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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 736 by tim, Thu Aug 28 21:09:47 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 12 | Line 16 | SimSetup::SimSetup(){
16		#include "mpiSimulation.hpp"
17		#endif
18
19	+	// some defines for ensemble and Forcefield  cases
20	+
21	+	#define NVE_ENS        0
22	+	#define NVT_ENS        1
23	+	#define NPTi_ENS       2
24	+	#define NPTf_ENS       3
25	+	#define NPTim_ENS      4
26	+	#define NPTfm_ENS      5
27	+
28	+	#define FF_DUFF 0
29	+	#define FF_LJ   1
30	+	#define FF_EAM  2
31	+
32	+	using namespace std;
33	+
34		SimSetup::SimSetup(){
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40	<
40	>
41	>
42		#ifdef IS_MPI
43	<	strcpy( checkPointMsg, "SimSetup creation successful" );
43	>	strcpy(checkPointMsg, "SimSetup creation successful");
44		MPIcheckPoint();
45		#endif // IS_MPI
46		}
#	Line 27 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	<	void SimSetup::parseFile( char* fileName ){
53	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
54	>	info = the_info;
55	>	nInfo = theNinfo;
56	>	isInfoArray = 1;
57	>	}
58
59	+
60	+	void SimSetup::parseFile(char* fileName){
61		#ifdef IS_MPI
62	<	if( worldRank == 0 ){
62	>	if (worldRank == 0){
63		#endif // is_mpi
64	<
64	>
65		inFileName = fileName;
66	<	set_interface_stamps( stamps, globals );
67	<
66	>	set_interface_stamps(stamps, globals);
67	>
68		#ifdef IS_MPI
69		mpiEventInit();
70		#endif
71
72	<	yacc_BASS( fileName );
72	>	yacc_BASS(fileName);
73
74		#ifdef IS_MPI
75		throwMPIEvent(NULL);
76		}
77	<	else receiveParse();
77	>	else{
78	>	receiveParse();
79	>	}
80		#endif
81
82		}
83
84		#ifdef IS_MPI
85		void SimSetup::receiveParse(void){
86	<
87	<	set_interface_stamps( stamps, globals );
88	<	mpiEventInit();
89	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
86	>	set_interface_stamps(stamps, globals);
87	>	mpiEventInit();
88	>	MPIcheckPoint();
89	>	mpiEventLoop();
90		}
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
94	>	void SimSetup::createSim(void){
95	>	int i, j, k, globalAtomIndex;
96
97	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
97	>	// gather all of the information from the Bass file
98
99	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
99	>	gatherInfo();
100
101	<	// 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();
101	>	// creation of complex system objects
102
103	<	// 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 );
103	>	sysObjectsCreation();
104
105	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
105	>	// check on the post processing info
106
107	+	finalInfoCheck();
108
109	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
109	>	// initialize the system coordinates
110
111	<	#ifdef IS_MPI
112	<	strcpy( checkPointMsg, "ForceField creation successful" );
113	<	MPIcheckPoint();
106	<	#endif // is_mpi
111	>	if (!isInfoArray){
112	>	initSystemCoords();
113	>	}
114
115	<
115	>	// make the output filenames
116
117	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
117	>	makeOutNames();
118
119	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
119	>	// make the integrator
120
121	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
121	>	makeIntegrator();
122
123	<	if( !the_components[i]->haveNMol() ){
124	<	// we have a problem
125	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
123	>	#ifdef IS_MPI
124	>	mpiSim->mpiRefresh();
125	>	#endif
126
127	<	tot_nmol += the_components[i]->getNMol();
132	<	components_nmol[i] = the_components[i]->getNMol();
133	<	}
134	<	}
135	<	else{
136	<	sprintf( painCave.errMsg,
137	<	"SimSetup error.\n"
138	<	"\tSorry, the ability to specify total"
139	<	" nMols and then give molfractions in the components\n"
140	<	"\tis not currently supported."
141	<	" Please give nMol in the components.\n" );
142	<	painCave.isFatal = 1;
143	<	simError();
144	<
145	<
146	<	//     tot_nmol = the_globals->getNMol();
147	<
148	<	//   //we have the total number of molecules, now we check for molfractions
149	<	//     for( i=0; i<n_components; i++ ){
150	<
151	<	//       if( !the_components[i]->haveMolFraction() ){
152	<
153	<	//  if( !the_components[i]->haveNMol() ){
154	<	//    //we have a problem
155	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	<	//              << " nMol was given in component
157	<
158	<	}
127	>	// initialize the Fortran
128
129	<	#ifdef IS_MPI
130	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
129	>	initFortran();
130	>	}
131
165	–	// make an array of molecule stamps that match the components used.
166	–	// also extract the used stamps out into a separate linked list
132
133	<	simnfo->nComponents = n_components;
134	<	simnfo->componentsNmol = components_nmol;
135	<	simnfo->compStamps = comp_stamps;
136	<	simnfo->headStamp = new LinkedMolStamp();
137	<
138	<	char* id;
139	<	LinkedMolStamp* headStamp = simnfo->headStamp;
140	<	LinkedMolStamp* currentStamp = NULL;
141	<	for( i=0; i<n_components; i++ ){
133	>	void SimSetup::makeMolecules(void){
134	>	int k, l;
135	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136	>	molInit molInfo;
137	>	DirectionalAtom* dAtom;
138	>	LinkedAssign* extras;
139	>	LinkedAssign* current_extra;
140	>	AtomStamp* currentAtom;
141	>	BondStamp* currentBond;
142	>	BendStamp* currentBend;
143	>	TorsionStamp* currentTorsion;
144
145	<	id = the_components[i]->getType();
146	<	comp_stamps[i] = NULL;
147	<
181	<	// check to make sure the component isn't already in the list
145	>	bond_pair* theBonds;
146	>	bend_set* theBends;
147	>	torsion_set* theTorsions;
148
183	–	comp_stamps[i] = headStamp->match( id );
184	–	if( comp_stamps[i] == NULL ){
185	–
186	–	// extract the component from the list;
187	–
188	–	currentStamp = the_stamps->extractMolStamp( id );
189	–	if( currentStamp == NULL ){
190	–	sprintf( painCave.errMsg,
191	–	"SimSetup error: Component \"%s\" was not found in the "
192	–	"list of declared molecules\n",
193	–	id );
194	–	painCave.isFatal = 1;
195	–	simError();
196	–	}
197	–
198	–	headStamp->add( currentStamp );
199	–	comp_stamps[i] = headStamp->match( id );
200	–	}
201	–	}
149
150	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
150	>	//init the forceField paramters
151
152	+	the_ff->readParams();
153
154
155	<	// caclulate the number of atoms, bonds, bends and torsions
155	>	// init the atoms
156
157	<	tot_atoms = 0;
214	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
218	<
219	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
157	>	double ux, uy, uz, u, uSqr;
158
159	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
159	>	for (k = 0; k < nInfo; k++){
160	>	the_ff->setSimInfo(&(info[k]));
161
162	<	simnfo->n_atoms = tot_atoms;
163	<	simnfo->n_bonds = tot_bonds;
164	<	simnfo->n_bends = tot_bends;
165	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
162	>	atomOffset = 0;
163	>	excludeOffset = 0;
164	>	for (i = 0; i < info[k].n_mol; i++){
165	>	stampID = info[k].molecules[i].getStampID();
166
167	<
168	<	#ifdef IS_MPI
167	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
168	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
169	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
170	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
171	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
172
173	<	// divide the molecules among processors here.
