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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 432 by chuckv, Thu Mar 27 23:33:40 2003 UTC vs.
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8		#include "parse_me.h"
#	Line 12 | Line 14 | SimSetup::SimSetup(){
14		#include "mpiSimulation.hpp"
15		#endif
16
17	+	// some defines for ensemble and Forcefield  cases
18	+
19	+	#define NVE_ENS        0
20	+	#define NVT_ENS        1
21	+	#define NPTi_ENS       2
22	+	#define NPTf_ENS       3
23	+	#define NPTim_ENS      4
24	+	#define NPTfm_ENS      5
25	+	#define NVEZCONS_ENS   6
26	+	#define NVTZCONS_ENS   7
27	+	#define NPTiZCONS_ENS  8
28	+	#define NPTfZCONS_ENS  9
29	+	#define NPTimZCONS_ENS 10
30	+	#define NPTfmZCONS_ENS 11
31	+
32	+	#define FF_DUFF 0
33	+	#define FF_LJ   1
34	+	#define FF_EAM  2
35	+
36	+	using namespace std;
37	+
38		SimSetup::SimSetup(){
39	+
40	+	isInfoArray = 0;
41	+	nInfo = 1;
42	+
43		stamps = new MakeStamps();
44		globals = new Globals();
45
46	+
47		#ifdef IS_MPI
48		strcpy( checkPointMsg, "SimSetup creation successful" );
49		MPIcheckPoint();
#	Line 27 | Line 55 | void SimSetup::parseFile( char* fileName ){
55		delete globals;
56		}
57
58	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
59	+	info = the_info;
60	+	nInfo = theNinfo;
61	+	isInfoArray = 1;
62	+	}
63	+
64	+
65		void SimSetup::parseFile( char* fileName ){
66
67		#ifdef IS_MPI
#	Line 62 | Line 97 | void SimSetup::createSim( void ){
97
98		#endif // is_mpi
99
100	<	void SimSetup::createSim( void ){
100	>	void SimSetup::createSim(void){
101
102	<	MakeStamps *the_stamps;
103	<	Globals* the_globals;
104	<	int i, j;
102	>	int i, j, k, globalAtomIndex;
103	>
104	>	// gather all of the information from the Bass file
105	>
106	>	gatherInfo();
107
108	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
108	>	// creation of complex system objects
109
110	<	// 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();
110	>	sysObjectsCreation();
111
112	<	// get the ones we know are there, yet still may need some work.
113	<	n_components = the_globals->getNComponents();
114	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
112	>	// check on the post processing info
113	>
114	>	finalInfoCheck();
115
116	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
116	>	// initialize the system coordinates
117
118	+	if( !isInfoArray ) initSystemCoords();
119
120	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
120	>	// make the output filenames
121
122	+	makeOutNames();
123	+
124	+	// make the integrator
125	+
126	+	makeIntegrator();
127	+
128		#ifdef IS_MPI
129	<	strcpy( checkPointMsg, "ForceField creation successful" );
130	<	MPIcheckPoint();
104	<	#endif // is_mpi
129	>	mpiSim->mpiRefresh();
130	>	#endif
131
132	<
132	>	// initialize the Fortran
133
134	<	// get the components and calculate the tot_nMol and indvidual n_mol
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
134	>	initFortran();
135
113	–	if( !the_globals->haveNMol() ){
114	–	// we don't have the total number of molecules, so we assume it is
115	–	// given in each component
136
117	–	tot_nmol = 0;
118	–	for( i=0; i<n_components; i++ ){
137
138	<	if( !the_components[i]->haveNMol() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
138	>	}
139
140	<	tot_nmol += the_components[i]->getNMol();
141	<	components_nmol[i] = the_components[i]->getNMol();
142	<	}
143	<	}
144	<	else{
145	<	sprintf( painCave.errMsg,
146	<	"SimSetup error.\n"
147	<	"\tSorry, the ability to specify total"
148	<	" nMols and then give molfractions in the components\n"
149	<	"\tis not currently supported."
150	<	" Please give nMol in the components.\n" );
151	<	painCave.isFatal = 1;
152	<	simError();
140	>
141	>	void SimSetup::makeMolecules( void ){
142	>
143	>	int k,l;
144	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
145	>	molInit molInfo;
146	>	DirectionalAtom* dAtom;
147	>	LinkedAssign* extras;
148	>	LinkedAssign* current_extra;
149	>	AtomStamp* currentAtom;
150	>	BondStamp* currentBond;
151	>	BendStamp* currentBend;
152	>	TorsionStamp* currentTorsion;
153	>
154	>	bond_pair* theBonds;
155	>	bend_set* theBends;
156	>	torsion_set* theTorsions;
157	>
158	>
159	>	//init the forceField paramters
160	>
161	>	the_ff->readParams();
162	>
163	>
164	>	// init the atoms
165	>
166	>	double ux, uy, uz, u, uSqr;
167	>
168	>	for(k=0; k<nInfo; k++){
169
170	+	the_ff->setSimInfo( &(info[k]) );
171	+
172	+	atomOffset = 0;
173	+	excludeOffset = 0;
174	+	for(i=0; i<info[k].n_mol; i++){
175
176	<	//     tot_nmol = the_globals->getNMol();
176	>	stampID = info[k].molecules[i].getStampID();
177	>
178	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
179	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
180	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
181	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
182	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
183	>
184	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
185	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
186	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
187	>	molInfo.myBends = new Bend*[molInfo.nBends];
188	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
189	>
190	>	theBonds = new bond_pair[molInfo.nBonds];
191	>	theBends = new bend_set[molInfo.nBends];
192	>	theTorsions = new torsion_set[molInfo.nTorsions];
193
194	<	//   //we have the total number of molecules, now we check for molfractions
147	<	//     for( i=0; i<n_components; i++ ){
194	>	// make the Atoms
195
196	<	//       if( !the_components[i]->haveMolFraction() ){
196	>	for(j=0; j<molInfo.nAtoms; j++){
197	>
198	>	currentAtom = comp_stamps[stampID]->getAtom( j );
199	>	if( currentAtom->haveOrientation() ){
200	>
201	>	dAtom = new DirectionalAtom( (j + atomOffset),
202	>	info[k].getConfiguration() );
203	>	info[k].n_oriented++;
204	>	molInfo.myAtoms[j] = dAtom;
205	>
206	>	ux = currentAtom->getOrntX();
207	>	uy = currentAtom->getOrntY();
208	>	uz = currentAtom->getOrntZ();
209	>
210	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
211	>
212	>	u = sqrt( uSqr );
213	>	ux = ux / u;
214	>	uy = uy / u;
215	>	uz = uz / u;
216	>
217	>	dAtom->setSUx( ux );
218	>	dAtom->setSUy( uy );
219	>	dAtom->setSUz( uz );
220	>	}
221	>	else{
222	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
223	>	info[k].getConfiguration() );
224	>	}
225	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
226
151	–	//  if( !the_components[i]->haveNMol() ){
152	–	//    //we have a problem
153	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	–	//              << " nMol was given in component
155	–
156	–	}
157	–
227		#ifdef IS_MPI
228	<	strcpy( checkPointMsg, "Have the number of components" );
229	<	MPIcheckPoint();
228	>
229	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
230	>
231		#endif // is_mpi
232	<
163	<	// make an array of molecule stamps that match the components used.
164	<	// also extract the used stamps out into a separate linked list
165	<
166	<	simnfo->nComponents = n_components;
167	<	simnfo->componentsNmol = components_nmol;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
170	<
171	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
175	<
176	<	id = the_components[i]->getType();
177	<	comp_stamps[i] = NULL;
232	>	}
233
234	<	// check to make sure the component isn't already in the list
235	<
181	<	comp_stamps[i] = headStamp->match( id );
182	<	if( comp_stamps[i] == NULL ){
234	>	// make the bonds
235	>	for(j=0; j<molInfo.nBonds; j++){
236
237	<	// extract the component from the list;
237	>	currentBond = comp_stamps[stampID]->getBond( j );
238	>	theBonds[j].a = currentBond->getA() + atomOffset;
239	>	theBonds[j].b = currentBond->getB() + atomOffset;
240	>
241	>	exI = theBonds[j].a;
242	>	exJ = theBonds[j].b;
243	>
244	>	// exclude_I must always be the smaller of the pair
245	>	if( exI > exJ ){
246	>	tempEx = exI;
247	>	exI = exJ;
248	>	exJ = tempEx;
249	>	}
250	>	#ifdef IS_MPI
251	>	tempEx = exI;
252	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
253	>	tempEx = exJ;
254	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
255	>
256	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
257	>	#else  // isn't MPI
258	>
259	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
260	>	#endif  //is_mpi
261	>	}
262	>	excludeOffset += molInfo.nBonds;
263
264	<	currentStamp = the_stamps->extractMolStamp( id );
265	<	if( currentStamp == NULL ){
266	<	sprintf( painCave.errMsg,
267	<	"SimSetup error: Component \"%s\" was not found in the "
268	<	"list of declared molecules\n",
269	<	id );
270	<	painCave.isFatal = 1;
271	<	simError();
264	>	//make the bends
265	>	for(j=0; j<molInfo.nBends; j++){
266	>
267	>	currentBend = comp_stamps[stampID]->getBend( j );
268	>	theBends[j].a = currentBend->getA() + atomOffset;
269	>	theBends[j].b = currentBend->getB() + atomOffset;
270	>	theBends[j].c = currentBend->getC() + atomOffset;
271	>
272	>	if( currentBend->haveExtras() ){
273	>
274	>	extras = currentBend->getExtras();
275	>	current_extra = extras;
276	>
277	>	while( current_extra != NULL ){
278	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
279	>
280	>	switch( current_extra->getType() ){
281	>
282	>	case 0:
283	>	theBends[j].ghost =
284	>	current_extra->getInt() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	case 1:
289	>	theBends[j].ghost =
290	>	(int)current_extra->getDouble() + atomOffset;
291	>	theBends[j].isGhost = 1;
292	>	break;
293	>
294	>	default:
295	>	sprintf( painCave.errMsg,
296	>	"SimSetup Error: ghostVectorSource was neither a "
297	>	"double nor an int.\n"
298	>	"-->Bend[%d] in %s\n",
299	>	j, comp_stamps[stampID]->getID() );
300	>	painCave.isFatal = 1;
301	>	simError();
302	>	}
303	>	}
304	>
305	>	else{
306	>
307	>	sprintf( painCave.errMsg,
308	>	"SimSetup Error: unhandled bend assignment:\n"
309	>	"    -->%s in Bend[%d] in %s\n",
310	>	current_extra->getlhs(),
311	>	j, comp_stamps[stampID]->getID() );
312	>	painCave.isFatal = 1;
313	>	simError();
314	>	}
315	>
316	>	current_extra = current_extra->getNext();
317	>	}
318	>	}
319	>
320	>	if( !theBends[j].isGhost ){
321	>
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].c;
324	>	}
325	>	else{
326	>
327	>	exI = theBends[j].a;
328	>	exJ = theBends[j].b;
329	>	}
330	>
331	>	// exclude_I must always be the smaller of the pair
332	>	if( exI > exJ ){
333	>	tempEx = exI;
334	>	exI = exJ;
335	>	exJ = tempEx;
336	>	}
337	>	#ifdef IS_MPI
338	>	tempEx = exI;
339	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
340	>	tempEx = exJ;
341	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
342	>
343	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
344	>	#else  // isn't MPI
345	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
346	>	#endif  //is_mpi
347		}
348	+	excludeOffset += molInfo.nBends;
349
350	<	headStamp->add( currentStamp );
351	<	comp_stamps[i] = headStamp->match( id );
350	>	for(j=0; j<molInfo.nTorsions; j++){
351	>
352	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
353	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
354	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
355	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
356	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
357	>
358	>	exI = theTorsions[j].a;
359	>	exJ = theTorsions[j].d;
360	>
361	>	// exclude_I must always be the smaller of the pair
362	>	if( exI > exJ ){
363	>	tempEx = exI;
364	>	exI = exJ;
365	>	exJ = tempEx;
366	>	}
367	>	#ifdef IS_MPI
368	>	tempEx = exI;
369	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
370	>	tempEx = exJ;
371	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
372	>
373	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
374	>	#else  // isn't MPI
375	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
376	>	#endif  //is_mpi
377	>	}
378	>	excludeOffset += molInfo.nTorsions;
379	>
380	>
381	>	// send the arrays off to the forceField for init.
