14 |
|
|
15 |
|
// some defines for ensemble and Forcefield cases |
16 |
|
|
17 |
< |
#define NVE_ENS 0 |
18 |
< |
#define NVT_ENS 1 |
19 |
< |
#define NPT_ENS 2 |
17 |
> |
#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 |
|
|
24 |
+ |
|
25 |
|
#define FF_DUFF 0 |
26 |
|
#define FF_LJ 1 |
27 |
+ |
#define FF_EAM 2 |
28 |
|
|
24 |
– |
|
29 |
|
SimSetup::SimSetup(){ |
30 |
+ |
|
31 |
+ |
isInfoArray = 0; |
32 |
+ |
nInfo = 1; |
33 |
+ |
|
34 |
|
stamps = new MakeStamps(); |
35 |
|
globals = new Globals(); |
36 |
|
|
37 |
+ |
|
38 |
|
#ifdef IS_MPI |
39 |
|
strcpy( checkPointMsg, "SimSetup creation successful" ); |
40 |
|
MPIcheckPoint(); |
46 |
|
delete globals; |
47 |
|
} |
48 |
|
|
49 |
+ |
void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
50 |
+ |
info = the_info; |
51 |
+ |
nInfo = theNinfo; |
52 |
+ |
isInfoArray = 1; |
53 |
+ |
} |
54 |
+ |
|
55 |
+ |
|
56 |
|
void SimSetup::parseFile( char* fileName ){ |
57 |
|
|
58 |
|
#ifdef IS_MPI |
90 |
|
|
91 |
|
void SimSetup::createSim( void ){ |
92 |
|
|
77 |
– |
MakeStamps *the_stamps; |
78 |
– |
Globals* the_globals; |
93 |
|
int i, j, k, globalAtomIndex; |
94 |
|
|
95 |
< |
int ensembleCase; |
82 |
< |
int ffCase; |
95 |
> |
// gather all of the information from the Bass file |
96 |
|
|
97 |
< |
ensembleCase = -1; |
85 |
< |
ffCase = -1; |
97 |
> |
gatherInfo(); |
98 |
|
|
99 |
< |
// get the stamps and globals; |
88 |
< |
the_stamps = stamps; |
89 |
< |
the_globals = globals; |
99 |
> |
// creation of complex system objects |
100 |
|
|
101 |
< |
// set the easy ones first |
92 |
< |
simnfo->target_temp = the_globals->getTargetTemp(); |
93 |
< |
simnfo->dt = the_globals->getDt(); |
94 |
< |
simnfo->run_time = the_globals->getRunTime(); |
101 |
> |
sysObjectsCreation(); |
102 |
|
|
103 |
< |
// get the ones we know are there, yet still may need some work. |
104 |
< |
n_components = the_globals->getNComponents(); |
105 |
< |
strcpy( force_field, the_globals->getForceField() ); |
103 |
> |
// check on the post processing info |
104 |
> |
|
105 |
> |
finalInfoCheck(); |
106 |
|
|
107 |
< |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
101 |
< |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
102 |
< |
else{ |
103 |
< |
sprintf( painCave.errMsg, |
104 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
105 |
< |
force_field ); |
106 |
< |
painCave.isFatal = 1; |
107 |
< |
simError(); |
108 |
< |
} |
107 |
> |
// initialize the system coordinates |
108 |
|
|
109 |
< |
// get the ensemble: |
111 |
< |
strcpy( ensemble, the_globals->getEnsemble() ); |
112 |
< |
|
113 |
< |
if( !strcasecmp( ensemble, "NVE" )) ffCase = NVE_ENS; |
114 |
< |
else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS; |
115 |
< |
else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS; |
116 |
< |
else{ |
117 |
< |
sprintf( painCave.errMsg, |
118 |
< |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
119 |
< |
"reverting to NVE for this simulation.\n", |
120 |
< |
ensemble ); |
121 |
< |
painCave.isFatal = 0; |
122 |
< |
simError(); |
123 |
< |
strcpy( ensemble, "NVE" ); |
124 |
< |
ensembleCase = NVE_ENS; |
125 |
< |
} |
126 |
< |
strcpy( simnfo->ensemble, ensemble ); |
127 |
< |
|
128 |
< |
|
129 |
< |
// if( !strcasecmp( ensemble, "NPT" ) ) { |
130 |
< |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
131 |
< |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
132 |
< |
// if (the_globals->haveTargetPressure()) |
133 |
< |
// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
134 |
< |
// else { |
135 |
< |
// sprintf( painCave.errMsg, |
136 |
< |
// "SimSetup error: If you use the constant pressure\n" |
137 |
< |
// " ensemble, you must set targetPressure.\n" |
138 |
< |
// " This was found in the BASS file.\n"); |
139 |
< |
// painCave.isFatal = 1; |
140 |
< |
// simError(); |
141 |
< |
// } |
142 |
< |
|
143 |
< |
// if (the_globals->haveTauThermostat()) |
144 |
< |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
145 |
< |
// else if (the_globals->haveQmass()) |
146 |
< |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
147 |
< |
// else { |
148 |
< |
// sprintf( painCave.errMsg, |
149 |
< |
// "SimSetup error: If you use one of the constant temperature\n" |
150 |
< |
// " ensembles, you must set either tauThermostat or qMass.\n" |
151 |
< |
// " Neither of these was found in the BASS file.\n"); |
152 |
< |
// painCave.isFatal = 1; |
153 |
< |
// simError(); |
154 |
< |
// } |
155 |
< |
|
156 |
< |
// if (the_globals->haveTauBarostat()) |
157 |
< |
// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
158 |
< |
// else { |
159 |
< |
// sprintf( painCave.errMsg, |
160 |
< |
// "SimSetup error: If you use the constant pressure\n" |
161 |
< |
// " ensemble, you must set tauBarostat.\n" |
162 |
< |
// " This was found in the BASS file.\n"); |
163 |
< |
// painCave.isFatal = 1; |
164 |
< |
// simError(); |
165 |
< |
// } |
166 |
< |
|
167 |
< |
// } else if ( !strcasecmp( ensemble, "NVT") ) { |
168 |
< |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
169 |
< |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
170 |
< |
|
171 |
< |
// if (the_globals->haveTauThermostat()) |
172 |
< |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
173 |
< |
// else if (the_globals->haveQmass()) |
174 |
< |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
175 |
< |
// else { |
176 |
< |
// sprintf( painCave.errMsg, |
177 |
< |
// "SimSetup error: If you use one of the constant temperature\n" |
178 |
< |
// " ensembles, you must set either tauThermostat or qMass.\n" |
179 |
< |
// " Neither of these was found in the BASS file.\n"); |
180 |
< |
// painCave.isFatal = 1; |
181 |
< |
// simError(); |
182 |
< |
// } |
183 |
< |
|
184 |
< |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
185 |
< |
simnfo->usePBC = the_globals->getPBC(); |
186 |
< |
|
187 |
< |
int usesDipoles = 0; |
188 |
< |
switch( ffCase ){ |
189 |
< |
|
190 |
< |
case FF_DUFF: |
191 |
< |
the_ff = new DUFF(); |
192 |
< |
usesDipoles = 1; |
193 |
< |
break; |
194 |
< |
|
195 |
< |
case FF_LJ: |
196 |
< |
the_ff = LJFF(); |
197 |
< |
break; |
198 |
< |
|
199 |
< |
default: |
200 |
< |
sprintf( painCave.errMsg, |
201 |
< |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
202 |
< |
painCave.isFatal = 1; |
203 |
< |
simError(); |
204 |
< |
} |
205 |
< |
|
206 |
< |
#ifdef IS_MPI |
207 |
< |
strcpy( checkPointMsg, "ForceField creation successful" ); |
208 |
< |
MPIcheckPoint(); |
209 |
< |
#endif // is_mpi |
210 |
< |
|
211 |
< |
// get the components and calculate the tot_nMol and indvidual n_mol |
212 |
< |
the_components = the_globals->getComponents(); |
213 |
< |
components_nmol = new int[n_components]; |
214 |
< |
comp_stamps = new MoleculeStamp*[n_components]; |
215 |
< |
|
216 |
< |
if( !the_globals->haveNMol() ){ |
217 |
< |
// we don't have the total number of molecules, so we assume it is |
218 |
< |
// given in each component |
219 |
< |
|
220 |
< |
tot_nmol = 0; |
221 |
< |
for( i=0; i<n_components; i++ ){ |
222 |
< |
|
223 |
< |
if( !the_components[i]->haveNMol() ){ |
224 |
< |
// we have a problem |
225 |
< |
sprintf( painCave.errMsg, |
226 |
< |
"SimSetup Error. No global NMol or component NMol" |
227 |
< |
" given. Cannot calculate the number of atoms.\n" ); |
228 |
< |
painCave.isFatal = 1; |
229 |
< |
simError(); |
230 |
< |
} |
231 |
< |
|
232 |
< |
tot_nmol += the_components[i]->getNMol(); |
233 |
< |
components_nmol[i] = the_components[i]->getNMol(); |
234 |
< |
} |
235 |
< |
} |
236 |
< |
else{ |
237 |
< |
sprintf( painCave.errMsg, |
238 |
< |
"SimSetup error.\n" |
239 |
< |
"\tSorry, the ability to specify total" |
240 |
< |
" nMols and then give molfractions in the components\n" |
241 |
< |
"\tis not currently supported." |
242 |
< |
" Please give nMol in the components.\n" ); |
243 |
< |
painCave.isFatal = 1; |
244 |
< |
simError(); |
245 |
< |
|
246 |
< |
|
247 |
< |
// tot_nmol = the_globals->getNMol(); |
248 |
< |
|
249 |
< |
// //we have the total number of molecules, now we check for molfractions |
250 |
< |
