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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 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;
83	>	int i, j, k, globalAtomIndex;
84	>
85	>	// gather all of the information from the Bass file
86	>
87	>	gatherInfo();
88
89	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
89	>	// creation of complex system objects
90
91	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
91	>	sysObjectsCreation();
92
80	–	// get the ones we know are there, yet still may need some work.
81	–	n_components = the_globals->getNComponents();
82	–	strcpy( force_field, the_globals->getForceField() );
83	–	strcpy( ensemble, the_globals->getEnsemble() );
84	–	strcpy( simnfo->ensemble, ensemble );
93
86	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	–	simnfo->usePBC = the_globals->getPBC();
88	–
94
95	+	// initialize the arrays
96
97	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
98	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
99	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
100	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
101	<	else{
102	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
97	>
98	>
99	>	makeMolecules();
100	>	info->identArray = new int[info->n_atoms];
101	>	for(i=0; i<info->n_atoms; i++){
102	>	info->identArray[i] = the_atoms[i]->getIdent();
103		}
104	+
105
106	<	#ifdef IS_MPI
104	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
107	<
106	>	// check on the post processing info
107
108	+	finalInfoCheck();
109
110	–	// get the components and calculate the tot_nMol and indvidual n_mol
111	–	the_components = the_globals->getComponents();
112	–	components_nmol = new int[n_components];
113	–	comp_stamps = new MoleculeStamp*[n_components];
110
115	–	if( !the_globals->haveNMol() ){
116	–	// we don't have the total number of molecules, so we assume it is
117	–	// given in each component
111
119	–	tot_nmol = 0;
120	–	for( i=0; i<n_components; i++ ){
112
113	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
113	>	// initialize the system coordinates
114
115	<	tot_nmol += the_components[i]->getNMol();
116	<	components_nmol[i] = the_components[i]->getNMol();
133	<	}
134	<	}
135	<	else{
136	<	sprintf( painCave.errMsg,
137	<	"SimSetup error.\n"
138	<	"\tSorry, the ability to specify total"
139	<	" nMols and then give molfractions in the components\n"
140	<	"\tis not currently supported."
141	<	" Please give nMol in the components.\n" );
142	<	painCave.isFatal = 1;
143	<	simError();
144	<
145	<
146	<	//     tot_nmol = the_globals->getNMol();
147	<
148	<	//   //we have the total number of molecules, now we check for molfractions
149	<	//     for( i=0; i<n_components; i++ ){
150	<
151	<	//       if( !the_components[i]->haveMolFraction() ){
152	<
153	<	//  if( !the_components[i]->haveNMol() ){
154	<	//    //we have a problem
155	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	<	//              << " nMol was given in component
157	<
158	<	}
115	>	initSystemCoords();
116	>
117
118	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
118	>	// make the output filenames
119
120	<	// make an array of molecule stamps that match the components used.
121	<	// also extract the used stamps out into a separate linked list
120	>	makeOutNames();
121	>
122	>
123	>
124
168	–	simnfo->nComponents = n_components;
169	–	simnfo->componentsNmol = components_nmol;
170	–	simnfo->compStamps = comp_stamps;
171	–	simnfo->headStamp = new LinkedMolStamp();
125
173	–	char* id;
174	–	LinkedMolStamp* headStamp = simnfo->headStamp;
175	–	LinkedMolStamp* currentStamp = NULL;
176	–	for( i=0; i<n_components; i++ ){
126
127	<	id = the_components[i]->getType();
179	<	comp_stamps[i] = NULL;
180	<
181	<	// check to make sure the component isn't already in the list
127	>
128
183	–	comp_stamps[i] = headStamp->match( id );
184	–	if( comp_stamps[i] == NULL ){
185	–
186	–	// extract the component from the list;
187	–
188	–	currentStamp = the_stamps->extractMolStamp( id );
189	–	if( currentStamp == NULL ){
190	–	sprintf( painCave.errMsg,
191	–	"SimSetup error: Component \"%s\" was not found in the "
192	–	"list of declared molecules\n",
193	–	id );
194	–	painCave.isFatal = 1;
195	–	simError();
196	–	}
197	–
198	–	headStamp->add( currentStamp );
199	–	comp_stamps[i] = headStamp->match( id );
200	–	}
201	–	}
129
130	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
130	>	// make the integrator
131
132	+
133	+	NVT*  myNVT = NULL;
134	+	NPTi* myNPTi = NULL;
135	+	NPTf* myNPTf = NULL;
136	+	NPTim* myNPTim = NULL;
137	+	NPTfm* myNPTfm = NULL;
138
139	+	switch( ensembleCase ){
140
141	+	case NVE_ENS:
142	+	new NVE( info, the_ff );
143	+	break;
144
145	<	// caclulate the number of atoms, bonds, bends and torsions
145	>	case NVT_ENS:
146	>	myNVT = new NVT( info, the_ff );
147	>	myNVT->setTargetTemp(the_globals->getTargetTemp());
148
149	<	tot_atoms = 0;
150	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
218	<
219	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
149	>	if (the_globals->haveTauThermostat())
150	>	myNVT->setTauThermostat(the_globals->getTauThermostat());
151
152	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
152	>	else {
153	>	sprintf( painCave.errMsg,
154	>	"SimSetup error: If you use the NVT\n"
155	>	"    ensemble, you must set tauThermostat.\n");
156	>	painCave.isFatal = 1;
157	>	simError();
158	>	}
159	>	break;
160
161	<	simnfo->n_atoms = tot_atoms;
162	<	simnfo->n_bonds = tot_bonds;
163	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
161	>	case NPTi_ENS:
162	>	myNPTi = new NPTi( info, the_ff );
163	>	myNPTi->setTargetTemp( the_globals->getTargetTemp() );
164
165	<
166	<	#ifdef IS_MPI
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	<	// divide the molecules among processors here.