174	<
175	<	mpiSim = new mpiSimulation( simnfo );
176	<
177	<
173	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
174	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
175	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
176	>	molInfo.myBends = new Bend * [molInfo.nBends];
177	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
178
179	<	globalIndex = mpiSim->divideLabor();
179	>	theBonds = new bond_pair[molInfo.nBonds];
180	>	theBends = new bend_set[molInfo.nBends];
181	>	theTorsions = new torsion_set[molInfo.nTorsions];
182
183	+	// make the Atoms
184
185	+	for (j = 0; j < molInfo.nAtoms; j++){
186	+	currentAtom = comp_stamps[stampID]->getAtom(j);
187	+	if (currentAtom->haveOrientation()){
188	+	dAtom = new DirectionalAtom((j + atomOffset),
189	+	info[k].getConfiguration());
190	+	info[k].n_oriented++;
191	+	molInfo.myAtoms[j] = dAtom;
192
193	<	// set up the local variables
194	<
195	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
193	>	ux = currentAtom->getOrntX();
194	>	uy = currentAtom->getOrntY();
195	>	uz = currentAtom->getOrntZ();
196
197	<	for( j=0; j<components_nmol[i]; j++ ){
261	<
262	<	if( mpiSim->getMyMolStart() <= allMol &&
263	<	allMol <= mpiSim->getMyMolEnd() ){
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	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
198
199	<	simnfo->n_atoms = mpiSim->getMyNlocal();
200	<
201	<	if( local_atoms != simnfo->n_atoms ){
202	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
199	>	u = sqrt(uSqr);
200	>	ux = ux / u;
201	>	uy = uy / u;
202	>	uz = uz / u;
203
204	<	simnfo->n_bonds = local_bonds;
205	<	simnfo->n_bends = local_bends;
206	<	simnfo->n_torsions = local_torsions;
207	<	simnfo->n_SRI = local_SRI;
208	<	simnfo->n_mol = localMol;
204	>	dAtom->setSUx(ux);
205	>	dAtom->setSUy(uy);
206	>	dAtom->setSUz(uz);
207	>	}
208	>	else{
209	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
210	>	info[k].getConfiguration());
211	>	}
212	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
213
214	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
296	<	MPIcheckPoint();
297	<
298	<
299	<	#endif // is_mpi
300	<
214	>	#ifdef IS_MPI
215
216	<	// create the atom and short range interaction arrays
216	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
217
218	<	Atom::createArrays(simnfo->n_atoms);
219	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
218	>	#endif // is_mpi
219	>	}
220
221	+	// make the bonds
222	+	for (j = 0; j < molInfo.nBonds; j++){
223	+	currentBond = comp_stamps[stampID]->getBond(j);
224	+	theBonds[j].a = currentBond->getA() + atomOffset;
225	+	theBonds[j].b = currentBond->getB() + atomOffset;
226
227	<	if( simnfo->n_SRI ){
228	<	the_sris = new SRI*[simnfo->n_SRI];
311	<	the_excludes = new int[2 * simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
227	>	exI = theBonds[j].a;
228	>	exJ = theBonds[j].b;
229
230	<	simnfo->n_exclude = 1;
231	<	}
230	>	// exclude_I must always be the smaller of the pair
231	>	if (exI > exJ){
232	>	tempEx = exI;
233	>	exI = exJ;
234	>	exJ = tempEx;
235	>	}
236	>	#ifdef IS_MPI
237	>	tempEx = exI;
238	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	>	tempEx = exJ;
240	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241
242	<	// set the arrays into the SimInfo object
242	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243	>	#else  // isn't MPI
244
245	<	simnfo->atoms = the_atoms;
246	<	simnfo->sr_interactions = the_sris;
247	<	simnfo->nGlobalExcludes = 0;
248	<	simnfo->excludes = the_excludes;
245	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246	>	#endif  //is_mpi
247	>	}
248	>	excludeOffset += molInfo.nBonds;
249
250	+	//make the bends
251	+	for (j = 0; j < molInfo.nBends; j++){
252	+	currentBend = comp_stamps[stampID]->getBend(j);
253	+	theBends[j].a = currentBend->getA() + atomOffset;
254	+	theBends[j].b = currentBend->getB() + atomOffset;
255	+	theBends[j].c = currentBend->getC() + atomOffset;
256
257	<	// get some of the tricky things that may still be in the globals
257	>	if (currentBend->haveExtras()){
258	>	extras = currentBend->getExtras();
259	>	current_extra = extras;
260
261	<	if( simnfo->n_dipoles ){
261	>	while (current_extra != NULL){
262	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
263	>	switch (current_extra->getType()){
264	>	case 0:
265	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
266	>	theBends[j].isGhost = 1;
267	>	break;
268
269	<	if( !the_globals->haveRRF() ){
270	<	sprintf( painCave.errMsg,
271	<	"SimSetup Error, system has dipoles, but no rRF was set.\n");
272	<	painCave.isFatal = 1;
273	<	simError();
343	<	}
344	<	if( !the_globals->haveDielectric() ){
345	<	sprintf( painCave.errMsg,
346	<	"SimSetup Error, system has dipoles, but no"
347	<	" dielectric was set.\n" );
348	<	painCave.isFatal = 1;
349	<	simError();
350	<	}
269	>	case 1:
270	>	theBends[j].ghost = (int) current_extra->getDouble() +
271	>	atomOffset;
272	>	theBends[j].isGhost = 1;
273	>	break;
274
275	<	simnfo->rRF        = the_globals->getRRF();
276	<	simnfo->dielectric = the_globals->getDielectric();
277	<	}
275	>	default:
276	>	sprintf(painCave.errMsg,
277	>	"SimSetup Error: ghostVectorSource was neither a "
278	>	"double nor an int.\n"
279	>	"-->Bend[%d] in %s\n",
280	>	j, comp_stamps[stampID]->getID());
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	}
285	>	else{
286	>	sprintf(painCave.errMsg,
287	>	"SimSetup Error: unhandled bend assignment:\n"
288	>	"    -->%s in Bend[%d] in %s\n",
289	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293
294	<	#ifdef IS_MPI
295	<	strcpy( checkPointMsg, "rRf and dielectric check out" );
296	<	MPIcheckPoint();
359	<	#endif // is_mpi
360	<
361	<	if( the_globals->haveBox() ){
362	<	simnfo->box_x = the_globals->getBox();
363	<	simnfo->box_y = the_globals->getBox();
364	<	simnfo->box_z = the_globals->getBox();
365	<	}
366	<	else if( the_globals->haveDensity() ){
294	>	current_extra = current_extra->getNext();
295	>	}
296	>	}
297
298	<	double vol;
299	<	vol = (double)tot_nmol / the_globals->getDensity();
300	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
301	<	simnfo->box_y = simnfo->box_x;
302	<	simnfo->box_z = simnfo->box_x;
303	<	}
304	<	else{
305	<	if( !the_globals->haveBoxX() ){
376	<	sprintf( painCave.errMsg,
377	<	"SimSetup error, no periodic BoxX size given.\n" );
378	<	painCave.isFatal = 1;
379	<	simError();
380	<	}
381	<	simnfo->box_x = the_globals->getBoxX();
298	>	if (!theBends[j].isGhost){
299	>	exI = theBends[j].a;
300	>	exJ = theBends[j].c;
301	>	}
302	>	else{
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].b;
305	>	}
306
307	<	if( !the_globals->haveBoxY() ){
308	<	sprintf( painCave.errMsg,
309	<	"SimSetup error, no periodic BoxY size given.\n" );
310	<	painCave.isFatal = 1;
311	<	simError();
312	<	}
389	<	simnfo->box_y = the_globals->getBoxY();
390	<
391	<	if( !the_globals->haveBoxZ() ){
392	<	sprintf( painCave.errMsg,
393	<	"SimSetup error, no periodic BoxZ size given.\n" );
394	<	painCave.isFatal = 1;
395	<	simError();
396	<	}
397	<	simnfo->box_z = the_globals->getBoxZ();
398	<	}
399	<
307	>	// exclude_I must always be the smaller of the pair
308	>	if (exI > exJ){
309	>	tempEx = exI;
310	>	exI = exJ;
311	>	exJ = tempEx;
312	>	}
313		#ifdef IS_MPI
314	<	strcpy( checkPointMsg, "Box size set up" );
315	<	MPIcheckPoint();
316	<	#endif // is_mpi
314	>	tempEx = exI;
315	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	>	tempEx = exJ;
317	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318
319	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
320	+	#else  // isn't MPI
321	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
322	+	#endif  //is_mpi
323	+	}
324	+	excludeOffset += molInfo.nBends;
325
326	<	// initialize the arrays
326	>	for (j = 0; j < molInfo.nTorsions; j++){
327	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
328	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
329	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
330	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
331	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
332
333	<	the_ff->setSimInfo( simnfo );
333	>	exI = theTorsions[j].a;
334	>	exJ = theTorsions[j].d;
335
336	<	makeAtoms();
337	<	simnfo->identArray = new int[simnfo->n_atoms];
338	<	for(i=0; i<simnfo->n_atoms; i++){
339	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
340	<	}
341	<
342	<	if( tot_bonds ){
343	<	makeBonds();
344	<	}
345	<
346	<	if( tot_bends ){
421	<	makeBends();
422	<	}
336	>	// exclude_I must always be the smaller of the pair
337	>	if (exI > exJ){
338	>	tempEx = exI;
339	>	exI = exJ;
340	>	exJ = tempEx;
341	>	}
342	>	#ifdef IS_MPI
343	>	tempEx = exI;
344	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>	tempEx = exJ;
346	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347
348	<	if( tot_torsions ){
349	<	makeTorsions();
350	<	}
348	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
349	>	#else  // isn't MPI
350	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
351	>	#endif  //is_mpi
352	>	}
353	>	excludeOffset += molInfo.nTorsions;
354
355
356	+	// send the arrays off to the forceField for init.
357
358	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
359	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
360	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
361	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
362	+	theTorsions);
363
364
365	+	info[k].molecules[i].initialize(molInfo);
366
433	–	if( the_globals->haveInitialConfig() ){
434	–
435	–	InitializeFromFile* fileInit;
436	–	#ifdef IS_MPI // is_mpi
437	–	if( worldRank == 0 ){
438	–	#endif //is_mpi
439	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
440	–	#ifdef IS_MPI
441	–	}else fileInit = new InitializeFromFile( NULL );
442	–	#endif
443	–	fileInit->read_xyz( simnfo ); // default velocities on
367
368	<	delete fileInit;
369	<	}
370	<	else{
368	>	atomOffset += molInfo.nAtoms;
369	>	delete[] theBonds;
370	>	delete[] theBends;
371	>	delete[] theTorsions;
372	>	}
373	>	}
374
375	<	#ifdef IS_MPI
375	>	#ifdef IS_MPI
376	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
377	>	MPIcheckPoint();
378	>	#endif // is_mpi
379
380	<	// no init from bass
452	<
453	<	sprintf( painCave.errMsg,
454	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
455	<	painCave.isFatal;
456	<	simError();
457	<
458	<	#else
380	>	// clean up the forcefield
381
382	<	initFromBass();
382	>	the_ff->calcRcut();
383	>	the_ff->cleanMe();
384	>	}
385
386	+	void SimSetup::initFromBass(void){
387	+	int i, j, k;
388	+	int n_cells;
389	+	double cellx, celly, cellz;
390	+	double temp1, temp2, temp3;
391	+	int n_per_extra;
392	+	int n_extra;
393	+	int have_extra, done;
394
395	<	#endif
396	<	}
395	>	double vel[3];
396	>	vel[0] = 0.0;
397	>	vel[1] = 0.0;
398	>	vel[2] = 0.0;
399
400	<	#ifdef IS_MPI
401	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
402	<	MPIcheckPoint();
