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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 483 by gezelter, Wed Apr 9 04:06:43 2003 UTC vs.
Revision 1229 by gezelter, Thu Jun 3 20:02:25 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 "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
19		#include "mpiSimulation.hpp"
20		#endif
21
22	+	// some defines for ensemble and Forcefield  cases
23	+
24	+	#define NVE_ENS        0
25	+	#define NVT_ENS        1
26	+	#define NPTi_ENS       2
27	+	#define NPTf_ENS       3
28	+	#define NPTxyz_ENS     4
29	+
30	+
31	+	#define FF_DUFF  0
32	+	#define FF_LJ    1
33	+	#define FF_EAM   2
34	+	#define FF_H2O   3
35	+
36	+	using namespace std;
37	+
38	+	/**
39	+	* Check whether dividend is divisble by divisor or not
40	+	*/
41	+	bool isDivisible(double dividend, double divisor){
42	+	double tolerance = 0.000001;
43	+	double quotient;
44	+	double diff;
45	+	int intQuotient;
46	+
47	+	quotient = dividend / divisor;
48	+
49	+	if (quotient < 0)
50	+	quotient = -quotient;
51	+
52	+	intQuotient = int (quotient + tolerance);
53	+
54	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
55	+
56	+	if (diff <= tolerance)
57	+	return true;
58	+	else
59	+	return false;
60	+	}
61	+
62		SimSetup::SimSetup(){
63	+
64	+	initSuspend = false;
65	+	isInfoArray = 0;
66	+	nInfo = 1;
67	+
68		stamps = new MakeStamps();
69		globals = new Globals();
70	<
70	>
71	>
72		#ifdef IS_MPI
73	<	strcpy( checkPointMsg, "SimSetup creation successful" );
73	>	strcpy(checkPointMsg, "SimSetup creation successful");
74		MPIcheckPoint();
75		#endif // IS_MPI
76		}
#	Line 27 | Line 80 | SimSetup::~SimSetup(){
80		delete globals;
81		}
82
83	<	void SimSetup::parseFile( char* fileName ){
83	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
84	>	info = the_info;
85	>	nInfo = theNinfo;
86	>	isInfoArray = 1;
87	>	initSuspend = true;
88	>	}
89
90	+
91	+	void SimSetup::parseFile(char* fileName){
92		#ifdef IS_MPI
93	<	if( worldRank == 0 ){
93	>	if (worldRank == 0){
94		#endif // is_mpi
95	<
95	>
96		inFileName = fileName;
97	<	set_interface_stamps( stamps, globals );
98	<
97	>	set_interface_stamps(stamps, globals);
98	>
99		#ifdef IS_MPI
100		mpiEventInit();
101		#endif
102
103	<	yacc_BASS( fileName );
103	>	yacc_BASS(fileName);
104
105		#ifdef IS_MPI
106		throwMPIEvent(NULL);
107		}
108	<	else receiveParse();
108	>	else{
109	>	receiveParse();
110	>	}
111		#endif
112
113		}
114
115		#ifdef IS_MPI
116		void SimSetup::receiveParse(void){
117	<
118	<	set_interface_stamps( stamps, globals );
119	<	mpiEventInit();
120	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
117	>	set_interface_stamps(stamps, globals);
118	>	mpiEventInit();
119	>	MPIcheckPoint();
120	>	mpiEventLoop();
121		}
122
123		#endif // is_mpi
124
125	<	void SimSetup::createSim( void ){
125	>	void SimSetup::createSim(void){
126
127	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
127	>	// gather all of the information from the Bass file
128
129	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
129	>	gatherInfo();
130
131	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	simnfo->run_time = the_globals->getRunTime();
131	>	// creation of complex system objects
132
133	<	// get the ones we know are there, yet still may need some work.
82	<	n_components = the_globals->getNComponents();
83	<	strcpy( force_field, the_globals->getForceField() );
133	>	sysObjectsCreation();
134
135	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	if (the_globals->haveTargetPressure())
91	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92	<	else {
93	<	sprintf( painCave.errMsg,
94	<	"SimSetup error: If you use the constant pressure\n"
95	<	"    ensemble, you must set targetPressure.\n"
96	<	"    This was found in the BASS file.\n");
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
135	>	// check on the post processing info
136
137	<	if (the_globals->haveTauThermostat())
102	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103	<	else if (the_globals->haveQmass())
104	<	the_extendedsystem->setQmass(the_globals->getQmass());
105	<	else {
106	<	sprintf( painCave.errMsg,
107	<	"SimSetup error: If you use one of the constant temperature\n"
108	<	"    ensembles, you must set either tauThermostat or qMass.\n"
109	<	"    Neither of these was found in the BASS file.\n");
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
137	>	finalInfoCheck();
138
139	<	if (the_globals->haveTauBarostat())
115	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116	<	else {
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup error: If you use the constant pressure\n"
119	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
139	>	// initialize the system coordinates
140
141	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
142	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
141	>	if ( !initSuspend ){
142	>	initSystemCoords();
143
144	<	if (the_globals->haveTauThermostat())
145	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131	<	else if (the_globals->haveQmass())
132	<	the_extendedsystem->setQmass(the_globals->getQmass());
133	<	else {
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error: If you use one of the constant temperature\n"
136	<	"    ensembles, you must set either tauThermostat or qMass.\n"
137	<	"    Neither of these was found in the BASS file.\n");
138	<	painCave.isFatal = 1;
139	<	simError();
140	<	}
141	<
142	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
143	<	} else {
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	<	"reverting to NVE for this simulation.\n",
147	<	ensemble );
148	<	painCave.isFatal = 0;
149	<	simError();
150	<	strcpy( ensemble, "NVE" );
144	>	if( !(globals->getUseInitTime()) )
145	>	info[0].currentTime = 0.0;
146		}
152	–	strcpy( simnfo->ensemble, ensemble );
147
148	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155	<	simnfo->usePBC = the_globals->getPBC();
156	<
157	<	int usesDipoles = 0;
158	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
159	<	the_ff = new TraPPE_ExFF();
160	<	usesDipoles = 1;
161	<	}
162	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163	<	else{
164	<	sprintf( painCave.errMsg,
165	<	"SimSetup Error. Unrecognized force field -> %s\n",
166	<	force_field );
167	<	painCave.isFatal = 1;
168	<	simError();
169	<	}
148	>	// make the output filenames
149
150	+	makeOutNames();
151	+
152		#ifdef IS_MPI
153	<	strcpy( checkPointMsg, "ForceField creation successful" );
154	<	MPIcheckPoint();
174	<	#endif // is_mpi
153	>	mpiSim->mpiRefresh();
154	>	#endif
155
156	<
156	>	// initialize the Fortran
157
158	<	// get the components and calculate the tot_nMol and indvidual n_mol
179	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
158	>	initFortran();
159
160	<	if( !the_globals->haveNMol() ){
161	<	// we don't have the total number of molecules, so we assume it is
162	<	// given in each component
160	>	if (globals->haveMinimizer())
161	>	// make minimizer
162	>	makeMinimizer();
163	>	else
164	>	// make the integrator
165	>	makeIntegrator();
166
167	<	tot_nmol = 0;
188	<	for( i=0; i<n_components; i++ ){
167	>	}
168
190	–	if( !the_components[i]->haveNMol() ){
191	–	// we have a problem
192	–	sprintf( painCave.errMsg,
193	–	"SimSetup Error. No global NMol or component NMol"
194	–	" given. Cannot calculate the number of atoms.\n" );
195	–	painCave.isFatal = 1;
196	–	simError();
197	–	}
169
170	<	tot_nmol += the_components[i]->getNMol();
171	<	components_nmol[i] = the_components[i]->getNMol();
172	<	}
173	<	}
174	<	else{
175	<	sprintf( painCave.errMsg,
176	<	"SimSetup error.\n"
177	<	"\tSorry, the ability to specify total"
178	<	" nMols and then give molfractions in the components\n"
179	<	"\tis not currently supported."
180	<	" Please give nMol in the components.\n" );
181	<	painCave.isFatal = 1;
182	<	simError();
183	<
184	<
185	<	//     tot_nmol = the_globals->getNMol();
186	<
187	<	//   //we have the total number of molecules, now we check for molfractions
188	<	//     for( i=0; i<n_components; i++ ){
189	<
190	<	//       if( !the_components[i]->haveMolFraction() ){
220	<
221	<	//  if( !the_components[i]->haveNMol() ){
222	<	//    //we have a problem
223	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	<	//              << " nMol was given in component
225	<
226	<	}
170	>	void SimSetup::makeMolecules(void){
171	>	int i, j, k;
172	>	int exI, exJ, exK, exL, slI, slJ;
173	>	int tempI, tempJ, tempK, tempL;
174	>	int molI, globalID;
175	>	int stampID, atomOffset, rbOffset, groupOffset;
176	>	molInit molInfo;
177	>	DirectionalAtom* dAtom;
178	>	RigidBody* myRB;
179	>	StuntDouble* mySD;
180	>	LinkedAssign* extras;
181	>	LinkedAssign* current_extra;
182	>	AtomStamp* currentAtom;
183	>	BondStamp* currentBond;
184	>	BendStamp* currentBend;
185	>	TorsionStamp* currentTorsion;
186	>	RigidBodyStamp* currentRigidBody;
187	>	CutoffGroupStamp* currentCutoffGroup;
188	>	CutoffGroup* myCutoffGroup;
189	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
190	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
191
192	<	#ifdef IS_MPI
193	<	strcpy( checkPointMsg, "Have the number of components" );
194	<	MPIcheckPoint();
231	<	#endif // is_mpi
232	<
233	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
192	>	bond_pair* theBonds;
193	>	bend_set* theBends;
194	>	torsion_set* theTorsions;
195
196	<	simnfo->nComponents = n_components;
237	<	simnfo->componentsNmol = components_nmol;
238	<	simnfo->compStamps = comp_stamps;
239	<	simnfo->headStamp = new LinkedMolStamp();
240	<
241	<	char* id;
242	<	LinkedMolStamp* headStamp = simnfo->headStamp;
243	<	LinkedMolStamp* currentStamp = NULL;
244	<	for( i=0; i<n_components; i++ ){
196	>	set<int> skipList;
197
198	<	id = the_components[i]->getType();
199	<	comp_stamps[i] = NULL;
200	<
249	<	// check to make sure the component isn't already in the list
198	>	double phi, theta, psi;
199	>	char* molName;
200	>	char rbName[100];
201
202	<	comp_stamps[i] = headStamp->match( id );
203	<	if( comp_stamps[i] == NULL ){
204	<
205	<	// extract the component from the list;
206	<
207	<	currentStamp = the_stamps->extractMolStamp( id );
208	<	if( currentStamp == NULL ){
258	<	sprintf( painCave.errMsg,
259	<	"SimSetup error: Component \"%s\" was not found in the "
260	<	"list of declared molecules\n",
261	<	id );
262	<	painCave.isFatal = 1;
263	<	simError();
264	<	}
265	<
266	<	headStamp->add( currentStamp );
267	<	comp_stamps[i] = headStamp->match( id );
268	<	}
269	<	}
202	>	//ConstraintPair* consPair; //constraint pair
203	>	//ConstraintElement* consElement1;  //first element of constraint pair
204	>	//ConstraintElement* consElement2;  //second element of constraint pair
205	>	//int whichRigidBody;
206	>	//int consAtomIndex;  //index of constraint atom in rigid body's atom array
207	>	//vector<pair<int, int> > jointAtoms;
208	>	//init the forceField paramters
209
210	<	#ifdef IS_MPI
272	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	<	MPIcheckPoint();
274	<	#endif // is_mpi
275	<
210	>	the_ff->readParams();
211
212	+	// init the atoms
213
214	+	int nMembers, nNew, rb1, rb2;
215
216	<	// caclulate the number of atoms, bonds, bends and torsions
216	>	for (k = 0; k < nInfo; k++){
217	>	the_ff->setSimInfo(&(info[k]));
218
219	<	tot_atoms = 0;
220	<	tot_bonds = 0;
221	<	tot_bends = 0;
222	<	tot_torsions = 0;
223	<	for( i=0; i<n_components; i++ ){
224	<
225	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
226	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
227	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
290	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
291	<	}
219	>	#ifdef IS_MPI
220	>	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
221	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
222	>	info[k].globalGroupMembership[i] = 0;
223	>	#else
224	>	info[k].globalGroupMembership = new int[info[k].n_atoms];
225	>	for (i = 0; i < info[k].n_atoms; i++)
226	>	info[k].globalGroupMembership[i] = 0;
227	>	#endif
228
229	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
229	>	atomOffset = 0;
230	>	groupOffset = 0;
231
232	<	simnfo->n_atoms = tot_atoms;
233	<	simnfo->n_bonds = tot_bonds;
234	<	simnfo->n_bends = tot_bends;
298	<	simnfo->n_torsions = tot_torsions;
299	<	simnfo->n_SRI = tot_SRI;
300	<	simnfo->n_mol = tot_nmol;
232	>	for (i = 0; i < info[k].n_mol; i++){
233	>	stampID = info[k].molecules[i].getStampID();
234	>	molName = comp_stamps[stampID]->getID();
235
236	<
237	<	#ifdef IS_MPI
236	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
237	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
238	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
239	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
240	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
241
242	<	// divide the molecules among processors here.
