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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 582 by mmeineke, Wed Jul 9 15:33:46 2003 UTC vs.
Revision 653 by chuckv, Fri Jul 25 20:00:17 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	+	#define FF_EAM  2
28
26	–
29		SimSetup::SimSetup(){
30		stamps = new MakeStamps();
31		globals = new Globals();
#	Line 76 | Line 78 | void SimSetup::createSim( void ){
78
79		void SimSetup::createSim( void ){
80
79	–	MakeStamps *the_stamps;
80	–	Globals* the_globals;
81		int i, j, k, globalAtomIndex;
82
83	<	int ensembleCase;
84	<	int ffCase;
83	>	// gather all of the information from the Bass file
84
85	<	ensembleCase = -1;
87	<	ffCase = -1;
85	>	gatherInfo();
86
87	<	// get the stamps and globals;
90	<	the_stamps = stamps;
91	<	the_globals = globals;
87	>	// creation of complex system objects
88
89	<	// set the easy ones first
94	<	simnfo->target_temp = the_globals->getTargetTemp();
95	<	simnfo->dt = the_globals->getDt();
96	<	simnfo->run_time = the_globals->getRunTime();
89	>	sysObjectsCreation();
90
91	<	// get the ones we know are there, yet still may need some work.
99	<	n_components = the_globals->getNComponents();
100	<	strcpy( force_field, the_globals->getForceField() );
101	<
102	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
103	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
104	<	else{
105	<	sprintf( painCave.errMsg,
106	<	"SimSetup Error. Unrecognized force field -> %s\n",
107	<	force_field );
108	<	painCave.isFatal = 1;
109	<	simError();
110	<	}
111	<
112	<	// get the ensemble:
113	<	strcpy( ensemble, the_globals->getEnsemble() );
114	<
115	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
116	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
117	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
118	<	ensembleCase = NPTi_ENS;
119	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
120	<	else{
121	<	sprintf( painCave.errMsg,
122	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
123	<	"reverting to NVE for this simulation.\n",
124	<	ensemble );
125	<	painCave.isFatal = 0;
126	<	simError();
127	<	strcpy( ensemble, "NVE" );
128	<	ensembleCase = NVE_ENS;
129	<	}
130	<	strcpy( simnfo->ensemble, ensemble );
131	<
132	<
133	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
134	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
135	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
136	<	//     if (the_globals->haveTargetPressure())
137	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
138	<	//     else {
139	<	//       sprintf( painCave.errMsg,
140	<	//                "SimSetup error: If you use the constant pressure\n"
141	<	//                "    ensemble, you must set targetPressure.\n"
142	<	//                "    This was found in the BASS file.\n");
143	<	//       painCave.isFatal = 1;
144	<	//       simError();
145	<	//     }
146	<
147	<	//     if (the_globals->haveTauThermostat())
148	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
149	<	//     else if (the_globals->haveQmass())
150	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
151	<	//     else {
152	<	//       sprintf( painCave.errMsg,
153	<	//                "SimSetup error: If you use one of the constant temperature\n"
154	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
155	<	//                "    Neither of these was found in the BASS file.\n");
156	<	//       painCave.isFatal = 1;
157	<	//       simError();
158	<	//     }
159	<
160	<	//     if (the_globals->haveTauBarostat())
161	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
162	<	//     else {
163	<	//       sprintf( painCave.errMsg,
164	<	//                "SimSetup error: If you use the constant pressure\n"
165	<	//                "    ensemble, you must set tauBarostat.\n"
166	<	//                "    This was found in the BASS file.\n");
167	<	//       painCave.isFatal = 1;
168	<	//       simError();
169	<	//     }
170	<
171	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
172	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
173	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
174	<
175	<	//     if (the_globals->haveTauThermostat())
176	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
177	<	//     else if (the_globals->haveQmass())
178	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
179	<	//     else {
180	<	//       sprintf( painCave.errMsg,
181	<	//                "SimSetup error: If you use one of the constant temperature\n"
182	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
183	<	//                "    Neither of these was found in the BASS file.\n");
184	<	//       painCave.isFatal = 1;
185	<	//       simError();
186	<	//     }
187	<
188	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
189	<	simnfo->usePBC = the_globals->getPBC();
190	<
191	<	int usesDipoles = 0;
192	<	switch( ffCase ){
193	<
194	<	case FF_DUFF:
195	<	the_ff = new DUFF();
196	<	usesDipoles = 1;
197	<	break;
198	<
199	<	case FF_LJ:
200	<	the_ff = new LJFF();
201	<	break;
202	<
203	<	default:
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup Error. Unrecognized force field in case statement.\n");
206	<	painCave.isFatal = 1;
207	<	simError();
208	<	}
209	<
210	<	#ifdef IS_MPI
211	<	strcpy( checkPointMsg, "ForceField creation successful" );
212	<	MPIcheckPoint();
213	<	#endif // is_mpi
214	<
215	<	// get the components and calculate the tot_nMol and indvidual n_mol
216	<	the_components = the_globals->getComponents();
217	<	components_nmol = new int[n_components];
218	<	comp_stamps = new MoleculeStamp*[n_components];
219	<
220	<	if( !the_globals->haveNMol() ){
221	<	// we don't have the total number of molecules, so we assume it is
222	<	// given in each component
223	<
224	<	tot_nmol = 0;
225	<	for( i=0; i<n_components; i++ ){
226	<
227	<	if( !the_components[i]->haveNMol() ){
228	<	// we have a problem
229	<	sprintf( painCave.errMsg,
230	<	"SimSetup Error. No global NMol or component NMol"
231	<	" given. Cannot calculate the number of atoms.\n" );
232	<	painCave.isFatal = 1;
233	<	simError();
234	<	}
235	<
236	<	tot_nmol += the_components[i]->getNMol();
237	<	components_nmol[i] = the_components[i]->getNMol();
238	<	}
239	<	}
240	<	else{
241	<	sprintf( painCave.errMsg,
242	<	"SimSetup error.\n"
243	<	"\tSorry, the ability to specify total"
244	<	" nMols and then give molfractions in the components\n"
245	<	"\tis not currently supported."
246	<	" Please give nMol in the components.\n" );
247	<	painCave.isFatal = 1;
248	<	simError();
249	<
250	<
251	<	//     tot_nmol = the_globals->getNMol();
252	<
253	<	//   //we have the total number of molecules, now we check for molfractions
254	<	//     for( i=0; i<n_components; i++ ){
255	<
256	<	//       if( !the_components[i]->haveMolFraction() ){
257	<
258	<	//  if( !the_components[i]->haveNMol() ){
259	<	//    //we have a problem
260	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
261	<	//              << " nMol was given in component
262	<
263	<	}
264	<
265	<	#ifdef IS_MPI
266	<	strcpy( checkPointMsg, "Have the number of components" );
267	<	MPIcheckPoint();
268	<	#endif // is_mpi
269	<
270	<	// make an array of molecule stamps that match the components used.