186	<
187	<	mpiSim = new mpiSimulation( simnfo );
188	<
189	<
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	<	globalIndex = mpiSim->divideLabor();
196	>	case NPTf_ENS:
197	>	myNPTf = new NPTf( info, the_ff );
198	>	myNPTf->setTargetTemp( the_globals->getTargetTemp());
199
200	<
201	<
202	<	// set up the local variables
203	<
204	<	int localMol, allMol;
205	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
206	<
207	<	allMol = 0;
208	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
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	<	for( j=0; j<components_nmol[i]; j++ ){
211	<
212	<	if( mpiSim->getMyMolStart() <= allMol &&
213	<	allMol <= mpiSim->getMyMolEnd() ){
214	<
215	<	local_atoms +=    comp_stamps[i]->getNAtoms();
216	<	local_bonds +=    comp_stamps[i]->getNBonds();
217	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
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	+	if( the_globals->haveTauBarostat() )
221	+	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
222	+	else{
223	+	sprintf( painCave.errMsg,
224	+	"SimSetup error: If you use an NPT\n"
225	+	"    ensemble, you must set tauBarostat.\n");
226	+	painCave.isFatal = 1;
227	+	simError();
228	+	}
229	+	break;
230	+
231	+	case NPTim_ENS:
232	+	myNPTim = new NPTim( info, the_ff );
233	+	myNPTim->setTargetTemp( the_globals->getTargetTemp());
234	+
235	+	if (the_globals->haveTargetPressure())
236	+	myNPTim->setTargetPressure(the_globals->getTargetPressure());
237	+	else {
238	+	sprintf( painCave.errMsg,
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	+
245	+	if( the_globals->haveTauThermostat() )
246	+	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
247	+	else{
248	+	sprintf( painCave.errMsg,
249	+	"SimSetup error: If you use an NPT\n"
250	+	"    ensemble, you must set tauThermostat.\n");
251	+	painCave.isFatal = 1;
252	+	simError();
253	+	}
254	+
255	+	if( the_globals->haveTauBarostat() )
256	+	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
257	+	else{
258	+	sprintf( painCave.errMsg,
259	+	"SimSetup error: If you use an NPT\n"
260	+	"    ensemble, you must set tauBarostat.\n");
261	+	painCave.isFatal = 1;
262	+	simError();
263	+	}
264	+	break;
265	+
266	+	case NPTfm_ENS:
267	+	myNPTfm = new NPTfm( info, the_ff );
268	+	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
269	+
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->haveTauThermostat() )
281	+	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
282	+	else{
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	+	if( the_globals->haveTauBarostat() )
291	+	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
292	+	else{
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	+	break;
300	+
301	+	default:
302	+	sprintf( painCave.errMsg,
303	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
304	+	painCave.isFatal = 1;
305	+	simError();
306		}
274	–	local_SRI = local_bonds + local_bends + local_torsions;
275	–
307
308	<	simnfo->n_atoms = mpiSim->getMyNlocal();
308	>
309	>	#ifdef IS_MPI
310	>	mpiSim->mpiRefresh();
311	>	#endif
312	>
313	>	// initialize the Fortran
314	>
315	>
316	>	info->refreshSim();
317
318	<	if( local_atoms != simnfo->n_atoms ){
318	>	if( !strcmp( info->mixingRule, "standard") ){
319	>	the_ff->initForceField( LB_MIXING_RULE );
320	>	}
321	>	else if( !strcmp( info->mixingRule, "explicit") ){
322	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
323	>	}
324	>	else{
325		sprintf( painCave.errMsg,
326	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
327	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
326	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
327	>	info->mixingRule );
328		painCave.isFatal = 1;
329		simError();
330		}
331
289	–	simnfo->n_bonds = local_bonds;
290	–	simnfo->n_bends = local_bends;
291	–	simnfo->n_torsions = local_torsions;
292	–	simnfo->n_SRI = local_SRI;
293	–	simnfo->n_mol = localMol;
332
333	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
333	>	#ifdef IS_MPI
334	>	strcpy( checkPointMsg,
335	>	"Successfully intialized the mixingRule for Fortran." );
336		MPIcheckPoint();
297	–
298	–
337		#endif // is_mpi
338	<
338	>	}
339
302	–	// create the atom and short range interaction arrays
340
341	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
341	>	void SimSetup::makeMolecules( void ){
342
343	+	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
344	+	molInit info;
345	+	DirectionalAtom* dAtom;
346	+	LinkedAssign* extras;
347	+	LinkedAssign* current_extra;
348	+	AtomStamp* currentAtom;
349	+	BondStamp* currentBond;
350	+	BendStamp* currentBend;
351	+	TorsionStamp* currentTorsion;
352
353	<	if( simnfo->n_SRI ){
354	<	the_sris = new SRI*[simnfo->n_SRI];
355	<	the_excludes = new int[2 * simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
353	>	bond_pair* theBonds;
354	>	bend_set* theBends;
355	>	torsion_set* theTorsions;
356
357	<	simnfo->n_exclude = 1;
358	<	}
357	>
358	>	//init the forceField paramters
359
360	<	// set the arrays into the SimInfo object
360	>	the_ff->readParams();
361
362	<	simnfo->atoms = the_atoms;
363	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
362	>
363	>	// init the atoms
364
365	+	double ux, uy, uz, u, uSqr;
366	+
367	+	atomOffset = 0;
368	+	excludeOffset = 0;
369	+	for(i=0; i<info->n_mol; i++){
370	+
371	+	stampID = the_molecules[i].getStampID();
372
373	<	// get some of the tricky things that may still be in the globals
373	>	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
374	>	info.nBonds    = comp_stamps[stampID]->getNBonds();
375	>	info.nBends    = comp_stamps[stampID]->getNBends();
