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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC vs.
Revision 626 by mmeineke, Wed Jul 16 21:30:56 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 NPT_ENS 2
17	>	#define NVE_ENS   0
18	>	#define NVT_ENS   1
19	>	#define NPTi_ENS  2
20	>	#define NPTf_ENS  3
21	>	#define NPTim_ENS 4
22	>	#define NPTfm_ENS 5
23
24	+
25		#define FF_DUFF 0
26		#define FF_LJ   1
27
#	Line 74 | Line 78 | void SimSetup::createSim( void ){
78
79		void SimSetup::createSim( void ){
80
77	–	MakeStamps *the_stamps;
78	–	Globals* the_globals;
81		int i, j, k, globalAtomIndex;
82
83	<	int ensembleCase;
82	<	int ffCase;
83	>	// gather all of the information from the Bass file
84
85	<	ensembleCase = -1;
85	<	ffCase = -1;
85	>	gatherInfo();
86
87	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
87	>	// creation of complex system objects
88
89	<	// set the easy ones first
92	<	simnfo->target_temp = the_globals->getTargetTemp();
93	<	simnfo->dt = the_globals->getDt();
94	<	simnfo->run_time = the_globals->getRunTime();
95	<
96	<	// get the ones we know are there, yet still may need some work.
97	<	n_components = the_globals->getNComponents();
98	<	strcpy( force_field, the_globals->getForceField() );
99	<
100	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
101	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102	<	else{
103	<	sprintf( painCave.errMsg,
104	<	"SimSetup Error. Unrecognized force field -> %s\n",
105	<	force_field );
106	<	painCave.isFatal = 1;
107	<	simError();
108	<	}
109	<
110	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
112	<
113	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
114	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
115	<	else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS;
116	<	else{
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
119	<	"reverting to NVE for this simulation.\n",
120	<	ensemble );
121	<	painCave.isFatal = 0;
122	<	simError();
123	<	strcpy( ensemble, "NVE" );
124	<	ensembleCase = NVE_ENS;
125	<	}
126	<	strcpy( simnfo->ensemble, ensemble );
127	<
128	<
129	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
130	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
131	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132	<	//     if (the_globals->haveTargetPressure())
133	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134	<	//     else {
135	<	//       sprintf( painCave.errMsg,
136	<	//                "SimSetup error: If you use the constant pressure\n"
137	<	//                "    ensemble, you must set targetPressure.\n"
138	<	//                "    This was found in the BASS file.\n");
139	<	//       painCave.isFatal = 1;
140	<	//       simError();
141	<	//     }
142	<
143	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
155	<
156	<	//     if (the_globals->haveTauBarostat())
157	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158	<	//     else {
159	<	//       sprintf( painCave.errMsg,
160	<	//                "SimSetup error: If you use the constant pressure\n"
161	<	//                "    ensemble, you must set tauBarostat.\n"
162	<	//                "    This was found in the BASS file.\n");
163	<	//       painCave.isFatal = 1;
164	<	//       simError();
165	<	//     }
166	<
167	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
168	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
169	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
170	<
171	<	//     if (the_globals->haveTauThermostat())
172	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173	<	//     else if (the_globals->haveQmass())
174	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
175	<	//     else {
176	<	//       sprintf( painCave.errMsg,
177	<	//                "SimSetup error: If you use one of the constant temperature\n"
178	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
179	<	//                "    Neither of these was found in the BASS file.\n");
180	<	//       painCave.isFatal = 1;
181	<	//       simError();
182	<	//     }
183	<
184	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185	<	simnfo->usePBC = the_globals->getPBC();
186	<
187	<	int usesDipoles = 0;
188	<	switch( ffCase ){
189	<
190	<	case FF_DUFF:
191	<	the_ff = new DUFF();
192	<	usesDipoles = 1;
193	<	break;
194	<
195	<	case FF_LJ:
196	<	the_ff = new LJFF();
197	<	break;
198	<
199	<	default:
200	<	sprintf( painCave.errMsg,
201	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
205	<
206	<	#ifdef IS_MPI
207	<	strcpy( checkPointMsg, "ForceField creation successful" );
208	<	MPIcheckPoint();
209	<	#endif // is_mpi
210	<
211	<	// get the components and calculate the tot_nMol and indvidual n_mol
212	<	the_components = the_globals->getComponents();
213	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
215	<
216	<	if( !the_globals->haveNMol() ){
217	<	// we don't have the total number of molecules, so we assume it is
218	<	// given in each component
219	<
220	<	tot_nmol = 0;
221	<	for( i=0; i<n_components; i++ ){
222	<
223	<	if( !the_components[i]->haveNMol() ){
224	<	// we have a problem
225	<	sprintf( painCave.errMsg,
226	<	"SimSetup Error. No global NMol or component NMol"
227	<	" given. Cannot calculate the number of atoms.\n" );
228	<	painCave.isFatal = 1;
229	<	simError();
230	<	}
231	<
232	<	tot_nmol += the_components[i]->getNMol();
233	<	components_nmol[i] = the_components[i]->getNMol();
234	<	}
235	<	}
236	<	else{
237	<	sprintf( painCave.errMsg,
238	<	"SimSetup error.\n"
239	<	"\tSorry, the ability to specify total"
240	<	" nMols and then give molfractions in the components\n"
241	<	"\tis not currently supported."
242	<	" Please give nMol in the components.\n" );
243	<	painCave.isFatal = 1;
244	<	simError();
245	<
246	<
247	<	//     tot_nmol = the_globals->getNMol();
248	<
249	<	//   //we have the total number of molecules, now we check for molfractions
250	<	//     for( i=0; i<n_components; i++ ){
251	<
252	<	//       if( !the_components[i]->haveMolFraction() ){
253	<
254	<	//  if( !the_components[i]->haveNMol() ){
255	<	//    //we have a problem
256	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	<	//              << " nMol was given in component
258	<
259	<	}
260	<
261	<	#ifdef IS_MPI
262	<	strcpy( checkPointMsg, "Have the number of components" );
263	<	MPIcheckPoint();
264	<	#endif // is_mpi
265	<
266	<	// make an array of molecule stamps that match the components used.
