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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 558 by mmeineke, Thu Jun 19 19:21:23 2003 UTC vs.
Revision 722 by tim, Tue Aug 26 20:02:29 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 14 | Line 18
18
19		// some defines for ensemble and Forcefield  cases
20
21	<	#define NVE_ENS 0
22	<	#define NVT_ENS 1
23	<	#define NPT_ENS 2
21	>	#define NVE_ENS        0
22	>	#define NVT_ENS        1
23	>	#define NPTi_ENS       2
24	>	#define NPTf_ENS       3
25	>	#define NPTim_ENS      4
26	>	#define NPTfm_ENS      5
27
28		#define FF_DUFF 0
29		#define FF_LJ   1
30	+	#define FF_EAM  2
31
32	+	using namespace std;
33
34		SimSetup::SimSetup(){
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40	<
40	>
41	>
42		#ifdef IS_MPI
43	<	strcpy( checkPointMsg, "SimSetup creation successful" );
43	>	strcpy(checkPointMsg, "SimSetup creation successful");
44		MPIcheckPoint();
45		#endif // IS_MPI
46		}
#	Line 37 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	<	void SimSetup::parseFile( char* fileName ){
53	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
54	>	info = the_info;
55	>	nInfo = theNinfo;
56	>	isInfoArray = 1;
57	>	}
58
59	+
60	+	void SimSetup::parseFile(char* fileName){
61		#ifdef IS_MPI
62	<	if( worldRank == 0 ){
62	>	if (worldRank == 0){
63		#endif // is_mpi
64	<
64	>
65		inFileName = fileName;
66	<	set_interface_stamps( stamps, globals );
67	<
66	>	set_interface_stamps(stamps, globals);
67	>
68		#ifdef IS_MPI
69		mpiEventInit();
70		#endif
71
72	<	yacc_BASS( fileName );
72	>	yacc_BASS(fileName);
73
74		#ifdef IS_MPI
75		throwMPIEvent(NULL);
76		}
77	<	else receiveParse();
77	>	else{
78	>	receiveParse();
79	>	}
80		#endif
81
82		}
83
84		#ifdef IS_MPI
85		void SimSetup::receiveParse(void){
86	<
87	<	set_interface_stamps( stamps, globals );
88	<	mpiEventInit();
89	<	MPIcheckPoint();
69	<	mpiEventLoop();
70	<
86	>	set_interface_stamps(stamps, globals);
87	>	mpiEventInit();
88	>	MPIcheckPoint();
89	>	mpiEventLoop();
90		}
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
76	<
77	<	MakeStamps *the_stamps;
78	<	Globals* the_globals;
94	>	void SimSetup::createSim(void){
95		int i, j, k, globalAtomIndex;
80	–
81	–	int ensembleCase;
82	–	int ffCase;
83	–
84	–	ensembleCase = -1;
85	–	ffCase = -1;
96
97	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
97	>	// gather all of the information from the Bass file
98
99	<	// set the easy ones first
92	<	simnfo->target_temp = the_globals->getTargetTemp();
93	<	simnfo->dt = the_globals->getDt();
94	<	simnfo->run_time = the_globals->getRunTime();
99	>	gatherInfo();
100
101	<	// get the ones we know are there, yet still may need some work.
97	<	n_components = the_globals->getNComponents();
98	<	strcpy( force_field, the_globals->getForceField() );
101	>	// creation of complex system objects
102
103	<	if( !strcasecmp( force_field, "DUFF" ))    ffCase = FF_DUFF;
101	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102	<	else{
103	<	sprintf( painCave.errMsg,
104	<	"SimSetup Error. Unrecognized force field -> %s\n",
105	<	force_field );
106	<	painCave.isFatal = 1;
107	<	simError();
108	<	}
103	>	sysObjectsCreation();
104
105	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
105	>	// check on the post processing info
106
107	<	if( !strcasecmp( ensemble, "NVE" ))      ffCase = NVE_ENS;
114	<	else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS;
115	<	else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS;
116	<	else{
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
119	<	"reverting to NVE for this simulation.\n",
120	<	ensemble );
121	<	painCave.isFatal = 0;
122	<	simError();
123	<	strcpy( ensemble, "NVE" );
124	<	ensembleCase = NVE_ENS;
125	<	}
126	<	strcpy( simnfo->ensemble, ensemble );
107	>	finalInfoCheck();
108
109	+	// initialize the system coordinates
110
111	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
112	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
113	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132	<	//     if (the_globals->haveTargetPressure())
133	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134	<	//     else {
135	<	//       sprintf( painCave.errMsg,
136	<	//                "SimSetup error: If you use the constant pressure\n"
137	<	//                "    ensemble, you must set targetPressure.\n"
138	<	//                "    This was found in the BASS file.\n");
139	<	//       painCave.isFatal = 1;
140	<	//       simError();
141	<	//     }
111	>	if (!isInfoArray){
112	>	initSystemCoords();
113	>	}
114
115	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
115	>	// make the output filenames
116
117	<	//     if (the_globals->haveTauBarostat())
157	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158	<	//     else {
159	<	//       sprintf( painCave.errMsg,
160	<	//                "SimSetup error: If you use the constant pressure\n"
161	<	//                "    ensemble, you must set tauBarostat.\n"
162	<	//                "    This was found in the BASS file.\n");
163	<	//       painCave.isFatal = 1;
164	<	//       simError();
165	<	//     }
117	>	makeOutNames();
118
119	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
168	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
169	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
119	>	// make the integrator
120
121	<	//     if (the_globals->haveTauThermostat())
172	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173	<	//     else if (the_globals->haveQmass())
174	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
175	<	//     else {
176	<	//       sprintf( painCave.errMsg,
177	<	//                "SimSetup error: If you use one of the constant temperature\n"
178	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
179	<	//                "    Neither of these was found in the BASS file.\n");
180	<	//       painCave.isFatal = 1;
181	<	//       simError();
182	<	//     }
121	>	makeIntegrator();
122
123	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
124	<	simnfo->usePBC = the_globals->getPBC();
125	<
187	<	int usesDipoles = 0;
188	<	switch( ffCase ){
123	>	#ifdef IS_MPI
124	>	mpiSim->mpiRefresh();
125	>	#endif
126
127	<	case FF_DUFF:
191	<	the_ff = new DUFF();
192	<	usesDipoles = 1;
193	<	break;
127	>	// initialize the Fortran
128
129	<	case FF_LJ:
130	<	the_ff = LJFF();
197	<	break;
129	>	initFortran();
130	>	}
131
199	–	default:
200	–	sprintf( painCave.errMsg,
201	–	"SimSetup Error. Unrecognized force field in case statement.\n");
202	–	painCave.isFatal = 1;
203	–	simError();
204	–	}
132
133	<	#ifdef IS_MPI
134	<	strcpy( checkPointMsg, "ForceField creation successful" );
135	<	MPIcheckPoint();
136	<	#endif // is_mpi
133	>	void SimSetup::makeMolecules(void){
134	>	int k, l;
135	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136	>	molInit molInfo;
137	>	DirectionalAtom* dAtom;
138	>	LinkedAssign* extras;
139	>	LinkedAssign* current_extra;
140	>	AtomStamp* currentAtom;
141	>	BondStamp* currentBond;
142	>	BendStamp* currentBend;
143	>	TorsionStamp* currentTorsion;
144
145	<	// get the components and calculate the tot_nMol and indvidual n_mol
146	<	the_components = the_globals->getComponents();
147	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
145	>	bond_pair* theBonds;
146	>	bend_set* theBends;
147	>	torsion_set* theTorsions;
148
216	–	if( !the_globals->haveNMol() ){
217	–	// we don't have the total number of molecules, so we assume it is
218	–	// given in each component
149
150	<	tot_nmol = 0;
221	<	for( i=0; i<n_components; i++ ){
150	>	//init the forceField paramters
151
152	<	if( !the_components[i]->haveNMol() ){
224	<	// we have a problem
225	<	sprintf( painCave.errMsg,
226	<	"SimSetup Error. No global NMol or component NMol"
227	<	" given. Cannot calculate the number of atoms.\n" );
228	<	painCave.isFatal = 1;
229	<	simError();
230	<	}
152	>	the_ff->readParams();
153
232	–	tot_nmol += the_components[i]->getNMol();
233	–	components_nmol[i] = the_components[i]->getNMol();
234	–	}
235	–	}
236	–	else{
237	–	sprintf( painCave.errMsg,
238	–	"SimSetup error.\n"
239	–	"\tSorry, the ability to specify total"
240	–	" nMols and then give molfractions in the components\n"
241	–	"\tis not currently supported."
242	–	" Please give nMol in the components.\n" );
243	–	painCave.isFatal = 1;
244	–	simError();
245	–
246	–
247	–	//     tot_nmol = the_globals->getNMol();
248	–
249	–	//   //we have the total number of molecules, now we check for molfractions
250	–	//     for( i=0; i<n_components; i++ ){
251	–
252	–	//       if( !the_components[i]->haveMolFraction() ){
253	–
254	–	//  if( !the_components[i]->haveNMol() ){
255	–	//    //we have a problem
256	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	–	//              << " nMol was given in component
258	–
259	–	}
154
155	<	#ifdef IS_MPI
262	<	strcpy( checkPointMsg, "Have the number of components" );
263	<	MPIcheckPoint();
264	<	#endif // is_mpi
155	>	// init the atoms
156
157	<	// make an array of molecule stamps that match the components used.
