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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC

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

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