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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 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	<	int i, j;
95	>	// gather all of the information from the Bass file
96
97	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
97	>	gatherInfo();
98
99	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	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.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
101	>	sysObjectsCreation();
102
103	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
103	>	// check on the post processing info
104
105	+	finalInfoCheck();
106
107	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
107	>	// initialize the system coordinates
108
109	<	#ifdef IS_MPI
110	<	strcpy( checkPointMsg, "ForceField creation successful" );
111	<	MPIcheckPoint();
106	<	#endif // is_mpi
109	>	if (!isInfoArray){
110	>	initSystemCoords();
111	>	}
112
113	<
113	>	// make the output filenames
114
115	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
115	>	makeOutNames();
116
117	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
117	>	// make the integrator
118
119	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
119	>	makeIntegrator();
120
122	–	if( !the_components[i]->haveNMol() ){
123	–	// we have a problem
124	–	sprintf( painCave.errMsg,
125	–	"SimSetup Error. No global NMol or component NMol"
126	–	" given. Cannot calculate the number of atoms.\n" );
127	–	painCave.isFatal = 1;
128	–	simError();
129	–	}
130	–
131	–	tot_nmol += the_components[i]->getNMol();
132	–	components_nmol[i] = the_components[i]->getNMol();
133	–	}
134	–	}
135	–	else{
136	–	sprintf( painCave.errMsg,
137	–	"SimSetup error.\n"
138	–	"\tSorry, the ability to specify total"
139	–	" nMols and then give molfractions in the components\n"
140	–	"\tis not currently supported."
141	–	" Please give nMol in the components.\n" );
142	–	painCave.isFatal = 1;
143	–	simError();
144	–
145	–
146	–	//     tot_nmol = the_globals->getNMol();
147	–
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
159	–
121		#ifdef IS_MPI
122	<	strcpy( checkPointMsg, "Have the number of components" );
123	<	MPIcheckPoint();
163	<	#endif // is_mpi
122	>	mpiSim->mpiRefresh();
123	>	#endif
124
125	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
125	>	// initialize the Fortran
126
127	<	simnfo->nComponents = n_components;
128	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
173	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
127	>	initFortran();
128	>	}
129
178	–	id = the_components[i]->getType();
179	–	comp_stamps[i] = NULL;
180	–
181	–	// check to make sure the component isn't already in the list
130
131	<	comp_stamps[i] = headStamp->match( id );
132	<	if( comp_stamps[i] == NULL ){
133	<
134	<	// extract the component from the list;
135	<
136	<	currentStamp = the_stamps->extractMolStamp( id );
137	<	if( currentStamp == NULL ){
138	<	sprintf( painCave.errMsg,
139	<	"SimSetup error: Component \"%s\" was not found in the "
140	<	"list of declared molecules\n",
141	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
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	<	#ifdef IS_MPI
144	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
145	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
143	>	bond_pair* theBonds;
144	>	bend_set* theBends;
145	>	torsion_set* theTorsions;
146
147
148	+	//init the forceField paramters
149
150	<	// caclulate the number of atoms, bonds, bends and torsions
150	>	the_ff->readParams();
151
213	–	tot_atoms = 0;
214	–	tot_bonds = 0;
215	–	tot_bends = 0;
216	–	tot_torsions = 0;
217	–	for( i=0; i<n_components; i++ ){
218	–
219	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	–	}
152
153	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
153	>	// init the atoms
154
155	<	simnfo->n_atoms = tot_atoms;
228	<	simnfo->n_bonds = tot_bonds;
229	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
155	>	double ux, uy, uz, u, uSqr;
156
157	<
158	<	#ifdef IS_MPI
157	>	for (k = 0; k < nInfo; k++){
158	>	the_ff->setSimInfo(&(info[k]));
159
160	<	// divide the molecules among processors here.