267	<	// also extract the used stamps out into a separate linked list
157	>	double ux, uy, uz, u, uSqr;
158
159	<	simnfo->nComponents = n_components;
160	<	simnfo->componentsNmol = components_nmol;
271	<	simnfo->compStamps = comp_stamps;
272	<	simnfo->headStamp = new LinkedMolStamp();
273	<
274	<	char* id;
275	<	LinkedMolStamp* headStamp = simnfo->headStamp;
276	<	LinkedMolStamp* currentStamp = NULL;
277	<	for( i=0; i<n_components; i++ ){
159	>	for (k = 0; k < nInfo; k++){
160	>	the_ff->setSimInfo(&(info[k]));
161
162	<	id = the_components[i]->getType();
163	<	comp_stamps[i] = NULL;
164	<
165	<	// check to make sure the component isn't already in the list
283	<
284	<	comp_stamps[i] = headStamp->match( id );
285	<	if( comp_stamps[i] == NULL ){
286	<
287	<	// extract the component from the list;
288	<
289	<	currentStamp = the_stamps->extractMolStamp( id );
290	<	if( currentStamp == NULL ){
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup error: Component \"%s\" was not found in the "
293	<	"list of declared molecules\n",
294	<	id );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	headStamp->add( currentStamp );
300	<	comp_stamps[i] = headStamp->match( id );
301	<	}
302	<	}
162	>	atomOffset = 0;
163	>	excludeOffset = 0;
164	>	for (i = 0; i < info[k].n_mol; i++){
165	>	stampID = info[k].molecules[i].getStampID();
166
167	<	#ifdef IS_MPI
168	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
169	<	MPIcheckPoint();
170	<	#endif // is_mpi
171	<
167	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
168	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
169	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
170	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
171	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
172
173	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
174	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
175	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
176	+	molInfo.myBends = new Bend * [molInfo.nBends];
177	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
178
179	+	theBonds = new bond_pair[molInfo.nBonds];
180	+	theBends = new bend_set[molInfo.nBends];
181	+	theTorsions = new torsion_set[molInfo.nTorsions];
182
183	<	// caclulate the number of atoms, bonds, bends and torsions
183	>	// make the Atoms
184
185	<	tot_atoms = 0;
186	<	tot_bonds = 0;
187	<	tot_bends = 0;
188	<	tot_torsions = 0;
189	<	for( i=0; i<n_components; i++ ){
190	<
191	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	<	}
185	>	for (j = 0; j < molInfo.nAtoms; j++){
186	>	currentAtom = comp_stamps[stampID]->getAtom(j);
187	>	if (currentAtom->haveOrientation()){
188	>	dAtom = new DirectionalAtom((j + atomOffset),
189	>	info[k].getConfiguration());
190	>	info[k].n_oriented++;
191	>	molInfo.myAtoms[j] = dAtom;
192
193	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
193	>	ux = currentAtom->getOrntX();
194	>	uy = currentAtom->getOrntY();
195	>	uz = currentAtom->getOrntZ();
196
197	<	simnfo->n_atoms = tot_atoms;
329	<	simnfo->n_bonds = tot_bonds;
330	<	simnfo->n_bends = tot_bends;
331	<	simnfo->n_torsions = tot_torsions;
332	<	simnfo->n_SRI = tot_SRI;
333	<	simnfo->n_mol = tot_nmol;
334	<
335	<	simnfo->molMembershipArray = new int[tot_atoms];
197	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
198
199	+	u = sqrt(uSqr);
200	+	ux = ux / u;
201	+	uy = uy / u;
202	+	uz = uz / u;
203	+
204	+	dAtom->setSUx(ux);
205	+	dAtom->setSUy(uy);
206	+	dAtom->setSUz(uz);
207	+	}
208	+	else{
209	+	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
210	+	info[k].getConfiguration());
211	+	}
212	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
213	+
214		#ifdef IS_MPI
215
216	<	// divide the molecules among processors here.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
216	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
217
218	<	// set up the local variables
219	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
218	>	#endif // is_mpi
219	>	}
220
221	<	int* mol2proc = mpiSim->getMolToProcMap();
222	<	int* molCompType = mpiSim->getMolComponentType();
223	<
224	<	allMol = 0;
225	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
221	>	// make the bonds
222	>	for (j = 0; j < molInfo.nBonds; j++){
223	>	currentBond = comp_stamps[stampID]->getBond(j);
224	>	theBonds[j].a = currentBond->getA() + atomOffset;
225	>	theBonds[j].b = currentBond->getB() + atomOffset;
226
227	+	exI = theBonds[j].a;
228	+	exJ = theBonds[j].b;
229
230	<	for( i=0; i<n_components; i++ ){
230	>	// exclude_I must always be the smaller of the pair
231	>	if (exI > exJ){
232	>	tempEx = exI;
233	>	exI = exJ;
234	>	exJ = tempEx;
235	>	}
236	>	#ifdef IS_MPI
237	>	tempEx = exI;
238	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	>	tempEx = exJ;
240	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241
242	<	for( j=0; j<components_nmol[i]; j++ ){
243	<
244	<	if( mol2proc[allMol] == worldRank ){
245	<
246	<	local_atoms +=    comp_stamps[i]->getNAtoms();
369	<	local_bonds +=    comp_stamps[i]->getNBonds();
370	<	local_bends +=    comp_stamps[i]->getNBends();
371	<	local_torsions += comp_stamps[i]->getNTorsions();
372	<	localMol++;
373	<	}
374	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
242	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243	>	#else  // isn't MPI
244	>
245	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246	>	#endif  //is_mpi
247		}
248	+	excludeOffset += molInfo.nBonds;
249
250	<	allMol++;
251	<	}
252	<	}
253	<	local_SRI = local_bonds + local_bends + local_torsions;
254	<
255	<	simnfo->n_atoms = mpiSim->getMyNlocal();
385	<
386	<	if( local_atoms != simnfo->n_atoms ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
250	>	//make the bends
251	>	for (j = 0; j < molInfo.nBends; j++){
252	>	currentBend = comp_stamps[stampID]->getBend(j);
253	>	theBends[j].a = currentBend->getA() + atomOffset;
254	>	theBends[j].b = currentBend->getB() + atomOffset;
255	>	theBends[j].c = currentBend->getC() + atomOffset;
256
257	<	simnfo->n_bonds = local_bonds;
258	<	simnfo->n_bends = local_bends;
259	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
257	>	if (currentBend->haveExtras()){
258	>	extras = currentBend->getExtras();
259	>	current_extra = extras;
260
261	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
262	<	MPIcheckPoint();
263	<
264	<
265	<	#endif // is_mpi
266	<
261	>	while (current_extra != NULL){
262	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
263	>	switch (current_extra->getType()){
264	>	case 0:
265	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
266	>	theBends[j].isGhost = 1;
267	>	break;
268
269	<	// create the atom and short range interaction arrays
269	>	case 1:
270	>	theBends[j].ghost = (int) current_extra->getDouble() +
271	>	atomOffset;
272	>	theBends[j].isGhost = 1;
273	>	break;
274
275	<	Atom::createArrays(simnfo->n_atoms);
276	<	the_atoms = new Atom*[simnfo->n_atoms];
277	<	the_molecules = new Molecule[simnfo->n_mol];
278	<	int molIndex;
275	>	default:
276	>	sprintf(painCave.errMsg,
277	>	"SimSetup Error: ghostVectorSource was neither a "
278	>	"double nor an int.\n"
279	>	"-->Bend[%d] in %s\n",
280	>	j, comp_stamps[stampID]->getID());
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	}
285	>	else{
286	>	sprintf(painCave.errMsg,
287	>	"SimSetup Error: unhandled bend assignment:\n"
288	>	"    -->%s in Bend[%d] in %s\n",
289	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293
294	<	// initialize the molecule's stampID's
294	>	current_extra = current_extra->getNext();
295	>	}
296	>	}
297
298	+	if (!theBends[j].isGhost){
299	+	exI = theBends[j].a;
300	+	exJ = theBends[j].c;
301	+	}
302	+	else{
303	+	exI = theBends[j].a;
304	+	exJ = theBends[j].b;
305	+	}
306	+
307	+	// exclude_I must always be the smaller of the pair
308	+	if (exI > exJ){
309	+	tempEx = exI;
310	+	exI = exJ;
311	+	exJ = tempEx;
312	+	}
313		#ifdef IS_MPI
314	<
314	>	tempEx = exI;
315	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	>	tempEx = exJ;
317	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318
319	<	molIndex = 0;
320	<	for(i=0; i<mpiSim->getTotNmol(); i++){
321	<
322	<	if(mol2proc[i] == worldRank ){
425	<	the_molecules[molIndex].setStampID( molCompType[i] );
426	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
429	<	}
430	<	}
431	<
432	<	#else // is_mpi
433	<
434	<	molIndex = 0;
435	<	globalAtomIndex = 0;
436	<	for(i=0; i<n_components; i++){
437	<	for(j=0; j<components_nmol[i]; j++ ){
438	<	the_molecules[molIndex].setStampID( i );
439	<	the_molecules[molIndex].setMyIndex( molIndex );
440	<	the_molecules[molIndex].setGlobalIndex( molIndex );
441	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443	<	globalAtomIndex++;
319	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
320	>	#else  // isn't MPI
321	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
322	>	#endif  //is_mpi
323		}
324	<	molIndex++;
446	<	}
447	<	}
448	<
324	>	excludeOffset += molInfo.nBends;
325
326	<	#endif // is_mpi
326	>	for (j = 0; j < molInfo.nTorsions; j++){
327	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
328	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
329	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
330	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
331	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
332
333	+	exI = theTorsions[j].a;
334	+	exJ = theTorsions[j].d;
335
336	<	if( simnfo->n_SRI ){
337	<
338	<	Exclude::createArray(simnfo->n_SRI);
339	<	the_excludes = new Exclude*[simnfo->n_SRI];
340	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
341	<	simnfo->globalExcludes = new int;
342	<	simnfo->n_exclude = simnfo->n_SRI;
343	<	}
344	<	else{
345	<
346	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
336	>	// exclude_I must always be the smaller of the pair
337	>	if (exI > exJ){
338	>	tempEx = exI;
339	>	exI = exJ;
340	>	exJ = tempEx;
341	>	}
342	>	#ifdef IS_MPI
343	>	tempEx = exI;
344	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>	tempEx = exJ;
346	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347
348	<	// set the arrays into the SimInfo object
348	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
349	>	#else  // isn't MPI
350	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
351	>	#endif  //is_mpi
352	>	}
353	>	excludeOffset += molInfo.nTorsions;
354
474	–	simnfo->atoms = the_atoms;
475	–	simnfo->molecules = the_molecules;
476	–	simnfo->nGlobalExcludes = 0;
477	–	simnfo->excludes = the_excludes;
355
356	+	// send the arrays off to the forceField for init.
