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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 621 by gezelter, Wed Jul 16 02:11:02 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 64 | Line 78 | void SimSetup::createSim( void ){
78
79		void SimSetup::createSim( void ){
80
81	<	MakeStamps *the_stamps;
82	<	Globals* the_globals;
83	<	int i, j;
81	>	int i, j, k, globalAtomIndex;
82	>
83	>	// gather all of the information from the Bass file
84	>
85	>	gatherInfo();
86
87	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
87	>	// creation of complex system objects
88
89	<	// 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();
89	>	sysObjectsCreation();
90
91	<	// get the ones we know are there, yet still may need some work.
92	<	n_components = the_globals->getNComponents();
93	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
91	>	// check on the post processing info
92	>
93	>	finalInfoCheck();
94
95	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
95	>	// initialize the system coordinates
96
97	+	initSystemCoords();
98	+
99
100	<	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	<	}
100	>	// make the output filenames
101
102	+	makeOutNames();
103	+
104	+	// make the integrator
105	+
106	+	makeIntegrator();
107	+
108		#ifdef IS_MPI
109	<	strcpy( checkPointMsg, "ForceField creation successful" );
110	<	MPIcheckPoint();
106	<	#endif // is_mpi
109	>	mpiSim->mpiRefresh();
110	>	#endif
111
112	<
112	>	// initialize the Fortran
113
114	<	// 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];
114	>	initFortran();
115
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
116
119	–	tot_nmol = 0;
120	–	for( i=0; i<n_components; i++ ){
117
118	<	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	<	}
118	>	}
119
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	–	}
120
121	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
121	>	void SimSetup::makeMolecules( void ){
122
123	<	// make an array of molecule stamps that match the components used.
124	<	// also extract the used stamps out into a separate linked list
123	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
124	>	molInit molInfo;
125	>	DirectionalAtom* dAtom;
126	>	LinkedAssign* extras;
127	>	LinkedAssign* current_extra;
128	>	AtomStamp* currentAtom;
129	>	BondStamp* currentBond;
130	>	BendStamp* currentBend;
131	>	TorsionStamp* currentTorsion;
132
133	<	simnfo->nComponents = n_components;
134	<	simnfo->componentsNmol = components_nmol;
135	<	simnfo->compStamps = comp_stamps;
136	<	simnfo->headStamp = new LinkedMolStamp();
133	>	bond_pair* theBonds;
134	>	bend_set* theBends;
135	>	torsion_set* theTorsions;
136	>
137
138	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
138	>	//init the forceField paramters
139
140	<	id = the_components[i]->getType();
179	<	comp_stamps[i] = NULL;
180	<
181	<	// check to make sure the component isn't already in the list
140	>	the_ff->readParams();
141
142	<	comp_stamps[i] = headStamp->match( id );
143	<	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	<	}
142	>
143	>	// init the atoms
144
145	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
145	>	double ux, uy, uz, u, uSqr;
146
147	+	atomOffset = 0;
148	+	excludeOffset = 0;
149	+	for(i=0; i<info->n_mol; i++){
150	+
151	+	stampID = the_molecules[i].getStampID();
152
153	+	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
154	+	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
155	+	molInfo.nBends    = comp_stamps[stampID]->getNBends();
156	+	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
157	+	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
158
159	+	molInfo.myAtoms = &the_atoms[atomOffset];
160	+	molInfo.myExcludes = &the_excludes[excludeOffset];
161	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
162	+	molInfo.myBends = new Bend*[molInfo.nBends];
163	+	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
164
165	<	// caclulate the number of atoms, bonds, bends and torsions
166	<
167	<	tot_atoms = 0;
214	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
165	>	theBonds = new bond_pair[molInfo.nBonds];
166	>	theBends = new bend_set[molInfo.nBends];
167	>	theTorsions = new torsion_set[molInfo.nTorsions];
168
169	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
170	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
171	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
172	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
173	<	}
169	>	// make the Atoms
170	>
171	>	for(j=0; j<molInfo.nAtoms; j++){
172	>
173	>	currentAtom = comp_stamps[stampID]->getAtom( j );
174	>	if( currentAtom->haveOrientation() ){
175	>
176	>	dAtom = new DirectionalAtom(j + atomOffset);
177	>	info->n_oriented++;
178	>	molInfo.myAtoms[j] = dAtom;
179	>
180	>	ux = currentAtom->getOrntX();
181	>	uy = currentAtom->getOrntY();
182	>	uz = currentAtom->getOrntZ();
183	>
184	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
185	>
186	>	u = sqrt( uSqr );
187	>	ux = ux / u;
188	>	uy = uy / u;
189	>	uz = uz / u;
190	>
191	>	dAtom->setSUx( ux );
192	>	dAtom->setSUy( uy );
193	>	dAtom->setSUz( uz );
194	>	}
195	>	else{
196	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
197	>	}
198	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
199	>
200	>	#ifdef IS_MPI
201	>
202	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
203	>
204	>	#endif // is_mpi
205	>	}
206	>
207	>	// make the bonds
208	>	for(j=0; j<molInfo.nBonds; j++){
209	>
210	>	currentBond = comp_stamps[stampID]->getBond( j );
211	>	theBonds[j].a = currentBond->getA() + atomOffset;
212	>	theBonds[j].b = currentBond->getB() + atomOffset;
213
214	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
214	>	exI = theBonds[j].a;
215	>	exJ = theBonds[j].b;
216
217	<	simnfo->n_atoms = tot_atoms;
218	<	simnfo->n_bonds = tot_bonds;
219	<	simnfo->n_bends = tot_bends;
220	<	simnfo->n_torsions = tot_torsions;
221	<	simnfo->n_SRI = tot_SRI;
222	<	simnfo->n_mol = tot_nmol;
233	<
234	<
217	>	// exclude_I must always be the smaller of the pair
218	>	if( exI > exJ ){
219	>	tempEx = exI;
220	>	exI = exJ;
221	>	exJ = tempEx;
222	>	}
223		#ifdef IS_MPI
224	+	tempEx = exI;
225	+	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
226	+	tempEx = exJ;
227	+	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
228	+
229	+	the_excludes[j+excludeOffset]->setPair( exI, exJ );
230	+	#else  // isn't MPI
231
232	<	// divide the molecules among processors here.
233	<
234	<	mpiSim = new mpiSimulation( simnfo );
235	<
241	<
232	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
233	>	#endif  //is_mpi
234	>	}
235	>	excludeOffset += molInfo.nBonds;
236
237	<	globalIndex = mpiSim->divideLabor();
237	>	//make the bends
238	>	for(j=0; j<molInfo.nBends; j++){
239	>
240	>	currentBend = comp_stamps[stampID]->getBend( j );
241	>	theBends[j].a = currentBend->getA() + atomOffset;
242	>	theBends[j].b = currentBend->getB() + atomOffset;
243	>	theBends[j].c = currentBend->getC() + atomOffset;
244	>
245	>	if( currentBend->haveExtras() ){
246	>
247	>	extras = currentBend->getExtras();
248	>	current_extra = extras;
249	>
250	>	while( current_extra != NULL ){
251	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
252	>
253	>	switch( current_extra->getType() ){
254	>
255	>	case 0:
256	>	theBends[j].ghost =
257	>	current_extra->getInt() + atomOffset;
258	>	theBends[j].isGhost = 1;
259	>	break;
260	>
261	>	case 1:
262	>	theBends[j].ghost =
263	>	(int)current_extra->getDouble() + atomOffset;
264	>	theBends[j].isGhost = 1;
265	>	break;
266	>
267	>	default:
268	>	sprintf( painCave.errMsg,
269	>	"SimSetup Error: ghostVectorSource was neither a "
270	>	"double nor an int.\n"
271	>	"-->Bend[%d] in %s\n",
272	>	j, comp_stamps[stampID]->getID() );
273	>	painCave.isFatal = 1;
274	>	simError();
275	>	}
276	>	}
277	>
278	>	else{
279	>
280	>	sprintf( painCave.errMsg,
281	>	"SimSetup Error: unhandled bend assignment:\n"
282	>	"    -->%s in Bend[%d] in %s\n",
283	>	current_extra->getlhs(),
284	>	j, comp_stamps[stampID]->getID() );
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>
289	>	current_extra = current_extra->getNext();
290	>	}
291	>	}
292	>
293	>	if( !theBends[j].isGhost ){
294	>
295	>	exI = theBends[j].a;
296	>	exJ = theBends[j].c;
297	>	}
298	>	else{
299	>
300	>	exI = theBends[j].a;
301	>	exJ = theBends[j].b;
302	>	}
303	>
304	>	// exclude_I must always be the smaller of the pair
305	>	if( exI > exJ ){
306	>	tempEx = exI;
307	>	exI = exJ;
308	>	exJ = tempEx;
309	>	}
310	>	#ifdef IS_MPI
311	>	tempEx = exI;
312	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
313	>	tempEx = exJ;
314	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
315	>
316	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
317	>	#else  // isn't MPI
318	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
319	>	#endif  //is_mpi
320	>	}
321	>	excludeOffset += molInfo.nBends;
322
323	+	for(j=0; j<molInfo.nTorsions; j++){
324	+
325	+	currentTorsion = comp_stamps[stampID]->getTorsion( j );
326	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
327	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
328	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
329	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
330	+
331	+	exI = theTorsions[j].a;
332	+	exJ = theTorsions[j].d;
333
334	<
335	<	// set up the local variables
336	<
337	<	int localMol, allMol;
338	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
339	<
340	<	allMol = 0;
341	<	localMol = 0;
342	<	local_atoms = 0;
343	<	local_bonds = 0;
344	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
259	<
260	<	for( j=0; j<components_nmol[i]; j++ ){
334	>	// exclude_I must always be the smaller of the pair
335	>	if( exI > exJ ){
336	>	tempEx = exI;
337	>	exI = exJ;
338	>	exJ = tempEx;
339	>	}
340	>	#ifdef IS_MPI
341	>	tempEx = exI;
342	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
343	>	tempEx = exJ;
344	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
345
346	<	if( mpiSim->getMyMolStart() <= allMol &&
347	<	allMol <= mpiSim->getMyMolEnd() ){
348	<
349	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
346	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
347	>	#else  // isn't MPI
348	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349	>	#endif  //is_mpi
350		}
351	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
351	>	excludeOffset += molInfo.nTorsions;
352
353	<	simnfo->n_atoms = mpiSim->getMyNlocal();
354	<
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();
287	<	}
353	>
354	>	// send the arrays off to the forceField for init.
