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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 605 by gezelter, Tue Jul 15 03:27:24 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 14 | Line 18
18
19		// some defines for ensemble and Forcefield  cases
20
21	<	#define NVE_ENS   0
22	<	#define NVT_ENS   1
23	<	#define NPTi_ENS  2
24	<	#define NPTf_ENS  3
21	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
21	>	#define NVE_ENS        0
22	>	#define NVT_ENS        1
23	>	#define NPTi_ENS       2
24	>	#define NPTf_ENS       3
25
24	–
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 41 | 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();
73	<	mpiEventLoop();
74	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92	<	void SimSetup::createSim( void ){
92	>	void SimSetup::createSim(void){
93
94	<	MakeStamps *the_stamps;
82	<	Globals* the_globals;
83	<	int i, j, k, globalAtomIndex;
84	<
85	<	int ensembleCase;
86	<	int ffCase;
87	<
88	<	ensembleCase = -1;
89	<	ffCase = -1;
94	>	// gather all of the information from the Bass file
95
96	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
96	>	gatherInfo();
97
98	<	// set the easy ones first
96	<	simnfo->target_temp = the_globals->getTargetTemp();
97	<	simnfo->dt = the_globals->getDt();
98	<	simnfo->run_time = the_globals->getRunTime();
98	>	// creation of complex system objects
99
100	<	// get the ones we know are there, yet still may need some work.
101	<	n_components = the_globals->getNComponents();
102	<	strcpy( force_field, the_globals->getForceField() );
100	>	sysObjectsCreation();
101
102	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106	<	else{
107	<	sprintf( painCave.errMsg,
108	<	"SimSetup Error. Unrecognized force field -> %s\n",
109	<	force_field );
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
102	>	// check on the post processing info
103
104	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
104	>	finalInfoCheck();
105
106	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
107	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
108	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
109	<	ensembleCase = NPTi_ENS;
121	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
122	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
123	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124	<	else{
125	<	sprintf( painCave.errMsg,
126	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
127	<	"reverting to NVE for this simulation.\n",
128	<	ensemble );
129	<	painCave.isFatal = 0;
130	<	simError();
131	<	strcpy( ensemble, "NVE" );
132	<	ensembleCase = NVE_ENS;
106	>	// initialize the system coordinates
107	>
108	>	if (!isInfoArray){
109	>	initSystemCoords();
110		}
134	–	strcpy( simnfo->ensemble, ensemble );
111
112	+	// make the output filenames
113
114	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
138	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
139	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140	<	//     if (the_globals->haveTargetPressure())
141	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142	<	//     else {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "SimSetup error: If you use the constant pressure\n"
145	<	//                "    ensemble, you must set targetPressure.\n"
146	<	//                "    This was found in the BASS file.\n");
147	<	//       painCave.isFatal = 1;
148	<	//       simError();
149	<	//     }
114	>	makeOutNames();
115
116	<	//     if (the_globals->haveTauThermostat())
152	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153	<	//     else if (the_globals->haveQmass())
154	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
155	<	//     else {
156	<	//       sprintf( painCave.errMsg,
157	<	//                "SimSetup error: If you use one of the constant temperature\n"
158	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
159	<	//                "    Neither of these was found in the BASS file.\n");
160	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
116	>	// make the integrator
117
118	<	//     if (the_globals->haveTauBarostat())
165	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166	<	//     else {
167	<	//       sprintf( painCave.errMsg,
168	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
118	>	makeIntegrator();
119
120	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
121	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
122	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
120	>	#ifdef IS_MPI
121	>	mpiSim->mpiRefresh();
122	>	#endif
123
124	<	//     if (the_globals->haveTauThermostat())
180	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181	<	//     else if (the_globals->haveQmass())
182	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
183	<	//     else {
184	<	//       sprintf( painCave.errMsg,
185	<	//                "SimSetup error: If you use one of the constant temperature\n"
186	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
187	<	//                "    Neither of these was found in the BASS file.\n");
188	<	//       painCave.isFatal = 1;
189	<	//       simError();
190	<	//     }
124	>	// initialize the Fortran
125
126	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
127	<	simnfo->usePBC = the_globals->getPBC();
194	<
195	<	int usesDipoles = 0;
196	<	switch( ffCase ){
126	>	initFortran();
127	>	}
128
198	–	case FF_DUFF:
199	–	the_ff = new DUFF();
200	–	usesDipoles = 1;
201	–	break;
129
130	<	case FF_LJ:
131	<	the_ff = new LJFF();
132	<	break;
130	>	void SimSetup::makeMolecules(void){
131	>	int k;
132	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
133	>	molInit molInfo;
134	>	DirectionalAtom* dAtom;
135	>	LinkedAssign* extras;
136	>	LinkedAssign* current_extra;
137	>	AtomStamp* currentAtom;
138	>	BondStamp* currentBond;
139	>	BendStamp* currentBend;
140	>	TorsionStamp* currentTorsion;
141
142	<	default:
143	<	sprintf( painCave.errMsg,
144	<	"SimSetup Error. Unrecognized force field in case statement.\n");
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
142	>	bond_pair* theBonds;
143	>	bend_set* theBends;
144	>	torsion_set* theTorsions;
145
214	–	#ifdef IS_MPI
215	–	strcpy( checkPointMsg, "ForceField creation successful" );
216	–	MPIcheckPoint();
217	–	#endif // is_mpi
146
147	<	// get the components and calculate the tot_nMol and indvidual n_mol
220	<	the_components = the_globals->getComponents();
221	<	components_nmol = new int[n_components];
222	<	comp_stamps = new MoleculeStamp*[n_components];
147	>	//init the forceField paramters
148
149	<	if( !the_globals->haveNMol() ){
225	<	// we don't have the total number of molecules, so we assume it is
226	<	// given in each component
149	>	the_ff->readParams();
150
228	–	tot_nmol = 0;
229	–	for( i=0; i<n_components; i++ ){
151
152	<	if( !the_components[i]->haveNMol() ){
232	<	// we have a problem
233	<	sprintf( painCave.errMsg,
234	<	"SimSetup Error. No global NMol or component NMol"
235	<	" given. Cannot calculate the number of atoms.\n" );
236	<	painCave.isFatal = 1;
237	<	simError();
238	<	}
152	>	// init the atoms
153
154	<	tot_nmol += the_components[i]->getNMol();
241	<	components_nmol[i] = the_components[i]->getNMol();
242	<	}
243	<	}
244	<	else{
245	<	sprintf( painCave.errMsg,
246	<	"SimSetup error.\n"
247	<	"\tSorry, the ability to specify total"
248	<	" nMols and then give molfractions in the components\n"
249	<	"\tis not currently supported."
250	<	" Please give nMol in the components.\n" );
251	<	painCave.isFatal = 1;
252	<	simError();
253	<
254	<
255	<	//     tot_nmol = the_globals->getNMol();
256	<
257	<	//   //we have the total number of molecules, now we check for molfractions
258	<	//     for( i=0; i<n_components; i++ ){
259	<
260	<	//       if( !the_components[i]->haveMolFraction() ){
261	<
262	<	//  if( !the_components[i]->haveNMol() ){
263	<	//    //we have a problem
264	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
265	<	//              << " nMol was given in component
266	<
267	<	}
154	>	double ux, uy, uz, u, uSqr;
155
156	<	#ifdef IS_MPI
157	<	strcpy( checkPointMsg, "Have the number of components" );
271	<	MPIcheckPoint();
272	<	#endif // is_mpi
156	>	for (k = 0; k < nInfo; k++){
157	>	the_ff->setSimInfo(&(info[k]));
158
159	<	// make an array of molecule stamps that match the components used.
160	<	// also extract the used stamps out into a separate linked list
159	>	atomOffset = 0;
160	>	excludeOffset = 0;
161	>	for (i = 0; i < info[k].n_mol; i++){
162	>	stampID = info[k].molecules[i].getStampID();
163
164	<	simnfo->nComponents = n_components;
165	<	simnfo->componentsNmol = components_nmol;
166	<	simnfo->compStamps = comp_stamps;
167	<	simnfo->headStamp = new LinkedMolStamp();
168	<
282	<	char* id;
283	<	LinkedMolStamp* headStamp = simnfo->headStamp;
284	<	LinkedMolStamp* currentStamp = NULL;
285	<	for( i=0; i<n_components; i++ ){
164	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
165	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
166	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
167	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
168	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
169
170	<	id = the_components[i]->getType();
171	<	comp_stamps[i] = NULL;
172	<
173	<	// check to make sure the component isn't already in the list
170	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
171	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
172	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
173	>	molInfo.myBends = new Bend * [molInfo.nBends];
174	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
175
176	<	comp_stamps[i] = headStamp->match( id );
177	<	if( comp_stamps[i] == NULL ){
178	<
295	<	// extract the component from the list;
296	<
297	<	currentStamp = the_stamps->extractMolStamp( id );
298	<	if( currentStamp == NULL ){
299	<	sprintf( painCave.errMsg,
300	<	"SimSetup error: Component \"%s\" was not found in the "
301	<	"list of declared molecules\n",
302	<	id );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<
307	<	headStamp->add( currentStamp );
308	<	comp_stamps[i] = headStamp->match( id );
309	<	}
310	<	}
176	>	theBonds = new bond_pair[molInfo.nBonds];
177	>	theBends = new bend_set[molInfo.nBends];
178	>	theTorsions = new torsion_set[molInfo.nTorsions];
179
180	<	#ifdef IS_MPI
313	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
314	<	MPIcheckPoint();
315	<	#endif // is_mpi
316	<
180	>	// make the Atoms
181
182	+	for (j = 0; j < molInfo.nAtoms; j++){
183	+	currentAtom = comp_stamps[stampID]->getAtom(j);
184	+	if (currentAtom->haveOrientation()){
185	+	dAtom = new DirectionalAtom((j + atomOffset),
186	+	info[k].getConfiguration());
187	+	info[k].n_oriented++;
188	+	molInfo.myAtoms[j] = dAtom;
189
190	+	ux = currentAtom->getOrntX();
191	+	uy = currentAtom->getOrntY();
192	+	uz = currentAtom->getOrntZ();
193
194	<	// caclulate the number of atoms, bonds, bends and torsions
194	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
195
196	<	tot_atoms = 0;
197	<	tot_bonds = 0;
198	<	tot_bends = 0;
199	<	tot_torsions = 0;
326	<	for( i=0; i<n_components; i++ ){
327	<
328	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
329	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
330	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
331	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
332	<	}
196	>	u = sqrt(uSqr);
197	>	ux = ux / u;
198	>	uy = uy / u;
199	>	uz = uz / u;
200
201	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
201	>	dAtom->setSUx(ux);
202	>	dAtom->setSUy(uy);
203	>	dAtom->setSUz(uz);
204	>	}
205	>	else{
206	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
207	>	info[k].getConfiguration());
208	>	}
209	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
210
336	–	simnfo->n_atoms = tot_atoms;
337	–	simnfo->n_bonds = tot_bonds;
338	–	simnfo->n_bends = tot_bends;
339	–	simnfo->n_torsions = tot_torsions;
340	–	simnfo->n_SRI = tot_SRI;
341	–	simnfo->n_mol = tot_nmol;
342	–
343	–	simnfo->molMembershipArray = new int[tot_atoms];
344	–
211		#ifdef IS_MPI
212
213	<	// divide the molecules among processors here.
