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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 489 by mmeineke, Thu Apr 10 20:08:56 2003 UTC vs.
Revision 782 by mmeineke, Tue Sep 23 20:34:31 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	>	int i, j, k, globalAtomIndex;
94
95	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
95	>	// gather all of the information from the Bass file
96
97	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
97	>	gatherInfo();
98
99	<	// 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();
99	>	// creation of complex system objects
100
101	<	// 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() );
101	>	sysObjectsCreation();
102
103	<	// 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	<	}
103	>	// check on the post processing info
104
105	<	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	<	}
105	>	finalInfoCheck();
106
107	<	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	<	}
107	>	// initialize the system coordinates
108
109	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
110	<	the_extendedsystem = new ExtendedSystem( simnfo );
111	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
109	>	if (!isInfoArray){
110	>	initSystemCoords();
111	>	}
112
113	<	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	<	}
113	>	// make the output filenames
114
115	<	} 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 );
115	>	makeOutNames();
116
117	<	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	<	}
117	>	// make the integrator
118
119	+	makeIntegrator();
120	+
121		#ifdef IS_MPI
122	<	strcpy( checkPointMsg, "ForceField creation successful" );
123	<	MPIcheckPoint();
174	<	#endif // is_mpi
122	>	mpiSim->mpiRefresh();
123	>	#endif
124
125	<
125	>	// initialize the Fortran
126
127	<	// get the components and calculate the tot_nMol and indvidual n_mol
128	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
127	>	initFortran();
128	>	}
129
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
130
131	<	tot_nmol = 0;
132	<	for( i=0; i<n_components; i++ ){
131	>	void SimSetup::makeMolecules(void){
132	>	int k, l;
133	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
134	>	molInit molInfo;
135	>	DirectionalAtom* dAtom;
136	>	LinkedAssign* extras;
137	>	LinkedAssign* current_extra;
138	>	AtomStamp* currentAtom;
139	>	BondStamp* currentBond;
140	>	BendStamp* currentBend;
141	>	TorsionStamp* currentTorsion;
142
143	<	if( !the_components[i]->haveNMol() ){
144	<	// we have a problem
145	<	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	<	}
143	>	bond_pair* theBonds;
144	>	bend_set* theBends;
145	>	torsion_set* theTorsions;
146
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	–	}
147
148	<	#ifdef IS_MPI
229	<	strcpy( checkPointMsg, "Have the number of components" );
230	<	MPIcheckPoint();
231	<	#endif // is_mpi
148	>	//init the forceField paramters
149
150	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
150	>	the_ff->readParams();
151
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++ ){
152
153	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
153	>	// init the atoms
154
155	<	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	<	}
155	>	double ux, uy, uz, u, uSqr;
156
157	<	#ifdef IS_MPI
158	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
159	<	MPIcheckPoint();
160	<	#endif // is_mpi
161	<
157	>	for (k = 0; k < nInfo; k++){
158	>	the_ff->setSimInfo(&(info[k]));
159	>
160	>	atomOffset = 0;
161	>	excludeOffset = 0;
162	>	for (i = 0; i < info[k].n_mol; i++){
163	>	stampID = info[k].molecules[i].getStampID();
164
165	+	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
166	+	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
167	+	molInfo.nBends = comp_stamps[stampID]->getNBends();
168	+	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
169	+	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
170
171	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
172	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
173	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
174	+	molInfo.myBends = new Bend * [molInfo.nBends];
175	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
176
177	<	// caclulate the number of atoms, bonds, bends and torsions
177	>	theBonds = new bond_pair[molInfo.nBonds];
178	>	theBends = new bend_set[molInfo.nBends];
179	>	theTorsions = new torsion_set[molInfo.nTorsions];
180
181	<	tot_atoms = 0;
282	<	tot_bonds = 0;
283	<	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	<	}
181	>	// make the Atoms
182
183	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
183	>	for (j = 0; j < molInfo.nAtoms; j++){
184	>	currentAtom = comp_stamps[stampID]->getAtom(j);
185	>	if (currentAtom->haveOrientation()){
186	>	dAtom = new DirectionalAtom((j + atomOffset),
187	>	info[k].getConfiguration());
188	>	info[k].n_oriented++;
189	>	molInfo.myAtoms[j] = dAtom;
190
191	<	simnfo->n_atoms = tot_atoms;
192	<	simnfo->n_bonds = tot_bonds;
193	<	simnfo->n_bends = tot_bends;
298	<	simnfo->n_torsions = tot_torsions;
299	<	simnfo->n_SRI = tot_SRI;
300	<	simnfo->n_mol = tot_nmol;
191	>	ux = currentAtom->getOrntX();
192	>	uy = currentAtom->getOrntY();
193	>	uz = currentAtom->getOrntZ();
194
195	<
303	<	#ifdef IS_MPI
195	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
196
197	<	// divide the molecules among processors here.
198	<
199	<	mpiSim = new mpiSimulation( simnfo );
200	<
309	<
197	>	u = sqrt(uSqr);
198	>	ux = ux / u;
199	>	uy = uy / u;
200	>	uz = uz / u;
201
202	<	globalIndex = mpiSim->divideLabor();
202	>	dAtom->setSUx(ux);
203	>	dAtom->setSUy(uy);
204	>	dAtom->setSUz(uz);
205	>	}
206	>	else{
207	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
208	>	info[k].getConfiguration());
209	>	}
210	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
211
212	<	// set up the local variables
314	<
315	<	int localMol, allMol;
316	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
212	>	#ifdef IS_MPI
213
214	<	int* mol2proc = mpiSim->getMolToProcMap();
319	<	int* molCompType = mpiSim->getMolComponentType();
320	<
321	<	allMol = 0;
322	<	localMol = 0;
323	<	local_atoms = 0;
324	<	local_bonds = 0;
325	<	local_bends = 0;
326	<	local_torsions = 0;
327	<	for( i=0; i<n_components; i++ ){
214	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
215
329	–	for( j=0; j<components_nmol[i]; j++ ){
330	–
331	–	if( mol2proc[allMol] == worldRank ){
332	–
333	–	local_atoms +=    comp_stamps[i]->getNAtoms();
334	–	local_bonds +=    comp_stamps[i]->getNBonds();
335	–	local_bends +=    comp_stamps[i]->getNBends();
336	–	local_torsions += comp_stamps[i]->getNTorsions();
337	–	localMol++;
338	–	}
339	–	allMol++;
340	–	}
341	–	}
342	–	local_SRI = local_bonds + local_bends + local_torsions;
343	–
344	–
345	–	simnfo->n_atoms = mpiSim->getMyNlocal();
346	–
347	–	if( local_atoms != simnfo->n_atoms ){
348	–	sprintf( painCave.errMsg,
349	–	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
350	–	" localAtom (%d) are not equal.\n",
351	–	simnfo->n_atoms,
352	–	local_atoms );
353	–	painCave.isFatal = 1;
354	–	simError();
355	–	}
356	–
357	–	simnfo->n_bonds = local_bonds;
358	–	simnfo->n_bends = local_bends;
359	–	simnfo->n_torsions = local_torsions;
360	–	simnfo->n_SRI = local_SRI;
361	–	simnfo->n_mol = localMol;
362	–
363	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
364	–	MPIcheckPoint();
365	–
366	–
216		#endif // is_mpi
217	<
217	>	}
218
219	<	// create the atom and short range interaction arrays
219	>	// make the bonds
220	>	for (j = 0; j < molInfo.nBonds; j++){
221	>	currentBond = comp_stamps[stampID]->getBond(j);
222	>	theBonds[j].a = currentBond->getA() + atomOffset;
223	>	theBonds[j].b = currentBond->getB() + atomOffset;
224
225	<	Atom::createArrays(simnfo->n_atoms);
226	<	the_atoms = new Atom*[simnfo->n_atoms];
374	<	the_molecules = new Molecule[simnfo->n_mol];
375	<	int molIndex;
225	>	exI = theBonds[j].a;
226	>	exJ = theBonds[j].b;
227
228	<	// initialize the molecule's stampID's
229	<
228	>	// exclude_I must always be the smaller of the pair
229	>	if (exI > exJ){
230	>	tempEx = exI;
231	>	exI = exJ;
232	>	exJ = tempEx;
233	>	}
234		#ifdef IS_MPI
235	<
235	>	tempEx = exI;
236	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
237	>	tempEx = exJ;
238	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239
240	<	molIndex = 0;
241	<	for(i=0; i<mpiSim->getTotNmol(); i++){
384	<
385	<	if(mol2proc[i] == worldRank ){
386	<	the_molecules[molIndex].setStampID( molCompType[i] );
387	<	the_molecules[molIndex].setMyIndex( molIndex );
388	<	the_molecules[molIndex].setGlobalIndex( i );
389	<	molIndex++;
390	<	}
391	<	}
240	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
241	>	#else  // isn't MPI
242
243	<	#else // is_mpi
244	<
245	<	molIndex = 0;
246	<	for(i=0; i<n_components; i++){
397	<	for(j=0; j<components_nmol[i]; j++ ){
398	<	the_molecules[molIndex].setStampID( i );