161	<
162	<	mpiSim = new mpiSimulation( simnfo );
163	<
241	<
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	<	globalIndex = mpiSim->divideLabor();
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	+	theBonds = new bond_pair[molInfo.nBonds];
178	+	theBends = new bend_set[molInfo.nBends];
179	+	theTorsions = new torsion_set[molInfo.nTorsions];
180
181	<	// set up the local variables
248	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
181	>	// make the Atoms
182
183	<	for( j=0; j<components_nmol[i]; j++ ){
184	<
185	<	if( mpiSim->getMyMolStart() <= allMol &&
186	<	allMol <= mpiSim->getMyMolEnd() ){
187	<
188	<	local_atoms +=    comp_stamps[i]->getNAtoms();
189	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
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 = mpiSim->getMyNlocal();
192	<
193	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
191	>	ux = currentAtom->getOrntX();
192	>	uy = currentAtom->getOrntY();
193	>	uz = currentAtom->getOrntZ();
194
195	<	simnfo->n_bonds = local_bonds;
290	<	simnfo->n_bends = local_bends;
291	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
195	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
196
197	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
198	<	MPIcheckPoint();
199	<
200	<
299	<	#endif // is_mpi
300	<
197	>	u = sqrt(uSqr);
198	>	ux = ux / u;
199	>	uy = uy / u;
200	>	uz = uz / u;
201
202	<	// create the atom and short range interaction arrays
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	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
212	>	#ifdef IS_MPI
213
214	+	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
215
216	<	if( simnfo->n_SRI ){
217	<	the_sris = new SRI*[simnfo->n_SRI];
311	<	the_excludes = new int[2 * simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
216	>	#endif // is_mpi
217	>	}
218
219	<	simnfo->n_exclude = 1;
220	<	}
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	<	// set the arrays into the SimInfo object
225	>	exI = theBonds[j].a;
226	>	exJ = theBonds[j].b;
227
228	<	simnfo->atoms = the_atoms;
229	<	simnfo->sr_interactions = the_sris;
230	<	simnfo->nGlobalExcludes = 0;
231	<	simnfo->excludes = the_excludes;
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	>	tempEx = exI;
236	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
237	>	tempEx = exJ;
238	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239
240	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
241	+	#else  // isn't MPI
242
243	<	// get some of the tricky things that may still be in the globals
243	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
244	>	#endif  //is_mpi
245	>	}
246	>	excludeOffset += molInfo.nBonds;
247
248	<
249	<	if( the_globals->haveBox() ){
250	<	simnfo->box_x = the_globals->getBox();
251	<	simnfo->box_y = the_globals->getBox();
252	<	simnfo->box_z = the_globals->getBox();
253	<	}
342	<	else if( the_globals->haveDensity() ){
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	<	double vol;
256	<	vol = (double)tot_nmol / the_globals->getDensity();
257	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	<	simnfo->box_y = simnfo->box_x;
348	<	simnfo->box_z = simnfo->box_x;
349	<	}
350	<	else{
351	<	if( !the_globals->haveBoxX() ){
352	<	sprintf( painCave.errMsg,
353	<	"SimSetup error, no periodic BoxX size given.\n" );
354	<	painCave.isFatal = 1;
355	<	simError();
356	<	}
357	<	simnfo->box_x = the_globals->getBoxX();
255	>	if (currentBend->haveExtras()){
256	>	extras = currentBend->getExtras();
257	>	current_extra = extras;
258
259	<	if( !the_globals->haveBoxY() ){
260	<	sprintf( painCave.errMsg,
261	<	"SimSetup error, no periodic BoxY size given.\n" );
262	<	painCave.isFatal = 1;
263	<	simError();
264	<	}
265	<	simnfo->box_y = the_globals->getBoxY();
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	<	if( !the_globals->haveBoxZ() ){
268	<	sprintf( painCave.errMsg,
269	<	"SimSetup error, no periodic BoxZ size given.\n" );
270	<	painCave.isFatal = 1;
271	<	simError();
372	<	}
373	<	simnfo->box_z = the_globals->getBoxZ();
374	<	}
267	>	case 1:
268	>	theBends[j].ghost = (int) current_extra->getDouble() +
269	>	atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272
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	+	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	+	// 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	<	strcpy( checkPointMsg, "Box size set up" );
313	<	MPIcheckPoint();
314	<	#endif // 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	+	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	<	// initialize the arrays
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	<	the_ff->setSimInfo( simnfo );
331	>	exI = theTorsions[j].a;
332	>	exJ = theTorsions[j].d;
333
334	<	makeAtoms();
335	<	simnfo->identArray = new int[simnfo->n_atoms];
336	<	for(i=0; i<simnfo->n_atoms; i++){
337	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
338	<	}
339	<
340	<	if( tot_bonds ){
341	<	makeBonds();
342	<	}
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	>	tempEx = exI;
342	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	>	tempEx = exJ;
344	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345
346	<	if( tot_bends ){
347	<	makeBends();
348	<	}
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
400	–	if( tot_torsions ){
401	–	makeTorsions();
402	–	}
353
354	+	// send the arrays off to the forceField for init.
