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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 435 by mmeineke, Fri Mar 28 19:33:37 2003 UTC vs.
Revision 676 by tim, Mon Aug 11 19:40:06 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	+
26	+	#define FF_DUFF 0
27	+	#define FF_LJ   1
28	+	#define FF_EAM  2
29	+
30	+	using namespace std;
31	+
32		SimSetup::SimSetup(){
33	+
34	+	isInfoArray = 0;
35	+	nInfo = 1;
36	+
37		stamps = new MakeStamps();
38		globals = new Globals();
39
40	+
41		#ifdef IS_MPI
42		strcpy( checkPointMsg, "SimSetup creation successful" );
43		MPIcheckPoint();
#	Line 27 | Line 49 | void SimSetup::parseFile( char* fileName ){
49		delete globals;
50		}
51
52	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
53	+	info = the_info;
54	+	nInfo = theNinfo;
55	+	isInfoArray = 1;
56	+	}
57	+
58	+
59		void SimSetup::parseFile( char* fileName ){
60
61		#ifdef IS_MPI
#	Line 62 | Line 91 | void SimSetup::createSim( void ){
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
94	>	void SimSetup::createSim(void){
95
96	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
70	<
71	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
74	<
75	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
79	<
80	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
85	<
86	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
89	<
90	<
91	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
100	<
101	<	#ifdef IS_MPI
102	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#endif // is_mpi
105	<
96	>	int i, j, k, globalAtomIndex;
97
98	<
108	<	// get the components and calculate the tot_nMol and indvidual n_mol
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
112	<
113	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// given in each component
116	<
117	<	tot_nmol = 0;
118	<	for( i=0; i<n_components; i++ ){
119	<
120	<	if( !the_components[i]->haveNMol() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
128	<
129	<	tot_nmol += the_components[i]->getNMol();
130	<	components_nmol[i] = the_components[i]->getNMol();
131	<	}
132	<	}
133	<	else{
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error.\n"
136	<	"\tSorry, the ability to specify total"
137	<	" nMols and then give molfractions in the components\n"
138	<	"\tis not currently supported."
139	<	" Please give nMol in the components.\n" );
140	<	painCave.isFatal = 1;
141	<	simError();
142	<
143	<
144	<	//     tot_nmol = the_globals->getNMol();
145	<
146	<	//   //we have the total number of molecules, now we check for molfractions
147	<	//     for( i=0; i<n_components; i++ ){
148	<
149	<	//       if( !the_components[i]->haveMolFraction() ){
150	<
151	<	//  if( !the_components[i]->haveNMol() ){
152	<	//    //we have a problem
153	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	<	//              << " nMol was given in component
155	<
156	<	}
157	<
158	<	#ifdef IS_MPI
159	<	strcpy( checkPointMsg, "Have the number of components" );
160	<	MPIcheckPoint();
161	<	#endif // is_mpi
162	<
163	<	// make an array of molecule stamps that match the components used.
164	<	// also extract the used stamps out into a separate linked list
165	<
166	<	simnfo->nComponents = n_components;
167	<	simnfo->componentsNmol = components_nmol;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
98	>	// gather all of the information from the Bass file
99
100	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
100	>	gatherInfo();
101
102	<	id = the_components[i]->getType();
177	<	comp_stamps[i] = NULL;
178	<
179	<	// check to make sure the component isn't already in the list
102	>	// creation of complex system objects
103
104	<	comp_stamps[i] = headStamp->match( id );
182	<	if( comp_stamps[i] == NULL ){
183	<
184	<	// extract the component from the list;
185	<
186	<	currentStamp = the_stamps->extractMolStamp( id );
187	<	if( currentStamp == NULL ){
188	<	sprintf( painCave.errMsg,
189	<	"SimSetup error: Component \"%s\" was not found in the "
190	<	"list of declared molecules\n",
191	<	id );
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	headStamp->add( currentStamp );
197	<	comp_stamps[i] = headStamp->match( id );
198	<	}
199	<	}
104	>	sysObjectsCreation();
105
106	<	#ifdef IS_MPI
202	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
203	<	MPIcheckPoint();
204	<	#endif // is_mpi
106	>	// check on the post processing info
107
108	+	finalInfoCheck();
109
110	+	// initialize the system coordinates
111
112	+	if( !isInfoArray ) initSystemCoords();
113
114	<	// caclulate the number of atoms, bonds, bends and torsions
210	<
211	<	tot_atoms = 0;
212	<	tot_bonds = 0;
213	<	tot_bends = 0;
214	<	tot_torsions = 0;
215	<	for( i=0; i<n_components; i++ ){
216	<
217	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	<	}
222	<
223	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
224	<
225	<	simnfo->n_atoms = tot_atoms;
226	<	simnfo->n_bonds = tot_bonds;
227	<	simnfo->n_bends = tot_bends;
228	<	simnfo->n_torsions = tot_torsions;
229	<	simnfo->n_SRI = tot_SRI;
230	<	simnfo->n_mol = tot_nmol;
231	<
232	<
233	<	#ifdef IS_MPI
234	<
235	<	// divide the molecules among processors here.
236	<
237	<	mpiSim = new mpiSimulation( simnfo );
238	<
239	<
240	<
241	<	globalIndex = mpiSim->divideLabor();
242	<
243	<	// set up the local variables
244	<
245	<	int localMol, allMol;
246	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
247	<
248	<	int* mol2proc = mpiSim->getMolToProcMap();
249	<	int* molCompType = mpiSim->getMolComponentType();
250	<
251	<	allMol = 0;
252	<	localMol = 0;
253	<	local_atoms = 0;
254	<	local_bonds = 0;
255	<	local_bends = 0;
256	<	local_torsions = 0;
257	<	for( i=0; i<n_components; i++ ){
258	<
259	<	for( j=0; j<components_nmol[i]; j++ ){
260	<
261	<	if( mol2proc[j] == worldRank ){
262	<
263	<	local_atoms +=    comp_stamps[i]->getNAtoms();
264	<	local_bonds +=    comp_stamps[i]->getNBonds();
265	<	local_bends +=    comp_stamps[i]->getNBends();
266	<	local_torsions += comp_stamps[i]->getNTorsions();
267	<	localMol++;
268	<	}
269	<	allMol++;
270	<	}
271	<	}
272	<	local_SRI = local_bonds + local_bends + local_torsions;
273	<
274	<
275	<	simnfo->n_atoms = mpiSim->getMyNlocal();
276	<
277	<	if( local_atoms != simnfo->n_atoms ){
278	<	sprintf( painCave.errMsg,
279	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
280	<	" localAtom (%d) are not equal.\n",
281	<	simnfo->n_atoms,
282	<	local_atoms );
283	<	painCave.isFatal = 1;
284	<	simError();
285	<	}
286	<
287	<	simnfo->n_bonds = local_bonds;
288	<	simnfo->n_bends = local_bends;
289	<	simnfo->n_torsions = local_torsions;
290	<	simnfo->n_SRI = local_SRI;
291	<	simnfo->n_mol = localMol;
292	<
293	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
294	<	MPIcheckPoint();
295	<
296	<
297	<	#endif // is_mpi
298	<
299	<
300	<	// create the atom and short range interaction arrays
301	<
302	<	Atom::createArrays(simnfo->n_atoms);
303	<	the_atoms = new Atom*[simnfo->n_atoms];
304	<	the_molecules = new Molecule[simnfo->n_mol];
305	<	int molIndex;
306	<
307	<	// initialize the molecule's stampID's
114	>	// make the output filenames
115
116	<	#ifdef IS_MPI
310	<
311	<
312	<	molIndex = 0;
313	<	for(i=0; i<mpiSim->getTotNmol(); i++){
314	<
315	<	if(mol2proc[i] == worldRank ){
316	<	the_molecules[molIndex].setStampID( molCompType[i] );
317	<	molIndex++;
318	<	}
319	<	}
320	<
321	<	#else // is_mpi
322	<
323	<	molIndex = 0;
324	<	for(i=0; i<n_components; i++){
325	<	for(j=0; j<components_nmol[i]; j++ ){
326	<	the_molecules[molIndex].setStampID( i );
327	<	molIndex++;
328	<	}
329	<	}
330	<
331	<
332	<	#endif // is_mpi
333	<
334	<
335	<	if( simnfo->n_SRI ){
336	<
337	<	std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
