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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC vs.
Revision 660 by tim, Thu Jul 31 19:59:34 2003 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
2	<	#include <iostream>
3	<	#include <cmath>
4	<
5	<	#include "SimSetup.hpp"
6	<	#include "parse_me.h"
7	<	#include "Integrator.hpp"
8	<	#include "simError.h"
9	<
10	<	#ifdef IS_MPI
11	<	#include "mpiBASS.h"
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	<
22	<
23	<	#define FF_DUFF 0
24	<	#define FF_LJ   1
25	<
26	<
27	<	SimSetup::SimSetup(){
28	<	stamps = new MakeStamps();
29	<	globals = new Globals();
30	<
31	<	#ifdef IS_MPI
32	<	strcpy( checkPointMsg, "SimSetup creation successful" );
33	<	MPIcheckPoint();
34	<	#endif // IS_MPI
35	<	}
36	<
37	<	SimSetup::~SimSetup(){
38	<	delete stamps;
39	<	delete globals;
40	<	}
41	<
42	<	void SimSetup::parseFile( char* fileName ){
43	<
44	<	#ifdef IS_MPI
45	<	if( worldRank == 0 ){
46	<	#endif // is_mpi
47	<
48	<	inFileName = fileName;
49	<	set_interface_stamps( stamps, globals );
50	<
51	<	#ifdef IS_MPI
52	<	mpiEventInit();
53	<	#endif
54	<
55	<	yacc_BASS( fileName );
56	<
57	<	#ifdef IS_MPI
58	<	throwMPIEvent(NULL);
59	<	}
60	<	else receiveParse();
61	<	#endif
62	<
63	<	}
64	<
65	<	#ifdef IS_MPI
66	<	void SimSetup::receiveParse(void){
67	<
68	<	set_interface_stamps( stamps, globals );
69	<	mpiEventInit();
70	<	MPIcheckPoint();
71	<	mpiEventLoop();
72	<
73	<	}
74	<
75	<	#endif // is_mpi
76	<
77	<	void SimSetup::createSim( void ){
78	<
79	<	MakeStamps *the_stamps;
80	<	Globals* the_globals;
81	<	int i, j, k, globalAtomIndex;
82	<
83	<	int ensembleCase;
84	<	int ffCase;
85	<
86	<	ensembleCase = -1;
87	<	ffCase = -1;
88	<
89	<	// get the stamps and globals;
90	<	the_stamps = stamps;
91	<	the_globals = globals;
92	<
93	<	// set the easy ones first
94	<	simnfo->target_temp = the_globals->getTargetTemp();
95	<	simnfo->dt = the_globals->getDt();
96	<	simnfo->run_time = the_globals->getRunTime();
97	<
98	<	// get the ones we know are there, yet still may need some work.
99	<	n_components = the_globals->getNComponents();
100	<	strcpy( force_field, the_globals->getForceField() );
101	<
102	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
103	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
104	<	else{
105	<	sprintf( painCave.errMsg,
106	<	"SimSetup Error. Unrecognized force field -> %s\n",
107	<	force_field );
108	<	painCave.isFatal = 1;
109	<	simError();
110	<	}
111	<
112	<	// get the ensemble:
113	<	strcpy( ensemble, the_globals->getEnsemble() );
114	<
115	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
116	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
117	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
118	<	ensembleCase = NPTi_ENS;
119	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
120	<	else{
121	<	sprintf( painCave.errMsg,
122	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
123	<	"reverting to NVE for this simulation.\n",
124	<	ensemble );
125	<	painCave.isFatal = 0;
126	<	simError();
127	<	strcpy( ensemble, "NVE" );
128	<	ensembleCase = NVE_ENS;
129	<	}
130	<	strcpy( simnfo->ensemble, ensemble );
131	<
132	<
133	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
134	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
135	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
136	<	//     if (the_globals->haveTargetPressure())
137	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
138	<	//     else {
139	<	//       sprintf( painCave.errMsg,
140	<	//                "SimSetup error: If you use the constant pressure\n"
141	<	//                "    ensemble, you must set targetPressure.\n"
142	<	//                "    This was found in the BASS file.\n");
143	<	//       painCave.isFatal = 1;
144	<	//       simError();
145	<	//     }
146	<
147	<	//     if (the_globals->haveTauThermostat())
148	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
149	<	//     else if (the_globals->haveQmass())
150	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
151	<	//     else {
152	<	//       sprintf( painCave.errMsg,
153	<	//                "SimSetup error: If you use one of the constant temperature\n"
154	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
155	<	//                "    Neither of these was found in the BASS file.\n");
156	<	//       painCave.isFatal = 1;
157	<	//       simError();
158	<	//     }
159	<
160	<	//     if (the_globals->haveTauBarostat())
161	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
162	<	//     else {
163	<	//       sprintf( painCave.errMsg,
164	<	//                "SimSetup error: If you use the constant pressure\n"
165	<	//                "    ensemble, you must set tauBarostat.\n"
166	<	//                "    This was found in the BASS file.\n");
167	<	//       painCave.isFatal = 1;
168	<	//       simError();
169	<	//     }
170	<
171	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
172	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
173	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
174	<
175	<	//     if (the_globals->haveTauThermostat())
176	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
177	<	//     else if (the_globals->haveQmass())
178	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
179	<	//     else {
180	<	//       sprintf( painCave.errMsg,
181	<	//                "SimSetup error: If you use one of the constant temperature\n"
182	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
183	<	//                "    Neither of these was found in the BASS file.\n");
184	<	//       painCave.isFatal = 1;
185	<	//       simError();
186	<	//     }
187	<
188	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
189	<	simnfo->usePBC = the_globals->getPBC();
190	<
191	<	int usesDipoles = 0;
192	<	switch( ffCase ){
193	<
194	<	case FF_DUFF:
195	<	the_ff = new DUFF();
196	<	usesDipoles = 1;
197	<	break;
198	<
199	<	case FF_LJ:
200	<	the_ff = new LJFF();
201	<	break;
202	<
203	<	default:
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup Error. Unrecognized force field in case statement.\n");
206	<	painCave.isFatal = 1;
207	<	simError();
208	<	}
209	<
210	<	#ifdef IS_MPI
211	<	strcpy( checkPointMsg, "ForceField creation successful" );
212	<	MPIcheckPoint();
213	<	#endif // is_mpi
214	<
215	<	// get the components and calculate the tot_nMol and indvidual n_mol
216	<	the_components = the_globals->getComponents();
217	<	components_nmol = new int[n_components];
218	<	comp_stamps = new MoleculeStamp*[n_components];
219	<
220	<	if( !the_globals->haveNMol() ){
221	<	// we don't have the total number of molecules, so we assume it is
222	<	// given in each component
223	<
224	<	tot_nmol = 0;
225	<	for( i=0; i<n_components; i++ ){
226	<
227	<	if( !the_components[i]->haveNMol() ){
228	<	// we have a problem
229	<	sprintf( painCave.errMsg,
230	<	"SimSetup Error. No global NMol or component NMol"
231	<	" given. Cannot calculate the number of atoms.\n" );
232	<	painCave.isFatal = 1;
233	<	simError();
234	<	}
235	<
236	<	tot_nmol += the_components[i]->getNMol();
237	<	components_nmol[i] = the_components[i]->getNMol();
238	<	}
239	<	}
240	<	else{
241	<	sprintf( painCave.errMsg,
242	<	"SimSetup error.\n"
243	<	"\tSorry, the ability to specify total"
244	<	" nMols and then give molfractions in the components\n"
245	<	"\tis not currently supported."
246	<	" Please give nMol in the components.\n" );
247	<	painCave.isFatal = 1;
248	<	simError();
249	<
250	<
251	<	//     tot_nmol = the_globals->getNMol();
252	<
253	<	//   //we have the total number of molecules, now we check for molfractions
254	<	//     for( i=0; i<n_components; i++ ){
255	<
256	<	//       if( !the_components[i]->haveMolFraction() ){
257	<
258	<	//  if( !the_components[i]->haveNMol() ){
259	<	//    //we have a problem
260	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
261	<	//              << " nMol was given in component
262	<
263	<	}
264	<
265	<	#ifdef IS_MPI
266	<	strcpy( checkPointMsg, "Have the number of components" );
267	<	MPIcheckPoint();
268	<	#endif // is_mpi
269	<
270	<	// make an array of molecule stamps that match the components used.
271	<	// also extract the used stamps out into a separate linked list
272	<
273	<	simnfo->nComponents = n_components;
274	<	simnfo->componentsNmol = components_nmol;
275	<	simnfo->compStamps = comp_stamps;
276	<	simnfo->headStamp = new LinkedMolStamp();
277	<
278	<	char* id;
279	<	LinkedMolStamp* headStamp = simnfo->headStamp;
280	<	LinkedMolStamp* currentStamp = NULL;
281	<	for( i=0; i<n_components; i++ ){
282	<
283	<	id = the_components[i]->getType();
284	<	comp_stamps[i] = NULL;
285	<
286	<	// check to make sure the component isn't already in the list
287	<
288	<	comp_stamps[i] = headStamp->match( id );
289	<	if( comp_stamps[i] == NULL ){
290	<
291	<	// extract the component from the list;
292	<
293	<	currentStamp = the_stamps->extractMolStamp( id );
294	<	if( currentStamp == NULL ){
295	<	sprintf( painCave.errMsg,
296	<	"SimSetup error: Component \"%s\" was not found in the "
297	<	"list of declared molecules\n",
298	<	id );
299	<	painCave.isFatal = 1;
300	<	simError();
301	<	}
302	<
303	<	headStamp->add( currentStamp );
304	<	comp_stamps[i] = headStamp->match( id );
305	<	}
306	<	}
307	<
308	<	#ifdef IS_MPI
309	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
310	<	MPIcheckPoint();
311	<	#endif // is_mpi
312	<
313	<
314	<
315	<
316	<	// caclulate the number of atoms, bonds, bends and torsions
317	<
318	<	tot_atoms = 0;
319	<	tot_bonds = 0;
320	<	tot_bends = 0;
321	<	tot_torsions = 0;
322	<	for( i=0; i<n_components; i++ ){
323	<
324	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
325	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
326	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
327	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
328	<	}
329	<
330	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
331	<
332	<	simnfo->n_atoms = tot_atoms;
333	<	simnfo->n_bonds = tot_bonds;
334	<	simnfo->n_bends = tot_bends;
335	<	simnfo->n_torsions = tot_torsions;
336	<	simnfo->n_SRI = tot_SRI;
337	<	simnfo->n_mol = tot_nmol;
338	<
339	<	simnfo->molMembershipArray = new int[tot_atoms];
340	<
341	<	#ifdef IS_MPI
342	<
343	<	// divide the molecules among processors here.
