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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC vs.
Revision 644 by mmeineke, Tue Jul 22 16:41:08 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	+
28	+
29		SimSetup::SimSetup(){
30		stamps = new MakeStamps();
31		globals = new Globals();
#	Line 64 | Line 78 | void SimSetup::createSim( void ){
78
79		void SimSetup::createSim( void ){
80
81	<	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	<
81	>	int i, j, k, globalAtomIndex;
82
83	<
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();
83	>	// gather all of the information from the Bass file
84
85	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
85	>	gatherInfo();
86
87	<	id = the_components[i]->getType();
179	<	comp_stamps[i] = NULL;
180	<
181	<	// check to make sure the component isn't already in the list
87	>	// creation of complex system objects
88
89	<	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	<	}
89	>	sysObjectsCreation();
90
91	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
91	>	// check on the post processing info
92
93	+	finalInfoCheck();
94
95	+	// initialize the system coordinates
96
97	<
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	<
97	>	initSystemCoords();
98
235	–	#ifdef IS_MPI
99
100	<	// divide the molecules among processors here.
238	<
239	<	mpiSim = new mpiSimulation( simnfo );
240	<
241	<
100	>	// make the output filenames
101
102	<	globalIndex = mpiSim->divideLabor();
103	<
104	<
246	<
247	<	// set up the local variables
102	>	makeOutNames();
103	>
104	>	// make the integrator
105
106	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
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	<
106	>	makeIntegrator();
107
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	–
108		#ifdef IS_MPI
109	<	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 );
109	>	mpiSim->mpiRefresh();
110		#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
111
112	<	delete fileInit;
497	<	}
498	<	else{
112	>	// initialize the Fortran
113
114	<	#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	<	}
114	>	initFortran();
115
624	–	if( the_globals->haveStatusTime() ){
625	–	simnfo->statusTime = the_globals->getStatusTime();
626	–	}
116
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
117
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
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 683 | Line 129 | void SimSetup::makeMolecules( void ){
129		BondStamp* currentBond;
130		BendStamp* currentBend;
131		TorsionStamp* currentTorsion;
132	+
133	+	bond_pair* theBonds;
134	+	bend_set* theBends;
135	+	torsion_set* theTorsions;
136	+
137
138		//init the forceField paramters
139
140		the_ff->readParams();
141
142
143	<	// init the molecules
143	>	// init the atoms
144
145	+	double ux, uy, uz, u, uSqr;
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 Torsions*[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 = theComponents[stampID]->getAtom( j );
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 740 | 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;
212		theBonds[j].b = currentBond->getB() + atomOffset;
213
214	<	exI = theBonds[i].a;
215	<	exJ = theBonds[i].b;
214	>	exI = theBonds[j].a;
215	>	exJ = theBonds[j].b;
216
217		// exclude_I must always be the smaller of the pair
218		if( exI > exJ ){
#	Line 775 | Line 228 | void SimSetup::makeMolecules( void ){
228
229		the_excludes[j+excludeOffset]->setPair( exI, exJ );
230		#else  // isn't MPI
231	+
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 790 | Line 244 | void SimSetup::makeMolecules( void ){
244
245		if( currentBend->haveExtras() ){
246
247	<	extras = current_bend->getExtras();
247	>	extras = currentBend->getExtras();
248		current_extra = extras;
249
250		while( current_extra != NULL ){
#	Line 812 | Line 266 | void SimSetup::makeMolecules( void ){
266
267		default:
268		sprintf( painCave.errMsg,
269	<	"SimSetup Error: ghostVectorSource was neiter a "
269	>	"SimSetup Error: ghostVectorSource was neither a "
270		"double nor an int.\n"
271		"-->Bend[%d] in %s\n",
272		j, comp_stamps[stampID]->getID() );
#	Line 864 | 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 894 | 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( 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	<
904	<
905	<
906	<	void SimSetup::makeAtoms( void ){
907	<
908	<	int i, j, k, index;
909	<	double ux, uy, uz, uSqr, u;
910	<	AtomStamp* current_atom;
911	<
912	<	DirectionalAtom* dAtom;
913	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
914	<
915	<	lMolIndex = 0;
916	<	molIndex = 0;
917	<	index = 0;
918	<	for( i=0; i<n_components; i++ ){
919	<
920	<	for( j=0; j<components_nmol[i]; j++ ){
921	<
922	<	#ifdef IS_MPI
923	<	if( mpiSim->getMyMolStart() <= molIndex &&
924	<	molIndex <= mpiSim->getMyMolEnd() ){
925	<	#endif // is_mpi
926	<
927	<	molStart = index;
928	<	nMemb = comp_stamps[i]->getNAtoms();
929	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
