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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 656 by mmeineke, Tue Jul 29 16:32:37 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	+	#define FF_EAM  2
28	+
29		SimSetup::SimSetup(){
30	+
31	+	isInfoArray = 0;
32	+	nInfo = 1;
33	+
34		stamps = new MakeStamps();
35		globals = new Globals();
36
37	+
38		#ifdef IS_MPI
39		strcpy( checkPointMsg, "SimSetup creation successful" );
40		MPIcheckPoint();
#	Line 27 | Line 46 | void SimSetup::parseFile( char* fileName ){
46		delete globals;
47		}
48
49	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
50	+	info = the_info;
51	+	nInfo = theNinfo;
52	+	isInfoArray = 1;
53	+	}
54	+
55	+
56		void SimSetup::parseFile( char* fileName ){
57
58		#ifdef IS_MPI
#	Line 64 | Line 90 | void SimSetup::createSim( void ){
90
91		void SimSetup::createSim( void ){
92
93	<	MakeStamps *the_stamps;
94	<	Globals* the_globals;
95	<	int i, j;
93	>	int i, j, k, globalAtomIndex;
94	>
95	>	// gather all of the information from the Bass file
96	>
97	>	gatherInfo();
98
99	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
99	>	// creation of complex system objects
100
101	<	// 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();
101	>	sysObjectsCreation();
102
103	<	// get the ones we know are there, yet still may need some work.
104	<	n_components = the_globals->getNComponents();
105	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
103	>	// check on the post processing info
104	>
105	>	finalInfoCheck();
106
107	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
107	>	// initialize the system coordinates
108
109	+	initSystemCoords();
110	+
111
112	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
112	>	// make the output filenames
113
114	+	makeOutNames();
115	+
116	+	// make the integrator
117	+
118	+	makeIntegrator();
119	+
120		#ifdef IS_MPI
121	<	strcpy( checkPointMsg, "ForceField creation successful" );
122	<	MPIcheckPoint();
106	<	#endif // is_mpi
121	>	mpiSim->mpiRefresh();
122	>	#endif
123
124	<
124	>	// initialize the Fortran
125
126	<	// 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];
126	>	initFortran();
127
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
128
119	–	tot_nmol = 0;
120	–	for( i=0; i<n_components; i++ ){
129
130	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
130	>	}
131
131	–	tot_nmol += the_components[i]->getNMol();
132	–	components_nmol[i] = the_components[i]->getNMol();
133	–	}
134	–	}
135	–	else{
136	–	sprintf( painCave.errMsg,
137	–	"SimSetup error.\n"
138	–	"\tSorry, the ability to specify total"
139	–	" nMols and then give molfractions in the components\n"
140	–	"\tis not currently supported."
141	–	" Please give nMol in the components.\n" );
142	–	painCave.isFatal = 1;
143	–	simError();
144	–
145	–
146	–	//     tot_nmol = the_globals->getNMol();
147	–
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
132
133	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
133	>	void SimSetup::makeMolecules( void ){
134
135	<	// make an array of molecule stamps that match the components used.
136	<	// also extract the used stamps out into a separate linked list
135	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136	>	molInit molInfo;
137	>	DirectionalAtom* dAtom;
138	>	LinkedAssign* extras;
139	>	LinkedAssign* current_extra;
140	>	AtomStamp* currentAtom;
141	>	BondStamp* currentBond;
142	>	BendStamp* currentBend;
143	>	TorsionStamp* currentTorsion;
144
145	<	simnfo->nComponents = n_components;
146	<	simnfo->componentsNmol = components_nmol;
147	<	simnfo->compStamps = comp_stamps;
148	<	simnfo->headStamp = new LinkedMolStamp();
145	>	bond_pair* theBonds;
146	>	bend_set* theBends;
147	>	torsion_set* theTorsions;
148	>
149
150	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
150	>	//init the forceField paramters
151
152	<	id = the_components[i]->getType();
153	<	comp_stamps[i] = NULL;
152	>	the_ff->readParams();
153	>
154	>
155	>	// init the atoms
156	>
157	>	double ux, uy, uz, u, uSqr;
158	>
159	>	atomOffset = 0;
160	>	excludeOffset = 0;
161	>	for(i=0; i<info->n_mol; i++){
162
163	<	// check to make sure the component isn't already in the list
163	>	stampID = the_molecules[i].getStampID();
164
165	<	comp_stamps[i] = headStamp->match( id );
166	<	if( comp_stamps[i] == NULL ){
165	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
166	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
167	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
168	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
169	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
170	>
171	>	molInfo.myAtoms = &the_atoms[atomOffset];
172	>	molInfo.myExcludes = &the_excludes[excludeOffset];
173	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
174	>	molInfo.myBends = new Bend*[molInfo.nBends];
175	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
176	>
177	>	theBonds = new bond_pair[molInfo.nBonds];
178	>	theBends = new bend_set[molInfo.nBends];
179	>	theTorsions = new torsion_set[molInfo.nTorsions];
180	>
181	>	// make the Atoms
182	>
183	>	for(j=0; j<molInfo.nAtoms; j++){
184
185	<	// extract the component from the list;
186	<
187	<	currentStamp = the_stamps->extractMolStamp( id );
188	<	if( currentStamp == NULL ){
189	<	sprintf( painCave.errMsg,
190	<	"SimSetup error: Component \"%s\" was not found in the "
191	<	"list of declared molecules\n",
192	<	id );
193	<	painCave.isFatal = 1;
194	<	simError();
185	>	currentAtom = comp_stamps[stampID]->getAtom( j );
186	>	if( currentAtom->haveOrientation() ){
187	>
188	>	dAtom = new DirectionalAtom(j + atomOffset);
189	>	info->n_oriented++;
190	>	molInfo.myAtoms[j] = dAtom;
191	>
192	>	ux = currentAtom->getOrntX();
193	>	uy = currentAtom->getOrntY();
194	>	uz = currentAtom->getOrntZ();
195	>
196	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
197	>
198	>	u = sqrt( uSqr );
199	>	ux = ux / u;
200	>	uy = uy / u;
201	>	uz = uz / u;
202	>
203	>	dAtom->setSUx( ux );
204	>	dAtom->setSUy( uy );
205	>	dAtom->setSUz( uz );
206		}
207	<
208	<	headStamp->add( currentStamp );
209	<	comp_stamps[i] = headStamp->match( id );
210	<	}
211	<	}
202	<
207	>	else{
208	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
209	>	}
210	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
211	>
212		#ifdef IS_MPI
213	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
214	<	MPIcheckPoint();
213	>
214	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
215	>
216		#endif // is_mpi
217	<
217	>	}
218	>
219	>	// make the bonds
220	>	for(j=0; j<molInfo.nBonds; j++){
221	>
222	>	currentBond = comp_stamps[stampID]->getBond( j );
223	>	theBonds[j].a = currentBond->getA() + atomOffset;
224	>	theBonds[j].b = currentBond->getB() + atomOffset;
225
226	+	exI = theBonds[j].a;
227	+	exJ = theBonds[j].b;
228
229	+	// exclude_I must always be the smaller of the pair
230	+	if( exI > exJ ){
231	+	tempEx = exI;
232	+	exI = exJ;
233	+	exJ = tempEx;
234	+	}
235	+	#ifdef IS_MPI
236	+	tempEx = exI;
237	+	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
238	+	tempEx = exJ;
239	+	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
