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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 420 by mmeineke, Thu Mar 27 17:32:03 2003 UTC vs.
Revision 689 by tim, Tue Aug 12 19:56:49 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 "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTim_ENS      4
25	+	#define NPTfm_ENS      5
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 27 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 62 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
97	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
70	<
71	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
74	<
75	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
79	<
80	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
85	<
86	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
89	<
90	<
91	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
102	<
103	<	#ifdef IS_MPI
104	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
107	<
97	>	int i, j, k, globalAtomIndex;
98
99	+	// gather all of the information from the Bass file
100
101	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
101	>	std::cerr << "gathering info\n";
102
103	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
103	>	gatherInfo();
104
105	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
105	>	// creation of complex system objects
106
107	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
107	>	std::cerr << "creating system objects\n";
108
109	<	tot_nmol += the_components[i]->getNMol();
132	<	components_nmol[i] = the_components[i]->getNMol();
133	<	}
134	<	}
135	<	else{
136	<	sprintf( painCave.errMsg,
137	<	"SimSetup error.\n"
138	<	"\tSorry, the ability to specify total"
139	<	" nMols and then give molfractions in the components\n"
140	<	"\tis not currently supported."
141	<	" Please give nMol in the components.\n" );
142	<	painCave.isFatal = 1;
143	<	simError();
144	<
145	<
146	<	//     tot_nmol = the_globals->getNMol();
147	<
148	<	//   //we have the total number of molecules, now we check for molfractions
149	<	//     for( i=0; i<n_components; i++ ){
150	<
151	<	//       if( !the_components[i]->haveMolFraction() ){
152	<
153	<	//  if( !the_components[i]->haveNMol() ){
154	<	//    //we have a problem
155	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	<	//              << " nMol was given in component
157	<
158	<	}
109	>	sysObjectsCreation();
110
111	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
164	<
165	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
167	<
168	<	simnfo->nComponents = n_components;
169	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
111	>	// check on the post processing info
112
113	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
113	>	std::cerr << "performing final info check.\n";
114
115	<	id = the_components[i]->getType();
179	<	comp_stamps[i] = NULL;
180	<
181	<	// check to make sure the component isn't already in the list
115	>	finalInfoCheck();
116
117	<	comp_stamps[i] = headStamp->match( id );
184	<	if( comp_stamps[i] == NULL ){
185	<
186	<	// extract the component from the list;
187	<
188	<	currentStamp = the_stamps->extractMolStamp( id );
189	<	if( currentStamp == NULL ){
190	<	sprintf( painCave.errMsg,
191	<	"SimSetup error: Component \"%s\" was not found in the "
192	<	"list of declared molecules\n",
193	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
117	>	// initialize the system coordinates
118
119	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
119	>	std::cerr << "about to init coords\n";
120
121	+	if( !isInfoArray ) initSystemCoords();
122
123	+	// make the output filenames
124
125	<	// caclulate the number of atoms, bonds, bends and torsions
126	<
127	<	tot_atoms = 0;
214	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
218	<
219	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
224	<
225	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
226	<
227	<	simnfo->n_atoms = tot_atoms;
228	<	simnfo->n_bonds = tot_bonds;
229	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
233	<
125	>	makeOutNames();
126	>
127	>	// make the integrator
128
129	<	#ifdef IS_MPI
236	<
237	<	// divide the molecules among processors here.
238	<
239	<	mpiSim = new mpiSimulation( simnfo );
240	<
241	<
242	<
243	<	globalIndex = mpiSim->divideLabor();
244	<
245	<
246	<
247	<	// set up the local variables
248	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
259	<
260	<	for( j=0; j<components_nmol[i]; j++ ){
261	<
262	<	if( mpiSim->getMyMolStart() <= allMol &&
263	<	allMol <= mpiSim->getMyMolEnd() ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
276	<
277	<	simnfo->n_atoms = mpiSim->getMyNlocal();
278	<
279	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
288	<
289	<	simnfo->n_bonds = local_bonds;
290	<	simnfo->n_bends = local_bends;
291	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
294	<
295	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
296	<	MPIcheckPoint();
297	<
298	<
299	<	#endif // is_mpi
300	<
301	<
302	<	// create the atom and short range interaction arrays
303	<
304	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
307	<
308	<
309	<	if( simnfo->n_SRI ){
310	<	Exclude::createArray(simnfo->n_SRI);
311	<	the_excludes = new Exclude*[simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	Exclude::createArray( 1 );
318	<	the_excludes = new Exclude*;
319	<	the_excludes[0] = new Exclude(0);
320	<	the_excludes[0]->setPair( 0,0 );
321	<	simnfo->globalExcludes = new int;
322	<	simnfo->globalExcludes[0] = 0;
323	<	simnfo->n_exclude = 0;
324	<	}
325	<
326	<	// set the arrays into the SimInfo object
327	<
328	<	simnfo->atoms = the_atoms;
329	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
332	<
333	<
334	<	// get some of the tricky things that may still be in the globals
335	<
129	>	makeIntegrator();
130
337	–	if( the_globals->haveBox() ){
338	–	simnfo->box_x = the_globals->getBox();
339	–	simnfo->box_y = the_globals->getBox();
340	–	simnfo->box_z = the_globals->getBox();
341	–	}
342	–	else if( the_globals->haveDensity() ){
343	–
344	–	double vol;
345	–	vol = (double)tot_nmol / the_globals->getDensity();
346	–	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	–	simnfo->box_y = simnfo->box_x;
348	–	simnfo->box_z = simnfo->box_x;
349	–	}
350	–	else{
351	–	if( !the_globals->haveBoxX() ){
352	–	sprintf( painCave.errMsg,
353	–	"SimSetup error, no periodic BoxX size given.\n" );
354	–	painCave.isFatal = 1;
355	–	simError();
356	–	}
357	–	simnfo->box_x = the_globals->getBoxX();
358	–
359	–	if( !the_globals->haveBoxY() ){
360	–	sprintf( painCave.errMsg,
361	–	"SimSetup error, no periodic BoxY size given.\n" );
362	–	painCave.isFatal = 1;
363	–	simError();
364	–	}
365	–	simnfo->box_y = the_globals->getBoxY();
366	–
367	–	if( !the_globals->haveBoxZ() ){
368	–	sprintf( painCave.errMsg,
369	–	"SimSetup error, no periodic BoxZ size given.\n" );
370	–	painCave.isFatal = 1;
371	–	simError();
372	–	}
373	–	simnfo->box_z = the_globals->getBoxZ();
374	–	}
375	–
131		#ifdef IS_MPI
132	<	strcpy( checkPointMsg, "Box size set up" );
378	<	MPIcheckPoint();
379	<	#endif // is_mpi
380	<
381	<
382	<	// initialize the arrays
383	<
384	<	the_ff->setSimInfo( simnfo );
385	<
386	<	makeAtoms();
387	<	simnfo->identArray = new int[simnfo->n_atoms];
388	<	for(i=0; i<simnfo->n_atoms; i++){
389	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
390	<	}
391	<
392	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
395	<
396	<	if( tot_bends ){
397	<	makeBends();
398	<	}
399	<
400	<	if( tot_torsions ){
401	<	makeTorsions();
402	<	}
403	<
404	<
405	<	if (the_globals->getUseRF() ) {
406	<	simnfo->useReactionField = 1;
407	<
408	<	if( !the_globals->haveECR() ){
409	<	sprintf( painCave.errMsg,
410	<	"SimSetup Warning: using default value of 1/2 the smallest "
411	<	"box length for the electrostaticCutoffRadius.\n"
412	<	"I hope you have a very fast processor!\n");
413	<	painCave.isFatal = 0;
414	<	simError();
415	<	double smallest;
416	<	smallest = simnfo->box_x;
417	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	<	simnfo->ecr = 0.5 * smallest;
420	<	} else {
421	<	simnfo->ecr        = the_globals->getECR();
422	<	}
423	<
424	<	if( !the_globals->haveEST() ){
425	<	sprintf( painCave.errMsg,
426	<	"SimSetup Warning: using default value of 0.05 * the "
427	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	<	);
429	<	painCave.isFatal = 0;
430	<	simError();
431	<	simnfo->est = 0.05 * simnfo->ecr;
432	<	} else {
