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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 487 by mmeineke, Thu Apr 10 16:27:21 2003 UTC vs.
Revision 626 by mmeineke, Wed Jul 16 21:30:56 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	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
71	<
72	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
75	<
76	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	simnfo->run_time = the_globals->getRunTime();
80	<
81	<	// get the ones we know are there, yet still may need some work.
82	<	n_components = the_globals->getNComponents();
83	<	strcpy( force_field, the_globals->getForceField() );
84	<
85	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	if (the_globals->haveTargetPressure())
91	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92	<	else {
93	<	sprintf( painCave.errMsg,
94	<	"SimSetup error: If you use the constant pressure\n"
95	<	"    ensemble, you must set targetPressure.\n"
96	<	"    This was found in the BASS file.\n");
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
100	<
101	<	if (the_globals->haveTauThermostat())
102	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103	<	else if (the_globals->haveQmass())
104	<	the_extendedsystem->setQmass(the_globals->getQmass());
105	<	else {
106	<	sprintf( painCave.errMsg,
107	<	"SimSetup error: If you use one of the constant temperature\n"
108	<	"    ensembles, you must set either tauThermostat or qMass.\n"
109	<	"    Neither of these was found in the BASS file.\n");
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
113	<
114	<	if (the_globals->haveTauBarostat())
115	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116	<	else {
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup error: If you use the constant pressure\n"
119	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
124	<
125	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
126	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
128	<
129	<	if (the_globals->haveTauThermostat())
130	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131	<	else if (the_globals->haveQmass())
132	<	the_extendedsystem->setQmass(the_globals->getQmass());
133	<	else {
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error: If you use one of the constant temperature\n"
136	<	"    ensembles, you must set either tauThermostat or qMass.\n"
137	<	"    Neither of these was found in the BASS file.\n");
138	<	painCave.isFatal = 1;
139	<	simError();
140	<	}
141	<
142	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
143	<	} else {
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	<	"reverting to NVE for this simulation.\n",
147	<	ensemble );
148	<	painCave.isFatal = 0;
149	<	simError();
150	<	strcpy( ensemble, "NVE" );
151	<	}
152	<	strcpy( simnfo->ensemble, ensemble );
153	<
154	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155	<	simnfo->usePBC = the_globals->getPBC();
156	<
157	<	int usesDipoles = 0;
158	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
159	<	the_ff = new TraPPE_ExFF();
160	<	usesDipoles = 1;
161	<	}
162	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163	<	else{
164	<	sprintf( painCave.errMsg,
165	<	"SimSetup Error. Unrecognized force field -> %s\n",
166	<	force_field );
167	<	painCave.isFatal = 1;
168	<	simError();
169	<	}
170	<
171	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "ForceField creation successful" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
175	<
81	>	int i, j, k, globalAtomIndex;
82
83	+	// gather all of the information from the Bass file
84	+
85	+	gatherInfo();
86
87	<	// get the components and calculate the tot_nMol and indvidual n_mol
179	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
87	>	// creation of complex system objects
88
89	<	if( !the_globals->haveNMol() ){
184	<	// we don't have the total number of molecules, so we assume it is
185	<	// given in each component
89	>	sysObjectsCreation();
90
91	<	tot_nmol = 0;
188	<	for( i=0; i<n_components; i++ ){
189	<
190	<	if( !the_components[i]->haveNMol() ){
191	<	// we have a problem
192	<	sprintf( painCave.errMsg,
193	<	"SimSetup Error. No global NMol or component NMol"
194	<	" given. Cannot calculate the number of atoms.\n" );
195	<	painCave.isFatal = 1;
196	<	simError();
197	<	}
198	<
199	<	tot_nmol += the_components[i]->getNMol();
200	<	components_nmol[i] = the_components[i]->getNMol();
201	<	}
202	<	}
203	<	else{
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup error.\n"
206	<	"\tSorry, the ability to specify total"
207	<	" nMols and then give molfractions in the components\n"
208	<	"\tis not currently supported."
209	<	" Please give nMol in the components.\n" );
210	<	painCave.isFatal = 1;
211	<	simError();
212	<
213	<
214	<	//     tot_nmol = the_globals->getNMol();
215	<
216	<	//   //we have the total number of molecules, now we check for molfractions
217	<	//     for( i=0; i<n_components; i++ ){
218	<
219	<	//       if( !the_components[i]->haveMolFraction() ){
220	<
221	<	//  if( !the_components[i]->haveNMol() ){
222	<	//    //we have a problem
223	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	<	//              << " nMol was given in component
225	<
226	<	}
227	<
228	<	#ifdef IS_MPI
229	<	strcpy( checkPointMsg, "Have the number of components" );
230	<	MPIcheckPoint();
231	<	#endif // is_mpi
232	<
233	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
235	<
236	<	simnfo->nComponents = n_components;
237	<	simnfo->componentsNmol = components_nmol;
238	<	simnfo->compStamps = comp_stamps;
239	<	simnfo->headStamp = new LinkedMolStamp();
91	>	// check on the post processing info
92
93	<	char* id;
242	<	LinkedMolStamp* headStamp = simnfo->headStamp;
243	<	LinkedMolStamp* currentStamp = NULL;
244	<	for( i=0; i<n_components; i++ ){
93	>	finalInfoCheck();
94
95	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
95	>	// initialize the system coordinates
96
97	<	comp_stamps[i] = headStamp->match( id );
252	<	if( comp_stamps[i] == NULL ){
253	<
254	<	// extract the component from the list;
255	<
256	<	currentStamp = the_stamps->extractMolStamp( id );
257	<	if( currentStamp == NULL ){
258	<	sprintf( painCave.errMsg,
259	<	"SimSetup error: Component \"%s\" was not found in the "
260	<	"list of declared molecules\n",
261	<	id );
262	<	painCave.isFatal = 1;
263	<	simError();
264	<	}
265	<
266	<	headStamp->add( currentStamp );
267	<	comp_stamps[i] = headStamp->match( id );
268	<	}
269	<	}
270	<
271	<	#ifdef IS_MPI
272	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	<	MPIcheckPoint();
274	<	#endif // is_mpi
97	>	initSystemCoords();
98
99
100	+	// make the output filenames
101
102	<
103	<	// caclulate the number of atoms, bonds, bends and torsions
104	<
281	<	tot_atoms = 0;
282	<	tot_bonds = 0;
283	<	tot_bends = 0;
284	<	tot_torsions = 0;
285	<	for( i=0; i<n_components; i++ ){
286	<
287	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
288	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
289	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
290	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
291	<	}
292	<
293	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
294	<
295	<	simnfo->n_atoms = tot_atoms;
296	<	simnfo->n_bonds = tot_bonds;
297	<	simnfo->n_bends = tot_bends;
298	<	simnfo->n_torsions = tot_torsions;
299	<	simnfo->n_SRI = tot_SRI;
300	<	simnfo->n_mol = tot_nmol;
301	<
102	>	makeOutNames();
103	>
104	>	// make the integrator
105
106	<	#ifdef IS_MPI
304	<
305	<	// divide the molecules among processors here.