399	<	the_molecules[molIndex].setMyIndex( molIndex );
400	<	the_molecules[molIndex].setGlobalIndex( molIndex );
401	<	molIndex++;
402	<	}
403	<	}
404	<
243	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
244	>	#endif  //is_mpi
245	>	}
246	>	excludeOffset += molInfo.nBonds;
247
248	<	#endif // is_mpi
248	>	//make the bends
249	>	for (j = 0; j < molInfo.nBends; j++){
250	>	currentBend = comp_stamps[stampID]->getBend(j);
251	>	theBends[j].a = currentBend->getA() + atomOffset;
252	>	theBends[j].b = currentBend->getB() + atomOffset;
253	>	theBends[j].c = currentBend->getC() + atomOffset;
254
255	+	if (currentBend->haveExtras()){
256	+	extras = currentBend->getExtras();
257	+	current_extra = extras;
258
259	<	if( simnfo->n_SRI ){
260	<
261	<	Exclude::createArray(simnfo->n_SRI);
262	<	the_excludes = new Exclude*[simnfo->n_SRI];
263	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
264	<	simnfo->globalExcludes = new int;
265	<	simnfo->n_exclude = simnfo->n_SRI;
416	<	}
417	<	else{
418	<
419	<	Exclude::createArray( 1 );
420	<	the_excludes = new Exclude*;
421	<	the_excludes[0] = new Exclude(0);
422	<	the_excludes[0]->setPair( 0,0 );
423	<	simnfo->globalExcludes = new int;
424	<	simnfo->globalExcludes[0] = 0;
425	<	simnfo->n_exclude = 0;
426	<	}
259	>	while (current_extra != NULL){
260	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
261	>	switch (current_extra->getType()){
262	>	case 0:
263	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
264	>	theBends[j].isGhost = 1;
265	>	break;
266
267	<	// set the arrays into the SimInfo object
267	>	case 1:
268	>	theBends[j].ghost = (int) current_extra->getDouble() +
269	>	atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272
273	<	simnfo->atoms = the_atoms;
274	<	simnfo->molecules = the_molecules;
275	<	simnfo->nGlobalExcludes = 0;
276	<	simnfo->excludes = the_excludes;
273	>	default:
274	>	sprintf(painCave.errMsg,
275	>	"SimSetup Error: ghostVectorSource was neither a "
276	>	"double nor an int.\n"
277	>	"-->Bend[%d] in %s\n",
278	>	j, comp_stamps[stampID]->getID());
279	>	painCave.isFatal = 1;
280	>	simError();
281	>	}
282	>	}
283	>	else{
284	>	sprintf(painCave.errMsg,
285	>	"SimSetup Error: unhandled bend assignment:\n"
286	>	"    -->%s in Bend[%d] in %s\n",
287	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
288	>	painCave.isFatal = 1;
289	>	simError();
290	>	}
291
292	+	current_extra = current_extra->getNext();
293	+	}
294	+	}
295
296	<	// get some of the tricky things that may still be in the globals
297	<
298	<
299	<	if( the_globals->haveBox() ){
300	<	simnfo->box_x = the_globals->getBox();
301	<	simnfo->box_y = the_globals->getBox();
302	<	simnfo->box_z = the_globals->getBox();
303	<	}
444	<	else if( the_globals->haveDensity() ){
296	>	if (!theBends[j].isGhost){
297	>	exI = theBends[j].a;
298	>	exJ = theBends[j].c;
299	>	}
300	>	else{
301	>	exI = theBends[j].a;
302	>	exJ = theBends[j].b;
303	>	}
304
305	<	double vol;
306	<	vol = (double)tot_nmol / the_globals->getDensity();
307	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
308	<	simnfo->box_y = simnfo->box_x;
309	<	simnfo->box_z = simnfo->box_x;
310	<	}
311	<	else{
312	<	if( !the_globals->haveBoxX() ){
313	<	sprintf( painCave.errMsg,
314	<	"SimSetup error, no periodic BoxX size given.\n" );
315	<	painCave.isFatal = 1;
457	<	simError();
458	<	}
459	<	simnfo->box_x = the_globals->getBoxX();
305	>	// exclude_I must always be the smaller of the pair
306	>	if (exI > exJ){
307	>	tempEx = exI;
308	>	exI = exJ;
309	>	exJ = tempEx;
310	>	}
311	>	#ifdef IS_MPI
312	>	tempEx = exI;
313	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
314	>	tempEx = exJ;
315	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316
317	<	if( !the_globals->haveBoxY() ){
318	<	sprintf( painCave.errMsg,
319	<	"SimSetup error, no periodic BoxY size given.\n" );
320	<	painCave.isFatal = 1;
321	<	simError();
322	<	}
467	<	simnfo->box_y = the_globals->getBoxY();
317	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
318	>	#else  // isn't MPI
319	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
320	>	#endif  //is_mpi
321	>	}
322	>	excludeOffset += molInfo.nBends;
323
324	<	if( !the_globals->haveBoxZ() ){
325	<	sprintf( painCave.errMsg,
326	<	"SimSetup error, no periodic BoxZ size given.\n" );
327	<	painCave.isFatal = 1;
328	<	simError();
329	<	}
475	<	simnfo->box_z = the_globals->getBoxZ();
476	<	}
324	>	for (j = 0; j < molInfo.nTorsions; j++){
325	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
326	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
327	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
328	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
329	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
330
331	+	exI = theTorsions[j].a;
332	+	exJ = theTorsions[j].d;
333	+
334	+	// exclude_I must always be the smaller of the pair
335	+	if (exI > exJ){
336	+	tempEx = exI;
337	+	exI = exJ;
338	+	exJ = tempEx;
339	+	}
340		#ifdef IS_MPI
341	<	strcpy( checkPointMsg, "Box size set up" );
342	<	MPIcheckPoint();
343	<	#endif // is_mpi
341	>	tempEx = exI;
342	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	>	tempEx = exJ;
344	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345
346	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
347	+	#else  // isn't MPI
348	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
349	+	#endif  //is_mpi
350	+	}
351	+	excludeOffset += molInfo.nTorsions;
352
484	–	// initialize the arrays
353
354	<	the_ff->setSimInfo( simnfo );
354	>	// send the arrays off to the forceField for init.
355
356	<	makeMolecules();
357	<	simnfo->identArray = new int[simnfo->n_atoms];
358	<	simnfo->molMembershipArray = new int[simnfo->n_atoms];
359	<	for(i=0; i<simnfo->n_atoms; i++){
360	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
493	<	}
494	<	for(i=0; i< simnfo->n_mol; i++) {
495	<	the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
496	<	}
497	<
498	<	if (the_globals->getUseRF() ) {
499	<	simnfo->useReactionField = 1;
500	<
501	<	if( !the_globals->haveECR() ){
502	<	sprintf( painCave.errMsg,
503	<	"SimSetup Warning: using default value of 1/2 the smallest "
504	<	"box length for the electrostaticCutoffRadius.\n"
505	<	"I hope you have a very fast processor!\n");
506	<	painCave.isFatal = 0;
507	<	simError();
508	<	double smallest;
509	<	smallest = simnfo->box_x;
510	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
511	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
512	<	simnfo->ecr = 0.5 * smallest;
513	<	} else {
514	<	simnfo->ecr        = the_globals->getECR();
515	<	}
356	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
357	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
358	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
359	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
360	>	theTorsions);
361
362	<	if( !the_globals->haveEST() ){
363	<	sprintf( painCave.errMsg,
364	<	"SimSetup Warning: using default value of 0.05 * the "
365	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
366	<	);
367	<	painCave.isFatal = 0;
368	<	simError();
369	<	simnfo->est = 0.05 * simnfo->ecr;
525	<	} else {
526	<	simnfo->est        = the_globals->getEST();
362	>
363	>	info[k].molecules[i].initialize(molInfo);
364	>
365	>
366	>	atomOffset += molInfo.nAtoms;
367	>	delete[] theBonds;
368	>	delete[] theBends;
369	>	delete[] theTorsions;
370		}
371	<
529	<	if(!the_globals->haveDielectric() ){
530	<	sprintf( painCave.errMsg,
531	<	"SimSetup Error: You are trying to use Reaction Field without"
532	<	"setting a dielectric constant!\n"
533	<	);
534	<	painCave.isFatal = 1;
535	<	simError();
536	<	}
537	<	simnfo->dielectric = the_globals->getDielectric();
538	<	} else {
539	<	if (usesDipoles) {
540	<
541	<	if( !the_globals->haveECR() ){
542	<	sprintf( painCave.errMsg,
543	<	"SimSetup Warning: using default value of 1/2 the smallest "
544	<	"box length for the electrostaticCutoffRadius.\n"
545	<	"I hope you have a very fast processor!\n");
546	<	painCave.isFatal = 0;
547	<	simError();
548	<	double smallest;
549	<	smallest = simnfo->box_x;
550	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
551	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
552	<	simnfo->ecr = 0.5 * smallest;
553	<	} else {
554	<	simnfo->ecr        = the_globals->getECR();
555	<	}
556	<
557	<	if( !the_globals->haveEST() ){
558	<	sprintf( painCave.errMsg,
559	<	"SimSetup Warning: using default value of 5%% of the "
560	<	"electrostaticCutoffRadius for the "
561	<	"electrostaticSkinThickness\n"
562	<	);
563	<	painCave.isFatal = 0;
564	<	simError();
565	<	simnfo->est = 0.05 * simnfo->ecr;
566	<	} else {
567	<	simnfo->est        = the_globals->getEST();
568	<	}
569	<	}
570	<	}
371	>	}
372
373		#ifdef IS_MPI
374	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
374	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
375		MPIcheckPoint();
376		#endif // is_mpi
