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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 474 by gezelter, Mon Apr 7 21:42:19 2003 UTC vs.
Revision 701 by tim, Wed Aug 20 14:34:04 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	<	the_extendedsystem->setQmass(the_globals->getQmass());
92	<	the_extendedsystem->setTauRelax(the_globals->getTauRelax());
93	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
94	<	the_extendedsystem = new ExtendedSystem( simnfo );
95	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
96	<	the_extendedsystem->setQmass(the_globals->getQmass());
97	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
98	<	} else {
99	<	sprintf( painCave.errMsg,
100	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
101	<	"reverting to NVE for this simulation.\n",
102	<	ensemble );
103	<	painCave.isFatal = 0;
104	<	simError();
105	<	strcpy( ensemble, "NVE" );
106	<	}
107	<	strcpy( simnfo->ensemble, ensemble );
108	<
109	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
110	<	simnfo->usePBC = the_globals->getPBC();
111	<
112	<	int usesDipoles = 0;
113	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
114	<	the_ff = new TraPPE_ExFF();
115	<	usesDipoles = 1;
116	<	}
117	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
118	<	else{
119	<	sprintf( painCave.errMsg,
120	<	"SimSetup Error. Unrecognized force field -> %s\n",
121	<	force_field );
122	<	painCave.isFatal = 1;
123	<	simError();
124	<	}
125	<
126	<	#ifdef IS_MPI
127	<	strcpy( checkPointMsg, "ForceField creation successful" );
128	<	MPIcheckPoint();
129	<	#endif // is_mpi
130	<
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
134	<	the_components = the_globals->getComponents();
135	<	components_nmol = new int[n_components];
136	<	comp_stamps = new MoleculeStamp*[n_components];
101	>	gatherInfo();
102
103	<	if( !the_globals->haveNMol() ){
139	<	// we don't have the total number of molecules, so we assume it is
140	<	// given in each component
103	>	// creation of complex system objects
104
105	<	tot_nmol = 0;
143	<	for( i=0; i<n_components; i++ ){
105	>	sysObjectsCreation();
106
107	<	if( !the_components[i]->haveNMol() ){
146	<	// we have a problem
147	<	sprintf( painCave.errMsg,
148	<	"SimSetup Error. No global NMol or component NMol"
149	<	" given. Cannot calculate the number of atoms.\n" );
150	<	painCave.isFatal = 1;
151	<	simError();
152	<	}
107	>	// check on the post processing info
108
109	<	tot_nmol += the_components[i]->getNMol();
155	<	components_nmol[i] = the_components[i]->getNMol();
156	<	}
157	<	}
158	<	else{
159	<	sprintf( painCave.errMsg,
160	<	"SimSetup error.\n"
161	<	"\tSorry, the ability to specify total"
162	<	" nMols and then give molfractions in the components\n"
163	<	"\tis not currently supported."
164	<	" Please give nMol in the components.\n" );
165	<	painCave.isFatal = 1;
166	<	simError();
167	<
168	<
169	<	//     tot_nmol = the_globals->getNMol();
170	<
171	<	//   //we have the total number of molecules, now we check for molfractions
172	<	//     for( i=0; i<n_components; i++ ){
173	<
174	<	//       if( !the_components[i]->haveMolFraction() ){
175	<
176	<	//  if( !the_components[i]->haveNMol() ){
177	<	//    //we have a problem
178	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
179	<	//              << " nMol was given in component
180	<
181	<	}
109	>	finalInfoCheck();
110
111	<	#ifdef IS_MPI
184	<	strcpy( checkPointMsg, "Have the number of components" );
185	<	MPIcheckPoint();
186	<	#endif // is_mpi
111	>	// initialize the system coordinates
112
113	<	// make an array of molecule stamps that match the components used.
189	<	// also extract the used stamps out into a separate linked list
113	>	if( !isInfoArray ) initSystemCoords();
114
115	<	simnfo->nComponents = n_components;
192	<	simnfo->componentsNmol = components_nmol;
193	<	simnfo->compStamps = comp_stamps;
194	<	simnfo->headStamp = new LinkedMolStamp();
195	<
196	<	char* id;
197	<	LinkedMolStamp* headStamp = simnfo->headStamp;
198	<	LinkedMolStamp* currentStamp = NULL;
199	<	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	<
204	<	// check to make sure the component isn't already in the list
205	<
206	<	comp_stamps[i] = headStamp->match( id );
207	<	if( comp_stamps[i] == NULL ){
208	<
209	<	// extract the component from the list;
210	<
211	<	currentStamp = the_stamps->extractMolStamp( id );
212	<	if( currentStamp == NULL ){
213	<	sprintf( painCave.errMsg,
214	<	"SimSetup error: Component \"%s\" was not found in the "
215	<	"list of declared molecules\n",
216	<	id );
217	<	painCave.isFatal = 1;
218	<	simError();
219	<	}
220	<
221	<	headStamp->add( currentStamp );
222	<	comp_stamps[i] = headStamp->match( id );
223	<	}
224	<	}
225	<
226	<	#ifdef IS_MPI
227	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
228	<	MPIcheckPoint();
229	<	#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
234	–	// caclulate the number of atoms, bonds, bends and torsions
131
236	–	tot_atoms = 0;
237	–	tot_bonds = 0;
238	–	tot_bends = 0;
239	–	tot_torsions = 0;
240	–	for( i=0; i<n_components; i++ ){
241	–
242	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
243	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
244	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
245	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
246	–	}
132
133	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
133	>	}
134
250	–	simnfo->n_atoms = tot_atoms;
251	–	simnfo->n_bonds = tot_bonds;
252	–	simnfo->n_bends = tot_bends;
253	–	simnfo->n_torsions = tot_torsions;
254	–	simnfo->n_SRI = tot_SRI;
255	–	simnfo->n_mol = tot_nmol;
135
136	<
258	<	#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
268	–	// set up the local variables
153
154	<	int localMol, allMol;
271	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
154	>	//init the forceField paramters
155
156	<	int* mol2proc = mpiSim->getMolToProcMap();
274	<	int* molCompType = mpiSim->getMolComponentType();
275	<
276	<	allMol = 0;
277	<	localMol = 0;
278	<	local_atoms = 0;
279	<	local_bonds = 0;
280	<	local_bends = 0;
281	<	local_torsions = 0;
282	<	for( i=0; i<n_components; i++ ){
156	>	the_ff->readParams();
157
284	–	for( j=0; j<components_nmol[i]; j++ ){
285	–
286	–	if( mol2proc[j] == worldRank ){
287	–
288	–	local_atoms +=    comp_stamps[i]->getNAtoms();
289	–	local_bonds +=    comp_stamps[i]->getNBonds();
290	–	local_bends +=    comp_stamps[i]->getNBends();
291	–	local_torsions += comp_stamps[i]->getNTorsions();
292	–	localMol++;
293	–	}
294	–	allMol++;
295	–	}
296	–	}
297	–	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"
305	<	" localAtom (%d) are not equal.\n",
306	<	simnfo->n_atoms,
307	<	local_atoms );
308	<	painCave.isFatal = 1;
309	<	simError();
310	<	}
163	>	for(k=0; k<nInfo; k++){
164	>
165	>	the_ff->setSimInfo( &(info[k]) );
166
167	<	simnfo->n_bonds = local_bonds;
168	<	simnfo->n_bends = local_bends;
169	<	simnfo->n_torsions = local_torsions;
170	<	simnfo->n_SRI = local_SRI;
171	<	simnfo->n_mol = localMol;
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	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
174	<	MPIcheckPoint();
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	>	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
333	<
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		}
346	–
347	–	#else // is_mpi
314
315	<	molIndex = 0;
350	<	for(i=0; i<n_components; i++){
351	<	for(j=0; j<components_nmol[i]; j++ ){
352	<	the_molecules[molIndex].setStampID( i );
353	<	the_molecules[molIndex].setMyIndex( molIndex );
354	<	molIndex++;
355	<	}
356	<	}
315	>	if( !theBends[j].isGhost ){
316
317	<
318	<	#endif // is_mpi
360	<
361	<
362	<	if( simnfo->n_SRI ){
363	<
364	<	Exclude::createArray(simnfo->n_SRI);
365	<	the_excludes = new Exclude*[simnfo->n_SRI];
366	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
367	<	simnfo->globalExcludes = new int;
368	<	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*;
374	<	the_excludes[0] = new Exclude(0);
375	<	the_excludes[0]->setPair( 0,0 );
376	<	simnfo->globalExcludes = new int;
377	<	simnfo->globalExcludes[0] = 0;
378	<	simnfo->n_exclude = 0;
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].b;
324		}
380	–
381	–	// set the arrays into the SimInfo object
382	–
383	–	simnfo->atoms = the_atoms;
384	–	simnfo->molecules = the_molecules;
385	–	simnfo->nGlobalExcludes = 0;
386	–	simnfo->excludes = the_excludes;
387	–
388	–
389	–	// get some of the tricky things that may still be in the globals
390	–
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;
426	<	simError();
427	<	}
428	<	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();
445	<	}
446	<
447	<	if (the_globals->getUseRF() ) {
448	<	simnfo->useReactionField = 1;
449	<
450	<	if( !the_globals->haveECR() ){
451	<	sprintf( painCave.errMsg,
452	<	"SimSetup Warning: using default value of 1/2 the smallest "
453	<	"box length for the electrostaticCutoffRadius.\n"
454	<	"I hope you have a very fast processor!\n");
455	<	painCave.isFatal = 0;
456	<	simError();
457	<	double smallest;
458	<	smallest = simnfo->box_x;
459	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
460	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
461	<	simnfo->ecr = 0.5 * smallest;
462	<	} else {
463	<	simnfo->ecr        = the_globals->getECR();
464	<	}
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"
470	<	);
471	<	painCave.isFatal = 0;
472	<	simError();
473	<	simnfo->est = 0.05 * simnfo->ecr;
474	<	} else {
475	<	simnfo->est        = the_globals->getEST();
476	<	}
477	<
478	<	if(!the_globals->haveDielectric() ){
479	<	sprintf( painCave.errMsg,
480	<	"SimSetup Error: You are trying to use Reaction Field without"
481	<	"setting a dielectric constant!\n"
482	<	);
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 (usesDipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest "
493	<	"box length for the electrostaticCutoffRadius.\n"
494	<	"I hope you have a very fast processor!\n");
495	<	painCave.isFatal = 0;
496	<	simError();
497	<	double smallest;
498	<	smallest = simnfo->box_x;
499	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
500	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
501	<	simnfo->ecr = 0.5 * smallest;
502	<	} else {
503	<	simnfo->ecr        = the_globals->getECR();
504	<	}
505	<
506	<	if( !the_globals->haveEST() ){
507	<	sprintf( painCave.errMsg,
508	<	"SimSetup Warning: using default value of 5%% of the "
509	<	"electrostaticCutoffRadius for the "
510	<	"electrostaticSkinThickness\n"
511	<	);
512	<	painCave.isFatal = 0;
513	<	simError();
514	<	simnfo->est = 0.05 * simnfo->ecr;
515	<	} else {
516	<	simnfo->est        = the_globals->getEST();
517	<	}
518	<	}
519	<	}
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;
529	<	#ifdef IS_MPI // is_mpi
530	<	if( worldRank == 0 ){
531	<	#endif //is_mpi
532	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
533	<	#ifdef IS_MPI
534	<	}else fileInit = new InitializeFromFile( NULL );
535	<	#endif
536	<	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,
547	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
548	<	painCave.isFatal;
549	<	simError();
550	<
551	<	#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
560	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
561	<	MPIcheckPoint();
562	<	#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	<
566	<
567	<
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" ) ){
583	<	strcpy( endTest, ".eor" );
584	<	}
585	<	else if( !strcmp( endTest, ".BASS" ) ){
586	<	strcpy( endTest, ".eor" );
587	<	}
588	<	else{
589	<	endTest = &(simnfo->finalName[nameLength - 4]);
590	<	if( !strcmp( endTest, ".bss" ) ){
591	<	strcpy( endTest, ".eor" );
592	<	}
593	<	else if( !strcmp( endTest, ".mdl" ) ){
594	<	strcpy( endTest, ".eor" );
595	<	}
596	<	else{
597	<	strcat( simnfo->finalName, ".eor" );
598	<	}
599	<	}
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 );
607	<	endTest = &(simnfo->sampleName[nameLength - 5]);
608	<	if( !strcmp( endTest, ".bass" ) ){
609	<	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" ) ){
612	<	strcpy( endTest, ".dump" );
613	<	}
614	<	else{
615	<	endTest = &(simnfo->sampleName[nameLength - 4]);
616	<	if( !strcmp( endTest, ".bss" ) ){
617	<	strcpy( endTest, ".dump" );
523	>	}
524		}
619	–	else if( !strcmp( endTest, ".mdl" ) ){
620	–	strcpy( endTest, ".dump" );
621	–	}
622	–	else{
623	–	strcat( simnfo->sampleName, ".dump" );
624	–	}
525		}
626	–
627	–	strcpy( simnfo->statusName, inFileName );
628	–	nameLength = strlen( simnfo->statusName );
629	–	endTest = &(simnfo->statusName[nameLength - 5]);
630	–	if( !strcmp( endTest, ".bass" ) ){
631	–	strcpy( endTest, ".stat" );
632	–	}
633	–	else if( !strcmp( endTest, ".BASS" ) ){
634	–	strcpy( endTest, ".stat" );
635	–	}
636	–	else{
637	–	endTest = &(simnfo->statusName[nameLength - 4]);
638	–	if( !strcmp( endTest, ".bss" ) ){
639	–	strcpy( endTest, ".stat" );
640	–	}
641	–	else if( !strcmp( endTest, ".mdl" ) ){
642	–	strcpy( endTest, ".stat" );
643	–	}
644	–	else{
645	–	strcat( simnfo->statusName, ".stat" );
646	–	}
647	–	}
648	–
649	–	#ifdef IS_MPI
526		}
651	–	#endif // is_mpi
652	–
653	–	// set the status, sample, and themal kick times
654	–
655	–	if( the_globals->haveSampleTime() ){
656	–	simnfo->sampleTime = the_globals->getSampleTime();
657	–	simnfo->statusTime = simnfo->sampleTime;
658	–	simnfo->thermalTime = simnfo->sampleTime;
659	–	}
660	–	else{
661	–	simnfo->sampleTime = the_globals->getRunTime();
662	–	simnfo->statusTime = simnfo->sampleTime;
663	–	simnfo->thermalTime = simnfo->sampleTime;
664	–	}
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() ){
671	<	simnfo->thermalTime = the_globals->getThermalTime();
672	<	}
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	+	rotMat[0][0] = 1.0;
567	+	rotMat[0][1] = 0.0;
568	+	rotMat[0][2] = 0.0;
569
570	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
571	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
572	<	std::cerr << "called new Symplecic\n";
573	<	fprintf( stderr, "called new Symplectic. stderr\n" );
570	>	rotMat[1][0] = 0.0;
571	>	rotMat[1][1] = 1.0;
572	>	rotMat[1][2] = 0.0;
573	>
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	>	current_atom_ndx++;
582		}
583	<	else if( !strcmp( force_field, "LJ" ) ){
584	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
585	<	std::cerr << "called new Verlet\n";
586	<	fprintf( stderr, "called new Verlet. stderr\n" );
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	<	else {
695	<	std::cerr << "I'm a bug.\n";
696	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
697	<	}
698	<	#ifdef IS_MPI
699	<	mpiSim->mpiRefresh();
700	<	#endif
592	>	}
593
702	–	// initialize the Fortran
594
595	+	void SimSetup::gatherInfo( void ){
596	+	int i,j,k;
597
598	<	simnfo->refreshSim();
599	<
600	<	if( !strcmp( simnfo->mixingRule, "standard") ){
601	<	the_ff->initForceField( LB_MIXING_RULE );
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	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
609	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
610	<	}
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
723	<	strcpy( checkPointMsg,
724	<	"Successfully intialized the mixingRule for Fortran." );
725	<	MPIcheckPoint();
726	<	#endif // is_mpi
727	<	}
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;
657	<	LinkedAssign* extras;
658	<	LinkedAssign* current_extra;
659	<	AtomStamp* currentAtom;
660	<	BondStamp* currentBond;
661	<	BendStamp* currentBend;
740	<	TorsionStamp* currentTorsion;
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657	>
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
742	–	bond_pair* theBonds;
743	–	bend_set* theBends;
744	–	torsion_set* theTorsions;
663
664	<
665	<	//init the forceField paramters
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	<	the_ff->readParams();
668	>	tot_nmol = 0;
669	>	for( i=0; i<n_components; i++ ){
670
671	<
672	<	// init the atoms
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	<	double ux, uy, uz, u, uSqr;
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();
763	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
764	<	info.nBends    = comp_stamps[stampID]->getNBends();
765	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
766	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
718	>	// check for the temperature set flag
719
720	<	info.myAtoms = &the_atoms[atomOffset];
769	<	info.myExcludes = &the_excludes[excludeOffset];
770	<	info.myBonds = new Bond*[info.nBonds];
771	<	info.myBends = new Bend*[info.nBends];
772	<	info.myTorsions = new Torsion*[info.nTorsions];
773	<
774	<	theBonds = new bond_pair[info.nBonds];
775	<	theBends = new bend_set[info.nBends];
776	<	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	<
800	<	dAtom->setSUx( ux );
801	<	dAtom->setSUy( uy );
802	<	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() );
808	<
809	<	#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 );
820	<	theBonds[j].a = currentBond->getA() + atomOffset;
821	<	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;
824	<	exJ = theBonds[j].b;
777	>	}
778
826	–	// exclude_I must always be the smaller of the pair
827	–	if( exI > exJ ){
828	–	tempEx = exI;
829	–	exI = exJ;
830	–	exJ = tempEx;
831	–	}
832	–	#ifdef IS_MPI
833	–	tempEx = exI;
834	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
835	–	tempEx = exJ;
836	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
837	–
838	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
839	–	#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() ){
863	<
864	<	case 0:
865	<	theBends[j].ghost =
866	<	current_extra->getInt() + atomOffset;
867	<	theBends[j].isGhost = 1;
868	<	break;
869	<
870	<	case 1:
871	<	theBends[j].ghost =
872	<	(int)current_extra->getDouble() + atomOffset;
873	<	theBends[j].isGhost = 1;
874	<	break;
875	<
876	<	default:
877	<	sprintf( painCave.errMsg,
878	<	"SimSetup Error: ghostVectorSource was neither a "
879	<	"double nor an int.\n"
880	<	"-->Bend[%d] in %s\n",
881	<	j, comp_stamps[stampID]->getID() );
882	<	painCave.isFatal = 1;
883	<	simError();
884	<	}
885	<	}
886	<
887	<	else{
888	<
889	<	sprintf( painCave.errMsg,
890	<	"SimSetup Error: unhandled bend assignment:\n"
891	<	"    -->%s in Bend[%d] in %s\n",
892	<	current_extra->getlhs(),
893	<	j, comp_stamps[stampID]->getID() );
894	<	painCave.isFatal = 1;
895	<	simError();
896	<	}
897	<
898	<	current_extra = current_extra->getNext();
899	<	}
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		}
901	–
902	–	if( !theBends[j].isGhost ){
903	–
904	–	exI = theBends[j].a;
905	–	exJ = theBends[j].c;
906	–	}
907	–	else{
908	–
909	–	exI = theBends[j].a;
910	–	exJ = theBends[j].b;
911	–	}
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		}
919	–	#ifdef IS_MPI
920	–	tempEx = exI;
921	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
922	–	tempEx = exJ;
923	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
832
833	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
926	<	#else  // isn't MPI
927	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
928	<	#endif  //is_mpi
929	<	}
930	<	excludeOffset += info.nBends;
931	<
932	<	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	>
895	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
896	>
897	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
898	>
899	>	if( globals->haveInitialConfig() ){
900	>
901	>	InitializeFromFile* fileInit;
902	>	#ifdef IS_MPI // is_mpi
903	>	if( worldRank == 0 ){
904	>	#endif //is_mpi
905	>	inName = globals->getInitialConfig();
906	>	double* tempDouble = new double[1000000];
907	>	fileInit = new InitializeFromFile( inName );
908	>	#ifdef IS_MPI
909	>	}else fileInit = new InitializeFromFile( NULL );
910	>	#endif
911	>	fileInit->readInit( info ); // default velocities on
912	>
913	>	delete fileInit;
914	>	}
915	>	else{
916	>
917	>	#ifdef IS_MPI
918	>
919	>	// no init from bass
920	>
921	>	sprintf( painCave.errMsg,
922	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923	>	painCave.isFatal;
924	>	simError();
925	>
926	>	#else
927	>
928	>	initFromBass();
929	>
930	>
931	>	#endif
932	>	}
933	>
934	>	#ifdef IS_MPI
935	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
936	>	MPIcheckPoint();
937	>	#endif // is_mpi
938	>
939	>	}
940	>
941	>
942	>	void SimSetup::makeOutNames( void ){
943	>
944	>	int k;
945	>
946	>
947	>	for(k=0; k<nInfo; k++){
948	>
949	>	#ifdef IS_MPI
950	>	if( worldRank == 0 ){
951	>	#endif // is_mpi
952
953	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
954	<	#else  // isn't MPI
955	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
956	<	#endif  //is_mpi
953	>	if( globals->haveFinalConfig() ){
954	>	strcpy( info[k].finalName, globals->getFinalConfig() );
955	>	}
956	>	else{
957	>	strcpy( info[k].finalName, inFileName );
958	>	char* endTest;
959	>	int nameLength = strlen( info[k].finalName );
960	>	endTest = &(info[k].finalName[nameLength - 5]);
961	>	if( !strcmp( endTest, ".bass" ) ){
962	>	strcpy( endTest, ".eor" );
963	>	}
964	>	else if( !strcmp( endTest, ".BASS" ) ){
965	>	strcpy( endTest, ".eor" );
966	>	}
967	>	else{
968	>	endTest = &(info[k].finalName[nameLength - 4]);
969	>	if( !strcmp( endTest, ".bss" ) ){
970	>	strcpy( endTest, ".eor" );
971		}
972	<	excludeOffset += info.nTorsions;
972	>	else if( !strcmp( endTest, ".mdl" ) ){
973	>	strcpy( endTest, ".eor" );
974	>	}
975	>	else{
976	>	strcat( info[k].finalName, ".eor" );
977	>	}
978	>	}
979	>	}
980	>
981	>	// make the sample and status out names
982	>
983	>	strcpy( info[k].sampleName, inFileName );
984	>	char* endTest;
985	>	int nameLength = strlen( info[k].sampleName );
986	>	endTest = &(info[k].sampleName[nameLength - 5]);
987	>	if( !strcmp( endTest, ".bass" ) ){
988	>	strcpy( endTest, ".dump" );
989	>	}
990	>	else if( !strcmp( endTest, ".BASS" ) ){
991	>	strcpy( endTest, ".dump" );
992	>	}
993	>	else{
994	>	endTest = &(info[k].sampleName[nameLength - 4]);
995	>	if( !strcmp( endTest, ".bss" ) ){
996	>	strcpy( endTest, ".dump" );
997	>	}
998	>	else if( !strcmp( endTest, ".mdl" ) ){
999	>	strcpy( endTest, ".dump" );
1000	>	}
1001	>	else{
1002	>	strcat( info[k].sampleName, ".dump" );
1003	>	}
1004	>	}
1005	>
1006	>	strcpy( info[k].statusName, inFileName );
1007	>	nameLength = strlen( info[k].statusName );
1008	>	endTest = &(info[k].statusName[nameLength - 5]);
1009	>	if( !strcmp( endTest, ".bass" ) ){
1010	>	strcpy( endTest, ".stat" );
1011	>	}
1012	>	else if( !strcmp( endTest, ".BASS" ) ){
1013	>	strcpy( endTest, ".stat" );
1014	>	}
1015	>	else{
1016	>	endTest = &(info[k].statusName[nameLength - 4]);
1017	>	if( !strcmp( endTest, ".bss" ) ){
1018	>	strcpy( endTest, ".stat" );
1019	>	}
1020	>	else if( !strcmp( endTest, ".mdl" ) ){
1021	>	strcpy( endTest, ".stat" );
1022	>	}
1023	>	else{
1024	>	strcat( info[k].statusName, ".stat" );
1025	>	}
1026	>	}
1027	>
1028	>	#ifdef IS_MPI
1029	>	}
1030	>	#endif // is_mpi
1031	>	}
1032	>	}
1033
962	–
963	–	// send the arrays off to the forceField for init.
1034
1035	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1036	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1037	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1038	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1035	>	void SimSetup::sysObjectsCreation( void ){
1036	>
1037	>	int i,k;
1038	>
1039	>	// create the forceField
1040
1041	+	createFF();
1042
1043	<	the_molecules[i].initialize( info );
1043	>	// extract componentList
1044
1045	+	compList();
1046
1047	<	atomOffset += info.nAtoms;
1048	<	delete[] theBonds;
1049	<	delete[] theBends;
1050	<	delete[] theTorsions;
1047	>	// calc the number of atoms, bond, bends, and torsions
1048	>
1049	>	calcSysValues();
1050	>
1051	>	#ifdef IS_MPI
1052	>	// divide the molecules among the processors
1053	>
1054	>	mpiMolDivide();
1055	>	#endif //is_mpi
1056	>
1057	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1058	>
1059	>	makeSysArrays();
1060	>
1061	>	// make and initialize the molecules (all but atomic coordinates)
1062	>
1063	>	makeMolecules();
1064	>
1065	>	for(k=0; k<nInfo; k++){
1066	>	info[k].identArray = new int[info[k].n_atoms];
1067	>	for(i=0; i<info[k].n_atoms; i++){
1068	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1069	>	}
1070		}
1071	+	}
1072
1073	+
1074	+	void SimSetup::createFF( void ){
1075	+
1076	+	switch( ffCase ){
1077	+
1078	+	case FF_DUFF:
1079	+	the_ff = new DUFF();
1080	+	break;
1081	+
1082	+	case FF_LJ:
1083	+	the_ff = new LJFF();
1084	+	break;
1085	+
1086	+	case FF_EAM:
1087	+	the_ff = new EAM_FF();
1088	+	break;
1089	+
1090	+	default:
1091	+	sprintf( painCave.errMsg,
1092	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	+	painCave.isFatal = 1;
1094	+	simError();
1095	+	}
1096	+
1097		#ifdef IS_MPI
1098	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1098	>	strcpy( checkPointMsg, "ForceField creation successful" );
1099		MPIcheckPoint();
1100		#endif // is_mpi
1101
985	–	// clean up the forcefield
986	–	the_ff->calcRcut();
987	–	the_ff->cleanMe();
988	–
1102		}
1103
991	–	void SimSetup::initFromBass( void ){
1104
1105	<	int i, j, k;
994	<	int n_cells;
995	<	double cellx, celly, cellz;
996	<	double temp1, temp2, temp3;
997	<	int n_per_extra;
998	<	int n_extra;
999	<	int have_extra, done;
1105	>	void SimSetup::compList( void ){
1106
1107	<	temp1 = (double)tot_nmol / 4.0;
1108	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1109	<	temp3 = ceil( temp2 );
1107	>	int i;
1108	>	char* id;
1109	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1110	>	LinkedMolStamp* currentStamp = NULL;
1111	>	comp_stamps = new MoleculeStamp*[n_components];
1112	>
1113	>	// make an array of molecule stamps that match the components used.
1114	>	// also extract the used stamps out into a separate linked list
1115	>
1116	>	for(i=0; i<nInfo; i++){
1117	>	info[i].nComponents = n_components;
1118	>	info[i].componentsNmol = components_nmol;
1119	>	info[i].compStamps = comp_stamps;
1120	>	info[i].headStamp = headStamp;
1121	>	}
1122	>
1123
1124	<	have_extra =0;
1006	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1007	<	have_extra =1;
1124	>	for( i=0; i<n_components; i++ ){
1125
1126	<	n_cells = (int)temp3 - 1;
1127	<	cellx = simnfo->box_x / temp3;
1128	<	celly = simnfo->box_y / temp3;
1129	<	cellz = simnfo->box_z / temp3;
1013	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1014	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1015	<	n_per_extra = (int)ceil( temp1 );
1126	>	id = the_components[i]->getType();
1127	>	comp_stamps[i] = NULL;
1128	>
1129	>	// check to make sure the component isn't already in the list
1130
1131	<	if( n_per_extra > 4){
1132	<	sprintf( painCave.errMsg,
1133	<	"SimSetup error. There has been an error in constructing"
1134	<	" the non-complete lattice.\n" );
1135	<	painCave.isFatal = 1;
1136	<	simError();
1131	>	comp_stamps[i] = headStamp->match( id );
1132	>	if( comp_stamps[i] == NULL ){
1133	>
1134	>	// extract the component from the list;
1135	>
1136	>	currentStamp = stamps->extractMolStamp( id );
1137	>	if( currentStamp == NULL ){
1138	>	sprintf( painCave.errMsg,
1139	>	"SimSetup error: Component \"%s\" was not found in the "
1140	>	"list of declared molecules\n",
1141	>	id );
1142	>	painCave.isFatal = 1;
1143	>	simError();
1144	>	}
1145	>
1146	>	headStamp->add( currentStamp );
1147	>	comp_stamps[i] = headStamp->match( id );
1148		}
1149		}
1150	<	else{
1151	<	n_cells = (int)temp3;
1152	<	cellx = simnfo->box_x / temp3;
1153	<	celly = simnfo->box_y / temp3;
1154	<	cellz = simnfo->box_z / temp3;
1150	>
1151	>	#ifdef IS_MPI
1152	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1153	>	MPIcheckPoint();
1154	>	#endif // is_mpi
1155	>
1156	>
1157	>	}
1158	>
1159	>	void SimSetup::calcSysValues( void ){
1160	>	int i, j, k;
1161	>
1162	>	int *molMembershipArray;
1163	>
1164	>	tot_atoms = 0;
1165	>	tot_bonds = 0;
1166	>	tot_bends = 0;
1167	>	tot_torsions = 0;
1168	>	for( i=0; i<n_components; i++ ){
1169	>
1170	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1172	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1173	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174		}
1175	+
1176	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	+	molMembershipArray = new int[tot_atoms];
1178	+
1179	+	for(i=0; i<nInfo; i++){
1180	+	info[i].n_atoms = tot_atoms;
1181	+	info[i].n_bonds = tot_bonds;
1182	+	info[i].n_bends = tot_bends;
1183	+	info[i].n_torsions = tot_torsions;
1184	+	info[i].n_SRI = tot_SRI;
1185	+	info[i].n_mol = tot_nmol;
1186	+
1187	+	info[i].molMembershipArray = molMembershipArray;
1188	+	}
1189	+	}
1190
1191	<	current_mol = 0;
1033	<	current_comp_mol = 0;
1034	<	current_comp = 0;
1035	<	current_atom_ndx = 0;
1191	>	#ifdef IS_MPI
1192
1193	<	for( i=0; i < n_cells ; i++ ){
1194	<	for( j=0; j < n_cells; j++ ){
1195	<	for( k=0; k < n_cells; k++ ){
1193	>	void SimSetup::mpiMolDivide( void ){
1194	>
1195	>	int i, j, k;
1196	>	int localMol, allMol;
1197	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1198
1199	<	makeElement( i * cellx,
1200	<	j * celly,
1201	<	k * cellz );
1199	>	mpiSim = new mpiSimulation( info );
1200	>
1201	>	globalIndex = mpiSim->divideLabor();
1202
1203	<	makeElement( i * cellx + 0.5 * cellx,
1204	<	j * celly + 0.5 * celly,
1205	<	k * cellz );
1203	>	// set up the local variables
1204	>
1205	>	mol2proc = mpiSim->getMolToProcMap();
1206	>	molCompType = mpiSim->getMolComponentType();
1207	>
1208	>	allMol = 0;
1209	>	localMol = 0;
1210	>	local_atoms = 0;
1211	>	local_bonds = 0;
1212	>	local_bends = 0;
1213	>	local_torsions = 0;
1214	>	globalAtomIndex = 0;
1215
1049	–	makeElement( i * cellx,
1050	–	j * celly + 0.5 * celly,
1051	–	k * cellz + 0.5 * cellz );
1216
1217	<	makeElement( i * cellx + 0.5 * cellx,
1218	<	j * celly,
1219	<	k * cellz + 0.5 * cellz );
1217	>	for( i=0; i<n_components; i++ ){
1218	>
1219	>	for( j=0; j<components_nmol[i]; j++ ){
1220	>
1221	>	if( mol2proc[allMol] == worldRank ){
1222	>
1223	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1224	>	local_bonds +=    comp_stamps[i]->getNBonds();
1225	>	local_bends +=    comp_stamps[i]->getNBends();
1226	>	local_torsions += comp_stamps[i]->getNTorsions();
1227	>	localMol++;
1228	>	}
1229	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1230	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1231	>	globalAtomIndex++;
1232		}
1233	+
1234	+	allMol++;
1235		}
1236		}
1237	+	local_SRI = local_bonds + local_bends + local_torsions;
1238	+
1239	+	info[0].n_atoms = mpiSim->getMyNlocal();
1240	+
1241	+	if( local_atoms != info[0].n_atoms ){
1242	+	sprintf( painCave.errMsg,
1243	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244	+	" localAtom (%d) are not equal.\n",
1245	+	info[0].n_atoms,
1246	+	local_atoms );
1247	+	painCave.isFatal = 1;
1248	+	simError();
1249	+	}
1250
1251	<	if( have_extra ){
1252	<	done = 0;
1251	>	info[0].n_bonds = local_bonds;
1252	>	info[0].n_bends = local_bends;
1253	>	info[0].n_torsions = local_torsions;
1254	>	info[0].n_SRI = local_SRI;
1255	>	info[0].n_mol = localMol;
1256
1257	<	int start_ndx;
1258	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1259	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1257	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1258	>	MPIcheckPoint();
1259	>	}
1260	>
1261	>	#endif // is_mpi
1262
1067	–	if( i < n_cells ){
1263
1264	<	if( j < n_cells ){
1265	<	start_ndx = n_cells;
1071	<	}
1072	<	else start_ndx = 0;
1073	<	}
1074	<	else start_ndx = 0;
1264	>	void SimSetup::makeSysArrays( void ){
1265	>	int i, j, k, l;
1266
1267	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1267	>	Atom** the_atoms;
1268	>	Molecule* the_molecules;
1269	>	Exclude** the_excludes;
1270
1271	<	makeElement( i * cellx,
1272	<	j * celly,
1273	<	k * cellz );
1274	<	done = ( current_mol >= tot_nmol );
1271	>
1272	>	for(l=0; l<nInfo; l++){
1273	>
1274	>	// create the atom and short range interaction arrays
1275	>
1276	>	the_atoms = new Atom*[info[l].n_atoms];
1277	>	the_molecules = new Molecule[info[l].n_mol];
1278	>	int molIndex;
1279
1280	<	if( !done && n_per_extra > 1 ){
1281	<	makeElement( i * cellx + 0.5 * cellx,
1282	<	j * celly + 0.5 * celly,
1283	<	k * cellz );
1284	<	done = ( current_mol >= tot_nmol );
1285	<	}
1280	>	// initialize the molecule's stampID's
1281	>
1282	>	#ifdef IS_MPI
1283	>
1284	>
1285	>	molIndex = 0;
1286	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1287	>
1288	>	if(mol2proc[i] == worldRank ){
1289	>	the_molecules[molIndex].setStampID( molCompType[i] );
1290	>	the_molecules[molIndex].setMyIndex( molIndex );
1291	>	the_molecules[molIndex].setGlobalIndex( i );
1292	>	molIndex++;
1293	>	}
1294	>	}
1295	>
1296	>	#else // is_mpi
1297	>
1298	>	molIndex = 0;
1299	>	globalAtomIndex = 0;
1300	>	for(i=0; i<n_components; i++){
1301	>	for(j=0; j<components_nmol[i]; j++ ){
1302	>	the_molecules[molIndex].setStampID( i );
1303	>	the_molecules[molIndex].setMyIndex( molIndex );
1304	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1305	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1306	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1307	>	globalAtomIndex++;
1308	>	}
1309	>	molIndex++;
1310	>	}
1311	>	}
1312	>
1313	>
1314	>	#endif // is_mpi
1315
1090	–	if( !done && n_per_extra > 2){
1091	–	makeElement( i * cellx,
1092	–	j * celly + 0.5 * celly,
1093	–	k * cellz + 0.5 * cellz );
1094	–	done = ( current_mol >= tot_nmol );
1095	–	}
1316
1317	<	if( !done && n_per_extra > 3){
1318	<	makeElement( i * cellx + 0.5 * cellx,
1319	<	j * celly,
1320	<	k * cellz + 0.5 * cellz );
1321	<	done = ( current_mol >= tot_nmol );
1322	<	}
1103	<	}
1317	>	if( info[l].n_SRI ){
1318	>
1319	>	Exclude::createArray(info[l].n_SRI);
1320	>	the_excludes = new Exclude*[info[l].n_SRI];
1321	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	>	the_excludes[ex] = new Exclude(ex);
1323		}
1324	+	info[l].globalExcludes = new int;
1325	+	info[l].n_exclude = info[l].n_SRI;
1326		}
1327	<	}
1327	>	else{
1328	>
1329	>	Exclude::createArray( 1 );
1330	>	the_excludes = new Exclude*;
1331	>	the_excludes[0] = new Exclude(0);
1332	>	the_excludes[0]->setPair( 0,0 );
1333	>	info[l].globalExcludes = new int;
1334	>	info[l].globalExcludes[0] = 0;
1335	>	info[l].n_exclude = 0;
1336	>	}
1337
1338	+	// set the arrays into the SimInfo object
1339
1340	<	for( i=0; i<simnfo->n_atoms; i++ ){
1341	<	simnfo->atoms[i]->set_vx( 0.0 );
1342	<	simnfo->atoms[i]->set_vy( 0.0 );
1343	<	simnfo->atoms[i]->set_vz( 0.0 );
1340	>	info[l].atoms = the_atoms;
1341	>	info[l].molecules = the_molecules;
1342	>	info[l].nGlobalExcludes = 0;
1343	>	info[l].excludes = the_excludes;
1344	>
1345	>	the_ff->setSimInfo( info );
1346	>
1347		}
1348		}
1349
1350	<	void SimSetup::makeElement( double x, double y, double z ){
1350	>	void SimSetup::makeIntegrator( void ){
1351
1352		int k;
1119	–	AtomStamp* current_atom;
1120	–	DirectionalAtom* dAtom;
1121	–	double rotMat[3][3];
1353
1354	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1354	>	NVT<RealIntegrator>*  myNVT = NULL;
1355	>	NPTi<RealIntegrator>* myNPTi = NULL;
1356	>	NPTf<RealIntegrator>* myNPTf = NULL;
1357	>	NPTim<RealIntegrator>* myNPTim = NULL;
1358	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1359	>
1360	>	for(k=0; k<nInfo; k++){
1361	>
1362	>	switch( ensembleCase ){
1363	>
1364	>	case NVE_ENS:
1365	>	if (globals->haveZconstraints()){
1366	>	setupZConstraint(info[k]);
1367	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1368	>	}
1369
1370	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1371	<	if( !current_atom->havePosition() ){
1370	>	else
1371	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1372	>	break;
1373	>
1374	>	case NVT_ENS:
1375	>	if (globals->haveZconstraints()){
1376	>	setupZConstraint(info[k]);
1377	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	>	}
1379	>	else
1380	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1381	>
1382	>	myNVT->setTargetTemp(globals->getTargetTemp());
1383	>
1384	>	if (globals->haveTauThermostat())
1385	>	myNVT->setTauThermostat(globals->getTauThermostat());
1386	>
1387	>	else {
1388	>	sprintf( painCave.errMsg,
1389	>	"SimSetup error: If you use the NVT\n"
1390	>	"    ensemble, you must set tauThermostat.\n");
1391	>	painCave.isFatal = 1;
1392	>	simError();
1393	>	}
1394	>	break;
1395	>
1396	>	case NPTi_ENS:
1397	>	if (globals->haveZconstraints()){
1398	>	setupZConstraint(info[k]);
1399	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	>	}
1401	>	else
1402	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403	>
1404	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	>
1406	>	if (globals->haveTargetPressure())
1407	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	>	else {
1409	>	sprintf( painCave.errMsg,
1410	>	"SimSetup error: If you use a constant pressure\n"
1411	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	>	painCave.isFatal = 1;
1413	>	simError();
1414	>	}
1415	>
1416	>	if( globals->haveTauThermostat() )
1417	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	>	else{
1419	>	sprintf( painCave.errMsg,
1420	>	"SimSetup error: If you use an NPT\n"
1421	>	"    ensemble, you must set tauThermostat.\n");
1422	>	painCave.isFatal = 1;
1423	>	simError();
1424	>	}
1425	>
1426	>	if( globals->haveTauBarostat() )
1427	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	>	else{
1429	>	sprintf( painCave.errMsg,
1430	>	"SimSetup error: If you use an NPT\n"
1431	>	"    ensemble, you must set tauBarostat.\n");
1432	>	painCave.isFatal = 1;
1433	>	simError();
1434	>	}
1435	>	break;
1436	>
1437	>	case NPTf_ENS:
1438	>	if (globals->haveZconstraints()){
1439	>	setupZConstraint(info[k]);
1440	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	>	}
1442	>	else
1443	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1444	>
1445	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1446	>
1447	>	if (globals->haveTargetPressure())
1448	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	>	else {
1450	>	sprintf( painCave.errMsg,
1451	>	"SimSetup error: If you use a constant pressure\n"
1452	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	>	painCave.isFatal = 1;
1454	>	simError();
1455	>	}
1456	>
1457	>	if( globals->haveTauThermostat() )
1458	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	>	else{
1460	>	sprintf( painCave.errMsg,
1461	>	"SimSetup error: If you use an NPT\n"
1462	>	"    ensemble, you must set tauThermostat.\n");
1463	>	painCave.isFatal = 1;
1464	>	simError();
1465	>	}
1466	>
1467	>	if( globals->haveTauBarostat() )
1468	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	>	else{
1470	>	sprintf( painCave.errMsg,
1471	>	"SimSetup error: If you use an NPT\n"
1472	>	"    ensemble, you must set tauBarostat.\n");
1473	>	painCave.isFatal = 1;
1474	>	simError();
1475	>	}
1476	>	break;
1477	>
1478	>	case NPTim_ENS:
1479	>	if (globals->haveZconstraints()){
1480	>	setupZConstraint(info[k]);
1481	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	>	}
1483	>	else
1484	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1485	>
1486	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1487	>
1488	>	if (globals->haveTargetPressure())
1489	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	>	else {
1491	>	sprintf( painCave.errMsg,
1492	>	"SimSetup error: If you use a constant pressure\n"
1493	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	>	painCave.isFatal = 1;
1495	>	simError();
1496	>	}
1497	>
1498	>	if( globals->haveTauThermostat() )
1499	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	>	else{
1501	>	sprintf( painCave.errMsg,
1502	>	"SimSetup error: If you use an NPT\n"
1503	>	"    ensemble, you must set tauThermostat.\n");
1504	>	painCave.isFatal = 1;
1505	>	simError();
1506	>	}
1507	>
1508	>	if( globals->haveTauBarostat() )
1509	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	>	else{
1511	>	sprintf( painCave.errMsg,
1512	>	"SimSetup error: If you use an NPT\n"
1513	>	"    ensemble, you must set tauBarostat.\n");
1514	>	painCave.isFatal = 1;
1515	>	simError();
1516	>	}
1517	>	break;
1518	>
1519	>	case NPTfm_ENS:
1520	>	if (globals->haveZconstraints()){
1521	>	setupZConstraint(info[k]);
1522	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	>	}
1524	>	else
1525	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1526	>
1527	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1528	>
1529	>	if (globals->haveTargetPressure())
1530	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1531	>	else {
1532	>	sprintf( painCave.errMsg,
1533	>	"SimSetup error: If you use a constant pressure\n"
1534	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1535	>	painCave.isFatal = 1;
1536	>	simError();
1537	>	}
