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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 434 by chuckv, Fri Mar 28 19:30:59 2003 UTC vs.
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8		#include "parse_me.h"
#	Line 12 | Line 14 | SimSetup::SimSetup(){
14		#include "mpiSimulation.hpp"
15		#endif
16
17	+	// some defines for ensemble and Forcefield  cases
18	+
19	+	#define NVE_ENS        0
20	+	#define NVT_ENS        1
21	+	#define NPTi_ENS       2
22	+	#define NPTf_ENS       3
23	+	#define NPTim_ENS      4
24	+	#define NPTfm_ENS      5
25	+	#define NVEZCONS_ENS   6
26	+	#define NVTZCONS_ENS   7
27	+	#define NPTiZCONS_ENS  8
28	+	#define NPTfZCONS_ENS  9
29	+	#define NPTimZCONS_ENS 10
30	+	#define NPTfmZCONS_ENS 11
31	+
32	+	#define FF_DUFF 0
33	+	#define FF_LJ   1
34	+	#define FF_EAM  2
35	+
36	+	using namespace std;
37	+
38		SimSetup::SimSetup(){
39	+
40	+	isInfoArray = 0;
41	+	nInfo = 1;
42	+
43		stamps = new MakeStamps();
44		globals = new Globals();
45
46	+
47		#ifdef IS_MPI
48		strcpy( checkPointMsg, "SimSetup creation successful" );
49		MPIcheckPoint();
#	Line 27 | Line 55 | void SimSetup::parseFile( char* fileName ){
55		delete globals;
56		}
57
58	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
59	+	info = the_info;
60	+	nInfo = theNinfo;
61	+	isInfoArray = 1;
62	+	}
63	+
64	+
65		void SimSetup::parseFile( char* fileName ){
66
67		#ifdef IS_MPI
#	Line 62 | Line 97 | void SimSetup::createSim( void ){
97
98		#endif // is_mpi
99
100	<	void SimSetup::createSim( void ){
100	>	void SimSetup::createSim(void){
101
102	<	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	<
102	>	int i, j, k, globalAtomIndex;
103
104	<
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();
104	>	// gather all of the information from the Bass file
105
106	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
106	>	gatherInfo();
107
108	<	id = the_components[i]->getType();
177	<	comp_stamps[i] = NULL;
178	<
179	<	// check to make sure the component isn't already in the list
108	>	// creation of complex system objects
109
110	<	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	<	}
110	>	sysObjectsCreation();
111
112	<	#ifdef IS_MPI
202	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
203	<	MPIcheckPoint();
204	<	#endif // is_mpi
112	>	// check on the post processing info
113
114	+	finalInfoCheck();
115
116	+	// initialize the system coordinates
117
118	<
209	<	// 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
118	>	if( !isInfoArray ) initSystemCoords();
119
120	<	Atom::createArrays(simnfo->n_atoms);
303	<	the_atoms = new Atom*[simnfo->n_atoms];
304	<	the_molecules = new Molecule[simnfo->n_mol];
305	<	int molIndex;
120	>	// make the output filenames
121
122	<	// initialize the molecule's stampID's
308	<
309	<	#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	<
122	>	makeOutNames();
123
124	<
124	>	// make the integrator
125
126	<
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
126	>	makeIntegrator();
127
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	–
128		#ifdef IS_MPI
129		mpiSim->mpiRefresh();
130		#endif
131
132		// initialize the Fortran
133
134	+	initFortran();
135
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	–	}
136
137
685	–	#ifdef IS_MPI
686	–	strcpy( checkPointMsg,
687	–	"Successfully intialized the mixingRule for Fortran." );
688	–	MPIcheckPoint();
689	–	#endif // is_mpi
138		}
139
140
141		void SimSetup::makeMolecules( void ){
142
143	+	int k,l;
144		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
145	<	molInit info;
145	>	molInit molInfo;
146		DirectionalAtom* dAtom;
147		LinkedAssign* extras;
148		LinkedAssign* current_extra;
#	Line 716 | Line 165 | void SimSetup::makeMolecules( void ){
165
166		double ux, uy, uz, u, uSqr;
167
168	<	atomOffset = 0;
720	<	excludeOffset = 0;
721	<	for(i=0; i<simnfo->n_mol; i++){
168	>	for(k=0; k<nInfo; k++){
169
170	<	stampID = the_molecules[i].getStampID();
170	>	the_ff->setSimInfo( &(info[k]) );
171
172	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
173	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
174	<	info.nBends    = comp_stamps[stampID]->getNBends();
175	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
176	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
172	>	atomOffset = 0;
173	>	excludeOffset = 0;
174	>	for(i=0; i<info[k].n_mol; i++){
175	>
176	>	stampID = info[k].molecules[i].getStampID();
177
178	<	info.myAtoms = &the_atoms[atomOffset];
179	<	info.myExcludes = &the_excludes[excludeOffset];
180	<	info.myBonds = new Bond*[info.nBonds];
181	<	info.myBends = new Bend*[info.nBends];
182	<	info.myTorsions = new Torsion*[info.nTorsions];
178	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
179	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
180	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
181	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
182	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
183	>
184	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
185	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
186	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
187	>	molInfo.myBends = new Bend*[molInfo.nBends];
188	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
189
190	<	theBonds = new bond_pair[info.nBonds];
191	<	theBends = new bend_set[info.nBends];
192	<	theTorsions = new torsion_set[info.nTorsions];
190	>	theBonds = new bond_pair[molInfo.nBonds];
191	>	theBends = new bend_set[molInfo.nBends];
192	>	theTorsions = new torsion_set[molInfo.nTorsions];
193
194	<	// make the Atoms
194	>	// make the Atoms
195
196	<	for(j=0; j<info.nAtoms; j++){
744	<
745	<	currentAtom = comp_stamps[stampID]->getAtom( j );
746	<	if( currentAtom->haveOrientation() ){
196	>	for(j=0; j<molInfo.nAtoms; j++){
197
198	<	dAtom = new DirectionalAtom(j + atomOffset);
199	<	simnfo->n_oriented++;
200	<	info.myAtoms[j] = dAtom;
201	<
202	<	ux = currentAtom->getOrntX();
203	<	uy = currentAtom->getOrntY();
204	<	uz = currentAtom->getOrntZ();
205	<
206	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
207	<
208	<	u = sqrt( uSqr );
209	<	ux = ux / u;
210	<	uy = uy / u;
211	<	uz = uz / u;
212	<
213	<	dAtom->setSUx( ux );
214	<	dAtom->setSUy( uy );
215	<	dAtom->setSUz( uz );
216	<	}
217	<	else{
218	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
219	<	}
220	<	info.myAtoms[j]->setType( currentAtom->getType() );
198	>	currentAtom = comp_stamps[stampID]->getAtom( j );
199	>	if( currentAtom->haveOrientation() ){
200	>
201	>	dAtom = new DirectionalAtom( (j + atomOffset),
202	>	info[k].getConfiguration() );
203	>	info[k].n_oriented++;
204	>	molInfo.myAtoms[j] = dAtom;
205	>
206	>	ux = currentAtom->getOrntX();
207	>	uy = currentAtom->getOrntY();
208	>	uz = currentAtom->getOrntZ();
209	>
210	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
211	>
212	>	u = sqrt( uSqr );
213	>	ux = ux / u;
214	>	uy = uy / u;
215	>	uz = uz / u;
216	>
217	>	dAtom->setSUx( ux );
218	>	dAtom->setSUy( uy );
219	>	dAtom->setSUz( uz );
220	>	}
221	>	else{
222	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
223	>	info[k].getConfiguration() );
224	>	}
225	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
226
227		#ifdef IS_MPI
228
