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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 614 by mmeineke, Tue Jul 15 17:57:04 2003 UTC vs.
Revision 707 by mmeineke, Wed Aug 20 19:42:31 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 "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 14 | Line 17
17
18		// some defines for ensemble and Forcefield  cases
19
20	<	#define NVE_ENS   0
21	<	#define NVT_ENS   1
22	<	#define NPTi_ENS  2
23	<	#define NPTf_ENS  3
24	<	#define NPTim_ENS 4
25	<	#define NPTfm_ENS 5
20	>	#define NVE_ENS        0
21	>	#define NVT_ENS        1
22	>	#define NPTi_ENS       2
23	>	#define NPTf_ENS       3
24	>	#define NPTim_ENS      4
25	>	#define NPTfm_ENS      5
26
24	–
27		#define FF_DUFF 0
28		#define FF_LJ   1
29	+	#define FF_EAM  2
30
31	+	using namespace std;
32
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 41 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 76 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
81	–	MakeStamps *the_stamps;
82	–	Globals* the_globals;
97		int i, j, k, globalAtomIndex;
98
99		// gather all of the information from the Bass file
100	<
100	>
101		gatherInfo();
102
103		// creation of complex system objects
104
105		sysObjectsCreation();
106
93	–
94	–
95	–	// initialize the arrays
96	–
97	–
98	–
99	–	makeMolecules();
100	–	info->identArray = new int[info->n_atoms];
101	–	for(i=0; i<info->n_atoms; i++){
102	–	info->identArray[i] = the_atoms[i]->getIdent();
103	–	}
104	–
105	–
107		// check on the post processing info
108	<
108	>
109		finalInfoCheck();
110
110	–
111	–
112	–
111		// initialize the system coordinates
112
113	<	initSystemCoords();
116	<
113	>	if( !isInfoArray ) initSystemCoords();
114
115		// make the output filenames
116
117		makeOutNames();
118
122	–
123	–
124	–
125	–
126	–
127	–
128	–
129	–
119		// make the integrator
120
121	+	makeIntegrator();
122
133	–	NVT*  myNVT = NULL;
134	–	NPTi* myNPTi = NULL;
135	–	NPTf* myNPTf = NULL;
136	–	NPTim* myNPTim = NULL;
137	–	NPTfm* myNPTfm = NULL;
138	–
139	–	switch( ensembleCase ){
140	–
141	–	case NVE_ENS:
142	–	new NVE( info, the_ff );
143	–	break;
144	–
145	–	case NVT_ENS:
146	–	myNVT = new NVT( info, the_ff );
147	–	myNVT->setTargetTemp(the_globals->getTargetTemp());
148	–
149	–	if (the_globals->haveTauThermostat())
150	–	myNVT->setTauThermostat(the_globals->getTauThermostat());
151	–
152	–	else {
153	–	sprintf( painCave.errMsg,
154	–	"SimSetup error: If you use the NVT\n"
155	–	"    ensemble, you must set tauThermostat.\n");
156	–	painCave.isFatal = 1;
157	–	simError();
158	–	}
159	–	break;
160	–
161	–	case NPTi_ENS:
162	–	myNPTi = new NPTi( info, the_ff );
163	–	myNPTi->setTargetTemp( the_globals->getTargetTemp() );
164	–
165	–	if (the_globals->haveTargetPressure())
166	–	myNPTi->setTargetPressure(the_globals->getTargetPressure());
167	–	else {
168	–	sprintf( painCave.errMsg,
169	–	"SimSetup error: If you use a constant pressure\n"
170	–	"    ensemble, you must set targetPressure in the BASS file.\n");
171	–	painCave.isFatal = 1;
172	–	simError();
173	–	}
174	–
175	–	if( the_globals->haveTauThermostat() )
176	–	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
177	–	else{
178	–	sprintf( painCave.errMsg,
179	–	"SimSetup error: If you use an NPT\n"
180	–	"    ensemble, you must set tauThermostat.\n");
181	–	painCave.isFatal = 1;
182	–	simError();
183	–	}
184	–
185	–	if( the_globals->haveTauBarostat() )
186	–	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
187	–	else{
188	–	sprintf( painCave.errMsg,
189	–	"SimSetup error: If you use an NPT\n"
190	–	"    ensemble, you must set tauBarostat.\n");
191	–	painCave.isFatal = 1;
192	–	simError();
193	–	}
194	–	break;
195	–
196	–	case NPTf_ENS:
197	–	myNPTf = new NPTf( info, the_ff );
198	–	myNPTf->setTargetTemp( the_globals->getTargetTemp());
199	–
200	–	if (the_globals->haveTargetPressure())
201	–	myNPTf->setTargetPressure(the_globals->getTargetPressure());
202	–	else {
203	–	sprintf( painCave.errMsg,
204	–	"SimSetup error: If you use a constant pressure\n"
205	–	"    ensemble, you must set targetPressure in the BASS file.\n");
206	–	painCave.isFatal = 1;
207	–	simError();
208	–	}
209	–
210	–	if( the_globals->haveTauThermostat() )
211	–	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
212	–	else{
213	–	sprintf( painCave.errMsg,
214	–	"SimSetup error: If you use an NPT\n"
215	–	"    ensemble, you must set tauThermostat.\n");
216	–	painCave.isFatal = 1;
217	–	simError();
218	–	}
219	–
220	–	if( the_globals->haveTauBarostat() )
221	–	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
222	–	else{
223	–	sprintf( painCave.errMsg,
224	–	"SimSetup error: If you use an NPT\n"
225	–	"    ensemble, you must set tauBarostat.\n");
226	–	painCave.isFatal = 1;
227	–	simError();
228	–	}
229	–	break;
230	–
231	–	case NPTim_ENS:
232	–	myNPTim = new NPTim( info, the_ff );
233	–	myNPTim->setTargetTemp( the_globals->getTargetTemp());
234	–
235	–	if (the_globals->haveTargetPressure())
236	–	myNPTim->setTargetPressure(the_globals->getTargetPressure());
237	–	else {
238	–	sprintf( painCave.errMsg,
239	–	"SimSetup error: If you use a constant pressure\n"
240	–	"    ensemble, you must set targetPressure in the BASS file.\n");
241	–	painCave.isFatal = 1;
242	–	simError();
243	–	}
244	–
245	–	if( the_globals->haveTauThermostat() )
246	–	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
247	–	else{
248	–	sprintf( painCave.errMsg,
249	–	"SimSetup error: If you use an NPT\n"
250	–	"    ensemble, you must set tauThermostat.\n");
251	–	painCave.isFatal = 1;
252	–	simError();
253	–	}
254	–
255	–	if( the_globals->haveTauBarostat() )
256	–	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
257	–	else{
258	–	sprintf( painCave.errMsg,
259	–	"SimSetup error: If you use an NPT\n"
260	–	"    ensemble, you must set tauBarostat.\n");
261	–	painCave.isFatal = 1;
262	–	simError();
263	–	}
264	–	break;
265	–
266	–	case NPTfm_ENS:
267	–	myNPTfm = new NPTfm( info, the_ff );
268	–	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
269	–
270	–	if (the_globals->haveTargetPressure())
271	–	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
272	–	else {
273	–	sprintf( painCave.errMsg,
274	–	"SimSetup error: If you use a constant pressure\n"
275	–	"    ensemble, you must set targetPressure in the BASS file.\n");
276	–	painCave.isFatal = 1;
277	–	simError();
278	–	}
279	–
280	–	if( the_globals->haveTauThermostat() )
281	–	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
282	–	else{
283	–	sprintf( painCave.errMsg,
284	–	"SimSetup error: If you use an NPT\n"
285	–	"    ensemble, you must set tauThermostat.\n");
286	–	painCave.isFatal = 1;
287	–	simError();
288	–	}
289	–
290	–	if( the_globals->haveTauBarostat() )
291	–	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
292	–	else{
293	–	sprintf( painCave.errMsg,
294	–	"SimSetup error: If you use an NPT\n"
295	–	"    ensemble, you must set tauBarostat.\n");
296	–	painCave.isFatal = 1;
297	–	simError();
298	–	}
299	–	break;
300	–
301	–	default:
302	–	sprintf( painCave.errMsg,
303	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
304	–	painCave.isFatal = 1;
305	–	simError();
306	–	}
307	–
308	–
123		#ifdef IS_MPI
124		mpiSim->mpiRefresh();
125		#endif
126
127		// initialize the Fortran
128
129	+	initFortran();
130
316	–	info->refreshSim();
317	–
318	–	if( !strcmp( info->mixingRule, "standard") ){
319	–	the_ff->initForceField( LB_MIXING_RULE );
320	–	}
321	–	else if( !strcmp( info->mixingRule, "explicit") ){
322	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
323	–	}
324	–	else{
325	–	sprintf( painCave.errMsg,
326	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
327	–	info->mixingRule );
328	–	painCave.isFatal = 1;
329	–	simError();
330	–	}
131
132
333	–	#ifdef IS_MPI
334	–	strcpy( checkPointMsg,
335	–	"Successfully intialized the mixingRule for Fortran." );
336	–	MPIcheckPoint();
337	–	#endif // is_mpi
133		}
134
135
136		void SimSetup::makeMolecules( void ){
137
138	+	int k,l;
139		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	<	molInit info;
140	>	molInit molInfo;
141		DirectionalAtom* dAtom;
142		LinkedAssign* extras;
143		LinkedAssign* current_extra;
#	Line 364 | Line 160 | void SimSetup::makeMolecules( void ){
160
161		double ux, uy, uz, u, uSqr;
162
163	<	atomOffset = 0;
368	<	excludeOffset = 0;
369	<	for(i=0; i<info->n_mol; i++){
163	>	for(k=0; k<nInfo; k++){
164
165	<	stampID = the_molecules[i].getStampID();
165	>	the_ff->setSimInfo( &(info[k]) );
166
167	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
168	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
169	<	info.nBends    = comp_stamps[stampID]->getNBends();
170	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
171	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
378	<
