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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 580 by gezelter, Wed Jul 9 13:56:36 2003 UTC vs.
Revision 814 by mmeineke, Thu Oct 23 19:57:25 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	<
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 14 | Line 17
17
18		// some defines for ensemble and Forcefield  cases
19
20	<	#define NVE_ENS 0
21	<	#define NVT_ENS 1
22	<	#define NPTi_ENS 2
23	<	#define NPTf_ENS 3
20	>	#define NVE_ENS        0
21	>	#define NVT_ENS        1
22	>	#define NPTi_ENS       2
23	>	#define NPTf_ENS       3
24	>	#define NPTxyz_ENS     4
25
26	+
27		#define FF_DUFF 0
28		#define FF_LJ   1
29	+	#define FF_EAM  2
30
31	+	using namespace std;
32
33		SimSetup::SimSetup(){
34	+	isInfoArray = 0;
35	+	nInfo = 1;
36	+
37		stamps = new MakeStamps();
38		globals = new Globals();
39	<
39	>
40	>
41		#ifdef IS_MPI
42	<	strcpy( checkPointMsg, "SimSetup creation successful" );
42	>	strcpy(checkPointMsg, "SimSetup creation successful");
43		MPIcheckPoint();
44		#endif // IS_MPI
45		}
#	Line 38 | Line 49 | void SimSetup::parseFile( char* fileName ){
49		delete globals;
50		}
51
52	<	void SimSetup::parseFile( char* fileName ){
52	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
53	>	info = the_info;
54	>	nInfo = theNinfo;
55	>	isInfoArray = 1;
56	>	}
57
58	+
59	+	void SimSetup::parseFile(char* fileName){
60		#ifdef IS_MPI
61	<	if( worldRank == 0 ){
61	>	if (worldRank == 0){
62		#endif // is_mpi
63	<
63	>
64		inFileName = fileName;
65	<	set_interface_stamps( stamps, globals );
66	<
65	>	set_interface_stamps(stamps, globals);
66	>
67		#ifdef IS_MPI
68		mpiEventInit();
69		#endif
70
71	<	yacc_BASS( fileName );
71	>	yacc_BASS(fileName);
72
73		#ifdef IS_MPI
74		throwMPIEvent(NULL);
75		}
76	<	else receiveParse();
76	>	else{
77	>	receiveParse();
78	>	}
79		#endif
80
81		}
82
83		#ifdef IS_MPI
84		void SimSetup::receiveParse(void){
85	<
86	<	set_interface_stamps( stamps, globals );
87	<	mpiEventInit();
88	<	MPIcheckPoint();
70	<	mpiEventLoop();
71	<
85	>	set_interface_stamps(stamps, globals);
86	>	mpiEventInit();
87	>	MPIcheckPoint();
88	>	mpiEventLoop();
89		}
90
91		#endif // is_mpi
92
93	<	void SimSetup::createSim( void ){
93	>	void SimSetup::createSim(void){
94
95	<	MakeStamps *the_stamps;
79	<	Globals* the_globals;
80	<	int i, j, k, globalAtomIndex;
81	<
82	<	int ensembleCase;
83	<	int ffCase;
84	<
85	<	ensembleCase = -1;
86	<	ffCase = -1;
95	>	// gather all of the information from the Bass file
96
97	<	// get the stamps and globals;
89	<	the_stamps = stamps;
90	<	the_globals = globals;
97	>	gatherInfo();
98
99	<	// set the easy ones first
93	<	simnfo->target_temp = the_globals->getTargetTemp();
94	<	simnfo->dt = the_globals->getDt();
95	<	simnfo->run_time = the_globals->getRunTime();
99	>	// creation of complex system objects
100
101	<	// get the ones we know are there, yet still may need some work.
98	<	n_components = the_globals->getNComponents();
99	<	strcpy( force_field, the_globals->getForceField() );
101	>	sysObjectsCreation();
102
103	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
102	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
103	<	else{
104	<	sprintf( painCave.errMsg,
105	<	"SimSetup Error. Unrecognized force field -> %s\n",
106	<	force_field );
107	<	painCave.isFatal = 1;
108	<	simError();
109	<	}
103	>	// check on the post processing info
104
105	<	// get the ensemble:
112	<	strcpy( ensemble, the_globals->getEnsemble() );
105	>	finalInfoCheck();
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{
113	<	sprintf( painCave.errMsg,
121	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
122	<	"reverting to NVE for this simulation.\n",
123	<	ensemble );
124	<	painCave.isFatal = 0;
125	<	simError();
126	<	strcpy( ensemble, "NVE" );
127	<	ensembleCase = NVE_ENS;
107	>	// initialize the system coordinates
108	>
109	>	if (!isInfoArray){
110	>	initSystemCoords();
111	>
112	>	if( !(globals->getUseInitTime()) )
113	>	info[0].currentTime = 0.0;
114		}
129	–	strcpy( simnfo->ensemble, ensemble );
115
116	+	// make the output filenames
117
118	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
133	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
134	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
135	<	//     if (the_globals->haveTargetPressure())
136	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
137	<	//     else {
138	<	//       sprintf( painCave.errMsg,
139	<	//                "SimSetup error: If you use the constant pressure\n"
140	<	//                "    ensemble, you must set targetPressure.\n"
141	<	//                "    This was found in the BASS file.\n");
142	<	//       painCave.isFatal = 1;
143	<	//       simError();
144	<	//     }
118	>	makeOutNames();
119
120	<	//     if (the_globals->haveTauThermostat())
147	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
148	<	//     else if (the_globals->haveQmass())
149	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
150	<	//     else {
151	<	//       sprintf( painCave.errMsg,
152	<	//                "SimSetup error: If you use one of the constant temperature\n"
153	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
154	<	//                "    Neither of these was found in the BASS file.\n");
155	<	//       painCave.isFatal = 1;
156	<	//       simError();
157	<	//     }
120	>	// make the integrator
121
122	<	//     if (the_globals->haveTauBarostat())
160	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
161	<	//     else {
162	<	//       sprintf( painCave.errMsg,
163	<	//                "SimSetup error: If you use the constant pressure\n"
164	<	//                "    ensemble, you must set tauBarostat.\n"
165	<	//                "    This was found in the BASS file.\n");
166	<	//       painCave.isFatal = 1;
167	<	//       simError();
168	<	//     }
122	>	makeIntegrator();
123
124	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
125	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
126	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
124	>	#ifdef IS_MPI
125	>	mpiSim->mpiRefresh();
126	>	#endif
127
128	<	//     if (the_globals->haveTauThermostat())
175	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
176	<	//     else if (the_globals->haveQmass())
177	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
178	<	//     else {
179	<	//       sprintf( painCave.errMsg,
180	<	//                "SimSetup error: If you use one of the constant temperature\n"
181	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
182	<	//                "    Neither of these was found in the BASS file.\n");
183	<	//       painCave.isFatal = 1;
184	<	//       simError();
185	<	//     }
128	>	// initialize the Fortran
129
130	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
131	<	simnfo->usePBC = the_globals->getPBC();
189	<
190	<	int usesDipoles = 0;
191	<	switch( ffCase ){
130	>	initFortran();
131	>	}
132
193	–	case FF_DUFF:
194	–	the_ff = new DUFF();
195	–	usesDipoles = 1;
196	–	break;
133
134	<	case FF_LJ:
135	<	the_ff = new LJFF();
136	<	break;
134	>	void SimSetup::makeMolecules(void){
135	>	int k;
136	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
137	>	molInit molInfo;
138	>	DirectionalAtom* dAtom;
139	>	LinkedAssign* extras;
140	>	LinkedAssign* current_extra;
141	>	AtomStamp* currentAtom;
142	>	BondStamp* currentBond;
143	>	BendStamp* currentBend;
144	>	TorsionStamp* currentTorsion;
145
146	<	default:
147	<	sprintf( painCave.errMsg,
148	<	"SimSetup Error. Unrecognized force field in case statement.\n");
205	<	painCave.isFatal = 1;
206	<	simError();
207	<	}
146	>	bond_pair* theBonds;
147	>	bend_set* theBends;
148	>	torsion_set* theTorsions;
149
209	–	#ifdef IS_MPI
210	–	strcpy( checkPointMsg, "ForceField creation successful" );
211	–	MPIcheckPoint();
212	–	#endif // is_mpi
150
151	<	// get the components and calculate the tot_nMol and indvidual n_mol
215	<	the_components = the_globals->getComponents();
216	<	components_nmol = new int[n_components];
217	<	comp_stamps = new MoleculeStamp*[n_components];
151	>	//init the forceField paramters
152
153	<	if( !the_globals->haveNMol() ){
220	<	// we don't have the total number of molecules, so we assume it is
221	<	// given in each component
153	>	the_ff->readParams();
154
223	–	tot_nmol = 0;
224	–	for( i=0; i<n_components; i++ ){
155
156	<	if( !the_components[i]->haveNMol() ){
227	<	// we have a problem
228	<	sprintf( painCave.errMsg,
229	<	"SimSetup Error. No global NMol or component NMol"
230	<	" given. Cannot calculate the number of atoms.\n" );
231	<	painCave.isFatal = 1;
232	<	simError();
233	<	}
156	>	// init the atoms
157
158	<	tot_nmol += the_components[i]->getNMol();
236	<	components_nmol[i] = the_components[i]->getNMol();
237	<	}
238	<	}
239	<	else{
240	<	sprintf( painCave.errMsg,
241	<	"SimSetup error.\n"
242	<	"\tSorry, the ability to specify total"
243	<	" nMols and then give molfractions in the components\n"
244	<	"\tis not currently supported."
245	<	" Please give nMol in the components.\n" );
246	<	painCave.isFatal = 1;
247	<	simError();
248	<
249	<
250	<	//     tot_nmol = the_globals->getNMol();
251	<
252	<	//   //we have the total number of molecules, now we check for molfractions
253	<	//     for( i=0; i<n_components; i++ ){
254	<
255	<	//       if( !the_components[i]->haveMolFraction() ){
256	<
257	<	//  if( !the_components[i]->haveNMol() ){
258	<	//    //we have a problem
259	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
260	<	//              << " nMol was given in component
261	<
262	<	}
158	>	double ux, uy, uz, u, uSqr;
159
160	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
266	<	MPIcheckPoint();
267	<	#endif // is_mpi
160	>	for (k = 0; k < nInfo; k++){
161	>	the_ff->setSimInfo(&(info[k]));
162
163	<	// make an array of molecule stamps that match the components used.
