFFF,true,stack);
1364
}
1365
mprintf("\n");
1366
BTOUT;
1367
}
1368
1369
1370
void CTimeStep::PrintMatrix(bool onlyfirst, bool onlybind)
1371
{
1372
BTIN;
1373
int z, z2, z3, z4, z5, z6, z7, z8, ti, ti2;
1374
float tf;
1375
bool b, c, noh;
1376
CxVector3 vec1, vec2;
1377
CSingleMolecule *sm;
1378
CMolecule *m;
1379
CMolAtom *ma, *ma0;
1380
CxIntArray *wa, *wat;
1381
1382
for (z=0;z<g_oaMolecules.GetSize();z++)
1383
{
1384
m = (CMolecule*)g_oaMolecules[z];
1385
for (z6=0;z6<(onlyfirst?1:m->m_laSingleMolIndex.GetSize());z6++)
1386
{
1387
mprintf(YELLOW,"\n*** Molecule %d: %s; Representant %d; Distances in pm ***\n",z+1,m->m_sName,z6+1);
1388
if ((m->m_baAtomIndex.GetSize() == 1) && (m->m_waAtomCount[0] == 1))
1389
{
1390
mprintf("[only 1 Atom]\n");
1391
continue;
1392
}
1393
if (m->m_iAtomGes > 200)
1394
{
1395
mprintf(WHITE,"\n This molecule has > 200 atoms. Output would flood the screen. Skipping.\n");
1396
continue;
1397
}
1398
noh = false;
1399
_matagain:
1400
if (m->m_oaRingAtoms.GetSize() != 0)
1401
mprintf(GREEN," (ring bonds are shown in green)\n");
1402
mprintf("\n");
1403
mprintf(" ");
1404
for (z2=0;z2<m->m_baAtomIndex.GetSize();z2++)
1405
{
1406
if (noh) // Skip H atoms
1407
if (mystricmp(((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,"H") == 0)
1408
continue;
1409
for (z3=0;z3<m->m_waAtomCount[z2];z3++)
1410
{
1411
if (((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName[1] == 0)
1412
mprintf(" ");
1413
mprintf(WHITE,"%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,z3+1);
1414
if (z3+1 < 10)
1415
mprintf(" ");
1416
}
1417
}
1418
mprintf("\n");
1419
for (z2=0;z2<m->m_baAtomIndex.GetSize();z2++)
1420
{
1421
if (noh) // Skip H atoms
1422
if (mystricmp(((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,"H") == 0)
1423
continue;
1424
for (z3=0;z3<m->m_waAtomCount[z2];z3++)
1425
{
1426
mprintf(WHITE,"%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,z3+1);
1427
if (((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName[1] == 0)
1428
mprintf(" ");
1429
if (z3+1 < 10)
1430
mprintf(" ");
1431
for (z4=0;z4<m->m_baAtomIndex.GetSize();z4++)
1432
{
1433
if (noh) // Skip H atoms
1434
if (mystricmp(((CAtom*)g_oaAtoms[m->m_baAtomIndex[z4]])->m_sName,"H") == 0)
1435
continue;
1436
for (z5=0;z5<m->m_waAtomCount[z4];z5++)
1437
{
1438
if ((z2 == z4) && (z3 == z5))
1439
{
1440
mprintf(BLUE,"*** ");
1441
continue;
1442
}
1443
ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z6]])->m_oaAtomOffset[z2])->GetAt(z3);
1444
vec1 = g_TimeStep.m_vaCoords[ti];
1445
ti2 = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z6]])->m_oaAtomOffset[z4])->GetAt(z5);
1446
vec2 = g_TimeStep.m_vaCoords[ti2];
1447
vec1 -= vec2;
1448
tf = vec1.GetLength();
1449
if ((g_TimeStep.BondRange(ti,ti2,NULL)) || (!onlybind))
1450
{
1451
for (z8=0;z8<m->m_oaRingAtomTypes.GetSize();z8++)
1452
{
1453
wat = (CxIntArray*)m->m_oaRingAtomTypes[z8];
1454
wa = (CxIntArray*)m->m_oaRingAtoms[z8];
1455
for (z7=0;z7<wa->GetSize();z7++)
1456
{
1457
if (((*wat)[z7] == z2) && ((*wa)[z7] == z3))
1458
{
1459
if (z7 == 0)
1460
{
1461
if (((*wat)[z7+1] == z4) && ((*wa)[z7+1] == z5))
1462
goto _green;
1463
if (((*wat)[wa->GetSize()-1] == z4) && ((*wa)[wa->GetSize()-1] == z5))
1464
goto _green;
1465
} else if (z7 == wa->GetSize()-1)
1466
{
1467
if (((*wat)[0] == z4) && ((*wa)[0] == z5))
1468
goto _green;
1469
if (((*wat)[z7-1] == z4) && ((*wa)[z7-1] == z5))
1470
goto _green;
1471
} else
1472
{
1473
if (((*wat)[z7+1] == z4) && ((*wa)[z7+1] == z5))
1474
goto _green;
1475
if (((*wat)[z7-1] == z4) && ((*wa)[z7-1] == z5))
1476
goto _green;
1477
}
1478
}
1479
}
1480
}
1481
mprintf("%3.0f ",tf);
1482
continue;
1483
_green:
1484
mprintf(GREEN,"%3.0f ",tf);
1485
} else mprintf(" - ");
1486
}
1487
}
1488
mprintf("\n");
1489
}
1490
}
1491
if ((!noh) && (m->m_iAtomGes > 30))
1492
{
1493
mprintf(WHITE,"\n This was a very large molecule.\n Printing the matrix again without H atoms.\n");
1494
noh = true;
1495
goto _matagain;
1496
}
1497
// if (((!onlyfirst) && ((z2 < ((CMolecule*)g_oaMolecules[z])->Elements-1) || (g_oaMolecules.GetSize()-1))) || (z < g_oaMolecules.GetSize()-1))
1498
// mprintf(">>>");
1499
}
1500
1501
if (m->m_oaRingAtoms.GetSize() != 0)
1502
{
1503
mprintf("\n");
1504
for (z2=0;z2<m->m_oaRingAtoms.GetSize();z2++)
1505
{
1506
mprintf(" %d-ring: ",((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize());
1507
if (((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize() > 20)
1508
{
1509
for (z3=0;z3<5;z3++)
1510
{
1511
mprintf("%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[((CxIntArray*)m->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)m->m_oaRingAtoms[z2])->GetAt(z3)+1);
1512
if (z3+1 < ((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize())
1513
mprintf(" - ");
1514
}
1515
mprintf(RED,"...");
1516
mprintf(" - ");
1517
for (z3=((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize()-5;z3<((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize();z3++)
1518
{
1519
mprintf("%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[((CxIntArray*)m->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)m->m_oaRingAtoms[z2])->GetAt(z3)+1);
1520
if (z3+1 < ((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize())
1521
mprintf(" - ");
1522
}
1523
} else
1524
{
1525
for (z3=0;z3<((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize();z3++)
1526
{
1527
mprintf("%s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[((CxIntArray*)m->m_oaRingAtomTypes[z2])->GetAt(z3)]])->m_sName,((CxIntArray*)m->m_oaRingAtoms[z2])->GetAt(z3)+1);
1528
if (z3+1 < ((CxIntArray*)m->m_oaRingAtoms[z2])->GetSize())
1529
mprintf(" - ");
1530
}
1531
}
1532
mprintf("\n");
1533
if (z2 >= 99)
1534
{
1535
mprintf(RED,"\n Only showing the first 100 rings.\n");
1536
break;
1537
}
1538
}
1539
}
1540
1541
c = false;
1542
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];
1543
for (z2=0;z2<m->m_baAtomIndex.GetSize();z2++)
1544
{
1545
b = false;
1546
ma = NULL;
1547
for (z3=0;z3<sm->m_oaMolAtoms.GetSize();z3++)
1548
{
1549
if (((CMolAtom*)sm->m_oaMolAtoms[z3])->m_iType != z2)
1550
continue;
1551
ma0 = ma;
1552
ma = (CMolAtom*)sm->m_oaMolAtoms[z3];
1553
if (ma0 == NULL)
1554
continue;
1555
z4 = ma0->m_iNumber;
1556
if (ma->m_fAtomCode == ma0->m_fAtomCode)
1557
{
1558
if (b)
1559
{
1560
mprintf(", %s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,ma->m_iNumber+1);
1561
} else
1562
{
1563
if (!c)
1564
{
1565
c = true;
1566
mprintf("\n");
1567
}
1568
mprintf(" Atoms %s%d, %s%d",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,z4+1,((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_sName,ma->m_iNumber+1);
1569
b = true;
1570
}
1571
} else if (b)
1572
{
1573
mprintf(" are equivalent.\n");
1574
b = false;
1575
}
1576
}
1577
if (b)
1578
mprintf(" are equivalent.\n");
1579
}
1580
} // Tabelle Ende
1581
BTOUT;
1582
}
1583
1584
1585
void CTimeStep::Transform(const CxMatrix3 &mat)
1586
{
1587
BTIN;
1588
int z;
1589
// CxVector3 v;
1590
1591
for (z=0;z<g_iGesVirtAtomCount;z++)
1592
{
1593
// if (z < g_iGesAtomCount)
1594
// mprintf("@ %2d: ( %g | %g | %g ) --> ",z,m_vaCoords[z][0],m_vaCoords[z][1],m_vaCoords[z][2]);
1595
m_vaCoords[z] = mat * m_vaCoords[z];
1596
// if (z < g_iGesAtomCount)
1597
// mprintf("( %g | %g | %g )\n",m_vaCoords[z][0],m_vaCoords[z][1],m_vaCoords[z][2]);
1598
}
1599
1600
if (g_bUseVelocities)
1601
for (z=0;z<g_iGesVirtAtomCount;z++)
1602
m_vaVelocities[z] = mat * m_vaVelocities[z];
1603
1604
if (g_bUseForces)
1605
for (z=0;z<g_iGesVirtAtomCount;z++)
1606
m_vaForces[z] = mat * m_vaForces[z];
1607
BTOUT;
1608
}
1609
1610
1611
void CTimeStep::Transform(const CxDMatrix3 &mat)
1612
{
1613
BTIN;
1614
int z;
1615
1616
for (z=0;z<g_iGesVirtAtomCount;z++)
1617
m_vaCoords[z] = mat * m_vaCoords[z];
1618
1619
if (g_bUseVelocities)
1620
for (z=0;z<g_iGesVirtAtomCount;z++)
1621
m_vaVelocities[z] = mat * m_vaVelocities[z];
1622
1623
if (g_bUseForces)
1624
for (z=0;z<g_iGesVirtAtomCount;z++)
1625
m_vaForces[z] = mat * m_vaForces[z];
1626
BTOUT;
1627
}
1628
1629
1630
void CTimeStep::Transform(const CxQuaternion &q)
1631
{
1632
BTIN;
1633
int z;
1634
1635
for (z=0;z<g_iGesVirtAtomCount;z++)
1636
m_vaCoords[z] = q.Transform(m_vaCoords[z]);
1637
1638
if (g_bUseVelocities)
1639
for (z=0;z<g_iGesVirtAtomCount;z++)
1640
m_vaVelocities[z] = q.Transform(m_vaVelocities[z]);
1641
1642
if (g_bUseForces)
1643
for (z=0;z<g_iGesVirtAtomCount;z++)
1644
m_vaForces[z] = q.Transform(m_vaForces[z]);
1645
BTOUT;
1646
}
1647
1648
1649
void CTimeStep::SubVelocities(const CxVector3 &vec)
1650
{
1651
BTIN;
1652
int z;
1653
1654
for (z=0;z<g_iGesVirtAtomCount;z++)
1655
m_vaVelocities[z] -= vec;
1656
BTOUT;
1657
}
1658
1659
1660
void CTimeStep::FoldMolecules()
1661
{
1662
BTIN;
1663
int z, z2, z3, z4;
1664
CxVector3 v, vc;
1665
CMolecule *m;
1666
CSingleMolecule *sm;
1667
1668
if (!g_bPeriodic)
1669
return;
1670
1671
// mprintf("*** Fold ***\n");
1672
1673
for (z=0;z<g_oaMolecules.GetSize();z++)
1674
{
1675
m = (CMolecule*)g_oaMolecules[z];
1676
if (m->m_bPseudo)
1677
continue;
1678
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1679
{
1680
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
1681
1682
// mprintf("\n%d, %d",m->m_baAtomIndex.GetSize(),((CxIntArray*)sm->m_oaAtomOffset[m->m_baAtomIndex.GetSize()-1])->GetAt(1));
1683
1684
// Massenzentrum
1685
v = m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[m->m_baAtomIndex.GetSize()-1])->GetAt(1)];
1686
1687
/* mprintf(" .Mol ");
1688
v.Dump();
1689
mprintf("\n");
1690
1691
*/ vc = CxVector3(0,0,0);
1692
1693
if (g_bPeriodicX)
1694
{
1695
while (v[0] < -g_fBoxX/2) { v[0] += g_fBoxX; vc[0] += g_fBoxX; }
1696
while (v[0] >= g_fBoxX/2) { v[0] -= g_fBoxX; vc[0] -= g_fBoxX; }
1697
}
1698
if (g_bPeriodicY)
1699
{
1700
while (v[1] < -g_fBoxY/2) { v[1] += g_fBoxY; vc[1] += g_fBoxY; }
1701
while (v[1] >= g_fBoxY/2) { v[1] -= g_fBoxY; vc[1] -= g_fBoxY; }
1702
}
1703
if (g_bPeriodicZ)
1704
{
1705
while (v[2] < -g_fBoxZ/2) { v[2] += g_fBoxZ; vc[2] += g_fBoxZ; }
1706
while (v[2] >= g_fBoxZ/2) { v[2] -= g_fBoxZ; vc[2] -= g_fBoxZ; }
1707
}
1708
1709
if ((vc[0] == 0) && (vc[1] == 0) && (vc[2] == 0))
1710
continue;
1711
1712
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
1713
for (z4=0;z4<m->m_waAtomCount[z3];z4++)
1714
m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)] += vc;
1715
1716
if (g_bWannier)
1717
for (z3=0;z3<sm->m_laWannier.GetSize();z3++)
1718
m_vaCoords[sm->m_laWannier[z3]] += vc;
1719
}
1720
}
1721
// mprintf(" Fold Done\n");
1722
BTOUT;
1723
}
1724
1725
1726
void CTimeStep::FoldAtoms()
1727
{
1728
BTIN;
1729
int z;
1730
1731
if (!g_bPeriodic)
1732
return;
1733
1734
for (z=0;z<g_iGesVirtAtomCount;z++)
1735
{
1736
if (g_bPeriodicX)
1737
{
1738
while (m_vaCoords[z][0] < -g_fBoxX/2) m_vaCoords[z][0] += g_fBoxX;
1739
while (m_vaCoords[z][0] >= g_fBoxX/2) m_vaCoords[z][0] -= g_fBoxX;
1740
}
1741
1742
if (g_bPeriodicY)
1743
{
1744
while (m_vaCoords[z][1] < -g_fBoxY/2) m_vaCoords[z][1] += g_fBoxY;
1745
while (m_vaCoords[z][1] >= g_fBoxY/2) m_vaCoords[z][1] -= g_fBoxY;
1746
}
1747
1748
if (g_bPeriodicZ)
1749
{
1750
while (m_vaCoords[z][2] < -g_fBoxZ/2) m_vaCoords[z][2] += g_fBoxZ;
1751
while (m_vaCoords[z][2] >= g_fBoxZ/2) m_vaCoords[z][2] -= g_fBoxZ;
1752
}
1753
}
1754
BTOUT;
1755
}
1756
1757
1758
void CTimeStep::CenterPos(const CxVector3 &vec)
1759
{
1760
BTIN;
1761
int z/*, z2, z3, z4*/;
1762
1763
/* for (z=0;z<g_oaMolecules.GetSize();z++)
1764
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->Count;z2++)
1765
for (z3=0;z3<((CMolecule*)g_oaMolecules[z])->Elements;z3++)
1766
for (z4=0;z4<((CMolecule*)g_oaMolecules[z])->AtomCount[z3];z4++)
1767
m_vaCoords[((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[z])->SingleMolIndex[z2]])->m_iAtomOffset[z3][z4]] -= vec;*/
1768
1769
for (z=0;z<g_iGesVirtAtomCount;z++)
1770
m_vaCoords[z] -= vec;
1771
BTOUT;
1772
}
1773
1774
1775
void CTimeStep::AddAtoms()
1776
{
1777
BTIN;
1778
char *q;
1779
int z;
1780
// bool labeledatoms;
1781
1782
// labeledatoms = false;
1783
for (z=0;z<(long)m_iGesAtomCount;z++)
1784
{
1785
q = (char*)m_paLabels[z];
1786
q+=strlen(q)-1;
1787
/* while ((*q >= '0') && (*q <= '9'))
1788
{
1789
if (!labeledatoms)
1790
{
1791
mprintf(">>>\n>>> The atoms in the input file are numbered.\n>>> Ignoring this, using own numbers ;-)\n>>>\n");
1792
labeledatoms = true;
1793
}
1794
*q = 0;
1795
q--;
1796
}*/
1797
// printf("AddAtoms: \"%s\"\n",q);
1798
xAddAtom((char*)m_paLabels[z]);
1799
}
1800
BTOUT;
1801
}
1802
1803
1804
void CTimeStep::WriteTimestep(FILE *a)
1805
{
1806
BTIN;
1807
int z, z2, z3, z4, z0;
1808
CMolecule *m;
1809
CSingleMolecule *sm;
1810
1811
if (g_bSaveVirtAtoms)
1812
mfprintf(a," %d\n",g_iGesVirtAtomCount);
1813
else mfprintf(a," %d\n",g_iGesAtomCount);
1814
if (m_pComment != NULL)
1815
mfprintf(a,"%s\n",m_pComment);
1816
else mfprintf(a,"\n");
1817
1818
if (g_bWriteAtomwise)
1819
{
1820
for (z0=0;z0<g_oaAtoms.GetSize();z0++)
1821
{
1822
for (z=0;z<g_oaMolecules.GetSize();z++)
1823
{
1824
m = (CMolecule*)g_oaMolecules[z];
1825
if (m->m_bPseudo)
1826
continue;
1827
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
1828
{
1829
if (m->m_baAtomIndex[z3] != z0)
1830
continue;
1831
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
1832
continue;
1833
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1834
{
1835
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
1836
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
1837
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
1838
}
1839
}
1840
}
1841
}
1842
} else
1843
{
1844
for (z=0;z<g_oaMolecules.GetSize();z++)
1845
{
1846
m = (CMolecule*)g_oaMolecules[z];
1847
if (m->m_bPseudo)
1848
continue;
1849
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1850
{
1851
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
1852
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
1853
{
1854
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
1855
continue;
1856
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
1857
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
1858
}
1859
}
1860
}
1861
}
1862
1863
BTOUT;
1864
}
1865
1866
1867
void CTimeStep::WriteTimestepNb(FILE *a, CNbSet *nbs, int singlemol)
1868
{
1869
BTIN;
1870
