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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 580 by gezelter, Wed Jul 9 13:56:36 2003 UTC vs.
Revision 616 by mmeineke, Tue Jul 15 18:52:16 2003 UTC

#	Line 14 | Line 14
14
15		// some defines for ensemble and Forcefield  cases
16
17	<	#define NVE_ENS 0
18	<	#define NVT_ENS 1
19	<	#define NPTi_ENS 2
20	<	#define NPTf_ENS 3
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
#	Line 75 | Line 78 | void SimSetup::createSim( void ){
78
79		void SimSetup::createSim( void ){
80
78	–	MakeStamps *the_stamps;
79	–	Globals* the_globals;
81		int i, j, k, globalAtomIndex;
82
83	<	int ensembleCase;
83	<	int ffCase;
83	>	// gather all of the information from the Bass file
84
85	<	ensembleCase = -1;
86	<	ffCase = -1;
85	>	gatherInfo();
86
87	<	// get the stamps and globals;
89	<	the_stamps = stamps;
90	<	the_globals = globals;
87	>	// creation of complex system objects
88
89	<	// set the easy ones first
93	<	simnfo->target_temp = the_globals->getTargetTemp();
94	<	simnfo->dt = the_globals->getDt();
95	<	simnfo->run_time = the_globals->getRunTime();
89	>	sysObjectsCreation();
90
91	<	// get the ones we know are there, yet still may need some work.
98	<	n_components = the_globals->getNComponents();
99	<	strcpy( force_field, the_globals->getForceField() );
100	<
101	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
102	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
103	<	else{
104	<	sprintf( painCave.errMsg,
105	<	"SimSetup Error. Unrecognized force field -> %s\n",
106	<	force_field );
107	<	painCave.isFatal = 1;
108	<	simError();
109	<	}
110	<
111	<	// get the ensemble:
112	<	strcpy( ensemble, the_globals->getEnsemble() );
113	<
114	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
115	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
116	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
117	<	ensembleCase = NPTi_ENS;
118	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
119	<	else{
120	<	sprintf( painCave.errMsg,
121	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
122	<	"reverting to NVE for this simulation.\n",
123	<	ensemble );
124	<	painCave.isFatal = 0;
125	<	simError();
126	<	strcpy( ensemble, "NVE" );
127	<	ensembleCase = NVE_ENS;
128	<	}
129	<	strcpy( simnfo->ensemble, ensemble );
130	<
131	<
132	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
133	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
134	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
135	<	//     if (the_globals->haveTargetPressure())
136	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
137	<	//     else {
138	<	//       sprintf( painCave.errMsg,
139	<	//                "SimSetup error: If you use the constant pressure\n"
140	<	//                "    ensemble, you must set targetPressure.\n"
141	<	//                "    This was found in the BASS file.\n");
142	<	//       painCave.isFatal = 1;
143	<	//       simError();
144	<	//     }
145	<
146	<	//     if (the_globals->haveTauThermostat())
147	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
148	<	//     else if (the_globals->haveQmass())
149	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
150	<	//     else {
151	<	//       sprintf( painCave.errMsg,
152	<	//                "SimSetup error: If you use one of the constant temperature\n"
153	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
154	<	//                "    Neither of these was found in the BASS file.\n");
155	<	//       painCave.isFatal = 1;
156	<	//       simError();
157	<	//     }
158	<
159	<	//     if (the_globals->haveTauBarostat())
160	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
161	<	//     else {
162	<	//       sprintf( painCave.errMsg,
163	<	//                "SimSetup error: If you use the constant pressure\n"
164	<	//                "    ensemble, you must set tauBarostat.\n"
165	<	//                "    This was found in the BASS file.\n");
166	<	//       painCave.isFatal = 1;
167	<	//       simError();
168	<	//     }
169	<
170	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
171	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
172	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
173	<
174	<	//     if (the_globals->haveTauThermostat())
175	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
176	<	//     else if (the_globals->haveQmass())
177	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
178	<	//     else {
179	<	//       sprintf( painCave.errMsg,
180	<	//                "SimSetup error: If you use one of the constant temperature\n"
181	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
182	<	//                "    Neither of these was found in the BASS file.\n");
183	<	//       painCave.isFatal = 1;
184	<	//       simError();
185	<	//     }
186	<
187	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
188	<	simnfo->usePBC = the_globals->getPBC();
189	<
190	<	int usesDipoles = 0;
191	<	switch( ffCase ){
192	<
193	<	case FF_DUFF:
194	<	the_ff = new DUFF();
195	<	usesDipoles = 1;
196	<	break;
197	<
198	<	case FF_LJ:
199	<	the_ff = new LJFF();
200	<	break;
201	<
202	<	default:
203	<	sprintf( painCave.errMsg,
204	<	"SimSetup Error. Unrecognized force field in case statement.\n");
205	<	painCave.isFatal = 1;
206	<	simError();
207	<	}
208	<
209	<	#ifdef IS_MPI
210	<	strcpy( checkPointMsg, "ForceField creation successful" );
211	<	MPIcheckPoint();
212	<	#endif // is_mpi
213	<
214	<	// get the components and calculate the tot_nMol and indvidual n_mol
215	<	the_components = the_globals->getComponents();
216	<	components_nmol = new int[n_components];
217	<	comp_stamps = new MoleculeStamp*[n_components];
218	<
219	<	if( !the_globals->haveNMol() ){
220	<	// we don't have the total number of molecules, so we assume it is
221	<	// given in each component
222	<
223	<	tot_nmol = 0;
224	<	for( i=0; i<n_components; i++ ){
225	<
226	<	if( !the_components[i]->haveNMol() ){
227	<	// we have a problem
228	<	sprintf( painCave.errMsg,
229	<	"SimSetup Error. No global NMol or component NMol"
230	<	" given. Cannot calculate the number of atoms.\n" );
231	<	painCave.isFatal = 1;
232	<	simError();
233	<	}
234	<
235	<	tot_nmol += the_components[i]->getNMol();
236	<	components_nmol[i] = the_components[i]->getNMol();
237	<	}
238	<	}
239	<	else{
240	<	sprintf( painCave.errMsg,
241	<	"SimSetup error.\n"
242	<	"\tSorry, the ability to specify total"
243	<	" nMols and then give molfractions in the components\n"
244	<	"\tis not currently supported."
245	<	" Please give nMol in the components.\n" );
246	<	painCave.isFatal = 1;
247	<	simError();
248	<
249	<
250	<	//     tot_nmol = the_globals->getNMol();
251	<
252	<	//   //we have the total number of molecules, now we check for molfractions
253	<	//     for( i=0; i<n_components; i++ ){
254	<
255	<	//       if( !the_components[i]->haveMolFraction() ){
256	<
257	<	//  if( !the_components[i]->haveNMol() ){
258	<	//    //we have a problem
259	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
260	<	//              << " nMol was given in component
261	<
262	<	}
263	<
264	<	#ifdef IS_MPI
265	<	strcpy( checkPointMsg, "Have the number of components" );
266	<	MPIcheckPoint();
267	<	#endif // is_mpi
268	<
269	<	// make an array of molecule stamps that match the components used.