469	<	#endif // is_mpi
400	>	temp1 = (double) tot_nmol / 4.0;
401	>	temp2 = pow(temp1, (1.0 / 3.0));
402	>	temp3 = ceil(temp2);
403
404	+	have_extra = 0;
405	+	if (temp2 < temp3){
406	+	// we have a non-complete lattice
407	+	have_extra = 1;
408
409	<
410	<
411	<
409	>	n_cells = (int) temp3 - 1;
410	>	cellx = info[0].boxL[0] / temp3;
411	>	celly = info[0].boxL[1] / temp3;
412	>	cellz = info[0].boxL[2] / temp3;
413	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
414	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
415	>	n_per_extra = (int) ceil(temp1);
416
417	<
418	<	#ifdef IS_MPI
419	<	if( worldRank == 0 ){
420	<	#endif // is_mpi
421	<
422	<	if( the_globals->haveFinalConfig() ){
482	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
417	>	if (n_per_extra > 4){
418	>	sprintf(painCave.errMsg,
419	>	"SimSetup error. There has been an error in constructing"
420	>	" the non-complete lattice.\n");
421	>	painCave.isFatal = 1;
422	>	simError();
423		}
484	–	else{
485	–	strcpy( simnfo->finalName, inFileName );
486	–	char* endTest;
487	–	int nameLength = strlen( simnfo->finalName );
488	–	endTest = &(simnfo->finalName[nameLength - 5]);
489	–	if( !strcmp( endTest, ".bass" ) ){
490	–	strcpy( endTest, ".eor" );
491	–	}
492	–	else if( !strcmp( endTest, ".BASS" ) ){
493	–	strcpy( endTest, ".eor" );
494	–	}
495	–	else{
496	–	endTest = &(simnfo->finalName[nameLength - 4]);
497	–	if( !strcmp( endTest, ".bss" ) ){
498	–	strcpy( endTest, ".eor" );
499	–	}
500	–	else if( !strcmp( endTest, ".mdl" ) ){
501	–	strcpy( endTest, ".eor" );
502	–	}
503	–	else{
504	–	strcat( simnfo->finalName, ".eor" );
505	–	}
506	–	}
507	–	}
508	–
509	–	// make the sample and status out names
510	–
511	–	strcpy( simnfo->sampleName, inFileName );
512	–	char* endTest;
513	–	int nameLength = strlen( simnfo->sampleName );
514	–	endTest = &(simnfo->sampleName[nameLength - 5]);
515	–	if( !strcmp( endTest, ".bass" ) ){
516	–	strcpy( endTest, ".dump" );
517	–	}
518	–	else if( !strcmp( endTest, ".BASS" ) ){
519	–	strcpy( endTest, ".dump" );
520	–	}
521	–	else{
522	–	endTest = &(simnfo->sampleName[nameLength - 4]);
523	–	if( !strcmp( endTest, ".bss" ) ){
524	–	strcpy( endTest, ".dump" );
525	–	}
526	–	else if( !strcmp( endTest, ".mdl" ) ){
527	–	strcpy( endTest, ".dump" );
528	–	}
529	–	else{
530	–	strcat( simnfo->sampleName, ".dump" );
531	–	}
532	–	}
533	–
534	–	strcpy( simnfo->statusName, inFileName );
535	–	nameLength = strlen( simnfo->statusName );
536	–	endTest = &(simnfo->statusName[nameLength - 5]);
537	–	if( !strcmp( endTest, ".bass" ) ){
538	–	strcpy( endTest, ".stat" );
539	–	}
540	–	else if( !strcmp( endTest, ".BASS" ) ){
541	–	strcpy( endTest, ".stat" );
542	–	}
543	–	else{
544	–	endTest = &(simnfo->statusName[nameLength - 4]);
545	–	if( !strcmp( endTest, ".bss" ) ){
546	–	strcpy( endTest, ".stat" );
547	–	}
548	–	else if( !strcmp( endTest, ".mdl" ) ){
549	–	strcpy( endTest, ".stat" );
550	–	}
551	–	else{
552	–	strcat( simnfo->statusName, ".stat" );
553	–	}
554	–	}
555	–
556	–	#ifdef IS_MPI
424		}
558	–	#endif // is_mpi
559	–
560	–	// set the status, sample, and themal kick times
561	–
562	–	if( the_globals->haveSampleTime() ){
563	–	simnfo->sampleTime = the_globals->getSampleTime();
564	–	simnfo->statusTime = simnfo->sampleTime;
565	–	simnfo->thermalTime = simnfo->sampleTime;
566	–	}
425		else{
426	<	simnfo->sampleTime = the_globals->getRunTime();
427	<	simnfo->statusTime = simnfo->sampleTime;
428	<	simnfo->thermalTime = simnfo->sampleTime;
426	>	n_cells = (int) temp3;
427	>	cellx = info[0].boxL[0] / temp3;
428	>	celly = info[0].boxL[1] / temp3;
429	>	cellz = info[0].boxL[2] / temp3;
430		}
431
432	<	if( the_globals->haveStatusTime() ){
433	<	simnfo->statusTime = the_globals->getStatusTime();
434	<	}
432	>	current_mol = 0;
433	>	current_comp_mol = 0;
434	>	current_comp = 0;
435	>	current_atom_ndx = 0;
436
437	<	if( the_globals->haveThermalTime() ){
438	<	simnfo->thermalTime = the_globals->getThermalTime();
437	>	for (i = 0; i < n_cells ; i++){
438	>	for (j = 0; j < n_cells; j++){
439	>	for (k = 0; k < n_cells; k++){
440	>	makeElement(i * cellx, j * celly, k * cellz);
441	>
442	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
443	>
444	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
445	>
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
447	>	}
448	>	}
449		}
450
451	<	// check for the temperature set flag
451	>	if (have_extra){
452	>	done = 0;
453
454	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
454	>	int start_ndx;
455	>	for (i = 0; i < (n_cells + 1) && !done; i++){
456	>	for (j = 0; j < (n_cells + 1) && !done; j++){
457	>	if (i < n_cells){
458	>	if (j < n_cells){
459	>	start_ndx = n_cells;
460	>	}
461	>	else
462	>	start_ndx = 0;
463	>	}
464	>	else
465	>	start_ndx = 0;
466
467	+	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
468	+	makeElement(i * cellx, j * celly, k * cellz);
469	+	done = (current_mol >= tot_nmol);
470
471	<	//   // make the longe range forces and the integrator
471	>	if (!done && n_per_extra > 1){
472	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
473	>	k * cellz);
474	>	done = (current_mol >= tot_nmol);
475	>	}
476
477	<	//   new AllLong( simnfo );
477	>	if (!done && n_per_extra > 2){
478	>	makeElement(i * cellx, j * celly + 0.5 * celly,
479	>	k * cellz + 0.5 * cellz);
480	>	done = (current_mol >= tot_nmol);
481	>	}
482
483	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
484	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
485	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
486	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
483	>	if (!done && n_per_extra > 3){
484	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
485	>	k * cellz + 0.5 * cellz);
486	>	done = (current_mol >= tot_nmol);
487	>	}
488	>	}
489	>	}
490	>	}
491	>	}
492
493	+	for (i = 0; i < info[0].n_atoms; i++){
494	+	info[0].atoms[i]->setVel(vel);
495	+	}
496	+	}
497
498	+	void SimSetup::makeElement(double x, double y, double z){
499	+	int k;
500	+	AtomStamp* current_atom;
501	+	DirectionalAtom* dAtom;
502	+	double rotMat[3][3];
503	+	double pos[3];
504
505	<	// initialize the Fortran
506	<
507	<	simnfo->refreshSim();
508	<
509	<	if( !strcmp( simnfo->mixingRule, "standard") ){
510	<	the_ff->initForceField( LB_MIXING_RULE );
505	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
506	>	current_atom = comp_stamps[current_comp]->getAtom(k);
507	>	if (!current_atom->havePosition()){
508	>	sprintf(painCave.errMsg,
509	>	"SimSetup:initFromBass error.\n"
510	>	"\tComponent %s, atom %s does not have a position specified.\n"
511	>	"\tThe initialization routine is unable to give a start"
512	>	" position.\n",
513	>	comp_stamps[current_comp]->getID(), current_atom->getType());
514	>	painCave.isFatal = 1;
515	>	simError();
516	>	}
517	>
518	>	pos[0] = x + current_atom->getPosX();
519	>	pos[1] = y + current_atom->getPosY();
520	>	pos[2] = z + current_atom->getPosZ();
521	>
522	>	info[0].atoms[current_atom_ndx]->setPos(pos);
523	>
524	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
525	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
526	>
527	>	rotMat[0][0] = 1.0;
528	>	rotMat[0][1] = 0.0;
529	>	rotMat[0][2] = 0.0;
530	>
531	>	rotMat[1][0] = 0.0;
532	>	rotMat[1][1] = 1.0;
533	>	rotMat[1][2] = 0.0;
534	>
535	>	rotMat[2][0] = 0.0;
536	>	rotMat[2][1] = 0.0;
537	>	rotMat[2][2] = 1.0;
538	>
539	>	dAtom->setA(rotMat);
540	>	}
541	>
542	>	current_atom_ndx++;
543		}
544	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
545	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
544	>
545	>	current_mol++;
546	>	current_comp_mol++;
547	>
548	>	if (current_comp_mol >= components_nmol[current_comp]){
549	>	current_comp_mol = 0;
550	>	current_comp++;
551		}
552	+	}
553	+
554	+
555	+	void SimSetup::gatherInfo(void){
556	+	int i, j, k;
557	+
558	+	ensembleCase = -1;
559	+	ffCase = -1;
560	+
561	+	// set the easy ones first
562	+
563	+	for (i = 0; i < nInfo; i++){
564	+	info[i].target_temp = globals->getTargetTemp();
565	+	info[i].dt = globals->getDt();
566	+	info[i].run_time = globals->getRunTime();
567	+	}
568	+	n_components = globals->getNComponents();
569	+
570	+
571	+	// get the forceField
572	+
573	+	strcpy(force_field, globals->getForceField());
574	+
575	+	if (!strcasecmp(force_field, "DUFF")){
576	+	ffCase = FF_DUFF;
577	+	}
578	+	else if (!strcasecmp(force_field, "LJ")){
579	+	ffCase = FF_LJ;
580	+	}
581	+	else if (!strcasecmp(force_field, "EAM")){
582	+	ffCase = FF_EAM;
583	+	}
584		else{
585	<	sprintf( painCave.errMsg,
586	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
587	<	simnfo->mixingRule );
585	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
586	>	force_field);
587	>	painCave.isFatal = 1;
588	>	simError();
589	>	}
590	>
591	>	// get the ensemble
592	>
593	>	strcpy(ensemble, globals->getEnsemble());
594	>
595	>	if (!strcasecmp(ensemble, "NVE")){
596	>	ensembleCase = NVE_ENS;
597	>	}
598	>	else if (!strcasecmp(ensemble, "NVT")){
599	>	ensembleCase = NVT_ENS;
600	>	}
601	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
602	>	ensembleCase = NPTi_ENS;
603	>	}
604	>	else if (!strcasecmp(ensemble, "NPTf")){
605	>	ensembleCase = NPTf_ENS;
606	>	}
607	>	else if (!strcasecmp(ensemble, "NPTim")){
608	>	ensembleCase = NPTim_ENS;
609	>	}
610	>	else if (!strcasecmp(ensemble, "NPTfm")){
611	>	ensembleCase = NPTfm_ENS;
612	>	}
613	>	else{
614	>	sprintf(painCave.errMsg,
615	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
616	>	"reverting to NVE for this simulation.\n",
617	>	ensemble);
618	>	painCave.isFatal = 0;
619	>	simError();
620	>	strcpy(ensemble, "NVE");
621	>	ensembleCase = NVE_ENS;
622	>	}
623	>
624	>	for (i = 0; i < nInfo; i++){
625	>	strcpy(info[i].ensemble, ensemble);
626	>
627	>	// get the mixing rule
628	>
629	>	strcpy(info[i].mixingRule, globals->getMixingRule());
630	>	info[i].usePBC = globals->getPBC();
631	>	}
632	>
633	>	// get the components and calculate the tot_nMol and indvidual n_mol
634	>
635	>	the_components = globals->getComponents();
636	>	components_nmol = new int[n_components];
637	>
638	>
639	>	if (!globals->haveNMol()){
640	>	// we don't have the total number of molecules, so we assume it is
641	>	// given in each component
642	>
643	>	tot_nmol = 0;
644	>	for (i = 0; i < n_components; i++){
645	>	if (!the_components[i]->haveNMol()){
646	>	// we have a problem
647	>	sprintf(painCave.errMsg,
648	>	"SimSetup Error. No global NMol or component NMol"
649	>	" given. Cannot calculate the number of atoms.\n");
650	>	painCave.isFatal = 1;
651	>	simError();
652	>	}
653	>
654	>	tot_nmol += the_components[i]->getNMol();
655	>	components_nmol[i] = the_components[i]->getNMol();
656	>	}
657	>	}
658	>	else{
659	>	sprintf(painCave.errMsg,
660	>	"SimSetup error.\n"
661	>	"\tSorry, the ability to specify total"
662	>	" nMols and then give molfractions in the components\n"
663	>	"\tis not currently supported."