357
358	<	// get some of the tricky things that may still be in the globals
358	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
359	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
360	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
361	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
362	>	theTorsions);
363
482	–
483	–	if( the_globals->haveBox() ){
484	–	simnfo->box_x = the_globals->getBox();
485	–	simnfo->box_y = the_globals->getBox();
486	–	simnfo->box_z = the_globals->getBox();
487	–	}
488	–	else if( the_globals->haveDensity() ){
364
365	<	double vol;
491	<	vol = (double)tot_nmol / the_globals->getDensity();
492	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
493	<	simnfo->box_y = simnfo->box_x;
494	<	simnfo->box_z = simnfo->box_x;
495	<	}
496	<	else{
497	<	if( !the_globals->haveBoxX() ){
498	<	sprintf( painCave.errMsg,
499	<	"SimSetup error, no periodic BoxX size given.\n" );
500	<	painCave.isFatal = 1;
501	<	simError();
502	<	}
503	<	simnfo->box_x = the_globals->getBoxX();
365	>	info[k].molecules[i].initialize(molInfo);
366
505	–	if( !the_globals->haveBoxY() ){
506	–	sprintf( painCave.errMsg,
507	–	"SimSetup error, no periodic BoxY size given.\n" );
508	–	painCave.isFatal = 1;
509	–	simError();
510	–	}
511	–	simnfo->box_y = the_globals->getBoxY();
367
368	<	if( !the_globals->haveBoxZ() ){
369	<	sprintf( painCave.errMsg,
370	<	"SimSetup error, no periodic BoxZ size given.\n" );
371	<	painCave.isFatal = 1;
517	<	simError();
368	>	atomOffset += molInfo.nAtoms;
369	>	delete[] theBonds;
370	>	delete[] theBends;
371	>	delete[] theTorsions;
372		}
519	–	simnfo->box_z = the_globals->getBoxZ();
373		}
374
375		#ifdef IS_MPI
376	<	strcpy( checkPointMsg, "Box size set up" );
376	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
377		MPIcheckPoint();
378		#endif // is_mpi
379
380	+	// clean up the forcefield
381
382	<	// initialize the arrays
382	>	the_ff->calcRcut();
383	>	the_ff->cleanMe();
384	>	}
385
386	<	the_ff->setSimInfo( simnfo );
386	>	void SimSetup::initFromBass(void){
387	>	int i, j, k;
388	>	int n_cells;
389	>	double cellx, celly, cellz;
390	>	double temp1, temp2, temp3;
391	>	int n_per_extra;
392	>	int n_extra;
393	>	int have_extra, done;
394
395	<	makeMolecules();
396	<	simnfo->identArray = new int[simnfo->n_atoms];
397	<	for(i=0; i<simnfo->n_atoms; i++){
398	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
536	<	}
537	<
538	<	if (the_globals->getUseRF() ) {
539	<	simnfo->useReactionField = 1;
540	<
541	<	if( !the_globals->haveECR() ){
542	<	sprintf( painCave.errMsg,
543	<	"SimSetup Warning: using default value of 1/2 the smallest "
544	<	"box length for the electrostaticCutoffRadius.\n"
545	<	"I hope you have a very fast processor!\n");
546	<	painCave.isFatal = 0;
547	<	simError();
548	<	double smallest;
549	<	smallest = simnfo->box_x;
550	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
551	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
552	<	simnfo->ecr = 0.5 * smallest;
553	<	} else {
554	<	simnfo->ecr        = the_globals->getECR();
555	<	}
395	>	double vel[3];
396	>	vel[0] = 0.0;
397	>	vel[1] = 0.0;
398	>	vel[2] = 0.0;
399
400	<	if( !the_globals->haveEST() ){
401	<	sprintf( painCave.errMsg,
402	<	"SimSetup Warning: using default value of 0.05 * the "
403	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
404	<	);
405	<	painCave.isFatal = 0;
406	<	simError();
407	<	simnfo->est = 0.05 * simnfo->ecr;
408	<	} else {
409	<	simnfo->est        = the_globals->getEST();
410	<	}
411	<
412	<	if(!the_globals->haveDielectric() ){
413	<	sprintf( painCave.errMsg,
414	<	"SimSetup Error: You are trying to use Reaction Field without"
415	<	"setting a dielectric constant!\n"
416	<	);
400	>	temp1 = (double) tot_nmol / 4.0;
401	>	temp2 = pow(temp1, (1.0 / 3.0));
402	>	temp3 = ceil(temp2);
403	>
404	>	have_extra = 0;
405	>	if (temp2 < temp3){
406	>	// we have a non-complete lattice
407	>	have_extra = 1;
408	>
409	>	n_cells = (int) temp3 - 1;
410	>	cellx = info[0].boxL[0] / temp3;
411	>	celly = info[0].boxL[1] / temp3;
412	>	cellz = info[0].boxL[2] / temp3;
413	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
414	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
415	>	n_per_extra = (int) ceil(temp1);
416	>
417	>	if (n_per_extra > 4){
418	>	sprintf(painCave.errMsg,
419	>	"SimSetup error. There has been an error in constructing"
420	>	" the non-complete lattice.\n");
421		painCave.isFatal = 1;
422		simError();
423		}
424	<	simnfo->dielectric = the_globals->getDielectric();
425	<	} else {
426	<	if (usesDipoles) {
427	<
428	<	if( !the_globals->haveECR() ){
429	<	sprintf( painCave.errMsg,
430	<	"SimSetup Warning: using default value of 1/2 the smallest "
584	<	"box length for the electrostaticCutoffRadius.\n"
585	<	"I hope you have a very fast processor!\n");
586	<	painCave.isFatal = 0;
587	<	simError();
588	<	double smallest;
589	<	smallest = simnfo->box_x;
590	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
591	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
592	<	simnfo->ecr = 0.5 * smallest;
593	<	} else {
594	<	simnfo->ecr        = the_globals->getECR();
595	<	}
596	<
597	<	if( !the_globals->haveEST() ){
598	<	sprintf( painCave.errMsg,
599	<	"SimSetup Warning: using default value of 5%% of the "
600	<	"electrostaticCutoffRadius for the "
601	<	"electrostaticSkinThickness\n"
602	<	);
603	<	painCave.isFatal = 0;
604	<	simError();
605	<	simnfo->est = 0.05 * simnfo->ecr;
606	<	} else {
607	<	simnfo->est        = the_globals->getEST();
608	<	}
609	<	}
610	<	}
424	>	}
425	>	else{
426	>	n_cells = (int) temp3;
427	>	cellx = info[0].boxL[0] / temp3;
428	>	celly = info[0].boxL[1] / temp3;
429	>	cellz = info[0].boxL[2] / temp3;
430	>	}
431
432	<	#ifdef IS_MPI
433	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
434	<	MPIcheckPoint();
435	<	#endif // is_mpi
432	>	current_mol = 0;
433	>	current_comp_mol = 0;
434	>	current_comp = 0;
435	>	current_atom_ndx = 0;
436
437	<	if( the_globals->haveInitialConfig() ){
438	<
439	<	InitializeFromFile* fileInit;
440	<	#ifdef IS_MPI // is_mpi
621	<	if( worldRank == 0 ){
622	<	#endif //is_mpi
623	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
624	<	#ifdef IS_MPI
625	<	}else fileInit = new InitializeFromFile( NULL );
626	<	#endif
627	<	fileInit->read_xyz( simnfo ); // default velocities on
437	>	for (i = 0; i < n_cells ; i++){
438	>	for (j = 0; j < n_cells; j++){
439	>	for (k = 0; k < n_cells; k++){
440	>	makeElement(i * cellx, j * celly, k * cellz);
441
442	<	delete fileInit;
630	<	}
631	<	else{
442	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
443
444	<	#ifdef IS_MPI
444	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
445
446	<	// no init from bass
447	<
448	<	sprintf( painCave.errMsg,
449	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
639	<	painCave.isFatal;
640	<	simError();
641	<
642	<	#else
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
447	>	}
448	>	}
449	>	}
450
451	<	initFromBass();
451	>	if (have_extra){
452	>	done = 0;
453
454	+	int start_ndx;
455	+	for (i = 0; i < (n_cells + 1) && !done; i++){
456	+	for (j = 0; j < (n_cells + 1) && !done; j++){
457	+	if (i < n_cells){
458	+	if (j < n_cells){
459	+	start_ndx = n_cells;
460	+	}
461	+	else
462	+	start_ndx = 0;
463	+	}
464	+	else
465	+	start_ndx = 0;
466
467	<	#endif
468	<	}
467	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469	>	done = (current_mol >= tot_nmol);
470
471	<	#ifdef IS_MPI
472	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
473	<	MPIcheckPoint();
474	<	#endif // is_mpi
471	>	if (!done && n_per_extra > 1){
472	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
473	>	k * cellz);
474	>	done = (current_mol >= tot_nmol);
475	>	}
476
477	+	if (!done && n_per_extra > 2){
478	+	makeElement(i * cellx, j * celly + 0.5 * celly,
479	+	k * cellz + 0.5 * cellz);
480	+	done = (current_mol >= tot_nmol);
481	+	}
482
483	<
484	<
485	<
486	<
487	<
488	<	#ifdef IS_MPI
662	<	if( worldRank == 0 ){
663	<	#endif // is_mpi
664	<
665	<	if( the_globals->haveFinalConfig() ){
666	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
667	<	}
668	<	else{
669	<	strcpy( simnfo->finalName, inFileName );
670	<	char* endTest;
671	<	int nameLength = strlen( simnfo->finalName );
672	<	endTest = &(simnfo->finalName[nameLength - 5]);
673	<	if( !strcmp( endTest, ".bass" ) ){
674	<	strcpy( endTest, ".eor" );
483	>	if (!done && n_per_extra > 3){
484	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
485	>	k * cellz + 0.5 * cellz);
486	>	done = (current_mol >= tot_nmol);
487	>	}
488	>	}
489		}
676	–	else if( !strcmp( endTest, ".BASS" ) ){
677	–	strcpy( endTest, ".eor" );
678	–	}
679	–	else{
680	–	endTest = &(simnfo->finalName[nameLength - 4]);
681	–	if( !strcmp( endTest, ".bss" ) ){
682	–	strcpy( endTest, ".eor" );
683	–	}
684	–	else if( !strcmp( endTest, ".mdl" ) ){
685	–	strcpy( endTest, ".eor" );
686	–	}
687	–	else{
688	–	strcat( simnfo->finalName, ".eor" );
689	–	}
690	–	}
490		}
692	–
693	–	// make the sample and status out names
694	–
695	–	strcpy( simnfo->sampleName, inFileName );
696	–	char* endTest;
697	–	int nameLength = strlen( simnfo->sampleName );
698	–	endTest = &(simnfo->sampleName[nameLength - 5]);
699	–	if( !strcmp( endTest, ".bass" ) ){
700	–	strcpy( endTest, ".dump" );
701	–	}
702	–	else if( !strcmp( endTest, ".BASS" ) ){
703	–	strcpy( endTest, ".dump" );
704	–	}
705	–	else{
706	–	endTest = &(simnfo->sampleName[nameLength - 4]);
707	–	if( !strcmp( endTest, ".bss" ) ){
708	–	strcpy( endTest, ".dump" );
709	–	}
710	–	else if( !strcmp( endTest, ".mdl" ) ){
711	–	strcpy( endTest, ".dump" );
712	–	}
713	–	else{
714	–	strcat( simnfo->sampleName, ".dump" );
715	–	}
716	–	}
717	–
718	–	strcpy( simnfo->statusName, inFileName );
719	–	nameLength = strlen( simnfo->statusName );
720	–	endTest = &(simnfo->statusName[nameLength - 5]);
721	–	if( !strcmp( endTest, ".bass" ) ){
722	–	strcpy( endTest, ".stat" );
723	–	}