270	<	// also extract the used stamps out into a separate linked list
271	<
272	<	simnfo->nComponents = n_components;
273	<	simnfo->componentsNmol = components_nmol;
274	<	simnfo->compStamps = comp_stamps;
275	<	simnfo->headStamp = new LinkedMolStamp();
91	>	// check on the post processing info
92
93	<	char* id;
278	<	LinkedMolStamp* headStamp = simnfo->headStamp;
279	<	LinkedMolStamp* currentStamp = NULL;
280	<	for( i=0; i<n_components; i++ ){
93	>	finalInfoCheck();
94
95	<	id = the_components[i]->getType();
283	<	comp_stamps[i] = NULL;
284	<
285	<	// check to make sure the component isn't already in the list
286	<
287	<	comp_stamps[i] = headStamp->match( id );
288	<	if( comp_stamps[i] == NULL ){
289	<
290	<	// extract the component from the list;
291	<
292	<	currentStamp = the_stamps->extractMolStamp( id );
293	<	if( currentStamp == NULL ){
294	<	sprintf( painCave.errMsg,
295	<	"SimSetup error: Component \"%s\" was not found in the "
296	<	"list of declared molecules\n",
297	<	id );
298	<	painCave.isFatal = 1;
299	<	simError();
300	<	}
301	<
302	<	headStamp->add( currentStamp );
303	<	comp_stamps[i] = headStamp->match( id );
304	<	}
305	<	}
95	>	// initialize the system coordinates
96
97	<	#ifdef IS_MPI
308	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
309	<	MPIcheckPoint();
310	<	#endif // is_mpi
97	>	initSystemCoords();
98
99
100	+	// make the output filenames
101
102	<
315	<	// caclulate the number of atoms, bonds, bends and torsions
316	<
317	<	tot_atoms = 0;
318	<	tot_bonds = 0;
319	<	tot_bends = 0;
320	<	tot_torsions = 0;
321	<	for( i=0; i<n_components; i++ ){
322	<
323	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
324	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
325	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
326	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
327	<	}
328	<
329	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
330	<
331	<	simnfo->n_atoms = tot_atoms;
332	<	simnfo->n_bonds = tot_bonds;
333	<	simnfo->n_bends = tot_bends;
334	<	simnfo->n_torsions = tot_torsions;
335	<	simnfo->n_SRI = tot_SRI;
336	<	simnfo->n_mol = tot_nmol;
337	<
338	<	simnfo->molMembershipArray = new int[tot_atoms];
339	<
340	<	#ifdef IS_MPI
341	<
342	<	// divide the molecules among processors here.
343	<
344	<	mpiSim = new mpiSimulation( simnfo );
345	<
346	<	globalIndex = mpiSim->divideLabor();
347	<
348	<	// set up the local variables
349	<
350	<	int localMol, allMol;
351	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
352	<
353	<	int* mol2proc = mpiSim->getMolToProcMap();
354	<	int* molCompType = mpiSim->getMolComponentType();
355	<
356	<	allMol = 0;
357	<	localMol = 0;
358	<	local_atoms = 0;
359	<	local_bonds = 0;
360	<	local_bends = 0;
361	<	local_torsions = 0;
362	<	globalAtomIndex = 0;
363	<
364	<
365	<	for( i=0; i<n_components; i++ ){
366	<
367	<	for( j=0; j<components_nmol[i]; j++ ){
368	<
369	<	if( mol2proc[allMol] == worldRank ){
370	<
371	<	local_atoms +=    comp_stamps[i]->getNAtoms();
372	<	local_bonds +=    comp_stamps[i]->getNBonds();
373	<	local_bends +=    comp_stamps[i]->getNBends();
374	<	local_torsions += comp_stamps[i]->getNTorsions();
375	<	localMol++;
376	<	}
377	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
378	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
379	<	globalAtomIndex++;
380	<	}
381	<
382	<	allMol++;
383	<	}
384	<	}
385	<	local_SRI = local_bonds + local_bends + local_torsions;
386	<
387	<	simnfo->n_atoms = mpiSim->getMyNlocal();
388	<
389	<	if( local_atoms != simnfo->n_atoms ){
390	<	sprintf( painCave.errMsg,
391	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
392	<	" localAtom (%d) are not equal.\n",
393	<	simnfo->n_atoms,
394	<	local_atoms );
395	<	painCave.isFatal = 1;
396	<	simError();
397	<	}
398	<
399	<	simnfo->n_bonds = local_bonds;
400	<	simnfo->n_bends = local_bends;
401	<	simnfo->n_torsions = local_torsions;
402	<	simnfo->n_SRI = local_SRI;
403	<	simnfo->n_mol = localMol;
404	<
405	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
406	<	MPIcheckPoint();
407	<
408	<
409	<	#endif // is_mpi
410	<
411	<
412	<	// create the atom and short range interaction arrays
413	<
414	<	Atom::createArrays(simnfo->n_atoms);
415	<	the_atoms = new Atom*[simnfo->n_atoms];
416	<	the_molecules = new Molecule[simnfo->n_mol];
417	<	int molIndex;
418	<
419	<	// initialize the molecule's stampID's
420	<
421	<	#ifdef IS_MPI
422	<
423	<
424	<	molIndex = 0;
425	<	for(i=0; i<mpiSim->getTotNmol(); i++){
426	<
427	<	if(mol2proc[i] == worldRank ){
428	<	the_molecules[molIndex].setStampID( molCompType[i] );
429	<	the_molecules[molIndex].setMyIndex( molIndex );
430	<	the_molecules[molIndex].setGlobalIndex( i );
431	<	molIndex++;
432	<	}
433	<	}
434	<
435	<	#else // is_mpi
436	<
437	<	molIndex = 0;
438	<	globalAtomIndex = 0;
439	<	for(i=0; i<n_components; i++){
440	<	for(j=0; j<components_nmol[i]; j++ ){
441	<	the_molecules[molIndex].setStampID( i );
442	<	the_molecules[molIndex].setMyIndex( molIndex );
443	<	the_molecules[molIndex].setGlobalIndex( molIndex );
444	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
445	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
446	<	globalAtomIndex++;
447	<	}
448	<	molIndex++;
449	<	}
450	<	}
451	<
452	<
453	<	#endif // is_mpi
454	<
455	<
456	<	if( simnfo->n_SRI ){
457	<
458	<	Exclude::createArray(simnfo->n_SRI);
459	<	the_excludes = new Exclude*[simnfo->n_SRI];
460	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
461	<	simnfo->globalExcludes = new int;
462	<	simnfo->n_exclude = simnfo->n_SRI;
463	<	}
464	<	else{
465	<
466	<	Exclude::createArray( 1 );
467	<	the_excludes = new Exclude*;
468	<	the_excludes[0] = new Exclude(0);
469	<	the_excludes[0]->setPair( 0,0 );
470	<	simnfo->globalExcludes = new int;
471	<	simnfo->globalExcludes[0] = 0;
472	<	simnfo->n_exclude = 0;
473	<	}
474	<
475	<	// set the arrays into the SimInfo object
476	<
477	<	simnfo->atoms = the_atoms;
478	<	simnfo->molecules = the_molecules;
479	<	simnfo->nGlobalExcludes = 0;
480	<	simnfo->excludes = the_excludes;
481	<
482	<
483	<	// get some of the tricky things that may still be in the globals
484	<
485	<	double boxVector[3];
486	<	if( the_globals->haveBox() ){
487	<	boxVector[0] = the_globals->getBox();
488	<	boxVector[1] = the_globals->getBox();
489	<	boxVector[2] = the_globals->getBox();
490	<
491	<	simnfo->setBox( boxVector );
492	<	}
493	<	else if( the_globals->haveDensity() ){
494	<
495	<	double vol;
496	<	vol = (double)tot_nmol / the_globals->getDensity();
497	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
498	<	boxVector[1] = boxVector[0];
499	<	boxVector[2] = boxVector[0];
500	<
501	<	simnfo->setBox( boxVector );
502	<	}
503	<	else{
504	<	if( !the_globals->haveBoxX() ){
505	<	sprintf( painCave.errMsg,
