ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC vs.
Revision 780 by mmeineke, Mon Sep 22 21:23:25 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 14 | Line 18
18
19		// some defines for ensemble and Forcefield  cases
20
21	<	#define NVE_ENS 0
22	<	#define NVT_ENS 1
23	<	#define NPT_ENS 2
21	>	#define NVE_ENS        0
22	>	#define NVT_ENS        1
23	>	#define NPTi_ENS       2
24	>	#define NPTf_ENS       3
25
26		#define FF_DUFF 0
27		#define FF_LJ   1
28	+	#define FF_EAM  2
29
30	+	using namespace std;
31
32		SimSetup::SimSetup(){
33	+	isInfoArray = 0;
34	+	nInfo = 1;
35	+
36		stamps = new MakeStamps();
37		globals = new Globals();
38	<
38	>
39	>
40		#ifdef IS_MPI
41	<	strcpy( checkPointMsg, "SimSetup creation successful" );
41	>	strcpy(checkPointMsg, "SimSetup creation successful");
42		MPIcheckPoint();
43		#endif // IS_MPI
44		}
#	Line 37 | Line 48 | void SimSetup::parseFile( char* fileName ){
48		delete globals;
49		}
50
51	<	void SimSetup::parseFile( char* fileName ){
51	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
52	>	info = the_info;
53	>	nInfo = theNinfo;
54	>	isInfoArray = 1;
55	>	}
56
57	+
58	+	void SimSetup::parseFile(char* fileName){
59		#ifdef IS_MPI
60	<	if( worldRank == 0 ){
60	>	if (worldRank == 0){
61		#endif // is_mpi
62	<
62	>
63		inFileName = fileName;
64	<	set_interface_stamps( stamps, globals );
65	<
64	>	set_interface_stamps(stamps, globals);
65	>
66		#ifdef IS_MPI
67		mpiEventInit();
68		#endif
69
70	<	yacc_BASS( fileName );
70	>	yacc_BASS(fileName);
71
72		#ifdef IS_MPI
73		throwMPIEvent(NULL);
74		}
75	<	else receiveParse();
75	>	else{
76	>	receiveParse();
77	>	}
78		#endif
79
80		}
81
82		#ifdef IS_MPI
83		void SimSetup::receiveParse(void){
84	<
85	<	set_interface_stamps( stamps, globals );
86	<	mpiEventInit();
87	<	MPIcheckPoint();
69	<	mpiEventLoop();
70	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92	<	void SimSetup::createSim( void ){
76	<
77	<	MakeStamps *the_stamps;
78	<	Globals* the_globals;
92	>	void SimSetup::createSim(void){
93		int i, j, k, globalAtomIndex;
80	–
81	–	int ensembleCase;
82	–	int ffCase;
83	–
84	–	ensembleCase = -1;
85	–	ffCase = -1;
94
95	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
95	>	// gather all of the information from the Bass file
96
97	<	// set the easy ones first
92	<	simnfo->target_temp = the_globals->getTargetTemp();
93	<	simnfo->dt = the_globals->getDt();
94	<	simnfo->run_time = the_globals->getRunTime();
97	>	gatherInfo();
98
99	<	// get the ones we know are there, yet still may need some work.
97	<	n_components = the_globals->getNComponents();
98	<	strcpy( force_field, the_globals->getForceField() );
99	>	// creation of complex system objects
100
101	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
101	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102	<	else{
103	<	sprintf( painCave.errMsg,
104	<	"SimSetup Error. Unrecognized force field -> %s\n",
105	<	force_field );
106	<	painCave.isFatal = 1;
107	<	simError();
108	<	}
101	>	sysObjectsCreation();
102
103	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
103	>	// check on the post processing info
104
105	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
114	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
115	<	else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS;
116	<	else{
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
119	<	"reverting to NVE for this simulation.\n",
120	<	ensemble );
121	<	painCave.isFatal = 0;
122	<	simError();
123	<	strcpy( ensemble, "NVE" );
124	<	ensembleCase = NVE_ENS;
125	<	}
126	<	strcpy( simnfo->ensemble, ensemble );
105	>	finalInfoCheck();
106
107	+	// initialize the system coordinates
108
109	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
110	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
111	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132	<	//     if (the_globals->haveTargetPressure())
133	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134	<	//     else {
135	<	//       sprintf( painCave.errMsg,
136	<	//                "SimSetup error: If you use the constant pressure\n"
137	<	//                "    ensemble, you must set targetPressure.\n"
138	<	//                "    This was found in the BASS file.\n");
139	<	//       painCave.isFatal = 1;
140	<	//       simError();
141	<	//     }
109	>	if (!isInfoArray){
110	>	initSystemCoords();
111	>	}
112
113	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
113	>	// make the output filenames
114
115	<	//     if (the_globals->haveTauBarostat())
157	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158	<	//     else {
159	<	//       sprintf( painCave.errMsg,
160	<	//                "SimSetup error: If you use the constant pressure\n"
161	<	//                "    ensemble, you must set tauBarostat.\n"
162	<	//                "    This was found in the BASS file.\n");
163	<	//       painCave.isFatal = 1;
164	<	//       simError();
165	<	//     }
115	>	makeOutNames();
116
117	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
168	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
169	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
117	>	// make the integrator
118
119	<	//     if (the_globals->haveTauThermostat())
172	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173	<	//     else if (the_globals->haveQmass())
174	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
175	<	//     else {
176	<	//       sprintf( painCave.errMsg,
177	<	//                "SimSetup error: If you use one of the constant temperature\n"
178	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
179	<	//                "    Neither of these was found in the BASS file.\n");
180	<	//       painCave.isFatal = 1;
181	<	//       simError();
182	<	//     }
119	>	makeIntegrator();
120
121	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
122	<	simnfo->usePBC = the_globals->getPBC();
123	<
187	<	int usesDipoles = 0;
188	<	switch( ffCase ){
121	>	#ifdef IS_MPI
122	>	mpiSim->mpiRefresh();
123	>	#endif
124
125	<	case FF_DUFF:
191	<	the_ff = new DUFF();
192	<	usesDipoles = 1;
193	<	break;
125	>	// initialize the Fortran
126
127	<	case FF_LJ:
128	<	the_ff = new LJFF();
197	<	break;
127	>	initFortran();
128	>	}
129
199	–	default:
200	–	sprintf( painCave.errMsg,
201	–	"SimSetup Error. Unrecognized force field in case statement.\n");
202	–	painCave.isFatal = 1;
203	–	simError();
204	–	}
130
131	<	#ifdef IS_MPI
132	<	strcpy( checkPointMsg, "ForceField creation successful" );
133	<	MPIcheckPoint();
134	<	#endif // is_mpi
131	>	void SimSetup::makeMolecules(void){
132	>	int k, l;
133	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
134	>	molInit molInfo;
135	>	DirectionalAtom* dAtom;
136	>	LinkedAssign* extras;
137	>	LinkedAssign* current_extra;
138	>	AtomStamp* currentAtom;
139	>	BondStamp* currentBond;
140	>	BendStamp* currentBend;
141	>	TorsionStamp* currentTorsion;
142
143	<	// get the components and calculate the tot_nMol and indvidual n_mol
144	<	the_components = the_globals->getComponents();
145	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
143	>	bond_pair* theBonds;
144	>	bend_set* theBends;
145	>	torsion_set* theTorsions;
146
216	–	if( !the_globals->haveNMol() ){
217	–	// we don't have the total number of molecules, so we assume it is
218	–	// given in each component
147
148	<	tot_nmol = 0;
221	<	for( i=0; i<n_components; i++ ){
148	>	//init the forceField paramters
149
150	<	if( !the_components[i]->haveNMol() ){
224	<	// we have a problem
225	<	sprintf( painCave.errMsg,
226	<	"SimSetup Error. No global NMol or component NMol"
227	<	" given. Cannot calculate the number of atoms.\n" );
228	<	painCave.isFatal = 1;
229	<	simError();
230	<	}
150	>	the_ff->readParams();
151
232	–	tot_nmol += the_components[i]->getNMol();
233	–	components_nmol[i] = the_components[i]->getNMol();
234	–	}
235	–	}
236	–	else{
237	–	sprintf( painCave.errMsg,
238	–	"SimSetup error.\n"
239	–	"\tSorry, the ability to specify total"
240	–	" nMols and then give molfractions in the components\n"
241	–	"\tis not currently supported."
242	–	" Please give nMol in the components.\n" );
243	–	painCave.isFatal = 1;
244	–	simError();
245	–
246	–
247	–	//     tot_nmol = the_globals->getNMol();
248	–
249	–	//   //we have the total number of molecules, now we check for molfractions
250	–	//     for( i=0; i<n_components; i++ ){
251	–
252	–	//       if( !the_components[i]->haveMolFraction() ){
253	–
254	–	//  if( !the_components[i]->haveNMol() ){
255	–	//    //we have a problem
256	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	–	//              << " nMol was given in component
258	–
259	–	}
152
153	<	#ifdef IS_MPI
262	<	strcpy( checkPointMsg, "Have the number of components" );
263	<	MPIcheckPoint();
264	<	#endif // is_mpi
153	>	// init the atoms
154
155	<	// make an array of molecule stamps that match the components used.