// for( i=0; i<n_components; i++ ){ |
251 |
< |
|
252 |
< |
// if( !the_components[i]->haveMolFraction() ){ |
253 |
< |
|
254 |
< |
// if( !the_components[i]->haveNMol() ){ |
255 |
< |
// //we have a problem |
256 |
< |
// std::cerr << "SimSetup error. Neither molFraction nor " |
257 |
< |
// << " nMol was given in component |
258 |
< |
|
259 |
< |
} |
260 |
< |
|
261 |
< |
#ifdef IS_MPI |
262 |
< |
strcpy( checkPointMsg, "Have the number of components" ); |
263 |
< |
MPIcheckPoint(); |
264 |
< |
#endif // is_mpi |
265 |
< |
|
266 |
< |
// make an array of molecule stamps that match the components used. |
267 |
< |
// also extract the used stamps out into a separate linked list |
268 |
< |
|
269 |
< |
simnfo->nComponents = n_components; |
270 |
< |
simnfo->componentsNmol = components_nmol; |
271 |
< |
simnfo->compStamps = comp_stamps; |
272 |
< |
simnfo->headStamp = new LinkedMolStamp(); |
273 |
< |
|
274 |
< |
char* id; |
275 |
< |
LinkedMolStamp* headStamp = simnfo->headStamp; |
276 |
< |
LinkedMolStamp* currentStamp = NULL; |
277 |
< |
for( i=0; i<n_components; i++ ){ |
278 |
< |
|
279 |
< |
id = the_components[i]->getType(); |
280 |
< |
comp_stamps[i] = NULL; |
281 |
< |
|
282 |
< |
// check to make sure the component isn't already in the list |
283 |
< |
|
284 |
< |
comp_stamps[i] = headStamp->match( id ); |
285 |
< |
if( comp_stamps[i] == NULL ){ |
286 |
< |
|
287 |
< |
// extract the component from the list; |
288 |
< |
|
289 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
290 |
< |
if( currentStamp == NULL ){ |
291 |
< |
sprintf( painCave.errMsg, |
292 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
293 |
< |
"list of declared molecules\n", |
294 |
< |
id ); |
295 |
< |
painCave.isFatal = 1; |
296 |
< |
simError(); |
297 |
< |
} |
298 |
< |
|
299 |
< |
headStamp->add( currentStamp ); |
300 |
< |
comp_stamps[i] = headStamp->match( id ); |
301 |
< |
} |
302 |
< |
} |
303 |
< |
|
304 |
< |
#ifdef IS_MPI |
305 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
306 |
< |
MPIcheckPoint(); |
307 |
< |
#endif // is_mpi |
109 |
> |
initSystemCoords(); |
110 |
|
|
111 |
|
|
112 |
+ |
// make the output filenames |
113 |
|
|
114 |
< |
|
115 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
116 |
< |
|
314 |
< |
tot_atoms = 0; |
315 |
< |
tot_bonds = 0; |
316 |
< |
tot_bends = 0; |
317 |
< |
tot_torsions = 0; |
318 |
< |
for( i=0; i<n_components; i++ ){ |
319 |
< |
|
320 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
321 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
322 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
323 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
324 |
< |
} |
325 |
< |
|
326 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
327 |
< |
|
328 |
< |
simnfo->n_atoms = tot_atoms; |
329 |
< |
simnfo->n_bonds = tot_bonds; |
330 |
< |
simnfo->n_bends = tot_bends; |
331 |
< |
simnfo->n_torsions = tot_torsions; |
332 |
< |
simnfo->n_SRI = tot_SRI; |
333 |
< |
simnfo->n_mol = tot_nmol; |
114 |
> |
makeOutNames(); |
115 |
> |
|
116 |
> |
// make the integrator |
117 |
|
|
118 |
< |
simnfo->molMembershipArray = new int[tot_atoms]; |
336 |
< |
|
337 |
< |
#ifdef IS_MPI |
338 |
< |
|
339 |
< |
// divide the molecules among processors here. |
340 |
< |
|
341 |
< |
mpiSim = new mpiSimulation( simnfo ); |
342 |
< |
|
343 |
< |
globalIndex = mpiSim->divideLabor(); |
344 |
< |
|
345 |
< |
// set up the local variables |
346 |
< |
|
347 |
< |
int localMol, allMol; |
348 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
349 |
< |
|
350 |
< |
int* mol2proc = mpiSim->getMolToProcMap(); |
351 |
< |
int* molCompType = mpiSim->getMolComponentType(); |
352 |
< |
|
353 |
< |
allMol = 0; |
354 |
< |
localMol = 0; |
355 |
< |
local_atoms = 0; |
356 |
< |
local_bonds = 0; |
357 |
< |
local_bends = 0; |
358 |
< |
local_torsions = 0; |
359 |
< |
globalAtomIndex = 0; |
360 |
< |
|
361 |
< |
|
362 |
< |
for( i=0; i<n_components; i++ ){ |
363 |
< |
|
364 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
365 |
< |
|
366 |
< |
if( mol2proc[allMol] == worldRank ){ |
367 |
< |
|
368 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
369 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
370 |
< |
local_bends += comp_stamps[i]->getNBends(); |
371 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
372 |
< |
localMol++; |
373 |
< |
} |
374 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
375 |
< |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
376 |
< |
globalAtomIndex++; |
377 |
< |
} |
378 |
< |
|
379 |
< |
allMol++; |
380 |
< |
} |
381 |
< |
} |
382 |
< |
local_SRI = local_bonds + local_bends + local_torsions; |
383 |
< |
|
384 |
< |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
385 |
< |
|
386 |
< |
if( local_atoms != simnfo->n_atoms ){ |
387 |
< |
sprintf( painCave.errMsg, |
388 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
389 |
< |
" localAtom (%d) are not equal.\n", |
390 |
< |
simnfo->n_atoms, |
391 |
< |
local_atoms ); |
392 |
< |
painCave.isFatal = 1; |
393 |
< |
simError(); |
394 |
< |
} |
395 |
< |
|
396 |
< |
simnfo->n_bonds = local_bonds; |
397 |
< |
simnfo->n_bends = local_bends; |
398 |
< |
simnfo->n_torsions = local_torsions; |
399 |
< |
simnfo->n_SRI = local_SRI; |
400 |
< |
simnfo->n_mol = localMol; |
401 |
< |
|
402 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
403 |
< |
MPIcheckPoint(); |
404 |
< |
|
405 |
< |
|
406 |
< |
#endif // is_mpi |
407 |
< |
|
408 |
< |
|
409 |
< |
// create the atom and short range interaction arrays |
410 |
< |
|
411 |
< |
Atom::createArrays(simnfo->n_atoms); |
412 |
< |
the_atoms = new Atom*[simnfo->n_atoms]; |
413 |
< |
the_molecules = new Molecule[simnfo->n_mol]; |
414 |
< |
int molIndex; |
415 |
< |
|
416 |
< |
// initialize the molecule's stampID's |
417 |
< |
|
418 |
< |
#ifdef IS_MPI |
419 |
< |
|
420 |
< |
|
421 |
< |
molIndex = 0; |
422 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
423 |
< |
|
424 |
< |
if(mol2proc[i] == worldRank ){ |
425 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
426 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
427 |
< |
the_molecules[molIndex].setGlobalIndex( i ); |
428 |
< |
molIndex++; |
429 |
< |
} |
430 |
< |
} |
431 |
< |
|
432 |
< |
#else // is_mpi |
433 |
< |
|
434 |
< |
molIndex = 0; |
435 |
< |
globalAtomIndex = 0; |
436 |
< |
for(i=0; i<n_components; i++){ |
437 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
438 |
< |
the_molecules[molIndex].setStampID( i ); |
439 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
440 |
< |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
441 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
442 |
< |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
443 |
< |
globalAtomIndex++; |
444 |
< |
} |
445 |
< |
molIndex++; |
446 |
< |
} |
447 |
< |
} |
448 |
< |
|
449 |
< |
|
450 |
< |
#endif // is_mpi |
451 |
< |
|
452 |
< |
|
453 |
< |
if( simnfo->n_SRI ){ |
454 |
< |
|
455 |
< |
Exclude::createArray(simnfo->n_SRI); |
456 |
< |
the_excludes = new Exclude*[simnfo->n_SRI]; |
457 |
< |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
458 |
< |
simnfo->globalExcludes = new int; |
459 |
< |
simnfo->n_exclude = simnfo->n_SRI; |
460 |
< |
} |
461 |
< |
else{ |
462 |
< |
|
463 |
< |
Exclude::createArray( 1 ); |
464 |
< |
the_excludes = new Exclude*; |
465 |
< |
the_excludes[0] = new Exclude(0); |
466 |
< |
the_excludes[0]->setPair( 0,0 ); |
467 |
< |
simnfo->globalExcludes = new int; |
468 |
< |
simnfo->globalExcludes[0] = 0; |
469 |
< |
simnfo->n_exclude = 0; |
470 |
< |
} |
471 |
< |
|
472 |
< |
// set the arrays into the SimInfo object |
473 |
< |
|
474 |
< |
simnfo->atoms = the_atoms; |
475 |
< |
simnfo->molecules = the_molecules; |
476 |
< |
simnfo->nGlobalExcludes = 0; |
477 |
< |
simnfo->excludes = the_excludes; |
478 |
< |
|
479 |
< |
|
480 |
< |
// get some of the tricky things that may still be in the globals |
481 |
< |
|
482 |
< |
|
483 |
< |
if( the_globals->haveBox() ){ |
484 |
< |
simnfo->box_x = the_globals->getBox(); |
485 |
< |
simnfo->box_y = the_globals->getBox(); |
