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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 427 by mmeineke, Thu Mar 27 20:48:37 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 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	<	int i, j;
98	>	// gather all of the information from the Bass file
99
100	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
100	>	gatherInfo();
101
102	<	// 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();
102	>	// creation of complex system objects
103
104	<	// 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 );
104	>	sysObjectsCreation();
105
106	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
106	>	// check on the post processing info
107
108	+	finalInfoCheck();
109
110	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
110	>	// initialize the system coordinates
111
112	<	#ifdef IS_MPI
113	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#endif // is_mpi
112	>	if ( !initSuspend ){
113	>	initSystemCoords();
114
115	<
115	>	if( !(globals->getUseInitTime()) )
116	>	info[0].currentTime = 0.0;
117	>	}
118
119	<	// get the components and calculate the tot_nMol and indvidual n_mol
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
119	>	// make the output filenames
120
121	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// given in each component
121	>	makeOutNames();
122
123	<	tot_nmol = 0;
118	<	for( i=0; i<n_components; i++ ){
123	>	// make the integrator
124
125	<	if( !the_components[i]->haveNMol() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
125	>	makeIntegrator();
126
129	–	tot_nmol += the_components[i]->getNMol();
130	–	components_nmol[i] = the_components[i]->getNMol();
131	–	}
132	–	}
133	–	else{
134	–	sprintf( painCave.errMsg,
135	–	"SimSetup error.\n"
136	–	"\tSorry, the ability to specify total"
137	–	" nMols and then give molfractions in the components\n"
138	–	"\tis not currently supported."
139	–	" Please give nMol in the components.\n" );
140	–	painCave.isFatal = 1;
141	–	simError();
142	–
143	–
144	–	//     tot_nmol = the_globals->getNMol();
145	–
146	–	//   //we have the total number of molecules, now we check for molfractions
147	–	//     for( i=0; i<n_components; i++ ){
148	–
149	–	//       if( !the_components[i]->haveMolFraction() ){
150	–
151	–	//  if( !the_components[i]->haveNMol() ){
152	–	//    //we have a problem
153	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	–	//              << " nMol was given in component
155	–
156	–	}
157	–
127		#ifdef IS_MPI
128	<	strcpy( checkPointMsg, "Have the number of components" );
129	<	MPIcheckPoint();
161	<	#endif // is_mpi
128	>	mpiSim->mpiRefresh();
129	>	#endif
130
131	<	// make an array of molecule stamps that match the components used.
164	<	// 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;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
170	<
171	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
133	>	initFortran();
134	>	}
135
176	–	id = the_components[i]->getType();
177	–	comp_stamps[i] = NULL;
178	–
179	–	// 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 );
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	headStamp->add( currentStamp );
197	<	comp_stamps[i] = headStamp->match( id );
198	<	}
199	<	}
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();
204	<	#endif // is_mpi
205	<
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
211	–	tot_atoms = 0;
212	–	tot_bonds = 0;
213	–	tot_bends = 0;
214	–	tot_torsions = 0;
215	–	for( i=0; i<n_components; i++ ){
216	–
217	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	–	}
158
159	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
159	>	// init the atoms
160
161	<	simnfo->n_atoms = tot_atoms;
226	<	simnfo->n_bonds = tot_bonds;
227	<	simnfo->n_bends = tot_bends;
228	<	simnfo->n_torsions = tot_torsions;
229	<	simnfo->n_SRI = tot_SRI;
230	<	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	<
239	<
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();
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	+	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	+	theBonds = new bond_pair[molInfo.nBonds];
184	+	theBends = new bend_set[molInfo.nBends];
185	+	theTorsions = new torsion_set[molInfo.nTorsions];
186
187	<	// set up the local variables
246	<
247	<	int localMol, allMol;
248	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
187	>	// make the Atoms
188
189	<	int* mol2proc = mpiSim->getMolToProcMap();
190	<	int* molCompType = mpiSim->getMolComponentType();
191	<
192	<	allMol = 0;
193	<	localMol = 0;
194	<	local_atoms = 0;
195	<	local_bonds = 0;
257	<	local_bends = 0;
258	<	local_torsions = 0;
259	<	for( i=0; i<n_components; i++ ){
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	<	for( j=0; j<components_nmol[i]; j++ ){
198	<
199	<	if( mol2proc[j] == worldRank ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	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	<
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200
201	<	simnfo->n_atoms = mpiSim->getMyNlocal();
278	<
279	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are not equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202
203	<	simnfo->n_bonds = local_bonds;
204	<	simnfo->n_bends = local_bends;
205	<	simnfo->n_torsions = local_torsions;
206	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207
208	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
209	<	MPIcheckPoint();
210	<
211	<
212	<	#endif // is_mpi
213	<
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	<	// create the atom and short range interaction arrays
218	>	#ifdef IS_MPI
219
220	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
307	<	int molIndex;
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221
222	<	// initialize the molecule's stampID's
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	+	exI = theBonds[j].a;
232	+	exJ = theBonds[j].b;
233	+
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	<
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245
246	<	molIndex = 0;
247	<	for(i=0; i<mpiSim->getTotNmol(); i++){
316	<
317	<	if(mol2proc[i] == worldRank ){
318	<	the_molecules[molIndex].setStampID( molCompType[i] );
319	<	molIndex++;
320	<	}
321	<	}
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	>	#else  // isn't MPI
248
249	<	#else // is_mpi
250	<
251	<	molIndex = 0;
252	<	for(i=0; i<n_components; i++){
327	<	for(j=0; j<components_nmol[i]; j++ ){
328	<	the_molecules[molIndex].setStampID( i );
329	<	molIndex++;
330	<	}
331	<	}
332	<
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	>	#endif  //is_mpi
251	>	}
252	>	excludeOffset += molInfo.nBonds;
253
254	<	#endif // is_mpi
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	+	if (currentBend->haveExtras()){
262	+	extras = currentBend->getExtras();
263	+	current_extra = extras;
264
265	<	if( simnfo->n_SRI ){
266	<	Exclude::createArray(simnfo->n_SRI);
267	<	the_excludes = new Exclude*[simnfo->n_SRI];
268	<	simnfo->globalExcludes = new int;
269	<	simnfo->n_exclude = tot_SRI;
270	<	}
271	<	else{
344	<
345	<	Exclude::createArray( 1 );
346	<	the_excludes = new Exclude*;
347	<	the_excludes[0] = new Exclude(0);
348	<	the_excludes[0]->setPair( 0,0 );
349	<	simnfo->globalExcludes = new int;
350	<	simnfo->globalExcludes[0] = 0;
351	<	simnfo->n_exclude = 0;
352	<	}
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	<	// set the arrays into the SimInfo object
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278
279	<	simnfo->atoms = the_atoms;
280	<	simnfo->nGlobalExcludes = 0;
281	<	simnfo->excludes = the_excludes;
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	<	// get some of the tricky things that may still be in the globals
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	<
312	<	if( the_globals->haveBox() ){
313	<	simnfo->box_x = the_globals->getBox();
314	<	simnfo->box_y = the_globals->getBox();
315	<	simnfo->box_z = the_globals->getBox();
316	<	}
317	<	else if( the_globals->haveDensity() ){