271	<	// also extract the used stamps out into a separate linked list
272	<
273	<	simnfo->nComponents = n_components;
274	<	simnfo->componentsNmol = components_nmol;
275	<	simnfo->compStamps = comp_stamps;
276	<	simnfo->headStamp = new LinkedMolStamp();
91	>	// check on the post processing info
92
93	<	char* id;
279	<	LinkedMolStamp* headStamp = simnfo->headStamp;
280	<	LinkedMolStamp* currentStamp = NULL;
281	<	for( i=0; i<n_components; i++ ){
282	<
283	<	id = the_components[i]->getType();
284	<	comp_stamps[i] = NULL;
285	<
286	<	// check to make sure the component isn't already in the list
287	<
288	<	comp_stamps[i] = headStamp->match( id );
289	<	if( comp_stamps[i] == NULL ){
290	<
291	<	// extract the component from the list;
292	<
293	<	currentStamp = the_stamps->extractMolStamp( id );
294	<	if( currentStamp == NULL ){
295	<	sprintf( painCave.errMsg,
296	<	"SimSetup error: Component \"%s\" was not found in the "
297	<	"list of declared molecules\n",
298	<	id );
299	<	painCave.isFatal = 1;
300	<	simError();
301	<	}
302	<
303	<	headStamp->add( currentStamp );
304	<	comp_stamps[i] = headStamp->match( id );
305	<	}
306	<	}
93	>	finalInfoCheck();
94
95	<	#ifdef IS_MPI
309	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
310	<	MPIcheckPoint();
311	<	#endif // is_mpi
312	<
95	>	// initialize the system coordinates
96
97	<
315	<
316	<	// caclulate the number of atoms, bonds, bends and torsions
317	<
318	<	tot_atoms = 0;
319	<	tot_bonds = 0;
320	<	tot_bends = 0;
321	<	tot_torsions = 0;
322	<	for( i=0; i<n_components; i++ ){
323	<
324	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
325	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
326	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
327	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
328	<	}
329	<
330	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
331	<
332	<	simnfo->n_atoms = tot_atoms;
333	<	simnfo->n_bonds = tot_bonds;
334	<	simnfo->n_bends = tot_bends;
335	<	simnfo->n_torsions = tot_torsions;
336	<	simnfo->n_SRI = tot_SRI;
337	<	simnfo->n_mol = tot_nmol;
97	>	initSystemCoords();
98
339	–	simnfo->molMembershipArray = new int[tot_atoms];
99
100	<	#ifdef IS_MPI
100	>	// make the output filenames
101
102	<	// divide the molecules among processors here.
344	<
345	<	mpiSim = new mpiSimulation( simnfo );
346	<
347	<	globalIndex = mpiSim->divideLabor();
348	<
349	<	// set up the local variables
350	<
351	<	int localMol, allMol;
352	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
353	<
354	<	int* mol2proc = mpiSim->getMolToProcMap();
355	<	int* molCompType = mpiSim->getMolComponentType();
356	<
357	<	allMol = 0;
358	<	localMol = 0;
359	<	local_atoms = 0;
360	<	local_bonds = 0;
361	<	local_bends = 0;
362	<	local_torsions = 0;
363	<	globalAtomIndex = 0;
364	<
365	<
366	<	for( i=0; i<n_components; i++ ){
367	<
368	<	for( j=0; j<components_nmol[i]; j++ ){
369	<
370	<	if( mol2proc[allMol] == worldRank ){
371	<
372	<	local_atoms +=    comp_stamps[i]->getNAtoms();
373	<	local_bonds +=    comp_stamps[i]->getNBonds();
374	<	local_bends +=    comp_stamps[i]->getNBends();
375	<	local_torsions += comp_stamps[i]->getNTorsions();
376	<	localMol++;
377	<	}
378	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
379	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
380	<	globalAtomIndex++;
381	<	}
382	<
383	<	allMol++;
384	<	}
385	<	}
386	<	local_SRI = local_bonds + local_bends + local_torsions;
387	<
388	<	simnfo->n_atoms = mpiSim->getMyNlocal();
389	<
390	<	if( local_atoms != simnfo->n_atoms ){
391	<	sprintf( painCave.errMsg,
392	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
393	<	" localAtom (%d) are not equal.\n",
394	<	simnfo->n_atoms,
395	<	local_atoms );
396	<	painCave.isFatal = 1;
397	<	simError();
398	<	}
399	<
400	<	simnfo->n_bonds = local_bonds;
401	<	simnfo->n_bends = local_bends;
402	<	simnfo->n_torsions = local_torsions;
403	<	simnfo->n_SRI = local_SRI;
404	<	simnfo->n_mol = localMol;
405	<
406	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
407	<	MPIcheckPoint();
408	<
409	<
410	<	#endif // is_mpi
411	<
412	<
413	<	// create the atom and short range interaction arrays
414	<
415	<	Atom::createArrays(simnfo->n_atoms);
416	<	the_atoms = new Atom*[simnfo->n_atoms];
417	<	the_molecules = new Molecule[simnfo->n_mol];
418	<	int molIndex;
419	<
420	<	// initialize the molecule's stampID's
421	<
422	<	#ifdef IS_MPI
423	<
424	<
425	<	molIndex = 0;
426	<	for(i=0; i<mpiSim->getTotNmol(); i++){
427	<
428	<	if(mol2proc[i] == worldRank ){
429	<	the_molecules[molIndex].setStampID( molCompType[i] );
430	<	the_molecules[molIndex].setMyIndex( molIndex );
431	<	the_molecules[molIndex].setGlobalIndex( i );
432	<	molIndex++;
433	<	}
434	<	}
435	<
436	<	#else // is_mpi
437	<
438	<	molIndex = 0;
439	<	globalAtomIndex = 0;
440	<	for(i=0; i<n_components; i++){
441	<	for(j=0; j<components_nmol[i]; j++ ){
442	<	the_molecules[molIndex].setStampID( i );
443	<	the_molecules[molIndex].setMyIndex( molIndex );
444	<	the_molecules[molIndex].setGlobalIndex( molIndex );
445	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
446	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
447	<	globalAtomIndex++;
448	<	}
449	<	molIndex++;
450	<	}
451	<	}
452	<
453	<
454	<	#endif // is_mpi
455	<
456	<
457	<	if( simnfo->n_SRI ){
458	<
459	<	Exclude::createArray(simnfo->n_SRI);
460	<	the_excludes = new Exclude*[simnfo->n_SRI];
461	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
462	<	simnfo->globalExcludes = new int;
463	<	simnfo->n_exclude = simnfo->n_SRI;
464	<	}
465	<	else{
466	<
467	<	Exclude::createArray( 1 );
468	<	the_excludes = new Exclude*;
469	<	the_excludes[0] = new Exclude(0);
470	<	the_excludes[0]->setPair( 0,0 );
471	<	simnfo->globalExcludes = new int;
472	<	simnfo->globalExcludes[0] = 0;
473	<	simnfo->n_exclude = 0;
474	<	}
475	<
476	<	// set the arrays into the SimInfo object
477	<
478	<	simnfo->atoms = the_atoms;
479	<	simnfo->molecules = the_molecules;
480	<	simnfo->nGlobalExcludes = 0;
481	<	simnfo->excludes = the_excludes;
482	<
483	<
484	<	// get some of the tricky things that may still be in the globals
485	<
486	<	double boxVector[3];
487	<	if( the_globals->haveBox() ){
488	<	boxVector[0] = the_globals->getBox();
489	<	boxVector[1] = the_globals->getBox();
