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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 435 by mmeineke, Fri Mar 28 19:33:37 2003 UTC vs.
Revision 614 by mmeineke, Tue Jul 15 17:57:04 2003 UTC

#	Line 12 | Line 12 | SimSetup::SimSetup(){
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;
70	<
71	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
74	<
75	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
79	<
80	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
85	<
86	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
89	<
90	<
91	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
100	<
101	<	#ifdef IS_MPI
102	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#endif // is_mpi
105	<
83	>	int i, j, k, globalAtomIndex;
84
85	+	// gather all of the information from the Bass file
86	+
87	+	gatherInfo();
88
89	<	// get the components and calculate the tot_nMol and indvidual n_mol
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
89	>	// creation of complex system objects
90
91	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// given in each component
91	>	sysObjectsCreation();
92
117	–	tot_nmol = 0;
118	–	for( i=0; i<n_components; i++ ){
93
120	–	if( !the_components[i]->haveNMol() ){
121	–	// we have a problem
122	–	sprintf( painCave.errMsg,
123	–	"SimSetup Error. No global NMol or component NMol"
124	–	" given. Cannot calculate the number of atoms.\n" );
125	–	painCave.isFatal = 1;
126	–	simError();
127	–	}
94
95	<	tot_nmol += the_components[i]->getNMol();
130	<	components_nmol[i] = the_components[i]->getNMol();
131	<	}
132	<	}
133	<	else{
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error.\n"
136	<	"\tSorry, the ability to specify total"
137	<	" nMols and then give molfractions in the components\n"
138	<	"\tis not currently supported."
139	<	" Please give nMol in the components.\n" );
140	<	painCave.isFatal = 1;
141	<	simError();
142	<
143	<
144	<	//     tot_nmol = the_globals->getNMol();
145	<
146	<	//   //we have the total number of molecules, now we check for molfractions
147	<	//     for( i=0; i<n_components; i++ ){
148	<
149	<	//       if( !the_components[i]->haveMolFraction() ){
150	<
151	<	//  if( !the_components[i]->haveNMol() ){
152	<	//    //we have a problem
153	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	<	//              << " nMol was given in component
155	<
156	<	}
95	>	// initialize the arrays
96
97	<	#ifdef IS_MPI
159	<	strcpy( checkPointMsg, "Have the number of components" );
160	<	MPIcheckPoint();
161	<	#endif // is_mpi
97	>
98
99	<	// make an array of molecule stamps that match the components used.
100	<	// also extract the used stamps out into a separate linked list
101	<
102	<	simnfo->nComponents = n_components;
103	<	simnfo->componentsNmol = components_nmol;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
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
171	–	char* id;
172	–	LinkedMolStamp* headStamp = simnfo->headStamp;
173	–	LinkedMolStamp* currentStamp = NULL;
174	–	for( i=0; i<n_components; i++ ){
105
106	<	id = the_components[i]->getType();
177	<	comp_stamps[i] = NULL;
178	<
179	<	// check to make sure the component isn't already in the list
180	<
181	<	comp_stamps[i] = headStamp->match( id );
182	<	if( comp_stamps[i] == NULL ){
183	<
184	<	// extract the component from the list;
185	<
186	<	currentStamp = the_stamps->extractMolStamp( id );
187	<	if( currentStamp == NULL ){
188	<	sprintf( painCave.errMsg,
189	<	"SimSetup error: Component \"%s\" was not found in the "
190	<	"list of declared molecules\n",
191	<	id );
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	headStamp->add( currentStamp );
197	<	comp_stamps[i] = headStamp->match( id );
198	<	}
199	<	}
200	<
201	<	#ifdef IS_MPI
202	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
203	<	MPIcheckPoint();
204	<	#endif // is_mpi
106	>	// check on the post processing info
107
108	+	finalInfoCheck();
109
110
111
209	–	// caclulate the number of atoms, bonds, bends and torsions
112
113	<	tot_atoms = 0;
212	<	tot_bonds = 0;
213	<	tot_bends = 0;
214	<	tot_torsions = 0;
215	<	for( i=0; i<n_components; i++ ){
216	<
217	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	<	}
113	>	// initialize the system coordinates
114
115	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
224	<
225	<	simnfo->n_atoms = tot_atoms;
226	<	simnfo->n_bonds = tot_bonds;
227	<	simnfo->n_bends = tot_bends;
228	<	simnfo->n_torsions = tot_torsions;
229	<	simnfo->n_SRI = tot_SRI;
230	<	simnfo->n_mol = tot_nmol;
231	<
115	>	initSystemCoords();
116
233	–	#ifdef IS_MPI
117
118	<	// divide the molecules among processors here.