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	<	double vol;
324	<	vol = (double)tot_nmol / the_globals->getDensity();
325	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
326	<	simnfo->box_y = simnfo->box_x;
327	<	simnfo->box_z = simnfo->box_x;
328	<	}
377	<	else{
378	<	if( !the_globals->haveBoxX() ){
379	<	sprintf( painCave.errMsg,
380	<	"SimSetup error, no periodic BoxX size given.\n" );
381	<	painCave.isFatal = 1;
382	<	simError();
383	<	}
384	<	simnfo->box_x = the_globals->getBoxX();
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	<	if( !the_globals->haveBoxY() ){
331	<	sprintf( painCave.errMsg,
332	<	"SimSetup error, no periodic BoxY size given.\n" );
333	<	painCave.isFatal = 1;
334	<	simError();
335	<	}
392	<	simnfo->box_y = the_globals->getBoxY();
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		}
400	–	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();
417	<	}
418	<
419	<	if (the_globals->getUseRF() ) {
420	<	simnfo->useReactionField = 1;
421	<
422	<	if( !the_globals->haveECR() ){
423	<	sprintf( painCave.errMsg,
424	<	"SimSetup Warning: using default value of 1/2 the smallest "
425	<	"box length for the electrostaticCutoffRadius.\n"
426	<	"I hope you have a very fast processor!\n");
427	<	painCave.isFatal = 0;
428	<	simError();
429	<	double smallest;
430	<	smallest = simnfo->box_x;
431	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
432	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
433	<	simnfo->ecr = 0.5 * smallest;
434	<	} else {
435	<	simnfo->ecr        = the_globals->getECR();
436	<	}
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 (simnfo->n_dipoles) {
431	<
432	<	if( !the_globals->haveECR() ){
433	<	sprintf( painCave.errMsg,
434	<	"SimSetup Warning: using default value of 1/2 the smallest"
435	<	"box length for the electrostaticCutoffRadius.\n"
436	<	"I hope you have a very fast processor!\n");
437	<	painCave.isFatal = 0;
438	<	simError();
439	<	double smallest;
440	<	smallest = simnfo->box_x;
441	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
442	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
443	<	simnfo->ecr = 0.5 * smallest;
444	<	} else {
445	<	simnfo->ecr        = the_globals->getECR();
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	>	current_mol = 0;
437	>	current_comp_mol = 0;
438	>	current_comp = 0;
439	>	current_atom_ndx = 0;
440	>
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	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447	>
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449	>
450	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
451		}
477	–
478	–	if( !the_globals->haveEST() ){
479	–	sprintf( painCave.errMsg,
480	–	"SimSetup Warning: using default value of 5% of the"
481	–	"electrostaticCutoffRadius for the "
482	–	"electrostaticSkinThickness\n"
483	–	);
484	–	painCave.isFatal = 0;
485	–	simError();
486	–	simnfo->est = 0.05 * simnfo->ecr;
487	–	} else {
488	–	simnfo->est        = the_globals->getEST();
489	–	}
452		}
453	<	}
453	>	}
454
455	<	#ifdef IS_MPI
456	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
495	<	MPIcheckPoint();
496	<	#endif // is_mpi
455	>	if (have_extra){
456	>	done = 0;
457
458	<	if( the_globals->haveInitialConfig() ){
459	<
460	<	InitializeFromFile* fileInit;
461	<	#ifdef IS_MPI // is_mpi
462	<	if( worldRank == 0 ){
463	<	#endif //is_mpi
464	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
465	<	#ifdef IS_MPI
466	<	}else fileInit = new InitializeFromFile( NULL );
467	<	#endif
468	<	fileInit->read_xyz( simnfo ); // default velocities on
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	<	delete fileInit;
472	<	}
473	<	else{
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
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	<	// no init from bass
482	<
483	<	sprintf( painCave.errMsg,
484	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
485	<	painCave.isFatal;
521	<	simError();
522	<
523	<	#else
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	<	initFromBass();
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	>	}
494	>	}
495	>	}
496
497	+	for (i = 0; i < info[0].n_atoms; i++){
498	+	info[0].atoms[i]->setVel(vel);
499	+	}
500	+	}
501
502	<	#endif
503	<	}
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	<	#ifdef IS_MPI
510	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
511	<	MPIcheckPoint();
512	<	#endif // is_mpi
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	+	pos[0] = x + current_atom->getPosX();
523	+	pos[1] = y + current_atom->getPosY();
524	+	pos[2] = z + current_atom->getPosZ();
525
526	<
538	<
539	<
526	>	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<
529	<	#ifdef IS_MPI
530	<	if( worldRank == 0 ){
531	<	#endif // is_mpi
532	<
533	<	if( the_globals->haveFinalConfig() ){
534	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530	>
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	>	rotMat[2][0] = 0.0;
540	>	rotMat[2][1] = 0.0;
541	>	rotMat[2][2] = 1.0;
542	>
543	>	dAtom->setA(rotMat);
544		}
549	–	else{
550	–	strcpy( simnfo->finalName, inFileName );
551	–	char* endTest;
552	–	int nameLength = strlen( simnfo->finalName );
553	–	endTest = &(simnfo->finalName[nameLength - 5]);
554	–	if( !strcmp( endTest, ".bass" ) ){
555	–	strcpy( endTest, ".eor" );
556	–	}
557	–	else if( !strcmp( endTest, ".BASS" ) ){
558	–	strcpy( endTest, ".eor" );
559	–	}
560	–	else{
561	–	endTest = &(simnfo->finalName[nameLength - 4]);
562	–	if( !strcmp( endTest, ".bss" ) ){
563	–	strcpy( endTest, ".eor" );
564	–	}
565	–	else if( !strcmp( endTest, ".mdl" ) ){
566	–	strcpy( endTest, ".eor" );
567	–	}
568	–	else{
569	–	strcat( simnfo->finalName, ".eor" );
570	–	}
571	–	}
572	–	}
573	–
574	–	// make the sample and status out names
575	–
576	–	strcpy( simnfo->sampleName, inFileName );
577	–	char* endTest;
578	–	int nameLength = strlen( simnfo->sampleName );
579	–	endTest = &(simnfo->sampleName[nameLength - 5]);
580	–	if( !strcmp( endTest, ".bass" ) ){
581	–	strcpy( endTest, ".dump" );
582	–	}
583	–	else if( !strcmp( endTest, ".BASS" ) ){
584	–	strcpy( endTest, ".dump" );
585	–	}
586	–	else{
587	–	endTest = &(simnfo->sampleName[nameLength - 4]);
588	–	if( !strcmp( endTest, ".bss" ) ){
589	–	strcpy( endTest, ".dump" );
590	–	}
591	–	else if( !strcmp( endTest, ".mdl" ) ){
592	–	strcpy( endTest, ".dump" );
593	–	}
594	–	else{
595	–	strcat( simnfo->sampleName, ".dump" );
596	–	}
597	–	}
598	–
599	–	strcpy( simnfo->statusName, inFileName );
600	–	nameLength = strlen( simnfo->statusName );
601	–	endTest = &(simnfo->statusName[nameLength - 5]);
602	–	if( !strcmp( endTest, ".bass" ) ){
603	–	strcpy( endTest, ".stat" );
604	–	}
605	–	else if( !strcmp( endTest, ".BASS" ) ){
606	–	strcpy( endTest, ".stat" );
607	–	}
608	–	else{
609	–	endTest = &(simnfo->statusName[nameLength - 4]);
610	–	if( !strcmp( endTest, ".bss" ) ){
611	–	strcpy( endTest, ".stat" );
612	–	}
613	–	else if( !strcmp( endTest, ".mdl" ) ){
614	–	strcpy( endTest, ".stat" );
615	–	}
616	–	else{
617	–	strcat( simnfo->statusName, ".stat" );
618	–	}
619	–	}
620	–
621	–	#ifdef IS_MPI
622	–	}
623	–	#endif // is_mpi
624	–
625	–	// set the status, sample, and themal kick times
626	–
627	–	if( the_globals->haveSampleTime() ){
628	–	simnfo->sampleTime = the_globals->getSampleTime();
629	–	simnfo->statusTime = simnfo->sampleTime;
630	–	simnfo->thermalTime = simnfo->sampleTime;
631	–	}
632	–	else{
633	–	simnfo->sampleTime = the_globals->getRunTime();
634	–	simnfo->statusTime = simnfo->sampleTime;
635	–	simnfo->thermalTime = simnfo->sampleTime;
636	–	}
545
546	<	if( the_globals->haveStatusTime() ){
639	<	simnfo->statusTime = the_globals->getStatusTime();
546	>	current_atom_ndx++;
547		}
548
549	<	if( the_globals->haveThermalTime() ){
550	<	simnfo->thermalTime = the_globals->getThermalTime();
549	>	current_mol++;
550	>	current_comp_mol++;
551	>
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553	>	current_comp_mol = 0;
554	>	current_comp++;
555		}
556	+	}
557
646	–	// check for the temperature set flag