int z, z2, z3, z4, z0, n, ti;
1871
CMolecule *m;
1872
CSingleMolecule *sm;
1873
CConditionGroup *cg;
1874
CConditionSubGroup *cs;
1875
CNbSearch *nb;
1876
1877
n = 0;
1878
1879
for (z=0;z<g_oaMolecules.GetSize();z++)
1880
{
1881
if (nbs->m_oaConditionGroups[z] == NULL)
1882
continue;
1883
m = (CMolecule*)g_oaMolecules[z];
1884
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1885
{
1886
if (((CConditionGroup*)nbs->m_oaConditionGroups[z])->Contains(z2))
1887
{
1888
n += m->m_iAtomGes;
1889
if (!g_bSaveVirtAtoms)
1890
n -= m->m_laVirtualAtoms.GetSize();
1891
}
1892
}
1893
}
1894
1895
mfprintf(a," %d\n",n);
1896
1897
mfprintf(a,"# Step %d",((int)g_iSteps));
1898
1899
if (singlemol >= 0)
1900
{
1901
sm = (CSingleMolecule*)g_oaSingleMolecules[singlemol];
1902
m = (CMolecule*)g_oaMolecules[sm->m_iMolType];
1903
if (!g_bSaveVirtAtoms)
1904
{
1905
if (g_bWriteAtomwise)
1906
mfprintf(a,", RM=%s[%d]",m->m_sName,sm->m_iMolSMIndex+1);
1907
else mfprintf(a,", RM=%s[%d] (%d atoms)",m->m_sName,sm->m_iMolSMIndex+1,m->m_iAtomGes-m->m_laVirtualAtoms.GetSize());
1908
} else
1909
{
1910
if (g_bWriteAtomwise)
1911
mfprintf(a,", RM=%s[%d]",m->m_sName,sm->m_iMolSMIndex+1);
1912
else mfprintf(a,", RM=%s[%d] (%d atoms)",m->m_sName,sm->m_iMolSMIndex+1,m->m_iAtomGes);
1913
}
1914
}
1915
1916
if (g_bEnvWriteDetailedInfo)
1917
{
1918
for (z=0;z<g_oaMolecules.GetSize();z++)
1919
{
1920
if (nbs->m_oaConditionGroups[z] == NULL)
1921
continue;
1922
m = (CMolecule*)g_oaMolecules[z];
1923
1924
cg = (CConditionGroup*)nbs->m_oaConditionGroups[z];
1925
1926
if (g_bEnvSortNb)
1927
{
1928
nb = NULL;
1929
if (cg->m_oaConditionSubGroups.GetSize() == 1)
1930
{
1931
cs = (CConditionSubGroup*)cg->m_oaConditionSubGroups[0];
1932
if (cs->m_oaConditions.GetSize() == 1)
1933
nb = (CNbSearch*)cs->m_oaConditions[0];
1934
}
1935
if (nb == NULL)
1936
goto _nosortinfo;
1937
1938
if (nb->m_iNbCountMin <= -1)
1939
goto _nosortinfo;
1940
1941
for (z2=nb->m_iNbCountMin;z2<=nb->m_iNbCountMax;z2++)
1942
{
1943
ti = nb->m_pNbSort[z2].m_iOM;
1944
if (!g_bSaveVirtAtoms)
1945
{
1946
if (m->m_laSingleMolIndex[ti] != singlemol)
1947
{
1948
if (g_bWriteAtomwise)
1949
mfprintf(a,", %s[%d] d=%.3fpm",m->m_sName,z2+1,nb->m_pNbSort[z2].m_fMinDist);
1950
else mfprintf(a,", %s[%d] d=%.3fpm (%d atoms)",m->m_sName,ti+1,nb->m_pNbSort[z2].m_fMinDist,m->m_iAtomGes-m->m_laVirtualAtoms.GetSize());
1951
}
1952
} else
1953
{
1954
if (m->m_laSingleMolIndex[ti] != singlemol)
1955
{
1956
if (g_bWriteAtomwise)
1957
mfprintf(a,", %s[%d] d=%.3fpm",m->m_sName,z2+1,nb->m_pNbSort[z2].m_fMinDist);
1958
else mfprintf(a,", %s[%d] d=%.3fpm (%d atoms)",m->m_sName,ti+1,nb->m_pNbSort[z2].m_fMinDist,m->m_iAtomGes);
1959
}
1960
}
1961
}
1962
} else
1963
{
1964
_nosortinfo:
1965
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
1966
{
1967
if (cg->Contains(z2))
1968
{
1969
if (!g_bSaveVirtAtoms)
1970
{
1971
if (m->m_laSingleMolIndex[z2] != singlemol)
1972
{
1973
if (g_bWriteAtomwise)
1974
mfprintf(a,", %s[%d]",m->m_sName,z2+1);
1975
else mfprintf(a,", %s[%d] (%d atoms)",m->m_sName,z2+1,m->m_iAtomGes-m->m_laVirtualAtoms.GetSize());
1976
}
1977
} else
1978
{
1979
if (m->m_laSingleMolIndex[z2] != singlemol)
1980
{
1981
if (g_bWriteAtomwise)
1982
mfprintf(a,", %s[%d]",m->m_sName,z2+1);
1983
else mfprintf(a,", %s[%d] (%d atoms)",m->m_sName,z2+1,m->m_iAtomGes);
1984
}
1985
}
1986
}
1987
}
1988
}
1989
}
1990
}
1991
1992
mfprintf(a,"\n");
1993
1994
if (g_bWriteAtomwise)
1995
{
1996
for (z0=0;z0<g_oaAtoms.GetSize();z0++)
1997
{
1998
for (z=0;z<g_oaMolecules.GetSize();z++)
1999
{
2000
if (nbs->m_oaConditionGroups[z] == NULL)
2001
continue;
2002
m = (CMolecule*)g_oaMolecules[z];
2003
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2004
{
2005
if (m->m_baAtomIndex[z3] != z0)
2006
continue;
2007
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
2008
continue;
2009
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
2010
{
2011
if (((CConditionGroup*)nbs->m_oaConditionGroups[z])->Contains(z2))
2012
{
2013
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
2014
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
2015
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
2016
}
2017
}
2018
}
2019
}
2020
}
2021
} else
2022
{
2023
if (singlemol >= 0)
2024
{
2025
sm = (CSingleMolecule*)g_oaSingleMolecules[singlemol];
2026
m = (CMolecule*)g_oaMolecules[sm->m_iMolType];
2027
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2028
{
2029
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
2030
continue;
2031
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
2032
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
2033
}
2034
}
2035
2036
for (z=0;z<g_oaMolecules.GetSize();z++)
2037
{
2038
if (nbs->m_oaConditionGroups[z] == NULL)
2039
continue;
2040
m = (CMolecule*)g_oaMolecules[z];
2041
cg = (CConditionGroup*)nbs->m_oaConditionGroups[z];
2042
2043
if (g_bEnvSortNb)
2044
{
2045
nb = NULL;
2046
if (cg->m_oaConditionSubGroups.GetSize() == 1)
2047
{
2048
cs = (CConditionSubGroup*)cg->m_oaConditionSubGroups[0];
2049
if (cs->m_oaConditions.GetSize() == 1)
2050
nb = (CNbSearch*)cs->m_oaConditions[0];
2051
}
2052
if (nb == NULL)
2053
goto _nosort;
2054
2055
if (nb->m_iNbCountMin <= -1)
2056
goto _nosort;
2057
2058
for (z2=nb->m_iNbCountMin;z2<=nb->m_iNbCountMax;z2++)
2059
{
2060
ti = nb->m_pNbSort[z2].m_iOM;
2061
2062
if (m->m_laSingleMolIndex[ti] == singlemol)
2063
continue;
2064
2065
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[ti]];
2066
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2067
{
2068
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
2069
continue;
2070
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
2071
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
2072
}
2073
}
2074
} else
2075
{
2076
_nosort:
2077
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
2078
{
2079
if (((CConditionGroup*)nbs->m_oaConditionGroups[z])->Contains(z2))
2080
{
2081
if (m->m_laSingleMolIndex[z2] == singlemol)
2082
continue;
2083
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
2084
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2085
{
2086
if ((!g_bSaveVirtAtoms) && (m->m_baAtomIndex[z3] == g_iVirtAtomType))
2087
continue;
2088
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
2089
mfprintf(a," %s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1]/100.0f,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]/100.0f);
2090
}
2091
}
2092
}
2093
}
2094
}
2095
}
2096
2097
BTOUT;
2098
}
2099
2100
2101
/*void CTimeStep::WriteTimestepNb(int refmol, FILE *a)
2102
{
2103
BTIN;
2104
int z, c, z2, z3, z4, z0;
2105
int ti;
2106
CMolecule *m, *m2;
2107
2108
m = (CMolecule*)g_oaMolecules[g_iFixMol];
2109
2110
c = 0;
2111
if (g_bRefEnvVirt)
2112
{
2113
for (z=0;z<g_oaMolecules.GetSize();z++)
2114
c += g_pNbAll->m_waScanNeighborCount[z]*((CMolecule*)g_oaMolecules[z])->m_iAtomGes;
2115
if (g_bSaveRefWithEnv)
2116
c += m->m_iAtomGes;
2117
} else
2118
{
2119
for (z=0;z<g_oaMolecules.GetSize();z++)
2120
c += g_pNbAll->m_waScanNeighborCount[z]*(((CMolecule*)g_oaMolecules[z])->m_iAtomGes-((CMolecule*)g_oaMolecules[z])->m_waVirtualAtoms.GetSize());
2121
if (g_bSaveRefWithEnv)
2122
c += m->m_iAtomGes - m->m_waVirtualAtoms.GetSize();
2123
}
2124
2125
mfprintf(a," %d\n\n",c);
2126
2127
if (g_bRefEnvAtomwise)
2128
{
2129
for (z0=0;z0<g_oaAtoms.GetSize();z0++)
2130
{
2131
if (g_bSaveRefWithEnv)
2132
{
2133
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2134
{
2135
if (m->m_baAtomIndex[z3] != z0)
2136
continue;
2137
if (!g_bRefEnvVirt)
2138
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
2139
continue;
2140
for (z4=0;z4<m->m_waAtomCount[z3];z4++)
2141
{
2142
ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[refmol]])->m_oaAtomOffset[z3])->GetAt(z4);
2143
mfprintf(a," %s %f %f %f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0f,m_vaCoords[ti][1]/100.0f,m_vaCoords[ti][2]/100.0f);
2144
}
2145
}
2146
}
2147
for (z=0;z<g_oaMolecules.GetSize();z++)
2148
{
2149
m2 = (CMolecule*)g_oaMolecules[z];
2150
for (z2=0;z2<g_pNbAll->m_waScanNeighborCount[z];z2++)
2151
{
2152
for (z3=0;z3<m2->m_baAtomIndex.GetSize();z3++)
2153
{
2154
if (m2->m_baAtomIndex[z3] != z0)
2155
continue;
2156
if (!g_bRefEnvVirt)
2157
if (m2->m_baAtomIndex[z3] == g_iVirtAtomType)
2158
continue;
2159
for (z4=0;z4<m2->m_waAtomCount[z3];z4++)
2160
{
2161
ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[((CxIntArray*)g_pNbAll->m_oaScanNeighbors[z])->GetAt(z2)]])->m_oaAtomOffset[z3])->GetAt(z4);
2162
mfprintf(a," %s %f %f %f\n",((CAtom*)g_oaAtoms[m2->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0f,m_vaCoords[ti][1]/100.0f,m_vaCoords[ti][2]/100.0f);
2163
}
2164
}
2165
}
2166
}
2167
}
2168
} else
2169
{
2170
if (g_bSaveRefWithEnv)
2171
{
2172
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
2173
{
2174
if (!g_bRefEnvVirt)
2175
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
2176
continue;
2177
for (z4=0;z4<m->m_waAtomCount[z3];z4++)
2178
{
2179
ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[refmol]])->m_oaAtomOffset[z3])->GetAt(z4);
2180
mfprintf(a," %s %f %f %f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0,m_vaCoords[ti][1]/100.0,m_vaCoords[ti][2]/100.0);
2181
}
2182
}
2183
}
2184
for (z=0;z<g_oaMolecules.GetSize();z++)
2185
{
2186
m2 = (CMolecule*)g_oaMolecules[z];
2187
for (z2=0;z2<g_pNbAll->m_waScanNeighborCount[z];z2++)
2188
{
2189
for (z3=0;z3<m2->m_baAtomIndex.GetSize();z3++)
2190
{
2191
if (!g_bRefEnvVirt)
2192
if (m2->m_baAtomIndex[z3] == g_iVirtAtomType)
2193
continue;
2194
for (z4=0;z4<m2->m_waAtomCount[z3];z4++)
2195
{
2196
ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[((CxIntArray*)g_pNbAll->m_oaScanNeighbors[z])->GetAt(z2)]])->m_oaAtomOffset[z3])->GetAt(z4);
2197
mfprintf(a," %s %f %f %f\n",((CAtom*)g_oaAtoms[m2->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0,m_vaCoords[ti][1]/100.0,m_vaCoords[ti][2]/100.0);
2198
}
2199
}
2200
}
2201
}
2202
}
2203
BTOUT;
2204
}*/
2205
2206
2207
/*float CTimeStep::MolDist(CSingleMolecule *ref, CSingleMolecule *sm2, CNbSearch *nb)
2208
{
2209
BXIN;
2210
int z3, z4;
2211
float d;
2212
CxVector3 vec;
2213
2214
d = 99999.0f;
2215
for (z3=0;z3<nb->m_waRefElements.GetSize();z3++)
2216
for (z4=0;z4<((CxIntArray*)nb->m_oaNbElements[sm2->m_iMolType])->GetSize();z4++)
2217
{
2218
vec = m_vaCoords[((CxIntArray*)ref->m_oaAtomOffset[nb->m_waRefElements[z3]])->GetAt(nb->m_waRefAtoms[z3])] - m_vaCoords[((CxIntArray*)sm2->m_oaAtomOffset[((CxIntArray*)nb->m_oaNbElements[sm2->m_iMolType])->GetAt(z4)])->GetAt(((CxIntArray*)nb->m_oaNbAtoms[sm2->m_iMolType])->GetAt(z4))];
2219
if (g_bFold)
2220
{
2221
while (vec[0] >= g_fBoxX/2) vec[0] -= g_fBoxX;
2222
while (vec[0] < -g_fBoxX/2) vec[0] += g_fBoxX;
2223
while (vec[1] >= g_fBoxY/2) vec[1] -= g_fBoxY;
2224
while (vec[1] < -g_fBoxY/2) vec[1] += g_fBoxY;
2225
while (vec[2] >= g_fBoxZ/2) vec[2] -= g_fBoxZ;
2226
while (vec[2] < -g_fBoxZ/2) vec[2] += g_fBoxZ;
2227
}
2228
if (vec.GetLength() < d)
2229
d = vec.GetLength();
2230
}
2231
BXOUT;
2232
if (d < 90000.0f)
2233
return d;
2234
else return -1.0f;
2235
}*/
2236
2237
2238
/*void CTimeStep::ScanNeighborhood(int fixmol, int refmol, CNbSearch *nb, CNbSearch *prev)
2239
{
2240
BTIN;
2241
float *del, d;
2242
int *best, b;
2243
int z, z2, z3, c;
2244
CMolecule *m, *m2;
2245
CSingleMolecule *sm, *sm2;
2246
CxVector3 vec;
2247
2248
m = (CMolecule*)g_oaMolecules[fixmol];
2249
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[refmol]];
2250
del = new float[g_oaSingleMolecules.GetSize()];
2251
best = new int[g_oaSingleMolecules.GetSize()];
2252
2253
// printf("Suche Nachbarschaft von Molekuel %d...\n",refmol+1);
2254
2255
for (z=0;z<g_oaMolecules.GetSize();z++)
2256
{
2257
if (((!nb->m_bDistMode) && (nb->m_waMolCount[z] == 0)) || (nb->m_bDistMode && (nb->m_faMolDist[z] == 0)))
2258
{
2259
nb->m_waScanNeighborCount[z] = 0;
2260
continue;
2261
}
2262
m2 = (CMolecule*)g_oaMolecules[z];
2263
// printf("*** Molekuel %d: %s\n",z+1,m2->Name);
2264
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)
2265
{
2266
del[z2] = 99999.0f;
2267
if ((z == fixmol) && (z2 == refmol))
2268
continue;
2269
if (prev != NULL)
2270
if (!prev->Contains(z,z2))
2271
continue;
2272
// printf(" - Vertreter %d\n",z2+1);
2273
sm2 = (CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[z2]];
2274
del[z2] = MolDist(sm,sm2,nb);
2275
// printf(" - Finaler Abstand: %f\n",del[z2]);
2276
}
2277
if (nb->m_bDistMode)
2278
{
2279
// printf("**DistMode**\n");
2280
// mprintf("Die Nachbarn: ");
2281
c = 0;
2282
for (z3=0;z3<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z3++)
2283
if ((del[z3] <= nb->m_faMolDist[z]) && (del[z3] >= nb->m_faMolMinDist[z]))
2284
{
2285
// mprintf("%d (%f), ",z3+1,del[z3]);
2286
best[c] = z3;
2287
c++;
2288
}
2289
// mprintf("\n");
2290
// printf(" # Die naechsten Nachbarn: ");
2291
for (z2=0;z2<c;z2++)
2292
{
2293
// printf("%d, ",best[z2]+1);
2294
nb->m_iNeighbourCount++;
2295
for (z3=0;z3<nb->m_waScanNeighborCount[z];z3++)
2296
if (((CxIntArray*)nb->m_oaScanNeighbors[z])->GetAt(z3) == best[z2])
2297
{
2298
((CxIntArray*)nb->m_oaScanNeighborHits[z])->GetAt(z3)++;
2299
goto _enddist;
2300
}
2301
((CxIntArray*)nb->m_oaScanNeighbors[z])->Add(best[z2]);
2302
((CxIntArray*)nb->m_oaScanNeighborHits[z])->Add(1);
2303
nb->m_waScanNeighborCount[z]++;
2304
_enddist:;
2305
}
2306
// printf("\n");
2307
} else
2308
{
2309
// printf("**CountMode**\n");
2310
for (z2=0;z2<nb->m_waMolCount[z];z2++)
2311
{
2312
d = 999999.0f;
2313
b = -1;
2314
for (z3=0;z3<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z3++)
2315
{
2316
if (del[z3] < d)
2317
{
2318
d = del[z3];
2319
b = z3;
2320
}
2321
}
2322
best[z2] = b;
2323
del[b] = 1000000.0f;
2324
}
2325
// printf(" # Die naechsten Nachbarn: ");
2326
for (z2=nb->m_waMolCountMin[z]-1;z2<nb->m_waMolCount[z];z2++)
2327
{
2328
// printf("%d, ",best[z2]);
2329
nb->m_iNeighbourCount++;
2330
for (z3=0;z3<nb->m_waScanNeighborCount[z];z3++)
2331
if (((CxIntArray*)nb->m_oaScanNeighbors[z])->GetAt(z3) == best[z2])
2332
{
2333
((CxIntArray*)nb->m_oaScanNeighborHits[z])->GetAt(z3)++;
2334
goto _end;
2335
}
2336
((CxIntArray*)nb->m_oaScanNeighbors[z])->Add(best[z2]);
2337
((CxIntArray*)nb->m_oaScanNeighborHits[z])->Add(1);
2338
nb->m_waScanNeighborCount[z]++;