344	<
345	<	mpiSim = new mpiSimulation( simnfo );
346	<
347	<	globalIndex = mpiSim->divideLabor();
348	<
349	<	// set up the local variables
350	<
351	<	int localMol, allMol;
352	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
353	<
354	<	int* mol2proc = mpiSim->getMolToProcMap();
355	<	int* molCompType = mpiSim->getMolComponentType();
356	<
357	<	allMol = 0;
358	<	localMol = 0;
359	<	local_atoms = 0;
360	<	local_bonds = 0;
361	<	local_bends = 0;
362	<	local_torsions = 0;
363	<	globalAtomIndex = 0;
364	<
365	<
366	<	for( i=0; i<n_components; i++ ){
367	<
368	<	for( j=0; j<components_nmol[i]; j++ ){
369	<
370	<	if( mol2proc[allMol] == worldRank ){
371	<
372	<	local_atoms +=    comp_stamps[i]->getNAtoms();
373	<	local_bonds +=    comp_stamps[i]->getNBonds();
374	<	local_bends +=    comp_stamps[i]->getNBends();
375	<	local_torsions += comp_stamps[i]->getNTorsions();
376	<	localMol++;
377	<	}
378	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
379	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
380	<	globalAtomIndex++;
381	<	}
382	<
383	<	allMol++;
384	<	}
385	<	}
386	<	local_SRI = local_bonds + local_bends + local_torsions;
387	<
388	<	simnfo->n_atoms = mpiSim->getMyNlocal();
389	<
390	<	if( local_atoms != simnfo->n_atoms ){
391	<	sprintf( painCave.errMsg,
392	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
393	<	" localAtom (%d) are not equal.\n",
394	<	simnfo->n_atoms,
395	<	local_atoms );
396	<	painCave.isFatal = 1;
397	<	simError();
398	<	}
399	<
400	<	simnfo->n_bonds = local_bonds;
401	<	simnfo->n_bends = local_bends;
402	<	simnfo->n_torsions = local_torsions;
403	<	simnfo->n_SRI = local_SRI;
404	<	simnfo->n_mol = localMol;
405	<
406	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
407	<	MPIcheckPoint();
408	<
409	<
410	<	#endif // is_mpi
411	<
412	<
413	<	// create the atom and short range interaction arrays
414	<
415	<	Atom::createArrays(simnfo->n_atoms);
416	<	the_atoms = new Atom*[simnfo->n_atoms];
417	<	the_molecules = new Molecule[simnfo->n_mol];
418	<	int molIndex;
419	<
420	<	// initialize the molecule's stampID's
421	<
422	<	#ifdef IS_MPI
423	<
424	<
425	<	molIndex = 0;
426	<	for(i=0; i<mpiSim->getTotNmol(); i++){
427	<
428	<	if(mol2proc[i] == worldRank ){
429	<	the_molecules[molIndex].setStampID( molCompType[i] );
430	<	the_molecules[molIndex].setMyIndex( molIndex );
431	<	the_molecules[molIndex].setGlobalIndex( i );
432	<	molIndex++;
433	<	}
434	<	}
435	<
436	<	#else // is_mpi
437	<
438	<	molIndex = 0;
439	<	globalAtomIndex = 0;
440	<	for(i=0; i<n_components; i++){
441	<	for(j=0; j<components_nmol[i]; j++ ){
442	<	the_molecules[molIndex].setStampID( i );
443	<	the_molecules[molIndex].setMyIndex( molIndex );
444	<	the_molecules[molIndex].setGlobalIndex( molIndex );
445	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
446	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
447	<	globalAtomIndex++;
448	<	}
449	<	molIndex++;
450	<	}
451	<	}
452	<
453	<
454	<	#endif // is_mpi
455	<
456	<
457	<	if( simnfo->n_SRI ){
458	<
459	<	Exclude::createArray(simnfo->n_SRI);
460	<	the_excludes = new Exclude*[simnfo->n_SRI];
461	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
462	<	simnfo->globalExcludes = new int;
463	<	simnfo->n_exclude = simnfo->n_SRI;
464	<	}
465	<	else{
466	<
467	<	Exclude::createArray( 1 );
468	<	the_excludes = new Exclude*;
469	<	the_excludes[0] = new Exclude(0);
470	<	the_excludes[0]->setPair( 0,0 );
471	<	simnfo->globalExcludes = new int;
472	<	simnfo->globalExcludes[0] = 0;
473	<	simnfo->n_exclude = 0;
474	<	}
475	<
476	<	// set the arrays into the SimInfo object
477	<
478	<	simnfo->atoms = the_atoms;
479	<	simnfo->molecules = the_molecules;
480	<	simnfo->nGlobalExcludes = 0;
481	<	simnfo->excludes = the_excludes;
482	<
483	<
484	<	// get some of the tricky things that may still be in the globals
485	<
486	<	double boxVector[3];
487	<	if( the_globals->haveBox() ){
488	<	boxVector[0] = the_globals->getBox();
489	<	boxVector[1] = the_globals->getBox();
490	<	boxVector[2] = the_globals->getBox();
491	<
492	<	simnfo->setBox( boxVector );
493	<	}
494	<	else if( the_globals->haveDensity() ){
495	<
496	<	double vol;
497	<	vol = (double)tot_nmol / the_globals->getDensity();
498	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
499	<	boxVector[1] = boxVector[0];
500	<	boxVector[2] = boxVector[0];
501	<
502	<	simnfo->setBox( boxVector );
503	<	}
504	<	else{
505	<	if( !the_globals->haveBoxX() ){
506	<	sprintf( painCave.errMsg,
507	<	"SimSetup error, no periodic BoxX size given.\n" );
508	<	painCave.isFatal = 1;
509	<	simError();
510	<	}
511	<	boxVector[0] = the_globals->getBoxX();
512	<
513	<	if( !the_globals->haveBoxY() ){
514	<	sprintf( painCave.errMsg,
515	<	"SimSetup error, no periodic BoxY size given.\n" );
516	<	painCave.isFatal = 1;
517	<	simError();
518	<	}
519	<	boxVector[1] = the_globals->getBoxY();
520	<
521	<	if( !the_globals->haveBoxZ() ){
522	<	sprintf( painCave.errMsg,
523	<	"SimSetup error, no periodic BoxZ size given.\n" );
524	<	painCave.isFatal = 1;
525	<	simError();
526	<	}
527	<	boxVector[2] = the_globals->getBoxZ();
528	<
529	<	simnfo->setBox( boxVector );
530	<	}
531	<
532	<	#ifdef IS_MPI
533	<	strcpy( checkPointMsg, "Box size set up" );
534	<	MPIcheckPoint();
535	<	#endif // is_mpi
536	<
537	<
538	<	// initialize the arrays
539	<
540	<	the_ff->setSimInfo( simnfo );
541	<
542	<	makeMolecules();
543	<	simnfo->identArray = new int[simnfo->n_atoms];
544	<	for(i=0; i<simnfo->n_atoms; i++){
545	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
546	<	}
547	<
548	<	if (the_globals->getUseRF() ) {
549	<	simnfo->useReactionField = 1;
550	<
551	<	if( !the_globals->haveECR() ){
552	<	sprintf( painCave.errMsg,
553	<	"SimSetup Warning: using default value of 1/2 the smallest "
554	<	"box length for the electrostaticCutoffRadius.\n"
555	<	"I hope you have a very fast processor!\n");
556	<	painCave.isFatal = 0;
557	<	simError();
558	<	double smallest;
559	<	smallest = simnfo->boxLx;
560	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
561	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
562	<	simnfo->ecr = 0.5 * smallest;
563	<	} else {
564	<	simnfo->ecr        = the_globals->getECR();
565	<	}
566	<
567	<	if( !the_globals->haveEST() ){
568	<	sprintf( painCave.errMsg,
569	<	"SimSetup Warning: using default value of 0.05 * the "
570	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
571	<	);
572	<	painCave.isFatal = 0;
573	<	simError();
574	<	simnfo->est = 0.05 * simnfo->ecr;
575	<	} else {
576	<	simnfo->est        = the_globals->getEST();
577	<	}
578	<
579	<	if(!the_globals->haveDielectric() ){
580	<	sprintf( painCave.errMsg,
581	<	"SimSetup Error: You are trying to use Reaction Field without"
582	<	"setting a dielectric constant!\n"
583	<	);
584	<	painCave.isFatal = 1;
585	<	simError();
586	<	}
587	<	simnfo->dielectric = the_globals->getDielectric();
588	<	} else {
589	<	if (usesDipoles) {
590	<
591	<	if( !the_globals->haveECR() ){
592	<	sprintf( painCave.errMsg,
593	<	"SimSetup Warning: using default value of 1/2 the smallest "
594	<	"box length for the electrostaticCutoffRadius.\n"
595	<	"I hope you have a very fast processor!\n");
596	<	painCave.isFatal = 0;
597	<	simError();
598	<	double smallest;
599	<	smallest = simnfo->boxLx;
600	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
601	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
602	<	simnfo->ecr = 0.5 * smallest;
603	<	} else {
604	<	simnfo->ecr        = the_globals->getECR();
605	<	}
606	<
607	<	if( !the_globals->haveEST() ){
608	<	sprintf( painCave.errMsg,
609	<	"SimSetup Warning: using default value of 5%% of the "
610	<	"electrostaticCutoffRadius for the "
611	<	"electrostaticSkinThickness\n"
612	<	);
613	<	painCave.isFatal = 0;
614	<	simError();
615	<	simnfo->est = 0.05 * simnfo->ecr;
616	<	} else {
617	<	simnfo->est        = the_globals->getEST();
618	<	}
619	<	}
620	<	}
621	<
622	<	#ifdef IS_MPI
623	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
624	<	MPIcheckPoint();
625	<	#endif // is_mpi
626	<
627	<	if( the_globals->haveInitialConfig() ){
628	<
629	<	InitializeFromFile* fileInit;
630	<	#ifdef IS_MPI // is_mpi
631	<	if( worldRank == 0 ){
632	<	#endif //is_mpi
633	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
634	<	#ifdef IS_MPI
635	<	}else fileInit = new InitializeFromFile( NULL );
636	<	#endif
637	<	fileInit->read_xyz( simnfo ); // default velocities on
638	<
639	<	delete fileInit;
640	<	}
641	<	else{
642	<
643	<	#ifdef IS_MPI
644	<
645	<	// no init from bass
646	<
647	<	sprintf( painCave.errMsg,
648	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
649	<	painCave.isFatal;
650	<	simError();
651	<
652	<	#else
653	<
654	<	initFromBass();
655	<
656	<
657	<	#endif
658	<	}
659	<
660	<	#ifdef IS_MPI
661	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
662	<	MPIcheckPoint();
663	<	#endif // is_mpi
664	<
665	<
666	<
667	<
668	<
669	<
670	<
671	<	#ifdef IS_MPI
672	<	if( worldRank == 0 ){
673	<	#endif // is_mpi
674	<
675	<	if( the_globals->haveFinalConfig() ){
676	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
677	<	}
678	<	else{
679	<	strcpy( simnfo->finalName, inFileName );
680	<	char* endTest;
681	<	int nameLength = strlen( simnfo->finalName );
682	<	endTest = &(simnfo->finalName[nameLength - 5]);
683	<	if( !strcmp( endTest, ".bass" ) ){
684	<	strcpy( endTest, ".eor" );
685	<	}
686	<	else if( !strcmp( endTest, ".BASS" ) ){
687	<	strcpy( endTest, ".eor" );
688	<	}
689	<	else{
690	<	endTest = &(simnfo->finalName[nameLength - 4]);
691	<	if( !strcmp( endTest, ".bss" ) ){
692	<	strcpy( endTest, ".eor" );
693	<	}
694	<	else if( !strcmp( endTest, ".mdl" ) ){
695	<	strcpy( endTest, ".eor" );
696	<	}
697	<	else{
698	<	strcat( simnfo->finalName, ".eor" );
699	<	}
700	<	}
701	<	}
702	<
703	<	// make the sample and status out names
704	<
705	<	strcpy( simnfo->sampleName, inFileName );
706	<	char* endTest;
707	<	int nameLength = strlen( simnfo->sampleName );
708	<	endTest = &(simnfo->sampleName[nameLength - 5]);
709	<	if( !strcmp( endTest, ".bass" ) ){
710	<	strcpy( endTest, ".dump" );
711	<	}
712	<	else if( !strcmp( endTest, ".BASS" ) ){
713	<	strcpy( endTest, ".dump" );
714	<	}
715	<	else{
716	<	endTest = &(simnfo->sampleName[nameLength - 4]);
717	<	if( !strcmp( endTest, ".bss" ) ){
718	<	strcpy( endTest, ".dump" );
719	<	}
720	<	else if( !strcmp( endTest, ".mdl" ) ){
721	<	strcpy( endTest, ".dump" );
722	<	}
723	<	else{
724	<	strcat( simnfo->sampleName, ".dump" );
725	<	}
726	<	}
727	<
728	<	strcpy( simnfo->statusName, inFileName );
729	<	nameLength = strlen( simnfo->statusName );
730	<	endTest = &(simnfo->statusName[nameLength - 5]);
731	<	if( !strcmp( endTest, ".bass" ) ){
732	<	strcpy( endTest, ".stat" );
733	<	}
734	<	else if( !strcmp( endTest, ".BASS" ) ){
735	<	strcpy( endTest, ".stat" );
736	<	}
737	<	else{
738	<	endTest = &(simnfo->statusName[nameLength - 4]);
739	<	if( !strcmp( endTest, ".bss" ) ){
740	<	strcpy( endTest, ".stat" );
741	<	}
742	<	else if( !strcmp( endTest, ".mdl" ) ){
743	<	strcpy( endTest, ".stat" );
744	<	}
745	<	else{
746	<	strcat( simnfo->statusName, ".stat" );
747	<	}
748	<	}
749	<
750	<	#ifdef IS_MPI
751	<	}
752	<	#endif // is_mpi