236	<
237	<	mpiSim = new mpiSimulation( simnfo );
238	<
239	<
118	>	// make the output filenames
119
120	<	globalIndex = mpiSim->divideLabor();
121	<
122	<	// set up the local variables
120	>	makeOutNames();
121	>
122	>
123
245	–	int localMol, allMol;
246	–	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
124
248	–	int* mol2proc = mpiSim->getMolToProcMap();
249	–	int* molCompType = mpiSim->getMolComponentType();
125
251	–	allMol = 0;
252	–	localMol = 0;
253	–	local_atoms = 0;
254	–	local_bonds = 0;
255	–	local_bends = 0;
256	–	local_torsions = 0;
257	–	for( i=0; i<n_components; i++ ){
126
259	–	for( j=0; j<components_nmol[i]; j++ ){
260	–
261	–	if( mol2proc[j] == worldRank ){
262	–
263	–	local_atoms +=    comp_stamps[i]->getNAtoms();
264	–	local_bonds +=    comp_stamps[i]->getNBonds();
265	–	local_bends +=    comp_stamps[i]->getNBends();
266	–	local_torsions += comp_stamps[i]->getNTorsions();
267	–	localMol++;
268	–	}
269	–	allMol++;
270	–	}
271	–	}
272	–	local_SRI = local_bonds + local_bends + local_torsions;
127
128
275	–	simnfo->n_atoms = mpiSim->getMyNlocal();
276	–
277	–	if( local_atoms != simnfo->n_atoms ){
278	–	sprintf( painCave.errMsg,
279	–	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
280	–	" localAtom (%d) are not equal.\n",
281	–	simnfo->n_atoms,
282	–	local_atoms );
283	–	painCave.isFatal = 1;
284	–	simError();
285	–	}
129
130	<	simnfo->n_bonds = local_bonds;
288	<	simnfo->n_bends = local_bends;
289	<	simnfo->n_torsions = local_torsions;
290	<	simnfo->n_SRI = local_SRI;
291	<	simnfo->n_mol = localMol;
292	<
293	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
294	<	MPIcheckPoint();
130	>	// make the integrator
131
132
133	<	#endif // is_mpi
134	<
133	>	NVT*  myNVT = NULL;
134	>	NPTi* myNPTi = NULL;
135	>	NPTf* myNPTf = NULL;
136	>	NPTim* myNPTim = NULL;
137	>	NPTfm* myNPTfm = NULL;
138
139	<	// create the atom and short range interaction arrays
139	>	switch( ensembleCase ){
140
141	<	Atom::createArrays(simnfo->n_atoms);
142	<	the_atoms = new Atom*[simnfo->n_atoms];
143	<	the_molecules = new Molecule[simnfo->n_mol];
305	<	int molIndex;
141	>	case NVE_ENS:
142	>	new NVE( info, the_ff );
143	>	break;
144
145	<	// initialize the molecule's stampID's
145	>	case NVT_ENS:
146	>	myNVT = new NVT( info, the_ff );
147	>	myNVT->setTargetTemp(the_globals->getTargetTemp());
148
149	<	#ifdef IS_MPI
150	<
149	>	if (the_globals->haveTauThermostat())
150	>	myNVT->setTauThermostat(the_globals->getTauThermostat());
151
152	<	molIndex = 0;
153	<	for(i=0; i<mpiSim->getTotNmol(); i++){
154	<
155	<	if(mol2proc[i] == worldRank ){
156	<	the_molecules[molIndex].setStampID( molCompType[i] );
157	<	molIndex++;
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	<	}
159	>	break;
160
161	<	#else // is_mpi
162	<
163	<	molIndex = 0;
324	<	for(i=0; i<n_components; i++){
325	<	for(j=0; j<components_nmol[i]; j++ ){
326	<	the_molecules[molIndex].setStampID( i );
327	<	molIndex++;
328	<	}
329	<	}
330	<
161	>	case NPTi_ENS:
162	>	myNPTi = new NPTi( info, the_ff );
163	>	myNPTi->setTargetTemp( the_globals->getTargetTemp() );
164
165	<	#endif // is_mpi
166	<
167	<
335	<	if( simnfo->n_SRI ){
336	<
337	<	std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
338	<
339	<	Exclude::createArray(simnfo->n_SRI);
340	<	the_excludes = new Exclude*[simnfo->n_SRI];
341	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
342	<	simnfo->globalExcludes = new int;
343	<	simnfo->n_exclude = tot_SRI;
344	<	}
345	<	else{
346	<
347	<	Exclude::createArray( 1 );
348	<	the_excludes = new Exclude*;
349	<	the_excludes[0] = new Exclude(0);
350	<	the_excludes[0]->setPair( 0,0 );
351	<	simnfo->globalExcludes = new int;
352	<	simnfo->globalExcludes[0] = 0;
353	<	simnfo->n_exclude = 0;
354	<	}
355	<
356	<	// set the arrays into the SimInfo object
357	<
358	<	simnfo->atoms = the_atoms;
