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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 605 by gezelter, Tue Jul 15 03:27:24 2003 UTC vs.
Revision 614 by mmeineke, Tue Jul 15 17:57:04 2003 UTC

#	Line 82 | Line 82 | void SimSetup::createSim( void ){
82		Globals* the_globals;
83		int i, j, k, globalAtomIndex;
84
85	<	int ensembleCase;
86	<	int ffCase;
85	>	// gather all of the information from the Bass file
86
87	<	ensembleCase = -1;
89	<	ffCase = -1;
87	>	gatherInfo();
88
89	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
89	>	// creation of complex system objects
90
91	<	// set the easy ones first
96	<	simnfo->target_temp = the_globals->getTargetTemp();
97	<	simnfo->dt = the_globals->getDt();
98	<	simnfo->run_time = the_globals->getRunTime();
91	>	sysObjectsCreation();
92
100	–	// get the ones we know are there, yet still may need some work.
101	–	n_components = the_globals->getNComponents();
102	–	strcpy( force_field, the_globals->getForceField() );
93
104	–	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105	–	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106	–	else{
107	–	sprintf( painCave.errMsg,
108	–	"SimSetup Error. Unrecognized force field -> %s\n",
109	–	force_field );
110	–	painCave.isFatal = 1;
111	–	simError();
112	–	}
94
95	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
95	>	// initialize the arrays
96
97	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
118	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
119	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
120	<	ensembleCase = NPTi_ENS;
121	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
122	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
123	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124	<	else{
125	<	sprintf( painCave.errMsg,
126	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
127	<	"reverting to NVE for this simulation.\n",
128	<	ensemble );
129	<	painCave.isFatal = 0;
130	<	simError();
131	<	strcpy( ensemble, "NVE" );
132	<	ensembleCase = NVE_ENS;
133	<	}
134	<	strcpy( simnfo->ensemble, ensemble );
97	>
98
99	<
100	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
101	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
102	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140	<	//     if (the_globals->haveTargetPressure())
141	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142	<	//     else {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "SimSetup error: If you use the constant pressure\n"
145	<	//                "    ensemble, you must set targetPressure.\n"
146	<	//                "    This was found in the BASS file.\n");
147	<	//       painCave.isFatal = 1;
148	<	//       simError();
149	<	//     }
150	<
151	<	//     if (the_globals->haveTauThermostat())
152	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153	<	//     else if (the_globals->haveQmass())
154	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
155	<	//     else {
156	<	//       sprintf( painCave.errMsg,
157	<	//                "SimSetup error: If you use one of the constant temperature\n"
158	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
159	<	//                "    Neither of these was found in the BASS file.\n");
160	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
163	<
164	<	//     if (the_globals->haveTauBarostat())
165	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166	<	//     else {
167	<	//       sprintf( painCave.errMsg,
168	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
174	<
175	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
176	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
177	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
178	<
179	<	//     if (the_globals->haveTauThermostat())
180	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181	<	//     else if (the_globals->haveQmass())
182	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
183	<	//     else {
184	<	//       sprintf( painCave.errMsg,
185	<	//                "SimSetup error: If you use one of the constant temperature\n"
186	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
187	<	//                "    Neither of these was found in the BASS file.\n");
188	<	//       painCave.isFatal = 1;
189	<	//       simError();
190	<	//     }
191	<
192	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
193	<	simnfo->usePBC = the_globals->getPBC();
194	<
195	<	int usesDipoles = 0;
196	<	switch( ffCase ){
197	<
198	<	case FF_DUFF:
199	<	the_ff = new DUFF();
200	<	usesDipoles = 1;
201	<	break;
202	<
203	<	case FF_LJ:
204	<	the_ff = new LJFF();
205	<	break;
206	<
207	<	default:
208	<	sprintf( painCave.errMsg,
209	<	"SimSetup Error. Unrecognized force field in case statement.\n");
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
213	<
214	<	#ifdef IS_MPI
215	<	strcpy( checkPointMsg, "ForceField creation successful" );
216	<	MPIcheckPoint();
217	<	#endif // is_mpi
218	<
219	<	// get the components and calculate the tot_nMol and indvidual n_mol
220	<	the_components = the_globals->getComponents();
221	<	components_nmol = new int[n_components];
222	<	comp_stamps = new MoleculeStamp*[n_components];
223	<
224	<	if( !the_globals->haveNMol() ){
225	<	// we don't have the total number of molecules, so we assume it is
226	<	// given in each component
227	<
228	<	tot_nmol = 0;
229	<	for( i=0; i<n_components; i++ ){
230	<
231	<	if( !the_components[i]->haveNMol() ){
232	<	// we have a problem
233	<	sprintf( painCave.errMsg,
234	<	"SimSetup Error. No global NMol or component NMol"
235	<	" given. Cannot calculate the number of atoms.\n" );
236	<	painCave.isFatal = 1;
237	<	simError();
238	<	}
239	<
240	<	tot_nmol += the_components[i]->getNMol();
241	<	components_nmol[i] = the_components[i]->getNMol();
242	<	}
243	<	}
244	<	else{
245	<	sprintf( painCave.errMsg,
246	<	"SimSetup error.\n"
247	<	"\tSorry, the ability to specify total"
248	<	" nMols and then give molfractions in the components\n"
249	<	"\tis not currently supported."
250	<	" Please give nMol in the components.\n" );
251	<	painCave.isFatal = 1;
252	<	simError();
253	<
254	<
255	<	//     tot_nmol = the_globals->getNMol();
256	<
257	<	//   //we have the total number of molecules, now we check for molfractions
258	<	//     for( i=0; i<n_components; i++ ){
259	<
260	<	//       if( !the_components[i]->haveMolFraction() ){
261	<
262	<	//  if( !the_components[i]->haveNMol() ){
263	<	//    //we have a problem
264	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
265	<	//              << " nMol was given in component
266	<
99	>	makeMolecules();
100	>	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		}
268	–
269	–	#ifdef IS_MPI
270	–	strcpy( checkPointMsg, "Have the number of components" );
271	–	MPIcheckPoint();
272	–	#endif // is_mpi
273	–
274	–	// make an array of molecule stamps that match the components used.
275	–	// also extract the used stamps out into a separate linked list
276	–
277	–	simnfo->nComponents = n_components;
278	–	simnfo->componentsNmol = components_nmol;
279	–	simnfo->compStamps = comp_stamps;
280	–	simnfo->headStamp = new LinkedMolStamp();
104
282	–	char* id;
283	–	LinkedMolStamp* headStamp = simnfo->headStamp;
284	–	LinkedMolStamp* currentStamp = NULL;
285	–	for( i=0; i<n_components; i++ ){
105
106	<	id = the_components[i]->getType();
288	<	comp_stamps[i] = NULL;
289	<
290	<	// check to make sure the component isn't already in the list
291	<
292	<	comp_stamps[i] = headStamp->match( id );
293	<	if( comp_stamps[i] == NULL ){
294	<
295	<	// extract the component from the list;
296	<
297	<	currentStamp = the_stamps->extractMolStamp( id );
298	<	if( currentStamp == NULL ){
299	<	sprintf( painCave.errMsg,
300	<	"SimSetup error: Component \"%s\" was not found in the "
301	<	"list of declared molecules\n",
302	<	id );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<
307	<	headStamp->add( currentStamp );
308	<	comp_stamps[i] = headStamp->match( id );
309	<	}
310	<	}
311	<
312	<	#ifdef IS_MPI
313	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
314	<	MPIcheckPoint();
315	<	#endif // is_mpi
106	>	// check on the post processing info
107
108	+	finalInfoCheck();
109
110
111
320	–	// caclulate the number of atoms, bonds, bends and torsions
112
113	<	tot_atoms = 0;
323	<	tot_bonds = 0;
324	<	tot_bends = 0;
325	<	tot_torsions = 0;
326	<	for( i=0; i<n_components; i++ ){
327	<
328	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
329	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
330	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
331	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
332	<	}
113	>	// initialize the system coordinates
114
115	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
335	<
336	<	simnfo->n_atoms = tot_atoms;
337	<	simnfo->n_bonds = tot_bonds;
338	<	simnfo->n_bends = tot_bends;
339	<	simnfo->n_torsions = tot_torsions;
340	<	simnfo->n_SRI = tot_SRI;
341	<	simnfo->n_mol = tot_nmol;
115	>	initSystemCoords();
116
343	–	simnfo->molMembershipArray = new int[tot_atoms];
117
118	<	#ifdef IS_MPI
118	>	// make the output filenames
119
120	<	// divide the molecules among processors here.