240	+
241	+	the_excludes[j+excludeOffset]->setPair( exI, exJ );
242	+	#else  // isn't MPI
243
244	<	// caclulate the number of atoms, bonds, bends and torsions
244	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
245	>	#endif  //is_mpi
246	>	}
247	>	excludeOffset += molInfo.nBonds;
248
249	<	tot_atoms = 0;
250	<	tot_bonds = 0;
251	<	tot_bends = 0;
252	<	tot_torsions = 0;
253	<	for( i=0; i<n_components; i++ ){
249	>	//make the bends
250	>	for(j=0; j<molInfo.nBends; j++){
251	>
252	>	currentBend = comp_stamps[stampID]->getBend( j );
253	>	theBends[j].a = currentBend->getA() + atomOffset;
254	>	theBends[j].b = currentBend->getB() + atomOffset;
255	>	theBends[j].c = currentBend->getC() + atomOffset;
256	>
257	>	if( currentBend->haveExtras() ){
258	>
259	>	extras = currentBend->getExtras();
260	>	current_extra = extras;
261	>
262	>	while( current_extra != NULL ){
263	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
264	>
265	>	switch( current_extra->getType() ){
266	>
267	>	case 0:
268	>	theBends[j].ghost =
269	>	current_extra->getInt() + atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272	>
273	>	case 1:
274	>	theBends[j].ghost =
275	>	(int)current_extra->getDouble() + atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278	>
279	>	default:
280	>	sprintf( painCave.errMsg,
281	>	"SimSetup Error: ghostVectorSource was neither a "
282	>	"double nor an int.\n"
283	>	"-->Bend[%d] in %s\n",
284	>	j, comp_stamps[stampID]->getID() );
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>	}
289	>
290	>	else{
291	>
292	>	sprintf( painCave.errMsg,
293	>	"SimSetup Error: unhandled bend assignment:\n"
294	>	"    -->%s in Bend[%d] in %s\n",
295	>	current_extra->getlhs(),
296	>	j, comp_stamps[stampID]->getID() );
297	>	painCave.isFatal = 1;
298	>	simError();
299	>	}
300	>
301	>	current_extra = current_extra->getNext();
302	>	}
303	>	}
304	>
305	>	if( !theBends[j].isGhost ){
306	>
307	>	exI = theBends[j].a;
308	>	exJ = theBends[j].c;
309	>	}
310	>	else{
311	>
312	>	exI = theBends[j].a;
313	>	exJ = theBends[j].b;
314	>	}
315	>
316	>	// exclude_I must always be the smaller of the pair
317	>	if( exI > exJ ){
318	>	tempEx = exI;
319	>	exI = exJ;
320	>	exJ = tempEx;
321	>	}
322	>	#ifdef IS_MPI
323	>	tempEx = exI;
324	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
325	>	tempEx = exJ;
326	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
327	>
328	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
329	>	#else  // isn't MPI
330	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
331	>	#endif  //is_mpi
332	>	}
333	>	excludeOffset += molInfo.nBends;
334	>
335	>	for(j=0; j<molInfo.nTorsions; j++){
336	>
337	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
338	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
339	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
340	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
341	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
342	>
343	>	exI = theTorsions[j].a;
344	>	exJ = theTorsions[j].d;
345	>
346	>	// exclude_I must always be the smaller of the pair
347	>	if( exI > exJ ){
348	>	tempEx = exI;
349	>	exI = exJ;
350	>	exJ = tempEx;
351	>	}
352	>	#ifdef IS_MPI
353	>	tempEx = exI;
354	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
355	>	tempEx = exJ;
356	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
357	>
358	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
359	>	#else  // isn't MPI
360	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
361	>	#endif  //is_mpi
362	>	}
363	>	excludeOffset += molInfo.nTorsions;
364	>
365
366	<	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	<	}
366	>	// send the arrays off to the forceField for init.
367
368	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
368	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
369	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
370	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
371	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
372
227	–	simnfo->n_atoms = tot_atoms;
228	–	simnfo->n_bonds = tot_bonds;
229	–	simnfo->n_bends = tot_bends;
230	–	simnfo->n_torsions = tot_torsions;
231	–	simnfo->n_SRI = tot_SRI;
232	–	simnfo->n_mol = tot_nmol;
373
374	<
374	>	the_molecules[i].initialize( molInfo );
375	>
376	>
377	>	atomOffset += molInfo.nAtoms;
378	>	delete[] theBonds;
379	>	delete[] theBends;
380	>	delete[] theTorsions;
381	>	}
382	>
383		#ifdef IS_MPI
384	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
385	+	MPIcheckPoint();
386	+	#endif // is_mpi
387
388	<	// divide the molecules among processors here.
389	<
390	<	mpiSim = new mpiSimulation( simnfo );
240	<
241	<
388	>	// clean up the forcefield
389	>	the_ff->calcRcut();
390	>	the_ff->cleanMe();
391
392	<	globalIndex = mpiSim->divideLabor();
392	>	}
393
394	+	void SimSetup::initFromBass( void ){
395
396	+	int i, j, k;
397	+	int n_cells;
398	+	double cellx, celly, cellz;
399	+	double temp1, temp2, temp3;
400	+	int n_per_extra;
401	+	int n_extra;
402	+	int have_extra, done;
403
404	<	// set up the local variables
405	<
406	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	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++ ){
404	>	temp1 = (double)tot_nmol / 4.0;
405	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
406	>	temp3 = ceil( temp2 );
407
408	<	for( j=0; j<components_nmol[i]; j++ ){
409	<
410	<	if( mpiSim->getMyMolStart() <= allMol &&
411	<	allMol <= mpiSim->getMyMolEnd() ){
412	<
413	<	local_atoms +=    comp_stamps[i]->getNAtoms();
414	<	local_bonds +=    comp_stamps[i]->getNBonds();
415	<	local_bends +=    comp_stamps[i]->getNBends();
416	<	local_torsions += comp_stamps[i]->getNTorsions();
417	<	localMol++;
418	<	}
419	<	allMol++;
408	>	have_extra =0;
409	>	if( temp2 < temp3 ){ // we have a non-complete lattice
410	>	have_extra =1;
411	>
412	>	n_cells = (int)temp3 - 1;
413	>	cellx = info->boxL[0] / temp3;
414	>	celly = info->boxL[1] / temp3;
415	>	cellz = info->boxL[2] / temp3;
416	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
417	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
418	>	n_per_extra = (int)ceil( temp1 );
419	>
420	>	if( n_per_extra > 4){
421	>	sprintf( painCave.errMsg,
422	>	"SimSetup error. There has been an error in constructing"
423	>	" the non-complete lattice.\n" );
424	>	painCave.isFatal = 1;
425	>	simError();
426		}
427		}
428	<	local_SRI = local_bonds + local_bends + local_torsions;
429	<
430	<
431	<	simnfo->n_atoms = mpiSim->getMyNlocal();
432	<
279	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
428	>	else{
429	>	n_cells = (int)temp3;
430	>	cellx = info->boxL[0] / temp3;
431	>	celly = info->boxL[1] / temp3;
432	>	cellz = info->boxL[2] / temp3;
433		}
434
435	<	simnfo->n_bonds = local_bonds;
436	<	simnfo->n_bends = local_bends;
437	<	simnfo->n_torsions = local_torsions;
438	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
435	>	current_mol = 0;
436	>	current_comp_mol = 0;
437	>	current_comp = 0;
438	>	current_atom_ndx = 0;
439
440	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
441	<	MPIcheckPoint();
442	<
298	<
299	<	#endif // is_mpi
300	<
440	>	for( i=0; i < n_cells ; i++ ){
