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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 491 by mmeineke, Fri Apr 11 18:46:37 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 12 | Line 16 | SimSetup::SimSetup(){
16		#include "mpiSimulation.hpp"
17		#endif
18
19	+	// some defines for ensemble and Forcefield  cases
20	+
21	+	#define NVE_ENS        0
22	+	#define NVT_ENS        1
23	+	#define NPTi_ENS       2
24	+	#define NPTf_ENS       3
25	+
26	+	#define FF_DUFF 0
27	+	#define FF_LJ   1
28	+	#define FF_EAM  2
29	+
30	+	using namespace std;
31	+
32		SimSetup::SimSetup(){
33	+	isInfoArray = 0;
34	+	nInfo = 1;
35	+
36		stamps = new MakeStamps();
37		globals = new Globals();
38	<
38	>
39	>
40		#ifdef IS_MPI
41	<	strcpy( checkPointMsg, "SimSetup creation successful" );
41	>	strcpy(checkPointMsg, "SimSetup creation successful");
42		MPIcheckPoint();
43		#endif // IS_MPI
44		}
#	Line 27 | Line 48 | void SimSetup::parseFile( char* fileName ){
48		delete globals;
49		}
50
51	<	void SimSetup::parseFile( char* fileName ){
51	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
52	>	info = the_info;
53	>	nInfo = theNinfo;
54	>	isInfoArray = 1;
55	>	}
56
57	+
58	+	void SimSetup::parseFile(char* fileName){
59		#ifdef IS_MPI
60	<	if( worldRank == 0 ){
60	>	if (worldRank == 0){
61		#endif // is_mpi
62	<
62	>
63		inFileName = fileName;
64	<	set_interface_stamps( stamps, globals );
65	<
64	>	set_interface_stamps(stamps, globals);
65	>
66		#ifdef IS_MPI
67		mpiEventInit();
68		#endif
69
70	<	yacc_BASS( fileName );
70	>	yacc_BASS(fileName);
71
72		#ifdef IS_MPI
73		throwMPIEvent(NULL);
74		}
75	<	else receiveParse();
75	>	else{
76	>	receiveParse();
77	>	}
78		#endif
79
80		}
81
82		#ifdef IS_MPI
83		void SimSetup::receiveParse(void){
84	<
85	<	set_interface_stamps( stamps, globals );
86	<	mpiEventInit();
87	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92	<	void SimSetup::createSim( void ){
92	>	void SimSetup::createSim(void){
93
94	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j, k, globalAtomIndex;
94	>	// gather all of the information from the Bass file
95
96	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
96	>	gatherInfo();
97
98	<	// 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();
98	>	// creation of complex system objects
99
100	<	// 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() );
100	>	sysObjectsCreation();
101
102	<	// 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	<	}
102	>	// check on the post processing info
103
104	<	if (the_globals->haveTauThermostat())
102	<	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	<	}
104	>	finalInfoCheck();
105
106	<	if (the_globals->haveTauBarostat())
115	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116	<	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	<	}
106	>	// initialize the system coordinates
107
108	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
109	<	the_extendedsystem = new ExtendedSystem( simnfo );
110	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
108	>	if (!isInfoArray){
109	>	initSystemCoords();
110	>	}
111
112	<	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	<	}
112	>	// make the output filenames
113
114	<	} 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 );
114	>	makeOutNames();
115
116	<	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	<	}
116	>	// make the integrator
117
118	+	makeIntegrator();
119	+
120		#ifdef IS_MPI
121	<	strcpy( checkPointMsg, "ForceField creation successful" );
122	<	MPIcheckPoint();
174	<	#endif // is_mpi
121	>	mpiSim->mpiRefresh();
122	>	#endif
123
124	<
124	>	// initialize the Fortran
125
126	<	// get the components and calculate the tot_nMol and indvidual n_mol
127	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
126	>	initFortran();
127	>	}
128
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
129
130	<	tot_nmol = 0;
131	<	for( i=0; i<n_components; i++ ){
130	>	void SimSetup::makeMolecules(void){
131	>	int k;
132	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
133	>	molInit molInfo;
134	>	DirectionalAtom* dAtom;
135	>	LinkedAssign* extras;
136	>	LinkedAssign* current_extra;
137	>	AtomStamp* currentAtom;
138	>	BondStamp* currentBond;
139	>	BendStamp* currentBend;
140	>	TorsionStamp* currentTorsion;
141
142	<	if( !the_components[i]->haveNMol() ){
143	<	// we have a problem
144	<	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	<	}
142	>	bond_pair* theBonds;
143	>	bend_set* theBends;
144	>	torsion_set* theTorsions;
145
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	–	}
146
147	<	#ifdef IS_MPI
229	<	strcpy( checkPointMsg, "Have the number of components" );
230	<	MPIcheckPoint();
231	<	#endif // is_mpi
147	>	//init the forceField paramters
148
149	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
149	>	the_ff->readParams();
150
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++ ){
151
152	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
152	>	// init the atoms
153
154	<	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	<	}
154	>	double ux, uy, uz, u, uSqr;
155
156	<	#ifdef IS_MPI
157	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	<	MPIcheckPoint();
274	<	#endif // is_mpi
275	<
156	>	for (k = 0; k < nInfo; k++){
157	>	the_ff->setSimInfo(&(info[k]));
158
159	+	atomOffset = 0;
160	+	excludeOffset = 0;
161	+	for (i = 0; i < info[k].n_mol; i++){
162	+	stampID = info[k].molecules[i].getStampID();
163
164	+	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
165	+	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
166	+	molInfo.nBends = comp_stamps[stampID]->getNBends();
167	+	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
168	+	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
169
170	<	// caclulate the number of atoms, bonds, bends and torsions
170	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
171	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
172	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
173	>	molInfo.myBends = new Bend * [molInfo.nBends];
174	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
175
176	<	tot_atoms = 0;
177	<	tot_bonds = 0;
178	<	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	<	}
176	>	theBonds = new bond_pair[molInfo.nBonds];
177	>	theBends = new bend_set[molInfo.nBends];
178	>	theTorsions = new torsion_set[molInfo.nTorsions];
179
180	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
180	>	// make the Atoms
181
182	<	simnfo->n_atoms = tot_atoms;
183	<	simnfo->n_bonds = tot_bonds;
184	<	simnfo->n_bends = tot_bends;
185	<	simnfo->n_torsions = tot_torsions;
186	<	simnfo->n_SRI = tot_SRI;
187	<	simnfo->n_mol = tot_nmol;
188	<
302	<	simnfo->molMembershipArray = new int[tot_atoms];
182	>	for (j = 0; j < molInfo.nAtoms; j++){
183	>	currentAtom = comp_stamps[stampID]->getAtom(j);
184	>	if (currentAtom->haveOrientation()){
185	>	dAtom = new DirectionalAtom((j + atomOffset),
186	>	info[k].getConfiguration());
187	>	info[k].n_oriented++;
188	>	molInfo.myAtoms[j] = dAtom;
189
190	<	#ifdef IS_MPI
190	>	ux = currentAtom->getOrntX();
191	>	uy = currentAtom->getOrntY();
192	>	uz = currentAtom->getOrntZ();
193
194	<	// divide the molecules among processors here.