506	<	"SimSetup error, no periodic BoxX size given.\n" );
507	<	painCave.isFatal = 1;
508	<	simError();
509	<	}
510	<	boxVector[0] = the_globals->getBoxX();
511	<
512	<	if( !the_globals->haveBoxY() ){
513	<	sprintf( painCave.errMsg,
514	<	"SimSetup error, no periodic BoxY size given.\n" );
515	<	painCave.isFatal = 1;
516	<	simError();
517	<	}
518	<	boxVector[1] = the_globals->getBoxY();
519	<
520	<	if( !the_globals->haveBoxZ() ){
521	<	sprintf( painCave.errMsg,
522	<	"SimSetup error, no periodic BoxZ size given.\n" );
523	<	painCave.isFatal = 1;
524	<	simError();
525	<	}
526	<	boxVector[2] = the_globals->getBoxZ();
527	<
528	<	simnfo->setBox( boxVector );
529	<	}
530	<
531	<	#ifdef IS_MPI
532	<	strcpy( checkPointMsg, "Box size set up" );
533	<	MPIcheckPoint();
534	<	#endif // is_mpi
535	<
536	<
537	<	// initialize the arrays
538	<
539	<	the_ff->setSimInfo( simnfo );
540	<
541	<	makeMolecules();
542	<	simnfo->identArray = new int[simnfo->n_atoms];
543	<	for(i=0; i<simnfo->n_atoms; i++){
544	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
545	<	}
546	<
547	<	if (the_globals->getUseRF() ) {
548	<	simnfo->useReactionField = 1;
549	<
550	<	if( !the_globals->haveECR() ){
551	<	sprintf( painCave.errMsg,
552	<	"SimSetup Warning: using default value of 1/2 the smallest "
553	<	"box length for the electrostaticCutoffRadius.\n"
554	<	"I hope you have a very fast processor!\n");
555	<	painCave.isFatal = 0;
556	<	simError();
557	<	double smallest;
558	<	smallest = simnfo->boxLx;
559	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
560	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
561	<	simnfo->ecr = 0.5 * smallest;
562	<	} else {
563	<	simnfo->ecr        = the_globals->getECR();
564	<	}
565	<
566	<	if( !the_globals->haveEST() ){
567	<	sprintf( painCave.errMsg,
568	<	"SimSetup Warning: using default value of 0.05 * the "
569	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
570	<	);
571	<	painCave.isFatal = 0;
572	<	simError();
573	<	simnfo->est = 0.05 * simnfo->ecr;
574	<	} else {
575	<	simnfo->est        = the_globals->getEST();
576	<	}
577	<
578	<	if(!the_globals->haveDielectric() ){
579	<	sprintf( painCave.errMsg,
580	<	"SimSetup Error: You are trying to use Reaction Field without"
581	<	"setting a dielectric constant!\n"
582	<	);
583	<	painCave.isFatal = 1;
584	<	simError();
585	<	}
586	<	simnfo->dielectric = the_globals->getDielectric();
587	<	} else {
588	<	if (usesDipoles) {
589	<
590	<	if( !the_globals->haveECR() ){
591	<	sprintf( painCave.errMsg,
592	<	"SimSetup Warning: using default value of 1/2 the smallest "
593	<	"box length for the electrostaticCutoffRadius.\n"
594	<	"I hope you have a very fast processor!\n");
595	<	painCave.isFatal = 0;
596	<	simError();
597	<	double smallest;
598	<	smallest = simnfo->boxLx;
599	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
600	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
601	<	simnfo->ecr = 0.5 * smallest;
602	<	} else {
603	<	simnfo->ecr        = the_globals->getECR();
604	<	}
605	<
606	<	if( !the_globals->haveEST() ){
607	<	sprintf( painCave.errMsg,
608	<	"SimSetup Warning: using default value of 5%% of the "
609	<	"electrostaticCutoffRadius for the "
610	<	"electrostaticSkinThickness\n"
611	<	);
612	<	painCave.isFatal = 0;
613	<	simError();
614	<	simnfo->est = 0.05 * simnfo->ecr;
615	<	} else {
616	<	simnfo->est        = the_globals->getEST();
617	<	}
618	<	}
619	<	}
620	<
621	<	#ifdef IS_MPI
622	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
623	<	MPIcheckPoint();
624	<	#endif // is_mpi
625	<
626	<	if( the_globals->haveInitialConfig() ){
627	<
628	<	InitializeFromFile* fileInit;
629	<	#ifdef IS_MPI // is_mpi
630	<	if( worldRank == 0 ){
631	<	#endif //is_mpi
632	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
633	<	#ifdef IS_MPI
634	<	}else fileInit = new InitializeFromFile( NULL );
635	<	#endif
636	<	fileInit->read_xyz( simnfo ); // default velocities on
637	<
638	<	delete fileInit;
639	<	}
640	<	else{
641	<
642	<	#ifdef IS_MPI
643	<
644	<	// no init from bass
645	<
646	<	sprintf( painCave.errMsg,
647	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
648	<	painCave.isFatal;
649	<	simError();
650	<
651	<	#else
652	<
653	<	initFromBass();
654	<
655	<
656	<	#endif
657	<	}
658	<
659	<	#ifdef IS_MPI
660	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
661	<	MPIcheckPoint();
662	<	#endif // is_mpi
663	<
664	<
102	>	makeOutNames();
103
666	–
667	–
668	–
669	–
670	–	#ifdef IS_MPI
671	–	if( worldRank == 0 ){
672	–	#endif // is_mpi
673	–
674	–	if( the_globals->haveFinalConfig() ){
675	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
676	–	}
677	–	else{
678	–	strcpy( simnfo->finalName, inFileName );
679	–	char* endTest;
680	–	int nameLength = strlen( simnfo->finalName );
681	–	endTest = &(simnfo->finalName[nameLength - 5]);
682	–	if( !strcmp( endTest, ".bass" ) ){
683	–	strcpy( endTest, ".eor" );
684	–	}
685	–	else if( !strcmp( endTest, ".BASS" ) ){
686	–	strcpy( endTest, ".eor" );
687	–	}
688	–	else{
689	–	endTest = &(simnfo->finalName[nameLength - 4]);
690	–	if( !strcmp( endTest, ".bss" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else if( !strcmp( endTest, ".mdl" ) ){
694	–	strcpy( endTest, ".eor" );
695	–	}
696	–	else{
697	–	strcat( simnfo->finalName, ".eor" );
698	–	}
699	–	}
700	–	}
701	–
702	–	// make the sample and status out names
703	–
704	–	strcpy( simnfo->sampleName, inFileName );
705	–	char* endTest;
706	–	int nameLength = strlen( simnfo->sampleName );
707	–	endTest = &(simnfo->sampleName[nameLength - 5]);
708	–	if( !strcmp( endTest, ".bass" ) ){
709	–	strcpy( endTest, ".dump" );
710	–	}
711	–	else if( !strcmp( endTest, ".BASS" ) ){
712	–	strcpy( endTest, ".dump" );
713	–	}
714	–	else{
715	–	endTest = &(simnfo->sampleName[nameLength - 4]);
716	–	if( !strcmp( endTest, ".bss" ) ){
717	–	strcpy( endTest, ".dump" );
718	–	}
719	–	else if( !strcmp( endTest, ".mdl" ) ){
720	–	strcpy( endTest, ".dump" );
721	–	}
722	–	else{
723	–	strcat( simnfo->sampleName, ".dump" );
724	–	}
725	–	}
726	–
727	–	strcpy( simnfo->statusName, inFileName );
728	–	nameLength = strlen( simnfo->statusName );
729	–	endTest = &(simnfo->statusName[nameLength - 5]);
730	–	if( !strcmp( endTest, ".bass" ) ){
731	–	strcpy( endTest, ".stat" );
732	–	}
733	–	else if( !strcmp( endTest, ".BASS" ) ){
734	–	strcpy( endTest, ".stat" );
735	–	}
736	–	else{
737	–	endTest = &(simnfo->statusName[nameLength - 4]);
738	–	if( !strcmp( endTest, ".bss" ) ){
739	–	strcpy( endTest, ".stat" );
740	–	}
741	–	else if( !strcmp( endTest, ".mdl" ) ){
742	–	strcpy( endTest, ".stat" );
743	–	}
744	–	else{
745	–	strcat( simnfo->statusName, ".stat" );
746	–	}
747	–	}
748	–
749	–	#ifdef IS_MPI
750	–	}
751	–	#endif // is_mpi
752	–
753	–	// set the status, sample, and themal kick times
