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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 555 by mmeineke, Tue Jun 17 21:56:15 2003 UTC vs.
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;
69	–	ExtendedSystem* the_extendedsystem;
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;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
89	>	// creation of complex system objects
90
91	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	simnfo->run_time = the_globals->getRunTime();
91	>	sysObjectsCreation();
92
81	–	// get the ones we know are there, yet still may need some work.
82	–	n_components = the_globals->getNComponents();
83	–	strcpy( force_field, the_globals->getForceField() );
93
85	–	// get the ensemble and set up an extended system if we need it:
86	–	strcpy( ensemble, the_globals->getEnsemble() );
87	–	if( !strcasecmp( ensemble, "NPT" ) ) {
88	–	the_extendedsystem = new ExtendedSystem( simnfo );
89	–	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	–	if (the_globals->haveTargetPressure())
91	–	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92	–	else {
93	–	sprintf( painCave.errMsg,
94	–	"SimSetup error: If you use the constant pressure\n"
95	–	"    ensemble, you must set targetPressure.\n"
96	–	"    This was found in the BASS file.\n");
97	–	painCave.isFatal = 1;
98	–	simError();
99	–	}
94
95	<	if (the_globals->haveTauThermostat())
102	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103	<	else if (the_globals->haveQmass())
104	<	the_extendedsystem->setQmass(the_globals->getQmass());
105	<	else {
106	<	sprintf( painCave.errMsg,
107	<	"SimSetup error: If you use one of the constant temperature\n"
108	<	"    ensembles, you must set either tauThermostat or qMass.\n"
109	<	"    Neither of these was found in the BASS file.\n");
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
95	>	// initialize the arrays
96
97	<	if (the_globals->haveTauBarostat())
115	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116	<	else {
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup error: If you use the constant pressure\n"
119	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
97	>
98
99	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
100	<	the_extendedsystem = new ExtendedSystem( simnfo );
101	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
102	<
129	<	if (the_globals->haveTauThermostat())
130	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131	<	else if (the_globals->haveQmass())
132	<	the_extendedsystem->setQmass(the_globals->getQmass());
133	<	else {
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error: If you use one of the constant temperature\n"
136	<	"    ensembles, you must set either tauThermostat or qMass.\n"
137	<	"    Neither of these was found in the BASS file.\n");
138	<	painCave.isFatal = 1;
139	<	simError();
140	<	}
141	<
142	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
143	<	} else {
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	<	"reverting to NVE for this simulation.\n",
147	<	ensemble );
148	<	painCave.isFatal = 0;
149	<	simError();
150	<	strcpy( ensemble, "NVE" );
151	<	}
152	<	strcpy( simnfo->ensemble, ensemble );
153	<
154	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155	<	simnfo->usePBC = the_globals->getPBC();
156	<
157	<	int usesDipoles = 0;
158	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
159	<	the_ff = new TraPPE_ExFF();
160	<	usesDipoles = 1;
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	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163	<	else{
164	<	sprintf( painCave.errMsg,
165	<	"SimSetup Error. Unrecognized force field -> %s\n",
166	<	force_field );
167	<	painCave.isFatal = 1;
168	<	simError();
169	<	}
104	>
105
106	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "ForceField creation successful" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
175	<
106	>	// check on the post processing info
107
108	+	finalInfoCheck();
109
178	–	// get the components and calculate the tot_nMol and indvidual n_mol
179	–	the_components = the_globals->getComponents();
180	–	components_nmol = new int[n_components];
181	–	comp_stamps = new MoleculeStamp*[n_components];
110
183	–	if( !the_globals->haveNMol() ){
184	–	// we don't have the total number of molecules, so we assume it is
185	–	// given in each component
111
187	–	tot_nmol = 0;
188	–	for( i=0; i<n_components; i++ ){
112
113	<	if( !the_components[i]->haveNMol() ){
191	<	// we have a problem
192	<	sprintf( painCave.errMsg,
193	<	"SimSetup Error. No global NMol or component NMol"
194	<	" given. Cannot calculate the number of atoms.\n" );
195	<	painCave.isFatal = 1;
196	<	simError();
197	<	}
113	>	// initialize the system coordinates
114
115	<	tot_nmol += the_components[i]->getNMol();
200	<	components_nmol[i] = the_components[i]->getNMol();
201	<	}
202	<	}
203	<	else{
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup error.\n"
206	<	"\tSorry, the ability to specify total"
207	<	" nMols and then give molfractions in the components\n"
208	<	"\tis not currently supported."
