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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 604 by gezelter, Tue Jul 15 03:08:00 2003 UTC vs.
Revision 778 by mmeineke, Fri Sep 19 20:00:27 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
25	<	#define NPTim_ENS 4
26	<	#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	>	#define NPTim_ENS      4
26	>	#define NPTfm_ENS      5
27
24	–
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 41 | 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();
73	<	mpiEventLoop();
74	<
86	>	set_interface_stamps(stamps, globals);
87	>	mpiEventInit();
88	>	MPIcheckPoint();
89	>	mpiEventLoop();
90		}
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
80	<
81	<	MakeStamps *the_stamps;
82	<	Globals* the_globals;
94	>	void SimSetup::createSim(void){
95		int i, j, k, globalAtomIndex;
84	–
85	–	int ensembleCase;
86	–	int ffCase;
87	–
88	–	ensembleCase = -1;
89	–	ffCase = -1;
96
97	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
97	>	// gather all of the information from the Bass file
98
99	<	// 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();
99	>	gatherInfo();
100
101	<	// 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() );
101	>	// creation of complex system objects
102
103	<	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	<	}
103	>	sysObjectsCreation();
104
105	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
105	>	// check on the post processing info
106
107	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
108	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
109	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
110	<	ensembleCase = NPTi_ENS;
111	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
112	<	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;
107	>	finalInfoCheck();
108	>
109	>	// initialize the system coordinates
110	>
111	>	if (!isInfoArray){
112	>	initSystemCoords();
113		}
134	–	strcpy( simnfo->ensemble, ensemble );
114
115	+	// make the output filenames
116
117	<	//   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	<	//     }
117	>	makeOutNames();
118
119	<	//     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	<	//     }
119	>	// make the integrator
120
121	<	//     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	<	//     }
121	>	makeIntegrator();
122
123	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
124	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
125	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
123	>	#ifdef IS_MPI
124	>	mpiSim->mpiRefresh();
125	>	#endif
126
127	<	//     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	<	//     }
127	>	// initialize the Fortran
128
129	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
130	<	simnfo->usePBC = the_globals->getPBC();
194	<
195	<	int usesDipoles = 0;
196	<	switch( ffCase ){
129	>	initFortran();
130	>	}
131
198	–	case FF_DUFF:
199	–	the_ff = new DUFF();
200	–	usesDipoles = 1;
201	–	break;
132
133	<	case FF_LJ:
134	<	the_ff = new LJFF();
135	<	break;
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	<	default:
146	<	sprintf( painCave.errMsg,
147	<	"SimSetup Error. Unrecognized force field in case statement.\n");
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
145	>	bond_pair* theBonds;
146	>	bend_set* theBends;
147	>	torsion_set* theTorsions;
148
214	–	#ifdef IS_MPI
215	–	strcpy( checkPointMsg, "ForceField creation successful" );
216	–	MPIcheckPoint();
217	–	#endif // is_mpi
149
150	<	// 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];
150	>	//init the forceField paramters
151
152	<	if( !the_globals->haveNMol() ){
225	<	// we don't have the total number of molecules, so we assume it is
226	<	// given in each component
152	>	the_ff->readParams();
153
228	–	tot_nmol = 0;
229	–	for( i=0; i<n_components; i++ ){
154
155	<	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	<	}
155	>	// init the atoms
156
157	<	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	<	}
157	>	double ux, uy, uz, u, uSqr;
158
159	<	#ifdef IS_MPI
160	<	strcpy( checkPointMsg, "Have the number of components" );
271	<	MPIcheckPoint();
272	<	#endif // is_mpi
159	>	for (k = 0; k < nInfo; k++){
160	>	the_ff->setSimInfo(&(info[k]));
161
162	<	// make an array of molecule stamps that match the components used.
163	<	// also extract the used stamps out into a separate linked list
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	<	simnfo->nComponents = n_components;
168	<	simnfo->componentsNmol = components_nmol;
169	<	simnfo->compStamps = comp_stamps;
170	<	simnfo->headStamp = new LinkedMolStamp();
171	<
282	<	char* id;
283	<	LinkedMolStamp* headStamp = simnfo->headStamp;
284	<	LinkedMolStamp* currentStamp = NULL;
285	<	for( i=0; i<n_components; i++ ){
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	<	id = the_components[i]->getType();
174	<	comp_stamps[i] = NULL;
175	<
176	<	// check to make sure the component isn't already in the list
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	<	comp_stamps[i] = headStamp->match( id );
180	<	if( comp_stamps[i] == NULL ){
181	<
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	<	}
179	>	theBonds = new bond_pair[molInfo.nBonds];
180	>	theBends = new bend_set[molInfo.nBends];
181	>	theTorsions = new torsion_set[molInfo.nTorsions];
182
183	<	#ifdef IS_MPI
313	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
314	<	MPIcheckPoint();
315	<	#endif // is_mpi
316	<
183	>	// make the Atoms
184
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	+	ux = currentAtom->getOrntX();
194	+	uy = currentAtom->getOrntY();
195	+	uz = currentAtom->getOrntZ();
196
197	<	// caclulate the number of atoms, bonds, bends and torsions
197	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
198
199	<	tot_atoms = 0;
200	<	tot_bonds = 0;
201	<	tot_bends = 0;
202	<	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	<	}
199	>	u = sqrt(uSqr);
200	>	ux = ux / u;
201	>	uy = uy / u;
202	>	uz = uz / u;
203
204	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
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
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	–
214		#ifdef IS_MPI
215
216	<	// divide the molecules among processors here.