753	<
754	<	// set the status, sample, and themal kick times
755	<
756	<	if( the_globals->haveSampleTime() ){
757	<	simnfo->sampleTime = the_globals->getSampleTime();
758	<	simnfo->statusTime = simnfo->sampleTime;
759	<	simnfo->thermalTime = simnfo->sampleTime;
760	<	}
761	<	else{
762	<	simnfo->sampleTime = the_globals->getRunTime();
763	<	simnfo->statusTime = simnfo->sampleTime;
764	<	simnfo->thermalTime = simnfo->sampleTime;
765	<	}
766	<
767	<	if( the_globals->haveStatusTime() ){
768	<	simnfo->statusTime = the_globals->getStatusTime();
769	<	}
770	<
771	<	if( the_globals->haveThermalTime() ){
772	<	simnfo->thermalTime = the_globals->getThermalTime();
773	<	}
774	<
775	<	// check for the temperature set flag
776	<
777	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
778	<
779	<
780	<	// make the integrator
781	<
782	<
783	<	NVT*  myNVT = NULL;
784	<	NPTi* myNPTi = NULL;
785	<	NPTf* myNPTf = NULL;
786	<	switch( ensembleCase ){
787	<
788	<	case NVE_ENS:
789	<	new NVE( simnfo, the_ff );
790	<	break;
791	<
792	<	case NVT_ENS:
793	<	myNVT = new NVT( simnfo, the_ff );
794	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
795	<
796	<	if (the_globals->haveTauThermostat())
797	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
798	<
799	<	else {
800	<	sprintf( painCave.errMsg,
801	<	"SimSetup error: If you use the NVT\n"
802	<	"    ensemble, you must set tauThermostat.\n");
803	<	painCave.isFatal = 1;
804	<	simError();
805	<	}
806	<	break;
807	<
808	<	case NPTi_ENS:
809	<	myNPTi = new NPTi( simnfo, the_ff );
810	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
811	<
812	<	if (the_globals->haveTargetPressure())
813	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
814	<	else {
815	<	sprintf( painCave.errMsg,
816	<	"SimSetup error: If you use a constant pressure\n"
817	<	"    ensemble, you must set targetPressure in the BASS file.\n");
818	<	painCave.isFatal = 1;
819	<	simError();
820	<	}
821	<
822	<	if( the_globals->haveTauThermostat() )
823	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
824	<	else{
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup error: If you use an NPT\n"
827	<	"    ensemble, you must set tauThermostat.\n");
828	<	painCave.isFatal = 1;
829	<	simError();
830	<	}
831	<
832	<	if( the_globals->haveTauBarostat() )
833	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
834	<	else{
835	<	sprintf( painCave.errMsg,
836	<	"SimSetup error: If you use an NPT\n"
837	<	"    ensemble, you must set tauBarostat.\n");
838	<	painCave.isFatal = 1;
839	<	simError();
840	<	}
841	<	break;
842	<
843	<	case NPTf_ENS:
844	<	myNPTf = new NPTf( simnfo, the_ff );
845	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
846	<
847	<	if (the_globals->haveTargetPressure())
848	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
849	<	else {
850	<	sprintf( painCave.errMsg,
851	<	"SimSetup error: If you use a constant pressure\n"
852	<	"    ensemble, you must set targetPressure in the BASS file.\n");
853	<	painCave.isFatal = 1;
854	<	simError();
855	<	}
856	<
857	<	if( the_globals->haveTauThermostat() )
858	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
859	<	else{
860	<	sprintf( painCave.errMsg,
861	<	"SimSetup error: If you use an NPT\n"
862	<	"    ensemble, you must set tauThermostat.\n");
863	<	painCave.isFatal = 1;
864	<	simError();
865	<	}
866	<
867	<	if( the_globals->haveTauBarostat() )
868	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
869	<	else{
870	<	sprintf( painCave.errMsg,
871	<	"SimSetup error: If you use an NPT\n"
872	<	"    ensemble, you must set tauBarostat.\n");
873	<	painCave.isFatal = 1;
874	<	simError();
875	<	}
876	<	break;
877	<
878	<
879	<
880	<	default:
881	<	sprintf( painCave.errMsg,
882	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
883	<	painCave.isFatal = 1;
884	<	simError();
885	<	}
886	<
887	<
888	<	#ifdef IS_MPI
889	<	mpiSim->mpiRefresh();
890	<	#endif
891	<
892	<	// initialize the Fortran
893	<
894	<
895	<	simnfo->refreshSim();
896	<
897	<	if( !strcmp( simnfo->mixingRule, "standard") ){
898	<	the_ff->initForceField( LB_MIXING_RULE );
899	<	}
900	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
901	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
902	<	}
903	<	else{
904	<	sprintf( painCave.errMsg,
905	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
906	<	simnfo->mixingRule );
907	<	painCave.isFatal = 1;
908	<	simError();
909	<	}
910	<
911	<
912	<	#ifdef IS_MPI
913	<	strcpy( checkPointMsg,
914	<	"Successfully intialized the mixingRule for Fortran." );
915	<	MPIcheckPoint();
916	<	#endif // is_mpi
917	<	}
918	<
919	<
920	<	void SimSetup::makeMolecules( void ){
921	<
922	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
923	<	molInit info;
924	<	DirectionalAtom* dAtom;
925	<	LinkedAssign* extras;
926	<	LinkedAssign* current_extra;
927	<	AtomStamp* currentAtom;
928	<	BondStamp* currentBond;
929	<	BendStamp* currentBend;
930	<	TorsionStamp* currentTorsion;
931	<
932	<	bond_pair* theBonds;
933	<	bend_set* theBends;
934	<	torsion_set* theTorsions;
935	<
936	<
937	<	//init the forceField paramters
938	<
939	<	the_ff->readParams();
940	<
941	<
942	<	// init the atoms
943	<
944	<	double ux, uy, uz, u, uSqr;
945	<
946	<	atomOffset = 0;
947	<	excludeOffset = 0;
948	<	for(i=0; i<simnfo->n_mol; i++){
949	<
950	<	stampID = the_molecules[i].getStampID();
951	<
952	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
953	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
954	<	info.nBends    = comp_stamps[stampID]->getNBends();
955	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
956	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
957	<
958	<	info.myAtoms = &the_atoms[atomOffset];
959	<	info.myExcludes = &the_excludes[excludeOffset];
960	<	info.myBonds = new Bond*[info.nBonds];
961	<	info.myBends = new Bend*[info.nBends];
962	<	info.myTorsions = new Torsion*[info.nTorsions];
963	<
964	<	theBonds = new bond_pair[info.nBonds];
965	<	theBends = new bend_set[info.nBends];
966	<	theTorsions = new torsion_set[info.nTorsions];
967	<
968	<	// make the Atoms
969	<
970	<	for(j=0; j<info.nAtoms; j++){
971	<
972	<	currentAtom = comp_stamps[stampID]->getAtom( j );
973	<	if( currentAtom->haveOrientation() ){
974	<
975	<	dAtom = new DirectionalAtom(j + atomOffset);
976	<	simnfo->n_oriented++;
977	<	info.myAtoms[j] = dAtom;
978	<
979	<	ux = currentAtom->getOrntX();
980	<	uy = currentAtom->getOrntY();
981	<	uz = currentAtom->getOrntZ();
982	<
983	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
984	<
985	<	u = sqrt( uSqr );
986	<	ux = ux / u;
987	<	uy = uy / u;
988	<	uz = uz / u;
989	<
990	<	dAtom->setSUx( ux );
991	<	dAtom->setSUy( uy );
992	<	dAtom->setSUz( uz );
993	<	}
994	<	else{
995	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
996	<	}
997	<	info.myAtoms[j]->setType( currentAtom->getType() );
998	<
999	<	#ifdef IS_MPI
1000	<
1001	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1002	<
1003	<	#endif // is_mpi
1004	<	}
1005	<
1006	<	// make the bonds
1007	<	for(j=0; j<info.nBonds; j++){
1008	<
1009	<	currentBond = comp_stamps[stampID]->getBond( j );
1010	<	theBonds[j].a = currentBond->getA() + atomOffset;
1011	<	theBonds[j].b = currentBond->getB() + atomOffset;
1012	<
1013	<	exI = theBonds[j].a;
1014	<	exJ = theBonds[j].b;
1015	<
1016	<	// exclude_I must always be the smaller of the pair
1017	<	if( exI > exJ ){
1018	<	tempEx = exI;
1019	<	exI = exJ;
1020	<	exJ = tempEx;
1021	<	}
1022	<	#ifdef IS_MPI
1023	<	tempEx = exI;
1024	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1025	<	tempEx = exJ;
1026	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1027	<
1028	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1029	<	#else  // isn't MPI
1030	<
1031	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1032	<	#endif  //is_mpi
1033	<	}
1034	<	excludeOffset += info.nBonds;
1035	<
1036	<	//make the bends
1037	<	for(j=0; j<info.nBends; j++){
1038	<
1039	<	currentBend = comp_stamps[stampID]->getBend( j );
1040	<	theBends[j].a = currentBend->getA() + atomOffset;
1041	<	theBends[j].b = currentBend->getB() + atomOffset;
1042	<	theBends[j].c = currentBend->getC() + atomOffset;
1043	<
1044	<	if( currentBend->haveExtras() ){
1045	<
1046	<	extras = currentBend->getExtras();
1047	<	current_extra = extras;
1048	<
1049	<	while( current_extra != NULL ){
1050	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1051	<
1052	<	switch( current_extra->getType() ){
1053	<
1054	<	case 0:
1055	<	theBends[j].ghost =
1056	<	current_extra->getInt() + atomOffset;
1057	<	theBends[j].isGhost = 1;
1058	<	break;
1059	<
1060	<	case 1:
1061	<	theBends[j].ghost =
1062	<	(int)current_extra->getDouble() + atomOffset;
1063	<	theBends[j].isGhost = 1;
1064	<	break;
1065	<
1066	<	default:
1067	<	sprintf( painCave.errMsg,
1068	<	"SimSetup Error: ghostVectorSource was neither a "
1069	<	"double nor an int.\n"
1070	<	"-->Bend[%d] in %s\n",
1071	<	j, comp_stamps[stampID]->getID() );
1072	<	painCave.isFatal = 1;
1073	<	simError();
1074	<	}
1075	<	}
1076	<
1077	<	else{
1078	<
1079	<	sprintf( painCave.errMsg,
1080	<	"SimSetup Error: unhandled bend assignment:\n"
1081	<	"    -->%s in Bend[%d] in %s\n",
1082	<	current_extra->getlhs(),
1083	<	j, comp_stamps[stampID]->getID() );
1084	<	painCave.isFatal = 1;
1085	<	simError();
1086	<	}
1087	<
1088	<	current_extra = current_extra->getNext();
1089	<	}
1090	<	}
1091	<
1092	<	if( !theBends[j].isGhost ){
1093	<
1094	<	exI = theBends[j].a;
1095	<	exJ = theBends[j].c;
1096	<	}
1097	<	else{
1098	<
1099	<	exI = theBends[j].a;
1100	<	exJ = theBends[j].b;
1101	<	}
1102	<
1103	<	// exclude_I must always be the smaller of the pair
1104	<	if( exI > exJ ){
1105	<	tempEx = exI;
1106	<	exI = exJ;
1107	<	exJ = tempEx;
1108	<	}
1109	<	#ifdef IS_MPI
1110	<	tempEx = exI;
1111	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1112	<	tempEx = exJ;
1113	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1114	<
1115	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1116	<	#else  // isn't MPI
1117	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1118	<	#endif  //is_mpi
1119	<	}
1120	<	excludeOffset += info.nBends;
1121	<
1122	<	for(j=0; j<info.nTorsions; j++){
1123	<
1124	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1125	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1126	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1127	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1128	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1129	<
1130	<	exI = theTorsions[j].a;
1131	<	exJ = theTorsions[j].d;
1132	<
1133	<	// exclude_I must always be the smaller of the pair
1134	<	if( exI > exJ ){
1135	<	tempEx = exI;
1136	<	exI = exJ;
1137	<	exJ = tempEx;
1138	<	}
1139	<	#ifdef IS_MPI
1140	<	tempEx = exI;
1141	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1142	<	tempEx = exJ;
1143	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1144	<
1145	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1146	<	#else  // isn't MPI
1147	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1148	<	#endif  //is_mpi
1149	<	}
1150	<	excludeOffset += info.nTorsions;
1151	<
1152	<
1153	<	// send the arrays off to the forceField for init.
