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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 414 by mmeineke, Wed Mar 26 22:02:36 2003 UTC vs.
Revision 656 by mmeineke, Tue Jul 29 16:32:37 2003 UTC

#	Line 12 | Line 12 | SimSetup::SimSetup(){
12		#include "mpiSimulation.hpp"
13		#endif
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
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	+
29		SimSetup::SimSetup(){
30	+
31	+	isInfoArray = 0;
32	+	nInfo = 1;
33	+
34		stamps = new MakeStamps();
35		globals = new Globals();
36
37	+
38		#ifdef IS_MPI
39		strcpy( checkPointMsg, "SimSetup creation successful" );
40		MPIcheckPoint();
#	Line 27 | Line 46 | void SimSetup::parseFile( char* fileName ){
46		delete globals;
47		}
48
49	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
50	+	info = the_info;
51	+	nInfo = theNinfo;
52	+	isInfoArray = 1;
53	+	}
54	+
55	+
56		void SimSetup::parseFile( char* fileName ){
57
58		#ifdef IS_MPI
#	Line 64 | Line 90 | void SimSetup::createSim( void ){
90
91		void SimSetup::createSim( void ){
92
93	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
70	<
71	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
74	<
75	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
79	<
80	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
85	<
86	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
89	<
90	<
91	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
102	<
103	<	#ifdef IS_MPI
104	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
107	<
93	>	int i, j, k, globalAtomIndex;
94
95	<
110	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
114	<
115	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
118	<
119	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
121	<
122	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
130	<
131	<	tot_nmol += the_components[i]->getNMol();
132	<	components_nmol[i] = the_components[i]->getNMol();
133	<	}
134	<	}
135	<	else{
136	<	sprintf( painCave.errMsg,
137	<	"SimSetup error.\n"
138	<	"\tSorry, the ability to specify total"
139	<	" nMols and then give molfractions in the components\n"
140	<	"\tis not currently supported."
141	<	" Please give nMol in the components.\n" );
142	<	painCave.isFatal = 1;
143	<	simError();
144	<
145	<
146	<	//     tot_nmol = the_globals->getNMol();
147	<
148	<	//   //we have the total number of molecules, now we check for molfractions
149	<	//     for( i=0; i<n_components; i++ ){
150	<
151	<	//       if( !the_components[i]->haveMolFraction() ){
152	<
153	<	//  if( !the_components[i]->haveNMol() ){
154	<	//    //we have a problem
155	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	<	//              << " nMol was given in component
157	<
158	<	}
159	<
160	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
164	<
165	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
167	<
168	<	simnfo->nComponents = n_components;
169	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
95	>	// gather all of the information from the Bass file
96
97	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
97	>	gatherInfo();
98
99	<	id = the_components[i]->getType();
179	<	comp_stamps[i] = NULL;
180	<
181	<	// check to make sure the component isn't already in the list
99	>	// creation of complex system objects
100
101	<	comp_stamps[i] = headStamp->match( id );
184	<	if( comp_stamps[i] == NULL ){
185	<
186	<	// extract the component from the list;
187	<
188	<	currentStamp = the_stamps->extractMolStamp( id );
189	<	if( currentStamp == NULL ){
190	<	sprintf( painCave.errMsg,
191	<	"SimSetup error: Component \"%s\" was not found in the "
192	<	"list of declared molecules\n",
193	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
101	>	sysObjectsCreation();
102
103	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
103	>	// check on the post processing info
104
105	+	finalInfoCheck();
106
107	+	// initialize the system coordinates
108
109	<
211	<	// caclulate the number of atoms, bonds, bends and torsions
212	<
213	<	tot_atoms = 0;
214	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
218	<
219	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
224	<
225	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
226	<
227	<	simnfo->n_atoms = tot_atoms;
228	<	simnfo->n_bonds = tot_bonds;
229	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
233	<
109	>	initSystemCoords();
110
235	–	#ifdef IS_MPI
111
112	<	// divide the molecules among processors here.
238	<
239	<	mpiSim = new mpiSimulation( simnfo );
240	<
241	<
112	>	// make the output filenames
113
114	<	globalIndex = mpiSim->divideLabor();
115	<
116	<
246	<
247	<	// set up the local variables
114	>	makeOutNames();
115	>
116	>	// make the integrator
117
118	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
118	>	makeIntegrator();
119
252	–	allMol = 0;
253	–	localMol = 0;
254	–	local_atoms = 0;
255	–	local_bonds = 0;
256	–	local_bends = 0;
257	–	local_torsions = 0;
258	–	for( i=0; i<n_components; i++ ){
259	–
260	–	for( j=0; j<components_nmol[i]; j++ ){
261	–
262	–	if( mpiSim->getMyMolStart() <= allMol &&
263	–	allMol <= mpiSim->getMyMolEnd() ){
264	–
265	–	local_atoms +=    comp_stamps[i]->getNAtoms();
266	–	local_bonds +=    comp_stamps[i]->getNBonds();
267	–	local_bends +=    comp_stamps[i]->getNBends();
268	–	local_torsions += comp_stamps[i]->getNTorsions();
269	–	localMol++;
270	–	}
271	–	allMol++;
272	–	}
273	–	}
274	–	local_SRI = local_bonds + local_bends + local_torsions;
275	–
276	–
277	–	simnfo->n_atoms = mpiSim->getMyNlocal();
278	–
279	–	if( local_atoms != simnfo->n_atoms ){
280	–	sprintf( painCave.errMsg,
281	–	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	–	" localAtom (%d) are note equal.\n",
283	–	simnfo->n_atoms,
284	–	local_atoms );
285	–	painCave.isFatal = 1;
286	–	simError();
287	–	}
288	–
289	–	simnfo->n_bonds = local_bonds;
290	–	simnfo->n_bends = local_bends;
291	–	simnfo->n_torsions = local_torsions;
292	–	simnfo->n_SRI = local_SRI;
293	–	simnfo->n_mol = localMol;
294	–
295	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
296	–	MPIcheckPoint();
297	–
298	–
299	–	#endif // is_mpi
300	–
301	–
302	–	// create the atom and short range interaction arrays
303	–
304	–	Atom::createArrays(simnfo->n_atoms);
305	–	the_atoms = new Atom*[simnfo->n_atoms];
306	–	the_molecules = new Molecule[simnfo->n_mol];
307	–
308	–
309	–	if( simnfo->n_SRI ){
310	–	Exclude::createArray(simnfo->n_SRI);
311	–	the_excludes = new Exclude*[simnfo->n_SRI];
312	–	simnfo->globalExcludes = new int;
313	–	simnfo->n_exclude = tot_SRI;
314	–	}
315	–	else{
316	–
317	–	Exclude::createArray( 1 );
318	–	the_excludes = new Exclude*;
319	–	the_excludes[0] = new Exclude(0);
320	–	the_excludes[0]->setPair( 0,0 );
321	–	simnfo->globalExcludes = new int;
322	–	simnfo->globalExcludes[0] = 0;
323	–	simnfo->n_exclude = 0;
324	–	}
325	–
326	–	// set the arrays into the SimInfo object
327	–
328	–	simnfo->atoms = the_atoms;
329	–	simnfo->sr_interactions = the_sris;
330	–	simnfo->nGlobalExcludes = 0;
331	–	simnfo->excludes = the_excludes;
332	–
333	–
334	–	// get some of the tricky things that may still be in the globals