355
356	<	simnfo->n_bonds = local_bonds;
357	<	simnfo->n_bends = local_bends;
358	<	simnfo->n_torsions = local_torsions;
359	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
356	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
357	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
358	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
359	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
360
361	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
361	>
362	>	the_molecules[i].initialize( molInfo );
363	>
364	>
365	>	atomOffset += molInfo.nAtoms;
366	>	delete[] theBonds;
367	>	delete[] theBends;
368	>	delete[] theTorsions;
369	>	}
370	>
371	>	#ifdef IS_MPI
372	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
373		MPIcheckPoint();
297	–
298	–
374		#endif // is_mpi
300	–
375
376	<	// create the atom and short range interaction arrays
376	>	// clean up the forcefield
377	>	the_ff->calcRcut();
378	>	the_ff->cleanMe();
379
380	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
380	>	}
381
382	+	void SimSetup::initFromBass( void ){
383
384	<	if( simnfo->n_SRI ){
385	<	the_sris = new SRI*[simnfo->n_SRI];
386	<	the_excludes = new int[2 * simnfo->n_SRI];
387	<	simnfo->globalExcludes = new int;
388	<	simnfo->n_exclude = tot_SRI;
384	>	int i, j, k;
385	>	int n_cells;
386	>	double cellx, celly, cellz;
387	>	double temp1, temp2, temp3;
388	>	int n_per_extra;
389	>	int n_extra;
390	>	int have_extra, done;
391	>
392	>	temp1 = (double)tot_nmol / 4.0;
393	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
394	>	temp3 = ceil( temp2 );
395	>
396	>	have_extra =0;
397	>	if( temp2 < temp3 ){ // we have a non-complete lattice
398	>	have_extra =1;
399	>
400	>	n_cells = (int)temp3 - 1;
401	>	cellx = info->boxL[0] / temp3;
402	>	celly = info->boxL[1] / temp3;
403	>	cellz = info->boxL[2] / temp3;
404	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
405	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
406	>	n_per_extra = (int)ceil( temp1 );
407	>
408	>	if( n_per_extra > 4){
409	>	sprintf( painCave.errMsg,
410	>	"SimSetup error. There has been an error in constructing"
411	>	" the non-complete lattice.\n" );
412	>	painCave.isFatal = 1;
413	>	simError();
414	>	}
415		}
416		else{
417	<
418	<	the_excludes = new int[2];
419	<	the_excludes[0] = 0;
420	<	the_excludes[1] = 0;
421	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
417	>	n_cells = (int)temp3;
418	>	cellx = info->boxL[0] / temp3;
419	>	celly = info->boxL[1] / temp3;
420	>	cellz = info->boxL[2] / temp3;
421	>	}
422
423	<	simnfo->n_exclude = 1;
423	>	current_mol = 0;
424	>	current_comp_mol = 0;
425	>	current_comp = 0;
426	>	current_atom_ndx = 0;
427	>
428	>	for( i=0; i < n_cells ; i++ ){
429	>	for( j=0; j < n_cells; j++ ){
430	>	for( k=0; k < n_cells; k++ ){
431	>
432	>	makeElement( i * cellx,
433	>	j * celly,
434	>	k * cellz );
435	>
436	>	makeElement( i * cellx + 0.5 * cellx,
437	>	j * celly + 0.5 * celly,
438	>	k * cellz );
439	>
440	>	makeElement( i * cellx,
441	>	j * celly + 0.5 * celly,
442	>	k * cellz + 0.5 * cellz );
443	>
444	>	makeElement( i * cellx + 0.5 * cellx,
445	>	j * celly,
446	>	k * cellz + 0.5 * cellz );
447	>	}
448	>	}
449		}
450
451	<	// set the arrays into the SimInfo object
451	>	if( have_extra ){
452	>	done = 0;
453
454	<	simnfo->atoms = the_atoms;
455	<	simnfo->sr_interactions = the_sris;
456	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
454	>	int start_ndx;
455	>	for( i=0; i < (n_cells+1) && !done; i++ ){
456	>	for( j=0; j < (n_cells+1) && !done; j++ ){
457
458	+	if( i < n_cells ){
459
460	<	// get some of the tricky things that may still be in the globals
460	>	if( j < n_cells ){
461	>	start_ndx = n_cells;
462	>	}
463	>	else start_ndx = 0;
464	>	}
465	>	else start_ndx = 0;
466
467	+	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
468	+
469	+	makeElement( i * cellx,
470	+	j * celly,
471	+	k * cellz );
472	+	done = ( current_mol >= tot_nmol );
473	+
474	+	if( !done && n_per_extra > 1 ){
475	+	makeElement( i * cellx + 0.5 * cellx,
476	+	j * celly + 0.5 * celly,
477	+	k * cellz );
478	+	done = ( current_mol >= tot_nmol );
479	+	}
480	+
481	+	if( !done && n_per_extra > 2){
482	+	makeElement( i * cellx,
483	+	j * celly + 0.5 * celly,
484	+	k * cellz + 0.5 * cellz );
485	+	done = ( current_mol >= tot_nmol );
486	+	}
487	+
488	+	if( !done && n_per_extra > 3){
489	+	makeElement( i * cellx + 0.5 * cellx,
490	+	j * celly,
491	+	k * cellz + 0.5 * cellz );
492	+	done = ( current_mol >= tot_nmol );
493	+	}
494	+	}
495	+	}
496	+	}
497	+	}
498	+
499	+
500	+	for( i=0; i<info->n_atoms; i++ ){
501	+	info->atoms[i]->set_vx( 0.0 );
502	+	info->atoms[i]->set_vy( 0.0 );
503	+	info->atoms[i]->set_vz( 0.0 );
504	+	}
505	+	}
506	+
507	+	void SimSetup::makeElement( double x, double y, double z ){
508	+
509	+	int k;
510	+	AtomStamp* current_atom;
511	+	DirectionalAtom* dAtom;
512	+	double rotMat[3][3];
513	+
514	+	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
515	+
516	+	current_atom = comp_stamps[current_comp]->getAtom( k );
517	+	if( !current_atom->havePosition() ){
518	+	sprintf( painCave.errMsg,
519	+	"SimSetup:initFromBass error.\n"
520	+	"\tComponent %s, atom %s does not have a position specified.\n"
521	+	"\tThe initialization routine is unable to give a start"
522	+	" position.\n",
523	+	comp_stamps[current_comp]->getID(),
524	+	current_atom->getType() );
525	+	painCave.isFatal = 1;
526	+	simError();
527	+	}
528	+
529	+	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
530	+	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
531	+	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
532	+
533	+	if( the_atoms[current_atom_ndx]->isDirectional() ){
534	+
535	+	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
536	+
537	+	rotMat[0][0] = 1.0;
538	+	rotMat[0][1] = 0.0;
539	+	rotMat[0][2] = 0.0;
540	+
541	+	rotMat[1][0] = 0.0;
542	+	rotMat[1][1] = 1.0;
543	+	rotMat[1][2] = 0.0;
544	+
545	+	rotMat[2][0] = 0.0;
546	+	rotMat[2][1] = 0.0;
547	+	rotMat[2][2] = 1.0;
548	+
549	+	dAtom->setA( rotMat );
550	+	}
551	+
552	+	current_atom_ndx++;
553	+	}
554	+
555	+	current_mol++;
556	+	current_comp_mol++;
557	+
558	+	if( current_comp_mol >= components_nmol[current_comp] ){
559	+
560	+	current_comp_mol = 0;
561	+	current_comp++;
562	+	}
563	+	}
564	+
565	+
566	+	void SimSetup::gatherInfo( void ){
567	+	int i,j,k;
568	+
569	+	ensembleCase = -1;
570	+	ffCase = -1;
571	+
572	+	// get the stamps and globals;
573	+	stamps = stamps;
574	+	globals = globals;
575	+
576	+	// set the easy ones first
577	+	info->target_temp = globals->getTargetTemp();
578	+	info->dt = globals->getDt();
579	+	info->run_time = globals->getRunTime();
580	+	n_components = globals->getNComponents();
581	+
582	+
583	+	// get the forceField
584	+
585	+	strcpy( force_field, globals->getForceField() );
586	+
587	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
588	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
589	+	else{
590	+	sprintf( painCave.errMsg,
591	+	"SimSetup Error. Unrecognized force field -> %s\n",
592	+	force_field );
593	+	painCave.isFatal = 1;
594	+	simError();
595	+	}
596	+
597	+	// get the ensemble
598	+
599	+	strcpy( ensemble, globals->getEnsemble() );
600	+
601	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
