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root/group/branches/new-templateless/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.
branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 850 by mmeineke, Mon Nov 3 22:07:17 2003 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
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	>	#define NPTxyz_ENS     4
26
27	+
28		#define FF_DUFF 0
29		#define FF_LJ   1
30	+	#define FF_EAM  2
31
32	+	using namespace std;
33
34		SimSetup::SimSetup(){
35	+
36	+	initSuspend = false;
37	+	isInfoArray = 0;
38	+	nInfo = 1;
39	+
40		stamps = new MakeStamps();
41		globals = new Globals();
42	<
42	>
43	>
44		#ifdef IS_MPI
45	<	strcpy( checkPointMsg, "SimSetup creation successful" );
45	>	strcpy(checkPointMsg, "SimSetup creation successful");
46		MPIcheckPoint();
47		#endif // IS_MPI
48		}
#	Line 38 | Line 52 | SimSetup::~SimSetup(){
52		delete globals;
53		}
54
55	<	void SimSetup::parseFile( char* fileName ){
55	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
56	>	info = the_info;
57	>	nInfo = theNinfo;
58	>	isInfoArray = 1;
59	>	initSuspend = true;
60	>	}
61
62	+
63	+	void SimSetup::parseFile(char* fileName){
64		#ifdef IS_MPI
65	<	if( worldRank == 0 ){
65	>	if (worldRank == 0){
66		#endif // is_mpi
67	<
67	>
68		inFileName = fileName;
69	<	set_interface_stamps( stamps, globals );
70	<
69	>	set_interface_stamps(stamps, globals);
70	>
71		#ifdef IS_MPI
72		mpiEventInit();
73		#endif
74
75	<	yacc_BASS( fileName );
75	>	yacc_BASS(fileName);
76
77		#ifdef IS_MPI
78		throwMPIEvent(NULL);
79		}
80	<	else receiveParse();
80	>	else{
81	>	receiveParse();
82	>	}
83		#endif
84
85		}
86
87		#ifdef IS_MPI
88		void SimSetup::receiveParse(void){
89	<
90	<	set_interface_stamps( stamps, globals );
91	<	mpiEventInit();
92	<	MPIcheckPoint();
70	<	mpiEventLoop();
71	<
89	>	set_interface_stamps(stamps, globals);
90	>	mpiEventInit();
91	>	MPIcheckPoint();
92	>	mpiEventLoop();
93		}
94
95		#endif // is_mpi
96
97	<	void SimSetup::createSim( void ){
97	>	void SimSetup::createSim(void){
98
99	<	MakeStamps *the_stamps;
79	<	Globals* the_globals;
80	<	int i, j, k, globalAtomIndex;
81	<
82	<	int ensembleCase;
83	<	int ffCase;
84	<
85	<	ensembleCase = -1;
86	<	ffCase = -1;
99	>	// gather all of the information from the Bass file
100
101	<	// get the stamps and globals;
89	<	the_stamps = stamps;
90	<	the_globals = globals;
101	>	gatherInfo();
102
103	<	// 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();
103	>	// creation of complex system objects
104
105	<	// 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() );
105	>	sysObjectsCreation();
106
107	<	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	<	}
107	>	// initialize the system coordinates
108
109	<	// get the ensemble:
110	<	strcpy( ensemble, the_globals->getEnsemble() );
109	>	if ( !initSuspend ){
110	>	initSystemCoords();
111
112	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
113	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
116	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
117	<	ensembleCase = NPTi_ENS;
118	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
119	<	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;
112	>	if( !(globals->getUseInitTime()) )
113	>	info[0].currentTime = 0.0;
114		}
129	–	strcpy( simnfo->ensemble, ensemble );
115
116	+	// check on the post processing info
117
118	<	//   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	<	//     }
118	>	finalInfoCheck();
119
120	<	//     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	<	//     }
120	>	// make the output filenames
121
122	<	//     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	<	//     }
122	>	makeOutNames();
123
124	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
171	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
172	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
124	>	// make the integrator
125
126	<	//     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	<	//     }
126	>	makeIntegrator();
127
128	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
129	<	simnfo->usePBC = the_globals->getPBC();
130	<
190	<	int usesDipoles = 0;
191	<	switch( ffCase ){
128	>	#ifdef IS_MPI
129	>	mpiSim->mpiRefresh();
130	>	#endif
131
132	<	case FF_DUFF:
194	<	the_ff = new DUFF();
195	<	usesDipoles = 1;
196	<	break;
132	>	// initialize the Fortran
133
134	<	case FF_LJ:
135	<	the_ff = new LJFF();
200	<	break;
134	>	initFortran();
135	>	}
136
202	–	default:
203	–	sprintf( painCave.errMsg,
204	–	"SimSetup Error. Unrecognized force field in case statement.\n");
205	–	painCave.isFatal = 1;
206	–	simError();
207	–	}
137
138	<	#ifdef IS_MPI
139	<	strcpy( checkPointMsg, "ForceField creation successful" );
140	<	MPIcheckPoint();
141	<	#endif // is_mpi
138	>	void SimSetup::makeMolecules(void){
139	>	int k;
140	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
141	>	molInit molInfo;
142	>	DirectionalAtom* dAtom;
143	>	LinkedAssign* extras;
144	>	LinkedAssign* current_extra;
145	>	AtomStamp* currentAtom;
146	>	BondStamp* currentBond;
147	>	BendStamp* currentBend;
148	>	TorsionStamp* currentTorsion;
149
150	<	// get the components and calculate the tot_nMol and indvidual n_mol
151	<	the_components = the_globals->getComponents();
152	<	components_nmol = new int[n_components];
217	<	comp_stamps = new MoleculeStamp*[n_components];
150	>	bond_pair* theBonds;
151	>	bend_set* theBends;
152	>	torsion_set* theTorsions;
153
219	–	if( !the_globals->haveNMol() ){
220	–	// we don't have the total number of molecules, so we assume it is
221	–	// given in each component
154
155	<	tot_nmol = 0;
224	<	for( i=0; i<n_components; i++ ){
155	>	//init the forceField paramters
156
157	<	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	<	}
157	>	the_ff->readParams();
158
235	–	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	–	}
159
160	<	#ifdef IS_MPI
265	<	strcpy( checkPointMsg, "Have the number of components" );
266	<	MPIcheckPoint();
267	<	#endif // is_mpi
160	>	// init the atoms
161
162	<	// make an array of molecule stamps that match the components used.
270	<	// also extract the used stamps out into a separate linked list
162	>	double ux, uy, uz, u, uSqr;
163
164	<	simnfo->nComponents = n_components;
165	<	simnfo->componentsNmol = components_nmol;
274	<	simnfo->compStamps = comp_stamps;
275	<	simnfo->headStamp = new LinkedMolStamp();
276	<
277	<	char* id;
278	<	LinkedMolStamp* headStamp = simnfo->headStamp;
279	<	LinkedMolStamp* currentStamp = NULL;
280	<	for( i=0; i<n_components; i++ ){
164	>	for (k = 0; k < nInfo; k++){
165	>	the_ff->setSimInfo(&(info[k]));
166
167	<	id = the_components[i]->getType();
168	<	comp_stamps[i] = NULL;
169	<
170	<	// check to make sure the component isn't already in the list
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for (i = 0; i < info[k].n_mol; i++){
170	>	stampID = info[k].molecules[i].getStampID();
171	>
172	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
173	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
174	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
175	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
177
178	<	comp_stamps[i] = headStamp->match( id );
179	<	if( comp_stamps[i] == NULL ){
180	<
181	<	// extract the component from the list;
182	<
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	<	}
178	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
181	>	molInfo.myBends = new Bend * [molInfo.nBends];
182	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
183
184	<	#ifdef IS_MPI
185	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
186	<	MPIcheckPoint();
310	<	#endif // is_mpi
311	<
184	>	theBonds = new bond_pair[molInfo.nBonds];
185	>	theBends = new bend_set[molInfo.nBends];
186	>	theTorsions = new torsion_set[molInfo.nTorsions];
187
188	+	// make the Atoms
189
190	+	for (j = 0; j < molInfo.nAtoms; j++){
191	+	currentAtom = comp_stamps[stampID]->getAtom(j);
192	+	if (currentAtom->haveOrientation()){
193	+	dAtom = new DirectionalAtom((j + atomOffset),
194	+	info[k].getConfiguration());
195	+	info[k].n_oriented++;
196	+	molInfo.myAtoms[j] = dAtom;
197
198	<	// caclulate the number of atoms, bonds, bends and torsions
198	>	ux = currentAtom->getOrntX();
199	>	uy = currentAtom->getOrntY();
200	>	uz = currentAtom->getOrntZ();
201
202	<	tot_atoms = 0;
318	<	tot_bonds = 0;
319	<	tot_bends = 0;
320	<	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	<	}
202	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
203
204	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
204	>	u = sqrt(uSqr);
205	>	ux = ux / u;
206	>	uy = uy / u;
207	>	uz = uz / u;
208
209	<	simnfo->n_atoms = tot_atoms;
210	<	simnfo->n_bonds = tot_bonds;
211	<	simnfo->n_bends = tot_bends;
212	<	simnfo->n_torsions = tot_torsions;
213	<	simnfo->n_SRI = tot_SRI;
214	<	simnfo->n_mol = tot_nmol;
215	<
216	<	simnfo->molMembershipArray = new int[tot_atoms];
209	>	dAtom->setSUx(ux);
210	>	dAtom->setSUy(uy);
211	>	dAtom->setSUz(uz);
212	>	}
213	>	else{
214	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
215	>	info[k].getConfiguration());
216	>	}
217	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
218
219		#ifdef IS_MPI
220
221	<	// divide the molecules among processors here.