348	<
349	<	mpiSim = new mpiSimulation( simnfo );
350	<
351	<	globalIndex = mpiSim->divideLabor();
213	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
214
215	<	// set up the local variables
216	<
355	<	int localMol, allMol;
356	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
215	>	#endif // is_mpi
216	>	}
217
218	<	int* mol2proc = mpiSim->getMolToProcMap();
219	<	int* molCompType = mpiSim->getMolComponentType();
220	<
221	<	allMol = 0;
222	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
218	>	// make the bonds
219	>	for (j = 0; j < molInfo.nBonds; j++){
220	>	currentBond = comp_stamps[stampID]->getBond(j);
221	>	theBonds[j].a = currentBond->getA() + atomOffset;
222	>	theBonds[j].b = currentBond->getB() + atomOffset;
223
224	+	exI = theBonds[j].a;
225	+	exJ = theBonds[j].b;
226
227	<	for( i=0; i<n_components; i++ ){
227	>	// exclude_I must always be the smaller of the pair
228	>	if (exI > exJ){
229	>	tempEx = exI;
230	>	exI = exJ;
231	>	exJ = tempEx;
232	>	}
233	>	#ifdef IS_MPI
234	>	tempEx = exI;
235	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
236	>	tempEx = exJ;
237	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
238
239	<	for( j=0; j<components_nmol[i]; j++ ){
240	<
241	<	if( mol2proc[allMol] == worldRank ){
242	<
243	<	local_atoms +=    comp_stamps[i]->getNAtoms();
377	<	local_bonds +=    comp_stamps[i]->getNBonds();
378	<	local_bends +=    comp_stamps[i]->getNBends();
379	<	local_torsions += comp_stamps[i]->getNTorsions();
380	<	localMol++;
381	<	}
382	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
384	<	globalAtomIndex++;
239	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
240	>	#else  // isn't MPI
241	>
242	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
243	>	#endif  //is_mpi
244		}
245	+	excludeOffset += molInfo.nBonds;
246
247	<	allMol++;
248	<	}
249	<	}
250	<	local_SRI = local_bonds + local_bends + local_torsions;
251	<
252	<	simnfo->n_atoms = mpiSim->getMyNlocal();
393	<
394	<	if( local_atoms != simnfo->n_atoms ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
397	<	" localAtom (%d) are not equal.\n",
398	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
247	>	//make the bends
248	>	for (j = 0; j < molInfo.nBends; j++){
249	>	currentBend = comp_stamps[stampID]->getBend(j);
250	>	theBends[j].a = currentBend->getA() + atomOffset;
251	>	theBends[j].b = currentBend->getB() + atomOffset;
252	>	theBends[j].c = currentBend->getC() + atomOffset;
253
254	<	simnfo->n_bonds = local_bonds;
255	<	simnfo->n_bends = local_bends;
256	<	simnfo->n_torsions = local_torsions;
407	<	simnfo->n_SRI = local_SRI;
408	<	simnfo->n_mol = localMol;
254	>	if (currentBend->haveExtras()){
255	>	extras = currentBend->getExtras();
256	>	current_extra = extras;
257
258	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
259	<	MPIcheckPoint();
260	<
261	<
262	<	#endif // is_mpi
263	<
258	>	while (current_extra != NULL){
259	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
260	>	switch (current_extra->getType()){
261	>	case 0:
262	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
263	>	theBends[j].isGhost = 1;
264	>	break;
265
266	<	// create the atom and short range interaction arrays
266	>	case 1:
267	>	theBends[j].ghost = (int) current_extra->getDouble() +
268	>	atomOffset;
269	>	theBends[j].isGhost = 1;
270	>	break;
271
272	<	Atom::createArrays(simnfo->n_atoms);
273	<	the_atoms = new Atom*[simnfo->n_atoms];
274	<	the_molecules = new Molecule[simnfo->n_mol];
275	<	int molIndex;
272	>	default:
273	>	sprintf(painCave.errMsg,
274	>	"SimSetup Error: ghostVectorSource was neither a "
275	>	"double nor an int.\n"
276	>	"-->Bend[%d] in %s\n",
277	>	j, comp_stamps[stampID]->getID());
278	>	painCave.isFatal = 1;
279	>	simError();
280	>	}
281	>	}
282	>	else{
283	>	sprintf(painCave.errMsg,
284	>	"SimSetup Error: unhandled bend assignment:\n"
285	>	"    -->%s in Bend[%d] in %s\n",
286	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290
291	<	// initialize the molecule's stampID's
291	>	current_extra = current_extra->getNext();
292	>	}
293	>	}
294
295	+	if (!theBends[j].isGhost){
296	+	exI = theBends[j].a;
297	+	exJ = theBends[j].c;
298	+	}
299	+	else{
300	+	exI = theBends[j].a;
301	+	exJ = theBends[j].b;
302	+	}
303	+
304	+	// exclude_I must always be the smaller of the pair
305	+	if (exI > exJ){
306	+	tempEx = exI;
307	+	exI = exJ;
308	+	exJ = tempEx;
309	+	}
310		#ifdef IS_MPI
311	<
311	>	tempEx = exI;
312	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
313	>	tempEx = exJ;
314	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
315
316	<	molIndex = 0;
317	<	for(i=0; i<mpiSim->getTotNmol(); i++){
318	<
319	<	if(mol2proc[i] == worldRank ){
320	<	the_molecules[molIndex].setStampID( molCompType[i] );
321	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
316	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
317	>	#else  // isn't MPI
318	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
319	>	#endif  //is_mpi
320	>	}
321	>	excludeOffset += molInfo.nBends;
322
323	<	#else // is_mpi
324	<
325	<	molIndex = 0;
326	<	globalAtomIndex = 0;
327	<	for(i=0; i<n_components; i++){
328	<	for(j=0; j<components_nmol[i]; j++ ){
446	<	the_molecules[molIndex].setStampID( i );
447	<	the_molecules[molIndex].setMyIndex( molIndex );
448	<	the_molecules[molIndex].setGlobalIndex( molIndex );
449	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
450	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
451	<	globalAtomIndex++;
452	<	}
453	<	molIndex++;
454	<	}
455	<	}
456	<
323	>	for (j = 0; j < molInfo.nTorsions; j++){
324	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
325	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
326	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
327	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
328	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
329
330	<	#endif // is_mpi
330	>	exI = theTorsions[j].a;
331	>	exJ = theTorsions[j].d;
332
333	+	// exclude_I must always be the smaller of the pair
334	+	if (exI > exJ){
335	+	tempEx = exI;
336	+	exI = exJ;
337	+	exJ = tempEx;
338	+	}
339	+	#ifdef IS_MPI
340	+	tempEx = exI;
341	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
342	+	tempEx = exJ;
343	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344
345	<	if( simnfo->n_SRI ){
346	<
347	<	Exclude::createArray(simnfo->n_SRI);
348	<	the_excludes = new Exclude*[simnfo->n_SRI];
349	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
350	<	simnfo->globalExcludes = new int;
467	<	simnfo->n_exclude = simnfo->n_SRI;
468	<	}
469	<	else{
470	<
471	<	Exclude::createArray( 1 );
472	<	the_excludes = new Exclude*;
473	<	the_excludes[0] = new Exclude(0);
474	<	the_excludes[0]->setPair( 0,0 );
475	<	simnfo->globalExcludes = new int;
476	<	simnfo->globalExcludes[0] = 0;
477	<	simnfo->n_exclude = 0;
478	<	}
345	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
346	>	#else  // isn't MPI
347	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
348	>	#endif  //is_mpi
349	>	}
350	>	excludeOffset += molInfo.nTorsions;
351
480	–	// set the arrays into the SimInfo object
352
353	<	simnfo->atoms = the_atoms;
483	<	simnfo->molecules = the_molecules;
484	<	simnfo->nGlobalExcludes = 0;
485	<	simnfo->excludes = the_excludes;
353	>	// send the arrays off to the forceField for init.
