1 |
mmeineke |
377 |
#include <cstdlib> |
2 |
|
|
#include <iostream> |
3 |
|
|
#include <cmath> |
4 |
|
|
|
5 |
|
|
#include "SimSetup.hpp" |
6 |
|
|
#include "parse_me.h" |
7 |
|
|
#include "Integrator.hpp" |
8 |
|
|
#include "simError.h" |
9 |
|
|
|
10 |
|
|
#ifdef IS_MPI |
11 |
|
|
#include "mpiBASS.h" |
12 |
|
|
#include "mpiSimulation.hpp" |
13 |
|
|
#endif |
14 |
|
|
|
15 |
mmeineke |
557 |
// some defines for ensemble and Forcefield cases |
16 |
|
|
|
17 |
gezelter |
604 |
#define NVE_ENS 0 |
18 |
|
|
#define NVT_ENS 1 |
19 |
|
|
#define NPTi_ENS 2 |
20 |
|
|
#define NPTf_ENS 3 |
21 |
|
|
#define NPTim_ENS 4 |
22 |
|
|
#define NPTfm_ENS 5 |
23 |
mmeineke |
557 |
|
24 |
mmeineke |
582 |
|
25 |
mmeineke |
557 |
#define FF_DUFF 0 |
26 |
|
|
#define FF_LJ 1 |
27 |
|
|
|
28 |
|
|
|
29 |
mmeineke |
377 |
SimSetup::SimSetup(){ |
30 |
|
|
stamps = new MakeStamps(); |
31 |
|
|
globals = new Globals(); |
32 |
|
|
|
33 |
|
|
#ifdef IS_MPI |
34 |
|
|
strcpy( checkPointMsg, "SimSetup creation successful" ); |
35 |
|
|
MPIcheckPoint(); |
36 |
|
|
#endif // IS_MPI |
37 |
|
|
} |
38 |
|
|
|
39 |
|
|
SimSetup::~SimSetup(){ |
40 |
|
|
delete stamps; |
41 |
|
|
delete globals; |
42 |
|
|
} |
43 |
|
|
|
44 |
|
|
void SimSetup::parseFile( char* fileName ){ |
45 |
|
|
|
46 |
|
|
#ifdef IS_MPI |
47 |
|
|
if( worldRank == 0 ){ |
48 |
|
|
#endif // is_mpi |
49 |
|
|
|
50 |
|
|
inFileName = fileName; |
51 |
|
|
set_interface_stamps( stamps, globals ); |
52 |
|
|
|
53 |
|
|
#ifdef IS_MPI |
54 |
|
|
mpiEventInit(); |
55 |
|
|
#endif |
56 |
|
|
|
57 |
|
|
yacc_BASS( fileName ); |
58 |
|
|
|
59 |
|
|
#ifdef IS_MPI |
60 |
|
|
throwMPIEvent(NULL); |
61 |
|
|
} |
62 |
|
|
else receiveParse(); |
63 |
|
|
#endif |
64 |
|
|
|
65 |
|
|
} |
66 |
|
|
|
67 |
|
|
#ifdef IS_MPI |
68 |
|
|
void SimSetup::receiveParse(void){ |
69 |
|
|
|
70 |
|
|
set_interface_stamps( stamps, globals ); |
71 |
|
|
mpiEventInit(); |
72 |
|
|
MPIcheckPoint(); |
73 |
|
|
mpiEventLoop(); |
74 |
|
|
|
75 |
|
|
} |
76 |
|
|
|
77 |
|
|
#endif // is_mpi |
78 |
|
|
|
79 |
|
|
void SimSetup::createSim( void ){ |
80 |
|
|
|
81 |
|
|
MakeStamps *the_stamps; |
82 |
|
|
Globals* the_globals; |
83 |
gezelter |
490 |
int i, j, k, globalAtomIndex; |
84 |
mmeineke |
557 |
|
85 |
mmeineke |
614 |
// gather all of the information from the Bass file |
86 |
mmeineke |
557 |
|
87 |
mmeineke |
614 |
gatherInfo(); |
88 |
mmeineke |
377 |
|
89 |
mmeineke |
614 |
// creation of complex system objects |
90 |
mmeineke |
377 |
|
91 |
mmeineke |
614 |
sysObjectsCreation(); |
92 |
mmeineke |
377 |
|
93 |
gezelter |
466 |
|
94 |
mmeineke |
557 |
|
95 |
mmeineke |
377 |
// initialize the arrays |
96 |
|
|
|
97 |
mmeineke |
614 |
|
98 |
mmeineke |
377 |
|
99 |
mmeineke |
422 |
makeMolecules(); |
100 |
mmeineke |
614 |
info->identArray = new int[info->n_atoms]; |
101 |
|
|
for(i=0; i<info->n_atoms; i++){ |
102 |
|
|
info->identArray[i] = the_atoms[i]->getIdent(); |
103 |
mmeineke |
377 |
} |
104 |
|
|
|
105 |
mmeineke |
614 |
|
106 |
|
|
// check on the post processing info |
107 |
gezelter |
394 |
|
108 |
mmeineke |
614 |
finalInfoCheck(); |
109 |
mmeineke |
377 |
|
110 |
|
|
|
111 |
|
|
|
112 |
|
|
|
113 |
mmeineke |
614 |
// initialize the system coordinates |
114 |
mmeineke |
377 |
|
115 |
mmeineke |
614 |
initSystemCoords(); |
116 |
mmeineke |
377 |
|
117 |
|
|
|
118 |
mmeineke |
614 |
// make the output filenames |
119 |
mmeineke |
377 |
|
120 |
mmeineke |
614 |
makeOutNames(); |
121 |
mmeineke |
377 |
|
122 |
|
|
|
123 |
|
|
|
124 |
|
|
|
125 |
|
|
|
126 |
mmeineke |
614 |
|
127 |
mmeineke |
377 |
|
128 |
|
|
|
129 |
|
|
|
130 |
mmeineke |
555 |
// make the integrator |
131 |
mmeineke |
561 |
|
132 |
|
|
|
133 |
mmeineke |
586 |
NVT* myNVT = NULL; |
134 |
|
|
NPTi* myNPTi = NULL; |
135 |
|
|
NPTf* myNPTf = NULL; |
136 |
gezelter |
604 |
NPTim* myNPTim = NULL; |
137 |
gezelter |
605 |
NPTfm* myNPTfm = NULL; |
138 |
gezelter |
604 |
|
139 |
mmeineke |
558 |
switch( ensembleCase ){ |
140 |
mmeineke |
377 |
|
141 |
mmeineke |
558 |
case NVE_ENS: |
142 |
mmeineke |
614 |
new NVE( info, the_ff ); |
143 |
mmeineke |
558 |
break; |
144 |
|
|
|
145 |
mmeineke |
561 |
case NVT_ENS: |
146 |
mmeineke |
614 |
myNVT = new NVT( info, the_ff ); |
147 |
mmeineke |
561 |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
148 |
|
|
|
149 |
|
|
if (the_globals->haveTauThermostat()) |
150 |
|
|
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
151 |
mmeineke |
586 |
|
152 |
mmeineke |
561 |
else { |
153 |
|
|
sprintf( painCave.errMsg, |
154 |
|
|
"SimSetup error: If you use the NVT\n" |
155 |
mmeineke |
586 |
" ensemble, you must set tauThermostat.\n"); |
156 |
mmeineke |
561 |
painCave.isFatal = 1; |
157 |
|
|
simError(); |
158 |
|
|
} |
159 |
|
|
break; |
160 |
|
|
|
161 |
mmeineke |
586 |
case NPTi_ENS: |
162 |
mmeineke |
614 |
myNPTi = new NPTi( info, the_ff ); |
163 |
|
|
myNPTi->setTargetTemp( the_globals->getTargetTemp() ); |
164 |
mmeineke |
586 |
|
165 |
|
|
if (the_globals->haveTargetPressure()) |
166 |
|
|
myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
167 |
|
|
else { |
168 |
|
|
sprintf( painCave.errMsg, |
169 |
|
|
"SimSetup error: If you use a constant pressure\n" |
170 |
|
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
171 |
|
|
painCave.isFatal = 1; |
172 |
|
|
simError(); |
173 |
|
|
} |
174 |
|
|
|
175 |
|
|
if( the_globals->haveTauThermostat() ) |
176 |
|
|
myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
177 |
|
|
else{ |
178 |
|
|
sprintf( painCave.errMsg, |
179 |
|
|
"SimSetup error: If you use an NPT\n" |
180 |
|
|
" ensemble, you must set tauThermostat.\n"); |
181 |
|
|
painCave.isFatal = 1; |
182 |
|
|
simError(); |
183 |
|
|
} |
184 |
|
|
|
185 |
|
|
if( the_globals->haveTauBarostat() ) |
186 |
|
|
myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
187 |
|
|
else{ |
188 |
|
|
sprintf( painCave.errMsg, |
189 |
|
|
"SimSetup error: If you use an NPT\n" |
190 |
|
|
" ensemble, you must set tauBarostat.\n"); |
191 |
|
|
painCave.isFatal = 1; |
192 |
|
|
simError(); |
193 |
|
|
} |
194 |
|
|
break; |
195 |
|
|
|
196 |
|
|
case NPTf_ENS: |
197 |
mmeineke |
614 |
myNPTf = new NPTf( info, the_ff ); |
198 |
mmeineke |
586 |
myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