602	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
603	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
604	+	ensembleCase = NPTi_ENS;
605	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
606	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
607	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
608	+	else{
609	+	sprintf( painCave.errMsg,
610	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
611	+	"reverting to NVE for this simulation.\n",
612	+	ensemble );
613	+	painCave.isFatal = 0;
614	+	simError();
615	+	strcpy( ensemble, "NVE" );
616	+	ensembleCase = NVE_ENS;
617	+	}
618	+	strcpy( info->ensemble, ensemble );
619	+
620	+	// get the mixing rule
621	+
622	+	strcpy( info->mixingRule, globals->getMixingRule() );
623	+	info->usePBC = globals->getPBC();
624	+
625
626	<	if( the_globals->haveBox() ){
627	<	simnfo->box_x = the_globals->getBox();
628	<	simnfo->box_y = the_globals->getBox();
629	<	simnfo->box_z = the_globals->getBox();
626	>	// get the components and calculate the tot_nMol and indvidual n_mol
627	>
628	>	the_components = globals->getComponents();
629	>	components_nmol = new int[n_components];
630	>
631	>
632	>	if( !globals->haveNMol() ){
633	>	// we don't have the total number of molecules, so we assume it is
634	>	// given in each component
635	>
636	>	tot_nmol = 0;
637	>	for( i=0; i<n_components; i++ ){
638	>
639	>	if( !the_components[i]->haveNMol() ){
640	>	// we have a problem
641	>	sprintf( painCave.errMsg,
642	>	"SimSetup Error. No global NMol or component NMol"
643	>	" given. Cannot calculate the number of atoms.\n" );
644	>	painCave.isFatal = 1;
645	>	simError();
646	>	}
647	>
648	>	tot_nmol += the_components[i]->getNMol();
649	>	components_nmol[i] = the_components[i]->getNMol();
650	>	}
651		}
652	<	else if( the_globals->haveDensity() ){
652	>	else{
653	>	sprintf( painCave.errMsg,
654	>	"SimSetup error.\n"
655	>	"\tSorry, the ability to specify total"
656	>	" nMols and then give molfractions in the components\n"
657	>	"\tis not currently supported."
658	>	" Please give nMol in the components.\n" );
659	>	painCave.isFatal = 1;
660	>	simError();
661	>	}
662
663	+	// set the status, sample, and thermal kick times
664	+
665	+	if( globals->haveSampleTime() ){
666	+	info->sampleTime = globals->getSampleTime();
667	+	info->statusTime = info->sampleTime;
668	+	info->thermalTime = info->sampleTime;
669	+	}
670	+	else{
671	+	info->sampleTime = globals->getRunTime();
672	+	info->statusTime = info->sampleTime;
673	+	info->thermalTime = info->sampleTime;
674	+	}
675	+
676	+	if( globals->haveStatusTime() ){
677	+	info->statusTime = globals->getStatusTime();
678	+	}
679	+
680	+	if( globals->haveThermalTime() ){
681	+	info->thermalTime = globals->getThermalTime();
682	+	}
683	+
684	+	// check for the temperature set flag
685	+
686	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
687	+
688	+	// get some of the tricky things that may still be in the globals
689	+
690	+	double boxVector[3];
691	+	if( globals->haveBox() ){
692	+	boxVector[0] = globals->getBox();
693	+	boxVector[1] = globals->getBox();
694	+	boxVector[2] = globals->getBox();
695	+
696	+	info->setBox( boxVector );
697	+	}
698	+	else if( globals->haveDensity() ){
699	+
700		double vol;
701	<	vol = (double)tot_nmol / the_globals->getDensity();
702	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
703	<	simnfo->box_y = simnfo->box_x;
704	<	simnfo->box_z = simnfo->box_x;
701	>	vol = (double)tot_nmol / globals->getDensity();
702	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
703	>	boxVector[1] = boxVector[0];
704	>	boxVector[2] = boxVector[0];
705	>
706	>	info->setBox( boxVector );
707		}
708		else{
709	<	if( !the_globals->haveBoxX() ){
709	>	if( !globals->haveBoxX() ){
710		sprintf( painCave.errMsg,
711		"SimSetup error, no periodic BoxX size given.\n" );
712		painCave.isFatal = 1;
713		simError();
714		}
715	<	simnfo->box_x = the_globals->getBoxX();
715	>	boxVector[0] = globals->getBoxX();
716
717	<	if( !the_globals->haveBoxY() ){
717	>	if( !globals->haveBoxY() ){
718		sprintf( painCave.errMsg,
719		"SimSetup error, no periodic BoxY size given.\n" );
720		painCave.isFatal = 1;
721		simError();
722		}
723	<	simnfo->box_y = the_globals->getBoxY();
723	>	boxVector[1] = globals->getBoxY();
724
725	<	if( !the_globals->haveBoxZ() ){
725	>	if( !globals->haveBoxZ() ){
726		sprintf( painCave.errMsg,
727		"SimSetup error, no periodic BoxZ size given.\n" );
728		painCave.isFatal = 1;
729		simError();
730		}
731	<	simnfo->box_z = the_globals->getBoxZ();
731	>	boxVector[2] = globals->getBoxZ();
732	>
733	>	info->setBox( boxVector );
734		}
735
736	+
737	+
738		#ifdef IS_MPI
739	<	strcpy( checkPointMsg, "Box size set up" );
739	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
740		MPIcheckPoint();
741		#endif // is_mpi
742
743	+	}
744
382	–	// initialize the arrays
745
746	<	the_ff->setSimInfo( simnfo );
746	>	void SimSetup::finalInfoCheck( void ){
747	>	int index;
748	>	int usesDipoles;
749	>
750
751	<	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	<	}
751	>	// check electrostatic parameters
752
753	<	if( tot_bonds ){
754	<	makeBonds();
753	>	index = 0;
754	>	usesDipoles = 0;
755	>	while( (index < info->n_atoms) && !usesDipoles ){
756	>	usesDipoles = ((info->atoms)[index])->hasDipole();
757	>	index++;
758		}
759	+
760	+	#ifdef IS_MPI
761	+	int myUse = usesDipoles;
762	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
763	+	#endif //is_mpi
764
396	–	if( tot_bends ){
397	–	makeBends();
398	–	}
765
766	<	if( tot_torsions ){
767	<	makeTorsions();
768	<	}
769	<
404	<
405	<	if (the_globals->getUseRF() ) {
406	<	simnfo->useReactionField = 1;
407	<
408	<	if( !the_globals->haveECR() ){
766	>	if (globals->getUseRF() ) {
767	>	info->useReactionField = 1;
768	>
769	>	if( !globals->haveECR() ){
770		sprintf( painCave.errMsg,
771		"SimSetup Warning: using default value of 1/2 the smallest "
772		"box length for the electrostaticCutoffRadius.\n"
#	Line 413 | Line 774 | void SimSetup::createSim( void ){
774		painCave.isFatal = 0;
775		simError();
776		double smallest;
777	<	smallest = simnfo->box_x;
778	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
779	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
780	<	simnfo->ecr = 0.5 * smallest;
777	>	smallest = info->boxL[0];
778	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
779	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
780	>	info->ecr = 0.5 * smallest;
781		} else {
782	<	simnfo->ecr        = the_globals->getECR();
782	>	info->ecr        = globals->getECR();
783		}
784
785	<	if( !the_globals->haveEST() ){
785	>	if( !globals->haveEST() ){
786		sprintf( painCave.errMsg,
787		"SimSetup Warning: using default value of 0.05 * the "
788		"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
789		);
790		painCave.isFatal = 0;
791		simError();
792	<	simnfo->est = 0.05 * simnfo->ecr;
792	>	info->est = 0.05 * info->ecr;
793		} else {
794	<	simnfo->est        = the_globals->getEST();
794	>	info->est        = globals->getEST();
795		}
796
797	<	if(!the_globals->haveDielectric() ){
797	>	if(!globals->haveDielectric() ){
798		sprintf( painCave.errMsg,
799		"SimSetup Error: You are trying to use Reaction Field without"
800		"setting a dielectric constant!\n"