441	>	for( j=0; j < n_cells; j++ ){
442	>	for( k=0; k < n_cells; k++ ){
443
444	<	// create the atom and short range interaction arrays
444	>	makeElement( i * cellx,
445	>	j * celly,
446	>	k * cellz );
447
448	<	Atom::createArrays(simnfo->n_atoms);
449	<	the_atoms = new Atom*[simnfo->n_atoms];
450	<	the_molecules = new Molecule[simnfo->n_mol];
448	>	makeElement( i * cellx + 0.5 * cellx,
449	>	j * celly + 0.5 * celly,
450	>	k * cellz );
451
452	+	makeElement( i * cellx,
453	+	j * celly + 0.5 * celly,
454	+	k * cellz + 0.5 * cellz );
455
456	<	if( simnfo->n_SRI ){
457	<	the_sris = new SRI*[simnfo->n_SRI];
458	<	the_excludes = new int[2 * simnfo->n_SRI];
459	<	simnfo->globalExcludes = new int;
460	<	simnfo->n_exclude = tot_SRI;
456	>	makeElement( i * cellx + 0.5 * cellx,
457	>	j * celly,
458	>	k * cellz + 0.5 * cellz );
459	>	}
460	>	}
461		}
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;
462
463	<	simnfo->n_exclude = 1;
463	>	if( have_extra ){
464	>	done = 0;
465	>
466	>	int start_ndx;
467	>	for( i=0; i < (n_cells+1) && !done; i++ ){
468	>	for( j=0; j < (n_cells+1) && !done; j++ ){
469	>
470	>	if( i < n_cells ){
471	>
472	>	if( j < n_cells ){
473	>	start_ndx = n_cells;
474	>	}
475	>	else start_ndx = 0;
476	>	}
477	>	else start_ndx = 0;
478	>
479	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
480	>
481	>	makeElement( i * cellx,
482	>	j * celly,
483	>	k * cellz );
484	>	done = ( current_mol >= tot_nmol );
485	>
486	>	if( !done && n_per_extra > 1 ){
487	>	makeElement( i * cellx + 0.5 * cellx,
488	>	j * celly + 0.5 * celly,
489	>	k * cellz );
490	>	done = ( current_mol >= tot_nmol );
491	>	}
492	>
493	>	if( !done && n_per_extra > 2){
494	>	makeElement( i * cellx,
495	>	j * celly + 0.5 * celly,
496	>	k * cellz + 0.5 * cellz );
497	>	done = ( current_mol >= tot_nmol );
498	>	}
499	>
500	>	if( !done && n_per_extra > 3){
501	>	makeElement( i * cellx + 0.5 * cellx,
502	>	j * celly,
503	>	k * cellz + 0.5 * cellz );
504	>	done = ( current_mol >= tot_nmol );
505	>	}
506	>	}
507	>	}
508	>	}
509		}
510
326	–	// set the arrays into the SimInfo object
511
512	<	simnfo->atoms = the_atoms;
513	<	simnfo->sr_interactions = the_sris;
514	<	simnfo->nGlobalExcludes = 0;
515	<	simnfo->excludes = the_excludes;
512	>	for( i=0; i<info->n_atoms; i++ ){
513	>	info->atoms[i]->set_vx( 0.0 );
514	>	info->atoms[i]->set_vy( 0.0 );
515	>	info->atoms[i]->set_vz( 0.0 );
516	>	}
517	>	}
518
519	+	void SimSetup::makeElement( double x, double y, double z ){
520
521	<	// get some of the tricky things that may still be in the globals
521	>	int k;
522	>	AtomStamp* current_atom;
523	>	DirectionalAtom* dAtom;
524	>	double rotMat[3][3];
525
526	+	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
527	+
528	+	current_atom = comp_stamps[current_comp]->getAtom( k );
529	+	if( !current_atom->havePosition() ){
530	+	sprintf( painCave.errMsg,
531	+	"SimSetup:initFromBass error.\n"
532	+	"\tComponent %s, atom %s does not have a position specified.\n"
533	+	"\tThe initialization routine is unable to give a start"
534	+	" position.\n",
535	+	comp_stamps[current_comp]->getID(),
536	+	current_atom->getType() );
537	+	painCave.isFatal = 1;
538	+	simError();
539	+	}
540	+
541	+	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
542	+	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
543	+	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
544	+
545	+	if( the_atoms[current_atom_ndx]->isDirectional() ){
546	+
547	+	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
548	+
549	+	rotMat[0][0] = 1.0;
550	+	rotMat[0][1] = 0.0;
551	+	rotMat[0][2] = 0.0;
552	+
553	+	rotMat[1][0] = 0.0;
554	+	rotMat[1][1] = 1.0;
555	+	rotMat[1][2] = 0.0;
556	+
557	+	rotMat[2][0] = 0.0;
558	+	rotMat[2][1] = 0.0;
559	+	rotMat[2][2] = 1.0;
560	+
561	+	dAtom->setA( rotMat );
562	+	}
563	+
564	+	current_atom_ndx++;
565	+	}
566	+
567	+	current_mol++;
568	+	current_comp_mol++;
569	+
570	+	if( current_comp_mol >= components_nmol[current_comp] ){
571	+
572	+	current_comp_mol = 0;
573	+	current_comp++;
574	+	}
575	+	}
576	+
577	+
578	+	void SimSetup::gatherInfo( void ){
579	+	int i,j,k;
580	+
581	+	ensembleCase = -1;
582	+	ffCase = -1;
583	+
584	+	// get the stamps and globals;
585	+	stamps = stamps;
586	+	globals = globals;
587	+
588	+	// set the easy ones first
589	+	info->target_temp = globals->getTargetTemp();
590	+	info->dt = globals->getDt();
591	+	info->run_time = globals->getRunTime();
592	+	n_components = globals->getNComponents();
593	+
594	+
595	+	// get the forceField
596	+
597	+	strcpy( force_field, globals->getForceField() );
598	+
599	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
600	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
601	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
602	+	else{
603	+	sprintf( painCave.errMsg,
604	+	"SimSetup Error. Unrecognized force field -> %s\n",
605	+	force_field );
606	+	painCave.isFatal = 1;
607	+	simError();
608	+	}
609	+
610	+	// get the ensemble
611	+
612	+	strcpy( ensemble, globals->getEnsemble() );
613	+
614	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
615	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
616	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
617	+	ensembleCase = NPTi_ENS;
618	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
619	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
620	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
621	+	else{
622	+	sprintf( painCave.errMsg,
623	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
624	+	"reverting to NVE for this simulation.\n",
625	+	ensemble );
626	+	painCave.isFatal = 0;
627	+	simError();
628	+	strcpy( ensemble, "NVE" );
629	+	ensembleCase = NVE_ENS;
630	+	}
631	+	strcpy( info->ensemble, ensemble );
632	+
633	+	// get the mixing rule
634	+
635	+	strcpy( info->mixingRule, globals->getMixingRule() );
636	+	info->usePBC = globals->getPBC();
637	+
638
639	<	if( the_globals->haveBox() ){
640	<	simnfo->box_x = the_globals->getBox();
641	<	simnfo->box_y = the_globals->getBox();
642	<	simnfo->box_z = the_globals->getBox();
639	>	// get the components and calculate the tot_nMol and indvidual n_mol
640	>
641	>	the_components = globals->getComponents();
642	>	components_nmol = new int[n_components];
643	>
644	>
645	>	if( !globals->haveNMol() ){
646	>	// we don't have the total number of molecules, so we assume it is
647	>	// given in each component
648	>
649	>	tot_nmol = 0;
650	>	for( i=0; i<n_components; i++ ){
651	>
652	>	if( !the_components[i]->haveNMol() ){
653	>	// we have a problem
654	>	sprintf( painCave.errMsg,
655	>	"SimSetup Error. No global NMol or component NMol"
656	>	" given. Cannot calculate the number of atoms.\n" );
657	>	painCave.isFatal = 1;
658	>	simError();
659	>	}
660	>
661	>	tot_nmol += the_components[i]->getNMol();
662	>	components_nmol[i] = the_components[i]->getNMol();
663	>	}
664		}
665	<	else if( the_globals->haveDensity() ){
665	>	else{
666	>	sprintf( painCave.errMsg,
667	>	"SimSetup error.\n"
668	>	"\tSorry, the ability to specify total"
669	>	" nMols and then give molfractions in the components\n"
670	>	"\tis not currently supported."