199 |
|
|
|
200 |
|
|
if (the_globals->haveTargetPressure()) |
201 |
|
|
myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
202 |
|
|
else { |
203 |
|
|
sprintf( painCave.errMsg, |
204 |
|
|
"SimSetup error: If you use a constant pressure\n" |
205 |
|
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
206 |
|
|
painCave.isFatal = 1; |
207 |
|
|
simError(); |
208 |
|
|
} |
209 |
|
|
|
210 |
|
|
if( the_globals->haveTauThermostat() ) |
211 |
|
|
myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
212 |
|
|
else{ |
213 |
|
|
sprintf( painCave.errMsg, |
214 |
|
|
"SimSetup error: If you use an NPT\n" |
215 |
|
|
" ensemble, you must set tauThermostat.\n"); |
216 |
|
|
painCave.isFatal = 1; |
217 |
|
|
simError(); |
218 |
|
|
} |
219 |
|
|
|
220 |
|
|
if( the_globals->haveTauBarostat() ) |
221 |
|
|
myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
222 |
|
|
else{ |
223 |
|
|
sprintf( painCave.errMsg, |
224 |
|
|
"SimSetup error: If you use an NPT\n" |
225 |
|
|
" ensemble, you must set tauBarostat.\n"); |
226 |
|
|
painCave.isFatal = 1; |
227 |
|
|
simError(); |
228 |
|
|
} |
229 |
|
|
break; |
230 |
|
|
|
231 |
gezelter |
604 |
case NPTim_ENS: |
232 |
mmeineke |
614 |
myNPTim = new NPTim( info, the_ff ); |
233 |
gezelter |
604 |
myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
234 |
|
|
|
235 |
|
|
if (the_globals->haveTargetPressure()) |
236 |
|
|
myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
237 |
|
|
else { |
238 |
|
|
sprintf( painCave.errMsg, |
239 |
|
|
"SimSetup error: If you use a constant pressure\n" |
240 |
|
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
241 |
|
|
painCave.isFatal = 1; |
242 |
|
|
simError(); |
243 |
|
|
} |
244 |
mmeineke |
586 |
|
245 |
gezelter |
604 |
if( the_globals->haveTauThermostat() ) |
246 |
|
|
myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
247 |
|
|
else{ |
248 |
|
|
sprintf( painCave.errMsg, |
249 |
|
|
"SimSetup error: If you use an NPT\n" |
250 |
|
|
" ensemble, you must set tauThermostat.\n"); |
251 |
|
|
painCave.isFatal = 1; |
252 |
|
|
simError(); |
253 |
|
|
} |
254 |
mmeineke |
586 |
|
255 |
gezelter |
604 |
if( the_globals->haveTauBarostat() ) |
256 |
|
|
myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
257 |
|
|
else{ |
258 |
|
|
sprintf( painCave.errMsg, |
259 |
|
|
"SimSetup error: If you use an NPT\n" |
260 |
|
|
" ensemble, you must set tauBarostat.\n"); |
261 |
|
|
painCave.isFatal = 1; |
262 |
|
|
simError(); |
263 |
|
|
} |
264 |
|
|
break; |
265 |
|
|
|
266 |
gezelter |
605 |
case NPTfm_ENS: |
267 |
mmeineke |
614 |
myNPTfm = new NPTfm( info, the_ff ); |
268 |
gezelter |
605 |
myNPTfm->setTargetTemp( the_globals->getTargetTemp()); |
269 |
|
|
|
270 |
|
|
if (the_globals->haveTargetPressure()) |
271 |
|
|
myNPTfm->setTargetPressure(the_globals->getTargetPressure()); |
272 |
|
|
else { |
273 |
|
|
sprintf( painCave.errMsg, |
274 |
|
|
"SimSetup error: If you use a constant pressure\n" |
275 |
|
|
" ensemble, you must set targetPressure in the BASS file.\n"); |
276 |
|
|
painCave.isFatal = 1; |
277 |
|
|
simError(); |
278 |
|
|
} |
279 |
gezelter |
604 |
|
280 |
gezelter |
605 |
if( the_globals->haveTauThermostat() ) |
281 |
|
|
myNPTfm->setTauThermostat( the_globals->getTauThermostat() ); |
282 |
|
|
else{ |
283 |
|
|
sprintf( painCave.errMsg, |
284 |
|
|
"SimSetup error: If you use an NPT\n" |
285 |
|
|
" ensemble, you must set tauThermostat.\n"); |
286 |
|
|
painCave.isFatal = 1; |
287 |
|
|
simError(); |
288 |
|
|
} |
289 |
gezelter |
604 |
|
290 |
gezelter |
605 |
if( the_globals->haveTauBarostat() ) |
291 |
|
|
myNPTfm->setTauBarostat( the_globals->getTauBarostat() ); |
292 |
|
|
else{ |
293 |
|
|
sprintf( painCave.errMsg, |
294 |
|
|
"SimSetup error: If you use an NPT\n" |
295 |
|
|
" ensemble, you must set tauBarostat.\n"); |
296 |
|
|
painCave.isFatal = 1; |
297 |
|
|
simError(); |
298 |
|
|
} |
299 |
|
|
break; |
300 |
|
|
|
301 |
mmeineke |
558 |
default: |
302 |
|
|
sprintf( painCave.errMsg, |
303 |
|
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
304 |
|
|
painCave.isFatal = 1; |
305 |
|
|
simError(); |
306 |
mmeineke |
469 |
} |
307 |
mmeineke |
504 |
|
308 |
mmeineke |
558 |
|
309 |
chuckv |
432 |
#ifdef IS_MPI |
310 |
|
|
mpiSim->mpiRefresh(); |
311 |
|
|
#endif |
312 |
mmeineke |
377 |
|
313 |
chuckv |
432 |
// initialize the Fortran |
314 |
mmeineke |
377 |
|
315 |
chuckv |
432 |
|
316 |
mmeineke |
614 |
info->refreshSim(); |
317 |
mmeineke |
377 |
|
318 |
mmeineke |
614 |
if( !strcmp( info->mixingRule, "standard") ){ |
319 |
mmeineke |
377 |
the_ff->initForceField( LB_MIXING_RULE ); |
320 |
|
|
} |
321 |
mmeineke |
614 |
else if( !strcmp( info->mixingRule, "explicit") ){ |
322 |
mmeineke |
377 |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
323 |
|
|
} |
324 |
|
|
else{ |
325 |
|
|
sprintf( painCave.errMsg, |
326 |
|
|
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
327 |
mmeineke |
614 |
info->mixingRule ); |
328 |
mmeineke |
377 |
painCave.isFatal = 1; |
329 |
|
|
simError(); |
330 |
|
|
} |
331 |
|
|
|
332 |
|
|
|
333 |
|
|
#ifdef IS_MPI |
334 |
|
|
strcpy( checkPointMsg, |
335 |
|
|
"Successfully intialized the mixingRule for Fortran." ); |
336 |
|
|
MPIcheckPoint(); |
337 |
|
|
#endif // is_mpi |
338 |
|
|
} |
339 |
|
|
|
340 |
mmeineke |
407 |
|
341 |
|
|
void SimSetup::makeMolecules( void ){ |
342 |
|
|
|
343 |
mmeineke |
412 |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
344 |
mmeineke |
407 |
molInit info; |
345 |
|
|
DirectionalAtom* dAtom; |
346 |
mmeineke |
412 |
LinkedAssign* extras; |
347 |
|
|
LinkedAssign* current_extra; |
348 |
mmeineke |
407 |
AtomStamp* currentAtom; |
349 |
|
|
BondStamp* currentBond; |
350 |
|
|
BendStamp* currentBend; |
351 |
|
|
TorsionStamp* currentTorsion; |
352 |
mmeineke |
427 |
|
353 |
|
|
bond_pair* theBonds; |
354 |
|
|
bend_set* theBends; |
355 |
|
|
torsion_set* theTorsions; |
356 |
|
|
|
357 |
mmeineke |
407 |
|
358 |
|
|
//init the forceField paramters |
359 |
|
|
|
360 |
|
|
the_ff->readParams(); |
361 |
|
|
|
362 |
|
|
|
363 |
mmeineke |
427 |
// init the atoms |
364 |
mmeineke |
407 |
|
365 |
mmeineke |
427 |
double ux, uy, uz, u, uSqr; |
366 |
|
|
|
367 |
mmeineke |
407 |
atomOffset = 0; |
368 |
mmeineke |
412 |