1154	<
1155	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1156	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1157	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1158	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1159	<
1160	<
1161	<	the_molecules[i].initialize( info );
1162	<
1163	<
1164	<	atomOffset += info.nAtoms;
1165	<	delete[] theBonds;
1166	<	delete[] theBends;
1167	<	delete[] theTorsions;
1168	<	}
1169	<
1170	<	#ifdef IS_MPI
1171	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1172	<	MPIcheckPoint();
1173	<	#endif // is_mpi
1174	<
1175	<	// clean up the forcefield
1176	<	the_ff->calcRcut();
1177	<	the_ff->cleanMe();
1178	<
1179	<	}
1180	<
1181	<	void SimSetup::initFromBass( void ){
1182	<
1183	<	int i, j, k;
1184	<	int n_cells;
1185	<	double cellx, celly, cellz;
1186	<	double temp1, temp2, temp3;
1187	<	int n_per_extra;
1188	<	int n_extra;
1189	<	int have_extra, done;
1190	<
1191	<	temp1 = (double)tot_nmol / 4.0;
1192	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1193	<	temp3 = ceil( temp2 );
1194	<
1195	<	have_extra =0;
1196	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1197	<	have_extra =1;
1198	<
1199	<	n_cells = (int)temp3 - 1;
1200	<	cellx = simnfo->boxLx / temp3;
1201	<	celly = simnfo->boxLy / temp3;
1202	<	cellz = simnfo->boxLz / temp3;
1203	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1204	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1205	<	n_per_extra = (int)ceil( temp1 );
1206	<
1207	<	if( n_per_extra > 4){
1208	<	sprintf( painCave.errMsg,
1209	<	"SimSetup error. There has been an error in constructing"
1210	<	" the non-complete lattice.\n" );
1211	<	painCave.isFatal = 1;
1212	<	simError();
1213	<	}
1214	<	}
1215	<	else{
1216	<	n_cells = (int)temp3;
1217	<	cellx = simnfo->boxLx / temp3;
1218	<	celly = simnfo->boxLy / temp3;
1219	<	cellz = simnfo->boxLz / temp3;
1220	<	}
1221	<
1222	<	current_mol = 0;
1223	<	current_comp_mol = 0;
1224	<	current_comp = 0;
1225	<	current_atom_ndx = 0;
1226	<
1227	<	for( i=0; i < n_cells ; i++ ){
1228	<	for( j=0; j < n_cells; j++ ){
1229	<	for( k=0; k < n_cells; k++ ){
1230	<
1231	<	makeElement( i * cellx,
1232	<	j * celly,
1233	<	k * cellz );
1234	<
1235	<	makeElement( i * cellx + 0.5 * cellx,
1236	<	j * celly + 0.5 * celly,
1237	<	k * cellz );
1238	<
1239	<	makeElement( i * cellx,
1240	<	j * celly + 0.5 * celly,
1241	<	k * cellz + 0.5 * cellz );
1242	<
1243	<	makeElement( i * cellx + 0.5 * cellx,
1244	<	j * celly,
1245	<	k * cellz + 0.5 * cellz );
1246	<	}
1247	<	}
1248	<	}
1249	<
1250	<	if( have_extra ){
1251	<	done = 0;
1252	<
1253	<	int start_ndx;
1254	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1255	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1256	<
1257	<	if( i < n_cells ){
1258	<
1259	<	if( j < n_cells ){
1260	<	start_ndx = n_cells;
1261	<	}
1262	<	else start_ndx = 0;
1263	<	}
1264	<	else start_ndx = 0;
1265	<
1266	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1267	<
1268	<	makeElement( i * cellx,
1269	<	j * celly,
1270	<	k * cellz );
1271	<	done = ( current_mol >= tot_nmol );
1272	<
1273	<	if( !done && n_per_extra > 1 ){
1274	<	makeElement( i * cellx + 0.5 * cellx,
1275	<	j * celly + 0.5 * celly,
1276	<	k * cellz );
1277	<	done = ( current_mol >= tot_nmol );
1278	<	}
1279	<
1280	<	if( !done && n_per_extra > 2){
1281	<	makeElement( i * cellx,
1282	<	j * celly + 0.5 * celly,
1283	<	k * cellz + 0.5 * cellz );
1284	<	done = ( current_mol >= tot_nmol );
1285	<	}
1286	<
1287	<	if( !done && n_per_extra > 3){
1288	<	makeElement( i * cellx + 0.5 * cellx,
1289	<	j * celly,
1290	<	k * cellz + 0.5 * cellz );
1291	<	done = ( current_mol >= tot_nmol );
1292	<	}
1293	<	}
1294	<	}
1295	<	}
1296	<	}
1297	<
1298	<
1299	<	for( i=0; i<simnfo->n_atoms; i++ ){
1300	<	simnfo->atoms[i]->set_vx( 0.0 );
1301	<	simnfo->atoms[i]->set_vy( 0.0 );
1302	<	simnfo->atoms[i]->set_vz( 0.0 );
1303	<	}
1304	<	}
1305	<
1306	<	void SimSetup::makeElement( double x, double y, double z ){
1307	<
1308	<	int k;
1309	<	AtomStamp* current_atom;
1310	<	DirectionalAtom* dAtom;
1311	<	double rotMat[3][3];
1312	<
1313	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1314	<
1315	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1316	<	if( !current_atom->havePosition() ){
1317	<	sprintf( painCave.errMsg,
1318	<	"SimSetup:initFromBass error.\n"
1319	<	"\tComponent %s, atom %s does not have a position specified.\n"
1320	<	"\tThe initialization routine is unable to give a start"
1321	<	" position.\n",
1322	<	comp_stamps[current_comp]->getID(),
1323	<	current_atom->getType() );
1324	<	painCave.isFatal = 1;
1325	<	simError();
1326	<	}
1327	<
1328	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1329	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1330	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1331	<
1332	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1333	<
1334	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1335	<
1336	<	rotMat[0][0] = 1.0;
1337	<	rotMat[0][1] = 0.0;
1338	<	rotMat[0][2] = 0.0;
1339	<
1340	<	rotMat[1][0] = 0.0;
1341	<	rotMat[1][1] = 1.0;
1342	<	rotMat[1][2] = 0.0;
1343	<
1344	<	rotMat[2][0] = 0.0;
1345	<	rotMat[2][1] = 0.0;
1346	<	rotMat[2][2] = 1.0;
1347	<
1348	<	dAtom->setA( rotMat );
1349	<	}
1350	<
1351	<	current_atom_ndx++;
1352	<	}
1353	<
1354	<	current_mol++;
1355	<	current_comp_mol++;
1356	<
1357	<	if( current_comp_mol >= components_nmol[current_comp] ){
1358	<
1359	<	current_comp_mol = 0;
1360	<	current_comp++;
1361	<	}
1	>	#include <algorithm>
2	>	#include <cstdlib>
3	>	#include <iostream>
4	>	#include <cmath>
5	>	#include <string>
6	>
7	>	#include "SimSetup.hpp"
8	>	#include "parse_me.h"
9	>	#include "Integrator.hpp"
10	>	#include "simError.h"
11	>
12	>	#ifdef IS_MPI
13	>	#include "mpiBASS.h"
14	>	#include "mpiSimulation.hpp"
15	>	#endif
16	>
17	>	// some defines for ensemble and Forcefield  cases
18	>
19	>	#define NVE_ENS        0
20	>	#define NVT_ENS        1
21	>	#define NPTi_ENS       2
22	>	#define NPTf_ENS       3
23	>	#define NPTim_ENS      4
24	>	#define NPTfm_ENS      5
25	>	#define NVEZCONS_ENS   6
26	>	#define NVTZCONS_ENS   7
27	>	#define NPTiZCONS_ENS  8
28	>	#define NPTfZCONS_ENS  9
29	>	#define NPTimZCONS_ENS 10
30	>	#define NPTfmZCONS_ENS 11
31	>
32	>	#define FF_DUFF 0
33	>	#define FF_LJ   1
34	>	#define FF_EAM  2
35	>
36	>	using namespace std;
37	>
38	>	SimSetup::SimSetup(){
39	>
40	>	isInfoArray = 0;
41	>	nInfo = 1;
42	>
43	>	stamps = new MakeStamps();
44	>	globals = new Globals();
45	>
46	>
47	>	#ifdef IS_MPI
48	>	strcpy( checkPointMsg, "SimSetup creation successful" );
49	>	MPIcheckPoint();
50	>	#endif // IS_MPI
51	>	}
52	>
53	>	SimSetup::~SimSetup(){
54	>	delete stamps;
55	>	delete globals;
56	>	}
57	>
58	>	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
59	>	info = the_info;
60	>	nInfo = theNinfo;
61	>	isInfoArray = 1;
62	>	}
63	>
64	>
65	>	void SimSetup::parseFile( char* fileName ){
66	>
67	>	#ifdef IS_MPI
68	>	if( worldRank == 0 ){
69	>	#endif // is_mpi
70	>
71	>	inFileName = fileName;
72	>	set_interface_stamps( stamps, globals );
73	>
74	>	#ifdef IS_MPI
75	>	mpiEventInit();
76	>	#endif
77	>
78	>	yacc_BASS( fileName );
79	>
80	>	#ifdef IS_MPI
81	>	throwMPIEvent(NULL);
82	>	}
83	>	else receiveParse();
84	>	#endif
85	>
86	>	}
87	>
88	>	#ifdef IS_MPI
89	>	void SimSetup::receiveParse(void){
90	>
91	>	set_interface_stamps( stamps, globals );
92	>	mpiEventInit();
93	>	MPIcheckPoint();
94	>	mpiEventLoop();
95	>
96	>	}
97	>
98	>	#endif // is_mpi
99	>
100	>	void SimSetup::createSim( void ){
101	>
102	>	int i, j, k, globalAtomIndex;
103	>
104	>	// gather all of the information from the Bass file
105	>
106	>	gatherInfo();
107	>
108	>	// creation of complex system objects
109	>
110	>	sysObjectsCreation();
111	>
112	>	// check on the post processing info
113	>
114	>	finalInfoCheck();
115	>
116	>	// initialize the system coordinates
117	>
118	>	initSystemCoords();
119	>
120	>
121	>	// make the output filenames
122	>
123	>	makeOutNames();
124	>
125	>	// make the integrator
126	>
127	>	makeIntegrator();
128	>
129	>	#ifdef IS_MPI
130	>	mpiSim->mpiRefresh();
131	>	#endif
132	>
133	>	// initialize the Fortran
134	>
135	>	initFortran();
136	>
137	>
138	>
139	>	}
140	>
141	>
142	>	void SimSetup::makeMolecules( void ){
143	>
144	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
145	>	molInit molInfo;
146	>	DirectionalAtom* dAtom;
147	>	LinkedAssign* extras;
148	>	LinkedAssign* current_extra;
149	>	AtomStamp* currentAtom;
150	>	BondStamp* currentBond;
151	>	BendStamp* currentBend;
152	>	TorsionStamp* currentTorsion;
153	>
154	>	bond_pair* theBonds;
155	>	bend_set* theBends;
156	>	torsion_set* theTorsions;
157	>
158	>
159	>	//init the forceField paramters
160	>
161	>	the_ff->readParams();
162	>
163	>
164	>	// init the atoms
165	>
166	>	double ux, uy, uz, u, uSqr;
167	>
168	>	atomOffset = 0;
169	>	excludeOffset = 0;
170	>	for(i=0; i<info->n_mol; i++){
171	>
172	>	stampID = the_molecules[i].getStampID();
173	>
174	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
175	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
176	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
177	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
178	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
179	>
180	>	molInfo.myAtoms = &the_atoms[atomOffset];
181	>	molInfo.myExcludes = &the_excludes[excludeOffset];
182	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
183	>	molInfo.myBends = new Bend*[molInfo.nBends];
184	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
185	>
186	>	theBonds = new bond_pair[molInfo.nBonds];
187	>	theBends = new bend_set[molInfo.nBends];
188	>	theTorsions = new torsion_set[molInfo.nTorsions];
189	>
190	>	// make the Atoms
191	>
192	>	for(j=0; j<molInfo.nAtoms; j++){
193	>
194	>	currentAtom = comp_stamps[stampID]->getAtom( j );
195	>	if( currentAtom->haveOrientation() ){
196	>
197	>	dAtom = new DirectionalAtom(j + atomOffset);
198	>	info->n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200	>
201	>	ux = currentAtom->getOrntX();
202	>	uy = currentAtom->getOrntY();
203	>	uz = currentAtom->getOrntZ();
204	>
205	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	>
207	>	u = sqrt( uSqr );
208	>	ux = ux / u;
209	>	uy = uy / u;
210	>	uz = uz / u;
211	>
212	>	dAtom->setSUx( ux );
213	>	dAtom->setSUy( uy );
214	>	dAtom->setSUz( uz );
215	>	}
216	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
218	>	}
219	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220	>
221	>	#ifdef IS_MPI
222	>
223	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>
225	>	#endif // is_mpi
226	>	}
227	>
228	>	// make the bonds
229	>	for(j=0; j<molInfo.nBonds; j++){
230	>
231	>	currentBond = comp_stamps[stampID]->getBond( j );
232	>	theBonds[j].a = currentBond->getA() + atomOffset;
233	>	theBonds[j].b = currentBond->getB() + atomOffset;
234	>
235	>	exI = theBonds[j].a;
236	>	exJ = theBonds[j].b;
237	>
238	>	// exclude_I must always be the smaller of the pair
239	>	if( exI > exJ ){
240	>	tempEx = exI;
241	>	exI = exJ;
242	>	exJ = tempEx;
243	>	}
244	>	#ifdef IS_MPI
245	>	tempEx = exI;
246	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
247	>	tempEx = exJ;
248	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
249	>
250	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
251	>	#else  // isn't MPI
252	>
253	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	>	#endif  //is_mpi
255	>	}