164	<	// also extract the used stamps out into a separate linked list
163	>	atomOffset = 0;
164	>	excludeOffset = 0;
165	>	for (i = 0; i < info[k].n_mol; i++){
166	>	stampID = info[k].molecules[i].getStampID();
167
168	<	simnfo->nComponents = n_components;
169	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
277	<	char* id;
278	<	LinkedMolStamp* headStamp = simnfo->headStamp;
279	<	LinkedMolStamp* currentStamp = NULL;
280	<	for( i=0; i<n_components; i++ ){
168	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
169	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
170	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
171	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
172	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
173
174	<	id = the_components[i]->getType();
175	<	comp_stamps[i] = NULL;
176	<
177	<	// check to make sure the component isn't already in the list
174	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
175	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
176	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
177	>	molInfo.myBends = new Bend * [molInfo.nBends];
178	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
179
180	<	comp_stamps[i] = headStamp->match( id );
181	<	if( comp_stamps[i] == NULL ){
182	<
290	<	// extract the component from the list;
291	<
292	<	currentStamp = the_stamps->extractMolStamp( id );
293	<	if( currentStamp == NULL ){
294	<	sprintf( painCave.errMsg,
295	<	"SimSetup error: Component \"%s\" was not found in the "
296	<	"list of declared molecules\n",
297	<	id );
298	<	painCave.isFatal = 1;
299	<	simError();
300	<	}
301	<
302	<	headStamp->add( currentStamp );
303	<	comp_stamps[i] = headStamp->match( id );
304	<	}
305	<	}
180	>	theBonds = new bond_pair[molInfo.nBonds];
181	>	theBends = new bend_set[molInfo.nBends];
182	>	theTorsions = new torsion_set[molInfo.nTorsions];
183
184	<	#ifdef IS_MPI
308	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
309	<	MPIcheckPoint();
310	<	#endif // is_mpi
311	<
184	>	// make the Atoms
185
186	+	for (j = 0; j < molInfo.nAtoms; j++){
187	+	currentAtom = comp_stamps[stampID]->getAtom(j);
188	+	if (currentAtom->haveOrientation()){
189	+	dAtom = new DirectionalAtom((j + atomOffset),
190	+	info[k].getConfiguration());
191	+	info[k].n_oriented++;
192	+	molInfo.myAtoms[j] = dAtom;
193
194	+	ux = currentAtom->getOrntX();
195	+	uy = currentAtom->getOrntY();
196	+	uz = currentAtom->getOrntZ();
197
198	<	// caclulate the number of atoms, bonds, bends and torsions
198	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
199
200	<	tot_atoms = 0;
201	<	tot_bonds = 0;
202	<	tot_bends = 0;
203	<	tot_torsions = 0;
321	<	for( i=0; i<n_components; i++ ){
322	<
323	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
324	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
325	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
326	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
327	<	}
200	>	u = sqrt(uSqr);
201	>	ux = ux / u;
202	>	uy = uy / u;
203	>	uz = uz / u;
204
205	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
205	>	dAtom->setSUx(ux);
206	>	dAtom->setSUy(uy);
207	>	dAtom->setSUz(uz);
208	>	}
209	>	else{
210	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
211	>	info[k].getConfiguration());
212	>	}
213	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
214
331	–	simnfo->n_atoms = tot_atoms;
332	–	simnfo->n_bonds = tot_bonds;
333	–	simnfo->n_bends = tot_bends;
334	–	simnfo->n_torsions = tot_torsions;
335	–	simnfo->n_SRI = tot_SRI;
336	–	simnfo->n_mol = tot_nmol;
337	–
338	–	simnfo->molMembershipArray = new int[tot_atoms];
339	–
215		#ifdef IS_MPI
216
217	<	// divide the molecules among processors here.
343	<
344	<	mpiSim = new mpiSimulation( simnfo );
345	<
346	<	globalIndex = mpiSim->divideLabor();
217	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
218
219	<	// set up the local variables
220	<
350	<	int localMol, allMol;
351	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
219	>	#endif // is_mpi
220	>	}
221
222	<	int* mol2proc = mpiSim->getMolToProcMap();
223	<	int* molCompType = mpiSim->getMolComponentType();
224	<
225	<	allMol = 0;
226	<	localMol = 0;
358	<	local_atoms = 0;
359	<	local_bonds = 0;
360	<	local_bends = 0;
361	<	local_torsions = 0;
362	<	globalAtomIndex = 0;
222	>	// make the bonds
223	>	for (j = 0; j < molInfo.nBonds; j++){
224	>	currentBond = comp_stamps[stampID]->getBond(j);
225	>	theBonds[j].a = currentBond->getA() + atomOffset;
226	>	theBonds[j].b = currentBond->getB() + atomOffset;
227
228	+	exI = theBonds[j].a;
229	+	exJ = theBonds[j].b;
230
231	<	for( i=0; i<n_components; i++ ){
231	>	// exclude_I must always be the smaller of the pair
232	>	if (exI > exJ){
233	>	tempEx = exI;
234	>	exI = exJ;
235	>	exJ = tempEx;
236	>	}
237	>	#ifdef IS_MPI
238	>	tempEx = exI;
239	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
240	>	tempEx = exJ;
241	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
242
243	<	for( j=0; j<components_nmol[i]; j++ ){
244	<
245	<	if( mol2proc[allMol] == worldRank ){
246	<
247	<	local_atoms +=    comp_stamps[i]->getNAtoms();
372	<	local_bonds +=    comp_stamps[i]->getNBonds();
373	<	local_bends +=    comp_stamps[i]->getNBends();
374	<	local_torsions += comp_stamps[i]->getNTorsions();
375	<	localMol++;
376	<	}
377	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
378	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
379	<	globalAtomIndex++;
243	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
244	>	#else  // isn't MPI
245	>
246	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
247	>	#endif  //is_mpi
248		}
249	+	excludeOffset += molInfo.nBonds;
250
251	<	allMol++;
252	<	}
253	<	}
254	<	local_SRI = local_bonds + local_bends + local_torsions;
255	<
256	<	simnfo->n_atoms = mpiSim->getMyNlocal();
388	<
389	<	if( local_atoms != simnfo->n_atoms ){
390	<	sprintf( painCave.errMsg,
391	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
392	<	" localAtom (%d) are not equal.\n",
393	<	simnfo->n_atoms,
394	<	local_atoms );
395	<	painCave.isFatal = 1;
396	<	simError();
397	<	}
251	>	//make the bends
252	>	for (j = 0; j < molInfo.nBends; j++){
253	>	currentBend = comp_stamps[stampID]->getBend(j);
254	>	theBends[j].a = currentBend->getA() + atomOffset;
255	>	theBends[j].b = currentBend->getB() + atomOffset;
256	>	theBends[j].c = currentBend->getC() + atomOffset;
257
258	<	simnfo->n_bonds = local_bonds;
259	<	simnfo->n_bends = local_bends;
260	<	simnfo->n_torsions = local_torsions;
402	<	simnfo->n_SRI = local_SRI;
403	<	simnfo->n_mol = localMol;
258	>	if (currentBend->haveExtras()){
259	>	extras = currentBend->getExtras();
260	>	current_extra = extras;
261
262	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
263	<	MPIcheckPoint();
264	<
265	<
266	<	#endif // is_mpi
267	<
262	>	while (current_extra != NULL){
263	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
264	>	switch (current_extra->getType()){
265	>	case 0:
266	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
267	>	theBends[j].isGhost = 1;
268	>	break;
269
270	<	// create the atom and short range interaction arrays
270	>	case 1:
271	>	theBends[j].ghost = (int) current_extra->getDouble() +
272	>	atomOffset;
273	>	theBends[j].isGhost = 1;
274	>	break;
275
276	<	Atom::createArrays(simnfo->n_atoms);
277	<	the_atoms = new Atom*[simnfo->n_atoms];
278	<	the_molecules = new Molecule[simnfo->n_mol];
279	<	int molIndex;
276	>	default:
277	>	sprintf(painCave.errMsg,
278	>	"SimSetup Error: ghostVectorSource was neither a "
279	>	"double nor an int.\n"
280	>	"-->Bend[%d] in %s\n",
281	>	j, comp_stamps[stampID]->getID());
282	>	painCave.isFatal = 1;
283	>	simError();
284	>	}
285	>	}
286	>	else{
287	>	sprintf(painCave.errMsg,
288	>	"SimSetup Error: unhandled bend assignment:\n"
289	>	"    -->%s in Bend[%d] in %s\n",
290	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
291	>	painCave.isFatal = 1;
292	>	simError();
293	>	}
294
295	<	// initialize the molecule's stampID's
295	>	current_extra = current_extra->getNext();
296	>	}
297	>	}
298
299	+	if (!theBends[j].isGhost){
300	+	exI = theBends[j].a;
301	+	exJ = theBends[j].c;
302	+	}
303	+	else{
304	+	exI = theBends[j].a;
305	+	exJ = theBends[j].b;
306	+	}
307	+
308	+	// exclude_I must always be the smaller of the pair
309	+	if (exI > exJ){
310	+	tempEx = exI;
311	+	exI = exJ;
312	+	exJ = tempEx;
313	+	}
314		#ifdef IS_MPI
315	<
315	>	tempEx = exI;
316	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
317	>	tempEx = exJ;
318	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
319
320	<	molIndex = 0;
321	<	for(i=0; i<mpiSim->getTotNmol(); i++){
322	<
323	<	if(mol2proc[i] == worldRank ){
428	<	the_molecules[molIndex].setStampID( molCompType[i] );
429	<	the_molecules[molIndex].setMyIndex( molIndex );
430	<	the_molecules[molIndex].setGlobalIndex( i );
431	<	molIndex++;
432	<	}
433	<	}
434	<
435	<	#else // is_mpi
436	<
437	<	molIndex = 0;
438	<	globalAtomIndex = 0;
439	<	for(i=0; i<n_components; i++){
440	<	for(j=0; j<components_nmol[i]; j++ ){
441	<	the_molecules[molIndex].setStampID( i );
442	<	the_molecules[molIndex].setMyIndex( molIndex );
443	<	the_molecules[molIndex].setGlobalIndex( molIndex );
444	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
445	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
446	<	globalAtomIndex++;
320	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
321	>	#else  // isn't MPI
322	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
323	>	#endif  //is_mpi
324		}
325	<	molIndex++;
449	<	}
450	<	}
451	<
325	>	excludeOffset += molInfo.nBends;
326
327	<	#endif // is_mpi
327	>	for (j = 0; j < molInfo.nTorsions; j++){
328	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
329	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
330	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
331	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
332	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
333
334	+	exI = theTorsions[j].a;
335	+	exJ = theTorsions[j].d;
336
337	<	if( simnfo->n_SRI ){
338	<
339	<	Exclude::createArray(simnfo->n_SRI);
340	<	the_excludes = new Exclude*[simnfo->n_SRI];
341	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
342	<	simnfo->globalExcludes = new int;
343	<	simnfo->n_exclude = simnfo->n_SRI;
344	<	}
345	<	else{
346	<
347	<	Exclude::createArray( 1 );
467	<	the_excludes = new Exclude*;
468	<	the_excludes[0] = new Exclude(0);
469	<	the_excludes[0]->setPair( 0,0 );
470	<	simnfo->globalExcludes = new int;
471	<	simnfo->globalExcludes[0] = 0;
472	<	simnfo->n_exclude = 0;
473	<	}
337	>	// exclude_I must always be the smaller of the pair
338	>	if (exI > exJ){
339	>	tempEx = exI;
340	>	exI = exJ;
341	>	exJ = tempEx;
342	>	}
343	>	#ifdef IS_MPI
344	>	tempEx = exI;
345	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346	>	tempEx = exJ;
347	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
348
349	<	// set the arrays into the SimInfo object
349	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
350	>	#else  // isn't MPI
351	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
352	>	#endif  //is_mpi
353	>	}
354	>	excludeOffset += molInfo.nTorsions;
355
477	–	simnfo->atoms = the_atoms;
478	–	simnfo->molecules = the_molecules;
479	–	simnfo->nGlobalExcludes = 0;
480	–	simnfo->excludes = the_excludes;
356
357	+	// send the arrays off to the forceField for init.
