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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 605 by gezelter, Tue Jul 15 03:27:24 2003 UTC vs.
Revision 1167 by tim, Wed May 12 16:38:45 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 14 | Line 20
20
21		// some defines for ensemble and Forcefield  cases
22
23	<	#define NVE_ENS   0
24	<	#define NVT_ENS   1
25	<	#define NPTi_ENS  2
26	<	#define NPTf_ENS  3
27	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
23	>	#define NVE_ENS        0
24	>	#define NVT_ENS        1
25	>	#define NPTi_ENS       2
26	>	#define NPTf_ENS       3
27	>	#define NPTxyz_ENS     4
28
29
30	<	#define FF_DUFF 0
31	<	#define FF_LJ   1
30	>	#define FF_DUFF  0
31	>	#define FF_LJ    1
32	>	#define FF_EAM   2
33	>	#define FF_H2O   3
34
35	+	using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 41 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
126	<	MakeStamps *the_stamps;
82	<	Globals* the_globals;
83	<	int i, j, k, globalAtomIndex;
84	<
85	<	int ensembleCase;
86	<	int ffCase;
87	<
88	<	ensembleCase = -1;
89	<	ffCase = -1;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
96	<	simnfo->target_temp = the_globals->getTargetTemp();
97	<	simnfo->dt = the_globals->getDt();
98	<	simnfo->run_time = the_globals->getRunTime();
130	>	// creation of complex system objects
131
132	<	// get the ones we know are there, yet still may need some work.
101	<	n_components = the_globals->getNComponents();
102	<	strcpy( force_field, the_globals->getForceField() );
132	>	sysObjectsCreation();
133
134	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106	<	else{
107	<	sprintf( painCave.errMsg,
108	<	"SimSetup Error. Unrecognized force field -> %s\n",
109	<	force_field );
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
134	>	// check on the post processing info
135
136	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
136	>	finalInfoCheck();
137
138	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
139	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
140	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
141	<	ensembleCase = NPTi_ENS;
142	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
143	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
144	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124	<	else{
125	<	sprintf( painCave.errMsg,
126	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
127	<	"reverting to NVE for this simulation.\n",
128	<	ensemble );
129	<	painCave.isFatal = 0;
130	<	simError();
131	<	strcpy( ensemble, "NVE" );
132	<	ensembleCase = NVE_ENS;
138	>	// initialize the system coordinates
139	>
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142	>
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145		}
134	–	strcpy( simnfo->ensemble, ensemble );
146
147	+	// make the output filenames
148
149	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
150	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
151	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
152	<	//     if (the_globals->haveTargetPressure())
153	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142	<	//     else {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "SimSetup error: If you use the constant pressure\n"
145	<	//                "    ensemble, you must set targetPressure.\n"
146	<	//                "    This was found in the BASS file.\n");
147	<	//       painCave.isFatal = 1;
148	<	//       simError();
149	<	//     }
149	>	makeOutNames();
150	>
151	>	#ifdef IS_MPI
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	//     if (the_globals->haveTauThermostat())
152	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153	<	//     else if (the_globals->haveQmass())
154	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
155	<	//     else {
156	<	//       sprintf( painCave.errMsg,
157	<	//                "SimSetup error: If you use one of the constant temperature\n"
158	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
159	<	//                "    Neither of these was found in the BASS file.\n");
160	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
155	>	// initialize the Fortran
156
157	<	//     if (the_globals->haveTauBarostat())
165	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166	<	//     else {
167	<	//       sprintf( painCave.errMsg,
168	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
157	>	initFortran();
158
159	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
160	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
161	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	//     if (the_globals->haveTauThermostat())
180	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181	<	//     else if (the_globals->haveQmass())
182	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
183	<	//     else {
184	<	//       sprintf( painCave.errMsg,
185	<	//                "SimSetup error: If you use one of the constant temperature\n"
186	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
187	<	//                "    Neither of these was found in the BASS file.\n");
188	<	//       painCave.isFatal = 1;
189	<	//       simError();
190	<	//     }
166	>	}
167
192	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
193	–	simnfo->usePBC = the_globals->getPBC();
194	–
195	–	int usesDipoles = 0;
196	–	switch( ffCase ){
168
169	<	case FF_DUFF:
170	<	the_ff = new DUFF();
171	<	usesDipoles = 1;
172	<	break;
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175	>	molInit molInfo;
176	>	DirectionalAtom* dAtom;
177	>	RigidBody* myRB;
178	>	StuntDouble* mySD;
179	>	LinkedAssign* extras;
180	>	LinkedAssign* current_extra;
181	>	AtomStamp* currentAtom;
182	>	BondStamp* currentBond;
183	>	BendStamp* currentBend;
184	>	TorsionStamp* currentTorsion;
185	>	RigidBodyStamp* currentRigidBody;
186	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191	<	case FF_LJ:
192	<	the_ff = new LJFF();
193	<	break;
191	>	bond_pair* theBonds;
192	>	bend_set* theBends;
193	>	torsion_set* theTorsions;
194
195	<	default:
208	<	sprintf( painCave.errMsg,
209	<	"SimSetup Error. Unrecognized force field in case statement.\n");
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
195	>	set<int> skipList;
196
197	<	#ifdef IS_MPI
198	<	strcpy( checkPointMsg, "ForceField creation successful" );
199	<	MPIcheckPoint();
217	<	#endif // is_mpi
197	>	double phi, theta, psi;
198	>	char* molName;
199	>	char rbName[100];
200
201	<	// get the components and calculate the tot_nMol and indvidual n_mol
220	<	the_components = the_globals->getComponents();
221	<	components_nmol = new int[n_components];
222	<	comp_stamps = new MoleculeStamp*[n_components];
201	>	//init the forceField paramters
202
203	<	if( !the_globals->haveNMol() ){
225	<	// we don't have the total number of molecules, so we assume it is
226	<	// given in each component
203	>	the_ff->readParams();
204
205	<	tot_nmol = 0;
229	<	for( i=0; i<n_components; i++ ){
205	>	// init the atoms
206
207	<	if( !the_components[i]->haveNMol() ){
208	<	// we have a problem
209	<	sprintf( painCave.errMsg,
210	<	"SimSetup Error. No global NMol or component NMol"
235	<	" given. Cannot calculate the number of atoms.\n" );
236	<	painCave.isFatal = 1;
237	<	simError();
238	<	}
207	>	int nMembers, nNew, rb1, rb2;
208	>
209	>	for (k = 0; k < nInfo; k++){
210	>	the_ff->setSimInfo(&(info[k]));
211
212	<	tot_nmol += the_components[i]->getNMol();
241	<	components_nmol[i] = the_components[i]->getNMol();
242	<	}
243	<	}
244	<	else{
245	<	sprintf( painCave.errMsg,
246	<	"SimSetup error.\n"
247	<	"\tSorry, the ability to specify total"
248	<	" nMols and then give molfractions in the components\n"
249	<	"\tis not currently supported."
250	<	" Please give nMol in the components.\n" );
251	<	painCave.isFatal = 1;
252	<	simError();
253	<
254	<
255	<	//     tot_nmol = the_globals->getNMol();
256	<
257	<	//   //we have the total number of molecules, now we check for molfractions
258	<	//     for( i=0; i<n_components; i++ ){
259	<
260	<	//       if( !the_components[i]->haveMolFraction() ){
261	<
262	<	//  if( !the_components[i]->haveNMol() ){
263	<	//    //we have a problem
264	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
265	<	//              << " nMol was given in component
266	<
267	<	}
212	>	atomOffset = 0;
213
214	<	#ifdef IS_MPI
215	<	strcpy( checkPointMsg, "Have the number of components" );
216	<	MPIcheckPoint();
272	<	#endif // is_mpi
214	>	for (i = 0; i < info[k].n_mol; i++){
215	>	stampID = info[k].molecules[i].getStampID();
216	>	molName = comp_stamps[stampID]->getID();
217
218	<	// make an array of molecule stamps that match the components used.
219	<	// also extract the used stamps out into a separate linked list
218	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
221	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223
224	<	simnfo->nComponents = n_components;
225	<	simnfo->componentsNmol = components_nmol;
226	<	simnfo->compStamps = comp_stamps;
280	<	simnfo->headStamp = new LinkedMolStamp();
281	<
282	<	char* id;
283	<	LinkedMolStamp* headStamp = simnfo->headStamp;
284	<	LinkedMolStamp* currentStamp = NULL;
285	<	for( i=0; i<n_components; i++ ){
224	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225	>
226	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
227
228	<	id = the_components[i]->getType();
229	<	comp_stamps[i] = NULL;
230	<
231	<	// check to make sure the component isn't already in the list
228	>	if (molInfo.nBonds > 0)
229	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
230	>	else
231	>	molInfo.myBonds = NULL;
232
233	<	comp_stamps[i] = headStamp->match( id );
234	<	if( comp_stamps[i] == NULL ){
233	>	if (molInfo.nBends > 0)
234	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
235	>	else
236	>	molInfo.myBends = NULL;
237	>
238	>	if (molInfo.nTorsions > 0)
239	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
240	>	else
241	>	molInfo.myTorsions = NULL;
242	>
243	>	theBonds = new bond_pair[molInfo.nBonds];
244	>	theBends = new bend_set[molInfo.nBends];
245	>	theTorsions = new torsion_set[molInfo.nTorsions];
246
247	<	// extract the component from the list;
296	<
297	<	currentStamp = the_stamps->extractMolStamp( id );
298	<	if( currentStamp == NULL ){
299	<	sprintf( painCave.errMsg,
300	<	"SimSetup error: Component \"%s\" was not found in the "
301	<	"list of declared molecules\n",
302	<	id );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<
307	<	headStamp->add( currentStamp );
308	<	comp_stamps[i] = headStamp->match( id );
309	<	}
310	<	}
247	>	// make the Atoms
248
249	<	#ifdef IS_MPI
250	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
314	<	MPIcheckPoint();
315	<	#endif // is_mpi
316	<
249	>	for (j = 0; j < molInfo.nAtoms; j++){
250	>	currentAtom = comp_stamps[stampID]->getAtom(j);
251
252	+	if (currentAtom->haveOrientation()){
253	+	dAtom = new DirectionalAtom((j + atomOffset),
254	+	info[k].getConfiguration());
255	+	info[k].n_oriented++;
256	+	molInfo.myAtoms[j] = dAtom;
257
258	+	// Directional Atoms have standard unit vectors which are oriented
259	+	// in space using the three Euler angles.  We assume the standard
260	+	// unit vector was originally along the z axis below.
261
262	<	// caclulate the number of atoms, bonds, bends and torsions
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265
266	<	tot_atoms = 0;
267	<	tot_bonds = 0;
268	<	tot_bends = 0;
269	<	tot_torsions = 0;
326	<	for( i=0; i<n_components; i++ ){
327	<
328	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
329	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
330	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
331	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
332	<	}
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268	>	}
269	>	else{
270
271	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272
273	<	simnfo->n_atoms = tot_atoms;
337	<	simnfo->n_bonds = tot_bonds;
338	<	simnfo->n_bends = tot_bends;
339	<	simnfo->n_torsions = tot_torsions;
340	<	simnfo->n_SRI = tot_SRI;
341	<	simnfo->n_mol = tot_nmol;
342	<
343	<	simnfo->molMembershipArray = new int[tot_atoms];
273	>	}
274
275	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
277
278	<	// divide the molecules among processors here.
