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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 707 by mmeineke, Wed Aug 20 19:42:31 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTim_ENS      4
25	+	#define NPTfm_ENS      5
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 27 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 62 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
97	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
71	<
72	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
75	<
76	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	simnfo->run_time = the_globals->getRunTime();
80	<
81	<	// get the ones we know are there, yet still may need some work.
82	<	n_components = the_globals->getNComponents();
83	<	strcpy( force_field, the_globals->getForceField() );
84	<
85	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
91	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
92	<	the_extendedsystem = new ExtendedSystem( simnfo );
93	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
94	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
95	<	} else {
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
98	<	"reverting to NVE for this simulation.\n",
99	<	ensemble );
100	<	painCave.isFatal = 0;
101	<	simError();
102	<	strcpy( ensemble, "NVE" );
103	<	}
104	<	strcpy( simnfo->ensemble, ensemble );
105	<
106	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
107	<	simnfo->usePBC = the_globals->getPBC();
108	<
109	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
110	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
111	<	else{
112	<	sprintf( painCave.errMsg,
113	<	"SimSetup Error. Unrecognized force field -> %s\n",
114	<	force_field );
115	<	painCave.isFatal = 1;
116	<	simError();
117	<	}
118	<
119	<	#ifdef IS_MPI
120	<	strcpy( checkPointMsg, "ForceField creation successful" );
121	<	MPIcheckPoint();
122	<	#endif // is_mpi
123	<
97	>	int i, j, k, globalAtomIndex;
98
99	+	// gather all of the information from the Bass file
100
101	<	// get the components and calculate the tot_nMol and indvidual n_mol
127	<	the_components = the_globals->getComponents();
128	<	components_nmol = new int[n_components];
129	<	comp_stamps = new MoleculeStamp*[n_components];
101	>	gatherInfo();
102
103	<	if( !the_globals->haveNMol() ){
132	<	// we don't have the total number of molecules, so we assume it is
133	<	// given in each component
103	>	// creation of complex system objects
104
105	<	tot_nmol = 0;
136	<	for( i=0; i<n_components; i++ ){
105	>	sysObjectsCreation();
106
107	<	if( !the_components[i]->haveNMol() ){
139	<	// we have a problem
140	<	sprintf( painCave.errMsg,
141	<	"SimSetup Error. No global NMol or component NMol"
142	<	" given. Cannot calculate the number of atoms.\n" );
143	<	painCave.isFatal = 1;
144	<	simError();
145	<	}
107	>	// check on the post processing info
108
109	<	tot_nmol += the_components[i]->getNMol();
148	<	components_nmol[i] = the_components[i]->getNMol();
149	<	}
150	<	}
151	<	else{
152	<	sprintf( painCave.errMsg,
153	<	"SimSetup error.\n"
154	<	"\tSorry, the ability to specify total"
155	<	" nMols and then give molfractions in the components\n"
156	<	"\tis not currently supported."
157	<	" Please give nMol in the components.\n" );
158	<	painCave.isFatal = 1;
159	<	simError();
160	<
161	<
162	<	//     tot_nmol = the_globals->getNMol();
163	<
164	<	//   //we have the total number of molecules, now we check for molfractions
165	<	//     for( i=0; i<n_components; i++ ){
166	<
167	<	//       if( !the_components[i]->haveMolFraction() ){
168	<
169	<	//  if( !the_components[i]->haveNMol() ){
170	<	//    //we have a problem
171	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
172	<	//              << " nMol was given in component
173	<
174	<	}
109	>	finalInfoCheck();
110
111	<	#ifdef IS_MPI
177	<	strcpy( checkPointMsg, "Have the number of components" );
178	<	MPIcheckPoint();
179	<	#endif // is_mpi
111	>	// initialize the system coordinates
112
113	<	// make an array of molecule stamps that match the components used.
182	<	// also extract the used stamps out into a separate linked list
113	>	if( !isInfoArray ) initSystemCoords();
114
115	<	simnfo->nComponents = n_components;
185	<	simnfo->componentsNmol = components_nmol;
186	<	simnfo->compStamps = comp_stamps;
187	<	simnfo->headStamp = new LinkedMolStamp();
188	<
189	<	char* id;
190	<	LinkedMolStamp* headStamp = simnfo->headStamp;
191	<	LinkedMolStamp* currentStamp = NULL;
192	<	for( i=0; i<n_components; i++ ){
115	>	// make the output filenames
116
117	<	id = the_components[i]->getType();
118	<	comp_stamps[i] = NULL;
119	<
197	<	// check to make sure the component isn't already in the list
198	<
199	<	comp_stamps[i] = headStamp->match( id );
200	<	if( comp_stamps[i] == NULL ){
201	<
202	<	// extract the component from the list;
203	<
204	<	currentStamp = the_stamps->extractMolStamp( id );
205	<	if( currentStamp == NULL ){
206	<	sprintf( painCave.errMsg,
207	<	"SimSetup error: Component \"%s\" was not found in the "
208	<	"list of declared molecules\n",
209	<	id );
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
213	<
214	<	headStamp->add( currentStamp );
215	<	comp_stamps[i] = headStamp->match( id );
216	<	}
217	<	}
218	<
219	<	#ifdef IS_MPI
220	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
221	<	MPIcheckPoint();
222	<	#endif // is_mpi
117	>	makeOutNames();
118	>
119	>	// make the integrator
120
121	+	makeIntegrator();
122	+
123	+	#ifdef IS_MPI
124	+	mpiSim->mpiRefresh();
125	+	#endif
126
127	+	// initialize the Fortran
128
129	+	initFortran();
130
227	–	// caclulate the number of atoms, bonds, bends and torsions
131
229	–	tot_atoms = 0;
230	–	tot_bonds = 0;
231	–	tot_bends = 0;
232	–	tot_torsions = 0;
233	–	for( i=0; i<n_components; i++ ){
234	–
235	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
236	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
237	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
238	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
239	–	}
132
133	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
133	>	}
134
243	–	simnfo->n_atoms = tot_atoms;
244	–	simnfo->n_bonds = tot_bonds;
245	–	simnfo->n_bends = tot_bends;
246	–	simnfo->n_torsions = tot_torsions;
247	–	simnfo->n_SRI = tot_SRI;
248	–	simnfo->n_mol = tot_nmol;
135
136	<
251	<	#ifdef IS_MPI
136	>	void SimSetup::makeMolecules( void ){
137
138	<	// divide the molecules among processors here.
139	<
140	<	mpiSim = new mpiSimulation( simnfo );
141	<
142	<
138	>	int k,l;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	globalIndex = mpiSim->divideLabor();
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
261	–	// set up the local variables
153
154	<	int localMol, allMol;
264	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
154	>	//init the forceField paramters
155
156	<	int* mol2proc = mpiSim->getMolToProcMap();
267	<	int* molCompType = mpiSim->getMolComponentType();
268	<
269	<	allMol = 0;
270	<	localMol = 0;
271	<	local_atoms = 0;
272	<	local_bonds = 0;
273	<	local_bends = 0;
274	<	local_torsions = 0;
275	<	for( i=0; i<n_components; i++ ){
156	>	the_ff->readParams();
157
277	–	for( j=0; j<components_nmol[i]; j++ ){
278	–
279	–	if( mol2proc[j] == worldRank ){
280	–
281	–	local_atoms +=    comp_stamps[i]->getNAtoms();
282	–	local_bonds +=    comp_stamps[i]->getNBonds();
283	–	local_bends +=    comp_stamps[i]->getNBends();
284	–	local_torsions += comp_stamps[i]->getNTorsions();
285	–	localMol++;
286	–	}
287	–	allMol++;
288	–	}
289	–	}
290	–	local_SRI = local_bonds + local_bends + local_torsions;
158
159	+	// init the atoms
160
161	<	simnfo->n_atoms = mpiSim->getMyNlocal();
161	>	double ux, uy, uz, u, uSqr;
162
163	<	if( local_atoms != simnfo->n_atoms ){
164	<	sprintf( painCave.errMsg,
165	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
166	<	" localAtom (%d) are not equal.\n",
167	<	simnfo->n_atoms,
168	<	local_atoms );
169	<	painCave.isFatal = 1;
170	<	simError();
171	<	}
163	>	for(k=0; k<nInfo; k++){
164	>
165	>	the_ff->setSimInfo( &(info[k]) );
166	>
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for(i=0; i<info[k].n_mol; i++){
170	>
171	>	stampID = info[k].molecules[i].getStampID();
172
173	<	simnfo->n_bonds = local_bonds;
174	<	simnfo->n_bends = local_bends;
175	<	simnfo->n_torsions = local_torsions;
176	<	simnfo->n_SRI = local_SRI;
177	<	simnfo->n_mol = localMol;
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178	>
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184
185	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
186	<	MPIcheckPoint();
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188	>
189	>	// make the Atoms
190	>
191	>	for(j=0; j<molInfo.nAtoms; j++){
192
193	<
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195	>