256	>	excludeOffset += molInfo.nBonds;
257	>
258	>	//make the bends
259	>	for(j=0; j<molInfo.nBends; j++){
260	>
261	>	currentBend = comp_stamps[stampID]->getBend( j );
262	>	theBends[j].a = currentBend->getA() + atomOffset;
263	>	theBends[j].b = currentBend->getB() + atomOffset;
264	>	theBends[j].c = currentBend->getC() + atomOffset;
265	>
266	>	if( currentBend->haveExtras() ){
267	>
268	>	extras = currentBend->getExtras();
269	>	current_extra = extras;
270	>
271	>	while( current_extra != NULL ){
272	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273	>
274	>	switch( current_extra->getType() ){
275	>
276	>	case 0:
277	>	theBends[j].ghost =
278	>	current_extra->getInt() + atomOffset;
279	>	theBends[j].isGhost = 1;
280	>	break;
281	>
282	>	case 1:
283	>	theBends[j].ghost =
284	>	(int)current_extra->getDouble() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	default:
289	>	sprintf( painCave.errMsg,
290	>	"SimSetup Error: ghostVectorSource was neither a "
291	>	"double nor an int.\n"
292	>	"-->Bend[%d] in %s\n",
293	>	j, comp_stamps[stampID]->getID() );
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	}
298	>
299	>	else{
300	>
301	>	sprintf( painCave.errMsg,
302	>	"SimSetup Error: unhandled bend assignment:\n"
303	>	"    -->%s in Bend[%d] in %s\n",
304	>	current_extra->getlhs(),
305	>	j, comp_stamps[stampID]->getID() );
306	>	painCave.isFatal = 1;
307	>	simError();
308	>	}
309	>
310	>	current_extra = current_extra->getNext();
311	>	}
312	>	}
313	>
314	>	if( !theBends[j].isGhost ){
315	>
316	>	exI = theBends[j].a;
317	>	exJ = theBends[j].c;
318	>	}
319	>	else{
320	>
321	>	exI = theBends[j].a;
322	>	exJ = theBends[j].b;
323	>	}
324	>
325	>	// exclude_I must always be the smaller of the pair
326	>	if( exI > exJ ){
327	>	tempEx = exI;
328	>	exI = exJ;
329	>	exJ = tempEx;
330	>	}
331	>	#ifdef IS_MPI
332	>	tempEx = exI;
333	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exJ;
335	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
336	>
337	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
338	>	#else  // isn't MPI
339	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340	>	#endif  //is_mpi
341	>	}
342	>	excludeOffset += molInfo.nBends;
343	>
344	>	for(j=0; j<molInfo.nTorsions; j++){
345	>
346	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	>
352	>	exI = theTorsions[j].a;
353	>	exJ = theTorsions[j].d;
354	>
355	>	// exclude_I must always be the smaller of the pair
356	>	if( exI > exJ ){
357	>	tempEx = exI;
358	>	exI = exJ;
359	>	exJ = tempEx;
360	>	}
361	>	#ifdef IS_MPI
362	>	tempEx = exI;
363	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
364	>	tempEx = exJ;
365	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
366	>
367	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
368	>	#else  // isn't MPI
369	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370	>	#endif  //is_mpi
371	>	}
372	>	excludeOffset += molInfo.nTorsions;
373	>
374	>
375	>	// send the arrays off to the forceField for init.
376	>
377	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381	>
382	>
383	>	the_molecules[i].initialize( molInfo );
384	>
385	>
386	>	atomOffset += molInfo.nAtoms;
387	>	delete[] theBonds;
388	>	delete[] theBends;
389	>	delete[] theTorsions;
390	>	}
391	>
392	>	#ifdef IS_MPI
393	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
394	>	MPIcheckPoint();
395	>	#endif // is_mpi
396	>
397	>	// clean up the forcefield
398	>	the_ff->calcRcut();
399	>	the_ff->cleanMe();
400	>
401	>	}
402	>
403	>	void SimSetup::initFromBass( void ){
404	>
405	>	int i, j, k;
406	>	int n_cells;
407	>	double cellx, celly, cellz;
408	>	double temp1, temp2, temp3;
409	>	int n_per_extra;
410	>	int n_extra;
411	>	int have_extra, done;
412	>
413	>	temp1 = (double)tot_nmol / 4.0;
414	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
415	>	temp3 = ceil( temp2 );
416	>
417	>	have_extra =0;
418	>	if( temp2 < temp3 ){ // we have a non-complete lattice
419	>	have_extra =1;
420	>
421	>	n_cells = (int)temp3 - 1;
422	>	cellx = info->boxL[0] / temp3;
423	>	celly = info->boxL[1] / temp3;
424	>	cellz = info->boxL[2] / temp3;
425	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
426	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
427	>	n_per_extra = (int)ceil( temp1 );
428	>
429	>	if( n_per_extra > 4){
430	>	sprintf( painCave.errMsg,
431	>	"SimSetup error. There has been an error in constructing"
432	>	" the non-complete lattice.\n" );
433	>	painCave.isFatal = 1;
434	>	simError();
435	>	}
436	>	}
437	>	else{
438	>	n_cells = (int)temp3;
439	>	cellx = info->boxL[0] / temp3;
440	>	celly = info->boxL[1] / temp3;
441	>	cellz = info->boxL[2] / temp3;
442	>	}
443	>
444	>	current_mol = 0;
445	>	current_comp_mol = 0;
446	>	current_comp = 0;
447	>	current_atom_ndx = 0;
448	>
449	>	for( i=0; i < n_cells ; i++ ){
450	>	for( j=0; j < n_cells; j++ ){
451	>	for( k=0; k < n_cells; k++ ){
452	>
453	>	makeElement( i * cellx,
454	>	j * celly,
455	>	k * cellz );
456	>
457	>	makeElement( i * cellx + 0.5 * cellx,
458	>	j * celly + 0.5 * celly,
459	>	k * cellz );
460	>
461	>	makeElement( i * cellx,
462	>	j * celly + 0.5 * celly,
463	>	k * cellz + 0.5 * cellz );
464	>
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly,
467	>	k * cellz + 0.5 * cellz );
468	>	}
469	>	}
470	>	}
471	>
472	>	if( have_extra ){
473	>	done = 0;
474	>
475	>	int start_ndx;
476	>	for( i=0; i < (n_cells+1) && !done; i++ ){
477	>	for( j=0; j < (n_cells+1) && !done; j++ ){
478	>
479	>	if( i < n_cells ){
480	>
481	>	if( j < n_cells ){
482	>	start_ndx = n_cells;
483	>	}
484	>	else start_ndx = 0;
485	>	}
486	>	else start_ndx = 0;
487	>
488	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
489	>
490	>	makeElement( i * cellx,
491	>	j * celly,
492	>	k * cellz );
493	>	done = ( current_mol >= tot_nmol );
494	>
495	>	if( !done && n_per_extra > 1 ){
496	>	makeElement( i * cellx + 0.5 * cellx,
497	>	j * celly + 0.5 * celly,
498	>	k * cellz );
499	>	done = ( current_mol >= tot_nmol );
500	>	}
501	>
502	>	if( !done && n_per_extra > 2){
503	>	makeElement( i * cellx,
504	>	j * celly + 0.5 * celly,
505	>	k * cellz + 0.5 * cellz );
506	>	done = ( current_mol >= tot_nmol );
507	>	}
508	>
509	>	if( !done && n_per_extra > 3){
510	>	makeElement( i * cellx + 0.5 * cellx,
511	>	j * celly,
512	>	k * cellz + 0.5 * cellz );
513	>	done = ( current_mol >= tot_nmol );
514	>	}
515	>	}
516	>	}
517	>	}
518	>	}
519	>
520	>
521	>	for( i=0; i<info->n_atoms; i++ ){
522	>	info->atoms[i]->set_vx( 0.0 );
523	>	info->atoms[i]->set_vy( 0.0 );
524	>	info->atoms[i]->set_vz( 0.0 );
525	>	}
526	>	}
527	>
528	>	void SimSetup::makeElement( double x, double y, double z ){
529	>
530	>	int k;
531	>	AtomStamp* current_atom;
532	>	DirectionalAtom* dAtom;
533	>	double rotMat[3][3];
534	>
535	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
536	>
537	>	current_atom = comp_stamps[current_comp]->getAtom( k );
538	>	if( !current_atom->havePosition() ){
539	>	sprintf( painCave.errMsg,
540	>	"SimSetup:initFromBass error.\n"
541	>	"\tComponent %s, atom %s does not have a position specified.\n"
542	>	"\tThe initialization routine is unable to give a start"
543	>	" position.\n",
544	>	comp_stamps[current_comp]->getID(),
545	>	current_atom->getType() );
546	>	painCave.isFatal = 1;
547	>	simError();
548	>	}
549	>
550	>	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
551	>	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
552	>	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
553	>
554	>	if( the_atoms[current_atom_ndx]->isDirectional() ){
555	>
556	>	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
557	>
558	>	rotMat[0][0] = 1.0;
559	>	rotMat[0][1] = 0.0;
560	>	rotMat[0][2] = 0.0;
561	>
562	>	rotMat[1][0] = 0.0;
563	>	rotMat[1][1] = 1.0;
564	>	rotMat[1][2] = 0.0;
565	>
566	>	rotMat[2][0] = 0.0;
567	>	rotMat[2][1] = 0.0;
568	>	rotMat[2][2] = 1.0;
569	>
570	>	dAtom->setA( rotMat );
571	>	}
572	>
573	>	current_atom_ndx++;
574	>	}
575	>
576	>	current_mol++;
577	>	current_comp_mol++;
578	>
579	>	if( current_comp_mol >= components_nmol[current_comp] ){
580	>
581	>	current_comp_mol = 0;
582	>	current_comp++;
583	>	}
584	>	}
585	>
586	>
587	>	void SimSetup::gatherInfo( void ){
588	>	int i,j,k;
589	>
590	>	ensembleCase = -1;
591	>	ffCase = -1;
592	>
593	>	// get the stamps and globals;
594	>	stamps = stamps;
595	>	globals = globals;
596	>
597	>	// set the easy ones first
598	>	info->target_temp = globals->getTargetTemp();
599	>	info->dt = globals->getDt();
600	>	info->run_time = globals->getRunTime();
601	>	n_components = globals->getNComponents();
602	>
603	>
604	>	// get the forceField
605	>
606	>	strcpy( force_field, globals->getForceField() );
607	>
608	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
609	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
610	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
611	>	else{
612	>	sprintf( painCave.errMsg,
613	>	"SimSetup Error. Unrecognized force field -> %s\n",
614	>	force_field );
615	>	painCave.isFatal = 1;
616	>	simError();
617	>	}
618	>
619	>	// get the ensemble
620	>
621	>	strcpy( ensemble, globals->getEnsemble() );
622	>
623	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
624	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
625	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
626	>	ensembleCase = NPTi_ENS;
627	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
628	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
629	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
630	>
631	>	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
632	>	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
633	>	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT"))
634	>	ensembleCase = NPTiZCONS_ENS;
635	>	else if( !strcasecmp( ensemble, "NPTfCONS"))  ensembleCase = NPTfZCONS_ENS;
636	>	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637	>	else if( !strcasecmp( ensemble, "NPTfmCONS"))  ensembleCase = NPTfmZCONS_ENS;
638	>
639	>	else{
640	>	sprintf( painCave.errMsg,
641	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
642	>	"reverting to NVE for this simulation.\n",
643	>	ensemble );
644	>	painCave.isFatal = 0;
645	>	simError();
646	>	strcpy( ensemble, "NVE" );
647	>	ensembleCase = NVE_ENS;
648	>	}
649	>	strcpy( info->ensemble, ensemble );
650	>
651	>	// get the mixing rule
652	>
653	>	strcpy( info->mixingRule, globals->getMixingRule() );
654	>	info->usePBC = globals->getPBC();
655	>
656	>
657	>	// get the components and calculate the tot_nMol and indvidual n_mol
658	>
659	>	the_components = globals->getComponents();
660	>	components_nmol = new int[n_components];
661	>
662	>
663	>	if( !globals->haveNMol() ){
664	>	// we don't have the total number of molecules, so we assume it is
665	>	// given in each component
666	>
667	>	tot_nmol = 0;
668	>	for( i=0; i<n_components; i++ ){
669	>
670	>	if( !the_components[i]->haveNMol() ){
671	>	// we have a problem
672	>	sprintf( painCave.errMsg,
673	>	"SimSetup Error. No global NMol or component NMol"
674	>	" given. Cannot calculate the number of atoms.\n" );
675	>	painCave.isFatal = 1;
676	>	simError();
677	>	}
678	>
679	>	tot_nmol += the_components[i]->getNMol();
680	>	components_nmol[i] = the_components[i]->getNMol();
681	>	}
682	>	}
683	>	else{
684	>	sprintf( painCave.errMsg,
685	>	"SimSetup error.\n"
686	>	"\tSorry, the ability to specify total"
687	>	" nMols and then give molfractions in the components\n"
688	>	"\tis not currently supported."
