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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 490 by gezelter, Fri Apr 11 15:16:59 2003 UTC vs.
Revision 845 by gezelter, Thu Oct 30 18:59:20 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 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
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
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 27 | 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();
59	<	mpiEventLoop();
60	<
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;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j, k, globalAtomIndex;
98	>	// gather all of the information from the Bass file
99
100	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
100	>	gatherInfo();
101
102	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	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.
82	<	n_components = the_globals->getNComponents();
83	<	strcpy( force_field, the_globals->getForceField() );
104	>	sysObjectsCreation();
105
106	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	if (the_globals->haveTargetPressure())
91	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92	<	else {
93	<	sprintf( painCave.errMsg,
94	<	"SimSetup error: If you use the constant pressure\n"
95	<	"    ensemble, you must set targetPressure.\n"
96	<	"    This was found in the BASS file.\n");
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
106	>	// initialize the system coordinates
107
108	<	if (the_globals->haveTauThermostat())
109	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103	<	else if (the_globals->haveQmass())
104	<	the_extendedsystem->setQmass(the_globals->getQmass());
105	<	else {
106	<	sprintf( painCave.errMsg,
107	<	"SimSetup error: If you use one of the constant temperature\n"
108	<	"    ensembles, you must set either tauThermostat or qMass.\n"
109	<	"    Neither of these was found in the BASS file.\n");
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
108	>	if ( !initSuspend ){
109	>	initSystemCoords();
110
111	<	if (the_globals->haveTauBarostat())
112	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
113	<	else {
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup error: If you use the constant pressure\n"
119	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
111	>	if( !(globals->getUseInitTime()) )
112	>	info[0].currentTime = 0.0;
113	>	}
114
115	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
126	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
115	>	// check on the post processing info
116
117	<	if (the_globals->haveTauThermostat())
130	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131	<	else if (the_globals->haveQmass())
132	<	the_extendedsystem->setQmass(the_globals->getQmass());
133	<	else {
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error: If you use one of the constant temperature\n"
136	<	"    ensembles, you must set either tauThermostat or qMass.\n"
137	<	"    Neither of these was found in the BASS file.\n");
138	<	painCave.isFatal = 1;
139	<	simError();
140	<	}
117	>	finalInfoCheck();
118
119	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
143	<	} else {
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	<	"reverting to NVE for this simulation.\n",
147	<	ensemble );
148	<	painCave.isFatal = 0;
149	<	simError();
150	<	strcpy( ensemble, "NVE" );
151	<	}
152	<	strcpy( simnfo->ensemble, ensemble );
119	>	// make the output filenames
120
121	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155	<	simnfo->usePBC = the_globals->getPBC();
156	<
157	<	int usesDipoles = 0;
158	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
159	<	the_ff = new TraPPE_ExFF();
160	<	usesDipoles = 1;
161	<	}
162	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163	<	else{
164	<	sprintf( painCave.errMsg,
165	<	"SimSetup Error. Unrecognized force field -> %s\n",
166	<	force_field );
167	<	painCave.isFatal = 1;
168	<	simError();
169	<	}
121	>	makeOutNames();
122
123	+	// make the integrator
124	+
125	+	makeIntegrator();
126	+
127		#ifdef IS_MPI
128	<	strcpy( checkPointMsg, "ForceField creation successful" );
129	<	MPIcheckPoint();
174	<	#endif // is_mpi
128	>	mpiSim->mpiRefresh();
129	>	#endif
130
131	<
131	>	// initialize the Fortran
132
133	<	// get the components and calculate the tot_nMol and indvidual n_mol
134	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
133	>	initFortran();
134	>	}
135
183	–	if( !the_globals->haveNMol() ){
184	–	// we don't have the total number of molecules, so we assume it is
185	–	// given in each component
136
137	<	tot_nmol = 0;
138	<	for( i=0; i<n_components; i++ ){
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	<	if( !the_components[i]->haveNMol() ){
150	<	// we have a problem
151	<	sprintf( painCave.errMsg,
193	<	"SimSetup Error. No global NMol or component NMol"
194	<	" given. Cannot calculate the number of atoms.\n" );
195	<	painCave.isFatal = 1;
196	<	simError();
197	<	}
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
199	–	tot_nmol += the_components[i]->getNMol();
200	–	components_nmol[i] = the_components[i]->getNMol();
201	–	}
202	–	}
203	–	else{
204	–	sprintf( painCave.errMsg,
205	–	"SimSetup error.\n"
206	–	"\tSorry, the ability to specify total"
207	–	" nMols and then give molfractions in the components\n"
208	–	"\tis not currently supported."
209	–	" Please give nMol in the components.\n" );
210	–	painCave.isFatal = 1;
211	–	simError();
212	–
213	–
214	–	//     tot_nmol = the_globals->getNMol();
215	–
216	–	//   //we have the total number of molecules, now we check for molfractions
217	–	//     for( i=0; i<n_components; i++ ){
218	–
219	–	//       if( !the_components[i]->haveMolFraction() ){
220	–
221	–	//  if( !the_components[i]->haveNMol() ){
222	–	//    //we have a problem
223	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	–	//              << " nMol was given in component
225	–
226	–	}
153
154	<	#ifdef IS_MPI
229	<	strcpy( checkPointMsg, "Have the number of components" );
230	<	MPIcheckPoint();
231	<	#endif // is_mpi
154	>	//init the forceField paramters
155
156	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
156	>	the_ff->readParams();
157
236	–	simnfo->nComponents = n_components;
237	–	simnfo->componentsNmol = components_nmol;
238	–	simnfo->compStamps = comp_stamps;
239	–	simnfo->headStamp = new LinkedMolStamp();
240	–
241	–	char* id;
242	–	LinkedMolStamp* headStamp = simnfo->headStamp;
243	–	LinkedMolStamp* currentStamp = NULL;
244	–	for( i=0; i<n_components; i++ ){
158
159	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
159	>	// init the atoms
160
161	<	comp_stamps[i] = headStamp->match( id );
252	<	if( comp_stamps[i] == NULL ){
253	<
254	<	// extract the component from the list;
255	<
256	<	currentStamp = the_stamps->extractMolStamp( id );
257	<	if( currentStamp == NULL ){
258	<	sprintf( painCave.errMsg,
259	<	"SimSetup error: Component \"%s\" was not found in the "
260	<	"list of declared molecules\n",
261	<	id );
262	<	painCave.isFatal = 1;
263	<	simError();
264	<	}
265	<
266	<	headStamp->add( currentStamp );
267	<	comp_stamps[i] = headStamp->match( id );
268	<	}
269	<	}
161	>	double ux, uy, uz, u, uSqr;
162
163	<	#ifdef IS_MPI
164	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	<	MPIcheckPoint();
274	<	#endif // is_mpi
275	<
163	>	for (k = 0; k < nInfo; k++){
164	>	the_ff->setSimInfo(&(info[k]));
165
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	<	// caclulate the number of atoms, bonds, bends and torsions
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	<	tot_atoms = 0;
184	<	tot_bonds = 0;
185	<	tot_bends = 0;
284	<	tot_torsions = 0;
285	<	for( i=0; i<n_components; i++ ){
286	<
287	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
288	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
289	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
290	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
291	<	}
183	>	theBonds = new bond_pair[molInfo.nBonds];
184	>	theBends = new bend_set[molInfo.nBends];
185	>	theTorsions = new torsion_set[molInfo.nTorsions];
186
187	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
187	>	// make the Atoms
188
189	<	simnfo->n_atoms = tot_atoms;
190	<	simnfo->n_bonds = tot_bonds;
191	<	simnfo->n_bends = tot_bends;
192	<	simnfo->n_torsions = tot_torsions;
193	<	simnfo->n_SRI = tot_SRI;
194	<	simnfo->n_mol = tot_nmol;
195	<	simnfo->molMembershipArray = new int[tot_atoms];
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	+	ux = currentAtom->getOrntX();
198	+	uy = currentAtom->getOrntY();
199	+	uz = currentAtom->getOrntZ();
200	+
201	+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	+
203	+	u = sqrt(uSqr);
204	+	ux = ux / u;
205	+	uy = uy / u;
206	+	uz = uz / u;
207	+
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.