267	<	// also extract the used stamps out into a separate linked list
268	<
269	<	simnfo->nComponents = n_components;
270	<	simnfo->componentsNmol = components_nmol;
271	<	simnfo->compStamps = comp_stamps;
272	<	simnfo->headStamp = new LinkedMolStamp();
273	<
274	<	char* id;
275	<	LinkedMolStamp* headStamp = simnfo->headStamp;
276	<	LinkedMolStamp* currentStamp = NULL;
277	<	for( i=0; i<n_components; i++ ){
278	<
279	<	id = the_components[i]->getType();
280	<	comp_stamps[i] = NULL;
281	<
282	<	// check to make sure the component isn't already in the list
283	<
284	<	comp_stamps[i] = headStamp->match( id );
285	<	if( comp_stamps[i] == NULL ){
286	<
287	<	// extract the component from the list;
288	<
289	<	currentStamp = the_stamps->extractMolStamp( id );
290	<	if( currentStamp == NULL ){
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup error: Component \"%s\" was not found in the "
293	<	"list of declared molecules\n",
294	<	id );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	headStamp->add( currentStamp );
300	<	comp_stamps[i] = headStamp->match( id );
301	<	}
302	<	}
89	>	sysObjectsCreation();
90
91	<	#ifdef IS_MPI
305	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
306	<	MPIcheckPoint();
307	<	#endif // is_mpi
91	>	// check on the post processing info
92
93	+	finalInfoCheck();
94
95	+	// initialize the system coordinates
96
97	<
312	<	// caclulate the number of atoms, bonds, bends and torsions
313	<
314	<	tot_atoms = 0;
315	<	tot_bonds = 0;
316	<	tot_bends = 0;
317	<	tot_torsions = 0;
318	<	for( i=0; i<n_components; i++ ){
319	<
320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	<	}
325	<
326	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
327	<
328	<	simnfo->n_atoms = tot_atoms;
329	<	simnfo->n_bonds = tot_bonds;
330	<	simnfo->n_bends = tot_bends;
331	<	simnfo->n_torsions = tot_torsions;
332	<	simnfo->n_SRI = tot_SRI;
333	<	simnfo->n_mol = tot_nmol;
97	>	initSystemCoords();
98
335	–	simnfo->molMembershipArray = new int[tot_atoms];
99
100	<	#ifdef IS_MPI
100	>	// make the output filenames
101
102	<	// divide the molecules among processors here.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
344	<
345	<	// set up the local variables
346	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
349	<
350	<	int* mol2proc = mpiSim->getMolToProcMap();
351	<	int* molCompType = mpiSim->getMolComponentType();
352	<
353	<	allMol = 0;
354	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
360	<
361	<
362	<	for( i=0; i<n_components; i++ ){
363	<
364	<	for( j=0; j<components_nmol[i]; j++ ){
365	<
366	<	if( mol2proc[allMol] == worldRank ){
367	<
368	<	local_atoms +=    comp_stamps[i]->getNAtoms();
369	<	local_bonds +=    comp_stamps[i]->getNBonds();
370	<	local_bends +=    comp_stamps[i]->getNBends();
371	<	local_torsions += comp_stamps[i]->getNTorsions();
372	<	localMol++;
373	<	}
374	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
377	<	}
378	<
379	<	allMol++;
380	<	}
381	<	}
382	<	local_SRI = local_bonds + local_bends + local_torsions;
383	<
384	<	simnfo->n_atoms = mpiSim->getMyNlocal();
385	<
386	<	if( local_atoms != simnfo->n_atoms ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
395	<
396	<	simnfo->n_bonds = local_bonds;
397	<	simnfo->n_bends = local_bends;
398	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
401	<
402	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
403	<	MPIcheckPoint();
404	<
405	<
406	<	#endif // is_mpi
407	<
408	<
409	<	// create the atom and short range interaction arrays
410	<
411	<	Atom::createArrays(simnfo->n_atoms);
412	<	the_atoms = new Atom*[simnfo->n_atoms];
413	<	the_molecules = new Molecule[simnfo->n_mol];
414	<	int molIndex;
415	<
416	<	// initialize the molecule's stampID's
417	<
418	<	#ifdef IS_MPI
419	<
420	<
421	<	molIndex = 0;
422	<	for(i=0; i<mpiSim->getTotNmol(); i++){
423	<
424	<	if(mol2proc[i] == worldRank ){
425	<	the_molecules[molIndex].setStampID( molCompType[i] );
426	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
429	<	}
430	<	}
431	<
432	<	#else // is_mpi
433	<
434	<	molIndex = 0;
435	<	globalAtomIndex = 0;
436	<	for(i=0; i<n_components; i++){
437	<	for(j=0; j<components_nmol[i]; j++ ){
438	<	the_molecules[molIndex].setStampID( i );
439	<	the_molecules[molIndex].setMyIndex( molIndex );
440	<	the_molecules[molIndex].setGlobalIndex( molIndex );
441	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443	<	globalAtomIndex++;
444	<	}
445	<	molIndex++;
446	<	}
447	<	}
448	<
449	<
450	<	#endif // is_mpi
451	<
452	<
453	<	if( simnfo->n_SRI ){
454	<
455	<	Exclude::createArray(simnfo->n_SRI);
456	<	the_excludes = new Exclude*[simnfo->n_SRI];
457	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
458	<	simnfo->globalExcludes = new int;
459	<	simnfo->n_exclude = simnfo->n_SRI;
460	<	}
461	<	else{
462	<
463	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
471	<
472	<	// set the arrays into the SimInfo object
473	<
474	<	simnfo->atoms = the_atoms;
475	<	simnfo->molecules = the_molecules;
476	<	simnfo->nGlobalExcludes = 0;
477	<	simnfo->excludes = the_excludes;
478	<
479	<
480	<	// get some of the tricky things that may still be in the globals