754	–
755	–	if( the_globals->haveSampleTime() ){
756	–	simnfo->sampleTime = the_globals->getSampleTime();
757	–	simnfo->statusTime = simnfo->sampleTime;
758	–	simnfo->thermalTime = simnfo->sampleTime;
759	–	}
760	–	else{
761	–	simnfo->sampleTime = the_globals->getRunTime();
762	–	simnfo->statusTime = simnfo->sampleTime;
763	–	simnfo->thermalTime = simnfo->sampleTime;
764	–	}
765	–
766	–	if( the_globals->haveStatusTime() ){
767	–	simnfo->statusTime = the_globals->getStatusTime();
768	–	}
769	–
770	–	if( the_globals->haveThermalTime() ){
771	–	simnfo->thermalTime = the_globals->getThermalTime();
772	–	}
773	–
774	–	// check for the temperature set flag
775	–
776	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
777	–
778	–
104		// make the integrator
105
106	+	makeIntegrator();
107
782	–	NVT* myNVT = NULL;
783	–	switch( ensembleCase ){
784	–
785	–	case NVE_ENS:
786	–	new NVE( simnfo, the_ff );
787	–	break;
788	–
789	–	case NVT_ENS:
790	–	myNVT = new NVT( simnfo, the_ff );
791	–	myNVT->setTargetTemp(the_globals->getTargetTemp());
792	–
793	–	if (the_globals->haveTauThermostat())
794	–	myNVT->setTauThermostat(the_globals->getTauThermostat());
795	–	//     else if (the_globals->haveQmass())
796	–	//       myNVT->setQmass(the_globals->getQmass());
797	–	else {
798	–	sprintf( painCave.errMsg,
799	–	"SimSetup error: If you use the NVT\n"
800	–	"    ensemble, you must set either tauThermostat or qMass.\n"
801	–	"    Neither of these was found in the BASS file.\n");
802	–	painCave.isFatal = 1;
803	–	simError();
804	–	}
805	–	break;
806	–
807	–	default:
808	–	sprintf( painCave.errMsg,
809	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
810	–	painCave.isFatal = 1;
811	–	simError();
812	–	}
813	–
814	–
108		#ifdef IS_MPI
109		mpiSim->mpiRefresh();
110		#endif
111
112		// initialize the Fortran
113
114	+	initFortran();
115
822	–	simnfo->refreshSim();
823	–
824	–	if( !strcmp( simnfo->mixingRule, "standard") ){
825	–	the_ff->initForceField( LB_MIXING_RULE );
826	–	}
827	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
828	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
829	–	}
830	–	else{
831	–	sprintf( painCave.errMsg,
832	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
833	–	simnfo->mixingRule );
834	–	painCave.isFatal = 1;
835	–	simError();
836	–	}
116
117
839	–	#ifdef IS_MPI
840	–	strcpy( checkPointMsg,
841	–	"Successfully intialized the mixingRule for Fortran." );
842	–	MPIcheckPoint();
843	–	#endif // is_mpi
118		}
119
120
121		void SimSetup::makeMolecules( void ){
122
123		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
124	<	molInit info;
124	>	molInit molInfo;
125		DirectionalAtom* dAtom;
126		LinkedAssign* extras;
127		LinkedAssign* current_extra;
#	Line 872 | Line 146 | void SimSetup::makeMolecules( void ){
146
147		atomOffset = 0;
148		excludeOffset = 0;
149	<	for(i=0; i<simnfo->n_mol; i++){
149	>	for(i=0; i<info->n_mol; i++){
150
151		stampID = the_molecules[i].getStampID();
152
153	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
154	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
155	<	info.nBends    = comp_stamps[stampID]->getNBends();
156	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
157	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
884	<
885	<	info.myAtoms = &the_atoms[atomOffset];
886	<	info.myExcludes = &the_excludes[excludeOffset];
887	<	info.myBonds = new Bond*[info.nBonds];
888	<	info.myBends = new Bend*[info.nBends];
889	<	info.myTorsions = new Torsion*[info.nTorsions];
153	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
154	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
155	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
156	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
157	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
158
159	<	theBonds = new bond_pair[info.nBonds];
160	<	theBends = new bend_set[info.nBends];
161	<	theTorsions = new torsion_set[info.nTorsions];
159	>	molInfo.myAtoms = &the_atoms[atomOffset];
160	>	molInfo.myExcludes = &the_excludes[excludeOffset];
161	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
162	>	molInfo.myBends = new Bend*[molInfo.nBends];
163	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
164	>
165	>	theBonds = new bond_pair[molInfo.nBonds];
166	>	theBends = new bend_set[molInfo.nBends];
167	>	theTorsions = new torsion_set[molInfo.nTorsions];
168
169		// make the Atoms
170
171	<	for(j=0; j<info.nAtoms; j++){
171	>	for(j=0; j<molInfo.nAtoms; j++){
172
173		currentAtom = comp_stamps[stampID]->getAtom( j );
174		if( currentAtom->haveOrientation() ){
175
176		dAtom = new DirectionalAtom(j + atomOffset);
177	<	simnfo->n_oriented++;
178	<	info.myAtoms[j] = dAtom;
177	>	info->n_oriented++;
178	>	molInfo.myAtoms[j] = dAtom;
179
180		ux = currentAtom->getOrntX();
181		uy = currentAtom->getOrntY();
#	Line 919 | Line 193 | void SimSetup::makeMolecules( void ){
193		dAtom->setSUz( uz );
194		}
195		else{
196	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
196	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
197		}
198	<	info.myAtoms[j]->setType( currentAtom->getType() );
198	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
199
200		#ifdef IS_MPI
201
202	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
202	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
203
204		#endif // is_mpi
205		}
206
207		// make the bonds
208	<	for(j=0; j<info.nBonds; j++){
208	>	for(j=0; j<molInfo.nBonds; j++){
209
210		currentBond = comp_stamps[stampID]->getBond( j );
211		theBonds[j].a = currentBond->getA() + atomOffset;
#	Line 958 | Line 232 | void SimSetup::makeMolecules( void ){
232		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
233		#endif  //is_mpi
234		}
235	<	excludeOffset += info.nBonds;
235	>	excludeOffset += molInfo.nBonds;
236
237		//make the bends
238	<	for(j=0; j<info.nBends; j++){
238	>	for(j=0; j<molInfo.nBends; j++){
239
240		currentBend = comp_stamps[stampID]->getBend( j );
241		theBends[j].a = currentBend->getA() + atomOffset;
#	Line 1044 | Line 318 | void SimSetup::makeMolecules( void ){
318		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
319		#endif  //is_mpi
320		}
321	<	excludeOffset += info.nBends;
321	>	excludeOffset += molInfo.nBends;
322
323	<	for(j=0; j<info.nTorsions; j++){
323	>	for(j=0; j<molInfo.nTorsions; j++){
324
325		currentTorsion = comp_stamps[stampID]->getTorsion( j );
326		theTorsions[j].a = currentTorsion->getA() + atomOffset;
#	Line 1074 | Line 348 | void SimSetup::makeMolecules( void ){
348		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349		#endif  //is_mpi
350		}
351	<	excludeOffset += info.nTorsions;
351	>	excludeOffset += molInfo.nTorsions;
352
353
354		// send the arrays off to the forceField for init.