209	<	" Please give nMol in the components.\n" );
210	<	painCave.isFatal = 1;
211	<	simError();
212	<
213	<
214	<	//     tot_nmol = the_globals->getNMol();
215	<
216	<	//   //we have the total number of molecules, now we check for molfractions
217	<	//     for( i=0; i<n_components; i++ ){
218	<
219	<	//       if( !the_components[i]->haveMolFraction() ){
220	<
221	<	//  if( !the_components[i]->haveNMol() ){
222	<	//    //we have a problem
223	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	<	//              << " nMol was given in component
225	<
226	<	}
227	<
228	<	#ifdef IS_MPI
229	<	strcpy( checkPointMsg, "Have the number of components" );
230	<	MPIcheckPoint();
231	<	#endif // is_mpi
232	<
233	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
235	<
236	<	simnfo->nComponents = n_components;
237	<	simnfo->componentsNmol = components_nmol;
238	<	simnfo->compStamps = comp_stamps;
239	<	simnfo->headStamp = new LinkedMolStamp();
240	<
241	<	char* id;
242	<	LinkedMolStamp* headStamp = simnfo->headStamp;
243	<	LinkedMolStamp* currentStamp = NULL;
244	<	for( i=0; i<n_components; i++ ){
245	<
246	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
250	<
251	<	comp_stamps[i] = headStamp->match( id );
252	<	if( comp_stamps[i] == NULL ){
253	<
254	<	// extract the component from the list;
255	<
256	<	currentStamp = the_stamps->extractMolStamp( id );
257	<	if( currentStamp == NULL ){
258	<	sprintf( painCave.errMsg,
259	<	"SimSetup error: Component \"%s\" was not found in the "
260	<	"list of declared molecules\n",
261	<	id );
262	<	painCave.isFatal = 1;
263	<	simError();
264	<	}
265	<
266	<	headStamp->add( currentStamp );
267	<	comp_stamps[i] = headStamp->match( id );
268	<	}
269	<	}
270	<
271	<	#ifdef IS_MPI
272	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	<	MPIcheckPoint();
274	<	#endif // is_mpi
115	>	initSystemCoords();
116
117
118	+	// make the output filenames
119
120	+	makeOutNames();
121	+
122	+
123	+
124
125	<	// caclulate the number of atoms, bonds, bends and torsions
125	>
126
281	–	tot_atoms = 0;
282	–	tot_bonds = 0;
283	–	tot_bends = 0;
284	–	tot_torsions = 0;
285	–	for( i=0; i<n_components; i++ ){
286	–
287	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
288	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
289	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
290	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
291	–	}
292	–
293	–	tot_SRI = tot_bonds + tot_bends + tot_torsions;
294	–
295	–	simnfo->n_atoms = tot_atoms;
296	–	simnfo->n_bonds = tot_bonds;
297	–	simnfo->n_bends = tot_bends;
298	–	simnfo->n_torsions = tot_torsions;
299	–	simnfo->n_SRI = tot_SRI;
300	–	simnfo->n_mol = tot_nmol;
127
302	–	simnfo->molMembershipArray = new int[tot_atoms];
128
304	–	#ifdef IS_MPI
129
130	<	// divide the molecules among processors here.