433	<	simnfo->est        = the_globals->getEST();
434	<	}
435	<
436	<	if(!the_globals->haveDielectric() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup Error: You are trying to use Reaction Field without"
439	<	"setting a dielectric constant!\n"
440	<	);
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
451	<	"box length for the electrostaticCutoffRadius.\n"
452	<	"I hope you have a very fast processor!\n");
453	<	painCave.isFatal = 0;
454	<	simError();
455	<	double smallest;
456	<	smallest = simnfo->box_x;
457	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	<	simnfo->ecr = 0.5 * smallest;
460	<	} else {
461	<	simnfo->ecr        = the_globals->getECR();
462	<	}
463	<
464	<	if( !the_globals->haveEST() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup Warning: using default value of 5% of the"
467	<	"electrostaticCutoffRadius for the "
468	<	"electrostaticSkinThickness\n"
469	<	);
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	simnfo->est = 0.05 * simnfo->ecr;
473	<	} else {
474	<	simnfo->est        = the_globals->getEST();
475	<	}
476	<	}
477	<	}
478	<
479	<	#ifdef IS_MPI
480	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
481	<	MPIcheckPoint();
482	<	#endif // is_mpi
483	<
484	<	if( the_globals->haveInitialConfig() ){
485	<
486	<	InitializeFromFile* fileInit;
487	<	#ifdef IS_MPI // is_mpi
488	<	if( worldRank == 0 ){
489	<	#endif //is_mpi
490	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
491	<	#ifdef IS_MPI
492	<	}else fileInit = new InitializeFromFile( NULL );
132	>	mpiSim->mpiRefresh();
133		#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
134
135	<	delete fileInit;
497	<	}
498	<	else{
135	>	// initialize the Fortran
136
137	<	#ifdef IS_MPI
501	<
502	<	// no init from bass
503	<
504	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
510	<
511	<	initFromBass();
512	<
513	<
514	<	#endif
515	<	}
516	<
517	<	#ifdef IS_MPI
518	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
519	<	MPIcheckPoint();
520	<	#endif // is_mpi
521	<
522	<
523	<
524	<
525	<
526	<
527	<
528	<	#ifdef IS_MPI
529	<	if( worldRank == 0 ){
530	<	#endif // is_mpi
531	<
532	<	if( the_globals->haveFinalConfig() ){
533	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
534	<	}
535	<	else{
536	<	strcpy( simnfo->finalName, inFileName );
537	<	char* endTest;
538	<	int nameLength = strlen( simnfo->finalName );
539	<	endTest = &(simnfo->finalName[nameLength - 5]);
540	<	if( !strcmp( endTest, ".bass" ) ){
541	<	strcpy( endTest, ".eor" );
542	<	}
543	<	else if( !strcmp( endTest, ".BASS" ) ){
544	<	strcpy( endTest, ".eor" );
545	<	}
546	<	else{
547	<	endTest = &(simnfo->finalName[nameLength - 4]);
548	<	if( !strcmp( endTest, ".bss" ) ){
549	<	strcpy( endTest, ".eor" );
550	<	}
551	<	else if( !strcmp( endTest, ".mdl" ) ){
552	<	strcpy( endTest, ".eor" );
553	<	}
554	<	else{
555	<	strcat( simnfo->finalName, ".eor" );
556	<	}
557	<	}
558	<	}
559	<
560	<	// make the sample and status out names
561	<
562	<	strcpy( simnfo->sampleName, inFileName );
563	<	char* endTest;
564	<	int nameLength = strlen( simnfo->sampleName );
565	<	endTest = &(simnfo->sampleName[nameLength - 5]);
566	<	if( !strcmp( endTest, ".bass" ) ){
567	<	strcpy( endTest, ".dump" );
568	<	}
569	<	else if( !strcmp( endTest, ".BASS" ) ){
570	<	strcpy( endTest, ".dump" );
571	<	}
572	<	else{
573	<	endTest = &(simnfo->sampleName[nameLength - 4]);
574	<	if( !strcmp( endTest, ".bss" ) ){
575	<	strcpy( endTest, ".dump" );
576	<	}
577	<	else if( !strcmp( endTest, ".mdl" ) ){
578	<	strcpy( endTest, ".dump" );
579	<	}
580	<	else{
581	<	strcat( simnfo->sampleName, ".dump" );
582	<	}
583	<	}
584	<
585	<	strcpy( simnfo->statusName, inFileName );
586	<	nameLength = strlen( simnfo->statusName );
587	<	endTest = &(simnfo->statusName[nameLength - 5]);
588	<	if( !strcmp( endTest, ".bass" ) ){
589	<	strcpy( endTest, ".stat" );
590	<	}
591	<	else if( !strcmp( endTest, ".BASS" ) ){
592	<	strcpy( endTest, ".stat" );
593	<	}
594	<	else{
595	<	endTest = &(simnfo->statusName[nameLength - 4]);
596	<	if( !strcmp( endTest, ".bss" ) ){
597	<	strcpy( endTest, ".stat" );
598	<	}
599	<	else if( !strcmp( endTest, ".mdl" ) ){
600	<	strcpy( endTest, ".stat" );
601	<	}
602	<	else{
603	<	strcat( simnfo->statusName, ".stat" );
604	<	}
605	<	}
606	<
607	<	#ifdef IS_MPI
608	<	}
609	<	#endif // is_mpi
610	<
611	<	// set the status, sample, and themal kick times
612	<
613	<	if( the_globals->haveSampleTime() ){
614	<	simnfo->sampleTime = the_globals->getSampleTime();
615	<	simnfo->statusTime = simnfo->sampleTime;
616	<	simnfo->thermalTime = simnfo->sampleTime;
617	<	}
618	<	else{
619	<	simnfo->sampleTime = the_globals->getRunTime();
620	<	simnfo->statusTime = simnfo->sampleTime;
621	<	simnfo->thermalTime = simnfo->sampleTime;
622	<	}
137	>	initFortran();
138
624	–	if( the_globals->haveStatusTime() ){
625	–	simnfo->statusTime = the_globals->getStatusTime();
626	–	}
139
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
140
632	–	// check for the temperature set flag
633	–
634	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
635	–
636	–
637	–	//   // make the longe range forces and the integrator
638	–
639	–	//   new AllLong( simnfo );
640	–
641	–	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642	–	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
645	–
646	–
647	–
648	–	// initialize the Fortran
649	–
650	–	simnfo->refreshSim();
651	–
652	–	if( !strcmp( simnfo->mixingRule, "standard") ){
653	–	the_ff->initForceField( LB_MIXING_RULE );
654	–	}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
658	–	else{
659	–	sprintf( painCave.errMsg,
660	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	–	simnfo->mixingRule );
662	–	painCave.isFatal = 1;
663	–	simError();
664	–	}
665	–
666	–
667	–	#ifdef IS_MPI
668	–	strcpy( checkPointMsg,
669	–	"Successfully intialized the mixingRule for Fortran." );
670	–	MPIcheckPoint();
671	–	#endif // is_mpi
141		}
142
143
144		void SimSetup::makeMolecules( void ){
145
146	+	int k,l;
147		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
148	<	molInit info;
148	>	molInit molInfo;
149		DirectionalAtom* dAtom;
150		LinkedAssign* extras;
151		LinkedAssign* current_extra;
#	Line 683 | Line 153 | void SimSetup::makeMolecules( void ){
153		BondStamp* currentBond;
154		BendStamp* currentBend;
155		TorsionStamp* currentTorsion;
156	+
157	+	bond_pair* theBonds;
158	+	bend_set* theBends;
159	+	torsion_set* theTorsions;
160	+
161
162		//init the forceField paramters
163
164		the_ff->readParams();
165
166
167	<	// init the molecules
167	>	// init the atoms
168
169	<	atomOffset = 0;
170	<	excludeOffset = 0;
171	<	for(i=0; i<simnfo->n_mol; i++){
169	>	double ux, uy, uz, u, uSqr;
170	>
171	>	for(k=0; k<nInfo; k++){
172
173	<	stampID = the_molecules[i].getStampID();
173	>	the_ff->setSimInfo( &(info[k]) );
174
175	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
176	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
177	<	info.nBends    = comp_stamps[stampID]->getNBends();
178	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
179	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
175	>	atomOffset = 0;
176	>	excludeOffset = 0;
177	>	for(i=0; i<info[k].n_mol; i++){
178	>
179	>	stampID = info[k].molecules[i].getStampID();
180
181	<	info.myAtoms = &the_atoms[atomOffset];
182	<	info.myExcludes = &the_excludes[excludeOffset];
183	<	info.myBonds = new Bond*[info.nBonds];
184	<	info.myBends = new Bend*[info.nBends];
185	<	info.myTorsions = new Torsions*[info.nTorsions];
181	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
182	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
183	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
184	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
185	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
186	>
187	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
188	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
189	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
190	>	molInfo.myBends = new Bend*[molInfo.nBends];
191	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
192
193	<	theBonds = new bond_pair[info.nBonds];
194	<	theBends = new bend_set[info.nBends];
195	<	theTorsions = new torsion_set[info.nTorsions];
193	>	theBonds = new bond_pair[molInfo.nBonds];
194	>	theBends = new bend_set[molInfo.nBends];
195	>	theTorsions = new torsion_set[molInfo.nTorsions];
196
197	<	// make the Atoms
197	>	// make the Atoms
198
199	<	for(j=0; j<info.nAtoms; j++){
