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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 580 by gezelter, Wed Jul 9 13:56:36 2003 UTC vs.
Revision 780 by mmeineke, Mon Sep 22 21:23:25 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
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 38 | 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();
70	<	mpiEventLoop();
71	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92	<	void SimSetup::createSim( void ){
77	<
78	<	MakeStamps *the_stamps;
79	<	Globals* the_globals;
92	>	void SimSetup::createSim(void){
93		int i, j, k, globalAtomIndex;
81	–
82	–	int ensembleCase;
83	–	int ffCase;
84	–
85	–	ensembleCase = -1;
86	–	ffCase = -1;
94
95	<	// get the stamps and globals;
89	<	the_stamps = stamps;
90	<	the_globals = globals;
95	>	// gather all of the information from the Bass file
96
97	<	// set the easy ones first
93	<	simnfo->target_temp = the_globals->getTargetTemp();
94	<	simnfo->dt = the_globals->getDt();
95	<	simnfo->run_time = the_globals->getRunTime();
97	>	gatherInfo();
98
99	<	// get the ones we know are there, yet still may need some work.
98	<	n_components = the_globals->getNComponents();
99	<	strcpy( force_field, the_globals->getForceField() );
99	>	// creation of complex system objects
100
101	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
102	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
103	<	else{
104	<	sprintf( painCave.errMsg,
105	<	"SimSetup Error. Unrecognized force field -> %s\n",
106	<	force_field );
107	<	painCave.isFatal = 1;
108	<	simError();
109	<	}
101	>	sysObjectsCreation();
102
103	<	// get the ensemble:
112	<	strcpy( ensemble, the_globals->getEnsemble() );
103	>	// check on the post processing info
104
105	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
106	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
107	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
108	<	ensembleCase = NPTi_ENS;
109	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
110	<	else{
120	<	sprintf( painCave.errMsg,
121	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
122	<	"reverting to NVE for this simulation.\n",
123	<	ensemble );
124	<	painCave.isFatal = 0;
125	<	simError();
126	<	strcpy( ensemble, "NVE" );
127	<	ensembleCase = NVE_ENS;
105	>	finalInfoCheck();
106	>
107	>	// initialize the system coordinates
108	>
109	>	if (!isInfoArray){
110	>	initSystemCoords();
111		}
129	–	strcpy( simnfo->ensemble, ensemble );
112
113	+	// make the output filenames
114
115	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
133	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
134	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
135	<	//     if (the_globals->haveTargetPressure())
136	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
137	<	//     else {
138	<	//       sprintf( painCave.errMsg,
139	<	//                "SimSetup error: If you use the constant pressure\n"
140	<	//                "    ensemble, you must set targetPressure.\n"
141	<	//                "    This was found in the BASS file.\n");
142	<	//       painCave.isFatal = 1;
143	<	//       simError();
144	<	//     }
115	>	makeOutNames();
116
117	<	//     if (the_globals->haveTauThermostat())
147	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
148	<	//     else if (the_globals->haveQmass())
149	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
150	<	//     else {
151	<	//       sprintf( painCave.errMsg,
152	<	//                "SimSetup error: If you use one of the constant temperature\n"
153	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
154	<	//                "    Neither of these was found in the BASS file.\n");
155	<	//       painCave.isFatal = 1;
156	<	//       simError();
157	<	//     }
117	>	// make the integrator
118
119	<	//     if (the_globals->haveTauBarostat())
160	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
161	<	//     else {
162	<	//       sprintf( painCave.errMsg,
163	<	//                "SimSetup error: If you use the constant pressure\n"
164	<	//                "    ensemble, you must set tauBarostat.\n"
165	<	//                "    This was found in the BASS file.\n");
166	<	//       painCave.isFatal = 1;
167	<	//       simError();
168	<	//     }
119	>	makeIntegrator();
120
121	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
122	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
123	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
121	>	#ifdef IS_MPI
122	>	mpiSim->mpiRefresh();
123	>	#endif
124
125	<	//     if (the_globals->haveTauThermostat())
175	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
176	<	//     else if (the_globals->haveQmass())
177	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
178	<	//     else {
179	<	//       sprintf( painCave.errMsg,
180	<	//                "SimSetup error: If you use one of the constant temperature\n"
181	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
182	<	//                "    Neither of these was found in the BASS file.\n");
183	<	//       painCave.isFatal = 1;
184	<	//       simError();
185	<	//     }
125	>	// initialize the Fortran
126
127	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
128	<	simnfo->usePBC = the_globals->getPBC();
189	<
190	<	int usesDipoles = 0;
191	<	switch( ffCase ){
127	>	initFortran();
128	>	}
129
193	–	case FF_DUFF:
194	–	the_ff = new DUFF();
195	–	usesDipoles = 1;
196	–	break;
130
131	<	case FF_LJ:
132	<	the_ff = new LJFF();
133	<	break;
131	>	void SimSetup::makeMolecules(void){
132	>	int k, l;
133	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
134	>	molInit molInfo;
135	>	DirectionalAtom* dAtom;
136	>	LinkedAssign* extras;
137	>	LinkedAssign* current_extra;
138	>	AtomStamp* currentAtom;
139	>	BondStamp* currentBond;
140	>	BendStamp* currentBend;
141	>	TorsionStamp* currentTorsion;
142
143	<	default:
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Error. Unrecognized force field in case statement.\n");
205	<	painCave.isFatal = 1;
206	<	simError();
207	<	}
143	>	bond_pair* theBonds;
144	>	bend_set* theBends;
145	>	torsion_set* theTorsions;
146
209	–	#ifdef IS_MPI
210	–	strcpy( checkPointMsg, "ForceField creation successful" );
211	–	MPIcheckPoint();
212	–	#endif // is_mpi
147
148	<	// get the components and calculate the tot_nMol and indvidual n_mol
215	<	the_components = the_globals->getComponents();
216	<	components_nmol = new int[n_components];
217	<	comp_stamps = new MoleculeStamp*[n_components];
148	>	//init the forceField paramters
149
150	<	if( !the_globals->haveNMol() ){
220	<	// we don't have the total number of molecules, so we assume it is
221	<	// given in each component
150	>	the_ff->readParams();
151
223	–	tot_nmol = 0;
224	–	for( i=0; i<n_components; i++ ){
152
153	<	if( !the_components[i]->haveNMol() ){
227	<	// we have a problem
228	<	sprintf( painCave.errMsg,
229	<	"SimSetup Error. No global NMol or component NMol"
230	<	" given. Cannot calculate the number of atoms.\n" );
231	<	painCave.isFatal = 1;
232	<	simError();
233	<	}
153	>	// init the atoms
154
155	<	tot_nmol += the_components[i]->getNMol();
236	<	components_nmol[i] = the_components[i]->getNMol();
237	<	}
238	<	}
239	<	else{
240	<	sprintf( painCave.errMsg,
241	<	"SimSetup error.\n"
242	<	"\tSorry, the ability to specify total"
243	<	" nMols and then give molfractions in the components\n"
244	<	"\tis not currently supported."
245	<	" Please give nMol in the components.\n" );
246	<	painCave.isFatal = 1;
247	<	simError();
248	<
249	<
250	<	//     tot_nmol = the_globals->getNMol();
251	<
252	<	//   //we have the total number of molecules, now we check for molfractions
253	<	//     for( i=0; i<n_components; i++ ){
254	<
255	<	//       if( !the_components[i]->haveMolFraction() ){
256	<
257	<	//  if( !the_components[i]->haveNMol() ){
258	<	//    //we have a problem
259	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
260	<	//              << " nMol was given in component
261	<
262	<	}
155	>	double ux, uy, uz, u, uSqr;
156
157	<	#ifdef IS_MPI
158	<	strcpy( checkPointMsg, "Have the number of components" );
266	<	MPIcheckPoint();
267	<	#endif // is_mpi
157	>	for (k = 0; k < nInfo; k++){
158	>	the_ff->setSimInfo(&(info[k]));
159
160	<	// make an array of molecule stamps that match the components used.
161	<	// also extract the used stamps out into a separate linked list
160	>	atomOffset = 0;
161	>	excludeOffset = 0;
162	>	for (i = 0; i < info[k].n_mol; i++){
163	>	stampID = info[k].molecules[i].getStampID();
164
165	<	simnfo->nComponents = n_components;
166	<	simnfo->componentsNmol = components_nmol;
167	<	simnfo->compStamps = comp_stamps;
168	<	simnfo->headStamp = new LinkedMolStamp();
169	<
277	<	char* id;
278	<	LinkedMolStamp* headStamp = simnfo->headStamp;
279	<	LinkedMolStamp* currentStamp = NULL;
280	<	for( i=0; i<n_components; i++ ){
165	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
166	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
167	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
168	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
169	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
170
171	<	id = the_components[i]->getType();
172	<	comp_stamps[i] = NULL;
173	<
174	<	// check to make sure the component isn't already in the list
171	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
172	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
173	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
174	>	molInfo.myBends = new Bend * [molInfo.nBends];
175	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
176
177	<	comp_stamps[i] = headStamp->match( id );
178	<	if( comp_stamps[i] == NULL ){
179	<
290	<	// extract the component from the list;
291	<
292	<	currentStamp = the_stamps->extractMolStamp( id );
293	<	if( currentStamp == NULL ){
294	<	sprintf( painCave.errMsg,
295	<	"SimSetup error: Component \"%s\" was not found in the "
296	<	"list of declared molecules\n",
297	<	id );
298	<	painCave.isFatal = 1;
299	<	simError();
300	<	}
301	<
302	<	headStamp->add( currentStamp );
303	<	comp_stamps[i] = headStamp->match( id );
304	<	}
305	<	}
177	>	theBonds = new bond_pair[molInfo.nBonds];
178	>	theBends = new bend_set[molInfo.nBends];
179	>	theTorsions = new torsion_set[molInfo.nTorsions];
180
181	<	#ifdef IS_MPI
308	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
309	<	MPIcheckPoint();
310	<	#endif // is_mpi
311	<
181	>	// make the Atoms
182
183	+	for (j = 0; j < molInfo.nAtoms; j++){
184	+	currentAtom = comp_stamps[stampID]->getAtom(j);
185	+	if (currentAtom->haveOrientation()){
186	+	dAtom = new DirectionalAtom((j + atomOffset),
187	+	info[k].getConfiguration());
188	+	info[k].n_oriented++;
189	+	molInfo.myAtoms[j] = dAtom;
190
191	+	ux = currentAtom->getOrntX();
192	+	uy = currentAtom->getOrntY();
193	+	uz = currentAtom->getOrntZ();
194
195	<	// caclulate the number of atoms, bonds, bends and torsions
195	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
196
197	<	tot_atoms = 0;
198	<	tot_bonds = 0;
199	<	tot_bends = 0;
200	<	tot_torsions = 0;
321	<	for( i=0; i<n_components; i++ ){
322	<
323	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
324	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
325	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
326	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
327	<	}
197	>	u = sqrt(uSqr);
198	>	ux = ux / u;
199	>	uy = uy / u;
200	>	uz = uz / u;
201
202	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
202	>	dAtom->setSUx(ux);
203	>	dAtom->setSUy(uy);
204	>	dAtom->setSUz(uz);
205	>	}
206	>	else{
207	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
208	>	info[k].getConfiguration());
209	>	}
210	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
211
331	–	simnfo->n_atoms = tot_atoms;
332	–	simnfo->n_bonds = tot_bonds;
333	–	simnfo->n_bends = tot_bends;
334	–	simnfo->n_torsions = tot_torsions;
335	–	simnfo->n_SRI = tot_SRI;
336	–	simnfo->n_mol = tot_nmol;
337	–
338	–	simnfo->molMembershipArray = new int[tot_atoms];
339	–
212		#ifdef IS_MPI
213
214	<	// divide the molecules among processors here.