306	<
307	<	mpiSim = new mpiSimulation( simnfo );
308	<
309	<
310	<
311	<	globalIndex = mpiSim->divideLabor();
312	<
313	<	// set up the local variables
314	<
315	<	int localMol, allMol;
316	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
317	<
318	<	int* mol2proc = mpiSim->getMolToProcMap();
319	<	int* molCompType = mpiSim->getMolComponentType();
320	<
321	<	allMol = 0;
322	<	localMol = 0;
323	<	local_atoms = 0;
324	<	local_bonds = 0;
325	<	local_bends = 0;
326	<	local_torsions = 0;
327	<	for( i=0; i<n_components; i++ ){
328	<
329	<	for( j=0; j<components_nmol[i]; j++ ){
330	<
331	<	if( mol2proc[allMol] == worldRank ){
332	<
333	<	local_atoms +=    comp_stamps[i]->getNAtoms();
334	<	local_bonds +=    comp_stamps[i]->getNBonds();
335	<	local_bends +=    comp_stamps[i]->getNBends();
336	<	local_torsions += comp_stamps[i]->getNTorsions();
337	<	localMol++;
338	<	}
339	<	allMol++;
340	<	}
341	<	}
342	<	local_SRI = local_bonds + local_bends + local_torsions;
343	<
344	<
345	<	simnfo->n_atoms = mpiSim->getMyNlocal();
346	<
347	<	if( local_atoms != simnfo->n_atoms ){
348	<	sprintf( painCave.errMsg,
349	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
350	<	" localAtom (%d) are not equal.\n",
351	<	simnfo->n_atoms,
352	<	local_atoms );
353	<	painCave.isFatal = 1;
354	<	simError();
355	<	}
356	<
357	<	simnfo->n_bonds = local_bonds;
358	<	simnfo->n_bends = local_bends;
359	<	simnfo->n_torsions = local_torsions;
360	<	simnfo->n_SRI = local_SRI;
361	<	simnfo->n_mol = localMol;
362	<
363	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
364	<	MPIcheckPoint();
365	<
366	<
367	<	#endif // is_mpi
368	<
369	<
370	<	// create the atom and short range interaction arrays
371	<
372	<	Atom::createArrays(simnfo->n_atoms);
373	<	the_atoms = new Atom*[simnfo->n_atoms];
374	<	the_molecules = new Molecule[simnfo->n_mol];
375	<	int molIndex;
376	<
377	<	// initialize the molecule's stampID's
378	<
379	<	#ifdef IS_MPI
380	<
381	<
382	<	molIndex = 0;
383	<	for(i=0; i<mpiSim->getTotNmol(); i++){
384	<
385	<	if(mol2proc[i] == worldRank ){
386	<	the_molecules[molIndex].setStampID( molCompType[i] );
387	<	the_molecules[molIndex].setMyIndex( molIndex );
388	<	molIndex++;
389	<	}
390	<	}
391	<
392	<	#else // is_mpi
393	<
394	<	molIndex = 0;
395	<	for(i=0; i<n_components; i++){
396	<	for(j=0; j<components_nmol[i]; j++ ){
397	<	the_molecules[molIndex].setStampID( i );
398	<	the_molecules[molIndex].setMyIndex( molIndex );
399	<	molIndex++;
400	<	}
401	<	}
402	<
403	<
404	<	#endif // is_mpi
405	<
406	<
407	<	if( simnfo->n_SRI ){
408	<
409	<	Exclude::createArray(simnfo->n_SRI);
410	<	the_excludes = new Exclude*[simnfo->n_SRI];
411	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
412	<	simnfo->globalExcludes = new int;
413	<	simnfo->n_exclude = simnfo->n_SRI;
414	<	}
415	<	else{
416	<
417	<	Exclude::createArray( 1 );
418	<	the_excludes = new Exclude*;
419	<	the_excludes[0] = new Exclude(0);
420	<	the_excludes[0]->setPair( 0,0 );
421	<	simnfo->globalExcludes = new int;
422	<	simnfo->globalExcludes[0] = 0;
423	<	simnfo->n_exclude = 0;
424	<	}
425	<
426	<	// set the arrays into the SimInfo object
427	<
428	<	simnfo->atoms = the_atoms;
429	<	simnfo->molecules = the_molecules;
430	<	simnfo->nGlobalExcludes = 0;
431	<	simnfo->excludes = the_excludes;
432	<
433	<
434	<	// get some of the tricky things that may still be in the globals
435	<
436	<
437	<	if( the_globals->haveBox() ){
438	<	simnfo->box_x = the_globals->getBox();
439	<	simnfo->box_y = the_globals->getBox();
440	<	simnfo->box_z = the_globals->getBox();
441	<	}
442	<	else if( the_globals->haveDensity() ){
443	<
444	<	double vol;
445	<	vol = (double)tot_nmol / the_globals->getDensity();
446	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
447	<	simnfo->box_y = simnfo->box_x;
448	<	simnfo->box_z = simnfo->box_x;
449	<	}
450	<	else{
451	<	if( !the_globals->haveBoxX() ){
452	<	sprintf( painCave.errMsg,
453	<	"SimSetup error, no periodic BoxX size given.\n" );
454	<	painCave.isFatal = 1;
455	<	simError();
456	<	}
457	<	simnfo->box_x = the_globals->getBoxX();
458	<
459	<	if( !the_globals->haveBoxY() ){
460	<	sprintf( painCave.errMsg,
461	<	"SimSetup error, no periodic BoxY size given.\n" );
462	<	painCave.isFatal = 1;
463	<	simError();
464	<	}
465	<	simnfo->box_y = the_globals->getBoxY();
466	<
467	<	if( !the_globals->haveBoxZ() ){
468	<	sprintf( painCave.errMsg,
469	<	"SimSetup error, no periodic BoxZ size given.\n" );
470	<	painCave.isFatal = 1;
471	<	simError();
472	<	}
473	<	simnfo->box_z = the_globals->getBoxZ();
474	<	}
475	<
476	<	#ifdef IS_MPI
477	<	strcpy( checkPointMsg, "Box size set up" );
478	<	MPIcheckPoint();
479	<	#endif // is_mpi
480	<
481	<
482	<	// initialize the arrays
483	<
484	<	the_ff->setSimInfo( simnfo );
485	<
486	<	makeMolecules();
487	<	simnfo->identArray = new int[simnfo->n_atoms];
488	<	simnfo->molMembershipArray = new int[simnfo->n_atoms];
489	<	for(i=0; i<simnfo->n_atoms; i++){
490	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
491	<	}
492	<	for(i=0; i< simnfo->n_mol; i++) {
493	<	the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
494	<	}
495	<
496	<	if (the_globals->getUseRF() ) {
497	<	simnfo->useReactionField = 1;
498	<
499	<	if( !the_globals->haveECR() ){
500	<	sprintf( painCave.errMsg,
501	<	"SimSetup Warning: using default value of 1/2 the smallest "
502	<	"box length for the electrostaticCutoffRadius.\n"
503	<	"I hope you have a very fast processor!\n");
504	<	painCave.isFatal = 0;
505	<	simError();
506	<	double smallest;
507	<	smallest = simnfo->box_x;
508	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
509	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
510	<	simnfo->ecr = 0.5 * smallest;
511	<	} else {
512	<	simnfo->ecr        = the_globals->getECR();
513	<	}
514	<
515	<	if( !the_globals->haveEST() ){
516	<	sprintf( painCave.errMsg,
517	<	"SimSetup Warning: using default value of 0.05 * the "
518	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
519	<	);
520	<	painCave.isFatal = 0;
521	<	simError();
522	<	simnfo->est = 0.05 * simnfo->ecr;