382	>
383	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
384	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
385	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
386	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
387	>
388	>
389	>	info[k].molecules[i].initialize( molInfo );
390	>
391	>
392	>	atomOffset += molInfo.nAtoms;
393	>	delete[] theBonds;
394	>	delete[] theBends;
395	>	delete[] theTorsions;
396		}
397		}
398	<
398	>
399		#ifdef IS_MPI
400	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
400	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
401		MPIcheckPoint();
402		#endif // is_mpi
403
404	+	// clean up the forcefield
405
406	+	the_ff->calcRcut();
407	+	the_ff->cleanMe();
408	+
409	+	}
410
411	+	void SimSetup::initFromBass( void ){
412
413	<	// caclulate the number of atoms, bonds, bends and torsions
413	>	int i, j, k;
414	>	int n_cells;
415	>	double cellx, celly, cellz;
416	>	double temp1, temp2, temp3;
417	>	int n_per_extra;
418	>	int n_extra;
419	>	int have_extra, done;
420
421	<	tot_atoms = 0;
422	<	tot_bonds = 0;
423	<	tot_bends = 0;
424	<	tot_torsions = 0;
215	<	for( i=0; i<n_components; i++ ){
216	<
217	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	<	}
421	>	double vel[3];
422	>	vel[0] = 0.0;
423	>	vel[1] = 0.0;
424	>	vel[2] = 0.0;
425
426	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
426	>	temp1 = (double)tot_nmol / 4.0;
427	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
428	>	temp3 = ceil( temp2 );
429
430	<	simnfo->n_atoms = tot_atoms;
431	<	simnfo->n_bonds = tot_bonds;
432	<	simnfo->n_bends = tot_bends;
228	<	simnfo->n_torsions = tot_torsions;
229	<	simnfo->n_SRI = tot_SRI;
230	<	simnfo->n_mol = tot_nmol;
430	>	have_extra =0;
431	>	if( temp2 < temp3 ){ // we have a non-complete lattice
432	>	have_extra =1;
433
434	<
435	<	#ifdef IS_MPI
434	>	n_cells = (int)temp3 - 1;
435	>	cellx = info[0].boxL[0] / temp3;
436	>	celly = info[0].boxL[1] / temp3;
437	>	cellz = info[0].boxL[2] / temp3;
438	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
439	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
440	>	n_per_extra = (int)ceil( temp1 );
441
442	<	// divide the molecules among processors here.
443	<
444	<	mpiSim = new mpiSimulation( simnfo );
445	<
446	<
442	>	if( n_per_extra > 4){
443	>	sprintf( painCave.errMsg,
444	>	"SimSetup error. There has been an error in constructing"
445	>	" the non-complete lattice.\n" );
446	>	painCave.isFatal = 1;
447	>	simError();
448	>	}
449	>	}
450	>	else{
451	>	n_cells = (int)temp3;
452	>	cellx = info[0].boxL[0] / temp3;
453	>	celly = info[0].boxL[1] / temp3;
454	>	cellz = info[0].boxL[2] / temp3;
455	>	}
456
457	<	globalIndex = mpiSim->divideLabor();
457	>	current_mol = 0;
458	>	current_comp_mol = 0;
459	>	current_comp = 0;
460	>	current_atom_ndx = 0;
461
462	<	// set up the local variables
463	<
464	<	int localMol, allMol;
246	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
462	>	for( i=0; i < n_cells ; i++ ){
463	>	for( j=0; j < n_cells; j++ ){
464	>	for( k=0; k < n_cells; k++ ){
465
466	<	int* mol2proc = mpiSim->getMolToProcMap();
467	<	int* molCompType = mpiSim->getMolComponentType();
468	<
251	<	allMol = 0;
252	<	localMol = 0;
253	<	local_atoms = 0;
254	<	local_bonds = 0;
255	<	local_bends = 0;
256	<	local_torsions = 0;
257	<	for( i=0; i<n_components; i++ ){
466	>	makeElement( i * cellx,
467	>	j * celly,
468	>	k * cellz );
469
470	<	for( j=0; j<components_nmol[i]; j++ ){
471	<
472	<	if( mol2proc[j] == worldRank ){
473	<
474	<	local_atoms +=    comp_stamps[i]->getNAtoms();
475	<	local_bonds +=    comp_stamps[i]->getNBonds();
476	<	local_bends +=    comp_stamps[i]->getNBends();
477	<	local_torsions += comp_stamps[i]->getNTorsions();
478	<	localMol++;
479	<	}
480	<	allMol++;
470	>	makeElement( i * cellx + 0.5 * cellx,
471	>	j * celly + 0.5 * celly,
472	>	k * cellz );
473	>
474	>	makeElement( i * cellx,
475	>	j * celly + 0.5 * celly,
476	>	k * cellz + 0.5 * cellz );
477	>
478	>	makeElement( i * cellx + 0.5 * cellx,
479	>	j * celly,
480	>	k * cellz + 0.5 * cellz );
481	>	}
482		}
483		}
272	–	local_SRI = local_bonds + local_bends + local_torsions;
273	–
484
485	<	simnfo->n_atoms = mpiSim->getMyNlocal();
486	<
277	<	if( local_atoms != simnfo->n_atoms ){
278	<	sprintf( painCave.errMsg,
279	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
280	<	" localAtom (%d) are not equal.\n",
281	<	simnfo->n_atoms,
282	<	local_atoms );
283	<	painCave.isFatal = 1;
284	<	simError();
285	<	}
485	>	if( have_extra ){
486	>	done = 0;
487
488	<	simnfo->n_bonds = local_bonds;
489	<	simnfo->n_bends = local_bends;
490	<	simnfo->n_torsions = local_torsions;
290	<	simnfo->n_SRI = local_SRI;
291	<	simnfo->n_mol = localMol;
488	>	int start_ndx;
489	>	for( i=0; i < (n_cells+1) && !done; i++ ){
490	>	for( j=0; j < (n_cells+1) && !done; j++ ){
491
492	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
294	<	MPIcheckPoint();
295	<
296	<
297	<	#endif // is_mpi
298	<
492	>	if( i < n_cells ){
493
494	<	// create the atom and short range interaction arrays
494	>	if( j < n_cells ){
495	>	start_ndx = n_cells;
496	>	}
497	>	else start_ndx = 0;
498	>	}
499	>	else start_ndx = 0;
500
501	<	Atom::createArrays(simnfo->n_atoms);
303	<	the_atoms = new Atom*[simnfo->n_atoms];
304	<	the_molecules = new Molecule[simnfo->n_mol];
305	<	int molIndex;
501	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
502
503	<	// initialize the molecule's stampID's
503	>	makeElement( i * cellx,
504	>	j * celly,
505	>	k * cellz );
506	>	done = ( current_mol >= tot_nmol );
507
508	<	#ifdef IS_MPI
509	<
508	>	if( !done && n_per_extra > 1 ){
509	>	makeElement( i * cellx + 0.5 * cellx,
510	>	j * celly + 0.5 * celly,
511	>	k * cellz );
512	>	done = ( current_mol >= tot_nmol );
513	>	}
514
515	<	molIndex = 0;
516	<	for(i=0; i<mpiSim->getTotNmol(); i++){
517	<
518	<	if(mol2proc[i] == worldRank ){
519	<	the_molecules[molIndex].setStampID( molCompType[i] );
520	<	molIndex++;
515	>	if( !done && n_per_extra > 2){
516	>	makeElement( i * cellx,
517	>	j * celly + 0.5 * celly,
518	>	k * cellz + 0.5 * cellz );
519	>	done = ( current_mol >= tot_nmol );
520	>	}
521	>
522	>	if( !done && n_per_extra > 3){
523	>	makeElement( i * cellx + 0.5 * cellx,
524	>	j * celly,
525	>	k * cellz + 0.5 * cellz );
526	>	done = ( current_mol >= tot_nmol );
527	>	}
528	>	}
529	>	}
530		}
531		}
532
533	<	#else // is_mpi
534	<
323	<	molIndex = 0;
324	<	for(i=0; i<n_components; i++){
325	<	for(j=0; j<components_nmol[i]; j++ ){
326	<	the_molecules[molIndex].setStampID( i );
327	<	molIndex++;
328	<	}
533	>	for( i=0; i<info[0].n_atoms; i++ ){
534	>	info[0].atoms[i]->setVel( vel );
535		}
536	<
536	>	}
537
538	<	#endif // is_mpi
538	>	void SimSetup::makeElement( double x, double y, double z ){
539
540	+	int k;
541	+	AtomStamp* current_atom;
542	+	DirectionalAtom* dAtom;
543	+	double rotMat[3][3];
544	+	double pos[3];
545
546	<	if( simnfo->n_SRI ){
546	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
547	>
548	>	current_atom = comp_stamps[current_comp]->getAtom( k );
549	>	if( !current_atom->havePosition() ){
550	>	sprintf( painCave.errMsg,
551	>	"SimSetup:initFromBass error.\n"
552	>	"\tComponent %s, atom %s does not have a position specified.\n"
553	>	"\tThe initialization routine is unable to give a start"
554	>	" position.\n",
555	>	comp_stamps[current_comp]->getID(),
556	>	current_atom->getType() );
557	>	painCave.isFatal = 1;
558	>	simError();
559	>	}
560
561	<	std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
561	>	pos[0] = x + current_atom->getPosX();
562	>	pos[1] = y + current_atom->getPosY();
563	>	pos[2] = z + current_atom->getPosZ();
564
565	<	Exclude::createArray(simnfo->n_SRI);
566	<	the_excludes = new Exclude*[simnfo->n_SRI];
567	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
568	<	simnfo->globalExcludes = new int;
569	<	simnfo->n_exclude = tot_SRI;
565	>	info[0].atoms[current_atom_ndx]->setPos( pos );
566	>
567	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
568	>
569	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
570	>
571	>	rotMat[0][0] = 1.0;
572	>	rotMat[0][1] = 0.0;
573	>	rotMat[0][2] = 0.0;
574	>
575	>	rotMat[1][0] = 0.0;
576	>	rotMat[1][1] = 1.0;
577	>	rotMat[1][2] = 0.0;
578	>
579	>	rotMat[2][0] = 0.0;
580	>	rotMat[2][1] = 0.0;
581	>	rotMat[2][2] = 1.0;
582	>
583	>	dAtom->setA( rotMat );
584	>	}
585	>
586	>	current_atom_ndx++;
587		}
588	<	else{
589	<
590	<	Exclude::createArray( 1 );
591	<	the_excludes = new Exclude*;
592	<	the_excludes[0] = new Exclude(0);