359	<	simnfo->molecules = the_molecules;
360	<	simnfo->nGlobalExcludes = 0;
361	<	simnfo->excludes = the_excludes;
362	<
363	<
364	<	// get some of the tricky things that may still be in the globals
365	<
366	<
367	<	if( the_globals->haveBox() ){
368	<	simnfo->box_x = the_globals->getBox();
369	<	simnfo->box_y = the_globals->getBox();
370	<	simnfo->box_z = the_globals->getBox();
371	<	}
372	<	else if( the_globals->haveDensity() ){
373	<
374	<	double vol;
375	<	vol = (double)tot_nmol / the_globals->getDensity();
376	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
377	<	simnfo->box_y = simnfo->box_x;
378	<	simnfo->box_z = simnfo->box_x;
379	<	}
380	<	else{
381	<	if( !the_globals->haveBoxX() ){
165	>	if (the_globals->haveTargetPressure())
166	>	myNPTi->setTargetPressure(the_globals->getTargetPressure());
167	>	else {
168		sprintf( painCave.errMsg,
169	<	"SimSetup error, no periodic BoxX size given.\n" );
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	<	simnfo->box_x = the_globals->getBoxX();
175	<
176	<	if( !the_globals->haveBoxY() ){
174	>
175	>	if( the_globals->haveTauThermostat() )
176	>	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
177	>	else{
178		sprintf( painCave.errMsg,
179	<	"SimSetup error, no periodic BoxY size given.\n" );
179	>	"SimSetup error: If you use an NPT\n"
180	>	"    ensemble, you must set tauThermostat.\n");
181		painCave.isFatal = 1;
182		simError();
183		}
395	–	simnfo->box_y = the_globals->getBoxY();
184
185	<	if( !the_globals->haveBoxZ() ){
185	>	if( the_globals->haveTauBarostat() )
186	>	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
187	>	else{
188		sprintf( painCave.errMsg,
189	<	"SimSetup error, no periodic BoxZ size given.\n" );
189	>	"SimSetup error: If you use an NPT\n"
190	>	"    ensemble, you must set tauBarostat.\n");
191		painCave.isFatal = 1;
192		simError();
193		}
194	<	simnfo->box_z = the_globals->getBoxZ();
404	<	}
194	>	break;
195
196	<	#ifdef IS_MPI
197	<	strcpy( checkPointMsg, "Box size set up" );
198	<	MPIcheckPoint();
409	<	#endif // is_mpi
196	>	case NPTf_ENS:
197	>	myNPTf = new NPTf( info, the_ff );
198	>	myNPTf->setTargetTemp( the_globals->getTargetTemp());
199
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	<	// initialize the arrays
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	<	the_ff->setSimInfo( simnfo );
221	<
222	<	makeMolecules();
417	<	simnfo->identArray = new int[simnfo->n_atoms];
418	<	for(i=0; i<simnfo->n_atoms; i++){
419	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
420	<	}
421	<
422	<	if (the_globals->getUseRF() ) {
423	<	simnfo->useReactionField = 1;
424	<
425	<	if( !the_globals->haveECR() ){
220	>	if( the_globals->haveTauBarostat() )
221	>	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
222	>	else{
223		sprintf( painCave.errMsg,
224	<	"SimSetup Warning: using default value of 1/2 the smallest "
225	<	"box length for the electrostaticCutoffRadius.\n"
226	<	"I hope you have a very fast processor!\n");
430	<	painCave.isFatal = 0;
224	>	"SimSetup error: If you use an NPT\n"
225	>	"    ensemble, you must set tauBarostat.\n");
226	>	painCave.isFatal = 1;
227		simError();
432	–	double smallest;
433	–	smallest = simnfo->box_x;
434	–	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
435	–	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
436	–	simnfo->ecr = 0.5 * smallest;
437	–	} else {
438	–	simnfo->ecr        = the_globals->getECR();
228		}
229	+	break;
230	+
231	+	case NPTim_ENS:
232	+	myNPTim = new NPTim( info, the_ff );
233	+	myNPTim->setTargetTemp( the_globals->getTargetTemp());
234
235	<	if( !the_globals->haveEST() ){
235	>	if (the_globals->haveTargetPressure())
236	>	myNPTim->setTargetPressure(the_globals->getTargetPressure());
237	>	else {
238		sprintf( painCave.errMsg,
239	<	"SimSetup Warning: using default value of 0.05 * the "
