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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 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 14 | Line 18
18
19		// some defines for ensemble and Forcefield  cases
20
21	<	#define NVE_ENS   0
22	<	#define NVT_ENS   1
23	<	#define NPTi_ENS  2
24	<	#define NPTf_ENS  3
25	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
21	>	#define NVE_ENS        0
22	>	#define NVT_ENS        1
23	>	#define NPTi_ENS       2
24	>	#define NPTf_ENS       3
25	>	#define NPTxyz_ENS     4
26
27
28		#define FF_DUFF 0
29		#define FF_LJ   1
30	+	#define FF_EAM  2
31
32	+	using namespace std;
33
34		SimSetup::SimSetup(){
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40	<
40	>
41	>
42		#ifdef IS_MPI
43	<	strcpy( checkPointMsg, "SimSetup creation successful" );
43	>	strcpy(checkPointMsg, "SimSetup creation successful");
44		MPIcheckPoint();
45		#endif // IS_MPI
46		}
#	Line 41 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	<	void SimSetup::parseFile( char* fileName ){
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		#ifdef IS_MPI
62	<	if( worldRank == 0 ){
62	>	if (worldRank == 0){
63		#endif // is_mpi
64	<
64	>
65		inFileName = fileName;
66	<	set_interface_stamps( stamps, globals );
67	<
66	>	set_interface_stamps(stamps, globals);
67	>
68		#ifdef IS_MPI
69		mpiEventInit();
70		#endif
71
72	<	yacc_BASS( fileName );
72	>	yacc_BASS(fileName);
73
74		#ifdef IS_MPI
75		throwMPIEvent(NULL);
76		}
77	<	else receiveParse();
77	>	else{
78	>	receiveParse();
79	>	}
80		#endif
81
82		}
83
84		#ifdef IS_MPI
85		void SimSetup::receiveParse(void){
86	<
87	<	set_interface_stamps( stamps, globals );
88	<	mpiEventInit();
89	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
86	>	set_interface_stamps(stamps, globals);
87	>	mpiEventInit();
88	>	MPIcheckPoint();
89	>	mpiEventLoop();
90		}
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;
83	–	int i, j, k, globalAtomIndex;
84	–
96		// gather all of the information from the Bass file
97	<
97	>
98		gatherInfo();
99
100		// creation of complex system objects
101
102		sysObjectsCreation();
103
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	–
104		// check on the post processing info
105	<
105	>
106		finalInfoCheck();
107
110	–
111	–
112	–
108		// initialize the system coordinates
109
110	<	initSystemCoords();
111	<
110	>	if (!isInfoArray){
111	>	initSystemCoords();
112
113	+	if( !(globals->getUseInitTime()) )
114	+	info[0].currentTime = 0.0;
115	+	}
116	+
117		// make the output filenames
118
119		makeOutNames();
121	–
122	–
123	–
120
125	–
126	–
127	–
128	–
129	–
121		// make the integrator
131	–
132	–
133	–	NVT*  myNVT = NULL;
134	–	NPTi* myNPTi = NULL;
135	–	NPTf* myNPTf = NULL;
136	–	NPTim* myNPTim = NULL;
137	–	NPTfm* myNPTfm = NULL;
122
123	<	switch( ensembleCase ){
123	>	makeIntegrator();
124
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	–
125		#ifdef IS_MPI
126		mpiSim->mpiRefresh();
127		#endif
128
129		// initialize the Fortran
130
131	<
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	<	}
331	<
332	<
333	<	#ifdef IS_MPI
334	<	strcpy( checkPointMsg,
335	<	"Successfully intialized the mixingRule for Fortran." );
336	<	MPIcheckPoint();
337	<	#endif // is_mpi
131	>	initFortran();
132		}
133
134
135	<	void SimSetup::makeMolecules( void ){
136	<
135	>	void SimSetup::makeMolecules(void){
136	>	int k;
137		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
138	<	molInit info;
138	>	molInit molInfo;
139		DirectionalAtom* dAtom;
140		LinkedAssign* extras;
141		LinkedAssign* current_extra;
#	Line 354 | Line 148 | void SimSetup::makeMolecules( void ){
148		bend_set* theBends;
149		torsion_set* theTorsions;
150
151	<
151	>
152		//init the forceField paramters
153
154		the_ff->readParams();
155
156	<
156	>
157		// init the atoms
158
159		double ux, uy, uz, u, uSqr;
366	–
367	–	atomOffset = 0;
368	–	excludeOffset = 0;
369	–	for(i=0; i<info->n_mol; i++){
370	–
371	–	stampID = the_molecules[i].getStampID();
160
161	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
162	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
375	<	info.nBends    = comp_stamps[stampID]->getNBends();
376	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
377	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
161	>	for (k = 0; k < nInfo; k++){
162	>	the_ff->setSimInfo(&(info[k]));
163
164	<	info.myAtoms = &the_atoms[atomOffset];
165	<	info.myExcludes = &the_excludes[excludeOffset];
166	<	info.myBonds = new Bond*[info.nBonds];
167	<	info.myBends = new Bend*[info.nBends];
383	<	info.myTorsions = new Torsion*[info.nTorsions];
164	>	atomOffset = 0;
165	>	excludeOffset = 0;
166	>	for (i = 0; i < info[k].n_mol; i++){
167	>	stampID = info[k].molecules[i].getStampID();
168
169	<	theBonds = new bond_pair[info.nBonds];
170	<	theBends = new bend_set[info.nBends];
171	<	theTorsions = new torsion_set[info.nTorsions];
172	<
173	<	// make the Atoms
174	<
175	<	for(j=0; j<info.nAtoms; j++){
176	<
177	<	currentAtom = comp_stamps[stampID]->getAtom( j );
178	<	if( currentAtom->haveOrientation() ){
179	<
180	<	dAtom = new DirectionalAtom(j + atomOffset);
181	<	info->n_oriented++;
182	<	info.myAtoms[j] = dAtom;
183	<
184	<	ux = currentAtom->getOrntX();
185	<	uy = currentAtom->getOrntY();
186	<	uz = currentAtom->getOrntZ();
187	<
188	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
189	<
190	<	u = sqrt( uSqr );
191	<	ux = ux / u;
192	<	uy = uy / u;
193	<	uz = uz / u;
194	<
195	<	dAtom->setSUx( ux );
196	<	dAtom->setSUy( uy );
197	<	dAtom->setSUz( uz );
198	<	}
199	<	else{
200	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
201	<	}
202	<	info.myAtoms[j]->setType( currentAtom->getType() );
203	<
169	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
170	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
171	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
172	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
173	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
174	>
175	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
176	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
177	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
178	>	molInfo.myBends = new Bend * [molInfo.nBends];
179	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
180	>
181	>	theBonds = new bond_pair[molInfo.nBonds];
182	>	theBends = new bend_set[molInfo.nBends];
183	>	theTorsions = new torsion_set[molInfo.nTorsions];
184	>
185	>	// make the Atoms
186	>
187	>	for (j = 0; j < molInfo.nAtoms; j++){
188	>	currentAtom = comp_stamps[stampID]->getAtom(j);
189	>	if (currentAtom->haveOrientation()){
190	>	dAtom = new DirectionalAtom((j + atomOffset),
191	>	info[k].getConfiguration());
192	>	info[k].n_oriented++;
193	>	molInfo.myAtoms[j] = dAtom;
194	>
195	>	ux = currentAtom->getOrntX();
196	>	uy = currentAtom->getOrntY();
197	>	uz = currentAtom->getOrntZ();
198	>
199	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
200	>
201	>	u = sqrt(uSqr);
202	>	ux = ux / u;
203	>	uy = uy / u;
204	>	uz = uz / u;
205	>
206	>	dAtom->setSUx(ux);
207	>	dAtom->setSUy(uy);
208	>	dAtom->setSUz(uz);
209	>	}
210	>	else{
211	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
212	>	info[k].getConfiguration());
213	>	}
214	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
215	>
216		#ifdef IS_MPI
217	<
218	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
219	<
217	>
218	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
219	>
220		#endif // is_mpi
221	<	}
426	<
427	<	// make the bonds
428	<	for(j=0; j<info.nBonds; j++){
429	<
430	<	currentBond = comp_stamps[stampID]->getBond( j );
431	<	theBonds[j].a = currentBond->getA() + atomOffset;
432	<	theBonds[j].b = currentBond->getB() + atomOffset;
221	>	}
222
223	<	exI = theBonds[j].a;
224	<	exJ = theBonds[j].b;
223	>	// make the bonds
224	>	for (j = 0; j < molInfo.nBonds; j++){
225	>	currentBond = comp_stamps[stampID]->getBond(j);
226	>	theBonds[j].a = currentBond->getA() + atomOffset;
227	>	theBonds[j].b = currentBond->getB() + atomOffset;
228
229	<	// exclude_I must always be the smaller of the pair
230	<	if( exI > exJ ){
231	<	tempEx = exI;
232	<	exI = exJ;
233	<	exJ = tempEx;
229	>	exI = theBonds[j].a;
230	>	exJ = theBonds[j].b;
231	>
232	>	// exclude_I must always be the smaller of the pair
233	>	if (exI > exJ){
234	>	tempEx = exI;
235	>	exI = exJ;
236	>	exJ = tempEx;
237	>	}
238	>	#ifdef IS_MPI
239	>	tempEx = exI;
240	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241	>	tempEx = exJ;
242	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>
244	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
245	>	#else  // isn't MPI
246	>
247	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
248	>	#endif  //is_mpi
249		}
250	+	excludeOffset += molInfo.nBonds;
251	+
252	+	//make the bends
253	+	for (j = 0; j < molInfo.nBends; j++){
254	+	currentBend = comp_stamps[stampID]->getBend(j);
255	+	theBends[j].a = currentBend->getA() + atomOffset;
256	+	theBends[j].b = currentBend->getB() + atomOffset;
257	+	theBends[j].c = currentBend->getC() + atomOffset;
258	+
259	+	if (currentBend->haveExtras()){
260	+	extras = currentBend->getExtras();
261	+	current_extra = extras;
262	+
263	+	while (current_extra != NULL){
264	+	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
265	+	switch (current_extra->getType()){
266	+	case 0:
267	+	theBends[j].ghost = current_extra->getInt() + atomOffset;
268	+	theBends[j].isGhost = 1;
269	+	break;
270	+
271	+	case 1:
272	+	theBends[j].ghost = (int) current_extra->getDouble() +
273	+	atomOffset;
274	+	theBends[j].isGhost = 1;
275	+	break;
276	+
277	+	default:
278	+	sprintf(painCave.errMsg,
279	+	"SimSetup Error: ghostVectorSource was neither a "
280	+	"double nor an int.\n"
281	+	"-->Bend[%d] in %s\n",
282	+	j, comp_stamps[stampID]->getID());
283	+	painCave.isFatal = 1;
284	+	simError();
285	+	}
286	+	}
287	+	else{
288	+	sprintf(painCave.errMsg,
289	+	"SimSetup Error: unhandled bend assignment:\n"
290	+	"    -->%s in Bend[%d] in %s\n",
291	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
292	+	painCave.isFatal = 1;
293	+	simError();
294	+	}
295	+
296	+	current_extra = current_extra->getNext();
297	+	}
298	+	}
299	+
300	+	if (!theBends[j].isGhost){
301	+	exI = theBends[j].a;
302	+	exJ = theBends[j].c;
303	+	}
304	+	else{
305	+	exI = theBends[j].a;
306	+	exJ = theBends[j].b;
307	+	}
308	+
309	+	// exclude_I must always be the smaller of the pair
310	+	if (exI > exJ){
311	+	tempEx = exI;
312	+	exI = exJ;
313	+	exJ = tempEx;
314	+	}
315	+	#ifdef IS_MPI
316	+	tempEx = exI;
317	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318	+	tempEx = exJ;
319	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	+
321	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
322	+	#else  // isn't MPI
323	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
324	+	#endif  //is_mpi
325	+	}
326	+	excludeOffset += molInfo.nBends;
327	+
328	+	for (j = 0; j < molInfo.nTorsions; j++){
329	+	currentTorsion = comp_stamps[stampID]->getTorsion(j);
330	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
331	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
332	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
333	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
334	+
335	+	exI = theTorsions[j].a;
336	+	exJ = theTorsions[j].d;
337	+
338	+	// exclude_I must always be the smaller of the pair
339	+	if (exI > exJ){
340	+	tempEx = exI;
341	+	exI = exJ;
342	+	exJ = tempEx;
343	+	}
344		#ifdef IS_MPI
345	<	tempEx = exI;
346	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
347	<	tempEx = exJ;
348	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
448	<
449	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
450	<	#else  // isn't MPI
345	>	tempEx = exI;
346	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	>	tempEx = exJ;
348	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349
350	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
453	<	#endif  //is_mpi
454	<	}
455	<	excludeOffset += info.nBonds;
456	<
457	<	//make the bends
458	<	for(j=0; j<info.nBends; j++){
459	<
460	<	currentBend = comp_stamps[stampID]->getBend( j );
461	<	theBends[j].a = currentBend->getA() + atomOffset;
462	<	theBends[j].b = currentBend->getB() + atomOffset;
463	<	theBends[j].c = currentBend->getC() + atomOffset;
464	<
465	<	if( currentBend->haveExtras() ){
466	<
467	<	extras = currentBend->getExtras();
468	<	current_extra = extras;
469	<
470	<	while( current_extra != NULL ){
471	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
472	<
473	<	switch( current_extra->getType() ){
474	<
475	<	case 0:
476	<	theBends[j].ghost =
477	<	current_extra->getInt() + atomOffset;
478	<	theBends[j].isGhost = 1;
479	<	break;
480	<
481	<	case 1:
482	<	theBends[j].ghost =
483	<	(int)current_extra->getDouble() + atomOffset;
484	<	theBends[j].isGhost = 1;
485	<	break;
486	<
487	<	default:
488	<	sprintf( painCave.errMsg,
489	<	"SimSetup Error: ghostVectorSource was neither a "
490	<	"double nor an int.\n"
491	<	"-->Bend[%d] in %s\n",
492	<	j, comp_stamps[stampID]->getID() );
493	<	painCave.isFatal = 1;
494	<	simError();
495	<	}
496	<	}
497	<
498	<	else{
499	<
500	<	sprintf( painCave.errMsg,
501	<	"SimSetup Error: unhandled bend assignment:\n"
502	<	"    -->%s in Bend[%d] in %s\n",
503	<	current_extra->getlhs(),
504	<	j, comp_stamps[stampID]->getID() );
505	<	painCave.isFatal = 1;
506	<	simError();
507	<	}
508	<
509	<	current_extra = current_extra->getNext();
510	<	}
511	<	}
512	<
513	<	if( !theBends[j].isGhost ){
514	<
515	<	exI = theBends[j].a;
516	<	exJ = theBends[j].c;
517	<	}
518	<	else{
519	<
520	<	exI = theBends[j].a;
521	<	exJ = theBends[j].b;
522	<	}
523	<
524	<	// exclude_I must always be the smaller of the pair
525	<	if( exI > exJ ){
526	<	tempEx = exI;
527	<	exI = exJ;
528	<	exJ = tempEx;
529	<	}
530	<	#ifdef IS_MPI
531	<	tempEx = exI;
532	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
533	<	tempEx = exJ;
534	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
535	<
536	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
350	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
351		#else  // isn't MPI
352	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
352	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
353		#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;
354		}
355	<	#ifdef IS_MPI
561	<	tempEx = exI;
562	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
563	<	tempEx = exJ;
564	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
565	<
566	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
567	<	#else  // isn't MPI
568	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
569	<	#endif  //is_mpi
570	<	}
571	<	excludeOffset += info.nTorsions;
355	>	excludeOffset += molInfo.nTorsions;
356
573	–
574	–	// send the arrays off to the forceField for init.
357
358	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
577	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
578	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
579	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
358	>	// send the arrays off to the forceField for init.
359
360	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
361	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
362	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
363	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
364	+	theTorsions);
365
582	–	the_molecules[i].initialize( info );
366
367	+	info[k].molecules[i].initialize(molInfo);
368
369	<	atomOffset += info.nAtoms;
370	<	delete[] theBonds;
371	<	delete[] theBends;
372	<	delete[] theTorsions;
369	>
370	>	atomOffset += molInfo.nAtoms;
371	>	delete[] theBonds;
372	>	delete[] theBends;
373	>	delete[] theTorsions;
374	>	}
375		}
376
377		#ifdef IS_MPI
378	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
378	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
379		MPIcheckPoint();
380		#endif // is_mpi
381
382		// clean up the forcefield
383	+
384		the_ff->calcRcut();
385		the_ff->cleanMe();
599	–
386		}
387
388	<	void SimSetup::initFromBass( void ){
603	<
388	>	void SimSetup::initFromBass(void){
389		int i, j, k;
390		int n_cells;
391		double cellx, celly, cellz;
#	Line 609 | Line 394 | void SimSetup::initFromBass( void ){
394		int n_extra;
395		int have_extra, done;
396
397	<	temp1 = (double)tot_nmol / 4.0;
398	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
399	<	temp3 = ceil( temp2 );
397	>	double vel[3];
398	>	vel[0] = 0.0;
399	>	vel[1] = 0.0;
400	>	vel[2] = 0.0;
401
402	<	have_extra =0;
403	<	if( temp2 < temp3 ){ // we have a non-complete lattice
404	<	have_extra =1;
402	>	temp1 = (double) tot_nmol / 4.0;
403	>	temp2 = pow(temp1, (1.0 / 3.0));
404	>	temp3 = ceil(temp2);
405
406	<	n_cells = (int)temp3 - 1;
407	<	cellx = info->boxLx / temp3;
408	<	celly = info->boxLy / temp3;
409	<	cellz = info->boxLz / temp3;
624	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
625	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
626	<	n_per_extra = (int)ceil( temp1 );
406	>	have_extra = 0;
407	>	if (temp2 < temp3){
408	>	// we have a non-complete lattice
409	>	have_extra = 1;
410
411	<	if( n_per_extra > 4){
412	<	sprintf( painCave.errMsg,
413	<	"SimSetup error. There has been an error in constructing"
414	<	" the non-complete lattice.\n" );
411	>	n_cells = (int) temp3 - 1;
412	>	cellx = info[0].boxL[0] / temp3;
413	>	celly = info[0].boxL[1] / temp3;
414	>	cellz = info[0].boxL[2] / temp3;
415	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
416	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
417	>	n_per_extra = (int) ceil(temp1);
418	>
419	>	if (n_per_extra > 4){
420	>	sprintf(painCave.errMsg,
421	>	"SimSetup error. There has been an error in constructing"
422	>	" the non-complete lattice.\n");
423		painCave.isFatal = 1;
424		simError();
425		}
426		}
427		else{
428	<	n_cells = (int)temp3;
429	<	cellx = info->boxLx / temp3;
430	<	celly = info->boxLy / temp3;
431	<	cellz = info->boxLz / temp3;
428	>	n_cells = (int) temp3;
429	>	cellx = info[0].boxL[0] / temp3;
430	>	celly = info[0].boxL[1] / temp3;
431	>	cellz = info[0].boxL[2] / temp3;
432		}
433
434		current_mol = 0;
#	Line 645 | Line 436 | void SimSetup::initFromBass( void ){
436		current_comp = 0;
437		current_atom_ndx = 0;
438
439	<	for( i=0; i < n_cells ; i++ ){
440	<	for( j=0; j < n_cells; j++ ){
441	<	for( k=0; k < n_cells; k++ ){
439	>	for (i = 0; i < n_cells ; i++){
440	>	for (j = 0; j < n_cells; j++){
441	>	for (k = 0; k < n_cells; k++){
442	>	makeElement(i * cellx, j * celly, k * cellz);
443
444	<	makeElement( i * cellx,
653	<	j * celly,
654	<	k * cellz );
444	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
445
446	<	makeElement( i * cellx + 0.5 * cellx,
657	<	j * celly + 0.5 * celly,
658	<	k * cellz );
446	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
447
448	<	makeElement( i * cellx,
661	<	j * celly + 0.5 * celly,
662	<	k * cellz + 0.5 * cellz );
663	<
664	<	makeElement( i * cellx + 0.5 * cellx,