excludeOffset = 0; |
369 |
mmeineke |
614 |
for(i=0; i<info->n_mol; i++){ |
370 |
mmeineke |
407 |
|
371 |
|
|
stampID = the_molecules[i].getStampID(); |
372 |
|
|
|
373 |
|
|
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
374 |
|
|
info.nBonds = comp_stamps[stampID]->getNBonds(); |
375 |
|
|
info.nBends = comp_stamps[stampID]->getNBends(); |
376 |
|
|
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
377 |
mmeineke |
412 |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
378 |
|
|
|
379 |
mmeineke |
407 |
info.myAtoms = &the_atoms[atomOffset]; |
380 |
mmeineke |
412 |
info.myExcludes = &the_excludes[excludeOffset]; |
381 |
mmeineke |
407 |
info.myBonds = new Bond*[info.nBonds]; |
382 |
|
|
info.myBends = new Bend*[info.nBends]; |
383 |
mmeineke |
427 |
info.myTorsions = new Torsion*[info.nTorsions]; |
384 |
mmeineke |
407 |
|
385 |
|
|
theBonds = new bond_pair[info.nBonds]; |
386 |
|
|
theBends = new bend_set[info.nBends]; |
387 |
|
|
theTorsions = new torsion_set[info.nTorsions]; |
388 |
|
|
|
389 |
|
|
// make the Atoms |
390 |
|
|
|
391 |
|
|
for(j=0; j<info.nAtoms; j++){ |
392 |
|
|
|
393 |
mmeineke |
427 |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
394 |
mmeineke |
407 |
if( currentAtom->haveOrientation() ){ |
395 |
|
|
|
396 |
|
|
dAtom = new DirectionalAtom(j + atomOffset); |
397 |
mmeineke |
614 |
info->n_oriented++; |
398 |
mmeineke |
407 |
info.myAtoms[j] = dAtom; |
399 |
|
|
|
400 |
|
|
ux = currentAtom->getOrntX(); |
401 |
|
|
uy = currentAtom->getOrntY(); |
402 |
|
|
uz = currentAtom->getOrntZ(); |
403 |
|
|
|
404 |
|
|
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
405 |
|
|
|
406 |
|
|
u = sqrt( uSqr ); |
407 |
|
|
ux = ux / u; |
408 |
|
|
uy = uy / u; |
409 |
|
|
uz = uz / u; |
410 |
|
|
|
411 |
|
|
dAtom->setSUx( ux ); |
412 |
|
|
dAtom->setSUy( uy ); |
413 |
|
|
dAtom->setSUz( uz ); |
414 |
|
|
} |
415 |
|
|
else{ |
416 |
|
|
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
417 |
|
|
} |
418 |
|
|
info.myAtoms[j]->setType( currentAtom->getType() ); |
419 |
|
|
|
420 |
|
|
#ifdef IS_MPI |
421 |
|
|
|
422 |
|
|
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
423 |
|
|
|
424 |
|
|
#endif // is_mpi |
425 |
|
|
} |
426 |
|
|
|
427 |
|
|
// make the bonds |
428 |
mmeineke |
412 |
for(j=0; j<info.nBonds; j++){ |
429 |
mmeineke |
407 |
|
430 |
|
|
currentBond = comp_stamps[stampID]->getBond( j ); |
431 |
|
|
theBonds[j].a = currentBond->getA() + atomOffset; |
432 |
|
|
theBonds[j].b = currentBond->getB() + atomOffset; |
433 |
|
|
|
434 |
mmeineke |
435 |
exI = theBonds[j].a; |
435 |
|
|
exJ = theBonds[j].b; |
436 |
mmeineke |
407 |
|
437 |
|
|
// exclude_I must always be the smaller of the pair |
438 |
|
|
if( exI > exJ ){ |
439 |
|
|
tempEx = exI; |
440 |
|
|
exI = exJ; |
441 |
|
|
exJ = tempEx; |
442 |
|
|
} |
443 |
|
|
#ifdef IS_MPI |
444 |
mmeineke |
412 |
tempEx = exI; |
445 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
446 |
|
|
tempEx = exJ; |
447 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
448 |
mmeineke |
407 |
|
449 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
450 |
|
|
#else // isn't MPI |
451 |
mmeineke |
435 |
|
452 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
453 |
|
|
#endif //is_mpi |
454 |
|
|
} |
455 |
|
|
excludeOffset += info.nBonds; |
456 |
|
|
|
457 |
|
|
//make the bends |
458 |
|
|
for(j=0; j<info.nBends; j++){ |
459 |
mmeineke |
407 |
|
460 |
mmeineke |
412 |
currentBend = comp_stamps[stampID]->getBend( j ); |
461 |
|
|
theBends[j].a = currentBend->getA() + atomOffset; |
462 |
|
|
theBends[j].b = currentBend->getB() + atomOffset; |
463 |
|
|
theBends[j].c = currentBend->getC() + atomOffset; |
464 |
|
|
|
465 |
|
|
if( currentBend->haveExtras() ){ |
466 |
|
|
|
467 |
mmeineke |
427 |
extras = currentBend->getExtras(); |
468 |
mmeineke |
412 |
current_extra = extras; |
469 |
|
|
|
470 |
|
|
while( current_extra != NULL ){ |
471 |
|
|
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
472 |
|
|
|
473 |
|
|
switch( current_extra->getType() ){ |
474 |
|
|
|
475 |
|
|
case 0: |
476 |
|
|
theBends[j].ghost = |
477 |
|
|
current_extra->getInt() + atomOffset; |
478 |
|
|
theBends[j].isGhost = 1; |
479 |
|
|
break; |
480 |
|
|
|
481 |
|
|
case 1: |
482 |
|
|
theBends[j].ghost = |
483 |
|
|
(int)current_extra->getDouble() + atomOffset; |
484 |
|
|
theBends[j].isGhost = 1; |
485 |
|
|
break; |
486 |
|
|
|
487 |
|
|
default: |
488 |
|
|
sprintf( painCave.errMsg, |
489 |
chuckv |
434 |
"SimSetup Error: ghostVectorSource was neither a " |
490 |
mmeineke |
412 |
"double nor an int.\n" |
491 |
|
|
"-->Bend[%d] in %s\n", |
492 |
|
|
j, comp_stamps[stampID]->getID() ); |
493 |
|
|
painCave.isFatal = 1; |
494 |
|
|
simError(); |
495 |
|
|
} |
496 |
|
|
} |
497 |
|
|
|
498 |
|
|
else{ |
499 |
|
|
|
500 |
|
|
sprintf( painCave.errMsg, |
501 |
|
|
"SimSetup Error: unhandled bend assignment:\n" |
502 |
|
|
" -->%s in Bend[%d] in %s\n", |
503 |
|
|
current_extra->getlhs(), |
504 |
|
|
j, comp_stamps[stampID]->getID() ); |
505 |
|
|
painCave.isFatal = 1; |
506 |
|
|
simError(); |
507 |
|
|
} |
508 |
|
|
|
509 |
|
|
current_extra = current_extra->getNext(); |
510 |
|
|
} |
511 |
|
|
} |
512 |
|
|
|
513 |
|
|
if( !theBends[j].isGhost ){ |
514 |
|
|
|
515 |
|
|
exI = theBends[j].a; |
516 |
|
|
exJ = theBends[j].c; |
517 |
|
|
} |
518 |
|
|
else{ |
519 |
|
|
|
520 |
|
|
exI = theBends[j].a; |
521 |
|
|
exJ = theBends[j].b; |
522 |
|
|
} |
523 |
|
|
|
524 |
|
|
// exclude_I must always be the smaller of the pair |
525 |
|
|
if( exI > exJ ){ |
526 |
|
|
tempEx = exI; |
527 |
|
|
exI = exJ; |
528 |
|
|
exJ = tempEx; |
529 |
|
|
} |
530 |
|
|
#ifdef IS_MPI |
531 |
|
|
tempEx = exI; |
532 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
533 |
|
|
tempEx = exJ; |
534 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
535 |
|
|
|
536 |
|
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
537 |
mmeineke |
407 |
#else // isn't MPI |
538 |
mmeineke |
412 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
539 |
|
|
#endif //is_mpi |
540 |
|
|
} |
541 |
|
|
excludeOffset += info.nBends; |
542 |
|
|
|
543 |
|
|
for(j=0; j<info.nTorsions; j++){ |
544 |
mmeineke |
407 |
|
545 |
mmeineke |
412 |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
