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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 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();
179	<	comp_stamps[i] = NULL;
180	<
181	<	// check to make sure the component isn't already in the list
152	>	the_ff->readParams();
153
154	<	comp_stamps[i] = headStamp->match( id );
155	<	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	<	}
154	>
155	>	// init the atoms
156
157	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
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	+	stampID = the_molecules[i].getStampID();
164
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	<	// caclulate the number of atoms, bonds, bends and torsions
178	<
179	<	tot_atoms = 0;
214	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
177	>	theBonds = new bond_pair[molInfo.nBonds];
178	>	theBends = new bend_set[molInfo.nBends];
179	>	theTorsions = new torsion_set[molInfo.nTorsions];
180
181	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
182	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
183	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
184	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
185	<	}
181	>	// make the Atoms
182	>
183	>	for(j=0; j<molInfo.nAtoms; j++){
184	>
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	>	else{
208	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
209	>	}
210	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
211	>
212	>	#ifdef IS_MPI
213	>
214	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
215	>
216	>	#endif // is_mpi
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	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
226	>	exI = theBonds[j].a;
227	>	exJ = theBonds[j].b;
228
229	<	simnfo->n_atoms = tot_atoms;
230	<	simnfo->n_bonds = tot_bonds;
231	<	simnfo->n_bends = tot_bends;
232	<	simnfo->n_torsions = tot_torsions;
233	<	simnfo->n_SRI = tot_SRI;
234	<	simnfo->n_mol = tot_nmol;
233	<
234	<
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	<	// divide the molecules among processors here.
245	<
246	<	mpiSim = new mpiSimulation( simnfo );
247	<
241	<
244	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
245	>	#endif  //is_mpi
246	>	}
247	>	excludeOffset += molInfo.nBonds;
248
249	<	globalIndex = mpiSim->divideLabor();
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	<
347	<	// set up the local variables
348	<
349	<	int localMol, allMol;
350	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
351	<
352	<	allMol = 0;
353	<	localMol = 0;
354	<	local_atoms = 0;
355	<	local_bonds = 0;
356	<	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++ ){
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	<	if( mpiSim->getMyMolStart() <= allMol &&
359	<	allMol <= mpiSim->getMyMolEnd() ){
360	<
361	<	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++;
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	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
363	>	excludeOffset += molInfo.nTorsions;
364
365	<	simnfo->n_atoms = mpiSim->getMyNlocal();
366	<
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	<	}
365	>
366	>	// send the arrays off to the forceField for init.
367
368	<	simnfo->n_bonds = local_bonds;
369	<	simnfo->n_bends = local_bends;
370	<	simnfo->n_torsions = local_torsions;
371	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
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
373	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
373	>
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();
297	–
298	–
386		#endif // is_mpi
300	–
387
388	<	// create the atom and short range interaction arrays
388	>	// clean up the forcefield
389	>	the_ff->calcRcut();
390	>	the_ff->cleanMe();
391
392	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
392	>	}
393
394	+	void SimSetup::initFromBass( void ){
395
396	<	if( simnfo->n_SRI ){
397	<	the_sris = new SRI*[simnfo->n_SRI];
398	<	the_excludes = new int[2 * simnfo->n_SRI];
399	<	simnfo->globalExcludes = new int;
400	<	simnfo->n_exclude = tot_SRI;
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	>	temp1 = (double)tot_nmol / 4.0;
405	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
406	>	temp3 = ceil( temp2 );
407	>
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		else{
429	<
430	<	the_excludes = new int[2];
431	<	the_excludes[0] = 0;
432	<	the_excludes[1] = 0;
433	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