593	<	the_excludes[0]->setPair( 0,0 );
594	<	simnfo->globalExcludes = new int;
595	<	simnfo->globalExcludes[0] = 0;
353	<	simnfo->n_exclude = 0;
588	>
589	>	current_mol++;
590	>	current_comp_mol++;
591	>
592	>	if( current_comp_mol >= components_nmol[current_comp] ){
593	>
594	>	current_comp_mol = 0;
595	>	current_comp++;
596		}
597	+	}
598
356	–	// set the arrays into the SimInfo object
599
600	<	simnfo->atoms = the_atoms;
601	<	simnfo->molecules = the_molecules;
360	<	simnfo->nGlobalExcludes = 0;
361	<	simnfo->excludes = the_excludes;
600	>	void SimSetup::gatherInfo( void ){
601	>	int i,j,k;
602
603	+	ensembleCase = -1;
604	+	ffCase = -1;
605
606	<	// get some of the tricky things that may still be in the globals
606	>	// set the easy ones first
607
608	<
609	<	if( the_globals->haveBox() ){
610	<	simnfo->box_x = the_globals->getBox();
611	<	simnfo->box_y = the_globals->getBox();
370	<	simnfo->box_z = the_globals->getBox();
608	>	for( i=0; i<nInfo; i++){
609	>	info[i].target_temp = globals->getTargetTemp();
610	>	info[i].dt = globals->getDt();
611	>	info[i].run_time = globals->getRunTime();
612		}
613	<	else if( the_globals->haveDensity() ){
613	>	n_components = globals->getNComponents();
614
374	–	double vol;
375	–	vol = (double)tot_nmol / the_globals->getDensity();
376	–	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
377	–	simnfo->box_y = simnfo->box_x;
378	–	simnfo->box_z = simnfo->box_x;
379	–	}
380	–	else{
381	–	if( !the_globals->haveBoxX() ){
382	–	sprintf( painCave.errMsg,
383	–	"SimSetup error, no periodic BoxX size given.\n" );
384	–	painCave.isFatal = 1;
385	–	simError();
386	–	}
387	–	simnfo->box_x = the_globals->getBoxX();
615
616	<	if( !the_globals->haveBoxY() ){
390	<	sprintf( painCave.errMsg,
391	<	"SimSetup error, no periodic BoxY size given.\n" );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
395	<	simnfo->box_y = the_globals->getBoxY();
616	>	// get the forceField
617
618	<	if( !the_globals->haveBoxZ() ){
619	<	sprintf( painCave.errMsg,
620	<	"SimSetup error, no periodic BoxZ size given.\n" );
621	<	painCave.isFatal = 1;
622	<	simError();
623	<	}
624	<	simnfo->box_z = the_globals->getBoxZ();
618	>	strcpy( force_field, globals->getForceField() );
619	>
620	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
621	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
622	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
623	>	else{
624	>	sprintf( painCave.errMsg,
625	>	"SimSetup Error. Unrecognized force field -> %s\n",
626	>	force_field );
627	>	painCave.isFatal = 1;
628	>	simError();
629		}
630
631	<	#ifdef IS_MPI
407	<	strcpy( checkPointMsg, "Box size set up" );
408	<	MPIcheckPoint();
409	<	#endif // is_mpi
631	>	// get the ensemble
632
633	+	strcpy( ensemble, globals->getEnsemble() );
634
635	<	// initialize the arrays
635	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
636	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
637	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
638	>	ensembleCase = NPTi_ENS;
639	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
640	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
641	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
642
643	<	the_ff->setSimInfo( simnfo );
643	>	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
644	>	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
645	>	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS"))
646	>	ensembleCase = NPTiZCONS_ENS;
647	>	else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
648	>	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
649	>	else if( !strcasecmp( ensemble, "NPTfmZCONS"))  ensembleCase = NPTfmZCONS_ENS;
650	>
651	>	else{
652	>	sprintf( painCave.errMsg,
653	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
654	>	"reverting to NVE for this simulation.\n",
655	>	ensemble );
656	>	painCave.isFatal = 0;
657	>	simError();
658	>	strcpy( ensemble, "NVE" );
659	>	ensembleCase = NVE_ENS;
660	>	}
661	>
662	>	for(i=0; i<nInfo; i++){
663	>
664	>	strcpy( info[i].ensemble, ensemble );
665
666	<	makeMolecules();
667	<	simnfo->identArray = new int[simnfo->n_atoms];
668	<	for(i=0; i<simnfo->n_atoms; i++){
669	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
666	>	// get the mixing rule
667	>
668	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
669	>	info[i].usePBC = globals->getPBC();
670		}
671
672	<	if (the_globals->getUseRF() ) {
423	<	simnfo->useReactionField = 1;
424	<
425	<	if( !the_globals->haveECR() ){
426	<	sprintf( painCave.errMsg,
427	<	"SimSetup Warning: using default value of 1/2 the smallest "
428	<	"box length for the electrostaticCutoffRadius.\n"
429	<	"I hope you have a very fast processor!\n");
430	<	painCave.isFatal = 0;
431	<	simError();
432	<	double smallest;
433	<	smallest = simnfo->box_x;
434	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
435	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
436	<	simnfo->ecr = 0.5 * smallest;
437	<	} else {
438	<	simnfo->ecr        = the_globals->getECR();
439	<	}
440	<
441	<	if( !the_globals->haveEST() ){
442	<	sprintf( painCave.errMsg,
443	<	"SimSetup Warning: using default value of 0.05 * the "
444	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
445	<	);
446	<	painCave.isFatal = 0;
447	<	simError();
448	<	simnfo->est = 0.05 * simnfo->ecr;
449	<	} else {
450	<	simnfo->est        = the_globals->getEST();
451	<	}
452	<
453	<	if(!the_globals->haveDielectric() ){
454	<	sprintf( painCave.errMsg,
455	<	"SimSetup Error: You are trying to use Reaction Field without"
456	<	"setting a dielectric constant!\n"
457	<	);
458	<	painCave.isFatal = 1;
459	<	simError();
460	<	}
461	<	simnfo->dielectric = the_globals->getDielectric();
462	<	} else {
463	<	if (simnfo->n_dipoles) {
464	<
465	<	if( !the_globals->haveECR() ){
466	<	sprintf( painCave.errMsg,
467	<	"SimSetup Warning: using default value of 1/2 the smallest"
468	<	"box length for the electrostaticCutoffRadius.\n"
469	<	"I hope you have a very fast processor!\n");
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	double smallest;
473	<	smallest = simnfo->box_x;
474	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
475	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
476	<	simnfo->ecr = 0.5 * smallest;
477	<	} else {
478	<	simnfo->ecr        = the_globals->getECR();
479	<	}
480	<
481	<	if( !the_globals->haveEST() ){
482	<	sprintf( painCave.errMsg,
483	<	"SimSetup Warning: using default value of 5% of the"
484	<	"electrostaticCutoffRadius for the "
485	<	"electrostaticSkinThickness\n"
486	<	);
487	<	painCave.isFatal = 0;
488	<	simError();
489	<	simnfo->est = 0.05 * simnfo->ecr;
490	<	} else {
491	<	simnfo->est        = the_globals->getEST();
492	<	}
493	<	}
494	<	}
495	<
496	<	#ifdef IS_MPI
497	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
498	<	MPIcheckPoint();
499	<	#endif // is_mpi
500	<
501	<	if( the_globals->haveInitialConfig() ){
672	>	// get the components and calculate the tot_nMol and indvidual n_mol
673
674	<	InitializeFromFile* fileInit;
675	<	#ifdef IS_MPI // is_mpi
505	<	if( worldRank == 0 ){
506	<	#endif //is_mpi
507	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
508	<	#ifdef IS_MPI
509	<	}else fileInit = new InitializeFromFile( NULL );
510	<	#endif
511	<	fileInit->read_xyz( simnfo ); // default velocities on
674	>	the_components = globals->getComponents();
675	>	components_nmol = new int[n_components];
676
513	–	delete fileInit;
514	–	}
515	–	else{
677
678	<	#ifdef IS_MPI
678	>	if( !globals->haveNMol() ){
679	>	// we don't have the total number of molecules, so we assume it is
680	>	// given in each component
681
682	<	// no init from bass
683	<
521	<	sprintf( painCave.errMsg,
522	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
523	<	painCave.isFatal;
524	<	simError();
525	<
526	<	#else
682	>	tot_nmol = 0;
683	>	for( i=0; i<n_components; i++ ){
684
685	<	initFromBass();
685	>	if( !the_components[i]->haveNMol() ){
686	>	// we have a problem
687	>	sprintf( painCave.errMsg,
688	>	"SimSetup Error. No global NMol or component NMol"
689	>	" given. Cannot calculate the number of atoms.\n" );
690	>	painCave.isFatal = 1;
691	>	simError();
692	>	}
693
694	+	tot_nmol += the_components[i]->getNMol();
695	+	components_nmol[i] = the_components[i]->getNMol();
696	+	}
697	+	}
698	+	else{
699	+	sprintf( painCave.errMsg,
700	+	"SimSetup error.\n"
701	+	"\tSorry, the ability to specify total"
702	+	" nMols and then give molfractions in the components\n"
703	+	"\tis not currently supported."
