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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 469 by mmeineke, Mon Apr 7 20:06:31 2003 UTC vs.
Revision 843 by mmeineke, Wed Oct 29 20:41:39 2003 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTxyz_ENS     4
25	+
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	initSuspend = false;
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41	<
41	>
42	>
43		#ifdef IS_MPI
44	<	strcpy( checkPointMsg, "SimSetup creation successful" );
44	>	strcpy(checkPointMsg, "SimSetup creation successful");
45		MPIcheckPoint();
46		#endif // IS_MPI
47		}
#	Line 27 | Line 51 | SimSetup::~SimSetup(){
51		delete globals;
52		}
53
54	<	void SimSetup::parseFile( char* fileName ){
54	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
55	>	info = the_info;
56	>	nInfo = theNinfo;
57	>	isInfoArray = 1;
58	>	initSuspend = true;
59	>	}
60
61	+
62	+	void SimSetup::parseFile(char* fileName){
63		#ifdef IS_MPI
64	<	if( worldRank == 0 ){
64	>	if (worldRank == 0){
65		#endif // is_mpi
66	<
66	>
67		inFileName = fileName;
68	<	set_interface_stamps( stamps, globals );
69	<
68	>	set_interface_stamps(stamps, globals);
69	>
70		#ifdef IS_MPI
71		mpiEventInit();
72		#endif
73
74	<	yacc_BASS( fileName );
74	>	yacc_BASS(fileName);
75
76		#ifdef IS_MPI
77		throwMPIEvent(NULL);
78		}
79	<	else receiveParse();
79	>	else{
80	>	receiveParse();
81	>	}
82		#endif
83
84		}
85
86		#ifdef IS_MPI
87		void SimSetup::receiveParse(void){
88	<
89	<	set_interface_stamps( stamps, globals );
90	<	mpiEventInit();
91	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
88	>	set_interface_stamps(stamps, globals);
89	>	mpiEventInit();
90	>	MPIcheckPoint();
91	>	mpiEventLoop();
92		}
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
98	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
98	>	// gather all of the information from the Bass file
99
100	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
100	>	gatherInfo();
101
102	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	simnfo->run_time = the_globals->getRunTime();
102	>	// creation of complex system objects
103
104	<	// get the ones we know are there, yet still may need some work.
82	<	n_components = the_globals->getNComponents();
83	<	strcpy( force_field, the_globals->getForceField() );
104	>	sysObjectsCreation();
105
106	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
91	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
92	<	the_extendedsystem = new ExtendedSystem( simnfo );
93	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
94	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
95	<	} else {
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
98	<	"reverting to NVE for this simulation.\n",
99	<	ensemble );
100	<	painCave.isFatal = 0;
101	<	simError();
102	<	strcpy( ensemble, "NVE" );
103	<	}
104	<	strcpy( simnfo->ensemble, ensemble );
106	>	// initialize the system coordinates
107
108	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
109	<	simnfo->usePBC = the_globals->getPBC();
108	<
109	<	int usesDipoles = 0;
110	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
111	<	the_ff = new TraPPE_ExFF();
112	<	usesDipoles = 1;
113	<	}
114	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
115	<	else{
116	<	sprintf( painCave.errMsg,
117	<	"SimSetup Error. Unrecognized force field -> %s\n",
118	<	force_field );
119	<	painCave.isFatal = 1;
120	<	simError();
121	<	}
108	>	if ( !initSuspend ){
109	>	initSystemCoords();
110
111	<	#ifdef IS_MPI
112	<	strcpy( checkPointMsg, "ForceField creation successful" );
113	<	MPIcheckPoint();
126	<	#endif // is_mpi
111	>	if( !(globals->getUseInitTime()) )
112	>	info[0].currentTime = 0.0;
113	>	}
114
115	<
115	>	// check on the post processing info
116
117	<	// get the components and calculate the tot_nMol and indvidual n_mol
131	<	the_components = the_globals->getComponents();
132	<	components_nmol = new int[n_components];
133	<	comp_stamps = new MoleculeStamp*[n_components];
117	>	finalInfoCheck();
118
119	<	if( !the_globals->haveNMol() ){
136	<	// we don't have the total number of molecules, so we assume it is
137	<	// given in each component
119	>	// make the output filenames
120
121	<	tot_nmol = 0;
140	<	for( i=0; i<n_components; i++ ){
121	>	makeOutNames();
122
123	<	if( !the_components[i]->haveNMol() ){
143	<	// we have a problem
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Error. No global NMol or component NMol"
146	<	" given. Cannot calculate the number of atoms.\n" );
147	<	painCave.isFatal = 1;
148	<	simError();
149	<	}
123	>	// make the integrator
124
125	<	tot_nmol += the_components[i]->getNMol();
152	<	components_nmol[i] = the_components[i]->getNMol();
153	<	}
154	<	}
155	<	else{
156	<	sprintf( painCave.errMsg,
157	<	"SimSetup error.\n"
158	<	"\tSorry, the ability to specify total"
159	<	" nMols and then give molfractions in the components\n"
160	<	"\tis not currently supported."
161	<	" Please give nMol in the components.\n" );
162	<	painCave.isFatal = 1;
163	<	simError();
164	<
165	<
166	<	//     tot_nmol = the_globals->getNMol();
167	<
168	<	//   //we have the total number of molecules, now we check for molfractions
169	<	//     for( i=0; i<n_components; i++ ){
170	<
171	<	//       if( !the_components[i]->haveMolFraction() ){
172	<
173	<	//  if( !the_components[i]->haveNMol() ){
174	<	//    //we have a problem
175	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
176	<	//              << " nMol was given in component
177	<
178	<	}
125	>	makeIntegrator();
126
127		#ifdef IS_MPI
128	<	strcpy( checkPointMsg, "Have the number of components" );
129	<	MPIcheckPoint();
183	<	#endif // is_mpi
128	>	mpiSim->mpiRefresh();
129	>	#endif
130
131	<	// make an array of molecule stamps that match the components used.
186	<	// also extract the used stamps out into a separate linked list
131	>	// initialize the Fortran
132
133	<	simnfo->nComponents = n_components;
134	<	simnfo->componentsNmol = components_nmol;
190	<	simnfo->compStamps = comp_stamps;
191	<	simnfo->headStamp = new LinkedMolStamp();
192	<
193	<	char* id;
194	<	LinkedMolStamp* headStamp = simnfo->headStamp;
195	<	LinkedMolStamp* currentStamp = NULL;
196	<	for( i=0; i<n_components; i++ ){
133	>	initFortran();
134	>	}
135
198	–	id = the_components[i]->getType();
199	–	comp_stamps[i] = NULL;
200	–
201	–	// check to make sure the component isn't already in the list
136
137	<	comp_stamps[i] = headStamp->match( id );
138	<	if( comp_stamps[i] == NULL ){
139	<
140	<	// extract the component from the list;
141	<
142	<	currentStamp = the_stamps->extractMolStamp( id );
143	<	if( currentStamp == NULL ){
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup error: Component \"%s\" was not found in the "
146	<	"list of declared molecules\n",
147	<	id );
214	<	painCave.isFatal = 1;
215	<	simError();
216	<	}
217	<
218	<	headStamp->add( currentStamp );
219	<	comp_stamps[i] = headStamp->match( id );
220	<	}
221	<	}
137	>	void SimSetup::makeMolecules(void){
138	>	int k;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	#ifdef IS_MPI
150	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
151	<	MPIcheckPoint();
226	<	#endif // is_mpi
227	<
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
153
154	+	//init the forceField paramters
155
156	<	// caclulate the number of atoms, bonds, bends and torsions
156	>	the_ff->readParams();
157
233	–	tot_atoms = 0;
234	–	tot_bonds = 0;
235	–	tot_bends = 0;
236	–	tot_torsions = 0;
237	–	for( i=0; i<n_components; i++ ){
238	–
239	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
240	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
241	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
242	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
243	–	}
158
159	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
159	>	// init the atoms
160
161	<	simnfo->n_atoms = tot_atoms;
248	<	simnfo->n_bonds = tot_bonds;
249	<	simnfo->n_bends = tot_bends;
250	<	simnfo->n_torsions = tot_torsions;
251	<	simnfo->n_SRI = tot_SRI;
252	<	simnfo->n_mol = tot_nmol;
161	>	double ux, uy, uz, u, uSqr;
162
163	<
164	<	#ifdef IS_MPI
163	>	for (k = 0; k < nInfo; k++){
164	>	the_ff->setSimInfo(&(info[k]));
165
166	<	// divide the molecules among processors here.