343	<
344	<	mpiSim = new mpiSimulation( simnfo );
345	<
346	<	globalIndex = mpiSim->divideLabor();
214	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
215
216	<	// set up the local variables
217	<
350	<	int localMol, allMol;
351	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
216	>	#endif // is_mpi
217	>	}
218
219	<	int* mol2proc = mpiSim->getMolToProcMap();
220	<	int* molCompType = mpiSim->getMolComponentType();
221	<
222	<	allMol = 0;
223	<	localMol = 0;
358	<	local_atoms = 0;
359	<	local_bonds = 0;
360	<	local_bends = 0;
361	<	local_torsions = 0;
362	<	globalAtomIndex = 0;
219	>	// make the bonds
220	>	for (j = 0; j < molInfo.nBonds; j++){
221	>	currentBond = comp_stamps[stampID]->getBond(j);
222	>	theBonds[j].a = currentBond->getA() + atomOffset;
223	>	theBonds[j].b = currentBond->getB() + atomOffset;
224
225	+	exI = theBonds[j].a;
226	+	exJ = theBonds[j].b;
227
228	<	for( i=0; i<n_components; i++ ){
228	>	// exclude_I must always be the smaller of the pair
229	>	if (exI > exJ){
230	>	tempEx = exI;
231	>	exI = exJ;
232	>	exJ = tempEx;
233	>	}
234	>	#ifdef IS_MPI
235	>	tempEx = exI;
236	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
237	>	tempEx = exJ;
238	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239
240	<	for( j=0; j<components_nmol[i]; j++ ){
241	<
242	<	if( mol2proc[allMol] == worldRank ){
243	<
244	<	local_atoms +=    comp_stamps[i]->getNAtoms();
372	<	local_bonds +=    comp_stamps[i]->getNBonds();
373	<	local_bends +=    comp_stamps[i]->getNBends();
374	<	local_torsions += comp_stamps[i]->getNTorsions();
375	<	localMol++;
376	<	}
377	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
378	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
379	<	globalAtomIndex++;
240	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
241	>	#else  // isn't MPI
242	>
243	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
244	>	#endif  //is_mpi
245		}
246	+	excludeOffset += molInfo.nBonds;
247
248	<	allMol++;
249	<	}
250	<	}
251	<	local_SRI = local_bonds + local_bends + local_torsions;
252	<
253	<	simnfo->n_atoms = mpiSim->getMyNlocal();
388	<
389	<	if( local_atoms != simnfo->n_atoms ){
390	<	sprintf( painCave.errMsg,
391	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
392	<	" localAtom (%d) are not equal.\n",
393	<	simnfo->n_atoms,
394	<	local_atoms );
395	<	painCave.isFatal = 1;
396	<	simError();
397	<	}
248	>	//make the bends
249	>	for (j = 0; j < molInfo.nBends; j++){
250	>	currentBend = comp_stamps[stampID]->getBend(j);
251	>	theBends[j].a = currentBend->getA() + atomOffset;
252	>	theBends[j].b = currentBend->getB() + atomOffset;
253	>	theBends[j].c = currentBend->getC() + atomOffset;
254
255	<	simnfo->n_bonds = local_bonds;
256	<	simnfo->n_bends = local_bends;
257	<	simnfo->n_torsions = local_torsions;
402	<	simnfo->n_SRI = local_SRI;
403	<	simnfo->n_mol = localMol;
255	>	if (currentBend->haveExtras()){
256	>	extras = currentBend->getExtras();
257	>	current_extra = extras;
258
259	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
260	<	MPIcheckPoint();
261	<
262	<
263	<	#endif // is_mpi
264	<
259	>	while (current_extra != NULL){
260	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
261	>	switch (current_extra->getType()){
262	>	case 0:
263	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
264	>	theBends[j].isGhost = 1;
265	>	break;
266
267	<	// create the atom and short range interaction arrays
267	>	case 1:
268	>	theBends[j].ghost = (int) current_extra->getDouble() +
269	>	atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272
273	<	Atom::createArrays(simnfo->n_atoms);
274	<	the_atoms = new Atom*[simnfo->n_atoms];
275	<	the_molecules = new Molecule[simnfo->n_mol];
276	<	int molIndex;
273	>	default:
274	>	sprintf(painCave.errMsg,
275	>	"SimSetup Error: ghostVectorSource was neither a "
276	>	"double nor an int.\n"
277	>	"-->Bend[%d] in %s\n",
278	>	j, comp_stamps[stampID]->getID());
279	>	painCave.isFatal = 1;
280	>	simError();
281	>	}
282	>	}
283	>	else{
284	>	sprintf(painCave.errMsg,
285	>	"SimSetup Error: unhandled bend assignment:\n"
286	>	"    -->%s in Bend[%d] in %s\n",
287	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
288	>	painCave.isFatal = 1;
289	>	simError();
290	>	}
291
292	<	// initialize the molecule's stampID's
292	>	current_extra = current_extra->getNext();
293	>	}
294	>	}
295
296	+	if (!theBends[j].isGhost){
297	+	exI = theBends[j].a;
298	+	exJ = theBends[j].c;
299	+	}
300	+	else{
301	+	exI = theBends[j].a;
302	+	exJ = theBends[j].b;
303	+	}
304	+
305	+	// exclude_I must always be the smaller of the pair
306	+	if (exI > exJ){
307	+	tempEx = exI;
308	+	exI = exJ;
309	+	exJ = tempEx;
310	+	}
311		#ifdef IS_MPI
312	<
312	>	tempEx = exI;
313	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
314	>	tempEx = exJ;
315	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316
317	<	molIndex = 0;
318	<	for(i=0; i<mpiSim->getTotNmol(); i++){
319	<
320	<	if(mol2proc[i] == worldRank ){
321	<	the_molecules[molIndex].setStampID( molCompType[i] );
322	<	the_molecules[molIndex].setMyIndex( molIndex );
430	<	the_molecules[molIndex].setGlobalIndex( i );
431	<	molIndex++;
432	<	}
433	<	}
317	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
318	>	#else  // isn't MPI
319	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
320	>	#endif  //is_mpi
321	>	}
322	>	excludeOffset += molInfo.nBends;
323
324	<	#else // is_mpi
325	<
326	<	molIndex = 0;
327	<	globalAtomIndex = 0;
328	<	for(i=0; i<n_components; i++){
329	<	for(j=0; j<components_nmol[i]; j++ ){
441	<	the_molecules[molIndex].setStampID( i );
442	<	the_molecules[molIndex].setMyIndex( molIndex );
443	<	the_molecules[molIndex].setGlobalIndex( molIndex );
444	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
445	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
446	<	globalAtomIndex++;
447	<	}
448	<	molIndex++;
449	<	}
450	<	}
451	<
324	>	for (j = 0; j < molInfo.nTorsions; j++){
325	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
326	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
327	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
328	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
329	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
330
331	<	#endif // is_mpi
331	>	exI = theTorsions[j].a;
332	>	exJ = theTorsions[j].d;
333
334	+	// exclude_I must always be the smaller of the pair
335	+	if (exI > exJ){
336	+	tempEx = exI;
337	+	exI = exJ;
338	+	exJ = tempEx;
339	+	}
340	+	#ifdef IS_MPI
341	+	tempEx = exI;
342	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	+	tempEx = exJ;
344	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345
346	<	if( simnfo->n_SRI ){
347	<
348	<	Exclude::createArray(simnfo->n_SRI);
349	<	the_excludes = new Exclude*[simnfo->n_SRI];
350	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
351	<	simnfo->globalExcludes = new int;
462	<	simnfo->n_exclude = simnfo->n_SRI;
463	<	}
464	<	else{
465	<
466	<	Exclude::createArray( 1 );
467	<	the_excludes = new Exclude*;
468	<	the_excludes[0] = new Exclude(0);
469	<	the_excludes[0]->setPair( 0,0 );
470	<	simnfo->globalExcludes = new int;
471	<	simnfo->globalExcludes[0] = 0;
472	<	simnfo->n_exclude = 0;
473	<	}
346	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
347	>	#else  // isn't MPI
348	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
349	>	#endif  //is_mpi
350	>	}
351	>	excludeOffset += molInfo.nTorsions;
352
475	–	// set the arrays into the SimInfo object
353
354	<	simnfo->atoms = the_atoms;
478	<	simnfo->molecules = the_molecules;
479	<	simnfo->nGlobalExcludes = 0;
480	<	simnfo->excludes = the_excludes;
354	>	// send the arrays off to the forceField for init.