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_exclude = 1;
435	>	current_mol = 0;
436	>	current_comp_mol = 0;
437	>	current_comp = 0;
438	>	current_atom_ndx = 0;
439	>
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	>	makeElement( i * cellx,
445	>	j * celly,
446	>	k * cellz );
447	>
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	>	makeElement( i * cellx + 0.5 * cellx,
457	>	j * celly,
458	>	k * cellz + 0.5 * cellz );
459	>	}
460	>	}
461		}
462
463	<	// set the arrays into the SimInfo object
463	>	if( have_extra ){
464	>	done = 0;
465
466	<	simnfo->atoms = the_atoms;
467	<	simnfo->sr_interactions = the_sris;
468	<	simnfo->nGlobalExcludes = 0;
469	<	simnfo->excludes = the_excludes;
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	<	// get some of the tricky things that may still be in the globals
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	+
511	+
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	+	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) {
821	>	info->dielectric = globals->getDielectric();
822	>	}
823	>	else {
824	>	if (usesDipoles) {
825
826	<	if( !the_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 = simnfo->box_x;
835	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
836	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
837	<	simnfo->ecr = 0.5 * smallest;
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
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	–	}
993
994	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
994	>	}
995
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
996
997	<	// check for the temperature set flag
997	>	void SimSetup::sysObjectsCreation( void ){
998
999	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
999	>	int i;
1000
1001	+	// create the forceField
1002
1003	<	//   // make the longe range forces and the integrator
1003	>	createFF();
1004
1005	<	//   new AllLong( simnfo );
1005	>	// extract componentList
1006
1007	<	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 );
1007	>	compList();
1008
1009	+	// calc the number of atoms, bond, bends, and torsions
1010
1011	+	calcSysValues();
1012
1013	<	// initialize the Fortran
1013	>	#ifdef IS_MPI
1014	>	// divide the molecules among the processors
1015
1016	<	simnfo->refreshSim();
1016	>	mpiMolDivide();
1017	>	#endif //is_mpi
1018
1019	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1020	<	the_ff->initForceField( LB_MIXING_RULE );
1021	<	}
1022	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
1023	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1024	<	}
1025	<	else{
1026	<	sprintf( painCave.errMsg,
1027	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1028	<	simnfo->mixingRule );
1019	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1020	>
1021	>	makeSysArrays();
1022	>
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	>
1032	>
1033	>	}
1034	>
1035	>
1036	>	void SimSetup::createFF( void ){
1037	>
1038	>	switch( ffCase ){
1039	>
1040	>	case FF_DUFF:
1041	>	the_ff = new DUFF();
1042	>	break;
1043	>
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	>	default:
1053	>	sprintf( painCave.errMsg,
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
1066
1067	<	void SimSetup::makeMolecules( void ){
1067	>	void SimSetup::compList( void ){
1068
1069	<	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;
684	<
685	<	//init the forceField paramters
1069	>	int i;
1070
1071	<	the_ff->readParams();
1071	>	comp_stamps = new MoleculeStamp*[n_components];
1072
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	+	info->nComponents = n_components;
1077	+	info->componentsNmol = components_nmol;
1078	+	info->compStamps = comp_stamps;
1079	+	info->headStamp = new LinkedMolStamp();
1080
1081	<	// init the molecules
1081	>	char* id;
1082	>	LinkedMolStamp* headStamp = info->headStamp;
1083	>	LinkedMolStamp* currentStamp = NULL;
1084	>	for( i=0; i<n_components; i++ ){
1085
1086	<	atomOffset = 0;
1087	<	for(i=0; i<simnfo->n_mol; i++){
1086	>	id = the_components[i]->getType();
1087	>	comp_stamps[i] = NULL;
1088
1089	<	stampID = the_molecules[i].getStampID();
1089	>	// check to make sure the component isn't already in the list
1090
1091	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
1092	<	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++){
1091	>	comp_stamps[i] = headStamp->match( id );
1092	>	if( comp_stamps[i] == NULL ){
1093
1094	<	currentAtom = theComponents[stampID]->getAtom( j );
1095	<	if( currentAtom->haveOrientation() ){