665	<	j * celly,
666	<	k * cellz + 0.5 * cellz );
448	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
449		}
450		}
451		}
452
453	<	if( have_extra ){
453	>	if (have_extra){
454		done = 0;
455
456		int start_ndx;
457	<	for( i=0; i < (n_cells+1) && !done; i++ ){
458	<	for( j=0; j < (n_cells+1) && !done; j++ ){
457	>	for (i = 0; i < (n_cells + 1) && !done; i++){
458	>	for (j = 0; j < (n_cells + 1) && !done; j++){
459	>	if (i < n_cells){
460	>	if (j < n_cells){
461	>	start_ndx = n_cells;
462	>	}
463	>	else
464	>	start_ndx = 0;
465	>	}
466	>	else
467	>	start_ndx = 0;
468
469	<	if( i < n_cells ){
470	<
471	<	if( j < n_cells ){
681	<	start_ndx = n_cells;
682	<	}
683	<	else start_ndx = 0;
684	<	}
685	<	else start_ndx = 0;
686	<
687	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
469	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
470	>	makeElement(i * cellx, j * celly, k * cellz);
471	>	done = (current_mol >= tot_nmol);
472
473	<	makeElement( i * cellx,
474	<	j * celly,
475	<	k * cellz );
476	<	done = ( current_mol >= tot_nmol );
473	>	if (!done && n_per_extra > 1){
474	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
475	>	k * cellz);
476	>	done = (current_mol >= tot_nmol);
477	>	}
478
479	<	if( !done && n_per_extra > 1 ){
480	<	makeElement( i * cellx + 0.5 * cellx,
481	<	j * celly + 0.5 * celly,
482	<	k * cellz );
483	<	done = ( current_mol >= tot_nmol );
699	<	}
479	>	if (!done && n_per_extra > 2){
480	>	makeElement(i * cellx, j * celly + 0.5 * celly,
481	>	k * cellz + 0.5 * cellz);
482	>	done = (current_mol >= tot_nmol);
483	>	}
484
485	<	if( !done && n_per_extra > 2){
486	<	makeElement( i * cellx,
487	<	j * celly + 0.5 * celly,
488	<	k * cellz + 0.5 * cellz );
489	<	done = ( current_mol >= tot_nmol );
490	<	}
707	<
708	<	if( !done && n_per_extra > 3){
709	<	makeElement( i * cellx + 0.5 * cellx,
710	<	j * celly,
711	<	k * cellz + 0.5 * cellz );
712	<	done = ( current_mol >= tot_nmol );
713	<	}
714	<	}
485	>	if (!done && n_per_extra > 3){
486	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
487	>	k * cellz + 0.5 * cellz);
488	>	done = (current_mol >= tot_nmol);
489	>	}
490	>	}
491		}
492		}
493		}
494
495	<
496	<	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 );
495	>	for (i = 0; i < info[0].n_atoms; i++){
496	>	info[0].atoms[i]->setVel(vel);
497		}
498		}
499
500	<	void SimSetup::makeElement( double x, double y, double z ){
728	<
500	>	void SimSetup::makeElement(double x, double y, double z){
501		int k;
502		AtomStamp* current_atom;
503		DirectionalAtom* dAtom;
504		double rotMat[3][3];
505	+	double pos[3];
506
507	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
508	<
509	<	current_atom = comp_stamps[current_comp]->getAtom( k );
510	<	if( !current_atom->havePosition() ){
511	<	sprintf( painCave.errMsg,
512	<	"SimSetup:initFromBass error.\n"
513	<	"\tComponent %s, atom %s does not have a position specified.\n"
514	<	"\tThe initialization routine is unable to give a start"
515	<	" position.\n",
743	<	comp_stamps[current_comp]->getID(),
744	<	current_atom->getType() );
507	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
508	>	current_atom = comp_stamps[current_comp]->getAtom(k);
509	>	if (!current_atom->havePosition()){
510	>	sprintf(painCave.errMsg,
511	>	"SimSetup:initFromBass error.\n"
512	>	"\tComponent %s, atom %s does not have a position specified.\n"
513	>	"\tThe initialization routine is unable to give a start"
514	>	" position.\n",
515	>	comp_stamps[current_comp]->getID(), current_atom->getType());
516		painCave.isFatal = 1;
517		simError();
518		}
519
520	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
521	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
522	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
520	>	pos[0] = x + current_atom->getPosX();
521	>	pos[1] = y + current_atom->getPosY();
522	>	pos[2] = z + current_atom->getPosZ();
523
524	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
524	>	info[0].atoms[current_atom_ndx]->setPos(pos);
525
526	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
526	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
527	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
528
529		rotMat[0][0] = 1.0;
530		rotMat[0][1] = 0.0;
#	Line 766 | Line 538 | void SimSetup::makeElement( double x, double y, double
538		rotMat[2][1] = 0.0;
539		rotMat[2][2] = 1.0;
540
541	<	dAtom->setA( rotMat );
541	>	dAtom->setA(rotMat);
542		}
543
544		current_atom_ndx++;
#	Line 775 | Line 547 | void SimSetup::makeElement( double x, double y, double
547		current_mol++;
548		current_comp_mol++;
549
550	<	if( current_comp_mol >= components_nmol[current_comp] ){
779	<
550	>	if (current_comp_mol >= components_nmol[current_comp]){
551		current_comp_mol = 0;
552		current_comp++;
553		}
554		}
555
556
557	<	void SimSetup::gatherInfo( void ){
557	>	void SimSetup::gatherInfo(void){
558	>	int i;
559
560		ensembleCase = -1;
561		ffCase = -1;
562
791	–	// get the stamps and globals;
792	–	the_stamps = stamps;
793	–	the_globals = globals;
794	–
563		// 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();
564
565	+	for (i = 0; i < nInfo; i++){
566	+	info[i].target_temp = globals->getTargetTemp();
567	+	info[i].dt = globals->getDt();
568	+	info[i].run_time = globals->getRunTime();
569	+	}
570	+	n_components = globals->getNComponents();
571
572	+
573		// get the forceField
574
575	<	strcpy( force_field, the_globals->getForceField() );
575	>	strcpy(force_field, globals->getForceField());
576
577	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
578	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
577	>	if (!strcasecmp(force_field, "DUFF")){
578	>	ffCase = FF_DUFF;
579	>	}
580	>	else if (!strcasecmp(force_field, "LJ")){
581	>	ffCase = FF_LJ;
582	>	}
583	>	else if (!strcasecmp(force_field, "EAM")){
584	>	ffCase = FF_EAM;
585	>	}
586		else{
587	<	sprintf( painCave.errMsg,
588	<	"SimSetup Error. Unrecognized force field -> %s\n",
589	<	force_field );
590	<	painCave.isFatal = 1;
813	<	simError();
587	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
588	>	force_field);
589	>	painCave.isFatal = 1;
590	>	simError();
591		}
592
593	<	// get the ensemble
593	>	// get the ensemble
594
595	<	strcpy( ensemble, the_globals->getEnsemble() );
595	>	strcpy(ensemble, globals->getEnsemble());
596
597	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
598	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
599	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
597	>	if (!strcasecmp(ensemble, "NVE")){
598	>	ensembleCase = NVE_ENS;
599	>	}
600	>	else if (!strcasecmp(ensemble, "NVT")){
601	>	ensembleCase = NVT_ENS;
602	>	}
603	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
604		ensembleCase = NPTi_ENS;
605	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
606	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
607	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
605	>	}
606	>	else if (!strcasecmp(ensemble, "NPTf")){
607	>	ensembleCase = NPTf_ENS;
608	>	}
609	>	else if (!strcasecmp(ensemble, "NPTxyz")){
610	>	ensembleCase = NPTxyz_ENS;
611	>	}
612		else{
613	<	sprintf( painCave.errMsg,
614	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
615	<	"reverting to NVE for this simulation.\n",
616	<	ensemble );
617	<	painCave.isFatal = 0;
618	<	simError();
619	<	strcpy( ensemble, "NVE" );
620	<	ensembleCase = NVE_ENS;
613	>	sprintf(painCave.errMsg,
614	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
615	>	"reverting to NVE for this simulation.\n",
616	>	ensemble);
617	>	painCave.isFatal = 0;
618	>	simError();
619	>	strcpy(ensemble, "NVE");
620	>	ensembleCase = NVE_ENS;
621		}
837	–	strcpy( info->ensemble, ensemble );
622
623	<	// get the mixing rule
623	>	for (i = 0; i < nInfo; i++){
624	>	strcpy(info[i].ensemble, ensemble);
625
626	<	strcpy( info->mixingRule, the_globals->getMixingRule() );
627	<	info->usePBC = the_globals->getPBC();
628	<
629	<
626	>	// get the mixing rule
627	>
628	>	strcpy(info[i].mixingRule, globals->getMixingRule());
629	>	info[i].usePBC = globals->getPBC();
630	>	}
631	>
632		// get the components and calculate the tot_nMol and indvidual n_mol
633	<
634	<	the_components = the_globals->getComponents();
633	>
634	>	the_components = globals->getComponents();
635		components_nmol = new int[n_components];
636
637
638	<	if( !the_globals->haveNMol() ){
638	>	if (!globals->haveNMol()){
639		// we don't have the total number of molecules, so we assume it is
640		// given in each component
641
642		tot_nmol = 0;
643	<	for( i=0; i<n_components; i++ ){
644	<
645	<	if( !the_components[i]->haveNMol() ){
646	<	// we have a problem
647	<	sprintf( painCave.errMsg,
648	<	"SimSetup Error. No global NMol or component NMol"
649	<	" given. Cannot calculate the number of atoms.\n" );
650	<	painCave.isFatal = 1;
864	<	simError();
643	>	for (i = 0; i < n_components; i++){
644	>	if (!the_components[i]->haveNMol()){
645	>	// we have a problem
646	>	sprintf(painCave.errMsg,
647	>	"SimSetup Error. No global NMol or component NMol"
648	>	" given. Cannot calculate the number of atoms.\n");
649	>	painCave.isFatal = 1;
650	>	simError();
651		}
652
653		tot_nmol += the_components[i]->getNMol();
#	Line 869 | Line 655 | void SimSetup::gatherInfo( void ){
655		}
656		}
657		else{
658	<	sprintf( painCave.errMsg,
659	<	"SimSetup error.\n"
660	<	"\tSorry, the ability to specify total"
661	<	" nMols and then give molfractions in the components\n"
662	<	"\tis not currently supported."
