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

Comparing:
branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 614 by mmeineke, Tue Jul 15 17:57:04 2003 UTC

#	Line 12 | Line 12
12		#include "mpiSimulation.hpp"
13		#endif
14
15	+	// some defines for ensemble and Forcefield  cases
16	+
17	+	#define NVE_ENS   0
18	+	#define NVT_ENS   1
19	+	#define NPTi_ENS  2
20	+	#define NPTf_ENS  3
21	+	#define NPTim_ENS 4
22	+	#define NPTfm_ENS 5
23	+
24	+
25	+	#define FF_DUFF 0
26	+	#define FF_LJ   1
27	+
28	+
29		SimSetup::SimSetup(){
30		stamps = new MakeStamps();
31		globals = new Globals();
#	Line 66 | Line 80 | void SimSetup::createSim( void ){
80
81		MakeStamps *the_stamps;
82		Globals* the_globals;
83	<	int i, j;
83	>	int i, j, k, globalAtomIndex;
84	>
85	>	// gather all of the information from the Bass file
86	>
87	>	gatherInfo();
88
89	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
89	>	// creation of complex system objects
90
91	<	// 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();
91	>	sysObjectsCreation();
92
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 );
93
86	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	–	simnfo->usePBC = the_globals->getPBC();
88	–
94
95	+	// initialize the arrays
96
97	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
98	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
99	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
100	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
101	<	else{
102	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
97	>
98	>
99	>	makeMolecules();
100	>	info->identArray = new int[info->n_atoms];
101	>	for(i=0; i<info->n_atoms; i++){
102	>	info->identArray[i] = the_atoms[i]->getIdent();
103		}
104	+
105
106	<	#ifdef IS_MPI
104	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
107	<
106	>	// check on the post processing info
107
108	+	finalInfoCheck();
109
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];
110
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
111
119	–	tot_nmol = 0;
120	–	for( i=0; i<n_components; i++ ){
112
113	<	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	<	}
113	>	// initialize the system coordinates
114
115	<	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();
115	>	initSystemCoords();
116
173	–	char* id;
174	–	LinkedMolStamp* headStamp = simnfo->headStamp;
175	–	LinkedMolStamp* currentStamp = NULL;
176	–	for( i=0; i<n_components; i++ ){
117
118	<	id = the_components[i]->getType();
179	<	comp_stamps[i] = NULL;
180	<
181	<	// check to make sure the component isn't already in the list
118	>	// make the output filenames
119
120	<	comp_stamps[i] = headStamp->match( id );
121	<	if( comp_stamps[i] == NULL ){
122	<
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	<	}
202	<
203	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
120	>	makeOutNames();
121	>
122	>
123
124
209	–
210	–
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	–
125
235	–	#ifdef IS_MPI
126
237	–	// divide the molecules among processors here.
127
239	–	mpiSim = new mpiSimulation( simnfo );
240	–
241	–
128
243	–	globalIndex = mpiSim->divideLabor();
129
130	<
246	<
247	<	// set up the local variables
130	>	// make the integrator
131
249	–	int localMol, allMol;
250	–	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
132
133	<	allMol = 0;
134	<	localMol = 0;
135	<	local_atoms = 0;
136	<	local_bonds = 0;
137	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
133	>	NVT*  myNVT = NULL;
134	>	NPTi* myNPTi = NULL;
135	>	NPTf* myNPTf = NULL;
136	>	NPTim* myNPTim = NULL;
137	>	NPTfm* myNPTfm = NULL;
138
139	<	for( j=0; j<components_nmol[i]; j++ ){
261	<
262	<	if( mpiSim->getMyMolStart() <= allMol &&
263	<	allMol <= mpiSim->getMyMolEnd() ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
139	>	switch( ensembleCase ){
140
141	<	simnfo->n_atoms = mpiSim->getMyNlocal();
142	<
143	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
141	>	case NVE_ENS:
142	>	new NVE( info, the_ff );
143	>	break;
144
145	<	simnfo->n_bonds = local_bonds;
146	<	simnfo->n_bends = local_bends;
147	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
145	>	case NVT_ENS:
146	>	myNVT = new NVT( info, the_ff );
147	>	myNVT->setTargetTemp(the_globals->getTargetTemp());
148
149	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
150	<	MPIcheckPoint();
297	<
298	<
299	<	#endif // is_mpi
300	<
149	>	if (the_globals->haveTauThermostat())
150	>	myNVT->setTauThermostat(the_globals->getTauThermostat());
151
152	<	// create the atom and short range interaction arrays
152	>	else {
153	>	sprintf( painCave.errMsg,
154	>	"SimSetup error: If you use the NVT\n"
155	>	"    ensemble, you must set tauThermostat.\n");
156	>	painCave.isFatal = 1;
157	>	simError();
158	>	}
159	>	break;
160
161	<	Atom::createArrays(simnfo->n_atoms);
162	<	the_atoms = new Atom*[simnfo->n_atoms];
163	<	the_molecules = new Molecule[simnfo->n_mol];
161	>	case NPTi_ENS:
162	>	myNPTi = new NPTi( info, the_ff );
163	>	myNPTi->setTargetTemp( the_globals->getTargetTemp() );
164
165	<
166	<	if( simnfo->n_SRI ){
167	<	the_sris = new SRI*[simnfo->n_SRI];
168	<	the_excludes = new int[2 * simnfo->n_SRI];
169	<	simnfo->globalExcludes = new int;
170	<	simnfo->n_exclude = tot_SRI;
171	<	}
172	<	else{
165	>	if (the_globals->haveTargetPressure())
166	>	myNPTi->setTargetPressure(the_globals->getTargetPressure());
167	>	else {
168	>	sprintf( painCave.errMsg,
169	>	"SimSetup error: If you use a constant pressure\n"
170	>	"    ensemble, you must set targetPressure in the BASS file.\n");
171	>	painCave.isFatal = 1;
172	>	simError();
173	>	}
174
175	<	the_excludes = new int[2];
176	<	the_excludes[0] = 0;
177	<	the_excludes[1] = 0;
178	<	simnfo->globalExcludes = new int;
179	<	simnfo->globalExcludes[0] = 0;
175	>	if( the_globals->haveTauThermostat() )
176	>	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
177	>	else{
178	>	sprintf( painCave.errMsg,
179	>	"SimSetup error: If you use an NPT\n"
180	>	"    ensemble, you must set tauThermostat.\n");
181	>	painCave.isFatal = 1;
182	>	simError();
183	>	}
184
185	<	simnfo->n_exclude = 1;
186	<	}
185	>	if( the_globals->haveTauBarostat() )
186	>	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
187	>	else{
188	>	sprintf( painCave.errMsg,
189	>	"SimSetup error: If you use an NPT\n"
190	>	"    ensemble, you must set tauBarostat.\n");
191	>	painCave.isFatal = 1;
192	>	simError();
193	>	}
194	>	break;
195
196	<	// set the arrays into the SimInfo object
196	>	case NPTf_ENS:
197	>	myNPTf = new NPTf( info, the_ff );
198	>	myNPTf->setTargetTemp( the_globals->getTargetTemp());
199
200	<	simnfo->atoms = the_atoms;
201	<	simnfo->sr_interactions = the_sris;
202	<	simnfo->nGlobalExcludes = 0;
203	<	simnfo->excludes = the_excludes;