1096	<
1097	<	dAtom = new DirectionalAtom(j + atomOffset);
1098	<	simnfo->n_oriented++;
1099	<	info.myAtoms[j] = dAtom;
1100	<
1101	<	ux = currentAtom->getOrntX();
1102	<	uy = currentAtom->getOrntY();
1103	<	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 );
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		}
737	–	else{
738	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
739	–	}
740	–	info.myAtoms[j]->setType( currentAtom->getType() );
741	–
742	–	#ifdef IS_MPI
1105
1106	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1107	<
1106	>	headStamp->add( currentStamp );
1107	>	comp_stamps[i] = headStamp->match( id );
1108	>	}
1109	>	}
1110	>
1111	>	#ifdef IS_MPI
1112	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1113	>	MPIcheckPoint();
1114		#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;
1115
756	–	exI = theBonds[i].a;
757	–	exJ = theBonds[i].b;
1116
1117	<	// 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)
1117	>	}
1118
1119	<	#endif  //is_mpi
1119	>	void SimSetup::calcSysValues( void ){
1120	>	int i, j, k;
1121	>
1122	>
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	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1136
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
1147
1148	+	#ifdef IS_MPI
1149
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	+	mpiSim = new mpiSimulation( info );
1157	+
1158	+	globalIndex = mpiSim->divideLabor();
1159
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
1174	+	for( i=0; i<n_components; i++ ){
1175
1176	+	for( j=0; j<components_nmol[i]; j++ ){
1177	+
1178	+	if( mol2proc[allMol] == worldRank ){
1179	+
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	+	}
1190
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	+	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	+	}
1217	+
1218	+	#endif // is_mpi
1219
1220
1221	<	void SimSetup::makeAtoms( void ){
1221	>	void SimSetup::makeSysArrays( void ){
1222	>	int i, j, k;
1223
798	–	int i, j, k, index;
799	–	double ux, uy, uz, uSqr, u;
800	–	AtomStamp* current_atom;
1224
1225	<	DirectionalAtom* dAtom;
803	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
1225	>	// create the atom and short range interaction arrays
1226
1227	<	lMolIndex = 0;
1228	<	molIndex = 0;
1229	<	index = 0;
1230	<	for( i=0; i<n_components; i++ ){
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	<	for( j=0; j<components_nmol[i]; j++ ){
1232	>	// initialize the molecule's stampID's
1233
1234		#ifdef IS_MPI
1235	<	if( mpiSim->getMyMolStart() <= molIndex &&
814	<	molIndex <= mpiSim->getMyMolEnd() ){
815	<	#endif // is_mpi
1235	>
1236
1237	<	molStart = index;
1238	<	nMemb = comp_stamps[i]->getNAtoms();
1239	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
1240	<
1241	<	current_atom = comp_stamps[i]->getAtom( k );
1242	<	if( current_atom->haveOrientation() ){
1243	<
1244	<	dAtom = new DirectionalAtom(index);
1245	<	simnfo->n_oriented++;
1246	<	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++;
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	<	#ifdef IS_MPI
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		}
862	–	#endif //is_mpi
863	–
1261		molIndex++;
1262		}
1263		}
867	–
868	–	#ifdef IS_MPI
869	–	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
1264
871	–	delete[] globalIndex;
1265
1266	<	mpiSim->mpiRefresh();
874	<	#endif //IS_MPI
875	<
876	<	the_ff->initializeAtoms();
877	<	}
1266	>	#endif // is_mpi
1267
879	–	void SimSetup::makeBonds( void ){
1268
1269	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1270	<	bond_pair* the_bonds;
1271	<	BondStamp* current_bond;
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	>
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	<	the_bonds = new bond_pair[tot_bonds];
886	<	index = 0;
887	<	offset = 0;
888	<	molIndex = 0;
1288	>	// set the arrays into the SimInfo object
1289
1290	<	for( i=0; i<n_components; i++ ){
1290	>	info->atoms = the_atoms;
1291	>	info->molecules = the_molecules;
1292	>	info->nGlobalExcludes = 0;
1293	>	info->excludes = the_excludes;
1294
1295	<	for( j=0; j<components_nmol[i]; j++ ){
1295	>	the_ff->setSimInfo( info );
1296
1297	<	#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;
1297	>	}
1298
1299	<	exI = the_bonds[index].a;
906	<	exJ = the_bonds[index].b;
1299	>	void SimSetup::makeIntegrator( void ){
1300
1301	<	// exclude_I must always be the smaller of the pair
1302	<	if( exI > exJ ){
1303	<	tempEx = exI;
1304	<	exI = exJ;
1305	<	exJ = tempEx;
