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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 429 by mmeineke, Thu Mar 27 21:52:21 2003 UTC vs.
Revision 653 by chuckv, Fri Jul 25 20:00:17 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		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_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
100	<
101	<	#ifdef IS_MPI
102	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#endif // is_mpi
105	<
81	>	int i, j, k, globalAtomIndex;
82
83	<
108	<	// get the components and calculate the tot_nMol and indvidual n_mol
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
112	<
113	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// given in each component
116	<
117	<	tot_nmol = 0;
118	<	for( i=0; i<n_components; i++ ){
119	<
120	<	if( !the_components[i]->haveNMol() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
128	<
129	<	tot_nmol += the_components[i]->getNMol();
130	<	components_nmol[i] = the_components[i]->getNMol();
131	<	}
132	<	}
133	<	else{
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error.\n"
136	<	"\tSorry, the ability to specify total"
137	<	" nMols and then give molfractions in the components\n"
138	<	"\tis not currently supported."
139	<	" Please give nMol in the components.\n" );
140	<	painCave.isFatal = 1;
141	<	simError();
142	<
143	<
144	<	//     tot_nmol = the_globals->getNMol();
145	<
146	<	//   //we have the total number of molecules, now we check for molfractions
147	<	//     for( i=0; i<n_components; i++ ){
148	<
149	<	//       if( !the_components[i]->haveMolFraction() ){
150	<
151	<	//  if( !the_components[i]->haveNMol() ){
152	<	//    //we have a problem
153	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	<	//              << " nMol was given in component
155	<
156	<	}
157	<
158	<	#ifdef IS_MPI
159	<	strcpy( checkPointMsg, "Have the number of components" );
160	<	MPIcheckPoint();
161	<	#endif // is_mpi
162	<
163	<	// make an array of molecule stamps that match the components used.
164	<	// also extract the used stamps out into a separate linked list
165	<
166	<	simnfo->nComponents = n_components;
167	<	simnfo->componentsNmol = components_nmol;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
83	>	// gather all of the information from the Bass file
84
85	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
85	>	gatherInfo();
86
87	<	id = the_components[i]->getType();
177	<	comp_stamps[i] = NULL;
178	<
179	<	// 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 );
182	<	if( comp_stamps[i] == NULL ){
183	<
184	<	// extract the component from the list;
185	<
186	<	currentStamp = the_stamps->extractMolStamp( id );
187	<	if( currentStamp == NULL ){
188	<	sprintf( painCave.errMsg,
189	<	"SimSetup error: Component \"%s\" was not found in the "
190	<	"list of declared molecules\n",
191	<	id );
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	headStamp->add( currentStamp );
197	<	comp_stamps[i] = headStamp->match( id );
198	<	}
199	<	}
89	>	sysObjectsCreation();
90
91	<	#ifdef IS_MPI
202	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
203	<	MPIcheckPoint();
204	<	#endif // is_mpi
91	>	// check on the post processing info
92
93	+	finalInfoCheck();
94
95	+	// initialize the system coordinates
96
97	<
209	<	// caclulate the number of atoms, bonds, bends and torsions
210	<
211	<	tot_atoms = 0;
212	<	tot_bonds = 0;
213	<	tot_bends = 0;
214	<	tot_torsions = 0;
215	<	for( i=0; i<n_components; i++ ){
216	<
217	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	<	}
222	<
223	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
224	<
225	<	simnfo->n_atoms = tot_atoms;
226	<	simnfo->n_bonds = tot_bonds;
227	<	simnfo->n_bends = tot_bends;
228	<	simnfo->n_torsions = tot_torsions;
229	<	simnfo->n_SRI = tot_SRI;
230	<	simnfo->n_mol = tot_nmol;
231	<
97	>	initSystemCoords();
98
233	–	#ifdef IS_MPI
99
100	<	// divide the molecules among processors here.
236	<
237	<	mpiSim = new mpiSimulation( simnfo );
238	<
239	<
100	>	// make the output filenames
101
102	<	globalIndex = mpiSim->divideLabor();
103	<
104	<
244	<
245	<	// set up the local variables
102	>	makeOutNames();
103	>
104	>	// make the integrator
105
106	<	int localMol, allMol;
248	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
249	<
250	<	int* mol2proc = mpiSim->getMolToProcMap();
251	<	int* molCompType = mpiSim->getMolComponentType();
106	>	makeIntegrator();
107
253	–	allMol = 0;
254	–	localMol = 0;
255	–	local_atoms = 0;
256	–	local_bonds = 0;
257	–	local_bends = 0;
258	–	local_torsions = 0;
259	–	for( i=0; i<n_components; i++ ){
260	–
261	–	for( j=0; j<components_nmol[i]; j++ ){
262	–
263	–	if( mol2proc[j] == worldRank ){
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 not 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	–	int molIndex;
308	–
309	–	// initialize the molecule's stampID's
310	–
108		#ifdef IS_MPI
109	<
109	>	mpiSim->mpiRefresh();
110	>	#endif
111
112	<	molIndex = 0;
315	<	for(i=0; i<mpiSim->getTotNmol(); i++){
316	<
317	<	if(mol2proc[i] == worldRank ){
318	<	the_molecules[molIndex].setStampID( molCompType[i] );
319	<	molIndex++;
320	<	}
321	<	}
112	>	// initialize the Fortran
113
114	<	#else // is_mpi
324	<
325	<	molIndex = 0;
326	<	for(i=0; i<n_components; i++){
327	<	for(j=0; j<components_nmol[i]; j++ ){
328	<	the_molecules[molIndex].setStampID( i );
329	<	molIndex++;
330	<	}
331	<	}
332	<
333	<
334	<	#endif // is_mpi
335	<
336	<
337	<	if( simnfo->n_SRI ){
338	<	Exclude::createArray(simnfo->n_SRI);
339	<	the_excludes = new Exclude*[simnfo->n_SRI];
340	<	simnfo->globalExcludes = new int;
341	<	simnfo->n_exclude = tot_SRI;
342	<	}
343	<	else{
344	<
345	<	Exclude::createArray( 1 );
346	<	the_excludes = new Exclude*;
347	<	the_excludes[0] = new Exclude(0);
348	<	the_excludes[0]->setPair( 0,0 );
349	<	simnfo->globalExcludes = new int;
350	<	simnfo->globalExcludes[0] = 0;
351	<	simnfo->n_exclude = 0;
352	<	}
353	<
