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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 558 by mmeineke, Thu Jun 19 19:21:23 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 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 NPT_ENS 2
21	>	#define NVE_ENS        0
22	>	#define NVT_ENS        1
23	>	#define NPTi_ENS       2
24	>	#define NPTf_ENS       3
25
26		#define FF_DUFF 0
27		#define FF_LJ   1
28	+	#define FF_EAM  2
29
30	+	using namespace std;
31
32		SimSetup::SimSetup(){
33	+	isInfoArray = 0;
34	+	nInfo = 1;
35	+
36		stamps = new MakeStamps();
37		globals = new Globals();
38	<
38	>
39	>
40		#ifdef IS_MPI
41	<	strcpy( checkPointMsg, "SimSetup creation successful" );
41	>	strcpy(checkPointMsg, "SimSetup creation successful");
42		MPIcheckPoint();
43		#endif // IS_MPI
44		}
#	Line 37 | Line 48 | void SimSetup::parseFile( char* fileName ){
48		delete globals;
49		}
50
51	<	void SimSetup::parseFile( char* fileName ){
51	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
52	>	info = the_info;
53	>	nInfo = theNinfo;
54	>	isInfoArray = 1;
55	>	}
56
57	+
58	+	void SimSetup::parseFile(char* fileName){
59		#ifdef IS_MPI
60	<	if( worldRank == 0 ){
60	>	if (worldRank == 0){
61		#endif // is_mpi
62	<
62	>
63		inFileName = fileName;
64	<	set_interface_stamps( stamps, globals );
65	<
64	>	set_interface_stamps(stamps, globals);
65	>
66		#ifdef IS_MPI
67		mpiEventInit();
68		#endif
69
70	<	yacc_BASS( fileName );
70	>	yacc_BASS(fileName);
71
72		#ifdef IS_MPI
73		throwMPIEvent(NULL);
74		}
75	<	else receiveParse();
75	>	else{
76	>	receiveParse();
77	>	}
78		#endif
79
80		}
81
82		#ifdef IS_MPI
83		void SimSetup::receiveParse(void){
84	<
85	<	set_interface_stamps( stamps, globals );
86	<	mpiEventInit();
87	<	MPIcheckPoint();
69	<	mpiEventLoop();
70	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92	<	void SimSetup::createSim( void ){
92	>	void SimSetup::createSim(void){
93
94	<	MakeStamps *the_stamps;
78	<	Globals* the_globals;
79	<	int i, j, k, globalAtomIndex;
80	<
81	<	int ensembleCase;
82	<	int ffCase;
83	<
84	<	ensembleCase = -1;
85	<	ffCase = -1;
94	>	// gather all of the information from the Bass file
95
96	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
96	>	gatherInfo();
97
98	<	// set the easy ones first
92	<	simnfo->target_temp = the_globals->getTargetTemp();
93	<	simnfo->dt = the_globals->getDt();
94	<	simnfo->run_time = the_globals->getRunTime();
98	>	// creation of complex system objects
99
100	<	// get the ones we know are there, yet still may need some work.
97	<	n_components = the_globals->getNComponents();
98	<	strcpy( force_field, the_globals->getForceField() );
100	>	sysObjectsCreation();
101
102	<	if( !strcasecmp( force_field, "DUFF" ))    ffCase = FF_DUFF;
101	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102	<	else{
103	<	sprintf( painCave.errMsg,
104	<	"SimSetup Error. Unrecognized force field -> %s\n",
105	<	force_field );
106	<	painCave.isFatal = 1;
107	<	simError();
108	<	}
102	>	// check on the post processing info
103
104	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
104	>	finalInfoCheck();
105
106	<	if( !strcasecmp( ensemble, "NVE" ))      ffCase = NVE_ENS;
107	<	else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS;
108	<	else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS;
109	<	else{
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
119	<	"reverting to NVE for this simulation.\n",
120	<	ensemble );
121	<	painCave.isFatal = 0;
122	<	simError();
123	<	strcpy( ensemble, "NVE" );
124	<	ensembleCase = NVE_ENS;
106	>	// initialize the system coordinates
107	>
108	>	if (!isInfoArray){
109	>	initSystemCoords();
110		}
126	–	strcpy( simnfo->ensemble, ensemble );
111
112	+	// make the output filenames
113
114	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
130	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
131	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132	<	//     if (the_globals->haveTargetPressure())
133	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134	<	//     else {
135	<	//       sprintf( painCave.errMsg,
136	<	//                "SimSetup error: If you use the constant pressure\n"
137	<	//                "    ensemble, you must set targetPressure.\n"
138	<	//                "    This was found in the BASS file.\n");
139	<	//       painCave.isFatal = 1;
140	<	//       simError();
141	<	//     }
114	>	makeOutNames();
115
116	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
116	>	// make the integrator
117
118	<	//     if (the_globals->haveTauBarostat())
157	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158	<	//     else {
159	<	//       sprintf( painCave.errMsg,
160	<	//                "SimSetup error: If you use the constant pressure\n"
161	<	//                "    ensemble, you must set tauBarostat.\n"
162	<	//                "    This was found in the BASS file.\n");
163	<	//       painCave.isFatal = 1;
164	<	//       simError();
165	<	//     }
118	>	makeIntegrator();
119
120	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
121	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
122	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
120	>	#ifdef IS_MPI
121	>	mpiSim->mpiRefresh();
122	>	#endif
123
124	<	//     if (the_globals->haveTauThermostat())
172	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173	<	//     else if (the_globals->haveQmass())
174	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
175	<	//     else {
176	<	//       sprintf( painCave.errMsg,
177	<	//                "SimSetup error: If you use one of the constant temperature\n"
178	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
179	<	//                "    Neither of these was found in the BASS file.\n");
180	<	//       painCave.isFatal = 1;
181	<	//       simError();
182	<	//     }
124	>	// initialize the Fortran
125
126	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
127	<	simnfo->usePBC = the_globals->getPBC();
186	<
187	<	int usesDipoles = 0;
188	<	switch( ffCase ){
126	>	initFortran();
127	>	}
128
190	–	case FF_DUFF:
191	–	the_ff = new DUFF();
192	–	usesDipoles = 1;
193	–	break;
129
130	<	case FF_LJ:
131	<	the_ff = LJFF();
132	<	break;
130	>	void SimSetup::makeMolecules(void){
131	>	int k;
132	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
133	>	molInit molInfo;
134	>	DirectionalAtom* dAtom;
135	>	LinkedAssign* extras;
136	>	LinkedAssign* current_extra;
137	>	AtomStamp* currentAtom;
138	>	BondStamp* currentBond;
139	>	BendStamp* currentBend;
140	>	TorsionStamp* currentTorsion;
141
142	<	default:
143	<	sprintf( painCave.errMsg,
144	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
142	>	bond_pair* theBonds;
143	>	bend_set* theBends;
144	>	torsion_set* theTorsions;
145
206	–	#ifdef IS_MPI
207	–	strcpy( checkPointMsg, "ForceField creation successful" );
208	–	MPIcheckPoint();
209	–	#endif // is_mpi
146
147	<	// get the components and calculate the tot_nMol and indvidual n_mol
212	<	the_components = the_globals->getComponents();
213	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
147	>	//init the forceField paramters
148
149	<	if( !the_globals->haveNMol() ){
217	<	// we don't have the total number of molecules, so we assume it is
218	<	// given in each component
149	>	the_ff->readParams();
150
220	–	tot_nmol = 0;
221	–	for( i=0; i<n_components; i++ ){
151
152	<	if( !the_components[i]->haveNMol() ){
224	<	// we have a problem
225	<	sprintf( painCave.errMsg,
226	<	"SimSetup Error. No global NMol or component NMol"
227	<	" given. Cannot calculate the number of atoms.\n" );
228	<	painCave.isFatal = 1;
229	<	simError();
230	<	}
152	>	// init the atoms
153
154	<	tot_nmol += the_components[i]->getNMol();
233	<	components_nmol[i] = the_components[i]->getNMol();
234	<	}
235	<	}
236	<	else{
237	<	sprintf( painCave.errMsg,
238	<	"SimSetup error.\n"
239	<	"\tSorry, the ability to specify total"
240	<	" nMols and then give molfractions in the components\n"
241	<	"\tis not currently supported."
242	<	" Please give nMol in the components.\n" );
243	<	painCave.isFatal = 1;
244	<	simError();
245	<
246	<
247	<	//     tot_nmol = the_globals->getNMol();
248	<
249	<	//   //we have the total number of molecules, now we check for molfractions
250	<	//     for( i=0; i<n_components; i++ ){
251	<
252	<	//       if( !the_components[i]->haveMolFraction() ){
253	<
254	<	//  if( !the_components[i]->haveNMol() ){
255	<	//    //we have a problem
256	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	<	//              << " nMol was given in component
258	<
259	<	}
154	>	double ux, uy, uz, u, uSqr;
155
156	<	#ifdef IS_MPI
157	<	strcpy( checkPointMsg, "Have the number of components" );
263	<	MPIcheckPoint();
264	<	#endif // is_mpi
156	>	for (k = 0; k < nInfo; k++){
157	>	the_ff->setSimInfo(&(info[k]));
158
159	<	// make an array of molecule stamps that match the components used.