689	>	" Please give nMol in the components.\n" );
690	>	painCave.isFatal = 1;
691	>	simError();
692	>	}
693	>
694	>	// set the status, sample, and thermal kick times
695	>
696	>	if( globals->haveSampleTime() ){
697	>	info->sampleTime = globals->getSampleTime();
698	>	info->statusTime = info->sampleTime;
699	>	info->thermalTime = info->sampleTime;
700	>	}
701	>	else{
702	>	info->sampleTime = globals->getRunTime();
703	>	info->statusTime = info->sampleTime;
704	>	info->thermalTime = info->sampleTime;
705	>	}
706	>
707	>	if( globals->haveStatusTime() ){
708	>	info->statusTime = globals->getStatusTime();
709	>	}
710	>
711	>	if( globals->haveThermalTime() ){
712	>	info->thermalTime = globals->getThermalTime();
713	>	}
714	>
715	>	// check for the temperature set flag
716	>
717	>	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
718	>
719	>	// get some of the tricky things that may still be in the globals
720	>
721	>	double boxVector[3];
722	>	if( globals->haveBox() ){
723	>	boxVector[0] = globals->getBox();
724	>	boxVector[1] = globals->getBox();
725	>	boxVector[2] = globals->getBox();
726	>
727	>	info->setBox( boxVector );
728	>	}
729	>	else if( globals->haveDensity() ){
730	>
731	>	double vol;
732	>	vol = (double)tot_nmol / globals->getDensity();
733	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
734	>	boxVector[1] = boxVector[0];
735	>	boxVector[2] = boxVector[0];
736	>
737	>	info->setBox( boxVector );
738	>	}
739	>	else{
740	>	if( !globals->haveBoxX() ){
741	>	sprintf( painCave.errMsg,
742	>	"SimSetup error, no periodic BoxX size given.\n" );
743	>	painCave.isFatal = 1;
744	>	simError();
745	>	}
746	>	boxVector[0] = globals->getBoxX();
747	>
748	>	if( !globals->haveBoxY() ){
749	>	sprintf( painCave.errMsg,
750	>	"SimSetup error, no periodic BoxY size given.\n" );
751	>	painCave.isFatal = 1;
752	>	simError();
753	>	}
754	>	boxVector[1] = globals->getBoxY();
755	>
756	>	if( !globals->haveBoxZ() ){
757	>	sprintf( painCave.errMsg,
758	>	"SimSetup error, no periodic BoxZ size given.\n" );
759	>	painCave.isFatal = 1;
760	>	simError();
761	>	}
762	>	boxVector[2] = globals->getBoxZ();
763	>
764	>	info->setBox( boxVector );
765	>	}
766	>
767	>
768	>
769	>	#ifdef IS_MPI
770	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
771	>	MPIcheckPoint();
772	>	#endif // is_mpi
773	>
774	>	}
775	>
776	>
777	>	void SimSetup::finalInfoCheck( void ){
778	>	int index;
779	>	int usesDipoles;
780	>
781	>
782	>	// check electrostatic parameters
783	>
784	>	index = 0;
785	>	usesDipoles = 0;
786	>	while( (index < info->n_atoms) && !usesDipoles ){
787	>	usesDipoles = ((info->atoms)[index])->hasDipole();
788	>	index++;
789	>	}
790	>
791	>	#ifdef IS_MPI
792	>	int myUse = usesDipoles;
793	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
794	>	#endif //is_mpi
795	>
796	>	double theEcr, theEst;
797	>
798	>	if (globals->getUseRF() ) {
799	>	info->useReactionField = 1;
800	>
801	>	if( !globals->haveECR() ){
802	>	sprintf( painCave.errMsg,
803	>	"SimSetup Warning: using default value of 1/2 the smallest "
804	>	"box length for the electrostaticCutoffRadius.\n"
805	>	"I hope you have a very fast processor!\n");
806	>	painCave.isFatal = 0;
807	>	simError();
808	>	double smallest;
809	>	smallest = info->boxL[0];
810	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
811	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
812	>	theEcr = 0.5 * smallest;
813	>	} else {
814	>	theEcr = globals->getECR();
815	>	}
816	>
817	>	if( !globals->haveEST() ){
818	>	sprintf( painCave.errMsg,
819	>	"SimSetup Warning: using default value of 0.05 * the "
820	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
821	>	);
822	>	painCave.isFatal = 0;
823	>	simError();
824	>	theEst = 0.05 * theEcr;
825	>	} else {
826	>	theEst= globals->getEST();
827	>	}
828	>
829	>	info->setEcr( theEcr, theEst );
830	>
831	>	if(!globals->haveDielectric() ){
832	>	sprintf( painCave.errMsg,
833	>	"SimSetup Error: You are trying to use Reaction Field without"
834	>	"setting a dielectric constant!\n"
835	>	);
836	>	painCave.isFatal = 1;
837	>	simError();
838	>	}
839	>	info->dielectric = globals->getDielectric();
840	>	}
841	>	else {
842	>	if (usesDipoles) {
843	>
844	>	if( !globals->haveECR() ){
845	>	sprintf( painCave.errMsg,
846	>	"SimSetup Warning: using default value of 1/2 the smallest "
847	>	"box length for the electrostaticCutoffRadius.\n"
848	>	"I hope you have a very fast processor!\n");
849	>	painCave.isFatal = 0;
850	>	simError();
851	>	double smallest;
852	>	smallest = info->boxL[0];
853	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
854	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
855	>	theEcr = 0.5 * smallest;
856	>	} else {
857	>	theEcr = globals->getECR();
858	>	}
859	>
860	>	if( !globals->haveEST() ){
861	>	sprintf( painCave.errMsg,
862	>	"SimSetup Warning: using default value of 0.05 * the "
863	>	"electrostaticCutoffRadius for the "
864	>	"electrostaticSkinThickness\n"
865	>	);
866	>	painCave.isFatal = 0;
867	>	simError();
868	>	theEst = 0.05 * theEcr;
869	>	} else {
870	>	theEst= globals->getEST();
871	>	}
872	>
873	>	info->setEcr( theEcr, theEst );
874	>	}
875	>	}
876	>
877	>	#ifdef IS_MPI
878	>	strcpy( checkPointMsg, "post processing checks out" );
879	>	MPIcheckPoint();
880	>	#endif // is_mpi
881	>
882	>	}
883	>
884	>	void SimSetup::initSystemCoords( void ){
885	>
886	>	if( globals->haveInitialConfig() ){
887	>
888	>	InitializeFromFile* fileInit;
889	>	#ifdef IS_MPI // is_mpi
890	>	if( worldRank == 0 ){
891	>	#endif //is_mpi
892	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
893	>	#ifdef IS_MPI
894	>	}else fileInit = new InitializeFromFile( NULL );
895	>	#endif
896	>	fileInit->readInit( info ); // default velocities on
897	>
898	>	delete fileInit;
899	>	}
900	>	else{
901	>
902	>	#ifdef IS_MPI
903	>
904	>	// no init from bass
905	>
906	>	sprintf( painCave.errMsg,
907	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
908	>	painCave.isFatal;
909	>	simError();
910	>
911	>	#else
912	>
913	>	initFromBass();
914	>
915	>
916	>	#endif
917	>	}
918	>
919	>	#ifdef IS_MPI
920	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
921	>	MPIcheckPoint();
922	>	#endif // is_mpi
923	>
924	>	}
925	>
926	>
927	>	void SimSetup::makeOutNames( void ){
928	>
929	>	#ifdef IS_MPI
930	>	if( worldRank == 0 ){
931	>	#endif // is_mpi
932	>
933	>	if( globals->haveFinalConfig() ){
934	>	strcpy( info->finalName, globals->getFinalConfig() );
935	>	}
936	>	else{
937	>	strcpy( info->finalName, inFileName );
938	>	char* endTest;
939	>	int nameLength = strlen( info->finalName );
940	>	endTest = &(info->finalName[nameLength - 5]);
941	>	if( !strcmp( endTest, ".bass" ) ){
942	>	strcpy( endTest, ".eor" );
943	>	}
944	>	else if( !strcmp( endTest, ".BASS" ) ){
945	>	strcpy( endTest, ".eor" );
946	>	}
947	>	else{
948	>	endTest = &(info->finalName[nameLength - 4]);
949	>	if( !strcmp( endTest, ".bss" ) ){
950	>	strcpy( endTest, ".eor" );
951	>	}
952	>	else if( !strcmp( endTest, ".mdl" ) ){
953	>	strcpy( endTest, ".eor" );
954	>	}
955	>	else{
956	>	strcat( info->finalName, ".eor" );
957	>	}
958	>	}
959	>	}
960	>
961	>	// make the sample and status out names
962	>
963	>	strcpy( info->sampleName, inFileName );
964	>	char* endTest;
965	>	int nameLength = strlen( info->sampleName );
966	>	endTest = &(info->sampleName[nameLength - 5]);
967	>	if( !strcmp( endTest, ".bass" ) ){
968	>	strcpy( endTest, ".dump" );
969	>	}
970	>	else if( !strcmp( endTest, ".BASS" ) ){
971	>	strcpy( endTest, ".dump" );
972	>	}
973	>	else{
974	>	endTest = &(info->sampleName[nameLength - 4]);
975	>	if( !strcmp( endTest, ".bss" ) ){
976	>	strcpy( endTest, ".dump" );
977	>	}
978	>	else if( !strcmp( endTest, ".mdl" ) ){
979	>	strcpy( endTest, ".dump" );
980	>	}
981	>	else{
982	>	strcat( info->sampleName, ".dump" );
983	>	}
984	>	}
985	>
986	>	strcpy( info->statusName, inFileName );
987	>	nameLength = strlen( info->statusName );
988	>	endTest = &(info->statusName[nameLength - 5]);
989	>	if( !strcmp( endTest, ".bass" ) ){
990	>	strcpy( endTest, ".stat" );
991	>	}
992	>	else if( !strcmp( endTest, ".BASS" ) ){
993	>	strcpy( endTest, ".stat" );
994	>	}
995	>	else{
996	>	endTest = &(info->statusName[nameLength - 4]);
997	>	if( !strcmp( endTest, ".bss" ) ){
998	>	strcpy( endTest, ".stat" );
999	>	}
1000	>	else if( !strcmp( endTest, ".mdl" ) ){
1001	>	strcpy( endTest, ".stat" );
1002	>	}
1003	>	else{
1004	>	strcat( info->statusName, ".stat" );
1005	>	}
1006	>	}
1007	>
1008	>	#ifdef IS_MPI
1009	>	}
1010	>	#endif // is_mpi
1011	>
1012	>	}
1013	>
1014	>
1015	>	void SimSetup::sysObjectsCreation( void ){
1016	>
1017	>	int i;
1018	>
1019	>	// create the forceField
1020	>
1021	>	createFF();
1022	>
1023	>	// extract componentList
1024	>
1025	>	compList();
1026	>
1027	>	// calc the number of atoms, bond, bends, and torsions
1028	>
1029	>	calcSysValues();
1030	>
1031	>	#ifdef IS_MPI
1032	>	// divide the molecules among the processors
1033	>
1034	>	mpiMolDivide();
1035	>	#endif //is_mpi
1036	>
1037	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1038	>
1039	>	makeSysArrays();
1040	>
1041	>	// make and initialize the molecules (all but atomic coordinates)
1042	>
1043	>	makeMolecules();
1044	>	info->identArray = new int[info->n_atoms];
1045	>	for(i=0; i<info->n_atoms; i++){
1046	>	info->identArray[i] = the_atoms[i]->getIdent();
1047	>	}
1048	>
1049	>
1050	>
1051	>	}
1052	>
1053	>
1054	>	void SimSetup::createFF( void ){
1055	>
1056	>	switch( ffCase ){
1057	>
1058	>	case FF_DUFF:
1059	>	the_ff = new DUFF();
1060	>	break;
1061	>
1062	>	case FF_LJ:
1063	>	the_ff = new LJFF();
1064	>	break;
1065	>
1066	>	case FF_EAM:
1067	>	the_ff = new EAM_FF();
1068	>	break;
1069	>
1070	>	default:
1071	>	sprintf( painCave.errMsg,
1072	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1073	>	painCave.isFatal = 1;
1074	>	simError();
1075	>	}
1076	>
1077	>	#ifdef IS_MPI
1078	>	strcpy( checkPointMsg, "ForceField creation successful" );
1079	>	MPIcheckPoint();
1080	>	#endif // is_mpi
1081	>
1082	>	}
1083	>
1084	>
1085	>	void SimSetup::compList( void ){
1086	>
1087	>	int i;
1088	>
1089	>	comp_stamps = new MoleculeStamp*[n_components];
1090	>
1091	>	// make an array of molecule stamps that match the components used.