354	<	// set the arrays into the SimInfo object
355	<
356	<	simnfo->atoms = the_atoms;
357	<	simnfo->molecules = the_molecules;
358	<	simnfo->nGlobalExcludes = 0;
359	<	simnfo->excludes = the_excludes;
360	<
361	<
362	<	// get some of the tricky things that may still be in the globals
363	<
364	<
365	<	if( the_globals->haveBox() ){
366	<	simnfo->box_x = the_globals->getBox();
367	<	simnfo->box_y = the_globals->getBox();
368	<	simnfo->box_z = the_globals->getBox();
369	<	}
370	<	else if( the_globals->haveDensity() ){
371	<
372	<	double vol;
373	<	vol = (double)tot_nmol / the_globals->getDensity();
374	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
375	<	simnfo->box_y = simnfo->box_x;
376	<	simnfo->box_z = simnfo->box_x;
377	<	}
378	<	else{
379	<	if( !the_globals->haveBoxX() ){
380	<	sprintf( painCave.errMsg,
381	<	"SimSetup error, no periodic BoxX size given.\n" );
382	<	painCave.isFatal = 1;
383	<	simError();
384	<	}
385	<	simnfo->box_x = the_globals->getBoxX();
386	<
387	<	if( !the_globals->haveBoxY() ){
388	<	sprintf( painCave.errMsg,
389	<	"SimSetup error, no periodic BoxY size given.\n" );
390	<	painCave.isFatal = 1;
391	<	simError();
392	<	}
393	<	simnfo->box_y = the_globals->getBoxY();
394	<
395	<	if( !the_globals->haveBoxZ() ){
396	<	sprintf( painCave.errMsg,
397	<	"SimSetup error, no periodic BoxZ size given.\n" );
398	<	painCave.isFatal = 1;
399	<	simError();
400	<	}
401	<	simnfo->box_z = the_globals->getBoxZ();
402	<	}
403	<
404	<	#ifdef IS_MPI
405	<	strcpy( checkPointMsg, "Box size set up" );
406	<	MPIcheckPoint();
407	<	#endif // is_mpi
408	<
409	<
410	<	// initialize the arrays
411	<
412	<	the_ff->setSimInfo( simnfo );
413	<
414	<	makeMolecules();
415	<	simnfo->identArray = new int[simnfo->n_atoms];
416	<	for(i=0; i<simnfo->n_atoms; i++){
417	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
418	<	}
419	<
420	<	if (the_globals->getUseRF() ) {
421	<	simnfo->useReactionField = 1;
422	<
423	<	if( !the_globals->haveECR() ){
424	<	sprintf( painCave.errMsg,
425	<	"SimSetup Warning: using default value of 1/2 the smallest "
426	<	"box length for the electrostaticCutoffRadius.\n"
427	<	"I hope you have a very fast processor!\n");
428	<	painCave.isFatal = 0;
429	<	simError();
430	<	double smallest;
431	<	smallest = simnfo->box_x;
432	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
433	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
434	<	simnfo->ecr = 0.5 * smallest;
435	<	} else {
436	<	simnfo->ecr        = the_globals->getECR();
437	<	}
438	<
439	<	if( !the_globals->haveEST() ){
440	<	sprintf( painCave.errMsg,
441	<	"SimSetup Warning: using default value of 0.05 * the "
442	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
443	<	);
444	<	painCave.isFatal = 0;
445	<	simError();
446	<	simnfo->est = 0.05 * simnfo->ecr;
447	<	} else {
448	<	simnfo->est        = the_globals->getEST();
449	<	}
450	<
451	<	if(!the_globals->haveDielectric() ){
452	<	sprintf( painCave.errMsg,
453	<	"SimSetup Error: You are trying to use Reaction Field without"
454	<	"setting a dielectric constant!\n"
455	<	);
456	<	painCave.isFatal = 1;
457	<	simError();
458	<	}
459	<	simnfo->dielectric = the_globals->getDielectric();
460	<	} else {
461	<	if (simnfo->n_dipoles) {
462	<
463	<	if( !the_globals->haveECR() ){
464	<	sprintf( painCave.errMsg,
465	<	"SimSetup Warning: using default value of 1/2 the smallest"
466	<	"box length for the electrostaticCutoffRadius.\n"
467	<	"I hope you have a very fast processor!\n");
468	<	painCave.isFatal = 0;
469	<	simError();
470	<	double smallest;
471	<	smallest = simnfo->box_x;
472	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
473	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
474	<	simnfo->ecr = 0.5 * smallest;
475	<	} else {
476	<	simnfo->ecr        = the_globals->getECR();
477	<	}
478	<
479	<	if( !the_globals->haveEST() ){
480	<	sprintf( painCave.errMsg,
481	<	"SimSetup Warning: using default value of 5% of the"
482	<	"electrostaticCutoffRadius for the "
483	<	"electrostaticSkinThickness\n"
484	<	);
485	<	painCave.isFatal = 0;
486	<	simError();
487	<	simnfo->est = 0.05 * simnfo->ecr;
488	<	} else {
489	<	simnfo->est        = the_globals->getEST();
490	<	}
491	<	}
492	<	}
114	>	initFortran();
115
494	–	#ifdef IS_MPI
495	–	strcpy( checkPointMsg, "electrostatic parameters check out" );
496	–	MPIcheckPoint();
497	–	#endif // is_mpi
116
499	–	if( the_globals->haveInitialConfig() ){
500	–
501	–	InitializeFromFile* fileInit;
502	–	#ifdef IS_MPI // is_mpi
503	–	if( worldRank == 0 ){
504	–	#endif //is_mpi
505	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
506	–	#ifdef IS_MPI
507	–	}else fileInit = new InitializeFromFile( NULL );
508	–	#endif
509	–	fileInit->read_xyz( simnfo ); // default velocities on
117
511	–	delete fileInit;
512	–	}
513	–	else{
514	–
515	–	#ifdef IS_MPI
516	–
517	–	// no init from bass
518	–
519	–	sprintf( painCave.errMsg,
520	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
521	–	painCave.isFatal;
522	–	simError();
523	–
524	–	#else
525	–
526	–	initFromBass();
527	–
528	–
529	–	#endif
530	–	}
531	–
532	–	#ifdef IS_MPI
533	–	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
534	–	MPIcheckPoint();
535	–	#endif // is_mpi
536	–
537	–
538	–
539	–
540	–
541	–
542	–
543	–	#ifdef IS_MPI
544	–	if( worldRank == 0 ){
545	–	#endif // is_mpi
546	–
547	–	if( the_globals->haveFinalConfig() ){
548	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
549	–	}
550	–	else{
551	–	strcpy( simnfo->finalName, inFileName );
552	–	char* endTest;
553	–	int nameLength = strlen( simnfo->finalName );
554	–	endTest = &(simnfo->finalName[nameLength - 5]);
555	–	if( !strcmp( endTest, ".bass" ) ){
556	–	strcpy( endTest, ".eor" );
557	–	}
558	–	else if( !strcmp( endTest, ".BASS" ) ){
559	–	strcpy( endTest, ".eor" );
560	–	}
561	–	else{
562	–	endTest = &(simnfo->finalName[nameLength - 4]);
563	–	if( !strcmp( endTest, ".bss" ) ){
564	–	strcpy( endTest, ".eor" );
565	–	}