167	<
168	<	mpiSim = new mpiSimulation( simnfo );
169	<
261	<
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for (i = 0; i < info[k].n_mol; i++){
169	>	stampID = info[k].molecules[i].getStampID();
170
171	<	globalIndex = mpiSim->divideLabor();
172	<
173	<	// set up the local variables
174	<
175	<	int localMol, allMol;
268	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
171	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
172	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
173	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
174	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
175	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
176
177	<	int* mol2proc = mpiSim->getMolToProcMap();
178	<	int* molCompType = mpiSim->getMolComponentType();
179	<
180	<	allMol = 0;
181	<	localMol = 0;
275	<	local_atoms = 0;
276	<	local_bonds = 0;
277	<	local_bends = 0;
278	<	local_torsions = 0;
279	<	for( i=0; i<n_components; i++ ){
177	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
178	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	>	molInfo.myBends = new Bend * [molInfo.nBends];
181	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
182
183	<	for( j=0; j<components_nmol[i]; j++ ){
184	<
185	<	if( mol2proc[j] == worldRank ){
284	<
285	<	local_atoms +=    comp_stamps[i]->getNAtoms();
286	<	local_bonds +=    comp_stamps[i]->getNBonds();
287	<	local_bends +=    comp_stamps[i]->getNBends();
288	<	local_torsions += comp_stamps[i]->getNTorsions();
289	<	localMol++;
290	<	}
291	<	allMol++;
292	<	}
293	<	}
294	<	local_SRI = local_bonds + local_bends + local_torsions;
295	<
183	>	theBonds = new bond_pair[molInfo.nBonds];
184	>	theBends = new bend_set[molInfo.nBends];
185	>	theTorsions = new torsion_set[molInfo.nTorsions];
186
187	<	simnfo->n_atoms = mpiSim->getMyNlocal();
298	<
299	<	if( local_atoms != simnfo->n_atoms ){
300	<	sprintf( painCave.errMsg,
301	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
302	<	" localAtom (%d) are not equal.\n",
303	<	simnfo->n_atoms,
304	<	local_atoms );
305	<	painCave.isFatal = 1;
306	<	simError();
307	<	}
187	>	// make the Atoms
188
189	<	simnfo->n_bonds = local_bonds;
190	<	simnfo->n_bends = local_bends;
191	<	simnfo->n_torsions = local_torsions;
192	<	simnfo->n_SRI = local_SRI;
193	<	simnfo->n_mol = localMol;
189	>	for (j = 0; j < molInfo.nAtoms; j++){
190	>	currentAtom = comp_stamps[stampID]->getAtom(j);
191	>	if (currentAtom->haveOrientation()){
192	>	dAtom = new DirectionalAtom((j + atomOffset),
193	>	info[k].getConfiguration());
194	>	info[k].n_oriented++;
195	>	molInfo.myAtoms[j] = dAtom;
196
197	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
198	<	MPIcheckPoint();
199	<
318	<
319	<	#endif // is_mpi
320	<
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200
201	<	// create the atom and short range interaction arrays
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202
203	<	Atom::createArrays(simnfo->n_atoms);
204	<	the_atoms = new Atom*[simnfo->n_atoms];
205	<	the_molecules = new Molecule[simnfo->n_mol];
206	<	int molIndex;
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207
208	<	// initialize the molecule's stampID's
208	>	dAtom->setSUx(ux);
209	>	dAtom->setSUy(uy);
210	>	dAtom->setSUz(uz);
211	>	}
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	>	info[k].getConfiguration());
215	>	}
216	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
217
218		#ifdef IS_MPI
332	–
219
220	<	molIndex = 0;
335	<	for(i=0; i<mpiSim->getTotNmol(); i++){
336	<
337	<	if(mol2proc[i] == worldRank ){
338	<	the_molecules[molIndex].setStampID( molCompType[i] );
339	<	the_molecules[molIndex].setMyIndex( molIndex );
340	<	molIndex++;
341	<	}
342	<	}
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221
344	–	#else // is_mpi
345	–
346	–	molIndex = 0;
347	–	for(i=0; i<n_components; i++){
348	–	for(j=0; j<components_nmol[i]; j++ ){
349	–	the_molecules[molIndex].setStampID( i );
350	–	the_molecules[molIndex].setMyIndex( molIndex );
351	–	molIndex++;
352	–	}
353	–	}
354	–
355	–
222		#endif // is_mpi
223	+	}
224
225	+	// make the bonds
226	+	for (j = 0; j < molInfo.nBonds; j++){
227	+	currentBond = comp_stamps[stampID]->getBond(j);
228	+	theBonds[j].a = currentBond->getA() + atomOffset;
229	+	theBonds[j].b = currentBond->getB() + atomOffset;
230
231	<	if( simnfo->n_SRI ){
232	<
361	<	Exclude::createArray(simnfo->n_SRI);
362	<	the_excludes = new Exclude*[simnfo->n_SRI];
363	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
364	<	simnfo->globalExcludes = new int;
365	<	simnfo->n_exclude = simnfo->n_SRI;
366	<	}
367	<	else{
368	<
369	<	Exclude::createArray( 1 );
370	<	the_excludes = new Exclude*;
371	<	the_excludes[0] = new Exclude(0);
372	<	the_excludes[0]->setPair( 0,0 );
373	<	simnfo->globalExcludes = new int;
374	<	simnfo->globalExcludes[0] = 0;
375	<	simnfo->n_exclude = 0;
376	<	}
231	>	exI = theBonds[j].a;
232	>	exJ = theBonds[j].b;
233
234	<	// set the arrays into the SimInfo object
234	>	// exclude_I must always be the smaller of the pair
235	>	if (exI > exJ){
236	>	tempEx = exI;
237	>	exI = exJ;
238	>	exJ = tempEx;
239	>	}
240	>	#ifdef IS_MPI
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245
246	<	simnfo->atoms = the_atoms;
247	<	simnfo->molecules = the_molecules;
382	<	simnfo->nGlobalExcludes = 0;
383	<	simnfo->excludes = the_excludes;
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	>	#else  // isn't MPI
248
249	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	+	#endif  //is_mpi
251	+	}
252	+	excludeOffset += molInfo.nBonds;
253
254	<	// get some of the tricky things that may still be in the globals
254	>	//make the bends
255	>	for (j = 0; j < molInfo.nBends; j++){
256	>	currentBend = comp_stamps[stampID]->getBend(j);
257	>	theBends[j].a = currentBend->getA() + atomOffset;
258	>	theBends[j].b = currentBend->getB() + atomOffset;
259	>	theBends[j].c = currentBend->getC() + atomOffset;
260
261	<
262	<	if( the_globals->haveBox() ){
263	<	simnfo->box_x = the_globals->getBox();
391	<	simnfo->box_y = the_globals->getBox();
392	<	simnfo->box_z = the_globals->getBox();
393	<	}
394	<	else if( the_globals->haveDensity() ){
261	>	if (currentBend->haveExtras()){
262	>	extras = currentBend->getExtras();
263	>	current_extra = extras;
264
265	<	double vol;
266	<	vol = (double)tot_nmol / the_globals->getDensity();
267	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
268	<	simnfo->box_y = simnfo->box_x;
269	<	simnfo->box_z = simnfo->box_x;
270	<	}
271	<	else{
403	<	if( !the_globals->haveBoxX() ){
404	<	sprintf( painCave.errMsg,
405	<	"SimSetup error, no periodic BoxX size given.\n" );
406	<	painCave.isFatal = 1;
407	<	simError();
408	<	}
409	<	simnfo->box_x = the_globals->getBoxX();
265	>	while (current_extra != NULL){
266	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
267	>	switch (current_extra->getType()){
268	>	case 0:
269	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272
273	<	if( !the_globals->haveBoxY() ){
274	<	sprintf( painCave.errMsg,
275	<	"SimSetup error, no periodic BoxY size given.\n" );
276	<	painCave.isFatal = 1;
277	<	simError();
278	<	}
279	<	simnfo->box_y = the_globals->getBoxY();
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278	>
279	>	default:
280	>	sprintf(painCave.errMsg,
281	>	"SimSetup Error: ghostVectorSource was neither a "
282	>	"double nor an int.\n"
283	>	"-->Bend[%d] in %s\n",
284	>	j, comp_stamps[stampID]->getID());
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>	}
289	>	else{
290	>	sprintf(painCave.errMsg,
291	>	"SimSetup Error: unhandled bend assignment:\n"
292	>	"    -->%s in Bend[%d] in %s\n",
293	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>
298	>	current_extra = current_extra->getNext();
299	>	}
300	>	}
301	>
302	>	if (!theBends[j].isGhost){
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].c;
305	>	}
306	>	else{
307	>	exI = theBends[j].a;
308	>	exJ = theBends[j].b;
309	>	}
310	>
311	>	// exclude_I must always be the smaller of the pair
312	>	if (exI > exJ){
313	>	tempEx = exI;
314	>	exI = exJ;
315	>	exJ = tempEx;
316	>	}
317	>	#ifdef IS_MPI
318	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322	>
323	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
324	>	#else  // isn't MPI
325	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
326	>	#endif  //is_mpi
327	>	}
328	>	excludeOffset += molInfo.nBends;
329	>
330	>	for (j = 0; j < molInfo.nTorsions; j++){
331	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
332	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
333	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
334	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
335	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
336
337	<	if( !the_globals->haveBoxZ() ){
338	<	sprintf( painCave.errMsg,
339	<	"SimSetup error, no periodic BoxZ size given.\n" );
340	<	painCave.isFatal = 1;
341	<	simError();
337	>	exI = theTorsions[j].a;
338	>	exJ = theTorsions[j].d;
339	>
340	>	// exclude_I must always be the smaller of the pair
341	>	if (exI > exJ){
342	>	tempEx = exI;
343	>	exI = exJ;
344	>	exJ = tempEx;
345	>	}
346	>	#ifdef IS_MPI
347	>	tempEx = exI;
348	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	>	tempEx = exJ;
350	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351	>
352	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
353	>	#else  // isn't MPI
354	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
355	>	#endif  //is_mpi
356	>	}
357	>	excludeOffset += molInfo.nTorsions;
358	>
359	>
360	>	// send the arrays off to the forceField for init.