664	>	" Please give nMol in the components.\n");
665		painCave.isFatal = 1;
666		simError();
667		}
668
669	+	// set the status, sample, and thermal kick times
670
671	<	#ifdef IS_MPI
672	<	strcpy( checkPointMsg,
673	<	"Successfully intialized the mixingRule for Fortran." );
674	<	MPIcheckPoint();
675	<	#endif // is_mpi
676	<	}
671	>	for (i = 0; i < nInfo; i++){
672	>	if (globals->haveSampleTime()){
673	>	info[i].sampleTime = globals->getSampleTime();
674	>	info[i].statusTime = info[i].sampleTime;
675	>	info[i].thermalTime = info[i].sampleTime;
676	>	}
677	>	else{
678	>	info[i].sampleTime = globals->getRunTime();
679	>	info[i].statusTime = info[i].sampleTime;
680	>	info[i].thermalTime = info[i].sampleTime;
681	>	}
682
683	<	void SimSetup::makeAtoms( void ){
683	>	if (globals->haveStatusTime()){
684	>	info[i].statusTime = globals->getStatusTime();
685	>	}
686
687	<	int i, j, k, index;
688	<	double ux, uy, uz, uSqr, u;
689	<	AtomStamp* current_atom;
687	>	if (globals->haveThermalTime()){
688	>	info[i].thermalTime = globals->getThermalTime();
689	>	}
690
691	<	DirectionalAtom* dAtom;
630	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
691	>	// check for the temperature set flag
692
693	<	lMolIndex = 0;
694	<	molIndex = 0;
634	<	index = 0;
635	<	for( i=0; i<n_components; i++ ){
693	>	if (globals->haveTempSet())
694	>	info[i].setTemp = globals->getTempSet();
695
696	<	for( j=0; j<components_nmol[i]; j++ ){
696	>	// get some of the tricky things that may still be in the globals
697
698	<	#ifdef IS_MPI
699	<	if( mpiSim->getMyMolStart() <= molIndex &&
700	<	molIndex <= mpiSim->getMyMolEnd() ){
701	<	#endif // is_mpi
698	>	double boxVector[3];
699	>	if (globals->haveBox()){
700	>	boxVector[0] = globals->getBox();
701	>	boxVector[1] = globals->getBox();
702	>	boxVector[2] = globals->getBox();
703
704	<	molStart = index;
705	<	nMemb = comp_stamps[i]->getNAtoms();
706	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
707	<
708	<	current_atom = comp_stamps[i]->getAtom( k );
709	<	if( current_atom->haveOrientation() ){
710	<
711	<	dAtom = new DirectionalAtom(index);
652	<	simnfo->n_oriented++;
653	<	the_atoms[index] = dAtom;
654	<
655	<	ux = current_atom->getOrntX();
656	<	uy = current_atom->getOrntY();
657	<	uz = current_atom->getOrntZ();
658	<
659	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
660	<
661	<	u = sqrt( uSqr );
662	<	ux = ux / u;
663	<	uy = uy / u;
664	<	uz = uz / u;
665	<
666	<	dAtom->setSUx( ux );
667	<	dAtom->setSUy( uy );
668	<	dAtom->setSUz( uz );
669	<	}
670	<	else{
671	<	the_atoms[index] = new GeneralAtom(index);
672	<	}
673	<	the_atoms[index]->setType( current_atom->getType() );
674	<	the_atoms[index]->setIndex( index );
675	<
676	<	// increment the index and repeat;
677	<	index++;
678	<	}
679	<
680	<	molEnd = index -1;
681	<	the_molecules[lMolIndex].setNMembers( nMemb );
682	<	the_molecules[lMolIndex].setStartAtom( molStart );
683	<	the_molecules[lMolIndex].setEndAtom( molEnd );
684	<	the_molecules[lMolIndex].setStampID( i );
685	<	lMolIndex++;
704	>	info[i].setBox(boxVector);
705	>	}
706	>	else if (globals->haveDensity()){
707	>	double vol;
708	>	vol = (double) tot_nmol / globals->getDensity();
709	>	boxVector[0] = pow(vol, (1.0 / 3.0));
710	>	boxVector[1] = boxVector[0];
711	>	boxVector[2] = boxVector[0];
712
713	<	#ifdef IS_MPI
688	<	}
689	<	#endif //is_mpi
690	<
691	<	molIndex++;
713	>	info[i].setBox(boxVector);
714		}
715	<	}
715	>	else{
716	>	if (!globals->haveBoxX()){
717	>	sprintf(painCave.errMsg,
718	>	"SimSetup error, no periodic BoxX size given.\n");
719	>	painCave.isFatal = 1;
720	>	simError();
721	>	}
722	>	boxVector[0] = globals->getBoxX();
723
724	<	#ifdef IS_MPI
725	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
726	<
727	<	delete[] globalIndex;
724	>	if (!globals->haveBoxY()){
725	>	sprintf(painCave.errMsg,
726	>	"SimSetup error, no periodic BoxY size given.\n");
727	>	painCave.isFatal = 1;
728	>	simError();
729	>	}
730	>	boxVector[1] = globals->getBoxY();
731
732	<	mpiSim->mpiRefresh();
733	<	#endif //IS_MPI
734	<
735	<	the_ff->initializeAtoms();
736	<	}
705	<
706	<	void SimSetup::makeBonds( void ){
707	<
708	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
709	<	bond_pair* the_bonds;
710	<	BondStamp* current_bond;
711	<
712	<	the_bonds = new bond_pair[tot_bonds];
713	<	index = 0;
714	<	offset = 0;
715	<	molIndex = 0;
716	<
717	<	for( i=0; i<n_components; i++ ){
718	<
719	<	for( j=0; j<components_nmol[i]; j++ ){
720	<
721	<	#ifdef IS_MPI
722	<	if( mpiSim->getMyMolStart() <= molIndex &&
723	<	molIndex <= mpiSim->getMyMolEnd() ){
724	<	#endif // is_mpi
725	<
726	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
727	<
728	<	current_bond = comp_stamps[i]->getBond( k );
729	<	the_bonds[index].a = current_bond->getA() + offset;
730	<	the_bonds[index].b = current_bond->getB() + offset;
731	<
732	<	exI = the_bonds[index].a;
733	<	exJ = the_bonds[index].b;
734	<
735	<	// exclude_I must always be the smaller of the pair
736	<	if( exI > exJ ){
737	<	tempEx = exI;
738	<	exI = exJ;
739	<	exJ = tempEx;
740	<	}
741	<
742	<
743	<	#ifdef IS_MPI
744	<
745	<	the_excludes[index*2] =
746	<	the_atoms[exI]->getGlobalIndex() + 1;
747	<	the_excludes[index*2 + 1] =
748	<	the_atoms[exJ]->getGlobalIndex() + 1;
749	<
750	<	#else  // isn't MPI
751	<
752	<	the_excludes[index*2] =     exI + 1;
753	<	the_excludes[index*2 + 1] = exJ + 1;
754	<	// fortran index from 1 (hence the +1 in the indexing)
755	<	#endif  //is_mpi
756	<
757	<	// increment the index and repeat;
758	<	index++;
759	<	}
760	<	offset += comp_stamps[i]->getNAtoms();
761	<
762	<	#ifdef IS_MPI
732	>	if (!globals->haveBoxZ()){
733	>	sprintf(painCave.errMsg,
734	>	"SimSetup error, no periodic BoxZ size given.\n");
735	>	painCave.isFatal = 1;
736	>	simError();
737		}
738	<	#endif //is_mpi
739	<
740	<	molIndex++;
741	<	}
738	>	boxVector[2] = globals->getBoxZ();
739	>
740	>	info[i].setBox(boxVector);
741	>	}
742		}
743
744	<	the_ff->initializeBonds( the_bonds );
745	<	}
744	>	//setup seed for random number generator
745	>	int seedValue;
746
747	<	void SimSetup::makeBends( void ){
747	>	if (globals->haveSeed()){
748	>	seedValue = globals->getSeed();
749
750	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
751	<	bend_set* the_bends;
752	<	BendStamp* current_bend;
753	<	LinkedAssign* extras;
754	<	LinkedAssign* current_extra;
755	<
750	>	if(seedValue / 1E9 == 0){
751	>	sprintf(painCave.errMsg,
752	>	"Seed for sprng library should contain at least 9 digits\n"
753	>	"OOPSE will generate a seed for user\n");
754	>	painCave.isFatal = 0;
755	>	simError();
756
757	<	the_bends = new bend_set[tot_bends];
758	<	index = 0;
759	<	offset = 0;
760	<	molIndex = 0;
761	<	for( i=0; i<n_components; i++ ){
762	<
788	<	for( j=0; j<components_nmol[i]; j++ ){
789	<
790	<	#ifdef IS_MPI
791	<	if( mpiSim->getMyMolStart() <= molIndex &&
792	<	molIndex <= mpiSim->getMyMolEnd() ){
793	<	#endif // is_mpi
794	<
795	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
796	<
797	<	current_bend = comp_stamps[i]->getBend( k );
798	<	the_bends[index].a = current_bend->getA() + offset;
799	<	the_bends[index].b = current_bend->getB() + offset;
800	<	the_bends[index].c = current_bend->getC() + offset;
801	<
802	<	if( current_bend->haveExtras() ){
803	<
804	<	extras = current_bend->getExtras();
805	<	current_extra = extras;
806	<
807	<	while( current_extra != NULL ){
808	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
809	<
810	<	switch( current_extra->getType() ){
811	<
812	<	case 0:
813	<	the_bends[index].ghost =
814	<	current_extra->getInt() + offset;
815	<	the_bends[index].isGhost = 1;
816	<	break;
817	<
818	<	case 1:
819	<	the_bends[index].ghost =
820	<	(int)current_extra->getDouble() + offset;