486 |
< |
simnfo->box_z = the_globals->getBox(); |
487 |
< |
} |
488 |
< |
else if( the_globals->haveDensity() ){ |
489 |
< |
|
490 |
< |
double vol; |
491 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
492 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
493 |
< |
simnfo->box_y = simnfo->box_x; |
494 |
< |
simnfo->box_z = simnfo->box_x; |
495 |
< |
} |
496 |
< |
else{ |
497 |
< |
if( !the_globals->haveBoxX() ){ |
498 |
< |
sprintf( painCave.errMsg, |
499 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
500 |
< |
painCave.isFatal = 1; |
501 |
< |
simError(); |
502 |
< |
} |
503 |
< |
simnfo->box_x = the_globals->getBoxX(); |
504 |
< |
|
505 |
< |
if( !the_globals->haveBoxY() ){ |
506 |
< |
sprintf( painCave.errMsg, |
507 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
508 |
< |
painCave.isFatal = 1; |
509 |
< |
simError(); |
510 |
< |
} |
511 |
< |
simnfo->box_y = the_globals->getBoxY(); |
512 |
< |
|
513 |
< |
if( !the_globals->haveBoxZ() ){ |
514 |
< |
sprintf( painCave.errMsg, |
515 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
516 |
< |
painCave.isFatal = 1; |
517 |
< |
simError(); |
518 |
< |
} |
519 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
520 |
< |
} |
521 |
< |
|
522 |
< |
#ifdef IS_MPI |
523 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
524 |
< |
MPIcheckPoint(); |
525 |
< |
#endif // is_mpi |
526 |
< |
|
527 |
< |
|
528 |
< |
// initialize the arrays |
529 |
< |
|
530 |
< |
the_ff->setSimInfo( simnfo ); |
531 |
< |
|
532 |
< |
makeMolecules(); |
533 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
534 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
535 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
536 |
< |
} |
537 |
< |
|
538 |
< |
if (the_globals->getUseRF() ) { |
539 |
< |
simnfo->useReactionField = 1; |
540 |
< |
|
541 |
< |
if( !the_globals->haveECR() ){ |
542 |
< |
sprintf( painCave.errMsg, |
543 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
544 |
< |
"box length for the electrostaticCutoffRadius.\n" |
545 |
< |
"I hope you have a very fast processor!\n"); |
546 |
< |
painCave.isFatal = 0; |
547 |
< |
simError(); |
548 |
< |
double smallest; |
549 |
< |
smallest = simnfo->box_x; |
550 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
551 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
552 |
< |
simnfo->ecr = 0.5 * smallest; |
553 |
< |
} else { |
554 |
< |
simnfo->ecr = the_globals->getECR(); |
555 |
< |
} |
556 |
< |
|
557 |
< |
if( !the_globals->haveEST() ){ |
558 |
< |
sprintf( painCave.errMsg, |
559 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
560 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
561 |
< |
); |
562 |
< |
painCave.isFatal = 0; |
563 |
< |
simError(); |
564 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
565 |
< |
} else { |
566 |
< |
simnfo->est = the_globals->getEST(); |
567 |
< |
} |
568 |
< |
|
569 |
< |
if(!the_globals->haveDielectric() ){ |
570 |
< |
sprintf( painCave.errMsg, |
571 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
572 |
< |
"setting a dielectric constant!\n" |
573 |
< |
); |
574 |
< |
painCave.isFatal = 1; |
575 |
< |
simError(); |
576 |
< |
} |
577 |
< |
simnfo->dielectric = the_globals->getDielectric(); |
578 |
< |
} else { |
579 |
< |
if (usesDipoles) { |
580 |
< |
|
581 |
< |
if( !the_globals->haveECR() ){ |
582 |
< |
sprintf( painCave.errMsg, |
583 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
584 |
< |
"box length for the electrostaticCutoffRadius.\n" |
585 |
< |
"I hope you have a very fast processor!\n"); |
586 |
< |
painCave.isFatal = 0; |
587 |
< |
simError(); |
588 |
< |
double smallest; |
589 |
< |
smallest = simnfo->box_x; |
590 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
591 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
592 |
< |
simnfo->ecr = 0.5 * smallest; |
593 |
< |
} else { |
594 |
< |
simnfo->ecr = the_globals->getECR(); |
595 |
< |
} |
596 |
< |
|
597 |
< |
if( !the_globals->haveEST() ){ |
598 |
< |
sprintf( painCave.errMsg, |
599 |
< |
"SimSetup Warning: using default value of 5%% of the " |
600 |
< |
"electrostaticCutoffRadius for the " |
601 |
< |
"electrostaticSkinThickness\n" |
602 |
< |
); |
603 |
< |
painCave.isFatal = 0; |
604 |
< |
simError(); |
605 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
606 |
< |
} else { |
607 |
< |
simnfo->est = the_globals->getEST(); |
608 |
< |
} |
609 |
< |
} |
610 |
< |
} |
611 |
< |
|
612 |
< |
#ifdef IS_MPI |
613 |
< |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
614 |
< |
MPIcheckPoint(); |
615 |
< |
#endif // is_mpi |
616 |
< |
|
617 |
< |
if( the_globals->haveInitialConfig() ){ |
618 |
< |
|
619 |
< |
InitializeFromFile* fileInit; |
620 |
< |
#ifdef IS_MPI // is_mpi |
621 |
< |
if( worldRank == 0 ){ |
622 |
< |
#endif //is_mpi |
623 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
624 |
< |
#ifdef IS_MPI |
625 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
626 |
< |
#endif |
627 |
< |
fileInit->read_xyz( simnfo ); // default velocities on |
628 |
< |
|
629 |
< |
delete fileInit; |
630 |
< |
} |
631 |
< |
else{ |
632 |
< |
|
633 |
< |
#ifdef IS_MPI |
634 |
< |
|
635 |
< |
// no init from bass |
636 |
< |
|
637 |
< |
sprintf( painCave.errMsg, |
638 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
639 |
< |
painCave.isFatal; |
640 |
< |
simError(); |
641 |
< |
|
642 |
< |
#else |
643 |
< |
|
644 |
< |
initFromBass(); |
645 |
< |
|
646 |
< |
|
647 |
< |
#endif |
648 |
< |
} |
649 |
< |
|
650 |
< |
#ifdef IS_MPI |
651 |
< |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
652 |
< |
MPIcheckPoint(); |
653 |
< |
#endif // is_mpi |
654 |
< |
|
655 |
< |
|
656 |
< |
|
657 |
< |
|
658 |
< |
|
659 |
< |
|
660 |
< |
|
661 |
< |
#ifdef IS_MPI |
662 |
< |
if( worldRank == 0 ){ |
663 |
< |
#endif // is_mpi |
664 |
< |
|
665 |
< |
if( the_globals->haveFinalConfig() ){ |
666 |
< |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
667 |
< |
} |
668 |
< |
else{ |
669 |
< |
strcpy( simnfo->finalName, inFileName ); |
670 |
< |
char* endTest; |
671 |
< |
int nameLength = strlen( simnfo->finalName ); |
672 |
< |
endTest = &(simnfo->finalName[nameLength - 5]); |
673 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
674 |
< |
strcpy( endTest, ".eor" ); |
675 |
< |
} |
676 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
677 |
< |
strcpy( endTest, ".eor" ); |
678 |
< |
} |
679 |
< |
else{ |
680 |
< |
endTest = &(simnfo->finalName[nameLength - 4]); |
681 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
682 |
< |
strcpy( endTest, ".eor" ); |
683 |
< |
} |
684 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
685 |
< |
strcpy( endTest, ".eor" ); |
686 |
< |
} |
687 |
< |
else{ |
688 |
< |
strcat( simnfo->finalName, ".eor" ); |
689 |
< |
} |
690 |
< |
} |
691 |
< |
} |
692 |
< |
|
693 |
< |
// make the sample and status out names |
694 |
< |
|
695 |
< |
strcpy( simnfo->sampleName, inFileName ); |
696 |
< |
char* endTest; |
697 |
< |
int nameLength = strlen( simnfo->sampleName ); |
698 |
< |
endTest = &(simnfo->sampleName[nameLength - 5]); |
699 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
700 |
< |
strcpy( endTest, ".dump" ); |
701 |
< |
} |
702 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
703 |
< |
strcpy( endTest, ".dump" ); |
704 |
< |
} |
705 |
< |
else{ |
706 |
< |
endTest = &(simnfo->sampleName[nameLength - 4]); |
707 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
708 |
< |
strcpy( endTest, ".dump" ); |
709 |
< |
} |
710 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
711 |
< |
strcpy( endTest, ".dump" ); |
712 |
< |
} |
713 |
< |
else{ |
714 |
< |
strcat( simnfo->sampleName, ".dump" ); |
715 |
< |
} |
716 |
< |
} |
717 |
< |
|
718 |
< |
strcpy( simnfo->statusName, inFileName ); |
719 |
< |
nameLength = strlen( simnfo->statusName ); |
720 |
< |
endTest = &(simnfo->statusName[nameLength - 5]); |
721 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
722 |
< |
strcpy( endTest, ".stat" ); |
723 |
< |
} |
724 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
725 |
< |