379	<	info.myAtoms = &the_atoms[atomOffset];
380	<	info.myExcludes = &the_excludes[excludeOffset];
381	<	info.myBonds = new Bond*[info.nBonds];
382	<	info.myBends = new Bend*[info.nBends];
383	<	info.myTorsions = new Torsion*[info.nTorsions];
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for(i=0; i<info[k].n_mol; i++){
170	>
171	>	stampID = info[k].molecules[i].getStampID();
172
173	<	theBonds = new bond_pair[info.nBonds];
174	<	theBends = new bend_set[info.nBends];
175	<	theTorsions = new torsion_set[info.nTorsions];
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178	>
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184	>
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188
189	<	// make the Atoms
189	>	// make the Atoms
190
191	<	for(j=0; j<info.nAtoms; j++){
192	<
193	<	currentAtom = comp_stamps[stampID]->getAtom( j );
194	<	if( currentAtom->haveOrientation() ){
395	<
396	<	dAtom = new DirectionalAtom(j + atomOffset);
397	<	info->n_oriented++;
398	<	info.myAtoms[j] = dAtom;
399	<
400	<	ux = currentAtom->getOrntX();
401	<	uy = currentAtom->getOrntY();
402	<	uz = currentAtom->getOrntZ();
403	<
404	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
405	<
406	<	u = sqrt( uSqr );
407	<	ux = ux / u;
408	<	uy = uy / u;
409	<	uz = uz / u;
410	<
411	<	dAtom->setSUx( ux );
412	<	dAtom->setSUy( uy );
413	<	dAtom->setSUz( uz );
414	<	}
415	<	else{
416	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
417	<	}
418	<	info.myAtoms[j]->setType( currentAtom->getType() );
191	>	for(j=0; j<molInfo.nAtoms; j++){
192	>
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195
196	+	dAtom = new DirectionalAtom( (j + atomOffset),
197	+	info[k].getConfiguration() );
198	+	info[k].n_oriented++;
199	+	molInfo.myAtoms[j] = dAtom;
200	+
201	+	ux = currentAtom->getOrntX();
202	+	uy = currentAtom->getOrntY();
203	+	uz = currentAtom->getOrntZ();
204	+
205	+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	+
207	+	u = sqrt( uSqr );
208	+	ux = ux / u;
209	+	uy = uy / u;
210	+	uz = uz / u;
211	+
212	+	dAtom->setSUx( ux );
213	+	dAtom->setSUy( uy );
214	+	dAtom->setSUz( uz );
215	+	}
216	+	else{
217	+	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	+	info[k].getConfiguration() );
219	+	}
220	+	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	+
222		#ifdef IS_MPI
223
224	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225
226		#endif // is_mpi
227	<	}
227	>	}
228
229		// make the bonds
230	<	for(j=0; j<info.nBonds; j++){
230	>	for(j=0; j<molInfo.nBonds; j++){
231
232	<	currentBond = comp_stamps[stampID]->getBond( j );
233	<	theBonds[j].a = currentBond->getA() + atomOffset;
234	<	theBonds[j].b = currentBond->getB() + atomOffset;
235	<
236	<	exI = theBonds[j].a;
237	<	exJ = theBonds[j].b;
238	<
239	<	// exclude_I must always be the smaller of the pair
240	<	if( exI > exJ ){
241	<	tempEx = exI;
242	<	exI = exJ;
243	<	exJ = tempEx;
244	<	}
232	>	currentBond = comp_stamps[stampID]->getBond( j );
233	>	theBonds[j].a = currentBond->getA() + atomOffset;
234	>	theBonds[j].b = currentBond->getB() + atomOffset;
235	>
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244	>	}
245		#ifdef IS_MPI
246	<	tempEx = exI;
247	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
248	<	tempEx = exJ;
249	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
250	<
251	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
246	>	tempEx = exI;
247	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	>	tempEx = exJ;
249	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	>
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252		#else  // isn't MPI
253	<
254	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
253	>
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255		#endif  //is_mpi
454	–	}
455	–	excludeOffset += info.nBonds;
456	–
457	–	//make the bends
458	–	for(j=0; j<info.nBends; j++){
459	–
460	–	currentBend = comp_stamps[stampID]->getBend( j );
461	–	theBends[j].a = currentBend->getA() + atomOffset;
462	–	theBends[j].b = currentBend->getB() + atomOffset;
463	–	theBends[j].c = currentBend->getC() + atomOffset;
464	–
465	–	if( currentBend->haveExtras() ){
466	–
467	–	extras = currentBend->getExtras();
468	–	current_extra = extras;
469	–
470	–	while( current_extra != NULL ){
471	–	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
472	–
473	–	switch( current_extra->getType() ){
474	–
475	–	case 0:
476	–	theBends[j].ghost =
477	–	current_extra->getInt() + atomOffset;
478	–	theBends[j].isGhost = 1;
479	–	break;
480	–
481	–	case 1:
482	–	theBends[j].ghost =
483	–	(int)current_extra->getDouble() + atomOffset;
484	–	theBends[j].isGhost = 1;
485	–	break;
486	–
487	–	default:
488	–	sprintf( painCave.errMsg,
489	–	"SimSetup Error: ghostVectorSource was neither a "
490	–	"double nor an int.\n"
491	–	"-->Bend[%d] in %s\n",
492	–	j, comp_stamps[stampID]->getID() );
493	–	painCave.isFatal = 1;
494	–	simError();
495	–	}
496	–	}
497	–
498	–	else{
499	–
500	–	sprintf( painCave.errMsg,
501	–	"SimSetup Error: unhandled bend assignment:\n"
502	–	"    -->%s in Bend[%d] in %s\n",
503	–	current_extra->getlhs(),
504	–	j, comp_stamps[stampID]->getID() );
505	–	painCave.isFatal = 1;
506	–	simError();
507	–	}
508	–
509	–	current_extra = current_extra->getNext();
510	–	}
256		}
257	<
513	<	if( !theBends[j].isGhost ){
514	<
515	<	exI = theBends[j].a;
516	<	exJ = theBends[j].c;
517	<	}
518	<	else{
519	<
520	<	exI = theBends[j].a;
521	<	exJ = theBends[j].b;
522	<	}
257	>	excludeOffset += molInfo.nBonds;
258
259	<	// exclude_I must always be the smaller of the pair
260	<	if( exI > exJ ){
261	<	tempEx = exI;
262	<	exI = exJ;
263	<	exJ = tempEx;
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261	>
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266	>
267	>	if( currentBend->haveExtras() ){
268	>
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276	>
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290	>	sprintf( painCave.errMsg,
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298		}
530	–	#ifdef IS_MPI
531	–	tempEx = exI;
532	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
533	–	tempEx = exJ;
534	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
299
300	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
301	<	#else  // isn't MPI
302	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
303	<	#endif  //is_mpi
300	>	else{
301	>
302	>	sprintf( painCave.errMsg,
303	>	"SimSetup Error: unhandled bend assignment:\n"
304	>	"    -->%s in Bend[%d] in %s\n",
305	>	current_extra->getlhs(),
306	>	j, comp_stamps[stampID]->getID() );
307	>	painCave.isFatal = 1;
308	>	simError();
309	>	}
310	>
311	>	current_extra = current_extra->getNext();
312		}
313	<	excludeOffset += info.nBends;
314	<
315	<	for(j=0; j<info.nTorsions; j++){
313	>	}
314	>
315	>	if( !theBends[j].isGhost ){
316	>
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].c;
319	>	}
320	>	else{
321	>
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].b;
324	>	}
325	>
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331	>	}
332	>	#ifdef IS_MPI
333	>	tempEx = exI;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337
338	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
339	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
340	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
341	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
549	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
550	<
551	<	exI = theTorsions[j].a;
552	<	exJ = theTorsions[j].d;
553	<
554	<	// exclude_I must always be the smaller of the pair
555	<	if( exI > exJ ){
556	<	tempEx = exI;
557	<	exI = exJ;
558	<	exJ = tempEx;
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	#else  // isn't MPI
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	#endif  //is_mpi
342		}
343	<	#ifdef IS_MPI
561	<	tempEx = exI;
562	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
563	<	tempEx = exJ;
564	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
343	>	excludeOffset += molInfo.nBends;
344
345	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
345	>	for(j=0; j<molInfo.nTorsions; j++){
346	>
347	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352	>
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355	>
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361	>	}
362	>	#ifdef IS_MPI
363	>	tempEx = exI;
364	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	>	tempEx = exJ;
366	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	>
368	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369		#else  // isn't MPI
370	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371		#endif  //is_mpi
372	<	}
373	<	excludeOffset += info.nTorsions;
372	>	}
373	>	excludeOffset += molInfo.nTorsions;
374	>
375	>
376	>	// send the arrays off to the forceField for init.