160	<	// also extract the used stamps out into a separate linked list
159	>	atomOffset = 0;
160	>	excludeOffset = 0;
161	>	for (i = 0; i < info[k].n_mol; i++){
162	>	stampID = info[k].molecules[i].getStampID();
163
164	<	simnfo->nComponents = n_components;
165	<	simnfo->componentsNmol = components_nmol;
166	<	simnfo->compStamps = comp_stamps;
167	<	simnfo->headStamp = new LinkedMolStamp();
168	<
274	<	char* id;
275	<	LinkedMolStamp* headStamp = simnfo->headStamp;
276	<	LinkedMolStamp* currentStamp = NULL;
277	<	for( i=0; i<n_components; i++ ){
164	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
165	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
166	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
167	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
168	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
169
170	<	id = the_components[i]->getType();
171	<	comp_stamps[i] = NULL;
172	<
173	<	// check to make sure the component isn't already in the list
174	<
284	<	comp_stamps[i] = headStamp->match( id );
285	<	if( comp_stamps[i] == NULL ){
286	<
287	<	// extract the component from the list;
288	<
289	<	currentStamp = the_stamps->extractMolStamp( id );
290	<	if( currentStamp == NULL ){
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup error: Component \"%s\" was not found in the "
293	<	"list of declared molecules\n",
294	<	id );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	headStamp->add( currentStamp );
300	<	comp_stamps[i] = headStamp->match( id );
301	<	}
302	<	}
170	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
171	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
172	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
173	>	molInfo.myBends = new Bend * [molInfo.nBends];
174	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
175
176	<	#ifdef IS_MPI
177	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
178	<	MPIcheckPoint();
307	<	#endif // is_mpi
308	<
176	>	theBonds = new bond_pair[molInfo.nBonds];
177	>	theBends = new bend_set[molInfo.nBends];
178	>	theTorsions = new torsion_set[molInfo.nTorsions];
179
180	+	// make the Atoms
181
182	+	for (j = 0; j < molInfo.nAtoms; j++){
183	+	currentAtom = comp_stamps[stampID]->getAtom(j);
184	+	if (currentAtom->haveOrientation()){
185	+	dAtom = new DirectionalAtom((j + atomOffset),
186	+	info[k].getConfiguration());
187	+	info[k].n_oriented++;
188	+	molInfo.myAtoms[j] = dAtom;
189
190	<	// caclulate the number of atoms, bonds, bends and torsions
190	>	ux = currentAtom->getOrntX();
191	>	uy = currentAtom->getOrntY();
192	>	uz = currentAtom->getOrntZ();
193
194	<	tot_atoms = 0;
315	<	tot_bonds = 0;
316	<	tot_bends = 0;
317	<	tot_torsions = 0;
318	<	for( i=0; i<n_components; i++ ){
319	<
320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	<	}
194	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
195
196	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
196	>	u = sqrt(uSqr);
197	>	ux = ux / u;
198	>	uy = uy / u;
199	>	uz = uz / u;
200
201	<	simnfo->n_atoms = tot_atoms;
202	<	simnfo->n_bonds = tot_bonds;
203	<	simnfo->n_bends = tot_bends;
204	<	simnfo->n_torsions = tot_torsions;
205	<	simnfo->n_SRI = tot_SRI;
206	<	simnfo->n_mol = tot_nmol;
207	<
208	<	simnfo->molMembershipArray = new int[tot_atoms];
201	>	dAtom->setSUx(ux);
202	>	dAtom->setSUy(uy);
203	>	dAtom->setSUz(uz);
204	>	}
205	>	else{
206	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
207	>	info[k].getConfiguration());
208	>	}
209	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
210
211		#ifdef IS_MPI
212
213	<	// divide the molecules among processors here.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
213	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
214
215	<	// set up the local variables
216	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
215	>	#endif // is_mpi
216	>	}
217
218	<	int* mol2proc = mpiSim->getMolToProcMap();
219	<	int* molCompType = mpiSim->getMolComponentType();
220	<
221	<	allMol = 0;
222	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
218	>	// make the bonds
219	>	for (j = 0; j < molInfo.nBonds; j++){
220	>	currentBond = comp_stamps[stampID]->getBond(j);
221	>	theBonds[j].a = currentBond->getA() + atomOffset;
222	>	theBonds[j].b = currentBond->getB() + atomOffset;
223
224	+	exI = theBonds[j].a;
225	+	exJ = theBonds[j].b;
226
227	<	for( i=0; i<n_components; i++ ){
227	>	// exclude_I must always be the smaller of the pair
228	>	if (exI > exJ){
229	>	tempEx = exI;
230	>	exI = exJ;
231	>	exJ = tempEx;
232	>	}
233	>	#ifdef IS_MPI
234	>	tempEx = exI;
235	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
236	>	tempEx = exJ;
237	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
238
239	<	for( j=0; j<components_nmol[i]; j++ ){
240	<
241	<	if( mol2proc[allMol] == worldRank ){
242	<
243	<	local_atoms +=    comp_stamps[i]->getNAtoms();
369	<	local_bonds +=    comp_stamps[i]->getNBonds();
370	<	local_bends +=    comp_stamps[i]->getNBends();
371	<	local_torsions += comp_stamps[i]->getNTorsions();
372	<	localMol++;
373	<	}
374	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
239	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
240	>	#else  // isn't MPI
241	>
242	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
243	>	#endif  //is_mpi
244		}
245	+	excludeOffset += molInfo.nBonds;
246
247	<	allMol++;
248	<	}
249	<	}
250	<	local_SRI = local_bonds + local_bends + local_torsions;
251	<
252	<	simnfo->n_atoms = mpiSim->getMyNlocal();
385	<
386	<	if( local_atoms != simnfo->n_atoms ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
247	>	//make the bends
248	>	for (j = 0; j < molInfo.nBends; j++){
249	>	currentBend = comp_stamps[stampID]->getBend(j);
250	>	theBends[j].a = currentBend->getA() + atomOffset;
251	>	theBends[j].b = currentBend->getB() + atomOffset;
252	>	theBends[j].c = currentBend->getC() + atomOffset;
253
254	<	simnfo->n_bonds = local_bonds;
255	<	simnfo->n_bends = local_bends;
256	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
254	>	if (currentBend->haveExtras()){
255	>	extras = currentBend->getExtras();
256	>	current_extra = extras;
257
258	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
259	<	MPIcheckPoint();
260	<
261	<
262	<	#endif // is_mpi
263	<
258	>	while (current_extra != NULL){
259	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
260	>	switch (current_extra->getType()){
261	>	case 0:
262	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
263	>	theBends[j].isGhost = 1;
264	>	break;
265
266	<	// create the atom and short range interaction arrays
266	>	case 1:
267	>	theBends[j].ghost = (int) current_extra->getDouble() +
268	>	atomOffset;
269	>	theBends[j].isGhost = 1;
270	>	break;
271
272	<	Atom::createArrays(simnfo->n_atoms);
273	<	the_atoms = new Atom*[simnfo->n_atoms];
274	<	the_molecules = new Molecule[simnfo->n_mol];
275	<	int molIndex;
272	>	default:
273	>	sprintf(painCave.errMsg,
274	>	"SimSetup Error: ghostVectorSource was neither a "
275	>	"double nor an int.\n"
276	>	"-->Bend[%d] in %s\n",
277	>	j, comp_stamps[stampID]->getID());
278	>	painCave.isFatal = 1;
279	>	simError();
280	>	}
281	>	}
282	>	else{
283	>	sprintf(painCave.errMsg,
284	>	"SimSetup Error: unhandled bend assignment:\n"
285	>	"    -->%s in Bend[%d] in %s\n",
286	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290
291	<	// initialize the molecule's stampID's
291	>	current_extra = current_extra->getNext();
292	>	}
293	>	}
294
295	+	if (!theBends[j].isGhost){
296	+	exI = theBends[j].a;
297	+	exJ = theBends[j].c;
298	+	}
299	+	else{
300	+	exI = theBends[j].a;
301	+	exJ = theBends[j].b;
302	+	}
303	+
304	+	// exclude_I must always be the smaller of the pair
305	+	if (exI > exJ){
306	+	tempEx = exI;
307	+	exI = exJ;
308	+	exJ = tempEx;
309	+	}
310		#ifdef IS_MPI
311	<
311	>	tempEx = exI;
312	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
313	>	tempEx = exJ;
314	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
315
316	<	molIndex = 0;
317	<	for(i=0; i<mpiSim->getTotNmol(); i++){
318	<
319	<	if(mol2proc[i] == worldRank ){
320	<	the_molecules[molIndex].setStampID( molCompType[i] );
321	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
429	<	}
430	<	}
316	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
317	>	#else  // isn't MPI
318	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
319	>	#endif  //is_mpi
320	>	}
321	>	excludeOffset += molInfo.nBends;
322
323	<	#else // is_mpi
324	<
325	<	molIndex = 0;
326	<	globalAtomIndex = 0;
327	<	for(i=0; i<n_components; i++){
328	<	for(j=0; j<components_nmol[i]; j++ ){
438	<	the_molecules[molIndex].setStampID( i );
439	<	the_molecules[molIndex].setMyIndex( molIndex );
440	<	the_molecules[molIndex].setGlobalIndex( molIndex );
441	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443	<	globalAtomIndex++;
444	<	}
445	<	molIndex++;
446	<	}
447	<	}
448	<
323	>	for (j = 0; j < molInfo.nTorsions; j++){
324	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
325	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
326	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
327	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
328	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
329
330	<	#endif // is_mpi
330	>	exI = theTorsions[j].a;
331	>	exJ = theTorsions[j].d;
332
333	+	// exclude_I must always be the smaller of the pair
334	+	if (exI > exJ){
335	+	tempEx = exI;
336	+	exI = exJ;
337	+	exJ = tempEx;
338	+	}
339	+	#ifdef IS_MPI
340	+	tempEx = exI;
341	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
342	+	tempEx = exJ;
343	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344
345	<	if( simnfo->n_SRI ){
346	<
347	<	Exclude::createArray(simnfo->n_SRI);
348	<	the_excludes = new Exclude*[simnfo->n_SRI];
349	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
350	<	simnfo->globalExcludes = new int;
459	<	simnfo->n_exclude = simnfo->n_SRI;
460	<	}
461	<	else{
462	<
463	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
345	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
346	>	#else  // isn't MPI
347	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
348	>	#endif  //is_mpi
349	>	}
350	>	excludeOffset += molInfo.nTorsions;
351
472	–	// set the arrays into the SimInfo object
352
353	<	simnfo->atoms = the_atoms;
475	<	simnfo->molecules = the_molecules;
476	<	simnfo->nGlobalExcludes = 0;
477	<	simnfo->excludes = the_excludes;
353	>	// send the arrays off to the forceField for init.