240	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
241	<	);
446	<	painCave.isFatal = 0;
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();
448	–	simnfo->est = 0.05 * simnfo->ecr;
449	–	} else {
450	–	simnfo->est        = the_globals->getEST();
243		}
244
245	<	if(!the_globals->haveDielectric() ){
245	>	if( the_globals->haveTauThermostat() )
246	>	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
247	>	else{
248		sprintf( painCave.errMsg,
249	<	"SimSetup Error: You are trying to use Reaction Field without"
250	<	"setting a dielectric constant!\n"
457	<	);
249	>	"SimSetup error: If you use an NPT\n"
250	>	"    ensemble, you must set tauThermostat.\n");
251		painCave.isFatal = 1;
252		simError();
253		}
254	<	simnfo->dielectric = the_globals->getDielectric();
255	<	} else {
256	<	if (simnfo->n_dipoles) {
257	<
258	<	if( !the_globals->haveECR() ){
259	<	sprintf( painCave.errMsg,
260	<	"SimSetup Warning: using default value of 1/2 the smallest"
261	<	"box length for the electrostaticCutoffRadius.\n"
262	<	"I hope you have a very fast processor!\n");
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	double smallest;
473	<	smallest = simnfo->box_x;
474	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
475	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
476	<	simnfo->ecr = 0.5 * smallest;
477	<	} else {
478	<	simnfo->ecr        = the_globals->getECR();
479	<	}
480	<
481	<	if( !the_globals->haveEST() ){
482	<	sprintf( painCave.errMsg,
483	<	"SimSetup Warning: using default value of 5% of the"
484	<	"electrostaticCutoffRadius for the "
485	<	"electrostaticSkinThickness\n"
486	<	);
487	<	painCave.isFatal = 0;
488	<	simError();
489	<	simnfo->est = 0.05 * simnfo->ecr;
490	<	} else {
491	<	simnfo->est        = the_globals->getEST();
492	<	}
254	>
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	<	}
264	>	break;
265
266	<	#ifdef IS_MPI
267	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
268	<	MPIcheckPoint();
499	<	#endif // is_mpi
266	>	case NPTfm_ENS:
267	>	myNPTfm = new NPTfm( info, the_ff );
268	>	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
269
270	<	if( the_globals->haveInitialConfig() ){
271	<
272	<	InitializeFromFile* fileInit;
273	<	#ifdef IS_MPI // is_mpi
274	<	if( worldRank == 0 ){
275	<	#endif //is_mpi
276	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
277	<	#ifdef IS_MPI
278	<	}else fileInit = new InitializeFromFile( NULL );
510	<	#endif
511	<	fileInit->read_xyz( simnfo ); // default velocities on
512	<
513	<	delete fileInit;
514	<	}
515	<	else{
516	<
517	<	#ifdef IS_MPI
518	<
519	<	// no init from bass
520	<
521	<	sprintf( painCave.errMsg,
522	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
523	<	painCave.isFatal;
524	<	simError();
525	<
526	<	#else
527	<
528	<	initFromBass();
529	<
530	<
531	<	#endif
532	<	}
533	<
534	<	#ifdef IS_MPI
535	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
536	<	MPIcheckPoint();
537	<	#endif // is_mpi
538	<
539	<
540	<
541	<
542	<
543	<
544	<
545	<	#ifdef IS_MPI
546	<	if( worldRank == 0 ){
547	<	#endif // is_mpi
270	>	if (the_globals->haveTargetPressure())
271	>	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
272	>	else {
273	>	sprintf( painCave.errMsg,
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
280	<	if( the_globals->haveFinalConfig() ){
281	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
551	<	}
280	>	if( the_globals->haveTauThermostat() )
281	>	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
282		else{
283	<	strcpy( simnfo->finalName, inFileName );
284	<	char* endTest;
285	<	int nameLength = strlen( simnfo->finalName );
286	<	endTest = &(simnfo->finalName[nameLength - 5]);
287	<	if( !strcmp( endTest, ".bass" ) ){
558	<	strcpy( endTest, ".eor" );
559	<	}
560	<	else if( !strcmp( endTest, ".BASS" ) ){
561	<	strcpy( endTest, ".eor" );
