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root/group/branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp

Comparing:
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 489 by mmeineke, Thu Apr 10 20:08:56 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 850 by mmeineke, Mon Nov 3 22:07:17 2003 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 12 | Line 16
16		#include "mpiSimulation.hpp"
17		#endif
18
19	+	// some defines for ensemble and Forcefield  cases
20	+
21	+	#define NVE_ENS        0
22	+	#define NVT_ENS        1
23	+	#define NPTi_ENS       2
24	+	#define NPTf_ENS       3
25	+	#define NPTxyz_ENS     4
26	+
27	+
28	+	#define FF_DUFF 0
29	+	#define FF_LJ   1
30	+	#define FF_EAM  2
31	+
32	+	using namespace std;
33	+
34		SimSetup::SimSetup(){
35	+
36	+	initSuspend = false;
37	+	isInfoArray = 0;
38	+	nInfo = 1;
39	+
40		stamps = new MakeStamps();
41		globals = new Globals();
42	<
42	>
43	>
44		#ifdef IS_MPI
45	<	strcpy( checkPointMsg, "SimSetup creation successful" );
45	>	strcpy(checkPointMsg, "SimSetup creation successful");
46		MPIcheckPoint();
47		#endif // IS_MPI
48		}
#	Line 27 | Line 52 | SimSetup::~SimSetup(){
52		delete globals;
53		}
54
55	<	void SimSetup::parseFile( char* fileName ){
55	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
56	>	info = the_info;
57	>	nInfo = theNinfo;
58	>	isInfoArray = 1;
59	>	initSuspend = true;
60	>	}
61
62	+
63	+	void SimSetup::parseFile(char* fileName){
64		#ifdef IS_MPI
65	<	if( worldRank == 0 ){
65	>	if (worldRank == 0){
66		#endif // is_mpi
67	<
67	>
68		inFileName = fileName;
69	<	set_interface_stamps( stamps, globals );
70	<
69	>	set_interface_stamps(stamps, globals);
70	>
71		#ifdef IS_MPI
72		mpiEventInit();
73		#endif
74
75	<	yacc_BASS( fileName );
75	>	yacc_BASS(fileName);
76
77		#ifdef IS_MPI
78		throwMPIEvent(NULL);
79		}
80	<	else receiveParse();
80	>	else{
81	>	receiveParse();
82	>	}
83		#endif
84
85		}
86
87		#ifdef IS_MPI
88		void SimSetup::receiveParse(void){
89	<
90	<	set_interface_stamps( stamps, globals );
91	<	mpiEventInit();
92	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
89	>	set_interface_stamps(stamps, globals);
90	>	mpiEventInit();
91	>	MPIcheckPoint();
92	>	mpiEventLoop();
93		}
94
95		#endif // is_mpi
96
97	<	void SimSetup::createSim( void ){
97	>	void SimSetup::createSim(void){
98
99	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
99	>	// gather all of the information from the Bass file
100
101	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
101	>	gatherInfo();
102
103	<	// 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();
103	>	// creation of complex system objects
104
105	<	// 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() );
105	>	sysObjectsCreation();
106
107	<	// 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	<	if (the_globals->haveTargetPressure())
91	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92	<	else {
93	<	sprintf( painCave.errMsg,
94	<	"SimSetup error: If you use the constant pressure\n"
95	<	"    ensemble, you must set targetPressure.\n"
96	<	"    This was found in the BASS file.\n");
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
107	>	// initialize the system coordinates
108
109	<	if (the_globals->haveTauThermostat())
110	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103	<	else if (the_globals->haveQmass())
104	<	the_extendedsystem->setQmass(the_globals->getQmass());
105	<	else {
106	<	sprintf( painCave.errMsg,
107	<	"SimSetup error: If you use one of the constant temperature\n"
108	<	"    ensembles, you must set either tauThermostat or qMass.\n"
109	<	"    Neither of these was found in the BASS file.\n");
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
109	>	if ( !initSuspend ){
110	>	initSystemCoords();
111
112	<	if (the_globals->haveTauBarostat())
113	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
114	<	else {
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup error: If you use the constant pressure\n"
119	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
112	>	if( !(globals->getUseInitTime()) )
113	>	info[0].currentTime = 0.0;
114	>	}
115
116	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
126	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
116	>	// check on the post processing info
117
118	<	if (the_globals->haveTauThermostat())
130	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131	<	else if (the_globals->haveQmass())
132	<	the_extendedsystem->setQmass(the_globals->getQmass());
133	<	else {
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error: If you use one of the constant temperature\n"
136	<	"    ensembles, you must set either tauThermostat or qMass.\n"
137	<	"    Neither of these was found in the BASS file.\n");
138	<	painCave.isFatal = 1;
139	<	simError();
140	<	}
118	>	finalInfoCheck();
119
120	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
143	<	} else {
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	<	"reverting to NVE for this simulation.\n",
147	<	ensemble );
148	<	painCave.isFatal = 0;
149	<	simError();
150	<	strcpy( ensemble, "NVE" );
151	<	}
152	<	strcpy( simnfo->ensemble, ensemble );
120	>	// make the output filenames
121
122	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155	<	simnfo->usePBC = the_globals->getPBC();
156	<
157	<	int usesDipoles = 0;
158	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
159	<	the_ff = new TraPPE_ExFF();
160	<	usesDipoles = 1;
161	<	}
162	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163	<	else{
164	<	sprintf( painCave.errMsg,
165	<	"SimSetup Error. Unrecognized force field -> %s\n",
166	<	force_field );
167	<	painCave.isFatal = 1;
168	<	simError();
169	<	}
122	>	makeOutNames();
123
124	+	// make the integrator
125	+
126	+	makeIntegrator();
127	+
128		#ifdef IS_MPI
129	<	strcpy( checkPointMsg, "ForceField creation successful" );
130	<	MPIcheckPoint();
174	<	#endif // is_mpi
129	>	mpiSim->mpiRefresh();
130	>	#endif
131
132	<
132	>	// initialize the Fortran
133
134	<	// get the components and calculate the tot_nMol and indvidual n_mol
135	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
134	>	initFortran();
135	>	}
136
183	–	if( !the_globals->haveNMol() ){
184	–	// we don't have the total number of molecules, so we assume it is
185	–	// given in each component
137
138	<	tot_nmol = 0;
139	<	for( i=0; i<n_components; i++ ){
138	>	void SimSetup::makeMolecules(void){
139	>	int k;
140	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
141	>	molInit molInfo;
142	>	DirectionalAtom* dAtom;
143	>	LinkedAssign* extras;
144	>	LinkedAssign* current_extra;
145	>	AtomStamp* currentAtom;
146	>	BondStamp* currentBond;
147	>	BendStamp* currentBend;
148	>	TorsionStamp* currentTorsion;
149
150	<	if( !the_components[i]->haveNMol() ){
151	<	// we have a problem
152	<	sprintf( painCave.errMsg,
193	<	"SimSetup Error. No global NMol or component NMol"
194	<	" given. Cannot calculate the number of atoms.\n" );
195	<	painCave.isFatal = 1;
196	<	simError();
197	<	}
150	>	bond_pair* theBonds;
151	>	bend_set* theBends;
152	>	torsion_set* theTorsions;
153
199	–	tot_nmol += the_components[i]->getNMol();
200	–	components_nmol[i] = the_components[i]->getNMol();
201	–	}
202	–	}
203	–	else{
204	–	sprintf( painCave.errMsg,
205	–	"SimSetup error.\n"
206	–	"\tSorry, the ability to specify total"
207	–	" nMols and then give molfractions in the components\n"
208	–	"\tis not currently supported."
209	–	" Please give nMol in the components.\n" );
210	–	painCave.isFatal = 1;
211	–	simError();
212	–
213	–
214	–	//     tot_nmol = the_globals->getNMol();
215	–
216	–	//   //we have the total number of molecules, now we check for molfractions
217	–	//     for( i=0; i<n_components; i++ ){
218	–
219	–	//       if( !the_components[i]->haveMolFraction() ){
220	–
221	–	//  if( !the_components[i]->haveNMol() ){
222	–	//    //we have a problem
223	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	–	//              << " nMol was given in component
225	–
226	–	}
154
155	<	#ifdef IS_MPI
229	<	strcpy( checkPointMsg, "Have the number of components" );
230	<	MPIcheckPoint();
231	<	#endif // is_mpi
155	>	//init the forceField paramters
156
157	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
157	>	the_ff->readParams();
158
236	–	simnfo->nComponents = n_components;
237	–	simnfo->componentsNmol = components_nmol;
238	–	simnfo->compStamps = comp_stamps;
239	–	simnfo->headStamp = new LinkedMolStamp();
240	–
241	–	char* id;
242	–	LinkedMolStamp* headStamp = simnfo->headStamp;
243	–	LinkedMolStamp* currentStamp = NULL;
244	–	for( i=0; i<n_components; i++ ){
159
160	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
160	>	// init the atoms
161
162	<	comp_stamps[i] = headStamp->match( id );
252	<	if( comp_stamps[i] == NULL ){
253	<
254	<	// extract the component from the list;
255	<
256	<	currentStamp = the_stamps->extractMolStamp( id );
257	<	if( currentStamp == NULL ){
258	<	sprintf( painCave.errMsg,
259	<	"SimSetup error: Component \"%s\" was not found in the "
260	<	"list of declared molecules\n",
261	<	id );
262	<	painCave.isFatal = 1;
263	<	simError();
264	<	}
265	<
266	<	headStamp->add( currentStamp );
267	<	comp_stamps[i] = headStamp->match( id );
268	<	}
269	<	}
162	>	double ux, uy, uz, u, uSqr;
163
164	<	#ifdef IS_MPI
165	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	<	MPIcheckPoint();
274	<	#endif // is_mpi
275	<
164	>	for (k = 0; k < nInfo; k++){
165	>	the_ff->setSimInfo(&(info[k]));
166
167	+	atomOffset = 0;
168	+	excludeOffset = 0;
169	+	for (i = 0; i < info[k].n_mol; i++){
170	+	stampID = info[k].molecules[i].getStampID();
171
172	+	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
173	+	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
174	+	molInfo.nBends = comp_stamps[stampID]->getNBends();
175	+	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176	+	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
177
178	<	// caclulate the number of atoms, bonds, bends and torsions
178	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
181	>	molInfo.myBends = new Bend * [molInfo.nBends];
182	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
183
184	<	tot_atoms = 0;
185	<	tot_bonds = 0;
186	<	tot_bends = 0;
284	<	tot_torsions = 0;
285	<	for( i=0; i<n_components; i++ ){
286	<
287	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
288	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
289	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
290	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
291	<	}
184	>	theBonds = new bond_pair[molInfo.nBonds];
185	>	theBends = new bend_set[molInfo.nBends];
186	>	theTorsions = new torsion_set[molInfo.nTorsions];
187
188	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
188	>	// make the Atoms
189
190	<	simnfo->n_atoms = tot_atoms;
191	<	simnfo->n_bonds = tot_bonds;
192	<	simnfo->n_bends = tot_bends;
193	<	simnfo->n_torsions = tot_torsions;
194	<	simnfo->n_SRI = tot_SRI;
195	<	simnfo->n_mol = tot_nmol;
190	>	for (j = 0; j < molInfo.nAtoms; j++){
191	>	currentAtom = comp_stamps[stampID]->getAtom(j);
192	>	if (currentAtom->haveOrientation()){
193	>	dAtom = new DirectionalAtom((j + atomOffset),
194	>	info[k].getConfiguration());
195	>	info[k].n_oriented++;
196	>	molInfo.myAtoms[j] = dAtom;
197
198	<
199	<	#ifdef IS_MPI
198	>	ux = currentAtom->getOrntX();
199	>	uy = currentAtom->getOrntY();
200	>	uz = currentAtom->getOrntZ();
201
202	<	// divide the molecules among processors here.