354
355	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
356	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
357	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
358	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
359	+	theTorsions);
360
480	–	// get some of the tricky things that may still be in the globals
361
362	<
483	<	if( the_globals->haveBox() ){
484	<	simnfo->box_x = the_globals->getBox();
485	<	simnfo->box_y = the_globals->getBox();
486	<	simnfo->box_z = the_globals->getBox();
487	<	}
488	<	else if( the_globals->haveDensity() ){
362	>	info[k].molecules[i].initialize(molInfo);
363
490	–	double vol;
491	–	vol = (double)tot_nmol / the_globals->getDensity();
492	–	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
493	–	simnfo->box_y = simnfo->box_x;
494	–	simnfo->box_z = simnfo->box_x;
495	–	}
496	–	else{
497	–	if( !the_globals->haveBoxX() ){
498	–	sprintf( painCave.errMsg,
499	–	"SimSetup error, no periodic BoxX size given.\n" );
500	–	painCave.isFatal = 1;
501	–	simError();
502	–	}
503	–	simnfo->box_x = the_globals->getBoxX();
364
365	<	if( !the_globals->haveBoxY() ){
366	<	sprintf( painCave.errMsg,
367	<	"SimSetup error, no periodic BoxY size given.\n" );
368	<	painCave.isFatal = 1;
509	<	simError();
365	>	atomOffset += molInfo.nAtoms;
366	>	delete[] theBonds;
367	>	delete[] theBends;
368	>	delete[] theTorsions;
369		}
511	–	simnfo->box_y = the_globals->getBoxY();
512	–
513	–	if( !the_globals->haveBoxZ() ){
514	–	sprintf( painCave.errMsg,
515	–	"SimSetup error, no periodic BoxZ size given.\n" );
516	–	painCave.isFatal = 1;
517	–	simError();
518	–	}
519	–	simnfo->box_z = the_globals->getBoxZ();
370		}
371
372		#ifdef IS_MPI
373	<	strcpy( checkPointMsg, "Box size set up" );
373	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
374		MPIcheckPoint();
375		#endif // is_mpi
376
377	+	// clean up the forcefield
378
379	<	// initialize the arrays
379	>	the_ff->calcRcut();
380	>	the_ff->cleanMe();
381	>	}
382
383	<	the_ff->setSimInfo( simnfo );
383	>	void SimSetup::initFromBass(void){
384	>	int i, j, k;
385	>	int n_cells;
386	>	double cellx, celly, cellz;
387	>	double temp1, temp2, temp3;
388	>	int n_per_extra;
389	>	int n_extra;
390	>	int have_extra, done;
391
392	<	makeMolecules();
393	<	simnfo->identArray = new int[simnfo->n_atoms];
394	<	for(i=0; i<simnfo->n_atoms; i++){
395	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
536	<	}
537	<
538	<	if (the_globals->getUseRF() ) {
539	<	simnfo->useReactionField = 1;
540	<
541	<	if( !the_globals->haveECR() ){
542	<	sprintf( painCave.errMsg,
543	<	"SimSetup Warning: using default value of 1/2 the smallest "
544	<	"box length for the electrostaticCutoffRadius.\n"
545	<	"I hope you have a very fast processor!\n");
546	<	painCave.isFatal = 0;
547	<	simError();
548	<	double smallest;
549	<	smallest = simnfo->box_x;
550	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
551	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
552	<	simnfo->ecr = 0.5 * smallest;
553	<	} else {
554	<	simnfo->ecr        = the_globals->getECR();
555	<	}
392	>	double vel[3];
393	>	vel[0] = 0.0;
394	>	vel[1] = 0.0;
395	>	vel[2] = 0.0;
396
397	<	if( !the_globals->haveEST() ){
398	<	sprintf( painCave.errMsg,
399	<	"SimSetup Warning: using default value of 0.05 * the "
400	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
401	<	);
402	<	painCave.isFatal = 0;
403	<	simError();
404	<	simnfo->est = 0.05 * simnfo->ecr;
405	<	} else {
406	<	simnfo->est        = the_globals->getEST();
407	<	}
408	<
409	<	if(!the_globals->haveDielectric() ){
410	<	sprintf( painCave.errMsg,
411	<	"SimSetup Error: You are trying to use Reaction Field without"
412	<	"setting a dielectric constant!\n"
413	<	);
397	>	temp1 = (double) tot_nmol / 4.0;
398	>	temp2 = pow(temp1, (1.0 / 3.0));
399	>	temp3 = ceil(temp2);
400	>
401	>	have_extra = 0;
402	>	if (temp2 < temp3){
403	>	// we have a non-complete lattice
404	>	have_extra = 1;
405	>
406	>	n_cells = (int) temp3 - 1;
407	>	cellx = info[0].boxL[0] / temp3;
408	>	celly = info[0].boxL[1] / temp3;
409	>	cellz = info[0].boxL[2] / temp3;
410	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
411	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
412	>	n_per_extra = (int) ceil(temp1);
413	>
414	>	if (n_per_extra > 4){
415	>	sprintf(painCave.errMsg,
416	>	"SimSetup error. There has been an error in constructing"
417	>	" the non-complete lattice.\n");
418		painCave.isFatal = 1;
419		simError();
420		}
421	<	simnfo->dielectric = the_globals->getDielectric();
422	<	} else {
423	<	if (usesDipoles) {
424	<
425	<	if( !the_globals->haveECR() ){
426	<	sprintf( painCave.errMsg,
427	<	"SimSetup Warning: using default value of 1/2 the smallest "
584	<	"box length for the electrostaticCutoffRadius.\n"
585	<	"I hope you have a very fast processor!\n");
586	<	painCave.isFatal = 0;
587	<	simError();
588	<	double smallest;
589	<	smallest = simnfo->box_x;
590	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
591	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
592	<	simnfo->ecr = 0.5 * smallest;
593	<	} else {
594	<	simnfo->ecr        = the_globals->getECR();
595	<	}
596	<
597	<	if( !the_globals->haveEST() ){
598	<	sprintf( painCave.errMsg,
599	<	"SimSetup Warning: using default value of 5%% of the "
600	<	"electrostaticCutoffRadius for the "
601	<	"electrostaticSkinThickness\n"
602	<	);
603	<	painCave.isFatal = 0;
604	<	simError();
605	<	simnfo->est = 0.05 * simnfo->ecr;
606	<	} else {
607	<	simnfo->est        = the_globals->getEST();
608	<	}
609	<	}
610	<	}
421	>	}
422	>	else{
423	>	n_cells = (int) temp3;
424	>	cellx = info[0].boxL[0] / temp3;
425	>	celly = info[0].boxL[1] / temp3;
426	>	cellz = info[0].boxL[2] / temp3;
427	>	}
428
429	<	#ifdef IS_MPI
430	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
431	<	MPIcheckPoint();
432	<	#endif // is_mpi
429	>	current_mol = 0;
430	>	current_comp_mol = 0;
431	>	current_comp = 0;
432	>	current_atom_ndx = 0;
433
434	<	if( the_globals->haveInitialConfig() ){
435	<
436	<	InitializeFromFile* fileInit;
437	<	#ifdef IS_MPI // is_mpi
621	<	if( worldRank == 0 ){
622	<	#endif //is_mpi
623	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
624	<	#ifdef IS_MPI
625	<	}else fileInit = new InitializeFromFile( NULL );
626	<	#endif
627	<	fileInit->read_xyz( simnfo ); // default velocities on
434	>	for (i = 0; i < n_cells ; i++){
435	>	for (j = 0; j < n_cells; j++){
436	>	for (k = 0; k < n_cells; k++){
437	>	makeElement(i * cellx, j * celly, k * cellz);
438
439	<	delete fileInit;
630	<	}
631	<	else{
439	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
440
441	<	#ifdef IS_MPI
634	<
635	<	// no init from bass
636	<
637	<	sprintf( painCave.errMsg,
638	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
639	<	painCave.isFatal;
640	<	simError();
641	<
642	<	#else
643	<
644	<	initFromBass();
441	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
442
443	+	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
444	+	}
445	+	}
446	+	}
447
448	<	#endif
449	<	}
448	>	if (have_extra){
449	>	done = 0;
450
451	<	#ifdef IS_MPI
452	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
453	<	MPIcheckPoint();
454	<	#endif // is_mpi
451	>	int start_ndx;
452	>	for (i = 0; i < (n_cells + 1) && !done; i++){
453	>	for (j = 0; j < (n_cells + 1) && !done; j++){
454	>	if (i < n_cells){
455	>	if (j < n_cells){
456	>	start_ndx = n_cells;
457	>	}
458	>	else
459	>	start_ndx = 0;
460	>	}
461	>	else
462	>	start_ndx = 0;
463
464	+	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
465	+	makeElement(i * cellx, j * celly, k * cellz);
466	+	done = (current_mol >= tot_nmol);
467
468	<
469	<
470	<
468	>	if (!done && n_per_extra > 1){
469	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
470	>	k * cellz);
471	>	done = (current_mol >= tot_nmol);
472	>	}
473
474	<
475	<	#ifdef IS_MPI
476	<	if( worldRank == 0 ){
477	<	#endif // is_mpi
478	<
479	<	if( the_globals->haveFinalConfig() ){
480	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
481	<	}
482	<	else{
483	<	strcpy( simnfo->finalName, inFileName );
484	<	char* endTest;
485	<	int nameLength = strlen( simnfo->finalName );
672	<	endTest = &(simnfo->finalName[nameLength - 5]);
673	<	if( !strcmp( endTest, ".bass" ) ){
674	<	strcpy( endTest, ".eor" );
474	>	if (!done && n_per_extra > 2){
475	>	makeElement(i * cellx, j * celly + 0.5 * celly,
476	>	k * cellz + 0.5 * cellz);
477	>	done = (current_mol >= tot_nmol);
478	>	}
479	>
480	>	if (!done && n_per_extra > 3){
481	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
482	>	k * cellz + 0.5 * cellz);
483	>	done = (current_mol >= tot_nmol);
484	>	}
485	>	}
486		}
676	–	else if( !strcmp( endTest, ".BASS" ) ){
677	–	strcpy( endTest, ".eor" );
678	–	}
679	–	else{
680	–	endTest = &(simnfo->finalName[nameLength - 4]);
681	–	if( !strcmp( endTest, ".bss" ) ){
682	–	strcpy( endTest, ".eor" );
683	–	}
684	–	else if( !strcmp( endTest, ".mdl" ) ){
685	–	strcpy( endTest, ".eor" );
686	–	}
687	–	else{
688	–	strcat( simnfo->finalName, ".eor" );
689	–	}
690	–	}
487		}
692	–
693	–	// make the sample and status out names
694	–
695	–	strcpy( simnfo->sampleName, inFileName );
696	–	char* endTest;
697	–	int nameLength = strlen( simnfo->sampleName );
698	–	endTest = &(simnfo->sampleName[nameLength - 5]);
699	–	if( !strcmp( endTest, ".bass" ) ){
700	–	strcpy( endTest, ".dump" );
701	–	}
702	–	else if( !strcmp( endTest, ".BASS" ) ){
703	–	strcpy( endTest, ".dump" );
704	–	}
705	–	else{
706	–	endTest = &(simnfo->sampleName[nameLength - 4]);
707	–	if( !strcmp( endTest, ".bss" ) ){
708	–	strcpy( endTest, ".dump" );
709	–	}
710	–	else if( !strcmp( endTest, ".mdl" ) ){
711	–	strcpy( endTest, ".dump" );
712	–	}
713	–	else{
714	–	strcat( simnfo->sampleName, ".dump" );
715	–	}
716	–	}
717	–
718	–	strcpy( simnfo->statusName, inFileName );
719	–	nameLength = strlen( simnfo->statusName );
