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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 855 by mmeineke, Thu Nov 6 22:01:37 2003 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
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	+
35	+	initSuspend = false;
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41	<
41	>
42	>
43		#ifdef IS_MPI
44	<	strcpy( checkPointMsg, "SimSetup creation successful" );
44	>	strcpy(checkPointMsg, "SimSetup creation successful");
45		MPIcheckPoint();
46		#endif // IS_MPI
47		}
#	Line 38 | Line 51 | void SimSetup::parseFile( char* fileName ){
51		delete globals;
52		}
53
54	<	void SimSetup::parseFile( char* fileName ){
54	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
55	>	info = the_info;
56	>	nInfo = theNinfo;
57	>	isInfoArray = 1;
58	>	initSuspend = true;
59	>	}
60
61	+
62	+	void SimSetup::parseFile(char* fileName){
63		#ifdef IS_MPI
64	<	if( worldRank == 0 ){
64	>	if (worldRank == 0){
65		#endif // is_mpi
66	<
66	>
67		inFileName = fileName;
68	<	set_interface_stamps( stamps, globals );
69	<
68	>	set_interface_stamps(stamps, globals);
69	>
70		#ifdef IS_MPI
71		mpiEventInit();
72		#endif
73
74	<	yacc_BASS( fileName );
74	>	yacc_BASS(fileName);
75
76		#ifdef IS_MPI
77		throwMPIEvent(NULL);
78		}
79	<	else receiveParse();
79	>	else{
80	>	receiveParse();
81	>	}
82		#endif
83
84		}
85
86		#ifdef IS_MPI
87		void SimSetup::receiveParse(void){
88	<
89	<	set_interface_stamps( stamps, globals );
90	<	mpiEventInit();
91	<	MPIcheckPoint();
70	<	mpiEventLoop();
71	<
88	>	set_interface_stamps(stamps, globals);
89	>	mpiEventInit();
90	>	MPIcheckPoint();
91	>	mpiEventLoop();
92		}
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
98	<	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;
98	>	// gather all of the information from the Bass file
99
100	<	// get the stamps and globals;
89	<	the_stamps = stamps;
90	<	the_globals = globals;
100	>	gatherInfo();
101
102	<	// 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();
102	>	// creation of complex system objects
103
104	<	// 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() );
104	>	sysObjectsCreation();
105
106	<	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	<	}
106	>	// initialize the system coordinates
107
108	<	// get the ensemble:
109	<	strcpy( ensemble, the_globals->getEnsemble() );
108	>	if ( !initSuspend ){
109	>	initSystemCoords();
110
111	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
112	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
116	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
117	<	ensembleCase = NPTi_ENS;
118	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
119	<	else{
120	<	sprintf( painCave.errMsg,
121	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
122	<	"reverting to NVE for this simulation.\n",
123	<	ensemble );
124	<	painCave.isFatal = 0;
125	<	simError();
126	<	strcpy( ensemble, "NVE" );
127	<	ensembleCase = NVE_ENS;
111	>	if( !(globals->getUseInitTime()) )
112	>	info[0].currentTime = 0.0;
113		}
129	–	strcpy( simnfo->ensemble, ensemble );
114
115	+	// check on the post processing info
116
117	<	//   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	<	//     }
117	>	finalInfoCheck();
118
119	<	//     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	<	//     }
119	>	// make the output filenames
120
121	<	//     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	<	//     }
121	>	makeOutNames();
122
123	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
171	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
172	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
123	>	// make the integrator
124
125	<	//     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	<	//     }
125	>	makeIntegrator();
126
127	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
128	<	simnfo->usePBC = the_globals->getPBC();
129	<
190	<	int usesDipoles = 0;
191	<	switch( ffCase ){
127	>	#ifdef IS_MPI
128	>	mpiSim->mpiRefresh();
129	>	#endif
130
131	<	case FF_DUFF:
194	<	the_ff = new DUFF();
195	<	usesDipoles = 1;
196	<	break;
131	>	// initialize the Fortran
132
133	<	case FF_LJ:
134	<	the_ff = new LJFF();
200	<	break;
133	>	initFortran();
134	>	}
135
202	–	default:
203	–	sprintf( painCave.errMsg,
204	–	"SimSetup Error. Unrecognized force field in case statement.\n");
205	–	painCave.isFatal = 1;
206	–	simError();
207	–	}
136
137	<	#ifdef IS_MPI
138	<	strcpy( checkPointMsg, "ForceField creation successful" );
139	<	MPIcheckPoint();
140	<	#endif // is_mpi
137	>	void SimSetup::makeMolecules(void){
138	>	int k;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	// get the components and calculate the tot_nMol and indvidual n_mol
150	<	the_components = the_globals->getComponents();
151	<	components_nmol = new int[n_components];
217	<	comp_stamps = new MoleculeStamp*[n_components];
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
219	–	if( !the_globals->haveNMol() ){
220	–	// we don't have the total number of molecules, so we assume it is
221	–	// given in each component
153
154	<	tot_nmol = 0;
224	<	for( i=0; i<n_components; i++ ){
154	>	//init the forceField paramters
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	>	the_ff->readParams();
157
235	–	tot_nmol += the_components[i]->getNMol();
236	–	components_nmol[i] = the_components[i]->getNMol();
237	–	}
238	–	}
239	–	else{
240	–	sprintf( painCave.errMsg,
241	–	"SimSetup error.\n"
242	–	"\tSorry, the ability to specify total"
243	–	" nMols and then give molfractions in the components\n"
244	–	"\tis not currently supported."
245	–	" Please give nMol in the components.\n" );
246	–	painCave.isFatal = 1;
247	–	simError();
248	–
249	–
250	–	//     tot_nmol = the_globals->getNMol();
251	–
252	–	//   //we have the total number of molecules, now we check for molfractions
253	–	//     for( i=0; i<n_components; i++ ){
254	–
255	–	//       if( !the_components[i]->haveMolFraction() ){
256	–
257	–	//  if( !the_components[i]->haveNMol() ){
258	–	//    //we have a problem
259	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
260	–	//              << " nMol was given in component
261	–
262	–	}
158
159	<	#ifdef IS_MPI
265	<	strcpy( checkPointMsg, "Have the number of components" );
266	<	MPIcheckPoint();
267	<	#endif // is_mpi
159	>	// init the atoms
160
161	<	// make an array of molecule stamps that match the components used.
270	<	// also extract the used stamps out into a separate linked list
161	>	double ux, uy, uz, u, uSqr;
162
163	<	simnfo->nComponents = n_components;
164	<	simnfo->componentsNmol = components_nmol;
274	<	simnfo->compStamps = comp_stamps;
275	<	simnfo->headStamp = new LinkedMolStamp();
276	<
277	<	char* id;
278	<	LinkedMolStamp* headStamp = simnfo->headStamp;
279	<	LinkedMolStamp* currentStamp = NULL;
280	<	for( i=0; i<n_components; i++ ){
163	>	for (k = 0; k < nInfo; k++){
164	>	the_ff->setSimInfo(&(info[k]));
165
166	<	id = the_components[i]->getType();
167	<	comp_stamps[i] = NULL;
168	<
169	<	// check to make sure the component isn't already in the list
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for (i = 0; i < info[k].n_mol; i++){
169	>	stampID = info[k].molecules[i].getStampID();
170	>
171	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
172	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
173	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
174	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
175	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
176
177	<	comp_stamps[i] = headStamp->match( id );
178	<	if( comp_stamps[i] == NULL ){
179	<
180	<	// extract the component from the list;
181	<
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	<	}
177	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
178	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	>	molInfo.myBends = new Bend * [molInfo.nBends];
181	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
182
183	<	#ifdef IS_MPI
184	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
185	<	MPIcheckPoint();
310	<	#endif // is_mpi
311	<
183	>	theBonds = new bond_pair[molInfo.nBonds];
184	>	theBends = new bend_set[molInfo.nBends];
185	>	theTorsions = new torsion_set[molInfo.nTorsions];
186
187	+	// make the Atoms
188
189	+	for (j = 0; j < molInfo.nAtoms; j++){
190	+	currentAtom = comp_stamps[stampID]->getAtom(j);
191	+	if (currentAtom->haveOrientation()){
192	+	dAtom = new DirectionalAtom((j + atomOffset),
193	+	info[k].getConfiguration());
194	+	info[k].n_oriented++;
195	+	molInfo.myAtoms[j] = dAtom;
196
197	<	// caclulate the number of atoms, bonds, bends and torsions
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200
201	<	tot_atoms = 0;
318	<	tot_bonds = 0;
319	<	tot_bends = 0;
320	<	tot_torsions = 0;
321	<	for( i=0; i<n_components; i++ ){
322	<
323	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
324	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
325	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
326	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
327	<	}
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202
203	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207
208	<	simnfo->n_atoms = tot_atoms;
209	<	simnfo->n_bonds = tot_bonds;
210	<	simnfo->n_bends = tot_bends;
211	<	simnfo->n_torsions = tot_torsions;
212	<	simnfo->n_SRI = tot_SRI;
213	<	simnfo->n_mol = tot_nmol;
214	<
215	<	simnfo->molMembershipArray = new int[tot_atoms];
208	>	dAtom->setSUx(ux);
209	>	dAtom->setSUy(uy);
210	>	dAtom->setSUz(uz);
211	>	}
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	>	info[k].getConfiguration());
215	>	}
216	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
217
218		#ifdef IS_MPI
219
220	<	// divide the molecules among processors here.