481	<
482	<	double boxVector[3];
483	<	if( the_globals->haveBox() ){
484	<	boxVector[0] = the_globals->getBox();
485	<	boxVector[1] = the_globals->getBox();
486	<	boxVector[2] = the_globals->getBox();
487	<
488	<	simnfo->setBox( boxVector );
489	<	}
490	<	else if( the_globals->haveDensity() ){
491	<
492	<	double vol;
493	<	vol = (double)tot_nmol / the_globals->getDensity();
494	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
495	<	boxVector[1] = boxVector[0];
496	<	boxVector[2] = boxVector[0];
497	<
498	<	simnfo->setBox( boxVector );
499	<	}
500	<	else{
501	<	if( !the_globals->haveBoxX() ){
502	<	sprintf( painCave.errMsg,
503	<	"SimSetup error, no periodic BoxX size given.\n" );
504	<	painCave.isFatal = 1;
505	<	simError();
506	<	}
507	<	boxVector[0] = the_globals->getBoxX();
508	<
509	<	if( !the_globals->haveBoxY() ){
510	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxY size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[1] = the_globals->getBoxY();
516	<
517	<	if( !the_globals->haveBoxZ() ){
518	<	sprintf( painCave.errMsg,
519	<	"SimSetup error, no periodic BoxZ size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	boxVector[2] = the_globals->getBoxZ();
524	<
525	<	simnfo->setBox( boxVector );
526	<	}
527	<
528	<	#ifdef IS_MPI
529	<	strcpy( checkPointMsg, "Box size set up" );
530	<	MPIcheckPoint();
531	<	#endif // is_mpi
532	<
533	<
534	<	// initialize the arrays
535	<
536	<	the_ff->setSimInfo( simnfo );
537	<
538	<	makeMolecules();
539	<	simnfo->identArray = new int[simnfo->n_atoms];
540	<	for(i=0; i<simnfo->n_atoms; i++){
541	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
542	<	}
543	<
544	<	if (the_globals->getUseRF() ) {
545	<	simnfo->useReactionField = 1;
546	<
547	<	if( !the_globals->haveECR() ){
548	<	sprintf( painCave.errMsg,
549	<	"SimSetup Warning: using default value of 1/2 the smallest "
550	<	"box length for the electrostaticCutoffRadius.\n"
551	<	"I hope you have a very fast processor!\n");
552	<	painCave.isFatal = 0;
553	<	simError();
554	<	double smallest;
555	<	smallest = simnfo->boxLx;
556	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
557	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
558	<	simnfo->ecr = 0.5 * smallest;
559	<	} else {
560	<	simnfo->ecr        = the_globals->getECR();
561	<	}
562	<
563	<	if( !the_globals->haveEST() ){
564	<	sprintf( painCave.errMsg,
565	<	"SimSetup Warning: using default value of 0.05 * the "
566	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
567	<	);
568	<	painCave.isFatal = 0;
569	<	simError();
570	<	simnfo->est = 0.05 * simnfo->ecr;
571	<	} else {
572	<	simnfo->est        = the_globals->getEST();
573	<	}
574	<
575	<	if(!the_globals->haveDielectric() ){
576	<	sprintf( painCave.errMsg,
577	<	"SimSetup Error: You are trying to use Reaction Field without"
578	<	"setting a dielectric constant!\n"
579	<	);
580	<	painCave.isFatal = 1;
581	<	simError();
582	<	}
583	<	simnfo->dielectric = the_globals->getDielectric();
584	<	} else {
585	<	if (usesDipoles) {
586	<
587	<	if( !the_globals->haveECR() ){
588	<	sprintf( painCave.errMsg,
589	<	"SimSetup Warning: using default value of 1/2 the smallest "
590	<	"box length for the electrostaticCutoffRadius.\n"
591	<	"I hope you have a very fast processor!\n");
592	<	painCave.isFatal = 0;
593	<	simError();
594	<	double smallest;
595	<	smallest = simnfo->boxLx;
596	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
597	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
598	<	simnfo->ecr = 0.5 * smallest;
599	<	} else {
600	<	simnfo->ecr        = the_globals->getECR();
601	<	}
602	<
603	<	if( !the_globals->haveEST() ){
604	<	sprintf( painCave.errMsg,
605	<	"SimSetup Warning: using default value of 5%% of the "
606	<	"electrostaticCutoffRadius for the "
607	<	"electrostaticSkinThickness\n"
608	<	);
609	<	painCave.isFatal = 0;
610	<	simError();
611	<	simnfo->est = 0.05 * simnfo->ecr;
612	<	} else {
613	<	simnfo->est        = the_globals->getEST();
614	<	}
615	<	}
616	<	}
617	<
618	<	#ifdef IS_MPI
619	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
620	<	MPIcheckPoint();
621	<	#endif // is_mpi
622	<
623	<	if( the_globals->haveInitialConfig() ){
624	<
625	<	InitializeFromFile* fileInit;
626	<	#ifdef IS_MPI // is_mpi
627	<	if( worldRank == 0 ){
628	<	#endif //is_mpi
629	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
630	<	#ifdef IS_MPI
631	<	}else fileInit = new InitializeFromFile( NULL );
632	<	#endif
633	<	fileInit->read_xyz( simnfo ); // default velocities on
634	<
635	<	delete fileInit;
636	<	}
637	<	else{
638	<
639	<	#ifdef IS_MPI
640	<
641	<	// no init from bass
642	<
643	<	sprintf( painCave.errMsg,
644	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
645	<	painCave.isFatal;
646	<	simError();
647	<
648	<	#else
649	<
650	<	initFromBass();
651	<
652	<
653	<	#endif
654	<	}
655	<
656	<	#ifdef IS_MPI
657	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
658	<	MPIcheckPoint();
659	<	#endif // is_mpi
660	<
661	<
102	>	makeOutNames();
103
663	–
664	–
665	–
666	–
667	–	#ifdef IS_MPI
668	–	if( worldRank == 0 ){
669	–	#endif // is_mpi
670	–