#	Line 441 | Line 802 | void SimSetup::createSim( void ){
802		painCave.isFatal = 1;
803		simError();
804		}
805	<	simnfo->dielectric = the_globals->getDielectric();
806	<	} else {
807	<	if (simnfo->n_dipoles) {
805	>	info->dielectric = globals->getDielectric();
806	>	}
807	>	else {
808	>	if (usesDipoles) {
809
810	<	if( !the_globals->haveECR() ){
810	>	if( !globals->haveECR() ){
811		sprintf( painCave.errMsg,
812	<	"SimSetup Warning: using default value of 1/2 the smallest"
812	>	"SimSetup Warning: using default value of 1/2 the smallest "
813		"box length for the electrostaticCutoffRadius.\n"
814		"I hope you have a very fast processor!\n");
815		painCave.isFatal = 0;
816		simError();
817		double smallest;
818	<	smallest = simnfo->box_x;
819	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
820	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
821	<	simnfo->ecr = 0.5 * smallest;
818	>	smallest = info->boxL[0];
819	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
820	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
821	>	info->ecr = 0.5 * smallest;
822		} else {
823	<	simnfo->ecr        = the_globals->getECR();
823	>	info->ecr        = globals->getECR();
824		}
825
826	<	if( !the_globals->haveEST() ){
826	>	if( !globals->haveEST() ){
827		sprintf( painCave.errMsg,
828	<	"SimSetup Warning: using default value of 5% of the"
828	>	"SimSetup Warning: using default value of 5%% of the "
829		"electrostaticCutoffRadius for the "
830		"electrostaticSkinThickness\n"
831		);
832		painCave.isFatal = 0;
833		simError();
834	<	simnfo->est = 0.05 * simnfo->ecr;
834	>	info->est = 0.05 * info->ecr;
835		} else {
836	<	simnfo->est        = the_globals->getEST();
836	>	info->est        = globals->getEST();
837		}
838		}
839		}
840
841		#ifdef IS_MPI
842	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
842	>	strcpy( checkPointMsg, "post processing checks out" );
843		MPIcheckPoint();
844		#endif // is_mpi
845
846	<	if( the_globals->haveInitialConfig() ){
846	>	}
847	>
848	>	void SimSetup::initSystemCoords( void ){
849	>
850	>	if( globals->haveInitialConfig() ){
851
852		InitializeFromFile* fileInit;
853		#ifdef IS_MPI // is_mpi
854		if( worldRank == 0 ){
855		#endif //is_mpi
856	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
856	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
857		#ifdef IS_MPI
858		}else fileInit = new InitializeFromFile( NULL );
859		#endif
860	<	fileInit->read_xyz( simnfo ); // default velocities on
860	>	fileInit->read_xyz( info ); // default velocities on
861
862		delete fileInit;
863		}
#	Line 519 | Line 885 | void SimSetup::createSim( void ){
885		MPIcheckPoint();
886		#endif // is_mpi
887
888	+	}
889
523	–
524	–
525	–
890
891	<
891	>	void SimSetup::makeOutNames( void ){
892	>
893		#ifdef IS_MPI
894		if( worldRank == 0 ){
895		#endif // is_mpi
896
897	<	if( the_globals->haveFinalConfig() ){
898	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
897	>	if( globals->haveFinalConfig() ){
898	>	strcpy( info->finalName, globals->getFinalConfig() );
899		}
900		else{
901	<	strcpy( simnfo->finalName, inFileName );
901	>	strcpy( info->finalName, inFileName );
902		char* endTest;
903	<	int nameLength = strlen( simnfo->finalName );
904	<	endTest = &(simnfo->finalName[nameLength - 5]);
903	>	int nameLength = strlen( info->finalName );
904	>	endTest = &(info->finalName[nameLength - 5]);
905		if( !strcmp( endTest, ".bass" ) ){
906		strcpy( endTest, ".eor" );
907		}
#	Line 544 | Line 909 | void SimSetup::createSim( void ){
909		strcpy( endTest, ".eor" );
910		}
911		else{
912	<	endTest = &(simnfo->finalName[nameLength - 4]);
912	>	endTest = &(info->finalName[nameLength - 4]);
913		if( !strcmp( endTest, ".bss" ) ){
914		strcpy( endTest, ".eor" );
915		}
#	Line 552 | Line 917 | void SimSetup::createSim( void ){
917		strcpy( endTest, ".eor" );
918		}
919		else{
920	<	strcat( simnfo->finalName, ".eor" );
920	>	strcat( info->finalName, ".eor" );
921		}
922		}
923		}
924
925		// make the sample and status out names
926
927	<	strcpy( simnfo->sampleName, inFileName );
927	>	strcpy( info->sampleName, inFileName );
928		char* endTest;
929	<	int nameLength = strlen( simnfo->sampleName );
930	<	endTest = &(simnfo->sampleName[nameLength - 5]);
929	>	int nameLength = strlen( info->sampleName );
930	>	endTest = &(info->sampleName[nameLength - 5]);
931		if( !strcmp( endTest, ".bass" ) ){
932		strcpy( endTest, ".dump" );
933		}
#	Line 570 | Line 935 | void SimSetup::createSim( void ){
935		strcpy( endTest, ".dump" );
936		}
937		else{
938	<	endTest = &(simnfo->sampleName[nameLength - 4]);
938	>	endTest = &(info->sampleName[nameLength - 4]);
939		if( !strcmp( endTest, ".bss" ) ){
940		strcpy( endTest, ".dump" );
941		}
#	Line 578 | Line 943 | void SimSetup::createSim( void ){
943		strcpy( endTest, ".dump" );
944		}
945		else{
946	<	strcat( simnfo->sampleName, ".dump" );
946	>	strcat( info->sampleName, ".dump" );
947		}
948		}
949
950	<	strcpy( simnfo->statusName, inFileName );
951	<	nameLength = strlen( simnfo->statusName );
952	<	endTest = &(simnfo->statusName[nameLength - 5]);
950	>	strcpy( info->statusName, inFileName );
951	>	nameLength = strlen( info->statusName );
952	>	endTest = &(info->statusName[nameLength - 5]);
953		if( !strcmp( endTest, ".bass" ) ){
954		strcpy( endTest, ".stat" );
955		}
#	Line 592 | Line 957 | void SimSetup::createSim( void ){
957		strcpy( endTest, ".stat" );
958		}
959		else{
960	<	endTest = &(simnfo->statusName[nameLength - 4]);
960	>	endTest = &(info->statusName[nameLength - 4]);
961		if( !strcmp( endTest, ".bss" ) ){
962		strcpy( endTest, ".stat" );
963		}
#	Line 600 | Line 965 | void SimSetup::createSim( void ){
965		strcpy( endTest, ".stat" );
966		}
967		else{
968	<	strcat( simnfo->statusName, ".stat" );
968	>	strcat( info->statusName, ".stat" );
969		}
970		}
971
972		#ifdef IS_MPI
973		}
974		#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	–	}
975
976	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
976	>	}
977
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
978
979	<	// check for the temperature set flag
979	>	void SimSetup::sysObjectsCreation( void ){
980
981	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
981	>	int i;
982
983	+	// create the forceField
984
985	<	//   // make the longe range forces and the integrator
985	>	createFF();
986
987	<	//   new AllLong( simnfo );
987	>	// extract componentList
988
989	<	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 );
989	>	compList();
990
991	+	// calc the number of atoms, bond, bends, and torsions
992
993	+	calcSysValues();
994
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{
659	–	sprintf( painCave.errMsg,
660	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	–	simnfo->mixingRule );
662	–	painCave.isFatal = 1;
663	–	simError();
664	–	}
665	–
666	–
995		#ifdef IS_MPI
996	<	strcpy( checkPointMsg,
997	<	"Successfully intialized the mixingRule for Fortran." );
998	<	MPIcheckPoint();
999	<	#endif // is_mpi
672	<	}
673	<
674	<
675	<	void SimSetup::makeMolecules( void ){
676	<
677	<	int i, j, exI, exJ, tempEx, stampID, atomOffset;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	AtomStamp* currentAtom;
681	<	BondStamp* currentBond;
682	<	BendStamp* currentBend;