1092	>	// also extract the used stamps out into a separate linked list
1093	>
1094	>	info->nComponents = n_components;
1095	>	info->componentsNmol = components_nmol;
1096	>	info->compStamps = comp_stamps;
1097	>	info->headStamp = new LinkedMolStamp();
1098	>
1099	>	char* id;
1100	>	LinkedMolStamp* headStamp = info->headStamp;
1101	>	LinkedMolStamp* currentStamp = NULL;
1102	>	for( i=0; i<n_components; i++ ){
1103	>
1104	>	id = the_components[i]->getType();
1105	>	comp_stamps[i] = NULL;
1106	>
1107	>	// check to make sure the component isn't already in the list
1108	>
1109	>	comp_stamps[i] = headStamp->match( id );
1110	>	if( comp_stamps[i] == NULL ){
1111	>
1112	>	// extract the component from the list;
1113	>
1114	>	currentStamp = stamps->extractMolStamp( id );
1115	>	if( currentStamp == NULL ){
1116	>	sprintf( painCave.errMsg,
1117	>	"SimSetup error: Component \"%s\" was not found in the "
1118	>	"list of declared molecules\n",
1119	>	id );
1120	>	painCave.isFatal = 1;
1121	>	simError();
1122	>	}
1123	>
1124	>	headStamp->add( currentStamp );
1125	>	comp_stamps[i] = headStamp->match( id );
1126	>	}
1127	>	}
1128	>
1129	>	#ifdef IS_MPI
1130	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1131	>	MPIcheckPoint();
1132	>	#endif // is_mpi
1133	>
1134	>
1135	>	}
1136	>
1137	>	void SimSetup::calcSysValues( void ){
1138	>	int i, j, k;
1139	>
1140	>
1141	>	tot_atoms = 0;
1142	>	tot_bonds = 0;
1143	>	tot_bends = 0;
1144	>	tot_torsions = 0;
1145	>	for( i=0; i<n_components; i++ ){
1146	>
1147	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1148	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1149	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1150	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1151	>	}
1152	>
1153	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1154	>
1155	>	info->n_atoms = tot_atoms;
1156	>	info->n_bonds = tot_bonds;
1157	>	info->n_bends = tot_bends;
1158	>	info->n_torsions = tot_torsions;
1159	>	info->n_SRI = tot_SRI;
1160	>	info->n_mol = tot_nmol;
1161	>
1162	>	info->molMembershipArray = new int[tot_atoms];
1163	>	}
1164	>
1165	>
1166	>	#ifdef IS_MPI
1167	>
1168	>	void SimSetup::mpiMolDivide( void ){
1169	>
1170	>	int i, j, k;
1171	>	int localMol, allMol;
1172	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1173	>
1174	>	mpiSim = new mpiSimulation( info );
1175	>
1176	>	globalIndex = mpiSim->divideLabor();
1177	>
1178	>	// set up the local variables
1179	>
1180	>	mol2proc = mpiSim->getMolToProcMap();
1181	>	molCompType = mpiSim->getMolComponentType();
1182	>
1183	>	allMol = 0;
1184	>	localMol = 0;
1185	>	local_atoms = 0;
1186	>	local_bonds = 0;
1187	>	local_bends = 0;
1188	>	local_torsions = 0;
1189	>	globalAtomIndex = 0;
1190	>
1191	>
1192	>	for( i=0; i<n_components; i++ ){
1193	>
1194	>	for( j=0; j<components_nmol[i]; j++ ){
1195	>
1196	>	if( mol2proc[allMol] == worldRank ){
1197	>
1198	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1199	>	local_bonds +=    comp_stamps[i]->getNBonds();
1200	>	local_bends +=    comp_stamps[i]->getNBends();
1201	>	local_torsions += comp_stamps[i]->getNTorsions();
1202	>	localMol++;
1203	>	}
1204	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1205	>	info->molMembershipArray[globalAtomIndex] = allMol;
1206	>	globalAtomIndex++;
1207	>	}
1208	>
1209	>	allMol++;
1210	>	}
1211	>	}
1212	>	local_SRI = local_bonds + local_bends + local_torsions;
1213	>
1214	>	info->n_atoms = mpiSim->getMyNlocal();
1215	>
1216	>	if( local_atoms != info->n_atoms ){
1217	>	sprintf( painCave.errMsg,
1218	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1219	>	" localAtom (%d) are not equal.\n",
1220	>	info->n_atoms,
1221	>	local_atoms );
1222	>	painCave.isFatal = 1;
1223	>	simError();
1224	>	}
1225	>
1226	>	info->n_bonds = local_bonds;
1227	>	info->n_bends = local_bends;
1228	>	info->n_torsions = local_torsions;
1229	>	info->n_SRI = local_SRI;
1230	>	info->n_mol = localMol;
1231	>
1232	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1233	>	MPIcheckPoint();
1234	>	}
1235	>
1236	>	#endif // is_mpi
1237	>
1238	>
1239	>	void SimSetup::makeSysArrays( void ){
1240	>	int i, j, k;
1241	>
1242	>
1243	>	// create the atom and short range interaction arrays
1244	>
1245	>	Atom::createArrays(info->n_atoms);
1246	>	the_atoms = new Atom*[info->n_atoms];
1247	>	the_molecules = new Molecule[info->n_mol];
1248	>	int molIndex;
1249	>
1250	>	// initialize the molecule's stampID's
1251	>
1252	>	#ifdef IS_MPI
1253	>
1254	>
1255	>	molIndex = 0;
1256	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1257	>
1258	>	if(mol2proc[i] == worldRank ){
1259	>	the_molecules[molIndex].setStampID( molCompType[i] );
1260	>	the_molecules[molIndex].setMyIndex( molIndex );
1261	>	the_molecules[molIndex].setGlobalIndex( i );
1262	>	molIndex++;
1263	>	}
1264	>	}
1265	>
1266	>	#else // is_mpi
1267	>
1268	>	molIndex = 0;
1269	>	globalAtomIndex = 0;
1270	>	for(i=0; i<n_components; i++){
1271	>	for(j=0; j<components_nmol[i]; j++ ){
1272	>	the_molecules[molIndex].setStampID( i );
1273	>	the_molecules[molIndex].setMyIndex( molIndex );
1274	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1275	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1276	>	info->molMembershipArray[globalAtomIndex] = molIndex;
1277	>	globalAtomIndex++;
1278	>	}
1279	>	molIndex++;
1280	>	}
1281	>	}
1282	>
1283	>
1284	>	#endif // is_mpi
1285	>
1286	>
1287	>	if( info->n_SRI ){
1288	>
1289	>	Exclude::createArray(info->n_SRI);
1290	>	the_excludes = new Exclude*[info->n_SRI];
1291	>	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1292	>	info->globalExcludes = new int;
1293	>	info->n_exclude = info->n_SRI;
1294	>	}
1295	>	else{
1296	>
1297	>	Exclude::createArray( 1 );
1298	>	the_excludes = new Exclude*;
1299	>	the_excludes[0] = new Exclude(0);
1300	>	the_excludes[0]->setPair( 0,0 );
1301	>	info->globalExcludes = new int;
1302	>	info->globalExcludes[0] = 0;
1303	>	info->n_exclude = 0;
1304	>	}
1305	>
1306	>	// set the arrays into the SimInfo object
1307	>
1308	>	info->atoms = the_atoms;
1309	>	info->molecules = the_molecules;
1310	>	info->nGlobalExcludes = 0;
1311	>	info->excludes = the_excludes;
1312	>
1313	>	the_ff->setSimInfo( info );
1314	>
1315	>	}
1316	>
1317	>	void SimSetup::makeIntegrator( void ){
1318	>
1319	>	NVT<RealIntegrator>*  myNVT = NULL;
1320	>	NPTi<RealIntegrator>* myNPTi = NULL;
1321	>	NPTf<RealIntegrator>* myNPTf = NULL;
1322	>	NPTim<RealIntegrator>* myNPTim = NULL;
1323	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1324	>	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1325	>	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1326	>	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1327	>	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1328	>	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1329	>	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1330	>
1331	>	cerr << "setting integrator" <<endl;
1332	>
1333	>	switch( ensembleCase ){
1334	>
1335	>	case NVE_ENS:
1336	>	new NVE<RealIntegrator>( info, the_ff );
1337	>	break;
1338	>
1339	>	case NVT_ENS:
1340	>	myNVT = new NVT<RealIntegrator>( info, the_ff );
1341	>	myNVT->setTargetTemp(globals->getTargetTemp());
1342	>
1343	>	if (globals->haveTauThermostat())
1344	>	myNVT->setTauThermostat(globals->getTauThermostat());
1345	>
1346	>	else {
1347	>	sprintf( painCave.errMsg,
1348	>	"SimSetup error: If you use the NVT\n"
1349	>	"    ensemble, you must set tauThermostat.\n");
1350	>	painCave.isFatal = 1;
1351	>	simError();
1352	>	}
1353	>	break;
1354	>
1355	>	case NPTi_ENS:
1356	>	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1357	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1358	>
1359	>	if (globals->haveTargetPressure())
1360	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1361	>	else {
1362	>	sprintf( painCave.errMsg,
1363	>	"SimSetup error: If you use a constant pressure\n"
1364	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1365	>	painCave.isFatal = 1;
1366	>	simError();
1367	>	}
1368	>
1369	>	if( globals->haveTauThermostat() )
1370	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1371	>	else{
1372	>	sprintf( painCave.errMsg,
1373	>	"SimSetup error: If you use an NPT\n"
1374	>	"    ensemble, you must set tauThermostat.\n");
1375	>	painCave.isFatal = 1;
1376	>	simError();
1377	>	}
1378	>
1379	>	if( globals->haveTauBarostat() )
1380	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1381	>	else{
1382	>	sprintf( painCave.errMsg,
1383	>	"SimSetup error: If you use an NPT\n"
1384	>	"    ensemble, you must set tauBarostat.\n");
1385	>	painCave.isFatal = 1;
1386	>	simError();
1387	>	}
1388	>	break;
1389	>
1390	>	case NPTf_ENS:
1391	>	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1392	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1393	>
1394	>	if (globals->haveTargetPressure())
1395	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1396	>	else {
1397	>	sprintf( painCave.errMsg,
1398	>	"SimSetup error: If you use a constant pressure\n"
1399	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1400	>	painCave.isFatal = 1;
1401	>	simError();
1402	>	}
1403	>
1404	>	if( globals->haveTauThermostat() )
1405	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1406	>	else{
1407	>	sprintf( painCave.errMsg,
1408	>	"SimSetup error: If you use an NPT\n"
1409	>	"    ensemble, you must set tauThermostat.\n");
1410	>	painCave.isFatal = 1;
1411	>	simError();
1412	>	}
1413	>
1414	>	if( globals->haveTauBarostat() )
1415	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1416	>	else{
1417	>	sprintf( painCave.errMsg,
1418	>	"SimSetup error: If you use an NPT\n"
1419	>	"    ensemble, you must set tauBarostat.\n");
1420	>	painCave.isFatal = 1;
1421	>	simError();
1422	>	}
1423	>	break;
1424	>
1425	>	case NPTim_ENS:
1426	>	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1427	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1428	>
1429	>	if (globals->haveTargetPressure())
1430	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1431	>	else {
1432	>	sprintf( painCave.errMsg,
1433	>	"SimSetup error: If you use a constant pressure\n"
1434	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	>	painCave.isFatal = 1;