348	<
349	<	mpiSim = new mpiSimulation( simnfo );
350	<
351	<	globalIndex = mpiSim->divideLabor();
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279
280	<	// set up the local variables
281	<
355	<	int localMol, allMol;
356	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
280	>	#endif // is_mpi
281	>	}
282
283	<	int* mol2proc = mpiSim->getMolToProcMap();
284	<	int* molCompType = mpiSim->getMolComponentType();
285	<
286	<	allMol = 0;
287	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
283	>	// make the bonds
284	>	for (j = 0; j < molInfo.nBonds; j++){
285	>	currentBond = comp_stamps[stampID]->getBond(j);
286	>	theBonds[j].a = currentBond->getA() + atomOffset;
287	>	theBonds[j].b = currentBond->getB() + atomOffset;
288
289	+	tempI = theBonds[j].a;
290	+	tempJ = theBonds[j].b;
291
292	<	for( i=0; i<n_components; i++ ){
292	>	#ifdef IS_MPI
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299
300	<	for( j=0; j<components_nmol[i]; j++ ){
373	<
374	<	if( mol2proc[allMol] == worldRank ){
375	<
376	<	local_atoms +=    comp_stamps[i]->getNAtoms();
377	<	local_bonds +=    comp_stamps[i]->getNBonds();
378	<	local_bends +=    comp_stamps[i]->getNBends();
379	<	local_torsions += comp_stamps[i]->getNTorsions();
380	<	localMol++;
381	<	}
382	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
384	<	globalAtomIndex++;
300	>	info[k].excludes->addPair(exI, exJ);
301		}
302
303	<	allMol++;
304	<	}
305	<	}
306	<	local_SRI = local_bonds + local_bends + local_torsions;
307	<
308	<	simnfo->n_atoms = mpiSim->getMyNlocal();
393	<
394	<	if( local_atoms != simnfo->n_atoms ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
397	<	" localAtom (%d) are not equal.\n",
398	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
303	>	//make the bends
304	>	for (j = 0; j < molInfo.nBends; j++){
305	>	currentBend = comp_stamps[stampID]->getBend(j);
306	>	theBends[j].a = currentBend->getA() + atomOffset;
307	>	theBends[j].b = currentBend->getB() + atomOffset;
308	>	theBends[j].c = currentBend->getC() + atomOffset;
309
310	<	simnfo->n_bonds = local_bonds;
311	<	simnfo->n_bends = local_bends;
312	<	simnfo->n_torsions = local_torsions;
407	<	simnfo->n_SRI = local_SRI;
408	<	simnfo->n_mol = localMol;
310	>	if (currentBend->haveExtras()){
311	>	extras = currentBend->getExtras();
312	>	current_extra = extras;
313
314	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
315	<	MPIcheckPoint();
316	<
317	<
318	<	#endif // is_mpi
319	<
314	>	while (current_extra != NULL){
315	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
316	>	switch (current_extra->getType()){
317	>	case 0:
318	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	// create the atom and short range interaction arrays
323	<
324	<	Atom::createArrays(simnfo->n_atoms);
325	<	the_atoms = new Atom*[simnfo->n_atoms];
326	<	the_molecules = new Molecule[simnfo->n_mol];
422	<	int molIndex;
423	<
424	<	// initialize the molecule's stampID's
322	>	case 1:
323	>	theBends[j].ghost = (int) current_extra->getDouble() +
324	>	atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327
328	+	default:
329	+	sprintf(painCave.errMsg,
330	+	"SimSetup Error: ghostVectorSource was neither a "
331	+	"double nor an int.\n"
332	+	"-->Bend[%d] in %s\n",
333	+	j, comp_stamps[stampID]->getID());
334	+	painCave.isFatal = 1;
335	+	simError();
336	+	}
337	+	}
338	+	else{
339	+	sprintf(painCave.errMsg,
340	+	"SimSetup Error: unhandled bend assignment:\n"
341	+	"    -->%s in Bend[%d] in %s\n",
342	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
343	+	painCave.isFatal = 1;
344	+	simError();
345	+	}
346	+
347	+	current_extra = current_extra->getNext();
348	+	}
349	+	}
350	+
351	+	if (theBends[j].isGhost) {
352	+
353	+	tempI = theBends[j].a;
354	+	tempJ = theBends[j].b;
355	+
356		#ifdef IS_MPI
357	<
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364
365	<	molIndex = 0;
430	<	for(i=0; i<mpiSim->getTotNmol(); i++){
431	<
432	<	if(mol2proc[i] == worldRank ){
433	<	the_molecules[molIndex].setStampID( molCompType[i] );
434	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
365	>	} else {
366
367	<	#else // is_mpi
368	<
369	<	molIndex = 0;
370	<	globalAtomIndex = 0;
371	<	for(i=0; i<n_components; i++){
372	<	for(j=0; j<components_nmol[i]; j++ ){
373	<	the_molecules[molIndex].setStampID( i );
374	<	the_molecules[molIndex].setMyIndex( molIndex );
375	<	the_molecules[molIndex].setGlobalIndex( molIndex );
376	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
377	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
378	<	globalAtomIndex++;
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371	>	#ifdef IS_MPI
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385		}
453	–	molIndex++;
454	–	}
455	–	}
456	–
386
387	<	#endif // is_mpi
387	>	for (j = 0; j < molInfo.nTorsions; j++){
388	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
389	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
390	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
391	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
392	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
393
394	+	tempI = theTorsions[j].a;
395	+	tempJ = theTorsions[j].b;
396	+	tempK = theTorsions[j].c;
397	+	tempL = theTorsions[j].d;
398
399	<	if( simnfo->n_SRI ){
400	<
401	<	Exclude::createArray(simnfo->n_SRI);
402	<	the_excludes = new Exclude*[simnfo->n_SRI];
403	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
404	<	simnfo->globalExcludes = new int;
405	<	simnfo->n_exclude = simnfo->n_SRI;
406	<	}
407	<	else{
408	<
409	<	Exclude::createArray( 1 );
472	<	the_excludes = new Exclude*;
473	<	the_excludes[0] = new Exclude(0);
474	<	the_excludes[0]->setPair( 0,0 );
475	<	simnfo->globalExcludes = new int;
476	<	simnfo->globalExcludes[0] = 0;
477	<	simnfo->n_exclude = 0;
478	<	}
399	>	#ifdef IS_MPI
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409	>	#endif
410
411	<	// set the arrays into the SimInfo object
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417	>	}
418
419	<	simnfo->atoms = the_atoms;
420	<	simnfo->molecules = the_molecules;
421	<	simnfo->nGlobalExcludes = 0;
422	<	simnfo->excludes = the_excludes;
419	>
420	>	molInfo.myRigidBodies.clear();
421	>
422	>	for (j = 0; j < molInfo.nRigidBodies; j++){
423
424	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	+	nMembers = currentRigidBody->getNMembers();
426
427	<	// get some of the tricky things that may still be in the globals
427	>	// Create the Rigid Body:
428
429	<	double boxVector[3];
491	<	if( the_globals->haveBox() ){
492	<	boxVector[0] = the_globals->getBox();
493	<	boxVector[1] = the_globals->getBox();
494	<	boxVector[2] = the_globals->getBox();
495	<
496	<	simnfo->setBox( boxVector );
497	<	}
498	<	else if( the_globals->haveDensity() ){
429	>	myRB = new RigidBody();
430
431	<	double vol;
432	<	vol = (double)tot_nmol / the_globals->getDensity();
433	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
434	<	boxVector[1] = boxVector[0];
504	<	boxVector[2] = boxVector[0];
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435
436	<	simnfo->setBox( boxVector );
437	<	}
508	<	else{
509	<	if( !the_globals->haveBoxX() ){
510	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxX size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[0] = the_globals->getBoxX();
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438
439	<	if( !the_globals->haveBoxY() ){
440	<	sprintf( painCave.errMsg,
519	<	"SimSetup error, no periodic BoxY size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	boxVector[1] = the_globals->getBoxY();
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441
442	<	if( !the_globals->haveBoxZ() ){
443	<	sprintf( painCave.errMsg,
444	<	"SimSetup error, no periodic BoxZ size given.\n" );
528	<	painCave.isFatal = 1;
529	<	simError();
530	<	}
531	<	boxVector[2] = the_globals->getBoxZ();
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445
446	<	simnfo->setBox( boxVector );
447	<	}
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448
449	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	+
451	+	// Add this atom to the Skip List for the integrators
452		#ifdef IS_MPI
453	<	strcpy( checkPointMsg, "Box size set up" );
454	<	MPIcheckPoint();
455	<	#endif // is_mpi
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472	>	#ifdef IS_MPI
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484
485	+	molInfo.myRigidBodies.push_back(myRB);
486	+	info[k].rigidBodies.push_back(myRB);
487	+	}
488	+
489
490	<	// initialize the arrays
490	>	//create cutoff group for molecule
491
492	<	the_ff->setSimInfo( simnfo );
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
495	>	for (j = 0; j < nCutoffGroups; j++){
496
497	<	makeMolecules();
498	<	simnfo->identArray = new int[simnfo->n_atoms];
548	<	for(i=0; i<simnfo->n_atoms; i++){
549	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
550	<	}
551	<
552	<	if (the_globals->getUseRF() ) {
553	<	simnfo->useReactionField = 1;
554	<
555	<	if( !the_globals->haveECR() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 1/2 the smallest "
558	<	"box length for the electrostaticCutoffRadius.\n"
559	<	"I hope you have a very fast processor!\n");
560	<	painCave.isFatal = 0;
561	<	simError();
562	<	double smallest;
563	<	smallest = simnfo->boxLx;
564	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566	<	simnfo->ecr = 0.5 * smallest;
567	<	} else {
568	<	simnfo->ecr        = the_globals->getECR();
569	<	}
497	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	>	nMembers = currentCutoffGroup->getNMembers();
499
500	<	if( !the_globals->haveEST() ){
501	<	sprintf( painCave.errMsg,
502	<	"SimSetup Warning: using default value of 0.05 * the "
503	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
504	<	);
505	<	painCave.isFatal = 0;
506	<	simError();
507	<	simnfo->est = 0.05 * simnfo->ecr;
508	<	} else {
509	<	simnfo->est        = the_globals->getEST();
510	<	}
511	<
512	<	if(!the_globals->haveDielectric() ){
513	<	sprintf( painCave.errMsg,
514	<	"SimSetup Error: You are trying to use Reaction Field without"
515	<	"setting a dielectric constant!\n"
516	<	);
517	<	painCave.isFatal = 1;
518	<	simError();
519	<	}
520	<	simnfo->dielectric = the_globals->getDielectric();
521	<	} else {
522	<	if (usesDipoles) {
523	<
524	<	if( !the_globals->haveECR() ){
525	<	sprintf( painCave.errMsg,
526	<	"SimSetup Warning: using default value of 1/2 the smallest "
527	<	"box length for the electrostaticCutoffRadius.\n"
599	<	"I hope you have a very fast processor!\n");
600	<	painCave.isFatal = 0;
601	<	simError();
602	<	double smallest;
603	<	smallest = simnfo->boxLx;
604	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
605	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
606	<	simnfo->ecr = 0.5 * smallest;
607	<	} else {
608	<	simnfo->ecr        = the_globals->getECR();
500	>	myCutoffGroup = new CutoffGroup();
501	>
502	>	for (int cg = 0; cg < nMembers; cg++) {
503	>
504	>	// molI is atom numbering inside this molecule
505	>	molI = currentCutoffGroup->getMember(cg);
506	>
507	>	// tempI is atom numbering on local processor
508	>	tempI = molI + atomOffset;
509	>
510	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511	>
512	>	cutoffAtomSet.insert(tempI);
513	>	}
514	>
515	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517	>
518	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519	>
520	>	for(j = 0; j < molInfo.nAtoms; j++){
521	>
522	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	>	myCutoffGroup = new CutoffGroup();
524	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	>	}
527	>
528		}
529	+
530	+
531	+
532	+
533	+	// After this is all set up, scan through the atoms to
534	+	// see if they can be added to the integrableObjects:
535	+
536	+	molInfo.myIntegrableObjects.clear();
537
611	–	if( !the_globals->haveEST() ){
612	–	sprintf( painCave.errMsg,
613	–	"SimSetup Warning: using default value of 5%% of the "
614	–	"electrostaticCutoffRadius for the "
615	–	"electrostaticSkinThickness\n"
616	–	);
617	–	painCave.isFatal = 0;
618	–	simError();
619	–	simnfo->est = 0.05 * simnfo->ecr;
620	–	} else {
621	–	simnfo->est        = the_globals->getEST();
622	–	}
623	–	}
624	–	}
538
539	<	#ifdef IS_MPI
627	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
628	<	MPIcheckPoint();
629	<	#endif // is_mpi
539	>	for (j = 0; j < molInfo.nAtoms; j++){
540
631	–	if( the_globals->haveInitialConfig() ){
632	–
633	–	InitializeFromFile* fileInit;
634	–	#ifdef IS_MPI // is_mpi
635	–	if( worldRank == 0 ){
636	–	#endif //is_mpi
637	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
541		#ifdef IS_MPI
542	<	}else fileInit = new InitializeFromFile( NULL );
542	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	>	#else
544	>	slJ = j+atomOffset;
545		#endif
641	–	fileInit->read_xyz( simnfo ); // default velocities on
546
547	<	delete fileInit;
644	<	}
645	<	else{
547	>	// if they aren't on the skip list, then they can be integrated
548
549	<	#ifdef IS_MPI
549	>	if (skipList.find(slJ) == skipList.end()) {
550	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	>	info[k].integrableObjects.push_back(mySD);
552	>	molInfo.myIntegrableObjects.push_back(mySD);
553	>	}
554	>	}
555
556	<	// no init from bass
650	<
651	<	sprintf( painCave.errMsg,
652	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
653	<	painCave.isFatal;
654	<	simError();
655	<
656	<	#else
556	>	// all rigid bodies are integrated:
557
558	<	initFromBass();
558	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	>	info[k].integrableObjects.push_back(mySD);
561	>	molInfo.myIntegrableObjects.push_back(mySD);
562	>	}
563	>
564	>
565	>	// send the arrays off to the forceField for init.