343	<
344	<	mpiSim = new mpiSimulation( simnfo );
345	<
346	<	globalIndex = mpiSim->divideLabor();
221	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
222
223	<	// set up the local variables
224	<
350	<	int localMol, allMol;
351	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
223	>	#endif // is_mpi
224	>	}
225
226	<	int* mol2proc = mpiSim->getMolToProcMap();
227	<	int* molCompType = mpiSim->getMolComponentType();
228	<
229	<	allMol = 0;
230	<	localMol = 0;
358	<	local_atoms = 0;
359	<	local_bonds = 0;
360	<	local_bends = 0;
361	<	local_torsions = 0;
362	<	globalAtomIndex = 0;
226	>	// make the bonds
227	>	for (j = 0; j < molInfo.nBonds; j++){
228	>	currentBond = comp_stamps[stampID]->getBond(j);
229	>	theBonds[j].a = currentBond->getA() + atomOffset;
230	>	theBonds[j].b = currentBond->getB() + atomOffset;
231
232	+	exI = theBonds[j].a;
233	+	exJ = theBonds[j].b;
234
235	<	for( i=0; i<n_components; i++ ){
235	>	// exclude_I must always be the smaller of the pair
236	>	if (exI > exJ){
237	>	tempEx = exI;
238	>	exI = exJ;
239	>	exJ = tempEx;
240	>	}
241	>	#ifdef IS_MPI
242	>	tempEx = exI;
243	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
244	>	tempEx = exJ;
245	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
246
247	<	for( j=0; j<components_nmol[i]; j++ ){
248	<
249	<	if( mol2proc[allMol] == worldRank ){
250	<
251	<	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++;
247	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
248	>	#else  // isn't MPI
249	>
250	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
251	>	#endif  //is_mpi
252		}
253	+	excludeOffset += molInfo.nBonds;
254
255	<	allMol++;
256	<	}
257	<	}
258	<	local_SRI = local_bonds + local_bends + local_torsions;
259	<
260	<	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	<	}
255	>	//make the bends
256	>	for (j = 0; j < molInfo.nBends; j++){
257	>	currentBend = comp_stamps[stampID]->getBend(j);
258	>	theBends[j].a = currentBend->getA() + atomOffset;
259	>	theBends[j].b = currentBend->getB() + atomOffset;
260	>	theBends[j].c = currentBend->getC() + atomOffset;
261
262	<	simnfo->n_bonds = local_bonds;
263	<	simnfo->n_bends = local_bends;
264	<	simnfo->n_torsions = local_torsions;
402	<	simnfo->n_SRI = local_SRI;
403	<	simnfo->n_mol = localMol;
262	>	if (currentBend->haveExtras()){
263	>	extras = currentBend->getExtras();
264	>	current_extra = extras;
265
266	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
267	<	MPIcheckPoint();
268	<
269	<
270	<	#endif // is_mpi
271	<
266	>	while (current_extra != NULL){
267	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
268	>	switch (current_extra->getType()){
269	>	case 0:
270	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
271	>	theBends[j].isGhost = 1;
272	>	break;
273
274	<	// create the atom and short range interaction arrays
274	>	case 1:
275	>	theBends[j].ghost = (int) current_extra->getDouble() +
276	>	atomOffset;
277	>	theBends[j].isGhost = 1;
278	>	break;
279
280	<	Atom::createArrays(simnfo->n_atoms);
281	<	the_atoms = new Atom*[simnfo->n_atoms];
282	<	the_molecules = new Molecule[simnfo->n_mol];
283	<	int molIndex;
280	>	default:
281	>	sprintf(painCave.errMsg,
282	>	"SimSetup Error: ghostVectorSource was neither a "
283	>	"double nor an int.\n"
284	>	"-->Bend[%d] in %s\n",
285	>	j, comp_stamps[stampID]->getID());
286	>	painCave.isFatal = 1;
287	>	simError();
288	>	}
289	>	}
290	>	else{
291	>	sprintf(painCave.errMsg,
292	>	"SimSetup Error: unhandled bend assignment:\n"
293	>	"    -->%s in Bend[%d] in %s\n",
294	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298
299	<	// initialize the molecule's stampID's
299	>	current_extra = current_extra->getNext();
300	>	}
301	>	}
302
303	<	#ifdef IS_MPI
304	<
303	>	if (!theBends[j].isGhost){
304	>	exI = theBends[j].a;
305	>	exJ = theBends[j].c;
306	>	}
307	>	else{
308	>	exI = theBends[j].a;
309	>	exJ = theBends[j].b;
310	>	}
311
312	<	molIndex = 0;
313	<	for(i=0; i<mpiSim->getTotNmol(); i++){
314	<
315	<	if(mol2proc[i] == worldRank ){
316	<	the_molecules[molIndex].setStampID( molCompType[i] );
317	<	the_molecules[molIndex].setMyIndex( molIndex );
318	<	the_molecules[molIndex].setGlobalIndex( i );
319	<	molIndex++;
320	<	}
321	<	}
312	>	// exclude_I must always be the smaller of the pair
313	>	if (exI > exJ){
314	>	tempEx = exI;
315	>	exI = exJ;
316	>	exJ = tempEx;
317	>	}
318	>	#ifdef IS_MPI
319	>	tempEx = exI;
320	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
321	>	tempEx = exJ;
322	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
323
324	<	#else // is_mpi
325	<
326	<	molIndex = 0;
327	<	globalAtomIndex = 0;
439	<	for(i=0; i<n_components; i++){
440	<	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++;
324	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
325	>	#else  // isn't MPI
326	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
327	>	#endif  //is_mpi
328		}
329	<	molIndex++;
449	<	}
450	<	}
451	<
329	>	excludeOffset += molInfo.nBends;
330
331	<	#endif // is_mpi
331	>	for (j = 0; j < molInfo.nTorsions; j++){
332	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
333	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
334	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
335	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
336	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
337
338	+	exI = theTorsions[j].a;
339	+	exJ = theTorsions[j].d;
340
341	<	if( simnfo->n_SRI ){
342	<
343	<	Exclude::createArray(simnfo->n_SRI);
344	<	the_excludes = new Exclude*[simnfo->n_SRI];
345	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
346	<	simnfo->globalExcludes = new int;
347	<	simnfo->n_exclude = simnfo->n_SRI;
348	<	}
349	<	else{
350	<
351	<	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	<	}
341	>	// exclude_I must always be the smaller of the pair
342	>	if (exI > exJ){
343	>	tempEx = exI;
344	>	exI = exJ;
345	>	exJ = tempEx;
346	>	}
347	>	#ifdef IS_MPI
348	>	tempEx = exI;
349	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
350	>	tempEx = exJ;
351	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
352
353	<	// set the arrays into the SimInfo object
353	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
354	>	#else  // isn't MPI
355	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
356	>	#endif  //is_mpi
357	>	}
358	>	excludeOffset += molInfo.nTorsions;
359
477	–	simnfo->atoms = the_atoms;
478	–	simnfo->molecules = the_molecules;
479	–	simnfo->nGlobalExcludes = 0;
480	–	simnfo->excludes = the_excludes;
360
361	+	// send the arrays off to the forceField for init.
