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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 689 by tim, Tue Aug 12 19:56:49 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	>	std::cerr << "gathering info\n";
102	>
103		gatherInfo();
104
105		// creation of complex system objects
106
107	+	std::cerr << "creating system objects\n";
108	+
109		sysObjectsCreation();
110
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	–
111		// check on the post processing info
112
113	+	std::cerr << "performing final info check.\n";
114	+
115		finalInfoCheck();
116
110	–
111	–
112	–
117		// initialize the system coordinates
118
119	<	initSystemCoords();
116	<
119	>	std::cerr << "about to init coords\n";
120
121	+	if( !isInfoArray ) initSystemCoords();
122	+
123		// make the output filenames
124
125		makeOutNames();
126
122	–
123	–
124	–
125	–
126	–
127	–
128	–
129	–
127		// make the integrator
128
129	+	makeIntegrator();
130
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	–
131		#ifdef IS_MPI
132		mpiSim->mpiRefresh();
133		#endif
134
135		// initialize the Fortran
136
137	+	initFortran();
138
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	–	}
139
140
333	–	#ifdef IS_MPI
334	–	strcpy( checkPointMsg,
335	–	"Successfully intialized the mixingRule for Fortran." );
336	–	MPIcheckPoint();
337	–	#endif // is_mpi
141		}
142
143
144		void SimSetup::makeMolecules( void ){
145
146	+	int k,l;
147		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
148	<	molInit info;
148	>	molInit molInfo;
149		DirectionalAtom* dAtom;
150		LinkedAssign* extras;
151		LinkedAssign* current_extra;
#	Line 364 | Line 168 | void SimSetup::makeMolecules( void ){
168
169		double ux, uy, uz, u, uSqr;
170
171	<	atomOffset = 0;
368	<	excludeOffset = 0;
369	<	for(i=0; i<info->n_mol; i++){
171	>	for(k=0; k<nInfo; k++){
172
173	<	stampID = the_molecules[i].getStampID();
173	>	the_ff->setSimInfo( &(info[k]) );
174
175	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
176	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
177	<	info.nBends    = comp_stamps[stampID]->getNBends();
178	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
179	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
175	>	atomOffset = 0;
176	>	excludeOffset = 0;
177	>	for(i=0; i<info[k].n_mol; i++){
178	>
179	>	stampID = info[k].molecules[i].getStampID();
180
181	<	info.myAtoms = &the_atoms[atomOffset];
182	<	info.myExcludes = &the_excludes[excludeOffset];
183	<	info.myBonds = new Bond*[info.nBonds];
184	<	info.myBends = new Bend*[info.nBends];
185	<	info.myTorsions = new Torsion*[info.nTorsions];
181	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
182	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
183	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
184	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
185	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
186	>
187	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
188	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
189	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
190	>	molInfo.myBends = new Bend*[molInfo.nBends];
191	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
192
193	<	theBonds = new bond_pair[info.nBonds];
194	<	theBends = new bend_set[info.nBends];
195	<	theTorsions = new torsion_set[info.nTorsions];
193	>	theBonds = new bond_pair[molInfo.nBonds];
194	>	theBends = new bend_set[molInfo.nBends];
195	>	theTorsions = new torsion_set[molInfo.nTorsions];
196
197	<	// make the Atoms
197	>	// make the Atoms
198
199	<	for(j=0; j<info.nAtoms; j++){
392	<
393	<	currentAtom = comp_stamps[stampID]->getAtom( j );
394	<	if( currentAtom->haveOrientation() ){
199	>	for(j=0; j<molInfo.nAtoms; j++){
200
201	<	dAtom = new DirectionalAtom(j + atomOffset);
202	<	info->n_oriented++;
203	<	info.myAtoms[j] = dAtom;
204	<
205	<	ux = currentAtom->getOrntX();
206	<	uy = currentAtom->getOrntY();
207	<	uz = currentAtom->getOrntZ();
208	<
209	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
210	<
211	<	u = sqrt( uSqr );
212	<	ux = ux / u;
213	<	uy = uy / u;
214	<	uz = uz / u;
215	<
216	<	dAtom->setSUx( ux );
217	<	dAtom->setSUy( uy );
218	<	dAtom->setSUz( uz );
219	<	}
220	<	else{
221	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
222	<	}
223	<	info.myAtoms[j]->setType( currentAtom->getType() );
201	>	currentAtom = comp_stamps[stampID]->getAtom( j );
202	>	if( currentAtom->haveOrientation() ){
203	>
204	>	dAtom = new DirectionalAtom( (j + atomOffset),
205	>	info[k].getConfiguration() );
206	>	info[k].n_oriented++;
207	>	molInfo.myAtoms[j] = dAtom;
208	>
209	>	ux = currentAtom->getOrntX();
210	>	uy = currentAtom->getOrntY();
211	>	uz = currentAtom->getOrntZ();
212	>
213	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
214	>
215	>	u = sqrt( uSqr );
216	>	ux = ux / u;
217	>	uy = uy / u;
218	>	uz = uz / u;
219	>
220	>	dAtom->setSUx( ux );
221	>	dAtom->setSUy( uy );
222	>	dAtom->setSUz( uz );
223	>	}
224	>	else{
225	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
226	>	info[k].getConfiguration() );
227	>	}
228	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
229
230		#ifdef IS_MPI
231
232	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
232	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
233
234		#endif // is_mpi
235	<	}
235	>	}
236
237		// make the bonds
238	<	for(j=0; j<info.nBonds; j++){
238	>	for(j=0; j<molInfo.nBonds; j++){
239
240	<	currentBond = comp_stamps[stampID]->getBond( j );
241	<	theBonds[j].a = currentBond->getA() + atomOffset;
242	<	theBonds[j].b = currentBond->getB() + atomOffset;
243	<
244	<	exI = theBonds[j].a;
245	<	exJ = theBonds[j].b;
246	<
247	<	// exclude_I must always be the smaller of the pair
248	<	if( exI > exJ ){
249	<	tempEx = exI;
250	<	exI = exJ;
251	<	exJ = tempEx;
252	<	}
240	>	currentBond = comp_stamps[stampID]->getBond( j );
241	>	theBonds[j].a = currentBond->getA() + atomOffset;
242	>	theBonds[j].b = currentBond->getB() + atomOffset;
243	>
244	>	exI = theBonds[j].a;
245	>	exJ = theBonds[j].b;
246	>
247	>	// exclude_I must always be the smaller of the pair