558
559	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
559	>	void SimSetup::gatherInfo(void){
560	>	int i;
561
562	+	ensembleCase = -1;
563	+	ffCase = -1;
564
565	<	//   // make the longe range forces and the integrator
565	>	// set the easy ones first
566
567	<	//   new AllLong( simnfo );
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
655	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
656	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
574
575	+	// get the forceField
576
577	+	strcpy(force_field, globals->getForceField());
578
579	<	// initialize the Fortran
580	<
662	<	simnfo->refreshSim();
663	<
664	<	if( !strcmp( simnfo->mixingRule, "standard") ){
665	<	the_ff->initForceField( LB_MIXING_RULE );
579	>	if (!strcasecmp(force_field, "DUFF")){
580	>	ffCase = FF_DUFF;
581		}
582	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
583	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
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,
590	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
591	<	simnfo->mixingRule );
592	<	painCave.isFatal = 1;
675	<	simError();
589	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
590	>	force_field);
591	>	painCave.isFatal = 1;
592	>	simError();
593		}
594
595	+	// get the ensemble
596
597	<	#ifdef IS_MPI
680	<	strcpy( checkPointMsg,
681	<	"Successfully intialized the mixingRule for Fortran." );
682	<	MPIcheckPoint();
683	<	#endif // is_mpi
684	<	}
685	<
686	<
687	<	void SimSetup::makeMolecules( void ){
688	<
689	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
690	<	molInit info;
691	<	DirectionalAtom* dAtom;
692	<	LinkedAssign* extras;
693	<	LinkedAssign* current_extra;
694	<	AtomStamp* currentAtom;
695	<	BondStamp* currentBond;
696	<	BendStamp* currentBend;
697	<	TorsionStamp* currentTorsion;
698	<
699	<	bond_pair* theBonds;
700	<	bend_set* theBends;
701	<	torsion_set* theTorsions;
702	<
703	<
704	<	//init the forceField paramters
705	<
706	<	the_ff->readParams();
707	<
708	<
709	<	// init the atoms
710	<
711	<	double ux, uy, uz, u, uSqr;
712	<
713	<	atomOffset = 0;
714	<	excludeOffset = 0;
715	<	for(i=0; i<simnfo->n_mol; i++){
716	<
717	<	stampID = the_molecules[i].getStampID();
718	<
719	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
720	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
721	<	info.nBends    = comp_stamps[stampID]->getNBends();
722	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
723	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
724	<
725	<	info.myAtoms = &the_atoms[atomOffset];
726	<	info.myExcludes = &the_excludes[excludeOffset];
727	<	info.myBonds = new Bond*[info.nBonds];
728	<	info.myBends = new Bend*[info.nBends];
729	<	info.myTorsions = new Torsion*[info.nTorsions];
730	<
731	<	theBonds = new bond_pair[info.nBonds];
732	<	theBends = new bend_set[info.nBends];
733	<	theTorsions = new torsion_set[info.nTorsions];
734	<
735	<	// make the Atoms
736	<
737	<	for(j=0; j<info.nAtoms; j++){
738	<
739	<	currentAtom = comp_stamps[stampID]->getAtom( j );
740	<	if( currentAtom->haveOrientation() ){
741	<
742	<	dAtom = new DirectionalAtom(j + atomOffset);
743	<	simnfo->n_oriented++;
744	<	info.myAtoms[j] = dAtom;
745	<
746	<	ux = currentAtom->getOrntX();
747	<	uy = currentAtom->getOrntY();
748	<	uz = currentAtom->getOrntZ();
749	<
750	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
751	<
752	<	u = sqrt( uSqr );
753	<	ux = ux / u;
754	<	uy = uy / u;
755	<	uz = uz / u;
756	<
757	<	dAtom->setSUx( ux );
758	<	dAtom->setSUy( uy );
759	<	dAtom->setSUz( uz );
760	<	}
761	<	else{
762	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
763	<	}
764	<	info.myAtoms[j]->setType( currentAtom->getType() );
765	<
766	<	#ifdef IS_MPI
767	<
768	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
769	<
770	<	#endif // is_mpi
771	<	}
772	<
773	<	// make the bonds
774	<	for(j=0; j<info.nBonds; j++){
775	<
776	<	currentBond = comp_stamps[stampID]->getBond( j );
777	<	theBonds[j].a = currentBond->getA() + atomOffset;
778	<	theBonds[j].b = currentBond->getB() + atomOffset;
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	<	exI = theBonds[i].a;
600	<	exJ = theBonds[i].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 ){
785	<	tempEx = exI;
786	<	exI = exJ;
787	<	exJ = tempEx;
788	<	}
789	<	#ifdef IS_MPI
790	<	tempEx = exI;
791	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
792	<	tempEx = exJ;
793	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
794	<
795	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
796	<	#else  // isn't MPI
797	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
798	<	#endif  //is_mpi
799	<	}
800	<	excludeOffset += info.nBonds;
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627
628	<	//make the bends
803	<	for(j=0; j<info.nBends; j++){
804	<
805	<	currentBend = comp_stamps[stampID]->getBend( j );
806	<	theBends[j].a = currentBend->getA() + atomOffset;
807	<	theBends[j].b = currentBend->getB() + atomOffset;
808	<	theBends[j].c = currentBend->getC() + atomOffset;
809	<
810	<	if( currentBend->haveExtras() ){
811	<
812	<	extras = currentBend->getExtras();
813	<	current_extra = extras;
814	<
815	<	while( current_extra != NULL ){
816	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
817	<
818	<	switch( current_extra->getType() ){
819	<
820	<	case 0:
821	<	theBends[j].ghost =
822	<	current_extra->getInt() + atomOffset;
823	<	theBends[j].isGhost = 1;
824	<	break;
825	<
826	<	case 1:
827	<	theBends[j].ghost =
828	<	(int)current_extra->getDouble() + atomOffset;
829	<	theBends[j].isGhost = 1;
830	<	break;
831	<
832	<	default:
833	<	sprintf( painCave.errMsg,
834	<	"SimSetup Error: ghostVectorSource was neiter a "
835	<	"double nor an int.\n"
836	<	"-->Bend[%d] in %s\n",
837	<	j, comp_stamps[stampID]->getID() );
838	<	painCave.isFatal = 1;
839	<	simError();
840	<	}
841	<	}
842	<
843	<	else{
844	<
845	<	sprintf( painCave.errMsg,
846	<	"SimSetup Error: unhandled bend assignment:\n"
847	<	"    -->%s in Bend[%d] in %s\n",
848	<	current_extra->getlhs(),
849	<	j, comp_stamps[stampID]->getID() );
850	<	painCave.isFatal = 1;
851	<	simError();
852	<	}
853	<
854	<	current_extra = current_extra->getNext();
855	<	}
856	<	}
857	<
858	<	if( !theBends[j].isGhost ){
859	<
860	<	exI = theBends[j].a;
861	<	exJ = theBends[j].c;
862	<	}
863	<	else{
864	<
865	<	exI = theBends[j].a;
866	<	exJ = theBends[j].b;
867	<	}
868	<
869	<	// exclude_I must always be the smaller of the pair
870	<	if( exI > exJ ){
871	<	tempEx = exI;
872	<	exI = exJ;
873	<	exJ = tempEx;
874	<	}
875	<	#ifdef IS_MPI
876	<	tempEx = exI;
877	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
878	<	tempEx = exJ;
879	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
880	<
881	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
882	<	#else  // isn't MPI
883	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
884	<	#endif  //is_mpi
885	<	}
886	<	excludeOffset += info.nBends;
628	>	// get the mixing rule
629
630	<	for(j=0; j<info.nTorsions; j++){
631	<
890	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
891	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
892	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
893	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
894	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
895	<
896	<	exI = theTorsions[j].a;
897	<	exJ = theTorsions[j].d;
898	<
899	<	// exclude_I must always be the smaller of the pair
900	<	if( exI > exJ ){
901	<	tempEx = exI;
902	<	exI = exJ;
903	<	exJ = tempEx;
904	<	}
905	<	#ifdef IS_MPI
906	<	tempEx = exI;
907	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
908	<	tempEx = exJ;
909	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
910	<
911	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
912	<	#else  // isn't MPI
913	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
914	<	#endif  //is_mpi
915	<	}
916	<	excludeOffset += info.nTorsions;
917	<
918	<
919	<	// send the arrays off to the forceField for init.