338	<
339	<	Exclude::createArray(simnfo->n_SRI);
340	<	the_excludes = new Exclude*[simnfo->n_SRI];
341	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
342	<	simnfo->globalExcludes = new int;
343	<	simnfo->n_exclude = tot_SRI;
344	<	}
345	<	else{
346	<
347	<	Exclude::createArray( 1 );
348	<	the_excludes = new Exclude*;
349	<	the_excludes[0] = new Exclude(0);
350	<	the_excludes[0]->setPair( 0,0 );
351	<	simnfo->globalExcludes = new int;
352	<	simnfo->globalExcludes[0] = 0;
353	<	simnfo->n_exclude = 0;
354	<	}
355	<
356	<	// set the arrays into the SimInfo object
357	<
358	<	simnfo->atoms = the_atoms;
359	<	simnfo->molecules = the_molecules;
360	<	simnfo->nGlobalExcludes = 0;
361	<	simnfo->excludes = the_excludes;
362	<
363	<
364	<	// get some of the tricky things that may still be in the globals
365	<
366	<
367	<	if( the_globals->haveBox() ){
368	<	simnfo->box_x = the_globals->getBox();
369	<	simnfo->box_y = the_globals->getBox();
370	<	simnfo->box_z = the_globals->getBox();
371	<	}
372	<	else if( the_globals->haveDensity() ){
373	<
374	<	double vol;
375	<	vol = (double)tot_nmol / the_globals->getDensity();
376	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
377	<	simnfo->box_y = simnfo->box_x;
378	<	simnfo->box_z = simnfo->box_x;
379	<	}
380	<	else{
381	<	if( !the_globals->haveBoxX() ){
382	<	sprintf( painCave.errMsg,
383	<	"SimSetup error, no periodic BoxX size given.\n" );
384	<	painCave.isFatal = 1;
385	<	simError();
386	<	}
387	<	simnfo->box_x = the_globals->getBoxX();
388	<
389	<	if( !the_globals->haveBoxY() ){
390	<	sprintf( painCave.errMsg,
391	<	"SimSetup error, no periodic BoxY size given.\n" );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
395	<	simnfo->box_y = the_globals->getBoxY();
396	<
397	<	if( !the_globals->haveBoxZ() ){
398	<	sprintf( painCave.errMsg,
399	<	"SimSetup error, no periodic BoxZ size given.\n" );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
403	<	simnfo->box_z = the_globals->getBoxZ();
404	<	}
405	<
406	<	#ifdef IS_MPI
407	<	strcpy( checkPointMsg, "Box size set up" );
408	<	MPIcheckPoint();
409	<	#endif // is_mpi
410	<
411	<
412	<	// initialize the arrays
413	<
414	<	the_ff->setSimInfo( simnfo );
415	<
416	<	makeMolecules();
417	<	simnfo->identArray = new int[simnfo->n_atoms];
418	<	for(i=0; i<simnfo->n_atoms; i++){
419	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
420	<	}
421	<
422	<	if (the_globals->getUseRF() ) {
423	<	simnfo->useReactionField = 1;
424	<
425	<	if( !the_globals->haveECR() ){
426	<	sprintf( painCave.errMsg,
427	<	"SimSetup Warning: using default value of 1/2 the smallest "
428	<	"box length for the electrostaticCutoffRadius.\n"
429	<	"I hope you have a very fast processor!\n");
430	<	painCave.isFatal = 0;
431	<	simError();
432	<	double smallest;
433	<	smallest = simnfo->box_x;
434	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
435	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
436	<	simnfo->ecr = 0.5 * smallest;
437	<	} else {
438	<	simnfo->ecr        = the_globals->getECR();
439	<	}
440	<
441	<	if( !the_globals->haveEST() ){
442	<	sprintf( painCave.errMsg,
443	<	"SimSetup Warning: using default value of 0.05 * the "
444	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
445	<	);
446	<	painCave.isFatal = 0;
447	<	simError();
448	<	simnfo->est = 0.05 * simnfo->ecr;
449	<	} else {
450	<	simnfo->est        = the_globals->getEST();
451	<	}
452	<
453	<	if(!the_globals->haveDielectric() ){
454	<	sprintf( painCave.errMsg,
455	<	"SimSetup Error: You are trying to use Reaction Field without"
456	<	"setting a dielectric constant!\n"
457	<	);
458	<	painCave.isFatal = 1;
459	<	simError();
460	<	}
461	<	simnfo->dielectric = the_globals->getDielectric();
462	<	} else {
463	<	if (simnfo->n_dipoles) {
464	<
465	<	if( !the_globals->haveECR() ){
466	<	sprintf( painCave.errMsg,
467	<	"SimSetup Warning: using default value of 1/2 the smallest"
468	<	"box length for the electrostaticCutoffRadius.\n"
469	<	"I hope you have a very fast processor!\n");
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	double smallest;
473	<	smallest = simnfo->box_x;
474	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
475	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
476	<	simnfo->ecr = 0.5 * smallest;
477	<	} else {
478	<	simnfo->ecr        = the_globals->getECR();
479	<	}
480	<
481	<	if( !the_globals->haveEST() ){
482	<	sprintf( painCave.errMsg,
483	<	"SimSetup Warning: using default value of 5% of the"
484	<	"electrostaticCutoffRadius for the "
485	<	"electrostaticSkinThickness\n"
486	<	);
487	<	painCave.isFatal = 0;
488	<	simError();
489	<	simnfo->est = 0.05 * simnfo->ecr;
490	<	} else {
491	<	simnfo->est        = the_globals->getEST();
492	<	}
493	<	}
494	<	}
495	<
496	<	#ifdef IS_MPI
497	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
498	<	MPIcheckPoint();
499	<	#endif // is_mpi
500	<
501	<	if( the_globals->haveInitialConfig() ){
502	<
503	<	InitializeFromFile* fileInit;
504	<	#ifdef IS_MPI // is_mpi
505	<	if( worldRank == 0 ){
506	<	#endif //is_mpi
507	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
508	<	#ifdef IS_MPI
509	<	}else fileInit = new InitializeFromFile( NULL );
510	<	#endif
511	<	fileInit->read_xyz( simnfo ); // default velocities on
512	<
513	<	delete fileInit;
514	<	}
515	<	else{
516	<
517	<	#ifdef IS_MPI
518	<
519	<	// no init from bass
520	<
521	<	sprintf( painCave.errMsg,
522	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
523	<	painCave.isFatal;
524	<	simError();
525	<
526	<	#else
527	<
528	<	initFromBass();
529	<
530	<
531	<	#endif
532	<	}
533	<
534	<	#ifdef IS_MPI
535	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
536	<	MPIcheckPoint();
537	<	#endif // is_mpi
538	<
539	<
116	>	makeOutNames();
117
118	<
118	>	// make the integrator
119
120	<
544	<
545	<	#ifdef IS_MPI
546	<	if( worldRank == 0 ){
547	<	#endif // is_mpi
548	<
549	<	if( the_globals->haveFinalConfig() ){
550	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
551	<	}
552	<	else{
553	<	strcpy( simnfo->finalName, inFileName );
554	<	char* endTest;
555	<	int nameLength = strlen( simnfo->finalName );
556	<	endTest = &(simnfo->finalName[nameLength - 5]);
557	<	if( !strcmp( endTest, ".bass" ) ){
558	<	strcpy( endTest, ".eor" );
559	<	}
560	<	else if( !strcmp( endTest, ".BASS" ) ){
561	<	strcpy( endTest, ".eor" );
562	<	}
563	<	else{
564	<	endTest = &(simnfo->finalName[nameLength - 4]);
565	<	if( !strcmp( endTest, ".bss" ) ){
566	<	strcpy( endTest, ".eor" );
567	<	}
568	<	else if( !strcmp( endTest, ".mdl" ) ){
569	<	strcpy( endTest, ".eor" );
570	<	}
571	<	else{
572	<	strcat( simnfo->finalName, ".eor" );
573	<	}
574	<	}
575	<	}
576	<
577	<	// make the sample and status out names
578	<
579	<	strcpy( simnfo->sampleName, inFileName );
580	<	char* endTest;
581	<	int nameLength = strlen( simnfo->sampleName );
582	<	endTest = &(simnfo->sampleName[nameLength - 5]);
583	<	if( !strcmp( endTest, ".bass" ) ){
584	<	strcpy( endTest, ".dump" );
585	<	}
586	<	else if( !strcmp( endTest, ".BASS" ) ){
587	<	strcpy( endTest, ".dump" );
588	<	}
589	<	else{
590	<	endTest = &(simnfo->sampleName[nameLength - 4]);
591	<	if( !strcmp( endTest, ".bss" ) ){
592	<	strcpy( endTest, ".dump" );
593	<	}
594	<	else if( !strcmp( endTest, ".mdl" ) ){
595	<	strcpy( endTest, ".dump" );
596	<	}
597	<	else{
598	<	strcat( simnfo->sampleName, ".dump" );
599	<	}
600	<	}
601	<
602	<	strcpy( simnfo->statusName, inFileName );
603	<	nameLength = strlen( simnfo->statusName );
604	<	endTest = &(simnfo->statusName[nameLength - 5]);
605	<	if( !strcmp( endTest, ".bass" ) ){
606	<	strcpy( endTest, ".stat" );
607	<	}
608	<	else if( !strcmp( endTest, ".BASS" ) ){
609	<	strcpy( endTest, ".stat" );