362
363	<	// get some of the tricky things that may still be in the globals
363	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
364	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
365	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
366	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
367	>	theTorsions);
368
485	–	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() ){
369
370	<	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];
370	>	info[k].molecules[i].initialize(molInfo);
371
501	–	simnfo->setBox( boxVector );
502	–	}
503	–	else{
504	–	if( !the_globals->haveBoxX() ){
505	–	sprintf( painCave.errMsg,
506	–	"SimSetup error, no periodic BoxX size given.\n" );
507	–	painCave.isFatal = 1;
508	–	simError();
509	–	}
510	–	boxVector[0] = the_globals->getBoxX();
372
373	<	if( !the_globals->haveBoxY() ){
374	<	sprintf( painCave.errMsg,
375	<	"SimSetup error, no periodic BoxY size given.\n" );
376	<	painCave.isFatal = 1;
516	<	simError();
373	>	atomOffset += molInfo.nAtoms;
374	>	delete[] theBonds;
375	>	delete[] theBends;
376	>	delete[] theTorsions;
377		}
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 );
378		}
379
380		#ifdef IS_MPI
381	<	strcpy( checkPointMsg, "Box size set up" );
381	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
382		MPIcheckPoint();
383		#endif // is_mpi
384
385	+	// clean up the forcefield
386
387	<	// initialize the arrays
387	>	the_ff->calcRcut();
388	>	the_ff->cleanMe();
389	>	}
390
391	<	the_ff->setSimInfo( simnfo );
391	>	void SimSetup::initFromBass(void){
392	>	int i, j, k;
393	>	int n_cells;
394	>	double cellx, celly, cellz;
395	>	double temp1, temp2, temp3;
396	>	int n_per_extra;
397	>	int n_extra;
398	>	int have_extra, done;
399
400	<	makeMolecules();
401	<	simnfo->identArray = new int[simnfo->n_atoms];
402	<	for(i=0; i<simnfo->n_atoms; i++){
403	<	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	<	}
400	>	double vel[3];
401	>	vel[0] = 0.0;
402	>	vel[1] = 0.0;
403	>	vel[2] = 0.0;
404
405	<	if( !the_globals->haveEST() ){
406	<	sprintf( painCave.errMsg,
407	<	"SimSetup Warning: using default value of 0.05 * the "
408	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
409	<	);
410	<	painCave.isFatal = 0;
411	<	simError();
412	<	simnfo->est = 0.05 * simnfo->ecr;
413	<	} else {
414	<	simnfo->est        = the_globals->getEST();
415	<	}
416	<
417	<	if(!the_globals->haveDielectric() ){
418	<	sprintf( painCave.errMsg,
419	<	"SimSetup Error: You are trying to use Reaction Field without"
420	<	"setting a dielectric constant!\n"
421	<	);
405	>	temp1 = (double) tot_nmol / 4.0;
406	>	temp2 = pow(temp1, (1.0 / 3.0));
407	>	temp3 = ceil(temp2);
408	>
409	>	have_extra = 0;
410	>	if (temp2 < temp3){
411	>	// we have a non-complete lattice
412	>	have_extra = 1;
413	>
414	>	n_cells = (int) temp3 - 1;
415	>	cellx = info[0].boxL[0] / temp3;
416	>	celly = info[0].boxL[1] / temp3;
417	>	cellz = info[0].boxL[2] / temp3;
418	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
419	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
420	>	n_per_extra = (int) ceil(temp1);
421	>
422	>	if (n_per_extra > 4){
423	>	sprintf(painCave.errMsg,
424	>	"SimSetup error. There has been an error in constructing"
425	>	" the non-complete lattice.\n");
426		painCave.isFatal = 1;
427		simError();
428		}
429	<	simnfo->dielectric = the_globals->getDielectric();
430	<	} else {
431	<	if (usesDipoles) {
432	<
433	<	if( !the_globals->haveECR() ){
434	<	sprintf( painCave.errMsg,
435	<	"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	<	}
429	>	}
430	>	else{
431	>	n_cells = (int) temp3;
432	>	cellx = info[0].boxL[0] / temp3;
433	>	celly = info[0].boxL[1] / temp3;
434	>	cellz = info[0].boxL[2] / temp3;
435	>	}
436
437	<	#ifdef IS_MPI
438	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
439	<	MPIcheckPoint();
440	<	#endif // is_mpi
437	>	current_mol = 0;
438	>	current_comp_mol = 0;
439	>	current_comp = 0;
440	>	current_atom_ndx = 0;
441
442	<	if( the_globals->haveInitialConfig() ){
443	<
444	<	InitializeFromFile* fileInit;
445	<	#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
442	>	for (i = 0; i < n_cells ; i++){
443	>	for (j = 0; j < n_cells; j++){
444	>	for (k = 0; k < n_cells; k++){
445	>	makeElement(i * cellx, j * celly, k * cellz);
446
447	<	delete fileInit;
639	<	}
640	<	else{
447	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
448
449	<	#ifdef IS_MPI
449	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
450
451	<	// no init from bass
452	<
453	<	sprintf( painCave.errMsg,
454	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
648	<	painCave.isFatal;
649	<	simError();
650	<
651	<	#else
451	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
452	>	}
453	>	}
454	>	}
455
456	<	initFromBass();
456	>	if (have_extra){
457	>	done = 0;
458
459	+	int start_ndx;
460	+	for (i = 0; i < (n_cells + 1) && !done; i++){
461	+	for (j = 0; j < (n_cells + 1) && !done; j++){
462	+	if (i < n_cells){
463	+	if (j < n_cells){
464	+	start_ndx = n_cells;
465	+	}
466	+	else
467	+	start_ndx = 0;
468	+	}
469	+	else
470	+	start_ndx = 0;
471
472	<	#endif
473	<	}
472	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
473	>	makeElement(i * cellx, j * celly, k * cellz);
474	>	done = (current_mol >= tot_nmol);
475
476	<	#ifdef IS_MPI
477	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
478	<	MPIcheckPoint();
479	<	#endif // is_mpi
476	>	if (!done && n_per_extra > 1){
477	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
478	>	k * cellz);
479	>	done = (current_mol >= tot_nmol);
480	>	}
481
482	+	if (!done && n_per_extra > 2){
483	+	makeElement(i * cellx, j * celly + 0.5 * celly,
484	+	k * cellz + 0.5 * cellz);
485	+	done = (current_mol >= tot_nmol);
486	+	}
487
488	<
489	<
490	<
491	<
492	<
493	<	#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" );
488	>	if (!done && n_per_extra > 3){
489	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
490	>	k * cellz + 0.5 * cellz);
491	>	done = (current_mol >= tot_nmol);
492	>	}
493	>	}
494		}
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	–	}
495		}
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
496		}
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	–	}
497
498	<	if( the_globals->haveStatusTime() ){
499	<	simnfo->statusTime = the_globals->getStatusTime();
498	>	for (i = 0; i < info[0].n_atoms; i++){
499	>	info[0].atoms[i]->setVel(vel);
500		}
501	+	}
502
503	<	if( the_globals->haveThermalTime() ){
504	<	simnfo->thermalTime = the_globals->getThermalTime();
505	<	}
503	>	void SimSetup::makeElement(double x, double y, double z){
504	>	int k;
505	>	AtomStamp* current_atom;
506	>	DirectionalAtom* dAtom;
507	>	double rotMat[3][3];
508	>	double pos[3];
509
510	<	// check for the temperature set flag
510	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
511	>	current_atom = comp_stamps[current_comp]->getAtom(k);
512	>	if (!current_atom->havePosition()){
513	>	sprintf(painCave.errMsg,
514	>	"SimSetup:initFromBass error.\n"
515	>	"\tComponent %s, atom %s does not have a position specified.\n"
516	>	"\tThe initialization routine is unable to give a start"
517	>	" position.\n",
518	>	comp_stamps[current_comp]->getID(), current_atom->getType());
519	>	painCave.isFatal = 1;
520	>	simError();
521	>	}
522
523	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
523	>	pos[0] = x + current_atom->getPosX();
524	>	pos[1] = y + current_atom->getPosY();
525	>	pos[2] = z + current_atom->getPosZ();
526
527	+	info[0].atoms[current_atom_ndx]->setPos(pos);
528
529	<	// make the integrator
530	<
781	<
782	<	NVT* myNVT = NULL;