920	<
921	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
922	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
923	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
924	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
925	<
926	<
927	<	the_molecules[i].initialize( info );
928	<	atomOffset += info.nAtoms;
929	<	delete[] theBonds;
930	<	delete[] theBends;
931	<	delete[] theTorsions;
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632		}
633
634	<	// clean up the forcefield
935	<	the_ff->calcRcut();
936	<	the_ff->cleanMe();
937	<	}
634	>	// get the components and calculate the tot_nMol and indvidual n_mol
635
636	<	void SimSetup::initFromBass( void ){
636	>	the_components = globals->getComponents();
637	>	components_nmol = new int[n_components];
638
941	–	int i, j, k;
942	–	int n_cells;
943	–	double cellx, celly, cellz;
944	–	double temp1, temp2, temp3;
945	–	int n_per_extra;
946	–	int n_extra;
947	–	int have_extra, done;
639
640	<	temp1 = (double)tot_nmol / 4.0;
641	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
642	<	temp3 = ceil( temp2 );
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	<	have_extra =0;
645	<	if( temp2 < temp3 ){ // we have a non-complete lattice
646	<	have_extra =1;
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	>	}
654
655	<	n_cells = (int)temp3 - 1;
656	<	cellx = simnfo->box_x / temp3;
959	<	celly = simnfo->box_y / temp3;
960	<	cellz = simnfo->box_z / temp3;
961	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
962	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
963	<	n_per_extra = (int)ceil( temp1 );
964	<
965	<	if( n_per_extra > 4){
966	<	sprintf( painCave.errMsg,
967	<	"SimSetup error. There has been an error in constructing"
968	<	" the non-complete lattice.\n" );
969	<	painCave.isFatal = 1;
970	<	simError();
655	>	tot_nmol += the_components[i]->getNMol();
656	>	components_nmol[i] = the_components[i]->getNMol();
657		}
658		}
659		else{
660	<	n_cells = (int)temp3;
661	<	cellx = simnfo->box_x / temp3;
662	<	celly = simnfo->box_y / temp3;
663	<	cellz = simnfo->box_z / temp3;
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	<	current_mol = 0;
981	<	current_comp_mol = 0;
982	<	current_comp = 0;
983	<	current_atom_ndx = 0;
670	>	// set the status, sample, and thermal kick times
671
672	<	for( i=0; i < n_cells ; i++ ){
673	<	for( j=0; j < n_cells; j++ ){
674	<	for( k=0; k < n_cells; k++ ){
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	>	else{
679	>	info[i].sampleTime = globals->getRunTime();
680	>	info[i].statusTime = info[i].sampleTime;
681	>	info[i].thermalTime = info[i].sampleTime;
682	>	}
683
684	<	makeElement( i * cellx,
685	<	j * celly,
686	<	k * cellz );
684	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686	>	}
687
688	<	makeElement( i * cellx + 0.5 * cellx,
689	<	j * celly + 0.5 * celly,
690	<	k * cellz );
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690	>	}
691
692	<	makeElement( i * cellx,
693	<	j * celly + 0.5 * celly,
694	<	k * cellz + 0.5 * cellz );
695	<
1001	<	makeElement( i * cellx + 0.5 * cellx,
1002	<	j * celly,
1003	<	k * cellz + 0.5 * cellz );
1004	<	}
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696		}
1006	–	}
697
698	<	if( have_extra ){
1009	<	done = 0;
698	>	// check for the temperature set flag
699
700	<	int start_ndx;
701	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1013	<	for( j=0; j < (n_cells+1) && !done; j++ ){
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702
703	<	if( i < n_cells ){
703	>	// get some of the tricky things that may still be in the globals
704
705	<	if( j < n_cells ){
706	<	start_ndx = n_cells;
707	<	}
708	<	else start_ndx = 0;
709	<	}
1022	<	else start_ndx = 0;
705	>	double boxVector[3];
706	>	if (globals->haveBox()){
707	>	boxVector[0] = globals->getBox();
708	>	boxVector[1] = globals->getBox();
709	>	boxVector[2] = globals->getBox();
710
711	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
712	<
713	<	makeElement( i * cellx,
714	<	j * celly,
715	<	k * cellz );
716	<	done = ( current_mol >= tot_nmol );
711	>	info[i].setBox(boxVector);
712	>	}
713	>	else if (globals->haveDensity()){
714	>	double vol;
715	>	vol = (double) tot_nmol / globals->getDensity();
716	>	boxVector[0] = pow(vol, (1.0 / 3.0));
717	>	boxVector[1] = boxVector[0];
718	>	boxVector[2] = boxVector[0];
719
720	<	if( !done && n_per_extra > 1 ){
721	<	makeElement( i * cellx + 0.5 * cellx,
722	<	j * celly + 0.5 * celly,
723	<	k * cellz );
724	<	done = ( current_mol >= tot_nmol );
725	<	}
720	>	info[i].setBox(boxVector);
721	>	}
722	>	else{
723	>	if (!globals->haveBoxX()){
724	>	sprintf(painCave.errMsg,
725	>	"SimSetup error, no periodic BoxX size given.\n");
726	>	painCave.isFatal = 1;
727	>	simError();
728	>	}
729	>	boxVector[0] = globals->getBoxX();
730
731	<	if( !done && n_per_extra > 2){
732	<	makeElement( i * cellx,
733	<	j * celly + 0.5 * celly,
734	<	k * cellz + 0.5 * cellz );
735	<	done = ( current_mol >= tot_nmol );
736	<	}
731	>	if (!globals->haveBoxY()){
732	>	sprintf(painCave.errMsg,
733	>	"SimSetup error, no periodic BoxY size given.\n");
734	>	painCave.isFatal = 1;
735	>	simError();
736	>	}
737	>	boxVector[1] = globals->getBoxY();
738
739	<	if( !done && n_per_extra > 3){
740	<	makeElement( i * cellx + 0.5 * cellx,
741	<	j * celly,
742	<	k * cellz + 0.5 * cellz );
743	<	done = ( current_mol >= tot_nmol );
1050	<	}
1051	<	}
739	>	if (!globals->haveBoxZ()){
740	>	sprintf(painCave.errMsg,
741	>	"SimSetup error, no periodic BoxZ size given.\n");
742	>	painCave.isFatal = 1;
743	>	simError();
744		}
745	+	boxVector[2] = globals->getBoxZ();
746	+
747	+	info[i].setBox(boxVector);
748		}
749		}
750
751	+	//setup seed for random number generator
752	+	int seedValue;
753
754	<	for( i=0; i<simnfo->n_atoms; i++ ){
755	<	simnfo->atoms[i]->set_vx( 0.0 );
756	<	simnfo->atoms[i]->set_vy( 0.0 );
757	<	simnfo->atoms[i]->set_vz( 0.0 );
754	>	if (globals->haveSeed()){
755	>	seedValue = globals->getSeed();
756	>
757	>	if(seedValue / 1E9 == 0){
758	>	sprintf(painCave.errMsg,
759	>	"Seed for sprng library should contain at least 9 digits\n"
760	>	"OOPSE will generate a seed for user\n");
761	>	painCave.isFatal = 0;
762	>	simError();
763	>
764	>	//using seed generated by system instead of invalid seed set by user
765	>	#ifndef IS_MPI
766	>	seedValue = make_sprng_seed();
767	>	#else
768	>	if (worldRank == 0){
769	>	seedValue = make_sprng_seed();
770	>	}
771	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
772	>	#endif
773	>	}
774	>	}//end of if branch of globals->haveSeed()
775	>	else{
776	>
777	>	#ifndef IS_MPI
