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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 490 by gezelter, Fri Apr 11 15:16:59 2003 UTC vs.
Revision 707 by mmeineke, Wed Aug 20 19:42:31 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTim_ENS      4
25	+	#define NPTfm_ENS      5
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 27 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 62 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
67	–	MakeStamps *the_stamps;
68	–	Globals* the_globals;
69	–	ExtendedSystem* the_extendedsystem;
97		int i, j, k, globalAtomIndex;
98	+
99	+	// gather all of the information from the Bass file
100
101	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
101	>	gatherInfo();
102
103	<	// 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();
103	>	// creation of complex system objects
104
105	<	// 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() );
105	>	sysObjectsCreation();
106
107	<	// 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	<	}
107	>	// check on the post processing info
108
109	<	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	<	}
109	>	finalInfoCheck();
110
111	<	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	<	}
111	>	// initialize the system coordinates
112
113	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
126	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
113	>	if( !isInfoArray ) initSystemCoords();
114
115	<	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	<	}
115	>	// make the output filenames
116
117	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
118	<	} else {
119	<	sprintf( painCave.errMsg,
120	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
121	<	"reverting to NVE for this simulation.\n",
122	<	ensemble );
123	<	painCave.isFatal = 0;
124	<	simError();
125	<	strcpy( ensemble, "NVE" );
151	<	}
152	<	strcpy( simnfo->ensemble, ensemble );
117	>	makeOutNames();
118	>
119	>	// make the integrator
120	>
121	>	makeIntegrator();
122	>
123	>	#ifdef IS_MPI
124	>	mpiSim->mpiRefresh();
125	>	#endif
126
127	<	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	<	}
127	>	// initialize the Fortran
128
129	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "ForceField creation successful" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
129	>	initFortran();
130
131	+
132	+
133	+	}
134	+
135	+
136	+	void SimSetup::makeMolecules( void ){
137	+
138	+	int k,l;
139	+	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	+	molInit molInfo;
141	+	DirectionalAtom* dAtom;
142	+	LinkedAssign* extras;
143	+	LinkedAssign* current_extra;
144	+	AtomStamp* currentAtom;
145	+	BondStamp* currentBond;
146	+	BendStamp* currentBend;
147	+	TorsionStamp* currentTorsion;
148	+
149	+	bond_pair* theBonds;
150	+	bend_set* theBends;
151	+	torsion_set* theTorsions;
152	+
153
154	+	//init the forceField paramters
155
156	<	// get the components and calculate the tot_nMol and indvidual n_mol
179	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
156	>	the_ff->readParams();
157
158	<	if( !the_globals->haveNMol() ){
159	<	// we don't have the total number of molecules, so we assume it is
185	<	// given in each component
158	>
159	>	// init the atoms
160
161	<	tot_nmol = 0;
162	<	for( i=0; i<n_components; i++ ){
161	>	double ux, uy, uz, u, uSqr;
162	>
163	>	for(k=0; k<nInfo; k++){
164	>
165	>	the_ff->setSimInfo( &(info[k]) );
166
167	<	if( !the_components[i]->haveNMol() ){
168	<	// we have a problem
169	<	sprintf( painCave.errMsg,
170	<	"SimSetup Error. No global NMol or component NMol"
171	<	" given. Cannot calculate the number of atoms.\n" );
195	<	painCave.isFatal = 1;
196	<	simError();
197	<	}
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for(i=0; i<info[k].n_mol; i++){
170	>
171	>	stampID = info[k].molecules[i].getStampID();
172
173	<	tot_nmol += the_components[i]->getNMol();
174	<	components_nmol[i] = the_components[i]->getNMol();
175	<	}
176	<	}
177	<	else{
178	<	sprintf( painCave.errMsg,
179	<	"SimSetup error.\n"
180	<	"\tSorry, the ability to specify total"
181	<	" nMols and then give molfractions in the components\n"
182	<	"\tis not currently supported."
183	<	" Please give nMol in the components.\n" );
184	<	painCave.isFatal = 1;
185	<	simError();
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178	>
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184	>
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188
189	+	// make the Atoms
190
191	<	//     tot_nmol = the_globals->getNMol();
191	>	for(j=0; j<molInfo.nAtoms; j++){
192	>
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195
196	<	//   //we have the total number of molecules, now we check for molfractions
197	<	//     for( i=0; i<n_components; i++ ){
196	>	dAtom = new DirectionalAtom( (j + atomOffset),
197	>	info[k].getConfiguration() );
198	>	info[k].n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200
201	<	//       if( !the_components[i]->haveMolFraction() ){
201	>	ux = currentAtom->getOrntX();
202	>	uy = currentAtom->getOrntY();
203	>	uz = currentAtom->getOrntZ();
204
205	<	//  if( !the_components[i]->haveNMol() ){
222	<	//    //we have a problem
223	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	<	//              << " nMol was given in component
205	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206
207	+	u = sqrt( uSqr );
208	+	ux = ux / u;
209	+	uy = uy / u;
210	+	uz = uz / u;
211	+
212	+	dAtom->setSUx( ux );
213	+	dAtom->setSUy( uy );
214	+	dAtom->setSUz( uz );
215		}
216	<
217	<	#ifdef IS_MPI
218	<	strcpy( checkPointMsg, "Have the number of components" );
219	<	MPIcheckPoint();
220	<	#endif // is_mpi
232	<
233	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
235	<
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++ ){
245	<
246	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
216	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	>	info[k].getConfiguration() );
219	>	}
220	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221
222	<	// check to make sure the component isn't already in the list
250	<
251	<	comp_stamps[i] = headStamp->match( id );
252	<	if( comp_stamps[i] == NULL ){
222	>	#ifdef IS_MPI
223
224	<	// extract the component from the list;
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225
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	–	}
270	–
271	–	#ifdef IS_MPI
272	–	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	–	MPIcheckPoint();
226		#endif // is_mpi
227	<
276	<
277	<
278	<
279	<	// caclulate the number of atoms, bonds, bends and torsions
280	<
281	<	tot_atoms = 0;
282	<	tot_bonds = 0;
283	<	tot_bends = 0;
284	<	tot_torsions = 0;
285	<	for( i=0; i<n_components; i++ ){
227	>	}
228
229	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
230	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
231	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
232	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
229	>	// make the bonds
230	>	for(j=0; j<molInfo.nBonds; j++){
231	>
232	>	currentBond = comp_stamps[stampID]->getBond( j );
233	>	theBonds[j].a = currentBond->getA() + atomOffset;
234	>	theBonds[j].b = currentBond->getB() + atomOffset;
235	>
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244		}
292	–
293	–	tot_SRI = tot_bonds + tot_bends + tot_torsions;
294	–
295	–	simnfo->n_atoms = tot_atoms;
296	–	simnfo->n_bonds = tot_bonds;
297	–	simnfo->n_bends = tot_bends;
298	–	simnfo->n_torsions = tot_torsions;
299	–	simnfo->n_SRI = tot_SRI;
300	–	simnfo->n_mol = tot_nmol;
301	–	simnfo->molMembershipArray = new int[tot_atoms];
302	–
245		#ifdef IS_MPI
246	<
247	<	// divide the molecules among processors here.
246	>	tempEx = exI;
247	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	>	tempEx = exJ;
249	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250
251	<	mpiSim = new mpiSimulation( simnfo );
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252	>	#else  // isn't MPI
253
254	<	globalIndex = mpiSim->divideLabor();
255	<
256	<	// set up the local variables
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	>	#endif  //is_mpi
256	>	}
257	>	excludeOffset += molInfo.nBonds;
258	>
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261
262	<	int localMol, allMol;
263	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
264	<
265	<	int* mol2proc = mpiSim->getMolToProcMap();
317	<	int* molCompType = mpiSim->getMolComponentType();
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266
267	<	allMol = 0;
268	<	localMol = 0;
269	<	local_atoms = 0;
270	<	local_bonds = 0;
271	<	local_bends = 0;
272	<	local_torsions = 0;
273	<	globalAtomIndex = 0;
274	<
275	<
276	<	for( i=0; i<n_components; i++ ){
277	<
278	<	for( j=0; j<components_nmol[i]; j++ ){
267	>	if( currentBend->haveExtras() ){
268	>
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276	>
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290	>	sprintf( painCave.errMsg,
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298	>	}
299
300	<	if( mol2proc[allMol] == worldRank ){
301	<
302	<	local_atoms +=    comp_stamps[i]->getNAtoms();
303	<	local_bonds +=    comp_stamps[i]->getNBonds();
304	<	local_bends +=    comp_stamps[i]->getNBends();
305	<	local_torsions += comp_stamps[i]->getNTorsions();
306	<	localMol++;
307	<	}
308	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
341	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
342	<	globalAtomIndex++;
300	>	else{
301	>
302	>	sprintf( painCave.errMsg,
303	>	"SimSetup Error: unhandled bend assignment:\n"
304	>	"    -->%s in Bend[%d] in %s\n",
305	>	current_extra->getlhs(),
306	>	j, comp_stamps[stampID]->getID() );
307	>	painCave.isFatal = 1;
308	>	simError();
309		}
310	<
311	<	allMol++;
310	>
311	>	current_extra = current_extra->getNext();
312		}
313		}
348	–	local_SRI = local_bonds + local_bends + local_torsions;
314
315	<	if (worldRank != 0) {
316	<	for (i =0; i < tot_atoms; i++){
317	<	std::cerr << "i = " << i << " molMembershipArray[i] = " << simnfo->molMembershipArray[i] << "\n";
318	<	}
315	>	if( !theBends[j].isGhost ){
316	>
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].c;
319		}
320	<
321	<	simnfo->n_atoms = mpiSim->getMyNlocal();
320	>	else{
321	>
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].b;
324	>	}
325
326	<	if( local_atoms != simnfo->n_atoms ){
327	<	sprintf( painCave.errMsg,
328	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
329	<	" localAtom (%d) are not equal.\n",
330	<	simnfo->n_atoms,
363	<	local_atoms );
364	<	painCave.isFatal = 1;
365	<	simError();
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331		}
332	<
333	<	simnfo->n_bonds = local_bonds;
334	<	simnfo->n_bends = local_bends;
335	<	simnfo->n_torsions = local_torsions;
336	<	simnfo->n_SRI = local_SRI;
337	<	simnfo->n_mol = localMol;
338	<
339	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
340	<	MPIcheckPoint();
332	>	#ifdef IS_MPI
333	>	tempEx = exI;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	>
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	#else  // isn't MPI
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	#endif  //is_mpi
342	>	}
343	>	excludeOffset += molInfo.nBends;
344	>
345	>	for(j=0; j<molInfo.nTorsions; j++){
346
347	+	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352
353	<	#endif // is_mpi
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355
356	<
357	<	// create the atom and short range interaction arrays
358	<
359	<	Atom::createArrays(simnfo->n_atoms);
360	<	the_atoms = new Atom*[simnfo->n_atoms];
361	<	the_molecules = new Molecule[simnfo->n_mol];
386	<	int molIndex;
387	<
388	<	// initialize the molecule's stampID's
389	<
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361	>	}
362		#ifdef IS_MPI
363	+	tempEx = exI;
364	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	+	tempEx = exJ;
366	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367
368	+	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369	+	#else  // isn't MPI
370	+	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371	+	#endif  //is_mpi
372	+	}
373	+	excludeOffset += molInfo.nTorsions;
374	+
375	+
376	+	// send the arrays off to the forceField for init.