2339
_end:;
2340
}
2341
// printf("\n");
2342
}
2343
}
2344
delete del;
2345
delete best;
2346
BTOUT;
2347
}*/
2348
2349
2350
/*void CTimeStep::ScanAngle(int fixmol, int refmol, CCondition *co, CNbSearch *prev)
2351
{
2352
BTIN;
2353
int z2, z3, z4;
2354
float tf;
2355
CMolecule *m, *m2;
2356
CSingleMolecule *sm, *sm2;
2357
CxVector3 vec0, vec1, vec2, vec3, vec4, vec5;
2358
CxIntArray tempwa;
2359
CNbSearch *nb;
2360
2361
// mprintf("*** ScanAngle ***\n");
2362
// mprintf(" FixMol = %d, RefMol = %d\n",fixmol,refmol);
2363
m = (CMolecule*)g_oaMolecules[fixmol];
2364
// mprintf(" m->m_laSingleMolIndex[refmol] = %d\n",m->m_laSingleMolIndex[refmol]);
2365
2366
nb = co->m_pTempNbS;
2367
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[refmol]];
2368
2369
// printf("Suche Nachbarschaft von Molekuel %d...\n",refmol+1);
2370
2371
// mprintf(" SecondMol = %d\n",co->m_iSecondMol);
2372
m2 = (CMolecule*)g_oaMolecules[co->m_iSecondMol];
2373
2374
// printf("*** Molekuel %d: %s\n",z+1,m2->Name);
2375
for (z2=0;z2<m2->m_laSingleMolIndex.GetSize();z2++)
2376
{
2377
if ((co->m_iSecondMol == fixmol) && (z2 == refmol))
2378
continue;
2379
if (prev != NULL)
2380
if (!prev->Contains(co->m_iSecondMol,z2))
2381
continue;
2382
// printf(" - Vertreter %d\n",z2+1);
2383
sm2 = (CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[z2]];
2384
2385
co->m_pADF->BuildAtomList(sm,sm2,NULL,&tempwa);
2386
2387
for (z4=0;z4<tempwa.GetSize();z4+=6)
2388
{
2389
if (co->m_pADF->m_bOrtho[0])
2390
{
2391
vec0 = m_vaCoords[tempwa[z4]];
2392
vec2 = m_vaCoords[tempwa[z4+1]];
2393
vec3 = m_vaCoords[tempwa[z4+2]];
2394
vec1 = CrossP(vec2-vec0,vec3-vec0);
2395
} else
2396
{
2397
vec0 = m_vaCoords[tempwa[z4]];
2398
vec2 = m_vaCoords[tempwa[z4+1]];
2399
vec1 = vec2-vec0;
2400
}
2401
if (co->m_pADF->m_bOrtho[1])
2402
{
2403
vec4 = m_vaCoords[tempwa[z4+3]];
2404
vec3 = m_vaCoords[tempwa[z4+4]];
2405
vec5 = m_vaCoords[tempwa[z4+5]];
2406
vec2 = CrossP(vec3-vec4,vec5-vec4);
2407
} else
2408
{
2409
vec4 = m_vaCoords[tempwa[z4+3]];
2410
vec3 = m_vaCoords[tempwa[z4+4]];
2411
vec2 = vec3-vec4;
2412
}
2413
2414
tf = Angle_Deg(vec1,vec2);
2415
2416
if ((tf >= co->m_pADF->m_fMinAngle) && (tf <= co->m_pADF->m_fMaxAngle))
2417
{
2418
nb->m_iNeighbourCount++;
2419
for (z3=0;z3<nb->m_waScanNeighborCount[co->m_iSecondMol];z3++)
2420
if (((CxIntArray*)nb->m_oaScanNeighbors[co->m_iSecondMol])->GetAt(z3) == z2)
2421
{
2422
((CxIntArray*)nb->m_oaScanNeighborHits[co->m_iSecondMol])->GetAt(z3)++;
2423
goto _endang;
2424
}
2425
((CxIntArray*)nb->m_oaScanNeighbors[co->m_iSecondMol])->Add(z2);
2426
((CxIntArray*)nb->m_oaScanNeighborHits[co->m_iSecondMol])->Add(1);
2427
nb->m_waScanNeighborCount[co->m_iSecondMol]++;
2428
_endang:; break;
2429
}
2430
}
2431
}
2432
BTOUT;
2433
}*/
2434
2435
/*void CTimeStep::GatherNbDiagram(int refmol, CNbSearch *nb)
2436
{
2437
BTIN;
2438
float *del, d;
2439
int *best, b;
2440
bool *done;
2441
int z, z2, z3, z4, c, z0;
2442
CMolecule *m, *m2;
2443
CSingleMolecule *sm, *sm2;
2444
CxVector3 vec;
2445
// FILE *a;
2446
2447
m = (CMolecule*)g_oaMolecules[g_iFixMol];
2448
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[refmol]];
2449
del = new float[g_oaSingleMolecules.GetSize()];
2450
best = new int[g_oaSingleMolecules.GetSize()];
2451
done = new bool[g_oaSingleMolecules.GetSize()];
2452
2453
// printf("Suche Nachbarschaft von Molekuel %d...\n",refmol+1);
2454
2455
for (z=0;z<g_oaMolecules.GetSize();z++)
2456
{
2457
if (nb->m_bDistMode && (nb->m_faMolDist[z] == 0))
2458
{
2459
nb->m_waScanNeighborCount[z] = 0;
2460
continue;
2461
}
2462
m2 = (CMolecule*)g_oaMolecules[z];
2463
// printf("*** Molekuel %d: %s\n",z+1,m2->Name);
2464
// for (z2=0;z2<=((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)
2465
// del[z2] = 99999.0f;
2466
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)
2467
{
2468
del[z2] = 99999.0f;
2469
if ((z == g_iFixMol) && (z2 == refmol))
2470
continue;
2471
// printf(" - Vertreter %d\n",z2+1);
2472
sm2 = (CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[z2]];
2473
for (z3=0;z3<nb->m_waRefElements.GetSize();z3++)
2474
for (z4=0;z4<((CxIntArray*)nb->m_oaNbElements[z])->GetSize();z4++)
2475
{
2476
vec = m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[nb->m_waRefElements[z3]])->GetAt(nb->m_waRefAtoms[z3])] - m_vaCoords[((CxIntArray*)sm2->m_oaAtomOffset[((CxIntArray*)nb->m_oaNbElements[z])->GetAt(z4)])->GetAt(((CxIntArray*)nb->m_oaNbAtoms[z])->GetAt(z4))];
2477
if (g_bFold)
2478
{
2479
while (vec[0] >= g_fBoxX/2) vec[0] -= g_fBoxX;
2480
while (vec[0] < -g_fBoxX/2) vec[0] += g_fBoxX;
2481
while (vec[1] >= g_fBoxY/2) vec[1] -= g_fBoxY;
2482
while (vec[1] < -g_fBoxY/2) vec[1] += g_fBoxY;
2483
while (vec[2] >= g_fBoxZ/2) vec[2] -= g_fBoxZ;
2484
while (vec[2] < -g_fBoxZ/2) vec[2] += g_fBoxZ;
2485
}
2486
d = vec.GetLength();
2487
// printf(" = m1 %d (%d|%d); m2 %d (%d|%d); Dist = %f\n",z3+1,m->m_waNbElements[z3]+1,m->m_waNbAtoms[z3]+1,z4+1,m2->m_waNbElements[z4]+1,m2->m_waNbAtoms[z4]+1,d);
2488
if (d < del[z2])
2489
del[z2] = d;
2490
}
2491
// printf(" - Finaler Abstand: %f\n",del[z2]);
2492
}
2493
2494
for (z0=0;z0<nb->m_pAF->m_iResolution;z0++)
2495
{
2496
c = 0;
2497
for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)
2498
done[z2] = false;
2499
while (true)
2500
{
2501
d = 999999.0f;
2502
b = -1;
2503
for (z3=0;z3<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z3++)
2504
{
2505
if (done[z3])
2506
continue;
2507
if (del[z3] < d)
2508
{
2509
d = del[z3];
2510
b = z3;
2511
}
2512
}
2513
if (d > nb->m_pAF->m_fMaxVal*z0/nb->m_pAF->m_iResolution)
2514
break;
2515
best[c] = b;
2516
done[b] = true;
2517
c++;
2518
// if (c >= ((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize())
2519
// break;
2520
}
2521
nb->m_pAF->AddToBin(nb->m_pAF->m_fMaxVal*z0/nb->m_pAF->m_iResolution,(float)c);
2522
// if (g_iSteps == 1)
2523
// mfprintf(a,"%f;%f\n",nb->m_pAF->m_fMaxVal*z0/nb->m_pAF->m_iResolution,(float)c);
2524
}
2525
// if (g_iSteps == 1)
2526
// fclose(a);
2527
}
2528
delete del;
2529
delete best;
2530
BTOUT;
2531
}*/
2532
2533
2534
int CTimeStep::REC_UniteMolecules(CSingleMolecule *sm, int i0, int depth)
2535
{
2536
int z, z2, n;
2537
CMolAtom *m;
2538
2539
n = 0;
2540
m = (CMolAtom*)sm->m_oaMolAtoms[i0];
2541
2542
/* if (g_bVerbose)
2543
{
2544
mprintf("# ");
2545
for (z2=0;z2<depth;z2++)
2546
mprintf(". ");
2547
mprintf(">>> REC_UniteMolecules MolAtom=%d, Offset=%d.\n",i0,m->m_iOffset);
2548
}*/
2549
2550
g_pUniteTemp[m->m_iOffset] = true;
2551
2552
for (z=0;z<m->m_oaBonds.GetSize();z++)
2553
{
2554
if (!g_pUniteTemp[((CMolAtom*)m->m_oaBonds[z])->m_iOffset])
2555
{
2556
if (MirrorBond(m->m_iOffset,((CMolAtom*)m->m_oaBonds[z])->m_iOffset))
2557
{
2558
if (g_bVerbose)
2559
{
2560
mprintf("# ");
2561
for (z2=0;z2<depth;z2++)
2562
mprintf(". ");
2563
mprintf(" Bond %s(%d) <--> %s(%d) unwrapped.\n",((CAtom*)g_oaAtoms[g_baAtomIndex[m->m_iOffset]])->m_sName,m->m_iOffset+1,((CAtom*)g_oaAtoms[g_baAtomIndex[((CMolAtom*)m->m_oaBonds[z])->m_iOffset]])->m_sName,((CMolAtom*)m->m_oaBonds[z])->m_iOffset+1);
2564
}
2565
n++;
2566
}
2567
n += REC_UniteMolecules(sm,((CMolAtom*)m->m_oaBonds[z])->m_iMolAtomNumber,depth+1);
2568
}
2569
}
2570
/* if (g_bVerbose)
2571
{
2572
mprintf("# ");
2573
for (z2=0;z2<depth;z2++)
2574
mprintf(". ");
2575
mprintf("<<< REC_UniteMolecules MolAtom=%d, Offset=%d.\n",i0,m->m_iOffset);
2576
}*/
2577
return n;
2578
}
2579
2580
2581
void CTimeStep::UniteMolecules(bool verbose)
2582
{
2583
BTIN;
2584
int z, z2, n;
2585
CMolecule *m;
2586
CSingleMolecule *sm;
2587
2588
for (z=0;z<g_iGesAtomCount;z++)
2589
g_pUniteTemp[z] = false;
2590
for (z=0;z<g_oaMolecules.GetSize();z++)
2591
{
2592
m = (CMolecule*)g_oaMolecules[z];
2593
if (m->m_bPseudo)
2594
continue;
2595
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
2596
{
2597
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
2598
2599
// if (g_bVerbose)
2600
// mprintf(" # UniteMolecules molecule %s (%d)\n",m->m_sName,z2+1);
2601
2602
n = REC_UniteMolecules(sm,0,0);
2603
2604
if ((n != 0) && verbose)
2605
mprintf(" - Molecule %s[%d] united, %d bonds unwrapped.\n",m->m_sName,z2+1,n);
2606
2607
if ((n != 0) && (!verbose) && g_bVerbose)
2608
mprintf("\n # UniteMolecules: Molecule %s[%d] united, %d bonds unwrapped.",m->m_sName,z2+1,n);
2609
2610
}
2611
}
2612
BTOUT;
2613
}
2614
2615
2616
bool CTimeStep::ReadTimestep(FILE *a, bool needinfo)
2617
{
2618
BTIN;
2619
switch(g_iTrajFormat)
2620
{
2621
case 0:
2622
if (!ReadXYZ(a,needinfo,&m_vaCoords))
2623
return false;
2624
break;
2625
2626
case 1:
2627
if (!ReadPDB(a,needinfo,&m_vaCoords))
2628
return false;
2629
break;
2630
2631
case 2:
2632
if (!ReadMol2(a,needinfo))
2633
return false;
2634
break;
2635
2636
case 3:
2637
if (!ReadLAMMPS(a,needinfo))
2638
return false;
2639
break;
2640
2641
case 4:
2642
if (!ReadDLPOLY(a,needinfo))
2643
return false;
2644
break;
2645
}
2646
if (g_bDoubleBox)
2647
DoubleBox();
2648
BTOUT;
2649
return true;
2650
}
2651
2652
2653
bool CTimeStep::SkipTimestep(FILE *a)
2654
{
2655
BTIN;
2656
switch(g_iTrajFormat)
2657
{
2658
case 0:
2659
if (!SkipXYZ(a))
2660
return false;
2661
break;
2662
2663
case 1:
2664
if (!SkipPDB(a))
2665
return false;
2666
break;
2667
2668
case 2:
2669
if (!SkipMol2(a))
2670
return false;
2671
break;
2672
2673
case 3:
2674
if (!SkipLAMMPS(a))
2675
return false;
2676
break;
2677
2678
case 4:
2679
if (!SkipDLPOLY(a))
2680
return false;
2681
break;
2682
}
2683
BTOUT;
2684
return true;
2685
}
2686
2687
2688
bool CTimeStep::ReadTimestepVel(FILE *a)
2689
{
2690
BTIN;
2691
char buf[256], *p, *q;
2692
int z, tc;
2693
2694
buf[0] = 0;
2695
fgets(buf,256,a);
2696
if (feof(a))
2697
{
2698
BTOUT;
2699
return false;
2700
}
2701
if (strlen(buf) > 0)
2702
buf[strlen(buf)-1] = 0;
2703
tc = atoi(buf);
2704
if (tc == 0)
2705
{
2706
BTOUT;
2707
return false;
2708
}
2709
m_vaVelocities.SetSize(tc);
2710
buf[0] = 0;
2711
fgets(buf,256,a); // Zeitschritt - egal hier
2712
if (strlen(buf) > 0)
2713
buf[strlen(buf)-1] = 0;
2714
for (z=0;z<tc;z++) // den ersten Zeitschritt einlesen
2715
{
2716
buf[0] = 0;
2717
fgets(buf,256,a);
2718
if (feof(a))
2719
{
2720
BTOUT;
2721
return false;
2722
}
2723
if (strlen(buf) > 0)
2724
buf[strlen(buf)-1] = 0;
2725
q = buf;
2726
while (*q == ' ')
2727
q++;
2728
p = strchr(q,' ');
2729
if (p == NULL)
2730
{
2731
eprintf("CTimeStep::ReadTimestepVel(): Error 1. %d, \"%s\"\n",z+1,buf);
2732
continue;
2733
}
2734
while (isdigit(*(p-1)) && (p > buf))
2735
p--;
2736
if (p == buf)
2737
{
2738
eprintf("CTimeStep::ReadTimestepVel(): No Atom laben found. %d, \"%s\"\n",z+1,buf);
2739
continue;
2740
}
2741
*p = 0;
2742
p++;
2743
q = strchr(p,' ');
2744
if (q == NULL)
2745
{
2746
eprintf("CTimeStep::ReadTimestepVel(): Error 2. %d, \"%s\"\n",z+1,p);
2747
continue;
2748
}
2749
while (*q == ' ')
2750
q++;
2751
p = strchr(q,' ');
2752
if (p == NULL)
2753
{
2754
eprintf("CTimeStep::ReadTimestepVel(): Error 3. %d, \"%s\"\n",z+1,q);
2755
continue;
2756
}
2757
*p = 0;
2758
m_vaVelocities[z][0] = (float)atof(q);
2759
q = p+1;
2760
while (*q == ' ')
2761
q++;
2762
p = strchr(q,' ');
2763
if (p == NULL)
2764
{
2765
eprintf("CTimeStep::ReadTimestepVel(): Error 4. %d, \"%s\"\n",z+1,q);
2766
continue;
2767
}
2768
*p = 0;
2769
m_vaVelocities[z][1] = (float)atof(q);
2770
q = p+1;
2771
while (*q == ' ')
2772
q++;
2773
p = strchr(q,' ');
2774
if (p != NULL)
2775
*p = 0;
2776
m_vaVelocities[z][2] = (float)atof(q);
2777
}
2778
if (g_bDoubleBox)
2779
DoubleBoxVelocity();
2780
BTOUT;
2781
return true;
2782
}
2783
2784
2785
bool CTimeStep::ReadTimestepForce(FILE *a)
2786
{
2787
BTIN;
2788
char buf[256], *p, *q;
2789
int z, tc;
2790
2791
buf[0] = 0;
2792
fgets(buf,256,a);
2793
if (feof(a))
2794
{
2795
BTOUT;
2796
return false;
2797
}
2798
if (strlen(buf) > 0)
2799
buf[strlen(buf)-1] = 0;
2800
tc = atoi(buf);
2801
if (tc == 0)
2802
{
2803
BTOUT;
2804
return false;
2805
}
2806
m_vaForces.SetSize(tc);
2807
buf[0] = 0;
2808
fgets(buf,256,a); // Zeitschritt - egal hier
2809
if (strlen(buf) > 0)
2810
buf[strlen(buf)-1] = 0;
2811
for (z=0;z<tc;z++) // den ersten Zeitschritt einlesen
2812
{
2813
buf[0] = 0;
2814
fgets(buf,256,a);
2815
if (feof(a))
2816
{
2817
BTOUT;
2818
return false;
2819
}
2820
if (strlen(buf) > 0)
2821
buf[strlen(buf)-1] = 0;
2822
q = buf;
2823
while (*q == ' ')
2824
q++;
2825
p = strchr(q,' ');
2826
if (p == NULL)
2827
{
2828
eprintf("CTimeStep::ReadTimestepForce(): Error 1. %d, \"%s\"\n",z+1,buf);
2829
continue;
2830
}
2831
while (isdigit(*(p-1)) && (p > buf))
2832
p--;
2833
if (p == buf)
2834
{
2835
eprintf("CTimeStep::ReadTimestepForce(): No Atom laben found. %d, \"%s\"\n",z+1,buf);
2836
continue;
2837
}
2838
*p = 0;
2839
p++;
2840
q = strchr(p,' ');
2841
if (q == NULL)
2842
{
2843
eprintf("CTimeStep::ReadTimestepForce(): Error 2. %d, \"%s\"\n",z+1,p);
2844
continue;
2845
}
2846
while (*q == ' ')
2847
q++;
2848
p = strchr(q,' ');
2849
if (p == NULL)
2850
{
2851
eprintf("CTimeStep::ReadTimestepForce(): Error 3. %d, \"%s\"\n",z+1,q);
2852
continue;
2853
}
2854
*p = 0;
2855
m_vaForces[z][0] = (float)atof(q);
2856
q = p+1;
2857
while (*q == ' ')
2858
q++;
2859
p = strchr(q,' ');
2860
if (p == NULL)
2861
{
2862
eprintf("CTimeStep::ReadTimestepForce(): Error 4. %d, \"%s\"\n",z+1,q);
2863
continue;
2864
}
2865
*p = 0;
2866
m_vaForces[z][1] = (float)atof(q);
2867
q = p+1;
2868
while (*q == ' ')
2869
q++;
2870
p = strchr(q,' ');
2871
if (p != NULL)
2872
*p = 0;
2873
m_vaForces[z][2] = (float)atof(q);
2874
}
2875
if (g_bDoubleBox)
2876
DoubleBoxForce();
2877
BTOUT;
2878
return true;
2879
}
2880
2881
2882
bool CTimeStep::SkipXYZ(FILE *a)
2883
{
2884
BTIN;
2885
char buf[256];
2886
int z, tc;
2887
2888
// mprintf("*** Skip Anfang ***\n");
2889
buf[0] = 0;
2890
fgets_bin(buf,256,a);
2891
if (feof(a))
2892
{
2893
BTOUT;
2894
return false;
2895
}
2896
if (strlen(buf)==0)
2897
{
2898
BTOUT;
2899
return false;
2900
}
2901
buf[strlen(buf)-1] = 0;
2902
tc = atoi(buf);
2903
// mprintf("SkipA: \"%s\".\n",buf);
2904
if (tc == 0)
2905
{
2906
BTOUT;
2907
return false;
2908
}
2909
// buf[0] = 0;
2910
fgets_bin(buf,256,a); // Zeitschritt - egal hier
2911
// mprintf("SkipB: \"%s\".\n",buf);
2912
for (z=0;z<tc;z++) // den ersten Zeitschritt einlesen
2913
{
2914
// buf[0] = 0;