355
356	<	if (the_globals->getUseRF() ) {
357	<	simnfo->useReactionField = 1;
358	<
359	<	if( !the_globals->haveECR() ){
360	<	sprintf( painCave.errMsg,
410	<	"SimSetup Warning: using default value of 1/2 the smallest "
411	<	"box length for the electrostaticCutoffRadius.\n"
412	<	"I hope you have a very fast processor!\n");
413	<	painCave.isFatal = 0;
414	<	simError();
415	<	double smallest;
416	<	smallest = simnfo->box_x;
417	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	<	simnfo->ecr = 0.5 * smallest;
420	<	} else {
421	<	simnfo->ecr        = the_globals->getECR();
422	<	}
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
424	–	if( !the_globals->haveEST() ){
425	–	sprintf( painCave.errMsg,
426	–	"SimSetup Warning: using default value of 0.05 * the "
427	–	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	–	);
429	–	painCave.isFatal = 0;
430	–	simError();
431	–	simnfo->est = 0.05 * simnfo->ecr;
432	–	} else {
433	–	simnfo->est        = the_globals->getEST();
434	–	}
435	–
436	–	if(!the_globals->haveDielectric() ){
437	–	sprintf( painCave.errMsg,
438	–	"SimSetup Error: You are trying to use Reaction Field without"
439	–	"setting a dielectric constant!\n"
440	–	);
441	–	painCave.isFatal = 1;
442	–	simError();
443	–	}
444	–	simnfo->dielectric = the_globals->getDielectric();
445	–	} else {
446	–	if (simnfo->n_dipoles) {
447	–
448	–	if( !the_globals->haveECR() ){
449	–	sprintf( painCave.errMsg,
450	–	"SimSetup Warning: using default value of 1/2 the smallest"
451	–	"box length for the electrostaticCutoffRadius.\n"
452	–	"I hope you have a very fast processor!\n");
453	–	painCave.isFatal = 0;
454	–	simError();
455	–	double smallest;
456	–	smallest = simnfo->box_x;
457	–	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	–	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	–	simnfo->ecr = 0.5 * smallest;
460	–	} else {
461	–	simnfo->ecr        = the_globals->getECR();
462	–	}
463	–
464	–	if( !the_globals->haveEST() ){
465	–	sprintf( painCave.errMsg,
466	–	"SimSetup Warning: using default value of 5% of the"
467	–	"electrostaticCutoffRadius for the "
468	–	"electrostaticSkinThickness\n"
469	–	);
470	–	painCave.isFatal = 0;
471	–	simError();
472	–	simnfo->est = 0.05 * simnfo->ecr;
473	–	} else {
474	–	simnfo->est        = the_globals->getEST();
475	–	}
476	–	}
477	–	}
362
363	<	#ifdef IS_MPI
480	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
481	<	MPIcheckPoint();
482	<	#endif // is_mpi
363	>	info[k].molecules[i].initialize(molInfo);
364
484	–	if( the_globals->haveInitialConfig() ){
485	–
486	–	InitializeFromFile* fileInit;
487	–	#ifdef IS_MPI // is_mpi
488	–	if( worldRank == 0 ){
489	–	#endif //is_mpi
490	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
491	–	#ifdef IS_MPI
492	–	}else fileInit = new InitializeFromFile( NULL );
493	–	#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
365
366	<	delete fileInit;
367	<	}
368	<	else{
366	>	atomOffset += molInfo.nAtoms;
367	>	delete[] theBonds;
368	>	delete[] theBends;
369	>	delete[] theTorsions;
370	>	}
371	>	}
372
500	–	#ifdef IS_MPI
501	–
502	–	// no init from bass
503	–
504	–	sprintf( painCave.errMsg,
505	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	–	painCave.isFatal;
507	–	simError();
508	–
509	–	#else
510	–
511	–	initFromBass();
512	–
513	–
514	–	#endif
515	–	}
516	–
373		#ifdef IS_MPI
374	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
374	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
375		MPIcheckPoint();
376		#endif // is_mpi
377
378	+	// clean up the forcefield
379
380	<
381	<
382	<
380	>	the_ff->calcRcut();
381	>	the_ff->cleanMe();
382	>	}
383
384	<
385	<	#ifdef IS_MPI
386	<	if( worldRank == 0 ){
387	<	#endif // is_mpi
388	<
389	<	if( the_globals->haveFinalConfig() ){
390	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
391	<	}
535	<	else{
536	<	strcpy( simnfo->finalName, inFileName );
537	<	char* endTest;
538	<	int nameLength = strlen( simnfo->finalName );
539	<	endTest = &(simnfo->finalName[nameLength - 5]);
540	<	if( !strcmp( endTest, ".bass" ) ){
541	<	strcpy( endTest, ".eor" );
542	<	}
543	<	else if( !strcmp( endTest, ".BASS" ) ){
544	<	strcpy( endTest, ".eor" );
545	<	}
546	<	else{
547	<	endTest = &(simnfo->finalName[nameLength - 4]);
548	<	if( !strcmp( endTest, ".bss" ) ){
549	<	strcpy( endTest, ".eor" );