248	>	if( exI > exJ ){
249	>	tempEx = exI;
250	>	exI = exJ;
251	>	exJ = tempEx;
252	>	}
253		#ifdef IS_MPI
254	<	tempEx = exI;
255	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
256	<	tempEx = exJ;
257	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
258	<
259	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
254	>	tempEx = exI;
255	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
256	>	tempEx = exJ;
257	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
258	>
259	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
260		#else  // isn't MPI
261	<
262	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
261	>
262	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
263		#endif  //is_mpi
264	<	}
265	<	excludeOffset += info.nBonds;
456	<
457	<	//make the bends
458	<	for(j=0; j<info.nBends; j++){
264	>	}
265	>	excludeOffset += molInfo.nBonds;
266
267	<	currentBend = comp_stamps[stampID]->getBend( j );
268	<	theBends[j].a = currentBend->getA() + atomOffset;
269	<	theBends[j].b = currentBend->getB() + atomOffset;
270	<	theBends[j].c = currentBend->getC() + atomOffset;
267	>	//make the bends
268	>	for(j=0; j<molInfo.nBends; j++){
269	>
270	>	currentBend = comp_stamps[stampID]->getBend( j );
271	>	theBends[j].a = currentBend->getA() + atomOffset;
272	>	theBends[j].b = currentBend->getB() + atomOffset;
273	>	theBends[j].c = currentBend->getC() + atomOffset;
274	>
275	>	if( currentBend->haveExtras() ){
276
277	<	if( currentBend->haveExtras() ){
278	<
279	<	extras = currentBend->getExtras();
280	<	current_extra = extras;
281	<
470	<	while( current_extra != NULL ){
471	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
472	<
473	<	switch( current_extra->getType() ){
277	>	extras = currentBend->getExtras();
278	>	current_extra = extras;
279	>
280	>	while( current_extra != NULL ){
281	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
282
283	<	case 0:
284	<	theBends[j].ghost =
285	<	current_extra->getInt() + atomOffset;
286	<	theBends[j].isGhost = 1;
287	<	break;
288	<
289	<	case 1:
290	<	theBends[j].ghost =
291	<	(int)current_extra->getDouble() + atomOffset;
292	<	theBends[j].isGhost = 1;
293	<	break;
294	<
295	<	default:
283	>	switch( current_extra->getType() ){
284	>
285	>	case 0:
286	>	theBends[j].ghost =
287	>	current_extra->getInt() + atomOffset;
288	>	theBends[j].isGhost = 1;
289	>	break;
290	>
291	>	case 1:
292	>	theBends[j].ghost =
293	>	(int)current_extra->getDouble() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296	>
297	>	default:
298	>	sprintf( painCave.errMsg,
299	>	"SimSetup Error: ghostVectorSource was neither a "
300	>	"double nor an int.\n"
301	>	"-->Bend[%d] in %s\n",
302	>	j, comp_stamps[stampID]->getID() );
303	>	painCave.isFatal = 1;
304	>	simError();
305	>	}
306	>	}
307	>
308	>	else{
309	>
310		sprintf( painCave.errMsg,
311	<	"SimSetup Error: ghostVectorSource was neither a "
312	<	"double nor an int.\n"
313	<	"-->Bend[%d] in %s\n",
311	>	"SimSetup Error: unhandled bend assignment:\n"
312	>	"    -->%s in Bend[%d] in %s\n",
313	>	current_extra->getlhs(),
314		j, comp_stamps[stampID]->getID() );
315		painCave.isFatal = 1;
316		simError();
317		}
496	–	}
497	–
498	–	else{
318
319	<	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();
319	>	current_extra = current_extra->getNext();
320		}
321	+	}
322	+
323	+	if( !theBends[j].isGhost ){
324
325	<	current_extra = current_extra->getNext();
325	>	exI = theBends[j].a;
326	>	exJ = theBends[j].c;
327		}
328	<	}
328	>	else{
329
330	<	if( !theBends[j].isGhost ){
331	<
332	<	exI = theBends[j].a;
516	<	exJ = theBends[j].c;
517	<	}
518	<	else{
330	>	exI = theBends[j].a;
331	>	exJ = theBends[j].b;
332	>	}
333
334	<	exI = theBends[j].a;
335	<	exJ = theBends[j].b;
336	<	}
337	<
338	<	// exclude_I must always be the smaller of the pair
339	<	if( exI > exJ ){
526	<	tempEx = exI;
527	<	exI = exJ;
528	<	exJ = tempEx;
529	<	}
334	>	// exclude_I must always be the smaller of the pair
335	>	if( exI > exJ ){
336	>	tempEx = exI;
337	>	exI = exJ;
338	>	exJ = tempEx;
339	>	}
340		#ifdef IS_MPI
341	<	tempEx = exI;
342	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
343	<	tempEx = exJ;
344	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
341	>	tempEx = exI;
342	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	>	tempEx = exJ;
344	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345
346	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
346	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
347		#else  // isn't MPI
348	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
348	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349		#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;
350		}
351	<	#ifdef IS_MPI
561	<	tempEx = exI;
562	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
563	<	tempEx = exJ;
564	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
351	>	excludeOffset += molInfo.nBends;
352
353	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
353	>	for(j=0; j<molInfo.nTorsions; j++){
354	>
355	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360	>
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363	>
364	>	// exclude_I must always be the smaller of the pair
365	>	if( exI > exJ ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370	>	#ifdef IS_MPI
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>
376	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
377		#else  // isn't MPI
378	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
378	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
379		#endif  //is_mpi
380	<	}
381	<	excludeOffset += info.nTorsions;
380	>	}
381	>	excludeOffset += molInfo.nTorsions;
382	>
383	>
384	>	// send the arrays off to the forceField for init.
385	>
386	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
387	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
388	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
389	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
390	>
391	>
392	>	info[k].molecules[i].initialize( molInfo );
393
394	<
395	<	// send the arrays off to the forceField for init.