306	<
307	<	mpiSim = new mpiSimulation( simnfo );
308	<
309	<
202	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
203
204	<	globalIndex = mpiSim->divideLabor();
204	>	u = sqrt(uSqr);
205	>	ux = ux / u;
206	>	uy = uy / u;
207	>	uz = uz / u;
208
209	<	// set up the local variables
210	<
211	<	int localMol, allMol;
212	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
209	>	dAtom->setSUx(ux);
210	>	dAtom->setSUy(uy);
211	>	dAtom->setSUz(uz);
212	>	}
213	>	else{
214	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
215	>	info[k].getConfiguration());
216	>	}
217	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
218
219	<	int* mol2proc = mpiSim->getMolToProcMap();
319	<	int* molCompType = mpiSim->getMolComponentType();
320	<
321	<	allMol = 0;
322	<	localMol = 0;
323	<	local_atoms = 0;
324	<	local_bonds = 0;
325	<	local_bends = 0;
326	<	local_torsions = 0;
327	<	for( i=0; i<n_components; i++ ){
219	>	#ifdef IS_MPI
220
221	<	for( j=0; j<components_nmol[i]; j++ ){
330	<
331	<	if( mol2proc[allMol] == worldRank ){
332	<
333	<	local_atoms +=    comp_stamps[i]->getNAtoms();
334	<	local_bonds +=    comp_stamps[i]->getNBonds();
335	<	local_bends +=    comp_stamps[i]->getNBends();
336	<	local_torsions += comp_stamps[i]->getNTorsions();
337	<	localMol++;
338	<	}
339	<	allMol++;
340	<	}
341	<	}
342	<	local_SRI = local_bonds + local_bends + local_torsions;
343	<
221	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
222
345	–	simnfo->n_atoms = mpiSim->getMyNlocal();
346	–
347	–	if( local_atoms != simnfo->n_atoms ){
348	–	sprintf( painCave.errMsg,
349	–	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
350	–	" localAtom (%d) are not equal.\n",
351	–	simnfo->n_atoms,
352	–	local_atoms );
353	–	painCave.isFatal = 1;
354	–	simError();
355	–	}
356	–
357	–	simnfo->n_bonds = local_bonds;
358	–	simnfo->n_bends = local_bends;
359	–	simnfo->n_torsions = local_torsions;
360	–	simnfo->n_SRI = local_SRI;
361	–	simnfo->n_mol = localMol;
362	–
363	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
364	–	MPIcheckPoint();
365	–
366	–
223		#endif // is_mpi
224	<
224	>	}
225
226	<	// create the atom and short range interaction arrays
226	>	// make the bonds
227	>	for (j = 0; j < molInfo.nBonds; j++){
228	>	currentBond = comp_stamps[stampID]->getBond(j);
229	>	theBonds[j].a = currentBond->getA() + atomOffset;
230	>	theBonds[j].b = currentBond->getB() + atomOffset;
231
232	<	Atom::createArrays(simnfo->n_atoms);
233	<	the_atoms = new Atom*[simnfo->n_atoms];
374	<	the_molecules = new Molecule[simnfo->n_mol];
375	<	int molIndex;
232	>	exI = theBonds[j].a;
233	>	exJ = theBonds[j].b;
234
235	<	// initialize the molecule's stampID's
236	<
235	>	// exclude_I must always be the smaller of the pair
236	>	if (exI > exJ){
237	>	tempEx = exI;
238	>	exI = exJ;
239	>	exJ = tempEx;
240	>	}
241		#ifdef IS_MPI
242	<
242	>	tempEx = exI;
243	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
244	>	tempEx = exJ;
245	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
246
247	<	molIndex = 0;
248	<	for(i=0; i<mpiSim->getTotNmol(); i++){
384	<
385	<	if(mol2proc[i] == worldRank ){
386	<	the_molecules[molIndex].setStampID( molCompType[i] );
387	<	the_molecules[molIndex].setMyIndex( molIndex );
388	<	the_molecules[molIndex].setGlobalIndex( i );
389	<	molIndex++;
390	<	}
391	<	}
247	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
248	>	#else  // isn't MPI
249
250	<	#else // is_mpi
251	<
252	<	molIndex = 0;
253	<	for(i=0; i<n_components; i++){
397	<	for(j=0; j<components_nmol[i]; j++ ){
398	<	the_molecules[molIndex].setStampID( i );
399	<	the_molecules[molIndex].setMyIndex( molIndex );
400	<	the_molecules[molIndex].setGlobalIndex( molIndex );
401	<	molIndex++;
402	<	}
403	<	}
404	<
250	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
251	>	#endif  //is_mpi
252	>	}
253	>	excludeOffset += molInfo.nBonds;
254
255	<	#endif // is_mpi
255	>	//make the bends
256	>	for (j = 0; j < molInfo.nBends; j++){
257	>	currentBend = comp_stamps[stampID]->getBend(j);
258	>	theBends[j].a = currentBend->getA() + atomOffset;
259	>	theBends[j].b = currentBend->getB() + atomOffset;
260	>	theBends[j].c = currentBend->getC() + atomOffset;
261
262	+	if (currentBend->haveExtras()){
263	+	extras = currentBend->getExtras();
264	+	current_extra = extras;
265
266	<	if( simnfo->n_SRI ){
267	<
268	<	Exclude::createArray(simnfo->n_SRI);
269	<	the_excludes = new Exclude*[simnfo->n_SRI];
270	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
271	<	simnfo->globalExcludes = new int;
272	<	simnfo->n_exclude = simnfo->n_SRI;
416	<	}
417	<	else{
418	<
419	<	Exclude::createArray( 1 );
420	<	the_excludes = new Exclude*;
421	<	the_excludes[0] = new Exclude(0);
422	<	the_excludes[0]->setPair( 0,0 );
423	<	simnfo->globalExcludes = new int;
424	<	simnfo->globalExcludes[0] = 0;
425	<	simnfo->n_exclude = 0;
426	<	}
266	>	while (current_extra != NULL){
267	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
268	>	switch (current_extra->getType()){
269	>	case 0:
270	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
271	>	theBends[j].isGhost = 1;
272	>	break;
273
274	<	// set the arrays into the SimInfo object
274	>	case 1:
275	>	theBends[j].ghost = (int) current_extra->getDouble() +
276	>	atomOffset;
277	>	theBends[j].isGhost = 1;
278	>	break;
279
280	<	simnfo->atoms = the_atoms;
281	<	simnfo->molecules = the_molecules;
282	<	simnfo->nGlobalExcludes = 0;
283	<	simnfo->excludes = the_excludes;
280	>	default:
281	>	sprintf(painCave.errMsg,
282	>	"SimSetup Error: ghostVectorSource was neither a "
283	>	"double nor an int.\n"
284	>	"-->Bend[%d] in %s\n",
285	>	j, comp_stamps[stampID]->getID());
286	>	painCave.isFatal = 1;
287	>	simError();
288	>	}
289	>	}
290	>	else{
291	>	sprintf(painCave.errMsg,
292	>	"SimSetup Error: unhandled bend assignment:\n"
293	>	"    -->%s in Bend[%d] in %s\n",
294	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298
299	+	current_extra = current_extra->getNext();
300	+	}
301	+	}
302
303	<	// get some of the tricky things that may still be in the globals
303	>	if (!theBends[j].isGhost){
304	>	exI = theBends[j].a;
305	>	exJ = theBends[j].c;
306	>	}
307	>	else{
308	>	exI = theBends[j].a;
309	>	exJ = theBends[j].b;
310	>	}
311
312	<
313	<	if( the_globals->haveBox() ){
314	<	simnfo->box_x = the_globals->getBox();
315	<	simnfo->box_y = the_globals->getBox();
316	<	simnfo->box_z = the_globals->getBox();
317	<	}
318	<	else if( the_globals->haveDensity() ){
312	>	// exclude_I must always be the smaller of the pair
313	>	if (exI > exJ){
314	>	tempEx = exI;
315	>	exI = exJ;
316	>	exJ = tempEx;
317	>	}
318	>	#ifdef IS_MPI
319	>	tempEx = exI;
320	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
321	>	tempEx = exJ;
322	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
323
324	<	double vol;
325	<	vol = (double)tot_nmol / the_globals->getDensity();
326	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
327	<	simnfo->box_y = simnfo->box_x;
328	<	simnfo->box_z = simnfo->box_x;
329	<	}
452	<	else{
453	<	if( !the_globals->haveBoxX() ){
454	<	sprintf( painCave.errMsg,
455	<	"SimSetup error, no periodic BoxX size given.\n" );
456	<	painCave.isFatal = 1;
457	<	simError();
458	<	}
459	<	simnfo->box_x = the_globals->getBoxX();
324	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
325	>	#else  // isn't MPI
326	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
327	>	#endif  //is_mpi
328	>	}
329	>	excludeOffset += molInfo.nBends;
330
331	<	if( !the_globals->haveBoxY() ){
332	<	sprintf( painCave.errMsg,
333	<	"SimSetup error, no periodic BoxY size given.\n" );
334	<	painCave.isFatal = 1;
335	<	simError();
336	<	}
467	<	simnfo->box_y = the_globals->getBoxY();
331	>	for (j = 0; j < molInfo.nTorsions; j++){
332	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
333	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
334	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
335	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
336	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
337
338	<	if( !the_globals->haveBoxZ() ){
339	<	sprintf( painCave.errMsg,
471	<	"SimSetup error, no periodic BoxZ size given.\n" );
472	<	painCave.isFatal = 1;
473	<	simError();
474	<	}
475	<	simnfo->box_z = the_globals->getBoxZ();
476	<	}
338	>	exI = theTorsions[j].a;
339	>	exJ = theTorsions[j].d;
340
341	+	// exclude_I must always be the smaller of the pair
342	+	if (exI > exJ){
343	+	tempEx = exI;
344	+	exI = exJ;
345	+	exJ = tempEx;
346	+	}
347		#ifdef IS_MPI
348	<	strcpy( checkPointMsg, "Box size set up" );
349	<	MPIcheckPoint();
350	<	#endif // is_mpi
348	>	tempEx = exI;
349	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
350	>	tempEx = exJ;
351	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
352
353	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
354	+	#else  // isn't MPI
355	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
356	+	#endif  //is_mpi
357	+	}
358	+	excludeOffset += molInfo.nTorsions;
359
484	–	// initialize the arrays
360
361	<	the_ff->setSimInfo( simnfo );
361	>	// send the arrays off to the forceField for init.