354
355	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
356	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
357	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
358	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
359	+	theTorsions);
360
488	–	// get some of the tricky things that may still be in the globals
361
362	<	double boxVector[3];
491	<	if( the_globals->haveBox() ){
492	<	boxVector[0] = the_globals->getBox();
493	<	boxVector[1] = the_globals->getBox();
494	<	boxVector[2] = the_globals->getBox();
495	<
496	<	simnfo->setBox( boxVector );
497	<	}
498	<	else if( the_globals->haveDensity() ){
362	>	info[k].molecules[i].initialize(molInfo);
363
500	–	double vol;
501	–	vol = (double)tot_nmol / the_globals->getDensity();
502	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
503	–	boxVector[1] = boxVector[0];
504	–	boxVector[2] = boxVector[0];
364
365	<	simnfo->setBox( boxVector );
366	<	}
367	<	else{
368	<	if( !the_globals->haveBoxX() ){
510	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxX size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
365	>	atomOffset += molInfo.nAtoms;
366	>	delete[] theBonds;
367	>	delete[] theBends;
368	>	delete[] theTorsions;
369		}
515	–	boxVector[0] = the_globals->getBoxX();
516	–
517	–	if( !the_globals->haveBoxY() ){
518	–	sprintf( painCave.errMsg,
519	–	"SimSetup error, no periodic BoxY size given.\n" );
520	–	painCave.isFatal = 1;
521	–	simError();
522	–	}
523	–	boxVector[1] = the_globals->getBoxY();
524	–
525	–	if( !the_globals->haveBoxZ() ){
526	–	sprintf( painCave.errMsg,
527	–	"SimSetup error, no periodic BoxZ size given.\n" );
528	–	painCave.isFatal = 1;
529	–	simError();
530	–	}
531	–	boxVector[2] = the_globals->getBoxZ();
532	–
533	–	simnfo->setBox( boxVector );
370		}
371
372		#ifdef IS_MPI
373	<	strcpy( checkPointMsg, "Box size set up" );
373	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
374		MPIcheckPoint();
375		#endif // is_mpi
376
377	+	// clean up the forcefield
378
379	<	// initialize the arrays
379	>	the_ff->calcRcut();
380	>	the_ff->cleanMe();
381	>	}
382
383	<	the_ff->setSimInfo( simnfo );
383	>	void SimSetup::initFromBass(void){
384	>	int i, j, k;
385	>	int n_cells;
386	>	double cellx, celly, cellz;
387	>	double temp1, temp2, temp3;
388	>	int n_per_extra;
389	>	int n_extra;
390	>	int have_extra, done;
391
392	<	makeMolecules();
393	<	simnfo->identArray = new int[simnfo->n_atoms];
394	<	for(i=0; i<simnfo->n_atoms; i++){
395	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
550	<	}
551	<
552	<	if (the_globals->getUseRF() ) {
553	<	simnfo->useReactionField = 1;
554	<
555	<	if( !the_globals->haveECR() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 1/2 the smallest "
558	<	"box length for the electrostaticCutoffRadius.\n"
559	<	"I hope you have a very fast processor!\n");
560	<	painCave.isFatal = 0;
561	<	simError();
562	<	double smallest;
563	<	smallest = simnfo->boxLx;
564	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566	<	simnfo->ecr = 0.5 * smallest;
567	<	} else {
568	<	simnfo->ecr        = the_globals->getECR();
569	<	}
392	>	double vel[3];
393	>	vel[0] = 0.0;
394	>	vel[1] = 0.0;
395	>	vel[2] = 0.0;
396
397	<	if( !the_globals->haveEST() ){
398	<	sprintf( painCave.errMsg,
399	<	"SimSetup Warning: using default value of 0.05 * the "
400	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
401	<	);
402	<	painCave.isFatal = 0;
403	<	simError();
404	<	simnfo->est = 0.05 * simnfo->ecr;
405	<	} else {
406	<	simnfo->est        = the_globals->getEST();
407	<	}
408	<
409	<	if(!the_globals->haveDielectric() ){
410	<	sprintf( painCave.errMsg,
411	<	"SimSetup Error: You are trying to use Reaction Field without"
412	<	"setting a dielectric constant!\n"
413	<	);
397	>	temp1 = (double) tot_nmol / 4.0;
398	>	temp2 = pow(temp1, (1.0 / 3.0));
399	>	temp3 = ceil(temp2);
400	>
401	>	have_extra = 0;
402	>	if (temp2 < temp3){
403	>	// we have a non-complete lattice
404	>	have_extra = 1;
405	>
406	>	n_cells = (int) temp3 - 1;
407	>	cellx = info[0].boxL[0] / temp3;
408	>	celly = info[0].boxL[1] / temp3;
409	>	cellz = info[0].boxL[2] / temp3;
410	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
411	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
412	>	n_per_extra = (int) ceil(temp1);
413	>
414	>	if (n_per_extra > 4){
415	>	sprintf(painCave.errMsg,
416	>	"SimSetup error. There has been an error in constructing"
417	>	" the non-complete lattice.\n");
418		painCave.isFatal = 1;
419		simError();
420		}
421	<	simnfo->dielectric = the_globals->getDielectric();
422	<	} else {
423	<	if (usesDipoles) {
424	<
425	<	if( !the_globals->haveECR() ){
426	<	sprintf( painCave.errMsg,
427	<	"SimSetup Warning: using default value of 1/2 the smallest "
428	<	"box length for the electrostaticCutoffRadius.\n"
429	<	"I hope you have a very fast processor!\n");
430	<	painCave.isFatal = 0;
431	<	simError();
432	<	double smallest;
433	<	smallest = simnfo->boxLx;
434	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
435	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
436	<	simnfo->ecr = 0.5 * smallest;
437	<	} else {
438	<	simnfo->ecr        = the_globals->getECR();
421	>	}
422	>	else{
423	>	n_cells = (int) temp3;
424	>	cellx = info[0].boxL[0] / temp3;
425	>	celly = info[0].boxL[1] / temp3;
426	>	cellz = info[0].boxL[2] / temp3;
427	>	}
428	>
429	>	current_mol = 0;
430	>	current_comp_mol = 0;
431	>	current_comp = 0;
432	>	current_atom_ndx = 0;
433	>
434	>	for (i = 0; i < n_cells ; i++){
435	>	for (j = 0; j < n_cells; j++){
436	>	for (k = 0; k < n_cells; k++){
437	>	makeElement(i * cellx, j * celly, k * cellz);
438	>
439	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
440	>
441	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
442	>
443	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
444		}
610	–
611	–	if( !the_globals->haveEST() ){
612	–	sprintf( painCave.errMsg,
613	–	"SimSetup Warning: using default value of 5%% of the "
614	–	"electrostaticCutoffRadius for the "
615	–	"electrostaticSkinThickness\n"
616	–	);
617	–	painCave.isFatal = 0;
618	–	simError();
619	–	simnfo->est = 0.05 * simnfo->ecr;
620	–	} else {
621	–	simnfo->est        = the_globals->getEST();
622	–	}
445		}
446	<	}
446	>	}
447
448	<	#ifdef IS_MPI
449	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
628	<	MPIcheckPoint();
629	<	#endif // is_mpi
448	>	if (have_extra){
449	>	done = 0;
450
451	<	if( the_globals->haveInitialConfig() ){
452	<
453	<	InitializeFromFile* fileInit;
454	<	#ifdef IS_MPI // is_mpi
455	<	if( worldRank == 0 ){
456	<	#endif //is_mpi
457	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
458	<	#ifdef IS_MPI
459	<	}else fileInit = new InitializeFromFile( NULL );
460	<	#endif
461	<	fileInit->read_xyz( simnfo ); // default velocities on
451	>	int start_ndx;
452	>	for (i = 0; i < (n_cells + 1) && !done; i++){
453	>	for (j = 0; j < (n_cells + 1) && !done; j++){
454	>	if (i < n_cells){
455	>	if (j < n_cells){
456	>	start_ndx = n_cells;
457	>	}
458	>	else
459	>	start_ndx = 0;
460	>	}
461	>	else
462	>	start_ndx = 0;
463
464	<	delete fileInit;
465	<	}
466	<	else{
464	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
465	>	makeElement(i * cellx, j * celly, k * cellz);
466	>	done = (current_mol >= tot_nmol);
467
468	<	#ifdef IS_MPI
468	>	if (!done && n_per_extra > 1){
469	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
470	>	k * cellz);
471	>	done = (current_mol >= tot_nmol);
472	>	}
473
474	<	// no init from bass
475	<
476	<	sprintf( painCave.errMsg,
477	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
478	<	painCave.isFatal;
654	<	simError();
655	<
656	<	#else
474	>	if (!done && n_per_extra > 2){
475	>	makeElement(i * cellx, j * celly + 0.5 * celly,
476	>	k * cellz + 0.5 * cellz);
477	>	done = (current_mol >= tot_nmol);
478	>	}
479
480	<	initFromBass();
481	<
482	<
483	<	#endif
484	<	}
485	<
664	<	#ifdef IS_MPI
665	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
666	<	MPIcheckPoint();
667	<	#endif // is_mpi
668	<
669	<
670	<
671	<
672	<
673	<
674	<
675	<	#ifdef IS_MPI
676	<	if( worldRank == 0 ){
677	<	#endif // is_mpi
678	<
679	<	if( the_globals->haveFinalConfig() ){
680	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
681	<	}
682	<	else{
683	<	strcpy( simnfo->finalName, inFileName );
684	<	char* endTest;
685	<	int nameLength = strlen( simnfo->finalName );
686	<	endTest = &(simnfo->finalName[nameLength - 5]);
687	<	if( !strcmp( endTest, ".bass" ) ){
688	<	strcpy( endTest, ".eor" );
480	>	if (!done && n_per_extra > 3){
481	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
482	>	k * cellz + 0.5 * cellz);
483	>	done = (current_mol >= tot_nmol);
484	>	}
485	>	}
486		}
690	–	else if( !strcmp( endTest, ".BASS" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else{
694	–	endTest = &(simnfo->finalName[nameLength - 4]);
695	–	if( !strcmp( endTest, ".bss" ) ){
696	–	strcpy( endTest, ".eor" );
697	–	}
698	–	else if( !strcmp( endTest, ".mdl" ) ){
699	–	strcpy( endTest, ".eor" );
700	–	}
701	–	else{
702	–	strcat( simnfo->finalName, ".eor" );
703	–	}
704	–	}
487		}
706	–
707	–	// make the sample and status out names
708	–
709	–	strcpy( simnfo->sampleName, inFileName );
710	–	char* endTest;
711	–	int nameLength = strlen( simnfo->sampleName );
712	–	endTest = &(simnfo->sampleName[nameLength - 5]);
713	–	if( !strcmp( endTest, ".bass" ) ){
714	–	strcpy( endTest, ".dump" );
715	–	}
716	–	else if( !strcmp( endTest, ".BASS" ) ){
717	–	strcpy( endTest, ".dump" );
718	–	}
719	–	else{
720	–	endTest = &(simnfo->sampleName[nameLength - 4]);
721	–	if( !strcmp( endTest, ".bss" ) ){
722	–	strcpy( endTest, ".dump" );
723	–	}
724	–	else if( !strcmp( endTest, ".mdl" ) ){
725	–	strcpy( endTest, ".dump" );
726	–	}
727	–	else{
728	–	strcat( simnfo->sampleName, ".dump" );
729	–	}
730	–	}
731	–
732	–	strcpy( simnfo->statusName, inFileName );
733	–	nameLength = strlen( simnfo->statusName );
734	–	endTest = &(simnfo->statusName[nameLength - 5]);
735	–	if( !strcmp( endTest, ".bass" ) ){
736	–	strcpy( endTest, ".stat" );
737	–	}
738	–	else if( !strcmp( endTest, ".BASS" ) ){
739	–	strcpy( endTest, ".stat" );
740	–	}
741	–	else{
742	–	endTest = &(simnfo->statusName[nameLength - 4]);
743	–	if( !strcmp( endTest, ".bss" ) ){
744	–	strcpy( endTest, ".stat" );
745	–	}
746	–	else if( !strcmp( endTest, ".mdl" ) ){
747	–	strcpy( endTest, ".stat" );
748	–	}
749	–	else{
750	–	strcat( simnfo->statusName, ".stat" );
751	–	}
752	–	}
753	–
754	–	#ifdef IS_MPI
488		}
756	–	#endif // is_mpi
757	–
758	–	// set the status, sample, and themal kick times
759	–
760	–	if( the_globals->haveSampleTime() ){
761	–	simnfo->sampleTime = the_globals->getSampleTime();