355
356	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
357	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
358	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
359	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
360	+	theTorsions);
361
483	–	// get some of the tricky things that may still be in the globals
362
363	<	double boxVector[3];
486	<	if( the_globals->haveBox() ){
487	<	boxVector[0] = the_globals->getBox();
488	<	boxVector[1] = the_globals->getBox();
489	<	boxVector[2] = the_globals->getBox();
490	<
491	<	simnfo->setBox( boxVector );
492	<	}
493	<	else if( the_globals->haveDensity() ){
363	>	info[k].molecules[i].initialize(molInfo);
364
495	–	double vol;
496	–	vol = (double)tot_nmol / the_globals->getDensity();
497	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
498	–	boxVector[1] = boxVector[0];
499	–	boxVector[2] = boxVector[0];
365
366	<	simnfo->setBox( boxVector );
367	<	}
368	<	else{
369	<	if( !the_globals->haveBoxX() ){
505	<	sprintf( painCave.errMsg,
506	<	"SimSetup error, no periodic BoxX size given.\n" );
507	<	painCave.isFatal = 1;
508	<	simError();
366	>	atomOffset += molInfo.nAtoms;
367	>	delete[] theBonds;
368	>	delete[] theBends;
369	>	delete[] theTorsions;
370		}
510	–	boxVector[0] = the_globals->getBoxX();
511	–
512	–	if( !the_globals->haveBoxY() ){
513	–	sprintf( painCave.errMsg,
514	–	"SimSetup error, no periodic BoxY size given.\n" );
515	–	painCave.isFatal = 1;
516	–	simError();
517	–	}
518	–	boxVector[1] = the_globals->getBoxY();
519	–
520	–	if( !the_globals->haveBoxZ() ){
521	–	sprintf( painCave.errMsg,
522	–	"SimSetup error, no periodic BoxZ size given.\n" );
523	–	painCave.isFatal = 1;
524	–	simError();
525	–	}
526	–	boxVector[2] = the_globals->getBoxZ();
527	–
528	–	simnfo->setBox( boxVector );
371		}
372
373		#ifdef IS_MPI
374	<	strcpy( checkPointMsg, "Box size set up" );
374	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
375		MPIcheckPoint();
376		#endif // is_mpi
377
378	+	// clean up the forcefield
379
380	<	// initialize the arrays
380	>	the_ff->calcRcut();
381	>	the_ff->cleanMe();
382	>	}
383
384	<	the_ff->setSimInfo( simnfo );
384	>	void SimSetup::initFromBass(void){
385	>	int i, j, k;
386	>	int n_cells;
387	>	double cellx, celly, cellz;
388	>	double temp1, temp2, temp3;
389	>	int n_per_extra;
390	>	int n_extra;
391	>	int have_extra, done;
392
393	<	makeMolecules();
394	<	simnfo->identArray = new int[simnfo->n_atoms];
395	<	for(i=0; i<simnfo->n_atoms; i++){
396	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
545	<	}
546	<
547	<	if (the_globals->getUseRF() ) {
548	<	simnfo->useReactionField = 1;
549	<
550	<	if( !the_globals->haveECR() ){
551	<	sprintf( painCave.errMsg,
552	<	"SimSetup Warning: using default value of 1/2 the smallest "
553	<	"box length for the electrostaticCutoffRadius.\n"
554	<	"I hope you have a very fast processor!\n");
555	<	painCave.isFatal = 0;
556	<	simError();
557	<	double smallest;
558	<	smallest = simnfo->boxLx;
559	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
560	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
561	<	simnfo->ecr = 0.5 * smallest;
562	<	} else {
563	<	simnfo->ecr        = the_globals->getECR();
564	<	}
393	>	double vel[3];
394	>	vel[0] = 0.0;
395	>	vel[1] = 0.0;
396	>	vel[2] = 0.0;
397
398	<	if( !the_globals->haveEST() ){
399	<	sprintf( painCave.errMsg,
400	<	"SimSetup Warning: using default value of 0.05 * the "
401	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
402	<	);
403	<	painCave.isFatal = 0;
404	<	simError();
405	<	simnfo->est = 0.05 * simnfo->ecr;
406	<	} else {
407	<	simnfo->est        = the_globals->getEST();
408	<	}
409	<
410	<	if(!the_globals->haveDielectric() ){
411	<	sprintf( painCave.errMsg,
412	<	"SimSetup Error: You are trying to use Reaction Field without"
413	<	"setting a dielectric constant!\n"
414	<	);
398	>	temp1 = (double) tot_nmol / 4.0;
399	>	temp2 = pow(temp1, (1.0 / 3.0));
400	>	temp3 = ceil(temp2);
401	>
402	>	have_extra = 0;
403	>	if (temp2 < temp3){
404	>	// we have a non-complete lattice
405	>	have_extra = 1;
406	>
407	>	n_cells = (int) temp3 - 1;
408	>	cellx = info[0].boxL[0] / temp3;
409	>	celly = info[0].boxL[1] / temp3;
410	>	cellz = info[0].boxL[2] / temp3;
411	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
412	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
413	>	n_per_extra = (int) ceil(temp1);
414	>
415	>	if (n_per_extra > 4){
416	>	sprintf(painCave.errMsg,
417	>	"SimSetup error. There has been an error in constructing"
418	>	" the non-complete lattice.\n");
419		painCave.isFatal = 1;
420		simError();
421		}
422	<	simnfo->dielectric = the_globals->getDielectric();
423	<	} else {
424	<	if (usesDipoles) {
425	<
426	<	if( !the_globals->haveECR() ){
427	<	sprintf( painCave.errMsg,
428	<	"SimSetup Warning: using default value of 1/2 the smallest "
593	<	"box length for the electrostaticCutoffRadius.\n"
594	<	"I hope you have a very fast processor!\n");
595	<	painCave.isFatal = 0;
596	<	simError();
597	<	double smallest;
598	<	smallest = simnfo->boxLx;
599	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
600	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
601	<	simnfo->ecr = 0.5 * smallest;
602	<	} else {
603	<	simnfo->ecr        = the_globals->getECR();
604	<	}
605	<
606	<	if( !the_globals->haveEST() ){
607	<	sprintf( painCave.errMsg,
608	<	"SimSetup Warning: using default value of 5%% of the "
609	<	"electrostaticCutoffRadius for the "
610	<	"electrostaticSkinThickness\n"
611	<	);
612	<	painCave.isFatal = 0;
613	<	simError();
614	<	simnfo->est = 0.05 * simnfo->ecr;
615	<	} else {
616	<	simnfo->est        = the_globals->getEST();
617	<	}
618	<	}
619	<	}
422	>	}
423	>	else{
424	>	n_cells = (int) temp3;
425	>	cellx = info[0].boxL[0] / temp3;
426	>	celly = info[0].boxL[1] / temp3;
427	>	cellz = info[0].boxL[2] / temp3;
428	>	}
429
430	<	#ifdef IS_MPI
431	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
432	<	MPIcheckPoint();
433	<	#endif // is_mpi
430	>	current_mol = 0;
431	>	current_comp_mol = 0;
432	>	current_comp = 0;
433	>	current_atom_ndx = 0;
434
435	<	if( the_globals->haveInitialConfig() ){
436	<
437	<	InitializeFromFile* fileInit;
438	<	#ifdef IS_MPI // is_mpi
630	<	if( worldRank == 0 ){
631	<	#endif //is_mpi
632	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
633	<	#ifdef IS_MPI
634	<	}else fileInit = new InitializeFromFile( NULL );
635	<	#endif
636	<	fileInit->read_xyz( simnfo ); // default velocities on
435	>	for (i = 0; i < n_cells ; i++){
436	>	for (j = 0; j < n_cells; j++){
437	>	for (k = 0; k < n_cells; k++){
438	>	makeElement(i * cellx, j * celly, k * cellz);
439
440	<	delete fileInit;
639	<	}
640	<	else{
440	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
441
442	<	#ifdef IS_MPI
442	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
443
444	<	// no init from bass
445	<
446	<	sprintf( painCave.errMsg,
447	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
648	<	painCave.isFatal;
649	<	simError();
650	<
651	<	#else
444	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
445	>	}
446	>	}
447	>	}
448
449	<	initFromBass();
449	>	if (have_extra){
450	>	done = 0;
451
452	+	int start_ndx;
453	+	for (i = 0; i < (n_cells + 1) && !done; i++){
454	+	for (j = 0; j < (n_cells + 1) && !done; j++){
455	+	if (i < n_cells){
456	+	if (j < n_cells){
457	+	start_ndx = n_cells;
458	+	}
459	+	else
460	+	start_ndx = 0;
461	+	}
462	+	else
463	+	start_ndx = 0;
464
465	<	#endif
466	<	}
465	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
466	>	makeElement(i * cellx, j * celly, k * cellz);
467	>	done = (current_mol >= tot_nmol);
468
469	<	#ifdef IS_MPI
470	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
471	<	MPIcheckPoint();
472	<	#endif // is_mpi
469	>	if (!done && n_per_extra > 1){
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
471	>	k * cellz);
472	>	done = (current_mol >= tot_nmol);
473	>	}
474
475	+	if (!done && n_per_extra > 2){
476	+	makeElement(i * cellx, j * celly + 0.5 * celly,
477	+	k * cellz + 0.5 * cellz);
478	+	done = (current_mol >= tot_nmol);
479	+	}
480
481	<
482	<
483	<
484	<
485	<
486	<	#ifdef IS_MPI
671	<	if( worldRank == 0 ){
672	<	#endif // is_mpi
673	<
674	<	if( the_globals->haveFinalConfig() ){
675	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
676	<	}
677	<	else{
678	<	strcpy( simnfo->finalName, inFileName );
679	<	char* endTest;
680	<	int nameLength = strlen( simnfo->finalName );
681	<	endTest = &(simnfo->finalName[nameLength - 5]);
682	<	if( !strcmp( endTest, ".bass" ) ){
683	<	strcpy( endTest, ".eor" );
481	>	if (!done && n_per_extra > 3){
482	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486	>	}
487		}
685	–	else if( !strcmp( endTest, ".BASS" ) ){
686	–	strcpy( endTest, ".eor" );
687	–	}
688	–	else{
689	–	endTest = &(simnfo->finalName[nameLength - 4]);
690	–	if( !strcmp( endTest, ".bss" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else if( !strcmp( endTest, ".mdl" ) ){
694	–	strcpy( endTest, ".eor" );
695	–	}
696	–	else{
697	–	strcat( simnfo->finalName, ".eor" );
698	–	}
699	–	}
488		}
701	–
702	–	// make the sample and status out names
703	–
704	–	strcpy( simnfo->sampleName, inFileName );
705	–	char* endTest;
706	–	int nameLength = strlen( simnfo->sampleName );
707	–	endTest = &(simnfo->sampleName[nameLength - 5]);
708	–	if( !strcmp( endTest, ".bass" ) ){
709	–	strcpy( endTest, ".dump" );
710	–	}
711	–	else if( !strcmp( endTest, ".BASS" ) ){
712	–	strcpy( endTest, ".dump" );
713	–	}
714	–	else{
715	–	endTest = &(simnfo->sampleName[nameLength - 4]);
716	–	if( !strcmp( endTest, ".bss" ) ){
717	–	strcpy( endTest, ".dump" );
718	–	}
719	–	else if( !strcmp( endTest, ".mdl" ) ){
720	–	strcpy( endTest, ".dump" );
721	–	}
722	–	else{
723	–	strcat( simnfo->sampleName, ".dump" );
724	–	}
725	–	}
726	–
727	–	strcpy( simnfo->statusName, inFileName );
728	–	nameLength = strlen( simnfo->statusName );
729	–	endTest = &(simnfo->statusName[nameLength - 5]);