704	+	" Please give nMol in the components.\n" );
705	+	painCave.isFatal = 1;
706	+	simError();
707	+	}
708
709	<	#endif
532	<	}
533	<
534	<	#ifdef IS_MPI
535	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
536	<	MPIcheckPoint();
537	<	#endif // is_mpi
538	<
539	<
540	<
541	<
709	>	// set the status, sample, and thermal kick times
710
711	+	for(i=0; i<nInfo; i++){
712
713	<
714	<	#ifdef IS_MPI
715	<	if( worldRank == 0 ){
716	<	#endif // is_mpi
548	<
549	<	if( the_globals->haveFinalConfig() ){
550	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
713	>	if( globals->haveSampleTime() ){
714	>	info[i].sampleTime = globals->getSampleTime();
715	>	info[i].statusTime = info[i].sampleTime;
716	>	info[i].thermalTime = info[i].sampleTime;
717		}
718		else{
719	<	strcpy( simnfo->finalName, inFileName );
720	<	char* endTest;
721	<	int nameLength = strlen( simnfo->finalName );
556	<	endTest = &(simnfo->finalName[nameLength - 5]);
557	<	if( !strcmp( endTest, ".bass" ) ){
558	<	strcpy( endTest, ".eor" );
559	<	}
560	<	else if( !strcmp( endTest, ".BASS" ) ){
561	<	strcpy( endTest, ".eor" );
562	<	}
563	<	else{
564	<	endTest = &(simnfo->finalName[nameLength - 4]);
565	<	if( !strcmp( endTest, ".bss" ) ){
566	<	strcpy( endTest, ".eor" );
567	<	}
568	<	else if( !strcmp( endTest, ".mdl" ) ){
569	<	strcpy( endTest, ".eor" );
570	<	}
571	<	else{
572	<	strcat( simnfo->finalName, ".eor" );
573	<	}
574	<	}
719	>	info[i].sampleTime = globals->getRunTime();
720	>	info[i].statusTime = info[i].sampleTime;
721	>	info[i].thermalTime = info[i].sampleTime;
722		}
723
724	<	// make the sample and status out names
724	>	if( globals->haveStatusTime() ){
725	>	info[i].statusTime = globals->getStatusTime();
726	>	}
727
728	<	strcpy( simnfo->sampleName, inFileName );
729	<	char* endTest;
581	<	int nameLength = strlen( simnfo->sampleName );
582	<	endTest = &(simnfo->sampleName[nameLength - 5]);
583	<	if( !strcmp( endTest, ".bass" ) ){
584	<	strcpy( endTest, ".dump" );
728	>	if( globals->haveThermalTime() ){
729	>	info[i].thermalTime = globals->getThermalTime();
730		}
731	<	else if( !strcmp( endTest, ".BASS" ) ){
732	<	strcpy( endTest, ".dump" );
731	>
732	>	// check for the temperature set flag
733	>
734	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
735	>
736	>	// get some of the tricky things that may still be in the globals
737	>
738	>	double boxVector[3];
739	>	if( globals->haveBox() ){
740	>	boxVector[0] = globals->getBox();
741	>	boxVector[1] = globals->getBox();
742	>	boxVector[2] = globals->getBox();
743	>
744	>	info[i].setBox( boxVector );
745		}
746	+	else if( globals->haveDensity() ){
747	+
748	+	double vol;
749	+	vol = (double)tot_nmol / globals->getDensity();
750	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
751	+	boxVector[1] = boxVector[0];
752	+	boxVector[2] = boxVector[0];
753	+
754	+	info[i].setBox( boxVector );
755	+	}
756		else{
757	<	endTest = &(simnfo->sampleName[nameLength - 4]);
758	<	if( !strcmp( endTest, ".bss" ) ){
759	<	strcpy( endTest, ".dump" );
757	>	if( !globals->haveBoxX() ){
758	>	sprintf( painCave.errMsg,
759	>	"SimSetup error, no periodic BoxX size given.\n" );
760	>	painCave.isFatal = 1;
761	>	simError();
762		}
763	<	else if( !strcmp( endTest, ".mdl" ) ){
764	<	strcpy( endTest, ".dump" );
765	<	}
766	<	else{
767	<	strcat( simnfo->sampleName, ".dump" );
768	<	}
769	<	}
601	<
602	<	strcpy( simnfo->statusName, inFileName );
603	<	nameLength = strlen( simnfo->statusName );
604	<	endTest = &(simnfo->statusName[nameLength - 5]);
605	<	if( !strcmp( endTest, ".bass" ) ){
606	<	strcpy( endTest, ".stat" );
607	<	}
608	<	else if( !strcmp( endTest, ".BASS" ) ){
609	<	strcpy( endTest, ".stat" );
610	<	}
611	<	else{
612	<	endTest = &(simnfo->statusName[nameLength - 4]);
613	<	if( !strcmp( endTest, ".bss" ) ){
614	<	strcpy( endTest, ".stat" );
763	>	boxVector[0] = globals->getBoxX();
764	>
765	>	if( !globals->haveBoxY() ){
766	>	sprintf( painCave.errMsg,
767	>	"SimSetup error, no periodic BoxY size given.\n" );
768	>	painCave.isFatal = 1;
769	>	simError();
770		}
771	<	else if( !strcmp( endTest, ".mdl" ) ){
772	<	strcpy( endTest, ".stat" );
771	>	boxVector[1] = globals->getBoxY();
772	>
773	>	if( !globals->haveBoxZ() ){
774	>	sprintf( painCave.errMsg,
775	>	"SimSetup error, no periodic BoxZ size given.\n" );
776	>	painCave.isFatal = 1;
777	>	simError();
778		}
779	<	else{
780	<	strcat( simnfo->statusName, ".stat" );
781	<	}
779	>	boxVector[2] = globals->getBoxZ();
780	>
781	>	info[i].setBox( boxVector );
782		}
783	+
784	+	}
785
786		#ifdef IS_MPI
787	<	}
787	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
788	>	MPIcheckPoint();
789		#endif // is_mpi
627	–
628	–	// set the status, sample, and themal kick times
629	–
630	–	if( the_globals->haveSampleTime() ){
631	–	simnfo->sampleTime = the_globals->getSampleTime();
632	–	simnfo->statusTime = simnfo->sampleTime;
633	–	simnfo->thermalTime = simnfo->sampleTime;
634	–	}
635	–	else{
636	–	simnfo->sampleTime = the_globals->getRunTime();
637	–	simnfo->statusTime = simnfo->sampleTime;
638	–	simnfo->thermalTime = simnfo->sampleTime;
639	–	}
790
791	<	if( the_globals->haveStatusTime() ){
642	<	simnfo->statusTime = the_globals->getStatusTime();
643	<	}
791	>	}
792
645	–	if( the_globals->haveThermalTime() ){
646	–	simnfo->thermalTime = the_globals->getThermalTime();
647	–	}
793
794	<	// check for the temperature set flag
794	>	void SimSetup::finalInfoCheck( void ){
795	>	int index;
796	>	int usesDipoles;
797	>	int i;
798
799	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
799	>	for(i=0; i<nInfo; i++){
800	>	// check electrostatic parameters
801	>
802	>	index = 0;
803	>	usesDipoles = 0;
804	>	while( (index < info[i].n_atoms) && !usesDipoles ){
805	>	usesDipoles = (info[i].atoms[index])->hasDipole();
806	>	index++;
807	>	}
808	>
809	>	#ifdef IS_MPI
810	>	int myUse = usesDipoles;
811	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
812	>	#endif //is_mpi
813	>
814	>	double theEcr, theEst;
815	>
816	>	if (globals->getUseRF() ) {
817	>	info[i].useReactionField = 1;
818	>
819	>	if( !globals->haveECR() ){
820	>	sprintf( painCave.errMsg,
821	>	"SimSetup Warning: using default value of 1/2 the smallest "
822	>	"box length for the electrostaticCutoffRadius.\n"
823	>	"I hope you have a very fast processor!\n");
824	>	painCave.isFatal = 0;
825	>	simError();
826	>	double smallest;
827	>	smallest = info[i].boxL[0];
828	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
829	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
830	>	theEcr = 0.5 * smallest;
831	>	} else {
832	>	theEcr = globals->getECR();
833	>	}
834	>
835	>	if( !globals->haveEST() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Warning: using default value of 0.05 * the "
838	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
839	>	);
840	>	painCave.isFatal = 0;
841	>	simError();
842	>	theEst = 0.05 * theEcr;
843	>	} else {
844	>	theEst= globals->getEST();
845	>	}
846	>
847	>	info[i].setEcr( theEcr, theEst );
848	>
849	>	if(!globals->haveDielectric() ){
850	>	sprintf( painCave.errMsg,
851	>	"SimSetup Error: You are trying to use Reaction Field without"
852	>	"setting a dielectric constant!\n"
853	>	);
854	>	painCave.isFatal = 1;
855	>	simError();
856	>	}
857	>	info[i].dielectric = globals->getDielectric();
858	>	}
859	>	else {
860	>	if (usesDipoles) {
861	>
862	>	if( !globals->haveECR() ){
863	>	sprintf( painCave.errMsg,
864	>	"SimSetup Warning: using default value of 1/2 the smallest "
865	>	"box length for the electrostaticCutoffRadius.\n"
866	>	"I hope you have a very fast processor!\n");
867	>	painCave.isFatal = 0;
868	>	simError();
869	>	double smallest;
870	>	smallest = info[i].boxL[0];
871	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
872	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
873	>	theEcr = 0.5 * smallest;
874	>	} else {
875	>	theEcr = globals->getECR();
876	>	}
877	>
878	>	if( !globals->haveEST() ){
879	>	sprintf( painCave.errMsg,
880	>	"SimSetup Warning: using default value of 0.05 * the "
881	>	"electrostaticCutoffRadius for the "
882	>	"electrostaticSkinThickness\n"
883	>	);
884	>	painCave.isFatal = 0;
885	>	simError();
886	>	theEst = 0.05 * theEcr;
887	>	} else {
888	>	theEst= globals->getEST();
889	>	}
890	>
891	>	info[i].setEcr( theEcr, theEst );
892	>	}
893	>	}
894	>	}
895
653	–
654	–	//   // make the longe range forces and the integrator
655	–
656	–	//   new AllLong( simnfo );
657	–
658	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
659	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
660	–
896		#ifdef IS_MPI
897	<	mpiSim->mpiRefresh();
898	<	#endif
897	>	strcpy( checkPointMsg, "post processing checks out" );
898	>	MPIcheckPoint();
899	>	#endif // is_mpi
900
901	<	// initialize the Fortran
901	>	}
902
903	+	void SimSetup::initSystemCoords( void ){
904	+	int i;
905	+
906	+	std::cerr << "Setting atom Coords\n";
907
908	<	simnfo->refreshSim();
908	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
909
910	<	if( !strcmp( simnfo->mixingRule, "standard") ){
911	<	the_ff->initForceField( LB_MIXING_RULE );
910	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
911	>
912	>	if( globals->haveInitialConfig() ){
913	>
914	>	InitializeFromFile* fileInit;
915	>	#ifdef IS_MPI // is_mpi
916	>	if( worldRank == 0 ){
917	>	#endif //is_mpi
918	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
919	>	#ifdef IS_MPI
920	>	}else fileInit = new InitializeFromFile( NULL );
921	>	#endif
922	>	fileInit->readInit( info ); // default velocities on
923	>
924	>	delete fileInit;
925		}
673	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