358
359	<	// get some of the tricky things that may still be in the globals
359	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
360	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
361	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
362	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
363	>	theTorsions);
364
485	–	double boxVector[3];
486	–	if( the_globals->haveBox() ){
487	–	boxVector[0] = the_globals->getBox();
488	–	boxVector[1] = the_globals->getBox();
489	–	boxVector[2] = the_globals->getBox();
490	–
491	–	simnfo->setBox( boxVector );
492	–	}
493	–	else if( the_globals->haveDensity() ){
365
366	<	double vol;
496	<	vol = (double)tot_nmol / the_globals->getDensity();
497	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
498	<	boxVector[1] = boxVector[0];
499	<	boxVector[2] = boxVector[0];
366	>	info[k].molecules[i].initialize(molInfo);
367
501	–	simnfo->setBox( boxVector );
502	–	}
503	–	else{
504	–	if( !the_globals->haveBoxX() ){
505	–	sprintf( painCave.errMsg,
506	–	"SimSetup error, no periodic BoxX size given.\n" );
507	–	painCave.isFatal = 1;
508	–	simError();
509	–	}
510	–	boxVector[0] = the_globals->getBoxX();
368
369	<	if( !the_globals->haveBoxY() ){
370	<	sprintf( painCave.errMsg,
371	<	"SimSetup error, no periodic BoxY size given.\n" );
372	<	painCave.isFatal = 1;
516	<	simError();
369	>	atomOffset += molInfo.nAtoms;
370	>	delete[] theBonds;
371	>	delete[] theBends;
372	>	delete[] theTorsions;
373		}
518	–	boxVector[1] = the_globals->getBoxY();
519	–
520	–	if( !the_globals->haveBoxZ() ){
521	–	sprintf( painCave.errMsg,
522	–	"SimSetup error, no periodic BoxZ size given.\n" );
523	–	painCave.isFatal = 1;
524	–	simError();
525	–	}
526	–	boxVector[2] = the_globals->getBoxZ();
527	–
528	–	simnfo->setBox( boxVector );
374		}
375
376		#ifdef IS_MPI
377	<	strcpy( checkPointMsg, "Box size set up" );
377	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
378		MPIcheckPoint();
379		#endif // is_mpi
380
381	+	// clean up the forcefield
382
383	<	// initialize the arrays
383	>	the_ff->calcRcut();
384	>	the_ff->cleanMe();
385	>	}
386
387	<	the_ff->setSimInfo( simnfo );
387	>	void SimSetup::initFromBass(void){
388	>	int i, j, k;
389	>	int n_cells;
390	>	double cellx, celly, cellz;
391	>	double temp1, temp2, temp3;
392	>	int n_per_extra;
393	>	int n_extra;
394	>	int have_extra, done;
395
396	<	makeMolecules();
397	<	simnfo->identArray = new int[simnfo->n_atoms];
398	<	for(i=0; i<simnfo->n_atoms; i++){
399	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
545	<	}
546	<
547	<	if (the_globals->getUseRF() ) {
548	<	simnfo->useReactionField = 1;
549	<
550	<	if( !the_globals->haveECR() ){
551	<	sprintf( painCave.errMsg,
552	<	"SimSetup Warning: using default value of 1/2 the smallest "
553	<	"box length for the electrostaticCutoffRadius.\n"
554	<	"I hope you have a very fast processor!\n");
555	<	painCave.isFatal = 0;
556	<	simError();
557	<	double smallest;
558	<	smallest = simnfo->boxLx;
559	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
560	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
561	<	simnfo->ecr = 0.5 * smallest;
562	<	} else {
563	<	simnfo->ecr        = the_globals->getECR();
564	<	}
396	>	double vel[3];
397	>	vel[0] = 0.0;
398	>	vel[1] = 0.0;
399	>	vel[2] = 0.0;
400
401	<	if( !the_globals->haveEST() ){
402	<	sprintf( painCave.errMsg,
403	<	"SimSetup Warning: using default value of 0.05 * the "
404	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
405	<	);
406	<	painCave.isFatal = 0;
407	<	simError();
408	<	simnfo->est = 0.05 * simnfo->ecr;
409	<	} else {
410	<	simnfo->est        = the_globals->getEST();
411	<	}
412	<
413	<	if(!the_globals->haveDielectric() ){
414	<	sprintf( painCave.errMsg,
415	<	"SimSetup Error: You are trying to use Reaction Field without"
416	<	"setting a dielectric constant!\n"
417	<	);
401	>	temp1 = (double) tot_nmol / 4.0;
402	>	temp2 = pow(temp1, (1.0 / 3.0));
403	>	temp3 = ceil(temp2);
404	>
405	>	have_extra = 0;
406	>	if (temp2 < temp3){
407	>	// we have a non-complete lattice
408	>	have_extra = 1;
409	>
410	>	n_cells = (int) temp3 - 1;
411	>	cellx = info[0].boxL[0] / temp3;
412	>	celly = info[0].boxL[1] / temp3;
413	>	cellz = info[0].boxL[2] / temp3;
414	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
415	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
416	>	n_per_extra = (int) ceil(temp1);
417	>
418	>	if (n_per_extra > 4){
419	>	sprintf(painCave.errMsg,
420	>	"SimSetup error. There has been an error in constructing"
421	>	" the non-complete lattice.\n");
422		painCave.isFatal = 1;
423		simError();
424		}
425	<	simnfo->dielectric = the_globals->getDielectric();
426	<	} else {
427	<	if (usesDipoles) {
428	<
429	<	if( !the_globals->haveECR() ){
430	<	sprintf( painCave.errMsg,
431	<	"SimSetup Warning: using default value of 1/2 the smallest "
432	<	"box length for the electrostaticCutoffRadius.\n"
433	<	"I hope you have a very fast processor!\n");
434	<	painCave.isFatal = 0;
435	<	simError();
436	<	double smallest;
437	<	smallest = simnfo->boxLx;
438	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
439	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
440	<	simnfo->ecr = 0.5 * smallest;
441	<	} else {
442	<	simnfo->ecr        = the_globals->getECR();
425	>	}
426	>	else{
427	>	n_cells = (int) temp3;
428	>	cellx = info[0].boxL[0] / temp3;
429	>	celly = info[0].boxL[1] / temp3;
430	>	cellz = info[0].boxL[2] / temp3;
431	>	}
432	>
433	>	current_mol = 0;
434	>	current_comp_mol = 0;
435	>	current_comp = 0;
436	>	current_atom_ndx = 0;
437	>
438	>	for (i = 0; i < n_cells ; i++){
439	>	for (j = 0; j < n_cells; j++){
440	>	for (k = 0; k < n_cells; k++){
441	>	makeElement(i * cellx, j * celly, k * cellz);
442	>
443	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
444	>
445	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
446	>
447	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
448		}
605	–
606	–	if( !the_globals->haveEST() ){
607	–	sprintf( painCave.errMsg,
608	–	"SimSetup Warning: using default value of 5%% of the "
609	–	"electrostaticCutoffRadius for the "
610	–	"electrostaticSkinThickness\n"
611	–	);
612	–	painCave.isFatal = 0;
613	–	simError();
614	–	simnfo->est = 0.05 * simnfo->ecr;
615	–	} else {
616	–	simnfo->est        = the_globals->getEST();
617	–	}
449		}
450	<	}
450	>	}
451
452	<	#ifdef IS_MPI
453	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
623	<	MPIcheckPoint();
624	<	#endif // is_mpi
452	>	if (have_extra){
453	>	done = 0;
454
455	<	if( the_globals->haveInitialConfig() ){
456	<
457	<	InitializeFromFile* fileInit;
458	<	#ifdef IS_MPI // is_mpi
459	<	if( worldRank == 0 ){
460	<	#endif //is_mpi
461	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
462	<	#ifdef IS_MPI
463	<	}else fileInit = new InitializeFromFile( NULL );
464	<	#endif
465	<	fileInit->read_xyz( simnfo ); // default velocities on
455	>	int start_ndx;
456	>	for (i = 0; i < (n_cells + 1) && !done; i++){
457	>	for (j = 0; j < (n_cells + 1) && !done; j++){
458	>	if (i < n_cells){
459	>	if (j < n_cells){
460	>	start_ndx = n_cells;
461	>	}
462	>	else
463	>	start_ndx = 0;
464	>	}
465	>	else
466	>	start_ndx = 0;
467
468	<	delete fileInit;
469	<	}
470	<	else{
468	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
469	>	makeElement(i * cellx, j * celly, k * cellz);
470	>	done = (current_mol >= tot_nmol);
471
472	<	#ifdef IS_MPI
472	>	if (!done && n_per_extra > 1){
473	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
474	>	k * cellz);
475	>	done = (current_mol >= tot_nmol);
476	>	}
477
478	<	// no init from bass
479	<
480	<	sprintf( painCave.errMsg,
481	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
482	<	painCave.isFatal;
649	<	simError();
650	<
651	<	#else
478	>	if (!done && n_per_extra > 2){
479	>	makeElement(i * cellx, j * celly + 0.5 * celly,
480	>	k * cellz + 0.5 * cellz);
481	>	done = (current_mol >= tot_nmol);
482	>	}
483
484	<	initFromBass();
485	<
486	<
487	<	#endif
488	<	}
489	<
659	<	#ifdef IS_MPI
660	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
661	<	MPIcheckPoint();
662	<	#endif // is_mpi
663	<
664	<
665	<
666	<
667	<
668	<
669	<
670	<	#ifdef IS_MPI
671	<	if( worldRank == 0 ){
672	<	#endif // is_mpi
673	<
674	<	if( the_globals->haveFinalConfig() ){
675	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
676	<	}
677	<	else{
678	<	strcpy( simnfo->finalName, inFileName );
679	<	char* endTest;
680	<	int nameLength = strlen( simnfo->finalName );
681	<	endTest = &(simnfo->finalName[nameLength - 5]);
682	<	if( !strcmp( endTest, ".bass" ) ){
683	<	strcpy( endTest, ".eor" );
484	>	if (!done && n_per_extra > 3){
485	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
486	>	k * cellz + 0.5 * cellz);
487	>	done = (current_mol >= tot_nmol);
488	>	}
489	>	}
490		}
685	–	else if( !strcmp( endTest, ".BASS" ) ){
686	–	strcpy( endTest, ".eor" );
687	–	}
688	–	else{
689	–	endTest = &(simnfo->finalName[nameLength - 4]);
690	–	if( !strcmp( endTest, ".bss" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else if( !strcmp( endTest, ".mdl" ) ){
694	–	strcpy( endTest, ".eor" );
695	–	}
696	–	else{
697	–	strcat( simnfo->finalName, ".eor" );
698	–	}
699	–	}
491		}
701	–
702	–	// make the sample and status out names
703	–
704	–	strcpy( simnfo->sampleName, inFileName );
705	–	char* endTest;
706	–	int nameLength = strlen( simnfo->sampleName );
707	–	endTest = &(simnfo->sampleName[nameLength - 5]);
708	–	if( !strcmp( endTest, ".bass" ) ){
709	–	strcpy( endTest, ".dump" );
710	–	}
711	–	else if( !strcmp( endTest, ".BASS" ) ){
712	–	strcpy( endTest, ".dump" );
713	–	}
714	–	else{
715	–	endTest = &(simnfo->sampleName[nameLength - 4]);
716	–	if( !strcmp( endTest, ".bss" ) ){
717	–	strcpy( endTest, ".dump" );
718	–	}
719	–	else if( !strcmp( endTest, ".mdl" ) ){
720	–	strcpy( endTest, ".dump" );
721	–	}
722	–	else{
723	–	strcat( simnfo->sampleName, ".dump" );
724	–	}
725	–	}
726	–
727	–	strcpy( simnfo->statusName, inFileName );
728	–	nameLength = strlen( simnfo->statusName );
729	–	endTest = &(simnfo->statusName[nameLength - 5]);
730	–	if( !strcmp( endTest, ".bass" ) ){
731	–	strcpy( endTest, ".stat" );
732	–	}
733	–	else if( !strcmp( endTest, ".BASS" ) ){
734	–	strcpy( endTest, ".stat" );
735	–	}
736	–	else{
737	–	endTest = &(simnfo->statusName[nameLength - 4]);