130	>	// make the integrator
131
308	–	mpiSim = new mpiSimulation( simnfo );
132
133	<	globalIndex = mpiSim->divideLabor();
133	>	NVT*  myNVT = NULL;
134	>	NPTi* myNPTi = NULL;
135	>	NPTf* myNPTf = NULL;
136	>	NPTim* myNPTim = NULL;
137	>	NPTfm* myNPTfm = NULL;
138
139	<	// set up the local variables
313	<
314	<	int localMol, allMol;
315	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
139	>	switch( ensembleCase ){
140
141	<	int* mol2proc = mpiSim->getMolToProcMap();
142	<	int* molCompType = mpiSim->getMolComponentType();
143	<
320	<	allMol = 0;
321	<	localMol = 0;
322	<	local_atoms = 0;
323	<	local_bonds = 0;
324	<	local_bends = 0;
325	<	local_torsions = 0;
326	<	globalAtomIndex = 0;
141	>	case NVE_ENS:
142	>	new NVE( info, the_ff );
143	>	break;
144
145	+	case NVT_ENS:
146	+	myNVT = new NVT( info, the_ff );
147	+	myNVT->setTargetTemp(the_globals->getTargetTemp());
148
149	<	for( i=0; i<n_components; i++ ){
149	>	if (the_globals->haveTauThermostat())
150	>	myNVT->setTauThermostat(the_globals->getTauThermostat());
151
152	<	for( j=0; j<components_nmol[i]; j++ ){
153	<
154	<	if( mol2proc[allMol] == worldRank ){
155	<
156	<	local_atoms +=    comp_stamps[i]->getNAtoms();
157	<	local_bonds +=    comp_stamps[i]->getNBonds();
337	<	local_bends +=    comp_stamps[i]->getNBends();
338	<	local_torsions += comp_stamps[i]->getNTorsions();
339	<	localMol++;
340	<	}
341	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
342	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
343	<	globalAtomIndex++;
344	<	}
345	<
346	<	allMol++;
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	<	}
349	<	local_SRI = local_bonds + local_bends + local_torsions;
350	<
351	<	simnfo->n_atoms = mpiSim->getMyNlocal();
352	<
353	<	if( local_atoms != simnfo->n_atoms ){
354	<	sprintf( painCave.errMsg,
355	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
356	<	" localAtom (%d) are not equal.\n",
357	<	simnfo->n_atoms,
358	<	local_atoms );
359	<	painCave.isFatal = 1;
360	<	simError();
361	<	}
159	>	break;
160
161	<	simnfo->n_bonds = local_bonds;
162	<	simnfo->n_bends = local_bends;
163	<	simnfo->n_torsions = local_torsions;
366	<	simnfo->n_SRI = local_SRI;
367	<	simnfo->n_mol = localMol;
161	>	case NPTi_ENS:
162	>	myNPTi = new NPTi( info, the_ff );
163	>	myNPTi->setTargetTemp( the_globals->getTargetTemp() );
164
165	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
166	<	MPIcheckPoint();
167	<
168	<
169	<	#endif // is_mpi
170	<
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	>	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	<	// create the atom and short range interaction arrays
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	<	Atom::createArrays(simnfo->n_atoms);
197	<	the_atoms = new Atom*[simnfo->n_atoms];
198	<	the_molecules = new Molecule[simnfo->n_mol];
381	<	int molIndex;
196	>	case NPTf_ENS:
197	>	myNPTf = new NPTf( info, the_ff );
198	>	myNPTf->setTargetTemp( the_globals->getTargetTemp());
199
200	<	// initialize the molecule's stampID's
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	<	#ifdef IS_MPI
211	<
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	<	molIndex = 0;
221	<	for(i=0; i<mpiSim->getTotNmol(); i++){
222	<
223	<	if(mol2proc[i] == worldRank ){
224	<	the_molecules[molIndex].setStampID( molCompType[i] );
225	<	the_molecules[molIndex].setMyIndex( molIndex );
226	<	the_molecules[molIndex].setGlobalIndex( i );
227	<	molIndex++;
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	<	}
398	<
399	<	#else // is_mpi
400	<
401	<	molIndex = 0;
402	<	globalAtomIndex = 0;
403	<	for(i=0; i<n_components; i++){
404	<	for(j=0; j<components_nmol[i]; j++ ){
405	<	the_molecules[molIndex].setStampID( i );
406	<	the_molecules[molIndex].setMyIndex( molIndex );
407	<	the_molecules[molIndex].setGlobalIndex( molIndex );
408	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
409	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
410	<	globalAtomIndex++;
411	<	}
412	<	molIndex++;