490	<	boxVector[2] = the_globals->getBox();
491	<
492	<	simnfo->setBox( boxVector );
493	<	}
494	<	else if( the_globals->haveDensity() ){
495	<
496	<	double vol;
497	<	vol = (double)tot_nmol / the_globals->getDensity();
498	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
499	<	boxVector[1] = boxVector[0];
500	<	boxVector[2] = boxVector[0];
501	<
502	<	simnfo->setBox( boxVector );
503	<	}
504	<	else{
505	<	if( !the_globals->haveBoxX() ){
506	<	sprintf( painCave.errMsg,
507	<	"SimSetup error, no periodic BoxX size given.\n" );
508	<	painCave.isFatal = 1;
509	<	simError();
510	<	}
511	<	boxVector[0] = the_globals->getBoxX();
512	<
513	<	if( !the_globals->haveBoxY() ){
514	<	sprintf( painCave.errMsg,
515	<	"SimSetup error, no periodic BoxY size given.\n" );
516	<	painCave.isFatal = 1;
517	<	simError();
518	<	}
519	<	boxVector[1] = the_globals->getBoxY();
520	<
521	<	if( !the_globals->haveBoxZ() ){
522	<	sprintf( painCave.errMsg,
523	<	"SimSetup error, no periodic BoxZ size given.\n" );
524	<	painCave.isFatal = 1;
525	<	simError();
526	<	}
527	<	boxVector[2] = the_globals->getBoxZ();
528	<
529	<	simnfo->setBox( boxVector );
530	<	}
531	<
532	<	#ifdef IS_MPI
533	<	strcpy( checkPointMsg, "Box size set up" );
534	<	MPIcheckPoint();
535	<	#endif // is_mpi
536	<
537	<
538	<	// initialize the arrays
539	<
540	<	the_ff->setSimInfo( simnfo );
541	<
542	<	makeMolecules();
543	<	simnfo->identArray = new int[simnfo->n_atoms];
544	<	for(i=0; i<simnfo->n_atoms; i++){
545	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
546	<	}
547	<
548	<	if (the_globals->getUseRF() ) {
549	<	simnfo->useReactionField = 1;
550	<
551	<	if( !the_globals->haveECR() ){
552	<	sprintf( painCave.errMsg,
553	<	"SimSetup Warning: using default value of 1/2 the smallest "
554	<	"box length for the electrostaticCutoffRadius.\n"
555	<	"I hope you have a very fast processor!\n");
556	<	painCave.isFatal = 0;
557	<	simError();
558	<	double smallest;
559	<	smallest = simnfo->boxLx;
560	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
561	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
562	<	simnfo->ecr = 0.5 * smallest;
563	<	} else {
564	<	simnfo->ecr        = the_globals->getECR();
565	<	}
566	<
567	<	if( !the_globals->haveEST() ){
568	<	sprintf( painCave.errMsg,
569	<	"SimSetup Warning: using default value of 0.05 * the "
570	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
571	<	);
572	<	painCave.isFatal = 0;
573	<	simError();
574	<	simnfo->est = 0.05 * simnfo->ecr;
575	<	} else {
576	<	simnfo->est        = the_globals->getEST();
577	<	}
578	<
579	<	if(!the_globals->haveDielectric() ){
580	<	sprintf( painCave.errMsg,
581	<	"SimSetup Error: You are trying to use Reaction Field without"
582	<	"setting a dielectric constant!\n"
583	<	);
584	<	painCave.isFatal = 1;
585	<	simError();
586	<	}
587	<	simnfo->dielectric = the_globals->getDielectric();
588	<	} else {
589	<	if (usesDipoles) {
590	<
591	<	if( !the_globals->haveECR() ){
592	<	sprintf( painCave.errMsg,
593	<	"SimSetup Warning: using default value of 1/2 the smallest "
594	<	"box length for the electrostaticCutoffRadius.\n"
595	<	"I hope you have a very fast processor!\n");
596	<	painCave.isFatal = 0;
597	<	simError();
598	<	double smallest;
599	<	smallest = simnfo->boxLx;
600	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
601	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
602	<	simnfo->ecr = 0.5 * smallest;
603	<	} else {
604	<	simnfo->ecr        = the_globals->getECR();
605	<	}
606	<
607	<	if( !the_globals->haveEST() ){
608	<	sprintf( painCave.errMsg,
609	<	"SimSetup Warning: using default value of 5%% of the "
610	<	"electrostaticCutoffRadius for the "
611	<	"electrostaticSkinThickness\n"
612	<	);
613	<	painCave.isFatal = 0;
614	<	simError();
615	<	simnfo->est = 0.05 * simnfo->ecr;
616	<	} else {
617	<	simnfo->est        = the_globals->getEST();
618	<	}
619	<	}
620	<	}
621	<
622	<	#ifdef IS_MPI
623	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
624	<	MPIcheckPoint();
625	<	#endif // is_mpi
626	<
627	<	if( the_globals->haveInitialConfig() ){
628	<
629	<	InitializeFromFile* fileInit;
630	<	#ifdef IS_MPI // is_mpi
631	<	if( worldRank == 0 ){
632	<	#endif //is_mpi
633	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
634	<	#ifdef IS_MPI
635	<	}else fileInit = new InitializeFromFile( NULL );
636	<	#endif
637	<	fileInit->read_xyz( simnfo ); // default velocities on
638	<
639	<	delete fileInit;
640	<	}
641	<	else{
642	<
643	<	#ifdef IS_MPI
644	<
645	<	// no init from bass
646	<
647	<	sprintf( painCave.errMsg,
648	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
649	<	painCave.isFatal;
650	<	simError();
651	<
652	<	#else
653	<
654	<	initFromBass();
655	<
656	<
657	<	#endif
658	<	}
659	<
660	<	#ifdef IS_MPI
661	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
662	<	MPIcheckPoint();
663	<	#endif // is_mpi
664	<
665	<
102	>	makeOutNames();
103
667	–
668	–
669	–
670	–
671	–	#ifdef IS_MPI
672	–	if( worldRank == 0 ){
673	–	#endif // is_mpi
674	–
675	–	if( the_globals->haveFinalConfig() ){
676	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
677	–	}
678	–	else{
679	–	strcpy( simnfo->finalName, inFileName );
680	–	char* endTest;
681	–	int nameLength = strlen( simnfo->finalName );
682	–	endTest = &(simnfo->finalName[nameLength - 5]);
683	–	if( !strcmp( endTest, ".bass" ) ){
684	–	strcpy( endTest, ".eor" );
685	–	}
686	–	else if( !strcmp( endTest, ".BASS" ) ){
687	–	strcpy( endTest, ".eor" );
688	–	}
689	–	else{
690	–	endTest = &(simnfo->finalName[nameLength - 4]);
691	–	if( !strcmp( endTest, ".bss" ) ){
692	–	strcpy( endTest, ".eor" );
693	–	}
694	–	else if( !strcmp( endTest, ".mdl" ) ){
695	–	strcpy( endTest, ".eor" );
696	–	}
697	–	else{
698	–	strcat( simnfo->finalName, ".eor" );
699	–	}
700	–	}
701	–	}
702	–
703	–	// make the sample and status out names
704	–
705	–	strcpy( simnfo->sampleName, inFileName );
706	–	char* endTest;
707	–	int nameLength = strlen( simnfo->sampleName );
708	–	endTest = &(simnfo->sampleName[nameLength - 5]);
709	–	if( !strcmp( endTest, ".bass" ) ){
710	–	strcpy( endTest, ".dump" );
711	–	}
712	–	else if( !strcmp( endTest, ".BASS" ) ){
713	–	strcpy( endTest, ".dump" );
714	–	}
715	–	else{
716	–	endTest = &(simnfo->sampleName[nameLength - 4]);
717	–	if( !strcmp( endTest, ".bss" ) ){