610	<	}
611	<	else{
612	<	endTest = &(simnfo->statusName[nameLength - 4]);
613	<	if( !strcmp( endTest, ".bss" ) ){
614	<	strcpy( endTest, ".stat" );
615	<	}
616	<	else if( !strcmp( endTest, ".mdl" ) ){
617	<	strcpy( endTest, ".stat" );
618	<	}
619	<	else{
620	<	strcat( simnfo->statusName, ".stat" );
621	<	}
622	<	}
623	<
624	<	#ifdef IS_MPI
625	<	}
626	<	#endif // is_mpi
120	>	makeIntegrator();
121
628	–	// set the status, sample, and themal kick times
629	–
630	–	if( the_globals->haveSampleTime() ){
631	–	simnfo->sampleTime = the_globals->getSampleTime();
632	–	simnfo->statusTime = simnfo->sampleTime;
633	–	simnfo->thermalTime = simnfo->sampleTime;
634	–	}
635	–	else{
636	–	simnfo->sampleTime = the_globals->getRunTime();
637	–	simnfo->statusTime = simnfo->sampleTime;
638	–	simnfo->thermalTime = simnfo->sampleTime;
639	–	}
640	–
641	–	if( the_globals->haveStatusTime() ){
642	–	simnfo->statusTime = the_globals->getStatusTime();
643	–	}
644	–
645	–	if( the_globals->haveThermalTime() ){
646	–	simnfo->thermalTime = the_globals->getThermalTime();
647	–	}
648	–
649	–	// check for the temperature set flag
650	–
651	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
652	–
653	–
654	–	//   // make the longe range forces and the integrator
655	–
656	–	//   new AllLong( simnfo );
657	–
658	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
659	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
660	–
122		#ifdef IS_MPI
123		mpiSim->mpiRefresh();
124		#endif
125
126		// initialize the Fortran
127
128	+	initFortran();
129
668	–	simnfo->refreshSim();
669	–
670	–	if( !strcmp( simnfo->mixingRule, "standard") ){
671	–	the_ff->initForceField( LB_MIXING_RULE );
672	–	}
673	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
674	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
675	–	}
676	–	else{
677	–	sprintf( painCave.errMsg,
678	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
679	–	simnfo->mixingRule );
680	–	painCave.isFatal = 1;
681	–	simError();
682	–	}
130
131
685	–	#ifdef IS_MPI
686	–	strcpy( checkPointMsg,
687	–	"Successfully intialized the mixingRule for Fortran." );
688	–	MPIcheckPoint();
689	–	#endif // is_mpi
132		}
133
134
135		void SimSetup::makeMolecules( void ){
136
137	+	int k,l;
138		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
139	<	molInit info;
139	>	molInit molInfo;
140		DirectionalAtom* dAtom;
141		LinkedAssign* extras;
142		LinkedAssign* current_extra;
#	Line 716 | Line 159 | void SimSetup::makeMolecules( void ){
159
160		double ux, uy, uz, u, uSqr;
161
162	<	atomOffset = 0;
720	<	excludeOffset = 0;
721	<	for(i=0; i<simnfo->n_mol; i++){
162	>	for(k=0; k<nInfo; k++){
163
164	<	stampID = the_molecules[i].getStampID();
164	>	the_ff->setSimInfo( &(info[k]) );
165
166	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
167	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
168	<	info.nBends    = comp_stamps[stampID]->getNBends();
169	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
170	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for(i=0; i<info[k].n_mol; i++){
169	>
170	>	stampID = info[k].molecules[i].getStampID();
171
172	<	info.myAtoms = &the_atoms[atomOffset];
173	<	info.myExcludes = &the_excludes[excludeOffset];
174	<	info.myBonds = new Bond*[info.nBonds];
175	<	info.myBends = new Bend*[info.nBends];
176	<	info.myTorsions = new Torsion*[info.nTorsions];
172	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
173	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
174	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
175	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
177	>
178	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	>	molInfo.myBends = new Bend*[molInfo.nBends];
182	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
183
184	<	theBonds = new bond_pair[info.nBonds];
185	<	theBends = new bend_set[info.nBends];
186	<	theTorsions = new torsion_set[info.nTorsions];
184	>	theBonds = new bond_pair[molInfo.nBonds];
185	>	theBends = new bend_set[molInfo.nBends];
186	>	theTorsions = new torsion_set[molInfo.nTorsions];
187
188	<	// make the Atoms
188	>	// make the Atoms
189
190	<	for(j=0; j<info.nAtoms; j++){
744	<
745	<	currentAtom = comp_stamps[stampID]->getAtom( j );
746	<	if( currentAtom->haveOrientation() ){
190	>	for(j=0; j<molInfo.nAtoms; j++){
191
192	<	dAtom = new DirectionalAtom(j + atomOffset);
193	<	simnfo->n_oriented++;
194	<	info.myAtoms[j] = dAtom;
195	<
196	<	ux = currentAtom->getOrntX();
197	<	uy = currentAtom->getOrntY();
198	<	uz = currentAtom->getOrntZ();
199	<
200	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
201	<
202	<	u = sqrt( uSqr );
203	<	ux = ux / u;
204	<	uy = uy / u;
205	<	uz = uz / u;
206	<
207	<	dAtom->setSUx( ux );
208	<	dAtom->setSUy( uy );
209	<	dAtom->setSUz( uz );
210	<	}
211	<	else{
212	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
213	<	}
214	<	info.myAtoms[j]->setType( currentAtom->getType() );
192	>	currentAtom = comp_stamps[stampID]->getAtom( j );
193	>	if( currentAtom->haveOrientation() ){
194	>
195	>	dAtom = new DirectionalAtom( (j + atomOffset),
196	>	info[k].getConfiguration() );
197	>	info[k].n_oriented++;
198	>	molInfo.myAtoms[j] = dAtom;
199	>
200	>	ux = currentAtom->getOrntX();
201	>	uy = currentAtom->getOrntY();
202	>	uz = currentAtom->getOrntZ();
203	>
204	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
205	>
206	>	u = sqrt( uSqr );
207	>	ux = ux / u;
208	>	uy = uy / u;
209	>	uz = uz / u;
210	>
211	>	dAtom->setSUx( ux );
212	>	dAtom->setSUy( uy );
213	>	dAtom->setSUz( uz );
214	>	}
215	>	else{
216	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
217	>	info[k].getConfiguration() );
218	>	}
219	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220
221		#ifdef IS_MPI
222
223	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
223	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224
225		#endif // is_mpi
226	<	}
226	>	}
227
228		// make the bonds
229	<	for(j=0; j<info.nBonds; j++){
229	>	for(j=0; j<molInfo.nBonds; j++){
230
231	<	currentBond = comp_stamps[stampID]->getBond( j );
232	<	theBonds[j].a = currentBond->getA() + atomOffset;
233	<	theBonds[j].b = currentBond->getB() + atomOffset;
234	<
235	<	exI = theBonds[j].a;
236	<	exJ = theBonds[j].b;
237	<
238	<	// exclude_I must always be the smaller of the pair
239	<	if( exI > exJ ){
240	<	tempEx = exI;
241	<	exI = exJ;
242	<	exJ = tempEx;
243	<	}
231	>	currentBond = comp_stamps[stampID]->getBond( j );
232	>	theBonds[j].a = currentBond->getA() + atomOffset;
233	>	theBonds[j].b = currentBond->getB() + atomOffset;
234	>
235	>	exI = theBonds[j].a;
236	>	exJ = theBonds[j].b;
237	>
238	>	// exclude_I must always be the smaller of the pair
239	>	if( exI > exJ ){
240	>	tempEx = exI;
241	>	exI = exJ;
242	>	exJ = tempEx;
243	>	}
244		#ifdef IS_MPI
245	<	tempEx = exI;
246	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
247	<	tempEx = exJ;
248	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
249	<
250	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
245	>	tempEx = exI;
246	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
247	>	tempEx = exJ;
248	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>
250	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
251		#else  // isn't MPI
252	<
253	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
252	>
253	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254		#endif  //is_mpi
255	<	}
256	<	excludeOffset += info.nBonds;
808	<
809	<	//make the bends
810	<	for(j=0; j<info.nBends; j++){
255	>	}
256	>	excludeOffset += molInfo.nBonds;
257
258	<	currentBend = comp_stamps[stampID]->getBend( j );
259	<	theBends[j].a = currentBend->getA() + atomOffset;