930	<
931	<	current_atom = comp_stamps[i]->getAtom( k );
932	<	if( current_atom->haveOrientation() ){
933	<
934	<	dAtom = new DirectionalAtom(index);
935	<	simnfo->n_oriented++;
936	<	the_atoms[index] = dAtom;
937	<
938	<	ux = current_atom->getOrntX();
939	<	uy = current_atom->getOrntY();
940	<	uz = current_atom->getOrntZ();
941	<
942	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
943	<
944	<	u = sqrt( uSqr );
945	<	ux = ux / u;
946	<	uy = uy / u;
947	<	uz = uz / u;
948	<
949	<	dAtom->setSUx( ux );
950	<	dAtom->setSUy( uy );
951	<	dAtom->setSUz( uz );
952	<	}
953	<	else{
954	<	the_atoms[index] = new GeneralAtom(index);
955	<	}
956	<	the_atoms[index]->setType( current_atom->getType() );
957	<	the_atoms[index]->setIndex( index );
958	<
959	<	// increment the index and repeat;
960	<	index++;
961	<	}
962	<
963	<	molEnd = index -1;
964	<	the_molecules[lMolIndex].setNMembers( nMemb );
965	<	the_molecules[lMolIndex].setStartAtom( molStart );
966	<	the_molecules[lMolIndex].setEndAtom( molEnd );
967	<	the_molecules[lMolIndex].setStampID( i );
968	<	lMolIndex++;
362	>	the_molecules[i].initialize( molInfo );
363
970	–	#ifdef IS_MPI
971	–	}
972	–	#endif //is_mpi
973	–
974	–	molIndex++;
975	–	}
976	–	}
364
365	<	#ifdef IS_MPI
366	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
367	<
368	<	delete[] globalIndex;
982	<
983	<	mpiSim->mpiRefresh();
984	<	#endif //IS_MPI
985	<
986	<	the_ff->initializeAtoms();
987	<	}
988	<
989	<	void SimSetup::makeBonds( void ){
990	<
991	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
992	<	bond_pair* the_bonds;
993	<	BondStamp* current_bond;
994	<
995	<	the_bonds = new bond_pair[tot_bonds];
996	<	index = 0;
997	<	offset = 0;
998	<	molIndex = 0;
999	<
1000	<	for( i=0; i<n_components; i++ ){
1001	<
1002	<	for( j=0; j<components_nmol[i]; j++ ){
1003	<
1004	<	#ifdef IS_MPI
1005	<	if( mpiSim->getMyMolStart() <= molIndex &&
1006	<	molIndex <= mpiSim->getMyMolEnd() ){
1007	<	#endif // is_mpi
1008	<
1009	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1010	<
1011	<	current_bond = comp_stamps[i]->getBond( k );
1012	<	the_bonds[index].a = current_bond->getA() + offset;
1013	<	the_bonds[index].b = current_bond->getB() + offset;
1014	<
1015	<	exI = the_bonds[index].a;
1016	<	exJ = the_bonds[index].b;
1017	<
1018	<	// exclude_I must always be the smaller of the pair
1019	<	if( exI > exJ ){
1020	<	tempEx = exI;
1021	<	exI = exJ;
1022	<	exJ = tempEx;
1023	<	}
1024	<
1025	<
1026	<	#ifdef IS_MPI
1027	<
1028	<	the_excludes[index*2] =
1029	<	the_atoms[exI]->getGlobalIndex() + 1;
1030	<	the_excludes[index*2 + 1] =
1031	<	the_atoms[exJ]->getGlobalIndex() + 1;
1032	<
1033	<	#else  // isn't MPI
1034	<
1035	<	the_excludes[index*2] =     exI + 1;
1036	<	the_excludes[index*2 + 1] = exJ + 1;
1037	<	// fortran index from 1 (hence the +1 in the indexing)
1038	<	#endif  //is_mpi
1039	<
1040	<	// increment the index and repeat;
1041	<	index++;
1042	<	}
1043	<	offset += comp_stamps[i]->getNAtoms();
1044	<
1045	<	#ifdef IS_MPI
1046	<	}
1047	<	#endif //is_mpi
1048	<
1049	<	molIndex++;
1050	<	}
365	>	atomOffset += molInfo.nAtoms;
366	>	delete[] theBonds;
367	>	delete[] theBends;
368	>	delete[] theTorsions;
369		}
370
1053	–	the_ff->initializeBonds( the_bonds );
1054	–	}
1055	–
1056	–	void SimSetup::makeBends( void ){
1057	–
1058	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1059	–	bend_set* the_bends;
1060	–	BendStamp* current_bend;
1061	–	LinkedAssign* extras;
1062	–	LinkedAssign* current_extra;
1063	–
1064	–
1065	–	the_bends = new bend_set[tot_bends];
1066	–	index = 0;
1067	–	offset = 0;
1068	–	molIndex = 0;
1069	–	for( i=0; i<n_components; i++ ){
1070	–
1071	–	for( j=0; j<components_nmol[i]; j++ ){
1072	–
371		#ifdef IS_MPI
372	<	if( mpiSim->getMyMolStart() <= molIndex &&
1075	<	molIndex <= mpiSim->getMyMolEnd() ){
1076	<	#endif // is_mpi
1077	<
1078	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1079	<
1080	<	current_bend = comp_stamps[i]->getBend( k );
1081	<	the_bends[index].a = current_bend->getA() + offset;
1082	<	the_bends[index].b = current_bend->getB() + offset;
1083	<	the_bends[index].c = current_bend->getC() + offset;
1084	<
1085	<	if( current_bend->haveExtras() ){
1086	<
1087	<	extras = current_bend->getExtras();
1088	<	current_extra = extras;
1089	<
1090	<	while( current_extra != NULL ){
1091	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092	<
1093	<	switch( current_extra->getType() ){
1094	<
1095	<	case 0:
1096	<	the_bends[index].ghost =
1097	<	current_extra->getInt() + offset;
1098	<	the_bends[index].isGhost = 1;
1099	<	break;
1100	<
1101	<	case 1:
1102	<	the_bends[index].ghost =
1103	<	(int)current_extra->getDouble() + offset;
1104	<	the_bends[index].isGhost = 1;
1105	<	break;
1106	<
1107	<	default:
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup Error: ghostVectorSource was neiter a "
1110	<	"double nor an int.\n"
1111	<	"-->Bend[%d] in %s\n",
1112	<	k, comp_stamps[i]->getID() );