783	<	switch( ensembleCase ){
529	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
530	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
531
532	<	case NVE_ENS:
533	<	new NVE( simnfo, the_ff );
534	<	break;
532	>	rotMat[0][0] = 1.0;
533	>	rotMat[0][1] = 0.0;
534	>	rotMat[0][2] = 0.0;
535
536	<	case NVT_ENS:
537	<	myNVT = new NVT( simnfo, the_ff );
538	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
536	>	rotMat[1][0] = 0.0;
537	>	rotMat[1][1] = 1.0;
538	>	rotMat[1][2] = 0.0;
539
540	<	if (the_globals->haveTauThermostat())
541	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
542	<	//     else if (the_globals->haveQmass())
543	<	//       myNVT->setQmass(the_globals->getQmass());
544	<	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();
540	>	rotMat[2][0] = 0.0;
541	>	rotMat[2][1] = 0.0;
542	>	rotMat[2][2] = 1.0;
543	>
544	>	dAtom->setA(rotMat);
545		}
805	–	break;
546
547	<	default:
808	<	sprintf( painCave.errMsg,
809	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
810	<	painCave.isFatal = 1;
811	<	simError();
547	>	current_atom_ndx++;
548		}
549
550	+	current_mol++;
551	+	current_comp_mol++;
552
553	<	#ifdef IS_MPI
554	<	mpiSim->mpiRefresh();
555	<	#endif
553	>	if (current_comp_mol >= components_nmol[current_comp]){
554	>	current_comp_mol = 0;
555	>	current_comp++;
556	>	}
557	>	}
558
819	–	// initialize the Fortran
559
560	+	void SimSetup::gatherInfo(void){
561	+	int i;
562
563	<	simnfo->refreshSim();
564	<
565	<	if( !strcmp( simnfo->mixingRule, "standard") ){
566	<	the_ff->initForceField( LB_MIXING_RULE );
563	>	ensembleCase = -1;
564	>	ffCase = -1;
565	>
566	>	// set the easy ones first
567	>
568	>	for (i = 0; i < nInfo; i++){
569	>	info[i].target_temp = globals->getTargetTemp();
570	>	info[i].dt = globals->getDt();
571	>	info[i].run_time = globals->getRunTime();
572		}
573	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
574	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
573	>	n_components = globals->getNComponents();
574	>
575	>
576	>	// get the forceField
577	>
578	>	strcpy(force_field, globals->getForceField());
579	>
580	>	if (!strcasecmp(force_field, "DUFF")){
581	>	ffCase = FF_DUFF;
582		}
583	+	else if (!strcasecmp(force_field, "LJ")){
584	+	ffCase = FF_LJ;
585	+	}
586	+	else if (!strcasecmp(force_field, "EAM")){
587	+	ffCase = FF_EAM;
588	+	}
589		else{
590	<	sprintf( painCave.errMsg,
591	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
592	<	simnfo->mixingRule );
593	<	painCave.isFatal = 1;
835	<	simError();
590	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
591	>	force_field);
592	>	painCave.isFatal = 1;
593	>	simError();
594		}
595
596	+	// get the ensemble
597
598	<	#ifdef IS_MPI
840	<	strcpy( checkPointMsg,
841	<	"Successfully intialized the mixingRule for Fortran." );
842	<	MPIcheckPoint();
843	<	#endif // is_mpi
844	<	}
598	>	strcpy(ensemble, globals->getEnsemble());
599
600	+	if (!strcasecmp(ensemble, "NVE")){
601	+	ensembleCase = NVE_ENS;
602	+	}
603	+	else if (!strcasecmp(ensemble, "NVT")){
604	+	ensembleCase = NVT_ENS;
605	+	}
606	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
607	+	ensembleCase = NPTi_ENS;
608	+	}
609	+	else if (!strcasecmp(ensemble, "NPTf")){
610	+	ensembleCase = NPTf_ENS;
611	+	}
612	+	else if (!strcasecmp(ensemble, "NPTxyz")){
613	+	ensembleCase = NPTxyz_ENS;
614	+	}
615	+	else{
616	+	sprintf(painCave.errMsg,
617	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
618	+	"reverting to NVE for this simulation.\n",
619	+	ensemble);
620	+	painCave.isFatal = 0;
621	+	simError();
622	+	strcpy(ensemble, "NVE");
623	+	ensembleCase = NVE_ENS;
624	+	}
625
626	<	void SimSetup::makeMolecules( void ){
626	>	for (i = 0; i < nInfo; i++){
627	>	strcpy(info[i].ensemble, ensemble);
628
629	<	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;
629	>	// get the mixing rule
630
631	<	bond_pair* theBonds;
632	<	bend_set* theBends;
633	<	torsion_set* theTorsions;
631	>	strcpy(info[i].mixingRule, globals->getMixingRule());
632	>	info[i].usePBC = globals->getPBC();
633	>	}
634
635	<
864	<	//init the forceField paramters
635	>	// get the components and calculate the tot_nMol and indvidual n_mol
636
637	<	the_ff->readParams();
637	>	the_components = globals->getComponents();
638	>	components_nmol = new int[n_components];
639
868	–
869	–	// init the atoms
640
641	<	double ux, uy, uz, u, uSqr;
642	<
643	<	atomOffset = 0;
874	<	excludeOffset = 0;
875	<	for(i=0; i<simnfo->n_mol; i++){
876	<
877	<	stampID = the_molecules[i].getStampID();
641	>	if (!globals->haveNMol()){
642	>	// we don't have the total number of molecules, so we assume it is
643	>	// given in each component
644
645	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
646	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
647	<	info.nBends    = comp_stamps[stampID]->getNBends();
648	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
649	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
650	<
651	<	info.myAtoms = &the_atoms[atomOffset];
652	<	info.myExcludes = &the_excludes[excludeOffset];
653	<	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 );
645	>	tot_nmol = 0;
646	>	for (i = 0; i < n_components; i++){
647	>	if (!the_components[i]->haveNMol()){
648	>	// we have a problem
649	>	sprintf(painCave.errMsg,
650	>	"SimSetup Error. No global NMol or component NMol"
651	>	" given. Cannot calculate the number of atoms.\n");
652	>	painCave.isFatal = 1;
653	>	simError();
654		}
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;
655
656	<	exI = theBonds[j].a;
657	<	exJ = theBonds[j].b;
656	>	tot_nmol += the_components[i]->getNMol();
657	>	components_nmol[i] = the_components[i]->getNMol();
658	>	}
659	>	}
660	>	else{
661	>	sprintf(painCave.errMsg,
662	>	"SimSetup error.\n"
663	>	"\tSorry, the ability to specify total"
664	>	" nMols and then give molfractions in the components\n"
665	>	"\tis not currently supported."
666	>	" Please give nMol in the components.\n");
667	>	painCave.isFatal = 1;
668	>	simError();
669	>	}
670
671	<	// 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
671	>	// set the status, sample, and thermal kick times
672
673	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
674	<	#endif  //is_mpi
673	>	for (i = 0; i < nInfo; i++){
674	>	if (globals->haveSampleTime()){
675	>	info[i].sampleTime = globals->getSampleTime();
676	>	info[i].statusTime = info[i].sampleTime;
677	>	info[i].thermalTime = info[i].sampleTime;
678		}
679	<	excludeOffset += info.nBonds;
679	>	else{
680	>	info[i].sampleTime = globals->getRunTime();
681	>	info[i].statusTime = info[i].sampleTime;
682	>	info[i].thermalTime = info[i].sampleTime;
683	>	}
684
685	<	//make the bends
686	<	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
685	>	if (globals->haveStatusTime()){
686	>	info[i].statusTime = globals->getStatusTime();
687		}
1047	–	excludeOffset += info.nBends;
688
689	<	for(j=0; j<info.nTorsions; j++){
690	<
691	<	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;
689	>	if (globals->haveThermalTime()){
690	>	info[i].thermalTime = globals->getThermalTime();
691	>	}
692
693	<	// exclude_I must always be the smaller of the pair
694	<	if( exI > exJ ){
695	<	tempEx = exI;
696	<	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
693	>	info[i].resetIntegrator = 0;
694	>	if( globals->haveResetTime() ){
695	>	info[i].resetTime = globals->getResetTime();
696	>	info[i].resetIntegrator = 1;
697		}
1077	–	excludeOffset += info.nTorsions;
698
699	+	// check for the temperature set flag
700
701	<	// send the arrays off to the forceField for init.