362
363	<	makeMolecules();
364	<	simnfo->identArray = new int[simnfo->n_atoms];
365	<	simnfo->molMembershipArray = new int[simnfo->n_atoms];
366	<	for(i=0; i<simnfo->n_atoms; i++){
367	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
493	<	}
494	<	for(i=0; i< simnfo->n_mol; i++) {
495	<	the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
496	<	}
497	<
498	<	if (the_globals->getUseRF() ) {
499	<	simnfo->useReactionField = 1;
500	<
501	<	if( !the_globals->haveECR() ){
502	<	sprintf( painCave.errMsg,
503	<	"SimSetup Warning: using default value of 1/2 the smallest "
504	<	"box length for the electrostaticCutoffRadius.\n"
505	<	"I hope you have a very fast processor!\n");
506	<	painCave.isFatal = 0;
507	<	simError();
508	<	double smallest;
509	<	smallest = simnfo->box_x;
510	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
511	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
512	<	simnfo->ecr = 0.5 * smallest;
513	<	} else {
514	<	simnfo->ecr        = the_globals->getECR();
515	<	}
363	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
364	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
365	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
366	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
367	>	theTorsions);
368
369	<	if( !the_globals->haveEST() ){
370	<	sprintf( painCave.errMsg,
371	<	"SimSetup Warning: using default value of 0.05 * the "
372	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
373	<	);
374	<	painCave.isFatal = 0;
375	<	simError();
376	<	simnfo->est = 0.05 * simnfo->ecr;
525	<	} else {
526	<	simnfo->est        = the_globals->getEST();
369	>
370	>	info[k].molecules[i].initialize(molInfo);
371	>
372	>
373	>	atomOffset += molInfo.nAtoms;
374	>	delete[] theBonds;
375	>	delete[] theBends;
376	>	delete[] theTorsions;
377		}
378	<
529	<	if(!the_globals->haveDielectric() ){
530	<	sprintf( painCave.errMsg,
531	<	"SimSetup Error: You are trying to use Reaction Field without"
532	<	"setting a dielectric constant!\n"
533	<	);
534	<	painCave.isFatal = 1;
535	<	simError();
536	<	}
537	<	simnfo->dielectric = the_globals->getDielectric();
538	<	} else {
539	<	if (usesDipoles) {
540	<
541	<	if( !the_globals->haveECR() ){
542	<	sprintf( painCave.errMsg,
543	<	"SimSetup Warning: using default value of 1/2 the smallest "
544	<	"box length for the electrostaticCutoffRadius.\n"
545	<	"I hope you have a very fast processor!\n");
546	<	painCave.isFatal = 0;
547	<	simError();
548	<	double smallest;
549	<	smallest = simnfo->box_x;
550	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
551	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
552	<	simnfo->ecr = 0.5 * smallest;
553	<	} else {
554	<	simnfo->ecr        = the_globals->getECR();
555	<	}
556	<
557	<	if( !the_globals->haveEST() ){
558	<	sprintf( painCave.errMsg,
559	<	"SimSetup Warning: using default value of 5%% of the "
560	<	"electrostaticCutoffRadius for the "
561	<	"electrostaticSkinThickness\n"
562	<	);
563	<	painCave.isFatal = 0;
564	<	simError();
565	<	simnfo->est = 0.05 * simnfo->ecr;
566	<	} else {
567	<	simnfo->est        = the_globals->getEST();
568	<	}
569	<	}
570	<	}
378	>	}
379
380		#ifdef IS_MPI
381	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
381	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
382		MPIcheckPoint();
383		#endif // is_mpi
384
385	<	if( the_globals->haveInitialConfig() ){
578	<
579	<	InitializeFromFile* fileInit;
580	<	#ifdef IS_MPI // is_mpi
581	<	if( worldRank == 0 ){
582	<	#endif //is_mpi
583	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
584	<	#ifdef IS_MPI
585	<	}else fileInit = new InitializeFromFile( NULL );
586	<	#endif
587	<	fileInit->read_xyz( simnfo ); // default velocities on
385	>	// clean up the forcefield
386
387	<	delete fileInit;
388	<	}
389	<	else{
387	>	the_ff->calcRcut();
388	>	the_ff->cleanMe();
389	>	}
390
391	<	#ifdef IS_MPI
391	>	void SimSetup::initFromBass(void){
392	>	int i, j, k;
393	>	int n_cells;
394	>	double cellx, celly, cellz;
395	>	double temp1, temp2, temp3;
396	>	int n_per_extra;
397	>	int n_extra;
398	>	int have_extra, done;
399
400	<	// no init from bass
401	<
402	<	sprintf( painCave.errMsg,
403	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
599	<	painCave.isFatal;
600	<	simError();
601	<
602	<	#else
400	>	double vel[3];
401	>	vel[0] = 0.0;
402	>	vel[1] = 0.0;
403	>	vel[2] = 0.0;
404
405	<	initFromBass();
405	>	temp1 = (double) tot_nmol / 4.0;
406	>	temp2 = pow(temp1, (1.0 / 3.0));
407	>	temp3 = ceil(temp2);
408
409	+	have_extra = 0;
410	+	if (temp2 < temp3){
411	+	// we have a non-complete lattice
412	+	have_extra = 1;
413
414	<	#endif
415	<	}
414	>	n_cells = (int) temp3 - 1;
415	>	cellx = info[0].boxL[0] / temp3;
416	>	celly = info[0].boxL[1] / temp3;
417	>	cellz = info[0].boxL[2] / temp3;
418	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
419	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
420	>	n_per_extra = (int) ceil(temp1);
421
422	<	#ifdef IS_MPI
423	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
424	<	MPIcheckPoint();
425	<	#endif // is_mpi
426	<
427	<
616	<
617	<
618	<
619	<
620	<
621	<	#ifdef IS_MPI
622	<	if( worldRank == 0 ){
623	<	#endif // is_mpi
624	<
625	<	if( the_globals->haveFinalConfig() ){
626	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
422	>	if (n_per_extra > 4){
423	>	sprintf(painCave.errMsg,
424	>	"SimSetup error. There has been an error in constructing"
425	>	" the non-complete lattice.\n");
426	>	painCave.isFatal = 1;
427	>	simError();
428		}
628	–	else{
629	–	strcpy( simnfo->finalName, inFileName );
630	–	char* endTest;
631	–	int nameLength = strlen( simnfo->finalName );
632	–	endTest = &(simnfo->finalName[nameLength - 5]);
633	–	if( !strcmp( endTest, ".bass" ) ){
634	–	strcpy( endTest, ".eor" );
635	–	}
636	–	else if( !strcmp( endTest, ".BASS" ) ){
637	–	strcpy( endTest, ".eor" );
638	–	}
639	–	else{
640	–	endTest = &(simnfo->finalName[nameLength - 4]);
641	–	if( !strcmp( endTest, ".bss" ) ){
642	–	strcpy( endTest, ".eor" );
643	–	}
644	–	else if( !strcmp( endTest, ".mdl" ) ){
645	–	strcpy( endTest, ".eor" );
646	–	}
647	–	else{
648	–	strcat( simnfo->finalName, ".eor" );
649	–	}
650	–	}
651	–	}
652	–
653	–	// make the sample and status out names
654	–
655	–	strcpy( simnfo->sampleName, inFileName );
656	–	char* endTest;
657	–	int nameLength = strlen( simnfo->sampleName );
658	–	endTest = &(simnfo->sampleName[nameLength - 5]);
659	–	if( !strcmp( endTest, ".bass" ) ){
660	–	strcpy( endTest, ".dump" );
661	–	}
662	–	else if( !strcmp( endTest, ".BASS" ) ){
663	–	strcpy( endTest, ".dump" );
664	–	}
665	–	else{
666	–	endTest = &(simnfo->sampleName[nameLength - 4]);
667	–	if( !strcmp( endTest, ".bss" ) ){
668	–	strcpy( endTest, ".dump" );
669	–	}
670	–	else if( !strcmp( endTest, ".mdl" ) ){
671	–	strcpy( endTest, ".dump" );
672	–	}
673	–	else{
674	–	strcat( simnfo->sampleName, ".dump" );
675	–	}
676	–	}
677	–
678	–	strcpy( simnfo->statusName, inFileName );
679	–	nameLength = strlen( simnfo->statusName );
680	–	endTest = &(simnfo->statusName[nameLength - 5]);
681	–	if( !strcmp( endTest, ".bass" ) ){
682	–	strcpy( endTest, ".stat" );
683	–	}
684	–	else if( !strcmp( endTest, ".BASS" ) ){
685	–	strcpy( endTest, ".stat" );
686	–	}
687	–	else{
688	–	endTest = &(simnfo->statusName[nameLength - 4]);
689	–	if( !strcmp( endTest, ".bss" ) ){
690	–	strcpy( endTest, ".stat" );
691	–	}
692	–	else if( !strcmp( endTest, ".mdl" ) ){
693	–	strcpy( endTest, ".stat" );
694	–	}
695	–	else{
696	–	strcat( simnfo->statusName, ".stat" );
697	–	}
698	–	}
699	–
700	–	#ifdef IS_MPI
429		}
702	–	#endif // is_mpi
703	–
704	–	// set the status, sample, and themal kick times
705	–
706	–	if( the_globals->haveSampleTime() ){
707	–	simnfo->sampleTime = the_globals->getSampleTime();
708	–	simnfo->statusTime = simnfo->sampleTime;
709	–	simnfo->thermalTime = simnfo->sampleTime;
710	–	}
430		else{
431	<	simnfo->sampleTime = the_globals->getRunTime();
432	<	simnfo->statusTime = simnfo->sampleTime;
433	<	simnfo->thermalTime = simnfo->sampleTime;
431	>	n_cells = (int) temp3;
432	>	cellx = info[0].boxL[0] / temp3;
433	>	celly = info[0].boxL[1] / temp3;
434	>	cellz = info[0].boxL[2] / temp3;
435		}
436
437	<	if( the_globals->haveStatusTime() ){
438	<	simnfo->statusTime = the_globals->getStatusTime();
439	<	}
437	>	current_mol = 0;
438	>	current_comp_mol = 0;
439	>	current_comp = 0;
440	>	current_atom_ndx = 0;
441
442	<	if( the_globals->haveThermalTime() ){
443	<	simnfo->thermalTime = the_globals->getThermalTime();
442	>	for (i = 0; i < n_cells ; i++){
443	>	for (j = 0; j < n_cells; j++){
444	>	for (k = 0; k < n_cells; k++){
445	>	makeElement(i * cellx, j * celly, k * cellz);
446	>
447	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
448	>
449	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
450	>
451	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
452	>	}
453	>	}
454		}
455
456	<	// check for the temperature set flag
456	>	if (have_extra){
457	>	done = 0;
458
459	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
459	>	int start_ndx;
460	>	for (i = 0; i < (n_cells + 1) && !done; i++){
461	>	for (j = 0; j < (n_cells + 1) && !done; j++){
462	>	if (i < n_cells){
463	>	if (j < n_cells){
464	>	start_ndx = n_cells;
465	>	}
466	>	else
467	>	start_ndx = 0;
468	>	}
469	>	else
470	>	start_ndx = 0;
471
472	+	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
473	+	makeElement(i * cellx, j * celly, k * cellz);