348	<
349	<	mpiSim = new mpiSimulation( simnfo );
350	<
351	<	globalIndex = mpiSim->divideLabor();
216	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
217
218	<	// set up the local variables
219	<
355	<	int localMol, allMol;
356	<	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;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	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();
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++;
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();
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	<	}
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;
407	<	simnfo->n_SRI = local_SRI;
408	<	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 ){
433	<	the_molecules[molIndex].setStampID( molCompType[i] );
434	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
439	<
440	<	#else // is_mpi
441	<
442	<	molIndex = 0;
443	<	globalAtomIndex = 0;
444	<	for(i=0; i<n_components; i++){
445	<	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++;
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++;
454	<	}
455	<	}
456	<
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 );
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	<	}
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
482	–	simnfo->atoms = the_atoms;
483	–	simnfo->molecules = the_molecules;
484	–	simnfo->nGlobalExcludes = 0;
485	–	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
490	–	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() ){
364
365	<	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];
365	>	info[k].molecules[i].initialize(molInfo);
366
506	–	simnfo->setBox( boxVector );
507	–	}
508	–	else{
509	–	if( !the_globals->haveBoxX() ){
510	–	sprintf( painCave.errMsg,
511	–	"SimSetup error, no periodic BoxX size given.\n" );
512	–	painCave.isFatal = 1;
513	–	simError();
514	–	}
515	–	boxVector[0] = the_globals->getBoxX();
367
368	<	if( !the_globals->haveBoxY() ){
369	<	sprintf( painCave.errMsg,
370	<	"SimSetup error, no periodic BoxY size given.\n" );
371	<	painCave.isFatal = 1;
521	<	simError();
368	>	atomOffset += molInfo.nAtoms;
369	>	delete[] theBonds;
370	>	delete[] theBends;
371	>	delete[] theTorsions;
372		}
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 );
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();
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	<	}
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 "
431	<	"box length for the electrostaticCutoffRadius.\n"
432	<	"I hope you have a very fast processor!\n");
433	<	painCave.isFatal = 0;
434	<	simError();
435	<	double smallest;
436	<	smallest = simnfo->boxLx;
437	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
438	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
439	<	simnfo->ecr = 0.5 * smallest;
440	<	} else {
441	<	simnfo->ecr        = the_globals->getECR();
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	>	current_mol = 0;
433	>	current_comp_mol = 0;
434	>	current_comp = 0;
435	>	current_atom_ndx = 0;
436	>
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	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
443	>
444	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
445	>
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
447		}
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	–	}
448		}
449	<	}
449	>	}
450
451	<	#ifdef IS_MPI
452	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
628	<	MPIcheckPoint();
629	<	#endif // is_mpi
451	>	if (have_extra){
452	>	done = 0;
453
454	<	if( the_globals->haveInitialConfig() ){
455	<
456	<	InitializeFromFile* fileInit;
457	<	#ifdef IS_MPI // is_mpi
458	<	if( worldRank == 0 ){
459	<	#endif //is_mpi
460	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
461	<	#ifdef IS_MPI
462	<	}else fileInit = new InitializeFromFile( NULL );
463	<	#endif
464	<	fileInit->read_xyz( simnfo ); // default velocities on
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	<	delete fileInit;
468	<	}
469	<	else{
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
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	<	// no init from bass
478	<
479	<	sprintf( painCave.errMsg,
480	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
481	<	painCave.isFatal;
654	<	simError();
655	<
656	<	#else
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	<	initFromBass();
484	<
485	<
486	<	#endif
487	<	}
488	<
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" );
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		}
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	–	}
490		}
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
491		}
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	–	}
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
525	<
786	<
787	<	NVT*  myNVT = NULL;
788	<	NPTi* myNPTi = NULL;
789	<	NPTf* myNPTf = NULL;
790	<	NPTim* myNPTim = NULL;
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	<	case NVT_ENS:
536	<	myNVT = new NVT( simnfo, the_ff );
537	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
535	>	rotMat[2][0] = 0.0;
536	>	rotMat[2][1] = 0.0;
537	>	rotMat[2][2] = 1.0;
538
539	<	if (the_globals->haveTauThermostat())
540	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
539	>	dAtom->setA(rotMat);
540	>	}
541
542	<	else {
543	<	sprintf( painCave.errMsg,
807	<	"SimSetup error: If you use the NVT\n"
808	<	"    ensemble, you must set tauThermostat.\n");
809	<	painCave.isFatal = 1;
810	<	simError();
811	<	}
812	<	break;
542	>	current_atom_ndx++;
543	>	}
544
545	<	case NPTi_ENS:
546	<	myNPTi = new NPTi( simnfo, the_ff );
816	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
545	>	current_mol++;
546	>	current_comp_mol++;
547
548	<	if (the_globals->haveTargetPressure())
549	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
550	<	else {
551	<	sprintf( painCave.errMsg,
552	<	"SimSetup error: If you use a constant pressure\n"
823	<	"    ensemble, you must set targetPressure in the BASS file.\n");
824	<	painCave.isFatal = 1;
825	<	simError();
826	<	}
827	<
828	<	if( the_globals->haveTauThermostat() )
829	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
830	<	else{
831	<	sprintf( painCave.errMsg,
832	<	"SimSetup error: If you use an NPT\n"
833	<	"    ensemble, you must set tauThermostat.\n");
834	<	painCave.isFatal = 1;
835	<	simError();
836	<	}
548	>	if (current_comp_mol >= components_nmol[current_comp]){
549	>	current_comp_mol = 0;
550	>	current_comp++;
551	>	}
552	>	}
553
838	–	if( the_globals->haveTauBarostat() )
839	–	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
840	–	else{
841	–	sprintf( painCave.errMsg,
842	–	"SimSetup error: If you use an NPT\n"
843	–	"    ensemble, you must set tauBarostat.\n");
844	–	painCave.isFatal = 1;
845	–	simError();
846	–	}
847	–	break;
554
555	<	case NPTf_ENS:
556	<	myNPTf = new NPTf( simnfo, the_ff );
851	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
555	>	void SimSetup::gatherInfo(void){
556	>	int i, j, k;
557
558	<	if (the_globals->haveTargetPressure())
559	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
855	<	else {
856	<	sprintf( painCave.errMsg,
857	<	"SimSetup error: If you use a constant pressure\n"
858	<	"    ensemble, you must set targetPressure in the BASS file.\n");
859	<	painCave.isFatal = 1;
860	<	simError();
861	<	}
558	>	ensembleCase = -1;
559	>	ffCase = -1;
560
561	<	if( the_globals->haveTauThermostat() )
864	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
865	<	else{
866	<	sprintf( painCave.errMsg,
867	<	"SimSetup error: If you use an NPT\n"
868	<	"    ensemble, you must set tauThermostat.\n");
869	<	painCave.isFatal = 1;
870	<	simError();
871	<	}
561	>	// set the easy ones first
562