762	–	simnfo->statusTime = simnfo->sampleTime;
763	–	simnfo->thermalTime = simnfo->sampleTime;
764	–	}
765	–	else{
766	–	simnfo->sampleTime = the_globals->getRunTime();
767	–	simnfo->statusTime = simnfo->sampleTime;
768	–	simnfo->thermalTime = simnfo->sampleTime;
769	–	}
489
490	<	if( the_globals->haveStatusTime() ){
491	<	simnfo->statusTime = the_globals->getStatusTime();
490	>	for (i = 0; i < info[0].n_atoms; i++){
491	>	info[0].atoms[i]->setVel(vel);
492		}
493	+	}
494
495	<	if( the_globals->haveThermalTime() ){
496	<	simnfo->thermalTime = the_globals->getThermalTime();
497	<	}
495	>	void SimSetup::makeElement(double x, double y, double z){
496	>	int k;
497	>	AtomStamp* current_atom;
498	>	DirectionalAtom* dAtom;
499	>	double rotMat[3][3];
500	>	double pos[3];
501
502	<	// check for the temperature set flag
502	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
503	>	current_atom = comp_stamps[current_comp]->getAtom(k);
504	>	if (!current_atom->havePosition()){
505	>	sprintf(painCave.errMsg,
506	>	"SimSetup:initFromBass error.\n"
507	>	"\tComponent %s, atom %s does not have a position specified.\n"
508	>	"\tThe initialization routine is unable to give a start"
509	>	" position.\n",
510	>	comp_stamps[current_comp]->getID(), current_atom->getType());
511	>	painCave.isFatal = 1;
512	>	simError();
513	>	}
514
515	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
515	>	pos[0] = x + current_atom->getPosX();
516	>	pos[1] = y + current_atom->getPosY();
517	>	pos[2] = z + current_atom->getPosZ();
518
519	+	info[0].atoms[current_atom_ndx]->setPos(pos);
520
521	<	// make the integrator
522	<
786	<
787	<	NVT*  myNVT = NULL;
788	<	NPTi* myNPTi = NULL;
789	<	NPTf* myNPTf = NULL;
790	<	NPTim* myNPTim = NULL;
791	<	NPTfm* myNPTfm = NULL;
521	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
522	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
523
524	<	switch( ensembleCase ){
524	>	rotMat[0][0] = 1.0;
525	>	rotMat[0][1] = 0.0;
526	>	rotMat[0][2] = 0.0;
527
528	<	case NVE_ENS:
529	<	new NVE( simnfo, the_ff );
530	<	break;
528	>	rotMat[1][0] = 0.0;
529	>	rotMat[1][1] = 1.0;
530	>	rotMat[1][2] = 0.0;
531
532	<	case NVT_ENS:
533	<	myNVT = new NVT( simnfo, the_ff );
534	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
532	>	rotMat[2][0] = 0.0;
533	>	rotMat[2][1] = 0.0;
534	>	rotMat[2][2] = 1.0;
535
536	<	if (the_globals->haveTauThermostat())
537	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
536	>	dAtom->setA(rotMat);
537	>	}
538
539	<	else {
540	<	sprintf( painCave.errMsg,
808	<	"SimSetup error: If you use the NVT\n"
809	<	"    ensemble, you must set tauThermostat.\n");
810	<	painCave.isFatal = 1;
811	<	simError();
812	<	}
813	<	break;
539	>	current_atom_ndx++;
540	>	}
541
542	<	case NPTi_ENS:
543	<	myNPTi = new NPTi( simnfo, the_ff );
817	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
542	>	current_mol++;
543	>	current_comp_mol++;
544
545	<	if (the_globals->haveTargetPressure())
546	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
547	<	else {
548	<	sprintf( painCave.errMsg,
549	<	"SimSetup error: If you use a constant pressure\n"
824	<	"    ensemble, you must set targetPressure in the BASS file.\n");
825	<	painCave.isFatal = 1;
826	<	simError();
827	<	}
828	<
829	<	if( the_globals->haveTauThermostat() )
830	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
831	<	else{
832	<	sprintf( painCave.errMsg,
833	<	"SimSetup error: If you use an NPT\n"
834	<	"    ensemble, you must set tauThermostat.\n");
835	<	painCave.isFatal = 1;
836	<	simError();
837	<	}
545	>	if (current_comp_mol >= components_nmol[current_comp]){
546	>	current_comp_mol = 0;
547	>	current_comp++;
548	>	}
549	>	}
550
839	–	if( the_globals->haveTauBarostat() )
840	–	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
841	–	else{
842	–	sprintf( painCave.errMsg,
843	–	"SimSetup error: If you use an NPT\n"
844	–	"    ensemble, you must set tauBarostat.\n");
845	–	painCave.isFatal = 1;
846	–	simError();
847	–	}
848	–	break;
551
552	<	case NPTf_ENS:
553	<	myNPTf = new NPTf( simnfo, the_ff );
852	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
552	>	void SimSetup::gatherInfo(void){
553	>	int i;
554
555	<	if (the_globals->haveTargetPressure())
556	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
856	<	else {
857	<	sprintf( painCave.errMsg,
858	<	"SimSetup error: If you use a constant pressure\n"
859	<	"    ensemble, you must set targetPressure in the BASS file.\n");
860	<	painCave.isFatal = 1;
861	<	simError();
862	<	}
555	>	ensembleCase = -1;
556	>	ffCase = -1;
557
558	<	if( the_globals->haveTauThermostat() )
865	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
866	<	else{
867	<	sprintf( painCave.errMsg,
868	<	"SimSetup error: If you use an NPT\n"
869	<	"    ensemble, you must set tauThermostat.\n");
870	<	painCave.isFatal = 1;
871	<	simError();
872	<	}
558	>	// set the easy ones first
559
560	<	if( the_globals->haveTauBarostat() )
561	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
562	<	else{
563	<	sprintf( painCave.errMsg,
564	<	"SimSetup error: If you use an NPT\n"
565	<	"    ensemble, you must set tauBarostat.\n");
880	<	painCave.isFatal = 1;
881	<	simError();
882	<	}
883	<	break;
884	<
885	<	case NPTim_ENS:
886	<	myNPTim = new NPTim( simnfo, the_ff );
887	<	myNPTim->setTargetTemp( the_globals->getTargetTemp());
560	>	for (i = 0; i < nInfo; i++){
561	>	info[i].target_temp = globals->getTargetTemp();
562	>	info[i].dt = globals->getDt();
563	>	info[i].run_time = globals->getRunTime();
564	>	}
565	>	n_components = globals->getNComponents();
566
889	–	if (the_globals->haveTargetPressure())
890	–	myNPTim->setTargetPressure(the_globals->getTargetPressure());
891	–	else {
892	–	sprintf( painCave.errMsg,
893	–	"SimSetup error: If you use a constant pressure\n"
894	–	"    ensemble, you must set targetPressure in the BASS file.\n");
895	–	painCave.isFatal = 1;
896	–	simError();
897	–	}
898	–
899	–	if( the_globals->haveTauThermostat() )
900	–	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
901	–	else{
902	–	sprintf( painCave.errMsg,
903	–	"SimSetup error: If you use an NPT\n"
904	–	"    ensemble, you must set tauThermostat.\n");
905	–	painCave.isFatal = 1;
906	–	simError();
907	–	}
567
568	<	if( the_globals->haveTauBarostat() )
910	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
911	<	else{
912	<	sprintf( painCave.errMsg,
913	<	"SimSetup error: If you use an NPT\n"
914	<	"    ensemble, you must set tauBarostat.\n");
915	<	painCave.isFatal = 1;
916	<	simError();
917	<	}
918	<	break;
568	>	// get the forceField
569
570	<	case NPTfm_ENS:
921	<	myNPTfm = new NPTfm( simnfo, the_ff );
922	<	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
570	>	strcpy(force_field, globals->getForceField());
571
572	<	if (the_globals->haveTargetPressure())
573	<	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
574	<	else {
575	<	sprintf( painCave.errMsg,
576	<	"SimSetup error: If you use a constant pressure\n"
577	<	"    ensemble, you must set targetPressure in the BASS file.\n");
578	<	painCave.isFatal = 1;
579	<	simError();
580	<	}
581	<
582	<	if( the_globals->haveTauThermostat() )
583	<	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
584	<	else{
585	<	sprintf( painCave.errMsg,
586	<	"SimSetup error: If you use an NPT\n"
939	<	"    ensemble, you must set tauThermostat.\n");
940	<	painCave.isFatal = 1;
941	<	simError();
942	<	}
572	>	if (!strcasecmp(force_field, "DUFF")){
573	>	ffCase = FF_DUFF;
574	>	}
575	>	else if (!strcasecmp(force_field, "LJ")){
576	>	ffCase = FF_LJ;
577	>	}
578	>	else if (!strcasecmp(force_field, "EAM")){
579	>	ffCase = FF_EAM;
580	>	}
581	>	else{
582	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
583	>	force_field);
584	>	painCave.isFatal = 1;
585	>	simError();
586	>	}
587
588	<	if( the_globals->haveTauBarostat() )
945	<	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
946	<	else{
947	<	sprintf( painCave.errMsg,
948	<	"SimSetup error: If you use an NPT\n"
949	<	"    ensemble, you must set tauBarostat.\n");
950	<	painCave.isFatal = 1;
951	<	simError();
952	<	}
953	<	break;
588	>	// get the ensemble
589
590	<	default:
591	<	sprintf( painCave.errMsg,
592	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
593	<	painCave.isFatal = 1;
959	<	simError();
590	>	strcpy(ensemble, globals->getEnsemble());
591	>
592	>	if (!strcasecmp(ensemble, "NVE")){
593	>	ensembleCase = NVE_ENS;
594		}
595	+	else if (!strcasecmp(ensemble, "NVT")){
596	+	ensembleCase = NVT_ENS;
597	+	}
598	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
599	+	ensembleCase = NPTi_ENS;
600	+	}
601	+	else if (!strcasecmp(ensemble, "NPTf")){
602	+	ensembleCase = NPTf_ENS;
603	+	}
604	+	else{
605	+	sprintf(painCave.errMsg,
606	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
607	+	"reverting to NVE for this simulation.\n",
608	+	ensemble);
609	+	painCave.isFatal = 0;
610	+	simError();
611	+	strcpy(ensemble, "NVE");
612	+	ensembleCase = NVE_ENS;
613	+	}
614
615	+	for (i = 0; i < nInfo; i++){
616	+	strcpy(info[i].ensemble, ensemble);
617
618	<	#ifdef IS_MPI
964	<	mpiSim->mpiRefresh();
965	<	#endif
618	>	// get the mixing rule
619
620	<	// initialize the Fortran
620	>	strcpy(info[i].mixingRule, globals->getMixingRule());
621	>	info[i].usePBC = globals->getPBC();
622	>	}
623
624	+	// get the components and calculate the tot_nMol and indvidual n_mol
625
626	<	simnfo->refreshSim();
627	<
628	<	if( !strcmp( simnfo->mixingRule, "standard") ){
629	<	the_ff->initForceField( LB_MIXING_RULE );
626	>	the_components = globals->getComponents();
627	>	components_nmol = new int[n_components];
628	>
629	>
630	>	if (!globals->haveNMol()){
631	>	// we don't have the total number of molecules, so we assume it is
632	>	// given in each component
633	>
634	>	tot_nmol = 0;
635	>	for (i = 0; i < n_components; i++){
636	>	if (!the_components[i]->haveNMol()){
637	>	// we have a problem
638	>	sprintf(painCave.errMsg,
639	>	"SimSetup Error. No global NMol or component NMol"
640	>	" given. Cannot calculate the number of atoms.\n");
641	>	painCave.isFatal = 1;
642	>	simError();
643	>	}
644	>
645	>	tot_nmol += the_components[i]->getNMol();
646	>	components_nmol[i] = the_components[i]->getNMol();
647	>	}
648		}
975	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
976	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
977	–	}
649		else{
650	<	sprintf( painCave.errMsg,
651	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
652	<	simnfo->mixingRule );
650	>	sprintf(painCave.errMsg,
651	>	"SimSetup error.\n"
652	>	"\tSorry, the ability to specify total"
653	>	" nMols and then give molfractions in the components\n"
654	>	"\tis not currently supported."