663	<	" Please give nMol in the components.\n" );
658	>	sprintf(painCave.errMsg,
659	>	"SimSetup error.\n"
660	>	"\tSorry, the ability to specify total"
661	>	" nMols and then give molfractions in the components\n"
662	>	"\tis not currently supported."
663	>	" Please give nMol in the components.\n");
664		painCave.isFatal = 1;
665		simError();
666		}
667
668		// set the status, sample, and thermal kick times
883	–
884	–	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	–	}
669
670	<	if( the_globals->haveStatusTime() ){
671	<	info->statusTime = the_globals->getStatusTime();
672	<	}
670	>	for (i = 0; i < nInfo; i++){
671	>	if (globals->haveSampleTime()){
672	>	info[i].sampleTime = globals->getSampleTime();
673	>	info[i].statusTime = info[i].sampleTime;
674	>	info[i].thermalTime = info[i].sampleTime;
675	>	}
676	>	else{
677	>	info[i].sampleTime = globals->getRunTime();
678	>	info[i].statusTime = info[i].sampleTime;
679	>	info[i].thermalTime = info[i].sampleTime;
680	>	}
681
682	<	if( the_globals->haveThermalTime() ){
683	<	info->thermalTime = the_globals->getThermalTime();
684	<	}
682	>	if (globals->haveStatusTime()){
683	>	info[i].statusTime = globals->getStatusTime();
684	>	}
685
686	<	// check for the temperature set flag
686	>	if (globals->haveThermalTime()){
687	>	info[i].thermalTime = globals->getThermalTime();
688	>	}
689
690	<	if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet();
690	>	info[i].resetIntegrator = 0;
691	>	if( globals->haveResetTime() ){
692	>	info[i].resetTime = globals->getResetTime();
693	>	info[i].resetIntegrator = 1;
694	>	}
695
696	<	// get some of the tricky things that may still be in the globals
696	>	// check for the temperature set flag
697
698	<	double boxVector[3];
699	<	if( the_globals->haveBox() ){
911	<	boxVector[0] = the_globals->getBox();
912	<	boxVector[1] = the_globals->getBox();
913	<	boxVector[2] = the_globals->getBox();
914	<
915	<	info->setBox( boxVector );
916	<	}
917	<	else if( the_globals->haveDensity() ){
698	>	if (globals->haveTempSet())
699	>	info[i].setTemp = globals->getTempSet();
700
701	<	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];
701	>	// get some of the tricky things that may still be in the globals
702
703	<	info->setBox( boxVector );
704	<	}
705	<	else{
706	<	if( !the_globals->haveBoxX() ){
707	<	sprintf( painCave.errMsg,
930	<	"SimSetup error, no periodic BoxX size given.\n" );
931	<	painCave.isFatal = 1;
932	<	simError();
933	<	}
934	<	boxVector[0] = the_globals->getBoxX();
703	>	double boxVector[3];
704	>	if (globals->haveBox()){
705	>	boxVector[0] = globals->getBox();
706	>	boxVector[1] = globals->getBox();
707	>	boxVector[2] = globals->getBox();
708
709	<	if( !the_globals->haveBoxY() ){
937	<	sprintf( painCave.errMsg,
938	<	"SimSetup error, no periodic BoxY size given.\n" );
939	<	painCave.isFatal = 1;
940	<	simError();
709	>	info[i].setBox(boxVector);
710		}
711	<	boxVector[1] = the_globals->getBoxY();
711	>	else if (globals->haveDensity()){
712	>	double vol;
713	>	vol = (double) tot_nmol / globals->getDensity();
714	>	boxVector[0] = pow(vol, (1.0 / 3.0));
715	>	boxVector[1] = boxVector[0];
716	>	boxVector[2] = boxVector[0];
717
718	<	if( !the_globals->haveBoxZ() ){
945	<	sprintf( painCave.errMsg,
946	<	"SimSetup error, no periodic BoxZ size given.\n" );
947	<	painCave.isFatal = 1;
948	<	simError();
718	>	info[i].setBox(boxVector);
719		}
720	<	boxVector[2] = the_globals->getBoxZ();
720	>	else{
721	>	if (!globals->haveBoxX()){
722	>	sprintf(painCave.errMsg,
723	>	"SimSetup error, no periodic BoxX size given.\n");
724	>	painCave.isFatal = 1;
725	>	simError();
726	>	}
727	>	boxVector[0] = globals->getBoxX();
728
729	<	info->setBox( boxVector );
729	>	if (!globals->haveBoxY()){
730	>	sprintf(painCave.errMsg,
731	>	"SimSetup error, no periodic BoxY size given.\n");
732	>	painCave.isFatal = 1;
733	>	simError();
734	>	}
735	>	boxVector[1] = globals->getBoxY();
736	>
737	>	if (!globals->haveBoxZ()){
738	>	sprintf(painCave.errMsg,
739	>	"SimSetup error, no periodic BoxZ size given.\n");
740	>	painCave.isFatal = 1;
741	>	simError();
742	>	}
743	>	boxVector[2] = globals->getBoxZ();
744	>
745	>	info[i].setBox(boxVector);
746	>	}
747		}
748
749	+	//setup seed for random number generator
750	+	int seedValue;
751
752	+	if (globals->haveSeed()){
753	+	seedValue = globals->getSeed();
754	+
755	+	if(seedValue / 1E9 == 0){
756	+	sprintf(painCave.errMsg,
757	+	"Seed for sprng library should contain at least 9 digits\n"
758	+	"OOPSE will generate a seed for user\n");
759	+	painCave.isFatal = 0;
760	+	simError();
761	+
762	+	//using seed generated by system instead of invalid seed set by user
763	+	#ifndef IS_MPI
764	+	seedValue = make_sprng_seed();
765	+	#else
766	+	if (worldRank == 0){
767	+	seedValue = make_sprng_seed();
768	+	}
769	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
770	+	#endif
771	+	}
772	+	}//end of if branch of globals->haveSeed()
773	+	else{
774
775	+	#ifndef IS_MPI
776	+	seedValue = make_sprng_seed();
777	+	#else
778	+	if (worldRank == 0){
779	+	seedValue = make_sprng_seed();
780	+	}
781	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
782	+	#endif
783	+	}//end of globals->haveSeed()
784	+
785	+	for (int i = 0; i < nInfo; i++){
786	+	info[i].setSeed(seedValue);
787	+	}
788	+
789		#ifdef IS_MPI
790	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
790	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
791		MPIcheckPoint();
792		#endif // is_mpi
961	–
793		}
794
795
796	<	void SimSetup::finalInfoCheck( void ){
796	>	void SimSetup::finalInfoCheck(void){
797		int index;
798		int usesDipoles;
799	<
799	>	int i;
800
801	<	// check electrostatic parameters
802	<
803	<	index = 0;
804	<	usesDipoles = 0;
805	<	while( (index < info->n_atoms) && !usesDipoles ){
806	<	usesDipoles = ((info->atoms)[index])->hasDipole();
807	<	index++;
808	<	}
809	<
801	>	for (i = 0; i < nInfo; i++){
802	>	// check electrostatic parameters
803	>
804	>	index = 0;
805	>	usesDipoles = 0;
806	>	while ((index < info[i].n_atoms) && !usesDipoles){
807	>	usesDipoles = (info[i].atoms[index])->hasDipole();
808	>	index++;
809	>	}
810	>
811		#ifdef IS_MPI
812	<	int myUse = usesDipoles
813	<	MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
812	>	int myUse = usesDipoles;
813	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814		#endif //is_mpi
815
816	+	double theEcr, theEst;
817
818	<	if (the_globals->getUseRF() ) {
819	<	info->useReactionField = 1;
987	<
988	<	if( !the_globals->haveECR() ){
989	<	sprintf( painCave.errMsg,
990	<	"SimSetup Warning: using default value of 1/2 the smallest "
991	<	"box length for the electrostaticCutoffRadius.\n"
992	<	"I hope you have a very fast processor!\n");
993	<	painCave.isFatal = 0;
994	<	simError();
995	<	double smallest;
996	<	smallest = info->boxLx;
997	<	if (info->boxLy <= smallest) smallest = info->boxLy;
998	<	if (info->boxLz <= smallest) smallest = info->boxLz;
999	<	info->ecr = 0.5 * smallest;
1000	<	} else {
1001	<	info->ecr        = the_globals->getECR();
1002	<	}
818	>	if (globals->getUseRF()){
819	>	info[i].useReactionField = 1;
820
821	<	if( !the_globals->haveEST() ){
822	<	sprintf( painCave.errMsg,
823	<	"SimSetup Warning: using default value of 0.05 * the "
824	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	<	);
1009	<	painCave.isFatal = 0;
1010	<	simError();
1011	<	info->est = 0.05 * info->ecr;
1012	<	} else {
1013	<	info->est        = the_globals->getEST();
1014	<	}
1015	<
1016	<	if(!the_globals->haveDielectric() ){
1017	<	sprintf( painCave.errMsg,
1018	<	"SimSetup Error: You are trying to use Reaction Field without"
1019	<	"setting a dielectric constant!\n"
1020	<	);
1021	<	painCave.isFatal = 1;
1022	<	simError();
1023	<	}
1024	<	info->dielectric = the_globals->getDielectric();
1025	<	}
1026	<	else {
1027	<	if (usesDipoles) {
1028	<
1029	<	if( !the_globals->haveECR() ){
1030	<	sprintf( painCave.errMsg,
1031	<	"SimSetup Warning: using default value of 1/2 the smallest "