348	<
349	<	mpiSim = new mpiSimulation( simnfo );
350	<
351	<	globalIndex = mpiSim->divideLabor();
352	<
353	<	// set up the local variables
354	<
355	<	int localMol, allMol;
356	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
357	<
358	<	int* mol2proc = mpiSim->getMolToProcMap();
359	<	int* molCompType = mpiSim->getMolComponentType();
360	<
361	<	allMol = 0;
362	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
368	<
369	<
370	<	for( i=0; i<n_components; i++ ){
371	<
372	<	for( j=0; j<components_nmol[i]; j++ ){
373	<
374	<	if( mol2proc[allMol] == worldRank ){
375	<
376	<	local_atoms +=    comp_stamps[i]->getNAtoms();
377	<	local_bonds +=    comp_stamps[i]->getNBonds();
378	<	local_bends +=    comp_stamps[i]->getNBends();
379	<	local_torsions += comp_stamps[i]->getNTorsions();
380	<	localMol++;
381	<	}
382	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
384	<	globalAtomIndex++;
385	<	}
386	<
387	<	allMol++;
388	<	}
389	<	}
390	<	local_SRI = local_bonds + local_bends + local_torsions;
391	<
392	<	simnfo->n_atoms = mpiSim->getMyNlocal();
393	<
394	<	if( local_atoms != simnfo->n_atoms ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
397	<	" localAtom (%d) are not equal.\n",
398	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
403	<
404	<	simnfo->n_bonds = local_bonds;
405	<	simnfo->n_bends = local_bends;
406	<	simnfo->n_torsions = local_torsions;
407	<	simnfo->n_SRI = local_SRI;
408	<	simnfo->n_mol = localMol;
409	<
410	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
411	<	MPIcheckPoint();
412	<
413	<
414	<	#endif // is_mpi
415	<
416	<
417	<	// create the atom and short range interaction arrays
418	<
419	<	Atom::createArrays(simnfo->n_atoms);
420	<	the_atoms = new Atom*[simnfo->n_atoms];
421	<	the_molecules = new Molecule[simnfo->n_mol];
422	<	int molIndex;
423	<
424	<	// initialize the molecule's stampID's
425	<
426	<	#ifdef IS_MPI
427	<
428	<
429	<	molIndex = 0;
430	<	for(i=0; i<mpiSim->getTotNmol(); i++){
431	<
432	<	if(mol2proc[i] == worldRank ){
433	<	the_molecules[molIndex].setStampID( molCompType[i] );
434	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
439	<
440	<	#else // is_mpi
441	<
442	<	molIndex = 0;
443	<	globalAtomIndex = 0;
444	<	for(i=0; i<n_components; i++){
445	<	for(j=0; j<components_nmol[i]; j++ ){
446	<	the_molecules[molIndex].setStampID( i );
447	<	the_molecules[molIndex].setMyIndex( molIndex );
448	<	the_molecules[molIndex].setGlobalIndex( molIndex );
449	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
450	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
451	<	globalAtomIndex++;
452	<	}
453	<	molIndex++;
454	<	}
455	<	}
456	<
457	<
458	<	#endif // is_mpi
459	<
460	<
461	<	if( simnfo->n_SRI ){
462	<
463	<	Exclude::createArray(simnfo->n_SRI);
464	<	the_excludes = new Exclude*[simnfo->n_SRI];
465	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
466	<	simnfo->globalExcludes = new int;
467	<	simnfo->n_exclude = simnfo->n_SRI;
468	<	}
469	<	else{
470	<
471	<	Exclude::createArray( 1 );
472	<	the_excludes = new Exclude*;
473	<	the_excludes[0] = new Exclude(0);
474	<	the_excludes[0]->setPair( 0,0 );
475	<	simnfo->globalExcludes = new int;