566	>
567	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571	>	theTorsions);
572
573	+	info[k].molecules[i].initialize(molInfo);
574
661	–	#endif
662	–	}
575
576	+	atomOffset += molInfo.nAtoms;
577	+	delete[] theBonds;
578	+	delete[] theBends;
579	+	delete[] theTorsions;
580	+	}
581	+	}
582	+
583		#ifdef IS_MPI
584	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
584	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
585		MPIcheckPoint();
586		#endif // is_mpi
587
588	+	}
589
590	<
591	<
592	<
590	>	void SimSetup::initFromBass(void){
591	>	int i, j, k;
592	>	int n_cells;
593	>	double cellx, celly, cellz;
594	>	double temp1, temp2, temp3;
595	>	int n_per_extra;
596	>	int n_extra;
597	>	int have_extra, done;
598
599	<
600	<	#ifdef IS_MPI
601	<	if( worldRank == 0 ){
602	<	#endif // is_mpi
603	<
604	<	if( the_globals->haveFinalConfig() ){
605	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
599	>	double vel[3];
600	>	vel[0] = 0.0;
601	>	vel[1] = 0.0;
602	>	vel[2] = 0.0;
603	>
604	>	temp1 = (double) tot_nmol / 4.0;
605	>	temp2 = pow(temp1, (1.0 / 3.0));
606	>	temp3 = ceil(temp2);
607	>
608	>	have_extra = 0;
609	>	if (temp2 < temp3){
610	>	// we have a non-complete lattice
611	>	have_extra = 1;
612	>
613	>	n_cells = (int) temp3 - 1;
614	>	cellx = info[0].boxL[0] / temp3;
615	>	celly = info[0].boxL[1] / temp3;
616	>	cellz = info[0].boxL[2] / temp3;
617	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
618	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
619	>	n_per_extra = (int) ceil(temp1);
620	>
621	>	if (n_per_extra > 4){
622	>	sprintf(painCave.errMsg,
623	>	"SimSetup error. There has been an error in constructing"
624	>	" the non-complete lattice.\n");
625	>	painCave.isFatal = 1;
626	>	simError();
627		}
682	–	else{
683	–	strcpy( simnfo->finalName, inFileName );
684	–	char* endTest;
685	–	int nameLength = strlen( simnfo->finalName );
686	–	endTest = &(simnfo->finalName[nameLength - 5]);
687	–	if( !strcmp( endTest, ".bass" ) ){
688	–	strcpy( endTest, ".eor" );
689	–	}
690	–	else if( !strcmp( endTest, ".BASS" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else{
694	–	endTest = &(simnfo->finalName[nameLength - 4]);
695	–	if( !strcmp( endTest, ".bss" ) ){
696	–	strcpy( endTest, ".eor" );
697	–	}
698	–	else if( !strcmp( endTest, ".mdl" ) ){
699	–	strcpy( endTest, ".eor" );
700	–	}
701	–	else{
702	–	strcat( simnfo->finalName, ".eor" );
703	–	}
704	–	}
705	–	}
706	–
707	–	// make the sample and status out names
708	–
709	–	strcpy( simnfo->sampleName, inFileName );
710	–	char* endTest;
711	–	int nameLength = strlen( simnfo->sampleName );
712	–	endTest = &(simnfo->sampleName[nameLength - 5]);
713	–	if( !strcmp( endTest, ".bass" ) ){
714	–	strcpy( endTest, ".dump" );
715	–	}
716	–	else if( !strcmp( endTest, ".BASS" ) ){
717	–	strcpy( endTest, ".dump" );
718	–	}
719	–	else{
720	–	endTest = &(simnfo->sampleName[nameLength - 4]);
721	–	if( !strcmp( endTest, ".bss" ) ){
722	–	strcpy( endTest, ".dump" );
723	–	}
724	–	else if( !strcmp( endTest, ".mdl" ) ){
725	–	strcpy( endTest, ".dump" );
726	–	}
727	–	else{
728	–	strcat( simnfo->sampleName, ".dump" );
729	–	}
730	–	}
731	–
732	–	strcpy( simnfo->statusName, inFileName );
733	–	nameLength = strlen( simnfo->statusName );
734	–	endTest = &(simnfo->statusName[nameLength - 5]);
735	–	if( !strcmp( endTest, ".bass" ) ){
736	–	strcpy( endTest, ".stat" );
737	–	}
738	–	else if( !strcmp( endTest, ".BASS" ) ){
739	–	strcpy( endTest, ".stat" );
740	–	}
741	–	else{
742	–	endTest = &(simnfo->statusName[nameLength - 4]);
743	–	if( !strcmp( endTest, ".bss" ) ){
744	–	strcpy( endTest, ".stat" );
745	–	}
746	–	else if( !strcmp( endTest, ".mdl" ) ){
747	–	strcpy( endTest, ".stat" );
748	–	}
749	–	else{
750	–	strcat( simnfo->statusName, ".stat" );
751	–	}
752	–	}
753	–
754	–	#ifdef IS_MPI
628		}
756	–	#endif // is_mpi
757	–
758	–	// set the status, sample, and themal kick times
759	–
760	–	if( the_globals->haveSampleTime() ){
761	–	simnfo->sampleTime = the_globals->getSampleTime();
762	–	simnfo->statusTime = simnfo->sampleTime;
763	–	simnfo->thermalTime = simnfo->sampleTime;
764	–	}
629		else{
630	<	simnfo->sampleTime = the_globals->getRunTime();
631	<	simnfo->statusTime = simnfo->sampleTime;
632	<	simnfo->thermalTime = simnfo->sampleTime;
630	>	n_cells = (int) temp3;
631	>	cellx = info[0].boxL[0] / temp3;
632	>	celly = info[0].boxL[1] / temp3;
633	>	cellz = info[0].boxL[2] / temp3;
634		}
635
636	<	if( the_globals->haveStatusTime() ){
637	<	simnfo->statusTime = the_globals->getStatusTime();
638	<	}
636	>	current_mol = 0;
637	>	current_comp_mol = 0;
638	>	current_comp = 0;
639	>	current_atom_ndx = 0;
640
641	<	if( the_globals->haveThermalTime() ){
642	<	simnfo->thermalTime = the_globals->getThermalTime();
643	<	}
641	>	for (i = 0; i < n_cells ; i++){
642	>	for (j = 0; j < n_cells; j++){
643	>	for (k = 0; k < n_cells; k++){
644	>	makeElement(i * cellx, j * celly, k * cellz);
645
646	<	// check for the temperature set flag
646	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
647
648	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
648	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
649
650	+	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
651	+	}
652	+	}
653	+	}
654
655	<	// make the integrator
656	<
786	<
787	<	NVT*  myNVT = NULL;
788	<	NPTi* myNPTi = NULL;
789	<	NPTf* myNPTf = NULL;
790	<	NPTim* myNPTim = NULL;
791	<	NPTfm* myNPTfm = NULL;
655	>	if (have_extra){
656	>	done = 0;
657
658	<	switch( ensembleCase ){
658	>	int start_ndx;
659	>	for (i = 0; i < (n_cells + 1) && !done; i++){
660	>	for (j = 0; j < (n_cells + 1) && !done; j++){
661	>	if (i < n_cells){
662	>	if (j < n_cells){
663	>	start_ndx = n_cells;
664	>	}
665	>	else
666	>	start_ndx = 0;
667	>	}
668	>	else
669	>	start_ndx = 0;
670
671	<	case NVE_ENS:
672	<	new NVE( simnfo, the_ff );
673	<	break;
671	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
672	>	makeElement(i * cellx, j * celly, k * cellz);
673	>	done = (current_mol >= tot_nmol);
674
675	<	case NVT_ENS:
676	<	myNVT = new NVT( simnfo, the_ff );
677	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
675	>	if (!done && n_per_extra > 1){
676	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
677	>	k * cellz);
678	>	done = (current_mol >= tot_nmol);
679	>	}
680
681	<	if (the_globals->haveTauThermostat())
682	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
681	>	if (!done && n_per_extra > 2){
682	>	makeElement(i * cellx, j * celly + 0.5 * celly,
683	>	k * cellz + 0.5 * cellz);
684	>	done = (current_mol >= tot_nmol);
685	>	}
686
687	<	else {
688	<	sprintf( painCave.errMsg,
689	<	"SimSetup error: If you use the NVT\n"
690	<	"    ensemble, you must set tauThermostat.\n");
691	<	painCave.isFatal = 1;
692	<	simError();
687	>	if (!done && n_per_extra > 3){
688	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
689	>	k * cellz + 0.5 * cellz);
690	>	done = (current_mol >= tot_nmol);
691	>	}
692	>	}
693	>	}
694		}
695	<	break;
695	>	}
696
697	<	case NPTi_ENS:
698	<	myNPTi = new NPTi( simnfo, the_ff );
699	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
697	>	for (i = 0; i < info[0].n_atoms; i++){
698	>	info[0].atoms[i]->setVel(vel);
699	>	}
700	>	}
701
702	<	if (the_globals->haveTargetPressure())
703	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
704	<	else {
705	<	sprintf( painCave.errMsg,
706	<	"SimSetup error: If you use a constant pressure\n"
707	<	"    ensemble, you must set targetPressure in the BASS file.\n");
825	<	painCave.isFatal = 1;
826	<	simError();
827	<	}
828	<
829	<	if( the_globals->haveTauThermostat() )
830	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
831	<	else{
832	<	sprintf( painCave.errMsg,
833	<	"SimSetup error: If you use an NPT\n"
834	<	"    ensemble, you must set tauThermostat.\n");
835	<	painCave.isFatal = 1;
836	<	simError();
837	<	}
702	>	void SimSetup::makeElement(double x, double y, double z){
703	>	int k;
704	>	AtomStamp* current_atom;
705	>	DirectionalAtom* dAtom;
706	>	double rotMat[3][3];
707	>	double pos[3];
708
709	<	if( the_globals->haveTauBarostat() )
710	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
711	<	else{
712	<	sprintf( painCave.errMsg,
713	<	"SimSetup error: If you use an NPT\n"
714	<	"    ensemble, you must set tauBarostat.\n");
709	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
710	>	current_atom = comp_stamps[current_comp]->getAtom(k);
711	>	if (!current_atom->havePosition()){
712	>	sprintf(painCave.errMsg,
713	>	"SimSetup:initFromBass error.\n"
714	>	"\tComponent %s, atom %s does not have a position specified.\n"
715	>	"\tThe initialization routine is unable to give a start"
716	>	" position.\n",
717	>	comp_stamps[current_comp]->getID(), current_atom->getType());
718		painCave.isFatal = 1;
719		simError();
720		}
848	–	break;
721
722	<	case NPTf_ENS:
723	<	myNPTf = new NPTf( simnfo, the_ff );
724	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
722	>	pos[0] = x + current_atom->getPosX();
723	>	pos[1] = y + current_atom->getPosY();
724	>	pos[2] = z + current_atom->getPosZ();
725
726	<	if (the_globals->haveTargetPressure())
855	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
856	<	else {
857	<	sprintf( painCave.errMsg,
858	<	"SimSetup error: If you use a constant pressure\n"
859	<	"    ensemble, you must set targetPressure in the BASS file.\n");
860	<	painCave.isFatal = 1;
861	<	simError();
862	<	}
726	>	info[0].atoms[current_atom_ndx]->setPos(pos);
727
728	<	if( the_globals->haveTauThermostat() )
729	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
866	<	else{
867	<	sprintf( painCave.errMsg,
868	<	"SimSetup error: If you use an NPT\n"
869	<	"    ensemble, you must set tauThermostat.\n");
870	<	painCave.isFatal = 1;
871	<	simError();
872	<	}
728	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
729	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
730
731	<	if( the_globals->haveTauBarostat() )
732	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