1436	>	simError();
1437	>	}
1438	>
1439	>	if( globals->haveTauThermostat() )
1440	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1441	>	else{
1442	>	sprintf( painCave.errMsg,
1443	>	"SimSetup error: If you use an NPT\n"
1444	>	"    ensemble, you must set tauThermostat.\n");
1445	>	painCave.isFatal = 1;
1446	>	simError();
1447	>	}
1448	>
1449	>	if( globals->haveTauBarostat() )
1450	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1451	>	else{
1452	>	sprintf( painCave.errMsg,
1453	>	"SimSetup error: If you use an NPT\n"
1454	>	"    ensemble, you must set tauBarostat.\n");
1455	>	painCave.isFatal = 1;
1456	>	simError();
1457	>	}
1458	>	break;
1459	>
1460	>	case NPTfm_ENS:
1461	>	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1462	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1463	>
1464	>	if (globals->haveTargetPressure())
1465	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1466	>	else {
1467	>	sprintf( painCave.errMsg,
1468	>	"SimSetup error: If you use a constant pressure\n"
1469	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1470	>	painCave.isFatal = 1;
1471	>	simError();
1472	>	}
1473	>
1474	>	if( globals->haveTauThermostat() )
1475	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1476	>	else{
1477	>	sprintf( painCave.errMsg,
1478	>	"SimSetup error: If you use an NPT\n"
1479	>	"    ensemble, you must set tauThermostat.\n");
1480	>	painCave.isFatal = 1;
1481	>	simError();
1482	>	}
1483	>
1484	>	if( globals->haveTauBarostat() )
1485	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1486	>	else{
1487	>	sprintf( painCave.errMsg,
1488	>	"SimSetup error: If you use an NPT\n"
1489	>	"    ensemble, you must set tauBarostat.\n");
1490	>	painCave.isFatal = 1;
1491	>	simError();
1492	>	}
1493	>	break;
1494	>
1495	>	case NVEZCONS_ENS:
1496	>
1497	>
1498	>	//setup index of z-constraint molecules, z-constraint sampel time
1499	>	//and z-constraint force output name. These parameter should be known
1500	>	//before constructing the z-constraint integrator
1501	>	setupZConstraint();
1502	>
1503	>	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1504	>
1505	>	break;
1506	>
1507	>
1508	>	case NVTZCONS_ENS:
1509	>
1510	>	setupZConstraint();
1511	>
1512	>	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1513	>	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1514	>
1515	>	if (globals->haveTauThermostat())
1516	>	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1517	>
1518	>	else {
1519	>	sprintf( painCave.errMsg,
1520	>	"SimSetup error: If you use the NVT\n"
1521	>	"    ensemble, you must set tauThermostat.\n");
1522	>	painCave.isFatal = 1;
1523	>	simError();
1524	>	}
1525	>	break;
1526	>
1527	>	case NPTiZCONS_ENS:
1528	>
1529	>	setupZConstraint();
1530	>
1531	>	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1532	>	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1533	>
1534	>	if (globals->haveTargetPressure())
1535	>	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1536	>	else {
1537	>	sprintf( painCave.errMsg,
1538	>	"SimSetup error: If you use a constant pressure\n"
1539	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1540	>	painCave.isFatal = 1;
1541	>	simError();
1542	>	}
1543	>
1544	>	if( globals->haveTauThermostat() )
1545	>	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1546	>	else{
1547	>	sprintf( painCave.errMsg,
1548	>	"SimSetup error: If you use an NPT\n"
1549	>	"    ensemble, you must set tauThermostat.\n");
1550	>	painCave.isFatal = 1;
1551	>	simError();
1552	>	}
1553	>
1554	>	if( globals->haveTauBarostat() )
1555	>	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1556	>	else{
1557	>	sprintf( painCave.errMsg,
1558	>	"SimSetup error: If you use an NPT\n"
1559	>	"    ensemble, you must set tauBarostat.\n");
1560	>	painCave.isFatal = 1;
1561	>	simError();
1562	>	}
1563	>
1564	>	break;
1565	>
1566	>	case NPTfZCONS_ENS:
1567	>
1568	>	setupZConstraint();
1569	>
1570	>	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1571	>	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1572	>
1573	>	if (globals->haveTargetPressure())
1574	>	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1575	>	else {
1576	>	sprintf( painCave.errMsg,
1577	>	"SimSetup error: If you use a constant pressure\n"
1578	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1579	>	painCave.isFatal = 1;
1580	>	simError();
1581	>	}
1582	>
1583	>	if( globals->haveTauThermostat() )
1584	>	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1585	>	else{
1586	>	sprintf( painCave.errMsg,
1587	>	"SimSetup error: If you use an NPT\n"
1588	>	"    ensemble, you must set tauThermostat.\n");
1589	>	painCave.isFatal = 1;
1590	>	simError();
1591	>	}
1592	>
1593	>	if( globals->haveTauBarostat() )
1594	>	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1595	>	else{
1596	>	sprintf( painCave.errMsg,
1597	>	"SimSetup error: If you use an NPT\n"
1598	>	"    ensemble, you must set tauBarostat.\n");
1599	>	painCave.isFatal = 1;
1600	>	simError();
1601	>	}
1602	>
1603	>	break;
1604	>
1605	>	case NPTimZCONS_ENS:
1606	>
1607	>	setupZConstraint();
1608	>
1609	>	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1610	>	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1611	>
1612	>	if (globals->haveTargetPressure())
1613	>	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1614	>	else {
1615	>	sprintf( painCave.errMsg,
1616	>	"SimSetup error: If you use a constant pressure\n"
1617	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1618	>	painCave.isFatal = 1;
1619	>	simError();
1620	>	}
1621	>
1622	>	if( globals->haveTauThermostat() )
1623	>	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1624	>	else{
1625	>	sprintf( painCave.errMsg,
1626	>	"SimSetup error: If you use an NPT\n"
1627	>	"    ensemble, you must set tauThermostat.\n");
1628	>	painCave.isFatal = 1;
1629	>	simError();
1630	>	}
1631	>
1632	>	if( globals->haveTauBarostat() )
1633	>	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1634	>	else{
1635	>	sprintf( painCave.errMsg,
1636	>	"SimSetup error: If you use an NPT\n"
1637	>	"    ensemble, you must set tauBarostat.\n");
1638	>	painCave.isFatal = 1;
1639	>	simError();
1640	>	}
1641	>
1642	>	break;
1643	>
1644	>	case NPTfmZCONS_ENS:
1645	>
1646	>	setupZConstraint();
1647	>
1648	>	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1649	>	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1650	>
1651	>	if (globals->haveTargetPressure())
1652	>	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1653	>	else {
1654	>	sprintf( painCave.errMsg,
1655	>	"SimSetup error: If you use a constant pressure\n"
1656	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1657	>	painCave.isFatal = 1;
1658	>	simError();
1659	>	}
1660	>
1661	>	if( globals->haveTauThermostat() )
1662	>	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1663	>	else{
1664	>	sprintf( painCave.errMsg,
1665	>	"SimSetup error: If you use an NPT\n"
1666	>	"    ensemble, you must set tauThermostat.\n");
1667	>	painCave.isFatal = 1;
1668	>	simError();
1669	>	}
1670	>
1671	>	if( globals->haveTauBarostat() )
1672	>	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1673	>	else{
1674	>	sprintf( painCave.errMsg,
1675	>	"SimSetup error: If you use an NPT\n"
1676	>	"    ensemble, you must set tauBarostat.\n");
1677	>	painCave.isFatal = 1;
1678	>	simError();
1679	>	}
1680	>	break;
1681	>
1682	>
1683	>
1684	>	default:
1685	>	sprintf( painCave.errMsg,
1686	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1687	>	painCave.isFatal = 1;
1688	>	simError();
1689	>	}
1690	>
1691	>	}
1692	>
1693	>	void SimSetup::initFortran( void ){
1694	>
1695	>	info->refreshSim();
1696	>
1697	>	if( !strcmp( info->mixingRule, "standard") ){
1698	>	the_ff->initForceField( LB_MIXING_RULE );
1699	>	}
1700	>	else if( !strcmp( info->mixingRule, "explicit") ){
1701	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1702	>	}
1703	>	else{
1704	>	sprintf( painCave.errMsg,
1705	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1706	>	info->mixingRule );
1707	>	painCave.isFatal = 1;
1708	>	simError();
1709	>	}
1710	>
1711	>
1712	>	#ifdef IS_MPI
1713	>	strcpy( checkPointMsg,
1714	>	"Successfully intialized the mixingRule for Fortran." );
1715	>	MPIcheckPoint();
1716	>	#endif // is_mpi
1717	>
1718	>	}
1719	>
1720	>	void SimSetup::setupZConstraint()
1721	>	{
1722	>	if(globals->haveZConsTime()){
1723	>
1724	>	//add sample time of z-constraint  into SimInfo's property list
1725	>	DoubleData* zconsTimeProp = new DoubleData();
1726	>	zconsTimeProp->setID("zconstime");
1727	>	zconsTimeProp->setData(globals->getZConsTime());
1728	>	info->addProperty(zconsTimeProp);
1729	>	}
1730	>	else{
1731	>	sprintf( painCave.errMsg,
1732	>	"ZConstraint error: If you use an ZConstraint\n"
1733	>	" , you must set sample time.\n");
1734	>	painCave.isFatal = 1;
1735	>	simError();
1736	>	}
1737	>
1738	>	if(globals->haveIndexOfAllZConsMols()){
1739	>
1740	>	//add index of z-constraint molecules into SimInfo's property list
1741	>	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1742	>
1743	>	//sort the index
1744	>	sort(tempIndex.begin(), tempIndex.end());
1745	>
1746	>	IndexData* zconsIndex = new IndexData();
1747	>	zconsIndex->setID("zconsindex");
1748	>	zconsIndex->setIndexData(tempIndex);
1749	>	info->addProperty(zconsIndex);
1750	>	}
1751	>	else{
1752	>	sprintf( painCave.errMsg,
1753	>	"SimSetup error: If you use an ZConstraint\n"
1754	>	" , you must set index of z-constraint molecules.\n");
1755	>	painCave.isFatal = 1;
1756	>	simError();
1757	>
1758	>	}
1759	>
1760	>	//Determine the name of ouput file and add it into SimInfo's property list
1761	>	//Be careful, do not use inFileName, since it is a pointer which
1762	>	//point to a string at master node, and slave nodes do not contain that string
1763	>
1764	>	string zconsOutput(info->finalName);
1765	>
1766	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1767	>
1768	>	StringData* zconsFilename = new StringData();
1769	>	zconsFilename->setID("zconsfilename");
1770	>	zconsFilename->setData(zconsOutput);
1771	>
1772	>	info->addProperty(zconsFilename);
1773	>
1774		}

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