strcpy( endTest, ".stat" ); |
726 |
< |
} |
727 |
< |
else{ |
728 |
< |
endTest = &(simnfo->statusName[nameLength - 4]); |
729 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
730 |
< |
strcpy( endTest, ".stat" ); |
731 |
< |
} |
732 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
733 |
< |
strcpy( endTest, ".stat" ); |
734 |
< |
} |
735 |
< |
else{ |
736 |
< |
strcat( simnfo->statusName, ".stat" ); |
737 |
< |
} |
738 |
< |
} |
739 |
< |
|
740 |
< |
#ifdef IS_MPI |
741 |
< |
} |
742 |
< |
#endif // is_mpi |
118 |
> |
makeIntegrator(); |
119 |
|
|
744 |
– |
// set the status, sample, and themal kick times |
745 |
– |
|
746 |
– |
if( the_globals->haveSampleTime() ){ |
747 |
– |
simnfo->sampleTime = the_globals->getSampleTime(); |
748 |
– |
simnfo->statusTime = simnfo->sampleTime; |
749 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
750 |
– |
} |
751 |
– |
else{ |
752 |
– |
simnfo->sampleTime = the_globals->getRunTime(); |
753 |
– |
simnfo->statusTime = simnfo->sampleTime; |
754 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
755 |
– |
} |
756 |
– |
|
757 |
– |
if( the_globals->haveStatusTime() ){ |
758 |
– |
simnfo->statusTime = the_globals->getStatusTime(); |
759 |
– |
} |
760 |
– |
|
761 |
– |
if( the_globals->haveThermalTime() ){ |
762 |
– |
simnfo->thermalTime = the_globals->getThermalTime(); |
763 |
– |
} |
764 |
– |
|
765 |
– |
// check for the temperature set flag |
766 |
– |
|
767 |
– |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
768 |
– |
|
769 |
– |
|
770 |
– |
// make the integrator |
771 |
– |
|
772 |
– |
|
773 |
– |
if( !strcmp( ensemble, "TraPPE_Ex" ) ){ |
774 |
– |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
775 |
– |
} |
776 |
– |
else if( !strcmp( force_field, "LJ" ) ){ |
777 |
– |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
778 |
– |
} |
779 |
– |
|
120 |
|
#ifdef IS_MPI |
121 |
|
mpiSim->mpiRefresh(); |
122 |
|
#endif |
123 |
|
|
124 |
|
// initialize the Fortran |
125 |
|
|
126 |
+ |
initFortran(); |
127 |
|
|
787 |
– |
simnfo->refreshSim(); |
788 |
– |
|
789 |
– |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
790 |
– |
the_ff->initForceField( LB_MIXING_RULE ); |
791 |
– |
} |
792 |
– |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
793 |
– |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
794 |
– |
} |
795 |
– |
else{ |
796 |
– |
sprintf( painCave.errMsg, |
797 |
– |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
798 |
– |
simnfo->mixingRule ); |
799 |
– |
painCave.isFatal = 1; |
800 |
– |
simError(); |
801 |
– |
} |
128 |
|
|
129 |
|
|
804 |
– |
#ifdef IS_MPI |
805 |
– |
strcpy( checkPointMsg, |
806 |
– |
"Successfully intialized the mixingRule for Fortran." ); |
807 |
– |
MPIcheckPoint(); |
808 |
– |
#endif // is_mpi |
130 |
|
} |
131 |
|
|
132 |
|
|
133 |
|
void SimSetup::makeMolecules( void ){ |
134 |
|
|
135 |
|
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
136 |
< |
molInit info; |
136 |
> |
molInit molInfo; |
137 |
|
DirectionalAtom* dAtom; |
138 |
|
LinkedAssign* extras; |
139 |
|
LinkedAssign* current_extra; |
158 |
|
|
159 |
|
atomOffset = 0; |
160 |
|
excludeOffset = 0; |
161 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
161 |
> |
for(i=0; i<info->n_mol; i++){ |
162 |
|
|
163 |
|
stampID = the_molecules[i].getStampID(); |
164 |
|
|
165 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
166 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
167 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
168 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
169 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
165 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
166 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
167 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
168 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
169 |
> |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
170 |
|
|
171 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
172 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
173 |
< |
info.myBonds = new Bond*[info.nBonds]; |
174 |
< |
info.myBends = new Bend*[info.nBends]; |
175 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
171 |
> |
molInfo.myAtoms = &the_atoms[atomOffset]; |
172 |
> |
molInfo.myExcludes = &the_excludes[excludeOffset]; |
173 |
> |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
174 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
175 |
> |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
176 |
|
|
177 |
< |
theBonds = new bond_pair[info.nBonds]; |
178 |
< |
theBends = new bend_set[info.nBends]; |
179 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
177 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
178 |
> |
theBends = new bend_set[molInfo.nBends]; |
179 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
180 |
|
|
181 |
|
// make the Atoms |
182 |
|
|
183 |
< |
for(j=0; j<info.nAtoms; j++){ |
183 |
> |
for(j=0; j<molInfo.nAtoms; j++){ |
184 |
|
|
185 |
|
currentAtom = comp_stamps[stampID]->getAtom( j ); |
186 |
|
if( currentAtom->haveOrientation() ){ |
187 |
|
|
188 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
189 |
< |
simnfo->n_oriented++; |
190 |
< |
info.myAtoms[j] = dAtom; |
189 |
> |
info->n_oriented++; |
190 |
> |
molInfo.myAtoms[j] = dAtom; |
191 |
|
|
192 |
|
ux = currentAtom->getOrntX(); |
193 |
|
uy = currentAtom->getOrntY(); |
205 |
|
dAtom->setSUz( uz ); |
206 |
|
} |
207 |
|
else{ |
208 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
208 |
> |
molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
209 |
|
} |
210 |
< |
info.myAtoms[j]->setType( currentAtom->getType() ); |
210 |
> |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
211 |
|
|
212 |
|
#ifdef IS_MPI |
213 |
|
|
214 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
214 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
215 |
|
|
216 |
|
#endif // is_mpi |
217 |
|
} |
218 |
|
|
219 |
|
// make the bonds |
220 |
< |
for(j=0; j<info.nBonds; j++){ |
220 |
> |
for(j=0; j<molInfo.nBonds; j++){ |
221 |
|
|
222 |
|
currentBond = comp_stamps[stampID]->getBond( j ); |
223 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
244 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
245 |
|
#endif //is_mpi |
246 |
|
} |
247 |
< |
excludeOffset += info.nBonds; |
247 |
> |
excludeOffset += molInfo.nBonds; |
248 |
|
|
249 |
|
//make the bends |
250 |
< |
for(j=0; j<info.nBends; j++){ |
250 |
> |
for(j=0; j<molInfo.nBends; j++){ |
251 |
|
|
252 |
|
currentBend = comp_stamps[stampID]->getBend( j ); |
253 |
|
theBends[j].a = currentBend->getA() + atomOffset; |
330 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
331 |
|
#endif //is_mpi |
332 |
|
} |
333 |
< |
excludeOffset += info.nBends; |
333 |
> |
excludeOffset += molInfo.nBends; |
334 |
|
|
335 |
< |
for(j=0; j<info.nTorsions; j++){ |
335 |
> |
for(j=0; j<molInfo.nTorsions; j++){ |
336 |
|
|
337 |
|
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
338 |
|
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
360 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
361 |
|
#endif //is_mpi |
362 |
|
} |
363 |
< |
excludeOffset += info.nTorsions; |
363 |
> |
excludeOffset += molInfo.nTorsions; |
364 |
|
|
365 |
|
|
366 |
|
// send the arrays off to the forceField for init. |
367 |
|
|
368 |
< |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
369 |
< |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
370 |
< |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
371 |
< |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
368 |
> |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
369 |
> |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
370 |
> |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
371 |
> |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
372 |
|
|
373 |
|
|
374 |
< |
the_molecules[i].initialize( info ); |
374 |
> |
the_molecules[i].initialize( molInfo ); |
375 |
|
|
376 |
|
|
377 |
< |
atomOffset += info.nAtoms; |
377 |
> |
atomOffset += molInfo.nAtoms; |
378 |
|
delete[] theBonds; |