671	>	" Please give nMol in the components.\n" );
672	>	painCave.isFatal = 1;
673	>	simError();
674	>	}
675
676	+	// set the status, sample, and thermal kick times
677	+
678	+	if( globals->haveSampleTime() ){
679	+	info->sampleTime = globals->getSampleTime();
680	+	info->statusTime = info->sampleTime;
681	+	info->thermalTime = info->sampleTime;
682	+	}
683	+	else{
684	+	info->sampleTime = globals->getRunTime();
685	+	info->statusTime = info->sampleTime;
686	+	info->thermalTime = info->sampleTime;
687	+	}
688	+
689	+	if( globals->haveStatusTime() ){
690	+	info->statusTime = globals->getStatusTime();
691	+	}
692	+
693	+	if( globals->haveThermalTime() ){
694	+	info->thermalTime = globals->getThermalTime();
695	+	}
696	+
697	+	// check for the temperature set flag
698	+
699	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
700	+
701	+	// get some of the tricky things that may still be in the globals
702	+
703	+	double boxVector[3];
704	+	if( globals->haveBox() ){
705	+	boxVector[0] = globals->getBox();
706	+	boxVector[1] = globals->getBox();
707	+	boxVector[2] = globals->getBox();
708	+
709	+	info->setBox( boxVector );
710	+	}
711	+	else if( globals->haveDensity() ){
712	+
713		double vol;
714	<	vol = (double)tot_nmol / the_globals->getDensity();
715	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
716	<	simnfo->box_y = simnfo->box_x;
717	<	simnfo->box_z = simnfo->box_x;
714	>	vol = (double)tot_nmol / globals->getDensity();
715	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
716	>	boxVector[1] = boxVector[0];
717	>	boxVector[2] = boxVector[0];
718	>
719	>	info->setBox( boxVector );
720		}
721		else{
722	<	if( !the_globals->haveBoxX() ){
722	>	if( !globals->haveBoxX() ){
723		sprintf( painCave.errMsg,
724		"SimSetup error, no periodic BoxX size given.\n" );
725		painCave.isFatal = 1;
726		simError();
727		}
728	<	simnfo->box_x = the_globals->getBoxX();
728	>	boxVector[0] = globals->getBoxX();
729
730	<	if( !the_globals->haveBoxY() ){
730	>	if( !globals->haveBoxY() ){
731		sprintf( painCave.errMsg,
732		"SimSetup error, no periodic BoxY size given.\n" );
733		painCave.isFatal = 1;
734		simError();
735		}
736	<	simnfo->box_y = the_globals->getBoxY();
736	>	boxVector[1] = globals->getBoxY();
737
738	<	if( !the_globals->haveBoxZ() ){
738	>	if( !globals->haveBoxZ() ){
739		sprintf( painCave.errMsg,
740		"SimSetup error, no periodic BoxZ size given.\n" );
741		painCave.isFatal = 1;
742		simError();
743		}
744	<	simnfo->box_z = the_globals->getBoxZ();
744	>	boxVector[2] = globals->getBoxZ();
745	>
746	>	info->setBox( boxVector );
747		}
748
749	+
750	+
751		#ifdef IS_MPI
752	<	strcpy( checkPointMsg, "Box size set up" );
752	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
753		MPIcheckPoint();
754		#endif // is_mpi
755
756	+	}
757
382	–	// initialize the arrays
758
759	<	the_ff->setSimInfo( simnfo );
759	>	void SimSetup::finalInfoCheck( void ){
760	>	int index;
761	>	int usesDipoles;
762	>
763
764	<	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	<	}
764	>	// check electrostatic parameters
765
766	<	if( tot_bonds ){
767	<	makeBonds();
766	>	index = 0;
767	>	usesDipoles = 0;
768	>	while( (index < info->n_atoms) && !usesDipoles ){
769	>	usesDipoles = ((info->atoms)[index])->hasDipole();
770	>	index++;
771		}
772	+
773	+	#ifdef IS_MPI
774	+	int myUse = usesDipoles;
775	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
776	+	#endif //is_mpi
777
778	<	if( tot_bends ){
397	<	makeBends();
398	<	}
778	>	double theEcr, theEst;
779
780	<	if( tot_torsions ){
781	<	makeTorsions();
782	<	}
783	<
404	<
405	<	if (the_globals->getUseRF() ) {
406	<	simnfo->useReactionField = 1;
407	<
408	<	if( !the_globals->haveECR() ){
780	>	if (globals->getUseRF() ) {
781	>	info->useReactionField = 1;
782	>
783	>	if( !globals->haveECR() ){
784		sprintf( painCave.errMsg,
785		"SimSetup Warning: using default value of 1/2 the smallest "
786		"box length for the electrostaticCutoffRadius.\n"
#	Line 413 | Line 788 | void SimSetup::createSim( void ){
788		painCave.isFatal = 0;
789		simError();
790		double smallest;
791	<	smallest = simnfo->box_x;
792	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
793	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
794	<	simnfo->ecr = 0.5 * smallest;
791	>	smallest = info->boxL[0];
792	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
793	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
794	>	theEcr = 0.5 * smallest;
795		} else {
796	<	simnfo->ecr        = the_globals->getECR();
796	>	theEcr = globals->getECR();
797		}
798
799	<	if( !the_globals->haveEST() ){
799	>	if( !globals->haveEST() ){
800		sprintf( painCave.errMsg,
801		"SimSetup Warning: using default value of 0.05 * the "
802		"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
803		);
804		painCave.isFatal = 0;
805		simError();
806	<	simnfo->est = 0.05 * simnfo->ecr;
806	>	theEst = 0.05 * theEcr;
807		} else {
808	<	simnfo->est        = the_globals->getEST();
808	>	theEst= globals->getEST();
809		}
810	+
811	+	info->setEcr( theEcr, theEst );
812
813	<	if(!the_globals->haveDielectric() ){
813	>	if(!globals->haveDielectric() ){
814		sprintf( painCave.errMsg,
815		"SimSetup Error: You are trying to use Reaction Field without"
816		"setting a dielectric constant!\n"
#	Line 441 | Line 818 | void SimSetup::createSim( void ){
818		painCave.isFatal = 1;
819		simError();
820		}
821	<	simnfo->dielectric = the_globals->getDielectric();
822	<	} else {
823	<	if (simnfo->n_dipoles) {
824	<
825	<	if( !the_globals->haveECR() ){
826	<	sprintf( painCave.errMsg,
827	<	"SimSetup Warning: using default value of 1/2 the smallest"
828	<	"box length for the electrostaticCutoffRadius.\n"
829	<	"I hope you have a very fast processor!\n");
830	<	painCave.isFatal = 0;
831	<	simError();
832	<	double smallest;
833	<	smallest = simnfo->box_x;
834	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
835	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
836	<	simnfo->ecr = 0.5 * smallest;
821	>	info->dielectric = globals->getDielectric();
822	>	}
823	>	else {
824	>	if (usesDipoles) {
825	>
826	>	if( !globals->haveECR() ){
827	>	sprintf( painCave.errMsg,
828	>	"SimSetup Warning: using default value of 1/2 the smallest "
829	>	"box length for the electrostaticCutoffRadius.\n"
830	>	"I hope you have a very fast processor!\n");
831	>	painCave.isFatal = 0;
832	>	simError();
833	>	double smallest;
834	>	smallest = info->boxL[0];
835	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
836	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
837	>	theEcr = 0.5 * smallest;
838		} else {
839	<	simnfo->ecr        = the_globals->getECR();
839	>	theEcr = globals->getECR();
840		}
841
842	<	if( !the_globals->haveEST() ){
843	<	sprintf( painCave.errMsg,
844	<	"SimSetup Warning: using default value of 5% of the"
845	<	"electrostaticCutoffRadius for the "
846	<	"electrostaticSkinThickness\n"
847	<	);
848	<	painCave.isFatal = 0;
849	<	simError();
850	<	simnfo->est = 0.05 * simnfo->ecr;
842	>	if( !globals->haveEST() ){
843	>	sprintf( painCave.errMsg,
844	>	"SimSetup Warning: using default value of 0.05 * the "
845	>	"electrostaticCutoffRadius for the "
846	>	"electrostaticSkinThickness\n"
847	>	);
848	>	painCave.isFatal = 0;
849	>	simError();
850	>	theEst = 0.05 * theEcr;
851		} else {
852	<	simnfo->est        = the_globals->getEST();
852	>	theEst= globals->getEST();
853		}
854	+
855	+	info->setEcr( theEcr, theEst );
856		}
857		}