720	–	endTest = &(simnfo->statusName[nameLength - 5]);
721	–	if( !strcmp( endTest, ".bass" ) ){
722	–	strcpy( endTest, ".stat" );
723	–	}
724	–	else if( !strcmp( endTest, ".BASS" ) ){
725	–	strcpy( endTest, ".stat" );
726	–	}
727	–	else{
728	–	endTest = &(simnfo->statusName[nameLength - 4]);
729	–	if( !strcmp( endTest, ".bss" ) ){
730	–	strcpy( endTest, ".stat" );
731	–	}
732	–	else if( !strcmp( endTest, ".mdl" ) ){
733	–	strcpy( endTest, ".stat" );
734	–	}
735	–	else{
736	–	strcat( simnfo->statusName, ".stat" );
737	–	}
738	–	}
739	–
740	–	#ifdef IS_MPI
488		}
742	–	#endif // is_mpi
743	–
744	–	// set the status, sample, and themal kick times
745	–
746	–	if( the_globals->haveSampleTime() ){
747	–	simnfo->sampleTime = the_globals->getSampleTime();
748	–	simnfo->statusTime = simnfo->sampleTime;
749	–	simnfo->thermalTime = simnfo->sampleTime;
750	–	}
751	–	else{
752	–	simnfo->sampleTime = the_globals->getRunTime();
753	–	simnfo->statusTime = simnfo->sampleTime;
754	–	simnfo->thermalTime = simnfo->sampleTime;
755	–	}
489
490	<	if( the_globals->haveStatusTime() ){
491	<	simnfo->statusTime = the_globals->getStatusTime();
490	>	for (i = 0; i < info[0].n_atoms; i++){
491	>	info[0].atoms[i]->setVel(vel);
492		}
493	+	}
494
495	<	if( the_globals->haveThermalTime() ){
496	<	simnfo->thermalTime = the_globals->getThermalTime();
497	<	}
495	>	void SimSetup::makeElement(double x, double y, double z){
496	>	int k;
497	>	AtomStamp* current_atom;
498	>	DirectionalAtom* dAtom;
499	>	double rotMat[3][3];
500	>	double pos[3];
501
502	<	// check for the temperature set flag
502	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
503	>	current_atom = comp_stamps[current_comp]->getAtom(k);
504	>	if (!current_atom->havePosition()){
505	>	sprintf(painCave.errMsg,
506	>	"SimSetup:initFromBass error.\n"
507	>	"\tComponent %s, atom %s does not have a position specified.\n"
508	>	"\tThe initialization routine is unable to give a start"
509	>	" position.\n",
510	>	comp_stamps[current_comp]->getID(), current_atom->getType());
511	>	painCave.isFatal = 1;
512	>	simError();
513	>	}
514
515	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
515	>	pos[0] = x + current_atom->getPosX();
516	>	pos[1] = y + current_atom->getPosY();
517	>	pos[2] = z + current_atom->getPosZ();
518
519	+	info[0].atoms[current_atom_ndx]->setPos(pos);
520
521	<	// make the integrator
521	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
522	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
523
524	<	switch( ensembleCase ){
524	>	rotMat[0][0] = 1.0;
525	>	rotMat[0][1] = 0.0;
526	>	rotMat[0][2] = 0.0;
527
528	<	case NVE_ENS:
529	<	new NVE( simnfo, the_ff );
530	<	break;
528	>	rotMat[1][0] = 0.0;
529	>	rotMat[1][1] = 1.0;
530	>	rotMat[1][2] = 0.0;
531
532	<	default:
533	<	sprintf( painCave.errMsg,
534	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
535	<	painCave.isFatal = 1;
536	<	simError();
532	>	rotMat[2][0] = 0.0;
533	>	rotMat[2][1] = 0.0;
534	>	rotMat[2][2] = 1.0;
535	>
536	>	dAtom->setA(rotMat);
537	>	}
538	>
539	>	current_atom_ndx++;
540		}
541
542	+	current_mol++;
543	+	current_comp_mol++;
544
545	<	#ifdef IS_MPI
546	<	mpiSim->mpiRefresh();
547	<	#endif
545	>	if (current_comp_mol >= components_nmol[current_comp]){
546	>	current_comp_mol = 0;
547	>	current_comp++;
548	>	}
549	>	}
550
790	–	// initialize the Fortran
551
552	+	void SimSetup::gatherInfo(void){
553	+	int i;
554
555	<	simnfo->refreshSim();
556	<
557	<	if( !strcmp( simnfo->mixingRule, "standard") ){
558	<	the_ff->initForceField( LB_MIXING_RULE );
559	<	}
560	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
561	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
562	<	}
563	<	else{
802	<	sprintf( painCave.errMsg,
803	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
804	<	simnfo->mixingRule );
805	<	painCave.isFatal = 1;
806	<	simError();
555	>	ensembleCase = -1;
556	>	ffCase = -1;
557	>
558	>	// set the easy ones first
559	>
560	>	for (i = 0; i < nInfo; i++){
561	>	info[i].target_temp = globals->getTargetTemp();
562	>	info[i].dt = globals->getDt();
563	>	info[i].run_time = globals->getRunTime();
564		}
565	+	n_components = globals->getNComponents();
566
567
568	<	#ifdef IS_MPI
811	<	strcpy( checkPointMsg,
812	<	"Successfully intialized the mixingRule for Fortran." );
813	<	MPIcheckPoint();
814	<	#endif // is_mpi
815	<	}
568	>	// get the forceField
569
570	+	strcpy(force_field, globals->getForceField());
571
572	<	void SimSetup::makeMolecules( void ){
572	>	if (!strcasecmp(force_field, "DUFF")){
573	>	ffCase = FF_DUFF;
574	>	}
575	>	else if (!strcasecmp(force_field, "LJ")){
576	>	ffCase = FF_LJ;
577	>	}
578	>	else if (!strcasecmp(force_field, "EAM")){
579	>	ffCase = FF_EAM;
580	>	}
581	>	else{
582	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
583	>	force_field);
584	>	painCave.isFatal = 1;
585	>	simError();
586	>	}
587
588	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
821	<	molInit info;
822	<	DirectionalAtom* dAtom;
823	<	LinkedAssign* extras;
824	<	LinkedAssign* current_extra;
825	<	AtomStamp* currentAtom;
826	<	BondStamp* currentBond;
827	<	BendStamp* currentBend;
828	<	TorsionStamp* currentTorsion;
588	>	// get the ensemble
589
590	<	bond_pair* theBonds;
831	<	bend_set* theBends;
832	<	torsion_set* theTorsions;
590	>	strcpy(ensemble, globals->getEnsemble());
591
592	<
593	<	//init the forceField paramters
592	>	if (!strcasecmp(ensemble, "NVE")){
593	>	ensembleCase = NVE_ENS;
594	>	}
595	>	else if (!strcasecmp(ensemble, "NVT")){
596	>	ensembleCase = NVT_ENS;
597	>	}
598	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
599	>	ensembleCase = NPTi_ENS;
600	>	}
601	>	else if (!strcasecmp(ensemble, "NPTf")){
602	>	ensembleCase = NPTf_ENS;
603	>	}
604	>	else{
605	>	sprintf(painCave.errMsg,
606	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
607	>	"reverting to NVE for this simulation.\n",
608	>	ensemble);
609	>	painCave.isFatal = 0;
610	>	simError();
611	>	strcpy(ensemble, "NVE");
612	>	ensembleCase = NVE_ENS;
613	>	}
614
615	<	the_ff->readParams();
615	>	for (i = 0; i < nInfo; i++){
616	>	strcpy(info[i].ensemble, ensemble);
617
618	<
840	<	// init the atoms
618	>	// get the mixing rule
619
620	<	double ux, uy, uz, u, uSqr;
621	<
622	<	atomOffset = 0;
845	<	excludeOffset = 0;
846	<	for(i=0; i<simnfo->n_mol; i++){
847	<
848	<	stampID = the_molecules[i].getStampID();
620	>	strcpy(info[i].mixingRule, globals->getMixingRule());
621	>	info[i].usePBC = globals->getPBC();
622	>	}
623
624	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
851	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
852	<	info.nBends    = comp_stamps[stampID]->getNBends();
853	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
854	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
624	>	// get the components and calculate the tot_nMol and indvidual n_mol
625
626	<	info.myAtoms = &the_atoms[atomOffset];
627	<	info.myExcludes = &the_excludes[excludeOffset];
858	<	info.myBonds = new Bond*[info.nBonds];
859	<	info.myBends = new Bend*[info.nBends];
860	<	info.myTorsions = new Torsion*[info.nTorsions];
626	>	the_components = globals->getComponents();
627	>	components_nmol = new int[n_components];
628
862	–	theBonds = new bond_pair[info.nBonds];
863	–	theBends = new bend_set[info.nBends];
864	–	theTorsions = new torsion_set[info.nTorsions];
865	–
866	–	// make the Atoms
867	–
868	–	for(j=0; j<info.nAtoms; j++){
869	–
870	–	currentAtom = comp_stamps[stampID]->getAtom( j );
871	–	if( currentAtom->haveOrientation() ){
872	–
873	–	dAtom = new DirectionalAtom(j + atomOffset);
874	–	simnfo->n_oriented++;
875	–	info.myAtoms[j] = dAtom;
876	–
877	–	ux = currentAtom->getOrntX();
878	–	uy = currentAtom->getOrntY();
879	–	uz = currentAtom->getOrntZ();
880	–
881	–	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
882	–
883	–	u = sqrt( uSqr );
884	–	ux = ux / u;
885	–	uy = uy / u;
886	–	uz = uz / u;
887	–
888	–	dAtom->setSUx( ux );
889	–	dAtom->setSUy( uy );
890	–	dAtom->setSUz( uz );
891	–	}
892	–	else{
893	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
894	–	}
895	–	info.myAtoms[j]->setType( currentAtom->getType() );
896	–
897	–	#ifdef IS_MPI
898	–
899	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
900	–
901	–	#endif // is_mpi
902	–	}
903	–
904	–	// make the bonds
905	–	for(j=0; j<info.nBonds; j++){
906	–
907	–	currentBond = comp_stamps[stampID]->getBond( j );
908	–	theBonds[j].a = currentBond->getA() + atomOffset;
909	–	theBonds[j].b = currentBond->getB() + atomOffset;
629
630	<	exI = theBonds[j].a;
631	<	exJ = theBonds[j].b;
630	>	if (!globals->haveNMol()){
631	>	// we don't have the total number of molecules, so we assume it is
632	>	// given in each component
633
634	<	// exclude_I must always be the smaller of the pair
635	<	if( exI > exJ ){
636	<	tempEx = exI;
637	<	exI = exJ;
638	<	exJ = tempEx;
634	>	tot_nmol = 0;
635	>	for (i = 0; i < n_components; i++){
636	>	if (!the_components[i]->haveNMol()){
637	>	// we have a problem
638	>	sprintf(painCave.errMsg,
639	>	"SimSetup Error. No global NMol or component NMol"
640	>	" given. Cannot calculate the number of atoms.\n");
641	>	painCave.isFatal = 1;
642	>	simError();
643		}
920	–	#ifdef IS_MPI
921	–	tempEx = exI;
922	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
923	–	tempEx = exJ;
924	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
925	–
926	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
927	–	#else  // isn't MPI
644
645	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
646	<	#endif  //is_mpi
645	>	tot_nmol += the_components[i]->getNMol();
646	>	components_nmol[i] = the_components[i]->getNMol();
647		}
648	<	excludeOffset += info.nBonds;
648	>	}
649	>	else{
650	>	sprintf(painCave.errMsg,
651	>	"SimSetup error.\n"
652	>	"\tSorry, the ability to specify total"
653	>	" nMols and then give molfractions in the components\n"
654	>	"\tis not currently supported."