307	<
308	<	mpiSim = new mpiSimulation( simnfo );
309	<
310	<	globalIndex = mpiSim->divideLabor();
194	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
195
196	<	// set up the local variables
197	<
198	<	int localMol, allMol;
199	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
196	>	u = sqrt(uSqr);
197	>	ux = ux / u;
198	>	uy = uy / u;
199	>	uz = uz / u;
200
201	<	int* mol2proc = mpiSim->getMolToProcMap();
202	<	int* molCompType = mpiSim->getMolComponentType();
203	<
204	<	allMol = 0;
205	<	localMol = 0;
206	<	local_atoms = 0;
207	<	local_bonds = 0;
208	<	local_bends = 0;
209	<	local_torsions = 0;
326	<	globalAtomIndex = 0;
201	>	dAtom->setSUx(ux);
202	>	dAtom->setSUy(uy);
203	>	dAtom->setSUz(uz);
204	>	}
205	>	else{
206	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
207	>	info[k].getConfiguration());
208	>	}
209	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
210
211	+	#ifdef IS_MPI
212
213	<	for( i=0; i<n_components; i++ ){
213	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
214
331	–	for( j=0; j<components_nmol[i]; j++ ){
332	–
333	–	if( mol2proc[allMol] == worldRank ){
334	–
335	–	local_atoms +=    comp_stamps[i]->getNAtoms();
336	–	local_bonds +=    comp_stamps[i]->getNBonds();
337	–	local_bends +=    comp_stamps[i]->getNBends();
338	–	local_torsions += comp_stamps[i]->getNTorsions();
339	–	localMol++;
340	–	}
341	–	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
342	–	simnfo->molMembershipArray[globalAtomIndex] = allMol;
343	–	globalAtomIndex++;
344	–	}
345	–
346	–	allMol++;
347	–	}
348	–	}
349	–	local_SRI = local_bonds + local_bends + local_torsions;
350	–
351	–	simnfo->n_atoms = mpiSim->getMyNlocal();
352	–
353	–	if( local_atoms != simnfo->n_atoms ){
354	–	sprintf( painCave.errMsg,
355	–	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
356	–	" localAtom (%d) are not equal.\n",
357	–	simnfo->n_atoms,
358	–	local_atoms );
359	–	painCave.isFatal = 1;
360	–	simError();
361	–	}
362	–
363	–	simnfo->n_bonds = local_bonds;
364	–	simnfo->n_bends = local_bends;
365	–	simnfo->n_torsions = local_torsions;
366	–	simnfo->n_SRI = local_SRI;
367	–	simnfo->n_mol = localMol;
368	–
369	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
370	–	MPIcheckPoint();
371	–
372	–
215		#endif // is_mpi
216	<
216	>	}
217
218	<	// create the atom and short range interaction arrays
218	>	// make the bonds
219	>	for (j = 0; j < molInfo.nBonds; j++){
220	>	currentBond = comp_stamps[stampID]->getBond(j);
221	>	theBonds[j].a = currentBond->getA() + atomOffset;
222	>	theBonds[j].b = currentBond->getB() + atomOffset;
223
224	<	Atom::createArrays(simnfo->n_atoms);
225	<	the_atoms = new Atom*[simnfo->n_atoms];
380	<	the_molecules = new Molecule[simnfo->n_mol];
381	<	int molIndex;
224	>	exI = theBonds[j].a;
225	>	exJ = theBonds[j].b;
226
227	<	// initialize the molecule's stampID's
228	<
227	>	// exclude_I must always be the smaller of the pair
228	>	if (exI > exJ){
229	>	tempEx = exI;
230	>	exI = exJ;
231	>	exJ = tempEx;
232	>	}
233		#ifdef IS_MPI
234	<
234	>	tempEx = exI;
235	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
236	>	tempEx = exJ;
237	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
238
239	<	molIndex = 0;
240	<	for(i=0; i<mpiSim->getTotNmol(); i++){
390	<
391	<	if(mol2proc[i] == worldRank ){
392	<	the_molecules[molIndex].setStampID( molCompType[i] );
393	<	the_molecules[molIndex].setMyIndex( molIndex );
394	<	the_molecules[molIndex].setGlobalIndex( i );
395	<	molIndex++;
396	<	}
397	<	}
239	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
240	>	#else  // isn't MPI
241
242	<	#else // is_mpi
243	<
401	<	molIndex = 0;
402	<	globalAtomIndex = 0;
403	<	for(i=0; i<n_components; i++){
404	<	for(j=0; j<components_nmol[i]; j++ ){
405	<	the_molecules[molIndex].setStampID( i );
406	<	the_molecules[molIndex].setMyIndex( molIndex );
407	<	the_molecules[molIndex].setGlobalIndex( molIndex );
408	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
409	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
410	<	globalAtomIndex++;
242	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
243	>	#endif  //is_mpi
244		}
245	<	molIndex++;
413	<	}
414	<	}
415	<
245	>	excludeOffset += molInfo.nBonds;
246
247	<	#endif // is_mpi
247	>	//make the bends
248	>	for (j = 0; j < molInfo.nBends; j++){
249	>	currentBend = comp_stamps[stampID]->getBend(j);
250	>	theBends[j].a = currentBend->getA() + atomOffset;
251	>	theBends[j].b = currentBend->getB() + atomOffset;
252	>	theBends[j].c = currentBend->getC() + atomOffset;
253
254	+	if (currentBend->haveExtras()){
255	+	extras = currentBend->getExtras();
256	+	current_extra = extras;
257
258	<	if( simnfo->n_SRI ){
259	<
260	<	Exclude::createArray(simnfo->n_SRI);
261	<	the_excludes = new Exclude*[simnfo->n_SRI];
262	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
263	<	simnfo->globalExcludes = new int;
264	<	simnfo->n_exclude = simnfo->n_SRI;
427	<	}
428	<	else{
429	<
430	<	Exclude::createArray( 1 );
431	<	the_excludes = new Exclude*;
432	<	the_excludes[0] = new Exclude(0);
433	<	the_excludes[0]->setPair( 0,0 );
434	<	simnfo->globalExcludes = new int;
435	<	simnfo->globalExcludes[0] = 0;
436	<	simnfo->n_exclude = 0;
437	<	}
258	>	while (current_extra != NULL){
259	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
260	>	switch (current_extra->getType()){
261	>	case 0:
262	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
263	>	theBends[j].isGhost = 1;
264	>	break;
265
266	<	// set the arrays into the SimInfo object
266	>	case 1:
267	>	theBends[j].ghost = (int) current_extra->getDouble() +
268	>	atomOffset;
269	>	theBends[j].isGhost = 1;
270	>	break;
271
272	<	simnfo->atoms = the_atoms;
273	<	simnfo->molecules = the_molecules;
274	<	simnfo->nGlobalExcludes = 0;
275	<	simnfo->excludes = the_excludes;
272	>	default:
273	>	sprintf(painCave.errMsg,
274	>	"SimSetup Error: ghostVectorSource was neither a "
275	>	"double nor an int.\n"
276	>	"-->Bend[%d] in %s\n",
277	>	j, comp_stamps[stampID]->getID());
278	>	painCave.isFatal = 1;
279	>	simError();
280	>	}
281	>	}
282	>	else{
283	>	sprintf(painCave.errMsg,
284	>	"SimSetup Error: unhandled bend assignment:\n"
285	>	"    -->%s in Bend[%d] in %s\n",
286	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290
291	+	current_extra = current_extra->getNext();
292	+	}
293	+	}
294
295	<	// get some of the tricky things that may still be in the globals
295	>	if (!theBends[j].isGhost){
296	>	exI = theBends[j].a;
297	>	exJ = theBends[j].c;
298	>	}
299	>	else{
300	>	exI = theBends[j].a;
301	>	exJ = theBends[j].b;
302	>	}
303
304	<
305	<	if( the_globals->haveBox() ){
306	<	simnfo->box_x = the_globals->getBox();
307	<	simnfo->box_y = the_globals->getBox();
308	<	simnfo->box_z = the_globals->getBox();
309	<	}
310	<	else if( the_globals->haveDensity() ){
304	>	// exclude_I must always be the smaller of the pair
305	>	if (exI > exJ){
306	>	tempEx = exI;
307	>	exI = exJ;
308	>	exJ = tempEx;
309	>	}
310	>	#ifdef IS_MPI
311	>	tempEx = exI;
312	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
313	>	tempEx = exJ;
314	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
315
316	<	double vol;
317	<	vol = (double)tot_nmol / the_globals->getDensity();
318	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
319	<	simnfo->box_y = simnfo->box_x;
320	<	simnfo->box_z = simnfo->box_x;
321	<	}
463	<	else{
464	<	if( !the_globals->haveBoxX() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup error, no periodic BoxX size given.\n" );
467	<	painCave.isFatal = 1;
468	<	simError();
469	<	}
470	<	simnfo->box_x = the_globals->getBoxX();
316	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
317	>	#else  // isn't MPI
318	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
319	>	#endif  //is_mpi
320	>	}
321	>	excludeOffset += molInfo.nBends;
322
323	<	if( !the_globals->haveBoxY() ){
324	<	sprintf( painCave.errMsg,
325	<	"SimSetup error, no periodic BoxY size given.\n" );
326	<	painCave.isFatal = 1;
327	<	simError();
328	<	}
478	<	simnfo->box_y = the_globals->getBoxY();
323	>	for (j = 0; j < molInfo.nTorsions; j++){
324	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
325	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
326	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
327	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
328	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
329
330	<	if( !the_globals->haveBoxZ() ){
331	<	sprintf( painCave.errMsg,
482	<	"SimSetup error, no periodic BoxZ size given.\n" );
483	<	painCave.isFatal = 1;
484	<	simError();
485	<	}
486	<	simnfo->box_z = the_globals->getBoxZ();
487	<	}
330	>	exI = theTorsions[j].a;
331	>	exJ = theTorsions[j].d;
332
333	+	// exclude_I must always be the smaller of the pair
334	+	if (exI > exJ){
335	+	tempEx = exI;
336	+	exI = exJ;
337	+	exJ = tempEx;
338	+	}
339		#ifdef IS_MPI
340	<	strcpy( checkPointMsg, "Box size set up" );
341	<	MPIcheckPoint();
342	<	#endif // is_mpi
340	>	tempEx = exI;
341	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
342	>	tempEx = exJ;
343	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344
345	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
346	+	#else  // isn't MPI
347	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
348	+	#endif  //is_mpi
349	+	}
350	+	excludeOffset += molInfo.nTorsions;
351
495	–	// initialize the arrays
352
353	<	the_ff->setSimInfo( simnfo );
353	>	// send the arrays off to the forceField for init.