355
356	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
357	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
358	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
359	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
356	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
357	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
358	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
359	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
360
361
362	<	the_molecules[i].initialize( info );
362	>	the_molecules[i].initialize( molInfo );
363
364
365	<	atomOffset += info.nAtoms;
365	>	atomOffset += molInfo.nAtoms;
366		delete[] theBonds;
367		delete[] theBends;
368		delete[] theTorsions;
#	Line 1124 | Line 398 | void SimSetup::initFromBass( void ){
398		have_extra =1;
399
400		n_cells = (int)temp3 - 1;
401	<	cellx = simnfo->boxLx / temp3;
402	<	celly = simnfo->boxLy / temp3;
403	<	cellz = simnfo->boxLz / temp3;
401	>	cellx = info->boxLx / temp3;
402	>	celly = info->boxLy / temp3;
403	>	cellz = info->boxLz / temp3;
404		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
405		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
406		n_per_extra = (int)ceil( temp1 );
#	Line 1141 | Line 415 | void SimSetup::initFromBass( void ){
415		}
416		else{
417		n_cells = (int)temp3;
418	<	cellx = simnfo->boxLx / temp3;
419	<	celly = simnfo->boxLy / temp3;
420	<	cellz = simnfo->boxLz / temp3;
418	>	cellx = info->boxLx / temp3;
419	>	celly = info->boxLy / temp3;
420	>	cellz = info->boxLz / temp3;
421		}
422
423		current_mol = 0;
#	Line 1223 | Line 497 | void SimSetup::initFromBass( void ){
497		}
498
499
500	<	for( i=0; i<simnfo->n_atoms; i++ ){
501	<	simnfo->atoms[i]->set_vx( 0.0 );
502	<	simnfo->atoms[i]->set_vy( 0.0 );
503	<	simnfo->atoms[i]->set_vz( 0.0 );
500	>	for( i=0; i<info->n_atoms; i++ ){
501	>	info->atoms[i]->set_vx( 0.0 );
502	>	info->atoms[i]->set_vy( 0.0 );
503	>	info->atoms[i]->set_vz( 0.0 );
504		}
505		}
506
#	Line 1285 | Line 559 | void SimSetup::makeElement( double x, double y, double
559
560		current_comp_mol = 0;
561		current_comp++;
562	+	}
563	+	}
564	+
565	+
566	+	void SimSetup::gatherInfo( void ){
567	+	int i,j,k;
568	+
569	+	ensembleCase = -1;
570	+	ffCase = -1;
571	+
572	+	// get the stamps and globals;
573	+	stamps = stamps;
574	+	globals = globals;
575	+
576	+	// set the easy ones first
577	+	info->target_temp = globals->getTargetTemp();
578	+	info->dt = globals->getDt();
579	+	info->run_time = globals->getRunTime();
580	+	n_components = globals->getNComponents();
581	+
582	+
583	+	// get the forceField
584	+
585	+	strcpy( force_field, globals->getForceField() );
586	+
587	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
588	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
589	+	else{
590	+	sprintf( painCave.errMsg,
591	+	"SimSetup Error. Unrecognized force field -> %s\n",
592	+	force_field );
593	+	painCave.isFatal = 1;
594	+	simError();
595	+	}
596	+
597	+	// get the ensemble
598	+
599	+	strcpy( ensemble, globals->getEnsemble() );
600	+
601	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
602	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
603	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
604	+	ensembleCase = NPTi_ENS;
605	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
606	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
607	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
608	+	else{
609	+	sprintf( painCave.errMsg,
610	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
611	+	"reverting to NVE for this simulation.\n",
612	+	ensemble );
613	+	painCave.isFatal = 0;
614	+	simError();
615	+	strcpy( ensemble, "NVE" );
616	+	ensembleCase = NVE_ENS;
617	+	}
618	+	strcpy( info->ensemble, ensemble );
619	+
620	+	// get the mixing rule
621	+
622	+	strcpy( info->mixingRule, globals->getMixingRule() );
623	+	info->usePBC = globals->getPBC();
624	+
625	+
626	+	// get the components and calculate the tot_nMol and indvidual n_mol
627	+
628	+	the_components = globals->getComponents();
629	+	components_nmol = new int[n_components];
630	+
631	+
632	+	if( !globals->haveNMol() ){
633	+	// we don't have the total number of molecules, so we assume it is
634	+	// given in each component
635	+
636	+	tot_nmol = 0;
637	+	for( i=0; i<n_components; i++ ){
638	+
639	+	if( !the_components[i]->haveNMol() ){
640	+	// we have a problem
641	+	sprintf( painCave.errMsg,
642	+	"SimSetup Error. No global NMol or component NMol"
643	+	" given. Cannot calculate the number of atoms.\n" );
644	+	painCave.isFatal = 1;
645	+	simError();
646	+	}
647	+
648	+	tot_nmol += the_components[i]->getNMol();
649	+	components_nmol[i] = the_components[i]->getNMol();
650	+	}
651		}
652	+	else{
653	+	sprintf( painCave.errMsg,
654	+	"SimSetup error.\n"
655	+	"\tSorry, the ability to specify total"
656	+	" nMols and then give molfractions in the components\n"
657	+	"\tis not currently supported."
658	+	" Please give nMol in the components.\n" );
659	+	painCave.isFatal = 1;
660	+	simError();
661	+	}
662	+
663	+	// set the status, sample, and thermal kick times
664	+
665	+	if( globals->haveSampleTime() ){
666	+	info->sampleTime = globals->getSampleTime();
667	+	info->statusTime = info->sampleTime;
668	+	info->thermalTime = info->sampleTime;
669	+	}
670	+	else{
671	+	info->sampleTime = globals->getRunTime();
672	+	info->statusTime = info->sampleTime;
673	+	info->thermalTime = info->sampleTime;
674	+	}
675	+
676	+	if( globals->haveStatusTime() ){
677	+	info->statusTime = globals->getStatusTime();
678	+	}
679	+
680	+	if( globals->haveThermalTime() ){
681	+	info->thermalTime = globals->getThermalTime();
682	+	}
683	+
684	+	// check for the temperature set flag
685	+
686	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
687	+
688	+	// get some of the tricky things that may still be in the globals
689	+
690	+	double boxVector[3];
691	+	if( globals->haveBox() ){
692	+	boxVector[0] = globals->getBox();
693	+	boxVector[1] = globals->getBox();
694	+	boxVector[2] = globals->getBox();
695	+
696	+	info->setBox( boxVector );
697	+	}
698	+	else if( globals->haveDensity() ){
699	+
700	+	double vol;
701	+	vol = (double)tot_nmol / globals->getDensity();
702	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
703	+	boxVector[1] = boxVector[0];
704	+	boxVector[2] = boxVector[0];
705	+
706	+	info->setBox( boxVector );
707	+	}
708	+	else{
709	+	if( !globals->haveBoxX() ){
710	+	sprintf( painCave.errMsg,
711	+	"SimSetup error, no periodic BoxX size given.\n" );
712	+	painCave.isFatal = 1;
713	+	simError();
714	+	}
715	+	boxVector[0] = globals->getBoxX();
716	+
717	+	if( !globals->haveBoxY() ){
718	+	sprintf( painCave.errMsg,
719	+	"SimSetup error, no periodic BoxY size given.\n" );
720	+	painCave.isFatal = 1;
721	+	simError();
722	+	}
723	+	boxVector[1] = globals->getBoxY();
724	+
725	+	if( !globals->haveBoxZ() ){
726	+	sprintf( painCave.errMsg,
727	+	"SimSetup error, no periodic BoxZ size given.\n" );
728	+	painCave.isFatal = 1;
729	+	simError();
730	+	}
731	+	boxVector[2] = globals->getBoxZ();
732	+
733	+	info->setBox( boxVector );
734	+	}
735	+
736	+
737	+
738	+	#ifdef IS_MPI
739	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
740	+	MPIcheckPoint();
741	+	#endif // is_mpi
742	+
743		}
744	+
745	+
746	+	void SimSetup::finalInfoCheck( void ){
747	+	int index;
748	+	int usesDipoles;
749	+
750	+
751	+	// check electrostatic parameters
752	+
753	+	index = 0;
754	+	usesDipoles = 0;
755	+	while( (index < info->n_atoms) && !usesDipoles ){