730	–	if( !strcmp( endTest, ".bass" ) ){
731	–	strcpy( endTest, ".stat" );
732	–	}
733	–	else if( !strcmp( endTest, ".BASS" ) ){
734	–	strcpy( endTest, ".stat" );
735	–	}
736	–	else{
737	–	endTest = &(simnfo->statusName[nameLength - 4]);
738	–	if( !strcmp( endTest, ".bss" ) ){
739	–	strcpy( endTest, ".stat" );
740	–	}
741	–	else if( !strcmp( endTest, ".mdl" ) ){
742	–	strcpy( endTest, ".stat" );
743	–	}
744	–	else{
745	–	strcat( simnfo->statusName, ".stat" );
746	–	}
747	–	}
748	–
749	–	#ifdef IS_MPI
489		}
751	–	#endif // is_mpi
752	–
753	–	// set the status, sample, and themal kick times
754	–
755	–	if( the_globals->haveSampleTime() ){
756	–	simnfo->sampleTime = the_globals->getSampleTime();
757	–	simnfo->statusTime = simnfo->sampleTime;
758	–	simnfo->thermalTime = simnfo->sampleTime;
759	–	}
760	–	else{
761	–	simnfo->sampleTime = the_globals->getRunTime();
762	–	simnfo->statusTime = simnfo->sampleTime;
763	–	simnfo->thermalTime = simnfo->sampleTime;
764	–	}
490
491	<	if( the_globals->haveStatusTime() ){
492	<	simnfo->statusTime = the_globals->getStatusTime();
491	>	for (i = 0; i < info[0].n_atoms; i++){
492	>	info[0].atoms[i]->setVel(vel);
493		}
494	+	}
495
496	<	if( the_globals->haveThermalTime() ){
497	<	simnfo->thermalTime = the_globals->getThermalTime();
498	<	}
496	>	void SimSetup::makeElement(double x, double y, double z){
497	>	int k;
498	>	AtomStamp* current_atom;
499	>	DirectionalAtom* dAtom;
500	>	double rotMat[3][3];
501	>	double pos[3];
502
503	<	// check for the temperature set flag
503	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
504	>	current_atom = comp_stamps[current_comp]->getAtom(k);
505	>	if (!current_atom->havePosition()){
506	>	sprintf(painCave.errMsg,
507	>	"SimSetup:initFromBass error.\n"
508	>	"\tComponent %s, atom %s does not have a position specified.\n"
509	>	"\tThe initialization routine is unable to give a start"
510	>	" position.\n",
511	>	comp_stamps[current_comp]->getID(), current_atom->getType());
512	>	painCave.isFatal = 1;
513	>	simError();
514	>	}
515
516	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
516	>	pos[0] = x + current_atom->getPosX();
517	>	pos[1] = y + current_atom->getPosY();
518	>	pos[2] = z + current_atom->getPosZ();
519
520	+	info[0].atoms[current_atom_ndx]->setPos(pos);
521
522	<	// make the integrator
523	<
781	<
782	<	NVT* myNVT = NULL;
783	<	switch( ensembleCase ){
522	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
523	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
524
525	<	case NVE_ENS:
526	<	new NVE( simnfo, the_ff );
527	<	break;
525	>	rotMat[0][0] = 1.0;
526	>	rotMat[0][1] = 0.0;
527	>	rotMat[0][2] = 0.0;
528
529	<	case NVT_ENS:
530	<	myNVT = new NVT( simnfo, the_ff );
531	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
529	>	rotMat[1][0] = 0.0;
530	>	rotMat[1][1] = 1.0;
531	>	rotMat[1][2] = 0.0;
532
533	<	if (the_globals->haveTauThermostat())
534	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
535	<	//     else if (the_globals->haveQmass())
536	<	//       myNVT->setQmass(the_globals->getQmass());
537	<	else {
798	<	sprintf( painCave.errMsg,
799	<	"SimSetup error: If you use the NVT\n"
800	<	"    ensemble, you must set either tauThermostat or qMass.\n"
801	<	"    Neither of these was found in the BASS file.\n");
802	<	painCave.isFatal = 1;
803	<	simError();
533	>	rotMat[2][0] = 0.0;
534	>	rotMat[2][1] = 0.0;
535	>	rotMat[2][2] = 1.0;
536	>
537	>	dAtom->setA(rotMat);
538		}
805	–	break;
539
540	<	default:
808	<	sprintf( painCave.errMsg,
809	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
810	<	painCave.isFatal = 1;
811	<	simError();
540	>	current_atom_ndx++;
541		}
542
543	+	current_mol++;
544	+	current_comp_mol++;
545
546	<	#ifdef IS_MPI
547	<	mpiSim->mpiRefresh();
548	<	#endif
546	>	if (current_comp_mol >= components_nmol[current_comp]){
547	>	current_comp_mol = 0;
548	>	current_comp++;
549	>	}
550	>	}
551
819	–	// initialize the Fortran
552
553	+	void SimSetup::gatherInfo(void){
554	+	int i, j, k;
555
556	<	simnfo->refreshSim();
557	<
558	<	if( !strcmp( simnfo->mixingRule, "standard") ){
559	<	the_ff->initForceField( LB_MIXING_RULE );
556	>	ensembleCase = -1;
557	>	ffCase = -1;
558	>
559	>	// set the easy ones first
560	>
561	>	for (i = 0; i < nInfo; i++){
562	>	info[i].target_temp = globals->getTargetTemp();
563	>	info[i].dt = globals->getDt();
564	>	info[i].run_time = globals->getRunTime();
565		}
566	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
567	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
566	>	n_components = globals->getNComponents();
567	>
568	>
569	>	// get the forceField
570	>
571	>	strcpy(force_field, globals->getForceField());
572	>
573	>	if (!strcasecmp(force_field, "DUFF")){
574	>	ffCase = FF_DUFF;
575		}
576	+	else if (!strcasecmp(force_field, "LJ")){
577	+	ffCase = FF_LJ;
578	+	}
579	+	else if (!strcasecmp(force_field, "EAM")){
580	+	ffCase = FF_EAM;
581	+	}
582		else{
583	<	sprintf( painCave.errMsg,
584	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
585	<	simnfo->mixingRule );
586	<	painCave.isFatal = 1;
835	<	simError();
583	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
584	>	force_field);
585	>	painCave.isFatal = 1;
586	>	simError();
587		}
588
589	+	// get the ensemble
590
591	<	#ifdef IS_MPI
840	<	strcpy( checkPointMsg,
841	<	"Successfully intialized the mixingRule for Fortran." );
842	<	MPIcheckPoint();
843	<	#endif // is_mpi
844	<	}
591	>	strcpy(ensemble, globals->getEnsemble());
592
593	+	if (!strcasecmp(ensemble, "NVE")){
594	+	ensembleCase = NVE_ENS;
595	+	}
596	+	else if (!strcasecmp(ensemble, "NVT")){
597	+	ensembleCase = NVT_ENS;
598	+	}
599	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
600	+	ensembleCase = NPTi_ENS;
601	+	}
602	+	else if (!strcasecmp(ensemble, "NPTf")){
603	+	ensembleCase = NPTf_ENS;
604	+	}
605	+	else{
606	+	sprintf(painCave.errMsg,
607	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
608	+	"reverting to NVE for this simulation.\n",
609	+	ensemble);
610	+	painCave.isFatal = 0;
611	+	simError();
612	+	strcpy(ensemble, "NVE");
613	+	ensembleCase = NVE_ENS;
614	+	}
615
616	<	void SimSetup::makeMolecules( void ){
616	>	for (i = 0; i < nInfo; i++){
617	>	strcpy(info[i].ensemble, ensemble);
618
619	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
850	<	molInit info;
851	<	DirectionalAtom* dAtom;
852	<	LinkedAssign* extras;
853	<	LinkedAssign* current_extra;
854	<	AtomStamp* currentAtom;
855	<	BondStamp* currentBond;
856	<	BendStamp* currentBend;
857	<	TorsionStamp* currentTorsion;
619	>	// get the mixing rule
620
621	<	bond_pair* theBonds;
622	<	bend_set* theBends;
623	<	torsion_set* theTorsions;
621	>	strcpy(info[i].mixingRule, globals->getMixingRule());
622	>	info[i].usePBC = globals->getPBC();
623	>	}
624
625	<
864	<	//init the forceField paramters
625	>	// get the components and calculate the tot_nMol and indvidual n_mol
626
627	<	the_ff->readParams();
627	>	the_components = globals->getComponents();
628	>	components_nmol = new int[n_components];
629
868	–
869	–	// init the atoms
630
631	<	double ux, uy, uz, u, uSqr;
632	<
633	<	atomOffset = 0;
874	<	excludeOffset = 0;
875	<	for(i=0; i<simnfo->n_mol; i++){
876	<
877	<	stampID = the_molecules[i].getStampID();
631	>	if (!globals->haveNMol()){
632	>	// we don't have the total number of molecules, so we assume it is
633	>	// given in each component
634
635	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
636	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
637	<	info.nBends    = comp_stamps[stampID]->getNBends();
638	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
639	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
640	<
641	<	info.myAtoms = &the_atoms[atomOffset];
642	<	info.myExcludes = &the_excludes[excludeOffset];
643	<	info.myBonds = new Bond*[info.nBonds];
888	<	info.myBends = new Bend*[info.nBends];
889	<	info.myTorsions = new Torsion*[info.nTorsions];
890	<
891	<	theBonds = new bond_pair[info.nBonds];
892	<	theBends = new bend_set[info.nBends];
893	<	theTorsions = new torsion_set[info.nTorsions];
894	<
895	<	// make the Atoms
896	<
897	<	for(j=0; j<info.nAtoms; j++){
898	<
899	<	currentAtom = comp_stamps[stampID]->getAtom( j );
900	<	if( currentAtom->haveOrientation() ){
901	<
902	<	dAtom = new DirectionalAtom(j + atomOffset);
903	<	simnfo->n_oriented++;
904	<	info.myAtoms[j] = dAtom;
905	<
906	<	ux = currentAtom->getOrntX();
907	<	uy = currentAtom->getOrntY();
908	<	uz = currentAtom->getOrntZ();
909	<
910	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
911	<
912	<	u = sqrt( uSqr );
913	<	ux = ux / u;
914	<	uy = uy / u;
915	<	uz = uz / u;
916	<
917	<	dAtom->setSUx( ux );
918	<	dAtom->setSUy( uy );
919	<	dAtom->setSUz( uz );
635	>	tot_nmol = 0;
636	>	for (i = 0; i < n_components; i++){
637	>	if (!the_components[i]->haveNMol()){
638	>	// we have a problem
639	>	sprintf(painCave.errMsg,
640	>	"SimSetup Error. No global NMol or component NMol"
641	>	" given. Cannot calculate the number of atoms.\n");
642	>	painCave.isFatal = 1;
643	>	simError();
644		}
921	–	else{
922	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
923	–	}
924	–	info.myAtoms[j]->setType( currentAtom->getType() );
925	–
926	–	#ifdef IS_MPI
927	–
928	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
929	–
930	–	#endif // is_mpi
931	–	}
932	–
933	–	// make the bonds
934	–	for(j=0; j<info.nBonds; j++){
935	–
936	–	currentBond = comp_stamps[stampID]->getBond( j );
937	–	theBonds[j].a = currentBond->getA() + atomOffset;
938	–	theBonds[j].b = currentBond->getB() + atomOffset;
645
646	<	exI = theBonds[j].a;
647	<	exJ = theBonds[j].b;
646	>	tot_nmol += the_components[i]->getNMol();
647	>	components_nmol[i] = the_components[i]->getNMol();
648	>	}
649	>	}
650	>	else{
651	>	sprintf(painCave.errMsg,
652	>	"SimSetup error.\n"
653	>	"\tSorry, the ability to specify total"
654	>	" nMols and then give molfractions in the components\n"
655	>	"\tis not currently supported."