200	>	if (the_globals->haveTargetPressure())
201	>	myNPTf->setTargetPressure(the_globals->getTargetPressure());
202	>	else {
203	>	sprintf( painCave.errMsg,
204	>	"SimSetup error: If you use a constant pressure\n"
205	>	"    ensemble, you must set targetPressure in the BASS file.\n");
206	>	painCave.isFatal = 1;
207	>	simError();
208	>	}
209
210	+	if( the_globals->haveTauThermostat() )
211	+	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
212	+	else{
213	+	sprintf( painCave.errMsg,
214	+	"SimSetup error: If you use an NPT\n"
215	+	"    ensemble, you must set tauThermostat.\n");
216	+	painCave.isFatal = 1;
217	+	simError();
218	+	}
219
220	<	// get some of the tricky things that may still be in the globals
220	>	if( the_globals->haveTauBarostat() )
221	>	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
222	>	else{
223	>	sprintf( painCave.errMsg,
224	>	"SimSetup error: If you use an NPT\n"
225	>	"    ensemble, you must set tauBarostat.\n");
226	>	painCave.isFatal = 1;
227	>	simError();
228	>	}
229	>	break;
230	>
231	>	case NPTim_ENS:
232	>	myNPTim = new NPTim( info, the_ff );
233	>	myNPTim->setTargetTemp( the_globals->getTargetTemp());
234
235	<	if( simnfo->n_dipoles ){
236	<
237	<	if( !the_globals->haveRRF() ){
235	>	if (the_globals->haveTargetPressure())
236	>	myNPTim->setTargetPressure(the_globals->getTargetPressure());
237	>	else {
238		sprintf( painCave.errMsg,
239	<	"SimSetup Error, system has dipoles, but no rRF was set.\n");
239	>	"SimSetup error: If you use a constant pressure\n"
240	>	"    ensemble, you must set targetPressure in the BASS file.\n");
241		painCave.isFatal = 1;
242		simError();
243		}
244	<	if( !the_globals->haveDielectric() ){
244	>
245	>	if( the_globals->haveTauThermostat() )
246	>	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
247	>	else{
248		sprintf( painCave.errMsg,
249	<	"SimSetup Error, system has dipoles, but no"
250	<	" dielectric was set.\n" );
249	>	"SimSetup error: If you use an NPT\n"
250	>	"    ensemble, you must set tauThermostat.\n");
251		painCave.isFatal = 1;
252		simError();
253		}
254
255	<	simnfo->rRF        = the_globals->getRRF();
256	<	simnfo->dielectric = the_globals->getDielectric();
257	<	}
255	>	if( the_globals->haveTauBarostat() )
256	>	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
257	>	else{
258	>	sprintf( painCave.errMsg,
259	>	"SimSetup error: If you use an NPT\n"
260	>	"    ensemble, you must set tauBarostat.\n");
261	>	painCave.isFatal = 1;
262	>	simError();
263	>	}
264	>	break;
265
266	<	#ifdef IS_MPI
267	<	strcpy( checkPointMsg, "rRf and dielectric check out" );
268	<	MPIcheckPoint();
359	<	#endif // is_mpi
360	<
361	<	if( the_globals->haveBox() ){
362	<	simnfo->box_x = the_globals->getBox();
363	<	simnfo->box_y = the_globals->getBox();
364	<	simnfo->box_z = the_globals->getBox();
365	<	}
366	<	else if( the_globals->haveDensity() ){
266	>	case NPTfm_ENS:
267	>	myNPTfm = new NPTfm( info, the_ff );
268	>	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
269
270	<	double vol;
271	<	vol = (double)tot_nmol / the_globals->getDensity();
272	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
371	<	simnfo->box_y = simnfo->box_x;
372	<	simnfo->box_z = simnfo->box_x;
373	<	}
374	<	else{
375	<	if( !the_globals->haveBoxX() ){
270	>	if (the_globals->haveTargetPressure())
271	>	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
272	>	else {
273		sprintf( painCave.errMsg,
274	<	"SimSetup error, no periodic BoxX size given.\n" );
274	>	"SimSetup error: If you use a constant pressure\n"
275	>	"    ensemble, you must set targetPressure in the BASS file.\n");
276		painCave.isFatal = 1;
277		simError();
278		}
279	<	simnfo->box_x = the_globals->getBoxX();
280	<
281	<	if( !the_globals->haveBoxY() ){
279	>
280	>	if( the_globals->haveTauThermostat() )
281	>	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
282	>	else{
283		sprintf( painCave.errMsg,
284	<	"SimSetup error, no periodic BoxY size given.\n" );
284	>	"SimSetup error: If you use an NPT\n"
285	>	"    ensemble, you must set tauThermostat.\n");
286		painCave.isFatal = 1;
287		simError();
288		}
389	–	simnfo->box_y = the_globals->getBoxY();
289
290	<	if( !the_globals->haveBoxZ() ){
290	>	if( the_globals->haveTauBarostat() )
291	>	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
292	>	else{
293		sprintf( painCave.errMsg,
294	<	"SimSetup error, no periodic BoxZ size given.\n" );
294	>	"SimSetup error: If you use an NPT\n"
295	>	"    ensemble, you must set tauBarostat.\n");
296		painCave.isFatal = 1;
297		simError();
298		}
299	<	simnfo->box_z = the_globals->getBoxZ();
398	<	}
299	>	break;
300
301	<	#ifdef IS_MPI
302	<	strcpy( checkPointMsg, "Box size set up" );
303	<	MPIcheckPoint();
304	<	#endif // is_mpi
305	<
405	<
406	<	// initialize the arrays
407	<
408	<	the_ff->setSimInfo( simnfo );
409	<
410	<	makeAtoms();
411	<	simnfo->identArray = new int[simnfo->n_atoms];
412	<	for(i=0; i<simnfo->n_atoms; i++){
413	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
301	>	default:
302	>	sprintf( painCave.errMsg,
303	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
304	>	painCave.isFatal = 1;
305	>	simError();
306		}
415	–
416	–	if( tot_bonds ){
417	–	makeBonds();
418	–	}
307
420	–	if( tot_bends ){
421	–	makeBends();
422	–	}
308
424	–	if( tot_torsions ){
425	–	makeTorsions();
426	–	}
427	–
428	–
429	–
430	–
431	–
432	–
433	–	if( the_globals->haveInitialConfig() ){
434	–
435	–	InitializeFromFile* fileInit;
436	–	#ifdef IS_MPI // is_mpi
437	–	if( worldRank == 0 ){
438	–	#endif //is_mpi
439	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
309		#ifdef IS_MPI
310	<	}else fileInit = new InitializeFromFile( NULL );
310	>	mpiSim->mpiRefresh();
311		#endif
443	–	fileInit->read_xyz( simnfo ); // default velocities on
312
313	<	delete fileInit;
446	<	}
447	<	else{
313	>	// initialize the Fortran
314
449	–	#ifdef IS_MPI
315
316	<	// no init from bass
316	>	info->refreshSim();
317
318	<	sprintf( painCave.errMsg,
454	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
455	<	painCave.isFatal;
456	<	simError();
457	<
458	<	#else
459	<
460	<	initFromBass();
461	<
462	<
463	<	#endif
464	<	}
465	<
466	<	#ifdef IS_MPI
467	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
468	<	MPIcheckPoint();
469	<	#endif // is_mpi
470	<
471	<
472	<
473	<
474	<
475	<
476	<
477	<	#ifdef IS_MPI
478	<	if( worldRank == 0 ){
479	<	#endif // is_mpi
480	<
481	<	if( the_globals->haveFinalConfig() ){
482	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
483	<	}
484	<	else{
485	<	strcpy( simnfo->finalName, inFileName );
486	<	char* endTest;
487	<	int nameLength = strlen( simnfo->finalName );
488	<	endTest = &(simnfo->finalName[nameLength - 5]);
489	<	if( !strcmp( endTest, ".bass" ) ){