229	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
229	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
230
231		#endif // is_mpi
232	<	}
232	>	}
233
234		// make the bonds
235	<	for(j=0; j<info.nBonds; j++){
235	>	for(j=0; j<molInfo.nBonds; j++){
236
237	<	currentBond = comp_stamps[stampID]->getBond( j );
238	<	theBonds[j].a = currentBond->getA() + atomOffset;
239	<	theBonds[j].b = currentBond->getB() + atomOffset;
240	<
241	<	exI = theBonds[i].a;
242	<	exJ = theBonds[i].b;
243	<
244	<	// exclude_I must always be the smaller of the pair
245	<	if( exI > exJ ){
246	<	tempEx = exI;
247	<	exI = exJ;
248	<	exJ = tempEx;
249	<	}
237	>	currentBond = comp_stamps[stampID]->getBond( j );
238	>	theBonds[j].a = currentBond->getA() + atomOffset;
239	>	theBonds[j].b = currentBond->getB() + atomOffset;
240	>
241	>	exI = theBonds[j].a;
242	>	exJ = theBonds[j].b;
243	>
244	>	// exclude_I must always be the smaller of the pair
245	>	if( exI > exJ ){
246	>	tempEx = exI;
247	>	exI = exJ;
248	>	exJ = tempEx;
249	>	}
250		#ifdef IS_MPI
251	<	tempEx = exI;
252	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
253	<	tempEx = exJ;
254	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
255	<
256	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
251	>	tempEx = exI;
252	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
253	>	tempEx = exJ;
254	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
255	>
256	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
257		#else  // isn't MPI
258	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
259	<	#endif  //is_mpi
260	<	}
261	<	excludeOffset += info.nBonds;
262	<
808	<	//make the bends
809	<	for(j=0; j<info.nBends; j++){
258	>
259	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
260	>	#endif  //is_mpi
261	>	}
262	>	excludeOffset += molInfo.nBonds;
263
264	<	currentBend = comp_stamps[stampID]->getBend( j );
265	<	theBends[j].a = currentBend->getA() + atomOffset;
266	<	theBends[j].b = currentBend->getB() + atomOffset;
267	<	theBends[j].c = currentBend->getC() + atomOffset;
264	>	//make the bends
265	>	for(j=0; j<molInfo.nBends; j++){
266	>
267	>	currentBend = comp_stamps[stampID]->getBend( j );
268	>	theBends[j].a = currentBend->getA() + atomOffset;
269	>	theBends[j].b = currentBend->getB() + atomOffset;
270	>	theBends[j].c = currentBend->getC() + atomOffset;
271	>
272	>	if( currentBend->haveExtras() ){
273
274	<	if( currentBend->haveExtras() ){
275	<
276	<	extras = currentBend->getExtras();
277	<	current_extra = extras;
278	<
279	<	while( current_extra != NULL ){
280	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>	extras = currentBend->getExtras();
275	>	current_extra = extras;
276	>
277	>	while( current_extra != NULL ){
278	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
279	>
280	>	switch( current_extra->getType() ){
281
282	<	switch( current_extra->getType() ){
282	>	case 0:
283	>	theBends[j].ghost =
284	>	current_extra->getInt() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	case 1:
289	>	theBends[j].ghost =
290	>	(int)current_extra->getDouble() + atomOffset;
291	>	theBends[j].isGhost = 1;
292	>	break;
293	>
294	>	default:
295	>	sprintf( painCave.errMsg,
296	>	"SimSetup Error: ghostVectorSource was neither a "
297	>	"double nor an int.\n"
298	>	"-->Bend[%d] in %s\n",
299	>	j, comp_stamps[stampID]->getID() );
300	>	painCave.isFatal = 1;
301	>	simError();
302	>	}
303	>	}
304	>
305	>	else{
306
826	–	case 0:
827	–	theBends[j].ghost =
828	–	current_extra->getInt() + atomOffset;
829	–	theBends[j].isGhost = 1;
830	–	break;
831	–
832	–	case 1:
833	–	theBends[j].ghost =
834	–	(int)current_extra->getDouble() + atomOffset;
835	–	theBends[j].isGhost = 1;
836	–	break;
837	–
838	–	default:
307		sprintf( painCave.errMsg,
308	<	"SimSetup Error: ghostVectorSource was neither a "
309	<	"double nor an int.\n"
310	<	"-->Bend[%d] in %s\n",
308	>	"SimSetup Error: unhandled bend assignment:\n"
309	>	"    -->%s in Bend[%d] in %s\n",
310	>	current_extra->getlhs(),
311		j, comp_stamps[stampID]->getID() );
312		painCave.isFatal = 1;
313		simError();
314		}
847	–	}
848	–
849	–	else{
315
316	<	sprintf( painCave.errMsg,
852	<	"SimSetup Error: unhandled bend assignment:\n"
853	<	"    -->%s in Bend[%d] in %s\n",
854	<	current_extra->getlhs(),
855	<	j, comp_stamps[stampID]->getID() );
856	<	painCave.isFatal = 1;
857	<	simError();
316	>	current_extra = current_extra->getNext();
317		}
318	+	}
319	+
320	+	if( !theBends[j].isGhost ){
321
322	<	current_extra = current_extra->getNext();
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].c;
324		}
325	<	}
325	>	else{
326
327	<	if( !theBends[j].isGhost ){
328	<
329	<	exI = theBends[j].a;
867	<	exJ = theBends[j].c;
868	<	}
869	<	else{
327	>	exI = theBends[j].a;
328	>	exJ = theBends[j].b;
329	>	}
330
331	<	exI = theBends[j].a;
332	<	exJ = theBends[j].b;
333	<	}
334	<
335	<	// exclude_I must always be the smaller of the pair
336	<	if( exI > exJ ){
331	>	// exclude_I must always be the smaller of the pair
332	>	if( exI > exJ ){
333	>	tempEx = exI;
334	>	exI = exJ;
335	>	exJ = tempEx;
336	>	}
337	>	#ifdef IS_MPI
338		tempEx = exI;
339	<	exI = exJ;
340	<	exJ = tempEx;
339	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
340	>	tempEx = exJ;
341	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
342	>
343	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
344	>	#else  // isn't MPI
345	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
346	>	#endif  //is_mpi
347		}
348	<	#ifdef IS_MPI
882	<	tempEx = exI;
883	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
884	<	tempEx = exJ;
885	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
348	>	excludeOffset += molInfo.nBends;
349
350	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
350	>	for(j=0; j<molInfo.nTorsions; j++){
351	>
352	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
353	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
354	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
355	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
356	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
357	>
358	>	exI = theTorsions[j].a;
359	>	exJ = theTorsions[j].d;
360	>
361	>	// exclude_I must always be the smaller of the pair
362	>	if( exI > exJ ){
363	>	tempEx = exI;
364	>	exI = exJ;
365	>	exJ = tempEx;
366	>	}
367	>	#ifdef IS_MPI
368	>	tempEx = exI;
369	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
370	>	tempEx = exJ;
371	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
372	>
373	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
374		#else  // isn't MPI
375	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
375	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
376		#endif  //is_mpi
377	<	}
378	<	excludeOffset += info.nBends;
893	<
894	<	for(j=0; j<info.nTorsions; j++){
377	>	}
378	>	excludeOffset += molInfo.nTorsions;
379
896	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
897	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
898	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
899	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
900	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
380
381	<	exI = theTorsions[j].a;
382	<	exJ = theTorsions[j].d;
381	>	// send the arrays off to the forceField for init.