523	<	} else {
524	<	simnfo->est        = the_globals->getEST();
525	<	}
526	<
527	<	if(!the_globals->haveDielectric() ){
528	<	sprintf( painCave.errMsg,
529	<	"SimSetup Error: You are trying to use Reaction Field without"
530	<	"setting a dielectric constant!\n"
531	<	);
532	<	painCave.isFatal = 1;
533	<	simError();
534	<	}
535	<	simnfo->dielectric = the_globals->getDielectric();
536	<	} else {
537	<	if (usesDipoles) {
538	<
539	<	if( !the_globals->haveECR() ){
540	<	sprintf( painCave.errMsg,
541	<	"SimSetup Warning: using default value of 1/2 the smallest "
542	<	"box length for the electrostaticCutoffRadius.\n"
543	<	"I hope you have a very fast processor!\n");
544	<	painCave.isFatal = 0;
545	<	simError();
546	<	double smallest;
547	<	smallest = simnfo->box_x;
548	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
549	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
550	<	simnfo->ecr = 0.5 * smallest;
551	<	} else {
552	<	simnfo->ecr        = the_globals->getECR();
553	<	}
554	<
555	<	if( !the_globals->haveEST() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 5%% of the "
558	<	"electrostaticCutoffRadius for the "
559	<	"electrostaticSkinThickness\n"
560	<	);
561	<	painCave.isFatal = 0;
562	<	simError();
563	<	simnfo->est = 0.05 * simnfo->ecr;
564	<	} else {
565	<	simnfo->est        = the_globals->getEST();
566	<	}
567	<	}
568	<	}
569	<
570	<	#ifdef IS_MPI
571	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
572	<	MPIcheckPoint();
573	<	#endif // is_mpi
574	<
575	<	if( the_globals->haveInitialConfig() ){
576	<
577	<	InitializeFromFile* fileInit;
578	<	#ifdef IS_MPI // is_mpi
579	<	if( worldRank == 0 ){
580	<	#endif //is_mpi
581	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
582	<	#ifdef IS_MPI
583	<	}else fileInit = new InitializeFromFile( NULL );
584	<	#endif
585	<	fileInit->read_xyz( simnfo ); // default velocities on
586	<
587	<	delete fileInit;
588	<	}
589	<	else{
590	<
591	<	#ifdef IS_MPI
592	<
593	<	// no init from bass
594	<
595	<	sprintf( painCave.errMsg,
596	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
597	<	painCave.isFatal;
598	<	simError();
599	<
600	<	#else
601	<
602	<	initFromBass();
603	<
604	<
605	<	#endif
606	<	}
607	<
608	<	#ifdef IS_MPI
609	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
610	<	MPIcheckPoint();
611	<	#endif // is_mpi
612	<
613	<
614	<
615	<
616	<
617	<
618	<
619	<	#ifdef IS_MPI
620	<	if( worldRank == 0 ){
621	<	#endif // is_mpi
622	<
623	<	if( the_globals->haveFinalConfig() ){
624	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
625	<	}
626	<	else{
627	<	strcpy( simnfo->finalName, inFileName );
628	<	char* endTest;
629	<	int nameLength = strlen( simnfo->finalName );
630	<	endTest = &(simnfo->finalName[nameLength - 5]);
631	<	if( !strcmp( endTest, ".bass" ) ){
632	<	strcpy( endTest, ".eor" );
633	<	}
634	<	else if( !strcmp( endTest, ".BASS" ) ){
635	<	strcpy( endTest, ".eor" );
636	<	}
637	<	else{
638	<	endTest = &(simnfo->finalName[nameLength - 4]);
639	<	if( !strcmp( endTest, ".bss" ) ){
640	<	strcpy( endTest, ".eor" );
641	<	}
642	<	else if( !strcmp( endTest, ".mdl" ) ){
643	<	strcpy( endTest, ".eor" );
644	<	}
645	<	else{
646	<	strcat( simnfo->finalName, ".eor" );
647	<	}
648	<	}
649	<	}
650	<
651	<	// make the sample and status out names
652	<
653	<	strcpy( simnfo->sampleName, inFileName );
654	<	char* endTest;
655	<	int nameLength = strlen( simnfo->sampleName );
656	<	endTest = &(simnfo->sampleName[nameLength - 5]);
657	<	if( !strcmp( endTest, ".bass" ) ){
658	<	strcpy( endTest, ".dump" );
659	<	}
660	<	else if( !strcmp( endTest, ".BASS" ) ){
661	<	strcpy( endTest, ".dump" );
662	<	}
663	<	else{
664	<	endTest = &(simnfo->sampleName[nameLength - 4]);
665	<	if( !strcmp( endTest, ".bss" ) ){
666	<	strcpy( endTest, ".dump" );
667	<	}
668	<	else if( !strcmp( endTest, ".mdl" ) ){
669	<	strcpy( endTest, ".dump" );
670	<	}
671	<	else{
672	<	strcat( simnfo->sampleName, ".dump" );
673	<	}
674	<	}
675	<
676	<	strcpy( simnfo->statusName, inFileName );
677	<	nameLength = strlen( simnfo->statusName );
678	<	endTest = &(simnfo->statusName[nameLength - 5]);
679	<	if( !strcmp( endTest, ".bass" ) ){
680	<	strcpy( endTest, ".stat" );
681	<	}
682	<	else if( !strcmp( endTest, ".BASS" ) ){
683	<	strcpy( endTest, ".stat" );
684	<	}
685	<	else{
686	<	endTest = &(simnfo->statusName[nameLength - 4]);
687	<	if( !strcmp( endTest, ".bss" ) ){
688	<	strcpy( endTest, ".stat" );
689	<	}
690	<	else if( !strcmp( endTest, ".mdl" ) ){
691	<	strcpy( endTest, ".stat" );
692	<	}
693	<	else{
694	<	strcat( simnfo->statusName, ".stat" );
695	<	}
696	<	}
697	<
698	<	#ifdef IS_MPI
699	<	}
700	<	#endif // is_mpi
701	<
702	<	// set the status, sample, and themal kick times
106	>	makeIntegrator();
107
704	–	if( the_globals->haveSampleTime() ){
705	–	simnfo->sampleTime = the_globals->getSampleTime();
706	–	simnfo->statusTime = simnfo->sampleTime;
707	–	simnfo->thermalTime = simnfo->sampleTime;
708	–	}
709	–	else{
710	–	simnfo->sampleTime = the_globals->getRunTime();
711	–	simnfo->statusTime = simnfo->sampleTime;
712	–	simnfo->thermalTime = simnfo->sampleTime;
713	–	}
714	–
715	–	if( the_globals->haveStatusTime() ){
716	–	simnfo->statusTime = the_globals->getStatusTime();
717	–	}
718	–
719	–	if( the_globals->haveThermalTime() ){
720	–	simnfo->thermalTime = the_globals->getThermalTime();
721	–	}
722	–
723	–	// check for the temperature set flag
724	–
725	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
726	–
727	–
728	–	//   // make the longe range forces and the integrator
729	–
730	–	//   new AllLong( simnfo );
731	–
732	–
733	–	if( !strcmp( force_field, "TraPPE_Ex" ) ){
734	–	new Symplectic(simnfo, the_ff, the_extendedsystem);
735	–	}
736	–	else if( !strcmp( force_field, "LJ" ) ){
737	–	new Verlet( *simnfo, the_ff, the_extendedsystem );
738	–	}
739	–	else {
740	–	std::cerr << "I'm a bug.\n";
741	–	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
742	–	}
108		#ifdef IS_MPI
109		mpiSim->mpiRefresh();
110		#endif
111
112		// initialize the Fortran
113
114	+	initFortran();
115