335	–
336	–
337	–	if( the_globals->haveBox() ){
338	–	simnfo->box_x = the_globals->getBox();
339	–	simnfo->box_y = the_globals->getBox();
340	–	simnfo->box_z = the_globals->getBox();
341	–	}
342	–	else if( the_globals->haveDensity() ){
343	–
344	–	double vol;
345	–	vol = (double)tot_nmol / the_globals->getDensity();
346	–	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	–	simnfo->box_y = simnfo->box_x;
348	–	simnfo->box_z = simnfo->box_x;
349	–	}
350	–	else{
351	–	if( !the_globals->haveBoxX() ){
352	–	sprintf( painCave.errMsg,
353	–	"SimSetup error, no periodic BoxX size given.\n" );
354	–	painCave.isFatal = 1;
355	–	simError();
356	–	}
357	–	simnfo->box_x = the_globals->getBoxX();
358	–
359	–	if( !the_globals->haveBoxY() ){
360	–	sprintf( painCave.errMsg,
361	–	"SimSetup error, no periodic BoxY size given.\n" );
362	–	painCave.isFatal = 1;
363	–	simError();
364	–	}
365	–	simnfo->box_y = the_globals->getBoxY();
366	–
367	–	if( !the_globals->haveBoxZ() ){
368	–	sprintf( painCave.errMsg,
369	–	"SimSetup error, no periodic BoxZ size given.\n" );
370	–	painCave.isFatal = 1;
371	–	simError();
372	–	}
373	–	simnfo->box_z = the_globals->getBoxZ();
374	–	}
375	–
120		#ifdef IS_MPI
121	<	strcpy( checkPointMsg, "Box size set up" );
378	<	MPIcheckPoint();
379	<	#endif // is_mpi
380	<
381	<
382	<	// initialize the arrays
383	<
384	<	the_ff->setSimInfo( simnfo );
385	<
386	<	makeAtoms();
387	<	simnfo->identArray = new int[simnfo->n_atoms];
388	<	for(i=0; i<simnfo->n_atoms; i++){
389	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
390	<	}
391	<
392	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
395	<
396	<	if( tot_bends ){
397	<	makeBends();
398	<	}
399	<
400	<	if( tot_torsions ){
401	<	makeTorsions();
402	<	}
403	<
404	<
405	<	if (the_globals->getUseRF() ) {
406	<	simnfo->useReactionField = 1;
407	<
408	<	if( !the_globals->haveECR() ){
409	<	sprintf( painCave.errMsg,
410	<	"SimSetup Warning: using default value of 1/2 the smallest "
411	<	"box length for the electrostaticCutoffRadius.\n"
412	<	"I hope you have a very fast processor!\n");
413	<	painCave.isFatal = 0;
414	<	simError();
415	<	double smallest;
416	<	smallest = simnfo->box_x;
417	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	<	simnfo->ecr = 0.5 * smallest;
420	<	} else {
421	<	simnfo->ecr        = the_globals->getECR();
422	<	}
423	<
424	<	if( !the_globals->haveEST() ){
425	<	sprintf( painCave.errMsg,
426	<	"SimSetup Warning: using default value of 0.05 * the "
427	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	<	);
429	<	painCave.isFatal = 0;
430	<	simError();
431	<	simnfo->est = 0.05 * simnfo->ecr;
432	<	} else {
433	<	simnfo->est        = the_globals->getEST();
434	<	}
435	<
436	<	if(!the_globals->haveDielectric() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup Error: You are trying to use Reaction Field without"
439	<	"setting a dielectric constant!\n"
440	<	);
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
451	<	"box length for the electrostaticCutoffRadius.\n"
452	<	"I hope you have a very fast processor!\n");
453	<	painCave.isFatal = 0;
454	<	simError();
455	<	double smallest;
456	<	smallest = simnfo->box_x;
457	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	<	simnfo->ecr = 0.5 * smallest;
460	<	} else {
461	<	simnfo->ecr        = the_globals->getECR();
462	<	}
463	<
464	<	if( !the_globals->haveEST() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup Warning: using default value of 5% of the"
467	<	"electrostaticCutoffRadius for the "
468	<	"electrostaticSkinThickness\n"
469	<	);
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	simnfo->est = 0.05 * simnfo->ecr;
473	<	} else {
474	<	simnfo->est        = the_globals->getEST();
475	<	}
476	<	}
477	<	}
478	<
479	<	#ifdef IS_MPI
480	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
481	<	MPIcheckPoint();
482	<	#endif // is_mpi
483	<
484	<	if( the_globals->haveInitialConfig() ){
485	<
486	<	InitializeFromFile* fileInit;
487	<	#ifdef IS_MPI // is_mpi
488	<	if( worldRank == 0 ){
489	<	#endif //is_mpi
490	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
491	<	#ifdef IS_MPI
492	<	}else fileInit = new InitializeFromFile( NULL );
121	>	mpiSim->mpiRefresh();
122		#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
123
124	<	delete fileInit;
497	<	}
498	<	else{
124	>	// initialize the Fortran
125
126	<	#ifdef IS_MPI
501	<
502	<	// no init from bass
503	<
504	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
510	<
511	<	initFromBass();
512	<
513	<
514	<	#endif
515	<	}
516	<
517	<	#ifdef IS_MPI
518	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
519	<	MPIcheckPoint();
520	<	#endif // is_mpi
521	<
522	<
523	<
524	<
525	<
526	<
527	<
528	<	#ifdef IS_MPI
529	<	if( worldRank == 0 ){
530	<	#endif // is_mpi
531	<
532	<	if( the_globals->haveFinalConfig() ){
533	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
534	<	}
535	<	else{
536	<	strcpy( simnfo->finalName, inFileName );
537	<	char* endTest;
538	<	int nameLength = strlen( simnfo->finalName );
539	<	endTest = &(simnfo->finalName[nameLength - 5]);
540	<	if( !strcmp( endTest, ".bass" ) ){
541	<	strcpy( endTest, ".eor" );
542	<	}
543	<	else if( !strcmp( endTest, ".BASS" ) ){
544	<	strcpy( endTest, ".eor" );
545	<	}
546	<	else{
547	<	endTest = &(simnfo->finalName[nameLength - 4]);
548	<	if( !strcmp( endTest, ".bss" ) ){
549	<	strcpy( endTest, ".eor" );
550	<	}
551	<	else if( !strcmp( endTest, ".mdl" ) ){
552	<	strcpy( endTest, ".eor" );
553	<	}
554	<	else{
555	<	strcat( simnfo->finalName, ".eor" );
556	<	}
557	<	}
558	<	}
559	<
560	<	// make the sample and status out names
561	<
562	<	strcpy( simnfo->sampleName, inFileName );
563	<	char* endTest;
564	<	int nameLength = strlen( simnfo->sampleName );
565	<	endTest = &(simnfo->sampleName[nameLength - 5]);
566	<	if( !strcmp( endTest, ".bass" ) ){
567	<	strcpy( endTest, ".dump" );
568	<	}
569	<	else if( !strcmp( endTest, ".BASS" ) ){
570	<	strcpy( endTest, ".dump" );
571	<	}
572	<	else{
573	<	endTest = &(simnfo->sampleName[nameLength - 4]);
574	<	if( !strcmp( endTest, ".bss" ) ){
575	<	strcpy( endTest, ".dump" );
576	<	}
577	<	else if( !strcmp( endTest, ".mdl" ) ){
578	<	strcpy( endTest, ".dump" );
579	<	}
580	<	else{
581	<	strcat( simnfo->sampleName, ".dump" );
582	<	}
583	<	}
584	<
585	<	strcpy( simnfo->statusName, inFileName );
586	<	nameLength = strlen( simnfo->statusName );
587	<	endTest = &(simnfo->statusName[nameLength - 5]);
588	<	if( !strcmp( endTest, ".bass" ) ){
589	<	strcpy( endTest, ".stat" );
590	<	}
591	<	else if( !strcmp( endTest, ".BASS" ) ){
592	<	strcpy( endTest, ".stat" );
593	<	}
594	<	else{
595	<	endTest = &(simnfo->statusName[nameLength - 4]);
596	<	if( !strcmp( endTest, ".bss" ) ){
597	<	strcpy( endTest, ".stat" );
598	<	}
599	<	else if( !strcmp( endTest, ".mdl" ) ){
600	<	strcpy( endTest, ".stat" );
601	<	}
602	<	else{
603	<	strcat( simnfo->statusName, ".stat" );
604	<	}
605	<	}
606	<
607	<	#ifdef IS_MPI
608	<	}
609	<	#endif // is_mpi
610	<
611	<	// set the status, sample, and themal kick times
612	<
613	<	if( the_globals->haveSampleTime() ){