382	>
383	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
384	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
385	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
386	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
387	>
388	>
389	>	info[k].molecules[i].initialize( molInfo );
390
905	–	// exclude_I must always be the smaller of the pair
906	–	if( exI > exJ ){
907	–	tempEx = exI;
908	–	exI = exJ;
909	–	exJ = tempEx;
910	–	}
911	–	#ifdef IS_MPI
912	–	tempEx = exI;
913	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
914	–	tempEx = exJ;
915	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
391
392	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
393	<	#else  // isn't MPI
394	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
395	<	#endif  //is_mpi
392	>	atomOffset += molInfo.nAtoms;
393	>	delete[] theBonds;
394	>	delete[] theBends;
395	>	delete[] theTorsions;
396		}
922	–	excludeOffset += info.nTorsions;
923	–
924	–
925	–	// send the arrays off to the forceField for init.
926	–
927	–	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
928	–	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
929	–	the_ff->initializeBends( info.nBends, info.myBends, theBends );
930	–	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
931	–
932	–
933	–	the_molecules[i].initialize( info );
934	–	atomOffset += info.nAtoms;
935	–	delete[] theBonds;
936	–	delete[] theBends;
937	–	delete[] theTorsions;
397		}
398	<
398	>
399		#ifdef IS_MPI
400		sprintf( checkPointMsg, "all molecules initialized succesfully" );
401		MPIcheckPoint();
402		#endif // is_mpi
403	<
403	>
404		// clean up the forcefield
405	+
406		the_ff->calcRcut();
407		the_ff->cleanMe();
408	<
408	>
409		}
410
411		void SimSetup::initFromBass( void ){
#	Line 958 | Line 418 | void SimSetup::initFromBass( void ){
418		int n_extra;
419		int have_extra, done;
420
421	<	temp1 = (double)tot_nmol / 4.0;
421	>	double vel[3];
422	>	vel[0] = 0.0;
423	>	vel[1] = 0.0;
424	>	vel[2] = 0.0;
425	>
426	>	temp1 = (double)tot_nmol / 4.0;
427		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
428		temp3 = ceil( temp2 );
429
#	Line 967 | Line 432 | void SimSetup::initFromBass( void ){
432		have_extra =1;
433
434		n_cells = (int)temp3 - 1;
435	<	cellx = simnfo->box_x / temp3;
436	<	celly = simnfo->box_y / temp3;
437	<	cellz = simnfo->box_z / temp3;
435	>	cellx = info[0].boxL[0] / temp3;
436	>	celly = info[0].boxL[1] / temp3;
437	>	cellz = info[0].boxL[2] / temp3;
438		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
439		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
440		n_per_extra = (int)ceil( temp1 );
#	Line 984 | Line 449 | void SimSetup::initFromBass( void ){
449		}
450		else{
451		n_cells = (int)temp3;
452	<	cellx = simnfo->box_x / temp3;
453	<	celly = simnfo->box_y / temp3;
454	<	cellz = simnfo->box_z / temp3;
452	>	cellx = info[0].boxL[0] / temp3;
453	>	celly = info[0].boxL[1] / temp3;
454	>	cellz = info[0].boxL[2] / temp3;
455		}
456
457		current_mol = 0;
#	Line 1065 | Line 530 | void SimSetup::initFromBass( void ){
530		}
531		}
532
533	<
534	<	for( i=0; i<simnfo->n_atoms; i++ ){
1070	<	simnfo->atoms[i]->set_vx( 0.0 );
1071	<	simnfo->atoms[i]->set_vy( 0.0 );
1072	<	simnfo->atoms[i]->set_vz( 0.0 );
533	>	for( i=0; i<info[0].n_atoms; i++ ){
534	>	info[0].atoms[i]->setVel( vel );
535		}
536		}
537
#	Line 1079 | Line 541 | void SimSetup::makeElement( double x, double y, double
541		AtomStamp* current_atom;
542		DirectionalAtom* dAtom;
543		double rotMat[3][3];
544	+	double pos[3];
545
546		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
547
#	Line 1094 | Line 557 | void SimSetup::makeElement( double x, double y, double
557		painCave.isFatal = 1;
558		simError();
559		}
560	+
561	+	pos[0] = x + current_atom->getPosX();
562	+	pos[1] = y + current_atom->getPosY();
563	+	pos[2] = z + current_atom->getPosZ();
564	+
565	+	info[0].atoms[current_atom_ndx]->setPos( pos );
566
567	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1099	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1100	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
567	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
568
569	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
569	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
570
1104	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1105	–
571		rotMat[0][0] = 1.0;
572		rotMat[0][1] = 0.0;
573		rotMat[0][2] = 0.0;
#	Line 1128 | Line 593 | void SimSetup::makeElement( double x, double y, double
593
594		current_comp_mol = 0;
595		current_comp++;
596	+	}
597	+	}
598	+
599	+
600	+	void SimSetup::gatherInfo( void ){
601	+	int i,j,k;
602	+
603	+	ensembleCase = -1;
604	+	ffCase = -1;
605	+
606	+	// set the easy ones first
607	+
608	+	for( i=0; i<nInfo; i++){
609	+	info[i].target_temp = globals->getTargetTemp();
610	+	info[i].dt = globals->getDt();
611	+	info[i].run_time = globals->getRunTime();
612	+	}
613	+	n_components = globals->getNComponents();
614	+
615	+
616	+	// get the forceField
617	+
618	+	strcpy( force_field, globals->getForceField() );
619	+
620	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
621	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
622	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
623	+	else{
624	+	sprintf( painCave.errMsg,
625	+	"SimSetup Error. Unrecognized force field -> %s\n",
626	+	force_field );
627	+	painCave.isFatal = 1;
628	+	simError();
629	+	}
630	+
631	+	// get the ensemble
632	+
633	+	strcpy( ensemble, globals->getEnsemble() );
634	+
635	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
636	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
637	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
638	+	ensembleCase = NPTi_ENS;
639	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
640	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
641	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
642	+
643	+	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
644	+	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
645	+	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS"))
646	+	ensembleCase = NPTiZCONS_ENS;
647	+	else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
648	+	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
649	+	else if( !strcasecmp( ensemble, "NPTfmZCONS"))  ensembleCase = NPTfmZCONS_ENS;
650	+
651	+	else{
652	+	sprintf( painCave.errMsg,
653	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
654	+	"reverting to NVE for this simulation.\n",
655	+	ensemble );
656	+	painCave.isFatal = 0;
657	+	simError();
658	+	strcpy( ensemble, "NVE" );
659	+	ensembleCase = NVE_ENS;
660	+	}
661	+
662	+	for(i=0; i<nInfo; i++){
663	+
664	+	strcpy( info[i].ensemble, ensemble );
665	+
666	+	// get the mixing rule
667	+
668	+	strcpy( info[i].mixingRule, globals->getMixingRule() );
669	+	info[i].usePBC = globals->getPBC();
670	+	}
671	+
672	+	// get the components and calculate the tot_nMol and indvidual n_mol
673	+
674	+	the_components = globals->getComponents();
675	+	components_nmol = new int[n_components];
676	+
677	+
678	+	if( !globals->haveNMol() ){
679	+	// we don't have the total number of molecules, so we assume it is
680	+	// given in each component
681	+
682	+	tot_nmol = 0;
683	+	for( i=0; i<n_components; i++ ){
684	+
685	+	if( !the_components[i]->haveNMol() ){
686	+	// we have a problem
687	+	sprintf( painCave.errMsg,
688	+	"SimSetup Error. No global NMol or component NMol"
689	+	" given. Cannot calculate the number of atoms.\n" );
690	+	painCave.isFatal = 1;
691	+	simError();
692	+	}
693	+
694	+	tot_nmol += the_components[i]->getNMol();
695	+	components_nmol[i] = the_components[i]->getNMol();
696	+	}
697	+	}
698	+	else{
699	+	sprintf( painCave.errMsg,
700	+	"SimSetup error.\n"
701	+	"\tSorry, the ability to specify total"
702	+	" nMols and then give molfractions in the components\n"
703	+	"\tis not currently supported."