719	<
720	<	currentAtom = theComponents[stampID]->getAtom( j );
721	<	if( currentAtom->haveOrientation() ){
199	>	for(j=0; j<molInfo.nAtoms; j++){
200
201	<	dAtom = new DirectionalAtom(j + atomOffset);
202	<	simnfo->n_oriented++;
203	<	info.myAtoms[j] = dAtom;
204	<
205	<	ux = currentAtom->getOrntX();
206	<	uy = currentAtom->getOrntY();
207	<	uz = currentAtom->getOrntZ();
208	<
209	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
210	<
211	<	u = sqrt( uSqr );
212	<	ux = ux / u;
213	<	uy = uy / u;
214	<	uz = uz / u;
215	<
216	<	dAtom->setSUx( ux );
217	<	dAtom->setSUy( uy );
218	<	dAtom->setSUz( uz );
219	<	}
220	<	else{
221	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
222	<	}
223	<	info.myAtoms[j]->setType( currentAtom->getType() );
201	>	currentAtom = comp_stamps[stampID]->getAtom( j );
202	>	if( currentAtom->haveOrientation() ){
203	>
204	>	dAtom = new DirectionalAtom( (j + atomOffset),
205	>	info[k].getConfiguration() );
206	>	info[k].n_oriented++;
207	>	molInfo.myAtoms[j] = dAtom;
208	>
209	>	ux = currentAtom->getOrntX();
210	>	uy = currentAtom->getOrntY();
211	>	uz = currentAtom->getOrntZ();
212	>
213	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
214	>
215	>	u = sqrt( uSqr );
216	>	ux = ux / u;
217	>	uy = uy / u;
218	>	uz = uz / u;
219	>
220	>	dAtom->setSUx( ux );
221	>	dAtom->setSUy( uy );
222	>	dAtom->setSUz( uz );
223	>	}
224	>	else{
225	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
226	>	info[k].getConfiguration() );
227	>	}
228	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
229
230		#ifdef IS_MPI
231
232	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
232	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
233
234		#endif // is_mpi
235	<	}
235	>	}
236
237		// make the bonds
238	<	for(j=0; j<info.nBonds; j++){
238	>	for(j=0; j<molInfo.nBonds; j++){
239
240	<	currentBond = comp_stamps[stampID]->getBond( j );
241	<	theBonds[j].a = currentBond->getA() + atomOffset;
242	<	theBonds[j].b = currentBond->getB() + atomOffset;
243	<
244	<	exI = theBonds[i].a;
245	<	exJ = theBonds[i].b;
246	<
247	<	// exclude_I must always be the smaller of the pair
248	<	if( exI > exJ ){
249	<	tempEx = exI;
250	<	exI = exJ;
251	<	exJ = tempEx;
252	<	}
240	>	currentBond = comp_stamps[stampID]->getBond( j );
241	>	theBonds[j].a = currentBond->getA() + atomOffset;
242	>	theBonds[j].b = currentBond->getB() + atomOffset;
243	>
244	>	exI = theBonds[j].a;
245	>	exJ = theBonds[j].b;
246	>
247	>	// exclude_I must always be the smaller of the pair
248	>	if( exI > exJ ){
249	>	tempEx = exI;
250	>	exI = exJ;
251	>	exJ = tempEx;
252	>	}
253		#ifdef IS_MPI
254	<	tempEx = exI;
255	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
256	<	tempEx = exJ;
257	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
258	<
259	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
254	>	tempEx = exI;
255	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
256	>	tempEx = exJ;
257	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
258	>
259	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
260		#else  // isn't MPI
261	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
261	>
262	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
263		#endif  //is_mpi
264	<	}
265	<	excludeOffset += info.nBonds;
266	<
267	<	//make the bends
268	<	for(j=0; j<info.nBends; j++){
269	<
270	<	currentBend = comp_stamps[stampID]->getBend( j );
271	<	theBends[j].a = currentBend->getA() + atomOffset;
272	<	theBends[j].b = currentBend->getB() + atomOffset;
273	<	theBends[j].c = currentBend->getC() + atomOffset;
264	>	}
265	>	excludeOffset += molInfo.nBonds;
266	>
267	>	//make the bends
268	>	for(j=0; j<molInfo.nBends; j++){
269	>
270	>	currentBend = comp_stamps[stampID]->getBend( j );
271	>	theBends[j].a = currentBend->getA() + atomOffset;
272	>	theBends[j].b = currentBend->getB() + atomOffset;
273	>	theBends[j].c = currentBend->getC() + atomOffset;
274	>
275	>	if( currentBend->haveExtras() ){
276
277	<	if( currentBend->haveExtras() ){
278	<
279	<	extras = current_bend->getExtras();
280	<	current_extra = extras;
281	<
282	<	while( current_extra != NULL ){
283	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
277	>	extras = currentBend->getExtras();
278	>	current_extra = extras;
279	>
280	>	while( current_extra != NULL ){
281	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
282	>
283	>	switch( current_extra->getType() ){
284
285	<	switch( current_extra->getType() ){
285	>	case 0:
286	>	theBends[j].ghost =
287	>	current_extra->getInt() + atomOffset;
288	>	theBends[j].isGhost = 1;
289	>	break;
290	>
291	>	case 1:
292	>	theBends[j].ghost =
293	>	(int)current_extra->getDouble() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296	>
297	>	default:
298	>	sprintf( painCave.errMsg,
299	>	"SimSetup Error: ghostVectorSource was neither a "
300	>	"double nor an int.\n"
301	>	"-->Bend[%d] in %s\n",
302	>	j, comp_stamps[stampID]->getID() );
303	>	painCave.isFatal = 1;
304	>	simError();
305	>	}
306	>	}
307	>
308	>	else{
309
801	–	case 0:
802	–	theBends[j].ghost =
803	–	current_extra->getInt() + atomOffset;
804	–	theBends[j].isGhost = 1;
805	–	break;
806	–
807	–	case 1:
808	–	theBends[j].ghost =
809	–	(int)current_extra->getDouble() + atomOffset;
810	–	theBends[j].isGhost = 1;
811	–	break;
812	–
813	–	default:
310		sprintf( painCave.errMsg,
311	<	"SimSetup Error: ghostVectorSource was neiter a "
312	<	"double nor an int.\n"
313	<	"-->Bend[%d] in %s\n",
311	>	"SimSetup Error: unhandled bend assignment:\n"
312	>	"    -->%s in Bend[%d] in %s\n",
313	>	current_extra->getlhs(),
314		j, comp_stamps[stampID]->getID() );
315		painCave.isFatal = 1;
316		simError();
317		}
822	–	}
823	–
824	–	else{
318
319	<	sprintf( painCave.errMsg,
827	<	"SimSetup Error: unhandled bend assignment:\n"
828	<	"    -->%s in Bend[%d] in %s\n",
829	<	current_extra->getlhs(),
830	<	j, comp_stamps[stampID]->getID() );
831	<	painCave.isFatal = 1;
832	<	simError();
319	>	current_extra = current_extra->getNext();
320		}
321	+	}
322	+
323	+	if( !theBends[j].isGhost ){
324
325	<	current_extra = current_extra->getNext();
325	>	exI = theBends[j].a;
326	>	exJ = theBends[j].c;
327		}
328	<	}
328	>	else{
329
330	<	if( !theBends[j].isGhost ){
331	<
332	<	exI = theBends[j].a;
842	<	exJ = theBends[j].c;
843	<	}
844	<	else{
330	>	exI = theBends[j].a;
331	>	exJ = theBends[j].b;
332	>	}
333
334	<	exI = theBends[j].a;
335	<	exJ = theBends[j].b;
336	<	}
337	<
338	<	// exclude_I must always be the smaller of the pair
339	<	if( exI > exJ ){
334	>	// exclude_I must always be the smaller of the pair
335	>	if( exI > exJ ){
336	>	tempEx = exI;
337	>	exI = exJ;
338	>	exJ = tempEx;
339	>	}
340	>	#ifdef IS_MPI
341		tempEx = exI;
342	<	exI = exJ;
343	<	exJ = tempEx;
342	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	>	tempEx = exJ;
344	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>
346	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
347	>	#else  // isn't MPI
348	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349	>	#endif  //is_mpi
350		}
351	<	#ifdef IS_MPI
857	<	tempEx = exI;
858	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
859	<	tempEx = exJ;
860	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
351	>	excludeOffset += molInfo.nBends;
352
353	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
353	>	for(j=0; j<molInfo.nTorsions; j++){
354	>
355	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360	>
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363	>
364	>	// exclude_I must always be the smaller of the pair
365	>	if( exI > exJ ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370	>	#ifdef IS_MPI
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>
376	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
377		#else  // isn't MPI
378	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
378	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
379		#endif  //is_mpi
380	<	}
381	<	excludeOffset += info.nBends;
868	<
869	<	for(j=0; j<info.nTorsions; j++){
380	>	}
381	>	excludeOffset += molInfo.nTorsions;
382
871	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
872	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
873	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
874	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
875	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
383
384	<	exI = theTorsions[j].a;
385	<	exJ = theTorsions[j].d;
384	>	// send the arrays off to the forceField for init.