1113	<	painCave.isFatal = 1;
1114	<	simError();
1115	<	}
1116	<	}
1117	<
1118	<	else{
1119	<
1120	<	sprintf( painCave.errMsg,
1121	<	"SimSetup Error: unhandled bend assignment:\n"
1122	<	"    -->%s in Bend[%d] in %s\n",
1123	<	current_extra->getlhs(),
1124	<	k, comp_stamps[i]->getID() );
1125	<	painCave.isFatal = 1;
1126	<	simError();
1127	<	}
1128	<
1129	<	current_extra = current_extra->getNext();
1130	<	}
1131	<	}
1132	<
1133	<	if( !the_bends[index].isGhost ){
1134	<
1135	<	exI = the_bends[index].a;
1136	<	exJ = the_bends[index].c;
1137	<	}
1138	<	else{
1139	<
1140	<	exI = the_bends[index].a;
1141	<	exJ = the_bends[index].b;
1142	<	}
1143	<
1144	<	// exclude_I must always be the smaller of the pair
1145	<	if( exI > exJ ){
1146	<	tempEx = exI;
1147	<	exI = exJ;
1148	<	exJ = tempEx;
1149	<	}
1150	<
1151	<
1152	<	#ifdef IS_MPI
1153	<
1154	<	the_excludes[(index + tot_bonds)*2] =
1155	<	the_atoms[exI]->getGlobalIndex() + 1;
1156	<	the_excludes[(index + tot_bonds)*2 + 1] =
1157	<	the_atoms[exJ]->getGlobalIndex() + 1;
1158	<
1159	<	#else  // isn't MPI
1160	<
1161	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1162	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1163	<	// fortran index from 1 (hence the +1 in the indexing)
1164	<	#endif  //is_mpi
1165	<
1166	<
1167	<	// increment the index and repeat;
1168	<	index++;
1169	<	}
1170	<	offset += comp_stamps[i]->getNAtoms();
1171	<
1172	<	#ifdef IS_MPI
1173	<	}
1174	<	#endif //is_mpi
1175	<
1176	<	molIndex++;
1177	<	}
1178	<	}
1179	<
1180	<	#ifdef IS_MPI
1181	<	sprintf( checkPointMsg,
1182	<	"Successfully created the bends list.\n" );
372	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
373		MPIcheckPoint();
374		#endif // is_mpi
1185	–
375
376	<	the_ff->initializeBends( the_bends );
377	<	}
378	<
1190	<	void SimSetup::makeTorsions( void ){
1191	<
1192	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1193	<	torsion_set* the_torsions;
1194	<	TorsionStamp* current_torsion;
1195	<
1196	<	the_torsions = new torsion_set[tot_torsions];
1197	<	index = 0;
1198	<	offset = 0;
1199	<	molIndex = 0;
1200	<	for( i=0; i<n_components; i++ ){
1201	<
1202	<	for( j=0; j<components_nmol[i]; j++ ){
1203	<
1204	<	#ifdef IS_MPI
1205	<	if( mpiSim->getMyMolStart() <= molIndex &&
1206	<	molIndex <= mpiSim->getMyMolEnd() ){
1207	<	#endif // is_mpi
376	>	// clean up the forcefield
377	>	the_ff->calcRcut();
378	>	the_ff->cleanMe();
379
1209	–	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1210	–
1211	–	current_torsion = comp_stamps[i]->getTorsion( k );
1212	–	the_torsions[index].a = current_torsion->getA() + offset;
1213	–	the_torsions[index].b = current_torsion->getB() + offset;
1214	–	the_torsions[index].c = current_torsion->getC() + offset;
1215	–	the_torsions[index].d = current_torsion->getD() + offset;
1216	–
1217	–	exI = the_torsions[index].a;
1218	–	exJ = the_torsions[index].d;
1219	–
1220	–
1221	–	// exclude_I must always be the smaller of the pair
1222	–	if( exI > exJ ){
1223	–	tempEx = exI;
1224	–	exI = exJ;
1225	–	exJ = tempEx;
1226	–	}
1227	–
1228	–
1229	–	#ifdef IS_MPI
1230	–
1231	–	the_excludes[(index + tot_bonds + tot_bends)*2] =
1232	–	the_atoms[exI]->getGlobalIndex() + 1;
1233	–	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1234	–	the_atoms[exJ]->getGlobalIndex() + 1;
1235	–
1236	–	#else  // isn't MPI
1237	–
1238	–	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1239	–	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1240	–	// fortran indexes from 1 (hence the +1 in the indexing)
1241	–	#endif  //is_mpi
1242	–
1243	–
1244	–	// increment the index and repeat;
1245	–	index++;
1246	–	}
1247	–	offset += comp_stamps[i]->getNAtoms();
1248	–
1249	–	#ifdef IS_MPI
1250	–	}
1251	–	#endif //is_mpi
1252	–
1253	–	molIndex++;
1254	–	}
1255	–	}
1256	–
1257	–	the_ff->initializeTorsions( the_torsions );
380		}
381
382		void SimSetup::initFromBass( void ){
#	Line 1276 | Line 398 | void SimSetup::initFromBass( void ){
398		have_extra =1;
399
400		n_cells = (int)temp3 - 1;
401	<	cellx = simnfo->box_x / temp3;
402	<	celly = simnfo->box_y / temp3;
403	<	cellz = simnfo->box_z / 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 1293 | Line 415 | void SimSetup::initFromBass( void ){
415		}
416		else{
417		n_cells = (int)temp3;
418	<	cellx = simnfo->box_x / temp3;
419	<	celly = simnfo->box_y / temp3;
420	<	cellz = simnfo->box_z / 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 1375 | 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 1437 | Line 559 | void SimSetup::makeElement( double x, double y, double
559
560		current_comp_mol = 0;
561		current_comp++;
562	+	}
563	+	}
564	+
565	+
566	+	void SimSetup::gatherInfo( void ){
567	+	int i,j,k;
568	+
569	+	ensembleCase = -1;
570	+	ffCase = -1;
571	+
572	+	// get the stamps and globals;
573	+	stamps = stamps;
574	+	globals = globals;
575	+
576	+	// set the easy ones first
577	+	info->target_temp = globals->getTargetTemp();
578	+	info->dt = globals->getDt();