306	<
307	<	mpiSim = new mpiSimulation( simnfo );
308	<
309	<	globalIndex = mpiSim->divideLabor();
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221
222	<	// set up the local variables
223	<
313	<	int localMol, allMol;
314	<	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;
321	<	local_atoms = 0;
322	<	local_bonds = 0;
323	<	local_bends = 0;
324	<	local_torsions = 0;
325	<	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();
335	<	local_bonds +=    comp_stamps[i]->getNBonds();
336	<	local_bends +=    comp_stamps[i]->getNBends();
337	<	local_torsions += comp_stamps[i]->getNTorsions();
338	<	localMol++;
339	<	}
340	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
341	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
342	<	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	<	if (worldRank != 0) {
351	<	for (i =0; i < tot_atoms; i++){
352	<	std::cerr << "i = " << i << " molMembershipArray[i] = " << simnfo->molMembershipArray[i] << "\n";
353	<	}
354	<	}
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_atoms = mpiSim->getMyNlocal();
262	<
263	<	if( local_atoms != simnfo->n_atoms ){
359	<	sprintf( painCave.errMsg,
360	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
361	<	" localAtom (%d) are not equal.\n",
362	<	simnfo->n_atoms,
363	<	local_atoms );
364	<	painCave.isFatal = 1;
365	<	simError();
366	<	}
261	>	if (currentBend->haveExtras()){
262	>	extras = currentBend->getExtras();
263	>	current_extra = extras;
264
265	<	simnfo->n_bonds = local_bonds;
266	<	simnfo->n_bends = local_bends;
267	<	simnfo->n_torsions = local_torsions;
268	<	simnfo->n_SRI = local_SRI;
269	<	simnfo->n_mol = localMol;
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	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
274	<	MPIcheckPoint();
275	<
276	<
277	<	#endif // is_mpi
379	<
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278
279	<	// create the atom and short range interaction arrays
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	<	Atom::createArrays(simnfo->n_atoms);
299	<	the_atoms = new Atom*[simnfo->n_atoms];
300	<	the_molecules = new Molecule[simnfo->n_mol];
386	<	int molIndex;
298	>	current_extra = current_extra->getNext();
299	>	}
300	>	}
301
302	<	// initialize the molecule's stampID's
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	+	// 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	<
318	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322
323	<	molIndex = 0;
324	<	for(i=0; i<mpiSim->getTotNmol(); i++){
325	<
326	<	if(mol2proc[i] == worldRank ){
397	<	the_molecules[molIndex].setStampID( molCompType[i] );
398	<	the_molecules[molIndex].setMyIndex( molIndex );
399	<	the_molecules[molIndex].setGlobalIndex( i );
400	<	molIndex++;
401	<	}
402	<	}
403	<
404	<	#else // is_mpi
405	<
406	<	molIndex = 0;
407	<	globalAtomIndex = 0;
408	<	for(i=0; i<n_components; i++){
409	<	for(j=0; j<components_nmol[i]; j++ ){
410	<	the_molecules[molIndex].setStampID( i );
411	<	the_molecules[molIndex].setMyIndex( molIndex );
412	<	the_molecules[molIndex].setGlobalIndex( molIndex );
413	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
414	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
415	<	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++;
418	<	}
419	<	}
420	<
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 );
436	<	the_excludes = new Exclude*;
437	<	the_excludes[0] = new Exclude(0);
438	<	the_excludes[0]->setPair( 0,0 );
439	<	simnfo->globalExcludes = new int;
440	<	simnfo->globalExcludes[0] = 0;
441	<	simnfo->n_exclude = 0;
442	<	}
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
446	–	simnfo->atoms = the_atoms;
447	–	simnfo->molecules = the_molecules;
448	–	simnfo->nGlobalExcludes = 0;
449	–	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
454	–
455	–	if( the_globals->haveBox() ){
456	–	simnfo->box_x = the_globals->getBox();
457	–	simnfo->box_y = the_globals->getBox();
458	–	simnfo->box_z = the_globals->getBox();
459	–	}
460	–	else if( the_globals->haveDensity() ){
368
369	<	double vol;
463	<	vol = (double)tot_nmol / the_globals->getDensity();
464	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
465	<	simnfo->box_y = simnfo->box_x;
466	<	simnfo->box_z = simnfo->box_x;
467	<	}
468	<	else{
469	<	if( !the_globals->haveBoxX() ){
470	<	sprintf( painCave.errMsg,
471	<	"SimSetup error, no periodic BoxX size given.\n" );
472	<	painCave.isFatal = 1;
473	<	simError();
474	<	}
475	<	simnfo->box_x = the_globals->getBoxX();
369	>	info[k].molecules[i].initialize(molInfo);
370
477	–	if( !the_globals->haveBoxY() ){
478	–	sprintf( painCave.errMsg,
479	–	"SimSetup error, no periodic BoxY size given.\n" );
480	–	painCave.isFatal = 1;
481	–	simError();
482	–	}
483	–	simnfo->box_y = the_globals->getBoxY();
371
372	<	if( !the_globals->haveBoxZ() ){
373	<	sprintf( painCave.errMsg,
374	<	"SimSetup error, no periodic BoxZ size given.\n" );
375	<	painCave.isFatal = 1;
489	<	simError();
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376		}
491	–	simnfo->box_z = the_globals->getBoxZ();
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();
508	<	}
509	<
510	<	if (the_globals->getUseRF() ) {
511	<	simnfo->useReactionField = 1;
512	<
513	<	if( !the_globals->haveECR() ){
514	<	sprintf( painCave.errMsg,
515	<	"SimSetup Warning: using default value of 1/2 the smallest "
516	<	"box length for the electrostaticCutoffRadius.\n"
517	<	"I hope you have a very fast processor!\n");
518	<	painCave.isFatal = 0;
519	<	simError();
520	<	double smallest;
521	<	smallest = simnfo->box_x;
522	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
523	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
524	<	simnfo->ecr = 0.5 * smallest;
525	<	} else {
526	<	simnfo->ecr        = the_globals->getECR();
527	<	}
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 "
556	<	"box length for the electrostaticCutoffRadius.\n"
557	<	"I hope you have a very fast processor!\n");
558	<	painCave.isFatal = 0;
559	<	simError();
560	<	double smallest;
561	<	smallest = simnfo->box_x;
562	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
563	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
564	<	simnfo->ecr = 0.5 * smallest;
565	<	} else {
566	<	simnfo->ecr        = the_globals->getECR();
567	<	}
568	<
569	<	if( !the_globals->haveEST() ){
570	<	sprintf( painCave.errMsg,
571	<	"SimSetup Warning: using default value of 5%% of the "
572	<	"electrostaticCutoffRadius for the "