655	>	" Please give nMol in the components.\n");
656		painCave.isFatal = 1;
657		simError();
658		}
659
660	+	// set the status, sample, and thermal kick times
661
662	<	#ifdef IS_MPI
663	<	strcpy( checkPointMsg,
664	<	"Successfully intialized the mixingRule for Fortran." );
665	<	MPIcheckPoint();
666	<	#endif // is_mpi
667	<	}
662	>	for (i = 0; i < nInfo; i++){
663	>	if (globals->haveSampleTime()){
664	>	info[i].sampleTime = globals->getSampleTime();
665	>	info[i].statusTime = info[i].sampleTime;
666	>	info[i].thermalTime = info[i].sampleTime;
667	>	}
668	>	else{
669	>	info[i].sampleTime = globals->getRunTime();
670	>	info[i].statusTime = info[i].sampleTime;
671	>	info[i].thermalTime = info[i].sampleTime;
672	>	}
673
674	+	if (globals->haveStatusTime()){
675	+	info[i].statusTime = globals->getStatusTime();
676	+	}
677
678	<	void SimSetup::makeMolecules( void ){
678	>	if (globals->haveThermalTime()){
679	>	info[i].thermalTime = globals->getThermalTime();
680	>	}
681
682	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
683	<	molInit info;
684	<	DirectionalAtom* dAtom;
685	<	LinkedAssign* extras;
686	<	LinkedAssign* current_extra;
1002	<	AtomStamp* currentAtom;
1003	<	BondStamp* currentBond;
1004	<	BendStamp* currentBend;
1005	<	TorsionStamp* currentTorsion;
682	>	info[i].resetIntegrator = 0;
683	>	if( globals->haveResetTime() ){
684	>	info[i].resetTime = globals->getResetTime();
685	>	info[i].resetIntegrator = 1;
686	>	}
687
688	<	bond_pair* theBonds;
1008	<	bend_set* theBends;
1009	<	torsion_set* theTorsions;
688	>	// check for the temperature set flag
689
690	<
691	<	//init the forceField paramters
690	>	if (globals->haveTempSet())
691	>	info[i].setTemp = globals->getTempSet();
692
693	<	the_ff->readParams();
693	>	// get some of the tricky things that may still be in the globals
694
695	<
696	<	// init the atoms
695	>	double boxVector[3];
696	>	if (globals->haveBox()){
697	>	boxVector[0] = globals->getBox();
698	>	boxVector[1] = globals->getBox();
699	>	boxVector[2] = globals->getBox();
700
701	<	double ux, uy, uz, u, uSqr;
702	<
703	<	atomOffset = 0;
704	<	excludeOffset = 0;
705	<	for(i=0; i<simnfo->n_mol; i++){
706	<
707	<	stampID = the_molecules[i].getStampID();
701	>	info[i].setBox(boxVector);
702	>	}
703	>	else if (globals->haveDensity()){
704	>	double vol;
705	>	vol = (double) tot_nmol / globals->getDensity();
706	>	boxVector[0] = pow(vol, (1.0 / 3.0));
707	>	boxVector[1] = boxVector[0];
708	>	boxVector[2] = boxVector[0];
709
710	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
711	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
712	<	info.nBends    = comp_stamps[stampID]->getNBends();
713	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
714	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
710	>	info[i].setBox(boxVector);
711	>	}
712	>	else{
713	>	if (!globals->haveBoxX()){
714	>	sprintf(painCave.errMsg,
715	>	"SimSetup error, no periodic BoxX size given.\n");
716	>	painCave.isFatal = 1;
717	>	simError();
718	>	}
719	>	boxVector[0] = globals->getBoxX();
720
721	<	info.myAtoms = &the_atoms[atomOffset];
722	<	info.myExcludes = &the_excludes[excludeOffset];
723	<	info.myBonds = new Bond*[info.nBonds];
724	<	info.myBends = new Bend*[info.nBends];
725	<	info.myTorsions = new Torsion*[info.nTorsions];
721	>	if (!globals->haveBoxY()){
722	>	sprintf(painCave.errMsg,
723	>	"SimSetup error, no periodic BoxY size given.\n");
724	>	painCave.isFatal = 1;
725	>	simError();
726	>	}
727	>	boxVector[1] = globals->getBoxY();
728
729	<	theBonds = new bond_pair[info.nBonds];
730	<	theBends = new bend_set[info.nBends];
731	<	theTorsions = new torsion_set[info.nTorsions];
732	<
733	<	// make the Atoms
1044	<
1045	<	for(j=0; j<info.nAtoms; j++){
1046	<
1047	<	currentAtom = comp_stamps[stampID]->getAtom( j );
1048	<	if( currentAtom->haveOrientation() ){
1049	<
1050	<	dAtom = new DirectionalAtom(j + atomOffset);
1051	<	simnfo->n_oriented++;
1052	<	info.myAtoms[j] = dAtom;
1053	<
1054	<	ux = currentAtom->getOrntX();
1055	<	uy = currentAtom->getOrntY();
1056	<	uz = currentAtom->getOrntZ();
1057	<
1058	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1059	<
1060	<	u = sqrt( uSqr );
1061	<	ux = ux / u;
1062	<	uy = uy / u;
1063	<	uz = uz / u;
1064	<
1065	<	dAtom->setSUx( ux );
1066	<	dAtom->setSUy( uy );
1067	<	dAtom->setSUz( uz );
729	>	if (!globals->haveBoxZ()){
730	>	sprintf(painCave.errMsg,
731	>	"SimSetup error, no periodic BoxZ size given.\n");
732	>	painCave.isFatal = 1;
733	>	simError();
734		}
735	<	else{
1070	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
1071	<	}
1072	<	info.myAtoms[j]->setType( currentAtom->getType() );
1073	<
1074	<	#ifdef IS_MPI
1075	<
1076	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1077	<
1078	<	#endif // is_mpi
1079	<	}
1080	<
1081	<	// make the bonds
1082	<	for(j=0; j<info.nBonds; j++){
1083	<
1084	<	currentBond = comp_stamps[stampID]->getBond( j );
1085	<	theBonds[j].a = currentBond->getA() + atomOffset;
1086	<	theBonds[j].b = currentBond->getB() + atomOffset;
735	>	boxVector[2] = globals->getBoxZ();
736
737	<	exI = theBonds[j].a;
738	<	exJ = theBonds[j].b;
737	>	info[i].setBox(boxVector);
738	>	}
739	>	}
740
741	<	// exclude_I must always be the smaller of the pair
742	<	if( exI > exJ ){
743	<	tempEx = exI;
744	<	exI = exJ;
745	<	exJ = tempEx;
741	>	//setup seed for random number generator
742	>	int seedValue;
743	>
744	>	if (globals->haveSeed()){
745	>	seedValue = globals->getSeed();
746	>
747	>	if(seedValue / 1E9 == 0){
748	>	sprintf(painCave.errMsg,
749	>	"Seed for sprng library should contain at least 9 digits\n"
750	>	"OOPSE will generate a seed for user\n");
751	>	painCave.isFatal = 0;
752	>	simError();
753	>
754	>	//using seed generated by system instead of invalid seed set by user
755	>	#ifndef IS_MPI
756	>	seedValue = make_sprng_seed();
757	>	#else
758	>	if (worldRank == 0){
759	>	seedValue = make_sprng_seed();
760		}
761	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
762	+	#endif
763	+	}
764	+	}//end of if branch of globals->haveSeed()
765	+	else{
766	+
767	+	#ifndef IS_MPI
768	+	seedValue = make_sprng_seed();
769	+	#else
770	+	if (worldRank == 0){
771	+	seedValue = make_sprng_seed();
772	+	}
773	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
774	+	#endif
775	+	}//end of globals->haveSeed()
776	+
777	+	for (int i = 0; i < nInfo; i++){
778	+	info[i].setSeed(seedValue);
779	+	}
780	+
781		#ifdef IS_MPI
782	<	tempEx = exI;
783	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
784	<	tempEx = exJ;
785	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1102	<
1103	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1104	<	#else  // isn't MPI
782	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
783	>	MPIcheckPoint();
784	>	#endif // is_mpi
785	>	}
786
787	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
788	<	#endif  //is_mpi
787	>
788	>	void SimSetup::finalInfoCheck(void){
789	>	int index;
790	>	int usesDipoles;
791	>	int i;
792	>
793	>	for (i = 0; i < nInfo; i++){
794	>	// check electrostatic parameters
795	>
796	>	index = 0;
797	>	usesDipoles = 0;
798	>	while ((index < info[i].n_atoms) && !usesDipoles){
799	>	usesDipoles = (info[i].atoms[index])->hasDipole();
800	>	index++;
801		}
1109	–	excludeOffset += info.nBonds;
802
803	<	//make the bends
804	<	for(j=0; j<info.nBends; j++){
805	<
806	<	currentBend = comp_stamps[stampID]->getBend( j );
807	<	theBends[j].a = currentBend->getA() + atomOffset;
808	<	theBends[j].b = currentBend->getB() + atomOffset;
809	<	theBends[j].c = currentBend->getC() + atomOffset;
810	<
811	<	if( currentBend->haveExtras() ){
812	<
813	<	extras = currentBend->getExtras();
814	<	current_extra = extras;
815	<
816	<	while( current_extra != NULL ){
817	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
818	<
819	<	switch( current_extra->getType() ){
820	<
821	<	case 0:
822	<	theBends[j].ghost =
823	<	current_extra->getInt() + atomOffset;
824	<	theBends[j].isGhost = 1;
825	<	break;
826	<
1135	<	case 1:
1136	<	theBends[j].ghost =
1137	<	(int)current_extra->getDouble() + atomOffset;
1138	<	theBends[j].isGhost = 1;
1139	<	break;
1140	<
1141	<	default:
1142	<	sprintf( painCave.errMsg,
1143	<	"SimSetup Error: ghostVectorSource was neither a "
1144	<	"double nor an int.\n"
1145	<	"-->Bend[%d] in %s\n",
1146	<	j, comp_stamps[stampID]->getID() );
1147	<	painCave.isFatal = 1;
1148	<	simError();
1149	<	}
1150	<	}
1151	<
1152	<	else{
1153	<
1154	<	sprintf( painCave.errMsg,
1155	<	"SimSetup Error: unhandled bend assignment:\n"
1156	<	"    -->%s in Bend[%d] in %s\n",
1157	<	current_extra->getlhs(),
1158	<	j, comp_stamps[stampID]->getID() );
1159	<	painCave.isFatal = 1;
1160	<	simError();
1161	<	}
1162	<
1163	<	current_extra = current_extra->getNext();
1164	<	}
803	>	#ifdef IS_MPI
804	>	int myUse = usesDipoles;
805	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806	>	#endif //is_mpi
807	>
808	>	double theEcr, theEst;
809	>
810	>	if (globals->getUseRF()){
811	>	info[i].useReactionField = 1;
812	>
813	>	if (!globals->haveECR()){
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Warning: using default value of 1/2 the smallest "
816	>	"box length for the electrostaticCutoffRadius.\n"
817	>	"I hope you have a very fast processor!\n");
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	double smallest;
821	>	smallest = info[i].boxL[0];
822	>	if (info[i].boxL[1] <= smallest)
823	>	smallest = info[i].boxL[1];
824	>	if (info[i].boxL[2] <= smallest)
825	>	smallest = info[i].boxL[2];