377	>
378	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	>
383	>
384	>	info[k].molecules[i].initialize( molInfo );
385
386	<
387	<	// send the arrays off to the forceField for init.
388	<
389	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
390	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
391	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
579	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
580	<
581	<
582	<	the_molecules[i].initialize( info );
583	<
584	<
585	<	atomOffset += info.nAtoms;
586	<	delete[] theBonds;
587	<	delete[] theBends;
588	<	delete[] theTorsions;
386	>
387	>	atomOffset += molInfo.nAtoms;
388	>	delete[] theBonds;
389	>	delete[] theBends;
390	>	delete[] theTorsions;
391	>	}
392		}
393	<
393	>
394		#ifdef IS_MPI
395		sprintf( checkPointMsg, "all molecules initialized succesfully" );
396		MPIcheckPoint();
397		#endif // is_mpi
398	<
398	>
399		// clean up the forcefield
400	+
401		the_ff->calcRcut();
402		the_ff->cleanMe();
403	<
403	>
404		}
405
406		void SimSetup::initFromBass( void ){
#	Line 609 | Line 413 | void SimSetup::initFromBass( void ){
413		int n_extra;
414		int have_extra, done;
415
416	+	double vel[3];
417	+	vel[0] = 0.0;
418	+	vel[1] = 0.0;
419	+	vel[2] = 0.0;
420	+
421		temp1 = (double)tot_nmol / 4.0;
422		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423		temp3 = ceil( temp2 );
#	Line 618 | Line 427 | void SimSetup::initFromBass( void ){
427		have_extra =1;
428
429		n_cells = (int)temp3 - 1;
430	<	cellx = info->boxLx / temp3;
431	<	celly = info->boxLy / temp3;
432	<	cellz = info->boxLz / temp3;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435		n_per_extra = (int)ceil( temp1 );
436
437		if( n_per_extra > 4){
438		sprintf( painCave.errMsg,
439	<	"SimSetup error. There has been an error in constructing"
440	<	" the non-complete lattice.\n" );
439	>	"SimSetup error. There has been an error in constructing"
440	>	" the non-complete lattice.\n" );
441		painCave.isFatal = 1;
442		simError();
443		}
444		}
445		else{
446		n_cells = (int)temp3;
447	<	cellx = info->boxLx / temp3;
448	<	celly = info->boxLy / temp3;
449	<	cellz = info->boxLz / temp3;
447	>	cellx = info[0].boxL[0] / temp3;
448	>	celly = info[0].boxL[1] / temp3;
449	>	cellz = info[0].boxL[2] / temp3;
450		}
451
452		current_mol = 0;
#	Line 649 | Line 458 | void SimSetup::initFromBass( void ){
458		for( j=0; j < n_cells; j++ ){
459		for( k=0; k < n_cells; k++ ){
460
461	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
461	>	makeElement( i * cellx,
462	>	j * celly,
463	>	k * cellz );
464
465	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly + 0.5 * celly,
467	>	k * cellz );
468
469	<	makeElement( i * cellx,
470	<	j * celly + 0.5 * celly,
471	<	k * cellz + 0.5 * cellz );
469	>	makeElement( i * cellx,
470	>	j * celly + 0.5 * celly,
471	>	k * cellz + 0.5 * cellz );
472
473	<	makeElement( i * cellx + 0.5 * cellx,
474	<	j * celly,
475	<	k * cellz + 0.5 * cellz );
473	>	makeElement( i * cellx + 0.5 * cellx,
474	>	j * celly,
475	>	k * cellz + 0.5 * cellz );
476		}
477		}
478		}
#	Line 675 | Line 484 | void SimSetup::initFromBass( void ){
484		for( i=0; i < (n_cells+1) && !done; i++ ){
485		for( j=0; j < (n_cells+1) && !done; j++ ){
486
487	<	if( i < n_cells ){
487	>	if( i < n_cells ){
488
489	<	if( j < n_cells ){
490	<	start_ndx = n_cells;
491	<	}
492	<	else start_ndx = 0;
493	<	}
494	<	else start_ndx = 0;
489	>	if( j < n_cells ){
490	>	start_ndx = n_cells;
491	>	}
492	>	else start_ndx = 0;
493	>	}
494	>	else start_ndx = 0;
495
496	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
496	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497
498	<	makeElement( i * cellx,
499	<	j * celly,
500	<	k * cellz );
501	<	done = ( current_mol >= tot_nmol );
498	>	makeElement( i * cellx,
499	>	j * celly,
500	>	k * cellz );
501	>	done = ( current_mol >= tot_nmol );
502
503	<	if( !done && n_per_extra > 1 ){
504	<	makeElement( i * cellx + 0.5 * cellx,
505	<	j * celly + 0.5 * celly,
506	<	k * cellz );
507	<	done = ( current_mol >= tot_nmol );
508	<	}
503	>	if( !done && n_per_extra > 1 ){
504	>	makeElement( i * cellx + 0.5 * cellx,
505	>	j * celly + 0.5 * celly,
506	>	k * cellz );
507	>	done = ( current_mol >= tot_nmol );
508	>	}
509
510	<	if( !done && n_per_extra > 2){
511	<	makeElement( i * cellx,
512	<	j * celly + 0.5 * celly,
513	<	k * cellz + 0.5 * cellz );
514	<	done = ( current_mol >= tot_nmol );
515	<	}
510	>	if( !done && n_per_extra > 2){
511	>	makeElement( i * cellx,
512	>	j * celly + 0.5 * celly,
513	>	k * cellz + 0.5 * cellz );
514	>	done = ( current_mol >= tot_nmol );
515	>	}
516
517	<	if( !done && n_per_extra > 3){
518	<	makeElement( i * cellx + 0.5 * cellx,
519	<	j * celly,
520	<	k * cellz + 0.5 * cellz );
521	<	done = ( current_mol >= tot_nmol );
522	<	}
523	<	}
517	>	if( !done && n_per_extra > 3){
518	>	makeElement( i * cellx + 0.5 * cellx,
519	>	j * celly,
520	>	k * cellz + 0.5 * cellz );
521	>	done = ( current_mol >= tot_nmol );
522	>	}
523	>	}
524		}
525		}
526		}
527
528	<
529	<	for( i=0; i<info->n_atoms; i++ ){
721	<	info->atoms[i]->set_vx( 0.0 );
722	<	info->atoms[i]->set_vy( 0.0 );
723	<	info->atoms[i]->set_vz( 0.0 );
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530		}
531		}
532
#	Line 730 | Line 536 | void SimSetup::makeElement( double x, double y, double
536		AtomStamp* current_atom;
537		DirectionalAtom* dAtom;
538		double rotMat[3][3];
539	+	double pos[3];
540
541		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542
543		current_atom = comp_stamps[current_comp]->getAtom( k );
544		if( !current_atom->havePosition() ){
545		sprintf( painCave.errMsg,
546	<	"SimSetup:initFromBass error.\n"
547	<	"\tComponent %s, atom %s does not have a position specified.\n"
548	<	"\tThe initialization routine is unable to give a start"
549	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
546	>	"SimSetup:initFromBass error.\n"
547	>	"\tComponent %s, atom %s does not have a position specified.\n"
548	>	"\tThe initialization routine is unable to give a start"
549	>	" position.\n",
550	>	comp_stamps[current_comp]->getID(),
551	>	current_atom->getType() );
552		painCave.isFatal = 1;
553		simError();
554		}
555	+
556	+	pos[0] = x + current_atom->getPosX();
557	+	pos[1] = y + current_atom->getPosY();
558	+	pos[2] = z + current_atom->getPosZ();
559	+
560	+	info[0].atoms[current_atom_ndx]->setPos( pos );
561
562	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
750	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
751	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563
564	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
564	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565
755	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
756	–
566		rotMat[0][0] = 1.0;
567		rotMat[0][1] = 0.0;
568		rotMat[0][2] = 0.0;
#	Line 784 | Line 593 | void SimSetup::gatherInfo( void ){
593
594
595		void SimSetup::gatherInfo( void ){
596	+	int i,j,k;
597
598		ensembleCase = -1;
599		ffCase = -1;
600
791	–	// get the stamps and globals;
792	–	the_stamps = stamps;
793	–	the_globals = globals;
794	–
601		// set the easy ones first
796	–	info->target_temp = the_globals->getTargetTemp();
797	–	info->dt = the_globals->getDt();
798	–	info->run_time = the_globals->getRunTime();
799	–	n_components = the_globals->getNComponents();
602
603	+	for( i=0; i<nInfo; i++){
604	+	info[i].target_temp = globals->getTargetTemp();
605	+	info[i].dt = globals->getDt();
606	+	info[i].run_time = globals->getRunTime();
607	+	}
608	+	n_components = globals->getNComponents();
609
610	+
611		// get the forceField
612
613	<	strcpy( force_field, the_globals->getForceField() );
613	>	strcpy( force_field, globals->getForceField() );
614
615		if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616		else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618		else{