566	–	else if( !strcmp( endTest, ".mdl" ) ){
567	–	strcpy( endTest, ".eor" );
568	–	}
569	–	else{
570	–	strcat( simnfo->finalName, ".eor" );
571	–	}
572	–	}
573	–	}
574	–
575	–	// make the sample and status out names
576	–
577	–	strcpy( simnfo->sampleName, inFileName );
578	–	char* endTest;
579	–	int nameLength = strlen( simnfo->sampleName );
580	–	endTest = &(simnfo->sampleName[nameLength - 5]);
581	–	if( !strcmp( endTest, ".bass" ) ){
582	–	strcpy( endTest, ".dump" );
583	–	}
584	–	else if( !strcmp( endTest, ".BASS" ) ){
585	–	strcpy( endTest, ".dump" );
586	–	}
587	–	else{
588	–	endTest = &(simnfo->sampleName[nameLength - 4]);
589	–	if( !strcmp( endTest, ".bss" ) ){
590	–	strcpy( endTest, ".dump" );
591	–	}
592	–	else if( !strcmp( endTest, ".mdl" ) ){
593	–	strcpy( endTest, ".dump" );
594	–	}
595	–	else{
596	–	strcat( simnfo->sampleName, ".dump" );
597	–	}
598	–	}
599	–
600	–	strcpy( simnfo->statusName, inFileName );
601	–	nameLength = strlen( simnfo->statusName );
602	–	endTest = &(simnfo->statusName[nameLength - 5]);
603	–	if( !strcmp( endTest, ".bass" ) ){
604	–	strcpy( endTest, ".stat" );
605	–	}
606	–	else if( !strcmp( endTest, ".BASS" ) ){
607	–	strcpy( endTest, ".stat" );
608	–	}
609	–	else{
610	–	endTest = &(simnfo->statusName[nameLength - 4]);
611	–	if( !strcmp( endTest, ".bss" ) ){
612	–	strcpy( endTest, ".stat" );
613	–	}
614	–	else if( !strcmp( endTest, ".mdl" ) ){
615	–	strcpy( endTest, ".stat" );
616	–	}
617	–	else{
618	–	strcat( simnfo->statusName, ".stat" );
619	–	}
620	–	}
621	–
622	–	#ifdef IS_MPI
623	–	}
624	–	#endif // is_mpi
625	–
626	–	// set the status, sample, and themal kick times
627	–
628	–	if( the_globals->haveSampleTime() ){
629	–	simnfo->sampleTime = the_globals->getSampleTime();
630	–	simnfo->statusTime = simnfo->sampleTime;
631	–	simnfo->thermalTime = simnfo->sampleTime;
632	–	}
633	–	else{
634	–	simnfo->sampleTime = the_globals->getRunTime();
635	–	simnfo->statusTime = simnfo->sampleTime;
636	–	simnfo->thermalTime = simnfo->sampleTime;
637	–	}
638	–
639	–	if( the_globals->haveStatusTime() ){
640	–	simnfo->statusTime = the_globals->getStatusTime();
641	–	}
642	–
643	–	if( the_globals->haveThermalTime() ){
644	–	simnfo->thermalTime = the_globals->getThermalTime();
645	–	}
646	–
647	–	// check for the temperature set flag
648	–
649	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
650	–
651	–
652	–	//   // make the longe range forces and the integrator
653	–
654	–	//   new AllLong( simnfo );
655	–
656	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
657	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
658	–
659	–
660	–
661	–	// initialize the Fortran
662	–
663	–	simnfo->refreshSim();
664	–
665	–	if( !strcmp( simnfo->mixingRule, "standard") ){
666	–	the_ff->initForceField( LB_MIXING_RULE );
667	–	}
668	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
669	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
670	–	}
671	–	else{
672	–	sprintf( painCave.errMsg,
673	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
674	–	simnfo->mixingRule );
675	–	painCave.isFatal = 1;
676	–	simError();
677	–	}
678	–
679	–
680	–	#ifdef IS_MPI
681	–	strcpy( checkPointMsg,
682	–	"Successfully intialized the mixingRule for Fortran." );
683	–	MPIcheckPoint();
684	–	#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 713 | Line 146 | void SimSetup::makeMolecules( void ){
146
147		atomOffset = 0;
148		excludeOffset = 0;
149	<	for(i=0; i<simnfo->n_mol; i++){
149	>	for(i=0; i<info->n_mol; i++){
150
151		stampID = the_molecules[i].getStampID();
152
153	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
154	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
155	<	info.nBends    = comp_stamps[stampID]->getNBends();
156	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
157	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
153	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
154	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
155	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
156	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
157	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
158
159	<	info.myAtoms = &the_atoms[atomOffset];
160	<	info.myExcludes = &the_excludes[excludeOffset];
161	<	info.myBonds = new Bond*[info.nBonds];
162	<	info.myBends = new Bend*[info.nBends];
163	<	info.myTorsions = new Torsion*[info.nTorsions];
159	>	molInfo.myAtoms = &the_atoms[atomOffset];
160	>	molInfo.myExcludes = &the_excludes[excludeOffset];
161	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
162	>	molInfo.myBends = new Bend*[molInfo.nBends];
163	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
164
165	<	theBonds = new bond_pair[info.nBonds];
166	<	theBends = new bend_set[info.nBends];
167	<	theTorsions = new torsion_set[info.nTorsions];
165	>	theBonds = new bond_pair[molInfo.nBonds];
166	>	theBends = new bend_set[molInfo.nBends];
167	>	theTorsions = new torsion_set[molInfo.nTorsions];
168
169		// make the Atoms
170
171	<	for(j=0; j<info.nAtoms; j++){
171	>	for(j=0; j<molInfo.nAtoms; j++){
172
173		currentAtom = comp_stamps[stampID]->getAtom( j );
174		if( currentAtom->haveOrientation() ){
175
176		dAtom = new DirectionalAtom(j + atomOffset);
177	<	simnfo->n_oriented++;
178	<	info.myAtoms[j] = dAtom;
177	>	info->n_oriented++;
178	>	molInfo.myAtoms[j] = dAtom;
179
180		ux = currentAtom->getOrntX();
181		uy = currentAtom->getOrntY();
#	Line 760 | 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 795 | 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 832 | 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 884 | 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 914 | Line 348 | void SimSetup::makeMolecules( void ){
348		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349		#endif  //is_mpi
350		}
351	<	excludeOffset += info.nTorsions;
351	>	excludeOffset += molInfo.nTorsions;
352
353
354		// send the arrays off to the forceField for init.