683	<	TorsionStamp* currentTorsion;
996	>	// divide the molecules among the processors
997	>
998	>	mpiMolDivide();
999	>	#endif //is_mpi
1000
1001	<	//init the forceField paramters
686	<
687	<	the_ff->readParams();
688	<
1001	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1002
1003	<	// init the molecules
1003	>	makeSysArrays();
1004
1005	<	atomOffset = 0;
1006	<	for(i=0; i<simnfo->n_mol; i++){
1007	<
1008	<	stampID = the_molecules[i].getStampID();
1009	<
1010	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
698	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
699	<	info.nBends    = comp_stamps[stampID]->getNBends();
700	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
701	<
702	<	info.myAtoms = &the_atoms[atomOffset];
703	<	info.myBonds = new Bond*[info.nBonds];
704	<	info.myBends = new Bend*[info.nBends];
705	<	info.myTorsions = new Torsions*[info.nTorsions];
706	<
707	<	theBonds = new bond_pair[info.nBonds];
708	<	theBends = new bend_set[info.nBends];
709	<	theTorsions = new torsion_set[info.nTorsions];
710	<
711	<	// make the Atoms
712	<
713	<	for(j=0; j<info.nAtoms; j++){
714	<
715	<	currentAtom = theComponents[stampID]->getAtom( j );
716	<	if( currentAtom->haveOrientation() ){
717	<
718	<	dAtom = new DirectionalAtom(j + atomOffset);
719	<	simnfo->n_oriented++;
720	<	info.myAtoms[j] = dAtom;
721	<
722	<	ux = currentAtom->getOrntX();
723	<	uy = currentAtom->getOrntY();
724	<	uz = currentAtom->getOrntZ();
725	<
726	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
727	<
728	<	u = sqrt( uSqr );
729	<	ux = ux / u;
730	<	uy = uy / u;
731	<	uz = uz / u;
732	<
733	<	dAtom->setSUx( ux );
734	<	dAtom->setSUy( uy );
735	<	dAtom->setSUz( uz );
736	<	}
737	<	else{
738	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
739	<	}
740	<	info.myAtoms[j]->setType( currentAtom->getType() );
741	<
742	<	#ifdef IS_MPI
743	<
744	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
745	<
746	<	#endif // is_mpi
747	<	}
748	<
749	<	// make the bonds
750	<	for(j=0; j<nBonds; j++){
751	<
752	<	currentBond = comp_stamps[stampID]->getBond( j );
753	<	theBonds[j].a = currentBond->getA() + atomOffset;
754	<	theBonds[j].b = currentBond->getB() + atomOffset;
755	<
756	<	exI = theBonds[i].a;
757	<	exJ = theBonds[i].b;
758	<
759	<	// exclude_I must always be the smaller of the pair
760	<	if( exI > exJ ){
761	<	tempEx = exI;
762	<	exI = exJ;
763	<	exJ = tempEx;
764	<	}
765	<	#ifdef IS_MPI
766	<
767	<	the_excludes[index*2] =
768	<	the_atoms[exI]->getGlobalIndex() + 1;
769	<	the_excludes[index*2 + 1] =
770	<	the_atoms[exJ]->getGlobalIndex() + 1;
771	<
772	<	#else  // isn't MPI
773	<
774	<	the_excludes[index*2] =     exI + 1;
775	<	the_excludes[index*2 + 1] = exJ + 1;
776	<	// fortran index from 1 (hence the +1 in the indexing)
777	<
778	<	#endif  //is_mpi
779	<
1005	>	// make and initialize the molecules (all but atomic coordinates)
1006	>
1007	>	makeMolecules();
1008	>	info->identArray = new int[info->n_atoms];
1009	>	for(i=0; i<info->n_atoms; i++){
1010	>	info->identArray[i] = the_atoms[i]->getIdent();
1011		}
1012	+
1013
1014
1015	+	}
1016
1017
1018	+	void SimSetup::createFF( void ){
1019
1020	+	switch( ffCase ){
1021
1022	+	case FF_DUFF:
1023	+	the_ff = new DUFF();
1024	+	break;
1025
1026	+	case FF_LJ:
1027	+	the_ff = new LJFF();
1028	+	break;
1029
1030	+	default:
1031	+	sprintf( painCave.errMsg,
1032	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1033	+	painCave.isFatal = 1;
1034	+	simError();
1035	+	}
1036
1037	+	#ifdef IS_MPI
1038	+	strcpy( checkPointMsg, "ForceField creation successful" );
1039	+	MPIcheckPoint();
1040	+	#endif // is_mpi
1041
1042	+	}
1043
1044
1045	+	void SimSetup::compList( void ){
1046
1047	+	int i;
1048
1049	+	comp_stamps = new MoleculeStamp*[n_components];
1050
1051	<	void SimSetup::makeAtoms( void ){
1051	>	// make an array of molecule stamps that match the components used.
1052	>	// also extract the used stamps out into a separate linked list
1053
1054	<	int i, j, k, index;
1055	<	double ux, uy, uz, uSqr, u;
1056	<	AtomStamp* current_atom;
1057	<
1058	<	DirectionalAtom* dAtom;
1059	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
1060	<
1061	<	lMolIndex = 0;
806	<	molIndex = 0;
807	<	index = 0;
1054	>	info->nComponents = n_components;
1055	>	info->componentsNmol = components_nmol;
1056	>	info->compStamps = comp_stamps;
1057	>	info->headStamp = new LinkedMolStamp();
1058	>
1059	>	char* id;
1060	>	LinkedMolStamp* headStamp = info->headStamp;
1061	>	LinkedMolStamp* currentStamp = NULL;
1062		for( i=0; i<n_components; i++ ){
1063
1064	<	for( j=0; j<components_nmol[i]; j++ ){
1064	>	id = the_components[i]->getType();
1065	>	comp_stamps[i] = NULL;
1066	>
1067	>	// check to make sure the component isn't already in the list
1068
1069	<	#ifdef IS_MPI
1070	<	if( mpiSim->getMyMolStart() <= molIndex &&
1071	<	molIndex <= mpiSim->getMyMolEnd() ){
1072	<	#endif // is_mpi
1073	<
1074	<	molStart = index;
1075	<	nMemb = comp_stamps[i]->getNAtoms();
1076	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
1077	<
1078	<	current_atom = comp_stamps[i]->getAtom( k );
1079	<	if( current_atom->haveOrientation() ){
1080	<
1081	<	dAtom = new DirectionalAtom(index);
825	<	simnfo->n_oriented++;
826	<	the_atoms[index] = dAtom;
827	<
828	<	ux = current_atom->getOrntX();
829	<	uy = current_atom->getOrntY();
830	<	uz = current_atom->getOrntZ();
831	<
832	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
833	<
834	<	u = sqrt( uSqr );
835	<	ux = ux / u;
836	<	uy = uy / u;
837	<	uz = uz / u;
838	<
839	<	dAtom->setSUx( ux );
840	<	dAtom->setSUy( uy );
841	<	dAtom->setSUz( uz );
842	<	}
843	<	else{
844	<	the_atoms[index] = new GeneralAtom(index);
845	<	}
846	<	the_atoms[index]->setType( current_atom->getType() );
847	<	the_atoms[index]->setIndex( index );
848	<
849	<	// increment the index and repeat;
850	<	index++;
851	<	}
852	<
853	<	molEnd = index -1;
854	<	the_molecules[lMolIndex].setNMembers( nMemb );
855	<	the_molecules[lMolIndex].setStartAtom( molStart );
856	<	the_molecules[lMolIndex].setEndAtom( molEnd );
857	<	the_molecules[lMolIndex].setStampID( i );
858	<	lMolIndex++;
859	<
860	<	#ifdef IS_MPI
1069	>	comp_stamps[i] = headStamp->match( id );
1070	>	if( comp_stamps[i] == NULL ){
1071	>
1072	>	// extract the component from the list;
1073	>
1074	>	currentStamp = stamps->extractMolStamp( id );
1075	>	if( currentStamp == NULL ){
1076	>	sprintf( painCave.errMsg,
1077	>	"SimSetup error: Component \"%s\" was not found in the "
1078	>	"list of declared molecules\n",
1079	>	id );
1080	>	painCave.isFatal = 1;
1081	>	simError();
1082		}
862	–	#endif //is_mpi
1083
1084	<	molIndex++;
1084	>	headStamp->add( currentStamp );
1085	>	comp_stamps[i] = headStamp->match( id );
1086		}
1087		}
1088
1089		#ifdef IS_MPI
1090	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
1091	<
1092	<	delete[] globalIndex;
1090	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1091	>	MPIcheckPoint();
1092	>	#endif // is_mpi
1093
1094	<	mpiSim->mpiRefresh();
874	<	#endif //IS_MPI
875	<
876	<	the_ff->initializeAtoms();
1094	>
1095		}
1096
1097	<	void SimSetup::makeBonds( void ){
1097	>	void SimSetup::calcSysValues( void ){
1098	>	int i, j, k;
1099
881	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