573	<	"electrostaticSkinThickness\n"
574	<	);
575	<	painCave.isFatal = 0;
576	<	simError();
577	<	simnfo->est = 0.05 * simnfo->ecr;
578	<	} else {
579	<	simnfo->est        = the_globals->getEST();
580	<	}
581	<	}
582	<	}
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
593	<	if( worldRank == 0 ){
594	<	#endif //is_mpi
595	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
596	<	#ifdef IS_MPI
597	<	}else fileInit = new InitializeFromFile( NULL );
598	<	#endif
599	<	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;
602	<	}
603	<	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" );
611	<	painCave.isFatal;
612	<	simError();
613	<
614	<	#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
634	<	if( worldRank == 0 ){
635	<	#endif // is_mpi
636	<
637	<	if( the_globals->haveFinalConfig() ){
638	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
639	<	}
640	<	else{
641	<	strcpy( simnfo->finalName, inFileName );
642	<	char* endTest;
643	<	int nameLength = strlen( simnfo->finalName );
644	<	endTest = &(simnfo->finalName[nameLength - 5]);
645	<	if( !strcmp( endTest, ".bass" ) ){
646	<	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		}
648	–	else if( !strcmp( endTest, ".BASS" ) ){
649	–	strcpy( endTest, ".eor" );
650	–	}
651	–	else{
652	–	endTest = &(simnfo->finalName[nameLength - 4]);
653	–	if( !strcmp( endTest, ".bss" ) ){
654	–	strcpy( endTest, ".eor" );
655	–	}
656	–	else if( !strcmp( endTest, ".mdl" ) ){
657	–	strcpy( endTest, ".eor" );
658	–	}
659	–	else{
660	–	strcat( simnfo->finalName, ".eor" );
661	–	}
662	–	}
494		}
664	–
665	–	// make the sample and status out names
666	–
667	–	strcpy( simnfo->sampleName, inFileName );
668	–	char* endTest;
669	–	int nameLength = strlen( simnfo->sampleName );
670	–	endTest = &(simnfo->sampleName[nameLength - 5]);
671	–	if( !strcmp( endTest, ".bass" ) ){
672	–	strcpy( endTest, ".dump" );
673	–	}
674	–	else if( !strcmp( endTest, ".BASS" ) ){
675	–	strcpy( endTest, ".dump" );
676	–	}
677	–	else{
678	–	endTest = &(simnfo->sampleName[nameLength - 4]);
679	–	if( !strcmp( endTest, ".bss" ) ){
680	–	strcpy( endTest, ".dump" );
681	–	}
682	–	else if( !strcmp( endTest, ".mdl" ) ){
683	–	strcpy( endTest, ".dump" );
684	–	}
685	–	else{
686	–	strcat( simnfo->sampleName, ".dump" );
687	–	}
688	–	}
689	–
690	–	strcpy( simnfo->statusName, inFileName );
691	–	nameLength = strlen( simnfo->statusName );
692	–	endTest = &(simnfo->statusName[nameLength - 5]);
693	–	if( !strcmp( endTest, ".bass" ) ){
694	–	strcpy( endTest, ".stat" );
695	–	}
696	–	else if( !strcmp( endTest, ".BASS" ) ){
697	–	strcpy( endTest, ".stat" );
698	–	}
699	–	else{
700	–	endTest = &(simnfo->statusName[nameLength - 4]);
701	–	if( !strcmp( endTest, ".bss" ) ){
702	–	strcpy( endTest, ".stat" );
703	–	}
704	–	else if( !strcmp( endTest, ".mdl" ) ){
705	–	strcpy( endTest, ".stat" );
706	–	}
707	–	else{
708	–	strcat( simnfo->statusName, ".stat" );
709	–	}
710	–	}
711	–
712	–	#ifdef IS_MPI
495		}
714	–	#endif // is_mpi
715	–
716	–	// set the status, sample, and themal kick times
717	–
718	–	if( the_globals->haveSampleTime() ){
719	–	simnfo->sampleTime = the_globals->getSampleTime();
720	–	simnfo->statusTime = simnfo->sampleTime;
721	–	simnfo->thermalTime = simnfo->sampleTime;
722	–	}
723	–	else{
724	–	simnfo->sampleTime = the_globals->getRunTime();
725	–	simnfo->statusTime = simnfo->sampleTime;
726	–	simnfo->thermalTime = simnfo->sampleTime;
727	–	}
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 longe range forces and the integrator
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530
531	<	//   new AllLong( simnfo );
531	>	rotMat[0][0] = 1.0;
532	>	rotMat[0][1] = 0.0;
533	>	rotMat[0][2] = 0.0;
534
535	+	rotMat[1][0] = 0.0;
536	+	rotMat[1][1] = 1.0;
537	+	rotMat[1][2] = 0.0;
538
539	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
540	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
539	>	rotMat[2][0] = 0.0;
540	>	rotMat[2][1] = 0.0;
541	>	rotMat[2][2] = 1.0;
542	>
543	>	dAtom->setA(rotMat);
544	>	}
545	>
546	>	current_atom_ndx++;
547		}
548	<	else if( !strcmp( force_field, "LJ" ) ){
549	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
548	>
549	>	current_mol++;
550	>	current_comp_mol++;
551	>
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553	>	current_comp_mol = 0;
554	>	current_comp++;
555		}
556	<	else {
754	<	std::cerr << "I'm a bug.\n";
755	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
756	<	}
757	<	#ifdef IS_MPI
758	<	mpiSim->mpiRefresh();
759	<	#endif
556	>	}
557
761	–	// 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;
777	<	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
782	<	strcpy( checkPointMsg,
783	<	"Successfully intialized the mixingRule for Fortran." );
784	<	MPIcheckPoint();
785	<	#endif // is_mpi
786	<	}
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;
792	<	molInit info;
793	<	DirectionalAtom* dAtom;
794	<	LinkedAssign* extras;
795	<	LinkedAssign* current_extra;
796	<	AtomStamp* currentAtom;
797	<	BondStamp* currentBond;
798	<	BendStamp* currentBend;
799	<	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	<
806	<	//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
810	–
811	–	// init the atoms
639
640	<	double ux, uy, uz, u, uSqr;
641	<
642	<	atomOffset = 0;
816	<	excludeOffset = 0;
817	<	for(i=0; i<simnfo->n_mol; i++){
818	<
819	<	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;
649	<
650	<	info.myAtoms = &the_atoms[atomOffset];
651	<	info.myExcludes = &the_excludes[excludeOffset];
652	<	info.myBonds = new Bond*[info.nBonds];
830	<	info.myBends = new Bend*[info.nBends];
831	<	info.myTorsions = new Torsion*[info.nTorsions];
832	<
833	<	theBonds = new bond_pair[info.nBonds];
834	<	theBends = new bend_set[info.nBends];
835	<	theTorsions = new torsion_set[info.nTorsions];
836	<
837	<	// make the Atoms
838	<
839	<	for(j=0; j<info.nAtoms; j++){
840	<
841	<	currentAtom = comp_stamps[stampID]->getAtom( j );
842	<	if( currentAtom->haveOrientation() ){
843	<
844	<	dAtom = new DirectionalAtom(j + atomOffset);
845	<	simnfo->n_oriented++;
846	<	info.myAtoms[j] = dAtom;
847	<
848	<	ux = currentAtom->getOrntX();
849	<	uy = currentAtom->getOrntY();
850	<	uz = currentAtom->getOrntZ();
851	<
852	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
853	<
854	<	u = sqrt( uSqr );
855	<	ux = ux / u;
856	<	uy = uy / u;
857	<	uz = uz / u;
858	<
859	<	dAtom->setSUx( ux );
860	<	dAtom->setSUy( uy );
861	<	dAtom->setSUz( uz );