355
356	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
357	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
358	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
359	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
356	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
357	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
358	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
359	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
360
361
362	<	the_molecules[i].initialize( info );
363	<	atomOffset += info.nAtoms;
362	>	the_molecules[i].initialize( molInfo );
363	>
364	>
365	>	atomOffset += molInfo.nAtoms;
366		delete[] theBonds;
367		delete[] theBends;
368		delete[] theTorsions;
369		}
370
371	+	#ifdef IS_MPI
372	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
373	+	MPIcheckPoint();
374	+	#endif // is_mpi
375	+
376		// clean up the forcefield
377		the_ff->calcRcut();
378		the_ff->cleanMe();
379	+
380		}
381
382		void SimSetup::initFromBass( void ){
#	Line 956 | 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 973 | 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 1055 | 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 1117 | 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 if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
590	+	else{
591	+	sprintf( painCave.errMsg,
592	+	"SimSetup Error. Unrecognized force field -> %s\n",
593	+	force_field );
594	+	painCave.isFatal = 1;
595	+	simError();
596	+	}
597	+
598	+	// get the ensemble
599	+
600	+	strcpy( ensemble, globals->getEnsemble() );
601	+
602	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
603	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
604	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
605	+	ensembleCase = NPTi_ENS;
606	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
607	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
608	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
609	+	else{
610	+	sprintf( painCave.errMsg,
611	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
612	+	"reverting to NVE for this simulation.\n",
613	+	ensemble );
614	+	painCave.isFatal = 0;
615	+	simError();
616	+	strcpy( ensemble, "NVE" );
617	+	ensembleCase = NVE_ENS;
618	+	}
619	+	strcpy( info->ensemble, ensemble );
620	+
621	+	// get the mixing rule
622	+
623	+	strcpy( info->mixingRule, globals->getMixingRule() );
624	+	info->usePBC = globals->getPBC();
625	+
626	+
627	+	// get the components and calculate the tot_nMol and indvidual n_mol
628	+
629	+	the_components = globals->getComponents();
630	+	components_nmol = new int[n_components];
631	+
632	+
633	+	if( !globals->haveNMol() ){
634	+	// we don't have the total number of molecules, so we assume it is
635	+	// given in each component
636	+
637	+	tot_nmol = 0;
638	+	for( i=0; i<n_components; i++ ){
639	+
640	+	if( !the_components[i]->haveNMol() ){
641	+	// we have a problem
642	+	sprintf( painCave.errMsg,
643	+	"SimSetup Error. No global NMol or component NMol"
644	+	" given. Cannot calculate the number of atoms.\n" );
645	+	painCave.isFatal = 1;
646	+	simError();
647	+	}
648	+
649	+	tot_nmol += the_components[i]->getNMol();
650	+	components_nmol[i] = the_components[i]->getNMol();
651	+	}
652	+	}
653	+	else{
654	+	sprintf( painCave.errMsg,
655	+	"SimSetup error.\n"
656	+	"\tSorry, the ability to specify total"
657	+	" nMols and then give molfractions in the components\n"
658	+	"\tis not currently supported."
659	+	" Please give nMol in the components.\n" );
660	+	painCave.isFatal = 1;
661	+	simError();
662	+	}
663	+
664	+	// set the status, sample, and thermal kick times
665	+
666	+	if( globals->haveSampleTime() ){
667	+	info->sampleTime = globals->getSampleTime();
668	+	info->statusTime = info->sampleTime;
669	+	info->thermalTime = info->sampleTime;
670	+	}
671	+	else{
672	+	info->sampleTime = globals->getRunTime();
673	+	info->statusTime = info->sampleTime;
674	+	info->thermalTime = info->sampleTime;
675	+	}
676	+
677	+	if( globals->haveStatusTime() ){
678	+	info->statusTime = globals->getStatusTime();
679	+	}
680	+
681	+	if( globals->haveThermalTime() ){
682	+	info->thermalTime = globals->getThermalTime();
683	+	}
684	+
685	+	// check for the temperature set flag
686	+
687	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
688	+
689	+	// get some of the tricky things that may still be in the globals
690	+
691	+	double boxVector[3];
692	+	if( globals->haveBox() ){
693	+	boxVector[0] = globals->getBox();
694	+	boxVector[1] = globals->getBox();
695	+	boxVector[2] = globals->getBox();