361	>
362	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
363	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
364	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
365	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
366	>	theTorsions);
367	>
368	>
369	>	info[k].molecules[i].initialize(molInfo);
370	>
371	>
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376		}
425	–	simnfo->box_z = the_globals->getBoxZ();
377		}
378
379		#ifdef IS_MPI
380	<	strcpy( checkPointMsg, "Box size set up" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383
384	+	// clean up the forcefield
385
386	<	// initialize the arrays
386	>	the_ff->calcRcut();
387	>	the_ff->cleanMe();
388	>	}
389
390	<	the_ff->setSimInfo( simnfo );
390	>	void SimSetup::initFromBass(void){
391	>	int i, j, k;
392	>	int n_cells;
393	>	double cellx, celly, cellz;
394	>	double temp1, temp2, temp3;
395	>	int n_per_extra;
396	>	int n_extra;
397	>	int have_extra, done;
398
399	<	makeMolecules();
400	<	simnfo->identArray = new int[simnfo->n_atoms];
401	<	for(i=0; i<simnfo->n_atoms; i++){
402	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
442	<	}
443	<
444	<	if (the_globals->getUseRF() ) {
445	<	simnfo->useReactionField = 1;
446	<
447	<	if( !the_globals->haveECR() ){
448	<	sprintf( painCave.errMsg,
449	<	"SimSetup Warning: using default value of 1/2 the smallest "
450	<	"box length for the electrostaticCutoffRadius.\n"
451	<	"I hope you have a very fast processor!\n");
452	<	painCave.isFatal = 0;
453	<	simError();
454	<	double smallest;
455	<	smallest = simnfo->box_x;
456	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
457	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
458	<	simnfo->ecr = 0.5 * smallest;
459	<	} else {
460	<	simnfo->ecr        = the_globals->getECR();
461	<	}
399	>	double vel[3];
400	>	vel[0] = 0.0;
401	>	vel[1] = 0.0;
402	>	vel[2] = 0.0;
403
404	<	if( !the_globals->haveEST() ){
405	<	sprintf( painCave.errMsg,
406	<	"SimSetup Warning: using default value of 0.05 * the "
407	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
408	<	);
409	<	painCave.isFatal = 0;
410	<	simError();
411	<	simnfo->est = 0.05 * simnfo->ecr;
412	<	} else {
413	<	simnfo->est        = the_globals->getEST();
414	<	}
415	<
416	<	if(!the_globals->haveDielectric() ){
417	<	sprintf( painCave.errMsg,
418	<	"SimSetup Error: You are trying to use Reaction Field without"
419	<	"setting a dielectric constant!\n"
420	<	);
404	>	temp1 = (double) tot_nmol / 4.0;
405	>	temp2 = pow(temp1, (1.0 / 3.0));
406	>	temp3 = ceil(temp2);
407	>
408	>	have_extra = 0;
409	>	if (temp2 < temp3){
410	>	// we have a non-complete lattice
411	>	have_extra = 1;
412	>
413	>	n_cells = (int) temp3 - 1;
414	>	cellx = info[0].boxL[0] / temp3;
415	>	celly = info[0].boxL[1] / temp3;
416	>	cellz = info[0].boxL[2] / temp3;
417	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
418	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
419	>	n_per_extra = (int) ceil(temp1);
420	>
421	>	if (n_per_extra > 4){
422	>	sprintf(painCave.errMsg,
423	>	"SimSetup error. There has been an error in constructing"
424	>	" the non-complete lattice.\n");
425		painCave.isFatal = 1;
426		simError();
427		}
428	<	simnfo->dielectric = the_globals->getDielectric();
429	<	} else {
430	<	if (usesDipoles) {
431	<
432	<	if( !the_globals->haveECR() ){
433	<	sprintf( painCave.errMsg,
434	<	"SimSetup Warning: using default value of 1/2 the smallest "
490	<	"box length for the electrostaticCutoffRadius.\n"
491	<	"I hope you have a very fast processor!\n");
492	<	painCave.isFatal = 0;
493	<	simError();
494	<	double smallest;
495	<	smallest = simnfo->box_x;
496	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
497	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
498	<	simnfo->ecr = 0.5 * smallest;
499	<	} else {
500	<	simnfo->ecr        = the_globals->getECR();
501	<	}
502	<
503	<	if( !the_globals->haveEST() ){
504	<	sprintf( painCave.errMsg,
505	<	"SimSetup Warning: using default value of 5%% of the "
506	<	"electrostaticCutoffRadius for the "
507	<	"electrostaticSkinThickness\n"
508	<	);
509	<	painCave.isFatal = 0;
510	<	simError();
511	<	simnfo->est = 0.05 * simnfo->ecr;
512	<	} else {
513	<	simnfo->est        = the_globals->getEST();
514	<	}
515	<	}
516	<	}
428	>	}
429	>	else{
430	>	n_cells = (int) temp3;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434	>	}
435
436	<	#ifdef IS_MPI
437	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
438	<	MPIcheckPoint();
439	<	#endif // is_mpi
436	>	current_mol = 0;
437	>	current_comp_mol = 0;
438	>	current_comp = 0;
439	>	current_atom_ndx = 0;
440
441	<	if( the_globals->haveInitialConfig() ){
442	<
443	<	InitializeFromFile* fileInit;
444	<	#ifdef IS_MPI // is_mpi
527	<	if( worldRank == 0 ){
528	<	#endif //is_mpi
529	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
530	<	#ifdef IS_MPI
531	<	}else fileInit = new InitializeFromFile( NULL );
532	<	#endif
533	<	fileInit->read_xyz( simnfo ); // default velocities on
441	>	for (i = 0; i < n_cells ; i++){
442	>	for (j = 0; j < n_cells; j++){
443	>	for (k = 0; k < n_cells; k++){
444	>	makeElement(i * cellx, j * celly, k * cellz);
445
446	<	delete fileInit;
536	<	}
537	<	else{
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447
448	<	#ifdef IS_MPI
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449
450	<	// no init from bass
451	<
452	<	sprintf( painCave.errMsg,
453	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
545	<	painCave.isFatal;
546	<	simError();
547	<
548	<	#else
450	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
451	>	}
452	>	}
453	>	}
454
455	<	initFromBass();
455	>	if (have_extra){
456	>	done = 0;
457
458	+	int start_ndx;
459	+	for (i = 0; i < (n_cells + 1) && !done; i++){
460	+	for (j = 0; j < (n_cells + 1) && !done; j++){
461	+	if (i < n_cells){
462	+	if (j < n_cells){
463	+	start_ndx = n_cells;
464	+	}
465	+	else
466	+	start_ndx = 0;
467	+	}
468	+	else
469	+	start_ndx = 0;
470
471	<	#endif
472	<	}
471	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
472	>	makeElement(i * cellx, j * celly, k * cellz);
473	>	done = (current_mol >= tot_nmol);
474
475	<	#ifdef IS_MPI
476	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
477	<	MPIcheckPoint();
478	<	#endif // is_mpi
475	>	if (!done && n_per_extra > 1){
476	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
477	>	k * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	+	if (!done && n_per_extra > 2){
482	+	makeElement(i * cellx, j * celly + 0.5 * celly,
483	+	k * cellz + 0.5 * cellz);
484	+	done = (current_mol >= tot_nmol);
485	+	}
486
487	<
488	<
489	<
490	<
491	<
492	<	#ifdef IS_MPI
568	<	if( worldRank == 0 ){
569	<	#endif // is_mpi
570	<
571	<	if( the_globals->haveFinalConfig() ){
572	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
573	<	}
574	<	else{
575	<	strcpy( simnfo->finalName, inFileName );
576	<	char* endTest;
577	<	int nameLength = strlen( simnfo->finalName );
578	<	endTest = &(simnfo->finalName[nameLength - 5]);
579	<	if( !strcmp( endTest, ".bass" ) ){
580	<	strcpy( endTest, ".eor" );
487	>	if (!done && n_per_extra > 3){
488	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
489	>	k * cellz + 0.5 * cellz);
490	>	done = (current_mol >= tot_nmol);
491	>	}
492	>	}
493		}
582	–	else if( !strcmp( endTest, ".BASS" ) ){
583	–	strcpy( endTest, ".eor" );
584	–	}
585	–	else{
586	–	endTest = &(simnfo->finalName[nameLength - 4]);
587	–	if( !strcmp( endTest, ".bss" ) ){
588	–	strcpy( endTest, ".eor" );
589	–	}
590	–	else if( !strcmp( endTest, ".mdl" ) ){
591	–	strcpy( endTest, ".eor" );
592	–	}
593	–	else{
594	–	strcat( simnfo->finalName, ".eor" );
595	–	}
596	–	}
494		}
598	–
599	–	// make the sample and status out names
600	–
601	–	strcpy( simnfo->sampleName, inFileName );
602	–	char* endTest;
603	–	int nameLength = strlen( simnfo->sampleName );
604	–	endTest = &(simnfo->sampleName[nameLength - 5]);
605	–	if( !strcmp( endTest, ".bass" ) ){
606	–	strcpy( endTest, ".dump" );
607	–	}
608	–	else if( !strcmp( endTest, ".BASS" ) ){
609	–	strcpy( endTest, ".dump" );
610	–	}
611	–	else{
612	–	endTest = &(simnfo->sampleName[nameLength - 4]);
613	–	if( !strcmp( endTest, ".bss" ) ){
614	–	strcpy( endTest, ".dump" );
615	–	}
616	–	else if( !strcmp( endTest, ".mdl" ) ){
617	–	strcpy( endTest, ".dump" );
618	–	}
619	–	else{
620	–	strcat( simnfo->sampleName, ".dump" );
621	–	}
622	–	}
623	–
624	–	strcpy( simnfo->statusName, inFileName );
625	–	nameLength = strlen( simnfo->statusName );
626	–	endTest = &(simnfo->statusName[nameLength - 5]);
627	–	if( !strcmp( endTest, ".bass" ) ){
628	–	strcpy( endTest, ".stat" );
629	–	}
630	–	else if( !strcmp( endTest, ".BASS" ) ){
631	–	strcpy( endTest, ".stat" );
632	–	}
633	–	else{
634	–	endTest = &(simnfo->statusName[nameLength - 4]);
635	–	if( !strcmp( endTest, ".bss" ) ){
636	–	strcpy( endTest, ".stat" );
637	–	}
638	–	else if( !strcmp( endTest, ".mdl" ) ){
639	–	strcpy( endTest, ".stat" );
640	–	}
641	–	else{
642	–	strcat( simnfo->statusName, ".stat" );
643	–	}
644	–	}
645	–
646	–	#ifdef IS_MPI
495		}
648	–	#endif // is_mpi
649	–
650	–	// set the status, sample, and themal kick times
651	–
652	–	if( the_globals->haveSampleTime() ){
653	–	simnfo->sampleTime = the_globals->getSampleTime();
654	–	simnfo->statusTime = simnfo->sampleTime;
655	–	simnfo->thermalTime = simnfo->sampleTime;
656	–	}