674	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
675	–	}
926		else{
927	+
928	+	#ifdef IS_MPI
929	+
930	+	// no init from bass
931	+
932		sprintf( painCave.errMsg,
933	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
934	<	simnfo->mixingRule );
680	<	painCave.isFatal = 1;
933	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
934	>	painCave.isFatal;
935		simError();
936	+
937	+	#else
938	+
939	+	initFromBass();
940	+
941	+
942	+	#endif
943		}
944	<
684	<
944	>
945		#ifdef IS_MPI
946	<	strcpy( checkPointMsg,
687	<	"Successfully intialized the mixingRule for Fortran." );
946	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
947		MPIcheckPoint();
948		#endif // is_mpi
949	+
950		}
951
952
953	<	void SimSetup::makeMolecules( void ){
694	<
695	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
696	<	molInit info;
697	<	DirectionalAtom* dAtom;
698	<	LinkedAssign* extras;
699	<	LinkedAssign* current_extra;
700	<	AtomStamp* currentAtom;
701	<	BondStamp* currentBond;
702	<	BendStamp* currentBend;
703	<	TorsionStamp* currentTorsion;
704	<
705	<	bond_pair* theBonds;
706	<	bend_set* theBends;
707	<	torsion_set* theTorsions;
708	<
953	>	void SimSetup::makeOutNames( void ){
954
955	<	//init the forceField paramters
955	>	int k;
956
712	–	the_ff->readParams();
713	–
957
958	<	// init the atoms
958	>	for(k=0; k<nInfo; k++){
959
960	<	double ux, uy, uz, u, uSqr;
961	<
962	<	atomOffset = 0;
720	<	excludeOffset = 0;
721	<	for(i=0; i<simnfo->n_mol; i++){
722	<
723	<	stampID = the_molecules[i].getStampID();
724	<
725	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
726	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
727	<	info.nBends    = comp_stamps[stampID]->getNBends();
728	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
729	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
730	<
731	<	info.myAtoms = &the_atoms[atomOffset];
732	<	info.myExcludes = &the_excludes[excludeOffset];
733	<	info.myBonds = new Bond*[info.nBonds];
734	<	info.myBends = new Bend*[info.nBends];
735	<	info.myTorsions = new Torsion*[info.nTorsions];
736	<
737	<	theBonds = new bond_pair[info.nBonds];
738	<	theBends = new bend_set[info.nBends];
739	<	theTorsions = new torsion_set[info.nTorsions];
740	<
741	<	// make the Atoms
742	<
743	<	for(j=0; j<info.nAtoms; j++){
960	>	#ifdef IS_MPI
961	>	if( worldRank == 0 ){
962	>	#endif // is_mpi
963
964	<	currentAtom = comp_stamps[stampID]->getAtom( j );
965	<	if( currentAtom->haveOrientation() ){
747	<
748	<	dAtom = new DirectionalAtom(j + atomOffset);
749	<	simnfo->n_oriented++;
750	<	info.myAtoms[j] = dAtom;
751	<
752	<	ux = currentAtom->getOrntX();
753	<	uy = currentAtom->getOrntY();
754	<	uz = currentAtom->getOrntZ();
755	<
756	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
757	<
758	<	u = sqrt( uSqr );
759	<	ux = ux / u;
760	<	uy = uy / u;
761	<	uz = uz / u;
762	<
763	<	dAtom->setSUx( ux );
764	<	dAtom->setSUy( uy );
765	<	dAtom->setSUz( uz );
964	>	if( globals->haveFinalConfig() ){
965	>	strcpy( info[k].finalName, globals->getFinalConfig() );
966		}
967		else{
968	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
968	>	strcpy( info[k].finalName, inFileName );
969	>	char* endTest;
970	>	int nameLength = strlen( info[k].finalName );
971	>	endTest = &(info[k].finalName[nameLength - 5]);
972	>	if( !strcmp( endTest, ".bass" ) ){
973	>	strcpy( endTest, ".eor" );
974	>	}
975	>	else if( !strcmp( endTest, ".BASS" ) ){
976	>	strcpy( endTest, ".eor" );
977	>	}
978	>	else{
979	>	endTest = &(info[k].finalName[nameLength - 4]);
980	>	if( !strcmp( endTest, ".bss" ) ){
981	>	strcpy( endTest, ".eor" );
982	>	}
983	>	else if( !strcmp( endTest, ".mdl" ) ){
984	>	strcpy( endTest, ".eor" );
985	>	}
986	>	else{
987	>	strcat( info[k].finalName, ".eor" );
988	>	}
989	>	}
990		}
770	–	info.myAtoms[j]->setType( currentAtom->getType() );
771	–
772	–	#ifdef IS_MPI
991
992	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
992	>	// make the sample and status out names
993
994	<	#endif // is_mpi
995	<	}
996	<
997	<	// make the bonds
998	<	for(j=0; j<info.nBonds; j++){
999	<
782	<	currentBond = comp_stamps[stampID]->getBond( j );
783	<	theBonds[j].a = currentBond->getA() + atomOffset;
784	<	theBonds[j].b = currentBond->getB() + atomOffset;
785	<
786	<	exI = theBonds[i].a;
787	<	exJ = theBonds[i].b;
788	<
789	<	// exclude_I must always be the smaller of the pair
790	<	if( exI > exJ ){
791	<	tempEx = exI;
792	<	exI = exJ;
793	<	exJ = tempEx;
994	>	strcpy( info[k].sampleName, inFileName );
995	>	char* endTest;
996	>	int nameLength = strlen( info[k].sampleName );
997	>	endTest = &(info[k].sampleName[nameLength - 5]);
998	>	if( !strcmp( endTest, ".bass" ) ){
999	>	strcpy( endTest, ".dump" );
1000		}
1001	<	#ifdef IS_MPI
1002	<	tempEx = exI;
1003	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1004	<	tempEx = exJ;
1005	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1006	<
1007	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
802	<	#else  // isn't MPI
803	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
804	<	#endif  //is_mpi
805	<	}
806	<	excludeOffset += info.nBonds;
807	<
808	<	//make the bends
809	<	for(j=0; j<info.nBends; j++){
810	<
811	<	currentBend = comp_stamps[stampID]->getBend( j );
812	<	theBends[j].a = currentBend->getA() + atomOffset;
813	<	theBends[j].b = currentBend->getB() + atomOffset;
814	<	theBends[j].c = currentBend->getC() + atomOffset;
815	<
816	<	if( currentBend->haveExtras() ){
817	<
818	<	extras = currentBend->getExtras();
819	<	current_extra = extras;
820	<
821	<	while( current_extra != NULL ){
822	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
823	<
824	<	switch( current_extra->getType() ){
825	<
826	<	case 0:
827	<	theBends[j].ghost =
828	<	current_extra->getInt() + atomOffset;
829	<	theBends[j].isGhost = 1;
830	<	break;
831	<
832	<	case 1:
833	<	theBends[j].ghost =
834	<	(int)current_extra->getDouble() + atomOffset;
835	<	theBends[j].isGhost = 1;
836	<	break;
837	<
838	<	default:
839	<	sprintf( painCave.errMsg,
840	<	"SimSetup Error: ghostVectorSource was neiter a "
841	<	"double nor an int.\n"
842	<	"-->Bend[%d] in %s\n",
843	<	j, comp_stamps[stampID]->getID() );
844	<	painCave.isFatal = 1;
845	<	simError();
846	<	}
847	<	}
848	<
849	<	else{
850	<
851	<	sprintf( painCave.errMsg,
852	<	"SimSetup Error: unhandled bend assignment:\n"
853	<	"    -->%s in Bend[%d] in %s\n",
854	<	current_extra->getlhs(),
855	<	j, comp_stamps[stampID]->getID() );
856	<	painCave.isFatal = 1;
857	<	simError();
858	<	}
859	<
860	<	current_extra = current_extra->getNext();
1001	>	else if( !strcmp( endTest, ".BASS" ) ){
1002	>	strcpy( endTest, ".dump" );
1003	>	}
1004	>	else{
1005	>	endTest = &(info[k].sampleName[nameLength - 4]);
1006	>	if( !strcmp( endTest, ".bss" ) ){
1007	>	strcpy( endTest, ".dump" );
1008		}
1009	+	else if( !strcmp( endTest, ".mdl" ) ){
1010	+	strcpy( endTest, ".dump" );
1011	+	}
1012	+	else{
1013	+	strcat( info[k].sampleName, ".dump" );
1014	+	}
1015		}
1016	<
1017	<	if( !theBends[j].isGhost ){
1018	<
1019	<	exI = theBends[j].a;
1020	<	exJ = theBends[j].c;
1016	>
1017	>	strcpy( info[k].statusName, inFileName );
1018	>	nameLength = strlen( info[k].statusName );
1019	>	endTest = &(info[k].statusName[nameLength - 5]);
1020	>	if( !strcmp( endTest, ".bass" ) ){
1021	>	strcpy( endTest, ".stat" );
1022		}
1023	+	else if( !strcmp( endTest, ".BASS" ) ){
1024	+	strcpy( endTest, ".stat" );
1025	+	}
1026		else{
1027	<
1028	<	exI = theBends[j].a;
1029	<	exJ = theBends[j].b;
1027	>	endTest = &(info[k].statusName[nameLength - 4]);
1028	>	if( !strcmp( endTest, ".bss" ) ){
1029	>	strcpy( endTest, ".stat" );
1030	>	}
1031	>	else if( !strcmp( endTest, ".mdl" ) ){
1032	>	strcpy( endTest, ".stat" );
1033	>	}
1034	>	else{
1035	>	strcat( info[k].statusName, ".stat" );
1036	>	}
1037		}
1038
875	–	// exclude_I must always be the smaller of the pair
876	–	if( exI > exJ ){
877	–	tempEx = exI;
878	–	exI = exJ;
879	–	exJ = tempEx;
880	–	}
1039		#ifdef IS_MPI
882	–	tempEx = exI;
883	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
884	–	tempEx = exJ;
885	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
886	–
887	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
888	–	#else  // isn't MPI
889	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
890	–	#endif  //is_mpi
1040		}
1041	<	excludeOffset += info.nBends;
1041	>	#endif // is_mpi
1042	>	}
1043	>	}
1044
894	–	for(j=0; j<info.nTorsions; j++){
895	–
896	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
897	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
898	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
899	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
900	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
901	–
902	–	exI = theTorsions[j].a;
903	–	exJ = theTorsions[j].d;
1045
1046	<	// exclude_I must always be the smaller of the pair
1047	<	if( exI > exJ ){
1048	<	tempEx = exI;
1049	<	exI = exJ;
1050	<	exJ = tempEx;
1051	<	}
1052	<	#ifdef IS_MPI
912	<	tempEx = exI;
913	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
914	<	tempEx = exJ;
915	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
916	<
917	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
918	<	#else  // isn't MPI
919	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
920	<	#endif  //is_mpi
921	<	}
922	<	excludeOffset += info.nTorsions;
1046	>	void SimSetup::sysObjectsCreation( void ){
1047	>
1048	>	int i,k;
1049	>
1050	>	// create the forceField
1051	>
1052	>	createFF();
1053
1054	<
925	<	// send the arrays off to the forceField for init.