196	>	dAtom = new DirectionalAtom( (j + atomOffset),
197	>	info[k].getConfiguration() );
198	>	info[k].n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200	>
201	>	ux = currentAtom->getOrntX();
202	>	uy = currentAtom->getOrntY();
203	>	uz = currentAtom->getOrntZ();
204	>
205	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	>
207	>	u = sqrt( uSqr );
208	>	ux = ux / u;
209	>	uy = uy / u;
210	>	uz = uz / u;
211	>
212	>	dAtom->setSUx( ux );
213	>	dAtom->setSUy( uy );
214	>	dAtom->setSUz( uz );
215	>	}
216	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	>	info[k].getConfiguration() );
219	>	}
220	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	>
222	>	#ifdef IS_MPI
223	>
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	>
226		#endif // is_mpi
227	+	}
228	+
229	+	// make the bonds
230	+	for(j=0; j<molInfo.nBonds; j++){
231	+
232	+	currentBond = comp_stamps[stampID]->getBond( j );
233	+	theBonds[j].a = currentBond->getA() + atomOffset;
234	+	theBonds[j].b = currentBond->getB() + atomOffset;
235
236	<
237	<	// create the atom and short range interaction arrays
238	<
239	<	Atom::createArrays(simnfo->n_atoms);
240	<	the_atoms = new Atom*[simnfo->n_atoms];
241	<	the_molecules = new Molecule[simnfo->n_mol];
242	<	int molIndex;
243	<
244	<	// initialize the molecule's stampID's
326	<
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244	>	}
245		#ifdef IS_MPI
246	+	tempEx = exI;
247	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	+	tempEx = exJ;
249	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250
251	<
252	<	molIndex = 0;
253	<	for(i=0; i<mpiSim->getTotNmol(); i++){
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252	>	#else  // isn't MPI
253	>
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	>	#endif  //is_mpi
256	>	}
257	>	excludeOffset += molInfo.nBonds;
258	>
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261	>
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266	>
267	>	if( currentBend->haveExtras() ){
268
269	<	if(mol2proc[i] == worldRank ){
270	<	the_molecules[molIndex].setStampID( molCompType[i] );
271	<	the_molecules[molIndex].setMyIndex( molIndex );
272	<	molIndex++;
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276	>
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290	>	sprintf( painCave.errMsg,
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298	>	}
299	>
300	>	else{
301	>
302	>	sprintf( painCave.errMsg,
303	>	"SimSetup Error: unhandled bend assignment:\n"
304	>	"    -->%s in Bend[%d] in %s\n",
305	>	current_extra->getlhs(),
306	>	j, comp_stamps[stampID]->getID() );
307	>	painCave.isFatal = 1;
308	>	simError();
309	>	}
310	>
311	>	current_extra = current_extra->getNext();
312		}
313		}
339	–
340	–	#else // is_mpi
314
315	<	molIndex = 0;
343	<	for(i=0; i<n_components; i++){
344	<	for(j=0; j<components_nmol[i]; j++ ){
345	<	the_molecules[molIndex].setStampID( i );
346	<	the_molecules[molIndex].setMyIndex( molIndex );
347	<	molIndex++;
348	<	}
349	<	}
315	>	if( !theBends[j].isGhost ){
316
317	<
318	<	#endif // is_mpi
353	<
354	<
355	<	if( simnfo->n_SRI ){
356	<
357	<	Exclude::createArray(simnfo->n_SRI);
358	<	the_excludes = new Exclude*[simnfo->n_SRI];
359	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
360	<	simnfo->globalExcludes = new int;
361	<	simnfo->n_exclude = simnfo->n_SRI;
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].c;
319		}
320		else{
321
322	<	Exclude::createArray( 1 );
323	<	the_excludes = new Exclude*;
367	<	the_excludes[0] = new Exclude(0);
368	<	the_excludes[0]->setPair( 0,0 );
369	<	simnfo->globalExcludes = new int;
370	<	simnfo->globalExcludes[0] = 0;
371	<	simnfo->n_exclude = 0;
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].b;
324		}
373	–
374	–	// set the arrays into the SimInfo object
375	–
376	–	simnfo->atoms = the_atoms;
377	–	simnfo->molecules = the_molecules;
378	–	simnfo->nGlobalExcludes = 0;
379	–	simnfo->excludes = the_excludes;
380	–
381	–
382	–	// get some of the tricky things that may still be in the globals
383	–
325
326	<	if( the_globals->haveBox() ){
327	<	simnfo->box_x = the_globals->getBox();
328	<	simnfo->box_y = the_globals->getBox();
329	<	simnfo->box_z = the_globals->getBox();
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331		}
332	<	else if( the_globals->haveDensity() ){
333	<
334	<	double vol;
335	<	vol = (double)tot_nmol / the_globals->getDensity();
336	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
337	<	simnfo->box_y = simnfo->box_x;
338	<	simnfo->box_z = simnfo->box_x;
339	<	}
340	<	else{
341	<	if( !the_globals->haveBoxX() ){
342	<	sprintf( painCave.errMsg,
343	<	"SimSetup error, no periodic BoxX size given.\n" );
344	<	painCave.isFatal = 1;
345	<	simError();
346	<	}
347	<	simnfo->box_x = the_globals->getBoxX();
348	<
349	<	if( !the_globals->haveBoxY() ){
350	<	sprintf( painCave.errMsg,
351	<	"SimSetup error, no periodic BoxY size given.\n" );
352	<	painCave.isFatal = 1;
353	<	simError();
354	<	}
355	<	simnfo->box_y = the_globals->getBoxY();
356	<
357	<	if( !the_globals->haveBoxZ() ){
358	<	sprintf( painCave.errMsg,
359	<	"SimSetup error, no periodic BoxZ size given.\n" );
360	<	painCave.isFatal = 1;
419	<	simError();
420	<	}
421	<	simnfo->box_z = the_globals->getBoxZ();
332	>	#ifdef IS_MPI
333	>	tempEx = exI;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	>
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	#else  // isn't MPI
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	#endif  //is_mpi
342	>	}
343	>	excludeOffset += molInfo.nBends;
344	>
345	>	for(j=0; j<molInfo.nTorsions; j++){
346	>
347	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352	>
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355	>
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361		}
362	+	#ifdef IS_MPI
363	+	tempEx = exI;
364	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	+	tempEx = exJ;
366	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	+
368	+	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369	+	#else  // isn't MPI
370	+	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371	+	#endif  //is_mpi
372	+	}
373	+	excludeOffset += molInfo.nTorsions;
374	+
375	+
376	+	// send the arrays off to the forceField for init.
377	+
378	+	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	+	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	+	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	+	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	+
383	+
384	+	info[k].molecules[i].initialize( molInfo );
385
386	+
387	+	atomOffset += molInfo.nAtoms;
388	+	delete[] theBonds;
389	+	delete[] theBends;
390	+	delete[] theTorsions;
391	+	}
392	+	}
393	+
394		#ifdef IS_MPI
395	<	strcpy( checkPointMsg, "Box size set up" );
395	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
396		MPIcheckPoint();
397		#endif // is_mpi
398	+
399	+	// clean up the forcefield
400
401	+	the_ff->calcRcut();
402	+	the_ff->cleanMe();
403	+
404	+	}
405
406	<	// initialize the arrays
406	>	void SimSetup::initFromBass( void ){
407
408	<	the_ff->setSimInfo( simnfo );
408	>	int i, j, k;
409	>	int n_cells;
410	>	double cellx, celly, cellz;
411	>	double temp1, temp2, temp3;
412	>	int n_per_extra;
413	>	int n_extra;
414	>	int have_extra, done;
415
416	<	makeMolecules();
417	<	simnfo->identArray = new int[simnfo->n_atoms];
418	<	for(i=0; i<simnfo->n_atoms; i++){
419	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
438	<	}
439	<
440	<	if (the_globals->getUseRF() ) {
441	<	simnfo->useReactionField = 1;
442	<
443	<	if( !the_globals->haveECR() ){
444	<	sprintf( painCave.errMsg,
445	<	"SimSetup Warning: using default value of 1/2 the smallest "
446	<	"box length for the electrostaticCutoffRadius.\n"
447	<	"I hope you have a very fast processor!\n");
448	<	painCave.isFatal = 0;
449	<	simError();
450	<	double smallest;
451	<	smallest = simnfo->box_x;
452	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
453	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
454	<	simnfo->ecr = 0.5 * smallest;
455	<	} else {
456	<	simnfo->ecr        = the_globals->getECR();
457	<	}
416	>	double vel[3];
417	>	vel[0] = 0.0;
418	>	vel[1] = 0.0;
419	>	vel[2] = 0.0;
420
421	<	if( !the_globals->haveEST() ){
421	>	temp1 = (double)tot_nmol / 4.0;
422	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423	>	temp3 = ceil( temp2 );
424	>
425	>	have_extra =0;
426	>	if( temp2 < temp3 ){ // we have a non-complete lattice
427	>	have_extra =1;
428	>
429	>	n_cells = (int)temp3 - 1;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435	>	n_per_extra = (int)ceil( temp1 );
436	>
437	>	if( n_per_extra > 4){
438		sprintf( painCave.errMsg,
439	<	"SimSetup Warning: using default value of 0.05 * the "
440	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
463	<	);
464	<	painCave.isFatal = 0;
465	<	simError();
466	<	simnfo->est = 0.05 * simnfo->ecr;