704	+	" Please give nMol in the components.\n" );
705	+	painCave.isFatal = 1;
706	+	simError();
707	+	}
708	+
709	+	// set the status, sample, and thermal kick times
710	+
711	+	for(i=0; i<nInfo; i++){
712	+
713	+	if( globals->haveSampleTime() ){
714	+	info[i].sampleTime = globals->getSampleTime();
715	+	info[i].statusTime = info[i].sampleTime;
716	+	info[i].thermalTime = info[i].sampleTime;
717	+	}
718	+	else{
719	+	info[i].sampleTime = globals->getRunTime();
720	+	info[i].statusTime = info[i].sampleTime;
721	+	info[i].thermalTime = info[i].sampleTime;
722	+	}
723	+
724	+	if( globals->haveStatusTime() ){
725	+	info[i].statusTime = globals->getStatusTime();
726	+	}
727	+
728	+	if( globals->haveThermalTime() ){
729	+	info[i].thermalTime = globals->getThermalTime();
730	+	}
731	+
732	+	// check for the temperature set flag
733	+
734	+	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
735	+
736	+	// get some of the tricky things that may still be in the globals
737	+
738	+	double boxVector[3];
739	+	if( globals->haveBox() ){
740	+	boxVector[0] = globals->getBox();
741	+	boxVector[1] = globals->getBox();
742	+	boxVector[2] = globals->getBox();
743	+
744	+	info[i].setBox( boxVector );
745	+	}
746	+	else if( globals->haveDensity() ){
747	+
748	+	double vol;
749	+	vol = (double)tot_nmol / globals->getDensity();
750	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
751	+	boxVector[1] = boxVector[0];
752	+	boxVector[2] = boxVector[0];
753	+
754	+	info[i].setBox( boxVector );
755		}
756	+	else{
757	+	if( !globals->haveBoxX() ){
758	+	sprintf( painCave.errMsg,
759	+	"SimSetup error, no periodic BoxX size given.\n" );
760	+	painCave.isFatal = 1;
761	+	simError();
762	+	}
763	+	boxVector[0] = globals->getBoxX();
764	+
765	+	if( !globals->haveBoxY() ){
766	+	sprintf( painCave.errMsg,
767	+	"SimSetup error, no periodic BoxY size given.\n" );
768	+	painCave.isFatal = 1;
769	+	simError();
770	+	}
771	+	boxVector[1] = globals->getBoxY();
772	+
773	+	if( !globals->haveBoxZ() ){
774	+	sprintf( painCave.errMsg,
775	+	"SimSetup error, no periodic BoxZ size given.\n" );
776	+	painCave.isFatal = 1;
777	+	simError();
778	+	}
779	+	boxVector[2] = globals->getBoxZ();
780	+
781	+	info[i].setBox( boxVector );
782	+	}
783	+
784	+	}
785	+
786	+	#ifdef IS_MPI
787	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
788	+	MPIcheckPoint();
789	+	#endif // is_mpi
790	+
791		}
792	+
793	+
794	+	void SimSetup::finalInfoCheck( void ){
795	+	int index;
796	+	int usesDipoles;
797	+	int i;
798	+
799	+	for(i=0; i<nInfo; i++){
800	+	// check electrostatic parameters
801	+
802	+	index = 0;
803	+	usesDipoles = 0;
804	+	while( (index < info[i].n_atoms) && !usesDipoles ){
805	+	usesDipoles = (info[i].atoms[index])->hasDipole();
806	+	index++;
807	+	}
808	+
809	+	#ifdef IS_MPI
810	+	int myUse = usesDipoles;
811	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
812	+	#endif //is_mpi
813	+
814	+	double theEcr, theEst;
815	+
816	+	if (globals->getUseRF() ) {
817	+	info[i].useReactionField = 1;
818	+
819	+	if( !globals->haveECR() ){
820	+	sprintf( painCave.errMsg,
821	+	"SimSetup Warning: using default value of 1/2 the smallest "
822	+	"box length for the electrostaticCutoffRadius.\n"
823	+	"I hope you have a very fast processor!\n");
824	+	painCave.isFatal = 0;
825	+	simError();
826	+	double smallest;
827	+	smallest = info[i].boxL[0];
828	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
829	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
830	+	theEcr = 0.5 * smallest;
831	+	} else {
832	+	theEcr = globals->getECR();
833	+	}
834	+
835	+	if( !globals->haveEST() ){
836	+	sprintf( painCave.errMsg,
837	+	"SimSetup Warning: using default value of 0.05 * the "
838	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
839	+	);
840	+	painCave.isFatal = 0;
841	+	simError();
842	+	theEst = 0.05 * theEcr;
843	+	} else {
844	+	theEst= globals->getEST();
845	+	}
846	+
847	+	info[i].setEcr( theEcr, theEst );
848	+
849	+	if(!globals->haveDielectric() ){
850	+	sprintf( painCave.errMsg,
851	+	"SimSetup Error: You are trying to use Reaction Field without"
852	+	"setting a dielectric constant!\n"
853	+	);
854	+	painCave.isFatal = 1;
855	+	simError();
856	+	}
857	+	info[i].dielectric = globals->getDielectric();
858	+	}
859	+	else {
860	+	if (usesDipoles) {
861	+
862	+	if( !globals->haveECR() ){
863	+	sprintf( painCave.errMsg,
864	+	"SimSetup Warning: using default value of 1/2 the smallest "
865	+	"box length for the electrostaticCutoffRadius.\n"
866	+	"I hope you have a very fast processor!\n");
867	+	painCave.isFatal = 0;
868	+	simError();
869	+	double smallest;
870	+	smallest = info[i].boxL[0];
871	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
872	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
873	+	theEcr = 0.5 * smallest;
874	+	} else {
875	+	theEcr = globals->getECR();
876	+	}
877	+
878	+	if( !globals->haveEST() ){
879	+	sprintf( painCave.errMsg,
880	+	"SimSetup Warning: using default value of 0.05 * the "
881	+	"electrostaticCutoffRadius for the "
882	+	"electrostaticSkinThickness\n"
883	+	);
884	+	painCave.isFatal = 0;
885	+	simError();
886	+	theEst = 0.05 * theEcr;
887	+	} else {
888	+	theEst= globals->getEST();
889	+	}
890	+
891	+	info[i].setEcr( theEcr, theEst );
892	+	}
893	+	}
894	+	}
895	+
896	+	#ifdef IS_MPI
897	+	strcpy( checkPointMsg, "post processing checks out" );
898	+	MPIcheckPoint();
899	+	#endif // is_mpi