550	<	}
551	<	else if( !strcmp( endTest, ".mdl" ) ){
552	<	strcpy( endTest, ".eor" );
553	<	}
554	<	else{
555	<	strcat( simnfo->finalName, ".eor" );
556	<	}
557	<	}
558	<	}
559	<
560	<	// make the sample and status out names
561	<
562	<	strcpy( simnfo->sampleName, inFileName );
563	<	char* endTest;
564	<	int nameLength = strlen( simnfo->sampleName );
565	<	endTest = &(simnfo->sampleName[nameLength - 5]);
566	<	if( !strcmp( endTest, ".bass" ) ){
567	<	strcpy( endTest, ".dump" );
568	<	}
569	<	else if( !strcmp( endTest, ".BASS" ) ){
570	<	strcpy( endTest, ".dump" );
571	<	}
572	<	else{
573	<	endTest = &(simnfo->sampleName[nameLength - 4]);
574	<	if( !strcmp( endTest, ".bss" ) ){
575	<	strcpy( endTest, ".dump" );
576	<	}
577	<	else if( !strcmp( endTest, ".mdl" ) ){
578	<	strcpy( endTest, ".dump" );
579	<	}
580	<	else{
581	<	strcat( simnfo->sampleName, ".dump" );
582	<	}
583	<	}
584	<
585	<	strcpy( simnfo->statusName, inFileName );
586	<	nameLength = strlen( simnfo->statusName );
587	<	endTest = &(simnfo->statusName[nameLength - 5]);
588	<	if( !strcmp( endTest, ".bass" ) ){
589	<	strcpy( endTest, ".stat" );
590	<	}
591	<	else if( !strcmp( endTest, ".BASS" ) ){
592	<	strcpy( endTest, ".stat" );
593	<	}
594	<	else{
595	<	endTest = &(simnfo->statusName[nameLength - 4]);
596	<	if( !strcmp( endTest, ".bss" ) ){
597	<	strcpy( endTest, ".stat" );
598	<	}
599	<	else if( !strcmp( endTest, ".mdl" ) ){
600	<	strcpy( endTest, ".stat" );
601	<	}
602	<	else{
603	<	strcat( simnfo->statusName, ".stat" );
604	<	}
605	<	}
606	<
607	<	#ifdef IS_MPI
608	<	}
609	<	#endif // is_mpi
610	<
611	<	// set the status, sample, and themal kick times
612	<
613	<	if( the_globals->haveSampleTime() ){
614	<	simnfo->sampleTime = the_globals->getSampleTime();
615	<	simnfo->statusTime = simnfo->sampleTime;
616	<	simnfo->thermalTime = simnfo->sampleTime;
617	<	}
618	<	else{
619	<	simnfo->sampleTime = the_globals->getRunTime();
620	<	simnfo->statusTime = simnfo->sampleTime;
621	<	simnfo->thermalTime = simnfo->sampleTime;
622	<	}
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	<	if( the_globals->haveStatusTime() ){
394	<	simnfo->statusTime = the_globals->getStatusTime();
395	<	}
393	>	double vel[3];
394	>	vel[0] = 0.0;
395	>	vel[1] = 0.0;
396	>	vel[2] = 0.0;
397
398	<	if( the_globals->haveThermalTime() ){
399	<	simnfo->thermalTime = the_globals->getThermalTime();
400	<	}
398	>	temp1 = (double) tot_nmol / 4.0;
399	>	temp2 = pow(temp1, (1.0 / 3.0));
400	>	temp3 = ceil(temp2);
401
402	<	// check for the temperature set flag
402	>	have_extra = 0;
403	>	if (temp2 < temp3){
404	>	// we have a non-complete lattice
405	>	have_extra = 1;
406
407	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
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	<
416	<	//   // make the longe range forces and the integrator
417	<
418	<	//   new AllLong( simnfo );
419	<
420	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
421	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
422	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
423	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
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	>	}
422	>	}
423	>	else{
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	+	current_mol = 0;
431	+	current_comp_mol = 0;
432	+	current_comp = 0;
433	+	current_atom_ndx = 0;
434
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	<	// initialize the Fortran
441	<
442	<	simnfo->refreshSim();
443	<
444	<	if( !strcmp( simnfo->mixingRule, "standard") ){
445	<	the_ff->initForceField( LB_MIXING_RULE );
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		}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
658	–	else{
659	–	sprintf( painCave.errMsg,
660	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	–	simnfo->mixingRule );
662	–	painCave.isFatal = 1;
663	–	simError();
664	–	}
448
449	+	if (have_extra){
450	+	done = 0;
451
452	<	#ifdef IS_MPI
453	<	strcpy( checkPointMsg,
454	<	"Successfully intialized the mixingRule for Fortran." );
455	<	MPIcheckPoint();
456	<	#endif // is_mpi
457	<	}
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	<	void SimSetup::makeAtoms( void ){
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	<	int i, j, k, index;
470	<	double ux, uy, uz, uSqr, u;
471	<	AtomStamp* current_atom;