733	<	else{
877	<	sprintf( painCave.errMsg,
878	<	"SimSetup error: If you use an NPT\n"
879	<	"    ensemble, you must set tauBarostat.\n");
880	<	painCave.isFatal = 1;
881	<	simError();
882	<	}
883	<	break;
884	<
885	<	case NPTim_ENS:
886	<	myNPTim = new NPTim( simnfo, the_ff );
887	<	myNPTim->setTargetTemp( the_globals->getTargetTemp());
731	>	rotMat[0][0] = 1.0;
732	>	rotMat[0][1] = 0.0;
733	>	rotMat[0][2] = 0.0;
734
735	<	if (the_globals->haveTargetPressure())
736	<	myNPTim->setTargetPressure(the_globals->getTargetPressure());
737	<	else {
738	<	sprintf( painCave.errMsg,
739	<	"SimSetup error: If you use a constant pressure\n"
740	<	"    ensemble, you must set targetPressure in the BASS file.\n");
741	<	painCave.isFatal = 1;
896	<	simError();
897	<	}
898	<
899	<	if( the_globals->haveTauThermostat() )
900	<	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
901	<	else{
902	<	sprintf( painCave.errMsg,
903	<	"SimSetup error: If you use an NPT\n"
904	<	"    ensemble, you must set tauThermostat.\n");
905	<	painCave.isFatal = 1;
906	<	simError();
907	<	}
735	>	rotMat[1][0] = 0.0;
736	>	rotMat[1][1] = 1.0;
737	>	rotMat[1][2] = 0.0;
738	>
739	>	rotMat[2][0] = 0.0;
740	>	rotMat[2][1] = 0.0;
741	>	rotMat[2][2] = 1.0;
742
743	<	if( the_globals->haveTauBarostat() )
910	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
911	<	else{
912	<	sprintf( painCave.errMsg,
913	<	"SimSetup error: If you use an NPT\n"
914	<	"    ensemble, you must set tauBarostat.\n");
915	<	painCave.isFatal = 1;
916	<	simError();
743	>	dAtom->setA(rotMat);
744		}
918	–	break;
745
746	<	case NPTfm_ENS:
747	<	myNPTfm = new NPTfm( simnfo, the_ff );
922	<	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
746	>	current_atom_ndx++;
747	>	}
748
749	<	if (the_globals->haveTargetPressure())
750	<	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
926	<	else {
927	<	sprintf( painCave.errMsg,
928	<	"SimSetup error: If you use a constant pressure\n"
929	<	"    ensemble, you must set targetPressure in the BASS file.\n");
930	<	painCave.isFatal = 1;
931	<	simError();
932	<	}
933	<
934	<	if( the_globals->haveTauThermostat() )
935	<	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
936	<	else{
937	<	sprintf( painCave.errMsg,
938	<	"SimSetup error: If you use an NPT\n"
939	<	"    ensemble, you must set tauThermostat.\n");
940	<	painCave.isFatal = 1;
941	<	simError();
942	<	}
749	>	current_mol++;
750	>	current_comp_mol++;
751
752	<	if( the_globals->haveTauBarostat() )
753	<	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
754	<	else{
947	<	sprintf( painCave.errMsg,
948	<	"SimSetup error: If you use an NPT\n"
949	<	"    ensemble, you must set tauBarostat.\n");
950	<	painCave.isFatal = 1;
951	<	simError();
952	<	}
953	<	break;
954	<
955	<	default:
956	<	sprintf( painCave.errMsg,
957	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
958	<	painCave.isFatal = 1;
959	<	simError();
752	>	if (current_comp_mol >= components_nmol[current_comp]){
753	>	current_comp_mol = 0;
754	>	current_comp++;
755		}
756	+	}
757
758
759	<	#ifdef IS_MPI
760	<	mpiSim->mpiRefresh();
965	<	#endif
759	>	void SimSetup::gatherInfo(void){
760	>	int i;
761
762	<	// initialize the Fortran
762	>	ensembleCase = -1;
763	>	ffCase = -1;
764
765	+	// set the easy ones first
766
767	<	simnfo->refreshSim();
768	<
769	<	if( !strcmp( simnfo->mixingRule, "standard") ){
770	<	the_ff->initForceField( LB_MIXING_RULE );
767	>	for (i = 0; i < nInfo; i++){
768	>	info[i].target_temp = globals->getTargetTemp();
769	>	info[i].dt = globals->getDt();
770	>	info[i].run_time = globals->getRunTime();
771		}
772	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
773	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
772	>	n_components = globals->getNComponents();
773	>
774	>
775	>	// get the forceField
776	>
777	>	strcpy(force_field, globals->getForceField());
778	>
779	>	if (!strcasecmp(force_field, "DUFF")){
780	>	ffCase = FF_DUFF;
781		}
782	+	else if (!strcasecmp(force_field, "LJ")){
783	+	ffCase = FF_LJ;
784	+	}
785	+	else if (!strcasecmp(force_field, "EAM")){
786	+	ffCase = FF_EAM;
787	+	}
788	+	else if (!strcasecmp(force_field, "WATER")){
789	+	ffCase = FF_H2O;
790	+	}
791		else{
792	<	sprintf( painCave.errMsg,
793	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
794	<	simnfo->mixingRule );
795	<	painCave.isFatal = 1;
983	<	simError();
792	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793	>	force_field);
794	>	painCave.isFatal = 1;
795	>	simError();
796		}
797
798	+	// get the ensemble
799
800	<	#ifdef IS_MPI
988	<	strcpy( checkPointMsg,
989	<	"Successfully intialized the mixingRule for Fortran." );
990	<	MPIcheckPoint();
991	<	#endif // is_mpi
992	<	}
800	>	strcpy(ensemble, globals->getEnsemble());
801
802	+	if (!strcasecmp(ensemble, "NVE")){
803	+	ensembleCase = NVE_ENS;
804	+	}
805	+	else if (!strcasecmp(ensemble, "NVT")){
806	+	ensembleCase = NVT_ENS;
807	+	}
808	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
809	+	ensembleCase = NPTi_ENS;
810	+	}
811	+	else if (!strcasecmp(ensemble, "NPTf")){
812	+	ensembleCase = NPTf_ENS;
813	+	}
814	+	else if (!strcasecmp(ensemble, "NPTxyz")){
815	+	ensembleCase = NPTxyz_ENS;
816	+	}
817	+	else{
818	+	sprintf(painCave.errMsg,
819	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	+	"\treverting to NVE for this simulation.\n",
821	+	ensemble);
822	+	painCave.isFatal = 0;
823	+	simError();
824	+	strcpy(ensemble, "NVE");
825	+	ensembleCase = NVE_ENS;
826	+	}
827
828	<	void SimSetup::makeMolecules( void ){
828	>	for (i = 0; i < nInfo; i++){
829	>	strcpy(info[i].ensemble, ensemble);
830
831	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
998	<	molInit info;
999	<	DirectionalAtom* dAtom;
1000	<	LinkedAssign* extras;
1001	<	LinkedAssign* current_extra;
1002	<	AtomStamp* currentAtom;
1003	<	BondStamp* currentBond;
1004	<	BendStamp* currentBend;
1005	<	TorsionStamp* currentTorsion;
831	>	// get the mixing rule
832
833	<	bond_pair* theBonds;
834	<	bend_set* theBends;
835	<	torsion_set* theTorsions;
833	>	strcpy(info[i].mixingRule, globals->getMixingRule());
834	>	info[i].usePBC = globals->getPBC();
835	>	}
836
837	<
1012	<	//init the forceField paramters
837	>	// get the components and calculate the tot_nMol and indvidual n_mol
838
839	<	the_ff->readParams();
839	>	the_components = globals->getComponents();
840	>	components_nmol = new int[n_components];
841
1016	–
1017	–	// init the atoms
842
843	<	double ux, uy, uz, u, uSqr;
844	<
845	<	atomOffset = 0;
1022	<	excludeOffset = 0;
1023	<	for(i=0; i<simnfo->n_mol; i++){
1024	<
1025	<	stampID = the_molecules[i].getStampID();
843	>	if (!globals->haveNMol()){
844	>	// we don't have the total number of molecules, so we assume it is
845	>	// given in each component
846
847	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
848	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
849	<	info.nBends    = comp_stamps[stampID]->getNBends();
850	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
851	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
852	<
853	<	info.myAtoms = &the_atoms[atomOffset];
854	<	info.myExcludes = &the_excludes[excludeOffset];
855	<	info.myBonds = new Bond*[info.nBonds];
1036	<	info.myBends = new Bend*[info.nBends];
1037	<	info.myTorsions = new Torsion*[info.nTorsions];
1038	<
1039	<	theBonds = new bond_pair[info.nBonds];
1040	<	theBends = new bend_set[info.nBends];
1041	<	theTorsions = new torsion_set[info.nTorsions];
1042	<
1043	<	// make the Atoms
1044	<
1045	<	for(j=0; j<info.nAtoms; j++){
1046	<
1047	<	currentAtom = comp_stamps[stampID]->getAtom( j );
1048	<	if( currentAtom->haveOrientation() ){
1049	<
1050	<	dAtom = new DirectionalAtom(j + atomOffset);
1051	<	simnfo->n_oriented++;
1052	<	info.myAtoms[j] = dAtom;
1053	<
1054	<	ux = currentAtom->getOrntX();
1055	<	uy = currentAtom->getOrntY();
1056	<	uz = currentAtom->getOrntZ();
1057	<
1058	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1059	<
1060	<	u = sqrt( uSqr );
1061	<	ux = ux / u;
1062	<	uy = uy / u;
1063	<	uz = uz / u;
1064	<
1065	<	dAtom->setSUx( ux );
1066	<	dAtom->setSUy( uy );
1067	<	dAtom->setSUz( uz );
1068	<	}
1069	<	else{
1070	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
1071	<	}
1072	<	info.myAtoms[j]->setType( currentAtom->getType() );
1073	<
1074	<	#ifdef IS_MPI
1075	<
1076	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1077	<
1078	<	#endif // is_mpi
1079	<	}
1080	<
1081	<	// make the bonds
1082	<	for(j=0; j<info.nBonds; j++){
1083	<
1084	<	currentBond = comp_stamps[stampID]->getBond( j );
1085	<	theBonds[j].a = currentBond->getA() + atomOffset;
1086	<	theBonds[j].b = currentBond->getB() + atomOffset;
1087	<
1088	<	exI = theBonds[j].a;
1089	<	exJ = theBonds[j].b;
1090	<
1091	<	// exclude_I must always be the smaller of the pair
1092	<	if( exI > exJ ){
1093	<	tempEx = exI;
1094	<	exI = exJ;
1095	<	exJ = tempEx;
847	>	tot_nmol = 0;
848	>	for (i = 0; i < n_components; i++){
849	>	if (!the_components[i]->haveNMol()){
850	>	// we have a problem
851	>	sprintf(painCave.errMsg,
852	>	"SimSetup Error. No global NMol or component NMol given.\n"
853	>	"\tCannot calculate the number of atoms.\n");
854	>	painCave.isFatal = 1;
855	>	simError();
856		}
1097	–	#ifdef IS_MPI
1098	–	tempEx = exI;
1099	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1100	–	tempEx = exJ;
1101	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1102	–
1103	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1104	–	#else  // isn't MPI
857
858	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
859	<	#endif  //is_mpi
858	>	tot_nmol += the_components[i]->getNMol();
859	>	components_nmol[i] = the_components[i]->getNMol();
860		}
861	<	excludeOffset += info.nBonds;
861	>	}
862	>	else{
863	>	sprintf(painCave.errMsg,
864	>	"SimSetup error.\n"
865	>	"\tSorry, the ability to specify total"
866	>	" nMols and then give molfractions in the components\n"
867	>	"\tis not currently supported."
