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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 422 by mmeineke, Thu Mar 27 19:21:42 2003 UTC vs.
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC

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

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