343	<
344	<	mpiSim = new mpiSimulation( simnfo );
345	<
346	<	globalIndex = mpiSim->divideLabor();
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221
222	<	// set up the local variables
223	<
350	<	int localMol, allMol;
351	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
222	>	#endif // is_mpi
223	>	}
224
225	<	int* mol2proc = mpiSim->getMolToProcMap();
226	<	int* molCompType = mpiSim->getMolComponentType();
227	<
228	<	allMol = 0;
229	<	localMol = 0;
358	<	local_atoms = 0;
359	<	local_bonds = 0;
360	<	local_bends = 0;
361	<	local_torsions = 0;
362	<	globalAtomIndex = 0;
225	>	// make the bonds
226	>	for (j = 0; j < molInfo.nBonds; j++){
227	>	currentBond = comp_stamps[stampID]->getBond(j);
228	>	theBonds[j].a = currentBond->getA() + atomOffset;
229	>	theBonds[j].b = currentBond->getB() + atomOffset;
230
231	+	exI = theBonds[j].a;
232	+	exJ = theBonds[j].b;
233
234	<	for( i=0; i<n_components; i++ ){
234	>	// exclude_I must always be the smaller of the pair
235	>	if (exI > exJ){
236	>	tempEx = exI;
237	>	exI = exJ;
238	>	exJ = tempEx;
239	>	}
240	>	#ifdef IS_MPI
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245
246	<	for( j=0; j<components_nmol[i]; j++ ){
247	<
248	<	if( mol2proc[allMol] == worldRank ){
249	<
250	<	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++;
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	>	#else  // isn't MPI
248	>
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	>	#endif  //is_mpi
251		}
252	+	excludeOffset += molInfo.nBonds;
253
254	<	allMol++;
255	<	}
256	<	}
257	<	local_SRI = local_bonds + local_bends + local_torsions;
258	<
259	<	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	<	}
254	>	//make the bends
255	>	for (j = 0; j < molInfo.nBends; j++){
256	>	currentBend = comp_stamps[stampID]->getBend(j);
257	>	theBends[j].a = currentBend->getA() + atomOffset;
258	>	theBends[j].b = currentBend->getB() + atomOffset;
259	>	theBends[j].c = currentBend->getC() + atomOffset;
260
261	<	simnfo->n_bonds = local_bonds;
262	<	simnfo->n_bends = local_bends;
263	<	simnfo->n_torsions = local_torsions;
402	<	simnfo->n_SRI = local_SRI;
403	<	simnfo->n_mol = localMol;
261	>	if (currentBend->haveExtras()){
262	>	extras = currentBend->getExtras();
263	>	current_extra = extras;
264
265	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
266	<	MPIcheckPoint();
267	<
268	<
269	<	#endif // is_mpi
270	<
265	>	while (current_extra != NULL){
266	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
267	>	switch (current_extra->getType()){
268	>	case 0:
269	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272
273	<	// create the atom and short range interaction arrays
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278
279	<	Atom::createArrays(simnfo->n_atoms);
280	<	the_atoms = new Atom*[simnfo->n_atoms];
281	<	the_molecules = new Molecule[simnfo->n_mol];
282	<	int molIndex;
279	>	default:
280	>	sprintf(painCave.errMsg,
281	>	"SimSetup Error: ghostVectorSource was neither a "
282	>	"double nor an int.\n"
283	>	"-->Bend[%d] in %s\n",
284	>	j, comp_stamps[stampID]->getID());
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>	}
289	>	else{
290	>	sprintf(painCave.errMsg,
291	>	"SimSetup Error: unhandled bend assignment:\n"
292	>	"    -->%s in Bend[%d] in %s\n",
293	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297
298	<	// initialize the molecule's stampID's
298	>	current_extra = current_extra->getNext();
299	>	}
300	>	}
301
302	<	#ifdef IS_MPI
303	<
302	>	if (!theBends[j].isGhost){
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].c;
305	>	}
306	>	else{
307	>	exI = theBends[j].a;
308	>	exJ = theBends[j].b;
309	>	}
310
311	<	molIndex = 0;
312	<	for(i=0; i<mpiSim->getTotNmol(); i++){
313	<
314	<	if(mol2proc[i] == worldRank ){
315	<	the_molecules[molIndex].setStampID( molCompType[i] );
316	<	the_molecules[molIndex].setMyIndex( molIndex );
317	<	the_molecules[molIndex].setGlobalIndex( i );
318	<	molIndex++;
319	<	}
320	<	}
311	>	// exclude_I must always be the smaller of the pair
312	>	if (exI > exJ){
313	>	tempEx = exI;
314	>	exI = exJ;
315	>	exJ = tempEx;
316	>	}
317	>	#ifdef IS_MPI
318	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322
323	<	#else // is_mpi
324	<
325	<	molIndex = 0;
326	<	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++;
323	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
324	>	#else  // isn't MPI
325	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
326	>	#endif  //is_mpi
327		}
328	<	molIndex++;
449	<	}
450	<	}
451	<
328	>	excludeOffset += molInfo.nBends;
329
330	<	#endif // is_mpi
330	>	for (j = 0; j < molInfo.nTorsions; j++){
331	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
332	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
333	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
334	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
335	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
336
337	+	exI = theTorsions[j].a;
338	+	exJ = theTorsions[j].d;
339
340	<	if( simnfo->n_SRI ){
341	<
342	<	Exclude::createArray(simnfo->n_SRI);
343	<	the_excludes = new Exclude*[simnfo->n_SRI];
344	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
345	<	simnfo->globalExcludes = new int;
346	<	simnfo->n_exclude = simnfo->n_SRI;
347	<	}
348	<	else{
349	<
350	<	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	<	}
340	>	// exclude_I must always be the smaller of the pair
341	>	if (exI > exJ){
342	>	tempEx = exI;
343	>	exI = exJ;
344	>	exJ = tempEx;
345	>	}
346	>	#ifdef IS_MPI
347	>	tempEx = exI;
348	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	>	tempEx = exJ;
350	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351
352	<	// set the arrays into the SimInfo object
352	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
353	>	#else  // isn't MPI
354	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
355	>	#endif  //is_mpi
356	>	}
357	>	excludeOffset += molInfo.nTorsions;
358
477	–	simnfo->atoms = the_atoms;
478	–	simnfo->molecules = the_molecules;
479	–	simnfo->nGlobalExcludes = 0;
480	–	simnfo->excludes = the_excludes;
359
360	+	// send the arrays off to the forceField for init.