1032	<	"box length for the electrostaticCutoffRadius.\n"
1033	<	"I hope you have a very fast processor!\n");
821	>	if (!globals->haveECR()){
822	>	sprintf(painCave.errMsg,
823	>	"SimSetup Warning: using default value of 1/2 the smallest "
824	>	"box length for the electrostaticCutoffRadius.\n"
825	>	"I hope you have a very fast processor!\n");
826		painCave.isFatal = 0;
827		simError();
828		double smallest;
829	<	smallest = info->boxLx;
830	<	if (info->boxLy <= smallest) smallest = info->boxLy;
831	<	if (info->boxLz <= smallest) smallest = info->boxLz;
832	<	info->ecr = 0.5 * smallest;
833	<	} else {
834	<	info->ecr        = the_globals->getECR();
829	>	smallest = info[i].boxL[0];
830	>	if (info[i].boxL[1] <= smallest)
831	>	smallest = info[i].boxL[1];
832	>	if (info[i].boxL[2] <= smallest)
833	>	smallest = info[i].boxL[2];
834	>	theEcr = 0.5 * smallest;
835		}
836	<
837	<	if( !the_globals->haveEST() ){
838	<	sprintf( painCave.errMsg,
839	<	"SimSetup Warning: using default value of 5%% of the "
840	<	"electrostaticCutoffRadius for the "
841	<	"electrostaticSkinThickness\n"
842	<	);
836	>	else{
837	>	theEcr = globals->getECR();
838	>	}
839	>
840	>	if (!globals->haveEST()){
841	>	sprintf(painCave.errMsg,
842	>	"SimSetup Warning: using default value of 0.05 * the "
843	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
844		painCave.isFatal = 0;
845		simError();
846	<	info->est = 0.05 * info->ecr;
1054	<	} else {
1055	<	info->est        = the_globals->getEST();
846	>	theEst = 0.05 * theEcr;
847		}
848	+	else{
849	+	theEst = globals->getEST();
850	+	}
851	+
852	+	info[i].setEcr(theEcr, theEst);
853	+
854	+	if (!globals->haveDielectric()){
855	+	sprintf(painCave.errMsg,
856	+	"SimSetup Error: You are trying to use Reaction Field without"
857	+	"setting a dielectric constant!\n");
858	+	painCave.isFatal = 1;
859	+	simError();
860	+	}
861	+	info[i].dielectric = globals->getDielectric();
862		}
863	<	}
863	>	else{
864	>	if (usesDipoles){
865	>	if (!globals->haveECR()){
866	>	sprintf(painCave.errMsg,
867	>	"SimSetup Warning: using default value of 1/2 the smallest "
868	>	"box length for the electrostaticCutoffRadius.\n"
869	>	"I hope you have a very fast processor!\n");
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	double smallest;
873	>	smallest = info[i].boxL[0];
874	>	if (info[i].boxL[1] <= smallest)
875	>	smallest = info[i].boxL[1];
876	>	if (info[i].boxL[2] <= smallest)
877	>	smallest = info[i].boxL[2];
878	>	theEcr = 0.5 * smallest;
879	>	}
880	>	else{
881	>	theEcr = globals->getECR();
882	>	}
883
884	+	if (!globals->haveEST()){
885	+	sprintf(painCave.errMsg,
886	+	"SimSetup Warning: using default value of 0.05 * the "
887	+	"electrostaticCutoffRadius for the "
888	+	"electrostaticSkinThickness\n");
889	+	painCave.isFatal = 0;
890	+	simError();
891	+	theEst = 0.05 * theEcr;
892	+	}
893	+	else{
894	+	theEst = globals->getEST();
895	+	}
896	+
897	+	info[i].setEcr(theEcr, theEst);
898	+	}
899	+	}
900	+	}
901	+
902		#ifdef IS_MPI
903	<	strcpy( checkPointMsg, "post processing checks out" );
903	>	strcpy(checkPointMsg, "post processing checks out");
904		MPIcheckPoint();
905		#endif // is_mpi
1064	–
906		}
907
908	<	void SimSetup::initSystemCoords( void ){
908	>	void SimSetup::initSystemCoords(void){
909	>	int i;
910
911	<	if( the_globals->haveInitialConfig() ){
912	<
913	<	InitializeFromFile* fileInit;
911	>	char* inName;
912	>
913	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
914	>
915	>	for (i = 0; i < info[0].n_atoms; i++)
916	>	info[0].atoms[i]->setCoords();
917	>
918	>	if (globals->haveInitialConfig()){
919	>	InitializeFromFile* fileInit;
920		#ifdef IS_MPI // is_mpi
921	<	if( worldRank == 0 ){
921	>	if (worldRank == 0){
922		#endif //is_mpi
923	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
923	>	inName = globals->getInitialConfig();
924	>	fileInit = new InitializeFromFile(inName);
925		#ifdef IS_MPI
926	<	}else fileInit = new InitializeFromFile( NULL );
926	>	}
927	>	else
928	>	fileInit = new InitializeFromFile(NULL);
929		#endif
930	<	fileInit->read_xyz( info ); // default velocities on
930	>	fileInit->readInit(info); // default velocities on
931
932	<	delete fileInit;
933	<	}
934	<	else{
1084	<
932	>	delete fileInit;
933	>	}
934	>	else{
935		#ifdef IS_MPI
936
937	<	// no init from bass
938	<
939	<	sprintf( painCave.errMsg,
940	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
941	<	painCave.isFatal;
942	<	simError();
943	<
937	>	// no init from bass
938	>
939	>	sprintf(painCave.errMsg,
940	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
941	>	painCave.isFatal = 1;;
942	>	simError();
943	>
944		#else
945
946	<	initFromBass();
946	>	initFromBass();
947
948
949		#endif
950	<	}
950	>	}
951
952		#ifdef IS_MPI
953	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
953	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
954		MPIcheckPoint();
955		#endif // is_mpi
1106	–
956		}
957
958
959	<	void SimSetup::makeOutNames( void ){
959	>	void SimSetup::makeOutNames(void){
960	>	int k;
961
962	+
963	+	for (k = 0; k < nInfo; k++){
964		#ifdef IS_MPI
965	<	if( worldRank == 0 ){
965	>	if (worldRank == 0){
966		#endif // is_mpi
967	<
968	<	if( the_globals->haveFinalConfig() ){
969	<	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" );
967	>
968	>	if (globals->haveFinalConfig()){
969	>	strcpy(info[k].finalName, globals->getFinalConfig());
970		}
1127	–	else if( !strcmp( endTest, ".BASS" ) ){
1128	–	strcpy( endTest, ".eor" );
1129	–	}
971		else{
972	<	endTest = &(info->finalName[nameLength - 4]);
973	<	if( !strcmp( endTest, ".bss" ) ){
974	<	strcpy( endTest, ".eor" );
975	<	}
976	<	else if( !strcmp( endTest, ".mdl" ) ){
977	<	strcpy( endTest, ".eor" );
978	<	}
979	<	else{
980	<	strcat( info->finalName, ".eor" );
981	<	}
972	>	strcpy(info[k].finalName, inFileName);
973	>	char* endTest;
974	>	int nameLength = strlen(info[k].finalName);
975	>	endTest = &(info[k].finalName[nameLength - 5]);
976	>	if (!strcmp(endTest, ".bass")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".BASS")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	endTest = &(info[k].finalName[nameLength - 4]);
984	>	if (!strcmp(endTest, ".bss")){
985	>	strcpy(endTest, ".eor");
986	>	}
987	>	else if (!strcmp(endTest, ".mdl")){
988	>	strcpy(endTest, ".eor");
989	>	}
990	>	else{
991	>	strcat(info[k].finalName, ".eor");
992	>	}
993	>	}
994		}
995	<	}
996	<
997	<	// make the sample and status out names
998	<
999	<	strcpy( info->sampleName, inFileName );
1000	<	char* endTest;
1001	<	int nameLength = strlen( info->sampleName );
1002	<	endTest = &(info->sampleName[nameLength - 5]);
1003	<	if( !strcmp( endTest, ".bass" ) ){
1151	<	strcpy( endTest, ".dump" );
1152	<	}
1153	<	else if( !strcmp( endTest, ".BASS" ) ){
1154	<	strcpy( endTest, ".dump" );
1155	<	}
1156	<	else{
1157	<	endTest = &(info->sampleName[nameLength - 4]);
1158	<	if( !strcmp( endTest, ".bss" ) ){
1159	<	strcpy( endTest, ".dump" );
995	>
996	>	// make the sample and status out names
997	>
998	>	strcpy(info[k].sampleName, inFileName);
999	>	char* endTest;
1000	>	int nameLength = strlen(info[k].sampleName);
1001	>	endTest = &(info[k].sampleName[nameLength - 5]);
1002	>	if (!strcmp(endTest, ".bass")){
1003	>	strcpy(endTest, ".dump");
1004		}
1005	<	else if( !strcmp( endTest, ".mdl" ) ){
1006	<	strcpy( endTest, ".dump" );
1005	>	else if (!strcmp(endTest, ".BASS")){
1006	>	strcpy(endTest, ".dump");
1007		}
1008		else{
1009	<	strcat( info->sampleName, ".dump" );
1009	>	endTest = &(info[k].sampleName[nameLength - 4]);
1010	>	if (!strcmp(endTest, ".bss")){
1011	>	strcpy(endTest, ".dump");
1012	>	}
1013	>	else if (!strcmp(endTest, ".mdl")){
1014	>	strcpy(endTest, ".dump");
1015	>	}
1016	>	else{
1017	>	strcat(info[k].sampleName, ".dump");
1018	>	}
1019		}
1020	<	}
1021	<
1022	<	strcpy( info->statusName, inFileName );
1023	<	nameLength = strlen( info->statusName );
1024	<	endTest = &(info->statusName[nameLength - 5]);