900	+
901	+	}
902	+
903	+	void SimSetup::initSystemCoords( void ){
904	+	int i;
905	+
906	+	std::cerr << "Setting atom Coords\n";
907	+
908	+	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
909	+
910	+	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
911	+
912	+	if( globals->haveInitialConfig() ){
913	+
914	+	InitializeFromFile* fileInit;
915	+	#ifdef IS_MPI // is_mpi
916	+	if( worldRank == 0 ){
917	+	#endif //is_mpi
918	+	fileInit = new InitializeFromFile( globals->getInitialConfig() );
919	+	#ifdef IS_MPI
920	+	}else fileInit = new InitializeFromFile( NULL );
921	+	#endif
922	+	fileInit->readInit( info ); // default velocities on
923	+
924	+	delete fileInit;
925	+	}
926	+	else{
927	+
928	+	#ifdef IS_MPI
929	+
930	+	// no init from bass
931	+
932	+	sprintf( painCave.errMsg,
933	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
934	+	painCave.isFatal;
935	+	simError();
936	+
937	+	#else
938	+
939	+	initFromBass();
940	+
941	+
942	+	#endif
943	+	}
944	+
945	+	#ifdef IS_MPI
946	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
947	+	MPIcheckPoint();
948	+	#endif // is_mpi
949	+
950	+	}
951	+
952	+
953	+	void SimSetup::makeOutNames( void ){
954	+
955	+	int k;
956	+
957	+
958	+	for(k=0; k<nInfo; k++){
959	+
960	+	#ifdef IS_MPI
961	+	if( worldRank == 0 ){
962	+	#endif // is_mpi
963	+
964	+	if( globals->haveFinalConfig() ){
965	+	strcpy( info[k].finalName, globals->getFinalConfig() );
966	+	}
967	+	else{
968	+	strcpy( info[k].finalName, inFileName );
969	+	char* endTest;
970	+	int nameLength = strlen( info[k].finalName );
971	+	endTest = &(info[k].finalName[nameLength - 5]);
972	+	if( !strcmp( endTest, ".bass" ) ){
973	+	strcpy( endTest, ".eor" );
974	+	}
975	+	else if( !strcmp( endTest, ".BASS" ) ){
976	+	strcpy( endTest, ".eor" );
977	+	}
978	+	else{
979	+	endTest = &(info[k].finalName[nameLength - 4]);
980	+	if( !strcmp( endTest, ".bss" ) ){
981	+	strcpy( endTest, ".eor" );
982	+	}
983	+	else if( !strcmp( endTest, ".mdl" ) ){
984	+	strcpy( endTest, ".eor" );
985	+	}
986	+	else{
987	+	strcat( info[k].finalName, ".eor" );
988	+	}
989	+	}
990	+	}
991	+
992	+	// make the sample and status out names
993	+
994	+	strcpy( info[k].sampleName, inFileName );
995	+	char* endTest;
996	+	int nameLength = strlen( info[k].sampleName );
997	+	endTest = &(info[k].sampleName[nameLength - 5]);
998	+	if( !strcmp( endTest, ".bass" ) ){
999	+	strcpy( endTest, ".dump" );
1000	+	}
1001	+	else if( !strcmp( endTest, ".BASS" ) ){
1002	+	strcpy( endTest, ".dump" );
1003	+	}
1004	+	else{
1005	+	endTest = &(info[k].sampleName[nameLength - 4]);
1006	+	if( !strcmp( endTest, ".bss" ) ){
1007	+	strcpy( endTest, ".dump" );
1008	+	}
1009	+	else if( !strcmp( endTest, ".mdl" ) ){
1010	+	strcpy( endTest, ".dump" );
1011	+	}
1012	+	else{
1013	+	strcat( info[k].sampleName, ".dump" );
1014	+	}
1015	+	}
1016	+
1017	+	strcpy( info[k].statusName, inFileName );
1018	+	nameLength = strlen( info[k].statusName );
1019	+	endTest = &(info[k].statusName[nameLength - 5]);
1020	+	if( !strcmp( endTest, ".bass" ) ){
1021	+	strcpy( endTest, ".stat" );
1022	+	}
1023	+	else if( !strcmp( endTest, ".BASS" ) ){
1024	+	strcpy( endTest, ".stat" );
1025	+	}
1026	+	else{
1027	+	endTest = &(info[k].statusName[nameLength - 4]);
1028	+	if( !strcmp( endTest, ".bss" ) ){
1029	+	strcpy( endTest, ".stat" );
1030	+	}
1031	+	else if( !strcmp( endTest, ".mdl" ) ){
1032	+	strcpy( endTest, ".stat" );
1033	+	}
1034	+	else{
1035	+	strcat( info[k].statusName, ".stat" );
1036	+	}
1037	+	}
1038	+
1039	+	#ifdef IS_MPI
1040	+	}
1041	+	#endif // is_mpi
1042	+	}
1043	+	}
1044	+
1045	+
1046	+	void SimSetup::sysObjectsCreation( void ){
1047	+
1048	+	int i,k;
1049	+
1050	+	// create the forceField
1051	+
1052	+	createFF();
1053	+
1054	+	// extract componentList
1055	+
1056	+	compList();
1057	+
1058	+	// calc the number of atoms, bond, bends, and torsions
1059	+
1060	+	calcSysValues();
1061	+
1062	+	#ifdef IS_MPI
1063	+	// divide the molecules among the processors
1064	+
1065	+	mpiMolDivide();
1066	+	#endif //is_mpi
1067	+
1068	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1069	+
1070	+	makeSysArrays();
1071	+
1072	+	// make and initialize the molecules (all but atomic coordinates)
1073	+
1074	+	makeMolecules();
1075	+
1076	+	for(k=0; k<nInfo; k++){
1077	+	info[k].identArray = new int[info[k].n_atoms];
1078	+	for(i=0; i<info[k].n_atoms; i++){
1079	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1080	+	}
1081	+	}
1082	+	}
1083	+
1084	+
1085	+	void SimSetup::createFF( void ){
1086	+
1087	+	switch( ffCase ){
1088	+
1089	+	case FF_DUFF:
1090	+	the_ff = new DUFF();
1091	+	break;
1092	+
1093	+	case FF_LJ:
1094	+	the_ff = new LJFF();
1095	+	break;
1096	+
1097	+	case FF_EAM:
1098	+	the_ff = new EAM_FF();
1099	+	break;
1100	+
1101	+	default:
1102	+	sprintf( painCave.errMsg,
1103	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1104	+	painCave.isFatal = 1;
1105	+	simError();
1106	+	}
1107	+
1108	+	#ifdef IS_MPI
1109	+	strcpy( checkPointMsg, "ForceField creation successful" );
1110	+	MPIcheckPoint();
1111	+	#endif // is_mpi
1112	+
1113	+	}
1114	+
1115	+
1116	+	void SimSetup::compList( void ){
1117	+
1118	+	int i;
1119	+	char* id;
1120	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1121	+	LinkedMolStamp* currentStamp = NULL;
1122	+	comp_stamps = new MoleculeStamp*[n_components];
1123	+
1124	+	// make an array of molecule stamps that match the components used.