377
378	<	if( the_globals->haveInitialConfig() ){
578	<
579	<	InitializeFromFile* fileInit;
580	<	#ifdef IS_MPI // is_mpi
581	<	if( worldRank == 0 ){
582	<	#endif //is_mpi
583	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
584	<	#ifdef IS_MPI
585	<	}else fileInit = new InitializeFromFile( NULL );
586	<	#endif
587	<	fileInit->read_xyz( simnfo ); // default velocities on
378	>	// clean up the forcefield
379
380	<	delete fileInit;
381	<	}
382	<	else{
380	>	the_ff->calcRcut();
381	>	the_ff->cleanMe();
382	>	}
383
384	<	#ifdef IS_MPI
384	>	void SimSetup::initFromBass(void){
385	>	int i, j, k;
386	>	int n_cells;
387	>	double cellx, celly, cellz;
388	>	double temp1, temp2, temp3;
389	>	int n_per_extra;
390	>	int n_extra;
391	>	int have_extra, done;
392
393	<	// no init from bass
394	<
395	<	sprintf( painCave.errMsg,
396	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
599	<	painCave.isFatal;
600	<	simError();
601	<
602	<	#else
393	>	double vel[3];
394	>	vel[0] = 0.0;
395	>	vel[1] = 0.0;
396	>	vel[2] = 0.0;
397
398	<	initFromBass();
398	>	temp1 = (double) tot_nmol / 4.0;
399	>	temp2 = pow(temp1, (1.0 / 3.0));
400	>	temp3 = ceil(temp2);
401
402	+	have_extra = 0;
403	+	if (temp2 < temp3){
404	+	// we have a non-complete lattice
405	+	have_extra = 1;
406
407	<	#endif
408	<	}
407	>	n_cells = (int) temp3 - 1;
408	>	cellx = info[0].boxL[0] / temp3;
409	>	celly = info[0].boxL[1] / temp3;
410	>	cellz = info[0].boxL[2] / temp3;
411	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
412	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
413	>	n_per_extra = (int) ceil(temp1);
414
415	<	#ifdef IS_MPI
416	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
417	<	MPIcheckPoint();
418	<	#endif // is_mpi
419	<
420	<
616	<
617	<
618	<
619	<
620	<
621	<	#ifdef IS_MPI
622	<	if( worldRank == 0 ){
623	<	#endif // is_mpi
624	<
625	<	if( the_globals->haveFinalConfig() ){
626	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
415	>	if (n_per_extra > 4){
416	>	sprintf(painCave.errMsg,
417	>	"SimSetup error. There has been an error in constructing"
418	>	" the non-complete lattice.\n");
419	>	painCave.isFatal = 1;
420	>	simError();
421		}
628	–	else{
629	–	strcpy( simnfo->finalName, inFileName );
630	–	char* endTest;
631	–	int nameLength = strlen( simnfo->finalName );
632	–	endTest = &(simnfo->finalName[nameLength - 5]);
633	–	if( !strcmp( endTest, ".bass" ) ){
634	–	strcpy( endTest, ".eor" );
635	–	}
636	–	else if( !strcmp( endTest, ".BASS" ) ){
637	–	strcpy( endTest, ".eor" );
638	–	}
639	–	else{
640	–	endTest = &(simnfo->finalName[nameLength - 4]);
641	–	if( !strcmp( endTest, ".bss" ) ){
642	–	strcpy( endTest, ".eor" );
643	–	}
644	–	else if( !strcmp( endTest, ".mdl" ) ){
645	–	strcpy( endTest, ".eor" );
646	–	}
647	–	else{
648	–	strcat( simnfo->finalName, ".eor" );
649	–	}
650	–	}
651	–	}
652	–
653	–	// make the sample and status out names
654	–
655	–	strcpy( simnfo->sampleName, inFileName );
656	–	char* endTest;
657	–	int nameLength = strlen( simnfo->sampleName );
658	–	endTest = &(simnfo->sampleName[nameLength - 5]);
659	–	if( !strcmp( endTest, ".bass" ) ){
660	–	strcpy( endTest, ".dump" );
661	–	}
662	–	else if( !strcmp( endTest, ".BASS" ) ){
663	–	strcpy( endTest, ".dump" );
664	–	}
665	–	else{
666	–	endTest = &(simnfo->sampleName[nameLength - 4]);
667	–	if( !strcmp( endTest, ".bss" ) ){
668	–	strcpy( endTest, ".dump" );
669	–	}
670	–	else if( !strcmp( endTest, ".mdl" ) ){
671	–	strcpy( endTest, ".dump" );
672	–	}
673	–	else{
674	–	strcat( simnfo->sampleName, ".dump" );
675	–	}
676	–	}
677	–
678	–	strcpy( simnfo->statusName, inFileName );
679	–	nameLength = strlen( simnfo->statusName );
680	–	endTest = &(simnfo->statusName[nameLength - 5]);
681	–	if( !strcmp( endTest, ".bass" ) ){
682	–	strcpy( endTest, ".stat" );
683	–	}
684	–	else if( !strcmp( endTest, ".BASS" ) ){
685	–	strcpy( endTest, ".stat" );
686	–	}
687	–	else{
688	–	endTest = &(simnfo->statusName[nameLength - 4]);
689	–	if( !strcmp( endTest, ".bss" ) ){
690	–	strcpy( endTest, ".stat" );
691	–	}
692	–	else if( !strcmp( endTest, ".mdl" ) ){
693	–	strcpy( endTest, ".stat" );
694	–	}
695	–	else{
696	–	strcat( simnfo->statusName, ".stat" );
697	–	}
698	–	}
699	–
700	–	#ifdef IS_MPI
422		}
702	–	#endif // is_mpi
703	–
704	–	// set the status, sample, and themal kick times
705	–
706	–	if( the_globals->haveSampleTime() ){
707	–	simnfo->sampleTime = the_globals->getSampleTime();
708	–	simnfo->statusTime = simnfo->sampleTime;
709	–	simnfo->thermalTime = simnfo->sampleTime;
710	–	}
423		else{
424	<	simnfo->sampleTime = the_globals->getRunTime();
425	<	simnfo->statusTime = simnfo->sampleTime;
426	<	simnfo->thermalTime = simnfo->sampleTime;
424	>	n_cells = (int) temp3;
425	>	cellx = info[0].boxL[0] / temp3;
426	>	celly = info[0].boxL[1] / temp3;
427	>	cellz = info[0].boxL[2] / temp3;
428		}
429
430	<	if( the_globals->haveStatusTime() ){
431	<	simnfo->statusTime = the_globals->getStatusTime();
432	<	}
430	>	current_mol = 0;
431	>	current_comp_mol = 0;
432	>	current_comp = 0;
433	>	current_atom_ndx = 0;
434
435	<	if( the_globals->haveThermalTime() ){
436	<	simnfo->thermalTime = the_globals->getThermalTime();
435	>	for (i = 0; i < n_cells ; i++){
436	>	for (j = 0; j < n_cells; j++){
437	>	for (k = 0; k < n_cells; k++){
438	>	makeElement(i * cellx, j * celly, k * cellz);
439	>
440	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
441	>
442	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
443	>
444	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
445	>	}
446	>	}
447		}
448
449	<	// check for the temperature set flag
449	>	if (have_extra){
450	>	done = 0;
451
452	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
452	>	int start_ndx;
453	>	for (i = 0; i < (n_cells + 1) && !done; i++){
454	>	for (j = 0; j < (n_cells + 1) && !done; j++){
455	>	if (i < n_cells){
456	>	if (j < n_cells){
457	>	start_ndx = n_cells;
458	>	}
459	>	else
460	>	start_ndx = 0;
461	>	}
462	>	else
463	>	start_ndx = 0;
464
465	+	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
466	+	makeElement(i * cellx, j * celly, k * cellz);
467	+	done = (current_mol >= tot_nmol);
468
469	<	//   // make the longe range forces and the integrator
469	>	if (!done && n_per_extra > 1){
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
471	>	k * cellz);
472	>	done = (current_mol >= tot_nmol);
473	>	}
474
475	<	//   new AllLong( simnfo );
475	>	if (!done && n_per_extra > 2){
476	>	makeElement(i * cellx, j * celly + 0.5 * celly,
477	>	k * cellz + 0.5 * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	+	if (!done && n_per_extra > 3){
482	+	makeElement(i * cellx + 0.5 * cellx, j * celly,
483	+	k * cellz + 0.5 * cellz);
484	+	done = (current_mol >= tot_nmol);
485	+	}
486	+	}
487	+	}
488	+	}
489	+	}
490
491	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
492	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
491	>	for (i = 0; i < info[0].n_atoms; i++){
492	>	info[0].atoms[i]->setVel(vel);
493		}
494	<	else if( !strcmp( force_field, "LJ" ) ){
739	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
740	<	}
741	<	else {
742	<	std::cerr << "I'm a bug.\n";
743	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
744	<	}
745	<	#ifdef IS_MPI
746	<	mpiSim->mpiRefresh();
747	<	#endif
494	>	}
495
496	<	// initialize the Fortran
496	>	void SimSetup::makeElement(double x, double y, double z){
497	>	int k;
498	>	AtomStamp* current_atom;
499	>	DirectionalAtom* dAtom;
500	>	double rotMat[3][3];
501	>	double pos[3];
502
503	+	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
504	+	current_atom = comp_stamps[current_comp]->getAtom(k);
505	+	if (!current_atom->havePosition()){
506	+	sprintf(painCave.errMsg,
507	+	"SimSetup:initFromBass error.\n"
508	+	"\tComponent %s, atom %s does not have a position specified.\n"
509	+	"\tThe initialization routine is unable to give a start"
510	+	" position.\n",
511	+	comp_stamps[current_comp]->getID(), current_atom->getType());
512	+	painCave.isFatal = 1;
513	+	simError();
514	+	}
515
516	<	simnfo->refreshSim();
517	<
518	<	if( !strcmp( simnfo->mixingRule, "standard") ){
519	<	the_ff->initForceField( LB_MIXING_RULE );
516	>	pos[0] = x + current_atom->getPosX();
517	>	pos[1] = y + current_atom->getPosY();
518	>	pos[2] = z + current_atom->getPosZ();
519	>
520	>	info[0].atoms[current_atom_ndx]->setPos(pos);
521	>
522	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
523	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
524	>
525	>	rotMat[0][0] = 1.0;
526	>	rotMat[0][1] = 0.0;
527	>	rotMat[0][2] = 0.0;
528	>
529	>	rotMat[1][0] = 0.0;
530	>	rotMat[1][1] = 1.0;
531	>	rotMat[1][2] = 0.0;
532	>
533	>	rotMat[2][0] = 0.0;
534	>	rotMat[2][1] = 0.0;
535	>	rotMat[2][2] = 1.0;
536	>
537	>	dAtom->setA(rotMat);
538	>	}
539	>
540	>	current_atom_ndx++;
541		}
757	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
758	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