750	–	simnfo->refreshSim();
751	–
752	–	if( !strcmp( simnfo->mixingRule, "standard") ){
753	–	the_ff->initForceField( LB_MIXING_RULE );
754	–	}
755	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
756	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
757	–	}
758	–	else{
759	–	sprintf( painCave.errMsg,
760	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
761	–	simnfo->mixingRule );
762	–	painCave.isFatal = 1;
763	–	simError();
764	–	}
116
117
767	–	#ifdef IS_MPI
768	–	strcpy( checkPointMsg,
769	–	"Successfully intialized the mixingRule for Fortran." );
770	–	MPIcheckPoint();
771	–	#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 800 | 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 847 | Line 193 | void SimSetup::makeMolecules( void ){
193		dAtom->setSUz( uz );
194		}
195		else{
196	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
196	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
197		}
198	<	info.myAtoms[j]->setType( currentAtom->getType() );
198	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
199
200		#ifdef IS_MPI
201
202	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
202	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
203
204		#endif // is_mpi
205		}
206
207		// make the bonds
208	<	for(j=0; j<info.nBonds; j++){
208	>	for(j=0; j<molInfo.nBonds; j++){
209
210		currentBond = comp_stamps[stampID]->getBond( j );
211		theBonds[j].a = currentBond->getA() + atomOffset;
#	Line 886 | Line 232 | void SimSetup::makeMolecules( void ){
232		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
233		#endif  //is_mpi
234		}
235	<	excludeOffset += info.nBonds;
235	>	excludeOffset += molInfo.nBonds;
236
237		//make the bends
238	<	for(j=0; j<info.nBends; j++){
238	>	for(j=0; j<molInfo.nBends; j++){
239
240		currentBend = comp_stamps[stampID]->getBend( j );
241		theBends[j].a = currentBend->getA() + atomOffset;
#	Line 972 | 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 1002 | Line 348 | void SimSetup::makeMolecules( void ){
348		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349		#endif  //is_mpi
350		}
351	<	excludeOffset += info.nTorsions;
351	>	excludeOffset += molInfo.nTorsions;
352
353
354		// send the arrays off to the forceField for init.
355
356	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
357	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
358	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
359	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
356	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
357	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
358	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
359	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
360
361
362	<	the_molecules[i].initialize( info );
362	>	the_molecules[i].initialize( molInfo );
363
364
365	<	atomOffset += info.nAtoms;
365	>	atomOffset += molInfo.nAtoms;
366		delete[] theBonds;
367		delete[] theBends;
368		delete[] theTorsions;
#	Line 1052 | 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 1069 | 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 1151 | 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 1215 | Line 561 | void SimSetup::makeElement( double x, double y, double
561		current_comp++;
562		}
563		}
564	+
565	+
566	+	void SimSetup::gatherInfo( void ){
567	+	int i,j,k;
568	+
569	+	ensembleCase = -1;
570	+	ffCase = -1;
571	+
572	+	// get the stamps and globals;
573	+	stamps = stamps;
574	+	globals = globals;
575	+
576	+	// set the easy ones first
577	+	info->target_temp = globals->getTargetTemp();
578	+	info->dt = globals->getDt();
579	+	info->run_time = globals->getRunTime();
580	+	n_components = globals->getNComponents();
581	+
582	+
583	+	// get the forceField
584	+
585	+	strcpy( force_field, globals->getForceField() );
586	+
587	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
588	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
589	+	else{
590	+	sprintf( painCave.errMsg,
591	+	"SimSetup Error. Unrecognized force field -> %s\n",
592	+	force_field );
593	+	painCave.isFatal = 1;
594	+	simError();
595	+	}
596	+
597	+	// get the ensemble
598	+
599	+	strcpy( ensemble, globals->getEnsemble() );
600	+
601	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
602	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
603	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
604	+	ensembleCase = NPTi_ENS;
605	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
606	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
607	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
608	+	else{
609	+	sprintf( painCave.errMsg,
610	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
611	+	"reverting to NVE for this simulation.\n",
612	+	ensemble );
613	+	painCave.isFatal = 0;
614	+	simError();
615	+	strcpy( ensemble, "NVE" );
616	+	ensembleCase = NVE_ENS;
617	+	}
618	+	strcpy( info->ensemble, ensemble );
619	+
620	+	// get the mixing rule
621	+
622	+	strcpy( info->mixingRule, globals->getMixingRule() );
623	+	info->usePBC = globals->getPBC();
624	+
625	+
626	+	// get the components and calculate the tot_nMol and indvidual n_mol
627	+
628	+	the_components = globals->getComponents();
629	+	components_nmol = new int[n_components];
630	+
631	+
632	+	if( !globals->haveNMol() ){
633	+	// we don't have the total number of molecules, so we assume it is
634	+	// given in each component
635	+
636	+	tot_nmol = 0;
637	+	for( i=0; i<n_components; i++ ){
638	+
639	+	if( !the_components[i]->haveNMol() ){
640	+	// we have a problem
641	+	sprintf( painCave.errMsg,
642	+	"SimSetup Error. No global NMol or component NMol"
643	+	" given. Cannot calculate the number of atoms.\n" );
644	+	painCave.isFatal = 1;
645	+	simError();
646	+	}
647	+
648	+	tot_nmol += the_components[i]->getNMol();
649	+	components_nmol[i] = the_components[i]->getNMol();
650	+	}
651	+	}
652	+	else{
653	+	sprintf( painCave.errMsg,
654	+	"SimSetup error.\n"
655	+	"\tSorry, the ability to specify total"
656	+	" nMols and then give molfractions in the components\n"
657	+	"\tis not currently supported."