868	>	" Please give nMol in the components.\n");
869	>	painCave.isFatal = 1;
870	>	simError();
871	>	}
872
873	<	//make the bends
874	<	for(j=0; j<info.nBends; j++){
875	<
876	<	currentBend = comp_stamps[stampID]->getBend( j );
877	<	theBends[j].a = currentBend->getA() + atomOffset;
878	<	theBends[j].b = currentBend->getB() + atomOffset;
879	<	theBends[j].c = currentBend->getC() + atomOffset;
880	<
881	<	if( currentBend->haveExtras() ){
882	<
1121	<	extras = currentBend->getExtras();
1122	<	current_extra = extras;
1123	<
1124	<	while( current_extra != NULL ){
1125	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1126	<
1127	<	switch( current_extra->getType() ){
1128	<
1129	<	case 0:
1130	<	theBends[j].ghost =
1131	<	current_extra->getInt() + atomOffset;
1132	<	theBends[j].isGhost = 1;
1133	<	break;
1134	<
1135	<	case 1:
1136	<	theBends[j].ghost =
1137	<	(int)current_extra->getDouble() + atomOffset;
1138	<	theBends[j].isGhost = 1;
1139	<	break;
1140	<
1141	<	default:
1142	<	sprintf( painCave.errMsg,
1143	<	"SimSetup Error: ghostVectorSource was neither a "
1144	<	"double nor an int.\n"
1145	<	"-->Bend[%d] in %s\n",
1146	<	j, comp_stamps[stampID]->getID() );
1147	<	painCave.isFatal = 1;
1148	<	simError();
1149	<	}
1150	<	}
1151	<
1152	<	else{
1153	<
1154	<	sprintf( painCave.errMsg,
1155	<	"SimSetup Error: unhandled bend assignment:\n"
1156	<	"    -->%s in Bend[%d] in %s\n",
1157	<	current_extra->getlhs(),
1158	<	j, comp_stamps[stampID]->getID() );
1159	<	painCave.isFatal = 1;
1160	<	simError();
1161	<	}
1162	<
1163	<	current_extra = current_extra->getNext();
1164	<	}
1165	<	}
1166	<
1167	<	if( !theBends[j].isGhost ){
1168	<
1169	<	exI = theBends[j].a;
1170	<	exJ = theBends[j].c;
1171	<	}
1172	<	else{
1173	<
1174	<	exI = theBends[j].a;
1175	<	exJ = theBends[j].b;
1176	<	}
1177	<
1178	<	// exclude_I must always be the smaller of the pair
1179	<	if( exI > exJ ){
1180	<	tempEx = exI;
1181	<	exI = exJ;
1182	<	exJ = tempEx;
1183	<	}
1184	<	#ifdef IS_MPI
1185	<	tempEx = exI;
1186	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1187	<	tempEx = exJ;
1188	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1189	<
1190	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1191	<	#else  // isn't MPI
1192	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1193	<	#endif  //is_mpi
1194	<	}
1195	<	excludeOffset += info.nBends;
873	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	>	sprintf(painCave.errMsg,
876	>	"Sample time is not divisible by dt.\n"
877	>	"\tThis will result in samples that are not uniformly\n"
878	>	"\tdistributed in time.  If this is a problem, change\n"
879	>	"\tyour sampleTime variable.\n");
880	>	painCave.isFatal = 0;
881	>	simError();
882	>	}
883
884	<	for(j=0; j<info.nTorsions; j++){
885	<
886	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
887	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
888	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
889	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
890	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
891	<
892	<	exI = theTorsions[j].a;
1206	<	exJ = theTorsions[j].d;
884	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	>	sprintf(painCave.errMsg,
886	>	"Status time is not divisible by dt.\n"
887	>	"\tThis will result in status reports that are not uniformly\n"
888	>	"\tdistributed in time.  If this is a problem, change \n"
889	>	"\tyour statusTime variable.\n");
890	>	painCave.isFatal = 0;
891	>	simError();
892	>	}
893
894	<	// exclude_I must always be the smaller of the pair
895	<	if( exI > exJ ){
896	<	tempEx = exI;
897	<	exI = exJ;
898	<	exJ = tempEx;
899	<	}
900	<	#ifdef IS_MPI
901	<	tempEx = exI;
902	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1217	<	tempEx = exJ;
1218	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1219	<
1220	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1221	<	#else  // isn't MPI
1222	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1223	<	#endif  //is_mpi
1224	<	}
1225	<	excludeOffset += info.nTorsions;
894	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	>	sprintf(painCave.errMsg,
896	>	"Thermal time is not divisible by dt.\n"
897	>	"\tThis will result in thermalizations that are not uniformly\n"
898	>	"\tdistributed in time.  If this is a problem, change \n"
899	>	"\tyour thermalTime variable.\n");
900	>	painCave.isFatal = 0;
901	>	simError();
902	>	}
903
904	<
905	<	// send the arrays off to the forceField for init.
904	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	>	sprintf(painCave.errMsg,
906	>	"Reset time is not divisible by dt.\n"
907	>	"\tThis will result in integrator resets that are not uniformly\n"
908	>	"\tdistributed in time.  If this is a problem, change\n"
909	>	"\tyour resetTime variable.\n");
910	>	painCave.isFatal = 0;
911	>	simError();
912	>	}
913
914	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1231	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1232	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1233	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
914	>	// set the status, sample, and thermal kick times
915
916	+	for (i = 0; i < nInfo; i++){
917	+	if (globals->haveSampleTime()){
918	+	info[i].sampleTime = globals->getSampleTime();
919	+	info[i].statusTime = info[i].sampleTime;
920	+	}
921	+	else{
922	+	info[i].sampleTime = globals->getRunTime();
923	+	info[i].statusTime = info[i].sampleTime;
924	+	}
925
926	<	the_molecules[i].initialize( info );
926	>	if (globals->haveStatusTime()){
927	>	info[i].statusTime = globals->getStatusTime();
928	>	}
929
930	+	if (globals->haveThermalTime()){
931	+	info[i].thermalTime = globals->getThermalTime();
932	+	} else {
933	+	info[i].thermalTime = globals->getRunTime();
934	+	}
935
936	<	atomOffset += info.nAtoms;
937	<	delete[] theBonds;
938	<	delete[] theBends;
939	<	delete[] theTorsions;
936	>	info[i].resetIntegrator = 0;
937	>	if( globals->haveResetTime() ){
938	>	info[i].resetTime = globals->getResetTime();
939	>	info[i].resetIntegrator = 1;
940	>	}
941	>
942	>	// check for the temperature set flag
943	>
944	>	if (globals->haveTempSet())
945	>	info[i].setTemp = globals->getTempSet();
946	>
947	>	// check for the extended State init
948	>
949	>	info[i].useInitXSstate = globals->getUseInitXSstate();
950	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951	>
952		}
953	+
954	+	//setup seed for random number generator
955	+	int seedValue;
956
957	+	if (globals->haveSeed()){
958	+	seedValue = globals->getSeed();
959	+
960	+	if(seedValue / 1E9 == 0){
961	+	sprintf(painCave.errMsg,
962	+	"Seed for sprng library should contain at least 9 digits\n"
963	+	"OOPSE will generate a seed for user\n");
964	+	painCave.isFatal = 0;
965	+	simError();
966	+
967	+	//using seed generated by system instead of invalid seed set by user
968	+	#ifndef IS_MPI
969	+	seedValue = make_sprng_seed();
970	+	#else
971	+	if (worldRank == 0){
972	+	seedValue = make_sprng_seed();
973	+	}
974	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
975	+	#endif
976	+	}
977	+	}//end of if branch of globals->haveSeed()
978	+	else{
979	+
980	+	#ifndef IS_MPI
981	+	seedValue = make_sprng_seed();
982	+	#else
983	+	if (worldRank == 0){
984	+	seedValue = make_sprng_seed();
985	+	}
986	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
987	+	#endif
988	+	}//end of globals->haveSeed()
989	+
990	+	for (int i = 0; i < nInfo; i++){
991	+	info[i].setSeed(seedValue);
992	+	}
993	+
994		#ifdef IS_MPI
995	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
995	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
996		MPIcheckPoint();
997		#endif // is_mpi
998	+	}
999
1000	+
1001	+	void SimSetup::finalInfoCheck(void){
1002	+	int index;
1003	+	int usesDipoles;
1004	+	int usesCharges;
1005	+	int i;
1006	+
1007	+	for (i = 0; i < nInfo; i++){
1008	+	// check electrostatic parameters
1009	+
1010	+	index = 0;
1011	+	usesDipoles = 0;
1012	+	while ((index < info[i].n_atoms) && !usesDipoles){
1013	+	usesDipoles = (info[i].atoms[index])->hasDipole();
1014	+	index++;
1015	+	}
1016	+	index = 0;
1017	+	usesCharges = 0;
1018	+	while ((index < info[i].n_atoms) && !usesCharges){
1019	+	usesCharges= (info[i].atoms[index])->hasCharge();
1020	+	index++;
1021	+	}
1022	+	#ifdef IS_MPI
1023	+	int myUse = usesDipoles;
1024	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1025	+	#endif //is_mpi
1026	+
1027	+	double theRcut, theRsw;
1028	+
1029	+	if (globals->haveRcut()) {
1030	+	theRcut = globals->getRcut();
1031	+
1032	+	if (globals->haveRsw())
1033	+	theRsw = globals->getRsw();
1034	+	else
1035	+	theRsw = theRcut;
1036	+
1037	+	info[i].setDefaultRcut(theRcut, theRsw);
1038	+
1039	+	} else {
1040	+
1041	+	the_ff->calcRcut();
1042	+	theRcut = info[i].getRcut();
1043	+
1044	+	if (globals->haveRsw())
1045	+	theRsw = globals->getRsw();
1046	+	else
1047	+	theRsw = theRcut;
1048	+
1049	+	info[i].setDefaultRcut(theRcut, theRsw);
1050	+	}
1051	+
1052	+	if (globals->getUseRF()){
1053	+	info[i].useReactionField = 1;
1054	+
1055	+	if (!globals->haveRcut()){
1056	+	sprintf(painCave.errMsg,
1057	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1058	+	"\tOOPSE will use a default value of 15.0 angstroms"
1059	+	"\tfor the cutoffRadius.\n");
1060	+	painCave.isFatal = 0;
1061	+	simError();
1062	+	theRcut = 15.0;
1063	+	}
1064	+	else{
1065	+	theRcut = globals->getRcut();
1066	+	}
1067	+
1068	+	if (!globals->haveRsw()){
1069	+	sprintf(painCave.errMsg,
1070	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1071	+	"\tOOPSE will use a default value of\n"
1072	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1073	+	painCave.isFatal = 0;
1074	+	simError();
1075	+	theRsw = 0.95 * theRcut;
1076	+	}
1077	+	else{
1078	+	theRsw = globals->getRsw();
1079	+	}
1080	+
1081	+	info[i].setDefaultRcut(theRcut, theRsw);
1082	+
1083	+	if (!globals->haveDielectric()){
1084	+	sprintf(painCave.errMsg,
1085	+	"SimSetup Error: No Dielectric constant was set.\n"
1086	+	"\tYou are trying to use Reaction Field without"
1087	+	"\tsetting a dielectric constant!\n");
1088	+	painCave.isFatal = 1;
1089	+	simError();
1090	+	}
1091	+	info[i].dielectric = globals->getDielectric();
1092	+	}
1093	+	else{
1094	+	if (usesDipoles || usesCharges){
1095	+
1096	+	if (!globals->haveRcut()){
1097	+	sprintf(painCave.errMsg,
1098	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1099	+	"\tOOPSE will use a default value of 15.0 angstroms"
1100	+	"\tfor the cutoffRadius.\n");
1101	+	painCave.isFatal = 0;
1102	+	simError();