563	<	if( the_globals->haveTauBarostat() )
564	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
565	<	else{
566	<	sprintf( painCave.errMsg,
567	<	"SimSetup error: If you use an NPT\n"
568	<	"    ensemble, you must set tauBarostat.\n");
879	<	painCave.isFatal = 1;
880	<	simError();
881	<	}
882	<	break;
883	<
884	<	case NPTim_ENS:
885	<	myNPTim = new NPTim( simnfo, the_ff );
886	<	myNPTim->setTargetTemp( the_globals->getTargetTemp());
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	>	n_components = globals->getNComponents();
569
888	–	if (the_globals->haveTargetPressure())
889	–	myNPTim->setTargetPressure(the_globals->getTargetPressure());
890	–	else {
891	–	sprintf( painCave.errMsg,
892	–	"SimSetup error: If you use a constant pressure\n"
893	–	"    ensemble, you must set targetPressure in the BASS file.\n");
894	–	painCave.isFatal = 1;
895	–	simError();
896	–	}
897	–
898	–	if( the_globals->haveTauThermostat() )
899	–	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
900	–	else{
901	–	sprintf( painCave.errMsg,
902	–	"SimSetup error: If you use an NPT\n"
903	–	"    ensemble, you must set tauThermostat.\n");
904	–	painCave.isFatal = 1;
905	–	simError();
906	–	}
570
571	<	if( the_globals->haveTauBarostat() )
909	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
910	<	else{
911	<	sprintf( painCave.errMsg,
912	<	"SimSetup error: If you use an NPT\n"
913	<	"    ensemble, you must set tauBarostat.\n");
914	<	painCave.isFatal = 1;
915	<	simError();
916	<	}
917	<	break;
571	>	// get the forceField
572
573	<
573	>	strcpy(force_field, globals->getForceField());
574
575	<	default:
576	<	sprintf( painCave.errMsg,
923	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
924	<	painCave.isFatal = 1;
925	<	simError();
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	+	// get the ensemble
592
593	<	#ifdef IS_MPI
930	<	mpiSim->mpiRefresh();
931	<	#endif
593	>	strcpy(ensemble, globals->getEnsemble());
594
595	<	// initialize the Fortran
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	+	for (i = 0; i < nInfo; i++){
625	+	strcpy(info[i].ensemble, ensemble);
626
627	<	simnfo->refreshSim();
628	<
629	<	if( !strcmp( simnfo->mixingRule, "standard") ){
630	<	the_ff->initForceField( LB_MIXING_RULE );
627	>	// get the mixing rule
628	>
629	>	strcpy(info[i].mixingRule, globals->getMixingRule());
630	>	info[i].usePBC = globals->getPBC();
631		}
632	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
633	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
632	>
633	>	// get the components and calculate the tot_nMol and indvidual n_mol
634	>
635	>	the_components = globals->getComponents();
636	>	components_nmol = new int[n_components];
637	>
638	>
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	>	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	>	}
653	>
654	>	tot_nmol += the_components[i]->getNMol();
655	>	components_nmol[i] = the_components[i]->getNMol();
656	>	}
657		}
658		else{
659	<	sprintf( painCave.errMsg,
660	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	<	simnfo->mixingRule );
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	+	// set the status, sample, and thermal kick times
670
671	<	#ifdef IS_MPI
672	<	strcpy( checkPointMsg,
673	<	"Successfully intialized the mixingRule for Fortran." );
674	<	MPIcheckPoint();
675	<	#endif // is_mpi
676	<	}
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	>	else{
678	>	info[i].sampleTime = globals->getRunTime();
679	>	info[i].statusTime = info[i].sampleTime;
680	>	info[i].thermalTime = info[i].sampleTime;
681	>	}
682
683	+	if (globals->haveStatusTime()){
684	+	info[i].statusTime = globals->getStatusTime();
685	+	}
686
687	<	void SimSetup::makeMolecules( void ){
687	>	if (globals->haveThermalTime()){
688	>	info[i].thermalTime = globals->getThermalTime();
689	>	}
690
691	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
692	<	molInit info;
693	<	DirectionalAtom* dAtom;
694	<	LinkedAssign* extras;
695	<	LinkedAssign* current_extra;
968	<	AtomStamp* currentAtom;
969	<	BondStamp* currentBond;
970	<	BendStamp* currentBend;
971	<	TorsionStamp* currentTorsion;
691	>	info[i].resetIntegrator = 0;
692	>	if( globals->haveResetTime() ){
693	>	info[i].resetTime = globals->getResetTime();
694	>	info[i].resetIntegrator = 1;
695	>	}
696
697	<	bond_pair* theBonds;
974	<	bend_set* theBends;
975	<	torsion_set* theTorsions;
697	>	// check for the temperature set flag
698
699	<
700	<	//init the forceField paramters
699	>	if (globals->haveTempSet())
700	>	info[i].setTemp = globals->getTempSet();
701
702	<	the_ff->readParams();
702	>	// get some of the tricky things that may still be in the globals
703
704	<
705	<	// init the atoms
704	>	double boxVector[3];
705	>	if (globals->haveBox()){
706	>	boxVector[0] = globals->getBox();
707	>	boxVector[1] = globals->getBox();
708	>	boxVector[2] = globals->getBox();
709
710	<	double ux, uy, uz, u, uSqr;
711	<
712	<	atomOffset = 0;
713	<	excludeOffset = 0;
714	<	for(i=0; i<simnfo->n_mol; i++){
715	<
716	<	stampID = the_molecules[i].getStampID();
710	>	info[i].setBox(boxVector);
711	>	}
712	>	else if (globals->haveDensity()){
713	>	double vol;
714	>	vol = (double) tot_nmol / globals->getDensity();
715	>	boxVector[0] = pow(vol, (1.0 / 3.0));
716	>	boxVector[1] = boxVector[0];
717	>	boxVector[2] = boxVector[0];
718
719	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
720	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
721	<	info.nBends    = comp_stamps[stampID]->getNBends();
722	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
723	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
719	>	info[i].setBox(boxVector);
720	>	}
721	>	else{
722	>	if (!globals->haveBoxX()){
723	>	sprintf(painCave.errMsg,
724	>	"SimSetup error, no periodic BoxX size given.\n");
725	>	painCave.isFatal = 1;
726	>	simError();
727	>	}
728	>	boxVector[0] = globals->getBoxX();
729
730	<	info.myAtoms = &the_atoms[atomOffset];
731	<	info.myExcludes = &the_excludes[excludeOffset];
732	<	info.myBonds = new Bond*[info.nBonds];
733	<	info.myBends = new Bend*[info.nBends];
734	<	info.myTorsions = new Torsion*[info.nTorsions];
730	>	if (!globals->haveBoxY()){
731	>	sprintf(painCave.errMsg,
732	>	"SimSetup error, no periodic BoxY size given.\n");
733	>	painCave.isFatal = 1;
734	>	simError();
735	>	}
736	>	boxVector[1] = globals->getBoxY();
737
738	<	theBonds = new bond_pair[info.nBonds];
739	<	theBends = new bend_set[info.nBends];
740	<	theTorsions = new torsion_set[info.nTorsions];
741	<
742	<	// make the Atoms
1010	<
1011	<	for(j=0; j<info.nAtoms; j++){
1012	<
1013	<	currentAtom = comp_stamps[stampID]->getAtom( j );
1014	<	if( currentAtom->haveOrientation() ){
1015	<
1016	<	dAtom = new DirectionalAtom(j + atomOffset);
1017	<	simnfo->n_oriented++;
1018	<	info.myAtoms[j] = dAtom;
1019	<
1020	<	ux = currentAtom->getOrntX();
1021	<	uy = currentAtom->getOrntY();
1022	<	uz = currentAtom->getOrntZ();
1023	<
1024	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1025	<
1026	<	u = sqrt( uSqr );
1027	<	ux = ux / u;
1028	<	uy = uy / u;
1029	<	uz = uz / u;
1030	<
1031	<	dAtom->setSUx( ux );
1032	<	dAtom->setSUy( uy );
1033	<	dAtom->setSUz( uz );
738	>	if (!globals->haveBoxZ()){
739	>	sprintf(painCave.errMsg,
740	>	"SimSetup error, no periodic BoxZ size given.\n");
741	>	painCave.isFatal = 1;
742	>	simError();
743		}
744	<	else{
745	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
744	>	boxVector[2] = globals->getBoxZ();
745	>
746	>	info[i].setBox(boxVector);
747	>	}
748	>	}
749	>
750	>	//setup seed for random number generator
751	>	int seedValue;
752	>
753	>	if (globals->haveSeed()){
754	>	seedValue = globals->getSeed();
755	>
756	>	if(seedValue / 1E9 == 0){