619		sprintf( painCave.errMsg,
620	<	"SimSetup Error. Unrecognized force field -> %s\n",
621	<	force_field );
620	>	"SimSetup Error. Unrecognized force field -> %s\n",
621	>	force_field );
622		painCave.isFatal = 1;
623		simError();
624		}
625
626		// get the ensemble
627
628	<	strcpy( ensemble, the_globals->getEnsemble() );
628	>	strcpy( ensemble, globals->getEnsemble() );
629
630		if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631		else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
#	Line 826 | Line 636 | void SimSetup::gatherInfo( void ){
636		else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637		else{
638		sprintf( painCave.errMsg,
639	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
639	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640		"reverting to NVE for this simulation.\n",
641	<	ensemble );
641	>	ensemble );
642		painCave.isFatal = 0;
643		simError();
644		strcpy( ensemble, "NVE" );
645		ensembleCase = NVE_ENS;
646		}
647	<	strcpy( info->ensemble, ensemble );
647	>
648	>	for(i=0; i<nInfo; i++){
649	>
650	>	strcpy( info[i].ensemble, ensemble );
651
652	<	// get the mixing rule
652	>	// get the mixing rule
653
654	<	strcpy( info->mixingRule, the_globals->getMixingRule() );
655	<	info->usePBC = the_globals->getPBC();
656	<
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657
658		// get the components and calculate the tot_nMol and indvidual n_mol
659
660	<	the_components = the_globals->getComponents();
660	>	the_components = globals->getComponents();
661		components_nmol = new int[n_components];
662
663
664	<	if( !the_globals->haveNMol() ){
664	>	if( !globals->haveNMol() ){
665		// we don't have the total number of molecules, so we assume it is
666		// given in each component
667
#	Line 856 | Line 669 | void SimSetup::gatherInfo( void ){
669		for( i=0; i<n_components; i++ ){
670
671		if( !the_components[i]->haveNMol() ){
672	<	// we have a problem
673	<	sprintf( painCave.errMsg,
674	<	"SimSetup Error. No global NMol or component NMol"
675	<	" given. Cannot calculate the number of atoms.\n" );
676	<	painCave.isFatal = 1;
677	<	simError();
672	>	// we have a problem
673	>	sprintf( painCave.errMsg,
674	>	"SimSetup Error. No global NMol or component NMol"
675	>	" given. Cannot calculate the number of atoms.\n" );
676	>	painCave.isFatal = 1;
677	>	simError();
678		}
679
680		tot_nmol += the_components[i]->getNMol();
#	Line 870 | Line 683 | void SimSetup::gatherInfo( void ){
683		}
684		else{
685		sprintf( painCave.errMsg,
686	<	"SimSetup error.\n"
687	<	"\tSorry, the ability to specify total"
688	<	" nMols and then give molfractions in the components\n"
689	<	"\tis not currently supported."
690	<	" Please give nMol in the components.\n" );
686	>	"SimSetup error.\n"
687	>	"\tSorry, the ability to specify total"
688	>	" nMols and then give molfractions in the components\n"
689	>	"\tis not currently supported."
690	>	" Please give nMol in the components.\n" );
691		painCave.isFatal = 1;
692		simError();
693		}
694
695		// set the status, sample, and thermal kick times
696
697	<	if( the_globals->haveSampleTime() ){
885	<	info->sampleTime = the_globals->getSampleTime();
886	<	info->statusTime = info->sampleTime;
887	<	info->thermalTime = info->sampleTime;
888	<	}
889	<	else{
890	<	info->sampleTime = the_globals->getRunTime();
891	<	info->statusTime = info->sampleTime;
892	<	info->thermalTime = info->sampleTime;
893	<	}
697	>	for(i=0; i<nInfo; i++){
698
699	<	if( the_globals->haveStatusTime() ){
700	<	info->statusTime = the_globals->getStatusTime();
701	<	}
702	<
703	<	if( the_globals->haveThermalTime() ){
704	<	info->thermalTime = the_globals->getThermalTime();
705	<	}
706	<
707	<	// check for the temperature set flag
708	<
905	<	if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet();
906	<
907	<	// get some of the tricky things that may still be in the globals
908	<
909	<	double boxVector[3];
910	<	if( the_globals->haveBox() ){
911	<	boxVector[0] = the_globals->getBox();
912	<	boxVector[1] = the_globals->getBox();
913	<	boxVector[2] = the_globals->getBox();
699	>	if( globals->haveSampleTime() ){
700	>	info[i].sampleTime = globals->getSampleTime();
701	>	info[i].statusTime = info[i].sampleTime;
702	>	info[i].thermalTime = info[i].sampleTime;
703	>	}
704	>	else{
705	>	info[i].sampleTime = globals->getRunTime();
706	>	info[i].statusTime = info[i].sampleTime;
707	>	info[i].thermalTime = info[i].sampleTime;
708	>	}
709
710	<	info->setBox( boxVector );
711	<	}
917	<	else if( the_globals->haveDensity() ){
918	<
919	<	double vol;
920	<	vol = (double)tot_nmol / the_globals->getDensity();
921	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
922	<	boxVector[1] = boxVector[0];
923	<	boxVector[2] = boxVector[0];
924	<
925	<	info->setBox( boxVector );
926	<	}
927	<	else{
928	<	if( !the_globals->haveBoxX() ){
929	<	sprintf( painCave.errMsg,
930	<	"SimSetup error, no periodic BoxX size given.\n" );
931	<	painCave.isFatal = 1;
932	<	simError();
710	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712		}
713	<	boxVector[0] = the_globals->getBoxX();
714	<
715	<	if( !the_globals->haveBoxY() ){
937	<	sprintf( painCave.errMsg,
938	<	"SimSetup error, no periodic BoxY size given.\n" );
939	<	painCave.isFatal = 1;
940	<	simError();
713	>
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716		}
942	–	boxVector[1] = the_globals->getBoxY();
717
718	<	if( !the_globals->haveBoxZ() ){
945	<	sprintf( painCave.errMsg,
946	<	"SimSetup error, no periodic BoxZ size given.\n" );
947	<	painCave.isFatal = 1;
948	<	simError();
949	<	}
950	<	boxVector[2] = the_globals->getBoxZ();
718	>	// check for the temperature set flag
719
720	<	info->setBox( boxVector );
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721	>
722	>	// get some of the tricky things that may still be in the globals
723	>
724	>	double boxVector[3];
725	>	if( globals->haveBox() ){
726	>	boxVector[0] = globals->getBox();
727	>	boxVector[1] = globals->getBox();
728	>	boxVector[2] = globals->getBox();
729	>
730	>	info[i].setBox( boxVector );
731	>	}
732	>	else if( globals->haveDensity() ){
733	>
734	>	double vol;
735	>	vol = (double)tot_nmol / globals->getDensity();
736	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	>	boxVector[1] = boxVector[0];
738	>	boxVector[2] = boxVector[0];
739	>
740	>	info[i].setBox( boxVector );
741		}
742	+	else{
743	+	if( !globals->haveBoxX() ){
744	+	sprintf( painCave.errMsg,
745	+	"SimSetup error, no periodic BoxX size given.\n" );
746	+	painCave.isFatal = 1;
747	+	simError();
748	+	}
749	+	boxVector[0] = globals->getBoxX();
750	+
751	+	if( !globals->haveBoxY() ){
752	+	sprintf( painCave.errMsg,
753	+	"SimSetup error, no periodic BoxY size given.\n" );
754	+	painCave.isFatal = 1;
755	+	simError();
756	+	}
757	+	boxVector[1] = globals->getBoxY();
758	+
759	+	if( !globals->haveBoxZ() ){
760	+	sprintf( painCave.errMsg,
761	+	"SimSetup error, no periodic BoxZ size given.\n" );
762	+	painCave.isFatal = 1;
763	+	simError();
764	+	}
765	+	boxVector[2] = globals->getBoxZ();
766	+
767	+	info[i].setBox( boxVector );
768	+	}
769
770	<
770	>	}
771
772		#ifdef IS_MPI
773		strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
#	Line 965 | Line 780 | void SimSetup::finalInfoCheck( void ){
780		void SimSetup::finalInfoCheck( void ){
781		int index;
782		int usesDipoles;
783	<
783	>	int i;
784
785	<	// check electrostatic parameters
786	<
787	<	index = 0;
788	<	usesDipoles = 0;
789	<	while( (index < info->n_atoms) && !usesDipoles ){
790	<	usesDipoles = ((info->atoms)[index])->hasDipole();
791	<	index++;
792	<	}
793	<
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787	>
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793	>	}
794	>
795		#ifdef IS_MPI
796	<	int myUse = usesDipoles