858
859		#ifdef IS_MPI
860	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
860	>	strcpy( checkPointMsg, "post processing checks out" );
861		MPIcheckPoint();
862		#endif // is_mpi
863
864	<	if( the_globals->haveInitialConfig() ){
864	>	}
865	>
866	>	void SimSetup::initSystemCoords( void ){
867	>
868	>	if( globals->haveInitialConfig() ){
869
870		InitializeFromFile* fileInit;
871		#ifdef IS_MPI // is_mpi
872		if( worldRank == 0 ){
873		#endif //is_mpi
874	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
874	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
875		#ifdef IS_MPI
876		}else fileInit = new InitializeFromFile( NULL );
877		#endif
878	<	fileInit->read_xyz( simnfo ); // default velocities on
878	>	fileInit->readInit( info ); // default velocities on
879
880		delete fileInit;
881		}
#	Line 519 | Line 903 | void SimSetup::createSim( void ){
903		MPIcheckPoint();
904		#endif // is_mpi
905
906	+	}
907
523	–
524	–
525	–
908
909	<
909	>	void SimSetup::makeOutNames( void ){
910	>
911		#ifdef IS_MPI
912		if( worldRank == 0 ){
913		#endif // is_mpi
914
915	<	if( the_globals->haveFinalConfig() ){
916	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
915	>	if( globals->haveFinalConfig() ){
916	>	strcpy( info->finalName, globals->getFinalConfig() );
917		}
918		else{
919	<	strcpy( simnfo->finalName, inFileName );
919	>	strcpy( info->finalName, inFileName );
920		char* endTest;
921	<	int nameLength = strlen( simnfo->finalName );
922	<	endTest = &(simnfo->finalName[nameLength - 5]);
921	>	int nameLength = strlen( info->finalName );
922	>	endTest = &(info->finalName[nameLength - 5]);
923		if( !strcmp( endTest, ".bass" ) ){
924		strcpy( endTest, ".eor" );
925		}
#	Line 544 | Line 927 | void SimSetup::createSim( void ){
927		strcpy( endTest, ".eor" );
928		}
929		else{
930	<	endTest = &(simnfo->finalName[nameLength - 4]);
930	>	endTest = &(info->finalName[nameLength - 4]);
931		if( !strcmp( endTest, ".bss" ) ){
932		strcpy( endTest, ".eor" );
933		}
#	Line 552 | Line 935 | void SimSetup::createSim( void ){
935		strcpy( endTest, ".eor" );
936		}
937		else{
938	<	strcat( simnfo->finalName, ".eor" );
938	>	strcat( info->finalName, ".eor" );
939		}
940		}
941		}
942
943		// make the sample and status out names
944
945	<	strcpy( simnfo->sampleName, inFileName );
945	>	strcpy( info->sampleName, inFileName );
946		char* endTest;
947	<	int nameLength = strlen( simnfo->sampleName );
948	<	endTest = &(simnfo->sampleName[nameLength - 5]);
947	>	int nameLength = strlen( info->sampleName );
948	>	endTest = &(info->sampleName[nameLength - 5]);
949		if( !strcmp( endTest, ".bass" ) ){
950		strcpy( endTest, ".dump" );
951		}
#	Line 570 | Line 953 | void SimSetup::createSim( void ){
953		strcpy( endTest, ".dump" );
954		}
955		else{
956	<	endTest = &(simnfo->sampleName[nameLength - 4]);
956	>	endTest = &(info->sampleName[nameLength - 4]);
957		if( !strcmp( endTest, ".bss" ) ){
958		strcpy( endTest, ".dump" );
959		}
#	Line 578 | Line 961 | void SimSetup::createSim( void ){
961		strcpy( endTest, ".dump" );
962		}
963		else{
964	<	strcat( simnfo->sampleName, ".dump" );
964	>	strcat( info->sampleName, ".dump" );
965		}
966		}
967
968	<	strcpy( simnfo->statusName, inFileName );
969	<	nameLength = strlen( simnfo->statusName );
970	<	endTest = &(simnfo->statusName[nameLength - 5]);
968	>	strcpy( info->statusName, inFileName );
969	>	nameLength = strlen( info->statusName );
970	>	endTest = &(info->statusName[nameLength - 5]);
971		if( !strcmp( endTest, ".bass" ) ){
972		strcpy( endTest, ".stat" );
973		}
#	Line 592 | Line 975 | void SimSetup::createSim( void ){
975		strcpy( endTest, ".stat" );
976		}
977		else{
978	<	endTest = &(simnfo->statusName[nameLength - 4]);
978	>	endTest = &(info->statusName[nameLength - 4]);
979		if( !strcmp( endTest, ".bss" ) ){
980		strcpy( endTest, ".stat" );
981		}
#	Line 600 | Line 983 | void SimSetup::createSim( void ){
983		strcpy( endTest, ".stat" );
984		}
985		else{
986	<	strcat( simnfo->statusName, ".stat" );
986	>	strcat( info->statusName, ".stat" );
987		}
988		}
989
990		#ifdef IS_MPI
991		}
992		#endif // is_mpi
993	<
994	<	// set the status, sample, and themal kick times
993	>
994	>	}
995	>
996	>
997	>	void SimSetup::sysObjectsCreation( void ){
998	>
999	>	int i;
1000	>
1001	>	// create the forceField
1002	>
1003	>	createFF();
1004	>
1005	>	// extract componentList
1006	>
1007	>	compList();
1008	>
1009	>	// calc the number of atoms, bond, bends, and torsions
1010	>
1011	>	calcSysValues();
1012	>
1013	>	#ifdef IS_MPI
1014	>	// divide the molecules among the processors
1015
1016	<	if( the_globals->haveSampleTime() ){
1017	<	simnfo->sampleTime = the_globals->getSampleTime();
1018	<	simnfo->statusTime = simnfo->sampleTime;
1019	<	simnfo->thermalTime = simnfo->sampleTime;
1020	<	}
1021	<	else{
619	<	simnfo->sampleTime = the_globals->getRunTime();
620	<	simnfo->statusTime = simnfo->sampleTime;
621	<	simnfo->thermalTime = simnfo->sampleTime;
622	<	}
1016	>	mpiMolDivide();
1017	>	#endif //is_mpi
1018	>
1019	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1020	>
1021	>	makeSysArrays();
1022
1023	<	if( the_globals->haveStatusTime() ){
1024	<	simnfo->statusTime = the_globals->getStatusTime();
1023	>	// make and initialize the molecules (all but atomic coordinates)
1024	>
1025	>	makeMolecules();
1026	>	info->identArray = new int[info->n_atoms];
1027	>	for(i=0; i<info->n_atoms; i++){
1028	>	info->identArray[i] = the_atoms[i]->getIdent();
1029		}
1030	+
1031
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
1032
1033	<	// check for the temperature set flag
1033	>	}
1034
634	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1035
1036	+	void SimSetup::createFF( void ){
1037
1038	<	//   // make the longe range forces and the integrator
1038	>	switch( ffCase ){
1039
1040	<	//   new AllLong( simnfo );
1040	>	case FF_DUFF:
1041	>	the_ff = new DUFF();
1042	>	break;
1043
1044	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
1045	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
1046	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
1044	>	case FF_LJ:
1045	>	the_ff = new LJFF();
1046	>	break;
1047
1048	+	case FF_EAM:
1049	+	the_ff = new EAM_FF();
1050	+	break;
1051
1052	<
648	<	// initialize the Fortran
649	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
654	<	}
655	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	<	}
658	<	else{
1052	>	default:
1053		sprintf( painCave.errMsg,
1054	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	<	simnfo->mixingRule );
1054	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1055		painCave.isFatal = 1;
1056		simError();
1057		}
1058
666	–
1059		#ifdef IS_MPI
1060	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
1060	>	strcpy( checkPointMsg, "ForceField creation successful" );
1061		MPIcheckPoint();
1062		#endif // is_mpi
1063	+
1064		}
1065
674	–	void SimSetup::makeAtoms( void ){
1066
1067	<	int i, j, k, index;
677	<	double ux, uy, uz, uSqr, u;
678	<	AtomStamp* current_atom;
1067	>	void SimSetup::compList( void ){
1068
1069	<	DirectionalAtom* dAtom;
681	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
1069	>	int i;
1070
1071	<	lMolIndex = 0;
684	<	molIndex = 0;
685	<	index = 0;
686	<	for( i=0; i<n_components; i++ ){
1071	>	comp_stamps = new MoleculeStamp*[n_components];
1072
1073	<	for( j=0; j<components_nmol[i]; j++ ){
1073	>	// make an array of molecule stamps that match the components used.