385	>
386	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
387	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
388	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
389	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
390	>
391	>
392	>	info[k].molecules[i].initialize( molInfo );
393
880	–	// exclude_I must always be the smaller of the pair
881	–	if( exI > exJ ){
882	–	tempEx = exI;
883	–	exI = exJ;
884	–	exJ = tempEx;
885	–	}
886	–	#ifdef IS_MPI
887	–	tempEx = exI;
888	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
889	–	tempEx = exJ;
890	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
394
395	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
396	<	#else  // isn't MPI
397	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
398	<	#endif  //is_mpi
395	>	atomOffset += molInfo.nAtoms;
396	>	delete[] theBonds;
397	>	delete[] theBends;
398	>	delete[] theTorsions;
399		}
897	–	excludeOffset += info.nTorsions;
898	–
899	–
900	–	// send the arrays off to the forceField for init.
901	–
902	–	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
903	–	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
904	–	the_ff->initializeBends( info.nBends, info.myBends, theBends );
905	–	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
906	–
907	–
908	–	the_molecules[i].initialize( info );
909	–	atomOffset += info.nAtoms;
400		}
401	<
401	>
402	>	#ifdef IS_MPI
403	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
404	>	MPIcheckPoint();
405	>	#endif // is_mpi
406	>
407		// clean up the forcefield
408	+
409		the_ff->calcRcut();
410		the_ff->cleanMe();
411	+
412		}
413
414		void SimSetup::initFromBass( void ){
#	Line 924 | Line 421 | void SimSetup::initFromBass( void ){
421		int n_extra;
422		int have_extra, done;
423
424	+	double vel[3];
425	+	vel[0] = 0.0;
426	+	vel[1] = 0.0;
427	+	vel[2] = 0.0;
428	+
429		temp1 = (double)tot_nmol / 4.0;
430		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
431		temp3 = ceil( temp2 );
#	Line 933 | Line 435 | void SimSetup::initFromBass( void ){
435		have_extra =1;
436
437		n_cells = (int)temp3 - 1;
438	<	cellx = simnfo->box_x / temp3;
439	<	celly = simnfo->box_y / temp3;
440	<	cellz = simnfo->box_z / temp3;
441	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
442	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
438	>	cellx = info[0].boxL[0] / temp3;
439	>	celly = info[0].boxL[1] / temp3;
440	>	cellz = info[0].boxL[2] / temp3;
441	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
442	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
443		n_per_extra = (int)ceil( temp1 );
444
445		if( n_per_extra > 4){
#	Line 950 | Line 452 | void SimSetup::initFromBass( void ){
452		}
453		else{
454		n_cells = (int)temp3;
455	<	cellx = simnfo->box_x / temp3;
456	<	celly = simnfo->box_y / temp3;
457	<	cellz = simnfo->box_z / temp3;
455	>	cellx = info[0].boxL[0] / temp3;
456	>	celly = info[0].boxL[1] / temp3;
457	>	cellz = info[0].boxL[2] / temp3;
458		}
459
460		current_mol = 0;
#	Line 1031 | Line 533 | void SimSetup::initFromBass( void ){
533		}
534		}
535
536	<
537	<	for( i=0; i<simnfo->n_atoms; i++ ){
1036	<	simnfo->atoms[i]->set_vx( 0.0 );
1037	<	simnfo->atoms[i]->set_vy( 0.0 );
1038	<	simnfo->atoms[i]->set_vz( 0.0 );
536	>	for( i=0; i<info[0].n_atoms; i++ ){
537	>	info[0].atoms[i]->setVel( vel );
538		}
539		}
540
#	Line 1045 | Line 544 | void SimSetup::makeElement( double x, double y, double
544		AtomStamp* current_atom;
545		DirectionalAtom* dAtom;
546		double rotMat[3][3];
547	+	double pos[3];
548
549		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
550
#	Line 1060 | Line 560 | void SimSetup::makeElement( double x, double y, double
560		painCave.isFatal = 1;
561		simError();
562		}
563	+
564	+	pos[0] = x + current_atom->getPosX();
565	+	pos[1] = y + current_atom->getPosY();
566	+	pos[2] = z + current_atom->getPosZ();
567	+
568	+	info[0].atoms[current_atom_ndx]->setPos( pos );
569
570	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1065	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1066	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
570	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
571
572	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
572	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
573
1070	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1071	–
574		rotMat[0][0] = 1.0;
575		rotMat[0][1] = 0.0;
576		rotMat[0][2] = 0.0;
#	Line 1094 | Line 596 | void SimSetup::makeElement( double x, double y, double
596
597		current_comp_mol = 0;
598		current_comp++;
599	+	}
600	+	}
601	+
602	+
603	+	void SimSetup::gatherInfo( void ){
604	+	int i,j,k;
605	+
606	+	ensembleCase = -1;
607	+	ffCase = -1;
608	+
609	+	// set the easy ones first
610	+
611	+	for( i=0; i<nInfo; i++){
612	+	info[i].target_temp = globals->getTargetTemp();
613	+	info[i].dt = globals->getDt();
614	+	info[i].run_time = globals->getRunTime();
615	+	}
616	+	n_components = globals->getNComponents();
617	+
618	+
619	+	// get the forceField
620	+
621	+	strcpy( force_field, globals->getForceField() );
622	+
623	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
624	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
625	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
626	+	else{
627	+	sprintf( painCave.errMsg,
628	+	"SimSetup Error. Unrecognized force field -> %s\n",
629	+	force_field );
630	+	painCave.isFatal = 1;
631	+	simError();
632	+	}
633	+
634	+	// get the ensemble
635	+
636	+	strcpy( ensemble, globals->getEnsemble() );
637	+
638	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
639	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
640	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
641	+	ensembleCase = NPTi_ENS;
642	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
643	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
644	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
645	+	else{
646	+	sprintf( painCave.errMsg,
647	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
648	+	"reverting to NVE for this simulation.\n",
649	+	ensemble );
650	+	painCave.isFatal = 0;
651	+	simError();
652	+	strcpy( ensemble, "NVE" );
653	+	ensembleCase = NVE_ENS;
654	+	}
655	+
656	+	for(i=0; i<nInfo; i++){
657	+
658	+	strcpy( info[i].ensemble, ensemble );
659	+
660	+	// get the mixing rule
661	+
662	+	strcpy( info[i].mixingRule, globals->getMixingRule() );
663	+	info[i].usePBC = globals->getPBC();
664	+	}
665	+
666	+	// get the components and calculate the tot_nMol and indvidual n_mol
667	+
668	+	the_components = globals->getComponents();
669	+	components_nmol = new int[n_components];
670	+
671	+
672	+	if( !globals->haveNMol() ){
673	+	// we don't have the total number of molecules, so we assume it is
674	+	// given in each component
675	+
676	+	tot_nmol = 0;
677	+	for( i=0; i<n_components; i++ ){
678	+
679	+	if( !the_components[i]->haveNMol() ){
680	+	// we have a problem
681	+	sprintf( painCave.errMsg,
682	+	"SimSetup Error. No global NMol or component NMol"
683	+	" given. Cannot calculate the number of atoms.\n" );
684	+	painCave.isFatal = 1;
685	+	simError();
686	+	}
687	+
688	+	tot_nmol += the_components[i]->getNMol();
689	+	components_nmol[i] = the_components[i]->getNMol();
690	+	}
691	+	}
692	+	else{
693	+	sprintf( painCave.errMsg,
694	+	"SimSetup error.\n"
695	+	"\tSorry, the ability to specify total"
696	+	" nMols and then give molfractions in the components\n"
697	+	"\tis not currently supported."