579	+	info->run_time = globals->getRunTime();
580	+	n_components = globals->getNComponents();
581	+
582	+
583	+	// get the forceField
584	+
585	+	strcpy( force_field, globals->getForceField() );
586	+
587	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
588	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
589	+	else{
590	+	sprintf( painCave.errMsg,
591	+	"SimSetup Error. Unrecognized force field -> %s\n",
592	+	force_field );
593	+	painCave.isFatal = 1;
594	+	simError();
595	+	}
596	+
597	+	// get the ensemble
598	+
599	+	strcpy( ensemble, globals->getEnsemble() );
600	+
601	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
602	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
603	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
604	+	ensembleCase = NPTi_ENS;
605	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
606	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
607	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
608	+	else{
609	+	sprintf( painCave.errMsg,
610	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
611	+	"reverting to NVE for this simulation.\n",
612	+	ensemble );
613	+	painCave.isFatal = 0;
614	+	simError();
615	+	strcpy( ensemble, "NVE" );
616	+	ensembleCase = NVE_ENS;
617	+	}
618	+	strcpy( info->ensemble, ensemble );
619	+
620	+	// get the mixing rule
621	+
622	+	strcpy( info->mixingRule, globals->getMixingRule() );
623	+	info->usePBC = globals->getPBC();
624	+
625	+
626	+	// get the components and calculate the tot_nMol and indvidual n_mol
627	+
628	+	the_components = globals->getComponents();
629	+	components_nmol = new int[n_components];
630	+
631	+
632	+	if( !globals->haveNMol() ){
633	+	// we don't have the total number of molecules, so we assume it is
634	+	// given in each component
635	+
636	+	tot_nmol = 0;
637	+	for( i=0; i<n_components; i++ ){
638	+
639	+	if( !the_components[i]->haveNMol() ){
640	+	// we have a problem
641	+	sprintf( painCave.errMsg,
642	+	"SimSetup Error. No global NMol or component NMol"
643	+	" given. Cannot calculate the number of atoms.\n" );
644	+	painCave.isFatal = 1;
645	+	simError();
646	+	}
647	+
648	+	tot_nmol += the_components[i]->getNMol();
649	+	components_nmol[i] = the_components[i]->getNMol();
650	+	}
651	+	}
652	+	else{
653	+	sprintf( painCave.errMsg,
654	+	"SimSetup error.\n"
655	+	"\tSorry, the ability to specify total"
656	+	" nMols and then give molfractions in the components\n"
657	+	"\tis not currently supported."
658	+	" Please give nMol in the components.\n" );
659	+	painCave.isFatal = 1;
660	+	simError();
661	+	}
662	+
663	+	// set the status, sample, and thermal kick times
664	+
665	+	if( globals->haveSampleTime() ){
666	+	info->sampleTime = globals->getSampleTime();
667	+	info->statusTime = info->sampleTime;
668	+	info->thermalTime = info->sampleTime;
669	+	}
670	+	else{
671	+	info->sampleTime = globals->getRunTime();
672	+	info->statusTime = info->sampleTime;
673	+	info->thermalTime = info->sampleTime;
674	+	}
675	+
676	+	if( globals->haveStatusTime() ){
677	+	info->statusTime = globals->getStatusTime();
678	+	}
679	+
680	+	if( globals->haveThermalTime() ){
681	+	info->thermalTime = globals->getThermalTime();
682	+	}
683	+
684	+	// check for the temperature set flag
685	+
686	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
687	+
688	+	// get some of the tricky things that may still be in the globals
689	+
690	+	double boxVector[3];
691	+	if( globals->haveBox() ){
692	+	boxVector[0] = globals->getBox();
693	+	boxVector[1] = globals->getBox();
694	+	boxVector[2] = globals->getBox();
695	+
696	+	info->setBox( boxVector );
697	+	}
698	+	else if( globals->haveDensity() ){
699	+
700	+	double vol;
701	+	vol = (double)tot_nmol / globals->getDensity();
702	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
703	+	boxVector[1] = boxVector[0];
704	+	boxVector[2] = boxVector[0];
705	+
706	+	info->setBox( boxVector );
707	+	}
708	+	else{
709	+	if( !globals->haveBoxX() ){
710	+	sprintf( painCave.errMsg,
711	+	"SimSetup error, no periodic BoxX size given.\n" );
712	+	painCave.isFatal = 1;
713	+	simError();
714	+	}
715	+	boxVector[0] = globals->getBoxX();
716	+
717	+	if( !globals->haveBoxY() ){
718	+	sprintf( painCave.errMsg,
719	+	"SimSetup error, no periodic BoxY size given.\n" );
720	+	painCave.isFatal = 1;
721	+	simError();
722	+	}
723	+	boxVector[1] = globals->getBoxY();
724	+
725	+	if( !globals->haveBoxZ() ){
726	+	sprintf( painCave.errMsg,
727	+	"SimSetup error, no periodic BoxZ size given.\n" );
728	+	painCave.isFatal = 1;
729	+	simError();
730	+	}
731	+	boxVector[2] = globals->getBoxZ();
732	+
733	+	info->setBox( boxVector );
734	+	}
735	+
736	+
737	+
738	+	#ifdef IS_MPI
739	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
740	+	MPIcheckPoint();
741	+	#endif // is_mpi
742	+
743	+	}
744	+
745	+
746	+	void SimSetup::finalInfoCheck( void ){
747	+	int index;
748	+	int usesDipoles;
749	+
750	+
751	+	// check electrostatic parameters
752	+
753	+	index = 0;
754	+	usesDipoles = 0;