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		}
863	–	else{
864	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
865	–	}
866	–	info.myAtoms[j]->setType( currentAtom->getType() );
867	–
868	–	#ifdef IS_MPI
869	–
870	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
871	–
872	–	#endif // is_mpi
873	–	}
874	–
875	–	// make the bonds
876	–	for(j=0; j<info.nBonds; j++){
877	–
878	–	currentBond = comp_stamps[stampID]->getBond( j );
879	–	theBonds[j].a = currentBond->getA() + atomOffset;
880	–	theBonds[j].b = currentBond->getB() + atomOffset;
654
655	<	exI = theBonds[j].a;
656	<	exJ = theBonds[j].b;
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	<	// exclude_I must always be the smaller of the pair
886	<	if( exI > exJ ){
887	<	tempEx = exI;
888	<	exI = exJ;
889	<	exJ = tempEx;
890	<	}
891	<	#ifdef IS_MPI
892	<	tempEx = exI;
893	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
894	<	tempEx = exJ;
895	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
896	<
897	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
898	<	#else  // isn't MPI
670	>	// set the status, sample, and thermal kick times
671
672	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
673	<	#endif  //is_mpi
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	<	excludeOffset += info.nBonds;
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	<	//make the bends
685	<	for(j=0; j<info.nBends; j++){
907	<
908	<	currentBend = comp_stamps[stampID]->getBend( j );
909	<	theBends[j].a = currentBend->getA() + atomOffset;
910	<	theBends[j].b = currentBend->getB() + atomOffset;
911	<	theBends[j].c = currentBend->getC() + atomOffset;
912	<
913	<	if( currentBend->haveExtras() ){
914	<
915	<	extras = currentBend->getExtras();
916	<	current_extra = extras;
917	<
918	<	while( current_extra != NULL ){
919	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
920	<
921	<	switch( current_extra->getType() ){
922	<
923	<	case 0:
924	<	theBends[j].ghost =
925	<	current_extra->getInt() + atomOffset;
926	<	theBends[j].isGhost = 1;
927	<	break;
928	<
929	<	case 1:
930	<	theBends[j].ghost =
931	<	(int)current_extra->getDouble() + atomOffset;
932	<	theBends[j].isGhost = 1;
933	<	break;
934	<
935	<	default:
936	<	sprintf( painCave.errMsg,
937	<	"SimSetup Error: ghostVectorSource was neither a "
938	<	"double nor an int.\n"
939	<	"-->Bend[%d] in %s\n",
940	<	j, comp_stamps[stampID]->getID() );
941	<	painCave.isFatal = 1;
942	<	simError();
943	<	}
944	<	}
945	<
946	<	else{
947	<
948	<	sprintf( painCave.errMsg,
949	<	"SimSetup Error: unhandled bend assignment:\n"
950	<	"    -->%s in Bend[%d] in %s\n",
951	<	current_extra->getlhs(),
952	<	j, comp_stamps[stampID]->getID() );
953	<	painCave.isFatal = 1;
954	<	simError();
955	<	}
956	<
957	<	current_extra = current_extra->getNext();
958	<	}
959	<	}
960	<
961	<	if( !theBends[j].isGhost ){
962	<
963	<	exI = theBends[j].a;
964	<	exJ = theBends[j].c;
965	<	}
966	<	else{
967	<
968	<	exI = theBends[j].a;
969	<	exJ = theBends[j].b;
970	<	}
971	<
972	<	// exclude_I must always be the smaller of the pair
973	<	if( exI > exJ ){
974	<	tempEx = exI;
975	<	exI = exJ;
976	<	exJ = tempEx;
977	<	}
978	<	#ifdef IS_MPI
979	<	tempEx = exI;
980	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
981	<	tempEx = exJ;
982	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
983	<
984	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
985	<	#else  // isn't MPI
986	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
987	<	#endif  //is_mpi
684	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686		}
989	–	excludeOffset += info.nBends;
687
688	<	for(j=0; j<info.nTorsions; j++){
689	<
690	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
994	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
995	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
996	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
997	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
998	<
999	<	exI = theTorsions[j].a;
1000	<	exJ = theTorsions[j].d;
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690	>	}
691
692	<	// exclude_I must always be the smaller of the pair
693	<	if( exI > exJ ){
694	<	tempEx = exI;
695	<	exI = exJ;
1006	<	exJ = tempEx;
1007	<	}
1008	<	#ifdef IS_MPI
1009	<	tempEx = exI;
1010	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1011	<	tempEx = exJ;
1012	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1013	<
1014	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1015	<	#else  // isn't MPI
1016	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1017	<	#endif  //is_mpi
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696		}
1019	–	excludeOffset += info.nTorsions;
697
698	+	// check for the temperature set flag
699
700	<	// send the arrays off to the forceField for init.
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702	>
703	>	}
704	>
705	>	//setup seed for random number generator
706	>	int seedValue;
707
708	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
709	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1026	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1027	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
708	>	if (globals->haveSeed()){
709	>	seedValue = globals->getSeed();
710
711	+	if(seedValue / 1E9 == 0){
712	+	sprintf(painCave.errMsg,
713	+	"Seed for sprng library should contain at least 9 digits\n"
714	+	"OOPSE will generate a seed for user\n");
715	+	painCave.isFatal = 0;
716	+	simError();
717
718	<	the_molecules[i].initialize( info );
718	>	//using seed generated by system instead of invalid seed set by user
719	>	#ifndef IS_MPI
720	>	seedValue = make_sprng_seed();
721	>	#else
722	>	if (worldRank == 0){
723	>	seedValue = make_sprng_seed();
724	>	}
725	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
726	>	#endif
727	>	}
728	>	}//end of if branch of globals->haveSeed()
729	>	else{
730	>
731	>	#ifndef IS_MPI
732	>	seedValue = make_sprng_seed();
733	>	#else
734	>	if (worldRank == 0){
735	>	seedValue = make_sprng_seed();
736	>	}
737	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
738	>	#endif
739	>	}//end of globals->haveSeed()
740
741	<
742	<	atomOffset += info.nAtoms;
1034	<	delete[] theBonds;
1035	<	delete[] theBends;
1036	<	delete[] theTorsions;
741	>	for (int i = 0; i < nInfo; i++){
742	>	info[i].setSeed(seedValue);
743		}
744
745		#ifdef IS_MPI
746	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
746	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