354
355	<	makeMolecules();
356	<	simnfo->identArray = new int[simnfo->n_atoms];
357	<	for(i=0; i<simnfo->n_atoms; i++){
358	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
359	<	}
504	<
505	<	if (the_globals->getUseRF() ) {
506	<	simnfo->useReactionField = 1;
507	<
508	<	if( !the_globals->haveECR() ){
509	<	sprintf( painCave.errMsg,
510	<	"SimSetup Warning: using default value of 1/2 the smallest "
511	<	"box length for the electrostaticCutoffRadius.\n"
512	<	"I hope you have a very fast processor!\n");
513	<	painCave.isFatal = 0;
514	<	simError();
515	<	double smallest;
516	<	smallest = simnfo->box_x;
517	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
518	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
519	<	simnfo->ecr = 0.5 * smallest;
520	<	} else {
521	<	simnfo->ecr        = the_globals->getECR();
522	<	}
355	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
356	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
357	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
358	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
359	>	theTorsions);
360
361	<	if( !the_globals->haveEST() ){
362	<	sprintf( painCave.errMsg,
363	<	"SimSetup Warning: using default value of 0.05 * the "
364	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
365	<	);
366	<	painCave.isFatal = 0;
367	<	simError();
368	<	simnfo->est = 0.05 * simnfo->ecr;
532	<	} else {
533	<	simnfo->est        = the_globals->getEST();
361	>
362	>	info[k].molecules[i].initialize(molInfo);
363	>
364	>
365	>	atomOffset += molInfo.nAtoms;
366	>	delete[] theBonds;
367	>	delete[] theBends;
368	>	delete[] theTorsions;
369		}
370	<
536	<	if(!the_globals->haveDielectric() ){
537	<	sprintf( painCave.errMsg,
538	<	"SimSetup Error: You are trying to use Reaction Field without"
539	<	"setting a dielectric constant!\n"
540	<	);
541	<	painCave.isFatal = 1;
542	<	simError();
543	<	}
544	<	simnfo->dielectric = the_globals->getDielectric();
545	<	} else {
546	<	if (usesDipoles) {
547	<
548	<	if( !the_globals->haveECR() ){
549	<	sprintf( painCave.errMsg,
550	<	"SimSetup Warning: using default value of 1/2 the smallest "
551	<	"box length for the electrostaticCutoffRadius.\n"
552	<	"I hope you have a very fast processor!\n");
553	<	painCave.isFatal = 0;
554	<	simError();
555	<	double smallest;
556	<	smallest = simnfo->box_x;
557	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
558	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
559	<	simnfo->ecr = 0.5 * smallest;
560	<	} else {
561	<	simnfo->ecr        = the_globals->getECR();
562	<	}
563	<
564	<	if( !the_globals->haveEST() ){
565	<	sprintf( painCave.errMsg,
566	<	"SimSetup Warning: using default value of 5%% of the "
567	<	"electrostaticCutoffRadius for the "
568	<	"electrostaticSkinThickness\n"
569	<	);
570	<	painCave.isFatal = 0;
571	<	simError();
572	<	simnfo->est = 0.05 * simnfo->ecr;
573	<	} else {
574	<	simnfo->est        = the_globals->getEST();
575	<	}
576	<	}
577	<	}
370	>	}
371
372		#ifdef IS_MPI
373	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
373	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
374		MPIcheckPoint();
375		#endif // is_mpi
376
377	<	if( the_globals->haveInitialConfig() ){
585	<
586	<	InitializeFromFile* fileInit;
587	<	#ifdef IS_MPI // is_mpi
588	<	if( worldRank == 0 ){
589	<	#endif //is_mpi
590	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
591	<	#ifdef IS_MPI
592	<	}else fileInit = new InitializeFromFile( NULL );
593	<	#endif
594	<	fileInit->read_xyz( simnfo ); // default velocities on
377	>	// clean up the forcefield
378
379	<	delete fileInit;
380	<	}
381	<	else{
379	>	the_ff->calcRcut();
380	>	the_ff->cleanMe();
381	>	}
382
383	<	#ifdef IS_MPI
383	>	void SimSetup::initFromBass(void){
384	>	int i, j, k;
385	>	int n_cells;
386	>	double cellx, celly, cellz;
387	>	double temp1, temp2, temp3;
388	>	int n_per_extra;
389	>	int n_extra;
390	>	int have_extra, done;
391
392	<	// no init from bass
393	<
394	<	sprintf( painCave.errMsg,
395	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
606	<	painCave.isFatal;
607	<	simError();
608	<
609	<	#else
392	>	double vel[3];
393	>	vel[0] = 0.0;
394	>	vel[1] = 0.0;
395	>	vel[2] = 0.0;
396
397	<	initFromBass();
397	>	temp1 = (double) tot_nmol / 4.0;
398	>	temp2 = pow(temp1, (1.0 / 3.0));
399	>	temp3 = ceil(temp2);
400
401	+	have_extra = 0;
402	+	if (temp2 < temp3){
403	+	// we have a non-complete lattice
404	+	have_extra = 1;
405
406	<	#endif
407	<	}
406	>	n_cells = (int) temp3 - 1;
407	>	cellx = info[0].boxL[0] / temp3;
408	>	celly = info[0].boxL[1] / temp3;
409	>	cellz = info[0].boxL[2] / temp3;
410	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
411	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
412	>	n_per_extra = (int) ceil(temp1);
413
414	<	#ifdef IS_MPI
415	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
416	<	MPIcheckPoint();
417	<	#endif // is_mpi
418	<
419	<
623	<
624	<
625	<
626	<
627	<
628	<	#ifdef IS_MPI
629	<	if( worldRank == 0 ){
630	<	#endif // is_mpi
631	<
632	<	if( the_globals->haveFinalConfig() ){
633	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
414	>	if (n_per_extra > 4){
415	>	sprintf(painCave.errMsg,
416	>	"SimSetup error. There has been an error in constructing"
417	>	" the non-complete lattice.\n");
418	>	painCave.isFatal = 1;
419	>	simError();
420		}
635	–	else{
636	–	strcpy( simnfo->finalName, inFileName );
637	–	char* endTest;
638	–	int nameLength = strlen( simnfo->finalName );
639	–	endTest = &(simnfo->finalName[nameLength - 5]);
640	–	if( !strcmp( endTest, ".bass" ) ){
641	–	strcpy( endTest, ".eor" );
642	–	}
643	–	else if( !strcmp( endTest, ".BASS" ) ){
644	–	strcpy( endTest, ".eor" );
645	–	}
646	–	else{
647	–	endTest = &(simnfo->finalName[nameLength - 4]);
648	–	if( !strcmp( endTest, ".bss" ) ){
649	–	strcpy( endTest, ".eor" );
650	–	}
651	–	else if( !strcmp( endTest, ".mdl" ) ){
652	–	strcpy( endTest, ".eor" );
653	–	}
654	–	else{
655	–	strcat( simnfo->finalName, ".eor" );
656	–	}
657	–	}
658	–	}
659	–
660	–	// make the sample and status out names
661	–
662	–	strcpy( simnfo->sampleName, inFileName );
663	–	char* endTest;
664	–	int nameLength = strlen( simnfo->sampleName );
665	–	endTest = &(simnfo->sampleName[nameLength - 5]);
666	–	if( !strcmp( endTest, ".bass" ) ){
667	–	strcpy( endTest, ".dump" );
668	–	}
669	–	else if( !strcmp( endTest, ".BASS" ) ){
670	–	strcpy( endTest, ".dump" );
671	–	}
672	–	else{
673	–	endTest = &(simnfo->sampleName[nameLength - 4]);
674	–	if( !strcmp( endTest, ".bss" ) ){
675	–	strcpy( endTest, ".dump" );
676	–	}
677	–	else if( !strcmp( endTest, ".mdl" ) ){
678	–	strcpy( endTest, ".dump" );
679	–	}
680	–	else{
681	–	strcat( simnfo->sampleName, ".dump" );
682	–	}
683	–	}
684	–
685	–	strcpy( simnfo->statusName, inFileName );
686	–	nameLength = strlen( simnfo->statusName );
687	–	endTest = &(simnfo->statusName[nameLength - 5]);
688	–	if( !strcmp( endTest, ".bass" ) ){
689	–	strcpy( endTest, ".stat" );
690	–	}
691	–	else if( !strcmp( endTest, ".BASS" ) ){
692	–	strcpy( endTest, ".stat" );
693	–	}
694	–	else{
695	–	endTest = &(simnfo->statusName[nameLength - 4]);
696	–	if( !strcmp( endTest, ".bss" ) ){
697	–	strcpy( endTest, ".stat" );
698	–	}
699	–	else if( !strcmp( endTest, ".mdl" ) ){
700	–	strcpy( endTest, ".stat" );
701	–	}
702	–	else{
703	–	strcat( simnfo->statusName, ".stat" );
704	–	}
705	–	}
706	–
707	–	#ifdef IS_MPI
421		}
709	–	#endif // is_mpi
710	–
711	–	// set the status, sample, and themal kick times
712	–
713	–	if( the_globals->haveSampleTime() ){
714	–	simnfo->sampleTime = the_globals->getSampleTime();
715	–	simnfo->statusTime = simnfo->sampleTime;
716	–	simnfo->thermalTime = simnfo->sampleTime;
717	–	}
422		else{
423	<	simnfo->sampleTime = the_globals->getRunTime();
424	<	simnfo->statusTime = simnfo->sampleTime;
425	<	simnfo->thermalTime = simnfo->sampleTime;
423	>	n_cells = (int) temp3;
424	>	cellx = info[0].boxL[0] / temp3;
425	>	celly = info[0].boxL[1] / temp3;
426	>	cellz = info[0].boxL[2] / temp3;
427		}
428
429	<	if( the_globals->haveStatusTime() ){
430	<	simnfo->statusTime = the_globals->getStatusTime();
431	<	}
429	>	current_mol = 0;
430	>	current_comp_mol = 0;
431	>	current_comp = 0;
432	>	current_atom_ndx = 0;
433
434	<	if( the_globals->haveThermalTime() ){
435	<	simnfo->thermalTime = the_globals->getThermalTime();
434	>	for (i = 0; i < n_cells ; i++){
435	>	for (j = 0; j < n_cells; j++){
436	>	for (k = 0; k < n_cells; k++){
437	>	makeElement(i * cellx, j * celly, k * cellz);
438	>
439	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
440	>
441	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
442	>
443	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
444	>	}
445	>	}
446		}
447
448	<	// check for the temperature set flag
448	>	if (have_extra){
449	>	done = 0;
450
451	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
451	>	int start_ndx;
452	>	for (i = 0; i < (n_cells + 1) && !done; i++){
453	>	for (j = 0; j < (n_cells + 1) && !done; j++){
454	>	if (i < n_cells){
455	>	if (j < n_cells){
456	>	start_ndx = n_cells;
457	>	}
458	>	else
459	>	start_ndx = 0;
460	>	}
461	>	else
462	>	start_ndx = 0;
463
464	+	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
465	+	makeElement(i * cellx, j * celly, k * cellz);
466	+	done = (current_mol >= tot_nmol);
467
468	<	//   // make the longe range forces and the integrator
468	>	if (!done && n_per_extra > 1){
469	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
470	>	k * cellz);
471	>	done = (current_mol >= tot_nmol);
472	>	}
473
474	<	//   new AllLong( simnfo );
474	>	if (!done && n_per_extra > 2){
475	>	makeElement(i * cellx, j * celly + 0.5 * celly,
476	>	k * cellz + 0.5 * cellz);
477	>	done = (current_mol >= tot_nmol);
478	>	}
479
480	+	if (!done && n_per_extra > 3){
481	+	makeElement(i * cellx + 0.5 * cellx, j * celly,
482	+	k * cellz + 0.5 * cellz);
483	+	done = (current_mol >= tot_nmol);
484	+	}
485	+	}
486	+	}
487	+	}
488	+	}
489
490	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
491	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
490	>	for (i = 0; i < info[0].n_atoms; i++){
491	>	info[0].atoms[i]->setVel(vel);
492		}
493	<	else if( !strcmp( force_field, "LJ" ) ){
746	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
747	<	}
748	<	else {
749	<	std::cerr << "I'm a bug.\n";
750	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
751	<	}
752	<	#ifdef IS_MPI
753	<	mpiSim->mpiRefresh();
754	<	#endif
493	>	}
494
495	<	// initialize the Fortran