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	+	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	+	for (i = 0; i < info[0].n_atoms; i++){
492	+	info[0].atoms[i]->setVel(vel);
493	+	}
494	+	}
495	+
496	+	void SimSetup::makeElement(double x, double y, double z){
497	+	int k;
498	+	AtomStamp* current_atom;
499		DirectionalAtom* dAtom;
500	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
500	>	double rotMat[3][3];
501	>	double pos[3];
502
503	<	lMolIndex = 0;
504	<	molIndex = 0;
505	<	index = 0;
506	<	for( i=0; i<n_components; i++ ){
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	<	for( j=0; j<components_nmol[i]; j++ ){
516	>	pos[0] = x + current_atom->getPosX();
517	>	pos[1] = y + current_atom->getPosY();
518	>	pos[2] = z + current_atom->getPosZ();
519
520	<	#ifdef IS_MPI
691	<	if( mpiSim->getMyMolStart() <= molIndex &&
692	<	molIndex <= mpiSim->getMyMolEnd() ){
693	<	#endif // is_mpi
520	>	info[0].atoms[current_atom_ndx]->setPos(pos);
521
522	<	molStart = index;
523	<	nMemb = comp_stamps[i]->getNAtoms();
697	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
698	<
699	<	current_atom = comp_stamps[i]->getAtom( k );
700	<	if( current_atom->haveOrientation() ){
701	<
702	<	dAtom = new DirectionalAtom(index);
703	<	simnfo->n_oriented++;
704	<	the_atoms[index] = dAtom;
705	<
706	<	ux = current_atom->getOrntX();
707	<	uy = current_atom->getOrntY();
708	<	uz = current_atom->getOrntZ();
709	<
710	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
711	<
712	<	u = sqrt( uSqr );
713	<	ux = ux / u;
714	<	uy = uy / u;
715	<	uz = uz / u;
716	<
717	<	dAtom->setSUx( ux );
718	<	dAtom->setSUy( uy );
719	<	dAtom->setSUz( uz );
720	<	}
721	<	else{
722	<	the_atoms[index] = new GeneralAtom(index);
723	<	}
724	<	the_atoms[index]->setType( current_atom->getType() );
725	<	the_atoms[index]->setIndex( index );
726	<
727	<	// increment the index and repeat;
728	<	index++;
729	<	}
730	<
731	<	molEnd = index -1;
732	<	the_molecules[lMolIndex].setNMembers( nMemb );
733	<	the_molecules[lMolIndex].setStartAtom( molStart );
734	<	the_molecules[lMolIndex].setEndAtom( molEnd );
735	<	the_molecules[lMolIndex].setStampID( i );
736	<	lMolIndex++;
522	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
523	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
524
525	<	#ifdef IS_MPI
526	<	}
527	<	#endif //is_mpi
528	<
529	<	molIndex++;
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		}
542
543	<	#ifdef IS_MPI
544	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
748	<
749	<	delete[] globalIndex;
543	>	current_mol++;
544	>	current_comp_mol++;
545
546	<	mpiSim->mpiRefresh();
547	<	#endif //IS_MPI
548	<
549	<	the_ff->initializeAtoms();
546	>	if (current_comp_mol >= components_nmol[current_comp]){
547	>	current_comp_mol = 0;
548	>	current_comp++;
549	>	}
550		}
551
757	–	void SimSetup::makeBonds( void ){
552
553	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
554	<	bond_pair* the_bonds;
761	<	BondStamp* current_bond;
553	>	void SimSetup::gatherInfo(void){
554	>	int i, j, k;
555
556	<	the_bonds = new bond_pair[tot_bonds];
557	<	index = 0;
765	<	offset = 0;
766	<	molIndex = 0;
556	>	ensembleCase = -1;
557	>	ffCase = -1;
558
559	<	for( i=0; i<n_components; i++ ){
559	>	// set the easy ones first
560
561	<	for( j=0; j<components_nmol[i]; j++ ){
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
772	–	#ifdef IS_MPI
773	–	if( mpiSim->getMyMolStart() <= molIndex &&
774	–	molIndex <= mpiSim->getMyMolEnd() ){
775	–	#endif // is_mpi
776	–
777	–	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
778	–
779	–	current_bond = comp_stamps[i]->getBond( k );
780	–	the_bonds[index].a = current_bond->getA() + offset;
781	–	the_bonds[index].b = current_bond->getB() + offset;
568
569	<	exI = the_bonds[index].a;
784	<	exJ = the_bonds[index].b;
569	>	// get the forceField
570
571	<	// exclude_I must always be the smaller of the pair
787	<	if( exI > exJ ){
788	<	tempEx = exI;
789	<	exI = exJ;
790	<	exJ = tempEx;
791	<	}
571	>	strcpy(force_field, globals->getForceField());
572
573	<
574	<	#ifdef IS_MPI
795	<
796	<	the_excludes[index*2] =
797	<	the_atoms[exI]->getGlobalIndex() + 1;
798	<	the_excludes[index*2 + 1] =
799	<	the_atoms[exJ]->getGlobalIndex() + 1;
800	<
801	<	#else  // isn't MPI
802	<
803	<	the_excludes[index*2] =     exI + 1;