671	–	if( the_globals->haveFinalConfig() ){
672	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
673	–	}
674	–	else{
675	–	strcpy( simnfo->finalName, inFileName );
676	–	char* endTest;
677	–	int nameLength = strlen( simnfo->finalName );
678	–	endTest = &(simnfo->finalName[nameLength - 5]);
679	–	if( !strcmp( endTest, ".bass" ) ){
680	–	strcpy( endTest, ".eor" );
681	–	}
682	–	else if( !strcmp( endTest, ".BASS" ) ){
683	–	strcpy( endTest, ".eor" );
684	–	}
685	–	else{
686	–	endTest = &(simnfo->finalName[nameLength - 4]);
687	–	if( !strcmp( endTest, ".bss" ) ){
688	–	strcpy( endTest, ".eor" );
689	–	}
690	–	else if( !strcmp( endTest, ".mdl" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else{
694	–	strcat( simnfo->finalName, ".eor" );
695	–	}
696	–	}
697	–	}
698	–
699	–	// make the sample and status out names
700	–
701	–	strcpy( simnfo->sampleName, inFileName );
702	–	char* endTest;
703	–	int nameLength = strlen( simnfo->sampleName );
704	–	endTest = &(simnfo->sampleName[nameLength - 5]);
705	–	if( !strcmp( endTest, ".bass" ) ){
706	–	strcpy( endTest, ".dump" );
707	–	}
708	–	else if( !strcmp( endTest, ".BASS" ) ){
709	–	strcpy( endTest, ".dump" );
710	–	}
711	–	else{
712	–	endTest = &(simnfo->sampleName[nameLength - 4]);
713	–	if( !strcmp( endTest, ".bss" ) ){
714	–	strcpy( endTest, ".dump" );
715	–	}
716	–	else if( !strcmp( endTest, ".mdl" ) ){
717	–	strcpy( endTest, ".dump" );
718	–	}
719	–	else{
720	–	strcat( simnfo->sampleName, ".dump" );
721	–	}
722	–	}
723	–
724	–	strcpy( simnfo->statusName, inFileName );
725	–	nameLength = strlen( simnfo->statusName );
726	–	endTest = &(simnfo->statusName[nameLength - 5]);
727	–	if( !strcmp( endTest, ".bass" ) ){
728	–	strcpy( endTest, ".stat" );
729	–	}
730	–	else if( !strcmp( endTest, ".BASS" ) ){
731	–	strcpy( endTest, ".stat" );
732	–	}
733	–	else{
734	–	endTest = &(simnfo->statusName[nameLength - 4]);
735	–	if( !strcmp( endTest, ".bss" ) ){
736	–	strcpy( endTest, ".stat" );
737	–	}
738	–	else if( !strcmp( endTest, ".mdl" ) ){
739	–	strcpy( endTest, ".stat" );
740	–	}
741	–	else{
742	–	strcat( simnfo->statusName, ".stat" );
743	–	}
744	–	}
745	–
746	–	#ifdef IS_MPI
747	–	}
748	–	#endif // is_mpi
749	–
750	–	// set the status, sample, and themal kick times
751	–
752	–	if( the_globals->haveSampleTime() ){
753	–	simnfo->sampleTime = the_globals->getSampleTime();
754	–	simnfo->statusTime = simnfo->sampleTime;
755	–	simnfo->thermalTime = simnfo->sampleTime;
756	–	}
757	–	else{
758	–	simnfo->sampleTime = the_globals->getRunTime();
759	–	simnfo->statusTime = simnfo->sampleTime;
760	–	simnfo->thermalTime = simnfo->sampleTime;
761	–	}
762	–
763	–	if( the_globals->haveStatusTime() ){
764	–	simnfo->statusTime = the_globals->getStatusTime();
765	–	}
766	–
767	–	if( the_globals->haveThermalTime() ){
768	–	simnfo->thermalTime = the_globals->getThermalTime();
769	–	}
770	–
771	–	// check for the temperature set flag
772	–
773	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
774	–
775	–
104		// make the integrator
105
106	+	makeIntegrator();
107
779	–	NVT* myNVT = NULL;
780	–	switch( ensembleCase ){
781	–
782	–	case NVE_ENS:
783	–	new NVE( simnfo, the_ff );
784	–	break;
785	–
786	–	case NVT_ENS:
787	–	myNVT = new NVT( simnfo, the_ff );
788	–	myNVT->setTargetTemp(the_globals->getTargetTemp());
789	–
790	–	if (the_globals->haveTauThermostat())
791	–	myNVT->setTauThermostat(the_globals->getTauThermostat());
792	–	//     else if (the_globals->haveQmass())
793	–	//       myNVT->setQmass(the_globals->getQmass());
794	–	else {
795	–	sprintf( painCave.errMsg,
796	–	"SimSetup error: If you use the NVT\n"
797	–	"    ensemble, you must set either tauThermostat or qMass.\n"
798	–	"    Neither of these was found in the BASS file.\n");
799	–	painCave.isFatal = 1;
800	–	simError();
801	–	}
802	–	break;
803	–
804	–	default:
805	–	sprintf( painCave.errMsg,
806	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
807	–	painCave.isFatal = 1;
808	–	simError();
809	–	}
810	–
811	–
108		#ifdef IS_MPI
109		mpiSim->mpiRefresh();
110		#endif
111
112		// initialize the Fortran
113
114	+	initFortran();
115
819	–	simnfo->refreshSim();
820	–
821	–	if( !strcmp( simnfo->mixingRule, "standard") ){
822	–	the_ff->initForceField( LB_MIXING_RULE );
823	–	}
824	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
825	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
826	–	}
827	–	else{
828	–	sprintf( painCave.errMsg,
829	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
830	–	simnfo->mixingRule );
831	–	painCave.isFatal = 1;
832	–	simError();
833	–	}
116
117
836	–	#ifdef IS_MPI
837	–	strcpy( checkPointMsg,
838	–	"Successfully intialized the mixingRule for Fortran." );
839	–	MPIcheckPoint();
840	–	#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 869 | 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;
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	<	info.myAtoms = &the_atoms[atomOffset];
160	<	info.myExcludes = &the_excludes[excludeOffset];
161	<	info.myBonds = new Bond*[info.nBonds];
162	<	info.myBends = new Bend*[info.nBends];
163	<	info.myTorsions = new Torsion*[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[info.nBonds];