656	>	" Please give nMol in the components.\n");
657	>	painCave.isFatal = 1;
658	>	simError();
659	>	}
660
661	<	// exclude_I must always be the smaller of the pair
944	<	if( exI > exJ ){
945	<	tempEx = exI;
946	<	exI = exJ;
947	<	exJ = tempEx;
948	<	}
949	<	#ifdef IS_MPI
950	<	tempEx = exI;
951	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
952	<	tempEx = exJ;
953	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
954	<
955	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
956	<	#else  // isn't MPI
661	>	// set the status, sample, and thermal kick times
662
663	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
664	<	#endif  //is_mpi
663	>	for (i = 0; i < nInfo; i++){
664	>	if (globals->haveSampleTime()){
665	>	info[i].sampleTime = globals->getSampleTime();
666	>	info[i].statusTime = info[i].sampleTime;
667	>	info[i].thermalTime = info[i].sampleTime;
668		}
669	<	excludeOffset += info.nBonds;
669	>	else{
670	>	info[i].sampleTime = globals->getRunTime();
671	>	info[i].statusTime = info[i].sampleTime;
672	>	info[i].thermalTime = info[i].sampleTime;
673	>	}
674
675	<	//make the bends
676	<	for(j=0; j<info.nBends; j++){
965	<
966	<	currentBend = comp_stamps[stampID]->getBend( j );
967	<	theBends[j].a = currentBend->getA() + atomOffset;
968	<	theBends[j].b = currentBend->getB() + atomOffset;
969	<	theBends[j].c = currentBend->getC() + atomOffset;
970	<
971	<	if( currentBend->haveExtras() ){
972	<
973	<	extras = currentBend->getExtras();
974	<	current_extra = extras;
975	<
976	<	while( current_extra != NULL ){
977	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
978	<
979	<	switch( current_extra->getType() ){
980	<
981	<	case 0:
982	<	theBends[j].ghost =
983	<	current_extra->getInt() + atomOffset;
984	<	theBends[j].isGhost = 1;
985	<	break;
986	<
987	<	case 1:
988	<	theBends[j].ghost =
989	<	(int)current_extra->getDouble() + atomOffset;
990	<	theBends[j].isGhost = 1;
991	<	break;
992	<
993	<	default:
994	<	sprintf( painCave.errMsg,
995	<	"SimSetup Error: ghostVectorSource was neither a "
996	<	"double nor an int.\n"
997	<	"-->Bend[%d] in %s\n",
998	<	j, comp_stamps[stampID]->getID() );
999	<	painCave.isFatal = 1;
1000	<	simError();
1001	<	}
1002	<	}
1003	<
1004	<	else{
1005	<
1006	<	sprintf( painCave.errMsg,
1007	<	"SimSetup Error: unhandled bend assignment:\n"
1008	<	"    -->%s in Bend[%d] in %s\n",
1009	<	current_extra->getlhs(),
1010	<	j, comp_stamps[stampID]->getID() );
1011	<	painCave.isFatal = 1;
1012	<	simError();
1013	<	}
1014	<
1015	<	current_extra = current_extra->getNext();
1016	<	}
1017	<	}
1018	<
1019	<	if( !theBends[j].isGhost ){
1020	<
1021	<	exI = theBends[j].a;
1022	<	exJ = theBends[j].c;
1023	<	}
1024	<	else{
1025	<
1026	<	exI = theBends[j].a;
1027	<	exJ = theBends[j].b;
1028	<	}
1029	<
1030	<	// exclude_I must always be the smaller of the pair
1031	<	if( exI > exJ ){
1032	<	tempEx = exI;
1033	<	exI = exJ;
1034	<	exJ = tempEx;
1035	<	}
1036	<	#ifdef IS_MPI
1037	<	tempEx = exI;
1038	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1039	<	tempEx = exJ;
1040	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1041	<
1042	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1043	<	#else  // isn't MPI
1044	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1045	<	#endif  //is_mpi
675	>	if (globals->haveStatusTime()){
676	>	info[i].statusTime = globals->getStatusTime();
677		}
1047	–	excludeOffset += info.nBends;
678
679	<	for(j=0; j<info.nTorsions; j++){
680	<
681	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1052	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1053	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1054	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1055	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1056	<
1057	<	exI = theTorsions[j].a;
1058	<	exJ = theTorsions[j].d;
679	>	if (globals->haveThermalTime()){
680	>	info[i].thermalTime = globals->getThermalTime();
681	>	}
682
683	<	// exclude_I must always be the smaller of the pair
684	<	if( exI > exJ ){
685	<	tempEx = exI;
686	<	exI = exJ;
1064	<	exJ = tempEx;
1065	<	}
1066	<	#ifdef IS_MPI
1067	<	tempEx = exI;
1068	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1069	<	tempEx = exJ;
1070	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1071	<
1072	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1073	<	#else  // isn't MPI
1074	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1075	<	#endif  //is_mpi
683	>	info[i].resetIntegrator = 0;
684	>	if( globals->haveResetTime() ){
685	>	info[i].resetTime = globals->getResetTime();
686	>	info[i].resetIntegrator = 1;
687		}
1077	–	excludeOffset += info.nTorsions;
688
689	<
1080	<	// send the arrays off to the forceField for init.
689	>	// check for the temperature set flag
690
691	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
692	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1084	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1085	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
691	>	if (globals->haveTempSet())
692	>	info[i].setTemp = globals->getTempSet();
693
694	+	// get some of the tricky things that may still be in the globals
695
696	<	the_molecules[i].initialize( info );
696	>	double boxVector[3];
697	>	if (globals->haveBox()){
698	>	boxVector[0] = globals->getBox();
699	>	boxVector[1] = globals->getBox();
700	>	boxVector[2] = globals->getBox();
701
702	+	info[i].setBox(boxVector);
703	+	}
704	+	else if (globals->haveDensity()){
705	+	double vol;
706	+	vol = (double) tot_nmol / globals->getDensity();
707	+	boxVector[0] = pow(vol, (1.0 / 3.0));
708	+	boxVector[1] = boxVector[0];
709	+	boxVector[2] = boxVector[0];
710
711	<	atomOffset += info.nAtoms;
712	<	delete[] theBonds;
713	<	delete[] theBends;
714	<	delete[] theTorsions;
711	>	info[i].setBox(boxVector);
712	>	}
713	>	else{
714	>	if (!globals->haveBoxX()){
715	>	sprintf(painCave.errMsg,
716	>	"SimSetup error, no periodic BoxX size given.\n");
717	>	painCave.isFatal = 1;
718	>	simError();
719	>	}
720	>	boxVector[0] = globals->getBoxX();
721	>
722	>	if (!globals->haveBoxY()){
723	>	sprintf(painCave.errMsg,
724	>	"SimSetup error, no periodic BoxY size given.\n");
725	>	painCave.isFatal = 1;
726	>	simError();
727	>	}
728	>	boxVector[1] = globals->getBoxY();
729	>
730	>	if (!globals->haveBoxZ()){
731	>	sprintf(painCave.errMsg,
732	>	"SimSetup error, no periodic BoxZ size given.\n");
733	>	painCave.isFatal = 1;
734	>	simError();
735	>	}
736	>	boxVector[2] = globals->getBoxZ();
737	>
738	>	info[i].setBox(boxVector);
739	>	}
740		}
741
742	+	//setup seed for random number generator
743	+	int seedValue;
744	+
745	+	if (globals->haveSeed()){
746	+	seedValue = globals->getSeed();
747	+
748	+	if(seedValue / 1E9 == 0){
749	+	sprintf(painCave.errMsg,
750	+	"Seed for sprng library should contain at least 9 digits\n"
751	+	"OOPSE will generate a seed for user\n");
752	+	painCave.isFatal = 0;
753	+	simError();
754	+
755	+	//using seed generated by system instead of invalid seed set by user
756	+	#ifndef IS_MPI
757	+	seedValue = make_sprng_seed();
758	+	#else
759	+	if (worldRank == 0){
760	+	seedValue = make_sprng_seed();
761	+	}
762	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
763	+	#endif
764	+	}
765	+	}//end of if branch of globals->haveSeed()
766	+	else{
767	+
768	+	#ifndef IS_MPI
769	+	seedValue = make_sprng_seed();
770	+	#else
771	+	if (worldRank == 0){
772	+	seedValue = make_sprng_seed();
773	+	}
774	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
775	+	#endif
776	+	}//end of globals->haveSeed()
777	+
778	+	for (int i = 0; i < nInfo; i++){
779	+	info[i].setSeed(seedValue);
780	+	}
781	+
782		#ifdef IS_MPI
783	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
783	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
784		MPIcheckPoint();
785		#endif // is_mpi
786	+	}
787
1102	–	// clean up the forcefield
1103	–	the_ff->calcRcut();
1104	–	the_ff->cleanMe();
788
789	<	}
789	>	void SimSetup::finalInfoCheck(void){
790	>	int index;
791	>	int usesDipoles;
792	>	int i;
793
794	<	void SimSetup::initFromBass( void ){
794	>	for (i = 0; i < nInfo; i++){
795	>	// check electrostatic parameters
796
797	<	int i, j, k;
798	<	int n_cells;
799	<	double cellx, celly, cellz;
800	<	double temp1, temp2, temp3;
801	<	int n_per_extra;
802	<	int n_extra;
1116	<	int have_extra, done;
797	>	index = 0;
798	>	usesDipoles = 0;
799	>	while ((index < info[i].n_atoms) && !usesDipoles){
800	>	usesDipoles = (info[i].atoms[index])->hasDipole();
801	>	index++;
802	>	}
803
804	<	temp1 = (double)tot_nmol / 4.0;
805	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
806	<	temp3 = ceil( temp2 );
804	>	#ifdef IS_MPI
805	>	int myUse = usesDipoles;
806	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>	#endif //is_mpi