696	+
697	+	info->setBox( boxVector );
698	+	}
699	+	else if( globals->haveDensity() ){
700	+
701	+	double vol;
702	+	vol = (double)tot_nmol / globals->getDensity();
703	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
704	+	boxVector[1] = boxVector[0];
705	+	boxVector[2] = boxVector[0];
706	+
707	+	info->setBox( boxVector );
708	+	}
709	+	else{
710	+	if( !globals->haveBoxX() ){
711	+	sprintf( painCave.errMsg,
712	+	"SimSetup error, no periodic BoxX size given.\n" );
713	+	painCave.isFatal = 1;
714	+	simError();
715	+	}
716	+	boxVector[0] = globals->getBoxX();
717	+
718	+	if( !globals->haveBoxY() ){
719	+	sprintf( painCave.errMsg,
720	+	"SimSetup error, no periodic BoxY size given.\n" );
721	+	painCave.isFatal = 1;
722	+	simError();
723	+	}
724	+	boxVector[1] = globals->getBoxY();
725	+
726	+	if( !globals->haveBoxZ() ){
727	+	sprintf( painCave.errMsg,
728	+	"SimSetup error, no periodic BoxZ size given.\n" );
729	+	painCave.isFatal = 1;
730	+	simError();
731	+	}
732	+	boxVector[2] = globals->getBoxZ();
733	+
734	+	info->setBox( boxVector );
735	+	}
736	+
737	+
738	+
739	+	#ifdef IS_MPI
740	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
741	+	MPIcheckPoint();
742	+	#endif // is_mpi
743	+
744	+	}
745	+
746	+
747	+	void SimSetup::finalInfoCheck( void ){
748	+	int index;
749	+	int usesDipoles;
750	+
751	+
752	+	// check electrostatic parameters
753	+
754	+	index = 0;
755	+	usesDipoles = 0;
756	+	while( (index < info->n_atoms) && !usesDipoles ){
757	+	usesDipoles = ((info->atoms)[index])->hasDipole();
758	+	index++;
759	+	}
760	+
761	+	#ifdef IS_MPI
762	+	int myUse = usesDipoles;
763	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
764	+	#endif //is_mpi
765	+
766	+	double theEcr, theEst;
767	+
768	+	if (globals->getUseRF() ) {
769	+	info->useReactionField = 1;
770	+
771	+	if( !globals->haveECR() ){
772	+	sprintf( painCave.errMsg,
773	+	"SimSetup Warning: using default value of 1/2 the smallest "
774	+	"box length for the electrostaticCutoffRadius.\n"
775	+	"I hope you have a very fast processor!\n");
776	+	painCave.isFatal = 0;
777	+	simError();
778	+	double smallest;
779	+	smallest = info->boxL[0];
780	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
781	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
782	+	theEcr = 0.5 * smallest;
783	+	} else {
784	+	theEcr = globals->getECR();
785	+	}
786	+
787	+	if( !globals->haveEST() ){
788	+	sprintf( painCave.errMsg,
789	+	"SimSetup Warning: using default value of 0.05 * the "
790	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
791	+	);
792	+	painCave.isFatal = 0;
793	+	simError();
794	+	theEst = 0.05 * theEcr;
795	+	} else {
796	+	theEst= globals->getEST();
797	+	}
798	+
799	+	info->setEcr( theEcr, theEst );
800	+
801	+	if(!globals->haveDielectric() ){
802	+	sprintf( painCave.errMsg,
803	+	"SimSetup Error: You are trying to use Reaction Field without"
804	+	"setting a dielectric constant!\n"
805	+	);
806	+	painCave.isFatal = 1;
807	+	simError();
808	+	}
809	+	info->dielectric = globals->getDielectric();
810	+	}
811	+	else {
812	+	if (usesDipoles) {
813	+
814	+	if( !globals->haveECR() ){
815	+	sprintf( painCave.errMsg,
816	+	"SimSetup Warning: using default value of 1/2 the smallest "
817	+	"box length for the electrostaticCutoffRadius.\n"
818	+	"I hope you have a very fast processor!\n");
819	+	painCave.isFatal = 0;
820	+	simError();
821	+	double smallest;
822	+	smallest = info->boxL[0];
823	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
824	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
825	+	theEcr = 0.5 * smallest;
826	+	} else {
827	+	theEcr = globals->getECR();
828	+	}
829	+
830	+	if( !globals->haveEST() ){
831	+	sprintf( painCave.errMsg,
832	+	"SimSetup Warning: using default value of 0.05 * the "
833	+	"electrostaticCutoffRadius for the "
834	+	"electrostaticSkinThickness\n"
835	+	);
836	+	painCave.isFatal = 0;
837	+	simError();
838	+	theEst = 0.05 * theEcr;
839	+	} else {
840	+	theEst= globals->getEST();
841	+	}
842	+
843	+	info->setEcr( theEcr, theEst );
844	+	}
845	+	}
846	+
847	+	#ifdef IS_MPI
848	+	strcpy( checkPointMsg, "post processing checks out" );
849	+	MPIcheckPoint();
850	+	#endif // is_mpi
851	+
852	+	}
853	+
854	+	void SimSetup::initSystemCoords( void ){
855	+
856	+	if( globals->haveInitialConfig() ){
857	+
858	+	InitializeFromFile* fileInit;
859	+	#ifdef IS_MPI // is_mpi
860	+	if( worldRank == 0 ){
861	+	#endif //is_mpi
862	+	fileInit = new InitializeFromFile( globals->getInitialConfig() );
863	+	#ifdef IS_MPI