658	+	" Please give nMol in the components.\n" );
659	+	painCave.isFatal = 1;
660	+	simError();
661	+	}
662	+
663	+	// set the status, sample, and thermal kick times
664	+
665	+	if( globals->haveSampleTime() ){
666	+	info->sampleTime = globals->getSampleTime();
667	+	info->statusTime = info->sampleTime;
668	+	info->thermalTime = info->sampleTime;
669	+	}
670	+	else{
671	+	info->sampleTime = globals->getRunTime();
672	+	info->statusTime = info->sampleTime;
673	+	info->thermalTime = info->sampleTime;
674	+	}
675	+
676	+	if( globals->haveStatusTime() ){
677	+	info->statusTime = globals->getStatusTime();
678	+	}
679	+
680	+	if( globals->haveThermalTime() ){
681	+	info->thermalTime = globals->getThermalTime();
682	+	}
683	+
684	+	// check for the temperature set flag
685	+
686	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
687	+
688	+	// get some of the tricky things that may still be in the globals
689	+
690	+	double boxVector[3];
691	+	if( globals->haveBox() ){
692	+	boxVector[0] = globals->getBox();
693	+	boxVector[1] = globals->getBox();
694	+	boxVector[2] = globals->getBox();
695	+
696	+	info->setBox( boxVector );
697	+	}
698	+	else if( globals->haveDensity() ){
699	+
700	+	double vol;
701	+	vol = (double)tot_nmol / globals->getDensity();
702	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
703	+	boxVector[1] = boxVector[0];
704	+	boxVector[2] = boxVector[0];
705	+
706	+	info->setBox( boxVector );
707	+	}
708	+	else{
709	+	if( !globals->haveBoxX() ){
710	+	sprintf( painCave.errMsg,
711	+	"SimSetup error, no periodic BoxX size given.\n" );
712	+	painCave.isFatal = 1;
713	+	simError();
714	+	}
715	+	boxVector[0] = globals->getBoxX();
716	+
717	+	if( !globals->haveBoxY() ){
718	+	sprintf( painCave.errMsg,
719	+	"SimSetup error, no periodic BoxY size given.\n" );
720	+	painCave.isFatal = 1;
721	+	simError();
722	+	}
723	+	boxVector[1] = globals->getBoxY();
724	+
725	+	if( !globals->haveBoxZ() ){
726	+	sprintf( painCave.errMsg,
727	+	"SimSetup error, no periodic BoxZ size given.\n" );
728	+	painCave.isFatal = 1;
729	+	simError();
730	+	}
731	+	boxVector[2] = globals->getBoxZ();
732	+
733	+	info->setBox( boxVector );
734	+	}
735	+
736	+
737	+
738	+	#ifdef IS_MPI
739	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
740	+	MPIcheckPoint();
741	+	#endif // is_mpi
742	+
743	+	}
744	+
745	+
746	+	void SimSetup::finalInfoCheck( void ){
747	+	int index;
748	+	int usesDipoles;
749	+
750	+
751	+	// check electrostatic parameters
752	+
753	+	index = 0;
754	+	usesDipoles = 0;
755	+	while( (index < info->n_atoms) && !usesDipoles ){
756	+	usesDipoles = ((info->atoms)[index])->hasDipole();
757	+	index++;
758	+	}
759	+
760	+	#ifdef IS_MPI
761	+	int myUse = usesDipoles;
762	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
763	+	#endif //is_mpi
764	+
765	+	double theEcr, theEst;
766	+
767	+	if (globals->getUseRF() ) {
768	+	info->useReactionField = 1;
769	+
770	+	if( !globals->haveECR() ){
771	+	sprintf( painCave.errMsg,
772	+	"SimSetup Warning: using default value of 1/2 the smallest "
773	+	"box length for the electrostaticCutoffRadius.\n"
774	+	"I hope you have a very fast processor!\n");
775	+	painCave.isFatal = 0;
776	+	simError();
777	+	double smallest;
778	+	smallest = info->boxL[0];
779	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
780	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
781	+	theEcr = 0.5 * smallest;
782	+	} else {
783	+	theEcr = globals->getECR();
784	+	}
785	+
786	+	if( !globals->haveEST() ){
787	+	sprintf( painCave.errMsg,
788	+	"SimSetup Warning: using default value of 0.05 * the "
789	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
790	+	);
791	+	painCave.isFatal = 0;
792	+	simError();
793	+	theEst = 0.05 * theEcr;
794	+	} else {
795	+	theEst= globals->getEST();
796	+	}
797	+
798	+	info->setEcr( theEcr, theEst );
799	+
800	+	if(!globals->haveDielectric() ){
801	+	sprintf( painCave.errMsg,
802	+	"SimSetup Error: You are trying to use Reaction Field without"
803	+	"setting a dielectric constant!\n"
804	+	);
805	+	painCave.isFatal = 1;
806	+	simError();
807	+	}
808	+	info->dielectric = globals->getDielectric();
809	+	}
810	+	else {
811	+	if (usesDipoles) {
812	+
813	+	if( !globals->haveECR() ){
814	+	sprintf( painCave.errMsg,
815	+	"SimSetup Warning: using default value of 1/2 the smallest "
816	+	"box length for the electrostaticCutoffRadius.\n"
817	+	"I hope you have a very fast processor!\n");
818	+	painCave.isFatal = 0;
819	+	simError();
820	+	double smallest;
821	+	smallest = info->boxL[0];
822	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
823	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
824	+	theEcr = 0.5 * smallest;
825	+	} else {
826	+	theEcr = globals->getECR();
827	+	}
828	+
829	+	if( !globals->haveEST() ){
830	+	sprintf( painCave.errMsg,
831	+	"SimSetup Warning: using default value of 0.05 * the "
832	+	"electrostaticCutoffRadius for the "
833	+	"electrostaticSkinThickness\n"
834	+	);
835	+	painCave.isFatal = 0;
836	+	simError();
837	+	theEst = 0.05 * theEcr;
838	+	} else {