1054	>	// extract componentList
1055
1056	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
928	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
929	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
930	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1056	>	compList();
1057
1058	+	// calc the number of atoms, bond, bends, and torsions
1059
1060	<	the_molecules[i].initialize( info );
934	<	atomOffset += info.nAtoms;
935	<	delete[] theBonds;
936	<	delete[] theBends;
937	<	delete[] theTorsions;
938	<	}
1060	>	calcSysValues();
1061
1062	<	// clean up the forcefield
1063	<	the_ff->calcRcut();
1064	<	the_ff->cleanMe();
1062	>	#ifdef IS_MPI
1063	>	// divide the molecules among the processors
1064	>
1065	>	mpiMolDivide();
1066	>	#endif //is_mpi
1067	>
1068	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1069	>
1070	>	makeSysArrays();
1071	>
1072	>	// make and initialize the molecules (all but atomic coordinates)
1073	>
1074	>	makeMolecules();
1075	>
1076	>	for(k=0; k<nInfo; k++){
1077	>	info[k].identArray = new int[info[k].n_atoms];
1078	>	for(i=0; i<info[k].n_atoms; i++){
1079	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1080	>	}
1081	>	}
1082		}
1083
945	–	void SimSetup::initFromBass( void ){
1084
1085	<	int i, j, k;
948	<	int n_cells;
949	<	double cellx, celly, cellz;
950	<	double temp1, temp2, temp3;
951	<	int n_per_extra;
952	<	int n_extra;
953	<	int have_extra, done;
1085	>	void SimSetup::createFF( void ){
1086
1087	<	temp1 = (double)tot_nmol / 4.0;
956	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
957	<	temp3 = ceil( temp2 );
1087	>	switch( ffCase ){
1088
1089	<	have_extra =0;
1090	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1091	<	have_extra =1;
1089	>	case FF_DUFF:
1090	>	the_ff = new DUFF();
1091	>	break;
1092
1093	<	n_cells = (int)temp3 - 1;
1094	<	cellx = simnfo->box_x / temp3;
1095	<	celly = simnfo->box_y / temp3;
966	<	cellz = simnfo->box_z / temp3;
967	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
968	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
969	<	n_per_extra = (int)ceil( temp1 );
1093	>	case FF_LJ:
1094	>	the_ff = new LJFF();
1095	>	break;
1096
1097	<	if( n_per_extra > 4){
1098	<	sprintf( painCave.errMsg,
1099	<	"SimSetup error. There has been an error in constructing"
1100	<	" the non-complete lattice.\n" );
1101	<	painCave.isFatal = 1;
1102	<	simError();
1103	<	}
1097	>	case FF_EAM:
1098	>	the_ff = new EAM_FF();
1099	>	break;
1100	>
1101	>	default:
1102	>	sprintf( painCave.errMsg,
1103	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1104	>	painCave.isFatal = 1;
1105	>	simError();
1106		}
979	–	else{
980	–	n_cells = (int)temp3;
981	–	cellx = simnfo->box_x / temp3;
982	–	celly = simnfo->box_y / temp3;
983	–	cellz = simnfo->box_z / temp3;
984	–	}
1107
1108	<	current_mol = 0;
1109	<	current_comp_mol = 0;
1110	<	current_comp = 0;
1111	<	current_atom_ndx = 0;
1108	>	#ifdef IS_MPI
1109	>	strcpy( checkPointMsg, "ForceField creation successful" );
1110	>	MPIcheckPoint();
1111	>	#endif // is_mpi
1112
1113	<	for( i=0; i < n_cells ; i++ ){
992	<	for( j=0; j < n_cells; j++ ){
993	<	for( k=0; k < n_cells; k++ ){
1113	>	}
1114
995	–	makeElement( i * cellx,
996	–	j * celly,
997	–	k * cellz );
1115
1116	<	makeElement( i * cellx + 0.5 * cellx,
1000	<	j * celly + 0.5 * celly,
1001	<	k * cellz );
1116	>	void SimSetup::compList( void ){
1117
1118	<	makeElement( i * cellx,
1119	<	j * celly + 0.5 * celly,
1120	<	k * cellz + 0.5 * cellz );
1118	>	int i;
1119	>	char* id;
1120	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1121	>	LinkedMolStamp* currentStamp = NULL;
1122	>	comp_stamps = new MoleculeStamp*[n_components];
1123	>
1124	>	// make an array of molecule stamps that match the components used.
1125	>	// also extract the used stamps out into a separate linked list
1126	>
1127	>	for(i=0; i<nInfo; i++){
1128	>	info[i].nComponents = n_components;
1129	>	info[i].componentsNmol = components_nmol;
1130	>	info[i].compStamps = comp_stamps;
1131	>	info[i].headStamp = headStamp;
1132	>	}
1133	>
1134
1135	<	makeElement( i * cellx + 0.5 * cellx,
1136	<	j * celly,
1137	<	k * cellz + 0.5 * cellz );
1135	>	for( i=0; i<n_components; i++ ){
1136	>
1137	>	id = the_components[i]->getType();
1138	>	comp_stamps[i] = NULL;
1139	>
1140	>	// check to make sure the component isn't already in the list
1141	>
1142	>	comp_stamps[i] = headStamp->match( id );
1143	>	if( comp_stamps[i] == NULL ){
1144	>
1145	>	// extract the component from the list;
1146	>
1147	>	currentStamp = stamps->extractMolStamp( id );
1148	>	if( currentStamp == NULL ){
1149	>	sprintf( painCave.errMsg,
1150	>	"SimSetup error: Component \"%s\" was not found in the "
1151	>	"list of declared molecules\n",
1152	>	id );
1153	>	painCave.isFatal = 1;
1154	>	simError();
1155		}
1156	+
1157	+	headStamp->add( currentStamp );
1158	+	comp_stamps[i] = headStamp->match( id );
1159		}
1160		}
1161
1162	<	if( have_extra ){
1163	<	done = 0;
1162	>	#ifdef IS_MPI
1163	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1164	>	MPIcheckPoint();
1165	>	#endif // is_mpi
1166
1017	–	int start_ndx;
1018	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1019	–	for( j=0; j < (n_cells+1) && !done; j++ ){
1167
1168	<	if( i < n_cells ){
1168	>	}
1169
1170	<	if( j < n_cells ){
1171	<	start_ndx = n_cells;
1172	<	}
1173	<	else start_ndx = 0;
1174	<	}
1175	<	else start_ndx = 0;
1176	<
1177	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1178	<
1179	<	makeElement( i * cellx,
1180	<	j * celly,
1181	<	k * cellz );
1182	<	done = ( current_mol >= tot_nmol );
1183	<
1184	<	if( !done && n_per_extra > 1 ){
1185	<	makeElement( i * cellx + 0.5 * cellx,
1186	<	j * celly + 0.5 * celly,
1187	<	k * cellz );
1188	<	done = ( current_mol >= tot_nmol );
1189	<	}
1170	>	void SimSetup::calcSysValues( void ){
1171	>	int i, j, k;
1172	>
1173	>	int *molMembershipArray;
1174	>
1175	>	tot_atoms = 0;
1176	>	tot_bonds = 0;
1177	>	tot_bends = 0;
1178	>	tot_torsions = 0;
1179	>	for( i=0; i<n_components; i++ ){
1180	>
1181	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1182	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1183	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1184	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1185	>	}
1186	>
1187	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1188	>	molMembershipArray = new int[tot_atoms];
1189	>
1190	>	for(i=0; i<nInfo; i++){
1191	>	info[i].n_atoms = tot_atoms;
1192	>	info[i].n_bonds = tot_bonds;
1193	>	info[i].n_bends = tot_bends;
1194	>	info[i].n_torsions = tot_torsions;
1195	>	info[i].n_SRI = tot_SRI;
1196	>	info[i].n_mol = tot_nmol;
1197	>
1198	>	info[i].molMembershipArray = molMembershipArray;
1199	>	}
1200	>	}
1201
1202	<	if( !done && n_per_extra > 2){
1045	<	makeElement( i * cellx,
1046	<	j * celly + 0.5 * celly,
1047	<	k * cellz + 0.5 * cellz );
1048	<	done = ( current_mol >= tot_nmol );
1049	<	}
1202	>	#ifdef IS_MPI
1203
1204	<	if( !done && n_per_extra > 3){
1205	<	makeElement( i * cellx + 0.5 * cellx,
1206	<	j * celly,
1207	<	k * cellz + 0.5 * cellz );
1208	<	done = ( current_mol >= tot_nmol );
1209	<	}
1210	<	}
1204	>	void SimSetup::mpiMolDivide( void ){
1205	>
1206	>	int i, j, k;
1207	>	int localMol, allMol;
1208	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1209	>
1210	>	mpiSim = new mpiSimulation( info );
1211	>
1212	>	globalIndex = mpiSim->divideLabor();
1213	>
1214	>	// set up the local variables
1215	>
1216	>	mol2proc = mpiSim->getMolToProcMap();
1217	>	molCompType = mpiSim->getMolComponentType();
1218	>
1219	>	allMol = 0;
1220	>	localMol = 0;
1221	>	local_atoms = 0;
1222	>	local_bonds = 0;
1223	>	local_bends = 0;
1224	>	local_torsions = 0;
1225	>	globalAtomIndex = 0;
1226	>
1227	>
1228	>	for( i=0; i<n_components; i++ ){
1229	>
1230	>	for( j=0; j<components_nmol[i]; j++ ){
1231	>
1232	>	if( mol2proc[allMol] == worldRank ){
1233	>
1234	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1235	>	local_bonds +=    comp_stamps[i]->getNBonds();
1236	>	local_bends +=    comp_stamps[i]->getNBends();
1237	>	local_torsions += comp_stamps[i]->getNTorsions();
1238	>	localMol++;
1239	>	}
1240	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1241	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1242	>	globalAtomIndex++;
1243		}
1244	+
1245	+	allMol++;
1246		}
1247		}
1248	+	local_SRI = local_bonds + local_bends + local_torsions;
1249	+
1250	+	info[0].n_atoms = mpiSim->getMyNlocal();
1251	+
1252	+	if( local_atoms != info[0].n_atoms ){
1253	+	sprintf( painCave.errMsg,
1254	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1255	+	" localAtom (%d) are not equal.\n",
1256	+	info[0].n_atoms,
1257	+	local_atoms );
1258	+	painCave.isFatal = 1;
1259	+	simError();
1260	+	}
1261
1262	+	info[0].n_bonds = local_bonds;
1263	+	info[0].n_bends = local_bends;
1264	+	info[0].n_torsions = local_torsions;
1265	+	info[0].n_SRI = local_SRI;
1266	+	info[0].n_mol = localMol;
1267
1268	<	for( i=0; i<simnfo->n_atoms; i++ ){