614	<	simnfo->sampleTime = the_globals->getSampleTime();
615	<	simnfo->statusTime = simnfo->sampleTime;
616	<	simnfo->thermalTime = simnfo->sampleTime;
617	<	}
618	<	else{
619	<	simnfo->sampleTime = the_globals->getRunTime();
620	<	simnfo->statusTime = simnfo->sampleTime;
621	<	simnfo->thermalTime = simnfo->sampleTime;
622	<	}
126	>	initFortran();
127
624	–	if( the_globals->haveStatusTime() ){
625	–	simnfo->statusTime = the_globals->getStatusTime();
626	–	}
128
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
129
632	–	// check for the temperature set flag
633	–
634	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
635	–
636	–
637	–	//   // make the longe range forces and the integrator
638	–
639	–	//   new AllLong( simnfo );
640	–
641	–	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642	–	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
645	–
646	–
647	–
648	–	// initialize the Fortran
649	–
650	–	simnfo->refreshSim();
651	–
652	–	if( !strcmp( simnfo->mixingRule, "standard") ){
653	–	the_ff->initForceField( LB_MIXING_RULE );
654	–	}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
658	–	else{
659	–	sprintf( painCave.errMsg,
660	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	–	simnfo->mixingRule );
662	–	painCave.isFatal = 1;
663	–	simError();
664	–	}
665	–
666	–
667	–	#ifdef IS_MPI
668	–	strcpy( checkPointMsg,
669	–	"Successfully intialized the mixingRule for Fortran." );
670	–	MPIcheckPoint();
671	–	#endif // is_mpi
130		}
131
132
133		void SimSetup::makeMolecules( void ){
134
135		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136	<	molInit info;
136	>	molInit molInfo;
137		DirectionalAtom* dAtom;
138		LinkedAssign* extras;
139		LinkedAssign* current_extra;
#	Line 683 | Line 141 | void SimSetup::makeMolecules( void ){
141		BondStamp* currentBond;
142		BendStamp* currentBend;
143		TorsionStamp* currentTorsion;
144	+
145	+	bond_pair* theBonds;
146	+	bend_set* theBends;
147	+	torsion_set* theTorsions;
148	+
149
150		//init the forceField paramters
151
152		the_ff->readParams();
153
154
155	<	// init the molecules
155	>	// init the atoms
156
157	+	double ux, uy, uz, u, uSqr;
158	+
159		atomOffset = 0;
160		excludeOffset = 0;
161	<	for(i=0; i<simnfo->n_mol; i++){
161	>	for(i=0; i<info->n_mol; i++){
162
163		stampID = the_molecules[i].getStampID();
164
165	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
166	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
167	<	info.nBends    = comp_stamps[stampID]->getNBends();
168	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
169	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
165	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
166	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
167	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
168	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
169	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
170
171	<	info.myAtoms = &the_atoms[atomOffset];
172	<	info.myExcludes = &the_excludes[excludeOffset];
173	<	info.myBonds = new Bond*[info.nBonds];
174	<	info.myBends = new Bend*[info.nBends];
175	<	info.myTorsions = new Torsions*[info.nTorsions];
171	>	molInfo.myAtoms = &the_atoms[atomOffset];
172	>	molInfo.myExcludes = &the_excludes[excludeOffset];
173	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
174	>	molInfo.myBends = new Bend*[molInfo.nBends];
175	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
176
177	<	theBonds = new bond_pair[info.nBonds];
178	<	theBends = new bend_set[info.nBends];
179	<	theTorsions = new torsion_set[info.nTorsions];
177	>	theBonds = new bond_pair[molInfo.nBonds];
178	>	theBends = new bend_set[molInfo.nBends];
179	>	theTorsions = new torsion_set[molInfo.nTorsions];
180
181		// make the Atoms
182
183	<	for(j=0; j<info.nAtoms; j++){
183	>	for(j=0; j<molInfo.nAtoms; j++){
184
185	<	currentAtom = theComponents[stampID]->getAtom( j );
185	>	currentAtom = comp_stamps[stampID]->getAtom( j );
186		if( currentAtom->haveOrientation() ){
187
188		dAtom = new DirectionalAtom(j + atomOffset);
189	<	simnfo->n_oriented++;
190	<	info.myAtoms[j] = dAtom;
189	>	info->n_oriented++;
190	>	molInfo.myAtoms[j] = dAtom;
191
192		ux = currentAtom->getOrntX();
193		uy = currentAtom->getOrntY();
#	Line 740 | Line 205 | void SimSetup::makeMolecules( void ){
205		dAtom->setSUz( uz );
206		}
207		else{
208	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
208	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
209		}
210	<	info.myAtoms[j]->setType( currentAtom->getType() );
210	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
211
212		#ifdef IS_MPI
213
214	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
214	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
215
216		#endif // is_mpi
217		}
218
219		// make the bonds
220	<	for(j=0; j<info.nBonds; j++){
220	>	for(j=0; j<molInfo.nBonds; j++){
221
222		currentBond = comp_stamps[stampID]->getBond( j );
223		theBonds[j].a = currentBond->getA() + atomOffset;
224		theBonds[j].b = currentBond->getB() + atomOffset;
225
226	<	exI = theBonds[i].a;
227	<	exJ = theBonds[i].b;
226	>	exI = theBonds[j].a;
227	>	exJ = theBonds[j].b;
228
229		// exclude_I must always be the smaller of the pair
230		if( exI > exJ ){
#	Line 775 | Line 240 | void SimSetup::makeMolecules( void ){
240
241		the_excludes[j+excludeOffset]->setPair( exI, exJ );
242		#else  // isn't MPI
243	+
244		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
245		#endif  //is_mpi
246		}
247	<	excludeOffset += info.nBonds;
247	>	excludeOffset += molInfo.nBonds;
248
249		//make the bends
250	<	for(j=0; j<info.nBends; j++){
250	>	for(j=0; j<molInfo.nBends; j++){
251
252		currentBend = comp_stamps[stampID]->getBend( j );
253		theBends[j].a = currentBend->getA() + atomOffset;
#	Line 790 | Line 256 | void SimSetup::makeMolecules( void ){
256
257		if( currentBend->haveExtras() ){
258
259	<	extras = current_bend->getExtras();
259	>	extras = currentBend->getExtras();
260		current_extra = extras;
261
262		while( current_extra != NULL ){
#	Line 812 | Line 278 | void SimSetup::makeMolecules( void ){
278
279		default:
280		sprintf( painCave.errMsg,
281	<	"SimSetup Error: ghostVectorSource was neiter a "
281	>	"SimSetup Error: ghostVectorSource was neither a "
282		"double nor an int.\n"
283		"-->Bend[%d] in %s\n",
284		j, comp_stamps[stampID]->getID() );
#	Line 864 | Line 330 | void SimSetup::makeMolecules( void ){
330		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
331		#endif  //is_mpi
332		}
333	<	excludeOffset += info.nBends;
333	>	excludeOffset += molInfo.nBends;
334
335	<	for(j=0; j<info.nTorsions; j++){
335	>	for(j=0; j<molInfo.nTorsions; j++){
336
337		currentTorsion = comp_stamps[stampID]->getTorsion( j );
338		theTorsions[j].a = currentTorsion->getA() + atomOffset;
#	Line 894 | Line 360 | void SimSetup::makeMolecules( void ){
360		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
361		#endif  //is_mpi
362		}
363	<	excludeOffset += info.nTorsions;
363	>	excludeOffset += molInfo.nTorsions;
364
365
366		// send the arrays off to the forceField for init.