1025	<	if( !strcmp( endTest, ".bass" ) ){
1173	<	strcpy( endTest, ".stat" );
1174	<	}
1175	<	else if( !strcmp( endTest, ".BASS" ) ){
1176	<	strcpy( endTest, ".stat" );
1177	<	}
1178	<	else{
1179	<	endTest = &(info->statusName[nameLength - 4]);
1180	<	if( !strcmp( endTest, ".bss" ) ){
1181	<	strcpy( endTest, ".stat" );
1020	>
1021	>	strcpy(info[k].statusName, inFileName);
1022	>	nameLength = strlen(info[k].statusName);
1023	>	endTest = &(info[k].statusName[nameLength - 5]);
1024	>	if (!strcmp(endTest, ".bass")){
1025	>	strcpy(endTest, ".stat");
1026		}
1027	<	else if( !strcmp( endTest, ".mdl" ) ){
1028	<	strcpy( endTest, ".stat" );
1027	>	else if (!strcmp(endTest, ".BASS")){
1028	>	strcpy(endTest, ".stat");
1029		}
1030		else{
1031	<	strcat( info->statusName, ".stat" );
1031	>	endTest = &(info[k].statusName[nameLength - 4]);
1032	>	if (!strcmp(endTest, ".bss")){
1033	>	strcpy(endTest, ".stat");
1034	>	}
1035	>	else if (!strcmp(endTest, ".mdl")){
1036	>	strcpy(endTest, ".stat");
1037	>	}
1038	>	else{
1039	>	strcat(info[k].statusName, ".stat");
1040	>	}
1041		}
1042	<	}
1190	<
1042	>
1043		#ifdef IS_MPI
1192	–	}
1193	–	#endif // is_mpi
1044
1045	+	}
1046	+	#endif // is_mpi
1047	+	}
1048		}
1049
1050
1051	<	void SimSetup::sysObjectsCreation( void ){
1051	>	void SimSetup::sysObjectsCreation(void){
1052	>	int i, k;
1053
1054		// create the forceField
1055
#	Line 1211 | Line 1065 | void SimSetup::sysObjectsCreation( void ){
1065
1066		#ifdef IS_MPI
1067		// divide the molecules among the processors
1068	<
1068	>
1069		mpiMolDivide();
1070		#endif //is_mpi
1071	<
1071	>
1072		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1073	<
1073	>
1074		makeSysArrays();
1075
1076	<
1076	>	// make and initialize the molecules (all but atomic coordinates)
1077
1078	+	makeMolecules();
1079
1080	+	for (k = 0; k < nInfo; k++){
1081	+	info[k].identArray = new int[info[k].n_atoms];
1082	+	for (i = 0; i < info[k].n_atoms; i++){
1083	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1084	+	}
1085	+	}
1086		}
1087
1088
1089	<	void SimSetup::createFF( void ){
1089	>	void SimSetup::createFF(void){
1090	>	switch (ffCase){
1091	>	case FF_DUFF:
1092	>	the_ff = new DUFF();
1093	>	break;
1094
1095	<	switch( ffCase ){
1095	>	case FF_LJ:
1096	>	the_ff = new LJFF();
1097	>	break;
1098
1099	<	case FF_DUFF:
1100	<	the_ff = new DUFF();
1101	<	break;
1099	>	case FF_EAM:
1100	>	the_ff = new EAM_FF();
1101	>	break;
1102
1103	<	case FF_LJ:
1104	<	the_ff = new LJFF();
1105	<	break;
1106	<
1107	<	default:
1241	<	sprintf( painCave.errMsg,
1242	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1243	<	painCave.isFatal = 1;
1244	<	simError();
1103	>	default:
1104	>	sprintf(painCave.errMsg,
1105	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1106	>	painCave.isFatal = 1;
1107	>	simError();
1108		}
1109
1110		#ifdef IS_MPI
1111	<	strcpy( checkPointMsg, "ForceField creation successful" );
1111	>	strcpy(checkPointMsg, "ForceField creation successful");
1112		MPIcheckPoint();
1113		#endif // is_mpi
1251	–
1114		}
1115
1116
1117	<	void SimSetup::compList( void ){
1117	>	void SimSetup::compList(void){
1118	>	int i;
1119	>	char* id;
1120	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1121	>	LinkedMolStamp* currentStamp = NULL;
1122	>	comp_stamps = new MoleculeStamp * [n_components];
1123
1257	–	comp_stamps = new MoleculeStamp*[n_components];
1258	–
1124		// make an array of molecule stamps that match the components used.
1125		// also extract the used stamps out into a separate linked list
1126
1127	<	info->nComponents = n_components;
1128	<	info->componentsNmol = components_nmol;
1129	<	info->compStamps = comp_stamps;
1130	<	info->headStamp = new LinkedMolStamp();
1131	<
1132	<	char* id;
1268	<	LinkedMolStamp* headStamp = info->headStamp;
1269	<	LinkedMolStamp* currentStamp = NULL;
1270	<	for( i=0; i<n_components; i++ ){
1127	>	for (i = 0; i < nInfo; i++){
1128	>	info[i].nComponents = n_components;
1129	>	info[i].componentsNmol = components_nmol;
1130	>	info[i].compStamps = comp_stamps;
1131	>	info[i].headStamp = headStamp;
1132	>	}
1133
1134	+
1135	+	for (i = 0; i < n_components; i++){
1136		id = the_components[i]->getType();
1137		comp_stamps[i] = NULL;
1138	<
1138	>
1139		// check to make sure the component isn't already in the list
1140
1141	<	comp_stamps[i] = headStamp->match( id );
1142	<	if( comp_stamps[i] == NULL ){
1279	<
1141	>	comp_stamps[i] = headStamp->match(id);
1142	>	if (comp_stamps[i] == NULL){
1143		// extract the component from the list;
1144	<
1145	<	currentStamp = the_stamps->extractMolStamp( id );
1146	<	if( currentStamp == NULL ){
1147	<	sprintf( painCave.errMsg,
1148	<	"SimSetup error: Component \"%s\" was not found in the "
1149	<	"list of declared molecules\n",
1150	<	id );
1151	<	painCave.isFatal = 1;
1152	<	simError();
1144	>
1145	>	currentStamp = stamps->extractMolStamp(id);
1146	>	if (currentStamp == NULL){
1147	>	sprintf(painCave.errMsg,
1148	>	"SimSetup error: Component \"%s\" was not found in the "
1149	>	"list of declared molecules\n",
1150	>	id);
1151	>	painCave.isFatal = 1;
1152	>	simError();
1153		}
1154	<
1155	<	headStamp->add( currentStamp );
1156	<	comp_stamps[i] = headStamp->match( id );
1154	>
1155	>	headStamp->add(currentStamp);
1156	>	comp_stamps[i] = headStamp->match(id);
1157		}
1158		}
1159
1160		#ifdef IS_MPI
1161	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1161	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1162		MPIcheckPoint();
1163		#endif // is_mpi
1301	–
1302	–
1164		}
1165
1166	<	void SimSetup::calcSysValues( void ){
1166	>	void SimSetup::calcSysValues(void){
1167	>	int i;
1168
1169	+	int* molMembershipArray;
1170	+
1171		tot_atoms = 0;
1172		tot_bonds = 0;
1173		tot_bends = 0;
1174		tot_torsions = 0;
1175	<	for( i=0; i<n_components; i++ ){
1176	<
1177	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1178	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1315	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1175	>	for (i = 0; i < n_components; i++){
1176	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1177	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1178	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1179		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1180		}
1181
1182		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1183	+	molMembershipArray = new int[tot_atoms];
1184
1185	<	info->n_atoms = tot_atoms;
1186	<	info->n_bonds = tot_bonds;
1187	<	info->n_bends = tot_bends;
1188	<	info->n_torsions = tot_torsions;
1189	<	info->n_SRI = tot_SRI;
1190	<	info->n_mol = tot_nmol;
1191	<
1192	<	info->molMembershipArray = new int[tot_atoms];
1185	>	for (i = 0; i < nInfo; i++){
1186	>	info[i].n_atoms = tot_atoms;
1187	>	info[i].n_bonds = tot_bonds;
1188	>	info[i].n_bends = tot_bends;
1189	>	info[i].n_torsions = tot_torsions;
1190	>	info[i].n_SRI = tot_SRI;
1191	>	info[i].n_mol = tot_nmol;
1192	>
1193	>	info[i].molMembershipArray = molMembershipArray;
1194	>	}
1195		}
1196
1331	–
1197		#ifdef IS_MPI
1198
1199	<	void SimSetup::mpiMolDivide( void ){
1200	<
1199	>	void SimSetup::mpiMolDivide(void){
1200	>	int i, j, k;
1201		int localMol, allMol;
1202		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1203
1204	<	mpiSim = new mpiSimulation( info );
1205	<
1204	>	mpiSim = new mpiSimulation(info);
1205	>
1206		globalIndex = mpiSim->divideLabor();
1207
1208		// set up the local variables
1209	<
1209	>
1210		mol2proc = mpiSim->getMolToProcMap();
1211		molCompType = mpiSim->getMolComponentType();
1212	<
1212	>
1213		allMol = 0;
1214		localMol = 0;
1215		local_atoms = 0;
#	Line 1354 | Line 1219 | void SimSetup::mpiMolDivide( void ){
1219		globalAtomIndex = 0;
1220
1221
1222	<	for( i=0; i<n_components; i++ ){
1223	<
1224	<	for( j=0; j<components_nmol[i]; j++ ){
1225	<
1226	<	if( mol2proc[allMol] == worldRank ){
1227	<
1228	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1229	<	local_bonds +=    comp_stamps[i]->getNBonds();