759	–	}
760	–	else{
761	–	sprintf( painCave.errMsg,
762	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
763	–	simnfo->mixingRule );
764	–	painCave.isFatal = 1;
765	–	simError();
766	–	}
542
543	+	current_mol++;
544	+	current_comp_mol++;
545
546	<	#ifdef IS_MPI
547	<	strcpy( checkPointMsg,
548	<	"Successfully intialized the mixingRule for Fortran." );
549	<	MPIcheckPoint();
773	<	#endif // is_mpi
546	>	if (current_comp_mol >= components_nmol[current_comp]){
547	>	current_comp_mol = 0;
548	>	current_comp++;
549	>	}
550		}
551
552
553	<	void SimSetup::makeMolecules( void ){
553	>	void SimSetup::gatherInfo(void){
554	>	int i, j, k;
555
556	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
557	<	molInit info;
781	<	DirectionalAtom* dAtom;
782	<	LinkedAssign* extras;
783	<	LinkedAssign* current_extra;
784	<	AtomStamp* currentAtom;
785	<	BondStamp* currentBond;
786	<	BendStamp* currentBend;
787	<	TorsionStamp* currentTorsion;
556	>	ensembleCase = -1;
557	>	ffCase = -1;
558
559	<	bond_pair* theBonds;
790	<	bend_set* theBends;
791	<	torsion_set* theTorsions;
559	>	// set the easy ones first
560
561	<
562	<	//init the forceField paramters
561	>	for (i = 0; i < nInfo; i++){
562	>	info[i].target_temp = globals->getTargetTemp();
563	>	info[i].dt = globals->getDt();
564	>	info[i].run_time = globals->getRunTime();
565	>	}
566	>	n_components = globals->getNComponents();
567
796	–	the_ff->readParams();
568
569	<
799	<	// init the atoms
569	>	// get the forceField
570
571	<	double ux, uy, uz, u, uSqr;
802	<
803	<	atomOffset = 0;
804	<	excludeOffset = 0;
805	<	for(i=0; i<simnfo->n_mol; i++){
806	<
807	<	stampID = the_molecules[i].getStampID();
571	>	strcpy(force_field, globals->getForceField());
572
573	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
574	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
575	<	info.nBends    = comp_stamps[stampID]->getNBends();
576	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
577	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
573	>	if (!strcasecmp(force_field, "DUFF")){
574	>	ffCase = FF_DUFF;
575	>	}
576	>	else if (!strcasecmp(force_field, "LJ")){
577	>	ffCase = FF_LJ;
578	>	}
579	>	else if (!strcasecmp(force_field, "EAM")){
580	>	ffCase = FF_EAM;
581	>	}
582	>	else{
583	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
584	>	force_field);
585	>	painCave.isFatal = 1;
586	>	simError();
587	>	}
588
589	<	info.myAtoms = &the_atoms[atomOffset];
816	<	info.myExcludes = &the_excludes[excludeOffset];
817	<	info.myBonds = new Bond*[info.nBonds];
818	<	info.myBends = new Bend*[info.nBends];
819	<	info.myTorsions = new Torsion*[info.nTorsions];
589	>	// get the ensemble
590
591	<	theBonds = new bond_pair[info.nBonds];
822	<	theBends = new bend_set[info.nBends];
823	<	theTorsions = new torsion_set[info.nTorsions];
824	<
825	<	// make the Atoms
826	<
827	<	for(j=0; j<info.nAtoms; j++){
828	<
829	<	currentAtom = comp_stamps[stampID]->getAtom( j );
830	<	if( currentAtom->haveOrientation() ){
831	<
832	<	dAtom = new DirectionalAtom(j + atomOffset);
833	<	simnfo->n_oriented++;
834	<	info.myAtoms[j] = dAtom;
835	<
836	<	ux = currentAtom->getOrntX();
837	<	uy = currentAtom->getOrntY();
838	<	uz = currentAtom->getOrntZ();
839	<
840	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
841	<
842	<	u = sqrt( uSqr );
843	<	ux = ux / u;
844	<	uy = uy / u;
845	<	uz = uz / u;
846	<
847	<	dAtom->setSUx( ux );
848	<	dAtom->setSUy( uy );
849	<	dAtom->setSUz( uz );
850	<	}
851	<	else{
852	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
853	<	}
854	<	info.myAtoms[j]->setType( currentAtom->getType() );
855	<
856	<	#ifdef IS_MPI
857	<
858	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
859	<
860	<	#endif // is_mpi
861	<	}
862	<
863	<	// make the bonds
864	<	for(j=0; j<info.nBonds; j++){
865	<
866	<	currentBond = comp_stamps[stampID]->getBond( j );
867	<	theBonds[j].a = currentBond->getA() + atomOffset;
868	<	theBonds[j].b = currentBond->getB() + atomOffset;
591	>	strcpy(ensemble, globals->getEnsemble());
592
593	<	exI = theBonds[j].a;
594	<	exJ = theBonds[j].b;
593	>	if (!strcasecmp(ensemble, "NVE")){
594	>	ensembleCase = NVE_ENS;
595	>	}
596	>	else if (!strcasecmp(ensemble, "NVT")){
597	>	ensembleCase = NVT_ENS;
598	>	}
599	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
600	>	ensembleCase = NPTi_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NPTf")){
603	>	ensembleCase = NPTf_ENS;
604	>	}
605	>	else{
606	>	sprintf(painCave.errMsg,
607	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
608	>	"reverting to NVE for this simulation.\n",
609	>	ensemble);
610	>	painCave.isFatal = 0;
611	>	simError();
612	>	strcpy(ensemble, "NVE");
613	>	ensembleCase = NVE_ENS;
614	>	}
615
616	<	// exclude_I must always be the smaller of the pair
617	<	if( exI > exJ ){
875	<	tempEx = exI;
876	<	exI = exJ;
877	<	exJ = tempEx;
878	<	}
879	<	#ifdef IS_MPI
880	<	tempEx = exI;
881	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
882	<	tempEx = exJ;
883	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
884	<
885	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
886	<	#else  // isn't MPI
616	>	for (i = 0; i < nInfo; i++){
617	>	strcpy(info[i].ensemble, ensemble);
618
619	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
889	<	#endif  //is_mpi
890	<	}
891	<	excludeOffset += info.nBonds;
619	>	// get the mixing rule
620
621	<	//make the bends
622	<	for(j=0; j<info.nBends; j++){
623	<
896	<	currentBend = comp_stamps[stampID]->getBend( j );
897	<	theBends[j].a = currentBend->getA() + atomOffset;
898	<	theBends[j].b = currentBend->getB() + atomOffset;
899	<	theBends[j].c = currentBend->getC() + atomOffset;
900	<
901	<	if( currentBend->haveExtras() ){
902	<
903	<	extras = currentBend->getExtras();
904	<	current_extra = extras;
905	<
906	<	while( current_extra != NULL ){
907	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
908	<
909	<	switch( current_extra->getType() ){
910	<
911	<	case 0:
912	<	theBends[j].ghost =
913	<	current_extra->getInt() + atomOffset;
914	<	theBends[j].isGhost = 1;
915	<	break;
916	<
917	<	case 1:
918	<	theBends[j].ghost =
919	<	(int)current_extra->getDouble() + atomOffset;
920	<	theBends[j].isGhost = 1;
921	<	break;
922	<
923	<	default:
924	<	sprintf( painCave.errMsg,
925	<	"SimSetup Error: ghostVectorSource was neither a "
926	<	"double nor an int.\n"
927	<	"-->Bend[%d] in %s\n",
928	<	j, comp_stamps[stampID]->getID() );
929	<	painCave.isFatal = 1;
930	<	simError();
931	<	}
932	<	}
933	<
934	<	else{
935	<
936	<	sprintf( painCave.errMsg,
937	<	"SimSetup Error: unhandled bend assignment:\n"
938	<	"    -->%s in Bend[%d] in %s\n",
939	<	current_extra->getlhs(),
940	<	j, comp_stamps[stampID]->getID() );
941	<	painCave.isFatal = 1;
942	<	simError();
943	<	}
944	<
945	<	current_extra = current_extra->getNext();
946	<	}
947	<	}
948	<
949	<	if( !theBends[j].isGhost ){
950	<
951	<	exI = theBends[j].a;
952	<	exJ = theBends[j].c;
953	<	}
954	<	else{
955	<
956	<	exI = theBends[j].a;
957	<	exJ = theBends[j].b;
958	<	}
959	<
960	<	// exclude_I must always be the smaller of the pair
961	<	if( exI > exJ ){
962	<	tempEx = exI;
963	<	exI = exJ;
964	<	exJ = tempEx;
965	<	}
966	<	#ifdef IS_MPI
967	<	tempEx = exI;
968	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
969	<	tempEx = exJ;
970	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
971	<
972	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
973	<	#else  // isn't MPI
974	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
975	<	#endif  //is_mpi
976	<	}
977	<	excludeOffset += info.nBends;
621	>	strcpy(info[i].mixingRule, globals->getMixingRule());
622	>	info[i].usePBC = globals->getPBC();
623	>	}
624
625	<	for(j=0; j<info.nTorsions; j++){
980	<
981	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
982	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
983	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
984	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
985	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
986	<
987	<	exI = theTorsions[j].a;
988	<	exJ = theTorsions[j].d;
625	>	// get the components and calculate the tot_nMol and indvidual n_mol
626
627	<	// exclude_I must always be the smaller of the pair
628	<	if( exI > exJ ){
992	<	tempEx = exI;
993	<	exI = exJ;
994	<	exJ = tempEx;
995	<	}
996	<	#ifdef IS_MPI
997	<	tempEx = exI;
998	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
999	<	tempEx = exJ;
1000	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1001	<
1002	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1003	<	#else  // isn't MPI
1004	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1005	<	#endif  //is_mpi
1006	<	}
1007	<	excludeOffset += info.nTorsions;
627	>	the_components = globals->getComponents();
628	>	components_nmol = new int[n_components];
629
1009	–
1010	–	// send the arrays off to the forceField for init.