718	–	strcpy( endTest, ".dump" );
719	–	}
720	–	else if( !strcmp( endTest, ".mdl" ) ){
721	–	strcpy( endTest, ".dump" );
722	–	}
723	–	else{
724	–	strcat( simnfo->sampleName, ".dump" );
725	–	}
726	–	}
727	–
728	–	strcpy( simnfo->statusName, inFileName );
729	–	nameLength = strlen( simnfo->statusName );
730	–	endTest = &(simnfo->statusName[nameLength - 5]);
731	–	if( !strcmp( endTest, ".bass" ) ){
732	–	strcpy( endTest, ".stat" );
733	–	}
734	–	else if( !strcmp( endTest, ".BASS" ) ){
735	–	strcpy( endTest, ".stat" );
736	–	}
737	–	else{
738	–	endTest = &(simnfo->statusName[nameLength - 4]);
739	–	if( !strcmp( endTest, ".bss" ) ){
740	–	strcpy( endTest, ".stat" );
741	–	}
742	–	else if( !strcmp( endTest, ".mdl" ) ){
743	–	strcpy( endTest, ".stat" );
744	–	}
745	–	else{
746	–	strcat( simnfo->statusName, ".stat" );
747	–	}
748	–	}
749	–
750	–	#ifdef IS_MPI
751	–	}
752	–	#endif // is_mpi
753	–
754	–	// set the status, sample, and themal kick times
755	–
756	–	if( the_globals->haveSampleTime() ){
757	–	simnfo->sampleTime = the_globals->getSampleTime();
758	–	simnfo->statusTime = simnfo->sampleTime;
759	–	simnfo->thermalTime = simnfo->sampleTime;
760	–	}
761	–	else{
762	–	simnfo->sampleTime = the_globals->getRunTime();
763	–	simnfo->statusTime = simnfo->sampleTime;
764	–	simnfo->thermalTime = simnfo->sampleTime;
765	–	}
766	–
767	–	if( the_globals->haveStatusTime() ){
768	–	simnfo->statusTime = the_globals->getStatusTime();
769	–	}
770	–
771	–	if( the_globals->haveThermalTime() ){
772	–	simnfo->thermalTime = the_globals->getThermalTime();
773	–	}
774	–
775	–	// check for the temperature set flag
776	–
777	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
778	–
779	–
104		// make the integrator
105
106	+	makeIntegrator();
107
783	–	NVT* myNVT = NULL;
784	–	switch( ensembleCase ){
785	–
786	–	case NVE_ENS:
787	–	new NVE( simnfo, the_ff );
788	–	break;
789	–
790	–	case NVT_ENS:
791	–	myNVT = new NVT( simnfo, the_ff );
792	–	myNVT->setTargetTemp(the_globals->getTargetTemp());
793	–
794	–	if (the_globals->haveTauThermostat())
795	–	myNVT->setTauThermostat(the_globals->getTauThermostat());
796	–	//     else if (the_globals->haveQmass())
797	–	//       myNVT->setQmass(the_globals->getQmass());
798	–	else {
799	–	sprintf( painCave.errMsg,
800	–	"SimSetup error: If you use the NVT\n"
801	–	"    ensemble, you must set either tauThermostat or qMass.\n"
802	–	"    Neither of these was found in the BASS file.\n");
803	–	painCave.isFatal = 1;
804	–	simError();
805	–	}
806	–	break;
807	–
808	–	default:
809	–	sprintf( painCave.errMsg,
810	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
811	–	painCave.isFatal = 1;
812	–	simError();
813	–	}
814	–
815	–
108		#ifdef IS_MPI
109		mpiSim->mpiRefresh();
110		#endif
111
112		// initialize the Fortran
113
114	+	initFortran();
115
823	–	simnfo->refreshSim();
824	–
825	–	if( !strcmp( simnfo->mixingRule, "standard") ){
826	–	the_ff->initForceField( LB_MIXING_RULE );
827	–	}
828	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
829	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
830	–	}
831	–	else{
832	–	sprintf( painCave.errMsg,
833	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
834	–	simnfo->mixingRule );
835	–	painCave.isFatal = 1;
836	–	simError();
837	–	}
116
117
840	–	#ifdef IS_MPI
841	–	strcpy( checkPointMsg,
842	–	"Successfully intialized the mixingRule for Fortran." );
843	–	MPIcheckPoint();
844	–	#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 873 | 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 920 | 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 959 | 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 1045 | 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 1075 | 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 1125 | 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 1142 | 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 1224 | 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 1288 | Line 561 | void SimSetup::makeElement( double x, double y, double
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 if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
590	+	else{
591	+	sprintf( painCave.errMsg,
592	+	"SimSetup Error. Unrecognized force field -> %s\n",
593	+	force_field );
594	+	painCave.isFatal = 1;
595	+	simError();
596	+	}
597	+
598	+	// get the ensemble
599	+
600	+	strcpy( ensemble, globals->getEnsemble() );
601	+
602	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
603	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
604	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
605	+	ensembleCase = NPTi_ENS;
606	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
607	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
608	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
609	+	else{
610	+	sprintf( painCave.errMsg,
611	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
612	+	"reverting to NVE for this simulation.\n",
613	+	ensemble );
614	+	painCave.isFatal = 0;
615	+	simError();
616	+	strcpy( ensemble, "NVE" );
617	+	ensembleCase = NVE_ENS;
618	+	}
619	+	strcpy( info->ensemble, ensemble );
620	+
621	+	// get the mixing rule
622	+
623	+	strcpy( info->mixingRule, globals->getMixingRule() );
624	+	info->usePBC = globals->getPBC();
625	+
626	+
627	+	// get the components and calculate the tot_nMol and indvidual n_mol
628	+
629	+	the_components = globals->getComponents();
630	+	components_nmol = new int[n_components];
631	+
632	+
633	+	if( !globals->haveNMol() ){
634	+	// we don't have the total number of molecules, so we assume it is
635	+	// given in each component
636	+
637	+	tot_nmol = 0;
638	+	for( i=0; i<n_components; i++ ){
639	+
640	+	if( !the_components[i]->haveNMol() ){
641	+	// we have a problem
642	+	sprintf( painCave.errMsg,
643	+	"SimSetup Error. No global NMol or component NMol"
644	+	" given. Cannot calculate the number of atoms.\n" );
645	+	painCave.isFatal = 1;
646	+	simError();
647	+	}
648	+
649	+	tot_nmol += the_components[i]->getNMol();
650	+	components_nmol[i] = the_components[i]->getNMol();
651	+	}
652	+	}
653	+	else{
654	+	sprintf( painCave.errMsg,
655	+	"SimSetup error.\n"
656	+	"\tSorry, the ability to specify total"
657	+	" nMols and then give molfractions in the components\n"
658	+	"\tis not currently supported."