267	<	// also extract the used stamps out into a separate linked list
155	>	double ux, uy, uz, u, uSqr;
156
157	<	simnfo->nComponents = n_components;
158	<	simnfo->componentsNmol = components_nmol;
271	<	simnfo->compStamps = comp_stamps;
272	<	simnfo->headStamp = new LinkedMolStamp();
273	<
274	<	char* id;
275	<	LinkedMolStamp* headStamp = simnfo->headStamp;
276	<	LinkedMolStamp* currentStamp = NULL;
277	<	for( i=0; i<n_components; i++ ){
157	>	for (k = 0; k < nInfo; k++){
158	>	the_ff->setSimInfo(&(info[k]));
159
160	<	id = the_components[i]->getType();
161	<	comp_stamps[i] = NULL;
162	<
163	<	// check to make sure the component isn't already in the list
160	>	atomOffset = 0;
161	>	excludeOffset = 0;
162	>	for (i = 0; i < info[k].n_mol; i++){
163	>	stampID = info[k].molecules[i].getStampID();
164
165	<	comp_stamps[i] = headStamp->match( id );
166	<	if( comp_stamps[i] == NULL ){
167	<
168	<	// extract the component from the list;
169	<
289	<	currentStamp = the_stamps->extractMolStamp( id );
290	<	if( currentStamp == NULL ){
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup error: Component \"%s\" was not found in the "
293	<	"list of declared molecules\n",
294	<	id );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	headStamp->add( currentStamp );
300	<	comp_stamps[i] = headStamp->match( id );
301	<	}
302	<	}
165	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
166	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
167	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
168	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
169	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
170
171	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
175	<
171	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
172	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
173	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
174	>	molInfo.myBends = new Bend * [molInfo.nBends];
175	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
176
177	+	theBonds = new bond_pair[molInfo.nBonds];
178	+	theBends = new bend_set[molInfo.nBends];
179	+	theTorsions = new torsion_set[molInfo.nTorsions];
180
181	+	// make the Atoms
182
183	<	// caclulate the number of atoms, bonds, bends and torsions
183	>	for (j = 0; j < molInfo.nAtoms; j++){
184	>	currentAtom = comp_stamps[stampID]->getAtom(j);
185	>	if (currentAtom->haveOrientation()){
186	>	dAtom = new DirectionalAtom((j + atomOffset),
187	>	info[k].getConfiguration());
188	>	info[k].n_oriented++;
189	>	molInfo.myAtoms[j] = dAtom;
190
191	<	tot_atoms = 0;
192	<	tot_bonds = 0;
193	<	tot_bends = 0;
317	<	tot_torsions = 0;
318	<	for( i=0; i<n_components; i++ ){
319	<
320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	<	}
191	>	ux = currentAtom->getOrntX();
192	>	uy = currentAtom->getOrntY();
193	>	uz = currentAtom->getOrntZ();
194
195	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
195	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
196
197	<	simnfo->n_atoms = tot_atoms;
198	<	simnfo->n_bonds = tot_bonds;
199	<	simnfo->n_bends = tot_bends;
200	<	simnfo->n_torsions = tot_torsions;
332	<	simnfo->n_SRI = tot_SRI;
333	<	simnfo->n_mol = tot_nmol;
334	<
335	<	simnfo->molMembershipArray = new int[tot_atoms];
197	>	u = sqrt(uSqr);
198	>	ux = ux / u;
199	>	uy = uy / u;
200	>	uz = uz / u;
201
202	+	dAtom->setSUx(ux);
203	+	dAtom->setSUy(uy);
204	+	dAtom->setSUz(uz);
205	+	}
206	+	else{
207	+	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
208	+	info[k].getConfiguration());
209	+	}
210	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
211	+
212		#ifdef IS_MPI
213
214	<	// divide the molecules among processors here.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
214	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
215
216	<	// set up the local variables
217	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
216	>	#endif // is_mpi
217	>	}
218
219	<	int* mol2proc = mpiSim->getMolToProcMap();
220	<	int* molCompType = mpiSim->getMolComponentType();
221	<
222	<	allMol = 0;
223	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
219	>	// make the bonds
220	>	for (j = 0; j < molInfo.nBonds; j++){
221	>	currentBond = comp_stamps[stampID]->getBond(j);
222	>	theBonds[j].a = currentBond->getA() + atomOffset;
223	>	theBonds[j].b = currentBond->getB() + atomOffset;
224
225	+	exI = theBonds[j].a;
226	+	exJ = theBonds[j].b;
227
228	<	for( i=0; i<n_components; i++ ){
228	>	// exclude_I must always be the smaller of the pair
229	>	if (exI > exJ){
230	>	tempEx = exI;
231	>	exI = exJ;
232	>	exJ = tempEx;
233	>	}
234	>	#ifdef IS_MPI
235	>	tempEx = exI;
236	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
237	>	tempEx = exJ;
238	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239
240	<	for( j=0; j<components_nmol[i]; j++ ){
241	<
242	<	if( mol2proc[allMol] == worldRank ){
243	<
244	<	local_atoms +=    comp_stamps[i]->getNAtoms();
369	<	local_bonds +=    comp_stamps[i]->getNBonds();
370	<	local_bends +=    comp_stamps[i]->getNBends();
371	<	local_torsions += comp_stamps[i]->getNTorsions();
372	<	localMol++;
373	<	}
374	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
240	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
241	>	#else  // isn't MPI
242	>
243	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
244	>	#endif  //is_mpi
245		}
246	+	excludeOffset += molInfo.nBonds;
247
248	<	allMol++;
249	<	}
250	<	}
251	<	local_SRI = local_bonds + local_bends + local_torsions;
252	<
253	<	simnfo->n_atoms = mpiSim->getMyNlocal();
385	<
386	<	if( local_atoms != simnfo->n_atoms ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
248	>	//make the bends
249	>	for (j = 0; j < molInfo.nBends; j++){
250	>	currentBend = comp_stamps[stampID]->getBend(j);
251	>	theBends[j].a = currentBend->getA() + atomOffset;
252	>	theBends[j].b = currentBend->getB() + atomOffset;
253	>	theBends[j].c = currentBend->getC() + atomOffset;
254
255	<	simnfo->n_bonds = local_bonds;
256	<	simnfo->n_bends = local_bends;
257	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
255	>	if (currentBend->haveExtras()){
256	>	extras = currentBend->getExtras();
257	>	current_extra = extras;
258
259	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
260	<	MPIcheckPoint();
261	<
262	<
263	<	#endif // is_mpi
264	<
259	>	while (current_extra != NULL){
260	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
261	>	switch (current_extra->getType()){
262	>	case 0:
263	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
264	>	theBends[j].isGhost = 1;
265	>	break;
266
267	<	// create the atom and short range interaction arrays
267	>	case 1:
268	>	theBends[j].ghost = (int) current_extra->getDouble() +
269	>	atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272
273	<	Atom::createArrays(simnfo->n_atoms);
274	<	the_atoms = new Atom*[simnfo->n_atoms];
275	<	the_molecules = new Molecule[simnfo->n_mol];
276	<	int molIndex;
273	>	default:
274	>	sprintf(painCave.errMsg,
275	>	"SimSetup Error: ghostVectorSource was neither a "
276	>	"double nor an int.\n"
277	>	"-->Bend[%d] in %s\n",
278	>	j, comp_stamps[stampID]->getID());
279	>	painCave.isFatal = 1;
280	>	simError();
281	>	}
282	>	}
283	>	else{
284	>	sprintf(painCave.errMsg,
285	>	"SimSetup Error: unhandled bend assignment:\n"
286	>	"    -->%s in Bend[%d] in %s\n",
287	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
288	>	painCave.isFatal = 1;
289	>	simError();
290	>	}
291
292	<	// initialize the molecule's stampID's
292	>	current_extra = current_extra->getNext();
293	>	}
294	>	}
295
296	+	if (!theBends[j].isGhost){
297	+	exI = theBends[j].a;
298	+	exJ = theBends[j].c;
299	+	}
300	+	else{
301	+	exI = theBends[j].a;
302	+	exJ = theBends[j].b;
303	+	}
304	+
305	+	// exclude_I must always be the smaller of the pair
306	+	if (exI > exJ){
307	+	tempEx = exI;
308	+	exI = exJ;
309	+	exJ = tempEx;
310	+	}
311		#ifdef IS_MPI
312	<
312	>	tempEx = exI;
313	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
314	>	tempEx = exJ;
315	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316
317	<	molIndex = 0;
318	<	for(i=0; i<mpiSim->getTotNmol(); i++){
319	<
320	<	if(mol2proc[i] == worldRank ){
321	<	the_molecules[molIndex].setStampID( molCompType[i] );
322	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
429	<	}
430	<	}
317	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
318	>	#else  // isn't MPI
319	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
320	>	#endif  //is_mpi
321	>	}
322	>	excludeOffset += molInfo.nBends;
323
324	<	#else // is_mpi
325	<
326	<	molIndex = 0;
327	<	globalAtomIndex = 0;
328	<	for(i=0; i<n_components; i++){
329	<	for(j=0; j<components_nmol[i]; j++ ){
438	<	the_molecules[molIndex].setStampID( i );
439	<	the_molecules[molIndex].setMyIndex( molIndex );
440	<	the_molecules[molIndex].setGlobalIndex( molIndex );
441	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443	<	globalAtomIndex++;
444	<	}
445	<	molIndex++;
446	<	}
447	<	}
448	<
324	>	for (j = 0; j < molInfo.nTorsions; j++){
325	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
326	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
327	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
328	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
329	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
330
331	<	#endif // is_mpi
331	>	exI = theTorsions[j].a;
332	>	exJ = theTorsions[j].d;
333
334	+	// exclude_I must always be the smaller of the pair
335	+	if (exI > exJ){
336	+	tempEx = exI;
337	+	exI = exJ;
338	+	exJ = tempEx;
339	+	}
340	+	#ifdef IS_MPI
341	+	tempEx = exI;
342	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	+	tempEx = exJ;
344	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345
346	<	if( simnfo->n_SRI ){
347	<
348	<	Exclude::createArray(simnfo->n_SRI);
349	<	the_excludes = new Exclude*[simnfo->n_SRI];
350	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
351	<	simnfo->globalExcludes = new int;
459	<	simnfo->n_exclude = simnfo->n_SRI;
460	<	}
461	<	else{
462	<
463	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
346	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
347	>	#else  // isn't MPI
348	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
349	>	#endif  //is_mpi
350	>	}
351	>	excludeOffset += molInfo.nTorsions;
352
472	–	// set the arrays into the SimInfo object
353
354	<	simnfo->atoms = the_atoms;
475	<	simnfo->molecules = the_molecules;
476	<	simnfo->nGlobalExcludes = 0;
477	<	simnfo->excludes = the_excludes;
354	>	// send the arrays off to the forceField for init.