778	>	seedValue = make_sprng_seed();
779	>	#else
780	>	if (worldRank == 0){
781	>	seedValue = make_sprng_seed();
782	>	}
783	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
784	>	#endif
785	>	}//end of globals->haveSeed()
786	>
787	>	for (int i = 0; i < nInfo; i++){
788	>	info[i].setSeed(seedValue);
789		}
790	+
791	+	#ifdef IS_MPI
792	+	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
793	+	MPIcheckPoint();
794	+	#endif // is_mpi
795		}
796
1064	–	void SimSetup::makeElement( double x, double y, double z ){
797
798	<	int k;
799	<	AtomStamp* current_atom;
800	<	DirectionalAtom* dAtom;
801	<	double rotMat[3][3];
798	>	void SimSetup::finalInfoCheck(void){
799	>	int index;
800	>	int usesDipoles;
801	>	int i;
802
803	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
803	>	for (i = 0; i < nInfo; i++){
804	>	// check electrostatic parameters
805
806	<	current_atom = comp_stamps[current_comp]->getAtom( k );
807	<	if( !current_atom->havePosition() ){
808	<	sprintf( painCave.errMsg,
809	<	"SimSetup:initFromBass error.\n"
810	<	"\tComponent %s, atom %s does not have a position specified.\n"
1078	<	"\tThe initialization routine is unable to give a start"
1079	<	" position.\n",
1080	<	comp_stamps[current_comp]->getID(),
1081	<	current_atom->getType() );
1082	<	painCave.isFatal = 1;
1083	<	simError();
806	>	index = 0;
807	>	usesDipoles = 0;
808	>	while ((index < info[i].n_atoms) && !usesDipoles){
809	>	usesDipoles = (info[i].atoms[index])->hasDipole();
810	>	index++;
811		}
812
813	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
814	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
815	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
813	>	#ifdef IS_MPI
814	>	int myUse = usesDipoles;
815	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>	#endif //is_mpi
817
818	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
818	>	double theEcr, theEst;
819
820	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
820	>	if (globals->getUseRF()){
821	>	info[i].useReactionField = 1;
822
823	<	rotMat[0][0] = 1.0;
824	<	rotMat[0][1] = 0.0;
825	<	rotMat[0][2] = 0.0;
823	>	if (!globals->haveECR()){
824	>	sprintf(painCave.errMsg,
825	>	"SimSetup Warning: using default value of 1/2 the smallest "
826	>	"box length for the electrostaticCutoffRadius.\n"
827	>	"I hope you have a very fast processor!\n");
828	>	painCave.isFatal = 0;
829	>	simError();
830	>	double smallest;
831	>	smallest = info[i].boxL[0];
832	>	if (info[i].boxL[1] <= smallest)
833	>	smallest = info[i].boxL[1];
834	>	if (info[i].boxL[2] <= smallest)
835	>	smallest = info[i].boxL[2];
836	>	theEcr = 0.5 * smallest;
837	>	}
838	>	else{
839	>	theEcr = globals->getECR();
840	>	}
841
842	<	rotMat[1][0] = 0.0;
843	<	rotMat[1][1] = 1.0;
844	<	rotMat[1][2] = 0.0;
842	>	if (!globals->haveEST()){
843	>	sprintf(painCave.errMsg,
844	>	"SimSetup Warning: using default value of 0.05 * the "
845	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
846	>	painCave.isFatal = 0;
847	>	simError();
848	>	theEst = 0.05 * theEcr;
849	>	}
850	>	else{
851	>	theEst = globals->getEST();
852	>	}
853
854	<	rotMat[2][0] = 0.0;
1103	<	rotMat[2][1] = 0.0;
1104	<	rotMat[2][2] = 1.0;
854	>	info[i].setEcr(theEcr, theEst);
855
856	<	dAtom->setA( rotMat );
856	>	if (!globals->haveDielectric()){
857	>	sprintf(painCave.errMsg,
858	>	"SimSetup Error: You are trying to use Reaction Field without"
859	>	"setting a dielectric constant!\n");
860	>	painCave.isFatal = 1;
861	>	simError();
862	>	}
863	>	info[i].dielectric = globals->getDielectric();
864		}
865	+	else{
866	+	if (usesDipoles){
867	+	if (!globals->haveECR()){
868	+	sprintf(painCave.errMsg,
869	+	"SimSetup Warning: using default value of 1/2 the smallest "
870	+	"box length for the electrostaticCutoffRadius.\n"
871	+	"I hope you have a very fast processor!\n");
872	+	painCave.isFatal = 0;
873	+	simError();
874	+	double smallest;
875	+	smallest = info[i].boxL[0];
876	+	if (info[i].boxL[1] <= smallest)
877	+	smallest = info[i].boxL[1];
878	+	if (info[i].boxL[2] <= smallest)
879	+	smallest = info[i].boxL[2];
880	+	theEcr = 0.5 * smallest;
881	+	}
882	+	else{
883	+	theEcr = globals->getECR();
884	+	}
885
886	<	current_atom_ndx++;
886	>	if (!globals->haveEST()){
887	>	sprintf(painCave.errMsg,
888	>	"SimSetup Warning: using default value of 0.05 * the "
889	>	"electrostaticCutoffRadius for the "
890	>	"electrostaticSkinThickness\n");
891	>	painCave.isFatal = 0;
892	>	simError();
893	>	theEst = 0.05 * theEcr;
894	>	}
895	>	else{
896	>	theEst = globals->getEST();
897	>	}
898	>
899	>	info[i].setEcr(theEcr, theEst);
900	>	}
901	>	}
902		}
903
904	<	current_mol++;
905	<	current_comp_mol++;
904	>	#ifdef IS_MPI
905	>	strcpy(checkPointMsg, "post processing checks out");
906	>	MPIcheckPoint();
907	>	#endif // is_mpi
908	>	}
909
910	<	if( current_comp_mol >= components_nmol[current_comp] ){
910	>	void SimSetup::initSystemCoords(void){
911	>	int i;
912
913	<	current_comp_mol = 0;
914	<	current_comp++;
913	>	char* inName;
914	>
915	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
916	>
917	>	for (i = 0; i < info[0].n_atoms; i++)
918	>	info[0].atoms[i]->setCoords();
919	>
920	>	if (globals->haveInitialConfig()){
921	>	InitializeFromFile* fileInit;
922	>	#ifdef IS_MPI // is_mpi
923	>	if (worldRank == 0){
924	>	#endif //is_mpi
925	>	inName = globals->getInitialConfig();
926	>	fileInit = new InitializeFromFile(inName);
927	>	#ifdef IS_MPI
928	>	}
929	>	else
930	>	fileInit = new InitializeFromFile(NULL);
931	>	#endif
932	>	fileInit->readInit(info); // default velocities on
933	>
934	>	delete fileInit;
935	>	}
936	>	else{
937	>	#ifdef IS_MPI
938	>
939	>	// no init from bass
940	>
941	>	sprintf(painCave.errMsg,
942	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
943	>	painCave.isFatal = 1;;
944	>	simError();
945	>
946	>	#else
947	>
948	>	initFromBass();
949	>
950	>
951	>	#endif
952	>	}
953	>
954	>	#ifdef IS_MPI
955	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
956	>	MPIcheckPoint();
957	>	#endif // is_mpi
958	>	}
959	>
960	>
961	>	void SimSetup::makeOutNames(void){
962	>	int k;
963	>
964	>
965	>	for (k = 0; k < nInfo; k++){
966	>	#ifdef IS_MPI
967	>	if (worldRank == 0){
968	>	#endif // is_mpi
969	>
970	>	if (globals->haveFinalConfig()){
971	>	strcpy(info[k].finalName, globals->getFinalConfig());
972	>	}
973	>	else{
974	>	strcpy(info[k].finalName, inFileName);
975	>	char* endTest;
976	>	int nameLength = strlen(info[k].finalName);
977	>	endTest = &(info[k].finalName[nameLength - 5]);