2915
fgets_bin(buf,256,a);
2916
// mprintf("SkipC%d: \"%s\".\n",z,buf);
2917
if (feof(a))
2918
{
2919
BTOUT;
2920
return false;
2921
}
2922
}
2923
// mprintf("*** Skip Ende ***\n");
2924
BTOUT;
2925
return true;
2926
}
2927
2928
2929
void CTimeStep::CopyFrom(CTimeStep *t)
2930
{
2931
BTIN;
2932
int z;
2933
char *p;
2934
CxVector3 v;
2935
2936
m_iGesAtomCount = t->m_iGesAtomCount;
2937
m_vaCoords.CopyFrom(&t->m_vaCoords);
2938
if (g_bKeepUnfoldedCoords)
2939
m_vaCoords_Unfolded.CopyFrom(&t->m_vaCoords_Unfolded);
2940
m_vaForces.CopyFrom(&t->m_vaForces);
2941
m_vaVelocities.CopyFrom(&t->m_vaVelocities);
2942
if (t->m_paLabels.GetSize() != 0)
2943
{
2944
for (z=0;z<m_paLabels.GetSize();z++)
2945
delete[] (char*)m_paLabels[z];
2946
m_paLabels.RemoveAll();
2947
for (z=0;z<t->m_paLabels.GetSize();z++)
2948
{
2949
try { p = new char[strlen((char*)t->m_paLabels[z])+1]; } catch(...) { p = NULL; }
2950
if (p == NULL) NewException((double)(strlen((char*)t->m_paLabels[z])+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2951
2952
strcpy(p,(char*)t->m_paLabels[z]);
2953
m_paLabels.Add(p);
2954
}
2955
}
2956
if (t->m_pComment != NULL)
2957
{
2958
if (m_pComment == NULL)
2959
{
2960
try { m_pComment = new char[256]; } catch(...) { m_pComment = NULL; }
2961
if (m_pComment == NULL) NewException((double)256*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
2962
}
2963
strcpy(m_pComment,t->m_pComment);
2964
}
2965
BTOUT;
2966
}
2967
2968
2969
long CTimeStep::ExtractNumber(int i)
2970
{
2971
BXIN;
2972
char *p, *q, buf[20];
2973
int z;
2974
long l;
2975
2976
if (m_pComment == NULL)
2977
return -1;
2978
p = m_pComment;
2979
for (z=0;z<i;z++)
2980
{
2981
while ((!isdigit(*p)) && (*p != 0))
2982
p++;
2983
if (*p == 0)
2984
{
2985
BXOUT;
2986
return -1;
2987
}
2988
q = p+1;
2989
while ((isdigit(*q)) && (*q != 0))
2990
q++;
2991
if (*q == 0)
2992
{
2993
BXOUT;
2994
return -1;
2995
}
2996
p = q+1;
2997
}
2998
while ((!isdigit(*p)) && (*p != 0))
2999
p++;
3000
if (*p == 0)
3001
{
3002
BXOUT;
3003
return -1;
3004
}
3005
q = p;
3006
while ((isdigit(*q)) && (*q != 0))
3007
q++;
3008
if (q == p)
3009
{
3010
BXOUT;
3011
return -1;
3012
}
3013
memcpy(buf,p,q-p);
3014
buf[q-p] = 0;
3015
l = atoi(buf);
3016
BXOUT;
3017
return l;
3018
}
3019
3020
3021
int CTimeStep::GetCommentNumberCount()
3022
{
3023
BXIN;
3024
char *p, *q;
3025
int z;
3026
3027
if (m_pComment == NULL)
3028
return 0;
3029
p = m_pComment;
3030
z = 0;
3031
while (true)
3032
{
3033
while ((!isdigit(*p)) && (*p != 0))
3034
p++;
3035
if (*p == 0)
3036
{
3037
// mprintf("GetCommentNumberCount 1: %d (p=\"%s\", q=\"%s\")\n",z,p,q);
3038
BXOUT;
3039
return z;
3040
}
3041
q = p;
3042
while ((isdigit(*q)) && (*q != 0))
3043
q++;
3044
if (q == p)
3045
{
3046
// mprintf("GetCommentNumberCount 2: %d (p=\"%s\", q=\"%s\")\n",z,p,q);
3047
BXOUT;
3048
return z;
3049
}
3050
z++;
3051
if (*q == 0)
3052
{
3053
// mprintf("GetCommentNumberCount 3: %d (p=\"%s\", q=\"%s\")\n",z,p,q);
3054
BXOUT;
3055
return z;
3056
}
3057
p = q+1;
3058
}
3059
return 0; // Never happens
3060
}
3061
3062
3063
bool CTimeStep::ScanWannier(bool verbose)
3064
{
3065
BTIN;
3066
int z, z2, z3;
3067
float td, d, dx, dy, dz;
3068
CMolecule *m;
3069
3070
if (g_bVerbose)
3071
{
3072
mprintf(WHITE,"\n*** ScanWannier ***\n\n");
3073
verbose = true;
3074
}
3075
3076
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
3077
((CSingleMolecule*)g_oaSingleMolecules[z])->m_laWannier.RemoveAll_KeepSize();
3078
3079
for (z=0;z<g_iGesAtomCount;z++)
3080
{
3081
if (g_baAtomIndex[z] != g_iWannierAtomType)
3082
continue;
3083
d = 9999.0f;
3084
z3 = -1;
3085
for (z2=0;z2<g_iGesAtomCount;z2++)
3086
{
3087
if (g_baAtomIndex[z2] == g_iWannierAtomType)
3088
continue;
3089
dx = m_vaCoords[z][0]-m_vaCoords[z2][0];
3090
dy = m_vaCoords[z][1]-m_vaCoords[z2][1];
3091
dz = m_vaCoords[z][2]-m_vaCoords[z2][2];
3092
if (g_bPeriodicX)
3093
{
3094
while (dx > g_fBoxX/2.0f) dx -= g_fBoxX;
3095
while (dx < -g_fBoxX/2.0f) dx += g_fBoxX;
3096
}
3097
if (g_bPeriodicY)
3098
{
3099
while (dy > g_fBoxY/2.0f) dy -= g_fBoxY;
3100
while (dy < -g_fBoxY/2.0f) dy += g_fBoxY;
3101
}
3102
if (g_bPeriodicZ)
3103
{
3104
while (dz > g_fBoxZ/2.0f) dz -= g_fBoxZ;
3105
while (dz < -g_fBoxZ/2.0f) dz += g_fBoxZ;
3106
}
3107
td = (float)sqrt(dx*dx+dy*dy+dz*dz);
3108
if (td < d)
3109
{
3110
d = td;
3111
z3 = z2;
3112
}
3113
}
3114
if (z3 == -1)
3115
abort();
3116
if (g_bPeriodicX)
3117
{
3118
while (m_vaCoords[z][0]-m_vaCoords[z3][0] > g_fBoxX/2.0f) m_vaCoords[z][0] -= g_fBoxX;
3119
while (m_vaCoords[z][0]-m_vaCoords[z3][0] < -g_fBoxX/2.0f) m_vaCoords[z][0] += g_fBoxX;
3120
}
3121
if (g_bPeriodicY)
3122
{
3123
while (m_vaCoords[z][1]-m_vaCoords[z3][1] > g_fBoxY/2.0f) m_vaCoords[z][1] -= g_fBoxY;
3124
while (m_vaCoords[z][1]-m_vaCoords[z3][1] < -g_fBoxY/2.0f) m_vaCoords[z][1] += g_fBoxY;
3125
}
3126
if (g_bPeriodicZ)
3127
{
3128
while (m_vaCoords[z][2]-m_vaCoords[z3][2] > g_fBoxZ/2.0f) m_vaCoords[z][2] -= g_fBoxZ;
3129
while (m_vaCoords[z][2]-m_vaCoords[z3][2] < -g_fBoxZ/2.0f) m_vaCoords[z][2] += g_fBoxZ;
3130
}
3131
z2 = g_laAtomSMIndex[z3];
3132
if (d > 100.0)
3133
{
3134
eprintf("Step %d: Wannier center at offset %d too far away from any atom (closest atom is %s[%d] %s%d, %.0f pm).\n",g_iSteps,z+1,((CMolecule*)g_oaMolecules[((CSingleMolecule*)g_oaSingleMolecules[z2])->m_iMolType])->m_sName,((CSingleMolecule*)g_oaSingleMolecules[z2])->m_iMolSMIndex+1,((CAtom*)g_oaAtoms[g_waAtomRealElement[z3]])->m_sName,g_waAtomMolNumber[z3]+1,d);
3135
} else if (verbose)
3136
mprintf(" - Wannier center %d belongs to %s[%d] %s%d (%.0f pm).\n",z+1,((CMolecule*)g_oaMolecules[((CSingleMolecule*)g_oaSingleMolecules[z2])->m_iMolType])->m_sName,((CSingleMolecule*)g_oaSingleMolecules[z2])->m_iMolSMIndex+1,((CAtom*)g_oaAtoms[g_waAtomRealElement[z3]])->m_sName,g_waAtomMolNumber[z3]+1,d);
3137
/* if (z2 == -1)
3138
{
3139
eprintf("Wannier center %d: Atom %d does not belong to any molecule.\n",z+1,z3+1);
3140
continue;
3141
}*/
3142
// mprintf("Wannier Center %d hat Abstand %.2f zu Atom %d in SM %d.\n",z+1,d,z3+1,z2+1);
3143
((CSingleMolecule*)g_oaSingleMolecules[z2])->m_laWannier.Add(z);
3144
}
3145
if (verbose)
3146
mprintf("\n\n");
3147
for (z=0;z<g_oaMolecules.GetSize();z++)
3148
{
3149
m = (CMolecule*)g_oaMolecules[z];
3150
if (m->m_iWannierCount == 0)
3151
{
3152
m->m_iWannierCount = ((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]])->m_laWannier.GetSize();
3153
td = 0;
3154
for (z2=0;z2<m->m_baAtomIndex.GetSize();z2++)
3155
{
3156
if (m->m_baAtomIndex[z2] == g_iWannierAtomType)
3157
continue;
3158
if (m->m_baAtomIndex[z2] == g_iVirtAtomType)
3159
continue;
3160
td += ((CAtom*)g_oaAtoms[m->m_baAtomIndex[z2]])->m_fCharge * m->m_waAtomCount[z2];
3161
}
3162
m->m_fCharge = td-m->m_iWannierCount*g_fWannierCharge;
3163
mprintf(" - Molecule %s contains %d wannier centers. Total charge is %.2f - %.2f = %.2f\n",m->m_sName,m->m_iWannierCount,td,m->m_iWannierCount*g_fWannierCharge,m->m_fCharge);
3164
if (m->m_fCharge > 5.0)
3165
{
3166
eprintf("\n This molecular charge seems to be too high.\n\n");
3167
if (!AskYesNo(" Do you want to continue (y/n)? [yes] ",true))
3168
return false;
3169
}
3170
}
3171
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
3172
{
3173
if (m->m_iWannierCount != ((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]])->m_laWannier.GetSize())
3174
eprintf("Step %d: Molecule %s[%d] contains %d instead of %d wannier centers.\n",g_iSteps,m->m_sName,z2+1,((CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]])->m_laWannier.GetSize(),m->m_iWannierCount);
3175
}
3176
}
3177
BTOUT;
3178
return true;
3179
}
3180
3181
3182
void CTimeStep::CalcDipoles()
3183
{
3184
BTIN;
3185
int z, z2, z3, z4;
3186
CMolecule *m;
3187
CSingleMolecule *sm;
3188
CAtom *a;
3189
CxVector3 dc;
3190
3191
// mprintf("\n*** CalcDipoles ***");
3192
3193
for (z=0;z<g_oaMolecules.GetSize();z++)
3194
{
3195
m = (CMolecule*)g_oaMolecules[z];
3196
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
3197
{
3198
if (g_bVerbose)
3199
mprintf("\nCalcDipoles %s (%d):\n",m->m_sName,z2+1);
3200
3201
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
3202
3203
sm->m_vDipole = CxVector3(0,0,0);
3204
3205
if ((!g_bWannier) && (!m->m_bChargesAssigned))
3206
continue;
3207
3208
if (g_bDipoleRefFixed)
3209
dc = CxVector3(0,0,0);
3210
else dc = m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[m->m_iDipoleCenterType])->GetAt(m->m_iDipoleCenterIndex)];
3211
3212
if (g_bVerbose)
3213
mprintf(" Ref. point is ( %f | %f | %f )\n",dc[0],dc[1],dc[2]);
3214
3215
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
3216
{
3217
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
3218
continue;
3219
3220
if (g_bWannier)
3221
if (m->m_baAtomIndex[z3] == g_iWannierAtomType)
3222
continue;
3223
3224
a = (CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]];
3225
for (z4=0;z4<m->m_waAtomCount[z3];z4++)
3226
{
3227
// mprintf(" %s%d %.2f x ",a->m_sName,z4+1,a->m_fCharge);
3228
// (m_vaCoords[sm->m_iAtomOffset[z3][z4]]-m_vaCoords[sm->m_iAtomOffset[m->Elements-1][0]]).Dump();
3229
// mprintf("\n");
3230
// mprintf(" %s%d %.2f (%d)\n",a->m_sName,z4+1,a->m_fCharge,((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4));
3231
3232
if (g_bWannier)
3233
{
3234
sm->m_vDipole += a->m_fCharge * (m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)] - dc);
3235
3236
if (g_bVerbose)
3237
mprintf(" %.2f: ( %f | %f | %f )\n",a->m_fCharge,m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]);
3238
} else
3239
{
3240
if (g_bReadChargesFrom4thXYZ)
3241
{
3242
// mprintf("Moep. z3=%d, z4=%d, c=%f.\n",z3,z4,m_faCharge[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)]);
3243
sm->m_vDipole += m_faCharge[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)] * (m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)] - dc);
3244
if (g_bVerbose)
3245
mprintf(" %.2f: ( %f | %f | %f )\n",m_faCharge[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]);
3246
} else
3247
{
3248
sm->m_vDipole += ((CxFloatArray*)m->m_oaCharges[z3])->GetAt(z4) * (m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)] - dc);
3249
if (g_bVerbose)
3250
mprintf(" %.2f: ( %f | %f | %f )\n",((CxFloatArray*)m->m_oaCharges[z3])->GetAt(z4),m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][0],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][1],m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4)][2]);
3251
}
3252
}
3253
}
3254
}
3255
for (z3=0;z3<sm->m_laWannier.GetSize();z3++)
3256
{
3257
// mprintf(" - %.2f x ",g_fWannierCharge);
3258
// (m_vaCoords[sm->m_waWannier[z3]] - m_vaCoords[sm->m_iAtomOffset[m->Elements-1][0]]).Dump();
3259
// mprintf("\n");
3260
sm->m_vDipole -= g_fWannierCharge * (m_vaCoords[sm->m_laWannier[z3]] - dc);
3261
3262
if (g_bVerbose)
3263
mprintf(" %.2f: ( %f | %f | %f )\n",-g_fWannierCharge,m_vaCoords[sm->m_laWannier[z3]][0],m_vaCoords[sm->m_laWannier[z3]][1],m_vaCoords[sm->m_laWannier[z3]][2]);
3264
}
3265
// mprintf(" = ");
3266
// sm->m_vDipole.Dump();
3267
// mprintf("\n");
3268
sm->m_vDipole *= 0.048008f; // Conversion e*pm --> Debye
3269
3270
if (g_bVerbose)
3271
mprintf(" Result: %f.\n",sm->m_vDipole.GetLength());
3272
3273
// mprintf("Molecule %s - Dipole %.3f\n",m->Name,sm->m_vDipole.GetLength());
3274
}
3275
}
3276
BTOUT;
3277
}
3278
3279
3280
void CTimeStep::DoubleBox()
3281
{
3282
int px, py, pz, z;
3283
char *p;
3284
3285
if (m_vaCoords.GetSize() < g_iGesAtomCount)
3286
m_vaCoords.SetSize(g_iGesAtomCount);
3287
3288
if (m_paLabels.GetSize() != 0)
3289
m_paLabels.SetSize(g_iGesAtomCount);
3290
3291
for (pz=0;pz<g_iDoubleBoxZ;pz++)
3292
{
3293
for (py=0;py<g_iDoubleBoxY;py++)
3294
{
3295
for (px=0;px<g_iDoubleBoxX;px++)
3296
{
3297
if ((px == 0) && (py == 0) && (pz == 0))
3298
continue;
3299
for (z=0;z<g_iGesAtomCount/g_iDoubleBoxFactor;z++)
3300
{
3301
m_vaCoords[(pz*g_iDoubleBoxX*g_iDoubleBoxY+py*g_iDoubleBoxX+px)*g_iGesAtomCount/g_iDoubleBoxFactor+z] = m_vaCoords[z] + CxVector3(px*g_fBoxX/g_iDoubleBoxX,py*g_fBoxY/g_iDoubleBoxY,pz*g_fBoxZ/g_iDoubleBoxZ);
3302
if (m_paLabels.GetSize() != 0)
3303
{
3304
try { p = new char[strlen((char*)m_paLabels[z])+1]; } catch(...) { p = NULL; }
3305
if (p == NULL) NewException((double)(strlen((char*)m_paLabels[z])+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3306
3307
strcpy(p,(char*)m_paLabels[z]);
3308
m_paLabels[(pz*g_iDoubleBoxX*g_iDoubleBoxY+py*g_iDoubleBoxX+px)*g_iGesAtomCount/g_iDoubleBoxFactor+z] = p;
3309
}
3310
}
3311
}
3312
}
3313
}
3314
m_iGesAtomCount = g_iGesAtomCount;
3315
}
3316
3317
3318
void CTimeStep::DoubleBoxVelocity()
3319
{
3320
int px, py, pz, z;
3321
3322
if (m_vaVelocities.GetSize() < g_iGesAtomCount)
3323
m_vaVelocities.SetSize(g_iGesAtomCount);
3324
3325
for (pz=0;pz<g_iDoubleBoxZ;pz++)
3326
{
3327
for (py=0;py<g_iDoubleBoxY;py++)
3328
{
3329
for (px=0;px<g_iDoubleBoxX;px++)
3330
{
3331
if ((px == 0) && (py == 0) && (pz == 0))
3332
continue;
3333
for (z=0;z<g_iGesAtomCount/g_iDoubleBoxFactor;z++)
3334
m_vaVelocities[(pz*g_iDoubleBoxX*g_iDoubleBoxY+py*g_iDoubleBoxX+px)*g_iGesAtomCount/g_iDoubleBoxFactor+z] = m_vaVelocities[z];
3335
}
3336
}
3337
}
3338
}
3339
3340
3341
void CTimeStep::DoubleBoxForce()
3342
{
3343
int px, py, pz, z;
3344
3345
if (m_vaForces.GetSize() < g_iGesAtomCount)
3346
m_vaForces.SetSize(g_iGesAtomCount);
3347
3348
for (pz=0;pz<g_iDoubleBoxZ;pz++)
3349
{
3350
for (py=0;py<g_iDoubleBoxY;py++)
3351
{
3352
for (px=0;px<g_iDoubleBoxX;px++)
3353
{
3354
if ((px == 0) && (py == 0) && (pz == 0))
3355
continue;
3356
for (z=0;z<g_iGesAtomCount/g_iDoubleBoxFactor;z++)
3357
m_vaForces[(pz*g_iDoubleBoxX*g_iDoubleBoxY+py*g_iDoubleBoxX+px)*g_iGesAtomCount/g_iDoubleBoxFactor+z] = m_vaForces[z];
3358
}
3359
}
3360
}
3361
}
3362
3363
3364
bool CTimeStep::ReadXYZ(FILE *a, bool needinfo, CxVec3Array *v)
3365
{
3366
BTIN;
3367
char buf[256], obuf[256], *p, *q, *r;
3368
int z, /*i,*/ j;
3369
const char *separators = " ,;\"'\t";
3370
3371
// mprintf("*** Read Anfang.\n");
3372
j = 0;
3373
// m_iSizeBytes = 0;
3374
_readagain:
3375
buf[0] = 0;
3376
fgets_bin(buf,256,a);
3377
// m_iSizeBytes += strlen(buf);
3378
if (strlen(buf) > 0)
3379
buf[strlen(buf)-1] = 0;
3380
// mprintf("Read1: \"%s\".\n",buf);
3381
goto _firsttry;
3382
_again:
3383
