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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 676 by tim, Mon Aug 11 19:40:06 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 14 | Line 16
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
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
24	–
26		#define FF_DUFF 0
27		#define FF_LJ   1
28	+	#define FF_EAM  2
29
30	+	using namespace std;
31
32		SimSetup::SimSetup(){
33	+
34	+	isInfoArray = 0;
35	+	nInfo = 1;
36	+
37		stamps = new MakeStamps();
38		globals = new Globals();
39
40	+
41		#ifdef IS_MPI
42		strcpy( checkPointMsg, "SimSetup creation successful" );
43		MPIcheckPoint();
#	Line 41 | Line 49 | void SimSetup::parseFile( char* fileName ){
49		delete globals;
50		}
51
52	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
53	+	info = the_info;
54	+	nInfo = theNinfo;
55	+	isInfoArray = 1;
56	+	}
57	+
58	+
59		void SimSetup::parseFile( char* fileName ){
60
61		#ifdef IS_MPI
#	Line 76 | Line 91 | void SimSetup::createSim( void ){
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
94	>	void SimSetup::createSim(void){
95
81	–	MakeStamps *the_stamps;
82	–	Globals* the_globals;
96		int i, j, k, globalAtomIndex;
97
98		// gather all of the information from the Bass file
#	Line 90 | Line 103 | void SimSetup::createSim( void ){
103
104		sysObjectsCreation();
105
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	–
106		// check on the post processing info
107
108		finalInfoCheck();
109
110	–
111	–
112	–
110		// initialize the system coordinates
111
112	<	initSystemCoords();
116	<
112	>	if( !isInfoArray ) initSystemCoords();
113
114		// make the output filenames
115
116		makeOutNames();
117
122	–
123	–
124	–
125	–
126	–
127	–
128	–
129	–
118		// make the integrator
119
120	+	makeIntegrator();
121
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	–
122		#ifdef IS_MPI
123		mpiSim->mpiRefresh();
124		#endif
125
126		// initialize the Fortran
127
128	+	initFortran();
129
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	–	}
130
131
333	–	#ifdef IS_MPI
334	–	strcpy( checkPointMsg,
335	–	"Successfully intialized the mixingRule for Fortran." );
336	–	MPIcheckPoint();
337	–	#endif // is_mpi
132		}
133
134
135		void SimSetup::makeMolecules( void ){
136
137	+	int k,l;
138		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
139	<	molInit info;
139	>	molInit molInfo;
140		DirectionalAtom* dAtom;
141		LinkedAssign* extras;
142		LinkedAssign* current_extra;
#	Line 364 | Line 159 | void SimSetup::makeMolecules( void ){
159
160		double ux, uy, uz, u, uSqr;
161
162	<	atomOffset = 0;
368	<	excludeOffset = 0;
369	<	for(i=0; i<info->n_mol; i++){
162	>	for(k=0; k<nInfo; k++){
163
164	<	stampID = the_molecules[i].getStampID();
164	>	the_ff->setSimInfo( &(info[k]) );
165
166	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
167	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
168	<	info.nBends    = comp_stamps[stampID]->getNBends();
169	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
170	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for(i=0; i<info[k].n_mol; i++){
169	>
170	>	stampID = info[k].molecules[i].getStampID();
171
172	<	info.myAtoms = &the_atoms[atomOffset];
173	<	info.myExcludes = &the_excludes[excludeOffset];
174	<	info.myBonds = new Bond*[info.nBonds];
175	<	info.myBends = new Bend*[info.nBends];
176	<	info.myTorsions = new Torsion*[info.nTorsions];
172	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
173	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
174	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
175	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
177	>
178	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	>	molInfo.myBends = new Bend*[molInfo.nBends];
182	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
183
184	<	theBonds = new bond_pair[info.nBonds];
185	<	theBends = new bend_set[info.nBends];
186	<	theTorsions = new torsion_set[info.nTorsions];
184	>	theBonds = new bond_pair[molInfo.nBonds];
185	>	theBends = new bend_set[molInfo.nBends];
186	>	theTorsions = new torsion_set[molInfo.nTorsions];
187
188	<	// make the Atoms
188	>	// make the Atoms
189
190	<	for(j=0; j<info.nAtoms; j++){
392	<
393	<	currentAtom = comp_stamps[stampID]->getAtom( j );
394	<	if( currentAtom->haveOrientation() ){
190	>	for(j=0; j<molInfo.nAtoms; j++){
191
192	<	dAtom = new DirectionalAtom(j + atomOffset);
193	<	info->n_oriented++;
194	<	info.myAtoms[j] = dAtom;
195	<
196	<	ux = currentAtom->getOrntX();
197	<	uy = currentAtom->getOrntY();
198	<	uz = currentAtom->getOrntZ();
199	<
200	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
201	<
202	<	u = sqrt( uSqr );
203	<	ux = ux / u;
204	<	uy = uy / u;
205	<	uz = uz / u;
206	<
207	<	dAtom->setSUx( ux );
208	<	dAtom->setSUy( uy );
209	<	dAtom->setSUz( uz );
210	<	}
211	<	else{
212	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
213	<	}
214	<	info.myAtoms[j]->setType( currentAtom->getType() );
192	>	currentAtom = comp_stamps[stampID]->getAtom( j );
193	>	if( currentAtom->haveOrientation() ){
194	>
195	>	dAtom = new DirectionalAtom( (j + atomOffset),
196	>	info[k].getConfiguration() );
197	>	info[k].n_oriented++;
198	>	molInfo.myAtoms[j] = dAtom;
199	>
200	>	ux = currentAtom->getOrntX();
201	>	uy = currentAtom->getOrntY();
202	>	uz = currentAtom->getOrntZ();
203	>
204	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
205	>
206	>	u = sqrt( uSqr );
207	>	ux = ux / u;
208	>	uy = uy / u;
209	>	uz = uz / u;
210	>
211	>	dAtom->setSUx( ux );
212	>	dAtom->setSUy( uy );
213	>	dAtom->setSUz( uz );
214	>	}
215	>	else{
216	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
217	>	info[k].getConfiguration() );
218	>	}
219	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220
221		#ifdef IS_MPI
222
223	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
223	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224
225		#endif // is_mpi
226	<	}
226	>	}
227
228		// make the bonds
229	<	for(j=0; j<info.nBonds; j++){
229	>	for(j=0; j<molInfo.nBonds; j++){
230
231	<	currentBond = comp_stamps[stampID]->getBond( j );
232	<	theBonds[j].a = currentBond->getA() + atomOffset;
233	<	theBonds[j].b = currentBond->getB() + atomOffset;
234	<
235	<	exI = theBonds[j].a;
236	<	exJ = theBonds[j].b;
237	<
238	<	// exclude_I must always be the smaller of the pair
239	<	if( exI > exJ ){
240	<	tempEx = exI;
241	<	exI = exJ;
242	<	exJ = tempEx;
243	<	}
231	>	currentBond = comp_stamps[stampID]->getBond( j );