808
809	<	have_extra =0;
1123	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1124	<	have_extra =1;
809	>	double theEcr, theEst;
810
811	<	n_cells = (int)temp3 - 1;
812	<	cellx = simnfo->boxLx / temp3;
1128	<	celly = simnfo->boxLy / temp3;
1129	<	cellz = simnfo->boxLz / temp3;
1130	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1131	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1132	<	n_per_extra = (int)ceil( temp1 );
811	>	if (globals->getUseRF()){
812	>	info[i].useReactionField = 1;
813
814	<	if( n_per_extra > 4){
815	<	sprintf( painCave.errMsg,
816	<	"SimSetup error. There has been an error in constructing"
817	<	" the non-complete lattice.\n" );
818	<	painCave.isFatal = 1;
819	<	simError();
814	>	if (!globals->haveECR()){
815	>	sprintf(painCave.errMsg,
816	>	"SimSetup Warning: using default value of 1/2 the smallest "
817	>	"box length for the electrostaticCutoffRadius.\n"
818	>	"I hope you have a very fast processor!\n");
819	>	painCave.isFatal = 0;
820	>	simError();
821	>	double smallest;
822	>	smallest = info[i].boxL[0];
823	>	if (info[i].boxL[1] <= smallest)
824	>	smallest = info[i].boxL[1];
825	>	if (info[i].boxL[2] <= smallest)
826	>	smallest = info[i].boxL[2];
827	>	theEcr = 0.5 * smallest;
828	>	}
829	>	else{
830	>	theEcr = globals->getECR();
831	>	}
832	>
833	>	if (!globals->haveEST()){
834	>	sprintf(painCave.errMsg,
835	>	"SimSetup Warning: using default value of 0.05 * the "
836	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
837	>	painCave.isFatal = 0;
838	>	simError();
839	>	theEst = 0.05 * theEcr;
840	>	}
841	>	else{
842	>	theEst = globals->getEST();
843	>	}
844	>
845	>	info[i].setEcr(theEcr, theEst);
846	>
847	>	if (!globals->haveDielectric()){
848	>	sprintf(painCave.errMsg,
849	>	"SimSetup Error: You are trying to use Reaction Field without"
850	>	"setting a dielectric constant!\n");
851	>	painCave.isFatal = 1;
852	>	simError();
853	>	}
854	>	info[i].dielectric = globals->getDielectric();
855		}
856	+	else{
857	+	if (usesDipoles){
858	+	if (!globals->haveECR()){
859	+	sprintf(painCave.errMsg,
860	+	"SimSetup Warning: using default value of 1/2 the smallest "
861	+	"box length for the electrostaticCutoffRadius.\n"
862	+	"I hope you have a very fast processor!\n");
863	+	painCave.isFatal = 0;
864	+	simError();
865	+	double smallest;
866	+	smallest = info[i].boxL[0];
867	+	if (info[i].boxL[1] <= smallest)
868	+	smallest = info[i].boxL[1];
869	+	if (info[i].boxL[2] <= smallest)
870	+	smallest = info[i].boxL[2];
871	+	theEcr = 0.5 * smallest;
872	+	}
873	+	else{
874	+	theEcr = globals->getECR();
875	+	}
876	+
877	+	if (!globals->haveEST()){
878	+	sprintf(painCave.errMsg,
879	+	"SimSetup Warning: using default value of 0.05 * the "
880	+	"electrostaticCutoffRadius for the "
881	+	"electrostaticSkinThickness\n");
882	+	painCave.isFatal = 0;
883	+	simError();
884	+	theEst = 0.05 * theEcr;
885	+	}
886	+	else{
887	+	theEst = globals->getEST();
888	+	}
889	+
890	+	info[i].setEcr(theEcr, theEst);
891	+	}
892	+	}
893		}
1142	–	else{
1143	–	n_cells = (int)temp3;
1144	–	cellx = simnfo->boxLx / temp3;
1145	–	celly = simnfo->boxLy / temp3;
1146	–	cellz = simnfo->boxLz / temp3;
1147	–	}
894
895	<	current_mol = 0;
896	<	current_comp_mol = 0;
897	<	current_comp = 0;
898	<	current_atom_ndx = 0;
895	>	#ifdef IS_MPI
896	>	strcpy(checkPointMsg, "post processing checks out");
897	>	MPIcheckPoint();
898	>	#endif // is_mpi
899	>	}
900
901	<	for( i=0; i < n_cells ; i++ ){
902	<	for( j=0; j < n_cells; j++ ){
1156	<	for( k=0; k < n_cells; k++ ){
901	>	void SimSetup::initSystemCoords(void){
902	>	int i;
903
904	<	makeElement( i * cellx,
1159	<	j * celly,
1160	<	k * cellz );
904	>	char* inName;
905
906	<	makeElement( i * cellx + 0.5 * cellx,
1163	<	j * celly + 0.5 * celly,
1164	<	k * cellz );
906	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
907
908	<	makeElement( i * cellx,
909	<	j * celly + 0.5 * celly,
1168	<	k * cellz + 0.5 * cellz );
908	>	for (i = 0; i < info[0].n_atoms; i++)
909	>	info[0].atoms[i]->setCoords();
910
911	<	makeElement( i * cellx + 0.5 * cellx,
912	<	j * celly,
913	<	k * cellz + 0.5 * cellz );
914	<	}
911	>	if (globals->haveInitialConfig()){
912	>	InitializeFromFile* fileInit;
913	>	#ifdef IS_MPI // is_mpi
914	>	if (worldRank == 0){
915	>	#endif //is_mpi
916	>	inName = globals->getInitialConfig();
917	>	double* tempDouble = new double[1000000];
918	>	fileInit = new InitializeFromFile(inName);
919	>	#ifdef IS_MPI
920		}
921	+	else
922	+	fileInit = new InitializeFromFile(NULL);
923	+	#endif
924	+	fileInit->readInit(info); // default velocities on
925	+
926	+	delete fileInit;
927		}
928	+	else{
929	+	#ifdef IS_MPI
930
931	<	if( have_extra ){
1178	<	done = 0;
931	>	// no init from bass
932
933	<	int start_ndx;
934	<	for( i=0; i < (n_cells+1) && !done; i++ ){
935	<	for( j=0; j < (n_cells+1) && !done; j++ ){
933	>	sprintf(painCave.errMsg,
934	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
935	>	painCave.isFatal;
936	>	simError();
937
938	<	if( i < n_cells ){
938	>	#else
939
940	<	if( j < n_cells ){
1187	<	start_ndx = n_cells;
1188	<	}
1189	<	else start_ndx = 0;
1190	<	}
1191	<	else start_ndx = 0;
940	>	initFromBass();
941
1193	–	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
942
943	<	makeElement( i * cellx,
944	<	j * celly,
1197	<	k * cellz );
1198	<	done = ( current_mol >= tot_nmol );
943	>	#endif
944	>	}
945
946	<	if( !done && n_per_extra > 1 ){
947	<	makeElement( i * cellx + 0.5 * cellx,
948	<	j * celly + 0.5 * celly,
949	<	k * cellz );
950	<	done = ( current_mol >= tot_nmol );
1205	<	}
946	>	#ifdef IS_MPI
947	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
948	>	MPIcheckPoint();
949	>	#endif // is_mpi
950	>	}
951
952	<	if( !done && n_per_extra > 2){
953	<	makeElement( i * cellx,
954	<	j * celly + 0.5 * celly,
955	<	k * cellz + 0.5 * cellz );
956	<	done = ( current_mol >= tot_nmol );
957	<	}
952	>
953	>	void SimSetup::makeOutNames(void){
954	>	int k;
955	>
956	>
957	>	for (k = 0; k < nInfo; k++){
958	>	#ifdef IS_MPI
959	>	if (worldRank == 0){
960	>	#endif // is_mpi
961	>
962	>	if (globals->haveFinalConfig()){
963	>	strcpy(info[k].finalName, globals->getFinalConfig());
964	>	}
965	>	else{
966	>	strcpy(info[k].finalName, inFileName);
967	>	char* endTest;
968	>	int nameLength = strlen(info[k].finalName);
969	>	endTest = &(info[k].finalName[nameLength - 5]);
970	>	if (!strcmp(endTest, ".bass")){
971	>	strcpy(endTest, ".eor");
972	>	}
973	>	else if (!strcmp(endTest, ".BASS")){
974	>	strcpy(endTest, ".eor");
975	>	}
976	>	else{
977	>	endTest = &(info[k].finalName[nameLength - 4]);
978	>	if (!strcmp(endTest, ".bss")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".mdl")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	strcat(info[k].finalName, ".eor");
986	>	}
987	>	}
988	>	}
989
990	<	if( !done && n_per_extra > 3){
991	<	makeElement( i * cellx + 0.5 * cellx,
992	<	j * celly,
993	<	k * cellz + 0.5 * cellz );
994	<	done = ( current_mol >= tot_nmol );
995	<	}
996	<	}
990	>	// make the sample and status out names
991	>
992	>	strcpy(info[k].sampleName, inFileName);
993	>	char* endTest;
994	>	int nameLength = strlen(info[k].sampleName);
995	>	endTest = &(info[k].sampleName[nameLength - 5]);
996	>	if (!strcmp(endTest, ".bass")){
997	>	strcpy(endTest, ".dump");
998		}
999	+	else if (!strcmp(endTest, ".BASS")){
1000	+	strcpy(endTest, ".dump");
1001	+	}
1002	+	else{
1003	+	endTest = &(info[k].sampleName[nameLength - 4]);
1004	+	if (!strcmp(endTest, ".bss")){
1005	+	strcpy(endTest, ".dump");
1006	+	}
1007	+	else if (!strcmp(endTest, ".mdl")){
1008	+	strcpy(endTest, ".dump");
1009	+	}
1010	+	else{
1011	+	strcat(info[k].sampleName, ".dump");
1012	+	}
1013	+	}
1014	+
1015	+	strcpy(info[k].statusName, inFileName);
1016	+	nameLength = strlen(info[k].statusName);
1017	+	endTest = &(info[k].statusName[nameLength - 5]);
1018	+	if (!strcmp(endTest, ".bass")){
1019	+	strcpy(endTest, ".stat");
1020	+	}
1021	+	else if (!strcmp(endTest, ".BASS")){
1022	+	strcpy(endTest, ".stat");
1023	+	}
1024	+	else{
1025	+	endTest = &(info[k].statusName[nameLength - 4]);
1026	+	if (!strcmp(endTest, ".bss")){
1027	+	strcpy(endTest, ".stat");
1028	+	}
1029	+	else if (!strcmp(endTest, ".mdl")){
1030	+	strcpy(endTest, ".stat");
1031	+	}
1032	+	else{
1033	+	strcat(info[k].statusName, ".stat");
1034	+	}
1035	+	}
1036	+
1037	+	#ifdef IS_MPI
1038	+
1039		}
1040	+	#endif // is_mpi
1041		}
1042	+	}
1043
1044
1045	<	for( i=0; i<simnfo->n_atoms; i++ ){
1046	<	simnfo->atoms[i]->set_vx( 0.0 );
1047	<	simnfo->atoms[i]->set_vy( 0.0 );
1048	<	simnfo->atoms[i]->set_vz( 0.0 );
1045	>	void SimSetup::sysObjectsCreation(void){
1046	>	int i, k;
1047	>
1048	>	// create the forceField
1049	>
1050	>	createFF();
1051	>