839	+	theEst= globals->getEST();
840	+	}
841	+
842	+	info->setEcr( theEcr, theEst );
843	+	}
844	+	}
845	+
846	+	#ifdef IS_MPI
847	+	strcpy( checkPointMsg, "post processing checks out" );
848	+	MPIcheckPoint();
849	+	#endif // is_mpi
850	+
851	+	}
852	+
853	+	void SimSetup::initSystemCoords( void ){
854	+
855	+	if( globals->haveInitialConfig() ){
856	+
857	+	InitializeFromFile* fileInit;
858	+	#ifdef IS_MPI // is_mpi
859	+	if( worldRank == 0 ){
860	+	#endif //is_mpi
861	+	fileInit = new InitializeFromFile( globals->getInitialConfig() );
862	+	#ifdef IS_MPI
863	+	}else fileInit = new InitializeFromFile( NULL );
864	+	#endif
865	+	fileInit->read_xyz( info ); // default velocities on
866	+
867	+	delete fileInit;
868	+	}
869	+	else{
870	+
871	+	#ifdef IS_MPI
872	+
873	+	// no init from bass
874	+
875	+	sprintf( painCave.errMsg,
876	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
877	+	painCave.isFatal;
878	+	simError();
879	+
880	+	#else
881	+
882	+	initFromBass();
883	+
884	+
885	+	#endif
886	+	}
887	+
888	+	#ifdef IS_MPI
889	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
890	+	MPIcheckPoint();
891	+	#endif // is_mpi
892	+
893	+	}
894	+
895	+
896	+	void SimSetup::makeOutNames( void ){
897	+
898	+	#ifdef IS_MPI
899	+	if( worldRank == 0 ){
900	+	#endif // is_mpi
901	+
902	+	if( globals->haveFinalConfig() ){
903	+	strcpy( info->finalName, globals->getFinalConfig() );
904	+	}
905	+	else{
906	+	strcpy( info->finalName, inFileName );
907	+	char* endTest;
908	+	int nameLength = strlen( info->finalName );
909	+	endTest = &(info->finalName[nameLength - 5]);
910	+	if( !strcmp( endTest, ".bass" ) ){
911	+	strcpy( endTest, ".eor" );
912	+	}
913	+	else if( !strcmp( endTest, ".BASS" ) ){
914	+	strcpy( endTest, ".eor" );
915	+	}
916	+	else{
917	+	endTest = &(info->finalName[nameLength - 4]);
918	+	if( !strcmp( endTest, ".bss" ) ){
919	+	strcpy( endTest, ".eor" );
920	+	}
921	+	else if( !strcmp( endTest, ".mdl" ) ){
922	+	strcpy( endTest, ".eor" );
923	+	}
924	+	else{
925	+	strcat( info->finalName, ".eor" );
926	+	}
927	+	}
928	+	}
929	+
930	+	// make the sample and status out names
931	+
932	+	strcpy( info->sampleName, inFileName );
933	+	char* endTest;
934	+	int nameLength = strlen( info->sampleName );
935	+	endTest = &(info->sampleName[nameLength - 5]);
936	+	if( !strcmp( endTest, ".bass" ) ){
937	+	strcpy( endTest, ".dump" );
938	+	}
939	+	else if( !strcmp( endTest, ".BASS" ) ){
940	+	strcpy( endTest, ".dump" );
941	+	}
942	+	else{
943	+	endTest = &(info->sampleName[nameLength - 4]);
944	+	if( !strcmp( endTest, ".bss" ) ){
945	+	strcpy( endTest, ".dump" );
946	+	}
947	+	else if( !strcmp( endTest, ".mdl" ) ){
948	+	strcpy( endTest, ".dump" );
949	+	}
950	+	else{
951	+	strcat( info->sampleName, ".dump" );
952	+	}
953	+	}
954	+
955	+	strcpy( info->statusName, inFileName );
956	+	nameLength = strlen( info->statusName );
957	+	endTest = &(info->statusName[nameLength - 5]);
958	+	if( !strcmp( endTest, ".bass" ) ){
959	+	strcpy( endTest, ".stat" );
960	+	}
961	+	else if( !strcmp( endTest, ".BASS" ) ){
962	+	strcpy( endTest, ".stat" );
963	+	}
964	+	else{
965	+	endTest = &(info->statusName[nameLength - 4]);
966	+	if( !strcmp( endTest, ".bss" ) ){
967	+	strcpy( endTest, ".stat" );
968	+	}
969	+	else if( !strcmp( endTest, ".mdl" ) ){
970	+	strcpy( endTest, ".stat" );
971	+	}
972	+	else{
973	+	strcat( info->statusName, ".stat" );
974	+	}
975	+	}
976	+
977	+	#ifdef IS_MPI
978	+	}
979	+	#endif // is_mpi
980	+
981	+	}
982	+
983	+
984	+	void SimSetup::sysObjectsCreation( void ){
985	+
986	+	int i;
987	+
988	+	// create the forceField
989	+
990	+	createFF();
991	+
992	+	// extract componentList
993	+
994	+	compList();
995	+
996	+	// calc the number of atoms, bond, bends, and torsions
997	+
998	+	calcSysValues();
999	+
1000	+	#ifdef IS_MPI
1001	+	// divide the molecules among the processors
1002	+
1003	+	mpiMolDivide();
1004	+	#endif //is_mpi
1005	+
1006	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1007	+
1008	+	makeSysArrays();
1009	+
1010	+	// make and initialize the molecules (all but atomic coordinates)
1011	+
1012	+	makeMolecules();
1013	+	info->identArray = new int[info->n_atoms];
1014	+	for(i=0; i<info->n_atoms; i++){
1015	+	info->identArray[i] = the_atoms[i]->getIdent();
1016	+	}
1017	+
1018	+
1019	+
1020	+	}
1021	+
1022	+
1023	+	void SimSetup::createFF( void ){
1024	+
1025	+	switch( ffCase ){
1026	+
1027	+	case FF_DUFF:
1028	+	the_ff = new DUFF();
1029	+	break;
1030	+
1031	+	case FF_LJ:
1032	+	the_ff = new LJFF();
1033	+	break;
1034	+
1035	+	default:
1036	+	sprintf( painCave.errMsg,
1037	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1038	+	painCave.isFatal = 1;
1039	+	simError();
1040	+	}
1041	+
1042	+	#ifdef IS_MPI
1043	+	strcpy( checkPointMsg, "ForceField creation successful" );
1044	+	MPIcheckPoint();
1045	+	#endif // is_mpi
1046	+
1047	+	}
1048	+
1049	+
1050	+	void SimSetup::compList( void ){
1051	+
1052	+	int i;
1053	+
1054	+	comp_stamps = new MoleculeStamp*[n_components];
1055	+
1056	+	// make an array of molecule stamps that match the components used.