630
631	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
632	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
633	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1015	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
631	>	if (!globals->haveNMol()){
632	>	// we don't have the total number of molecules, so we assume it is
633	>	// given in each component
634
635	+	tot_nmol = 0;
636	+	for (i = 0; i < n_components; i++){
637	+	if (!the_components[i]->haveNMol()){
638	+	// we have a problem
639	+	sprintf(painCave.errMsg,
640	+	"SimSetup Error. No global NMol or component NMol"
641	+	" given. Cannot calculate the number of atoms.\n");
642	+	painCave.isFatal = 1;
643	+	simError();
644	+	}
645
646	<	the_molecules[i].initialize( info );
646	>	tot_nmol += the_components[i]->getNMol();
647	>	components_nmol[i] = the_components[i]->getNMol();
648	>	}
649	>	}
650	>	else{
651	>	sprintf(painCave.errMsg,
652	>	"SimSetup error.\n"
653	>	"\tSorry, the ability to specify total"
654	>	" nMols and then give molfractions in the components\n"
655	>	"\tis not currently supported."
656	>	" Please give nMol in the components.\n");
657	>	painCave.isFatal = 1;
658	>	simError();
659	>	}
660
661	+	// set the status, sample, and thermal kick times
662
663	<	atomOffset += info.nAtoms;
664	<	delete[] theBonds;
665	<	delete[] theBends;
666	<	delete[] theTorsions;
667	<	}
663	>	for (i = 0; i < nInfo; i++){
664	>	if (globals->haveSampleTime()){
665	>	info[i].sampleTime = globals->getSampleTime();
666	>	info[i].statusTime = info[i].sampleTime;
667	>	info[i].thermalTime = info[i].sampleTime;
668	>	}
669	>	else{
670	>	info[i].sampleTime = globals->getRunTime();
671	>	info[i].statusTime = info[i].sampleTime;
672	>	info[i].thermalTime = info[i].sampleTime;
673	>	}
674
675	<	#ifdef IS_MPI
676	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
677	<	MPIcheckPoint();
1030	<	#endif // is_mpi
675	>	if (globals->haveStatusTime()){
676	>	info[i].statusTime = globals->getStatusTime();
677	>	}
678
679	<	// clean up the forcefield
680	<	the_ff->calcRcut();
681	<	the_ff->cleanMe();
679	>	if (globals->haveThermalTime()){
680	>	info[i].thermalTime = globals->getThermalTime();
681	>	}
682
683	<	}
683	>	info[i].resetIntegrator = 0;
684	>	if( globals->haveResetTime() ){
685	>	info[i].resetTime = globals->getResetTime();
686	>	info[i].resetIntegrator = 1;
687	>	}
688
689	<	void SimSetup::initFromBass( void ){
689	>	// check for the temperature set flag
690
691	<	int i, j, k;
692	<	int n_cells;
1042	<	double cellx, celly, cellz;
1043	<	double temp1, temp2, temp3;
1044	<	int n_per_extra;
1045	<	int n_extra;
1046	<	int have_extra, done;
691	>	if (globals->haveTempSet())
692	>	info[i].setTemp = globals->getTempSet();
693
694	<	temp1 = (double)tot_nmol / 4.0;
1049	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1050	<	temp3 = ceil( temp2 );
694	>	// get some of the tricky things that may still be in the globals
695
696	<	have_extra =0;
697	<	if( temp2 < temp3 ){ // we have a non-complete lattice
698	<	have_extra =1;
696	>	double boxVector[3];
697	>	if (globals->haveBox()){
698	>	boxVector[0] = globals->getBox();
699	>	boxVector[1] = globals->getBox();
700	>	boxVector[2] = globals->getBox();
701
702	<	n_cells = (int)temp3 - 1;
703	<	cellx = simnfo->box_x / temp3;
704	<	celly = simnfo->box_y / temp3;
705	<	cellz = simnfo->box_z / temp3;
706	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
707	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
708	<	n_per_extra = (int)ceil( temp1 );
702	>	info[i].setBox(boxVector);
703	>	}
704	>	else if (globals->haveDensity()){
705	>	double vol;
706	>	vol = (double) tot_nmol / globals->getDensity();
707	>	boxVector[0] = pow(vol, (1.0 / 3.0));
708	>	boxVector[1] = boxVector[0];
709	>	boxVector[2] = boxVector[0];
710
711	<	if( n_per_extra > 4){
1065	<	sprintf( painCave.errMsg,
1066	<	"SimSetup error. There has been an error in constructing"
1067	<	" the non-complete lattice.\n" );
1068	<	painCave.isFatal = 1;
1069	<	simError();
711	>	info[i].setBox(boxVector);
712		}
713	<	}
714	<	else{
715	<	n_cells = (int)temp3;
716	<	cellx = simnfo->box_x / temp3;
717	<	celly = simnfo->box_y / temp3;
718	<	cellz = simnfo->box_z / temp3;
719	<	}
713	>	else{
714	>	if (!globals->haveBoxX()){
715	>	sprintf(painCave.errMsg,
716	>	"SimSetup error, no periodic BoxX size given.\n");
717	>	painCave.isFatal = 1;
718	>	simError();
719	>	}
720	>	boxVector[0] = globals->getBoxX();
721
722	<	current_mol = 0;
723	<	current_comp_mol = 0;
724	<	current_comp = 0;
725	<	current_atom_ndx = 0;
722	>	if (!globals->haveBoxY()){
723	>	sprintf(painCave.errMsg,
724	>	"SimSetup error, no periodic BoxY size given.\n");
725	>	painCave.isFatal = 1;
726	>	simError();
727	>	}
728	>	boxVector[1] = globals->getBoxY();
729
730	<	for( i=0; i < n_cells ; i++ ){
731	<	for( j=0; j < n_cells; j++ ){
732	<	for( k=0; k < n_cells; k++ ){
730	>	if (!globals->haveBoxZ()){
731	>	sprintf(painCave.errMsg,
732	>	"SimSetup error, no periodic BoxZ size given.\n");
733	>	painCave.isFatal = 1;
734	>	simError();
735	>	}
736	>	boxVector[2] = globals->getBoxZ();
737
738	<	makeElement( i * cellx,
739	<	j * celly,
740	<	k * cellz );
738	>	info[i].setBox(boxVector);
739	>	}
740	>	}
741
742	<	makeElement( i * cellx + 0.5 * cellx,
743	<	j * celly + 0.5 * celly,
1094	<	k * cellz );
742	>	//setup seed for random number generator
743	>	int seedValue;
744
745	<	makeElement( i * cellx,
746	<	j * celly + 0.5 * celly,
1098	<	k * cellz + 0.5 * cellz );
745	>	if (globals->haveSeed()){
746	>	seedValue = globals->getSeed();
747
748	<	makeElement( i * cellx + 0.5 * cellx,
749	<	j * celly,
750	<	k * cellz + 0.5 * cellz );
748	>	if(seedValue / 1E9 == 0){
749	>	sprintf(painCave.errMsg,
750	>	"Seed for sprng library should contain at least 9 digits\n"
751	>	"OOPSE will generate a seed for user\n");
752	>	painCave.isFatal = 0;
753	>	simError();
754	>
755	>	//using seed generated by system instead of invalid seed set by user
756	>	#ifndef IS_MPI
757	>	seedValue = make_sprng_seed();
758	>	#else
759	>	if (worldRank == 0){
760	>	seedValue = make_sprng_seed();
761		}
762	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
763	+	#endif
764		}
765	+	}//end of if branch of globals->haveSeed()
766	+	else{
767	+
768	+	#ifndef IS_MPI
769	+	seedValue = make_sprng_seed();
770	+	#else
771	+	if (worldRank == 0){
772	+	seedValue = make_sprng_seed();
773	+	}
774	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
775	+	#endif
776	+	}//end of globals->haveSeed()
777	+
778	+	for (int i = 0; i < nInfo; i++){
779	+	info[i].setSeed(seedValue);
780		}
781
782	<	if( have_extra ){
783	<	done = 0;
782	>	#ifdef IS_MPI
783	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
784	>	MPIcheckPoint();
785	>	#endif // is_mpi
786	>	}
787
1110	–	int start_ndx;
1111	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1112	–	for( j=0; j < (n_cells+1) && !done; j++ ){
788
789	<	if( i < n_cells ){
789	>	void SimSetup::finalInfoCheck(void){
790	>	int index;
791	>	int usesDipoles;
792	>	int i;
793
794	<	if( j < n_cells ){
795	<	start_ndx = n_cells;
1118	<	}
1119	<	else start_ndx = 0;
1120	<	}
1121	<	else start_ndx = 0;
794	>	for (i = 0; i < nInfo; i++){
795	>	// check electrostatic parameters
796
797	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
797	>	index = 0;
798	>	usesDipoles = 0;
799	>	while ((index < info[i].n_atoms) && !usesDipoles){
800	>	usesDipoles = (info[i].atoms[index])->hasDipole();
801	>	index++;
802	>	}
803
804	<	makeElement( i * cellx,
805	<	j * celly,
806	<	k * cellz );
807	<	done = ( current_mol >= tot_nmol );
804	>	#ifdef IS_MPI
805	>	int myUse = usesDipoles;
806	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>	#endif //is_mpi
808
809	<	if( !done && n_per_extra > 1 ){
1131	<	makeElement( i * cellx + 0.5 * cellx,
1132	<	j * celly + 0.5 * celly,
1133	<	k * cellz );
1134	<	done = ( current_mol >= tot_nmol );
1135	<	}
809	>	double theEcr, theEst;
810
811	<	if( !done && n_per_extra > 2){
812	<	makeElement( i * cellx,
1139	<	j * celly + 0.5 * celly,
1140	<	k * cellz + 0.5 * cellz );
1141	<	done = ( current_mol >= tot_nmol );
1142	<	}
811	>	if (globals->getUseRF()){
812	>	info[i].useReactionField = 1;
813
814	<	if( !done && n_per_extra > 3){
815	<	makeElement( i * cellx + 0.5 * cellx,
816	<	j * celly,
817	<	k * cellz + 0.5 * cellz );
818	<	done = ( current_mol >= tot_nmol );
819	<	}
820	<	}
814	>	if (!globals->haveECR()){
815	>	sprintf(painCave.errMsg,
816	>	"SimSetup Warning: using default value of 1/2 the smallest "
817	>	"box length for the electrostaticCutoffRadius.\n"
818	>	"I hope you have a very fast processor!\n");
819	>	painCave.isFatal = 0;
820	>	simError();
821	>	double smallest;
822	>	smallest = info[i].boxL[0];
823	>	if (info[i].boxL[1] <= smallest)
824	>	smallest = info[i].boxL[1];
825	>	if (info[i].boxL[2] <= smallest)
826	>	smallest = info[i].boxL[2];