747		MPIcheckPoint();
748		#endif // is_mpi
1043	–
1044	–	// clean up the forcefield
1045	–	the_ff->calcRcut();
1046	–	the_ff->cleanMe();
1047	–
749		}
750
1050	–	void SimSetup::initFromBass( void ){
751
752	<	int i, j, k;
753	<	int n_cells;
754	<	double cellx, celly, cellz;
755	<	double temp1, temp2, temp3;
1056	<	int n_per_extra;
1057	<	int n_extra;
1058	<	int have_extra, done;
752	>	void SimSetup::finalInfoCheck(void){
753	>	int index;
754	>	int usesDipoles;
755	>	int i;
756
757	<	temp1 = (double)tot_nmol / 4.0;
758	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1062	<	temp3 = ceil( temp2 );
757	>	for (i = 0; i < nInfo; i++){
758	>	// check electrostatic parameters
759
760	<	have_extra =0;
761	<	if( temp2 < temp3 ){ // we have a non-complete lattice
762	<	have_extra =1;
760	>	index = 0;
761	>	usesDipoles = 0;
762	>	while ((index < info[i].n_atoms) && !usesDipoles){
763	>	usesDipoles = (info[i].atoms[index])->hasDipole();
764	>	index++;
765	>	}
766
767	<	n_cells = (int)temp3 - 1;
768	<	cellx = simnfo->box_x / temp3;
769	<	celly = simnfo->box_y / temp3;
770	<	cellz = simnfo->box_z / temp3;
1072	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1073	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1074	<	n_per_extra = (int)ceil( temp1 );
767	>	#ifdef IS_MPI
768	>	int myUse = usesDipoles;
769	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>	#endif //is_mpi
771
772	<	if( n_per_extra > 4){
1077	<	sprintf( painCave.errMsg,
1078	<	"SimSetup error. There has been an error in constructing"
1079	<	" the non-complete lattice.\n" );
1080	<	painCave.isFatal = 1;
1081	<	simError();
1082	<	}
1083	<	}
1084	<	else{
1085	<	n_cells = (int)temp3;
1086	<	cellx = simnfo->box_x / temp3;
1087	<	celly = simnfo->box_y / temp3;
1088	<	cellz = simnfo->box_z / temp3;
1089	<	}
772	>	double theEcr, theEst;
773
774	<	current_mol = 0;
775	<	current_comp_mol = 0;
1093	<	current_comp = 0;
1094	<	current_atom_ndx = 0;
774	>	if (globals->getUseRF()){
775	>	info[i].useReactionField = 1;
776
777	<	for( i=0; i < n_cells ; i++ ){
778	<	for( j=0; j < n_cells; j++ ){
779	<	for( k=0; k < n_cells; k++ ){
777	>	if (!globals->haveECR()){
778	>	sprintf(painCave.errMsg,
779	>	"SimSetup Warning: using default value of 1/2 the smallest "
780	>	"box length for the electrostaticCutoffRadius.\n"
781	>	"I hope you have a very fast processor!\n");
782	>	painCave.isFatal = 0;
783	>	simError();
784	>	double smallest;
785	>	smallest = info[i].boxL[0];
786	>	if (info[i].boxL[1] <= smallest)
787	>	smallest = info[i].boxL[1];
788	>	if (info[i].boxL[2] <= smallest)
789	>	smallest = info[i].boxL[2];
790	>	theEcr = 0.5 * smallest;
791	>	}
792	>	else{
793	>	theEcr = globals->getECR();
794	>	}
795
796	<	makeElement( i * cellx,
797	<	j * celly,
798	<	k * cellz );
796	>	if (!globals->haveEST()){
797	>	sprintf(painCave.errMsg,
798	>	"SimSetup Warning: using default value of 0.05 * the "
799	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
800	>	painCave.isFatal = 0;
801	>	simError();
802	>	theEst = 0.05 * theEcr;
803	>	}
804	>	else{
805	>	theEst = globals->getEST();
806	>	}
807
808	<	makeElement( i * cellx + 0.5 * cellx,
1105	<	j * celly + 0.5 * celly,
1106	<	k * cellz );
808	>	info[i].setDefaultEcr(theEcr, theEst);
809
810	<	makeElement( i * cellx,
811	<	j * celly + 0.5 * celly,
812	<	k * cellz + 0.5 * cellz );
810	>	if (!globals->haveDielectric()){
811	>	sprintf(painCave.errMsg,
812	>	"SimSetup Error: You are trying to use Reaction Field without"
813	>	"setting a dielectric constant!\n");
814	>	painCave.isFatal = 1;
815	>	simError();
816	>	}
817	>	info[i].dielectric = globals->getDielectric();
818	>	}
819	>	else{
820	>	if (usesDipoles){
821	>	if (!globals->haveECR()){
822	>	sprintf(painCave.errMsg,
823	>	"SimSetup Warning: using default value of 1/2 the smallest "
824	>	"box length for the electrostaticCutoffRadius.\n"
825	>	"I hope you have a very fast processor!\n");
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	double smallest;
829	>	smallest = info[i].boxL[0];
830	>	if (info[i].boxL[1] <= smallest)
831	>	smallest = info[i].boxL[1];
832	>	if (info[i].boxL[2] <= smallest)
833	>	smallest = info[i].boxL[2];
834	>	theEcr = 0.5 * smallest;
835	>	}
836	>	else{
837	>	theEcr = globals->getECR();
838	>	}
839
840	<	makeElement( i * cellx + 0.5 * cellx,
841	<	j * celly,
842	<	k * cellz + 0.5 * cellz );
840	>	if (!globals->haveEST()){
841	>	sprintf(painCave.errMsg,
842	>	"SimSetup Warning: using default value of 0.05 * the "
843	>	"electrostaticCutoffRadius for the "
844	>	"electrostaticSkinThickness\n");
845	>	painCave.isFatal = 0;
846	>	simError();
847	>	theEst = 0.05 * theEcr;
848	>	}
849	>	else{
850	>	theEst = globals->getEST();
851	>	}
852	>
853	>	info[i].setDefaultEcr(theEcr, theEst);
854		}
855		}
856	+	info[i].checkCutOffs();
857		}
858
859	<	if( have_extra ){
860	<	done = 0;
859	>	#ifdef IS_MPI
860	>	strcpy(checkPointMsg, "post processing checks out");
861	>	MPIcheckPoint();
862	>	#endif // is_mpi
863	>	}
864
865	<	int start_ndx;
866	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1124	<	for( j=0; j < (n_cells+1) && !done; j++ ){
865	>	void SimSetup::initSystemCoords(void){
866	>	int i;
867
868	<	if( i < n_cells ){
868	>	char* inName;
869
870	<	if( j < n_cells ){
1129	<	start_ndx = n_cells;
1130	<	}
1131	<	else start_ndx = 0;
1132	<	}
1133	<	else start_ndx = 0;
870	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
871
872	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
872	>	for (i = 0; i < info[0].n_atoms; i++)
873	>	info[0].atoms[i]->setCoords();
874
875	<	makeElement( i * cellx,
876	<	j * celly,
877	<	k * cellz );
878	<	done = ( current_mol >= tot_nmol );
879	<
880	<	if( !done && n_per_extra > 1 ){
881	<	makeElement( i * cellx + 0.5 * cellx,
882	<	j * celly + 0.5 * celly,
1145	<	k * cellz );
1146	<	done = ( current_mol >= tot_nmol );
1147	<	}
1148	<
1149	<	if( !done && n_per_extra > 2){
1150	<	makeElement( i * cellx,
1151	<	j * celly + 0.5 * celly,
1152	<	k * cellz + 0.5 * cellz );
1153	<	done = ( current_mol >= tot_nmol );
1154	<	}
1155	<
1156	<	if( !done && n_per_extra > 3){
1157	<	makeElement( i * cellx + 0.5 * cellx,
1158	<	j * celly,
1159	<	k * cellz + 0.5 * cellz );
1160	<	done = ( current_mol >= tot_nmol );
1161	<	}
1162	<	}
1163	<	}
875	>	if (globals->haveInitialConfig()){
876	>	InitializeFromFile* fileInit;
877	>	#ifdef IS_MPI // is_mpi
878	>	if (worldRank == 0){
879	>	#endif //is_mpi