1103	+	theRcut = 15.0;
1104	+	}
1105	+	else{
1106	+	theRcut = globals->getRcut();
1107	+	}
1108	+
1109	+	if (!globals->haveRsw()){
1110	+	sprintf(painCave.errMsg,
1111	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1112	+	"\tOOPSE will use a default value of\n"
1113	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1114	+	painCave.isFatal = 0;
1115	+	simError();
1116	+	theRsw = 0.95 * theRcut;
1117	+	}
1118	+	else{
1119	+	theRsw = globals->getRsw();
1120	+	}
1121	+
1122	+	info[i].setDefaultRcut(theRcut, theRsw);
1123	+
1124	+	}
1125	+	}
1126	+	}
1127	+	#ifdef IS_MPI
1128	+	strcpy(checkPointMsg, "post processing checks out");
1129	+	MPIcheckPoint();
1130	+	#endif // is_mpi
1131	+
1132		// clean up the forcefield
1251	–	the_ff->calcRcut();
1133		the_ff->cleanMe();
1253	–
1134		}
1135	+
1136	+	void SimSetup::initSystemCoords(void){
1137	+	int i;
1138
1139	<	void SimSetup::initFromBass( void ){
1139	>	char* inName;
1140
1141	<	int i, j, k;
1259	<	int n_cells;
1260	<	double cellx, celly, cellz;
1261	<	double temp1, temp2, temp3;
1262	<	int n_per_extra;
1263	<	int n_extra;
1264	<	int have_extra, done;
1141	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1142
1143	<	temp1 = (double)tot_nmol / 4.0;
1144	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1268	<	temp3 = ceil( temp2 );
1143	>	for (i = 0; i < info[0].n_atoms; i++)
1144	>	info[0].atoms[i]->setCoords();
1145
1146	<	have_extra =0;
1147	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1148	<	have_extra =1;
1146	>	if (globals->haveInitialConfig()){
1147	>	InitializeFromFile* fileInit;
1148	>	#ifdef IS_MPI // is_mpi
1149	>	if (worldRank == 0){
1150	>	#endif //is_mpi
1151	>	inName = globals->getInitialConfig();
1152	>	fileInit = new InitializeFromFile(inName);
1153	>	#ifdef IS_MPI
1154	>	}
1155	>	else
1156	>	fileInit = new InitializeFromFile(NULL);
1157	>	#endif
1158	>	fileInit->readInit(info); // default velocities on
1159
1160	<	n_cells = (int)temp3 - 1;
1161	<	cellx = simnfo->boxLx / temp3;
1162	<	celly = simnfo->boxLy / temp3;
1163	<	cellz = simnfo->boxLz / temp3;
1164	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1165	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1166	<	n_per_extra = (int)ceil( temp1 );
1167	<
1168	<	if( n_per_extra > 4){
1169	<	sprintf( painCave.errMsg,
1170	<	"SimSetup error. There has been an error in constructing"
1285	<	" the non-complete lattice.\n" );
1286	<	painCave.isFatal = 1;
1287	<	simError();
1288	<	}
1160	>	delete fileInit;
1161	>	}
1162	>	else{
1163	>
1164	>	// no init from bass
1165	>
1166	>	sprintf(painCave.errMsg,
1167	>	"Cannot intialize a simulation without an initial configuration file.\n");
1168	>	painCave.isFatal = 1;;
1169	>	simError();
1170	>
1171		}
1290	–	else{
1291	–	n_cells = (int)temp3;
1292	–	cellx = simnfo->boxLx / temp3;
1293	–	celly = simnfo->boxLy / temp3;
1294	–	cellz = simnfo->boxLz / temp3;
1295	–	}
1172
1173	<	current_mol = 0;
1174	<	current_comp_mol = 0;
1175	<	current_comp = 0;
1176	<	current_atom_ndx = 0;
1173	>	#ifdef IS_MPI
1174	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1175	>	MPIcheckPoint();
1176	>	#endif // is_mpi
1177	>	}
1178
1302	–	for( i=0; i < n_cells ; i++ ){
1303	–	for( j=0; j < n_cells; j++ ){
1304	–	for( k=0; k < n_cells; k++ ){
1179
1180	<	makeElement( i * cellx,
1181	<	j * celly,
1308	<	k * cellz );
1180	>	void SimSetup::makeOutNames(void){
1181	>	int k;
1182
1310	–	makeElement( i * cellx + 0.5 * cellx,
1311	–	j * celly + 0.5 * celly,
1312	–	k * cellz );
1183
1184	<	makeElement( i * cellx,
1185	<	j * celly + 0.5 * celly,
1186	<	k * cellz + 0.5 * cellz );
1184	>	for (k = 0; k < nInfo; k++){
1185	>	#ifdef IS_MPI
1186	>	if (worldRank == 0){
1187	>	#endif // is_mpi
1188
1189	<	makeElement( i * cellx + 0.5 * cellx,
1190	<	j * celly,
1320	<	k * cellz + 0.5 * cellz );
1189	>	if (globals->haveFinalConfig()){
1190	>	strcpy(info[k].finalName, globals->getFinalConfig());
1191		}
1192	<	}
1193	<	}
1192	>	else{
1193	>	strcpy(info[k].finalName, inFileName);
1194	>	char* endTest;
1195	>	int nameLength = strlen(info[k].finalName);
1196	>	endTest = &(info[k].finalName[nameLength - 5]);
1197	>	if (!strcmp(endTest, ".bass")){
1198	>	strcpy(endTest, ".eor");
1199	>	}
1200	>	else if (!strcmp(endTest, ".BASS")){
1201	>	strcpy(endTest, ".eor");
1202	>	}
1203	>	else{
1204	>	endTest = &(info[k].finalName[nameLength - 4]);
1205	>	if (!strcmp(endTest, ".bss")){
1206	>	strcpy(endTest, ".eor");
1207	>	}
1208	>	else if (!strcmp(endTest, ".mdl")){
1209	>	strcpy(endTest, ".eor");
1210	>	}
1211	>	else{
1212	>	strcat(info[k].finalName, ".eor");
1213	>	}
1214	>	}
1215	>	}
1216
1217	<	if( have_extra ){
1326	<	done = 0;
1217	>	// make the sample and status out names
1218
1219	<	int start_ndx;
1220	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1221	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1219	>	strcpy(info[k].sampleName, inFileName);
1220	>	char* endTest;
1221	>	int nameLength = strlen(info[k].sampleName);
1222	>	endTest = &(info[k].sampleName[nameLength - 5]);
1223	>	if (!strcmp(endTest, ".bass")){
1224	>	strcpy(endTest, ".dump");
1225	>	}
1226	>	else if (!strcmp(endTest, ".BASS")){
1227	>	strcpy(endTest, ".dump");
1228	>	}
1229	>	else{
1230	>	endTest = &(info[k].sampleName[nameLength - 4]);
1231	>	if (!strcmp(endTest, ".bss")){
1232	>	strcpy(endTest, ".dump");
1233	>	}
1234	>	else if (!strcmp(endTest, ".mdl")){
1235	>	strcpy(endTest, ".dump");
1236	>	}
1237	>	else{
1238	>	strcat(info[k].sampleName, ".dump");
1239	>	}
1240	>	}
1241
1242	<	if( i < n_cells ){
1242	>	strcpy(info[k].statusName, inFileName);
1243	>	nameLength = strlen(info[k].statusName);
1244	>	endTest = &(info[k].statusName[nameLength - 5]);
1245	>	if (!strcmp(endTest, ".bass")){
1246	>	strcpy(endTest, ".stat");
1247	>	}
1248	>	else if (!strcmp(endTest, ".BASS")){
1249	>	strcpy(endTest, ".stat");
1250	>	}
1251	>	else{
1252	>	endTest = &(info[k].statusName[nameLength - 4]);
1253	>	if (!strcmp(endTest, ".bss")){
1254	>	strcpy(endTest, ".stat");
1255	>	}
1256	>	else if (!strcmp(endTest, ".mdl")){
1257	>	strcpy(endTest, ".stat");
1258	>	}
1259	>	else{
1260	>	strcat(info[k].statusName, ".stat");
1261	>	}
1262	>	}
1263
1264	<	if( j < n_cells ){
1335	<	start_ndx = n_cells;
1336	<	}
1337	<	else start_ndx = 0;
1338	<	}
1339	<	else start_ndx = 0;
1264	>	#ifdef IS_MPI
1265
1266	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1266	>	}
1267	>	#endif // is_mpi
1268	>	}
1269	>	}
1270
1343	–	makeElement( i * cellx,
1344	–	j * celly,
1345	–	k * cellz );
1346	–	done = ( current_mol >= tot_nmol );
1271
1272	<	if( !done && n_per_extra > 1 ){
1273	<	makeElement( i * cellx + 0.5 * cellx,
1350	<	j * celly + 0.5 * celly,
1351	<	k * cellz );
1352	<	done = ( current_mol >= tot_nmol );
1353	<	}
1272	>	void SimSetup::sysObjectsCreation(void){
1273	>	int i, k;
1274
1275	<	if( !done && n_per_extra > 2){
1356	<	makeElement( i * cellx,
1357	<	j * celly + 0.5 * celly,
1358	<	k * cellz + 0.5 * cellz );
1359	<	done = ( current_mol >= tot_nmol );
1360	<	}
1275	>	// create the forceField
1276
1277	<	if( !done && n_per_extra > 3){
1363	<	makeElement( i * cellx + 0.5 * cellx,
1364	<	j * celly,
1365	<	k * cellz + 0.5 * cellz );
1366	<	done = ( current_mol >= tot_nmol );
1367	<	}
1368	<	}
1369	<	}
1370	<	}
1371	<	}
1277	>	createFF();
1278
1279	+	// extract componentList
1280
1281	<	for( i=0; i<simnfo->n_atoms; i++ ){
1375	<	simnfo->atoms[i]->set_vx( 0.0 );
1376	<	simnfo->atoms[i]->set_vy( 0.0 );
1377	<	simnfo->atoms[i]->set_vz( 0.0 );
1378	<	}
1379	<	}
1281	>	compList();
1282
1283	<	void SimSetup::makeElement( double x, double y, double z ){
1283	>	// calc the number of atoms, bond, bends, and torsions
1284
1285	<	int k;
1384	<	AtomStamp* current_atom;
1385	<	DirectionalAtom* dAtom;
1386	<	double rotMat[3][3];
1285	>	calcSysValues();
1286
1287	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1287	>	#ifdef IS_MPI
1288	>	// divide the molecules among the processors
1289
1290	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1291	<	if( !current_atom->havePosition() ){
1392	<	sprintf( painCave.errMsg,
1393	<	"SimSetup:initFromBass error.\n"
1394	<	"\tComponent %s, atom %s does not have a position specified.\n"
1395	<	"\tThe initialization routine is unable to give a start"
1396	<	" position.\n",
1397	<	comp_stamps[current_comp]->getID(),
1398	<	current_atom->getType() );
1399	<	painCave.isFatal = 1;
1400	<	simError();
1401	<	}
1290	>	mpiMolDivide();
1291	>	#endif //is_mpi
1292
1293	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1404	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1405	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1293	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1294
1295	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1295	>	makeSysArrays();
1296
1297	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1297	>	// make and initialize the molecules (all but atomic coordinates)
1298
1299	<	rotMat[0][0] = 1.0;
1412	<	rotMat[0][1] = 0.0;
1413	<	rotMat[0][2] = 0.0;
1299	>	makeMolecules();
1300
1301	<	rotMat[1][0] = 0.0;
1302	<	rotMat[1][1] = 1.0;
1303	<	rotMat[1][2] = 0.0;
1301	>	for (k = 0; k < nInfo; k++){
1302	>	info[k].identArray = new int[info[k].n_atoms];
1303	>	for (i = 0; i < info[k].n_atoms; i++){
1304	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1305	>	}
1306	>	}
1307	>	}
1308
1419	–	rotMat[2][0] = 0.0;
1420	–	rotMat[2][1] = 0.0;
1421	–	rotMat[2][2] = 1.0;
1309
1310	<	dAtom->setA( rotMat );
1310	>	void SimSetup::createFF(void){
1311	>	switch (ffCase){
1312	>	case FF_DUFF:
1313	>	the_ff = new DUFF();
1314	>	break;
1315	>
1316	>	case FF_LJ:
1317	>	the_ff = new LJFF();
1318	>	break;
1319	>
1320	>	case FF_EAM:
1321	>	the_ff = new EAM_FF();
1322	>	break;
1323	>
1324	>	case FF_H2O:
1325	>	the_ff = new WATER();
1326	>	break;
1327	>
1328	>	default:
1329	>	sprintf(painCave.errMsg,
1330	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1331	>	painCave.isFatal = 1;
1332	>	simError();
1333	>	}
1334	>
1335	>	#ifdef IS_MPI
1336	>	strcpy(checkPointMsg, "ForceField creation successful");
1337	>	MPIcheckPoint();
1338	>	#endif // is_mpi
1339	>	}
1340	>
1341	>
1342	>	void SimSetup::compList(void){
1343	>	int i;
1344	>	char* id;
1345	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1346	>	LinkedMolStamp* currentStamp = NULL;
1347	>	comp_stamps = new MoleculeStamp * [n_components];
1348	>	bool haveCutoffGroups;
1349	>
1350	>	haveCutoffGroups = false;
1351	>
1352	>	// make an array of molecule stamps that match the components used.