377	+
378	+	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	+	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	+	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	+	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	+
383	+
384	+	info[k].molecules[i].initialize( molInfo );
385
386	<	molIndex = 0;
387	<	for(i=0; i<mpiSim->getTotNmol(); i++){
388	<
389	<	if(mol2proc[i] == worldRank ){
390	<	the_molecules[molIndex].setStampID( molCompType[i] );
398	<	the_molecules[molIndex].setMyIndex( molIndex );
399	<	the_molecules[molIndex].setGlobalIndex( i );
400	<	molIndex++;
386	>
387	>	atomOffset += molInfo.nAtoms;
388	>	delete[] theBonds;
389	>	delete[] theBends;
390	>	delete[] theTorsions;
391		}
392		}
393	+
394	+	#ifdef IS_MPI
395	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
396	+	MPIcheckPoint();
397	+	#endif // is_mpi
398	+
399	+	// clean up the forcefield
400
401	<	#else // is_mpi
401	>	the_ff->calcRcut();
402	>	the_ff->cleanMe();
403
404	<	molIndex = 0;
407	<	globalAtomIndex = 0;
408	<	for(i=0; i<n_components; i++){
409	<	for(j=0; j<components_nmol[i]; j++ ){
410	<	the_molecules[molIndex].setStampID( i );
411	<	the_molecules[molIndex].setMyIndex( molIndex );
412	<	the_molecules[molIndex].setGlobalIndex( molIndex );
413	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
414	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
415	<	globalAtomIndex++;
416	<	}
417	<	molIndex++;
418	<	}
419	<	}
420	<
404	>	}
405
406	<	#endif // is_mpi
406	>	void SimSetup::initFromBass( void ){
407
408	+	int i, j, k;
409	+	int n_cells;
410	+	double cellx, celly, cellz;
411	+	double temp1, temp2, temp3;
412	+	int n_per_extra;
413	+	int n_extra;
414	+	int have_extra, done;
415
416	<	if( simnfo->n_SRI ){
417	<
418	<	Exclude::createArray(simnfo->n_SRI);
419	<	the_excludes = new Exclude*[simnfo->n_SRI];
420	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
421	<	simnfo->globalExcludes = new int;
422	<	simnfo->n_exclude = simnfo->n_SRI;
416	>	double vel[3];
417	>	vel[0] = 0.0;
418	>	vel[1] = 0.0;
419	>	vel[2] = 0.0;
420	>
421	>	temp1 = (double)tot_nmol / 4.0;
422	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423	>	temp3 = ceil( temp2 );
424	>
425	>	have_extra =0;
426	>	if( temp2 < temp3 ){ // we have a non-complete lattice
427	>	have_extra =1;
428	>
429	>	n_cells = (int)temp3 - 1;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435	>	n_per_extra = (int)ceil( temp1 );
436	>
437	>	if( n_per_extra > 4){
438	>	sprintf( painCave.errMsg,
439	>	"SimSetup error. There has been an error in constructing"
440	>	" the non-complete lattice.\n" );
441	>	painCave.isFatal = 1;
442	>	simError();
443	>	}
444		}
445		else{
446	<
447	<	Exclude::createArray( 1 );
448	<	the_excludes = new Exclude*;
449	<	the_excludes[0] = new Exclude(0);
438	<	the_excludes[0]->setPair( 0,0 );
439	<	simnfo->globalExcludes = new int;
440	<	simnfo->globalExcludes[0] = 0;
441	<	simnfo->n_exclude = 0;
446	>	n_cells = (int)temp3;
447	>	cellx = info[0].boxL[0] / temp3;
448	>	celly = info[0].boxL[1] / temp3;
449	>	cellz = info[0].boxL[2] / temp3;
450		}
451
452	<	// set the arrays into the SimInfo object
452	>	current_mol = 0;
453	>	current_comp_mol = 0;
454	>	current_comp = 0;
455	>	current_atom_ndx = 0;
456
457	<	simnfo->atoms = the_atoms;
458	<	simnfo->molecules = the_molecules;
459	<	simnfo->nGlobalExcludes = 0;
449	<	simnfo->excludes = the_excludes;
457	>	for( i=0; i < n_cells ; i++ ){
458	>	for( j=0; j < n_cells; j++ ){
459	>	for( k=0; k < n_cells; k++ ){
460
461	+	makeElement( i * cellx,
462	+	j * celly,
463	+	k * cellz );
464
465	<	// get some of the tricky things that may still be in the globals
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly + 0.5 * celly,
467	>	k * cellz );
468
469	<
470	<	if( the_globals->haveBox() ){
471	<	simnfo->box_x = the_globals->getBox();
472	<	simnfo->box_y = the_globals->getBox();
473	<	simnfo->box_z = the_globals->getBox();
469	>	makeElement( i * cellx,
470	>	j * celly + 0.5 * celly,
471	>	k * cellz + 0.5 * cellz );
472	>
473	>	makeElement( i * cellx + 0.5 * cellx,
474	>	j * celly,
475	>	k * cellz + 0.5 * cellz );
476	>	}
477	>	}
478		}
460	–	else if( the_globals->haveDensity() ){
479
480	<	double vol;
481	<	vol = (double)tot_nmol / the_globals->getDensity();
482	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
483	<	simnfo->box_y = simnfo->box_x;
484	<	simnfo->box_z = simnfo->box_x;
480	>	if( have_extra ){
481	>	done = 0;
482	>
483	>	int start_ndx;
484	>	for( i=0; i < (n_cells+1) && !done; i++ ){
485	>	for( j=0; j < (n_cells+1) && !done; j++ ){
486	>
487	>	if( i < n_cells ){
488	>
489	>	if( j < n_cells ){
490	>	start_ndx = n_cells;
491	>	}
492	>	else start_ndx = 0;
493		}
494	<	else{
495	<	if( !the_globals->haveBoxX() ){
496	<	sprintf( painCave.errMsg,
497	<	"SimSetup error, no periodic BoxX size given.\n" );
498	<	painCave.isFatal = 1;
499	<	simError();
494	>	else start_ndx = 0;
495	>
496	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497	>
498	>	makeElement( i * cellx,
499	>	j * celly,
500	>	k * cellz );
501	>	done = ( current_mol >= tot_nmol );
502	>
503	>	if( !done && n_per_extra > 1 ){
504	>	makeElement( i * cellx + 0.5 * cellx,
505	>	j * celly + 0.5 * celly,
506	>	k * cellz );
507	>	done = ( current_mol >= tot_nmol );
508		}
475	–	simnfo->box_x = the_globals->getBoxX();
509
510	<	if( !the_globals->haveBoxY() ){
511	<	sprintf( painCave.errMsg,
512	<	"SimSetup error, no periodic BoxY size given.\n" );
513	<	painCave.isFatal = 1;
514	<	simError();
510	>	if( !done && n_per_extra > 2){
511	>	makeElement( i * cellx,
512	>	j * celly + 0.5 * celly,
513	>	k * cellz + 0.5 * cellz );
514	>	done = ( current_mol >= tot_nmol );
515		}
483	–	simnfo->box_y = the_globals->getBoxY();
516
517	<	if( !the_globals->haveBoxZ() ){
518	<	sprintf( painCave.errMsg,
519	<	"SimSetup error, no periodic BoxZ size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
517	>	if( !done && n_per_extra > 3){
518	>	makeElement( i * cellx + 0.5 * cellx,
519	>	j * celly,
520	>	k * cellz + 0.5 * cellz );
521	>	done = ( current_mol >= tot_nmol );
522		}
491	–	simnfo->box_z = the_globals->getBoxZ();
523		}
524	+	}
525	+	}
526	+	}
527
528	<	#ifdef IS_MPI
529	<	strcpy( checkPointMsg, "Box size set up" );
530	<	MPIcheckPoint();
531	<	#endif // is_mpi
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530	>	}
531	>	}
532
533	+	void SimSetup::makeElement( double x, double y, double z ){
534
535	<	// initialize the arrays
535	>	int k;
536	>	AtomStamp* current_atom;
537	>	DirectionalAtom* dAtom;
538	>	double rotMat[3][3];
539	>	double pos[3];
540
541	<	the_ff->setSimInfo( simnfo );
541	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542
543	<	makeMolecules();
544	<	simnfo->identArray = new int[simnfo->n_atoms];
506	<	for(i=0; i<simnfo->n_atoms; i++){
507	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
508	<	}
509	<
510	<	if (the_globals->getUseRF() ) {