655	>	" Please give nMol in the components.\n");
656	>	painCave.isFatal = 1;
657	>	simError();
658	>	}
659
660	<	//make the bends
661	<	for(j=0; j<info.nBends; j++){
662	<
663	<	currentBend = comp_stamps[stampID]->getBend( j );
664	<	theBends[j].a = currentBend->getA() + atomOffset;
665	<	theBends[j].b = currentBend->getB() + atomOffset;
666	<	theBends[j].c = currentBend->getC() + atomOffset;
941	<
942	<	if( currentBend->haveExtras() ){
943	<
944	<	extras = currentBend->getExtras();
945	<	current_extra = extras;
946	<
947	<	while( current_extra != NULL ){
948	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
949	<
950	<	switch( current_extra->getType() ){
951	<
952	<	case 0:
953	<	theBends[j].ghost =
954	<	current_extra->getInt() + atomOffset;
955	<	theBends[j].isGhost = 1;
956	<	break;
957	<
958	<	case 1:
959	<	theBends[j].ghost =
960	<	(int)current_extra->getDouble() + atomOffset;
961	<	theBends[j].isGhost = 1;
962	<	break;
963	<
964	<	default:
965	<	sprintf( painCave.errMsg,
966	<	"SimSetup Error: ghostVectorSource was neither a "
967	<	"double nor an int.\n"
968	<	"-->Bend[%d] in %s\n",
969	<	j, comp_stamps[stampID]->getID() );
970	<	painCave.isFatal = 1;
971	<	simError();
972	<	}
973	<	}
974	<
975	<	else{
976	<
977	<	sprintf( painCave.errMsg,
978	<	"SimSetup Error: unhandled bend assignment:\n"
979	<	"    -->%s in Bend[%d] in %s\n",
980	<	current_extra->getlhs(),
981	<	j, comp_stamps[stampID]->getID() );
982	<	painCave.isFatal = 1;
983	<	simError();
984	<	}
985	<
986	<	current_extra = current_extra->getNext();
987	<	}
988	<	}
989	<
990	<	if( !theBends[j].isGhost ){
991	<
992	<	exI = theBends[j].a;
993	<	exJ = theBends[j].c;
994	<	}
995	<	else{
996	<
997	<	exI = theBends[j].a;
998	<	exJ = theBends[j].b;
999	<	}
1000	<
1001	<	// exclude_I must always be the smaller of the pair
1002	<	if( exI > exJ ){
1003	<	tempEx = exI;
1004	<	exI = exJ;
1005	<	exJ = tempEx;
1006	<	}
1007	<	#ifdef IS_MPI
1008	<	tempEx = exI;
1009	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1010	<	tempEx = exJ;
1011	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1012	<
1013	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1014	<	#else  // isn't MPI
1015	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1016	<	#endif  //is_mpi
660	>	// set the status, sample, and thermal kick times
661	>
662	>	for (i = 0; i < nInfo; i++){
663	>	if (globals->haveSampleTime()){
664	>	info[i].sampleTime = globals->getSampleTime();
665	>	info[i].statusTime = info[i].sampleTime;
666	>	info[i].thermalTime = info[i].sampleTime;
667		}
668	<	excludeOffset += info.nBends;
668	>	else{
669	>	info[i].sampleTime = globals->getRunTime();
670	>	info[i].statusTime = info[i].sampleTime;
671	>	info[i].thermalTime = info[i].sampleTime;
672	>	}
673
674	<	for(j=0; j<info.nTorsions; j++){
675	<
676	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1023	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1024	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1025	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1026	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1027	<
1028	<	exI = theTorsions[j].a;
1029	<	exJ = theTorsions[j].d;
674	>	if (globals->haveStatusTime()){
675	>	info[i].statusTime = globals->getStatusTime();
676	>	}
677
678	<	// exclude_I must always be the smaller of the pair
679	<	if( exI > exJ ){
1033	<	tempEx = exI;
1034	<	exI = exJ;
1035	<	exJ = tempEx;
1036	<	}
1037	<	#ifdef IS_MPI
1038	<	tempEx = exI;
1039	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1040	<	tempEx = exJ;
1041	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1042	<
1043	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1044	<	#else  // isn't MPI
1045	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1046	<	#endif  //is_mpi
678	>	if (globals->haveThermalTime()){
679	>	info[i].thermalTime = globals->getThermalTime();
680		}
1048	–	excludeOffset += info.nTorsions;
681
682	<
683	<	// send the arrays off to the forceField for init.
682	>	info[i].resetIntegrator = 0;
683	>	if( globals->haveResetTime() ){
684	>	info[i].resetTime = globals->getResetTime();
685	>	info[i].resetIntegrator = 1;
686	>	}
687
688	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1054	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1055	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1056	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
688	>	// check for the temperature set flag
689
690	+	if (globals->haveTempSet())
691	+	info[i].setTemp = globals->getTempSet();
692
693	<	the_molecules[i].initialize( info );
693	>	// get some of the tricky things that may still be in the globals
694
695	+	double boxVector[3];
696	+	if (globals->haveBox()){
697	+	boxVector[0] = globals->getBox();
698	+	boxVector[1] = globals->getBox();
699	+	boxVector[2] = globals->getBox();
700
701	<	atomOffset += info.nAtoms;
702	<	delete[] theBonds;
703	<	delete[] theBends;
704	<	delete[] theTorsions;
705	<	}
701	>	info[i].setBox(boxVector);
702	>	}
703	>	else if (globals->haveDensity()){
704	>	double vol;
705	>	vol = (double) tot_nmol / globals->getDensity();
706	>	boxVector[0] = pow(vol, (1.0 / 3.0));
707	>	boxVector[1] = boxVector[0];
708	>	boxVector[2] = boxVector[0];
709
710	<	#ifdef IS_MPI
711	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
712	<	MPIcheckPoint();
713	<	#endif // is_mpi
710	>	info[i].setBox(boxVector);
711	>	}
712	>	else{
713	>	if (!globals->haveBoxX()){
714	>	sprintf(painCave.errMsg,
715	>	"SimSetup error, no periodic BoxX size given.\n");
716	>	painCave.isFatal = 1;
717	>	simError();
718	>	}
719	>	boxVector[0] = globals->getBoxX();
720
721	<	// clean up the forcefield
722	<	the_ff->calcRcut();
723	<	the_ff->cleanMe();
721	>	if (!globals->haveBoxY()){
722	>	sprintf(painCave.errMsg,
723	>	"SimSetup error, no periodic BoxY size given.\n");
724	>	painCave.isFatal = 1;
725	>	simError();
726	>	}
727	>	boxVector[1] = globals->getBoxY();
728
729	<	}
729	>	if (!globals->haveBoxZ()){
730	>	sprintf(painCave.errMsg,
731	>	"SimSetup error, no periodic BoxZ size given.\n");
732	>	painCave.isFatal = 1;
733	>	simError();
734	>	}
735	>	boxVector[2] = globals->getBoxZ();
736
737	<	void SimSetup::initFromBass( void ){
737	>	info[i].setBox(boxVector);
738	>	}
739	>	}
740
741	<	int i, j, k;
742	<	int n_cells;
1083	<	double cellx, celly, cellz;
1084	<	double temp1, temp2, temp3;
1085	<	int n_per_extra;
1086	<	int n_extra;
1087	<	int have_extra, done;
741	>	//setup seed for random number generator
742	>	int seedValue;
743
744	<	temp1 = (double)tot_nmol / 4.0;
745	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1091	<	temp3 = ceil( temp2 );
744	>	if (globals->haveSeed()){
745	>	seedValue = globals->getSeed();
746
747	<	have_extra =0;
748	<	if( temp2 < temp3 ){ // we have a non-complete lattice
749	<	have_extra =1;
750	<
751	<	n_cells = (int)temp3 - 1;
1098	<	cellx = simnfo->box_x / temp3;
1099	<	celly = simnfo->box_y / temp3;
1100	<	cellz = simnfo->box_z / temp3;
1101	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1102	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1103	<	n_per_extra = (int)ceil( temp1 );
1104	<
1105	<	if( n_per_extra > 4){
1106	<	sprintf( painCave.errMsg,
1107	<	"SimSetup error. There has been an error in constructing"
1108	<	" the non-complete lattice.\n" );
1109	<	painCave.isFatal = 1;
747	>	if(seedValue / 1E9 == 0){
748	>	sprintf(painCave.errMsg,
749	>	"Seed for sprng library should contain at least 9 digits\n"
750	>	"OOPSE will generate a seed for user\n");
751	>	painCave.isFatal = 0;
752		simError();
753	+
754	+	//using seed generated by system instead of invalid seed set by user
755	+	#ifndef IS_MPI
756	+	seedValue = make_sprng_seed();
757	+	#else
758	+	if (worldRank == 0){
759	+	seedValue = make_sprng_seed();
760	+	}
761	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
762	+	#endif
763		}
764	<	}
764	>	}//end of if branch of globals->haveSeed()
765		else{
766	<	n_cells = (int)temp3;
767	<	cellx = simnfo->box_x / temp3;
768	<	celly = simnfo->box_y / temp3;
769	<	cellz = simnfo->box_z / temp3;
766	>
767	>	#ifndef IS_MPI
768	>	seedValue = make_sprng_seed();
769	>	#else
770	>	if (worldRank == 0){
771	>	seedValue = make_sprng_seed();
772	>	}
773	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
774	>	#endif
775	>	}//end of globals->haveSeed()
776	>
777	>	for (int i = 0; i < nInfo; i++){
778	>	info[i].setSeed(seedValue);
779		}
780
781	<	current_mol = 0;
782	<	current_comp_mol = 0;
783	<	current_comp = 0;
784	<	current_atom_ndx = 0;
781	>	#ifdef IS_MPI
782	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