827	>	theEcr = 0.5 * smallest;
828		}
829	+	else{
830	+	theEcr = globals->getECR();
831	+	}
832	+
833	+	if (!globals->haveEST()){
834	+	sprintf(painCave.errMsg,
835	+	"SimSetup Warning: using default value of 0.05 * the "
836	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
837	+	painCave.isFatal = 0;
838	+	simError();
839	+	theEst = 0.05 * theEcr;
840	+	}
841	+	else{
842	+	theEst = globals->getEST();
843	+	}
844	+
845	+	info[i].setEcr(theEcr, theEst);
846	+
847	+	if (!globals->haveDielectric()){
848	+	sprintf(painCave.errMsg,
849	+	"SimSetup Error: You are trying to use Reaction Field without"
850	+	"setting a dielectric constant!\n");
851	+	painCave.isFatal = 1;
852	+	simError();
853	+	}
854	+	info[i].dielectric = globals->getDielectric();
855		}
856	<	}
856	>	else{
857	>	if (usesDipoles){
858	>	if (!globals->haveECR()){
859	>	sprintf(painCave.errMsg,
860	>	"SimSetup Warning: using default value of 1/2 the smallest "
861	>	"box length for the electrostaticCutoffRadius.\n"
862	>	"I hope you have a very fast processor!\n");
863	>	painCave.isFatal = 0;
864	>	simError();
865	>	double smallest;
866	>	smallest = info[i].boxL[0];
867	>	if (info[i].boxL[1] <= smallest)
868	>	smallest = info[i].boxL[1];
869	>	if (info[i].boxL[2] <= smallest)
870	>	smallest = info[i].boxL[2];
871	>	theEcr = 0.5 * smallest;
872	>	}
873	>	else{
874	>	theEcr = globals->getECR();
875	>	}
876
877	+	if (!globals->haveEST()){
878	+	sprintf(painCave.errMsg,
879	+	"SimSetup Warning: using default value of 0.05 * the "
880	+	"electrostaticCutoffRadius for the "
881	+	"electrostaticSkinThickness\n");
882	+	painCave.isFatal = 0;
883	+	simError();
884	+	theEst = 0.05 * theEcr;
885	+	}
886	+	else{
887	+	theEst = globals->getEST();
888	+	}
889
890	<	for( i=0; i<simnfo->n_atoms; i++ ){
891	<	simnfo->atoms[i]->set_vx( 0.0 );
892	<	simnfo->atoms[i]->set_vy( 0.0 );
1159	<	simnfo->atoms[i]->set_vz( 0.0 );
890	>	info[i].setEcr(theEcr, theEst);
891	>	}
892	>	}
893		}
894	+
895	+	#ifdef IS_MPI
896	+	strcpy(checkPointMsg, "post processing checks out");
897	+	MPIcheckPoint();
898	+	#endif // is_mpi
899		}
900
901	<	void SimSetup::makeElement( double x, double y, double z ){
901	>	void SimSetup::initSystemCoords(void){
902	>	int i;
903
904	<	int k;
1166	<	AtomStamp* current_atom;
1167	<	DirectionalAtom* dAtom;
1168	<	double rotMat[3][3];
904	>	char* inName;
905
906	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
906	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
907
908	<	current_atom = comp_stamps[current_comp]->getAtom( k );
909	<	if( !current_atom->havePosition() ){
910	<	sprintf( painCave.errMsg,
911	<	"SimSetup:initFromBass error.\n"
912	<	"\tComponent %s, atom %s does not have a position specified.\n"
913	<	"\tThe initialization routine is unable to give a start"
914	<	" position.\n",
915	<	comp_stamps[current_comp]->getID(),
916	<	current_atom->getType() );
917	<	painCave.isFatal = 1;
918	<	simError();
908	>	for (i = 0; i < info[0].n_atoms; i++)
909	>	info[0].atoms[i]->setCoords();
910	>
911	>	if (globals->haveInitialConfig()){
912	>	InitializeFromFile* fileInit;
913	>	#ifdef IS_MPI // is_mpi
914	>	if (worldRank == 0){
915	>	#endif //is_mpi
916	>	inName = globals->getInitialConfig();
917	>	double* tempDouble = new double[1000000];
918	>	fileInit = new InitializeFromFile(inName);
919	>	#ifdef IS_MPI
920		}
921	+	else
922	+	fileInit = new InitializeFromFile(NULL);
923	+	#endif
924	+	fileInit->readInit(info); // default velocities on
925
926	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
927	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
928	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
926	>	delete fileInit;
927	>	}
928	>	else{
929	>	#ifdef IS_MPI
930
931	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
931	>	// no init from bass
932
933	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
934	<
935	<	rotMat[0][0] = 1.0;
936	<	rotMat[0][1] = 0.0;
1195	<	rotMat[0][2] = 0.0;
1196	<
1197	<	rotMat[1][0] = 0.0;
1198	<	rotMat[1][1] = 1.0;
1199	<	rotMat[1][2] = 0.0;
1200	<
1201	<	rotMat[2][0] = 0.0;
1202	<	rotMat[2][1] = 0.0;
1203	<	rotMat[2][2] = 1.0;
933	>	sprintf(painCave.errMsg,
934	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
935	>	painCave.isFatal;
936	>	simError();
937
938	<	dAtom->setA( rotMat );
938	>	#else
939	>
940	>	initFromBass();
941	>
942	>
943	>	#endif
944	>	}
945	>
946	>	#ifdef IS_MPI
947	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
948	>	MPIcheckPoint();
949	>	#endif // is_mpi
950	>	}
951	>
952	>
953	>	void SimSetup::makeOutNames(void){
954	>	int k;
955	>
956	>
957	>	for (k = 0; k < nInfo; k++){
958	>	#ifdef IS_MPI
959	>	if (worldRank == 0){
960	>	#endif // is_mpi
961	>
962	>	if (globals->haveFinalConfig()){
963	>	strcpy(info[k].finalName, globals->getFinalConfig());
964	>	}
965	>	else{
966	>	strcpy(info[k].finalName, inFileName);
967	>	char* endTest;
968	>	int nameLength = strlen(info[k].finalName);
969	>	endTest = &(info[k].finalName[nameLength - 5]);
970	>	if (!strcmp(endTest, ".bass")){
971	>	strcpy(endTest, ".eor");
972	>	}
973	>	else if (!strcmp(endTest, ".BASS")){
974	>	strcpy(endTest, ".eor");
975	>	}
976	>	else{
977	>	endTest = &(info[k].finalName[nameLength - 4]);
978	>	if (!strcmp(endTest, ".bss")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".mdl")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	strcat(info[k].finalName, ".eor");
986	>	}
987	>	}
988	>	}
989	>
990	>	// make the sample and status out names
991	>
992	>	strcpy(info[k].sampleName, inFileName);
993	>	char* endTest;
994	>	int nameLength = strlen(info[k].sampleName);
995	>	endTest = &(info[k].sampleName[nameLength - 5]);
996	>	if (!strcmp(endTest, ".bass")){
997	>	strcpy(endTest, ".dump");
998	>	}
999	>	else if (!strcmp(endTest, ".BASS")){
1000	>	strcpy(endTest, ".dump");
1001	>	}
1002	>	else{
1003	>	endTest = &(info[k].sampleName[nameLength - 4]);
1004	>	if (!strcmp(endTest, ".bss")){
1005	>	strcpy(endTest, ".dump");
1006	>	}
1007	>	else if (!strcmp(endTest, ".mdl")){
1008	>	strcpy(endTest, ".dump");
1009	>	}
1010	>	else{
1011	>	strcat(info[k].sampleName, ".dump");
1012	>	}
1013	>	}
1014	>
1015	>	strcpy(info[k].statusName, inFileName);
1016	>	nameLength = strlen(info[k].statusName);
1017	>	endTest = &(info[k].statusName[nameLength - 5]);
1018	>	if (!strcmp(endTest, ".bass")){
1019	>	strcpy(endTest, ".stat");
1020	>	}
1021	>	else if (!strcmp(endTest, ".BASS")){
1022	>	strcpy(endTest, ".stat");
1023	>	}
1024	>	else{
1025	>	endTest = &(info[k].statusName[nameLength - 4]);
1026	>	if (!strcmp(endTest, ".bss")){
1027	>	strcpy(endTest, ".stat");
1028	>	}
1029	>	else if (!strcmp(endTest, ".mdl")){
1030	>	strcpy(endTest, ".stat");
1031	>	}
1032	>	else{
1033	>	strcat(info[k].statusName, ".stat");
1034	>	}
1035	>	}
1036	>
1037	>	#ifdef IS_MPI
1038	>
1039		}
1040	+	#endif // is_mpi
1041	+	}
1042	+	}
1043
1044	<	current_atom_ndx++;
1044	>
1045	>	void SimSetup::sysObjectsCreation(void){
1046	>	int i, k;
1047	>
1048	>	// create the forceField
1049	>
1050	>	createFF();
1051	>
1052	>	// extract componentList
1053	>
1054	>	compList();
1055	>
1056	>	// calc the number of atoms, bond, bends, and torsions
1057	>
1058	>	calcSysValues();
1059	>
1060	>	#ifdef IS_MPI
1061	>	// divide the molecules among the processors
1062	>
1063	>	mpiMolDivide();
1064	>	#endif //is_mpi
1065	>
1066	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1067	>
1068	>	makeSysArrays();
1069	>
1070	>	// make and initialize the molecules (all but atomic coordinates)
1071	>
1072	>	makeMolecules();
1073	>
1074	>	for (k = 0; k < nInfo; k++){
1075	>	info[k].identArray = new int[info[k].n_atoms];
1076	>	for (i = 0; i < info[k].n_atoms; i++){
1077	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1078	>	}
1079		}
1080	+	}
1081
1211	–	current_mol++;
1212	–	current_comp_mol++;
1082
1083	<	if( current_comp_mol >= components_nmol[current_comp] ){
1083	>	void SimSetup::createFF(void){
1084	>	switch (ffCase){
1085	>	case FF_DUFF:
1086	>	the_ff = new DUFF();
1087	>	break;
1088
1089	<	current_comp_mol = 0;
1090	<	current_comp++;
1089	>	case FF_LJ:
1090	>	the_ff = new LJFF();
1091	>	break;
1092	>
1093	>	case FF_EAM:
1094	>	the_ff = new EAM_FF();
1095	>	break;
1096	>
1097	>	default:
1098	>	sprintf(painCave.errMsg,
1099	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1100	>	painCave.isFatal = 1;
1101	>	simError();
1102		}
1103	+
1104	+	#ifdef IS_MPI
1105	+	strcpy(checkPointMsg, "ForceField creation successful");
1106	+	MPIcheckPoint();
1107	+	#endif // is_mpi
1108		}
1109	+
1110	+
1111	+	void SimSetup::compList(void){
1112	+	int i;
1113	+	char* id;
1114	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1115	+	LinkedMolStamp* currentStamp = NULL;
1116	+	comp_stamps = new MoleculeStamp * [n_components];
1117	+
1118	+	// make an array of molecule stamps that match the components used.