361
362	<	// get some of the tricky things that may still be in the globals
362	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
363	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
364	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
365	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
366	>	theTorsions);
367
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() ){
368
369	<	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];
369	>	info[k].molecules[i].initialize(molInfo);
370
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();
371
372	<	if( !the_globals->haveBoxY() ){
373	<	sprintf( painCave.errMsg,
374	<	"SimSetup error, no periodic BoxY size given.\n" );
375	<	painCave.isFatal = 1;
516	<	simError();
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376		}
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 );
377		}
378
379		#ifdef IS_MPI
380	<	strcpy( checkPointMsg, "Box size set up" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383
384	+	// clean up the forcefield
385
386	<	// initialize the arrays
386	>	the_ff->calcRcut();
387	>	the_ff->cleanMe();
388	>	}
389
390	<	the_ff->setSimInfo( simnfo );
390	>	void SimSetup::initFromBass(void){
391	>	int i, j, k;
392	>	int n_cells;
393	>	double cellx, celly, cellz;
394	>	double temp1, temp2, temp3;
395	>	int n_per_extra;
396	>	int n_extra;
397	>	int have_extra, done;
398
399	<	makeMolecules();
400	<	simnfo->identArray = new int[simnfo->n_atoms];
401	<	for(i=0; i<simnfo->n_atoms; i++){
402	<	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	<	}
399	>	double vel[3];
400	>	vel[0] = 0.0;
401	>	vel[1] = 0.0;
402	>	vel[2] = 0.0;
403
404	<	if( !the_globals->haveEST() ){
405	<	sprintf( painCave.errMsg,
406	<	"SimSetup Warning: using default value of 0.05 * the "
407	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
408	<	);
409	<	painCave.isFatal = 0;
410	<	simError();
411	<	simnfo->est = 0.05 * simnfo->ecr;
412	<	} else {
413	<	simnfo->est        = the_globals->getEST();
414	<	}
415	<
416	<	if(!the_globals->haveDielectric() ){
417	<	sprintf( painCave.errMsg,
418	<	"SimSetup Error: You are trying to use Reaction Field without"
419	<	"setting a dielectric constant!\n"
420	<	);
404	>	temp1 = (double) tot_nmol / 4.0;
405	>	temp2 = pow(temp1, (1.0 / 3.0));
406	>	temp3 = ceil(temp2);
407	>
408	>	have_extra = 0;
409	>	if (temp2 < temp3){
410	>	// we have a non-complete lattice
411	>	have_extra = 1;
412	>
413	>	n_cells = (int) temp3 - 1;
414	>	cellx = info[0].boxL[0] / temp3;
415	>	celly = info[0].boxL[1] / temp3;
416	>	cellz = info[0].boxL[2] / temp3;
417	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
418	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
419	>	n_per_extra = (int) ceil(temp1);
420	>
421	>	if (n_per_extra > 4){
422	>	sprintf(painCave.errMsg,
423	>	"SimSetup error. There has been an error in constructing"
424	>	" the non-complete lattice.\n");
425		painCave.isFatal = 1;
426		simError();
427		}
428	<	simnfo->dielectric = the_globals->getDielectric();
429	<	} else {
430	<	if (usesDipoles) {
431	<
432	<	if( !the_globals->haveECR() ){
433	<	sprintf( painCave.errMsg,
434	<	"SimSetup Warning: using default value of 1/2 the smallest "
593	<	"box length for the electrostaticCutoffRadius.\n"
594	<	"I hope you have a very fast processor!\n");
595	<	painCave.isFatal = 0;
596	<	simError();
597	<	double smallest;
598	<	smallest = simnfo->boxLx;
599	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
600	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
601	<	simnfo->ecr = 0.5 * smallest;
602	<	} else {
603	<	simnfo->ecr        = the_globals->getECR();
604	<	}
605	<
606	<	if( !the_globals->haveEST() ){
607	<	sprintf( painCave.errMsg,
608	<	"SimSetup Warning: using default value of 5%% of the "
609	<	"electrostaticCutoffRadius for the "
610	<	"electrostaticSkinThickness\n"
611	<	);
612	<	painCave.isFatal = 0;
613	<	simError();
614	<	simnfo->est = 0.05 * simnfo->ecr;
615	<	} else {
616	<	simnfo->est        = the_globals->getEST();
617	<	}
618	<	}
619	<	}
428	>	}
429	>	else{
430	>	n_cells = (int) temp3;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434	>	}
435
436	<	#ifdef IS_MPI
437	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
438	<	MPIcheckPoint();
439	<	#endif // is_mpi
436	>	current_mol = 0;
437	>	current_comp_mol = 0;
438	>	current_comp = 0;
439	>	current_atom_ndx = 0;
440
441	<	if( the_globals->haveInitialConfig() ){
442	<
443	<	InitializeFromFile* fileInit;
444	<	#ifdef IS_MPI // is_mpi
630	<	if( worldRank == 0 ){
631	<	#endif //is_mpi
632	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
633	<	#ifdef IS_MPI
634	<	}else fileInit = new InitializeFromFile( NULL );
635	<	#endif
636	<	fileInit->read_xyz( simnfo ); // default velocities on
441	>	for (i = 0; i < n_cells ; i++){
442	>	for (j = 0; j < n_cells; j++){
443	>	for (k = 0; k < n_cells; k++){
444	>	makeElement(i * cellx, j * celly, k * cellz);
445
446	<	delete fileInit;
639	<	}
640	<	else{
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447
448	<	#ifdef IS_MPI
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449
450	<	// no init from bass
451	<
452	<	sprintf( painCave.errMsg,
453	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
648	<	painCave.isFatal;
649	<	simError();
650	<
651	<	#else
450	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
451	>	}
452	>	}
453	>	}
454
455	<	initFromBass();
455	>	if (have_extra){
456	>	done = 0;
457
458	+	int start_ndx;
459	+	for (i = 0; i < (n_cells + 1) && !done; i++){
460	+	for (j = 0; j < (n_cells + 1) && !done; j++){
461	+	if (i < n_cells){
462	+	if (j < n_cells){
463	+	start_ndx = n_cells;
464	+	}
465	+	else
466	+	start_ndx = 0;
467	+	}
468	+	else
469	+	start_ndx = 0;
470
471	<	#endif
472	<	}
471	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
472	>	makeElement(i * cellx, j * celly, k * cellz);
473	>	done = (current_mol >= tot_nmol);
474
475	<	#ifdef IS_MPI
476	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
477	<	MPIcheckPoint();
478	<	#endif // is_mpi
475	>	if (!done && n_per_extra > 1){
476	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
477	>	k * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	+	if (!done && n_per_extra > 2){
482	+	makeElement(i * cellx, j * celly + 0.5 * celly,
483	+	k * cellz + 0.5 * cellz);
484	+	done = (current_mol >= tot_nmol);
485	+	}
486
487	<
488	<
489	<
490	<
491	<
492	<	#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" );
487	>	if (!done && n_per_extra > 3){
488	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
489	>	k * cellz + 0.5 * cellz);
490	>	done = (current_mol >= tot_nmol);
491	>	}
492	>	}
493		}
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	–	}
494		}
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
495		}
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	–	}
496
497	<	if( the_globals->haveStatusTime() ){
498	<	simnfo->statusTime = the_globals->getStatusTime();
497	>	for (i = 0; i < info[0].n_atoms; i++){
498	>	info[0].atoms[i]->setVel(vel);
499		}
500	+	}
501
502	<	if( the_globals->haveThermalTime() ){
503	<	simnfo->thermalTime = the_globals->getThermalTime();
504	<	}
502	>	void SimSetup::makeElement(double x, double y, double z){
503	>	int k;
504	>	AtomStamp* current_atom;
505	>	DirectionalAtom* dAtom;
506	>	double rotMat[3][3];
507	>	double pos[3];
508
509	<	// check for the temperature set flag
509	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
510	>	current_atom = comp_stamps[current_comp]->getAtom(k);
511	>	if (!current_atom->havePosition()){
512	>	sprintf(painCave.errMsg,
513	>	"SimSetup:initFromBass error.\n"
514	>	"\tComponent %s, atom %s does not have a position specified.\n"
515	>	"\tThe initialization routine is unable to give a start"
516	>	" position.\n",
517	>	comp_stamps[current_comp]->getID(), current_atom->getType());
518	>	painCave.isFatal = 1;
519	>	simError();
520	>	}
521
522	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
522	>	pos[0] = x + current_atom->getPosX();
523	>	pos[1] = y + current_atom->getPosY();
524	>	pos[2] = z + current_atom->getPosZ();
525
526	+	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<	// make the integrator
529	<