562	<	}
563	<	else{
564	<	endTest = &(simnfo->finalName[nameLength - 4]);
565	<	if( !strcmp( endTest, ".bss" ) ){
566	<	strcpy( endTest, ".eor" );
567	<	}
568	<	else if( !strcmp( endTest, ".mdl" ) ){
569	<	strcpy( endTest, ".eor" );
570	<	}
571	<	else{
572	<	strcat( simnfo->finalName, ".eor" );
573	<	}
574	<	}
283	>	sprintf( painCave.errMsg,
284	>	"SimSetup error: If you use an NPT\n"
285	>	"    ensemble, you must set tauThermostat.\n");
286	>	painCave.isFatal = 1;
287	>	simError();
288		}
289	<
290	<	// make the sample and status out names
291	<
579	<	strcpy( simnfo->sampleName, inFileName );
580	<	char* endTest;
581	<	int nameLength = strlen( simnfo->sampleName );
582	<	endTest = &(simnfo->sampleName[nameLength - 5]);
583	<	if( !strcmp( endTest, ".bass" ) ){
584	<	strcpy( endTest, ".dump" );
585	<	}
586	<	else if( !strcmp( endTest, ".BASS" ) ){
587	<	strcpy( endTest, ".dump" );
588	<	}
289	>
290	>	if( the_globals->haveTauBarostat() )
291	>	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
292		else{
293	<	endTest = &(simnfo->sampleName[nameLength - 4]);
294	<	if( !strcmp( endTest, ".bss" ) ){
295	<	strcpy( endTest, ".dump" );
296	<	}
297	<	else if( !strcmp( endTest, ".mdl" ) ){
595	<	strcpy( endTest, ".dump" );
596	<	}
597	<	else{
598	<	strcat( simnfo->sampleName, ".dump" );
599	<	}
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	<
602	<	strcpy( simnfo->statusName, inFileName );
603	<	nameLength = strlen( simnfo->statusName );
604	<	endTest = &(simnfo->statusName[nameLength - 5]);
605	<	if( !strcmp( endTest, ".bass" ) ){
606	<	strcpy( endTest, ".stat" );
607	<	}
608	<	else if( !strcmp( endTest, ".BASS" ) ){
609	<	strcpy( endTest, ".stat" );
610	<	}
611	<	else{
612	<	endTest = &(simnfo->statusName[nameLength - 4]);
613	<	if( !strcmp( endTest, ".bss" ) ){
614	<	strcpy( endTest, ".stat" );
615	<	}
616	<	else if( !strcmp( endTest, ".mdl" ) ){
617	<	strcpy( endTest, ".stat" );
618	<	}
619	<	else{
620	<	strcat( simnfo->statusName, ".stat" );
621	<	}
622	<	}
623	<
624	<	#ifdef IS_MPI
625	<	}
626	<	#endif // is_mpi
627	<
628	<	// set the status, sample, and themal kick times
629	<
630	<	if( the_globals->haveSampleTime() ){
631	<	simnfo->sampleTime = the_globals->getSampleTime();
632	<	simnfo->statusTime = simnfo->sampleTime;
633	<	simnfo->thermalTime = simnfo->sampleTime;
634	<	}
635	<	else{
636	<	simnfo->sampleTime = the_globals->getRunTime();
637	<	simnfo->statusTime = simnfo->sampleTime;
638	<	simnfo->thermalTime = simnfo->sampleTime;
639	<	}
299	>	break;
300
301	<	if( the_globals->haveStatusTime() ){
302	<	simnfo->statusTime = the_globals->getStatusTime();
303	<	}
304	<
305	<	if( the_globals->haveThermalTime() ){
646	<	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
649	–	// check for the temperature set flag
308
651	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
652	–
653	–
654	–	//   // make the longe range forces and the integrator
655	–
656	–	//   new AllLong( simnfo );
657	–
658	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
659	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
660	–
309		#ifdef IS_MPI
310		mpiSim->mpiRefresh();
311		#endif
#	Line 665 | 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 718 | 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 746 | 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 932 | Line 580 | void SimSetup::makeMolecules( void ){
580
581
582		the_molecules[i].initialize( info );
583	+
584	+
585		atomOffset += info.nAtoms;
586		delete[] theBonds;
587		delete[] theBends;
#	Line 968 | 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 985 | 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 1067 | 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 1129 | 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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