657	–	else{
658	–	simnfo->sampleTime = the_globals->getRunTime();
659	–	simnfo->statusTime = simnfo->sampleTime;
660	–	simnfo->thermalTime = simnfo->sampleTime;
661	–	}
496
497	<	if( the_globals->haveStatusTime() ){
498	<	simnfo->statusTime = the_globals->getStatusTime();
497	>	for (i = 0; i < info[0].n_atoms; i++){
498	>	info[0].atoms[i]->setVel(vel);
499		}
500	+	}
501
502	<	if( the_globals->haveThermalTime() ){
503	<	simnfo->thermalTime = the_globals->getThermalTime();
504	<	}
502	>	void SimSetup::makeElement(double x, double y, double z){
503	>	int k;
504	>	AtomStamp* current_atom;
505	>	DirectionalAtom* dAtom;
506	>	double rotMat[3][3];
507	>	double pos[3];
508
509	<	// check for the temperature set flag
509	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
510	>	current_atom = comp_stamps[current_comp]->getAtom(k);
511	>	if (!current_atom->havePosition()){
512	>	sprintf(painCave.errMsg,
513	>	"SimSetup:initFromBass error.\n"
514	>	"\tComponent %s, atom %s does not have a position specified.\n"
515	>	"\tThe initialization routine is unable to give a start"
516	>	" position.\n",
517	>	comp_stamps[current_comp]->getID(), current_atom->getType());
518	>	painCave.isFatal = 1;
519	>	simError();
520	>	}
521
522	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
522	>	pos[0] = x + current_atom->getPosX();
523	>	pos[1] = y + current_atom->getPosY();
524	>	pos[2] = z + current_atom->getPosZ();
525
526	+	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<	//   // make the longe range forces and the integrator
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530
531	<	//   new AllLong( simnfo );
531	>	rotMat[0][0] = 1.0;
532	>	rotMat[0][1] = 0.0;
533	>	rotMat[0][2] = 0.0;
534
535	+	rotMat[1][0] = 0.0;
536	+	rotMat[1][1] = 1.0;
537	+	rotMat[1][2] = 0.0;
538
539	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
540	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
541	<	std::cerr << "called new Symplecic\n";
684	<	fprintf( stderr, "called new Symplectic. stderr\n" );
685	<	}
686	<	else if( !strcmp( force_field, "LJ" ) ){
687	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
688	<	std::cerr << "called new Verlet\n";
689	<	fprintf( stderr, "called new Verlet. stderr\n" );
690	<	}
691	<	else {
692	<	std::cerr << "I'm a bug.\n";
693	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
694	<	}
695	<	#ifdef IS_MPI
696	<	mpiSim->mpiRefresh();
697	<	#endif
539	>	rotMat[2][0] = 0.0;
540	>	rotMat[2][1] = 0.0;
541	>	rotMat[2][2] = 1.0;
542
543	<	// initialize the Fortran
543	>	dAtom->setA(rotMat);
544	>	}
545
546	<
702	<	simnfo->refreshSim();
703	<
704	<	if( !strcmp( simnfo->mixingRule, "standard") ){
705	<	the_ff->initForceField( LB_MIXING_RULE );
546	>	current_atom_ndx++;
547		}
707	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
708	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
709	–	}
710	–	else{
711	–	sprintf( painCave.errMsg,
712	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
713	–	simnfo->mixingRule );
714	–	painCave.isFatal = 1;
715	–	simError();
716	–	}
548
549	+	current_mol++;
550	+	current_comp_mol++;
551
552	<	#ifdef IS_MPI
553	<	strcpy( checkPointMsg,
554	<	"Successfully intialized the mixingRule for Fortran." );
555	<	MPIcheckPoint();
723	<	#endif // is_mpi
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553	>	current_comp_mol = 0;
554	>	current_comp++;
555	>	}
556		}
557
558
559	<	void SimSetup::makeMolecules( void ){
559	>	void SimSetup::gatherInfo(void){
560	>	int i;
561
562	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
563	<	molInit info;
731	<	DirectionalAtom* dAtom;
732	<	LinkedAssign* extras;
733	<	LinkedAssign* current_extra;
734	<	AtomStamp* currentAtom;
735	<	BondStamp* currentBond;
736	<	BendStamp* currentBend;
737	<	TorsionStamp* currentTorsion;
562	>	ensembleCase = -1;
563	>	ffCase = -1;
564
565	<	bond_pair* theBonds;
740	<	bend_set* theBends;
741	<	torsion_set* theTorsions;
565	>	// set the easy ones first
566
567	<
568	<	//init the forceField paramters
567	>	for (i = 0; i < nInfo; i++){
568	>	info[i].target_temp = globals->getTargetTemp();
569	>	info[i].dt = globals->getDt();
570	>	info[i].run_time = globals->getRunTime();
571	>	}
572	>	n_components = globals->getNComponents();
573
746	–	the_ff->readParams();
574
575	<
749	<	// init the atoms
575	>	// get the forceField
576
577	<	double ux, uy, uz, u, uSqr;
752	<
753	<	atomOffset = 0;
754	<	excludeOffset = 0;
755	<	for(i=0; i<simnfo->n_mol; i++){
756	<
757	<	stampID = the_molecules[i].getStampID();
577	>	strcpy(force_field, globals->getForceField());
578
579	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
580	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
581	<	info.nBends    = comp_stamps[stampID]->getNBends();
582	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
583	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
579	>	if (!strcasecmp(force_field, "DUFF")){
580	>	ffCase = FF_DUFF;
581	>	}
582	>	else if (!strcasecmp(force_field, "LJ")){
583	>	ffCase = FF_LJ;
584	>	}
585	>	else if (!strcasecmp(force_field, "EAM")){
586	>	ffCase = FF_EAM;
587	>	}
588	>	else{
589	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
590	>	force_field);
591	>	painCave.isFatal = 1;
592	>	simError();
593	>	}
594
595	<	info.myAtoms = &the_atoms[atomOffset];
766	<	info.myExcludes = &the_excludes[excludeOffset];
767	<	info.myBonds = new Bond*[info.nBonds];
768	<	info.myBends = new Bend*[info.nBends];
769	<	info.myTorsions = new Torsion*[info.nTorsions];
595	>	// get the ensemble
596
597	<	theBonds = new bond_pair[info.nBonds];
772	<	theBends = new bend_set[info.nBends];
773	<	theTorsions = new torsion_set[info.nTorsions];
774	<
775	<	// make the Atoms
776	<
777	<	for(j=0; j<info.nAtoms; j++){
778	<
779	<	currentAtom = comp_stamps[stampID]->getAtom( j );
780	<	if( currentAtom->haveOrientation() ){
781	<
782	<	dAtom = new DirectionalAtom(j + atomOffset);
783	<	simnfo->n_oriented++;
784	<	info.myAtoms[j] = dAtom;
785	<
786	<	ux = currentAtom->getOrntX();
787	<	uy = currentAtom->getOrntY();
788	<	uz = currentAtom->getOrntZ();
789	<
790	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
791	<
792	<	u = sqrt( uSqr );
793	<	ux = ux / u;
794	<	uy = uy / u;
795	<	uz = uz / u;
796	<
797	<	dAtom->setSUx( ux );
798	<	dAtom->setSUy( uy );
799	<	dAtom->setSUz( uz );
800	<	}
801	<	else{
802	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
803	<	}
804	<	info.myAtoms[j]->setType( currentAtom->getType() );
805	<
806	<	#ifdef IS_MPI
807	<
808	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
809	<
810	<	#endif // is_mpi
811	<	}
812	<
813	<	// make the bonds
814	<	for(j=0; j<info.nBonds; j++){
815	<
816	<	currentBond = comp_stamps[stampID]->getBond( j );
817	<	theBonds[j].a = currentBond->getA() + atomOffset;
818	<	theBonds[j].b = currentBond->getB() + atomOffset;
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	<	exI = theBonds[j].a;
600	<	exJ = theBonds[j].b;
599	>	if (!strcasecmp(ensemble, "NVE")){
600	>	ensembleCase = NVE_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NVT")){
603	>	ensembleCase = NVT_ENS;
604	>	}
605	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
606	>	ensembleCase = NPTi_ENS;
607	>	}
608	>	else if (!strcasecmp(ensemble, "NPTf")){
609	>	ensembleCase = NPTf_ENS;
610	>	}
611	>	else if (!strcasecmp(ensemble, "NPTxyz")){
612	>	ensembleCase = NPTxyz_ENS;
613	>	}
614	>	else{
615	>	sprintf(painCave.errMsg,
616	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	>	"reverting to NVE for this simulation.\n",
618	>	ensemble);
619	>	painCave.isFatal = 0;
620	>	simError();
621	>	strcpy(ensemble, "NVE");
622	>	ensembleCase = NVE_ENS;
623	>	}
624
625	<	// exclude_I must always be the smaller of the pair
626	<	if( exI > exJ ){
627	<	tempEx = exI;
628	<	exI = exJ;
629	<	exJ = tempEx;
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627	>
628	>	// get the mixing rule
629	>
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632	>	}
633	>
634	>	// get the components and calculate the tot_nMol and indvidual n_mol
635	>
636	>	the_components = globals->getComponents();
637	>	components_nmol = new int[n_components];
638	>
639	>
640	>	if (!globals->haveNMol()){
641	>	// we don't have the total number of molecules, so we assume it is
642	>	// given in each component
643	>
644	>	tot_nmol = 0;
645	>	for (i = 0; i < n_components; i++){
646	>	if (!the_components[i]->haveNMol()){
647	>	// we have a problem
648	>	sprintf(painCave.errMsg,
649	>	"SimSetup Error. No global NMol or component NMol"
650	>	" given. Cannot calculate the number of atoms.\n");
651	>	painCave.isFatal = 1;
652	>	simError();
653		}
829	–	#ifdef IS_MPI
830	–	tempEx = exI;
831	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
832	–	tempEx = exJ;
833	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
834	–
835	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
836	–	#else  // isn't MPI
654
655	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
656	<	#endif  //is_mpi
655	>	tot_nmol += the_components[i]->getNMol();
656	>	components_nmol[i] = the_components[i]->getNMol();
657		}
658	<	excludeOffset += info.nBonds;
658	>	}
659	>	else{
660	>	sprintf(painCave.errMsg,
661	>	"SimSetup error.\n"
662	>	"\tSorry, the ability to specify total"
663	>	" nMols and then give molfractions in the components\n"
664	>	"\tis not currently supported."