757	>	sprintf(painCave.errMsg,
758	>	"Seed for sprng library should contain at least 9 digits\n"
759	>	"OOPSE will generate a seed for user\n");
760	>	painCave.isFatal = 0;
761	>	simError();
762	>
763	>	//using seed generated by system instead of invalid seed set by user
764	>	#ifndef IS_MPI
765	>	seedValue = make_sprng_seed();
766	>	#else
767	>	if (worldRank == 0){
768	>	seedValue = make_sprng_seed();
769		}
770	<	info.myAtoms[j]->setType( currentAtom->getType() );
770	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
771	>	#endif
772	>	}
773	>	}//end of if branch of globals->haveSeed()
774	>	else{
775
776	+	#ifndef IS_MPI
777	+	seedValue = make_sprng_seed();
778	+	#else
779	+	if (worldRank == 0){
780	+	seedValue = make_sprng_seed();
781	+	}
782	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
783	+	#endif
784	+	}//end of globals->haveSeed()
785	+
786	+	for (int i = 0; i < nInfo; i++){
787	+	info[i].setSeed(seedValue);
788	+	}
789	+
790		#ifdef IS_MPI
791	<
792	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1043	<
791	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
792	>	MPIcheckPoint();
793		#endif // is_mpi
794	<	}
1046	<
1047	<	// make the bonds
1048	<	for(j=0; j<info.nBonds; j++){
1049	<
1050	<	currentBond = comp_stamps[stampID]->getBond( j );
1051	<	theBonds[j].a = currentBond->getA() + atomOffset;
1052	<	theBonds[j].b = currentBond->getB() + atomOffset;
794	>	}
795
1054	–	exI = theBonds[j].a;
1055	–	exJ = theBonds[j].b;
796
797	<	// exclude_I must always be the smaller of the pair
798	<	if( exI > exJ ){
799	<	tempEx = exI;
800	<	exI = exJ;
1061	<	exJ = tempEx;
1062	<	}
1063	<	#ifdef IS_MPI
1064	<	tempEx = exI;
1065	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1066	<	tempEx = exJ;
1067	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1068	<
1069	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1070	<	#else  // isn't MPI
797	>	void SimSetup::finalInfoCheck(void){
798	>	int index;
799	>	int usesDipoles;
800	>	int i;
801
802	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
803	<	#endif  //is_mpi
802	>	for (i = 0; i < nInfo; i++){
803	>	// check electrostatic parameters
804	>
805	>	index = 0;
806	>	usesDipoles = 0;
807	>	while ((index < info[i].n_atoms) && !usesDipoles){
808	>	usesDipoles = (info[i].atoms[index])->hasDipole();
809	>	index++;
810		}
1075	–	excludeOffset += info.nBonds;
811
812	<	//make the bends
813	<	for(j=0; j<info.nBends; j++){
814	<
815	<	currentBend = comp_stamps[stampID]->getBend( j );
816	<	theBends[j].a = currentBend->getA() + atomOffset;
817	<	theBends[j].b = currentBend->getB() + atomOffset;
818	<	theBends[j].c = currentBend->getC() + atomOffset;
819	<
820	<	if( currentBend->haveExtras() ){
821	<
822	<	extras = currentBend->getExtras();
823	<	current_extra = extras;
824	<
825	<	while( current_extra != NULL ){
826	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
827	<
828	<	switch( current_extra->getType() ){
829	<
830	<	case 0:
831	<	theBends[j].ghost =
832	<	current_extra->getInt() + atomOffset;
833	<	theBends[j].isGhost = 1;
834	<	break;
835	<
1101	<	case 1:
1102	<	theBends[j].ghost =
1103	<	(int)current_extra->getDouble() + atomOffset;
1104	<	theBends[j].isGhost = 1;
1105	<	break;
1106	<
1107	<	default:
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup Error: ghostVectorSource was neither a "
1110	<	"double nor an int.\n"
1111	<	"-->Bend[%d] in %s\n",
1112	<	j, comp_stamps[stampID]->getID() );
1113	<	painCave.isFatal = 1;
1114	<	simError();
1115	<	}
1116	<	}
1117	<
1118	<	else{
1119	<
1120	<	sprintf( painCave.errMsg,
1121	<	"SimSetup Error: unhandled bend assignment:\n"
1122	<	"    -->%s in Bend[%d] in %s\n",
1123	<	current_extra->getlhs(),
1124	<	j, comp_stamps[stampID]->getID() );
1125	<	painCave.isFatal = 1;
1126	<	simError();
1127	<	}
1128	<
1129	<	current_extra = current_extra->getNext();
1130	<	}
812	>	#ifdef IS_MPI
813	>	int myUse = usesDipoles;
814	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815	>	#endif //is_mpi
816	>
817	>	double theEcr, theEst;
818	>
819	>	if (globals->getUseRF()){
820	>	info[i].useReactionField = 1;
821	>
822	>	if (!globals->haveECR()){
823	>	sprintf(painCave.errMsg,
824	>	"SimSetup Warning: using default value of 1/2 the smallest "
825	>	"box length for the electrostaticCutoffRadius.\n"
826	>	"I hope you have a very fast processor!\n");
827	>	painCave.isFatal = 0;
828	>	simError();
829	>	double smallest;
830	>	smallest = info[i].boxL[0];
831	>	if (info[i].boxL[1] <= smallest)
832	>	smallest = info[i].boxL[1];
833	>	if (info[i].boxL[2] <= smallest)
834	>	smallest = info[i].boxL[2];
835	>	theEcr = 0.5 * smallest;
836		}
1132	–
1133	–	if( !theBends[j].isGhost ){
1134	–
1135	–	exI = theBends[j].a;
1136	–	exJ = theBends[j].c;
1137	–	}
837		else{
838	<
1140	<	exI = theBends[j].a;
1141	<	exJ = theBends[j].b;
838	>	theEcr = globals->getECR();
839		}
840	<
841	<	// exclude_I must always be the smaller of the pair
842	<	if( exI > exJ ){
843	<	tempEx = exI;
844	<	exI = exJ;
845	<	exJ = tempEx;
840	>
841	>	if (!globals->haveEST()){
842	>	sprintf(painCave.errMsg,
843	>	"SimSetup Warning: using default value of 0.05 * the "
844	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
845	>	painCave.isFatal = 0;
846	>	simError();
847	>	theEst = 0.05 * theEcr;
848		}
849	<	#ifdef IS_MPI
850	<	tempEx = exI;
851	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1153	<	tempEx = exJ;
1154	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1155	<
1156	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1157	<	#else  // isn't MPI
1158	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1159	<	#endif  //is_mpi
1160	<	}
1161	<	excludeOffset += info.nBends;
849	>	else{
850	>	theEst = globals->getEST();
851	>	}
852
853	<	for(j=0; j<info.nTorsions; j++){
1164	<
1165	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1166	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1167	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1168	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1169	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1170	<
1171	<	exI = theTorsions[j].a;
1172	<	exJ = theTorsions[j].d;
853	>	info[i].setEcr(theEcr, theEst);
854
855	<	// exclude_I must always be the smaller of the pair
856	<	if( exI > exJ ){
857	<	tempEx = exI;
858	<	exI = exJ;
859	<	exJ = tempEx;
855	>	if (!globals->haveDielectric()){
856	>	sprintf(painCave.errMsg,
857	>	"SimSetup Error: You are trying to use Reaction Field without"
858	>	"setting a dielectric constant!\n");
859	>	painCave.isFatal = 1;
860	>	simError();
861		}
862	<	#ifdef IS_MPI
1181	<	tempEx = exI;
1182	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1183	<	tempEx = exJ;
1184	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1185	<
1186	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1187	<	#else  // isn't MPI
1188	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1189	<	#endif  //is_mpi
862	>	info[i].dielectric = globals->getDielectric();
863		}
864	<	excludeOffset += info.nTorsions;
864	>	else{
865	>	if (usesDipoles){
866	>	if (!globals->haveECR()){
867	>	sprintf(painCave.errMsg,
868	>	"SimSetup Warning: using default value of 1/2 the smallest "
869	>	"box length for the electrostaticCutoffRadius.\n"
870	>	"I hope you have a very fast processor!\n");
871	>	painCave.isFatal = 0;
872	>	simError();
873	>	double smallest;
874	>	smallest = info[i].boxL[0];
875	>	if (info[i].boxL[1] <= smallest)
876	>	smallest = info[i].boxL[1];
877	>	if (info[i].boxL[2] <= smallest)
878	>	smallest = info[i].boxL[2];
879	>	theEcr = 0.5 * smallest;
880	>	}
881	>	else{
882	>	theEcr = globals->getECR();
883	>	}
884
885	<
886	<	// send the arrays off to the forceField for init.