376	>	info.nTorsions = comp_stamps[stampID]->getNTorsions();
377	>	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
378
379	+	info.myAtoms = &the_atoms[atomOffset];
380	+	info.myExcludes = &the_excludes[excludeOffset];
381	+	info.myBonds = new Bond*[info.nBonds];
382	+	info.myBends = new Bend*[info.nBends];
383	+	info.myTorsions = new Torsion*[info.nTorsions];
384	+
385	+	theBonds = new bond_pair[info.nBonds];
386	+	theBends = new bend_set[info.nBends];
387	+	theTorsions = new torsion_set[info.nTorsions];
388	+
389	+	// make the Atoms
390	+
391	+	for(j=0; j<info.nAtoms; j++){
392	+
393	+	currentAtom = comp_stamps[stampID]->getAtom( j );
394	+	if( currentAtom->haveOrientation() ){
395	+
396	+	dAtom = new DirectionalAtom(j + atomOffset);
397	+	info->n_oriented++;
398	+	info.myAtoms[j] = dAtom;
399	+
400	+	ux = currentAtom->getOrntX();
401	+	uy = currentAtom->getOrntY();
402	+	uz = currentAtom->getOrntZ();
403	+
404	+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
405	+
406	+	u = sqrt( uSqr );
407	+	ux = ux / u;
408	+	uy = uy / u;
409	+	uz = uz / u;
410	+
411	+	dAtom->setSUx( ux );
412	+	dAtom->setSUy( uy );
413	+	dAtom->setSUz( uz );
414	+	}
415	+	else{
416	+	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
417	+	}
418	+	info.myAtoms[j]->setType( currentAtom->getType() );
419	+
420	+	#ifdef IS_MPI
421	+
422	+	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
423	+
424	+	#endif // is_mpi
425	+	}
426	+
427	+	// make the bonds
428	+	for(j=0; j<info.nBonds; j++){
429	+
430	+	currentBond = comp_stamps[stampID]->getBond( j );
431	+	theBonds[j].a = currentBond->getA() + atomOffset;
432	+	theBonds[j].b = currentBond->getB() + atomOffset;
433	+
434	+	exI = theBonds[j].a;
435	+	exJ = theBonds[j].b;
436	+
437	+	// exclude_I must always be the smaller of the pair
438	+	if( exI > exJ ){
439	+	tempEx = exI;
440	+	exI = exJ;
441	+	exJ = tempEx;
442	+	}
443	+	#ifdef IS_MPI
444	+	tempEx = exI;
445	+	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
446	+	tempEx = exJ;
447	+	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
448	+
449	+	the_excludes[j+excludeOffset]->setPair( exI, exJ );
450	+	#else  // isn't MPI
451	+
452	+	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
453	+	#endif  //is_mpi
454	+	}
455	+	excludeOffset += info.nBonds;
456	+
457	+	//make the bends
458	+	for(j=0; j<info.nBends; j++){
459	+
460	+	currentBend = comp_stamps[stampID]->getBend( j );
461	+	theBends[j].a = currentBend->getA() + atomOffset;
462	+	theBends[j].b = currentBend->getB() + atomOffset;
463	+	theBends[j].c = currentBend->getC() + atomOffset;
464	+
465	+	if( currentBend->haveExtras() ){
466	+
467	+	extras = currentBend->getExtras();
468	+	current_extra = extras;
469	+
470	+	while( current_extra != NULL ){
471	+	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
472	+
473	+	switch( current_extra->getType() ){
474	+
475	+	case 0:
476	+	theBends[j].ghost =
477	+	current_extra->getInt() + atomOffset;
478	+	theBends[j].isGhost = 1;
479	+	break;
480	+
481	+	case 1:
482	+	theBends[j].ghost =
483	+	(int)current_extra->getDouble() + atomOffset;
484	+	theBends[j].isGhost = 1;
485	+	break;
486	+
487	+	default:
488	+	sprintf( painCave.errMsg,
489	+	"SimSetup Error: ghostVectorSource was neither a "
490	+	"double nor an int.\n"
491	+	"-->Bend[%d] in %s\n",
492	+	j, comp_stamps[stampID]->getID() );
493	+	painCave.isFatal = 1;
494	+	simError();
495	+	}
496	+	}
497	+
498	+	else{
499	+
500	+	sprintf( painCave.errMsg,
501	+	"SimSetup Error: unhandled bend assignment:\n"
502	+	"    -->%s in Bend[%d] in %s\n",
503	+	current_extra->getlhs(),
504	+	j, comp_stamps[stampID]->getID() );
505	+	painCave.isFatal = 1;
506	+	simError();
507	+	}
508	+
509	+	current_extra = current_extra->getNext();
510	+	}
511	+	}
512	+
513	+	if( !theBends[j].isGhost ){
514	+
515	+	exI = theBends[j].a;
516	+	exJ = theBends[j].c;
517	+	}
518	+	else{
519	+
520	+	exI = theBends[j].a;
521	+	exJ = theBends[j].b;
522	+	}
523	+
524	+	// exclude_I must always be the smaller of the pair
525	+	if( exI > exJ ){
526	+	tempEx = exI;
527	+	exI = exJ;
528	+	exJ = tempEx;
529	+	}
530	+	#ifdef IS_MPI
531	+	tempEx = exI;
532	+	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
533	+	tempEx = exJ;
534	+	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
535	+
536	+	the_excludes[j+excludeOffset]->setPair( exI, exJ );
537	+	#else  // isn't MPI
538	+	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
539	+	#endif  //is_mpi
540	+	}
541	+	excludeOffset += info.nBends;
542	+
543	+	for(j=0; j<info.nTorsions; j++){
544	+
545	+	currentTorsion = comp_stamps[stampID]->getTorsion( j );
546	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
547	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
548	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
549	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
550	+
551	+	exI = theTorsions[j].a;
552	+	exJ = theTorsions[j].d;
553	+
554	+	// exclude_I must always be the smaller of the pair
555	+	if( exI > exJ ){
556	+	tempEx = exI;
557	+	exI = exJ;
558	+	exJ = tempEx;
559	+	}
560	+	#ifdef IS_MPI
561	+	tempEx = exI;
562	+	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
563	+	tempEx = exJ;
564	+	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
565	+
566	+	the_excludes[j+excludeOffset]->setPair( exI, exJ );
567	+	#else  // isn't MPI
568	+	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
569	+	#endif  //is_mpi
570	+	}
571	+	excludeOffset += info.nTorsions;
572	+
573	+
574	+	// send the arrays off to the forceField for init.