1125	+	// also extract the used stamps out into a separate linked list
1126	+
1127	+	for(i=0; i<nInfo; i++){
1128	+	info[i].nComponents = n_components;
1129	+	info[i].componentsNmol = components_nmol;
1130	+	info[i].compStamps = comp_stamps;
1131	+	info[i].headStamp = headStamp;
1132	+	}
1133	+
1134	+
1135	+	for( i=0; i<n_components; i++ ){
1136	+
1137	+	id = the_components[i]->getType();
1138	+	comp_stamps[i] = NULL;
1139	+
1140	+	// check to make sure the component isn't already in the list
1141	+
1142	+	comp_stamps[i] = headStamp->match( id );
1143	+	if( comp_stamps[i] == NULL ){
1144	+
1145	+	// extract the component from the list;
1146	+
1147	+	currentStamp = stamps->extractMolStamp( id );
1148	+	if( currentStamp == NULL ){
1149	+	sprintf( painCave.errMsg,
1150	+	"SimSetup error: Component \"%s\" was not found in the "
1151	+	"list of declared molecules\n",
1152	+	id );
1153	+	painCave.isFatal = 1;
1154	+	simError();
1155	+	}
1156	+
1157	+	headStamp->add( currentStamp );
1158	+	comp_stamps[i] = headStamp->match( id );
1159	+	}
1160	+	}
1161	+
1162	+	#ifdef IS_MPI
1163	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1164	+	MPIcheckPoint();
1165	+	#endif // is_mpi
1166	+
1167	+
1168	+	}
1169	+
1170	+	void SimSetup::calcSysValues( void ){
1171	+	int i, j, k;
1172	+
1173	+	int *molMembershipArray;
1174	+
1175	+	tot_atoms = 0;
1176	+	tot_bonds = 0;
1177	+	tot_bends = 0;
1178	+	tot_torsions = 0;
1179	+	for( i=0; i<n_components; i++ ){
1180	+
1181	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1182	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1183	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1184	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1185	+	}
1186	+
1187	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1188	+	molMembershipArray = new int[tot_atoms];
1189	+
1190	+	for(i=0; i<nInfo; i++){
1191	+	info[i].n_atoms = tot_atoms;
1192	+	info[i].n_bonds = tot_bonds;
1193	+	info[i].n_bends = tot_bends;
1194	+	info[i].n_torsions = tot_torsions;
1195	+	info[i].n_SRI = tot_SRI;
1196	+	info[i].n_mol = tot_nmol;
1197	+
1198	+	info[i].molMembershipArray = molMembershipArray;
1199	+	}
1200	+	}
1201	+
1202	+	#ifdef IS_MPI
1203	+
1204	+	void SimSetup::mpiMolDivide( void ){
1205	+
1206	+	int i, j, k;
1207	+	int localMol, allMol;
1208	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1209	+
1210	+	mpiSim = new mpiSimulation( info );
1211	+
1212	+	globalIndex = mpiSim->divideLabor();
1213	+
1214	+	// set up the local variables
1215	+
1216	+	mol2proc = mpiSim->getMolToProcMap();
1217	+	molCompType = mpiSim->getMolComponentType();
1218	+
1219	+	allMol = 0;
1220	+	localMol = 0;
1221	+	local_atoms = 0;
1222	+	local_bonds = 0;
1223	+	local_bends = 0;
1224	+	local_torsions = 0;
1225	+	globalAtomIndex = 0;
1226	+
1227	+
1228	+	for( i=0; i<n_components; i++ ){
1229	+
1230	+	for( j=0; j<components_nmol[i]; j++ ){
1231	+
1232	+	if( mol2proc[allMol] == worldRank ){
1233	+
1234	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1235	+	local_bonds +=    comp_stamps[i]->getNBonds();
1236	+	local_bends +=    comp_stamps[i]->getNBends();
1237	+	local_torsions += comp_stamps[i]->getNTorsions();
1238	+	localMol++;
1239	+	}
1240	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1241	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1242	+	globalAtomIndex++;
1243	+	}
1244	+
1245	+	allMol++;
1246	+	}
1247	+	}
1248	+	local_SRI = local_bonds + local_bends + local_torsions;
1249	+
1250	+	info[0].n_atoms = mpiSim->getMyNlocal();
1251	+
1252	+	if( local_atoms != info[0].n_atoms ){
1253	+	sprintf( painCave.errMsg,
1254	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1255	+	" localAtom (%d) are not equal.\n",
1256	+	info[0].n_atoms,
1257	+	local_atoms );
1258	+	painCave.isFatal = 1;
1259	+	simError();
1260	+	}
1261	+
1262	+	info[0].n_bonds = local_bonds;
1263	+	info[0].n_bends = local_bends;
1264	+	info[0].n_torsions = local_torsions;
1265	+	info[0].n_SRI = local_SRI;
1266	+	info[0].n_mol = localMol;
1267	+
1268	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1269	+	MPIcheckPoint();
1270	+	}
1271	+
1272	+	#endif // is_mpi
1273	+
1274	+
1275	+	void SimSetup::makeSysArrays( void ){
1276	+	int i, j, k, l;
1277	+
1278	+	Atom** the_atoms;
1279	+	Molecule* the_molecules;
1280	+	Exclude** the_excludes;
1281	+
1282	+
1283	+	for(l=0; l<nInfo; l++){
1284	+
1285	+	// create the atom and short range interaction arrays
1286	+
1287	+	the_atoms = new Atom*[info[l].n_atoms];
1288	+	the_molecules = new Molecule[info[l].n_mol];
1289	+	int molIndex;
1290	+
1291	+	// initialize the molecule's stampID's
1292	+
1293	+	#ifdef IS_MPI
1294	+
1295	+
1296	+	molIndex = 0;
1297	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1298	+
1299	+	if(mol2proc[i] == worldRank ){
1300	+	the_molecules[molIndex].setStampID( molCompType[i] );
1301	+	the_molecules[molIndex].setMyIndex( molIndex );
1302	+	the_molecules[molIndex].setGlobalIndex( i );
1303	+	molIndex++;
1304	+	}
1305	+	}
1306	+
1307	+	#else // is_mpi
1308	+
1309	+	molIndex = 0;
1310	+	globalAtomIndex = 0;
1311	+	for(i=0; i<n_components; i++){
1312	+	for(j=0; j<components_nmol[i]; j++ ){
1313	+	the_molecules[molIndex].setStampID( i );
1314	+	the_molecules[molIndex].setMyIndex( molIndex );
1315	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1316	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1317	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1318	+	globalAtomIndex++;
1319	+	}
1320	+	molIndex++;
1321	+	}
1322	+	}
1323	+
1324	+
1325	+	#endif // is_mpi
1326	+
1327	+
1328	+	if( info[l].n_SRI ){
1329	+
1330	+	Exclude::createArray(info[l].n_SRI);
1331	+	the_excludes = new Exclude*[info[l].n_SRI];
1332	+	for( int ex=0; ex<info[l].n_SRI; ex++){
1333	+	the_excludes[ex] = new Exclude(ex);
1334	+	}
1335	+	info[l].globalExcludes = new int;
1336	+	info[l].n_exclude = info[l].n_SRI;
1337	+	}
1338	+	else{
1339	+
1340	+	Exclude::createArray( 1 );
1341	+	the_excludes = new Exclude*;
1342	+	the_excludes[0] = new Exclude(0);
1343	+	the_excludes[0]->setPair( 0,0 );
1344	+	info[l].globalExcludes = new int;
1345	+	info[l].globalExcludes[0] = 0;
1346	+	info[l].n_exclude = 0;
1347	+	}
1348	+
1349	+	// set the arrays into the SimInfo object
1350	+
1351	+	info[l].atoms = the_atoms;
1352	+	info[l].molecules = the_molecules;
1353	+	info[l].nGlobalExcludes = 0;
1354	+	info[l].excludes = the_excludes;
1355	+
1356	+	the_ff->setSimInfo( info );
1357	+
1358	+	}
1359	+	}
1360	+
1361	+	void SimSetup::makeIntegrator( void ){
1362	+
1363	+	int k;
1364	+
1365	+	NVT<RealIntegrator>*  myNVT = NULL;
1366	+	NPTi<RealIntegrator>* myNPTi = NULL;
1367	+	NPTf<RealIntegrator>* myNPTf = NULL;
1368	+	NPTim<RealIntegrator>* myNPTim = NULL;