413	<	}
414	<	}
229	>	break;
230
231	+	case NPTim_ENS:
232	+	myNPTim = new NPTim( info, the_ff );
233	+	myNPTim->setTargetTemp( the_globals->getTargetTemp());
234
235	<	#endif // is_mpi
236	<
237	<
420	<	if( simnfo->n_SRI ){
421	<
422	<	Exclude::createArray(simnfo->n_SRI);
423	<	the_excludes = new Exclude*[simnfo->n_SRI];
424	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
425	<	simnfo->globalExcludes = new int;
426	<	simnfo->n_exclude = simnfo->n_SRI;
427	<	}
428	<	else{
429	<
430	<	Exclude::createArray( 1 );
431	<	the_excludes = new Exclude*;
432	<	the_excludes[0] = new Exclude(0);
433	<	the_excludes[0]->setPair( 0,0 );
434	<	simnfo->globalExcludes = new int;
435	<	simnfo->globalExcludes[0] = 0;
436	<	simnfo->n_exclude = 0;
437	<	}
438	<
439	<	// set the arrays into the SimInfo object
440	<
441	<	simnfo->atoms = the_atoms;
442	<	simnfo->molecules = the_molecules;
443	<	simnfo->nGlobalExcludes = 0;
444	<	simnfo->excludes = the_excludes;
445	<
446	<
447	<	// get some of the tricky things that may still be in the globals
448	<
449	<
450	<	if( the_globals->haveBox() ){
451	<	simnfo->box_x = the_globals->getBox();
452	<	simnfo->box_y = the_globals->getBox();
453	<	simnfo->box_z = the_globals->getBox();
454	<	}
455	<	else if( the_globals->haveDensity() ){
456	<
457	<	double vol;
458	<	vol = (double)tot_nmol / the_globals->getDensity();
459	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
460	<	simnfo->box_y = simnfo->box_x;
461	<	simnfo->box_z = simnfo->box_x;
462	<	}
463	<	else{
464	<	if( !the_globals->haveBoxX() ){
235	>	if (the_globals->haveTargetPressure())
236	>	myNPTim->setTargetPressure(the_globals->getTargetPressure());
237	>	else {
238		sprintf( painCave.errMsg,
239	<	"SimSetup error, no periodic BoxX size given.\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	<	simnfo->box_x = the_globals->getBoxX();
245	<
246	<	if( !the_globals->haveBoxY() ){
244	>
245	>	if( the_globals->haveTauThermostat() )
246	>	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
247	>	else{
248		sprintf( painCave.errMsg,
249	<	"SimSetup error, no periodic BoxY size given.\n" );
249	>	"SimSetup error: If you use an NPT\n"
250	>	"    ensemble, you must set tauThermostat.\n");
251		painCave.isFatal = 1;
252		simError();
253		}
478	–	simnfo->box_y = the_globals->getBoxY();
254
255	<	if( !the_globals->haveBoxZ() ){
255	>	if( the_globals->haveTauBarostat() )
256	>	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
257	>	else{
258		sprintf( painCave.errMsg,
259	<	"SimSetup error, no periodic BoxZ size given.\n" );
259	>	"SimSetup error: If you use an NPT\n"
260	>	"    ensemble, you must set tauBarostat.\n");
261		painCave.isFatal = 1;
262		simError();
263		}
264	<	simnfo->box_z = the_globals->getBoxZ();
487	<	}
264	>	break;
265
266	<	#ifdef IS_MPI
267	<	strcpy( checkPointMsg, "Box size set up" );
268	<	MPIcheckPoint();
492	<	#endif // is_mpi
266	>	case NPTfm_ENS:
267	>	myNPTfm = new NPTfm( info, the_ff );
268	>	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
269
270	<
271	<	// initialize the arrays
272	<
497	<	the_ff->setSimInfo( simnfo );
498	<
499	<	makeMolecules();
500	<	simnfo->identArray = new int[simnfo->n_atoms];
501	<	for(i=0; i<simnfo->n_atoms; i++){
502	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
503	<	}
504	<
505	<	if (the_globals->getUseRF() ) {
506	<	simnfo->useReactionField = 1;
507	<
508	<	if( !the_globals->haveECR() ){
270	>	if (the_globals->haveTargetPressure())
271	>	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
272	>	else {
273		sprintf( painCave.errMsg,
274	<	"SimSetup Warning: using default value of 1/2 the smallest "
275	<	"box length for the electrostaticCutoffRadius.\n"
276	<	"I hope you have a very fast processor!\n");
513	<	painCave.isFatal = 0;
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();
515	–	double smallest;
516	–	smallest = simnfo->box_x;
517	–	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