367
368	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
369	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
370	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
371	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
368	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
369	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
370	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
371	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
372
373
374	<	the_molecules[i].initialize( info );
909	<	atomOffset += info.nAtoms;
910	<	}
911	<
912	<	// clean up the forcefield
913	<
914	<	the_ff->cleanMe();
915	<	}
916	<
917	<
918	<
919	<	void SimSetup::makeAtoms( void ){
920	<
921	<	int i, j, k, index;
922	<	double ux, uy, uz, uSqr, u;
923	<	AtomStamp* current_atom;
924	<
925	<	DirectionalAtom* dAtom;
926	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
927	<
928	<	lMolIndex = 0;
929	<	molIndex = 0;
930	<	index = 0;
931	<	for( i=0; i<n_components; i++ ){
932	<
933	<	for( j=0; j<components_nmol[i]; j++ ){
934	<
935	<	#ifdef IS_MPI
936	<	if( mpiSim->getMyMolStart() <= molIndex &&
937	<	molIndex <= mpiSim->getMyMolEnd() ){
938	<	#endif // is_mpi
939	<
940	<	molStart = index;
941	<	nMemb = comp_stamps[i]->getNAtoms();
942	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
943	<
944	<	current_atom = comp_stamps[i]->getAtom( k );
945	<	if( current_atom->haveOrientation() ){
946	<
947	<	dAtom = new DirectionalAtom(index);
948	<	simnfo->n_oriented++;
949	<	the_atoms[index] = dAtom;
950	<
951	<	ux = current_atom->getOrntX();
952	<	uy = current_atom->getOrntY();
953	<	uz = current_atom->getOrntZ();
954	<
955	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
956	<
957	<	u = sqrt( uSqr );
958	<	ux = ux / u;
959	<	uy = uy / u;
960	<	uz = uz / u;
961	<
962	<	dAtom->setSUx( ux );
963	<	dAtom->setSUy( uy );
964	<	dAtom->setSUz( uz );
965	<	}
966	<	else{
967	<	the_atoms[index] = new GeneralAtom(index);
968	<	}
969	<	the_atoms[index]->setType( current_atom->getType() );
970	<	the_atoms[index]->setIndex( index );
971	<
972	<	// increment the index and repeat;
973	<	index++;
974	<	}
975	<
976	<	molEnd = index -1;
977	<	the_molecules[lMolIndex].setNMembers( nMemb );
978	<	the_molecules[lMolIndex].setStartAtom( molStart );
979	<	the_molecules[lMolIndex].setEndAtom( molEnd );
980	<	the_molecules[lMolIndex].setStampID( i );
981	<	lMolIndex++;
374	>	the_molecules[i].initialize( molInfo );
375
983	–	#ifdef IS_MPI
984	–	}
985	–	#endif //is_mpi
986	–
987	–	molIndex++;
988	–	}
989	–	}
376
377	<	#ifdef IS_MPI
378	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
379	<
380	<	delete[] globalIndex;
995	<
996	<	mpiSim->mpiRefresh();
997	<	#endif //IS_MPI
998	<
999	<	the_ff->initializeAtoms();
1000	<	}
1001	<
1002	<	void SimSetup::makeBonds( void ){
1003	<
1004	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1005	<	bond_pair* the_bonds;
1006	<	BondStamp* current_bond;
1007	<
1008	<	the_bonds = new bond_pair[tot_bonds];
1009	<	index = 0;
1010	<	offset = 0;
1011	<	molIndex = 0;
1012	<
1013	<	for( i=0; i<n_components; i++ ){
1014	<
1015	<	for( j=0; j<components_nmol[i]; j++ ){
1016	<
1017	<	#ifdef IS_MPI
1018	<	if( mpiSim->getMyMolStart() <= molIndex &&
1019	<	molIndex <= mpiSim->getMyMolEnd() ){
1020	<	#endif // is_mpi
1021	<
1022	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1023	<
1024	<	current_bond = comp_stamps[i]->getBond( k );
1025	<	the_bonds[index].a = current_bond->getA() + offset;
1026	<	the_bonds[index].b = current_bond->getB() + offset;
1027	<
1028	<	exI = the_bonds[index].a;
1029	<	exJ = the_bonds[index].b;
1030	<
1031	<	// exclude_I must always be the smaller of the pair
1032	<	if( exI > exJ ){
1033	<	tempEx = exI;
1034	<	exI = exJ;
1035	<	exJ = tempEx;
1036	<	}
1037	<
1038	<
1039	<	#ifdef IS_MPI
1040	<
1041	<	the_excludes[index*2] =
1042	<	the_atoms[exI]->getGlobalIndex() + 1;
1043	<	the_excludes[index*2 + 1] =
1044	<	the_atoms[exJ]->getGlobalIndex() + 1;
1045	<
1046	<	#else  // isn't MPI
1047	<
1048	<	the_excludes[index*2] =     exI + 1;
1049	<	the_excludes[index*2 + 1] = exJ + 1;
1050	<	// fortran index from 1 (hence the +1 in the indexing)
1051	<	#endif  //is_mpi
1052	<
1053	<	// increment the index and repeat;
1054	<	index++;
1055	<	}
1056	<	offset += comp_stamps[i]->getNAtoms();
1057	<
1058	<	#ifdef IS_MPI
1059	<	}
1060	<	#endif //is_mpi
1061	<
1062	<	molIndex++;
1063	<	}
377	>	atomOffset += molInfo.nAtoms;
378	>	delete[] theBonds;
379	>	delete[] theBends;
380	>	delete[] theTorsions;
381		}
382
1066	–	the_ff->initializeBonds( the_bonds );
1067	–	}
1068	–
1069	–	void SimSetup::makeBends( void ){
1070	–
1071	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1072	–	bend_set* the_bends;
1073	–	BendStamp* current_bend;
1074	–	LinkedAssign* extras;
1075	–	LinkedAssign* current_extra;
1076	–
1077	–
1078	–	the_bends = new bend_set[tot_bends];
1079	–	index = 0;
1080	–	offset = 0;
1081	–	molIndex = 0;
1082	–	for( i=0; i<n_components; i++ ){
1083	–
1084	–	for( j=0; j<components_nmol[i]; j++ ){
1085	–
383		#ifdef IS_MPI
384	<	if( mpiSim->getMyMolStart() <= molIndex &&
1088	<	molIndex <= mpiSim->getMyMolEnd() ){
1089	<	#endif // is_mpi
1090	<
1091	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1092	<
1093	<	current_bend = comp_stamps[i]->getBend( k );
1094	<	the_bends[index].a = current_bend->getA() + offset;
1095	<	the_bends[index].b = current_bend->getB() + offset;
1096	<	the_bends[index].c = current_bend->getC() + offset;
1097	<
1098	<	if( current_bend->haveExtras() ){
1099	<
1100	<	extras = current_bend->getExtras();
1101	<	current_extra = extras;
1102	<
1103	<	while( current_extra != NULL ){
1104	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1105	<
1106	<	switch( current_extra->getType() ){
1107	<
1108	<	case 0:
1109	<	the_bends[index].ghost =
1110	<	current_extra->getInt() + offset;
1111	<	the_bends[index].isGhost = 1;
1112	<	break;
1113	<
1114	<	case 1:
1115	<	the_bends[index].ghost =
1116	<	(int)current_extra->getDouble() + offset;
1117	<	the_bends[index].isGhost = 1;
1118	<	break;
1119	<
1120	<	default:
1121	<	sprintf( painCave.errMsg,
1122	<	"SimSetup Error: ghostVectorSource was neiter a "
1123	<	"double nor an int.\n"
1124	<	"-->Bend[%d] in %s\n",
1125	<	k, comp_stamps[i]->getID() );
1126	<	painCave.isFatal = 1;
1127	<	simError();
1128	<	}
1129	<	}
1130	<
1131	<	else{
1132	<
1133	<	sprintf( painCave.errMsg,
1134	<	"SimSetup Error: unhandled bend assignment:\n"
1135	<	"    -->%s in Bend[%d] in %s\n",
1136	<	current_extra->getlhs(),
1137	<	k, comp_stamps[i]->getID() );
1138	<	painCave.isFatal = 1;
1139	<	simError();
1140	<	}
1141	<
1142	<	current_extra = current_extra->getNext();
1143	<	}
1144	<	}
1145	<
1146	<	if( !the_bends[index].isGhost ){
1147	<
1148	<	exI = the_bends[index].a;
1149	<	exJ = the_bends[index].c;
1150	<	}
1151	<	else{
1152	<
1153	<	exI = the_bends[index].a;
1154	<	exJ = the_bends[index].b;
1155	<	}
1156	<
1157	<	// exclude_I must always be the smaller of the pair
1158	<	if( exI > exJ ){
1159	<	tempEx = exI;
1160	<	exI = exJ;
1161	<	exJ = tempEx;
1162	<	}
1163	<
1164	<
1165	<	#ifdef IS_MPI
1166	<
1167	<	the_excludes[(index + tot_bonds)*2] =
1168	<	the_atoms[exI]->getGlobalIndex() + 1;