355
356	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
357	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
358	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
359	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
360	+	theTorsions);
361
480	–	// get some of the tricky things that may still be in the globals
362
363	<	double boxVector[3];
483	<	if( the_globals->haveBox() ){
484	<	boxVector[0] = the_globals->getBox();
485	<	boxVector[1] = the_globals->getBox();
486	<	boxVector[2] = the_globals->getBox();
487	<
488	<	simnfo->setBox( boxVector );
489	<	}
490	<	else if( the_globals->haveDensity() ){
363	>	info[k].molecules[i].initialize(molInfo);
364
492	–	double vol;
493	–	vol = (double)tot_nmol / the_globals->getDensity();
494	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
495	–	boxVector[1] = boxVector[0];
496	–	boxVector[2] = boxVector[0];
365
366	<	simnfo->setBox( boxVector );
367	<	}
368	<	else{
369	<	if( !the_globals->haveBoxX() ){
502	<	sprintf( painCave.errMsg,
503	<	"SimSetup error, no periodic BoxX size given.\n" );
504	<	painCave.isFatal = 1;
505	<	simError();
366	>	atomOffset += molInfo.nAtoms;
367	>	delete[] theBonds;
368	>	delete[] theBends;
369	>	delete[] theTorsions;
370		}
507	–	boxVector[0] = the_globals->getBoxX();
508	–
509	–	if( !the_globals->haveBoxY() ){
510	–	sprintf( painCave.errMsg,
511	–	"SimSetup error, no periodic BoxY size given.\n" );
512	–	painCave.isFatal = 1;
513	–	simError();
514	–	}
515	–	boxVector[1] = the_globals->getBoxY();
516	–
517	–	if( !the_globals->haveBoxZ() ){
518	–	sprintf( painCave.errMsg,
519	–	"SimSetup error, no periodic BoxZ size given.\n" );
520	–	painCave.isFatal = 1;
521	–	simError();
522	–	}
523	–	boxVector[2] = the_globals->getBoxZ();
524	–
525	–	simnfo->setBox( boxVector );
371		}
372
373		#ifdef IS_MPI
374	<	strcpy( checkPointMsg, "Box size set up" );
374	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
375		MPIcheckPoint();
376		#endif // is_mpi
377
378	+	// clean up the forcefield
379
380	<	// initialize the arrays
380	>	the_ff->calcRcut();
381	>	the_ff->cleanMe();
382	>	}
383
384	<	the_ff->setSimInfo( simnfo );
384	>	void SimSetup::initFromBass(void){
385	>	int i, j, k;
386	>	int n_cells;
387	>	double cellx, celly, cellz;
388	>	double temp1, temp2, temp3;
389	>	int n_per_extra;
390	>	int n_extra;
391	>	int have_extra, done;
392
393	<	makeMolecules();
394	<	simnfo->identArray = new int[simnfo->n_atoms];
395	<	for(i=0; i<simnfo->n_atoms; i++){
396	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
542	<	}
543	<
544	<	if (the_globals->getUseRF() ) {
545	<	simnfo->useReactionField = 1;
546	<
547	<	if( !the_globals->haveECR() ){
548	<	sprintf( painCave.errMsg,
549	<	"SimSetup Warning: using default value of 1/2 the smallest "
550	<	"box length for the electrostaticCutoffRadius.\n"
551	<	"I hope you have a very fast processor!\n");
552	<	painCave.isFatal = 0;
553	<	simError();
554	<	double smallest;
555	<	smallest = simnfo->boxLx;
556	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
557	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
558	<	simnfo->ecr = 0.5 * smallest;
559	<	} else {
560	<	simnfo->ecr        = the_globals->getECR();
561	<	}
393	>	double vel[3];
394	>	vel[0] = 0.0;
395	>	vel[1] = 0.0;
396	>	vel[2] = 0.0;
397
398	<	if( !the_globals->haveEST() ){
399	<	sprintf( painCave.errMsg,
400	<	"SimSetup Warning: using default value of 0.05 * the "
401	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
402	<	);
403	<	painCave.isFatal = 0;
404	<	simError();
405	<	simnfo->est = 0.05 * simnfo->ecr;
406	<	} else {
407	<	simnfo->est        = the_globals->getEST();
408	<	}
409	<
410	<	if(!the_globals->haveDielectric() ){
411	<	sprintf( painCave.errMsg,
412	<	"SimSetup Error: You are trying to use Reaction Field without"
413	<	"setting a dielectric constant!\n"
414	<	);
398	>	temp1 = (double) tot_nmol / 4.0;
399	>	temp2 = pow(temp1, (1.0 / 3.0));
400	>	temp3 = ceil(temp2);
401	>
402	>	have_extra = 0;
403	>	if (temp2 < temp3){
404	>	// we have a non-complete lattice
405	>	have_extra = 1;
406	>
407	>	n_cells = (int) temp3 - 1;
408	>	cellx = info[0].boxL[0] / temp3;
409	>	celly = info[0].boxL[1] / temp3;
410	>	cellz = info[0].boxL[2] / temp3;
411	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
412	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
413	>	n_per_extra = (int) ceil(temp1);
414	>
415	>	if (n_per_extra > 4){
416	>	sprintf(painCave.errMsg,
417	>	"SimSetup error. There has been an error in constructing"
418	>	" the non-complete lattice.\n");
419		painCave.isFatal = 1;
420		simError();
421		}
422	<	simnfo->dielectric = the_globals->getDielectric();
423	<	} else {
424	<	if (usesDipoles) {
425	<
426	<	if( !the_globals->haveECR() ){
427	<	sprintf( painCave.errMsg,
428	<	"SimSetup Warning: using default value of 1/2 the smallest "
429	<	"box length for the electrostaticCutoffRadius.\n"
430	<	"I hope you have a very fast processor!\n");
431	<	painCave.isFatal = 0;
432	<	simError();
433	<	double smallest;
434	<	smallest = simnfo->boxLx;
435	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
436	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
437	<	simnfo->ecr = 0.5 * smallest;
438	<	} else {
439	<	simnfo->ecr        = the_globals->getECR();
422	>	}
423	>	else{
424	>	n_cells = (int) temp3;
425	>	cellx = info[0].boxL[0] / temp3;
426	>	celly = info[0].boxL[1] / temp3;
427	>	cellz = info[0].boxL[2] / temp3;
428	>	}
429	>
430	>	current_mol = 0;
431	>	current_comp_mol = 0;
432	>	current_comp = 0;
433	>	current_atom_ndx = 0;
434	>
435	>	for (i = 0; i < n_cells ; i++){
436	>	for (j = 0; j < n_cells; j++){
437	>	for (k = 0; k < n_cells; k++){
438	>	makeElement(i * cellx, j * celly, k * cellz);
439	>
440	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
441	>
442	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
443	>
444	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
445		}
602	–
603	–	if( !the_globals->haveEST() ){
604	–	sprintf( painCave.errMsg,
605	–	"SimSetup Warning: using default value of 5%% of the "
606	–	"electrostaticCutoffRadius for the "
607	–	"electrostaticSkinThickness\n"
608	–	);
609	–	painCave.isFatal = 0;
610	–	simError();
611	–	simnfo->est = 0.05 * simnfo->ecr;
612	–	} else {
613	–	simnfo->est        = the_globals->getEST();
614	–	}
446		}
447	<	}
447	>	}
448
449	<	#ifdef IS_MPI
450	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
620	<	MPIcheckPoint();
621	<	#endif // is_mpi
449	>	if (have_extra){
450	>	done = 0;
451
452	<	if( the_globals->haveInitialConfig() ){
453	<
454	<	InitializeFromFile* fileInit;
455	<	#ifdef IS_MPI // is_mpi
456	<	if( worldRank == 0 ){
457	<	#endif //is_mpi
458	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
459	<	#ifdef IS_MPI
460	<	}else fileInit = new InitializeFromFile( NULL );
461	<	#endif
462	<	fileInit->read_xyz( simnfo ); // default velocities on
452	>	int start_ndx;
453	>	for (i = 0; i < (n_cells + 1) && !done; i++){
454	>	for (j = 0; j < (n_cells + 1) && !done; j++){
455	>	if (i < n_cells){
456	>	if (j < n_cells){
457	>	start_ndx = n_cells;
458	>	}
459	>	else
460	>	start_ndx = 0;
461	>	}
462	>	else
463	>	start_ndx = 0;
464
465	<	delete fileInit;
466	<	}
467	<	else{
465	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
466	>	makeElement(i * cellx, j * celly, k * cellz);
467	>	done = (current_mol >= tot_nmol);
468
469	<	#ifdef IS_MPI
469	>	if (!done && n_per_extra > 1){
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
471	>	k * cellz);
472	>	done = (current_mol >= tot_nmol);
473	>	}
474
475	<	// no init from bass
476	<
477	<	sprintf( painCave.errMsg,
478	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
479	<	painCave.isFatal;
646	<	simError();
647	<
648	<	#else
475	>	if (!done && n_per_extra > 2){
476	>	makeElement(i * cellx, j * celly + 0.5 * celly,
477	>	k * cellz + 0.5 * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	<	initFromBass();
482	<
483	<
484	<	#endif
485	<	}
486	<
656	<	#ifdef IS_MPI
657	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
658	<	MPIcheckPoint();
659	<	#endif // is_mpi
660	<
661	<
662	<
663	<
664	<
665	<
666	<
667	<	#ifdef IS_MPI
668	<	if( worldRank == 0 ){
669	<	#endif // is_mpi
670	<
671	<	if( the_globals->haveFinalConfig() ){
672	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
673	<	}
674	<	else{
675	<	strcpy( simnfo->finalName, inFileName );
676	<	char* endTest;
677	<	int nameLength = strlen( simnfo->finalName );
678	<	endTest = &(simnfo->finalName[nameLength - 5]);
679	<	if( !strcmp( endTest, ".bass" ) ){
680	<	strcpy( endTest, ".eor" );
481	>	if (!done && n_per_extra > 3){
482	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486	>	}
487		}
682	–	else if( !strcmp( endTest, ".BASS" ) ){
683	–	strcpy( endTest, ".eor" );
684	–	}
685	–	else{
686	–	endTest = &(simnfo->finalName[nameLength - 4]);
687	–	if( !strcmp( endTest, ".bss" ) ){
688	–	strcpy( endTest, ".eor" );
689	–	}
690	–	else if( !strcmp( endTest, ".mdl" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else{
694	–	strcat( simnfo->finalName, ".eor" );
695	–	}
696	–	}
488		}
698	–
699	–	// make the sample and status out names
700	–
701	–	strcpy( simnfo->sampleName, inFileName );
702	–	char* endTest;
703	–	int nameLength = strlen( simnfo->sampleName );
704	–	endTest = &(simnfo->sampleName[nameLength - 5]);
705	–	if( !strcmp( endTest, ".bass" ) ){
706	–	strcpy( endTest, ".dump" );
707	–	}
708	–	else if( !strcmp( endTest, ".BASS" ) ){
709	–	strcpy( endTest, ".dump" );
710	–	}
711	–	else{
712	–	endTest = &(simnfo->sampleName[nameLength - 4]);
713	–	if( !strcmp( endTest, ".bss" ) ){
714	–	strcpy( endTest, ".dump" );
715	–	}
716	–	else if( !strcmp( endTest, ".mdl" ) ){
717	–	strcpy( endTest, ".dump" );
718	–	}
719	–	else{
720	–	strcat( simnfo->sampleName, ".dump" );
721	–	}
722	–	}
723	–
724	–	strcpy( simnfo->statusName, inFileName );
725	–	nameLength = strlen( simnfo->statusName );
726	–	endTest = &(simnfo->statusName[nameLength - 5]);
727	–	if( !strcmp( endTest, ".bass" ) ){
728	–	strcpy( endTest, ".stat" );
729	–	}
730	–	else if( !strcmp( endTest, ".BASS" ) ){
731	–	strcpy( endTest, ".stat" );
732	–	}
733	–	else{
734	–	endTest = &(simnfo->statusName[nameLength - 4]);
735	–	if( !strcmp( endTest, ".bss" ) ){