379 |
|
delete[] theBends; |
380 |
|
delete[] theTorsions; |
410 |
|
have_extra =1; |
411 |
|
|
412 |
|
n_cells = (int)temp3 - 1; |
413 |
< |
cellx = simnfo->box_x / temp3; |
414 |
< |
celly = simnfo->box_y / temp3; |
415 |
< |
cellz = simnfo->box_z / temp3; |
413 |
> |
cellx = info->boxL[0] / temp3; |
414 |
> |
celly = info->boxL[1] / temp3; |
415 |
> |
cellz = info->boxL[2] / temp3; |
416 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
417 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
418 |
|
n_per_extra = (int)ceil( temp1 ); |
427 |
|
} |
428 |
|
else{ |
429 |
|
n_cells = (int)temp3; |
430 |
< |
cellx = simnfo->box_x / temp3; |
431 |
< |
celly = simnfo->box_y / temp3; |
432 |
< |
cellz = simnfo->box_z / temp3; |
430 |
> |
cellx = info->boxL[0] / temp3; |
431 |
> |
celly = info->boxL[1] / temp3; |
432 |
> |
cellz = info->boxL[2] / temp3; |
433 |
|
} |
434 |
|
|
435 |
|
current_mol = 0; |
509 |
|
} |
510 |
|
|
511 |
|
|
512 |
< |
for( i=0; i<simnfo->n_atoms; i++ ){ |
513 |
< |
simnfo->atoms[i]->set_vx( 0.0 ); |
514 |
< |
simnfo->atoms[i]->set_vy( 0.0 ); |
515 |
< |
simnfo->atoms[i]->set_vz( 0.0 ); |
512 |
> |
for( i=0; i<info->n_atoms; i++ ){ |
513 |
> |
info->atoms[i]->set_vx( 0.0 ); |
514 |
> |
info->atoms[i]->set_vy( 0.0 ); |
515 |
> |
info->atoms[i]->set_vz( 0.0 ); |
516 |
|
} |
517 |
|
} |
518 |
|
|
573 |
|
current_comp++; |
574 |
|
} |
575 |
|
} |
576 |
+ |
|
577 |
+ |
|
578 |
+ |
void SimSetup::gatherInfo( void ){ |
579 |
+ |
int i,j,k; |
580 |
+ |
|
581 |
+ |
ensembleCase = -1; |
582 |
+ |
ffCase = -1; |
583 |
+ |
|
584 |
+ |
// get the stamps and globals; |
585 |
+ |
stamps = stamps; |
586 |
+ |
globals = globals; |
587 |
+ |
|
588 |
+ |
// set the easy ones first |
589 |
+ |
info->target_temp = globals->getTargetTemp(); |
590 |
+ |
info->dt = globals->getDt(); |
591 |
+ |
info->run_time = globals->getRunTime(); |
592 |
+ |
n_components = globals->getNComponents(); |
593 |
+ |
|
594 |
+ |
|
595 |
+ |
// get the forceField |
596 |
+ |
|
597 |
+ |
strcpy( force_field, globals->getForceField() ); |
598 |
+ |
|
599 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
600 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
601 |
+ |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
602 |
+ |
else{ |
603 |
+ |
sprintf( painCave.errMsg, |
604 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
605 |
+ |
force_field ); |
606 |
+ |
painCave.isFatal = 1; |
607 |
+ |
simError(); |
608 |
+ |
} |
609 |
+ |
|
610 |
+ |
// get the ensemble |
611 |
+ |
|
612 |
+ |
strcpy( ensemble, globals->getEnsemble() ); |
613 |
+ |
|
614 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
615 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
616 |
+ |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
617 |
+ |
ensembleCase = NPTi_ENS; |
618 |
+ |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
619 |
+ |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
620 |
+ |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
621 |
+ |
else{ |
622 |
+ |
sprintf( painCave.errMsg, |
623 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
624 |
+ |
"reverting to NVE for this simulation.\n", |
625 |
+ |
ensemble ); |
626 |
+ |
painCave.isFatal = 0; |
627 |
+ |
simError(); |
628 |
+ |
strcpy( ensemble, "NVE" ); |
629 |
+ |
ensembleCase = NVE_ENS; |
630 |
+ |
} |
631 |
+ |
strcpy( info->ensemble, ensemble ); |
632 |
+ |
|
633 |
+ |
// get the mixing rule |
634 |
+ |
|
635 |
+ |
strcpy( info->mixingRule, globals->getMixingRule() ); |
636 |
+ |
info->usePBC = globals->getPBC(); |
637 |
+ |
|
638 |
+ |
|
639 |
+ |
// get the components and calculate the tot_nMol and indvidual n_mol |
640 |
+ |
|
641 |
+ |
the_components = globals->getComponents(); |
642 |
+ |
components_nmol = new int[n_components]; |
643 |
+ |
|
644 |
+ |
|
645 |
+ |
if( !globals->haveNMol() ){ |
646 |
+ |
// we don't have the total number of molecules, so we assume it is |
647 |
+ |
// given in each component |
648 |
+ |
|
649 |
+ |
tot_nmol = 0; |
650 |
+ |
for( i=0; i<n_components; i++ ){ |
651 |
+ |
|
652 |
+ |
if( !the_components[i]->haveNMol() ){ |
653 |
+ |
// we have a problem |
654 |
+ |
sprintf( painCave.errMsg, |
655 |
+ |
"SimSetup Error. No global NMol or component NMol" |
656 |
+ |
" given. Cannot calculate the number of atoms.\n" ); |
657 |
+ |
painCave.isFatal = 1; |
658 |
+ |
simError(); |
659 |
+ |
} |
660 |
+ |
|
661 |
+ |
tot_nmol += the_components[i]->getNMol(); |
662 |
+ |
components_nmol[i] = the_components[i]->getNMol(); |
663 |
+ |
} |
664 |
+ |
} |
665 |
+ |
else{ |
666 |
+ |
sprintf( painCave.errMsg, |
667 |
+ |
"SimSetup error.\n" |
668 |
+ |
"\tSorry, the ability to specify total" |
669 |
+ |
" nMols and then give molfractions in the components\n" |
670 |
+ |
"\tis not currently supported." |
671 |
+ |
" Please give nMol in the components.\n" ); |
672 |
+ |
painCave.isFatal = 1; |
673 |
+ |
simError(); |
674 |
+ |
} |
675 |
+ |
|
676 |
+ |
// set the status, sample, and thermal kick times |
677 |
+ |
|
678 |
+ |
if( globals->haveSampleTime() ){ |
679 |
+ |
info->sampleTime = globals->getSampleTime(); |
680 |
+ |
info->statusTime = info->sampleTime; |
681 |
+ |
info->thermalTime = info->sampleTime; |
682 |
+ |
} |
683 |
+ |
else{ |
684 |
+ |
info->sampleTime = globals->getRunTime(); |
685 |
+ |
info->statusTime = info->sampleTime; |
686 |
+ |
info->thermalTime = info->sampleTime; |
687 |
+ |
} |
688 |
+ |
|
689 |
+ |
if( globals->haveStatusTime() ){ |
690 |
+ |
info->statusTime = globals->getStatusTime(); |
691 |
+ |
} |
692 |
+ |
|
693 |
+ |
if( globals->haveThermalTime() ){ |
694 |
+ |
info->thermalTime = globals->getThermalTime(); |
695 |
+ |
} |
696 |
+ |
|
697 |
+ |
// check for the temperature set flag |
698 |
+ |
|
699 |
+ |
if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
700 |
+ |
|
701 |
+ |
// get some of the tricky things that may still be in the globals |
702 |
+ |
|
703 |
+ |
double boxVector[3]; |
704 |
+ |
if( globals->haveBox() ){ |
705 |
+ |
boxVector[0] = globals->getBox(); |
706 |
+ |
boxVector[1] = globals->getBox(); |
707 |
+ |
boxVector[2] = globals->getBox(); |
708 |
+ |
|
709 |
+ |
info->setBox( boxVector ); |
710 |
+ |
} |
711 |
+ |
else if( globals->haveDensity() ){ |
712 |
+ |
|
713 |
+ |
double vol; |
714 |
+ |
vol = (double)tot_nmol / globals->getDensity(); |
715 |
+ |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
716 |
+ |
boxVector[1] = boxVector[0]; |
717 |
+ |
boxVector[2] = boxVector[0]; |
718 |
+ |
|
719 |
+ |
info->setBox( boxVector ); |
720 |
+ |
} |
721 |
+ |
else{ |
722 |
+ |
if( !globals->haveBoxX() ){ |
723 |
+ |
sprintf( painCave.errMsg, |
724 |
+ |
"SimSetup error, no periodic BoxX size given.\n" ); |
725 |
+ |
painCave.isFatal = 1; |
726 |
+ |
simError(); |
727 |
+ |
} |
728 |
+ |
boxVector[0] = globals->getBoxX(); |
729 |
+ |
|
730 |
+ |
if( !globals->haveBoxY() ){ |
731 |
+ |
sprintf( painCave.errMsg, |
732 |
+ |
"SimSetup error, no periodic BoxY size given.\n" ); |
733 |
+ |
painCave.isFatal = 1; |
734 |
+ |
simError(); |
735 |
+ |
} |
736 |
+ |
boxVector[1] = globals->getBoxY(); |
737 |
+ |
|
738 |
+ |
if( !globals->haveBoxZ() ){ |
739 |
+ |
sprintf( painCave.errMsg, |
740 |
+ |
"SimSetup error, no periodic BoxZ size given.\n" ); |
741 |
+ |
painCave.isFatal = 1; |
742 |
+ |
simError(); |
743 |
+ |
} |
744 |
+ |
boxVector[2] = globals->getBoxZ(); |
745 |
+ |
|
746 |
+ |
info->setBox( boxVector ); |
747 |
+ |
} |
748 |
+ |
|
749 |
+ |
|
750 |
+ |
|
751 |
+ |
#ifdef IS_MPI |
752 |
+ |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
753 |
+ |
MPIcheckPoint(); |
754 |
+ |
#endif // is_mpi |
755 |
+ |
|
756 |
+ |
} |
757 |
+ |
|
758 |
+ |
|
759 |
+ |
void SimSetup::finalInfoCheck( void ){ |
760 |
+ |
int index; |
761 |
+ |
int usesDipoles; |
762 |
+ |
|
763 |
+ |
|
764 |
+ |
// check electrostatic parameters |
765 |
+ |
|
766 |
+ |
index = 0; |
767 |
+ |
usesDipoles = 0; |
768 |
+ |
while( (index < info->n_atoms) && !usesDipoles ){ |
769 |
+ |
usesDipoles = ((info->atoms)[index])->hasDipole(); |
770 |
+ |
index++; |
771 |
+ |
} |
772 |