702	<
703	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
704	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
705	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
706	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
701	>	if (globals->haveTempSet())
702	>	info[i].setTemp = globals->getTempSet();
703	>
704	>	}
705	>
706	>	//setup seed for random number generator
707	>	int seedValue;
708
709	+	if (globals->haveSeed()){
710	+	seedValue = globals->getSeed();
711
712	<	the_molecules[i].initialize( info );
712	>	if(seedValue / 1E9 == 0){
713	>	sprintf(painCave.errMsg,
714	>	"Seed for sprng library should contain at least 9 digits\n"
715	>	"OOPSE will generate a seed for user\n");
716	>	painCave.isFatal = 0;
717	>	simError();
718
719	+	//using seed generated by system instead of invalid seed set by user
720	+	#ifndef IS_MPI
721	+	seedValue = make_sprng_seed();
722	+	#else
723	+	if (worldRank == 0){
724	+	seedValue = make_sprng_seed();
725	+	}
726	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
727	+	#endif
728	+	}
729	+	}//end of if branch of globals->haveSeed()
730	+	else{
731	+
732	+	#ifndef IS_MPI
733	+	seedValue = make_sprng_seed();
734	+	#else
735	+	if (worldRank == 0){
736	+	seedValue = make_sprng_seed();
737	+	}
738	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
739	+	#endif
740	+	}//end of globals->haveSeed()
741
742	<	atomOffset += info.nAtoms;
743	<	delete[] theBonds;
1093	<	delete[] theBends;
1094	<	delete[] theTorsions;
742	>	for (int i = 0; i < nInfo; i++){
743	>	info[i].setSeed(seedValue);
744		}
745
746		#ifdef IS_MPI
747	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
747	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
748		MPIcheckPoint();
749		#endif // is_mpi
750	+	}
751
1102	–	// clean up the forcefield
1103	–	the_ff->calcRcut();
1104	–	the_ff->cleanMe();
752
753	<	}
753	>	void SimSetup::finalInfoCheck(void){
754	>	int index;
755	>	int usesDipoles;
756	>	int i;
757
758	<	void SimSetup::initFromBass( void ){
758	>	for (i = 0; i < nInfo; i++){
759	>	// check electrostatic parameters
760
761	<	int i, j, k;
762	<	int n_cells;
763	<	double cellx, celly, cellz;
764	<	double temp1, temp2, temp3;
765	<	int n_per_extra;
766	<	int n_extra;
1116	<	int have_extra, done;
761	>	index = 0;
762	>	usesDipoles = 0;
763	>	while ((index < info[i].n_atoms) && !usesDipoles){
764	>	usesDipoles = (info[i].atoms[index])->hasDipole();
765	>	index++;
766	>	}
767
768	<	temp1 = (double)tot_nmol / 4.0;
769	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
770	<	temp3 = ceil( temp2 );
768	>	#ifdef IS_MPI
769	>	int myUse = usesDipoles;
770	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
771	>	#endif //is_mpi
772
773	<	have_extra =0;
1123	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1124	<	have_extra =1;
773	>	double theEcr, theEst;
774
775	<	n_cells = (int)temp3 - 1;
776	<	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 );
775	>	if (globals->getUseRF()){
776	>	info[i].useReactionField = 1;
777
778	<	if( n_per_extra > 4){
779	<	sprintf( painCave.errMsg,
780	<	"SimSetup error. There has been an error in constructing"
781	<	" the non-complete lattice.\n" );
782	<	painCave.isFatal = 1;
783	<	simError();
778	>	if (!globals->haveECR()){
779	>	sprintf(painCave.errMsg,
780	>	"SimSetup Warning: using default value of 1/2 the smallest "
781	>	"box length for the electrostaticCutoffRadius.\n"
782	>	"I hope you have a very fast processor!\n");
783	>	painCave.isFatal = 0;
784	>	simError();
785	>	double smallest;
786	>	smallest = info[i].boxL[0];
787	>	if (info[i].boxL[1] <= smallest)
788	>	smallest = info[i].boxL[1];
789	>	if (info[i].boxL[2] <= smallest)
790	>	smallest = info[i].boxL[2];
791	>	theEcr = 0.5 * smallest;
792	>	}
793	>	else{
794	>	theEcr = globals->getECR();
795	>	}
796	>
797	>	if (!globals->haveEST()){
798	>	sprintf(painCave.errMsg,
799	>	"SimSetup Warning: using default value of 0.05 * the "
800	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
801	>	painCave.isFatal = 0;
802	>	simError();
803	>	theEst = 0.05 * theEcr;
804	>	}
805	>	else{
806	>	theEst = globals->getEST();
807	>	}
808	>
809	>	info[i].setDefaultEcr(theEcr, theEst);
810	>
811	>	if (!globals->haveDielectric()){
812	>	sprintf(painCave.errMsg,
813	>	"SimSetup Error: You are trying to use Reaction Field without"
814	>	"setting a dielectric constant!\n");
815	>	painCave.isFatal = 1;
816	>	simError();
817	>	}
818	>	info[i].dielectric = globals->getDielectric();
819		}
820	+	else{
821	+	if (usesDipoles){
822	+	if (!globals->haveECR()){
823	+	sprintf(painCave.errMsg,
824	+	"SimSetup Warning: using default value of 1/2 the smallest "
825	+	"box length for the electrostaticCutoffRadius.\n"
826	+	"I hope you have a very fast processor!\n");
827	+	painCave.isFatal = 0;
828	+	simError();
829	+	double smallest;
830	+	smallest = info[i].boxL[0];
831	+	if (info[i].boxL[1] <= smallest)
832	+	smallest = info[i].boxL[1];
833	+	if (info[i].boxL[2] <= smallest)
834	+	smallest = info[i].boxL[2];
835	+	theEcr = 0.5 * smallest;
836	+	}
837	+	else{
838	+	theEcr = globals->getECR();
839	+	}
840	+
841	+	if (!globals->haveEST()){
842	+	sprintf(painCave.errMsg,
843	+	"SimSetup Warning: using default value of 0.05 * the "
844	+	"electrostaticCutoffRadius for the "
845	+	"electrostaticSkinThickness\n");
846	+	painCave.isFatal = 0;
847	+	simError();
848	+	theEst = 0.05 * theEcr;
849	+	}
850	+	else{
851	+	theEst = globals->getEST();
852	+	}
853	+
854	+	info[i].setDefaultEcr(theEcr, theEst);
855	+	}
856	+	}
857	+	info[i].checkCutOffs();
858		}
859	+
860	+	#ifdef IS_MPI
861	+	strcpy(checkPointMsg, "post processing checks out");
862	+	MPIcheckPoint();
863	+	#endif // is_mpi
864	+	}
865	+
866	+	void SimSetup::initSystemCoords(void){
867	+	int i;
868	+
869	+	char* inName;
870	+
871	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
872	+
873	+	for (i = 0; i < info[0].n_atoms; i++)
874	+	info[0].atoms[i]->setCoords();
875	+
876	+	if (globals->haveInitialConfig()){
877	+	InitializeFromFile* fileInit;
878	+	#ifdef IS_MPI // is_mpi
879	+	if (worldRank == 0){
880	+	#endif //is_mpi
881	+	inName = globals->getInitialConfig();
882	+	fileInit = new InitializeFromFile(inName);
883	+	#ifdef IS_MPI
884	+	}
885	+	else
886	+	fileInit = new InitializeFromFile(NULL);
887	+	#endif
888	+	fileInit->readInit(info); // default velocities on
889	+
890	+	delete fileInit;
891	+	}
892		else{
893	<	n_cells = (int)temp3;
894	<	cellx = simnfo->boxLx / temp3;
895	<	celly = simnfo->boxLy / temp3;
896	<	cellz = simnfo->boxLz / temp3;
893	>	#ifdef IS_MPI
894	>
895	>	// no init from bass
896	>
897	>	sprintf(painCave.errMsg,
898	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
899	>	painCave.isFatal = 1;;
900	>	simError();
901	>
902	>	#else
903	>
904	>	initFromBass();
905	>
906	>
907	>	#endif
908		}
909
910	<	current_mol = 0;
911	<	current_comp_mol = 0;
912	<	current_comp = 0;
913	<	current_atom_ndx = 0;
910	>	#ifdef IS_MPI
911	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
912	>	MPIcheckPoint();
913	>	#endif // is_mpi
914	>	}
915
1154	–	for( i=0; i < n_cells ; i++ ){
1155	–	for( j=0; j < n_cells; j++ ){
1156	–	for( k=0; k < n_cells; k++ ){
916
917	<	makeElement( i * cellx,
918	<	j * celly,
1160	<	k * cellz );
917	>	void SimSetup::makeOutNames(void){
918	>	int k;
919
1162	–	makeElement( i * cellx + 0.5 * cellx,
1163	–	j * celly + 0.5 * celly,
1164	–	k * cellz );
920
921	<	makeElement( i * cellx,
922	<	j * celly + 0.5 * celly,
923	<	k * cellz + 0.5 * cellz );
921	>	for (k = 0; k < nInfo; k++){
922	>	#ifdef IS_MPI
923	>	if (worldRank == 0){
924	>	#endif // is_mpi
925
926	<	makeElement( i * cellx + 0.5 * cellx,
927	<	j * celly,
928	<	k * cellz + 0.5 * cellz );
929	<	}
926	>	if (globals->haveFinalConfig()){
927	>	strcpy(info[k].finalName, globals->getFinalConfig());
928	>	}
929	>	else{
930	>	strcpy(info[k].finalName, inFileName);