738	–	if( !strcmp( endTest, ".bss" ) ){
739	–	strcpy( endTest, ".stat" );
740	–	}
741	–	else if( !strcmp( endTest, ".mdl" ) ){
742	–	strcpy( endTest, ".stat" );
743	–	}
744	–	else{
745	–	strcat( simnfo->statusName, ".stat" );
746	–	}
747	–	}
748	–
749	–	#ifdef IS_MPI
492		}
751	–	#endif // is_mpi
752	–
753	–	// set the status, sample, and themal kick times
754	–
755	–	if( the_globals->haveSampleTime() ){
756	–	simnfo->sampleTime = the_globals->getSampleTime();
757	–	simnfo->statusTime = simnfo->sampleTime;
758	–	simnfo->thermalTime = simnfo->sampleTime;
759	–	}
760	–	else{
761	–	simnfo->sampleTime = the_globals->getRunTime();
762	–	simnfo->statusTime = simnfo->sampleTime;
763	–	simnfo->thermalTime = simnfo->sampleTime;
764	–	}
493
494	<	if( the_globals->haveStatusTime() ){
495	<	simnfo->statusTime = the_globals->getStatusTime();
494	>	for (i = 0; i < info[0].n_atoms; i++){
495	>	info[0].atoms[i]->setVel(vel);
496		}
497	+	}
498
499	<	if( the_globals->haveThermalTime() ){
500	<	simnfo->thermalTime = the_globals->getThermalTime();
501	<	}
499	>	void SimSetup::makeElement(double x, double y, double z){
500	>	int k;
501	>	AtomStamp* current_atom;
502	>	DirectionalAtom* dAtom;
503	>	double rotMat[3][3];
504	>	double pos[3];
505
506	<	// check for the temperature set flag
507	<
508	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
509	<
510	<
511	<	// make the integrator
512	<
513	<
514	<	NVT* myNVT = NULL;
783	<	switch( ensembleCase ){
784	<
785	<	case NVE_ENS:
786	<	new NVE( simnfo, the_ff );
787	<	break;
788	<
789	<	case NVT_ENS:
790	<	myNVT = new NVT( simnfo, the_ff );
791	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
792	<
793	<	if (the_globals->haveTauThermostat())
794	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
795	<	//     else if (the_globals->haveQmass())
796	<	//       myNVT->setQmass(the_globals->getQmass());
797	<	else {
798	<	sprintf( painCave.errMsg,
799	<	"SimSetup error: If you use the NVT\n"
800	<	"    ensemble, you must set either tauThermostat or qMass.\n"
801	<	"    Neither of these was found in the BASS file.\n");
506	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
507	>	current_atom = comp_stamps[current_comp]->getAtom(k);
508	>	if (!current_atom->havePosition()){
509	>	sprintf(painCave.errMsg,
510	>	"SimSetup:initFromBass error.\n"
511	>	"\tComponent %s, atom %s does not have a position specified.\n"
512	>	"\tThe initialization routine is unable to give a start"
513	>	" position.\n",
514	>	comp_stamps[current_comp]->getID(), current_atom->getType());
515		painCave.isFatal = 1;
516		simError();
517		}
805	–	break;
518
519	<	default:
520	<	sprintf( painCave.errMsg,
521	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
810	<	painCave.isFatal = 1;
811	<	simError();
812	<	}
519	>	pos[0] = x + current_atom->getPosX();
520	>	pos[1] = y + current_atom->getPosY();
521	>	pos[2] = z + current_atom->getPosZ();
522
523	+	info[0].atoms[current_atom_ndx]->setPos(pos);
524
525	<	#ifdef IS_MPI
526	<	mpiSim->mpiRefresh();
817	<	#endif
525	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
526	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
527
528	<	// initialize the Fortran
528	>	rotMat[0][0] = 1.0;
529	>	rotMat[0][1] = 0.0;
530	>	rotMat[0][2] = 0.0;
531
532	+	rotMat[1][0] = 0.0;
533	+	rotMat[1][1] = 1.0;
534	+	rotMat[1][2] = 0.0;
535
536	<	simnfo->refreshSim();
537	<
538	<	if( !strcmp( simnfo->mixingRule, "standard") ){
539	<	the_ff->initForceField( LB_MIXING_RULE );
536	>	rotMat[2][0] = 0.0;
537	>	rotMat[2][1] = 0.0;
538	>	rotMat[2][2] = 1.0;
539	>
540	>	dAtom->setA(rotMat);
541	>	}
542	>
543	>	current_atom_ndx++;
544		}
545	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
546	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
545	>
546	>	current_mol++;
547	>	current_comp_mol++;
548	>
549	>	if (current_comp_mol >= components_nmol[current_comp]){
550	>	current_comp_mol = 0;
551	>	current_comp++;
552		}
553	<	else{
554	<	sprintf( painCave.errMsg,
555	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
556	<	simnfo->mixingRule );
557	<	painCave.isFatal = 1;
558	<	simError();
553	>	}
554	>
555	>
556	>	void SimSetup::gatherInfo(void){
557	>	int i;
558	>
559	>	ensembleCase = -1;
560	>	ffCase = -1;
561	>
562	>	// set the easy ones first
563	>
564	>	for (i = 0; i < nInfo; i++){
565	>	info[i].target_temp = globals->getTargetTemp();
566	>	info[i].dt = globals->getDt();
567	>	info[i].run_time = globals->getRunTime();
568		}
569	+	n_components = globals->getNComponents();
570
571
572	<	#ifdef IS_MPI
840	<	strcpy( checkPointMsg,
841	<	"Successfully intialized the mixingRule for Fortran." );
842	<	MPIcheckPoint();
843	<	#endif // is_mpi
844	<	}
572	>	// get the forceField
573
574	+	strcpy(force_field, globals->getForceField());
575
576	<	void SimSetup::makeMolecules( void ){
576	>	if (!strcasecmp(force_field, "DUFF")){
577	>	ffCase = FF_DUFF;
578	>	}
579	>	else if (!strcasecmp(force_field, "LJ")){
580	>	ffCase = FF_LJ;
581	>	}
582	>	else if (!strcasecmp(force_field, "EAM")){
583	>	ffCase = FF_EAM;
584	>	}
585	>	else{
586	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
587	>	force_field);
588	>	painCave.isFatal = 1;
589	>	simError();
590	>	}
591
592	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
850	<	molInit info;
851	<	DirectionalAtom* dAtom;
852	<	LinkedAssign* extras;
853	<	LinkedAssign* current_extra;
854	<	AtomStamp* currentAtom;
855	<	BondStamp* currentBond;
856	<	BendStamp* currentBend;
857	<	TorsionStamp* currentTorsion;
592	>	// get the ensemble
593
594	<	bond_pair* theBonds;
860	<	bend_set* theBends;
861	<	torsion_set* theTorsions;
594	>	strcpy(ensemble, globals->getEnsemble());
595
596	<
597	<	//init the forceField paramters
596	>	if (!strcasecmp(ensemble, "NVE")){
597	>	ensembleCase = NVE_ENS;
598	>	}
599	>	else if (!strcasecmp(ensemble, "NVT")){
600	>	ensembleCase = NVT_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
603	>	ensembleCase = NPTi_ENS;
604	>	}
605	>	else if (!strcasecmp(ensemble, "NPTf")){
606	>	ensembleCase = NPTf_ENS;
607	>	}
608	>	else if (!strcasecmp(ensemble, "NPTxyz")){
609	>	ensembleCase = NPTxyz_ENS;
610	>	}
611	>	else{
612	>	sprintf(painCave.errMsg,
613	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
614	>	"reverting to NVE for this simulation.\n",
615	>	ensemble);
616	>	painCave.isFatal = 0;
617	>	simError();
618	>	strcpy(ensemble, "NVE");
619	>	ensembleCase = NVE_ENS;
620	>	}
621
622	<	the_ff->readParams();
622	>	for (i = 0; i < nInfo; i++){
623	>	strcpy(info[i].ensemble, ensemble);
624
625	<
869	<	// init the atoms
625	>	// get the mixing rule
626
627	<	double ux, uy, uz, u, uSqr;
628	<
629	<	atomOffset = 0;
874	<	excludeOffset = 0;
875	<	for(i=0; i<simnfo->n_mol; i++){
876	<
877	<	stampID = the_molecules[i].getStampID();
627	>	strcpy(info[i].mixingRule, globals->getMixingRule());
628	>	info[i].usePBC = globals->getPBC();
629	>	}
630
631	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
880	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
881	<	info.nBends    = comp_stamps[stampID]->getNBends();
882	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
883	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
631	>	// get the components and calculate the tot_nMol and indvidual n_mol
632
633	<	info.myAtoms = &the_atoms[atomOffset];
634	<	info.myExcludes = &the_excludes[excludeOffset];
887	<	info.myBonds = new Bond*[info.nBonds];
888	<	info.myBends = new Bend*[info.nBends];
889	<	info.myTorsions = new Torsion*[info.nTorsions];
633	>	the_components = globals->getComponents();
634	>	components_nmol = new int[n_components];
635
891	–	theBonds = new bond_pair[info.nBonds];
892	–	theBends = new bend_set[info.nBends];
893	–	theTorsions = new torsion_set[info.nTorsions];
894	–
895	–	// make the Atoms
896	–
897	–	for(j=0; j<info.nAtoms; j++){
898	–
899	–	currentAtom = comp_stamps[stampID]->getAtom( j );
900	–	if( currentAtom->haveOrientation() ){
901	–
902	–	dAtom = new DirectionalAtom(j + atomOffset);
903	–	simnfo->n_oriented++;
904	–	info.myAtoms[j] = dAtom;
905	–
906	–	ux = currentAtom->getOrntX();
907	–	uy = currentAtom->getOrntY();
908	–	uz = currentAtom->getOrntZ();
909	–
910	–	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
911	–
912	–	u = sqrt( uSqr );
913	–	ux = ux / u;
914	–	uy = uy / u;
915	–	uz = uz / u;
916	–
917	–	dAtom->setSUx( ux );
918	–	dAtom->setSUy( uy );
919	–	dAtom->setSUz( uz );
920	–	}
921	–	else{
922	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
923	–	}
924	–	info.myAtoms[j]->setType( currentAtom->getType() );
925	–
926	–	#ifdef IS_MPI
927	–
928	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
929	–
930	–	#endif // is_mpi
931	–	}
932	–
933	–	// make the bonds
934	–	for(j=0; j<info.nBonds; j++){
935	–
936	–	currentBond = comp_stamps[stampID]->getBond( j );
937	–	theBonds[j].a = currentBond->getA() + atomOffset;
938	–	theBonds[j].b = currentBond->getB() + atomOffset;
636
637	<	exI = theBonds[j].a;
638	<	exJ = theBonds[j].b;
637	>	if (!globals->haveNMol()){
638	>	// we don't have the total number of molecules, so we assume it is
639	>	// given in each component
640
641	<	// exclude_I must always be the smaller of the pair
642	<	if( exI > exJ ){
643	<	tempEx = exI;
644	<	exI = exJ;
645	<	exJ = tempEx;
641	>	tot_nmol = 0;
642	>	for (i = 0; i < n_components; i++){
643	>	if (!the_components[i]->haveNMol()){
644	>	// we have a problem
645	>	sprintf(painCave.errMsg,
646	>	"SimSetup Error. No global NMol or component NMol"
647	>	" given. Cannot calculate the number of atoms.\n");
648	>	painCave.isFatal = 1;
649	>	simError();
650		}
949	–	#ifdef IS_MPI
950	–	tempEx = exI;
951	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
952	–	tempEx = exJ;
953	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
954	–
955	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
956	–	#else  // isn't MPI
651
652	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
653	<	#endif  //is_mpi
652	>	tot_nmol += the_components[i]->getNMol();
653	>	components_nmol[i] = the_components[i]->getNMol();
654		}
655	<	excludeOffset += info.nBonds;
655	>	}
656	>	else{
657	>	sprintf(painCave.errMsg,
658	>	"SimSetup error.\n"
659	>	"\tSorry, the ability to specify total"
660	>	" nMols and then give molfractions in the components\n"
661	>	"\tis not currently supported."