797	<	MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
796	>	int myUse = usesDipoles;
797	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798		#endif //is_mpi
983	–
984	–
985	–	if (the_globals->getUseRF() ) {
986	–	info->useReactionField = 1;
799
800	<	if( !the_globals->haveECR() ){
801	<	sprintf( painCave.errMsg,
802	<	"SimSetup Warning: using default value of 1/2 the smallest "
803	<	"box length for the electrostaticCutoffRadius.\n"
992	<	"I hope you have a very fast processor!\n");
993	<	painCave.isFatal = 0;
994	<	simError();
995	<	double smallest;
996	<	smallest = info->boxLx;
997	<	if (info->boxLy <= smallest) smallest = info->boxLy;
998	<	if (info->boxLz <= smallest) smallest = info->boxLz;
999	<	info->ecr = 0.5 * smallest;
1000	<	} else {
1001	<	info->ecr        = the_globals->getECR();
1002	<	}
1003	<
1004	<	if( !the_globals->haveEST() ){
1005	<	sprintf( painCave.errMsg,
1006	<	"SimSetup Warning: using default value of 0.05 * the "
1007	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
1008	<	);
1009	<	painCave.isFatal = 0;
1010	<	simError();
1011	<	info->est = 0.05 * info->ecr;
1012	<	} else {
1013	<	info->est        = the_globals->getEST();
1014	<	}
1015	<
1016	<	if(!the_globals->haveDielectric() ){
1017	<	sprintf( painCave.errMsg,
1018	<	"SimSetup Error: You are trying to use Reaction Field without"
1019	<	"setting a dielectric constant!\n"
1020	<	);
1021	<	painCave.isFatal = 1;
1022	<	simError();
1023	<	}
1024	<	info->dielectric = the_globals->getDielectric();
1025	<	}
1026	<	else {
1027	<	if (usesDipoles) {
800	>	double theEcr, theEst;
801	>
802	>	if (globals->getUseRF() ) {
803	>	info[i].useReactionField = 1;
804
805	<	if( !the_globals->haveECR() ){
806	<	sprintf( painCave.errMsg,
807	<	"SimSetup Warning: using default value of 1/2 the smallest "
808	<	"box length for the electrostaticCutoffRadius.\n"
809	<	"I hope you have a very fast processor!\n");
810	<	painCave.isFatal = 0;
811	<	simError();
812	<	double smallest;
813	<	smallest = info->boxLx;
814	<	if (info->boxLy <= smallest) smallest = info->boxLy;
815	<	if (info->boxLz <= smallest) smallest = info->boxLz;
816	<	info->ecr = 0.5 * smallest;
805	>	if( !globals->haveECR() ){
806	>	sprintf( painCave.errMsg,
807	>	"SimSetup Warning: using default value of 1/2 the smallest "
808	>	"box length for the electrostaticCutoffRadius.\n"
809	>	"I hope you have a very fast processor!\n");
810	>	painCave.isFatal = 0;
811	>	simError();
812	>	double smallest;
813	>	smallest = info[i].boxL[0];
814	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	>	theEcr = 0.5 * smallest;
817		} else {
818	<	info->ecr        = the_globals->getECR();
818	>	theEcr = globals->getECR();
819		}
820
821	<	if( !the_globals->haveEST() ){
822	<	sprintf( painCave.errMsg,
823	<	"SimSetup Warning: using default value of 5%% of the "
824	<	"electrostaticCutoffRadius for the "
825	<	"electrostaticSkinThickness\n"
826	<	);
827	<	painCave.isFatal = 0;
828	<	simError();
1053	<	info->est = 0.05 * info->ecr;
821	>	if( !globals->haveEST() ){
822	>	sprintf( painCave.errMsg,
823	>	"SimSetup Warning: using default value of 0.05 * the "
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	>	);
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	theEst = 0.05 * theEcr;
829		} else {
830	<	info->est        = the_globals->getEST();
830	>	theEst= globals->getEST();
831		}
832	<	}
833	<	}
832	>
833	>	info[i].setEcr( theEcr, theEst );
834	>
835	>	if(!globals->haveDielectric() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Error: You are trying to use Reaction Field without"
838	>	"setting a dielectric constant!\n"
839	>	);
840	>	painCave.isFatal = 1;
841	>	simError();
842	>	}
843	>	info[i].dielectric = globals->getDielectric();
844	>	}
845	>	else {
846	>	if (usesDipoles) {
847	>
848	>	if( !globals->haveECR() ){
849	>	sprintf( painCave.errMsg,
850	>	"SimSetup Warning: using default value of 1/2 the smallest "
851	>	"box length for the electrostaticCutoffRadius.\n"
852	>	"I hope you have a very fast processor!\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	double smallest;
856	>	smallest = info[i].boxL[0];
857	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	>	theEcr = 0.5 * smallest;
860	>	} else {
861	>	theEcr = globals->getECR();
862	>	}
863	>
864	>	if( !globals->haveEST() ){
865	>	sprintf( painCave.errMsg,
866	>	"SimSetup Warning: using default value of 0.05 * the "
867	>	"electrostaticCutoffRadius for the "
868	>	"electrostaticSkinThickness\n"
869	>	);
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	theEst = 0.05 * theEcr;
873	>	} else {
874	>	theEst= globals->getEST();
875	>	}
876	>
877	>	info[i].setEcr( theEcr, theEst );
878	>	}
879	>	}
880	>	}
881
882		#ifdef IS_MPI
883		strcpy( checkPointMsg, "post processing checks out" );
#	Line 1065 | Line 887 | void SimSetup::initSystemCoords( void ){
887		}
888
889		void SimSetup::initSystemCoords( void ){
890	+	int i;
891	+
892	+	char* inName;
893
894	<	if( the_globals->haveInitialConfig() ){
895	<
896	<	InitializeFromFile* fileInit;
894	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
895	>
896	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
897	>
898	>	if( globals->haveInitialConfig() ){
899	>
900	>	InitializeFromFile* fileInit;
901		#ifdef IS_MPI // is_mpi
902	<	if( worldRank == 0 ){
902	>	if( worldRank == 0 ){
903		#endif //is_mpi
904	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
904	>	inName = globals->getInitialConfig();
905	>	double* tempDouble = new double[1000000];
906	>	fileInit = new InitializeFromFile( inName );
907		#ifdef IS_MPI
908	<	}else fileInit = new InitializeFromFile( NULL );
908	>	}else fileInit = new InitializeFromFile( NULL );
909		#endif
910	<	fileInit->read_xyz( info ); // default velocities on
911	<
912	<	delete fileInit;
913	<	}
914	<	else{
915	<
910	>	fileInit->readInit( info ); // default velocities on
911	>
912	>	delete fileInit;
913	>	}
914	>	else{
915	>
916		#ifdef IS_MPI
917	<
918	<	// no init from bass
919	<
920	<	sprintf( painCave.errMsg,
921	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
922	<	painCave.isFatal;
923	<	simError();
924	<
917	>
918	>	// no init from bass
919	>
920	>	sprintf( painCave.errMsg,
921	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
922	>	painCave.isFatal;
923	>	simError();
924	>
925		#else
926	<
927	<	initFromBass();
928	<
929	<
926	>
927	>	initFromBass();
928	>
929	>
930		#endif
931	<	}
932	<
931	>	}
932	>
933		#ifdef IS_MPI
934		strcpy( checkPointMsg, "Successfully read in the initial configuration" );
935		MPIcheckPoint();
936		#endif // is_mpi
937	<
937	>
938		}
939
940
941		void SimSetup::makeOutNames( void ){
942	+
943	+	int k;
944
945	+
946	+	for(k=0; k<nInfo; k++){
947	+
948		#ifdef IS_MPI
949	<	if( worldRank == 0 ){
949	>	if( worldRank == 0 ){
950		#endif // is_mpi
951	<
952	<	if( the_globals->haveFinalConfig() ){
953	<	strcpy( info->finalName, the_globals->getFinalConfig() );
951	>
952	>	if( globals->haveFinalConfig() ){
953	>	strcpy( info[k].finalName, globals->getFinalConfig() );
954	>	}
955	>	else{
956	>	strcpy( info[k].finalName, inFileName );
957	>	char* endTest;
958	>	int nameLength = strlen( info[k].finalName );
959	>	endTest = &(info[k].finalName[nameLength - 5]);
960	>	if( !strcmp( endTest, ".bass" ) ){
961	>	strcpy( endTest, ".eor" );
962	>	}
963	>	else if( !strcmp( endTest, ".BASS" ) ){
964	>	strcpy( endTest, ".eor" );
965	>	}
966	>	else{
967	>	endTest = &(info[k].finalName[nameLength - 4]);
968	>	if( !strcmp( endTest, ".bss" ) ){
969	>	strcpy( endTest, ".eor" );
970		}
971	+	else if( !strcmp( endTest, ".mdl" ) ){
972	+	strcpy( endTest, ".eor" );
973	+	}
974		else{
975	<	strcpy( info->finalName, inFileName );
975	>	strcat( info[k].finalName, ".eor" );
976	>	}
977	>	}
978	>	}
979	>
980	>	// make the sample and status out names
981	>