885	>	if (!globals->haveEST()){
886	>	sprintf(painCave.errMsg,
887	>	"SimSetup Warning: using default value of 0.05 * the "
888	>	"electrostaticCutoffRadius for the "
889	>	"electrostaticSkinThickness\n");
890	>	painCave.isFatal = 0;
891	>	simError();
892	>	theEst = 0.05 * theEcr;
893	>	}
894	>	else{
895	>	theEst = globals->getEST();
896	>	}
897
898	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
899	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
900	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1199	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1200	<
1201	<
1202	<	the_molecules[i].initialize( info );
1203	<
1204	<
1205	<	atomOffset += info.nAtoms;
1206	<	delete[] theBonds;
1207	<	delete[] theBends;
1208	<	delete[] theTorsions;
898	>	info[i].setEcr(theEcr, theEst);
899	>	}
900	>	}
901		}
902
903		#ifdef IS_MPI
904	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
904	>	strcpy(checkPointMsg, "post processing checks out");
905		MPIcheckPoint();
906		#endif // is_mpi
1215	–
1216	–	// clean up the forcefield
1217	–	the_ff->calcRcut();
1218	–	the_ff->cleanMe();
1219	–
907		}
908
909	<	void SimSetup::initFromBass( void ){
909	>	void SimSetup::initSystemCoords(void){
910	>	int i;
911
912	<	int i, j, k;
1225	<	int n_cells;
1226	<	double cellx, celly, cellz;
1227	<	double temp1, temp2, temp3;
1228	<	int n_per_extra;
1229	<	int n_extra;
1230	<	int have_extra, done;
912	>	char* inName;
913
914	<	temp1 = (double)tot_nmol / 4.0;
1233	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1234	<	temp3 = ceil( temp2 );
914	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
915
916	<	have_extra =0;
917	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1238	<	have_extra =1;
916	>	for (i = 0; i < info[0].n_atoms; i++)
917	>	info[0].atoms[i]->setCoords();
918
919	<	n_cells = (int)temp3 - 1;
920	<	cellx = simnfo->boxLx / temp3;
921	<	celly = simnfo->boxLy / temp3;
922	<	cellz = simnfo->boxLz / temp3;
923	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
924	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
925	<	n_per_extra = (int)ceil( temp1 );
926	<
927	<	if( n_per_extra > 4){
1249	<	sprintf( painCave.errMsg,
1250	<	"SimSetup error. There has been an error in constructing"
1251	<	" the non-complete lattice.\n" );
1252	<	painCave.isFatal = 1;
1253	<	simError();
919	>	if (globals->haveInitialConfig()){
920	>	InitializeFromFile* fileInit;
921	>	#ifdef IS_MPI // is_mpi
922	>	if (worldRank == 0){
923	>	#endif //is_mpi
924	>	inName = globals->getInitialConfig();
925	>	double* tempDouble = new double[1000000];
926	>	fileInit = new InitializeFromFile(inName);
927	>	#ifdef IS_MPI
928		}
929	+	else
930	+	fileInit = new InitializeFromFile(NULL);
931	+	#endif
932	+	fileInit->readInit(info); // default velocities on
933	+
934	+	delete fileInit;
935		}
936		else{
937	<	n_cells = (int)temp3;
1258	<	cellx = simnfo->boxLx / temp3;
1259	<	celly = simnfo->boxLy / temp3;
1260	<	cellz = simnfo->boxLz / temp3;
1261	<	}
937	>	#ifdef IS_MPI
938
939	<	current_mol = 0;
1264	<	current_comp_mol = 0;
1265	<	current_comp = 0;
1266	<	current_atom_ndx = 0;
939	>	// no init from bass
940
941	<	for( i=0; i < n_cells ; i++ ){
942	<	for( j=0; j < n_cells; j++ ){
943	<	for( k=0; k < n_cells; k++ ){
941	>	sprintf(painCave.errMsg,
942	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
943	>	painCave.isFatal;
944	>	simError();
945
946	<	makeElement( i * cellx,
1273	<	j * celly,
1274	<	k * cellz );
946	>	#else
947
948	<	makeElement( i * cellx + 0.5 * cellx,
1277	<	j * celly + 0.5 * celly,
1278	<	k * cellz );
948	>	initFromBass();
949
1280	–	makeElement( i * cellx,
1281	–	j * celly + 0.5 * celly,
1282	–	k * cellz + 0.5 * cellz );
950
951	<	makeElement( i * cellx + 0.5 * cellx,
1285	<	j * celly,
1286	<	k * cellz + 0.5 * cellz );
1287	<	}
1288	<	}
951	>	#endif
952		}
953
954	<	if( have_extra ){
955	<	done = 0;
954	>	#ifdef IS_MPI
955	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
956	>	MPIcheckPoint();
957	>	#endif // is_mpi
958	>	}
959
1294	–	int start_ndx;
1295	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1296	–	for( j=0; j < (n_cells+1) && !done; j++ ){
960
961	<	if( i < n_cells ){
961	>	void SimSetup::makeOutNames(void){
962	>	int k;
963
1300	–	if( j < n_cells ){
1301	–	start_ndx = n_cells;
1302	–	}
1303	–	else start_ndx = 0;
1304	–	}
1305	–	else start_ndx = 0;
964
965	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
966	<
967	<	makeElement( i * cellx,
968	<	j * celly,
1311	<	k * cellz );
1312	<	done = ( current_mol >= tot_nmol );
1313	<
1314	<	if( !done && n_per_extra > 1 ){
1315	<	makeElement( i * cellx + 0.5 * cellx,
1316	<	j * celly + 0.5 * celly,
1317	<	k * cellz );
1318	<	done = ( current_mol >= tot_nmol );
1319	<	}
1320	<
1321	<	if( !done && n_per_extra > 2){
1322	<	makeElement( i * cellx,
1323	<	j * celly + 0.5 * celly,
1324	<	k * cellz + 0.5 * cellz );
1325	<	done = ( current_mol >= tot_nmol );
1326	<	}
965	>	for (k = 0; k < nInfo; k++){
966	>	#ifdef IS_MPI
967	>	if (worldRank == 0){
968	>	#endif // is_mpi
969
970	<	if( !done && n_per_extra > 3){
971	<	makeElement( i * cellx + 0.5 * cellx,
1330	<	j * celly,
1331	<	k * cellz + 0.5 * cellz );
1332	<	done = ( current_mol >= tot_nmol );
1333	<	}
1334	<	}
970	>	if (globals->haveFinalConfig()){
971	>	strcpy(info[k].finalName, globals->getFinalConfig());
972		}
973	+	else{
974	+	strcpy(info[k].finalName, inFileName);
975	+	char* endTest;
976	+	int nameLength = strlen(info[k].finalName);
977	+	endTest = &(info[k].finalName[nameLength - 5]);
978	+	if (!strcmp(endTest, ".bass")){
979	+	strcpy(endTest, ".eor");
980	+	}
981	+	else if (!strcmp(endTest, ".BASS")){
982	+	strcpy(endTest, ".eor");
983	+	}
984	+	else{
985	+	endTest = &(info[k].finalName[nameLength - 4]);
986	+	if (!strcmp(endTest, ".bss")){
987	+	strcpy(endTest, ".eor");
988	+	}
989	+	else if (!strcmp(endTest, ".mdl")){
990	+	strcpy(endTest, ".eor");
991	+	}
992	+	else{
993	+	strcat(info[k].finalName, ".eor");
994	+	}
995	+	}
996	+	}
997	+
998	+	// make the sample and status out names
999	+
1000	+	strcpy(info[k].sampleName, inFileName);
1001	+	char* endTest;
1002	+	int nameLength = strlen(info[k].sampleName);
1003	+	endTest = &(info[k].sampleName[nameLength - 5]);
1004	+	if (!strcmp(endTest, ".bass")){
1005	+	strcpy(endTest, ".dump");
1006	+	}
1007	+	else if (!strcmp(endTest, ".BASS")){
1008	+	strcpy(endTest, ".dump");
1009	+	}
1010	+	else{
1011	+	endTest = &(info[k].sampleName[nameLength - 4]);
1012	+	if (!strcmp(endTest, ".bss")){
1013	+	strcpy(endTest, ".dump");
1014	+	}
1015	+	else if (!strcmp(endTest, ".mdl")){
1016	+	strcpy(endTest, ".dump");
1017	+	}
1018	+	else{
1019	+	strcat(info[k].sampleName, ".dump");
1020	+	}
1021	+	}
1022	+