166	<	theBends = new bend_set[info.nBends];
167	<	theTorsions = new torsion_set[info.nTorsions];
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 916 | 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 955 | 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 1041 | 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 1071 | 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 1121 | 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->boxL[0] / temp3;
402	>	celly = info->boxL[1] / temp3;
403	>	cellz = info->boxL[2] / 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 1138 | 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->boxL[0] / temp3;
419	>	celly = info->boxL[1] / temp3;
420	>	cellz = info->boxL[2] / temp3;
421		}
422
423		current_mol = 0;
#	Line 1220 | 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 1282 | 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	+	double theEcr, theEst;
766	+
767	+	if (globals->getUseRF() ) {
768	+	info->useReactionField = 1;
769	+
770	+	if( !globals->haveECR() ){
771	+	sprintf( painCave.errMsg,
772	+	"SimSetup Warning: using default value of 1/2 the smallest "
773	+	"box length for the electrostaticCutoffRadius.\n"
774	+	"I hope you have a very fast processor!\n");
775	+	painCave.isFatal = 0;
776	+	simError();
777	+	double smallest;
778	+	smallest = info->boxL[0];
779	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
780	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
781	+	theEcr = 0.5 * smallest;
782	+	} else {
783	+	theEcr = globals->getECR();
784	+	}
785	+
786	+	if( !globals->haveEST() ){
787	+	sprintf( painCave.errMsg,
788	+	"SimSetup Warning: using default value of 0.05 * the "
789	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
790	+	);
791	+	painCave.isFatal = 0;
792	+	simError();
793	+	theEst = 0.05 * theEcr;
794	+	} else {
795	+	theEst= globals->getEST();
796	+	}
797	+
798	+	info->setEcr( theEcr, theEst );
799	+
800	+	if(!globals->haveDielectric() ){
801	+	sprintf( painCave.errMsg,
802	+	"SimSetup Error: You are trying to use Reaction Field without"
803	+	"setting a dielectric constant!\n"
804	+	);
805	+	painCave.isFatal = 1;
806	+	simError();
807	+	}
808	+	info->dielectric = globals->getDielectric();
809	+	}
810	+	else {
811	+	if (usesDipoles) {
812	+
813	+	if( !globals->haveECR() ){
814	+	sprintf( painCave.errMsg,
815	+	"SimSetup Warning: using default value of 1/2 the smallest "
816	+	"box length for the electrostaticCutoffRadius.\n"
817	+	"I hope you have a very fast processor!\n");
818	+	painCave.isFatal = 0;
819	+	simError();
820	+	double smallest;
821	+	smallest = info->boxL[0];
822	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
823	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
824	+	theEcr = 0.5 * smallest;
825	+	} else {
826	+	theEcr = globals->getECR();
827	+	}
828	+
829	+	if( !globals->haveEST() ){
830	+	sprintf( painCave.errMsg,
831	+	"SimSetup Warning: using default value of 0.05 * the "
832	+	"electrostaticCutoffRadius for the "
833	+	"electrostaticSkinThickness\n"
834	+	);
835	+	painCave.isFatal = 0;
836	+	simError();
837	+	theEst = 0.05 * theEcr;
838	+	} else {
839	+	theEst= globals->getEST();
840	+	}
841	+
842	+	info->setEcr( theEcr, theEst );
843	+	}
844	+	}
845	+
846	+	#ifdef IS_MPI
847	+	strcpy( checkPointMsg, "post processing checks out" );
848	+	MPIcheckPoint();
849	+	#endif // is_mpi
850	+
851	+	}
852	+
853	+	void SimSetup::initSystemCoords( void ){
854	+
855	+	if( globals->haveInitialConfig() ){
856	+
857	+	InitializeFromFile* fileInit;
858	+	#ifdef IS_MPI // is_mpi
859	+	if( worldRank == 0 ){
860	+	#endif //is_mpi
861	+	fileInit = new InitializeFromFile( globals->getInitialConfig() );
862	+	#ifdef IS_MPI
863	+	}else fileInit = new InitializeFromFile( NULL );
864	+	#endif
865	+	fileInit->read_xyz( info ); // default velocities on
866	+
867	+	delete fileInit;
868	+	}
869	+	else{
870	+
871	+	#ifdef IS_MPI
872	+
873	+	// no init from bass
874	+
875	+	sprintf( painCave.errMsg,
876	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
877	+	painCave.isFatal;
878	+	simError();
879	+
880	+	#else
881	+
882	+	initFromBass();
883	+
884	+
885	+	#endif
886	+	}
887	+
888	+	#ifdef IS_MPI
889	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
890	+	MPIcheckPoint();
891	+	#endif // is_mpi
892	+
893	+	}
894	+
895	+
896	+	void SimSetup::makeOutNames( void ){
897	+
898	+	#ifdef IS_MPI
899	+	if( worldRank == 0 ){
900	+	#endif // is_mpi
901	+
902	+	if( globals->haveFinalConfig() ){
903	+	strcpy( info->finalName, globals->getFinalConfig() );
904	+	}
905	+	else{
906	+	strcpy( info->finalName, inFileName );
907	+	char* endTest;
908	+	int nameLength = strlen( info->finalName );
909	+	endTest = &(info->finalName[nameLength - 5]);
910	+	if( !strcmp( endTest, ".bass" ) ){
911	+	strcpy( endTest, ".eor" );
912	+	}
913	+	else if( !strcmp( endTest, ".BASS" ) ){
914	+	strcpy( endTest, ".eor" );
915	+	}
916	+	else{
917	+	endTest = &(info->finalName[nameLength - 4]);
918	+	if( !strcmp( endTest, ".bss" ) ){
919	+	strcpy( endTest, ".eor" );
920	+	}
921	+	else if( !strcmp( endTest, ".mdl" ) ){