546 |
|
|
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
547 |
|
|
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
548 |
|
|
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
549 |
|
|
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
550 |
|
|
|
551 |
|
|
exI = theTorsions[j].a; |
552 |
|
|
exJ = theTorsions[j].d; |
553 |
mmeineke |
407 |
|
554 |
mmeineke |
412 |
// exclude_I must always be the smaller of the pair |
555 |
|
|
if( exI > exJ ){ |
556 |
|
|
tempEx = exI; |
557 |
|
|
exI = exJ; |
558 |
|
|
exJ = tempEx; |
559 |
|
|
} |
560 |
|
|
#ifdef IS_MPI |
561 |
|
|
tempEx = exI; |
562 |
|
|
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
563 |
|
|
tempEx = exJ; |
564 |
|
|
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
565 |
|
|
|
566 |
|
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
567 |
|
|
#else // isn't MPI |
568 |
|
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
569 |
mmeineke |
407 |
#endif //is_mpi |
570 |
mmeineke |
412 |
} |
571 |
|
|
excludeOffset += info.nTorsions; |
572 |
|
|
|
573 |
mmeineke |
407 |
|
574 |
mmeineke |
414 |
// send the arrays off to the forceField for init. |
575 |
mmeineke |
407 |
|
576 |
mmeineke |
414 |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
577 |
|
|
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
578 |
|
|
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
579 |
|
|
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
580 |
mmeineke |
407 |
|
581 |
|
|
|
582 |
mmeineke |
414 |
the_molecules[i].initialize( info ); |
583 |
chuckv |
438 |
|
584 |
|
|
|
585 |
mmeineke |
414 |
atomOffset += info.nAtoms; |
586 |
mmeineke |
427 |
delete[] theBonds; |
587 |
|
|
delete[] theBends; |
588 |
|
|
delete[] theTorsions; |
589 |
mmeineke |
414 |
} |
590 |
mmeineke |
407 |
|
591 |
chuckv |
434 |
#ifdef IS_MPI |
592 |
|
|
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
593 |
|
|
MPIcheckPoint(); |
594 |
|
|
#endif // is_mpi |
595 |
|
|
|
596 |
mmeineke |
414 |
// clean up the forcefield |
597 |
mmeineke |
420 |
the_ff->calcRcut(); |
598 |
mmeineke |
414 |
the_ff->cleanMe(); |
599 |
chuckv |
434 |
|
600 |
mmeineke |
414 |
} |
601 |
mmeineke |
407 |
|
602 |
mmeineke |
377 |
void SimSetup::initFromBass( void ){ |
603 |
|
|
|
604 |
|
|
int i, j, k; |
605 |
|
|
int n_cells; |
606 |
|
|
double cellx, celly, cellz; |
607 |
|
|
double temp1, temp2, temp3; |
608 |
|
|
int n_per_extra; |
609 |
|
|
int n_extra; |
610 |
|
|
int have_extra, done; |
611 |
|
|
|
612 |
|
|
temp1 = (double)tot_nmol / 4.0; |
613 |
|
|
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
614 |
|
|
temp3 = ceil( temp2 ); |
615 |
|
|
|
616 |
|
|
have_extra =0; |
617 |
|
|
if( temp2 < temp3 ){ // we have a non-complete lattice |
618 |
|
|
have_extra =1; |
619 |
|
|
|
620 |
|
|
n_cells = (int)temp3 - 1; |
621 |
mmeineke |
614 |
cellx = info->boxLx / temp3; |
622 |
|
|
celly = info->boxLy / temp3; |
623 |
|
|
cellz = info->boxLz / temp3; |
624 |
mmeineke |
377 |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
625 |
|
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
626 |
|
|
n_per_extra = (int)ceil( temp1 ); |
627 |
|
|
|
628 |
|
|
if( n_per_extra > 4){ |
629 |
|
|
sprintf( painCave.errMsg, |
630 |
|
|
"SimSetup error. There has been an error in constructing" |
631 |
|
|
" the non-complete lattice.\n" ); |
632 |
|
|
painCave.isFatal = 1; |
633 |
|
|
simError(); |
634 |
|
|
} |
635 |
|
|
} |
636 |
|
|
else{ |
637 |
|
|
n_cells = (int)temp3; |
638 |
mmeineke |
614 |
cellx = info->boxLx / temp3; |
639 |
|
|
celly = info->boxLy / temp3; |
640 |
|
|
cellz = info->boxLz / temp3; |
641 |
mmeineke |
377 |
} |
642 |
|
|
|
643 |
|
|
current_mol = 0; |
644 |
|
|
current_comp_mol = 0; |
645 |
|
|
current_comp = 0; |
646 |
|
|
current_atom_ndx = 0; |
647 |
|
|
|
648 |
|
|
for( i=0; i < n_cells ; i++ ){ |
649 |
|
|
for( j=0; j < n_cells; j++ ){ |
650 |
|
|
for( k=0; k < n_cells; k++ ){ |
651 |
|
|
|
652 |
|
|
makeElement( i * cellx, |
653 |
|
|
j * celly, |
654 |
|
|
k * cellz ); |
655 |
|
|
|
656 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
657 |
|
|
j * celly + 0.5 * celly, |
658 |
|
|
k * cellz ); |
659 |
|
|
|
660 |
|
|
makeElement( i * cellx, |
661 |
|
|
j * celly + 0.5 * celly, |
662 |
|
|
k * cellz + 0.5 * cellz ); |
663 |
|
|
|
664 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
665 |
|
|
j * celly, |
666 |
|
|
k * cellz + 0.5 * cellz ); |
667 |
|
|
} |
668 |
|
|
} |
669 |
|
|
} |
670 |
|
|
|
671 |
|
|
if( have_extra ){ |
672 |
|
|
done = 0; |
673 |
|
|
|
674 |
|
|
int start_ndx; |
675 |
|
|
for( i=0; i < (n_cells+1) && !done; i++ ){ |
676 |
|
|
for( j=0; j < (n_cells+1) && !done; j++ ){ |
677 |
|
|
|
678 |
|
|
if( i < n_cells ){ |
679 |
|
|
|
680 |
|
|
if( j < n_cells ){ |
681 |
|
|
start_ndx = n_cells; |
682 |
|
|
} |
683 |
|
|
else start_ndx = 0; |
684 |
|
|
} |
685 |
|
|
else start_ndx = 0; |
686 |
|
|
|
687 |
|
|
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
688 |
|
|
|
689 |
|
|
makeElement( i * cellx, |
690 |
|
|
j * celly, |
691 |
|
|
k * cellz ); |
692 |
|
|
done = ( current_mol >= tot_nmol ); |
693 |
|
|
|
694 |
|
|
if( !done && n_per_extra > 1 ){ |
695 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
696 |
|
|
j * celly + 0.5 * celly, |
697 |
|
|
k * cellz ); |
698 |
|
|
done = ( current_mol >= tot_nmol ); |
699 |
|
|
} |
700 |
|
|
|
701 |
|
|
if( !done && n_per_extra > 2){ |
702 |
|
|
makeElement( i * cellx, |
703 |
|
|
j * celly + 0.5 * celly, |
704 |
|
|
k * cellz + 0.5 * cellz ); |
705 |
|
|
done = ( current_mol >= tot_nmol ); |
706 |
|
|
} |
707 |
|
|
|
708 |
|
|
if( !done && n_per_extra > 3){ |
709 |
|
|
makeElement( i * cellx + 0.5 * cellx, |
710 |
|
|
j * celly, |
711 |
|
|
k * cellz + 0.5 * cellz ); |
712 |
|
|
done = ( current_mol >= tot_nmol ); |
713 |
|
|
} |
714 |
|
|
} |
715 |
|
|
} |
716 |
|
|
} |
717 |
|
|
} |
718 |
|
|
|
719 |
|
|
|
720 |
mmeineke |
614 |
for( i=0; i<info->n_atoms; i++ ){ |
721 |
|
|
info->atoms[i]->set_vx( 0.0 ); |
722 |
|
|
info->atoms[i]->set_vy( 0.0 ); |
723 |
|
|
info->atoms[i]->set_vz( 0.0 ); |
724 |
mmeineke |
377 |
} |
725 |
|
|
} |
726 |
|
|
|
727 |
|
|
void SimSetup::makeElement( double x, double y, double z ){ |
728 |
|
|
|
729 |
|
|
int k; |
730 |
|
|
AtomStamp* current_atom; |