260	<	theBends[j].b = currentBend->getB() + atomOffset;
261	<	theBends[j].c = currentBend->getC() + atomOffset;
258	>	//make the bends
259	>	for(j=0; j<molInfo.nBends; j++){
260	>
261	>	currentBend = comp_stamps[stampID]->getBend( j );
262	>	theBends[j].a = currentBend->getA() + atomOffset;
263	>	theBends[j].b = currentBend->getB() + atomOffset;
264	>	theBends[j].c = currentBend->getC() + atomOffset;
265	>
266	>	if( currentBend->haveExtras() ){
267
268	<	if( currentBend->haveExtras() ){
269	<
270	<	extras = currentBend->getExtras();
271	<	current_extra = extras;
272	<
273	<	while( current_extra != NULL ){
274	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
268	>	extras = currentBend->getExtras();
269	>	current_extra = extras;
270	>
271	>	while( current_extra != NULL ){
272	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273	>
274	>	switch( current_extra->getType() ){
275
276	<	switch( current_extra->getType() ){
276	>	case 0:
277	>	theBends[j].ghost =
278	>	current_extra->getInt() + atomOffset;
279	>	theBends[j].isGhost = 1;
280	>	break;
281	>
282	>	case 1:
283	>	theBends[j].ghost =
284	>	(int)current_extra->getDouble() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	default:
289	>	sprintf( painCave.errMsg,
290	>	"SimSetup Error: ghostVectorSource was neither a "
291	>	"double nor an int.\n"
292	>	"-->Bend[%d] in %s\n",
293	>	j, comp_stamps[stampID]->getID() );
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	}
298	>
299	>	else{
300
827	–	case 0:
828	–	theBends[j].ghost =
829	–	current_extra->getInt() + atomOffset;
830	–	theBends[j].isGhost = 1;
831	–	break;
832	–
833	–	case 1:
834	–	theBends[j].ghost =
835	–	(int)current_extra->getDouble() + atomOffset;
836	–	theBends[j].isGhost = 1;
837	–	break;
838	–
839	–	default:
301		sprintf( painCave.errMsg,
302	<	"SimSetup Error: ghostVectorSource was neither a "
303	<	"double nor an int.\n"
304	<	"-->Bend[%d] in %s\n",
302	>	"SimSetup Error: unhandled bend assignment:\n"
303	>	"    -->%s in Bend[%d] in %s\n",
304	>	current_extra->getlhs(),
305		j, comp_stamps[stampID]->getID() );
306		painCave.isFatal = 1;
307		simError();
308		}
848	–	}
849	–
850	–	else{
309
310	<	sprintf( painCave.errMsg,
853	<	"SimSetup Error: unhandled bend assignment:\n"
854	<	"    -->%s in Bend[%d] in %s\n",
855	<	current_extra->getlhs(),
856	<	j, comp_stamps[stampID]->getID() );
857	<	painCave.isFatal = 1;
858	<	simError();
310	>	current_extra = current_extra->getNext();
311		}
312	+	}
313	+
314	+	if( !theBends[j].isGhost ){
315
316	<	current_extra = current_extra->getNext();
316	>	exI = theBends[j].a;
317	>	exJ = theBends[j].c;
318		}
319	<	}
319	>	else{
320
321	<	if( !theBends[j].isGhost ){
322	<
323	<	exI = theBends[j].a;
868	<	exJ = theBends[j].c;
869	<	}
870	<	else{
321	>	exI = theBends[j].a;
322	>	exJ = theBends[j].b;
323	>	}
324
325	<	exI = theBends[j].a;
326	<	exJ = theBends[j].b;
327	<	}
328	<
329	<	// exclude_I must always be the smaller of the pair
330	<	if( exI > exJ ){
325	>	// exclude_I must always be the smaller of the pair
326	>	if( exI > exJ ){
327	>	tempEx = exI;
328	>	exI = exJ;
329	>	exJ = tempEx;
330	>	}
331	>	#ifdef IS_MPI
332		tempEx = exI;
333	<	exI = exJ;
334	<	exJ = tempEx;
333	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exJ;
335	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>
337	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
338	>	#else  // isn't MPI
339	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340	>	#endif  //is_mpi
341		}
342	<	#ifdef IS_MPI
883	<	tempEx = exI;
884	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
885	<	tempEx = exJ;
886	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
342	>	excludeOffset += molInfo.nBends;
343
344	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
344	>	for(j=0; j<molInfo.nTorsions; j++){
345	>
346	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	>
352	>	exI = theTorsions[j].a;
353	>	exJ = theTorsions[j].d;
354	>
355	>	// exclude_I must always be the smaller of the pair
356	>	if( exI > exJ ){
357	>	tempEx = exI;
358	>	exI = exJ;
359	>	exJ = tempEx;
360	>	}
361	>	#ifdef IS_MPI
362	>	tempEx = exI;
363	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
364	>	tempEx = exJ;
365	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	>
367	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
368		#else  // isn't MPI
369	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
369	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370		#endif  //is_mpi
371	<	}
372	<	excludeOffset += info.nBends;
894	<
895	<	for(j=0; j<info.nTorsions; j++){
371	>	}
372	>	excludeOffset += molInfo.nTorsions;
373
897	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
898	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
899	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
900	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
901	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
374
375	<	exI = theTorsions[j].a;
376	<	exJ = theTorsions[j].d;
375	>	// send the arrays off to the forceField for init.
376	>
377	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381	>
382	>
383	>	info[k].molecules[i].initialize( molInfo );
384
906	–	// exclude_I must always be the smaller of the pair
907	–	if( exI > exJ ){
908	–	tempEx = exI;
909	–	exI = exJ;
910	–	exJ = tempEx;
911	–	}
912	–	#ifdef IS_MPI
913	–	tempEx = exI;
914	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
915	–	tempEx = exJ;
916	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
385
386	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
387	<	#else  // isn't MPI
388	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
389	<	#endif  //is_mpi
386	>	atomOffset += molInfo.nAtoms;
387	>	delete[] theBonds;
388	>	delete[] theBends;
389	>	delete[] theTorsions;
390		}
923	–	excludeOffset += info.nTorsions;
924	–
925	–
926	–	// send the arrays off to the forceField for init.
927	–
928	–	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
929	–	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
930	–	the_ff->initializeBends( info.nBends, info.myBends, theBends );
931	–	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
932	–
933	–
934	–	the_molecules[i].initialize( info );
935	–	atomOffset += info.nAtoms;
936	–	delete[] theBonds;
937	–	delete[] theBends;
938	–	delete[] theTorsions;
391		}
392	<
392	>
393		#ifdef IS_MPI
394		sprintf( checkPointMsg, "all molecules initialized succesfully" );
395		MPIcheckPoint();
396		#endif // is_mpi
397	<
397	>
398		// clean up the forcefield
399	+
400		the_ff->calcRcut();
401		the_ff->cleanMe();
402	<
402	>
403		}
404
405		void SimSetup::initFromBass( void ){
#	Line 959 | Line 412 | void SimSetup::initFromBass( void ){
412		int n_extra;
413		int have_extra, done;
414
415	+	double vel[3];
416	+	vel[0] = 0.0;
417	+	vel[1] = 0.0;
418	+	vel[2] = 0.0;
419	+
420		temp1 = (double)tot_nmol / 4.0;
421		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
422		temp3 = ceil( temp2 );
#	Line 968 | Line 426 | void SimSetup::initFromBass( void ){
426		have_extra =1;
427
428		n_cells = (int)temp3 - 1;
429	<	cellx = simnfo->box_x / temp3;
430	<	celly = simnfo->box_y / temp3;
431	<	cellz = simnfo->box_z / temp3;
429	>	cellx = info[0].boxL[0] / temp3;
430	>	celly = info[0].boxL[1] / temp3;
431	>	cellz = info[0].boxL[2] / temp3;
432		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
433		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
434		n_per_extra = (int)ceil( temp1 );
#	Line 985 | Line 443 | void SimSetup::initFromBass( void ){
443		}
444		else{
445		n_cells = (int)temp3;
446	<	cellx = simnfo->box_x / temp3;
447	<	celly = simnfo->box_y / temp3;
448	<	cellz = simnfo->box_z / temp3;
446	>	cellx = info[0].boxL[0] / temp3;