495	>	void SimSetup::makeElement(double x, double y, double z){
496	>	int k;
497	>	AtomStamp* current_atom;
498	>	DirectionalAtom* dAtom;
499	>	double rotMat[3][3];
500	>	double pos[3];
501
502	+	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
503	+	current_atom = comp_stamps[current_comp]->getAtom(k);
504	+	if (!current_atom->havePosition()){
505	+	sprintf(painCave.errMsg,
506	+	"SimSetup:initFromBass error.\n"
507	+	"\tComponent %s, atom %s does not have a position specified.\n"
508	+	"\tThe initialization routine is unable to give a start"
509	+	" position.\n",
510	+	comp_stamps[current_comp]->getID(), current_atom->getType());
511	+	painCave.isFatal = 1;
512	+	simError();
513	+	}
514
515	<	simnfo->refreshSim();
516	<
517	<	if( !strcmp( simnfo->mixingRule, "standard") ){
518	<	the_ff->initForceField( LB_MIXING_RULE );
515	>	pos[0] = x + current_atom->getPosX();
516	>	pos[1] = y + current_atom->getPosY();
517	>	pos[2] = z + current_atom->getPosZ();
518	>
519	>	info[0].atoms[current_atom_ndx]->setPos(pos);
520	>
521	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
522	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
523	>
524	>	rotMat[0][0] = 1.0;
525	>	rotMat[0][1] = 0.0;
526	>	rotMat[0][2] = 0.0;
527	>
528	>	rotMat[1][0] = 0.0;
529	>	rotMat[1][1] = 1.0;
530	>	rotMat[1][2] = 0.0;
531	>
532	>	rotMat[2][0] = 0.0;
533	>	rotMat[2][1] = 0.0;
534	>	rotMat[2][2] = 1.0;
535	>
536	>	dAtom->setA(rotMat);
537	>	}
538	>
539	>	current_atom_ndx++;
540		}
764	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
765	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
766	–	}
767	–	else{
768	–	sprintf( painCave.errMsg,
769	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
770	–	simnfo->mixingRule );
771	–	painCave.isFatal = 1;
772	–	simError();
773	–	}
541
542	+	current_mol++;
543	+	current_comp_mol++;
544
545	<	#ifdef IS_MPI
546	<	strcpy( checkPointMsg,
547	<	"Successfully intialized the mixingRule for Fortran." );
548	<	MPIcheckPoint();
780	<	#endif // is_mpi
545	>	if (current_comp_mol >= components_nmol[current_comp]){
546	>	current_comp_mol = 0;
547	>	current_comp++;
548	>	}
549		}
550
551
552	<	void SimSetup::makeMolecules( void ){
552	>	void SimSetup::gatherInfo(void){
553	>	int i;
554
555	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
556	<	molInit info;
788	<	DirectionalAtom* dAtom;
789	<	LinkedAssign* extras;
790	<	LinkedAssign* current_extra;
791	<	AtomStamp* currentAtom;
792	<	BondStamp* currentBond;
793	<	BendStamp* currentBend;
794	<	TorsionStamp* currentTorsion;
555	>	ensembleCase = -1;
556	>	ffCase = -1;
557
558	<	bond_pair* theBonds;
797	<	bend_set* theBends;
798	<	torsion_set* theTorsions;
558	>	// set the easy ones first
559
560	<
561	<	//init the forceField paramters
560	>	for (i = 0; i < nInfo; i++){
561	>	info[i].target_temp = globals->getTargetTemp();
562	>	info[i].dt = globals->getDt();
563	>	info[i].run_time = globals->getRunTime();
564	>	}
565	>	n_components = globals->getNComponents();
566
803	–	the_ff->readParams();
567
568	<
806	<	// init the atoms
568	>	// get the forceField
569
570	<	double ux, uy, uz, u, uSqr;
809	<
810	<	atomOffset = 0;
811	<	excludeOffset = 0;
812	<	for(i=0; i<simnfo->n_mol; i++){
813	<
814	<	stampID = the_molecules[i].getStampID();
570	>	strcpy(force_field, globals->getForceField());
571
572	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
573	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
574	<	info.nBends    = comp_stamps[stampID]->getNBends();
575	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
576	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
572	>	if (!strcasecmp(force_field, "DUFF")){
573	>	ffCase = FF_DUFF;
574	>	}
575	>	else if (!strcasecmp(force_field, "LJ")){
576	>	ffCase = FF_LJ;
577	>	}
578	>	else if (!strcasecmp(force_field, "EAM")){
579	>	ffCase = FF_EAM;
580	>	}
581	>	else{
582	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
583	>	force_field);
584	>	painCave.isFatal = 1;
585	>	simError();
586	>	}
587
588	<	info.myAtoms = &the_atoms[atomOffset];
823	<	info.myExcludes = &the_excludes[excludeOffset];
824	<	info.myBonds = new Bond*[info.nBonds];
825	<	info.myBends = new Bend*[info.nBends];
826	<	info.myTorsions = new Torsion*[info.nTorsions];
588	>	// get the ensemble
589
590	<	theBonds = new bond_pair[info.nBonds];
829	<	theBends = new bend_set[info.nBends];
830	<	theTorsions = new torsion_set[info.nTorsions];
831	<
832	<	// make the Atoms
833	<
834	<	for(j=0; j<info.nAtoms; j++){
835	<
836	<	currentAtom = comp_stamps[stampID]->getAtom( j );
837	<	if( currentAtom->haveOrientation() ){
838	<
839	<	dAtom = new DirectionalAtom(j + atomOffset);
840	<	simnfo->n_oriented++;
841	<	info.myAtoms[j] = dAtom;
842	<
843	<	ux = currentAtom->getOrntX();
844	<	uy = currentAtom->getOrntY();
845	<	uz = currentAtom->getOrntZ();
846	<
847	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
848	<
849	<	u = sqrt( uSqr );
850	<	ux = ux / u;
851	<	uy = uy / u;
852	<	uz = uz / u;
853	<
854	<	dAtom->setSUx( ux );
855	<	dAtom->setSUy( uy );
856	<	dAtom->setSUz( uz );
857	<	}
858	<	else{
859	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
860	<	}
861	<	info.myAtoms[j]->setType( currentAtom->getType() );
862	<
863	<	#ifdef IS_MPI
864	<
865	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
866	<
867	<	#endif // is_mpi
868	<	}
869	<
870	<	// make the bonds
871	<	for(j=0; j<info.nBonds; j++){
872	<
873	<	currentBond = comp_stamps[stampID]->getBond( j );
874	<	theBonds[j].a = currentBond->getA() + atomOffset;
875	<	theBonds[j].b = currentBond->getB() + atomOffset;
590	>	strcpy(ensemble, globals->getEnsemble());
591
592	<	exI = theBonds[j].a;
593	<	exJ = theBonds[j].b;
592	>	if (!strcasecmp(ensemble, "NVE")){
593	>	ensembleCase = NVE_ENS;
594	>	}
595	>	else if (!strcasecmp(ensemble, "NVT")){
596	>	ensembleCase = NVT_ENS;
597	>	}
598	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
599	>	ensembleCase = NPTi_ENS;
600	>	}
601	>	else if (!strcasecmp(ensemble, "NPTf")){
602	>	ensembleCase = NPTf_ENS;
603	>	}
604	>	else{
605	>	sprintf(painCave.errMsg,
606	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
607	>	"reverting to NVE for this simulation.\n",
608	>	ensemble);
609	>	painCave.isFatal = 0;
610	>	simError();
611	>	strcpy(ensemble, "NVE");
612	>	ensembleCase = NVE_ENS;
613	>	}
614
615	<	// exclude_I must always be the smaller of the pair
616	<	if( exI > exJ ){
882	<	tempEx = exI;
883	<	exI = exJ;
884	<	exJ = tempEx;
885	<	}
886	<	#ifdef IS_MPI
887	<	tempEx = exI;
888	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
889	<	tempEx = exJ;
890	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
891	<
892	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
893	<	#else  // isn't MPI
615	>	for (i = 0; i < nInfo; i++){
616	>	strcpy(info[i].ensemble, ensemble);
617
618	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
896	<	#endif  //is_mpi
897	<	}
898	<	excludeOffset += info.nBonds;
618	>	// get the mixing rule
619
620	<	//make the bends
621	<	for(j=0; j<info.nBends; j++){
622	<
903	<	currentBend = comp_stamps[stampID]->getBend( j );
904	<	theBends[j].a = currentBend->getA() + atomOffset;
905	<	theBends[j].b = currentBend->getB() + atomOffset;
906	<	theBends[j].c = currentBend->getC() + atomOffset;
907	<
908	<	if( currentBend->haveExtras() ){
909	<
910	<	extras = currentBend->getExtras();
911	<	current_extra = extras;
912	<
913	<	while( current_extra != NULL ){
914	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
915	<
916	<	switch( current_extra->getType() ){
917	<
918	<	case 0:
919	<	theBends[j].ghost =
920	<	current_extra->getInt() + atomOffset;
921	<	theBends[j].isGhost = 1;
922	<	break;
923	<
924	<	case 1:
925	<	theBends[j].ghost =
926	<	(int)current_extra->getDouble() + atomOffset;
927	<	theBends[j].isGhost = 1;
928	<	break;
929	<
930	<	default:
931	<	sprintf( painCave.errMsg,
932	<	"SimSetup Error: ghostVectorSource was neither a "
933	<	"double nor an int.\n"
934	<	"-->Bend[%d] in %s\n",
935	<	j, comp_stamps[stampID]->getID() );
936	<	painCave.isFatal = 1;
937	<	simError();
938	<	}
939	<	}
940	<
941	<	else{
942	<
943	<	sprintf( painCave.errMsg,
944	<	"SimSetup Error: unhandled bend assignment:\n"
945	<	"    -->%s in Bend[%d] in %s\n",
946	<	current_extra->getlhs(),
947	<	j, comp_stamps[stampID]->getID() );
948	<	painCave.isFatal = 1;
949	<	simError();
950	<	}
951	<
952	<	current_extra = current_extra->getNext();
953	<	}
954	<	}
955	<
956	<	if( !theBends[j].isGhost ){
957	<
958	<	exI = theBends[j].a;
959	<	exJ = theBends[j].c;
960	<	}
961	<	else{
962	<
963	<	exI = theBends[j].a;
964	<	exJ = theBends[j].b;
965	<	}
966	<
967	<	// exclude_I must always be the smaller of the pair
968	<	if( exI > exJ ){
969	<	tempEx = exI;
970	<	exI = exJ;
971	<	exJ = tempEx;
972	<	}
973	<	#ifdef IS_MPI
974	<	tempEx = exI;
975	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
976	<	tempEx = exJ;
977	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
978	<
979	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
980	<	#else  // isn't MPI
981	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
982	<	#endif  //is_mpi
983	<	}
984	<	excludeOffset += info.nBends;
620	>	strcpy(info[i].mixingRule, globals->getMixingRule());
621	>	info[i].usePBC = globals->getPBC();
622	>	}
623
624	<	for(j=0; j<info.nTorsions; j++){
987	<
988	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
989	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
990	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
991	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
992	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
993	<
994	<	exI = theTorsions[j].a;
995	<	exJ = theTorsions[j].d;
624	>	// get the components and calculate the tot_nMol and indvidual n_mol
625
626	<	// exclude_I must always be the smaller of the pair
627	<	if( exI > exJ ){
999	<	tempEx = exI;
1000	<	exI = exJ;
1001	<	exJ = tempEx;
1002	<	}
1003	<	#ifdef IS_MPI
1004	<	tempEx = exI;
1005	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1006	<	tempEx = exJ;
1007	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1008	<
1009	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1010	<	#else  // isn't MPI
1011	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1012	<	#endif  //is_mpi
1013	<	}
1014	<	excludeOffset += info.nTorsions;
626	>	the_components = globals->getComponents();
627	>	components_nmol = new int[n_components];
628
1016	–
1017	–	// send the arrays off to the forceField for init.