232	>	theBonds[j].a = currentBond->getA() + atomOffset;
233	>	theBonds[j].b = currentBond->getB() + atomOffset;
234	>
235	>	exI = theBonds[j].a;
236	>	exJ = theBonds[j].b;
237	>
238	>	// exclude_I must always be the smaller of the pair
239	>	if( exI > exJ ){
240	>	tempEx = exI;
241	>	exI = exJ;
242	>	exJ = tempEx;
243	>	}
244		#ifdef IS_MPI
245	<	tempEx = exI;
246	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
247	<	tempEx = exJ;
248	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
249	<
250	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
245	>	tempEx = exI;
246	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
247	>	tempEx = exJ;
248	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>
250	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
251		#else  // isn't MPI
252	<
253	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
252	>
253	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254		#endif  //is_mpi
255	<	}
256	<	excludeOffset += info.nBonds;
456	<
457	<	//make the bends
458	<	for(j=0; j<info.nBends; j++){
255	>	}
256	>	excludeOffset += molInfo.nBonds;
257
258	<	currentBend = comp_stamps[stampID]->getBend( j );
259	<	theBends[j].a = currentBend->getA() + atomOffset;
260	<	theBends[j].b = currentBend->getB() + atomOffset;
261	<	theBends[j].c = currentBend->getC() + atomOffset;
258	>	//make the bends
259	>	for(j=0; j<molInfo.nBends; j++){
260	>
261	>	currentBend = comp_stamps[stampID]->getBend( j );
262	>	theBends[j].a = currentBend->getA() + atomOffset;
263	>	theBends[j].b = currentBend->getB() + atomOffset;
264	>	theBends[j].c = currentBend->getC() + atomOffset;
265	>
266	>	if( currentBend->haveExtras() ){
267
268	<	if( currentBend->haveExtras() ){
269	<
270	<	extras = currentBend->getExtras();
271	<	current_extra = extras;
272	<
470	<	while( current_extra != NULL ){
471	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
472	<
473	<	switch( current_extra->getType() ){
268	>	extras = currentBend->getExtras();
269	>	current_extra = extras;
270	>
271	>	while( current_extra != NULL ){
272	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273
274	<	case 0:
275	<	theBends[j].ghost =
276	<	current_extra->getInt() + atomOffset;
277	<	theBends[j].isGhost = 1;
278	<	break;
279	<
280	<	case 1:
281	<	theBends[j].ghost =
282	<	(int)current_extra->getDouble() + atomOffset;
283	<	theBends[j].isGhost = 1;
284	<	break;
285	<
286	<	default:
274	>	switch( current_extra->getType() ){
275	>
276	>	case 0:
277	>	theBends[j].ghost =
278	>	current_extra->getInt() + atomOffset;
279	>	theBends[j].isGhost = 1;
280	>	break;
281	>
282	>	case 1:
283	>	theBends[j].ghost =
284	>	(int)current_extra->getDouble() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	default:
289	>	sprintf( painCave.errMsg,
290	>	"SimSetup Error: ghostVectorSource was neither a "
291	>	"double nor an int.\n"
292	>	"-->Bend[%d] in %s\n",
293	>	j, comp_stamps[stampID]->getID() );
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	}
298	>
299	>	else{
300	>
301		sprintf( painCave.errMsg,
302	<	"SimSetup Error: ghostVectorSource was neither a "
303	<	"double nor an int.\n"
304	<	"-->Bend[%d] in %s\n",
302	>	"SimSetup Error: unhandled bend assignment:\n"
303	>	"    -->%s in Bend[%d] in %s\n",
304	>	current_extra->getlhs(),
305		j, comp_stamps[stampID]->getID() );
306		painCave.isFatal = 1;
307		simError();
308		}
496	–	}
497	–
498	–	else{
309
310	<	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();
310	>	current_extra = current_extra->getNext();
311		}
312	+	}
313	+
314	+	if( !theBends[j].isGhost ){
315
316	<	current_extra = current_extra->getNext();
316	>	exI = theBends[j].a;
317	>	exJ = theBends[j].c;
318		}
319	<	}
319	>	else{
320
321	<	if( !theBends[j].isGhost ){
322	<
323	<	exI = theBends[j].a;
516	<	exJ = theBends[j].c;
517	<	}
518	<	else{
321	>	exI = theBends[j].a;
322	>	exJ = theBends[j].b;
323	>	}
324
325	<	exI = theBends[j].a;
326	<	exJ = theBends[j].b;
327	<	}
328	<
329	<	// exclude_I must always be the smaller of the pair
330	<	if( exI > exJ ){
526	<	tempEx = exI;
527	<	exI = exJ;
528	<	exJ = tempEx;
529	<	}
325	>	// exclude_I must always be the smaller of the pair
326	>	if( exI > exJ ){
327	>	tempEx = exI;
328	>	exI = exJ;
329	>	exJ = tempEx;
330	>	}
331		#ifdef IS_MPI
332	<	tempEx = exI;
333	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
334	<	tempEx = exJ;
335	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
332	>	tempEx = exI;
333	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exJ;
335	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336
337	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
337	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
338		#else  // isn't MPI
339	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
339	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340		#endif  //is_mpi
540	–	}
541	–	excludeOffset += info.nBends;
542	–
543	–	for(j=0; j<info.nTorsions; j++){
544	–
545	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
546	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
547	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
548	–	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;
341		}
342	<	#ifdef IS_MPI
561	<	tempEx = exI;
562	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
563	<	tempEx = exJ;
564	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
342	>	excludeOffset += molInfo.nBends;
343
344	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
344	>	for(j=0; j<molInfo.nTorsions; j++){
345	>
346	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	>
352	>	exI = theTorsions[j].a;
353	>	exJ = theTorsions[j].d;
354	>
355	>	// exclude_I must always be the smaller of the pair
356	>	if( exI > exJ ){
357	>	tempEx = exI;
358	>	exI = exJ;
359	>	exJ = tempEx;
360	>	}
361	>	#ifdef IS_MPI
362	>	tempEx = exI;
363	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
364	>	tempEx = exJ;
365	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	>
367	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
368		#else  // isn't MPI
369	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
369	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370		#endif  //is_mpi
371	<	}
372	<	excludeOffset += info.nTorsions;
371	>	}
372	>	excludeOffset += molInfo.nTorsions;
373	>
374	>
375	>	// send the arrays off to the forceField for init.
376	>
377	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381	>
382	>
383	>	info[k].molecules[i].initialize( molInfo );
384
385	<
386	<	// send the arrays off to the forceField for init.