243	<
244	<	mpiSim = new mpiSimulation( simnfo );
308	<
309	<
242	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
243	>
244	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
245
246	<	globalIndex = mpiSim->divideLabor();
246	>	if (molInfo.nBonds > 0)
247	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
248	>	else
249	>	molInfo.myBonds = NULL;
250
251	<	// set up the local variables
252	<
253	<	int localMol, allMol;
254	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	>	if (molInfo.nBends > 0)
252	>	molInfo.myBends = new Bend*[molInfo.nBends];
253	>	else
254	>	molInfo.myBends = NULL;
255
256	<	int* mol2proc = mpiSim->getMolToProcMap();
257	<	int* molCompType = mpiSim->getMolComponentType();
258	<
259	<	allMol = 0;
322	<	localMol = 0;
323	<	local_atoms = 0;
324	<	local_bonds = 0;
325	<	local_bends = 0;
326	<	local_torsions = 0;
327	<	for( i=0; i<n_components; i++ ){
256	>	if (molInfo.nTorsions > 0)
257	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
258	>	else
259	>	molInfo.myTorsions = NULL;
260
261	<	for( j=0; j<components_nmol[i]; j++ ){
261	>	theBonds = new bond_pair[molInfo.nBonds];
262	>	theBends = new bend_set[molInfo.nBends];
263	>	theTorsions = new torsion_set[molInfo.nTorsions];
264
265	<	if( mol2proc[j] == worldRank ){
332	<
333	<	local_atoms +=    comp_stamps[i]->getNAtoms();
334	<	local_bonds +=    comp_stamps[i]->getNBonds();
335	<	local_bends +=    comp_stamps[i]->getNBends();
336	<	local_torsions += comp_stamps[i]->getNTorsions();
337	<	localMol++;
338	<	}
339	<	allMol++;
340	<	}
341	<	}
342	<	local_SRI = local_bonds + local_bends + local_torsions;
343	<
265	>	// make the Atoms
266
267	<	simnfo->n_atoms = mpiSim->getMyNlocal();
268	<
347	<	if( local_atoms != simnfo->n_atoms ){
348	<	sprintf( painCave.errMsg,
349	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
350	<	" localAtom (%d) are not equal.\n",
351	<	simnfo->n_atoms,
352	<	local_atoms );
353	<	painCave.isFatal = 1;
354	<	simError();
355	<	}
267	>	for (j = 0; j < molInfo.nAtoms; j++){
268	>	currentAtom = comp_stamps[stampID]->getAtom(j);
269
270	<	simnfo->n_bonds = local_bonds;
271	<	simnfo->n_bends = local_bends;
272	<	simnfo->n_torsions = local_torsions;
273	<	simnfo->n_SRI = local_SRI;
274	<	simnfo->n_mol = localMol;
270	>	if (currentAtom->haveOrientation()){
271	>	dAtom = new DirectionalAtom((j + atomOffset),
272	>	info[k].getConfiguration());
273	>	info[k].n_oriented++;
274	>	molInfo.myAtoms[j] = dAtom;
275
276	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
277	<	MPIcheckPoint();
278	<
366	<
367	<	#endif // is_mpi
368	<
276	>	// Directional Atoms have standard unit vectors which are oriented
277	>	// in space using the three Euler angles.  We assume the standard
278	>	// unit vector was originally along the z axis below.
279
280	<	// create the atom and short range interaction arrays
280	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
281	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
282	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
283
284	<	Atom::createArrays(simnfo->n_atoms);
285	<	the_atoms = new Atom*[simnfo->n_atoms];
286	<	the_molecules = new Molecule[simnfo->n_mol];
287	<	int molIndex;
284	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
285	>
286	>	}
287	>	else{
288
289	<	// initialize the molecule's stampID's
289	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
290
291	<	#ifdef IS_MPI
380	<
291	>	}
292
293	<	molIndex = 0;
294	<	for(i=0; i<mpiSim->getTotNmol(); i++){
295	<
385	<	if(mol2proc[i] == worldRank ){
386	<	the_molecules[molIndex].setStampID( molCompType[i] );
387	<	the_molecules[molIndex].setMyIndex( molIndex );
388	<	molIndex++;
389	<	}
390	<	}
391	<
392	<	#else // is_mpi
393	<
394	<	molIndex = 0;
395	<	for(i=0; i<n_components; i++){
396	<	for(j=0; j<components_nmol[i]; j++ ){
397	<	the_molecules[molIndex].setStampID( i );
398	<	the_molecules[molIndex].setMyIndex( molIndex );
399	<	molIndex++;
400	<	}
401	<	}
402	<
403	<
293	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
294	>	#ifdef IS_MPI
295	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
296		#endif // is_mpi
297	+	}
298
299	+	// make the bonds
300	+	for (j = 0; j < molInfo.nBonds; j++){
301	+	currentBond = comp_stamps[stampID]->getBond(j);
302	+	theBonds[j].a = currentBond->getA() + atomOffset;
303	+	theBonds[j].b = currentBond->getB() + atomOffset;
304
305	<	if( simnfo->n_SRI ){
306	<
409	<	Exclude::createArray(simnfo->n_SRI);
410	<	the_excludes = new Exclude*[simnfo->n_SRI];
411	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
412	<	simnfo->globalExcludes = new int;
413	<	simnfo->n_exclude = simnfo->n_SRI;
414	<	}
415	<	else{
416	<
417	<	Exclude::createArray( 1 );
418	<	the_excludes = new Exclude*;
419	<	the_excludes[0] = new Exclude(0);
420	<	the_excludes[0]->setPair( 0,0 );
421	<	simnfo->globalExcludes = new int;
422	<	simnfo->globalExcludes[0] = 0;
423	<	simnfo->n_exclude = 0;
424	<	}
305	>	tempI = theBonds[j].a;
306	>	tempJ = theBonds[j].b;
307
308	<	// set the arrays into the SimInfo object
309	<
310	<	simnfo->atoms = the_atoms;
311	<	simnfo->molecules = the_molecules;
312	<	simnfo->nGlobalExcludes = 0;
313	<	simnfo->excludes = the_excludes;
308	>	#ifdef IS_MPI
309	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
310	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
311	>	#else
312	>	exI = tempI + 1;
313	>	exJ = tempJ + 1;
314	>	#endif
315
316	+	info[k].excludes->addPair(exI, exJ);
317	+	}
318
319	<	// get some of the tricky things that may still be in the globals
319	>	//make the bends
320	>	for (j = 0; j < molInfo.nBends; j++){
321	>	currentBend = comp_stamps[stampID]->getBend(j);
322	>	theBends[j].a = currentBend->getA() + atomOffset;
323	>	theBends[j].b = currentBend->getB() + atomOffset;
324	>	theBends[j].c = currentBend->getC() + atomOffset;
325
326	<
327	<	if( the_globals->haveBox() ){
328	<	simnfo->box_x = the_globals->getBox();
439	<	simnfo->box_y = the_globals->getBox();
440	<	simnfo->box_z = the_globals->getBox();
441	<	}
442	<	else if( the_globals->haveDensity() ){
326	>	if (currentBend->haveExtras()){
327	>	extras = currentBend->getExtras();
328	>	current_extra = extras;
329
330	<	double vol;
331	<	vol = (double)tot_nmol / the_globals->getDensity();
332	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
333	<	simnfo->box_y = simnfo->box_x;
334	<	simnfo->box_z = simnfo->box_x;
335	<	}
336	<	else{
451	<	if( !the_globals->haveBoxX() ){
452	<	sprintf( painCave.errMsg,
453	<	"SimSetup error, no periodic BoxX size given.\n" );
454	<	painCave.isFatal = 1;
455	<	simError();
456	<	}
457	<	simnfo->box_x = the_globals->getBoxX();
330	>	while (current_extra != NULL){
331	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
332	>	switch (current_extra->getType()){
333	>	case 0:
334	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
335	>	theBends[j].isGhost = 1;
336	>	break;
337
338	<	if( !the_globals->haveBoxY() ){
339	<	sprintf( painCave.errMsg,
340	<	"SimSetup error, no periodic BoxY size given.\n" );
341	<	painCave.isFatal = 1;
342	<	simError();
464	<	}
465	<	simnfo->box_y = the_globals->getBoxY();
338	>	case 1:
339	>	theBends[j].ghost = (int) current_extra->getDouble() +
340	>	atomOffset;
341	>	theBends[j].isGhost = 1;
342	>	break;
343
344	<	if( !the_globals->haveBoxZ() ){
345	<	sprintf( painCave.errMsg,
346	<	"SimSetup error, no periodic BoxZ size given.\n" );
347	<	painCave.isFatal = 1;
348	<	simError();
349	<	}
350	<	simnfo->box_z = the_globals->getBoxZ();
351	<	}
344	>	default:
345	>	sprintf(painCave.errMsg,
346	>	"SimSetup Error: ghostVectorSource was neither a "
347	>	"double nor an int.\n"
348	>	"-->Bend[%d] in %s\n",
349	>	j, comp_stamps[stampID]->getID());
350	>	painCave.isFatal = 1;
351	>	simError();
352	>	}
353	>	}
354	>	else{
355	>	sprintf(painCave.errMsg,
356	>	"SimSetup Error: unhandled bend assignment:\n"
357	>	"    -->%s in Bend[%d] in %s\n",
358	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
359	>	painCave.isFatal = 1;
360	>	simError();
361	>	}
362
363	+	current_extra = current_extra->getNext();
364	+	}
365	+	}
366	+
367	+	if (theBends[j].isGhost) {
368	+
369	+	tempI = theBends[j].a;
370	+	tempJ = theBends[j].b;
371	+
372		#ifdef IS_MPI
373	<	strcpy( checkPointMsg, "Box size set up" );
374	<	MPIcheckPoint();
375	<	#endif // is_mpi
373	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
374	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	#endif
379	>	info[k].excludes->addPair(exI, exJ);
380
381	+	} else {
382
383	<	// initialize the arrays
384	<
385	<	the_ff->setSimInfo( simnfo );
386	<
486	<	makeMolecules();
487	<	simnfo->identArray = new int[simnfo->n_atoms];
488	<	simnfo->molMembershipArray = new int[simnfo->n_atoms];
489	<	for(i=0; i<simnfo->n_atoms; i++){
490	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
491	<	}
492	<	for(i=0; i< simnfo->n_mol; i++) {
493	<	the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
494	<	}
495	<
496	<	if (the_globals->getUseRF() ) {
497	<	simnfo->useReactionField = 1;
498	<
499	<	if( !the_globals->haveECR() ){
500	<	sprintf( painCave.errMsg,
501	<	"SimSetup Warning: using default value of 1/2 the smallest "
502	<	"box length for the electrostaticCutoffRadius.\n"
503	<	"I hope you have a very fast processor!\n");
504	<	painCave.isFatal = 0;
505	<	simError();
506	<	double smallest;
507	<	smallest = simnfo->box_x;
508	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
509	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
510	<	simnfo->ecr = 0.5 * smallest;
511	<	} else {
512	<	simnfo->ecr        = the_globals->getECR();
513	<	}
514	<
515	<	if( !the_globals->haveEST() ){
516	<	sprintf( painCave.errMsg,
517	<	"SimSetup Warning: using default value of 0.05 * the "
518	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
519	<	);
520	<	painCave.isFatal = 0;
521	<	simError();
522	<	simnfo->est = 0.05 * simnfo->ecr;
523	<	} else {
524	<	simnfo->est        = the_globals->getEST();
525	<	}
526	<
527	<	if(!the_globals->haveDielectric() ){
528	<	sprintf( painCave.errMsg,
529	<	"SimSetup Error: You are trying to use Reaction Field without"
530	<	"setting a dielectric constant!\n"
531	<	);
532	<	painCave.isFatal = 1;
533	<	simError();
534	<	}
535	<	simnfo->dielectric = the_globals->getDielectric();
536	<	} else {
537	<	if (usesDipoles) {
538	<
539	<	if( !the_globals->haveECR() ){
540	<	sprintf( painCave.errMsg,
541	<	"SimSetup Warning: using default value of 1/2 the smallest "
542	<	"box length for the electrostaticCutoffRadius.\n"
543	<	"I hope you have a very fast processor!\n");
544	<	painCave.isFatal = 0;
545	<	simError();
546	<	double smallest;
547	<	smallest = simnfo->box_x;
548	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
549	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
550	<	simnfo->ecr = 0.5 * smallest;
551	<	} else {
552	<	simnfo->ecr        = the_globals->getECR();
553	<	}
554	<
555	<	if( !the_globals->haveEST() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 5%% of the "
558	<	"electrostaticCutoffRadius for the "
559	<	"electrostaticSkinThickness\n"
560	<	);
561	<	painCave.isFatal = 0;
562	<	simError();
563	<	simnfo->est = 0.05 * simnfo->ecr;
564	<	} else {
565	<	simnfo->est        = the_globals->getEST();
566	<	}
567	<	}
568	<	}
569	<
383	>	tempI = theBends[j].a;
384	>	tempJ = theBends[j].b;
385	>	tempK = theBends[j].c;
386	>
387		#ifdef IS_MPI
388	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
389	<	MPIcheckPoint();
390	<	#endif // is_mpi
391	<
392	<	if( the_globals->haveInitialConfig() ){
393	<
394	<	InitializeFromFile* fileInit;
578	<	#ifdef IS_MPI // is_mpi
579	<	if( worldRank == 0 ){
580	<	#endif //is_mpi
581	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
582	<	#ifdef IS_MPI
583	<	}else fileInit = new InitializeFromFile( NULL );
388	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