698	+	" Please give nMol in the components.\n" );
699	+	painCave.isFatal = 1;
700	+	simError();
701	+	}
702	+
703	+	// set the status, sample, and thermal kick times
704	+
705	+	for(i=0; i<nInfo; i++){
706	+
707	+	if( globals->haveSampleTime() ){
708	+	info[i].sampleTime = globals->getSampleTime();
709	+	info[i].statusTime = info[i].sampleTime;
710	+	info[i].thermalTime = info[i].sampleTime;
711	+	}
712	+	else{
713	+	info[i].sampleTime = globals->getRunTime();
714	+	info[i].statusTime = info[i].sampleTime;
715	+	info[i].thermalTime = info[i].sampleTime;
716	+	}
717	+
718	+	if( globals->haveStatusTime() ){
719	+	info[i].statusTime = globals->getStatusTime();
720	+	}
721	+
722	+	if( globals->haveThermalTime() ){
723	+	info[i].thermalTime = globals->getThermalTime();
724	+	}
725	+
726	+	// check for the temperature set flag
727	+
728	+	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
729	+
730	+	// get some of the tricky things that may still be in the globals
731	+
732	+	double boxVector[3];
733	+	if( globals->haveBox() ){
734	+	boxVector[0] = globals->getBox();
735	+	boxVector[1] = globals->getBox();
736	+	boxVector[2] = globals->getBox();
737	+
738	+	info[i].setBox( boxVector );
739	+	}
740	+	else if( globals->haveDensity() ){
741	+
742	+	double vol;
743	+	vol = (double)tot_nmol / globals->getDensity();
744	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
745	+	boxVector[1] = boxVector[0];
746	+	boxVector[2] = boxVector[0];
747	+
748	+	info[i].setBox( boxVector );
749	+	}
750	+	else{
751	+	if( !globals->haveBoxX() ){
752	+	sprintf( painCave.errMsg,
753	+	"SimSetup error, no periodic BoxX size given.\n" );
754	+	painCave.isFatal = 1;
755	+	simError();
756	+	}
757	+	boxVector[0] = globals->getBoxX();
758	+
759	+	if( !globals->haveBoxY() ){
760	+	sprintf( painCave.errMsg,
761	+	"SimSetup error, no periodic BoxY size given.\n" );
762	+	painCave.isFatal = 1;
763	+	simError();
764	+	}
765	+	boxVector[1] = globals->getBoxY();
766	+
767	+	if( !globals->haveBoxZ() ){
768	+	sprintf( painCave.errMsg,
769	+	"SimSetup error, no periodic BoxZ size given.\n" );
770	+	painCave.isFatal = 1;
771	+	simError();
772	+	}
773	+	boxVector[2] = globals->getBoxZ();
774	+
775	+	info[i].setBox( boxVector );
776	+	}
777	+
778	+	}
779	+
780	+	#ifdef IS_MPI
781	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
782	+	MPIcheckPoint();
783	+	#endif // is_mpi
784	+
785	+	}
786	+
787	+
788	+	void SimSetup::finalInfoCheck( void ){
789	+	int index;
790	+	int usesDipoles;
791	+	int i;
792	+
793	+	for(i=0; i<nInfo; i++){
794	+	// check electrostatic parameters
795	+
796	+	index = 0;
797	+	usesDipoles = 0;
798	+	while( (index < info[i].n_atoms) && !usesDipoles ){
799	+	usesDipoles = (info[i].atoms[index])->hasDipole();
800	+	index++;
801	+	}
802	+
803	+	#ifdef IS_MPI
804	+	int myUse = usesDipoles;
805	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
806	+	#endif //is_mpi
807	+
808	+	double theEcr, theEst;
809	+
810	+	if (globals->getUseRF() ) {
811	+	info[i].useReactionField = 1;
812	+
813	+	if( !globals->haveECR() ){
814	+	sprintf( painCave.errMsg,
815	+	"SimSetup Warning: using default value of 1/2 the smallest "
816	+	"box length for the electrostaticCutoffRadius.\n"
817	+	"I hope you have a very fast processor!\n");
818	+	painCave.isFatal = 0;
819	+	simError();
820	+	double smallest;
821	+	smallest = info[i].boxL[0];
822	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
823	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
824	+	theEcr = 0.5 * smallest;
825	+	} else {
826	+	theEcr = globals->getECR();
827	+	}
828	+
829	+	if( !globals->haveEST() ){
830	+	sprintf( painCave.errMsg,
831	+	"SimSetup Warning: using default value of 0.05 * the "
832	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
833	+	);
834	+	painCave.isFatal = 0;
835	+	simError();
836	+	theEst = 0.05 * theEcr;
837	+	} else {
838	+	theEst= globals->getEST();
839	+	}
840	+
841	+	info[i].setEcr( theEcr, theEst );
842	+
843	+	if(!globals->haveDielectric() ){
844	+	sprintf( painCave.errMsg,
845	+	"SimSetup Error: You are trying to use Reaction Field without"
846	+	"setting a dielectric constant!\n"
847	+	);
848	+	painCave.isFatal = 1;
849	+	simError();
850	+	}
851	+	info[i].dielectric = globals->getDielectric();
852	+	}
853	+	else {
854	+	if (usesDipoles) {
855	+
856	+	if( !globals->haveECR() ){
857	+	sprintf( painCave.errMsg,
858	+	"SimSetup Warning: using default value of 1/2 the smallest "
859	+	"box length for the electrostaticCutoffRadius.\n"
860	+	"I hope you have a very fast processor!\n");
861	+	painCave.isFatal = 0;
862	+	simError();
863	+	double smallest;
864	+	smallest = info[i].boxL[0];
865	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
866	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
867	+	theEcr = 0.5 * smallest;
868	+	} else {
869	+	theEcr = globals->getECR();
870	+	}
871	+
872	+	if( !globals->haveEST() ){
873	+	sprintf( painCave.errMsg,
874	+	"SimSetup Warning: using default value of 0.05 * the "
875	+	"electrostaticCutoffRadius for the "
876	+	"electrostaticSkinThickness\n"
877	+	);
878	+	painCave.isFatal = 0;
879	+	simError();
880	+	theEst = 0.05 * theEcr;
881	+	} else {
882	+	theEst= globals->getEST();
883	+	}
884	+
885	+	info[i].setEcr( theEcr, theEst );
886	+	}
887	+	}
888		}
889	+
890	+	#ifdef IS_MPI
891	+	strcpy( checkPointMsg, "post processing checks out" );
892	+	MPIcheckPoint();
893	+	#endif // is_mpi
894	+
895		}
896	+