882	–	bond_pair* the_bonds;
883	–	BondStamp* current_bond;
1100
1101	<	the_bonds = new bond_pair[tot_bonds];
1102	<	index = 0;
1103	<	offset = 0;
1104	<	molIndex = 0;
889	<
1101	>	tot_atoms = 0;
1102	>	tot_bonds = 0;
1103	>	tot_bends = 0;
1104	>	tot_torsions = 0;
1105		for( i=0; i<n_components; i++ ){
1106	+
1107	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1108	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1109	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1110	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1111	+	}
1112
1113	<	for( j=0; j<components_nmol[i]; j++ ){
1113	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1114
1115	+	info->n_atoms = tot_atoms;
1116	+	info->n_bonds = tot_bonds;
1117	+	info->n_bends = tot_bends;
1118	+	info->n_torsions = tot_torsions;
1119	+	info->n_SRI = tot_SRI;
1120	+	info->n_mol = tot_nmol;
1121	+
1122	+	info->molMembershipArray = new int[tot_atoms];
1123	+	}
1124	+
1125	+
1126		#ifdef IS_MPI
895	–	if( mpiSim->getMyMolStart() <= molIndex &&
896	–	molIndex <= mpiSim->getMyMolEnd() ){
897	–	#endif // is_mpi
898	–
899	–	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
900	–
901	–	current_bond = comp_stamps[i]->getBond( k );
902	–	the_bonds[index].a = current_bond->getA() + offset;
903	–	the_bonds[index].b = current_bond->getB() + offset;
1127
1128	<	exI = the_bonds[index].a;
1129	<	exJ = the_bonds[index].b;
1128	>	void SimSetup::mpiMolDivide( void ){
1129	>
1130	>	int i, j, k;
1131	>	int localMol, allMol;
1132	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1133
1134	<	// exclude_I must always be the smaller of the pair
1135	<	if( exI > exJ ){
1136	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
913	<	}
1134	>	mpiSim = new mpiSimulation( info );
1135	>
1136	>	globalIndex = mpiSim->divideLabor();
1137
1138	<
1139	<	#ifdef IS_MPI
1138	>	// set up the local variables
1139	>
1140	>	mol2proc = mpiSim->getMolToProcMap();
1141	>	molCompType = mpiSim->getMolComponentType();
1142	>
1143	>	allMol = 0;
1144	>	localMol = 0;
1145	>	local_atoms = 0;
1146	>	local_bonds = 0;
1147	>	local_bends = 0;
1148	>	local_torsions = 0;
1149	>	globalAtomIndex = 0;
1150
918	–	the_excludes[index*2] =
919	–	the_atoms[exI]->getGlobalIndex() + 1;
920	–	the_excludes[index*2 + 1] =
921	–	the_atoms[exJ]->getGlobalIndex() + 1;
1151
1152	<	#else  // isn't MPI
1153	<
1154	<	the_excludes[index*2] =     exI + 1;
1155	<	the_excludes[index*2 + 1] = exJ + 1;
1156	<	// fortran index from 1 (hence the +1 in the indexing)
928	<	#endif  //is_mpi
929	<
930	<	// increment the index and repeat;
931	<	index++;
932	<	}
933	<	offset += comp_stamps[i]->getNAtoms();
1152	>	for( i=0; i<n_components; i++ ){
1153	>
1154	>	for( j=0; j<components_nmol[i]; j++ ){
1155	>
1156	>	if( mol2proc[allMol] == worldRank ){
1157
1158	<	#ifdef IS_MPI
1158	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1159	>	local_bonds +=    comp_stamps[i]->getNBonds();
1160	>	local_bends +=    comp_stamps[i]->getNBends();
1161	>	local_torsions += comp_stamps[i]->getNTorsions();
1162	>	localMol++;
1163	>	}
1164	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1165	>	info->molMembershipArray[globalAtomIndex] = allMol;
1166	>	globalAtomIndex++;
1167		}
1168	<	#endif //is_mpi
1169	<
1170	<	molIndex++;
940	<	}
1168	>
1169	>	allMol++;
1170	>	}
1171		}
1172	+	local_SRI = local_bonds + local_bends + local_torsions;
1173	+
1174	+	info->n_atoms = mpiSim->getMyNlocal();
1175	+
1176	+	if( local_atoms != info->n_atoms ){
1177	+	sprintf( painCave.errMsg,
1178	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1179	+	" localAtom (%d) are not equal.\n",
1180	+	info->n_atoms,
1181	+	local_atoms );
1182	+	painCave.isFatal = 1;
1183	+	simError();
1184	+	}
1185
1186	<	the_ff->initializeBonds( the_bonds );
1187	<	}
1186	>	info->n_bonds = local_bonds;
1187	>	info->n_bends = local_bends;
1188	>	info->n_torsions = local_torsions;
1189	>	info->n_SRI = local_SRI;
1190	>	info->n_mol = localMol;
1191
1192	<	void SimSetup::makeBends( void ){
1193	<
1194	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
949	<	bend_set* the_bends;
950	<	BendStamp* current_bend;
951	<	LinkedAssign* extras;
952	<	LinkedAssign* current_extra;
1192	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1193	>	MPIcheckPoint();
1194	>	}
1195
1196	+	#endif // is_mpi
1197
955	–	the_bends = new bend_set[tot_bends];
956	–	index = 0;
957	–	offset = 0;
958	–	molIndex = 0;
959	–	for( i=0; i<n_components; i++ ){
1198
1199	<	for( j=0; j<components_nmol[i]; j++ ){
1199	>	void SimSetup::makeSysArrays( void ){
1200	>	int i, j, k;
1201
963	–	#ifdef IS_MPI
964	–	if( mpiSim->getMyMolStart() <= molIndex &&
965	–	molIndex <= mpiSim->getMyMolEnd() ){
966	–	#endif // is_mpi
1202
1203	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
969	<
970	<	current_bend = comp_stamps[i]->getBend( k );
971	<	the_bends[index].a = current_bend->getA() + offset;
972	<	the_bends[index].b = current_bend->getB() + offset;
973	<	the_bends[index].c = current_bend->getC() + offset;
974	<
975	<	if( current_bend->haveExtras() ){
976	<
977	<	extras = current_bend->getExtras();
978	<	current_extra = extras;
979	<
980	<	while( current_extra != NULL ){
981	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
982	<
983	<	switch( current_extra->getType() ){
984	<
985	<	case 0:
986	<	the_bends[index].ghost =
987	<	current_extra->getInt() + offset;
988	<	the_bends[index].isGhost = 1;
989	<	break;
990	<
991	<	case 1:
992	<	the_bends[index].ghost =
993	<	(int)current_extra->getDouble() + offset;
994	<	the_bends[index].isGhost = 1;
995	<	break;
996	<
997	<	default:
998	<	sprintf( painCave.errMsg,
999	<	"SimSetup Error: ghostVectorSource was neiter a "
1000	<	"double nor an int.\n"
1001	<	"-->Bend[%d] in %s\n",
1002	<	k, comp_stamps[i]->getID() );
1003	<	painCave.isFatal = 1;
1004	<	simError();
1005	<	}
1006	<	}
1007	<
1008	<	else{
1009	<
1010	<	sprintf( painCave.errMsg,
1011	<	"SimSetup Error: unhandled bend assignment:\n"
1012	<	"    -->%s in Bend[%d] in %s\n",
1013	<	current_extra->getlhs(),
1014	<	k, comp_stamps[i]->getID() );
1015	<	painCave.isFatal = 1;
1016	<	simError();
1017	<	}
1018	<
1019	<	current_extra = current_extra->getNext();
1020	<	}
1021	<	}
1022	<
1023	<	if( !the_bends[index].isGhost ){
1024	<
1025	<	exI = the_bends[index].a;
1026	<	exJ = the_bends[index].c;
1027	<	}
1028	<	else{
1029	<
1030	<	exI = the_bends[index].a;
1031	<	exJ = the_bends[index].b;
1032	<	}
1033	<
1034	<	// exclude_I must always be the smaller of the pair
1035	<	if( exI > exJ ){
1036	<	tempEx = exI;
1037	<	exI = exJ;
1038	<	exJ = tempEx;
1039	<	}
1203	>	// create the atom and short range interaction arrays
1204
1205	+	Atom::createArrays(info->n_atoms);
1206	+	the_atoms = new Atom*[info->n_atoms];
1207	+	the_molecules = new Molecule[info->n_mol];
1208	+	int molIndex;
1209
1210	<	#ifdef IS_MPI
1210	>	// initialize the molecule's stampID's
1211
1044	–	the_excludes[(index + tot_bonds)*2] =
1045	–	the_atoms[exI]->getGlobalIndex() + 1;
1046	–	the_excludes[(index + tot_bonds)*2 + 1] =
1047	–	the_atoms[exJ]->getGlobalIndex() + 1;
1048	–
1049	–	#else  // isn't MPI
1050	–
1051	–	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1052	–	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1053	–	// fortran index from 1 (hence the +1 in the indexing)