826	>	theEcr = 0.5 * smallest;
827		}
828	<
829	<	if( !theBends[j].isGhost ){
1168	<
1169	<	exI = theBends[j].a;
1170	<	exJ = theBends[j].c;
828	>	else{
829	>	theEcr = globals->getECR();
830		}
831	+
832	+	if (!globals->haveEST()){
833	+	sprintf(painCave.errMsg,
834	+	"SimSetup Warning: using default value of 0.05 * the "
835	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
836	+	painCave.isFatal = 0;
837	+	simError();
838	+	theEst = 0.05 * theEcr;
839	+	}
840		else{
841	<
1174	<	exI = theBends[j].a;
1175	<	exJ = theBends[j].b;
841	>	theEst = globals->getEST();
842		}
843	<
844	<	// exclude_I must always be the smaller of the pair
845	<	if( exI > exJ ){
846	<	tempEx = exI;
847	<	exI = exJ;
848	<	exJ = tempEx;
843	>
844	>	info[i].setEcr(theEcr, theEst);
845	>
846	>	if (!globals->haveDielectric()){
847	>	sprintf(painCave.errMsg,
848	>	"SimSetup Error: You are trying to use Reaction Field without"
849	>	"setting a dielectric constant!\n");
850	>	painCave.isFatal = 1;
851	>	simError();
852		}
853	<	#ifdef IS_MPI
1185	<	tempEx = exI;
1186	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1187	<	tempEx = exJ;
1188	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1189	<
1190	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1191	<	#else  // isn't MPI
1192	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1193	<	#endif  //is_mpi
853	>	info[i].dielectric = globals->getDielectric();
854		}
855	<	excludeOffset += info.nBends;
855	>	else{
856	>	if (usesDipoles){
857	>	if (!globals->haveECR()){
858	>	sprintf(painCave.errMsg,
859	>	"SimSetup Warning: using default value of 1/2 the smallest "
860	>	"box length for the electrostaticCutoffRadius.\n"
861	>	"I hope you have a very fast processor!\n");
862	>	painCave.isFatal = 0;
863	>	simError();
864	>	double smallest;
865	>	smallest = info[i].boxL[0];
866	>	if (info[i].boxL[1] <= smallest)
867	>	smallest = info[i].boxL[1];
868	>	if (info[i].boxL[2] <= smallest)
869	>	smallest = info[i].boxL[2];
870	>	theEcr = 0.5 * smallest;
871	>	}
872	>	else{
873	>	theEcr = globals->getECR();
874	>	}
875
876	<	for(j=0; j<info.nTorsions; j++){
877	<
878	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
879	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
880	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
881	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
882	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
883	<
884	<	exI = theTorsions[j].a;
885	<	exJ = theTorsions[j].d;
876	>	if (!globals->haveEST()){
877	>	sprintf(painCave.errMsg,
878	>	"SimSetup Warning: using default value of 0.05 * the "
879	>	"electrostaticCutoffRadius for the "
880	>	"electrostaticSkinThickness\n");
881	>	painCave.isFatal = 0;
882	>	simError();
883	>	theEst = 0.05 * theEcr;
884	>	}
885	>	else{
886	>	theEst = globals->getEST();
887	>	}
888
889	<	// exclude_I must always be the smaller of the pair
1209	<	if( exI > exJ ){
1210	<	tempEx = exI;
1211	<	exI = exJ;
1212	<	exJ = tempEx;
889	>	info[i].setEcr(theEcr, theEst);
890		}
891	+	}
892	+	}
893	+
894		#ifdef IS_MPI
895	<	tempEx = exI;
896	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
897	<	tempEx = exJ;
898	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
899	<
900	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
901	<	#else  // isn't MPI
902	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
903	<	#endif  //is_mpi
895	>	strcpy(checkPointMsg, "post processing checks out");
896	>	MPIcheckPoint();
897	>	#endif // is_mpi
898	>	}
899	>
900	>	void SimSetup::initSystemCoords(void){
901	>	int i;
902	>
903	>	char* inName;
904	>
905	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
906	>
907	>	for (i = 0; i < info[0].n_atoms; i++)
908	>	info[0].atoms[i]->setCoords();
909	>
910	>	if (globals->haveInitialConfig()){
911	>	InitializeFromFile* fileInit;
912	>	#ifdef IS_MPI // is_mpi
913	>	if (worldRank == 0){
914	>	#endif //is_mpi
915	>	inName = globals->getInitialConfig();
916	>	fileInit = new InitializeFromFile(inName);
917	>	#ifdef IS_MPI
918		}
919	<	excludeOffset += info.nTorsions;
919	>	else
920	>	fileInit = new InitializeFromFile(NULL);
921	>	#endif
922	>	fileInit->readInit(info); // default velocities on
923
924	<
925	<	// send the arrays off to the forceField for init.
924	>	delete fileInit;
925	>	}
926	>	else{
927	>	#ifdef IS_MPI
928
929	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1231	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1232	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1233	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
929	>	// no init from bass
930
931	+	sprintf(painCave.errMsg,
932	+	"Cannot intialize a parallel simulation without an initial configuration file.\n");
933	+	painCave.isFatal = 1;;
934	+	simError();
935
936	<	the_molecules[i].initialize( info );
936	>	#else
937
938	+	initFromBass();
939
940	<	atomOffset += info.nAtoms;
941	<	delete[] theBonds;
1241	<	delete[] theBends;
1242	<	delete[] theTorsions;
940	>
941	>	#endif
942		}
943
944		#ifdef IS_MPI
945	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
945	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
946		MPIcheckPoint();
947		#endif // is_mpi
1249	–
1250	–	// clean up the forcefield
1251	–	the_ff->calcRcut();
1252	–	the_ff->cleanMe();
1253	–
948		}
949
1256	–	void SimSetup::initFromBass( void ){
950
951	<	int i, j, k;
952	<	int n_cells;
1260	<	double cellx, celly, cellz;
1261	<	double temp1, temp2, temp3;
1262	<	int n_per_extra;
1263	<	int n_extra;
1264	<	int have_extra, done;
951	>	void SimSetup::makeOutNames(void){
952	>	int k;
953
1266	–	temp1 = (double)tot_nmol / 4.0;
1267	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1268	–	temp3 = ceil( temp2 );
954
955	<	have_extra =0;
956	<	if( temp2 < temp3 ){ // we have a non-complete lattice
957	<	have_extra =1;
955	>	for (k = 0; k < nInfo; k++){
956	>	#ifdef IS_MPI
957	>	if (worldRank == 0){
958	>	#endif // is_mpi
959
960	<	n_cells = (int)temp3 - 1;
961	<	cellx = simnfo->boxLx / temp3;
962	<	celly = simnfo->boxLy / temp3;
963	<	cellz = simnfo->boxLz / temp3;
964	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
965	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
966	<	n_per_extra = (int)ceil( temp1 );
960	>	if (globals->haveFinalConfig()){
961	>	strcpy(info[k].finalName, globals->getFinalConfig());
962	>	}
963	>	else{
964	>	strcpy(info[k].finalName, inFileName);
965	>	char* endTest;
966	>	int nameLength = strlen(info[k].finalName);
967	>	endTest = &(info[k].finalName[nameLength - 5]);
968	>	if (!strcmp(endTest, ".bass")){
969	>	strcpy(endTest, ".eor");
970	>	}
971	>	else if (!strcmp(endTest, ".BASS")){
972	>	strcpy(endTest, ".eor");
973	>	}
974	>	else{
975	>	endTest = &(info[k].finalName[nameLength - 4]);
976	>	if (!strcmp(endTest, ".bss")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".mdl")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	strcat(info[k].finalName, ".eor");
984	>	}
985	>	}
986	>	}
987
988	<	if( n_per_extra > 4){
989	<	sprintf( painCave.errMsg,
990	<	"SimSetup error. There has been an error in constructing"
991	<	" the non-complete lattice.\n" );
992	<	painCave.isFatal = 1;
993	<	simError();
988	>	// make the sample and status out names
989	>
990	>	strcpy(info[k].sampleName, inFileName);
991	>	char* endTest;
992	>	int nameLength = strlen(info[k].sampleName);
993	>	endTest = &(info[k].sampleName[nameLength - 5]);
994	>	if (!strcmp(endTest, ".bass")){
995	>	strcpy(endTest, ".dump");
996	>	}
997	>	else if (!strcmp(endTest, ".BASS")){
998	>	strcpy(endTest, ".dump");
999	>	}
1000	>	else{
1001	>	endTest = &(info[k].sampleName[nameLength - 4]);
1002	>	if (!strcmp(endTest, ".bss")){
1003	>	strcpy(endTest, ".dump");
1004	>	}
1005	>	else if (!strcmp(endTest, ".mdl")){
1006	>	strcpy(endTest, ".dump");
1007	>	}
1008	>	else{
1009	>	strcat(info[k].sampleName, ".dump");
1010	>	}
1011	>	}
1012	>
1013	>	strcpy(info[k].statusName, inFileName);
1014	>	nameLength = strlen(info[k].statusName);
1015	>	endTest = &(info[k].statusName[nameLength - 5]);
1016	>	if (!strcmp(endTest, ".bass")){
1017	>	strcpy(endTest, ".stat");
1018	>	}
1019	>	else if (!strcmp(endTest, ".BASS")){
1020	>	strcpy(endTest, ".stat");
1021	>	}
1022	>	else{
1023	>	endTest = &(info[k].statusName[nameLength - 4]);
1024	>	if (!strcmp(endTest, ".bss")){
1025	>	strcpy(endTest, ".stat");
1026	>	}
1027	>	else if (!strcmp(endTest, ".mdl")){
1028	>	strcpy(endTest, ".stat");
1029	>	}
1030	>	else{
1031	>	strcat(info[k].statusName, ".stat");
1032	>	}
1033	>	}
1034	>
1035	>	#ifdef IS_MPI
1036	>
1037		}
1038	+	#endif // is_mpi
1039		}
1040	<	else{
1291	<	n_cells = (int)temp3;
1292	<	cellx = simnfo->boxLx / temp3;
1293	<	celly = simnfo->boxLy / temp3;
1294	<	cellz = simnfo->boxLz / temp3;
1295	<	}
1040	>	}
1041
1297	–	current_mol = 0;
1298	–	current_comp_mol = 0;
1299	–	current_comp = 0;
1300	–	current_atom_ndx = 0;
1042
1043	<	for( i=0; i < n_cells ; i++ ){
1044	<	for( j=0; j < n_cells; j++ ){
1304	<	for( k=0; k < n_cells; k++ ){
1043	>	void SimSetup::sysObjectsCreation(void){
1044	>	int i, k;
1045
1046	<	makeElement( i * cellx,
1307	<	j * celly,
1308	<	k * cellz );
1046	>	// create the forceField
1047
1048	<	makeElement( i * cellx + 0.5 * cellx,
1311	<	j * celly + 0.5 * celly,
1312	<	k * cellz );
1048	>	createFF();
1049
1050	<	makeElement( i * cellx,
1315	<	j * celly + 0.5 * celly,
1316	<	k * cellz + 0.5 * cellz );
1050	>	// extract componentList
1051
1052	<	makeElement( i * cellx + 0.5 * cellx,
1053	<	j * celly,
1054	<	k * cellz + 0.5 * cellz );