575	+
576	+	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
577	+	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
578	+	the_ff->initializeBends( info.nBends, info.myBends, theBends );
579	+	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
580	+
581	+
582	+	the_molecules[i].initialize( info );
583	+
584	+
585	+	atomOffset += info.nAtoms;
586	+	delete[] theBonds;
587	+	delete[] theBends;
588	+	delete[] theTorsions;
589	+	}
590	+
591	+	#ifdef IS_MPI
592	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
593	+	MPIcheckPoint();
594	+	#endif // is_mpi
595	+
596	+	// clean up the forcefield
597	+	the_ff->calcRcut();
598	+	the_ff->cleanMe();
599	+
600	+	}
601	+
602	+	void SimSetup::initFromBass( void ){
603	+
604	+	int i, j, k;
605	+	int n_cells;
606	+	double cellx, celly, cellz;
607	+	double temp1, temp2, temp3;
608	+	int n_per_extra;
609	+	int n_extra;
610	+	int have_extra, done;
611	+
612	+	temp1 = (double)tot_nmol / 4.0;
613	+	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
614	+	temp3 = ceil( temp2 );
615	+
616	+	have_extra =0;
617	+	if( temp2 < temp3 ){ // we have a non-complete lattice
618	+	have_extra =1;
619	+
620	+	n_cells = (int)temp3 - 1;
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 );
627	+
628	+	if( n_per_extra > 4){
629	+	sprintf( painCave.errMsg,
630	+	"SimSetup error. There has been an error in constructing"
631	+	" the non-complete lattice.\n" );
632	+	painCave.isFatal = 1;
633	+	simError();
634	+	}
635	+	}
636	+	else{
637	+	n_cells = (int)temp3;
638	+	cellx = info->boxLx / temp3;
639	+	celly = info->boxLy / temp3;
640	+	cellz = info->boxLz / temp3;
641	+	}
642	+
643	+	current_mol = 0;
644	+	current_comp_mol = 0;
645	+	current_comp = 0;
646	+	current_atom_ndx = 0;
647	+
648	+	for( i=0; i < n_cells ; i++ ){
649	+	for( j=0; j < n_cells; j++ ){
650	+	for( k=0; k < n_cells; k++ ){
651	+
652	+	makeElement( i * cellx,
653	+	j * celly,
654	+	k * cellz );
655	+
656	+	makeElement( i * cellx + 0.5 * cellx,
657	+	j * celly + 0.5 * celly,
658	+	k * cellz );
659	+
660	+	makeElement( i * cellx,
661	+	j * celly + 0.5 * celly,
662	+	k * cellz + 0.5 * cellz );
663	+
664	+	makeElement( i * cellx + 0.5 * cellx,
665	+	j * celly,
666	+	k * cellz + 0.5 * cellz );
667	+	}
668	+	}
669	+	}
670	+
671	+	if( have_extra ){
672	+	done = 0;
673	+
674	+	int start_ndx;
675	+	for( i=0; i < (n_cells+1) && !done; i++ ){
676	+	for( j=0; j < (n_cells+1) && !done; j++ ){
677	+
678	+	if( i < n_cells ){
679	+
680	+	if( j < n_cells ){
681	+	start_ndx = n_cells;
682	+	}
683	+	else start_ndx = 0;
684	+	}
685	+	else start_ndx = 0;
686	+
687	+	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
688	+
689	+	makeElement( i * cellx,
690	+	j * celly,
691	+	k * cellz );
692	+	done = ( current_mol >= tot_nmol );
693	+
694	+	if( !done && n_per_extra > 1 ){
695	+	makeElement( i * cellx + 0.5 * cellx,
696	+	j * celly + 0.5 * celly,
697	+	k * cellz );
698	+	done = ( current_mol >= tot_nmol );
699	+	}
700	+
701	+	if( !done && n_per_extra > 2){
702	+	makeElement( i * cellx,
703	+	j * celly + 0.5 * celly,
704	+	k * cellz + 0.5 * cellz );
705	+	done = ( current_mol >= tot_nmol );
706	+	}
707	+
708	+	if( !done && n_per_extra > 3){
709	+	makeElement( i * cellx + 0.5 * cellx,
710	+	j * celly,
711	+	k * cellz + 0.5 * cellz );
712	+	done = ( current_mol >= tot_nmol );
713	+	}
714	+	}
715	+	}
716	+	}
717	+	}
718	+
719	+
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	+
727	+	void SimSetup::makeElement( double x, double y, double z ){
728	+
729	+	int k;
730	+	AtomStamp* current_atom;
731	+	DirectionalAtom* dAtom;
732	+	double rotMat[3][3];
733	+
734	+	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
735	+
736	+	current_atom = comp_stamps[current_comp]->getAtom( k );
737	+	if( !current_atom->havePosition() ){
738	+	sprintf( painCave.errMsg,
739	+	"SimSetup:initFromBass error.\n"
740	+	"\tComponent %s, atom %s does not have a position specified.\n"
741	+	"\tThe initialization routine is unable to give a start"
742	+	" position.\n",
743	+	comp_stamps[current_comp]->getID(),
744	+	current_atom->getType() );
745	+	painCave.isFatal = 1;
746	+	simError();
747	+	}
748	+
749	+	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
750	+	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
751	+	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
752	+
753	+	if( the_atoms[current_atom_ndx]->isDirectional() ){
754	+
755	+	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
756	+
757	+	rotMat[0][0] = 1.0;
758	+	rotMat[0][1] = 0.0;
759	+	rotMat[0][2] = 0.0;
760	+
761	+	rotMat[1][0] = 0.0;
762	+	rotMat[1][1] = 1.0;
763	+	rotMat[1][2] = 0.0;
764	+
765	+	rotMat[2][0] = 0.0;
766	+	rotMat[2][1] = 0.0;
767	+	rotMat[2][2] = 1.0;
768	+
769	+	dAtom->setA( rotMat );
770	+	}
771	+
772	+	current_atom_ndx++;
773	+	}
774	+
775	+	current_mol++;
776	+	current_comp_mol++;
777	+
778	+	if( current_comp_mol >= components_nmol[current_comp] ){
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	<	simnfo->box_x = the_globals->getBox();
912	<	simnfo->box_y = the_globals->getBox();
913	<	simnfo->box_z = the_globals->getBox();
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	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
922	<	simnfo->box_y = simnfo->box_x;
923	<	simnfo->box_z = simnfo->box_x;
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() ){
#	Line 354 | Line 931 | void SimSetup::createSim( void ){
931		painCave.isFatal = 1;
932		simError();
933		}
934	<	simnfo->box_x = the_globals->getBoxX();
934	>	boxVector[0] = the_globals->getBoxX();
935
936		if( !the_globals->haveBoxY() ){
937		sprintf( painCave.errMsg,
#	Line 362 | Line 939 | void SimSetup::createSim( void ){
939		painCave.isFatal = 1;
940		simError();
941		}
942	<	simnfo->box_y = the_globals->getBoxY();
942	>	boxVector[1] = the_globals->getBoxY();
943
944		if( !the_globals->haveBoxZ() ){
945		sprintf( painCave.errMsg,