629
630	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
631	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
632	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1022	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
630	>	if (!globals->haveNMol()){
631	>	// we don't have the total number of molecules, so we assume it is
632	>	// given in each component
633
634	+	tot_nmol = 0;
635	+	for (i = 0; i < n_components; i++){
636	+	if (!the_components[i]->haveNMol()){
637	+	// we have a problem
638	+	sprintf(painCave.errMsg,
639	+	"SimSetup Error. No global NMol or component NMol"
640	+	" given. Cannot calculate the number of atoms.\n");
641	+	painCave.isFatal = 1;
642	+	simError();
643	+	}
644
645	<	the_molecules[i].initialize( info );
645	>	tot_nmol += the_components[i]->getNMol();
646	>	components_nmol[i] = the_components[i]->getNMol();
647	>	}
648	>	}
649	>	else{
650	>	sprintf(painCave.errMsg,
651	>	"SimSetup error.\n"
652	>	"\tSorry, the ability to specify total"
653	>	" nMols and then give molfractions in the components\n"
654	>	"\tis not currently supported."
655	>	" Please give nMol in the components.\n");
656	>	painCave.isFatal = 1;
657	>	simError();
658	>	}
659
660	+	// set the status, sample, and thermal kick times
661
662	<	atomOffset += info.nAtoms;
663	<	delete[] theBonds;
664	<	delete[] theBends;
665	<	delete[] theTorsions;
666	<	}
662	>	for (i = 0; i < nInfo; i++){
663	>	if (globals->haveSampleTime()){
664	>	info[i].sampleTime = globals->getSampleTime();
665	>	info[i].statusTime = info[i].sampleTime;
666	>	info[i].thermalTime = info[i].sampleTime;
667	>	}
668	>	else{
669	>	info[i].sampleTime = globals->getRunTime();
670	>	info[i].statusTime = info[i].sampleTime;
671	>	info[i].thermalTime = info[i].sampleTime;
672	>	}
673
674	<	#ifdef IS_MPI
675	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
676	<	MPIcheckPoint();
1037	<	#endif // is_mpi
674	>	if (globals->haveStatusTime()){
675	>	info[i].statusTime = globals->getStatusTime();
676	>	}
677
678	<	// clean up the forcefield
679	<	the_ff->calcRcut();
680	<	the_ff->cleanMe();
678	>	if (globals->haveThermalTime()){
679	>	info[i].thermalTime = globals->getThermalTime();
680	>	}
681
682	<	}
682	>	info[i].resetIntegrator = 0;
683	>	if( globals->haveResetTime() ){
684	>	info[i].resetTime = globals->getResetTime();
685	>	info[i].resetIntegrator = 1;
686	>	}
687
688	<	void SimSetup::initFromBass( void ){
688	>	// check for the temperature set flag
689
690	<	int i, j, k;
691	<	int n_cells;
1049	<	double cellx, celly, cellz;
1050	<	double temp1, temp2, temp3;
1051	<	int n_per_extra;
1052	<	int n_extra;
1053	<	int have_extra, done;
690	>	if (globals->haveTempSet())
691	>	info[i].setTemp = globals->getTempSet();
692
693	<	temp1 = (double)tot_nmol / 4.0;
1056	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1057	<	temp3 = ceil( temp2 );
693	>	// get some of the tricky things that may still be in the globals
694
695	<	have_extra =0;
696	<	if( temp2 < temp3 ){ // we have a non-complete lattice
697	<	have_extra =1;
695	>	double boxVector[3];
696	>	if (globals->haveBox()){
697	>	boxVector[0] = globals->getBox();
698	>	boxVector[1] = globals->getBox();
699	>	boxVector[2] = globals->getBox();
700
701	<	n_cells = (int)temp3 - 1;
702	<	cellx = simnfo->box_x / temp3;
703	<	celly = simnfo->box_y / temp3;
704	<	cellz = simnfo->box_z / temp3;
705	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
706	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
707	<	n_per_extra = (int)ceil( temp1 );
701	>	info[i].setBox(boxVector);
702	>	}
703	>	else if (globals->haveDensity()){
704	>	double vol;
705	>	vol = (double) tot_nmol / globals->getDensity();
706	>	boxVector[0] = pow(vol, (1.0 / 3.0));
707	>	boxVector[1] = boxVector[0];
708	>	boxVector[2] = boxVector[0];
709
710	<	if( n_per_extra > 4){
1072	<	sprintf( painCave.errMsg,
1073	<	"SimSetup error. There has been an error in constructing"
1074	<	" the non-complete lattice.\n" );
1075	<	painCave.isFatal = 1;
1076	<	simError();
710	>	info[i].setBox(boxVector);
711		}
712	<	}
713	<	else{
714	<	n_cells = (int)temp3;
715	<	cellx = simnfo->box_x / temp3;
716	<	celly = simnfo->box_y / temp3;
717	<	cellz = simnfo->box_z / temp3;
718	<	}
712	>	else{
713	>	if (!globals->haveBoxX()){
714	>	sprintf(painCave.errMsg,
715	>	"SimSetup error, no periodic BoxX size given.\n");
716	>	painCave.isFatal = 1;
717	>	simError();
718	>	}
719	>	boxVector[0] = globals->getBoxX();
720
721	<	current_mol = 0;
722	<	current_comp_mol = 0;
723	<	current_comp = 0;
724	<	current_atom_ndx = 0;
721	>	if (!globals->haveBoxY()){
722	>	sprintf(painCave.errMsg,
723	>	"SimSetup error, no periodic BoxY size given.\n");
724	>	painCave.isFatal = 1;
725	>	simError();
726	>	}
727	>	boxVector[1] = globals->getBoxY();
728
729	<	for( i=0; i < n_cells ; i++ ){
730	<	for( j=0; j < n_cells; j++ ){
731	<	for( k=0; k < n_cells; k++ ){
729	>	if (!globals->haveBoxZ()){
730	>	sprintf(painCave.errMsg,
731	>	"SimSetup error, no periodic BoxZ size given.\n");
732	>	painCave.isFatal = 1;
733	>	simError();
734	>	}
735	>	boxVector[2] = globals->getBoxZ();
736
737	<	makeElement( i * cellx,
738	<	j * celly,
739	<	k * cellz );
737	>	info[i].setBox(boxVector);
738	>	}
739	>	}
740
741	<	makeElement( i * cellx + 0.5 * cellx,
742	<	j * celly + 0.5 * celly,
1101	<	k * cellz );
741	>	//setup seed for random number generator
742	>	int seedValue;
743
744	<	makeElement( i * cellx,
745	<	j * celly + 0.5 * celly,
1105	<	k * cellz + 0.5 * cellz );
744	>	if (globals->haveSeed()){
745	>	seedValue = globals->getSeed();
746
747	<	makeElement( i * cellx + 0.5 * cellx,
748	<	j * celly,
749	<	k * cellz + 0.5 * cellz );
747	>	if(seedValue / 1E9 == 0){
748	>	sprintf(painCave.errMsg,
749	>	"Seed for sprng library should contain at least 9 digits\n"
750	>	"OOPSE will generate a seed for user\n");
751	>	painCave.isFatal = 0;
752	>	simError();
753	>
754	>	//using seed generated by system instead of invalid seed set by user
755	>	#ifndef IS_MPI
756	>	seedValue = make_sprng_seed();
757	>	#else
758	>	if (worldRank == 0){
759	>	seedValue = make_sprng_seed();
760		}
761	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
762	+	#endif
763		}
764	+	}//end of if branch of globals->haveSeed()
765	+	else{
766	+
767	+	#ifndef IS_MPI
768	+	seedValue = make_sprng_seed();
769	+	#else
770	+	if (worldRank == 0){
771	+	seedValue = make_sprng_seed();
772	+	}
773	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
774	+	#endif
775	+	}//end of globals->haveSeed()
776	+
777	+	for (int i = 0; i < nInfo; i++){
778	+	info[i].setSeed(seedValue);
779		}
780
781	<	if( have_extra ){
782	<	done = 0;
781	>	#ifdef IS_MPI
782	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
783	>	MPIcheckPoint();
784	>	#endif // is_mpi
785	>	}
786
1117	–	int start_ndx;
1118	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1119	–	for( j=0; j < (n_cells+1) && !done; j++ ){
787
788	<	if( i < n_cells ){
788	>	void SimSetup::finalInfoCheck(void){
789	>	int index;
790	>	int usesDipoles;
791	>	int i;
792
793	<	if( j < n_cells ){
794	<	start_ndx = n_cells;
1125	<	}
1126	<	else start_ndx = 0;
1127	<	}
1128	<	else start_ndx = 0;
793	>	for (i = 0; i < nInfo; i++){
794	>	// check electrostatic parameters
795
796	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
796	>	index = 0;
797	>	usesDipoles = 0;
798	>	while ((index < info[i].n_atoms) && !usesDipoles){
799	>	usesDipoles = (info[i].atoms[index])->hasDipole();
800	>	index++;
801	>	}
802
803	<	makeElement( i * cellx,
804	<	j * celly,
805	<	k * cellz );
806	<	done = ( current_mol >= tot_nmol );
803	>	#ifdef IS_MPI
804	>	int myUse = usesDipoles;
805	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806	>	#endif //is_mpi
807
808	<	if( !done && n_per_extra > 1 ){
1138	<	makeElement( i * cellx + 0.5 * cellx,
1139	<	j * celly + 0.5 * celly,
1140	<	k * cellz );
1141	<	done = ( current_mol >= tot_nmol );
1142	<	}
808	>	double theEcr, theEst;
809
810	<	if( !done && n_per_extra > 2){
811	<	makeElement( i * cellx,
1146	<	j * celly + 0.5 * celly,
1147	<	k * cellz + 0.5 * cellz );
1148	<	done = ( current_mol >= tot_nmol );