821	<	the_bends[index].isGhost = 1;
822	<	break;
823	<
824	<	default:
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup Error: ghostVectorSource was neiter a "
827	<	"double nor an int.\n"
828	<	"-->Bend[%d] in %s\n",
829	<	k, comp_stamps[i]->getID() );
830	<	painCave.isFatal = 1;
831	<	simError();
832	<	}
833	<	}
834	<
835	<	else{
836	<
837	<	sprintf( painCave.errMsg,
838	<	"SimSetup Error: unhandled bend assignment:\n"
839	<	"    -->%s in Bend[%d] in %s\n",
840	<	current_extra->getlhs(),
841	<	k, comp_stamps[i]->getID() );
842	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<
846	<	current_extra = current_extra->getNext();
847	<	}
848	<	}
849	<
850	<	if( !the_bends[index].isGhost ){
851	<
852	<	exI = the_bends[index].a;
853	<	exJ = the_bends[index].c;
854	<	}
855	<	else{
856	<
857	<	exI = the_bends[index].a;
858	<	exJ = the_bends[index].b;
859	<	}
860	<
861	<	// exclude_I must always be the smaller of the pair
862	<	if( exI > exJ ){
863	<	tempEx = exI;
864	<	exI = exJ;
865	<	exJ = tempEx;
866	<	}
867	<
868	<
869	<	#ifdef IS_MPI
870	<
871	<	the_excludes[(index + tot_bonds)*2] =
872	<	the_atoms[exI]->getGlobalIndex() + 1;
873	<	the_excludes[(index + tot_bonds)*2 + 1] =
874	<	the_atoms[exJ]->getGlobalIndex() + 1;
875	<
876	<	#else  // isn't MPI
877	<
878	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
879	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
880	<	// fortran index from 1 (hence the +1 in the indexing)
881	<	#endif  //is_mpi
882	<
883	<
884	<	// increment the index and repeat;
885	<	index++;
886	<	}
887	<	offset += comp_stamps[i]->getNAtoms();
888	<
889	<	#ifdef IS_MPI
757	>	//using seed generated by system instead of invalid seed set by user
758	>	#ifndef IS_MPI
759	>	seedValue = make_sprng_seed();
760	>	#else
761	>	if (worldRank == 0){
762	>	seedValue = make_sprng_seed();
763		}
764	<	#endif //is_mpi
765	<
893	<	molIndex++;
764	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
765	>	#endif
766		}
767	+	}//end of if branch of globals->haveSeed()
768	+	else{
769	+
770	+	#ifndef IS_MPI
771	+	seedValue = make_sprng_seed();
772	+	#else
773	+	if (worldRank == 0){
774	+	seedValue = make_sprng_seed();
775	+	}
776	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
777	+	#endif
778	+	}//end of globals->haveSeed()
779	+
780	+	for (int i = 0; i < nInfo; i++){
781	+	info[i].setSeed(seedValue);
782		}
783
784		#ifdef IS_MPI
785	<	sprintf( checkPointMsg,
899	<	"Successfully created the bends list.\n" );
785	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
786		MPIcheckPoint();
787		#endif // is_mpi
902	–
903	–
904	–	the_ff->initializeBends( the_bends );
788		}
789
907	–	void SimSetup::makeTorsions( void ){
790
791	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
792	<	torsion_set* the_torsions;
793	<	TorsionStamp* current_torsion;
791	>	void SimSetup::finalInfoCheck(void){
792	>	int index;
793	>	int usesDipoles;
794	>	int i;
795
796	<	the_torsions = new torsion_set[tot_torsions];
797	<	index = 0;
915	<	offset = 0;
916	<	molIndex = 0;
917	<	for( i=0; i<n_components; i++ ){
796	>	for (i = 0; i < nInfo; i++){
797	>	// check electrostatic parameters
798
799	<	for( j=0; j<components_nmol[i]; j++ ){
799	>	index = 0;
800	>	usesDipoles = 0;
801	>	while ((index < info[i].n_atoms) && !usesDipoles){
802	>	usesDipoles = (info[i].atoms[index])->hasDipole();
803	>	index++;
804	>	}
805
806		#ifdef IS_MPI
807	<	if( mpiSim->getMyMolStart() <= molIndex &&
808	<	molIndex <= mpiSim->getMyMolEnd() ){
809	<	#endif // is_mpi
807	>	int myUse = usesDipoles;
808	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809	>	#endif //is_mpi
810
811	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
811	>	double theEcr, theEst;
812
813	<	current_torsion = comp_stamps[i]->getTorsion( k );
814	<	the_torsions[index].a = current_torsion->getA() + offset;
930	<	the_torsions[index].b = current_torsion->getB() + offset;
931	<	the_torsions[index].c = current_torsion->getC() + offset;
932	<	the_torsions[index].d = current_torsion->getD() + offset;
813	>	if (globals->getUseRF()){
814	>	info[i].useReactionField = 1;
815
816	<	exI = the_torsions[index].a;
817	<	exJ = the_torsions[index].d;
816	>	if (!globals->haveECR()){
817	>	sprintf(painCave.errMsg,
818	>	"SimSetup Warning: using default value of 1/2 the smallest "
819	>	"box length for the electrostaticCutoffRadius.\n"
820	>	"I hope you have a very fast processor!\n");
821	>	painCave.isFatal = 0;
822	>	simError();
823	>	double smallest;
824	>	smallest = info[i].boxL[0];
825	>	if (info[i].boxL[1] <= smallest)
826	>	smallest = info[i].boxL[1];
827	>	if (info[i].boxL[2] <= smallest)
828	>	smallest = info[i].boxL[2];
829	>	theEcr = 0.5 * smallest;
830	>	}
831	>	else{
832	>	theEcr = globals->getECR();
833	>	}
834
835	<
836	<	// exclude_I must always be the smaller of the pair
837	<	if( exI > exJ ){
838	<	tempEx = exI;
839	<	exI = exJ;
840	<	exJ = tempEx;
841	<	}
835	>	if (!globals->haveEST()){
836	>	sprintf(painCave.errMsg,
837	>	"SimSetup Warning: using default value of 0.05 * the "
838	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
839	>	painCave.isFatal = 0;
840	>	simError();
841	>	theEst = 0.05 * theEcr;
842	>	}
843	>	else{
844	>	theEst = globals->getEST();
845	>	}
846
847	+	info[i].setEcr(theEcr, theEst);
848
849	<	#ifdef IS_MPI
850	<
851	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
852	<	the_atoms[exI]->getGlobalIndex() + 1;
853	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
854	<	the_atoms[exJ]->getGlobalIndex() + 1;
952	<
953	<	#else  // isn't MPI
954	<
955	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957	<	// fortran indexes from 1 (hence the +1 in the indexing)
958	<	#endif  //is_mpi
959	<
960	<
961	<	// increment the index and repeat;
962	<	index++;
849	>	if (!globals->haveDielectric()){
850	>	sprintf(painCave.errMsg,
851	>	"SimSetup Error: You are trying to use Reaction Field without"
852	>	"setting a dielectric constant!\n");
853	>	painCave.isFatal = 1;
854	>	simError();
855		}
856	<	offset += comp_stamps[i]->getNAtoms();
856	>	info[i].dielectric = globals->getDielectric();
857	>	}
858	>	else{
859	>	if (usesDipoles){
860	>	if (!globals->haveECR()){
861	>	sprintf(painCave.errMsg,
862	>	"SimSetup Warning: using default value of 1/2 the smallest "
863	>	"box length for the electrostaticCutoffRadius.\n"
864	>	"I hope you have a very fast processor!\n");
865	>	painCave.isFatal = 0;
866	>	simError();
867	>	double smallest;
868	>	smallest = info[i].boxL[0];
869	>	if (info[i].boxL[1] <= smallest)
870	>	smallest = info[i].boxL[1];
871	>	if (info[i].boxL[2] <= smallest)
872	>	smallest = info[i].boxL[2];
873	>	theEcr = 0.5 * smallest;
874	>	}
875	>	else{
876	>	theEcr = globals->getECR();
877	>	}
878
879	<	#ifdef IS_MPI
880	<	}
881	<	#endif //is_mpi
879	>	if (!globals->haveEST()){
880	>	sprintf(painCave.errMsg,
881	>	"SimSetup Warning: using default value of 0.05 * the "
882	>	"electrostaticCutoffRadius for the "
883	>	"electrostaticSkinThickness\n");
884	>	painCave.isFatal = 0;
885	>	simError();
886	>	theEst = 0.05 * theEcr;
887	>	}
888	>	else{
889	>	theEst = globals->getEST();
890	>	}
891
892	<	molIndex++;
892	>	info[i].setEcr(theEcr, theEst);
893	>	}
894		}
895		}
896
897	<	the_ff->initializeTorsions( the_torsions );
897	>	#ifdef IS_MPI
898	>	strcpy(checkPointMsg, "post processing checks out");
899	>	MPIcheckPoint();
900	>	#endif // is_mpi
901		}
902
903	<	void SimSetup::initFromBass( void ){
903	>	void SimSetup::initSystemCoords(void){
904	>	int i;
905
906	<	int i, j, k;
980	<	int n_cells;
981	<	double cellx, celly, cellz;
982	<	double temp1, temp2, temp3;
983	<	int n_per_extra;
984	<	int n_extra;
985	<	int have_extra, done;
906	>	char* inName;
907