662	>	" Please give nMol in the components.\n");
663	>	painCave.isFatal = 1;
664	>	simError();
665	>	}
666
667	<	//make the bends
668	<	for(j=0; j<info.nBends; j++){
669	<
670	<	currentBend = comp_stamps[stampID]->getBend( j );
671	<	theBends[j].a = currentBend->getA() + atomOffset;
672	<	theBends[j].b = currentBend->getB() + atomOffset;
673	<	theBends[j].c = currentBend->getC() + atomOffset;
970	<
971	<	if( currentBend->haveExtras() ){
972	<
973	<	extras = currentBend->getExtras();
974	<	current_extra = extras;
975	<
976	<	while( current_extra != NULL ){
977	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
978	<
979	<	switch( current_extra->getType() ){
980	<
981	<	case 0:
982	<	theBends[j].ghost =
983	<	current_extra->getInt() + atomOffset;
984	<	theBends[j].isGhost = 1;
985	<	break;
986	<
987	<	case 1:
988	<	theBends[j].ghost =
989	<	(int)current_extra->getDouble() + atomOffset;
990	<	theBends[j].isGhost = 1;
991	<	break;
992	<
993	<	default:
994	<	sprintf( painCave.errMsg,
995	<	"SimSetup Error: ghostVectorSource was neither a "
996	<	"double nor an int.\n"
997	<	"-->Bend[%d] in %s\n",
998	<	j, comp_stamps[stampID]->getID() );
999	<	painCave.isFatal = 1;
1000	<	simError();
1001	<	}
1002	<	}
1003	<
1004	<	else{
1005	<
1006	<	sprintf( painCave.errMsg,
1007	<	"SimSetup Error: unhandled bend assignment:\n"
1008	<	"    -->%s in Bend[%d] in %s\n",
1009	<	current_extra->getlhs(),
1010	<	j, comp_stamps[stampID]->getID() );
1011	<	painCave.isFatal = 1;
1012	<	simError();
1013	<	}
1014	<
1015	<	current_extra = current_extra->getNext();
1016	<	}
1017	<	}
1018	<
1019	<	if( !theBends[j].isGhost ){
1020	<
1021	<	exI = theBends[j].a;
1022	<	exJ = theBends[j].c;
1023	<	}
1024	<	else{
1025	<
1026	<	exI = theBends[j].a;
1027	<	exJ = theBends[j].b;
1028	<	}
1029	<
1030	<	// exclude_I must always be the smaller of the pair
1031	<	if( exI > exJ ){
1032	<	tempEx = exI;
1033	<	exI = exJ;
1034	<	exJ = tempEx;
1035	<	}
1036	<	#ifdef IS_MPI
1037	<	tempEx = exI;
1038	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1039	<	tempEx = exJ;
1040	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1041	<
1042	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1043	<	#else  // isn't MPI
1044	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1045	<	#endif  //is_mpi
667	>	// set the status, sample, and thermal kick times
668	>
669	>	for (i = 0; i < nInfo; i++){
670	>	if (globals->haveSampleTime()){
671	>	info[i].sampleTime = globals->getSampleTime();
672	>	info[i].statusTime = info[i].sampleTime;
673	>	info[i].thermalTime = info[i].sampleTime;
674		}
675	<	excludeOffset += info.nBends;
675	>	else{
676	>	info[i].sampleTime = globals->getRunTime();
677	>	info[i].statusTime = info[i].sampleTime;
678	>	info[i].thermalTime = info[i].sampleTime;
679	>	}
680
681	<	for(j=0; j<info.nTorsions; j++){
682	<
683	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1052	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1053	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1054	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1055	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1056	<
1057	<	exI = theTorsions[j].a;
1058	<	exJ = theTorsions[j].d;
681	>	if (globals->haveStatusTime()){
682	>	info[i].statusTime = globals->getStatusTime();
683	>	}
684
685	<	// exclude_I must always be the smaller of the pair
686	<	if( exI > exJ ){
1062	<	tempEx = exI;
1063	<	exI = exJ;
1064	<	exJ = tempEx;
1065	<	}
1066	<	#ifdef IS_MPI
1067	<	tempEx = exI;
1068	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1069	<	tempEx = exJ;
1070	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1071	<
1072	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1073	<	#else  // isn't MPI
1074	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1075	<	#endif  //is_mpi
685	>	if (globals->haveThermalTime()){
686	>	info[i].thermalTime = globals->getThermalTime();
687		}
1077	–	excludeOffset += info.nTorsions;
688
689	<
690	<	// send the arrays off to the forceField for init.
689	>	info[i].resetIntegrator = 0;
690	>	if( globals->haveResetTime() ){
691	>	info[i].resetTime = globals->getResetTime();
692	>	info[i].resetIntegrator = 1;
693	>	}
694
695	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1083	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1084	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1085	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
695	>	// check for the temperature set flag
696
697	+	if (globals->haveTempSet())
698	+	info[i].setTemp = globals->getTempSet();
699
700	<	the_molecules[i].initialize( info );
700	>	// get some of the tricky things that may still be in the globals
701	>
702	>	double boxVector[3];
703	>	if (globals->haveBox()){
704	>	boxVector[0] = globals->getBox();
705	>	boxVector[1] = globals->getBox();
706	>	boxVector[2] = globals->getBox();
707
708	+	info[i].setBox(boxVector);
709	+	}
710	+	else if (globals->haveDensity()){
711	+	double vol;
712	+	vol = (double) tot_nmol / globals->getDensity();
713	+	boxVector[0] = pow(vol, (1.0 / 3.0));
714	+	boxVector[1] = boxVector[0];
715	+	boxVector[2] = boxVector[0];
716
717	<	atomOffset += info.nAtoms;
718	<	delete[] theBonds;
719	<	delete[] theBends;
720	<	delete[] theTorsions;
717	>	info[i].setBox(boxVector);
718	>	}
719	>	else{
720	>	if (!globals->haveBoxX()){
721	>	sprintf(painCave.errMsg,
722	>	"SimSetup error, no periodic BoxX size given.\n");
723	>	painCave.isFatal = 1;
724	>	simError();
725	>	}
726	>	boxVector[0] = globals->getBoxX();
727	>
728	>	if (!globals->haveBoxY()){
729	>	sprintf(painCave.errMsg,
730	>	"SimSetup error, no periodic BoxY size given.\n");
731	>	painCave.isFatal = 1;
732	>	simError();
733	>	}
734	>	boxVector[1] = globals->getBoxY();
735	>
736	>	if (!globals->haveBoxZ()){
737	>	sprintf(painCave.errMsg,
738	>	"SimSetup error, no periodic BoxZ size given.\n");
739	>	painCave.isFatal = 1;
740	>	simError();
741	>	}
742	>	boxVector[2] = globals->getBoxZ();
743	>
744	>	info[i].setBox(boxVector);
745	>	}
746		}
747
748	+	//setup seed for random number generator
749	+	int seedValue;
750	+
751	+	if (globals->haveSeed()){
752	+	seedValue = globals->getSeed();
753	+
754	+	if(seedValue / 1E9 == 0){
755	+	sprintf(painCave.errMsg,
756	+	"Seed for sprng library should contain at least 9 digits\n"
757	+	"OOPSE will generate a seed for user\n");
758	+	painCave.isFatal = 0;
759	+	simError();
760	+
761	+	//using seed generated by system instead of invalid seed set by user
762	+	#ifndef IS_MPI
763	+	seedValue = make_sprng_seed();
764	+	#else
765	+	if (worldRank == 0){
766	+	seedValue = make_sprng_seed();
767	+	}
768	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
769	+	#endif
770	+	}
771	+	}//end of if branch of globals->haveSeed()
772	+	else{
773	+
774	+	#ifndef IS_MPI
775	+	seedValue = make_sprng_seed();
776	+	#else
777	+	if (worldRank == 0){
778	+	seedValue = make_sprng_seed();
779	+	}
780	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
781	+	#endif
782	+	}//end of globals->haveSeed()
783	+
784	+	for (int i = 0; i < nInfo; i++){
785	+	info[i].setSeed(seedValue);
786	+	}
787	+
788		#ifdef IS_MPI
789	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
789	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
790		MPIcheckPoint();
791		#endif // is_mpi
1101	–
1102	–	// clean up the forcefield
1103	–	the_ff->calcRcut();
1104	–	the_ff->cleanMe();
1105	–
792		}
793
1108	–	void SimSetup::initFromBass( void ){
794
795	<	int i, j, k;
796	<	int n_cells;
797	<	double cellx, celly, cellz;
798	<	double temp1, temp2, temp3;
1114	<	int n_per_extra;
1115	<	int n_extra;
1116	<	int have_extra, done;
795	>	void SimSetup::finalInfoCheck(void){
796	>	int index;
797	>	int usesDipoles;
798	>	int i;
799
800	<	temp1 = (double)tot_nmol / 4.0;
801	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1120	<	temp3 = ceil( temp2 );
800	>	for (i = 0; i < nInfo; i++){
801	>	// check electrostatic parameters
802
803	<	have_extra =0;
804	<	if( temp2 < temp3 ){ // we have a non-complete lattice
805	<	have_extra =1;
803	>	index = 0;
804	>	usesDipoles = 0;
805	>	while ((index < info[i].n_atoms) && !usesDipoles){
806	>	usesDipoles = (info[i].atoms[index])->hasDipole();
807	>	index++;
808	>	}
809
810	<	n_cells = (int)temp3 - 1;
811	<	cellx = simnfo->boxLx / temp3;
812	<	celly = simnfo->boxLy / temp3;
813	<	cellz = simnfo->boxLz / temp3;
1130	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1131	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1132	<	n_per_extra = (int)ceil( temp1 );
810	>	#ifdef IS_MPI
811	>	int myUse = usesDipoles;
812	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	>	#endif //is_mpi
814
815	<	if( n_per_extra > 4){
1135	<	sprintf( painCave.errMsg,
1136	<	"SimSetup error. There has been an error in constructing"
1137	<	" the non-complete lattice.\n" );
1138	<	painCave.isFatal = 1;
1139	<	simError();
1140	<	}
1141	<	}
1142	<	else{
1143	<	n_cells = (int)temp3;
1144	<	cellx = simnfo->boxLx / temp3;
1145	<	celly = simnfo->boxLy / temp3;
1146	<	cellz = simnfo->boxLz / temp3;
1147	<	}