490	<	strcpy( endTest, ".eor" );
491	<	}
492	<	else if( !strcmp( endTest, ".BASS" ) ){
493	<	strcpy( endTest, ".eor" );
494	<	}
495	<	else{
496	<	endTest = &(simnfo->finalName[nameLength - 4]);
497	<	if( !strcmp( endTest, ".bss" ) ){
498	<	strcpy( endTest, ".eor" );
499	<	}
500	<	else if( !strcmp( endTest, ".mdl" ) ){
501	<	strcpy( endTest, ".eor" );
502	<	}
503	<	else{
504	<	strcat( simnfo->finalName, ".eor" );
505	<	}
506	<	}
507	<	}
508	<
509	<	// make the sample and status out names
510	<
511	<	strcpy( simnfo->sampleName, inFileName );
512	<	char* endTest;
513	<	int nameLength = strlen( simnfo->sampleName );
514	<	endTest = &(simnfo->sampleName[nameLength - 5]);
515	<	if( !strcmp( endTest, ".bass" ) ){
516	<	strcpy( endTest, ".dump" );
517	<	}
518	<	else if( !strcmp( endTest, ".BASS" ) ){
519	<	strcpy( endTest, ".dump" );
520	<	}
521	<	else{
522	<	endTest = &(simnfo->sampleName[nameLength - 4]);
523	<	if( !strcmp( endTest, ".bss" ) ){
524	<	strcpy( endTest, ".dump" );
525	<	}
526	<	else if( !strcmp( endTest, ".mdl" ) ){
527	<	strcpy( endTest, ".dump" );
528	<	}
529	<	else{
530	<	strcat( simnfo->sampleName, ".dump" );
531	<	}
532	<	}
533	<
534	<	strcpy( simnfo->statusName, inFileName );
535	<	nameLength = strlen( simnfo->statusName );
536	<	endTest = &(simnfo->statusName[nameLength - 5]);
537	<	if( !strcmp( endTest, ".bass" ) ){
538	<	strcpy( endTest, ".stat" );
539	<	}
540	<	else if( !strcmp( endTest, ".BASS" ) ){
541	<	strcpy( endTest, ".stat" );
542	<	}
543	<	else{
544	<	endTest = &(simnfo->statusName[nameLength - 4]);
545	<	if( !strcmp( endTest, ".bss" ) ){
546	<	strcpy( endTest, ".stat" );
547	<	}
548	<	else if( !strcmp( endTest, ".mdl" ) ){
549	<	strcpy( endTest, ".stat" );
550	<	}
551	<	else{
552	<	strcat( simnfo->statusName, ".stat" );
553	<	}
554	<	}
555	<
556	<	#ifdef IS_MPI
557	<	}
558	<	#endif // is_mpi
559	<
560	<	// set the status, sample, and themal kick times
561	<
562	<	if( the_globals->haveSampleTime() ){
563	<	simnfo->sampleTime = the_globals->getSampleTime();
564	<	simnfo->statusTime = simnfo->sampleTime;
565	<	simnfo->thermalTime = simnfo->sampleTime;
566	<	}
567	<	else{
568	<	simnfo->sampleTime = the_globals->getRunTime();
569	<	simnfo->statusTime = simnfo->sampleTime;
570	<	simnfo->thermalTime = simnfo->sampleTime;
571	<	}
572	<
573	<	if( the_globals->haveStatusTime() ){
574	<	simnfo->statusTime = the_globals->getStatusTime();
575	<	}
576	<
577	<	if( the_globals->haveThermalTime() ){
578	<	simnfo->thermalTime = the_globals->getThermalTime();
579	<	}
580	<
581	<	// check for the temperature set flag
582	<
583	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
584	<
585	<
586	<	//   // make the longe range forces and the integrator
587	<
588	<	//   new AllLong( simnfo );
589	<
590	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
591	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
592	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
593	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
594	<
595	<
596	<
597	<	// initialize the Fortran
598	<
599	<	simnfo->refreshSim();
600	<
601	<	if( !strcmp( simnfo->mixingRule, "standard") ){
318	>	if( !strcmp( info->mixingRule, "standard") ){
319		the_ff->initForceField( LB_MIXING_RULE );
320		}
321	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
321	>	else if( !strcmp( info->mixingRule, "explicit") ){
322		the_ff->initForceField( EXPLICIT_MIXING_RULE );
323		}
324		else{
325		sprintf( painCave.errMsg,
326		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
327	<	simnfo->mixingRule );
327	>	info->mixingRule );
328		painCave.isFatal = 1;
329		simError();
330		}
#	Line 620 | Line 337 | void SimSetup::createSim( void ){
337		#endif // is_mpi
338		}
339
623	–	void SimSetup::makeAtoms( void ){
340
341	<	int i, j, k, index;
626	<	double ux, uy, uz, uSqr, u;
627	<	AtomStamp* current_atom;
341	>	void SimSetup::makeMolecules( void ){
342
343	+	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
344	+	molInit info;
345		DirectionalAtom* dAtom;
346	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
346	>	LinkedAssign* extras;
347	>	LinkedAssign* current_extra;
348	>	AtomStamp* currentAtom;
349	>	BondStamp* currentBond;
350	>	BendStamp* currentBend;
351	>	TorsionStamp* currentTorsion;
352
353	<	lMolIndex = 0;
354	<	molIndex = 0;
355	<	index = 0;
635	<	for( i=0; i<n_components; i++ ){
353	>	bond_pair* theBonds;
354	>	bend_set* theBends;
355	>	torsion_set* theTorsions;
356
357	<	for( j=0; j<components_nmol[i]; j++ ){
357	>
358	>	//init the forceField paramters
359
360	<	#ifdef IS_MPI
640	<	if( mpiSim->getMyMolStart() <= molIndex &&
641	<	molIndex <= mpiSim->getMyMolEnd() ){
642	<	#endif // is_mpi
360	>	the_ff->readParams();
361
362	<	molStart = index;
363	<	nMemb = comp_stamps[i]->getNAtoms();
646	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
647	<
648	<	current_atom = comp_stamps[i]->getAtom( k );
649	<	if( current_atom->haveOrientation() ){
650	<
651	<	dAtom = new DirectionalAtom(index);
652	<	simnfo->n_oriented++;
653	<	the_atoms[index] = dAtom;
654	<
655	<	ux = current_atom->getOrntX();
656	<	uy = current_atom->getOrntY();
657	<	uz = current_atom->getOrntZ();
658	<
659	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
660	<
661	<	u = sqrt( uSqr );
662	<	ux = ux / u;
663	<	uy = uy / u;
664	<	uz = uz / u;
665	<
666	<	dAtom->setSUx( ux );
667	<	dAtom->setSUy( uy );
668	<	dAtom->setSUz( uz );
669	<	}
670	<	else{
671	<	the_atoms[index] = new GeneralAtom(index);
672	<	}
673	<	the_atoms[index]->setType( current_atom->getType() );
674	<	the_atoms[index]->setIndex( index );
675	<
676	<	// increment the index and repeat;
677	<	index++;
678	<	}
679	<
680	<	molEnd = index -1;
681	<	the_molecules[lMolIndex].setNMembers( nMemb );
682	<	the_molecules[lMolIndex].setStartAtom( molStart );
683	<	the_molecules[lMolIndex].setEndAtom( molEnd );
684	<	the_molecules[lMolIndex].setStampID( i );
685	<	lMolIndex++;
362	>
363	>	// init the atoms
364
365	<	#ifdef IS_MPI
366	<	}
367	<	#endif //is_mpi
368	<
369	<	molIndex++;
692	<	}
693	<	}
694	<
695	<	#ifdef IS_MPI
696	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
365	>	double ux, uy, uz, u, uSqr;
366	>
367	>	atomOffset = 0;
368	>	excludeOffset = 0;
369	>	for(i=0; i<info->n_mol; i++){
370
371	<	delete[] globalIndex;
371	>	stampID = the_molecules[i].getStampID();
372
373	<	mpiSim->mpiRefresh();
374	<	#endif //IS_MPI
375	<
376	<	the_ff->initializeAtoms();
377	<	}
373	>	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
374	>	info.nBonds    = comp_stamps[stampID]->getNBonds();
375	>	info.nBends    = comp_stamps[stampID]->getNBends();
376	>	info.nTorsions = comp_stamps[stampID]->getNTorsions();
377	>	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