1057	+	// also extract the used stamps out into a separate linked list
1058	+
1059	+	info->nComponents = n_components;
1060	+	info->componentsNmol = components_nmol;
1061	+	info->compStamps = comp_stamps;
1062	+	info->headStamp = new LinkedMolStamp();
1063	+
1064	+	char* id;
1065	+	LinkedMolStamp* headStamp = info->headStamp;
1066	+	LinkedMolStamp* currentStamp = NULL;
1067	+	for( i=0; i<n_components; i++ ){
1068	+
1069	+	id = the_components[i]->getType();
1070	+	comp_stamps[i] = NULL;
1071	+
1072	+	// check to make sure the component isn't already in the list
1073	+
1074	+	comp_stamps[i] = headStamp->match( id );
1075	+	if( comp_stamps[i] == NULL ){
1076	+
1077	+	// extract the component from the list;
1078	+
1079	+	currentStamp = stamps->extractMolStamp( id );
1080	+	if( currentStamp == NULL ){
1081	+	sprintf( painCave.errMsg,
1082	+	"SimSetup error: Component \"%s\" was not found in the "
1083	+	"list of declared molecules\n",
1084	+	id );
1085	+	painCave.isFatal = 1;
1086	+	simError();
1087	+	}
1088	+
1089	+	headStamp->add( currentStamp );
1090	+	comp_stamps[i] = headStamp->match( id );
1091	+	}
1092	+	}
1093	+
1094	+	#ifdef IS_MPI
1095	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1096	+	MPIcheckPoint();
1097	+	#endif // is_mpi
1098	+
1099	+
1100	+	}
1101	+
1102	+	void SimSetup::calcSysValues( void ){
1103	+	int i, j, k;
1104	+
1105	+
1106	+	tot_atoms = 0;
1107	+	tot_bonds = 0;
1108	+	tot_bends = 0;
1109	+	tot_torsions = 0;
1110	+	for( i=0; i<n_components; i++ ){
1111	+
1112	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1113	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1114	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1115	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1116	+	}
1117	+
1118	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1119	+
1120	+	info->n_atoms = tot_atoms;
1121	+	info->n_bonds = tot_bonds;
1122	+	info->n_bends = tot_bends;
1123	+	info->n_torsions = tot_torsions;
1124	+	info->n_SRI = tot_SRI;
1125	+	info->n_mol = tot_nmol;
1126	+
1127	+	info->molMembershipArray = new int[tot_atoms];
1128	+	}
1129	+
1130	+
1131	+	#ifdef IS_MPI
1132	+
1133	+	void SimSetup::mpiMolDivide( void ){
1134	+
1135	+	int i, j, k;
1136	+	int localMol, allMol;
1137	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1138	+
1139	+	mpiSim = new mpiSimulation( info );
1140	+
1141	+	globalIndex = mpiSim->divideLabor();
1142	+
1143	+	// set up the local variables
1144	+
1145	+	mol2proc = mpiSim->getMolToProcMap();
1146	+	molCompType = mpiSim->getMolComponentType();
1147	+
1148	+	allMol = 0;
1149	+	localMol = 0;
1150	+	local_atoms = 0;
1151	+	local_bonds = 0;
1152	+	local_bends = 0;
1153	+	local_torsions = 0;
1154	+	globalAtomIndex = 0;
1155	+
1156	+
1157	+	for( i=0; i<n_components; i++ ){
1158	+
1159	+	for( j=0; j<components_nmol[i]; j++ ){
1160	+
1161	+	if( mol2proc[allMol] == worldRank ){
1162	+
1163	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1164	+	local_bonds +=    comp_stamps[i]->getNBonds();
1165	+	local_bends +=    comp_stamps[i]->getNBends();
1166	+	local_torsions += comp_stamps[i]->getNTorsions();
1167	+	localMol++;
1168	+	}
1169	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1170	+	info->molMembershipArray[globalAtomIndex] = allMol;
1171	+	globalAtomIndex++;
1172	+	}
1173	+
1174	+	allMol++;
1175	+	}
1176	+	}
1177	+	local_SRI = local_bonds + local_bends + local_torsions;
1178	+
1179	+	info->n_atoms = mpiSim->getMyNlocal();
1180	+
1181	+	if( local_atoms != info->n_atoms ){
1182	+	sprintf( painCave.errMsg,
1183	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1184	+	" localAtom (%d) are not equal.\n",
1185	+	info->n_atoms,
1186	+	local_atoms );
1187	+	painCave.isFatal = 1;
1188	+	simError();
1189	+	}
1190	+
1191	+	info->n_bonds = local_bonds;
1192	+	info->n_bends = local_bends;
1193	+	info->n_torsions = local_torsions;
1194	+	info->n_SRI = local_SRI;
1195	+	info->n_mol = localMol;
1196	+
1197	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1198	+	MPIcheckPoint();
1199	+	}
1200	+
1201	+	#endif // is_mpi
1202	+
1203	+
1204	+	void SimSetup::makeSysArrays( void ){
1205	+	int i, j, k;
1206	+
1207	+
1208	+	// create the atom and short range interaction arrays
1209	+
1210	+	Atom::createArrays(info->n_atoms);
1211	+	the_atoms = new Atom*[info->n_atoms];
1212	+	the_molecules = new Molecule[info->n_mol];
1213	+	int molIndex;
1214	+
1215	+	// initialize the molecule's stampID's
1216	+
1217	+	#ifdef IS_MPI
1218	+
1219	+
1220	+	molIndex = 0;
1221	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1222	+
1223	+	if(mol2proc[i] == worldRank ){
1224	+	the_molecules[molIndex].setStampID( molCompType[i] );
1225	+	the_molecules[molIndex].setMyIndex( molIndex );
1226	+	the_molecules[molIndex].setGlobalIndex( i );
1227	+	molIndex++;
1228	+	}
1229	+	}
1230	+
1231	+	#else // is_mpi
1232	+
1233	+	molIndex = 0;
1234	+	globalAtomIndex = 0;
1235	+	for(i=0; i<n_components; i++){
1236	+	for(j=0; j<components_nmol[i]; j++ ){
1237	+	the_molecules[molIndex].setStampID( i );
1238	+	the_molecules[molIndex].setMyIndex( molIndex );
1239	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1240	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1241	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1242	+	globalAtomIndex++;
1243	+	}
1244	+	molIndex++;
1245	+	}
1246	+	}
1247	+
1248	+
1249	+	#endif // is_mpi
1250	+
1251	+
1252	+	if( info->n_SRI ){
1253	+
1254	+	Exclude::createArray(info->n_SRI);
1255	+	the_excludes = new Exclude*[info->n_SRI];
1256	+	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1257	+	info->globalExcludes = new int;
1258	+	info->n_exclude = info->n_SRI;
1259	+	}
1260	+	else{
1261	+
1262	+	Exclude::createArray( 1 );
1263	+	the_excludes = new Exclude*;
1264	+	the_excludes[0] = new Exclude(0);
1265	+	the_excludes[0]->setPair( 0,0 );
1266	+	info->globalExcludes = new int;
1267	+	info->globalExcludes[0] = 0;
1268	+	info->n_exclude = 0;
1269	+	}
1270	+
1271	+	// set the arrays into the SimInfo object
1272	+
1273	+	info->atoms = the_atoms;
1274	+	info->molecules = the_molecules;
1275	+	info->nGlobalExcludes = 0;
1276	+	info->excludes = the_excludes;
1277	+