908	<	temp1 = (double)tot_nmol / 4.0;
988	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
989	<	temp3 = ceil( temp2 );
908	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
909
910	<	have_extra =0;
911	<	if( temp2 < temp3 ){ // we have a non-complete lattice
993	<	have_extra =1;
910	>	for (i = 0; i < info[0].n_atoms; i++)
911	>	info[0].atoms[i]->setCoords();
912
913	<	n_cells = (int)temp3 - 1;
914	<	cellx = simnfo->box_x / temp3;
915	<	celly = simnfo->box_y / temp3;
916	<	cellz = simnfo->box_z / temp3;
917	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
918	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
919	<	n_per_extra = (int)ceil( temp1 );
920	<
921	<	if( n_per_extra > 4){
1004	<	sprintf( painCave.errMsg,
1005	<	"SimSetup error. There has been an error in constructing"
1006	<	" the non-complete lattice.\n" );
1007	<	painCave.isFatal = 1;
1008	<	simError();
913	>	if (globals->haveInitialConfig()){
914	>	InitializeFromFile* fileInit;
915	>	#ifdef IS_MPI // is_mpi
916	>	if (worldRank == 0){
917	>	#endif //is_mpi
918	>	inName = globals->getInitialConfig();
919	>	double* tempDouble = new double[1000000];
920	>	fileInit = new InitializeFromFile(inName);
921	>	#ifdef IS_MPI
922		}
923	+	else
924	+	fileInit = new InitializeFromFile(NULL);
925	+	#endif
926	+	fileInit->readInit(info); // default velocities on
927	+
928	+	delete fileInit;
929		}
930		else{
931	<	n_cells = (int)temp3;
932	<	cellx = simnfo->box_x / temp3;
933	<	celly = simnfo->box_y / temp3;
934	<	cellz = simnfo->box_z / temp3;
931	>	#ifdef IS_MPI
932	>
933	>	// no init from bass
934	>
935	>	sprintf(painCave.errMsg,
936	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
937	>	painCave.isFatal;
938	>	simError();
939	>
940	>	#else
941	>
942	>	initFromBass();
943	>
944	>
945	>	#endif
946		}
947
948	<	current_mol = 0;
949	<	current_comp_mol = 0;
950	<	current_comp = 0;
951	<	current_atom_ndx = 0;
948	>	#ifdef IS_MPI
949	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
950	>	MPIcheckPoint();
951	>	#endif // is_mpi
952	>	}
953
1023	–	for( i=0; i < n_cells ; i++ ){
1024	–	for( j=0; j < n_cells; j++ ){
1025	–	for( k=0; k < n_cells; k++ ){
954
955	<	makeElement( i * cellx,
956	<	j * celly,
1029	<	k * cellz );
955	>	void SimSetup::makeOutNames(void){
956	>	int k;
957
1031	–	makeElement( i * cellx + 0.5 * cellx,
1032	–	j * celly + 0.5 * celly,
1033	–	k * cellz );
958
959	<	makeElement( i * cellx,
960	<	j * celly + 0.5 * celly,
961	<	k * cellz + 0.5 * cellz );
959	>	for (k = 0; k < nInfo; k++){
960	>	#ifdef IS_MPI
961	>	if (worldRank == 0){
962	>	#endif // is_mpi
963
964	<	makeElement( i * cellx + 0.5 * cellx,
965	<	j * celly,
1041	<	k * cellz + 0.5 * cellz );
964	>	if (globals->haveFinalConfig()){
965	>	strcpy(info[k].finalName, globals->getFinalConfig());
966		}
967	+	else{
968	+	strcpy(info[k].finalName, inFileName);
969	+	char* endTest;
970	+	int nameLength = strlen(info[k].finalName);
971	+	endTest = &(info[k].finalName[nameLength - 5]);
972	+	if (!strcmp(endTest, ".bass")){
973	+	strcpy(endTest, ".eor");
974	+	}
975	+	else if (!strcmp(endTest, ".BASS")){
976	+	strcpy(endTest, ".eor");
977	+	}
978	+	else{
979	+	endTest = &(info[k].finalName[nameLength - 4]);
980	+	if (!strcmp(endTest, ".bss")){
981	+	strcpy(endTest, ".eor");
982	+	}
983	+	else if (!strcmp(endTest, ".mdl")){
984	+	strcpy(endTest, ".eor");
985	+	}
986	+	else{
987	+	strcat(info[k].finalName, ".eor");
988	+	}
989	+	}
990	+	}
991	+
992	+	// make the sample and status out names
993	+
994	+	strcpy(info[k].sampleName, inFileName);
995	+	char* endTest;
996	+	int nameLength = strlen(info[k].sampleName);
997	+	endTest = &(info[k].sampleName[nameLength - 5]);
998	+	if (!strcmp(endTest, ".bass")){
999	+	strcpy(endTest, ".dump");
1000	+	}
1001	+	else if (!strcmp(endTest, ".BASS")){
1002	+	strcpy(endTest, ".dump");
1003	+	}
1004	+	else{
1005	+	endTest = &(info[k].sampleName[nameLength - 4]);
1006	+	if (!strcmp(endTest, ".bss")){
1007	+	strcpy(endTest, ".dump");
1008	+	}
1009	+	else if (!strcmp(endTest, ".mdl")){
1010	+	strcpy(endTest, ".dump");
1011	+	}
1012	+	else{
1013	+	strcat(info[k].sampleName, ".dump");
1014	+	}
1015	+	}
1016	+
1017	+	strcpy(info[k].statusName, inFileName);
1018	+	nameLength = strlen(info[k].statusName);
1019	+	endTest = &(info[k].statusName[nameLength - 5]);
1020	+	if (!strcmp(endTest, ".bass")){
1021	+	strcpy(endTest, ".stat");
1022	+	}
1023	+	else if (!strcmp(endTest, ".BASS")){
1024	+	strcpy(endTest, ".stat");
1025	+	}
1026	+	else{
1027	+	endTest = &(info[k].statusName[nameLength - 4]);
1028	+	if (!strcmp(endTest, ".bss")){
1029	+	strcpy(endTest, ".stat");
1030	+	}
1031	+	else if (!strcmp(endTest, ".mdl")){
1032	+	strcpy(endTest, ".stat");
1033	+	}
1034	+	else{
1035	+	strcat(info[k].statusName, ".stat");
1036	+	}
1037	+	}
1038	+
1039	+	#ifdef IS_MPI
1040	+
1041		}
1042	+	#endif // is_mpi
1043		}
1044	+	}
1045
1046	–	if( have_extra ){
1047	–	done = 0;
1046
1047	<	int start_ndx;
1048	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1051	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1047	>	void SimSetup::sysObjectsCreation(void){
1048	>	int i, k;
1049
1050	<	if( i < n_cells ){
1050	>	// create the forceField
1051
1052	<	if( j < n_cells ){
1056	<	start_ndx = n_cells;
1057	<	}
1058	<	else start_ndx = 0;
1059	<	}
1060	<	else start_ndx = 0;
1052	>	createFF();
1053
1054	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1054	>	// extract componentList
1055
1056	<	makeElement( i * cellx,
1065	<	j * celly,
1066	<	k * cellz );
1067	<	done = ( current_mol >= tot_nmol );
1056	>	compList();
1057
1058	<	if( !done && n_per_extra > 1 ){
1070	<	makeElement( i * cellx + 0.5 * cellx,
1071	<	j * celly + 0.5 * celly,
1072	<	k * cellz );
1073	<	done = ( current_mol >= tot_nmol );
1074	<	}
1058	>	// calc the number of atoms, bond, bends, and torsions
1059
1060	<	if( !done && n_per_extra > 2){
1077	<	makeElement( i * cellx,
1078	<	j * celly + 0.5 * celly,
1079	<	k * cellz + 0.5 * cellz );
1080	<	done = ( current_mol >= tot_nmol );
1081	<	}
1060	>	calcSysValues();
1061
1062	<	if( !done && n_per_extra > 3){
1063	<	makeElement( i * cellx + 0.5 * cellx,
1064	<	j * celly,
1065	<	k * cellz + 0.5 * cellz );
1066	<	done = ( current_mol >= tot_nmol );
1067	<	}
1068	<	}
1062	>	#ifdef IS_MPI
1063	>	// divide the molecules among the processors
1064	>
1065	>	mpiMolDivide();
1066	>	#endif //is_mpi
1067	>
1068	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1069	>
1070	>	makeSysArrays();
1071	>
1072	>	// make and initialize the molecules (all but atomic coordinates)
1073	>
1074	>	makeMolecules();
1075	>
1076	>	for (k = 0; k < nInfo; k++){
1077	>	info[k].identArray = new int[info[k].n_atoms];
1078	>	for (i = 0; i < info[k].n_atoms; i++){
1079	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1080	>	}
1081	>	}
1082	>	}
1083	>
1084	>
1085	>	void SimSetup::createFF(void){
1086	>	switch (ffCase){
1087	>	case FF_DUFF:
1088	>	the_ff = new DUFF();
1089	>	break;
1090	>
1091	>	case FF_LJ:
1092	>	the_ff = new LJFF();
1093	>	break;
1094	>
1095	>	case FF_EAM:
1096	>	the_ff = new EAM_FF();
1097	>	break;
1098	>
1099	>	default:
1100	>	sprintf(painCave.errMsg,
1101	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1102	>	painCave.isFatal = 1;
1103	>	simError();
1104	>	}
1105	>
1106	>	#ifdef IS_MPI
1107	>	strcpy(checkPointMsg, "ForceField creation successful");
1108	>	MPIcheckPoint();
1109	>	#endif // is_mpi
1110	>	}
1111	>
1112	>
1113	>	void SimSetup::compList(void){
1114	>	int i;
1115	>	char* id;
1116	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1117	>	LinkedMolStamp* currentStamp = NULL;
1118	>	comp_stamps = new MoleculeStamp * [n_components];
1119	>
1120	>	// make an array of molecule stamps that match the components used.