387	<
388	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
389	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
390	<	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;
385	>
386	>	atomOffset += molInfo.nAtoms;
387	>	delete[] theBonds;
388	>	delete[] theBends;
389	>	delete[] theTorsions;
390	>	}
391		}
392	<
392	>
393		#ifdef IS_MPI
394		sprintf( checkPointMsg, "all molecules initialized succesfully" );
395		MPIcheckPoint();
396		#endif // is_mpi
397	<
397	>
398		// clean up the forcefield
399	+
400		the_ff->calcRcut();
401		the_ff->cleanMe();
402	<
402	>
403		}
404
405		void SimSetup::initFromBass( void ){
#	Line 609 | Line 412 | void SimSetup::initFromBass( void ){
412		int n_extra;
413		int have_extra, done;
414
415	+	double vel[3];
416	+	vel[0] = 0.0;
417	+	vel[1] = 0.0;
418	+	vel[2] = 0.0;
419	+
420		temp1 = (double)tot_nmol / 4.0;
421		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
422		temp3 = ceil( temp2 );
#	Line 618 | Line 426 | void SimSetup::initFromBass( void ){
426		have_extra =1;
427
428		n_cells = (int)temp3 - 1;
429	<	cellx = info->boxLx / temp3;
430	<	celly = info->boxLy / temp3;
431	<	cellz = info->boxLz / temp3;
429	>	cellx = info[0].boxL[0] / temp3;
430	>	celly = info[0].boxL[1] / temp3;
431	>	cellz = info[0].boxL[2] / temp3;
432		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
433		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
434		n_per_extra = (int)ceil( temp1 );
#	Line 635 | Line 443 | void SimSetup::initFromBass( void ){
443		}
444		else{
445		n_cells = (int)temp3;
446	<	cellx = info->boxLx / temp3;
447	<	celly = info->boxLy / temp3;
448	<	cellz = info->boxLz / temp3;
446	>	cellx = info[0].boxL[0] / temp3;
447	>	celly = info[0].boxL[1] / temp3;
448	>	cellz = info[0].boxL[2] / temp3;
449		}
450
451		current_mol = 0;
#	Line 716 | Line 524 | void SimSetup::initFromBass( void ){
524		}
525		}
526
527	<
528	<	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 );
527	>	for( i=0; i<info[0].n_atoms; i++ ){
528	>	info[0].atoms[i]->setVel( vel );
529		}
530		}
531
#	Line 730 | Line 535 | void SimSetup::makeElement( double x, double y, double
535		AtomStamp* current_atom;
536		DirectionalAtom* dAtom;
537		double rotMat[3][3];
538	+	double pos[3];
539
540		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
541
#	Line 745 | Line 551 | void SimSetup::makeElement( double x, double y, double
551		painCave.isFatal = 1;
552		simError();
553		}
554	+
555	+	pos[0] = x + current_atom->getPosX();
556	+	pos[1] = y + current_atom->getPosY();
557	+	pos[2] = z + current_atom->getPosZ();
558	+
559	+	info[0].atoms[current_atom_ndx]->setPos( pos );
560
561	<	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() );
561	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
562
563	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
563	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
564
755	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
756	–
565		rotMat[0][0] = 1.0;
566		rotMat[0][1] = 0.0;
567		rotMat[0][2] = 0.0;
#	Line 784 | Line 592 | void SimSetup::gatherInfo( void ){
592
593
594		void SimSetup::gatherInfo( void ){
595	+	int i,j,k;
596
597		ensembleCase = -1;
598		ffCase = -1;
599
791	–	// get the stamps and globals;
792	–	the_stamps = stamps;
793	–	the_globals = globals;
794	–
600		// 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();
601
602	+	for( i=0; i<nInfo; i++){
603	+	info[i].target_temp = globals->getTargetTemp();
604	+	info[i].dt = globals->getDt();
605	+	info[i].run_time = globals->getRunTime();
606	+	}
607	+	n_components = globals->getNComponents();
608
609	+
610		// get the forceField
611
612	<	strcpy( force_field, the_globals->getForceField() );
612	>	strcpy( force_field, globals->getForceField() );
613
614		if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
615		else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
616	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
617		else{
618		sprintf( painCave.errMsg,
619		"SimSetup Error. Unrecognized force field -> %s\n",
#	Line 815 | Line 624 | void SimSetup::gatherInfo( void ){
624
625		// get the ensemble
626
627	<	strcpy( ensemble, the_globals->getEnsemble() );
627	>	strcpy( ensemble, globals->getEnsemble() );
628
629		if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
630		else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
#	Line 834 | Line 643 | void SimSetup::gatherInfo( void ){
643		strcpy( ensemble, "NVE" );
644		ensembleCase = NVE_ENS;
645		}
646	<	strcpy( info->ensemble, ensemble );
646	>
647	>	for(i=0; i<nInfo; i++){
648	>
649	>	strcpy( info[i].ensemble, ensemble );
650
651	<	// get the mixing rule
651	>	// get the mixing rule
652
653	<	strcpy( info->mixingRule, the_globals->getMixingRule() );
654	<	info->usePBC = the_globals->getPBC();
655	<
653	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
654	>	info[i].usePBC = globals->getPBC();
655	>	}
656
657		// get the components and calculate the tot_nMol and indvidual n_mol
658
659	<	the_components = the_globals->getComponents();
659	>	the_components = globals->getComponents();
660		components_nmol = new int[n_components];
661
662
663	<	if( !the_globals->haveNMol() ){
663	>	if( !globals->haveNMol() ){
664		// we don't have the total number of molecules, so we assume it is
665		// given in each component
666
#	Line 881 | Line 693 | void SimSetup::gatherInfo( void ){
693
694		// set the status, sample, and thermal kick times
695
696	<	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	<	}
696	>	for(i=0; i<nInfo; i++){
697
698	<	if( the_globals->haveStatusTime() ){
699	<	info->statusTime = the_globals->getStatusTime();
700	<	}
701	<
702	<	if( the_globals->haveThermalTime() ){
703	<	info->thermalTime = the_globals->getThermalTime();
704	<	}
705	<
706	<	// check for the temperature set flag
707	<
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();
698	>	if( globals->haveSampleTime() ){
699	>	info[i].sampleTime = globals->getSampleTime();
700	>	info[i].statusTime = info[i].sampleTime;
701	>	info[i].thermalTime = info[i].sampleTime;
702	>	}
703	>	else{
704	>	info[i].sampleTime = globals->getRunTime();