1278	+	the_ff->setSimInfo( info );
1279	+
1280	+	}
1281	+
1282	+	void SimSetup::makeIntegrator( void ){
1283	+
1284	+	NVT*  myNVT = NULL;
1285	+	NPTi* myNPTi = NULL;
1286	+	NPTf* myNPTf = NULL;
1287	+	NPTim* myNPTim = NULL;
1288	+	NPTfm* myNPTfm = NULL;
1289	+
1290	+	switch( ensembleCase ){
1291	+
1292	+	case NVE_ENS:
1293	+	new NVE( info, the_ff );
1294	+	break;
1295	+
1296	+	case NVT_ENS:
1297	+	myNVT = new NVT( info, the_ff );
1298	+	myNVT->setTargetTemp(globals->getTargetTemp());
1299	+
1300	+	if (globals->haveTauThermostat())
1301	+	myNVT->setTauThermostat(globals->getTauThermostat());
1302	+
1303	+	else {
1304	+	sprintf( painCave.errMsg,
1305	+	"SimSetup error: If you use the NVT\n"
1306	+	"    ensemble, you must set tauThermostat.\n");
1307	+	painCave.isFatal = 1;
1308	+	simError();
1309	+	}
1310	+	break;
1311	+
1312	+	case NPTi_ENS:
1313	+	myNPTi = new NPTi( info, the_ff );
1314	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1315	+
1316	+	if (globals->haveTargetPressure())
1317	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1318	+	else {
1319	+	sprintf( painCave.errMsg,
1320	+	"SimSetup error: If you use a constant pressure\n"
1321	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1322	+	painCave.isFatal = 1;
1323	+	simError();
1324	+	}
1325	+
1326	+	if( globals->haveTauThermostat() )
1327	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1328	+	else{
1329	+	sprintf( painCave.errMsg,
1330	+	"SimSetup error: If you use an NPT\n"
1331	+	"    ensemble, you must set tauThermostat.\n");
1332	+	painCave.isFatal = 1;
1333	+	simError();
1334	+	}
1335	+
1336	+	if( globals->haveTauBarostat() )
1337	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1338	+	else{
1339	+	sprintf( painCave.errMsg,
1340	+	"SimSetup error: If you use an NPT\n"
1341	+	"    ensemble, you must set tauBarostat.\n");
1342	+	painCave.isFatal = 1;
1343	+	simError();
1344	+	}
1345	+	break;
1346	+
1347	+	case NPTf_ENS:
1348	+	myNPTf = new NPTf( info, the_ff );
1349	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1350	+
1351	+	if (globals->haveTargetPressure())
1352	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1353	+	else {
1354	+	sprintf( painCave.errMsg,
1355	+	"SimSetup error: If you use a constant pressure\n"
1356	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1357	+	painCave.isFatal = 1;
1358	+	simError();
1359	+	}
1360	+
1361	+	if( globals->haveTauThermostat() )
1362	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1363	+	else{
1364	+	sprintf( painCave.errMsg,
1365	+	"SimSetup error: If you use an NPT\n"
1366	+	"    ensemble, you must set tauThermostat.\n");
1367	+	painCave.isFatal = 1;
1368	+	simError();
1369	+	}
1370	+
1371	+	if( globals->haveTauBarostat() )
1372	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1373	+	else{
1374	+	sprintf( painCave.errMsg,
1375	+	"SimSetup error: If you use an NPT\n"
1376	+	"    ensemble, you must set tauBarostat.\n");
1377	+	painCave.isFatal = 1;
1378	+	simError();
1379	+	}
1380	+	break;
1381	+
1382	+	case NPTim_ENS:
1383	+	myNPTim = new NPTim( info, the_ff );
1384	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1385	+
1386	+	if (globals->haveTargetPressure())
1387	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1388	+	else {
1389	+	sprintf( painCave.errMsg,
1390	+	"SimSetup error: If you use a constant pressure\n"
1391	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1392	+	painCave.isFatal = 1;
1393	+	simError();
1394	+	}
1395	+
1396	+	if( globals->haveTauThermostat() )
1397	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1398	+	else{
1399	+	sprintf( painCave.errMsg,
1400	+	"SimSetup error: If you use an NPT\n"
1401	+	"    ensemble, you must set tauThermostat.\n");
1402	+	painCave.isFatal = 1;
1403	+	simError();
1404	+	}
1405	+
1406	+	if( globals->haveTauBarostat() )
1407	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1408	+	else{
1409	+	sprintf( painCave.errMsg,
1410	+	"SimSetup error: If you use an NPT\n"
1411	+	"    ensemble, you must set tauBarostat.\n");
1412	+	painCave.isFatal = 1;
1413	+	simError();
1414	+	}
1415	+	break;
1416	+
1417	+	case NPTfm_ENS:
1418	+	myNPTfm = new NPTfm( info, the_ff );
1419	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1420	+
1421	+	if (globals->haveTargetPressure())
1422	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1423	+	else {
1424	+	sprintf( painCave.errMsg,
1425	+	"SimSetup error: If you use a constant pressure\n"
1426	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1427	+	painCave.isFatal = 1;
1428	+	simError();
1429	+	}
1430	+
1431	+	if( globals->haveTauThermostat() )
1432	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1433	+	else{
1434	+	sprintf( painCave.errMsg,
1435	+	"SimSetup error: If you use an NPT\n"
1436	+	"    ensemble, you must set tauThermostat.\n");
1437	+	painCave.isFatal = 1;
1438	+	simError();
1439	+	}
1440	+
1441	+	if( globals->haveTauBarostat() )
1442	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1443	+	else{
1444	+	sprintf( painCave.errMsg,
1445	+	"SimSetup error: If you use an NPT\n"
1446	+	"    ensemble, you must set tauBarostat.\n");
1447	+	painCave.isFatal = 1;
1448	+	simError();
1449	+	}
1450	+	break;
1451	+
1452	+	default:
1453	+	sprintf( painCave.errMsg,
1454	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1455	+	painCave.isFatal = 1;
1456	+	simError();
1457	+	}
1458	+
1459	+	}
1460	+
1461	+	void SimSetup::initFortran( void ){
1462	+
1463	+	info->refreshSim();
1464	+
1465	+	if( !strcmp( info->mixingRule, "standard") ){
1466	+	the_ff->initForceField( LB_MIXING_RULE );
1467	+	}
1468	+	else if( !strcmp( info->mixingRule, "explicit") ){
1469	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1470	+	}
1471	+	else{
1472	+	sprintf( painCave.errMsg,
1473	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1474	+	info->mixingRule );
1475	+	painCave.isFatal = 1;
1476	+	simError();
1477	+	}
1478	+
1479	+
1480	+	#ifdef IS_MPI
1481	+	strcpy( checkPointMsg,
1482	+	"Successfully intialized the mixingRule for Fortran." );
1483	+	MPIcheckPoint();
1484	+	#endif // is_mpi
1485	+
1486	+	}

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