931	>	char* endTest;
932	>	int nameLength = strlen(info[k].finalName);
933	>	endTest = &(info[k].finalName[nameLength - 5]);
934	>	if (!strcmp(endTest, ".bass")){
935	>	strcpy(endTest, ".eor");
936	>	}
937	>	else if (!strcmp(endTest, ".BASS")){
938	>	strcpy(endTest, ".eor");
939	>	}
940	>	else{
941	>	endTest = &(info[k].finalName[nameLength - 4]);
942	>	if (!strcmp(endTest, ".bss")){
943	>	strcpy(endTest, ".eor");
944	>	}
945	>	else if (!strcmp(endTest, ".mdl")){
946	>	strcpy(endTest, ".eor");
947	>	}
948	>	else{
949	>	strcat(info[k].finalName, ".eor");
950	>	}
951	>	}
952	>	}
953	>
954	>	// make the sample and status out names
955	>
956	>	strcpy(info[k].sampleName, inFileName);
957	>	char* endTest;
958	>	int nameLength = strlen(info[k].sampleName);
959	>	endTest = &(info[k].sampleName[nameLength - 5]);
960	>	if (!strcmp(endTest, ".bass")){
961	>	strcpy(endTest, ".dump");
962	>	}
963	>	else if (!strcmp(endTest, ".BASS")){
964	>	strcpy(endTest, ".dump");
965	>	}
966	>	else{
967	>	endTest = &(info[k].sampleName[nameLength - 4]);
968	>	if (!strcmp(endTest, ".bss")){
969	>	strcpy(endTest, ".dump");
970	>	}
971	>	else if (!strcmp(endTest, ".mdl")){
972	>	strcpy(endTest, ".dump");
973	>	}
974	>	else{
975	>	strcat(info[k].sampleName, ".dump");
976	>	}
977	>	}
978	>
979	>	strcpy(info[k].statusName, inFileName);
980	>	nameLength = strlen(info[k].statusName);
981	>	endTest = &(info[k].statusName[nameLength - 5]);
982	>	if (!strcmp(endTest, ".bass")){
983	>	strcpy(endTest, ".stat");
984	>	}
985	>	else if (!strcmp(endTest, ".BASS")){
986	>	strcpy(endTest, ".stat");
987	>	}
988	>	else{
989	>	endTest = &(info[k].statusName[nameLength - 4]);
990	>	if (!strcmp(endTest, ".bss")){
991	>	strcpy(endTest, ".stat");
992	>	}
993	>	else if (!strcmp(endTest, ".mdl")){
994	>	strcpy(endTest, ".stat");
995	>	}
996	>	else{
997	>	strcat(info[k].statusName, ".stat");
998	>	}
999	>	}
1000	>
1001	>	#ifdef IS_MPI
1002	>
1003	>	}
1004	>	#endif // is_mpi
1005	>	}
1006	>	}
1007	>
1008	>
1009	>	void SimSetup::sysObjectsCreation(void){
1010	>	int i, k;
1011	>
1012	>	// create the forceField
1013	>
1014	>	createFF();
1015	>
1016	>	// extract componentList
1017	>
1018	>	compList();
1019	>
1020	>	// calc the number of atoms, bond, bends, and torsions
1021	>
1022	>	calcSysValues();
1023	>
1024	>	#ifdef IS_MPI
1025	>	// divide the molecules among the processors
1026	>
1027	>	mpiMolDivide();
1028	>	#endif //is_mpi
1029	>
1030	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1031	>
1032	>	makeSysArrays();
1033	>
1034	>	// make and initialize the molecules (all but atomic coordinates)
1035	>
1036	>	makeMolecules();
1037	>
1038	>	for (k = 0; k < nInfo; k++){
1039	>	info[k].identArray = new int[info[k].n_atoms];
1040	>	for (i = 0; i < info[k].n_atoms; i++){
1041	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1042		}
1043		}
1044	+	}
1045
1177	–	if( have_extra ){
1178	–	done = 0;
1046
1047	<	int start_ndx;
1048	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1049	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1047	>	void SimSetup::createFF(void){
1048	>	switch (ffCase){
1049	>	case FF_DUFF:
1050	>	the_ff = new DUFF();
1051	>	break;
1052
1053	<	if( i < n_cells ){
1053	>	case FF_LJ:
1054	>	the_ff = new LJFF();
1055	>	break;
1056
1057	<	if( j < n_cells ){
1058	<	start_ndx = n_cells;
1059	<	}
1189	<	else start_ndx = 0;
1190	<	}
1191	<	else start_ndx = 0;
1057	>	case FF_EAM:
1058	>	the_ff = new EAM_FF();
1059	>	break;
1060
1061	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1061	>	default:
1062	>	sprintf(painCave.errMsg,
1063	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1064	>	painCave.isFatal = 1;
1065	>	simError();
1066	>	}
1067
1068	<	makeElement( i * cellx,
1069	<	j * celly,
1070	<	k * cellz );
1071	<	done = ( current_mol >= tot_nmol );
1068	>	#ifdef IS_MPI
1069	>	strcpy(checkPointMsg, "ForceField creation successful");
1070	>	MPIcheckPoint();
1071	>	#endif // is_mpi
1072	>	}
1073
1200	–	if( !done && n_per_extra > 1 ){
1201	–	makeElement( i * cellx + 0.5 * cellx,
1202	–	j * celly + 0.5 * celly,
1203	–	k * cellz );
1204	–	done = ( current_mol >= tot_nmol );
1205	–	}
1074
1075	<	if( !done && n_per_extra > 2){
1076	<	makeElement( i * cellx,
1077	<	j * celly + 0.5 * celly,
1078	<	k * cellz + 0.5 * cellz );
1079	<	done = ( current_mol >= tot_nmol );
1080	<	}
1075	>	void SimSetup::compList(void){
1076	>	int i;
1077	>	char* id;
1078	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1079	>	LinkedMolStamp* currentStamp = NULL;
1080	>	comp_stamps = new MoleculeStamp * [n_components];
1081
1082	<	if( !done && n_per_extra > 3){
1083	<	makeElement( i * cellx + 0.5 * cellx,
1084	<	j * celly,
1085	<	k * cellz + 0.5 * cellz );
1086	<	done = ( current_mol >= tot_nmol );
1087	<	}
1088	<	}
1082	>	// make an array of molecule stamps that match the components used.
1083	>	// also extract the used stamps out into a separate linked list
1084	>
1085	>	for (i = 0; i < nInfo; i++){
1086	>	info[i].nComponents = n_components;
1087	>	info[i].componentsNmol = components_nmol;
1088	>	info[i].compStamps = comp_stamps;
1089	>	info[i].headStamp = headStamp;
1090	>	}
1091	>
1092	>
1093	>	for (i = 0; i < n_components; i++){
1094	>	id = the_components[i]->getType();
1095	>	comp_stamps[i] = NULL;
1096	>
1097	>	// check to make sure the component isn't already in the list
1098	>
1099	>	comp_stamps[i] = headStamp->match(id);
1100	>	if (comp_stamps[i] == NULL){
1101	>	// extract the component from the list;
1102	>
1103	>	currentStamp = stamps->extractMolStamp(id);
1104	>	if (currentStamp == NULL){
1105	>	sprintf(painCave.errMsg,
1106	>	"SimSetup error: Component \"%s\" was not found in the "
1107	>	"list of declared molecules\n",
1108	>	id);
1109	>	painCave.isFatal = 1;
1110	>	simError();
1111		}
1112	+
1113	+	headStamp->add(currentStamp);
1114	+	comp_stamps[i] = headStamp->match(id);
1115		}
1116		}
1117
1118	+	#ifdef IS_MPI
1119	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1120	+	MPIcheckPoint();
1121	+	#endif // is_mpi
1122	+	}
1123
1124	<	for( i=0; i<simnfo->n_atoms; i++ ){
1125	<	simnfo->atoms[i]->set_vx( 0.0 );
1126	<	simnfo->atoms[i]->set_vy( 0.0 );
1127	<	simnfo->atoms[i]->set_vz( 0.0 );
1124	>	void SimSetup::calcSysValues(void){
1125	>	int i;
1126	>
1127	>	int* molMembershipArray;
1128	>
1129	>	tot_atoms = 0;
1130	>	tot_bonds = 0;
1131	>	tot_bends = 0;
1132	>	tot_torsions = 0;
1133	>	for (i = 0; i < n_components; i++){
1134	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1135	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1136	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1137	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1138		}
1139	+
1140	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1141	+	molMembershipArray = new int[tot_atoms];
1142	+
1143	+	for (i = 0; i < nInfo; i++){
1144	+	info[i].n_atoms = tot_atoms;
1145	+	info[i].n_bonds = tot_bonds;
1146	+	info[i].n_bends = tot_bends;
1147	+	info[i].n_torsions = tot_torsions;
1148	+	info[i].n_SRI = tot_SRI;
1149	+	info[i].n_mol = tot_nmol;
1150	+
1151	+	info[i].molMembershipArray = molMembershipArray;
1152	+	}
1153		}
1154
1155	<	void SimSetup::makeElement( double x, double y, double z ){
1155	>	#ifdef IS_MPI
1156
1157	<	int k;
1158	<	AtomStamp* current_atom;
1159	<	DirectionalAtom* dAtom;
1160	<	double rotMat[3][3];
1157	>	void SimSetup::mpiMolDivide(void){
1158	>	int i, j, k;
1159	>	int localMol, allMol;
1160	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1161
1162	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1162	>	mpiSim = new mpiSimulation(info);
1163
1164	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1165	<	if( !current_atom->havePosition() ){
1166	<	sprintf( painCave.errMsg,
1167	<	"SimSetup:initFromBass error.\n"
1168	<	"\tComponent %s, atom %s does not have a position specified.\n"