736	–	strcpy( endTest, ".stat" );
737	–	}
738	–	else if( !strcmp( endTest, ".mdl" ) ){
739	–	strcpy( endTest, ".stat" );
740	–	}
741	–	else{
742	–	strcat( simnfo->statusName, ".stat" );
743	–	}
744	–	}
745	–
746	–	#ifdef IS_MPI
489		}
748	–	#endif // is_mpi
749	–
750	–	// set the status, sample, and themal kick times
751	–
752	–	if( the_globals->haveSampleTime() ){
753	–	simnfo->sampleTime = the_globals->getSampleTime();
754	–	simnfo->statusTime = simnfo->sampleTime;
755	–	simnfo->thermalTime = simnfo->sampleTime;
756	–	}
757	–	else{
758	–	simnfo->sampleTime = the_globals->getRunTime();
759	–	simnfo->statusTime = simnfo->sampleTime;
760	–	simnfo->thermalTime = simnfo->sampleTime;
761	–	}
490
491	<	if( the_globals->haveStatusTime() ){
492	<	simnfo->statusTime = the_globals->getStatusTime();
491	>	for (i = 0; i < info[0].n_atoms; i++){
492	>	info[0].atoms[i]->setVel(vel);
493		}
494	+	}
495
496	<	if( the_globals->haveThermalTime() ){
497	<	simnfo->thermalTime = the_globals->getThermalTime();
498	<	}
496	>	void SimSetup::makeElement(double x, double y, double z){
497	>	int k;
498	>	AtomStamp* current_atom;
499	>	DirectionalAtom* dAtom;
500	>	double rotMat[3][3];
501	>	double pos[3];
502
503	<	// check for the temperature set flag
504	<
505	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
506	<
507	<
508	<	// make the integrator
509	<
510	<
511	<	NVT* myNVT = NULL;
780	<	switch( ensembleCase ){
781	<
782	<	case NVE_ENS:
783	<	new NVE( simnfo, the_ff );
784	<	break;
785	<
786	<	case NVT_ENS:
787	<	myNVT = new NVT( simnfo, the_ff );
788	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
789	<
790	<	if (the_globals->haveTauThermostat())
791	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
792	<	//     else if (the_globals->haveQmass())
793	<	//       myNVT->setQmass(the_globals->getQmass());
794	<	else {
795	<	sprintf( painCave.errMsg,
796	<	"SimSetup error: If you use the NVT\n"
797	<	"    ensemble, you must set either tauThermostat or qMass.\n"
798	<	"    Neither of these was found in the BASS file.\n");
503	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
504	>	current_atom = comp_stamps[current_comp]->getAtom(k);
505	>	if (!current_atom->havePosition()){
506	>	sprintf(painCave.errMsg,
507	>	"SimSetup:initFromBass error.\n"
508	>	"\tComponent %s, atom %s does not have a position specified.\n"
509	>	"\tThe initialization routine is unable to give a start"
510	>	" position.\n",
511	>	comp_stamps[current_comp]->getID(), current_atom->getType());
512		painCave.isFatal = 1;
513		simError();
514		}
802	–	break;
515
516	<	default:
517	<	sprintf( painCave.errMsg,
518	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
807	<	painCave.isFatal = 1;
808	<	simError();
809	<	}
516	>	pos[0] = x + current_atom->getPosX();
517	>	pos[1] = y + current_atom->getPosY();
518	>	pos[2] = z + current_atom->getPosZ();
519
520	+	info[0].atoms[current_atom_ndx]->setPos(pos);
521
522	<	#ifdef IS_MPI
523	<	mpiSim->mpiRefresh();
814	<	#endif
522	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
523	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
524
525	<	// initialize the Fortran
525	>	rotMat[0][0] = 1.0;
526	>	rotMat[0][1] = 0.0;
527	>	rotMat[0][2] = 0.0;
528
529	<
530	<	simnfo->refreshSim();
531	<
532	<	if( !strcmp( simnfo->mixingRule, "standard") ){
533	<	the_ff->initForceField( LB_MIXING_RULE );
529	>	rotMat[1][0] = 0.0;
530	>	rotMat[1][1] = 1.0;
531	>	rotMat[1][2] = 0.0;
532	>
533	>	rotMat[2][0] = 0.0;
534	>	rotMat[2][1] = 0.0;
535	>	rotMat[2][2] = 1.0;
536	>
537	>	dAtom->setA(rotMat);
538	>	}
539	>
540	>	current_atom_ndx++;
541		}
542	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
543	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
542	>
543	>	current_mol++;
544	>	current_comp_mol++;
545	>
546	>	if (current_comp_mol >= components_nmol[current_comp]){
547	>	current_comp_mol = 0;
548	>	current_comp++;
549		}
550	<	else{
551	<	sprintf( painCave.errMsg,
552	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
553	<	simnfo->mixingRule );
554	<	painCave.isFatal = 1;
555	<	simError();
550	>	}
551	>
552	>
553	>	void SimSetup::gatherInfo(void){
554	>	int i, j, k;
555	>
556	>	ensembleCase = -1;
557	>	ffCase = -1;
558	>
559	>	// set the easy ones first
560	>
561	>	for (i = 0; i < nInfo; i++){
562	>	info[i].target_temp = globals->getTargetTemp();
563	>	info[i].dt = globals->getDt();
564	>	info[i].run_time = globals->getRunTime();
565		}
566	+	n_components = globals->getNComponents();
567
568
569	<	#ifdef IS_MPI
837	<	strcpy( checkPointMsg,
838	<	"Successfully intialized the mixingRule for Fortran." );
839	<	MPIcheckPoint();
840	<	#endif // is_mpi
841	<	}
569	>	// get the forceField
570
571	+	strcpy(force_field, globals->getForceField());
572
573	<	void SimSetup::makeMolecules( void ){
573	>	if (!strcasecmp(force_field, "DUFF")){
574	>	ffCase = FF_DUFF;
575	>	}
576	>	else if (!strcasecmp(force_field, "LJ")){
577	>	ffCase = FF_LJ;
578	>	}
579	>	else if (!strcasecmp(force_field, "EAM")){
580	>	ffCase = FF_EAM;
581	>	}
582	>	else{
583	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
584	>	force_field);
585	>	painCave.isFatal = 1;
586	>	simError();
587	>	}
588
589	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
847	<	molInit info;
848	<	DirectionalAtom* dAtom;
849	<	LinkedAssign* extras;
850	<	LinkedAssign* current_extra;
851	<	AtomStamp* currentAtom;
852	<	BondStamp* currentBond;
853	<	BendStamp* currentBend;
854	<	TorsionStamp* currentTorsion;
589	>	// get the ensemble
590
591	<	bond_pair* theBonds;
857	<	bend_set* theBends;
858	<	torsion_set* theTorsions;
591	>	strcpy(ensemble, globals->getEnsemble());
592
593	<
594	<	//init the forceField paramters
593	>	if (!strcasecmp(ensemble, "NVE")){
594	>	ensembleCase = NVE_ENS;
595	>	}
596	>	else if (!strcasecmp(ensemble, "NVT")){
597	>	ensembleCase = NVT_ENS;
598	>	}
599	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
600	>	ensembleCase = NPTi_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NPTf")){
603	>	ensembleCase = NPTf_ENS;
604	>	}
605	>	else{
606	>	sprintf(painCave.errMsg,
607	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
608	>	"reverting to NVE for this simulation.\n",
609	>	ensemble);
610	>	painCave.isFatal = 0;
611	>	simError();
612	>	strcpy(ensemble, "NVE");
613	>	ensembleCase = NVE_ENS;
614	>	}
615
616	<	the_ff->readParams();
616	>	for (i = 0; i < nInfo; i++){
617	>	strcpy(info[i].ensemble, ensemble);
618
619	<
866	<	// init the atoms
619	>	// get the mixing rule
620
621	<	double ux, uy, uz, u, uSqr;
622	<
623	<	atomOffset = 0;
871	<	excludeOffset = 0;
872	<	for(i=0; i<simnfo->n_mol; i++){
873	<
874	<	stampID = the_molecules[i].getStampID();
621	>	strcpy(info[i].mixingRule, globals->getMixingRule());
622	>	info[i].usePBC = globals->getPBC();
623	>	}
624
625	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
877	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
878	<	info.nBends    = comp_stamps[stampID]->getNBends();
879	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
880	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
625	>	// get the components and calculate the tot_nMol and indvidual n_mol
626
627	<	info.myAtoms = &the_atoms[atomOffset];
628	<	info.myExcludes = &the_excludes[excludeOffset];
884	<	info.myBonds = new Bond*[info.nBonds];
885	<	info.myBends = new Bend*[info.nBends];
886	<	info.myTorsions = new Torsion*[info.nTorsions];
627	>	the_components = globals->getComponents();
628	>	components_nmol = new int[n_components];
629
888	–	theBonds = new bond_pair[info.nBonds];
889	–	theBends = new bend_set[info.nBends];
890	–	theTorsions = new torsion_set[info.nTorsions];
891	–
892	–	// make the Atoms
893	–
894	–	for(j=0; j<info.nAtoms; j++){
895	–
896	–	currentAtom = comp_stamps[stampID]->getAtom( j );
897	–	if( currentAtom->haveOrientation() ){
898	–
899	–	dAtom = new DirectionalAtom(j + atomOffset);
900	–	simnfo->n_oriented++;
901	–	info.myAtoms[j] = dAtom;
902	–
903	–	ux = currentAtom->getOrntX();
904	–	uy = currentAtom->getOrntY();
905	–	uz = currentAtom->getOrntZ();
906	–
907	–	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
908	–
909	–	u = sqrt( uSqr );
910	–	ux = ux / u;
911	–	uy = uy / u;
912	–	uz = uz / u;
913	–
914	–	dAtom->setSUx( ux );
915	–	dAtom->setSUy( uy );
916	–	dAtom->setSUz( uz );
917	–	}
918	–	else{
919	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
920	–	}
921	–	info.myAtoms[j]->setType( currentAtom->getType() );
922	–
923	–	#ifdef IS_MPI
924	–
925	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
926	–
927	–	#endif // is_mpi
928	–	}
929	–
930	–	// make the bonds
931	–	for(j=0; j<info.nBonds; j++){
932	–
933	–	currentBond = comp_stamps[stampID]->getBond( j );
934	–	theBonds[j].a = currentBond->getA() + atomOffset;
935	–	theBonds[j].b = currentBond->getB() + atomOffset;
630
631	<	exI = theBonds[j].a;
632	<	exJ = theBonds[j].b;
631	>	if (!globals->haveNMol()){
632	>	// we don't have the total number of molecules, so we assume it is
633	>	// given in each component
634
635	<	// exclude_I must always be the smaller of the pair
636	<	if( exI > exJ ){
637	<	tempEx = exI;
638	<	exI = exJ;
639	<	exJ = tempEx;
635	>	tot_nmol = 0;
636	>	for (i = 0; i < n_components; i++){
637	>	if (!the_components[i]->haveNMol()){
638	>	// we have a problem
639	>	sprintf(painCave.errMsg,
640	>	"SimSetup Error. No global NMol or component NMol"
641	>	" given. Cannot calculate the number of atoms.\n");
642	>	painCave.isFatal = 1;
643	>	simError();
644		}
946	–	#ifdef IS_MPI
947	–	tempEx = exI;
948	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
949	–	tempEx = exJ;
950	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
951	–
952	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
953	–	#else  // isn't MPI
645
646	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
647	<	#endif  //is_mpi
646	>	tot_nmol += the_components[i]->getNMol();
647	>	components_nmol[i] = the_components[i]->getNMol();
648		}
649	<	excludeOffset += info.nBonds;
649	>	}
650	>	else{
651	>	sprintf(painCave.errMsg,
652	>	"SimSetup error.\n"
653	>	"\tSorry, the ability to specify total"
654	>	" nMols and then give molfractions in the components\n"
655	>	"\tis not currently supported."