447	>	celly = info[0].boxL[1] / temp3;
448	>	cellz = info[0].boxL[2] / temp3;
449		}
450
451		current_mol = 0;
#	Line 1066 | Line 524 | void SimSetup::initFromBass( void ){
524		}
525		}
526
527	<
528	<	for( i=0; i<simnfo->n_atoms; i++ ){
1071	<	simnfo->atoms[i]->set_vx( 0.0 );
1072	<	simnfo->atoms[i]->set_vy( 0.0 );
1073	<	simnfo->atoms[i]->set_vz( 0.0 );
527	>	for( i=0; i<info[0].n_atoms; i++ ){
528	>	info[0].atoms[i]->setVel( vel );
529		}
530		}
531
#	Line 1080 | Line 535 | void SimSetup::makeElement( double x, double y, double
535		AtomStamp* current_atom;
536		DirectionalAtom* dAtom;
537		double rotMat[3][3];
538	+	double pos[3];
539
540		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
541
#	Line 1095 | Line 551 | void SimSetup::makeElement( double x, double y, double
551		painCave.isFatal = 1;
552		simError();
553		}
554	+
555	+	pos[0] = x + current_atom->getPosX();
556	+	pos[1] = y + current_atom->getPosY();
557	+	pos[2] = z + current_atom->getPosZ();
558	+
559	+	info[0].atoms[current_atom_ndx]->setPos( pos );
560
561	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1100	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1101	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
561	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
562
563	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
563	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
564
1105	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1106	–
565		rotMat[0][0] = 1.0;
566		rotMat[0][1] = 0.0;
567		rotMat[0][2] = 0.0;
#	Line 1129 | Line 587 | void SimSetup::makeElement( double x, double y, double
587
588		current_comp_mol = 0;
589		current_comp++;
590	+	}
591	+	}
592	+
593	+
594	+	void SimSetup::gatherInfo( void ){
595	+	int i,j,k;
596	+
597	+	ensembleCase = -1;
598	+	ffCase = -1;
599	+
600	+	// set the easy ones first
601	+
602	+	for( i=0; i<nInfo; i++){
603	+	info[i].target_temp = globals->getTargetTemp();
604	+	info[i].dt = globals->getDt();
605	+	info[i].run_time = globals->getRunTime();
606	+	}
607	+	n_components = globals->getNComponents();
608	+
609	+
610	+	// get the forceField
611	+
612	+	strcpy( force_field, globals->getForceField() );
613	+
614	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
615	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
616	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
617	+	else{
618	+	sprintf( painCave.errMsg,
619	+	"SimSetup Error. Unrecognized force field -> %s\n",
620	+	force_field );
621	+	painCave.isFatal = 1;
622	+	simError();
623	+	}
624	+
625	+	// get the ensemble
626	+
627	+	strcpy( ensemble, globals->getEnsemble() );
628	+
629	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
630	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
631	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
632	+	ensembleCase = NPTi_ENS;
633	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
634	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
635	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
636	+	else{
637	+	sprintf( painCave.errMsg,
638	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
639	+	"reverting to NVE for this simulation.\n",
640	+	ensemble );
641	+	painCave.isFatal = 0;
642	+	simError();
643	+	strcpy( ensemble, "NVE" );
644	+	ensembleCase = NVE_ENS;
645	+	}
646	+
647	+	for(i=0; i<nInfo; i++){
648	+
649	+	strcpy( info[i].ensemble, ensemble );
650	+
651	+	// get the mixing rule
652	+
653	+	strcpy( info[i].mixingRule, globals->getMixingRule() );
654	+	info[i].usePBC = globals->getPBC();
655	+	}
656	+
657	+	// get the components and calculate the tot_nMol and indvidual n_mol
658	+
659	+	the_components = globals->getComponents();
660	+	components_nmol = new int[n_components];
661	+
662	+
663	+	if( !globals->haveNMol() ){
664	+	// we don't have the total number of molecules, so we assume it is
665	+	// given in each component
666	+
667	+	tot_nmol = 0;
668	+	for( i=0; i<n_components; i++ ){
669	+
670	+	if( !the_components[i]->haveNMol() ){
671	+	// we have a problem
672	+	sprintf( painCave.errMsg,
673	+	"SimSetup Error. No global NMol or component NMol"
674	+	" given. Cannot calculate the number of atoms.\n" );
675	+	painCave.isFatal = 1;
676	+	simError();
677	+	}
678	+
679	+	tot_nmol += the_components[i]->getNMol();
680	+	components_nmol[i] = the_components[i]->getNMol();
681	+	}
682	+	}
683	+	else{
684	+	sprintf( painCave.errMsg,
685	+	"SimSetup error.\n"
686	+	"\tSorry, the ability to specify total"
687	+	" nMols and then give molfractions in the components\n"
688	+	"\tis not currently supported."
689	+	" Please give nMol in the components.\n" );
690	+	painCave.isFatal = 1;
691	+	simError();
692	+	}
693	+
694	+	// set the status, sample, and thermal kick times
695	+
696	+	for(i=0; i<nInfo; i++){
697	+
698	+	if( globals->haveSampleTime() ){
699	+	info[i].sampleTime = globals->getSampleTime();
700	+	info[i].statusTime = info[i].sampleTime;
701	+	info[i].thermalTime = info[i].sampleTime;
702	+	}
703	+	else{
704	+	info[i].sampleTime = globals->getRunTime();
705	+	info[i].statusTime = info[i].sampleTime;
706	+	info[i].thermalTime = info[i].sampleTime;
707	+	}
708	+
709	+	if( globals->haveStatusTime() ){
710	+	info[i].statusTime = globals->getStatusTime();
711	+	}
712	+
713	+	if( globals->haveThermalTime() ){
714	+	info[i].thermalTime = globals->getThermalTime();
715	+	}
716	+
717	+	// check for the temperature set flag
718	+
719	+	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
720	+
721	+	// get some of the tricky things that may still be in the globals
722	+
723	+	double boxVector[3];
724	+	if( globals->haveBox() ){
725	+	boxVector[0] = globals->getBox();
726	+	boxVector[1] = globals->getBox();
727	+	boxVector[2] = globals->getBox();
728	+
729	+	info[i].setBox( boxVector );
730	+	}
731	+	else if( globals->haveDensity() ){
732	+
733	+	double vol;
734	+	vol = (double)tot_nmol / globals->getDensity();
735	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
736	+	boxVector[1] = boxVector[0];
737	+	boxVector[2] = boxVector[0];
738	+
739	+	info[i].setBox( boxVector );
740	+	}
741	+	else{
742	+	if( !globals->haveBoxX() ){
743	+	sprintf( painCave.errMsg,
744	+	"SimSetup error, no periodic BoxX size given.\n" );
745	+	painCave.isFatal = 1;
746	+	simError();
747	+	}
748	+	boxVector[0] = globals->getBoxX();
749	+
750	+	if( !globals->haveBoxY() ){
751	+	sprintf( painCave.errMsg,
752	+	"SimSetup error, no periodic BoxY size given.\n" );
753	+	painCave.isFatal = 1;
754	+	simError();
755	+	}
756	+	boxVector[1] = globals->getBoxY();
757	+
758	+	if( !globals->haveBoxZ() ){
759	+	sprintf( painCave.errMsg,
760	+	"SimSetup error, no periodic BoxZ size given.\n" );
761	+	painCave.isFatal = 1;
762	+	simError();
763	+	}
764	+	boxVector[2] = globals->getBoxZ();
765	+
766	+	info[i].setBox( boxVector );
767	+	}
768	+
769	+	}
770	+
771	+	#ifdef IS_MPI
772	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
773	+	MPIcheckPoint();
774	+	#endif // is_mpi
775	+
776	+	}
777	+
778	+
779	+	void SimSetup::finalInfoCheck( void ){
780	+	int index;
781	+	int usesDipoles;
782	+	int i;
783	+
784	+	for(i=0; i<nInfo; i++){
785	+	// check electrostatic parameters
786	+
787	+	index = 0;
788	+	usesDipoles = 0;
789	+	while( (index < info[i].n_atoms) && !usesDipoles ){
790	+	usesDipoles = (info[i].atoms[index])->hasDipole();
791	+	index++;
792	+	}
793	+
794	+	#ifdef IS_MPI
795	+	int myUse = usesDipoles;
796	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
797	+	#endif //is_mpi
798	+
799	+	double theEcr, theEst;
800	+
801	+	if (globals->getUseRF() ) {
802	+	info[i].useReactionField = 1;
803	+
804	+	if( !globals->haveECR() ){
805	+	sprintf( painCave.errMsg,