781	<
782	<	NVT* myNVT = NULL;
783	<	switch( ensembleCase ){
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530
531	<	case NVE_ENS:
532	<	new NVE( simnfo, the_ff );
533	<	break;
531	>	rotMat[0][0] = 1.0;
532	>	rotMat[0][1] = 0.0;
533	>	rotMat[0][2] = 0.0;
534
535	<	case NVT_ENS:
536	<	myNVT = new NVT( simnfo, the_ff );
537	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
535	>	rotMat[1][0] = 0.0;
536	>	rotMat[1][1] = 1.0;
537	>	rotMat[1][2] = 0.0;
538
539	<	if (the_globals->haveTauThermostat())
540	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
541	<	//     else if (the_globals->haveQmass())
542	<	//       myNVT->setQmass(the_globals->getQmass());
543	<	else {
798	<	sprintf( painCave.errMsg,
799	<	"SimSetup error: If you use the NVT\n"
800	<	"    ensemble, you must set either tauThermostat or qMass.\n"
801	<	"    Neither of these was found in the BASS file.\n");
802	<	painCave.isFatal = 1;
803	<	simError();
539	>	rotMat[2][0] = 0.0;
540	>	rotMat[2][1] = 0.0;
541	>	rotMat[2][2] = 1.0;
542	>
543	>	dAtom->setA(rotMat);
544		}
805	–	break;
545
546	<	default:
808	<	sprintf( painCave.errMsg,
809	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
810	<	painCave.isFatal = 1;
811	<	simError();
546	>	current_atom_ndx++;
547		}
548
549	+	current_mol++;
550	+	current_comp_mol++;
551
552	<	#ifdef IS_MPI
553	<	mpiSim->mpiRefresh();
554	<	#endif
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553	>	current_comp_mol = 0;
554	>	current_comp++;
555	>	}
556	>	}
557
819	–	// initialize the Fortran
558
559	+	void SimSetup::gatherInfo(void){
560	+	int i;
561
562	<	simnfo->refreshSim();
563	<
564	<	if( !strcmp( simnfo->mixingRule, "standard") ){
565	<	the_ff->initForceField( LB_MIXING_RULE );
562	>	ensembleCase = -1;
563	>	ffCase = -1;
564	>
565	>	// set the easy ones first
566	>
567	>	for (i = 0; i < nInfo; i++){
568	>	info[i].target_temp = globals->getTargetTemp();
569	>	info[i].dt = globals->getDt();
570	>	info[i].run_time = globals->getRunTime();
571		}
572	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
573	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
572	>	n_components = globals->getNComponents();
573	>
574	>
575	>	// get the forceField
576	>
577	>	strcpy(force_field, globals->getForceField());
578	>
579	>	if (!strcasecmp(force_field, "DUFF")){
580	>	ffCase = FF_DUFF;
581		}
582	+	else if (!strcasecmp(force_field, "LJ")){
583	+	ffCase = FF_LJ;
584	+	}
585	+	else if (!strcasecmp(force_field, "EAM")){
586	+	ffCase = FF_EAM;
587	+	}
588		else{
589	<	sprintf( painCave.errMsg,
590	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
591	<	simnfo->mixingRule );
592	<	painCave.isFatal = 1;
835	<	simError();
589	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
590	>	force_field);
591	>	painCave.isFatal = 1;
592	>	simError();
593		}
594
595	+	// get the ensemble
596
597	<	#ifdef IS_MPI
840	<	strcpy( checkPointMsg,
841	<	"Successfully intialized the mixingRule for Fortran." );
842	<	MPIcheckPoint();
843	<	#endif // is_mpi
844	<	}
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	+	if (!strcasecmp(ensemble, "NVE")){
600	+	ensembleCase = NVE_ENS;
601	+	}
602	+	else if (!strcasecmp(ensemble, "NVT")){
603	+	ensembleCase = NVT_ENS;
604	+	}
605	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
606	+	ensembleCase = NPTi_ENS;
607	+	}
608	+	else if (!strcasecmp(ensemble, "NPTf")){
609	+	ensembleCase = NPTf_ENS;
610	+	}
611	+	else if (!strcasecmp(ensemble, "NPTxyz")){
612	+	ensembleCase = NPTxyz_ENS;
613	+	}
614	+	else{
615	+	sprintf(painCave.errMsg,
616	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	+	"reverting to NVE for this simulation.\n",
618	+	ensemble);
619	+	painCave.isFatal = 0;
620	+	simError();
621	+	strcpy(ensemble, "NVE");
622	+	ensembleCase = NVE_ENS;
623	+	}
624
625	<	void SimSetup::makeMolecules( void ){
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627
628	<	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;
628	>	// get the mixing rule
629
630	<	bond_pair* theBonds;
631	<	bend_set* theBends;
632	<	torsion_set* theTorsions;
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632	>	}
633
634	<
864	<	//init the forceField paramters
634	>	// get the components and calculate the tot_nMol and indvidual n_mol
635
636	<	the_ff->readParams();
636	>	the_components = globals->getComponents();
637	>	components_nmol = new int[n_components];
638
868	–
869	–	// init the atoms
639
640	<	double ux, uy, uz, u, uSqr;
641	<
642	<	atomOffset = 0;
874	<	excludeOffset = 0;
875	<	for(i=0; i<simnfo->n_mol; i++){
876	<
877	<	stampID = the_molecules[i].getStampID();
640	>	if (!globals->haveNMol()){
641	>	// we don't have the total number of molecules, so we assume it is
642	>	// given in each component
643
644	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
645	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
646	<	info.nBends    = comp_stamps[stampID]->getNBends();
647	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
648	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
644	>	tot_nmol = 0;
645	>	for (i = 0; i < n_components; i++){
646	>	if (!the_components[i]->haveNMol()){
647	>	// we have a problem
648	>	sprintf(painCave.errMsg,
649	>	"SimSetup Error. No global NMol or component NMol"
650	>	" given. Cannot calculate the number of atoms.\n");
651	>	painCave.isFatal = 1;
652	>	simError();
653	>	}
654
655	<	info.myAtoms = &the_atoms[atomOffset];
656	<	info.myExcludes = &the_excludes[excludeOffset];
657	<	info.myBonds = new Bond*[info.nBonds];
658	<	info.myBends = new Bend*[info.nBends];
659	<	info.myTorsions = new Torsion*[info.nTorsions];
655	>	tot_nmol += the_components[i]->getNMol();
656	>	components_nmol[i] = the_components[i]->getNMol();
657	>	}
658	>	}
659	>	else{
660	>	sprintf(painCave.errMsg,
661	>	"SimSetup error.\n"
662	>	"\tSorry, the ability to specify total"
663	>	" nMols and then give molfractions in the components\n"
664	>	"\tis not currently supported."
665	>	" Please give nMol in the components.\n");
666	>	painCave.isFatal = 1;
667	>	simError();
668	>	}
669
670	<	theBonds = new bond_pair[info.nBonds];
671	<	theBends = new bend_set[info.nBends];
672	<	theTorsions = new torsion_set[info.nTorsions];
670	>	// set the status, sample, and thermal kick times
671	>
672	>	for (i = 0; i < nInfo; i++){
673	>	if (globals->haveSampleTime()){
674	>	info[i].sampleTime = globals->getSampleTime();
675	>	info[i].statusTime = info[i].sampleTime;
676	>	info[i].thermalTime = info[i].sampleTime;
677	>	}
678	>	else{
679	>	info[i].sampleTime = globals->getRunTime();
680	>	info[i].statusTime = info[i].sampleTime;
681	>	info[i].thermalTime = info[i].sampleTime;
682	>	}
683	>
684	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686	>	}
687	>
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690	>	}
691	>
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696	>	}
697	>
698	>	// check for the temperature set flag
699
700	<	// make the Atoms
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702	>
703	>	// check for the extended State init
704	>
705	>	info[i].useInitXSstate = globals->getUseInitXSstate();
706	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
707
708	<	for(j=0; j<info.nAtoms; j++){
709	<
710	<	currentAtom = comp_stamps[stampID]->getAtom( j );
711	<	if( currentAtom->haveOrientation() ){
712	<
713	<	dAtom = new DirectionalAtom(j + atomOffset);
714	<	simnfo->n_oriented++;
715	<	info.myAtoms[j] = dAtom;
716	<
717	<	ux = currentAtom->getOrntX();
718	<	uy = currentAtom->getOrntY();
719	<	uz = currentAtom->getOrntZ();
720	<
721	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
722	<
723	<	u = sqrt( uSqr );
724	<	ux = ux / u;
725	<	uy = uy / u;
726	<	uz = uz / u;
727	<
728	<	dAtom->setSUx( ux );
918	<	dAtom->setSUy( uy );
919	<	dAtom->setSUz( uz );
708	>	}
709	>
710	>	//setup seed for random number generator
711	>	int seedValue;
712	>
713	>	if (globals->haveSeed()){
714	>	seedValue = globals->getSeed();
715	>
716	>	if(seedValue / 1E9 == 0){
717	>	sprintf(painCave.errMsg,
718	>	"Seed for sprng library should contain at least 9 digits\n"
719	>	"OOPSE will generate a seed for user\n");
720	>	painCave.isFatal = 0;
721	>	simError();