eprintf("\nTrajectory file seems to be damaged. Searching for next time step...");
3384
_firsttry:
3385
if (feof(a))
3386
{
3387
// mprintf("CTimeStep::ReadTimestep(): Unexpected End of File (1).\n");
3388
BTOUT;
3389
return false;
3390
}
3391
if (strchr(buf,'.') != NULL)
3392
{
3393
if (j < 10)
3394
eprintf("x",j,buf);
3395
// mprintf("x: %d - \"%s\"\n",j,buf);
3396
j++;
3397
goto _readagain;
3398
}
3399
m_iGesAtomCount = atoi(buf);
3400
if (m_iGesAtomCount == 0)
3401
{
3402
eprintf("\nCTimeStep::ReadXYZ(): Error - atom count = 0. \"%s\"",buf);
3403
goto _readagain;
3404
}
3405
if (m_pComment == NULL)
3406
{
3407
try { m_pComment = new char[128]; } catch(...) { m_pComment = NULL; }
3408
if (m_pComment == NULL) NewException((double)128*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3409
}
3410
if (needinfo)
3411
{
3412
for (z=0;z<m_paLabels.GetSize();z++)
3413
delete[] (char*)m_paLabels[z];
3414
m_paLabels.RemoveAll();
3415
if (g_bDoubleBox)
3416
m_paLabels.SetSize(m_iGesAtomCount*g_iDoubleBoxFactor);
3417
else m_paLabels.SetSize(m_iGesAtomCount);
3418
}
3419
if (v->GetSize() < (long)m_iGesAtomCount)
3420
v->SetSize(m_iGesAtomCount);
3421
3422
if (g_bKeepOriginalCoords)
3423
{
3424
if (m_vaCoords_Original.GetSize() < (long)m_iGesAtomCount)
3425
m_vaCoords_Original.SetSize(m_iGesAtomCount);
3426
}
3427
3428
m_pComment[0] = 0;
3429
fgets_bin(m_pComment,128,a); // Zeitschritt - egal hier
3430
// if (strlen(m_pComment) > 0)
3431
// m_pComment[strlen(m_pComment)-1] = 0;
3432
3433
p = m_pComment;
3434
while (*p != 0)
3435
{
3436
if ((*p == 10) || (*p == 13))
3437
*p = 0;
3438
p++;
3439
}
3440
// mprintf("Comment: \"%s\".\n",m_pComment);
3441
// m_iSizeBytes += strlen(m_pComment);
3442
3443
if (g_bReadChargesFrom4thXYZ)
3444
m_faCharge.SetSize(m_iGesAtomCount);
3445
3446
for (z=0;z<(long)m_iGesAtomCount;z++) // den ersten Zeitschritt einlesen
3447
{
3448
buf[0] = 0;
3449
fgets_bin(buf,256,a);
3450
if (feof(a))
3451
{
3452
eprintf("\nCTimeStep::ReadXYZ(): Unexpected end of file (2). \"%s\"\n",buf);
3453
BTOUT;
3454
return false;
3455
}
3456
// m_iSizeBytes += strlen(buf);
3457
buf[strlen(buf)-1] = 0;
3458
// mprintf(" %d: \"%s\".\n",z,buf);
3459
strcpy(obuf,buf);
3460
// i = 0;
3461
3462
p = &buf[0];
3463
while (strchr(separators,*p) != NULL)
3464
p++;
3465
q = p+1;
3466
while ((strchr(separators,*q) == NULL) && (*q != 0))
3467
q++;
3468
if (*q == 0)
3469
{
3470
eprintf("\nCTimeStep::ReadXYZ(): %d: Incomplete line (1): \"%s\"\n",z+1,obuf);
3471
BTOUT;
3472
return false;
3473
}
3474
*q = 0;
3475
3476
if (needinfo)
3477
{
3478
if (strlen(p) > 7)
3479
{
3480
eprintf("\nCTimeStep::ReadXYZ(): \"%s\" - Maximum length of atom labels is 7 chars; truncating.\n",p);
3481
p[7] = 0;
3482
}
3483
3484
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
3485
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3486
3487
strcpy(r,p);
3488
m_paLabels[z] = r;
3489
}
3490
3491
q++;
3492
while (strchr(separators,*q) != NULL)
3493
q++;
3494
p = q;
3495
while ((strchr(separators,*p) == NULL) && (*p != 0))
3496
p++;
3497
if (*p == 0)
3498
{
3499
eprintf("\nCTimeStep::ReadXYZ(): %d: Incomplete line (2): \"%s\"",z+1,obuf);
3500
goto _again;
3501
}
3502
*p = 0;
3503
(*v)[z][0] = (float)atof(q) * 100.0f;
3504
3505
if (g_bKeepOriginalCoords)
3506
m_vaCoords_Original[z][0] = (double)atof(q) * 100.0;
3507
3508
q = p+1;
3509
while (strchr(separators,*q) != NULL)
3510
q++;
3511
p = q;
3512
while ((strchr(separators,*p) == NULL) && (*p != 0))
3513
p++;
3514
if (*p == 0)
3515
{
3516
eprintf("\nCTimeStep::ReadXYZ(): %d: Incomplete line (3) \"%s\"",z+1,obuf);
3517
goto _again;
3518
}
3519
*p = 0;
3520
(*v)[z][1] = (float)atof(q) * 100.0f;
3521
3522
if (g_bKeepOriginalCoords)
3523
m_vaCoords_Original[z][1] = (double)atof(q) * 100.0;
3524
3525
q = p+1;
3526
while (strchr(separators,*q) != NULL)
3527
q++;
3528
p = q;
3529
while ((strchr(separators,*p) == NULL) && (*p != 0))
3530
p++;
3531
if (g_bReadChargesFrom4thXYZ)
3532
{
3533
if (*p == 0)
3534
{
3535
eprintf("\nCTimeStep::ReadXYZ(): %d: Incomplete line (4) \"%s\"",z+1,obuf);
3536
goto _again;
3537
}
3538
*p = 0;
3539
} else
3540
{
3541
if (*p != 0)
3542
*p = 0;
3543
}
3544
(*v)[z][2] = (float)atof(q) * 100.0f;
3545
3546
if (g_bKeepOriginalCoords)
3547
m_vaCoords_Original[z][2] = (double)atof(q) * 100.0;
3548
3549
if (g_bReadChargesFrom4thXYZ)
3550
{
3551
q = p+1;
3552
while (strchr(separators,*q) != NULL)
3553
q++;
3554
p = q;
3555
while ((strchr(separators,*p) == NULL) && (*p != 0))
3556
p++;
3557
if (*p != 0)
3558
*p = 0;
3559
m_faCharge[z] = (float)atof(q);
3560
} else if (needinfo && (z==0))
3561
{
3562
if (*p == 0)
3563
goto _no4;
3564
q = p+1;
3565
if (*q == 0)
3566
goto _no4;
3567
while (strchr(separators,*q) != NULL)
3568
q++;
3569
p = q;
3570
while ((strchr(separators,*p) == NULL) && (*p != 0))
3571
p++;
3572
if ((p-q) > 3)
3573
{
3574
for (;q<p;q++)
3575
if (!(((*q >= '0') && (*q <= '9')) || (*q == '-') || (*q == '.')))
3576
goto _no4;
3577
g_bXYZ4thCol = true;
3578
_no4:;
3579
}
3580
}
3581
3582
/* q = strchr(buf,'.');
3583
if (q != NULL)
3584
{
3585
i++;
3586
q = strchr(q+1,'.');
3587
}
3588
if (q != NULL)
3589
{
3590
i++;
3591
q = strchr(q+1,'.');
3592
}
3593
if (q==NULL)
3594
{
3595
eprintf("\nCTimeStep::ReadXYZ(): Error - only %d/3 dots. %d, \"%s\"",i,z+1,buf);
3596
goto _again;
3597
}
3598
q = buf;
3599
while (*q == ' ')
3600
q++;
3601
p = strchr(q,' ');
3602
if (p == NULL)
3603
{
3604
eprintf("\nCTimeStep::ReadXYZ(): Error 1. %d, \"%s\"",z+1,buf);
3605
goto _again;
3606
}
3607
while (isdigit(*(p-1)) && (p > buf))
3608
p--;
3609
if (p == buf)
3610
{
3611
eprintf("\nCTimeStep::ReadXYZ(): No Atom label found. %d, \"%s\"",z+1,buf);
3612
goto _again;
3613
}
3614
*p = 0;
3615
if (needinfo)
3616
{
3617
r = new char[strlen(q)+1];
3618
strcpy(r,q);
3619
m_paLabels[z] = r;
3620
}
3621
q = p+1;
3622
while (*q == ' ')
3623
q++;
3624
p = strchr(q,' ');
3625
if (p == NULL)
3626
{
3627
eprintf("\nCTimeStep::ReadXYZ(): Error 3. %d, \"%s\"",z+1,q);
3628
goto _again;
3629
}
3630
*p = 0;
3631
(*v)[z][0] = (float)atof(q) * 100.0f;
3632
q = p+1;
3633
while (*q == ' ')
3634
q++;
3635
p = strchr(q,' ');
3636
if (p == NULL)
3637
{
3638
eprintf("\nCTimeStep::ReadXYZ(): Error 4. %d, \"%s\"",z+1,q);
3639
goto _again;
3640
}
3641
*p = 0;
3642
(*v)[z][1] = (float)atof(q) * 100.0f;
3643
q = p+1;
3644
while (*q == ' ')
3645
q++;
3646
p = strchr(q,' ');
3647
if (p != NULL)
3648
*p = 0;
3649
(*v)[z][2] = (float)atof(q) * 100.0f;*/
3650
3651
3652
}
3653
// mprintf("*** Read Ende.\n");
3654
BTOUT;
3655
return true;
3656
}
3657
3658
3659
bool CTimeStep::ReadPDB(FILE *a, bool needinfo, CxVec3Array *v)
3660
{
3661
int i;
3662
static char buf[256], obuf[256], buf2[64];
3663
char *p, *q, *r;
3664
float x, y, z;
3665
bool b;
3666
3667
v->RemoveAll_KeepSize();
3668
for (i=0;i<m_paLabels.GetSize();i++)
3669
delete[] (char*)m_paLabels[i];
3670
m_paLabels.RemoveAll();
3671
while (true)
3672
{
3673
fgets_bin(buf,256,a);
3674
if (feof(a))
3675
return false;
3676
if (strlen(buf) == 0)
3677
continue;
3678
buf[strlen(buf)-1] = 0;
3679
strcpy(obuf,buf);
3680
if (g_bNPT)
3681
{
3682
if (strstr(buf,"CRYST1") != 0) // Boxlaenge
3683
{
3684
// mprintf(GREY,"\"%s\".\n",buf);
3685
p = &buf[6];
3686
while (*p == ' ')
3687
p++;
3688
q = p;
3689
while ((*q != ' ') && (*q != 0))
3690
q++;
3691
if (*q == 0)
3692
{
3693
eprintf("Error 5 reading PDB line: \"%s\".\n",obuf);
3694
return false;
3695
}
3696
*q = 0;
3697
g_fBoxX = (float)(atof(p)*100.0);
3698
p = q+1;
3699
3700
while (*p == ' ')
3701
p++;
3702
q = p;
3703
while ((*q != ' ') && (*q != 0))
3704
q++;
3705
if (*q == 0)
3706
{
3707
eprintf("Error 6 reading PDB line: \"%s\".\n",obuf);
3708
return false;
3709
}
3710
*q = 0;
3711
g_fBoxY = (float)(atof(p)*100.0);
3712
p = q+1;
3713
3714
while (*p == ' ')
3715
p++;
3716
q = p;
3717
while ((*q != ' ') && (*q != 0))
3718
q++;
3719
if (*q != 0)
3720
*q = 0;
3721
g_fBoxZ = (float)(atof(p)*100.0);
3722
// mprintf(GREY,"--> %f %f %f\n",g_fBoxX,g_fBoxY,g_fBoxZ);
3723
}
3724
}
3725
3726
if (strstr(buf,"END") == buf)
3727
break;
3728
3729
if ((strstr(buf,"ATOM")==0) && (strstr(buf,"HETATM")==0))
3730
continue;
3731
3732
p = &buf[7];
3733
while (!(isalpha(*p) || (*p == '_')) && (*p != 0))
3734
p++;
3735
if (*p == 0)
3736
{
3737
eprintf("Error 4 reading PDB line: \"%s\".\n",obuf);
3738
return false;
3739
}
3740
q = p;
3741
while (isalpha(*q) || (*q == '_'))
3742
q++;
3743
if (needinfo)
3744
{
3745
*q = 0;
3746
if (strlen(p) > 7)
3747
{
3748
eprintf("\nCTimeStep::ReadPDB(): \"%s\" - maximum length for atom labels is 7 chars; truncating.\n",p);
3749
p[7] = 0;
3750
}
3751
3752
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
3753
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3754
3755
strcpy(r,p);
3756
m_paLabels.Add(r);
3757
}
3758
p = q+1;
3759
3760
while ((*p != '.') && (*p != 0))
3761
p++;
3762
3763
while (*p != ' ')
3764
p--;
3765
3766
p++;
3767
3768
q = p;
3769
b = false;
3770
while (*q != 0)
3771
{
3772
if (b)
3773
{
3774
if ((*q == ' ') || (*q == '-'))
3775
break;
3776
}
3777
if (*q == 0)
3778
break;
3779
if ((*q == '-') || (*q == '.') || ((*q >= '0') && (*q <= '9')))
3780
b = true;
3781
q++;
3782
}
3783
// q = strchr(p,' ');
3784
if (*q == 0)
3785
{
3786
eprintf("\nCTimeStep::ReadPDB(): Error 1. \"%s\".",obuf);
3787
return false;
3788
}
3789
memcpy(buf2,p,q-p);
3790
buf2[q-p] = 0;
3791
x = (float)atof(buf2) * 100.0f;
3792
// mprintf("\n \"%s\".",buf2);
3793
3794
p = q;
3795
b = false;
3796
while (*q != 0)
3797
{
3798
if (b)
3799
{
3800
if ((*q == ' ') || (*q == '-'))
3801
break;
3802
}
3803
if (*q == 0)
3804
break;
3805
if ((*q == '-') || (*q == '.') || ((*q >= '0') && (*q <= '9')))
3806
b = true;
3807
q++;
3808
}
3809
// q = strchr(p,' ');
3810
if (*q == 0)
3811
{
3812
eprintf("\nCTimeStep::ReadPDB(): Error 2. \"%s\".",obuf);
3813
return false;
3814
}
3815
memcpy(buf2,p,q-p);
3816
buf2[q-p] = 0;
3817
y = (float)atof(buf2) * 100.0f;
3818
// mprintf("\n \"%s\".",buf2);
3819
3820
z = (float)atof(q) * 100.0f;
3821
// mprintf("\n \"%s\".",q);
3822
3823
// mprintf("\n%f, %f, %f",x,y,z);
3824
3825
m_vaCoords.Add(CxVector3(x,y,z));
3826
}
3827
m_iGesAtomCount = m_vaCoords.GetSize();
3828
3829
return true;
3830
}
3831
3832
3833
bool CTimeStep::SkipPDB(FILE *a)
3834
{
3835
char buf[256];
3836
// bool b;
3837
3838
while (true)
3839
{
3840
fgets_bin(buf,256,a);
3841
if (feof(a))
3842
return false;
3843
if (strlen(buf) == 0)
3844
continue;
3845
buf[strlen(buf)-1] = 0;
3846
if (strstr(buf,"END") == buf)
3847
break;
3848
}
3849
return true;
3850
}
3851
3852
3853
bool CTimeStep::ReadLAMMPS(FILE *a, bool needinfo)
3854
{
3855
int i;
3856
char buf[256], obuf[256], *p, *q, *r;
3857
float x, y, z;
3858
3859
m_vaCoords.RemoveAll_KeepSize();
3860
for (i=0;i<m_paLabels.GetSize();i++)
3861
delete[] (char*)m_paLabels[i];
3862
m_paLabels.RemoveAll();
3863
m_iGesAtomCount = 0;
3864
while (true)
3865
{
3866
fgets_bin(buf,256,a);
3867
if (feof(a))
3868
return false;
3869
if (strlen(buf) == 0)
3870
continue;
3871
buf[strlen(buf)-1] = 0;
3872
strcpy(obuf,buf);
3873
if (g_bNPT)
3874
{
3875
if (strstr(buf,"ITEM: BOX BOUNDS") != 0) // Boxlaenge
3876
{
3877
for (i=0;i<3;i++)
3878
{
3879
fgets_bin(buf,256,a);
3880
if (feof(a))
3881
return false;
3882
3883
p = &buf[0];
3884
while (strchr(" ",*p) != NULL)
3885
p++;
3886
q = p+1;
3887
while ((strchr(" ",*q) == NULL) && (*q != 0))
3888
q++;
3889
if (*q == 0)
3890
{
3891
eprintf("\nCTimeStep::ReadLAMMPS(): Incomplete line: \"%s\"\n",obuf);
3892
return false;
3893
}
3894
*q = 0;
3895
x = atof(p);
3896
3897
p = q+1;
3898
while (strchr(" ",*p) != NULL)
3899
p++;
3900
3901
y = atof(p);
3902
3903
switch(i)
3904
{
3905
case 0: g_fBoxX = (y-x)*100.0f; break;
3906
case 1: g_fBoxY = (y-x)*100.0f; break;
3907
case 2: g_fBoxZ = (y-x)*100.0f; break;
3908
}
3909
}
3910
}
3911
}
3912
if (strstr(buf,"ITEM: NUMBER OF ATOMS") != 0)
3913
{
3914
fgets_bin(buf,256,a);
3915
if (feof(a))
3916
return false;
3917
buf[strlen(buf)-1] = 0;
3918
m_iGesAtomCount = atoi(buf);
3919
continue;
3920
}
3921
if (strstr(buf,"ITEM: ATOMS") != 0)
3922
{
3923
if (strstr(buf,"ITEM: ATOMS element xu yu zu") == 0)
3924
{
3925
eprintf("CTimeStep::ReadLAMMPS(): Wrong LAMMPS dump style: \"%s\".\n",buf);
3926
eprintf("You need to use \"dump custom element xu yu zu\".\n");
3927
return false;
3928
}
3929
3930
if (m_iGesAtomCount == 0)
3931
{
3932
eprintf("CTimeStep::ReadLAMMPS(): \"ITEM: ATOMS\" before \"ITEM: NUMBER OF ATOMS\".\n");
3933
return false;
3934
}
3935
3936
if (needinfo)
3937
{
3938
if (g_bDoubleBox)
3939
m_paLabels.SetSize(m_iGesAtomCount*g_iDoubleBoxFactor);
3940
else m_paLabels.SetSize(m_iGesAtomCount);
3941
}
3942
3943
for (i=0;i<(int)m_iGesAtomCount;i++)
3944
{
3945
fgets_bin(buf,256,a);
3946
if (feof(a))
3947
return false;
3948
3949
p = &buf[0];
3950
while (strchr(" ",*p) != NULL)
3951
p++;
3952
q = p+1;
3953
while ((strchr(" ",*q) == NULL) && (*q != 0))
3954
q++;
3955
if (*q == 0)
3956
{
3957
eprintf("\nCTimeStep::ReadLAMMPS(): %d: Incomplete line (1): \"%s\"\n",i+1,obuf);
3958
BTOUT;
3959
return false;
3960
}
3961
*q = 0;
3962
3963
if (needinfo)
3964
{
3965
if (strlen(p) > 7)
3966
{
3967
eprintf("\nCTimeStep::ReadLAMMPS(): \"%s\" - maximum length for atom labels is 7 chars; truncating.\n",p);
3968
p[7] = 0;
3969
}
3970
3971
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
3972
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
3973
3974
strcpy(r,p);
3975
m_paLabels[i] = r;
3976
}
3977
3978
q++;
3979
while (strchr(" ",*q) != NULL)
3980
q++;
3981
p = q;
3982
while ((strchr(" ",*p) == NULL) && (*p != 0))
3983
p++;
3984
if (*p == 0)
3985
{
3986
eprintf("\nCTimeStep::ReadLAMMPS(): %d: Incomplete line (2): \"%s\"",i+1,obuf);
3987
return false;
3988
}
3989
*p = 0;
3990
x = (float)atof(q) * 100.0f;
3991
q = p+1;
3992
while (strchr(" ",*q) != NULL)
3993
q++;
3994
p = q;
3995
while ((strchr(" ",*p) == NULL) && (*p != 0))
3996
p++;
3997
if (*p == 0)
3998
{
3999
eprintf("\nCTimeStep::ReadLAMMPS(): %d: Incomplete line (3) \"%s\"",i+1,obuf);
4000
return false;
4001
}
4002
*p = 0;
4003
y = (float)atof(q) * 100.0f;
4004
q = p+1;
4005
while (strchr(" ",*q) != NULL)
4006
q++;
4007
p = q;
4008
while ((strchr(" ",*p) == NULL) && (*p != 0))
4009
p++;
4010