897	+	void SimSetup::initSystemCoords( void ){
898	+	int i;
899	+
900	+	char* inName;
901	+
902	+	std::cerr << "Setting atom Coords\n";
903	+
904	+	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
905	+
906	+	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
907	+
908	+	if( globals->haveInitialConfig() ){
909	+
910	+	InitializeFromFile* fileInit;
911	+	#ifdef IS_MPI // is_mpi
912	+	if( worldRank == 0 ){
913	+	#endif //is_mpi
914	+	inName = globals->getInitialConfig();
915	+	fileInit = new InitializeFromFile( inName );
916	+	#ifdef IS_MPI
917	+	}else fileInit = new InitializeFromFile( NULL );
918	+	#endif
919	+	fileInit->readInit( info ); // default velocities on
920	+
921	+	delete fileInit;
922	+	}
923	+	else{
924	+
925	+	#ifdef IS_MPI
926	+
927	+	// no init from bass
928	+
929	+	sprintf( painCave.errMsg,
930	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
931	+	painCave.isFatal;
932	+	simError();
933	+
934	+	#else
935	+
936	+	initFromBass();
937	+
938	+
939	+	#endif
940	+	}
941	+
942	+	#ifdef IS_MPI
943	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
944	+	MPIcheckPoint();
945	+	#endif // is_mpi
946	+
947	+	}
948	+
949	+
950	+	void SimSetup::makeOutNames( void ){
951	+
952	+	int k;
953	+
954	+
955	+	for(k=0; k<nInfo; k++){
956	+
957	+	#ifdef IS_MPI
958	+	if( worldRank == 0 ){
959	+	#endif // is_mpi
960	+
961	+	if( globals->haveFinalConfig() ){
962	+	strcpy( info[k].finalName, globals->getFinalConfig() );
963	+	}
964	+	else{
965	+	strcpy( info[k].finalName, inFileName );
966	+	char* endTest;
967	+	int nameLength = strlen( info[k].finalName );
968	+	endTest = &(info[k].finalName[nameLength - 5]);
969	+	if( !strcmp( endTest, ".bass" ) ){
970	+	strcpy( endTest, ".eor" );
971	+	}
972	+	else if( !strcmp( endTest, ".BASS" ) ){
973	+	strcpy( endTest, ".eor" );
974	+	}
975	+	else{
976	+	endTest = &(info[k].finalName[nameLength - 4]);
977	+	if( !strcmp( endTest, ".bss" ) ){
978	+	strcpy( endTest, ".eor" );
979	+	}
980	+	else if( !strcmp( endTest, ".mdl" ) ){
981	+	strcpy( endTest, ".eor" );
982	+	}
983	+	else{
984	+	strcat( info[k].finalName, ".eor" );
985	+	}
986	+	}
987	+	}
988	+
989	+	// make the sample and status out names
990	+
991	+	strcpy( info[k].sampleName, inFileName );
992	+	char* endTest;
993	+	int nameLength = strlen( info[k].sampleName );
994	+	endTest = &(info[k].sampleName[nameLength - 5]);
995	+	if( !strcmp( endTest, ".bass" ) ){
996	+	strcpy( endTest, ".dump" );
997	+	}
998	+	else if( !strcmp( endTest, ".BASS" ) ){
999	+	strcpy( endTest, ".dump" );
1000	+	}
1001	+	else{
1002	+	endTest = &(info[k].sampleName[nameLength - 4]);
1003	+	if( !strcmp( endTest, ".bss" ) ){
1004	+	strcpy( endTest, ".dump" );
1005	+	}
1006	+	else if( !strcmp( endTest, ".mdl" ) ){
1007	+	strcpy( endTest, ".dump" );
1008	+	}
1009	+	else{
1010	+	strcat( info[k].sampleName, ".dump" );
1011	+	}
1012	+	}
1013	+
1014	+	strcpy( info[k].statusName, inFileName );
1015	+	nameLength = strlen( info[k].statusName );
1016	+	endTest = &(info[k].statusName[nameLength - 5]);
1017	+	if( !strcmp( endTest, ".bass" ) ){
1018	+	strcpy( endTest, ".stat" );
1019	+	}
1020	+	else if( !strcmp( endTest, ".BASS" ) ){
1021	+	strcpy( endTest, ".stat" );
1022	+	}
1023	+	else{
1024	+	endTest = &(info[k].statusName[nameLength - 4]);
1025	+	if( !strcmp( endTest, ".bss" ) ){
1026	+	strcpy( endTest, ".stat" );
1027	+	}
1028	+	else if( !strcmp( endTest, ".mdl" ) ){
1029	+	strcpy( endTest, ".stat" );
1030	+	}
1031	+	else{
1032	+	strcat( info[k].statusName, ".stat" );
1033	+	}
1034	+	}
1035	+
1036	+	#ifdef IS_MPI
1037	+	}
1038	+	#endif // is_mpi
1039	+	}
1040	+	}
1041	+
1042	+
1043	+	void SimSetup::sysObjectsCreation( void ){
1044	+
1045	+	int i,k;
1046	+
1047	+	// create the forceField
1048	+
1049	+	createFF();
1050	+
1051	+	// extract componentList
1052	+
1053	+	compList();
1054	+
1055	+	// calc the number of atoms, bond, bends, and torsions
1056	+
1057	+	calcSysValues();
1058	+
1059	+	#ifdef IS_MPI
1060	+	// divide the molecules among the processors
1061	+
1062	+	mpiMolDivide();
1063	+	#endif //is_mpi
1064	+
1065	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1066	+
1067	+	makeSysArrays();
1068	+
1069	+	// make and initialize the molecules (all but atomic coordinates)
1070	+
1071	+	makeMolecules();
1072	+
1073	+	for(k=0; k<nInfo; k++){
1074	+	info[k].identArray = new int[info[k].n_atoms];
1075	+	for(i=0; i<info[k].n_atoms; i++){
1076	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1077	+	}
1078	+	}
1079	+	}
1080	+
1081	+
1082	+	void SimSetup::createFF( void ){
1083	+
1084	+	switch( ffCase ){
1085	+
1086	+	case FF_DUFF:
1087	+	the_ff = new DUFF();
1088	+	break;
1089	+
1090	+	case FF_LJ:
1091	+	the_ff = new LJFF();
1092	+	break;
1093	+
1094	+	case FF_EAM:
1095	+	the_ff = new EAM_FF();
1096	+	break;
1097	+
1098	+	default:
1099	+	sprintf( painCave.errMsg,
1100	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1101	+	painCave.isFatal = 1;
1102	+	simError();
1103	+	}
1104	+
1105	+	#ifdef IS_MPI
1106	+	strcpy( checkPointMsg, "ForceField creation successful" );
1107	+	MPIcheckPoint();
1108	+	#endif // is_mpi
1109	+
1110	+	}
1111	+
1112	+
1113	+	void SimSetup::compList( void ){
1114	+
1115	+	int i;
1116	+	char* id;
1117	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1118	+	LinkedMolStamp* currentStamp = NULL;
1119	+	comp_stamps = new MoleculeStamp*[n_components];
1120	+
1121	+	// make an array of molecule stamps that match the components used.