806	+	"SimSetup Warning: using default value of 1/2 the smallest "
807	+	"box length for the electrostaticCutoffRadius.\n"
808	+	"I hope you have a very fast processor!\n");
809	+	painCave.isFatal = 0;
810	+	simError();
811	+	double smallest;
812	+	smallest = info[i].boxL[0];
813	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
814	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
815	+	theEcr = 0.5 * smallest;
816	+	} else {
817	+	theEcr = globals->getECR();
818	+	}
819	+
820	+	if( !globals->haveEST() ){
821	+	sprintf( painCave.errMsg,
822	+	"SimSetup Warning: using default value of 0.05 * the "
823	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
824	+	);
825	+	painCave.isFatal = 0;
826	+	simError();
827	+	theEst = 0.05 * theEcr;
828	+	} else {
829	+	theEst= globals->getEST();
830	+	}
831	+
832	+	info[i].setEcr( theEcr, theEst );
833	+
834	+	if(!globals->haveDielectric() ){
835	+	sprintf( painCave.errMsg,
836	+	"SimSetup Error: You are trying to use Reaction Field without"
837	+	"setting a dielectric constant!\n"
838	+	);
839	+	painCave.isFatal = 1;
840	+	simError();
841	+	}
842	+	info[i].dielectric = globals->getDielectric();
843	+	}
844	+	else {
845	+	if (usesDipoles) {
846	+
847	+	if( !globals->haveECR() ){
848	+	sprintf( painCave.errMsg,
849	+	"SimSetup Warning: using default value of 1/2 the smallest "
850	+	"box length for the electrostaticCutoffRadius.\n"
851	+	"I hope you have a very fast processor!\n");
852	+	painCave.isFatal = 0;
853	+	simError();
854	+	double smallest;
855	+	smallest = info[i].boxL[0];
856	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
857	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
858	+	theEcr = 0.5 * smallest;
859	+	} else {
860	+	theEcr = globals->getECR();
861	+	}
862	+
863	+	if( !globals->haveEST() ){
864	+	sprintf( painCave.errMsg,
865	+	"SimSetup Warning: using default value of 0.05 * the "
866	+	"electrostaticCutoffRadius for the "
867	+	"electrostaticSkinThickness\n"
868	+	);
869	+	painCave.isFatal = 0;
870	+	simError();
871	+	theEst = 0.05 * theEcr;
872	+	} else {
873	+	theEst= globals->getEST();
874	+	}
875	+
876	+	info[i].setEcr( theEcr, theEst );
877	+	}
878	+	}
879	+	}
880	+
881	+	#ifdef IS_MPI
882	+	strcpy( checkPointMsg, "post processing checks out" );
883	+	MPIcheckPoint();
884	+	#endif // is_mpi
885	+
886	+	}
887	+
888	+	void SimSetup::initSystemCoords( void ){
889	+	int i;
890	+
891	+	std::cerr << "Setting atom Coords\n";
892	+
893	+	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
894	+
895	+	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
896	+
897	+	if( globals->haveInitialConfig() ){
898	+
899	+	InitializeFromFile* fileInit;
900	+	#ifdef IS_MPI // is_mpi
901	+	if( worldRank == 0 ){
902	+	#endif //is_mpi
903	+	fileInit = new InitializeFromFile( globals->getInitialConfig() );
904	+	#ifdef IS_MPI
905	+	}else fileInit = new InitializeFromFile( NULL );
906	+	#endif
907	+	fileInit->readInit( info ); // default velocities on
908	+
909	+	delete fileInit;
910	+	}
911	+	else{
912	+
913	+	#ifdef IS_MPI
914	+
915	+	// no init from bass
916	+
917	+	sprintf( painCave.errMsg,
918	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
919	+	painCave.isFatal;
920	+	simError();
921	+
922	+	#else
923	+
924	+	initFromBass();
925	+
926	+
927	+	#endif
928	+	}
929	+
930	+	#ifdef IS_MPI
931	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
932	+	MPIcheckPoint();
933	+	#endif // is_mpi
934	+
935	+	}
936	+
937	+
938	+	void SimSetup::makeOutNames( void ){
939	+
940	+	int k;
941	+
942	+
943	+	for(k=0; k<nInfo; k++){
944	+
945	+	#ifdef IS_MPI
946	+	if( worldRank == 0 ){
947	+	#endif // is_mpi
948	+
949	+	if( globals->haveFinalConfig() ){
950	+	strcpy( info[k].finalName, globals->getFinalConfig() );
951	+	}
952	+	else{
953	+	strcpy( info[k].finalName, inFileName );
954	+	char* endTest;
955	+	int nameLength = strlen( info[k].finalName );
956	+	endTest = &(info[k].finalName[nameLength - 5]);
957	+	if( !strcmp( endTest, ".bass" ) ){
958	+	strcpy( endTest, ".eor" );
959	+	}
960	+	else if( !strcmp( endTest, ".BASS" ) ){
961	+	strcpy( endTest, ".eor" );
962	+	}
963	+	else{
964	+	endTest = &(info[k].finalName[nameLength - 4]);
965	+	if( !strcmp( endTest, ".bss" ) ){
966	+	strcpy( endTest, ".eor" );
967	+	}
968	+	else if( !strcmp( endTest, ".mdl" ) ){
969	+	strcpy( endTest, ".eor" );
970	+	}
971	+	else{
972	+	strcat( info[k].finalName, ".eor" );
973	+	}
974	+	}
975	+	}
976	+
977	+	// make the sample and status out names
978	+
979	+	strcpy( info[k].sampleName, inFileName );
980	+	char* endTest;
981	+	int nameLength = strlen( info[k].sampleName );
982	+	endTest = &(info[k].sampleName[nameLength - 5]);
983	+	if( !strcmp( endTest, ".bass" ) ){
984	+	strcpy( endTest, ".dump" );
985	+	}
986	+	else if( !strcmp( endTest, ".BASS" ) ){
987	+	strcpy( endTest, ".dump" );
988	+	}
989	+	else{
990	+	endTest = &(info[k].sampleName[nameLength - 4]);
991	+	if( !strcmp( endTest, ".bss" ) ){
992	+	strcpy( endTest, ".dump" );
993	+	}
994	+	else if( !strcmp( endTest, ".mdl" ) ){
995	+	strcpy( endTest, ".dump" );
996	+	}
997	+	else{
998	+	strcat( info[k].sampleName, ".dump" );
999	+	}
1000	+	}
1001	+
1002	+	strcpy( info[k].statusName, inFileName );
1003	+	nameLength = strlen( info[k].statusName );
1004	+	endTest = &(info[k].statusName[nameLength - 5]);
1005	+	if( !strcmp( endTest, ".bass" ) ){
1006	+	strcpy( endTest, ".stat" );
1007	+	}
1008	+	else if( !strcmp( endTest, ".BASS" ) ){
1009	+	strcpy( endTest, ".stat" );
1010	+	}
1011	+	else{
1012	+	endTest = &(info[k].statusName[nameLength - 4]);
1013	+	if( !strcmp( endTest, ".bss" ) ){
1014	+	strcpy( endTest, ".stat" );
1015	+	}
1016	+	else if( !strcmp( endTest, ".mdl" ) ){
1017	+	strcpy( endTest, ".stat" );
1018	+	}
1019	+	else{
1020	+	strcat( info[k].statusName, ".stat" );
1021	+	}
1022	+	}
1023	+
1024	+	#ifdef IS_MPI
1025	+	}
1026	+	#endif // is_mpi
1027	+	}
1028	+	}
1029	+
1030	+
1031	+	void SimSetup::sysObjectsCreation( void ){
1032	+
1033	+	int i,k;
1034	+
1035	+	// create the forceField
1036	+
1037	+	createFF();
1038	+
1039	+	// extract componentList
1040	+
1041	+	compList();
1042	+
1043	+	// calc the number of atoms, bond, bends, and torsions
1044	+
1045	+	calcSysValues();
1046	+
1047	+	#ifdef IS_MPI
1048	+	// divide the molecules among the processors
1049	+
1050	+	mpiMolDivide();
1051	+	#endif //is_mpi
1052	+
1053	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1054	+
1055	+	makeSysArrays();
1056	+
1057	+	// make and initialize the molecules (all but atomic coordinates)
1058	+
1059	+	makeMolecules();
1060	+
1061	+	for(k=0; k<nInfo; k++){
1062	+	info[k].identArray = new int[info[k].n_atoms];
1063	+	for(i=0; i<info[k].n_atoms; i++){
1064	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1065	+	}
1066	+	}
1067	+	}
1068	+
1069	+
1070	+	void SimSetup::createFF( void ){
1071	+
1072	+	switch( ffCase ){
1073	+
1074	+	case FF_DUFF:
1075	+	the_ff = new DUFF();
1076	+	break;
1077	+
1078	+	case FF_LJ:
1079	+	the_ff = new LJFF();
1080	+	break;
1081	+
1082	+	case FF_EAM:
1083	+	the_ff = new EAM_FF();
1084	+	break;
1085	+
1086	+	default:
1087	+	sprintf( painCave.errMsg,
1088	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1089	+	painCave.isFatal = 1;
1090	+	simError();
1091	+	}
1092	+
1093	+	#ifdef IS_MPI
1094	+	strcpy( checkPointMsg, "ForceField creation successful" );
1095	+	MPIcheckPoint();
1096	+	#endif // is_mpi
1097	+
1098	+	}
1099	+
1100	+
1101	+	void SimSetup::compList( void ){
1102	+
1103	+	int i;
1104	+	char* id;
1105	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1106	+	LinkedMolStamp* currentStamp = NULL;
1107	+	comp_stamps = new MoleculeStamp*[n_components];
1108	+
1109	+	// make an array of molecule stamps that match the components used.