+ |
|
773 |
+ |
#ifdef IS_MPI |
774 |
+ |
int myUse = usesDipoles; |
775 |
+ |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
776 |
+ |
#endif //is_mpi |
777 |
+ |
|
778 |
+ |
double theEcr, theEst; |
779 |
+ |
|
780 |
+ |
if (globals->getUseRF() ) { |
781 |
+ |
info->useReactionField = 1; |
782 |
+ |
|
783 |
+ |
if( !globals->haveECR() ){ |
784 |
+ |
sprintf( painCave.errMsg, |
785 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
786 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
787 |
+ |
"I hope you have a very fast processor!\n"); |
788 |
+ |
painCave.isFatal = 0; |
789 |
+ |
simError(); |
790 |
+ |
double smallest; |
791 |
+ |
smallest = info->boxL[0]; |
792 |
+ |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
793 |
+ |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
794 |
+ |
theEcr = 0.5 * smallest; |
795 |
+ |
} else { |
796 |
+ |
theEcr = globals->getECR(); |
797 |
+ |
} |
798 |
+ |
|
799 |
+ |
if( !globals->haveEST() ){ |
800 |
+ |
sprintf( painCave.errMsg, |
801 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
802 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
803 |
+ |
); |
804 |
+ |
painCave.isFatal = 0; |
805 |
+ |
simError(); |
806 |
+ |
theEst = 0.05 * theEcr; |
807 |
+ |
} else { |
808 |
+ |
theEst= globals->getEST(); |
809 |
+ |
} |
810 |
+ |
|
811 |
+ |
info->setEcr( theEcr, theEst ); |
812 |
+ |
|
813 |
+ |
if(!globals->haveDielectric() ){ |
814 |
+ |
sprintf( painCave.errMsg, |
815 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
816 |
+ |
"setting a dielectric constant!\n" |
817 |
+ |
); |
818 |
+ |
painCave.isFatal = 1; |
819 |
+ |
simError(); |
820 |
+ |
} |
821 |
+ |
info->dielectric = globals->getDielectric(); |
822 |
+ |
} |
823 |
+ |
else { |
824 |
+ |
if (usesDipoles) { |
825 |
+ |
|
826 |
+ |
if( !globals->haveECR() ){ |
827 |
+ |
sprintf( painCave.errMsg, |
828 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
829 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
830 |
+ |
"I hope you have a very fast processor!\n"); |
831 |
+ |
painCave.isFatal = 0; |
832 |
+ |
simError(); |
833 |
+ |
double smallest; |
834 |
+ |
smallest = info->boxL[0]; |
835 |
+ |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
836 |
+ |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
837 |
+ |
theEcr = 0.5 * smallest; |
838 |
+ |
} else { |
839 |
+ |
theEcr = globals->getECR(); |
840 |
+ |
} |
841 |
+ |
|
842 |
+ |
if( !globals->haveEST() ){ |
843 |
+ |
sprintf( painCave.errMsg, |
844 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
845 |
+ |
"electrostaticCutoffRadius for the " |
846 |
+ |
"electrostaticSkinThickness\n" |
847 |
+ |
); |
848 |
+ |
painCave.isFatal = 0; |
849 |
+ |
simError(); |
850 |
+ |
theEst = 0.05 * theEcr; |
851 |
+ |
} else { |
852 |
+ |
theEst= globals->getEST(); |
853 |
+ |
} |
854 |
+ |
|
855 |
+ |
info->setEcr( theEcr, theEst ); |
856 |
+ |
} |
857 |
+ |
} |
858 |
+ |
|
859 |
+ |
#ifdef IS_MPI |
860 |
+ |
strcpy( checkPointMsg, "post processing checks out" ); |
861 |
+ |
MPIcheckPoint(); |
862 |
+ |
#endif // is_mpi |
863 |
+ |
|
864 |
+ |
} |
865 |
+ |
|
866 |
+ |
void SimSetup::initSystemCoords( void ){ |
867 |
+ |
|
868 |
+ |
if( globals->haveInitialConfig() ){ |
869 |
+ |
|
870 |
+ |
InitializeFromFile* fileInit; |
871 |
+ |
#ifdef IS_MPI // is_mpi |
872 |
+ |
if( worldRank == 0 ){ |
873 |
+ |
#endif //is_mpi |
874 |
+ |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
875 |
+ |
#ifdef IS_MPI |
876 |
+ |
}else fileInit = new InitializeFromFile( NULL ); |
877 |
+ |
#endif |
878 |
+ |
fileInit->readInit( info ); // default velocities on |
879 |
+ |
|
880 |
+ |
delete fileInit; |
881 |
+ |
} |
882 |
+ |
else{ |
883 |
+ |
|
884 |
+ |
#ifdef IS_MPI |
885 |
+ |
|
886 |
+ |
// no init from bass |
887 |
+ |
|
888 |
+ |
sprintf( painCave.errMsg, |
889 |
+ |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
890 |
+ |
painCave.isFatal; |
891 |
+ |
simError(); |
892 |
+ |
|
893 |
+ |
#else |
894 |
+ |
|
895 |
+ |
initFromBass(); |
896 |
+ |
|
897 |
+ |
|
898 |
+ |
#endif |
899 |
+ |
} |
900 |
+ |
|
901 |
+ |
#ifdef IS_MPI |
902 |
+ |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
903 |
+ |
MPIcheckPoint(); |
904 |
+ |
#endif // is_mpi |
905 |
+ |
|
906 |
+ |
} |
907 |
+ |
|
908 |
+ |
|
909 |
+ |
void SimSetup::makeOutNames( void ){ |
910 |
+ |
|
911 |
+ |
#ifdef IS_MPI |
912 |
+ |
if( worldRank == 0 ){ |
913 |
+ |
#endif // is_mpi |
914 |
+ |
|
915 |
+ |
if( globals->haveFinalConfig() ){ |
916 |
+ |
strcpy( info->finalName, globals->getFinalConfig() ); |
917 |
+ |
} |
918 |
+ |
else{ |
919 |
+ |
strcpy( info->finalName, inFileName ); |
920 |
+ |
char* endTest; |
921 |
+ |
int nameLength = strlen( info->finalName ); |
922 |
+ |
endTest = &(info->finalName[nameLength - 5]); |
923 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
924 |
+ |
strcpy( endTest, ".eor" ); |
925 |
+ |
} |
926 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
927 |
+ |
strcpy( endTest, ".eor" ); |
928 |
+ |
} |
929 |
+ |
else{ |
930 |
+ |
endTest = &(info->finalName[nameLength - 4]); |
931 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
932 |
+ |
strcpy( endTest, ".eor" ); |
933 |
+ |
} |
934 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
935 |
+ |
strcpy( endTest, ".eor" ); |
936 |
+ |
} |
937 |
+ |
else{ |
938 |
+ |
strcat( info->finalName, ".eor" ); |
939 |
+ |
} |
940 |
+ |
} |
941 |
+ |
} |
942 |
+ |
|
943 |
+ |
// make the sample and status out names |
944 |
+ |
|
945 |
+ |
strcpy( info->sampleName, inFileName ); |
946 |
+ |
char* endTest; |
947 |
+ |
int nameLength = strlen( info->sampleName ); |
948 |
+ |
endTest = &(info->sampleName[nameLength - 5]); |
949 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
950 |
+ |
strcpy( endTest, ".dump" ); |
951 |
+ |
} |
952 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
953 |
+ |
strcpy( endTest, ".dump" ); |
954 |
+ |
} |
955 |
+ |
else{ |
956 |
+ |
endTest = &(info->sampleName[nameLength - 4]); |
957 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
958 |
+ |
strcpy( endTest, ".dump" ); |
959 |
+ |
} |
960 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
961 |
+ |
strcpy( endTest, ".dump" ); |
962 |
+ |
} |
963 |
+ |
else{ |
964 |
+ |
strcat( info->sampleName, ".dump" ); |
965 |
+ |
} |
966 |
+ |
} |
967 |
+ |
|
968 |
+ |
strcpy( info->statusName, inFileName ); |
969 |
+ |
nameLength = strlen( info->statusName ); |
970 |
+ |
endTest = &(info->statusName[nameLength - 5]); |
971 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
972 |
+ |
strcpy( endTest, ".stat" ); |
973 |
+ |
} |
974 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
975 |
+ |
strcpy( endTest, ".stat" ); |
976 |
+ |
} |
977 |
+ |
else{ |
978 |
+ |
endTest = &(info->statusName[nameLength - 4]); |
979 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
980 |
+ |
strcpy( endTest, ".stat" ); |
981 |
+ |
} |
982 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
983 |
+ |
strcpy( endTest, ".stat" ); |
984 |
+ |
} |
985 |
+ |
else{ |
986 |
+ |
strcat( info->statusName, ".stat" ); |
987 |
+ |
} |
988 |
+ |
} |
989 |
+ |
|
990 |
+ |
#ifdef IS_MPI |
991 |
+ |
} |
992 |
+ |
#endif // is_mpi |
993 |
+ |
|
994 |
+ |
} |
995 |
+ |
|
996 |
+ |
|
997 |
+ |
void SimSetup::sysObjectsCreation( void ){ |
998 |
+ |
|
999 |
+ |
int i; |
1000 |
+ |
|
1001 |
+ |
// create the forceField |
1002 |
+ |
|
1003 |
+ |
createFF(); |
1004 |
+ |
|
1005 |
+ |
// extract componentList |
1006 |
+ |
|
1007 |
+ |
compList(); |
1008 |
+ |
|
1009 |
+ |
// calc the number of atoms, bond, bends, and torsions |
1010 |
+ |
|
1011 |
+ |
calcSysValues(); |
1012 |
+ |
|
1013 |
+ |
#ifdef IS_MPI |
1014 |
+ |
// divide the molecules among the processors |
1015 |
+ |
|
1016 |
+ |
mpiMolDivide(); |
1017 |
+ |
#endif //is_mpi |
1018 |
+ |
|
1019 |
+ |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1020 |
+ |
|
1021 |
+ |
makeSysArrays(); |
1022 |
+ |
|
1023 |
+ |
// make and initialize the molecules (all but atomic coordinates) |
1024 |
+ |
|
1025 |
+ |
makeMolecules(); |
1026 |
+ |