511	<	simnfo->useReactionField = 1;
512	<
513	<	if( !the_globals->haveECR() ){
543	>	current_atom = comp_stamps[current_comp]->getAtom( k );
544	>	if( !current_atom->havePosition() ){
545		sprintf( painCave.errMsg,
546	<	"SimSetup Warning: using default value of 1/2 the smallest "
547	<	"box length for the electrostaticCutoffRadius.\n"
548	<	"I hope you have a very fast processor!\n");
549	<	painCave.isFatal = 0;
546	>	"SimSetup:initFromBass error.\n"
547	>	"\tComponent %s, atom %s does not have a position specified.\n"
548	>	"\tThe initialization routine is unable to give a start"
549	>	" position.\n",
550	>	comp_stamps[current_comp]->getID(),
551	>	current_atom->getType() );
552	>	painCave.isFatal = 1;
553		simError();
520	–	double smallest;
521	–	smallest = simnfo->box_x;
522	–	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
523	–	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
524	–	simnfo->ecr = 0.5 * smallest;
525	–	} else {
526	–	simnfo->ecr        = the_globals->getECR();
554		}
528	–
529	–	if( !the_globals->haveEST() ){
530	–	sprintf( painCave.errMsg,
531	–	"SimSetup Warning: using default value of 0.05 * the "
532	–	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
533	–	);
534	–	painCave.isFatal = 0;
535	–	simError();
536	–	simnfo->est = 0.05 * simnfo->ecr;
537	–	} else {
538	–	simnfo->est        = the_globals->getEST();
539	–	}
555
556	<	if(!the_globals->haveDielectric() ){
557	<	sprintf( painCave.errMsg,
558	<	"SimSetup Error: You are trying to use Reaction Field without"
559	<	"setting a dielectric constant!\n"
560	<	);
561	<	painCave.isFatal = 1;
562	<	simError();
556	>	pos[0] = x + current_atom->getPosX();
557	>	pos[1] = y + current_atom->getPosY();
558	>	pos[2] = z + current_atom->getPosZ();
559	>
560	>	info[0].atoms[current_atom_ndx]->setPos( pos );
561	>
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563	>
564	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565	>
566	>	rotMat[0][0] = 1.0;
567	>	rotMat[0][1] = 0.0;
568	>	rotMat[0][2] = 0.0;
569	>
570	>	rotMat[1][0] = 0.0;
571	>	rotMat[1][1] = 1.0;
572	>	rotMat[1][2] = 0.0;
573	>
574	>	rotMat[2][0] = 0.0;
575	>	rotMat[2][1] = 0.0;
576	>	rotMat[2][2] = 1.0;
577	>
578	>	dAtom->setA( rotMat );
579		}
549	–	simnfo->dielectric = the_globals->getDielectric();
550	–	} else {
551	–	if (usesDipoles) {
552	–
553	–	if( !the_globals->haveECR() ){
554	–	sprintf( painCave.errMsg,
555	–	"SimSetup Warning: using default value of 1/2 the smallest "
556	–	"box length for the electrostaticCutoffRadius.\n"
557	–	"I hope you have a very fast processor!\n");
558	–	painCave.isFatal = 0;
559	–	simError();
560	–	double smallest;
561	–	smallest = simnfo->box_x;
562	–	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
563	–	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
564	–	simnfo->ecr = 0.5 * smallest;
565	–	} else {
566	–	simnfo->ecr        = the_globals->getECR();
567	–	}
568	–
569	–	if( !the_globals->haveEST() ){
570	–	sprintf( painCave.errMsg,
571	–	"SimSetup Warning: using default value of 5%% of the "
572	–	"electrostaticCutoffRadius for the "
573	–	"electrostaticSkinThickness\n"
574	–	);
575	–	painCave.isFatal = 0;
576	–	simError();
577	–	simnfo->est = 0.05 * simnfo->ecr;
578	–	} else {
579	–	simnfo->est        = the_globals->getEST();
580	–	}
581	–	}
582	–	}
580
581	<	#ifdef IS_MPI
582	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
586	<	MPIcheckPoint();
587	<	#endif // is_mpi
581	>	current_atom_ndx++;
582	>	}
583
584	<	if( the_globals->haveInitialConfig() ){
585	<
591	<	InitializeFromFile* fileInit;
592	<	#ifdef IS_MPI // is_mpi
593	<	if( worldRank == 0 ){
594	<	#endif //is_mpi
595	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
596	<	#ifdef IS_MPI
597	<	}else fileInit = new InitializeFromFile( NULL );
598	<	#endif
599	<	fileInit->read_xyz( simnfo ); // default velocities on
584	>	current_mol++;
585	>	current_comp_mol++;
586
587	<	delete fileInit;
602	<	}
603	<	else{
587	>	if( current_comp_mol >= components_nmol[current_comp] ){
588
589	<	#ifdef IS_MPI
589	>	current_comp_mol = 0;
590	>	current_comp++;
591	>	}
592	>	}
593
594	<	// no init from bass
594	>
595	>	void SimSetup::gatherInfo( void ){
596	>	int i,j,k;
597	>
598	>	ensembleCase = -1;
599	>	ffCase = -1;
600	>
601	>	// set the easy ones first
602	>
603	>	for( i=0; i<nInfo; i++){
604	>	info[i].target_temp = globals->getTargetTemp();
605	>	info[i].dt = globals->getDt();
606	>	info[i].run_time = globals->getRunTime();
607	>	}
608	>	n_components = globals->getNComponents();
609	>
610	>
611	>	// get the forceField
612	>
613	>	strcpy( force_field, globals->getForceField() );
614	>
615	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618	>	else{
619	>	sprintf( painCave.errMsg,
620	>	"SimSetup Error. Unrecognized force field -> %s\n",
621	>	force_field );
622	>	painCave.isFatal = 1;
623	>	simError();
624	>	}
625	>
626	>	// get the ensemble
627	>
628	>	strcpy( ensemble, globals->getEnsemble() );
629	>
630	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633	>	ensembleCase = NPTi_ENS;
634	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637	>	else{
638	>	sprintf( painCave.errMsg,
639	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	>	"reverting to NVE for this simulation.\n",
641	>	ensemble );
642	>	painCave.isFatal = 0;
643	>	simError();
644	>	strcpy( ensemble, "NVE" );
645	>	ensembleCase = NVE_ENS;
646	>	}
647
648	<	sprintf( painCave.errMsg,
649	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
650	<	painCave.isFatal;
651	<	simError();
648	>	for(i=0; i<nInfo; i++){
649	>
650	>	strcpy( info[i].ensemble, ensemble );
651	>
652	>	// get the mixing rule
653	>
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657
658	<	#else
658	>	// get the components and calculate the tot_nMol and indvidual n_mol
659	>
660	>	the_components = globals->getComponents();
661	>	components_nmol = new int[n_components];
662
616	–	initFromBass();
663
664	+	if( !globals->haveNMol() ){
665	+	// we don't have the total number of molecules, so we assume it is
666	+	// given in each component
667
668	<	#endif
669	<	}
668	>	tot_nmol = 0;
669	>	for( i=0; i<n_components; i++ ){
670
671	<	#ifdef IS_MPI
672	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
673	<	MPIcheckPoint();
674	<	#endif // is_mpi
671	>	if( !the_components[i]->haveNMol() ){
672	>	// we have a problem
673	>	sprintf( painCave.errMsg,
674	>	"SimSetup Error. No global NMol or component NMol"
675	>	" given. Cannot calculate the number of atoms.\n" );
676	>	painCave.isFatal = 1;
677	>	simError();
678	>	}
679
680	+	tot_nmol += the_components[i]->getNMol();
681	+	components_nmol[i] = the_components[i]->getNMol();
682	+	}
683	+	}
684	+	else{
685	+	sprintf( painCave.errMsg,
686	+	"SimSetup error.\n"
687	+	"\tSorry, the ability to specify total"
688	+	" nMols and then give molfractions in the components\n"
689	+	"\tis not currently supported."
690	+	" Please give nMol in the components.\n" );
691	+	painCave.isFatal = 1;
692	+	simError();
693	+	}
694
695	<
629	<
695	>	// set the status, sample, and thermal kick times
696
697	+	for(i=0; i<nInfo; i++){
698
699	<
700	<	#ifdef IS_MPI
701	<	if( worldRank == 0 ){
702	<	#endif // is_mpi
636	<
637	<	if( the_globals->haveFinalConfig() ){
638	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
699	>	if( globals->haveSampleTime() ){
700	>	info[i].sampleTime = globals->getSampleTime();
701	>	info[i].statusTime = info[i].sampleTime;
702	>	info[i].thermalTime = info[i].sampleTime;
703		}
704		else{
705	<	strcpy( simnfo->finalName, inFileName );
706	<	char* endTest;
707	<	int nameLength = strlen( simnfo->finalName );
644	<	endTest = &(simnfo->finalName[nameLength - 5]);
645	<	if( !strcmp( endTest, ".bass" ) ){
646	<	strcpy( endTest, ".eor" );
647	<	}
648	<	else if( !strcmp( endTest, ".BASS" ) ){
649	<	strcpy( endTest, ".eor" );
650	<	}
651	<	else{
652	<	endTest = &(simnfo->finalName[nameLength - 4]);
653	<	if( !strcmp( endTest, ".bss" ) ){
654	<	strcpy( endTest, ".eor" );
655	<	}
656	<	else if( !strcmp( endTest, ".mdl" ) ){
657	<	strcpy( endTest, ".eor" );
658	<	}
659	<	else{
660	<	strcat( simnfo->finalName, ".eor" );
661	<	}
662	<	}
705	>	info[i].sampleTime = globals->getRunTime();
706	>	info[i].statusTime = info[i].sampleTime;
707	>	info[i].thermalTime = info[i].sampleTime;
708		}
709
710	<	// make the sample and status out names
711	<
667	<	strcpy( simnfo->sampleName, inFileName );
668	<	char* endTest;
669	<	int nameLength = strlen( simnfo->sampleName );
670	<	endTest = &(simnfo->sampleName[nameLength - 5]);
671	<	if( !strcmp( endTest, ".bass" ) ){
672	<	strcpy( endTest, ".dump" );
710	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712		}
713	<	else if( !strcmp( endTest, ".BASS" ) ){
714	<	strcpy( endTest, ".dump" );
713	>
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716		}
717	<	else{
718	<	endTest = &(simnfo->sampleName[nameLength - 4]);
719	<	if( !strcmp( endTest, ".bss" ) ){
720	<	strcpy( endTest, ".dump" );
681	<	}
682	<	else if( !strcmp( endTest, ".mdl" ) ){
683	<	strcpy( endTest, ".dump" );
684	<	}
685	<	else{
686	<	strcat( simnfo->sampleName, ".dump" );
687	<	}
688	<	}
717	>
718	>	// check for the temperature set flag
719	>
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721
722	<	strcpy( simnfo->statusName, inFileName );
723	<	nameLength = strlen( simnfo->statusName );
724	<	endTest = &(simnfo->statusName[nameLength - 5]);
725	<	if( !strcmp( endTest, ".bass" ) ){
726	<	strcpy( endTest, ".stat" );
722	>	// get some of the tricky things that may still be in the globals
723	>
724	>	double boxVector[3];
725	>	if( globals->haveBox() ){
726	>	boxVector[0] = globals->getBox();
727	>	boxVector[1] = globals->getBox();
728	>	boxVector[2] = globals->getBox();
729	>
730	>	info[i].setBox( boxVector );
731		}
732	<	else if( !strcmp( endTest, ".BASS" ) ){
733	<	strcpy( endTest, ".stat" );
734	<	}
732	>	else if( globals->haveDensity() ){
733	>
734	>	double vol;
735	>	vol = (double)tot_nmol / globals->getDensity();
736	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	>	boxVector[1] = boxVector[0];
738	>	boxVector[2] = boxVector[0];
739	>
740	>	info[i].setBox( boxVector );
741	>	}
742		else{
743	<	endTest = &(simnfo->statusName[nameLength - 4]);
744	<	if( !strcmp( endTest, ".bss" ) ){
745	<	strcpy( endTest, ".stat" );
743	>	if( !globals->haveBoxX() ){
744	>	sprintf( painCave.errMsg,
745	>	"SimSetup error, no periodic BoxX size given.\n" );
746	>	painCave.isFatal = 1;
747	>	simError();
748		}
749	<	else if( !strcmp( endTest, ".mdl" ) ){
750	<	strcpy( endTest, ".stat" );
749	>	boxVector[0] = globals->getBoxX();
750	>
751	>	if( !globals->haveBoxY() ){
752	>	sprintf( painCave.errMsg,
753	>	"SimSetup error, no periodic BoxY size given.\n" );
754	>	painCave.isFatal = 1;
755	>	simError();
756		}
757	<	else{
758	<	strcat( simnfo->statusName, ".stat" );
757	>	boxVector[1] = globals->getBoxY();
758	>
759	>	if( !globals->haveBoxZ() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxZ size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764		}
765	+	boxVector[2] = globals->getBoxZ();
766	+
767	+	info[i].setBox( boxVector );
768		}
769	+
770	+	}
771
772		#ifdef IS_MPI
773	<	}
773	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
774	>	MPIcheckPoint();
775		#endif // is_mpi
715	–
716	–	// set the status, sample, and themal kick times
717	–
718	–	if( the_globals->haveSampleTime() ){
719	–	simnfo->sampleTime = the_globals->getSampleTime();
720	–	simnfo->statusTime = simnfo->sampleTime;
721	–	simnfo->thermalTime = simnfo->sampleTime;
722	–	}
723	–	else{
724	–	simnfo->sampleTime = the_globals->getRunTime();
725	–	simnfo->statusTime = simnfo->sampleTime;
726	–	simnfo->thermalTime = simnfo->sampleTime;
727	–	}
776
777	<	if( the_globals->haveStatusTime() ){
730	<	simnfo->statusTime = the_globals->getStatusTime();
731	<	}
777	>	}
778
733	–	if( the_globals->haveThermalTime() ){
734	–	simnfo->thermalTime = the_globals->getThermalTime();
735	–	}
779
780	<	// check for the temperature set flag
780	>	void SimSetup::finalInfoCheck( void ){
781	>	int index;
782	>	int usesDipoles;
783	>	int i;
784
785	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
786	<
787	<
788	<	//   // make the longe range forces and the integrator
789	<
790	<	//   new AllLong( simnfo );
791	<
792	<
793	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
794	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787	>
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793	>	}
794	>
795	>	#ifdef IS_MPI
796	>	int myUse = usesDipoles;
797	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798	>	#endif //is_mpi
799	>
800	>	double theEcr, theEst;
801	>
802	>	if (globals->getUseRF() ) {
803	>	info[i].useReactionField = 1;
804	>
805	>	if( !globals->haveECR() ){
806	>	sprintf( painCave.errMsg,
807	>	"SimSetup Warning: using default value of 1/2 the smallest "
808	>	"box length for the electrostaticCutoffRadius.\n"
809	>	"I hope you have a very fast processor!\n");
810	>	painCave.isFatal = 0;
811	>	simError();
812	>	double smallest;
813	>	smallest = info[i].boxL[0];
814	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	>	theEcr = 0.5 * smallest;
817	>	} else {
818	>	theEcr = globals->getECR();
819	>	}
820	>
821	>	if( !globals->haveEST() ){
822	>	sprintf( painCave.errMsg,
823	>	"SimSetup Warning: using default value of 0.05 * the "
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	>	);
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	theEst = 0.05 * theEcr;
829	>	} else {
830	>	theEst= globals->getEST();
831	>	}
832	>
833	>	info[i].setEcr( theEcr, theEst );
834	>
835	>	if(!globals->haveDielectric() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Error: You are trying to use Reaction Field without"
838	>	"setting a dielectric constant!\n"
839	>	);
840	>	painCave.isFatal = 1;
841	>	simError();
842	>	}
843	>	info[i].dielectric = globals->getDielectric();
844	>	}
845	>	else {
846	>	if (usesDipoles) {
847	>
848	>	if( !globals->haveECR() ){
849	>	sprintf( painCave.errMsg,
850	>	"SimSetup Warning: using default value of 1/2 the smallest "
851	>	"box length for the electrostaticCutoffRadius.\n"
852	>	"I hope you have a very fast processor!\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	double smallest;
856	>	smallest = info[i].boxL[0];
857	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	>	theEcr = 0.5 * smallest;
860	>	} else {
861	>	theEcr = globals->getECR();
862		}
863	<	else if( !strcmp( force_field, "LJ" ) ){
864	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
863	>
864	>	if( !globals->haveEST() ){
865	>	sprintf( painCave.errMsg,
866	>	"SimSetup Warning: using default value of 0.05 * the "
867	>	"electrostaticCutoffRadius for the "
868	>	"electrostaticSkinThickness\n"
869	>	);
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	theEst = 0.05 * theEcr;
873	>	} else {
874	>	theEst= globals->getEST();
875		}
876	<	else {
877	<	std::cerr << "I'm a bug.\n";
878	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
876	>
877	>	info[i].setEcr( theEcr, theEst );
878	>	}
879	>	}
880		}
881	+
882		#ifdef IS_MPI
883	<	mpiSim->mpiRefresh();
884	<	#endif
883	>	strcpy( checkPointMsg, "post processing checks out" );
884	>	MPIcheckPoint();
885	>	#endif // is_mpi
886
887	<	// initialize the Fortran
887	>	}
888
889	+	void SimSetup::initSystemCoords( void ){
890	+	int i;
891	+
892	+	char* inName;
893
894	<	simnfo->refreshSim();
894	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
895	>
896	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
897
898	<	if( !strcmp( simnfo->mixingRule, "standard") ){
899	<	the_ff->initForceField( LB_MIXING_RULE );
898	>	if( globals->haveInitialConfig() ){
899	>
900	>	InitializeFromFile* fileInit;
901	>	#ifdef IS_MPI // is_mpi
902	>	if( worldRank == 0 ){
903	>	#endif //is_mpi
904	>	inName = globals->getInitialConfig();
905	>	double* tempDouble = new double[1000000];
906	>	fileInit = new InitializeFromFile( inName );
907	>	#ifdef IS_MPI
908	>	}else fileInit = new InitializeFromFile( NULL );
909	>	#endif
910	>	fileInit->readInit( info ); // default velocities on
911	>
912	>	delete fileInit;
913		}
769	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
770	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
771	–	}
914		else{
915	+
916	+	#ifdef IS_MPI
917	+
918	+	// no init from bass
919	+
920		sprintf( painCave.errMsg,
921	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
922	<	simnfo->mixingRule );
776	<	painCave.isFatal = 1;
921	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
922	>	painCave.isFatal;
923		simError();
924	+
925	+	#else
926	+
927	+	initFromBass();
928	+
929	+
930	+	#endif
931		}
932	<
780	<
932	>
933		#ifdef IS_MPI
934	<	strcpy( checkPointMsg,
783	<	"Successfully intialized the mixingRule for Fortran." );
934	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
935		MPIcheckPoint();
936		#endif // is_mpi
937	+
938		}
939
940
941	<	void SimSetup::makeMolecules( void ){
790	<
791	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
792	<	molInit info;
793	<	DirectionalAtom* dAtom;
794	<	LinkedAssign* extras;
795	<	LinkedAssign* current_extra;
796	<	AtomStamp* currentAtom;
797	<	BondStamp* currentBond;
798	<	BendStamp* currentBend;
799	<	TorsionStamp* currentTorsion;
800	<
801	<	bond_pair* theBonds;
802	<	bend_set* theBends;
803	<	torsion_set* theTorsions;
804	<
941	>	void SimSetup::makeOutNames( void ){
942
943	<	//init the forceField paramters
943	>	int k;
944
808	–	the_ff->readParams();
809	–
945
946	<	// init the atoms
946	>	for(k=0; k<nInfo; k++){
947
948	<	double ux, uy, uz, u, uSqr;
949	<
950	<	atomOffset = 0;
816	<	excludeOffset = 0;
817	<	for(i=0; i<simnfo->n_mol; i++){
818	<
819	<	stampID = the_molecules[i].getStampID();
820	<
821	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
822	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
823	<	info.nBends    = comp_stamps[stampID]->getNBends();
824	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
825	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
826	<
827	<	info.myAtoms = &the_atoms[atomOffset];
828	<	info.myExcludes = &the_excludes[excludeOffset];
829	<	info.myBonds = new Bond*[info.nBonds];
830	<	info.myBends = new Bend*[info.nBends];
831	<	info.myTorsions = new Torsion*[info.nTorsions];
832	<
833	<	theBonds = new bond_pair[info.nBonds];
834	<	theBends = new bend_set[info.nBends];
835	<	theTorsions = new torsion_set[info.nTorsions];
836	<
837	<	// make the Atoms
838	<
839	<	for(j=0; j<info.nAtoms; j++){
948	>	#ifdef IS_MPI
949	>	if( worldRank == 0 ){
950	>	#endif // is_mpi
951
952	<	currentAtom = comp_stamps[stampID]->getAtom( j );
953	<	if( currentAtom->haveOrientation() ){
954	<
844	<	dAtom = new DirectionalAtom(j + atomOffset);
845	<	simnfo->n_oriented++;
846	<	info.myAtoms[j] = dAtom;
847	<
848	<	ux = currentAtom->getOrntX();
849	<	uy = currentAtom->getOrntY();
850	<	uz = currentAtom->getOrntZ();
851	<
852	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
853	<
854	<	u = sqrt( uSqr );
855	<	ux = ux / u;
856	<	uy = uy / u;
857	<	uz = uz / u;
858	<
859	<	dAtom->setSUx( ux );
860	<	dAtom->setSUy( uy );
861	<	dAtom->setSUz( uz );
862	<	}
952	>	if( globals->haveFinalConfig() ){
953	>	strcpy( info[k].finalName, globals->getFinalConfig() );
954	>	}
955		else{
956	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
956	>	strcpy( info[k].finalName, inFileName );
957	>	char* endTest;
958	>	int nameLength = strlen( info[k].finalName );
959	>	endTest = &(info[k].finalName[nameLength - 5]);
960	>	if( !strcmp( endTest, ".bass" ) ){
961	>	strcpy( endTest, ".eor" );
962	>	}
963	>	else if( !strcmp( endTest, ".BASS" ) ){
964	>	strcpy( endTest, ".eor" );
965	>	}
966	>	else{
967	>	endTest = &(info[k].finalName[nameLength - 4]);
968	>	if( !strcmp( endTest, ".bss" ) ){
969	>	strcpy( endTest, ".eor" );
970	>	}
971	>	else if( !strcmp( endTest, ".mdl" ) ){
972	>	strcpy( endTest, ".eor" );
973	>	}
974	>	else{
975	>	strcat( info[k].finalName, ".eor" );
976	>	}
977	>	}
978		}
866	–	info.myAtoms[j]->setType( currentAtom->getType() );
867	–
868	–	#ifdef IS_MPI
979
980	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
980	>	// make the sample and status out names
981
982	<	#endif // is_mpi
983	<	}
984	<
985	<	// make the bonds
986	<	for(j=0; j<info.nBonds; j++){
987	<
878	<	currentBond = comp_stamps[stampID]->getBond( j );
879	<	theBonds[j].a = currentBond->getA() + atomOffset;
880	<	theBonds[j].b = currentBond->getB() + atomOffset;
881	<
882	<	exI = theBonds[j].a;
883	<	exJ = theBonds[j].b;
884	<
885	<	// exclude_I must always be the smaller of the pair
886	<	if( exI > exJ ){
887	<	tempEx = exI;
888	<	exI = exJ;
889	<	exJ = tempEx;
982	>	strcpy( info[k].sampleName, inFileName );
983	>	char* endTest;
984	>	int nameLength = strlen( info[k].sampleName );
985	>	endTest = &(info[k].sampleName[nameLength - 5]);
986	>	if( !strcmp( endTest, ".bass" ) ){
987	>	strcpy( endTest, ".dump" );
988		}
989	<	#ifdef IS_MPI
990	<	tempEx = exI;
991	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
992	<	tempEx = exJ;
993	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
989	>	else if( !strcmp( endTest, ".BASS" ) ){
990	>	strcpy( endTest, ".dump" );
991	>	}
992	>	else{
993	>	endTest = &(info[k].sampleName[nameLength - 4]);
994	>	if( !strcmp( endTest, ".bss" ) ){
995	>	strcpy( endTest, ".dump" );
996	>	}
997	>	else if( !strcmp( endTest, ".mdl" ) ){
998	>	strcpy( endTest, ".dump" );
999	>	}
1000	>	else{
1001	>	strcat( info[k].sampleName, ".dump" );
1002	>	}
1003	>	}
1004
1005	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1006	<	#else  // isn't MPI
1007	<
1008	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1009	<	#endif  //is_mpi
902	<	}
903	<	excludeOffset += info.nBonds;
904	<
905	<	//make the bends
906	<	for(j=0; j<info.nBends; j++){
907	<
908	<	currentBend = comp_stamps[stampID]->getBend( j );
909	<	theBends[j].a = currentBend->getA() + atomOffset;
910	<	theBends[j].b = currentBend->getB() + atomOffset;
911	<	theBends[j].c = currentBend->getC() + atomOffset;
912	<
913	<	if( currentBend->haveExtras() ){
914	<
915	<	extras = currentBend->getExtras();
916	<	current_extra = extras;
917	<
918	<	while( current_extra != NULL ){
919	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
920	<
921	<	switch( current_extra->getType() ){
922	<
923	<	case 0:
924	<	theBends[j].ghost =
925	<	current_extra->getInt() + atomOffset;
926	<	theBends[j].isGhost = 1;
927	<	break;
928	<
929	<	case 1:
930	<	theBends[j].ghost =
931	<	(int)current_extra->getDouble() + atomOffset;
932	<	theBends[j].isGhost = 1;
933	<	break;
934	<
935	<	default:
936	<	sprintf( painCave.errMsg,
937	<	"SimSetup Error: ghostVectorSource was neither a "
938	<	"double nor an int.\n"
939	<	"-->Bend[%d] in %s\n",
940	<	j, comp_stamps[stampID]->getID() );
941	<	painCave.isFatal = 1;
942	<	simError();
943	<	}
944	<	}
945	<
946	<	else{
947	<
948	<	sprintf( painCave.errMsg,
949	<	"SimSetup Error: unhandled bend assignment:\n"
950	<	"    -->%s in Bend[%d] in %s\n",
951	<	current_extra->getlhs(),
952	<	j, comp_stamps[stampID]->getID() );
953	<	painCave.isFatal = 1;
954	<	simError();
955	<	}
956	<
957	<	current_extra = current_extra->getNext();
958	<	}
1005	>	strcpy( info[k].statusName, inFileName );
1006	>	nameLength = strlen( info[k].statusName );
1007	>	endTest = &(info[k].statusName[nameLength - 5]);
1008	>	if( !strcmp( endTest, ".bass" ) ){
1009	>	strcpy( endTest, ".stat" );
1010		}
1011	<
1012	<	if( !theBends[j].isGhost ){
962	<
963	<	exI = theBends[j].a;
964	<	exJ = theBends[j].c;
1011	>	else if( !strcmp( endTest, ".BASS" ) ){
1012	>	strcpy( endTest, ".stat" );
1013		}
1014		else{
1015	<
1016	<	exI = theBends[j].a;
1017	<	exJ = theBends[j].b;
1015	>	endTest = &(info[k].statusName[nameLength - 4]);
1016	>	if( !strcmp( endTest, ".bss" ) ){
1017	>	strcpy( endTest, ".stat" );
1018	>	}
1019	>	else if( !strcmp( endTest, ".mdl" ) ){
1020	>	strcpy( endTest, ".stat" );
1021	>	}
1022	>	else{
1023	>	strcat( info[k].statusName, ".stat" );
1024	>	}
1025		}
1026
972	–	// exclude_I must always be the smaller of the pair
973	–	if( exI > exJ ){
974	–	tempEx = exI;
975	–	exI = exJ;
976	–	exJ = tempEx;
977	–	}
1027		#ifdef IS_MPI
979	–	tempEx = exI;
980	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
981	–	tempEx = exJ;
982	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
983	–
984	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
985	–	#else  // isn't MPI
986	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
987	–	#endif  //is_mpi
1028		}
1029	<	excludeOffset += info.nBends;
1029	>	#endif // is_mpi
1030	>	}
1031	>	}
1032
991	–	for(j=0; j<info.nTorsions; j++){
992	–
993	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
994	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
995	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
996	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
997	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
998	–
999	–	exI = theTorsions[j].a;
1000	–	exJ = theTorsions[j].d;
1033
1034	<	// exclude_I must always be the smaller of the pair
1035	<	if( exI > exJ ){
1036	<	tempEx = exI;
1037	<	exI = exJ;
1038	<	exJ = tempEx;
1039	<	}
1034	>	void SimSetup::sysObjectsCreation( void ){
1035	>
1036	>	int i,k;
1037	>
1038	>	// create the forceField
1039	>
1040	>	createFF();
1041	>
1042	>	// extract componentList
1043	>
1044	>	compList();
1045	>
1046	>	// calc the number of atoms, bond, bends, and torsions
1047	>
1048	>	calcSysValues();
1049	>
1050		#ifdef IS_MPI
1051	<	tempEx = exI;
1052	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1053	<	tempEx = exJ;
1054	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1055	<
1056	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1057	<	#else  // isn't MPI
1058	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1059	<	#endif  //is_mpi
1051	>	// divide the molecules among the processors
1052	>
1053	>	mpiMolDivide();
1054	>	#endif //is_mpi
1055	>
1056	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1057	>
1058	>	makeSysArrays();
1059	>
1060	>	// make and initialize the molecules (all but atomic coordinates)
1061	>
1062	>	makeMolecules();
1063	>
1064	>	for(k=0; k<nInfo; k++){
1065	>	info[k].identArray = new int[info[k].n_atoms];
1066	>	for(i=0; i<info[k].n_atoms; i++){
1067	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1068		}
1069	<	excludeOffset += info.nTorsions;
1069	>	}
1070	>	}
1071
1021	–
1022	–	// send the arrays off to the forceField for init.
1072
1073	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1025	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1026	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1027	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1073	>	void SimSetup::createFF( void ){
1074
1075	+	switch( ffCase ){
1076
1077	<	the_molecules[i].initialize( info );
1077	>	case FF_DUFF:
1078	>	the_ff = new DUFF();
1079	>	break;
1080
1081	+	case FF_LJ:
1082	+	the_ff = new LJFF();
1083	+	break;
1084
1085	<	atomOffset += info.nAtoms;
1086	<	delete[] theBonds;
1087	<	delete[] theBends;
1088	<	delete[] theTorsions;
1085	>	case FF_EAM:
1086	>	the_ff = new EAM_FF();
1087	>	break;
1088	>
1089	>	default:
1090	>	sprintf( painCave.errMsg,
1091	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	>	painCave.isFatal = 1;
1093	>	simError();
1094		}
1095
1096		#ifdef IS_MPI
1097	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1097	>	strcpy( checkPointMsg, "ForceField creation successful" );
1098		MPIcheckPoint();
1099		#endif // is_mpi
1100
1044	–	// clean up the forcefield
1045	–	the_ff->calcRcut();
1046	–	the_ff->cleanMe();
1047	–
1101		}
1102
1050	–	void SimSetup::initFromBass( void ){
1103
1104	<	int i, j, k;
1053	<	int n_cells;
1054	<	double cellx, celly, cellz;
1055	<	double temp1, temp2, temp3;
1056	<	int n_per_extra;
1057	<	int n_extra;
1058	<	int have_extra, done;
1104	>	void SimSetup::compList( void ){
1105
1106	<	temp1 = (double)tot_nmol / 4.0;
1107	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1108	<	temp3 = ceil( temp2 );
1106	>	int i;
1107	>	char* id;
1108	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1109	>	LinkedMolStamp* currentStamp = NULL;
1110	>	comp_stamps = new MoleculeStamp*[n_components];
1111	>
1112	>	// make an array of molecule stamps that match the components used.
1113	>	// also extract the used stamps out into a separate linked list
1114	>
1115	>	for(i=0; i<nInfo; i++){
1116	>	info[i].nComponents = n_components;
1117	>	info[i].componentsNmol = components_nmol;
1118	>	info[i].compStamps = comp_stamps;
1119	>	info[i].headStamp = headStamp;
1120	>	}
1121	>
1122
1123	<	have_extra =0;
1065	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1066	<	have_extra =1;
1123	>	for( i=0; i<n_components; i++ ){
1124
1125	<	n_cells = (int)temp3 - 1;
1126	<	cellx = simnfo->box_x / temp3;
1127	<	celly = simnfo->box_y / temp3;
1128	<	cellz = simnfo->box_z / temp3;
1072	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1073	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1074	<	n_per_extra = (int)ceil( temp1 );
1125	>	id = the_components[i]->getType();
1126	>	comp_stamps[i] = NULL;
1127	>
1128	>	// check to make sure the component isn't already in the list
1129
1130	<	if( n_per_extra > 4){
1131	<	sprintf( painCave.errMsg,
1132	<	"SimSetup error. There has been an error in constructing"
1133	<	" the non-complete lattice.\n" );
1134	<	painCave.isFatal = 1;
1135	<	simError();
1130	>	comp_stamps[i] = headStamp->match( id );
1131	>	if( comp_stamps[i] == NULL ){
1132	>
1133	>	// extract the component from the list;
1134	>
1135	>	currentStamp = stamps->extractMolStamp( id );
1136	>	if( currentStamp == NULL ){
1137	>	sprintf( painCave.errMsg,
1138	>	"SimSetup error: Component \"%s\" was not found in the "
1139	>	"list of declared molecules\n",
1140	>	id );
1141	>	painCave.isFatal = 1;
1142	>	simError();
1143	>	}
1144	>
1145	>	headStamp->add( currentStamp );
1146	>	comp_stamps[i] = headStamp->match( id );
1147		}
1148		}
1149	<	else{
1150	<	n_cells = (int)temp3;
1151	<	cellx = simnfo->box_x / temp3;
1152	<	celly = simnfo->box_y / temp3;
1153	<	cellz = simnfo->box_z / temp3;
1149	>
1150	>	#ifdef IS_MPI
1151	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1152	>	MPIcheckPoint();
1153	>	#endif // is_mpi
1154	>
1155	>
1156	>	}
1157	>
1158	>	void SimSetup::calcSysValues( void ){
1159	>	int i, j, k;
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	>
1169	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1170	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1171	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1172	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1173		}
1174	+
1175	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1176	+	molMembershipArray = new int[tot_atoms];
1177	+
1178	+	for(i=0; i<nInfo; i++){
1179	+	info[i].n_atoms = tot_atoms;
1180	+	info[i].n_bonds = tot_bonds;
1181	+	info[i].n_bends = tot_bends;
1182	+	info[i].n_torsions = tot_torsions;
1183	+	info[i].n_SRI = tot_SRI;
1184	+	info[i].n_mol = tot_nmol;
1185	+
1186	+	info[i].molMembershipArray = molMembershipArray;
1187	+	}
1188	+	}
1189
1190	<	current_mol = 0;
1092	<	current_comp_mol = 0;
1093	<	current_comp = 0;
1094	<	current_atom_ndx = 0;
1190	>	#ifdef IS_MPI
1191
1192	<	for( i=0; i < n_cells ; i++ ){
1193	<	for( j=0; j < n_cells; j++ ){
1194	<	for( k=0; k < n_cells; k++ ){
1192	>	void SimSetup::mpiMolDivide( void ){
1193	>
1194	>	int i, j, k;
1195	>	int localMol, allMol;
1196	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1197
1198	<	makeElement( i * cellx,
1199	<	j * celly,
1200	<	k * cellz );
1198	>	mpiSim = new mpiSimulation( info );
1199	>
1200	>	globalIndex = mpiSim->divideLabor();
1201
1202	<	makeElement( i * cellx + 0.5 * cellx,
1203	<	j * celly + 0.5 * celly,
1204	<	k * cellz );
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
1108	–	makeElement( i * cellx,
1109	–	j * celly + 0.5 * celly,
1110	–	k * cellz + 0.5 * cellz );
1215
1216	<	makeElement( i * cellx + 0.5 * cellx,
1217	<	j * celly,
1218	<	k * cellz + 0.5 * cellz );
1216	>	for( i=0; i<n_components; i++ ){
1217	>
1218	>	for( j=0; j<components_nmol[i]; j++ ){
1219	>
1220	>	if( mol2proc[allMol] == worldRank ){
1221	>
1222	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1223	>	local_bonds +=    comp_stamps[i]->getNBonds();
1224	>	local_bends +=    comp_stamps[i]->getNBends();
1225	>	local_torsions += comp_stamps[i]->getNTorsions();
1226	>	localMol++;
1227	>	}
1228	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1229	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1230	>	globalAtomIndex++;
1231		}
1232	+
1233	+	allMol++;
1234		}
1235		}
1236	+	local_SRI = local_bonds + local_bends + local_torsions;
1237	+
1238	+	info[0].n_atoms = mpiSim->getMyNlocal();
1239	+
1240	+	if( local_atoms != info[0].n_atoms ){
1241	+	sprintf( painCave.errMsg,
1242	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1243	+	" localAtom (%d) are not equal.\n",
1244	+	info[0].n_atoms,
1245	+	local_atoms );
1246	+	painCave.isFatal = 1;
1247	+	simError();
1248	+	}
1249
1250	<	if( have_extra ){
1251	<	done = 0;
1250	>	info[0].n_bonds = local_bonds;
1251	>	info[0].n_bends = local_bends;
1252	>	info[0].n_torsions = local_torsions;
1253	>	info[0].n_SRI = local_SRI;
1254	>	info[0].n_mol = localMol;
1255
1256	<	int start_ndx;
1257	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1258	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1256	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1257	>	MPIcheckPoint();
1258	>	}
1259	>
1260	>	#endif // is_mpi
1261
1126	–	if( i < n_cells ){
1262
1263	<	if( j < n_cells ){
1264	<	start_ndx = n_cells;
1130	<	}
1131	<	else start_ndx = 0;
1132	<	}
1133	<	else start_ndx = 0;
1263	>	void SimSetup::makeSysArrays( void ){
1264	>	int i, j, k, l;
1265
1266	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1266	>	Atom** the_atoms;
1267	>	Molecule* the_molecules;
1268	>	Exclude** the_excludes;
1269
1270	<	makeElement( i * cellx,
1271	<	j * celly,
1272	<	k * cellz );
1273	<	done = ( current_mol >= tot_nmol );
1270	>
1271	>	for(l=0; l<nInfo; l++){
1272	>
1273	>	// create the atom and short range interaction arrays
1274	>
1275	>	the_atoms = new Atom*[info[l].n_atoms];
1276	>	the_molecules = new Molecule[info[l].n_mol];
1277	>	int molIndex;
1278
1279	<	if( !done && n_per_extra > 1 ){
1280	<	makeElement( i * cellx + 0.5 * cellx,
1281	<	j * celly + 0.5 * celly,
1282	<	k * cellz );
1283	<	done = ( current_mol >= tot_nmol );
1284	<	}
1279	>	// initialize the molecule's stampID's
1280	>
1281	>	#ifdef IS_MPI
1282	>
1283	>
1284	>	molIndex = 0;
1285	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1286	>
1287	>	if(mol2proc[i] == worldRank ){
1288	>	the_molecules[molIndex].setStampID( molCompType[i] );
1289	>	the_molecules[molIndex].setMyIndex( molIndex );
1290	>	the_molecules[molIndex].setGlobalIndex( i );
1291	>	molIndex++;
1292	>	}
1293	>	}
1294	>
1295	>	#else // is_mpi
1296	>
1297	>	molIndex = 0;
1298	>	globalAtomIndex = 0;
1299	>	for(i=0; i<n_components; i++){
1300	>	for(j=0; j<components_nmol[i]; j++ ){
1301	>	the_molecules[molIndex].setStampID( i );
1302	>	the_molecules[molIndex].setMyIndex( molIndex );
1303	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1304	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1305	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1306	>	globalAtomIndex++;
1307	>	}
1308	>	molIndex++;
1309	>	}
1310	>	}
1311	>
1312	>
1313	>	#endif // is_mpi
1314
1149	–	if( !done && n_per_extra > 2){
1150	–	makeElement( i * cellx,
1151	–	j * celly + 0.5 * celly,
1152	–	k * cellz + 0.5 * cellz );
1153	–	done = ( current_mol >= tot_nmol );
1154	–	}
1315
1316	<	if( !done && n_per_extra > 3){
1317	<	makeElement( i * cellx + 0.5 * cellx,
1318	<	j * celly,
1319	<	k * cellz + 0.5 * cellz );
1320	<	done = ( current_mol >= tot_nmol );
1321	<	}
1162	<	}
1316	>	if( info[l].n_SRI ){
1317	>
1318	>	Exclude::createArray(info[l].n_SRI);
1319	>	the_excludes = new Exclude*[info[l].n_SRI];
1320	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1321	>	the_excludes[ex] = new Exclude(ex);
1322		}
1323	+	info[l].globalExcludes = new int;
1324	+	info[l].n_exclude = info[l].n_SRI;
1325		}
1326	<	}
1326	>	else{
1327	>
1328	>	Exclude::createArray( 1 );
1329	>	the_excludes = new Exclude*;
1330	>	the_excludes[0] = new Exclude(0);
1331	>	the_excludes[0]->setPair( 0,0 );
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].globalExcludes[0] = 0;
1334	>	info[l].n_exclude = 0;
1335	>	}
1336
1337	+	// set the arrays into the SimInfo object
1338
1339	<	for( i=0; i<simnfo->n_atoms; i++ ){
1340	<	simnfo->atoms[i]->set_vx( 0.0 );
1341	<	simnfo->atoms[i]->set_vy( 0.0 );
1342	<	simnfo->atoms[i]->set_vz( 0.0 );
1339	>	info[l].atoms = the_atoms;
1340	>	info[l].molecules = the_molecules;
1341	>	info[l].nGlobalExcludes = 0;
1342	>	info[l].excludes = the_excludes;
1343	>
1344	>	the_ff->setSimInfo( info );
1345	>
1346		}
1347		}
1348
1349	<	void SimSetup::makeElement( double x, double y, double z ){
1349	>	void SimSetup::makeIntegrator( void ){
1350
1351		int k;
1178	–	AtomStamp* current_atom;
1179	–	DirectionalAtom* dAtom;
1180	–	double rotMat[3][3];
1352
1353	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1353	>	NVT<RealIntegrator>*  myNVT = NULL;
1354	>	NPTi<RealIntegrator>* myNPTi = NULL;
1355	>	NPTf<RealIntegrator>* myNPTf = NULL;
1356	>	NPTim<RealIntegrator>* myNPTim = NULL;
1357	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1358	>
1359	>	for(k=0; k<nInfo; k++){
1360	>
1361	>	switch( ensembleCase ){
1362	>
1363	>	case NVE_ENS:
1364	>	if (globals->haveZconstraints()){
1365	>	setupZConstraint(info[k]);
1366	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1367	>	}
1368
1369	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1370	<	if( !current_atom->havePosition() ){
1369	>	else
1370	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1371	>	break;
1372	>
1373	>	case NVT_ENS:
1374	>	if (globals->haveZconstraints()){
1375	>	setupZConstraint(info[k]);
1376	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377	>	}
1378	>	else
1379	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1380	>
1381	>	myNVT->setTargetTemp(globals->getTargetTemp());
1382	>
1383	>	if (globals->haveTauThermostat())
1384	>	myNVT->setTauThermostat(globals->getTauThermostat());
1385	>
1386	>	else {
1387	>	sprintf( painCave.errMsg,
1388	>	"SimSetup error: If you use the NVT\n"
1389	>	"    ensemble, you must set tauThermostat.\n");
1390	>	painCave.isFatal = 1;
1391	>	simError();
1392	>	}
1393	>	break;
1394	>
1395	>	case NPTi_ENS:
1396	>	if (globals->haveZconstraints()){
1397	>	setupZConstraint(info[k]);
1398	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399	>	}
1400	>	else
1401	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1402	>
1403	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	>	else {
1408	>	sprintf( painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413	>	}
1414	>
1415	>	if( globals->haveTauThermostat() )
1416	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	>	else{
1418	>	sprintf( painCave.errMsg,
1419	>	"SimSetup error: If you use an NPT\n"
1420	>	"    ensemble, you must set tauThermostat.\n");
1421	>	painCave.isFatal = 1;
1422	>	simError();
1423	>	}
1424	>
1425	>	if( globals->haveTauBarostat() )
1426	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	>	else{
1428	>	sprintf( painCave.errMsg,
1429	>	"SimSetup error: If you use an NPT\n"
1430	>	"    ensemble, you must set tauBarostat.\n");
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433	>	}
1434	>	break;
1435	>
1436	>	case NPTf_ENS:
1437	>	if (globals->haveZconstraints()){
1438	>	setupZConstraint(info[k]);
1439	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440	>	}
1441	>	else
1442	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1443	>
1444	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1445	>
1446	>	if (globals->haveTargetPressure())
1447	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1448	>	else {
1449	>	sprintf( painCave.errMsg,
1450	>	"SimSetup error: If you use a constant pressure\n"
1451	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1452	>	painCave.isFatal = 1;
1453	>	simError();
1454	>	}
1455	>
1456	>	if( globals->haveTauThermostat() )
1457	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1458	>	else{
1459	>	sprintf( painCave.errMsg,
1460	>	"SimSetup error: If you use an NPT\n"
1461	>	"    ensemble, you must set tauThermostat.\n");
1462	>	painCave.isFatal = 1;
1463	>	simError();
1464	>	}
1465	>
1466	>	if( globals->haveTauBarostat() )
1467	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1468	>	else{
1469	>	sprintf( painCave.errMsg,
1470	>	"SimSetup error: If you use an NPT\n"
1471	>	"    ensemble, you must set tauBarostat.\n");
1472	>	painCave.isFatal = 1;
1473	>	simError();
1474	>	}
1475	>	break;
1476	>
1477	>	case NPTim_ENS:
1478	>	if (globals->haveZconstraints()){
1479	>	setupZConstraint(info[k]);
1480	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481	>	}
1482	>	else
1483	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1484	>
1485	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1486	>
1487	>	if (globals->haveTargetPressure())
1488	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1489	>	else {
1490	>	sprintf( painCave.errMsg,
1491	>	"SimSetup error: If you use a constant pressure\n"
1492	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1493	>	painCave.isFatal = 1;
1494	>	simError();
1495	>	}
1496	>
1497	>	if( globals->haveTauThermostat() )
1498	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1499	>	else{
1500	>	sprintf( painCave.errMsg,
1501	>	"SimSetup error: If you use an NPT\n"
1502	>	"    ensemble, you must set tauThermostat.\n");
1503	>	painCave.isFatal = 1;
1504	>	simError();
1505	>	}
1506	>
1507	>	if( globals->haveTauBarostat() )
1508	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509	>	else{
1510	>	sprintf( painCave.errMsg,
1511	>	"SimSetup error: If you use an NPT\n"
1512	>	"    ensemble, you must set tauBarostat.\n");
1513	>	painCave.isFatal = 1;
1514	>	simError();
1515	>	}
1516	>	break;
1517	>
1518	>	case NPTfm_ENS:
1519	>	if (globals->haveZconstraints()){
1520	>	setupZConstraint(info[k]);
1521	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522	>	}
1523	>	else
1524	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1525	>
1526	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1527	>
1528	>	if (globals->haveTargetPressure())
1529	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1530	>	else {
1531	>	sprintf( painCave.errMsg,
1532	>	"SimSetup error: If you use a constant pressure\n"
1533	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1534	>	painCave.isFatal = 1;
1535	>	simError();
1536	>	}
1537	>
1538	>	if( globals->haveTauThermostat() )
1539	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1540	>	else{
1541	>	sprintf( painCave.errMsg,
1542	>	"SimSetup error: If you use an NPT\n"
1543	>	"    ensemble, you must set tauThermostat.\n");
1544	>	painCave.isFatal = 1;
1545	>	simError();
1546	>	}
1547	>
1548	>	if( globals->haveTauBarostat() )
1549	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1550	>	else{
1551	>	sprintf( painCave.errMsg,
1552	>	"SimSetup error: If you use an NPT\n"
1553	>	"    ensemble, you must set tauBarostat.\n");
1554	>	painCave.isFatal = 1;
1555	>	simError();
1556	>	}
1557	>	break;
1558	>
1559	>	default:
1560		sprintf( painCave.errMsg,
1561	<	"SimSetup:initFromBass error.\n"
1188	<	"\tComponent %s, atom %s does not have a position specified.\n"
1189	<	"\tThe initialization routine is unable to give a start"
1190	<	" position.\n",
1191	<	comp_stamps[current_comp]->getID(),
1192	<	current_atom->getType() );
1561	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1562		painCave.isFatal = 1;
1563		simError();
1564		}
1565	+	}
1566	+	}
1567
1568	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1198	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1199	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1568	>	void SimSetup::initFortran( void ){
1569
1570	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1570	>	info[0].refreshSim();
1571	>
1572	>	if( !strcmp( info[0].mixingRule, "standard") ){
1573	>	the_ff->initForceField( LB_MIXING_RULE );
1574	>	}
1575	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1576	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1577	>	}
1578	>	else{
1579	>	sprintf( painCave.errMsg,
1580	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	>	info[0].mixingRule );
1582	>	painCave.isFatal = 1;
1583	>	simError();
1584	>	}
1585
1203	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1586
1587	<	rotMat[0][0] = 1.0;
1588	<	rotMat[0][1] = 0.0;
1589	<	rotMat[0][2] = 0.0;
1587	>	#ifdef IS_MPI
1588	>	strcpy( checkPointMsg,
1589	>	"Successfully intialized the mixingRule for Fortran." );
1590	>	MPIcheckPoint();
1591	>	#endif // is_mpi
1592
1593	<	rotMat[1][0] = 0.0;
1210	<	rotMat[1][1] = 1.0;
1211	<	rotMat[1][2] = 0.0;
1593	>	}
1594
1595	<	rotMat[2][0] = 0.0;
1596	<	rotMat[2][1] = 0.0;
1597	<	rotMat[2][2] = 1.0;
1595	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596	>	{
1597	>	int nZConstraints;
1598	>	ZconStamp** zconStamp;
1599
1600	<	dAtom->setA( rotMat );
1601	<	}
1600	>	if(globals->haveZconstraintTime()){
1601	>
1602	>	//add sample time of z-constraint  into SimInfo's property list
1603	>	DoubleData* zconsTimeProp = new DoubleData();
1604	>	zconsTimeProp->setID(ZCONSTIME_ID);
1605	>	zconsTimeProp->setData(globals->getZconsTime());
1606	>	theInfo.addProperty(zconsTimeProp);
1607	>	}
1608	>	else{
1609	>	sprintf( painCave.errMsg,
1610	>	"ZConstraint error: If you use an ZConstraint\n"
1611	>	" , you must set sample time.\n");
1612	>	painCave.isFatal = 1;
1613	>	simError();
1614	>	}
1615
1616	<	current_atom_ndx++;
1616	>	//push zconsTol into siminfo, if user does not specify
1617	>	//value for zconsTol, a default value will be used
1618	>	DoubleData* zconsTol = new DoubleData();
1619	>	zconsTol->setID(ZCONSTOL_ID);
1620	>	if(globals->haveZconsTol()){
1621	>	zconsTol->setData(globals->getZconsTol());
1622		}
1623	+	else{
1624	+	double defaultZConsTol = 0.01;
1625	+	sprintf( painCave.errMsg,
1626	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1627	+	" , default value %f is used.\n", defaultZConsTol);
1628	+	painCave.isFatal = 0;
1629	+	simError();
1630
1631	<	current_mol++;
1632	<	current_comp_mol++;
1631	>	zconsTol->setData(defaultZConsTol);
1632	>	}
1633	>	theInfo.addProperty(zconsTol);
1634
1635	<	if( current_comp_mol >= components_nmol[current_comp] ){
1635	>	//set Force Substraction Policy
1636	>	StringData* zconsForcePolicy =  new StringData();
1637	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1638	>
1639	>	if(globals->haveZconsForcePolicy()){
1640	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1641	>	}
1642	>	else{
1643	>	sprintf( painCave.errMsg,
1644	>	"ZConstraint Warning: User does not set force substraction policy, "
1645	>	"average force substraction policy is used\n");
1646	>	painCave.isFatal = 0;
1647	>	simError();
1648	>	zconsForcePolicy->setData("BYNUMBER");
1649	>	}
1650	>
1651	>	theInfo.addProperty(zconsForcePolicy);
1652	>
1653	>	//Determine the name of ouput file and add it into SimInfo's property list
1654	>	//Be careful, do not use inFileName, since it is a pointer which
1655	>	//point to a string at master node, and slave nodes do not contain that string
1656	>
1657	>	string zconsOutput(theInfo.finalName);
1658	>
1659	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1660	>
1661	>	StringData* zconsFilename = new StringData();
1662	>	zconsFilename->setID(ZCONSFILENAME_ID);
1663	>	zconsFilename->setData(zconsOutput);
1664	>
1665	>	theInfo.addProperty(zconsFilename);
1666	>
1667	>	//setup index, pos and other parameters of z-constraint molecules
1668	>	nZConstraints = globals->getNzConstraints();
1669	>	theInfo.nZconstraints = nZConstraints;
1670
1671	<	current_comp_mol = 0;
1672	<	current_comp++;
1671	>	zconStamp = globals->getZconStamp();
1672	>	ZConsParaItem tempParaItem;
1673	>
1674	>	ZConsParaData* zconsParaData = new ZConsParaData();
1675	>	zconsParaData->setID(ZCONSPARADATA_ID);
1676	>
1677	>	for(int i = 0; i < nZConstraints; i++){
1678	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1679	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1680	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1681	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1682	>
1683	>	zconsParaData->addItem(tempParaItem);
1684		}
1685	+
1686	+	//sort the parameters by index of molecules
1687	+	zconsParaData->sortByIndex();
1688	+
1689	+	//push data into siminfo, therefore, we can retrieve later
1690	+	theInfo.addProperty(zconsParaData);
1691	+
1692		}

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