389	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
390	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
391	>	#else
392	>	exI = tempI + 1;
393	>	exJ = tempJ + 1;
394	>	exK = tempK + 1;
395		#endif
396	<	fileInit->read_xyz( simnfo ); // default velocities on
396	>
397	>	info[k].excludes->addPair(exI, exK);
398	>	info[k].excludes->addPair(exI, exJ);
399	>	info[k].excludes->addPair(exJ, exK);
400	>	}
401	>	}
402
403	<	delete fileInit;
404	<	}
405	<	else{
403	>	for (j = 0; j < molInfo.nTorsions; j++){
404	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
405	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
406	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
407	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
408	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
409
410	<	#ifdef IS_MPI
410	>	tempI = theTorsions[j].a;
411	>	tempJ = theTorsions[j].b;
412	>	tempK = theTorsions[j].c;
413	>	tempL = theTorsions[j].d;
414
415	<	// no init from bass
416	<
417	<	sprintf( painCave.errMsg,
418	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
419	<	painCave.isFatal;
598	<	simError();
599	<
415	>	#ifdef IS_MPI
416	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
417	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
418	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
419	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
420		#else
421	+	exI = tempI + 1;
422	+	exJ = tempJ + 1;
423	+	exK = tempK + 1;
424	+	exL = tempL + 1;
425	+	#endif
426
427	<	initFromBass();
427	>	info[k].excludes->addPair(exI, exJ);
428	>	info[k].excludes->addPair(exI, exK);
429	>	info[k].excludes->addPair(exI, exL);
430	>	info[k].excludes->addPair(exJ, exK);
431	>	info[k].excludes->addPair(exJ, exL);
432	>	info[k].excludes->addPair(exK, exL);
433	>	}
434
435	+
436	+	molInfo.myRigidBodies.clear();
437	+
438	+	for (j = 0; j < molInfo.nRigidBodies; j++){
439
440	<	#endif
441	<	}
440	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
441	>	nMembers = currentRigidBody->getNMembers();
442
443	<	#ifdef IS_MPI
609	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
610	<	MPIcheckPoint();
611	<	#endif // is_mpi
443	>	// Create the Rigid Body:
444
445	+	myRB = new RigidBody();
446
447	<
448	<
449	<
447	>	sprintf(rbName,"%s_RB_%d", molName, j);
448	>	myRB->setType(rbName);
449	>
450	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
451
452	<
453	<	#ifdef IS_MPI
620	<	if( worldRank == 0 ){
621	<	#endif // is_mpi
622	<
623	<	if( the_globals->haveFinalConfig() ){
624	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
625	<	}
626	<	else{
627	<	strcpy( simnfo->finalName, inFileName );
628	<	char* endTest;
629	<	int nameLength = strlen( simnfo->finalName );
630	<	endTest = &(simnfo->finalName[nameLength - 5]);
631	<	if( !strcmp( endTest, ".bass" ) ){
632	<	strcpy( endTest, ".eor" );
633	<	}
634	<	else if( !strcmp( endTest, ".BASS" ) ){
635	<	strcpy( endTest, ".eor" );
636	<	}
637	<	else{
638	<	endTest = &(simnfo->finalName[nameLength - 4]);
639	<	if( !strcmp( endTest, ".bss" ) ){
640	<	strcpy( endTest, ".eor" );
641	<	}
642	<	else if( !strcmp( endTest, ".mdl" ) ){
643	<	strcpy( endTest, ".eor" );
644	<	}
645	<	else{
646	<	strcat( simnfo->finalName, ".eor" );
647	<	}
648	<	}
649	<	}
650	<
651	<	// make the sample and status out names
652	<
653	<	strcpy( simnfo->sampleName, inFileName );
654	<	char* endTest;
655	<	int nameLength = strlen( simnfo->sampleName );
656	<	endTest = &(simnfo->sampleName[nameLength - 5]);
657	<	if( !strcmp( endTest, ".bass" ) ){
658	<	strcpy( endTest, ".dump" );
659	<	}
660	<	else if( !strcmp( endTest, ".BASS" ) ){
661	<	strcpy( endTest, ".dump" );
662	<	}
663	<	else{
664	<	endTest = &(simnfo->sampleName[nameLength - 4]);
665	<	if( !strcmp( endTest, ".bss" ) ){
666	<	strcpy( endTest, ".dump" );
667	<	}
668	<	else if( !strcmp( endTest, ".mdl" ) ){
669	<	strcpy( endTest, ".dump" );
670	<	}
671	<	else{
672	<	strcat( simnfo->sampleName, ".dump" );
673	<	}
674	<	}
675	<
676	<	strcpy( simnfo->statusName, inFileName );
677	<	nameLength = strlen( simnfo->statusName );
678	<	endTest = &(simnfo->statusName[nameLength - 5]);
679	<	if( !strcmp( endTest, ".bass" ) ){
680	<	strcpy( endTest, ".stat" );
681	<	}
682	<	else if( !strcmp( endTest, ".BASS" ) ){
683	<	strcpy( endTest, ".stat" );
684	<	}
685	<	else{
686	<	endTest = &(simnfo->statusName[nameLength - 4]);
687	<	if( !strcmp( endTest, ".bss" ) ){
688	<	strcpy( endTest, ".stat" );
689	<	}
690	<	else if( !strcmp( endTest, ".mdl" ) ){
691	<	strcpy( endTest, ".stat" );
692	<	}
693	<	else{
694	<	strcat( simnfo->statusName, ".stat" );
695	<	}
696	<	}
697	<
698	<	#ifdef IS_MPI
699	<	}
700	<	#endif // is_mpi
701	<
702	<	// set the status, sample, and themal kick times
703	<
704	<	if( the_globals->haveSampleTime() ){
705	<	simnfo->sampleTime = the_globals->getSampleTime();
706	<	simnfo->statusTime = simnfo->sampleTime;
707	<	simnfo->thermalTime = simnfo->sampleTime;
708	<	}
709	<	else{
710	<	simnfo->sampleTime = the_globals->getRunTime();
711	<	simnfo->statusTime = simnfo->sampleTime;
712	<	simnfo->thermalTime = simnfo->sampleTime;
713	<	}
452	>	// molI is atom numbering inside this molecule
453	>	molI = currentRigidBody->getMember(rb1);
454
455	<	if( the_globals->haveStatusTime() ){
456	<	simnfo->statusTime = the_globals->getStatusTime();
717	<	}
455	>	// tempI is atom numbering on local processor
456	>	tempI = molI + atomOffset;
457
458	<	if( the_globals->haveThermalTime() ){
459	<	simnfo->thermalTime = the_globals->getThermalTime();
460	<	}
458	>	// currentAtom is the AtomStamp (which we need for
459	>	// rigid body reference positions)
460	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
461
462	<	// check for the temperature set flag
462	>	// When we add to the rigid body, add the atom itself and
463	>	// the stamp info:
464
465	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
465	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
466	>
467	>	// Add this atom to the Skip List for the integrators
468	>	#ifdef IS_MPI
469	>	slI = info[k].atoms[tempI]->getGlobalIndex();
470	>	#else
471	>	slI = tempI;
472	>	#endif
473	>	skipList.insert(slI);
474	>
475	>	}
476	>
477	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
478	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
479	>
480	>	tempI = currentRigidBody->getMember(rb1);
481	>	tempJ = currentRigidBody->getMember(rb2);
482	>
483	>	// Some explanation is required here.
484	>	// Fortran indexing starts at 1, while c indexing starts at 0
485	>	// Also, in parallel computations, the GlobalIndex is
486	>	// used for the exclude list:
487	>
488	>	#ifdef IS_MPI
489	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
490	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
491	>	#else
492	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
493	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
494	>	#endif
495	>
496	>	info[k].excludes->addPair(exI, exJ);
497	>
498	>	}
499	>	}
500
501	+	molInfo.myRigidBodies.push_back(myRB);
502	+	info[k].rigidBodies.push_back(myRB);
503	+	}
504	+
505
506	<	//   // make the longe range forces and the integrator
506	>	//create cutoff group for molecule
507
508	<	//   new AllLong( simnfo );
508	>	cutoffAtomSet.clear();
509	>	molInfo.myCutoffGroups.clear();
510	>
511	>	for (j = 0; j < nCutoffGroups; j++){
512
513	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
514	+	nMembers = currentCutoffGroup->getNMembers();
515
516	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
517	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
735	<	}
736	<	else if( !strcmp( force_field, "LJ" ) ){
737	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
738	<	}
739	<	else {
740	<	std::cerr << "I'm a bug.\n";
741	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
742	<	}
516	>	myCutoffGroup = new CutoffGroup();
517	>
518		#ifdef IS_MPI
519	<	mpiSim->mpiRefresh();
519	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
520	>	#else
521	>	myCutoffGroup->setGlobalIndex(groupOffset);
522		#endif
523	+
524	+	for (int cg = 0; cg < nMembers; cg++) {
525
526	<	// initialize the Fortran
526	>	// molI is atom numbering inside this molecule
527	>	molI = currentCutoffGroup->getMember(cg);
528
529	+	// tempI is atom numbering on local processor
530	+	tempI = molI + atomOffset;
531
532	<	simnfo->refreshSim();
533	<
534	<	if( !strcmp( simnfo->mixingRule, "standard") ){
535	<	the_ff->initForceField( LB_MIXING_RULE );
536	<	}
537	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
538	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
539	<	}
540	<	else{
541	<	sprintf( painCave.errMsg,
542	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
543	<	simnfo->mixingRule );
544	<	painCave.isFatal = 1;
763	<	simError();
764	<	}
532	>	#ifdef IS_MPI
533	>	globalID = info[k].atoms[tempI]->getGlobalIndex();
534	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
535	>	#else
536	>	globalID = info[k].atoms[tempI]->getIndex();
537	>	info[k].globalGroupMembership[globalID] = groupOffset;
538	>	#endif
539	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
540	>	cutoffAtomSet.insert(tempI);
541	>	}
542	>
543	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
544	>	groupOffset++;
545
546	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
547	+
548	+
549	+	// create a cutoff group for every atom in current molecule which
550	+	// does not belong to cutoffgroup defined at mdl file
551	+
552	+	for(j = 0; j < molInfo.nAtoms; j++){
553	+
554	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
555	+	myCutoffGroup = new CutoffGroup();
556	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
557	+
558	+	#ifdef IS_MPI
559	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
560	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
561	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
562	+	#else
563	+	myCutoffGroup->setGlobalIndex(groupOffset);
564	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
565	+	info[k].globalGroupMembership[globalID] = groupOffset;
566	+	#endif
567	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
568	+	groupOffset++;
569	+	}
570	+	}
571
572	+	// After this is all set up, scan through the atoms to
573	+	// see if they can be added to the integrableObjects:
574	+
575	+	molInfo.myIntegrableObjects.clear();
576	+
577	+
578	+	for (j = 0; j < molInfo.nAtoms; j++){
579	+
580		#ifdef IS_MPI
581	<	strcpy( checkPointMsg,
582	<	"Successfully intialized the mixingRule for Fortran." );
583	<	MPIcheckPoint();
584	<	#endif // is_mpi
772	<	}
581	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
582	>	#else
583	>	slJ = j+atomOffset;
584	>	#endif
585
586	+	// if they aren't on the skip list, then they can be integrated
587
588	<	void SimSetup::makeMolecules( void ){
588	>	if (skipList.find(slJ) == skipList.end()) {
589	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
590	>	info[k].integrableObjects.push_back(mySD);
591	>	molInfo.myIntegrableObjects.push_back(mySD);
592	>	}
593	>	}
594
595	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
778	<	molInit info;
779	<	DirectionalAtom* dAtom;
780	<	LinkedAssign* extras;
781	<	LinkedAssign* current_extra;
782	<	AtomStamp* currentAtom;
783	<	BondStamp* currentBond;
784	<	BendStamp* currentBend;
785	<	TorsionStamp* currentTorsion;
595	>	// all rigid bodies are integrated:
596
597	<	bond_pair* theBonds;
598	<	bend_set* theBends;
599	<	torsion_set* theTorsions;
597	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
598	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
599	>	info[k].integrableObjects.push_back(mySD);
600	>	molInfo.myIntegrableObjects.push_back(mySD);
601	>	}
602
791	–
792	–	//init the forceField paramters
603
604	<	the_ff->readParams();
604	>	/*
605
606	<
607	<	// init the atoms
606	>	//creat ConstraintPair.