659	+	" Please give nMol in the components.\n" );
660	+	painCave.isFatal = 1;
661	+	simError();
662	+	}
663	+
664	+	// set the status, sample, and thermal kick times
665	+
666	+	if( globals->haveSampleTime() ){
667	+	info->sampleTime = globals->getSampleTime();
668	+	info->statusTime = info->sampleTime;
669	+	info->thermalTime = info->sampleTime;
670	+	}
671	+	else{
672	+	info->sampleTime = globals->getRunTime();
673	+	info->statusTime = info->sampleTime;
674	+	info->thermalTime = info->sampleTime;
675	+	}
676	+
677	+	if( globals->haveStatusTime() ){
678	+	info->statusTime = globals->getStatusTime();
679	+	}
680	+
681	+	if( globals->haveThermalTime() ){
682	+	info->thermalTime = globals->getThermalTime();
683	+	}
684	+
685	+	// check for the temperature set flag
686	+
687	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
688	+
689	+	// get some of the tricky things that may still be in the globals
690	+
691	+	double boxVector[3];
692	+	if( globals->haveBox() ){
693	+	boxVector[0] = globals->getBox();
694	+	boxVector[1] = globals->getBox();
695	+	boxVector[2] = globals->getBox();
696	+
697	+	info->setBox( boxVector );
698	+	}
699	+	else if( globals->haveDensity() ){
700	+
701	+	double vol;
702	+	vol = (double)tot_nmol / globals->getDensity();
703	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
704	+	boxVector[1] = boxVector[0];
705	+	boxVector[2] = boxVector[0];
706	+
707	+	info->setBox( boxVector );
708	+	}
709	+	else{
710	+	if( !globals->haveBoxX() ){
711	+	sprintf( painCave.errMsg,
712	+	"SimSetup error, no periodic BoxX size given.\n" );
713	+	painCave.isFatal = 1;
714	+	simError();
715	+	}
716	+	boxVector[0] = globals->getBoxX();
717	+
718	+	if( !globals->haveBoxY() ){
719	+	sprintf( painCave.errMsg,
720	+	"SimSetup error, no periodic BoxY size given.\n" );
721	+	painCave.isFatal = 1;
722	+	simError();
723	+	}
724	+	boxVector[1] = globals->getBoxY();
725	+
726	+	if( !globals->haveBoxZ() ){
727	+	sprintf( painCave.errMsg,
728	+	"SimSetup error, no periodic BoxZ size given.\n" );
729	+	painCave.isFatal = 1;
730	+	simError();
731	+	}
732	+	boxVector[2] = globals->getBoxZ();
733	+
734	+	info->setBox( boxVector );
735	+	}
736	+
737	+
738	+
739	+	#ifdef IS_MPI
740	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
741	+	MPIcheckPoint();
742	+	#endif // is_mpi
743	+
744	+	}
745	+
746	+
747	+	void SimSetup::finalInfoCheck( void ){
748	+	int index;
749	+	int usesDipoles;
750	+
751	+
752	+	// check electrostatic parameters
753	+
754	+	index = 0;
755	+	usesDipoles = 0;
756	+	while( (index < info->n_atoms) && !usesDipoles ){
757	+	usesDipoles = ((info->atoms)[index])->hasDipole();
758	+	index++;
759	+	}
760	+
761	+	#ifdef IS_MPI
762	+	int myUse = usesDipoles;
763	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
764	+	#endif //is_mpi
765	+
766	+	double theEcr, theEst;
767	+
768	+	if (globals->getUseRF() ) {
769	+	info->useReactionField = 1;
770	+
771	+	if( !globals->haveECR() ){
772	+	sprintf( painCave.errMsg,
773	+	"SimSetup Warning: using default value of 1/2 the smallest "
774	+	"box length for the electrostaticCutoffRadius.\n"
775	+	"I hope you have a very fast processor!\n");
776	+	painCave.isFatal = 0;
777	+	simError();
778	+	double smallest;
779	+	smallest = info->boxL[0];
780	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
781	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
782	+	theEcr = 0.5 * smallest;
783	+	} else {
784	+	theEcr = globals->getECR();
785	+	}
786	+
787	+	if( !globals->haveEST() ){
788	+	sprintf( painCave.errMsg,
789	+	"SimSetup Warning: using default value of 0.05 * the "
790	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
791	+	);
792	+	painCave.isFatal = 0;
793	+	simError();
794	+	theEst = 0.05 * theEcr;
795	+	} else {
796	+	theEst= globals->getEST();
797	+	}
798	+
799	+	info->setEcr( theEcr, theEst );
800	+
801	+	if(!globals->haveDielectric() ){
802	+	sprintf( painCave.errMsg,
803	+	"SimSetup Error: You are trying to use Reaction Field without"
804	+	"setting a dielectric constant!\n"
805	+	);
806	+	painCave.isFatal = 1;
807	+	simError();
808	+	}
809	+	info->dielectric = globals->getDielectric();
810	+	}
811	+	else {
812	+	if (usesDipoles) {
813	+
814	+	if( !globals->haveECR() ){
815	+	sprintf( painCave.errMsg,
816	+	"SimSetup Warning: using default value of 1/2 the smallest "
817	+	"box length for the electrostaticCutoffRadius.\n"
818	+	"I hope you have a very fast processor!\n");
819	+	painCave.isFatal = 0;
820	+	simError();
821	+	double smallest;
822	+	smallest = info->boxL[0];
823	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
824	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
825	+	theEcr = 0.5 * smallest;
826	+	} else {
827	+	theEcr = globals->getECR();
828	+	}
829	+
830	+	if( !globals->haveEST() ){
831	+	sprintf( painCave.errMsg,
832	+	"SimSetup Warning: using default value of 0.05 * the "
833	+	"electrostaticCutoffRadius for the "
834	+	"electrostaticSkinThickness\n"
835	+	);
836	+	painCave.isFatal = 0;
837	+	simError();
838	+	theEst = 0.05 * theEcr;
839	+	} else {
840	+	theEst= globals->getEST();
841	+	}
842	+