1023	+	strcpy(info[k].statusName, inFileName);
1024	+	nameLength = strlen(info[k].statusName);
1025	+	endTest = &(info[k].statusName[nameLength - 5]);
1026	+	if (!strcmp(endTest, ".bass")){
1027	+	strcpy(endTest, ".stat");
1028	+	}
1029	+	else if (!strcmp(endTest, ".BASS")){
1030	+	strcpy(endTest, ".stat");
1031	+	}
1032	+	else{
1033	+	endTest = &(info[k].statusName[nameLength - 4]);
1034	+	if (!strcmp(endTest, ".bss")){
1035	+	strcpy(endTest, ".stat");
1036	+	}
1037	+	else if (!strcmp(endTest, ".mdl")){
1038	+	strcpy(endTest, ".stat");
1039	+	}
1040	+	else{
1041	+	strcat(info[k].statusName, ".stat");
1042	+	}
1043	+	}
1044	+
1045	+	#ifdef IS_MPI
1046	+
1047		}
1048	+	#endif // is_mpi
1049		}
1050	+	}
1051
1052
1053	<	for( i=0; i<simnfo->n_atoms; i++ ){
1054	<	simnfo->atoms[i]->set_vx( 0.0 );
1055	<	simnfo->atoms[i]->set_vy( 0.0 );
1056	<	simnfo->atoms[i]->set_vz( 0.0 );
1053	>	void SimSetup::sysObjectsCreation(void){
1054	>	int i, k;
1055	>
1056	>	// create the forceField
1057	>
1058	>	createFF();
1059	>
1060	>	// extract componentList
1061	>
1062	>	compList();
1063	>
1064	>	// calc the number of atoms, bond, bends, and torsions
1065	>
1066	>	calcSysValues();
1067	>
1068	>	#ifdef IS_MPI
1069	>	// divide the molecules among the processors
1070	>
1071	>	mpiMolDivide();
1072	>	#endif //is_mpi
1073	>
1074	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1075	>
1076	>	makeSysArrays();
1077	>
1078	>	// make and initialize the molecules (all but atomic coordinates)
1079	>
1080	>	makeMolecules();
1081	>
1082	>	for (k = 0; k < nInfo; k++){
1083	>	info[k].identArray = new int[info[k].n_atoms];
1084	>	for (i = 0; i < info[k].n_atoms; i++){
1085	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1086	>	}
1087		}
1088		}
1089
1347	–	void SimSetup::makeElement( double x, double y, double z ){
1090
1091	<	int k;
1092	<	AtomStamp* current_atom;
1093	<	DirectionalAtom* dAtom;
1094	<	double rotMat[3][3];
1091	>	void SimSetup::createFF(void){
1092	>	switch (ffCase){
1093	>	case FF_DUFF:
1094	>	the_ff = new DUFF();
1095	>	break;
1096
1097	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1097	>	case FF_LJ:
1098	>	the_ff = new LJFF();
1099	>	break;
1100
1101	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1102	<	if( !current_atom->havePosition() ){
1103	<	sprintf( painCave.errMsg,
1104	<	"SimSetup:initFromBass error.\n"
1105	<	"\tComponent %s, atom %s does not have a position specified.\n"
1106	<	"\tThe initialization routine is unable to give a start"
1107	<	" position.\n",
1363	<	comp_stamps[current_comp]->getID(),
1364	<	current_atom->getType() );
1101	>	case FF_EAM:
1102	>	the_ff = new EAM_FF();
1103	>	break;
1104	>
1105	>	default:
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1108		painCave.isFatal = 1;
1109		simError();
1110	+	}
1111	+
1112	+	#ifdef IS_MPI
1113	+	strcpy(checkPointMsg, "ForceField creation successful");
1114	+	MPIcheckPoint();
1115	+	#endif // is_mpi
1116	+	}
1117	+
1118	+
1119	+	void SimSetup::compList(void){
1120	+	int i;
1121	+	char* id;
1122	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1123	+	LinkedMolStamp* currentStamp = NULL;
1124	+	comp_stamps = new MoleculeStamp * [n_components];
1125	+
1126	+	// make an array of molecule stamps that match the components used.
1127	+	// also extract the used stamps out into a separate linked list
1128	+
1129	+	for (i = 0; i < nInfo; i++){
1130	+	info[i].nComponents = n_components;
1131	+	info[i].componentsNmol = components_nmol;
1132	+	info[i].compStamps = comp_stamps;
1133	+	info[i].headStamp = headStamp;
1134	+	}
1135	+
1136	+
1137	+	for (i = 0; i < n_components; i++){
1138	+	id = the_components[i]->getType();
1139	+	comp_stamps[i] = NULL;
1140	+
1141	+	// check to make sure the component isn't already in the list
1142	+
1143	+	comp_stamps[i] = headStamp->match(id);
1144	+	if (comp_stamps[i] == NULL){
1145	+	// extract the component from the list;
1146	+
1147	+	currentStamp = stamps->extractMolStamp(id);
1148	+	if (currentStamp == NULL){
1149	+	sprintf(painCave.errMsg,
1150	+	"SimSetup error: Component \"%s\" was not found in the "
1151	+	"list of declared molecules\n",
1152	+	id);
1153	+	painCave.isFatal = 1;
1154	+	simError();
1155	+	}
1156	+
1157	+	headStamp->add(currentStamp);
1158	+	comp_stamps[i] = headStamp->match(id);
1159		}
1160	+	}
1161
1162	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1163	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1164	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1162	>	#ifdef IS_MPI
1163	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1164	>	MPIcheckPoint();
1165	>	#endif // is_mpi
1166	>	}
1167
1168	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1168	>	void SimSetup::calcSysValues(void){
1169	>	int i, j, k;
1170
1171	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1171	>	int* molMembershipArray;
1172
1173	<	rotMat[0][0] = 1.0;
1174	<	rotMat[0][1] = 0.0;
1175	<	rotMat[0][2] = 0.0;
1173	>	tot_atoms = 0;
1174	>	tot_bonds = 0;
1175	>	tot_bends = 0;
1176	>	tot_torsions = 0;
1177	>	for (i = 0; i < n_components; i++){
1178	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1180	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1181	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182	>	}
1183
1184	<	rotMat[1][0] = 0.0;
1185	<	rotMat[1][1] = 1.0;
1383	<	rotMat[1][2] = 0.0;
1184	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	>	molMembershipArray = new int[tot_atoms];
1186
1187	<	rotMat[2][0] = 0.0;
1188	<	rotMat[2][1] = 0.0;
1189	<	rotMat[2][2] = 1.0;
1187	>	for (i = 0; i < nInfo; i++){
1188	>	info[i].n_atoms = tot_atoms;
1189	>	info[i].n_bonds = tot_bonds;
1190	>	info[i].n_bends = tot_bends;
1191	>	info[i].n_torsions = tot_torsions;
1192	>	info[i].n_SRI = tot_SRI;
1193	>	info[i].n_mol = tot_nmol;
1194
1195	<	dAtom->setA( rotMat );
1195	>	info[i].molMembershipArray = molMembershipArray;
1196	>	}
1197	>	}
1198	>
1199	>	#ifdef IS_MPI
1200	>
1201	>	void SimSetup::mpiMolDivide(void){
1202	>	int i, j, k;
1203	>	int localMol, allMol;
1204	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1205	>
1206	>	mpiSim = new mpiSimulation(info);
1207	>
1208	>	globalIndex = mpiSim->divideLabor();
1209	>
1210	>	// set up the local variables
1211	>
1212	>	mol2proc = mpiSim->getMolToProcMap();
1213	>	molCompType = mpiSim->getMolComponentType();
1214	>
1215	>	allMol = 0;
1216	>	localMol = 0;
1217	>	local_atoms = 0;
1218	>	local_bonds = 0;
1219	>	local_bends = 0;
1220	>	local_torsions = 0;
1221	>	globalAtomIndex = 0;
1222	>
1223	>
1224	>	for (i = 0; i < n_components; i++){
1225	>	for (j = 0; j < components_nmol[i]; j++){
1226	>	if (mol2proc[allMol] == worldRank){
1227	>	local_atoms += comp_stamps[i]->getNAtoms();