722	>
723	>	//using seed generated by system instead of invalid seed set by user
724	>	#ifndef IS_MPI
725	>	seedValue = make_sprng_seed();
726	>	#else
727	>	if (worldRank == 0){
728	>	seedValue = make_sprng_seed();
729		}
730	<	else{
731	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
732	<	}
733	<	info.myAtoms[j]->setType( currentAtom->getType() );
730	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
731	>	#endif
732	>	}
733	>	}//end of if branch of globals->haveSeed()
734	>	else{
735
736	+	#ifndef IS_MPI
737	+	seedValue = make_sprng_seed();
738	+	#else
739	+	if (worldRank == 0){
740	+	seedValue = make_sprng_seed();
741	+	}
742	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
743	+	#endif
744	+	}//end of globals->haveSeed()
745	+
746	+	for (int i = 0; i < nInfo; i++){
747	+	info[i].setSeed(seedValue);
748	+	}
749	+
750		#ifdef IS_MPI
751	<
752	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
929	<
751	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
752	>	MPIcheckPoint();
753		#endif // is_mpi
754	<	}
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;
754	>	}
755
940	–	exI = theBonds[j].a;
941	–	exJ = theBonds[j].b;
756
757	<	// exclude_I must always be the smaller of the pair
758	<	if( exI > exJ ){
759	<	tempEx = exI;
760	<	exI = exJ;
947	<	exJ = tempEx;
948	<	}
949	<	#ifdef IS_MPI
950	<	tempEx = exI;
951	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
952	<	tempEx = exJ;
953	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
954	<
955	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
956	<	#else  // isn't MPI
757	>	void SimSetup::finalInfoCheck(void){
758	>	int index;
759	>	int usesDipoles;
760	>	int i;
761
762	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
763	<	#endif  //is_mpi
762	>	for (i = 0; i < nInfo; i++){
763	>	// check electrostatic parameters
764	>
765	>	index = 0;
766	>	usesDipoles = 0;
767	>	while ((index < info[i].n_atoms) && !usesDipoles){
768	>	usesDipoles = (info[i].atoms[index])->hasDipole();
769	>	index++;
770		}
961	–	excludeOffset += info.nBonds;
771
772	<	//make the bends
773	<	for(j=0; j<info.nBends; j++){
774	<
775	<	currentBend = comp_stamps[stampID]->getBend( j );
776	<	theBends[j].a = currentBend->getA() + atomOffset;
777	<	theBends[j].b = currentBend->getB() + atomOffset;
778	<	theBends[j].c = currentBend->getC() + atomOffset;
779	<
780	<	if( currentBend->haveExtras() ){
781	<
782	<	extras = currentBend->getExtras();
783	<	current_extra = extras;
784	<
785	<	while( current_extra != NULL ){
786	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
787	<
788	<	switch( current_extra->getType() ){
789	<
790	<	case 0:
791	<	theBends[j].ghost =
792	<	current_extra->getInt() + atomOffset;
793	<	theBends[j].isGhost = 1;
794	<	break;
795	<
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;
772	>	#ifdef IS_MPI
773	>	int myUse = usesDipoles;
774	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775	>	#endif //is_mpi
776	>
777	>	double theEcr, theEst;
778	>
779	>	if (globals->getUseRF()){
780	>	info[i].useReactionField = 1;
781	>
782	>	if (!globals->haveECR()){
783	>	sprintf(painCave.errMsg,
784	>	"SimSetup Warning: using default value of 1/2 the smallest "
785	>	"box length for the electrostaticCutoffRadius.\n"
786	>	"I hope you have a very fast processor!\n");
787	>	painCave.isFatal = 0;
788	>	simError();
789	>	double smallest;
790	>	smallest = info[i].boxL[0];
791	>	if (info[i].boxL[1] <= smallest)
792	>	smallest = info[i].boxL[1];
793	>	if (info[i].boxL[2] <= smallest)
794	>	smallest = info[i].boxL[2];
795	>	theEcr = 0.5 * smallest;
796		}
797		else{
798	<
1026	<	exI = theBends[j].a;
1027	<	exJ = theBends[j].b;
798	>	theEcr = globals->getECR();
799		}
800	<
801	<	// exclude_I must always be the smaller of the pair
802	<	if( exI > exJ ){
803	<	tempEx = exI;
804	<	exI = exJ;
805	<	exJ = tempEx;
800	>
801	>	if (!globals->haveEST()){
802	>	sprintf(painCave.errMsg,
803	>	"SimSetup Warning: using default value of 0.05 * the "
804	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
805	>	painCave.isFatal = 0;
806	>	simError();
807	>	theEst = 0.05 * theEcr;
808		}
809	<	#ifdef IS_MPI
810	<	tempEx = exI;
811	<	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
1046	<	}
1047	<	excludeOffset += info.nBends;
809	>	else{
810	>	theEst = globals->getEST();
811	>	}
812
813	<	for(j=0; j<info.nTorsions; j++){
1050	<
1051	<	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;
813	>	info[i].setDefaultEcr(theEcr, theEst);
814
815	<	// exclude_I must always be the smaller of the pair
816	<	if( exI > exJ ){
817	<	tempEx = exI;
818	<	exI = exJ;
819	<	exJ = tempEx;
815	>	if (!globals->haveDielectric()){
816	>	sprintf(painCave.errMsg,
817	>	"SimSetup Error: You are trying to use Reaction Field without"
818	>	"setting a dielectric constant!\n");
819	>	painCave.isFatal = 1;
820	>	simError();
821		}
822	<	#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
822	>	info[i].dielectric = globals->getDielectric();
823		}
824	<	excludeOffset += info.nTorsions;
824	>	else{
825	>	if (usesDipoles){
826	>	if (!globals->haveECR()){
827	>	sprintf(painCave.errMsg,
828	>	"SimSetup Warning: using default value of 1/2 the smallest "
829	>	"box length for the electrostaticCutoffRadius.\n"
830	>	"I hope you have a very fast processor!\n");
831	>	painCave.isFatal = 0;
832	>	simError();
833	>	double smallest;
834	>	smallest = info[i].boxL[0];
835	>	if (info[i].boxL[1] <= smallest)
836	>	smallest = info[i].boxL[1];
837	>	if (info[i].boxL[2] <= smallest)
838	>	smallest = info[i].boxL[2];
839	>	theEcr = 0.5 * smallest;
840	>	}
841	>	else{
842	>	theEcr = globals->getECR();
843	>	}
844
845	<
846	<	// send the arrays off to the forceField for init.
845	>	if (!globals->haveEST()){
846	>	sprintf(painCave.errMsg,
847	>	"SimSetup Warning: using default value of 0.05 * the "
848	>	"electrostaticCutoffRadius for the "
849	>	"electrostaticSkinThickness\n");
850	>	painCave.isFatal = 0;
851	>	simError();
852	>	theEst = 0.05 * theEcr;
853	>	}
854	>	else{
855	>	theEst = globals->getEST();
856	>	}
857
858	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
859	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
860	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1085	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
858	>	info[i].setDefaultEcr(theEcr, theEst);
859	>	}
860	>	}
861
862	<
863	<	the_molecules[i].initialize( info );
1089	<
1090	<
1091	<	atomOffset += info.nAtoms;
1092	<	delete[] theBonds;
1093	<	delete[] theBends;
1094	<	delete[] theTorsions;
862	>	if( !initSuspend )
863	>	info[i].checkCutOffs();
864		}
865
866		#ifdef IS_MPI
867	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
867	>	strcpy(checkPointMsg, "post processing checks out");
868		MPIcheckPoint();
869		#endif // is_mpi
1101	–
1102	–	// clean up the forcefield
1103	–	the_ff->calcRcut();
1104	–	the_ff->cleanMe();
1105	–
870		}
871
872	<	void SimSetup::initFromBass( void ){
872	>	void SimSetup::initSystemCoords(void){
873	>	int i;
874
875	<	int i, j, k;
1111	<	int n_cells;
1112	<	double cellx, celly, cellz;
1113	<	double temp1, temp2, temp3;
1114	<	int n_per_extra;
1115	<	int n_extra;
1116	<	int have_extra, done;
875	>	char* inName;
876
877	<	temp1 = (double)tot_nmol / 4.0;
1119	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1120	<	temp3 = ceil( temp2 );
877	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
878
879	<	have_extra =0;
880	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1124	<	have_extra =1;
879	>	for (i = 0; i < info[0].n_atoms; i++)
880	>	info[0].atoms[i]->setCoords();
881
882	<	n_cells = (int)temp3 - 1;
883	<	cellx = simnfo->boxLx / temp3;
884	<	celly = simnfo->boxLy / temp3;
885	<	cellz = simnfo->boxLz / temp3;
886	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
887	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
888	<	n_per_extra = (int)ceil( temp1 );
889	<
1134	<	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();
882	>	if (globals->haveInitialConfig()){
883	>	InitializeFromFile* fileInit;
884	>	#ifdef IS_MPI // is_mpi
885	>	if (worldRank == 0){
886	>	#endif //is_mpi
887	>	inName = globals->getInitialConfig();
888	>	fileInit = new InitializeFromFile(inName);