804	<	the_excludes[index*2 + 1] = exJ + 1;
805	<	// fortran index from 1 (hence the +1 in the indexing)
806	<	#endif  //is_mpi
807	<
808	<	// increment the index and repeat;
809	<	index++;
810	<	}
811	<	offset += comp_stamps[i]->getNAtoms();
812	<
813	<	#ifdef IS_MPI
814	<	}
815	<	#endif //is_mpi
816	<
817	<	molIndex++;
818	<	}
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	<	the_ff->initializeBonds( the_bonds );
822	<	}
589	>	// get the ensemble
590
591	<	void SimSetup::makeBends( void ){
591	>	strcpy(ensemble, globals->getEnsemble());
592
593	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
594	<	bend_set* the_bends;
595	<	BendStamp* current_bend;
596	<	LinkedAssign* extras;
597	<	LinkedAssign* current_extra;
598	<
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	<	the_bends = new bend_set[tot_bends];
617	<	index = 0;
835	<	offset = 0;
836	<	molIndex = 0;
837	<	for( i=0; i<n_components; i++ ){
616	>	for (i = 0; i < nInfo; i++){
617	>	strcpy(info[i].ensemble, ensemble);
618
619	<	for( j=0; j<components_nmol[i]; j++ ){
619	>	// get the mixing rule
620
621	<	#ifdef IS_MPI
622	<	if( mpiSim->getMyMolStart() <= molIndex &&
623	<	molIndex <= mpiSim->getMyMolEnd() ){
844	<	#endif // is_mpi
621	>	strcpy(info[i].mixingRule, globals->getMixingRule());
622	>	info[i].usePBC = globals->getPBC();
623	>	}
624
625	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
847	<
848	<	current_bend = comp_stamps[i]->getBend( k );
849	<	the_bends[index].a = current_bend->getA() + offset;
850	<	the_bends[index].b = current_bend->getB() + offset;
851	<	the_bends[index].c = current_bend->getC() + offset;
852	<
853	<	if( current_bend->haveExtras() ){
854	<
855	<	extras = current_bend->getExtras();
856	<	current_extra = extras;
857	<
858	<	while( current_extra != NULL ){
859	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
860	<
861	<	switch( current_extra->getType() ){
862	<
863	<	case 0:
864	<	the_bends[index].ghost =
865	<	current_extra->getInt() + offset;
866	<	the_bends[index].isGhost = 1;
867	<	break;
868	<
869	<	case 1:
870	<	the_bends[index].ghost =
871	<	(int)current_extra->getDouble() + offset;
872	<	the_bends[index].isGhost = 1;
873	<	break;
874	<
875	<	default:
876	<	sprintf( painCave.errMsg,
877	<	"SimSetup Error: ghostVectorSource was neiter a "
878	<	"double nor an int.\n"
879	<	"-->Bend[%d] in %s\n",
880	<	k, comp_stamps[i]->getID() );
881	<	painCave.isFatal = 1;
882	<	simError();
883	<	}
884	<	}
885	<
886	<	else{
887	<
888	<	sprintf( painCave.errMsg,
889	<	"SimSetup Error: unhandled bend assignment:\n"
890	<	"    -->%s in Bend[%d] in %s\n",
891	<	current_extra->getlhs(),
892	<	k, comp_stamps[i]->getID() );
893	<	painCave.isFatal = 1;
894	<	simError();
895	<	}
896	<
897	<	current_extra = current_extra->getNext();
898	<	}
899	<	}
900	<
901	<	if( !the_bends[index].isGhost ){
902	<
903	<	exI = the_bends[index].a;
904	<	exJ = the_bends[index].c;
905	<	}
906	<	else{
907	<
908	<	exI = the_bends[index].a;
909	<	exJ = the_bends[index].b;
910	<	}
911	<
912	<	// exclude_I must always be the smaller of the pair
913	<	if( exI > exJ ){
914	<	tempEx = exI;
915	<	exI = exJ;
916	<	exJ = tempEx;
917	<	}
625	>	// get the components and calculate the tot_nMol and indvidual n_mol
626
627	+	the_components = globals->getComponents();
628	+	components_nmol = new int[n_components];
629
920	–	#ifdef IS_MPI
630
631	<	the_excludes[(index + tot_bonds)*2] =
632	<	the_atoms[exI]->getGlobalIndex() + 1;
633	<	the_excludes[(index + tot_bonds)*2 + 1] =
634	<	the_atoms[exJ]->getGlobalIndex() + 1;
635	<
636	<	#else  // isn't MPI
637	<
638	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
639	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
640	<	// fortran index from 1 (hence the +1 in the indexing)
641	<	#endif  //is_mpi
642	<
643	<
935	<	// increment the index and repeat;
936	<	index++;
937	<	}
938	<	offset += comp_stamps[i]->getNAtoms();
939	<
940	<	#ifdef IS_MPI
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		}
942	–	#endif //is_mpi
645
646	<	molIndex++;
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	<	#ifdef IS_MPI
949	<	sprintf( checkPointMsg,
950	<	"Successfully created the bends list.\n" );
951	<	MPIcheckPoint();
952	<	#endif // is_mpi
953	<
661	>	// set the status, sample, and thermal kick times
662