474	+	done = (current_mol >= tot_nmol);
475
476	<	//   // make the longe range forces and the integrator
476	>	if (!done && n_per_extra > 1){
477	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
478	>	k * cellz);
479	>	done = (current_mol >= tot_nmol);
480	>	}
481
482	<	//   new AllLong( simnfo );
482	>	if (!done && n_per_extra > 2){
483	>	makeElement(i * cellx, j * celly + 0.5 * celly,
484	>	k * cellz + 0.5 * cellz);
485	>	done = (current_mol >= tot_nmol);
486	>	}
487
488	+	if (!done && n_per_extra > 3){
489	+	makeElement(i * cellx + 0.5 * cellx, j * celly,
490	+	k * cellz + 0.5 * cellz);
491	+	done = (current_mol >= tot_nmol);
492	+	}
493	+	}
494	+	}
495	+	}
496	+	}
497
498	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
499	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
498	>	for (i = 0; i < info[0].n_atoms; i++){
499	>	info[0].atoms[i]->setVel(vel);
500		}
501	<	else if( !strcmp( force_field, "LJ" ) ){
739	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
740	<	}
741	<	else {
742	<	std::cerr << "I'm a bug.\n";
743	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
744	<	}
745	<	#ifdef IS_MPI
746	<	mpiSim->mpiRefresh();
747	<	#endif
501	>	}
502
503	<	// initialize the Fortran
503	>	void SimSetup::makeElement(double x, double y, double z){
504	>	int k;
505	>	AtomStamp* current_atom;
506	>	DirectionalAtom* dAtom;
507	>	double rotMat[3][3];
508	>	double pos[3];
509
510	+	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
511	+	current_atom = comp_stamps[current_comp]->getAtom(k);
512	+	if (!current_atom->havePosition()){
513	+	sprintf(painCave.errMsg,
514	+	"SimSetup:initFromBass error.\n"
515	+	"\tComponent %s, atom %s does not have a position specified.\n"
516	+	"\tThe initialization routine is unable to give a start"
517	+	" position.\n",
518	+	comp_stamps[current_comp]->getID(), current_atom->getType());
519	+	painCave.isFatal = 1;
520	+	simError();
521	+	}
522
523	<	simnfo->refreshSim();
524	<
525	<	if( !strcmp( simnfo->mixingRule, "standard") ){
526	<	the_ff->initForceField( LB_MIXING_RULE );
523	>	pos[0] = x + current_atom->getPosX();
524	>	pos[1] = y + current_atom->getPosY();
525	>	pos[2] = z + current_atom->getPosZ();
526	>
527	>	info[0].atoms[current_atom_ndx]->setPos(pos);
528	>
529	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
530	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
531	>
532	>	rotMat[0][0] = 1.0;
533	>	rotMat[0][1] = 0.0;
534	>	rotMat[0][2] = 0.0;
535	>
536	>	rotMat[1][0] = 0.0;
537	>	rotMat[1][1] = 1.0;
538	>	rotMat[1][2] = 0.0;
539	>
540	>	rotMat[2][0] = 0.0;
541	>	rotMat[2][1] = 0.0;
542	>	rotMat[2][2] = 1.0;
543	>
544	>	dAtom->setA(rotMat);
545	>	}
546	>
547	>	current_atom_ndx++;
548		}
757	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
758	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
759	–	}
760	–	else{
761	–	sprintf( painCave.errMsg,
762	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
763	–	simnfo->mixingRule );
764	–	painCave.isFatal = 1;
765	–	simError();
766	–	}
549
550	+	current_mol++;
551	+	current_comp_mol++;
552
553	<	#ifdef IS_MPI
554	<	strcpy( checkPointMsg,
555	<	"Successfully intialized the mixingRule for Fortran." );
556	<	MPIcheckPoint();
773	<	#endif // is_mpi
553	>	if (current_comp_mol >= components_nmol[current_comp]){
554	>	current_comp_mol = 0;
555	>	current_comp++;
556	>	}
557		}
558
559
560	<	void SimSetup::makeMolecules( void ){
560	>	void SimSetup::gatherInfo(void){
561	>	int i;
562
563	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
564	<	molInit info;
781	<	DirectionalAtom* dAtom;
782	<	LinkedAssign* extras;
783	<	LinkedAssign* current_extra;
784	<	AtomStamp* currentAtom;
785	<	BondStamp* currentBond;
786	<	BendStamp* currentBend;
787	<	TorsionStamp* currentTorsion;
563	>	ensembleCase = -1;
564	>	ffCase = -1;
565
566	<	bond_pair* theBonds;
790	<	bend_set* theBends;
791	<	torsion_set* theTorsions;
566	>	// set the easy ones first
567
568	<
569	<	//init the forceField paramters
568	>	for (i = 0; i < nInfo; i++){
569	>	info[i].target_temp = globals->getTargetTemp();
570	>	info[i].dt = globals->getDt();
571	>	info[i].run_time = globals->getRunTime();
572	>	}
573	>	n_components = globals->getNComponents();
574
796	–	the_ff->readParams();
575
576	<
799	<	// init the atoms
576	>	// get the forceField
577
578	<	double ux, uy, uz, u, uSqr;
802	<
803	<	atomOffset = 0;
804	<	excludeOffset = 0;
805	<	for(i=0; i<simnfo->n_mol; i++){
806	<
807	<	stampID = the_molecules[i].getStampID();
578	>	strcpy(force_field, globals->getForceField());
579
580	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
581	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
582	<	info.nBends    = comp_stamps[stampID]->getNBends();
583	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
584	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
580	>	if (!strcasecmp(force_field, "DUFF")){
581	>	ffCase = FF_DUFF;
582	>	}
583	>	else if (!strcasecmp(force_field, "LJ")){
584	>	ffCase = FF_LJ;
585	>	}
586	>	else if (!strcasecmp(force_field, "EAM")){
587	>	ffCase = FF_EAM;
588	>	}
589	>	else{
590	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
591	>	force_field);
592	>	painCave.isFatal = 1;
593	>	simError();
594	>	}
595
596	<	info.myAtoms = &the_atoms[atomOffset];
816	<	info.myExcludes = &the_excludes[excludeOffset];
817	<	info.myBonds = new Bond*[info.nBonds];
818	<	info.myBends = new Bend*[info.nBends];
819	<	info.myTorsions = new Torsion*[info.nTorsions];
596	>	// get the ensemble
597
598	<	theBonds = new bond_pair[info.nBonds];
822	<	theBends = new bend_set[info.nBends];
823	<	theTorsions = new torsion_set[info.nTorsions];
824	<
825	<	// make the Atoms
826	<
827	<	for(j=0; j<info.nAtoms; j++){
828	<
829	<	currentAtom = comp_stamps[stampID]->getAtom( j );
830	<	if( currentAtom->haveOrientation() ){
831	<
832	<	dAtom = new DirectionalAtom(j + atomOffset);
833	<	simnfo->n_oriented++;
834	<	info.myAtoms[j] = dAtom;
835	<
836	<	ux = currentAtom->getOrntX();
837	<	uy = currentAtom->getOrntY();
838	<	uz = currentAtom->getOrntZ();
839	<
840	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
841	<
842	<	u = sqrt( uSqr );
843	<	ux = ux / u;
844	<	uy = uy / u;
845	<	uz = uz / u;
846	<
847	<	dAtom->setSUx( ux );
848	<	dAtom->setSUy( uy );
849	<	dAtom->setSUz( uz );
850	<	}
851	<	else{
852	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
853	<	}
854	<	info.myAtoms[j]->setType( currentAtom->getType() );
855	<
856	<	#ifdef IS_MPI
857	<
858	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
859	<
860	<	#endif // is_mpi
861	<	}
862	<
863	<	// make the bonds
864	<	for(j=0; j<info.nBonds; j++){
865	<
866	<	currentBond = comp_stamps[stampID]->getBond( j );
867	<	theBonds[j].a = currentBond->getA() + atomOffset;
868	<	theBonds[j].b = currentBond->getB() + atomOffset;
598	>	strcpy(ensemble, globals->getEnsemble());
599
600	<	exI = theBonds[j].a;
601	<	exJ = theBonds[j].b;
600	>	if (!strcasecmp(ensemble, "NVE")){
601	>	ensembleCase = NVE_ENS;
602	>	}
603	>	else if (!strcasecmp(ensemble, "NVT")){
604	>	ensembleCase = NVT_ENS;
605	>	}
606	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
607	>	ensembleCase = NPTi_ENS;
608	>	}
609	>	else if (!strcasecmp(ensemble, "NPTf")){
610	>	ensembleCase = NPTf_ENS;
611	>	}
612	>	else if (!strcasecmp(ensemble, "NPTxyz")){
613	>	ensembleCase = NPTxyz_ENS;
614	>	}
615	>	else{
616	>	sprintf(painCave.errMsg,
617	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
618	>	"reverting to NVE for this simulation.\n",
619	>	ensemble);
620	>	painCave.isFatal = 0;
621	>	simError();
622	>	strcpy(ensemble, "NVE");
623	>	ensembleCase = NVE_ENS;
624	>	}
625
626	<	// exclude_I must always be the smaller of the pair
627	<	if( exI > exJ ){
628	<	tempEx = exI;
629	<	exI = exJ;
630	<	exJ = tempEx;
626	>	for (i = 0; i < nInfo; i++){
627	>	strcpy(info[i].ensemble, ensemble);
628	>
629	>	// get the mixing rule
630	>
631	>	strcpy(info[i].mixingRule, globals->getMixingRule());
632	>	info[i].usePBC = globals->getPBC();
633	>	}
634	>
635	>	// get the components and calculate the tot_nMol and indvidual n_mol
636	>
637	>	the_components = globals->getComponents();
638	>	components_nmol = new int[n_components];
639	>
640	>
641	>	if (!globals->haveNMol()){
642	>	// we don't have the total number of molecules, so we assume it is
643	>	// given in each component
644	>
645	>	tot_nmol = 0;
646	>	for (i = 0; i < n_components; i++){
647	>	if (!the_components[i]->haveNMol()){
648	>	// we have a problem
649	>	sprintf(painCave.errMsg,
650	>	"SimSetup Error. No global NMol or component NMol"
651	>	" given. Cannot calculate the number of atoms.\n");
652	>	painCave.isFatal = 1;
653	>	simError();
654		}
879	–	#ifdef IS_MPI
880	–	tempEx = exI;
881	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
882	–	tempEx = exJ;
883	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
884	–
885	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
886	–	#else  // isn't MPI
655
656	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
657	<	#endif  //is_mpi
656	>	tot_nmol += the_components[i]->getNMol();
657	>	components_nmol[i] = the_components[i]->getNMol();
658		}
659	<	excludeOffset += info.nBonds;
659	>	}
660	>	else{
661	>	sprintf(painCave.errMsg,
662	>	"SimSetup error.\n"
663	>	"\tSorry, the ability to specify total"
664	>	" nMols and then give molfractions in the components\n"
665	>	"\tis not currently supported."