467	<	} else {
468	<	simnfo->est        = the_globals->getEST();
469	<	}
470	<
471	<	if(!the_globals->haveDielectric() ){
472	<	sprintf( painCave.errMsg,
473	<	"SimSetup Error: You are trying to use Reaction Field without"
474	<	"setting a dielectric constant!\n"
475	<	);
439	>	"SimSetup error. There has been an error in constructing"
440	>	" the non-complete lattice.\n" );
441		painCave.isFatal = 1;
442		simError();
443		}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
486	<	"box length for the electrostaticCutoffRadius.\n"
487	<	"I hope you have a very fast processor!\n");
488	<	painCave.isFatal = 0;
489	<	simError();
490	<	double smallest;
491	<	smallest = simnfo->box_x;
492	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
493	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
494	<	simnfo->ecr = 0.5 * smallest;
495	<	} else {
496	<	simnfo->ecr        = the_globals->getECR();
497	<	}
498	<
499	<	if( !the_globals->haveEST() ){
500	<	sprintf( painCave.errMsg,
501	<	"SimSetup Warning: using default value of 5% of the"
502	<	"electrostaticCutoffRadius for the "
503	<	"electrostaticSkinThickness\n"
504	<	);
505	<	painCave.isFatal = 0;
506	<	simError();
507	<	simnfo->est = 0.05 * simnfo->ecr;
508	<	} else {
509	<	simnfo->est        = the_globals->getEST();
510	<	}
511	<	}
512	<	}
444	>	}
445	>	else{
446	>	n_cells = (int)temp3;
447	>	cellx = info[0].boxL[0] / temp3;
448	>	celly = info[0].boxL[1] / temp3;
449	>	cellz = info[0].boxL[2] / temp3;
450	>	}
451
452	<	#ifdef IS_MPI
453	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
454	<	MPIcheckPoint();
455	<	#endif // is_mpi
452	>	current_mol = 0;
453	>	current_comp_mol = 0;
454	>	current_comp = 0;
455	>	current_atom_ndx = 0;
456
457	<	if( the_globals->haveInitialConfig() ){
458	<
459	<	InitializeFromFile* fileInit;
522	<	#ifdef IS_MPI // is_mpi
523	<	if( worldRank == 0 ){
524	<	#endif //is_mpi
525	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
526	<	#ifdef IS_MPI
527	<	}else fileInit = new InitializeFromFile( NULL );
528	<	#endif
529	<	fileInit->read_xyz( simnfo ); // default velocities on
457	>	for( i=0; i < n_cells ; i++ ){
458	>	for( j=0; j < n_cells; j++ ){
459	>	for( k=0; k < n_cells; k++ ){
460
461	<	delete fileInit;
462	<	}
463	<	else{
461	>	makeElement( i * cellx,
462	>	j * celly,
463	>	k * cellz );
464
465	<	#ifdef IS_MPI
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly + 0.5 * celly,
467	>	k * cellz );
468
469	<	// no init from bass
470	<
471	<	sprintf( painCave.errMsg,
540	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
541	<	painCave.isFatal;
542	<	simError();
543	<
544	<	#else
469	>	makeElement( i * cellx,
470	>	j * celly + 0.5 * celly,
471	>	k * cellz + 0.5 * cellz );
472
473	<	initFromBass();
473	>	makeElement( i * cellx + 0.5 * cellx,
474	>	j * celly,
475	>	k * cellz + 0.5 * cellz );
476	>	}
477	>	}
478	>	}
479
480	+	if( have_extra ){
481	+	done = 0;
482
483	<	#endif
484	<	}
483	>	int start_ndx;
484	>	for( i=0; i < (n_cells+1) && !done; i++ ){
485	>	for( j=0; j < (n_cells+1) && !done; j++ ){
486
487	<	#ifdef IS_MPI
553	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
554	<	MPIcheckPoint();
555	<	#endif // is_mpi
487	>	if( i < n_cells ){
488
489	+	if( j < n_cells ){
490	+	start_ndx = n_cells;
491	+	}
492	+	else start_ndx = 0;
493	+	}
494	+	else start_ndx = 0;
495
496	<
559	<
560	<
496	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497
498	<
499	<	#ifdef IS_MPI
500	<	if( worldRank == 0 ){
501	<	#endif // is_mpi
502	<
503	<	if( the_globals->haveFinalConfig() ){
504	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
498	>	makeElement( i * cellx,
499	>	j * celly,
500	>	k * cellz );
501	>	done = ( current_mol >= tot_nmol );
502	>
503	>	if( !done && n_per_extra > 1 ){
504	>	makeElement( i * cellx + 0.5 * cellx,
505	>	j * celly + 0.5 * celly,
506	>	k * cellz );
507	>	done = ( current_mol >= tot_nmol );
508		}
509	<	else{
510	<	strcpy( simnfo->finalName, inFileName );
511	<	char* endTest;
512	<	int nameLength = strlen( simnfo->finalName );
513	<	endTest = &(simnfo->finalName[nameLength - 5]);
514	<	if( !strcmp( endTest, ".bass" ) ){
576	<	strcpy( endTest, ".eor" );
577	<	}
578	<	else if( !strcmp( endTest, ".BASS" ) ){
579	<	strcpy( endTest, ".eor" );
580	<	}
581	<	else{
582	<	endTest = &(simnfo->finalName[nameLength - 4]);
583	<	if( !strcmp( endTest, ".bss" ) ){
584	<	strcpy( endTest, ".eor" );
585	<	}
586	<	else if( !strcmp( endTest, ".mdl" ) ){
587	<	strcpy( endTest, ".eor" );
588	<	}
589	<	else{
590	<	strcat( simnfo->finalName, ".eor" );
591	<	}
592	<	}
509	>
510	>	if( !done && n_per_extra > 2){
511	>	makeElement( i * cellx,
512	>	j * celly + 0.5 * celly,
513	>	k * cellz + 0.5 * cellz );
514	>	done = ( current_mol >= tot_nmol );
515		}
516	<
517	<	// make the sample and status out names
518	<
519	<	strcpy( simnfo->sampleName, inFileName );
520	<	char* endTest;
521	<	int nameLength = strlen( simnfo->sampleName );
600	<	endTest = &(simnfo->sampleName[nameLength - 5]);
601	<	if( !strcmp( endTest, ".bass" ) ){
602	<	strcpy( endTest, ".dump" );
516	>
517	>	if( !done && n_per_extra > 3){
518	>	makeElement( i * cellx + 0.5 * cellx,
519	>	j * celly,
520	>	k * cellz + 0.5 * cellz );
521	>	done = ( current_mol >= tot_nmol );
522		}
523	<	else if( !strcmp( endTest, ".BASS" ) ){
605	<	strcpy( endTest, ".dump" );
606	<	}
607	<	else{
608	<	endTest = &(simnfo->sampleName[nameLength - 4]);
609	<	if( !strcmp( endTest, ".bss" ) ){
610	<	strcpy( endTest, ".dump" );
523	>	}
524		}
612	–	else if( !strcmp( endTest, ".mdl" ) ){
613	–	strcpy( endTest, ".dump" );
614	–	}
615	–	else{
616	–	strcat( simnfo->sampleName, ".dump" );
617	–	}
525		}
619	–
620	–	strcpy( simnfo->statusName, inFileName );
621	–	nameLength = strlen( simnfo->statusName );
622	–	endTest = &(simnfo->statusName[nameLength - 5]);
623	–	if( !strcmp( endTest, ".bass" ) ){
624	–	strcpy( endTest, ".stat" );
625	–	}
626	–	else if( !strcmp( endTest, ".BASS" ) ){
627	–	strcpy( endTest, ".stat" );
628	–	}
629	–	else{
630	–	endTest = &(simnfo->statusName[nameLength - 4]);
631	–	if( !strcmp( endTest, ".bss" ) ){
632	–	strcpy( endTest, ".stat" );
633	–	}
634	–	else if( !strcmp( endTest, ".mdl" ) ){
635	–	strcpy( endTest, ".stat" );
636	–	}
637	–	else{
638	–	strcat( simnfo->statusName, ".stat" );
639	–	}
640	–	}
641	–
642	–	#ifdef IS_MPI
526		}
644	–	#endif // is_mpi
645	–
646	–	// set the status, sample, and themal kick times
647	–
648	–	if( the_globals->haveSampleTime() ){
649	–	simnfo->sampleTime = the_globals->getSampleTime();
650	–	simnfo->statusTime = simnfo->sampleTime;
651	–	simnfo->thermalTime = simnfo->sampleTime;
652	–	}
653	–	else{
654	–	simnfo->sampleTime = the_globals->getRunTime();
655	–	simnfo->statusTime = simnfo->sampleTime;
656	–	simnfo->thermalTime = simnfo->sampleTime;
657	–	}
527
528	<	if( the_globals->haveStatusTime() ){
529	<	simnfo->statusTime = the_globals->getStatusTime();
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530		}
531	+	}
532
533	<	if( the_globals->haveThermalTime() ){
664	<	simnfo->thermalTime = the_globals->getThermalTime();
665	<	}
533	>	void SimSetup::makeElement( double x, double y, double z ){
534
535	<	// check for the temperature set flag
535	>	int k;
536	>	AtomStamp* current_atom;
537	>	DirectionalAtom* dAtom;
538	>	double rotMat[3][3];
539	>	double pos[3];
540
541	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
541	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542
543	+	current_atom = comp_stamps[current_comp]->getAtom( k );
544	+	if( !current_atom->havePosition() ){
545	+	sprintf( painCave.errMsg,
546	+	"SimSetup:initFromBass error.\n"
547	+	"\tComponent %s, atom %s does not have a position specified.\n"
548	+	"\tThe initialization routine is unable to give a start"
549	+	" position.\n",
550	+	comp_stamps[current_comp]->getID(),
551	+	current_atom->getType() );
552	+	painCave.isFatal = 1;
553	+	simError();
554	+	}
555	+
556	+	pos[0] = x + current_atom->getPosX();
557	+	pos[1] = y + current_atom->getPosY();
558	+	pos[2] = z + current_atom->getPosZ();
559	+
560	+	info[0].atoms[current_atom_ndx]->setPos( pos );
561
562	<	//   // make the longe range forces and the integrator
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563
564	<	//   new AllLong( simnfo );
564	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565
566	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo,
567	<	the_ff,
568	<	the_extendedsystem);
679	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo,
680	<	the_ff,
681	<	the_extendedsystem );
566	>	rotMat[0][0] = 1.0;
567	>	rotMat[0][1] = 0.0;
568	>	rotMat[0][2] = 0.0;
569
570	<	#ifdef IS_MPI
571	<	mpiSim->mpiRefresh();
572	<	#endif
570	>	rotMat[1][0] = 0.0;
571	>	rotMat[1][1] = 1.0;
572	>	rotMat[1][2] = 0.0;
573
574	<	// initialize the Fortran
574	>	rotMat[2][0] = 0.0;