1353	>	// also extract the used stamps out into a separate linked list
1354	>
1355	>	for (i = 0; i < nInfo; i++){
1356	>	info[i].nComponents = n_components;
1357	>	info[i].componentsNmol = components_nmol;
1358	>	info[i].compStamps = comp_stamps;
1359	>	info[i].headStamp = headStamp;
1360	>	}
1361	>
1362	>
1363	>	for (i = 0; i < n_components; i++){
1364	>	id = the_components[i]->getType();
1365	>	comp_stamps[i] = NULL;
1366	>
1367	>	// check to make sure the component isn't already in the list
1368	>
1369	>	comp_stamps[i] = headStamp->match(id);
1370	>	if (comp_stamps[i] == NULL){
1371	>	// extract the component from the list;
1372	>
1373	>	currentStamp = stamps->extractMolStamp(id);
1374	>	if (currentStamp == NULL){
1375	>	sprintf(painCave.errMsg,
1376	>	"SimSetup error: Component \"%s\" was not found in the "
1377	>	"list of declared molecules\n",
1378	>	id);
1379	>	painCave.isFatal = 1;
1380	>	simError();
1381	>	}
1382	>
1383	>	headStamp->add(currentStamp);
1384	>	comp_stamps[i] = headStamp->match(id);
1385		}
1386
1387	<	current_atom_ndx++;
1387	>	if(comp_stamps[i]->getNCutoffGroups() > 0)
1388	>	haveCutoffGroups = true;
1389		}
1390	+
1391	+	for (i = 0; i < nInfo; i++)
1392	+	info[i].haveCutoffGroups = haveCutoffGroups;
1393
1394	<	current_mol++;
1395	<	current_comp_mol++;
1394	>	#ifdef IS_MPI
1395	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1396	>	MPIcheckPoint();
1397	>	#endif // is_mpi
1398	>	}
1399
1400	<	if( current_comp_mol >= components_nmol[current_comp] ){
1400	>	void SimSetup::calcSysValues(void){
1401	>	int i;
1402
1403	<	current_comp_mol = 0;
1404	<	current_comp++;
1403	>	int* molMembershipArray;
1404	>
1405	>	tot_atoms = 0;
1406	>	tot_bonds = 0;
1407	>	tot_bends = 0;
1408	>	tot_torsions = 0;
1409	>	tot_rigid = 0;
1410	>	for (i = 0; i < n_components; i++){
1411	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1412	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1413	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1414	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1415	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1416	>	}
1417	>
1418	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1419	>	molMembershipArray = new int[tot_atoms];
1420	>
1421	>	for (i = 0; i < nInfo; i++){
1422	>	info[i].n_atoms = tot_atoms;
1423	>	info[i].n_bonds = tot_bonds;
1424	>	info[i].n_bends = tot_bends;
1425	>	info[i].n_torsions = tot_torsions;
1426	>	info[i].n_SRI = tot_SRI;
1427	>	info[i].n_mol = tot_nmol;
1428	>
1429	>	info[i].molMembershipArray = molMembershipArray;
1430	>	}
1431	>	}
1432	>
1433	>	#ifdef IS_MPI
1434	>
1435	>	void SimSetup::mpiMolDivide(void){
1436	>	int i, j, k;
1437	>	int localMol, allMol;
1438	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1439	>	int local_rigid;
1440	>	vector<int> globalMolIndex;
1441	>
1442	>	mpiSim = new mpiSimulation(info);
1443	>
1444	>	mpiSim->divideLabor();
1445	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1446	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1447	>
1448	>	// set up the local variables
1449	>
1450	>	mol2proc = mpiSim->getMolToProcMap();
1451	>	molCompType = mpiSim->getMolComponentType();
1452	>
1453	>	allMol = 0;
1454	>	localMol = 0;
1455	>	local_atoms = 0;
1456	>	local_bonds = 0;
1457	>	local_bends = 0;
1458	>	local_torsions = 0;
1459	>	local_rigid = 0;
1460	>	globalAtomCounter = 0;
1461	>
1462	>	for (i = 0; i < n_components; i++){
1463	>	for (j = 0; j < components_nmol[i]; j++){
1464	>	if (mol2proc[allMol] == worldRank){
1465	>	local_atoms += comp_stamps[i]->getNAtoms();
1466	>	local_bonds += comp_stamps[i]->getNBonds();
1467	>	local_bends += comp_stamps[i]->getNBends();
1468	>	local_torsions += comp_stamps[i]->getNTorsions();
1469	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1470	>	localMol++;
1471	>	}
1472	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1473	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1474	>	globalAtomCounter++;
1475	>	}
1476	>
1477	>	allMol++;
1478	>	}
1479	>	}
1480	>	local_SRI = local_bonds + local_bends + local_torsions;
1481	>
1482	>	info[0].n_atoms = mpiSim->getMyNlocal();
1483	>
1484	>
1485	>	if (local_atoms != info[0].n_atoms){
1486	>	sprintf(painCave.errMsg,
1487	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1488	>	"\tlocalAtom (%d) are not equal.\n",
1489	>	info[0].n_atoms, local_atoms);
1490	>	painCave.isFatal = 1;
1491	>	simError();
1492	>	}
1493	>
1494	>	info[0].n_bonds = local_bonds;
1495	>	info[0].n_bends = local_bends;
1496	>	info[0].n_torsions = local_torsions;
1497	>	info[0].n_SRI = local_SRI;
1498	>	info[0].n_mol = localMol;
1499	>
1500	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1501	>	MPIcheckPoint();
1502	>	}
1503	>
1504	>	#endif // is_mpi
1505	>
1506	>
1507	>	void SimSetup::makeSysArrays(void){
1508	>
1509	>	#ifndef IS_MPI
1510	>	int k, j;
1511	>	#endif // is_mpi
1512	>	int i, l;
1513	>
1514	>	Atom** the_atoms;
1515	>	Molecule* the_molecules;
1516	>
1517	>	for (l = 0; l < nInfo; l++){
1518	>	// create the atom and short range interaction arrays
1519	>
1520	>	the_atoms = new Atom * [info[l].n_atoms];
1521	>	the_molecules = new Molecule[info[l].n_mol];
1522	>	int molIndex;
1523	>
1524	>	// initialize the molecule's stampID's
1525	>
1526	>	#ifdef IS_MPI
1527	>
1528	>
1529	>	molIndex = 0;
1530	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1531	>	if (mol2proc[i] == worldRank){
1532	>	the_molecules[molIndex].setStampID(molCompType[i]);
1533	>	the_molecules[molIndex].setMyIndex(molIndex);
1534	>	the_molecules[molIndex].setGlobalIndex(i);
1535	>	molIndex++;
1536	>	}
1537	>	}
1538	>
1539	>	#else // is_mpi
1540	>
1541	>	molIndex = 0;
1542	>	globalAtomCounter = 0;
1543	>	for (i = 0; i < n_components; i++){
1544	>	for (j = 0; j < components_nmol[i]; j++){
1545	>	the_molecules[molIndex].setStampID(i);
1546	>	the_molecules[molIndex].setMyIndex(molIndex);
1547	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1548	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1549	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1550	>	globalAtomCounter++;
1551	>	}
1552	>	molIndex++;
1553	>	}
1554	>	}
1555	>
1556	>
1557	>	#endif // is_mpi
1558	>
1559	>	info[l].globalExcludes = new int;
1560	>	info[l].globalExcludes[0] = 0;
1561	>
1562	>	// set the arrays into the SimInfo object
1563	>
1564	>	info[l].atoms = the_atoms;
1565	>	info[l].molecules = the_molecules;
1566	>	info[l].nGlobalExcludes = 0;
1567	>
1568	>	the_ff->setSimInfo(info);
1569		}
1570		}
1571	+
1572	+	void SimSetup::makeIntegrator(void){
1573	+	int k;
1574	+
1575	+	NVE<RealIntegrator>* myNVE = NULL;
1576	+	NVT<RealIntegrator>* myNVT = NULL;
1577	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1578	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1579	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1580	+
1581	+	for (k = 0; k < nInfo; k++){
1582	+	switch (ensembleCase){
1583	+	case NVE_ENS:
1584	+	if (globals->haveZconstraints()){
1585	+	setupZConstraint(info[k]);
1586	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1587	+	}
1588	+	else{
1589	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1590	+	}
1591	+
1592	+	info->the_integrator = myNVE;
1593	+	break;
1594	+
1595	+	case NVT_ENS:
1596	+	if (globals->haveZconstraints()){
1597	+	setupZConstraint(info[k]);
1598	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1599	+	}
1600	+	else
1601	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1602	+
1603	+	myNVT->setTargetTemp(globals->getTargetTemp());
1604	+
1605	+	if (globals->haveTauThermostat())
1606	+	myNVT->setTauThermostat(globals->getTauThermostat());
1607	+	else{
1608	+	sprintf(painCave.errMsg,
1609	+	"SimSetup error: If you use the NVT\n"
1610	+	"\tensemble, you must set tauThermostat.\n");
1611	+	painCave.isFatal = 1;
1612	+	simError();
1613	+	}
1614	+
1615	+	info->the_integrator = myNVT;
1616	+	break;
1617	+
1618	+	case NPTi_ENS:
1619	+	if (globals->haveZconstraints()){
1620	+	setupZConstraint(info[k]);
1621	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1622	+	}
1623	+	else
1624	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1625	+
1626	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1627	+
1628	+	if (globals->haveTargetPressure())
1629	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1630	+	else{
1631	+	sprintf(painCave.errMsg,
1632	+	"SimSetup error: If you use a constant pressure\n"
1633	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1634	+	painCave.isFatal = 1;
1635	+	simError();
1636	+	}
1637	+
1638	+	if (globals->haveTauThermostat())
1639	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1640	+	else{
1641	+	sprintf(painCave.errMsg,
1642	+	"SimSetup error: If you use an NPT\n"
1643	+	"\tensemble, you must set tauThermostat.\n");
1644	+	painCave.isFatal = 1;
1645	+	simError();
1646	+	}
1647	+
1648	+	if (globals->haveTauBarostat())
1649	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1650	+	else{
1651	+	sprintf(painCave.errMsg,
1652	+	"SimSetup error: If you use an NPT\n"
1653	+	"\tensemble, you must set tauBarostat.\n");
1654	+	painCave.isFatal = 1;
1655	+	simError();
1656	+	}
1657	+
1658	+	info->the_integrator = myNPTi;
1659	+	break;
1660	+
1661	+	case NPTf_ENS:
1662	+	if (globals->haveZconstraints()){
1663	+	setupZConstraint(info[k]);
1664	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1665	+	}
1666	+	else
1667	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1668	+
1669	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1670	+
1671	+	if (globals->haveTargetPressure())
1672	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1673	+	else{
1674	+	sprintf(painCave.errMsg,
1675	+	"SimSetup error: If you use a constant pressure\n"