705	>	info[i].statusTime = info[i].sampleTime;
706	>	info[i].thermalTime = info[i].sampleTime;
707	>	}
708
709	<	info->setBox( boxVector );
710	<	}
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();
709	>	if( globals->haveStatusTime() ){
710	>	info[i].statusTime = globals->getStatusTime();
711		}
712	<	boxVector[0] = the_globals->getBoxX();
713	<
714	<	if( !the_globals->haveBoxY() ){
937	<	sprintf( painCave.errMsg,
938	<	"SimSetup error, no periodic BoxY size given.\n" );
939	<	painCave.isFatal = 1;
940	<	simError();
712	>
713	>	if( globals->haveThermalTime() ){
714	>	info[i].thermalTime = globals->getThermalTime();
715		}
942	–	boxVector[1] = the_globals->getBoxY();
716
717	<	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();
717	>	// check for the temperature set flag
718
719	<	info->setBox( boxVector );
719	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
720	>
721	>	// get some of the tricky things that may still be in the globals
722	>
723	>	double boxVector[3];
724	>	if( globals->haveBox() ){
725	>	boxVector[0] = globals->getBox();
726	>	boxVector[1] = globals->getBox();
727	>	boxVector[2] = globals->getBox();
728	>
729	>	info[i].setBox( boxVector );
730	>	}
731	>	else if( globals->haveDensity() ){
732	>
733	>	double vol;
734	>	vol = (double)tot_nmol / globals->getDensity();
735	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
736	>	boxVector[1] = boxVector[0];
737	>	boxVector[2] = boxVector[0];
738	>
739	>	info[i].setBox( boxVector );
740		}
741	+	else{
742	+	if( !globals->haveBoxX() ){
743	+	sprintf( painCave.errMsg,
744	+	"SimSetup error, no periodic BoxX size given.\n" );
745	+	painCave.isFatal = 1;
746	+	simError();
747	+	}
748	+	boxVector[0] = globals->getBoxX();
749	+
750	+	if( !globals->haveBoxY() ){
751	+	sprintf( painCave.errMsg,
752	+	"SimSetup error, no periodic BoxY size given.\n" );
753	+	painCave.isFatal = 1;
754	+	simError();
755	+	}
756	+	boxVector[1] = globals->getBoxY();
757	+
758	+	if( !globals->haveBoxZ() ){
759	+	sprintf( painCave.errMsg,
760	+	"SimSetup error, no periodic BoxZ size given.\n" );
761	+	painCave.isFatal = 1;
762	+	simError();
763	+	}
764	+	boxVector[2] = globals->getBoxZ();
765	+
766	+	info[i].setBox( boxVector );
767	+	}
768
769	<
769	>	}
770
771		#ifdef IS_MPI
772		strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
#	Line 965 | Line 779 | void SimSetup::finalInfoCheck( void ){
779		void SimSetup::finalInfoCheck( void ){
780		int index;
781		int usesDipoles;
782	<
782	>	int i;
783
784	<	// check electrostatic parameters
785	<
972	<	index = 0;
973	<	usesDipoles = 0;
974	<	while( (index < info->n_atoms) && !usesDipoles ){
975	<	usesDipoles = ((info->atoms)[index])->hasDipole();
976	<	index++;
977	<	}
978	<
979	<	#ifdef IS_MPI
980	<	int myUse = usesDipoles
981	<	MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
982	<	#endif //is_mpi
983	<
984	<
985	<	if (the_globals->getUseRF() ) {
986	<	info->useReactionField = 1;
784	>	for(i=0; i<nInfo; i++){
785	>	// check electrostatic parameters
786
787	<	if( !the_globals->haveECR() ){
788	<	sprintf( painCave.errMsg,
789	<	"SimSetup Warning: using default value of 1/2 the smallest "
790	<	"box length for the electrostaticCutoffRadius.\n"
791	<	"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();
787	>	index = 0;
788	>	usesDipoles = 0;
789	>	while( (index < info[i].n_atoms) && !usesDipoles ){
790	>	usesDipoles = (info[i].atoms[index])->hasDipole();
791	>	index++;
792		}
793
794	<	if(!the_globals->haveDielectric() ){
795	<	sprintf( painCave.errMsg,
796	<	"SimSetup Error: You are trying to use Reaction Field without"
797	<	"setting a dielectric constant!\n"
798	<	);
799	<	painCave.isFatal = 1;
800	<	simError();
801	<	}
802	<	info->dielectric = the_globals->getDielectric();
1025	<	}
1026	<	else {
1027	<	if (usesDipoles) {
794	>	#ifdef IS_MPI
795	>	int myUse = usesDipoles;
796	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
797	>	#endif //is_mpi
798	>
799	>	double theEcr, theEst;
800	>
801	>	if (globals->getUseRF() ) {
802	>	info[i].useReactionField = 1;
803
804	<	if( !the_globals->haveECR() ){
805	<	sprintf( painCave.errMsg,
806	<	"SimSetup Warning: using default value of 1/2 the smallest "
807	<	"box length for the electrostaticCutoffRadius.\n"
808	<	"I hope you have a very fast processor!\n");
809	<	painCave.isFatal = 0;
810	<	simError();
811	<	double smallest;
812	<	smallest = info->boxLx;
813	<	if (info->boxLy <= smallest) smallest = info->boxLy;
814	<	if (info->boxLz <= smallest) smallest = info->boxLz;
815	<	info->ecr = 0.5 * smallest;
804	>	if( !globals->haveECR() ){
805	>	sprintf( painCave.errMsg,
806	>	"SimSetup Warning: using default value of 1/2 the smallest "
807	>	"box length for the electrostaticCutoffRadius.\n"
808	>	"I hope you have a very fast processor!\n");
809	>	painCave.isFatal = 0;
810	>	simError();
811	>	double smallest;
812	>	smallest = info[i].boxL[0];
813	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
814	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
815	>	theEcr = 0.5 * smallest;
816		} else {
817	<	info->ecr        = the_globals->getECR();
817	>	theEcr = globals->getECR();
818		}
819
820	<	if( !the_globals->haveEST() ){
821	<	sprintf( painCave.errMsg,
822	<	"SimSetup Warning: using default value of 5%% of the "
823	<	"electrostaticCutoffRadius for the "
824	<	"electrostaticSkinThickness\n"
825	<	);
826	<	painCave.isFatal = 0;
827	<	simError();
1053	<	info->est = 0.05 * info->ecr;
820	>	if( !globals->haveEST() ){
821	>	sprintf( painCave.errMsg,
822	>	"SimSetup Warning: using default value of 0.05 * the "
823	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
824	>	);
825	>	painCave.isFatal = 0;
826	>	simError();
827	>	theEst = 0.05 * theEcr;
828		} else {
829	<	info->est        = the_globals->getEST();
829	>	theEst= globals->getEST();
830		}
831	<	}
832	<	}
831	>
832	>	info[i].setEcr( theEcr, theEst );
833	>
834	>	if(!globals->haveDielectric() ){
835	>	sprintf( painCave.errMsg,
836	>	"SimSetup Error: You are trying to use Reaction Field without"
837	>	"setting a dielectric constant!\n"
838	>	);
839	>	painCave.isFatal = 1;
840	>	simError();
841	>	}