518	–	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
519	–	simnfo->ecr = 0.5 * smallest;
520	–	} else {
521	–	simnfo->ecr        = the_globals->getECR();
278		}
523	–
524	–	if( !the_globals->haveEST() ){
525	–	sprintf( painCave.errMsg,
526	–	"SimSetup Warning: using default value of 0.05 * the "
527	–	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
528	–	);
529	–	painCave.isFatal = 0;
530	–	simError();
531	–	simnfo->est = 0.05 * simnfo->ecr;
532	–	} else {
533	–	simnfo->est        = the_globals->getEST();
534	–	}
279
280	<	if(!the_globals->haveDielectric() ){
280	>	if( the_globals->haveTauThermostat() )
281	>	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
282	>	else{
283		sprintf( painCave.errMsg,
284	<	"SimSetup Error: You are trying to use Reaction Field without"
285	<	"setting a dielectric constant!\n"
540	<	);
284	>	"SimSetup error: If you use an NPT\n"
285	>	"    ensemble, you must set tauThermostat.\n");
286		painCave.isFatal = 1;
287		simError();
288		}
544	–	simnfo->dielectric = the_globals->getDielectric();
545	–	} else {
546	–	if (usesDipoles) {
547	–
548	–	if( !the_globals->haveECR() ){
549	–	sprintf( painCave.errMsg,
550	–	"SimSetup Warning: using default value of 1/2 the smallest "
551	–	"box length for the electrostaticCutoffRadius.\n"
552	–	"I hope you have a very fast processor!\n");
553	–	painCave.isFatal = 0;
554	–	simError();
555	–	double smallest;
556	–	smallest = simnfo->box_x;
557	–	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
558	–	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
559	–	simnfo->ecr = 0.5 * smallest;
560	–	} else {
561	–	simnfo->ecr        = the_globals->getECR();
562	–	}
563	–
564	–	if( !the_globals->haveEST() ){
565	–	sprintf( painCave.errMsg,
566	–	"SimSetup Warning: using default value of 5%% of the "
567	–	"electrostaticCutoffRadius for the "
568	–	"electrostaticSkinThickness\n"
569	–	);
570	–	painCave.isFatal = 0;
571	–	simError();
572	–	simnfo->est = 0.05 * simnfo->ecr;
573	–	} else {
574	–	simnfo->est        = the_globals->getEST();
575	–	}
576	–	}
577	–	}
289
290	<	#ifdef IS_MPI
291	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
581	<	MPIcheckPoint();
582	<	#endif // is_mpi
583	<
584	<	if( the_globals->haveInitialConfig() ){
585	<
586	<	InitializeFromFile* fileInit;
587	<	#ifdef IS_MPI // is_mpi
588	<	if( worldRank == 0 ){
589	<	#endif //is_mpi
590	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
591	<	#ifdef IS_MPI
592	<	}else fileInit = new InitializeFromFile( NULL );
593	<	#endif
594	<	fileInit->read_xyz( simnfo ); // default velocities on
595	<
596	<	delete fileInit;
597	<	}
598	<	else{
599	<
600	<	#ifdef IS_MPI
601	<
602	<	// no init from bass
603	<
604	<	sprintf( painCave.errMsg,
605	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
606	<	painCave.isFatal;
607	<	simError();
608	<
609	<	#else
610	<
611	<	initFromBass();
612	<
613	<
614	<	#endif
615	<	}
616	<
617	<	#ifdef IS_MPI
618	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
619	<	MPIcheckPoint();
620	<	#endif // is_mpi
621	<
622	<
623	<
624	<
625	<
626	<
627	<
628	<	#ifdef IS_MPI
629	<	if( worldRank == 0 ){
630	<	#endif // is_mpi
631	<
632	<	if( the_globals->haveFinalConfig() ){
633	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
634	<	}
290	>	if( the_globals->haveTauBarostat() )
291	>	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
292		else{
293	<	strcpy( simnfo->finalName, inFileName );
294	<	char* endTest;
295	<	int nameLength = strlen( simnfo->finalName );
296	<	endTest = &(simnfo->finalName[nameLength - 5]);
297	<	if( !strcmp( endTest, ".bass" ) ){
641	<	strcpy( endTest, ".eor" );
642	<	}
643	<	else if( !strcmp( endTest, ".BASS" ) ){
644	<	strcpy( endTest, ".eor" );
645	<	}
646	<	else{
647	<	endTest = &(simnfo->finalName[nameLength - 4]);
648	<	if( !strcmp( endTest, ".bss" ) ){
649	<	strcpy( endTest, ".eor" );
650	<	}
651	<	else if( !strcmp( endTest, ".mdl" ) ){
652	<	strcpy( endTest, ".eor" );
653	<	}
654	<	else{