1052	>	// extract componentList
1053	>
1054	>	compList();
1055	>
1056	>	// calc the number of atoms, bond, bends, and torsions
1057	>
1058	>	calcSysValues();
1059	>
1060	>	#ifdef IS_MPI
1061	>	// divide the molecules among the processors
1062	>
1063	>	mpiMolDivide();
1064	>	#endif //is_mpi
1065	>
1066	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1067	>
1068	>	makeSysArrays();
1069	>
1070	>	// make and initialize the molecules (all but atomic coordinates)
1071	>
1072	>	makeMolecules();
1073	>
1074	>	for (k = 0; k < nInfo; k++){
1075	>	info[k].identArray = new int[info[k].n_atoms];
1076	>	for (i = 0; i < info[k].n_atoms; i++){
1077	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1078	>	}
1079		}
1080		}
1081
1233	–	void SimSetup::makeElement( double x, double y, double z ){
1082
1083	<	int k;
1084	<	AtomStamp* current_atom;
1085	<	DirectionalAtom* dAtom;
1086	<	double rotMat[3][3];
1083	>	void SimSetup::createFF(void){
1084	>	switch (ffCase){
1085	>	case FF_DUFF:
1086	>	the_ff = new DUFF();
1087	>	break;
1088
1089	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1089	>	case FF_LJ:
1090	>	the_ff = new LJFF();
1091	>	break;
1092
1093	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1094	<	if( !current_atom->havePosition() ){
1095	<	sprintf( painCave.errMsg,
1096	<	"SimSetup:initFromBass error.\n"
1097	<	"\tComponent %s, atom %s does not have a position specified.\n"
1098	<	"\tThe initialization routine is unable to give a start"
1099	<	" position.\n",
1249	<	comp_stamps[current_comp]->getID(),
1250	<	current_atom->getType() );
1093	>	case FF_EAM:
1094	>	the_ff = new EAM_FF();
1095	>	break;
1096	>
1097	>	default:
1098	>	sprintf(painCave.errMsg,
1099	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1100		painCave.isFatal = 1;
1101		simError();
1102	+	}
1103	+
1104	+	#ifdef IS_MPI
1105	+	strcpy(checkPointMsg, "ForceField creation successful");
1106	+	MPIcheckPoint();
1107	+	#endif // is_mpi
1108	+	}
1109	+
1110	+
1111	+	void SimSetup::compList(void){
1112	+	int i;
1113	+	char* id;
1114	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1115	+	LinkedMolStamp* currentStamp = NULL;
1116	+	comp_stamps = new MoleculeStamp * [n_components];
1117	+
1118	+	// make an array of molecule stamps that match the components used.
1119	+	// also extract the used stamps out into a separate linked list
1120	+
1121	+	for (i = 0; i < nInfo; i++){
1122	+	info[i].nComponents = n_components;
1123	+	info[i].componentsNmol = components_nmol;
1124	+	info[i].compStamps = comp_stamps;
1125	+	info[i].headStamp = headStamp;
1126	+	}
1127	+
1128	+
1129	+	for (i = 0; i < n_components; i++){
1130	+	id = the_components[i]->getType();
1131	+	comp_stamps[i] = NULL;
1132	+
1133	+	// check to make sure the component isn't already in the list
1134	+
1135	+	comp_stamps[i] = headStamp->match(id);
1136	+	if (comp_stamps[i] == NULL){
1137	+	// extract the component from the list;
1138	+
1139	+	currentStamp = stamps->extractMolStamp(id);
1140	+	if (currentStamp == NULL){
1141	+	sprintf(painCave.errMsg,
1142	+	"SimSetup error: Component \"%s\" was not found in the "
1143	+	"list of declared molecules\n",
1144	+	id);
1145	+	painCave.isFatal = 1;
1146	+	simError();
1147	+	}
1148	+
1149	+	headStamp->add(currentStamp);
1150	+	comp_stamps[i] = headStamp->match(id);
1151		}
1152	+	}
1153
1154	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1155	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1156	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1154	>	#ifdef IS_MPI
1155	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1156	>	MPIcheckPoint();
1157	>	#endif // is_mpi
1158	>	}
1159
1160	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1160	>	void SimSetup::calcSysValues(void){
1161	>	int i, j, k;
1162
1163	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1163	>	int* molMembershipArray;
1164
1165	<	rotMat[0][0] = 1.0;
1166	<	rotMat[0][1] = 0.0;
1167	<	rotMat[0][2] = 0.0;
1165	>	tot_atoms = 0;
1166	>	tot_bonds = 0;
1167	>	tot_bends = 0;
1168	>	tot_torsions = 0;
1169	>	for (i = 0; i < n_components; i++){
1170	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1172	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1173	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174	>	}
1175
1176	<	rotMat[1][0] = 0.0;
1177	<	rotMat[1][1] = 1.0;
1269	<	rotMat[1][2] = 0.0;
1176	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	>	molMembershipArray = new int[tot_atoms];
1178
1179	<	rotMat[2][0] = 0.0;
1180	<	rotMat[2][1] = 0.0;
1181	<	rotMat[2][2] = 1.0;
1179	>	for (i = 0; i < nInfo; i++){
1180	>	info[i].n_atoms = tot_atoms;
1181	>	info[i].n_bonds = tot_bonds;
1182	>	info[i].n_bends = tot_bends;
1183	>	info[i].n_torsions = tot_torsions;
1184	>	info[i].n_SRI = tot_SRI;
1185	>	info[i].n_mol = tot_nmol;
1186
1187	<	dAtom->setA( rotMat );
1187	>	info[i].molMembershipArray = molMembershipArray;
1188	>	}
1189	>	}
1190	>
1191	>	#ifdef IS_MPI
1192	>
1193	>	void SimSetup::mpiMolDivide(void){
1194	>	int i, j, k;
1195	>	int localMol, allMol;
1196	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1197	>
1198	>	mpiSim = new mpiSimulation(info);
1199	>
1200	>	globalIndex = mpiSim->divideLabor();
1201	>
1202	>	// set up the local variables
1203	>
1204	>	mol2proc = mpiSim->getMolToProcMap();
1205	>	molCompType = mpiSim->getMolComponentType();
1206	>
1207	>	allMol = 0;
1208	>	localMol = 0;
1209	>	local_atoms = 0;
1210	>	local_bonds = 0;
1211	>	local_bends = 0;
1212	>	local_torsions = 0;
1213	>	globalAtomIndex = 0;
1214	>
1215	>
1216	>	for (i = 0; i < n_components; i++){
1217	>	for (j = 0; j < components_nmol[i]; j++){
1218	>	if (mol2proc[allMol] == worldRank){
1219	>	local_atoms += comp_stamps[i]->getNAtoms();
1220	>	local_bonds += comp_stamps[i]->getNBonds();
1221	>	local_bends += comp_stamps[i]->getNBends();
1222	>	local_torsions += comp_stamps[i]->getNTorsions();
1223	>	localMol++;
1224	>	}
1225	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1226	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1227	>	globalAtomIndex++;
1228	>	}
1229	>
1230	>	allMol++;
1231		}
1232	+	}
1233	+	local_SRI = local_bonds + local_bends + local_torsions;
1234
1235	<	current_atom_ndx++;
1235	>	info[0].n_atoms = mpiSim->getMyNlocal();
1236	>
1237	>	if (local_atoms != info[0].n_atoms){
1238	>	sprintf(painCave.errMsg,
1239	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	>	" localAtom (%d) are not equal.\n",
1241	>	info[0].n_atoms, local_atoms);
1242	>	painCave.isFatal = 1;
1243	>	simError();
1244		}
1245
1246	<	current_mol++;
1247	<	current_comp_mol++;
1246	>	info[0].n_bonds = local_bonds;
1247	>	info[0].n_bends = local_bends;
1248	>	info[0].n_torsions = local_torsions;
1249	>	info[0].n_SRI = local_SRI;
1250	>	info[0].n_mol = localMol;
1251
1252	<	if( current_comp_mol >= components_nmol[current_comp] ){
1252	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1253	>	MPIcheckPoint();
1254	>	}
1255
1256	<	current_comp_mol = 0;
1257	<	current_comp++;
1256	>	#endif // is_mpi
1257	>
1258	>
1259	>	void SimSetup::makeSysArrays(void){
1260	>	int i, j, k, l;
1261	>
1262	>	Atom** the_atoms;
1263	>	Molecule* the_molecules;
1264	>	Exclude** the_excludes;
1265	>
1266	>
1267	>	for (l = 0; l < nInfo; l++){
1268	>	// create the atom and short range interaction arrays
1269	>
1270	>	the_atoms = new Atom * [info[l].n_atoms];
1271	>	the_molecules = new Molecule[info[l].n_mol];
1272	>	int molIndex;
1273	>
1274	>	// initialize the molecule's stampID's
1275	>
1276	>	#ifdef IS_MPI
1277	>
1278	>
1279	>	molIndex = 0;
1280	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1281	>	if (mol2proc[i] == worldRank){
1282	>	the_molecules[molIndex].setStampID(molCompType[i]);
1283	>	the_molecules[molIndex].setMyIndex(molIndex);
1284	>	the_molecules[molIndex].setGlobalIndex(i);
1285	>	molIndex++;
1286	>	}
1287	>	}
1288	>
1289	>	#else // is_mpi
1290	>
1291	>	molIndex = 0;
1292	>	globalAtomIndex = 0;
1293	>	for (i = 0; i < n_components; i++){
1294	>	for (j = 0; j < components_nmol[i]; j++){
1295	>	the_molecules[molIndex].setStampID(i);
1296	>	the_molecules[molIndex].setMyIndex(molIndex);
1297	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1298	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1299	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1300	>	globalAtomIndex++;
1301	>	}
1302	>	molIndex++;
1303	>	}
1304	>	}
1305	>
1306	>
1307	>	#endif // is_mpi
1308	>
1309	>
1310	>	if (info[l].n_SRI){
1311	>	Exclude::createArray(info[l].n_SRI);
1312	>	the_excludes = new Exclude * [info[l].n_SRI];
1313	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1314	>	the_excludes[ex] = new Exclude(ex);
1315	>	}
1316	>	info[l].globalExcludes = new int;
1317	>	info[l].n_exclude = info[l].n_SRI;
1318	>	}
1319	>	else{