1122	+	// also extract the used stamps out into a separate linked list
1123	+
1124	+	for(i=0; i<nInfo; i++){
1125	+	info[i].nComponents = n_components;
1126	+	info[i].componentsNmol = components_nmol;
1127	+	info[i].compStamps = comp_stamps;
1128	+	info[i].headStamp = headStamp;
1129	+	}
1130	+
1131	+
1132	+	for( i=0; i<n_components; i++ ){
1133	+
1134	+	id = the_components[i]->getType();
1135	+	comp_stamps[i] = NULL;
1136	+
1137	+	// check to make sure the component isn't already in the list
1138	+
1139	+	comp_stamps[i] = headStamp->match( id );
1140	+	if( comp_stamps[i] == NULL ){
1141	+
1142	+	// extract the component from the list;
1143	+
1144	+	currentStamp = stamps->extractMolStamp( id );
1145	+	if( currentStamp == NULL ){
1146	+	sprintf( painCave.errMsg,
1147	+	"SimSetup error: Component \"%s\" was not found in the "
1148	+	"list of declared molecules\n",
1149	+	id );
1150	+	painCave.isFatal = 1;
1151	+	simError();
1152	+	}
1153	+
1154	+	headStamp->add( currentStamp );
1155	+	comp_stamps[i] = headStamp->match( id );
1156	+	}
1157	+	}
1158	+
1159	+	#ifdef IS_MPI
1160	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1161	+	MPIcheckPoint();
1162	+	#endif // is_mpi
1163	+
1164	+
1165	+	}
1166	+
1167	+	void SimSetup::calcSysValues( void ){
1168	+	int i, j, k;
1169	+
1170	+	int *molMembershipArray;
1171	+
1172	+	tot_atoms = 0;
1173	+	tot_bonds = 0;
1174	+	tot_bends = 0;
1175	+	tot_torsions = 0;
1176	+	for( i=0; i<n_components; i++ ){
1177	+
1178	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1180	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1181	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182	+	}
1183	+
1184	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	+	molMembershipArray = new int[tot_atoms];
1186	+
1187	+	for(i=0; i<nInfo; i++){
1188	+	info[i].n_atoms = tot_atoms;
1189	+	info[i].n_bonds = tot_bonds;
1190	+	info[i].n_bends = tot_bends;
1191	+	info[i].n_torsions = tot_torsions;
1192	+	info[i].n_SRI = tot_SRI;
1193	+	info[i].n_mol = tot_nmol;
1194	+
1195	+	info[i].molMembershipArray = molMembershipArray;
1196	+	}
1197	+	}
1198	+
1199	+	#ifdef IS_MPI
1200	+
1201	+	void SimSetup::mpiMolDivide( void ){
1202	+
1203	+	int i, j, k;
1204	+	int localMol, allMol;
1205	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1206	+
1207	+	mpiSim = new mpiSimulation( info );
1208	+
1209	+	globalIndex = mpiSim->divideLabor();
1210	+
1211	+	// set up the local variables
1212	+
1213	+	mol2proc = mpiSim->getMolToProcMap();
1214	+	molCompType = mpiSim->getMolComponentType();
1215	+
1216	+	allMol = 0;
1217	+	localMol = 0;
1218	+	local_atoms = 0;
1219	+	local_bonds = 0;
1220	+	local_bends = 0;
1221	+	local_torsions = 0;
1222	+	globalAtomIndex = 0;
1223	+
1224	+
1225	+	for( i=0; i<n_components; i++ ){
1226	+
1227	+	for( j=0; j<components_nmol[i]; j++ ){
1228	+
1229	+	if( mol2proc[allMol] == worldRank ){
1230	+
1231	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1232	+	local_bonds +=    comp_stamps[i]->getNBonds();
1233	+	local_bends +=    comp_stamps[i]->getNBends();
1234	+	local_torsions += comp_stamps[i]->getNTorsions();
1235	+	localMol++;
1236	+	}
1237	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1238	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1239	+	globalAtomIndex++;
1240	+	}
1241	+
1242	+	allMol++;
1243	+	}
1244	+	}
1245	+	local_SRI = local_bonds + local_bends + local_torsions;
1246	+
1247	+	info[0].n_atoms = mpiSim->getMyNlocal();
1248	+
1249	+	if( local_atoms != info[0].n_atoms ){
1250	+	sprintf( painCave.errMsg,
1251	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1252	+	" localAtom (%d) are not equal.\n",
1253	+	info[0].n_atoms,
1254	+	local_atoms );
1255	+	painCave.isFatal = 1;
1256	+	simError();
1257	+	}
1258	+
1259	+	info[0].n_bonds = local_bonds;
1260	+	info[0].n_bends = local_bends;
1261	+	info[0].n_torsions = local_torsions;
1262	+	info[0].n_SRI = local_SRI;
1263	+	info[0].n_mol = localMol;
1264	+
1265	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1266	+	MPIcheckPoint();
1267	+	}
1268	+
1269	+	#endif // is_mpi
1270	+
1271	+
1272	+	void SimSetup::makeSysArrays( void ){
1273	+	int i, j, k, l;
1274	+
1275	+	Atom** the_atoms;
1276	+	Molecule* the_molecules;
1277	+	Exclude** the_excludes;
1278	+
1279	+
1280	+	for(l=0; l<nInfo; l++){
1281	+
1282	+	// create the atom and short range interaction arrays
1283	+
1284	+	the_atoms = new Atom*[info[l].n_atoms];
1285	+	the_molecules = new Molecule[info[l].n_mol];
1286	+	int molIndex;
1287	+
1288	+	// initialize the molecule's stampID's
1289	+
1290	+	#ifdef IS_MPI
1291	+
1292	+
1293	+	molIndex = 0;
1294	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1295	+
1296	+	if(mol2proc[i] == worldRank ){
1297	+	the_molecules[molIndex].setStampID( molCompType[i] );
1298	+	the_molecules[molIndex].setMyIndex( molIndex );
1299	+	the_molecules[molIndex].setGlobalIndex( i );
1300	+	molIndex++;
1301	+	}
1302	+	}
1303	+
1304	+	#else // is_mpi
1305	+
1306	+	molIndex = 0;
1307	+	globalAtomIndex = 0;
1308	+	for(i=0; i<n_components; i++){
1309	+	for(j=0; j<components_nmol[i]; j++ ){
1310	+	the_molecules[molIndex].setStampID( i );
1311	+	the_molecules[molIndex].setMyIndex( molIndex );
1312	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1313	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1314	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1315	+	globalAtomIndex++;
1316	+	}
1317	+	molIndex++;
1318	+	}
1319	+	}
1320	+
1321	+
1322	+	#endif // is_mpi
1323	+
1324	+
1325	+	if( info[l].n_SRI ){
1326	+
1327	+	Exclude::createArray(info[l].n_SRI);
1328	+	the_excludes = new Exclude*[info[l].n_SRI];
1329	+	for( int ex=0; ex<info[l].n_SRI; ex++){
1330	+	the_excludes[ex] = new Exclude(ex);
1331	+	}
1332	+	info[l].globalExcludes = new int;
1333	+	info[l].n_exclude = info[l].n_SRI;
1334	+	}
1335	+	else{
1336	+
1337	+	Exclude::createArray( 1 );
1338	+	the_excludes = new Exclude*;
1339	+	the_excludes[0] = new Exclude(0);
1340	+	the_excludes[0]->setPair( 0,0 );
1341	+	info[l].globalExcludes = new int;
1342	+	info[l].globalExcludes[0] = 0;
1343	+	info[l].n_exclude = 0;
1344	+	}
1345	+
1346	+	// set the arrays into the SimInfo object
1347	+
1348	+	info[l].atoms = the_atoms;
1349	+	info[l].molecules = the_molecules;
1350	+	info[l].nGlobalExcludes = 0;
1351	+	info[l].excludes = the_excludes;
1352	+
1353	+	the_ff->setSimInfo( info );
1354	+
1355	+	}
1356	+	}
1357	+
1358	+	void SimSetup::makeIntegrator( void ){
1359	+
1360	+	int k;
1361	+
1362	+	NVT<RealIntegrator>*  myNVT = NULL;
1363	+	NPTi<RealIntegrator>* myNPTi = NULL;
1364	+	NPTf<RealIntegrator>* myNPTf = NULL;
1365	+	NPTim<RealIntegrator>* myNPTim = NULL;
1366	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1367	+
1368	+	for(k=0; k<nInfo; k++){
1369	+
1370	+	switch( ensembleCase ){
1371	+
1372	+	case NVE_ENS:
1373	+	if (globals->haveZconstraints()){
1374	+	setupZConstraint(info[k]);
1375	+	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1376	+	}
1377	+
1378	+	else
1379	+	new NVE<RealIntegrator>( &(info[k]), the_ff );
1380	+	break;
1381	+
1382	+	case NVT_ENS:
1383	+	if (globals->haveZconstraints()){
1384	+	setupZConstraint(info[k]);
1385	+	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1386	+	}
1387	+	else
1388	+	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1389	+
1390	+	myNVT->setTargetTemp(globals->getTargetTemp());
1391	+
1392	+	if (globals->haveTauThermostat())
1393	+	myNVT->setTauThermostat(globals->getTauThermostat());
1394	+
1395	+	else {
1396	+	sprintf( painCave.errMsg,
1397	+	"SimSetup error: If you use the NVT\n"
1398	+	"    ensemble, you must set tauThermostat.\n");
1399	+	painCave.isFatal = 1;
1400	+	simError();
1401	+	}
1402	+	break;
1403	+
1404	+	case NPTi_ENS:
1405	+	if (globals->haveZconstraints()){
1406	+	setupZConstraint(info[k]);
1407	+	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1408	+	}
1409	+	else
1410	+	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1411	+
1412	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1413	+
1414	+	if (globals->haveTargetPressure())
1415	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1416	+	else {
1417	+	sprintf( painCave.errMsg,
1418	+	"SimSetup error: If you use a constant pressure\n"