731 |
|
|
DirectionalAtom* dAtom; |
732 |
|
|
double rotMat[3][3]; |
733 |
|
|
|
734 |
|
|
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
735 |
|
|
|
736 |
|
|
current_atom = comp_stamps[current_comp]->getAtom( k ); |
737 |
|
|
if( !current_atom->havePosition() ){ |
738 |
|
|
sprintf( painCave.errMsg, |
739 |
|
|
"SimSetup:initFromBass error.\n" |
740 |
|
|
"\tComponent %s, atom %s does not have a position specified.\n" |
741 |
|
|
"\tThe initialization routine is unable to give a start" |
742 |
|
|
" position.\n", |
743 |
|
|
comp_stamps[current_comp]->getID(), |
744 |
|
|
current_atom->getType() ); |
745 |
|
|
painCave.isFatal = 1; |
746 |
|
|
simError(); |
747 |
|
|
} |
748 |
|
|
|
749 |
|
|
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
750 |
|
|
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
751 |
|
|
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
752 |
|
|
|
753 |
|
|
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
754 |
|
|
|
755 |
|
|
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
756 |
|
|
|
757 |
|
|
rotMat[0][0] = 1.0; |
758 |
|
|
rotMat[0][1] = 0.0; |
759 |
|
|
rotMat[0][2] = 0.0; |
760 |
|
|
|
761 |
|
|
rotMat[1][0] = 0.0; |
762 |
|
|
rotMat[1][1] = 1.0; |
763 |
|
|
rotMat[1][2] = 0.0; |
764 |
|
|
|
765 |
|
|
rotMat[2][0] = 0.0; |
766 |
|
|
rotMat[2][1] = 0.0; |
767 |
|
|
rotMat[2][2] = 1.0; |
768 |
|
|
|
769 |
|
|
dAtom->setA( rotMat ); |
770 |
|
|
} |
771 |
|
|
|
772 |
|
|
current_atom_ndx++; |
773 |
|
|
} |
774 |
|
|
|
775 |
|
|
current_mol++; |
776 |
|
|
current_comp_mol++; |
777 |
|
|
|
778 |
|
|
if( current_comp_mol >= components_nmol[current_comp] ){ |
779 |
|
|
|
780 |
|
|
current_comp_mol = 0; |
781 |
|
|
current_comp++; |
782 |
|
|
} |
783 |
|
|
} |
784 |
mmeineke |
614 |
|
785 |
|
|
|
786 |
|
|
void SimSetup::gatherInfo( void ){ |
787 |
|
|
|
788 |
|
|
ensembleCase = -1; |
789 |
|
|
ffCase = -1; |
790 |
|
|
|
791 |
|
|
// get the stamps and globals; |
792 |
|
|
the_stamps = stamps; |
793 |
|
|
the_globals = globals; |
794 |
|
|
|
795 |
|
|
// set the easy ones first |
796 |
|
|
info->target_temp = the_globals->getTargetTemp(); |
797 |
|
|
info->dt = the_globals->getDt(); |
798 |
|
|
info->run_time = the_globals->getRunTime(); |
799 |
|
|
n_components = the_globals->getNComponents(); |
800 |
|
|
|
801 |
|
|
|
802 |
|
|
// get the forceField |
803 |
|
|
|
804 |
|
|
strcpy( force_field, the_globals->getForceField() ); |
805 |
|
|
|
806 |
|
|
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
807 |
|
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
808 |
|
|
else{ |
809 |
|
|
sprintf( painCave.errMsg, |
810 |
|
|
"SimSetup Error. Unrecognized force field -> %s\n", |
811 |
|
|
force_field ); |
812 |
|
|
painCave.isFatal = 1; |
813 |
|
|
simError(); |
814 |
|
|
} |
815 |
|
|
|
816 |
|
|
// get the ensemble |
817 |
|
|
|
818 |
|
|
strcpy( ensemble, the_globals->getEnsemble() ); |
819 |
|
|
|
820 |
|
|
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
821 |
|
|
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
822 |
|
|
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
823 |
|
|
ensembleCase = NPTi_ENS; |
824 |
|
|
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
825 |
|
|
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
826 |
|
|
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
827 |
|
|
else{ |
828 |
|
|
sprintf( painCave.errMsg, |
829 |
|
|
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
830 |
|
|
"reverting to NVE for this simulation.\n", |
831 |
|
|
ensemble ); |
832 |
|
|
painCave.isFatal = 0; |
833 |
|
|
simError(); |
834 |
|
|
strcpy( ensemble, "NVE" ); |
835 |
|
|
ensembleCase = NVE_ENS; |
836 |
|
|
} |
837 |
|
|
strcpy( info->ensemble, ensemble ); |
838 |
|
|
|
839 |
|
|
// get the mixing rule |
840 |
|
|
|
841 |
|
|
strcpy( info->mixingRule, the_globals->getMixingRule() ); |
842 |
|
|
info->usePBC = the_globals->getPBC(); |
843 |
|
|
|
844 |
|
|
|
845 |
|
|
// get the components and calculate the tot_nMol and indvidual n_mol |
846 |
|
|
|
847 |
|
|
the_components = the_globals->getComponents(); |
848 |
|
|
components_nmol = new int[n_components]; |
849 |
|
|
|
850 |
|
|
|
851 |
|
|
if( !the_globals->haveNMol() ){ |
852 |
|
|
// we don't have the total number of molecules, so we assume it is |
853 |
|
|
// given in each component |
854 |
|
|
|
855 |
|
|
tot_nmol = 0; |
856 |
|
|
for( i=0; i<n_components; i++ ){ |
857 |
|
|
|
858 |
|
|
if( !the_components[i]->haveNMol() ){ |
859 |
|
|
// we have a problem |
860 |
|
|
sprintf( painCave.errMsg, |
861 |
|
|
"SimSetup Error. No global NMol or component NMol" |
862 |
|
|
" given. Cannot calculate the number of atoms.\n" ); |
863 |
|
|
painCave.isFatal = 1; |
864 |
|
|
simError(); |
865 |
|
|
} |
866 |
|
|
|
867 |
|
|
tot_nmol += the_components[i]->getNMol(); |
868 |
|
|
components_nmol[i] = the_components[i]->getNMol(); |
869 |
|
|
} |
870 |
|
|
} |
871 |
|
|
else{ |
872 |
|
|
sprintf( painCave.errMsg, |
873 |
|
|
"SimSetup error.\n" |
874 |
|
|
"\tSorry, the ability to specify total" |
875 |
|
|
" nMols and then give molfractions in the components\n" |
876 |
|
|
"\tis not currently supported." |
877 |
|
|
" Please give nMol in the components.\n" ); |
878 |
|
|
painCave.isFatal = 1; |
879 |
|
|
simError(); |
880 |
|
|
} |
881 |
|
|
|
882 |
|
|
// set the status, sample, and thermal kick times |
883 |
|
|
|
884 |
|
|
if( the_globals->haveSampleTime() ){ |
885 |
|
|
info->sampleTime = the_globals->getSampleTime(); |
886 |
|
|
info->statusTime = info->sampleTime; |
887 |
|
|
info->thermalTime = info->sampleTime; |
888 |
|
|
} |
889 |
|
|
else{ |
890 |
|
|
info->sampleTime = the_globals->getRunTime(); |
891 |
|
|
info->statusTime = info->sampleTime; |
892 |
|
|
info->thermalTime = info->sampleTime; |
893 |
|
|
} |
894 |
|
|
|
895 |
|
|
if( the_globals->haveStatusTime() ){ |
896 |
|
|
info->statusTime = the_globals->getStatusTime(); |
897 |
|
|
} |
898 |
|
|
|
899 |
|
|
if( the_globals->haveThermalTime() ){ |
900 |
|
|
info->thermalTime = the_globals->getThermalTime(); |
901 |
|
|
} |
902 |
|
|
|
903 |
|
|
// check for the temperature set flag |
904 |
|
|
|
905 |
|
|
if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet(); |
906 |
|
|
|
907 |
|
|