889	>	#ifdef IS_MPI
890		}
891	+	else
892	+	fileInit = new InitializeFromFile(NULL);
893	+	#endif
894	+	fileInit->readInit(info); // default velocities on
895	+
896	+	delete fileInit;
897		}
898		else{
899	<	n_cells = (int)temp3;
1144	<	cellx = simnfo->boxLx / temp3;
1145	<	celly = simnfo->boxLy / temp3;
1146	<	cellz = simnfo->boxLz / temp3;
1147	<	}
899	>	#ifdef IS_MPI
900
901	<	current_mol = 0;
1150	<	current_comp_mol = 0;
1151	<	current_comp = 0;
1152	<	current_atom_ndx = 0;
901	>	// no init from bass
902
903	<	for( i=0; i < n_cells ; i++ ){
904	<	for( j=0; j < n_cells; j++ ){
905	<	for( k=0; k < n_cells; k++ ){
903	>	sprintf(painCave.errMsg,
904	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
905	>	painCave.isFatal = 1;;
906	>	simError();
907
908	<	makeElement( i * cellx,
1159	<	j * celly,
1160	<	k * cellz );
908	>	#else
909
910	<	makeElement( i * cellx + 0.5 * cellx,
1163	<	j * celly + 0.5 * celly,
1164	<	k * cellz );
910	>	initFromBass();
911
1166	–	makeElement( i * cellx,
1167	–	j * celly + 0.5 * celly,
1168	–	k * cellz + 0.5 * cellz );
912
913	<	makeElement( i * cellx + 0.5 * cellx,
1171	<	j * celly,
1172	<	k * cellz + 0.5 * cellz );
1173	<	}
1174	<	}
913	>	#endif
914		}
915
916	<	if( have_extra ){
917	<	done = 0;
918	<
919	<	int start_ndx;
1181	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1182	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1183	<
1184	<	if( i < n_cells ){
1185	<
1186	<	if( j < n_cells ){
1187	<	start_ndx = n_cells;
1188	<	}
1189	<	else start_ndx = 0;
1190	<	}
1191	<	else start_ndx = 0;
1192	<
1193	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1194	<
1195	<	makeElement( i * cellx,
1196	<	j * celly,
1197	<	k * cellz );
1198	<	done = ( current_mol >= tot_nmol );
1199	<
1200	<	if( !done && n_per_extra > 1 ){
1201	<	makeElement( i * cellx + 0.5 * cellx,
1202	<	j * celly + 0.5 * celly,
1203	<	k * cellz );
1204	<	done = ( current_mol >= tot_nmol );
1205	<	}
1206	<
1207	<	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	<	}
1213	<
1214	<	if( !done && n_per_extra > 3){
1215	<	makeElement( i * cellx + 0.5 * cellx,
1216	<	j * celly,
1217	<	k * cellz + 0.5 * cellz );
1218	<	done = ( current_mol >= tot_nmol );
1219	<	}
1220	<	}
1221	<	}
1222	<	}
1223	<	}
1224	<
1225	<
1226	<	for( i=0; i<simnfo->n_atoms; i++ ){
1227	<	simnfo->atoms[i]->set_vx( 0.0 );
1228	<	simnfo->atoms[i]->set_vy( 0.0 );
1229	<	simnfo->atoms[i]->set_vz( 0.0 );
1230	<	}
916	>	#ifdef IS_MPI
917	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
918	>	MPIcheckPoint();
919	>	#endif // is_mpi
920		}
921
1233	–	void SimSetup::makeElement( double x, double y, double z ){
922
923	+	void SimSetup::makeOutNames(void){
924		int k;
1236	–	AtomStamp* current_atom;
1237	–	DirectionalAtom* dAtom;
1238	–	double rotMat[3][3];
925
1240	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
926
927	<	current_atom = comp_stamps[current_comp]->getAtom( k );
928	<	if( !current_atom->havePosition() ){
929	<	sprintf( painCave.errMsg,
930	<	"SimSetup:initFromBass error.\n"
931	<	"\tComponent %s, atom %s does not have a position specified.\n"
932	<	"\tThe initialization routine is unable to give a start"
933	<	" position.\n",
934	<	comp_stamps[current_comp]->getID(),
935	<	current_atom->getType() );
936	<	painCave.isFatal = 1;
937	<	simError();
938	<	}
939	<
940	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
941	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
942	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
943	<
944	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
945	<
946	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
947	<
948	<	rotMat[0][0] = 1.0;
949	<	rotMat[0][1] = 0.0;
950	<	rotMat[0][2] = 0.0;
951	<
952	<	rotMat[1][0] = 0.0;
953	<	rotMat[1][1] = 1.0;
954	<	rotMat[1][2] = 0.0;
955	<
956	<	rotMat[2][0] = 0.0;
957	<	rotMat[2][1] = 0.0;
958	<	rotMat[2][2] = 1.0;
959	<
960	<	dAtom->setA( rotMat );
927	>	for (k = 0; k < nInfo; k++){
928	>	#ifdef IS_MPI
929	>	if (worldRank == 0){
930	>	#endif // is_mpi
931	>
932	>	if (globals->haveFinalConfig()){
933	>	strcpy(info[k].finalName, globals->getFinalConfig());
934	>	}
935	>	else{
936	>	strcpy(info[k].finalName, inFileName);
937	>	char* endTest;
938	>	int nameLength = strlen(info[k].finalName);
939	>	endTest = &(info[k].finalName[nameLength - 5]);
940	>	if (!strcmp(endTest, ".bass")){
941	>	strcpy(endTest, ".eor");
942	>	}
943	>	else if (!strcmp(endTest, ".BASS")){
944	>	strcpy(endTest, ".eor");
945	>	}
946	>	else{
947	>	endTest = &(info[k].finalName[nameLength - 4]);
948	>	if (!strcmp(endTest, ".bss")){
949	>	strcpy(endTest, ".eor");
950	>	}
951	>	else if (!strcmp(endTest, ".mdl")){
952	>	strcpy(endTest, ".eor");
953	>	}
954	>	else{
955	>	strcat(info[k].finalName, ".eor");
956	>	}
957	>	}
958	>	}
959	>
960	>	// make the sample and status out names
961	>
962	>	strcpy(info[k].sampleName, inFileName);
963	>	char* endTest;
964	>	int nameLength = strlen(info[k].sampleName);
965	>	endTest = &(info[k].sampleName[nameLength - 5]);
966	>	if (!strcmp(endTest, ".bass")){
967	>	strcpy(endTest, ".dump");
968	>	}
969	>	else if (!strcmp(endTest, ".BASS")){
970	>	strcpy(endTest, ".dump");
971	>	}
972	>	else{
973	>	endTest = &(info[k].sampleName[nameLength - 4]);
974	>	if (!strcmp(endTest, ".bss")){
975	>	strcpy(endTest, ".dump");
976	>	}
977	>	else if (!strcmp(endTest, ".mdl")){
978	>	strcpy(endTest, ".dump");
979	>	}
980	>	else{
981	>	strcat(info[k].sampleName, ".dump");
982	>	}
983	>	}
984	>
985	>	strcpy(info[k].statusName, inFileName);
986	>	nameLength = strlen(info[k].statusName);
987	>	endTest = &(info[k].statusName[nameLength - 5]);
988	>	if (!strcmp(endTest, ".bass")){
989	>	strcpy(endTest, ".stat");
990	>	}
991	>	else if (!strcmp(endTest, ".BASS")){
992	>	strcpy(endTest, ".stat");
993	>	}
994	>	else{
995	>	endTest = &(info[k].statusName[nameLength - 4]);
996	>	if (!strcmp(endTest, ".bss")){
997	>	strcpy(endTest, ".stat");
998	>	}
999	>	else if (!strcmp(endTest, ".mdl")){
1000	>	strcpy(endTest, ".stat");
1001	>	}
1002	>	else{
1003	>	strcat(info[k].statusName, ".stat");
1004	>	}
1005	>	}
1006	>
1007	>	#ifdef IS_MPI
1008	>
1009		}
1010	+	#endif // is_mpi
1011	+	}
1012	+	}
1013
1014	<	current_atom_ndx++;
1014	>
1015	>	void SimSetup::sysObjectsCreation(void){
1016	>	int i, k;
1017	>
1018	>	// create the forceField
1019	>
1020	>	createFF();
1021	>
1022	>	// extract componentList
1023	>
1024	>	compList();
1025	>
1026	>	// calc the number of atoms, bond, bends, and torsions
1027	>
1028	>	calcSysValues();
1029	>
1030	>	#ifdef IS_MPI
1031	>	// divide the molecules among the processors
1032	>
1033	>	mpiMolDivide();
1034	>	#endif //is_mpi
1035	>
1036	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1037	>
1038	>	makeSysArrays();
1039	>
1040	>	// make and initialize the molecules (all but atomic coordinates)
1041	>
1042	>	makeMolecules();
1043	>
1044	>	for (k = 0; k < nInfo; k++){
1045	>	info[k].identArray = new int[info[k].n_atoms];
1046	>	for (i = 0; i < info[k].n_atoms; i++){
1047	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1048	>	}
1049		}
1050	+	}
1051
1281	–	current_mol++;
1282	–	current_comp_mol++;
1052
1053	<	if( current_comp_mol >= components_nmol[current_comp] ){
1053	>	void SimSetup::createFF(void){
1054	>	switch (ffCase){
1055	>	case FF_DUFF:
1056	>	the_ff = new DUFF();
1057	>	break;
1058
1059	<	current_comp_mol = 0;
1060	<	current_comp++;
1059	>	case FF_LJ:
1060	>	the_ff = new LJFF();
1061	>	break;
1062	>
1063	>	case FF_EAM:
1064	>	the_ff = new EAM_FF();
1065	>	break;
1066	>
1067	>	default:
1068	>	sprintf(painCave.errMsg,
1069	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1070	>	painCave.isFatal = 1;
1071	>	simError();
1072	>	}
1073	>
1074	>	#ifdef IS_MPI
1075	>	strcpy(checkPointMsg, "ForceField creation successful");
1076	>	MPIcheckPoint();
1077	>	#endif // is_mpi
1078	>	}
1079	>
1080	>
1081	>	void SimSetup::compList(void){
1082	>	int i;
1083	>	char* id;
1084	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1085	>	LinkedMolStamp* currentStamp = NULL;
1086	>	comp_stamps = new MoleculeStamp * [n_components];
1087	>
1088	>	// make an array of molecule stamps that match the components used.