1320	>	Exclude::createArray(1);
1321	>	the_excludes = new Exclude * ;
1322	>	the_excludes[0] = new Exclude(0);
1323	>	the_excludes[0]->setPair(0, 0);
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].globalExcludes[0] = 0;
1326	>	info[l].n_exclude = 0;
1327	>	}
1328	>
1329	>	// set the arrays into the SimInfo object
1330	>
1331	>	info[l].atoms = the_atoms;
1332	>	info[l].molecules = the_molecules;
1333	>	info[l].nGlobalExcludes = 0;
1334	>	info[l].excludes = the_excludes;
1335	>
1336	>	the_ff->setSimInfo(info);
1337		}
1338		}
1339	+
1340	+	void SimSetup::makeIntegrator(void){
1341	+	int k;
1342	+
1343	+	NVT<RealIntegrator>* myNVT = NULL;
1344	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1345	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1346	+
1347	+	for (k = 0; k < nInfo; k++){
1348	+	switch (ensembleCase){
1349	+	case NVE_ENS:
1350	+	if (globals->haveZconstraints()){
1351	+	setupZConstraint(info[k]);
1352	+	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1353	+	}
1354	+	else
1355	+	new NVE<RealIntegrator>(&(info[k]), the_ff);
1356	+	break;
1357	+
1358	+	case NVT_ENS:
1359	+	if (globals->haveZconstraints()){
1360	+	setupZConstraint(info[k]);
1361	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1362	+	}
1363	+	else
1364	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1365	+
1366	+	myNVT->setTargetTemp(globals->getTargetTemp());
1367	+
1368	+	if (globals->haveTauThermostat())
1369	+	myNVT->setTauThermostat(globals->getTauThermostat());
1370	+	else{
1371	+	sprintf(painCave.errMsg,
1372	+	"SimSetup error: If you use the NVT\n"
1373	+	"    ensemble, you must set tauThermostat.\n");
1374	+	painCave.isFatal = 1;
1375	+	simError();
1376	+	}
1377	+	break;
1378	+
1379	+	case NPTi_ENS:
1380	+	if (globals->haveZconstraints()){
1381	+	setupZConstraint(info[k]);
1382	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1383	+	}
1384	+	else
1385	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1386	+
1387	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1388	+
1389	+	if (globals->haveTargetPressure())
1390	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1391	+	else{
1392	+	sprintf(painCave.errMsg,
1393	+	"SimSetup error: If you use a constant pressure\n"
1394	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1395	+	painCave.isFatal = 1;
1396	+	simError();
1397	+	}
1398	+
1399	+	if (globals->haveTauThermostat())
1400	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1401	+	else{
1402	+	sprintf(painCave.errMsg,
1403	+	"SimSetup error: If you use an NPT\n"
1404	+	"    ensemble, you must set tauThermostat.\n");
1405	+	painCave.isFatal = 1;
1406	+	simError();
1407	+	}
1408	+
1409	+	if (globals->haveTauBarostat())
1410	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1411	+	else{
1412	+	sprintf(painCave.errMsg,
1413	+	"SimSetup error: If you use an NPT\n"
1414	+	"    ensemble, you must set tauBarostat.\n");
1415	+	painCave.isFatal = 1;
1416	+	simError();
1417	+	}
1418	+	break;
1419	+
1420	+	case NPTf_ENS:
1421	+	if (globals->haveZconstraints()){
1422	+	setupZConstraint(info[k]);
1423	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1424	+	}
1425	+	else
1426	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1427	+
1428	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1429	+
1430	+	if (globals->haveTargetPressure())
1431	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1432	+	else{
1433	+	sprintf(painCave.errMsg,
1434	+	"SimSetup error: If you use a constant pressure\n"
1435	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1436	+	painCave.isFatal = 1;
1437	+	simError();
1438	+	}
1439	+
1440	+	if (globals->haveTauThermostat())
1441	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1442	+	else{
1443	+	sprintf(painCave.errMsg,
1444	+	"SimSetup error: If you use an NPT\n"
1445	+	"    ensemble, you must set tauThermostat.\n");
1446	+	painCave.isFatal = 1;
1447	+	simError();
1448	+	}
1449	+
1450	+	if (globals->haveTauBarostat())
1451	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1452	+	else{
1453	+	sprintf(painCave.errMsg,
1454	+	"SimSetup error: If you use an NPT\n"
1455	+	"    ensemble, you must set tauBarostat.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+	break;
1460	+
1461	+	default:
1462	+	sprintf(painCave.errMsg,
1463	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1464	+	painCave.isFatal = 1;
1465	+	simError();
1466	+	}
1467	+	}
1468	+	}
1469	+
1470	+	void SimSetup::initFortran(void){
1471	+	info[0].refreshSim();
1472	+
1473	+	if (!strcmp(info[0].mixingRule, "standard")){
1474	+	the_ff->initForceField(LB_MIXING_RULE);
1475	+	}
1476	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1477	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1478	+	}
1479	+	else{
1480	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1481	+	info[0].mixingRule);
1482	+	painCave.isFatal = 1;
1483	+	simError();
1484	+	}
1485	+
1486	+
1487	+	#ifdef IS_MPI
1488	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1489	+	MPIcheckPoint();
1490	+	#endif // is_mpi
1491	+	}
1492	+
1493	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1494	+	int nZConstraints;
1495	+	ZconStamp** zconStamp;
1496	+
1497	+	if (globals->haveZconstraintTime()){
1498	+	//add sample time of z-constraint  into SimInfo's property list
1499	+	DoubleData* zconsTimeProp = new DoubleData();
1500	+	zconsTimeProp->setID(ZCONSTIME_ID);
1501	+	zconsTimeProp->setData(globals->getZconsTime());
1502	+	theInfo.addProperty(zconsTimeProp);
1503	+	}
1504	+	else{
1505	+	sprintf(painCave.errMsg,
1506	+	"ZConstraint error: If you use an ZConstraint\n"
1507	+	" , you must set sample time.\n");
1508	+	painCave.isFatal = 1;
1509	+	simError();
1510	+	}
1511	+
1512	+	//push zconsTol into siminfo, if user does not specify
1513	+	//value for zconsTol, a default value will be used
1514	+	DoubleData* zconsTol = new DoubleData();
1515	+	zconsTol->setID(ZCONSTOL_ID);
1516	+	if (globals->haveZconsTol()){
1517	+	zconsTol->setData(globals->getZconsTol());
1518	+	}
1519	+	else{
1520	+	double defaultZConsTol = 0.01;
1521	+	sprintf(painCave.errMsg,
1522	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1523	+	" , default value %f is used.\n",
1524	+	defaultZConsTol);
1525	+	painCave.isFatal = 0;
1526	+	simError();
1527	+
1528	+	zconsTol->setData(defaultZConsTol);
1529	+	}
1530	+	theInfo.addProperty(zconsTol);
1531	+
1532	+	//set Force Subtraction Policy
1533	+	StringData* zconsForcePolicy = new StringData();
1534	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1535	+
1536	+	if (globals->haveZconsForcePolicy()){
1537	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1538	+	}
1539	+	else{
1540	+	sprintf(painCave.errMsg,
1541	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1542	+	"PolicyByMass is used\n");
1543	+	painCave.isFatal = 0;
1544	+	simError();
1545	+	zconsForcePolicy->setData("BYMASS");
1546	+	}
1547	+
1548	+	theInfo.addProperty(zconsForcePolicy);
1549	+
1550	+	//Determine the name of ouput file and add it into SimInfo's property list
1551	+	//Be careful, do not use inFileName, since it is a pointer which
1552	+	//point to a string at master node, and slave nodes do not contain that string
1553	+
1554	+	string zconsOutput(theInfo.finalName);
1555	+
1556	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1557	+
1558	+	StringData* zconsFilename = new StringData();
1559	+	zconsFilename->setID(ZCONSFILENAME_ID);
1560	+	zconsFilename->setData(zconsOutput);
1561	+
1562	+	theInfo.addProperty(zconsFilename);
1563	+
1564	+	//setup index, pos and other parameters of z-constraint molecules
1565	+	nZConstraints = globals->getNzConstraints();
1566	+	theInfo.nZconstraints = nZConstraints;
1567	+
1568	+	zconStamp = globals->getZconStamp();
1569	+	ZConsParaItem tempParaItem;
1570	+
1571	+	ZConsParaData* zconsParaData = new ZConsParaData();
1572	+	zconsParaData->setID(ZCONSPARADATA_ID);
1573	+
1574	+	for (int i = 0; i < nZConstraints; i++){
1575	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1576	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1577	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1578	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1579	+
1580	+	zconsParaData->addItem(tempParaItem);
1581	+	}
1582	+
1583	+	//check the uniqueness of index
1584	+	if(!zconsParaData->isIndexUnique()){
1585	+	sprintf(painCave.errMsg,
1586	+	"ZConstraint Error: molIndex is not unique\n");
1587	+	painCave.isFatal = 1;
1588	+	simError();
1589	+	}
1590	+
1591	+	//sort the parameters by index of molecules
1592	+	zconsParaData->sortByIndex();
1593	+
1594	+	//push data into siminfo, therefore, we can retrieve later
1595	+	theInfo.addProperty(zconsParaData);
1596	+	}

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