1054	–	#endif  //is_mpi
1055	–
1056	–
1057	–	// increment the index and repeat;
1058	–	index++;
1059	–	}
1060	–	offset += comp_stamps[i]->getNAtoms();
1061	–
1212		#ifdef IS_MPI
1213	<	}
1064	<	#endif //is_mpi
1213	>
1214
1215	+	molIndex = 0;
1216	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1217	+
1218	+	if(mol2proc[i] == worldRank ){
1219	+	the_molecules[molIndex].setStampID( molCompType[i] );
1220	+	the_molecules[molIndex].setMyIndex( molIndex );
1221	+	the_molecules[molIndex].setGlobalIndex( i );
1222		molIndex++;
1223		}
1224		}
1225
1226	<	#ifdef IS_MPI
1071	<	sprintf( checkPointMsg,
1072	<	"Successfully created the bends list.\n" );
1073	<	MPIcheckPoint();
1074	<	#endif // is_mpi
1226	>	#else // is_mpi
1227
1228	+	molIndex = 0;
1229	+	globalAtomIndex = 0;
1230	+	for(i=0; i<n_components; i++){
1231	+	for(j=0; j<components_nmol[i]; j++ ){
1232	+	the_molecules[molIndex].setStampID( i );
1233	+	the_molecules[molIndex].setMyIndex( molIndex );
1234	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1235	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1236	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1237	+	globalAtomIndex++;
1238	+	}
1239	+	molIndex++;
1240	+	}
1241	+	}
1242	+
1243
1244	<	the_ff->initializeBends( the_bends );
1078	<	}
1244	>	#endif // is_mpi
1245
1080	–	void SimSetup::makeTorsions( void ){
1246
1247	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1248	<	torsion_set* the_torsions;
1249	<	TorsionStamp* current_torsion;
1247	>	if( info->n_SRI ){
1248	>
1249	>	Exclude::createArray(info->n_SRI);
1250	>	the_excludes = new Exclude*[info->n_SRI];
1251	>	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1252	>	info->globalExcludes = new int;
1253	>	info->n_exclude = info->n_SRI;
1254	>	}
1255	>	else{
1256	>
1257	>	Exclude::createArray( 1 );
1258	>	the_excludes = new Exclude*;
1259	>	the_excludes[0] = new Exclude(0);
1260	>	the_excludes[0]->setPair( 0,0 );
1261	>	info->globalExcludes = new int;
1262	>	info->globalExcludes[0] = 0;
1263	>	info->n_exclude = 0;
1264	>	}
1265
1266	<	the_torsions = new torsion_set[tot_torsions];
1087	<	index = 0;
1088	<	offset = 0;
1089	<	molIndex = 0;
1090	<	for( i=0; i<n_components; i++ ){
1266	>	// set the arrays into the SimInfo object
1267
1268	<	for( j=0; j<components_nmol[i]; j++ ){
1268	>	info->atoms = the_atoms;
1269	>	info->molecules = the_molecules;
1270	>	info->nGlobalExcludes = 0;
1271	>	info->excludes = the_excludes;
1272
1273	<	#ifdef IS_MPI
1095	<	if( mpiSim->getMyMolStart() <= molIndex &&
1096	<	molIndex <= mpiSim->getMyMolEnd() ){
1097	<	#endif // is_mpi
1273	>	the_ff->setSimInfo( info );
1274
1275	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1275	>	}
1276
1277	<	current_torsion = comp_stamps[i]->getTorsion( k );
1102	<	the_torsions[index].a = current_torsion->getA() + offset;
1103	<	the_torsions[index].b = current_torsion->getB() + offset;
1104	<	the_torsions[index].c = current_torsion->getC() + offset;
1105	<	the_torsions[index].d = current_torsion->getD() + offset;
1277	>	void SimSetup::makeIntegrator( void ){
1278
1279	<	exI = the_torsions[index].a;
1280	<	exJ = the_torsions[index].d;
1279	>	NVT*  myNVT = NULL;
1280	>	NPTi* myNPTi = NULL;
1281	>	NPTf* myNPTf = NULL;
1282	>	NPTim* myNPTim = NULL;
1283	>	NPTfm* myNPTfm = NULL;
1284
1285	<
1111	<	// exclude_I must always be the smaller of the pair
1112	<	if( exI > exJ ){
1113	<	tempEx = exI;
1114	<	exI = exJ;
1115	<	exJ = tempEx;
1116	<	}
1285	>	switch( ensembleCase ){
1286
1287	+	case NVE_ENS:
1288	+	new NVE( info, the_ff );
1289	+	break;
1290
1291	<	#ifdef IS_MPI
1292	<
1293	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1122	<	the_atoms[exI]->getGlobalIndex() + 1;
1123	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1124	<	the_atoms[exJ]->getGlobalIndex() + 1;
1125	<
1126	<	#else  // isn't MPI
1127	<
1128	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1129	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1130	<	// fortran indexes from 1 (hence the +1 in the indexing)
1131	<	#endif  //is_mpi
1132	<
1291	>	case NVT_ENS:
1292	>	myNVT = new NVT( info, the_ff );
1293	>	myNVT->setTargetTemp(globals->getTargetTemp());
1294
1295	<	// increment the index and repeat;
1296	<	index++;
1136	<	}
1137	<	offset += comp_stamps[i]->getNAtoms();
1295	>	if (globals->haveTauThermostat())
1296	>	myNVT->setTauThermostat(globals->getTauThermostat());
1297
1298	<	#ifdef IS_MPI
1299	<	}
1300	<	#endif //is_mpi
1301	<
1302	<	molIndex++;
1298	>	else {
1299	>	sprintf( painCave.errMsg,
1300	>	"SimSetup error: If you use the NVT\n"
1301	>	"    ensemble, you must set tauThermostat.\n");
1302	>	painCave.isFatal = 1;
1303	>	simError();
1304		}
1305	<	}
1305	>	break;
1306
1307	<	the_ff->initializeTorsions( the_torsions );
1308	<	}
1307	>	case NPTi_ENS:
1308	>	myNPTi = new NPTi( info, the_ff );
1309	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1310
1311	<	void SimSetup::initFromBass( void ){
1311	>	if (globals->haveTargetPressure())
1312	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1313	>	else {
1314	>	sprintf( painCave.errMsg,
1315	>	"SimSetup error: If you use a constant pressure\n"
1316	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1317	>	painCave.isFatal = 1;
1318	>	simError();
1319	>	}
1320	>
1321	>	if( globals->haveTauThermostat() )
1322	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1323	>	else{
1324	>	sprintf( painCave.errMsg,
1325	>	"SimSetup error: If you use an NPT\n"
1326	>	"    ensemble, you must set tauThermostat.\n");
1327	>	painCave.isFatal = 1;
1328	>	simError();
1329	>	}
1330
1331	<	int i, j, k;
1332	<	int n_cells;
1333	<	double cellx, celly, cellz;
1334	<	double temp1, temp2, temp3;
1335	<	int n_per_extra;
1336	<	int n_extra;
1337	<	int have_extra, done;
1331	>	if( globals->haveTauBarostat() )
1332	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1333	>	else{
1334	>	sprintf( painCave.errMsg,
1335	>	"SimSetup error: If you use an NPT\n"
1336	>	"    ensemble, you must set tauBarostat.\n");
1337	>	painCave.isFatal = 1;
1338	>	simError();
1339	>	}
1340	>	break;
1341
1342	<	temp1 = (double)tot_nmol / 4.0;
1343	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1344	<	temp3 = ceil( temp2 );
1342	>	case NPTf_ENS:
1343	>	myNPTf = new NPTf( info, the_ff );
1344	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1345
1346	<	have_extra =0;
1347	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1348	<	have_extra =1;
1346	>	if (globals->haveTargetPressure())
1347	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1348	>	else {
1349	>	sprintf( painCave.errMsg,
1350	>	"SimSetup error: If you use a constant pressure\n"
1351	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1352	>	painCave.isFatal = 1;
1353	>	simError();
1354	>	}
1355
1356	<	n_cells = (int)temp3 - 1;
1357	<	cellx = simnfo->box_x / temp3;
1358	<	celly = simnfo->box_y / temp3;
1171	<	cellz = simnfo->box_z / temp3;
1172	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1173	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1174	<	n_per_extra = (int)ceil( temp1 );
1175	<
1176	<	if( n_per_extra > 4){
1356	>	if( globals->haveTauThermostat() )
1357	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1358	>	else{
1359		sprintf( painCave.errMsg,