1089	>	// also extract the used stamps out into a separate linked list
1090	>
1091	>	for (i = 0; i < nInfo; i++){
1092	>	info[i].nComponents = n_components;
1093	>	info[i].componentsNmol = components_nmol;
1094	>	info[i].compStamps = comp_stamps;
1095	>	info[i].headStamp = headStamp;
1096	>	}
1097	>
1098	>
1099	>	for (i = 0; i < n_components; i++){
1100	>	id = the_components[i]->getType();
1101	>	comp_stamps[i] = NULL;
1102	>
1103	>	// check to make sure the component isn't already in the list
1104	>
1105	>	comp_stamps[i] = headStamp->match(id);
1106	>	if (comp_stamps[i] == NULL){
1107	>	// extract the component from the list;
1108	>
1109	>	currentStamp = stamps->extractMolStamp(id);
1110	>	if (currentStamp == NULL){
1111	>	sprintf(painCave.errMsg,
1112	>	"SimSetup error: Component \"%s\" was not found in the "
1113	>	"list of declared molecules\n",
1114	>	id);
1115	>	painCave.isFatal = 1;
1116	>	simError();
1117	>	}
1118	>
1119	>	headStamp->add(currentStamp);
1120	>	comp_stamps[i] = headStamp->match(id);
1121	>	}
1122	>	}
1123	>
1124	>	#ifdef IS_MPI
1125	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1126	>	MPIcheckPoint();
1127	>	#endif // is_mpi
1128	>	}
1129	>
1130	>	void SimSetup::calcSysValues(void){
1131	>	int i;
1132	>
1133	>	int* molMembershipArray;
1134	>
1135	>	tot_atoms = 0;
1136	>	tot_bonds = 0;
1137	>	tot_bends = 0;
1138	>	tot_torsions = 0;
1139	>	for (i = 0; i < n_components; i++){
1140	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1141	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1142	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1143	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1144	>	}
1145	>
1146	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1147	>	molMembershipArray = new int[tot_atoms];
1148	>
1149	>	for (i = 0; i < nInfo; i++){
1150	>	info[i].n_atoms = tot_atoms;
1151	>	info[i].n_bonds = tot_bonds;
1152	>	info[i].n_bends = tot_bends;
1153	>	info[i].n_torsions = tot_torsions;
1154	>	info[i].n_SRI = tot_SRI;
1155	>	info[i].n_mol = tot_nmol;
1156	>
1157	>	info[i].molMembershipArray = molMembershipArray;
1158	>	}
1159	>	}
1160	>
1161	>	#ifdef IS_MPI
1162	>
1163	>	void SimSetup::mpiMolDivide(void){
1164	>	int i, j, k;
1165	>	int localMol, allMol;
1166	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1167	>
1168	>	mpiSim = new mpiSimulation(info);
1169	>
1170	>	globalIndex = mpiSim->divideLabor();
1171	>
1172	>	// set up the local variables
1173	>
1174	>	mol2proc = mpiSim->getMolToProcMap();
1175	>	molCompType = mpiSim->getMolComponentType();
1176	>
1177	>	allMol = 0;
1178	>	localMol = 0;
1179	>	local_atoms = 0;
1180	>	local_bonds = 0;
1181	>	local_bends = 0;
1182	>	local_torsions = 0;
1183	>	globalAtomIndex = 0;
1184	>
1185	>
1186	>	for (i = 0; i < n_components; i++){
1187	>	for (j = 0; j < components_nmol[i]; j++){
1188	>	if (mol2proc[allMol] == worldRank){
1189	>	local_atoms += comp_stamps[i]->getNAtoms();
1190	>	local_bonds += comp_stamps[i]->getNBonds();
1191	>	local_bends += comp_stamps[i]->getNBends();
1192	>	local_torsions += comp_stamps[i]->getNTorsions();
1193	>	localMol++;
1194	>	}
1195	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1196	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1197	>	globalAtomIndex++;
1198	>	}
1199	>
1200	>	allMol++;
1201	>	}
1202	>	}
1203	>	local_SRI = local_bonds + local_bends + local_torsions;
1204	>
1205	>	info[0].n_atoms = mpiSim->getMyNlocal();
1206	>
1207	>	if (local_atoms != info[0].n_atoms){
1208	>	sprintf(painCave.errMsg,
1209	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1210	>	" localAtom (%d) are not equal.\n",
1211	>	info[0].n_atoms, local_atoms);
1212	>	painCave.isFatal = 1;
1213	>	simError();
1214	>	}
1215	>
1216	>	info[0].n_bonds = local_bonds;
1217	>	info[0].n_bends = local_bends;
1218	>	info[0].n_torsions = local_torsions;
1219	>	info[0].n_SRI = local_SRI;
1220	>	info[0].n_mol = localMol;
1221	>
1222	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1223	>	MPIcheckPoint();
1224	>	}
1225	>
1226	>	#endif // is_mpi
1227	>
1228	>
1229	>	void SimSetup::makeSysArrays(void){
1230	>
1231	>	#ifndef IS_MPI
1232	>	int k, j;
1233	>	#endif // is_mpi
1234	>	int i, l;
1235	>
1236	>	Atom** the_atoms;
1237	>	Molecule* the_molecules;
1238	>	Exclude** the_excludes;
1239	>
1240	>
1241	>	for (l = 0; l < nInfo; l++){
1242	>	// create the atom and short range interaction arrays
1243	>
1244	>	the_atoms = new Atom * [info[l].n_atoms];
1245	>	the_molecules = new Molecule[info[l].n_mol];
1246	>	int molIndex;
1247	>
1248	>	// initialize the molecule's stampID's
1249	>
1250	>	#ifdef IS_MPI
1251	>
1252	>
1253	>	molIndex = 0;
1254	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1255	>	if (mol2proc[i] == worldRank){
1256	>	the_molecules[molIndex].setStampID(molCompType[i]);
1257	>	the_molecules[molIndex].setMyIndex(molIndex);
1258	>	the_molecules[molIndex].setGlobalIndex(i);
1259	>	molIndex++;
1260	>	}
1261	>	}
1262	>
1263	>	#else // is_mpi
1264	>
1265	>	molIndex = 0;
1266	>	globalAtomIndex = 0;
1267	>	for (i = 0; i < n_components; i++){
1268	>	for (j = 0; j < components_nmol[i]; j++){
1269	>	the_molecules[molIndex].setStampID(i);
1270	>	the_molecules[molIndex].setMyIndex(molIndex);
1271	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1272	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1273	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1274	>	globalAtomIndex++;
1275	>	}
1276	>	molIndex++;
1277	>	}
1278	>	}
1279	>
1280	>
1281	>	#endif // is_mpi
1282	>
1283	>
1284	>	if (info[l].n_SRI){
1285	>	Exclude::createArray(info[l].n_SRI);
1286	>	the_excludes = new Exclude * [info[l].n_SRI];
1287	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1288	>	the_excludes[ex] = new Exclude(ex);
1289	>	}
1290	>	info[l].globalExcludes = new int;
1291	>	info[l].n_exclude = info[l].n_SRI;
1292	>	}
1293	>	else{
1294	>	Exclude::createArray(1);
1295	>	the_excludes = new Exclude * ;
1296	>	the_excludes[0] = new Exclude(0);
1297	>	the_excludes[0]->setPair(0, 0);
1298	>	info[l].globalExcludes = new int;
1299	>	info[l].globalExcludes[0] = 0;
1300	>	info[l].n_exclude = 0;
1301	>	}
1302	>
1303	>	// set the arrays into the SimInfo object
1304	>
1305	>	info[l].atoms = the_atoms;
1306	>	info[l].molecules = the_molecules;
1307	>	info[l].nGlobalExcludes = 0;
1308	>	info[l].excludes = the_excludes;
1309	>
1310	>	the_ff->setSimInfo(info);
1311		}
1312		}
1313	+
1314	+	void SimSetup::makeIntegrator(void){
1315	+	int k;
1316	+
1317	+	NVE<RealIntegrator>* myNVE = NULL;
1318	+	NVT<RealIntegrator>* myNVT = NULL;
1319	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1320	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1321	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1322	+
1323	+	for (k = 0; k < nInfo; k++){
1324	+	switch (ensembleCase){
1325	+	case NVE_ENS:
1326	+	if (globals->haveZconstraints()){
1327	+	setupZConstraint(info[k]);
1328	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1329	+	}
1330	+	else{
1331	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1332	+	}
1333	+
1334	+	info->the_integrator = myNVE;
1335	+	break;
1336	+
1337	+	case NVT_ENS:
1338	+	if (globals->haveZconstraints()){
1339	+	setupZConstraint(info[k]);
1340	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1341	+	}
1342	+	else
1343	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1344	+
1345	+	myNVT->setTargetTemp(globals->getTargetTemp());
1346	+
1347	+	if (globals->haveTauThermostat())
1348	+	myNVT->setTauThermostat(globals->getTauThermostat());
1349	+	else{
1350	+	sprintf(painCave.errMsg,
1351	+	"SimSetup error: If you use the NVT\n"
1352	+	"    ensemble, you must set tauThermostat.\n");
1353	+	painCave.isFatal = 1;
1354	+	simError();
1355	+	}
1356	+
1357	+	info->the_integrator = myNVT;
1358	+	break;
1359	+
1360	+	case NPTi_ENS:
1361	+	if (globals->haveZconstraints()){
1362	+	setupZConstraint(info[k]);
1363	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1364	+	}
1365	+	else
1366	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1367	+
1368	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1369	+