843	+	info->setEcr( theEcr, theEst );
844	+	}
845	+	}
846	+
847	+	#ifdef IS_MPI
848	+	strcpy( checkPointMsg, "post processing checks out" );
849	+	MPIcheckPoint();
850	+	#endif // is_mpi
851	+
852	+	}
853	+
854	+	void SimSetup::initSystemCoords( void ){
855	+
856	+	if( globals->haveInitialConfig() ){
857	+
858	+	InitializeFromFile* fileInit;
859	+	#ifdef IS_MPI // is_mpi
860	+	if( worldRank == 0 ){
861	+	#endif //is_mpi
862	+	fileInit = new InitializeFromFile( globals->getInitialConfig() );
863	+	#ifdef IS_MPI
864	+	}else fileInit = new InitializeFromFile( NULL );
865	+	#endif
866	+	fileInit->readInit( info ); // default velocities on
867	+
868	+	delete fileInit;
869	+	}
870	+	else{
871	+
872	+	#ifdef IS_MPI
873	+
874	+	// no init from bass
875	+
876	+	sprintf( painCave.errMsg,
877	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
878	+	painCave.isFatal;
879	+	simError();
880	+
881	+	#else
882	+
883	+	initFromBass();
884	+
885	+
886	+	#endif
887	+	}
888	+
889	+	#ifdef IS_MPI
890	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
891	+	MPIcheckPoint();
892	+	#endif // is_mpi
893	+
894	+	}
895	+
896	+
897	+	void SimSetup::makeOutNames( void ){
898	+
899	+	#ifdef IS_MPI
900	+	if( worldRank == 0 ){
901	+	#endif // is_mpi
902	+
903	+	if( globals->haveFinalConfig() ){
904	+	strcpy( info->finalName, globals->getFinalConfig() );
905	+	}
906	+	else{
907	+	strcpy( info->finalName, inFileName );
908	+	char* endTest;
909	+	int nameLength = strlen( info->finalName );
910	+	endTest = &(info->finalName[nameLength - 5]);
911	+	if( !strcmp( endTest, ".bass" ) ){
912	+	strcpy( endTest, ".eor" );
913	+	}
914	+	else if( !strcmp( endTest, ".BASS" ) ){
915	+	strcpy( endTest, ".eor" );
916	+	}
917	+	else{
918	+	endTest = &(info->finalName[nameLength - 4]);
919	+	if( !strcmp( endTest, ".bss" ) ){
920	+	strcpy( endTest, ".eor" );
921	+	}
922	+	else if( !strcmp( endTest, ".mdl" ) ){
923	+	strcpy( endTest, ".eor" );
924	+	}
925	+	else{
926	+	strcat( info->finalName, ".eor" );
927	+	}
928	+	}
929	+	}
930	+
931	+	// make the sample and status out names
932	+
933	+	strcpy( info->sampleName, inFileName );
934	+	char* endTest;
935	+	int nameLength = strlen( info->sampleName );
936	+	endTest = &(info->sampleName[nameLength - 5]);
937	+	if( !strcmp( endTest, ".bass" ) ){
938	+	strcpy( endTest, ".dump" );
939	+	}
940	+	else if( !strcmp( endTest, ".BASS" ) ){
941	+	strcpy( endTest, ".dump" );
942	+	}
943	+	else{
944	+	endTest = &(info->sampleName[nameLength - 4]);
945	+	if( !strcmp( endTest, ".bss" ) ){
946	+	strcpy( endTest, ".dump" );
947	+	}
948	+	else if( !strcmp( endTest, ".mdl" ) ){
949	+	strcpy( endTest, ".dump" );
950	+	}
951	+	else{
952	+	strcat( info->sampleName, ".dump" );
953	+	}
954	+	}
955	+
956	+	strcpy( info->statusName, inFileName );
957	+	nameLength = strlen( info->statusName );
958	+	endTest = &(info->statusName[nameLength - 5]);
959	+	if( !strcmp( endTest, ".bass" ) ){
960	+	strcpy( endTest, ".stat" );
961	+	}
962	+	else if( !strcmp( endTest, ".BASS" ) ){
963	+	strcpy( endTest, ".stat" );
964	+	}
965	+	else{
966	+	endTest = &(info->statusName[nameLength - 4]);
967	+	if( !strcmp( endTest, ".bss" ) ){
968	+	strcpy( endTest, ".stat" );
969	+	}
970	+	else if( !strcmp( endTest, ".mdl" ) ){
971	+	strcpy( endTest, ".stat" );
972	+	}
973	+	else{
974	+	strcat( info->statusName, ".stat" );
975	+	}
976	+	}
977	+
978	+	#ifdef IS_MPI
979	+	}
980	+	#endif // is_mpi
981	+
982	+	}
983	+
984	+
985	+	void SimSetup::sysObjectsCreation( void ){
986	+
987	+	int i;
988	+
989	+	// create the forceField
990	+
991	+	createFF();
992	+
993	+	// extract componentList
994	+
995	+	compList();
996	+
997	+	// calc the number of atoms, bond, bends, and torsions
998	+
999	+	calcSysValues();
1000	+
1001	+	#ifdef IS_MPI
1002	+	// divide the molecules among the processors
1003	+
1004	+	mpiMolDivide();
1005	+	#endif //is_mpi
1006	+
1007	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1008	+
1009	+	makeSysArrays();
1010	+
1011	+	// make and initialize the molecules (all but atomic coordinates)
1012	+
1013	+	makeMolecules();
1014	+	info->identArray = new int[info->n_atoms];
1015	+	for(i=0; i<info->n_atoms; i++){
1016	+	info->identArray[i] = the_atoms[i]->getIdent();
1017	+	}
1018	+
1019	+
1020	+
1021	+	}
1022	+
1023	+
1024	+	void SimSetup::createFF( void ){
1025	+
1026	+	switch( ffCase ){
1027	+
1028	+	case FF_DUFF:
1029	+	the_ff = new DUFF();
1030	+	break;
1031	+
1032	+	case FF_LJ:
1033	+	the_ff = new LJFF();
1034	+	break;
1035	+
1036	+	case FF_EAM:
1037	+	the_ff = new EAM_FF();
1038	+	break;
1039	+
1040	+	default:
1041	+	sprintf( painCave.errMsg,
1042	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1043	+	painCave.isFatal = 1;
1044	+	simError();
1045	+	}
1046	+
1047	+	#ifdef IS_MPI
1048	+	strcpy( checkPointMsg, "ForceField creation successful" );
1049	+	MPIcheckPoint();
1050	+	#endif // is_mpi
1051	+
1052	+	}
1053	+
1054	+
1055	+	void SimSetup::compList( void ){
1056	+
1057	+	int i;
1058	+
1059	+	comp_stamps = new MoleculeStamp*[n_components];
1060	+
1061	+	// make an array of molecule stamps that match the components used.