913	<	}
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	<
916	<	#ifdef IS_MPI
1307	>	switch( ensembleCase ){
1308
1309	<	the_excludes[index*2] =
1310	<	the_atoms[exI]->getGlobalIndex() + 1;
1311	<	the_excludes[index*2 + 1] =
921	<	the_atoms[exJ]->getGlobalIndex() + 1;
1309	>	case NVE_ENS:
1310	>	new NVE<RealIntegrator>( info, the_ff );
1311	>	break;
1312
1313	<	#else  // isn't MPI
1314	<
1315	<	the_excludes[index*2] =     exI + 1;
926	<	the_excludes[index*2 + 1] = exJ + 1;
927	<	// 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();
934	<
935	<	#ifdef IS_MPI
936	<	}
937	<	#endif //is_mpi
938	<
939	<	molIndex++;
940	<	}
941	<	}
1313	>	case NVT_ENS:
1314	>	myNVT = new NVT<RealIntegrator>( info, the_ff );
1315	>	myNVT->setTargetTemp(globals->getTargetTemp());
1316
1317	<	the_ff->initializeBonds( the_bonds );
1318	<	}
1317	>	if (globals->haveTauThermostat())
1318	>	myNVT->setTauThermostat(globals->getTauThermostat());
1319
1320	<	void SimSetup::makeBends( void ){
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	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1330	<	bend_set* the_bends;
1331	<	BendStamp* current_bend;
951	<	LinkedAssign* extras;
952	<	LinkedAssign* current_extra;
953	<
1329	>	case NPTi_ENS:
1330	>	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1331	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1332
1333	<	the_bends = new bend_set[tot_bends];
1334	<	index = 0;
1335	<	offset = 0;
1336	<	molIndex = 0;
1337	<	for( i=0; i<n_components; i++ ){
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	<	for( j=0; j<components_nmol[i]; j++ ){
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	>	break;
1363
1364	<	#ifdef IS_MPI
1365	<	if( mpiSim->getMyMolStart() <= molIndex &&
1366	<	molIndex <= mpiSim->getMyMolEnd() ){
966	<	#endif // is_mpi
1364	>	case NPTf_ENS:
1365	>	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1366	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1367
1368	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1369	<
1370	<	current_bend = comp_stamps[i]->getBend( k );
1371	<	the_bends[index].a = current_bend->getA() + offset;
1372	<	the_bends[index].b = current_bend->getB() + offset;
1373	<	the_bends[index].c = current_bend->getC() + offset;
1374	<
1375	<	if( current_bend->haveExtras() ){
1376	<
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	<	}
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	+	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	<	#ifdef IS_MPI
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	<	the_excludes[(index + tot_bonds)*2] =
1404	<	the_atoms[exI]->getGlobalIndex() + 1;
1405	<	the_excludes[(index + tot_bonds)*2 + 1] =
1406	<	the_atoms[exJ]->getGlobalIndex() + 1;
1407	<
1408	<	#else  // isn't MPI
1409	<
1410	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1411	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1412	<	// fortran index from 1 (hence the +1 in the indexing)
1413	<	#endif  //is_mpi
1414	<
1415	<
1416	<	// increment the index and repeat;
1417	<	index++;
1418	<	}
1419	<	offset += comp_stamps[i]->getNAtoms();
1420	<
1421	<	#ifdef IS_MPI
1063	<	}
1064	<	#endif //is_mpi
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	<	molIndex++;
1423	>	if( globals->haveTauBarostat() )
1424	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1425	>	else{
1426	>	sprintf( painCave.errMsg,
1427	>	"SimSetup error: If you use an NPT\n"
1428	>	"    ensemble, you must set tauBarostat.\n");
1429	>	painCave.isFatal = 1;
1430	>	simError();
1431		}
1432	<	}
1432	>	break;
1433
1434	<	#ifdef IS_MPI
1435	<	sprintf( checkPointMsg,
1436	<	"Successfully created the bends list.\n" );
1073	<	MPIcheckPoint();
1074	<	#endif // is_mpi
1075	<
1434	>	case NPTfm_ENS:
1435	>	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1436	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1437
1438	<	the_ff->initializeBends( the_bends );
1439	<	}
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	<	void SimSetup::makeTorsions( void ){
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	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1470	<	torsion_set* the_torsions;
1471	<	TorsionStamp* current_torsion;
1472	<
1473	<	the_torsions = new torsion_set[tot_torsions];
1087	<	index = 0;
1088	<	offset = 0;
1089	<	molIndex = 0;
1090	<	for( i=0; i<n_components; i++ ){
1091	<
1092	<	for( j=0; j<components_nmol[i]; j++ ){
1093	<
1094	<	#ifdef IS_MPI
1095	<	if( mpiSim->getMyMolStart() <= molIndex &&