665	>	" Please give nMol in the components.\n");
666	>	painCave.isFatal = 1;
667	>	simError();
668	>	}
669
670	<	//make the bends
671	<	for(j=0; j<info.nBends; j++){
672	<
673	<	currentBend = comp_stamps[stampID]->getBend( j );
674	<	theBends[j].a = currentBend->getA() + atomOffset;
675	<	theBends[j].b = currentBend->getB() + atomOffset;
676	<	theBends[j].c = currentBend->getC() + atomOffset;
850	<
851	<	if( currentBend->haveExtras() ){
852	<
853	<	extras = currentBend->getExtras();
854	<	current_extra = extras;
855	<
856	<	while( current_extra != NULL ){
857	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
858	<
859	<	switch( current_extra->getType() ){
860	<
861	<	case 0:
862	<	theBends[j].ghost =
863	<	current_extra->getInt() + atomOffset;
864	<	theBends[j].isGhost = 1;
865	<	break;
866	<
867	<	case 1:
868	<	theBends[j].ghost =
869	<	(int)current_extra->getDouble() + atomOffset;
870	<	theBends[j].isGhost = 1;
871	<	break;
872	<
873	<	default:
874	<	sprintf( painCave.errMsg,
875	<	"SimSetup Error: ghostVectorSource was neither a "
876	<	"double nor an int.\n"
877	<	"-->Bend[%d] in %s\n",
878	<	j, comp_stamps[stampID]->getID() );
879	<	painCave.isFatal = 1;
880	<	simError();
881	<	}
882	<	}
883	<
884	<	else{
885	<
886	<	sprintf( painCave.errMsg,
887	<	"SimSetup Error: unhandled bend assignment:\n"
888	<	"    -->%s in Bend[%d] in %s\n",
889	<	current_extra->getlhs(),
890	<	j, comp_stamps[stampID]->getID() );
891	<	painCave.isFatal = 1;
892	<	simError();
893	<	}
894	<
895	<	current_extra = current_extra->getNext();
896	<	}
897	<	}
898	<
899	<	if( !theBends[j].isGhost ){
900	<
901	<	exI = theBends[j].a;
902	<	exJ = theBends[j].c;
903	<	}
904	<	else{
905	<
906	<	exI = theBends[j].a;
907	<	exJ = theBends[j].b;
908	<	}
909	<
910	<	// exclude_I must always be the smaller of the pair
911	<	if( exI > exJ ){
912	<	tempEx = exI;
913	<	exI = exJ;
914	<	exJ = tempEx;
915	<	}
916	<	#ifdef IS_MPI
917	<	tempEx = exI;
918	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
919	<	tempEx = exJ;
920	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
921	<
922	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
923	<	#else  // isn't MPI
924	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
925	<	#endif  //is_mpi
670	>	// set the status, sample, and thermal kick times
671	>
672	>	for (i = 0; i < nInfo; i++){
673	>	if (globals->haveSampleTime()){
674	>	info[i].sampleTime = globals->getSampleTime();
675	>	info[i].statusTime = info[i].sampleTime;
676	>	info[i].thermalTime = info[i].sampleTime;
677		}
678	<	excludeOffset += info.nBends;
678	>	else{
679	>	info[i].sampleTime = globals->getRunTime();
680	>	info[i].statusTime = info[i].sampleTime;
681	>	info[i].thermalTime = info[i].sampleTime;
682	>	}
683
684	<	for(j=0; j<info.nTorsions; j++){
685	<
686	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
932	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
933	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
934	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
935	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
936	<
937	<	exI = theTorsions[j].a;
938	<	exJ = theTorsions[j].d;
684	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686	>	}
687
688	<	// exclude_I must always be the smaller of the pair
689	<	if( exI > exJ ){
942	<	tempEx = exI;
943	<	exI = exJ;
944	<	exJ = tempEx;
945	<	}
946	<	#ifdef IS_MPI
947	<	tempEx = exI;
948	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
949	<	tempEx = exJ;
950	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
951	<
952	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
953	<	#else  // isn't MPI
954	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
955	<	#endif  //is_mpi
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690		}
957	–	excludeOffset += info.nTorsions;
691
692	+	info[i].resetIntegrator = 0;
693	+	if( globals->haveResetTime() ){
694	+	info[i].resetTime = globals->getResetTime();
695	+	info[i].resetIntegrator = 1;
696	+	}
697	+
698	+	// check for the temperature set flag
699
700	<	// send the arrays off to the forceField for init.
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702	>
703	>	}
704	>
705	>	//setup seed for random number generator
706	>	int seedValue;
707
708	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
709	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
964	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
965	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
708	>	if (globals->haveSeed()){
709	>	seedValue = globals->getSeed();
710
711	+	if(seedValue / 1E9 == 0){
712	+	sprintf(painCave.errMsg,
713	+	"Seed for sprng library should contain at least 9 digits\n"
714	+	"OOPSE will generate a seed for user\n");
715	+	painCave.isFatal = 0;
716	+	simError();
717
718	<	the_molecules[i].initialize( info );
718	>	//using seed generated by system instead of invalid seed set by user
719	>	#ifndef IS_MPI
720	>	seedValue = make_sprng_seed();
721	>	#else
722	>	if (worldRank == 0){
723	>	seedValue = make_sprng_seed();
724	>	}
725	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
726	>	#endif
727	>	}
728	>	}//end of if branch of globals->haveSeed()
729	>	else{
730	>
731	>	#ifndef IS_MPI
732	>	seedValue = make_sprng_seed();
733	>	#else
734	>	if (worldRank == 0){
735	>	seedValue = make_sprng_seed();
736	>	}
737	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
738	>	#endif
739	>	}//end of globals->haveSeed()
740
741	<
742	<	atomOffset += info.nAtoms;
972	<	delete[] theBonds;
973	<	delete[] theBends;
974	<	delete[] theTorsions;
741	>	for (int i = 0; i < nInfo; i++){
742	>	info[i].setSeed(seedValue);
743		}
744
745		#ifdef IS_MPI
746	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
746	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
747		MPIcheckPoint();
748		#endif // is_mpi
749	+	}
750
751	<	// clean up the forcefield
752	<	the_ff->calcRcut();
753	<	the_ff->cleanMe();
751	>
752	>	void SimSetup::finalInfoCheck(void){
753	>	int index;
754	>	int usesDipoles;
755	>	int i;
756	>
757	>	for (i = 0; i < nInfo; i++){
758	>	// check electrostatic parameters
759
760	<	}
760	>	index = 0;
761	>	usesDipoles = 0;
762	>	while ((index < info[i].n_atoms) && !usesDipoles){
763	>	usesDipoles = (info[i].atoms[index])->hasDipole();
764	>	index++;
765	>	}
766
767	<	void SimSetup::initFromBass( void ){
767	>	#ifdef IS_MPI
768	>	int myUse = usesDipoles;
769	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>	#endif //is_mpi
771
772	<	int i, j, k;
991	<	int n_cells;
992	<	double cellx, celly, cellz;
993	<	double temp1, temp2, temp3;
994	<	int n_per_extra;
995	<	int n_extra;
996	<	int have_extra, done;
772	>	double theEcr, theEst;
773
774	<	temp1 = (double)tot_nmol / 4.0;
775	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1000	<	temp3 = ceil( temp2 );
774	>	if (globals->getUseRF()){
775	>	info[i].useReactionField = 1;
776
777	<	have_extra =0;
778	<	if( temp2 < temp3 ){ // we have a non-complete lattice
779	<	have_extra =1;
777	>	if (!globals->haveECR()){
778	>	sprintf(painCave.errMsg,
779	>	"SimSetup Warning: using default value of 1/2 the smallest "
780	>	"box length for the electrostaticCutoffRadius.\n"
781	>	"I hope you have a very fast processor!\n");
782	>	painCave.isFatal = 0;
783	>	simError();
784	>	double smallest;
785	>	smallest = info[i].boxL[0];
786	>	if (info[i].boxL[1] <= smallest)
787	>	smallest = info[i].boxL[1];
788	>	if (info[i].boxL[2] <= smallest)
789	>	smallest = info[i].boxL[2];
790	>	theEcr = 0.5 * smallest;
791	>	}
792	>	else{
793	>	theEcr = globals->getECR();
794	>	}
795
796	<	n_cells = (int)temp3 - 1;
797	<	cellx = simnfo->box_x / temp3;
798	<	celly = simnfo->box_y / temp3;
799	<	cellz = simnfo->box_z / temp3;
800	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
801	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
802	<	n_per_extra = (int)ceil( temp1 );
796	>	if (!globals->haveEST()){
797	>	sprintf(painCave.errMsg,
798	>	"SimSetup Warning: using default value of 0.05 * the "
799	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
800	>	painCave.isFatal = 0;
801	>	simError();
802	>	theEst = 0.05 * theEcr;
803	>	}
804	>	else{
805	>	theEst = globals->getEST();
806	>	}
807
808	<	if( n_per_extra > 4){
809	<	sprintf( painCave.errMsg,
810	<	"SimSetup error. There has been an error in constructing"
811	<	" the non-complete lattice.\n" );
812	<	painCave.isFatal = 1;
813	<	simError();
808	>	info[i].setDefaultEcr(theEcr, theEst);
809	>
810	>	if (!globals->haveDielectric()){
811	>	sprintf(painCave.errMsg,
812	>	"SimSetup Error: You are trying to use Reaction Field without"
813	>	"setting a dielectric constant!\n");
814	>	painCave.isFatal = 1;
815	>	simError();
816	>	}
817	>	info[i].dielectric = globals->getDielectric();
818		}
819	<	}
820	<	else{
821	<	n_cells = (int)temp3;
822	<	cellx = simnfo->box_x / temp3;
823	<	celly = simnfo->box_y / temp3;
824	<	cellz = simnfo->box_z / temp3;
825	<	}
819	>	else{
820	>	if (usesDipoles){
821	>	if (!globals->haveECR()){
822	>	sprintf(painCave.errMsg,
823	>	"SimSetup Warning: using default value of 1/2 the smallest "
824	>	"box length for the electrostaticCutoffRadius.\n"
825	>	"I hope you have a very fast processor!\n");
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	double smallest;
829	>	smallest = info[i].boxL[0];