if (*p != 0)
4011
*p = 0;
4012
z = (float)atof(q) * 100.0f;
4013
4014
m_vaCoords.Add(CxVector3(x,y,z));
4015
}
4016
break;
4017
}
4018
}
4019
return true;
4020
}
4021
4022
4023
bool CTimeStep::SkipLAMMPS(FILE *a)
4024
{
4025
int i, j;
4026
char buf[256];
4027
4028
j = 0;
4029
while (true)
4030
{
4031
fgets_bin(buf,256,a);
4032
if (feof(a))
4033
return false;
4034
if (strlen(buf) == 0)
4035
continue;
4036
buf[strlen(buf)-1] = 0;
4037
if (strstr(buf,"ITEM: NUMBER OF ATOMS") != 0)
4038
{
4039
fgets_bin(buf,256,a);
4040
if (feof(a))
4041
return false;
4042
buf[strlen(buf)-1] = 0;
4043
j = atoi(buf);
4044
continue;
4045
}
4046
if (strstr(buf,"ITEM: ATOMS") != 0)
4047
{
4048
if (j == 0)
4049
{
4050
eprintf("CTimeStep::SkipLAMMPS(): \"ITEM: ATOMS\" before \"ITEM: NUMBER OF ATOMS\".\n");
4051
return false;
4052
}
4053
for (i=0;i<j;i++)
4054
{
4055
fgets_bin(buf,256,a);
4056
if (feof(a))
4057
return false;
4058
}
4059
break;
4060
}
4061
}
4062
return true;
4063
}
4064
4065
4066
bool CTimeStep::ReadDLPOLY(FILE *a, bool needinfo)
4067
{
4068
int i;
4069
char buf[256], obuf[256], *p, *q, *r;
4070
float x, y, z;
4071
4072
m_vaCoords.RemoveAll_KeepSize();
4073
for (i=0;i<m_paLabels.GetSize();i++)
4074
delete[] (char*)m_paLabels[i];
4075
m_paLabels.RemoveAll();
4076
m_iGesAtomCount = 0;
4077
while (true)
4078
{
4079
fgets_bin(buf,256,a);
4080
if (feof(a))
4081
return false;
4082
if (strlen(buf) == 0)
4083
continue;
4084
buf[strlen(buf)-1] = 0;
4085
strcpy(obuf,buf);
4086
4087
if (strstr(buf,"timestep") != 0)
4088
{
4089
p = &buf[0];
4090
while (*p == ' ')
4091
p++;
4092
q = p;
4093
while ((*q != ' ') && (*q != 0))
4094
q++;
4095
if (*q == 0)
4096
{
4097
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line A: \"%s\"\n",obuf);
4098
return false;
4099
}
4100
*q = 0;
4101
p=q+1;
4102
4103
while (*p == ' ')
4104
p++;
4105
q = p;
4106
while ((*q != ' ') && (*q != 0))
4107
q++;
4108
if (*q == 0)
4109
{
4110
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line B: \"%s\"\n",obuf);
4111
return false;
4112
}
4113
*q = 0;
4114
p=q+1;
4115
4116
while (*p == ' ')
4117
p++;
4118
q = p;
4119
while ((*q != ' ') && (*q != 0))
4120
q++;
4121
if (*q == 0)
4122
{
4123
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line C: \"%s\"\n",obuf);
4124
return false;
4125
}
4126
*q = 0;
4127
m_iGesAtomCount = atoi(p);
4128
4129
if (g_bNPT)
4130
{
4131
for (i=0;i<3;i++)
4132
{
4133
fgets_bin(buf,256,a);
4134
if (feof(a))
4135
return false;
4136
4137
p = &buf[0];
4138
4139
while (*p == ' ')
4140
p++;
4141
q = p;
4142
while ((*q != ' ') && (*q != 0))
4143
q++;
4144
if (*q == 0)
4145
{
4146
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line D: \"%s\"\n",obuf);
4147
return false;
4148
}
4149
*q = 0;
4150
x = atof(p);
4151
p = q+1;
4152
4153
while (*p == ' ')
4154
p++;
4155
q = p;
4156
while ((*q != ' ') && (*q != 0))
4157
q++;
4158
if (*q == 0)
4159
{
4160
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line E: \"%s\"\n",obuf);
4161
return false;
4162
}
4163
*q = 0;
4164
y = atof(p);
4165
p = q+1;
4166
4167
while (*p == ' ')
4168
p++;
4169
q = p;
4170
while ((*q != ' ') && (*q != 0))
4171
q++;
4172
*q = 0;
4173
z = atof(p);
4174
4175
switch(i)
4176
{
4177
case 0:
4178
if ((y != 0) || (z != 0))
4179
{
4180
eprintf("\nCTimeStep::ReadDLPOLY(): X: Only orthorhombic cells are supported.\n");
4181
return false;
4182
}
4183
g_fBoxX = x*100.0f;
4184
break;
4185
4186
case 1:
4187
if ((x != 0) || (z != 0))
4188
{
4189
eprintf("\nCTimeStep::ReadDLPOLY(): Y: Only orthorhombic cells are supported.\n");
4190
return false;
4191
}
4192
g_fBoxY = y*100.0f;
4193
break;
4194
4195
case 2:
4196
if ((x != 0) || (y != 0))
4197
{
4198
eprintf("\nCTimeStep::ReadDLPOLY(): Z: Only orthorhombic cells are supported.\n");
4199
return false;
4200
}
4201
g_fBoxZ = z*100.0f;
4202
break;
4203
4204
}
4205
}
4206
} else
4207
{
4208
fgets_bin(buf,256,a);
4209
fgets_bin(buf,256,a);
4210
fgets_bin(buf,256,a);
4211
}
4212
4213
if (m_iGesAtomCount == 0)
4214
{
4215
eprintf("CTimeStep::ReadDLPOLY(): Error: Atom count is 0.\n");
4216
return false;
4217
}
4218
4219
if (needinfo)
4220
{
4221
if (g_bDoubleBox)
4222
m_paLabels.SetSize(m_iGesAtomCount*g_iDoubleBoxFactor);
4223
else m_paLabels.SetSize(m_iGesAtomCount);
4224
}
4225
4226
for (i=0;i<(int)m_iGesAtomCount;i++)
4227
{
4228
_readagain:
4229
fgets_bin(buf,256,a);
4230
if (feof(a))
4231
return false;
4232
4233
p = &buf[0];
4234
while (*p == ' ')
4235
p++;
4236
q = p;
4237
4238
// Numer at beginning of line: Likely velocities. Skip that line
4239
if ((*p == '-') || (*p == '.') || ((*p >= '0') && (*p <= '9')))
4240
goto _readagain;
4241
4242
while ((*q != ' ') && (*q != 0))
4243
q++;
4244
if (*q == 0)
4245
{
4246
eprintf("\nCTimeStep::ReadDLPOLY(): %d: Incomplete line F: \"%s\"\n",i+1,obuf);
4247
return false;
4248
}
4249
*q = 0;
4250
4251
if (needinfo)
4252
{
4253
if (strlen(p) > 7)
4254
{
4255
eprintf("\nCTimeStep::ReadDLPOLY(): \"%s\" - maximum length for atom labels is 7 chars; truncating.\n",p);
4256
p[7] = 0;
4257
}
4258
4259
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
4260
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4261
4262
strcpy(r,p);
4263
m_paLabels[i] = r;
4264
}
4265
4266
fgets_bin(buf,256,a);
4267
if (feof(a))
4268
return false;
4269
4270
p = &buf[0];
4271
4272
while (*p == ' ')
4273
p++;
4274
q = p;
4275
while ((*q != ' ') && (*q != 0))
4276
q++;
4277
if (*q == 0)
4278
{
4279
eprintf("\nCTimeStep::ReadDLPOLY(): %d: Incomplete line G: \"%s\"\n",i+1,obuf);
4280
return false;
4281
}
4282
*q = 0;
4283
x = atof(p)*100.0f;
4284
p = q+1;
4285
4286
while (*p == ' ')
4287
p++;
4288
q = p;
4289
while ((*q != ' ') && (*q != 0))
4290
q++;
4291
if (*q == 0)
4292
{
4293
eprintf("\nCTimeStep::ReadDLPOLY(): %d: Incomplete line H: \"%s\"\n",i+1,obuf);
4294
return false;
4295
}
4296
*q = 0;
4297
y = atof(p)*100.0f;
4298
p = q+1;
4299
4300
while (*p == ' ')
4301
p++;
4302
q = p;
4303
while ((*q != ' ') && (*q != 0))
4304
q++;
4305
*q = 0;
4306
z = atof(p)*100.0f;
4307
4308
m_vaCoords.Add(CxVector3(x,y,z));
4309
}
4310
break;
4311
}
4312
}
4313
return true;
4314
}
4315
4316
4317
bool CTimeStep::SkipDLPOLY(FILE *a)
4318
{
4319
int i, j;
4320
char buf[256], obuf[256], *p, *q;
4321
4322
while (true)
4323
{
4324
fgets_bin(buf,256,a);
4325
if (feof(a))
4326
return false;
4327
if (strlen(buf) == 0)
4328
continue;
4329
buf[strlen(buf)-1] = 0;
4330
strcpy(obuf,buf);
4331
4332
if (strstr(buf,"timestep") != 0)
4333
{
4334
p = &buf[0];
4335
while (*p == ' ')
4336
p++;
4337
q = p;
4338
while ((*q != ' ') && (*q != 0))
4339
q++;
4340
if (*q == 0)
4341
{
4342
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line A: \"%s\"\n",obuf);
4343
return false;
4344
}
4345
*q = 0;
4346
p=q+1;
4347
4348
while (*p == ' ')
4349
p++;
4350
q = p;
4351
while ((*q != ' ') && (*q != 0))
4352
q++;
4353
if (*q == 0)
4354
{
4355
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line B: \"%s\"\n",obuf);
4356
return false;
4357
}
4358
*q = 0;
4359
p=q+1;
4360
4361
while (*p == ' ')
4362
p++;
4363
q = p;
4364
while ((*q != ' ') && (*q != 0))
4365
q++;
4366
if (*q == 0)
4367
{
4368
eprintf("\nCTimeStep::ReadDLPOLY(): Incomplete line C: \"%s\"\n",obuf);
4369
return false;
4370
}
4371
*q = 0;
4372
j = atoi(p);
4373
4374
fgets_bin(buf,256,a);
4375
fgets_bin(buf,256,a);
4376
fgets_bin(buf,256,a);
4377
4378
if (j == 0)
4379
{
4380
eprintf("CTimeStep::ReadDLPOLY(): Error: Atom count is 0.\n");
4381
return false;
4382
}
4383
4384
for (i=0;i<j;i++)
4385
{
4386
fgets_bin(buf,256,a);
4387
fgets_bin(buf,256,a);
4388
if (feof(a))
4389
return false;
4390
}
4391
break;
4392
}
4393
}
4394
return true;
4395
}
4396
4397
4398
bool CTimeStep::ReadMol2(FILE *a, bool needinfo)
4399
{
4400
int i;
4401
char buf[256], obuf[256], *p, *q, *r;
4402
float x, y, z;
4403
4404
fgets_bin(buf,256,a);
4405
fgets_bin(buf,256,a);
4406
fgets_bin(buf,256,a);
4407
p = buf;
4408
while (*p == ' ')
4409
p++;
4410
q = p;
4411
while ((*q != ' ') && (*q != 0))
4412
q++;
4413
*q = 0;
4414
m_iGesAtomCount = atoi(p);
4415
4416
if (needinfo)
4417
{
4418
m_vaCoords.RemoveAll_KeepSize();
4419
for (i=0;i<m_paLabels.GetSize();i++)
4420
delete[] (char*)m_paLabels[i];
4421
m_paLabels.RemoveAll();
4422
m_paLabels.SetSize(m_iGesAtomCount);
4423
for (i=0;i<m_paMol2Types.GetSize();i++)
4424
delete[] (char*)m_paMol2Types[i];
4425
m_paMol2Types.RemoveAll();
4426
m_paMol2Types.SetSize(m_iGesAtomCount);
4427
}
4428
fgets_bin(buf,256,a);
4429
fgets_bin(buf,256,a);
4430
fgets_bin(buf,256,a);
4431
fgets_bin(buf,256,a);
4432
fgets_bin(buf,256,a);
4433
4434
for (i=0;i<(long)m_iGesAtomCount;i++)
4435
{
4436
fgets_bin(buf,256,a);
4437
if (feof(a))
4438
return false;
4439
buf[strlen(buf)-1] = 0;
4440
strcpy(obuf,buf);
4441
// mprintf(" \"%s\"\n",buf);
4442
p = buf;
4443
while (*p == ' ')
4444
p++;
4445
while ((*p != ' ') && (*p != 0))
4446
p++;
4447
while (*p == ' ')
4448
p++;
4449
q = p;
4450
while (isalpha(*q) || (*q == '_'))
4451
q++;
4452
if (needinfo)
4453
{
4454
*q = 0;
4455
if (strlen(p) > 7)
4456
{
4457
eprintf("\nCTimeStep::ReadMol2(): \"%s\" - maximum length for atom labels is 7 chars; truncating.\n",p);
4458
p[7] = 0;
4459
}
4460
4461
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
4462
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4463
4464
strcpy(r,p);
4465
m_paLabels[i] = r;
4466
}
4467
p = q+1;
4468
while ((*p != ' ') && (*p != 0))
4469
p++;
4470
while (*p == ' ')
4471
p++;
4472
4473
q = strchr(p,' ');
4474
if (q == NULL)
4475
{
4476
eprintf("\nCTimeStep::ReadMol2(): Error 1. %d. \"%s\".",i+1,obuf);
4477
return false;
4478
}
4479
*q = 0;
4480
x = (float)atof(p) * 100.0f;
4481
p = q+1;
4482
while (*p == ' ')
4483
p++;
4484
4485
q = strchr(p,' ');
4486
if (q == NULL)
4487
{
4488
eprintf("\nCTimeStep::ReadMol2(): Error 2. %d. \"%s\".",i+1,obuf);
4489
return false;
4490
}
4491
*q = 0;
4492
y = (float)atof(p) * 100.0f;
4493
p = q+1;
4494
while (*p == ' ')
4495
p++;
4496
4497
q = strchr(p,' ');
4498
if (q == NULL)
4499
{
4500
eprintf("\nCTimeStep::ReadMol2(): Error 3. %d. \"%s\".",i+1,obuf);
4501
return false;
4502
}
4503
*q = 0;
4504
z = (float)atof(p) * 100.0f;
4505
m_vaCoords.Add(CxVector3(x,y,z));
4506
4507
p = q+1;
4508
while (*p == ' ')
4509
p++;
4510
q = p;
4511
while ((*q != ' ') && (*q != 0))
4512
q++;
4513
if (needinfo)
4514
{
4515
*q = 0;
4516
4517
try { r = new char[strlen(p)+1]; } catch(...) { r = NULL; }
4518
if (r == NULL) NewException((double)(strlen(p)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4519
4520
strcpy(r,p);
4521
m_paMol2Types[i] = r;
4522
}
4523
/* mprintf(" X=%f, Y=%f, Z=%f",x,y,z);
4524
if (needinfo)
4525
mprintf(", A=%s, B=%s",(char*)m_paLabels[i],(char*)m_paMol2Types[i]);
4526
mprintf("\n");*/
4527
}
4528
m_iGesAtomCount = m_vaCoords.GetSize();
4529
4530
return true;
4531
}
4532
4533
4534
bool CTimeStep::SkipMol2(FILE *a)
4535
{
4536
int i;
4537
char buf[256];
4538
4539
fgets_bin(buf,256,a);
4540
fgets_bin(buf,256,a);
4541
fgets_bin(buf,256,a);
4542
fgets_bin(buf,256,a);
4543
fgets_bin(buf,256,a);
4544
fgets_bin(buf,256,a);
4545
fgets_bin(buf,256,a);
4546
fgets_bin(buf,256,a);
4547
4548
for (i=0;i<(long)m_iGesAtomCount;i++)
4549
{
4550
fgets_bin(buf,256,a);
4551
if (feof(a))
4552
return false;
4553
}
4554
4555
return true;
4556
}
4557
4558
4559
void CTimeStep::CalcMinMax()
4560
{
4561
int z;
4562
4563
m_vMin[0] = 1E20f;
4564
m_vMin[1] = 1E20f;
4565
m_vMin[2] = 1E20f;
4566
m_vMax[0] = -1E20f;
4567
m_vMax[1] = -1E20f;
4568
m_vMax[2] = -1E20f;
4569
4570
for (z=0;z<(long)m_iGesAtomCount;z++)
4571
{
4572
if (m_vMin[0] > m_vaCoords[z][0])
4573
m_vMin[0] = m_vaCoords[z][0];
4574
if (m_vMin[1] > m_vaCoords[z][1])
4575
m_vMin[1] = m_vaCoords[z][1];
4576
if (m_vMin[2] > m_vaCoords[z][2])
4577
m_vMin[2] = m_vaCoords[z][2];
4578
if (m_vMax[0] < m_vaCoords[z][0])
4579
m_vMax[0] = m_vaCoords[z][0];
4580
if (m_vMax[1] < m_vaCoords[z][1])
4581
m_vMax[1] = m_vaCoords[z][1];
4582
if (m_vMax[2] < m_vaCoords[z][2])
4583
m_vMax[2] = m_vaCoords[z][2];
4584
}
4585
}
4586
4587
4588
void CTimeStep::WriteMol2(FILE *a)
4589
{
4590
int z, z2, z3, z4, ti, c, mc;
4591
CMolecule *m;
4592
CSingleMolecule *sm;
4593
int bonds;
4594
int *tpi;
4595
char *cc;
4596
4597
bonds = 0;
4598
for (z=0;z<g_oaSingleMolecules.GetSize();z++)
4599
bonds += ((CSingleMolecule*)g_oaSingleMolecules[z])->m_oaBonds.GetSize();
4600
4601
try { tpi = new int[g_iGesAtomCount]; } catch(...) { tpi = NULL; }
4602
if (tpi == NULL) NewException((double)g_iGesAtomCount*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);
4603
4604
mfprintf(a," @<TRIPOS>MOLECULE\n");
4605
mfprintf(a,"MOL\n");
4606
mfprintf(a," %d %d %d 0 0\n",g_iGesAtomCount,bonds,g_oaSingleMolecules.GetSize());
4607
mfprintf(a," SMALL\n");
4608
mfprintf(a,"resp\n\n\n");
4609
mfprintf(a," @<TRIPOS>ATOM\n");
4610
c = 0;
4611
mc = 0;
4612
if (m_faCharge.GetSize() != g_iGesAtomCount)
4613
{
4614
m_faCharge.SetSize(g_iGesAtomCount);
4615
for (z=0;z<g_iGesAtomCount;z++)
4616
m_faCharge[z] = 0;
4617
}
4618
for (z=0;z<g_oaMolecules.GetSize();z++)
4619
{
4620
m = (CMolecule*)g_oaMolecules[z];
4621
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
4622
{
4623
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
4624
mc++;
4625
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
4626
{
4627
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
4628
continue;
4629
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
4630
{
4631
ti = ((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4);
4632
if (m_paMol2Types.GetSize() != 0)
4633
cc = (char*)m_paMol2Types[ti];
4634
else cc = ((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName;
4635
tpi[ti] = c++;
4636
mfprintf(a," %6d %2s % 11.4f % 11.4f % 11.4f %2s %4d MOL % 8.4f\n",c,((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0,m_vaCoords[ti][1]/100.0,m_vaCoords[ti][2]/100.0,cc,mc,m_faCharge[ti]);
4637
}
4638
}
4639
}
4640
}
4641
mfprintf(a," @<TRIPOS>BOND\n");
4642
c = 0;
4643
for (z=0;z<g_oaMolecules.GetSize();z++)
4644
{
4645
m = (CMolecule*)g_oaMolecules[z];
4646
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
4647
{
4648
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
4649
for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)
4650