1119	+	// also extract the used stamps out into a separate linked list
1120	+
1121	+	for (i = 0; i < nInfo; i++){
1122	+	info[i].nComponents = n_components;
1123	+	info[i].componentsNmol = components_nmol;
1124	+	info[i].compStamps = comp_stamps;
1125	+	info[i].headStamp = headStamp;
1126	+	}
1127	+
1128	+
1129	+	for (i = 0; i < n_components; i++){
1130	+	id = the_components[i]->getType();
1131	+	comp_stamps[i] = NULL;
1132	+
1133	+	// check to make sure the component isn't already in the list
1134	+
1135	+	comp_stamps[i] = headStamp->match(id);
1136	+	if (comp_stamps[i] == NULL){
1137	+	// extract the component from the list;
1138	+
1139	+	currentStamp = stamps->extractMolStamp(id);
1140	+	if (currentStamp == NULL){
1141	+	sprintf(painCave.errMsg,
1142	+	"SimSetup error: Component \"%s\" was not found in the "
1143	+	"list of declared molecules\n",
1144	+	id);
1145	+	painCave.isFatal = 1;
1146	+	simError();
1147	+	}
1148	+
1149	+	headStamp->add(currentStamp);
1150	+	comp_stamps[i] = headStamp->match(id);
1151	+	}
1152	+	}
1153	+
1154	+	#ifdef IS_MPI
1155	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1156	+	MPIcheckPoint();
1157	+	#endif // is_mpi
1158	+	}
1159	+
1160	+	void SimSetup::calcSysValues(void){
1161	+	int i, j, k;
1162	+
1163	+	int* molMembershipArray;
1164	+
1165	+	tot_atoms = 0;
1166	+	tot_bonds = 0;
1167	+	tot_bends = 0;
1168	+	tot_torsions = 0;
1169	+	for (i = 0; i < n_components; i++){
1170	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1172	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1173	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174	+	}
1175	+
1176	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	+	molMembershipArray = new int[tot_atoms];
1178	+
1179	+	for (i = 0; i < nInfo; i++){
1180	+	info[i].n_atoms = tot_atoms;
1181	+	info[i].n_bonds = tot_bonds;
1182	+	info[i].n_bends = tot_bends;
1183	+	info[i].n_torsions = tot_torsions;
1184	+	info[i].n_SRI = tot_SRI;
1185	+	info[i].n_mol = tot_nmol;
1186	+
1187	+	info[i].molMembershipArray = molMembershipArray;
1188	+	}
1189	+	}
1190	+
1191	+	#ifdef IS_MPI
1192	+
1193	+	void SimSetup::mpiMolDivide(void){
1194	+	int i, j, k;
1195	+	int localMol, allMol;
1196	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1197	+
1198	+	mpiSim = new mpiSimulation(info);
1199	+
1200	+	globalIndex = mpiSim->divideLabor();
1201	+
1202	+	// set up the local variables
1203	+
1204	+	mol2proc = mpiSim->getMolToProcMap();
1205	+	molCompType = mpiSim->getMolComponentType();
1206	+
1207	+	allMol = 0;
1208	+	localMol = 0;
1209	+	local_atoms = 0;
1210	+	local_bonds = 0;
1211	+	local_bends = 0;
1212	+	local_torsions = 0;
1213	+	globalAtomIndex = 0;
1214	+
1215	+
1216	+	for (i = 0; i < n_components; i++){
1217	+	for (j = 0; j < components_nmol[i]; j++){
1218	+	if (mol2proc[allMol] == worldRank){
1219	+	local_atoms += comp_stamps[i]->getNAtoms();
1220	+	local_bonds += comp_stamps[i]->getNBonds();
1221	+	local_bends += comp_stamps[i]->getNBends();
1222	+	local_torsions += comp_stamps[i]->getNTorsions();
1223	+	localMol++;
1224	+	}
1225	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1226	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1227	+	globalAtomIndex++;
1228	+	}
1229	+
1230	+	allMol++;
1231	+	}
1232	+	}
1233	+	local_SRI = local_bonds + local_bends + local_torsions;
1234	+
1235	+	info[0].n_atoms = mpiSim->getMyNlocal();
1236	+
1237	+	if (local_atoms != info[0].n_atoms){
1238	+	sprintf(painCave.errMsg,
1239	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	+	" localAtom (%d) are not equal.\n",
1241	+	info[0].n_atoms, local_atoms);
1242	+	painCave.isFatal = 1;
1243	+	simError();
1244	+	}
1245	+
1246	+	info[0].n_bonds = local_bonds;
1247	+	info[0].n_bends = local_bends;
1248	+	info[0].n_torsions = local_torsions;
1249	+	info[0].n_SRI = local_SRI;
1250	+	info[0].n_mol = localMol;
1251	+
1252	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1253	+	MPIcheckPoint();
1254	+	}
1255	+
1256	+	#endif // is_mpi
1257	+
1258	+
1259	+	void SimSetup::makeSysArrays(void){
1260	+	int i, j, k, l;
1261	+
1262	+	Atom** the_atoms;
1263	+	Molecule* the_molecules;
1264	+	Exclude** the_excludes;
1265	+
1266	+
1267	+	for (l = 0; l < nInfo; l++){
1268	+	// create the atom and short range interaction arrays
1269	+
1270	+	the_atoms = new Atom * [info[l].n_atoms];
1271	+	the_molecules = new Molecule[info[l].n_mol];
1272	+	int molIndex;
1273	+
1274	+	// initialize the molecule's stampID's
1275	+
1276	+	#ifdef IS_MPI
1277	+
1278	+
1279	+	molIndex = 0;
1280	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1281	+	if (mol2proc[i] == worldRank){
1282	+	the_molecules[molIndex].setStampID(molCompType[i]);
1283	+	the_molecules[molIndex].setMyIndex(molIndex);
1284	+	the_molecules[molIndex].setGlobalIndex(i);
1285	+	molIndex++;
1286	+	}
1287	+	}
1288	+
1289	+	#else // is_mpi
1290	+
1291	+	molIndex = 0;
1292	+	globalAtomIndex = 0;
1293	+	for (i = 0; i < n_components; i++){
1294	+	for (j = 0; j < components_nmol[i]; j++){
1295	+	the_molecules[molIndex].setStampID(i);
1296	+	the_molecules[molIndex].setMyIndex(molIndex);
1297	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1298	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1299	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1300	+	globalAtomIndex++;
1301	+	}
1302	+	molIndex++;
1303	+	}
1304	+	}
1305	+
1306	+
1307	+	#endif // is_mpi
1308	+
1309	+
1310	+	if (info[l].n_SRI){
1311	+	Exclude::createArray(info[l].n_SRI);
1312	+	the_excludes = new Exclude * [info[l].n_SRI];
1313	+	for (int ex = 0; ex < info[l].n_SRI; ex++){
1314	+	the_excludes[ex] = new Exclude(ex);
1315	+	}
1316	+	info[l].globalExcludes = new int;
1317	+	info[l].n_exclude = info[l].n_SRI;
1318	+	}
1319	+	else{
1320	+	Exclude::createArray(1);
1321	+	the_excludes = new Exclude * ;
1322	+	the_excludes[0] = new Exclude(0);
1323	+	the_excludes[0]->setPair(0, 0);
1324	+	info[l].globalExcludes = new int;
1325	+	info[l].globalExcludes[0] = 0;
1326	+	info[l].n_exclude = 0;
1327	+	}
1328	+
1329	+	// set the arrays into the SimInfo object
1330	+
1331	+	info[l].atoms = the_atoms;
1332	+	info[l].molecules = the_molecules;
1333	+	info[l].nGlobalExcludes = 0;
1334	+	info[l].excludes = the_excludes;
1335	+
1336	+	the_ff->setSimInfo(info);
1337	+	}
1338	+	}
1339	+
1340	+	void SimSetup::makeIntegrator(void){
1341	+	int k;
1342	+
1343	+	NVE<RealIntegrator>* myNVE = NULL;
1344	+	NVT<RealIntegrator>* myNVT = NULL;
1345	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1346	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1347	+
1348	+	for (k = 0; k < nInfo; k++){
1349	+	switch (ensembleCase){
1350	+	case NVE_ENS:
1351	+	if (globals->haveZconstraints()){
1352	+	setupZConstraint(info[k]);
1353	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1354	+	}
1355	+	else{
1356	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1357	+	}
1358	+
1359	+	info->the_integrator = myNVE;
1360	+	break;
1361	+
1362	+	case NVT_ENS:
1363	+	if (globals->haveZconstraints()){
1364	+	setupZConstraint(info[k]);
1365	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1366	+	}
1367	+	else
1368	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1369	+
1370	+	myNVT->setTargetTemp(globals->getTargetTemp());
1371	+
1372	+	if (globals->haveTauThermostat())
1373	+	myNVT->setTauThermostat(globals->getTauThermostat());
1374	+	else{