1055	<	}
1052	>	compList();
1053	>
1054	>	// calc the number of atoms, bond, bends, and torsions
1055	>
1056	>	calcSysValues();
1057	>
1058	>	#ifdef IS_MPI
1059	>	// divide the molecules among the processors
1060	>
1061	>	mpiMolDivide();
1062	>	#endif //is_mpi
1063	>
1064	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1065	>
1066	>	makeSysArrays();
1067	>
1068	>	// make and initialize the molecules (all but atomic coordinates)
1069	>
1070	>	makeMolecules();
1071	>
1072	>	for (k = 0; k < nInfo; k++){
1073	>	info[k].identArray = new int[info[k].n_atoms];
1074	>	for (i = 0; i < info[k].n_atoms; i++){
1075	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1076		}
1077		}
1078	+	}
1079
1325	–	if( have_extra ){
1326	–	done = 0;
1080
1081	<	int start_ndx;
1082	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1083	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1081	>	void SimSetup::createFF(void){
1082	>	switch (ffCase){
1083	>	case FF_DUFF:
1084	>	the_ff = new DUFF();
1085	>	break;
1086
1087	<	if( i < n_cells ){
1087	>	case FF_LJ:
1088	>	the_ff = new LJFF();
1089	>	break;
1090
1091	<	if( j < n_cells ){
1092	<	start_ndx = n_cells;
1093	<	}
1337	<	else start_ndx = 0;
1338	<	}
1339	<	else start_ndx = 0;
1091	>	case FF_EAM:
1092	>	the_ff = new EAM_FF();
1093	>	break;
1094
1095	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1095	>	default:
1096	>	sprintf(painCave.errMsg,
1097	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1098	>	painCave.isFatal = 1;
1099	>	simError();
1100	>	}
1101
1102	<	makeElement( i * cellx,
1103	<	j * celly,
1104	<	k * cellz );
1105	<	done = ( current_mol >= tot_nmol );
1102	>	#ifdef IS_MPI
1103	>	strcpy(checkPointMsg, "ForceField creation successful");
1104	>	MPIcheckPoint();
1105	>	#endif // is_mpi
1106	>	}
1107
1348	–	if( !done && n_per_extra > 1 ){
1349	–	makeElement( i * cellx + 0.5 * cellx,
1350	–	j * celly + 0.5 * celly,
1351	–	k * cellz );
1352	–	done = ( current_mol >= tot_nmol );
1353	–	}
1108
1109	<	if( !done && n_per_extra > 2){
1110	<	makeElement( i * cellx,
1111	<	j * celly + 0.5 * celly,
1112	<	k * cellz + 0.5 * cellz );
1113	<	done = ( current_mol >= tot_nmol );
1114	<	}
1109	>	void SimSetup::compList(void){
1110	>	int i;
1111	>	char* id;
1112	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1113	>	LinkedMolStamp* currentStamp = NULL;
1114	>	comp_stamps = new MoleculeStamp * [n_components];
1115
1116	<	if( !done && n_per_extra > 3){
1117	<	makeElement( i * cellx + 0.5 * cellx,
1118	<	j * celly,
1119	<	k * cellz + 0.5 * cellz );
1120	<	done = ( current_mol >= tot_nmol );
1121	<	}
1122	<	}
1116	>	// make an array of molecule stamps that match the components used.
1117	>	// also extract the used stamps out into a separate linked list
1118	>
1119	>	for (i = 0; i < nInfo; i++){
1120	>	info[i].nComponents = n_components;
1121	>	info[i].componentsNmol = components_nmol;
1122	>	info[i].compStamps = comp_stamps;
1123	>	info[i].headStamp = headStamp;
1124	>	}
1125	>
1126	>
1127	>	for (i = 0; i < n_components; i++){
1128	>	id = the_components[i]->getType();
1129	>	comp_stamps[i] = NULL;
1130	>
1131	>	// check to make sure the component isn't already in the list
1132	>
1133	>	comp_stamps[i] = headStamp->match(id);
1134	>	if (comp_stamps[i] == NULL){
1135	>	// extract the component from the list;
1136	>
1137	>	currentStamp = stamps->extractMolStamp(id);
1138	>	if (currentStamp == NULL){
1139	>	sprintf(painCave.errMsg,
1140	>	"SimSetup error: Component \"%s\" was not found in the "
1141	>	"list of declared molecules\n",
1142	>	id);
1143	>	painCave.isFatal = 1;
1144	>	simError();
1145		}
1146	+
1147	+	headStamp->add(currentStamp);
1148	+	comp_stamps[i] = headStamp->match(id);
1149		}
1150		}
1151
1152	+	#ifdef IS_MPI
1153	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1154	+	MPIcheckPoint();
1155	+	#endif // is_mpi
1156	+	}
1157
1158	<	for( i=0; i<simnfo->n_atoms; i++ ){
1159	<	simnfo->atoms[i]->set_vx( 0.0 );
1160	<	simnfo->atoms[i]->set_vy( 0.0 );
1161	<	simnfo->atoms[i]->set_vz( 0.0 );
1158	>	void SimSetup::calcSysValues(void){
1159	>	int i;
1160	>
1161	>	int* molMembershipArray;
1162	>
1163	>	tot_atoms = 0;
1164	>	tot_bonds = 0;
1165	>	tot_bends = 0;
1166	>	tot_torsions = 0;
1167	>	for (i = 0; i < n_components; i++){
1168	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1169	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1170	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1171	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1172		}
1379	–	}
1173
1174	<	void SimSetup::makeElement( double x, double y, double z ){
1174	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1175	>	molMembershipArray = new int[tot_atoms];
1176
1177	<	int k;
1178	<	AtomStamp* current_atom;
1179	<	DirectionalAtom* dAtom;
1180	<	double rotMat[3][3];
1177	>	for (i = 0; i < nInfo; i++){
1178	>	info[i].n_atoms = tot_atoms;
1179	>	info[i].n_bonds = tot_bonds;
1180	>	info[i].n_bends = tot_bends;
1181	>	info[i].n_torsions = tot_torsions;
1182	>	info[i].n_SRI = tot_SRI;
1183	>	info[i].n_mol = tot_nmol;
1184
1185	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1185	>	info[i].molMembershipArray = molMembershipArray;
1186	>	}
1187	>	}
1188
1189	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1391	<	if( !current_atom->havePosition() ){
1392	<	sprintf( painCave.errMsg,
1393	<	"SimSetup:initFromBass error.\n"
1394	<	"\tComponent %s, atom %s does not have a position specified.\n"
1395	<	"\tThe initialization routine is unable to give a start"
1396	<	" position.\n",
1397	<	comp_stamps[current_comp]->getID(),
1398	<	current_atom->getType() );
1399	<	painCave.isFatal = 1;
1400	<	simError();
1401	<	}
1189	>	#ifdef IS_MPI
1190
1191	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1192	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1193	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1191	>	void SimSetup::mpiMolDivide(void){
1192	>	int i, j, k;
1193	>	int localMol, allMol;
1194	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1195
1196	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1196	>	mpiSim = new mpiSimulation(info);
1197
1198	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1198	>	globalIndex = mpiSim->divideLabor();
1199
1200	<	rotMat[0][0] = 1.0;
1412	<	rotMat[0][1] = 0.0;
1413	<	rotMat[0][2] = 0.0;
1200	>	// set up the local variables
1201
1202	<	rotMat[1][0] = 0.0;
1203	<	rotMat[1][1] = 1.0;
1417	<	rotMat[1][2] = 0.0;
1202	>	mol2proc = mpiSim->getMolToProcMap();
1203	>	molCompType = mpiSim->getMolComponentType();
1204
1205	<	rotMat[2][0] = 0.0;
1206	<	rotMat[2][1] = 0.0;
1207	<	rotMat[2][2] = 1.0;
1205	>	allMol = 0;
1206	>	localMol = 0;
1207	>	local_atoms = 0;
1208	>	local_bonds = 0;
1209	>	local_bends = 0;
1210	>	local_torsions = 0;
1211	>	globalAtomIndex = 0;
1212
1213	<	dAtom->setA( rotMat );
1213	>
1214	>	for (i = 0; i < n_components; i++){
1215	>	for (j = 0; j < components_nmol[i]; j++){
1216	>	if (mol2proc[allMol] == worldRank){
1217	>	local_atoms += comp_stamps[i]->getNAtoms();
1218	>	local_bonds += comp_stamps[i]->getNBonds();
1219	>	local_bends += comp_stamps[i]->getNBends();
1220	>	local_torsions += comp_stamps[i]->getNTorsions();
1221	>	localMol++;
1222	>	}
1223	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1224	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1225	>	globalAtomIndex++;
1226	>	}
1227	>
1228	>	allMol++;
1229		}
1230	+	}
1231	+	local_SRI = local_bonds + local_bends + local_torsions;
1232
1233	<	current_atom_ndx++;
1233	>	info[0].n_atoms = mpiSim->getMyNlocal();
1234	>
1235	>	if (local_atoms != info[0].n_atoms){
1236	>	sprintf(painCave.errMsg,
1237	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	>	" localAtom (%d) are not equal.\n",
1239	>	info[0].n_atoms, local_atoms);
1240	>	painCave.isFatal = 1;
1241	>	simError();
1242		}
1243
1244	<	current_mol++;
1245	<	current_comp_mol++;
1244	>	info[0].n_bonds = local_bonds;
1245	>	info[0].n_bends = local_bends;
1246	>	info[0].n_torsions = local_torsions;
1247	>	info[0].n_SRI = local_SRI;
1248	>	info[0].n_mol = localMol;
1249
1250	<	if( current_comp_mol >= components_nmol[current_comp] ){
1250	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1251	>	MPIcheckPoint();
1252	>	}
1253
1254	<	current_comp_mol = 0;
1255	<	current_comp++;
1254	>	#endif // is_mpi
1255	>
1256	>
1257	>	void SimSetup::makeSysArrays(void){
1258	>
1259	>	#ifndef IS_MPI
1260	>	int k, j;
1261	>	#endif // is_mpi
1262	>	int i, l;
1263	>
1264	>	Atom** the_atoms;
1265	>	Molecule* the_molecules;
1266	>	Exclude** the_excludes;
1267	>
1268	>
1269	>	for (l = 0; l < nInfo; l++){
1270	>	// create the atom and short range interaction arrays
1271	>
1272	>	the_atoms = new Atom * [info[l].n_atoms];
1273	>	the_molecules = new Molecule[info[l].n_mol];
1274	>	int molIndex;
1275	>
1276	>	// initialize the molecule's stampID's
1277	>
1278	>	#ifdef IS_MPI
1279	>
1280	>
1281	>	molIndex = 0;
1282	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1283	>	if (mol2proc[i] == worldRank){
1284	>	the_molecules[molIndex].setStampID(molCompType[i]);
1285	>	the_molecules[molIndex].setMyIndex(molIndex);
1286	>	the_molecules[molIndex].setGlobalIndex(i);
1287	>	molIndex++;
1288	>	}
1289	>	}
1290	>
1291	>	#else // is_mpi
1292	>
1293	>	molIndex = 0;
1294	>	globalAtomIndex = 0;
1295	>	for (i = 0; i < n_components; i++){
1296	>	for (j = 0; j < components_nmol[i]; j++){
1297	>	the_molecules[molIndex].setStampID(i);
1298	>	the_molecules[molIndex].setMyIndex(molIndex);