1110	+	// also extract the used stamps out into a separate linked list
1111	+
1112	+	for(i=0; i<nInfo; i++){
1113	+	info[i].nComponents = n_components;
1114	+	info[i].componentsNmol = components_nmol;
1115	+	info[i].compStamps = comp_stamps;
1116	+	info[i].headStamp = headStamp;
1117		}
1118	+
1119	+
1120	+	for( i=0; i<n_components; i++ ){
1121	+
1122	+	id = the_components[i]->getType();
1123	+	comp_stamps[i] = NULL;
1124	+
1125	+	// check to make sure the component isn't already in the list
1126	+
1127	+	comp_stamps[i] = headStamp->match( id );
1128	+	if( comp_stamps[i] == NULL ){
1129	+
1130	+	// extract the component from the list;
1131	+
1132	+	currentStamp = stamps->extractMolStamp( id );
1133	+	if( currentStamp == NULL ){
1134	+	sprintf( painCave.errMsg,
1135	+	"SimSetup error: Component \"%s\" was not found in the "
1136	+	"list of declared molecules\n",
1137	+	id );
1138	+	painCave.isFatal = 1;
1139	+	simError();
1140	+	}
1141	+
1142	+	headStamp->add( currentStamp );
1143	+	comp_stamps[i] = headStamp->match( id );
1144	+	}
1145	+	}
1146	+
1147	+	#ifdef IS_MPI
1148	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1149	+	MPIcheckPoint();
1150	+	#endif // is_mpi
1151	+
1152	+
1153		}
1154	+
1155	+	void SimSetup::calcSysValues( void ){
1156	+	int i, j, k;
1157	+
1158	+	int *molMembershipArray;
1159	+
1160	+	tot_atoms = 0;
1161	+	tot_bonds = 0;
1162	+	tot_bends = 0;
1163	+	tot_torsions = 0;
1164	+	for( i=0; i<n_components; i++ ){
1165	+
1166	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1167	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1168	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1169	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1170	+	}
1171	+
1172	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1173	+	molMembershipArray = new int[tot_atoms];
1174	+
1175	+	for(i=0; i<nInfo; i++){
1176	+	info[i].n_atoms = tot_atoms;
1177	+	info[i].n_bonds = tot_bonds;
1178	+	info[i].n_bends = tot_bends;
1179	+	info[i].n_torsions = tot_torsions;
1180	+	info[i].n_SRI = tot_SRI;
1181	+	info[i].n_mol = tot_nmol;
1182	+
1183	+	info[i].molMembershipArray = molMembershipArray;
1184	+	}
1185	+	}
1186	+
1187	+	#ifdef IS_MPI
1188	+
1189	+	void SimSetup::mpiMolDivide( void ){
1190	+
1191	+	int i, j, k;
1192	+	int localMol, allMol;
1193	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1194	+
1195	+	mpiSim = new mpiSimulation( info );
1196	+
1197	+	globalIndex = mpiSim->divideLabor();
1198	+
1199	+	// set up the local variables
1200	+
1201	+	mol2proc = mpiSim->getMolToProcMap();
1202	+	molCompType = mpiSim->getMolComponentType();
1203	+
1204	+	allMol = 0;
1205	+	localMol = 0;
1206	+	local_atoms = 0;
1207	+	local_bonds = 0;
1208	+	local_bends = 0;
1209	+	local_torsions = 0;
1210	+	globalAtomIndex = 0;
1211	+
1212	+
1213	+	for( i=0; i<n_components; i++ ){
1214	+
1215	+	for( j=0; j<components_nmol[i]; j++ ){
1216	+
1217	+	if( mol2proc[allMol] == worldRank ){
1218	+
1219	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1220	+	local_bonds +=    comp_stamps[i]->getNBonds();
1221	+	local_bends +=    comp_stamps[i]->getNBends();
1222	+	local_torsions += comp_stamps[i]->getNTorsions();
1223	+	localMol++;
1224	+	}
1225	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1226	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1227	+	globalAtomIndex++;
1228	+	}
1229	+
1230	+	allMol++;
1231	+	}
1232	+	}
1233	+	local_SRI = local_bonds + local_bends + local_torsions;
1234	+
1235	+	info[0].n_atoms = mpiSim->getMyNlocal();
1236	+
1237	+	if( local_atoms != info[0].n_atoms ){
1238	+	sprintf( painCave.errMsg,
1239	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	+	" localAtom (%d) are not equal.\n",
1241	+	info[0].n_atoms,
1242	+	local_atoms );
1243	+	painCave.isFatal = 1;
1244	+	simError();
1245	+	}
1246	+
1247	+	info[0].n_bonds = local_bonds;
1248	+	info[0].n_bends = local_bends;
1249	+	info[0].n_torsions = local_torsions;
1250	+	info[0].n_SRI = local_SRI;
1251	+	info[0].n_mol = localMol;
1252	+
1253	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1254	+	MPIcheckPoint();
1255	+	}
1256	+
1257	+	#endif // is_mpi
1258	+
1259	+
1260	+	void SimSetup::makeSysArrays( void ){
1261	+	int i, j, k, l;
1262	+
1263	+	Atom** the_atoms;
1264	+	Molecule* the_molecules;
1265	+	Exclude** the_excludes;
1266	+
1267	+
1268	+	for(l=0; l<nInfo; l++){
1269	+
1270	+	// create the atom and short range interaction arrays
1271	+
1272	+	the_atoms = new Atom*[info[l].n_atoms];
1273	+	the_molecules = new Molecule[info[l].n_mol];
1274	+	int molIndex;
1275	+
1276	+	// initialize the molecule's stampID's
1277	+
1278	+	#ifdef IS_MPI
1279	+
1280	+
1281	+	molIndex = 0;
1282	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1283	+
1284	+	if(mol2proc[i] == worldRank ){
1285	+	the_molecules[molIndex].setStampID( molCompType[i] );
1286	+	the_molecules[molIndex].setMyIndex( molIndex );
1287	+	the_molecules[molIndex].setGlobalIndex( i );
1288	+	molIndex++;
1289	+	}
1290	+	}
1291	+
1292	+	#else // is_mpi
1293	+
1294	+	molIndex = 0;
1295	+	globalAtomIndex = 0;
1296	+	for(i=0; i<n_components; i++){
1297	+	for(j=0; j<components_nmol[i]; j++ ){
1298	+	the_molecules[molIndex].setStampID( i );
1299	+	the_molecules[molIndex].setMyIndex( molIndex );
1300	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1301	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1302	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1303	+	globalAtomIndex++;
1304	+	}
1305	+	molIndex++;
1306	+	}
1307	+	}
1308	+
1309	+
1310	+	#endif // is_mpi
1311	+
1312	+
1313	+	if( info[l].n_SRI ){
1314	+
1315	+	Exclude::createArray(info[l].n_SRI);
1316	+	the_excludes = new Exclude*[info[l].n_SRI];
1317	+	for( int ex=0; ex<info[l].n_SRI; ex++){
1318	+	the_excludes[ex] = new Exclude(ex);
1319	+	}
1320	+	info[l].globalExcludes = new int;
1321	+	info[l].n_exclude = info[l].n_SRI;
1322	+	}
1323	+	else{
1324	+
1325	+	Exclude::createArray( 1 );
1326	+	the_excludes = new Exclude*;
1327	+	the_excludes[0] = new Exclude(0);
1328	+	the_excludes[0]->setPair( 0,0 );
1329	+	info[l].globalExcludes = new int;
1330	+	info[l].globalExcludes[0] = 0;
1331	+	info[l].n_exclude = 0;
1332	+	}
1333	+
1334	+	// set the arrays into the SimInfo object
1335	+
1336	+	info[l].atoms = the_atoms;
1337	+	info[l].molecules = the_molecules;
1338	+	info[l].nGlobalExcludes = 0;
1339	+	info[l].excludes = the_excludes;
1340	+
1341	+	the_ff->setSimInfo( info );
1342	+
1343	+	}
1344	+	}
1345	+
1346	+	void SimSetup::makeIntegrator( void ){
1347	+
1348	+	int k;
1349	+
1350	+	NVT<RealIntegrator>*  myNVT = NULL;
1351	+	NPTi<RealIntegrator>* myNPTi = NULL;
1352	+	NPTf<RealIntegrator>* myNPTf = NULL;
1353	+	NPTim<RealIntegrator>* myNPTim = NULL;
1354	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1355	+
1356	+	for(k=0; k<nInfo; k++){
1357	+
1358	+	switch( ensembleCase ){
1359	+
1360	+	case NVE_ENS:
1361	+	if (haveZConstraint){
1362	+	setupZConstraint();
1363	+	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1364	+	}
1365	+
1366	+	else
1367	+	new NVE<RealIntegrator>( &(info[k]), the_ff );
1368	+	break;
1369	+
1370	+	case NVT_ENS:
1371	+	if (haveZConstraint){
1372	+	setupZConstraint();
1373	+	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1374	+	}
1375	+	else
1376	+	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1377	+
1378	+	myNVT->setTargetTemp(globals->getTargetTemp());
1379	+
1380	+	if (globals->haveTauThermostat())
1381	+	myNVT->setTauThermostat(globals->getTauThermostat());
1382	+
1383	+	else {
1384	+	sprintf( painCave.errMsg,
1385	+	"SimSetup error: If you use the NVT\n"
1386	+	"    ensemble, you must set tauThermostat.\n");
1387	+	painCave.isFatal = 1;
1388	+	simError();
1389	+	}
1390	+	break;
1391	+
1392	+	case NPTi_ENS:
1393	+	if (haveZConstraint){
1394	+	setupZConstraint();