830	>	if (info[i].boxL[1] <= smallest)
831	>	smallest = info[i].boxL[1];
832	>	if (info[i].boxL[2] <= smallest)
833	>	smallest = info[i].boxL[2];
834	>	theEcr = 0.5 * smallest;
835	>	}
836	>	else{
837	>	theEcr = globals->getECR();
838	>	}
839
840	<	current_mol = 0;
841	<	current_comp_mol = 0;
842	<	current_comp = 0;
843	<	current_atom_ndx = 0;
840	>	if (!globals->haveEST()){
841	>	sprintf(painCave.errMsg,
842	>	"SimSetup Warning: using default value of 0.05 * the "
843	>	"electrostaticCutoffRadius for the "
844	>	"electrostaticSkinThickness\n");
845	>	painCave.isFatal = 0;
846	>	simError();
847	>	theEst = 0.05 * theEcr;
848	>	}
849	>	else{
850	>	theEst = globals->getEST();
851	>	}
852
853	<	for( i=0; i < n_cells ; i++ ){
1035	<	for( j=0; j < n_cells; j++ ){
1036	<	for( k=0; k < n_cells; k++ ){
1037	<
1038	<	makeElement( i * cellx,
1039	<	j * celly,
1040	<	k * cellz );
1041	<
1042	<	makeElement( i * cellx + 0.5 * cellx,
1043	<	j * celly + 0.5 * celly,
1044	<	k * cellz );
1045	<
1046	<	makeElement( i * cellx,
1047	<	j * celly + 0.5 * celly,
1048	<	k * cellz + 0.5 * cellz );
1049	<
1050	<	makeElement( i * cellx + 0.5 * cellx,
1051	<	j * celly,
1052	<	k * cellz + 0.5 * cellz );
853	>	info[i].setDefaultEcr(theEcr, theEst);
854		}
855		}
856		}
857
858	<	if( have_extra ){
859	<	done = 0;
858	>	#ifdef IS_MPI
859	>	strcpy(checkPointMsg, "post processing checks out");
860	>	MPIcheckPoint();
861	>	#endif // is_mpi
862	>	}
863
864	<	int start_ndx;
865	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1062	<	for( j=0; j < (n_cells+1) && !done; j++ ){
864	>	void SimSetup::initSystemCoords(void){
865	>	int i;
866
867	<	if( i < n_cells ){
867	>	char* inName;
868
869	<	if( j < n_cells ){
1067	<	start_ndx = n_cells;
1068	<	}
1069	<	else start_ndx = 0;
1070	<	}
1071	<	else start_ndx = 0;
869	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
870
871	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
871	>	for (i = 0; i < info[0].n_atoms; i++)
872	>	info[0].atoms[i]->setCoords();
873
874	<	makeElement( i * cellx,
875	<	j * celly,
876	<	k * cellz );
877	<	done = ( current_mol >= tot_nmol );
874	>	if (globals->haveInitialConfig()){
875	>	InitializeFromFile* fileInit;
876	>	#ifdef IS_MPI // is_mpi
877	>	if (worldRank == 0){
878	>	#endif //is_mpi
879	>	inName = globals->getInitialConfig();
880	>	fileInit = new InitializeFromFile(inName);
881	>	#ifdef IS_MPI
882	>	}
883	>	else
884	>	fileInit = new InitializeFromFile(NULL);
885	>	#endif
886	>	fileInit->readInit(info); // default velocities on
887
888	<	if( !done && n_per_extra > 1 ){
889	<	makeElement( i * cellx + 0.5 * cellx,
890	<	j * celly + 0.5 * celly,
891	<	k * cellz );
1084	<	done = ( current_mol >= tot_nmol );
1085	<	}
888	>	delete fileInit;
889	>	}
890	>	else{
891	>	#ifdef IS_MPI
892
893	<	if( !done && n_per_extra > 2){
1088	<	makeElement( i * cellx,
1089	<	j * celly + 0.5 * celly,
1090	<	k * cellz + 0.5 * cellz );
1091	<	done = ( current_mol >= tot_nmol );
1092	<	}
893	>	// no init from bass
894
895	<	if( !done && n_per_extra > 3){
896	<	makeElement( i * cellx + 0.5 * cellx,
897	<	j * celly,
898	<	k * cellz + 0.5 * cellz );
1098	<	done = ( current_mol >= tot_nmol );
1099	<	}
1100	<	}
1101	<	}
1102	<	}
1103	<	}
895	>	sprintf(painCave.errMsg,
896	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
897	>	painCave.isFatal = 1;;
898	>	simError();
899
900	+	#else
901
902	<	for( i=0; i<simnfo->n_atoms; i++ ){
903	<	simnfo->atoms[i]->set_vx( 0.0 );
904	<	simnfo->atoms[i]->set_vy( 0.0 );
905	<	simnfo->atoms[i]->set_vz( 0.0 );
902	>	initFromBass();
903	>
904	>
905	>	#endif
906		}
907	+
908	+	#ifdef IS_MPI
909	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
910	+	MPIcheckPoint();
911	+	#endif // is_mpi
912		}
913
1113	–	void SimSetup::makeElement( double x, double y, double z ){
914
915	+	void SimSetup::makeOutNames(void){
916		int k;
1116	–	AtomStamp* current_atom;
1117	–	DirectionalAtom* dAtom;
1118	–	double rotMat[3][3];
917
1120	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
918
919	<	current_atom = comp_stamps[current_comp]->getAtom( k );
920	<	if( !current_atom->havePosition() ){
921	<	sprintf( painCave.errMsg,
922	<	"SimSetup:initFromBass error.\n"
1126	<	"\tComponent %s, atom %s does not have a position specified.\n"
1127	<	"\tThe initialization routine is unable to give a start"
1128	<	" position.\n",
1129	<	comp_stamps[current_comp]->getID(),
1130	<	current_atom->getType() );
1131	<	painCave.isFatal = 1;
1132	<	simError();
1133	<	}
919	>	for (k = 0; k < nInfo; k++){
920	>	#ifdef IS_MPI
921	>	if (worldRank == 0){
922	>	#endif // is_mpi
923
924	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
925	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
926	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
924	>	if (globals->haveFinalConfig()){
925	>	strcpy(info[k].finalName, globals->getFinalConfig());
926	>	}
927	>	else{
928	>	strcpy(info[k].finalName, inFileName);
929	>	char* endTest;
930	>	int nameLength = strlen(info[k].finalName);
931	>	endTest = &(info[k].finalName[nameLength - 5]);
932	>	if (!strcmp(endTest, ".bass")){
933	>	strcpy(endTest, ".eor");
934	>	}
935	>	else if (!strcmp(endTest, ".BASS")){
936	>	strcpy(endTest, ".eor");
937	>	}
938	>	else{
939	>	endTest = &(info[k].finalName[nameLength - 4]);
940	>	if (!strcmp(endTest, ".bss")){
941	>	strcpy(endTest, ".eor");
942	>	}
943	>	else if (!strcmp(endTest, ".mdl")){
944	>	strcpy(endTest, ".eor");
945	>	}
946	>	else{
947	>	strcat(info[k].finalName, ".eor");
948	>	}
949	>	}
950	>	}
951
952	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
952	>	// make the sample and status out names
953
954	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
955	<
956	<	rotMat[0][0] = 1.0;
957	<	rotMat[0][1] = 0.0;
958	<	rotMat[0][2] = 0.0;
959	<
960	<	rotMat[1][0] = 0.0;
961	<	rotMat[1][1] = 1.0;
962	<	rotMat[1][2] = 0.0;
963	<
964	<	rotMat[2][0] = 0.0;
965	<	rotMat[2][1] = 0.0;
966	<	rotMat[2][2] = 1.0;
954	>	strcpy(info[k].sampleName, inFileName);
955	>	char* endTest;
956	>	int nameLength = strlen(info[k].sampleName);
957	>	endTest = &(info[k].sampleName[nameLength - 5]);
958	>	if (!strcmp(endTest, ".bass")){
959	>	strcpy(endTest, ".dump");
960	>	}
961	>	else if (!strcmp(endTest, ".BASS")){
962	>	strcpy(endTest, ".dump");
963	>	}
964	>	else{
965	>	endTest = &(info[k].sampleName[nameLength - 4]);
966	>	if (!strcmp(endTest, ".bss")){
967	>	strcpy(endTest, ".dump");
968	>	}
969	>	else if (!strcmp(endTest, ".mdl")){
970	>	strcpy(endTest, ".dump");
971	>	}
972	>	else{
973	>	strcat(info[k].sampleName, ".dump");
974	>	}
975	>	}
976
977	<	dAtom->setA( rotMat );
977	>	strcpy(info[k].statusName, inFileName);
978	>	nameLength = strlen(info[k].statusName);
979	>	endTest = &(info[k].statusName[nameLength - 5]);
980	>	if (!strcmp(endTest, ".bass")){
981	>	strcpy(endTest, ".stat");
982	>	}
983	>	else if (!strcmp(endTest, ".BASS")){
984	>	strcpy(endTest, ".stat");
985	>	}
986	>	else{
987	>	endTest = &(info[k].statusName[nameLength - 4]);
988	>	if (!strcmp(endTest, ".bss")){
989	>	strcpy(endTest, ".stat");
990	>	}
991	>	else if (!strcmp(endTest, ".mdl")){
992	>	strcpy(endTest, ".stat");
993	>	}
994	>	else{
995	>	strcat(info[k].statusName, ".stat");
996	>	}
997	>	}
998	>
999	>	#ifdef IS_MPI
1000	>
1001		}
1002	+	#endif // is_mpi
1003	+	}
1004	+	}
1005
1006	<	current_atom_ndx++;
1006	>
1007	>	void SimSetup::sysObjectsCreation(void){
1008	>	int i, k;
1009	>
1010	>	// create the forceField
1011	>
1012	>	createFF();
1013	>
1014	>	// extract componentList
1015	>
1016	>	compList();
1017	>
1018	>	// calc the number of atoms, bond, bends, and torsions
1019	>
1020	>	calcSysValues();
1021	>
1022	>	#ifdef IS_MPI
1023	>	// divide the molecules among the processors
1024	>
1025	>	mpiMolDivide();
1026	>	#endif //is_mpi
1027	>
1028	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1029	>
1030	>	makeSysArrays();
1031	>
1032	>	// make and initialize the molecules (all but atomic coordinates)
1033	>
1034	>	makeMolecules();
1035	>
1036	>	for (k = 0; k < nInfo; k++){
1037	>	info[k].identArray = new int[info[k].n_atoms];
1038	>	for (i = 0; i < info[k].n_atoms; i++){
1039	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1040	>	}
1041		}
1042	+	}
1043
1161	–	current_mol++;
1162	–	current_comp_mol++;
1044
1045	<	if( current_comp_mol >= components_nmol[current_comp] ){
1045	>	void SimSetup::createFF(void){
1046	>	switch (ffCase){
1047	>	case FF_DUFF:
1048	>	the_ff = new DUFF();
1049	>	break;
1050
1051	<	current_comp_mol = 0;
1052	<	current_comp++;
1051	>	case FF_LJ:
1052	>	the_ff = new LJFF();
1053	>	break;
1054	>
1055	>	case FF_EAM:
1056	>	the_ff = new EAM_FF();
1057	>	break;
1058	>
1059	>	default:
1060	>	sprintf(painCave.errMsg,
1061	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1062	>	painCave.isFatal = 1;
1063	>	simError();
1064		}
1065	+
1066	+	#ifdef IS_MPI
1067	+	strcpy(checkPointMsg, "ForceField creation successful");
1068	+	MPIcheckPoint();
1069	+	#endif // is_mpi
1070		}
1071	+
1072	+
1073	+	void SimSetup::compList(void){
1074	+	int i;
1075	+	char* id;
1076	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1077	+	LinkedMolStamp* currentStamp = NULL;
1078	+	comp_stamps = new MoleculeStamp * [n_components];
1079	+
1080	+	// make an array of molecule stamps that match the components used.