1121	>	// also extract the used stamps out into a separate linked list
1122	>
1123	>	for (i = 0; i < nInfo; i++){
1124	>	info[i].nComponents = n_components;
1125	>	info[i].componentsNmol = components_nmol;
1126	>	info[i].compStamps = comp_stamps;
1127	>	info[i].headStamp = headStamp;
1128	>	}
1129	>
1130	>
1131	>	for (i = 0; i < n_components; i++){
1132	>	id = the_components[i]->getType();
1133	>	comp_stamps[i] = NULL;
1134	>
1135	>	// check to make sure the component isn't already in the list
1136	>
1137	>	comp_stamps[i] = headStamp->match(id);
1138	>	if (comp_stamps[i] == NULL){
1139	>	// extract the component from the list;
1140	>
1141	>	currentStamp = stamps->extractMolStamp(id);
1142	>	if (currentStamp == NULL){
1143	>	sprintf(painCave.errMsg,
1144	>	"SimSetup error: Component \"%s\" was not found in the "
1145	>	"list of declared molecules\n",
1146	>	id);
1147	>	painCave.isFatal = 1;
1148	>	simError();
1149		}
1150	+
1151	+	headStamp->add(currentStamp);
1152	+	comp_stamps[i] = headStamp->match(id);
1153		}
1154		}
1155
1156	+	#ifdef IS_MPI
1157	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1158	+	MPIcheckPoint();
1159	+	#endif // is_mpi
1160	+	}
1161
1162	<	for( i=0; i<simnfo->n_atoms; i++ ){
1163	<	simnfo->atoms[i]->set_vx( 0.0 );
1164	<	simnfo->atoms[i]->set_vy( 0.0 );
1165	<	simnfo->atoms[i]->set_vz( 0.0 );
1162	>	void SimSetup::calcSysValues(void){
1163	>	int i, j, k;
1164	>
1165	>	int* molMembershipArray;
1166	>
1167	>	tot_atoms = 0;
1168	>	tot_bonds = 0;
1169	>	tot_bends = 0;
1170	>	tot_torsions = 0;
1171	>	for (i = 0; i < n_components; i++){
1172	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1173	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1174	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1175	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1176		}
1177	+
1178	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1179	+	molMembershipArray = new int[tot_atoms];
1180	+
1181	+	for (i = 0; i < nInfo; i++){
1182	+	info[i].n_atoms = tot_atoms;
1183	+	info[i].n_bonds = tot_bonds;
1184	+	info[i].n_bends = tot_bends;
1185	+	info[i].n_torsions = tot_torsions;
1186	+	info[i].n_SRI = tot_SRI;
1187	+	info[i].n_mol = tot_nmol;
1188	+
1189	+	info[i].molMembershipArray = molMembershipArray;
1190	+	}
1191		}
1192
1193	<	void SimSetup::makeElement( double x, double y, double z ){
1193	>	#ifdef IS_MPI
1194
1195	<	int k;
1196	<	AtomStamp* current_atom;
1197	<	DirectionalAtom* dAtom;
1198	<	double rotMat[3][3];
1195	>	void SimSetup::mpiMolDivide(void){
1196	>	int i, j, k;
1197	>	int localMol, allMol;
1198	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1199
1200	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1200	>	mpiSim = new mpiSimulation(info);
1201
1202	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1203	<	if( !current_atom->havePosition() ){
1204	<	sprintf( painCave.errMsg,
1205	<	"SimSetup:initFromBass error.\n"
1206	<	"\tComponent %s, atom %s does not have a position specified.\n"
1207	<	"\tThe initialization routine is unable to give a start"
1208	<	" position.\n",
1209	<	comp_stamps[current_comp]->getID(),
1210	<	current_atom->getType() );
1211	<	painCave.isFatal = 1;
1212	<	simError();
1202	>	globalIndex = mpiSim->divideLabor();
1203	>
1204	>	// set up the local variables
1205	>
1206	>	mol2proc = mpiSim->getMolToProcMap();
1207	>	molCompType = mpiSim->getMolComponentType();
1208	>
1209	>	allMol = 0;
1210	>	localMol = 0;
1211	>	local_atoms = 0;
1212	>	local_bonds = 0;
1213	>	local_bends = 0;
1214	>	local_torsions = 0;
1215	>	globalAtomIndex = 0;
1216	>
1217	>
1218	>	for (i = 0; i < n_components; i++){
1219	>	for (j = 0; j < components_nmol[i]; j++){
1220	>	if (mol2proc[allMol] == worldRank){
1221	>	local_atoms += comp_stamps[i]->getNAtoms();
1222	>	local_bonds += comp_stamps[i]->getNBonds();
1223	>	local_bends += comp_stamps[i]->getNBends();
1224	>	local_torsions += comp_stamps[i]->getNTorsions();
1225	>	localMol++;
1226	>	}
1227	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1228	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1229	>	globalAtomIndex++;
1230	>	}
1231	>
1232	>	allMol++;
1233		}
1234	+	}
1235	+	local_SRI = local_bonds + local_bends + local_torsions;
1236
1237	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1125	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1126	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1237	>	info[0].n_atoms = mpiSim->getMyNlocal();
1238
1239	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1239	>	if (local_atoms != info[0].n_atoms){
1240	>	sprintf(painCave.errMsg,
1241	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1242	>	" localAtom (%d) are not equal.\n",
1243	>	info[0].n_atoms, local_atoms);
1244	>	painCave.isFatal = 1;
1245	>	simError();
1246	>	}
1247
1248	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1248	>	info[0].n_bonds = local_bonds;
1249	>	info[0].n_bends = local_bends;
1250	>	info[0].n_torsions = local_torsions;
1251	>	info[0].n_SRI = local_SRI;
1252	>	info[0].n_mol = localMol;
1253
1254	<	rotMat[0][0] = 1.0;
1255	<	rotMat[0][1] = 0.0;
1256	<	rotMat[0][2] = 0.0;
1254	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1255	>	MPIcheckPoint();
1256	>	}
1257
1258	<	rotMat[1][0] = 0.0;
1137	<	rotMat[1][1] = 1.0;
1138	<	rotMat[1][2] = 0.0;
1258	>	#endif // is_mpi
1259
1140	–	rotMat[2][0] = 0.0;
1141	–	rotMat[2][1] = 0.0;
1142	–	rotMat[2][2] = 1.0;
1260
1261	<	dAtom->setA( rotMat );
1261	>	void SimSetup::makeSysArrays(void){
1262	>	int i, j, k, l;
1263	>
1264	>	Atom** the_atoms;
1265	>	Molecule* the_molecules;
1266	>	Exclude** the_excludes;
1267	>
1268	>
1269	>	for (l = 0; l < nInfo; l++){
1270	>	// create the atom and short range interaction arrays
1271	>
1272	>	the_atoms = new Atom * [info[l].n_atoms];
1273	>	the_molecules = new Molecule[info[l].n_mol];
1274	>	int molIndex;
1275	>
1276	>	// initialize the molecule's stampID's
1277	>
1278	>	#ifdef IS_MPI
1279	>
1280	>
1281	>	molIndex = 0;
1282	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1283	>	if (mol2proc[i] == worldRank){
1284	>	the_molecules[molIndex].setStampID(molCompType[i]);
1285	>	the_molecules[molIndex].setMyIndex(molIndex);
1286	>	the_molecules[molIndex].setGlobalIndex(i);
1287	>	molIndex++;
1288	>	}
1289		}
1290
1291	<	current_atom_ndx++;
1291	>	#else // is_mpi
1292	>
1293	>	molIndex = 0;
1294	>	globalAtomIndex = 0;
1295	>	for (i = 0; i < n_components; i++){
1296	>	for (j = 0; j < components_nmol[i]; j++){
1297	>	the_molecules[molIndex].setStampID(i);
1298	>	the_molecules[molIndex].setMyIndex(molIndex);
1299	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1300	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1301	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	>	globalAtomIndex++;
1303	>	}
1304	>	molIndex++;
1305	>	}
1306	>	}
1307	>
1308	>
1309	>	#endif // is_mpi
1310	>
1311	>
1312	>	if (info[l].n_SRI){
1313	>	Exclude::createArray(info[l].n_SRI);
1314	>	the_excludes = new Exclude * [info[l].n_SRI];
1315	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	>	the_excludes[ex] = new Exclude(ex);
1317	>	}
1318	>	info[l].globalExcludes = new int;
1319	>	info[l].n_exclude = info[l].n_SRI;
1320	>	}
1321	>	else{
1322	>	Exclude::createArray(1);
1323	>	the_excludes = new Exclude * ;
1324	>	the_excludes[0] = new Exclude(0);
1325	>	the_excludes[0]->setPair(0, 0);
1326	>	info[l].globalExcludes = new int;
1327	>	info[l].globalExcludes[0] = 0;
1328	>	info[l].n_exclude = 0;
1329	>	}
1330	>
1331	>	// set the arrays into the SimInfo object
1332	>
1333	>	info[l].atoms = the_atoms;
1334	>	info[l].molecules = the_molecules;
1335	>	info[l].nGlobalExcludes = 0;
1336	>	info[l].excludes = the_excludes;
1337	>
1338	>	the_ff->setSimInfo(info);
1339		}
1340	+	}
1341
1342	<	current_mol++;
1343	<	current_comp_mol++;
1342	>	void SimSetup::makeIntegrator(void){
1343	>	int k;
1344
1345	<	if( current_comp_mol >= components_nmol[current_comp] ){
1345	>	NVT<RealIntegrator>* myNVT = NULL;
1346	>	NPTi<RealIntegrator>* myNPTi = NULL;
1347	>	NPTf<RealIntegrator>* myNPTf = NULL;
1348	>	NPTim<RealIntegrator>* myNPTim = NULL;
1349	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1350	>
1351	>	for (k = 0; k < nInfo; k++){
1352	>	switch (ensembleCase){
1353	>	case NVE_ENS:
1354	>	if (globals->haveZconstraints()){
1355	>	setupZConstraint(info[k]);
1356	>	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1357	>	}
1358	>	else
1359	>	new NVE<RealIntegrator>(&(info[k]), the_ff);
1360	>	break;
1361
1362	<	current_comp_mol = 0;
1363	<	current_comp++;
1362	>	case NVT_ENS:
1363	>	if (globals->haveZconstraints()){
1364	>	setupZConstraint(info[k]);
1365	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1366	>	}
1367	>	else
1368	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1369	>
1370	>	myNVT->setTargetTemp(globals->getTargetTemp());
1371	>
1372	>	if (globals->haveTauThermostat())
1373	>	myNVT->setTauThermostat(globals->getTauThermostat());
1374	>	else{
1375	>	sprintf(painCave.errMsg,
1376	>	"SimSetup error: If you use the NVT\n"
1377	>	"    ensemble, you must set tauThermostat.\n");
1378	>	painCave.isFatal = 1;
1379	>	simError();
1380	>	}
1381	>	break;
1382	>
1383	>	case NPTi_ENS:
1384	>	if (globals->haveZconstraints()){
1385	>	setupZConstraint(info[k]);
1386	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1387	>	}
1388	>	else
1389	>	myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1390	>