922	+	strcpy( endTest, ".eor" );
923	+	}
924	+	else{
925	+	strcat( info->finalName, ".eor" );
926	+	}
927	+	}
928	+	}
929	+
930	+	// make the sample and status out names
931	+
932	+	strcpy( info->sampleName, inFileName );
933	+	char* endTest;
934	+	int nameLength = strlen( info->sampleName );
935	+	endTest = &(info->sampleName[nameLength - 5]);
936	+	if( !strcmp( endTest, ".bass" ) ){
937	+	strcpy( endTest, ".dump" );
938	+	}
939	+	else if( !strcmp( endTest, ".BASS" ) ){
940	+	strcpy( endTest, ".dump" );
941	+	}
942	+	else{
943	+	endTest = &(info->sampleName[nameLength - 4]);
944	+	if( !strcmp( endTest, ".bss" ) ){
945	+	strcpy( endTest, ".dump" );
946	+	}
947	+	else if( !strcmp( endTest, ".mdl" ) ){
948	+	strcpy( endTest, ".dump" );
949	+	}
950	+	else{
951	+	strcat( info->sampleName, ".dump" );
952	+	}
953	+	}
954	+
955	+	strcpy( info->statusName, inFileName );
956	+	nameLength = strlen( info->statusName );
957	+	endTest = &(info->statusName[nameLength - 5]);
958	+	if( !strcmp( endTest, ".bass" ) ){
959	+	strcpy( endTest, ".stat" );
960	+	}
961	+	else if( !strcmp( endTest, ".BASS" ) ){
962	+	strcpy( endTest, ".stat" );
963	+	}
964	+	else{
965	+	endTest = &(info->statusName[nameLength - 4]);
966	+	if( !strcmp( endTest, ".bss" ) ){
967	+	strcpy( endTest, ".stat" );
968	+	}
969	+	else if( !strcmp( endTest, ".mdl" ) ){
970	+	strcpy( endTest, ".stat" );
971	+	}
972	+	else{
973	+	strcat( info->statusName, ".stat" );
974	+	}
975	+	}
976	+
977	+	#ifdef IS_MPI
978	+	}
979	+	#endif // is_mpi
980	+
981	+	}
982	+
983	+
984	+	void SimSetup::sysObjectsCreation( void ){
985	+
986	+	int i;
987	+
988	+	// create the forceField
989	+
990	+	createFF();
991	+
992	+	// extract componentList
993	+
994	+	compList();
995	+
996	+	// calc the number of atoms, bond, bends, and torsions
997	+
998	+	calcSysValues();
999	+
1000	+	#ifdef IS_MPI
1001	+	// divide the molecules among the processors
1002	+
1003	+	mpiMolDivide();
1004	+	#endif //is_mpi
1005	+
1006	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1007	+
1008	+	makeSysArrays();
1009	+
1010	+	// make and initialize the molecules (all but atomic coordinates)
1011	+
1012	+	makeMolecules();
1013	+	info->identArray = new int[info->n_atoms];
1014	+	for(i=0; i<info->n_atoms; i++){
1015	+	info->identArray[i] = the_atoms[i]->getIdent();
1016	+	}
1017	+
1018	+
1019	+
1020	+	}
1021	+
1022	+
1023	+	void SimSetup::createFF( void ){
1024	+
1025	+	switch( ffCase ){
1026	+
1027	+	case FF_DUFF:
1028	+	the_ff = new DUFF();
1029	+	break;
1030	+
1031	+	case FF_LJ:
1032	+	the_ff = new LJFF();
1033	+	break;
1034	+
1035	+	default:
1036	+	sprintf( painCave.errMsg,
1037	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1038	+	painCave.isFatal = 1;
1039	+	simError();
1040	+	}
1041	+
1042	+	#ifdef IS_MPI
1043	+	strcpy( checkPointMsg, "ForceField creation successful" );
1044	+	MPIcheckPoint();
1045	+	#endif // is_mpi
1046	+
1047	+	}
1048	+
1049	+
1050	+	void SimSetup::compList( void ){
1051	+
1052	+	int i;
1053	+
1054	+	comp_stamps = new MoleculeStamp*[n_components];
1055	+
1056	+	// make an array of molecule stamps that match the components used.
1057	+	// also extract the used stamps out into a separate linked list
1058	+
1059	+	info->nComponents = n_components;
1060	+	info->componentsNmol = components_nmol;
1061	+	info->compStamps = comp_stamps;
1062	+	info->headStamp = new LinkedMolStamp();
1063	+
1064	+	char* id;
1065	+	LinkedMolStamp* headStamp = info->headStamp;
1066	+	LinkedMolStamp* currentStamp = NULL;
1067	+	for( i=0; i<n_components; i++ ){
1068	+
1069	+	id = the_components[i]->getType();
1070	+	comp_stamps[i] = NULL;
1071	+
1072	+	// check to make sure the component isn't already in the list
1073	+
1074	+	comp_stamps[i] = headStamp->match( id );
1075	+	if( comp_stamps[i] == NULL ){
1076	+
1077	+	// extract the component from the list;
1078	+
1079	+	currentStamp = stamps->extractMolStamp( id );
1080	+	if( currentStamp == NULL ){
1081	+	sprintf( painCave.errMsg,
1082	+	"SimSetup error: Component \"%s\" was not found in the "
1083	+	"list of declared molecules\n",
1084	+	id );
1085	+	painCave.isFatal = 1;
1086	+	simError();
1087	+	}
1088	+
1089	+	headStamp->add( currentStamp );
1090	+	comp_stamps[i] = headStamp->match( id );
1091	+	}
1092		}
1093	+
1094	+	#ifdef IS_MPI
1095	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1096	+	MPIcheckPoint();
1097	+	#endif // is_mpi
1098	+
1099	+
1100		}
1101	+
1102	+	void SimSetup::calcSysValues( void ){
1103	+	int i, j, k;
1104	+
1105	+
1106	+	tot_atoms = 0;
1107	+	tot_bonds = 0;
1108	+	tot_bends = 0;
1109	+	tot_torsions = 0;
1110	+	for( i=0; i<n_components; i++ ){
1111	+
1112	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1113	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1114	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1115	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1116	+	}
1117	+
1118	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1119	+
1120	+	info->n_atoms = tot_atoms;
1121	+	info->n_bonds = tot_bonds;
1122	+	info->n_bends = tot_bends;
1123	+	info->n_torsions = tot_torsions;
1124	+	info->n_SRI = tot_SRI;