1369	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1370	+	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1371	+	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1372	+	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1373	+	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1374	+	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1375	+	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1376	+
1377	+	for(k=0; k<nInfo; k++){
1378	+
1379	+	switch( ensembleCase ){
1380	+
1381	+	case NVE_ENS:
1382	+	new NVE<RealIntegrator>( &(info[k]), the_ff );
1383	+	break;
1384	+
1385	+	case NVT_ENS:
1386	+	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1387	+	myNVT->setTargetTemp(globals->getTargetTemp());
1388	+
1389	+	if (globals->haveTauThermostat())
1390	+	myNVT->setTauThermostat(globals->getTauThermostat());
1391	+
1392	+	else {
1393	+	sprintf( painCave.errMsg,
1394	+	"SimSetup error: If you use the NVT\n"
1395	+	"    ensemble, you must set tauThermostat.\n");
1396	+	painCave.isFatal = 1;
1397	+	simError();
1398	+	}
1399	+	break;
1400	+
1401	+	case NPTi_ENS:
1402	+	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1404	+
1405	+	if (globals->haveTargetPressure())
1406	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	+	else {
1408	+	sprintf( painCave.errMsg,
1409	+	"SimSetup error: If you use a constant pressure\n"
1410	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	+	painCave.isFatal = 1;
1412	+	simError();
1413	+	}
1414	+
1415	+	if( globals->haveTauThermostat() )
1416	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	+	else{
1418	+	sprintf( painCave.errMsg,
1419	+	"SimSetup error: If you use an NPT\n"
1420	+	"    ensemble, you must set tauThermostat.\n");
1421	+	painCave.isFatal = 1;
1422	+	simError();
1423	+	}
1424	+
1425	+	if( globals->haveTauBarostat() )
1426	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	+	else{
1428	+	sprintf( painCave.errMsg,
1429	+	"SimSetup error: If you use an NPT\n"
1430	+	"    ensemble, you must set tauBarostat.\n");
1431	+	painCave.isFatal = 1;
1432	+	simError();
1433	+	}
1434	+	break;
1435	+
1436	+	case NPTf_ENS:
1437	+	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1438	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1439	+
1440	+	if (globals->haveTargetPressure())
1441	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	+	else {
1443	+	sprintf( painCave.errMsg,
1444	+	"SimSetup error: If you use a constant pressure\n"
1445	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1446	+	painCave.isFatal = 1;
1447	+	simError();
1448	+	}
1449	+
1450	+	if( globals->haveTauThermostat() )
1451	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1452	+	else{
1453	+	sprintf( painCave.errMsg,
1454	+	"SimSetup error: If you use an NPT\n"
1455	+	"    ensemble, you must set tauThermostat.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+
1460	+	if( globals->haveTauBarostat() )
1461	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1462	+	else{
1463	+	sprintf( painCave.errMsg,
1464	+	"SimSetup error: If you use an NPT\n"
1465	+	"    ensemble, you must set tauBarostat.\n");
1466	+	painCave.isFatal = 1;
1467	+	simError();
1468	+	}
1469	+	break;
1470	+
1471	+	case NPTim_ENS:
1472	+	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1473	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1474	+
1475	+	if (globals->haveTargetPressure())
1476	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1477	+	else {
1478	+	sprintf( painCave.errMsg,
1479	+	"SimSetup error: If you use a constant pressure\n"
1480	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1481	+	painCave.isFatal = 1;
1482	+	simError();
1483	+	}
1484	+
1485	+	if( globals->haveTauThermostat() )
1486	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1487	+	else{
1488	+	sprintf( painCave.errMsg,
1489	+	"SimSetup error: If you use an NPT\n"
1490	+	"    ensemble, you must set tauThermostat.\n");
1491	+	painCave.isFatal = 1;
1492	+	simError();
1493	+	}
1494	+
1495	+	if( globals->haveTauBarostat() )
1496	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1497	+	else{
1498	+	sprintf( painCave.errMsg,
1499	+	"SimSetup error: If you use an NPT\n"
1500	+	"    ensemble, you must set tauBarostat.\n");
1501	+	painCave.isFatal = 1;
1502	+	simError();
1503	+	}
1504	+	break;
1505	+
1506	+	case NPTfm_ENS:
1507	+	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1508	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1509	+
1510	+	if (globals->haveTargetPressure())
1511	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1512	+	else {
1513	+	sprintf( painCave.errMsg,
1514	+	"SimSetup error: If you use a constant pressure\n"
1515	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1516	+	painCave.isFatal = 1;
1517	+	simError();
1518	+	}
1519	+
1520	+	if( globals->haveTauThermostat() )
1521	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1522	+	else{
1523	+	sprintf( painCave.errMsg,
1524	+	"SimSetup error: If you use an NPT\n"
1525	+	"    ensemble, you must set tauThermostat.\n");
1526	+	painCave.isFatal = 1;
1527	+	simError();
1528	+	}
1529	+
1530	+	if( globals->haveTauBarostat() )
1531	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1532	+	else{
1533	+	sprintf( painCave.errMsg,
1534	+	"SimSetup error: If you use an NPT\n"
1535	+	"    ensemble, you must set tauBarostat.\n");
1536	+	painCave.isFatal = 1;
1537	+	simError();
1538	+	}
1539	+	break;
1540	+
1541	+	case NVEZCONS_ENS:
1542	+
1543	+
1544	+	//setup index of z-constraint molecules, z-constraint sampel time
1545	+	//and z-constraint force output name. These parameter should be known
1546	+	//before constructing the z-constraint integrator
1547	+	setupZConstraint();
1548	+
1549	+	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1550	+
1551	+	break;
1552	+
1553	+
1554	+	case NVTZCONS_ENS:
1555	+
1556	+	setupZConstraint();
1557	+
1558	+	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1559	+	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1560	+
1561	+	if (globals->haveTauThermostat())
1562	+	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1563	+
1564	+	else {
1565	+	sprintf( painCave.errMsg,
1566	+	"SimSetup error: If you use the NVT\n"
1567	+	"    ensemble, you must set tauThermostat.\n");
1568	+	painCave.isFatal = 1;
1569	+	simError();
1570	+	}
1571	+	break;
1572	+
1573	+	case NPTiZCONS_ENS:
1574	+
1575	+	setupZConstraint();
1576	+
1577	+	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1578	+	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1579	+
1580	+	if (globals->haveTargetPressure())
1581	+	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1582	+	else {
1583	+	sprintf( painCave.errMsg,
1584	+	"SimSetup error: If you use a constant pressure\n"
1585	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1586	+	painCave.isFatal = 1;
1587	+	simError();
1588	+	}
1589	+
1590	+	if( globals->haveTauThermostat() )
1591	+	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1592	+	else{
1593	+	sprintf( painCave.errMsg,