663	<	the_ff->initializeBends( the_bends );
664	<	}
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	<	void SimSetup::makeTorsions( void ){
675	>	if (globals->haveStatusTime()){
676	>	info[i].statusTime = globals->getStatusTime();
677	>	}
678
679	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
680	<	torsion_set* the_torsions;
681	<	TorsionStamp* current_torsion;
679	>	if (globals->haveThermalTime()){
680	>	info[i].thermalTime = globals->getThermalTime();
681	>	}
682
683	<	the_torsions = new torsion_set[tot_torsions];
684	<	index = 0;
685	<	offset = 0;
686	<	molIndex = 0;
687	<	for( i=0; i<n_components; i++ ){
683	>	info[i].resetIntegrator = 0;
684	>	if( globals->haveResetTime() ){
685	>	info[i].resetTime = globals->getResetTime();
686	>	info[i].resetIntegrator = 1;
687	>	}
688
689	<	for( j=0; j<components_nmol[i]; j++ ){
689	>	// check for the temperature set flag
690
691	<	#ifdef IS_MPI
692	<	if( mpiSim->getMyMolStart() <= molIndex &&
974	<	molIndex <= mpiSim->getMyMolEnd() ){
975	<	#endif // is_mpi
691	>	if (globals->haveTempSet())
692	>	info[i].setTemp = globals->getTempSet();
693
694	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
694	>	// get some of the tricky things that may still be in the globals
695
696	<	current_torsion = comp_stamps[i]->getTorsion( k );
697	<	the_torsions[index].a = current_torsion->getA() + offset;
698	<	the_torsions[index].b = current_torsion->getB() + offset;
699	<	the_torsions[index].c = current_torsion->getC() + offset;
700	<	the_torsions[index].d = current_torsion->getD() + offset;
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	<	exI = the_torsions[index].a;
703	<	exJ = the_torsions[index].d;
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	<
712	<	// exclude_I must always be the smaller of the pair
713	<	if( exI > exJ ){
714	<	tempEx = exI;
715	<	exI = exJ;
716	<	exJ = tempEx;
717	<	}
711	>	info[i].setBox(boxVector);
712	>	}
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	<
723	<	#ifdef IS_MPI
724	<
725	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
726	<	the_atoms[exI]->getGlobalIndex() + 1;
1001	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1002	<	the_atoms[exJ]->getGlobalIndex() + 1;
1003	<
1004	<	#else  // isn't MPI
1005	<
1006	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1007	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1008	<	// fortran indexes from 1 (hence the +1 in the indexing)
1009	<	#endif  //is_mpi
1010	<
1011	<
1012	<	// increment the index and repeat;
1013	<	index++;
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	<	offset += comp_stamps[i]->getNAtoms();
728	>	boxVector[1] = globals->getBoxY();
729
730	<	#ifdef IS_MPI
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	<	#endif //is_mpi
736	>	boxVector[2] = globals->getBoxZ();
737
738	<	molIndex++;
738	>	info[i].setBox(boxVector);
739		}
740		}
741
742	<	the_ff->initializeTorsions( the_torsions );
743	<	}
742	>	//setup seed for random number generator
743	>	int seedValue;
744
745	<	void SimSetup::initFromBass( void ){
745	>	if (globals->haveSeed()){
746	>	seedValue = globals->getSeed();
747
748	<	int i, j, k;
749	<	int n_cells;
750	<	double cellx, celly, cellz;
751	<	double temp1, temp2, temp3;
752	<	int n_per_extra;
1035	<	int n_extra;
1036	<	int have_extra, done;
1037	<
1038	<	temp1 = (double)tot_nmol / 4.0;
1039	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1040	<	temp3 = ceil( temp2 );
1041	<
1042	<	have_extra =0;
1043	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1044	<	have_extra =1;
1045	<
1046	<	n_cells = (int)temp3 - 1;
1047	<	cellx = simnfo->box_x / temp3;
1048	<	celly = simnfo->box_y / temp3;
1049	<	cellz = simnfo->box_z / temp3;
1050	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1051	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1052	<	n_per_extra = (int)ceil( temp1 );
1053	<
1054	<	if( n_per_extra > 4){
1055	<	sprintf( painCave.errMsg,
1056	<	"SimSetup error. There has been an error in constructing"
1057	<	" the non-complete lattice.\n" );
1058	<	painCave.isFatal = 1;
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	<	}
765	>	}//end of if branch of globals->haveSeed()
766		else{
767	<	n_cells = (int)temp3;
768	<	cellx = simnfo->box_x / temp3;
769	<	celly = simnfo->box_y / temp3;
770	<	cellz = simnfo->box_z / temp3;