783	>	MPIcheckPoint();
784	>	#endif // is_mpi
785	>	}
786
1125	–	for( i=0; i < n_cells ; i++ ){
1126	–	for( j=0; j < n_cells; j++ ){
1127	–	for( k=0; k < n_cells; k++ ){
787
788	<	makeElement( i * cellx,
789	<	j * celly,
790	<	k * cellz );
788	>	void SimSetup::finalInfoCheck(void){
789	>	int index;
790	>	int usesDipoles;
791	>	int i;
792
793	<	makeElement( i * cellx + 0.5 * cellx,
794	<	j * celly + 0.5 * celly,
1135	<	k * cellz );
793	>	for (i = 0; i < nInfo; i++){
794	>	// check electrostatic parameters
795
796	<	makeElement( i * cellx,
797	<	j * celly + 0.5 * celly,
798	<	k * cellz + 0.5 * cellz );
799	<
800	<	makeElement( i * cellx + 0.5 * cellx,
1142	<	j * celly,
1143	<	k * cellz + 0.5 * cellz );
1144	<	}
796	>	index = 0;
797	>	usesDipoles = 0;
798	>	while ((index < info[i].n_atoms) && !usesDipoles){
799	>	usesDipoles = (info[i].atoms[index])->hasDipole();
800	>	index++;
801		}
1146	–	}
802
803	<	if( have_extra ){
804	<	done = 0;
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	<	int start_ndx;
1152	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1153	<	for( j=0; j < (n_cells+1) && !done; j++ ){
808	>	double theEcr, theEst;
809
810	<	if( i < n_cells ){
810	>	if (globals->getUseRF()){
811	>	info[i].useReactionField = 1;
812
813	<	if( j < n_cells ){
814	<	start_ndx = n_cells;
815	<	}
816	<	else start_ndx = 0;
817	<	}
818	<	else start_ndx = 0;
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)
823	>	smallest = info[i].boxL[1];
824	>	if (info[i].boxL[2] <= smallest)
825	>	smallest = info[i].boxL[2];
826	>	theEcr = 0.5 * smallest;
827	>	}
828	>	else{
829	>	theEcr = globals->getECR();
830	>	}
831
832	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
832	>	if (!globals->haveEST()){
833	>	sprintf(painCave.errMsg,
834	>	"SimSetup Warning: using default value of 0.05 * the "
835	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
836	>	painCave.isFatal = 0;
837	>	simError();
838	>	theEst = 0.05 * theEcr;
839	>	}
840	>	else{
841	>	theEst = globals->getEST();
842	>	}
843
844	<	makeElement( i * cellx,
1167	<	j * celly,
1168	<	k * cellz );
1169	<	done = ( current_mol >= tot_nmol );
844	>	info[i].setEcr(theEcr, theEst);
845
846	<	if( !done && n_per_extra > 1 ){
847	<	makeElement( i * cellx + 0.5 * cellx,
848	<	j * celly + 0.5 * celly,
849	<	k * cellz );
850	<	done = ( current_mol >= tot_nmol );
851	<	}
846	>	if (!globals->haveDielectric()){
847	>	sprintf(painCave.errMsg,
848	>	"SimSetup Error: You are trying to use Reaction Field without"
849	>	"setting a dielectric constant!\n");
850	>	painCave.isFatal = 1;
851	>	simError();
852	>	}
853	>	info[i].dielectric = globals->getDielectric();
854	>	}
855	>	else{
856	>	if (usesDipoles){
857	>	if (!globals->haveECR()){
858	>	sprintf(painCave.errMsg,
859	>	"SimSetup Warning: using default value of 1/2 the smallest "
860	>	"box length for the electrostaticCutoffRadius.\n"
861	>	"I hope you have a very fast processor!\n");
862	>	painCave.isFatal = 0;
863	>	simError();
864	>	double smallest;
865	>	smallest = info[i].boxL[0];
866	>	if (info[i].boxL[1] <= smallest)
867	>	smallest = info[i].boxL[1];
868	>	if (info[i].boxL[2] <= smallest)
869	>	smallest = info[i].boxL[2];
870	>	theEcr = 0.5 * smallest;
871	>	}
872	>	else{
873	>	theEcr = globals->getECR();
874	>	}
875
876	<	if( !done && n_per_extra > 2){
877	<	makeElement( i * cellx,
878	<	j * celly + 0.5 * celly,
879	<	k * cellz + 0.5 * cellz );
880	<	done = ( current_mol >= tot_nmol );
881	<	}
876	>	if (!globals->haveEST()){
877	>	sprintf(painCave.errMsg,
878	>	"SimSetup Warning: using default value of 0.05 * the "
879	>	"electrostaticCutoffRadius for the "
880	>	"electrostaticSkinThickness\n");
881	>	painCave.isFatal = 0;
882	>	simError();
883	>	theEst = 0.05 * theEcr;
884	>	}
885	>	else{
886	>	theEst = globals->getEST();
887	>	}
888
889	<	if( !done && n_per_extra > 3){
1186	<	makeElement( i * cellx + 0.5 * cellx,
1187	<	j * celly,
1188	<	k * cellz + 0.5 * cellz );
1189	<	done = ( current_mol >= tot_nmol );
1190	<	}
1191	<	}
889	>	info[i].setEcr(theEcr, theEst);
890		}
891		}
892		}
893
894	+	#ifdef IS_MPI
895	+	strcpy(checkPointMsg, "post processing checks out");
896	+	MPIcheckPoint();
897	+	#endif // is_mpi
898	+	}
899
900	<	for( i=0; i<simnfo->n_atoms; i++ ){
901	<	simnfo->atoms[i]->set_vx( 0.0 );
902	<	simnfo->atoms[i]->set_vy( 0.0 );
903	<	simnfo->atoms[i]->set_vz( 0.0 );
900	>	void SimSetup::initSystemCoords(void){
901	>	int i;
902	>
903	>	char* inName;
904	>
905	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
906	>
907	>	for (i = 0; i < info[0].n_atoms; i++)
908	>	info[0].atoms[i]->setCoords();
909	>
910	>	if (globals->haveInitialConfig()){
911	>	InitializeFromFile* fileInit;
912	>	#ifdef IS_MPI // is_mpi
913	>	if (worldRank == 0){
914	>	#endif //is_mpi
915	>	inName = globals->getInitialConfig();
916	>	fileInit = new InitializeFromFile(inName);
917	>	#ifdef IS_MPI
918	>	}
919	>	else
920	>	fileInit = new InitializeFromFile(NULL);
921	>	#endif
922	>	fileInit->readInit(info); // default velocities on
923	>
924	>	delete fileInit;
925		}
926	+	else{
927	+	#ifdef IS_MPI
928	+
929	+	// no init from bass
930	+
931	+	sprintf(painCave.errMsg,
932	+	"Cannot intialize a parallel simulation without an initial configuration file.\n");
933	+	painCave.isFatal = 1;;
934	+	simError();
935	+
936	+	#else
937	+
938	+	initFromBass();
939	+
940	+
941	+	#endif
942	+	}
943	+
944	+	#ifdef IS_MPI
945	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
946	+	MPIcheckPoint();
947	+	#endif // is_mpi
948		}
949
1204	–	void SimSetup::makeElement( double x, double y, double z ){
950
951	+	void SimSetup::makeOutNames(void){
952		int k;
1207	–	AtomStamp* current_atom;
1208	–	DirectionalAtom* dAtom;
1209	–	double rotMat[3][3];
953
1211	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
954
955	<	current_atom = comp_stamps[current_comp]->getAtom( k );
956	<	if( !current_atom->havePosition() ){
957	<	sprintf( painCave.errMsg,
958	<	"SimSetup:initFromBass error.\n"
959	<	"\tComponent %s, atom %s does not have a position specified.\n"
960	<	"\tThe initialization routine is unable to give a start"
961	<	" position.\n",
962	<	comp_stamps[current_comp]->getID(),
963	<	current_atom->getType() );
955	>	for (k = 0; k < nInfo; k++){
956	>	#ifdef IS_MPI
957	>	if (worldRank == 0){
958	>	#endif // is_mpi
959	>
960	>	if (globals->haveFinalConfig()){
961	>	strcpy(info[k].finalName, globals->getFinalConfig());
962	>	}
963	>	else{
964	>	strcpy(info[k].finalName, inFileName);
965	>	char* endTest;
966	>	int nameLength = strlen(info[k].finalName);
967	>	endTest = &(info[k].finalName[nameLength - 5]);
968	>	if (!strcmp(endTest, ".bass")){
969	>	strcpy(endTest, ".eor");
970	>	}
971	>	else if (!strcmp(endTest, ".BASS")){
972	>	strcpy(endTest, ".eor");
973	>	}
974	>	else{
975	>	endTest = &(info[k].finalName[nameLength - 4]);
976	>	if (!strcmp(endTest, ".bss")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".mdl")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	strcat(info[k].finalName, ".eor");
984	>	}
985	>	}
986	>	}
987	>
988	>	// make the sample and status out names
989	>
990	>	strcpy(info[k].sampleName, inFileName);
991	>	char* endTest;
992	>	int nameLength = strlen(info[k].sampleName);
993	>	endTest = &(info[k].sampleName[nameLength - 5]);
994	>	if (!strcmp(endTest, ".bass")){
995	>	strcpy(endTest, ".dump");
996	>	}
997	>	else if (!strcmp(endTest, ".BASS")){
998	>	strcpy(endTest, ".dump");
999	>	}
1000	>	else{
1001	>	endTest = &(info[k].sampleName[nameLength - 4]);
1002	>	if (!strcmp(endTest, ".bss")){
1003	>	strcpy(endTest, ".dump");
1004	>	}
1005	>	else if (!strcmp(endTest, ".mdl")){
1006	>	strcpy(endTest, ".dump");
1007	>	}
1008	>	else{
1009	>	strcat(info[k].sampleName, ".dump");
1010	>	}
1011	>	}
1012	>
1013	>	strcpy(info[k].statusName, inFileName);
1014	>	nameLength = strlen(info[k].statusName);
1015	>	endTest = &(info[k].statusName[nameLength - 5]);
1016	>	if (!strcmp(endTest, ".bass")){
1017	>	strcpy(endTest, ".stat");
1018	>	}
1019	>	else if (!strcmp(endTest, ".BASS")){
1020	>	strcpy(endTest, ".stat");
1021	>	}
1022	>	else{
1023	>	endTest = &(info[k].statusName[nameLength - 4]);
1024	>	if (!strcmp(endTest, ".bss")){
1025	>	strcpy(endTest, ".stat");
1026	>	}
1027	>	else if (!strcmp(endTest, ".mdl")){
1028	>	strcpy(endTest, ".stat");
1029	>	}
1030	>	else{
1031	>	strcat(info[k].statusName, ".stat");
1032	>	}
1033	>	}
1034	>
1035	>	#ifdef IS_MPI
1036	>
1037	>	}
1038	>	#endif // is_mpi
1039	>	}
1040	>	}
1041	>
1042	>
1043	>	void SimSetup::sysObjectsCreation(void){
1044	>	int i, k;
1045	>
1046	>	// create the forceField