864	+	}else fileInit = new InitializeFromFile( NULL );
865	+	#endif
866	+	fileInit->readInit( info ); // default velocities on
867	+
868	+	delete fileInit;
869	+	}
870	+	else{
871	+
872	+	#ifdef IS_MPI
873	+
874	+	// no init from bass
875	+
876	+	sprintf( painCave.errMsg,
877	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
878	+	painCave.isFatal;
879	+	simError();
880	+
881	+	#else
882	+
883	+	initFromBass();
884	+
885	+
886	+	#endif
887	+	}
888	+
889	+	#ifdef IS_MPI
890	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
891	+	MPIcheckPoint();
892	+	#endif // is_mpi
893	+
894	+	}
895	+
896	+
897	+	void SimSetup::makeOutNames( void ){
898	+
899	+	#ifdef IS_MPI
900	+	if( worldRank == 0 ){
901	+	#endif // is_mpi
902	+
903	+	if( globals->haveFinalConfig() ){
904	+	strcpy( info->finalName, globals->getFinalConfig() );
905	+	}
906	+	else{
907	+	strcpy( info->finalName, inFileName );
908	+	char* endTest;
909	+	int nameLength = strlen( info->finalName );
910	+	endTest = &(info->finalName[nameLength - 5]);
911	+	if( !strcmp( endTest, ".bass" ) ){
912	+	strcpy( endTest, ".eor" );
913	+	}
914	+	else if( !strcmp( endTest, ".BASS" ) ){
915	+	strcpy( endTest, ".eor" );
916	+	}
917	+	else{
918	+	endTest = &(info->finalName[nameLength - 4]);
919	+	if( !strcmp( endTest, ".bss" ) ){
920	+	strcpy( endTest, ".eor" );
921	+	}
922	+	else if( !strcmp( endTest, ".mdl" ) ){
923	+	strcpy( endTest, ".eor" );
924	+	}
925	+	else{
926	+	strcat( info->finalName, ".eor" );
927	+	}
928	+	}
929	+	}
930	+
931	+	// make the sample and status out names
932	+
933	+	strcpy( info->sampleName, inFileName );
934	+	char* endTest;
935	+	int nameLength = strlen( info->sampleName );
936	+	endTest = &(info->sampleName[nameLength - 5]);
937	+	if( !strcmp( endTest, ".bass" ) ){
938	+	strcpy( endTest, ".dump" );
939	+	}
940	+	else if( !strcmp( endTest, ".BASS" ) ){
941	+	strcpy( endTest, ".dump" );
942	+	}
943	+	else{
944	+	endTest = &(info->sampleName[nameLength - 4]);
945	+	if( !strcmp( endTest, ".bss" ) ){
946	+	strcpy( endTest, ".dump" );
947	+	}
948	+	else if( !strcmp( endTest, ".mdl" ) ){
949	+	strcpy( endTest, ".dump" );
950	+	}
951	+	else{
952	+	strcat( info->sampleName, ".dump" );
953	+	}
954	+	}
955	+
956	+	strcpy( info->statusName, inFileName );
957	+	nameLength = strlen( info->statusName );
958	+	endTest = &(info->statusName[nameLength - 5]);
959	+	if( !strcmp( endTest, ".bass" ) ){
960	+	strcpy( endTest, ".stat" );
961	+	}
962	+	else if( !strcmp( endTest, ".BASS" ) ){
963	+	strcpy( endTest, ".stat" );
964	+	}
965	+	else{
966	+	endTest = &(info->statusName[nameLength - 4]);
967	+	if( !strcmp( endTest, ".bss" ) ){
968	+	strcpy( endTest, ".stat" );
969	+	}
970	+	else if( !strcmp( endTest, ".mdl" ) ){
971	+	strcpy( endTest, ".stat" );
972	+	}
973	+	else{
974	+	strcat( info->statusName, ".stat" );
975	+	}
976	+	}
977	+
978	+	#ifdef IS_MPI
979	+	}
980	+	#endif // is_mpi
981	+
982	+	}
983	+
984	+
985	+	void SimSetup::sysObjectsCreation( void ){
986	+
987	+	int i;
988	+
989	+	// create the forceField
990	+
991	+	createFF();
992	+
993	+	// extract componentList
994	+
995	+	compList();
996	+
997	+	// calc the number of atoms, bond, bends, and torsions
998	+
999	+	calcSysValues();
1000	+
1001	+	#ifdef IS_MPI
1002	+	// divide the molecules among the processors
1003	+
1004	+	mpiMolDivide();
1005	+	#endif //is_mpi
1006	+
1007	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1008	+
1009	+	makeSysArrays();
1010	+
1011	+	// make and initialize the molecules (all but atomic coordinates)
1012	+
1013	+	makeMolecules();
1014	+	info->identArray = new int[info->n_atoms];
1015	+	for(i=0; i<info->n_atoms; i++){
1016	+	info->identArray[i] = the_atoms[i]->getIdent();
1017	+	}
1018	+
1019	+
1020	+
1021	+	}
1022	+
1023	+
1024	+	void SimSetup::createFF( void ){
1025	+
1026	+	switch( ffCase ){
1027	+
1028	+	case FF_DUFF:
1029	+	the_ff = new DUFF();
1030	+	break;
1031	+
1032	+	case FF_LJ:
1033	+	the_ff = new LJFF();
1034	+	break;
1035	+
1036	+	case FF_EAM:
1037	+	the_ff = new EAM_FF();
1038	+	break;
1039	+
1040	+	default:
1041	+	sprintf( painCave.errMsg,
1042	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1043	+	painCave.isFatal = 1;
1044	+	simError();
1045	+	}
1046	+
1047	+	#ifdef IS_MPI
1048	+	strcpy( checkPointMsg, "ForceField creation successful" );
1049	+	MPIcheckPoint();
1050	+	#endif // is_mpi
1051	+
1052	+	}
1053	+
1054	+
1055	+	void SimSetup::compList( void ){
1056	+
1057	+	int i;
1058	+
1059	+	comp_stamps = new MoleculeStamp*[n_components];
1060	+
1061	+	// make an array of molecule stamps that match the components used.