607	>	molInfo.myConstraintPair.clear();
608	>
609	>	for (j = 0; j < molInfo.nBonds; j++){
610
611	<	double ux, uy, uz, u, uSqr;
612	<
613	<	atomOffset = 0;
802	<	excludeOffset = 0;
803	<	for(i=0; i<simnfo->n_mol; i++){
804	<
805	<	stampID = the_molecules[i].getStampID();
611	>	//if both atoms are in the same rigid body, just skip it
612	>	currentBond = comp_stamps[stampID]->getBond(j);
613	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
614
615	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
616	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
617	<	info.nBends    = comp_stamps[stampID]->getNBends();
618	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
619	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
615	>	tempI = currentBond->getA() + atomOffset;
616	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
617	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
618	>	else
619	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
620
621	<	info.myAtoms = &the_atoms[atomOffset];
622	<	info.myExcludes = &the_excludes[excludeOffset];
623	<	info.myBonds = new Bond*[info.nBonds];
624	<	info.myBends = new Bend*[info.nBends];
625	<	info.myTorsions = new Torsion*[info.nTorsions];
621	>	tempJ =  currentBond->getB() + atomOffset;
622	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
623	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
624	>	else
625	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
626
627	<	theBonds = new bond_pair[info.nBonds];
628	<	theBends = new bend_set[info.nBends];
629	<	theTorsions = new torsion_set[info.nTorsions];
630	<
823	<	// make the Atoms
824	<
825	<	for(j=0; j<info.nAtoms; j++){
627	>	consPair = new DistanceConstraintPair(consElement1, consElement2);
628	>	molInfo.myConstraintPairs.push_back(consPair);
629	>	}
630	>	}
631
632	<	currentAtom = comp_stamps[stampID]->getAtom( j );
633	<	if( currentAtom->haveOrientation() ){
634	<
635	<	dAtom = new DirectionalAtom(j + atomOffset);
636	<	simnfo->n_oriented++;
637	<	info.myAtoms[j] = dAtom;
638	<
639	<	ux = currentAtom->getOrntX();
640	<	uy = currentAtom->getOrntY();
641	<	uz = currentAtom->getOrntZ();
642	<
643	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
644	<
645	<	u = sqrt( uSqr );
646	<	ux = ux / u;
842	<	uy = uy / u;
843	<	uz = uz / u;
844	<
845	<	dAtom->setSUx( ux );
846	<	dAtom->setSUy( uy );
847	<	dAtom->setSUz( uz );
632	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
633	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
634	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
635	>
636	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
637	>
638	>	for(size_t m = 0; m < jointAtoms.size(); m++){
639	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
640	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
641	>
642	>	consPair = new JointConstraintPair(consElement1, consElement2);
643	>	molInfo.myConstraintPairs.push_back(consPair);
644	>	}
645	>
646	>	}
647		}
849	–	else{
850	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
851	–	}
852	–	info.myAtoms[j]->setType( currentAtom->getType() );
853	–
854	–	#ifdef IS_MPI
648
649	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
649	>	*/
650	>	// send the arrays off to the forceField for init.
651
652	<	#endif // is_mpi
653	<	}
654	<
655	<	// make the bonds
656	<	for(j=0; j<info.nBonds; j++){
652	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
653	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
654	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
655	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
656	>	theTorsions);
657	>
658	>	info[k].molecules[i].initialize(molInfo);
659
660	<	currentBond = comp_stamps[stampID]->getBond( j );
661	<	theBonds[j].a = currentBond->getA() + atomOffset;
662	<	theBonds[j].b = currentBond->getB() + atomOffset;
660	>
661	>	atomOffset += molInfo.nAtoms;
662	>	delete[] theBonds;
663	>	delete[] theBends;
664	>	delete[] theTorsions;
665	>	}
666
868	–	exI = theBonds[j].a;
869	–	exJ = theBonds[j].b;
667
871	–	// exclude_I must always be the smaller of the pair
872	–	if( exI > exJ ){
873	–	tempEx = exI;
874	–	exI = exJ;
875	–	exJ = tempEx;
876	–	}
877	–	#ifdef IS_MPI
878	–	tempEx = exI;
879	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
880	–	tempEx = exJ;
881	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
882	–
883	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
884	–	#else  // isn't MPI
668
669	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
670	<	#endif  //is_mpi
671	<	}
672	<	excludeOffset += info.nBonds;
669	>	#ifdef IS_MPI
670	>	// Since the globalGroupMembership has been zero filled and we've only
671	>	// poked values into the atoms we know, we can do an Allreduce
672	>	// to get the full globalGroupMembership array (We think).
673	>	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
674	>	// docs said we could.
675
676	<	//make the bends
892	<	for(j=0; j<info.nBends; j++){
893	<
894	<	currentBend = comp_stamps[stampID]->getBend( j );
895	<	theBends[j].a = currentBend->getA() + atomOffset;
896	<	theBends[j].b = currentBend->getB() + atomOffset;
897	<	theBends[j].c = currentBend->getC() + atomOffset;
898	<
899	<	if( currentBend->haveExtras() ){
900	<
901	<	extras = currentBend->getExtras();
902	<	current_extra = extras;
903	<
904	<	while( current_extra != NULL ){
905	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
906	<
907	<	switch( current_extra->getType() ){
908	<
909	<	case 0:
910	<	theBends[j].ghost =
911	<	current_extra->getInt() + atomOffset;
912	<	theBends[j].isGhost = 1;
913	<	break;
914	<
915	<	case 1:
916	<	theBends[j].ghost =
917	<	(int)current_extra->getDouble() + atomOffset;
918	<	theBends[j].isGhost = 1;
919	<	break;
920	<
921	<	default:
922	<	sprintf( painCave.errMsg,
923	<	"SimSetup Error: ghostVectorSource was neither a "
924	<	"double nor an int.\n"
925	<	"-->Bend[%d] in %s\n",
926	<	j, comp_stamps[stampID]->getID() );
927	<	painCave.isFatal = 1;
928	<	simError();
929	<	}
930	<	}
931	<
932	<	else{
933	<
934	<	sprintf( painCave.errMsg,
935	<	"SimSetup Error: unhandled bend assignment:\n"
936	<	"    -->%s in Bend[%d] in %s\n",
937	<	current_extra->getlhs(),
938	<	j, comp_stamps[stampID]->getID() );
939	<	painCave.isFatal = 1;
940	<	simError();
941	<	}
942	<
943	<	current_extra = current_extra->getNext();
944	<	}
945	<	}
946	<
947	<	if( !theBends[j].isGhost ){
948	<
949	<	exI = theBends[j].a;
950	<	exJ = theBends[j].c;
951	<	}
952	<	else{
953	<
954	<	exI = theBends[j].a;
955	<	exJ = theBends[j].b;
956	<	}
957	<
958	<	// exclude_I must always be the smaller of the pair
959	<	if( exI > exJ ){
960	<	tempEx = exI;
961	<	exI = exJ;
962	<	exJ = tempEx;
963	<	}
964	<	#ifdef IS_MPI
965	<	tempEx = exI;
966	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
967	<	tempEx = exJ;
968	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
969	<
970	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
971	<	#else  // isn't MPI
972	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
973	<	#endif  //is_mpi
974	<	}
975	<	excludeOffset += info.nBends;
676	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
677
678	<	for(j=0; j<info.nTorsions; j++){
679	<
680	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
681	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
981	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
982	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
983	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
984	<
985	<	exI = theTorsions[j].a;
986	<	exJ = theTorsions[j].d;
678	>	MPI_Allreduce(info[k].globalGroupMembership,
679	>	ggMjunk,
680	>	mpiSim->getNAtomsGlobal(),
681	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
682
683	<	// exclude_I must always be the smaller of the pair
684	<	if( exI > exJ ){
990	<	tempEx = exI;
991	<	exI = exJ;
992	<	exJ = tempEx;
993	<	}
994	<	#ifdef IS_MPI
995	<	tempEx = exI;
996	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
997	<	tempEx = exJ;
998	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
999	<
1000	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1001	<	#else  // isn't MPI
1002	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1003	<	#endif  //is_mpi
1004	<	}
1005	<	excludeOffset += info.nTorsions;
683	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
684	>	info[k].globalGroupMembership[i] = ggMjunk[i];
685
686	+	delete[] ggMjunk;
687
688	<	// send the arrays off to the forceField for init.
688	>	#endif
689
1010	–	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1011	–	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1012	–	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1013	–	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
690
691
1016	–	the_molecules[i].initialize( info );
1017	–
1018	–
1019	–	atomOffset += info.nAtoms;
1020	–	delete[] theBonds;
1021	–	delete[] theBends;
1022	–	delete[] theTorsions;
692		}
693
694		#ifdef IS_MPI
695	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
695	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
696		MPIcheckPoint();
697		#endif // is_mpi
698
1030	–	// clean up the forcefield
1031	–	the_ff->calcRcut();
1032	–	the_ff->cleanMe();
1033	–
699		}
700
701	<	void SimSetup::initFromBass( void ){
1037	<
701	>	void SimSetup::initFromBass(void){
702		int i, j, k;
703		int n_cells;
704		double cellx, celly, cellz;
#	Line 1043 | Line 707 | void SimSetup::initFromBass( void ){
707		int n_extra;
708		int have_extra, done;
709
710	<	temp1 = (double)tot_nmol / 4.0;
711	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
712	<	temp3 = ceil( temp2 );
710	>	double vel[3];
711	>	vel[0] = 0.0;
712	>	vel[1] = 0.0;
713	>	vel[2] = 0.0;
714
715	<	have_extra =0;
716	<	if( temp2 < temp3 ){ // we have a non-complete lattice
717	<	have_extra =1;
715	>	temp1 = (double) tot_nmol / 4.0;
716	>	temp2 = pow(temp1, (1.0 / 3.0));
717	>	temp3 = ceil(temp2);
718
719	<	n_cells = (int)temp3 - 1;
720	<	cellx = simnfo->box_x / temp3;
721	<	celly = simnfo->box_y / temp3;
722	<	cellz = simnfo->box_z / temp3;