1228	>	local_bonds += comp_stamps[i]->getNBonds();
1229	>	local_bends += comp_stamps[i]->getNBends();
1230	>	local_torsions += comp_stamps[i]->getNTorsions();
1231	>	localMol++;
1232	>	}
1233	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1234	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1235	>	globalAtomIndex++;
1236	>	}
1237	>
1238	>	allMol++;
1239		}
1240	+	}
1241	+	local_SRI = local_bonds + local_bends + local_torsions;
1242
1243	<	current_atom_ndx++;
1243	>	info[0].n_atoms = mpiSim->getMyNlocal();
1244	>
1245	>	if (local_atoms != info[0].n_atoms){
1246	>	sprintf(painCave.errMsg,
1247	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1248	>	" localAtom (%d) are not equal.\n",
1249	>	info[0].n_atoms, local_atoms);
1250	>	painCave.isFatal = 1;
1251	>	simError();
1252		}
1253
1254	<	current_mol++;
1255	<	current_comp_mol++;
1254	>	info[0].n_bonds = local_bonds;
1255	>	info[0].n_bends = local_bends;
1256	>	info[0].n_torsions = local_torsions;
1257	>	info[0].n_SRI = local_SRI;
1258	>	info[0].n_mol = localMol;
1259
1260	<	if( current_comp_mol >= components_nmol[current_comp] ){
1260	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1261	>	MPIcheckPoint();
1262	>	}
1263
1264	<	current_comp_mol = 0;
1265	<	current_comp++;
1264	>	#endif // is_mpi
1265	>
1266	>
1267	>	void SimSetup::makeSysArrays(void){
1268	>	int i, j, k, l;
1269	>
1270	>	Atom** the_atoms;
1271	>	Molecule* the_molecules;
1272	>	Exclude** the_excludes;
1273	>
1274	>
1275	>	for (l = 0; l < nInfo; l++){
1276	>	// create the atom and short range interaction arrays
1277	>
1278	>	the_atoms = new Atom * [info[l].n_atoms];
1279	>	the_molecules = new Molecule[info[l].n_mol];
1280	>	int molIndex;
1281	>
1282	>	// initialize the molecule's stampID's
1283	>
1284	>	#ifdef IS_MPI
1285	>
1286	>
1287	>	molIndex = 0;
1288	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1289	>	if (mol2proc[i] == worldRank){
1290	>	the_molecules[molIndex].setStampID(molCompType[i]);
1291	>	the_molecules[molIndex].setMyIndex(molIndex);
1292	>	the_molecules[molIndex].setGlobalIndex(i);
1293	>	molIndex++;
1294	>	}
1295	>	}
1296	>
1297	>	#else // is_mpi
1298	>
1299	>	molIndex = 0;
1300	>	globalAtomIndex = 0;
1301	>	for (i = 0; i < n_components; i++){
1302	>	for (j = 0; j < components_nmol[i]; j++){
1303	>	the_molecules[molIndex].setStampID(i);
1304	>	the_molecules[molIndex].setMyIndex(molIndex);
1305	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1306	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1307	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1308	>	globalAtomIndex++;
1309	>	}
1310	>	molIndex++;
1311	>	}
1312	>	}
1313	>
1314	>
1315	>	#endif // is_mpi
1316	>
1317	>
1318	>	if (info[l].n_SRI){
1319	>	Exclude::createArray(info[l].n_SRI);
1320	>	the_excludes = new Exclude * [info[l].n_SRI];
1321	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1322	>	the_excludes[ex] = new Exclude(ex);
1323	>	}
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].n_exclude = info[l].n_SRI;
1326	>	}
1327	>	else{
1328	>	Exclude::createArray(1);
1329	>	the_excludes = new Exclude * ;
1330	>	the_excludes[0] = new Exclude(0);
1331	>	the_excludes[0]->setPair(0, 0);
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].globalExcludes[0] = 0;
1334	>	info[l].n_exclude = 0;
1335	>	}
1336	>
1337	>	// set the arrays into the SimInfo object
1338	>
1339	>	info[l].atoms = the_atoms;
1340	>	info[l].molecules = the_molecules;
1341	>	info[l].nGlobalExcludes = 0;
1342	>	info[l].excludes = the_excludes;
1343	>
1344	>	the_ff->setSimInfo(info);
1345		}
1346		}
1347	+
1348	+	void SimSetup::makeIntegrator(void){
1349	+	int k;
1350	+
1351	+	NVT<RealIntegrator>* myNVT = NULL;
1352	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1353	+	NPTf<RealIntegrator>* myNPTf = NULL;
1354	+	NPTim<RealIntegrator>* myNPTim = NULL;
1355	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1356	+
1357	+	for (k = 0; k < nInfo; k++){
1358	+	switch (ensembleCase){
1359	+	case NVE_ENS:
1360	+	if (globals->haveZconstraints()){
1361	+	setupZConstraint(info[k]);
1362	+	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1363	+	}
1364	+	else
1365	+	new NVE<RealIntegrator>(&(info[k]), the_ff);
1366	+	break;
1367	+
1368	+	case NVT_ENS:
1369	+	if (globals->haveZconstraints()){
1370	+	setupZConstraint(info[k]);
1371	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1372	+	}
1373	+	else
1374	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1375	+
1376	+	myNVT->setTargetTemp(globals->getTargetTemp());
1377	+
1378	+	if (globals->haveTauThermostat())
1379	+	myNVT->setTauThermostat(globals->getTauThermostat());
1380	+	else{
1381	+	sprintf(painCave.errMsg,
1382	+	"SimSetup error: If you use the NVT\n"
1383	+	"    ensemble, you must set tauThermostat.\n");
1384	+	painCave.isFatal = 1;
1385	+	simError();
1386	+	}
1387	+	break;
1388	+
1389	+	case NPTi_ENS:
1390	+	if (globals->haveZconstraints()){
1391	+	setupZConstraint(info[k]);
1392	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1393	+	}
1394	+	else
1395	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1396	+
1397	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1398	+
1399	+	if (globals->haveTargetPressure())
1400	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1401	+	else{
1402	+	sprintf(painCave.errMsg,
1403	+	"SimSetup error: If you use a constant pressure\n"
1404	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1405	+	painCave.isFatal = 1;
1406	+	simError();
1407	+	}
1408	+
1409	+	if (globals->haveTauThermostat())
1410	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1411	+	else{
1412	+	sprintf(painCave.errMsg,
1413	+	"SimSetup error: If you use an NPT\n"
1414	+	"    ensemble, you must set tauThermostat.\n");
1415	+	painCave.isFatal = 1;
1416	+	simError();
1417	+	}
1418	+
1419	+	if (globals->haveTauBarostat())
1420	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1421	+	else{
1422	+	sprintf(painCave.errMsg,
1423	+	"SimSetup error: If you use an NPT\n"
1424	+	"    ensemble, you must set tauBarostat.\n");
1425	+	painCave.isFatal = 1;
1426	+	simError();
1427	+	}
1428	+	break;
1429	+
1430	+	case NPTf_ENS:
1431	+	if (globals->haveZconstraints()){
1432	+	setupZConstraint(info[k]);
1433	+	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1434	+	}
1435	+	else
1436	+	myNPTf = new NPTf<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	+	break;
1470	+
1471	+	case NPTim_ENS:
1472	+	if (globals->haveZconstraints()){
1473	+	setupZConstraint(info[k]);
1474	+	myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1475	+	}
1476	+	else
1477	+	myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1478	+
1479	+	myNPTim->setTargetTemp(globals->getTargetTemp());
1480	+