880	>	inName = globals->getInitialConfig();
881	>	fileInit = new InitializeFromFile(inName);
882	>	#ifdef IS_MPI
883		}
884	+	else
885	+	fileInit = new InitializeFromFile(NULL);
886	+	#endif
887	+	fileInit->readInit(info); // default velocities on
888	+
889	+	delete fileInit;
890		}
891	+	else{
892	+	#ifdef IS_MPI
893
894	+	// no init from bass
895
896	<	for( i=0; i<simnfo->n_atoms; i++ ){
897	<	simnfo->atoms[i]->set_vx( 0.0 );
898	<	simnfo->atoms[i]->set_vy( 0.0 );
899	<	simnfo->atoms[i]->set_vz( 0.0 );
1172	<	}
1173	<	}
896	>	sprintf(painCave.errMsg,
897	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
898	>	painCave.isFatal = 1;;
899	>	simError();
900
901	<	void SimSetup::makeElement( double x, double y, double z ){
901	>	#else
902
903	<	int k;
1178	<	AtomStamp* current_atom;
1179	<	DirectionalAtom* dAtom;
1180	<	double rotMat[3][3];
903	>	initFromBass();
904
1182	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
905
906	<	current_atom = comp_stamps[current_comp]->getAtom( k );
907	<	if( !current_atom->havePosition() ){
1186	<	sprintf( painCave.errMsg,
1187	<	"SimSetup:initFromBass error.\n"
1188	<	"\tComponent %s, atom %s does not have a position specified.\n"
1189	<	"\tThe initialization routine is unable to give a start"
1190	<	" position.\n",
1191	<	comp_stamps[current_comp]->getID(),
1192	<	current_atom->getType() );
1193	<	painCave.isFatal = 1;
1194	<	simError();
1195	<	}
906	>	#endif
907	>	}
908
909	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
910	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
911	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
909	>	#ifdef IS_MPI
910	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
911	>	MPIcheckPoint();
912	>	#endif // is_mpi
913	>	}
914
1201	–	if( the_atoms[current_atom_ndx]->isDirectional() ){
915
916	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
916	>	void SimSetup::makeOutNames(void){
917	>	int k;
918
1205	–	rotMat[0][0] = 1.0;
1206	–	rotMat[0][1] = 0.0;
1207	–	rotMat[0][2] = 0.0;
919
920	<	rotMat[1][0] = 0.0;
921	<	rotMat[1][1] = 1.0;
922	<	rotMat[1][2] = 0.0;
920	>	for (k = 0; k < nInfo; k++){
921	>	#ifdef IS_MPI
922	>	if (worldRank == 0){
923	>	#endif // is_mpi
924
925	<	rotMat[2][0] = 0.0;
926	<	rotMat[2][1] = 0.0;
927	<	rotMat[2][2] = 1.0;
925	>	if (globals->haveFinalConfig()){
926	>	strcpy(info[k].finalName, globals->getFinalConfig());
927	>	}
928	>	else{
929	>	strcpy(info[k].finalName, inFileName);
930	>	char* endTest;
931	>	int nameLength = strlen(info[k].finalName);
932	>	endTest = &(info[k].finalName[nameLength - 5]);
933	>	if (!strcmp(endTest, ".bass")){
934	>	strcpy(endTest, ".eor");
935	>	}
936	>	else if (!strcmp(endTest, ".BASS")){
937	>	strcpy(endTest, ".eor");
938	>	}
939	>	else{
940	>	endTest = &(info[k].finalName[nameLength - 4]);
941	>	if (!strcmp(endTest, ".bss")){
942	>	strcpy(endTest, ".eor");
943	>	}
944	>	else if (!strcmp(endTest, ".mdl")){
945	>	strcpy(endTest, ".eor");
946	>	}
947	>	else{
948	>	strcat(info[k].finalName, ".eor");
949	>	}
950	>	}
951	>	}
952
953	<	dAtom->setA( rotMat );
953	>	// make the sample and status out names
954	>
955	>	strcpy(info[k].sampleName, inFileName);
956	>	char* endTest;
957	>	int nameLength = strlen(info[k].sampleName);
958	>	endTest = &(info[k].sampleName[nameLength - 5]);
959	>	if (!strcmp(endTest, ".bass")){
960	>	strcpy(endTest, ".dump");
961	>	}
962	>	else if (!strcmp(endTest, ".BASS")){
963	>	strcpy(endTest, ".dump");
964	>	}
965	>	else{
966	>	endTest = &(info[k].sampleName[nameLength - 4]);
967	>	if (!strcmp(endTest, ".bss")){
968	>	strcpy(endTest, ".dump");
969	>	}
970	>	else if (!strcmp(endTest, ".mdl")){
971	>	strcpy(endTest, ".dump");
972	>	}
973	>	else{
974	>	strcat(info[k].sampleName, ".dump");
975	>	}
976	>	}
977	>
978	>	strcpy(info[k].statusName, inFileName);
979	>	nameLength = strlen(info[k].statusName);
980	>	endTest = &(info[k].statusName[nameLength - 5]);
981	>	if (!strcmp(endTest, ".bass")){
982	>	strcpy(endTest, ".stat");
983	>	}
984	>	else if (!strcmp(endTest, ".BASS")){
985	>	strcpy(endTest, ".stat");
986	>	}
987	>	else{
988	>	endTest = &(info[k].statusName[nameLength - 4]);
989	>	if (!strcmp(endTest, ".bss")){
990	>	strcpy(endTest, ".stat");
991	>	}
992	>	else if (!strcmp(endTest, ".mdl")){
993	>	strcpy(endTest, ".stat");
994	>	}
995	>	else{
996	>	strcat(info[k].statusName, ".stat");
997	>	}
998	>	}
999	>
1000	>	#ifdef IS_MPI
1001	>
1002		}
1003	+	#endif // is_mpi
1004	+	}
1005	+	}
1006
1007	<	current_atom_ndx++;
1007	>
1008	>	void SimSetup::sysObjectsCreation(void){
1009	>	int i, k;
1010	>
1011	>	// create the forceField
1012	>
1013	>	createFF();
1014	>
1015	>	// extract componentList
1016	>
1017	>	compList();
1018	>
1019	>	// calc the number of atoms, bond, bends, and torsions
1020	>
1021	>	calcSysValues();
1022	>
1023	>	#ifdef IS_MPI
1024	>	// divide the molecules among the processors
1025	>
1026	>	mpiMolDivide();
1027	>	#endif //is_mpi
1028	>
1029	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1030	>
1031	>	makeSysArrays();
1032	>
1033	>	// make and initialize the molecules (all but atomic coordinates)
1034	>
1035	>	makeMolecules();
1036	>
1037	>	for (k = 0; k < nInfo; k++){
1038	>	info[k].identArray = new int[info[k].n_atoms];
1039	>	for (i = 0; i < info[k].n_atoms; i++){
1040	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1041	>	}
1042		}
1043	+	}
1044
1223	–	current_mol++;
1224	–	current_comp_mol++;
1045
1046	<	if( current_comp_mol >= components_nmol[current_comp] ){
1046	>	void SimSetup::createFF(void){
1047	>	switch (ffCase){
1048	>	case FF_DUFF:
1049	>	the_ff = new DUFF();
1050	>	break;
1051
1052	<	current_comp_mol = 0;
1053	<	current_comp++;
1052	>	case FF_LJ:
1053	>	the_ff = new LJFF();
1054	>	break;
1055	>
1056	>	case FF_EAM:
1057	>	the_ff = new EAM_FF();
1058	>	break;
1059	>
1060	>	default:
1061	>	sprintf(painCave.errMsg,
1062	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1063	>	painCave.isFatal = 1;
1064	>	simError();
1065		}
1066	+
1067	+	#ifdef IS_MPI
1068	+	strcpy(checkPointMsg, "ForceField creation successful");
1069	+	MPIcheckPoint();
1070	+	#endif // is_mpi
1071		}
1072	+
1073	+
1074	+	void SimSetup::compList(void){
1075	+	int i;
1076	+	char* id;
1077	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1078	+	LinkedMolStamp* currentStamp = NULL;
1079	+	comp_stamps = new MoleculeStamp * [n_components];
1080	+
1081	+	// make an array of molecule stamps that match the components used.