755	+	while( (index < info->n_atoms) && !usesDipoles ){
756	+	usesDipoles = ((info->atoms)[index])->hasDipole();
757	+	index++;
758	+	}
759	+
760	+	#ifdef IS_MPI
761	+	int myUse = usesDipoles;
762	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
763	+	#endif //is_mpi
764	+
765	+	double theEcr, theEst;
766	+
767	+	if (globals->getUseRF() ) {
768	+	info->useReactionField = 1;
769	+
770	+	if( !globals->haveECR() ){
771	+	sprintf( painCave.errMsg,
772	+	"SimSetup Warning: using default value of 1/2 the smallest "
773	+	"box length for the electrostaticCutoffRadius.\n"
774	+	"I hope you have a very fast processor!\n");
775	+	painCave.isFatal = 0;
776	+	simError();
777	+	double smallest;
778	+	smallest = info->boxL[0];
779	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
780	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
781	+	theEcr = 0.5 * smallest;
782	+	} else {
783	+	theEcr = globals->getECR();
784	+	}
785	+
786	+	if( !globals->haveEST() ){
787	+	sprintf( painCave.errMsg,
788	+	"SimSetup Warning: using default value of 0.05 * the "
789	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
790	+	);
791	+	painCave.isFatal = 0;
792	+	simError();
793	+	theEst = 0.05 * theEcr;
794	+	} else {
795	+	theEst= globals->getEST();
796	+	}
797	+
798	+	info->setEcr( theEcr, theEst );
799	+
800	+	if(!globals->haveDielectric() ){
801	+	sprintf( painCave.errMsg,
802	+	"SimSetup Error: You are trying to use Reaction Field without"
803	+	"setting a dielectric constant!\n"
804	+	);
805	+	painCave.isFatal = 1;
806	+	simError();
807	+	}
808	+	info->dielectric = globals->getDielectric();
809	+	}
810	+	else {
811	+	if (usesDipoles) {
812	+
813	+	if( !globals->haveECR() ){
814	+	sprintf( painCave.errMsg,
815	+	"SimSetup Warning: using default value of 1/2 the smallest "
816	+	"box length for the electrostaticCutoffRadius.\n"
817	+	"I hope you have a very fast processor!\n");
818	+	painCave.isFatal = 0;
819	+	simError();
820	+	double smallest;
821	+	smallest = info->boxL[0];
822	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
823	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
824	+	theEcr = 0.5 * smallest;
825	+	} else {
826	+	theEcr = globals->getECR();
827	+	}
828	+
829	+	if( !globals->haveEST() ){
830	+	sprintf( painCave.errMsg,
831	+	"SimSetup Warning: using default value of 0.05 * the "
832	+	"electrostaticCutoffRadius for the "
833	+	"electrostaticSkinThickness\n"
834	+	);
835	+	painCave.isFatal = 0;
836	+	simError();
837	+	theEst = 0.05 * theEcr;
838	+	} else {
839	+	theEst= globals->getEST();
840	+	}
841	+
842	+	info->setEcr( theEcr, theEst );
843	+	}
844	+	}
845	+
846	+	#ifdef IS_MPI
847	+	strcpy( checkPointMsg, "post processing checks out" );
848	+	MPIcheckPoint();
849	+	#endif // is_mpi
850	+
851	+	}
852	+
853	+	void SimSetup::initSystemCoords( void ){
854	+
855	+	if( globals->haveInitialConfig() ){
856	+
857	+	InitializeFromFile* fileInit;
858	+	#ifdef IS_MPI // is_mpi
859	+	if( worldRank == 0 ){
860	+	#endif //is_mpi
861	+	fileInit = new InitializeFromFile( globals->getInitialConfig() );
862	+	#ifdef IS_MPI
863	+	}else fileInit = new InitializeFromFile( NULL );
864	+	#endif
865	+	fileInit->readInit( info ); // default velocities on
866	+
867	+	delete fileInit;
868	+	}
869	+	else{
870	+
871	+	#ifdef IS_MPI
872	+
873	+	// no init from bass
874	+
875	+	sprintf( painCave.errMsg,
876	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
877	+	painCave.isFatal;
878	+	simError();
879	+
880	+	#else
881	+
882	+	initFromBass();
883	+
884	+
885	+	#endif
886	+	}
887	+
888	+	#ifdef IS_MPI
889	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
890	+	MPIcheckPoint();
891	+	#endif // is_mpi
892	+
893	+	}
894	+
895	+
896	+	void SimSetup::makeOutNames( void ){
897	+
898	+	#ifdef IS_MPI
899	+	if( worldRank == 0 ){
900	+	#endif // is_mpi
901	+
902	+	if( globals->haveFinalConfig() ){
903	+	strcpy( info->finalName, globals->getFinalConfig() );
904	+	}
905	+	else{
906	+	strcpy( info->finalName, inFileName );
907	+	char* endTest;
908	+	int nameLength = strlen( info->finalName );
909	+	endTest = &(info->finalName[nameLength - 5]);
910	+	if( !strcmp( endTest, ".bass" ) ){
911	+	strcpy( endTest, ".eor" );
912	+	}
913	+	else if( !strcmp( endTest, ".BASS" ) ){
914	+	strcpy( endTest, ".eor" );
915	+	}
916	+	else{
917	+	endTest = &(info->finalName[nameLength - 4]);
918	+	if( !strcmp( endTest, ".bss" ) ){
919	+	strcpy( endTest, ".eor" );
920	+	}
921	+	else if( !strcmp( endTest, ".mdl" ) ){
922	+	strcpy( endTest, ".eor" );
923	+	}
924	+	else{
925	+	strcat( info->finalName, ".eor" );
926	+	}
927	+	}
928	+	}
929	+
930	+	// make the sample and status out names
931	+
932	+	strcpy( info->sampleName, inFileName );
933	+	char* endTest;
934	+	int nameLength = strlen( info->sampleName );
935	+	endTest = &(info->sampleName[nameLength - 5]);
936	+	if( !strcmp( endTest, ".bass" ) ){
937	+	strcpy( endTest, ".dump" );
938	+	}
939	+	else if( !strcmp( endTest, ".BASS" ) ){