378
379	<	void SimSetup::makeBonds( void ){
379	>	info.myAtoms = &the_atoms[atomOffset];
380	>	info.myExcludes = &the_excludes[excludeOffset];
381	>	info.myBonds = new Bond*[info.nBonds];
382	>	info.myBends = new Bend*[info.nBends];
383	>	info.myTorsions = new Torsion*[info.nTorsions];
384
385	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
386	<	bond_pair* the_bonds;
387	<	BondStamp* current_bond;
388	<
389	<	the_bonds = new bond_pair[tot_bonds];
390	<	index = 0;
391	<	offset = 0;
392	<	molIndex = 0;
393	<
394	<	for( i=0; i<n_components; i++ ){
718	<
719	<	for( j=0; j<components_nmol[i]; j++ ){
720	<
721	<	#ifdef IS_MPI
722	<	if( mpiSim->getMyMolStart() <= molIndex &&
723	<	molIndex <= mpiSim->getMyMolEnd() ){
724	<	#endif // is_mpi
385	>	theBonds = new bond_pair[info.nBonds];
386	>	theBends = new bend_set[info.nBends];
387	>	theTorsions = new torsion_set[info.nTorsions];
388	>
389	>	// make the Atoms
390	>
391	>	for(j=0; j<info.nAtoms; j++){
392	>
393	>	currentAtom = comp_stamps[stampID]->getAtom( j );
394	>	if( currentAtom->haveOrientation() ){
395
396	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
397	<
398	<	current_bond = comp_stamps[i]->getBond( k );
729	<	the_bonds[index].a = current_bond->getA() + offset;
730	<	the_bonds[index].b = current_bond->getB() + offset;
731	<
732	<	exI = the_bonds[index].a;
733	<	exJ = the_bonds[index].b;
734	<
735	<	// exclude_I must always be the smaller of the pair
736	<	if( exI > exJ ){
737	<	tempEx = exI;
738	<	exI = exJ;
739	<	exJ = tempEx;
740	<	}
741	<
742	<
743	<	#ifdef IS_MPI
744	<
745	<	the_excludes[index*2] =
746	<	the_atoms[exI]->getGlobalIndex() + 1;
747	<	the_excludes[index*2 + 1] =
748	<	the_atoms[exJ]->getGlobalIndex() + 1;
749	<
750	<	#else  // isn't MPI
751	<
752	<	the_excludes[index*2] =     exI + 1;
753	<	the_excludes[index*2 + 1] = exJ + 1;
754	<	// fortran index from 1 (hence the +1 in the indexing)
755	<	#endif  //is_mpi
756	<
757	<	// increment the index and repeat;
758	<	index++;
759	<	}
760	<	offset += comp_stamps[i]->getNAtoms();
396	>	dAtom = new DirectionalAtom(j + atomOffset);
397	>	info->n_oriented++;
398	>	info.myAtoms[j] = dAtom;
399
400	<	#ifdef IS_MPI
400	>	ux = currentAtom->getOrntX();
401	>	uy = currentAtom->getOrntY();
402	>	uz = currentAtom->getOrntZ();
403	>
404	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
405	>
406	>	u = sqrt( uSqr );
407	>	ux = ux / u;
408	>	uy = uy / u;
409	>	uz = uz / u;
410	>
411	>	dAtom->setSUx( ux );
412	>	dAtom->setSUy( uy );
413	>	dAtom->setSUz( uz );
414		}
415	<	#endif //is_mpi
415	>	else{
416	>	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
417	>	}
418	>	info.myAtoms[j]->setType( currentAtom->getType() );
419	>
420	>	#ifdef IS_MPI
421
422	<	molIndex++;
423	<	}
424	<	}
422	>	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
423	>
424	>	#endif // is_mpi
425	>	}
426	>
427	>	// make the bonds
428	>	for(j=0; j<info.nBonds; j++){
429	>
430	>	currentBond = comp_stamps[stampID]->getBond( j );
431	>	theBonds[j].a = currentBond->getA() + atomOffset;
432	>	theBonds[j].b = currentBond->getB() + atomOffset;
433
434	<	the_ff->initializeBonds( the_bonds );
435	<	}
434	>	exI = theBonds[j].a;
435	>	exJ = theBonds[j].b;
436
437	<	void SimSetup::makeBends( void ){
438	<
439	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
440	<	bend_set* the_bends;
441	<	BendStamp* current_bend;
442	<	LinkedAssign* extras;
779	<	LinkedAssign* current_extra;
780	<
781	<
782	<	the_bends = new bend_set[tot_bends];
783	<	index = 0;
784	<	offset = 0;
785	<	molIndex = 0;
786	<	for( i=0; i<n_components; i++ ){
787	<
788	<	for( j=0; j<components_nmol[i]; j++ ){
789	<
437	>	// exclude_I must always be the smaller of the pair
438	>	if( exI > exJ ){
439	>	tempEx = exI;
440	>	exI = exJ;
441	>	exJ = tempEx;
442	>	}
443		#ifdef IS_MPI
444	<	if( mpiSim->getMyMolStart() <= molIndex &&
445	<	molIndex <= mpiSim->getMyMolEnd() ){
446	<	#endif // is_mpi
444	>	tempEx = exI;
445	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
446	>	tempEx = exJ;
447	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
448	>
449	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
450	>	#else  // isn't MPI
451
452	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
452	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
453	>	#endif  //is_mpi
454	>	}
455	>	excludeOffset += info.nBonds;
456	>
457	>	//make the bends
458	>	for(j=0; j<info.nBends; j++){
459	>
460	>	currentBend = comp_stamps[stampID]->getBend( j );
461	>	theBends[j].a = currentBend->getA() + atomOffset;
462	>	theBends[j].b = currentBend->getB() + atomOffset;
463	>	theBends[j].c = currentBend->getC() + atomOffset;
464
465	<	current_bend = comp_stamps[i]->getBend( k );
798	<	the_bends[index].a = current_bend->getA() + offset;
799	<	the_bends[index].b = current_bend->getB() + offset;
800	<	the_bends[index].c = current_bend->getC() + offset;
801	<
802	<	if( current_bend->haveExtras() ){
465	>	if( currentBend->haveExtras() ){
466
467	<	extras = current_bend->getExtras();
468	<	current_extra = extras;
467	>	extras = currentBend->getExtras();
468	>	current_extra = extras;
469
470	<	while( current_extra != NULL ){
471	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
470	>	while( current_extra != NULL ){
471	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
472
473	<	switch( current_extra->getType() ){
473	>	switch( current_extra->getType() ){
474	>
475	>	case 0:
476	>	theBends[j].ghost =
477	>	current_extra->getInt() + atomOffset;
478	>	theBends[j].isGhost = 1;
479	>	break;
480
481	<	case 0:
482	<	the_bends[index].ghost =
483	<	current_extra->getInt() + offset;
484	<	the_bends[index].isGhost = 1;
485	<	break;
817	<
818	<	case 1:
819	<	the_bends[index].ghost =
820	<	(int)current_extra->getDouble() + offset;
821	<	the_bends[index].isGhost = 1;
822	<	break;
823	<
824	<	default:
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup Error: ghostVectorSource was neiter a "
827	<	"double nor an int.\n"
828	<	"-->Bend[%d] in %s\n",
829	<	k, comp_stamps[i]->getID() );
830	<	painCave.isFatal = 1;
831	<	simError();
832	<	}
833	<	}
481	>	case 1:
482	>	theBends[j].ghost =
483	>	(int)current_extra->getDouble() + atomOffset;
484	>	theBends[j].isGhost = 1;
485	>	break;
486
487	<	else{
488	<
489	<	sprintf( painCave.errMsg,
490	<	"SimSetup Error: unhandled bend assignment:\n"
491	<	"    -->%s in Bend[%d] in %s\n",
492	<	current_extra->getlhs(),
493	<	k, comp_stamps[i]->getID() );
494	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<
846	<	current_extra = current_extra->getNext();
487	>	default:
488	>	sprintf( painCave.errMsg,
489	>	"SimSetup Error: ghostVectorSource was neither a "
490	>	"double nor an int.\n"
491	>	"-->Bend[%d] in %s\n",