1062	+	// also extract the used stamps out into a separate linked list
1063	+
1064	+	info->nComponents = n_components;
1065	+	info->componentsNmol = components_nmol;
1066	+	info->compStamps = comp_stamps;
1067	+	info->headStamp = new LinkedMolStamp();
1068	+
1069	+	char* id;
1070	+	LinkedMolStamp* headStamp = info->headStamp;
1071	+	LinkedMolStamp* currentStamp = NULL;
1072	+	for( i=0; i<n_components; i++ ){
1073	+
1074	+	id = the_components[i]->getType();
1075	+	comp_stamps[i] = NULL;
1076	+
1077	+	// check to make sure the component isn't already in the list
1078	+
1079	+	comp_stamps[i] = headStamp->match( id );
1080	+	if( comp_stamps[i] == NULL ){
1081	+
1082	+	// extract the component from the list;
1083	+
1084	+	currentStamp = stamps->extractMolStamp( id );
1085	+	if( currentStamp == NULL ){
1086	+	sprintf( painCave.errMsg,
1087	+	"SimSetup error: Component \"%s\" was not found in the "
1088	+	"list of declared molecules\n",
1089	+	id );
1090	+	painCave.isFatal = 1;
1091	+	simError();
1092	+	}
1093	+
1094	+	headStamp->add( currentStamp );
1095	+	comp_stamps[i] = headStamp->match( id );
1096	+	}
1097	+	}
1098	+
1099	+	#ifdef IS_MPI
1100	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1101	+	MPIcheckPoint();
1102	+	#endif // is_mpi
1103	+
1104	+
1105	+	}
1106	+
1107	+	void SimSetup::calcSysValues( void ){
1108	+	int i, j, k;
1109	+
1110	+
1111	+	tot_atoms = 0;
1112	+	tot_bonds = 0;
1113	+	tot_bends = 0;
1114	+	tot_torsions = 0;
1115	+	for( i=0; i<n_components; i++ ){
1116	+
1117	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1118	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1119	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1120	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1121	+	}
1122	+
1123	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1124	+
1125	+	info->n_atoms = tot_atoms;
1126	+	info->n_bonds = tot_bonds;
1127	+	info->n_bends = tot_bends;
1128	+	info->n_torsions = tot_torsions;
1129	+	info->n_SRI = tot_SRI;
1130	+	info->n_mol = tot_nmol;
1131	+
1132	+	info->molMembershipArray = new int[tot_atoms];
1133	+	}
1134	+
1135	+
1136	+	#ifdef IS_MPI
1137	+
1138	+	void SimSetup::mpiMolDivide( void ){
1139	+
1140	+	int i, j, k;
1141	+	int localMol, allMol;
1142	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1143	+
1144	+	mpiSim = new mpiSimulation( info );
1145	+
1146	+	globalIndex = mpiSim->divideLabor();
1147	+
1148	+	// set up the local variables
1149	+
1150	+	mol2proc = mpiSim->getMolToProcMap();
1151	+	molCompType = mpiSim->getMolComponentType();
1152	+
1153	+	allMol = 0;
1154	+	localMol = 0;
1155	+	local_atoms = 0;
1156	+	local_bonds = 0;
1157	+	local_bends = 0;
1158	+	local_torsions = 0;
1159	+	globalAtomIndex = 0;
1160	+
1161	+
1162	+	for( i=0; i<n_components; i++ ){
1163	+
1164	+	for( j=0; j<components_nmol[i]; j++ ){
1165	+
1166	+	if( mol2proc[allMol] == worldRank ){
1167	+
1168	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1169	+	local_bonds +=    comp_stamps[i]->getNBonds();
1170	+	local_bends +=    comp_stamps[i]->getNBends();
1171	+	local_torsions += comp_stamps[i]->getNTorsions();
1172	+	localMol++;
1173	+	}
1174	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1175	+	info->molMembershipArray[globalAtomIndex] = allMol;
1176	+	globalAtomIndex++;
1177	+	}
1178	+
1179	+	allMol++;
1180	+	}
1181	+	}
1182	+	local_SRI = local_bonds + local_bends + local_torsions;
1183	+
1184	+	info->n_atoms = mpiSim->getMyNlocal();
1185	+
1186	+	if( local_atoms != info->n_atoms ){
1187	+	sprintf( painCave.errMsg,
1188	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1189	+	" localAtom (%d) are not equal.\n",
1190	+	info->n_atoms,
1191	+	local_atoms );
1192	+	painCave.isFatal = 1;
1193	+	simError();
1194	+	}
1195	+
1196	+	info->n_bonds = local_bonds;
1197	+	info->n_bends = local_bends;
1198	+	info->n_torsions = local_torsions;
1199	+	info->n_SRI = local_SRI;
1200	+	info->n_mol = localMol;
1201	+
1202	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1203	+	MPIcheckPoint();
1204	+	}
1205	+
1206	+	#endif // is_mpi
1207	+
1208	+
1209	+	void SimSetup::makeSysArrays( void ){
1210	+	int i, j, k;
1211	+
1212	+
1213	+	// create the atom and short range interaction arrays
1214	+
1215	+	Atom::createArrays(info->n_atoms);
1216	+	the_atoms = new Atom*[info->n_atoms];
1217	+	the_molecules = new Molecule[info->n_mol];
1218	+	int molIndex;
1219	+
1220	+	// initialize the molecule's stampID's
1221	+
1222	+	#ifdef IS_MPI
1223	+
1224	+
1225	+	molIndex = 0;
1226	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1227	+
1228	+	if(mol2proc[i] == worldRank ){
1229	+	the_molecules[molIndex].setStampID( molCompType[i] );
1230	+	the_molecules[molIndex].setMyIndex( molIndex );
1231	+	the_molecules[molIndex].setGlobalIndex( i );
1232	+	molIndex++;
1233	+	}
1234	+	}
1235	+
1236	+	#else // is_mpi
1237	+
1238	+	molIndex = 0;
1239	+	globalAtomIndex = 0;
1240	+	for(i=0; i<n_components; i++){
1241	+	for(j=0; j<components_nmol[i]; j++ ){
1242	+	the_molecules[molIndex].setStampID( i );
1243	+	the_molecules[molIndex].setMyIndex( molIndex );
1244	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1245	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1246	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1247	+	globalAtomIndex++;
1248	+	}
1249	+	molIndex++;
1250	+	}
1251	+	}
1252	+
1253	+
1254	+	#endif // is_mpi
1255	+
1256	+
1257	+	if( info->n_SRI ){
1258	+
1259	+	Exclude::createArray(info->n_SRI);
1260	+	the_excludes = new Exclude*[info->n_SRI];
1261	+	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1262	+	info->globalExcludes = new int;
1263	+	info->n_exclude = info->n_SRI;
1264	+	}
1265	+	else{
1266	+
1267	+	Exclude::createArray( 1 );
1268	+	the_excludes = new Exclude*;
1269	+	the_excludes[0] = new Exclude(0);
1270	+	the_excludes[0]->setPair( 0,0 );
1271	+	info->globalExcludes = new int;
1272	+	info->globalExcludes[0] = 0;
1273	+	info->n_exclude = 0;
1274	+	}
1275	+
1276	+	// set the arrays into the SimInfo object
1277	+
1278	+	info->atoms = the_atoms;
1279	+	info->molecules = the_molecules;
1280	+	info->nGlobalExcludes = 0;
1281	+	info->excludes = the_excludes;
1282	+
1283	+	the_ff->setSimInfo( info );
1284	+
1285	+	}
1286	+
1287	+	void SimSetup::makeIntegrator( void ){