940	+	strcpy( endTest, ".dump" );
941	+	}
942	+	else{
943	+	endTest = &(info->sampleName[nameLength - 4]);
944	+	if( !strcmp( endTest, ".bss" ) ){
945	+	strcpy( endTest, ".dump" );
946	+	}
947	+	else if( !strcmp( endTest, ".mdl" ) ){
948	+	strcpy( endTest, ".dump" );
949	+	}
950	+	else{
951	+	strcat( info->sampleName, ".dump" );
952	+	}
953	+	}
954	+
955	+	strcpy( info->statusName, inFileName );
956	+	nameLength = strlen( info->statusName );
957	+	endTest = &(info->statusName[nameLength - 5]);
958	+	if( !strcmp( endTest, ".bass" ) ){
959	+	strcpy( endTest, ".stat" );
960	+	}
961	+	else if( !strcmp( endTest, ".BASS" ) ){
962	+	strcpy( endTest, ".stat" );
963	+	}
964	+	else{
965	+	endTest = &(info->statusName[nameLength - 4]);
966	+	if( !strcmp( endTest, ".bss" ) ){
967	+	strcpy( endTest, ".stat" );
968	+	}
969	+	else if( !strcmp( endTest, ".mdl" ) ){
970	+	strcpy( endTest, ".stat" );
971	+	}
972	+	else{
973	+	strcat( info->statusName, ".stat" );
974	+	}
975	+	}
976	+
977	+	#ifdef IS_MPI
978	+	}
979	+	#endif // is_mpi
980	+
981	+	}
982	+
983	+
984	+	void SimSetup::sysObjectsCreation( void ){
985	+
986	+	int i;
987	+
988	+	// create the forceField
989	+
990	+	createFF();
991	+
992	+	// extract componentList
993	+
994	+	compList();
995	+
996	+	// calc the number of atoms, bond, bends, and torsions
997	+
998	+	calcSysValues();
999	+
1000	+	#ifdef IS_MPI
1001	+	// divide the molecules among the processors
1002	+
1003	+	mpiMolDivide();
1004	+	#endif //is_mpi
1005	+
1006	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1007	+
1008	+	makeSysArrays();
1009	+
1010	+	// make and initialize the molecules (all but atomic coordinates)
1011	+
1012	+	makeMolecules();
1013	+	info->identArray = new int[info->n_atoms];
1014	+	for(i=0; i<info->n_atoms; i++){
1015	+	info->identArray[i] = the_atoms[i]->getIdent();
1016		}
1017	+
1018	+
1019	+
1020		}
1021	+
1022	+
1023	+	void SimSetup::createFF( void ){
1024	+
1025	+	switch( ffCase ){
1026	+
1027	+	case FF_DUFF:
1028	+	the_ff = new DUFF();
1029	+	break;
1030	+
1031	+	case FF_LJ:
1032	+	the_ff = new LJFF();
1033	+	break;
1034	+
1035	+	default:
1036	+	sprintf( painCave.errMsg,
1037	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1038	+	painCave.isFatal = 1;
1039	+	simError();
1040	+	}
1041	+
1042	+	#ifdef IS_MPI
1043	+	strcpy( checkPointMsg, "ForceField creation successful" );
1044	+	MPIcheckPoint();
1045	+	#endif // is_mpi
1046	+
1047	+	}
1048	+
1049	+
1050	+	void SimSetup::compList( void ){
1051	+
1052	+	int i;
1053	+
1054	+	comp_stamps = new MoleculeStamp*[n_components];
1055	+
1056	+	// make an array of molecule stamps that match the components used.
1057	+	// also extract the used stamps out into a separate linked list
1058	+
1059	+	info->nComponents = n_components;
1060	+	info->componentsNmol = components_nmol;
1061	+	info->compStamps = comp_stamps;
1062	+	info->headStamp = new LinkedMolStamp();
1063	+
1064	+	char* id;
1065	+	LinkedMolStamp* headStamp = info->headStamp;
1066	+	LinkedMolStamp* currentStamp = NULL;
1067	+	for( i=0; i<n_components; i++ ){
1068	+
1069	+	id = the_components[i]->getType();
1070	+	comp_stamps[i] = NULL;
1071	+
1072	+	// check to make sure the component isn't already in the list
1073	+
1074	+	comp_stamps[i] = headStamp->match( id );
1075	+	if( comp_stamps[i] == NULL ){
1076	+
1077	+	// extract the component from the list;
1078	+
1079	+	currentStamp = stamps->extractMolStamp( id );
1080	+	if( currentStamp == NULL ){
1081	+	sprintf( painCave.errMsg,
1082	+	"SimSetup error: Component \"%s\" was not found in the "
1083	+	"list of declared molecules\n",
1084	+	id );
1085	+	painCave.isFatal = 1;
1086	+	simError();
1087	+	}
1088	+
1089	+	headStamp->add( currentStamp );
1090	+	comp_stamps[i] = headStamp->match( id );
1091	+	}
1092	+	}
1093	+
1094	+	#ifdef IS_MPI
1095	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1096	+	MPIcheckPoint();
1097	+	#endif // is_mpi
1098	+
1099	+
1100	+	}
1101	+
1102	+	void SimSetup::calcSysValues( void ){
1103	+	int i, j, k;
1104	+
1105	+
1106	+	tot_atoms = 0;
1107	+	tot_bonds = 0;
1108	+	tot_bends = 0;
1109	+	tot_torsions = 0;
1110	+	for( i=0; i<n_components; i++ ){
1111	+
1112	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1113	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1114	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1115	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1116	+	}
1117	+
1118	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1119	+
1120	+	info->n_atoms = tot_atoms;
1121	+	info->n_bonds = tot_bonds;
1122	+	info->n_bends = tot_bends;
1123	+	info->n_torsions = tot_torsions;
1124	+	info->n_SRI = tot_SRI;
1125	+	info->n_mol = tot_nmol;
1126	+
1127	+	info->molMembershipArray = new int[tot_atoms];
1128	+	}
1129	+
1130	+
1131	+	#ifdef IS_MPI
1132	+
1133	+	void SimSetup::mpiMolDivide( void ){
1134	+
1135	+	int i, j, k;
1136	+	int localMol, allMol;
1137	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1138	+
1139	+	mpiSim = new mpiSimulation( info );