492	>	j, comp_stamps[stampID]->getID() );
493	>	painCave.isFatal = 1;
494	>	simError();
495		}
496		}
497
850	–	if( !the_bends[index].isGhost ){
851	–
852	–	exI = the_bends[index].a;
853	–	exJ = the_bends[index].c;
854	–	}
498		else{
499
500	<	exI = the_bends[index].a;
501	<	exJ = the_bends[index].b;
500	>	sprintf( painCave.errMsg,
501	>	"SimSetup Error: unhandled bend assignment:\n"
502	>	"    -->%s in Bend[%d] in %s\n",
503	>	current_extra->getlhs(),
504	>	j, comp_stamps[stampID]->getID() );
505	>	painCave.isFatal = 1;
506	>	simError();
507		}
508
509	<	// exclude_I must always be the smaller of the pair
510	<	if( exI > exJ ){
511	<	tempEx = exI;
512	<	exI = exJ;
513	<	exJ = tempEx;
514	<	}
509	>	current_extra = current_extra->getNext();
510	>	}
511	>	}
512	>
513	>	if( !theBends[j].isGhost ){
514	>
515	>	exI = theBends[j].a;
516	>	exJ = theBends[j].c;
517	>	}
518	>	else{
519	>
520	>	exI = theBends[j].a;
521	>	exJ = theBends[j].b;
522	>	}
523	>
524	>	// exclude_I must always be the smaller of the pair
525	>	if( exI > exJ ){
526	>	tempEx = exI;
527	>	exI = exJ;
528	>	exJ = tempEx;
529	>	}
530	>	#ifdef IS_MPI
531	>	tempEx = exI;
532	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
533	>	tempEx = exJ;
534	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
535	>
536	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
537	>	#else  // isn't MPI
538	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
539	>	#endif  //is_mpi
540	>	}
541	>	excludeOffset += info.nBends;
542
543	+	for(j=0; j<info.nTorsions; j++){
544	+
545	+	currentTorsion = comp_stamps[stampID]->getTorsion( j );
546	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
547	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
548	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
549	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
550	+
551	+	exI = theTorsions[j].a;
552	+	exJ = theTorsions[j].d;
553
554	+	// exclude_I must always be the smaller of the pair
555	+	if( exI > exJ ){
556	+	tempEx = exI;
557	+	exI = exJ;
558	+	exJ = tempEx;
559	+	}
560		#ifdef IS_MPI
561	<
562	<	the_excludes[(index + tot_bonds)*2] =
563	<	the_atoms[exI]->getGlobalIndex() + 1;
564	<	the_excludes[(index + tot_bonds)*2 + 1] =
565	<	the_atoms[exJ]->getGlobalIndex() + 1;
566	<
561	>	tempEx = exI;
562	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
563	>	tempEx = exJ;
564	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
565	>
566	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
567		#else  // isn't MPI
568	<
878	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
879	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
880	<	// fortran index from 1 (hence the +1 in the indexing)
568	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
569		#endif  //is_mpi
882	–
883	–
884	–	// increment the index and repeat;
885	–	index++;
886	–	}
887	–	offset += comp_stamps[i]->getNAtoms();
888	–
889	–	#ifdef IS_MPI
890	–	}
891	–	#endif //is_mpi
892	–
893	–	molIndex++;
570		}
571	<	}
571	>	excludeOffset += info.nTorsions;
572	>
573	>
574	>	// send the arrays off to the forceField for init.
575
576	<	#ifdef IS_MPI
577	<	sprintf( checkPointMsg,
578	<	"Successfully created the bends list.\n" );
579	<	MPIcheckPoint();
901	<	#endif // is_mpi
902	<
576	>	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
577	>	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
578	>	the_ff->initializeBends( info.nBends, info.myBends, theBends );
579	>	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
580
904	–	the_ff->initializeBends( the_bends );
905	–	}
581
582	<	void SimSetup::makeTorsions( void ){
582	>	the_molecules[i].initialize( info );
583
909	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
910	–	torsion_set* the_torsions;
911	–	TorsionStamp* current_torsion;
584
585	<	the_torsions = new torsion_set[tot_torsions];
586	<	index = 0;
587	<	offset = 0;
588	<	molIndex = 0;
589	<	for( i=0; i<n_components; i++ ){
585	>	atomOffset += info.nAtoms;
586	>	delete[] theBonds;
587	>	delete[] theBends;
588	>	delete[] theTorsions;
589	>	}
590
919	–	for( j=0; j<components_nmol[i]; j++ ){
920	–
591		#ifdef IS_MPI
592	<	if( mpiSim->getMyMolStart() <= molIndex &&
593	<	molIndex <= mpiSim->getMyMolEnd() ){
594	<	#endif // is_mpi
592	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
593	>	MPIcheckPoint();
594	>	#endif // is_mpi
595
596	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
596	>	// clean up the forcefield
597	>	the_ff->calcRcut();
598	>	the_ff->cleanMe();
599
928	–	current_torsion = comp_stamps[i]->getTorsion( k );
929	–	the_torsions[index].a = current_torsion->getA() + offset;
930	–	the_torsions[index].b = current_torsion->getB() + offset;
931	–	the_torsions[index].c = current_torsion->getC() + offset;
932	–	the_torsions[index].d = current_torsion->getD() + offset;
933	–
934	–	exI = the_torsions[index].a;
935	–	exJ = the_torsions[index].d;
936	–
937	–
938	–	// exclude_I must always be the smaller of the pair
939	–	if( exI > exJ ){
940	–	tempEx = exI;
941	–	exI = exJ;
942	–	exJ = tempEx;
943	–	}
944	–
945	–
946	–	#ifdef IS_MPI
947	–
948	–	the_excludes[(index + tot_bonds + tot_bends)*2] =
949	–	the_atoms[exI]->getGlobalIndex() + 1;
950	–	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
951	–	the_atoms[exJ]->getGlobalIndex() + 1;
952	–
953	–	#else  // isn't MPI
954	–
955	–	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956	–	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957	–	// fortran indexes from 1 (hence the +1 in the indexing)
958	–	#endif  //is_mpi
959	–
960	–
961	–	// increment the index and repeat;
962	–	index++;
963	–	}
964	–	offset += comp_stamps[i]->getNAtoms();
965	–
966	–	#ifdef IS_MPI
967	–	}
968	–	#endif //is_mpi
969	–
970	–	molIndex++;
971	–	}
972	–	}
973	–
974	–	the_ff->initializeTorsions( the_torsions );
600		}
601
602		void SimSetup::initFromBass( void ){
#	Line 993 | Line 618 | void SimSetup::initFromBass( void ){
618		have_extra =1;
619
620		n_cells = (int)temp3 - 1;
621	<	cellx = simnfo->box_x / temp3;
622	<	celly = simnfo->box_y / temp3;
623	<	cellz = simnfo->box_z / temp3;
621	>	cellx = info->boxLx / temp3;
622	>	celly = info->boxLy / temp3;
623	>	cellz = info->boxLz / temp3;
624		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
625		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
626		n_per_extra = (int)ceil( temp1 );
#	Line 1010 | Line 635 | void SimSetup::initFromBass( void ){
635		}
636		else{
637		n_cells = (int)temp3;
638	<	cellx = simnfo->box_x / temp3;
639	<	celly = simnfo->box_y / temp3;
640	<	cellz = simnfo->box_z / temp3;
638	>	cellx = info->boxLx / temp3;
639	>	celly = info->boxLy / temp3;
640	>	cellz = info->boxLz / temp3;
641		}
642
643		current_mol = 0;