1481	+	if (globals->haveTargetPressure())
1482	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1483	+	else{
1484	+	sprintf(painCave.errMsg,
1485	+	"SimSetup error: If you use a constant pressure\n"
1486	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1487	+	painCave.isFatal = 1;
1488	+	simError();
1489	+	}
1490	+
1491	+	if (globals->haveTauThermostat())
1492	+	myNPTim->setTauThermostat(globals->getTauThermostat());
1493	+	else{
1494	+	sprintf(painCave.errMsg,
1495	+	"SimSetup error: If you use an NPT\n"
1496	+	"    ensemble, you must set tauThermostat.\n");
1497	+	painCave.isFatal = 1;
1498	+	simError();
1499	+	}
1500	+
1501	+	if (globals->haveTauBarostat())
1502	+	myNPTim->setTauBarostat(globals->getTauBarostat());
1503	+	else{
1504	+	sprintf(painCave.errMsg,
1505	+	"SimSetup error: If you use an NPT\n"
1506	+	"    ensemble, you must set tauBarostat.\n");
1507	+	painCave.isFatal = 1;
1508	+	simError();
1509	+	}
1510	+	break;
1511	+
1512	+	case NPTfm_ENS:
1513	+	if (globals->haveZconstraints()){
1514	+	setupZConstraint(info[k]);
1515	+	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1516	+	}
1517	+	else
1518	+	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1519	+
1520	+	myNPTfm->setTargetTemp(globals->getTargetTemp());
1521	+
1522	+	if (globals->haveTargetPressure())
1523	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1524	+	else{
1525	+	sprintf(painCave.errMsg,
1526	+	"SimSetup error: If you use a constant pressure\n"
1527	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1528	+	painCave.isFatal = 1;
1529	+	simError();
1530	+	}
1531	+
1532	+	if (globals->haveTauThermostat())
1533	+	myNPTfm->setTauThermostat(globals->getTauThermostat());
1534	+	else{
1535	+	sprintf(painCave.errMsg,
1536	+	"SimSetup error: If you use an NPT\n"
1537	+	"    ensemble, you must set tauThermostat.\n");
1538	+	painCave.isFatal = 1;
1539	+	simError();
1540	+	}
1541	+
1542	+	if (globals->haveTauBarostat())
1543	+	myNPTfm->setTauBarostat(globals->getTauBarostat());
1544	+	else{
1545	+	sprintf(painCave.errMsg,
1546	+	"SimSetup error: If you use an NPT\n"
1547	+	"    ensemble, you must set tauBarostat.\n");
1548	+	painCave.isFatal = 1;
1549	+	simError();
1550	+	}
1551	+	break;
1552	+
1553	+	default:
1554	+	sprintf(painCave.errMsg,
1555	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1556	+	painCave.isFatal = 1;
1557	+	simError();
1558	+	}
1559	+	}
1560	+	}
1561	+
1562	+	void SimSetup::initFortran(void){
1563	+	info[0].refreshSim();
1564	+
1565	+	if (!strcmp(info[0].mixingRule, "standard")){
1566	+	the_ff->initForceField(LB_MIXING_RULE);
1567	+	}
1568	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1569	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1570	+	}
1571	+	else{
1572	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1573	+	info[0].mixingRule);
1574	+	painCave.isFatal = 1;
1575	+	simError();
1576	+	}
1577	+
1578	+
1579	+	#ifdef IS_MPI
1580	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1581	+	MPIcheckPoint();
1582	+	#endif // is_mpi
1583	+	}
1584	+
1585	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1586	+	int nZConstraints;
1587	+	ZconStamp** zconStamp;
1588	+
1589	+	if (globals->haveZconstraintTime()){
1590	+	//add sample time of z-constraint  into SimInfo's property list
1591	+	DoubleData* zconsTimeProp = new DoubleData();
1592	+	zconsTimeProp->setID(ZCONSTIME_ID);
1593	+	zconsTimeProp->setData(globals->getZconsTime());
1594	+	theInfo.addProperty(zconsTimeProp);
1595	+	}
1596	+	else{
1597	+	sprintf(painCave.errMsg,
1598	+	"ZConstraint error: If you use an ZConstraint\n"
1599	+	" , you must set sample time.\n");
1600	+	painCave.isFatal = 1;
1601	+	simError();
1602	+	}
1603	+
1604	+	//push zconsTol into siminfo, if user does not specify
1605	+	//value for zconsTol, a default value will be used
1606	+	DoubleData* zconsTol = new DoubleData();
1607	+	zconsTol->setID(ZCONSTOL_ID);
1608	+	if (globals->haveZconsTol()){
1609	+	zconsTol->setData(globals->getZconsTol());
1610	+	}
1611	+	else{
1612	+	double defaultZConsTol = 0.01;
1613	+	sprintf(painCave.errMsg,
1614	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1615	+	" , default value %f is used.\n",
1616	+	defaultZConsTol);
1617	+	painCave.isFatal = 0;
1618	+	simError();
1619	+
1620	+	zconsTol->setData(defaultZConsTol);
1621	+	}
1622	+	theInfo.addProperty(zconsTol);
1623	+
1624	+	//set Force Subtraction Policy
1625	+	StringData* zconsForcePolicy = new StringData();
1626	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1627	+
1628	+	if (globals->haveZconsForcePolicy()){
1629	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1630	+	}
1631	+	else{
1632	+	sprintf(painCave.errMsg,
1633	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1634	+	"PolicyByMass is used\n");
1635	+	painCave.isFatal = 0;
1636	+	simError();
1637	+	zconsForcePolicy->setData("BYMASS");
1638	+	}
1639	+
1640	+	theInfo.addProperty(zconsForcePolicy);
1641	+
1642	+	//Determine the name of ouput file and add it into SimInfo's property list
1643	+	//Be careful, do not use inFileName, since it is a pointer which
1644	+	//point to a string at master node, and slave nodes do not contain that string
1645	+
1646	+	string zconsOutput(theInfo.finalName);
1647	+
1648	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1649	+
1650	+	StringData* zconsFilename = new StringData();
1651	+	zconsFilename->setID(ZCONSFILENAME_ID);
1652	+	zconsFilename->setData(zconsOutput);
1653	+
1654	+	theInfo.addProperty(zconsFilename);
1655	+
1656	+	//setup index, pos and other parameters of z-constraint molecules
1657	+	nZConstraints = globals->getNzConstraints();
1658	+	theInfo.nZconstraints = nZConstraints;
1659	+
1660	+	zconStamp = globals->getZconStamp();
1661	+	ZConsParaItem tempParaItem;
1662	+
1663	+	ZConsParaData* zconsParaData = new ZConsParaData();
1664	+	zconsParaData->setID(ZCONSPARADATA_ID);
1665	+
1666	+	for (int i = 0; i < nZConstraints; i++){
1667	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1668	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1669	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1670	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1671	+
1672	+	zconsParaData->addItem(tempParaItem);
1673	+	}
1674	+
1675	+	//check the uniqueness of index
1676	+	if(!zconsParaData->isIndexUnique()){
1677	+	sprintf(painCave.errMsg,
1678	+	"ZConstraint Error: molIndex is not unique\n");
1679	+	painCave.isFatal = 1;
1680	+	simError();
1681	+	}
1682	+
1683	+	//sort the parameters by index of molecules
1684	+	zconsParaData->sortByIndex();
1685	+
1686	+	//push data into siminfo, therefore, we can retrieve later
1687	+	theInfo.addProperty(zconsParaData);
1688	+	}

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