// get some of the tricky things that may still be in the globals |
908 |
|
|
|
909 |
|
|
double boxVector[3]; |
910 |
|
|
if( the_globals->haveBox() ){ |
911 |
|
|
boxVector[0] = the_globals->getBox(); |
912 |
|
|
boxVector[1] = the_globals->getBox(); |
913 |
|
|
boxVector[2] = the_globals->getBox(); |
914 |
|
|
|
915 |
|
|
info->setBox( boxVector ); |
916 |
|
|
} |
917 |
|
|
else if( the_globals->haveDensity() ){ |
918 |
|
|
|
919 |
|
|
double vol; |
920 |
|
|
vol = (double)tot_nmol / the_globals->getDensity(); |
921 |
|
|
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
922 |
|
|
boxVector[1] = boxVector[0]; |
923 |
|
|
boxVector[2] = boxVector[0]; |
924 |
|
|
|
925 |
|
|
info->setBox( boxVector ); |
926 |
|
|
} |
927 |
|
|
else{ |
928 |
|
|
if( !the_globals->haveBoxX() ){ |
929 |
|
|
sprintf( painCave.errMsg, |
930 |
|
|
"SimSetup error, no periodic BoxX size given.\n" ); |
931 |
|
|
painCave.isFatal = 1; |
932 |
|
|
simError(); |
933 |
|
|
} |
934 |
|
|
boxVector[0] = the_globals->getBoxX(); |
935 |
|
|
|
936 |
|
|
if( !the_globals->haveBoxY() ){ |
937 |
|
|
sprintf( painCave.errMsg, |
938 |
|
|
"SimSetup error, no periodic BoxY size given.\n" ); |
939 |
|
|
painCave.isFatal = 1; |
940 |
|
|
simError(); |
941 |
|
|
} |
942 |
|
|
boxVector[1] = the_globals->getBoxY(); |
943 |
|
|
|
944 |
|
|
if( !the_globals->haveBoxZ() ){ |
945 |
|
|
sprintf( painCave.errMsg, |
946 |
|
|
"SimSetup error, no periodic BoxZ size given.\n" ); |
947 |
|
|
painCave.isFatal = 1; |
948 |
|
|
simError(); |
949 |
|
|
} |
950 |
|
|
boxVector[2] = the_globals->getBoxZ(); |
951 |
|
|
|
952 |
|
|
info->setBox( boxVector ); |
953 |
|
|
} |
954 |
|
|
|
955 |
|
|
|
956 |
|
|
|
957 |
|
|
#ifdef IS_MPI |
958 |
|
|
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
959 |
|
|
MPIcheckPoint(); |
960 |
|
|
#endif // is_mpi |
961 |
|
|
|
962 |
|
|
} |
963 |
|
|
|
964 |
|
|
|
965 |
|
|
void SimSetup::finalInfoCheck( void ){ |
966 |
|
|
int index; |
967 |
|
|
int usesDipoles; |
968 |
|
|
|
969 |
|
|
|
970 |
|
|
// check electrostatic parameters |
971 |
|
|
|
972 |
|
|
index = 0; |
973 |
|
|
usesDipoles = 0; |
974 |
|
|
while( (index < info->n_atoms) && !usesDipoles ){ |
975 |
|
|
usesDipoles = ((info->atoms)[index])->hasDipole(); |
976 |
|
|
index++; |
977 |
|
|
} |
978 |
|
|
|
979 |
|
|
#ifdef IS_MPI |
980 |
|
|
int myUse = usesDipoles |
981 |
|
|
MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
982 |
|
|
#endif //is_mpi |
983 |
|
|
|
984 |
|
|
|
985 |
|
|
if (the_globals->getUseRF() ) { |
986 |
|
|
info->useReactionField = 1; |
987 |
|
|
|
988 |
|
|
if( !the_globals->haveECR() ){ |
989 |
|
|
sprintf( painCave.errMsg, |
990 |
|
|
"SimSetup Warning: using default value of 1/2 the smallest " |
991 |
|
|
"box length for the electrostaticCutoffRadius.\n" |
992 |
|
|
"I hope you have a very fast processor!\n"); |
993 |
|
|
painCave.isFatal = 0; |
994 |
|
|
simError(); |
995 |
|
|
double smallest; |
996 |
|
|
smallest = info->boxLx; |
997 |
|
|
if (info->boxLy <= smallest) smallest = info->boxLy; |
998 |
|
|
if (info->boxLz <= smallest) smallest = info->boxLz; |
999 |
|
|
info->ecr = 0.5 * smallest; |
1000 |
|
|
} else { |
1001 |
|
|
info->ecr = the_globals->getECR(); |
1002 |
|
|
} |
1003 |
|
|
|
1004 |
|
|
if( !the_globals->haveEST() ){ |
1005 |
|
|
sprintf( painCave.errMsg, |
1006 |
|
|
"SimSetup Warning: using default value of 0.05 * the " |
1007 |
|
|
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
1008 |
|
|
); |
1009 |
|
|
painCave.isFatal = 0; |
1010 |
|
|
simError(); |
1011 |
|
|
info->est = 0.05 * info->ecr; |
1012 |
|
|
} else { |
1013 |
|
|
info->est = the_globals->getEST(); |
1014 |
|
|
} |
1015 |
|
|
|
1016 |
|
|
if(!the_globals->haveDielectric() ){ |
1017 |
|
|
sprintf( painCave.errMsg, |
1018 |
|
|
"SimSetup Error: You are trying to use Reaction Field without" |
1019 |
|
|
"setting a dielectric constant!\n" |
1020 |
|
|
); |
1021 |
|
|
painCave.isFatal = 1; |
1022 |
|
|
simError(); |
1023 |
|
|
} |
1024 |
|
|
info->dielectric = the_globals->getDielectric(); |
1025 |
|
|
} |
1026 |
|
|
else { |
1027 |
|
|
if (usesDipoles) { |
1028 |
|
|
|
1029 |
|
|
if( !the_globals->haveECR() ){ |
1030 |
|
|
sprintf( painCave.errMsg, |
1031 |
|
|
"SimSetup Warning: using default value of 1/2 the smallest " |
1032 |
|
|
"box length for the electrostaticCutoffRadius.\n" |
1033 |
|
|
"I hope you have a very fast processor!\n"); |
1034 |
|
|
painCave.isFatal = 0; |
1035 |
|
|
simError(); |
1036 |
|
|
double smallest; |
1037 |
|
|
smallest = info->boxLx; |
1038 |
|
|
if (info->boxLy <= smallest) smallest = info->boxLy; |
1039 |
|
|
if (info->boxLz <= smallest) smallest = info->boxLz; |
1040 |
|
|
info->ecr = 0.5 * smallest; |
1041 |
|
|
} else { |
1042 |
|
|
info->ecr = the_globals->getECR(); |
1043 |
|
|
} |
1044 |
|
|
|
1045 |
|
|
if( !the_globals->haveEST() ){ |
1046 |
|
|
sprintf( painCave.errMsg, |
1047 |
|
|
"SimSetup Warning: using default value of 5%% of the " |
1048 |
|
|
"electrostaticCutoffRadius for the " |
1049 |
|
|
"electrostaticSkinThickness\n" |
1050 |
|
|
); |
1051 |
|
|
painCave.isFatal = 0; |
1052 |
|
|
simError(); |
1053 |
|
|
info->est = 0.05 * info->ecr; |
1054 |
|
|
} else { |
1055 |
|
|
info->est = the_globals->getEST(); |
1056 |
|
|
} |
1057 |
|
|
} |
1058 |
|
|
} |
1059 |
|
|
|
1060 |
|
|
#ifdef IS_MPI |
1061 |
|
|
strcpy( checkPointMsg, "post processing checks out" ); |
1062 |
|
|
MPIcheckPoint(); |
1063 |
|
|
#endif // is_mpi |
1064 |
|
|
|
1065 |
|
|
} |
1066 |
|
|
|
1067 |
|
|
void SimSetup::initSystemCoords( void ){ |
1068 |
|
|
|
1069 |
|
|
if( the_globals->haveInitialConfig() ){ |
1070 |
|
|
|
1071 |
|
|
InitializeFromFile* fileInit; |
1072 |
|
|
#ifdef IS_MPI // is_mpi |
1073 |
|
|
if( worldRank == 0 ){ |
1074 |
|
|
#endif //is_mpi |
1075 |
|
|
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
1076 |
|
|
#ifdef IS_MPI |
1077 |
|
|
}else fileInit = new InitializeFromFile( NULL ); |
1078 |
|
|
#endif |
1079 |
|
|
fileInit->read_xyz( info ); // default velocities on |
1080 |
|
|
|
1081 |
|
|
delete fileInit; |
1082 |
|
|
} |
1083 |
|
|
else{ |
1084 |
|
|
|
1085 |
|
|
#ifdef IS_MPI |
1086 |
|
|
|
1087 |
|
|
// no init from bass |
1088 |
|
|
|
1089 |
|
|
sprintf( painCave.errMsg, |
1090 |
|
|
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