666	>	" Please give nMol in the components.\n");
667	>	painCave.isFatal = 1;
668	>	simError();
669	>	}
670
671	<	//make the bends
672	<	for(j=0; j<info.nBends; j++){
673	<
674	<	currentBend = comp_stamps[stampID]->getBend( j );
675	<	theBends[j].a = currentBend->getA() + atomOffset;
676	<	theBends[j].b = currentBend->getB() + atomOffset;
677	<	theBends[j].c = currentBend->getC() + atomOffset;
900	<
901	<	if( currentBend->haveExtras() ){
902	<
903	<	extras = currentBend->getExtras();
904	<	current_extra = extras;
905	<
906	<	while( current_extra != NULL ){
907	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
908	<
909	<	switch( current_extra->getType() ){
910	<
911	<	case 0:
912	<	theBends[j].ghost =
913	<	current_extra->getInt() + atomOffset;
914	<	theBends[j].isGhost = 1;
915	<	break;
916	<
917	<	case 1:
918	<	theBends[j].ghost =
919	<	(int)current_extra->getDouble() + atomOffset;
920	<	theBends[j].isGhost = 1;
921	<	break;
922	<
923	<	default:
924	<	sprintf( painCave.errMsg,
925	<	"SimSetup Error: ghostVectorSource was neither a "
926	<	"double nor an int.\n"
927	<	"-->Bend[%d] in %s\n",
928	<	j, comp_stamps[stampID]->getID() );
929	<	painCave.isFatal = 1;
930	<	simError();
931	<	}
932	<	}
933	<
934	<	else{
935	<
936	<	sprintf( painCave.errMsg,
937	<	"SimSetup Error: unhandled bend assignment:\n"
938	<	"    -->%s in Bend[%d] in %s\n",
939	<	current_extra->getlhs(),
940	<	j, comp_stamps[stampID]->getID() );
941	<	painCave.isFatal = 1;
942	<	simError();
943	<	}
944	<
945	<	current_extra = current_extra->getNext();
946	<	}
947	<	}
948	<
949	<	if( !theBends[j].isGhost ){
950	<
951	<	exI = theBends[j].a;
952	<	exJ = theBends[j].c;
953	<	}
954	<	else{
955	<
956	<	exI = theBends[j].a;
957	<	exJ = theBends[j].b;
958	<	}
959	<
960	<	// exclude_I must always be the smaller of the pair
961	<	if( exI > exJ ){
962	<	tempEx = exI;
963	<	exI = exJ;
964	<	exJ = tempEx;
965	<	}
966	<	#ifdef IS_MPI
967	<	tempEx = exI;
968	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
969	<	tempEx = exJ;
970	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
971	<
972	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
973	<	#else  // isn't MPI
974	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
975	<	#endif  //is_mpi
671	>	// set the status, sample, and thermal kick times
672	>
673	>	for (i = 0; i < nInfo; i++){
674	>	if (globals->haveSampleTime()){
675	>	info[i].sampleTime = globals->getSampleTime();
676	>	info[i].statusTime = info[i].sampleTime;
677	>	info[i].thermalTime = info[i].sampleTime;
678		}
679	<	excludeOffset += info.nBends;
679	>	else{
680	>	info[i].sampleTime = globals->getRunTime();
681	>	info[i].statusTime = info[i].sampleTime;
682	>	info[i].thermalTime = info[i].sampleTime;
683	>	}
684
685	<	for(j=0; j<info.nTorsions; j++){
686	<
687	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
982	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
983	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
984	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
985	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
986	<
987	<	exI = theTorsions[j].a;
988	<	exJ = theTorsions[j].d;
685	>	if (globals->haveStatusTime()){
686	>	info[i].statusTime = globals->getStatusTime();
687	>	}
688
689	<	// exclude_I must always be the smaller of the pair
690	<	if( exI > exJ ){
992	<	tempEx = exI;
993	<	exI = exJ;
994	<	exJ = tempEx;
995	<	}
996	<	#ifdef IS_MPI
997	<	tempEx = exI;
998	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
999	<	tempEx = exJ;
1000	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1001	<
1002	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1003	<	#else  // isn't MPI
1004	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1005	<	#endif  //is_mpi
689	>	if (globals->haveThermalTime()){
690	>	info[i].thermalTime = globals->getThermalTime();
691		}
1007	–	excludeOffset += info.nTorsions;
692
693	+	info[i].resetIntegrator = 0;
694	+	if( globals->haveResetTime() ){
695	+	info[i].resetTime = globals->getResetTime();
696	+	info[i].resetIntegrator = 1;
697	+	}
698	+
699	+	// check for the temperature set flag
700
701	<	// send the arrays off to the forceField for init.
701	>	if (globals->haveTempSet())
702	>	info[i].setTemp = globals->getTempSet();
703	>
704	>	}
705	>
706	>	//setup seed for random number generator
707	>	int seedValue;
708
709	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
710	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1014	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1015	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
709	>	if (globals->haveSeed()){
710	>	seedValue = globals->getSeed();
711
712	+	if(seedValue / 1E9 == 0){
713	+	sprintf(painCave.errMsg,
714	+	"Seed for sprng library should contain at least 9 digits\n"
715	+	"OOPSE will generate a seed for user\n");
716	+	painCave.isFatal = 0;
717	+	simError();
718
719	<	the_molecules[i].initialize( info );
719	>	//using seed generated by system instead of invalid seed set by user
720	>	#ifndef IS_MPI
721	>	seedValue = make_sprng_seed();
722	>	#else
723	>	if (worldRank == 0){
724	>	seedValue = make_sprng_seed();
725	>	}
726	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
727	>	#endif
728	>	}
729	>	}//end of if branch of globals->haveSeed()
730	>	else{
731	>
732	>	#ifndef IS_MPI
733	>	seedValue = make_sprng_seed();
734	>	#else
735	>	if (worldRank == 0){
736	>	seedValue = make_sprng_seed();
737	>	}
738	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
739	>	#endif
740	>	}//end of globals->haveSeed()
741
742	<
743	<	atomOffset += info.nAtoms;
1022	<	delete[] theBonds;
1023	<	delete[] theBends;
1024	<	delete[] theTorsions;
742	>	for (int i = 0; i < nInfo; i++){
743	>	info[i].setSeed(seedValue);
744		}
745
746		#ifdef IS_MPI
747	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
747	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
748		MPIcheckPoint();
749		#endif // is_mpi
750	+	}
751
1032	–	// clean up the forcefield
1033	–	the_ff->calcRcut();
1034	–	the_ff->cleanMe();
752
753	<	}
753	>	void SimSetup::finalInfoCheck(void){
754	>	int index;
755	>	int usesDipoles;
756	>	int i;
757
758	<	void SimSetup::initFromBass( void ){
758	>	for (i = 0; i < nInfo; i++){
759	>	// check electrostatic parameters
760
761	<	int i, j, k;
762	<	int n_cells;
763	<	double cellx, celly, cellz;
764	<	double temp1, temp2, temp3;
765	<	int n_per_extra;
766	<	int n_extra;
1046	<	int have_extra, done;
761	>	index = 0;
762	>	usesDipoles = 0;
763	>	while ((index < info[i].n_atoms) && !usesDipoles){
764	>	usesDipoles = (info[i].atoms[index])->hasDipole();
765	>	index++;
766	>	}
767
768	<	temp1 = (double)tot_nmol / 4.0;
769	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
770	<	temp3 = ceil( temp2 );
768	>	#ifdef IS_MPI
769	>	int myUse = usesDipoles;
770	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
771	>	#endif //is_mpi
772
773	<	have_extra =0;
1053	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1054	<	have_extra =1;
773	>	double theEcr, theEst;
774
775	<	n_cells = (int)temp3 - 1;
776	<	cellx = simnfo->box_x / temp3;
1058	<	celly = simnfo->box_y / temp3;
1059	<	cellz = simnfo->box_z / temp3;
1060	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1061	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1062	<	n_per_extra = (int)ceil( temp1 );
775	>	if (globals->getUseRF()){
776	>	info[i].useReactionField = 1;
777
778	<	if( n_per_extra > 4){
779	<	sprintf( painCave.errMsg,
780	<	"SimSetup error. There has been an error in constructing"
781	<	" the non-complete lattice.\n" );
782	<	painCave.isFatal = 1;
783	<	simError();
778	>	if (!globals->haveECR()){
779	>	sprintf(painCave.errMsg,
780	>	"SimSetup Warning: using default value of 1/2 the smallest "
781	>	"box length for the electrostaticCutoffRadius.\n"
782	>	"I hope you have a very fast processor!\n");
783	>	painCave.isFatal = 0;
784	>	simError();
785	>	double smallest;
786	>	smallest = info[i].boxL[0];
787	>	if (info[i].boxL[1] <= smallest)
788	>	smallest = info[i].boxL[1];
789	>	if (info[i].boxL[2] <= smallest)
790	>	smallest = info[i].boxL[2];
791	>	theEcr = 0.5 * smallest;
792	>	}
793	>	else{
794	>	theEcr = globals->getECR();
795	>	}
796	>
797	>	if (!globals->haveEST()){
798	>	sprintf(painCave.errMsg,
799	>	"SimSetup Warning: using default value of 0.05 * the "
800	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
801	>	painCave.isFatal = 0;
802	>	simError();
803	>	theEst = 0.05 * theEcr;
804	>	}
805	>	else{
806	>	theEst = globals->getEST();
807	>	}
808	>