#	Line 370 | Line 947 | void SimSetup::createSim( void ){
947		painCave.isFatal = 1;
948		simError();
949		}
950	<	simnfo->box_z = the_globals->getBoxZ();
950	>	boxVector[2] = the_globals->getBoxZ();
951	>
952	>	info->setBox( boxVector );
953		}
954
955	+
956	+
957		#ifdef IS_MPI
958	<	strcpy( checkPointMsg, "Box size set up" );
958	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
959		MPIcheckPoint();
960		#endif // is_mpi
961
962	+	}
963
382	–	// initialize the arrays
964
965	<	the_ff->setSimInfo( simnfo );
965	>	void SimSetup::finalInfoCheck( void ){
966	>	int index;
967	>	int usesDipoles;
968	>
969
970	<	makeAtoms();
387	<	simnfo->identArray = new int[simnfo->n_atoms];
388	<	for(i=0; i<simnfo->n_atoms; i++){
389	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
390	<	}
970	>	// check electrostatic parameters
971
972	<	if( tot_bonds ){
973	<	makeBonds();
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
396	–	if( tot_bends ){
397	–	makeBends();
398	–	}
984
400	–	if( tot_torsions ){
401	–	makeTorsions();
402	–	}
403	–
404	–
985		if (the_globals->getUseRF() ) {
986	<	simnfo->useReactionField = 1;
987	<
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 "
#	Line 413 | Line 993 | void SimSetup::createSim( void ){
993		painCave.isFatal = 0;
994		simError();
995		double smallest;
996	<	smallest = simnfo->box_x;
997	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
998	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
999	<	simnfo->ecr = 0.5 * 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	<	simnfo->ecr        = the_globals->getECR();
1001	>	info->ecr        = the_globals->getECR();
1002		}
1003
1004		if( !the_globals->haveEST() ){
#	Line 428 | Line 1008 | void SimSetup::createSim( void ){
1008		);
1009		painCave.isFatal = 0;
1010		simError();
1011	<	simnfo->est = 0.05 * simnfo->ecr;
1011	>	info->est = 0.05 * info->ecr;
1012		} else {
1013	<	simnfo->est        = the_globals->getEST();
1013	>	info->est        = the_globals->getEST();
1014		}
1015
1016		if(!the_globals->haveDielectric() ){
#	Line 441 | Line 1021 | void SimSetup::createSim( void ){
1021		painCave.isFatal = 1;
1022		simError();
1023		}
1024	<	simnfo->dielectric = the_globals->getDielectric();
1025	<	} else {
1026	<	if (simnfo->n_dipoles) {
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"
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 = simnfo->box_x;
1038	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
1039	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
1040	<	simnfo->ecr = 0.5 * 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	<	simnfo->ecr        = the_globals->getECR();
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"
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	<	simnfo->est = 0.05 * simnfo->ecr;
1053	>	info->est = 0.05 * info->ecr;
1054		} else {
1055	<	simnfo->est        = the_globals->getEST();
1055	>	info->est        = the_globals->getEST();
1056		}
1057		}
1058		}
1059
1060		#ifdef IS_MPI
1061	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
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;
#	Line 491 | Line 1076 | void SimSetup::createSim( void ){
1076		#ifdef IS_MPI
1077		}else fileInit = new InitializeFromFile( NULL );
1078		#endif
1079	<	fileInit->read_xyz( simnfo ); // default velocities on
1079	>	fileInit->read_xyz( info ); // default velocities on
1080
1081		delete fileInit;
1082		}
#	Line 519 | Line 1104 | void SimSetup::createSim( void ){
1104		MPIcheckPoint();
1105		#endif // is_mpi
1106
1107	+	}
1108
523	–
524	–
525	–
1109
1110	<
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( simnfo->finalName, the_globals->getFinalConfig() );
1117	>	strcpy( info->finalName, the_globals->getFinalConfig() );
1118		}
1119		else{
1120	<	strcpy( simnfo->finalName, inFileName );
1120	>	strcpy( info->finalName, inFileName );
1121		char* endTest;
1122	<	int nameLength = strlen( simnfo->finalName );
1123	<	endTest = &(simnfo->finalName[nameLength - 5]);
1122	>	int nameLength = strlen( info->finalName );
1123	>	endTest = &(info->finalName[nameLength - 5]);
1124		if( !strcmp( endTest, ".bass" ) ){
1125		strcpy( endTest, ".eor" );
1126		}
#	Line 544 | Line 1128 | void SimSetup::createSim( void ){
1128		strcpy( endTest, ".eor" );
1129		}
1130		else{
1131	<	endTest = &(simnfo->finalName[nameLength - 4]);
1131	>	endTest = &(info->finalName[nameLength - 4]);
1132		if( !strcmp( endTest, ".bss" ) ){
1133		strcpy( endTest, ".eor" );
1134		}
#	Line 552 | Line 1136 | void SimSetup::createSim( void ){
1136		strcpy( endTest, ".eor" );
1137		}
1138		else{
1139	<	strcat( simnfo->finalName, ".eor" );
1139	>	strcat( info->finalName, ".eor" );
1140		}
1141		}
1142		}
1143
1144		// make the sample and status out names
1145
1146	<	strcpy( simnfo->sampleName, inFileName );
1146	>	strcpy( info->sampleName, inFileName );
1147		char* endTest;
1148	<	int nameLength = strlen( simnfo->sampleName );
1149	<	endTest = &(simnfo->sampleName[nameLength - 5]);
1148	>	int nameLength = strlen( info->sampleName );
1149	>	endTest = &(info->sampleName[nameLength - 5]);
1150		if( !strcmp( endTest, ".bass" ) ){
1151		strcpy( endTest, ".dump" );
1152		}
#	Line 570 | Line 1154 | void SimSetup::createSim( void ){
1154		strcpy( endTest, ".dump" );
1155		}
1156		else{
1157	<	endTest = &(simnfo->sampleName[nameLength - 4]);
1157	>	endTest = &(info->sampleName[nameLength - 4]);
1158		if( !strcmp( endTest, ".bss" ) ){
1159		strcpy( endTest, ".dump" );
1160		}
#	Line 578 | Line 1162 | void SimSetup::createSim( void ){
1162		strcpy( endTest, ".dump" );
1163		}
1164		else{
1165	<	strcat( simnfo->sampleName, ".dump" );
1165	>	strcat( info->sampleName, ".dump" );
1166		}
1167		}
1168
1169	<	strcpy( simnfo->statusName, inFileName );
1170	<	nameLength = strlen( simnfo->statusName );
1171	<	endTest = &(simnfo->statusName[nameLength - 5]);