1594	+	"SimSetup error: If you use an NPT\n"
1595	+	"    ensemble, you must set tauThermostat.\n");
1596	+	painCave.isFatal = 1;
1597	+	simError();
1598	+	}
1599	+
1600	+	if( globals->haveTauBarostat() )
1601	+	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1602	+	else{
1603	+	sprintf( painCave.errMsg,
1604	+	"SimSetup error: If you use an NPT\n"
1605	+	"    ensemble, you must set tauBarostat.\n");
1606	+	painCave.isFatal = 1;
1607	+	simError();
1608	+	}
1609	+
1610	+	break;
1611	+
1612	+	case NPTfZCONS_ENS:
1613	+
1614	+	setupZConstraint();
1615	+
1616	+	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1617	+	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1618	+
1619	+	if (globals->haveTargetPressure())
1620	+	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1621	+	else {
1622	+	sprintf( painCave.errMsg,
1623	+	"SimSetup error: If you use a constant pressure\n"
1624	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1625	+	painCave.isFatal = 1;
1626	+	simError();
1627	+	}
1628	+
1629	+	if( globals->haveTauThermostat() )
1630	+	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1631	+	else{
1632	+	sprintf( painCave.errMsg,
1633	+	"SimSetup error: If you use an NPT\n"
1634	+	"    ensemble, you must set tauThermostat.\n");
1635	+	painCave.isFatal = 1;
1636	+	simError();
1637	+	}
1638	+
1639	+	if( globals->haveTauBarostat() )
1640	+	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1641	+	else{
1642	+	sprintf( painCave.errMsg,
1643	+	"SimSetup error: If you use an NPT\n"
1644	+	"    ensemble, you must set tauBarostat.\n");
1645	+	painCave.isFatal = 1;
1646	+	simError();
1647	+	}
1648	+
1649	+	break;
1650	+
1651	+	case NPTimZCONS_ENS:
1652	+
1653	+	setupZConstraint();
1654	+
1655	+	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1656	+	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1657	+
1658	+	if (globals->haveTargetPressure())
1659	+	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1660	+	else {
1661	+	sprintf( painCave.errMsg,
1662	+	"SimSetup error: If you use a constant pressure\n"
1663	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1664	+	painCave.isFatal = 1;
1665	+	simError();
1666	+	}
1667	+
1668	+	if( globals->haveTauThermostat() )
1669	+	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1670	+	else{
1671	+	sprintf( painCave.errMsg,
1672	+	"SimSetup error: If you use an NPT\n"
1673	+	"    ensemble, you must set tauThermostat.\n");
1674	+	painCave.isFatal = 1;
1675	+	simError();
1676	+	}
1677	+
1678	+	if( globals->haveTauBarostat() )
1679	+	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1680	+	else{
1681	+	sprintf( painCave.errMsg,
1682	+	"SimSetup error: If you use an NPT\n"
1683	+	"    ensemble, you must set tauBarostat.\n");
1684	+	painCave.isFatal = 1;
1685	+	simError();
1686	+	}
1687	+
1688	+	break;
1689	+
1690	+	case NPTfmZCONS_ENS:
1691	+
1692	+	setupZConstraint();
1693	+
1694	+	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1695	+	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1696	+
1697	+	if (globals->haveTargetPressure())
1698	+	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1699	+	else {
1700	+	sprintf( painCave.errMsg,
1701	+	"SimSetup error: If you use a constant pressure\n"
1702	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1703	+	painCave.isFatal = 1;
1704	+	simError();
1705	+	}
1706	+
1707	+	if( globals->haveTauThermostat() )
1708	+	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1709	+	else{
1710	+	sprintf( painCave.errMsg,
1711	+	"SimSetup error: If you use an NPT\n"
1712	+	"    ensemble, you must set tauThermostat.\n");
1713	+	painCave.isFatal = 1;
1714	+	simError();
1715	+	}
1716	+
1717	+	if( globals->haveTauBarostat() )
1718	+	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1719	+	else{
1720	+	sprintf( painCave.errMsg,
1721	+	"SimSetup error: If you use an NPT\n"
1722	+	"    ensemble, you must set tauBarostat.\n");
1723	+	painCave.isFatal = 1;
1724	+	simError();
1725	+	}
1726	+	break;
1727	+
1728	+
1729	+
1730	+	default:
1731	+	sprintf( painCave.errMsg,
1732	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1733	+	painCave.isFatal = 1;
1734	+	simError();
1735	+	}
1736	+	}
1737	+	}
1738	+
1739	+	void SimSetup::initFortran( void ){
1740	+
1741	+	info[0].refreshSim();
1742	+
1743	+	if( !strcmp( info[0].mixingRule, "standard") ){
1744	+	the_ff->initForceField( LB_MIXING_RULE );
1745	+	}
1746	+	else if( !strcmp( info[0].mixingRule, "explicit") ){
1747	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1748	+	}
1749	+	else{
1750	+	sprintf( painCave.errMsg,
1751	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1752	+	info[0].mixingRule );
1753	+	painCave.isFatal = 1;
1754	+	simError();
1755	+	}
1756	+
1757	+
1758	+	#ifdef IS_MPI
1759	+	strcpy( checkPointMsg,
1760	+	"Successfully intialized the mixingRule for Fortran." );
1761	+	MPIcheckPoint();
1762	+	#endif // is_mpi
1763	+
1764	+	}
1765	+
1766	+	void SimSetup::setupZConstraint()
1767	+	{
1768	+	int k;
1769	+
1770	+	for(k=0; k<nInfo; k++){
1771	+
1772	+	if(globals->haveZConsTime()){
1773	+
1774	+	//add sample time of z-constraint  into SimInfo's property list
1775	+	DoubleData* zconsTimeProp = new DoubleData();
1776	+	zconsTimeProp->setID("zconstime");
1777	+	zconsTimeProp->setData(globals->getZConsTime());
1778	+	info[k].addProperty(zconsTimeProp);
1779	+	}
1780	+	else{
1781	+	sprintf( painCave.errMsg,
1782	+	"ZConstraint error: If you use an ZConstraint\n"
1783	+	" , you must set sample time.\n");
1784	+	painCave.isFatal = 1;
1785	+	simError();
1786	+	}
1787	+
1788	+	if(globals->haveIndexOfAllZConsMols()){
1789	+
1790	+	//add index of z-constraint molecules into SimInfo's property list
1791	+	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1792	+
1793	+	//sort the index
1794	+	sort(tempIndex.begin(), tempIndex.end());
1795	+
1796	+	IndexData* zconsIndex = new IndexData();
1797	+	zconsIndex->setID("zconsindex");
1798	+	zconsIndex->setIndexData(tempIndex);
1799	+	info[k].addProperty(zconsIndex);
1800	+	}
1801	+	else{
1802	+	sprintf( painCave.errMsg,
1803	+	"SimSetup error: If you use an ZConstraint\n"
1804	+	" , you must set index of z-constraint molecules.\n");
1805	+	painCave.isFatal = 1;
1806	+	simError();
1807	+
1808	+	}
1809	+
1810	+	//Determine the name of ouput file and add it into SimInfo's property list
1811	+	//Be careful, do not use inFileName, since it is a pointer which
1812	+	//point to a string at master node, and slave nodes do not contain that string
1813	+
1814	+	string zconsOutput(info[k].finalName);
1815	+
1816	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1817	+
1818	+	StringData* zconsFilename = new StringData();
1819	+	zconsFilename->setID("zconsfilename");
1820	+	zconsFilename->setData(zconsOutput);
1821	+
1822	+	info[k].addProperty(zconsFilename);
1823	+	}
1824	+	}

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