656	>	" Please give nMol in the components.\n");
657	>	painCave.isFatal = 1;
658	>	simError();
659	>	}
660
661	<	//make the bends
662	<	for(j=0; j<info.nBends; j++){
663	<
664	<	currentBend = comp_stamps[stampID]->getBend( j );
665	<	theBends[j].a = currentBend->getA() + atomOffset;
666	<	theBends[j].b = currentBend->getB() + atomOffset;
667	<	theBends[j].c = currentBend->getC() + atomOffset;
967	<
968	<	if( currentBend->haveExtras() ){
969	<
970	<	extras = currentBend->getExtras();
971	<	current_extra = extras;
972	<
973	<	while( current_extra != NULL ){
974	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
975	<
976	<	switch( current_extra->getType() ){
977	<
978	<	case 0:
979	<	theBends[j].ghost =
980	<	current_extra->getInt() + atomOffset;
981	<	theBends[j].isGhost = 1;
982	<	break;
983	<
984	<	case 1:
985	<	theBends[j].ghost =
986	<	(int)current_extra->getDouble() + atomOffset;
987	<	theBends[j].isGhost = 1;
988	<	break;
989	<
990	<	default:
991	<	sprintf( painCave.errMsg,
992	<	"SimSetup Error: ghostVectorSource was neither a "
993	<	"double nor an int.\n"
994	<	"-->Bend[%d] in %s\n",
995	<	j, comp_stamps[stampID]->getID() );
996	<	painCave.isFatal = 1;
997	<	simError();
998	<	}
999	<	}
1000	<
1001	<	else{
1002	<
1003	<	sprintf( painCave.errMsg,
1004	<	"SimSetup Error: unhandled bend assignment:\n"
1005	<	"    -->%s in Bend[%d] in %s\n",
1006	<	current_extra->getlhs(),
1007	<	j, comp_stamps[stampID]->getID() );
1008	<	painCave.isFatal = 1;
1009	<	simError();
1010	<	}
1011	<
1012	<	current_extra = current_extra->getNext();
1013	<	}
1014	<	}
1015	<
1016	<	if( !theBends[j].isGhost ){
1017	<
1018	<	exI = theBends[j].a;
1019	<	exJ = theBends[j].c;
1020	<	}
1021	<	else{
1022	<
1023	<	exI = theBends[j].a;
1024	<	exJ = theBends[j].b;
1025	<	}
1026	<
1027	<	// exclude_I must always be the smaller of the pair
1028	<	if( exI > exJ ){
1029	<	tempEx = exI;
1030	<	exI = exJ;
1031	<	exJ = tempEx;
1032	<	}
1033	<	#ifdef IS_MPI
1034	<	tempEx = exI;
1035	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1036	<	tempEx = exJ;
1037	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1038	<
1039	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1040	<	#else  // isn't MPI
1041	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1042	<	#endif  //is_mpi
661	>	// set the status, sample, and thermal kick times
662	>
663	>	for (i = 0; i < nInfo; i++){
664	>	if (globals->haveSampleTime()){
665	>	info[i].sampleTime = globals->getSampleTime();
666	>	info[i].statusTime = info[i].sampleTime;
667	>	info[i].thermalTime = info[i].sampleTime;
668		}
669	<	excludeOffset += info.nBends;
669	>	else{
670	>	info[i].sampleTime = globals->getRunTime();
671	>	info[i].statusTime = info[i].sampleTime;
672	>	info[i].thermalTime = info[i].sampleTime;
673	>	}
674
675	<	for(j=0; j<info.nTorsions; j++){
676	<
677	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1049	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1050	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1051	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1052	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1053	<
1054	<	exI = theTorsions[j].a;
1055	<	exJ = theTorsions[j].d;
675	>	if (globals->haveStatusTime()){
676	>	info[i].statusTime = globals->getStatusTime();
677	>	}
678
679	<	// exclude_I must always be the smaller of the pair
680	<	if( exI > exJ ){
1059	<	tempEx = exI;
1060	<	exI = exJ;
1061	<	exJ = tempEx;
1062	<	}
1063	<	#ifdef IS_MPI
1064	<	tempEx = exI;
1065	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1066	<	tempEx = exJ;
1067	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1068	<
1069	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1070	<	#else  // isn't MPI
1071	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1072	<	#endif  //is_mpi
679	>	if (globals->haveThermalTime()){
680	>	info[i].thermalTime = globals->getThermalTime();
681		}
1074	–	excludeOffset += info.nTorsions;
682
683	<
684	<	// send the arrays off to the forceField for init.
683	>	info[i].resetIntegrator = 0;
684	>	if( globals->haveResetTime() ){
685	>	info[i].resetTime = globals->getResetTime();
686	>	info[i].resetIntegrator = 1;
687	>	}
688
689	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1080	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1081	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1082	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
689	>	// check for the temperature set flag
690
691	+	if (globals->haveTempSet())
692	+	info[i].setTemp = globals->getTempSet();
693
694	<	the_molecules[i].initialize( info );
694	>	// get some of the tricky things that may still be in the globals
695
696	+	double boxVector[3];
697	+	if (globals->haveBox()){
698	+	boxVector[0] = globals->getBox();
699	+	boxVector[1] = globals->getBox();
700	+	boxVector[2] = globals->getBox();
701
702	<	atomOffset += info.nAtoms;
703	<	delete[] theBonds;
704	<	delete[] theBends;
705	<	delete[] theTorsions;
706	<	}
702	>	info[i].setBox(boxVector);
703	>	}
704	>	else if (globals->haveDensity()){
705	>	double vol;
706	>	vol = (double) tot_nmol / globals->getDensity();
707	>	boxVector[0] = pow(vol, (1.0 / 3.0));
708	>	boxVector[1] = boxVector[0];
709	>	boxVector[2] = boxVector[0];
710
711	<	#ifdef IS_MPI
712	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
713	<	MPIcheckPoint();
714	<	#endif // is_mpi
711	>	info[i].setBox(boxVector);
712	>	}
713	>	else{
714	>	if (!globals->haveBoxX()){
715	>	sprintf(painCave.errMsg,
716	>	"SimSetup error, no periodic BoxX size given.\n");
717	>	painCave.isFatal = 1;
718	>	simError();
719	>	}
720	>	boxVector[0] = globals->getBoxX();
721
722	<	// clean up the forcefield
723	<	the_ff->calcRcut();
724	<	the_ff->cleanMe();
722	>	if (!globals->haveBoxY()){
723	>	sprintf(painCave.errMsg,
724	>	"SimSetup error, no periodic BoxY size given.\n");
725	>	painCave.isFatal = 1;
726	>	simError();
727	>	}
728	>	boxVector[1] = globals->getBoxY();
729
730	<	}
730	>	if (!globals->haveBoxZ()){
731	>	sprintf(painCave.errMsg,
732	>	"SimSetup error, no periodic BoxZ size given.\n");
733	>	painCave.isFatal = 1;
734	>	simError();
735	>	}
736	>	boxVector[2] = globals->getBoxZ();
737
738	<	void SimSetup::initFromBass( void ){
738	>	info[i].setBox(boxVector);
739	>	}
740	>	}
741
742	<	int i, j, k;
743	<	int n_cells;
1109	<	double cellx, celly, cellz;
1110	<	double temp1, temp2, temp3;
1111	<	int n_per_extra;
1112	<	int n_extra;
1113	<	int have_extra, done;
742	>	//setup seed for random number generator
743	>	int seedValue;
744
745	<	temp1 = (double)tot_nmol / 4.0;
746	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1117	<	temp3 = ceil( temp2 );
745	>	if (globals->haveSeed()){
746	>	seedValue = globals->getSeed();
747
748	<	have_extra =0;
749	<	if( temp2 < temp3 ){ // we have a non-complete lattice
750	<	have_extra =1;
751	<
752	<	n_cells = (int)temp3 - 1;
1124	<	cellx = simnfo->boxLx / temp3;
1125	<	celly = simnfo->boxLy / temp3;
1126	<	cellz = simnfo->boxLz / temp3;
1127	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1128	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1129	<	n_per_extra = (int)ceil( temp1 );
1130	<
1131	<	if( n_per_extra > 4){
1132	<	sprintf( painCave.errMsg,
1133	<	"SimSetup error. There has been an error in constructing"
1134	<	" the non-complete lattice.\n" );
1135	<	painCave.isFatal = 1;
748	>	if(seedValue / 1E9 == 0){
749	>	sprintf(painCave.errMsg,
750	>	"Seed for sprng library should contain at least 9 digits\n"
751	>	"OOPSE will generate a seed for user\n");
752	>	painCave.isFatal = 0;
753		simError();
754	+
755	+	//using seed generated by system instead of invalid seed set by user
756	+	#ifndef IS_MPI
757	+	seedValue = make_sprng_seed();
758	+	#else
759	+	if (worldRank == 0){
760	+	seedValue = make_sprng_seed();
761	+	}
762	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
763	+	#endif
764		}
765	<	}
765	>	}//end of if branch of globals->haveSeed()
766		else{
767	<	n_cells = (int)temp3;
768	<	cellx = simnfo->boxLx / temp3;
769	<	celly = simnfo->boxLy / temp3;
770	<	cellz = simnfo->boxLz / temp3;
767	>
768	>	#ifndef IS_MPI
769	>	seedValue = make_sprng_seed();
770	>	#else
771	>	if (worldRank == 0){
772	>	seedValue = make_sprng_seed();
773	>	}
774	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
775	>	#endif
776	>	}//end of globals->haveSeed()
777	>
778	>	for (int i = 0; i < nInfo; i++){
779	>	info[i].setSeed(seedValue);
780		}
781
782	<	current_mol = 0;
783	<	current_comp_mol = 0;
784	<	current_comp = 0;
785	<	current_atom_ndx = 0;
782	>	#ifdef IS_MPI
783	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
784	>	MPIcheckPoint();