842	>	info[i].dielectric = globals->getDielectric();
843	>	}
844	>	else {
845	>	if (usesDipoles) {
846	>
847	>	if( !globals->haveECR() ){
848	>	sprintf( painCave.errMsg,
849	>	"SimSetup Warning: using default value of 1/2 the smallest "
850	>	"box length for the electrostaticCutoffRadius.\n"
851	>	"I hope you have a very fast processor!\n");
852	>	painCave.isFatal = 0;
853	>	simError();
854	>	double smallest;
855	>	smallest = info[i].boxL[0];
856	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
857	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
858	>	theEcr = 0.5 * smallest;
859	>	} else {
860	>	theEcr = globals->getECR();
861	>	}
862	>
863	>	if( !globals->haveEST() ){
864	>	sprintf( painCave.errMsg,
865	>	"SimSetup Warning: using default value of 0.05 * the "
866	>	"electrostaticCutoffRadius for the "
867	>	"electrostaticSkinThickness\n"
868	>	);
869	>	painCave.isFatal = 0;
870	>	simError();
871	>	theEst = 0.05 * theEcr;
872	>	} else {
873	>	theEst= globals->getEST();
874	>	}
875	>
876	>	info[i].setEcr( theEcr, theEst );
877	>	}
878	>	}
879	>	}
880
881		#ifdef IS_MPI
882		strcpy( checkPointMsg, "post processing checks out" );
#	Line 1065 | Line 886 | void SimSetup::initSystemCoords( void ){
886		}
887
888		void SimSetup::initSystemCoords( void ){
889	+	int i;
890	+
891	+	std::cerr << "Setting atom Coords\n";
892
893	<	if( the_globals->haveInitialConfig() ){
894	<
895	<	InitializeFromFile* fileInit;
893	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
894	>
895	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
896	>
897	>	if( globals->haveInitialConfig() ){
898	>
899	>	InitializeFromFile* fileInit;
900		#ifdef IS_MPI // is_mpi
901	<	if( worldRank == 0 ){
901	>	if( worldRank == 0 ){
902		#endif //is_mpi
903	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
903	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
904		#ifdef IS_MPI
905	<	}else fileInit = new InitializeFromFile( NULL );
905	>	}else fileInit = new InitializeFromFile( NULL );
906		#endif
907	<	fileInit->read_xyz( info ); // default velocities on
908	<
909	<	delete fileInit;
910	<	}
911	<	else{
912	<
907	>	fileInit->readInit( info ); // default velocities on
908	>
909	>	delete fileInit;
910	>	}
911	>	else{
912	>
913		#ifdef IS_MPI
914	<
915	<	// no init from bass
916	<
917	<	sprintf( painCave.errMsg,
918	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
919	<	painCave.isFatal;
920	<	simError();
921	<
914	>
915	>	// no init from bass
916	>
917	>	sprintf( painCave.errMsg,
918	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
919	>	painCave.isFatal;
920	>	simError();
921	>
922		#else
923	<
924	<	initFromBass();
925	<
926	<
923	>
924	>	initFromBass();
925	>
926	>
927		#endif
928	<	}
929	<
928	>	}
929	>
930		#ifdef IS_MPI
931		strcpy( checkPointMsg, "Successfully read in the initial configuration" );
932		MPIcheckPoint();
933		#endif // is_mpi
934	<
934	>
935		}
936
937
938		void SimSetup::makeOutNames( void ){
939	+
940	+	int k;
941
942	+
943	+	for(k=0; k<nInfo; k++){
944	+
945		#ifdef IS_MPI
946	<	if( worldRank == 0 ){
946	>	if( worldRank == 0 ){
947		#endif // is_mpi
948	<
949	<	if( the_globals->haveFinalConfig() ){
950	<	strcpy( info->finalName, the_globals->getFinalConfig() );
1118	<	}
1119	<	else{
1120	<	strcpy( info->finalName, inFileName );
1121	<	char* endTest;
1122	<	int nameLength = strlen( info->finalName );
1123	<	endTest = &(info->finalName[nameLength - 5]);
1124	<	if( !strcmp( endTest, ".bass" ) ){
1125	<	strcpy( endTest, ".eor" );
948	>
949	>	if( globals->haveFinalConfig() ){
950	>	strcpy( info[k].finalName, globals->getFinalConfig() );
951		}
1127	–	else if( !strcmp( endTest, ".BASS" ) ){
1128	–	strcpy( endTest, ".eor" );
1129	–	}
952		else{
953	<	endTest = &(info->finalName[nameLength - 4]);
954	<	if( !strcmp( endTest, ".bss" ) ){
953	>	strcpy( info[k].finalName, inFileName );
954	>	char* endTest;
955	>	int nameLength = strlen( info[k].finalName );
956	>	endTest = &(info[k].finalName[nameLength - 5]);
957	>	if( !strcmp( endTest, ".bass" ) ){
958		strcpy( endTest, ".eor" );
959		}
960	<	else if( !strcmp( endTest, ".mdl" ) ){
960	>	else if( !strcmp( endTest, ".BASS" ) ){
961		strcpy( endTest, ".eor" );
962		}
963		else{
964	<	strcat( info->finalName, ".eor" );
964	>	endTest = &(info[k].finalName[nameLength - 4]);
965	>	if( !strcmp( endTest, ".bss" ) ){
966	>	strcpy( endTest, ".eor" );
967	>	}
968	>	else if( !strcmp( endTest, ".mdl" ) ){
969	>	strcpy( endTest, ".eor" );
970	>	}
971	>	else{
972	>	strcat( info[k].finalName, ".eor" );
973	>	}
974		}
975		}
976	<	}
977	<
978	<	// make the sample and status out names
979	<
980	<	strcpy( info->sampleName, inFileName );
981	<	char* endTest;
982	<	int nameLength = strlen( info->sampleName );
983	<	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" ) ){
976	>
977	>	// make the sample and status out names
978	>
979	>	strcpy( info[k].sampleName, inFileName );
980	>	char* endTest;
981	>	int nameLength = strlen( info[k].sampleName );
982	>	endTest = &(info[k].sampleName[nameLength - 5]);
983	>	if( !strcmp( endTest, ".bass" ) ){
984		strcpy( endTest, ".dump" );
985		}
986	<	else if( !strcmp( endTest, ".mdl" ) ){
986	>	else if( !strcmp( endTest, ".BASS" ) ){
987		strcpy( endTest, ".dump" );
988		}
989		else{
990	<	strcat( info->sampleName, ".dump" );
990	>	endTest = &(info[k].sampleName[nameLength - 4]);
991	>	if( !strcmp( endTest, ".bss" ) ){
992	>	strcpy( endTest, ".dump" );
993	>	}
994	>	else if( !strcmp( endTest, ".mdl" ) ){
995	>	strcpy( endTest, ".dump" );
996	>	}
997	>	else{
998	>	strcat( info[k].sampleName, ".dump" );
999	>	}
1000		}
1001	<	}
1002	<
1003	<	strcpy( info->statusName, inFileName );
1004	<	nameLength = strlen( info->statusName );
1005	<	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" ) ){
1001	>
1002	>	strcpy( info[k].statusName, inFileName );
1003	>	nameLength = strlen( info[k].statusName );
1004	>	endTest = &(info[k].statusName[nameLength - 5]);
1005	>	if( !strcmp( endTest, ".bass" ) ){
1006		strcpy( endTest, ".stat" );
1007		}
1008	<	else if( !strcmp( endTest, ".mdl" ) ){
1008	>	else if( !strcmp( endTest, ".BASS" ) ){
1009		strcpy( endTest, ".stat" );
1010		}