809	>	info[i].setDefaultEcr(theEcr, theEst);
810	>
811	>	if (!globals->haveDielectric()){
812	>	sprintf(painCave.errMsg,
813	>	"SimSetup Error: You are trying to use Reaction Field without"
814	>	"setting a dielectric constant!\n");
815	>	painCave.isFatal = 1;
816	>	simError();
817	>	}
818	>	info[i].dielectric = globals->getDielectric();
819		}
820	+	else{
821	+	if (usesDipoles){
822	+	if (!globals->haveECR()){
823	+	sprintf(painCave.errMsg,
824	+	"SimSetup Warning: using default value of 1/2 the smallest "
825	+	"box length for the electrostaticCutoffRadius.\n"
826	+	"I hope you have a very fast processor!\n");
827	+	painCave.isFatal = 0;
828	+	simError();
829	+	double smallest;
830	+	smallest = info[i].boxL[0];
831	+	if (info[i].boxL[1] <= smallest)
832	+	smallest = info[i].boxL[1];
833	+	if (info[i].boxL[2] <= smallest)
834	+	smallest = info[i].boxL[2];
835	+	theEcr = 0.5 * smallest;
836	+	}
837	+	else{
838	+	theEcr = globals->getECR();
839	+	}
840	+
841	+	if (!globals->haveEST()){
842	+	sprintf(painCave.errMsg,
843	+	"SimSetup Warning: using default value of 0.05 * the "
844	+	"electrostaticCutoffRadius for the "
845	+	"electrostaticSkinThickness\n");
846	+	painCave.isFatal = 0;
847	+	simError();
848	+	theEst = 0.05 * theEcr;
849	+	}
850	+	else{
851	+	theEst = globals->getEST();
852	+	}
853	+
854	+	info[i].setDefaultEcr(theEcr, theEst);
855	+	}
856	+	}
857	+	info[i].checkCutOffs();
858		}
859	+
860	+	#ifdef IS_MPI
861	+	strcpy(checkPointMsg, "post processing checks out");
862	+	MPIcheckPoint();
863	+	#endif // is_mpi
864	+	}
865	+
866	+	void SimSetup::initSystemCoords(void){
867	+	int i;
868	+
869	+	char* inName;
870	+
871	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
872	+
873	+	for (i = 0; i < info[0].n_atoms; i++)
874	+	info[0].atoms[i]->setCoords();
875	+
876	+	if (globals->haveInitialConfig()){
877	+	InitializeFromFile* fileInit;
878	+	#ifdef IS_MPI // is_mpi
879	+	if (worldRank == 0){
880	+	#endif //is_mpi
881	+	inName = globals->getInitialConfig();
882	+	fileInit = new InitializeFromFile(inName);
883	+	#ifdef IS_MPI
884	+	}
885	+	else
886	+	fileInit = new InitializeFromFile(NULL);
887	+	#endif
888	+	fileInit->readInit(info); // default velocities on
889	+
890	+	delete fileInit;
891	+	}
892		else{
893	<	n_cells = (int)temp3;
894	<	cellx = simnfo->box_x / temp3;
895	<	celly = simnfo->box_y / temp3;
896	<	cellz = simnfo->box_z / temp3;
893	>	#ifdef IS_MPI
894	>
895	>	// no init from bass
896	>
897	>	sprintf(painCave.errMsg,
898	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
899	>	painCave.isFatal = 1;;
900	>	simError();
901	>
902	>	#else
903	>
904	>	initFromBass();
905	>
906	>
907	>	#endif
908		}
909
910	<	current_mol = 0;
911	<	current_comp_mol = 0;
912	<	current_comp = 0;
913	<	current_atom_ndx = 0;
910	>	#ifdef IS_MPI
911	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
912	>	MPIcheckPoint();
913	>	#endif // is_mpi
914	>	}
915
1084	–	for( i=0; i < n_cells ; i++ ){
1085	–	for( j=0; j < n_cells; j++ ){
1086	–	for( k=0; k < n_cells; k++ ){
916
917	<	makeElement( i * cellx,
918	<	j * celly,
1090	<	k * cellz );
917	>	void SimSetup::makeOutNames(void){
918	>	int k;
919
1092	–	makeElement( i * cellx + 0.5 * cellx,
1093	–	j * celly + 0.5 * celly,
1094	–	k * cellz );
920
921	<	makeElement( i * cellx,
922	<	j * celly + 0.5 * celly,
923	<	k * cellz + 0.5 * cellz );
921	>	for (k = 0; k < nInfo; k++){
922	>	#ifdef IS_MPI
923	>	if (worldRank == 0){
924	>	#endif // is_mpi
925
926	<	makeElement( i * cellx + 0.5 * cellx,
927	<	j * celly,
1102	<	k * cellz + 0.5 * cellz );
926	>	if (globals->haveFinalConfig()){
927	>	strcpy(info[k].finalName, globals->getFinalConfig());
928		}
929	+	else{
930	+	strcpy(info[k].finalName, inFileName);
931	+	char* endTest;
932	+	int nameLength = strlen(info[k].finalName);
933	+	endTest = &(info[k].finalName[nameLength - 5]);
934	+	if (!strcmp(endTest, ".bass")){
935	+	strcpy(endTest, ".eor");
936	+	}
937	+	else if (!strcmp(endTest, ".BASS")){
938	+	strcpy(endTest, ".eor");
939	+	}
940	+	else{
941	+	endTest = &(info[k].finalName[nameLength - 4]);
942	+	if (!strcmp(endTest, ".bss")){
943	+	strcpy(endTest, ".eor");
944	+	}
945	+	else if (!strcmp(endTest, ".mdl")){
946	+	strcpy(endTest, ".eor");
947	+	}
948	+	else{
949	+	strcat(info[k].finalName, ".eor");
950	+	}
951	+	}
952	+	}
953	+
954	+	// make the sample and status out names
955	+
956	+	strcpy(info[k].sampleName, inFileName);
957	+	char* endTest;
958	+	int nameLength = strlen(info[k].sampleName);
959	+	endTest = &(info[k].sampleName[nameLength - 5]);
960	+	if (!strcmp(endTest, ".bass")){
961	+	strcpy(endTest, ".dump");
962	+	}
963	+	else if (!strcmp(endTest, ".BASS")){
964	+	strcpy(endTest, ".dump");
965	+	}
966	+	else{
967	+	endTest = &(info[k].sampleName[nameLength - 4]);
968	+	if (!strcmp(endTest, ".bss")){
969	+	strcpy(endTest, ".dump");
970	+	}
971	+	else if (!strcmp(endTest, ".mdl")){
972	+	strcpy(endTest, ".dump");
973	+	}
974	+	else{
975	+	strcat(info[k].sampleName, ".dump");
976	+	}
977	+	}
978	+
979	+	strcpy(info[k].statusName, inFileName);
980	+	nameLength = strlen(info[k].statusName);
981	+	endTest = &(info[k].statusName[nameLength - 5]);
982	+	if (!strcmp(endTest, ".bass")){
983	+	strcpy(endTest, ".stat");
984	+	}
985	+	else if (!strcmp(endTest, ".BASS")){
986	+	strcpy(endTest, ".stat");
987	+	}
988	+	else{
989	+	endTest = &(info[k].statusName[nameLength - 4]);
990	+	if (!strcmp(endTest, ".bss")){
991	+	strcpy(endTest, ".stat");
992	+	}
993	+	else if (!strcmp(endTest, ".mdl")){
994	+	strcpy(endTest, ".stat");
995	+	}
996	+	else{
997	+	strcat(info[k].statusName, ".stat");
998	+	}
999	+	}
1000	+
1001	+	#ifdef IS_MPI
1002	+
1003		}
1004	+	#endif // is_mpi
1005		}
1006	+	}
1007
1107	–	if( have_extra ){
1108	–	done = 0;
1008
1009	<	int start_ndx;
1010	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1112	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1009	>	void SimSetup::sysObjectsCreation(void){
1010	>	int i, k;
1011
1012	<	if( i < n_cells ){
1012	>	// create the forceField
1013	>
1014	>	createFF();
1015	>
1016	>	// extract componentList
1017	>
1018	>	compList();
1019	>
1020	>	// calc the number of atoms, bond, bends, and torsions
1021	>
1022	>	calcSysValues();
1023	>
1024	>	#ifdef IS_MPI
1025	>	// divide the molecules among the processors
1026
1027	<	if( j < n_cells ){
1028	<	start_ndx = n_cells;
1118	<	}
1119	<	else start_ndx = 0;
1120	<	}
1121	<	else start_ndx = 0;
1027	>	mpiMolDivide();
1028	>	#endif //is_mpi
1029
1030	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1030	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1031
1032	<	makeElement( i * cellx,
1126	<	j * celly,
1127	<	k * cellz );
1128	<	done = ( current_mol >= tot_nmol );
1032	>	makeSysArrays();
1033
1034	<	if( !done && n_per_extra > 1 ){
1131	<	makeElement( i * cellx + 0.5 * cellx,
1132	<	j * celly + 0.5 * celly,
1133	<	k * cellz );
1134	<	done = ( current_mol >= tot_nmol );
1135	<	}
1034	>	// make and initialize the molecules (all but atomic coordinates)
1035
1036	<	if( !done && n_per_extra > 2){
1138	<	makeElement( i * cellx,
1139	<	j * celly + 0.5 * celly,
1140	<	k * cellz + 0.5 * cellz );
1141	<	done = ( current_mol >= tot_nmol );
1142	<	}
1036	>	makeMolecules();
1037
1038	<	if( !done && n_per_extra > 3){
1039	<	makeElement( i * cellx + 0.5 * cellx,
1040	<	j * celly,
1041	<	k * cellz + 0.5 * cellz );
1042	<	done = ( current_mol >= tot_nmol );
1043	<	}
1044	<	}
1038	>	for (k = 0; k < nInfo; k++){
1039	>	info[k].identArray = new int[info[k].n_atoms];
1040	>	for (i = 0; i < info[k].n_atoms; i++){
1041	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1042	>	}
1043	>	}
1044	>	}
1045	>
1046	>
1047	>	void SimSetup::createFF(void){
1048	>	switch (ffCase){
1049	>	case FF_DUFF:
1050	>	the_ff = new DUFF();
1051	>	break;
1052	>
1053	>	case FF_LJ:
1054	>	the_ff = new LJFF();
1055	>	break;
1056	>
1057	>	case FF_EAM:
1058	>	the_ff = new EAM_FF();
1059	>	break;
1060	>
1061	>	default:
1062	>	sprintf(painCave.errMsg,
1063	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1064	>	painCave.isFatal = 1;
1065	>	simError();
1066	>	}
1067	>
1068	>	#ifdef IS_MPI
1069	>	strcpy(checkPointMsg, "ForceField creation successful");
1070	>	MPIcheckPoint();
1071	>	#endif // is_mpi
1072	>	}
1073	>
1074	>
1075	>	void SimSetup::compList(void){
1076	>	int i;
1077	>	char* id;
1078	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1079	>	LinkedMolStamp* currentStamp = NULL;
1080	>	comp_stamps = new MoleculeStamp * [n_components];
1081	>
1082	>	// make an array of molecule stamps that match the components used.