575	>	rotMat[2][1] = 0.0;
576	>	rotMat[2][2] = 1.0;
577
578	+	dAtom->setA( rotMat );
579	+	}
580
581	<	simnfo->refreshSim();
691	<
692	<	if( !strcmp( simnfo->mixingRule, "standard") ){
693	<	the_ff->initForceField( LB_MIXING_RULE );
581	>	current_atom_ndx++;
582		}
583	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
584	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
583	>
584	>	current_mol++;
585	>	current_comp_mol++;
586	>
587	>	if( current_comp_mol >= components_nmol[current_comp] ){
588	>
589	>	current_comp_mol = 0;
590	>	current_comp++;
591		}
592	+	}
593	+
594	+
595	+	void SimSetup::gatherInfo( void ){
596	+	int i,j,k;
597	+
598	+	ensembleCase = -1;
599	+	ffCase = -1;
600	+
601	+	// set the easy ones first
602	+
603	+	for( i=0; i<nInfo; i++){
604	+	info[i].target_temp = globals->getTargetTemp();
605	+	info[i].dt = globals->getDt();
606	+	info[i].run_time = globals->getRunTime();
607	+	}
608	+	n_components = globals->getNComponents();
609	+
610	+
611	+	// get the forceField
612	+
613	+	strcpy( force_field, globals->getForceField() );
614	+
615	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618		else{
619		sprintf( painCave.errMsg,
620	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
621	<	simnfo->mixingRule );
620	>	"SimSetup Error. Unrecognized force field -> %s\n",
621	>	force_field );
622		painCave.isFatal = 1;
623		simError();
624		}
625
626	+	// get the ensemble
627
628	<	#ifdef IS_MPI
708	<	strcpy( checkPointMsg,
709	<	"Successfully intialized the mixingRule for Fortran." );
710	<	MPIcheckPoint();
711	<	#endif // is_mpi
712	<	}
628	>	strcpy( ensemble, globals->getEnsemble() );
629
630	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633	+	ensembleCase = NPTi_ENS;
634	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637	+	else{
638	+	sprintf( painCave.errMsg,
639	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	+	"reverting to NVE for this simulation.\n",
641	+	ensemble );
642	+	painCave.isFatal = 0;
643	+	simError();
644	+	strcpy( ensemble, "NVE" );
645	+	ensembleCase = NVE_ENS;
646	+	}
647	+
648	+	for(i=0; i<nInfo; i++){
649	+
650	+	strcpy( info[i].ensemble, ensemble );
651
652	<	void SimSetup::makeMolecules( void ){
652	>	// get the mixing rule
653
654	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
655	<	molInit info;
656	<	DirectionalAtom* dAtom;
720	<	LinkedAssign* extras;
721	<	LinkedAssign* current_extra;
722	<	AtomStamp* currentAtom;
723	<	BondStamp* currentBond;
724	<	BendStamp* currentBend;
725	<	TorsionStamp* currentTorsion;
726	<
727	<	bond_pair* theBonds;
728	<	bend_set* theBends;
729	<	torsion_set* theTorsions;
730	<
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657
658	<	//init the forceField paramters
658	>	// get the components and calculate the tot_nMol and indvidual n_mol
659	>
660	>	the_components = globals->getComponents();
661	>	components_nmol = new int[n_components];
662
734	–	the_ff->readParams();
663
664	<
665	<	// init the atoms
664	>	if( !globals->haveNMol() ){
665	>	// we don't have the total number of molecules, so we assume it is
666	>	// given in each component
667
668	<	double ux, uy, uz, u, uSqr;
668	>	tot_nmol = 0;
669	>	for( i=0; i<n_components; i++ ){
670	>
671	>	if( !the_components[i]->haveNMol() ){
672	>	// we have a problem
673	>	sprintf( painCave.errMsg,
674	>	"SimSetup Error. No global NMol or component NMol"
675	>	" given. Cannot calculate the number of atoms.\n" );
676	>	painCave.isFatal = 1;
677	>	simError();
678	>	}
679	>
680	>	tot_nmol += the_components[i]->getNMol();
681	>	components_nmol[i] = the_components[i]->getNMol();
682	>	}
683	>	}
684	>	else{
685	>	sprintf( painCave.errMsg,
686	>	"SimSetup error.\n"
687	>	"\tSorry, the ability to specify total"
688	>	" nMols and then give molfractions in the components\n"
689	>	"\tis not currently supported."
690	>	" Please give nMol in the components.\n" );
691	>	painCave.isFatal = 1;
692	>	simError();
693	>	}
694	>
695	>	// set the status, sample, and thermal kick times
696
697	<	atomOffset = 0;
698	<	excludeOffset = 0;
699	<	for(i=0; i<simnfo->n_mol; i++){
697	>	for(i=0; i<nInfo; i++){
698	>
699	>	if( globals->haveSampleTime() ){
700	>	info[i].sampleTime = globals->getSampleTime();
701	>	info[i].statusTime = info[i].sampleTime;
702	>	info[i].thermalTime = info[i].sampleTime;
703	>	}
704	>	else{
705	>	info[i].sampleTime = globals->getRunTime();
706	>	info[i].statusTime = info[i].sampleTime;
707	>	info[i].thermalTime = info[i].sampleTime;
708	>	}
709
710	<	stampID = the_molecules[i].getStampID();
710	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712	>	}
713	>
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716	>	}
717
718	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
748	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
749	<	info.nBends    = comp_stamps[stampID]->getNBends();
750	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
751	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
718	>	// check for the temperature set flag
719
720	<	info.myAtoms = &the_atoms[atomOffset];
754	<	info.myExcludes = &the_excludes[excludeOffset];
755	<	info.myBonds = new Bond*[info.nBonds];
756	<	info.myBends = new Bend*[info.nBends];
757	<	info.myTorsions = new Torsion*[info.nTorsions];
758	<
759	<	theBonds = new bond_pair[info.nBonds];
760	<	theBends = new bend_set[info.nBends];
761	<	theTorsions = new torsion_set[info.nTorsions];
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721
722	<	// make the Atoms
722	>	// get some of the tricky things that may still be in the globals
723
724	<	for(j=0; j<info.nAtoms; j++){
724	>	double boxVector[3];
725	>	if( globals->haveBox() ){
726	>	boxVector[0] = globals->getBox();
727	>	boxVector[1] = globals->getBox();
728	>	boxVector[2] = globals->getBox();
729
730	<	currentAtom = comp_stamps[stampID]->getAtom( j );
731	<	if( currentAtom->haveOrientation() ){
732	<
733	<	dAtom = new DirectionalAtom(j + atomOffset);
734	<	simnfo->n_oriented++;
735	<	info.myAtoms[j] = dAtom;
736	<
737	<	ux = currentAtom->getOrntX();
738	<	uy = currentAtom->getOrntY();
739	<	uz = currentAtom->getOrntZ();
740	<
741	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
742	<
743	<	u = sqrt( uSqr );
744	<	ux = ux / u;
745	<	uy = uy / u;
746	<	uz = uz / u;
747	<
785	<	dAtom->setSUx( ux );
786	<	dAtom->setSUy( uy );
787	<	dAtom->setSUz( uz );
730	>	info[i].setBox( boxVector );
731	>	}
732	>	else if( globals->haveDensity() ){
733	>
734	>	double vol;
735	>	vol = (double)tot_nmol / globals->getDensity();
736	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	>	boxVector[1] = boxVector[0];
738	>	boxVector[2] = boxVector[0];
739	>
740	>	info[i].setBox( boxVector );
741	>	}
742	>	else{
743	>	if( !globals->haveBoxX() ){
744	>	sprintf( painCave.errMsg,
745	>	"SimSetup error, no periodic BoxX size given.\n" );
746	>	painCave.isFatal = 1;
747	>	simError();
748		}
749	<	else{
750	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
749	>	boxVector[0] = globals->getBoxX();
750	>
751	>	if( !globals->haveBoxY() ){
752	>	sprintf( painCave.errMsg,
753	>	"SimSetup error, no periodic BoxY size given.\n" );
754	>	painCave.isFatal = 1;
755	>	simError();
756		}
757	<	info.myAtoms[j]->setType( currentAtom->getType() );
793	<
794	<	#ifdef IS_MPI
757	>	boxVector[1] = globals->getBoxY();
758
759	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
759	>	if( !globals->haveBoxZ() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxZ size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764	>	}
765	>	boxVector[2] = globals->getBoxZ();
766
767	<	#endif // is_mpi
768	<	}
767	>	info[i].setBox( boxVector );
768	>	}
769	>
770	>	}
771
772	<	// make the bonds
773	<	for(j=0; j<info.nBonds; j++){
774	<
775	<	currentBond = comp_stamps[stampID]->getBond( j );
805	<	theBonds[j].a = currentBond->getA() + atomOffset;
806	<	theBonds[j].b = currentBond->getB() + atomOffset;
772	>	#ifdef IS_MPI
773	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
774	>	MPIcheckPoint();
775	>	#endif // is_mpi
776
777	<	exI = theBonds[j].a;
809	<	exJ = theBonds[j].b;
777	>	}
778
811	–	// exclude_I must always be the smaller of the pair
812	–	if( exI > exJ ){
813	–	tempEx = exI;
814	–	exI = exJ;
815	–	exJ = tempEx;
816	–	}
817	–	#ifdef IS_MPI
818	–	tempEx = exI;
819	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
820	–	tempEx = exJ;
821	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
822	–
823	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
824	–	#else  // isn't MPI
779
780	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
781	<	#endif  //is_mpi
782	<	}
783	<	excludeOffset += info.nBonds;
780	>	void SimSetup::finalInfoCheck( void ){
781	>	int index;
782	>	int usesDipoles;
783	>	int i;
784
785	<	//make the bends
786	<	for(j=0; j<info.nBends; j++){
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787	>