1081	+	// also extract the used stamps out into a separate linked list
1082	+
1083	+	for (i = 0; i < nInfo; i++){
1084	+	info[i].nComponents = n_components;
1085	+	info[i].componentsNmol = components_nmol;
1086	+	info[i].compStamps = comp_stamps;
1087	+	info[i].headStamp = headStamp;
1088	+	}
1089	+
1090	+
1091	+	for (i = 0; i < n_components; i++){
1092	+	id = the_components[i]->getType();
1093	+	comp_stamps[i] = NULL;
1094	+
1095	+	// check to make sure the component isn't already in the list
1096	+
1097	+	comp_stamps[i] = headStamp->match(id);
1098	+	if (comp_stamps[i] == NULL){
1099	+	// extract the component from the list;
1100	+
1101	+	currentStamp = stamps->extractMolStamp(id);
1102	+	if (currentStamp == NULL){
1103	+	sprintf(painCave.errMsg,
1104	+	"SimSetup error: Component \"%s\" was not found in the "
1105	+	"list of declared molecules\n",
1106	+	id);
1107	+	painCave.isFatal = 1;
1108	+	simError();
1109	+	}
1110	+
1111	+	headStamp->add(currentStamp);
1112	+	comp_stamps[i] = headStamp->match(id);
1113	+	}
1114	+	}
1115	+
1116	+	#ifdef IS_MPI
1117	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1118	+	MPIcheckPoint();
1119	+	#endif // is_mpi
1120	+	}
1121	+
1122	+	void SimSetup::calcSysValues(void){
1123	+	int i;
1124	+
1125	+	int* molMembershipArray;
1126	+
1127	+	tot_atoms = 0;
1128	+	tot_bonds = 0;
1129	+	tot_bends = 0;
1130	+	tot_torsions = 0;
1131	+	for (i = 0; i < n_components; i++){
1132	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1133	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1134	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1135	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1136	+	}
1137	+
1138	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1139	+	molMembershipArray = new int[tot_atoms];
1140	+
1141	+	for (i = 0; i < nInfo; i++){
1142	+	info[i].n_atoms = tot_atoms;
1143	+	info[i].n_bonds = tot_bonds;
1144	+	info[i].n_bends = tot_bends;
1145	+	info[i].n_torsions = tot_torsions;
1146	+	info[i].n_SRI = tot_SRI;
1147	+	info[i].n_mol = tot_nmol;
1148	+
1149	+	info[i].molMembershipArray = molMembershipArray;
1150	+	}
1151	+	}
1152	+
1153	+	#ifdef IS_MPI
1154	+
1155	+	void SimSetup::mpiMolDivide(void){
1156	+	int i, j, k;
1157	+	int localMol, allMol;
1158	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1159	+
1160	+	mpiSim = new mpiSimulation(info);
1161	+
1162	+	globalIndex = mpiSim->divideLabor();
1163	+
1164	+	// set up the local variables
1165	+
1166	+	mol2proc = mpiSim->getMolToProcMap();
1167	+	molCompType = mpiSim->getMolComponentType();
1168	+
1169	+	allMol = 0;
1170	+	localMol = 0;
1171	+	local_atoms = 0;
1172	+	local_bonds = 0;
1173	+	local_bends = 0;
1174	+	local_torsions = 0;
1175	+	globalAtomIndex = 0;
1176	+
1177	+
1178	+	for (i = 0; i < n_components; i++){
1179	+	for (j = 0; j < components_nmol[i]; j++){
1180	+	if (mol2proc[allMol] == worldRank){
1181	+	local_atoms += comp_stamps[i]->getNAtoms();
1182	+	local_bonds += comp_stamps[i]->getNBonds();
1183	+	local_bends += comp_stamps[i]->getNBends();
1184	+	local_torsions += comp_stamps[i]->getNTorsions();
1185	+	localMol++;
1186	+	}
1187	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1188	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1189	+	globalAtomIndex++;
1190	+	}
1191	+
1192	+	allMol++;
1193	+	}
1194	+	}
1195	+	local_SRI = local_bonds + local_bends + local_torsions;
1196	+
1197	+	info[0].n_atoms = mpiSim->getMyNlocal();
1198	+
1199	+	if (local_atoms != info[0].n_atoms){
1200	+	sprintf(painCave.errMsg,
1201	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1202	+	" localAtom (%d) are not equal.\n",
1203	+	info[0].n_atoms, local_atoms);
1204	+	painCave.isFatal = 1;
1205	+	simError();
1206	+	}
1207	+
1208	+	info[0].n_bonds = local_bonds;
1209	+	info[0].n_bends = local_bends;
1210	+	info[0].n_torsions = local_torsions;
1211	+	info[0].n_SRI = local_SRI;
1212	+	info[0].n_mol = localMol;
1213	+
1214	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1215	+	MPIcheckPoint();
1216	+	}
1217	+
1218	+	#endif // is_mpi
1219	+
1220	+
1221	+	void SimSetup::makeSysArrays(void){
1222	+
1223	+	#ifndef IS_MPI
1224	+	int k, j;
1225	+	#endif // is_mpi
1226	+	int i, l;
1227	+
1228	+	Atom** the_atoms;
1229	+	Molecule* the_molecules;
1230	+	Exclude** the_excludes;
1231	+
1232	+
1233	+	for (l = 0; l < nInfo; l++){
1234	+	// create the atom and short range interaction arrays
1235	+
1236	+	the_atoms = new Atom * [info[l].n_atoms];
1237	+	the_molecules = new Molecule[info[l].n_mol];
1238	+	int molIndex;
1239	+
1240	+	// initialize the molecule's stampID's
1241	+
1242	+	#ifdef IS_MPI
1243	+
1244	+
1245	+	molIndex = 0;
1246	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1247	+	if (mol2proc[i] == worldRank){
1248	+	the_molecules[molIndex].setStampID(molCompType[i]);
1249	+	the_molecules[molIndex].setMyIndex(molIndex);
1250	+	the_molecules[molIndex].setGlobalIndex(i);
1251	+	molIndex++;
1252	+	}
1253	+	}
1254	+
1255	+	#else // is_mpi
1256	+
1257	+	molIndex = 0;
1258	+	globalAtomIndex = 0;
1259	+	for (i = 0; i < n_components; i++){
1260	+	for (j = 0; j < components_nmol[i]; j++){
1261	+	the_molecules[molIndex].setStampID(i);
1262	+	the_molecules[molIndex].setMyIndex(molIndex);
1263	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1264	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1265	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1266	+	globalAtomIndex++;
1267	+	}
1268	+	molIndex++;
1269	+	}
1270	+	}
1271	+
1272	+
1273	+	#endif // is_mpi
1274	+
1275	+
1276	+	if (info[l].n_SRI){
1277	+	Exclude::createArray(info[l].n_SRI);
1278	+	the_excludes = new Exclude * [info[l].n_SRI];
1279	+	for (int ex = 0; ex < info[l].n_SRI; ex++){
1280	+	the_excludes[ex] = new Exclude(ex);
1281	+	}
1282	+	info[l].globalExcludes = new int;
1283	+	info[l].n_exclude = info[l].n_SRI;
1284	+	}
1285	+	else{
1286	+	Exclude::createArray(1);
1287	+	the_excludes = new Exclude * ;
1288	+	the_excludes[0] = new Exclude(0);
1289	+	the_excludes[0]->setPair(0, 0);
1290	+	info[l].globalExcludes = new int;
1291	+	info[l].globalExcludes[0] = 0;
1292	+	info[l].n_exclude = 0;
1293	+	}
1294	+
1295	+	// set the arrays into the SimInfo object
1296	+
1297	+	info[l].atoms = the_atoms;
1298	+	info[l].molecules = the_molecules;
1299	+	info[l].nGlobalExcludes = 0;
1300	+	info[l].excludes = the_excludes;
1301	+
1302	+	the_ff->setSimInfo(info);
1303	+	}
1304	+	}
1305	+
1306	+	void SimSetup::makeIntegrator(void){
1307	+	int k;
1308	+
1309	+	NVE<RealIntegrator>* myNVE = NULL;
1310	+	NVT<RealIntegrator>* myNVT = NULL;
1311	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1312	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1313	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1314	+
1315	+	for (k = 0; k < nInfo; k++){
1316	+	switch (ensembleCase){
1317	+	case NVE_ENS:
1318	+	if (globals->haveZconstraints()){
1319	+	setupZConstraint(info[k]);
1320	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1321	+	}
1322	+	else{
1323	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1324	+	}
1325	+
1326	+	info->the_integrator = myNVE;
1327	+	break;
1328	+
1329	+	case NVT_ENS:
1330	+	if (globals->haveZconstraints()){
1331	+	setupZConstraint(info[k]);
1332	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1333	+	}
1334	+	else
1335	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1336	+
1337	+	myNVT->setTargetTemp(globals->getTargetTemp());
1338	+
1339	+	if (globals->haveTauThermostat())
1340	+	myNVT->setTauThermostat(globals->getTauThermostat());
1341	+	else{
1342	+	sprintf(painCave.errMsg,
1343	+	"SimSetup error: If you use the NVT\n"
1344	+	"    ensemble, you must set tauThermostat.\n");
1345	+	painCave.isFatal = 1;
1346	+	simError();
1347	+	}
1348	+
1349	+	info->the_integrator = myNVT;
1350	+	break;
1351	+
1352	+	case NPTi_ENS:
1353	+	if (globals->haveZconstraints()){
1354	+	setupZConstraint(info[k]);
1355	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1356	+	}