1058	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1059	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1060	<	n_per_extra = (int)ceil( temp1 );
719	>	have_extra = 0;
720	>	if (temp2 < temp3){
721	>	// we have a non-complete lattice
722	>	have_extra = 1;
723
724	<	if( n_per_extra > 4){
725	<	sprintf( painCave.errMsg,
726	<	"SimSetup error. There has been an error in constructing"
727	<	" the non-complete lattice.\n" );
724	>	n_cells = (int) temp3 - 1;
725	>	cellx = info[0].boxL[0] / temp3;
726	>	celly = info[0].boxL[1] / temp3;
727	>	cellz = info[0].boxL[2] / temp3;
728	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
729	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
730	>	n_per_extra = (int) ceil(temp1);
731	>
732	>	if (n_per_extra > 4){
733	>	sprintf(painCave.errMsg,
734	>	"SimSetup error. There has been an error in constructing"
735	>	" the non-complete lattice.\n");
736		painCave.isFatal = 1;
737		simError();
738		}
739		}
740		else{
741	<	n_cells = (int)temp3;
742	<	cellx = simnfo->box_x / temp3;
743	<	celly = simnfo->box_y / temp3;
744	<	cellz = simnfo->box_z / temp3;
741	>	n_cells = (int) temp3;
742	>	cellx = info[0].boxL[0] / temp3;
743	>	celly = info[0].boxL[1] / temp3;
744	>	cellz = info[0].boxL[2] / temp3;
745		}
746
747		current_mol = 0;
#	Line 1079 | Line 749 | void SimSetup::initFromBass( void ){
749		current_comp = 0;
750		current_atom_ndx = 0;
751
752	<	for( i=0; i < n_cells ; i++ ){
753	<	for( j=0; j < n_cells; j++ ){
754	<	for( k=0; k < n_cells; k++ ){
752	>	for (i = 0; i < n_cells ; i++){
753	>	for (j = 0; j < n_cells; j++){
754	>	for (k = 0; k < n_cells; k++){
755	>	makeElement(i * cellx, j * celly, k * cellz);
756
757	<	makeElement( i * cellx,
1087	<	j * celly,
1088	<	k * cellz );
757	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
758
759	<	makeElement( i * cellx + 0.5 * cellx,
1091	<	j * celly + 0.5 * celly,
1092	<	k * cellz );
759	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
760
761	<	makeElement( i * cellx,
1095	<	j * celly + 0.5 * celly,
1096	<	k * cellz + 0.5 * cellz );
1097	<
1098	<	makeElement( i * cellx + 0.5 * cellx,
1099	<	j * celly,
1100	<	k * cellz + 0.5 * cellz );
761	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
762		}
763		}
764		}
765
766	<	if( have_extra ){
766	>	if (have_extra){
767		done = 0;
768
769		int start_ndx;
770	<	for( i=0; i < (n_cells+1) && !done; i++ ){
771	<	for( j=0; j < (n_cells+1) && !done; j++ ){
770	>	for (i = 0; i < (n_cells + 1) && !done; i++){
771	>	for (j = 0; j < (n_cells + 1) && !done; j++){
772	>	if (i < n_cells){
773	>	if (j < n_cells){
774	>	start_ndx = n_cells;
775	>	}
776	>	else
777	>	start_ndx = 0;
778	>	}
779	>	else
780	>	start_ndx = 0;
781
782	<	if( i < n_cells ){
782	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
783	>	makeElement(i * cellx, j * celly, k * cellz);
784	>	done = (current_mol >= tot_nmol);
785
786	<	if( j < n_cells ){
787	<	start_ndx = n_cells;
788	<	}
789	<	else start_ndx = 0;
790	<	}
1119	<	else start_ndx = 0;
786	>	if (!done && n_per_extra > 1){
787	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
788	>	k * cellz);
789	>	done = (current_mol >= tot_nmol);
790	>	}
791
792	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
793	<
794	<	makeElement( i * cellx,
795	<	j * celly,
796	<	k * cellz );
1126	<	done = ( current_mol >= tot_nmol );
1127	<
1128	<	if( !done && n_per_extra > 1 ){
1129	<	makeElement( i * cellx + 0.5 * cellx,
1130	<	j * celly + 0.5 * celly,
1131	<	k * cellz );
1132	<	done = ( current_mol >= tot_nmol );
1133	<	}
792	>	if (!done && n_per_extra > 2){
793	>	makeElement(i * cellx, j * celly + 0.5 * celly,
794	>	k * cellz + 0.5 * cellz);
795	>	done = (current_mol >= tot_nmol);
796	>	}
797
798	<	if( !done && n_per_extra > 2){
799	<	makeElement( i * cellx,
800	<	j * celly + 0.5 * celly,
801	<	k * cellz + 0.5 * cellz );
802	<	done = ( current_mol >= tot_nmol );
803	<	}
1141	<
1142	<	if( !done && n_per_extra > 3){
1143	<	makeElement( i * cellx + 0.5 * cellx,
1144	<	j * celly,
1145	<	k * cellz + 0.5 * cellz );
1146	<	done = ( current_mol >= tot_nmol );
1147	<	}
1148	<	}
798	>	if (!done && n_per_extra > 3){
799	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
800	>	k * cellz + 0.5 * cellz);
801	>	done = (current_mol >= tot_nmol);
802	>	}
803	>	}
804		}
805		}
806		}
807
808	<
809	<	for( i=0; i<simnfo->n_atoms; i++ ){
1155	<	simnfo->atoms[i]->set_vx( 0.0 );
1156	<	simnfo->atoms[i]->set_vy( 0.0 );
1157	<	simnfo->atoms[i]->set_vz( 0.0 );
808	>	for (i = 0; i < info[0].n_atoms; i++){
809	>	info[0].atoms[i]->setVel(vel);
810		}
811		}
812
813	<	void SimSetup::makeElement( double x, double y, double z ){
1162	<
813	>	void SimSetup::makeElement(double x, double y, double z){
814		int k;
815		AtomStamp* current_atom;
816		DirectionalAtom* dAtom;
817		double rotMat[3][3];
818	+	double pos[3];
819
820	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
821	<
822	<	current_atom = comp_stamps[current_comp]->getAtom( k );
823	<	if( !current_atom->havePosition() ){
824	<	sprintf( painCave.errMsg,
825	<	"SimSetup:initFromBass error.\n"
826	<	"\tComponent %s, atom %s does not have a position specified.\n"
827	<	"\tThe initialization routine is unable to give a start"
828	<	" position.\n",
1177	<	comp_stamps[current_comp]->getID(),
1178	<	current_atom->getType() );
820	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
821	>	current_atom = comp_stamps[current_comp]->getAtom(k);
822	>	if (!current_atom->havePosition()){
823	>	sprintf(painCave.errMsg,
824	>	"SimSetup:initFromBass error.\n"
825	>	"\tComponent %s, atom %s does not have a position specified.\n"
826	>	"\tThe initialization routine is unable to give a start"
827	>	" position.\n",
828	>	comp_stamps[current_comp]->getID(), current_atom->getType());
829		painCave.isFatal = 1;
830		simError();
831		}
832
833	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
834	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
835	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
833	>	pos[0] = x + current_atom->getPosX();
834	>	pos[1] = y + current_atom->getPosY();
835	>	pos[2] = z + current_atom->getPosZ();
836
837	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
837	>	info[0].atoms[current_atom_ndx]->setPos(pos);
838
839	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
839	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
840	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
841
842		rotMat[0][0] = 1.0;
843		rotMat[0][1] = 0.0;
#	Line 1200 | Line 851 | void SimSetup::makeElement( double x, double y, double
851		rotMat[2][1] = 0.0;
852		rotMat[2][2] = 1.0;
853
854	<	dAtom->setA( rotMat );
854	>	dAtom->setA(rotMat);
855		}
856
857		current_atom_ndx++;
#	Line 1209 | Line 860 | void SimSetup::makeElement( double x, double y, double
860		current_mol++;
861		current_comp_mol++;
862
863	<	if( current_comp_mol >= components_nmol[current_comp] ){
1213	<
863	>	if (current_comp_mol >= components_nmol[current_comp]){
864		current_comp_mol = 0;
865		current_comp++;
866	+	}
867	+	}
868	+
869	+
870	+	void SimSetup::gatherInfo(void){
871	+	int i;
872	+
873	+	ensembleCase = -1;
874	+	ffCase = -1;
875	+
876	+	// set the easy ones first
877	+
878	+	for (i = 0; i < nInfo; i++){
879	+	info[i].target_temp = globals->getTargetTemp();
880	+	info[i].dt = globals->getDt();
881	+	info[i].run_time = globals->getRunTime();
882	+	}
883	+	n_components = globals->getNComponents();
884	+
885	+
886	+	// get the forceField
887	+
888	+	strcpy(force_field, globals->getForceField());
889	+
890	+	if (!strcasecmp(force_field, "DUFF")){
891	+	ffCase = FF_DUFF;
892	+	}
893	+	else if (!strcasecmp(force_field, "LJ")){
894	+	ffCase = FF_LJ;
895	+	}
896	+	else if (!strcasecmp(force_field, "EAM")){
897	+	ffCase = FF_EAM;
898	+	}
899	+	else if (!strcasecmp(force_field, "WATER")){
900	+	ffCase = FF_H2O;
901	+	}
902	+	else{
903	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
904	+	force_field);
905	+	painCave.isFatal = 1;
906	+	simError();
907	+	}
908	+
909	+	// get the ensemble
910	+
911	+	strcpy(ensemble, globals->getEnsemble());
912	+
913	+	if (!strcasecmp(ensemble, "NVE")){
914	+	ensembleCase = NVE_ENS;
915	+	}
916	+	else if (!strcasecmp(ensemble, "NVT")){
917	+	ensembleCase = NVT_ENS;
918	+	}
919	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
920	+	ensembleCase = NPTi_ENS;
921	+	}
922	+	else if (!strcasecmp(ensemble, "NPTf")){
923	+	ensembleCase = NPTf_ENS;
924	+	}
925	+	else if (!strcasecmp(ensemble, "NPTxyz")){
926	+	ensembleCase = NPTxyz_ENS;
927	+	}
928	+	else{
929	+	sprintf(painCave.errMsg,
930	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
931	+	"\treverting to NVE for this simulation.\n",
932	+	ensemble);
933	+	painCave.isFatal = 0;
934	+	simError();
935	+	strcpy(ensemble, "NVE");
936	+	ensembleCase = NVE_ENS;
937	+	}
938	+
939	+	for (i = 0; i < nInfo; i++){
940	+	strcpy(info[i].ensemble, ensemble);
941	+
942	+	// get the mixing rule
943	+
944	+	strcpy(info[i].mixingRule, globals->getMixingRule());
945	+	info[i].usePBC = globals->getPBC();
946	+	}
947	+
948	+	// get the components and calculate the tot_nMol and indvidual n_mol
949	+
950	+	the_components = globals->getComponents();
951	+	components_nmol = new int[n_components];
952	+
953	+
954	+	if (!globals->haveNMol()){
955	+	// we don't have the total number of molecules, so we assume it is
956	+	// given in each component
957	+
958	+	tot_nmol = 0;
959	+	for (i = 0; i < n_components; i++){
960	+	if (!the_components[i]->haveNMol()){
961	+	// we have a problem
962	+	sprintf(painCave.errMsg,
963	+	"SimSetup Error. No global NMol or component NMol given.\n"
964	+	"\tCannot calculate the number of atoms.\n");
965	+	painCave.isFatal = 1;
966	+	simError();
967	+	}
968	+
969	+	tot_nmol += the_components[i]->getNMol();
970	+	components_nmol[i] = the_components[i]->getNMol();
971	+	}
972	+	}
973	+	else{
974	+	sprintf(painCave.errMsg,
975	+	"SimSetup error.\n"
976	+	"\tSorry, the ability to specify total"
977	+	" nMols and then give molfractions in the components\n"
978	+	"\tis not currently supported."