1149	<	}
810	>	if (globals->getUseRF()){
811	>	info[i].useReactionField = 1;
812
813	<	if( !done && n_per_extra > 3){
814	<	makeElement( i * cellx + 0.5 * cellx,
815	<	j * celly,
816	<	k * cellz + 0.5 * cellz );
817	<	done = ( current_mol >= tot_nmol );
818	<	}
819	<	}
813	>	if (!globals->haveECR()){
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Warning: using default value of 1/2 the smallest "
816	>	"box length for the electrostaticCutoffRadius.\n"
817	>	"I hope you have a very fast processor!\n");
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	double smallest;
821	>	smallest = info[i].boxL[0];
822	>	if (info[i].boxL[1] <= smallest)
823	>	smallest = info[i].boxL[1];
824	>	if (info[i].boxL[2] <= smallest)
825	>	smallest = info[i].boxL[2];
826	>	theEcr = 0.5 * smallest;
827		}
828	+	else{
829	+	theEcr = globals->getECR();
830	+	}
831	+
832	+	if (!globals->haveEST()){
833	+	sprintf(painCave.errMsg,
834	+	"SimSetup Warning: using default value of 0.05 * the "
835	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
836	+	painCave.isFatal = 0;
837	+	simError();
838	+	theEst = 0.05 * theEcr;
839	+	}
840	+	else{
841	+	theEst = globals->getEST();
842	+	}
843	+
844	+	info[i].setEcr(theEcr, theEst);
845	+
846	+	if (!globals->haveDielectric()){
847	+	sprintf(painCave.errMsg,
848	+	"SimSetup Error: You are trying to use Reaction Field without"
849	+	"setting a dielectric constant!\n");
850	+	painCave.isFatal = 1;
851	+	simError();
852	+	}
853	+	info[i].dielectric = globals->getDielectric();
854		}
855	<	}
855	>	else{
856	>	if (usesDipoles){
857	>	if (!globals->haveECR()){
858	>	sprintf(painCave.errMsg,
859	>	"SimSetup Warning: using default value of 1/2 the smallest "
860	>	"box length for the electrostaticCutoffRadius.\n"
861	>	"I hope you have a very fast processor!\n");
862	>	painCave.isFatal = 0;
863	>	simError();
864	>	double smallest;
865	>	smallest = info[i].boxL[0];
866	>	if (info[i].boxL[1] <= smallest)
867	>	smallest = info[i].boxL[1];
868	>	if (info[i].boxL[2] <= smallest)
869	>	smallest = info[i].boxL[2];
870	>	theEcr = 0.5 * smallest;
871	>	}
872	>	else{
873	>	theEcr = globals->getECR();
874	>	}
875
876	+	if (!globals->haveEST()){
877	+	sprintf(painCave.errMsg,
878	+	"SimSetup Warning: using default value of 0.05 * the "
879	+	"electrostaticCutoffRadius for the "
880	+	"electrostaticSkinThickness\n");
881	+	painCave.isFatal = 0;
882	+	simError();
883	+	theEst = 0.05 * theEcr;
884	+	}
885	+	else{
886	+	theEst = globals->getEST();
887	+	}
888
889	<	for( i=0; i<simnfo->n_atoms; i++ ){
890	<	simnfo->atoms[i]->set_vx( 0.0 );
891	<	simnfo->atoms[i]->set_vy( 0.0 );
1166	<	simnfo->atoms[i]->set_vz( 0.0 );
889	>	info[i].setEcr(theEcr, theEst);
890	>	}
891	>	}
892		}
893	+
894	+	#ifdef IS_MPI
895	+	strcpy(checkPointMsg, "post processing checks out");
896	+	MPIcheckPoint();
897	+	#endif // is_mpi
898		}
899
900	<	void SimSetup::makeElement( double x, double y, double z ){
900	>	void SimSetup::initSystemCoords(void){
901	>	int i;
902
903	<	int k;
1173	<	AtomStamp* current_atom;
1174	<	DirectionalAtom* dAtom;
1175	<	double rotMat[3][3];
903	>	char* inName;
904
905	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
905	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
906
907	<	current_atom = comp_stamps[current_comp]->getAtom( k );
908	<	if( !current_atom->havePosition() ){
909	<	sprintf( painCave.errMsg,
910	<	"SimSetup:initFromBass error.\n"
911	<	"\tComponent %s, atom %s does not have a position specified.\n"
912	<	"\tThe initialization routine is unable to give a start"
913	<	" position.\n",
914	<	comp_stamps[current_comp]->getID(),
915	<	current_atom->getType() );
916	<	painCave.isFatal = 1;
917	<	simError();
907	>	for (i = 0; i < info[0].n_atoms; i++)
908	>	info[0].atoms[i]->setCoords();
909	>
910	>	if (globals->haveInitialConfig()){
911	>	InitializeFromFile* fileInit;
912	>	#ifdef IS_MPI // is_mpi
913	>	if (worldRank == 0){
914	>	#endif //is_mpi
915	>	inName = globals->getInitialConfig();
916	>	fileInit = new InitializeFromFile(inName);
917	>	#ifdef IS_MPI
918		}
919	+	else
920	+	fileInit = new InitializeFromFile(NULL);
921	+	#endif
922	+	fileInit->readInit(info); // default velocities on
923
924	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
925	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
926	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
924	>	delete fileInit;
925	>	}
926	>	else{
927	>	#ifdef IS_MPI
928
929	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
929	>	// no init from bass
930
931	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
931	>	sprintf(painCave.errMsg,
932	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
933	>	painCave.isFatal = 1;;
934	>	simError();
935
936	<	rotMat[0][0] = 1.0;
1201	<	rotMat[0][1] = 0.0;
1202	<	rotMat[0][2] = 0.0;
936	>	#else
937
938	<	rotMat[1][0] = 0.0;
1205	<	rotMat[1][1] = 1.0;
1206	<	rotMat[1][2] = 0.0;
1207	<
1208	<	rotMat[2][0] = 0.0;
1209	<	rotMat[2][1] = 0.0;
1210	<	rotMat[2][2] = 1.0;
938	>	initFromBass();
939
940	<	dAtom->setA( rotMat );
940	>
941	>	#endif
942	>	}
943	>
944	>	#ifdef IS_MPI
945	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
946	>	MPIcheckPoint();
947	>	#endif // is_mpi
948	>	}
949	>
950	>
951	>	void SimSetup::makeOutNames(void){
952	>	int k;
953	>
954	>
955	>	for (k = 0; k < nInfo; k++){
956	>	#ifdef IS_MPI
957	>	if (worldRank == 0){
958	>	#endif // is_mpi
959	>
960	>	if (globals->haveFinalConfig()){
961	>	strcpy(info[k].finalName, globals->getFinalConfig());
962	>	}
963	>	else{
964	>	strcpy(info[k].finalName, inFileName);
965	>	char* endTest;
966	>	int nameLength = strlen(info[k].finalName);
967	>	endTest = &(info[k].finalName[nameLength - 5]);
968	>	if (!strcmp(endTest, ".bass")){
969	>	strcpy(endTest, ".eor");
970	>	}
971	>	else if (!strcmp(endTest, ".BASS")){
972	>	strcpy(endTest, ".eor");
973	>	}
974	>	else{
975	>	endTest = &(info[k].finalName[nameLength - 4]);
976	>	if (!strcmp(endTest, ".bss")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".mdl")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	strcat(info[k].finalName, ".eor");
984	>	}
985	>	}
986	>	}
987	>
988	>	// make the sample and status out names
989	>
990	>	strcpy(info[k].sampleName, inFileName);
991	>	char* endTest;
992	>	int nameLength = strlen(info[k].sampleName);
993	>	endTest = &(info[k].sampleName[nameLength - 5]);
994	>	if (!strcmp(endTest, ".bass")){
995	>	strcpy(endTest, ".dump");
996	>	}
997	>	else if (!strcmp(endTest, ".BASS")){
998	>	strcpy(endTest, ".dump");
999	>	}
1000	>	else{
1001	>	endTest = &(info[k].sampleName[nameLength - 4]);
1002	>	if (!strcmp(endTest, ".bss")){
1003	>	strcpy(endTest, ".dump");
1004	>	}
1005	>	else if (!strcmp(endTest, ".mdl")){
1006	>	strcpy(endTest, ".dump");
1007	>	}
1008	>	else{
1009	>	strcat(info[k].sampleName, ".dump");
1010	>	}
1011	>	}
1012	>
1013	>	strcpy(info[k].statusName, inFileName);
1014	>	nameLength = strlen(info[k].statusName);
1015	>	endTest = &(info[k].statusName[nameLength - 5]);
1016	>	if (!strcmp(endTest, ".bass")){
1017	>	strcpy(endTest, ".stat");
1018	>	}
1019	>	else if (!strcmp(endTest, ".BASS")){
1020	>	strcpy(endTest, ".stat");
1021	>	}
1022	>	else{
1023	>	endTest = &(info[k].statusName[nameLength - 4]);
1024	>	if (!strcmp(endTest, ".bss")){
1025	>	strcpy(endTest, ".stat");
1026	>	}
1027	>	else if (!strcmp(endTest, ".mdl")){
1028	>	strcpy(endTest, ".stat");
1029	>	}
1030	>	else{
1031	>	strcat(info[k].statusName, ".stat");
1032	>	}
1033	>	}
1034	>
1035	>	#ifdef IS_MPI
1036	>
1037		}
1038	+	#endif // is_mpi
1039	+	}
1040	+	}
1041
1042	<	current_atom_ndx++;
1042	>
1043	>	void SimSetup::sysObjectsCreation(void){
1044	>	int i, k;
1045	>
1046	>	// create the forceField
1047	>
1048	>	createFF();
1049	>
1050	>	// extract componentList
1051	>
1052	>	compList();
1053	>
1054	>	// calc the number of atoms, bond, bends, and torsions
1055	>
1056	>	calcSysValues();
1057	>
1058	>	#ifdef IS_MPI
1059	>	// divide the molecules among the processors
1060	>
1061	>	mpiMolDivide();
1062	>	#endif //is_mpi
1063	>
1064	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1065	>