1096	<	molIndex <= mpiSim->getMyMolEnd() ){
1097	<	#endif // is_mpi
1098	<
1099	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1100	<
1101	<	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;
1106	<
1107	<	exI = the_torsions[index].a;
1108	<	exJ = the_torsions[index].d;
1109	<
1110	<
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	<	}
1117	<
1118	<
1119	<	#ifdef IS_MPI
1120	<
1121	<	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	<
1133	<
1134	<	// increment the index and repeat;
1135	<	index++;
1136	<	}
1137	<	offset += comp_stamps[i]->getNAtoms();
1138	<
1139	<	#ifdef IS_MPI
1140	<	}
1141	<	#endif //is_mpi
1142	<
1143	<	molIndex++;
1144	<	}
1469	>	default:
1470	>	sprintf( painCave.errMsg,
1471	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1472	>	painCave.isFatal = 1;
1473	>	simError();
1474		}
1475
1147	–	the_ff->initializeTorsions( the_torsions );
1476		}
1477
1478	<	void SimSetup::initFromBass( void ){
1478	>	void SimSetup::initFortran( void ){
1479
1480	<	int i, j, k;
1481	<	int n_cells;
1482	<	double cellx, celly, cellz;
1483	<	double temp1, temp2, temp3;
1156	<	int n_per_extra;
1157	<	int n_extra;
1158	<	int have_extra, done;
1159	<
1160	<	temp1 = (double)tot_nmol / 4.0;
1161	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1162	<	temp3 = ceil( temp2 );
1163	<
1164	<	have_extra =0;
1165	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1166	<	have_extra =1;
1167	<
1168	<	n_cells = (int)temp3 - 1;
1169	<	cellx = simnfo->box_x / temp3;
1170	<	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){
1177	<	sprintf( painCave.errMsg,
1178	<	"SimSetup error. There has been an error in constructing"
1179	<	" the non-complete lattice.\n" );
1180	<	painCave.isFatal = 1;
1181	<	simError();
1182	<	}
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	<	n_cells = (int)temp3;
1490	<	cellx = simnfo->box_x / temp3;
1491	<	celly = simnfo->box_y / temp3;
1492	<	cellz = simnfo->box_z / temp3;
1489	>	sprintf( painCave.errMsg,
1490	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1491	>	info->mixingRule );
1492	>	painCave.isFatal = 1;
1493	>	simError();
1494		}
1495
1191	–	current_mol = 0;
1192	–	current_comp_mol = 0;
1193	–	current_comp = 0;
1194	–	current_atom_ndx = 0;
1496
1497	<	for( i=0; i < n_cells ; i++ ){
1498	<	for( j=0; j < n_cells; j++ ){
1499	<	for( k=0; k < n_cells; k++ ){
1497	>	#ifdef IS_MPI
1498	>	strcpy( checkPointMsg,
1499	>	"Successfully intialized the mixingRule for Fortran." );
1500	>	MPIcheckPoint();
1501	>	#endif // is_mpi
1502
1200	–	makeElement( i * cellx,
1201	–	j * celly,
1202	–	k * cellz );
1203	–
1204	–	makeElement( i * cellx + 0.5 * cellx,
1205	–	j * celly + 0.5 * celly,
1206	–	k * cellz );
1207	–
1208	–	makeElement( i * cellx,
1209	–	j * celly + 0.5 * celly,
1210	–	k * cellz + 0.5 * cellz );
1211	–
1212	–	makeElement( i * cellx + 0.5 * cellx,
1213	–	j * celly,
1214	–	k * cellz + 0.5 * cellz );
1215	–	}
1216	–	}
1217	–	}
1218	–
1219	–	if( have_extra ){
1220	–	done = 0;
1221	–
1222	–	int start_ndx;
1223	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1224	–	for( j=0; j < (n_cells+1) && !done; j++ ){
1225	–
1226	–	if( i < n_cells ){
1227	–
1228	–	if( j < n_cells ){
1229	–	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	–	}
1264	–	}
1265	–	}
1266	–
1267	–
1268	–	for( i=0; i<simnfo->n_atoms; i++ ){
1269	–	simnfo->atoms[i]->set_vx( 0.0 );
1270	–	simnfo->atoms[i]->set_vy( 0.0 );
1271	–	simnfo->atoms[i]->set_vz( 0.0 );
1272	–	}
1503		}
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() ){
1286	–	sprintf( painCave.errMsg,
1287	–	"SimSetup:initFromBass error.\n"
1288	–	"\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() );
1293	–	painCave.isFatal = 1;
1294	–	simError();
1295	–	}
1296	–
1297	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1298	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1299	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1300	–
1301	–	if( the_atoms[current_atom_ndx]->isDirectional() ){
1302	–
1303	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1304	–
1305	–	rotMat[0][0] = 1.0;
1306	–	rotMat[0][1] = 0.0;
1307	–	rotMat[0][2] = 0.0;
1308	–
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++;
1321	–	}
1322	–
1323	–	current_mol++;
1324	–	current_comp_mol++;
1325	–
1326	–	if( current_comp_mol >= components_nmol[current_comp] ){
1327	–
1328	–	current_comp_mol = 0;
1329	–	current_comp++;
1330	–	}
1331	–	}

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