1062	+	// also extract the used stamps out into a separate linked list
1063	+
1064	+	info->nComponents = n_components;
1065	+	info->componentsNmol = components_nmol;
1066	+	info->compStamps = comp_stamps;
1067	+	info->headStamp = new LinkedMolStamp();
1068	+
1069	+	char* id;
1070	+	LinkedMolStamp* headStamp = info->headStamp;
1071	+	LinkedMolStamp* currentStamp = NULL;
1072	+	for( i=0; i<n_components; i++ ){
1073	+
1074	+	id = the_components[i]->getType();
1075	+	comp_stamps[i] = NULL;
1076	+
1077	+	// check to make sure the component isn't already in the list
1078	+
1079	+	comp_stamps[i] = headStamp->match( id );
1080	+	if( comp_stamps[i] == NULL ){
1081	+
1082	+	// extract the component from the list;
1083	+
1084	+	currentStamp = stamps->extractMolStamp( id );
1085	+	if( currentStamp == NULL ){
1086	+	sprintf( painCave.errMsg,
1087	+	"SimSetup error: Component \"%s\" was not found in the "
1088	+	"list of declared molecules\n",
1089	+	id );
1090	+	painCave.isFatal = 1;
1091	+	simError();
1092	+	}
1093	+
1094	+	headStamp->add( currentStamp );
1095	+	comp_stamps[i] = headStamp->match( id );
1096	+	}
1097		}
1098	+
1099	+	#ifdef IS_MPI
1100	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1101	+	MPIcheckPoint();
1102	+	#endif // is_mpi
1103	+
1104	+
1105		}
1106	+
1107	+	void SimSetup::calcSysValues( void ){
1108	+	int i, j, k;
1109	+
1110	+
1111	+	tot_atoms = 0;
1112	+	tot_bonds = 0;
1113	+	tot_bends = 0;
1114	+	tot_torsions = 0;
1115	+	for( i=0; i<n_components; i++ ){
1116	+
1117	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1118	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1119	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1120	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1121	+	}
1122	+
1123	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1124	+
1125	+	info->n_atoms = tot_atoms;
1126	+	info->n_bonds = tot_bonds;
1127	+	info->n_bends = tot_bends;
1128	+	info->n_torsions = tot_torsions;
1129	+	info->n_SRI = tot_SRI;
1130	+	info->n_mol = tot_nmol;
1131	+
1132	+	info->molMembershipArray = new int[tot_atoms];
1133	+	}
1134	+
1135	+
1136	+	#ifdef IS_MPI
1137	+
1138	+	void SimSetup::mpiMolDivide( void ){
1139	+
1140	+	int i, j, k;
1141	+	int localMol, allMol;
1142	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1143	+
1144	+	mpiSim = new mpiSimulation( info );
1145	+
1146	+	globalIndex = mpiSim->divideLabor();
1147	+
1148	+	// set up the local variables
1149	+
1150	+	mol2proc = mpiSim->getMolToProcMap();
1151	+	molCompType = mpiSim->getMolComponentType();
1152	+
1153	+	allMol = 0;
1154	+	localMol = 0;
1155	+	local_atoms = 0;
1156	+	local_bonds = 0;
1157	+	local_bends = 0;
1158	+	local_torsions = 0;
1159	+	globalAtomIndex = 0;
1160	+
1161	+
1162	+	for( i=0; i<n_components; i++ ){
1163	+
1164	+	for( j=0; j<components_nmol[i]; j++ ){
1165	+
1166	+	if( mol2proc[allMol] == worldRank ){
1167	+
1168	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1169	+	local_bonds +=    comp_stamps[i]->getNBonds();
1170	+	local_bends +=    comp_stamps[i]->getNBends();
1171	+	local_torsions += comp_stamps[i]->getNTorsions();
1172	+	localMol++;
1173	+	}
1174	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1175	+	info->molMembershipArray[globalAtomIndex] = allMol;
1176	+	globalAtomIndex++;
1177	+	}
1178	+
1179	+	allMol++;
1180	+	}
1181	+	}
1182	+	local_SRI = local_bonds + local_bends + local_torsions;
1183	+
1184	+	info->n_atoms = mpiSim->getMyNlocal();
1185	+
1186	+	if( local_atoms != info->n_atoms ){
1187	+	sprintf( painCave.errMsg,
1188	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1189	+	" localAtom (%d) are not equal.\n",
1190	+	info->n_atoms,
1191	+	local_atoms );
1192	+	painCave.isFatal = 1;
1193	+	simError();
1194	+	}
1195	+
1196	+	info->n_bonds = local_bonds;
1197	+	info->n_bends = local_bends;
1198	+	info->n_torsions = local_torsions;
1199	+	info->n_SRI = local_SRI;
1200	+	info->n_mol = localMol;
1201	+
1202	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1203	+	MPIcheckPoint();
1204	+	}
1205	+
1206	+	#endif // is_mpi
1207	+
1208	+
1209	+	void SimSetup::makeSysArrays( void ){
1210	+	int i, j, k;
1211	+
1212	+
1213	+	// create the atom and short range interaction arrays
1214	+
1215	+	Atom::createArrays(info->n_atoms);
1216	+	the_atoms = new Atom*[info->n_atoms];
1217	+	the_molecules = new Molecule[info->n_mol];
1218	+	int molIndex;
1219	+
1220	+	// initialize the molecule's stampID's
1221	+
1222	+	#ifdef IS_MPI
1223	+
1224	+
1225	+	molIndex = 0;
1226	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1227	+
1228	+	if(mol2proc[i] == worldRank ){
1229	+	the_molecules[molIndex].setStampID( molCompType[i] );
1230	+	the_molecules[molIndex].setMyIndex( molIndex );
1231	+	the_molecules[molIndex].setGlobalIndex( i );
1232	+	molIndex++;
1233	+	}
1234	+	}
1235	+
1236	+	#else // is_mpi
1237	+
1238	+	molIndex = 0;
1239	+	globalAtomIndex = 0;
1240	+	for(i=0; i<n_components; i++){
1241	+	for(j=0; j<components_nmol[i]; j++ ){
1242	+	the_molecules[molIndex].setStampID( i );
1243	+	the_molecules[molIndex].setMyIndex( molIndex );
1244	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1245	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1246	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1247	+	globalAtomIndex++;
1248	+	}
1249	+	molIndex++;
1250	+	}
1251	+	}
1252	+
1253	+
1254	+	#endif // is_mpi
1255	+
1256	+
1257	+	if( info->n_SRI ){
1258	+
1259	+	Exclude::createArray(info->n_SRI);
1260	+	the_excludes = new Exclude*[info->n_SRI];
1261	+	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1262	+	info->globalExcludes = new int;
1263	+	info->n_exclude = info->n_SRI;
1264	+	}
1265	+	else{
1266	+
1267	+	Exclude::createArray( 1 );
1268	+	the_excludes = new Exclude*;
1269	+	the_excludes[0] = new Exclude(0);
1270	+	the_excludes[0]->setPair( 0,0 );
1271	+	info->globalExcludes = new int;
1272	+	info->globalExcludes[0] = 0;
1273	+	info->n_exclude = 0;
1274	+	}
1275	+
1276	+	// set the arrays into the SimInfo object
1277	+
1278	+	info->atoms = the_atoms;
1279	+	info->molecules = the_molecules;
1280	+	info->nGlobalExcludes = 0;
1281	+	info->excludes = the_excludes;
1282	+
1283	+	the_ff->setSimInfo( info );
1284	+
1285	+	}
1286	+
1287	+	void SimSetup::makeIntegrator( void ){