1074	>	// also extract the used stamps out into a separate linked list
1075
1076	<	#ifdef IS_MPI
1077	<	if( mpiSim->getMyMolStart() <= molIndex &&
1078	<	molIndex <= mpiSim->getMyMolEnd() ){
1079	<	#endif // is_mpi
1076	>	info->nComponents = n_components;
1077	>	info->componentsNmol = components_nmol;
1078	>	info->compStamps = comp_stamps;
1079	>	info->headStamp = new LinkedMolStamp();
1080	>
1081	>	char* id;
1082	>	LinkedMolStamp* headStamp = info->headStamp;
1083	>	LinkedMolStamp* currentStamp = NULL;
1084	>	for( i=0; i<n_components; i++ ){
1085
1086	<	molStart = index;
1087	<	nMemb = comp_stamps[i]->getNAtoms();
1088	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
1089	<
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++;
1086	>	id = the_components[i]->getType();
1087	>	comp_stamps[i] = NULL;
1088	>
1089	>	// check to make sure the component isn't already in the list
1090
1091	<	#ifdef IS_MPI
1091	>	comp_stamps[i] = headStamp->match( id );
1092	>	if( comp_stamps[i] == NULL ){
1093	>
1094	>	// extract the component from the list;
1095	>
1096	>	currentStamp = stamps->extractMolStamp( id );
1097	>	if( currentStamp == NULL ){
1098	>	sprintf( painCave.errMsg,
1099	>	"SimSetup error: Component \"%s\" was not found in the "
1100	>	"list of declared molecules\n",
1101	>	id );
1102	>	painCave.isFatal = 1;
1103	>	simError();
1104		}
740	–	#endif //is_mpi
1105
1106	<	molIndex++;
1106	>	headStamp->add( currentStamp );
1107	>	comp_stamps[i] = headStamp->match( id );
1108		}
1109		}
1110
1111		#ifdef IS_MPI
1112	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
1113	<
1114	<	delete[] globalIndex;
1112	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1113	>	MPIcheckPoint();
1114	>	#endif // is_mpi
1115
1116	<	mpiSim->mpiRefresh();
752	<	#endif //IS_MPI
753	<
754	<	the_ff->initializeAtoms();
1116	>
1117		}
1118
1119	<	void SimSetup::makeBonds( void ){
1119	>	void SimSetup::calcSysValues( void ){
1120	>	int i, j, k;
1121
759	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
760	–	bond_pair* the_bonds;
761	–	BondStamp* current_bond;
1122
1123	<	the_bonds = new bond_pair[tot_bonds];
1124	<	index = 0;
1125	<	offset = 0;
1126	<	molIndex = 0;
767	<
1123	>	tot_atoms = 0;
1124	>	tot_bonds = 0;
1125	>	tot_bends = 0;
1126	>	tot_torsions = 0;
1127		for( i=0; i<n_components; i++ ){
1128	+
1129	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1130	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1131	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1132	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1133	+	}
1134
1135	<	for( j=0; j<components_nmol[i]; j++ ){
1135	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1136
1137	<	#ifdef IS_MPI
1138	<	if( mpiSim->getMyMolStart() <= molIndex &&
1139	<	molIndex <= mpiSim->getMyMolEnd() ){
1140	<	#endif // is_mpi
1141	<
1142	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1143	<
1144	<	current_bond = comp_stamps[i]->getBond( k );
1145	<	the_bonds[index].a = current_bond->getA() + offset;
781	<	the_bonds[index].b = current_bond->getB() + offset;
1137	>	info->n_atoms = tot_atoms;
1138	>	info->n_bonds = tot_bonds;
1139	>	info->n_bends = tot_bends;
1140	>	info->n_torsions = tot_torsions;
1141	>	info->n_SRI = tot_SRI;
1142	>	info->n_mol = tot_nmol;
1143	>
1144	>	info->molMembershipArray = new int[tot_atoms];
1145	>	}
1146
783	–	exI = the_bonds[index].a;
784	–	exJ = the_bonds[index].b;
1147
786	–	// exclude_I must always be the smaller of the pair
787	–	if( exI > exJ ){
788	–	tempEx = exI;
789	–	exI = exJ;
790	–	exJ = tempEx;
791	–	}
792	–
793	–
1148		#ifdef IS_MPI
1149
1150	<	the_excludes[index*2] =
1151	<	the_atoms[exI]->getGlobalIndex() + 1;
1152	<	the_excludes[index*2 + 1] =
1153	<	the_atoms[exJ]->getGlobalIndex() + 1;
1150	>	void SimSetup::mpiMolDivide( void ){
1151	>
1152	>	int i, j, k;
1153	>	int localMol, allMol;
1154	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1155
1156	<	#else  // isn't MPI
1157	<
1158	<	the_excludes[index*2] =     exI + 1;
804	<	the_excludes[index*2 + 1] = exJ + 1;
805	<	// 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	<	}
819	<	}
1156	>	mpiSim = new mpiSimulation( info );
1157	>
1158	>	globalIndex = mpiSim->divideLabor();
1159
1160	<	the_ff->initializeBonds( the_bonds );
822	<	}
823	<
824	<	void SimSetup::makeBends( void ){
825	<
826	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
827	<	bend_set* the_bends;
828	<	BendStamp* current_bend;
829	<	LinkedAssign* extras;
830	<	LinkedAssign* current_extra;
1160	>	// set up the local variables
1161
1162	+	mol2proc = mpiSim->getMolToProcMap();
1163	+	molCompType = mpiSim->getMolComponentType();
1164	+
1165	+	allMol = 0;
1166	+	localMol = 0;
1167	+	local_atoms = 0;
1168	+	local_bonds = 0;
1169	+	local_bends = 0;
1170	+	local_torsions = 0;
1171	+	globalAtomIndex = 0;
1172
1173	<	the_bends = new bend_set[tot_bends];
834	<	index = 0;
835	<	offset = 0;
836	<	molIndex = 0;
1173	>
1174		for( i=0; i<n_components; i++ ){
1175
1176		for( j=0; j<components_nmol[i]; j++ ){
1177	<
1178	<	#ifdef IS_MPI
842	<	if( mpiSim->getMyMolStart() <= molIndex &&
843	<	molIndex <= mpiSim->getMyMolEnd() ){
844	<	#endif // is_mpi
845	<
846	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
847	<
848	<	current_bend = comp_stamps[i]->getBend( k );
849	<	the_bends[index].a = current_bend->getA() + offset;
850	<	the_bends[index].b = current_bend->getB() + offset;
851	<	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();
1177	>
1178	>	if( mol2proc[allMol] == worldRank ){
1179
1180	<	#ifdef IS_MPI
1180	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1181	>	local_bonds +=    comp_stamps[i]->getNBonds();
1182	>	local_bends +=    comp_stamps[i]->getNBends();
1183	>	local_torsions += comp_stamps[i]->getNTorsions();
1184	>	localMol++;
1185	>	}
1186	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1187	>	info->molMembershipArray[globalAtomIndex] = allMol;
1188	>	globalAtomIndex++;
1189		}
942	–	#endif //is_mpi
1190
1191	<	molIndex++;
1191	>	allMol++;
1192		}
1193		}
1194	+	local_SRI = local_bonds + local_bends + local_torsions;
1195	+
1196	+	info->n_atoms = mpiSim->getMyNlocal();
1197	+
1198	+	if( local_atoms != info->n_atoms ){
1199	+	sprintf( painCave.errMsg,
1200	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1201	+	" localAtom (%d) are not equal.\n",
1202	+	info->n_atoms,
1203	+	local_atoms );
1204	+	painCave.isFatal = 1;
1205	+	simError();
1206	+	}
1207
1208	<	#ifdef IS_MPI
1209	<	sprintf( checkPointMsg,
1210	<	"Successfully created the bends list.\n" );
1208	>	info->n_bonds = local_bonds;
1209	>	info->n_bends = local_bends;
1210	>	info->n_torsions = local_torsions;