396	<
397	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
398	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
399	<	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;
394	>
395	>	atomOffset += molInfo.nAtoms;
396	>	delete[] theBonds;
397	>	delete[] theBends;
398	>	delete[] theTorsions;
399	>	}
400		}
401	<
401	>
402		#ifdef IS_MPI
403		sprintf( checkPointMsg, "all molecules initialized succesfully" );
404		MPIcheckPoint();
405		#endif // is_mpi
406	<
406	>
407		// clean up the forcefield
408	+
409		the_ff->calcRcut();
410		the_ff->cleanMe();
411	<
411	>
412		}
413
414		void SimSetup::initFromBass( void ){
#	Line 609 | Line 421 | void SimSetup::initFromBass( void ){
421		int n_extra;
422		int have_extra, done;
423
424	+	double vel[3];
425	+	vel[0] = 0.0;
426	+	vel[1] = 0.0;
427	+	vel[2] = 0.0;
428	+
429		temp1 = (double)tot_nmol / 4.0;
430		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
431		temp3 = ceil( temp2 );
#	Line 618 | Line 435 | void SimSetup::initFromBass( void ){
435		have_extra =1;
436
437		n_cells = (int)temp3 - 1;
438	<	cellx = info->boxLx / temp3;
439	<	celly = info->boxLy / temp3;
440	<	cellz = info->boxLz / temp3;
438	>	cellx = info[0].boxL[0] / temp3;
439	>	celly = info[0].boxL[1] / temp3;
440	>	cellz = info[0].boxL[2] / temp3;
441		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
442		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
443		n_per_extra = (int)ceil( temp1 );
#	Line 635 | Line 452 | void SimSetup::initFromBass( void ){
452		}
453		else{
454		n_cells = (int)temp3;
455	<	cellx = info->boxLx / temp3;
456	<	celly = info->boxLy / temp3;
457	<	cellz = info->boxLz / temp3;
455	>	cellx = info[0].boxL[0] / temp3;
456	>	celly = info[0].boxL[1] / temp3;
457	>	cellz = info[0].boxL[2] / temp3;
458		}
459
460		current_mol = 0;
#	Line 716 | Line 533 | void SimSetup::initFromBass( void ){
533		}
534		}
535
536	<
537	<	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 );
536	>	for( i=0; i<info[0].n_atoms; i++ ){
537	>	info[0].atoms[i]->setVel( vel );
538		}
539		}
540
#	Line 730 | Line 544 | void SimSetup::makeElement( double x, double y, double
544		AtomStamp* current_atom;
545		DirectionalAtom* dAtom;
546		double rotMat[3][3];
547	+	double pos[3];
548
549		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
550
#	Line 745 | Line 560 | void SimSetup::makeElement( double x, double y, double
560		painCave.isFatal = 1;
561		simError();
562		}
563	+
564	+	pos[0] = x + current_atom->getPosX();
565	+	pos[1] = y + current_atom->getPosY();
566	+	pos[2] = z + current_atom->getPosZ();
567	+
568	+	info[0].atoms[current_atom_ndx]->setPos( pos );
569
570	<	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() );
570	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
571
572	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
572	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
573
755	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
756	–
574		rotMat[0][0] = 1.0;
575		rotMat[0][1] = 0.0;
576		rotMat[0][2] = 0.0;
#	Line 784 | Line 601 | void SimSetup::gatherInfo( void ){
601
602
603		void SimSetup::gatherInfo( void ){
604	+	int i,j,k;
605
606		ensembleCase = -1;
607		ffCase = -1;
608
791	–	// get the stamps and globals;
792	–	the_stamps = stamps;
793	–	the_globals = globals;
794	–
609		// set the easy ones first
610	<	info->target_temp = the_globals->getTargetTemp();
611	<	info->dt = the_globals->getDt();
612	<	info->run_time = the_globals->getRunTime();
613	<	n_components = the_globals->getNComponents();
610	>
611	>	for( i=0; i<nInfo; i++){
612	>	info[i].target_temp = globals->getTargetTemp();
613	>	info[i].dt = globals->getDt();
614	>	info[i].run_time = globals->getRunTime();
615	>	}
616	>	n_components = globals->getNComponents();
617
618
619		// get the forceField
620
621	<	strcpy( force_field, the_globals->getForceField() );
621	>	strcpy( force_field, globals->getForceField() );
622
623		if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
624		else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
625	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
626		else{
627		sprintf( painCave.errMsg,
628		"SimSetup Error. Unrecognized force field -> %s\n",
#	Line 815 | Line 633 | void SimSetup::gatherInfo( void ){
633
634		// get the ensemble
635
636	<	strcpy( ensemble, the_globals->getEnsemble() );
636	>	strcpy( ensemble, globals->getEnsemble() );
637
638		if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
639		else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
#	Line 834 | Line 652 | void SimSetup::gatherInfo( void ){
652		strcpy( ensemble, "NVE" );
653		ensembleCase = NVE_ENS;
654		}
655	<	strcpy( info->ensemble, ensemble );
655	>
656	>	for(i=0; i<nInfo; i++){
657	>
658	>	strcpy( info[i].ensemble, ensemble );
659
660	<	// get the mixing rule
660	>	// get the mixing rule
661
662	<	strcpy( info->mixingRule, the_globals->getMixingRule() );
663	<	info->usePBC = the_globals->getPBC();
664	<
662	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
663	>	info[i].usePBC = globals->getPBC();
664	>	}
665
666		// get the components and calculate the tot_nMol and indvidual n_mol
667
668	<	the_components = the_globals->getComponents();
668	>	the_components = globals->getComponents();
669		components_nmol = new int[n_components];
670
671
672	<	if( !the_globals->haveNMol() ){
672	>	if( !globals->haveNMol() ){
673		// we don't have the total number of molecules, so we assume it is
674		// given in each component
675
#	Line 881 | Line 702 | void SimSetup::gatherInfo( void ){
702
703		// set the status, sample, and thermal kick times
704
705	<	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	<	}
705	>	for(i=0; i<nInfo; i++){
706
707	<	if( the_globals->haveStatusTime() ){
708	<	info->statusTime = the_globals->getStatusTime();
709	<	}
710	<
711	<	if( the_globals->haveThermalTime() ){
712	<	info->thermalTime = the_globals->getThermalTime();
713	<	}
714	<
715	<	// check for the temperature set flag
716	<
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();
707	>	if( globals->haveSampleTime() ){
708	>	info[i].sampleTime = globals->getSampleTime();
709	>	info[i].statusTime = info[i].sampleTime;
710	>	info[i].thermalTime = info[i].sampleTime;
711	>	}
712	>	else{
713	>	info[i].sampleTime = globals->getRunTime();
714	>	info[i].statusTime = info[i].sampleTime;
715	>	info[i].thermalTime = info[i].sampleTime;
716	>	}
717
718	<	info->setBox( boxVector );
719	<	}
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();
718	>	if( globals->haveStatusTime() ){
719	>	info[i].statusTime = globals->getStatusTime();
720		}
721	<	boxVector[0] = the_globals->getBoxX();