1357	+	else
1358	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1359	+
1360	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1361	+
1362	+	if (globals->haveTargetPressure())
1363	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1364	+	else{
1365	+	sprintf(painCave.errMsg,
1366	+	"SimSetup error: If you use a constant pressure\n"
1367	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1368	+	painCave.isFatal = 1;
1369	+	simError();
1370	+	}
1371	+
1372	+	if (globals->haveTauThermostat())
1373	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1374	+	else{
1375	+	sprintf(painCave.errMsg,
1376	+	"SimSetup error: If you use an NPT\n"
1377	+	"    ensemble, you must set tauThermostat.\n");
1378	+	painCave.isFatal = 1;
1379	+	simError();
1380	+	}
1381	+
1382	+	if (globals->haveTauBarostat())
1383	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1384	+	else{
1385	+	sprintf(painCave.errMsg,
1386	+	"SimSetup error: If you use an NPT\n"
1387	+	"    ensemble, you must set tauBarostat.\n");
1388	+	painCave.isFatal = 1;
1389	+	simError();
1390	+	}
1391	+
1392	+	info->the_integrator = myNPTi;
1393	+	break;
1394	+
1395	+	case NPTf_ENS:
1396	+	if (globals->haveZconstraints()){
1397	+	setupZConstraint(info[k]);
1398	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1399	+	}
1400	+	else
1401	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1402	+
1403	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1404	+
1405	+	if (globals->haveTargetPressure())
1406	+	myNPTf->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	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1417	+
1418	+	else{
1419	+	sprintf(painCave.errMsg,
1420	+	"SimSetup error: If you use an NPT\n"
1421	+	"    ensemble, you must set tauThermostat.\n");
1422	+	painCave.isFatal = 1;
1423	+	simError();
1424	+	}
1425	+
1426	+	if (globals->haveTauBarostat())
1427	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1428	+
1429	+	else{
1430	+	sprintf(painCave.errMsg,
1431	+	"SimSetup error: If you use an NPT\n"
1432	+	"    ensemble, you must set tauBarostat.\n");
1433	+	painCave.isFatal = 1;
1434	+	simError();
1435	+	}
1436	+
1437	+	info->the_integrator = myNPTf;
1438	+	break;
1439	+
1440	+	case NPTxyz_ENS:
1441	+	if (globals->haveZconstraints()){
1442	+	setupZConstraint(info[k]);
1443	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1444	+	}
1445	+	else
1446	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1447	+
1448	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1449	+
1450	+	if (globals->haveTargetPressure())
1451	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1452	+	else{
1453	+	sprintf(painCave.errMsg,
1454	+	"SimSetup error: If you use a constant pressure\n"
1455	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+
1460	+	if (globals->haveTauThermostat())
1461	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1462	+	else{
1463	+	sprintf(painCave.errMsg,
1464	+	"SimSetup error: If you use an NPT\n"
1465	+	"    ensemble, you must set tauThermostat.\n");
1466	+	painCave.isFatal = 1;
1467	+	simError();
1468	+	}
1469	+
1470	+	if (globals->haveTauBarostat())
1471	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1472	+	else{
1473	+	sprintf(painCave.errMsg,
1474	+	"SimSetup error: If you use an NPT\n"
1475	+	"    ensemble, you must set tauBarostat.\n");
1476	+	painCave.isFatal = 1;
1477	+	simError();
1478	+	}
1479	+
1480	+	info->the_integrator = myNPTxyz;
1481	+	break;
1482	+
1483	+	default:
1484	+	sprintf(painCave.errMsg,
1485	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1486	+	painCave.isFatal = 1;
1487	+	simError();
1488	+	}
1489	+	}
1490	+	}
1491	+
1492	+	void SimSetup::initFortran(void){
1493	+	info[0].refreshSim();
1494	+
1495	+	if (!strcmp(info[0].mixingRule, "standard")){
1496	+	the_ff->initForceField(LB_MIXING_RULE);
1497	+	}
1498	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1499	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1500	+	}
1501	+	else{
1502	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1503	+	info[0].mixingRule);
1504	+	painCave.isFatal = 1;
1505	+	simError();
1506	+	}
1507	+
1508	+
1509	+	#ifdef IS_MPI
1510	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1511	+	MPIcheckPoint();
1512	+	#endif // is_mpi
1513	+	}
1514	+
1515	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1516	+	int nZConstraints;
1517	+	ZconStamp** zconStamp;
1518	+
1519	+	if (globals->haveZconstraintTime()){
1520	+	//add sample time of z-constraint  into SimInfo's property list
1521	+	DoubleData* zconsTimeProp = new DoubleData();
1522	+	zconsTimeProp->setID(ZCONSTIME_ID);
1523	+	zconsTimeProp->setData(globals->getZconsTime());
1524	+	theInfo.addProperty(zconsTimeProp);
1525	+	}
1526	+	else{
1527	+	sprintf(painCave.errMsg,
1528	+	"ZConstraint error: If you use an ZConstraint\n"
1529	+	" , you must set sample time.\n");
1530	+	painCave.isFatal = 1;
1531	+	simError();
1532	+	}
1533	+
1534	+	//push zconsTol into siminfo, if user does not specify
1535	+	//value for zconsTol, a default value will be used
1536	+	DoubleData* zconsTol = new DoubleData();
1537	+	zconsTol->setID(ZCONSTOL_ID);
1538	+	if (globals->haveZconsTol()){
1539	+	zconsTol->setData(globals->getZconsTol());
1540	+	}
1541	+	else{
1542	+	double defaultZConsTol = 0.01;
1543	+	sprintf(painCave.errMsg,
1544	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1545	+	" , default value %f is used.\n",
1546	+	defaultZConsTol);
1547	+	painCave.isFatal = 0;
1548	+	simError();
1549	+
1550	+	zconsTol->setData(defaultZConsTol);
1551	+	}
1552	+	theInfo.addProperty(zconsTol);
1553	+
1554	+	//set Force Subtraction Policy
1555	+	StringData* zconsForcePolicy = new StringData();
1556	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1557	+
1558	+	if (globals->haveZconsForcePolicy()){
1559	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1560	+	}
1561	+	else{
1562	+	sprintf(painCave.errMsg,
1563	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1564	+	"PolicyByMass is used\n");
1565	+	painCave.isFatal = 0;
1566	+	simError();
1567	+	zconsForcePolicy->setData("BYMASS");
1568	+	}
1569	+
1570	+	theInfo.addProperty(zconsForcePolicy);
1571	+
1572	+	//Determine the name of ouput file and add it into SimInfo's property list
1573	+	//Be careful, do not use inFileName, since it is a pointer which
1574	+	//point to a string at master node, and slave nodes do not contain that string
1575	+
1576	+	string zconsOutput(theInfo.finalName);
1577	+
1578	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1579	+
1580	+	StringData* zconsFilename = new StringData();
1581	+	zconsFilename->setID(ZCONSFILENAME_ID);
1582	+	zconsFilename->setData(zconsOutput);
1583	+
1584	+	theInfo.addProperty(zconsFilename);
1585	+
1586	+	//setup index, pos and other parameters of z-constraint molecules
1587	+	nZConstraints = globals->getNzConstraints();
1588	+	theInfo.nZconstraints = nZConstraints;
1589	+
1590	+	zconStamp = globals->getZconStamp();
1591	+	ZConsParaItem tempParaItem;
1592	+
1593	+	ZConsParaData* zconsParaData = new ZConsParaData();
1594	+	zconsParaData->setID(ZCONSPARADATA_ID);
1595	+
1596	+	for (int i = 0; i < nZConstraints; i++){
1597	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1598	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1599	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1600	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1601	+
1602	+	zconsParaData->addItem(tempParaItem);
1603	+	}
1604	+
1605	+	//check the uniqueness of index
1606	+	if(!zconsParaData->isIndexUnique()){
1607	+	sprintf(painCave.errMsg,
1608	+	"ZConstraint Error: molIndex is not unique\n");
1609	+	painCave.isFatal = 1;
1610	+	simError();
1611	+	}
1612	+
1613	+	//sort the parameters by index of molecules
1614	+	zconsParaData->sortByIndex();
1615	+
1616	+	//push data into siminfo, therefore, we can retrieve later
1617	+	theInfo.addProperty(zconsParaData);
1618	+	}

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