982	>	strcpy( info[k].sampleName, inFileName );
983		char* endTest;
984	<	int nameLength = strlen( info->finalName );
985	<	endTest = &(info->finalName[nameLength - 5]);
984	>	int nameLength = strlen( info[k].sampleName );
985	>	endTest = &(info[k].sampleName[nameLength - 5]);
986		if( !strcmp( endTest, ".bass" ) ){
987	<	strcpy( endTest, ".eor" );
987	>	strcpy( endTest, ".dump" );
988		}
989		else if( !strcmp( endTest, ".BASS" ) ){
990	<	strcpy( endTest, ".eor" );
990	>	strcpy( endTest, ".dump" );
991		}
992		else{
993	<	endTest = &(info->finalName[nameLength - 4]);
994	<	if( !strcmp( endTest, ".bss" ) ){
995	<	strcpy( endTest, ".eor" );
996	<	}
997	<	else if( !strcmp( endTest, ".mdl" ) ){
998	<	strcpy( endTest, ".eor" );
999	<	}
1000	<	else{
1001	<	strcat( info->finalName, ".eor" );
1002	<	}
993	>	endTest = &(info[k].sampleName[nameLength - 4]);
994	>	if( !strcmp( endTest, ".bss" ) ){
995	>	strcpy( endTest, ".dump" );
996	>	}
997	>	else if( !strcmp( endTest, ".mdl" ) ){
998	>	strcpy( endTest, ".dump" );
999	>	}
1000	>	else{
1001	>	strcat( info[k].sampleName, ".dump" );
1002	>	}
1003		}
1004	<	}
1005	<
1006	<	// make the sample and status out names
1007	<
1008	<	strcpy( info->sampleName, inFileName );
1009	<	char* endTest;
1148	<	int nameLength = strlen( info->sampleName );
1149	<	endTest = &(info->sampleName[nameLength - 5]);
1150	<	if( !strcmp( endTest, ".bass" ) ){
1151	<	strcpy( endTest, ".dump" );
1152	<	}
1153	<	else if( !strcmp( endTest, ".BASS" ) ){
1154	<	strcpy( endTest, ".dump" );
1155	<	}
1156	<	else{
1157	<	endTest = &(info->sampleName[nameLength - 4]);
1158	<	if( !strcmp( endTest, ".bss" ) ){
1159	<	strcpy( endTest, ".dump" );
1004	>
1005	>	strcpy( info[k].statusName, inFileName );
1006	>	nameLength = strlen( info[k].statusName );
1007	>	endTest = &(info[k].statusName[nameLength - 5]);
1008	>	if( !strcmp( endTest, ".bass" ) ){
1009	>	strcpy( endTest, ".stat" );
1010		}
1011	<	else if( !strcmp( endTest, ".mdl" ) ){
1012	<	strcpy( endTest, ".dump" );
1011	>	else if( !strcmp( endTest, ".BASS" ) ){
1012	>	strcpy( endTest, ".stat" );
1013		}
1014		else{
1015	<	strcat( info->sampleName, ".dump" );
1015	>	endTest = &(info[k].statusName[nameLength - 4]);
1016	>	if( !strcmp( endTest, ".bss" ) ){
1017	>	strcpy( endTest, ".stat" );
1018	>	}
1019	>	else if( !strcmp( endTest, ".mdl" ) ){
1020	>	strcpy( endTest, ".stat" );
1021	>	}
1022	>	else{
1023	>	strcat( info[k].statusName, ".stat" );
1024	>	}
1025		}
1026	<	}
1168	<
1169	<	strcpy( info->statusName, inFileName );
1170	<	nameLength = strlen( info->statusName );
1171	<	endTest = &(info->statusName[nameLength - 5]);
1172	<	if( !strcmp( endTest, ".bass" ) ){
1173	<	strcpy( endTest, ".stat" );
1174	<	}
1175	<	else if( !strcmp( endTest, ".BASS" ) ){
1176	<	strcpy( endTest, ".stat" );
1177	<	}
1178	<	else{
1179	<	endTest = &(info->statusName[nameLength - 4]);
1180	<	if( !strcmp( endTest, ".bss" ) ){
1181	<	strcpy( endTest, ".stat" );
1182	<	}
1183	<	else if( !strcmp( endTest, ".mdl" ) ){
1184	<	strcpy( endTest, ".stat" );
1185	<	}
1186	<	else{
1187	<	strcat( info->statusName, ".stat" );
1188	<	}
1189	<	}
1190	<
1026	>
1027		#ifdef IS_MPI
1028	<	}
1028	>	}
1029		#endif // is_mpi
1030	<
1030	>	}
1031		}
1032
1033
1034		void SimSetup::sysObjectsCreation( void ){
1035	<
1035	>
1036	>	int i,k;
1037	>
1038		// create the forceField
1039
1040		createFF();
#	Line 1216 | Line 1054 | void SimSetup::sysObjectsCreation( void ){
1054		#endif //is_mpi
1055
1056		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1057	<
1057	>
1058		makeSysArrays();
1059
1060	+	// make and initialize the molecules (all but atomic coordinates)
1061	+
1062	+	makeMolecules();
1063
1064	<
1065	<
1064	>	for(k=0; k<nInfo; k++){
1065	>	info[k].identArray = new int[info[k].n_atoms];
1066	>	for(i=0; i<info[k].n_atoms; i++){
1067	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1068	>	}
1069	>	}
1070		}
1071
1072
#	Line 1237 | Line 1082 | void SimSetup::createFF( void ){
1082		the_ff = new LJFF();
1083		break;
1084
1085	+	case FF_EAM:
1086	+	the_ff = new EAM_FF();
1087	+	break;
1088	+
1089		default:
1090		sprintf( painCave.errMsg,
1091	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1091	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1092		painCave.isFatal = 1;
1093		simError();
1094		}
#	Line 1254 | Line 1103 | void SimSetup::compList( void ){
1103
1104		void SimSetup::compList( void ){
1105
1106	+	int i;
1107	+	char* id;
1108	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1109	+	LinkedMolStamp* currentStamp = NULL;
1110		comp_stamps = new MoleculeStamp*[n_components];
1111	<
1111	>
1112		// make an array of molecule stamps that match the components used.
1113		// also extract the used stamps out into a separate linked list
1261	–
1262	–	info->nComponents = n_components;
1263	–	info->componentsNmol = components_nmol;
1264	–	info->compStamps = comp_stamps;
1265	–	info->headStamp = new LinkedMolStamp();
1114
1115	<	char* id;
1116	<	LinkedMolStamp* headStamp = info->headStamp;
1117	<	LinkedMolStamp* currentStamp = NULL;
1115	>	for(i=0; i<nInfo; i++){
1116	>	info[i].nComponents = n_components;
1117	>	info[i].componentsNmol = components_nmol;
1118	>	info[i].compStamps = comp_stamps;
1119	>	info[i].headStamp = headStamp;
1120	>	}
1121	>
1122	>
1123		for( i=0; i<n_components; i++ ){
1124
1125		id = the_components[i]->getType();
#	Line 1279 | Line 1132 | void SimSetup::compList( void ){
1132
1133		// extract the component from the list;
1134
1135	<	currentStamp = the_stamps->extractMolStamp( id );
1135	>	currentStamp = stamps->extractMolStamp( id );
1136		if( currentStamp == NULL ){
1137	<	sprintf( painCave.errMsg,
1138	<	"SimSetup error: Component \"%s\" was not found in the "
1139	<	"list of declared molecules\n",
1140	<	id );
1141	<	painCave.isFatal = 1;
1142	<	simError();
1137	>	sprintf( painCave.errMsg,
1138	>	"SimSetup error: Component \"%s\" was not found in the "
1139	>	"list of declared molecules\n",
1140	>	id );
1141	>	painCave.isFatal = 1;
1142	>	simError();
1143		}
1144
1145		headStamp->add( currentStamp );
#	Line 1303 | Line 1156 | void SimSetup::calcSysValues( void ){
1156		}
1157
1158		void SimSetup::calcSysValues( void ){
1159	<
1159	>	int i, j, k;
1160	>
1161	>	int *molMembershipArray;
1162	>
1163		tot_atoms = 0;
1164		tot_bonds = 0;
1165		tot_bends = 0;
#	Line 1315 | Line 1171 | void SimSetup::calcSysValues( void ){
1171		tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1172		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1173		}
1174	<
1174	>
1175		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1176	<
1321	<	info->n_atoms = tot_atoms;
1322	<	info->n_bonds = tot_bonds;
1323	<	info->n_bends = tot_bends;
1324	<	info->n_torsions = tot_torsions;
1325	<	info->n_SRI = tot_SRI;
1326	<	info->n_mol = tot_nmol;
1176	>	molMembershipArray = new int[tot_atoms];
1177
1178	<	info->molMembershipArray = new int[tot_atoms];
1178	>	for(i=0; i<nInfo; i++){
1179	>	info[i].n_atoms = tot_atoms;
1180	>	info[i].n_bonds = tot_bonds;
1181	>	info[i].n_bends = tot_bends;
1182	>	info[i].n_torsions = tot_torsions;
1183	>	info[i].n_SRI = tot_SRI;
1184	>	info[i].n_mol = tot_nmol;
1185	>
1186	>	info[i].molMembershipArray = molMembershipArray;
1187	>	}
1188		}
1189
1331	–
1190		#ifdef IS_MPI
1191
1192		void SimSetup::mpiMolDivide( void ){
1193
1194	+	int i, j, k;
1195		int localMol, allMol;
1196		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1197
#	Line 1359 | Line 1218 | void SimSetup::mpiMolDivide( void ){
1218		for( j=0; j<components_nmol[i]; j++ ){
1219
1220		if( mol2proc[allMol] == worldRank ){
1221	<
1222	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1223	<	local_bonds +=    comp_stamps[i]->getNBonds();
1224	<	local_bends +=    comp_stamps[i]->getNBends();
1225	<	local_torsions += comp_stamps[i]->getNTorsions();