1047	>
1048	>	createFF();
1049	>
1050	>	// extract componentList
1051	>
1052	>	compList();
1053	>
1054	>	// calc the number of atoms, bond, bends, and torsions
1055	>
1056	>	calcSysValues();
1057	>
1058	>	#ifdef IS_MPI
1059	>	// divide the molecules among the processors
1060	>
1061	>	mpiMolDivide();
1062	>	#endif //is_mpi
1063	>
1064	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1065	>
1066	>	makeSysArrays();
1067	>
1068	>	// make and initialize the molecules (all but atomic coordinates)
1069	>
1070	>	makeMolecules();
1071	>
1072	>	for (k = 0; k < nInfo; k++){
1073	>	info[k].identArray = new int[info[k].n_atoms];
1074	>	for (i = 0; i < info[k].n_atoms; i++){
1075	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1076	>	}
1077	>	}
1078	>	}
1079	>
1080	>
1081	>	void SimSetup::createFF(void){
1082	>	switch (ffCase){
1083	>	case FF_DUFF:
1084	>	the_ff = new DUFF();
1085	>	break;
1086	>
1087	>	case FF_LJ:
1088	>	the_ff = new LJFF();
1089	>	break;
1090	>
1091	>	case FF_EAM:
1092	>	the_ff = new EAM_FF();
1093	>	break;
1094	>
1095	>	default:
1096	>	sprintf(painCave.errMsg,
1097	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1098		painCave.isFatal = 1;
1099		simError();
1100	+	}
1101	+
1102	+	#ifdef IS_MPI
1103	+	strcpy(checkPointMsg, "ForceField creation successful");
1104	+	MPIcheckPoint();
1105	+	#endif // is_mpi
1106	+	}
1107	+
1108	+
1109	+	void SimSetup::compList(void){
1110	+	int i;
1111	+	char* id;
1112	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1113	+	LinkedMolStamp* currentStamp = NULL;
1114	+	comp_stamps = new MoleculeStamp * [n_components];
1115	+
1116	+	// make an array of molecule stamps that match the components used.
1117	+	// also extract the used stamps out into a separate linked list
1118	+
1119	+	for (i = 0; i < nInfo; i++){
1120	+	info[i].nComponents = n_components;
1121	+	info[i].componentsNmol = components_nmol;
1122	+	info[i].compStamps = comp_stamps;
1123	+	info[i].headStamp = headStamp;
1124	+	}
1125	+
1126	+
1127	+	for (i = 0; i < n_components; i++){
1128	+	id = the_components[i]->getType();
1129	+	comp_stamps[i] = NULL;
1130	+
1131	+	// check to make sure the component isn't already in the list
1132	+
1133	+	comp_stamps[i] = headStamp->match(id);
1134	+	if (comp_stamps[i] == NULL){
1135	+	// extract the component from the list;
1136	+
1137	+	currentStamp = stamps->extractMolStamp(id);
1138	+	if (currentStamp == NULL){
1139	+	sprintf(painCave.errMsg,
1140	+	"SimSetup error: Component \"%s\" was not found in the "
1141	+	"list of declared molecules\n",
1142	+	id);
1143	+	painCave.isFatal = 1;
1144	+	simError();
1145	+	}
1146	+
1147	+	headStamp->add(currentStamp);
1148	+	comp_stamps[i] = headStamp->match(id);
1149		}
1150	+	}
1151
1152	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1153	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1154	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1152	>	#ifdef IS_MPI
1153	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1154	>	MPIcheckPoint();
1155	>	#endif // is_mpi
1156	>	}
1157
1158	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1158	>	void SimSetup::calcSysValues(void){
1159	>	int i;
1160
1161	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1161	>	int* molMembershipArray;
1162
1163	<	rotMat[0][0] = 1.0;
1164	<	rotMat[0][1] = 0.0;
1165	<	rotMat[0][2] = 0.0;
1163	>	tot_atoms = 0;
1164	>	tot_bonds = 0;
1165	>	tot_bends = 0;
1166	>	tot_torsions = 0;
1167	>	for (i = 0; i < n_components; i++){
1168	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1169	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1170	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1171	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1172	>	}
1173
1174	<	rotMat[1][0] = 0.0;
1175	<	rotMat[1][1] = 1.0;
1240	<	rotMat[1][2] = 0.0;
1174	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1175	>	molMembershipArray = new int[tot_atoms];
1176
1177	<	rotMat[2][0] = 0.0;
1178	<	rotMat[2][1] = 0.0;
1179	<	rotMat[2][2] = 1.0;
1177	>	for (i = 0; i < nInfo; i++){
1178	>	info[i].n_atoms = tot_atoms;
1179	>	info[i].n_bonds = tot_bonds;
1180	>	info[i].n_bends = tot_bends;
1181	>	info[i].n_torsions = tot_torsions;
1182	>	info[i].n_SRI = tot_SRI;
1183	>	info[i].n_mol = tot_nmol;
1184
1185	<	dAtom->setA( rotMat );
1185	>	info[i].molMembershipArray = molMembershipArray;
1186	>	}
1187	>	}
1188	>
1189	>	#ifdef IS_MPI
1190	>
1191	>	void SimSetup::mpiMolDivide(void){
1192	>	int i, j, k;
1193	>	int localMol, allMol;
1194	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1195	>
1196	>	mpiSim = new mpiSimulation(info);
1197	>
1198	>	globalIndex = mpiSim->divideLabor();
1199	>
1200	>	// set up the local variables
1201	>
1202	>	mol2proc = mpiSim->getMolToProcMap();
1203	>	molCompType = mpiSim->getMolComponentType();
1204	>
1205	>	allMol = 0;
1206	>	localMol = 0;
1207	>	local_atoms = 0;
1208	>	local_bonds = 0;
1209	>	local_bends = 0;
1210	>	local_torsions = 0;
1211	>	globalAtomIndex = 0;
1212	>
1213	>
1214	>	for (i = 0; i < n_components; i++){
1215	>	for (j = 0; j < components_nmol[i]; j++){
1216	>	if (mol2proc[allMol] == worldRank){
1217	>	local_atoms += comp_stamps[i]->getNAtoms();
1218	>	local_bonds += comp_stamps[i]->getNBonds();
1219	>	local_bends += comp_stamps[i]->getNBends();
1220	>	local_torsions += comp_stamps[i]->getNTorsions();
1221	>	localMol++;
1222	>	}
1223	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1224	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1225	>	globalAtomIndex++;
1226	>	}
1227	>
1228	>	allMol++;
1229		}
1230	+	}
1231	+	local_SRI = local_bonds + local_bends + local_torsions;
1232
1233	<	current_atom_ndx++;
1233	>	info[0].n_atoms = mpiSim->getMyNlocal();
1234	>
1235	>	if (local_atoms != info[0].n_atoms){
1236	>	sprintf(painCave.errMsg,
1237	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	>	" localAtom (%d) are not equal.\n",
1239	>	info[0].n_atoms, local_atoms);
1240	>	painCave.isFatal = 1;
1241	>	simError();
1242		}
1243
1244	<	current_mol++;
1245	<	current_comp_mol++;
1244	>	info[0].n_bonds = local_bonds;
1245	>	info[0].n_bends = local_bends;
1246	>	info[0].n_torsions = local_torsions;
1247	>	info[0].n_SRI = local_SRI;
1248	>	info[0].n_mol = localMol;
1249
1250	<	if( current_comp_mol >= components_nmol[current_comp] ){
1250	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1251	>	MPIcheckPoint();
1252	>	}
1253
1254	<	current_comp_mol = 0;
1255	<	current_comp++;
1254	>	#endif // is_mpi
1255	>
1256	>
1257	>	void SimSetup::makeSysArrays(void){
1258	>
1259	>	#ifndef IS_MPI
1260	>	int k, j;
1261	>	#endif // is_mpi
1262	>	int i, l;
1263	>
1264	>	Atom** the_atoms;
1265	>	Molecule* the_molecules;
1266	>	Exclude** the_excludes;
1267	>
1268	>
1269	>	for (l = 0; l < nInfo; l++){
1270	>	// create the atom and short range interaction arrays
1271	>
1272	>	the_atoms = new Atom * [info[l].n_atoms];
1273	>	the_molecules = new Molecule[info[l].n_mol];
1274	>	int molIndex;
1275	>
1276	>	// initialize the molecule's stampID's
1277	>
1278	>	#ifdef IS_MPI
1279	>
1280	>
1281	>	molIndex = 0;
1282	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1283	>	if (mol2proc[i] == worldRank){
1284	>	the_molecules[molIndex].setStampID(molCompType[i]);
1285	>	the_molecules[molIndex].setMyIndex(molIndex);
1286	>	the_molecules[molIndex].setGlobalIndex(i);
1287	>	molIndex++;
1288	>	}
1289	>	}
1290	>
1291	>	#else // is_mpi
1292	>
1293	>	molIndex = 0;
1294	>	globalAtomIndex = 0;
1295	>	for (i = 0; i < n_components; i++){
1296	>	for (j = 0; j < components_nmol[i]; j++){
1297	>	the_molecules[molIndex].setStampID(i);
1298	>	the_molecules[molIndex].setMyIndex(molIndex);
1299	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1300	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1301	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	>	globalAtomIndex++;
1303	>	}
1304	>	molIndex++;
1305	>	}
1306	>	}
1307	>
1308	>
1309	>	#endif // is_mpi
1310	>
1311	>
1312	>	if (info[l].n_SRI){
1313	>	Exclude::createArray(info[l].n_SRI);
1314	>	the_excludes = new Exclude * [info[l].n_SRI];
1315	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	>	the_excludes[ex] = new Exclude(ex);
1317	>	}
1318	>	info[l].globalExcludes = new int;
1319	>	info[l].n_exclude = info[l].n_SRI;
1320	>	}
1321	>	else{
1322	>	Exclude::createArray(1);
1323	>	the_excludes = new Exclude * ;
1324	>	the_excludes[0] = new Exclude(0);
1325	>	the_excludes[0]->setPair(0, 0);
1326	>	info[l].globalExcludes = new int;
1327	>	info[l].globalExcludes[0] = 0;
1328	>	info[l].n_exclude = 0;
1329	>	}
1330	>
1331	>	// set the arrays into the SimInfo object