1011		else{
1012	<	strcat( info->statusName, ".stat" );
1012	>	endTest = &(info[k].statusName[nameLength - 4]);
1013	>	if( !strcmp( endTest, ".bss" ) ){
1014	>	strcpy( endTest, ".stat" );
1015	>	}
1016	>	else if( !strcmp( endTest, ".mdl" ) ){
1017	>	strcpy( endTest, ".stat" );
1018	>	}
1019	>	else{
1020	>	strcat( info[k].statusName, ".stat" );
1021	>	}
1022		}
1023	<	}
1190	<
1023	>
1024		#ifdef IS_MPI
1025	<	}
1025	>	}
1026		#endif // is_mpi
1027	<
1027	>	}
1028		}
1029
1030
1031		void SimSetup::sysObjectsCreation( void ){
1032	<
1032	>
1033	>	int i,k;
1034	>
1035		// create the forceField
1036	<
1036	>
1037		createFF();
1038
1039		// extract componentList
#	Line 1219 | Line 1054 | void SimSetup::sysObjectsCreation( void ){
1054
1055		makeSysArrays();
1056
1057	+	// make and initialize the molecules (all but atomic coordinates)
1058
1059	<
1060	<
1059	>	makeMolecules();
1060	>
1061	>	for(k=0; k<nInfo; k++){
1062	>	info[k].identArray = new int[info[k].n_atoms];
1063	>	for(i=0; i<info[k].n_atoms; i++){
1064	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1065	>	}
1066	>	}
1067		}
1068
1069
#	Line 1237 | Line 1079 | void SimSetup::createFF( void ){
1079		the_ff = new LJFF();
1080		break;
1081
1082	+	case FF_EAM:
1083	+	the_ff = new EAM_FF();
1084	+	break;
1085	+
1086		default:
1087		sprintf( painCave.errMsg,
1088		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1254 | Line 1100 | void SimSetup::compList( void ){
1100
1101		void SimSetup::compList( void ){
1102
1103	+	int i;
1104	+	char* id;
1105	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1106	+	LinkedMolStamp* currentStamp = NULL;
1107		comp_stamps = new MoleculeStamp*[n_components];
1108	<
1108	>
1109		// make an array of molecule stamps that match the components used.
1110		// 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();
1111
1112	<	char* id;
1113	<	LinkedMolStamp* headStamp = info->headStamp;
1114	<	LinkedMolStamp* currentStamp = NULL;
1112	>	for(i=0; i<nInfo; i++){
1113	>	info[i].nComponents = n_components;
1114	>	info[i].componentsNmol = components_nmol;
1115	>	info[i].compStamps = comp_stamps;
1116	>	info[i].headStamp = headStamp;
1117	>	}
1118	>
1119	>
1120		for( i=0; i<n_components; i++ ){
1121
1122		id = the_components[i]->getType();
#	Line 1279 | Line 1129 | void SimSetup::compList( void ){
1129
1130		// extract the component from the list;
1131
1132	<	currentStamp = the_stamps->extractMolStamp( id );
1132	>	currentStamp = stamps->extractMolStamp( id );
1133		if( currentStamp == NULL ){
1134		sprintf( painCave.errMsg,
1135		"SimSetup error: Component \"%s\" was not found in the "
#	Line 1303 | Line 1153 | void SimSetup::calcSysValues( void ){
1153		}
1154
1155		void SimSetup::calcSysValues( void ){
1156	<
1156	>	int i, j, k;
1157	>
1158	>	int *molMembershipArray;
1159	>
1160		tot_atoms = 0;
1161		tot_bonds = 0;
1162		tot_bends = 0;
#	Line 1315 | Line 1168 | void SimSetup::calcSysValues( void ){
1168		tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1169		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1170		}
1171	<
1171	>
1172		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1173	<
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;
1173	>	molMembershipArray = new int[tot_atoms];
1174
1175	<	info->molMembershipArray = new int[tot_atoms];
1175	>	for(i=0; i<nInfo; i++){
1176	>	info[i].n_atoms = tot_atoms;
1177	>	info[i].n_bonds = tot_bonds;
1178	>	info[i].n_bends = tot_bends;
1179	>	info[i].n_torsions = tot_torsions;
1180	>	info[i].n_SRI = tot_SRI;
1181	>	info[i].n_mol = tot_nmol;
1182	>
1183	>	info[i].molMembershipArray = molMembershipArray;
1184	>	}
1185		}
1186
1331	–
1187		#ifdef IS_MPI
1188
1189		void SimSetup::mpiMolDivide( void ){
1190
1191	+	int i, j, k;
1192		int localMol, allMol;
1193		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1194
#	Line 1367 | Line 1223 | void SimSetup::mpiMolDivide( void ){
1223		localMol++;
1224		}
1225		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1226	<	info->molMembershipArray[globalAtomIndex] = allMol;
1226	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1227		globalAtomIndex++;
1228		}
1229
#	Line 1376 | Line 1232 | void SimSetup::mpiMolDivide( void ){
1232		}
1233		local_SRI = local_bonds + local_bends + local_torsions;
1234
1235	<	info->n_atoms = mpiSim->getMyNlocal();
1235	>	info[0].n_atoms = mpiSim->getMyNlocal();
1236
1237	<	if( local_atoms != info->n_atoms ){
1237	>	if( local_atoms != info[0].n_atoms ){
1238		sprintf( painCave.errMsg,
1239		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240		" localAtom (%d) are not equal.\n",
1241	<	info->n_atoms,
1241	>	info[0].n_atoms,
1242		local_atoms );
1243		painCave.isFatal = 1;
1244		simError();
1245		}
1246
1247	<	info->n_bonds = local_bonds;
1248	<	info->n_bends = local_bends;
1249	<	info->n_torsions = local_torsions;
1250	<	info->n_SRI = local_SRI;
1251	<	info->n_mol = localMol;
1247	>	info[0].n_bonds = local_bonds;
1248	>	info[0].n_bends = local_bends;
1249	>	info[0].n_torsions = local_torsions;
1250	>	info[0].n_SRI = local_SRI;
1251	>	info[0].n_mol = localMol;
1252
1253		strcpy( checkPointMsg, "Passed nlocal consistency check." );
1254		MPIcheckPoint();
1255		}
1256	<
1256	>
1257		#endif // is_mpi
1258
1259
1260		void SimSetup::makeSysArrays( void ){
1261	+	int i, j, k, l;
1262
1263	<	// create the atom and short range interaction arrays
1263	>	Atom** the_atoms;
1264	>	Molecule* the_molecules;
1265	>	Exclude** the_excludes;
1266
1267	<	Atom::createArrays(info->n_atoms);
1268	<	the_atoms = new Atom*[info->n_atoms];
1269	<	the_molecules = new Molecule[info->n_mol];
1270	<	int molIndex;
1267	>
1268	>	for(l=0; l<nInfo; l++){
1269	>
1270	>	// create the atom and short range interaction arrays
1271	>
1272	>	the_atoms = new Atom*[info[l].n_atoms];
1273	>	the_molecules = new Molecule[info[l].n_mol];
1274	>	int molIndex;
1275
1276	<	// initialize the molecule's stampID's
1277	<
1276	>	// initialize the molecule's stampID's
1277	>
1278		#ifdef IS_MPI
1416	–
1417	–
1418	–	molIndex = 0;
1419	–	for(i=0; i<mpiSim->getTotNmol(); i++){
1279
1280	<	if(mol2proc[i] == worldRank ){
1281	<	the_molecules[molIndex].setStampID( molCompType[i] );