1360	<	"SimSetup error. There has been an error in constructing"
1361	<	" the non-complete lattice.\n" );
1360	>	"SimSetup error: If you use an NPT\n"
1361	>	"    ensemble, you must set tauThermostat.\n");
1362		painCave.isFatal = 1;
1363		simError();
1364		}
1183	–	}
1184	–	else{
1185	–	n_cells = (int)temp3;
1186	–	cellx = simnfo->box_x / temp3;
1187	–	celly = simnfo->box_y / temp3;
1188	–	cellz = simnfo->box_z / temp3;
1189	–	}
1365
1366	<	current_mol = 0;
1367	<	current_comp_mol = 0;
1368	<	current_comp = 0;
1369	<	current_atom_ndx = 0;
1370	<
1371	<	for( i=0; i < n_cells ; i++ ){
1372	<	for( j=0; j < n_cells; j++ ){
1373	<	for( k=0; k < n_cells; k++ ){
1374	<
1375	<	makeElement( i * cellx,
1376	<	j * celly,
1377	<	k * cellz );
1366	>	if( globals->haveTauBarostat() )
1367	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1368	>	else{
1369	>	sprintf( painCave.errMsg,
1370	>	"SimSetup error: If you use an NPT\n"
1371	>	"    ensemble, you must set tauBarostat.\n");
1372	>	painCave.isFatal = 1;
1373	>	simError();
1374	>	}
1375	>	break;
1376	>
1377	>	case NPTim_ENS:
1378	>	myNPTim = new NPTim( info, the_ff );
1379	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1380
1381	<	makeElement( i * cellx + 0.5 * cellx,
1382	<	j * celly + 0.5 * celly,
1383	<	k * cellz );
1381	>	if (globals->haveTargetPressure())
1382	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1383	>	else {
1384	>	sprintf( painCave.errMsg,
1385	>	"SimSetup error: If you use a constant pressure\n"
1386	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1387	>	painCave.isFatal = 1;
1388	>	simError();
1389	>	}
1390	>
1391	>	if( globals->haveTauThermostat() )
1392	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1393	>	else{
1394	>	sprintf( painCave.errMsg,
1395	>	"SimSetup error: If you use an NPT\n"
1396	>	"    ensemble, you must set tauThermostat.\n");
1397	>	painCave.isFatal = 1;
1398	>	simError();
1399	>	}
1400
1401	<	makeElement( i * cellx,
1402	<	j * celly + 0.5 * celly,
1403	<	k * cellz + 0.5 * cellz );
1404	<
1405	<	makeElement( i * cellx + 0.5 * cellx,
1406	<	j * celly,
1407	<	k * cellz + 0.5 * cellz );
1408	<	}
1401	>	if( globals->haveTauBarostat() )
1402	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1403	>	else{
1404	>	sprintf( painCave.errMsg,
1405	>	"SimSetup error: If you use an NPT\n"
1406	>	"    ensemble, you must set tauBarostat.\n");
1407	>	painCave.isFatal = 1;
1408	>	simError();
1409		}
1410	<	}
1410	>	break;
1411
1412	<	if( have_extra ){
1413	<	done = 0;
1412	>	case NPTfm_ENS:
1413	>	myNPTfm = new NPTfm( info, the_ff );
1414	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1415
1416	<	int start_ndx;
1417	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1418	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1419	<
1420	<	if( i < n_cells ){
1421	<
1422	<	if( j < n_cells ){
1423	<	start_ndx = n_cells;
1230	<	}
1231	<	else start_ndx = 0;
1232	<	}
1233	<	else start_ndx = 0;
1234	<
1235	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1236	<
1237	<	makeElement( i * cellx,
1238	<	j * celly,
1239	<	k * cellz );
1240	<	done = ( current_mol >= tot_nmol );
1241	<
1242	<	if( !done && n_per_extra > 1 ){
1243	<	makeElement( i * cellx + 0.5 * cellx,
1244	<	j * celly + 0.5 * celly,
1245	<	k * cellz );
1246	<	done = ( current_mol >= tot_nmol );
1247	<	}
1248	<
1249	<	if( !done && n_per_extra > 2){
1250	<	makeElement( i * cellx,
1251	<	j * celly + 0.5 * celly,
1252	<	k * cellz + 0.5 * cellz );
1253	<	done = ( current_mol >= tot_nmol );
1254	<	}
1255	<
1256	<	if( !done && n_per_extra > 3){
1257	<	makeElement( i * cellx + 0.5 * cellx,
1258	<	j * celly,
1259	<	k * cellz + 0.5 * cellz );
1260	<	done = ( current_mol >= tot_nmol );
1261	<	}
1262	<	}
1263	<	}
1416	>	if (globals->haveTargetPressure())
1417	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1418	>	else {
1419	>	sprintf( painCave.errMsg,
1420	>	"SimSetup error: If you use a constant pressure\n"
1421	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1422	>	painCave.isFatal = 1;
1423	>	simError();
1424		}
1425	<	}
1425	>
1426	>	if( globals->haveTauThermostat() )
1427	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1428	>	else{
1429	>	sprintf( painCave.errMsg,
1430	>	"SimSetup error: If you use an NPT\n"
1431	>	"    ensemble, you must set tauThermostat.\n");
1432	>	painCave.isFatal = 1;
1433	>	simError();
1434	>	}
1435
1436	<
1437	<	for( i=0; i<simnfo->n_atoms; i++ ){
1438	<	simnfo->atoms[i]->set_vx( 0.0 );
1270	<	simnfo->atoms[i]->set_vy( 0.0 );
1271	<	simnfo->atoms[i]->set_vz( 0.0 );
1272	<	}
1273	<	}
1274	<
1275	<	void SimSetup::makeElement( double x, double y, double z ){
1276	<
1277	<	int k;
1278	<	AtomStamp* current_atom;
1279	<	DirectionalAtom* dAtom;
1280	<	double rotMat[3][3];
1281	<
1282	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1283	<
1284	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1285	<	if( !current_atom->havePosition() ){
1436	>	if( globals->haveTauBarostat() )
1437	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1438	>	else{
1439		sprintf( painCave.errMsg,
1440	<	"SimSetup:initFromBass error.\n"
1441	<	"\tComponent %s, atom %s does not have a position specified.\n"
1289	<	"\tThe initialization routine is unable to give a start"
1290	<	" position.\n",
1291	<	comp_stamps[current_comp]->getID(),
1292	<	current_atom->getType() );
1440	>	"SimSetup error: If you use an NPT\n"
1441	>	"    ensemble, you must set tauBarostat.\n");
1442		painCave.isFatal = 1;
1443		simError();
1444		}
1445	+	break;
1446
1447	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1448	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1449	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1447	>	default:
1448	>	sprintf( painCave.errMsg,
1449	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1450	>	painCave.isFatal = 1;
1451	>	simError();
1452	>	}
1453
1454	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1454	>	}
1455
1456	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1456	>	void SimSetup::initFortran( void ){
1457
1458	<	rotMat[0][0] = 1.0;
1459	<	rotMat[0][1] = 0.0;
1460	<	rotMat[0][2] = 0.0;
1461	<
1309	<	rotMat[1][0] = 0.0;
1310	<	rotMat[1][1] = 1.0;
1311	<	rotMat[1][2] = 0.0;
1312	<
1313	<	rotMat[2][0] = 0.0;
1314	<	rotMat[2][1] = 0.0;
1315	<	rotMat[2][2] = 1.0;
1316	<
1317	<	dAtom->setA( rotMat );
1318	<	}
1319	<
1320	<	current_atom_ndx++;
1458	>	info->refreshSim();
1459	>
1460	>	if( !strcmp( info->mixingRule, "standard") ){
1461	>	the_ff->initForceField( LB_MIXING_RULE );
1462		}
1463	+	else if( !strcmp( info->mixingRule, "explicit") ){
1464	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1465	+	}
1466	+	else{
1467	+	sprintf( painCave.errMsg,
1468	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1469	+	info->mixingRule );
1470	+	painCave.isFatal = 1;
1471	+	simError();
1472	+	}
1473
1323	–	current_mol++;
1324	–	current_comp_mol++;
1474
1475	<	if( current_comp_mol >= components_nmol[current_comp] ){
1475	>	#ifdef IS_MPI
1476	>	strcpy( checkPointMsg,
1477	>	"Successfully intialized the mixingRule for Fortran." );
1478	>	MPIcheckPoint();
1479	>	#endif // is_mpi
1480
1328	–	current_comp_mol = 0;
1329	–	current_comp++;
1330	–	}
1481		}

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