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		}
#	Line 592 | Line 1176 | void SimSetup::createSim( void ){
1176		strcpy( endTest, ".stat" );
1177		}
1178		else{
1179	<	endTest = &(simnfo->statusName[nameLength - 4]);
1179	>	endTest = &(info->statusName[nameLength - 4]);
1180		if( !strcmp( endTest, ".bss" ) ){
1181		strcpy( endTest, ".stat" );
1182		}
#	Line 600 | Line 1184 | void SimSetup::createSim( void ){
1184		strcpy( endTest, ".stat" );
1185		}
1186		else{
1187	<	strcat( simnfo->statusName, ".stat" );
1187	>	strcat( info->statusName, ".stat" );
1188		}
1189		}
1190
1191		#ifdef IS_MPI
1192		}
1193		#endif // is_mpi
610	–
611	–	// set the status, sample, and themal kick times
612	–
613	–	if( the_globals->haveSampleTime() ){
614	–	simnfo->sampleTime = the_globals->getSampleTime();
615	–	simnfo->statusTime = simnfo->sampleTime;
616	–	simnfo->thermalTime = simnfo->sampleTime;
617	–	}
618	–	else{
619	–	simnfo->sampleTime = the_globals->getRunTime();
620	–	simnfo->statusTime = simnfo->sampleTime;
621	–	simnfo->thermalTime = simnfo->sampleTime;
622	–	}
1194
1195	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
1195	>	}
1196
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
1197
1198	<	// check for the temperature set flag
1198	>	void SimSetup::sysObjectsCreation( void ){
1199
1200	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1200	>	// create the forceField
1201
1202	+	createFF();
1203
1204	<	//   // make the longe range forces and the integrator
1204	>	// extract componentList
1205
1206	<	//   new AllLong( simnfo );
1206	>	compList();
1207
1208	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
1208	>	// calc the number of atoms, bond, bends, and torsions
1209
1210	+	calcSysValues();
1211
1212	<
1213	<	// initialize the Fortran
1212	>	#ifdef IS_MPI
1213	>	// divide the molecules among the processors
1214
1215	<	simnfo->refreshSim();
1215	>	mpiMolDivide();
1216	>	#endif //is_mpi
1217
1218	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1219	<	the_ff->initForceField( LB_MIXING_RULE );
1220	<	}
655	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	<	}
658	<	else{
659	<	sprintf( painCave.errMsg,
660	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	<	simnfo->mixingRule );
662	<	painCave.isFatal = 1;
663	<	simError();
664	<	}
1218	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1219	>
1220	>	makeSysArrays();
1221
1222	+
1223
1224	<	#ifdef IS_MPI
668	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
1224	>
1225		}
1226
674	–	void SimSetup::makeAtoms( void ){
1227
1228	<	int i, j, k, index;
677	<	double ux, uy, uz, uSqr, u;
678	<	AtomStamp* current_atom;
1228	>	void SimSetup::createFF( void ){
1229
1230	<	DirectionalAtom* dAtom;
681	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
1230	>	switch( ffCase ){
1231
1232	<	lMolIndex = 0;
1233	<	molIndex = 0;
1234	<	index = 0;
686	<	for( i=0; i<n_components; i++ ){
1232	>	case FF_DUFF:
1233	>	the_ff = new DUFF();
1234	>	break;
1235
1236	<	for( j=0; j<components_nmol[i]; j++ ){
1236	>	case FF_LJ:
1237	>	the_ff = new LJFF();
1238	>	break;
1239
1240	<	#ifdef IS_MPI
1241	<	if( mpiSim->getMyMolStart() <= molIndex &&
1242	<	molIndex <= mpiSim->getMyMolEnd() ){
1243	<	#endif // is_mpi
1244	<
695	<	molStart = index;
696	<	nMemb = comp_stamps[i]->getNAtoms();
697	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
698	<
699	<	current_atom = comp_stamps[i]->getAtom( k );
700	<	if( current_atom->haveOrientation() ){
701	<
702	<	dAtom = new DirectionalAtom(index);
703	<	simnfo->n_oriented++;
704	<	the_atoms[index] = dAtom;
705	<
706	<	ux = current_atom->getOrntX();
707	<	uy = current_atom->getOrntY();
708	<	uz = current_atom->getOrntZ();
709	<
710	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
711	<
712	<	u = sqrt( uSqr );
713	<	ux = ux / u;
714	<	uy = uy / u;
715	<	uz = uz / u;
716	<
717	<	dAtom->setSUx( ux );
718	<	dAtom->setSUy( uy );
719	<	dAtom->setSUz( uz );
720	<	}
721	<	else{
722	<	the_atoms[index] = new GeneralAtom(index);
723	<	}
724	<	the_atoms[index]->setType( current_atom->getType() );
725	<	the_atoms[index]->setIndex( index );
726	<
727	<	// increment the index and repeat;
728	<	index++;
729	<	}
730	<
731	<	molEnd = index -1;
732	<	the_molecules[lMolIndex].setNMembers( nMemb );
733	<	the_molecules[lMolIndex].setStartAtom( molStart );
734	<	the_molecules[lMolIndex].setEndAtom( molEnd );
735	<	the_molecules[lMolIndex].setStampID( i );
736	<	lMolIndex++;
737	<
738	<	#ifdef IS_MPI
739	<	}
740	<	#endif //is_mpi
741	<
742	<	molIndex++;
743	<	}
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	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
1249	<
1250	<	delete[] globalIndex;
1248	>	strcpy( checkPointMsg, "ForceField creation successful" );
1249	>	MPIcheckPoint();
1250	>	#endif // is_mpi
1251
751	–	mpiSim->mpiRefresh();
752	–	#endif //IS_MPI
753	–
754	–	the_ff->initializeAtoms();
1252		}
1253
757	–	void SimSetup::makeBonds( void ){
1254
1255	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
760	<	bond_pair* the_bonds;
761	<	BondStamp* current_bond;
1255	>	void SimSetup::compList( void ){
1256
1257	<	the_bonds = new bond_pair[tot_bonds];
764	<	index = 0;
765	<	offset = 0;
766	<	molIndex = 0;
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	<	for( j=0; j<components_nmol[i]; j++ ){
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	<	if( mpiSim->getMyMolStart() <= molIndex &&
1299	<	molIndex <= mpiSim->getMyMolEnd() ){
1300	<	#endif // is_mpi
776	<
777	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
778	<
779	<	current_bond = comp_stamps[i]->getBond( k );
780	<	the_bonds[index].a = current_bond->getA() + offset;
781	<	the_bonds[index].b = current_bond->getB() + offset;
1298	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1299	>	MPIcheckPoint();
1300	>	#endif // is_mpi
1301
783	–	exI = the_bonds[index].a;
784	–	exJ = the_bonds[index].b;
1302