1391	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1392	>
1393	>	if (globals->haveTargetPressure())
1394	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1395	>	else{
1396	>	sprintf(painCave.errMsg,
1397	>	"SimSetup error: If you use a constant pressure\n"
1398	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1399	>	painCave.isFatal = 1;
1400	>	simError();
1401	>	}
1402	>
1403	>	if (globals->haveTauThermostat())
1404	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1405	>	else{
1406	>	sprintf(painCave.errMsg,
1407	>	"SimSetup error: If you use an NPT\n"
1408	>	"    ensemble, you must set tauThermostat.\n");
1409	>	painCave.isFatal = 1;
1410	>	simError();
1411	>	}
1412	>
1413	>	if (globals->haveTauBarostat())
1414	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1415	>	else{
1416	>	sprintf(painCave.errMsg,
1417	>	"SimSetup error: If you use an NPT\n"
1418	>	"    ensemble, you must set tauBarostat.\n");
1419	>	painCave.isFatal = 1;
1420	>	simError();
1421	>	}
1422	>	break;
1423	>
1424	>	case NPTf_ENS:
1425	>	if (globals->haveZconstraints()){
1426	>	setupZConstraint(info[k]);
1427	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1428	>	}
1429	>	else
1430	>	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1431	>
1432	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1433	>
1434	>	if (globals->haveTargetPressure())
1435	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1436	>	else{
1437	>	sprintf(painCave.errMsg,
1438	>	"SimSetup error: If you use a constant pressure\n"
1439	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1440	>	painCave.isFatal = 1;
1441	>	simError();
1442	>	}
1443	>
1444	>	if (globals->haveTauThermostat())
1445	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1446	>	else{
1447	>	sprintf(painCave.errMsg,
1448	>	"SimSetup error: If you use an NPT\n"
1449	>	"    ensemble, you must set tauThermostat.\n");
1450	>	painCave.isFatal = 1;
1451	>	simError();
1452	>	}
1453	>
1454	>	if (globals->haveTauBarostat())
1455	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1456	>	else{
1457	>	sprintf(painCave.errMsg,
1458	>	"SimSetup error: If you use an NPT\n"
1459	>	"    ensemble, you must set tauBarostat.\n");
1460	>	painCave.isFatal = 1;
1461	>	simError();
1462	>	}
1463	>	break;
1464	>
1465	>	case NPTim_ENS:
1466	>	if (globals->haveZconstraints()){
1467	>	setupZConstraint(info[k]);
1468	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1469	>	}
1470	>	else
1471	>	myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1472	>
1473	>	myNPTim->setTargetTemp(globals->getTargetTemp());
1474	>
1475	>	if (globals->haveTargetPressure())
1476	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1477	>	else{
1478	>	sprintf(painCave.errMsg,
1479	>	"SimSetup error: If you use a constant pressure\n"
1480	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1481	>	painCave.isFatal = 1;
1482	>	simError();
1483	>	}
1484	>
1485	>	if (globals->haveTauThermostat())
1486	>	myNPTim->setTauThermostat(globals->getTauThermostat());
1487	>	else{
1488	>	sprintf(painCave.errMsg,
1489	>	"SimSetup error: If you use an NPT\n"
1490	>	"    ensemble, you must set tauThermostat.\n");
1491	>	painCave.isFatal = 1;
1492	>	simError();
1493	>	}
1494	>
1495	>	if (globals->haveTauBarostat())
1496	>	myNPTim->setTauBarostat(globals->getTauBarostat());
1497	>	else{
1498	>	sprintf(painCave.errMsg,
1499	>	"SimSetup error: If you use an NPT\n"
1500	>	"    ensemble, you must set tauBarostat.\n");
1501	>	painCave.isFatal = 1;
1502	>	simError();
1503	>	}
1504	>	break;
1505	>
1506	>	case NPTfm_ENS:
1507	>	if (globals->haveZconstraints()){
1508	>	setupZConstraint(info[k]);
1509	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1510	>	}
1511	>	else
1512	>	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1513	>
1514	>	myNPTfm->setTargetTemp(globals->getTargetTemp());
1515	>
1516	>	if (globals->haveTargetPressure())
1517	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1518	>	else{
1519	>	sprintf(painCave.errMsg,
1520	>	"SimSetup error: If you use a constant pressure\n"
1521	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1522	>	painCave.isFatal = 1;
1523	>	simError();
1524	>	}
1525	>
1526	>	if (globals->haveTauThermostat())
1527	>	myNPTfm->setTauThermostat(globals->getTauThermostat());
1528	>	else{
1529	>	sprintf(painCave.errMsg,
1530	>	"SimSetup error: If you use an NPT\n"
1531	>	"    ensemble, you must set tauThermostat.\n");
1532	>	painCave.isFatal = 1;
1533	>	simError();
1534	>	}
1535	>
1536	>	if (globals->haveTauBarostat())
1537	>	myNPTfm->setTauBarostat(globals->getTauBarostat());
1538	>	else{
1539	>	sprintf(painCave.errMsg,
1540	>	"SimSetup error: If you use an NPT\n"
1541	>	"    ensemble, you must set tauBarostat.\n");
1542	>	painCave.isFatal = 1;
1543	>	simError();
1544	>	}
1545	>	break;
1546	>
1547	>	default:
1548	>	sprintf(painCave.errMsg,
1549	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1550	>	painCave.isFatal = 1;
1551	>	simError();
1552	>	}
1553		}
1554		}
1555	+
1556	+	void SimSetup::initFortran(void){
1557	+	info[0].refreshSim();
1558	+
1559	+	if (!strcmp(info[0].mixingRule, "standard")){
1560	+	the_ff->initForceField(LB_MIXING_RULE);
1561	+	}
1562	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1563	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1564	+	}
1565	+	else{
1566	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1567	+	info[0].mixingRule);
1568	+	painCave.isFatal = 1;
1569	+	simError();
1570	+	}
1571	+
1572	+
1573	+	#ifdef IS_MPI
1574	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1575	+	MPIcheckPoint();
1576	+	#endif // is_mpi
1577	+	}
1578	+
1579	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1580	+	int nZConstraints;
1581	+	ZconStamp** zconStamp;
1582	+
1583	+	if (globals->haveZconstraintTime()){
1584	+	//add sample time of z-constraint  into SimInfo's property list
1585	+	DoubleData* zconsTimeProp = new DoubleData();
1586	+	zconsTimeProp->setID(ZCONSTIME_ID);
1587	+	zconsTimeProp->setData(globals->getZconsTime());
1588	+	theInfo.addProperty(zconsTimeProp);
1589	+	}
1590	+	else{
1591	+	sprintf(painCave.errMsg,
1592	+	"ZConstraint error: If you use an ZConstraint\n"
1593	+	" , you must set sample time.\n");
1594	+	painCave.isFatal = 1;
1595	+	simError();
1596	+	}
1597	+
1598	+	//push zconsTol into siminfo, if user does not specify
1599	+	//value for zconsTol, a default value will be used
1600	+	DoubleData* zconsTol = new DoubleData();
1601	+	zconsTol->setID(ZCONSTOL_ID);
1602	+	if (globals->haveZconsTol()){
1603	+	zconsTol->setData(globals->getZconsTol());
1604	+	}
1605	+	else{
1606	+	double defaultZConsTol = 0.01;
1607	+	sprintf(painCave.errMsg,
1608	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1609	+	" , default value %f is used.\n",
1610	+	defaultZConsTol);
1611	+	painCave.isFatal = 0;
1612	+	simError();
1613	+
1614	+	zconsTol->setData(defaultZConsTol);
1615	+	}
1616	+	theInfo.addProperty(zconsTol);
1617	+
1618	+	//set Force Substraction Policy
1619	+	StringData* zconsForcePolicy = new StringData();
1620	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1621	+
1622	+	if (globals->haveZconsForcePolicy()){
1623	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1624	+	}
1625	+	else{
1626	+	sprintf(painCave.errMsg,
1627	+	"ZConstraint Warning: User does not set force substraction policy, "
1628	+	"PolicyByMass is used\n");
1629	+	painCave.isFatal = 0;
1630	+	simError();
1631	+	zconsForcePolicy->setData("BYMASS");
1632	+	}
1633	+
1634	+	theInfo.addProperty(zconsForcePolicy);
1635	+
1636	+	//Determine the name of ouput file and add it into SimInfo's property list
1637	+	//Be careful, do not use inFileName, since it is a pointer which
1638	+	//point to a string at master node, and slave nodes do not contain that string
1639	+
1640	+	string zconsOutput(theInfo.finalName);
1641	+
1642	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1643	+
1644	+	StringData* zconsFilename = new StringData();
1645	+	zconsFilename->setID(ZCONSFILENAME_ID);
1646	+	zconsFilename->setData(zconsOutput);
1647	+
1648	+	theInfo.addProperty(zconsFilename);
1649	+
1650	+	//setup index, pos and other parameters of z-constraint molecules
1651	+	nZConstraints = globals->getNzConstraints();
1652	+	theInfo.nZconstraints = nZConstraints;
1653	+
1654	+	zconStamp = globals->getZconStamp();
1655	+	ZConsParaItem tempParaItem;
1656	+
1657	+	ZConsParaData* zconsParaData = new ZConsParaData();
1658	+	zconsParaData->setID(ZCONSPARADATA_ID);
1659	+
1660	+	for (int i = 0; i < nZConstraints; i++){
1661	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1662	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1663	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1664	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1665	+
1666	+	zconsParaData->addItem(tempParaItem);
1667	+	}
1668	+
1669	+	//check the uniqueness of index
1670	+	if(!zconsParaData->isIndexUnique()){
1671	+	sprintf(painCave.errMsg,
1672	+	"ZConstraint Error: molIndex is not unique\n");
1673	+	painCave.isFatal = 1;
1674	+	simError();
1675	+	}
1676	+
1677	+	//sort the parameters by index of molecules
1678	+	zconsParaData->sortByIndex();
1679	+
1680	+	//push data into siminfo, therefore, we can retrieve later
1681	+	theInfo.addProperty(zconsParaData);
1682	+	}

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