info->identArray = new int[info->n_atoms]; |
1027 |
+ |
for(i=0; i<info->n_atoms; i++){ |
1028 |
+ |
info->identArray[i] = the_atoms[i]->getIdent(); |
1029 |
+ |
} |
1030 |
+ |
|
1031 |
+ |
|
1032 |
+ |
|
1033 |
+ |
} |
1034 |
+ |
|
1035 |
+ |
|
1036 |
+ |
void SimSetup::createFF( void ){ |
1037 |
+ |
|
1038 |
+ |
switch( ffCase ){ |
1039 |
+ |
|
1040 |
+ |
case FF_DUFF: |
1041 |
+ |
the_ff = new DUFF(); |
1042 |
+ |
break; |
1043 |
+ |
|
1044 |
+ |
case FF_LJ: |
1045 |
+ |
the_ff = new LJFF(); |
1046 |
+ |
break; |
1047 |
+ |
|
1048 |
+ |
case FF_EAM: |
1049 |
+ |
the_ff = new EAM_FF(); |
1050 |
+ |
break; |
1051 |
+ |
|
1052 |
+ |
default: |
1053 |
+ |
sprintf( painCave.errMsg, |
1054 |
+ |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1055 |
+ |
painCave.isFatal = 1; |
1056 |
+ |
simError(); |
1057 |
+ |
} |
1058 |
+ |
|
1059 |
+ |
#ifdef IS_MPI |
1060 |
+ |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1061 |
+ |
MPIcheckPoint(); |
1062 |
+ |
#endif // is_mpi |
1063 |
+ |
|
1064 |
+ |
} |
1065 |
+ |
|
1066 |
+ |
|
1067 |
+ |
void SimSetup::compList( void ){ |
1068 |
+ |
|
1069 |
+ |
int i; |
1070 |
+ |
|
1071 |
+ |
comp_stamps = new MoleculeStamp*[n_components]; |
1072 |
+ |
|
1073 |
+ |
// make an array of molecule stamps that match the components used. |
1074 |
+ |
// also extract the used stamps out into a separate linked list |
1075 |
+ |
|
1076 |
+ |
info->nComponents = n_components; |
1077 |
+ |
info->componentsNmol = components_nmol; |
1078 |
+ |
info->compStamps = comp_stamps; |
1079 |
+ |
info->headStamp = new LinkedMolStamp(); |
1080 |
+ |
|
1081 |
+ |
char* id; |
1082 |
+ |
LinkedMolStamp* headStamp = info->headStamp; |
1083 |
+ |
LinkedMolStamp* currentStamp = NULL; |
1084 |
+ |
for( i=0; i<n_components; i++ ){ |
1085 |
+ |
|
1086 |
+ |
id = the_components[i]->getType(); |
1087 |
+ |
comp_stamps[i] = NULL; |
1088 |
+ |
|
1089 |
+ |
// check to make sure the component isn't already in the list |
1090 |
+ |
|
1091 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1092 |
+ |
if( comp_stamps[i] == NULL ){ |
1093 |
+ |
|
1094 |
+ |
// extract the component from the list; |
1095 |
+ |
|
1096 |
+ |
currentStamp = stamps->extractMolStamp( id ); |
1097 |
+ |
if( currentStamp == NULL ){ |
1098 |
+ |
sprintf( painCave.errMsg, |
1099 |
+ |
"SimSetup error: Component \"%s\" was not found in the " |
1100 |
+ |
"list of declared molecules\n", |
1101 |
+ |
id ); |
1102 |
+ |
painCave.isFatal = 1; |
1103 |
+ |
simError(); |
1104 |
+ |
} |
1105 |
+ |
|
1106 |
+ |
headStamp->add( currentStamp ); |
1107 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1108 |
+ |
} |
1109 |
+ |
} |
1110 |
+ |
|
1111 |
+ |
#ifdef IS_MPI |
1112 |
+ |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1113 |
+ |
MPIcheckPoint(); |
1114 |
+ |
#endif // is_mpi |
1115 |
+ |
|
1116 |
+ |
|
1117 |
+ |
} |
1118 |
+ |
|
1119 |
+ |
void SimSetup::calcSysValues( void ){ |
1120 |
+ |
int i, j, k; |
1121 |
+ |
|
1122 |
+ |
|
1123 |
+ |
tot_atoms = 0; |
1124 |
+ |
tot_bonds = 0; |
1125 |
+ |
tot_bends = 0; |
1126 |
+ |
tot_torsions = 0; |
1127 |
+ |
for( i=0; i<n_components; i++ ){ |
1128 |
+ |
|
1129 |
+ |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1130 |
+ |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1131 |
+ |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1132 |
+ |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1133 |
+ |
} |
1134 |
+ |
|
1135 |
+ |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1136 |
+ |
|
1137 |
+ |
info->n_atoms = tot_atoms; |
1138 |
+ |
info->n_bonds = tot_bonds; |
1139 |
+ |
info->n_bends = tot_bends; |
1140 |
+ |
info->n_torsions = tot_torsions; |
1141 |
+ |
info->n_SRI = tot_SRI; |
1142 |
+ |
info->n_mol = tot_nmol; |
1143 |
+ |
|
1144 |
+ |
info->molMembershipArray = new int[tot_atoms]; |
1145 |
+ |
} |
1146 |
+ |
|
1147 |
+ |
|
1148 |
+ |
#ifdef IS_MPI |
1149 |
+ |
|
1150 |
+ |
void SimSetup::mpiMolDivide( void ){ |
1151 |
+ |
|
1152 |
+ |
int i, j, k; |
1153 |
+ |
int localMol, allMol; |
1154 |
+ |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1155 |
+ |
|
1156 |
+ |
mpiSim = new mpiSimulation( info ); |
1157 |
+ |
|
1158 |
+ |
globalIndex = mpiSim->divideLabor(); |
1159 |
+ |
|
1160 |
+ |
// set up the local variables |
1161 |
+ |
|
1162 |
+ |
mol2proc = mpiSim->getMolToProcMap(); |
1163 |
+ |
molCompType = mpiSim->getMolComponentType(); |
1164 |
+ |
|
1165 |
+ |
allMol = 0; |
1166 |
+ |
localMol = 0; |
1167 |
+ |
local_atoms = 0; |
1168 |
+ |
local_bonds = 0; |
1169 |
+ |
local_bends = 0; |
1170 |
+ |
local_torsions = 0; |
1171 |
+ |
globalAtomIndex = 0; |
1172 |
+ |
|
1173 |
+ |
|
1174 |
+ |
for( i=0; i<n_components; i++ ){ |
1175 |
+ |
|
1176 |
+ |
for( j=0; j<components_nmol[i]; j++ ){ |
1177 |
+ |
|
1178 |
+ |
if( mol2proc[allMol] == worldRank ){ |
1179 |
+ |
|
1180 |
+ |
local_atoms += comp_stamps[i]->getNAtoms(); |
1181 |
+ |
local_bonds += comp_stamps[i]->getNBonds(); |
1182 |
+ |
local_bends += comp_stamps[i]->getNBends(); |
1183 |
+ |
local_torsions += comp_stamps[i]->getNTorsions(); |
1184 |
+ |
localMol++; |
1185 |
+ |
} |
1186 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1187 |
+ |
info->molMembershipArray[globalAtomIndex] = allMol; |
1188 |
+ |
globalAtomIndex++; |
1189 |
+ |
} |
1190 |
+ |
|
1191 |
+ |
allMol++; |
1192 |
+ |
} |
1193 |
+ |
} |
1194 |
+ |
local_SRI = local_bonds + local_bends + local_torsions; |
1195 |
+ |
|
1196 |
+ |
info->n_atoms = mpiSim->getMyNlocal(); |
1197 |
+ |
|
1198 |
+ |
if( local_atoms != info->n_atoms ){ |
1199 |
+ |
sprintf( painCave.errMsg, |
1200 |
+ |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1201 |
+ |
" localAtom (%d) are not equal.\n", |
1202 |
+ |
info->n_atoms, |
1203 |
+ |
local_atoms ); |
1204 |
+ |
painCave.isFatal = 1; |
1205 |
+ |
simError(); |
1206 |
+ |
} |
1207 |
+ |
|
1208 |
+ |
info->n_bonds = local_bonds; |
1209 |
+ |
info->n_bends = local_bends; |
1210 |
+ |
info->n_torsions = local_torsions; |
1211 |
+ |
info->n_SRI = local_SRI; |
1212 |
+ |
info->n_mol = localMol; |
1213 |
+ |
|
1214 |
+ |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1215 |
+ |
MPIcheckPoint(); |
1216 |
+ |
} |
1217 |
+ |
|
1218 |
+ |
#endif // is_mpi |
1219 |
+ |
|
1220 |
+ |
|
1221 |
+ |
void SimSetup::makeSysArrays( void ){ |
1222 |
+ |
int i, j, k; |
1223 |
+ |
|
1224 |
+ |
|
1225 |
+ |
// create the atom and short range interaction arrays |
1226 |
+ |
|
1227 |
+ |
Atom::createArrays(info->n_atoms); |
1228 |
+ |
the_atoms = new Atom*[info->n_atoms]; |
1229 |
+ |
the_molecules = new Molecule[info->n_mol]; |
1230 |
+ |
int molIndex; |
1231 |
+ |
|
1232 |
+ |
// initialize the molecule's stampID's |
1233 |
+ |
|
1234 |
+ |
#ifdef IS_MPI |
1235 |
+ |
|
1236 |
+ |
|
1237 |
+ |
molIndex = 0; |
1238 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1239 |
+ |
|
1240 |
+ |
if(mol2proc[i] == worldRank ){ |
1241 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1242 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1243 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
1244 |
+ |
molIndex++; |
1245 |
+ |
} |
1246 |
+ |
} |
1247 |
+ |
|
1248 |
+ |
#else // is_mpi |
1249 |
+ |
|
1250 |
+ |
molIndex = 0; |
1251 |
+ |
globalAtomIndex = 0; |
1252 |
+ |
for(i=0; i<n_components; i++){ |
1253 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
1254 |
+ |
the_molecules[molIndex].setStampID( i ); |
1255 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1256 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1257 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1258 |
+ |
info->molMembershipArray[globalAtomIndex] = molIndex; |
1259 |
+ |
globalAtomIndex++; |
1260 |
+ |
} |
1261 |
+ |
molIndex++; |
1262 |
+ |
} |
1263 |
+ |
} |
1264 |
+ |
|
1265 |
+ |
|
1266 |
+ |
#endif // is_mpi |
1267 |
+ |
|
1268 |
+ |
|
1269 |
+ |
if( info->n_SRI ){ |
1270 |
+ |
|
1271 |
+ |
Exclude::createArray(info->n_SRI); |
1272 |
+ |
the_excludes = new Exclude*[info->n_SRI]; |
1273 |
+ |
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1274 |
+ |
info->globalExcludes = new int; |
1275 |
+ |
info->n_exclude = info->n_SRI; |