1169	<	the_excludes[(index + tot_bonds)*2 + 1] =
1170	<	the_atoms[exJ]->getGlobalIndex() + 1;
1171	<
1172	<	#else  // isn't MPI
1173	<
1174	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1175	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1176	<	// fortran index from 1 (hence the +1 in the indexing)
1177	<	#endif  //is_mpi
1178	<
1179	<
1180	<	// increment the index and repeat;
1181	<	index++;
1182	<	}
1183	<	offset += comp_stamps[i]->getNAtoms();
1184	<
1185	<	#ifdef IS_MPI
1186	<	}
1187	<	#endif //is_mpi
1188	<
1189	<	molIndex++;
1190	<	}
1191	<	}
1192	<
1193	<	#ifdef IS_MPI
1194	<	sprintf( checkPointMsg,
1195	<	"Successfully created the bends list.\n" );
384	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
385		MPIcheckPoint();
386		#endif // is_mpi
1198	–
387
388	<	the_ff->initializeBends( the_bends );
389	<	}
390	<
1203	<	void SimSetup::makeTorsions( void ){
1204	<
1205	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1206	<	torsion_set* the_torsions;
1207	<	TorsionStamp* current_torsion;
1208	<
1209	<	the_torsions = new torsion_set[tot_torsions];
1210	<	index = 0;
1211	<	offset = 0;
1212	<	molIndex = 0;
1213	<	for( i=0; i<n_components; i++ ){
388	>	// clean up the forcefield
389	>	the_ff->calcRcut();
390	>	the_ff->cleanMe();
391
1215	–	for( j=0; j<components_nmol[i]; j++ ){
1216	–
1217	–	#ifdef IS_MPI
1218	–	if( mpiSim->getMyMolStart() <= molIndex &&
1219	–	molIndex <= mpiSim->getMyMolEnd() ){
1220	–	#endif // is_mpi
1221	–
1222	–	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1223	–
1224	–	current_torsion = comp_stamps[i]->getTorsion( k );
1225	–	the_torsions[index].a = current_torsion->getA() + offset;
1226	–	the_torsions[index].b = current_torsion->getB() + offset;
1227	–	the_torsions[index].c = current_torsion->getC() + offset;
1228	–	the_torsions[index].d = current_torsion->getD() + offset;
1229	–
1230	–	exI = the_torsions[index].a;
1231	–	exJ = the_torsions[index].d;
1232	–
1233	–
1234	–	// exclude_I must always be the smaller of the pair
1235	–	if( exI > exJ ){
1236	–	tempEx = exI;
1237	–	exI = exJ;
1238	–	exJ = tempEx;
1239	–	}
1240	–
1241	–
1242	–	#ifdef IS_MPI
1243	–
1244	–	the_excludes[(index + tot_bonds + tot_bends)*2] =
1245	–	the_atoms[exI]->getGlobalIndex() + 1;
1246	–	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1247	–	the_atoms[exJ]->getGlobalIndex() + 1;
1248	–
1249	–	#else  // isn't MPI
1250	–
1251	–	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1252	–	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1253	–	// fortran indexes from 1 (hence the +1 in the indexing)
1254	–	#endif  //is_mpi
1255	–
1256	–
1257	–	// increment the index and repeat;
1258	–	index++;
1259	–	}
1260	–	offset += comp_stamps[i]->getNAtoms();
1261	–
1262	–	#ifdef IS_MPI
1263	–	}
1264	–	#endif //is_mpi
1265	–
1266	–	molIndex++;
1267	–	}
1268	–	}
1269	–
1270	–	the_ff->initializeTorsions( the_torsions );
392		}
393
394		void SimSetup::initFromBass( void ){
#	Line 1289 | Line 410 | void SimSetup::initFromBass( void ){
410		have_extra =1;
411
412		n_cells = (int)temp3 - 1;
413	<	cellx = simnfo->box_x / temp3;
414	<	celly = simnfo->box_y / temp3;
415	<	cellz = simnfo->box_z / temp3;
413	>	cellx = info->boxL[0] / temp3;
414	>	celly = info->boxL[1] / temp3;
415	>	cellz = info->boxL[2] / temp3;
416		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
417		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
418		n_per_extra = (int)ceil( temp1 );
#	Line 1306 | Line 427 | void SimSetup::initFromBass( void ){
427		}
428		else{
429		n_cells = (int)temp3;
430	<	cellx = simnfo->box_x / temp3;
431	<	celly = simnfo->box_y / temp3;
432	<	cellz = simnfo->box_z / temp3;
430	>	cellx = info->boxL[0] / temp3;
431	>	celly = info->boxL[1] / temp3;
432	>	cellz = info->boxL[2] / temp3;
433		}
434
435		current_mol = 0;
#	Line 1388 | Line 509 | void SimSetup::initFromBass( void ){
509		}
510
511
512	<	for( i=0; i<simnfo->n_atoms; i++ ){
513	<	simnfo->atoms[i]->set_vx( 0.0 );
514	<	simnfo->atoms[i]->set_vy( 0.0 );
515	<	simnfo->atoms[i]->set_vz( 0.0 );
512	>	for( i=0; i<info->n_atoms; i++ ){
513	>	info->atoms[i]->set_vx( 0.0 );
514	>	info->atoms[i]->set_vy( 0.0 );
515	>	info->atoms[i]->set_vz( 0.0 );
516		}
517		}
518
#	Line 1450 | Line 571 | void SimSetup::makeElement( double x, double y, double
571
572		current_comp_mol = 0;
573		current_comp++;
574	+	}
575	+	}
576	+
577	+
578	+	void SimSetup::gatherInfo( void ){
579	+	int i,j,k;
580	+
581	+	ensembleCase = -1;
582	+	ffCase = -1;
583	+
584	+	// get the stamps and globals;
585	+	stamps = stamps;
586	+	globals = globals;
587	+
588	+	// set the easy ones first
589	+	info->target_temp = globals->getTargetTemp();
590	+	info->dt = globals->getDt();
591	+	info->run_time = globals->getRunTime();
592	+	n_components = globals->getNComponents();
593	+
594	+
595	+	// get the forceField
596	+
597	+	strcpy( force_field, globals->getForceField() );
598	+
599	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
600	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
601	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
602	+	else{
603	+	sprintf( painCave.errMsg,
604	+	"SimSetup Error. Unrecognized force field -> %s\n",
605	+	force_field );
606	+	painCave.isFatal = 1;
607	+	simError();
608	+	}
609	+
610	+	// get the ensemble
611	+
612	+	strcpy( ensemble, globals->getEnsemble() );
613	+
614	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
615	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
616	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
617	+	ensembleCase = NPTi_ENS;
618	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
619	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
620	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
621	+	else{
622	+	sprintf( painCave.errMsg,
623	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
624	+	"reverting to NVE for this simulation.\n",
625	+	ensemble );
626	+	painCave.isFatal = 0;
627	+	simError();
628	+	strcpy( ensemble, "NVE" );
629	+	ensembleCase = NVE_ENS;
630	+	}
631	+	strcpy( info->ensemble, ensemble );
632	+
633	+	// get the mixing rule
634	+
635	+	strcpy( info->mixingRule, globals->getMixingRule() );
636	+	info->usePBC = globals->getPBC();
637	+
638	+
639	+	// get the components and calculate the tot_nMol and indvidual n_mol
640	+
641	+	the_components = globals->getComponents();
642	+	components_nmol = new int[n_components];
643	+
644	+
645	+	if( !globals->haveNMol() ){
646	+	// we don't have the total number of molecules, so we assume it is
647	+	// given in each component
648	+
649	+	tot_nmol = 0;
650	+	for( i=0; i<n_components; i++ ){
651	+
652	+	if( !the_components[i]->haveNMol() ){
653	+	// we have a problem
654	+	sprintf( painCave.errMsg,
655	+	"SimSetup Error. No global NMol or component NMol"
656	+	" given. Cannot calculate the number of atoms.\n" );
657	+	painCave.isFatal = 1;
658	+	simError();
659	+	}
660	+
661	+	tot_nmol += the_components[i]->getNMol();
662	+	components_nmol[i] = the_components[i]->getNMol();
663	+	}
664	+	}
665	+	else{
666	+	sprintf( painCave.errMsg,
667	+	"SimSetup error.\n"
668	+	"\tSorry, the ability to specify total"
669	+	" nMols and then give molfractions in the components\n"
670	+	"\tis not currently supported."