1091 |
|
|
painCave.isFatal; |
1092 |
|
|
simError(); |
1093 |
|
|
|
1094 |
|
|
#else |
1095 |
|
|
|
1096 |
|
|
initFromBass(); |
1097 |
|
|
|
1098 |
|
|
|
1099 |
|
|
#endif |
1100 |
|
|
} |
1101 |
|
|
|
1102 |
|
|
#ifdef IS_MPI |
1103 |
|
|
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
1104 |
|
|
MPIcheckPoint(); |
1105 |
|
|
#endif // is_mpi |
1106 |
|
|
|
1107 |
|
|
} |
1108 |
|
|
|
1109 |
|
|
|
1110 |
|
|
void SimSetup::makeOutNames( void ){ |
1111 |
|
|
|
1112 |
|
|
#ifdef IS_MPI |
1113 |
|
|
if( worldRank == 0 ){ |
1114 |
|
|
#endif // is_mpi |
1115 |
|
|
|
1116 |
|
|
if( the_globals->haveFinalConfig() ){ |
1117 |
|
|
strcpy( info->finalName, the_globals->getFinalConfig() ); |
1118 |
|
|
} |
1119 |
|
|
else{ |
1120 |
|
|
strcpy( info->finalName, inFileName ); |
1121 |
|
|
char* endTest; |
1122 |
|
|
int nameLength = strlen( info->finalName ); |
1123 |
|
|
endTest = &(info->finalName[nameLength - 5]); |
1124 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
1125 |
|
|
strcpy( endTest, ".eor" ); |
1126 |
|
|
} |
1127 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
1128 |
|
|
strcpy( endTest, ".eor" ); |
1129 |
|
|
} |
1130 |
|
|
else{ |
1131 |
|
|
endTest = &(info->finalName[nameLength - 4]); |
1132 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
1133 |
|
|
strcpy( endTest, ".eor" ); |
1134 |
|
|
} |
1135 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
1136 |
|
|
strcpy( endTest, ".eor" ); |
1137 |
|
|
} |
1138 |
|
|
else{ |
1139 |
|
|
strcat( info->finalName, ".eor" ); |
1140 |
|
|
} |
1141 |
|
|
} |
1142 |
|
|
} |
1143 |
|
|
|
1144 |
|
|
// make the sample and status out names |
1145 |
|
|
|
1146 |
|
|
strcpy( info->sampleName, inFileName ); |
1147 |
|
|
char* endTest; |
1148 |
|
|
int nameLength = strlen( info->sampleName ); |
1149 |
|
|
endTest = &(info->sampleName[nameLength - 5]); |
1150 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
1151 |
|
|
strcpy( endTest, ".dump" ); |
1152 |
|
|
} |
1153 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
1154 |
|
|
strcpy( endTest, ".dump" ); |
1155 |
|
|
} |
1156 |
|
|
else{ |
1157 |
|
|
endTest = &(info->sampleName[nameLength - 4]); |
1158 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
1159 |
|
|
strcpy( endTest, ".dump" ); |
1160 |
|
|
} |
1161 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
1162 |
|
|
strcpy( endTest, ".dump" ); |
1163 |
|
|
} |
1164 |
|
|
else{ |
1165 |
|
|
strcat( info->sampleName, ".dump" ); |
1166 |
|
|
} |
1167 |
|
|
} |
1168 |
|
|
|
1169 |
|
|
strcpy( info->statusName, inFileName ); |
1170 |
|
|
nameLength = strlen( info->statusName ); |
1171 |
|
|
endTest = &(info->statusName[nameLength - 5]); |
1172 |
|
|
if( !strcmp( endTest, ".bass" ) ){ |
1173 |
|
|
strcpy( endTest, ".stat" ); |
1174 |
|
|
} |
1175 |
|
|
else if( !strcmp( endTest, ".BASS" ) ){ |
1176 |
|
|
strcpy( endTest, ".stat" ); |
1177 |
|
|
} |
1178 |
|
|
else{ |
1179 |
|
|
endTest = &(info->statusName[nameLength - 4]); |
1180 |
|
|
if( !strcmp( endTest, ".bss" ) ){ |
1181 |
|
|
strcpy( endTest, ".stat" ); |
1182 |
|
|
} |
1183 |
|
|
else if( !strcmp( endTest, ".mdl" ) ){ |
1184 |
|
|
strcpy( endTest, ".stat" ); |
1185 |
|
|
} |
1186 |
|
|
else{ |
1187 |
|
|
strcat( info->statusName, ".stat" ); |
1188 |
|
|
} |
1189 |
|
|
} |
1190 |
|
|
|
1191 |
|
|
#ifdef IS_MPI |
1192 |
|
|
} |
1193 |
|
|
#endif // is_mpi |
1194 |
|
|
|
1195 |
|
|
} |
1196 |
|
|
|
1197 |
|
|
|
1198 |
|
|
void SimSetup::sysObjectsCreation( void ){ |
1199 |
|
|
|
1200 |
|
|
// create the forceField |
1201 |
|
|
|
1202 |
|
|
createFF(); |
1203 |
|
|
|
1204 |
|
|
// extract componentList |
1205 |
|
|
|
1206 |
|
|
compList(); |
1207 |
|
|
|
1208 |
|
|
// calc the number of atoms, bond, bends, and torsions |
1209 |
|
|
|
1210 |
|
|
calcSysValues(); |
1211 |
|
|
|
1212 |
|
|
#ifdef IS_MPI |
1213 |
|
|
// divide the molecules among the processors |
1214 |
|
|
|
1215 |
|
|
mpiMolDivide(); |
1216 |
|
|
#endif //is_mpi |
1217 |
|
|
|
1218 |
|
|
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1219 |
|
|
|
1220 |
|
|
makeSysArrays(); |
1221 |
|
|
|
1222 |
|
|
|
1223 |
|
|
|
1224 |
|
|
|
1225 |
|
|
} |
1226 |
|
|
|
1227 |
|
|
|
1228 |
|
|
void SimSetup::createFF( void ){ |
1229 |
|
|
|
1230 |
|
|
switch( ffCase ){ |
1231 |
|
|
|
1232 |
|
|
case FF_DUFF: |
1233 |
|
|
the_ff = new DUFF(); |
1234 |
|
|
break; |
1235 |
|
|
|
1236 |
|
|
case FF_LJ: |
1237 |
|
|
the_ff = new LJFF(); |
1238 |
|
|
break; |
1239 |
|
|
|
1240 |
|
|
default: |
1241 |
|
|
sprintf( painCave.errMsg, |
1242 |
|
|
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1243 |
|
|
painCave.isFatal = 1; |
1244 |
|
|
simError(); |
1245 |
|
|
} |
1246 |
|
|
|
1247 |
|
|
#ifdef IS_MPI |
1248 |
|
|
strcpy( checkPointMsg, "ForceField creation successful" ); |
1249 |
|
|
MPIcheckPoint(); |
1250 |
|
|
#endif // is_mpi |
1251 |
|
|
|
1252 |
|
|
} |
1253 |
|
|
|
1254 |
|
|
|
1255 |
|
|
void SimSetup::compList( void ){ |
1256 |
|
|
|
1257 |
|
|
comp_stamps = new MoleculeStamp*[n_components]; |
1258 |
|
|
|
1259 |
|
|
// make an array of molecule stamps that match the components used. |
1260 |
|
|
// also extract the used stamps out into a separate linked list |
1261 |
|
|
|
1262 |
|
|
info->nComponents = n_components; |
1263 |
|
|
info->componentsNmol = components_nmol; |
1264 |
|
|
info->compStamps = comp_stamps; |
1265 |
|
|
info->headStamp = new LinkedMolStamp(); |
1266 |
|
|
|
1267 |
|
|
char* id; |
1268 |
|
|
LinkedMolStamp* headStamp = info->headStamp; |
1269 |
|
|
LinkedMolStamp* currentStamp = NULL; |
1270 |
|
|
for( i=0; i<n_components; i++ ){ |
1271 |
|
|
|
1272 |
|
|
id = the_components[i]->getType(); |
1273 |
|
|
comp_stamps[i] = NULL; |
1274 |
|
|
|
1275 |
|
|
// check to make sure the component isn't already in the list |
1276 |
|
|
|
1277 |
|
|
comp_stamps[i] = headStamp->match( id ); |
1278 |
|
|
if( comp_stamps[i] == NULL ){ |
1279 |
|
|
|
1280 |
|
|
// extract the component from the list; |
1281 |
|
|
|
1282 |
|
|
currentStamp = the_stamps->extractMolStamp( id ); |
1283 |
|
|
if( currentStamp == NULL ){ |
1284 |
|
|
sprintf( painCave.errMsg, |
1285 |
|
|
"SimSetup error: Component \"%s\" was not found in the " |
1286 |
|
|
"list of declared molecules\n", |
1287 |
|
|
id ); |
1288 |
|
|
painCave.isFatal = 1; |