1332	>
1333	>	info[l].atoms = the_atoms;
1334	>	info[l].molecules = the_molecules;
1335	>	info[l].nGlobalExcludes = 0;
1336	>	info[l].excludes = the_excludes;
1337	>
1338	>	the_ff->setSimInfo(info);
1339		}
1340		}
1341	+
1342	+	void SimSetup::makeIntegrator(void){
1343	+	int k;
1344	+
1345	+	NVE<RealIntegrator>* myNVE = NULL;
1346	+	NVT<RealIntegrator>* myNVT = NULL;
1347	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1349	+
1350	+	for (k = 0; k < nInfo; k++){
1351	+	switch (ensembleCase){
1352	+	case NVE_ENS:
1353	+	if (globals->haveZconstraints()){
1354	+	setupZConstraint(info[k]);
1355	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1356	+	}
1357	+	else{
1358	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1359	+	}
1360	+
1361	+	info->the_integrator = myNVE;
1362	+	break;
1363	+
1364	+	case NVT_ENS:
1365	+	if (globals->haveZconstraints()){
1366	+	setupZConstraint(info[k]);
1367	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1368	+	}
1369	+	else
1370	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1371	+
1372	+	myNVT->setTargetTemp(globals->getTargetTemp());
1373	+
1374	+	if (globals->haveTauThermostat())
1375	+	myNVT->setTauThermostat(globals->getTauThermostat());
1376	+	else{
1377	+	sprintf(painCave.errMsg,
1378	+	"SimSetup error: If you use the NVT\n"
1379	+	"    ensemble, you must set tauThermostat.\n");
1380	+	painCave.isFatal = 1;
1381	+	simError();
1382	+	}
1383	+
1384	+	info->the_integrator = myNVT;
1385	+	break;
1386	+
1387	+	case NPTi_ENS:
1388	+	if (globals->haveZconstraints()){
1389	+	setupZConstraint(info[k]);
1390	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1391	+	}
1392	+	else
1393	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1394	+
1395	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1396	+
1397	+	if (globals->haveTargetPressure())
1398	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1399	+	else{
1400	+	sprintf(painCave.errMsg,
1401	+	"SimSetup error: If you use a constant pressure\n"
1402	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1403	+	painCave.isFatal = 1;
1404	+	simError();
1405	+	}
1406	+
1407	+	if (globals->haveTauThermostat())
1408	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1409	+	else{
1410	+	sprintf(painCave.errMsg,
1411	+	"SimSetup error: If you use an NPT\n"
1412	+	"    ensemble, you must set tauThermostat.\n");
1413	+	painCave.isFatal = 1;
1414	+	simError();
1415	+	}
1416	+
1417	+	if (globals->haveTauBarostat())
1418	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1419	+	else{
1420	+	sprintf(painCave.errMsg,
1421	+	"SimSetup error: If you use an NPT\n"
1422	+	"    ensemble, you must set tauBarostat.\n");
1423	+	painCave.isFatal = 1;
1424	+	simError();
1425	+	}
1426	+
1427	+	info->the_integrator = myNPTi;
1428	+	break;
1429	+
1430	+	case NPTf_ENS:
1431	+	if (globals->haveZconstraints()){
1432	+	setupZConstraint(info[k]);
1433	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1434	+	}
1435	+	else
1436	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1437	+
1438	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1439	+
1440	+	if (globals->haveTargetPressure())
1441	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	+	else{
1443	+	sprintf(painCave.errMsg,
1444	+	"SimSetup error: If you use a constant pressure\n"
1445	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1446	+	painCave.isFatal = 1;
1447	+	simError();
1448	+	}
1449	+
1450	+	if (globals->haveTauThermostat())
1451	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1452	+	else{
1453	+	sprintf(painCave.errMsg,
1454	+	"SimSetup error: If you use an NPT\n"
1455	+	"    ensemble, you must set tauThermostat.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+
1460	+	if (globals->haveTauBarostat())
1461	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1462	+	else{
1463	+	sprintf(painCave.errMsg,
1464	+	"SimSetup error: If you use an NPT\n"
1465	+	"    ensemble, you must set tauBarostat.\n");
1466	+	painCave.isFatal = 1;
1467	+	simError();
1468	+	}
1469	+
1470	+	info->the_integrator = myNPTf;
1471	+	break;
1472	+
1473	+	default:
1474	+	sprintf(painCave.errMsg,
1475	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1476	+	painCave.isFatal = 1;
1477	+	simError();
1478	+	}
1479	+	}
1480	+	}
1481	+
1482	+	void SimSetup::initFortran(void){
1483	+	info[0].refreshSim();
1484	+
1485	+	if (!strcmp(info[0].mixingRule, "standard")){
1486	+	the_ff->initForceField(LB_MIXING_RULE);
1487	+	}
1488	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1489	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1490	+	}
1491	+	else{
1492	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1493	+	info[0].mixingRule);
1494	+	painCave.isFatal = 1;
1495	+	simError();
1496	+	}
1497	+
1498	+
1499	+	#ifdef IS_MPI
1500	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1501	+	MPIcheckPoint();
1502	+	#endif // is_mpi
1503	+	}
1504	+
1505	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1506	+	int nZConstraints;
1507	+	ZconStamp** zconStamp;
1508	+
1509	+	if (globals->haveZconstraintTime()){
1510	+	//add sample time of z-constraint  into SimInfo's property list
1511	+	DoubleData* zconsTimeProp = new DoubleData();
1512	+	zconsTimeProp->setID(ZCONSTIME_ID);
1513	+	zconsTimeProp->setData(globals->getZconsTime());
1514	+	theInfo.addProperty(zconsTimeProp);
1515	+	}
1516	+	else{
1517	+	sprintf(painCave.errMsg,
1518	+	"ZConstraint error: If you use an ZConstraint\n"
1519	+	" , you must set sample time.\n");
1520	+	painCave.isFatal = 1;
1521	+	simError();
1522	+	}
1523	+
1524	+	//push zconsTol into siminfo, if user does not specify
1525	+	//value for zconsTol, a default value will be used
1526	+	DoubleData* zconsTol = new DoubleData();
1527	+	zconsTol->setID(ZCONSTOL_ID);
1528	+	if (globals->haveZconsTol()){
1529	+	zconsTol->setData(globals->getZconsTol());
1530	+	}
1531	+	else{
1532	+	double defaultZConsTol = 0.01;
1533	+	sprintf(painCave.errMsg,
1534	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1535	+	" , default value %f is used.\n",
1536	+	defaultZConsTol);
1537	+	painCave.isFatal = 0;
1538	+	simError();
1539	+
1540	+	zconsTol->setData(defaultZConsTol);
1541	+	}
1542	+	theInfo.addProperty(zconsTol);
1543	+
1544	+	//set Force Subtraction Policy
1545	+	StringData* zconsForcePolicy = new StringData();
1546	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1547	+
1548	+	if (globals->haveZconsForcePolicy()){
1549	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1550	+	}
1551	+	else{
1552	+	sprintf(painCave.errMsg,
1553	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1554	+	"PolicyByMass is used\n");
1555	+	painCave.isFatal = 0;
1556	+	simError();
1557	+	zconsForcePolicy->setData("BYMASS");
1558	+	}
1559	+
1560	+	theInfo.addProperty(zconsForcePolicy);
1561	+
1562	+	//Determine the name of ouput file and add it into SimInfo's property list
1563	+	//Be careful, do not use inFileName, since it is a pointer which
1564	+	//point to a string at master node, and slave nodes do not contain that string
1565	+
1566	+	string zconsOutput(theInfo.finalName);
1567	+
1568	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1569	+
1570	+	StringData* zconsFilename = new StringData();
1571	+	zconsFilename->setID(ZCONSFILENAME_ID);
1572	+	zconsFilename->setData(zconsOutput);
1573	+
1574	+	theInfo.addProperty(zconsFilename);
1575	+
1576	+	//setup index, pos and other parameters of z-constraint molecules
1577	+	nZConstraints = globals->getNzConstraints();
1578	+	theInfo.nZconstraints = nZConstraints;
1579	+
1580	+	zconStamp = globals->getZconStamp();
1581	+	ZConsParaItem tempParaItem;
1582	+
1583	+	ZConsParaData* zconsParaData = new ZConsParaData();
1584	+	zconsParaData->setID(ZCONSPARADATA_ID);
1585	+
1586	+	for (int i = 0; i < nZConstraints; i++){
1587	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1588	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1589	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1590	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1591	+
1592	+	zconsParaData->addItem(tempParaItem);
1593	+	}
1594	+
1595	+	//check the uniqueness of index
1596	+	if(!zconsParaData->isIndexUnique()){
1597	+	sprintf(painCave.errMsg,
1598	+	"ZConstraint Error: molIndex is not unique\n");
1599	+	painCave.isFatal = 1;
1600	+	simError();
1601	+	}
1602	+
1603	+	//sort the parameters by index of molecules
1604	+	zconsParaData->sortByIndex();
1605	+
1606	+	//push data into siminfo, therefore, we can retrieve later
1607	+	theInfo.addProperty(zconsParaData);
1608	+	}

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