655	<	strcat( simnfo->finalName, ".eor" );
656	<	}
657	<	}
293	>	sprintf( painCave.errMsg,
294	>	"SimSetup error: If you use an NPT\n"
295	>	"    ensemble, you must set tauBarostat.\n");
296	>	painCave.isFatal = 1;
297	>	simError();
298		}
299	<
660	<	// make the sample and status out names
661	<
662	<	strcpy( simnfo->sampleName, inFileName );
663	<	char* endTest;
664	<	int nameLength = strlen( simnfo->sampleName );
665	<	endTest = &(simnfo->sampleName[nameLength - 5]);
666	<	if( !strcmp( endTest, ".bass" ) ){
667	<	strcpy( endTest, ".dump" );
668	<	}
669	<	else if( !strcmp( endTest, ".BASS" ) ){
670	<	strcpy( endTest, ".dump" );
671	<	}
672	<	else{
673	<	endTest = &(simnfo->sampleName[nameLength - 4]);
674	<	if( !strcmp( endTest, ".bss" ) ){
675	<	strcpy( endTest, ".dump" );
676	<	}
677	<	else if( !strcmp( endTest, ".mdl" ) ){
678	<	strcpy( endTest, ".dump" );
679	<	}
680	<	else{
681	<	strcat( simnfo->sampleName, ".dump" );
682	<	}
683	<	}
684	<
685	<	strcpy( simnfo->statusName, inFileName );
686	<	nameLength = strlen( simnfo->statusName );
687	<	endTest = &(simnfo->statusName[nameLength - 5]);
688	<	if( !strcmp( endTest, ".bass" ) ){
689	<	strcpy( endTest, ".stat" );
690	<	}
691	<	else if( !strcmp( endTest, ".BASS" ) ){
692	<	strcpy( endTest, ".stat" );
693	<	}
694	<	else{
695	<	endTest = &(simnfo->statusName[nameLength - 4]);
696	<	if( !strcmp( endTest, ".bss" ) ){
697	<	strcpy( endTest, ".stat" );
698	<	}
699	<	else if( !strcmp( endTest, ".mdl" ) ){
700	<	strcpy( endTest, ".stat" );
701	<	}
702	<	else{
703	<	strcat( simnfo->statusName, ".stat" );
704	<	}
705	<	}
706	<
707	<	#ifdef IS_MPI
708	<	}
709	<	#endif // is_mpi
710	<
711	<	// set the status, sample, and themal kick times
712	<
713	<	if( the_globals->haveSampleTime() ){
714	<	simnfo->sampleTime = the_globals->getSampleTime();
715	<	simnfo->statusTime = simnfo->sampleTime;
716	<	simnfo->thermalTime = simnfo->sampleTime;
717	<	}
718	<	else{
719	<	simnfo->sampleTime = the_globals->getRunTime();
720	<	simnfo->statusTime = simnfo->sampleTime;
721	<	simnfo->thermalTime = simnfo->sampleTime;
722	<	}
299	>	break;
300
301	<	if( the_globals->haveStatusTime() ){
302	<	simnfo->statusTime = the_globals->getStatusTime();
303	<	}
304	<
305	<	if( the_globals->haveThermalTime() ){
729	<	simnfo->thermalTime = the_globals->getThermalTime();
301	>	default:
302	>	sprintf( painCave.errMsg,
303	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
304	>	painCave.isFatal = 1;
305	>	simError();
306		}
307
732	–	// check for the temperature set flag
308
734	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
735	–
736	–
737	–	// make the integrator
738	–
739	–
740	–	if( !strcmp( ensemble, "TraPPE_Ex" ) ){
741	–	new Symplectic(simnfo, the_ff, the_extendedsystem);
742	–	}
743	–	else if( !strcmp( force_field, "LJ" ) ){
744	–	new Verlet( *simnfo, the_ff, the_extendedsystem );
745	–	}
746	–
309		#ifdef IS_MPI
310		mpiSim->mpiRefresh();
311		#endif
#	Line 751 | Line 313 | void SimSetup::createSim( void ){
313		// initialize the Fortran
314
315
316	<	simnfo->refreshSim();
316	>	info->refreshSim();
317
318	<	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 804 | Line 366 | void SimSetup::makeMolecules( void ){
366
367		atomOffset = 0;
368		excludeOffset = 0;
369	<	for(i=0; i<simnfo->n_mol; i++){
369	>	for(i=0; i<info->n_mol; i++){
370
371		stampID = the_molecules[i].getStampID();
372
#	Line 832 | Line 394 | void SimSetup::makeMolecules( void ){
394		if( currentAtom->haveOrientation() ){
395
396		dAtom = new DirectionalAtom(j + atomOffset);
397	<	simnfo->n_oriented++;
397	>	info->n_oriented++;
398		info.myAtoms[j] = dAtom;
399
400		ux = currentAtom->getOrntX();
#	Line 1056 | 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 1073 | 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 1155 | 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 1217 | 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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