1419	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1420	+	painCave.isFatal = 1;
1421	+	simError();
1422	+	}
1423	+
1424	+	if( globals->haveTauThermostat() )
1425	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1426	+	else{
1427	+	sprintf( painCave.errMsg,
1428	+	"SimSetup error: If you use an NPT\n"
1429	+	"    ensemble, you must set tauThermostat.\n");
1430	+	painCave.isFatal = 1;
1431	+	simError();
1432	+	}
1433	+
1434	+	if( globals->haveTauBarostat() )
1435	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1436	+	else{
1437	+	sprintf( painCave.errMsg,
1438	+	"SimSetup error: If you use an NPT\n"
1439	+	"    ensemble, you must set tauBarostat.\n");
1440	+	painCave.isFatal = 1;
1441	+	simError();
1442	+	}
1443	+	break;
1444	+
1445	+	case NPTf_ENS:
1446	+	if (globals->haveZconstraints()){
1447	+	setupZConstraint(info[k]);
1448	+	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1449	+	}
1450	+	else
1451	+	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1452	+
1453	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1454	+
1455	+	if (globals->haveTargetPressure())
1456	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1457	+	else {
1458	+	sprintf( painCave.errMsg,
1459	+	"SimSetup error: If you use a constant pressure\n"
1460	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1461	+	painCave.isFatal = 1;
1462	+	simError();
1463	+	}
1464	+
1465	+	if( globals->haveTauThermostat() )
1466	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1467	+	else{
1468	+	sprintf( painCave.errMsg,
1469	+	"SimSetup error: If you use an NPT\n"
1470	+	"    ensemble, you must set tauThermostat.\n");
1471	+	painCave.isFatal = 1;
1472	+	simError();
1473	+	}
1474	+
1475	+	if( globals->haveTauBarostat() )
1476	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1477	+	else{
1478	+	sprintf( painCave.errMsg,
1479	+	"SimSetup error: If you use an NPT\n"
1480	+	"    ensemble, you must set tauBarostat.\n");
1481	+	painCave.isFatal = 1;
1482	+	simError();
1483	+	}
1484	+	break;
1485	+
1486	+	case NPTim_ENS:
1487	+	if (globals->haveZconstraints()){
1488	+	setupZConstraint(info[k]);
1489	+	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1490	+	}
1491	+	else
1492	+	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1493	+
1494	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1495	+
1496	+	if (globals->haveTargetPressure())
1497	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1498	+	else {
1499	+	sprintf( painCave.errMsg,
1500	+	"SimSetup error: If you use a constant pressure\n"
1501	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1502	+	painCave.isFatal = 1;
1503	+	simError();
1504	+	}
1505	+
1506	+	if( globals->haveTauThermostat() )
1507	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1508	+	else{
1509	+	sprintf( painCave.errMsg,
1510	+	"SimSetup error: If you use an NPT\n"
1511	+	"    ensemble, you must set tauThermostat.\n");
1512	+	painCave.isFatal = 1;
1513	+	simError();
1514	+	}
1515	+
1516	+	if( globals->haveTauBarostat() )
1517	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1518	+	else{
1519	+	sprintf( painCave.errMsg,
1520	+	"SimSetup error: If you use an NPT\n"
1521	+	"    ensemble, you must set tauBarostat.\n");
1522	+	painCave.isFatal = 1;
1523	+	simError();
1524	+	}
1525	+	break;
1526	+
1527	+	case NPTfm_ENS:
1528	+	if (globals->haveZconstraints()){
1529	+	setupZConstraint(info[k]);
1530	+	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1531	+	}
1532	+	else
1533	+	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1534	+
1535	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1536	+
1537	+	if (globals->haveTargetPressure())
1538	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1539	+	else {
1540	+	sprintf( painCave.errMsg,
1541	+	"SimSetup error: If you use a constant pressure\n"
1542	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1543	+	painCave.isFatal = 1;
1544	+	simError();
1545	+	}
1546	+
1547	+	if( globals->haveTauThermostat() )
1548	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1549	+	else{
1550	+	sprintf( painCave.errMsg,
1551	+	"SimSetup error: If you use an NPT\n"
1552	+	"    ensemble, you must set tauThermostat.\n");
1553	+	painCave.isFatal = 1;
1554	+	simError();
1555	+	}
1556	+
1557	+	if( globals->haveTauBarostat() )
1558	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1559	+	else{
1560	+	sprintf( painCave.errMsg,
1561	+	"SimSetup error: If you use an NPT\n"
1562	+	"    ensemble, you must set tauBarostat.\n");
1563	+	painCave.isFatal = 1;
1564	+	simError();
1565	+	}
1566	+	break;
1567	+
1568	+	default:
1569	+	sprintf( painCave.errMsg,
1570	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1571	+	painCave.isFatal = 1;
1572	+	simError();
1573	+	}
1574	+	}
1575	+	}
1576	+
1577	+	void SimSetup::initFortran( void ){
1578	+
1579	+	info[0].refreshSim();
1580	+
1581	+	if( !strcmp( info[0].mixingRule, "standard") ){
1582	+	the_ff->initForceField( LB_MIXING_RULE );
1583	+	}
1584	+	else if( !strcmp( info[0].mixingRule, "explicit") ){
1585	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1586	+	}
1587	+	else{
1588	+	sprintf( painCave.errMsg,
1589	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1590	+	info[0].mixingRule );
1591	+	painCave.isFatal = 1;
1592	+	simError();
1593	+	}
1594	+
1595	+
1596	+	#ifdef IS_MPI
1597	+	strcpy( checkPointMsg,
1598	+	"Successfully intialized the mixingRule for Fortran." );
1599	+	MPIcheckPoint();
1600	+	#endif // is_mpi
1601	+
1602	+	}
1603	+
1604	+	void SimSetup::setupZConstraint(SimInfo& theInfo)
1605	+	{
1606	+	int nZConstraints;
1607	+	ZconStamp** zconStamp;
1608	+
1609	+	if(globals->haveZconstraintTime()){
1610	+
1611	+	//add sample time of z-constraint  into SimInfo's property list
1612	+	DoubleData* zconsTimeProp = new DoubleData();
1613	+	zconsTimeProp->setID(ZCONSTIME_ID);
1614	+	zconsTimeProp->setData(globals->getZconsTime());
1615	+	theInfo.addProperty(zconsTimeProp);
1616	+	}
1617	+	else{
1618	+	sprintf( painCave.errMsg,
1619	+	"ZConstraint error: If you use an ZConstraint\n"
1620	+	" , you must set sample time.\n");
1621	+	painCave.isFatal = 1;
1622	+	simError();
1623	+	}
1624	+
1625	+	//
1626	+	nZConstraints = globals->getNzConstraints();
1627	+	zconStamp = globals->getZconStamp();
1628	+	ZConsParaItem tempParaItem;
1629	+
1630	+	ZConsParaData* zconsParaData = new ZConsParaData();
1631	+	zconsParaData->setID(ZCONSPARADATA_ID);
1632	+
1633	+	for(int i = 0; i < nZConstraints; i++){
1634	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1635	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1636	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1637	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1638	+
1639	+	zconsParaData->addItem(tempParaItem);
1640	+	}
1641	+
1642	+	//sort the parameters by index of molecules
1643	+	zconsParaData->sortByIndex();
1644	+
1645	+	//push data into siminfo, therefore, we can retrieve later
1646	+	theInfo.addProperty(zconsParaData);
1647	+
1648	+	//push zconsTol into siminfo, if user does not specify
1649	+	//value for zconsTol, a default value will be used
1650	+	DoubleData* zconsTol = new DoubleData();
1651	+	zconsTol->setID(ZCONSTOL_ID);
1652	+	if(globals->haveZconsTol()){
1653	+	zconsTol->setData(globals->getZconsTol());
1654	+	}
1655	+	else{
1656	+	double defaultZConsTol = 1E-6;
1657	+	sprintf( painCave.errMsg,
1658	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1659	+	" , default value %f is used.\n", defaultZConsTol);
1660	+	painCave.isFatal = 0;
1661	+	simError();
1662	+
1663	+	zconsTol->setData(defaultZConsTol);
1664	+	}
1665	+	theInfo.addProperty(zconsTol);
1666	+
1667	+	//Determine the name of ouput file and add it into SimInfo's property list
1668	+	//Be careful, do not use inFileName, since it is a pointer which
1669	+	//point to a string at master node, and slave nodes do not contain that string
1670	+
1671	+	string zconsOutput(theInfo.finalName);
1672	+
1673	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1674	+
1675	+	StringData* zconsFilename = new StringData();
1676	+	zconsFilename->setID(ZCONSFILENAME_ID);
1677	+	zconsFilename->setData(zconsOutput);
1678	+
1679	+	theInfo.addProperty(zconsFilename);
1680	+	}

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