671	+	" Please give nMol in the components.\n" );
672	+	painCave.isFatal = 1;
673	+	simError();
674	+	}
675	+
676	+	// set the status, sample, and thermal kick times
677	+
678	+	if( globals->haveSampleTime() ){
679	+	info->sampleTime = globals->getSampleTime();
680	+	info->statusTime = info->sampleTime;
681	+	info->thermalTime = info->sampleTime;
682	+	}
683	+	else{
684	+	info->sampleTime = globals->getRunTime();
685	+	info->statusTime = info->sampleTime;
686	+	info->thermalTime = info->sampleTime;
687	+	}
688	+
689	+	if( globals->haveStatusTime() ){
690	+	info->statusTime = globals->getStatusTime();
691	+	}
692	+
693	+	if( globals->haveThermalTime() ){
694	+	info->thermalTime = globals->getThermalTime();
695	+	}
696	+
697	+	// check for the temperature set flag
698	+
699	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
700	+
701	+	// get some of the tricky things that may still be in the globals
702	+
703	+	double boxVector[3];
704	+	if( globals->haveBox() ){
705	+	boxVector[0] = globals->getBox();
706	+	boxVector[1] = globals->getBox();
707	+	boxVector[2] = globals->getBox();
708	+
709	+	info->setBox( boxVector );
710	+	}
711	+	else if( globals->haveDensity() ){
712	+
713	+	double vol;
714	+	vol = (double)tot_nmol / globals->getDensity();
715	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
716	+	boxVector[1] = boxVector[0];
717	+	boxVector[2] = boxVector[0];
718	+
719	+	info->setBox( boxVector );
720	+	}
721	+	else{
722	+	if( !globals->haveBoxX() ){
723	+	sprintf( painCave.errMsg,
724	+	"SimSetup error, no periodic BoxX size given.\n" );
725	+	painCave.isFatal = 1;
726	+	simError();
727	+	}
728	+	boxVector[0] = globals->getBoxX();
729	+
730	+	if( !globals->haveBoxY() ){
731	+	sprintf( painCave.errMsg,
732	+	"SimSetup error, no periodic BoxY size given.\n" );
733	+	painCave.isFatal = 1;
734	+	simError();
735	+	}
736	+	boxVector[1] = globals->getBoxY();
737	+
738	+	if( !globals->haveBoxZ() ){
739	+	sprintf( painCave.errMsg,
740	+	"SimSetup error, no periodic BoxZ size given.\n" );
741	+	painCave.isFatal = 1;
742	+	simError();
743	+	}
744	+	boxVector[2] = globals->getBoxZ();
745	+
746	+	info->setBox( boxVector );
747	+	}
748	+
749	+
750	+
751	+	#ifdef IS_MPI
752	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
753	+	MPIcheckPoint();
754	+	#endif // is_mpi
755	+
756	+	}
757	+
758	+
759	+	void SimSetup::finalInfoCheck( void ){
760	+	int index;
761	+	int usesDipoles;
762	+
763	+
764	+	// check electrostatic parameters
765	+
766	+	index = 0;
767	+	usesDipoles = 0;
768	+	while( (index < info->n_atoms) && !usesDipoles ){
769	+	usesDipoles = ((info->atoms)[index])->hasDipole();
770	+	index++;
771	+	}
772	+
773	+	#ifdef IS_MPI
774	+	int myUse = usesDipoles;
775	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
776	+	#endif //is_mpi
777	+
778	+	double theEcr, theEst;
779	+
780	+	if (globals->getUseRF() ) {
781	+	info->useReactionField = 1;
782	+
783	+	if( !globals->haveECR() ){
784	+	sprintf( painCave.errMsg,
785	+	"SimSetup Warning: using default value of 1/2 the smallest "
786	+	"box length for the electrostaticCutoffRadius.\n"
787	+	"I hope you have a very fast processor!\n");
788	+	painCave.isFatal = 0;
789	+	simError();
790	+	double smallest;
791	+	smallest = info->boxL[0];
792	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
793	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
794	+	theEcr = 0.5 * smallest;
795	+	} else {
796	+	theEcr = globals->getECR();
797	+	}
798	+
799	+	if( !globals->haveEST() ){
800	+	sprintf( painCave.errMsg,
801	+	"SimSetup Warning: using default value of 0.05 * the "
802	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
803	+	);
804	+	painCave.isFatal = 0;
805	+	simError();
806	+	theEst = 0.05 * theEcr;
807	+	} else {
808	+	theEst= globals->getEST();
809	+	}
810	+
811	+	info->setEcr( theEcr, theEst );
812	+
813	+	if(!globals->haveDielectric() ){
814	+	sprintf( painCave.errMsg,
815	+	"SimSetup Error: You are trying to use Reaction Field without"
816	+	"setting a dielectric constant!\n"
817	+	);
818	+	painCave.isFatal = 1;
819	+	simError();
820	+	}
821	+	info->dielectric = globals->getDielectric();
822	+	}
823	+	else {
824	+	if (usesDipoles) {
825	+
826	+	if( !globals->haveECR() ){
827	+	sprintf( painCave.errMsg,
828	+	"SimSetup Warning: using default value of 1/2 the smallest "
829	+	"box length for the electrostaticCutoffRadius.\n"
830	+	"I hope you have a very fast processor!\n");
831	+	painCave.isFatal = 0;
832	+	simError();
833	+	double smallest;
834	+	smallest = info->boxL[0];
835	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
836	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
837	+	theEcr = 0.5 * smallest;
838	+	} else {
839	+	theEcr = globals->getECR();
840	+	}
841	+
842	+	if( !globals->haveEST() ){
843	+	sprintf( painCave.errMsg,
844	+	"SimSetup Warning: using default value of 0.05 * the "
845	+	"electrostaticCutoffRadius for the "
846	+	"electrostaticSkinThickness\n"
847	+	);
848	+	painCave.isFatal = 0;
849	+	simError();
850	+	theEst = 0.05 * theEcr;
851	+	} else {
852	+	theEst= globals->getEST();
853	+	}
854	+
855	+	info->setEcr( theEcr, theEst );
856	+	}
857	+	}
858	+
859	+	#ifdef IS_MPI
860	+	strcpy( checkPointMsg, "post processing checks out" );
861	+	MPIcheckPoint();
862	+	#endif // is_mpi
863	+
864	+	}
865	+
866	+	void SimSetup::initSystemCoords( void ){
867	+
868	+	if( globals->haveInitialConfig() ){
869	+
870	+	InitializeFromFile* fileInit;
871	+	#ifdef IS_MPI // is_mpi
872	+	if( worldRank == 0 ){
873	+	#endif //is_mpi
874	+	fileInit = new InitializeFromFile( globals->getInitialConfig() );
875	+	#ifdef IS_MPI
876	+	}else fileInit = new InitializeFromFile( NULL );
877	+	#endif
878	+	fileInit->readInit( info ); // default velocities on
879	+
880	+	delete fileInit;
881	+	}
882	+	else{
883	+
884	+	#ifdef IS_MPI
885	+
886	+	// no init from bass
887	+
888	+	sprintf( painCave.errMsg,
889	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
890	+	painCave.isFatal;
891	+	simError();
892	+
893	+	#else
894	+
895	+	initFromBass();
896	+
897	+
898	+	#endif
899	+	}
900	+
901	+	#ifdef IS_MPI
902	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
903	+	MPIcheckPoint();
904	+	#endif // is_mpi
905	+
906	+	}
907	+
908	+
909	+	void SimSetup::makeOutNames( void ){
910	+
911	+	#ifdef IS_MPI
912	+	if( worldRank == 0 ){
913	+	#endif // is_mpi
914	+
915	+	if( globals->haveFinalConfig() ){
916	+	strcpy( info->finalName, globals->getFinalConfig() );
917	+	}
918	+	else{
919	+	strcpy( info->finalName, inFileName );
920	+	char* endTest;
921	+	int nameLength = strlen( info->finalName );
922	+	endTest = &(info->finalName[nameLength - 5]);
923	+	if( !strcmp( endTest, ".bass" ) ){
924	+	strcpy( endTest, ".eor" );
925	+	}
926	+	else if( !strcmp( endTest, ".BASS" ) ){
927	+	strcpy( endTest, ".eor" );
928	+	}
929	+	else{
930	+	endTest = &(info->finalName[nameLength - 4]);
931	+	if( !strcmp( endTest, ".bss" ) ){
932	+	strcpy( endTest, ".eor" );
933	+	}
934	+	else if( !strcmp( endTest, ".mdl" ) ){
935	+	strcpy( endTest, ".eor" );
936	+	}
937	+	else{
938	+	strcat( info->finalName, ".eor" );
939	+	}
940	+	}
941	+	}
942	+
943	+	// make the sample and status out names
944	+
945	+	strcpy( info->sampleName, inFileName );
946	+	char* endTest;
947	+	int nameLength = strlen( info->sampleName );
948	+	endTest = &(info->sampleName[nameLength - 5]);
949	+	if( !strcmp( endTest, ".bass" ) ){
950	+	strcpy( endTest, ".dump" );
951	+	}
952	+	else if( !strcmp( endTest, ".BASS" ) ){
953	+	strcpy( endTest, ".dump" );
954	+	}
955	+	else{
956	+	endTest = &(info->sampleName[nameLength - 4]);