1226	<	localMol++;
1221	>
1222	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1223	>	local_bonds +=    comp_stamps[i]->getNBonds();
1224	>	local_bends +=    comp_stamps[i]->getNBends();
1225	>	local_torsions += comp_stamps[i]->getNTorsions();
1226	>	localMol++;
1227		}
1228		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1229	<	info->molMembershipArray[globalAtomIndex] = allMol;
1229	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1230		globalAtomIndex++;
1231		}
1232
#	Line 1376 | Line 1235 | void SimSetup::mpiMolDivide( void ){
1235		}
1236		local_SRI = local_bonds + local_bends + local_torsions;
1237
1238	<	info->n_atoms = mpiSim->getMyNlocal();
1238	>	info[0].n_atoms = mpiSim->getMyNlocal();
1239
1240	<	if( local_atoms != info->n_atoms ){
1240	>	if( local_atoms != info[0].n_atoms ){
1241		sprintf( painCave.errMsg,
1242	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1243	<	" localAtom (%d) are not equal.\n",
1244	<	info->n_atoms,
1245	<	local_atoms );
1242	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1243	>	" localAtom (%d) are not equal.\n",
1244	>	info[0].n_atoms,
1245	>	local_atoms );
1246		painCave.isFatal = 1;
1247		simError();
1248		}
1249
1250	<	info->n_bonds = local_bonds;
1251	<	info->n_bends = local_bends;
1252	<	info->n_torsions = local_torsions;
1253	<	info->n_SRI = local_SRI;
1254	<	info->n_mol = localMol;
1250	>	info[0].n_bonds = local_bonds;
1251	>	info[0].n_bends = local_bends;
1252	>	info[0].n_torsions = local_torsions;
1253	>	info[0].n_SRI = local_SRI;
1254	>	info[0].n_mol = localMol;
1255
1256		strcpy( checkPointMsg, "Passed nlocal consistency check." );
1257		MPIcheckPoint();
1258		}
1259	<
1259	>
1260		#endif // is_mpi
1261
1262
1263		void SimSetup::makeSysArrays( void ){
1264	+	int i, j, k, l;
1265	+
1266	+	Atom** the_atoms;
1267	+	Molecule* the_molecules;
1268	+	Exclude** the_excludes;
1269
1406	–	// create the atom and short range interaction arrays
1407	–
1408	–	Atom::createArrays(info->n_atoms);
1409	–	the_atoms = new Atom*[info->n_atoms];
1410	–	the_molecules = new Molecule[info->n_mol];
1411	–	int molIndex;
1412	–
1413	–	// initialize the molecule's stampID's
1414	–
1415	–	#ifdef IS_MPI
1270
1271	+	for(l=0; l<nInfo; l++){
1272	+
1273	+	// create the atom and short range interaction arrays
1274	+
1275	+	the_atoms = new Atom*[info[l].n_atoms];
1276	+	the_molecules = new Molecule[info[l].n_mol];
1277	+	int molIndex;
1278
1279	<	molIndex = 0;
1419	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1279	>	// initialize the molecule's stampID's
1280
1281	<	if(mol2proc[i] == worldRank ){
1282	<	the_molecules[molIndex].setStampID( molCompType[i] );
1283	<	the_molecules[molIndex].setMyIndex( molIndex );
1284	<	the_molecules[molIndex].setGlobalIndex( i );
1285	<	molIndex++;
1281	>	#ifdef IS_MPI
1282	>
1283	>
1284	>	molIndex = 0;
1285	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1286	>
1287	>	if(mol2proc[i] == worldRank ){
1288	>	the_molecules[molIndex].setStampID( molCompType[i] );
1289	>	the_molecules[molIndex].setMyIndex( molIndex );
1290	>	the_molecules[molIndex].setGlobalIndex( i );
1291	>	molIndex++;
1292	>	}
1293		}
1294	+
1295	+	#else // is_mpi
1296	+
1297	+	molIndex = 0;
1298	+	globalAtomIndex = 0;
1299	+	for(i=0; i<n_components; i++){
1300	+	for(j=0; j<components_nmol[i]; j++ ){
1301	+	the_molecules[molIndex].setStampID( i );
1302	+	the_molecules[molIndex].setMyIndex( molIndex );
1303	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1304	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1305	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1306	+	globalAtomIndex++;
1307		}
1308	+	molIndex++;
1309	+	}
1310	+	}
1311	+
1312	+
1313	+	#endif // is_mpi
1314
1315	<	#else // is_mpi
1316	<
1317	<	molIndex = 0;
1318	<	globalAtomIndex = 0;
1319	<	for(i=0; i<n_components; i++){
1320	<	for(j=0; j<components_nmol[i]; j++ ){
1321	<	the_molecules[molIndex].setStampID( i );
1436	<	the_molecules[molIndex].setMyIndex( molIndex );
1437	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1438	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1439	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1440	<	globalAtomIndex++;
1315	>
1316	>	if( info[l].n_SRI ){
1317	>
1318	>	Exclude::createArray(info[l].n_SRI);
1319	>	the_excludes = new Exclude*[info[l].n_SRI];
1320	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1321	>	the_excludes[ex] = new Exclude(ex);
1322		}
1323	<	molIndex++;
1323	>	info[l].globalExcludes = new int;
1324	>	info[l].n_exclude = info[l].n_SRI;
1325		}
1326	+	else{
1327	+
1328	+	Exclude::createArray( 1 );
1329	+	the_excludes = new Exclude*;
1330	+	the_excludes[0] = new Exclude(0);
1331	+	the_excludes[0]->setPair( 0,0 );
1332	+	info[l].globalExcludes = new int;
1333	+	info[l].globalExcludes[0] = 0;
1334	+	info[l].n_exclude = 0;
1335	+	}
1336	+
1337	+	// set the arrays into the SimInfo object
1338	+
1339	+	info[l].atoms = the_atoms;
1340	+	info[l].molecules = the_molecules;
1341	+	info[l].nGlobalExcludes = 0;
1342	+	info[l].excludes = the_excludes;
1343	+
1344	+	the_ff->setSimInfo( info );
1345	+
1346		}
1347	+	}
1348	+
1349	+	void SimSetup::makeIntegrator( void ){
1350	+
1351	+	int k;
1352	+
1353	+	NVT<RealIntegrator>*  myNVT = NULL;
1354	+	NPTi<RealIntegrator>* myNPTi = NULL;
1355	+	NPTf<RealIntegrator>* myNPTf = NULL;
1356	+	NPTim<RealIntegrator>* myNPTim = NULL;
1357	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1358	+
1359	+	for(k=0; k<nInfo; k++){
1360
1361	+	switch( ensembleCase ){
1362	+
1363	+	case NVE_ENS:
1364	+	if (globals->haveZconstraints()){
1365	+	setupZConstraint(info[k]);
1366	+	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1367	+	}
1368
1369	+	else
1370	+	new NVE<RealIntegrator>( &(info[k]), the_ff );
1371	+	break;
1372	+
1373	+	case NVT_ENS:
1374	+	if (globals->haveZconstraints()){
1375	+	setupZConstraint(info[k]);
1376	+	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377	+	}
1378	+	else
1379	+	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1380	+
1381	+	myNVT->setTargetTemp(globals->getTargetTemp());
1382	+
1383	+	if (globals->haveTauThermostat())
1384	+	myNVT->setTauThermostat(globals->getTauThermostat());
1385	+
1386	+	else {
1387	+	sprintf( painCave.errMsg,
1388	+	"SimSetup error: If you use the NVT\n"
1389	+	"    ensemble, you must set tauThermostat.\n");
1390	+	painCave.isFatal = 1;
1391	+	simError();
1392	+	}
1393	+	break;
1394	+
1395	+	case NPTi_ENS:
1396	+	if (globals->haveZconstraints()){
1397	+	setupZConstraint(info[k]);
1398	+	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399	+	}
1400	+	else
1401	+	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1402	+
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	+	if (globals->haveZconstraints()){
1438	+	setupZConstraint(info[k]);
1439	+	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440	+	}
1441	+	else
1442	+	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1443	+
1444	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1445	+
1446	+	if (globals->haveTargetPressure())
1447	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1448	+	else {
1449	+	sprintf( painCave.errMsg,
1450	+	"SimSetup error: If you use a constant pressure\n"
1451	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1452	+	painCave.isFatal = 1;
1453	+	simError();
1454	+	}
1455	+
1456	+	if( globals->haveTauThermostat() )
1457	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1458	+	else{
1459	+	sprintf( painCave.errMsg,
1460	+	"SimSetup error: If you use an NPT\n"
1461	+	"    ensemble, you must set tauThermostat.\n");
1462	+	painCave.isFatal = 1;
1463	+	simError();
1464	+	}
1465	+
1466	+	if( globals->haveTauBarostat() )
1467	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1468	+	else{
1469	+	sprintf( painCave.errMsg,
1470	+	"SimSetup error: If you use an NPT\n"