1083	>	// also extract the used stamps out into a separate linked list
1084	>
1085	>	for (i = 0; i < nInfo; i++){
1086	>	info[i].nComponents = n_components;
1087	>	info[i].componentsNmol = components_nmol;
1088	>	info[i].compStamps = comp_stamps;
1089	>	info[i].headStamp = headStamp;
1090	>	}
1091	>
1092	>
1093	>	for (i = 0; i < n_components; i++){
1094	>	id = the_components[i]->getType();
1095	>	comp_stamps[i] = NULL;
1096	>
1097	>	// check to make sure the component isn't already in the list
1098	>
1099	>	comp_stamps[i] = headStamp->match(id);
1100	>	if (comp_stamps[i] == NULL){
1101	>	// extract the component from the list;
1102	>
1103	>	currentStamp = stamps->extractMolStamp(id);
1104	>	if (currentStamp == NULL){
1105	>	sprintf(painCave.errMsg,
1106	>	"SimSetup error: Component \"%s\" was not found in the "
1107	>	"list of declared molecules\n",
1108	>	id);
1109	>	painCave.isFatal = 1;
1110	>	simError();
1111		}
1112	+
1113	+	headStamp->add(currentStamp);
1114	+	comp_stamps[i] = headStamp->match(id);
1115		}
1116		}
1117
1118	+	#ifdef IS_MPI
1119	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1120	+	MPIcheckPoint();
1121	+	#endif // is_mpi
1122	+	}
1123
1124	<	for( i=0; i<simnfo->n_atoms; i++ ){
1125	<	simnfo->atoms[i]->set_vx( 0.0 );
1126	<	simnfo->atoms[i]->set_vy( 0.0 );
1127	<	simnfo->atoms[i]->set_vz( 0.0 );
1124	>	void SimSetup::calcSysValues(void){
1125	>	int i;
1126	>
1127	>	int* molMembershipArray;
1128	>
1129	>	tot_atoms = 0;
1130	>	tot_bonds = 0;
1131	>	tot_bends = 0;
1132	>	tot_torsions = 0;
1133	>	for (i = 0; i < n_components; i++){
1134	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1135	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1136	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1137	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1138		}
1139	+
1140	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1141	+	molMembershipArray = new int[tot_atoms];
1142	+
1143	+	for (i = 0; i < nInfo; i++){
1144	+	info[i].n_atoms = tot_atoms;
1145	+	info[i].n_bonds = tot_bonds;
1146	+	info[i].n_bends = tot_bends;
1147	+	info[i].n_torsions = tot_torsions;
1148	+	info[i].n_SRI = tot_SRI;
1149	+	info[i].n_mol = tot_nmol;
1150	+
1151	+	info[i].molMembershipArray = molMembershipArray;
1152	+	}
1153		}
1154
1155	<	void SimSetup::makeElement( double x, double y, double z ){
1155	>	#ifdef IS_MPI
1156
1157	<	int k;
1158	<	AtomStamp* current_atom;
1159	<	DirectionalAtom* dAtom;
1160	<	double rotMat[3][3];
1157	>	void SimSetup::mpiMolDivide(void){
1158	>	int i, j, k;
1159	>	int localMol, allMol;
1160	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1161
1162	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1162	>	mpiSim = new mpiSimulation(info);
1163
1164	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1165	<	if( !current_atom->havePosition() ){
1166	<	sprintf( painCave.errMsg,
1167	<	"SimSetup:initFromBass error.\n"
1168	<	"\tComponent %s, atom %s does not have a position specified.\n"
1169	<	"\tThe initialization routine is unable to give a start"
1170	<	" position.\n",
1171	<	comp_stamps[current_comp]->getID(),
1172	<	current_atom->getType() );
1173	<	painCave.isFatal = 1;
1174	<	simError();
1164	>	globalIndex = mpiSim->divideLabor();
1165	>
1166	>	// set up the local variables
1167	>
1168	>	mol2proc = mpiSim->getMolToProcMap();
1169	>	molCompType = mpiSim->getMolComponentType();
1170	>
1171	>	allMol = 0;
1172	>	localMol = 0;
1173	>	local_atoms = 0;
1174	>	local_bonds = 0;
1175	>	local_bends = 0;
1176	>	local_torsions = 0;
1177	>	globalAtomIndex = 0;
1178	>
1179	>
1180	>	for (i = 0; i < n_components; i++){
1181	>	for (j = 0; j < components_nmol[i]; j++){
1182	>	if (mol2proc[allMol] == worldRank){
1183	>	local_atoms += comp_stamps[i]->getNAtoms();
1184	>	local_bonds += comp_stamps[i]->getNBonds();
1185	>	local_bends += comp_stamps[i]->getNBends();
1186	>	local_torsions += comp_stamps[i]->getNTorsions();
1187	>	localMol++;
1188	>	}
1189	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1190	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1191	>	globalAtomIndex++;
1192	>	}
1193	>
1194	>	allMol++;
1195		}
1196	+	}
1197	+	local_SRI = local_bonds + local_bends + local_torsions;
1198
1199	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1186	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1187	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1199	>	info[0].n_atoms = mpiSim->getMyNlocal();
1200
1201	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1201	>	if (local_atoms != info[0].n_atoms){
1202	>	sprintf(painCave.errMsg,
1203	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1204	>	" localAtom (%d) are not equal.\n",
1205	>	info[0].n_atoms, local_atoms);
1206	>	painCave.isFatal = 1;
1207	>	simError();
1208	>	}
1209
1210	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1210	>	info[0].n_bonds = local_bonds;
1211	>	info[0].n_bends = local_bends;
1212	>	info[0].n_torsions = local_torsions;
1213	>	info[0].n_SRI = local_SRI;
1214	>	info[0].n_mol = localMol;
1215
1216	<	rotMat[0][0] = 1.0;
1217	<	rotMat[0][1] = 0.0;
1218	<	rotMat[0][2] = 0.0;
1216	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1217	>	MPIcheckPoint();
1218	>	}
1219
1220	<	rotMat[1][0] = 0.0;
1198	<	rotMat[1][1] = 1.0;
1199	<	rotMat[1][2] = 0.0;
1220	>	#endif // is_mpi
1221
1201	–	rotMat[2][0] = 0.0;
1202	–	rotMat[2][1] = 0.0;
1203	–	rotMat[2][2] = 1.0;
1222
1223	<	dAtom->setA( rotMat );
1223	>	void SimSetup::makeSysArrays(void){
1224	>
1225	>	#ifndef IS_MPI
1226	>	int k, j;
1227	>	#endif // is_mpi
1228	>	int i, l;
1229	>
1230	>	Atom** the_atoms;
1231	>	Molecule* the_molecules;
1232	>	Exclude** the_excludes;
1233	>
1234	>
1235	>	for (l = 0; l < nInfo; l++){
1236	>	// create the atom and short range interaction arrays
1237	>
1238	>	the_atoms = new Atom * [info[l].n_atoms];
1239	>	the_molecules = new Molecule[info[l].n_mol];
1240	>	int molIndex;
1241	>
1242	>	// initialize the molecule's stampID's
1243	>
1244	>	#ifdef IS_MPI
1245	>
1246	>
1247	>	molIndex = 0;
1248	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1249	>	if (mol2proc[i] == worldRank){
1250	>	the_molecules[molIndex].setStampID(molCompType[i]);
1251	>	the_molecules[molIndex].setMyIndex(molIndex);
1252	>	the_molecules[molIndex].setGlobalIndex(i);
1253	>	molIndex++;
1254	>	}
1255		}
1256
1257	<	current_atom_ndx++;
1257	>	#else // is_mpi
1258	>
1259	>	molIndex = 0;
1260	>	globalAtomIndex = 0;
1261	>	for (i = 0; i < n_components; i++){
1262	>	for (j = 0; j < components_nmol[i]; j++){
1263	>	the_molecules[molIndex].setStampID(i);
1264	>	the_molecules[molIndex].setMyIndex(molIndex);
1265	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1266	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1267	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1268	>	globalAtomIndex++;
1269	>	}
1270	>	molIndex++;
1271	>	}
1272	>	}
1273	>
1274	>
1275	>	#endif // is_mpi
1276	>
1277	>
1278	>	if (info[l].n_SRI){
1279	>	Exclude::createArray(info[l].n_SRI);
1280	>	the_excludes = new Exclude * [info[l].n_SRI];
1281	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1282	>	the_excludes[ex] = new Exclude(ex);
1283	>	}
1284	>	info[l].globalExcludes = new int;
1285	>	info[l].n_exclude = info[l].n_SRI;
1286	>	}
1287	>	else{
1288	>	Exclude::createArray(1);
1289	>	the_excludes = new Exclude * ;
1290	>	the_excludes[0] = new Exclude(0);
1291	>	the_excludes[0]->setPair(0, 0);
1292	>	info[l].globalExcludes = new int;
1293	>	info[l].globalExcludes[0] = 0;
1294	>	info[l].n_exclude = 0;
1295	>	}
1296	>
1297	>	// set the arrays into the SimInfo object
1298	>
1299	>	info[l].atoms = the_atoms;
1300	>	info[l].molecules = the_molecules;
1301	>	info[l].nGlobalExcludes = 0;
1302	>	info[l].excludes = the_excludes;
1303	>
1304	>	the_ff->setSimInfo(info);
1305		}
1306	+	}
1307
1308	<	current_mol++;
1309	<	current_comp_mol++;
1308	>	void SimSetup::makeIntegrator(void){
1309	>	int k;
1310
1311	<	if( current_comp_mol >= components_nmol[current_comp] ){
1311	>	NVE* myNVE = NULL;
1312	>	NVT* myNVT = NULL;
1313	>	NPTi* myNPTi = NULL;
1314	>	NPTf* myNPTf = NULL;
1315	>	NPTxyz* myNPTxyz = NULL;
1316	>
1317	>	for (k = 0; k < nInfo; k++){
1318	>	switch (ensembleCase){
1319	>	case NVE_ENS:
1320	>	if (globals->haveZconstraints()){
1321	>
1322	>	std::cerr << "ZConstraint is temporarily disabled\n";
1323	>
1324	>	//      setupZConstraint(info[k]);
1325	>	//      myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1326	>	}
1327	>
1328	>	//       else{
1329	>	myNVE = new NVE(&(info[k]), the_ff);
1330	>	//       }
1331	>
1332	>	info->the_integrator = myNVE;
1333	>	break;
1334	>
1335	>	case NVT_ENS:
1336	>	if (globals->haveZconstraints()){
1337	>
1338	>	std::cerr << "ZConstraint is temporarily disabled\n";
1339	>
1340	>	//      setupZConstraint(info[k]);
1341	>	//      myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1342	>	}
1343	>	// else
1344	>	myNVT = new NVT(&(info[k]), the_ff);
1345	>
1346	>	myNVT->setTargetTemp(globals->getTargetTemp());
1347	>
1348	>	if (globals->haveTauThermostat())
1349	>	myNVT->setTauThermostat(globals->getTauThermostat());
1350	>	else{
1351	>	sprintf(painCave.errMsg,
1352	>	"SimSetup error: If you use the NVT\n"
1353	>	"    ensemble, you must set tauThermostat.\n");
1354	>	painCave.isFatal = 1;
1355	>	simError();
1356	>	}
1357	>
1358	>	info->the_integrator = myNVT;
1359	>	break;