#	Line 1092 | Line 717 | void SimSetup::initFromBass( void ){
717		}
718
719
720	<	for( i=0; i<simnfo->n_atoms; i++ ){
721	<	simnfo->atoms[i]->set_vx( 0.0 );
722	<	simnfo->atoms[i]->set_vy( 0.0 );
723	<	simnfo->atoms[i]->set_vz( 0.0 );
720	>	for( i=0; i<info->n_atoms; i++ ){
721	>	info->atoms[i]->set_vx( 0.0 );
722	>	info->atoms[i]->set_vy( 0.0 );
723	>	info->atoms[i]->set_vz( 0.0 );
724		}
725		}
726
#	Line 1154 | Line 779 | void SimSetup::makeElement( double x, double y, double
779
780		current_comp_mol = 0;
781		current_comp++;
782	+	}
783	+	}
784	+
785	+
786	+	void SimSetup::gatherInfo( void ){
787	+
788	+	ensembleCase = -1;
789	+	ffCase = -1;
790	+
791	+	// get the stamps and globals;
792	+	the_stamps = stamps;
793	+	the_globals = globals;
794	+
795	+	// set the easy ones first
796	+	info->target_temp = the_globals->getTargetTemp();
797	+	info->dt = the_globals->getDt();
798	+	info->run_time = the_globals->getRunTime();
799	+	n_components = the_globals->getNComponents();
800	+
801	+
802	+	// get the forceField
803	+
804	+	strcpy( force_field, the_globals->getForceField() );
805	+
806	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
807	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
808	+	else{
809	+	sprintf( painCave.errMsg,
810	+	"SimSetup Error. Unrecognized force field -> %s\n",
811	+	force_field );
812	+	painCave.isFatal = 1;
813	+	simError();
814		}
815	+
816	+	// get the ensemble
817	+
818	+	strcpy( ensemble, the_globals->getEnsemble() );
819	+
820	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
821	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
822	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
823	+	ensembleCase = NPTi_ENS;
824	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
825	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
826	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
827	+	else{
828	+	sprintf( painCave.errMsg,
829	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
830	+	"reverting to NVE for this simulation.\n",
831	+	ensemble );
832	+	painCave.isFatal = 0;
833	+	simError();
834	+	strcpy( ensemble, "NVE" );
835	+	ensembleCase = NVE_ENS;
836	+	}
837	+	strcpy( info->ensemble, ensemble );
838	+
839	+	// get the mixing rule
840	+
841	+	strcpy( info->mixingRule, the_globals->getMixingRule() );
842	+	info->usePBC = the_globals->getPBC();
843	+
844	+
845	+	// get the components and calculate the tot_nMol and indvidual n_mol
846	+
847	+	the_components = the_globals->getComponents();
848	+	components_nmol = new int[n_components];
849	+
850	+
851	+	if( !the_globals->haveNMol() ){
852	+	// we don't have the total number of molecules, so we assume it is
853	+	// given in each component
854	+
855	+	tot_nmol = 0;
856	+	for( i=0; i<n_components; i++ ){
857	+
858	+	if( !the_components[i]->haveNMol() ){
859	+	// we have a problem
860	+	sprintf( painCave.errMsg,
861	+	"SimSetup Error. No global NMol or component NMol"
862	+	" given. Cannot calculate the number of atoms.\n" );
863	+	painCave.isFatal = 1;
864	+	simError();
865	+	}
866	+
867	+	tot_nmol += the_components[i]->getNMol();
868	+	components_nmol[i] = the_components[i]->getNMol();
869	+	}
870	+	}
871	+	else{
872	+	sprintf( painCave.errMsg,
873	+	"SimSetup error.\n"
874	+	"\tSorry, the ability to specify total"
875	+	" nMols and then give molfractions in the components\n"
876	+	"\tis not currently supported."
877	+	" Please give nMol in the components.\n" );
878	+	painCave.isFatal = 1;
879	+	simError();
880	+	}
881	+
882	+	// set the status, sample, and thermal kick times
883	+
884	+	if( the_globals->haveSampleTime() ){
885	+	info->sampleTime = the_globals->getSampleTime();
886	+	info->statusTime = info->sampleTime;
887	+	info->thermalTime = info->sampleTime;
888	+	}
889	+	else{
890	+	info->sampleTime = the_globals->getRunTime();
891	+	info->statusTime = info->sampleTime;
892	+	info->thermalTime = info->sampleTime;
893	+	}
894	+
895	+	if( the_globals->haveStatusTime() ){
896	+	info->statusTime = the_globals->getStatusTime();
897	+	}
898	+
899	+	if( the_globals->haveThermalTime() ){
900	+	info->thermalTime = the_globals->getThermalTime();
901	+	}
902	+
903	+	// check for the temperature set flag
904	+
905	+	if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet();
906	+
907	+	// get some of the tricky things that may still be in the globals
908	+
909	+	double boxVector[3];
910	+	if( the_globals->haveBox() ){
911	+	boxVector[0] = the_globals->getBox();
912	+	boxVector[1] = the_globals->getBox();
913	+	boxVector[2] = the_globals->getBox();
914	+
915	+	info->setBox( boxVector );
916	+	}
917	+	else if( the_globals->haveDensity() ){
918	+
919	+	double vol;
920	+	vol = (double)tot_nmol / the_globals->getDensity();
921	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
922	+	boxVector[1] = boxVector[0];
923	+	boxVector[2] = boxVector[0];
924	+
925	+	info->setBox( boxVector );
926	+	}
927	+	else{
928	+	if( !the_globals->haveBoxX() ){
929	+	sprintf( painCave.errMsg,
930	+	"SimSetup error, no periodic BoxX size given.\n" );
931	+	painCave.isFatal = 1;
932	+	simError();
933	+	}
934	+	boxVector[0] = the_globals->getBoxX();
935	+
936	+	if( !the_globals->haveBoxY() ){
937	+	sprintf( painCave.errMsg,
938	+	"SimSetup error, no periodic BoxY size given.\n" );
939	+	painCave.isFatal = 1;
940	+	simError();
941	+	}
942	+	boxVector[1] = the_globals->getBoxY();
943	+
944	+	if( !the_globals->haveBoxZ() ){
945	+	sprintf( painCave.errMsg,
946	+	"SimSetup error, no periodic BoxZ size given.\n" );
947	+	painCave.isFatal = 1;
948	+	simError();
949	+	}
950	+	boxVector[2] = the_globals->getBoxZ();
951	+
952	+	info->setBox( boxVector );
953	+	}
954	+
955	+
956	+
957	+	#ifdef IS_MPI
958	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
959	+	MPIcheckPoint();
960	+	#endif // is_mpi
961	+
962		}
963	+
964	+
965	+	void SimSetup::finalInfoCheck( void ){
966	+	int index;
967	+	int usesDipoles;
968	+
969	+
970	+	// check electrostatic parameters
971	+
972	+	index = 0;
973	+	usesDipoles = 0;
974	+	while( (index < info->n_atoms) && !usesDipoles ){
975	+	usesDipoles = ((info->atoms)[index])->hasDipole();
976	+	index++;
977	+	}
978	+
979	+	#ifdef IS_MPI
980	+	int myUse = usesDipoles
981	+	MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
982	+	#endif //is_mpi
983	+
984	+
985	+	if (the_globals->getUseRF() ) {
986	+	info->useReactionField = 1;
987	+
988	+	if( !the_globals->haveECR() ){
989	+	sprintf( painCave.errMsg,
990	+	"SimSetup Warning: using default value of 1/2 the smallest "
991	+	"box length for the electrostaticCutoffRadius.\n"
992	+	"I hope you have a very fast processor!\n");
993	+	painCave.isFatal = 0;
994	+	simError();
995	+	double smallest;
996	+	smallest = info->boxLx;
997	+	if (info->boxLy <= smallest) smallest = info->boxLy;