1471	+	"    ensemble, you must set tauBarostat.\n");
1472	+	painCave.isFatal = 1;
1473	+	simError();
1474	+	}
1475	+	break;
1476	+
1477	+	case NPTim_ENS:
1478	+	if (globals->haveZconstraints()){
1479	+	setupZConstraint(info[k]);
1480	+	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481	+	}
1482	+	else
1483	+	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1484	+
1485	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1486	+
1487	+	if (globals->haveTargetPressure())
1488	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1489	+	else {
1490	+	sprintf( painCave.errMsg,
1491	+	"SimSetup error: If you use a constant pressure\n"
1492	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1493	+	painCave.isFatal = 1;
1494	+	simError();
1495	+	}
1496	+
1497	+	if( globals->haveTauThermostat() )
1498	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1499	+	else{
1500	+	sprintf( painCave.errMsg,
1501	+	"SimSetup error: If you use an NPT\n"
1502	+	"    ensemble, you must set tauThermostat.\n");
1503	+	painCave.isFatal = 1;
1504	+	simError();
1505	+	}
1506	+
1507	+	if( globals->haveTauBarostat() )
1508	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509	+	else{
1510	+	sprintf( painCave.errMsg,
1511	+	"SimSetup error: If you use an NPT\n"
1512	+	"    ensemble, you must set tauBarostat.\n");
1513	+	painCave.isFatal = 1;
1514	+	simError();
1515	+	}
1516	+	break;
1517	+
1518	+	case NPTfm_ENS:
1519	+	if (globals->haveZconstraints()){
1520	+	setupZConstraint(info[k]);
1521	+	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522	+	}
1523	+	else
1524	+	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1525	+
1526	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1527	+
1528	+	if (globals->haveTargetPressure())
1529	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1530	+	else {
1531	+	sprintf( painCave.errMsg,
1532	+	"SimSetup error: If you use a constant pressure\n"
1533	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1534	+	painCave.isFatal = 1;
1535	+	simError();
1536	+	}
1537	+
1538	+	if( globals->haveTauThermostat() )
1539	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1540	+	else{
1541	+	sprintf( painCave.errMsg,
1542	+	"SimSetup error: If you use an NPT\n"
1543	+	"    ensemble, you must set tauThermostat.\n");
1544	+	painCave.isFatal = 1;
1545	+	simError();
1546	+	}
1547	+
1548	+	if( globals->haveTauBarostat() )
1549	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1550	+	else{
1551	+	sprintf( painCave.errMsg,
1552	+	"SimSetup error: If you use an NPT\n"
1553	+	"    ensemble, you must set tauBarostat.\n");
1554	+	painCave.isFatal = 1;
1555	+	simError();
1556	+	}
1557	+	break;
1558	+
1559	+	default:
1560	+	sprintf( painCave.errMsg,
1561	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1562	+	painCave.isFatal = 1;
1563	+	simError();
1564	+	}
1565	+	}
1566	+	}
1567	+
1568	+	void SimSetup::initFortran( void ){
1569	+
1570	+	info[0].refreshSim();
1571	+
1572	+	if( !strcmp( info[0].mixingRule, "standard") ){
1573	+	the_ff->initForceField( LB_MIXING_RULE );
1574	+	}
1575	+	else if( !strcmp( info[0].mixingRule, "explicit") ){
1576	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1577	+	}
1578	+	else{
1579	+	sprintf( painCave.errMsg,
1580	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	+	info[0].mixingRule );
1582	+	painCave.isFatal = 1;
1583	+	simError();
1584	+	}
1585	+
1586	+
1587	+	#ifdef IS_MPI
1588	+	strcpy( checkPointMsg,
1589	+	"Successfully intialized the mixingRule for Fortran." );
1590	+	MPIcheckPoint();
1591		#endif // is_mpi
1592
1593	+	}
1594
1595	<	if( info->n_SRI ){
1595	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596	>	{
1597	>	int nZConstraints;
1598	>	ZconStamp** zconStamp;
1599	>
1600	>	if(globals->haveZconstraintTime()){
1601
1602	<	Exclude::createArray(info->n_SRI);
1603	<	the_excludes = new Exclude*[info->n_SRI];
1604	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1605	<	info->globalExcludes = new int;
1606	<	info->n_exclude = info->n_SRI;
1602	>	//add sample time of z-constraint  into SimInfo's property list
1603	>	DoubleData* zconsTimeProp = new DoubleData();
1604	>	zconsTimeProp->setID(ZCONSTIME_ID);
1605	>	zconsTimeProp->setData(globals->getZconsTime());
1606	>	theInfo.addProperty(zconsTimeProp);
1607		}
1608		else{
1609	<
1610	<	Exclude::createArray( 1 );
1611	<	the_excludes = new Exclude*;
1612	<	the_excludes[0] = new Exclude(0);
1613	<	the_excludes[0]->setPair( 0,0 );
1464	<	info->globalExcludes = new int;
1465	<	info->globalExcludes[0] = 0;
1466	<	info->n_exclude = 0;
1609	>	sprintf( painCave.errMsg,
1610	>	"ZConstraint error: If you use an ZConstraint\n"
1611	>	" , you must set sample time.\n");
1612	>	painCave.isFatal = 1;
1613	>	simError();
1614		}
1615
1616	<	// set the arrays into the SimInfo object
1616	>	//push zconsTol into siminfo, if user does not specify
1617	>	//value for zconsTol, a default value will be used
1618	>	DoubleData* zconsTol = new DoubleData();
1619	>	zconsTol->setID(ZCONSTOL_ID);
1620	>	if(globals->haveZconsTol()){
1621	>	zconsTol->setData(globals->getZconsTol());
1622	>	}
1623	>	else{
1624	>	double defaultZConsTol = 0.01;
1625	>	sprintf( painCave.errMsg,
1626	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1627	>	" , default value %f is used.\n", defaultZConsTol);
1628	>	painCave.isFatal = 0;
1629	>	simError();
1630
1631	<	info->atoms = the_atoms;
1632	<	info->molecules = the_molecules;
1633	<	info->nGlobalExcludes = 0;
1474	<	info->excludes = the_excludes;
1631	>	zconsTol->setData(defaultZConsTol);
1632	>	}
1633	>	theInfo.addProperty(zconsTol);
1634
1635	<	the_ff->setSimInfo( info );
1635	>	//set Force Substraction Policy
1636	>	StringData* zconsForcePolicy =  new StringData();
1637	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1638	>
1639	>	if(globals->haveZconsForcePolicy()){
1640	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1641	>	}
1642	>	else{
1643	>	sprintf( painCave.errMsg,
1644	>	"ZConstraint Warning: User does not set force substraction policy, "
1645	>	"average force substraction policy is used\n");
1646	>	painCave.isFatal = 0;
1647	>	simError();
1648	>	zconsForcePolicy->setData("BYNUMBER");
1649	>	}
1650	>
1651	>	theInfo.addProperty(zconsForcePolicy);
1652	>
1653	>	//Determine the name of ouput file and add it into SimInfo's property list
1654	>	//Be careful, do not use inFileName, since it is a pointer which
1655	>	//point to a string at master node, and slave nodes do not contain that string
1656	>
1657	>	string zconsOutput(theInfo.finalName);
1658	>
1659	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1660	>
1661	>	StringData* zconsFilename = new StringData();
1662	>	zconsFilename->setID(ZCONSFILENAME_ID);
1663	>	zconsFilename->setData(zconsOutput);
1664	>
1665	>	theInfo.addProperty(zconsFilename);
1666	>
1667	>	//setup index, pos and other parameters of z-constraint molecules
1668	>	nZConstraints = globals->getNzConstraints();
1669	>	theInfo.nZconstraints = nZConstraints;
1670
1671	+	zconStamp = globals->getZconStamp();
1672	+	ZConsParaItem tempParaItem;
1673	+
1674	+	ZConsParaData* zconsParaData = new ZConsParaData();
1675	+	zconsParaData->setID(ZCONSPARADATA_ID);
1676	+
1677	+	for(int i = 0; i < nZConstraints; i++){
1678	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1679	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1680	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1681	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1682	+
1683	+	zconsParaData->addItem(tempParaItem);
1684	+	}
1685	+
1686	+	//sort the parameters by index of molecules
1687	+	zconsParaData->sortByIndex();
1688	+
1689	+	//push data into siminfo, therefore, we can retrieve later
1690	+	theInfo.addProperty(zconsParaData);
1691	+
1692		}

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