1269	<	simnfo->atoms[i]->set_vx( 0.0 );
1065	<	simnfo->atoms[i]->set_vy( 0.0 );
1066	<	simnfo->atoms[i]->set_vz( 0.0 );
1067	<	}
1268	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1269	>	MPIcheckPoint();
1270		}
1271	+
1272	+	#endif // is_mpi
1273
1070	–	void SimSetup::makeElement( double x, double y, double z ){
1274
1275	<	int k;
1276	<	AtomStamp* current_atom;
1074	<	DirectionalAtom* dAtom;
1075	<	double rotMat[3][3];
1275	>	void SimSetup::makeSysArrays( void ){
1276	>	int i, j, k, l;
1277
1278	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1278	>	Atom** the_atoms;
1279	>	Molecule* the_molecules;
1280	>	Exclude** the_excludes;
1281
1282	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1283	<	if( !current_atom->havePosition() ){
1284	<	sprintf( painCave.errMsg,
1285	<	"SimSetup:initFromBass error.\n"
1286	<	"\tComponent %s, atom %s does not have a position specified.\n"
1287	<	"\tThe initialization routine is unable to give a start"
1288	<	" position.\n",
1289	<	comp_stamps[current_comp]->getID(),
1290	<	current_atom->getType() );
1291	<	painCave.isFatal = 1;
1292	<	simError();
1282	>
1283	>	for(l=0; l<nInfo; l++){
1284	>
1285	>	// create the atom and short range interaction arrays
1286	>
1287	>	the_atoms = new Atom*[info[l].n_atoms];
1288	>	the_molecules = new Molecule[info[l].n_mol];
1289	>	int molIndex;
1290	>
1291	>	// initialize the molecule's stampID's
1292	>
1293	>	#ifdef IS_MPI
1294	>
1295	>
1296	>	molIndex = 0;
1297	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1298	>
1299	>	if(mol2proc[i] == worldRank ){
1300	>	the_molecules[molIndex].setStampID( molCompType[i] );
1301	>	the_molecules[molIndex].setMyIndex( molIndex );
1302	>	the_molecules[molIndex].setGlobalIndex( i );
1303	>	molIndex++;
1304	>	}
1305		}
1306	+
1307	+	#else // is_mpi
1308	+
1309	+	molIndex = 0;
1310	+	globalAtomIndex = 0;
1311	+	for(i=0; i<n_components; i++){
1312	+	for(j=0; j<components_nmol[i]; j++ ){
1313	+	the_molecules[molIndex].setStampID( i );
1314	+	the_molecules[molIndex].setMyIndex( molIndex );
1315	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1316	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1317	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1318	+	globalAtomIndex++;
1319	+	}
1320	+	molIndex++;
1321	+	}
1322	+	}
1323	+
1324	+
1325	+	#endif // is_mpi
1326
1092	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1093	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1094	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1327
1328	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1328	>	if( info[l].n_SRI ){
1329	>
1330	>	Exclude::createArray(info[l].n_SRI);
1331	>	the_excludes = new Exclude*[info[l].n_SRI];
1332	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1333	>	the_excludes[ex] = new Exclude(ex);
1334	>	}
1335	>	info[l].globalExcludes = new int;
1336	>	info[l].n_exclude = info[l].n_SRI;
1337	>	}
1338	>	else{
1339	>
1340	>	Exclude::createArray( 1 );
1341	>	the_excludes = new Exclude*;
1342	>	the_excludes[0] = new Exclude(0);
1343	>	the_excludes[0]->setPair( 0,0 );
1344	>	info[l].globalExcludes = new int;
1345	>	info[l].globalExcludes[0] = 0;
1346	>	info[l].n_exclude = 0;
1347	>	}
1348
1349	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1349	>	// set the arrays into the SimInfo object
1350
1351	<	rotMat[0][0] = 1.0;
1352	<	rotMat[0][1] = 0.0;
1353	<	rotMat[0][2] = 0.0;
1351	>	info[l].atoms = the_atoms;
1352	>	info[l].molecules = the_molecules;
1353	>	info[l].nGlobalExcludes = 0;
1354	>	info[l].excludes = the_excludes;
1355
1356	<	rotMat[1][0] = 0.0;
1357	<	rotMat[1][1] = 1.0;
1358	<	rotMat[1][2] = 0.0;
1356	>	the_ff->setSimInfo( info );
1357	>
1358	>	}
1359	>	}
1360
1361	<	rotMat[2][0] = 0.0;
1109	<	rotMat[2][1] = 0.0;
1110	<	rotMat[2][2] = 1.0;
1361	>	void SimSetup::makeIntegrator( void ){
1362
1363	<	dAtom->setA( rotMat );
1363	>	int k;
1364	>
1365	>	NVT<RealIntegrator>*  myNVT = NULL;
1366	>	NPTi<RealIntegrator>* myNPTi = NULL;
1367	>	NPTf<RealIntegrator>* myNPTf = NULL;
1368	>	NPTim<RealIntegrator>* myNPTim = NULL;
1369	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1370	>	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1371	>	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1372	>	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1373	>	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1374	>	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1375	>	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1376	>
1377	>	for(k=0; k<nInfo; k++){
1378	>
1379	>	switch( ensembleCase ){
1380	>
1381	>	case NVE_ENS:
1382	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1383	>	break;
1384	>
1385	>	case NVT_ENS:
1386	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1387	>	myNVT->setTargetTemp(globals->getTargetTemp());
1388	>
1389	>	if (globals->haveTauThermostat())
1390	>	myNVT->setTauThermostat(globals->getTauThermostat());
1391	>
1392	>	else {
1393	>	sprintf( painCave.errMsg,
1394	>	"SimSetup error: If you use the NVT\n"
1395	>	"    ensemble, you must set tauThermostat.\n");
1396	>	painCave.isFatal = 1;
1397	>	simError();
1398	>	}
1399	>	break;
1400	>
1401	>	case NPTi_ENS:
1402	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	>	else {
1408	>	sprintf( painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413	>	}
1414	>
1415	>	if( globals->haveTauThermostat() )
1416	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	>	else{
1418	>	sprintf( painCave.errMsg,
1419	>	"SimSetup error: If you use an NPT\n"
1420	>	"    ensemble, you must set tauThermostat.\n");
1421	>	painCave.isFatal = 1;
1422	>	simError();
1423	>	}
1424	>
1425	>	if( globals->haveTauBarostat() )
1426	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	>	else{
1428	>	sprintf( painCave.errMsg,
1429	>	"SimSetup error: If you use an NPT\n"
1430	>	"    ensemble, you must set tauBarostat.\n");
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433	>	}
1434	>	break;
1435	>
1436	>	case NPTf_ENS:
1437	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1438	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1439	>
1440	>	if (globals->haveTargetPressure())
1441	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	>	else {
1443	>	sprintf( painCave.errMsg,
1444	>	"SimSetup error: If you use a constant pressure\n"
1445	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1446	>	painCave.isFatal = 1;
1447	>	simError();
1448	>	}
1449	>
1450	>	if( globals->haveTauThermostat() )
1451	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1452	>	else{
1453	>	sprintf( painCave.errMsg,
1454	>	"SimSetup error: If you use an NPT\n"
1455	>	"    ensemble, you must set tauThermostat.\n");
1456	>	painCave.isFatal = 1;
1457	>	simError();
1458	>	}
1459	>
1460	>	if( globals->haveTauBarostat() )
1461	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1462	>	else{
1463	>	sprintf( painCave.errMsg,
1464	>	"SimSetup error: If you use an NPT\n"
1465	>	"    ensemble, you must set tauBarostat.\n");
1466	>	painCave.isFatal = 1;
1467	>	simError();
1468	>	}
1469	>	break;
1470	>
1471	>	case NPTim_ENS:
1472	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1473	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1474	>
1475	>	if (globals->haveTargetPressure())
1476	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1477	>	else {
1478	>	sprintf( painCave.errMsg,
1479	>	"SimSetup error: If you use a constant pressure\n"
1480	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1481	>	painCave.isFatal = 1;
1482	>	simError();
1483	>	}
1484	>
1485	>	if( globals->haveTauThermostat() )
1486	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1487	>	else{
1488	>	sprintf( painCave.errMsg,
1489	>	"SimSetup error: If you use an NPT\n"
1490	>	"    ensemble, you must set tauThermostat.\n");
1491	>	painCave.isFatal = 1;
1492	>	simError();
1493	>	}
1494	>
1495	>	if( globals->haveTauBarostat() )
1496	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1497	>	else{
1498	>	sprintf( painCave.errMsg,
1499	>	"SimSetup error: If you use an NPT\n"
1500	>	"    ensemble, you must set tauBarostat.\n");
1501	>	painCave.isFatal = 1;
1502	>	simError();
1503	>	}
1504	>	break;
1505	>
1506	>	case NPTfm_ENS:
1507	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1508	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1509	>
1510	>	if (globals->haveTargetPressure())
1511	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1512	>	else {
1513	>	sprintf( painCave.errMsg,
1514	>	"SimSetup error: If you use a constant pressure\n"
1515	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1516	>	painCave.isFatal = 1;
1517	>	simError();
1518	>	}
1519	>
1520	>	if( globals->haveTauThermostat() )
1521	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1522	>	else{
1523	>	sprintf( painCave.errMsg,
1524	>	"SimSetup error: If you use an NPT\n"
1525	>	"    ensemble, you must set tauThermostat.\n");
1526	>	painCave.isFatal = 1;
1527	>	simError();
1528	>	}
1529	>