979	+	" Please give nMol in the components.\n");
980	+	painCave.isFatal = 1;
981	+	simError();
982	+	}
983	+
984	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
985	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
986	+	sprintf(painCave.errMsg,
987	+	"Sample time is not divisible by dt.\n"
988	+	"\tThis will result in samples that are not uniformly\n"
989	+	"\tdistributed in time.  If this is a problem, change\n"
990	+	"\tyour sampleTime variable.\n");
991	+	painCave.isFatal = 0;
992	+	simError();
993	+	}
994	+
995	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
996	+	sprintf(painCave.errMsg,
997	+	"Status time is not divisible by dt.\n"
998	+	"\tThis will result in status reports that are not uniformly\n"
999	+	"\tdistributed in time.  If this is a problem, change \n"
1000	+	"\tyour statusTime variable.\n");
1001	+	painCave.isFatal = 0;
1002	+	simError();
1003	+	}
1004	+
1005	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1006	+	sprintf(painCave.errMsg,
1007	+	"Thermal time is not divisible by dt.\n"
1008	+	"\tThis will result in thermalizations that are not uniformly\n"
1009	+	"\tdistributed in time.  If this is a problem, change \n"
1010	+	"\tyour thermalTime variable.\n");
1011	+	painCave.isFatal = 0;
1012	+	simError();
1013	+	}
1014	+
1015	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1016	+	sprintf(painCave.errMsg,
1017	+	"Reset time is not divisible by dt.\n"
1018	+	"\tThis will result in integrator resets that are not uniformly\n"
1019	+	"\tdistributed in time.  If this is a problem, change\n"
1020	+	"\tyour resetTime variable.\n");
1021	+	painCave.isFatal = 0;
1022	+	simError();
1023	+	}
1024	+
1025	+	// set the status, sample, and thermal kick times
1026	+
1027	+	for (i = 0; i < nInfo; i++){
1028	+	if (globals->haveSampleTime()){
1029	+	info[i].sampleTime = globals->getSampleTime();
1030	+	info[i].statusTime = info[i].sampleTime;
1031	+	}
1032	+	else{
1033	+	info[i].sampleTime = globals->getRunTime();
1034	+	info[i].statusTime = info[i].sampleTime;
1035	+	}
1036	+
1037	+	if (globals->haveStatusTime()){
1038	+	info[i].statusTime = globals->getStatusTime();
1039	+	}
1040	+
1041	+	if (globals->haveThermalTime()){
1042	+	info[i].thermalTime = globals->getThermalTime();
1043	+	} else {
1044	+	info[i].thermalTime = globals->getRunTime();
1045	+	}
1046	+
1047	+	info[i].resetIntegrator = 0;
1048	+	if( globals->haveResetTime() ){
1049	+	info[i].resetTime = globals->getResetTime();
1050	+	info[i].resetIntegrator = 1;
1051	+	}
1052	+
1053	+	// check for the temperature set flag
1054	+
1055	+	if (globals->haveTempSet())
1056	+	info[i].setTemp = globals->getTempSet();
1057	+
1058	+	// check for the extended State init
1059	+
1060	+	info[i].useInitXSstate = globals->getUseInitXSstate();
1061	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1062	+
1063	+	// check for thermodynamic integration
1064	+	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1065	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1066	+	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1067	+	info[i].thermIntLambda = globals->getThermIntLambda();
1068	+	info[i].thermIntK = globals->getThermIntK();
1069	+
1070	+	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1071	+	info[i].restraint = myRestraint;
1072	+	}
1073	+	else {
1074	+	sprintf(painCave.errMsg,
1075	+	"SimSetup Error:\n"
1076	+	"\tKeyword useSolidThermInt was set to 'true' but\n"
1077	+	"\tthermodynamicIntegrationLambda (and/or\n"
1078	+	"\tthermodynamicIntegrationK) was not specified.\n"
1079	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1080	+	painCave.isFatal = 1;
1081	+	simError();
1082	+	}
1083	+	}
1084	+	else if(globals->getUseLiquidThermInt()) {
1085	+	if (globals->getUseSolidThermInt()) {
1086	+	sprintf( painCave.errMsg,
1087	+	"SimSetup Warning: It appears that you have both solid and\n"
1088	+	"\tliquid thermodynamic integration activated in your .bass\n"
1089	+	"\tfile. To avoid confusion, specify only one technique in\n"
1090	+	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1091	+	"\twill be assumed for the current simulation. If this is not\n"
1092	+	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1093	+	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1094	+	painCave.isFatal = 0;
1095	+	simError();
1096	+	}
1097	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1098	+	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1099	+	info[i].thermIntLambda = globals->getThermIntLambda();
1100	+	info[i].thermIntK = globals->getThermIntK();
1101	+	}
1102	+	else {
1103	+	sprintf(painCave.errMsg,
1104	+	"SimSetup Error:\n"
1105	+	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1106	+	"\tthermodynamicIntegrationLambda (and/or\n"
1107	+	"\tthermodynamicIntegrationK) was not specified.\n"
1108	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1109	+	painCave.isFatal = 1;
1110	+	simError();
1111	+	}
1112	+	}
1113	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1114	+	sprintf(painCave.errMsg,
1115	+	"SimSetup Warning: If you want to use Thermodynamic\n"
1116	+	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1117	+	"\t'true' in your .bass file.  These keywords are set to\n"
1118	+	"\t'false' by default, so your lambda and/or k values are\n"
1119	+	"\tbeing ignored.\n");
1120	+	painCave.isFatal = 0;
1121	+	simError();
1122	+	}
1123		}
1124	+
1125	+	//setup seed for random number generator
1126	+	int seedValue;
1127	+
1128	+	if (globals->haveSeed()){
1129	+	seedValue = globals->getSeed();
1130	+
1131	+	if(seedValue / 1E9 == 0){
1132	+	sprintf(painCave.errMsg,
1133	+	"Seed for sprng library should contain at least 9 digits\n"
1134	+	"OOPSE will generate a seed for user\n");
1135	+	painCave.isFatal = 0;
1136	+	simError();
1137	+
1138	+	//using seed generated by system instead of invalid seed set by user
1139	+	#ifndef IS_MPI
1140	+	seedValue = make_sprng_seed();
1141	+	#else
1142	+	if (worldRank == 0){
1143	+	seedValue = make_sprng_seed();
1144	+	}
1145	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1146	+	#endif
1147	+	}
1148	+	}//end of if branch of globals->haveSeed()
1149	+	else{
1150	+
1151	+	#ifndef IS_MPI
1152	+	seedValue = make_sprng_seed();
1153	+	#else
1154	+	if (worldRank == 0){
1155	+	seedValue = make_sprng_seed();
1156	+	}
1157	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1158	+	#endif
1159	+	}//end of globals->haveSeed()
1160	+
1161	+	for (int i = 0; i < nInfo; i++){
1162	+	info[i].setSeed(seedValue);
1163	+	}
1164	+
1165	+	#ifdef IS_MPI
1166	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1167	+	MPIcheckPoint();
1168	+	#endif // is_mpi
1169		}
1170	+
1171	+
1172	+	void SimSetup::finalInfoCheck(void){
1173	+	int index;
1174	+	int usesDipoles;
1175	+	int usesCharges;
1176	+	int i;
1177	+
1178	+	for (i = 0; i < nInfo; i++){
1179	+	// check electrostatic parameters
1180	+
1181	+	index = 0;
1182	+	usesDipoles = 0;
1183	+	while ((index < info[i].n_atoms) && !usesDipoles){
1184	+	usesDipoles = (info[i].atoms[index])->hasDipole();
1185	+	index++;
1186	+	}
1187	+	index = 0;
1188	+	usesCharges = 0;
1189	+	while ((index < info[i].n_atoms) && !usesCharges){
1190	+	usesCharges= (info[i].atoms[index])->hasCharge();
1191	+	index++;
1192	+	}
1193	+	#ifdef IS_MPI
1194	+	int myUse = usesDipoles;
1195	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1196	+	#endif //is_mpi
1197	+
1198	+	double theRcut, theRsw;
1199	+
1200	+	if (globals->haveRcut()) {
1201	+	theRcut = globals->getRcut();
1202	+
1203	+	if (globals->haveRsw())
1204	+	theRsw = globals->getRsw();
1205	+	else
1206	+	theRsw = theRcut;
1207	+
1208	+	info[i].setDefaultRcut(theRcut, theRsw);
1209	+
1210	+	} else {
1211	+
1212	+	the_ff->calcRcut();
1213	+	theRcut = info[i].getRcut();
1214	+
1215	+	if (globals->haveRsw())
1216	+	theRsw = globals->getRsw();
1217	+	else
1218	+	theRsw = theRcut;
1219	+
1220	+	info[i].setDefaultRcut(theRcut, theRsw);
1221	+	}
1222	+
1223	+	if (globals->getUseRF()){
1224	+	info[i].useReactionField = 1;
1225	+
1226	+	if (!globals->haveRcut()){
1227	+	sprintf(painCave.errMsg,
1228	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1229	+	"\tOOPSE will use a default value of 15.0 angstroms"
1230	+	"\tfor the cutoffRadius.\n");
1231	+	painCave.isFatal = 0;
1232	+	simError();
1233	+	theRcut = 15.0;
1234	+	}
1235	+	else{
1236	+	theRcut = globals->getRcut();
1237	+	}
1238	+
1239	+	if (!globals->haveRsw()){
1240	+	sprintf(painCave.errMsg,
1241	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1242	+	"\tOOPSE will use a default value of\n"
1243	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1244	+	painCave.isFatal = 0;
1245	+	simError();
1246	+	theRsw = 0.95 * theRcut;
1247	+	}
1248	+	else{
1249	+	theRsw = globals->getRsw();
1250	+	}
1251	+
1252	+	info[i].setDefaultRcut(theRcut, theRsw);
1253	+
1254	+	if (!globals->haveDielectric()){
1255	+	sprintf(painCave.errMsg,
1256	+	"SimSetup Error: No Dielectric constant was set.\n"
1257	+	"\tYou are trying to use Reaction Field without"
1258	+	"\tsetting a dielectric constant!\n");
1259	+	painCave.isFatal = 1;
1260	+	simError();
1261	+	}
1262	+	info[i].dielectric = globals->getDielectric();
1263	+	}
1264	+	else{
1265	+	if (usesDipoles || usesCharges){
1266	+
1267	+	if (!globals->haveRcut()){
1268	+	sprintf(painCave.errMsg,
1269	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1270	+	"\tOOPSE will use a default value of 15.0 angstroms"
1271	+	"\tfor the cutoffRadius.\n");
1272	+	painCave.isFatal = 0;
1273	+	simError();
1274	+	theRcut = 15.0;
1275	+	}
1276	+	else{
1277	+	theRcut = globals->getRcut();
1278	+	}
1279	+
1280	+	if (!globals->haveRsw()){
1281	+	sprintf(painCave.errMsg,
1282	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1283	+	"\tOOPSE will use a default value of\n"
1284	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1285	+	painCave.isFatal = 0;
1286	+	simError();
1287	+	theRsw = 0.95 * theRcut;
1288	+	}
1289	+	else{
1290	+	theRsw = globals->getRsw();
1291	+	}
1292	+
1293	+	info[i].setDefaultRcut(theRcut, theRsw);
1294	+
1295	+	}
1296	+	}
1297	+	}
1298	+	#ifdef IS_MPI
1299	+	strcpy(checkPointMsg, "post processing checks out");
1300	+	MPIcheckPoint();
1301	+	#endif // is_mpi
1302	+
1303	+	// clean up the forcefield
1304	+	the_ff->cleanMe();
1305	+	}
1306	+
1307	+	void SimSetup::initSystemCoords(void){
1308	+	int i;
1309	+
1310	+	char* inName;
1311	+
1312	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1313	+
1314	+	for (i = 0; i < info[0].n_atoms; i++)
1315	+	info[0].atoms[i]->setCoords();
1316	+
1317	+	if (globals->haveInitialConfig()){
1318	+	InitializeFromFile* fileInit;
1319	+	#ifdef IS_MPI // is_mpi
1320	+	if (worldRank == 0){
1321	+	#endif //is_mpi
1322	+	inName = globals->getInitialConfig();
1323	+	fileInit = new InitializeFromFile(inName);
1324	+	#ifdef IS_MPI
1325	+	}
1326	+	else
1327	+	fileInit = new InitializeFromFile(NULL);
1328	+	#endif
1329	+	fileInit->readInit(info); // default velocities on
1330	+
1331	+	delete fileInit;
1332	+	}
1333	+	else{
1334	+
1335	+	// no init from bass
1336	+
1337	+	sprintf(painCave.errMsg,
1338	+	"Cannot intialize a simulation without an initial configuration file.\n");
1339	+	painCave.isFatal = 1;;
1340	+	simError();
1341	+
1342	+	}
1343	+
1344	+	#ifdef IS_MPI
1345	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1346	+	MPIcheckPoint();
1347	+	#endif // is_mpi
1348	+	}
1349	+
1350	+
1351	+	void SimSetup::makeOutNames(void){
1352	+	int k;
1353	+
1354	+
1355	+	for (k = 0; k < nInfo; k++){
1356	+	#ifdef IS_MPI
1357	+	if (worldRank == 0){
1358	+	#endif // is_mpi
1359	+
1360	+	if (globals->haveFinalConfig()){
1361	+	strcpy(info[k].finalName, globals->getFinalConfig());
1362	+	}
1363	+	else{
1364	+	strcpy(info[k].finalName, inFileName);
1365	+	char* endTest;
1366	+	int nameLength = strlen(info[k].finalName);
1367	+	endTest = &(info[k].finalName[nameLength - 5]);
1368	+	if (!strcmp(endTest, ".bass")){
1369	+	strcpy(endTest, ".eor");
1370	+	}
1371	+	else if (!strcmp(endTest, ".BASS")){
1372	+	strcpy(endTest, ".eor");
1373	+	}
1374	+	else{
1375	+	endTest = &(info[k].finalName[nameLength - 4]);
1376	+	if (!strcmp(endTest, ".bss")){
1377	+	strcpy(endTest, ".eor");
1378	+	}
1379	+	else if (!strcmp(endTest, ".mdl")){
1380	+	strcpy(endTest, ".eor");
1381	+	}
1382	+	else{
1383	+	strcat(info[k].finalName, ".eor");
1384	+	}
1385	+	}
1386	+	}
1387	+
1388	+	// make the sample and status out names
1389	+
1390	+	strcpy(info[k].sampleName, inFileName);
1391	+	char* endTest;
1392	+	int nameLength = strlen(info[k].sampleName);
1393	+	endTest = &(info[k].sampleName[nameLength - 5]);
1394	+	if (!strcmp(endTest, ".bass")){
1395	+	strcpy(endTest, ".dump");
1396	+	}
1397	+	else if (!strcmp(endTest, ".BASS")){
1398	+	strcpy(endTest, ".dump");
1399	+	}
1400	+	else{
1401	+	endTest = &(info[k].sampleName[nameLength - 4]);
1402	+	if (!strcmp(endTest, ".bss")){
1403	+	strcpy(endTest, ".dump");
1404	+	}
1405	+	else if (!strcmp(endTest, ".mdl")){
1406	+	strcpy(endTest, ".dump");
1407	+	}
1408	+	else{
1409	+	strcat(info[k].sampleName, ".dump");
1410	+	}
1411	+	}
1412	+
1413	+	strcpy(info[k].statusName, inFileName);
1414	+	nameLength = strlen(info[k].statusName);
1415	+	endTest = &(info[k].statusName[nameLength - 5]);
1416	+	if (!strcmp(endTest, ".bass")){
1417	+	strcpy(endTest, ".stat");
1418	+	}
1419	+	else if (!strcmp(endTest, ".BASS")){
1420	+	strcpy(endTest, ".stat");
1421	+	}
1422	+	else{
1423	+	endTest = &(info[k].statusName[nameLength - 4]);
1424	+	if (!strcmp(endTest, ".bss")){
1425	+	strcpy(endTest, ".stat");
1426	+	}
1427	+	else if (!strcmp(endTest, ".mdl")){
1428	+	strcpy(endTest, ".stat");
1429	+	}
1430	+	else{
1431	+	strcat(info[k].statusName, ".stat");
1432	+	}
1433	+	}
1434	+
1435	+	strcpy(info[k].rawPotName, inFileName);
1436	+	nameLength = strlen(info[k].rawPotName);
1437	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1438	+	if (!strcmp(endTest, ".bass")){
1439	+	strcpy(endTest, ".raw");
1440	+	}
1441	+	else if (!strcmp(endTest, ".BASS")){
1442	+	strcpy(endTest, ".raw");
1443	+	}
1444	+	else{
1445	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1446	+	if (!strcmp(endTest, ".bss")){
1447	+	strcpy(endTest, ".raw");
1448	+	}
1449	+	else if (!strcmp(endTest, ".mdl")){
1450	+	strcpy(endTest, ".raw");
1451	+	}
1452	+	else{
1453	+	strcat(info[k].rawPotName, ".raw");
1454	+	}
1455	+	}
1456	+
1457	+	#ifdef IS_MPI
1458	+
1459	+	}
1460	+	#endif // is_mpi
1461	+	}
1462	+	}
1463	+
1464	+
1465	+	void SimSetup::sysObjectsCreation(void){
1466	+	int i, k;
1467	+
1468	+	// create the forceField
1469	+
1470	+	createFF();
1471	+
1472	+	// extract componentList
1473	+
1474	+	compList();
1475	+
1476	+	// calc the number of atoms, bond, bends, and torsions
1477	+
1478	+	calcSysValues();
1479	+
1480	+	#ifdef IS_MPI
1481	+	// divide the molecules among the processors
1482	+
1483	+	mpiMolDivide();
1484	+	#endif //is_mpi
1485	+
1486	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1487	+
1488	+	makeSysArrays();
1489	+
1490	+	// make and initialize the molecules (all but atomic coordinates)
1491	+
1492	+	makeMolecules();
1493	+
1494	+	for (k = 0; k < nInfo; k++){
1495	+	info[k].identArray = new int[info[k].n_atoms];
1496	+	for (i = 0; i < info[k].n_atoms; i++){
1497	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1498	+	}
1499	+	}
1500	+	}
1501	+
1502	+
1503	+	void SimSetup::createFF(void){
1504	+	switch (ffCase){
1505	+	case FF_DUFF:
1506	+	the_ff = new DUFF();
1507	+	break;
1508	+
1509	+	case FF_LJ:
1510	+	the_ff = new LJFF();
1511	+	break;
1512	+
1513	+	case FF_EAM:
1514	+	the_ff = new EAM_FF();
1515	+	break;
1516	+
1517	+	case FF_H2O:
1518	+	the_ff = new WATER();
1519	+	break;
1520	+
1521	+	default:
1522	+	sprintf(painCave.errMsg,
1523	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1524	+	painCave.isFatal = 1;
1525	+	simError();
1526	+	}
1527	+
1528	+	#ifdef IS_MPI
1529	+	strcpy(checkPointMsg, "ForceField creation successful");
1530	+	MPIcheckPoint();
1531	+	#endif // is_mpi
1532	+	}
1533	+
1534	+
1535	+	void SimSetup::compList(void){
1536	+	int i;
1537	+	char* id;
1538	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1539	+	LinkedMolStamp* currentStamp = NULL;
1540	+	comp_stamps = new MoleculeStamp * [n_components];
1541	+	bool haveCutoffGroups;
1542	+
1543	+	haveCutoffGroups = false;
1544	+
1545	+	// make an array of molecule stamps that match the components used.