1282	<	the_molecules[molIndex].setMyIndex( molIndex );
1283	<	the_molecules[molIndex].setGlobalIndex( i );
1284	<	molIndex++;
1280	>
1281	>	molIndex = 0;
1282	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1283	>
1284	>	if(mol2proc[i] == worldRank ){
1285	>	the_molecules[molIndex].setStampID( molCompType[i] );
1286	>	the_molecules[molIndex].setMyIndex( molIndex );
1287	>	the_molecules[molIndex].setGlobalIndex( i );
1288	>	molIndex++;
1289	>	}
1290		}
1291	<	}
1428	<
1291	>
1292		#else // is_mpi
1293	<
1294	<	molIndex = 0;
1295	<	globalAtomIndex = 0;
1296	<	for(i=0; i<n_components; i++){
1297	<	for(j=0; j<components_nmol[i]; j++ ){
1298	<	the_molecules[molIndex].setStampID( i );
1299	<	the_molecules[molIndex].setMyIndex( molIndex );
1300	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1301	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1302	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1303	<	globalAtomIndex++;
1293	>
1294	>	molIndex = 0;
1295	>	globalAtomIndex = 0;
1296	>	for(i=0; i<n_components; i++){
1297	>	for(j=0; j<components_nmol[i]; j++ ){
1298	>	the_molecules[molIndex].setStampID( i );
1299	>	the_molecules[molIndex].setMyIndex( molIndex );
1300	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1301	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1302	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1303	>	globalAtomIndex++;
1304	>	}
1305	>	molIndex++;
1306		}
1442	–	molIndex++;
1307		}
1444	–	}
1308
1309	<
1309	>
1310		#endif // is_mpi
1311
1312
1313	<	if( info->n_SRI ){
1313	>	if( info[l].n_SRI ){
1314
1315	<	Exclude::createArray(info->n_SRI);
1316	<	the_excludes = new Exclude*[info->n_SRI];
1317	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1318	<	info->globalExcludes = new int;
1319	<	info->n_exclude = info->n_SRI;
1315	>	Exclude::createArray(info[l].n_SRI);
1316	>	the_excludes = new Exclude*[info[l].n_SRI];
1317	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1318	>	the_excludes[ex] = new Exclude(ex);
1319	>	}
1320	>	info[l].globalExcludes = new int;
1321	>	info[l].n_exclude = info[l].n_SRI;
1322	>	}
1323	>	else{
1324	>
1325	>	Exclude::createArray( 1 );
1326	>	the_excludes = new Exclude*;
1327	>	the_excludes[0] = new Exclude(0);
1328	>	the_excludes[0]->setPair( 0,0 );
1329	>	info[l].globalExcludes = new int;
1330	>	info[l].globalExcludes[0] = 0;
1331	>	info[l].n_exclude = 0;
1332	>	}
1333	>
1334	>	// set the arrays into the SimInfo object
1335	>
1336	>	info[l].atoms = the_atoms;
1337	>	info[l].molecules = the_molecules;
1338	>	info[l].nGlobalExcludes = 0;
1339	>	info[l].excludes = the_excludes;
1340	>
1341	>	the_ff->setSimInfo( info );
1342	>
1343		}
1344	<	else{
1344	>	}
1345	>
1346	>	void SimSetup::makeIntegrator( void ){
1347	>
1348	>	int k;
1349	>
1350	>	NVT<RealIntegrator>*  myNVT = NULL;
1351	>	NPTi<RealIntegrator>* myNPTi = NULL;
1352	>	NPTf<RealIntegrator>* myNPTf = NULL;
1353	>	NPTim<RealIntegrator>* myNPTim = NULL;
1354	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1355	>
1356	>	for(k=0; k<nInfo; k++){
1357
1358	<	Exclude::createArray( 1 );
1359	<	the_excludes = new Exclude*;
1360	<	the_excludes[0] = new Exclude(0);
1361	<	the_excludes[0]->setPair( 0,0 );
1362	<	info->globalExcludes = new int;
1363	<	info->globalExcludes[0] = 0;
1364	<	info->n_exclude = 0;
1358	>	switch( ensembleCase ){
1359	>
1360	>	case NVE_ENS:
1361	>	if (haveZConstraint){
1362	>	setupZConstraint();
1363	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1364	>	}
1365	>
1366	>	else
1367	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1368	>	break;
1369	>
1370	>	case NVT_ENS:
1371	>	if (haveZConstraint){
1372	>	setupZConstraint();
1373	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1374	>	}
1375	>	else
1376	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1377	>
1378	>	myNVT->setTargetTemp(globals->getTargetTemp());
1379	>
1380	>	if (globals->haveTauThermostat())
1381	>	myNVT->setTauThermostat(globals->getTauThermostat());
1382	>
1383	>	else {
1384	>	sprintf( painCave.errMsg,
1385	>	"SimSetup error: If you use the NVT\n"
1386	>	"    ensemble, you must set tauThermostat.\n");
1387	>	painCave.isFatal = 1;
1388	>	simError();
1389	>	}
1390	>	break;
1391	>
1392	>	case NPTi_ENS:
1393	>	if (haveZConstraint){
1394	>	setupZConstraint();
1395	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1396	>	}
1397	>	else
1398	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1399	>
1400	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1401	>
1402	>	if (globals->haveTargetPressure())
1403	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1404	>	else {
1405	>	sprintf( painCave.errMsg,
1406	>	"SimSetup error: If you use a constant pressure\n"
1407	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1408	>	painCave.isFatal = 1;
1409	>	simError();
1410	>	}
1411	>
1412	>	if( globals->haveTauThermostat() )
1413	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1414	>	else{
1415	>	sprintf( painCave.errMsg,
1416	>	"SimSetup error: If you use an NPT\n"
1417	>	"    ensemble, you must set tauThermostat.\n");
1418	>	painCave.isFatal = 1;
1419	>	simError();
1420	>	}
1421	>
1422	>	if( globals->haveTauBarostat() )
1423	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1424	>	else{
1425	>	sprintf( painCave.errMsg,
1426	>	"SimSetup error: If you use an NPT\n"
1427	>	"    ensemble, you must set tauBarostat.\n");
1428	>	painCave.isFatal = 1;
1429	>	simError();
1430	>	}
1431	>	break;
1432	>
1433	>	case NPTf_ENS:
1434	>	if (haveZConstraint){
1435	>	setupZConstraint();
1436	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1437	>	}
1438	>	else
1439	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1440	>
1441	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1442	>
1443	>	if (globals->haveTargetPressure())
1444	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1445	>	else {
1446	>	sprintf( painCave.errMsg,
1447	>	"SimSetup error: If you use a constant pressure\n"
1448	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	>	painCave.isFatal = 1;
1450	>	simError();
1451	>	}
1452	>
1453	>	if( globals->haveTauThermostat() )