1066	>	makeSysArrays();
1067	>
1068	>	// make and initialize the molecules (all but atomic coordinates)
1069	>
1070	>	makeMolecules();
1071	>
1072	>	for (k = 0; k < nInfo; k++){
1073	>	info[k].identArray = new int[info[k].n_atoms];
1074	>	for (i = 0; i < info[k].n_atoms; i++){
1075	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1076	>	}
1077		}
1078	+	}
1079
1218	–	current_mol++;
1219	–	current_comp_mol++;
1080
1081	<	if( current_comp_mol >= components_nmol[current_comp] ){
1081	>	void SimSetup::createFF(void){
1082	>	switch (ffCase){
1083	>	case FF_DUFF:
1084	>	the_ff = new DUFF();
1085	>	break;
1086
1087	<	current_comp_mol = 0;
1088	<	current_comp++;
1087	>	case FF_LJ:
1088	>	the_ff = new LJFF();
1089	>	break;
1090	>
1091	>	case FF_EAM:
1092	>	the_ff = new EAM_FF();
1093	>	break;
1094	>
1095	>	default:
1096	>	sprintf(painCave.errMsg,
1097	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1098	>	painCave.isFatal = 1;
1099	>	simError();
1100		}
1101	+
1102	+	#ifdef IS_MPI
1103	+	strcpy(checkPointMsg, "ForceField creation successful");
1104	+	MPIcheckPoint();
1105	+	#endif // is_mpi
1106		}
1107	+
1108	+
1109	+	void SimSetup::compList(void){
1110	+	int i;
1111	+	char* id;
1112	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1113	+	LinkedMolStamp* currentStamp = NULL;
1114	+	comp_stamps = new MoleculeStamp * [n_components];
1115	+
1116	+	// make an array of molecule stamps that match the components used.
1117	+	// also extract the used stamps out into a separate linked list
1118	+
1119	+	for (i = 0; i < nInfo; i++){
1120	+	info[i].nComponents = n_components;
1121	+	info[i].componentsNmol = components_nmol;
1122	+	info[i].compStamps = comp_stamps;
1123	+	info[i].headStamp = headStamp;
1124	+	}
1125	+
1126	+
1127	+	for (i = 0; i < n_components; i++){
1128	+	id = the_components[i]->getType();
1129	+	comp_stamps[i] = NULL;
1130	+
1131	+	// check to make sure the component isn't already in the list
1132	+
1133	+	comp_stamps[i] = headStamp->match(id);
1134	+	if (comp_stamps[i] == NULL){
1135	+	// extract the component from the list;
1136	+
1137	+	currentStamp = stamps->extractMolStamp(id);
1138	+	if (currentStamp == NULL){
1139	+	sprintf(painCave.errMsg,
1140	+	"SimSetup error: Component \"%s\" was not found in the "
1141	+	"list of declared molecules\n",
1142	+	id);
1143	+	painCave.isFatal = 1;
1144	+	simError();
1145	+	}
1146	+
1147	+	headStamp->add(currentStamp);
1148	+	comp_stamps[i] = headStamp->match(id);
1149	+	}
1150	+	}
1151	+
1152	+	#ifdef IS_MPI
1153	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1154	+	MPIcheckPoint();
1155	+	#endif // is_mpi
1156	+	}
1157	+
1158	+	void SimSetup::calcSysValues(void){
1159	+	int i;
1160	+
1161	+	int* molMembershipArray;
1162	+
1163	+	tot_atoms = 0;
1164	+	tot_bonds = 0;
1165	+	tot_bends = 0;
1166	+	tot_torsions = 0;
1167	+	for (i = 0; i < n_components; i++){
1168	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1169	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1170	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1171	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1172	+	}
1173	+
1174	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1175	+	molMembershipArray = new int[tot_atoms];
1176	+
1177	+	for (i = 0; i < nInfo; i++){
1178	+	info[i].n_atoms = tot_atoms;
1179	+	info[i].n_bonds = tot_bonds;
1180	+	info[i].n_bends = tot_bends;
1181	+	info[i].n_torsions = tot_torsions;
1182	+	info[i].n_SRI = tot_SRI;
1183	+	info[i].n_mol = tot_nmol;
1184	+
1185	+	info[i].molMembershipArray = molMembershipArray;
1186	+	}
1187	+	}
1188	+
1189	+	#ifdef IS_MPI
1190	+
1191	+	void SimSetup::mpiMolDivide(void){
1192	+	int i, j, k;
1193	+	int localMol, allMol;
1194	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1195	+
1196	+	mpiSim = new mpiSimulation(info);
1197	+
1198	+	globalIndex = mpiSim->divideLabor();
1199	+
1200	+	// set up the local variables
1201	+
1202	+	mol2proc = mpiSim->getMolToProcMap();
1203	+	molCompType = mpiSim->getMolComponentType();
1204	+
1205	+	allMol = 0;
1206	+	localMol = 0;
1207	+	local_atoms = 0;
1208	+	local_bonds = 0;
1209	+	local_bends = 0;
1210	+	local_torsions = 0;
1211	+	globalAtomIndex = 0;
1212	+
1213	+
1214	+	for (i = 0; i < n_components; i++){
1215	+	for (j = 0; j < components_nmol[i]; j++){
1216	+	if (mol2proc[allMol] == worldRank){
1217	+	local_atoms += comp_stamps[i]->getNAtoms();
1218	+	local_bonds += comp_stamps[i]->getNBonds();
1219	+	local_bends += comp_stamps[i]->getNBends();
1220	+	local_torsions += comp_stamps[i]->getNTorsions();
1221	+	localMol++;
1222	+	}
1223	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1224	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1225	+	globalAtomIndex++;
1226	+	}
1227	+
1228	+	allMol++;
1229	+	}
1230	+	}
1231	+	local_SRI = local_bonds + local_bends + local_torsions;
1232	+
1233	+	info[0].n_atoms = mpiSim->getMyNlocal();
1234	+
1235	+	if (local_atoms != info[0].n_atoms){
1236	+	sprintf(painCave.errMsg,
1237	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	+	" localAtom (%d) are not equal.\n",
1239	+	info[0].n_atoms, local_atoms);
1240	+	painCave.isFatal = 1;
1241	+	simError();
1242	+	}
1243	+
1244	+	info[0].n_bonds = local_bonds;
1245	+	info[0].n_bends = local_bends;
1246	+	info[0].n_torsions = local_torsions;
1247	+	info[0].n_SRI = local_SRI;
1248	+	info[0].n_mol = localMol;
1249	+
1250	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1251	+	MPIcheckPoint();
1252	+	}
1253	+
1254	+	#endif // is_mpi
1255	+
1256	+
1257	+	void SimSetup::makeSysArrays(void){
1258	+
1259	+	#ifndef IS_MPI
1260	+	int k, j;
1261	+	#endif // is_mpi
1262	+	int i, l;
1263	+
1264	+	Atom** the_atoms;
1265	+	Molecule* the_molecules;
1266	+	Exclude** the_excludes;
1267	+
1268	+
1269	+	for (l = 0; l < nInfo; l++){
1270	+	// create the atom and short range interaction arrays
1271	+
1272	+	the_atoms = new Atom * [info[l].n_atoms];
1273	+	the_molecules = new Molecule[info[l].n_mol];
1274	+	int molIndex;
1275	+
1276	+	// initialize the molecule's stampID's
1277	+
1278	+	#ifdef IS_MPI
1279	+
1280	+
1281	+	molIndex = 0;
1282	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1283	+	if (mol2proc[i] == worldRank){
1284	+	the_molecules[molIndex].setStampID(molCompType[i]);
1285	+	the_molecules[molIndex].setMyIndex(molIndex);
1286	+	the_molecules[molIndex].setGlobalIndex(i);
1287	+	molIndex++;
1288	+	}
1289	+	}
1290	+
1291	+	#else // is_mpi
1292	+
1293	+	molIndex = 0;
1294	+	globalAtomIndex = 0;
1295	+	for (i = 0; i < n_components; i++){
1296	+	for (j = 0; j < components_nmol[i]; j++){
1297	+	the_molecules[molIndex].setStampID(i);
1298	+	the_molecules[molIndex].setMyIndex(molIndex);
1299	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1300	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1301	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	+	globalAtomIndex++;
1303	+	}
1304	+	molIndex++;
1305	+	}
1306	+	}
1307	+
1308	+
1309	+	#endif // is_mpi
1310	+
1311	+
1312	+	if (info[l].n_SRI){
1313	+	Exclude::createArray(info[l].n_SRI);
1314	+	the_excludes = new Exclude * [info[l].n_SRI];
1315	+	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	+	the_excludes[ex] = new Exclude(ex);
1317	+	}
1318	+	info[l].globalExcludes = new int;
1319	+	info[l].n_exclude = info[l].n_SRI;
1320	+	}
1321	+	else{
1322	+	Exclude::createArray(1);
1323	+	the_excludes = new Exclude * ;
1324	+	the_excludes[0] = new Exclude(0);
1325	+	the_excludes[0]->setPair(0, 0);
1326	+	info[l].globalExcludes = new int;
1327	+	info[l].globalExcludes[0] = 0;
1328	+	info[l].n_exclude = 0;
1329	+	}
1330	+
1331	+	// set the arrays into the SimInfo object
1332	+
1333	+	info[l].atoms = the_atoms;
1334	+	info[l].molecules = the_molecules;
1335	+	info[l].nGlobalExcludes = 0;
1336	+	info[l].excludes = the_excludes;
1337	+
1338	+	the_ff->setSimInfo(info);
1339	+	}
1340	+	}
1341	+
1342	+	void SimSetup::makeIntegrator(void){
1343	+	int k;
1344	+
1345	+	NVE<RealIntegrator>* myNVE = NULL;
1346	+	NVT<RealIntegrator>* myNVT = NULL;
1347	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1349	+
1350	+	for (k = 0; k < nInfo; k++){