1288	+
1289	+	NVT<RealIntegrator>*  myNVT = NULL;
1290	+	NPTi<RealIntegrator>* myNPTi = NULL;
1291	+	NPTf<RealIntegrator>* myNPTf = NULL;
1292	+	NPTim<RealIntegrator>* myNPTim = NULL;
1293	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1294	+
1295	+	switch( ensembleCase ){
1296	+
1297	+	case NVE_ENS:
1298	+	new NVE<RealIntegrator>( info, the_ff );
1299	+	break;
1300	+
1301	+	case NVT_ENS:
1302	+	myNVT = new NVT<RealIntegrator>( info, the_ff );
1303	+	myNVT->setTargetTemp(globals->getTargetTemp());
1304	+
1305	+	if (globals->haveTauThermostat())
1306	+	myNVT->setTauThermostat(globals->getTauThermostat());
1307	+
1308	+	else {
1309	+	sprintf( painCave.errMsg,
1310	+	"SimSetup error: If you use the NVT\n"
1311	+	"    ensemble, you must set tauThermostat.\n");
1312	+	painCave.isFatal = 1;
1313	+	simError();
1314	+	}
1315	+	break;
1316	+
1317	+	case NPTi_ENS:
1318	+	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1319	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1320	+
1321	+	if (globals->haveTargetPressure())
1322	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1323	+	else {
1324	+	sprintf( painCave.errMsg,
1325	+	"SimSetup error: If you use a constant pressure\n"
1326	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1327	+	painCave.isFatal = 1;
1328	+	simError();
1329	+	}
1330	+
1331	+	if( globals->haveTauThermostat() )
1332	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1333	+	else{
1334	+	sprintf( painCave.errMsg,
1335	+	"SimSetup error: If you use an NPT\n"
1336	+	"    ensemble, you must set tauThermostat.\n");
1337	+	painCave.isFatal = 1;
1338	+	simError();
1339	+	}
1340	+
1341	+	if( globals->haveTauBarostat() )
1342	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1343	+	else{
1344	+	sprintf( painCave.errMsg,
1345	+	"SimSetup error: If you use an NPT\n"
1346	+	"    ensemble, you must set tauBarostat.\n");
1347	+	painCave.isFatal = 1;
1348	+	simError();
1349	+	}
1350	+	break;
1351	+
1352	+	case NPTf_ENS:
1353	+	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1354	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1355	+
1356	+	if (globals->haveTargetPressure())
1357	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1358	+	else {
1359	+	sprintf( painCave.errMsg,
1360	+	"SimSetup error: If you use a constant pressure\n"
1361	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1362	+	painCave.isFatal = 1;
1363	+	simError();
1364	+	}
1365	+
1366	+	if( globals->haveTauThermostat() )
1367	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1368	+	else{
1369	+	sprintf( painCave.errMsg,
1370	+	"SimSetup error: If you use an NPT\n"
1371	+	"    ensemble, you must set tauThermostat.\n");
1372	+	painCave.isFatal = 1;
1373	+	simError();
1374	+	}
1375	+
1376	+	if( globals->haveTauBarostat() )
1377	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1378	+	else{
1379	+	sprintf( painCave.errMsg,
1380	+	"SimSetup error: If you use an NPT\n"
1381	+	"    ensemble, you must set tauBarostat.\n");
1382	+	painCave.isFatal = 1;
1383	+	simError();
1384	+	}
1385	+	break;
1386	+
1387	+	case NPTim_ENS:
1388	+	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1389	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1390	+
1391	+	if (globals->haveTargetPressure())
1392	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1393	+	else {
1394	+	sprintf( painCave.errMsg,
1395	+	"SimSetup error: If you use a constant pressure\n"
1396	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1397	+	painCave.isFatal = 1;
1398	+	simError();
1399	+	}
1400	+
1401	+	if( globals->haveTauThermostat() )
1402	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1403	+	else{
1404	+	sprintf( painCave.errMsg,
1405	+	"SimSetup error: If you use an NPT\n"
1406	+	"    ensemble, you must set tauThermostat.\n");
1407	+	painCave.isFatal = 1;
1408	+	simError();
1409	+	}
1410	+
1411	+	if( globals->haveTauBarostat() )
1412	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1413	+	else{
1414	+	sprintf( painCave.errMsg,
1415	+	"SimSetup error: If you use an NPT\n"
1416	+	"    ensemble, you must set tauBarostat.\n");
1417	+	painCave.isFatal = 1;
1418	+	simError();
1419	+	}
1420	+	break;
1421	+
1422	+	case NPTfm_ENS:
1423	+	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1424	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1425	+
1426	+	if (globals->haveTargetPressure())
1427	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1428	+	else {
1429	+	sprintf( painCave.errMsg,
1430	+	"SimSetup error: If you use a constant pressure\n"
1431	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1432	+	painCave.isFatal = 1;
1433	+	simError();
1434	+	}
1435	+
1436	+	if( globals->haveTauThermostat() )
1437	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1438	+	else{
1439	+	sprintf( painCave.errMsg,
1440	+	"SimSetup error: If you use an NPT\n"
1441	+	"    ensemble, you must set tauThermostat.\n");
1442	+	painCave.isFatal = 1;
1443	+	simError();
1444	+	}
1445	+
1446	+	if( globals->haveTauBarostat() )
1447	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1448	+	else{
1449	+	sprintf( painCave.errMsg,
1450	+	"SimSetup error: If you use an NPT\n"
1451	+	"    ensemble, you must set tauBarostat.\n");
1452	+	painCave.isFatal = 1;
1453	+	simError();
1454	+	}
1455	+	break;
1456	+
1457	+	default:
1458	+	sprintf( painCave.errMsg,
1459	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1460	+	painCave.isFatal = 1;
1461	+	simError();
1462	+	}
1463	+
1464	+	}
1465	+
1466	+	void SimSetup::initFortran( void ){
1467	+
1468	+	info->refreshSim();
1469	+
1470	+	if( !strcmp( info->mixingRule, "standard") ){
1471	+	the_ff->initForceField( LB_MIXING_RULE );
1472	+	}
1473	+	else if( !strcmp( info->mixingRule, "explicit") ){
1474	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1475	+	}
1476	+	else{
1477	+	sprintf( painCave.errMsg,
1478	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1479	+	info->mixingRule );
1480	+	painCave.isFatal = 1;
1481	+	simError();
1482	+	}
1483	+
1484	+
1485	+	#ifdef IS_MPI
1486	+	strcpy( checkPointMsg,
1487	+	"Successfully intialized the mixingRule for Fortran." );
1488	+	MPIcheckPoint();
1489	+	#endif // is_mpi
1490	+
1491	+	}

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