1082	+	// also extract the used stamps out into a separate linked list
1083	+
1084	+	for (i = 0; i < nInfo; i++){
1085	+	info[i].nComponents = n_components;
1086	+	info[i].componentsNmol = components_nmol;
1087	+	info[i].compStamps = comp_stamps;
1088	+	info[i].headStamp = headStamp;
1089	+	}
1090	+
1091	+
1092	+	for (i = 0; i < n_components; i++){
1093	+	id = the_components[i]->getType();
1094	+	comp_stamps[i] = NULL;
1095	+
1096	+	// check to make sure the component isn't already in the list
1097	+
1098	+	comp_stamps[i] = headStamp->match(id);
1099	+	if (comp_stamps[i] == NULL){
1100	+	// extract the component from the list;
1101	+
1102	+	currentStamp = stamps->extractMolStamp(id);
1103	+	if (currentStamp == NULL){
1104	+	sprintf(painCave.errMsg,
1105	+	"SimSetup error: Component \"%s\" was not found in the "
1106	+	"list of declared molecules\n",
1107	+	id);
1108	+	painCave.isFatal = 1;
1109	+	simError();
1110	+	}
1111	+
1112	+	headStamp->add(currentStamp);
1113	+	comp_stamps[i] = headStamp->match(id);
1114	+	}
1115	+	}
1116	+
1117	+	#ifdef IS_MPI
1118	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1119	+	MPIcheckPoint();
1120	+	#endif // is_mpi
1121	+	}
1122	+
1123	+	void SimSetup::calcSysValues(void){
1124	+	int i;
1125	+
1126	+	int* molMembershipArray;
1127	+
1128	+	tot_atoms = 0;
1129	+	tot_bonds = 0;
1130	+	tot_bends = 0;
1131	+	tot_torsions = 0;
1132	+	for (i = 0; i < n_components; i++){
1133	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1134	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1135	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1136	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1137	+	}
1138	+
1139	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1140	+	molMembershipArray = new int[tot_atoms];
1141	+
1142	+	for (i = 0; i < nInfo; i++){
1143	+	info[i].n_atoms = tot_atoms;
1144	+	info[i].n_bonds = tot_bonds;
1145	+	info[i].n_bends = tot_bends;
1146	+	info[i].n_torsions = tot_torsions;
1147	+	info[i].n_SRI = tot_SRI;
1148	+	info[i].n_mol = tot_nmol;
1149	+
1150	+	info[i].molMembershipArray = molMembershipArray;
1151	+	}
1152	+	}
1153	+
1154	+	#ifdef IS_MPI
1155	+
1156	+	void SimSetup::mpiMolDivide(void){
1157	+	int i, j, k;
1158	+	int localMol, allMol;
1159	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1160	+
1161	+	mpiSim = new mpiSimulation(info);
1162	+
1163	+	globalIndex = mpiSim->divideLabor();
1164	+
1165	+	// set up the local variables
1166	+
1167	+	mol2proc = mpiSim->getMolToProcMap();
1168	+	molCompType = mpiSim->getMolComponentType();
1169	+
1170	+	allMol = 0;
1171	+	localMol = 0;
1172	+	local_atoms = 0;
1173	+	local_bonds = 0;
1174	+	local_bends = 0;
1175	+	local_torsions = 0;
1176	+	globalAtomIndex = 0;
1177	+
1178	+
1179	+	for (i = 0; i < n_components; i++){
1180	+	for (j = 0; j < components_nmol[i]; j++){
1181	+	if (mol2proc[allMol] == worldRank){
1182	+	local_atoms += comp_stamps[i]->getNAtoms();
1183	+	local_bonds += comp_stamps[i]->getNBonds();
1184	+	local_bends += comp_stamps[i]->getNBends();
1185	+	local_torsions += comp_stamps[i]->getNTorsions();
1186	+	localMol++;
1187	+	}
1188	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1189	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1190	+	globalAtomIndex++;
1191	+	}
1192	+
1193	+	allMol++;
1194	+	}
1195	+	}
1196	+	local_SRI = local_bonds + local_bends + local_torsions;
1197	+
1198	+	info[0].n_atoms = mpiSim->getMyNlocal();
1199	+
1200	+	if (local_atoms != info[0].n_atoms){
1201	+	sprintf(painCave.errMsg,
1202	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1203	+	" localAtom (%d) are not equal.\n",
1204	+	info[0].n_atoms, local_atoms);
1205	+	painCave.isFatal = 1;
1206	+	simError();
1207	+	}
1208	+
1209	+	info[0].n_bonds = local_bonds;
1210	+	info[0].n_bends = local_bends;
1211	+	info[0].n_torsions = local_torsions;
1212	+	info[0].n_SRI = local_SRI;
1213	+	info[0].n_mol = localMol;
1214	+
1215	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1216	+	MPIcheckPoint();
1217	+	}
1218	+
1219	+	#endif // is_mpi
1220	+
1221	+
1222	+	void SimSetup::makeSysArrays(void){
1223	+
1224	+	#ifndef IS_MPI
1225	+	int k, j;
1226	+	#endif // is_mpi
1227	+	int i, l;
1228	+
1229	+	Atom** the_atoms;
1230	+	Molecule* the_molecules;
1231	+	Exclude** the_excludes;
1232	+
1233	+
1234	+	for (l = 0; l < nInfo; l++){
1235	+	// create the atom and short range interaction arrays
1236	+
1237	+	the_atoms = new Atom * [info[l].n_atoms];
1238	+	the_molecules = new Molecule[info[l].n_mol];
1239	+	int molIndex;
1240	+
1241	+	// initialize the molecule's stampID's
1242	+
1243	+	#ifdef IS_MPI
1244	+
1245	+
1246	+	molIndex = 0;
1247	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1248	+	if (mol2proc[i] == worldRank){
1249	+	the_molecules[molIndex].setStampID(molCompType[i]);
1250	+	the_molecules[molIndex].setMyIndex(molIndex);
1251	+	the_molecules[molIndex].setGlobalIndex(i);
1252	+	molIndex++;
1253	+	}
1254	+	}
1255	+
1256	+	#else // is_mpi
1257	+
1258	+	molIndex = 0;
1259	+	globalAtomIndex = 0;
1260	+	for (i = 0; i < n_components; i++){
1261	+	for (j = 0; j < components_nmol[i]; j++){
1262	+	the_molecules[molIndex].setStampID(i);
1263	+	the_molecules[molIndex].setMyIndex(molIndex);
1264	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1265	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1266	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1267	+	globalAtomIndex++;
1268	+	}
1269	+	molIndex++;
1270	+	}
1271	+	}
1272	+
1273	+
1274	+	#endif // is_mpi
1275	+
1276	+
1277	+	if (info[l].n_SRI){
1278	+	Exclude::createArray(info[l].n_SRI);
1279	+	the_excludes = new Exclude * [info[l].n_SRI];
1280	+	for (int ex = 0; ex < info[l].n_SRI; ex++){
1281	+	the_excludes[ex] = new Exclude(ex);
1282	+	}
1283	+	info[l].globalExcludes = new int;
1284	+	info[l].n_exclude = info[l].n_SRI;
1285	+	}
1286	+	else{
1287	+	Exclude::createArray(1);
1288	+	the_excludes = new Exclude * ;
1289	+	the_excludes[0] = new Exclude(0);
1290	+	the_excludes[0]->setPair(0, 0);
1291	+	info[l].globalExcludes = new int;
1292	+	info[l].globalExcludes[0] = 0;
1293	+	info[l].n_exclude = 0;
1294	+	}
1295	+
1296	+	// set the arrays into the SimInfo object
1297	+
1298	+	info[l].atoms = the_atoms;
1299	+	info[l].molecules = the_molecules;
1300	+	info[l].nGlobalExcludes = 0;
1301	+	info[l].excludes = the_excludes;
1302	+
1303	+	the_ff->setSimInfo(info);
1304	+	}
1305	+	}
1306	+
1307	+	void SimSetup::makeIntegrator(void){
1308	+	int k;
1309	+
1310	+	NVE<RealIntegrator>* myNVE = NULL;
1311	+	NVT<RealIntegrator>* myNVT = NULL;
1312	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1313	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1314	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1315	+
1316	+	for (k = 0; k < nInfo; k++){
1317	+	switch (ensembleCase){
1318	+	case NVE_ENS:
1319	+	if (globals->haveZconstraints()){
1320	+	setupZConstraint(info[k]);
1321	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1322	+	}
1323	+	else{
1324	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1325	+	}
1326	+
1327	+	info->the_integrator = myNVE;
1328	+	break;
1329	+
1330	+	case NVT_ENS:
1331	+	if (globals->haveZconstraints()){
1332	+	setupZConstraint(info[k]);
1333	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1334	+	}
1335	+	else
1336	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1337	+
1338	+	myNVT->setTargetTemp(globals->getTargetTemp());
1339	+
1340	+	if (globals->haveTauThermostat())
1341	+	myNVT->setTauThermostat(globals->getTauThermostat());
1342	+	else{
1343	+	sprintf(painCave.errMsg,
1344	+	"SimSetup error: If you use the NVT\n"
1345	+	"    ensemble, you must set tauThermostat.\n");
1346	+	painCave.isFatal = 1;
1347	+	simError();
1348	+	}
1349	+
1350	+	info->the_integrator = myNVT;
1351	+	break;
1352	+
1353	+	case NPTi_ENS:
1354	+	if (globals->haveZconstraints()){
1355	+	setupZConstraint(info[k]);
1356	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1357	+	}
1358	+	else
1359	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1360	+
1361	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1362	+
1363	+	if (globals->haveTargetPressure())