724	–	else if( !strcmp( endTest, ".BASS" ) ){
725	–	strcpy( endTest, ".stat" );
726	–	}
727	–	else{
728	–	endTest = &(simnfo->statusName[nameLength - 4]);
729	–	if( !strcmp( endTest, ".bss" ) ){
730	–	strcpy( endTest, ".stat" );
731	–	}
732	–	else if( !strcmp( endTest, ".mdl" ) ){
733	–	strcpy( endTest, ".stat" );
734	–	}
735	–	else{
736	–	strcat( simnfo->statusName, ".stat" );
737	–	}
738	–	}
739	–
740	–	#ifdef IS_MPI
491		}
742	–	#endif // is_mpi
743	–
744	–	// set the status, sample, and themal kick times
745	–
746	–	if( the_globals->haveSampleTime() ){
747	–	simnfo->sampleTime = the_globals->getSampleTime();
748	–	simnfo->statusTime = simnfo->sampleTime;
749	–	simnfo->thermalTime = simnfo->sampleTime;
750	–	}
751	–	else{
752	–	simnfo->sampleTime = the_globals->getRunTime();
753	–	simnfo->statusTime = simnfo->sampleTime;
754	–	simnfo->thermalTime = simnfo->sampleTime;
755	–	}
492
493	<	if( the_globals->haveStatusTime() ){
494	<	simnfo->statusTime = the_globals->getStatusTime();
493	>	for (i = 0; i < info[0].n_atoms; i++){
494	>	info[0].atoms[i]->setVel(vel);
495		}
496	+	}
497
498	<	if( the_globals->haveThermalTime() ){
499	<	simnfo->thermalTime = the_globals->getThermalTime();
500	<	}
498	>	void SimSetup::makeElement(double x, double y, double z){
499	>	int k;
500	>	AtomStamp* current_atom;
501	>	DirectionalAtom* dAtom;
502	>	double rotMat[3][3];
503	>	double pos[3];
504
505	<	// check for the temperature set flag
505	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
506	>	current_atom = comp_stamps[current_comp]->getAtom(k);
507	>	if (!current_atom->havePosition()){
508	>	sprintf(painCave.errMsg,
509	>	"SimSetup:initFromBass error.\n"
510	>	"\tComponent %s, atom %s does not have a position specified.\n"
511	>	"\tThe initialization routine is unable to give a start"
512	>	" position.\n",
513	>	comp_stamps[current_comp]->getID(), current_atom->getType());
514	>	painCave.isFatal = 1;
515	>	simError();
516	>	}
517
518	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
518	>	pos[0] = x + current_atom->getPosX();
519	>	pos[1] = y + current_atom->getPosY();
520	>	pos[2] = z + current_atom->getPosZ();
521
522	+	info[0].atoms[current_atom_ndx]->setPos(pos);
523
524	<	// make the integrator
524	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
525	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
526
527	<	switch( ensembleCase ){
527	>	rotMat[0][0] = 1.0;
528	>	rotMat[0][1] = 0.0;
529	>	rotMat[0][2] = 0.0;
530
531	<	case NVE_ENS:
532	<	new NVE( simnfo, the_ff );
533	<	break;
531	>	rotMat[1][0] = 0.0;
532	>	rotMat[1][1] = 1.0;
533	>	rotMat[1][2] = 0.0;
534
535	<	default:
536	<	sprintf( painCave.errMsg,
537	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
538	<	painCave.isFatal = 1;
539	<	simError();
535	>	rotMat[2][0] = 0.0;
536	>	rotMat[2][1] = 0.0;
537	>	rotMat[2][2] = 1.0;
538	>
539	>	dAtom->setA(rotMat);
540	>	}
541	>
542	>	current_atom_ndx++;
543		}
544
545	+	current_mol++;
546	+	current_comp_mol++;
547
548	<	#ifdef IS_MPI
549	<	mpiSim->mpiRefresh();
550	<	#endif
548	>	if (current_comp_mol >= components_nmol[current_comp]){
549	>	current_comp_mol = 0;
550	>	current_comp++;
551	>	}
552	>	}
553
790	–	// initialize the Fortran
554
555	+	void SimSetup::gatherInfo(void){
556	+	int i, j, k;
557
558	<	simnfo->refreshSim();
559	<
560	<	if( !strcmp( simnfo->mixingRule, "standard") ){
561	<	the_ff->initForceField( LB_MIXING_RULE );
562	<	}
563	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
564	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
558	>	ensembleCase = -1;
559	>	ffCase = -1;
560	>
561	>	// set the easy ones first
562	>
563	>	for (i = 0; i < nInfo; i++){
564	>	info[i].target_temp = globals->getTargetTemp();
565	>	info[i].dt = globals->getDt();
566	>	info[i].run_time = globals->getRunTime();
567		}
568	<	else{
802	<	sprintf( painCave.errMsg,
803	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
804	<	simnfo->mixingRule );
805	<	painCave.isFatal = 1;
806	<	simError();
807	<	}
568	>	n_components = globals->getNComponents();
569
570
571	<	#ifdef IS_MPI
811	<	strcpy( checkPointMsg,
812	<	"Successfully intialized the mixingRule for Fortran." );
813	<	MPIcheckPoint();
814	<	#endif // is_mpi
815	<	}
571	>	// get the forceField
572
573	+	strcpy(force_field, globals->getForceField());
574
575	<	void SimSetup::makeMolecules( void ){
575	>	if (!strcasecmp(force_field, "DUFF")){
576	>	ffCase = FF_DUFF;
577	>	}
578	>	else if (!strcasecmp(force_field, "LJ")){
579	>	ffCase = FF_LJ;
580	>	}
581	>	else if (!strcasecmp(force_field, "EAM")){
582	>	ffCase = FF_EAM;
583	>	}
584	>	else{
585	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
586	>	force_field);
587	>	painCave.isFatal = 1;
588	>	simError();
589	>	}
590
591	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
821	<	molInit info;
822	<	DirectionalAtom* dAtom;
823	<	LinkedAssign* extras;
824	<	LinkedAssign* current_extra;
825	<	AtomStamp* currentAtom;
826	<	BondStamp* currentBond;
827	<	BendStamp* currentBend;
828	<	TorsionStamp* currentTorsion;
591	>	// get the ensemble
592
593	<	bond_pair* theBonds;
831	<	bend_set* theBends;
832	<	torsion_set* theTorsions;
593	>	strcpy(ensemble, globals->getEnsemble());
594
595	<
596	<	//init the forceField paramters
595	>	if (!strcasecmp(ensemble, "NVE")){
596	>	ensembleCase = NVE_ENS;
597	>	}
598	>	else if (!strcasecmp(ensemble, "NVT")){
599	>	ensembleCase = NVT_ENS;
600	>	}
601	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
602	>	ensembleCase = NPTi_ENS;
603	>	}
604	>	else if (!strcasecmp(ensemble, "NPTf")){
605	>	ensembleCase = NPTf_ENS;
606	>	}
607	>	else if (!strcasecmp(ensemble, "NPTim")){
608	>	ensembleCase = NPTim_ENS;
609	>	}
610	>	else if (!strcasecmp(ensemble, "NPTfm")){
611	>	ensembleCase = NPTfm_ENS;
612	>	}
613	>	else{
614	>	sprintf(painCave.errMsg,
615	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
616	>	"reverting to NVE for this simulation.\n",
617	>	ensemble);
618	>	painCave.isFatal = 0;
619	>	simError();
620	>	strcpy(ensemble, "NVE");
621	>	ensembleCase = NVE_ENS;
622	>	}
623
624	<	the_ff->readParams();
624	>	for (i = 0; i < nInfo; i++){
625	>	strcpy(info[i].ensemble, ensemble);
626
627	<
840	<	// init the atoms
627	>	// get the mixing rule
628
629	<	double ux, uy, uz, u, uSqr;
630	<
631	<	atomOffset = 0;
845	<	excludeOffset = 0;
846	<	for(i=0; i<simnfo->n_mol; i++){
847	<
848	<	stampID = the_molecules[i].getStampID();
629	>	strcpy(info[i].mixingRule, globals->getMixingRule());
630	>	info[i].usePBC = globals->getPBC();
631	>	}
632
633	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
851	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
852	<	info.nBends    = comp_stamps[stampID]->getNBends();
853	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
854	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
633	>	// get the components and calculate the tot_nMol and indvidual n_mol
634
635	<	info.myAtoms = &the_atoms[atomOffset];
636	<	info.myExcludes = &the_excludes[excludeOffset];
858	<	info.myBonds = new Bond*[info.nBonds];
859	<	info.myBends = new Bend*[info.nBends];
860	<	info.myTorsions = new Torsion*[info.nTorsions];
635	>	the_components = globals->getComponents();
636	>	components_nmol = new int[n_components];
637
862	–	theBonds = new bond_pair[info.nBonds];
863	–	theBends = new bend_set[info.nBends];
864	–	theTorsions = new torsion_set[info.nTorsions];
865	–
866	–	// make the Atoms
867	–
868	–	for(j=0; j<info.nAtoms; j++){
869	–
870	–	currentAtom = comp_stamps[stampID]->getAtom( j );
871	–	if( currentAtom->haveOrientation() ){
872	–
873	–	dAtom = new DirectionalAtom(j + atomOffset);
874	–	simnfo->n_oriented++;
875	–	info.myAtoms[j] = dAtom;
876	–
877	–	ux = currentAtom->getOrntX();
878	–	uy = currentAtom->getOrntY();
879	–	uz = currentAtom->getOrntZ();
880	–
881	–	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
882	–
883	–	u = sqrt( uSqr );
884	–	ux = ux / u;
885	–	uy = uy / u;
886	–	uz = uz / u;
887	–
888	–	dAtom->setSUx( ux );
889	–	dAtom->setSUy( uy );
890	–	dAtom->setSUz( uz );
891	–	}
892	–	else{
893	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
894	–	}
895	–	info.myAtoms[j]->setType( currentAtom->getType() );
896	–
897	–	#ifdef IS_MPI
898	–
899	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
900	–
901	–	#endif // is_mpi
902	–	}
903	–
904	–	// make the bonds
905	–	for(j=0; j<info.nBonds; j++){
906	–
907	–	currentBond = comp_stamps[stampID]->getBond( j );
908	–	theBonds[j].a = currentBond->getA() + atomOffset;
909	–	theBonds[j].b = currentBond->getB() + atomOffset;
638
639	<	exI = theBonds[j].a;
640	<	exJ = theBonds[j].b;
639	>	if (!globals->haveNMol()){
640	>	// we don't have the total number of molecules, so we assume it is
641	>	// given in each component
642
643	<	// exclude_I must always be the smaller of the pair
644	<	if( exI > exJ ){
645	<	tempEx = exI;
646	<	exI = exJ;
647	<	exJ = tempEx;
643	>	tot_nmol = 0;
644	>	for (i = 0; i < n_components; i++){
645	>	if (!the_components[i]->haveNMol()){
646	>	// we have a problem
647	>	sprintf(painCave.errMsg,
648	>	"SimSetup Error. No global NMol or component NMol"
649	>	" given. Cannot calculate the number of atoms.\n");
650	>	painCave.isFatal = 1;
651	>	simError();
652		}
920	–	#ifdef IS_MPI
921	–	tempEx = exI;
922	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
923	–	tempEx = exJ;
924	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
925	–
926	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
927	–	#else  // isn't MPI
653
654	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
655	<	#endif  //is_mpi
654	>	tot_nmol += the_components[i]->getNMol();
655	>	components_nmol[i] = the_components[i]->getNMol();
656		}
657	<	excludeOffset += info.nBonds;
657	>	}
658	>	else{
659	>	sprintf(painCave.errMsg,
660	>	"SimSetup error.\n"
661	>	"\tSorry, the ability to specify total"
662	>	" nMols and then give molfractions in the components\n"
663	>	"\tis not currently supported."