1125	+	info->n_mol = tot_nmol;
1126	+
1127	+	info->molMembershipArray = new int[tot_atoms];
1128	+	}
1129	+
1130	+
1131	+	#ifdef IS_MPI
1132	+
1133	+	void SimSetup::mpiMolDivide( void ){
1134	+
1135	+	int i, j, k;
1136	+	int localMol, allMol;
1137	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1138	+
1139	+	mpiSim = new mpiSimulation( info );
1140	+
1141	+	globalIndex = mpiSim->divideLabor();
1142	+
1143	+	// set up the local variables
1144	+
1145	+	mol2proc = mpiSim->getMolToProcMap();
1146	+	molCompType = mpiSim->getMolComponentType();
1147	+
1148	+	allMol = 0;
1149	+	localMol = 0;
1150	+	local_atoms = 0;
1151	+	local_bonds = 0;
1152	+	local_bends = 0;
1153	+	local_torsions = 0;
1154	+	globalAtomIndex = 0;
1155	+
1156	+
1157	+	for( i=0; i<n_components; i++ ){
1158	+
1159	+	for( j=0; j<components_nmol[i]; j++ ){
1160	+
1161	+	if( mol2proc[allMol] == worldRank ){
1162	+
1163	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1164	+	local_bonds +=    comp_stamps[i]->getNBonds();
1165	+	local_bends +=    comp_stamps[i]->getNBends();
1166	+	local_torsions += comp_stamps[i]->getNTorsions();
1167	+	localMol++;
1168	+	}
1169	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1170	+	info->molMembershipArray[globalAtomIndex] = allMol;
1171	+	globalAtomIndex++;
1172	+	}
1173	+
1174	+	allMol++;
1175	+	}
1176	+	}
1177	+	local_SRI = local_bonds + local_bends + local_torsions;
1178	+
1179	+	info->n_atoms = mpiSim->getMyNlocal();
1180	+
1181	+	if( local_atoms != info->n_atoms ){
1182	+	sprintf( painCave.errMsg,
1183	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1184	+	" localAtom (%d) are not equal.\n",
1185	+	info->n_atoms,
1186	+	local_atoms );
1187	+	painCave.isFatal = 1;
1188	+	simError();
1189	+	}
1190	+
1191	+	info->n_bonds = local_bonds;
1192	+	info->n_bends = local_bends;
1193	+	info->n_torsions = local_torsions;
1194	+	info->n_SRI = local_SRI;
1195	+	info->n_mol = localMol;
1196	+
1197	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1198	+	MPIcheckPoint();
1199	+	}
1200	+
1201	+	#endif // is_mpi
1202	+
1203	+
1204	+	void SimSetup::makeSysArrays( void ){
1205	+	int i, j, k;
1206	+
1207	+
1208	+	// create the atom and short range interaction arrays
1209	+
1210	+	Atom::createArrays(info->n_atoms);
1211	+	the_atoms = new Atom*[info->n_atoms];
1212	+	the_molecules = new Molecule[info->n_mol];
1213	+	int molIndex;
1214	+
1215	+	// initialize the molecule's stampID's
1216	+
1217	+	#ifdef IS_MPI
1218	+
1219	+
1220	+	molIndex = 0;
1221	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1222	+
1223	+	if(mol2proc[i] == worldRank ){
1224	+	the_molecules[molIndex].setStampID( molCompType[i] );
1225	+	the_molecules[molIndex].setMyIndex( molIndex );
1226	+	the_molecules[molIndex].setGlobalIndex( i );
1227	+	molIndex++;
1228	+	}
1229	+	}
1230	+
1231	+	#else // is_mpi
1232	+
1233	+	molIndex = 0;
1234	+	globalAtomIndex = 0;
1235	+	for(i=0; i<n_components; i++){
1236	+	for(j=0; j<components_nmol[i]; j++ ){
1237	+	the_molecules[molIndex].setStampID( i );
1238	+	the_molecules[molIndex].setMyIndex( molIndex );
1239	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1240	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1241	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1242	+	globalAtomIndex++;
1243	+	}
1244	+	molIndex++;
1245	+	}
1246	+	}
1247	+
1248	+
1249	+	#endif // is_mpi
1250	+
1251	+
1252	+	if( info->n_SRI ){
1253	+
1254	+	Exclude::createArray(info->n_SRI);
1255	+	the_excludes = new Exclude*[info->n_SRI];
1256	+	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1257	+	info->globalExcludes = new int;
1258	+	info->n_exclude = info->n_SRI;
1259	+	}
1260	+	else{
1261	+
1262	+	Exclude::createArray( 1 );
1263	+	the_excludes = new Exclude*;
1264	+	the_excludes[0] = new Exclude(0);
1265	+	the_excludes[0]->setPair( 0,0 );
1266	+	info->globalExcludes = new int;
1267	+	info->globalExcludes[0] = 0;
1268	+	info->n_exclude = 0;
1269	+	}
1270	+
1271	+	// set the arrays into the SimInfo object
1272	+
1273	+	info->atoms = the_atoms;
1274	+	info->molecules = the_molecules;
1275	+	info->nGlobalExcludes = 0;
1276	+	info->excludes = the_excludes;
1277	+
1278	+	the_ff->setSimInfo( info );
1279	+
1280	+	}
1281	+
1282	+	void SimSetup::makeIntegrator( void ){
1283	+
1284	+	NVT*  myNVT = NULL;
1285	+	NPTi* myNPTi = NULL;
1286	+	NPTf* myNPTf = NULL;
1287	+	NPTim* myNPTim = NULL;
1288	+	NPTfm* myNPTfm = NULL;
1289	+
1290	+	switch( ensembleCase ){
1291	+
1292	+	case NVE_ENS:
1293	+	new NVE( info, the_ff );
1294	+	break;
1295	+
1296	+	case NVT_ENS:
1297	+	myNVT = new NVT( info, the_ff );
1298	+	myNVT->setTargetTemp(globals->getTargetTemp());
1299	+
1300	+	if (globals->haveTauThermostat())
1301	+	myNVT->setTauThermostat(globals->getTauThermostat());
1302	+
1303	+	else {
1304	+	sprintf( painCave.errMsg,
1305	+	"SimSetup error: If you use the NVT\n"
1306	+	"    ensemble, you must set tauThermostat.\n");
1307	+	painCave.isFatal = 1;
1308	+	simError();
1309	+	}
1310	+	break;
1311	+
1312	+	case NPTi_ENS:
1313	+	myNPTi = new NPTi( info, the_ff );
1314	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1315	+
1316	+	if (globals->haveTargetPressure())