1454	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1455	>	else{
1456	>	sprintf( painCave.errMsg,
1457	>	"SimSetup error: If you use an NPT\n"
1458	>	"    ensemble, you must set tauThermostat.\n");
1459	>	painCave.isFatal = 1;
1460	>	simError();
1461	>	}
1462	>
1463	>	if( globals->haveTauBarostat() )
1464	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1465	>	else{
1466	>	sprintf( painCave.errMsg,
1467	>	"SimSetup error: If you use an NPT\n"
1468	>	"    ensemble, you must set tauBarostat.\n");
1469	>	painCave.isFatal = 1;
1470	>	simError();
1471	>	}
1472	>	break;
1473	>
1474	>	case NPTim_ENS:
1475	>	if (haveZConstraint){
1476	>	setupZConstraint();
1477	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1478	>	}
1479	>	else
1480	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1481	>
1482	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1483	>
1484	>	if (globals->haveTargetPressure())
1485	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1486	>	else {
1487	>	sprintf( painCave.errMsg,
1488	>	"SimSetup error: If you use a constant pressure\n"
1489	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1490	>	painCave.isFatal = 1;
1491	>	simError();
1492	>	}
1493	>
1494	>	if( globals->haveTauThermostat() )
1495	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1496	>	else{
1497	>	sprintf( painCave.errMsg,
1498	>	"SimSetup error: If you use an NPT\n"
1499	>	"    ensemble, you must set tauThermostat.\n");
1500	>	painCave.isFatal = 1;
1501	>	simError();
1502	>	}
1503	>
1504	>	if( globals->haveTauBarostat() )
1505	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1506	>	else{
1507	>	sprintf( painCave.errMsg,
1508	>	"SimSetup error: If you use an NPT\n"
1509	>	"    ensemble, you must set tauBarostat.\n");
1510	>	painCave.isFatal = 1;
1511	>	simError();
1512	>	}
1513	>	break;
1514	>
1515	>	case NPTfm_ENS:
1516	>	if (haveZConstraint){
1517	>	setupZConstraint();
1518	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1519	>	}
1520	>	else
1521	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1522	>
1523	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1524	>
1525	>	if (globals->haveTargetPressure())
1526	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1527	>	else {
1528	>	sprintf( painCave.errMsg,
1529	>	"SimSetup error: If you use a constant pressure\n"
1530	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1531	>	painCave.isFatal = 1;
1532	>	simError();
1533	>	}
1534	>
1535	>	if( globals->haveTauThermostat() )
1536	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1537	>	else{
1538	>	sprintf( painCave.errMsg,
1539	>	"SimSetup error: If you use an NPT\n"
1540	>	"    ensemble, you must set tauThermostat.\n");
1541	>	painCave.isFatal = 1;
1542	>	simError();
1543	>	}
1544	>
1545	>	if( globals->haveTauBarostat() )
1546	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1547	>	else{
1548	>	sprintf( painCave.errMsg,
1549	>	"SimSetup error: If you use an NPT\n"
1550	>	"    ensemble, you must set tauBarostat.\n");
1551	>	painCave.isFatal = 1;
1552	>	simError();
1553	>	}
1554	>	break;
1555	>
1556	>	default:
1557	>	sprintf( painCave.errMsg,
1558	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1559	>	painCave.isFatal = 1;
1560	>	simError();
1561	>	}
1562		}
1563	+	}
1564
1565	<	// set the arrays into the SimInfo object
1565	>	void SimSetup::initFortran( void ){
1566
1567	<	info->atoms = the_atoms;
1568	<	info->molecules = the_molecules;
1569	<	info->nGlobalExcludes = 0;
1570	<	info->excludes = the_excludes;
1567	>	info[0].refreshSim();
1568	>
1569	>	if( !strcmp( info[0].mixingRule, "standard") ){
1570	>	the_ff->initForceField( LB_MIXING_RULE );
1571	>	}
1572	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1573	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1574	>	}
1575	>	else{
1576	>	sprintf( painCave.errMsg,
1577	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1578	>	info[0].mixingRule );
1579	>	painCave.isFatal = 1;
1580	>	simError();
1581	>	}
1582
1476	–	the_ff->setSimInfo( info );
1583
1584	+	#ifdef IS_MPI
1585	+	strcpy( checkPointMsg,
1586	+	"Successfully intialized the mixingRule for Fortran." );
1587	+	MPIcheckPoint();
1588	+	#endif // is_mpi
1589	+
1590		}
1591	+
1592	+	void SimSetup::setupZConstraint()
1593	+	{
1594	+	int k;
1595	+
1596	+	for(k=0; k<nInfo; k++){
1597	+
1598	+	if(globals->haveZConsTime()){
1599	+
1600	+	//add sample time of z-constraint  into SimInfo's property list
1601	+	DoubleData* zconsTimeProp = new DoubleData();
1602	+	zconsTimeProp->setID("zconstime");
1603	+	zconsTimeProp->setData(globals->getZConsTime());
1604	+	info[k].addProperty(zconsTimeProp);
1605	+	}
1606	+	else{
1607	+	sprintf( painCave.errMsg,
1608	+	"ZConstraint error: If you use an ZConstraint\n"
1609	+	" , you must set sample time.\n");
1610	+	painCave.isFatal = 1;
1611	+	simError();
1612	+	}
1613	+
1614	+	if(globals->haveIndexOfAllZConsMols()){
1615	+
1616	+	//add index of z-constraint molecules into SimInfo's property list
1617	+	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1618	+
1619	+	//sort the index
1620	+	sort(tempIndex.begin(), tempIndex.end());
1621	+
1622	+	IndexData* zconsIndex = new IndexData();
1623	+	zconsIndex->setID("zconsindex");
1624	+	zconsIndex->setIndexData(tempIndex);
1625	+	info[k].addProperty(zconsIndex);
1626	+	}
1627	+	else{
1628	+	sprintf( painCave.errMsg,
1629	+	"SimSetup error: If you use an ZConstraint\n"
1630	+	" , you must set index of z-constraint molecules.\n");
1631	+	painCave.isFatal = 1;
1632	+	simError();
1633	+
1634	+	}
1635	+
1636	+	//Determine the name of ouput file and add it into SimInfo's property list
1637	+	//Be careful, do not use inFileName, since it is a pointer which
1638	+	//point to a string at master node, and slave nodes do not contain that string
1639	+
1640	+	string zconsOutput(info[k].finalName);
1641	+
1642	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1643	+
1644	+	StringData* zconsFilename = new StringData();
1645	+	zconsFilename->setID("zconsfilename");
1646	+	zconsFilename->setData(zconsOutput);
1647	+
1648	+	info[k].addProperty(zconsFilename);
1649	+	}
1650	+	}

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