mfprintf(a," %6d %6d %6d 1\n",++c,tpi[((CMolBond*)sm->m_oaBonds[z3])->m_iAtomOffset[0]]+1,tpi[((CMolBond*)sm->m_oaBonds[z3])->m_iAtomOffset[1]]+1);
4651
}
4652
}
4653
mfprintf(a," @<TRIPOS>SUBSTRUCTURE\n");
4654
c = 0;
4655
for (z=0;z<g_oaMolecules.GetSize();z++)
4656
{
4657
m = (CMolecule*)g_oaMolecules[z];
4658
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
4659
{
4660
mfprintf(a," %4d MOL %4d TEMP 0 **** **** 0 ROOT\n",c+1,c+1);
4661
c++;
4662
}
4663
}
4664
delete[] tpi;
4665
}
4666
4667
4668
void CTimeStep::ReadCellVector(FILE *a)
4669
{
4670
char buf[256], obuf[256];
4671
char *p, *q;
4672
float tf;
4673
4674
fgets(buf,256,a);
4675
if (feof(a))
4676
{
4677
eprintf("\nReadCellVector: End of file.\n");
4678
eprintf("Your cell vector text file is too short.\n");
4679
return;
4680
}
4681
if (strlen(buf) == 0)
4682
{
4683
eprintf("\nReadCellVector: Empty line.\n");
4684
return;
4685
}
4686
buf[strlen(buf)-1] = 0;
4687
strcpy(obuf,buf);
4688
// mprintf(GREY,"\nReadCellVector: \"%s\".\n",buf);
4689
p = buf;
4690
while ((!isnumeric(*p)) && (*p != 0))
4691
p++;
4692
if (*p == 0)
4693
{
4694
eprintf("\nReadCellVector: Incomplete line (1) \"%s\".\n",obuf);
4695
return;
4696
}
4697
q = p;
4698
while (isnumeric(*q))
4699
q++;
4700
if (*q == 0)
4701
{
4702
eprintf("\nReadCellVector: Incomplete line (2) \"%s\".\n",obuf);
4703
return;
4704
}
4705
*q = 0;
4706
tf = (float)(atof(p)*100.0);
4707
if (tf <= 0)
4708
{
4709
eprintf("\nReadCellVector: Cell vectors need to be > 0 (X) \"%s\".\n",obuf);
4710
return;
4711
}
4712
g_fBoxX = tf;
4713
4714
p = q+1;
4715
while ((!isnumeric(*p)) && (*p != 0))
4716
p++;
4717
if (*p == 0)
4718
{
4719
eprintf("\nReadCellVector: Incomplete line (3) \"%s\".\n",obuf);
4720
return;
4721
}
4722
q = p;
4723
while (isnumeric(*q))
4724
q++;
4725
if (*q == 0)
4726
{
4727
eprintf("\nReadCellVector: Incomplete line (4) \"%s\".\n",obuf);
4728
return;
4729
}
4730
*q = 0;
4731
tf = (float)(atof(p)*100.0);
4732
if (tf <= 0)
4733
{
4734
eprintf("\nReadCellVector: Cell vectors need to be > 0 (Y) \"%s\".\n",obuf);
4735
return;
4736
}
4737
g_fBoxY = tf;
4738
p = q+1;
4739
4740
while ((!isnumeric(*p)) && (*p != 0))
4741
p++;
4742
if (*p == 0)
4743
{
4744
eprintf("\nReadCellVector: Incomplete line (5) \"%s\".\n",obuf);
4745
return;
4746
}
4747
q = p;
4748
while (isnumeric(*q))
4749
q++;
4750
if (*q != 0)
4751
*q = 0;
4752
tf = (float)(atof(p)*100.0);
4753
if (tf <= 0)
4754
{
4755
eprintf("\nReadCellVector: Cell vectors need to be > 0 (Z) \"%s\".\n",obuf);
4756
return;
4757
}
4758
g_fBoxZ = tf;
4759
4760
// mprintf(GREY," --> %f %f %f\n",g_fBoxX,g_fBoxY,g_fBoxZ);
4761
}
4762
4763
4764
void CTimeStep::CenterCOM()
4765
{
4766
CxVector3 vc;
4767
double m;
4768
int z;
4769
4770
vc = CxVector3(0,0,0);
4771
m = 0;
4772
for (z=0;z<g_iGesAtomCount;z++)
4773
{
4774
if (g_bWannier)
4775
if (g_baAtomIndex[z] == g_iWannierAtomType)
4776
continue;
4777
vc += m_vaCoords[z] * ((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_pElement->m_fMass;
4778
m += ((CAtom*)g_oaAtoms[g_baAtomIndex[z]])->m_pElement->m_fMass;
4779
}
4780
vc /= m;
4781
for (z=0;z<g_iGesAtomCount;z++)
4782
m_vaCoords[z] -= vc;
4783
}
4784
4785
4786
float CTimeStep::FoldedDistance(int i1, int i2)
4787
{
4788
CxVector3 t;
4789
4790
t = m_vaCoords[i2]-m_vaCoords[i1];
4791
4792
if (g_bPeriodicX)
4793
{
4794
while (t[0] < -g_fBoxX/2) t[0] += g_fBoxX;
4795
while (t[0] >= g_fBoxX/2) t[0] -= g_fBoxX;
4796
}
4797
4798
if (g_bPeriodicY)
4799
{
4800
while (t[1] < -g_fBoxY/2) t[1] += g_fBoxY;
4801
while (t[1] >= g_fBoxY/2) t[1] -= g_fBoxY;
4802
}
4803
4804
if (g_bPeriodicZ)
4805
{
4806
while (t[2] < -g_fBoxZ/2) t[2] += g_fBoxZ;
4807
while (t[2] >= g_fBoxZ/2) t[2] -= g_fBoxZ;
4808
}
4809
4810
return t.GetLength();
4811
}
4812
4813
4814
void CTimeStep::FoldAtomsPositive()
4815
{
4816
BTIN;
4817
int z;
4818
4819
if (!g_bPeriodic)
4820
return;
4821
4822
for (z=0;z<g_iGesVirtAtomCount;z++)
4823
{
4824
if (g_bPeriodicX)
4825
{
4826
while (m_vaCoords[z][0] < 0) m_vaCoords[z][0] += g_fBoxX;
4827
while (m_vaCoords[z][0] >= g_fBoxX) m_vaCoords[z][0] -= g_fBoxX;
4828
}
4829
4830
if (g_bPeriodicX)
4831
{
4832
while (m_vaCoords[z][1] < 0) m_vaCoords[z][1] += g_fBoxY;
4833
while (m_vaCoords[z][1] >= g_fBoxY) m_vaCoords[z][1] -= g_fBoxY;
4834
}
4835
4836
if (g_bPeriodicX)
4837
{
4838
while (m_vaCoords[z][2] < 0) m_vaCoords[z][2] += g_fBoxZ;
4839
while (m_vaCoords[z][2] >= g_fBoxZ) m_vaCoords[z][2] -= g_fBoxZ;
4840
}
4841
}
4842
BTOUT;
4843
}
4844
4845
4846
void CTimeStep::WritePOV(const char *s)
4847
{
4848
FILE *b;
4849
CMolecule *m;
4850
CSingleMolecule *sm;
4851
CElement *el, *el2;
4852
int z, z2, z3, z4, o, o2;
4853
CxVector3 vec1, vec2, vec3, vec1b, vec2b, vec3b, vecA, vecB, vecC, vecD;
4854
CMolBond *mb;
4855
CxVector3 cam;
4856
// float cr, cg, cb;
4857
4858
b = OpenFileWrite(s,true);
4859
4860
mfprintf(b,"// Written by TRAVIS\n");
4861
mfprintf(b,"// See http://www.travis-analyzer.de\n\n");
4862
mfprintf(b,"#version 3.6;\n");
4863
mfprintf(b,"\n");
4864
4865
mfprintf(b,"/**** Atoms ****/\n");
4866
4867
mfprintf(b,"#declare atom_draw = true;\n");
4868
mfprintf(b,"#declare atom_r = 0.65;\n");
4869
mfprintf(b,"#declare atom_specular = 0.7;\n");
4870
mfprintf(b,"#declare atom_reflect = 0;\n");
4871
mfprintf(b,"#declare atom_ambient = 0.2;\n");
4872
mfprintf(b,"#declare atom_diffuse = 0.7;\n");
4873
mfprintf(b,"//#declare atom_color = < 1.0, 1.0, 1.0, 0, 0 >;\n");
4874
mfprintf(b,"//#declare atom_trans = 0.7;\n");
4875
4876
mfprintf(b,"\n");
4877
4878
mfprintf(b,"#declare atom_draw_halo1 = true;\n");
4879
mfprintf(b,"#declare atom_r_halo1 = 0.008;\n");
4880
mfprintf(b,"#declare atom_d_halo1 = 0.0125;\n");
4881
mfprintf(b,"#declare atom_color_halo1 = < 0, 0, 0, 0, 0 >;\n");
4882
mfprintf(b,"#declare atom_specular_halo1 = 0;\n");
4883
mfprintf(b,"#declare atom_reflect_halo1 = 0;\n");
4884
mfprintf(b,"#declare atom_ambient_halo1 = 1.0;\n");
4885
mfprintf(b,"#declare atom_diffuse_halo1 = 0;\n");
4886
4887
mfprintf(b,"\n");
4888
4889
mfprintf(b,"#declare atom_draw_halo2 = true;\n");
4890
mfprintf(b,"#declare atom_r_halo2 = 0.003;\n");
4891
mfprintf(b,"#declare atom_d_halo2 = 0.01875;\n");
4892
mfprintf(b,"#declare atom_color_halo2 = < 1, 1, 1, 0, 0 >;\n");
4893
mfprintf(b,"#declare atom_specular_halo2 = 0;\n");
4894
mfprintf(b,"#declare atom_reflect_halo2 = 0;\n");
4895
mfprintf(b,"#declare atom_ambient_halo2 = 1.0;\n");
4896
mfprintf(b,"#declare atom_diffuse_halo2 = 0;\n");
4897
4898
mfprintf(b,"\n");
4899
4900
mfprintf(b,"#declare atom_draw_halo3 = true;\n");
4901
mfprintf(b,"#declare atom_r_halo3 = 0.003;\n");
4902
mfprintf(b,"#declare atom_d_halo3 = 0.025;\n");
4903
mfprintf(b,"#declare atom_color_halo3 = < 1, 1, 1, 0, 0.5 >;\n");
4904
mfprintf(b,"#declare atom_specular_halo3 = 0;\n");
4905
mfprintf(b,"#declare atom_reflect_halo3 = 0;\n");
4906
mfprintf(b,"#declare atom_ambient_halo3 = 1.0;\n");
4907
mfprintf(b,"#declare atom_diffuse_halo3 = 0;\n");
4908
4909
mfprintf(b,"\n");
4910
4911
mfprintf(b,"/**** Bonds ****/\n");
4912
4913
mfprintf(b,"#declare bond_draw = true;\n");
4914
mfprintf(b,"#declare bond_r = 0.015;\n");
4915
mfprintf(b,"#declare bond_specular = 0.7;\n");
4916
mfprintf(b,"#declare bond_reflect = 0;\n");
4917
mfprintf(b,"#declare bond_ambient = 0.2;\n");
4918
mfprintf(b,"#declare bond_diffuse = 0.7;\n");
4919
4920
mfprintf(b,"\n");
4921
4922
mfprintf(b,"#declare bond_draw_halo1 = true;\n");
4923
mfprintf(b,"#declare bond_r_halo1 = 0.008;\n");
4924
mfprintf(b,"#declare bond_d_halo1 = 0;\n");
4925
mfprintf(b,"#declare bond_color_halo1 = < 0, 0, 0, 0, 0 >;\n");
4926
mfprintf(b,"#declare bond_specular_halo1 = 0;\n");
4927
mfprintf(b,"#declare bond_reflect_halo1 = 0;\n");
4928
mfprintf(b,"#declare bond_ambient_halo1 = 1.0;\n");
4929
mfprintf(b,"#declare bond_diffuse_halo1 = 0;\n");
4930
4931
mfprintf(b,"\n");
4932
4933
mfprintf(b,"#declare bond_draw_halo2 = true;\n");
4934
mfprintf(b,"#declare bond_r_halo2 = 0.003;\n");
4935
mfprintf(b,"#declare bond_d_halo2 = 0.0286;\n");
4936
mfprintf(b,"#declare bond_color_halo2 = < 1, 1, 1, 0, 0 >;\n");
4937
mfprintf(b,"#declare bond_specular_halo2 = 0;\n");
4938
mfprintf(b,"#declare bond_reflect_halo2 = 0;\n");
4939
mfprintf(b,"#declare bond_ambient_halo2 = 1.0;\n");
4940
mfprintf(b,"#declare bond_diffuse_halo2 = 0;\n");
4941
4942
mfprintf(b,"\n");
4943
4944
mfprintf(b,"#declare bond_draw_halo3 = true;\n");
4945
mfprintf(b,"#declare bond_r_halo3 = 0.003;\n");
4946
mfprintf(b,"#declare bond_d_halo3 = 0.0333;\n");
4947
mfprintf(b,"#declare bond_color_halo3 = < 1, 1, 1, 0, 0.5 >;\n");
4948
mfprintf(b,"#declare bond_specular_halo3 = 0;\n");
4949
mfprintf(b,"#declare bond_reflect_halo3 = 0;\n");
4950
mfprintf(b,"#declare bond_ambient_halo3 = 1.0;\n");
4951
mfprintf(b,"#declare bond_diffuse_halo3 = 0;\n");
4952
4953
mfprintf(b,"\n");
4954
4955
mfprintf(b,"#declare bond_draw_stub = true;\n");
4956
mfprintf(b,"#declare bond_r_stub = 0.004;\n");
4957
mfprintf(b,"#declare bond_l_stub = 0.004;\n");
4958
mfprintf(b,"#declare bond_color_stub = < 0, 0, 0, 0, 0 >;\n");
4959
mfprintf(b,"#declare bond_specular_stub = 0;\n");
4960
mfprintf(b,"#declare bond_reflect_stub = 0;\n");
4961
mfprintf(b,"#declare bond_ambient_stub = 1.0;\n");
4962
mfprintf(b,"#declare bond_diffuse_stub = 0;\n");
4963
4964
mfprintf(b,"\n");
4965
4966
mfprintf(b,"/**** Element Colors ****/\n");
4967
for (z=0;z<g_oaAtoms.GetSize();z++)
4968
{
4969
if (z == g_iVirtAtomType)
4970
continue;
4971
el = ((CAtom*)g_oaAtoms[z])->m_pElement;
4972
mfprintf(b,"#declare elem_%s_col = < %f, %f, %f, 0, 0 >;\n",el->m_sLabel,el->m_iColorR/255.0,el->m_iColorG/255.0,el->m_iColorB/255.0);
4973
}
4974
4975
mfprintf(b,"\n/**** Element Radii ****/\n");
4976
for (z=0;z<g_oaAtoms.GetSize();z++)
4977
{
4978
if (z == g_iVirtAtomType)
4979
continue;
4980
el = ((CAtom*)g_oaAtoms[z])->m_pElement;
4981
mfprintf(b,"#declare elem_%s_r = %f;\n",el->m_sLabel,el->m_fRadius/1000.0);
4982
}
4983
mfprintf(b,"\n");
4984
4985
cam[0] = 0;
4986
cam[1] = 0;
4987
cam[2] = 40.0;
4988
4989
mfprintf(b,"global_settings {\n");
4990
mfprintf(b," assumed_gamma 1\n");
4991
mfprintf(b,"/* radiosity {\n");
4992
mfprintf(b," pretrace_start 0.08\n");
4993
mfprintf(b," pretrace_end 0.04\n");
4994
mfprintf(b," count 100\n\n");
4995
mfprintf(b," nearest_count 5\n");
4996
mfprintf(b," error_bound 0.4\n");
4997
mfprintf(b," recursion_limit 1\n\n");
4998
mfprintf(b," low_error_factor .5\n");
4999
mfprintf(b," gray_threshold 0.0\n");
5000
mfprintf(b," minimum_reuse 0.015\n");
5001
mfprintf(b," brightness 1\n\n");
5002
mfprintf(b," adc_bailout 0.01/2\n");
5003
mfprintf(b," }*/\n");
5004
mfprintf(b,"}\n");
5005
5006
mfprintf(b,"\ncamera {\n");
5007
mfprintf(b," location <%f, %f, %f>\n",cam[0],cam[1],cam[2]);
5008
mfprintf(b," sky y\n");
5009
mfprintf(b," right -0.06*x*image_width/image_height\n");
5010
mfprintf(b," up 0.06*y\n");
5011
mfprintf(b," look_at <0, 0, 0>\n");
5012
mfprintf(b,"}\n");
5013
mfprintf(b,"\n");
5014
5015
mfprintf(b,"// Solid background\n");
5016
mfprintf(b,"background { rgb < 0.15, 0.1, 0.3 > }\n");
5017
mfprintf(b,"\n");
5018
5019
mfprintf(b,"// Gradient background\n");
5020
mfprintf(b,"sky_sphere {\n");
5021
mfprintf(b," pigment {\n");
5022
mfprintf(b," gradient y\n");
5023
mfprintf(b," color_map {\n");
5024
mfprintf(b," [ 0 color rgb < 0.05, 0.05, 0.05 > ]\n");
5025
mfprintf(b," [ 1 color rgb < 0.20, 0.16, 0.50 > ]\n");
5026
mfprintf(b," }\n");
5027
mfprintf(b," scale 0.1\n");
5028
mfprintf(b," translate -0.05\n");
5029
mfprintf(b," }\n");
5030
mfprintf(b,"}\n\n");
5031
5032
mfprintf(b,"/**** Invisible, only for Radiosity ****/\n");
5033
mfprintf(b,"sphere {\n");
5034
mfprintf(b," <0, 0, 0>, 1\n");
5035
mfprintf(b," texture {\n");
5036
mfprintf(b," pigment {color rgb < 1.0, 1.0, 1.0 > }\n");
5037
mfprintf(b," finish { diffuse 0 ambient 1 }\n");
5038
mfprintf(b," }\n");
5039
mfprintf(b," hollow on\n");
5040
mfprintf(b," no_shadow\n");
5041
mfprintf(b," no_image\n");
5042
mfprintf(b," scale 30000\n");
5043
mfprintf(b,"}\n\n");
5044
5045
mfprintf(b,"light_source { < -8, 20, 20 > color rgb 0.8 }\n");
5046
mfprintf(b,"//light_source { < 25, 12, 20 > color rgb 0.5 }\n\n");
5047
5048
mfprintf(b,"#macro m_atom_color(col)\n");
5049
mfprintf(b," #ifdef(atom_color)\n");
5050
mfprintf(b," atom_color\n");
5051
mfprintf(b," #else #if (defined(atom_trans))\n");
5052
mfprintf(b," col + < 0, 0, 0, 0, atom_trans >\n");
5053
mfprintf(b," #else\n");
5054
mfprintf(b," col\n");
5055
mfprintf(b," #end #end\n");
5056
mfprintf(b,"#end\n");
5057
5058
mfprintf(b,"\nunion {\n");
5059
5060
for (z=0;z<g_oaMolecules.GetSize();z++)
5061
{
5062
m = (CMolecule*)g_oaMolecules[z];
5063
5064
for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)
5065
{
5066
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];
5067
5068
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
5069
{
5070
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
5071
continue;
5072
5073
el = ((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_pElement;
5074
5075
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
5076
{
5077
o = ((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4);
5078
vec1 = m_vaCoords[o];
5079
vec1 /= 1000.0;
5080
5081
mfprintf(b,"#if (atom_draw)\n");
5082
mfprintf(b," sphere { <%g, %g, %g>, elem_%s_r*atom_r\n",vec1[0],vec1[1],vec1[2],el->m_sLabel);
5083
mfprintf(b," pigment { rgbft m_atom_color(elem_%s_col) } finish { reflection atom_reflect specular atom_specular ambient atom_ambient diffuse atom_diffuse } }\n",el->m_sLabel);
5084
mfprintf(b,"#end\n");
5085
5086
vec2 = cam - vec1;
5087
vec2.Normalize();
5088
5089
// if (shadow)
5090
{
5091
mfprintf(b,"#if (atom_draw_halo1)\n");
5092
mfprintf(b," disc { < %g - (%g) * atom_d_halo1, %g - (%g) * atom_d_halo1, %g - (%g) * atom_d_halo1 >,\n",vec1[0],vec2[0],vec1[1],vec2[1],vec1[2],vec2[2]);
5093
mfprintf(b," < %g, %g, %g >, (elem_%s_r * atom_r) + atom_r_halo1, elem_%s_r * atom_r\n",vec2[0],vec2[1],vec2[2],el->m_sLabel,el->m_sLabel);
5094
mfprintf(b," pigment { rgbft atom_color_halo1 } finish { reflection atom_reflect_halo1 specular atom_specular_halo1 ambient atom_ambient_halo1 diffuse atom_diffuse_halo1 } no_reflection no_radiosity }\n");
5095
mfprintf(b,"#end\n");
5096
}
5097
5098
// if (halo)
5099
{
5100
mfprintf(b,"#if (atom_draw_halo2)\n");