664	>	" Please give nMol in the components.\n");
665	>	painCave.isFatal = 1;
666	>	simError();
667	>	}
668
669	<	//make the bends
670	<	for(j=0; j<info.nBends; j++){
671	<
672	<	currentBend = comp_stamps[stampID]->getBend( j );
673	<	theBends[j].a = currentBend->getA() + atomOffset;
674	<	theBends[j].b = currentBend->getB() + atomOffset;
675	<	theBends[j].c = currentBend->getC() + atomOffset;
941	<
942	<	if( currentBend->haveExtras() ){
943	<
944	<	extras = currentBend->getExtras();
945	<	current_extra = extras;
946	<
947	<	while( current_extra != NULL ){
948	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
949	<
950	<	switch( current_extra->getType() ){
951	<
952	<	case 0:
953	<	theBends[j].ghost =
954	<	current_extra->getInt() + atomOffset;
955	<	theBends[j].isGhost = 1;
956	<	break;
957	<
958	<	case 1:
959	<	theBends[j].ghost =
960	<	(int)current_extra->getDouble() + atomOffset;
961	<	theBends[j].isGhost = 1;
962	<	break;
963	<
964	<	default:
965	<	sprintf( painCave.errMsg,
966	<	"SimSetup Error: ghostVectorSource was neither a "
967	<	"double nor an int.\n"
968	<	"-->Bend[%d] in %s\n",
969	<	j, comp_stamps[stampID]->getID() );
970	<	painCave.isFatal = 1;
971	<	simError();
972	<	}
973	<	}
974	<
975	<	else{
976	<
977	<	sprintf( painCave.errMsg,
978	<	"SimSetup Error: unhandled bend assignment:\n"
979	<	"    -->%s in Bend[%d] in %s\n",
980	<	current_extra->getlhs(),
981	<	j, comp_stamps[stampID]->getID() );
982	<	painCave.isFatal = 1;
983	<	simError();
984	<	}
985	<
986	<	current_extra = current_extra->getNext();
987	<	}
988	<	}
989	<
990	<	if( !theBends[j].isGhost ){
991	<
992	<	exI = theBends[j].a;
993	<	exJ = theBends[j].c;
994	<	}
995	<	else{
996	<
997	<	exI = theBends[j].a;
998	<	exJ = theBends[j].b;
999	<	}
1000	<
1001	<	// exclude_I must always be the smaller of the pair
1002	<	if( exI > exJ ){
1003	<	tempEx = exI;
1004	<	exI = exJ;
1005	<	exJ = tempEx;
1006	<	}
1007	<	#ifdef IS_MPI
1008	<	tempEx = exI;
1009	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1010	<	tempEx = exJ;
1011	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1012	<
1013	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1014	<	#else  // isn't MPI
1015	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1016	<	#endif  //is_mpi
669	>	// set the status, sample, and thermal kick times
670	>
671	>	for (i = 0; i < nInfo; i++){
672	>	if (globals->haveSampleTime()){
673	>	info[i].sampleTime = globals->getSampleTime();
674	>	info[i].statusTime = info[i].sampleTime;
675	>	info[i].thermalTime = info[i].sampleTime;
676		}
677	<	excludeOffset += info.nBends;
677	>	else{
678	>	info[i].sampleTime = globals->getRunTime();
679	>	info[i].statusTime = info[i].sampleTime;
680	>	info[i].thermalTime = info[i].sampleTime;
681	>	}
682
683	<	for(j=0; j<info.nTorsions; j++){
684	<
685	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1023	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1024	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1025	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1026	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1027	<
1028	<	exI = theTorsions[j].a;
1029	<	exJ = theTorsions[j].d;
683	>	if (globals->haveStatusTime()){
684	>	info[i].statusTime = globals->getStatusTime();
685	>	}
686
687	<	// exclude_I must always be the smaller of the pair
688	<	if( exI > exJ ){
1033	<	tempEx = exI;
1034	<	exI = exJ;
1035	<	exJ = tempEx;
1036	<	}
1037	<	#ifdef IS_MPI
1038	<	tempEx = exI;
1039	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1040	<	tempEx = exJ;
1041	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1042	<
1043	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1044	<	#else  // isn't MPI
1045	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1046	<	#endif  //is_mpi
687	>	if (globals->haveThermalTime()){
688	>	info[i].thermalTime = globals->getThermalTime();
689		}
1048	–	excludeOffset += info.nTorsions;
690
691	<
1051	<	// send the arrays off to the forceField for init.
691	>	// check for the temperature set flag
692
693	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
694	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1055	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1056	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
693	>	if (globals->haveTempSet())
694	>	info[i].setTemp = globals->getTempSet();
695
696	+	// get some of the tricky things that may still be in the globals
697
698	<	the_molecules[i].initialize( info );
698	>	double boxVector[3];
699	>	if (globals->haveBox()){
700	>	boxVector[0] = globals->getBox();
701	>	boxVector[1] = globals->getBox();
702	>	boxVector[2] = globals->getBox();
703
704	+	info[i].setBox(boxVector);
705	+	}
706	+	else if (globals->haveDensity()){
707	+	double vol;
708	+	vol = (double) tot_nmol / globals->getDensity();
709	+	boxVector[0] = pow(vol, (1.0 / 3.0));
710	+	boxVector[1] = boxVector[0];
711	+	boxVector[2] = boxVector[0];
712
713	<	atomOffset += info.nAtoms;
714	<	delete[] theBonds;
715	<	delete[] theBends;
716	<	delete[] theTorsions;
713	>	info[i].setBox(boxVector);
714	>	}
715	>	else{
716	>	if (!globals->haveBoxX()){
717	>	sprintf(painCave.errMsg,
718	>	"SimSetup error, no periodic BoxX size given.\n");
719	>	painCave.isFatal = 1;
720	>	simError();
721	>	}
722	>	boxVector[0] = globals->getBoxX();
723	>
724	>	if (!globals->haveBoxY()){
725	>	sprintf(painCave.errMsg,
726	>	"SimSetup error, no periodic BoxY size given.\n");
727	>	painCave.isFatal = 1;
728	>	simError();
729	>	}
730	>	boxVector[1] = globals->getBoxY();
731	>
732	>	if (!globals->haveBoxZ()){
733	>	sprintf(painCave.errMsg,
734	>	"SimSetup error, no periodic BoxZ size given.\n");
735	>	painCave.isFatal = 1;
736	>	simError();
737	>	}
738	>	boxVector[2] = globals->getBoxZ();
739	>
740	>	info[i].setBox(boxVector);
741	>	}
742		}
743
744	+	//setup seed for random number generator
745	+	int seedValue;
746	+
747	+	if (globals->haveSeed()){
748	+	seedValue = globals->getSeed();
749	+
750	+	if(seedValue / 1E9 == 0){
751	+	sprintf(painCave.errMsg,
752	+	"Seed for sprng library should contain at least 9 digits\n"
753	+	"OOPSE will generate a seed for user\n");
754	+	painCave.isFatal = 0;
755	+	simError();
756	+
757	+	//using seed generated by system instead of invalid seed set by user
758	+	#ifndef IS_MPI
759	+	seedValue = make_sprng_seed();
760	+	#else
761	+	if (worldRank == 0){
762	+	seedValue = make_sprng_seed();
763	+	}
764	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
765	+	#endif
766	+	}
767	+	}//end of if branch of globals->haveSeed()
768	+	else{
769	+
770	+	#ifndef IS_MPI
771	+	seedValue = make_sprng_seed();
772	+	#else
773	+	if (worldRank == 0){
774	+	seedValue = make_sprng_seed();
775	+	}
776	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
777	+	#endif
778	+	}//end of globals->haveSeed()
779	+
780	+	for (int i = 0; i < nInfo; i++){
781	+	info[i].setSeed(seedValue);
782	+	}
783	+
784		#ifdef IS_MPI
785	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
785	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
786		MPIcheckPoint();
787		#endif // is_mpi
788	+	}
789
1073	–	// clean up the forcefield
1074	–	the_ff->calcRcut();
1075	–	the_ff->cleanMe();
790
791	<	}
791	>	void SimSetup::finalInfoCheck(void){
792	>	int index;
793	>	int usesDipoles;
794	>	int i;
795
796	<	void SimSetup::initFromBass( void ){
796	>	for (i = 0; i < nInfo; i++){
797	>	// check electrostatic parameters
798
799	<	int i, j, k;
800	<	int n_cells;
801	<	double cellx, celly, cellz;
802	<	double temp1, temp2, temp3;
803	<	int n_per_extra;
804	<	int n_extra;
1087	<	int have_extra, done;
799	>	index = 0;
800	>	usesDipoles = 0;
801	>	while ((index < info[i].n_atoms) && !usesDipoles){
802	>	usesDipoles = (info[i].atoms[index])->hasDipole();
803	>	index++;
804	>	}
805
806	<	temp1 = (double)tot_nmol / 4.0;
807	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
808	<	temp3 = ceil( temp2 );
806	>	#ifdef IS_MPI
807	>	int myUse = usesDipoles;
808	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809	>	#endif //is_mpi
810
811	<	have_extra =0;
1094	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1095	<	have_extra =1;
811	>	double theEcr, theEst;
812
813	<	n_cells = (int)temp3 - 1;
814	<	cellx = simnfo->box_x / temp3;
1099	<	celly = simnfo->box_y / temp3;
1100	<	cellz = simnfo->box_z / temp3;
1101	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1102	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1103	<	n_per_extra = (int)ceil( temp1 );
813	>	if (globals->getUseRF()){
814	>	info[i].useReactionField = 1;
815
816	<	if( n_per_extra > 4){
817	<	sprintf( painCave.errMsg,
818	<	"SimSetup error. There has been an error in constructing"
819	<	" the non-complete lattice.\n" );
820	<	painCave.isFatal = 1;
821	<	simError();
816	>	if (!globals->haveECR()){
817	>	sprintf(painCave.errMsg,
818	>	"SimSetup Warning: using default value of 1/2 the smallest "
819	>	"box length for the electrostaticCutoffRadius.\n"
820	>	"I hope you have a very fast processor!\n");
821	>	painCave.isFatal = 0;
822	>	simError();
823	>	double smallest;
824	>	smallest = info[i].boxL[0];
825	>	if (info[i].boxL[1] <= smallest)