1360	>
1361	>	case NPTi_ENS:
1362	>	if (globals->haveZconstraints()){
1363	>
1364	>	std::cerr << "ZConstraint is temporarily disabled\n";
1365	>
1366	>	//        setupZConstraint(info[k]);
1367	>	//           myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1368	>	}
1369	>	// else
1370	>	myNPTi = new NPTi(&(info[k]), the_ff);
1371	>
1372	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1373	>
1374	>	if (globals->haveTargetPressure())
1375	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1376	>	else{
1377	>	sprintf(painCave.errMsg,
1378	>	"SimSetup error: If you use a constant pressure\n"
1379	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1380	>	painCave.isFatal = 1;
1381	>	simError();
1382	>	}
1383	>
1384	>	if (globals->haveTauThermostat())
1385	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1386	>	else{
1387	>	sprintf(painCave.errMsg,
1388	>	"SimSetup error: If you use an NPT\n"
1389	>	"    ensemble, you must set tauThermostat.\n");
1390	>	painCave.isFatal = 1;
1391	>	simError();
1392	>	}
1393	>
1394	>	if (globals->haveTauBarostat())
1395	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1396	>	else{
1397	>	sprintf(painCave.errMsg,
1398	>	"SimSetup error: If you use an NPT\n"
1399	>	"    ensemble, you must set tauBarostat.\n");
1400	>	painCave.isFatal = 1;
1401	>	simError();
1402	>	}
1403	>
1404	>	info->the_integrator = myNPTi;
1405	>	break;
1406	>
1407	>	case NPTf_ENS:
1408	>	if (globals->haveZconstraints()){
1409
1410	<	current_comp_mol = 0;
1411	<	current_comp++;
1410	>	std::cerr << "ZConstraint is temporarily disabled\n";
1411	>
1412	>	//      setupZConstraint(info[k]);
1413	>	//      myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1414	>	}
1415	>	//       else
1416	>	myNPTf = new NPTf(&(info[k]), the_ff);
1417	>
1418	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1419	>
1420	>	if (globals->haveTargetPressure())
1421	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1422	>	else{
1423	>	sprintf(painCave.errMsg,
1424	>	"SimSetup error: If you use a constant pressure\n"
1425	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1426	>	painCave.isFatal = 1;
1427	>	simError();
1428	>	}
1429	>
1430	>	if (globals->haveTauThermostat())
1431	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1432	>
1433	>	else{
1434	>	sprintf(painCave.errMsg,
1435	>	"SimSetup error: If you use an NPT\n"
1436	>	"    ensemble, you must set tauThermostat.\n");
1437	>	painCave.isFatal = 1;
1438	>	simError();
1439	>	}
1440	>
1441	>	if (globals->haveTauBarostat())
1442	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1443	>
1444	>	else{
1445	>	sprintf(painCave.errMsg,
1446	>	"SimSetup error: If you use an NPT\n"
1447	>	"    ensemble, you must set tauBarostat.\n");
1448	>	painCave.isFatal = 1;
1449	>	simError();
1450	>	}
1451	>
1452	>	info->the_integrator = myNPTf;
1453	>	break;
1454	>
1455	>	case NPTxyz_ENS:
1456	>	if (globals->haveZconstraints()){
1457	>
1458	>	std::cerr << "ZConstraint is temporarily disabled\n";
1459	>
1460	>	//      setupZConstraint(info[k]);
1461	>	//      myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1462	>	}
1463	>	//       else
1464	>	myNPTxyz = new NPTxyz(&(info[k]), the_ff);
1465	>
1466	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1467	>
1468	>	if (globals->haveTargetPressure())
1469	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1470	>	else{
1471	>	sprintf(painCave.errMsg,
1472	>	"SimSetup error: If you use a constant pressure\n"
1473	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1474	>	painCave.isFatal = 1;
1475	>	simError();
1476	>	}
1477	>
1478	>	if (globals->haveTauThermostat())
1479	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1480	>	else{
1481	>	sprintf(painCave.errMsg,
1482	>	"SimSetup error: If you use an NPT\n"
1483	>	"    ensemble, you must set tauThermostat.\n");
1484	>	painCave.isFatal = 1;
1485	>	simError();
1486	>	}
1487	>
1488	>	if (globals->haveTauBarostat())
1489	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1490	>	else{
1491	>	sprintf(painCave.errMsg,
1492	>	"SimSetup error: If you use an NPT\n"
1493	>	"    ensemble, you must set tauBarostat.\n");
1494	>	painCave.isFatal = 1;
1495	>	simError();
1496	>	}
1497	>
1498	>	info->the_integrator = myNPTxyz;
1499	>	break;
1500	>
1501	>	default:
1502	>	sprintf(painCave.errMsg,
1503	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1504	>	painCave.isFatal = 1;
1505	>	simError();
1506	>	}
1507		}
1508		}
1509	+
1510	+	void SimSetup::initFortran(void){
1511	+	info[0].refreshSim();
1512	+
1513	+	if (!strcmp(info[0].mixingRule, "standard")){
1514	+	the_ff->initForceField(LB_MIXING_RULE);
1515	+	}
1516	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1517	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1518	+	}
1519	+	else{
1520	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1521	+	info[0].mixingRule);
1522	+	painCave.isFatal = 1;
1523	+	simError();
1524	+	}
1525	+
1526	+
1527	+	#ifdef IS_MPI
1528	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1529	+	MPIcheckPoint();
1530	+	#endif // is_mpi
1531	+	}
1532	+
1533	+	// void SimSetup::setupZConstraint(SimInfo& theInfo){
1534	+	//   int nZConstraints;
1535	+	//   ZconStamp** zconStamp;
1536	+
1537	+	//   if (globals->haveZconstraintTime()){
1538	+	//     //add sample time of z-constraint  into SimInfo's property list
1539	+	//     DoubleData* zconsTimeProp = new DoubleData();
1540	+	//     zconsTimeProp->setID(ZCONSTIME_ID);
1541	+	//     zconsTimeProp->setData(globals->getZconsTime());
1542	+	//     theInfo.addProperty(zconsTimeProp);
1543	+	//   }
1544	+	//   else{
1545	+	//     sprintf(painCave.errMsg,
1546	+	//             "ZConstraint error: If you use an ZConstraint\n"
1547	+	//             " , you must set sample time.\n");
1548	+	//     painCave.isFatal = 1;
1549	+	//     simError();
1550	+	//   }
1551	+
1552	+	//   //push zconsTol into siminfo, if user does not specify
1553	+	//   //value for zconsTol, a default value will be used
1554	+	//   DoubleData* zconsTol = new DoubleData();
1555	+	//   zconsTol->setID(ZCONSTOL_ID);
1556	+	//   if (globals->haveZconsTol()){
1557	+	//     zconsTol->setData(globals->getZconsTol());
1558	+	//   }
1559	+	//   else{
1560	+	//     double defaultZConsTol = 0.01;
1561	+	//     sprintf(painCave.errMsg,
1562	+	//             "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1563	+	//             " , default value %f is used.\n",
1564	+	//             defaultZConsTol);
1565	+	//     painCave.isFatal = 0;
1566	+	//     simError();
1567	+
1568	+	//     zconsTol->setData(defaultZConsTol);
1569	+	//   }
1570	+	//   theInfo.addProperty(zconsTol);
1571	+
1572	+	//   //set Force Subtraction Policy
1573	+	//   StringData* zconsForcePolicy = new StringData();
1574	+	//   zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1575	+
1576	+	//   if (globals->haveZconsForcePolicy()){
1577	+	//     zconsForcePolicy->setData(globals->getZconsForcePolicy());
1578	+	//   }
1579	+	//   else{
1580	+	//     sprintf(painCave.errMsg,
1581	+	//             "ZConstraint Warning: User does not set force Subtraction policy, "
1582	+	//             "PolicyByMass is used\n");
1583	+	//     painCave.isFatal = 0;
1584	+	//     simError();
1585	+	//     zconsForcePolicy->setData("BYMASS");
1586	+	//   }
1587	+
1588	+	//   theInfo.addProperty(zconsForcePolicy);
1589	+
1590	+	//   //Determine the name of ouput file and add it into SimInfo's property list
1591	+	//   //Be careful, do not use inFileName, since it is a pointer which
1592	+	//   //point to a string at master node, and slave nodes do not contain that string
1593	+
1594	+	//   string zconsOutput(theInfo.finalName);
1595	+
1596	+	//   zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1597	+
1598	+	//   StringData* zconsFilename = new StringData();
1599	+	//   zconsFilename->setID(ZCONSFILENAME_ID);
1600	+	//   zconsFilename->setData(zconsOutput);
1601	+
1602	+	//   theInfo.addProperty(zconsFilename);
1603	+
1604	+	//   //setup index, pos and other parameters of z-constraint molecules
1605	+	//   nZConstraints = globals->getNzConstraints();
1606	+	//   theInfo.nZconstraints = nZConstraints;
1607	+
1608	+	//   zconStamp = globals->getZconStamp();
1609	+	//   ZConsParaItem tempParaItem;
1610	+
1611	+	//   ZConsParaData* zconsParaData = new ZConsParaData();
1612	+	//   zconsParaData->setID(ZCONSPARADATA_ID);
1613	+
1614	+	//   for (int i = 0; i < nZConstraints; i++){
1615	+	//     tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1616	+	//     tempParaItem.zPos = zconStamp[i]->getZpos();
1617	+	//     tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1618	+	//     tempParaItem.kRatio = zconStamp[i]->getKratio();
1619	+
1620	+	//     zconsParaData->addItem(tempParaItem);
1621	+	//   }
1622	+
1623	+	//   //check the uniqueness of index
1624	+	//   if(!zconsParaData->isIndexUnique()){
1625	+	//     sprintf(painCave.errMsg,
1626	+	//             "ZConstraint Error: molIndex is not unique\n");
1627	+	//     painCave.isFatal = 1;
1628	+	//     simError();
1629	+	//   }
1630	+
1631	+	//   //sort the parameters by index of molecules
1632	+	//   zconsParaData->sortByIndex();
1633	+
1634	+	//   //push data into siminfo, therefore, we can retrieve later
1635	+	//   theInfo.addProperty(zconsParaData);
1636	+	// }

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