1546	+	// also extract the used stamps out into a separate linked list
1547	+
1548	+	for (i = 0; i < nInfo; i++){
1549	+	info[i].nComponents = n_components;
1550	+	info[i].componentsNmol = components_nmol;
1551	+	info[i].compStamps = comp_stamps;
1552	+	info[i].headStamp = headStamp;
1553	+	}
1554	+
1555	+
1556	+	for (i = 0; i < n_components; i++){
1557	+	id = the_components[i]->getType();
1558	+	comp_stamps[i] = NULL;
1559	+
1560	+	// check to make sure the component isn't already in the list
1561	+
1562	+	comp_stamps[i] = headStamp->match(id);
1563	+	if (comp_stamps[i] == NULL){
1564	+	// extract the component from the list;
1565	+
1566	+	currentStamp = stamps->extractMolStamp(id);
1567	+	if (currentStamp == NULL){
1568	+	sprintf(painCave.errMsg,
1569	+	"SimSetup error: Component \"%s\" was not found in the "
1570	+	"list of declared molecules\n",
1571	+	id);
1572	+	painCave.isFatal = 1;
1573	+	simError();
1574	+	}
1575	+
1576	+	headStamp->add(currentStamp);
1577	+	comp_stamps[i] = headStamp->match(id);
1578	+	}
1579	+
1580	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1581	+	haveCutoffGroups = true;
1582	+	}
1583	+
1584	+	for (i = 0; i < nInfo; i++)
1585	+	info[i].haveCutoffGroups = haveCutoffGroups;
1586	+
1587	+	#ifdef IS_MPI
1588	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1589	+	MPIcheckPoint();
1590	+	#endif // is_mpi
1591	+	}
1592	+
1593	+	void SimSetup::calcSysValues(void){
1594	+	int i, j;
1595	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1596	+
1597	+	int* molMembershipArray;
1598	+	CutoffGroupStamp* cg;
1599	+
1600	+	tot_atoms = 0;
1601	+	tot_bonds = 0;
1602	+	tot_bends = 0;
1603	+	tot_torsions = 0;
1604	+	tot_rigid = 0;
1605	+	tot_groups = 0;
1606	+	for (i = 0; i < n_components; i++){
1607	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1608	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1609	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1610	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1611	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1612	+
1613	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1614	+	atomsingroups = 0;
1615	+	for (j=0; j < ncutgroups; j++) {
1616	+	cg = comp_stamps[i]->getCutoffGroup(j);
1617	+	atomsingroups += cg->getNMembers();
1618	+	}
1619	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1620	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1621	+	}
1622	+
1623	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1624	+	molMembershipArray = new int[tot_atoms];
1625	+
1626	+	for (i = 0; i < nInfo; i++){
1627	+	info[i].n_atoms = tot_atoms;
1628	+	info[i].n_bonds = tot_bonds;
1629	+	info[i].n_bends = tot_bends;
1630	+	info[i].n_torsions = tot_torsions;
1631	+	info[i].n_SRI = tot_SRI;
1632	+	info[i].n_mol = tot_nmol;
1633	+	info[i].ngroup = tot_groups;
1634	+	info[i].molMembershipArray = molMembershipArray;
1635	+	}
1636	+	}
1637	+
1638	+	#ifdef IS_MPI
1639	+
1640	+	void SimSetup::mpiMolDivide(void){
1641	+	int i, j, k;
1642	+	int localMol, allMol;
1643	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1644	+	int local_rigid, local_groups;
1645	+	vector<int> globalMolIndex;
1646	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1647	+	CutoffGroupStamp* cg;
1648	+
1649	+	mpiSim = new mpiSimulation(info);
1650	+
1651	+	mpiSim->divideLabor();
1652	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1653	+	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1654	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1655	+
1656	+	// set up the local variables
1657	+
1658	+	mol2proc = mpiSim->getMolToProcMap();
1659	+	molCompType = mpiSim->getMolComponentType();
1660	+
1661	+	allMol = 0;
1662	+	localMol = 0;
1663	+	local_atoms = 0;
1664	+	local_bonds = 0;
1665	+	local_bends = 0;
1666	+	local_torsions = 0;
1667	+	local_rigid = 0;
1668	+	local_groups = 0;
1669	+	globalAtomCounter = 0;
1670	+
1671	+	for (i = 0; i < n_components; i++){
1672	+	for (j = 0; j < components_nmol[i]; j++){
1673	+	if (mol2proc[allMol] == worldRank){
1674	+	local_atoms += comp_stamps[i]->getNAtoms();
1675	+	local_bonds += comp_stamps[i]->getNBonds();
1676	+	local_bends += comp_stamps[i]->getNBends();
1677	+	local_torsions += comp_stamps[i]->getNTorsions();
1678	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1679	+
1680	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1681	+	atomsingroups = 0;
1682	+	for (k=0; k < ncutgroups; k++) {
1683	+	cg = comp_stamps[i]->getCutoffGroup(k);
1684	+	atomsingroups += cg->getNMembers();
1685	+	}
1686	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1687	+	ncutgroups;
1688	+	local_groups += ngroupsinstamp;
1689	+
1690	+	localMol++;
1691	+	}
1692	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1693	+	info[0].molMembershipArray[globalAtomCounter] = allMol;
1694	+	globalAtomCounter++;
1695	+	}
1696	+
1697	+	allMol++;
1698	+	}
1699	+	}
1700	+	local_SRI = local_bonds + local_bends + local_torsions;
1701	+
1702	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1703	+
1704	+	if (local_atoms != info[0].n_atoms){
1705	+	sprintf(painCave.errMsg,
1706	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1707	+	"\tlocalAtom (%d) are not equal.\n",
1708	+	info[0].n_atoms, local_atoms);
1709	+	painCave.isFatal = 1;
1710	+	simError();
1711	+	}
1712	+
1713	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1714	+	if (local_groups != info[0].ngroup){
1715	+	sprintf(painCave.errMsg,
1716	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1717	+	"\tlocalGroups (%d) are not equal.\n",
1718	+	info[0].ngroup, local_groups);
1719	+	painCave.isFatal = 1;
1720	+	simError();
1721	+	}
1722	+
1723	+	info[0].n_bonds = local_bonds;
1724	+	info[0].n_bends = local_bends;
1725	+	info[0].n_torsions = local_torsions;
1726	+	info[0].n_SRI = local_SRI;
1727	+	info[0].n_mol = localMol;
1728	+
1729	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1730	+	MPIcheckPoint();
1731	+	}
1732	+
1733	+	#endif // is_mpi
1734	+
1735	+
1736	+	void SimSetup::makeSysArrays(void){
1737	+
1738	+	#ifndef IS_MPI
1739	+	int k, j;
1740	+	#endif // is_mpi
1741	+	int i, l;
1742	+
1743	+	Atom** the_atoms;
1744	+	Molecule* the_molecules;
1745	+
1746	+	for (l = 0; l < nInfo; l++){
1747	+	// create the atom and short range interaction arrays
1748	+
1749	+	the_atoms = new Atom * [info[l].n_atoms];
1750	+	the_molecules = new Molecule[info[l].n_mol];
1751	+	int molIndex;
1752	+
1753	+	// initialize the molecule's stampID's
1754	+
1755	+	#ifdef IS_MPI
1756	+
1757	+
1758	+	molIndex = 0;
1759	+	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1760	+	if (mol2proc[i] == worldRank){
1761	+	the_molecules[molIndex].setStampID(molCompType[i]);
1762	+	the_molecules[molIndex].setMyIndex(molIndex);
1763	+	the_molecules[molIndex].setGlobalIndex(i);
1764	+	molIndex++;
1765	+	}
1766	+	}
1767	+
1768	+	#else // is_mpi
1769	+
1770	+	molIndex = 0;
1771	+	globalAtomCounter = 0;
1772	+	for (i = 0; i < n_components; i++){
1773	+	for (j = 0; j < components_nmol[i]; j++){
1774	+	the_molecules[molIndex].setStampID(i);
1775	+	the_molecules[molIndex].setMyIndex(molIndex);
1776	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1777	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1778	+	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1779	+	globalAtomCounter++;
1780	+	}
1781	+	molIndex++;
1782	+	}
1783	+	}
1784	+
1785	+
1786	+	#endif // is_mpi
1787	+
1788	+	info[l].globalExcludes = new int;
1789	+	info[l].globalExcludes[0] = 0;
1790	+
1791	+	// set the arrays into the SimInfo object
1792	+
1793	+	info[l].atoms = the_atoms;
1794	+	info[l].molecules = the_molecules;
1795	+	info[l].nGlobalExcludes = 0;
1796	+
1797	+	the_ff->setSimInfo(info);
1798	+	}
1799	+	}
1800	+
1801	+	void SimSetup::makeIntegrator(void){
1802	+	int k;
1803	+
1804	+	NVE<RealIntegrator>* myNVE = NULL;
1805	+	NVT<RealIntegrator>* myNVT = NULL;
1806	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1807	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1808	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1809	+
1810	+	for (k = 0; k < nInfo; k++){
1811	+	switch (ensembleCase){
1812	+	case NVE_ENS:
1813	+	if (globals->haveZconstraints()){
1814	+	setupZConstraint(info[k]);
1815	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1816	+	}
1817	+	else{
1818	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1819	+	}
1820	+
1821	+	info->the_integrator = myNVE;
1822	+	break;
1823	+
1824	+	case NVT_ENS:
1825	+	if (globals->haveZconstraints()){
1826	+	setupZConstraint(info[k]);
1827	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1828	+	}
1829	+	else
1830	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1831	+
1832	+	myNVT->setTargetTemp(globals->getTargetTemp());
1833	+
1834	+	if (globals->haveTauThermostat())
1835	+	myNVT->setTauThermostat(globals->getTauThermostat());
1836	+	else{
1837	+	sprintf(painCave.errMsg,
1838	+	"SimSetup error: If you use the NVT\n"
1839	+	"\tensemble, you must set tauThermostat.\n");
1840	+	painCave.isFatal = 1;
1841	+	simError();
1842	+	}
1843	+
1844	+	info->the_integrator = myNVT;
1845	+	break;
1846	+
1847	+	case NPTi_ENS:
1848	+	if (globals->haveZconstraints()){
1849	+	setupZConstraint(info[k]);
1850	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1851	+	}
1852	+	else
1853	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1854	+
1855	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1856	+
1857	+	if (globals->haveTargetPressure())
1858	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1859	+	else{
1860	+	sprintf(painCave.errMsg,
1861	+	"SimSetup error: If you use a constant pressure\n"
1862	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1863	+	painCave.isFatal = 1;
1864	+	simError();
1865	+	}
1866	+
1867	+	if (globals->haveTauThermostat())
1868	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1869	+	else{
1870	+	sprintf(painCave.errMsg,
1871	+	"SimSetup error: If you use an NPT\n"
1872	+	"\tensemble, you must set tauThermostat.\n");
1873	+	painCave.isFatal = 1;
1874	+	simError();
1875	+	}
1876	+
1877	+	if (globals->haveTauBarostat())
1878	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1879	+	else{
1880	+	sprintf(painCave.errMsg,
1881	+	"SimSetup error: If you use an NPT\n"
1882	+	"\tensemble, you must set tauBarostat.\n");
1883	+	painCave.isFatal = 1;
1884	+	simError();
