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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 722 by tim, Tue Aug 26 20:02:29 2003 UTC

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

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