815	>	double theEcr, theEst;
816
817	<	current_mol = 0;
818	<	current_comp_mol = 0;
1151	<	current_comp = 0;
1152	<	current_atom_ndx = 0;
817	>	if (globals->getUseRF()){
818	>	info[i].useReactionField = 1;
819
820	<	for( i=0; i < n_cells ; i++ ){
821	<	for( j=0; j < n_cells; j++ ){
822	<	for( k=0; k < n_cells; k++ ){
820	>	if (!globals->haveECR()){
821	>	sprintf(painCave.errMsg,
822	>	"SimSetup Warning: using default value of 1/2 the smallest "
823	>	"box length for the electrostaticCutoffRadius.\n"
824	>	"I hope you have a very fast processor!\n");
825	>	painCave.isFatal = 0;
826	>	simError();
827	>	double smallest;
828	>	smallest = info[i].boxL[0];
829	>	if (info[i].boxL[1] <= smallest)
830	>	smallest = info[i].boxL[1];
831	>	if (info[i].boxL[2] <= smallest)
832	>	smallest = info[i].boxL[2];
833	>	theEcr = 0.5 * smallest;
834	>	}
835	>	else{
836	>	theEcr = globals->getECR();
837	>	}
838
839	<	makeElement( i * cellx,
840	<	j * celly,
841	<	k * cellz );
839	>	if (!globals->haveEST()){
840	>	sprintf(painCave.errMsg,
841	>	"SimSetup Warning: using default value of 0.05 * the "
842	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
843	>	painCave.isFatal = 0;
844	>	simError();
845	>	theEst = 0.05 * theEcr;
846	>	}
847	>	else{
848	>	theEst = globals->getEST();
849	>	}
850
851	<	makeElement( i * cellx + 0.5 * cellx,
1163	<	j * celly + 0.5 * celly,
1164	<	k * cellz );
851	>	info[i].setEcr(theEcr, theEst);
852
853	<	makeElement( i * cellx,
854	<	j * celly + 0.5 * celly,
855	<	k * cellz + 0.5 * cellz );
853	>	if (!globals->haveDielectric()){
854	>	sprintf(painCave.errMsg,
855	>	"SimSetup Error: You are trying to use Reaction Field without"
856	>	"setting a dielectric constant!\n");
857	>	painCave.isFatal = 1;
858	>	simError();
859	>	}
860	>	info[i].dielectric = globals->getDielectric();
861	>	}
862	>	else{
863	>	if (usesDipoles){
864	>	if (!globals->haveECR()){
865	>	sprintf(painCave.errMsg,
866	>	"SimSetup Warning: using default value of 1/2 the smallest "
867	>	"box length for the electrostaticCutoffRadius.\n"
868	>	"I hope you have a very fast processor!\n");
869	>	painCave.isFatal = 0;
870	>	simError();
871	>	double smallest;
872	>	smallest = info[i].boxL[0];
873	>	if (info[i].boxL[1] <= smallest)
874	>	smallest = info[i].boxL[1];
875	>	if (info[i].boxL[2] <= smallest)
876	>	smallest = info[i].boxL[2];
877	>	theEcr = 0.5 * smallest;
878	>	}
879	>	else{
880	>	theEcr = globals->getECR();
881	>	}
882
883	<	makeElement( i * cellx + 0.5 * cellx,
884	<	j * celly,
885	<	k * cellz + 0.5 * cellz );
883	>	if (!globals->haveEST()){
884	>	sprintf(painCave.errMsg,
885	>	"SimSetup Warning: using default value of 0.05 * the "
886	>	"electrostaticCutoffRadius for the "
887	>	"electrostaticSkinThickness\n");
888	>	painCave.isFatal = 0;
889	>	simError();
890	>	theEst = 0.05 * theEcr;
891	>	}
892	>	else{
893	>	theEst = globals->getEST();
894	>	}
895	>
896	>	info[i].setEcr(theEcr, theEst);
897		}
898		}
899		}
900
901	<	if( have_extra ){
902	<	done = 0;
901	>	#ifdef IS_MPI
902	>	strcpy(checkPointMsg, "post processing checks out");
903	>	MPIcheckPoint();
904	>	#endif // is_mpi
905	>	}
906
907	<	int start_ndx;
908	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1182	<	for( j=0; j < (n_cells+1) && !done; j++ ){
907	>	void SimSetup::initSystemCoords(void){
908	>	int i;
909
910	<	if( i < n_cells ){
910	>	char* inName;
911
912	<	if( j < n_cells ){
1187	<	start_ndx = n_cells;
1188	<	}
1189	<	else start_ndx = 0;
1190	<	}
1191	<	else start_ndx = 0;
912	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
913
914	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
914	>	for (i = 0; i < info[0].n_atoms; i++)
915	>	info[0].atoms[i]->setCoords();
916
917	<	makeElement( i * cellx,
918	<	j * celly,
919	<	k * cellz );
920	<	done = ( current_mol >= tot_nmol );
917	>	if (globals->haveInitialConfig()){
918	>	InitializeFromFile* fileInit;
919	>	#ifdef IS_MPI // is_mpi
920	>	if (worldRank == 0){
921	>	#endif //is_mpi
922	>	inName = globals->getInitialConfig();
923	>	fileInit = new InitializeFromFile(inName);
924	>	#ifdef IS_MPI
925	>	}
926	>	else
927	>	fileInit = new InitializeFromFile(NULL);
928	>	#endif
929	>	fileInit->readInit(info); // default velocities on
930
931	<	if( !done && n_per_extra > 1 ){
932	<	makeElement( i * cellx + 0.5 * cellx,
933	<	j * celly + 0.5 * celly,
934	<	k * cellz );
1204	<	done = ( current_mol >= tot_nmol );
1205	<	}
931	>	delete fileInit;
932	>	}
933	>	else{
934	>	#ifdef IS_MPI
935
936	<	if( !done && n_per_extra > 2){
1208	<	makeElement( i * cellx,
1209	<	j * celly + 0.5 * celly,
1210	<	k * cellz + 0.5 * cellz );
1211	<	done = ( current_mol >= tot_nmol );
1212	<	}
936	>	// no init from bass
937
938	<	if( !done && n_per_extra > 3){
939	<	makeElement( i * cellx + 0.5 * cellx,
940	<	j * celly,
941	<	k * cellz + 0.5 * cellz );
1218	<	done = ( current_mol >= tot_nmol );
1219	<	}
1220	<	}
1221	<	}
1222	<	}
1223	<	}
938	>	sprintf(painCave.errMsg,
939	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
940	>	painCave.isFatal = 1;;
941	>	simError();
942
943	+	#else
944
945	<	for( i=0; i<simnfo->n_atoms; i++ ){
946	<	simnfo->atoms[i]->set_vx( 0.0 );
947	<	simnfo->atoms[i]->set_vy( 0.0 );
948	<	simnfo->atoms[i]->set_vz( 0.0 );
945	>	initFromBass();
946	>
947	>
948	>	#endif
949		}
950	+
951	+	#ifdef IS_MPI
952	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
953	+	MPIcheckPoint();
954	+	#endif // is_mpi
955		}
956
1233	–	void SimSetup::makeElement( double x, double y, double z ){
957
958	+	void SimSetup::makeOutNames(void){
959		int k;
1236	–	AtomStamp* current_atom;
1237	–	DirectionalAtom* dAtom;
1238	–	double rotMat[3][3];
960
1240	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
961
962	<	current_atom = comp_stamps[current_comp]->getAtom( k );
963	<	if( !current_atom->havePosition() ){
964	<	sprintf( painCave.errMsg,
965	<	"SimSetup:initFromBass error.\n"
966	<	"\tComponent %s, atom %s does not have a position specified.\n"
967	<	"\tThe initialization routine is unable to give a start"
968	<	" position.\n",
969	<	comp_stamps[current_comp]->getID(),
970	<	current_atom->getType() );
962	>	for (k = 0; k < nInfo; k++){
963	>	#ifdef IS_MPI
964	>	if (worldRank == 0){
965	>	#endif // is_mpi
966	>
967	>	if (globals->haveFinalConfig()){
968	>	strcpy(info[k].finalName, globals->getFinalConfig());
969	>	}
970	>	else{
971	>	strcpy(info[k].finalName, inFileName);
972	>	char* endTest;
973	>	int nameLength = strlen(info[k].finalName);
974	>	endTest = &(info[k].finalName[nameLength - 5]);
975	>	if (!strcmp(endTest, ".bass")){
976	>	strcpy(endTest, ".eor");
977	>	}
978	>	else if (!strcmp(endTest, ".BASS")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else{
982	>	endTest = &(info[k].finalName[nameLength - 4]);
983	>	if (!strcmp(endTest, ".bss")){
984	>	strcpy(endTest, ".eor");
985	>	}
986	>	else if (!strcmp(endTest, ".mdl")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else{
990	>	strcat(info[k].finalName, ".eor");
991	>	}
992	>	}
993	>	}
994	>
995	>	// make the sample and status out names
996	>
997	>	strcpy(info[k].sampleName, inFileName);
998	>	char* endTest;
999	>	int nameLength = strlen(info[k].sampleName);
1000	>	endTest = &(info[k].sampleName[nameLength - 5]);
1001	>	if (!strcmp(endTest, ".bass")){
1002	>	strcpy(endTest, ".dump");
1003	>	}
1004	>	else if (!strcmp(endTest, ".BASS")){
1005	>	strcpy(endTest, ".dump");
1006	>	}
1007	>	else{
1008	>	endTest = &(info[k].sampleName[nameLength - 4]);
1009	>	if (!strcmp(endTest, ".bss")){
1010	>	strcpy(endTest, ".dump");
1011	>	}
1012	>	else if (!strcmp(endTest, ".mdl")){
1013	>	strcpy(endTest, ".dump");
1014	>	}
1015	>	else{
1016	>	strcat(info[k].sampleName, ".dump");
1017	>	}
1018	>	}
1019	>
1020	>	strcpy(info[k].statusName, inFileName);
1021	>	nameLength = strlen(info[k].statusName);
1022	>	endTest = &(info[k].statusName[nameLength - 5]);
1023	>	if (!strcmp(endTest, ".bass")){
1024	>	strcpy(endTest, ".stat");
1025	>	}
1026	>	else if (!strcmp(endTest, ".BASS")){
1027	>	strcpy(endTest, ".stat");
1028	>	}
1029	>	else{
1030	>	endTest = &(info[k].statusName[nameLength - 4]);
1031	>	if (!strcmp(endTest, ".bss")){
1032	>	strcpy(endTest, ".stat");
1033	>	}
1034	>	else if (!strcmp(endTest, ".mdl")){
1035	>	strcpy(endTest, ".stat");
1036	>	}
1037	>	else{
1038	>	strcat(info[k].statusName, ".stat");
1039	>	}
1040	>	}
1041	>
1042	>	#ifdef IS_MPI
1043	>
1044	>	}
1045	>	#endif // is_mpi
1046	>	}
1047	>	}
1048	>
1049	>
1050	>	void SimSetup::sysObjectsCreation(void){
1051	>	int i, k;
1052	>
1053	>	// create the forceField
1054	>
1055	>	createFF();
1056	>
1057	>	// extract componentList
1058	>
1059	>	compList();
1060	>
1061	>	// calc the number of atoms, bond, bends, and torsions
1062	>
1063	>	calcSysValues();
1064	>
1065	>	#ifdef IS_MPI
1066	>	// divide the molecules among the processors
1067	>
1068	>	mpiMolDivide();
1069	>	#endif //is_mpi
1070	>
1071	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1072	>
1073	>	makeSysArrays();
1074	>
1075	>	// make and initialize the molecules (all but atomic coordinates)
1076	>