826	>	smallest = info[i].boxL[1];
827	>	if (info[i].boxL[2] <= smallest)
828	>	smallest = info[i].boxL[2];
829	>	theEcr = 0.5 * smallest;
830	>	}
831	>	else{
832	>	theEcr = globals->getECR();
833	>	}
834	>
835	>	if (!globals->haveEST()){
836	>	sprintf(painCave.errMsg,
837	>	"SimSetup Warning: using default value of 0.05 * the "
838	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
839	>	painCave.isFatal = 0;
840	>	simError();
841	>	theEst = 0.05 * theEcr;
842	>	}
843	>	else{
844	>	theEst = globals->getEST();
845	>	}
846	>
847	>	info[i].setEcr(theEcr, theEst);
848	>
849	>	if (!globals->haveDielectric()){
850	>	sprintf(painCave.errMsg,
851	>	"SimSetup Error: You are trying to use Reaction Field without"
852	>	"setting a dielectric constant!\n");
853	>	painCave.isFatal = 1;
854	>	simError();
855	>	}
856	>	info[i].dielectric = globals->getDielectric();
857		}
858	+	else{
859	+	if (usesDipoles){
860	+	if (!globals->haveECR()){
861	+	sprintf(painCave.errMsg,
862	+	"SimSetup Warning: using default value of 1/2 the smallest "
863	+	"box length for the electrostaticCutoffRadius.\n"
864	+	"I hope you have a very fast processor!\n");
865	+	painCave.isFatal = 0;
866	+	simError();
867	+	double smallest;
868	+	smallest = info[i].boxL[0];
869	+	if (info[i].boxL[1] <= smallest)
870	+	smallest = info[i].boxL[1];
871	+	if (info[i].boxL[2] <= smallest)
872	+	smallest = info[i].boxL[2];
873	+	theEcr = 0.5 * smallest;
874	+	}
875	+	else{
876	+	theEcr = globals->getECR();
877	+	}
878	+
879	+	if (!globals->haveEST()){
880	+	sprintf(painCave.errMsg,
881	+	"SimSetup Warning: using default value of 0.05 * the "
882	+	"electrostaticCutoffRadius for the "
883	+	"electrostaticSkinThickness\n");
884	+	painCave.isFatal = 0;
885	+	simError();
886	+	theEst = 0.05 * theEcr;
887	+	}
888	+	else{
889	+	theEst = globals->getEST();
890	+	}
891	+
892	+	info[i].setEcr(theEcr, theEst);
893	+	}
894	+	}
895		}
896	+
897	+	#ifdef IS_MPI
898	+	strcpy(checkPointMsg, "post processing checks out");
899	+	MPIcheckPoint();
900	+	#endif // is_mpi
901	+	}
902	+
903	+	void SimSetup::initSystemCoords(void){
904	+	int i;
905	+
906	+	char* inName;
907	+
908	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
909	+
910	+	for (i = 0; i < info[0].n_atoms; i++)
911	+	info[0].atoms[i]->setCoords();
912	+
913	+	if (globals->haveInitialConfig()){
914	+	InitializeFromFile* fileInit;
915	+	#ifdef IS_MPI // is_mpi
916	+	if (worldRank == 0){
917	+	#endif //is_mpi
918	+	inName = globals->getInitialConfig();
919	+	double* tempDouble = new double[1000000];
920	+	fileInit = new InitializeFromFile(inName);
921	+	#ifdef IS_MPI
922	+	}
923	+	else
924	+	fileInit = new InitializeFromFile(NULL);
925	+	#endif
926	+	fileInit->readInit(info); // default velocities on
927	+
928	+	delete fileInit;
929	+	}
930		else{
931	<	n_cells = (int)temp3;
932	<	cellx = simnfo->box_x / temp3;
933	<	celly = simnfo->box_y / temp3;
934	<	cellz = simnfo->box_z / temp3;
931	>	#ifdef IS_MPI
932	>
933	>	// no init from bass
934	>
935	>	sprintf(painCave.errMsg,
936	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
937	>	painCave.isFatal;
938	>	simError();
939	>
940	>	#else
941	>
942	>	initFromBass();
943	>
944	>
945	>	#endif
946		}
947
948	<	current_mol = 0;
949	<	current_comp_mol = 0;
950	<	current_comp = 0;
951	<	current_atom_ndx = 0;
948	>	#ifdef IS_MPI
949	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
950	>	MPIcheckPoint();
951	>	#endif // is_mpi
952	>	}
953
1125	–	for( i=0; i < n_cells ; i++ ){
1126	–	for( j=0; j < n_cells; j++ ){
1127	–	for( k=0; k < n_cells; k++ ){
954
955	<	makeElement( i * cellx,
956	<	j * celly,
1131	<	k * cellz );
955	>	void SimSetup::makeOutNames(void){
956	>	int k;
957
1133	–	makeElement( i * cellx + 0.5 * cellx,
1134	–	j * celly + 0.5 * celly,
1135	–	k * cellz );
958
959	<	makeElement( i * cellx,
960	<	j * celly + 0.5 * celly,
961	<	k * cellz + 0.5 * cellz );
959	>	for (k = 0; k < nInfo; k++){
960	>	#ifdef IS_MPI
961	>	if (worldRank == 0){
962	>	#endif // is_mpi
963	>
964	>	if (globals->haveFinalConfig()){
965	>	strcpy(info[k].finalName, globals->getFinalConfig());
966	>	}
967	>	else{
968	>	strcpy(info[k].finalName, inFileName);
969	>	char* endTest;
970	>	int nameLength = strlen(info[k].finalName);
971	>	endTest = &(info[k].finalName[nameLength - 5]);
972	>	if (!strcmp(endTest, ".bass")){
973	>	strcpy(endTest, ".eor");
974	>	}
975	>	else if (!strcmp(endTest, ".BASS")){
976	>	strcpy(endTest, ".eor");
977	>	}
978	>	else{
979	>	endTest = &(info[k].finalName[nameLength - 4]);
980	>	if (!strcmp(endTest, ".bss")){
981	>	strcpy(endTest, ".eor");
982	>	}
983	>	else if (!strcmp(endTest, ".mdl")){
984	>	strcpy(endTest, ".eor");
985	>	}
986	>	else{
987	>	strcat(info[k].finalName, ".eor");
988	>	}
989	>	}
990	>	}
991	>
992	>	// make the sample and status out names
993	>
994	>	strcpy(info[k].sampleName, inFileName);
995	>	char* endTest;
996	>	int nameLength = strlen(info[k].sampleName);
997	>	endTest = &(info[k].sampleName[nameLength - 5]);
998	>	if (!strcmp(endTest, ".bass")){
999	>	strcpy(endTest, ".dump");
1000	>	}
1001	>	else if (!strcmp(endTest, ".BASS")){
1002	>	strcpy(endTest, ".dump");
1003	>	}
1004	>	else{
1005	>	endTest = &(info[k].sampleName[nameLength - 4]);
1006	>	if (!strcmp(endTest, ".bss")){
1007	>	strcpy(endTest, ".dump");
1008	>	}
1009	>	else if (!strcmp(endTest, ".mdl")){
1010	>	strcpy(endTest, ".dump");
1011	>	}
1012	>	else{
1013	>	strcat(info[k].sampleName, ".dump");
1014	>	}
1015	>	}
1016	>
1017	>	strcpy(info[k].statusName, inFileName);
1018	>	nameLength = strlen(info[k].statusName);
1019	>	endTest = &(info[k].statusName[nameLength - 5]);
1020	>	if (!strcmp(endTest, ".bass")){
1021	>	strcpy(endTest, ".stat");
1022	>	}
1023	>	else if (!strcmp(endTest, ".BASS")){
1024	>	strcpy(endTest, ".stat");
1025	>	}
1026	>	else{
1027	>	endTest = &(info[k].statusName[nameLength - 4]);
1028	>	if (!strcmp(endTest, ".bss")){
1029	>	strcpy(endTest, ".stat");
1030	>	}
1031	>	else if (!strcmp(endTest, ".mdl")){
1032	>	strcpy(endTest, ".stat");
1033	>	}
1034	>	else{
1035	>	strcat(info[k].statusName, ".stat");
1036	>	}
1037	>	}
1038	>
1039	>	#ifdef IS_MPI
1040	>
1041	>	}
1042	>	#endif // is_mpi
1043	>	}
1044	>	}
1045	>
1046	>
1047	>	void SimSetup::sysObjectsCreation(void){
1048	>	int i, k;
1049	>
1050	>	// create the forceField
1051	>
1052	>	createFF();
1053
1054	<	makeElement( i * cellx + 0.5 * cellx,
1055	<	j * celly,
1056	<	k * cellz + 0.5 * cellz );
1057	<	}
1054	>	// extract componentList
1055	>
1056	>	compList();
1057	>
1058	>	// calc the number of atoms, bond, bends, and torsions
1059	>
1060	>	calcSysValues();
1061	>
1062	>	#ifdef IS_MPI
1063	>	// divide the molecules among the processors
1064	>
1065	>	mpiMolDivide();
1066	>	#endif //is_mpi
1067	>
1068	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1069	>
1070	>	makeSysArrays();
1071	>
1072	>	// make and initialize the molecules (all but atomic coordinates)
1073	>
1074	>	makeMolecules();
1075	>
1076	>	for (k = 0; k < nInfo; k++){
1077	>	info[k].identArray = new int[info[k].n_atoms];
1078	>	for (i = 0; i < info[k].n_atoms; i++){
1079	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1080		}
1081		}
1082	+	}
1083
1148	–	if( have_extra ){
1149	–	done = 0;
1084
1085	<	int start_ndx;
1086	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1087	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1085	>	void SimSetup::createFF(void){
1086	>	switch (ffCase){
1087	>	case FF_DUFF:
1088	>	the_ff = new DUFF();
1089	>	break;
1090
1091	<	if( i < n_cells ){
1091	>	case FF_LJ:
1092	>	the_ff = new LJFF();
1093	>	break;
1094
1095	<	if( j < n_cells ){
1096	<	start_ndx = n_cells;
1097	<	}
1160	<	else start_ndx = 0;
1161	<	}
1162	<	else start_ndx = 0;
1095	>	case FF_EAM:
1096	>	the_ff = new EAM_FF();
1097	>	break;
1098
1099	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1099	>	default:
1100	>	sprintf(painCave.errMsg,
1101	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1102	>	painCave.isFatal = 1;
1103	>	simError();
1104	>	}
1105
1106	<	makeElement( i * cellx,
1107	<	j * celly,
1108	<	k * cellz );
1109	<	done = ( current_mol >= tot_nmol );
1106	>	#ifdef IS_MPI
1107	>	strcpy(checkPointMsg, "ForceField creation successful");
1108	>	MPIcheckPoint();
1109	>	#endif // is_mpi
1110	>	}
1111
1171	–	if( !done && n_per_extra > 1 ){
1172	–	makeElement( i * cellx + 0.5 * cellx,
1173	–	j * celly + 0.5 * celly,
1174	–	k * cellz );
1175	–	done = ( current_mol >= tot_nmol );
1176	–	}
1112
1113	<	if( !done && n_per_extra > 2){
1114	<	makeElement( i * cellx,
1115	<	j * celly + 0.5 * celly,
1116	<	k * cellz + 0.5 * cellz );
1117	<	done = ( current_mol >= tot_nmol );
1118	<	}
1113	>	void SimSetup::compList(void){
1114	>	int i;
1115	>	char* id;
1116	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1117	>	LinkedMolStamp* currentStamp = NULL;
1118	>	comp_stamps = new MoleculeStamp * [n_components];
1119
1120	<	if( !done && n_per_extra > 3){
1121	<	makeElement( i * cellx + 0.5 * cellx,
1122	<	j * celly,
1123	<	k * cellz + 0.5 * cellz );
1124	<	done = ( current_mol >= tot_nmol );
1125	<	}
1126	<	}
1120	>	// make an array of molecule stamps that match the components used.