1169	<	"\tThe initialization routine is unable to give a start"
1170	<	" position.\n",
1171	<	comp_stamps[current_comp]->getID(),
1172	<	current_atom->getType() );
1173	<	painCave.isFatal = 1;
1174	<	simError();
1164	>	globalIndex = mpiSim->divideLabor();
1165	>
1166	>	// set up the local variables
1167	>
1168	>	mol2proc = mpiSim->getMolToProcMap();
1169	>	molCompType = mpiSim->getMolComponentType();
1170	>
1171	>	allMol = 0;
1172	>	localMol = 0;
1173	>	local_atoms = 0;
1174	>	local_bonds = 0;
1175	>	local_bends = 0;
1176	>	local_torsions = 0;
1177	>	globalAtomIndex = 0;
1178	>
1179	>
1180	>	for (i = 0; i < n_components; i++){
1181	>	for (j = 0; j < components_nmol[i]; j++){
1182	>	if (mol2proc[allMol] == worldRank){
1183	>	local_atoms += comp_stamps[i]->getNAtoms();
1184	>	local_bonds += comp_stamps[i]->getNBonds();
1185	>	local_bends += comp_stamps[i]->getNBends();
1186	>	local_torsions += comp_stamps[i]->getNTorsions();
1187	>	localMol++;
1188	>	}
1189	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1190	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1191	>	globalAtomIndex++;
1192	>	}
1193	>
1194	>	allMol++;
1195		}
1196	+	}
1197	+	local_SRI = local_bonds + local_bends + local_torsions;
1198
1199	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1256	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1257	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1199	>	info[0].n_atoms = mpiSim->getMyNlocal();
1200
1201	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1201	>	if (local_atoms != info[0].n_atoms){
1202	>	sprintf(painCave.errMsg,
1203	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1204	>	" localAtom (%d) are not equal.\n",
1205	>	info[0].n_atoms, local_atoms);
1206	>	painCave.isFatal = 1;
1207	>	simError();
1208	>	}
1209
1210	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1210	>	info[0].n_bonds = local_bonds;
1211	>	info[0].n_bends = local_bends;
1212	>	info[0].n_torsions = local_torsions;
1213	>	info[0].n_SRI = local_SRI;
1214	>	info[0].n_mol = localMol;
1215
1216	<	rotMat[0][0] = 1.0;
1217	<	rotMat[0][1] = 0.0;
1218	<	rotMat[0][2] = 0.0;
1216	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1217	>	MPIcheckPoint();
1218	>	}
1219
1220	<	rotMat[1][0] = 0.0;
1268	<	rotMat[1][1] = 1.0;
1269	<	rotMat[1][2] = 0.0;
1220	>	#endif // is_mpi
1221
1271	–	rotMat[2][0] = 0.0;
1272	–	rotMat[2][1] = 0.0;
1273	–	rotMat[2][2] = 1.0;
1222
1223	<	dAtom->setA( rotMat );
1223	>	void SimSetup::makeSysArrays(void){
1224	>
1225	>	#ifndef IS_MPI
1226	>	int k, j;
1227	>	#endif // is_mpi
1228	>	int i, l;
1229	>
1230	>	Atom** the_atoms;
1231	>	Molecule* the_molecules;
1232	>	Exclude** the_excludes;
1233	>
1234	>
1235	>	for (l = 0; l < nInfo; l++){
1236	>	// create the atom and short range interaction arrays
1237	>
1238	>	the_atoms = new Atom * [info[l].n_atoms];
1239	>	the_molecules = new Molecule[info[l].n_mol];
1240	>	int molIndex;
1241	>
1242	>	// initialize the molecule's stampID's
1243	>
1244	>	#ifdef IS_MPI
1245	>
1246	>
1247	>	molIndex = 0;
1248	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1249	>	if (mol2proc[i] == worldRank){
1250	>	the_molecules[molIndex].setStampID(molCompType[i]);
1251	>	the_molecules[molIndex].setMyIndex(molIndex);
1252	>	the_molecules[molIndex].setGlobalIndex(i);
1253	>	molIndex++;
1254	>	}
1255		}
1256
1257	<	current_atom_ndx++;
1279	<	}
1257	>	#else // is_mpi
1258
1259	<	current_mol++;
1260	<	current_comp_mol++;
1259	>	molIndex = 0;
1260	>	globalAtomIndex = 0;
1261	>	for (i = 0; i < n_components; i++){
1262	>	for (j = 0; j < components_nmol[i]; j++){
1263	>	the_molecules[molIndex].setStampID(i);
1264	>	the_molecules[molIndex].setMyIndex(molIndex);
1265	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1266	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1267	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1268	>	globalAtomIndex++;
1269	>	}
1270	>	molIndex++;
1271	>	}
1272	>	}
1273
1284	–	if( current_comp_mol >= components_nmol[current_comp] ){
1274
1275	<	current_comp_mol = 0;
1276	<	current_comp++;
1275	>	#endif // is_mpi
1276	>
1277	>
1278	>	if (info[l].n_SRI){
1279	>	Exclude::createArray(info[l].n_SRI);
1280	>	the_excludes = new Exclude * [info[l].n_SRI];
1281	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1282	>	the_excludes[ex] = new Exclude(ex);
1283	>	}
1284	>	info[l].globalExcludes = new int;
1285	>	info[l].n_exclude = info[l].n_SRI;
1286	>	}
1287	>	else{
1288	>	Exclude::createArray(1);
1289	>	the_excludes = new Exclude * ;
1290	>	the_excludes[0] = new Exclude(0);
1291	>	the_excludes[0]->setPair(0, 0);
1292	>	info[l].globalExcludes = new int;
1293	>	info[l].globalExcludes[0] = 0;
1294	>	info[l].n_exclude = 0;
1295	>	}
1296	>
1297	>	// set the arrays into the SimInfo object
1298	>
1299	>	info[l].atoms = the_atoms;
1300	>	info[l].molecules = the_molecules;
1301	>	info[l].nGlobalExcludes = 0;
1302	>	info[l].excludes = the_excludes;
1303	>
1304	>	the_ff->setSimInfo(info);
1305		}
1306		}
1307	+
1308	+	void SimSetup::makeIntegrator(void){
1309	+	int k;
1310	+
1311	+	NVE* myNVE = NULL;
1312	+	NVT* myNVT = NULL;
1313	+	NPTi* myNPTi = NULL;
1314	+	NPTf* myNPTf = NULL;
1315	+	NPTxyz* myNPTxyz = NULL;
1316	+
1317	+	for (k = 0; k < nInfo; k++){
1318	+	switch (ensembleCase){
1319	+	case NVE_ENS:
1320	+	if (globals->haveZconstraints()){
1321	+
1322	+	std::cerr << "ZConstraint is temporarily disabled\n";
1323	+
1324	+	//      setupZConstraint(info[k]);
1325	+	//      myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1326	+	}
1327	+
1328	+	//       else{
1329	+	myNVE = new NVE(&(info[k]), the_ff);
1330	+	//       }
1331	+
1332	+	info->the_integrator = myNVE;
1333	+	break;
1334	+
1335	+	case NVT_ENS:
1336	+	if (globals->haveZconstraints()){
1337	+
1338	+	std::cerr << "ZConstraint is temporarily disabled\n";
1339	+
1340	+	//      setupZConstraint(info[k]);
1341	+	//      myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1342	+	}
1343	+	// else
1344	+	myNVT = new NVT(&(info[k]), the_ff);
1345	+
1346	+	myNVT->setTargetTemp(globals->getTargetTemp());
1347	+
1348	+	if (globals->haveTauThermostat())
1349	+	myNVT->setTauThermostat(globals->getTauThermostat());
1350	+	else{
1351	+	sprintf(painCave.errMsg,
1352	+	"SimSetup error: If you use the NVT\n"
1353	+	"    ensemble, you must set tauThermostat.\n");
1354	+	painCave.isFatal = 1;
1355	+	simError();
1356	+	}
1357	+
1358	+	info->the_integrator = myNVT;
1359	+	break;
1360	+
1361	+	case NPTi_ENS:
1362	+	if (globals->haveZconstraints()){
1363	+
1364	+	std::cerr << "ZConstraint is temporarily disabled\n";
1365	+
1366	+	//        setupZConstraint(info[k]);
1367	+	//           myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1368	+	}
1369	+	// else
1370	+	myNPTi = new NPTi(&(info[k]), the_ff);
1371	+
1372	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1373	+
1374	+	if (globals->haveTargetPressure())
1375	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1376	+	else{
1377	+	sprintf(painCave.errMsg,
1378	+	"SimSetup error: If you use a constant pressure\n"
1379	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1380	+	painCave.isFatal = 1;
1381	+	simError();
1382	+	}
1383	+
1384	+	if (globals->haveTauThermostat())
1385	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1386	+	else{
1387	+	sprintf(painCave.errMsg,
1388	+	"SimSetup error: If you use an NPT\n"
1389	+	"    ensemble, you must set tauThermostat.\n");
1390	+	painCave.isFatal = 1;
1391	+	simError();
1392	+	}
1393	+
1394	+	if (globals->haveTauBarostat())
1395	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1396	+	else{
1397	+	sprintf(painCave.errMsg,
1398	+	"SimSetup error: If you use an NPT\n"
1399	+	"    ensemble, you must set tauBarostat.\n");
1400	+	painCave.isFatal = 1;
1401	+	simError();
1402	+	}
1403	+
1404	+	info->the_integrator = myNPTi;
1405	+	break;
1406	+
1407	+	case NPTf_ENS:
1408	+	if (globals->haveZconstraints()){