1303	<	// exclude_I must always be the smaller of the pair
787	<	if( exI > exJ ){
788	<	tempEx = exI;
789	<	exI = exJ;
790	<	exJ = tempEx;
791	<	}
1303	>	}
1304
1305	<
794	<	#ifdef IS_MPI
1305	>	void SimSetup::calcSysValues( void ){
1306
1307	<	the_excludes[index*2] =
1308	<	the_atoms[exI]->getGlobalIndex() + 1;
1309	<	the_excludes[index*2 + 1] =
1310	<	the_atoms[exJ]->getGlobalIndex() + 1;
1311	<
1312	<	#else  // isn't MPI
1313	<
1314	<	the_excludes[index*2] =     exI + 1;
1315	<	the_excludes[index*2 + 1] = exJ + 1;
1316	<	// fortran index from 1 (hence the +1 in the indexing)
806	<	#endif  //is_mpi
807	<
808	<	// increment the index and repeat;
809	<	index++;
810	<	}
811	<	offset += comp_stamps[i]->getNAtoms();
812	<
813	<	#ifdef IS_MPI
814	<	}
815	<	#endif //is_mpi
816	<
817	<	molIndex++;
818	<	}
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	<	the_ff->initializeBonds( the_bonds );
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
824	–	void SimSetup::makeBends( void ){
1331
1332	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1333	<	bend_set* the_bends;
1334	<	BendStamp* current_bend;
829	<	LinkedAssign* extras;
830	<	LinkedAssign* current_extra;
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	<	the_bends = new bend_set[tot_bends];
1340	<	index = 0;
1341	<	offset = 0;
1342	<	molIndex = 0;
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	<	#ifdef IS_MPI
1362	<	if( mpiSim->getMyMolStart() <= molIndex &&
1363	<	molIndex <= mpiSim->getMyMolEnd() ){
1364	<	#endif // is_mpi
1365	<
1366	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1367	<
1368	<	current_bend = comp_stamps[i]->getBend( k );
1369	<	the_bends[index].a = current_bend->getA() + offset;
1370	<	the_bends[index].b = current_bend->getB() + offset;
1371	<	the_bends[index].c = current_bend->getC() + offset;
852	<
853	<	if( current_bend->haveExtras() ){
854	<
855	<	extras = current_bend->getExtras();
856	<	current_extra = extras;
857	<
858	<	while( current_extra != NULL ){
859	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
860	<
861	<	switch( current_extra->getType() ){
862	<
863	<	case 0:
864	<	the_bends[index].ghost =
865	<	current_extra->getInt() + offset;
866	<	the_bends[index].isGhost = 1;
867	<	break;
868	<
869	<	case 1:
870	<	the_bends[index].ghost =
871	<	(int)current_extra->getDouble() + offset;
872	<	the_bends[index].isGhost = 1;
873	<	break;
874	<
875	<	default:
876	<	sprintf( painCave.errMsg,
877	<	"SimSetup Error: ghostVectorSource was neiter a "
878	<	"double nor an int.\n"
879	<	"-->Bend[%d] in %s\n",
880	<	k, comp_stamps[i]->getID() );
881	<	painCave.isFatal = 1;
882	<	simError();
883	<	}
884	<	}
885	<
886	<	else{
887	<
888	<	sprintf( painCave.errMsg,
889	<	"SimSetup Error: unhandled bend assignment:\n"
890	<	"    -->%s in Bend[%d] in %s\n",
891	<	current_extra->getlhs(),
892	<	k, comp_stamps[i]->getID() );
893	<	painCave.isFatal = 1;
894	<	simError();
895	<	}
896	<
897	<	current_extra = current_extra->getNext();
898	<	}
899	<	}
900	<
901	<	if( !the_bends[index].isGhost ){
902	<
903	<	exI = the_bends[index].a;
904	<	exJ = the_bends[index].c;
905	<	}
906	<	else{
907	<
908	<	exI = the_bends[index].a;
909	<	exJ = the_bends[index].b;
910	<	}
911	<
912	<	// exclude_I must always be the smaller of the pair
913	<	if( exI > exJ ){
914	<	tempEx = exI;
915	<	exI = exJ;
916	<	exJ = tempEx;
917	<	}
918	<
919	<
920	<	#ifdef IS_MPI
921	<
922	<	the_excludes[(index + tot_bonds)*2] =
923	<	the_atoms[exI]->getGlobalIndex() + 1;
924	<	the_excludes[(index + tot_bonds)*2 + 1] =
925	<	the_atoms[exJ]->getGlobalIndex() + 1;
926	<
927	<	#else  // isn't MPI
928	<
929	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
930	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
931	<	// fortran index from 1 (hence the +1 in the indexing)
932	<	#endif  //is_mpi
933	<
934	<
935	<	// increment the index and repeat;
936	<	index++;
937	<	}
938	<	offset += comp_stamps[i]->getNAtoms();
939	<
940	<	#ifdef IS_MPI
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		}
942	–	#endif //is_mpi
1373
1374	<	molIndex++;
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	<	#ifdef IS_MPI
1392	<	sprintf( checkPointMsg,
1393	<	"Successfully created the bends list.\n" );
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	<	#endif // is_mpi
1399	>	}
1400
1401	+	#endif // is_mpi
1402
955	–	the_ff->initializeBends( the_bends );
956	–	}
1403
1404	<	void SimSetup::makeTorsions( void ){
1404	>	void SimSetup::makeSysArrays( void ){
1405
1406	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
961	<	torsion_set* the_torsions;
962	<	TorsionStamp* current_torsion;
1406	>	// create the atom and short range interaction arrays
1407
1408	<	the_torsions = new torsion_set[tot_torsions];
1409	<	index = 0;
1410	<	offset = 0;
1411	<	molIndex = 0;
968	<	for( i=0; i<n_components; i++ ){
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	<	for( j=0; j<components_nmol[i]; j++ ){
1413	>	// initialize the molecule's stampID's
1414
1415		#ifdef IS_MPI
1416	<	if( mpiSim->getMyMolStart() <= molIndex &&
974	<	molIndex <= mpiSim->getMyMolEnd() ){
975	<	#endif // is_mpi
1416	>
1417
1418	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1419	<
1420	<	current_torsion = comp_stamps[i]->getTorsion( k );
1421	<	the_torsions[index].a = current_torsion->getA() + offset;
1422	<	the_torsions[index].b = current_torsion->getB() + offset;
1423	<	the_torsions[index].c = current_torsion->getC() + offset;
1424	<	the_torsions[index].d = current_torsion->getD() + offset;
984	<
985	<	exI = the_torsions[index].a;
986	<	exJ = the_torsions[index].d;
987	<
988	<
989	<	// exclude_I must always be the smaller of the pair
990	<	if( exI > exJ ){
991	<	tempEx = exI;
992	<	exI = exJ;
993	<	exJ = tempEx;
994	<	}
995	<
996	<
997	<	#ifdef IS_MPI
998	<
999	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1000	<	the_atoms[exI]->getGlobalIndex() + 1;