5101
mfprintf(b," disc { < %g - (%g) * atom_d_halo2, %g - (%g) * atom_d_halo2, %g - (%g) * atom_d_halo2 >,\n",vec1[0],vec2[0],vec1[1],vec2[1],vec1[2],vec2[2]);
5102
mfprintf(b," < %g, %g, %g >, (elem_%s_r * atom_r) + atom_r_halo1 + atom_r_halo2, elem_%s_r * atom_r\n",vec2[0],vec2[1],vec2[2],el->m_sLabel,el->m_sLabel);
5103
mfprintf(b," pigment { rgbft atom_color_halo2 } finish { reflection atom_reflect_halo2 specular atom_specular_halo2 ambient atom_ambient_halo2 diffuse atom_diffuse_halo2 } no_reflection no_radiosity }\n");
5104
mfprintf(b,"#end\n");
5105
5106
mfprintf(b,"#if (atom_draw_halo3)\n");
5107
mfprintf(b," disc { < %g - (%g) * atom_d_halo3, %g - (%g) * atom_d_halo3, %g - (%g) * atom_d_halo3 >,\n",vec1[0],vec2[0],vec1[1],vec2[1],vec1[2],vec2[2]);
5108
mfprintf(b," < %g, %g, %g >, (elem_%s_r * atom_r) + atom_r_halo1 + atom_r_halo2 + atom_r_halo3, elem_%s_r * atom_r\n",vec2[0],vec2[1],vec2[2],el->m_sLabel,el->m_sLabel);
5109
mfprintf(b," pigment { rgbft atom_color_halo3 } finish { reflection atom_reflect_halo3 specular atom_specular_halo3 ambient atom_ambient_halo3 diffuse atom_diffuse_halo3 } no_reflection no_radiosity }\n");
5110
mfprintf(b,"#end\n");
5111
}
5112
}
5113
}
5114
5115
for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)
5116
{
5117
mb = (CMolBond*)sm->m_oaBonds[z3];
5118
o = mb->m_iAtomOffset[0];
5119
o2 = mb->m_iAtomOffset[1];
5120
5121
el = ((CAtom*)g_oaAtoms[g_waAtomRealElement[o]])->m_pElement;
5122
el2 = ((CAtom*)g_oaAtoms[g_waAtomRealElement[o2]])->m_pElement;
5123
5124
vec1 = m_vaCoords[o];
5125
vec1 /= 1000.0;
5126
5127
vec2 = m_vaCoords[o2];
5128
vec2 /= 1000.0;
5129
5130
if ((vec1-vec2).GetLength() > 0.3)
5131
continue;
5132
5133
vec3 = (vec1/el->m_fRadius + vec2/el2->m_fRadius) / (1.0/el->m_fRadius+1.0/el2->m_fRadius);
5134
5135
vec3b = vec2 - vec1;
5136
vec3b.Normalize();
5137
5138
mfprintf(b,"#local vec1c = < %g + (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ),\n",vec1[0],vec3b[0],el->m_sLabel,el->m_sLabel,el->m_sLabel,el->m_sLabel);
5139
mfprintf(b," %g + (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ),\n",vec1[1],vec3b[1],el->m_sLabel,el->m_sLabel,el->m_sLabel,el->m_sLabel);
5140
mfprintf(b," %g + (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ) >;\n",vec1[2],vec3b[2],el->m_sLabel,el->m_sLabel,el->m_sLabel,el->m_sLabel);
5141
mfprintf(b,"#local vec2c = < %g - (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ),\n",vec2[0],vec3b[0],el2->m_sLabel,el2->m_sLabel,el2->m_sLabel,el2->m_sLabel);
5142
mfprintf(b," %g - (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ),\n",vec2[1],vec3b[1],el2->m_sLabel,el2->m_sLabel,el2->m_sLabel,el2->m_sLabel);
5143
mfprintf(b," %g - (%g) * ( elem_%s_r*atom_r - ( elem_%s_r*atom_r - 0.5*sqrt(4*elem_%s_r*elem_%s_r*atom_r*atom_r - 4*bond_r*bond_r ) ) ) >;\n",vec2[2],vec3b[2],el2->m_sLabel,el2->m_sLabel,el2->m_sLabel,el2->m_sLabel);
5144
5145
mfprintf(b,"#if (bond_draw)\n");
5146
mfprintf(b," cylinder { < %g, %g, %g >, vec1c, bond_r open\n",vec3[0],vec3[1],vec3[2]);
5147
mfprintf(b," pigment { rgbft m_atom_color(elem_%s_col) } finish { reflection bond_reflect specular bond_specular ambient bond_ambient diffuse bond_diffuse } }\n",el->m_sLabel);
5148
mfprintf(b," cylinder { < %g, %g, %g >, vec2c, bond_r open\n",vec3[0],vec3[1],vec3[2]);
5149
mfprintf(b," pigment { rgbft m_atom_color(elem_%s_col) } finish { reflection bond_reflect specular bond_specular ambient bond_ambient diffuse bond_diffuse } }\n",el2->m_sLabel);
5150
mfprintf(b,"#end\n");
5151
5152
vec3 = cam - (vec1 + vec2) / 2.0;
5153
vec3.Normalize();
5154
5155
vec2b = vec2-vec1;
5156
vec1b = CrossP(vec3,vec2b);
5157
vec1b.Normalize();
5158
5159
mfprintf(b,"#local vec3 = < %g, %g, %g >;\n",vec3[0],vec3[1],vec3[2]);
5160
mfprintf(b,"#local vec1b = < %g, %g, %g >;\n",vec1b[0],vec1b[1],vec1b[2]);
5161
5162
// if (shadow)
5163
{
5164
mfprintf(b,"#if (bond_draw_halo1)\n");
5165
mfprintf(b," #local vecA = vec1c + vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo1;\n");
5166
mfprintf(b," #local vecB = vec2c + vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo1;\n");
5167
mfprintf(b," #local vecC = vec2c + vec1b * (bond_r) - vec3 * bond_d_halo1;\n");
5168
mfprintf(b," #local vecD = vec1c + vec1b * (bond_r) - vec3 * bond_d_halo1;\n");
5169
mfprintf(b," triangle { vecA, vecB, vecC\n");
5170
mfprintf(b," pigment { rgbft bond_color_halo1 } finish { reflection bond_reflect_halo1 specular bond_specular_halo1 ambient bond_ambient_halo1 diffuse bond_diffuse_halo1 } no_reflection no_radiosity }\n");
5171
mfprintf(b," triangle { vecA, vecD, vecC\n");
5172
mfprintf(b," pigment { rgbft bond_color_halo1 } finish { reflection bond_reflect_halo1 specular bond_specular_halo1 ambient bond_ambient_halo1 diffuse bond_diffuse_halo1 } no_reflection no_radiosity }\n");
5173
mfprintf(b," #local vecA = vec1c - vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo1;\n");
5174
mfprintf(b," #local vecB = vec2c - vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo1;\n");
5175
mfprintf(b," #local vecC = vec2c - vec1b * (bond_r) - vec3 * bond_d_halo1;\n");
5176
mfprintf(b," #local vecD = vec1c - vec1b * (bond_r) - vec3 * bond_d_halo1;\n");
5177
mfprintf(b," triangle { vecA, vecB, vecC\n");
5178
mfprintf(b," pigment { rgbft bond_color_halo1 } finish { reflection bond_reflect_halo1 specular bond_specular_halo1 ambient bond_ambient_halo1 diffuse bond_diffuse_halo1 } no_reflection no_radiosity }\n");
5179
mfprintf(b," triangle { vecA, vecD, vecC\n");
5180
mfprintf(b," pigment { rgbft bond_color_halo1 } finish { reflection bond_reflect_halo1 specular bond_specular_halo1 ambient bond_ambient_halo1 diffuse bond_diffuse_halo1 } no_reflection no_radiosity }\n");
5181
mfprintf(b,"#end\n");
5182
}
5183
5184
// if (halo)
5185
{
5186
mfprintf(b,"#if (bond_draw_halo2)\n");
5187
mfprintf(b," #local vecA = vec1c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5188
mfprintf(b," #local vecB = vec2c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5189
mfprintf(b," #local vecC = vec2c + vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo2;\n");
5190
mfprintf(b," #local vecD = vec1c + vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo2;\n");
5191
mfprintf(b," triangle { vecA, vecB, vecC\n");
5192
mfprintf(b," pigment { rgbft bond_color_halo2 } finish { reflection bond_reflect_halo2 specular bond_specular_halo2 ambient bond_ambient_halo2 diffuse bond_diffuse_halo2 } no_reflection no_radiosity }\n");
5193
mfprintf(b," triangle { vecA, vecD, vecC\n");
5194
mfprintf(b," pigment { rgbft bond_color_halo2 } finish { reflection bond_reflect_halo2 specular bond_specular_halo2 ambient bond_ambient_halo2 diffuse bond_diffuse_halo2 } no_reflection no_radiosity }\n");
5195
mfprintf(b," #local vecA = vec1c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5196
mfprintf(b," #local vecB = vec2c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5197
mfprintf(b," #local vecC = vec2c - vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo2;\n");
5198
mfprintf(b," #local vecD = vec1c - vec1b * (bond_r + bond_r_halo1) - vec3 * bond_d_halo2;\n");
5199
mfprintf(b," triangle { vecA, vecB, vecC\n");
5200
mfprintf(b," pigment { rgbft bond_color_halo2 } finish { reflection bond_reflect_halo2 specular bond_specular_halo2 ambient bond_ambient_halo2 diffuse bond_diffuse_halo2 } no_reflection no_radiosity }\n");
5201
mfprintf(b," triangle { vecA, vecD, vecC\n");
5202
mfprintf(b," pigment { rgbft bond_color_halo2 } finish { reflection bond_reflect_halo2 specular bond_specular_halo2 ambient bond_ambient_halo2 diffuse bond_diffuse_halo2 } no_reflection no_radiosity }\n");
5203
mfprintf(b,"#end\n");
5204
5205
mfprintf(b,"#if (bond_draw_halo3)\n");
5206
mfprintf(b," #local vecA = vec1c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2 + bond_r_halo3) - vec3 * bond_d_halo2;\n");
5207
mfprintf(b," #local vecB = vec2c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2 + bond_r_halo3) - vec3 * bond_d_halo2;\n");
5208
mfprintf(b," #local vecC = vec2c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5209
mfprintf(b," #local vecD = vec1c + vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5210
mfprintf(b," triangle { vecA, vecB, vecC\n");
5211
mfprintf(b," pigment { rgbft bond_color_halo3 } finish { reflection bond_reflect_halo3 specular bond_specular_halo3 ambient bond_ambient_halo3 diffuse bond_diffuse_halo3 } no_reflection no_radiosity }\n");
5212
mfprintf(b," triangle { vecA, vecD, vecC\n");
5213
mfprintf(b," pigment { rgbft bond_color_halo3 } finish { reflection bond_reflect_halo3 specular bond_specular_halo3 ambient bond_ambient_halo3 diffuse bond_diffuse_halo3 } no_reflection no_radiosity }\n");
5214
mfprintf(b," #local vecA = vec1c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2 + bond_r_halo3) - vec3 * bond_d_halo2;\n");
5215
mfprintf(b," #local vecB = vec2c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2 + bond_r_halo3) - vec3 * bond_d_halo2;\n");
5216
mfprintf(b," #local vecC = vec2c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5217
mfprintf(b," #local vecD = vec1c - vec1b * (bond_r + bond_r_halo1 + bond_r_halo2) - vec3 * bond_d_halo2;\n");
5218
mfprintf(b," triangle { vecA, vecB, vecC\n");
5219
mfprintf(b," pigment { rgbft bond_color_halo3 } finish { reflection bond_reflect_halo3 specular bond_specular_halo3 ambient bond_ambient_halo3 diffuse bond_diffuse_halo3 } no_reflection no_radiosity }\n");
5220
mfprintf(b," triangle { vecA, vecD, vecC\n");
5221
mfprintf(b," pigment { rgbft bond_color_halo3 } finish { reflection bond_reflect_halo3 specular bond_specular_halo3 ambient bond_ambient_halo3 diffuse bond_diffuse_halo3 } no_reflection no_radiosity }\n");
5222
mfprintf(b,"#end\n");
5223
}
5224
5225
// if (shadow)
5226
{
5227
vec3 = vec2 - vec1;
5228
vec3.Normalize();
5229
5230
mfprintf(b,"#if (bond_draw_stub)\n");
5231
mfprintf(b," #local vec3 = < %g, %g, %g >;\n",vec3[0],vec3[1],vec3[2]);
5232
mfprintf(b," difference {\n");
5233
mfprintf(b," cylinder { vec1c, vec1c + vec3 * bond_l_stub, bond_r + bond_r_stub }\n");
5234
mfprintf(b," cylinder { vec1c - vec3 * (bond_l_stub+0.001), vec1c + vec3 * (bond_l_stub+0.001), bond_r }\n");
5235
mfprintf(b," pigment { rgbft bond_color_stub } finish { reflection bond_reflect_stub specular bond_specular_stub ambient bond_ambient_stub diffuse bond_diffuse_stub } }\n");
5236
mfprintf(b," difference {\n");
5237
mfprintf(b," cylinder { vec2c, vec2c - vec3 * bond_l_stub, bond_r + bond_r_stub }\n");
5238
mfprintf(b," cylinder { vec2c + vec3 * (bond_l_stub+0.001), vec2c - vec3 * (bond_l_stub+0.001), bond_r }\n");
5239
mfprintf(b," pigment { rgbft bond_color_stub } finish { reflection bond_reflect_stub specular bond_specular_stub ambient bond_ambient_stub diffuse bond_diffuse_stub } }\n");
5240
mfprintf(b,"#end\n");
5241
}
5242
}
5243
}
5244
}
5245
5246
mfprintf(b,"\n no_shadow\n}\n\n");
5247
5248
fclose(b);
5249
}
5250
5251
5252
void CTimeStep::DumpDipoles()
5253
{
5254
int z, z2, z3, z4, ti;
5255
CMolecule *m;
5256
CSingleMolecule *sm;
5257
CxVector3 dc;
5258
5259
if (!(g_bDipole && g_bDumpDipoleVector))
5260
return;
5261
5262
fprintf(g_fDumpDipole,"%lu",g_iSteps);
5263
for (z=0;z<g_oaMolecules.GetSize();z++)
5264
{
5265
if (g_oaDumpDipoleVector[z] == NULL)
5266
continue;
5267
m = (CMolecule*)g_oaMolecules[z];
5268
for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)
5269
{
5270
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[((CxIntArray*)g_oaDumpDipoleVector[z])->GetAt(z2)]];
5271
fprintf(g_fDumpDipole,"; %10G; %10G; %10G",sm->m_vDipole[0],sm->m_vDipole[1],sm->m_vDipole[2]);
5272
if (g_bDumpDipoleAbs)
5273
fprintf(g_fDumpDipole,"; %10G",sm->m_vDipole.GetLength());
5274
}
5275
}
5276
fprintf(g_fDumpDipole,"\n");
5277
5278
if (g_bDumpDipoleXYZ)
5279
{
5280
fprintf(g_fDumpDipoleXYZ,"%d\n\n",g_iDumpDipoleXYZAtoms);
5281
for (z=0;z<g_oaMolecules.GetSize();z++)
5282
{
5283
if (g_oaDumpDipoleVector[z] == NULL)
5284
continue;
5285
m = (CMolecule*)g_oaMolecules[z];
5286
for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)
5287
{
5288
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[((CxIntArray*)g_oaDumpDipoleVector[z])->GetAt(z2)]];
5289
5290
for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)
5291
{
5292
if (m->m_baAtomIndex[z3] == g_iVirtAtomType)
5293
continue;
5294
for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)
5295
{
5296
ti = ((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4);
5297
fprintf(g_fDumpDipoleXYZ,"%s %12f %12f %12f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,m_vaCoords[ti][0]/100.0,m_vaCoords[ti][1]/100.0,m_vaCoords[ti][2]/100.0);
5298
}
5299
}
5300
}
5301
}
5302
5303
for (z=0;z<g_oaMolecules.GetSize();z++)
5304
{
5305
if (g_oaDumpDipoleVector[z] == NULL)
5306
continue;
5307
m = (CMolecule*)g_oaMolecules[z];
5308
for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)
5309
{
5310
sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[((CxIntArray*)g_oaDumpDipoleVector[z])->GetAt(z2)]];
5311
dc = m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[m->m_iDipoleCenterType])->GetAt(m->m_iDipoleCenterIndex)];
5312
fprintf(g_fDumpDipoleXYZ,"B %12f %12f %12f\n",dc[0]/100.0,dc[1]/100.0,dc[2]/100.0);
5313
fprintf(g_fDumpDipoleXYZ,"B %12f %12f %12f\n",dc[0]/100.0+sm->m_vDipole[0]*g_fDumpDipoleScale,dc[1]/100.0+sm->m_vDipole[1]*g_fDumpDipoleScale,dc[2]/100.0+sm->m_vDipole[2]*g_fDumpDipoleScale);
5314
}
5315
}
5316
}
5317
}
5318
5319
5320
CTimeStep::CTimeStep()
5321
{
5322
m_pComment = NULL;
5323
5324
m_vaCoords.SetName("CTimeStep::m_vaCoords");
5325
m_vaCoords_Unfolded.SetName("CTimeStep::m_vaCoords_Unfolded");
5326
m_vaCoords_Original.SetName("CTimeStep::m_vaCoords_Original");
5327
m_vaVelocities.SetName("CTimeStep::m_vaVelocities");
5328
m_vaForces.SetName("CTimeStep::m_vaForces");
5329
m_paLabels.SetName("CTimeStep::m_paLabels");
5330
m_paMol2Types.SetName("CTimeStep::m_paMol2Types");
5331
m_faCharge.SetName("CTimeStep::m_faCharge");
5332
}
5333
5334
5335
CTimeStep::~CTimeStep()
5336
{
5337
/* if (m_pLabels != NULL)
5338
delete[] m_pLabels;*/
5339
if (m_pComment != NULL)
5340
delete[] m_pComment;
5341
}
5342
Loggerhead is a web-based interface for Breezy
Version: 2.0.1