756	+	usesDipoles = ((info->atoms)[index])->hasDipole();
757	+	index++;
758	+	}
759	+
760	+	#ifdef IS_MPI
761	+	int myUse = usesDipoles;
762	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
763	+	#endif //is_mpi
764	+
765	+
766	+	if (globals->getUseRF() ) {
767	+	info->useReactionField = 1;
768	+
769	+	if( !globals->haveECR() ){
770	+	sprintf( painCave.errMsg,
771	+	"SimSetup Warning: using default value of 1/2 the smallest "
772	+	"box length for the electrostaticCutoffRadius.\n"
773	+	"I hope you have a very fast processor!\n");
774	+	painCave.isFatal = 0;
775	+	simError();
776	+	double smallest;
777	+	smallest = info->boxLx;
778	+	if (info->boxLy <= smallest) smallest = info->boxLy;
779	+	if (info->boxLz <= smallest) smallest = info->boxLz;
780	+	info->ecr = 0.5 * smallest;
781	+	} else {
782	+	info->ecr        = globals->getECR();
783	+	}
784	+
785	+	if( !globals->haveEST() ){
786	+	sprintf( painCave.errMsg,
787	+	"SimSetup Warning: using default value of 0.05 * the "
788	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
789	+	);
790	+	painCave.isFatal = 0;
791	+	simError();
792	+	info->est = 0.05 * info->ecr;
793	+	} else {
794	+	info->est        = globals->getEST();
795	+	}
796	+
797	+	if(!globals->haveDielectric() ){
798	+	sprintf( painCave.errMsg,
799	+	"SimSetup Error: You are trying to use Reaction Field without"
800	+	"setting a dielectric constant!\n"
801	+	);
802	+	painCave.isFatal = 1;
803	+	simError();
804	+	}
805	+	info->dielectric = globals->getDielectric();
806	+	}
807	+	else {
808	+	if (usesDipoles) {
809	+
810	+	if( !globals->haveECR() ){
811	+	sprintf( painCave.errMsg,
812	+	"SimSetup Warning: using default value of 1/2 the smallest "
813	+	"box length for the electrostaticCutoffRadius.\n"
814	+	"I hope you have a very fast processor!\n");
815	+	painCave.isFatal = 0;
816	+	simError();
817	+	double smallest;
818	+	smallest = info->boxLx;
819	+	if (info->boxLy <= smallest) smallest = info->boxLy;
820	+	if (info->boxLz <= smallest) smallest = info->boxLz;
821	+	info->ecr = 0.5 * smallest;
822	+	} else {
823	+	info->ecr        = globals->getECR();
824	+	}
825	+
826	+	if( !globals->haveEST() ){
827	+	sprintf( painCave.errMsg,
828	+	"SimSetup Warning: using default value of 5%% of the "
829	+	"electrostaticCutoffRadius for the "
830	+	"electrostaticSkinThickness\n"
831	+	);
832	+	painCave.isFatal = 0;
833	+	simError();
834	+	info->est = 0.05 * info->ecr;
835	+	} else {
836	+	info->est        = globals->getEST();
837	+	}
838	+	}
839	+	}
840	+
841	+	#ifdef IS_MPI
842	+	strcpy( checkPointMsg, "post processing checks out" );
843	+	MPIcheckPoint();
844	+	#endif // is_mpi
845	+
846	+	}
847	+
848	+	void SimSetup::initSystemCoords( void ){
849	+
850	+	if( globals->haveInitialConfig() ){
851	+
852	+	InitializeFromFile* fileInit;
853	+	#ifdef IS_MPI // is_mpi
854	+	if( worldRank == 0 ){
855	+	#endif //is_mpi
856	+	fileInit = new InitializeFromFile( globals->getInitialConfig() );
857	+	#ifdef IS_MPI
858	+	}else fileInit = new InitializeFromFile( NULL );
859	+	#endif
860	+	fileInit->read_xyz( info ); // default velocities on
861	+
862	+	delete fileInit;
863	+	}
864	+	else{
865	+
866	+	#ifdef IS_MPI
867	+
868	+	// no init from bass
869	+
870	+	sprintf( painCave.errMsg,
871	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
872	+	painCave.isFatal;
873	+	simError();
874	+
875	+	#else
876	+
877	+	initFromBass();
878	+
879	+
880	+	#endif
881	+	}
882	+
883	+	#ifdef IS_MPI
884	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
885	+	MPIcheckPoint();
886	+	#endif // is_mpi
887	+
888	+	}
889	+
890	+
891	+	void SimSetup::makeOutNames( void ){
892	+
893	+	#ifdef IS_MPI
894	+	if( worldRank == 0 ){
895	+	#endif // is_mpi
896	+
897	+	if( globals->haveFinalConfig() ){
898	+	strcpy( info->finalName, globals->getFinalConfig() );
899	+	}
900	+	else{
901	+	strcpy( info->finalName, inFileName );
902	+	char* endTest;
903	+	int nameLength = strlen( info->finalName );
904	+	endTest = &(info->finalName[nameLength - 5]);
905	+	if( !strcmp( endTest, ".bass" ) ){
906	+	strcpy( endTest, ".eor" );
907	+	}
908	+	else if( !strcmp( endTest, ".BASS" ) ){
909	+	strcpy( endTest, ".eor" );
910	+	}
911	+	else{
912	+	endTest = &(info->finalName[nameLength - 4]);
913	+	if( !strcmp( endTest, ".bss" ) ){
914	+	strcpy( endTest, ".eor" );
915	+	}
916	+	else if( !strcmp( endTest, ".mdl" ) ){
917	+	strcpy( endTest, ".eor" );
918	+	}
919	+	else{
920	+	strcat( info->finalName, ".eor" );
921	+	}
922	+	}
923	+	}
924	+
925	+	// make the sample and status out names
926	+
927	+	strcpy( info->sampleName, inFileName );
928	+	char* endTest;
929	+	int nameLength = strlen( info->sampleName );
930	+	endTest = &(info->sampleName[nameLength - 5]);
931	+	if( !strcmp( endTest, ".bass" ) ){
932	+	strcpy( endTest, ".dump" );
933	+	}
934	+	else if( !strcmp( endTest, ".BASS" ) ){
935	+	strcpy( endTest, ".dump" );
936	+	}
937	+	else{
938	+	endTest = &(info->sampleName[nameLength - 4]);
939	+	if( !strcmp( endTest, ".bss" ) ){
940	+	strcpy( endTest, ".dump" );
941	+	}
942	+	else if( !strcmp( endTest, ".mdl" ) ){
943	+	strcpy( endTest, ".dump" );
944	+	}
945	+	else{
946	+	strcat( info->sampleName, ".dump" );
947	+	}
948	+	}
949	+
950	+	strcpy( info->statusName, inFileName );
951	+	nameLength = strlen( info->statusName );
952	+	endTest = &(info->statusName[nameLength - 5]);
953	+	if( !strcmp( endTest, ".bass" ) ){
954	+	strcpy( endTest, ".stat" );
955	+	}
956	+	else if( !strcmp( endTest, ".BASS" ) ){
957	+	strcpy( endTest, ".stat" );
958	+	}
959	+	else{
960	+	endTest = &(info->statusName[nameLength - 4]);
961	+	if( !strcmp( endTest, ".bss" ) ){
962	+	strcpy( endTest, ".stat" );
963	+	}
964	+	else if( !strcmp( endTest, ".mdl" ) ){
965	+	strcpy( endTest, ".stat" );
966	+	}
967	+	else{
968	+	strcat( info->statusName, ".stat" );
969	+	}
970	+	}
971	+
972	+	#ifdef IS_MPI
973	+	}
974	+	#endif // is_mpi
975	+
976	+	}
977	+
978	+
979	+	void SimSetup::sysObjectsCreation( void ){
980	+
981	+	int i;
982	+
983	+	// create the forceField
984	+
985	+	createFF();
986	+
987	+	// extract componentList
988	+
989	+	compList();
990	+
991	+	// calc the number of atoms, bond, bends, and torsions
992	+
993	+	calcSysValues();
994	+
995	+	#ifdef IS_MPI
996	+	// divide the molecules among the processors
997	+
998	+	mpiMolDivide();
999	+	#endif //is_mpi
1000	+
1001	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1002	+
1003	+	makeSysArrays();
1004	+
1005	+	// make and initialize the molecules (all but atomic coordinates)
1006	+
1007	+	makeMolecules();
1008	+	info->identArray = new int[info->n_atoms];
1009	+	for(i=0; i<info->n_atoms; i++){
1010	+	info->identArray[i] = the_atoms[i]->getIdent();
1011	+	}
1012	+
1013	+
1014	+
1015	+	}
1016	+
1017	+
1018	+	void SimSetup::createFF( void ){
1019	+
1020	+	switch( ffCase ){
1021	+
1022	+	case FF_DUFF:
1023	+	the_ff = new DUFF();
1024	+	break;
1025	+
1026	+	case FF_LJ:
1027	+	the_ff = new LJFF();
1028	+	break;
1029	+
1030	+	default:
1031	+	sprintf( painCave.errMsg,
1032	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1033	+	painCave.isFatal = 1;
1034	+	simError();
1035	+	}
1036	+
1037	+	#ifdef IS_MPI
1038	+	strcpy( checkPointMsg, "ForceField creation successful" );
1039	+	MPIcheckPoint();
1040	+	#endif // is_mpi
1041	+
1042	+	}
1043	+
1044	+
1045	+	void SimSetup::compList( void ){
1046	+
1047	+	int i;
1048	+
1049	+	comp_stamps = new MoleculeStamp*[n_components];
1050	+
1051	+	// make an array of molecule stamps that match the components used.