1365	<	local_bends +=    comp_stamps[i]->getNBends();
1366	<	local_torsions += comp_stamps[i]->getNTorsions();
1367	<	localMol++;
1222	>	for (i = 0; i < n_components; i++){
1223	>	for (j = 0; j < components_nmol[i]; j++){
1224	>	if (mol2proc[allMol] == worldRank){
1225	>	local_atoms += comp_stamps[i]->getNAtoms();
1226	>	local_bonds += comp_stamps[i]->getNBonds();
1227	>	local_bends += comp_stamps[i]->getNBends();
1228	>	local_torsions += comp_stamps[i]->getNTorsions();
1229	>	localMol++;
1230		}
1231	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1232	<	info->molMembershipArray[globalAtomIndex] = allMol;
1231	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1232	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1233		globalAtomIndex++;
1234		}
1235
1236	<	allMol++;
1236	>	allMol++;
1237		}
1238		}
1239		local_SRI = local_bonds + local_bends + local_torsions;
1240	<
1241	<	info->n_atoms = mpiSim->getMyNlocal();
1242	<
1243	<	if( local_atoms != info->n_atoms ){
1244	<	sprintf( painCave.errMsg,
1245	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1246	<	" localAtom (%d) are not equal.\n",
1247	<	info->n_atoms,
1386	<	local_atoms );
1240	>
1241	>	info[0].n_atoms = mpiSim->getMyNlocal();
1242	>
1243	>	if (local_atoms != info[0].n_atoms){
1244	>	sprintf(painCave.errMsg,
1245	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1246	>	" localAtom (%d) are not equal.\n",
1247	>	info[0].n_atoms, local_atoms);
1248		painCave.isFatal = 1;
1249		simError();
1250		}
1251
1252	<	info->n_bonds = local_bonds;
1253	<	info->n_bends = local_bends;
1254	<	info->n_torsions = local_torsions;
1255	<	info->n_SRI = local_SRI;
1256	<	info->n_mol = localMol;
1252	>	info[0].n_bonds = local_bonds;
1253	>	info[0].n_bends = local_bends;
1254	>	info[0].n_torsions = local_torsions;
1255	>	info[0].n_SRI = local_SRI;
1256	>	info[0].n_mol = localMol;
1257
1258	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1258	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1259		MPIcheckPoint();
1260		}
1261	<
1261	>
1262		#endif // is_mpi
1263
1264
1265	<	void SimSetup::makeSysArrays( void ){
1265	>	void SimSetup::makeSysArrays(void){
1266	>
1267	>	#ifndef IS_MPI
1268	>	int k, j;
1269	>	#endif // is_mpi
1270	>	int i, l;
1271
1272	<	// create the atom and short range interaction arrays
1272	>	Atom** the_atoms;
1273	>	Molecule* the_molecules;
1274	>	Exclude** the_excludes;
1275
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;
1276
1277	<	// initialize the molecule's stampID's
1277	>	for (l = 0; l < nInfo; l++){
1278	>	// create the atom and short range interaction arrays
1279
1280	+	the_atoms = new Atom * [info[l].n_atoms];
1281	+	the_molecules = new Molecule[info[l].n_mol];
1282	+	int molIndex;
1283	+
1284	+	// initialize the molecule's stampID's
1285	+
1286		#ifdef IS_MPI
1416	–
1287
1288	<	molIndex = 0;
1289	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1290	<
1291	<	if(mol2proc[i] == worldRank ){
1292	<	the_molecules[molIndex].setStampID( molCompType[i] );
1293	<	the_molecules[molIndex].setMyIndex( molIndex );
1294	<	the_molecules[molIndex].setGlobalIndex( i );
1295	<	molIndex++;
1288	>
1289	>	molIndex = 0;
1290	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1291	>	if (mol2proc[i] == worldRank){
1292	>	the_molecules[molIndex].setStampID(molCompType[i]);
1293	>	the_molecules[molIndex].setMyIndex(molIndex);
1294	>	the_molecules[molIndex].setGlobalIndex(i);
1295	>	molIndex++;
1296	>	}
1297		}
1427	–	}
1298
1299		#else // is_mpi
1300	<
1301	<	molIndex = 0;
1302	<	globalAtomIndex = 0;
1303	<	for(i=0; i<n_components; i++){
1304	<	for(j=0; j<components_nmol[i]; j++ ){
1305	<	the_molecules[molIndex].setStampID( i );
1306	<	the_molecules[molIndex].setMyIndex( molIndex );
1307	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1308	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1309	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1310	<	globalAtomIndex++;
1300	>
1301	>	molIndex = 0;
1302	>	globalAtomIndex = 0;
1303	>	for (i = 0; i < n_components; i++){
1304	>	for (j = 0; j < components_nmol[i]; j++){
1305	>	the_molecules[molIndex].setStampID(i);
1306	>	the_molecules[molIndex].setMyIndex(molIndex);
1307	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1308	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1309	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1310	>	globalAtomIndex++;
1311	>	}
1312	>	molIndex++;
1313		}
1442	–	molIndex++;
1314		}
1444	–	}
1445	–
1315
1316	+
1317		#endif // is_mpi
1318
1319
1320	<	if( info->n_SRI ){
1321	<
1322	<	Exclude::createArray(info->n_SRI);
1323	<	the_excludes = new Exclude*[info->n_SRI];
1324	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1325	<	info->globalExcludes = new int;
1326	<	info->n_exclude = info->n_SRI;
1320	>	if (info[l].n_SRI){
1321	>	Exclude::createArray(info[l].n_SRI);
1322	>	the_excludes = new Exclude * [info[l].n_SRI];
1323	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1324	>	the_excludes[ex] = new Exclude(ex);
1325	>	}
1326	>	info[l].globalExcludes = new int;
1327	>	info[l].n_exclude = info[l].n_SRI;
1328	>	}
1329	>	else{
1330	>	Exclude::createArray(1);
1331	>	the_excludes = new Exclude * ;
1332	>	the_excludes[0] = new Exclude(0);
1333	>	the_excludes[0]->setPair(0, 0);
1334	>	info[l].globalExcludes = new int;
1335	>	info[l].globalExcludes[0] = 0;
1336	>	info[l].n_exclude = 0;
1337	>	}
1338	>
1339	>	// set the arrays into the SimInfo object
1340	>
1341	>	info[l].atoms = the_atoms;
1342	>	info[l].molecules = the_molecules;
1343	>	info[l].nGlobalExcludes = 0;
1344	>	info[l].excludes = the_excludes;
1345	>
1346	>	the_ff->setSimInfo(info);
1347		}
1348	<	else{
1459	<
1460	<	Exclude::createArray( 1 );
1461	<	the_excludes = new Exclude*;
1462	<	the_excludes[0] = new Exclude(0);
1463	<	the_excludes[0]->setPair( 0,0 );
1464	<	info->globalExcludes = new int;
1465	<	info->globalExcludes[0] = 0;
1466	<	info->n_exclude = 0;
1467	<	}
1348	>	}
1349
1350	<	// set the arrays into the SimInfo object
1350	>	void SimSetup::makeIntegrator(void){
1351	>	int k;
1352
1353	<	info->atoms = the_atoms;
1354	<	info->molecules = the_molecules;
1355	<	info->nGlobalExcludes = 0;
1356	<	info->excludes = the_excludes;
1353	>	NVE<RealIntegrator>* myNVE = NULL;
1354	>	NVT<RealIntegrator>* myNVT = NULL;
1355	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1356	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1357	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1358	>
1359	>	for (k = 0; k < nInfo; k++){
1360	>	switch (ensembleCase){
1361	>	case NVE_ENS:
1362	>	if (globals->haveZconstraints()){
1363	>	setupZConstraint(info[k]);
1364	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1365	>	}
1366	>	else{
1367	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1368	>	}
1369	>
1370	>	info->the_integrator = myNVE;
1371	>	break;
1372
1373	<	the_ff->setSimInfo( info );
1373	>	case NVT_ENS:
1374	>	if (globals->haveZconstraints()){
1375	>	setupZConstraint(info[k]);
1376	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1377	>	}
1378	>	else
1379	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1380
1381	+	myNVT->setTargetTemp(globals->getTargetTemp());
1382	+
1383	+	if (globals->haveTauThermostat())
1384	+	myNVT->setTauThermostat(globals->getTauThermostat());
1385	+	else{
1386	+	sprintf(painCave.errMsg,
1387	+	"SimSetup error: If you use the NVT\n"
1388	+	"    ensemble, you must set tauThermostat.\n");
1389	+	painCave.isFatal = 1;
1390	+	simError();
1391	+	}
1392	+
1393	+	info->the_integrator = myNVT;
1394	+	break;
1395	+
1396	+	case NPTi_ENS:
1397	+	if (globals->haveZconstraints()){
1398	+	setupZConstraint(info[k]);
1399	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1400	+	}
1401	+	else
1402	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1403	+
1404	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1405	+
1406	+	if (globals->haveTargetPressure())
1407	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	+	else{
1409	+	sprintf(painCave.errMsg,