1276 |
+ |
} |
1277 |
+ |
else{ |
1278 |
+ |
|
1279 |
+ |
Exclude::createArray( 1 ); |
1280 |
+ |
the_excludes = new Exclude*; |
1281 |
+ |
the_excludes[0] = new Exclude(0); |
1282 |
+ |
the_excludes[0]->setPair( 0,0 ); |
1283 |
+ |
info->globalExcludes = new int; |
1284 |
+ |
info->globalExcludes[0] = 0; |
1285 |
+ |
info->n_exclude = 0; |
1286 |
+ |
} |
1287 |
+ |
|
1288 |
+ |
// set the arrays into the SimInfo object |
1289 |
+ |
|
1290 |
+ |
info->atoms = the_atoms; |
1291 |
+ |
info->molecules = the_molecules; |
1292 |
+ |
info->nGlobalExcludes = 0; |
1293 |
+ |
info->excludes = the_excludes; |
1294 |
+ |
|
1295 |
+ |
the_ff->setSimInfo( info ); |
1296 |
+ |
|
1297 |
+ |
} |
1298 |
+ |
|
1299 |
+ |
void SimSetup::makeIntegrator( void ){ |
1300 |
+ |
|
1301 |
+ |
NVT<RealIntegrator>* myNVT = NULL; |
1302 |
+ |
NPTi<RealIntegrator>* myNPTi = NULL; |
1303 |
+ |
NPTf<RealIntegrator>* myNPTf = NULL; |
1304 |
+ |
NPTim<RealIntegrator>* myNPTim = NULL; |
1305 |
+ |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1306 |
+ |
|
1307 |
+ |
switch( ensembleCase ){ |
1308 |
+ |
|
1309 |
+ |
case NVE_ENS: |
1310 |
+ |
new NVE<RealIntegrator>( info, the_ff ); |
1311 |
+ |
break; |
1312 |
+ |
|
1313 |
+ |
case NVT_ENS: |
1314 |
+ |
myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1315 |
+ |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1316 |
+ |
|
1317 |
+ |
if (globals->haveTauThermostat()) |
1318 |
+ |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1319 |
+ |
|
1320 |
+ |
else { |
1321 |
+ |
sprintf( painCave.errMsg, |
1322 |
+ |
"SimSetup error: If you use the NVT\n" |
1323 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1324 |
+ |
painCave.isFatal = 1; |
1325 |
+ |
simError(); |
1326 |
+ |
} |
1327 |
+ |
break; |
1328 |
+ |
|
1329 |
+ |
case NPTi_ENS: |
1330 |
+ |
myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1331 |
+ |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1332 |
+ |
|
1333 |
+ |
if (globals->haveTargetPressure()) |
1334 |
+ |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1335 |
+ |
else { |
1336 |
+ |
sprintf( painCave.errMsg, |
1337 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1338 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1339 |
+ |
painCave.isFatal = 1; |
1340 |
+ |
simError(); |
1341 |
+ |
} |
1342 |
+ |
|
1343 |
+ |
if( globals->haveTauThermostat() ) |
1344 |
+ |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1345 |
+ |
else{ |
1346 |
+ |
sprintf( painCave.errMsg, |
1347 |
+ |
"SimSetup error: If you use an NPT\n" |
1348 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1349 |
+ |
painCave.isFatal = 1; |
1350 |
+ |
simError(); |
1351 |
+ |
} |
1352 |
+ |
|
1353 |
+ |
if( globals->haveTauBarostat() ) |
1354 |
+ |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1355 |
+ |
else{ |
1356 |
+ |
sprintf( painCave.errMsg, |
1357 |
+ |
"SimSetup error: If you use an NPT\n" |
1358 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1359 |
+ |
painCave.isFatal = 1; |
1360 |
+ |
simError(); |
1361 |
+ |
} |
1362 |
+ |
break; |
1363 |
+ |
|
1364 |
+ |
case NPTf_ENS: |
1365 |
+ |
myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1366 |
+ |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1367 |
+ |
|
1368 |
+ |
if (globals->haveTargetPressure()) |
1369 |
+ |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1370 |
+ |
else { |
1371 |
+ |
sprintf( painCave.errMsg, |
1372 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1373 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1374 |
+ |
painCave.isFatal = 1; |
1375 |
+ |
simError(); |
1376 |
+ |
} |
1377 |
+ |
|
1378 |
+ |
if( globals->haveTauThermostat() ) |
1379 |
+ |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1380 |
+ |
else{ |
1381 |
+ |
sprintf( painCave.errMsg, |
1382 |
+ |
"SimSetup error: If you use an NPT\n" |
1383 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1384 |
+ |
painCave.isFatal = 1; |
1385 |
+ |
simError(); |
1386 |
+ |
} |
1387 |
+ |
|
1388 |
+ |
if( globals->haveTauBarostat() ) |
1389 |
+ |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1390 |
+ |
else{ |
1391 |
+ |
sprintf( painCave.errMsg, |
1392 |
+ |
"SimSetup error: If you use an NPT\n" |
1393 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1394 |
+ |
painCave.isFatal = 1; |
1395 |
+ |
simError(); |
1396 |
+ |
} |
1397 |
+ |
break; |
1398 |
+ |
|
1399 |
+ |
case NPTim_ENS: |
1400 |
+ |
myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1401 |
+ |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1402 |
+ |
|
1403 |
+ |
if (globals->haveTargetPressure()) |
1404 |
+ |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1405 |
+ |
else { |
1406 |
+ |
sprintf( painCave.errMsg, |
1407 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1408 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1409 |
+ |
painCave.isFatal = 1; |
1410 |
+ |
simError(); |
1411 |
+ |
} |
1412 |
+ |
|
1413 |
+ |
if( globals->haveTauThermostat() ) |
1414 |
+ |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1415 |
+ |
else{ |
1416 |
+ |
sprintf( painCave.errMsg, |
1417 |
+ |
"SimSetup error: If you use an NPT\n" |
1418 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1419 |
+ |
painCave.isFatal = 1; |
1420 |
+ |
simError(); |
1421 |
+ |
} |
1422 |
+ |
|
1423 |
+ |
if( globals->haveTauBarostat() ) |
1424 |
+ |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1425 |
+ |
else{ |
1426 |
+ |
sprintf( painCave.errMsg, |
1427 |
+ |
"SimSetup error: If you use an NPT\n" |
1428 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1429 |
+ |
painCave.isFatal = 1; |
1430 |
+ |
simError(); |
1431 |
+ |
} |
1432 |
+ |
break; |
1433 |
+ |
|
1434 |
+ |
case NPTfm_ENS: |
1435 |
+ |
myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1436 |
+ |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1437 |
+ |
|
1438 |
+ |
if (globals->haveTargetPressure()) |
1439 |
+ |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1440 |
+ |
else { |
1441 |
+ |
sprintf( painCave.errMsg, |
1442 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1443 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1444 |
+ |
painCave.isFatal = 1; |
1445 |
+ |
simError(); |
1446 |
+ |
} |
1447 |
+ |
|
1448 |
+ |
if( globals->haveTauThermostat() ) |
1449 |
+ |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1450 |
+ |
else{ |
1451 |
+ |
sprintf( painCave.errMsg, |
1452 |
+ |
"SimSetup error: If you use an NPT\n" |
1453 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1454 |
+ |
painCave.isFatal = 1; |
1455 |
+ |
simError(); |
1456 |
+ |
} |
1457 |
+ |
|
1458 |
+ |
if( globals->haveTauBarostat() ) |
1459 |
+ |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1460 |
+ |
else{ |
1461 |
+ |
sprintf( painCave.errMsg, |
1462 |
+ |
"SimSetup error: If you use an NPT\n" |
1463 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1464 |
+ |
painCave.isFatal = 1; |
1465 |
+ |
simError(); |
1466 |
+ |
} |
1467 |
+ |
break; |
1468 |
+ |
|
1469 |
+ |
default: |
1470 |
+ |
sprintf( painCave.errMsg, |
1471 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1472 |
+ |
painCave.isFatal = 1; |
1473 |
+ |
simError(); |
1474 |
+ |
} |
1475 |
+ |
|
1476 |
+ |
} |
1477 |
+ |
|
1478 |
+ |
void SimSetup::initFortran( void ){ |
1479 |
+ |
|
1480 |
+ |
info->refreshSim(); |
1481 |
+ |
|
1482 |
+ |
if( !strcmp( info->mixingRule, "standard") ){ |
1483 |
+ |
the_ff->initForceField( LB_MIXING_RULE ); |
1484 |
+ |
} |
1485 |
+ |
else if( !strcmp( info->mixingRule, "explicit") ){ |
1486 |
+ |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1487 |
+ |
} |
1488 |
+ |
else{ |
1489 |
+ |
sprintf( painCave.errMsg, |
1490 |
+ |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1491 |
+ |
info->mixingRule ); |
1492 |
+ |
painCave.isFatal = 1; |
1493 |
+ |
simError(); |
1494 |
+ |
} |
1495 |
+ |
|
1496 |
+ |
|
1497 |
+ |
#ifdef IS_MPI |
1498 |
+ |
strcpy( checkPointMsg, |
1499 |
+ |
"Successfully intialized the mixingRule for Fortran." ); |
1500 |
+ |
MPIcheckPoint(); |
1501 |
+ |
#endif // is_mpi |
1502 |
+ |
|
1503 |
+ |
} |