1052	+	// also extract the used stamps out into a separate linked list
1053	+
1054	+	info->nComponents = n_components;
1055	+	info->componentsNmol = components_nmol;
1056	+	info->compStamps = comp_stamps;
1057	+	info->headStamp = new LinkedMolStamp();
1058	+
1059	+	char* id;
1060	+	LinkedMolStamp* headStamp = info->headStamp;
1061	+	LinkedMolStamp* currentStamp = NULL;
1062	+	for( i=0; i<n_components; i++ ){
1063	+
1064	+	id = the_components[i]->getType();
1065	+	comp_stamps[i] = NULL;
1066	+
1067	+	// check to make sure the component isn't already in the list
1068	+
1069	+	comp_stamps[i] = headStamp->match( id );
1070	+	if( comp_stamps[i] == NULL ){
1071	+
1072	+	// extract the component from the list;
1073	+
1074	+	currentStamp = stamps->extractMolStamp( id );
1075	+	if( currentStamp == NULL ){
1076	+	sprintf( painCave.errMsg,
1077	+	"SimSetup error: Component \"%s\" was not found in the "
1078	+	"list of declared molecules\n",
1079	+	id );
1080	+	painCave.isFatal = 1;
1081	+	simError();
1082	+	}
1083	+
1084	+	headStamp->add( currentStamp );
1085	+	comp_stamps[i] = headStamp->match( id );
1086	+	}
1087	+	}
1088	+
1089	+	#ifdef IS_MPI
1090	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1091	+	MPIcheckPoint();
1092	+	#endif // is_mpi
1093	+
1094	+
1095	+	}
1096	+
1097	+	void SimSetup::calcSysValues( void ){
1098	+	int i, j, k;
1099	+
1100	+
1101	+	tot_atoms = 0;
1102	+	tot_bonds = 0;
1103	+	tot_bends = 0;
1104	+	tot_torsions = 0;
1105	+	for( i=0; i<n_components; i++ ){
1106	+
1107	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1108	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1109	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1110	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1111	+	}
1112	+
1113	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1114	+
1115	+	info->n_atoms = tot_atoms;
1116	+	info->n_bonds = tot_bonds;
1117	+	info->n_bends = tot_bends;
1118	+	info->n_torsions = tot_torsions;
1119	+	info->n_SRI = tot_SRI;
1120	+	info->n_mol = tot_nmol;
1121	+
1122	+	info->molMembershipArray = new int[tot_atoms];
1123	+	}
1124	+
1125	+
1126	+	#ifdef IS_MPI
1127	+
1128	+	void SimSetup::mpiMolDivide( void ){
1129	+
1130	+	int i, j, k;
1131	+	int localMol, allMol;
1132	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1133	+
1134	+	mpiSim = new mpiSimulation( info );
1135	+
1136	+	globalIndex = mpiSim->divideLabor();
1137	+
1138	+	// set up the local variables
1139	+
1140	+	mol2proc = mpiSim->getMolToProcMap();
1141	+	molCompType = mpiSim->getMolComponentType();
1142	+
1143	+	allMol = 0;
1144	+	localMol = 0;
1145	+	local_atoms = 0;
1146	+	local_bonds = 0;
1147	+	local_bends = 0;
1148	+	local_torsions = 0;
1149	+	globalAtomIndex = 0;
1150	+
1151	+
1152	+	for( i=0; i<n_components; i++ ){
1153	+
1154	+	for( j=0; j<components_nmol[i]; j++ ){
1155	+
1156	+	if( mol2proc[allMol] == worldRank ){
1157	+
1158	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1159	+	local_bonds +=    comp_stamps[i]->getNBonds();
1160	+	local_bends +=    comp_stamps[i]->getNBends();
1161	+	local_torsions += comp_stamps[i]->getNTorsions();
1162	+	localMol++;
1163	+	}
1164	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1165	+	info->molMembershipArray[globalAtomIndex] = allMol;
1166	+	globalAtomIndex++;
1167	+	}
1168	+
1169	+	allMol++;
1170	+	}
1171	+	}
1172	+	local_SRI = local_bonds + local_bends + local_torsions;
1173	+
1174	+	info->n_atoms = mpiSim->getMyNlocal();
1175	+
1176	+	if( local_atoms != info->n_atoms ){
1177	+	sprintf( painCave.errMsg,
1178	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1179	+	" localAtom (%d) are not equal.\n",
1180	+	info->n_atoms,
1181	+	local_atoms );
1182	+	painCave.isFatal = 1;
1183	+	simError();
1184	+	}
1185	+
1186	+	info->n_bonds = local_bonds;
1187	+	info->n_bends = local_bends;
1188	+	info->n_torsions = local_torsions;
1189	+	info->n_SRI = local_SRI;
1190	+	info->n_mol = localMol;
1191	+
1192	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1193	+	MPIcheckPoint();
1194	+	}
1195	+
1196	+	#endif // is_mpi
1197	+
1198	+
1199	+	void SimSetup::makeSysArrays( void ){
1200	+	int i, j, k;
1201	+
1202	+
1203	+	// create the atom and short range interaction arrays
1204	+
1205	+	Atom::createArrays(info->n_atoms);
1206	+	the_atoms = new Atom*[info->n_atoms];
1207	+	the_molecules = new Molecule[info->n_mol];
1208	+	int molIndex;
1209	+
1210	+	// initialize the molecule's stampID's
1211	+
1212	+	#ifdef IS_MPI
1213	+
1214	+
1215	+	molIndex = 0;
1216	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1217	+
1218	+	if(mol2proc[i] == worldRank ){
1219	+	the_molecules[molIndex].setStampID( molCompType[i] );
1220	+	the_molecules[molIndex].setMyIndex( molIndex );
1221	+	the_molecules[molIndex].setGlobalIndex( i );
1222	+	molIndex++;
1223	+	}
1224	+	}
1225	+
1226	+	#else // is_mpi
1227	+
1228	+	molIndex = 0;
1229	+	globalAtomIndex = 0;
1230	+	for(i=0; i<n_components; i++){
1231	+	for(j=0; j<components_nmol[i]; j++ ){
1232	+	the_molecules[molIndex].setStampID( i );
1233	+	the_molecules[molIndex].setMyIndex( molIndex );
1234	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1235	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1236	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1237	+	globalAtomIndex++;
1238	+	}
1239	+	molIndex++;
1240	+	}
1241	+	}
1242	+
1243	+
1244	+	#endif // is_mpi
1245	+
1246	+
1247	+	if( info->n_SRI ){
1248	+
1249	+	Exclude::createArray(info->n_SRI);
1250	+	the_excludes = new Exclude*[info->n_SRI];
1251	+	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1252	+	info->globalExcludes = new int;
1253	+	info->n_exclude = info->n_SRI;
1254	+	}
1255	+	else{
1256	+
1257	+	Exclude::createArray( 1 );
1258	+	the_excludes = new Exclude*;
1259	+	the_excludes[0] = new Exclude(0);
1260	+	the_excludes[0]->setPair( 0,0 );
1261	+	info->globalExcludes = new int;
1262	+	info->globalExcludes[0] = 0;
1263	+	info->n_exclude = 0;
1264	+	}
1265	+
1266	+	// set the arrays into the SimInfo object
1267	+
1268	+	info->atoms = the_atoms;
1269	+	info->molecules = the_molecules;
1270	+	info->nGlobalExcludes = 0;
1271	+	info->excludes = the_excludes;
1272	+