1077	>	makeMolecules();
1078	>
1079	>	for (k = 0; k < nInfo; k++){
1080	>	info[k].identArray = new int[info[k].n_atoms];
1081	>	for (i = 0; i < info[k].n_atoms; i++){
1082	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1083	>	}
1084	>	}
1085	>	}
1086	>
1087	>
1088	>	void SimSetup::createFF(void){
1089	>	switch (ffCase){
1090	>	case FF_DUFF:
1091	>	the_ff = new DUFF();
1092	>	break;
1093	>
1094	>	case FF_LJ:
1095	>	the_ff = new LJFF();
1096	>	break;
1097	>
1098	>	case FF_EAM:
1099	>	the_ff = new EAM_FF();
1100	>	break;
1101	>
1102	>	default:
1103	>	sprintf(painCave.errMsg,
1104	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1105		painCave.isFatal = 1;
1106		simError();
1107	+	}
1108	+
1109	+	#ifdef IS_MPI
1110	+	strcpy(checkPointMsg, "ForceField creation successful");
1111	+	MPIcheckPoint();
1112	+	#endif // is_mpi
1113	+	}
1114	+
1115	+
1116	+	void SimSetup::compList(void){
1117	+	int i;
1118	+	char* id;
1119	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1120	+	LinkedMolStamp* currentStamp = NULL;
1121	+	comp_stamps = new MoleculeStamp * [n_components];
1122	+
1123	+	// make an array of molecule stamps that match the components used.
1124	+	// also extract the used stamps out into a separate linked list
1125	+
1126	+	for (i = 0; i < nInfo; i++){
1127	+	info[i].nComponents = n_components;
1128	+	info[i].componentsNmol = components_nmol;
1129	+	info[i].compStamps = comp_stamps;
1130	+	info[i].headStamp = headStamp;
1131	+	}
1132	+
1133	+
1134	+	for (i = 0; i < n_components; i++){
1135	+	id = the_components[i]->getType();
1136	+	comp_stamps[i] = NULL;
1137	+
1138	+	// check to make sure the component isn't already in the list
1139	+
1140	+	comp_stamps[i] = headStamp->match(id);
1141	+	if (comp_stamps[i] == NULL){
1142	+	// extract the component from the list;
1143	+
1144	+	currentStamp = stamps->extractMolStamp(id);
1145	+	if (currentStamp == NULL){
1146	+	sprintf(painCave.errMsg,
1147	+	"SimSetup error: Component \"%s\" was not found in the "
1148	+	"list of declared molecules\n",
1149	+	id);
1150	+	painCave.isFatal = 1;
1151	+	simError();
1152	+	}
1153	+
1154	+	headStamp->add(currentStamp);
1155	+	comp_stamps[i] = headStamp->match(id);
1156		}
1157	+	}
1158
1159	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1160	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1161	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1159	>	#ifdef IS_MPI
1160	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1161	>	MPIcheckPoint();
1162	>	#endif // is_mpi
1163	>	}
1164
1165	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1165	>	void SimSetup::calcSysValues(void){
1166	>	int i;
1167
1168	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1168	>	int* molMembershipArray;
1169
1170	<	rotMat[0][0] = 1.0;
1171	<	rotMat[0][1] = 0.0;
1172	<	rotMat[0][2] = 0.0;
1170	>	tot_atoms = 0;
1171	>	tot_bonds = 0;
1172	>	tot_bends = 0;
1173	>	tot_torsions = 0;
1174	>	for (i = 0; i < n_components; i++){
1175	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1176	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1177	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1178	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1179	>	}
1180
1181	<	rotMat[1][0] = 0.0;
1182	<	rotMat[1][1] = 1.0;
1269	<	rotMat[1][2] = 0.0;
1181	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1182	>	molMembershipArray = new int[tot_atoms];
1183
1184	<	rotMat[2][0] = 0.0;
1185	<	rotMat[2][1] = 0.0;
1186	<	rotMat[2][2] = 1.0;
1184	>	for (i = 0; i < nInfo; i++){
1185	>	info[i].n_atoms = tot_atoms;
1186	>	info[i].n_bonds = tot_bonds;
1187	>	info[i].n_bends = tot_bends;
1188	>	info[i].n_torsions = tot_torsions;
1189	>	info[i].n_SRI = tot_SRI;
1190	>	info[i].n_mol = tot_nmol;
1191
1192	<	dAtom->setA( rotMat );
1192	>	info[i].molMembershipArray = molMembershipArray;
1193	>	}
1194	>	}
1195	>
1196	>	#ifdef IS_MPI
1197	>
1198	>	void SimSetup::mpiMolDivide(void){
1199	>	int i, j, k;
1200	>	int localMol, allMol;
1201	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1202	>
1203	>	mpiSim = new mpiSimulation(info);
1204	>
1205	>	globalIndex = mpiSim->divideLabor();
1206	>
1207	>	// set up the local variables
1208	>
1209	>	mol2proc = mpiSim->getMolToProcMap();
1210	>	molCompType = mpiSim->getMolComponentType();
1211	>
1212	>	allMol = 0;
1213	>	localMol = 0;
1214	>	local_atoms = 0;
1215	>	local_bonds = 0;
1216	>	local_bends = 0;
1217	>	local_torsions = 0;
1218	>	globalAtomIndex = 0;
1219	>
1220	>
1221	>	for (i = 0; i < n_components; i++){
1222	>	for (j = 0; j < components_nmol[i]; j++){
1223	>	if (mol2proc[allMol] == worldRank){
1224	>	local_atoms += comp_stamps[i]->getNAtoms();
1225	>	local_bonds += comp_stamps[i]->getNBonds();
1226	>	local_bends += comp_stamps[i]->getNBends();
1227	>	local_torsions += comp_stamps[i]->getNTorsions();
1228	>	localMol++;
1229	>	}
1230	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1231	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1232	>	globalAtomIndex++;
1233	>	}
1234	>
1235	>	allMol++;
1236		}
1237	+	}
1238	+	local_SRI = local_bonds + local_bends + local_torsions;
1239
1240	<	current_atom_ndx++;
1240	>	info[0].n_atoms = mpiSim->getMyNlocal();
1241	>
1242	>	if (local_atoms != info[0].n_atoms){
1243	>	sprintf(painCave.errMsg,
1244	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1245	>	" localAtom (%d) are not equal.\n",
1246	>	info[0].n_atoms, local_atoms);
1247	>	painCave.isFatal = 1;
1248	>	simError();
1249		}
1250
1251	<	current_mol++;
1252	<	current_comp_mol++;
1251	>	info[0].n_bonds = local_bonds;
1252	>	info[0].n_bends = local_bends;
1253	>	info[0].n_torsions = local_torsions;
1254	>	info[0].n_SRI = local_SRI;
1255	>	info[0].n_mol = localMol;
1256
1257	<	if( current_comp_mol >= components_nmol[current_comp] ){
1257	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1258	>	MPIcheckPoint();
1259	>	}
1260
1261	<	current_comp_mol = 0;
1262	<	current_comp++;
1261	>	#endif // is_mpi
1262	>
1263	>
1264	>	void SimSetup::makeSysArrays(void){
1265	>
1266	>	#ifndef IS_MPI
1267	>	int k, j;
1268	>	#endif // is_mpi
1269	>	int i, l;
1270	>
1271	>	Atom** the_atoms;
1272	>	Molecule* the_molecules;
1273	>	Exclude** the_excludes;
1274	>
1275	>
1276	>	for (l = 0; l < nInfo; l++){
1277	>	// create the atom and short range interaction arrays
1278	>
1279	>	the_atoms = new Atom * [info[l].n_atoms];
1280	>	the_molecules = new Molecule[info[l].n_mol];
1281	>	int molIndex;
1282	>
1283	>	// initialize the molecule's stampID's
1284	>
1285	>	#ifdef IS_MPI
1286	>
1287	>
1288	>	molIndex = 0;
1289	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1290	>	if (mol2proc[i] == worldRank){
1291	>	the_molecules[molIndex].setStampID(molCompType[i]);
1292	>	the_molecules[molIndex].setMyIndex(molIndex);
1293	>	the_molecules[molIndex].setGlobalIndex(i);
1294	>	molIndex++;
1295	>	}
1296	>	}
1297	>
1298	>	#else // is_mpi
1299	>
1300	>	molIndex = 0;
1301	>	globalAtomIndex = 0;
1302	>	for (i = 0; i < n_components; i++){
1303	>	for (j = 0; j < components_nmol[i]; j++){
1304	>	the_molecules[molIndex].setStampID(i);
1305	>	the_molecules[molIndex].setMyIndex(molIndex);
1306	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1307	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1308	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1309	>	globalAtomIndex++;
1310	>	}
1311	>	molIndex++;
1312	>	}
1313	>	}
1314	>
1315	>
1316	>	#endif // is_mpi
1317	>
1318	>
1319	>	if (info[l].n_SRI){
1320	>	Exclude::createArray(info[l].n_SRI);
1321	>	the_excludes = new Exclude * [info[l].n_SRI];
1322	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1323	>	the_excludes[ex] = new Exclude(ex);
1324	>	}
1325	>	info[l].globalExcludes = new int;
1326	>	info[l].n_exclude = info[l].n_SRI;
1327	>	}
1328	>	else{
1329	>	Exclude::createArray(1);
1330	>	the_excludes = new Exclude * ;
1331	>	the_excludes[0] = new Exclude(0);
1332	>	the_excludes[0]->setPair(0, 0);
1333	>	info[l].globalExcludes = new int;
1334	>	info[l].globalExcludes[0] = 0;
1335	>	info[l].n_exclude = 0;
1336	>	}
1337	>
1338	>	// set the arrays into the SimInfo object
1339	>
1340	>	info[l].atoms = the_atoms;
1341	>	info[l].molecules = the_molecules;
1342	>	info[l].nGlobalExcludes = 0;
1343	>	info[l].excludes = the_excludes;
1344	>
1345	>	the_ff->setSimInfo(info);
1346		}
1347		}
1348	+
1349	+	void SimSetup::makeIntegrator(void){
1350	+	int k;
1351	+
1352	+	NVE<RealIntegrator>* myNVE = NULL;
1353	+	NVT<RealIntegrator>* myNVT = NULL;
1354	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1355	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1356	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1357	+
1358	+	for (k = 0; k < nInfo; k++){
1359	+	switch (ensembleCase){
1360	+	case NVE_ENS:
1361	+	if (globals->haveZconstraints()){
1362	+	setupZConstraint(info[k]);
1363	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1364	+	}
1365	+	else{
1366	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1367	+	}
1368	+
1369	+	info->the_integrator = myNVE;
1370	+	break;
1371	+
1372	+	case NVT_ENS:
1373	+	if (globals->haveZconstraints()){
1374	+	setupZConstraint(info[k]);
1375	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1376	+	}
1377	+	else
1378	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1379	+
1380	+	myNVT->setTargetTemp(globals->getTargetTemp());
1381	+
1382	+	if (globals->haveTauThermostat())
1383	+	myNVT->setTauThermostat(globals->getTauThermostat());
1384	+	else{
1385	+	sprintf(painCave.errMsg,
1386	+	"SimSetup error: If you use the NVT\n"
1387	+	"    ensemble, you must set tauThermostat.\n");
1388	+	painCave.isFatal = 1;
1389	+	simError();
1390	+	}
1391	+
1392	+	info->the_integrator = myNVT;
1393	+	break;
1394	+
1395	+	case NPTi_ENS:
1396	+	if (globals->haveZconstraints()){
1397	+	setupZConstraint(info[k]);
1398	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1399	+	}
1400	+	else
1401	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1402	+
1403	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1404	+
1405	+	if (globals->haveTargetPressure())
1406	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	+	else{
1408	+	sprintf(painCave.errMsg,
1409	+	"SimSetup error: If you use a constant pressure\n"
1410	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	+	painCave.isFatal = 1;
1412	+	simError();
1413	+	}
1414	+
1415	+	if (globals->haveTauThermostat())
1416	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1417	+	else{
1418	+	sprintf(painCave.errMsg,
1419	+	"SimSetup error: If you use an NPT\n"
1420	+	"    ensemble, you must set tauThermostat.\n");
1421	+	painCave.isFatal = 1;
1422	+	simError();
1423	+	}
1424	+
1425	+	if (globals->haveTauBarostat())
1426	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1427	+	else{
1428	+	sprintf(painCave.errMsg,
1429	+	"SimSetup error: If you use an NPT\n"
1430	+	"    ensemble, you must set tauBarostat.\n");
1431	+	painCave.isFatal = 1;
1432	+	simError();
1433	+	}
1434	+
1435	+	info->the_integrator = myNPTi;
1436	+	break;
1437	+
1438	+	case NPTf_ENS:
1439	+	if (globals->haveZconstraints()){
1440	+	setupZConstraint(info[k]);
1441	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1442	+	}
1443	+	else
1444	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1445	+
1446	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1447	+
1448	+	if (globals->haveTargetPressure())
1449	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1450	+	else{
1451	+	sprintf(painCave.errMsg,
1452	+	"SimSetup error: If you use a constant pressure\n"
1453	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1454	+	painCave.isFatal = 1;
1455	+	simError();
1456	+	}
1457	+
1458	+	if (globals->haveTauThermostat())
1459	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1460	+	else{
1461	+	sprintf(painCave.errMsg,
1462	+	"SimSetup error: If you use an NPT\n"
1463	+	"    ensemble, you must set tauThermostat.\n");
1464	+	painCave.isFatal = 1;
1465	+	simError();
1466	+	}
1467	+
1468	+	if (globals->haveTauBarostat())
1469	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1470	+	else{
1471	+	sprintf(painCave.errMsg,
1472	+	"SimSetup error: If you use an NPT\n"
1473	+	"    ensemble, you must set tauBarostat.\n");
1474	+	painCave.isFatal = 1;
1475	+	simError();
1476	+	}
1477	+
1478	+	info->the_integrator = myNPTf;
1479	+	break;
1480	+
1481	+	case NPTxyz_ENS:
1482	+	if (globals->haveZconstraints()){
1483	+	setupZConstraint(info[k]);
1484	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1485	+	}
1486	+	else
1487	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1488	+
1489	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1490	+
1491	+	if (globals->haveTargetPressure())
1492	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1493	+	else{
1494	+	sprintf(painCave.errMsg,
1495	+	"SimSetup error: If you use a constant pressure\n"
1496	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1497	+	painCave.isFatal = 1;
1498	+	simError();
1499	+	}
1500	+
1501	+	if (globals->haveTauThermostat())
1502	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1503	+	else{
1504	+	sprintf(painCave.errMsg,
1505	+	"SimSetup error: If you use an NPT\n"
1506	+	"    ensemble, you must set tauThermostat.\n");
1507	+	painCave.isFatal = 1;
1508	+	simError();
1509	+	}
1510	+
1511	+	if (globals->haveTauBarostat())
1512	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1513	+	else{
1514	+	sprintf(painCave.errMsg,
1515	+	"SimSetup error: If you use an NPT\n"
1516	+	"    ensemble, you must set tauBarostat.\n");
1517	+	painCave.isFatal = 1;
1518	+	simError();
1519	+	}
1520	+
1521	+	info->the_integrator = myNPTxyz;
1522	+	break;
1523	+
1524	+	default:
1525	+	sprintf(painCave.errMsg,
1526	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1527	+	painCave.isFatal = 1;
1528	+	simError();
1529	+	}
1530	+	}
1531	+	}
1532	+
1533	+	void SimSetup::initFortran(void){
1534	+	info[0].refreshSim();
1535	+
1536	+	if (!strcmp(info[0].mixingRule, "standard")){
1537	+	the_ff->initForceField(LB_MIXING_RULE);
1538	+	}
1539	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1540	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1541	+	}
1542	+	else{
1543	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1544	+	info[0].mixingRule);
1545	+	painCave.isFatal = 1;
1546	+	simError();
1547	+	}
1548	+
1549	+
1550	+	#ifdef IS_MPI
1551	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1552	+	MPIcheckPoint();
1553	+	#endif // is_mpi
1554	+	}
1555	+
1556	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1557	+	int nZConstraints;
1558	+	ZconStamp** zconStamp;
1559	+
1560	+	if (globals->haveZconstraintTime()){
1561	+	//add sample time of z-constraint  into SimInfo's property list
1562	+	DoubleData* zconsTimeProp = new DoubleData();
1563	+	zconsTimeProp->setID(ZCONSTIME_ID);
1564	+	zconsTimeProp->setData(globals->getZconsTime());
1565	+	theInfo.addProperty(zconsTimeProp);
1566	+	}
1567	+	else{
1568	+	sprintf(painCave.errMsg,
1569	+	"ZConstraint error: If you use an ZConstraint\n"
1570	+	" , you must set sample time.\n");
1571	+	painCave.isFatal = 1;
1572	+	simError();
1573	+	}
1574	+
1575	+	//push zconsTol into siminfo, if user does not specify
1576	+	//value for zconsTol, a default value will be used
1577	+	DoubleData* zconsTol = new DoubleData();
1578	+	zconsTol->setID(ZCONSTOL_ID);
1579	+	if (globals->haveZconsTol()){
1580	+	zconsTol->setData(globals->getZconsTol());
1581	+	}
1582	+	else{
1583	+	double defaultZConsTol = 0.01;
1584	+	sprintf(painCave.errMsg,
1585	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1586	+	" , default value %f is used.\n",
1587	+	defaultZConsTol);
1588	+	painCave.isFatal = 0;
1589	+	simError();
1590	+
1591	+	zconsTol->setData(defaultZConsTol);
1592	+	}
1593	+	theInfo.addProperty(zconsTol);
1594	+
1595	+	//set Force Subtraction Policy
1596	+	StringData* zconsForcePolicy = new StringData();
1597	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1598	+
1599	+	if (globals->haveZconsForcePolicy()){
1600	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1601	+	}
1602	+	else{
1603	+	sprintf(painCave.errMsg,
1604	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1605	+	"PolicyByMass is used\n");
1606	+	painCave.isFatal = 0;
1607	+	simError();
1608	+	zconsForcePolicy->setData("BYMASS");
1609	+	}
1610	+
1611	+	theInfo.addProperty(zconsForcePolicy);
1612	+
1613	+	//Determine the name of ouput file and add it into SimInfo's property list
1614	+	//Be careful, do not use inFileName, since it is a pointer which
1615	+	//point to a string at master node, and slave nodes do not contain that string
1616	+
1617	+	string zconsOutput(theInfo.finalName);
1618	+
1619	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1620	+
1621	+	StringData* zconsFilename = new StringData();
1622	+	zconsFilename->setID(ZCONSFILENAME_ID);
1623	+	zconsFilename->setData(zconsOutput);
1624	+
1625	+	theInfo.addProperty(zconsFilename);
1626	+
1627	+	//setup index, pos and other parameters of z-constraint molecules
1628	+	nZConstraints = globals->getNzConstraints();
1629	+	theInfo.nZconstraints = nZConstraints;
1630	+
1631	+	zconStamp = globals->getZconStamp();
1632	+	ZConsParaItem tempParaItem;
1633	+
1634	+	ZConsParaData* zconsParaData = new ZConsParaData();
1635	+	zconsParaData->setID(ZCONSPARADATA_ID);
1636	+
1637	+	for (int i = 0; i < nZConstraints; i++){
1638	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1639	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1640	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1641	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1642	+
1643	+	zconsParaData->addItem(tempParaItem);
1644	+	}
1645	+
1646	+	//check the uniqueness of index
1647	+	if(!zconsParaData->isIndexUnique()){
1648	+	sprintf(painCave.errMsg,
1649	+	"ZConstraint Error: molIndex is not unique\n");
1650	+	painCave.isFatal = 1;
1651	+	simError();
1652	+	}
1653	+
1654	+	//sort the parameters by index of molecules
1655	+	zconsParaData->sortByIndex();
1656	+
1657	+	//push data into siminfo, therefore, we can retrieve later
1658	+	theInfo.addProperty(zconsParaData);
1659	+	}

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