957	+	if( !strcmp( endTest, ".bss" ) ){
958	+	strcpy( endTest, ".dump" );
959	+	}
960	+	else if( !strcmp( endTest, ".mdl" ) ){
961	+	strcpy( endTest, ".dump" );
962	+	}
963	+	else{
964	+	strcat( info->sampleName, ".dump" );
965	+	}
966	+	}
967	+
968	+	strcpy( info->statusName, inFileName );
969	+	nameLength = strlen( info->statusName );
970	+	endTest = &(info->statusName[nameLength - 5]);
971	+	if( !strcmp( endTest, ".bass" ) ){
972	+	strcpy( endTest, ".stat" );
973	+	}
974	+	else if( !strcmp( endTest, ".BASS" ) ){
975	+	strcpy( endTest, ".stat" );
976	+	}
977	+	else{
978	+	endTest = &(info->statusName[nameLength - 4]);
979	+	if( !strcmp( endTest, ".bss" ) ){
980	+	strcpy( endTest, ".stat" );
981	+	}
982	+	else if( !strcmp( endTest, ".mdl" ) ){
983	+	strcpy( endTest, ".stat" );
984	+	}
985	+	else{
986	+	strcat( info->statusName, ".stat" );
987	+	}
988	+	}
989	+
990	+	#ifdef IS_MPI
991	+	}
992	+	#endif // is_mpi
993	+
994	+	}
995	+
996	+
997	+	void SimSetup::sysObjectsCreation( void ){
998	+
999	+	int i;
1000	+
1001	+	// create the forceField
1002	+
1003	+	createFF();
1004	+
1005	+	// extract componentList
1006	+
1007	+	compList();
1008	+
1009	+	// calc the number of atoms, bond, bends, and torsions
1010	+
1011	+	calcSysValues();
1012	+
1013	+	#ifdef IS_MPI
1014	+	// divide the molecules among the processors
1015	+
1016	+	mpiMolDivide();
1017	+	#endif //is_mpi
1018	+
1019	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1020	+
1021	+	makeSysArrays();
1022	+
1023	+	// make and initialize the molecules (all but atomic coordinates)
1024	+
1025	+	makeMolecules();
1026	+	info->identArray = new int[info->n_atoms];
1027	+	for(i=0; i<info->n_atoms; i++){
1028	+	info->identArray[i] = the_atoms[i]->getIdent();
1029		}
1030	+
1031	+
1032	+
1033		}
1034	+
1035	+
1036	+	void SimSetup::createFF( void ){
1037	+
1038	+	switch( ffCase ){
1039	+
1040	+	case FF_DUFF:
1041	+	the_ff = new DUFF();
1042	+	break;
1043	+
1044	+	case FF_LJ:
1045	+	the_ff = new LJFF();
1046	+	break;
1047	+
1048	+	case FF_EAM:
1049	+	the_ff = new EAM_FF();
1050	+	break;
1051	+
1052	+	default:
1053	+	sprintf( painCave.errMsg,
1054	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1055	+	painCave.isFatal = 1;
1056	+	simError();
1057	+	}
1058	+
1059	+	#ifdef IS_MPI
1060	+	strcpy( checkPointMsg, "ForceField creation successful" );
1061	+	MPIcheckPoint();
1062	+	#endif // is_mpi
1063	+
1064	+	}
1065	+
1066	+
1067	+	void SimSetup::compList( void ){
1068	+
1069	+	int i;
1070	+
1071	+	comp_stamps = new MoleculeStamp*[n_components];
1072	+
1073	+	// make an array of molecule stamps that match the components used.
1074	+	// also extract the used stamps out into a separate linked list
1075	+
1076	+	info->nComponents = n_components;
1077	+	info->componentsNmol = components_nmol;
1078	+	info->compStamps = comp_stamps;
1079	+	info->headStamp = new LinkedMolStamp();
1080	+
1081	+	char* id;
1082	+	LinkedMolStamp* headStamp = info->headStamp;
1083	+	LinkedMolStamp* currentStamp = NULL;
1084	+	for( i=0; i<n_components; i++ ){
1085	+
1086	+	id = the_components[i]->getType();
1087	+	comp_stamps[i] = NULL;
1088	+
1089	+	// check to make sure the component isn't already in the list
1090	+
1091	+	comp_stamps[i] = headStamp->match( id );
1092	+	if( comp_stamps[i] == NULL ){
1093	+
1094	+	// extract the component from the list;
1095	+
1096	+	currentStamp = stamps->extractMolStamp( id );
1097	+	if( currentStamp == NULL ){
1098	+	sprintf( painCave.errMsg,
1099	+	"SimSetup error: Component \"%s\" was not found in the "
1100	+	"list of declared molecules\n",
1101	+	id );
1102	+	painCave.isFatal = 1;
1103	+	simError();
1104	+	}
1105	+
1106	+	headStamp->add( currentStamp );
1107	+	comp_stamps[i] = headStamp->match( id );
1108	+	}
1109	+	}
1110	+
1111	+	#ifdef IS_MPI
1112	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1113	+	MPIcheckPoint();
1114	+	#endif // is_mpi
1115	+
1116	+
1117	+	}
1118	+
1119	+	void SimSetup::calcSysValues( void ){
1120	+	int i, j, k;
1121	+
1122	+
1123	+	tot_atoms = 0;
1124	+	tot_bonds = 0;
1125	+	tot_bends = 0;
1126	+	tot_torsions = 0;
1127	+	for( i=0; i<n_components; i++ ){
1128	+
1129	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1130	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1131	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1132	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1133	+	}
1134	+
1135	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1136	+
1137	+	info->n_atoms = tot_atoms;
1138	+	info->n_bonds = tot_bonds;
1139	+	info->n_bends = tot_bends;
1140	+	info->n_torsions = tot_torsions;
1141	+	info->n_SRI = tot_SRI;
1142	+	info->n_mol = tot_nmol;
1143	+
1144	+	info->molMembershipArray = new int[tot_atoms];
1145	+	}
1146	+
1147	+
1148	+	#ifdef IS_MPI
1149	+
1150	+	void SimSetup::mpiMolDivide( void ){
1151	+
1152	+	int i, j, k;
1153	+	int localMol, allMol;
1154	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1155	+
1156	+	mpiSim = new mpiSimulation( info );
1157	+
1158	+	globalIndex = mpiSim->divideLabor();
1159	+
1160	+	// set up the local variables
1161	+
1162	+	mol2proc = mpiSim->getMolToProcMap();
1163	+	molCompType = mpiSim->getMolComponentType();
1164	+
1165	+	allMol = 0;
1166	+	localMol = 0;
1167	+	local_atoms = 0;
1168	+	local_bonds = 0;
1169	+	local_bends = 0;
1170	+	local_torsions = 0;
1171	+	globalAtomIndex = 0;
1172	+
1173	+
1174	+	for( i=0; i<n_components; i++ ){
1175	+
1176	+	for( j=0; j<components_nmol[i]; j++ ){
1177	+
1178	+	if( mol2proc[allMol] == worldRank ){
1179	+
1180	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1181	+	local_bonds +=    comp_stamps[i]->getNBonds();
1182	+	local_bends +=    comp_stamps[i]->getNBends();
1183	+	local_torsions += comp_stamps[i]->getNTorsions();
1184	+	localMol++;
1185	+	}
1186	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1187	+	info->molMembershipArray[globalAtomIndex] = allMol;
1188	+	globalAtomIndex++;
1189	+	}
1190	+
1191	+	allMol++;
1192	+	}
1193	+	}
1194	+	local_SRI = local_bonds + local_bends + local_torsions;
1195	+
1196	+	info->n_atoms = mpiSim->getMyNlocal();
1197	+
1198	+	if( local_atoms != info->n_atoms ){
1199	+	sprintf( painCave.errMsg,
1200	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1201	+	" localAtom (%d) are not equal.\n",
1202	+	info->n_atoms,
1203	+	local_atoms );
1204	+	painCave.isFatal = 1;
1205	+	simError();
1206	+	}
1207	+
1208	+	info->n_bonds = local_bonds;
1209	+	info->n_bends = local_bends;
1210	+	info->n_torsions = local_torsions;
1211	+	info->n_SRI = local_SRI;
1212	+	info->n_mol = localMol;
1213	+
1214	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1215	+	MPIcheckPoint();
1216	+	}
1217	+
1218	+	#endif // is_mpi
1219	+
1220	+
1221	+	void SimSetup::makeSysArrays( void ){
1222	+	int i, j, k;
1223	+
1224	+
1225	+	// create the atom and short range interaction arrays
1226	+
1227	+	Atom::createArrays(info->n_atoms);
1228	+	the_atoms = new Atom*[info->n_atoms];
1229	+	the_molecules = new Molecule[info->n_mol];
1230	+	int molIndex;
1231	+
1232	+	// initialize the molecule's stampID's
1233	+
1234	+	#ifdef IS_MPI
1235	+
1236	+
1237	+	molIndex = 0;
1238	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1239	+
1240	+	if(mol2proc[i] == worldRank ){
1241	+	the_molecules[molIndex].setStampID( molCompType[i] );
1242	+	the_molecules[molIndex].setMyIndex( molIndex );
1243	+	the_molecules[molIndex].setGlobalIndex( i );
1244	+	molIndex++;
1245	+	}
1246	+	}
1247	+
1248	+	#else // is_mpi
1249	+
1250	+	molIndex = 0;
1251	+	globalAtomIndex = 0;
1252	+	for(i=0; i<n_components; i++){