1288	+
1289	+	NVT<RealIntegrator>*  myNVT = NULL;
1290	+	NPTi<RealIntegrator>* myNPTi = NULL;
1291	+	NPTf<RealIntegrator>* myNPTf = NULL;
1292	+	NPTim<RealIntegrator>* myNPTim = NULL;
1293	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1294	+
1295	+	switch( ensembleCase ){
1296	+
1297	+	case NVE_ENS:
1298	+	new NVE<RealIntegrator>( info, the_ff );
1299	+	break;
1300	+
1301	+	case NVT_ENS:
1302	+	myNVT = new NVT<RealIntegrator>( info, the_ff );
1303	+	myNVT->setTargetTemp(globals->getTargetTemp());
1304	+
1305	+	if (globals->haveTauThermostat())
1306	+	myNVT->setTauThermostat(globals->getTauThermostat());
1307	+
1308	+	else {
1309	+	sprintf( painCave.errMsg,
1310	+	"SimSetup error: If you use the NVT\n"
1311	+	"    ensemble, you must set tauThermostat.\n");
1312	+	painCave.isFatal = 1;
1313	+	simError();
1314	+	}
1315	+	break;
1316	+
1317	+	case NPTi_ENS:
1318	+	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1319	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1320	+
1321	+	if (globals->haveTargetPressure())
1322	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1323	+	else {
1324	+	sprintf( painCave.errMsg,
1325	+	"SimSetup error: If you use a constant pressure\n"
1326	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1327	+	painCave.isFatal = 1;
1328	+	simError();
1329	+	}
1330	+
1331	+	if( globals->haveTauThermostat() )
1332	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1333	+	else{
1334	+	sprintf( painCave.errMsg,
1335	+	"SimSetup error: If you use an NPT\n"
1336	+	"    ensemble, you must set tauThermostat.\n");
1337	+	painCave.isFatal = 1;
1338	+	simError();
1339	+	}
1340	+
1341	+	if( globals->haveTauBarostat() )
1342	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1343	+	else{
1344	+	sprintf( painCave.errMsg,
1345	+	"SimSetup error: If you use an NPT\n"
1346	+	"    ensemble, you must set tauBarostat.\n");
1347	+	painCave.isFatal = 1;
1348	+	simError();
1349	+	}
1350	+	break;
1351	+
1352	+	case NPTf_ENS:
1353	+	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1354	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1355	+
1356	+	if (globals->haveTargetPressure())
1357	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1358	+	else {
1359	+	sprintf( painCave.errMsg,
1360	+	"SimSetup error: If you use a constant pressure\n"
1361	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1362	+	painCave.isFatal = 1;
1363	+	simError();
1364	+	}
1365	+
1366	+	if( globals->haveTauThermostat() )
1367	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1368	+	else{
1369	+	sprintf( painCave.errMsg,
1370	+	"SimSetup error: If you use an NPT\n"
1371	+	"    ensemble, you must set tauThermostat.\n");
1372	+	painCave.isFatal = 1;
1373	+	simError();
1374	+	}
1375	+
1376	+	if( globals->haveTauBarostat() )
1377	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1378	+	else{
1379	+	sprintf( painCave.errMsg,
1380	+	"SimSetup error: If you use an NPT\n"
1381	+	"    ensemble, you must set tauBarostat.\n");
1382	+	painCave.isFatal = 1;
1383	+	simError();
1384	+	}
1385	+	break;
1386	+
1387	+	case NPTim_ENS:
1388	+	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1389	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1390	+
1391	+	if (globals->haveTargetPressure())
1392	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1393	+	else {
1394	+	sprintf( painCave.errMsg,
1395	+	"SimSetup error: If you use a constant pressure\n"
1396	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1397	+	painCave.isFatal = 1;
1398	+	simError();
1399	+	}
1400	+
1401	+	if( globals->haveTauThermostat() )
1402	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1403	+	else{
1404	+	sprintf( painCave.errMsg,
1405	+	"SimSetup error: If you use an NPT\n"
1406	+	"    ensemble, you must set tauThermostat.\n");
1407	+	painCave.isFatal = 1;
1408	+	simError();
1409	+	}
1410	+
1411	+	if( globals->haveTauBarostat() )
1412	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1413	+	else{
1414	+	sprintf( painCave.errMsg,
1415	+	"SimSetup error: If you use an NPT\n"
1416	+	"    ensemble, you must set tauBarostat.\n");
1417	+	painCave.isFatal = 1;
1418	+	simError();
1419	+	}
1420	+	break;
1421	+
1422	+	case NPTfm_ENS:
1423	+	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1424	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1425	+
1426	+	if (globals->haveTargetPressure())
1427	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1428	+	else {
1429	+	sprintf( painCave.errMsg,
1430	+	"SimSetup error: If you use a constant pressure\n"
1431	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1432	+	painCave.isFatal = 1;
1433	+	simError();
1434	+	}
1435	+
1436	+	if( globals->haveTauThermostat() )
1437	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1438	+	else{
1439	+	sprintf( painCave.errMsg,
1440	+	"SimSetup error: If you use an NPT\n"
1441	+	"    ensemble, you must set tauThermostat.\n");
1442	+	painCave.isFatal = 1;
1443	+	simError();
1444	+	}
1445	+
1446	+	if( globals->haveTauBarostat() )
1447	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1448	+	else{
1449	+	sprintf( painCave.errMsg,
1450	+	"SimSetup error: If you use an NPT\n"
1451	+	"    ensemble, you must set tauBarostat.\n");
1452	+	painCave.isFatal = 1;
1453	+	simError();
1454	+	}
1455	+	break;
1456	+
1457	+	default:
1458	+	sprintf( painCave.errMsg,
1459	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1460	+	painCave.isFatal = 1;
1461	+	simError();
1462	+	}
1463	+
1464	+	}
1465	+
1466	+	void SimSetup::initFortran( void ){
1467	+
1468	+	info->refreshSim();
1469	+
1470	+	if( !strcmp( info->mixingRule, "standard") ){
1471	+	the_ff->initForceField( LB_MIXING_RULE );
1472	+	}
1473	+	else if( !strcmp( info->mixingRule, "explicit") ){
1474	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1475	+	}
1476	+	else{
1477	+	sprintf( painCave.errMsg,
1478	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1479	+	info->mixingRule );
1480	+	painCave.isFatal = 1;
1481	+	simError();
1482	+	}
1483	+
1484	+
1485	+	#ifdef IS_MPI
1486	+	strcpy( checkPointMsg,
1487	+	"Successfully intialized the mixingRule for Fortran." );
1488	+	MPIcheckPoint();
1489	+	#endif // is_mpi
1490	+
1491	+	}

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