1885	+	}
1886	+
1887	+	info->the_integrator = myNPTi;
1888	+	break;
1889	+
1890	+	case NPTf_ENS:
1891	+	if (globals->haveZconstraints()){
1892	+	setupZConstraint(info[k]);
1893	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1894	+	}
1895	+	else
1896	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1897	+
1898	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1899	+
1900	+	if (globals->haveTargetPressure())
1901	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1902	+	else{
1903	+	sprintf(painCave.errMsg,
1904	+	"SimSetup error: If you use a constant pressure\n"
1905	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1906	+	painCave.isFatal = 1;
1907	+	simError();
1908	+	}
1909	+
1910	+	if (globals->haveTauThermostat())
1911	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1912	+
1913	+	else{
1914	+	sprintf(painCave.errMsg,
1915	+	"SimSetup error: If you use an NPT\n"
1916	+	"\tensemble, you must set tauThermostat.\n");
1917	+	painCave.isFatal = 1;
1918	+	simError();
1919	+	}
1920	+
1921	+	if (globals->haveTauBarostat())
1922	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1923	+
1924	+	else{
1925	+	sprintf(painCave.errMsg,
1926	+	"SimSetup error: If you use an NPT\n"
1927	+	"\tensemble, you must set tauBarostat.\n");
1928	+	painCave.isFatal = 1;
1929	+	simError();
1930	+	}
1931	+
1932	+	info->the_integrator = myNPTf;
1933	+	break;
1934	+
1935	+	case NPTxyz_ENS:
1936	+	if (globals->haveZconstraints()){
1937	+	setupZConstraint(info[k]);
1938	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1939	+	}
1940	+	else
1941	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1942	+
1943	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1944	+
1945	+	if (globals->haveTargetPressure())
1946	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1947	+	else{
1948	+	sprintf(painCave.errMsg,
1949	+	"SimSetup error: If you use a constant pressure\n"
1950	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1951	+	painCave.isFatal = 1;
1952	+	simError();
1953	+	}
1954	+
1955	+	if (globals->haveTauThermostat())
1956	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1957	+	else{
1958	+	sprintf(painCave.errMsg,
1959	+	"SimSetup error: If you use an NPT\n"
1960	+	"\tensemble, you must set tauThermostat.\n");
1961	+	painCave.isFatal = 1;
1962	+	simError();
1963	+	}
1964	+
1965	+	if (globals->haveTauBarostat())
1966	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1967	+	else{
1968	+	sprintf(painCave.errMsg,
1969	+	"SimSetup error: If you use an NPT\n"
1970	+	"\tensemble, you must set tauBarostat.\n");
1971	+	painCave.isFatal = 1;
1972	+	simError();
1973	+	}
1974	+
1975	+	info->the_integrator = myNPTxyz;
1976	+	break;
1977	+
1978	+	default:
1979	+	sprintf(painCave.errMsg,
1980	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1981	+	painCave.isFatal = 1;
1982	+	simError();
1983	+	}
1984	+	}
1985	+	}
1986	+
1987	+	void SimSetup::initFortran(void){
1988	+	info[0].refreshSim();
1989	+
1990	+	if (!strcmp(info[0].mixingRule, "standard")){
1991	+	the_ff->initForceField(LB_MIXING_RULE);
1992	+	}
1993	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1994	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1995	+	}
1996	+	else{
1997	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1998	+	info[0].mixingRule);
1999	+	painCave.isFatal = 1;
2000	+	simError();
2001	+	}
2002	+
2003	+
2004	+	#ifdef IS_MPI
2005	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2006	+	MPIcheckPoint();
2007	+	#endif // is_mpi
2008	+	}
2009	+
2010	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
2011	+	int nZConstraints;
2012	+	ZconStamp** zconStamp;
2013	+
2014	+	if (globals->haveZconstraintTime()){
2015	+	//add sample time of z-constraint  into SimInfo's property list
2016	+	DoubleData* zconsTimeProp = new DoubleData();
2017	+	zconsTimeProp->setID(ZCONSTIME_ID);
2018	+	zconsTimeProp->setData(globals->getZconsTime());
2019	+	theInfo.addProperty(zconsTimeProp);
2020	+	}
2021	+	else{
2022	+	sprintf(painCave.errMsg,
2023	+	"ZConstraint error: If you use a ZConstraint,\n"
2024	+	"\tyou must set zconsTime.\n");
2025	+	painCave.isFatal = 1;
2026	+	simError();
2027	+	}
2028	+
2029	+	//push zconsTol into siminfo, if user does not specify
2030	+	//value for zconsTol, a default value will be used
2031	+	DoubleData* zconsTol = new DoubleData();
2032	+	zconsTol->setID(ZCONSTOL_ID);
2033	+	if (globals->haveZconsTol()){
2034	+	zconsTol->setData(globals->getZconsTol());
2035	+	}
2036	+	else{
2037	+	double defaultZConsTol = 0.01;
2038	+	sprintf(painCave.errMsg,
2039	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2040	+	"\tOOPSE will use a default value of %f.\n"
2041	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2042	+	defaultZConsTol);
2043	+	painCave.isFatal = 0;
2044	+	simError();
2045	+
2046	+	zconsTol->setData(defaultZConsTol);
2047	+	}
2048	+	theInfo.addProperty(zconsTol);
2049	+
2050	+	//set Force Subtraction Policy
2051	+	StringData* zconsForcePolicy = new StringData();
2052	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2053	+
2054	+	if (globals->haveZconsForcePolicy()){
2055	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2056	+	}
2057	+	else{
2058	+	sprintf(painCave.errMsg,
2059	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2060	+	"\tOOPSE will use PolicyByMass.\n"
2061	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2062	+	painCave.isFatal = 0;
2063	+	simError();
2064	+	zconsForcePolicy->setData("BYMASS");
2065	+	}
2066	+
2067	+	theInfo.addProperty(zconsForcePolicy);
2068	+
2069	+	//set zcons gap
2070	+	DoubleData* zconsGap = new DoubleData();
2071	+	zconsGap->setID(ZCONSGAP_ID);
2072	+
2073	+	if (globals->haveZConsGap()){
2074	+	zconsGap->setData(globals->getZconsGap());
2075	+	theInfo.addProperty(zconsGap);
2076	+	}
2077	+
2078	+	//set zcons fixtime
2079	+	DoubleData* zconsFixtime = new DoubleData();
2080	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2081	+
2082	+	if (globals->haveZConsFixTime()){
2083	+	zconsFixtime->setData(globals->getZconsFixtime());
2084	+	theInfo.addProperty(zconsFixtime);
2085	+	}
2086	+
2087	+	//set zconsUsingSMD
2088	+	IntData* zconsUsingSMD = new IntData();
2089	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2090	+
2091	+	if (globals->haveZConsUsingSMD()){
2092	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2093	+	theInfo.addProperty(zconsUsingSMD);
2094	+	}
2095	+
2096	+	//Determine the name of ouput file and add it into SimInfo's property list
2097	+	//Be careful, do not use inFileName, since it is a pointer which
2098	+	//point to a string at master node, and slave nodes do not contain that string
2099	+
2100	+	string zconsOutput(theInfo.finalName);
2101	+
2102	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2103	+
2104	+	StringData* zconsFilename = new StringData();
2105	+	zconsFilename->setID(ZCONSFILENAME_ID);
2106	+	zconsFilename->setData(zconsOutput);
2107	+
2108	+	theInfo.addProperty(zconsFilename);
2109	+
2110	+	//setup index, pos and other parameters of z-constraint molecules
2111	+	nZConstraints = globals->getNzConstraints();
2112	+	theInfo.nZconstraints = nZConstraints;
2113	+
2114	+	zconStamp = globals->getZconStamp();
2115	+	ZConsParaItem tempParaItem;
2116	+
2117	+	ZConsParaData* zconsParaData = new ZConsParaData();
2118	+	zconsParaData->setID(ZCONSPARADATA_ID);
2119	+
2120	+	for (int i = 0; i < nZConstraints; i++){
2121	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2122	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2123	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2124	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2125	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2126	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2127	+	zconsParaData->addItem(tempParaItem);
2128	+	}
2129	+
2130	+	//check the uniqueness of index
2131	+	if(!zconsParaData->isIndexUnique()){
2132	+	sprintf(painCave.errMsg,
2133	+	"ZConstraint Error: molIndex is not unique!\n");
2134	+	painCave.isFatal = 1;
2135	+	simError();
2136	+	}
2137	+
2138	+	//sort the parameters by index of molecules
2139	+	zconsParaData->sortByIndex();
2140	+
2141	+	//push data into siminfo, therefore, we can retrieve later
2142	+	theInfo.addProperty(zconsParaData);
2143	+	}
2144	+
2145	+	void SimSetup::makeMinimizer(){
2146	+
2147	+	OOPSEMinimizer* myOOPSEMinimizer;
2148	+	MinimizerParameterSet* param;
2149	+	char minimizerName[100];
2150	+
2151	+	for (int i = 0; i < nInfo; i++){
2152	+
2153	+	//prepare parameter set for minimizer
2154	+	param = new MinimizerParameterSet();
2155	+	param->setDefaultParameter();
2156	+
2157	+	if (globals->haveMinimizer()){
2158	+	param->setFTol(globals->getMinFTol());
2159	+	}
2160	+
2161	+	if (globals->haveMinGTol()){
2162	+	param->setGTol(globals->getMinGTol());
2163	+	}
2164	+
2165	+	if (globals->haveMinMaxIter()){
2166	+	param->setMaxIteration(globals->getMinMaxIter());
2167	+	}
2168	+
2169	+	if (globals->haveMinWriteFrq()){
2170	+	param->setMaxIteration(globals->getMinMaxIter());
2171	+	}
2172	+
2173	+	if (globals->haveMinWriteFrq()){
2174	+	param->setWriteFrq(globals->getMinWriteFrq());
2175	+	}
2176	+
2177	+	if (globals->haveMinStepSize()){
2178	+	param->setStepSize(globals->getMinStepSize());
2179	+	}
2180	+
2181	+	if (globals->haveMinLSMaxIter()){
2182	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2183	+	}
2184	+
2185	+	if (globals->haveMinLSTol()){
2186	+	param->setLineSearchTol(globals->getMinLSTol());
2187	+	}
2188	+
2189	+	strcpy(minimizerName, globals->getMinimizer());
2190	+
2191	+	if (!strcasecmp(minimizerName, "CG")){
2192	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2193	+	}
2194	+	else if (!strcasecmp(minimizerName, "SD")){
2195	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2196	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2197	+	}
2198	+	else{
2199	+	sprintf(painCave.errMsg,
2200	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2201	+	painCave.isFatal = 0;
2202	+	simError();
2203	+
2204	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2205	+	}
2206	+	info[i].the_integrator = myOOPSEMinimizer;
2207	+
2208	+	//store the minimizer into simInfo
2209	+	info[i].the_minimizer = myOOPSEMinimizer;
2210	+	info[i].has_minimizer = true;
2211	+	}
2212	+
2213	+	}

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