1140	+
1141	+	globalIndex = mpiSim->divideLabor();
1142	+
1143	+	// set up the local variables
1144	+
1145	+	mol2proc = mpiSim->getMolToProcMap();
1146	+	molCompType = mpiSim->getMolComponentType();
1147	+
1148	+	allMol = 0;
1149	+	localMol = 0;
1150	+	local_atoms = 0;
1151	+	local_bonds = 0;
1152	+	local_bends = 0;
1153	+	local_torsions = 0;
1154	+	globalAtomIndex = 0;
1155	+
1156	+
1157	+	for( i=0; i<n_components; i++ ){
1158	+
1159	+	for( j=0; j<components_nmol[i]; j++ ){
1160	+
1161	+	if( mol2proc[allMol] == worldRank ){
1162	+
1163	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1164	+	local_bonds +=    comp_stamps[i]->getNBonds();
1165	+	local_bends +=    comp_stamps[i]->getNBends();
1166	+	local_torsions += comp_stamps[i]->getNTorsions();
1167	+	localMol++;
1168	+	}
1169	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1170	+	info->molMembershipArray[globalAtomIndex] = allMol;
1171	+	globalAtomIndex++;
1172	+	}
1173	+
1174	+	allMol++;
1175	+	}
1176	+	}
1177	+	local_SRI = local_bonds + local_bends + local_torsions;
1178	+
1179	+	info->n_atoms = mpiSim->getMyNlocal();
1180	+
1181	+	if( local_atoms != info->n_atoms ){
1182	+	sprintf( painCave.errMsg,
1183	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1184	+	" localAtom (%d) are not equal.\n",
1185	+	info->n_atoms,
1186	+	local_atoms );
1187	+	painCave.isFatal = 1;
1188	+	simError();
1189	+	}
1190	+
1191	+	info->n_bonds = local_bonds;
1192	+	info->n_bends = local_bends;
1193	+	info->n_torsions = local_torsions;
1194	+	info->n_SRI = local_SRI;
1195	+	info->n_mol = localMol;
1196	+
1197	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1198	+	MPIcheckPoint();
1199	+	}
1200	+
1201	+	#endif // is_mpi
1202	+
1203	+
1204	+	void SimSetup::makeSysArrays( void ){
1205	+	int i, j, k;
1206	+
1207	+
1208	+	// create the atom and short range interaction arrays
1209	+
1210	+	Atom::createArrays(info->n_atoms);
1211	+	the_atoms = new Atom*[info->n_atoms];
1212	+	the_molecules = new Molecule[info->n_mol];
1213	+	int molIndex;
1214	+
1215	+	// initialize the molecule's stampID's
1216	+
1217	+	#ifdef IS_MPI
1218	+
1219	+
1220	+	molIndex = 0;
1221	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1222	+
1223	+	if(mol2proc[i] == worldRank ){
1224	+	the_molecules[molIndex].setStampID( molCompType[i] );
1225	+	the_molecules[molIndex].setMyIndex( molIndex );
1226	+	the_molecules[molIndex].setGlobalIndex( i );
1227	+	molIndex++;
1228	+	}
1229	+	}
1230	+
1231	+	#else // is_mpi
1232	+
1233	+	molIndex = 0;
1234	+	globalAtomIndex = 0;
1235	+	for(i=0; i<n_components; i++){
1236	+	for(j=0; j<components_nmol[i]; j++ ){
1237	+	the_molecules[molIndex].setStampID( i );
1238	+	the_molecules[molIndex].setMyIndex( molIndex );
1239	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1240	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1241	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1242	+	globalAtomIndex++;
1243	+	}
1244	+	molIndex++;
1245	+	}
1246	+	}
1247	+
1248	+
1249	+	#endif // is_mpi
1250	+
1251	+
1252	+	if( info->n_SRI ){
1253	+
1254	+	Exclude::createArray(info->n_SRI);
1255	+	the_excludes = new Exclude*[info->n_SRI];
1256	+	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1257	+	info->globalExcludes = new int;
1258	+	info->n_exclude = info->n_SRI;
1259	+	}
1260	+	else{
1261	+
1262	+	Exclude::createArray( 1 );
1263	+	the_excludes = new Exclude*;
1264	+	the_excludes[0] = new Exclude(0);
1265	+	the_excludes[0]->setPair( 0,0 );
1266	+	info->globalExcludes = new int;
1267	+	info->globalExcludes[0] = 0;
1268	+	info->n_exclude = 0;
1269	+	}
1270	+
1271	+	// set the arrays into the SimInfo object
1272	+
1273	+	info->atoms = the_atoms;
1274	+	info->molecules = the_molecules;
1275	+	info->nGlobalExcludes = 0;
1276	+	info->excludes = the_excludes;
1277	+
1278	+	the_ff->setSimInfo( info );
1279	+
1280	+	}
1281	+
1282	+	void SimSetup::makeIntegrator( void ){
1283	+
1284	+	NVT*  myNVT = NULL;
1285	+	NPTi* myNPTi = NULL;
1286	+	NPTf* myNPTf = NULL;
1287	+	NPTim* myNPTim = NULL;
1288	+	NPTfm* myNPTfm = NULL;
1289	+
1290	+	switch( ensembleCase ){
1291	+
1292	+	case NVE_ENS:
1293	+	new NVE( info, the_ff );
1294	+	break;
1295	+
1296	+	case NVT_ENS:
1297	+	myNVT = new NVT( info, the_ff );
1298	+	myNVT->setTargetTemp(globals->getTargetTemp());
1299	+
1300	+	if (globals->haveTauThermostat())
1301	+	myNVT->setTauThermostat(globals->getTauThermostat());
1302	+
1303	+	else {
1304	+	sprintf( painCave.errMsg,
1305	+	"SimSetup error: If you use the NVT\n"
1306	+	"    ensemble, you must set tauThermostat.\n");
1307	+	painCave.isFatal = 1;
1308	+	simError();
1309	+	}
1310	+	break;
1311	+
1312	+	case NPTi_ENS:
1313	+	myNPTi = new NPTi( info, the_ff );
1314	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1315	+
1316	+	if (globals->haveTargetPressure())
1317	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1318	+	else {
1319	+	sprintf( painCave.errMsg,
1320	+	"SimSetup error: If you use a constant pressure\n"