1121	>	// also extract the used stamps out into a separate linked list
1122	>
1123	>	for (i = 0; i < nInfo; i++){
1124	>	info[i].nComponents = n_components;
1125	>	info[i].componentsNmol = components_nmol;
1126	>	info[i].compStamps = comp_stamps;
1127	>	info[i].headStamp = headStamp;
1128	>	}
1129	>
1130	>
1131	>	for (i = 0; i < n_components; i++){
1132	>	id = the_components[i]->getType();
1133	>	comp_stamps[i] = NULL;
1134	>
1135	>	// check to make sure the component isn't already in the list
1136	>
1137	>	comp_stamps[i] = headStamp->match(id);
1138	>	if (comp_stamps[i] == NULL){
1139	>	// extract the component from the list;
1140	>
1141	>	currentStamp = stamps->extractMolStamp(id);
1142	>	if (currentStamp == NULL){
1143	>	sprintf(painCave.errMsg,
1144	>	"SimSetup error: Component \"%s\" was not found in the "
1145	>	"list of declared molecules\n",
1146	>	id);
1147	>	painCave.isFatal = 1;
1148	>	simError();
1149		}
1150	+
1151	+	headStamp->add(currentStamp);
1152	+	comp_stamps[i] = headStamp->match(id);
1153		}
1154		}
1155
1156	+	#ifdef IS_MPI
1157	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1158	+	MPIcheckPoint();
1159	+	#endif // is_mpi
1160	+	}
1161
1162	<	for( i=0; i<simnfo->n_atoms; i++ ){
1163	<	simnfo->atoms[i]->set_vx( 0.0 );
1164	<	simnfo->atoms[i]->set_vy( 0.0 );
1165	<	simnfo->atoms[i]->set_vz( 0.0 );
1162	>	void SimSetup::calcSysValues(void){
1163	>	int i, j, k;
1164	>
1165	>	int* molMembershipArray;
1166	>
1167	>	tot_atoms = 0;
1168	>	tot_bonds = 0;
1169	>	tot_bends = 0;
1170	>	tot_torsions = 0;
1171	>	for (i = 0; i < n_components; i++){
1172	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1173	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1174	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1175	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1176		}
1177	+
1178	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1179	+	molMembershipArray = new int[tot_atoms];
1180	+
1181	+	for (i = 0; i < nInfo; i++){
1182	+	info[i].n_atoms = tot_atoms;
1183	+	info[i].n_bonds = tot_bonds;
1184	+	info[i].n_bends = tot_bends;
1185	+	info[i].n_torsions = tot_torsions;
1186	+	info[i].n_SRI = tot_SRI;
1187	+	info[i].n_mol = tot_nmol;
1188	+
1189	+	info[i].molMembershipArray = molMembershipArray;
1190	+	}
1191		}
1192
1193	<	void SimSetup::makeElement( double x, double y, double z ){
1193	>	#ifdef IS_MPI
1194
1195	<	int k;
1196	<	AtomStamp* current_atom;
1197	<	DirectionalAtom* dAtom;
1198	<	double rotMat[3][3];
1195	>	void SimSetup::mpiMolDivide(void){
1196	>	int i, j, k;
1197	>	int localMol, allMol;
1198	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1199
1200	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1200	>	mpiSim = new mpiSimulation(info);
1201
1202	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1203	<	if( !current_atom->havePosition() ){
1204	<	sprintf( painCave.errMsg,
1205	<	"SimSetup:initFromBass error.\n"
1206	<	"\tComponent %s, atom %s does not have a position specified.\n"
1207	<	"\tThe initialization routine is unable to give a start"
1208	<	" position.\n",
1209	<	comp_stamps[current_comp]->getID(),
1210	<	current_atom->getType() );
1211	<	painCave.isFatal = 1;
1212	<	simError();
1202	>	globalIndex = mpiSim->divideLabor();
1203	>
1204	>	// set up the local variables
1205	>
1206	>	mol2proc = mpiSim->getMolToProcMap();
1207	>	molCompType = mpiSim->getMolComponentType();
1208	>
1209	>	allMol = 0;
1210	>	localMol = 0;
1211	>	local_atoms = 0;
1212	>	local_bonds = 0;
1213	>	local_bends = 0;
1214	>	local_torsions = 0;
1215	>	globalAtomIndex = 0;
1216	>
1217	>
1218	>	for (i = 0; i < n_components; i++){
1219	>	for (j = 0; j < components_nmol[i]; j++){
1220	>	if (mol2proc[allMol] == worldRank){
1221	>	local_atoms += comp_stamps[i]->getNAtoms();
1222	>	local_bonds += comp_stamps[i]->getNBonds();
1223	>	local_bends += comp_stamps[i]->getNBends();
1224	>	local_torsions += comp_stamps[i]->getNTorsions();
1225	>	localMol++;
1226	>	}
1227	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1228	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1229	>	globalAtomIndex++;
1230	>	}
1231	>
1232	>	allMol++;
1233		}
1234	+	}
1235	+	local_SRI = local_bonds + local_bends + local_torsions;
1236
1237	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1227	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1228	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1237	>	info[0].n_atoms = mpiSim->getMyNlocal();
1238
1239	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1239	>	if (local_atoms != info[0].n_atoms){
1240	>	sprintf(painCave.errMsg,
1241	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1242	>	" localAtom (%d) are not equal.\n",
1243	>	info[0].n_atoms, local_atoms);
1244	>	painCave.isFatal = 1;
1245	>	simError();
1246	>	}
1247
1248	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1248	>	info[0].n_bonds = local_bonds;
1249	>	info[0].n_bends = local_bends;
1250	>	info[0].n_torsions = local_torsions;
1251	>	info[0].n_SRI = local_SRI;
1252	>	info[0].n_mol = localMol;
1253
1254	<	rotMat[0][0] = 1.0;
1255	<	rotMat[0][1] = 0.0;
1256	<	rotMat[0][2] = 0.0;
1254	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1255	>	MPIcheckPoint();
1256	>	}
1257
1258	<	rotMat[1][0] = 0.0;
1239	<	rotMat[1][1] = 1.0;
1240	<	rotMat[1][2] = 0.0;
1258	>	#endif // is_mpi
1259
1242	–	rotMat[2][0] = 0.0;
1243	–	rotMat[2][1] = 0.0;
1244	–	rotMat[2][2] = 1.0;
1260
1261	<	dAtom->setA( rotMat );
1261	>	void SimSetup::makeSysArrays(void){
1262	>	int i, j, k, 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	<	current_atom_ndx++;
1250	<	}
1291	>	#else // is_mpi
1292
1293	<	current_mol++;
1294	<	current_comp_mol++;
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
1255	–	if( current_comp_mol >= components_nmol[current_comp] ){
1308
1309	<	current_comp_mol = 0;
1310	<	current_comp++;
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	>	NVT<RealIntegrator>* myNVT = NULL;
1346	>	NPTi<RealIntegrator>* myNPTi = NULL;
1347	>	NPTf<RealIntegrator>* myNPTf = NULL;
1348	>	NPTim<RealIntegrator>* myNPTim = NULL;
1349	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1350	>
1351	>	for (k = 0; k < nInfo; k++){
1352	>	switch (ensembleCase){
1353	>	case NVE_ENS:
1354	>	if (globals->haveZconstraints()){
1355	>	setupZConstraint(info[k]);
1356	>	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1357	>	}
1358	>	else
1359	>	new NVE<RealIntegrator>(&(info[k]), the_ff);
1360	>	break;
1361	>
1362	>	case NVT_ENS:
1363	>	if (globals->haveZconstraints()){
1364	>	setupZConstraint(info[k]);
1365	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1366	>	}
1367	>	else
1368	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1369	>
1370	>	myNVT->setTargetTemp(globals->getTargetTemp());
1371	>
1372	>	if (globals->haveTauThermostat())
1373	>	myNVT->setTauThermostat(globals->getTauThermostat());
1374	>	else{
1375	>	sprintf(painCave.errMsg,
1376	>	"SimSetup error: If you use the NVT\n"
1377	>	"    ensemble, you must set tauThermostat.\n");
1378	>	painCave.isFatal = 1;
1379	>	simError();
1380	>	}
1381	>	break;
1382	>
1383	>	case NPTi_ENS:
1384	>	if (globals->haveZconstraints()){
1385	>	setupZConstraint(info[k]);
1386	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1387	>	}
1388	>	else
1389	>	myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1390	>
1391	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1392	>
1393	>	if (globals->haveTargetPressure())
1394	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1395	>	else{
1396	>	sprintf(painCave.errMsg,
1397	>	"SimSetup error: If you use a constant pressure\n"
1398	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1399	>	painCave.isFatal = 1;
1400	>	simError();
1401	>	}
1402	>
1403	>	if (globals->haveTauThermostat())
1404	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1405	>	else{
1406	>	sprintf(painCave.errMsg,
1407	>	"SimSetup error: If you use an NPT\n"
1408	>	"    ensemble, you must set tauThermostat.\n");
1409	>	painCave.isFatal = 1;
1410	>	simError();
1411	>	}
1412	>
1413	>	if (globals->haveTauBarostat())
1414	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1415	>	else{
1416	>	sprintf(painCave.errMsg,
1417	>	"SimSetup error: If you use an NPT\n"