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793	>	}
794	>
795	>	#ifdef IS_MPI
796	>	int myUse = usesDipoles;
797	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798	>	#endif //is_mpi
799	>
800	>	double theEcr, theEst;
801	>
802	>	if (globals->getUseRF() ) {
803	>	info[i].useReactionField = 1;
804
805	<	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() ){
848	<
849	<	case 0:
850	<	theBends[j].ghost =
851	<	current_extra->getInt() + atomOffset;
852	<	theBends[j].isGhost = 1;
853	<	break;
854	<
855	<	case 1:
856	<	theBends[j].ghost =
857	<	(int)current_extra->getDouble() + atomOffset;
858	<	theBends[j].isGhost = 1;
859	<	break;
860	<
861	<	default:
862	<	sprintf( painCave.errMsg,
863	<	"SimSetup Error: ghostVectorSource was neither a "
864	<	"double nor an int.\n"
865	<	"-->Bend[%d] in %s\n",
866	<	j, comp_stamps[stampID]->getID() );
867	<	painCave.isFatal = 1;
868	<	simError();
869	<	}
870	<	}
871	<
872	<	else{
873	<
874	<	sprintf( painCave.errMsg,
875	<	"SimSetup Error: unhandled bend assignment:\n"
876	<	"    -->%s in Bend[%d] in %s\n",
877	<	current_extra->getlhs(),
878	<	j, comp_stamps[stampID]->getID() );
879	<	painCave.isFatal = 1;
880	<	simError();
881	<	}
882	<
883	<	current_extra = current_extra->getNext();
884	<	}
805	>	if( !globals->haveECR() ){
806	>	sprintf( painCave.errMsg,
807	>	"SimSetup Warning: using default value of 1/2 the smallest "
808	>	"box length for the electrostaticCutoffRadius.\n"
809	>	"I hope you have a very fast processor!\n");
810	>	painCave.isFatal = 0;
811	>	simError();
812	>	double smallest;
813	>	smallest = info[i].boxL[0];
814	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	>	theEcr = 0.5 * smallest;
817	>	} else {
818	>	theEcr = globals->getECR();
819		}
886	–
887	–	if( !theBends[j].isGhost ){
888	–
889	–	exI = theBends[j].a;
890	–	exJ = theBends[j].c;
891	–	}
892	–	else{
893	–
894	–	exI = theBends[j].a;
895	–	exJ = theBends[j].b;
896	–	}
820
821	<	// exclude_I must always be the smaller of the pair
822	<	if( exI > exJ ){
823	<	tempEx = exI;
824	<	exI = exJ;
825	<	exJ = tempEx;
821	>	if( !globals->haveEST() ){
822	>	sprintf( painCave.errMsg,
823	>	"SimSetup Warning: using default value of 0.05 * the "
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	>	);
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	theEst = 0.05 * theEcr;
829	>	} else {
830	>	theEst= globals->getEST();
831		}
904	–	#ifdef IS_MPI
905	–	tempEx = exI;
906	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
907	–	tempEx = exJ;
908	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
832
833	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
911	<	#else  // isn't MPI
912	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
913	<	#endif  //is_mpi
914	<	}
915	<	excludeOffset += info.nBends;
916	<
917	<	for(j=0; j<info.nTorsions; j++){
833	>	info[i].setEcr( theEcr, theEst );
834
835	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
836	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
837	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
838	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
839	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
840	<
841	<	exI = theTorsions[j].a;
842	<	exJ = theTorsions[j].d;
843	<
844	<	// exclude_I must always be the smaller of the pair
845	<	if( exI > exJ ){
846	<	tempEx = exI;
847	<	exI = exJ;
848	<	exJ = tempEx;
835	>	if(!globals->haveDielectric() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Error: You are trying to use Reaction Field without"
838	>	"setting a dielectric constant!\n"
839	>	);
840	>	painCave.isFatal = 1;
841	>	simError();
842	>	}
843	>	info[i].dielectric = globals->getDielectric();
844	>	}
845	>	else {
846	>	if (usesDipoles) {
847	>
848	>	if( !globals->haveECR() ){
849	>	sprintf( painCave.errMsg,
850	>	"SimSetup Warning: using default value of 1/2 the smallest "
851	>	"box length for the electrostaticCutoffRadius.\n"
852	>	"I hope you have a very fast processor!\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	double smallest;
856	>	smallest = info[i].boxL[0];
857	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	>	theEcr = 0.5 * smallest;
860	>	} else {
861	>	theEcr = globals->getECR();
862	>	}
863	>
864	>	if( !globals->haveEST() ){
865	>	sprintf( painCave.errMsg,
866	>	"SimSetup Warning: using default value of 0.05 * the "
867	>	"electrostaticCutoffRadius for the "
868	>	"electrostaticSkinThickness\n"
869	>	);
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	theEst = 0.05 * theEcr;
873	>	} else {
874	>	theEst= globals->getEST();
875	>	}
876	>
877	>	info[i].setEcr( theEcr, theEst );
878		}
879	+	}
880	+	}
881	+
882		#ifdef IS_MPI
883	<	tempEx = exI;
884	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
885	<	tempEx = exJ;
886	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
883	>	strcpy( checkPointMsg, "post processing checks out" );
884	>	MPIcheckPoint();
885	>	#endif // is_mpi
886	>
887	>	}
888	>
889	>	void SimSetup::initSystemCoords( void ){
890	>	int i;
891	>
892	>	char* inName;
893	>
894	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
895	>
896	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
897	>
898	>	if( globals->haveInitialConfig() ){
899	>
900	>	InitializeFromFile* fileInit;
901	>	#ifdef IS_MPI // is_mpi
902	>	if( worldRank == 0 ){
903	>	#endif //is_mpi
904	>	inName = globals->getInitialConfig();
905	>	double* tempDouble = new double[1000000];
906	>	fileInit = new InitializeFromFile( inName );
907	>	#ifdef IS_MPI
908	>	}else fileInit = new InitializeFromFile( NULL );
909	>	#endif
910	>	fileInit->readInit( info ); // default velocities on
911	>
912	>	delete fileInit;
913	>	}
914	>	else{
915	>
916	>	#ifdef IS_MPI
917	>
918	>	// no init from bass
919	>
920	>	sprintf( painCave.errMsg,
921	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
922	>	painCave.isFatal;
923	>	simError();
924	>
925	>	#else
926	>
927	>	initFromBass();
928	>
929	>
930	>	#endif
931	>	}
932	>
933	>	#ifdef IS_MPI
934	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
935	>	MPIcheckPoint();
936	>	#endif // is_mpi
937	>
938	>	}
939	>
940	>
941	>	void SimSetup::makeOutNames( void ){
942	>
943	>	int k;
944	>
945	>
946	>	for(k=0; k<nInfo; k++){
947	>
948	>	#ifdef IS_MPI
949	>	if( worldRank == 0 ){
950	>	#endif // is_mpi
951
952	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
953	<	#else  // isn't MPI
954	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
955	<	#endif  //is_mpi
952	>	if( globals->haveFinalConfig() ){
953	>	strcpy( info[k].finalName, globals->getFinalConfig() );
954	>	}
955	>	else{
956	>	strcpy( info[k].finalName, inFileName );
957	>	char* endTest;
958	>	int nameLength = strlen( info[k].finalName );
959	>	endTest = &(info[k].finalName[nameLength - 5]);
960	>	if( !strcmp( endTest, ".bass" ) ){
961	>	strcpy( endTest, ".eor" );
962	>	}
963	>	else if( !strcmp( endTest, ".BASS" ) ){
964	>	strcpy( endTest, ".eor" );
965	>	}
966	>	else{
967	>	endTest = &(info[k].finalName[nameLength - 4]);
968	>	if( !strcmp( endTest, ".bss" ) ){
969	>	strcpy( endTest, ".eor" );
970		}
971	<	excludeOffset += info.nTorsions;
971	>	else if( !strcmp( endTest, ".mdl" ) ){
972	>	strcpy( endTest, ".eor" );
973	>	}
974	>	else{
975	>	strcat( info[k].finalName, ".eor" );
976	>	}
977	>	}
978	>	}
979	>
980	>	// make the sample and status out names
981	>
982	>	strcpy( info[k].sampleName, inFileName );
983	>	char* endTest;
984	>	int nameLength = strlen( info[k].sampleName );
985	>	endTest = &(info[k].sampleName[nameLength - 5]);
986	>	if( !strcmp( endTest, ".bass" ) ){
987	>	strcpy( endTest, ".dump" );
988	>	}
989	>	else if( !strcmp( endTest, ".BASS" ) ){
990	>	strcpy( endTest, ".dump" );
991	>	}
992	>	else{
993	>	endTest = &(info[k].sampleName[nameLength - 4]);
994	>	if( !strcmp( endTest, ".bss" ) ){
995	>	strcpy( endTest, ".dump" );
996	>	}
997	>	else if( !strcmp( endTest, ".mdl" ) ){
998	>	strcpy( endTest, ".dump" );
999	>	}
1000	>	else{
1001	>	strcat( info[k].sampleName, ".dump" );
1002	>	}
1003	>	}
1004	>
1005	>	strcpy( info[k].statusName, inFileName );
1006	>	nameLength = strlen( info[k].statusName );
1007	>	endTest = &(info[k].statusName[nameLength - 5]);
1008	>	if( !strcmp( endTest, ".bass" ) ){
1009	>	strcpy( endTest, ".stat" );
1010	>	}
1011	>	else if( !strcmp( endTest, ".BASS" ) ){
1012	>	strcpy( endTest, ".stat" );
1013	>	}
1014	>	else{
1015	>	endTest = &(info[k].statusName[nameLength - 4]);
1016	>	if( !strcmp( endTest, ".bss" ) ){
1017	>	strcpy( endTest, ".stat" );
1018	>	}
1019	>	else if( !strcmp( endTest, ".mdl" ) ){
1020	>	strcpy( endTest, ".stat" );
1021	>	}
1022	>	else{
1023	>	strcat( info[k].statusName, ".stat" );
1024	>	}
1025	>	}
1026	>
1027	>	#ifdef IS_MPI
1028	>	}
1029	>	#endif // is_mpi
1030	>	}
1031	>	}
1032
947	–
948	–	// send the arrays off to the forceField for init.
1033
1034	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1035	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1036	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1037	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1034	>	void SimSetup::sysObjectsCreation( void ){
1035	>
1036	>	int i,k;
1037	>
1038	>	// create the forceField
1039
1040	+	createFF();
1041
1042	<	the_molecules[i].initialize( info );
1042	>	// extract componentList
1043
1044	+	compList();
1045
1046	<	atomOffset += info.nAtoms;
1047	<	delete[] theBonds;
1048	<	delete[] theBends;
1049	<	delete[] theTorsions;
1046	>	// calc the number of atoms, bond, bends, and torsions
1047	>
1048	>	calcSysValues();
1049	>
1050	>	#ifdef IS_MPI
1051	>	// divide the molecules among the processors
1052	>
1053	>	mpiMolDivide();
1054	>	#endif //is_mpi
1055	>
1056	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1057	>
1058	>	makeSysArrays();
1059	>
1060	>	// make and initialize the molecules (all but atomic coordinates)
1061	>
1062	>	makeMolecules();
1063	>
1064	>	for(k=0; k<nInfo; k++){
1065	>	info[k].identArray = new int[info[k].n_atoms];
1066	>	for(i=0; i<info[k].n_atoms; i++){
1067	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1068	>	}
1069		}
1070	+	}
1071
1072	+
1073	+	void SimSetup::createFF( void ){
1074	+
1075	+	switch( ffCase ){
1076	+
1077	+	case FF_DUFF:
1078	+	the_ff = new DUFF();
1079	+	break;
1080	+
1081	+	case FF_LJ:
1082	+	the_ff = new LJFF();
1083	+	break;
1084	+
1085	+	case FF_EAM:
1086	+	the_ff = new EAM_FF();
1087	+	break;
1088	+
1089	+	default:
1090	+	sprintf( painCave.errMsg,
1091	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	+	painCave.isFatal = 1;
1093	+	simError();
1094	+	}
1095	+
1096		#ifdef IS_MPI
1097	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1097	>	strcpy( checkPointMsg, "ForceField creation successful" );
1098		MPIcheckPoint();
1099		#endif // is_mpi
1100
970	–	// clean up the forcefield
971	–	the_ff->calcRcut();
972	–	the_ff->cleanMe();
973	–
1101		}
1102
976	–	void SimSetup::initFromBass( void ){
1103
1104	<	int i, j, k;
979	<	int n_cells;
980	<	double cellx, celly, cellz;
981	<	double temp1, temp2, temp3;
982	<	int n_per_extra;
983	<	int n_extra;
984	<	int have_extra, done;
1104	>	void SimSetup::compList( void ){
1105
1106	<	temp1 = (double)tot_nmol / 4.0;
1107	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1108	<	temp3 = ceil( temp2 );
1106	>	int i;
1107	>	char* id;
1108	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1109	>	LinkedMolStamp* currentStamp = NULL;
1110	>	comp_stamps = new MoleculeStamp*[n_components];
1111	>
1112	>	// make an array of molecule stamps that match the components used.
1113	>	// also extract the used stamps out into a separate linked list
1114	>
1115	>	for(i=0; i<nInfo; i++){
1116	>	info[i].nComponents = n_components;
1117	>	info[i].componentsNmol = components_nmol;
1118	>	info[i].compStamps = comp_stamps;
1119	>	info[i].headStamp = headStamp;
1120	>	}
1121	>
1122
1123	<	have_extra =0;
991	<	if( temp2 < temp3 ){ // we have a non-complete lattice
992	<	have_extra =1;
1123	>	for( i=0; i<n_components; i++ ){
1124
1125	<	n_cells = (int)temp3 - 1;
1126	<	cellx = simnfo->box_x / temp3;
1127	<	celly = simnfo->box_y / temp3;
1128	<	cellz = simnfo->box_z / temp3;
998	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
999	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1000	<	n_per_extra = (int)ceil( temp1 );
1125	>	id = the_components[i]->getType();
1126	>	comp_stamps[i] = NULL;
1127	>
1128	>	// check to make sure the component isn't already in the list
1129
1130	<	if( n_per_extra > 4){
1131	<	sprintf( painCave.errMsg,
1132	<	"SimSetup error. There has been an error in constructing"
1133	<	" the non-complete lattice.\n" );
1134	<	painCave.isFatal = 1;
1135	<	simError();
1130	>	comp_stamps[i] = headStamp->match( id );
1131	>	if( comp_stamps[i] == NULL ){
1132	>
1133	>	// extract the component from the list;
1134	>
1135	>	currentStamp = stamps->extractMolStamp( id );
1136	>	if( currentStamp == NULL ){
1137	>	sprintf( painCave.errMsg,
1138	>	"SimSetup error: Component \"%s\" was not found in the "
1139	>	"list of declared molecules\n",
1140	>	id );
1141	>	painCave.isFatal = 1;
1142	>	simError();
1143	>	}
1144	>
1145	>	headStamp->add( currentStamp );
1146	>	comp_stamps[i] = headStamp->match( id );
1147		}
1148		}
1149	<	else{
1150	<	n_cells = (int)temp3;
1151	<	cellx = simnfo->box_x / temp3;
1152	<	celly = simnfo->box_y / temp3;
1153	<	cellz = simnfo->box_z / temp3;
1149	>
1150	>	#ifdef IS_MPI
1151	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1152	>	MPIcheckPoint();
1153	>	#endif // is_mpi
1154	>
1155	>
1156	>	}
1157	>
1158	>	void SimSetup::calcSysValues( void ){
1159	>	int i, j, k;
1160	>
1161	>	int *molMembershipArray;
1162	>
1163	>	tot_atoms = 0;
1164	>	tot_bonds = 0;
1165	>	tot_bends = 0;
1166	>	tot_torsions = 0;
1167	>	for( i=0; i<n_components; i++ ){
1168	>
1169	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1170	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1171	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1172	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1173		}
1174	+
1175	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1176	+	molMembershipArray = new int[tot_atoms];
1177	+
1178	+	for(i=0; i<nInfo; i++){
1179	+	info[i].n_atoms = tot_atoms;
1180	+	info[i].n_bonds = tot_bonds;
1181	+	info[i].n_bends = tot_bends;
1182	+	info[i].n_torsions = tot_torsions;
1183	+	info[i].n_SRI = tot_SRI;
1184	+	info[i].n_mol = tot_nmol;
1185	+
1186	+	info[i].molMembershipArray = molMembershipArray;
1187	+	}
1188	+	}
1189
1190	<	current_mol = 0;
1018	<	current_comp_mol = 0;
1019	<	current_comp = 0;
1020	<	current_atom_ndx = 0;
1190	>	#ifdef IS_MPI
1191
1192	<	for( i=0; i < n_cells ; i++ ){
1193	<	for( j=0; j < n_cells; j++ ){
1194	<	for( k=0; k < n_cells; k++ ){
1192	>	void SimSetup::mpiMolDivide( void ){
1193	>
1194	>	int i, j, k;
1195	>	int localMol, allMol;
1196	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1197
1198	<	makeElement( i * cellx,
1199	<	j * celly,
1200	<	k * cellz );
1198	>	mpiSim = new mpiSimulation( info );
1199	>
1200	>	globalIndex = mpiSim->divideLabor();
1201
1202	<	makeElement( i * cellx + 0.5 * cellx,
1203	<	j * celly + 0.5 * celly,
1204	<	k * cellz );
1202	>	// set up the local variables
1203	>
1204	>	mol2proc = mpiSim->getMolToProcMap();
1205	>	molCompType = mpiSim->getMolComponentType();
1206	>
1207	>	allMol = 0;
1208	>	localMol = 0;
1209	>	local_atoms = 0;
1210	>	local_bonds = 0;
1211	>	local_bends = 0;
1212	>	local_torsions = 0;
1213	>	globalAtomIndex = 0;
1214
1034	–	makeElement( i * cellx,
1035	–	j * celly + 0.5 * celly,
1036	–	k * cellz + 0.5 * cellz );
1215
1216	<	makeElement( i * cellx + 0.5 * cellx,
1217	<	j * celly,
1218	<	k * cellz + 0.5 * cellz );
1216	>	for( i=0; i<n_components; i++ ){
1217	>
1218	>	for( j=0; j<components_nmol[i]; j++ ){
1219	>
1220	>	if( mol2proc[allMol] == worldRank ){
1221	>
1222	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1223	>	local_bonds +=    comp_stamps[i]->getNBonds();
1224	>	local_bends +=    comp_stamps[i]->getNBends();
1225	>	local_torsions += comp_stamps[i]->getNTorsions();
1226	>	localMol++;
1227	>	}
1228	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1229	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1230	>	globalAtomIndex++;
1231		}
1232	+
1233	+	allMol++;
1234		}
1235		}
1236	+	local_SRI = local_bonds + local_bends + local_torsions;
1237	+
1238	+	info[0].n_atoms = mpiSim->getMyNlocal();
1239	+
1240	+	if( local_atoms != info[0].n_atoms ){
1241	+	sprintf( painCave.errMsg,
1242	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1243	+	" localAtom (%d) are not equal.\n",
1244	+	info[0].n_atoms,
1245	+	local_atoms );
1246	+	painCave.isFatal = 1;
1247	+	simError();
1248	+	}
1249
1250	<	if( have_extra ){
1251	<	done = 0;
1250	>	info[0].n_bonds = local_bonds;
1251	>	info[0].n_bends = local_bends;
1252	>	info[0].n_torsions = local_torsions;
1253	>	info[0].n_SRI = local_SRI;
1254	>	info[0].n_mol = localMol;
1255
1256	<	int start_ndx;
1257	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1258	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1256	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1257	>	MPIcheckPoint();
1258	>	}
1259	>
1260	>	#endif // is_mpi
1261
1052	–	if( i < n_cells ){
1262
1263	<	if( j < n_cells ){
1264	<	start_ndx = n_cells;
1056	<	}
1057	<	else start_ndx = 0;
1058	<	}
1059	<	else start_ndx = 0;
1263	>	void SimSetup::makeSysArrays( void ){
1264	>	int i, j, k, l;
1265
1266	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1266	>	Atom** the_atoms;
1267	>	Molecule* the_molecules;
1268	>	Exclude** the_excludes;
1269
1270	<	makeElement( i * cellx,
1271	<	j * celly,
1272	<	k * cellz );
1273	<	done = ( current_mol >= tot_nmol );
1270	>
1271	>	for(l=0; l<nInfo; l++){
1272	>
1273	>	// create the atom and short range interaction arrays
1274	>
1275	>	the_atoms = new Atom*[info[l].n_atoms];
1276	>	the_molecules = new Molecule[info[l].n_mol];
1277	>	int molIndex;
1278
1279	<	if( !done && n_per_extra > 1 ){
1280	<	makeElement( i * cellx + 0.5 * cellx,
1281	<	j * celly + 0.5 * celly,
1282	<	k * cellz );
1283	<	done = ( current_mol >= tot_nmol );
1284	<	}
1279	>	// initialize the molecule's stampID's
1280	>
1281	>	#ifdef IS_MPI
1282	>
1283	>
1284	>	molIndex = 0;
1285	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1286	>
1287	>	if(mol2proc[i] == worldRank ){
1288	>	the_molecules[molIndex].setStampID( molCompType[i] );
1289	>	the_molecules[molIndex].setMyIndex( molIndex );
1290	>	the_molecules[molIndex].setGlobalIndex( i );
1291	>	molIndex++;
1292	>	}
1293	>	}
1294	>
1295	>	#else // is_mpi
1296	>
1297	>	molIndex = 0;
1298	>	globalAtomIndex = 0;
1299	>	for(i=0; i<n_components; i++){
1300	>	for(j=0; j<components_nmol[i]; j++ ){
1301	>	the_molecules[molIndex].setStampID( i );
1302	>	the_molecules[molIndex].setMyIndex( molIndex );
1303	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1304	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1305	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1306	>	globalAtomIndex++;
1307	>	}
1308	>	molIndex++;
1309	>	}
1310	>	}
1311	>
1312	>
1313	>	#endif // is_mpi
1314
1075	–	if( !done && n_per_extra > 2){
1076	–	makeElement( i * cellx,
1077	–	j * celly + 0.5 * celly,
1078	–	k * cellz + 0.5 * cellz );
1079	–	done = ( current_mol >= tot_nmol );
1080	–	}
1315
1316	<	if( !done && n_per_extra > 3){
1317	<	makeElement( i * cellx + 0.5 * cellx,
1318	<	j * celly,
1319	<	k * cellz + 0.5 * cellz );
1320	<	done = ( current_mol >= tot_nmol );
1321	<	}
1088	<	}
1316	>	if( info[l].n_SRI ){
1317	>
1318	>	Exclude::createArray(info[l].n_SRI);
1319	>	the_excludes = new Exclude*[info[l].n_SRI];
1320	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1321	>	the_excludes[ex] = new Exclude(ex);
1322		}
1323	+	info[l].globalExcludes = new int;
1324	+	info[l].n_exclude = info[l].n_SRI;
1325		}
1326	<	}
1326	>	else{
1327	>
1328	>	Exclude::createArray( 1 );
1329	>	the_excludes = new Exclude*;
1330	>	the_excludes[0] = new Exclude(0);
1331	>	the_excludes[0]->setPair( 0,0 );
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].globalExcludes[0] = 0;
1334	>	info[l].n_exclude = 0;
1335	>	}
1336
1337	+	// set the arrays into the SimInfo object
1338
1339	<	for( i=0; i<simnfo->n_atoms; i++ ){
1340	<	simnfo->atoms[i]->set_vx( 0.0 );
1341	<	simnfo->atoms[i]->set_vy( 0.0 );
1342	<	simnfo->atoms[i]->set_vz( 0.0 );
1339	>	info[l].atoms = the_atoms;
1340	>	info[l].molecules = the_molecules;
1341	>	info[l].nGlobalExcludes = 0;
1342	>	info[l].excludes = the_excludes;
1343	>
1344	>	the_ff->setSimInfo( info );
1345	>
1346		}
1347		}
1348
1349	<	void SimSetup::makeElement( double x, double y, double z ){
1349	>	void SimSetup::makeIntegrator( void ){
1350
1351		int k;
1104	–	AtomStamp* current_atom;
1105	–	DirectionalAtom* dAtom;
1106	–	double rotMat[3][3];
1352
1353	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1353	>	NVT<RealIntegrator>*  myNVT = NULL;
1354	>	NPTi<RealIntegrator>* myNPTi = NULL;
1355	>	NPTf<RealIntegrator>* myNPTf = NULL;
1356	>	NPTim<RealIntegrator>* myNPTim = NULL;
1357	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1358	>
1359	>	for(k=0; k<nInfo; k++){
1360	>
1361	>	switch( ensembleCase ){
1362	>
1363	>	case NVE_ENS:
1364	>	if (globals->haveZconstraints()){
1365	>	setupZConstraint(info[k]);
1366	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1367	>	}
1368
1369	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1370	<	if( !current_atom->havePosition() ){
1369	>	else
1370	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1371	>	break;
1372	>
1373	>	case NVT_ENS:
1374	>	if (globals->haveZconstraints()){
1375	>	setupZConstraint(info[k]);
1376	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377	>	}
1378	>	else
1379	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1380	>
1381	>	myNVT->setTargetTemp(globals->getTargetTemp());
1382	>
1383	>	if (globals->haveTauThermostat())
1384	>	myNVT->setTauThermostat(globals->getTauThermostat());
1385	>
1386	>	else {
1387	>	sprintf( painCave.errMsg,
1388	>	"SimSetup error: If you use the NVT\n"
1389	>	"    ensemble, you must set tauThermostat.\n");
1390	>	painCave.isFatal = 1;
1391	>	simError();
1392	>	}
1393	>	break;
1394	>
1395	>	case NPTi_ENS:
1396	>	if (globals->haveZconstraints()){
1397	>	setupZConstraint(info[k]);
1398	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399	>	}
1400	>	else
1401	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1402	>
1403	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	>	else {
1408	>	sprintf( painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413	>	}
1414	>
1415	>	if( globals->haveTauThermostat() )
1416	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	>	else{
1418	>	sprintf( painCave.errMsg,
1419	>	"SimSetup error: If you use an NPT\n"
1420	>	"    ensemble, you must set tauThermostat.\n");
1421	>	painCave.isFatal = 1;
1422	>	simError();
1423	>	}
1424	>
1425	>	if( globals->haveTauBarostat() )
1426	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	>	else{
1428	>	sprintf( painCave.errMsg,
1429	>	"SimSetup error: If you use an NPT\n"
1430	>	"    ensemble, you must set tauBarostat.\n");
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433	>	}
1434	>	break;
1435	>
1436	>	case NPTf_ENS:
1437	>	if (globals->haveZconstraints()){
1438	>	setupZConstraint(info[k]);
1439	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440	>	}
1441	>	else
1442	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1443	>
1444	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1445	>
1446	>	if (globals->haveTargetPressure())
1447	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1448	>	else {
1449	>	sprintf( painCave.errMsg,
1450	>	"SimSetup error: If you use a constant pressure\n"
1451	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1452	>	painCave.isFatal = 1;
1453	>	simError();
1454	>	}
1455	>
1456	>	if( globals->haveTauThermostat() )
1457	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1458	>	else{
1459	>	sprintf( painCave.errMsg,
1460	>	"SimSetup error: If you use an NPT\n"
1461	>	"    ensemble, you must set tauThermostat.\n");
1462	>	painCave.isFatal = 1;
1463	>	simError();
1464	>	}
1465	>
1466	>	if( globals->haveTauBarostat() )
1467	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1468	>	else{
1469	>	sprintf( painCave.errMsg,
1470	>	"SimSetup error: If you use an NPT\n"
1471	>	"    ensemble, you must set tauBarostat.\n");
1472	>	painCave.isFatal = 1;
1473	>	simError();
1474	>	}
1475	>	break;
1476	>
1477	>	case NPTim_ENS:
1478	>	if (globals->haveZconstraints()){
1479	>	setupZConstraint(info[k]);
1480	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481	>	}
1482	>	else
1483	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1484	>
1485	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1486	>
1487	>	if (globals->haveTargetPressure())
1488	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1489	>	else {
1490	>	sprintf( painCave.errMsg,
1491	>	"SimSetup error: If you use a constant pressure\n"
1492	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1493	>	painCave.isFatal = 1;
1494	>	simError();
1495	>	}
1496	>
1497	>	if( globals->haveTauThermostat() )
1498	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1499	>	else{
1500	>	sprintf( painCave.errMsg,
1501	>	"SimSetup error: If you use an NPT\n"
1502	>	"    ensemble, you must set tauThermostat.\n");
1503	>	painCave.isFatal = 1;
1504	>	simError();
1505	>	}
1506	>
1507	>	if( globals->haveTauBarostat() )
1508	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509	>	else{
1510	>	sprintf( painCave.errMsg,
1511	>	"SimSetup error: If you use an NPT\n"
1512	>	"    ensemble, you must set tauBarostat.\n");
1513	>	painCave.isFatal = 1;
1514	>	simError();
1515	>	}
1516	>	break;
1517	>
1518	>	case NPTfm_ENS:
1519	>	if (globals->haveZconstraints()){
1520	>	setupZConstraint(info[k]);
1521	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522	>	}
1523	>	else
1524	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1525	>
1526	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1527	>
1528	>	if (globals->haveTargetPressure())
1529	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1530	>	else {
1531	>	sprintf( painCave.errMsg,
1532	>	"SimSetup error: If you use a constant pressure\n"
1533	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1534	>	painCave.isFatal = 1;
1535	>	simError();
1536	>	}
1537	>
1538	>	if( globals->haveTauThermostat() )
1539	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1540	>	else{
1541	>	sprintf( painCave.errMsg,
1542	>	"SimSetup error: If you use an NPT\n"
1543	>	"    ensemble, you must set tauThermostat.\n");
1544	>	painCave.isFatal = 1;
1545	>	simError();
1546	>	}
1547	>
1548	>	if( globals->haveTauBarostat() )
1549	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1550	>	else{
1551	>	sprintf( painCave.errMsg,
1552	>	"SimSetup error: If you use an NPT\n"
1553	>	"    ensemble, you must set tauBarostat.\n");
1554	>	painCave.isFatal = 1;
1555	>	simError();
1556	>	}
1557	>	break;
1558	>
1559	>	default:
1560		sprintf( painCave.errMsg,
1561	<	"SimSetup:initFromBass error.\n"
1114	<	"\tComponent %s, atom %s does not have a position specified.\n"
1115	<	"\tThe initialization routine is unable to give a start"
1116	<	" position.\n",
1117	<	comp_stamps[current_comp]->getID(),
1118	<	current_atom->getType() );
1561	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1562		painCave.isFatal = 1;
1563		simError();
1564		}
1565	+	}
1566	+	}
1567
1568	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1124	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1125	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1568	>	void SimSetup::initFortran( void ){
1569
1570	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1570	>	info[0].refreshSim();
1571	>
1572	>	if( !strcmp( info[0].mixingRule, "standard") ){
1573	>	the_ff->initForceField( LB_MIXING_RULE );
1574	>	}
1575	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1576	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1577	>	}
1578	>	else{
1579	>	sprintf( painCave.errMsg,
1580	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	>	info[0].mixingRule );
1582	>	painCave.isFatal = 1;
1583	>	simError();
1584	>	}
1585
1129	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1586
1587	<	rotMat[0][0] = 1.0;
1588	<	rotMat[0][1] = 0.0;
1589	<	rotMat[0][2] = 0.0;
1587	>	#ifdef IS_MPI
1588	>	strcpy( checkPointMsg,
1589	>	"Successfully intialized the mixingRule for Fortran." );
1590	>	MPIcheckPoint();
1591	>	#endif // is_mpi
1592
1593	<	rotMat[1][0] = 0.0;
1136	<	rotMat[1][1] = 1.0;
1137	<	rotMat[1][2] = 0.0;
1593	>	}
1594
1595	<	rotMat[2][0] = 0.0;
1596	<	rotMat[2][1] = 0.0;
1597	<	rotMat[2][2] = 1.0;
1595	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596	>	{
1597	>	int nZConstraints;
1598	>	ZconStamp** zconStamp;
1599
1600	<	dAtom->setA( rotMat );
1601	<	}
1600	>	if(globals->haveZconstraintTime()){
1601	>
1602	>	//add sample time of z-constraint  into SimInfo's property list
1603	>	DoubleData* zconsTimeProp = new DoubleData();
1604	>	zconsTimeProp->setID(ZCONSTIME_ID);
1605	>	zconsTimeProp->setData(globals->getZconsTime());
1606	>	theInfo.addProperty(zconsTimeProp);
1607	>	}
1608	>	else{
1609	>	sprintf( painCave.errMsg,
1610	>	"ZConstraint error: If you use an ZConstraint\n"
1611	>	" , you must set sample time.\n");
1612	>	painCave.isFatal = 1;
1613	>	simError();
1614	>	}
1615
1616	<	current_atom_ndx++;
1616	>	//push zconsTol into siminfo, if user does not specify
1617	>	//value for zconsTol, a default value will be used
1618	>	DoubleData* zconsTol = new DoubleData();
1619	>	zconsTol->setID(ZCONSTOL_ID);
1620	>	if(globals->haveZconsTol()){
1621	>	zconsTol->setData(globals->getZconsTol());
1622		}
1623	+	else{
1624	+	double defaultZConsTol = 0.01;
1625	+	sprintf( painCave.errMsg,
1626	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1627	+	" , default value %f is used.\n", defaultZConsTol);
1628	+	painCave.isFatal = 0;
1629	+	simError();
1630
1631	<	current_mol++;
1632	<	current_comp_mol++;
1631	>	zconsTol->setData(defaultZConsTol);
1632	>	}
1633	>	theInfo.addProperty(zconsTol);
1634
1635	<	if( current_comp_mol >= components_nmol[current_comp] ){
1635	>	//set Force Substraction Policy
1636	>	StringData* zconsForcePolicy =  new StringData();
1637	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1638	>
1639	>	if(globals->haveZconsForcePolicy()){
1640	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1641	>	}
1642	>	else{
1643	>	sprintf( painCave.errMsg,
1644	>	"ZConstraint Warning: User does not set force substraction policy, "
1645	>	"average force substraction policy is used\n");
1646	>	painCave.isFatal = 0;
1647	>	simError();
1648	>	zconsForcePolicy->setData("BYNUMBER");
1649	>	}
1650	>
1651	>	theInfo.addProperty(zconsForcePolicy);
1652	>
1653	>	//Determine the name of ouput file and add it into SimInfo's property list
1654	>	//Be careful, do not use inFileName, since it is a pointer which
1655	>	//point to a string at master node, and slave nodes do not contain that string
1656	>
1657	>	string zconsOutput(theInfo.finalName);
1658	>
1659	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1660	>
1661	>	StringData* zconsFilename = new StringData();
1662	>	zconsFilename->setID(ZCONSFILENAME_ID);
1663	>	zconsFilename->setData(zconsOutput);
1664	>
1665	>	theInfo.addProperty(zconsFilename);
1666	>
1667	>	//setup index, pos and other parameters of z-constraint molecules
1668	>	nZConstraints = globals->getNzConstraints();
1669	>	theInfo.nZconstraints = nZConstraints;
1670
1671	<	current_comp_mol = 0;
1672	<	current_comp++;
1671	>	zconStamp = globals->getZconStamp();
1672	>	ZConsParaItem tempParaItem;
1673	>
1674	>	ZConsParaData* zconsParaData = new ZConsParaData();
1675	>	zconsParaData->setID(ZCONSPARADATA_ID);
1676	>
1677	>	for(int i = 0; i < nZConstraints; i++){
1678	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1679	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1680	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1681	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1682	>
1683	>	zconsParaData->addItem(tempParaItem);
1684		}
1685	+
1686	+	//sort the parameters by index of molecules
1687	+	zconsParaData->sortByIndex();
1688	+
1689	+	//push data into siminfo, therefore, we can retrieve later
1690	+	theInfo.addProperty(zconsParaData);
1691	+
1692		}

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