1409	+
1410	+	std::cerr << "ZConstraint is temporarily disabled\n";
1411	+
1412	+	//      setupZConstraint(info[k]);
1413	+	//      myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1414	+	}
1415	+	//       else
1416	+	myNPTf = new NPTf(&(info[k]), the_ff);
1417	+
1418	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1419	+
1420	+	if (globals->haveTargetPressure())
1421	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1422	+	else{
1423	+	sprintf(painCave.errMsg,
1424	+	"SimSetup error: If you use a constant pressure\n"
1425	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1426	+	painCave.isFatal = 1;
1427	+	simError();
1428	+	}
1429	+
1430	+	if (globals->haveTauThermostat())
1431	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1432	+
1433	+	else{
1434	+	sprintf(painCave.errMsg,
1435	+	"SimSetup error: If you use an NPT\n"
1436	+	"    ensemble, you must set tauThermostat.\n");
1437	+	painCave.isFatal = 1;
1438	+	simError();
1439	+	}
1440	+
1441	+	if (globals->haveTauBarostat())
1442	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1443	+
1444	+	else{
1445	+	sprintf(painCave.errMsg,
1446	+	"SimSetup error: If you use an NPT\n"
1447	+	"    ensemble, you must set tauBarostat.\n");
1448	+	painCave.isFatal = 1;
1449	+	simError();
1450	+	}
1451	+
1452	+	info->the_integrator = myNPTf;
1453	+	break;
1454	+
1455	+	case NPTxyz_ENS:
1456	+	if (globals->haveZconstraints()){
1457	+
1458	+	std::cerr << "ZConstraint is temporarily disabled\n";
1459	+
1460	+	//      setupZConstraint(info[k]);
1461	+	//      myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1462	+	}
1463	+	//       else
1464	+	myNPTxyz = new NPTxyz(&(info[k]), the_ff);
1465	+
1466	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1467	+
1468	+	if (globals->haveTargetPressure())
1469	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1470	+	else{
1471	+	sprintf(painCave.errMsg,
1472	+	"SimSetup error: If you use a constant pressure\n"
1473	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1474	+	painCave.isFatal = 1;
1475	+	simError();
1476	+	}
1477	+
1478	+	if (globals->haveTauThermostat())
1479	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1480	+	else{
1481	+	sprintf(painCave.errMsg,
1482	+	"SimSetup error: If you use an NPT\n"
1483	+	"    ensemble, you must set tauThermostat.\n");
1484	+	painCave.isFatal = 1;
1485	+	simError();
1486	+	}
1487	+
1488	+	if (globals->haveTauBarostat())
1489	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1490	+	else{
1491	+	sprintf(painCave.errMsg,
1492	+	"SimSetup error: If you use an NPT\n"
1493	+	"    ensemble, you must set tauBarostat.\n");
1494	+	painCave.isFatal = 1;
1495	+	simError();
1496	+	}
1497	+
1498	+	info->the_integrator = myNPTxyz;
1499	+	break;
1500	+
1501	+	default:
1502	+	sprintf(painCave.errMsg,
1503	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1504	+	painCave.isFatal = 1;
1505	+	simError();
1506	+	}
1507	+	}
1508	+	}
1509	+
1510	+	void SimSetup::initFortran(void){
1511	+	info[0].refreshSim();
1512	+
1513	+	if (!strcmp(info[0].mixingRule, "standard")){
1514	+	the_ff->initForceField(LB_MIXING_RULE);
1515	+	}
1516	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1517	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1518	+	}
1519	+	else{
1520	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1521	+	info[0].mixingRule);
1522	+	painCave.isFatal = 1;
1523	+	simError();
1524	+	}
1525	+
1526	+
1527	+	#ifdef IS_MPI
1528	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1529	+	MPIcheckPoint();
1530	+	#endif // is_mpi
1531	+	}
1532	+
1533	+	// void SimSetup::setupZConstraint(SimInfo& theInfo){
1534	+	//   int nZConstraints;
1535	+	//   ZconStamp** zconStamp;
1536	+
1537	+	//   if (globals->haveZconstraintTime()){
1538	+	//     //add sample time of z-constraint  into SimInfo's property list
1539	+	//     DoubleData* zconsTimeProp = new DoubleData();
1540	+	//     zconsTimeProp->setID(ZCONSTIME_ID);
1541	+	//     zconsTimeProp->setData(globals->getZconsTime());
1542	+	//     theInfo.addProperty(zconsTimeProp);
1543	+	//   }
1544	+	//   else{
1545	+	//     sprintf(painCave.errMsg,
1546	+	//             "ZConstraint error: If you use an ZConstraint\n"
1547	+	//             " , you must set sample time.\n");
1548	+	//     painCave.isFatal = 1;
1549	+	//     simError();
1550	+	//   }
1551	+
1552	+	//   //push zconsTol into siminfo, if user does not specify
1553	+	//   //value for zconsTol, a default value will be used
1554	+	//   DoubleData* zconsTol = new DoubleData();
1555	+	//   zconsTol->setID(ZCONSTOL_ID);
1556	+	//   if (globals->haveZconsTol()){
1557	+	//     zconsTol->setData(globals->getZconsTol());
1558	+	//   }
1559	+	//   else{
1560	+	//     double defaultZConsTol = 0.01;
1561	+	//     sprintf(painCave.errMsg,
1562	+	//             "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1563	+	//             " , default value %f is used.\n",
1564	+	//             defaultZConsTol);
1565	+	//     painCave.isFatal = 0;
1566	+	//     simError();
1567	+
1568	+	//     zconsTol->setData(defaultZConsTol);
1569	+	//   }
1570	+	//   theInfo.addProperty(zconsTol);
1571	+
1572	+	//   //set Force Subtraction Policy
1573	+	//   StringData* zconsForcePolicy = new StringData();
1574	+	//   zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1575	+
1576	+	//   if (globals->haveZconsForcePolicy()){
1577	+	//     zconsForcePolicy->setData(globals->getZconsForcePolicy());
1578	+	//   }
1579	+	//   else{
1580	+	//     sprintf(painCave.errMsg,
1581	+	//             "ZConstraint Warning: User does not set force Subtraction policy, "
1582	+	//             "PolicyByMass is used\n");
1583	+	//     painCave.isFatal = 0;
1584	+	//     simError();
1585	+	//     zconsForcePolicy->setData("BYMASS");
1586	+	//   }
1587	+
1588	+	//   theInfo.addProperty(zconsForcePolicy);
1589	+
1590	+	//   //Determine the name of ouput file and add it into SimInfo's property list
1591	+	//   //Be careful, do not use inFileName, since it is a pointer which
1592	+	//   //point to a string at master node, and slave nodes do not contain that string
1593	+
1594	+	//   string zconsOutput(theInfo.finalName);
1595	+
1596	+	//   zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1597	+
1598	+	//   StringData* zconsFilename = new StringData();
1599	+	//   zconsFilename->setID(ZCONSFILENAME_ID);
1600	+	//   zconsFilename->setData(zconsOutput);
1601	+
1602	+	//   theInfo.addProperty(zconsFilename);
1603	+
1604	+	//   //setup index, pos and other parameters of z-constraint molecules
1605	+	//   nZConstraints = globals->getNzConstraints();
1606	+	//   theInfo.nZconstraints = nZConstraints;
1607	+
1608	+	//   zconStamp = globals->getZconStamp();
1609	+	//   ZConsParaItem tempParaItem;
1610	+
1611	+	//   ZConsParaData* zconsParaData = new ZConsParaData();
1612	+	//   zconsParaData->setID(ZCONSPARADATA_ID);
1613	+
1614	+	//   for (int i = 0; i < nZConstraints; i++){
1615	+	//     tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1616	+	//     tempParaItem.zPos = zconStamp[i]->getZpos();
1617	+	//     tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1618	+	//     tempParaItem.kRatio = zconStamp[i]->getKratio();
1619	+
1620	+	//     zconsParaData->addItem(tempParaItem);
1621	+	//   }
1622	+
1623	+	//   //check the uniqueness of index
1624	+	//   if(!zconsParaData->isIndexUnique()){
1625	+	//     sprintf(painCave.errMsg,
1626	+	//             "ZConstraint Error: molIndex is not unique\n");
1627	+	//     painCave.isFatal = 1;
1628	+	//     simError();
1629	+	//   }
1630	+
1631	+	//   //sort the parameters by index of molecules
1632	+	//   zconsParaData->sortByIndex();
1633	+
1634	+	//   //push data into siminfo, therefore, we can retrieve later
1635	+	//   theInfo.addProperty(zconsParaData);
1636	+	// }

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