1299	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1300	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1301	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	>	globalAtomIndex++;
1303	>	}
1304	>	molIndex++;
1305	>	}
1306	>	}
1307	>
1308	>
1309	>	#endif // is_mpi
1310	>
1311	>
1312	>	if (info[l].n_SRI){
1313	>	Exclude::createArray(info[l].n_SRI);
1314	>	the_excludes = new Exclude * [info[l].n_SRI];
1315	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	>	the_excludes[ex] = new Exclude(ex);
1317	>	}
1318	>	info[l].globalExcludes = new int;
1319	>	info[l].n_exclude = info[l].n_SRI;
1320	>	}
1321	>	else{
1322	>	Exclude::createArray(1);
1323	>	the_excludes = new Exclude * ;
1324	>	the_excludes[0] = new Exclude(0);
1325	>	the_excludes[0]->setPair(0, 0);
1326	>	info[l].globalExcludes = new int;
1327	>	info[l].globalExcludes[0] = 0;
1328	>	info[l].n_exclude = 0;
1329	>	}
1330	>
1331	>	// set the arrays into the SimInfo object
1332	>
1333	>	info[l].atoms = the_atoms;
1334	>	info[l].molecules = the_molecules;
1335	>	info[l].nGlobalExcludes = 0;
1336	>	info[l].excludes = the_excludes;
1337	>
1338	>	the_ff->setSimInfo(info);
1339		}
1340		}
1341	+
1342	+	void SimSetup::makeIntegrator(void){
1343	+	int k;
1344	+
1345	+	NVE<RealIntegrator>* myNVE = NULL;
1346	+	NVT<RealIntegrator>* myNVT = NULL;
1347	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1349	+
1350	+	for (k = 0; k < nInfo; k++){
1351	+	switch (ensembleCase){
1352	+	case NVE_ENS:
1353	+	if (globals->haveZconstraints()){
1354	+	setupZConstraint(info[k]);
1355	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1356	+	}
1357	+	else{
1358	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1359	+	}
1360	+
1361	+	info->the_integrator = myNVE;
1362	+	break;
1363	+
1364	+	case NVT_ENS:
1365	+	if (globals->haveZconstraints()){
1366	+	setupZConstraint(info[k]);
1367	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1368	+	}
1369	+	else
1370	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1371	+
1372	+	myNVT->setTargetTemp(globals->getTargetTemp());
1373	+
1374	+	if (globals->haveTauThermostat())
1375	+	myNVT->setTauThermostat(globals->getTauThermostat());
1376	+	else{
1377	+	sprintf(painCave.errMsg,
1378	+	"SimSetup error: If you use the NVT\n"
1379	+	"    ensemble, you must set tauThermostat.\n");
1380	+	painCave.isFatal = 1;
1381	+	simError();
1382	+	}
1383	+
1384	+	info->the_integrator = myNVT;
1385	+	break;
1386	+
1387	+	case NPTi_ENS:
1388	+	if (globals->haveZconstraints()){
1389	+	setupZConstraint(info[k]);
1390	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1391	+	}
1392	+	else
1393	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1394	+
1395	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1396	+
1397	+	if (globals->haveTargetPressure())
1398	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1399	+	else{
1400	+	sprintf(painCave.errMsg,
1401	+	"SimSetup error: If you use a constant pressure\n"
1402	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1403	+	painCave.isFatal = 1;
1404	+	simError();
1405	+	}
1406	+
1407	+	if (globals->haveTauThermostat())
1408	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1409	+	else{
1410	+	sprintf(painCave.errMsg,
1411	+	"SimSetup error: If you use an NPT\n"
1412	+	"    ensemble, you must set tauThermostat.\n");
1413	+	painCave.isFatal = 1;
1414	+	simError();
1415	+	}
1416	+
1417	+	if (globals->haveTauBarostat())
1418	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1419	+	else{
1420	+	sprintf(painCave.errMsg,
1421	+	"SimSetup error: If you use an NPT\n"
1422	+	"    ensemble, you must set tauBarostat.\n");
1423	+	painCave.isFatal = 1;
1424	+	simError();
1425	+	}
1426	+
1427	+	info->the_integrator = myNPTi;
1428	+	break;
1429	+
1430	+	case NPTf_ENS:
1431	+	if (globals->haveZconstraints()){
1432	+	setupZConstraint(info[k]);
1433	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1434	+	}
1435	+	else
1436	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1437	+
1438	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1439	+
1440	+	if (globals->haveTargetPressure())
1441	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	+	else{
1443	+	sprintf(painCave.errMsg,
1444	+	"SimSetup error: If you use a constant pressure\n"
1445	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1446	+	painCave.isFatal = 1;
1447	+	simError();
1448	+	}
1449	+
1450	+	if (globals->haveTauThermostat())
1451	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1452	+	else{
1453	+	sprintf(painCave.errMsg,
1454	+	"SimSetup error: If you use an NPT\n"
1455	+	"    ensemble, you must set tauThermostat.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+
1460	+	if (globals->haveTauBarostat())
1461	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1462	+	else{
1463	+	sprintf(painCave.errMsg,
1464	+	"SimSetup error: If you use an NPT\n"
1465	+	"    ensemble, you must set tauBarostat.\n");
1466	+	painCave.isFatal = 1;
1467	+	simError();
1468	+	}
1469	+
1470	+	info->the_integrator = myNPTf;
1471	+	break;
1472	+
1473	+	default:
1474	+	sprintf(painCave.errMsg,
1475	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1476	+	painCave.isFatal = 1;
1477	+	simError();
1478	+	}
1479	+	}
1480	+	}
1481	+
1482	+	void SimSetup::initFortran(void){
1483	+	info[0].refreshSim();
1484	+
1485	+	if (!strcmp(info[0].mixingRule, "standard")){
1486	+	the_ff->initForceField(LB_MIXING_RULE);
1487	+	}
1488	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1489	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1490	+	}
1491	+	else{
1492	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1493	+	info[0].mixingRule);
1494	+	painCave.isFatal = 1;
1495	+	simError();
1496	+	}
1497	+
1498	+
1499	+	#ifdef IS_MPI
1500	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1501	+	MPIcheckPoint();
1502	+	#endif // is_mpi
1503	+	}
1504	+
1505	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1506	+	int nZConstraints;
1507	+	ZconStamp** zconStamp;
1508	+
1509	+	if (globals->haveZconstraintTime()){
1510	+	//add sample time of z-constraint  into SimInfo's property list
1511	+	DoubleData* zconsTimeProp = new DoubleData();
1512	+	zconsTimeProp->setID(ZCONSTIME_ID);
1513	+	zconsTimeProp->setData(globals->getZconsTime());
1514	+	theInfo.addProperty(zconsTimeProp);
1515	+	}
1516	+	else{
1517	+	sprintf(painCave.errMsg,
1518	+	"ZConstraint error: If you use an ZConstraint\n"
1519	+	" , you must set sample time.\n");
1520	+	painCave.isFatal = 1;
1521	+	simError();
1522	+	}
1523	+
1524	+	//push zconsTol into siminfo, if user does not specify
1525	+	//value for zconsTol, a default value will be used
1526	+	DoubleData* zconsTol = new DoubleData();
1527	+	zconsTol->setID(ZCONSTOL_ID);
1528	+	if (globals->haveZconsTol()){
1529	+	zconsTol->setData(globals->getZconsTol());
1530	+	}
1531	+	else{
1532	+	double defaultZConsTol = 0.01;
1533	+	sprintf(painCave.errMsg,
1534	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1535	+	" , default value %f is used.\n",
1536	+	defaultZConsTol);
1537	+	painCave.isFatal = 0;
1538	+	simError();
1539	+
1540	+	zconsTol->setData(defaultZConsTol);
1541	+	}
1542	+	theInfo.addProperty(zconsTol);
1543	+
1544	+	//set Force Subtraction Policy
1545	+	StringData* zconsForcePolicy = new StringData();
1546	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1547	+
1548	+	if (globals->haveZconsForcePolicy()){
1549	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1550	+	}
1551	+	else{
1552	+	sprintf(painCave.errMsg,
1553	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1554	+	"PolicyByMass is used\n");
1555	+	painCave.isFatal = 0;
1556	+	simError();
1557	+	zconsForcePolicy->setData("BYMASS");
1558	+	}
1559	+
1560	+	theInfo.addProperty(zconsForcePolicy);
1561	+
1562	+	//Determine the name of ouput file and add it into SimInfo's property list
1563	+	//Be careful, do not use inFileName, since it is a pointer which
1564	+	//point to a string at master node, and slave nodes do not contain that string
1565	+
1566	+	string zconsOutput(theInfo.finalName);
1567	+
1568	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1569	+
1570	+	StringData* zconsFilename = new StringData();
1571	+	zconsFilename->setID(ZCONSFILENAME_ID);
1572	+	zconsFilename->setData(zconsOutput);
1573	+
1574	+	theInfo.addProperty(zconsFilename);
1575	+
1576	+	//setup index, pos and other parameters of z-constraint molecules
1577	+	nZConstraints = globals->getNzConstraints();
1578	+	theInfo.nZconstraints = nZConstraints;
1579	+
1580	+	zconStamp = globals->getZconStamp();
1581	+	ZConsParaItem tempParaItem;
1582	+
1583	+	ZConsParaData* zconsParaData = new ZConsParaData();
1584	+	zconsParaData->setID(ZCONSPARADATA_ID);
1585	+
1586	+	for (int i = 0; i < nZConstraints; i++){
1587	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1588	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1589	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1590	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1591	+
1592	+	zconsParaData->addItem(tempParaItem);
1593	+	}
1594	+
1595	+	//check the uniqueness of index
1596	+	if(!zconsParaData->isIndexUnique()){
1597	+	sprintf(painCave.errMsg,
1598	+	"ZConstraint Error: molIndex is not unique\n");
1599	+	painCave.isFatal = 1;
1600	+	simError();
1601	+	}
1602	+
1603	+	//sort the parameters by index of molecules
1604	+	zconsParaData->sortByIndex();
1605	+
1606	+	//push data into siminfo, therefore, we can retrieve later
1607	+	theInfo.addProperty(zconsParaData);
1608	+	}

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