1289 |
|
|
simError(); |
1290 |
|
|
} |
1291 |
|
|
|
1292 |
|
|
headStamp->add( currentStamp ); |
1293 |
|
|
comp_stamps[i] = headStamp->match( id ); |
1294 |
|
|
} |
1295 |
|
|
} |
1296 |
|
|
|
1297 |
|
|
#ifdef IS_MPI |
1298 |
|
|
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1299 |
|
|
MPIcheckPoint(); |
1300 |
|
|
#endif // is_mpi |
1301 |
|
|
|
1302 |
|
|
|
1303 |
|
|
} |
1304 |
|
|
|
1305 |
|
|
void SimSetup::calcSysValues( void ){ |
1306 |
|
|
|
1307 |
|
|
tot_atoms = 0; |
1308 |
|
|
tot_bonds = 0; |
1309 |
|
|
tot_bends = 0; |
1310 |
|
|
tot_torsions = 0; |
1311 |
|
|
for( i=0; i<n_components; i++ ){ |
1312 |
|
|
|
1313 |
|
|
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1314 |
|
|
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1315 |
|
|
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1316 |
|
|
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1317 |
|
|
} |
1318 |
|
|
|
1319 |
|
|
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1320 |
|
|
|
1321 |
|
|
info->n_atoms = tot_atoms; |
1322 |
|
|
info->n_bonds = tot_bonds; |
1323 |
|
|
info->n_bends = tot_bends; |
1324 |
|
|
info->n_torsions = tot_torsions; |
1325 |
|
|
info->n_SRI = tot_SRI; |
1326 |
|
|
info->n_mol = tot_nmol; |
1327 |
|
|
|
1328 |
|
|
info->molMembershipArray = new int[tot_atoms]; |
1329 |
|
|
} |
1330 |
|
|
|
1331 |
|
|
|
1332 |
|
|
#ifdef IS_MPI |
1333 |
|
|
|
1334 |
|
|
void SimSetup::mpiMolDivide( void ){ |
1335 |
|
|
|
1336 |
|
|
int localMol, allMol; |
1337 |
|
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1338 |
|
|
|
1339 |
|
|
mpiSim = new mpiSimulation( info ); |
1340 |
|
|
|
1341 |
|
|
globalIndex = mpiSim->divideLabor(); |
1342 |
|
|
|
1343 |
|
|
// set up the local variables |
1344 |
|
|
|
1345 |
|
|
mol2proc = mpiSim->getMolToProcMap(); |
1346 |
|
|
molCompType = mpiSim->getMolComponentType(); |
1347 |
|
|
|
1348 |
|
|
allMol = 0; |
1349 |
|
|
localMol = 0; |
1350 |
|
|
local_atoms = 0; |
1351 |
|
|
local_bonds = 0; |
1352 |
|
|
local_bends = 0; |
1353 |
|
|
local_torsions = 0; |
1354 |
|
|
globalAtomIndex = 0; |
1355 |
|
|
|
1356 |
|
|
|
1357 |
|
|
for( i=0; i<n_components; i++ ){ |
1358 |
|
|
|
1359 |
|
|
for( j=0; j<components_nmol[i]; j++ ){ |
1360 |
|
|
|
1361 |
|
|
if( mol2proc[allMol] == worldRank ){ |
1362 |
|
|
|
1363 |
|
|
local_atoms += comp_stamps[i]->getNAtoms(); |
1364 |
|
|
local_bonds += comp_stamps[i]->getNBonds(); |
1365 |
|
|
local_bends += comp_stamps[i]->getNBends(); |
1366 |
|
|
local_torsions += comp_stamps[i]->getNTorsions(); |
1367 |
|
|
localMol++; |
1368 |
|
|
} |
1369 |
|
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1370 |
|
|
info->molMembershipArray[globalAtomIndex] = allMol; |
1371 |
|
|
globalAtomIndex++; |
1372 |
|
|
} |
1373 |
|
|
|
1374 |
|
|
allMol++; |
1375 |
|
|
} |
1376 |
|
|
} |
1377 |
|
|
local_SRI = local_bonds + local_bends + local_torsions; |
1378 |
|
|
|
1379 |
|
|
info->n_atoms = mpiSim->getMyNlocal(); |
1380 |
|
|
|
1381 |
|
|
if( local_atoms != info->n_atoms ){ |
1382 |
|
|
sprintf( painCave.errMsg, |
1383 |
|
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1384 |
|
|
" localAtom (%d) are not equal.\n", |
1385 |
|
|
info->n_atoms, |
1386 |
|
|
local_atoms ); |
1387 |
|
|
painCave.isFatal = 1; |
1388 |
|
|
simError(); |
1389 |
|
|
} |
1390 |
|
|
|
1391 |
|
|
info->n_bonds = local_bonds; |
1392 |
|
|
info->n_bends = local_bends; |
1393 |
|
|
info->n_torsions = local_torsions; |
1394 |
|
|
info->n_SRI = local_SRI; |
1395 |
|
|
info->n_mol = localMol; |
1396 |
|
|
|
1397 |
|
|
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1398 |
|
|
MPIcheckPoint(); |
1399 |
|
|
} |
1400 |
|
|
|
1401 |
|
|
#endif // is_mpi |
1402 |
|
|
|
1403 |
|
|
|
1404 |
|
|
void SimSetup::makeSysArrays( void ){ |
1405 |
|
|
|
1406 |
|
|
// create the atom and short range interaction arrays |
1407 |
|
|
|
1408 |
|
|
Atom::createArrays(info->n_atoms); |
1409 |
|
|
the_atoms = new Atom*[info->n_atoms]; |
1410 |
|
|
the_molecules = new Molecule[info->n_mol]; |
1411 |
|
|
int molIndex; |
1412 |
|
|
|
1413 |
|
|
// initialize the molecule's stampID's |
1414 |
|
|
|
1415 |
|
|
#ifdef IS_MPI |
1416 |
|
|
|
1417 |
|
|
|
1418 |
|
|
molIndex = 0; |
1419 |
|
|
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1420 |
|
|
|
1421 |
|
|
if(mol2proc[i] == worldRank ){ |
1422 |
|
|
the_molecules[molIndex].setStampID( molCompType[i] ); |
1423 |
|
|
the_molecules[molIndex].setMyIndex( molIndex ); |
1424 |
|
|
the_molecules[molIndex].setGlobalIndex( i ); |
1425 |
|
|
molIndex++; |
1426 |
|
|
} |
1427 |
|
|
} |
1428 |
|
|
|
1429 |
|
|
#else // is_mpi |
1430 |
|
|
|
1431 |
|
|
molIndex = 0; |
1432 |
|
|
globalAtomIndex = 0; |
1433 |
|
|
for(i=0; i<n_components; i++){ |
1434 |
|
|
for(j=0; j<components_nmol[i]; j++ ){ |
1435 |
|
|
the_molecules[molIndex].setStampID( i ); |
1436 |
|
|
the_molecules[molIndex].setMyIndex( molIndex ); |
1437 |
|
|
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1438 |
|
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1439 |
|
|
info->molMembershipArray[globalAtomIndex] = molIndex; |
1440 |
|
|
globalAtomIndex++; |
1441 |
|
|
} |
1442 |
|
|
molIndex++; |
1443 |
|
|
} |
1444 |
|
|
} |
1445 |
|
|
|
1446 |
|
|
|
1447 |
|
|
#endif // is_mpi |
1448 |
|
|
|
1449 |
|
|
|
1450 |
|
|
if( info->n_SRI ){ |
1451 |
|
|
|
1452 |
|
|
Exclude::createArray(info->n_SRI); |
1453 |
|
|
the_excludes = new Exclude*[info->n_SRI]; |
1454 |
|
|
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1455 |
|
|
info->globalExcludes = new int; |
1456 |
|
|
info->n_exclude = info->n_SRI; |
1457 |
|
|
} |
1458 |
|
|
else{ |
1459 |
|
|
|
1460 |
|
|
Exclude::createArray( 1 ); |
1461 |
|
|
the_excludes = new Exclude*; |
1462 |
|
|
the_excludes[0] = new Exclude(0); |
1463 |
|
|
the_excludes[0]->setPair( 0,0 ); |
1464 |
|
|
info->globalExcludes = new int; |
1465 |
|
|
info->globalExcludes[0] = 0; |
1466 |
|
|
info->n_exclude = 0; |
1467 |
|
|
} |
1468 |
|
|
|
1469 |
|
|
// set the arrays into the SimInfo object |
1470 |
|
|
|
1471 |
|
|
info->atoms = the_atoms; |
1472 |
|
|
info->molecules = the_molecules; |
1473 |
|
|
info->nGlobalExcludes = 0; |
1474 |
|
|
info->excludes = the_excludes; |
1475 |
|
|
|
1476 |
|
|
the_ff->setSimInfo( info ); |
1477 |
|
|
|
1478 |
|
|
} |