998	+	if (info->boxLz <= smallest) smallest = info->boxLz;
999	+	info->ecr = 0.5 * smallest;
1000	+	} else {
1001	+	info->ecr        = the_globals->getECR();
1002	+	}
1003	+
1004	+	if( !the_globals->haveEST() ){
1005	+	sprintf( painCave.errMsg,
1006	+	"SimSetup Warning: using default value of 0.05 * the "
1007	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1008	+	);
1009	+	painCave.isFatal = 0;
1010	+	simError();
1011	+	info->est = 0.05 * info->ecr;
1012	+	} else {
1013	+	info->est        = the_globals->getEST();
1014	+	}
1015	+
1016	+	if(!the_globals->haveDielectric() ){
1017	+	sprintf( painCave.errMsg,
1018	+	"SimSetup Error: You are trying to use Reaction Field without"
1019	+	"setting a dielectric constant!\n"
1020	+	);
1021	+	painCave.isFatal = 1;
1022	+	simError();
1023	+	}
1024	+	info->dielectric = the_globals->getDielectric();
1025	+	}
1026	+	else {
1027	+	if (usesDipoles) {
1028	+
1029	+	if( !the_globals->haveECR() ){
1030	+	sprintf( painCave.errMsg,
1031	+	"SimSetup Warning: using default value of 1/2 the smallest "
1032	+	"box length for the electrostaticCutoffRadius.\n"
1033	+	"I hope you have a very fast processor!\n");
1034	+	painCave.isFatal = 0;
1035	+	simError();
1036	+	double smallest;
1037	+	smallest = info->boxLx;
1038	+	if (info->boxLy <= smallest) smallest = info->boxLy;
1039	+	if (info->boxLz <= smallest) smallest = info->boxLz;
1040	+	info->ecr = 0.5 * smallest;
1041	+	} else {
1042	+	info->ecr        = the_globals->getECR();
1043	+	}
1044	+
1045	+	if( !the_globals->haveEST() ){
1046	+	sprintf( painCave.errMsg,
1047	+	"SimSetup Warning: using default value of 5%% of the "
1048	+	"electrostaticCutoffRadius for the "
1049	+	"electrostaticSkinThickness\n"
1050	+	);
1051	+	painCave.isFatal = 0;
1052	+	simError();
1053	+	info->est = 0.05 * info->ecr;
1054	+	} else {
1055	+	info->est        = the_globals->getEST();
1056	+	}
1057	+	}
1058	+	}
1059	+
1060	+	#ifdef IS_MPI
1061	+	strcpy( checkPointMsg, "post processing checks out" );
1062	+	MPIcheckPoint();
1063	+	#endif // is_mpi
1064	+
1065	+	}
1066	+
1067	+	void SimSetup::initSystemCoords( void ){
1068	+
1069	+	if( the_globals->haveInitialConfig() ){
1070	+
1071	+	InitializeFromFile* fileInit;
1072	+	#ifdef IS_MPI // is_mpi
1073	+	if( worldRank == 0 ){
1074	+	#endif //is_mpi
1075	+	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
1076	+	#ifdef IS_MPI
1077	+	}else fileInit = new InitializeFromFile( NULL );
1078	+	#endif
1079	+	fileInit->read_xyz( info ); // default velocities on
1080	+
1081	+	delete fileInit;
1082	+	}
1083	+	else{
1084	+
1085	+	#ifdef IS_MPI
1086	+
1087	+	// no init from bass
1088	+
1089	+	sprintf( painCave.errMsg,
1090	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1091	+	painCave.isFatal;
1092	+	simError();
1093	+
1094	+	#else
1095	+
1096	+	initFromBass();
1097	+
1098	+
1099	+	#endif
1100	+	}
1101	+
1102	+	#ifdef IS_MPI
1103	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1104	+	MPIcheckPoint();
1105	+	#endif // is_mpi
1106	+
1107	+	}
1108	+
1109	+
1110	+	void SimSetup::makeOutNames( void ){
1111	+
1112	+	#ifdef IS_MPI
1113	+	if( worldRank == 0 ){
1114	+	#endif // is_mpi
1115	+
1116	+	if( the_globals->haveFinalConfig() ){
1117	+	strcpy( info->finalName, the_globals->getFinalConfig() );
1118	+	}
1119	+	else{
1120	+	strcpy( info->finalName, inFileName );
1121	+	char* endTest;
1122	+	int nameLength = strlen( info->finalName );
1123	+	endTest = &(info->finalName[nameLength - 5]);
1124	+	if( !strcmp( endTest, ".bass" ) ){
1125	+	strcpy( endTest, ".eor" );
1126	+	}
1127	+	else if( !strcmp( endTest, ".BASS" ) ){
1128	+	strcpy( endTest, ".eor" );
1129	+	}
1130	+	else{
1131	+	endTest = &(info->finalName[nameLength - 4]);
1132	+	if( !strcmp( endTest, ".bss" ) ){
1133	+	strcpy( endTest, ".eor" );
1134	+	}
1135	+	else if( !strcmp( endTest, ".mdl" ) ){
1136	+	strcpy( endTest, ".eor" );
1137	+	}
1138	+	else{
1139	+	strcat( info->finalName, ".eor" );
1140	+	}
1141	+	}
1142	+	}
1143	+
1144	+	// make the sample and status out names
1145	+
1146	+	strcpy( info->sampleName, inFileName );
1147	+	char* endTest;
1148	+	int nameLength = strlen( info->sampleName );
1149	+	endTest = &(info->sampleName[nameLength - 5]);
1150	+	if( !strcmp( endTest, ".bass" ) ){
1151	+	strcpy( endTest, ".dump" );
1152	+	}
1153	+	else if( !strcmp( endTest, ".BASS" ) ){
1154	+	strcpy( endTest, ".dump" );
1155	+	}
1156	+	else{
1157	+	endTest = &(info->sampleName[nameLength - 4]);
1158	+	if( !strcmp( endTest, ".bss" ) ){
1159	+	strcpy( endTest, ".dump" );
1160	+	}
1161	+	else if( !strcmp( endTest, ".mdl" ) ){
1162	+	strcpy( endTest, ".dump" );
1163	+	}
1164	+	else{
1165	+	strcat( info->sampleName, ".dump" );
1166	+	}
1167	+	}
1168	+
1169	+	strcpy( info->statusName, inFileName );
1170	+	nameLength = strlen( info->statusName );
1171	+	endTest = &(info->statusName[nameLength - 5]);
1172	+	if( !strcmp( endTest, ".bass" ) ){
1173	+	strcpy( endTest, ".stat" );
1174	+	}
1175	+	else if( !strcmp( endTest, ".BASS" ) ){
1176	+	strcpy( endTest, ".stat" );
1177	+	}
1178	+	else{
1179	+	endTest = &(info->statusName[nameLength - 4]);
1180	+	if( !strcmp( endTest, ".bss" ) ){
1181	+	strcpy( endTest, ".stat" );
1182	+	}
1183	+	else if( !strcmp( endTest, ".mdl" ) ){
1184	+	strcpy( endTest, ".stat" );
1185	+	}
1186	+	else{
1187	+	strcat( info->statusName, ".stat" );
1188	+	}
1189	+	}
1190	+
1191	+	#ifdef IS_MPI
1192	+	}
1193	+	#endif // is_mpi
1194	+
1195	+	}
1196	+
1197	+
1198	+	void SimSetup::sysObjectsCreation( void ){
1199	+
1200	+	// create the forceField
1201	+
1202	+	createFF();
1203	+
1204	+	// extract componentList
1205	+
1206	+	compList();
1207	+
1208	+	// calc the number of atoms, bond, bends, and torsions
1209	+
1210	+	calcSysValues();
1211	+
1212	+	#ifdef IS_MPI
1213	+	// divide the molecules among the processors
1214	+
1215	+	mpiMolDivide();
1216	+	#endif //is_mpi
1217	+
1218	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1219	+
1220	+	makeSysArrays();
1221	+
1222	+
1223	+
1224	+
1225	+	}
1226	+
1227	+
1228	+	void SimSetup::createFF( void ){
1229	+
1230	+	switch( ffCase ){
1231	+
1232	+	case FF_DUFF:
1233	+	the_ff = new DUFF();
1234	+	break;
1235	+
1236	+	case FF_LJ:
1237	+	the_ff = new LJFF();
1238	+	break;
1239	+
1240	+	default:
1241	+	sprintf( painCave.errMsg,
1242	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1243	+	painCave.isFatal = 1;
1244	+	simError();
1245	+	}
1246	+
1247	+	#ifdef IS_MPI
1248	+	strcpy( checkPointMsg, "ForceField creation successful" );
1249	+	MPIcheckPoint();
1250	+	#endif // is_mpi
1251	+
1252	+	}
1253	+
1254	+
1255	+	void SimSetup::compList( void ){
1256	+
1257	+	comp_stamps = new MoleculeStamp*[n_components];
1258	+
1259	+	// make an array of molecule stamps that match the components used.