1375	+	sprintf(painCave.errMsg,
1376	+	"SimSetup error: If you use the NVT\n"
1377	+	"    ensemble, you must set tauThermostat.\n");
1378	+	painCave.isFatal = 1;
1379	+	simError();
1380	+	}
1381	+
1382	+	info->the_integrator = myNVT;
1383	+	break;
1384	+
1385	+	case NPTi_ENS:
1386	+	if (globals->haveZconstraints()){
1387	+	setupZConstraint(info[k]);
1388	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1389	+	}
1390	+	else
1391	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1392	+
1393	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1394	+
1395	+	if (globals->haveTargetPressure())
1396	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1397	+	else{
1398	+	sprintf(painCave.errMsg,
1399	+	"SimSetup error: If you use a constant pressure\n"
1400	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1401	+	painCave.isFatal = 1;
1402	+	simError();
1403	+	}
1404	+
1405	+	if (globals->haveTauThermostat())
1406	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1407	+	else{
1408	+	sprintf(painCave.errMsg,
1409	+	"SimSetup error: If you use an NPT\n"
1410	+	"    ensemble, you must set tauThermostat.\n");
1411	+	painCave.isFatal = 1;
1412	+	simError();
1413	+	}
1414	+
1415	+	if (globals->haveTauBarostat())
1416	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1417	+	else{
1418	+	sprintf(painCave.errMsg,
1419	+	"SimSetup error: If you use an NPT\n"
1420	+	"    ensemble, you must set tauBarostat.\n");
1421	+	painCave.isFatal = 1;
1422	+	simError();
1423	+	}
1424	+
1425	+	info->the_integrator = myNPTi;
1426	+	break;
1427	+
1428	+	case NPTf_ENS:
1429	+	if (globals->haveZconstraints()){
1430	+	setupZConstraint(info[k]);
1431	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1432	+	}
1433	+	else
1434	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1435	+
1436	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1437	+
1438	+	if (globals->haveTargetPressure())
1439	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1440	+	else{
1441	+	sprintf(painCave.errMsg,
1442	+	"SimSetup error: If you use a constant pressure\n"
1443	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1444	+	painCave.isFatal = 1;
1445	+	simError();
1446	+	}
1447	+
1448	+	if (globals->haveTauThermostat())
1449	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1450	+	else{
1451	+	sprintf(painCave.errMsg,
1452	+	"SimSetup error: If you use an NPT\n"
1453	+	"    ensemble, you must set tauThermostat.\n");
1454	+	painCave.isFatal = 1;
1455	+	simError();
1456	+	}
1457	+
1458	+	if (globals->haveTauBarostat())
1459	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1460	+	else{
1461	+	sprintf(painCave.errMsg,
1462	+	"SimSetup error: If you use an NPT\n"
1463	+	"    ensemble, you must set tauBarostat.\n");
1464	+	painCave.isFatal = 1;
1465	+	simError();
1466	+	}
1467	+
1468	+	info->the_integrator = myNPTf;
1469	+	break;
1470	+
1471	+	default:
1472	+	sprintf(painCave.errMsg,
1473	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1474	+	painCave.isFatal = 1;
1475	+	simError();
1476	+	}
1477	+	}
1478	+	}
1479	+
1480	+	void SimSetup::initFortran(void){
1481	+	info[0].refreshSim();
1482	+
1483	+	if (!strcmp(info[0].mixingRule, "standard")){
1484	+	the_ff->initForceField(LB_MIXING_RULE);
1485	+	}
1486	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1487	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1488	+	}
1489	+	else{
1490	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1491	+	info[0].mixingRule);
1492	+	painCave.isFatal = 1;
1493	+	simError();
1494	+	}
1495	+
1496	+
1497	+	#ifdef IS_MPI
1498	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1499	+	MPIcheckPoint();
1500	+	#endif // is_mpi
1501	+	}
1502	+
1503	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1504	+	int nZConstraints;
1505	+	ZconStamp** zconStamp;
1506	+
1507	+	if (globals->haveZconstraintTime()){
1508	+	//add sample time of z-constraint  into SimInfo's property list
1509	+	DoubleData* zconsTimeProp = new DoubleData();
1510	+	zconsTimeProp->setID(ZCONSTIME_ID);
1511	+	zconsTimeProp->setData(globals->getZconsTime());
1512	+	theInfo.addProperty(zconsTimeProp);
1513	+	}
1514	+	else{
1515	+	sprintf(painCave.errMsg,
1516	+	"ZConstraint error: If you use an ZConstraint\n"
1517	+	" , you must set sample time.\n");
1518	+	painCave.isFatal = 1;
1519	+	simError();
1520	+	}
1521	+
1522	+	//push zconsTol into siminfo, if user does not specify
1523	+	//value for zconsTol, a default value will be used
1524	+	DoubleData* zconsTol = new DoubleData();
1525	+	zconsTol->setID(ZCONSTOL_ID);
1526	+	if (globals->haveZconsTol()){
1527	+	zconsTol->setData(globals->getZconsTol());
1528	+	}
1529	+	else{
1530	+	double defaultZConsTol = 0.01;
1531	+	sprintf(painCave.errMsg,
1532	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1533	+	" , default value %f is used.\n",
1534	+	defaultZConsTol);
1535	+	painCave.isFatal = 0;
1536	+	simError();
1537	+
1538	+	zconsTol->setData(defaultZConsTol);
1539	+	}
1540	+	theInfo.addProperty(zconsTol);
1541	+
1542	+	//set Force Subtraction Policy
1543	+	StringData* zconsForcePolicy = new StringData();
1544	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1545	+
1546	+	if (globals->haveZconsForcePolicy()){
1547	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1548	+	}
1549	+	else{
1550	+	sprintf(painCave.errMsg,
1551	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1552	+	"PolicyByMass is used\n");
1553	+	painCave.isFatal = 0;
1554	+	simError();
1555	+	zconsForcePolicy->setData("BYMASS");
1556	+	}
1557	+
1558	+	theInfo.addProperty(zconsForcePolicy);
1559	+
1560	+	//Determine the name of ouput file and add it into SimInfo's property list
1561	+	//Be careful, do not use inFileName, since it is a pointer which
1562	+	//point to a string at master node, and slave nodes do not contain that string
1563	+
1564	+	string zconsOutput(theInfo.finalName);
1565	+
1566	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1567	+
1568	+	StringData* zconsFilename = new StringData();
1569	+	zconsFilename->setID(ZCONSFILENAME_ID);
1570	+	zconsFilename->setData(zconsOutput);
1571	+
1572	+	theInfo.addProperty(zconsFilename);
1573	+
1574	+	//setup index, pos and other parameters of z-constraint molecules
1575	+	nZConstraints = globals->getNzConstraints();
1576	+	theInfo.nZconstraints = nZConstraints;
1577	+
1578	+	zconStamp = globals->getZconStamp();
1579	+	ZConsParaItem tempParaItem;
1580	+
1581	+	ZConsParaData* zconsParaData = new ZConsParaData();
1582	+	zconsParaData->setID(ZCONSPARADATA_ID);
1583	+
1584	+	for (int i = 0; i < nZConstraints; i++){
1585	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1586	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1587	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1588	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1589	+
1590	+	zconsParaData->addItem(tempParaItem);
1591	+	}
1592	+
1593	+	//check the uniqueness of index
1594	+	if(!zconsParaData->isIndexUnique()){
1595	+	sprintf(painCave.errMsg,
1596	+	"ZConstraint Error: molIndex is not unique\n");
1597	+	painCave.isFatal = 1;
1598	+	simError();
1599	+	}
1600	+
1601	+	//sort the parameters by index of molecules
1602	+	zconsParaData->sortByIndex();
1603	+
1604	+	//push data into siminfo, therefore, we can retrieve later
1605	+	theInfo.addProperty(zconsParaData);
1606	+	}

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