476	<	simnfo->globalExcludes[0] = 0;
477	<	simnfo->n_exclude = 0;
478	<	}
479	<
480	<	// set the arrays into the SimInfo object
481	<
482	<	simnfo->atoms = the_atoms;
483	<	simnfo->molecules = the_molecules;
484	<	simnfo->nGlobalExcludes = 0;
485	<	simnfo->excludes = the_excludes;
486	<
487	<
488	<	// get some of the tricky things that may still be in the globals
489	<
490	<	double boxVector[3];
491	<	if( the_globals->haveBox() ){
492	<	boxVector[0] = the_globals->getBox();
493	<	boxVector[1] = the_globals->getBox();
494	<	boxVector[2] = the_globals->getBox();
495	<
496	<	simnfo->setBox( boxVector );
497	<	}
498	<	else if( the_globals->haveDensity() ){
499	<
500	<	double vol;
501	<	vol = (double)tot_nmol / the_globals->getDensity();
502	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
503	<	boxVector[1] = boxVector[0];
504	<	boxVector[2] = boxVector[0];
505	<
506	<	simnfo->setBox( boxVector );
507	<	}
508	<	else{
509	<	if( !the_globals->haveBoxX() ){
510	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxX size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[0] = the_globals->getBoxX();
516	<
517	<	if( !the_globals->haveBoxY() ){
518	<	sprintf( painCave.errMsg,
519	<	"SimSetup error, no periodic BoxY size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	boxVector[1] = the_globals->getBoxY();
524	<
525	<	if( !the_globals->haveBoxZ() ){
526	<	sprintf( painCave.errMsg,
527	<	"SimSetup error, no periodic BoxZ size given.\n" );
528	<	painCave.isFatal = 1;
529	<	simError();
530	<	}
531	<	boxVector[2] = the_globals->getBoxZ();
532	<
533	<	simnfo->setBox( boxVector );
534	<	}
535	<
536	<	#ifdef IS_MPI
537	<	strcpy( checkPointMsg, "Box size set up" );
538	<	MPIcheckPoint();
539	<	#endif // is_mpi
540	<
541	<
542	<	// initialize the arrays
543	<
544	<	the_ff->setSimInfo( simnfo );
545	<
546	<	makeMolecules();
547	<	simnfo->identArray = new int[simnfo->n_atoms];
548	<	for(i=0; i<simnfo->n_atoms; i++){
549	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
550	<	}
551	<
552	<	if (the_globals->getUseRF() ) {
553	<	simnfo->useReactionField = 1;
554	<
555	<	if( !the_globals->haveECR() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 1/2 the smallest "
558	<	"box length for the electrostaticCutoffRadius.\n"
559	<	"I hope you have a very fast processor!\n");
560	<	painCave.isFatal = 0;
561	<	simError();
562	<	double smallest;
563	<	smallest = simnfo->boxLx;
564	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566	<	simnfo->ecr = 0.5 * smallest;
567	<	} else {
568	<	simnfo->ecr        = the_globals->getECR();
569	<	}
570	<
571	<	if( !the_globals->haveEST() ){
572	<	sprintf( painCave.errMsg,
573	<	"SimSetup Warning: using default value of 0.05 * the "
574	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
575	<	);
576	<	painCave.isFatal = 0;
577	<	simError();
578	<	simnfo->est = 0.05 * simnfo->ecr;
579	<	} else {
580	<	simnfo->est        = the_globals->getEST();
581	<	}
582	<
583	<	if(!the_globals->haveDielectric() ){
584	<	sprintf( painCave.errMsg,
585	<	"SimSetup Error: You are trying to use Reaction Field without"
586	<	"setting a dielectric constant!\n"
587	<	);