1317	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1318	+	else {
1319	+	sprintf( painCave.errMsg,
1320	+	"SimSetup error: If you use a constant pressure\n"
1321	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1322	+	painCave.isFatal = 1;
1323	+	simError();
1324	+	}
1325	+
1326	+	if( globals->haveTauThermostat() )
1327	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1328	+	else{
1329	+	sprintf( painCave.errMsg,
1330	+	"SimSetup error: If you use an NPT\n"
1331	+	"    ensemble, you must set tauThermostat.\n");
1332	+	painCave.isFatal = 1;
1333	+	simError();
1334	+	}
1335	+
1336	+	if( globals->haveTauBarostat() )
1337	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1338	+	else{
1339	+	sprintf( painCave.errMsg,
1340	+	"SimSetup error: If you use an NPT\n"
1341	+	"    ensemble, you must set tauBarostat.\n");
1342	+	painCave.isFatal = 1;
1343	+	simError();
1344	+	}
1345	+	break;
1346	+
1347	+	case NPTf_ENS:
1348	+	myNPTf = new NPTf( info, the_ff );
1349	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1350	+
1351	+	if (globals->haveTargetPressure())
1352	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1353	+	else {
1354	+	sprintf( painCave.errMsg,
1355	+	"SimSetup error: If you use a constant pressure\n"
1356	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1357	+	painCave.isFatal = 1;
1358	+	simError();
1359	+	}
1360	+
1361	+	if( globals->haveTauThermostat() )
1362	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1363	+	else{
1364	+	sprintf( painCave.errMsg,
1365	+	"SimSetup error: If you use an NPT\n"
1366	+	"    ensemble, you must set tauThermostat.\n");
1367	+	painCave.isFatal = 1;
1368	+	simError();
1369	+	}
1370	+
1371	+	if( globals->haveTauBarostat() )
1372	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1373	+	else{
1374	+	sprintf( painCave.errMsg,
1375	+	"SimSetup error: If you use an NPT\n"
1376	+	"    ensemble, you must set tauBarostat.\n");
1377	+	painCave.isFatal = 1;
1378	+	simError();
1379	+	}
1380	+	break;
1381	+
1382	+	case NPTim_ENS:
1383	+	myNPTim = new NPTim( info, the_ff );
1384	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1385	+
1386	+	if (globals->haveTargetPressure())
1387	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1388	+	else {
1389	+	sprintf( painCave.errMsg,
1390	+	"SimSetup error: If you use a constant pressure\n"
1391	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1392	+	painCave.isFatal = 1;
1393	+	simError();
1394	+	}
1395	+
1396	+	if( globals->haveTauThermostat() )
1397	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1398	+	else{
1399	+	sprintf( painCave.errMsg,
1400	+	"SimSetup error: If you use an NPT\n"
1401	+	"    ensemble, you must set tauThermostat.\n");
1402	+	painCave.isFatal = 1;
1403	+	simError();
1404	+	}
1405	+
1406	+	if( globals->haveTauBarostat() )
1407	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1408	+	else{
1409	+	sprintf( painCave.errMsg,
1410	+	"SimSetup error: If you use an NPT\n"
1411	+	"    ensemble, you must set tauBarostat.\n");
1412	+	painCave.isFatal = 1;
1413	+	simError();
1414	+	}
1415	+	break;
1416	+
1417	+	case NPTfm_ENS:
1418	+	myNPTfm = new NPTfm( info, the_ff );
1419	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1420	+
1421	+	if (globals->haveTargetPressure())
1422	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1423	+	else {
1424	+	sprintf( painCave.errMsg,
1425	+	"SimSetup error: If you use a constant pressure\n"
1426	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1427	+	painCave.isFatal = 1;
1428	+	simError();
1429	+	}
1430	+
1431	+	if( globals->haveTauThermostat() )
1432	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1433	+	else{
1434	+	sprintf( painCave.errMsg,
1435	+	"SimSetup error: If you use an NPT\n"
1436	+	"    ensemble, you must set tauThermostat.\n");
1437	+	painCave.isFatal = 1;
1438	+	simError();
1439	+	}
1440	+
1441	+	if( globals->haveTauBarostat() )
1442	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1443	+	else{
1444	+	sprintf( painCave.errMsg,
1445	+	"SimSetup error: If you use an NPT\n"
1446	+	"    ensemble, you must set tauBarostat.\n");
1447	+	painCave.isFatal = 1;
1448	+	simError();
1449	+	}
1450	+	break;
1451	+
1452	+	default:
1453	+	sprintf( painCave.errMsg,
1454	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1455	+	painCave.isFatal = 1;
1456	+	simError();
1457	+	}
1458	+
1459	+	}
1460	+
1461	+	void SimSetup::initFortran( void ){
1462	+
1463	+	info->refreshSim();
1464	+
1465	+	if( !strcmp( info->mixingRule, "standard") ){
1466	+	the_ff->initForceField( LB_MIXING_RULE );
1467	+	}
1468	+	else if( !strcmp( info->mixingRule, "explicit") ){
1469	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1470	+	}
1471	+	else{
1472	+	sprintf( painCave.errMsg,
1473	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1474	+	info->mixingRule );
1475	+	painCave.isFatal = 1;
1476	+	simError();
1477	+	}
1478	+
1479	+
1480	+	#ifdef IS_MPI
1481	+	strcpy( checkPointMsg,
1482	+	"Successfully intialized the mixingRule for Fortran." );
1483	+	MPIcheckPoint();
1484	+	#endif // is_mpi
1485	+
1486	+	}

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