1370	+	if (globals->haveTargetPressure())
1371	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1372	+	else{
1373	+	sprintf(painCave.errMsg,
1374	+	"SimSetup error: If you use a constant pressure\n"
1375	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1376	+	painCave.isFatal = 1;
1377	+	simError();
1378	+	}
1379	+
1380	+	if (globals->haveTauThermostat())
1381	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1382	+	else{
1383	+	sprintf(painCave.errMsg,
1384	+	"SimSetup error: If you use an NPT\n"
1385	+	"    ensemble, you must set tauThermostat.\n");
1386	+	painCave.isFatal = 1;
1387	+	simError();
1388	+	}
1389	+
1390	+	if (globals->haveTauBarostat())
1391	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1392	+	else{
1393	+	sprintf(painCave.errMsg,
1394	+	"SimSetup error: If you use an NPT\n"
1395	+	"    ensemble, you must set tauBarostat.\n");
1396	+	painCave.isFatal = 1;
1397	+	simError();
1398	+	}
1399	+
1400	+	info->the_integrator = myNPTi;
1401	+	break;
1402	+
1403	+	case NPTf_ENS:
1404	+	if (globals->haveZconstraints()){
1405	+	setupZConstraint(info[k]);
1406	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1407	+	}
1408	+	else
1409	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1410	+
1411	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1412	+
1413	+	if (globals->haveTargetPressure())
1414	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1415	+	else{
1416	+	sprintf(painCave.errMsg,
1417	+	"SimSetup error: If you use a constant pressure\n"
1418	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1419	+	painCave.isFatal = 1;
1420	+	simError();
1421	+	}
1422	+
1423	+	if (globals->haveTauThermostat())
1424	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1425	+
1426	+	else{
1427	+	sprintf(painCave.errMsg,
1428	+	"SimSetup error: If you use an NPT\n"
1429	+	"    ensemble, you must set tauThermostat.\n");
1430	+	painCave.isFatal = 1;
1431	+	simError();
1432	+	}
1433	+
1434	+	if (globals->haveTauBarostat())
1435	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1436	+
1437	+	else{
1438	+	sprintf(painCave.errMsg,
1439	+	"SimSetup error: If you use an NPT\n"
1440	+	"    ensemble, you must set tauBarostat.\n");
1441	+	painCave.isFatal = 1;
1442	+	simError();
1443	+	}
1444	+
1445	+	info->the_integrator = myNPTf;
1446	+	break;
1447	+
1448	+	case NPTxyz_ENS:
1449	+	if (globals->haveZconstraints()){
1450	+	setupZConstraint(info[k]);
1451	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1452	+	}
1453	+	else
1454	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1455	+
1456	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1457	+
1458	+	if (globals->haveTargetPressure())
1459	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1460	+	else{
1461	+	sprintf(painCave.errMsg,
1462	+	"SimSetup error: If you use a constant pressure\n"
1463	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1464	+	painCave.isFatal = 1;
1465	+	simError();
1466	+	}
1467	+
1468	+	if (globals->haveTauThermostat())
1469	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1470	+	else{
1471	+	sprintf(painCave.errMsg,
1472	+	"SimSetup error: If you use an NPT\n"
1473	+	"    ensemble, you must set tauThermostat.\n");
1474	+	painCave.isFatal = 1;
1475	+	simError();
1476	+	}
1477	+
1478	+	if (globals->haveTauBarostat())
1479	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1480	+	else{
1481	+	sprintf(painCave.errMsg,
1482	+	"SimSetup error: If you use an NPT\n"
1483	+	"    ensemble, you must set tauBarostat.\n");
1484	+	painCave.isFatal = 1;
1485	+	simError();
1486	+	}
1487	+
1488	+	info->the_integrator = myNPTxyz;
1489	+	break;
1490	+
1491	+	default:
1492	+	sprintf(painCave.errMsg,
1493	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1494	+	painCave.isFatal = 1;
1495	+	simError();
1496	+	}
1497	+	}
1498	+	}
1499	+
1500	+	void SimSetup::initFortran(void){
1501	+	info[0].refreshSim();
1502	+
1503	+	if (!strcmp(info[0].mixingRule, "standard")){
1504	+	the_ff->initForceField(LB_MIXING_RULE);
1505	+	}
1506	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1507	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1508	+	}
1509	+	else{
1510	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1511	+	info[0].mixingRule);
1512	+	painCave.isFatal = 1;
1513	+	simError();
1514	+	}
1515	+
1516	+
1517	+	#ifdef IS_MPI
1518	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1519	+	MPIcheckPoint();
1520	+	#endif // is_mpi
1521	+	}
1522	+
1523	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1524	+	int nZConstraints;
1525	+	ZconStamp** zconStamp;
1526	+
1527	+	if (globals->haveZconstraintTime()){
1528	+	//add sample time of z-constraint  into SimInfo's property list
1529	+	DoubleData* zconsTimeProp = new DoubleData();
1530	+	zconsTimeProp->setID(ZCONSTIME_ID);
1531	+	zconsTimeProp->setData(globals->getZconsTime());
1532	+	theInfo.addProperty(zconsTimeProp);
1533	+	}
1534	+	else{
1535	+	sprintf(painCave.errMsg,
1536	+	"ZConstraint error: If you use an ZConstraint\n"
1537	+	" , you must set sample time.\n");
1538	+	painCave.isFatal = 1;
1539	+	simError();
1540	+	}
1541	+
1542	+	//push zconsTol into siminfo, if user does not specify
1543	+	//value for zconsTol, a default value will be used
1544	+	DoubleData* zconsTol = new DoubleData();
1545	+	zconsTol->setID(ZCONSTOL_ID);
1546	+	if (globals->haveZconsTol()){
1547	+	zconsTol->setData(globals->getZconsTol());
1548	+	}
1549	+	else{
1550	+	double defaultZConsTol = 0.01;
1551	+	sprintf(painCave.errMsg,
1552	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1553	+	" , default value %f is used.\n",
1554	+	defaultZConsTol);
1555	+	painCave.isFatal = 0;
1556	+	simError();
1557	+
1558	+	zconsTol->setData(defaultZConsTol);
1559	+	}
1560	+	theInfo.addProperty(zconsTol);
1561	+
1562	+	//set Force Subtraction Policy
1563	+	StringData* zconsForcePolicy = new StringData();
1564	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1565	+
1566	+	if (globals->haveZconsForcePolicy()){
1567	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1568	+	}
1569	+	else{
1570	+	sprintf(painCave.errMsg,
1571	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1572	+	"PolicyByMass is used\n");
1573	+	painCave.isFatal = 0;
1574	+	simError();
1575	+	zconsForcePolicy->setData("BYMASS");
1576	+	}
1577	+
1578	+	theInfo.addProperty(zconsForcePolicy);
1579	+
1580	+	//Determine the name of ouput file and add it into SimInfo's property list
1581	+	//Be careful, do not use inFileName, since it is a pointer which
1582	+	//point to a string at master node, and slave nodes do not contain that string
1583	+
1584	+	string zconsOutput(theInfo.finalName);
1585	+
1586	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1587	+
1588	+	StringData* zconsFilename = new StringData();
1589	+	zconsFilename->setID(ZCONSFILENAME_ID);
1590	+	zconsFilename->setData(zconsOutput);
1591	+
1592	+	theInfo.addProperty(zconsFilename);
1593	+
1594	+	//setup index, pos and other parameters of z-constraint molecules
1595	+	nZConstraints = globals->getNzConstraints();
1596	+	theInfo.nZconstraints = nZConstraints;
1597	+
1598	+	zconStamp = globals->getZconStamp();
1599	+	ZConsParaItem tempParaItem;
1600	+
1601	+	ZConsParaData* zconsParaData = new ZConsParaData();
1602	+	zconsParaData->setID(ZCONSPARADATA_ID);
1603	+
1604	+	for (int i = 0; i < nZConstraints; i++){
1605	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1606	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1607	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1608	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1609	+
1610	+	zconsParaData->addItem(tempParaItem);
1611	+	}
1612	+
1613	+	//check the uniqueness of index
1614	+	if(!zconsParaData->isIndexUnique()){
1615	+	sprintf(painCave.errMsg,
1616	+	"ZConstraint Error: molIndex is not unique\n");
1617	+	painCave.isFatal = 1;
1618	+	simError();
1619	+	}
1620	+
1621	+	//sort the parameters by index of molecules
1622	+	zconsParaData->sortByIndex();
1623	+
1624	+	//push data into siminfo, therefore, we can retrieve later
1625	+	theInfo.addProperty(zconsParaData);
1626	+	}

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