1001	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1002	<	the_atoms[exJ]->getGlobalIndex() + 1;
1003	<
1004	<	#else  // isn't MPI
1005	<
1006	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1007	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1008	<	// fortran indexes from 1 (hence the +1 in the indexing)
1009	<	#endif  //is_mpi
1010	<
1011	<
1012	<	// increment the index and repeat;
1013	<	index++;
1014	<	}
1015	<	offset += comp_stamps[i]->getNAtoms();
1016	<
1017	<	#ifdef IS_MPI
1018	<	}
1019	<	#endif //is_mpi
1020	<
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	<	the_ff->initializeTorsions( the_torsions );
1430	<	}
1431	<
1432	<	void SimSetup::initFromBass( void ){
1433	<
1434	<	int i, j, k;
1435	<	int n_cells;
1436	<	double cellx, celly, cellz;
1437	<	double temp1, temp2, temp3;
1438	<	int n_per_extra;
1439	<	int n_extra;
1440	<	int have_extra, done;
1037	<
1038	<	temp1 = (double)tot_nmol / 4.0;
1039	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1040	<	temp3 = ceil( temp2 );
1041	<
1042	<	have_extra =0;
1043	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1044	<	have_extra =1;
1045	<
1046	<	n_cells = (int)temp3 - 1;
1047	<	cellx = simnfo->box_x / temp3;
1048	<	celly = simnfo->box_y / temp3;
1049	<	cellz = simnfo->box_z / temp3;
1050	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1051	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1052	<	n_per_extra = (int)ceil( temp1 );
1053	<
1054	<	if( n_per_extra > 4){
1055	<	sprintf( painCave.errMsg,
1056	<	"SimSetup error. There has been an error in constructing"
1057	<	" the non-complete lattice.\n" );
1058	<	painCave.isFatal = 1;
1059	<	simError();
1060	<	}
1061	<	}
1062	<	else{
1063	<	n_cells = (int)temp3;
1064	<	cellx = simnfo->box_x / temp3;
1065	<	celly = simnfo->box_y / temp3;
1066	<	cellz = simnfo->box_z / temp3;
1067	<	}
1068	<
1069	<	current_mol = 0;
1070	<	current_comp_mol = 0;
1071	<	current_comp = 0;
1072	<	current_atom_ndx = 0;
1073	<
1074	<	for( i=0; i < n_cells ; i++ ){
1075	<	for( j=0; j < n_cells; j++ ){
1076	<	for( k=0; k < n_cells; k++ ){
1077	<
1078	<	makeElement( i * cellx,
1079	<	j * celly,
1080	<	k * cellz );
1081	<
1082	<	makeElement( i * cellx + 0.5 * cellx,
1083	<	j * celly + 0.5 * celly,
1084	<	k * cellz );
1085	<
1086	<	makeElement( i * cellx,
1087	<	j * celly + 0.5 * celly,
1088	<	k * cellz + 0.5 * cellz );
1089	<
1090	<	makeElement( i * cellx + 0.5 * cellx,
1091	<	j * celly,
1092	<	k * cellz + 0.5 * cellz );
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	<	if( have_extra ){
1098	<	done = 0;
1447	>	#endif // is_mpi
1448
1100	–	int start_ndx;
1101	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1102	–	for( j=0; j < (n_cells+1) && !done; j++ ){
1449
1450	<	if( i < n_cells ){
1451	<
1452	<	if( j < n_cells ){
1453	<	start_ndx = n_cells;
1454	<	}
1455	<	else start_ndx = 0;
1456	<	}
1111	<	else start_ndx = 0;
1112	<
1113	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1114	<
1115	<	makeElement( i * cellx,
1116	<	j * celly,
1117	<	k * cellz );
1118	<	done = ( current_mol >= tot_nmol );
1119	<
1120	<	if( !done && n_per_extra > 1 ){
1121	<	makeElement( i * cellx + 0.5 * cellx,
1122	<	j * celly + 0.5 * celly,
1123	<	k * cellz );
1124	<	done = ( current_mol >= tot_nmol );
1125	<	}
1126	<
1127	<	if( !done && n_per_extra > 2){
1128	<	makeElement( i * cellx,
1129	<	j * celly + 0.5 * celly,
1130	<	k * cellz + 0.5 * cellz );
1131	<	done = ( current_mol >= tot_nmol );
1132	<	}
1133	<
1134	<	if( !done && n_per_extra > 3){
1135	<	makeElement( i * cellx + 0.5 * cellx,
1136	<	j * celly,
1137	<	k * cellz + 0.5 * cellz );
1138	<	done = ( current_mol >= tot_nmol );
1139	<	}
1140	<	}
1141	<	}
1142	<	}
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	<
1459	<
1460	<	for( i=0; i<simnfo->n_atoms; i++ ){
1461	<	simnfo->atoms[i]->set_vx( 0.0 );
1462	<	simnfo->atoms[i]->set_vy( 0.0 );
1463	<	simnfo->atoms[i]->set_vz( 0.0 );
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		}
1151	–	}
1468
1469	<	void SimSetup::makeElement( double x, double y, double z ){
1469	>	// set the arrays into the SimInfo object
1470
1471	<	int k;
1472	<	AtomStamp* current_atom;
1473	<	DirectionalAtom* dAtom;
1474	<	double rotMat[3][3];
1471	>	info->atoms = the_atoms;
1472	>	info->molecules = the_molecules;
1473	>	info->nGlobalExcludes = 0;
1474	>	info->excludes = the_excludes;
1475
1476	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1476	>	the_ff->setSimInfo( info );
1477
1162	–	current_atom = comp_stamps[current_comp]->getAtom( k );
1163	–	if( !current_atom->havePosition() ){
1164	–	sprintf( painCave.errMsg,
1165	–	"SimSetup:initFromBass error.\n"
1166	–	"\tComponent %s, atom %s does not have a position specified.\n"
1167	–	"\tThe initialization routine is unable to give a start"
1168	–	" position.\n",
1169	–	comp_stamps[current_comp]->getID(),
1170	–	current_atom->getType() );
1171	–	painCave.isFatal = 1;
1172	–	simError();
1173	–	}
1174	–
1175	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1176	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1177	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1178	–
1179	–	if( the_atoms[current_atom_ndx]->isDirectional() ){
1180	–
1181	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1182	–
1183	–	rotMat[0][0] = 1.0;
1184	–	rotMat[0][1] = 0.0;
1185	–	rotMat[0][2] = 0.0;
1186	–
1187	–	rotMat[1][0] = 0.0;
1188	–	rotMat[1][1] = 1.0;
1189	–	rotMat[1][2] = 0.0;
1190	–
1191	–	rotMat[2][0] = 0.0;
1192	–	rotMat[2][1] = 0.0;
1193	–	rotMat[2][2] = 1.0;
1194	–
1195	–	dAtom->setA( rotMat );
1196	–	}
1197	–
1198	–	current_atom_ndx++;
1199	–	}
1200	–
1201	–	current_mol++;
1202	–	current_comp_mol++;
1203	–
1204	–	if( current_comp_mol >= components_nmol[current_comp] ){
1205	–
1206	–	current_comp_mol = 0;
1207	–	current_comp++;
1208	–	}
1478		}

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