1538	>
1539	>	if( globals->haveTauThermostat() )
1540	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1541	>	else{
1542	>	sprintf( painCave.errMsg,
1543	>	"SimSetup error: If you use an NPT\n"
1544	>	"    ensemble, you must set tauThermostat.\n");
1545	>	painCave.isFatal = 1;
1546	>	simError();
1547	>	}
1548	>
1549	>	if( globals->haveTauBarostat() )
1550	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1551	>	else{
1552	>	sprintf( painCave.errMsg,
1553	>	"SimSetup error: If you use an NPT\n"
1554	>	"    ensemble, you must set tauBarostat.\n");
1555	>	painCave.isFatal = 1;
1556	>	simError();
1557	>	}
1558	>	break;
1559	>
1560	>	default:
1561		sprintf( painCave.errMsg,
1562	<	"SimSetup:initFromBass error.\n"
1129	<	"\tComponent %s, atom %s does not have a position specified.\n"
1130	<	"\tThe initialization routine is unable to give a start"
1131	<	" position.\n",
1132	<	comp_stamps[current_comp]->getID(),
1133	<	current_atom->getType() );
1562	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1563		painCave.isFatal = 1;
1564		simError();
1565		}
1566	+	}
1567	+	}
1568
1569	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1139	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1140	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1569	>	void SimSetup::initFortran( void ){
1570
1571	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1571	>	info[0].refreshSim();
1572	>
1573	>	if( !strcmp( info[0].mixingRule, "standard") ){
1574	>	the_ff->initForceField( LB_MIXING_RULE );
1575	>	}
1576	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1577	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1578	>	}
1579	>	else{
1580	>	sprintf( painCave.errMsg,
1581	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	>	info[0].mixingRule );
1583	>	painCave.isFatal = 1;
1584	>	simError();
1585	>	}
1586
1144	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1587
1588	<	rotMat[0][0] = 1.0;
1589	<	rotMat[0][1] = 0.0;
1590	<	rotMat[0][2] = 0.0;
1588	>	#ifdef IS_MPI
1589	>	strcpy( checkPointMsg,
1590	>	"Successfully intialized the mixingRule for Fortran." );
1591	>	MPIcheckPoint();
1592	>	#endif // is_mpi
1593
1594	<	rotMat[1][0] = 0.0;
1151	<	rotMat[1][1] = 1.0;
1152	<	rotMat[1][2] = 0.0;
1594	>	}
1595
1596	<	rotMat[2][0] = 0.0;
1597	<	rotMat[2][1] = 0.0;
1598	<	rotMat[2][2] = 1.0;
1596	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1597	>	{
1598	>	int nZConstraints;
1599	>	ZconStamp** zconStamp;
1600
1601	<	dAtom->setA( rotMat );
1602	<	}
1601	>	if(globals->haveZconstraintTime()){
1602	>
1603	>	//add sample time of z-constraint  into SimInfo's property list
1604	>	DoubleData* zconsTimeProp = new DoubleData();
1605	>	zconsTimeProp->setID(ZCONSTIME_ID);
1606	>	zconsTimeProp->setData(globals->getZconsTime());
1607	>	theInfo.addProperty(zconsTimeProp);
1608	>	}
1609	>	else{
1610	>	sprintf( painCave.errMsg,
1611	>	"ZConstraint error: If you use an ZConstraint\n"
1612	>	" , you must set sample time.\n");
1613	>	painCave.isFatal = 1;
1614	>	simError();
1615	>	}
1616
1617	<	current_atom_ndx++;
1617	>	//push zconsTol into siminfo, if user does not specify
1618	>	//value for zconsTol, a default value will be used
1619	>	DoubleData* zconsTol = new DoubleData();
1620	>	zconsTol->setID(ZCONSTOL_ID);
1621	>	if(globals->haveZconsTol()){
1622	>	zconsTol->setData(globals->getZconsTol());
1623		}
1624	+	else{
1625	+	double defaultZConsTol = 0.01;
1626	+	sprintf( painCave.errMsg,
1627	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628	+	" , default value %f is used.\n", defaultZConsTol);
1629	+	painCave.isFatal = 0;
1630	+	simError();
1631
1632	<	current_mol++;
1633	<	current_comp_mol++;
1632	>	zconsTol->setData(defaultZConsTol);
1633	>	}
1634	>	theInfo.addProperty(zconsTol);
1635
1636	<	if( current_comp_mol >= components_nmol[current_comp] ){
1636	>	//set Force Substraction Policy
1637	>	StringData* zconsForcePolicy =  new StringData();
1638	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	>
1640	>	if(globals->haveZconsForcePolicy()){
1641	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	>	}
1643	>	else{
1644	>	sprintf( painCave.errMsg,
1645	>	"ZConstraint Warning: User does not set force substraction policy, "
1646	>	"average force substraction policy is used\n");
1647	>	painCave.isFatal = 0;
1648	>	simError();
1649	>	zconsForcePolicy->setData("BYNUMBER");
1650	>	}
1651	>
1652	>	theInfo.addProperty(zconsForcePolicy);
1653	>
1654	>	//Determine the name of ouput file and add it into SimInfo's property list
1655	>	//Be careful, do not use inFileName, since it is a pointer which
1656	>	//point to a string at master node, and slave nodes do not contain that string
1657	>
1658	>	string zconsOutput(theInfo.finalName);
1659	>
1660	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	>
1662	>	StringData* zconsFilename = new StringData();
1663	>	zconsFilename->setID(ZCONSFILENAME_ID);
1664	>	zconsFilename->setData(zconsOutput);
1665	>
1666	>	theInfo.addProperty(zconsFilename);
1667	>
1668	>	//setup index, pos and other parameters of z-constraint molecules
1669	>	nZConstraints = globals->getNzConstraints();
1670	>	theInfo.nZconstraints = nZConstraints;
1671
1672	<	current_comp_mol = 0;
1673	<	current_comp++;
1672	>	zconStamp = globals->getZconStamp();
1673	>	ZConsParaItem tempParaItem;
1674	>
1675	>	ZConsParaData* zconsParaData = new ZConsParaData();
1676	>	zconsParaData->setID(ZCONSPARADATA_ID);
1677	>
1678	>	for(int i = 0; i < nZConstraints; i++){
1679	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1683	>
1684	>	zconsParaData->addItem(tempParaItem);
1685		}
1686	+
1687	+	//sort the parameters by index of molecules
1688	+	zconsParaData->sortByIndex();
1689	+
1690	+	//push data into siminfo, therefore, we can retrieve later
1691	+	theInfo.addProperty(zconsParaData);
1692	+
1693		}

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