978	>	if (!strcmp(endTest, ".bass")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".BASS")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	endTest = &(info[k].finalName[nameLength - 4]);
986	>	if (!strcmp(endTest, ".bss")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else if (!strcmp(endTest, ".mdl")){
990	>	strcpy(endTest, ".eor");
991	>	}
992	>	else{
993	>	strcat(info[k].finalName, ".eor");
994	>	}
995	>	}
996	>	}
997	>
998	>	// make the sample and status out names
999	>
1000	>	strcpy(info[k].sampleName, inFileName);
1001	>	char* endTest;
1002	>	int nameLength = strlen(info[k].sampleName);
1003	>	endTest = &(info[k].sampleName[nameLength - 5]);
1004	>	if (!strcmp(endTest, ".bass")){
1005	>	strcpy(endTest, ".dump");
1006	>	}
1007	>	else if (!strcmp(endTest, ".BASS")){
1008	>	strcpy(endTest, ".dump");
1009	>	}
1010	>	else{
1011	>	endTest = &(info[k].sampleName[nameLength - 4]);
1012	>	if (!strcmp(endTest, ".bss")){
1013	>	strcpy(endTest, ".dump");
1014	>	}
1015	>	else if (!strcmp(endTest, ".mdl")){
1016	>	strcpy(endTest, ".dump");
1017	>	}
1018	>	else{
1019	>	strcat(info[k].sampleName, ".dump");
1020	>	}
1021	>	}
1022	>
1023	>	strcpy(info[k].statusName, inFileName);
1024	>	nameLength = strlen(info[k].statusName);
1025	>	endTest = &(info[k].statusName[nameLength - 5]);
1026	>	if (!strcmp(endTest, ".bass")){
1027	>	strcpy(endTest, ".stat");
1028	>	}
1029	>	else if (!strcmp(endTest, ".BASS")){
1030	>	strcpy(endTest, ".stat");
1031	>	}
1032	>	else{
1033	>	endTest = &(info[k].statusName[nameLength - 4]);
1034	>	if (!strcmp(endTest, ".bss")){
1035	>	strcpy(endTest, ".stat");
1036	>	}
1037	>	else if (!strcmp(endTest, ".mdl")){
1038	>	strcpy(endTest, ".stat");
1039	>	}
1040	>	else{
1041	>	strcat(info[k].statusName, ".stat");
1042	>	}
1043	>	}
1044	>
1045	>	#ifdef IS_MPI
1046	>
1047	>	}
1048	>	#endif // is_mpi
1049		}
1050		}
1051	+
1052	+
1053	+	void SimSetup::sysObjectsCreation(void){
1054	+	int i, k;
1055	+
1056	+	// create the forceField
1057	+
1058	+	createFF();
1059	+
1060	+	// extract componentList
1061	+
1062	+	compList();
1063	+
1064	+	// calc the number of atoms, bond, bends, and torsions
1065	+
1066	+	calcSysValues();
1067	+
1068	+	#ifdef IS_MPI
1069	+	// divide the molecules among the processors
1070	+
1071	+	mpiMolDivide();
1072	+	#endif //is_mpi
1073	+
1074	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1075	+
1076	+	makeSysArrays();
1077	+
1078	+	// make and initialize the molecules (all but atomic coordinates)
1079	+
1080	+	makeMolecules();
1081	+
1082	+	for (k = 0; k < nInfo; k++){
1083	+	info[k].identArray = new int[info[k].n_atoms];
1084	+	for (i = 0; i < info[k].n_atoms; i++){
1085	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1086	+	}
1087	+	}
1088	+	}
1089	+
1090	+
1091	+	void SimSetup::createFF(void){
1092	+	switch (ffCase){
1093	+	case FF_DUFF:
1094	+	the_ff = new DUFF();
1095	+	break;
1096	+
1097	+	case FF_LJ:
1098	+	the_ff = new LJFF();
1099	+	break;
1100	+
1101	+	case FF_EAM:
1102	+	the_ff = new EAM_FF();
1103	+	break;
1104	+
1105	+	default:
1106	+	sprintf(painCave.errMsg,
1107	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1108	+	painCave.isFatal = 1;
1109	+	simError();
1110	+	}
1111	+
1112	+	#ifdef IS_MPI
1113	+	strcpy(checkPointMsg, "ForceField creation successful");
1114	+	MPIcheckPoint();
1115	+	#endif // is_mpi
1116	+	}
1117	+
1118	+
1119	+	void SimSetup::compList(void){
1120	+	int i;
1121	+	char* id;
1122	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1123	+	LinkedMolStamp* currentStamp = NULL;
1124	+	comp_stamps = new MoleculeStamp * [n_components];
1125	+
1126	+	// make an array of molecule stamps that match the components used.
1127	+	// also extract the used stamps out into a separate linked list
1128	+
1129	+	for (i = 0; i < nInfo; i++){
1130	+	info[i].nComponents = n_components;
1131	+	info[i].componentsNmol = components_nmol;
1132	+	info[i].compStamps = comp_stamps;
1133	+	info[i].headStamp = headStamp;
1134	+	}
1135	+
1136	+
1137	+	for (i = 0; i < n_components; i++){
1138	+	id = the_components[i]->getType();
1139	+	comp_stamps[i] = NULL;
1140	+
1141	+	// check to make sure the component isn't already in the list
1142	+
1143	+	comp_stamps[i] = headStamp->match(id);
1144	+	if (comp_stamps[i] == NULL){
1145	+	// extract the component from the list;
1146	+
1147	+	currentStamp = stamps->extractMolStamp(id);
1148	+	if (currentStamp == NULL){
1149	+	sprintf(painCave.errMsg,
1150	+	"SimSetup error: Component \"%s\" was not found in the "
1151	+	"list of declared molecules\n",
1152	+	id);
1153	+	painCave.isFatal = 1;
1154	+	simError();
1155	+	}
1156	+
1157	+	headStamp->add(currentStamp);
1158	+	comp_stamps[i] = headStamp->match(id);
1159	+	}
1160	+	}
1161	+
1162	+	#ifdef IS_MPI
1163	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1164	+	MPIcheckPoint();
1165	+	#endif // is_mpi
1166	+	}
1167	+
1168	+	void SimSetup::calcSysValues(void){
1169	+	int i;
1170	+
1171	+	int* molMembershipArray;
1172	+
1173	+	tot_atoms = 0;
1174	+	tot_bonds = 0;
1175	+	tot_bends = 0;
1176	+	tot_torsions = 0;
1177	+	for (i = 0; i < n_components; i++){
1178	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1180	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1181	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182	+	}
1183	+
1184	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	+	molMembershipArray = new int[tot_atoms];
1186	+
1187	+	for (i = 0; i < nInfo; i++){
1188	+	info[i].n_atoms = tot_atoms;
1189	+	info[i].n_bonds = tot_bonds;
1190	+	info[i].n_bends = tot_bends;
1191	+	info[i].n_torsions = tot_torsions;
1192	+	info[i].n_SRI = tot_SRI;
1193	+	info[i].n_mol = tot_nmol;
1194	+
1195	+	info[i].molMembershipArray = molMembershipArray;
1196	+	}
1197	+	}
1198	+
1199	+	#ifdef IS_MPI
1200	+
1201	+	void SimSetup::mpiMolDivide(void){
1202	+	int i, j, k;
1203	+	int localMol, allMol;
1204	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1205	+
1206	+	mpiSim = new mpiSimulation(info);
1207	+
1208	+	globalIndex = mpiSim->divideLabor();
1209	+
1210	+	// set up the local variables
1211	+
1212	+	mol2proc = mpiSim->getMolToProcMap();
1213	+	molCompType = mpiSim->getMolComponentType();
1214	+
1215	+	allMol = 0;
1216	+	localMol = 0;
1217	+	local_atoms = 0;
1218	+	local_bonds = 0;
1219	+	local_bends = 0;
1220	+	local_torsions = 0;
1221	+	globalAtomIndex = 0;
1222	+
1223	+
1224	+	for (i = 0; i < n_components; i++){
1225	+	for (j = 0; j < components_nmol[i]; j++){
1226	+	if (mol2proc[allMol] == worldRank){
1227	+	local_atoms += comp_stamps[i]->getNAtoms();
1228	+	local_bonds += comp_stamps[i]->getNBonds();
1229	+	local_bends += comp_stamps[i]->getNBends();