1211	>	info->n_SRI = local_SRI;
1212	>	info->n_mol = localMol;
1213	>
1214	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1215		MPIcheckPoint();
1216	<	#endif // is_mpi
1216	>	}
1217
1218	+	#endif // is_mpi
1219
955	–	the_ff->initializeBends( the_bends );
956	–	}
1220
1221	<	void SimSetup::makeTorsions( void ){
1221	>	void SimSetup::makeSysArrays( void ){
1222	>	int i, j, k;
1223
960	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
961	–	torsion_set* the_torsions;
962	–	TorsionStamp* current_torsion;
1224
1225	<	the_torsions = new torsion_set[tot_torsions];
965	<	index = 0;
966	<	offset = 0;
967	<	molIndex = 0;
968	<	for( i=0; i<n_components; i++ ){
1225	>	// create the atom and short range interaction arrays
1226
1227	<	for( j=0; j<components_nmol[i]; j++ ){
1227	>	Atom::createArrays(info->n_atoms);
1228	>	the_atoms = new Atom*[info->n_atoms];
1229	>	the_molecules = new Molecule[info->n_mol];
1230	>	int molIndex;
1231
1232	<	#ifdef IS_MPI
973	<	if( mpiSim->getMyMolStart() <= molIndex &&
974	<	molIndex <= mpiSim->getMyMolEnd() ){
975	<	#endif // is_mpi
1232	>	// initialize the molecule's stampID's
1233
1234	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1234	>	#ifdef IS_MPI
1235	>
1236
1237	<	current_torsion = comp_stamps[i]->getTorsion( k );
1238	<	the_torsions[index].a = current_torsion->getA() + offset;
1239	<	the_torsions[index].b = current_torsion->getB() + offset;
1240	<	the_torsions[index].c = current_torsion->getC() + offset;
1241	<	the_torsions[index].d = current_torsion->getD() + offset;
1237	>	molIndex = 0;
1238	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1239	>
1240	>	if(mol2proc[i] == worldRank ){
1241	>	the_molecules[molIndex].setStampID( molCompType[i] );
1242	>	the_molecules[molIndex].setMyIndex( molIndex );
1243	>	the_molecules[molIndex].setGlobalIndex( i );
1244	>	molIndex++;
1245	>	}
1246	>	}
1247
1248	<	exI = the_torsions[index].a;
1249	<	exJ = the_torsions[index].d;
1250	<
1251	<
1252	<	// exclude_I must always be the smaller of the pair
1253	<	if( exI > exJ ){
1254	<	tempEx = exI;
1255	<	exI = exJ;
1256	<	exJ = tempEx;
1257	<	}
1258	<
1259	<
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++;
1248	>	#else // is_mpi
1249	>
1250	>	molIndex = 0;
1251	>	globalAtomIndex = 0;
1252	>	for(i=0; i<n_components; i++){
1253	>	for(j=0; j<components_nmol[i]; j++ ){
1254	>	the_molecules[molIndex].setStampID( i );
1255	>	the_molecules[molIndex].setMyIndex( molIndex );
1256	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1257	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1258	>	info->molMembershipArray[globalAtomIndex] = molIndex;
1259	>	globalAtomIndex++;
1260		}
1015	–	offset += comp_stamps[i]->getNAtoms();
1016	–
1017	–	#ifdef IS_MPI
1018	–	}
1019	–	#endif //is_mpi
1020	–
1261		molIndex++;
1262		}
1263		}
1264	+
1265
1266	<	the_ff->initializeTorsions( the_torsions );
1026	<	}
1266	>	#endif // is_mpi
1267
1028	–	void SimSetup::initFromBass( void ){
1268
1269	<	int i, j, k;
1270	<	int n_cells;
1271	<	double cellx, celly, cellz;
1272	<	double temp1, temp2, temp3;
1273	<	int n_per_extra;
1274	<	int n_extra;
1275	<	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	<	}
1269	>	if( info->n_SRI ){
1270	>
1271	>	Exclude::createArray(info->n_SRI);
1272	>	the_excludes = new Exclude*[info->n_SRI];
1273	>	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1274	>	info->globalExcludes = new int;
1275	>	info->n_exclude = info->n_SRI;
1276		}
1277		else{
1278	<	n_cells = (int)temp3;
1279	<	cellx = simnfo->box_x / temp3;
1280	<	celly = simnfo->box_y / temp3;
1281	<	cellz = simnfo->box_z / temp3;
1278	>
1279	>	Exclude::createArray( 1 );
1280	>	the_excludes = new Exclude*;
1281	>	the_excludes[0] = new Exclude(0);
1282	>	the_excludes[0]->setPair( 0,0 );
1283	>	info->globalExcludes = new int;
1284	>	info->globalExcludes[0] = 0;
1285	>	info->n_exclude = 0;
1286		}
1287
1288	<	current_mol = 0;
1070	<	current_comp_mol = 0;
1071	<	current_comp = 0;
1072	<	current_atom_ndx = 0;
1288	>	// set the arrays into the SimInfo object
1289
1290	<	for( i=0; i < n_cells ; i++ ){
1291	<	for( j=0; j < n_cells; j++ ){
1292	<	for( k=0; k < n_cells; k++ ){
1290	>	info->atoms = the_atoms;
1291	>	info->molecules = the_molecules;
1292	>	info->nGlobalExcludes = 0;
1293	>	info->excludes = the_excludes;
1294
1295	<	makeElement( i * cellx,
1079	<	j * celly,
1080	<	k * cellz );
1295	>	the_ff->setSimInfo( info );
1296
1297	<	makeElement( i * cellx + 0.5 * cellx,
1083	<	j * celly + 0.5 * celly,
1084	<	k * cellz );
1297	>	}
1298
1299	<	makeElement( i * cellx,
1087	<	j * celly + 0.5 * celly,
1088	<	k * cellz + 0.5 * cellz );
1299	>	void SimSetup::makeIntegrator( void ){
1300
1301	<	makeElement( i * cellx + 0.5 * cellx,
1302	<	j * celly,
1303	<	k * cellz + 0.5 * cellz );
1304	<	}
1305	<	}
1095	<	}
1301	>	NVT<RealIntegrator>*  myNVT = NULL;
1302	>	NPTi<RealIntegrator>* myNPTi = NULL;
1303	>	NPTf<RealIntegrator>* myNPTf = NULL;
1304	>	NPTim<RealIntegrator>* myNPTim = NULL;
1305	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1306
1307	<	if( have_extra ){
1098	<	done = 0;
1307	>	switch( ensembleCase ){
1308
1309	<	int start_ndx;
1310	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1311	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1309	>	case NVE_ENS:
1310	>	new NVE<RealIntegrator>( info, the_ff );
1311	>	break;
1312
1313	<	if( i < n_cells ){
1313	>	case NVT_ENS:
1314	>	myNVT = new NVT<RealIntegrator>( info, the_ff );
1315	>	myNVT->setTargetTemp(globals->getTargetTemp());
1316
1317	<	if( j < n_cells ){
1318	<	start_ndx = n_cells;
1108	<	}
1109	<	else start_ndx = 0;
1110	<	}
1111	<	else start_ndx = 0;
1317	>	if (globals->haveTauThermostat())
1318	>	myNVT->setTauThermostat(globals->getTauThermostat());
1319
1320	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1320	>	else {
1321	>	sprintf( painCave.errMsg,
1322	>	"SimSetup error: If you use the NVT\n"
1323	>	"    ensemble, you must set tauThermostat.\n");
1324	>	painCave.isFatal = 1;
1325	>	simError();
1326	>	}
1327	>	break;
1328
1329	<	makeElement( i * cellx,
1330	<	j * celly,
1331	<	k * cellz );
1118	<	done = ( current_mol >= tot_nmol );
1329	>	case NPTi_ENS:
1330	>	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1331	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1332
1333	<	if( !done && n_per_extra > 1 ){
1334	<	makeElement( i * cellx + 0.5 * cellx,
1335	<	j * celly + 0.5 * celly,
1336	<	k * cellz );
1337	<	done = ( current_mol >= tot_nmol );
1338	<	}
1333	>	if (globals->haveTargetPressure())
1334	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1335	>	else {
1336	>	sprintf( painCave.errMsg,
1337	>	"SimSetup error: If you use a constant pressure\n"
1338	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1339	>	painCave.isFatal = 1;
1340	>	simError();
1341	>	}
1342	>
1343	>	if( globals->haveTauThermostat() )
1344	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1345	>	else{
1346	>	sprintf( painCave.errMsg,
1347	>	"SimSetup error: If you use an NPT\n"
1348	>	"    ensemble, you must set tauThermostat.\n");
1349	>	painCave.isFatal = 1;
1350	>	simError();
1351	>	}
1352
1353	<	if( !done && n_per_extra > 2){
1354	<	makeElement( i * cellx,
1355	<	j * celly + 0.5 * celly,
1356	<	k * cellz + 0.5 * cellz );
1357	<	done = ( current_mol >= tot_nmol );
1358	<	}
1359	<
1360	<	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	<	}
1353	>	if( globals->haveTauBarostat() )
1354	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1355	>	else{
1356	>	sprintf( painCave.errMsg,
1357	>	"SimSetup error: If you use an NPT\n"
1358	>	"    ensemble, you must set tauBarostat.\n");
1359	>	painCave.isFatal = 1;
1360	>	simError();
1361		}
1362	<	}
1362	>	break;
1363
1364	+	case NPTf_ENS:
1365	+	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1366	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1367
1368	<	for( i=0; i<simnfo->n_atoms; i++ ){
1369	<	simnfo->atoms[i]->set_vx( 0.0 );
1370	<	simnfo->atoms[i]->set_vy( 0.0 );
1371	<	simnfo->atoms[i]->set_vz( 0.0 );
1372	<	}
1373	<	}
1368	>	if (globals->haveTargetPressure())
1369	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1370	>	else {
1371	>	sprintf( painCave.errMsg,
1372	>	"SimSetup error: If you use a constant pressure\n"
1373	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1374	>	painCave.isFatal = 1;
1375	>	simError();
1376	>	}
1377
1378	<	void SimSetup::makeElement( double x, double y, double z ){
1378	>	if( globals->haveTauThermostat() )
1379	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1380	>	else{
1381	>	sprintf( painCave.errMsg,
1382	>	"SimSetup error: If you use an NPT\n"
1383	>	"    ensemble, you must set tauThermostat.\n");
1384	>	painCave.isFatal = 1;
1385	>	simError();
1386	>	}
1387
1388	<	int k;
1389	<	AtomStamp* current_atom;
1390	<	DirectionalAtom* dAtom;
1391	<	double rotMat[3][3];
1388	>	if( globals->haveTauBarostat() )
1389	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1390	>	else{
1391	>	sprintf( painCave.errMsg,
1392	>	"SimSetup error: If you use an NPT\n"
1393	>	"    ensemble, you must set tauBarostat.\n");
1394	>	painCave.isFatal = 1;
1395	>	simError();
1396	>	}
1397	>	break;
1398	>
1399	>	case NPTim_ENS:
1400	>	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1401	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1402
1403	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1403	>	if (globals->haveTargetPressure())
1404	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1405	>	else {
1406	>	sprintf( painCave.errMsg,
1407	>	"SimSetup error: If you use a constant pressure\n"
1408	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1409	>	painCave.isFatal = 1;
1410	>	simError();
1411	>	}
1412	>
1413	>	if( globals->haveTauThermostat() )
1414	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1415	>	else{
1416	>	sprintf( painCave.errMsg,
1417	>	"SimSetup error: If you use an NPT\n"
1418	>	"    ensemble, you must set tauThermostat.\n");
1419	>	painCave.isFatal = 1;
1420	>	simError();
1421	>	}
1422
1423	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1424	<	if( !current_atom->havePosition() ){
1423	>	if( globals->haveTauBarostat() )
1424	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1425	>	else{
1426		sprintf( painCave.errMsg,
1427	<	"SimSetup:initFromBass error.\n"
1428	<	"\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() );
1427	>	"SimSetup error: If you use an NPT\n"
1428	>	"    ensemble, you must set tauBarostat.\n");
1429		painCave.isFatal = 1;
1430		simError();
1431		}
1432	+	break;
1433
1434	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1435	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1436	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1434	>	case NPTfm_ENS:
1435	>	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1436	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1437
1438	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1438	>	if (globals->haveTargetPressure())
1439	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1440	>	else {
1441	>	sprintf( painCave.errMsg,
1442	>	"SimSetup error: If you use a constant pressure\n"
1443	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1444	>	painCave.isFatal = 1;
1445	>	simError();
1446	>	}
1447	>
1448	>	if( globals->haveTauThermostat() )
1449	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1450	>	else{
1451	>	sprintf( painCave.errMsg,
1452	>	"SimSetup error: If you use an NPT\n"
1453	>	"    ensemble, you must set tauThermostat.\n");
1454	>	painCave.isFatal = 1;
1455	>	simError();
1456	>	}
1457
1458	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1458	>	if( globals->haveTauBarostat() )
1459	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1460	>	else{
1461	>	sprintf( painCave.errMsg,
1462	>	"SimSetup error: If you use an NPT\n"
1463	>	"    ensemble, you must set tauBarostat.\n");
1464	>	painCave.isFatal = 1;
1465	>	simError();
1466	>	}
1467	>	break;
1468
1469	<	rotMat[0][0] = 1.0;
1470	<	rotMat[0][1] = 0.0;
1471	<	rotMat[0][2] = 0.0;
1469	>	default:
1470	>	sprintf( painCave.errMsg,
1471	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1472	>	painCave.isFatal = 1;
1473	>	simError();
1474	>	}
1475
1476	<	rotMat[1][0] = 0.0;
1188	<	rotMat[1][1] = 1.0;
1189	<	rotMat[1][2] = 0.0;
1476	>	}
1477
1478	<	rotMat[2][0] = 0.0;
1192	<	rotMat[2][1] = 0.0;
1193	<	rotMat[2][2] = 1.0;
1478	>	void SimSetup::initFortran( void ){
1479
1480	<	dAtom->setA( rotMat );
1481	<	}
1482	<
1483	<	current_atom_ndx++;
1480	>	info->refreshSim();
1481	>
1482	>	if( !strcmp( info->mixingRule, "standard") ){
1483	>	the_ff->initForceField( LB_MIXING_RULE );
1484		}
1485	+	else if( !strcmp( info->mixingRule, "explicit") ){
1486	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1487	+	}
1488	+	else{
1489	+	sprintf( painCave.errMsg,
1490	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1491	+	info->mixingRule );
1492	+	painCave.isFatal = 1;
1493	+	simError();
1494	+	}
1495
1201	–	current_mol++;
1202	–	current_comp_mol++;
1496
1497	<	if( current_comp_mol >= components_nmol[current_comp] ){
1497	>	#ifdef IS_MPI
1498	>	strcpy( checkPointMsg,
1499	>	"Successfully intialized the mixingRule for Fortran." );
1500	>	MPIcheckPoint();
1501	>	#endif // is_mpi
1502
1206	–	current_comp_mol = 0;
1207	–	current_comp++;
1208	–	}
1503		}

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