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	<	current_mol = 0;
783	<	current_comp_mol = 0;
784	<	current_comp = 0;
785	<	current_atom_ndx = 0;
782	>	#ifdef IS_MPI
783	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
784	>	MPIcheckPoint();
785	>	#endif // is_mpi
786	>	}
787
1074	–	for( i=0; i < n_cells ; i++ ){
1075	–	for( j=0; j < n_cells; j++ ){
1076	–	for( k=0; k < n_cells; k++ ){
788
789	<	makeElement( i * cellx,
790	<	j * celly,
791	<	k * cellz );
789	>	void SimSetup::finalInfoCheck(void){
790	>	int index;
791	>	int usesDipoles;
792	>	int i;
793
794	<	makeElement( i * cellx + 0.5 * cellx,
795	<	j * celly + 0.5 * celly,
1084	<	k * cellz );
794	>	for (i = 0; i < nInfo; i++){
795	>	// check electrostatic parameters
796
797	<	makeElement( i * cellx,
798	<	j * celly + 0.5 * celly,
799	<	k * cellz + 0.5 * cellz );
800	<
801	<	makeElement( i * cellx + 0.5 * cellx,
1091	<	j * celly,
1092	<	k * cellz + 0.5 * cellz );
1093	<	}
797	>	index = 0;
798	>	usesDipoles = 0;
799	>	while ((index < info[i].n_atoms) && !usesDipoles){
800	>	usesDipoles = (info[i].atoms[index])->hasDipole();
801	>	index++;
802		}
1095	–	}
803
804	<	if( have_extra ){
805	<	done = 0;
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	<	int start_ndx;
1101	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1102	<	for( j=0; j < (n_cells+1) && !done; j++ ){
809	>	double theEcr, theEst;
810
811	<	if( i < n_cells ){
811	>	if (globals->getUseRF()){
812	>	info[i].useReactionField = 1;
813
814	<	if( j < n_cells ){
815	<	start_ndx = n_cells;
816	<	}
817	<	else start_ndx = 0;
818	<	}
819	<	else start_ndx = 0;
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	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
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	<	makeElement( i * cellx,
1116	<	j * celly,
1117	<	k * cellz );
1118	<	done = ( current_mol >= tot_nmol );
845	>	info[i].setEcr(theEcr, theEst);
846
847	<	if( !done && n_per_extra > 1 ){
848	<	makeElement( i * cellx + 0.5 * cellx,
849	<	j * celly + 0.5 * celly,
850	<	k * cellz );
851	<	done = ( current_mol >= tot_nmol );
852	<	}
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	>	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( !done && n_per_extra > 2){
878	<	makeElement( i * cellx,
879	<	j * celly + 0.5 * celly,
880	<	k * cellz + 0.5 * cellz );
881	<	done = ( current_mol >= tot_nmol );
882	<	}
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	<	if( !done && n_per_extra > 3){
1135	<	makeElement( i * cellx + 0.5 * cellx,
1136	<	j * celly,
1137	<	k * cellz + 0.5 * cellz );
1138	<	done = ( current_mol >= tot_nmol );
1139	<	}
1140	<	}
890	>	info[i].setEcr(theEcr, theEst);
891		}
892		}
893		}
894
895	<
896	<	for( i=0; i<simnfo->n_atoms; i++ ){
897	<	simnfo->atoms[i]->set_vx( 0.0 );
898	<	simnfo->atoms[i]->set_vy( 0.0 );
1149	<	simnfo->atoms[i]->set_vz( 0.0 );
1150	<	}
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;
1156	<	AtomStamp* current_atom;
1157	<	DirectionalAtom* dAtom;
1158	<	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];
933	>	sprintf(painCave.errMsg,
934	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
935	>	painCave.isFatal;
936	>	simError();
937
938	<	rotMat[0][0] = 1.0;
1184	<	rotMat[0][1] = 0.0;
1185	<	rotMat[0][2] = 0.0;
938	>	#else
939
940	<	rotMat[1][0] = 0.0;
1188	<	rotMat[1][1] = 1.0;
1189	<	rotMat[1][2] = 0.0;
940	>	initFromBass();
941
1191	–	rotMat[2][0] = 0.0;
1192	–	rotMat[2][1] = 0.0;
1193	–	rotMat[2][2] = 1.0;
942
943	<	dAtom->setA( rotMat );
1196	<	}
1197	<
1198	<	current_atom_ndx++;
943	>	#endif
944		}
945
946	<	current_mol++;
947	<	current_comp_mol++;
946	>	#ifdef IS_MPI
947	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
948	>	MPIcheckPoint();
949	>	#endif // is_mpi
950	>	}
951
952	<	if( current_comp_mol >= components_nmol[current_comp] ){
952	>
953	>	void SimSetup::makeOutNames(void){
954	>	int k;
955
956	<	current_comp_mol = 0;
957	<	current_comp++;
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	+
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	+
1082	+
1083	+	void SimSetup::createFF(void){
1084	+	switch (ffCase){
1085	+	case FF_DUFF:
1086	+	the_ff = new DUFF();
1087	+	break;
1088	+
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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