1530	>	if( globals->haveTauBarostat() )
1531	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1532	>	else{
1533	>	sprintf( painCave.errMsg,
1534	>	"SimSetup error: If you use an NPT\n"
1535	>	"    ensemble, you must set tauBarostat.\n");
1536	>	painCave.isFatal = 1;
1537	>	simError();
1538	>	}
1539	>	break;
1540	>
1541	>	case NVEZCONS_ENS:
1542	>
1543	>
1544	>	//setup index of z-constraint molecules, z-constraint sampel time
1545	>	//and z-constraint force output name. These parameter should be known
1546	>	//before constructing the z-constraint integrator
1547	>	setupZConstraint();
1548	>
1549	>	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1550	>
1551	>	break;
1552	>
1553	>
1554	>	case NVTZCONS_ENS:
1555	>
1556	>	setupZConstraint();
1557	>
1558	>	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1559	>	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1560	>
1561	>	if (globals->haveTauThermostat())
1562	>	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1563	>
1564	>	else {
1565	>	sprintf( painCave.errMsg,
1566	>	"SimSetup error: If you use the NVT\n"
1567	>	"    ensemble, you must set tauThermostat.\n");
1568	>	painCave.isFatal = 1;
1569	>	simError();
1570	>	}
1571	>	break;
1572	>
1573	>	case NPTiZCONS_ENS:
1574	>
1575	>	setupZConstraint();
1576	>
1577	>	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1578	>	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1579	>
1580	>	if (globals->haveTargetPressure())
1581	>	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1582	>	else {
1583	>	sprintf( painCave.errMsg,
1584	>	"SimSetup error: If you use a constant pressure\n"
1585	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1586	>	painCave.isFatal = 1;
1587	>	simError();
1588	>	}
1589	>
1590	>	if( globals->haveTauThermostat() )
1591	>	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1592	>	else{
1593	>	sprintf( painCave.errMsg,
1594	>	"SimSetup error: If you use an NPT\n"
1595	>	"    ensemble, you must set tauThermostat.\n");
1596	>	painCave.isFatal = 1;
1597	>	simError();
1598	>	}
1599	>
1600	>	if( globals->haveTauBarostat() )
1601	>	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1602	>	else{
1603	>	sprintf( painCave.errMsg,
1604	>	"SimSetup error: If you use an NPT\n"
1605	>	"    ensemble, you must set tauBarostat.\n");
1606	>	painCave.isFatal = 1;
1607	>	simError();
1608	>	}
1609	>
1610	>	break;
1611	>
1612	>	case NPTfZCONS_ENS:
1613	>
1614	>	setupZConstraint();
1615	>
1616	>	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1617	>	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1618	>
1619	>	if (globals->haveTargetPressure())
1620	>	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1621	>	else {
1622	>	sprintf( painCave.errMsg,
1623	>	"SimSetup error: If you use a constant pressure\n"
1624	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1625	>	painCave.isFatal = 1;
1626	>	simError();
1627	>	}
1628	>
1629	>	if( globals->haveTauThermostat() )
1630	>	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1631	>	else{
1632	>	sprintf( painCave.errMsg,
1633	>	"SimSetup error: If you use an NPT\n"
1634	>	"    ensemble, you must set tauThermostat.\n");
1635	>	painCave.isFatal = 1;
1636	>	simError();
1637	>	}
1638	>
1639	>	if( globals->haveTauBarostat() )
1640	>	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1641	>	else{
1642	>	sprintf( painCave.errMsg,
1643	>	"SimSetup error: If you use an NPT\n"
1644	>	"    ensemble, you must set tauBarostat.\n");
1645	>	painCave.isFatal = 1;
1646	>	simError();
1647	>	}
1648	>
1649	>	break;
1650	>
1651	>	case NPTimZCONS_ENS:
1652	>
1653	>	setupZConstraint();
1654	>
1655	>	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1656	>	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1657	>
1658	>	if (globals->haveTargetPressure())
1659	>	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1660	>	else {
1661	>	sprintf( painCave.errMsg,
1662	>	"SimSetup error: If you use a constant pressure\n"
1663	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1664	>	painCave.isFatal = 1;
1665	>	simError();
1666	>	}
1667	>
1668	>	if( globals->haveTauThermostat() )
1669	>	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1670	>	else{
1671	>	sprintf( painCave.errMsg,
1672	>	"SimSetup error: If you use an NPT\n"
1673	>	"    ensemble, you must set tauThermostat.\n");
1674	>	painCave.isFatal = 1;
1675	>	simError();
1676	>	}
1677	>
1678	>	if( globals->haveTauBarostat() )
1679	>	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1680	>	else{
1681	>	sprintf( painCave.errMsg,
1682	>	"SimSetup error: If you use an NPT\n"
1683	>	"    ensemble, you must set tauBarostat.\n");
1684	>	painCave.isFatal = 1;
1685	>	simError();
1686	>	}
1687	>
1688	>	break;
1689	>
1690	>	case NPTfmZCONS_ENS:
1691	>
1692	>	setupZConstraint();
1693	>
1694	>	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1695	>	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1696	>
1697	>	if (globals->haveTargetPressure())
1698	>	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1699	>	else {
1700	>	sprintf( painCave.errMsg,
1701	>	"SimSetup error: If you use a constant pressure\n"
1702	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1703	>	painCave.isFatal = 1;
1704	>	simError();
1705	>	}
1706	>
1707	>	if( globals->haveTauThermostat() )
1708	>	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1709	>	else{
1710	>	sprintf( painCave.errMsg,
1711	>	"SimSetup error: If you use an NPT\n"
1712	>	"    ensemble, you must set tauThermostat.\n");
1713	>	painCave.isFatal = 1;
1714	>	simError();
1715	>	}
1716	>
1717	>	if( globals->haveTauBarostat() )
1718	>	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1719	>	else{
1720	>	sprintf( painCave.errMsg,
1721	>	"SimSetup error: If you use an NPT\n"
1722	>	"    ensemble, you must set tauBarostat.\n");
1723	>	painCave.isFatal = 1;
1724	>	simError();
1725	>	}
1726	>	break;
1727	>
1728	>
1729	>
1730	>	default:
1731	>	sprintf( painCave.errMsg,
1732	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1733	>	painCave.isFatal = 1;
1734	>	simError();
1735		}
1736	+	}
1737	+	}
1738
1739	<	current_atom_ndx++;
1739	>	void SimSetup::initFortran( void ){
1740	>
1741	>	info[0].refreshSim();
1742	>
1743	>	if( !strcmp( info[0].mixingRule, "standard") ){
1744	>	the_ff->initForceField( LB_MIXING_RULE );
1745		}
1746	+	else if( !strcmp( info[0].mixingRule, "explicit") ){
1747	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1748	+	}
1749	+	else{
1750	+	sprintf( painCave.errMsg,
1751	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1752	+	info[0].mixingRule );
1753	+	painCave.isFatal = 1;
1754	+	simError();
1755	+	}
1756
1118	–	current_mol++;
1119	–	current_comp_mol++;
1757
1758	<	if( current_comp_mol >= components_nmol[current_comp] ){
1758	>	#ifdef IS_MPI
1759	>	strcpy( checkPointMsg,
1760	>	"Successfully intialized the mixingRule for Fortran." );
1761	>	MPIcheckPoint();
1762	>	#endif // is_mpi
1763
1764	<	current_comp_mol = 0;
1765	<	current_comp++;
1764	>	}
1765	>
1766	>	void SimSetup::setupZConstraint()
1767	>	{
1768	>	int k;
1769	>
1770	>	for(k=0; k<nInfo; k++){
1771	>
1772	>	if(globals->haveZConsTime()){
1773	>
1774	>	//add sample time of z-constraint  into SimInfo's property list
1775	>	DoubleData* zconsTimeProp = new DoubleData();
1776	>	zconsTimeProp->setID("zconstime");
1777	>	zconsTimeProp->setData(globals->getZConsTime());
1778	>	info[k].addProperty(zconsTimeProp);
1779	>	}
1780	>	else{
1781	>	sprintf( painCave.errMsg,
1782	>	"ZConstraint error: If you use an ZConstraint\n"
1783	>	" , you must set sample time.\n");
1784	>	painCave.isFatal = 1;
1785	>	simError();
1786	>	}
1787	>
1788	>	if(globals->haveIndexOfAllZConsMols()){
1789	>
1790	>	//add index of z-constraint molecules into SimInfo's property list
1791	>	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1792	>
1793	>	//sort the index
1794	>	sort(tempIndex.begin(), tempIndex.end());
1795	>
1796	>	IndexData* zconsIndex = new IndexData();
1797	>	zconsIndex->setID("zconsindex");
1798	>	zconsIndex->setIndexData(tempIndex);
1799	>	info[k].addProperty(zconsIndex);
1800	>	}
1801	>	else{
1802	>	sprintf( painCave.errMsg,
1803	>	"SimSetup error: If you use an ZConstraint\n"
1804	>	" , you must set index of z-constraint molecules.\n");
1805	>	painCave.isFatal = 1;
1806	>	simError();
1807	>
1808	>	}
1809	>
1810	>	//Determine the name of ouput file and add it into SimInfo's property list
1811	>	//Be careful, do not use inFileName, since it is a pointer which
1812	>	//point to a string at master node, and slave nodes do not contain that string
1813	>
1814	>	string zconsOutput(info[k].finalName);
1815	>
1816	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1817	>
1818	>	StringData* zconsFilename = new StringData();
1819	>	zconsFilename->setID("zconsfilename");
1820	>	zconsFilename->setData(zconsOutput);
1821	>
1822	>	info[k].addProperty(zconsFilename);
1823		}
1824		}

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