1230	+	local_torsions += comp_stamps[i]->getNTorsions();
1231	+	localMol++;
1232	+	}
1233	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1234	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1235	+	globalAtomIndex++;
1236	+	}
1237	+
1238	+	allMol++;
1239	+	}
1240	+	}
1241	+	local_SRI = local_bonds + local_bends + local_torsions;
1242	+
1243	+	info[0].n_atoms = mpiSim->getMyNlocal();
1244	+
1245	+	if (local_atoms != info[0].n_atoms){
1246	+	sprintf(painCave.errMsg,
1247	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1248	+	" localAtom (%d) are not equal.\n",
1249	+	info[0].n_atoms, local_atoms);
1250	+	painCave.isFatal = 1;
1251	+	simError();
1252	+	}
1253	+
1254	+	info[0].n_bonds = local_bonds;
1255	+	info[0].n_bends = local_bends;
1256	+	info[0].n_torsions = local_torsions;
1257	+	info[0].n_SRI = local_SRI;
1258	+	info[0].n_mol = localMol;
1259	+
1260	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1261	+	MPIcheckPoint();
1262	+	}
1263	+
1264	+	#endif // is_mpi
1265	+
1266	+
1267	+	void SimSetup::makeSysArrays(void){
1268	+
1269	+	#ifndef IS_MPI
1270	+	int k, j;
1271	+	#endif // is_mpi
1272	+	int i, l;
1273	+
1274	+	Atom** the_atoms;
1275	+	Molecule* the_molecules;
1276	+	Exclude** the_excludes;
1277	+
1278	+
1279	+	for (l = 0; l < nInfo; l++){
1280	+	// create the atom and short range interaction arrays
1281	+
1282	+	the_atoms = new Atom * [info[l].n_atoms];
1283	+	the_molecules = new Molecule[info[l].n_mol];
1284	+	int molIndex;
1285	+
1286	+	// initialize the molecule's stampID's
1287	+
1288	+	#ifdef IS_MPI
1289	+
1290	+
1291	+	molIndex = 0;
1292	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1293	+	if (mol2proc[i] == worldRank){
1294	+	the_molecules[molIndex].setStampID(molCompType[i]);
1295	+	the_molecules[molIndex].setMyIndex(molIndex);
1296	+	the_molecules[molIndex].setGlobalIndex(i);
1297	+	molIndex++;
1298	+	}
1299	+	}
1300	+
1301	+	#else // is_mpi
1302	+
1303	+	molIndex = 0;
1304	+	globalAtomIndex = 0;
1305	+	for (i = 0; i < n_components; i++){
1306	+	for (j = 0; j < components_nmol[i]; j++){
1307	+	the_molecules[molIndex].setStampID(i);
1308	+	the_molecules[molIndex].setMyIndex(molIndex);
1309	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1310	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1311	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1312	+	globalAtomIndex++;
1313	+	}
1314	+	molIndex++;
1315	+	}
1316	+	}
1317	+
1318	+
1319	+	#endif // is_mpi
1320	+
1321	+
1322	+	if (info[l].n_SRI){
1323	+	Exclude::createArray(info[l].n_SRI);
1324	+	the_excludes = new Exclude * [info[l].n_SRI];
1325	+	for (int ex = 0; ex < info[l].n_SRI; ex++){
1326	+	the_excludes[ex] = new Exclude(ex);
1327	+	}
1328	+	info[l].globalExcludes = new int;
1329	+	info[l].n_exclude = info[l].n_SRI;
1330	+	}
1331	+	else{
1332	+	Exclude::createArray(1);
1333	+	the_excludes = new Exclude * ;
1334	+	the_excludes[0] = new Exclude(0);
1335	+	the_excludes[0]->setPair(0, 0);
1336	+	info[l].globalExcludes = new int;
1337	+	info[l].globalExcludes[0] = 0;
1338	+	info[l].n_exclude = 0;
1339	+	}
1340	+
1341	+	// set the arrays into the SimInfo object
1342	+
1343	+	info[l].atoms = the_atoms;
1344	+	info[l].molecules = the_molecules;
1345	+	info[l].nGlobalExcludes = 0;
1346	+	info[l].excludes = the_excludes;
1347	+
1348	+	the_ff->setSimInfo(info);
1349	+	}
1350	+	}
1351	+
1352	+	void SimSetup::makeIntegrator(void){
1353	+	int k;
1354	+
1355	+	NVE<RealIntegrator>* myNVE = NULL;
1356	+	NVT<RealIntegrator>* myNVT = NULL;
1357	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1358	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1359	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1360	+
1361	+	for (k = 0; k < nInfo; k++){
1362	+	switch (ensembleCase){
1363	+	case NVE_ENS:
1364	+	if (globals->haveZconstraints()){
1365	+	setupZConstraint(info[k]);
1366	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1367	+	}
1368	+	else{
1369	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1370	+	}
1371	+
1372	+	info->the_integrator = myNVE;
1373	+	break;
1374	+
1375	+	case NVT_ENS:
1376	+	if (globals->haveZconstraints()){
1377	+	setupZConstraint(info[k]);
1378	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1379	+	}
1380	+	else
1381	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1382	+
1383	+	myNVT->setTargetTemp(globals->getTargetTemp());
1384	+
1385	+	if (globals->haveTauThermostat())
1386	+	myNVT->setTauThermostat(globals->getTauThermostat());
1387	+	else{
1388	+	sprintf(painCave.errMsg,
1389	+	"SimSetup error: If you use the NVT\n"
1390	+	"    ensemble, you must set tauThermostat.\n");
1391	+	painCave.isFatal = 1;
1392	+	simError();
1393	+	}
1394	+
1395	+	info->the_integrator = myNVT;
1396	+	break;
1397	+
1398	+	case NPTi_ENS:
1399	+	if (globals->haveZconstraints()){
1400	+	setupZConstraint(info[k]);
1401	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1402	+	}
1403	+	else
1404	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1405	+
1406	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1407	+
1408	+	if (globals->haveTargetPressure())
1409	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1410	+	else{
1411	+	sprintf(painCave.errMsg,
1412	+	"SimSetup error: If you use a constant pressure\n"
1413	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1414	+	painCave.isFatal = 1;
1415	+	simError();
1416	+	}
1417	+
1418	+	if (globals->haveTauThermostat())
1419	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1420	+	else{
1421	+	sprintf(painCave.errMsg,
1422	+	"SimSetup error: If you use an NPT\n"
1423	+	"    ensemble, you must set tauThermostat.\n");
1424	+	painCave.isFatal = 1;
1425	+	simError();
1426	+	}
1427	+
1428	+	if (globals->haveTauBarostat())
1429	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1430	+	else{
1431	+	sprintf(painCave.errMsg,
1432	+	"SimSetup error: If you use an NPT\n"
1433	+	"    ensemble, you must set tauBarostat.\n");
1434	+	painCave.isFatal = 1;
1435	+	simError();
1436	+	}
1437	+
1438	+	info->the_integrator = myNPTi;
1439	+	break;
1440	+
1441	+	case NPTf_ENS:
1442	+	if (globals->haveZconstraints()){
1443	+	setupZConstraint(info[k]);
1444	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1445	+	}
1446	+	else
1447	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1448	+
1449	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1450	+
1451	+	if (globals->haveTargetPressure())
1452	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1453	+	else{
1454	+	sprintf(painCave.errMsg,
1455	+	"SimSetup error: If you use a constant pressure\n"