1351	+	switch (ensembleCase){
1352	+	case NVE_ENS:
1353	+	if (globals->haveZconstraints()){
1354	+	setupZConstraint(info[k]);
1355	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1356	+	}
1357	+	else{
1358	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1359	+	}
1360	+
1361	+	info->the_integrator = myNVE;
1362	+	break;
1363	+
1364	+	case NVT_ENS:
1365	+	if (globals->haveZconstraints()){
1366	+	setupZConstraint(info[k]);
1367	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1368	+	}
1369	+	else
1370	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1371	+
1372	+	myNVT->setTargetTemp(globals->getTargetTemp());
1373	+
1374	+	if (globals->haveTauThermostat())
1375	+	myNVT->setTauThermostat(globals->getTauThermostat());
1376	+	else{
1377	+	sprintf(painCave.errMsg,
1378	+	"SimSetup error: If you use the NVT\n"
1379	+	"    ensemble, you must set tauThermostat.\n");
1380	+	painCave.isFatal = 1;
1381	+	simError();
1382	+	}
1383	+
1384	+	info->the_integrator = myNVT;
1385	+	break;
1386	+
1387	+	case NPTi_ENS:
1388	+	if (globals->haveZconstraints()){
1389	+	setupZConstraint(info[k]);
1390	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1391	+	}
1392	+	else
1393	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1394	+
1395	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1396	+
1397	+	if (globals->haveTargetPressure())
1398	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1399	+	else{
1400	+	sprintf(painCave.errMsg,
1401	+	"SimSetup error: If you use a constant pressure\n"
1402	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1403	+	painCave.isFatal = 1;
1404	+	simError();
1405	+	}
1406	+
1407	+	if (globals->haveTauThermostat())
1408	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1409	+	else{
1410	+	sprintf(painCave.errMsg,
1411	+	"SimSetup error: If you use an NPT\n"
1412	+	"    ensemble, you must set tauThermostat.\n");
1413	+	painCave.isFatal = 1;
1414	+	simError();
1415	+	}
1416	+
1417	+	if (globals->haveTauBarostat())
1418	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1419	+	else{
1420	+	sprintf(painCave.errMsg,
1421	+	"SimSetup error: If you use an NPT\n"
1422	+	"    ensemble, you must set tauBarostat.\n");
1423	+	painCave.isFatal = 1;
1424	+	simError();
1425	+	}
1426	+
1427	+	info->the_integrator = myNPTi;
1428	+	break;
1429	+
1430	+	case NPTf_ENS:
1431	+	if (globals->haveZconstraints()){
1432	+	setupZConstraint(info[k]);
1433	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1434	+	}
1435	+	else
1436	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1437	+
1438	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1439	+
1440	+	if (globals->haveTargetPressure())
1441	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	+	else{
1443	+	sprintf(painCave.errMsg,
1444	+	"SimSetup error: If you use a constant pressure\n"
1445	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1446	+	painCave.isFatal = 1;
1447	+	simError();
1448	+	}
1449	+
1450	+	if (globals->haveTauThermostat())
1451	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1452	+	else{
1453	+	sprintf(painCave.errMsg,
1454	+	"SimSetup error: If you use an NPT\n"
1455	+	"    ensemble, you must set tauThermostat.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+
1460	+	if (globals->haveTauBarostat())
1461	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1462	+	else{
1463	+	sprintf(painCave.errMsg,
1464	+	"SimSetup error: If you use an NPT\n"
1465	+	"    ensemble, you must set tauBarostat.\n");
1466	+	painCave.isFatal = 1;
1467	+	simError();
1468	+	}
1469	+
1470	+	info->the_integrator = myNPTf;
1471	+	break;
1472	+
1473	+	default:
1474	+	sprintf(painCave.errMsg,
1475	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1476	+	painCave.isFatal = 1;
1477	+	simError();
1478	+	}
1479	+	}
1480	+	}
1481	+
1482	+	void SimSetup::initFortran(void){
1483	+	info[0].refreshSim();
1484	+
1485	+	if (!strcmp(info[0].mixingRule, "standard")){
1486	+	the_ff->initForceField(LB_MIXING_RULE);
1487	+	}
1488	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1489	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1490	+	}
1491	+	else{
1492	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1493	+	info[0].mixingRule);
1494	+	painCave.isFatal = 1;
1495	+	simError();
1496	+	}
1497	+
1498	+
1499	+	#ifdef IS_MPI
1500	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1501	+	MPIcheckPoint();
1502	+	#endif // is_mpi
1503	+	}
1504	+
1505	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1506	+	int nZConstraints;
1507	+	ZconStamp** zconStamp;
1508	+
1509	+	if (globals->haveZconstraintTime()){
1510	+	//add sample time of z-constraint  into SimInfo's property list
1511	+	DoubleData* zconsTimeProp = new DoubleData();
1512	+	zconsTimeProp->setID(ZCONSTIME_ID);
1513	+	zconsTimeProp->setData(globals->getZconsTime());
1514	+	theInfo.addProperty(zconsTimeProp);
1515	+	}
1516	+	else{
1517	+	sprintf(painCave.errMsg,
1518	+	"ZConstraint error: If you use an ZConstraint\n"
1519	+	" , you must set sample time.\n");
1520	+	painCave.isFatal = 1;
1521	+	simError();
1522	+	}
1523	+
1524	+	//push zconsTol into siminfo, if user does not specify
1525	+	//value for zconsTol, a default value will be used
1526	+	DoubleData* zconsTol = new DoubleData();
1527	+	zconsTol->setID(ZCONSTOL_ID);
1528	+	if (globals->haveZconsTol()){
1529	+	zconsTol->setData(globals->getZconsTol());
1530	+	}
1531	+	else{
1532	+	double defaultZConsTol = 0.01;
1533	+	sprintf(painCave.errMsg,
1534	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1535	+	" , default value %f is used.\n",
1536	+	defaultZConsTol);
1537	+	painCave.isFatal = 0;
1538	+	simError();
1539	+
1540	+	zconsTol->setData(defaultZConsTol);
1541	+	}
1542	+	theInfo.addProperty(zconsTol);
1543	+
1544	+	//set Force Subtraction Policy
1545	+	StringData* zconsForcePolicy = new StringData();
1546	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1547	+
1548	+	if (globals->haveZconsForcePolicy()){
1549	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1550	+	}
1551	+	else{
1552	+	sprintf(painCave.errMsg,
1553	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1554	+	"PolicyByMass is used\n");
1555	+	painCave.isFatal = 0;
1556	+	simError();
1557	+	zconsForcePolicy->setData("BYMASS");
1558	+	}
1559	+
1560	+	theInfo.addProperty(zconsForcePolicy);
1561	+
1562	+	//Determine the name of ouput file and add it into SimInfo's property list
1563	+	//Be careful, do not use inFileName, since it is a pointer which
1564	+	//point to a string at master node, and slave nodes do not contain that string
1565	+
1566	+	string zconsOutput(theInfo.finalName);
1567	+
1568	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1569	+
1570	+	StringData* zconsFilename = new StringData();
1571	+	zconsFilename->setID(ZCONSFILENAME_ID);
1572	+	zconsFilename->setData(zconsOutput);
1573	+
1574	+	theInfo.addProperty(zconsFilename);
1575	+
1576	+	//setup index, pos and other parameters of z-constraint molecules
1577	+	nZConstraints = globals->getNzConstraints();
1578	+	theInfo.nZconstraints = nZConstraints;
1579	+
1580	+	zconStamp = globals->getZconStamp();
1581	+	ZConsParaItem tempParaItem;
1582	+
1583	+	ZConsParaData* zconsParaData = new ZConsParaData();
1584	+	zconsParaData->setID(ZCONSPARADATA_ID);
1585	+
1586	+	for (int i = 0; i < nZConstraints; i++){
1587	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1588	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1589	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1590	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1591	+
1592	+	zconsParaData->addItem(tempParaItem);
1593	+	}
1594	+
1595	+	//check the uniqueness of index
1596	+	if(!zconsParaData->isIndexUnique()){
1597	+	sprintf(painCave.errMsg,
1598	+	"ZConstraint Error: molIndex is not unique\n");
1599	+	painCave.isFatal = 1;
1600	+	simError();
1601	+	}
1602	+
1603	+	//sort the parameters by index of molecules
1604	+	zconsParaData->sortByIndex();
1605	+
1606	+	//push data into siminfo, therefore, we can retrieve later
1607	+	theInfo.addProperty(zconsParaData);
1608	+	}

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