1418	>	"    ensemble, you must set tauBarostat.\n");
1419	>	painCave.isFatal = 1;
1420	>	simError();
1421	>	}
1422	>	break;
1423	>
1424	>	case NPTf_ENS:
1425	>	if (globals->haveZconstraints()){
1426	>	setupZConstraint(info[k]);
1427	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1428	>	}
1429	>	else
1430	>	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1431	>
1432	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1433	>
1434	>	if (globals->haveTargetPressure())
1435	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1436	>	else{
1437	>	sprintf(painCave.errMsg,
1438	>	"SimSetup error: If you use a constant pressure\n"
1439	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1440	>	painCave.isFatal = 1;
1441	>	simError();
1442	>	}
1443	>
1444	>	if (globals->haveTauThermostat())
1445	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1446	>	else{
1447	>	sprintf(painCave.errMsg,
1448	>	"SimSetup error: If you use an NPT\n"
1449	>	"    ensemble, you must set tauThermostat.\n");
1450	>	painCave.isFatal = 1;
1451	>	simError();
1452	>	}
1453	>
1454	>	if (globals->haveTauBarostat())
1455	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1456	>	else{
1457	>	sprintf(painCave.errMsg,
1458	>	"SimSetup error: If you use an NPT\n"
1459	>	"    ensemble, you must set tauBarostat.\n");
1460	>	painCave.isFatal = 1;
1461	>	simError();
1462	>	}
1463	>	break;
1464	>
1465	>	case NPTim_ENS:
1466	>	if (globals->haveZconstraints()){
1467	>	setupZConstraint(info[k]);
1468	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1469	>	}
1470	>	else
1471	>	myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1472	>
1473	>	myNPTim->setTargetTemp(globals->getTargetTemp());
1474	>
1475	>	if (globals->haveTargetPressure())
1476	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1477	>	else{
1478	>	sprintf(painCave.errMsg,
1479	>	"SimSetup error: If you use a constant pressure\n"
1480	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1481	>	painCave.isFatal = 1;
1482	>	simError();
1483	>	}
1484	>
1485	>	if (globals->haveTauThermostat())
1486	>	myNPTim->setTauThermostat(globals->getTauThermostat());
1487	>	else{
1488	>	sprintf(painCave.errMsg,
1489	>	"SimSetup error: If you use an NPT\n"
1490	>	"    ensemble, you must set tauThermostat.\n");
1491	>	painCave.isFatal = 1;
1492	>	simError();
1493	>	}
1494	>
1495	>	if (globals->haveTauBarostat())
1496	>	myNPTim->setTauBarostat(globals->getTauBarostat());
1497	>	else{
1498	>	sprintf(painCave.errMsg,
1499	>	"SimSetup error: If you use an NPT\n"
1500	>	"    ensemble, you must set tauBarostat.\n");
1501	>	painCave.isFatal = 1;
1502	>	simError();
1503	>	}
1504	>	break;
1505	>
1506	>	case NPTfm_ENS:
1507	>	if (globals->haveZconstraints()){
1508	>	setupZConstraint(info[k]);
1509	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1510	>	}
1511	>	else
1512	>	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1513	>
1514	>	myNPTfm->setTargetTemp(globals->getTargetTemp());
1515	>
1516	>	if (globals->haveTargetPressure())
1517	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1518	>	else{
1519	>	sprintf(painCave.errMsg,
1520	>	"SimSetup error: If you use a constant pressure\n"
1521	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1522	>	painCave.isFatal = 1;
1523	>	simError();
1524	>	}
1525	>
1526	>	if (globals->haveTauThermostat())
1527	>	myNPTfm->setTauThermostat(globals->getTauThermostat());
1528	>	else{
1529	>	sprintf(painCave.errMsg,
1530	>	"SimSetup error: If you use an NPT\n"
1531	>	"    ensemble, you must set tauThermostat.\n");
1532	>	painCave.isFatal = 1;
1533	>	simError();
1534	>	}
1535	>
1536	>	if (globals->haveTauBarostat())
1537	>	myNPTfm->setTauBarostat(globals->getTauBarostat());
1538	>	else{
1539	>	sprintf(painCave.errMsg,
1540	>	"SimSetup error: If you use an NPT\n"
1541	>	"    ensemble, you must set tauBarostat.\n");
1542	>	painCave.isFatal = 1;
1543	>	simError();
1544	>	}
1545	>	break;
1546	>
1547	>	default:
1548	>	sprintf(painCave.errMsg,
1549	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1550	>	painCave.isFatal = 1;
1551	>	simError();
1552	>	}
1553		}
1554		}
1555	+
1556	+	void SimSetup::initFortran(void){
1557	+	info[0].refreshSim();
1558	+
1559	+	if (!strcmp(info[0].mixingRule, "standard")){
1560	+	the_ff->initForceField(LB_MIXING_RULE);
1561	+	}
1562	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1563	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1564	+	}
1565	+	else{
1566	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1567	+	info[0].mixingRule);
1568	+	painCave.isFatal = 1;
1569	+	simError();
1570	+	}
1571	+
1572	+
1573	+	#ifdef IS_MPI
1574	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1575	+	MPIcheckPoint();
1576	+	#endif // is_mpi
1577	+	}
1578	+
1579	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1580	+	int nZConstraints;
1581	+	ZconStamp** zconStamp;
1582	+
1583	+	if (globals->haveZconstraintTime()){
1584	+	//add sample time of z-constraint  into SimInfo's property list
1585	+	DoubleData* zconsTimeProp = new DoubleData();
1586	+	zconsTimeProp->setID(ZCONSTIME_ID);
1587	+	zconsTimeProp->setData(globals->getZconsTime());
1588	+	theInfo.addProperty(zconsTimeProp);
1589	+	}
1590	+	else{
1591	+	sprintf(painCave.errMsg,
1592	+	"ZConstraint error: If you use an ZConstraint\n"
1593	+	" , you must set sample time.\n");
1594	+	painCave.isFatal = 1;
1595	+	simError();
1596	+	}
1597	+
1598	+	//push zconsTol into siminfo, if user does not specify
1599	+	//value for zconsTol, a default value will be used
1600	+	DoubleData* zconsTol = new DoubleData();
1601	+	zconsTol->setID(ZCONSTOL_ID);
1602	+	if (globals->haveZconsTol()){
1603	+	zconsTol->setData(globals->getZconsTol());
1604	+	}
1605	+	else{
1606	+	double defaultZConsTol = 0.01;
1607	+	sprintf(painCave.errMsg,
1608	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1609	+	" , default value %f is used.\n",
1610	+	defaultZConsTol);
1611	+	painCave.isFatal = 0;
1612	+	simError();
1613	+
1614	+	zconsTol->setData(defaultZConsTol);
1615	+	}
1616	+	theInfo.addProperty(zconsTol);
1617	+
1618	+	//set Force Substraction Policy
1619	+	StringData* zconsForcePolicy = new StringData();
1620	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1621	+
1622	+	if (globals->haveZconsForcePolicy()){
1623	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1624	+	}
1625	+	else{
1626	+	sprintf(painCave.errMsg,
1627	+	"ZConstraint Warning: User does not set force substraction policy, "
1628	+	"average force substraction policy is used\n");
1629	+	painCave.isFatal = 0;
1630	+	simError();
1631	+	zconsForcePolicy->setData("BYNUMBER");
1632	+	}
1633	+
1634	+	theInfo.addProperty(zconsForcePolicy);
1635	+
1636	+	//Determine the name of ouput file and add it into SimInfo's property list
1637	+	//Be careful, do not use inFileName, since it is a pointer which
1638	+	//point to a string at master node, and slave nodes do not contain that string
1639	+
1640	+	string zconsOutput(theInfo.finalName);
1641	+
1642	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1643	+
1644	+	StringData* zconsFilename = new StringData();
1645	+	zconsFilename->setID(ZCONSFILENAME_ID);
1646	+	zconsFilename->setData(zconsOutput);
1647	+
1648	+	theInfo.addProperty(zconsFilename);
1649	+
1650	+	//setup index, pos and other parameters of z-constraint molecules
1651	+	nZConstraints = globals->getNzConstraints();
1652	+	theInfo.nZconstraints = nZConstraints;
1653	+
1654	+	zconStamp = globals->getZconStamp();
1655	+	ZConsParaItem tempParaItem;
1656	+
1657	+	ZConsParaData* zconsParaData = new ZConsParaData();
1658	+	zconsParaData->setID(ZCONSPARADATA_ID);
1659	+
1660	+	for (int i = 0; i < nZConstraints; i++){
1661	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1662	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1663	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1664	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1665	+
1666	+	zconsParaData->addItem(tempParaItem);
1667	+	}
1668	+
1669	+	//sort the parameters by index of molecules
1670	+	zconsParaData->sortByIndex();
1671	+
1672	+	//push data into siminfo, therefore, we can retrieve later
1673	+	theInfo.addProperty(zconsParaData);
1674	+	}

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