1395	+	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1396	+	}
1397	+	else
1398	+	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1399	+
1400	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1401	+
1402	+	if (globals->haveTargetPressure())
1403	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1404	+	else {
1405	+	sprintf( painCave.errMsg,
1406	+	"SimSetup error: If you use a constant pressure\n"
1407	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1408	+	painCave.isFatal = 1;
1409	+	simError();
1410	+	}
1411	+
1412	+	if( globals->haveTauThermostat() )
1413	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1414	+	else{
1415	+	sprintf( painCave.errMsg,
1416	+	"SimSetup error: If you use an NPT\n"
1417	+	"    ensemble, you must set tauThermostat.\n");
1418	+	painCave.isFatal = 1;
1419	+	simError();
1420	+	}
1421	+
1422	+	if( globals->haveTauBarostat() )
1423	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1424	+	else{
1425	+	sprintf( painCave.errMsg,
1426	+	"SimSetup error: If you use an NPT\n"
1427	+	"    ensemble, you must set tauBarostat.\n");
1428	+	painCave.isFatal = 1;
1429	+	simError();
1430	+	}
1431	+	break;
1432	+
1433	+	case NPTf_ENS:
1434	+	if (haveZConstraint){
1435	+	setupZConstraint();
1436	+	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1437	+	}
1438	+	else
1439	+	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1440	+
1441	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1442	+
1443	+	if (globals->haveTargetPressure())
1444	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1445	+	else {
1446	+	sprintf( painCave.errMsg,
1447	+	"SimSetup error: If you use a constant pressure\n"
1448	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	+	painCave.isFatal = 1;
1450	+	simError();
1451	+	}
1452	+
1453	+	if( globals->haveTauThermostat() )
1454	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1455	+	else{
1456	+	sprintf( painCave.errMsg,
1457	+	"SimSetup error: If you use an NPT\n"
1458	+	"    ensemble, you must set tauThermostat.\n");
1459	+	painCave.isFatal = 1;
1460	+	simError();
1461	+	}
1462	+
1463	+	if( globals->haveTauBarostat() )
1464	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1465	+	else{
1466	+	sprintf( painCave.errMsg,
1467	+	"SimSetup error: If you use an NPT\n"
1468	+	"    ensemble, you must set tauBarostat.\n");
1469	+	painCave.isFatal = 1;
1470	+	simError();
1471	+	}
1472	+	break;
1473	+
1474	+	case NPTim_ENS:
1475	+	if (haveZConstraint){
1476	+	setupZConstraint();
1477	+	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1478	+	}
1479	+	else
1480	+	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1481	+
1482	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1483	+
1484	+	if (globals->haveTargetPressure())
1485	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1486	+	else {
1487	+	sprintf( painCave.errMsg,
1488	+	"SimSetup error: If you use a constant pressure\n"
1489	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1490	+	painCave.isFatal = 1;
1491	+	simError();
1492	+	}
1493	+
1494	+	if( globals->haveTauThermostat() )
1495	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1496	+	else{
1497	+	sprintf( painCave.errMsg,
1498	+	"SimSetup error: If you use an NPT\n"
1499	+	"    ensemble, you must set tauThermostat.\n");
1500	+	painCave.isFatal = 1;
1501	+	simError();
1502	+	}
1503	+
1504	+	if( globals->haveTauBarostat() )
1505	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1506	+	else{
1507	+	sprintf( painCave.errMsg,
1508	+	"SimSetup error: If you use an NPT\n"
1509	+	"    ensemble, you must set tauBarostat.\n");
1510	+	painCave.isFatal = 1;
1511	+	simError();
1512	+	}
1513	+	break;
1514	+
1515	+	case NPTfm_ENS:
1516	+	if (haveZConstraint){
1517	+	setupZConstraint();
1518	+	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1519	+	}
1520	+	else
1521	+	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1522	+
1523	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1524	+
1525	+	if (globals->haveTargetPressure())
1526	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1527	+	else {
1528	+	sprintf( painCave.errMsg,
1529	+	"SimSetup error: If you use a constant pressure\n"
1530	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1531	+	painCave.isFatal = 1;
1532	+	simError();
1533	+	}
1534	+
1535	+	if( globals->haveTauThermostat() )
1536	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1537	+	else{
1538	+	sprintf( painCave.errMsg,
1539	+	"SimSetup error: If you use an NPT\n"
1540	+	"    ensemble, you must set tauThermostat.\n");
1541	+	painCave.isFatal = 1;
1542	+	simError();
1543	+	}
1544	+
1545	+	if( globals->haveTauBarostat() )
1546	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1547	+	else{
1548	+	sprintf( painCave.errMsg,
1549	+	"SimSetup error: If you use an NPT\n"
1550	+	"    ensemble, you must set tauBarostat.\n");
1551	+	painCave.isFatal = 1;
1552	+	simError();
1553	+	}
1554	+	break;
1555	+
1556	+	default:
1557	+	sprintf( painCave.errMsg,
1558	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1559	+	painCave.isFatal = 1;
1560	+	simError();
1561	+	}
1562	+	}
1563	+	}
1564	+
1565	+	void SimSetup::initFortran( void ){
1566	+
1567	+	info[0].refreshSim();
1568	+
1569	+	if( !strcmp( info[0].mixingRule, "standard") ){
1570	+	the_ff->initForceField( LB_MIXING_RULE );
1571	+	}
1572	+	else if( !strcmp( info[0].mixingRule, "explicit") ){
1573	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1574	+	}
1575	+	else{
1576	+	sprintf( painCave.errMsg,
1577	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1578	+	info[0].mixingRule );
1579	+	painCave.isFatal = 1;
1580	+	simError();
1581	+	}
1582	+
1583	+
1584	+	#ifdef IS_MPI
1585	+	strcpy( checkPointMsg,
1586	+	"Successfully intialized the mixingRule for Fortran." );
1587	+	MPIcheckPoint();
1588	+	#endif // is_mpi
1589	+
1590	+	}
1591	+
1592	+	void SimSetup::setupZConstraint()
1593	+	{
1594	+	int k;
1595	+
1596	+	for(k=0; k<nInfo; k++){
1597	+
1598	+	if(globals->haveZConsTime()){
1599	+
1600	+	//add sample time of z-constraint  into SimInfo's property list
1601	+	DoubleData* zconsTimeProp = new DoubleData();
1602	+	zconsTimeProp->setID("zconstime");
1603	+	zconsTimeProp->setData(globals->getZConsTime());
1604	+	info[k].addProperty(zconsTimeProp);
1605	+	}
1606	+	else{
1607	+	sprintf( painCave.errMsg,
1608	+	"ZConstraint error: If you use an ZConstraint\n"
1609	+	" , you must set sample time.\n");
1610	+	painCave.isFatal = 1;
1611	+	simError();
1612	+	}
1613	+
1614	+	if(globals->haveIndexOfAllZConsMols()){
1615	+
1616	+	//add index of z-constraint molecules into SimInfo's property list
1617	+	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1618	+
1619	+	//sort the index
1620	+	sort(tempIndex.begin(), tempIndex.end());
1621	+
1622	+	IndexData* zconsIndex = new IndexData();
1623	+	zconsIndex->setID("zconsindex");
1624	+	zconsIndex->setIndexData(tempIndex);
1625	+	info[k].addProperty(zconsIndex);
1626	+	}
1627	+	else{
1628	+	sprintf( painCave.errMsg,
1629	+	"SimSetup error: If you use an ZConstraint\n"
1630	+	" , you must set index of z-constraint molecules.\n");
1631	+	painCave.isFatal = 1;
1632	+	simError();
1633	+
1634	+	}
1635	+
1636	+	//Determine the name of ouput file and add it into SimInfo's property list
1637	+	//Be careful, do not use inFileName, since it is a pointer which
1638	+	//point to a string at master node, and slave nodes do not contain that string
1639	+
1640	+	string zconsOutput(info[k].finalName);
1641	+
1642	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1643	+
1644	+	StringData* zconsFilename = new StringData();
1645	+	zconsFilename->setID("zconsfilename");
1646	+	zconsFilename->setData(zconsOutput);
1647	+
1648	+	info[k].addProperty(zconsFilename);
1649	+	}
1650	+	}

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