785	>	#endif // is_mpi
786	>	}
787
1151	–	for( i=0; i < n_cells ; i++ ){
1152	–	for( j=0; j < n_cells; j++ ){
1153	–	for( k=0; k < n_cells; k++ ){
788
789	<	makeElement( i * cellx,
790	<	j * celly,
791	<	k * cellz );
789	>	void SimSetup::finalInfoCheck(void){
790	>	int index;
791	>	int usesDipoles;
792	>	int i;
793
794	<	makeElement( i * cellx + 0.5 * cellx,
795	<	j * celly + 0.5 * celly,
1161	<	k * cellz );
794	>	for (i = 0; i < nInfo; i++){
795	>	// check electrostatic parameters
796
797	<	makeElement( i * cellx,
798	<	j * celly + 0.5 * celly,
799	<	k * cellz + 0.5 * cellz );
800	<
801	<	makeElement( i * cellx + 0.5 * cellx,
1168	<	j * celly,
1169	<	k * cellz + 0.5 * cellz );
1170	<	}
797	>	index = 0;
798	>	usesDipoles = 0;
799	>	while ((index < info[i].n_atoms) && !usesDipoles){
800	>	usesDipoles = (info[i].atoms[index])->hasDipole();
801	>	index++;
802		}
1172	–	}
803
804	<	if( have_extra ){
805	<	done = 0;
804	>	#ifdef IS_MPI
805	>	int myUse = usesDipoles;
806	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>	#endif //is_mpi
808
809	<	int start_ndx;
1178	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1179	<	for( j=0; j < (n_cells+1) && !done; j++ ){
809	>	double theEcr, theEst;
810
811	<	if( i < n_cells ){
811	>	if (globals->getUseRF()){
812	>	info[i].useReactionField = 1;
813
814	<	if( j < n_cells ){
815	<	start_ndx = n_cells;
816	<	}
817	<	else start_ndx = 0;
818	<	}
819	<	else start_ndx = 0;
814	>	if (!globals->haveECR()){
815	>	sprintf(painCave.errMsg,
816	>	"SimSetup Warning: using default value of 1/2 the smallest "
817	>	"box length for the electrostaticCutoffRadius.\n"
818	>	"I hope you have a very fast processor!\n");
819	>	painCave.isFatal = 0;
820	>	simError();
821	>	double smallest;
822	>	smallest = info[i].boxL[0];
823	>	if (info[i].boxL[1] <= smallest)
824	>	smallest = info[i].boxL[1];
825	>	if (info[i].boxL[2] <= smallest)
826	>	smallest = info[i].boxL[2];
827	>	theEcr = 0.5 * smallest;
828	>	}
829	>	else{
830	>	theEcr = globals->getECR();
831	>	}
832
833	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
833	>	if (!globals->haveEST()){
834	>	sprintf(painCave.errMsg,
835	>	"SimSetup Warning: using default value of 0.05 * the "
836	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
837	>	painCave.isFatal = 0;
838	>	simError();
839	>	theEst = 0.05 * theEcr;
840	>	}
841	>	else{
842	>	theEst = globals->getEST();
843	>	}
844
845	<	makeElement( i * cellx,
1193	<	j * celly,
1194	<	k * cellz );
1195	<	done = ( current_mol >= tot_nmol );
845	>	info[i].setEcr(theEcr, theEst);
846
847	<	if( !done && n_per_extra > 1 ){
848	<	makeElement( i * cellx + 0.5 * cellx,
849	<	j * celly + 0.5 * celly,
850	<	k * cellz );
851	<	done = ( current_mol >= tot_nmol );
852	<	}
847	>	if (!globals->haveDielectric()){
848	>	sprintf(painCave.errMsg,
849	>	"SimSetup Error: You are trying to use Reaction Field without"
850	>	"setting a dielectric constant!\n");
851	>	painCave.isFatal = 1;
852	>	simError();
853	>	}
854	>	info[i].dielectric = globals->getDielectric();
855	>	}
856	>	else{
857	>	if (usesDipoles){
858	>	if (!globals->haveECR()){
859	>	sprintf(painCave.errMsg,
860	>	"SimSetup Warning: using default value of 1/2 the smallest "
861	>	"box length for the electrostaticCutoffRadius.\n"
862	>	"I hope you have a very fast processor!\n");
863	>	painCave.isFatal = 0;
864	>	simError();
865	>	double smallest;
866	>	smallest = info[i].boxL[0];
867	>	if (info[i].boxL[1] <= smallest)
868	>	smallest = info[i].boxL[1];
869	>	if (info[i].boxL[2] <= smallest)
870	>	smallest = info[i].boxL[2];
871	>	theEcr = 0.5 * smallest;
872	>	}
873	>	else{
874	>	theEcr = globals->getECR();
875	>	}
876
877	<	if( !done && n_per_extra > 2){
878	<	makeElement( i * cellx,
879	<	j * celly + 0.5 * celly,
880	<	k * cellz + 0.5 * cellz );
881	<	done = ( current_mol >= tot_nmol );
882	<	}
877	>	if (!globals->haveEST()){
878	>	sprintf(painCave.errMsg,
879	>	"SimSetup Warning: using default value of 0.05 * the "
880	>	"electrostaticCutoffRadius for the "
881	>	"electrostaticSkinThickness\n");
882	>	painCave.isFatal = 0;
883	>	simError();
884	>	theEst = 0.05 * theEcr;
885	>	}
886	>	else{
887	>	theEst = globals->getEST();
888	>	}
889
890	<	if( !done && n_per_extra > 3){
1212	<	makeElement( i * cellx + 0.5 * cellx,
1213	<	j * celly,
1214	<	k * cellz + 0.5 * cellz );
1215	<	done = ( current_mol >= tot_nmol );
1216	<	}
1217	<	}
890	>	info[i].setEcr(theEcr, theEst);
891		}
892		}
893		}
894
895	+	#ifdef IS_MPI
896	+	strcpy(checkPointMsg, "post processing checks out");
897	+	MPIcheckPoint();
898	+	#endif // is_mpi
899	+	}
900
901	<	for( i=0; i<simnfo->n_atoms; i++ ){
902	<	simnfo->atoms[i]->set_vx( 0.0 );
903	<	simnfo->atoms[i]->set_vy( 0.0 );
904	<	simnfo->atoms[i]->set_vz( 0.0 );
901	>	void SimSetup::initSystemCoords(void){
902	>	int i;
903	>
904	>	char* inName;
905	>
906	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
907	>
908	>	for (i = 0; i < info[0].n_atoms; i++)
909	>	info[0].atoms[i]->setCoords();
910	>
911	>	if (globals->haveInitialConfig()){
912	>	InitializeFromFile* fileInit;
913	>	#ifdef IS_MPI // is_mpi
914	>	if (worldRank == 0){
915	>	#endif //is_mpi
916	>	inName = globals->getInitialConfig();
917	>	double* tempDouble = new double[1000000];
918	>	fileInit = new InitializeFromFile(inName);
919	>	#ifdef IS_MPI
920	>	}
921	>	else
922	>	fileInit = new InitializeFromFile(NULL);
923	>	#endif
924	>	fileInit->readInit(info); // default velocities on
925	>
926	>	delete fileInit;
927		}
928	<	}
928	>	else{
929	>	#ifdef IS_MPI
930
931	<	void SimSetup::makeElement( double x, double y, double z ){
931	>	// no init from bass
932
933	<	int k;
934	<	AtomStamp* current_atom;
935	<	DirectionalAtom* dAtom;
936	<	double rotMat[3][3];
933	>	sprintf(painCave.errMsg,
934	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
935	>	painCave.isFatal;
936	>	simError();
937
938	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
938	>	#else
939
940	<	current_atom = comp_stamps[current_comp]->getAtom( k );
941	<	if( !current_atom->havePosition() ){
942	<	sprintf( painCave.errMsg,
943	<	"SimSetup:initFromBass error.\n"
944	<	"\tComponent %s, atom %s does not have a position specified.\n"
945	<	"\tThe initialization routine is unable to give a start"
946	<	" position.\n",
947	<	comp_stamps[current_comp]->getID(),
948	<	current_atom->getType() );
940	>	initFromBass();
941	>
942	>
943	>	#endif
944	>	}
945	>
946	>	#ifdef IS_MPI
947	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
948	>	MPIcheckPoint();
949	>	#endif // is_mpi
950	>	}
951	>
952	>
953	>	void SimSetup::makeOutNames(void){
954	>	int k;
955	>
956	>
957	>	for (k = 0; k < nInfo; k++){
958	>	#ifdef IS_MPI
959	>	if (worldRank == 0){
960	>	#endif // is_mpi
961	>
962	>	if (globals->haveFinalConfig()){
963	>	strcpy(info[k].finalName, globals->getFinalConfig());
964	>	}
965	>	else{
966	>	strcpy(info[k].finalName, inFileName);
967	>	char* endTest;
968	>	int nameLength = strlen(info[k].finalName);
969	>	endTest = &(info[k].finalName[nameLength - 5]);
970	>	if (!strcmp(endTest, ".bass")){
971	>	strcpy(endTest, ".eor");
972	>	}
973	>	else if (!strcmp(endTest, ".BASS")){
974	>	strcpy(endTest, ".eor");
975	>	}
976	>	else{
977	>	endTest = &(info[k].finalName[nameLength - 4]);
978	>	if (!strcmp(endTest, ".bss")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".mdl")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	strcat(info[k].finalName, ".eor");
986	>	}
987	>	}
988	>	}
989	>
990	>	// make the sample and status out names
991	>
992	>	strcpy(info[k].sampleName, inFileName);
993	>	char* endTest;
994	>	int nameLength = strlen(info[k].sampleName);
995	>	endTest = &(info[k].sampleName[nameLength - 5]);
996	>	if (!strcmp(endTest, ".bass")){
997	>	strcpy(endTest, ".dump");
998	>	}
999	>	else if (!strcmp(endTest, ".BASS")){
1000	>	strcpy(endTest, ".dump");
1001	>	}
1002	>	else{
1003	>	endTest = &(info[k].sampleName[nameLength - 4]);
1004	>	if (!strcmp(endTest, ".bss")){
1005	>	strcpy(endTest, ".dump");
1006	>	}
1007	>	else if (!strcmp(endTest, ".mdl")){
1008	>	strcpy(endTest, ".dump");
1009	>	}
1010	>	else{
1011	>	strcat(info[k].sampleName, ".dump");
1012	>	}
1013	>	}
1014	>
1015	>	strcpy(info[k].statusName, inFileName);
1016	>	nameLength = strlen(info[k].statusName);
1017	>	endTest = &(info[k].statusName[nameLength - 5]);
1018	>	if (!strcmp(endTest, ".bass")){
1019	>	strcpy(endTest, ".stat");
1020	>	}
1021	>	else if (!strcmp(endTest, ".BASS")){
1022	>	strcpy(endTest, ".stat");
1023	>	}
1024	>	else{
1025	>	endTest = &(info[k].statusName[nameLength - 4]);
1026	>	if (!strcmp(endTest, ".bss")){
1027	>	strcpy(endTest, ".stat");