1676	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1677	+	painCave.isFatal = 1;
1678	+	simError();
1679	+	}
1680	+
1681	+	if (globals->haveTauThermostat())
1682	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1683	+
1684	+	else{
1685	+	sprintf(painCave.errMsg,
1686	+	"SimSetup error: If you use an NPT\n"
1687	+	"\tensemble, you must set tauThermostat.\n");
1688	+	painCave.isFatal = 1;
1689	+	simError();
1690	+	}
1691	+
1692	+	if (globals->haveTauBarostat())
1693	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1694	+
1695	+	else{
1696	+	sprintf(painCave.errMsg,
1697	+	"SimSetup error: If you use an NPT\n"
1698	+	"\tensemble, you must set tauBarostat.\n");
1699	+	painCave.isFatal = 1;
1700	+	simError();
1701	+	}
1702	+
1703	+	info->the_integrator = myNPTf;
1704	+	break;
1705	+
1706	+	case NPTxyz_ENS:
1707	+	if (globals->haveZconstraints()){
1708	+	setupZConstraint(info[k]);
1709	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1710	+	}
1711	+	else
1712	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1713	+
1714	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1715	+
1716	+	if (globals->haveTargetPressure())
1717	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1718	+	else{
1719	+	sprintf(painCave.errMsg,
1720	+	"SimSetup error: If you use a constant pressure\n"
1721	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1722	+	painCave.isFatal = 1;
1723	+	simError();
1724	+	}
1725	+
1726	+	if (globals->haveTauThermostat())
1727	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1728	+	else{
1729	+	sprintf(painCave.errMsg,
1730	+	"SimSetup error: If you use an NPT\n"
1731	+	"\tensemble, you must set tauThermostat.\n");
1732	+	painCave.isFatal = 1;
1733	+	simError();
1734	+	}
1735	+
1736	+	if (globals->haveTauBarostat())
1737	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1738	+	else{
1739	+	sprintf(painCave.errMsg,
1740	+	"SimSetup error: If you use an NPT\n"
1741	+	"\tensemble, you must set tauBarostat.\n");
1742	+	painCave.isFatal = 1;
1743	+	simError();
1744	+	}
1745	+
1746	+	info->the_integrator = myNPTxyz;
1747	+	break;
1748	+
1749	+	default:
1750	+	sprintf(painCave.errMsg,
1751	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1752	+	painCave.isFatal = 1;
1753	+	simError();
1754	+	}
1755	+	}
1756	+	}
1757	+
1758	+	void SimSetup::initFortran(void){
1759	+	info[0].refreshSim();
1760	+
1761	+	if (!strcmp(info[0].mixingRule, "standard")){
1762	+	the_ff->initForceField(LB_MIXING_RULE);
1763	+	}
1764	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1765	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1766	+	}
1767	+	else{
1768	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1769	+	info[0].mixingRule);
1770	+	painCave.isFatal = 1;
1771	+	simError();
1772	+	}
1773	+
1774	+
1775	+	#ifdef IS_MPI
1776	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1777	+	MPIcheckPoint();
1778	+	#endif // is_mpi
1779	+	}
1780	+
1781	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1782	+	int nZConstraints;
1783	+	ZconStamp** zconStamp;
1784	+
1785	+	if (globals->haveZconstraintTime()){
1786	+	//add sample time of z-constraint  into SimInfo's property list
1787	+	DoubleData* zconsTimeProp = new DoubleData();
1788	+	zconsTimeProp->setID(ZCONSTIME_ID);
1789	+	zconsTimeProp->setData(globals->getZconsTime());
1790	+	theInfo.addProperty(zconsTimeProp);
1791	+	}
1792	+	else{
1793	+	sprintf(painCave.errMsg,
1794	+	"ZConstraint error: If you use a ZConstraint,\n"
1795	+	"\tyou must set zconsTime.\n");
1796	+	painCave.isFatal = 1;
1797	+	simError();
1798	+	}
1799	+
1800	+	//push zconsTol into siminfo, if user does not specify
1801	+	//value for zconsTol, a default value will be used
1802	+	DoubleData* zconsTol = new DoubleData();
1803	+	zconsTol->setID(ZCONSTOL_ID);
1804	+	if (globals->haveZconsTol()){
1805	+	zconsTol->setData(globals->getZconsTol());
1806	+	}
1807	+	else{
1808	+	double defaultZConsTol = 0.01;
1809	+	sprintf(painCave.errMsg,
1810	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1811	+	"\tOOPSE will use a default value of %f.\n"
1812	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1813	+	defaultZConsTol);
1814	+	painCave.isFatal = 0;
1815	+	simError();
1816	+
1817	+	zconsTol->setData(defaultZConsTol);
1818	+	}
1819	+	theInfo.addProperty(zconsTol);
1820	+
1821	+	//set Force Subtraction Policy
1822	+	StringData* zconsForcePolicy = new StringData();
1823	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1824	+
1825	+	if (globals->haveZconsForcePolicy()){
1826	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1827	+	}
1828	+	else{
1829	+	sprintf(painCave.errMsg,
1830	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1831	+	"\tOOPSE will use PolicyByMass.\n"
1832	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1833	+	painCave.isFatal = 0;
1834	+	simError();
1835	+	zconsForcePolicy->setData("BYMASS");
1836	+	}
1837	+
1838	+	theInfo.addProperty(zconsForcePolicy);
1839	+
1840	+	//set zcons gap
1841	+	DoubleData* zconsGap = new DoubleData();
1842	+	zconsGap->setID(ZCONSGAP_ID);
1843	+
1844	+	if (globals->haveZConsGap()){
1845	+	zconsGap->setData(globals->getZconsGap());
1846	+	theInfo.addProperty(zconsGap);
1847	+	}
1848	+
1849	+	//set zcons fixtime
1850	+	DoubleData* zconsFixtime = new DoubleData();
1851	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1852	+
1853	+	if (globals->haveZConsFixTime()){
1854	+	zconsFixtime->setData(globals->getZconsFixtime());
1855	+	theInfo.addProperty(zconsFixtime);
1856	+	}
1857	+
1858	+	//set zconsUsingSMD
1859	+	IntData* zconsUsingSMD = new IntData();
1860	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1861	+
1862	+	if (globals->haveZConsUsingSMD()){
1863	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1864	+	theInfo.addProperty(zconsUsingSMD);
1865	+	}
1866	+
1867	+	//Determine the name of ouput file and add it into SimInfo's property list
1868	+	//Be careful, do not use inFileName, since it is a pointer which
1869	+	//point to a string at master node, and slave nodes do not contain that string
1870	+
1871	+	string zconsOutput(theInfo.finalName);
1872	+
1873	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1874	+
1875	+	StringData* zconsFilename = new StringData();
1876	+	zconsFilename->setID(ZCONSFILENAME_ID);
1877	+	zconsFilename->setData(zconsOutput);
1878	+
1879	+	theInfo.addProperty(zconsFilename);
1880	+
1881	+	//setup index, pos and other parameters of z-constraint molecules
1882	+	nZConstraints = globals->getNzConstraints();
1883	+	theInfo.nZconstraints = nZConstraints;
1884	+
1885	+	zconStamp = globals->getZconStamp();
1886	+	ZConsParaItem tempParaItem;
1887	+
1888	+	ZConsParaData* zconsParaData = new ZConsParaData();
1889	+	zconsParaData->setID(ZCONSPARADATA_ID);
1890	+
1891	+	for (int i = 0; i < nZConstraints; i++){
1892	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1893	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1894	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1895	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1896	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1897	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1898	+	zconsParaData->addItem(tempParaItem);
1899	+	}
1900	+
1901	+	//check the uniqueness of index
1902	+	if(!zconsParaData->isIndexUnique()){
1903	+	sprintf(painCave.errMsg,
1904	+	"ZConstraint Error: molIndex is not unique!\n");
1905	+	painCave.isFatal = 1;
1906	+	simError();
1907	+	}
1908	+
1909	+	//sort the parameters by index of molecules
1910	+	zconsParaData->sortByIndex();
1911	+
1912	+	//push data into siminfo, therefore, we can retrieve later
1913	+	theInfo.addProperty(zconsParaData);
1914	+	}
1915	+
1916	+	void SimSetup::makeMinimizer(){
1917	+
1918	+	OOPSEMinimizer* myOOPSEMinimizer;
1919	+	MinimizerParameterSet* param;
1920	+	char minimizerName[100];
1921	+
1922	+	for (int i = 0; i < nInfo; i++){
1923	+
1924	+	//prepare parameter set for minimizer
1925	+	param = new MinimizerParameterSet();
1926	+	param->setDefaultParameter();
1927	+
1928	+	if (globals->haveMinimizer()){
1929	+	param->setFTol(globals->getMinFTol());
1930	+	}
1931	+
1932	+	if (globals->haveMinGTol()){
1933	+	param->setGTol(globals->getMinGTol());
1934	+	}
1935	+
1936	+	if (globals->haveMinMaxIter()){
1937	+	param->setMaxIteration(globals->getMinMaxIter());
1938	+	}
1939	+
1940	+	if (globals->haveMinWriteFrq()){
1941	+	param->setMaxIteration(globals->getMinMaxIter());
1942	+	}
1943	+
1944	+	if (globals->haveMinWriteFrq()){
1945	+	param->setWriteFrq(globals->getMinWriteFrq());
1946	+	}
1947	+
1948	+	if (globals->haveMinStepSize()){
1949	+	param->setStepSize(globals->getMinStepSize());
1950	+	}
1951	+
1952	+	if (globals->haveMinLSMaxIter()){
1953	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1954	+	}
1955	+
1956	+	if (globals->haveMinLSTol()){
1957	+	param->setLineSearchTol(globals->getMinLSTol());
1958	+	}
1959	+
1960	+	strcpy(minimizerName, globals->getMinimizer());
1961	+
1962	+	if (!strcasecmp(minimizerName, "CG")){
1963	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1964	+	}
1965	+	else if (!strcasecmp(minimizerName, "SD")){
1966	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1967	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1968	+	}
1969	+	else{
1970	+	sprintf(painCave.errMsg,
1971	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1972	+	painCave.isFatal = 0;
1973	+	simError();
1974	+
1975	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1976	+	}
1977	+	info[i].the_integrator = myOOPSEMinimizer;
1978	+
1979	+	//store the minimizer into simInfo
1980	+	info[i].the_minimizer = myOOPSEMinimizer;
1981	+	info[i].has_minimizer = true;
1982	+	}
1983	+
1984	+	}

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