722	<
723	<	if( !the_globals->haveBoxY() ){
937	<	sprintf( painCave.errMsg,
938	<	"SimSetup error, no periodic BoxY size given.\n" );
939	<	painCave.isFatal = 1;
940	<	simError();
721	>
722	>	if( globals->haveThermalTime() ){
723	>	info[i].thermalTime = globals->getThermalTime();
724		}
942	–	boxVector[1] = the_globals->getBoxY();
725
726	<	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();
726	>	// check for the temperature set flag
727
728	<	info->setBox( boxVector );
728	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
729	>
730	>	// get some of the tricky things that may still be in the globals
731	>
732	>	double boxVector[3];
733	>	if( globals->haveBox() ){
734	>	boxVector[0] = globals->getBox();
735	>	boxVector[1] = globals->getBox();
736	>	boxVector[2] = globals->getBox();
737	>
738	>	info[i].setBox( boxVector );
739	>	}
740	>	else if( globals->haveDensity() ){
741	>
742	>	double vol;
743	>	vol = (double)tot_nmol / globals->getDensity();
744	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
745	>	boxVector[1] = boxVector[0];
746	>	boxVector[2] = boxVector[0];
747	>
748	>	info[i].setBox( boxVector );
749		}
750	+	else{
751	+	if( !globals->haveBoxX() ){
752	+	sprintf( painCave.errMsg,
753	+	"SimSetup error, no periodic BoxX size given.\n" );
754	+	painCave.isFatal = 1;
755	+	simError();
756	+	}
757	+	boxVector[0] = globals->getBoxX();
758	+
759	+	if( !globals->haveBoxY() ){
760	+	sprintf( painCave.errMsg,
761	+	"SimSetup error, no periodic BoxY size given.\n" );
762	+	painCave.isFatal = 1;
763	+	simError();
764	+	}
765	+	boxVector[1] = globals->getBoxY();
766	+
767	+	if( !globals->haveBoxZ() ){
768	+	sprintf( painCave.errMsg,
769	+	"SimSetup error, no periodic BoxZ size given.\n" );
770	+	painCave.isFatal = 1;
771	+	simError();
772	+	}
773	+	boxVector[2] = globals->getBoxZ();
774	+
775	+	info[i].setBox( boxVector );
776	+	}
777
778	<
778	>	}
779
780		#ifdef IS_MPI
781		strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
#	Line 965 | Line 788 | void SimSetup::finalInfoCheck( void ){
788		void SimSetup::finalInfoCheck( void ){
789		int index;
790		int usesDipoles;
791	<
791	>	int i;
792
793	<	// check electrostatic parameters
794	<
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;
793	>	for(i=0; i<nInfo; i++){
794	>	// check electrostatic parameters
795
796	<	if( !the_globals->haveECR() ){
797	<	sprintf( painCave.errMsg,
798	<	"SimSetup Warning: using default value of 1/2 the smallest "
799	<	"box length for the electrostaticCutoffRadius.\n"
800	<	"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();
796	>	index = 0;
797	>	usesDipoles = 0;
798	>	while( (index < info[i].n_atoms) && !usesDipoles ){
799	>	usesDipoles = (info[i].atoms[index])->hasDipole();
800	>	index++;
801		}
802
803	<	if(!the_globals->haveDielectric() ){
804	<	sprintf( painCave.errMsg,
805	<	"SimSetup Error: You are trying to use Reaction Field without"
806	<	"setting a dielectric constant!\n"
807	<	);
808	<	painCave.isFatal = 1;
809	<	simError();
810	<	}
811	<	info->dielectric = the_globals->getDielectric();
1025	<	}
1026	<	else {
1027	<	if (usesDipoles) {
803	>	#ifdef IS_MPI
804	>	int myUse = usesDipoles;
805	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
806	>	#endif //is_mpi
807	>
808	>	double theEcr, theEst;
809	>
810	>	if (globals->getUseRF() ) {
811	>	info[i].useReactionField = 1;
812
813	<	if( !the_globals->haveECR() ){
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup Warning: using default value of 1/2 the smallest "
816	<	"box length for the electrostaticCutoffRadius.\n"
817	<	"I hope you have a very fast processor!\n");
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	double smallest;
821	<	smallest = info->boxLx;
822	<	if (info->boxLy <= smallest) smallest = info->boxLy;
823	<	if (info->boxLz <= smallest) smallest = info->boxLz;
824	<	info->ecr = 0.5 * smallest;
813	>	if( !globals->haveECR() ){
814	>	sprintf( painCave.errMsg,
815	>	"SimSetup Warning: using default value of 1/2 the smallest "
816	>	"box length for the electrostaticCutoffRadius.\n"
817	>	"I hope you have a very fast processor!\n");
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	double smallest;
821	>	smallest = info[i].boxL[0];
822	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
823	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
824	>	theEcr = 0.5 * smallest;
825		} else {
826	<	info->ecr        = the_globals->getECR();
826	>	theEcr = globals->getECR();
827		}
828
829	<	if( !the_globals->haveEST() ){
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Warning: using default value of 5%% of the "
832	<	"electrostaticCutoffRadius for the "
833	<	"electrostaticSkinThickness\n"
834	<	);
835	<	painCave.isFatal = 0;
836	<	simError();
1053	<	info->est = 0.05 * info->ecr;
829	>	if( !globals->haveEST() ){
830	>	sprintf( painCave.errMsg,
831	>	"SimSetup Warning: using default value of 0.05 * the "
832	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
833	>	);
834	>	painCave.isFatal = 0;
835	>	simError();
836	>	theEst = 0.05 * theEcr;
837		} else {
838	<	info->est        = the_globals->getEST();
838	>	theEst= globals->getEST();
839		}
840	<	}
841	<	}
840	>
841	>	info[i].setEcr( theEcr, theEst );
842	>
843	>	if(!globals->haveDielectric() ){
844	>	sprintf( painCave.errMsg,
845	>	"SimSetup Error: You are trying to use Reaction Field without"
846	>	"setting a dielectric constant!\n"
847	>	);
848	>	painCave.isFatal = 1;
849	>	simError();
850	>	}
851	>	info[i].dielectric = globals->getDielectric();
852	>	}
853	>	else {
854	>	if (usesDipoles) {
855	>
856	>	if( !globals->haveECR() ){
857	>	sprintf( painCave.errMsg,
858	>	"SimSetup Warning: using default value of 1/2 the smallest "
859	>	"box length for the electrostaticCutoffRadius.\n"
860	>	"I hope you have a very fast processor!\n");
861	>	painCave.isFatal = 0;
862	>	simError();
863	>	double smallest;
864	>	smallest = info[i].boxL[0];
865	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
866	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
867	>	theEcr = 0.5 * smallest;
868	>	} else {
869	>	theEcr = globals->getECR();
870	>	}
871	>
872	>	if( !globals->haveEST() ){
873	>	sprintf( painCave.errMsg,
874	>	"SimSetup Warning: using default value of 0.05 * the "
875	>	"electrostaticCutoffRadius for the "
876	>	"electrostaticSkinThickness\n"
877	>	);
878	>	painCave.isFatal = 0;
879	>	simError();
880	>	theEst = 0.05 * theEcr;
881	>	} else {
882	>	theEst= globals->getEST();
883	>	}
884	>
885	>	info[i].setEcr( theEcr, theEst );
886	>	}
887	>	}
888	>	}
889
890		#ifdef IS_MPI
891		strcpy( checkPointMsg, "post processing checks out" );
#	Line 1065 | Line 895 | void SimSetup::initSystemCoords( void ){
895		}
896
897		void SimSetup::initSystemCoords( void ){
898	+	int i;
899	+
900	+	char* inName;
901
902	<	if( the_globals->haveInitialConfig() ){
903	<
904	<	InitializeFromFile* fileInit;
902	>	std::cerr << "Setting atom Coords\n";
903	>
904	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
905	>
906	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
907	>
908	>	if( globals->haveInitialConfig() ){
909	>
910	>	InitializeFromFile* fileInit;
911		#ifdef IS_MPI // is_mpi
912	<	if( worldRank == 0 ){
912	>	if( worldRank == 0 ){
913		#endif //is_mpi
914	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
914	>	inName = globals->getInitialConfig();
915	>	fileInit = new InitializeFromFile( inName );
916		#ifdef IS_MPI
917	<	}else fileInit = new InitializeFromFile( NULL );
917	>	}else fileInit = new InitializeFromFile( NULL );
918		#endif
919	<	fileInit->read_xyz( info ); // default velocities on
920	<
921	<	delete fileInit;
922	<	}
923	<	else{
924	<
919	>	fileInit->readInit( info ); // default velocities on
920	>
921	>	delete fileInit;
922	>	}
923	>	else{
924	>
925		#ifdef IS_MPI
926	<
927	<	// no init from bass
928	<
929	<	sprintf( painCave.errMsg,
930	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
931	<	painCave.isFatal;
932	<	simError();
933	<
926	>
927	>	// no init from bass
928	>
929	>	sprintf( painCave.errMsg,
930	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
931	>	painCave.isFatal;
932	>	simError();
933	>
934		#else
935	<
936	<	initFromBass();
937	<
938	<
935	>
936	>	initFromBass();
937	>
938	>
939		#endif
940	<	}
941	<
940	>	}
941	>
942		#ifdef IS_MPI
943		strcpy( checkPointMsg, "Successfully read in the initial configuration" );
944		MPIcheckPoint();
945		#endif // is_mpi
946	<
946	>
947		}
948
949
950		void SimSetup::makeOutNames( void ){
951	+
952	+	int k;
953
954	+
955	+	for(k=0; k<nInfo; k++){
956	+
957		#ifdef IS_MPI
958	<	if( worldRank == 0 ){
958	>	if( worldRank == 0 ){
959		#endif // is_mpi
960	<
961	<	if( the_globals->haveFinalConfig() ){
962	<	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" );
960	>
961	>	if( globals->haveFinalConfig() ){
962	>	strcpy( info[k].finalName, globals->getFinalConfig() );
963		}
1127	–	else if( !strcmp( endTest, ".BASS" ) ){
1128	–	strcpy( endTest, ".eor" );
1129	–	}
964		else{
965	<	endTest = &(info->finalName[nameLength - 4]);
966	<	if( !strcmp( endTest, ".bss" ) ){
965	>	strcpy( info[k].finalName, inFileName );
966	>	char* endTest;
967	>	int nameLength = strlen( info[k].finalName );
968	>	endTest = &(info[k].finalName[nameLength - 5]);
969	>	if( !strcmp( endTest, ".bass" ) ){
970		strcpy( endTest, ".eor" );
971		}
972	<	else if( !strcmp( endTest, ".mdl" ) ){
972	>	else if( !strcmp( endTest, ".BASS" ) ){
973		strcpy( endTest, ".eor" );
974		}
975		else{
976	<	strcat( info->finalName, ".eor" );
976	>	endTest = &(info[k].finalName[nameLength - 4]);
977	>	if( !strcmp( endTest, ".bss" ) ){
978	>	strcpy( endTest, ".eor" );
979	>	}
980	>	else if( !strcmp( endTest, ".mdl" ) ){
981	>	strcpy( endTest, ".eor" );
982	>	}
983	>	else{
984	>	strcat( info[k].finalName, ".eor" );
985	>	}
986		}
987		}
988	<	}
989	<
990	<	// make the sample and status out names
991	<
992	<	strcpy( info->sampleName, inFileName );
993	<	char* endTest;
994	<	int nameLength = strlen( info->sampleName );
995	<	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" ) ){
988	>
989	>	// make the sample and status out names
990	>
991	>	strcpy( info[k].sampleName, inFileName );
992	>	char* endTest;
993	>	int nameLength = strlen( info[k].sampleName );
994	>	endTest = &(info[k].sampleName[nameLength - 5]);
995	>	if( !strcmp( endTest, ".bass" ) ){
996		strcpy( endTest, ".dump" );
997		}
998	<	else if( !strcmp( endTest, ".mdl" ) ){
998	>	else if( !strcmp( endTest, ".BASS" ) ){
999		strcpy( endTest, ".dump" );
1000		}
1001		else{
1002	<	strcat( info->sampleName, ".dump" );
1002	>	endTest = &(info[k].sampleName[nameLength - 4]);
1003	>	if( !strcmp( endTest, ".bss" ) ){
1004	>	strcpy( endTest, ".dump" );
1005	>	}
1006	>	else if( !strcmp( endTest, ".mdl" ) ){
1007	>	strcpy( endTest, ".dump" );
1008	>	}
1009	>	else{
1010	>	strcat( info[k].sampleName, ".dump" );
1011	>	}
1012		}
1013	<	}
1014	<
1015	<	strcpy( info->statusName, inFileName );
1016	<	nameLength = strlen( info->statusName );
1017	<	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" ) ){
1013	>
1014	>	strcpy( info[k].statusName, inFileName );
1015	>	nameLength = strlen( info[k].statusName );
1016	>	endTest = &(info[k].statusName[nameLength - 5]);
1017	>	if( !strcmp( endTest, ".bass" ) ){
1018		strcpy( endTest, ".stat" );
1019		}
1020	<	else if( !strcmp( endTest, ".mdl" ) ){
1020	>	else if( !strcmp( endTest, ".BASS" ) ){
1021		strcpy( endTest, ".stat" );
1022		}
1023		else{
1024	<	strcat( info->statusName, ".stat" );
1024	>	endTest = &(info[k].statusName[nameLength - 4]);
1025	>	if( !strcmp( endTest, ".bss" ) ){
1026	>	strcpy( endTest, ".stat" );
1027	>	}
1028	>	else if( !strcmp( endTest, ".mdl" ) ){
1029	>	strcpy( endTest, ".stat" );
1030	>	}
1031	>	else{
1032	>	strcat( info[k].statusName, ".stat" );
1033	>	}
1034		}
1035	<	}
1190	<
1035	>
1036		#ifdef IS_MPI
1037	<	}
1037	>	}
1038		#endif // is_mpi
1039	<
1039	>	}
1040		}
1041
1042
1043		void SimSetup::sysObjectsCreation( void ){
1044	<
1044	>
1045	>	int i,k;
1046	>
1047		// create the forceField
1048
1049		createFF();
#	Line 1216 | Line 1063 | void SimSetup::sysObjectsCreation( void ){
1063		#endif //is_mpi
1064
1065		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1066	<
1066	>
1067		makeSysArrays();
1068
1069	+	// make and initialize the molecules (all but atomic coordinates)
1070	+
1071	+	makeMolecules();
1072
1073	<
1074	<
1073	>	for(k=0; k<nInfo; k++){
1074	>	info[k].identArray = new int[info[k].n_atoms];
1075	>	for(i=0; i<info[k].n_atoms; i++){
1076	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1077	>	}
1078	>	}
1079		}
1080
1081
#	Line 1237 | Line 1091 | void SimSetup::createFF( void ){
1091		the_ff = new LJFF();
1092		break;
1093
1094	+	case FF_EAM:
1095	+	the_ff = new EAM_FF();
1096	+	break;
1097	+
1098		default:
1099		sprintf( painCave.errMsg,
1100		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1254 | Line 1112 | void SimSetup::compList( void ){
1112
1113		void SimSetup::compList( void ){
1114
1115	+	int i;
1116	+	char* id;
1117	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1118	+	LinkedMolStamp* currentStamp = NULL;
1119		comp_stamps = new MoleculeStamp*[n_components];
1120	<
1120	>
1121		// make an array of molecule stamps that match the components used.
1122		// 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();
1123
1124	<	char* id;
1125	<	LinkedMolStamp* headStamp = info->headStamp;
1126	<	LinkedMolStamp* currentStamp = NULL;
1124	>	for(i=0; i<nInfo; i++){
1125	>	info[i].nComponents = n_components;
1126	>	info[i].componentsNmol = components_nmol;
1127	>	info[i].compStamps = comp_stamps;
1128	>	info[i].headStamp = headStamp;
1129	>	}
1130	>
1131	>
1132		for( i=0; i<n_components; i++ ){
1133
1134		id = the_components[i]->getType();
#	Line 1279 | Line 1141 | void SimSetup::compList( void ){
1141
1142		// extract the component from the list;
1143
1144	<	currentStamp = the_stamps->extractMolStamp( id );
1144	>	currentStamp = stamps->extractMolStamp( id );
1145		if( currentStamp == NULL ){
1146		sprintf( painCave.errMsg,
1147		"SimSetup error: Component \"%s\" was not found in the "
#	Line 1303 | Line 1165 | void SimSetup::calcSysValues( void ){
1165		}
1166
1167		void SimSetup::calcSysValues( void ){
1168	<
1168	>	int i, j, k;
1169	>
1170	>	int *molMembershipArray;
1171	>
1172		tot_atoms = 0;
1173		tot_bonds = 0;
1174		tot_bends = 0;
#	Line 1315 | Line 1180 | void SimSetup::calcSysValues( void ){
1180		tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1181		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182		}
1183	<
1183	>
1184		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	<
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;
1185	>	molMembershipArray = new int[tot_atoms];
1186
1187	<	info->molMembershipArray = new int[tot_atoms];
1187	>	for(i=0; i<nInfo; i++){
1188	>	info[i].n_atoms = tot_atoms;
1189	>	info[i].n_bonds = tot_bonds;
1190	>	info[i].n_bends = tot_bends;
1191	>	info[i].n_torsions = tot_torsions;
1192	>	info[i].n_SRI = tot_SRI;
1193	>	info[i].n_mol = tot_nmol;
1194	>
1195	>	info[i].molMembershipArray = molMembershipArray;
1196	>	}
1197		}
1198
1331	–
1199		#ifdef IS_MPI
1200
1201		void SimSetup::mpiMolDivide( void ){
1202
1203	+	int i, j, k;
1204		int localMol, allMol;
1205		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1206
#	Line 1367 | Line 1235 | void SimSetup::mpiMolDivide( void ){
1235		localMol++;
1236		}
1237		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1238	<	info->molMembershipArray[globalAtomIndex] = allMol;
1238	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1239		globalAtomIndex++;
1240		}
1241
#	Line 1376 | Line 1244 | void SimSetup::mpiMolDivide( void ){
1244		}
1245		local_SRI = local_bonds + local_bends + local_torsions;
1246
1247	<	info->n_atoms = mpiSim->getMyNlocal();
1247	>	info[0].n_atoms = mpiSim->getMyNlocal();
1248
1249	<	if( local_atoms != info->n_atoms ){
1249	>	if( local_atoms != info[0].n_atoms ){
1250		sprintf( painCave.errMsg,
1251		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1252		" localAtom (%d) are not equal.\n",
1253	<	info->n_atoms,
1253	>	info[0].n_atoms,
1254		local_atoms );
1255		painCave.isFatal = 1;
1256		simError();
1257		}
1258
1259	<	info->n_bonds = local_bonds;
1260	<	info->n_bends = local_bends;
1261	<	info->n_torsions = local_torsions;
1262	<	info->n_SRI = local_SRI;
1263	<	info->n_mol = localMol;
1259	>	info[0].n_bonds = local_bonds;
1260	>	info[0].n_bends = local_bends;
1261	>	info[0].n_torsions = local_torsions;
1262	>	info[0].n_SRI = local_SRI;
1263	>	info[0].n_mol = localMol;
1264
1265		strcpy( checkPointMsg, "Passed nlocal consistency check." );
1266		MPIcheckPoint();
1267		}
1268	<
1268	>
1269		#endif // is_mpi
1270
1271
1272		void SimSetup::makeSysArrays( void ){
1273	+	int i, j, k, l;
1274
1275	<	// create the atom and short range interaction arrays
1275	>	Atom** the_atoms;
1276	>	Molecule* the_molecules;
1277	>	Exclude** the_excludes;
1278
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
1279
1280	<
1418	<	molIndex = 0;
1419	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1280	>	for(l=0; l<nInfo; l++){
1281
1282	<	if(mol2proc[i] == worldRank ){
1283	<	the_molecules[molIndex].setStampID( molCompType[i] );
1284	<	the_molecules[molIndex].setMyIndex( molIndex );
1285	<	the_molecules[molIndex].setGlobalIndex( i );
1286	<	molIndex++;
1426	<	}
1427	<	}
1282	>	// create the atom and short range interaction arrays
1283	>
1284	>	the_atoms = new Atom*[info[l].n_atoms];
1285	>	the_molecules = new Molecule[info[l].n_mol];
1286	>	int molIndex;
1287
1288	+	// initialize the molecule's stampID's
1289	+
1290	+	#ifdef IS_MPI
1291	+
1292	+
1293	+	molIndex = 0;
1294	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1295	+
1296	+	if(mol2proc[i] == worldRank ){
1297	+	the_molecules[molIndex].setStampID( molCompType[i] );
1298	+	the_molecules[molIndex].setMyIndex( molIndex );
1299	+	the_molecules[molIndex].setGlobalIndex( i );
1300	+	molIndex++;
1301	+	}
1302	+	}
1303	+
1304		#else // is_mpi
1305	<
1306	<	molIndex = 0;
1307	<	globalAtomIndex = 0;
1308	<	for(i=0; i<n_components; i++){
1309	<	for(j=0; j<components_nmol[i]; j++ ){
1310	<	the_molecules[molIndex].setStampID( i );
1311	<	the_molecules[molIndex].setMyIndex( molIndex );
1312	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1313	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1314	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1315	<	globalAtomIndex++;
1305	>
1306	>	molIndex = 0;
1307	>	globalAtomIndex = 0;
1308	>	for(i=0; i<n_components; i++){
1309	>	for(j=0; j<components_nmol[i]; j++ ){
1310	>	the_molecules[molIndex].setStampID( i );
1311	>	the_molecules[molIndex].setMyIndex( molIndex );
1312	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1313	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1314	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1315	>	globalAtomIndex++;
1316	>	}
1317	>	molIndex++;
1318		}
1442	–	molIndex++;
1319		}
1444	–	}
1320
1321	<
1321	>
1322		#endif // is_mpi
1323
1324
1325	<	if( info->n_SRI ){
1325	>	if( info[l].n_SRI ){
1326
1327	<	Exclude::createArray(info->n_SRI);
1328	<	the_excludes = new Exclude*[info->n_SRI];
1329	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1330	<	info->globalExcludes = new int;
1331	<	info->n_exclude = info->n_SRI;
1327	>	Exclude::createArray(info[l].n_SRI);
1328	>	the_excludes = new Exclude*[info[l].n_SRI];
1329	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1330	>	the_excludes[ex] = new Exclude(ex);
1331	>	}
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].n_exclude = info[l].n_SRI;
1334	>	}
1335	>	else{
1336	>
1337	>	Exclude::createArray( 1 );
1338	>	the_excludes = new Exclude*;
1339	>	the_excludes[0] = new Exclude(0);
1340	>	the_excludes[0]->setPair( 0,0 );
1341	>	info[l].globalExcludes = new int;
1342	>	info[l].globalExcludes[0] = 0;
1343	>	info[l].n_exclude = 0;
1344	>	}
1345	>
1346	>	// set the arrays into the SimInfo object
1347	>
1348	>	info[l].atoms = the_atoms;
1349	>	info[l].molecules = the_molecules;
1350	>	info[l].nGlobalExcludes = 0;
1351	>	info[l].excludes = the_excludes;
1352	>
1353	>	the_ff->setSimInfo( info );
1354	>
1355		}
1356	<	else{
1356	>	}
1357	>
1358	>	void SimSetup::makeIntegrator( void ){
1359	>
1360	>	int k;
1361	>
1362	>	NVT<RealIntegrator>*  myNVT = NULL;
1363	>	NPTi<RealIntegrator>* myNPTi = NULL;
1364	>	NPTf<RealIntegrator>* myNPTf = NULL;
1365	>	NPTim<RealIntegrator>* myNPTim = NULL;
1366	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1367	>
1368	>	for(k=0; k<nInfo; k++){
1369
1370	<	Exclude::createArray( 1 );
1371	<	the_excludes = new Exclude*;
1372	<	the_excludes[0] = new Exclude(0);
1373	<	the_excludes[0]->setPair( 0,0 );
1374	<	info->globalExcludes = new int;
1375	<	info->globalExcludes[0] = 0;
1376	<	info->n_exclude = 0;
1370	>	switch( ensembleCase ){
1371	>
1372	>	case NVE_ENS:
1373	>	if (globals->haveZconstraints()){
1374	>	setupZConstraint(info[k]);
1375	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1376	>	}
1377	>
1378	>	else
1379	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1380	>	break;
1381	>
1382	>	case NVT_ENS:
1383	>	if (globals->haveZconstraints()){
1384	>	setupZConstraint(info[k]);
1385	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1386	>	}
1387	>	else
1388	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1389	>
1390	>	myNVT->setTargetTemp(globals->getTargetTemp());
1391	>
1392	>	if (globals->haveTauThermostat())
1393	>	myNVT->setTauThermostat(globals->getTauThermostat());
1394	>
1395	>	else {
1396	>	sprintf( painCave.errMsg,
1397	>	"SimSetup error: If you use the NVT\n"
1398	>	"    ensemble, you must set tauThermostat.\n");
1399	>	painCave.isFatal = 1;
1400	>	simError();
1401	>	}
1402	>	break;
1403	>
1404	>	case NPTi_ENS:
1405	>	if (globals->haveZconstraints()){
1406	>	setupZConstraint(info[k]);
1407	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1408	>	}
1409	>	else
1410	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1411	>
1412	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1413	>
1414	>	if (globals->haveTargetPressure())
1415	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1416	>	else {
1417	>	sprintf( painCave.errMsg,
1418	>	"SimSetup error: If you use a constant pressure\n"
1419	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1420	>	painCave.isFatal = 1;
1421	>	simError();
1422	>	}
1423	>
1424	>	if( globals->haveTauThermostat() )
1425	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1426	>	else{
1427	>	sprintf( painCave.errMsg,
1428	>	"SimSetup error: If you use an NPT\n"
1429	>	"    ensemble, you must set tauThermostat.\n");
1430	>	painCave.isFatal = 1;
1431	>	simError();
1432	>	}
1433	>
1434	>	if( globals->haveTauBarostat() )
1435	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1436	>	else{
1437	>	sprintf( painCave.errMsg,
1438	>	"SimSetup error: If you use an NPT\n"
1439	>	"    ensemble, you must set tauBarostat.\n");
1440	>	painCave.isFatal = 1;
1441	>	simError();
1442	>	}
1443	>	break;
1444	>
1445	>	case NPTf_ENS:
1446	>	if (globals->haveZconstraints()){
1447	>	setupZConstraint(info[k]);
1448	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1449	>	}
1450	>	else
1451	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1452	>
1453	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1454	>
1455	>	if (globals->haveTargetPressure())
1456	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1457	>	else {
1458	>	sprintf( painCave.errMsg,
1459	>	"SimSetup error: If you use a constant pressure\n"
1460	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1461	>	painCave.isFatal = 1;
1462	>	simError();
1463	>	}
1464	>
1465	>	if( globals->haveTauThermostat() )
1466	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1467	>	else{
1468	>	sprintf( painCave.errMsg,
1469	>	"SimSetup error: If you use an NPT\n"
1470	>	"    ensemble, you must set tauThermostat.\n");
1471	>	painCave.isFatal = 1;
1472	>	simError();
1473	>	}
1474	>
1475	>	if( globals->haveTauBarostat() )
1476	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1477	>	else{
1478	>	sprintf( painCave.errMsg,
1479	>	"SimSetup error: If you use an NPT\n"
1480	>	"    ensemble, you must set tauBarostat.\n");
1481	>	painCave.isFatal = 1;
1482	>	simError();
1483	>	}
1484	>	break;
1485	>
1486	>	case NPTim_ENS:
1487	>	if (globals->haveZconstraints()){
1488	>	setupZConstraint(info[k]);
1489	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1490	>	}
1491	>	else
1492	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1493	>
1494	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1495	>
1496	>	if (globals->haveTargetPressure())
1497	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1498	>	else {
1499	>	sprintf( painCave.errMsg,
1500	>	"SimSetup error: If you use a constant pressure\n"
1501	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1502	>	painCave.isFatal = 1;
1503	>	simError();
1504	>	}
1505	>
1506	>	if( globals->haveTauThermostat() )
1507	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1508	>	else{
1509	>	sprintf( painCave.errMsg,
1510	>	"SimSetup error: If you use an NPT\n"
1511	>	"    ensemble, you must set tauThermostat.\n");
1512	>	painCave.isFatal = 1;
1513	>	simError();
1514	>	}
1515	>
1516	>	if( globals->haveTauBarostat() )
1517	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1518	>	else{
1519	>	sprintf( painCave.errMsg,
1520	>	"SimSetup error: If you use an NPT\n"
1521	>	"    ensemble, you must set tauBarostat.\n");
1522	>	painCave.isFatal = 1;
1523	>	simError();
1524	>	}
1525	>	break;
1526	>
1527	>	case NPTfm_ENS:
1528	>	if (globals->haveZconstraints()){
1529	>	setupZConstraint(info[k]);
1530	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1531	>	}
1532	>	else
1533	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1534	>
1535	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1536	>
1537	>	if (globals->haveTargetPressure())
1538	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1539	>	else {
1540	>	sprintf( painCave.errMsg,
1541	>	"SimSetup error: If you use a constant pressure\n"
1542	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1543	>	painCave.isFatal = 1;
1544	>	simError();
1545	>	}
1546	>
1547	>	if( globals->haveTauThermostat() )
1548	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1549	>	else{
1550	>	sprintf( painCave.errMsg,
1551	>	"SimSetup error: If you use an NPT\n"
1552	>	"    ensemble, you must set tauThermostat.\n");
1553	>	painCave.isFatal = 1;
1554	>	simError();
1555	>	}
1556	>
1557	>	if( globals->haveTauBarostat() )
1558	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1559	>	else{
1560	>	sprintf( painCave.errMsg,
1561	>	"SimSetup error: If you use an NPT\n"
1562	>	"    ensemble, you must set tauBarostat.\n");
1563	>	painCave.isFatal = 1;
1564	>	simError();
1565	>	}
1566	>	break;
1567	>
1568	>	default:
1569	>	sprintf( painCave.errMsg,
1570	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1571	>	painCave.isFatal = 1;
1572	>	simError();
1573	>	}
1574		}
1575	+	}
1576
1577	<	// set the arrays into the SimInfo object
1577	>	void SimSetup::initFortran( void ){
1578
1579	<	info->atoms = the_atoms;
1580	<	info->molecules = the_molecules;
1581	<	info->nGlobalExcludes = 0;
1582	<	info->excludes = the_excludes;
1579	>	info[0].refreshSim();
1580	>
1581	>	if( !strcmp( info[0].mixingRule, "standard") ){
1582	>	the_ff->initForceField( LB_MIXING_RULE );
1583	>	}
1584	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1585	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1586	>	}
1587	>	else{
1588	>	sprintf( painCave.errMsg,
1589	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1590	>	info[0].mixingRule );
1591	>	painCave.isFatal = 1;
1592	>	simError();
1593	>	}
1594
1476	–	the_ff->setSimInfo( info );
1595
1596	+	#ifdef IS_MPI
1597	+	strcpy( checkPointMsg,
1598	+	"Successfully intialized the mixingRule for Fortran." );
1599	+	MPIcheckPoint();
1600	+	#endif // is_mpi
1601	+
1602		}
1603	+
1604	+	void SimSetup::setupZConstraint(SimInfo& theInfo)
1605	+	{
1606	+	int nZConstraints;
1607	+	ZconStamp** zconStamp;
1608	+
1609	+	if(globals->haveZconstraintTime()){
1610	+
1611	+	//add sample time of z-constraint  into SimInfo's property list
1612	+	DoubleData* zconsTimeProp = new DoubleData();
1613	+	zconsTimeProp->setID(ZCONSTIME_ID);
1614	+	zconsTimeProp->setData(globals->getZconsTime());
1615	+	theInfo.addProperty(zconsTimeProp);
1616	+	}
1617	+	else{
1618	+	sprintf( painCave.errMsg,
1619	+	"ZConstraint error: If you use an ZConstraint\n"
1620	+	" , you must set sample time.\n");
1621	+	painCave.isFatal = 1;
1622	+	simError();
1623	+	}
1624	+
1625	+	//
1626	+	nZConstraints = globals->getNzConstraints();
1627	+	zconStamp = globals->getZconStamp();
1628	+	ZConsParaItem tempParaItem;
1629	+
1630	+	ZConsParaData* zconsParaData = new ZConsParaData();
1631	+	zconsParaData->setID(ZCONSPARADATA_ID);
1632	+
1633	+	for(int i = 0; i < nZConstraints; i++){
1634	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1635	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1636	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1637	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1638	+
1639	+	zconsParaData->addItem(tempParaItem);
1640	+	}
1641	+
1642	+	//sort the parameters by index of molecules
1643	+	zconsParaData->sortByIndex();
1644	+
1645	+	//push data into siminfo, therefore, we can retrieve later
1646	+	theInfo.addProperty(zconsParaData);
1647	+
1648	+	//push zconsTol into siminfo, if user does not specify
1649	+	//value for zconsTol, a default value will be used
1650	+	DoubleData* zconsTol = new DoubleData();
1651	+	zconsTol->setID(ZCONSTOL_ID);
1652	+	if(globals->haveZconsTol()){
1653	+	zconsTol->setData(globals->getZconsTol());
1654	+	}
1655	+	else{
1656	+	double defaultZConsTol = 1E-6;
1657	+	sprintf( painCave.errMsg,
1658	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1659	+	" , default value %f is used.\n", defaultZConsTol);
1660	+	painCave.isFatal = 0;
1661	+	simError();
1662	+
1663	+	zconsTol->setData(defaultZConsTol);
1664	+	}
1665	+	theInfo.addProperty(zconsTol);
1666	+
1667	+	//Determine the name of ouput file and add it into SimInfo's property list
1668	+	//Be careful, do not use inFileName, since it is a pointer which
1669	+	//point to a string at master node, and slave nodes do not contain that string
1670	+
1671	+	string zconsOutput(theInfo.finalName);
1672	+
1673	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1674	+
1675	+	StringData* zconsFilename = new StringData();
1676	+	zconsFilename->setID(ZCONSFILENAME_ID);
1677	+	zconsFilename->setData(zconsOutput);
1678	+
1679	+	theInfo.addProperty(zconsFilename);
1680	+	}

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