1410	+	"SimSetup error: If you use a constant pressure\n"
1411	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	+	painCave.isFatal = 1;
1413	+	simError();
1414	+	}
1415	+
1416	+	if (globals->haveTauThermostat())
1417	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1418	+	else{
1419	+	sprintf(painCave.errMsg,
1420	+	"SimSetup error: If you use an NPT\n"
1421	+	"    ensemble, you must set tauThermostat.\n");
1422	+	painCave.isFatal = 1;
1423	+	simError();
1424	+	}
1425	+
1426	+	if (globals->haveTauBarostat())
1427	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1428	+	else{
1429	+	sprintf(painCave.errMsg,
1430	+	"SimSetup error: If you use an NPT\n"
1431	+	"    ensemble, you must set tauBarostat.\n");
1432	+	painCave.isFatal = 1;
1433	+	simError();
1434	+	}
1435	+
1436	+	info->the_integrator = myNPTi;
1437	+	break;
1438	+
1439	+	case NPTf_ENS:
1440	+	if (globals->haveZconstraints()){
1441	+	setupZConstraint(info[k]);
1442	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1443	+	}
1444	+	else
1445	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1446	+
1447	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1448	+
1449	+	if (globals->haveTargetPressure())
1450	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1451	+	else{
1452	+	sprintf(painCave.errMsg,
1453	+	"SimSetup error: If you use a constant pressure\n"
1454	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1455	+	painCave.isFatal = 1;
1456	+	simError();
1457	+	}
1458	+
1459	+	if (globals->haveTauThermostat())
1460	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1461	+	else{
1462	+	sprintf(painCave.errMsg,
1463	+	"SimSetup error: If you use an NPT\n"
1464	+	"    ensemble, you must set tauThermostat.\n");
1465	+	painCave.isFatal = 1;
1466	+	simError();
1467	+	}
1468	+
1469	+	if (globals->haveTauBarostat())
1470	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1471	+	else{
1472	+	sprintf(painCave.errMsg,
1473	+	"SimSetup error: If you use an NPT\n"
1474	+	"    ensemble, you must set tauBarostat.\n");
1475	+	painCave.isFatal = 1;
1476	+	simError();
1477	+	}
1478	+
1479	+	info->the_integrator = myNPTf;
1480	+	break;
1481	+
1482	+	case NPTxyz_ENS:
1483	+	if (globals->haveZconstraints()){
1484	+	setupZConstraint(info[k]);
1485	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1486	+	}
1487	+	else
1488	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1489	+
1490	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1491	+
1492	+	if (globals->haveTargetPressure())
1493	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1494	+	else{
1495	+	sprintf(painCave.errMsg,
1496	+	"SimSetup error: If you use a constant pressure\n"
1497	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1498	+	painCave.isFatal = 1;
1499	+	simError();
1500	+	}
1501	+
1502	+	if (globals->haveTauThermostat())
1503	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1504	+	else{
1505	+	sprintf(painCave.errMsg,
1506	+	"SimSetup error: If you use an NPT\n"
1507	+	"    ensemble, you must set tauThermostat.\n");
1508	+	painCave.isFatal = 1;
1509	+	simError();
1510	+	}
1511	+
1512	+	if (globals->haveTauBarostat())
1513	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1514	+	else{
1515	+	sprintf(painCave.errMsg,
1516	+	"SimSetup error: If you use an NPT\n"
1517	+	"    ensemble, you must set tauBarostat.\n");
1518	+	painCave.isFatal = 1;
1519	+	simError();
1520	+	}
1521	+
1522	+	info->the_integrator = myNPTxyz;
1523	+	break;
1524	+
1525	+	default:
1526	+	sprintf(painCave.errMsg,
1527	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1528	+	painCave.isFatal = 1;
1529	+	simError();
1530	+	}
1531	+	}
1532		}
1533	+
1534	+	void SimSetup::initFortran(void){
1535	+	info[0].refreshSim();
1536	+
1537	+	if (!strcmp(info[0].mixingRule, "standard")){
1538	+	the_ff->initForceField(LB_MIXING_RULE);
1539	+	}
1540	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1541	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1542	+	}
1543	+	else{
1544	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1545	+	info[0].mixingRule);
1546	+	painCave.isFatal = 1;
1547	+	simError();
1548	+	}
1549	+
1550	+
1551	+	#ifdef IS_MPI
1552	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1553	+	MPIcheckPoint();
1554	+	#endif // is_mpi
1555	+	}
1556	+
1557	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1558	+	int nZConstraints;
1559	+	ZconStamp** zconStamp;
1560	+
1561	+	if (globals->haveZconstraintTime()){
1562	+	//add sample time of z-constraint  into SimInfo's property list
1563	+	DoubleData* zconsTimeProp = new DoubleData();
1564	+	zconsTimeProp->setID(ZCONSTIME_ID);
1565	+	zconsTimeProp->setData(globals->getZconsTime());
1566	+	theInfo.addProperty(zconsTimeProp);
1567	+	}
1568	+	else{
1569	+	sprintf(painCave.errMsg,
1570	+	"ZConstraint error: If you use an ZConstraint\n"
1571	+	" , you must set sample time.\n");
1572	+	painCave.isFatal = 1;
1573	+	simError();
1574	+	}
1575	+
1576	+	//push zconsTol into siminfo, if user does not specify
1577	+	//value for zconsTol, a default value will be used
1578	+	DoubleData* zconsTol = new DoubleData();
1579	+	zconsTol->setID(ZCONSTOL_ID);
1580	+	if (globals->haveZconsTol()){
1581	+	zconsTol->setData(globals->getZconsTol());
1582	+	}
1583	+	else{
1584	+	double defaultZConsTol = 0.01;
1585	+	sprintf(painCave.errMsg,
1586	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1587	+	" , default value %f is used.\n",
1588	+	defaultZConsTol);
1589	+	painCave.isFatal = 0;
1590	+	simError();
1591	+
1592	+	zconsTol->setData(defaultZConsTol);
1593	+	}
1594	+	theInfo.addProperty(zconsTol);
1595	+
1596	+	//set Force Subtraction Policy
1597	+	StringData* zconsForcePolicy = new StringData();
1598	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1599	+
1600	+	if (globals->haveZconsForcePolicy()){
1601	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1602	+	}
1603	+	else{
1604	+	sprintf(painCave.errMsg,
1605	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1606	+	"PolicyByMass is used\n");
1607	+	painCave.isFatal = 0;
1608	+	simError();
1609	+	zconsForcePolicy->setData("BYMASS");
1610	+	}
1611	+
1612	+	theInfo.addProperty(zconsForcePolicy);
1613	+
1614	+	//Determine the name of ouput file and add it into SimInfo's property list
1615	+	//Be careful, do not use inFileName, since it is a pointer which
1616	+	//point to a string at master node, and slave nodes do not contain that string
1617	+
1618	+	string zconsOutput(theInfo.finalName);
1619	+
1620	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1621	+
1622	+	StringData* zconsFilename = new StringData();
1623	+	zconsFilename->setID(ZCONSFILENAME_ID);
1624	+	zconsFilename->setData(zconsOutput);
1625	+
1626	+	theInfo.addProperty(zconsFilename);
1627	+
1628	+	//setup index, pos and other parameters of z-constraint molecules
1629	+	nZConstraints = globals->getNzConstraints();
1630	+	theInfo.nZconstraints = nZConstraints;
1631	+
1632	+	zconStamp = globals->getZconStamp();
1633	+	ZConsParaItem tempParaItem;
1634	+
1635	+	ZConsParaData* zconsParaData = new ZConsParaData();
1636	+	zconsParaData->setID(ZCONSPARADATA_ID);
1637	+
1638	+	for (int i = 0; i < nZConstraints; i++){
1639	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1640	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1641	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1642	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1643	+
1644	+	zconsParaData->addItem(tempParaItem);
1645	+	}
1646	+
1647	+	//check the uniqueness of index
1648	+	if(!zconsParaData->isIndexUnique()){
1649	+	sprintf(painCave.errMsg,
1650	+	"ZConstraint Error: molIndex is not unique\n");
1651	+	painCave.isFatal = 1;
1652	+	simError();
1653	+	}
1654	+
1655	+	//sort the parameters by index of molecules
1656	+	zconsParaData->sortByIndex();
1657	+
1658	+	//push data into siminfo, therefore, we can retrieve later
1659	+	theInfo.addProperty(zconsParaData);
1660	+	}

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