1364	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1365	+	else{
1366	+	sprintf(painCave.errMsg,
1367	+	"SimSetup error: If you use a constant pressure\n"
1368	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1369	+	painCave.isFatal = 1;
1370	+	simError();
1371	+	}
1372	+
1373	+	if (globals->haveTauThermostat())
1374	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1375	+	else{
1376	+	sprintf(painCave.errMsg,
1377	+	"SimSetup error: If you use an NPT\n"
1378	+	"    ensemble, you must set tauThermostat.\n");
1379	+	painCave.isFatal = 1;
1380	+	simError();
1381	+	}
1382	+
1383	+	if (globals->haveTauBarostat())
1384	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1385	+	else{
1386	+	sprintf(painCave.errMsg,
1387	+	"SimSetup error: If you use an NPT\n"
1388	+	"    ensemble, you must set tauBarostat.\n");
1389	+	painCave.isFatal = 1;
1390	+	simError();
1391	+	}
1392	+
1393	+	info->the_integrator = myNPTi;
1394	+	break;
1395	+
1396	+	case NPTf_ENS:
1397	+	if (globals->haveZconstraints()){
1398	+	setupZConstraint(info[k]);
1399	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1400	+	}
1401	+	else
1402	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1403	+
1404	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1405	+
1406	+	if (globals->haveTargetPressure())
1407	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1408	+	else{
1409	+	sprintf(painCave.errMsg,
1410	+	"SimSetup error: If you use a constant pressure\n"
1411	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	+	painCave.isFatal = 1;
1413	+	simError();
1414	+	}
1415	+
1416	+	if (globals->haveTauThermostat())
1417	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1418	+
1419	+	else{
1420	+	sprintf(painCave.errMsg,
1421	+	"SimSetup error: If you use an NPT\n"
1422	+	"    ensemble, you must set tauThermostat.\n");
1423	+	painCave.isFatal = 1;
1424	+	simError();
1425	+	}
1426	+
1427	+	if (globals->haveTauBarostat())
1428	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1429	+
1430	+	else{
1431	+	sprintf(painCave.errMsg,
1432	+	"SimSetup error: If you use an NPT\n"
1433	+	"    ensemble, you must set tauBarostat.\n");
1434	+	painCave.isFatal = 1;
1435	+	simError();
1436	+	}
1437	+
1438	+	info->the_integrator = myNPTf;
1439	+	break;
1440	+
1441	+	case NPTxyz_ENS:
1442	+	if (globals->haveZconstraints()){
1443	+	setupZConstraint(info[k]);
1444	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1445	+	}
1446	+	else
1447	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1448	+
1449	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1450	+
1451	+	if (globals->haveTargetPressure())
1452	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1453	+	else{
1454	+	sprintf(painCave.errMsg,
1455	+	"SimSetup error: If you use a constant pressure\n"
1456	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1457	+	painCave.isFatal = 1;
1458	+	simError();
1459	+	}
1460	+
1461	+	if (globals->haveTauThermostat())
1462	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1463	+	else{
1464	+	sprintf(painCave.errMsg,
1465	+	"SimSetup error: If you use an NPT\n"
1466	+	"    ensemble, you must set tauThermostat.\n");
1467	+	painCave.isFatal = 1;
1468	+	simError();
1469	+	}
1470	+
1471	+	if (globals->haveTauBarostat())
1472	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1473	+	else{
1474	+	sprintf(painCave.errMsg,
1475	+	"SimSetup error: If you use an NPT\n"
1476	+	"    ensemble, you must set tauBarostat.\n");
1477	+	painCave.isFatal = 1;
1478	+	simError();
1479	+	}
1480	+
1481	+	info->the_integrator = myNPTxyz;
1482	+	break;
1483	+
1484	+	default:
1485	+	sprintf(painCave.errMsg,
1486	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1487	+	painCave.isFatal = 1;
1488	+	simError();
1489	+	}
1490	+	}
1491	+	}
1492	+
1493	+	void SimSetup::initFortran(void){
1494	+	info[0].refreshSim();
1495	+
1496	+	if (!strcmp(info[0].mixingRule, "standard")){
1497	+	the_ff->initForceField(LB_MIXING_RULE);
1498	+	}
1499	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1500	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1501	+	}
1502	+	else{
1503	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1504	+	info[0].mixingRule);
1505	+	painCave.isFatal = 1;
1506	+	simError();
1507	+	}
1508	+
1509	+
1510	+	#ifdef IS_MPI
1511	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1512	+	MPIcheckPoint();
1513	+	#endif // is_mpi
1514	+	}
1515	+
1516	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1517	+	int nZConstraints;
1518	+	ZconStamp** zconStamp;
1519	+
1520	+	if (globals->haveZconstraintTime()){
1521	+	//add sample time of z-constraint  into SimInfo's property list
1522	+	DoubleData* zconsTimeProp = new DoubleData();
1523	+	zconsTimeProp->setID(ZCONSTIME_ID);
1524	+	zconsTimeProp->setData(globals->getZconsTime());
1525	+	theInfo.addProperty(zconsTimeProp);
1526	+	}
1527	+	else{
1528	+	sprintf(painCave.errMsg,
1529	+	"ZConstraint error: If you use an ZConstraint\n"
1530	+	" , you must set sample time.\n");
1531	+	painCave.isFatal = 1;
1532	+	simError();
1533	+	}
1534	+
1535	+	//push zconsTol into siminfo, if user does not specify
1536	+	//value for zconsTol, a default value will be used
1537	+	DoubleData* zconsTol = new DoubleData();
1538	+	zconsTol->setID(ZCONSTOL_ID);
1539	+	if (globals->haveZconsTol()){
1540	+	zconsTol->setData(globals->getZconsTol());
1541	+	}
1542	+	else{
1543	+	double defaultZConsTol = 0.01;
1544	+	sprintf(painCave.errMsg,
1545	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1546	+	" , default value %f is used.\n",
1547	+	defaultZConsTol);
1548	+	painCave.isFatal = 0;
1549	+	simError();
1550	+
1551	+	zconsTol->setData(defaultZConsTol);
1552	+	}
1553	+	theInfo.addProperty(zconsTol);
1554	+
1555	+	//set Force Subtraction Policy
1556	+	StringData* zconsForcePolicy = new StringData();
1557	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1558	+
1559	+	if (globals->haveZconsForcePolicy()){
1560	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1561	+	}
1562	+	else{
1563	+	sprintf(painCave.errMsg,
1564	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1565	+	"PolicyByMass is used\n");
1566	+	painCave.isFatal = 0;
1567	+	simError();
1568	+	zconsForcePolicy->setData("BYMASS");
1569	+	}
1570	+
1571	+	theInfo.addProperty(zconsForcePolicy);
1572	+
1573	+	//Determine the name of ouput file and add it into SimInfo's property list
1574	+	//Be careful, do not use inFileName, since it is a pointer which
1575	+	//point to a string at master node, and slave nodes do not contain that string
1576	+
1577	+	string zconsOutput(theInfo.finalName);
1578	+
1579	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1580	+
1581	+	StringData* zconsFilename = new StringData();
1582	+	zconsFilename->setID(ZCONSFILENAME_ID);
1583	+	zconsFilename->setData(zconsOutput);
1584	+
1585	+	theInfo.addProperty(zconsFilename);
1586	+
1587	+	//setup index, pos and other parameters of z-constraint molecules
1588	+	nZConstraints = globals->getNzConstraints();
1589	+	theInfo.nZconstraints = nZConstraints;
1590	+
1591	+	zconStamp = globals->getZconStamp();
1592	+	ZConsParaItem tempParaItem;
1593	+
1594	+	ZConsParaData* zconsParaData = new ZConsParaData();
1595	+	zconsParaData->setID(ZCONSPARADATA_ID);
1596	+
1597	+	for (int i = 0; i < nZConstraints; i++){
1598	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1599	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1600	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1601	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1602	+
1603	+	zconsParaData->addItem(tempParaItem);
1604	+	}
1605	+
1606	+	//check the uniqueness of index
1607	+	if(!zconsParaData->isIndexUnique()){
1608	+	sprintf(painCave.errMsg,
1609	+	"ZConstraint Error: molIndex is not unique\n");
1610	+	painCave.isFatal = 1;
1611	+	simError();
1612	+	}
1613	+
1614	+	//sort the parameters by index of molecules
1615	+	zconsParaData->sortByIndex();
1616	+
1617	+	//push data into siminfo, therefore, we can retrieve later
1618	+	theInfo.addProperty(zconsParaData);
1619	+	}

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