1321	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1322	+	painCave.isFatal = 1;
1323	+	simError();
1324	+	}
1325	+
1326	+	if( globals->haveTauThermostat() )
1327	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1328	+	else{
1329	+	sprintf( painCave.errMsg,
1330	+	"SimSetup error: If you use an NPT\n"
1331	+	"    ensemble, you must set tauThermostat.\n");
1332	+	painCave.isFatal = 1;
1333	+	simError();
1334	+	}
1335	+
1336	+	if( globals->haveTauBarostat() )
1337	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1338	+	else{
1339	+	sprintf( painCave.errMsg,
1340	+	"SimSetup error: If you use an NPT\n"
1341	+	"    ensemble, you must set tauBarostat.\n");
1342	+	painCave.isFatal = 1;
1343	+	simError();
1344	+	}
1345	+	break;
1346	+
1347	+	case NPTf_ENS:
1348	+	myNPTf = new NPTf( info, the_ff );
1349	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1350	+
1351	+	if (globals->haveTargetPressure())
1352	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1353	+	else {
1354	+	sprintf( painCave.errMsg,
1355	+	"SimSetup error: If you use a constant pressure\n"
1356	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1357	+	painCave.isFatal = 1;
1358	+	simError();
1359	+	}
1360	+
1361	+	if( globals->haveTauThermostat() )
1362	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1363	+	else{
1364	+	sprintf( painCave.errMsg,
1365	+	"SimSetup error: If you use an NPT\n"
1366	+	"    ensemble, you must set tauThermostat.\n");
1367	+	painCave.isFatal = 1;
1368	+	simError();
1369	+	}
1370	+
1371	+	if( globals->haveTauBarostat() )
1372	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1373	+	else{
1374	+	sprintf( painCave.errMsg,
1375	+	"SimSetup error: If you use an NPT\n"
1376	+	"    ensemble, you must set tauBarostat.\n");
1377	+	painCave.isFatal = 1;
1378	+	simError();
1379	+	}
1380	+	break;
1381	+
1382	+	case NPTim_ENS:
1383	+	myNPTim = new NPTim( info, the_ff );
1384	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1385	+
1386	+	if (globals->haveTargetPressure())
1387	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1388	+	else {
1389	+	sprintf( painCave.errMsg,
1390	+	"SimSetup error: If you use a constant pressure\n"
1391	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1392	+	painCave.isFatal = 1;
1393	+	simError();
1394	+	}
1395	+
1396	+	if( globals->haveTauThermostat() )
1397	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1398	+	else{
1399	+	sprintf( painCave.errMsg,
1400	+	"SimSetup error: If you use an NPT\n"
1401	+	"    ensemble, you must set tauThermostat.\n");
1402	+	painCave.isFatal = 1;
1403	+	simError();
1404	+	}
1405	+
1406	+	if( globals->haveTauBarostat() )
1407	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1408	+	else{
1409	+	sprintf( painCave.errMsg,
1410	+	"SimSetup error: If you use an NPT\n"
1411	+	"    ensemble, you must set tauBarostat.\n");
1412	+	painCave.isFatal = 1;
1413	+	simError();
1414	+	}
1415	+	break;
1416	+
1417	+	case NPTfm_ENS:
1418	+	myNPTfm = new NPTfm( info, the_ff );
1419	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1420	+
1421	+	if (globals->haveTargetPressure())
1422	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1423	+	else {
1424	+	sprintf( painCave.errMsg,
1425	+	"SimSetup error: If you use a constant pressure\n"
1426	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1427	+	painCave.isFatal = 1;
1428	+	simError();
1429	+	}
1430	+
1431	+	if( globals->haveTauThermostat() )
1432	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1433	+	else{
1434	+	sprintf( painCave.errMsg,
1435	+	"SimSetup error: If you use an NPT\n"
1436	+	"    ensemble, you must set tauThermostat.\n");
1437	+	painCave.isFatal = 1;
1438	+	simError();
1439	+	}
1440	+
1441	+	if( globals->haveTauBarostat() )
1442	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1443	+	else{
1444	+	sprintf( painCave.errMsg,
1445	+	"SimSetup error: If you use an NPT\n"
1446	+	"    ensemble, you must set tauBarostat.\n");
1447	+	painCave.isFatal = 1;
1448	+	simError();
1449	+	}
1450	+	break;
1451	+
1452	+	default:
1453	+	sprintf( painCave.errMsg,
1454	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1455	+	painCave.isFatal = 1;
1456	+	simError();
1457	+	}
1458	+
1459	+	}
1460	+
1461	+	void SimSetup::initFortran( void ){
1462	+
1463	+	info->refreshSim();
1464	+
1465	+	if( !strcmp( info->mixingRule, "standard") ){
1466	+	the_ff->initForceField( LB_MIXING_RULE );
1467	+	}
1468	+	else if( !strcmp( info->mixingRule, "explicit") ){
1469	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1470	+	}
1471	+	else{
1472	+	sprintf( painCave.errMsg,
1473	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1474	+	info->mixingRule );
1475	+	painCave.isFatal = 1;
1476	+	simError();
1477	+	}
1478	+
1479	+
1480	+	#ifdef IS_MPI
1481	+	strcpy( checkPointMsg,
1482	+	"Successfully intialized the mixingRule for Fortran." );
1483	+	MPIcheckPoint();
1484	+	#endif // is_mpi
1485	+
1486	+	}

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