1260	+	// also extract the used stamps out into a separate linked list
1261	+
1262	+	info->nComponents = n_components;
1263	+	info->componentsNmol = components_nmol;
1264	+	info->compStamps = comp_stamps;
1265	+	info->headStamp = new LinkedMolStamp();
1266	+
1267	+	char* id;
1268	+	LinkedMolStamp* headStamp = info->headStamp;
1269	+	LinkedMolStamp* currentStamp = NULL;
1270	+	for( i=0; i<n_components; i++ ){
1271	+
1272	+	id = the_components[i]->getType();
1273	+	comp_stamps[i] = NULL;
1274	+
1275	+	// check to make sure the component isn't already in the list
1276	+
1277	+	comp_stamps[i] = headStamp->match( id );
1278	+	if( comp_stamps[i] == NULL ){
1279	+
1280	+	// extract the component from the list;
1281	+
1282	+	currentStamp = the_stamps->extractMolStamp( id );
1283	+	if( currentStamp == NULL ){
1284	+	sprintf( painCave.errMsg,
1285	+	"SimSetup error: Component \"%s\" was not found in the "
1286	+	"list of declared molecules\n",
1287	+	id );
1288	+	painCave.isFatal = 1;
1289	+	simError();
1290	+	}
1291	+
1292	+	headStamp->add( currentStamp );
1293	+	comp_stamps[i] = headStamp->match( id );
1294	+	}
1295	+	}
1296	+
1297	+	#ifdef IS_MPI
1298	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1299	+	MPIcheckPoint();
1300	+	#endif // is_mpi
1301	+
1302	+
1303	+	}
1304	+
1305	+	void SimSetup::calcSysValues( void ){
1306	+
1307	+	tot_atoms = 0;
1308	+	tot_bonds = 0;
1309	+	tot_bends = 0;
1310	+	tot_torsions = 0;
1311	+	for( i=0; i<n_components; i++ ){
1312	+
1313	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1314	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1315	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1316	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1317	+	}
1318	+
1319	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1320	+
1321	+	info->n_atoms = tot_atoms;
1322	+	info->n_bonds = tot_bonds;
1323	+	info->n_bends = tot_bends;
1324	+	info->n_torsions = tot_torsions;
1325	+	info->n_SRI = tot_SRI;
1326	+	info->n_mol = tot_nmol;
1327	+
1328	+	info->molMembershipArray = new int[tot_atoms];
1329	+	}
1330	+
1331	+
1332	+	#ifdef IS_MPI
1333	+
1334	+	void SimSetup::mpiMolDivide( void ){
1335	+
1336	+	int localMol, allMol;
1337	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1338	+
1339	+	mpiSim = new mpiSimulation( info );
1340	+
1341	+	globalIndex = mpiSim->divideLabor();
1342	+
1343	+	// set up the local variables
1344	+
1345	+	mol2proc = mpiSim->getMolToProcMap();
1346	+	molCompType = mpiSim->getMolComponentType();
1347	+
1348	+	allMol = 0;
1349	+	localMol = 0;
1350	+	local_atoms = 0;
1351	+	local_bonds = 0;
1352	+	local_bends = 0;
1353	+	local_torsions = 0;
1354	+	globalAtomIndex = 0;
1355	+
1356	+
1357	+	for( i=0; i<n_components; i++ ){
1358	+
1359	+	for( j=0; j<components_nmol[i]; j++ ){
1360	+
1361	+	if( mol2proc[allMol] == worldRank ){
1362	+
1363	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1364	+	local_bonds +=    comp_stamps[i]->getNBonds();
1365	+	local_bends +=    comp_stamps[i]->getNBends();
1366	+	local_torsions += comp_stamps[i]->getNTorsions();
1367	+	localMol++;
1368	+	}
1369	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1370	+	info->molMembershipArray[globalAtomIndex] = allMol;
1371	+	globalAtomIndex++;
1372	+	}
1373	+
1374	+	allMol++;
1375	+	}
1376	+	}
1377	+	local_SRI = local_bonds + local_bends + local_torsions;
1378	+
1379	+	info->n_atoms = mpiSim->getMyNlocal();
1380	+
1381	+	if( local_atoms != info->n_atoms ){
1382	+	sprintf( painCave.errMsg,
1383	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1384	+	" localAtom (%d) are not equal.\n",
1385	+	info->n_atoms,
1386	+	local_atoms );
1387	+	painCave.isFatal = 1;
1388	+	simError();
1389	+	}
1390	+
1391	+	info->n_bonds = local_bonds;
1392	+	info->n_bends = local_bends;
1393	+	info->n_torsions = local_torsions;
1394	+	info->n_SRI = local_SRI;
1395	+	info->n_mol = localMol;
1396	+
1397	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1398	+	MPIcheckPoint();
1399	+	}
1400	+
1401	+	#endif // is_mpi
1402	+
1403	+
1404	+	void SimSetup::makeSysArrays( void ){
1405	+
1406	+	// create the atom and short range interaction arrays
1407	+
1408	+	Atom::createArrays(info->n_atoms);
1409	+	the_atoms = new Atom*[info->n_atoms];
1410	+	the_molecules = new Molecule[info->n_mol];
1411	+	int molIndex;
1412	+
1413	+	// initialize the molecule's stampID's
1414	+
1415	+	#ifdef IS_MPI
1416	+
1417	+
1418	+	molIndex = 0;
1419	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1420	+
1421	+	if(mol2proc[i] == worldRank ){
1422	+	the_molecules[molIndex].setStampID( molCompType[i] );
1423	+	the_molecules[molIndex].setMyIndex( molIndex );
1424	+	the_molecules[molIndex].setGlobalIndex( i );
1425	+	molIndex++;
1426	+	}
1427	+	}
1428	+
1429	+	#else // is_mpi
1430	+
1431	+	molIndex = 0;
1432	+	globalAtomIndex = 0;
1433	+	for(i=0; i<n_components; i++){
1434	+	for(j=0; j<components_nmol[i]; j++ ){
1435	+	the_molecules[molIndex].setStampID( i );
1436	+	the_molecules[molIndex].setMyIndex( molIndex );
1437	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1438	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1439	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1440	+	globalAtomIndex++;
1441	+	}
1442	+	molIndex++;
1443	+	}
1444	+	}
1445	+
1446	+
1447	+	#endif // is_mpi
1448	+
1449	+
1450	+	if( info->n_SRI ){
1451	+
1452	+	Exclude::createArray(info->n_SRI);
1453	+	the_excludes = new Exclude*[info->n_SRI];
1454	+	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1455	+	info->globalExcludes = new int;
1456	+	info->n_exclude = info->n_SRI;
1457	+	}
1458	+	else{
1459	+
1460	+	Exclude::createArray( 1 );
1461	+	the_excludes = new Exclude*;
1462	+	the_excludes[0] = new Exclude(0);
1463	+	the_excludes[0]->setPair( 0,0 );
1464	+	info->globalExcludes = new int;
1465	+	info->globalExcludes[0] = 0;
1466	+	info->n_exclude = 0;
1467	+	}
1468	+
1469	+	// set the arrays into the SimInfo object
1470	+
1471	+	info->atoms = the_atoms;
1472	+	info->molecules = the_molecules;
1473	+	info->nGlobalExcludes = 0;
1474	+	info->excludes = the_excludes;
1475	+
1476	+	the_ff->setSimInfo( info );
1477	+
1478	+	}

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