1253	+	for(j=0; j<components_nmol[i]; j++ ){
1254	+	the_molecules[molIndex].setStampID( i );
1255	+	the_molecules[molIndex].setMyIndex( molIndex );
1256	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1257	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1258	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1259	+	globalAtomIndex++;
1260	+	}
1261	+	molIndex++;
1262	+	}
1263	+	}
1264	+
1265	+
1266	+	#endif // is_mpi
1267	+
1268	+
1269	+	if( info->n_SRI ){
1270	+
1271	+	Exclude::createArray(info->n_SRI);
1272	+	the_excludes = new Exclude*[info->n_SRI];
1273	+	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1274	+	info->globalExcludes = new int;
1275	+	info->n_exclude = info->n_SRI;
1276	+	}
1277	+	else{
1278	+
1279	+	Exclude::createArray( 1 );
1280	+	the_excludes = new Exclude*;
1281	+	the_excludes[0] = new Exclude(0);
1282	+	the_excludes[0]->setPair( 0,0 );
1283	+	info->globalExcludes = new int;
1284	+	info->globalExcludes[0] = 0;
1285	+	info->n_exclude = 0;
1286	+	}
1287	+
1288	+	// set the arrays into the SimInfo object
1289	+
1290	+	info->atoms = the_atoms;
1291	+	info->molecules = the_molecules;
1292	+	info->nGlobalExcludes = 0;
1293	+	info->excludes = the_excludes;
1294	+
1295	+	the_ff->setSimInfo( info );
1296	+
1297	+	}
1298	+
1299	+	void SimSetup::makeIntegrator( void ){
1300	+
1301	+	NVT<RealIntegrator>*  myNVT = NULL;
1302	+	NPTi<RealIntegrator>* myNPTi = NULL;
1303	+	NPTf<RealIntegrator>* myNPTf = NULL;
1304	+	NPTim<RealIntegrator>* myNPTim = NULL;
1305	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1306	+
1307	+	switch( ensembleCase ){
1308	+
1309	+	case NVE_ENS:
1310	+	new NVE<RealIntegrator>( info, the_ff );
1311	+	break;
1312	+
1313	+	case NVT_ENS:
1314	+	myNVT = new NVT<RealIntegrator>( info, the_ff );
1315	+	myNVT->setTargetTemp(globals->getTargetTemp());
1316	+
1317	+	if (globals->haveTauThermostat())
1318	+	myNVT->setTauThermostat(globals->getTauThermostat());
1319	+
1320	+	else {
1321	+	sprintf( painCave.errMsg,
1322	+	"SimSetup error: If you use the NVT\n"
1323	+	"    ensemble, you must set tauThermostat.\n");
1324	+	painCave.isFatal = 1;
1325	+	simError();
1326	+	}
1327	+	break;
1328	+
1329	+	case NPTi_ENS:
1330	+	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1331	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1332	+
1333	+	if (globals->haveTargetPressure())
1334	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1335	+	else {
1336	+	sprintf( painCave.errMsg,
1337	+	"SimSetup error: If you use a constant pressure\n"
1338	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1339	+	painCave.isFatal = 1;
1340	+	simError();
1341	+	}
1342	+
1343	+	if( globals->haveTauThermostat() )
1344	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1345	+	else{
1346	+	sprintf( painCave.errMsg,
1347	+	"SimSetup error: If you use an NPT\n"
1348	+	"    ensemble, you must set tauThermostat.\n");
1349	+	painCave.isFatal = 1;
1350	+	simError();
1351	+	}
1352	+
1353	+	if( globals->haveTauBarostat() )
1354	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1355	+	else{
1356	+	sprintf( painCave.errMsg,
1357	+	"SimSetup error: If you use an NPT\n"
1358	+	"    ensemble, you must set tauBarostat.\n");
1359	+	painCave.isFatal = 1;
1360	+	simError();
1361	+	}
1362	+	break;
1363	+
1364	+	case NPTf_ENS:
1365	+	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1366	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1367	+
1368	+	if (globals->haveTargetPressure())
1369	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1370	+	else {
1371	+	sprintf( painCave.errMsg,
1372	+	"SimSetup error: If you use a constant pressure\n"
1373	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1374	+	painCave.isFatal = 1;
1375	+	simError();
1376	+	}
1377	+
1378	+	if( globals->haveTauThermostat() )
1379	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1380	+	else{
1381	+	sprintf( painCave.errMsg,
1382	+	"SimSetup error: If you use an NPT\n"
1383	+	"    ensemble, you must set tauThermostat.\n");
1384	+	painCave.isFatal = 1;
1385	+	simError();
1386	+	}
1387	+
1388	+	if( globals->haveTauBarostat() )
1389	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1390	+	else{
1391	+	sprintf( painCave.errMsg,
1392	+	"SimSetup error: If you use an NPT\n"
1393	+	"    ensemble, you must set tauBarostat.\n");
1394	+	painCave.isFatal = 1;
1395	+	simError();
1396	+	}
1397	+	break;
1398	+
1399	+	case NPTim_ENS:
1400	+	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1401	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1402	+
1403	+	if (globals->haveTargetPressure())
1404	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1405	+	else {
1406	+	sprintf( painCave.errMsg,
1407	+	"SimSetup error: If you use a constant pressure\n"
1408	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1409	+	painCave.isFatal = 1;
1410	+	simError();
1411	+	}
1412	+
1413	+	if( globals->haveTauThermostat() )
1414	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1415	+	else{
1416	+	sprintf( painCave.errMsg,
1417	+	"SimSetup error: If you use an NPT\n"
1418	+	"    ensemble, you must set tauThermostat.\n");
1419	+	painCave.isFatal = 1;
1420	+	simError();
1421	+	}
1422	+
1423	+	if( globals->haveTauBarostat() )
1424	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1425	+	else{
1426	+	sprintf( painCave.errMsg,
1427	+	"SimSetup error: If you use an NPT\n"
1428	+	"    ensemble, you must set tauBarostat.\n");
1429	+	painCave.isFatal = 1;
1430	+	simError();
1431	+	}
1432	+	break;
1433	+
1434	+	case NPTfm_ENS:
1435	+	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1436	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1437	+
1438	+	if (globals->haveTargetPressure())
1439	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1440	+	else {
1441	+	sprintf( painCave.errMsg,
1442	+	"SimSetup error: If you use a constant pressure\n"
1443	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1444	+	painCave.isFatal = 1;
1445	+	simError();
1446	+	}
1447	+
1448	+	if( globals->haveTauThermostat() )
1449	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1450	+	else{
1451	+	sprintf( painCave.errMsg,
1452	+	"SimSetup error: If you use an NPT\n"
1453	+	"    ensemble, you must set tauThermostat.\n");
1454	+	painCave.isFatal = 1;
1455	+	simError();
1456	+	}
1457	+
1458	+	if( globals->haveTauBarostat() )
1459	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1460	+	else{
1461	+	sprintf( painCave.errMsg,
1462	+	"SimSetup error: If you use an NPT\n"
1463	+	"    ensemble, you must set tauBarostat.\n");
1464	+	painCave.isFatal = 1;
1465	+	simError();
1466	+	}
1467	+	break;
1468	+
1469	+	default:
1470	+	sprintf( painCave.errMsg,
1471	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1472	+	painCave.isFatal = 1;
1473	+	simError();
1474	+	}
1475	+
1476	+	}
1477	+
1478	+	void SimSetup::initFortran( void ){
1479	+
1480	+	info->refreshSim();
1481	+
1482	+	if( !strcmp( info->mixingRule, "standard") ){
1483	+	the_ff->initForceField( LB_MIXING_RULE );
1484	+	}
1485	+	else if( !strcmp( info->mixingRule, "explicit") ){
1486	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1487	+	}
1488	+	else{
1489	+	sprintf( painCave.errMsg,
1490	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1491	+	info->mixingRule );
1492	+	painCave.isFatal = 1;
1493	+	simError();
1494	+	}
1495	+
1496	+
1497	+	#ifdef IS_MPI
1498	+	strcpy( checkPointMsg,
1499	+	"Successfully intialized the mixingRule for Fortran." );
1500	+	MPIcheckPoint();
1501	+	#endif // is_mpi
1502	+
1503	+	}

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