1456	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1457	+	painCave.isFatal = 1;
1458	+	simError();
1459	+	}
1460	+
1461	+	if (globals->haveTauThermostat())
1462	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1463	+	else{
1464	+	sprintf(painCave.errMsg,
1465	+	"SimSetup error: If you use an NPT\n"
1466	+	"    ensemble, you must set tauThermostat.\n");
1467	+	painCave.isFatal = 1;
1468	+	simError();
1469	+	}
1470	+
1471	+	if (globals->haveTauBarostat())
1472	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1473	+	else{
1474	+	sprintf(painCave.errMsg,
1475	+	"SimSetup error: If you use an NPT\n"
1476	+	"    ensemble, you must set tauBarostat.\n");
1477	+	painCave.isFatal = 1;
1478	+	simError();
1479	+	}
1480	+
1481	+	info->the_integrator = myNPTf;
1482	+	break;
1483	+
1484	+	case NPTxyz_ENS:
1485	+	if (globals->haveZconstraints()){
1486	+	setupZConstraint(info[k]);
1487	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1488	+	}
1489	+	else
1490	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1491	+
1492	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1493	+
1494	+	if (globals->haveTargetPressure())
1495	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1496	+	else{
1497	+	sprintf(painCave.errMsg,
1498	+	"SimSetup error: If you use a constant pressure\n"
1499	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1500	+	painCave.isFatal = 1;
1501	+	simError();
1502	+	}
1503	+
1504	+	if (globals->haveTauThermostat())
1505	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1506	+	else{
1507	+	sprintf(painCave.errMsg,
1508	+	"SimSetup error: If you use an NPT\n"
1509	+	"    ensemble, you must set tauThermostat.\n");
1510	+	painCave.isFatal = 1;
1511	+	simError();
1512	+	}
1513	+
1514	+	if (globals->haveTauBarostat())
1515	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1516	+	else{
1517	+	sprintf(painCave.errMsg,
1518	+	"SimSetup error: If you use an NPT\n"
1519	+	"    ensemble, you must set tauBarostat.\n");
1520	+	painCave.isFatal = 1;
1521	+	simError();
1522	+	}
1523	+
1524	+	info->the_integrator = myNPTxyz;
1525	+	break;
1526	+
1527	+	default:
1528	+	sprintf(painCave.errMsg,
1529	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1530	+	painCave.isFatal = 1;
1531	+	simError();
1532	+	}
1533	+	}
1534	+	}
1535	+
1536	+	void SimSetup::initFortran(void){
1537	+	info[0].refreshSim();
1538	+
1539	+	if (!strcmp(info[0].mixingRule, "standard")){
1540	+	the_ff->initForceField(LB_MIXING_RULE);
1541	+	}
1542	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1543	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1544	+	}
1545	+	else{
1546	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1547	+	info[0].mixingRule);
1548	+	painCave.isFatal = 1;
1549	+	simError();
1550	+	}
1551	+
1552	+
1553	+	#ifdef IS_MPI
1554	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1555	+	MPIcheckPoint();
1556	+	#endif // is_mpi
1557	+	}
1558	+
1559	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1560	+	int nZConstraints;
1561	+	ZconStamp** zconStamp;
1562	+
1563	+	if (globals->haveZconstraintTime()){
1564	+	//add sample time of z-constraint  into SimInfo's property list
1565	+	DoubleData* zconsTimeProp = new DoubleData();
1566	+	zconsTimeProp->setID(ZCONSTIME_ID);
1567	+	zconsTimeProp->setData(globals->getZconsTime());
1568	+	theInfo.addProperty(zconsTimeProp);
1569	+	}
1570	+	else{
1571	+	sprintf(painCave.errMsg,
1572	+	"ZConstraint error: If you use an ZConstraint\n"
1573	+	" , you must set sample time.\n");
1574	+	painCave.isFatal = 1;
1575	+	simError();
1576	+	}
1577	+
1578	+	//push zconsTol into siminfo, if user does not specify
1579	+	//value for zconsTol, a default value will be used
1580	+	DoubleData* zconsTol = new DoubleData();
1581	+	zconsTol->setID(ZCONSTOL_ID);
1582	+	if (globals->haveZconsTol()){
1583	+	zconsTol->setData(globals->getZconsTol());
1584	+	}
1585	+	else{
1586	+	double defaultZConsTol = 0.01;
1587	+	sprintf(painCave.errMsg,
1588	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1589	+	" , default value %f is used.\n",
1590	+	defaultZConsTol);
1591	+	painCave.isFatal = 0;
1592	+	simError();
1593	+
1594	+	zconsTol->setData(defaultZConsTol);
1595	+	}
1596	+	theInfo.addProperty(zconsTol);
1597	+
1598	+	//set Force Subtraction Policy
1599	+	StringData* zconsForcePolicy = new StringData();
1600	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1601	+
1602	+	if (globals->haveZconsForcePolicy()){
1603	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1604	+	}
1605	+	else{
1606	+	sprintf(painCave.errMsg,
1607	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1608	+	"PolicyByMass is used\n");
1609	+	painCave.isFatal = 0;
1610	+	simError();
1611	+	zconsForcePolicy->setData("BYMASS");
1612	+	}
1613	+
1614	+	theInfo.addProperty(zconsForcePolicy);
1615	+
1616	+	//Determine the name of ouput file and add it into SimInfo's property list
1617	+	//Be careful, do not use inFileName, since it is a pointer which
1618	+	//point to a string at master node, and slave nodes do not contain that string
1619	+
1620	+	string zconsOutput(theInfo.finalName);
1621	+
1622	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1623	+
1624	+	StringData* zconsFilename = new StringData();
1625	+	zconsFilename->setID(ZCONSFILENAME_ID);
1626	+	zconsFilename->setData(zconsOutput);
1627	+
1628	+	theInfo.addProperty(zconsFilename);
1629	+
1630	+	//setup index, pos and other parameters of z-constraint molecules
1631	+	nZConstraints = globals->getNzConstraints();
1632	+	theInfo.nZconstraints = nZConstraints;
1633	+
1634	+	zconStamp = globals->getZconStamp();
1635	+	ZConsParaItem tempParaItem;
1636	+
1637	+	ZConsParaData* zconsParaData = new ZConsParaData();
1638	+	zconsParaData->setID(ZCONSPARADATA_ID);
1639	+
1640	+	for (int i = 0; i < nZConstraints; i++){
1641	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1642	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1643	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1644	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1645	+
1646	+	zconsParaData->addItem(tempParaItem);
1647	+	}
1648	+
1649	+	//check the uniqueness of index
1650	+	if(!zconsParaData->isIndexUnique()){
1651	+	sprintf(painCave.errMsg,
1652	+	"ZConstraint Error: molIndex is not unique\n");
1653	+	painCave.isFatal = 1;
1654	+	simError();
1655	+	}
1656	+
1657	+	//sort the parameters by index of molecules
1658	+	zconsParaData->sortByIndex();
1659	+
1660	+	//push data into siminfo, therefore, we can retrieve later
1661	+	theInfo.addProperty(zconsParaData);
1662	+	}

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