588	<	painCave.isFatal = 1;
589	<	simError();
590	<	}
591	<	simnfo->dielectric = the_globals->getDielectric();
592	<	} else {
593	<	if (usesDipoles) {
594	<
595	<	if( !the_globals->haveECR() ){
596	<	sprintf( painCave.errMsg,
597	<	"SimSetup Warning: using default value of 1/2 the smallest "
598	<	"box length for the electrostaticCutoffRadius.\n"
599	<	"I hope you have a very fast processor!\n");
600	<	painCave.isFatal = 0;
601	<	simError();
602	<	double smallest;
603	<	smallest = simnfo->boxLx;
604	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
605	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
606	<	simnfo->ecr = 0.5 * smallest;
607	<	} else {
608	<	simnfo->ecr        = the_globals->getECR();
609	<	}
610	<
611	<	if( !the_globals->haveEST() ){
612	<	sprintf( painCave.errMsg,
613	<	"SimSetup Warning: using default value of 5%% of the "
614	<	"electrostaticCutoffRadius for the "
615	<	"electrostaticSkinThickness\n"
616	<	);
617	<	painCave.isFatal = 0;
618	<	simError();
619	<	simnfo->est = 0.05 * simnfo->ecr;
620	<	} else {
621	<	simnfo->est        = the_globals->getEST();
622	<	}
623	<	}
624	<	}
625	<
626	<	#ifdef IS_MPI
627	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
628	<	MPIcheckPoint();
629	<	#endif // is_mpi
630	<
631	<	if( the_globals->haveInitialConfig() ){
632	<
633	<	InitializeFromFile* fileInit;
634	<	#ifdef IS_MPI // is_mpi
635	<	if( worldRank == 0 ){
636	<	#endif //is_mpi
637	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
638	<	#ifdef IS_MPI
639	<	}else fileInit = new InitializeFromFile( NULL );
640	<	#endif
641	<	fileInit->read_xyz( simnfo ); // default velocities on
642	<
643	<	delete fileInit;
644	<	}
645	<	else{
646	<
647	<	#ifdef IS_MPI
648	<
649	<	// no init from bass
650	<
651	<	sprintf( painCave.errMsg,
652	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
653	<	painCave.isFatal;
654	<	simError();
655	<
656	<	#else
657	<
658	<	initFromBass();
659	<
660	<
661	<	#endif
662	<	}
663	<
664	<	#ifdef IS_MPI
665	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
666	<	MPIcheckPoint();
667	<	#endif // is_mpi
668	<
669	<
120	>	makeOutNames();
121
122
123
124
125
126	<	#ifdef IS_MPI
676	<	if( worldRank == 0 ){
677	<	#endif // is_mpi
678	<
679	<	if( the_globals->haveFinalConfig() ){
680	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
681	<	}
682	<	else{
683	<	strcpy( simnfo->finalName, inFileName );
684	<	char* endTest;
685	<	int nameLength = strlen( simnfo->finalName );
686	<	endTest = &(simnfo->finalName[nameLength - 5]);
687	<	if( !strcmp( endTest, ".bass" ) ){
688	<	strcpy( endTest, ".eor" );
689	<	}
690	<	else if( !strcmp( endTest, ".BASS" ) ){
691	<	strcpy( endTest, ".eor" );
692	<	}
693	<	else{
694	<	endTest = &(simnfo->finalName[nameLength - 4]);
695	<	if( !strcmp( endTest, ".bss" ) ){
696	<	strcpy( endTest, ".eor" );
697	<	}
698	<	else if( !strcmp( endTest, ".mdl" ) ){
699	<	strcpy( endTest, ".eor" );
700	<	}
701	<	else{
702	<	strcat( simnfo->finalName, ".eor" );
703	<	}
704	<	}
705	<	}
706	<
707	<	// make the sample and status out names
708	<
709	<	strcpy( simnfo->sampleName, inFileName );
710	<	char* endTest;
711	<	int nameLength = strlen( simnfo->sampleName );