1028	>	}
1029	>	else if (!strcmp(endTest, ".mdl")){
1030	>	strcpy(endTest, ".stat");
1031	>	}
1032	>	else{
1033	>	strcat(info[k].statusName, ".stat");
1034	>	}
1035	>	}
1036	>
1037	>	#ifdef IS_MPI
1038	>
1039	>	}
1040	>	#endif // is_mpi
1041	>	}
1042	>	}
1043	>
1044	>
1045	>	void SimSetup::sysObjectsCreation(void){
1046	>	int i, k;
1047	>
1048	>	// create the forceField
1049	>
1050	>	createFF();
1051	>
1052	>	// extract componentList
1053	>
1054	>	compList();
1055	>
1056	>	// calc the number of atoms, bond, bends, and torsions
1057	>
1058	>	calcSysValues();
1059	>
1060	>	#ifdef IS_MPI
1061	>	// divide the molecules among the processors
1062	>
1063	>	mpiMolDivide();
1064	>	#endif //is_mpi
1065	>
1066	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1067	>
1068	>	makeSysArrays();
1069	>
1070	>	// make and initialize the molecules (all but atomic coordinates)
1071	>
1072	>	makeMolecules();
1073	>
1074	>	for (k = 0; k < nInfo; k++){
1075	>	info[k].identArray = new int[info[k].n_atoms];
1076	>	for (i = 0; i < info[k].n_atoms; i++){
1077	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1078	>	}
1079	>	}
1080	>	}
1081	>
1082	>
1083	>	void SimSetup::createFF(void){
1084	>	switch (ffCase){
1085	>	case FF_DUFF:
1086	>	the_ff = new DUFF();
1087	>	break;
1088	>
1089	>	case FF_LJ:
1090	>	the_ff = new LJFF();
1091	>	break;
1092	>
1093	>	case FF_EAM:
1094	>	the_ff = new EAM_FF();
1095	>	break;
1096	>
1097	>	default:
1098	>	sprintf(painCave.errMsg,
1099	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1100		painCave.isFatal = 1;
1101		simError();
1102	+	}
1103	+
1104	+	#ifdef IS_MPI
1105	+	strcpy(checkPointMsg, "ForceField creation successful");
1106	+	MPIcheckPoint();
1107	+	#endif // is_mpi
1108	+	}
1109	+
1110	+
1111	+	void SimSetup::compList(void){
1112	+	int i;
1113	+	char* id;
1114	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1115	+	LinkedMolStamp* currentStamp = NULL;
1116	+	comp_stamps = new MoleculeStamp * [n_components];
1117	+
1118	+	// make an array of molecule stamps that match the components used.
1119	+	// also extract the used stamps out into a separate linked list
1120	+
1121	+	for (i = 0; i < nInfo; i++){
1122	+	info[i].nComponents = n_components;
1123	+	info[i].componentsNmol = components_nmol;
1124	+	info[i].compStamps = comp_stamps;
1125	+	info[i].headStamp = headStamp;
1126	+	}
1127	+
1128	+
1129	+	for (i = 0; i < n_components; i++){
1130	+	id = the_components[i]->getType();
1131	+	comp_stamps[i] = NULL;
1132	+
1133	+	// check to make sure the component isn't already in the list
1134	+
1135	+	comp_stamps[i] = headStamp->match(id);
1136	+	if (comp_stamps[i] == NULL){
1137	+	// extract the component from the list;
1138	+
1139	+	currentStamp = stamps->extractMolStamp(id);
1140	+	if (currentStamp == NULL){
1141	+	sprintf(painCave.errMsg,
1142	+	"SimSetup error: Component \"%s\" was not found in the "
1143	+	"list of declared molecules\n",
1144	+	id);
1145	+	painCave.isFatal = 1;
1146	+	simError();
1147	+	}
1148	+
1149	+	headStamp->add(currentStamp);
1150	+	comp_stamps[i] = headStamp->match(id);
1151		}
1152	+	}
1153
1154	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1155	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1156	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1154	>	#ifdef IS_MPI
1155	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1156	>	MPIcheckPoint();
1157	>	#endif // is_mpi
1158	>	}
1159
1160	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1160	>	void SimSetup::calcSysValues(void){
1161	>	int i, j, k;
1162
1163	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1163	>	int* molMembershipArray;
1164
1165	<	rotMat[0][0] = 1.0;
1166	<	rotMat[0][1] = 0.0;
1167	<	rotMat[0][2] = 0.0;
1165	>	tot_atoms = 0;
1166	>	tot_bonds = 0;
1167	>	tot_bends = 0;
1168	>	tot_torsions = 0;
1169	>	for (i = 0; i < n_components; i++){
1170	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1172	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1173	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174	>	}
1175
1176	<	rotMat[1][0] = 0.0;
1177	<	rotMat[1][1] = 1.0;
1266	<	rotMat[1][2] = 0.0;
1176	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	>	molMembershipArray = new int[tot_atoms];
1178
1179	<	rotMat[2][0] = 0.0;
1180	<	rotMat[2][1] = 0.0;
1181	<	rotMat[2][2] = 1.0;
1179	>	for (i = 0; i < nInfo; i++){
1180	>	info[i].n_atoms = tot_atoms;
1181	>	info[i].n_bonds = tot_bonds;
1182	>	info[i].n_bends = tot_bends;
1183	>	info[i].n_torsions = tot_torsions;
1184	>	info[i].n_SRI = tot_SRI;
1185	>	info[i].n_mol = tot_nmol;
1186
1187	<	dAtom->setA( rotMat );
1187	>	info[i].molMembershipArray = molMembershipArray;
1188	>	}
1189	>	}
1190	>
1191	>	#ifdef IS_MPI
1192	>
1193	>	void SimSetup::mpiMolDivide(void){
1194	>	int i, j, k;
1195	>	int localMol, allMol;
1196	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1197	>
1198	>	mpiSim = new mpiSimulation(info);
1199	>
1200	>	globalIndex = mpiSim->divideLabor();
1201	>
1202	>	// set up the local variables
1203	>
1204	>	mol2proc = mpiSim->getMolToProcMap();
1205	>	molCompType = mpiSim->getMolComponentType();
1206	>
1207	>	allMol = 0;
1208	>	localMol = 0;
1209	>	local_atoms = 0;
1210	>	local_bonds = 0;
1211	>	local_bends = 0;
1212	>	local_torsions = 0;
1213	>	globalAtomIndex = 0;
1214	>
1215	>
1216	>	for (i = 0; i < n_components; i++){
1217	>	for (j = 0; j < components_nmol[i]; j++){
1218	>	if (mol2proc[allMol] == worldRank){
1219	>	local_atoms += comp_stamps[i]->getNAtoms();
1220	>	local_bonds += comp_stamps[i]->getNBonds();
1221	>	local_bends += comp_stamps[i]->getNBends();
1222	>	local_torsions += comp_stamps[i]->getNTorsions();
1223	>	localMol++;
1224	>	}
1225	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1226	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1227	>	globalAtomIndex++;
1228	>	}
1229	>
1230	>	allMol++;
1231		}
1232	+	}
1233	+	local_SRI = local_bonds + local_bends + local_torsions;
1234
1235	<	current_atom_ndx++;
1235	>	info[0].n_atoms = mpiSim->getMyNlocal();
1236	>
1237	>	if (local_atoms != info[0].n_atoms){
1238	>	sprintf(painCave.errMsg,
1239	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	>	" localAtom (%d) are not equal.\n",
1241	>	info[0].n_atoms, local_atoms);
1242	>	painCave.isFatal = 1;
1243	>	simError();
1244		}
1245
1246	<	current_mol++;
1247	<	current_comp_mol++;
1246	>	info[0].n_bonds = local_bonds;
1247	>	info[0].n_bends = local_bends;
1248	>	info[0].n_torsions = local_torsions;
1249	>	info[0].n_SRI = local_SRI;
1250	>	info[0].n_mol = localMol;
1251
1252	<	if( current_comp_mol >= components_nmol[current_comp] ){
1252	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1253	>	MPIcheckPoint();
1254	>	}
1255
1256	<	current_comp_mol = 0;
1257	<	current_comp++;
1256	>	#endif // is_mpi
1257	>
1258	>
1259	>	void SimSetup::makeSysArrays(void){
1260	>	int i, j, k, l;
1261	>
1262	>	Atom** the_atoms;
1263	>	Molecule* the_molecules;
1264	>	Exclude** the_excludes;
1265	>
1266	>
1267	>	for (l = 0; l < nInfo; l++){
1268	>	// create the atom and short range interaction arrays
1269	>
1270	>	the_atoms = new Atom * [info[l].n_atoms];
1271	>	the_molecules = new Molecule[info[l].n_mol];
1272	>	int molIndex;
1273	>
1274	>	// initialize the molecule's stampID's
1275	>
1276	>	#ifdef IS_MPI
1277	>
1278	>
1279	>	molIndex = 0;
1280	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1281	>	if (mol2proc[i] == worldRank){
1282	>	the_molecules[molIndex].setStampID(molCompType[i]);
1283	>	the_molecules[molIndex].setMyIndex(molIndex);
1284	>	the_molecules[molIndex].setGlobalIndex(i);
1285	>	molIndex++;
1286	>	}
1287	>	}
1288	>
1289	>	#else // is_mpi
1290	>
1291	>	molIndex = 0;
1292	>	globalAtomIndex = 0;
1293	>	for (i = 0; i < n_components; i++){
1294	>	for (j = 0; j < components_nmol[i]; j++){
1295	>	the_molecules[molIndex].setStampID(i);
1296	>	the_molecules[molIndex].setMyIndex(molIndex);
1297	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1298	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1299	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1300	>	globalAtomIndex++;
1301	>	}
1302	>	molIndex++;
1303	>	}
1304	>	}
1305	>
1306	>
1307	>	#endif // is_mpi
1308	>
1309	>
1310	>	if (info[l].n_SRI){
1311	>	Exclude::createArray(info[l].n_SRI);
1312	>	the_excludes = new Exclude * [info[l].n_SRI];
1313	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1314	>	the_excludes[ex] = new Exclude(ex);
1315	>	}
1316	>	info[l].globalExcludes = new int;
1317	>	info[l].n_exclude = info[l].n_SRI;
1318	>	}
1319	>	else{
1320	>	Exclude::createArray(1);
1321	>	the_excludes = new Exclude * ;
1322	>	the_excludes[0] = new Exclude(0);