1273	+	the_ff->setSimInfo( info );
1274	+
1275	+	}
1276	+
1277	+	void SimSetup::makeIntegrator( void ){
1278	+
1279	+	NVT*  myNVT = NULL;
1280	+	NPTi* myNPTi = NULL;
1281	+	NPTf* myNPTf = NULL;
1282	+	NPTim* myNPTim = NULL;
1283	+	NPTfm* myNPTfm = NULL;
1284	+
1285	+	switch( ensembleCase ){
1286	+
1287	+	case NVE_ENS:
1288	+	new NVE( info, the_ff );
1289	+	break;
1290	+
1291	+	case NVT_ENS:
1292	+	myNVT = new NVT( info, the_ff );
1293	+	myNVT->setTargetTemp(globals->getTargetTemp());
1294	+
1295	+	if (globals->haveTauThermostat())
1296	+	myNVT->setTauThermostat(globals->getTauThermostat());
1297	+
1298	+	else {
1299	+	sprintf( painCave.errMsg,
1300	+	"SimSetup error: If you use the NVT\n"
1301	+	"    ensemble, you must set tauThermostat.\n");
1302	+	painCave.isFatal = 1;
1303	+	simError();
1304	+	}
1305	+	break;
1306	+
1307	+	case NPTi_ENS:
1308	+	myNPTi = new NPTi( info, the_ff );
1309	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1310	+
1311	+	if (globals->haveTargetPressure())
1312	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1313	+	else {
1314	+	sprintf( painCave.errMsg,
1315	+	"SimSetup error: If you use a constant pressure\n"
1316	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1317	+	painCave.isFatal = 1;
1318	+	simError();
1319	+	}
1320	+
1321	+	if( globals->haveTauThermostat() )
1322	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1323	+	else{
1324	+	sprintf( painCave.errMsg,
1325	+	"SimSetup error: If you use an NPT\n"
1326	+	"    ensemble, you must set tauThermostat.\n");
1327	+	painCave.isFatal = 1;
1328	+	simError();
1329	+	}
1330	+
1331	+	if( globals->haveTauBarostat() )
1332	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1333	+	else{
1334	+	sprintf( painCave.errMsg,
1335	+	"SimSetup error: If you use an NPT\n"
1336	+	"    ensemble, you must set tauBarostat.\n");
1337	+	painCave.isFatal = 1;
1338	+	simError();
1339	+	}
1340	+	break;
1341	+
1342	+	case NPTf_ENS:
1343	+	myNPTf = new NPTf( info, the_ff );
1344	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1345	+
1346	+	if (globals->haveTargetPressure())
1347	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1348	+	else {
1349	+	sprintf( painCave.errMsg,
1350	+	"SimSetup error: If you use a constant pressure\n"
1351	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1352	+	painCave.isFatal = 1;
1353	+	simError();
1354	+	}
1355	+
1356	+	if( globals->haveTauThermostat() )
1357	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1358	+	else{
1359	+	sprintf( painCave.errMsg,
1360	+	"SimSetup error: If you use an NPT\n"
1361	+	"    ensemble, you must set tauThermostat.\n");
1362	+	painCave.isFatal = 1;
1363	+	simError();
1364	+	}
1365	+
1366	+	if( globals->haveTauBarostat() )
1367	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1368	+	else{
1369	+	sprintf( painCave.errMsg,
1370	+	"SimSetup error: If you use an NPT\n"
1371	+	"    ensemble, you must set tauBarostat.\n");
1372	+	painCave.isFatal = 1;
1373	+	simError();
1374	+	}
1375	+	break;
1376	+
1377	+	case NPTim_ENS:
1378	+	myNPTim = new NPTim( info, the_ff );
1379	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1380	+
1381	+	if (globals->haveTargetPressure())
1382	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1383	+	else {
1384	+	sprintf( painCave.errMsg,
1385	+	"SimSetup error: If you use a constant pressure\n"
1386	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1387	+	painCave.isFatal = 1;
1388	+	simError();
1389	+	}
1390	+
1391	+	if( globals->haveTauThermostat() )
1392	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1393	+	else{
1394	+	sprintf( painCave.errMsg,
1395	+	"SimSetup error: If you use an NPT\n"
1396	+	"    ensemble, you must set tauThermostat.\n");
1397	+	painCave.isFatal = 1;
1398	+	simError();
1399	+	}
1400	+
1401	+	if( globals->haveTauBarostat() )
1402	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1403	+	else{
1404	+	sprintf( painCave.errMsg,
1405	+	"SimSetup error: If you use an NPT\n"
1406	+	"    ensemble, you must set tauBarostat.\n");
1407	+	painCave.isFatal = 1;
1408	+	simError();
1409	+	}
1410	+	break;
1411	+
1412	+	case NPTfm_ENS:
1413	+	myNPTfm = new NPTfm( info, the_ff );
1414	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1415	+
1416	+	if (globals->haveTargetPressure())
1417	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1418	+	else {
1419	+	sprintf( painCave.errMsg,
1420	+	"SimSetup error: If you use a constant pressure\n"
1421	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1422	+	painCave.isFatal = 1;
1423	+	simError();
1424	+	}
1425	+
1426	+	if( globals->haveTauThermostat() )
1427	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1428	+	else{
1429	+	sprintf( painCave.errMsg,
1430	+	"SimSetup error: If you use an NPT\n"
1431	+	"    ensemble, you must set tauThermostat.\n");
1432	+	painCave.isFatal = 1;
1433	+	simError();
1434	+	}
1435	+
1436	+	if( globals->haveTauBarostat() )
1437	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1438	+	else{
1439	+	sprintf( painCave.errMsg,
1440	+	"SimSetup error: If you use an NPT\n"
1441	+	"    ensemble, you must set tauBarostat.\n");
1442	+	painCave.isFatal = 1;
1443	+	simError();
1444	+	}
1445	+	break;
1446	+
1447	+	default:
1448	+	sprintf( painCave.errMsg,
1449	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1450	+	painCave.isFatal = 1;
1451	+	simError();
1452	+	}
1453	+
1454	+	}
1455	+
1456	+	void SimSetup::initFortran( void ){
1457	+
1458	+	info->refreshSim();
1459	+
1460	+	if( !strcmp( info->mixingRule, "standard") ){
1461	+	the_ff->initForceField( LB_MIXING_RULE );
1462	+	}
1463	+	else if( !strcmp( info->mixingRule, "explicit") ){
1464	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1465	+	}
1466	+	else{
1467	+	sprintf( painCave.errMsg,
1468	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1469	+	info->mixingRule );
1470	+	painCave.isFatal = 1;
1471	+	simError();
1472	+	}
1473	+
1474	+
1475	+	#ifdef IS_MPI
1476	+	strcpy( checkPointMsg,
1477	+	"Successfully intialized the mixingRule for Fortran." );
1478	+	MPIcheckPoint();
1479	+	#endif // is_mpi
1480	+
1481	+	}

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