712	<	endTest = &(simnfo->sampleName[nameLength - 5]);
713	<	if( !strcmp( endTest, ".bass" ) ){
714	<	strcpy( endTest, ".dump" );
715	<	}
716	<	else if( !strcmp( endTest, ".BASS" ) ){
717	<	strcpy( endTest, ".dump" );
718	<	}
719	<	else{
720	<	endTest = &(simnfo->sampleName[nameLength - 4]);
721	<	if( !strcmp( endTest, ".bss" ) ){
722	<	strcpy( endTest, ".dump" );
723	<	}
724	<	else if( !strcmp( endTest, ".mdl" ) ){
725	<	strcpy( endTest, ".dump" );
726	<	}
727	<	else{
728	<	strcat( simnfo->sampleName, ".dump" );
729	<	}
730	<	}
731	<
732	<	strcpy( simnfo->statusName, inFileName );
733	<	nameLength = strlen( simnfo->statusName );
734	<	endTest = &(simnfo->statusName[nameLength - 5]);
735	<	if( !strcmp( endTest, ".bass" ) ){
736	<	strcpy( endTest, ".stat" );
737	<	}
738	<	else if( !strcmp( endTest, ".BASS" ) ){
739	<	strcpy( endTest, ".stat" );
740	<	}
741	<	else{
742	<	endTest = &(simnfo->statusName[nameLength - 4]);
743	<	if( !strcmp( endTest, ".bss" ) ){
744	<	strcpy( endTest, ".stat" );
745	<	}
746	<	else if( !strcmp( endTest, ".mdl" ) ){
747	<	strcpy( endTest, ".stat" );
748	<	}
749	<	else{
750	<	strcat( simnfo->statusName, ".stat" );
751	<	}
752	<	}
753	<
754	<	#ifdef IS_MPI
755	<	}
756	<	#endif // is_mpi
126	>
127
758	–	// set the status, sample, and themal kick times
759	–
760	–	if( the_globals->haveSampleTime() ){
761	–	simnfo->sampleTime = the_globals->getSampleTime();
762	–	simnfo->statusTime = simnfo->sampleTime;
763	–	simnfo->thermalTime = simnfo->sampleTime;
764	–	}
765	–	else{
766	–	simnfo->sampleTime = the_globals->getRunTime();
767	–	simnfo->statusTime = simnfo->sampleTime;
768	–	simnfo->thermalTime = simnfo->sampleTime;
769	–	}
128
771	–	if( the_globals->haveStatusTime() ){
772	–	simnfo->statusTime = the_globals->getStatusTime();
773	–	}
129
775	–	if( the_globals->haveThermalTime() ){
776	–	simnfo->thermalTime = the_globals->getThermalTime();
777	–	}
778	–
779	–	// check for the temperature set flag
780	–
781	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
782	–
783	–
130		// make the integrator
131
132
#	Line 793 | Line 139 | void SimSetup::createSim( void ){
139		switch( ensembleCase ){
140
141		case NVE_ENS:
142	<	new NVE( simnfo, the_ff );
142	>	new NVE( info, the_ff );
143		break;
144
145		case NVT_ENS:
146	<	myNVT = new NVT( simnfo, the_ff );
146	>	myNVT = new NVT( info, the_ff );
147		myNVT->setTargetTemp(the_globals->getTargetTemp());
148
149		if (the_globals->haveTauThermostat())
#	Line 813 | Line 159 | void SimSetup::createSim( void ){
159		break;
160
161		case NPTi_ENS:
162	<	myNPTi = new NPTi( simnfo, the_ff );
163	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
162	>	myNPTi = new NPTi( info, the_ff );
163	>	myNPTi->setTargetTemp( the_globals->getTargetTemp() );
164
165		if (the_globals->haveTargetPressure())
166		myNPTi->setTargetPressure(the_globals->getTargetPressure());
#	Line 848 | Line 194 | void SimSetup::createSim( void ){
194		break;
195
196		case NPTf_ENS:
197	<	myNPTf = new NPTf( simnfo, the_ff );
197	>	myNPTf = new NPTf( info, the_ff );
198		myNPTf->setTargetTemp( the_globals->getTargetTemp());
199
200		if (the_globals->haveTargetPressure())
#	Line 883 | Line 229 | void SimSetup::createSim( void ){
229		break;
230
231		case NPTim_ENS:
232	<	myNPTim = new NPTim( simnfo, the_ff );
232	>	myNPTim = new NPTim( info, the_ff );
233		myNPTim->setTargetTemp( the_globals->getTargetTemp());
234
235		if (the_globals->haveTargetPressure())
#	Line 918 | Line 264 | void SimSetup::createSim( void ){
264		break;
265
266		case NPTfm_ENS:
267	<	myNPTfm = new NPTfm( simnfo, the_ff );
267	>	myNPTfm = new NPTfm( info, the_ff );
268		myNPTfm->setTargetTemp( the_globals->getTargetTemp());
269
270		if (the_globals->haveTargetPressure())
#	Line 967 | Line 313 | void SimSetup::createSim( void ){
313		// initialize the Fortran
314
315
316	<	simnfo->refreshSim();
316	>	info->refreshSim();
317
318	<	if( !strcmp( simnfo->mixingRule, "standard") ){
318	>	if( !strcmp( info->mixingRule, "standard") ){
319		the_ff->initForceField( LB_MIXING_RULE );
320		}
321	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
321	>	else if( !strcmp( info->mixingRule, "explicit") ){
322		the_ff->initForceField( EXPLICIT_MIXING_RULE );
323		}
324		else{
325		sprintf( painCave.errMsg,
326		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
327	<	simnfo->mixingRule );
327	>	info->mixingRule );
328		painCave.isFatal = 1;
329		simError();
330		}
#	Line 1020 | Line 366 | void SimSetup::makeMolecules( void ){
366
367		atomOffset = 0;
368		excludeOffset = 0;
369	<	for(i=0; i<simnfo->n_mol; i++){
369	>	for(i=0; i<info->n_mol; i++){
370
371		stampID = the_molecules[i].getStampID();
372
#	Line 1048 | Line 394 | void SimSetup::makeMolecules( void ){
394		if( currentAtom->haveOrientation() ){
395
396		dAtom = new DirectionalAtom(j + atomOffset);
397	<	simnfo->n_oriented++;
397	>	info->n_oriented++;
398		info.myAtoms[j] = dAtom;
399
400		ux = currentAtom->getOrntX();
#	Line 1272 | Line 618 | void SimSetup::initFromBass( void ){
618		have_extra =1;
619
620		n_cells = (int)temp3 - 1;
621	<	cellx = simnfo->boxLx / temp3;
622	<	celly = simnfo->boxLy / temp3;
623	<	cellz = simnfo->boxLz / temp3;
621	>	cellx = info->boxLx / temp3;
622	>	celly = info->boxLy / temp3;
623	>	cellz = info->boxLz / temp3;
624		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 );
#	Line 1289 | Line 635 | void SimSetup::initFromBass( void ){
635		}
636		else{
637		n_cells = (int)temp3;
638	<	cellx = simnfo->boxLx / temp3;
639	<	celly = simnfo->boxLy / temp3;
640	<	cellz = simnfo->boxLz / temp3;
638	>	cellx = info->boxLx / temp3;
639	>	celly = info->boxLy / temp3;
640	>	cellz = info->boxLz / temp3;
641		}
642
643		current_mol = 0;
#	Line 1371 | Line 717 | void SimSetup::initFromBass( void ){
717		}
718
719
720	<	for( i=0; i<simnfo->n_atoms; i++ ){
721	<	simnfo->atoms[i]->set_vx( 0.0 );
722	<	simnfo->atoms[i]->set_vy( 0.0 );
723	<	simnfo->atoms[i]->set_vz( 0.0 );
720	>	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		}
725		}
726
#	Line 1433 | Line 779 | void SimSetup::makeElement( double x, double y, double
779
780		current_comp_mol = 0;
781		current_comp++;
782	+	}
783	+	}
784	+
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	+	}

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