1323	>	the_excludes[0]->setPair(0, 0);
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].globalExcludes[0] = 0;
1326	>	info[l].n_exclude = 0;
1327	>	}
1328	>
1329	>	// set the arrays into the SimInfo object
1330	>
1331	>	info[l].atoms = the_atoms;
1332	>	info[l].molecules = the_molecules;
1333	>	info[l].nGlobalExcludes = 0;
1334	>	info[l].excludes = the_excludes;
1335	>
1336	>	the_ff->setSimInfo(info);
1337		}
1338		}
1339	+
1340	+	void SimSetup::makeIntegrator(void){
1341	+	int k;
1342	+
1343	+	NVT<RealIntegrator>* myNVT = NULL;
1344	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1345	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1346	+
1347	+	for (k = 0; k < nInfo; k++){
1348	+	switch (ensembleCase){
1349	+	case NVE_ENS:
1350	+	if (globals->haveZconstraints()){
1351	+	setupZConstraint(info[k]);
1352	+	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1353	+	}
1354	+	else
1355	+	new NVE<RealIntegrator>(&(info[k]), the_ff);
1356	+	break;
1357	+
1358	+	case NVT_ENS:
1359	+	if (globals->haveZconstraints()){
1360	+	setupZConstraint(info[k]);
1361	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1362	+	}
1363	+	else
1364	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1365	+
1366	+	myNVT->setTargetTemp(globals->getTargetTemp());
1367	+
1368	+	if (globals->haveTauThermostat())
1369	+	myNVT->setTauThermostat(globals->getTauThermostat());
1370	+	else{
1371	+	sprintf(painCave.errMsg,
1372	+	"SimSetup error: If you use the NVT\n"
1373	+	"    ensemble, you must set tauThermostat.\n");
1374	+	painCave.isFatal = 1;
1375	+	simError();
1376	+	}
1377	+	break;
1378	+
1379	+	case NPTi_ENS:
1380	+	if (globals->haveZconstraints()){
1381	+	setupZConstraint(info[k]);
1382	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1383	+	}
1384	+	else
1385	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1386	+
1387	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1388	+
1389	+	if (globals->haveTargetPressure())
1390	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1391	+	else{
1392	+	sprintf(painCave.errMsg,
1393	+	"SimSetup error: If you use a constant pressure\n"
1394	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1395	+	painCave.isFatal = 1;
1396	+	simError();
1397	+	}
1398	+
1399	+	if (globals->haveTauThermostat())
1400	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1401	+	else{
1402	+	sprintf(painCave.errMsg,
1403	+	"SimSetup error: If you use an NPT\n"
1404	+	"    ensemble, you must set tauThermostat.\n");
1405	+	painCave.isFatal = 1;
1406	+	simError();
1407	+	}
1408	+
1409	+	if (globals->haveTauBarostat())
1410	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1411	+	else{
1412	+	sprintf(painCave.errMsg,
1413	+	"SimSetup error: If you use an NPT\n"
1414	+	"    ensemble, you must set tauBarostat.\n");
1415	+	painCave.isFatal = 1;
1416	+	simError();
1417	+	}
1418	+	break;
1419	+
1420	+	case NPTf_ENS:
1421	+	if (globals->haveZconstraints()){
1422	+	setupZConstraint(info[k]);
1423	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1424	+	}
1425	+	else
1426	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1427	+
1428	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1429	+
1430	+	if (globals->haveTargetPressure())
1431	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1432	+	else{
1433	+	sprintf(painCave.errMsg,
1434	+	"SimSetup error: If you use a constant pressure\n"
1435	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1436	+	painCave.isFatal = 1;
1437	+	simError();
1438	+	}
1439	+
1440	+	if (globals->haveTauThermostat())
1441	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1442	+	else{
1443	+	sprintf(painCave.errMsg,
1444	+	"SimSetup error: If you use an NPT\n"
1445	+	"    ensemble, you must set tauThermostat.\n");
1446	+	painCave.isFatal = 1;
1447	+	simError();
1448	+	}
1449	+
1450	+	if (globals->haveTauBarostat())
1451	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1452	+	else{
1453	+	sprintf(painCave.errMsg,
1454	+	"SimSetup error: If you use an NPT\n"
1455	+	"    ensemble, you must set tauBarostat.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+	break;
1460	+
1461	+	default:
1462	+	sprintf(painCave.errMsg,
1463	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1464	+	painCave.isFatal = 1;
1465	+	simError();
1466	+	}
1467	+	}
1468	+	}
1469	+
1470	+	void SimSetup::initFortran(void){
1471	+	info[0].refreshSim();
1472	+
1473	+	if (!strcmp(info[0].mixingRule, "standard")){
1474	+	the_ff->initForceField(LB_MIXING_RULE);
1475	+	}
1476	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1477	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1478	+	}
1479	+	else{
1480	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1481	+	info[0].mixingRule);
1482	+	painCave.isFatal = 1;
1483	+	simError();
1484	+	}
1485	+
1486	+
1487	+	#ifdef IS_MPI
1488	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1489	+	MPIcheckPoint();
1490	+	#endif // is_mpi
1491	+	}
1492	+
1493	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1494	+	int nZConstraints;
1495	+	ZconStamp** zconStamp;
1496	+
1497	+	if (globals->haveZconstraintTime()){
1498	+	//add sample time of z-constraint  into SimInfo's property list
1499	+	DoubleData* zconsTimeProp = new DoubleData();
1500	+	zconsTimeProp->setID(ZCONSTIME_ID);
1501	+	zconsTimeProp->setData(globals->getZconsTime());
1502	+	theInfo.addProperty(zconsTimeProp);
1503	+	}
1504	+	else{
1505	+	sprintf(painCave.errMsg,
1506	+	"ZConstraint error: If you use an ZConstraint\n"
1507	+	" , you must set sample time.\n");
1508	+	painCave.isFatal = 1;
1509	+	simError();
1510	+	}
1511	+
1512	+	//push zconsTol into siminfo, if user does not specify
1513	+	//value for zconsTol, a default value will be used
1514	+	DoubleData* zconsTol = new DoubleData();
1515	+	zconsTol->setID(ZCONSTOL_ID);
1516	+	if (globals->haveZconsTol()){
1517	+	zconsTol->setData(globals->getZconsTol());
1518	+	}
1519	+	else{
1520	+	double defaultZConsTol = 0.01;
1521	+	sprintf(painCave.errMsg,
1522	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1523	+	" , default value %f is used.\n",
1524	+	defaultZConsTol);
1525	+	painCave.isFatal = 0;
1526	+	simError();
1527	+
1528	+	zconsTol->setData(defaultZConsTol);
1529	+	}
1530	+	theInfo.addProperty(zconsTol);
1531	+
1532	+	//set Force Subtraction Policy
1533	+	StringData* zconsForcePolicy = new StringData();
1534	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1535	+
1536	+	if (globals->haveZconsForcePolicy()){
1537	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1538	+	}
1539	+	else{
1540	+	sprintf(painCave.errMsg,
1541	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1542	+	"PolicyByMass is used\n");
1543	+	painCave.isFatal = 0;
1544	+	simError();
1545	+	zconsForcePolicy->setData("BYMASS");
1546	+	}
1547	+
1548	+	theInfo.addProperty(zconsForcePolicy);
1549	+
1550	+	//Determine the name of ouput file and add it into SimInfo's property list
1551	+	//Be careful, do not use inFileName, since it is a pointer which
1552	+	//point to a string at master node, and slave nodes do not contain that string
1553	+
1554	+	string zconsOutput(theInfo.finalName);
1555	+
1556	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1557	+
1558	+	StringData* zconsFilename = new StringData();
1559	+	zconsFilename->setID(ZCONSFILENAME_ID);
1560	+	zconsFilename->setData(zconsOutput);
1561	+
1562	+	theInfo.addProperty(zconsFilename);
1563	+
1564	+	//setup index, pos and other parameters of z-constraint molecules
1565	+	nZConstraints = globals->getNzConstraints();
1566	+	theInfo.nZconstraints = nZConstraints;
1567	+
1568	+	zconStamp = globals->getZconStamp();
1569	+	ZConsParaItem tempParaItem;
1570	+
1571	+	ZConsParaData* zconsParaData = new ZConsParaData();
1572	+	zconsParaData->setID(ZCONSPARADATA_ID);
1573	+
1574	+	for (int i = 0; i < nZConstraints; i++){
1575	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1576	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1577	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1578	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1579	+
1580	+	zconsParaData->addItem(tempParaItem);
1581	+	}
1582	+
1583	+	//check the uniqueness of index
1584	+	if(!zconsParaData->isIndexUnique()){
1585	+	sprintf(painCave.errMsg,
1586	+	"ZConstraint Error: molIndex is not unique\n");
1587	+	painCave.isFatal = 1;
1588	+	simError();
1589	+	}
1590	+
1591	+	//sort the parameters by index of molecules
1592	+	zconsParaData->sortByIndex();
1593	+
1594	+	//push data into siminfo, therefore, we can retrieve later
1595	+	theInfo.addProperty(zconsParaData);
1596	+	}

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines