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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 469 by mmeineke, Mon Apr 7 20:06:31 2003 UTC vs.
Revision 1330 by gezelter, Fri Jul 16 16:29:44 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	+	#include "ConstraintManager.hpp"
17
18		#ifdef IS_MPI
19		#include "mpiBASS.h"
20		#include "mpiSimulation.hpp"
21		#endif
22
23	+	// some defines for ensemble and Forcefield  cases
24	+
25	+	#define NVE_ENS        0
26	+	#define NVT_ENS        1
27	+	#define NPTi_ENS       2
28	+	#define NPTf_ENS       3
29	+	#define NPTxyz_ENS     4
30	+
31	+
32	+	#define FF_DUFF  0
33	+	#define FF_LJ    1
34	+	#define FF_EAM   2
35	+	#define FF_H2O   3
36	+
37	+	using namespace std;
38	+
39	+	/**
40	+	* Check whether dividend is divisble by divisor or not
41	+	*/
42	+	bool isDivisible(double dividend, double divisor){
43	+	double tolerance = 0.000001;
44	+	double quotient;
45	+	double diff;
46	+	int intQuotient;
47	+
48	+	quotient = dividend / divisor;
49	+
50	+	if (quotient < 0)
51	+	quotient = -quotient;
52	+
53	+	intQuotient = int (quotient + tolerance);
54	+
55	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
56	+
57	+	if (diff <= tolerance)
58	+	return true;
59	+	else
60	+	return false;
61	+	}
62	+
63		SimSetup::SimSetup(){
64	+
65	+	initSuspend = false;
66	+	isInfoArray = 0;
67	+	nInfo = 1;
68	+
69		stamps = new MakeStamps();
70		globals = new Globals();
71	<
71	>
72	>
73		#ifdef IS_MPI
74	<	strcpy( checkPointMsg, "SimSetup creation successful" );
74	>	strcpy(checkPointMsg, "SimSetup creation successful");
75		MPIcheckPoint();
76		#endif // IS_MPI
77		}
#	Line 27 | Line 81 | SimSetup::~SimSetup(){
81		delete globals;
82		}
83
84	<	void SimSetup::parseFile( char* fileName ){
84	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
85	>	info = the_info;
86	>	nInfo = theNinfo;
87	>	isInfoArray = 1;
88	>	initSuspend = true;
89	>	}
90
91	+
92	+	void SimSetup::parseFile(char* fileName){
93		#ifdef IS_MPI
94	<	if( worldRank == 0 ){
94	>	if (worldRank == 0){
95		#endif // is_mpi
96	<
96	>
97		inFileName = fileName;
98	<	set_interface_stamps( stamps, globals );
99	<
98	>	set_interface_stamps(stamps, globals);
99	>
100		#ifdef IS_MPI
101		mpiEventInit();
102		#endif
103
104	<	yacc_BASS( fileName );
104	>	yacc_BASS(fileName);
105
106		#ifdef IS_MPI
107		throwMPIEvent(NULL);
108		}
109	<	else receiveParse();
109	>	else{
110	>	receiveParse();
111	>	}
112		#endif
113
114		}
115
116		#ifdef IS_MPI
117		void SimSetup::receiveParse(void){
118	<
119	<	set_interface_stamps( stamps, globals );
120	<	mpiEventInit();
121	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
118	>	set_interface_stamps(stamps, globals);
119	>	mpiEventInit();
120	>	MPIcheckPoint();
121	>	mpiEventLoop();
122		}
123
124		#endif // is_mpi
125
126	<	void SimSetup::createSim( void ){
126	>	void SimSetup::createSim(void){
127
128	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
128	>	// gather all of the information from the Bass file
129
130	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
130	>	gatherInfo();
131
132	<	// 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();
132	>	// creation of complex system objects
133
134	<	// 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() );
134	>	sysObjectsCreation();
135
136	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
91	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
92	<	the_extendedsystem = new ExtendedSystem( simnfo );
93	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
94	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
95	<	} else {
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
98	<	"reverting to NVE for this simulation.\n",
99	<	ensemble );
100	<	painCave.isFatal = 0;
101	<	simError();
102	<	strcpy( ensemble, "NVE" );
103	<	}
104	<	strcpy( simnfo->ensemble, ensemble );
136	>	// check on the post processing info
137
138	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
107	<	simnfo->usePBC = the_globals->getPBC();
108	<
109	<	int usesDipoles = 0;
110	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
111	<	the_ff = new TraPPE_ExFF();
112	<	usesDipoles = 1;
113	<	}
114	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
115	<	else{
116	<	sprintf( painCave.errMsg,
117	<	"SimSetup Error. Unrecognized force field -> %s\n",
118	<	force_field );
119	<	painCave.isFatal = 1;
120	<	simError();
121	<	}
138	>	finalInfoCheck();
139
140	<	#ifdef IS_MPI
124	<	strcpy( checkPointMsg, "ForceField creation successful" );
125	<	MPIcheckPoint();
126	<	#endif // is_mpi
140	>	// initialize the system coordinates
141
142	<
142	>	if ( !initSuspend ){
143	>	initSystemCoords();
144
145	<	// get the components and calculate the tot_nMol and indvidual n_mol
146	<	the_components = the_globals->getComponents();
147	<	components_nmol = new int[n_components];
133	<	comp_stamps = new MoleculeStamp*[n_components];
145	>	if( !(globals->getUseInitTime()) )
146	>	info[0].currentTime = 0.0;
147	>	}
148
149	<	if( !the_globals->haveNMol() ){
136	<	// we don't have the total number of molecules, so we assume it is
137	<	// given in each component
149	>	// make the output filenames
150
151	<	tot_nmol = 0;
152	<	for( i=0; i<n_components; i++ ){
151	>	makeOutNames();
152	>
153	>	#ifdef IS_MPI
154	>	mpiSim->mpiRefresh();
155	>	#endif
156
157	<	if( !the_components[i]->haveNMol() ){
143	<	// we have a problem
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Error. No global NMol or component NMol"
146	<	" given. Cannot calculate the number of atoms.\n" );
147	<	painCave.isFatal = 1;
148	<	simError();
149	<	}
157	>	// initialize the Fortran
158
159	<	tot_nmol += the_components[i]->getNMol();
152	<	components_nmol[i] = the_components[i]->getNMol();
153	<	}
154	<	}
155	<	else{
156	<	sprintf( painCave.errMsg,
157	<	"SimSetup error.\n"
158	<	"\tSorry, the ability to specify total"
159	<	" nMols and then give molfractions in the components\n"
160	<	"\tis not currently supported."
161	<	" Please give nMol in the components.\n" );
162	<	painCave.isFatal = 1;
163	<	simError();
164	<
165	<
166	<	//     tot_nmol = the_globals->getNMol();
167	<
168	<	//   //we have the total number of molecules, now we check for molfractions
169	<	//     for( i=0; i<n_components; i++ ){
170	<
171	<	//       if( !the_components[i]->haveMolFraction() ){
172	<
173	<	//  if( !the_components[i]->haveNMol() ){
174	<	//    //we have a problem
175	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
176	<	//              << " nMol was given in component
177	<
178	<	}
159	>	initFortran();
160
161	<	#ifdef IS_MPI
162	<	strcpy( checkPointMsg, "Have the number of components" );
163	<	MPIcheckPoint();
183	<	#endif // is_mpi
161	>	//creat constraint manager
162	>	for(int i = 0; i < nInfo; i++)
163	>	info[i].consMan = new ConstraintManager(&info[i]);
164
165	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
165	>	if (globals->haveMinimizer())
166	>	// make minimizer
167	>	makeMinimizer();
168	>	else
169	>	// make the integrator
170	>	makeIntegrator();
171
172	<	simnfo->nComponents = n_components;
189	<	simnfo->componentsNmol = components_nmol;
190	<	simnfo->compStamps = comp_stamps;
191	<	simnfo->headStamp = new LinkedMolStamp();
192	<
193	<	char* id;
194	<	LinkedMolStamp* headStamp = simnfo->headStamp;
195	<	LinkedMolStamp* currentStamp = NULL;
196	<	for( i=0; i<n_components; i++ ){
172	>	}
173
198	–	id = the_components[i]->getType();
199	–	comp_stamps[i] = NULL;
200	–
201	–	// check to make sure the component isn't already in the list
174
175	<	comp_stamps[i] = headStamp->match( id );
176	<	if( comp_stamps[i] == NULL ){
177	<
178	<	// extract the component from the list;
179	<
180	<	currentStamp = the_stamps->extractMolStamp( id );
181	<	if( currentStamp == NULL ){
182	<	sprintf( painCave.errMsg,
183	<	"SimSetup error: Component \"%s\" was not found in the "
184	<	"list of declared molecules\n",
185	<	id );
186	<	painCave.isFatal = 1;
187	<	simError();
188	<	}
189	<
190	<	headStamp->add( currentStamp );
191	<	comp_stamps[i] = headStamp->match( id );
192	<	}
193	<	}
175	>	void SimSetup::makeMolecules(void){
176	>	int i, j, k;
177	>	int exI, exJ, exK, exL, slI, slJ;
178	>	int tempI, tempJ, tempK, tempL;
179	>	int molI, globalID;
180	>	int stampID, atomOffset, rbOffset, groupOffset;
181	>	molInit molInfo;
182	>	DirectionalAtom* dAtom;
183	>	RigidBody* myRB;
184	>	StuntDouble* mySD;
185	>	LinkedAssign* extras;
186	>	LinkedAssign* current_extra;
187	>	AtomStamp* currentAtom;
188	>	BondStamp* currentBond;
189	>	BendStamp* currentBend;
190	>	TorsionStamp* currentTorsion;
191	>	RigidBodyStamp* currentRigidBody;
192	>	CutoffGroupStamp* currentCutoffGroup;
193	>	CutoffGroup* myCutoffGroup;
194	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
195	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
196
197	<	#ifdef IS_MPI
198	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
199	<	MPIcheckPoint();
226	<	#endif // is_mpi
227	<
197	>	bond_pair* theBonds;
198	>	bend_set* theBends;
199	>	torsion_set* theTorsions;
200
201	+	set<int> skipList;
202
203	+	double phi, theta, psi;
204	+	char* molName;
205	+	char rbName[100];
206
207	<	// caclulate the number of atoms, bonds, bends and torsions
207	>	ConstraintPair* consPair; //constraint pair
208	>	ConstraintElement* consElement1;  //first element of constraint pair
209	>	ConstraintElement* consElement2;  //second element of constraint pair
210	>	int whichRigidBody;
211	>	int consAtomIndex;  //index of constraint atom in rigid body's atom array
212	>	vector<pair<int, int> > jointAtoms;
213	>	double bondLength2;
214	>	//init the forceField paramters
215
216	<	tot_atoms = 0;
234	<	tot_bonds = 0;
235	<	tot_bends = 0;
236	<	tot_torsions = 0;
237	<	for( i=0; i<n_components; i++ ){
238	<
239	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
240	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
241	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
242	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
243	<	}
216	>	the_ff->readParams();
217
218	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
218	>	// init the atoms
219
220	<	simnfo->n_atoms = tot_atoms;
248	<	simnfo->n_bonds = tot_bonds;
249	<	simnfo->n_bends = tot_bends;
250	<	simnfo->n_torsions = tot_torsions;
251	<	simnfo->n_SRI = tot_SRI;
252	<	simnfo->n_mol = tot_nmol;
220	>	int nMembers, nNew, rb1, rb2;
221
222	<
222	>	for (k = 0; k < nInfo; k++){
223	>	the_ff->setSimInfo(&(info[k]));
224	>
225		#ifdef IS_MPI
226	+	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
227	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
228	+	info[k].globalGroupMembership[i] = 0;
229	+	#else
230	+	info[k].globalGroupMembership = new int[info[k].n_atoms];
231	+	for (i = 0; i < info[k].n_atoms; i++)
232	+	info[k].globalGroupMembership[i] = 0;
233	+	#endif
234
235	<	// divide the molecules among processors here.
236	<
259	<	mpiSim = new mpiSimulation( simnfo );
260	<
261	<
235	>	atomOffset = 0;
236	>	groupOffset = 0;
237
238	<	globalIndex = mpiSim->divideLabor();
238	>	for (i = 0; i < info[k].n_mol; i++){
239	>	stampID = info[k].molecules[i].getStampID();
240	>	molName = comp_stamps[stampID]->getID();
241
242	<	// set up the local variables
243	<
244	<	int localMol, allMol;
245	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
242	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
243	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
244	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
245	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
246	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
247
248	<	int* mol2proc = mpiSim->getMolToProcMap();
249	<	int* molCompType = mpiSim->getMolComponentType();
250	<
273	<	allMol = 0;
274	<	localMol = 0;
275	<	local_atoms = 0;
276	<	local_bonds = 0;
277	<	local_bends = 0;
278	<	local_torsions = 0;
279	<	for( i=0; i<n_components; i++ ){
248	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
249	>
250	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
251
252	<	for( j=0; j<components_nmol[i]; j++ ){
252	>	if (molInfo.nBonds > 0)
253	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
254	>	else
255	>	molInfo.myBonds = NULL;
256	>
257	>	if (molInfo.nBends > 0)
258	>	molInfo.myBends = new Bend*[molInfo.nBends];
259	>	else
260	>	molInfo.myBends = NULL;
261	>
262	>	if (molInfo.nTorsions > 0)
263	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
264	>	else
265	>	molInfo.myTorsions = NULL;
266	>
267	>	theBonds = new bond_pair[molInfo.nBonds];
268	>	theBends = new bend_set[molInfo.nBends];
269	>	theTorsions = new torsion_set[molInfo.nTorsions];
270
271	<	if( mol2proc[j] == worldRank ){
284	<
285	<	local_atoms +=    comp_stamps[i]->getNAtoms();
286	<	local_bonds +=    comp_stamps[i]->getNBonds();
287	<	local_bends +=    comp_stamps[i]->getNBends();
288	<	local_torsions += comp_stamps[i]->getNTorsions();
289	<	localMol++;
290	<	}
291	<	allMol++;
292	<	}
293	<	}
294	<	local_SRI = local_bonds + local_bends + local_torsions;
295	<
271	>	// make the Atoms
272
273	<	simnfo->n_atoms = mpiSim->getMyNlocal();
274	<
299	<	if( local_atoms != simnfo->n_atoms ){
300	<	sprintf( painCave.errMsg,
301	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
302	<	" localAtom (%d) are not equal.\n",
303	<	simnfo->n_atoms,
304	<	local_atoms );
305	<	painCave.isFatal = 1;
306	<	simError();
307	<	}
273	>	for (j = 0; j < molInfo.nAtoms; j++){
274	>	currentAtom = comp_stamps[stampID]->getAtom(j);
275
276	<	simnfo->n_bonds = local_bonds;
277	<	simnfo->n_bends = local_bends;
278	<	simnfo->n_torsions = local_torsions;
279	<	simnfo->n_SRI = local_SRI;
280	<	simnfo->n_mol = localMol;
276	>	if (currentAtom->haveOrientation()){
277	>	dAtom = new DirectionalAtom((j + atomOffset),
278	>	info[k].getConfiguration());
279	>	info[k].n_oriented++;
280	>	molInfo.myAtoms[j] = dAtom;
281
282	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
283	<	MPIcheckPoint();
284	<
318	<
319	<	#endif // is_mpi
320	<
282	>	// Directional Atoms have standard unit vectors which are oriented
283	>	// in space using the three Euler angles.  We assume the standard
284	>	// unit vector was originally along the z axis below.
285
286	<	// create the atom and short range interaction arrays
286	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
287	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
288	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
289
290	<	Atom::createArrays(simnfo->n_atoms);
291	<	the_atoms = new Atom*[simnfo->n_atoms];
292	<	the_molecules = new Molecule[simnfo->n_mol];
293	<	int molIndex;
290	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
291	>
292	>	}
293	>	else{
294
295	<	// initialize the molecule's stampID's
295	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
296
297	+	}
298	+
299	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
300		#ifdef IS_MPI
301	<
301	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
302	>	#endif // is_mpi
303	>	}
304
305	<	molIndex = 0;
306	<	for(i=0; i<mpiSim->getTotNmol(); i++){
307	<
308	<	if(mol2proc[i] == worldRank ){
309	<	the_molecules[molIndex].setStampID( molCompType[i] );
339	<	the_molecules[molIndex].setMyIndex( molIndex );
340	<	molIndex++;
341	<	}
342	<	}
305	>	// make the bonds
306	>	for (j = 0; j < molInfo.nBonds; j++){
307	>	currentBond = comp_stamps[stampID]->getBond(j);
308	>	theBonds[j].a = currentBond->getA() + atomOffset;
309	>	theBonds[j].b = currentBond->getB() + atomOffset;
310
311	<	#else // is_mpi
312	<
346	<	molIndex = 0;
347	<	for(i=0; i<n_components; i++){
348	<	for(j=0; j<components_nmol[i]; j++ ){
349	<	the_molecules[molIndex].setStampID( i );
350	<	the_molecules[molIndex].setMyIndex( molIndex );
351	<	molIndex++;
352	<	}
353	<	}
354	<
311	>	tempI = theBonds[j].a;
312	>	tempJ = theBonds[j].b;
313
314	<	#endif // is_mpi
314	>	#ifdef IS_MPI
315	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
316	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
317	>	#else
318	>	exI = tempI + 1;
319	>	exJ = tempJ + 1;
320	>	#endif
321
322	+	info[k].excludes->addPair(exI, exJ);
323	+	}
324
325	<	if( simnfo->n_SRI ){
326	<
327	<	Exclude::createArray(simnfo->n_SRI);
328	<	the_excludes = new Exclude*[simnfo->n_SRI];
329	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
330	<	simnfo->globalExcludes = new int;
365	<	simnfo->n_exclude = simnfo->n_SRI;
366	<	}
367	<	else{
368	<
369	<	Exclude::createArray( 1 );
370	<	the_excludes = new Exclude*;
371	<	the_excludes[0] = new Exclude(0);
372	<	the_excludes[0]->setPair( 0,0 );
373	<	simnfo->globalExcludes = new int;
374	<	simnfo->globalExcludes[0] = 0;
375	<	simnfo->n_exclude = 0;
376	<	}
325	>	//make the bends
326	>	for (j = 0; j < molInfo.nBends; j++){
327	>	currentBend = comp_stamps[stampID]->getBend(j);
328	>	theBends[j].a = currentBend->getA() + atomOffset;
329	>	theBends[j].b = currentBend->getB() + atomOffset;
330	>	theBends[j].c = currentBend->getC() + atomOffset;
331
332	<	// set the arrays into the SimInfo object
332	>	if (currentBend->haveExtras()){
333	>	extras = currentBend->getExtras();
334	>	current_extra = extras;
335
336	<	simnfo->atoms = the_atoms;
337	<	simnfo->molecules = the_molecules;
338	<	simnfo->nGlobalExcludes = 0;
339	<	simnfo->excludes = the_excludes;
336	>	while (current_extra != NULL){
337	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
338	>	switch (current_extra->getType()){
339	>	case 0:
340	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
341	>	theBends[j].isGhost = 1;
342	>	break;
343
344	+	case 1:
345	+	theBends[j].ghost = (int) current_extra->getDouble() +
346	+	atomOffset;
347	+	theBends[j].isGhost = 1;
348	+	break;
349
350	<	// get some of the tricky things that may still be in the globals
350	>	default:
351	>	sprintf(painCave.errMsg,
352	>	"SimSetup Error: ghostVectorSource was neither a "
353	>	"double nor an int.\n"
354	>	"-->Bend[%d] in %s\n",
355	>	j, comp_stamps[stampID]->getID());
356	>	painCave.isFatal = 1;
357	>	simError();
358	>	}
359	>	}
360	>	else{
361	>	sprintf(painCave.errMsg,
362	>	"SimSetup Error: unhandled bend assignment:\n"
363	>	"    -->%s in Bend[%d] in %s\n",
364	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
365	>	painCave.isFatal = 1;
366	>	simError();
367	>	}
368
369	<
370	<	if( the_globals->haveBox() ){
371	<	simnfo->box_x = the_globals->getBox();
391	<	simnfo->box_y = the_globals->getBox();
392	<	simnfo->box_z = the_globals->getBox();
393	<	}
394	<	else if( the_globals->haveDensity() ){
369	>	current_extra = current_extra->getNext();
370	>	}
371	>	}
372
373	<	double vol;
374	<	vol = (double)tot_nmol / the_globals->getDensity();
375	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
376	<	simnfo->box_y = simnfo->box_x;
377	<	simnfo->box_z = simnfo->box_x;
378	<	}
379	<	else{
380	<	if( !the_globals->haveBoxX() ){
381	<	sprintf( painCave.errMsg,
382	<	"SimSetup error, no periodic BoxX size given.\n" );
383	<	painCave.isFatal = 1;
384	<	simError();
385	<	}
409	<	simnfo->box_x = the_globals->getBoxX();
373	>	if (theBends[j].isGhost) {
374	>
375	>	tempI = theBends[j].a;
376	>	tempJ = theBends[j].b;
377	>
378	>	#ifdef IS_MPI
379	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
380	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
381	>	#else
382	>	exI = tempI + 1;
383	>	exJ = tempJ + 1;
384	>	#endif
385	>	info[k].excludes->addPair(exI, exJ);
386
387	<	if( !the_globals->haveBoxY() ){
412	<	sprintf( painCave.errMsg,
413	<	"SimSetup error, no periodic BoxY size given.\n" );
414	<	painCave.isFatal = 1;
415	<	simError();
416	<	}
417	<	simnfo->box_y = the_globals->getBoxY();
387	>	} else {
388
389	<	if( !the_globals->haveBoxZ() ){
390	<	sprintf( painCave.errMsg,
391	<	"SimSetup error, no periodic BoxZ size given.\n" );
392	<	painCave.isFatal = 1;
423	<	simError();
424	<	}
425	<	simnfo->box_z = the_globals->getBoxZ();
426	<	}
427	<
389	>	tempI = theBends[j].a;
390	>	tempJ = theBends[j].b;
391	>	tempK = theBends[j].c;
392	>
393		#ifdef IS_MPI
394	<	strcpy( checkPointMsg, "Box size set up" );
395	<	MPIcheckPoint();
396	<	#endif // is_mpi
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	#else
398	>	exI = tempI + 1;
399	>	exJ = tempJ + 1;
400	>	exK = tempK + 1;
401	>	#endif
402	>
403	>	info[k].excludes->addPair(exI, exK);
404	>	info[k].excludes->addPair(exI, exJ);
405	>	info[k].excludes->addPair(exJ, exK);
406	>	}
407	>	}
408
409	+	for (j = 0; j < molInfo.nTorsions; j++){
410	+	currentTorsion = comp_stamps[stampID]->getTorsion(j);
411	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
412	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
413	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
414	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
415
416	<	// initialize the arrays
416	>	tempI = theTorsions[j].a;
417	>	tempJ = theTorsions[j].b;
418	>	tempK = theTorsions[j].c;
419	>	tempL = theTorsions[j].d;
420
421	<	the_ff->setSimInfo( simnfo );
421	>	#ifdef IS_MPI
422	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
423	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
424	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
425	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
426	>	#else
427	>	exI = tempI + 1;
428	>	exJ = tempJ + 1;
429	>	exK = tempK + 1;
430	>	exL = tempL + 1;
431	>	#endif
432
433	<	makeMolecules();
434	<	simnfo->identArray = new int[simnfo->n_atoms];
435	<	for(i=0; i<simnfo->n_atoms; i++){
436	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
437	<	}
438	<
439	<	if (the_globals->getUseRF() ) {
445	<	simnfo->useReactionField = 1;
446	<
447	<	if( !the_globals->haveECR() ){
448	<	sprintf( painCave.errMsg,
449	<	"SimSetup Warning: using default value of 1/2 the smallest "
450	<	"box length for the electrostaticCutoffRadius.\n"
451	<	"I hope you have a very fast processor!\n");
452	<	painCave.isFatal = 0;
453	<	simError();
454	<	double smallest;
455	<	smallest = simnfo->box_x;
456	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
457	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
458	<	simnfo->ecr = 0.5 * smallest;
459	<	} else {
460	<	simnfo->ecr        = the_globals->getECR();
461	<	}
433	>	info[k].excludes->addPair(exI, exJ);
434	>	info[k].excludes->addPair(exI, exK);
435	>	info[k].excludes->addPair(exI, exL);
436	>	info[k].excludes->addPair(exJ, exK);
437	>	info[k].excludes->addPair(exJ, exL);
438	>	info[k].excludes->addPair(exK, exL);
439	>	}
440
463	–	if( !the_globals->haveEST() ){
464	–	sprintf( painCave.errMsg,
465	–	"SimSetup Warning: using default value of 0.05 * the "
466	–	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
467	–	);
468	–	painCave.isFatal = 0;
469	–	simError();
470	–	simnfo->est = 0.05 * simnfo->ecr;
471	–	} else {
472	–	simnfo->est        = the_globals->getEST();
473	–	}
474	–
475	–	if(!the_globals->haveDielectric() ){
476	–	sprintf( painCave.errMsg,
477	–	"SimSetup Error: You are trying to use Reaction Field without"
478	–	"setting a dielectric constant!\n"
479	–	);
480	–	painCave.isFatal = 1;
481	–	simError();
482	–	}
483	–	simnfo->dielectric = the_globals->getDielectric();
484	–	} else {
485	–	if (usesDipoles) {
441
442	<	if( !the_globals->haveECR() ){
488	<	sprintf( painCave.errMsg,
489	<	"SimSetup Warning: using default value of 1/2 the smallest "
490	<	"box length for the electrostaticCutoffRadius.\n"
491	<	"I hope you have a very fast processor!\n");
492	<	painCave.isFatal = 0;
493	<	simError();
494	<	double smallest;
495	<	smallest = simnfo->box_x;
496	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
497	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
498	<	simnfo->ecr = 0.5 * smallest;
499	<	} else {
500	<	simnfo->ecr        = the_globals->getECR();
501	<	}
442	>	molInfo.myRigidBodies.clear();
443
444	<	if( !the_globals->haveEST() ){
504	<	sprintf( painCave.errMsg,
505	<	"SimSetup Warning: using default value of 5%% of the "
506	<	"electrostaticCutoffRadius for the "
507	<	"electrostaticSkinThickness\n"
508	<	);
509	<	painCave.isFatal = 0;
510	<	simError();
511	<	simnfo->est = 0.05 * simnfo->ecr;
512	<	} else {
513	<	simnfo->est        = the_globals->getEST();
514	<	}
515	<	}
516	<	}
444	>	for (j = 0; j < molInfo.nRigidBodies; j++){
445
446	<	#ifdef IS_MPI
447	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
520	<	MPIcheckPoint();
521	<	#endif // is_mpi
446	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
447	>	nMembers = currentRigidBody->getNMembers();
448
449	<	if( the_globals->haveInitialConfig() ){
524	<
525	<	InitializeFromFile* fileInit;
526	<	#ifdef IS_MPI // is_mpi
527	<	if( worldRank == 0 ){
528	<	#endif //is_mpi
529	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
530	<	#ifdef IS_MPI
531	<	}else fileInit = new InitializeFromFile( NULL );
532	<	#endif
533	<	fileInit->read_xyz( simnfo ); // default velocities on
449	>	// Create the Rigid Body:
450
451	<	delete fileInit;
536	<	}
537	<	else{
451	>	myRB = new RigidBody();
452
453	<	#ifdef IS_MPI
453	>	sprintf(rbName,"%s_RB_%d", molName, j);
454	>	myRB->setType(rbName);
455	>
456	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
457
458	<	// no init from bass
459	<
543	<	sprintf( painCave.errMsg,
544	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
545	<	painCave.isFatal;
546	<	simError();
547	<
548	<	#else
458	>	// molI is atom numbering inside this molecule
459	>	molI = currentRigidBody->getMember(rb1);
460
461	<	initFromBass();
461	>	// tempI is atom numbering on local processor
462	>	tempI = molI + atomOffset;
463
464	+	// currentAtom is the AtomStamp (which we need for
465	+	// rigid body reference positions)
466	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
467
468	<	#endif
469	<	}
468	>	// When we add to the rigid body, add the atom itself and
469	>	// the stamp info:
470
471	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
472	+
473	+	// Add this atom to the Skip List for the integrators
474		#ifdef IS_MPI
475	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
476	<	MPIcheckPoint();
477	<	#endif // is_mpi
475	>	slI = info[k].atoms[tempI]->getGlobalIndex();
476	>	#else
477	>	slI = tempI;
478	>	#endif
479	>	skipList.insert(slI);
480	>
481	>	}
482	>
483	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
484	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
485	>
486	>	tempI = currentRigidBody->getMember(rb1);
487	>	tempJ = currentRigidBody->getMember(rb2);
488	>
489	>	// Some explanation is required here.
490	>	// Fortran indexing starts at 1, while c indexing starts at 0
491	>	// Also, in parallel computations, the GlobalIndex is
492	>	// used for the exclude list:
493	>
494	>	#ifdef IS_MPI
495	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
496	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
497	>	#else
498	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
499	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
500	>	#endif
501	>
502	>	info[k].excludes->addPair(exI, exJ);
503	>
504	>	}
505	>	}
506
507	+	molInfo.myRigidBodies.push_back(myRB);
508	+	info[k].rigidBodies.push_back(myRB);
509	+	}
510	+
511
512	<
563	<
564	<
512	>	//create cutoff group for molecule
513
514	<
515	<	#ifdef IS_MPI
516	<	if( worldRank == 0 ){
517	<	#endif // is_mpi
570	<
571	<	if( the_globals->haveFinalConfig() ){
572	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
573	<	}
574	<	else{
575	<	strcpy( simnfo->finalName, inFileName );
576	<	char* endTest;
577	<	int nameLength = strlen( simnfo->finalName );
578	<	endTest = &(simnfo->finalName[nameLength - 5]);
579	<	if( !strcmp( endTest, ".bass" ) ){
580	<	strcpy( endTest, ".eor" );
581	<	}
582	<	else if( !strcmp( endTest, ".BASS" ) ){
583	<	strcpy( endTest, ".eor" );
584	<	}
585	<	else{
586	<	endTest = &(simnfo->finalName[nameLength - 4]);
587	<	if( !strcmp( endTest, ".bss" ) ){
588	<	strcpy( endTest, ".eor" );
589	<	}
590	<	else if( !strcmp( endTest, ".mdl" ) ){
591	<	strcpy( endTest, ".eor" );
592	<	}
593	<	else{
594	<	strcat( simnfo->finalName, ".eor" );
595	<	}
596	<	}
597	<	}
598	<
599	<	// make the sample and status out names
600	<
601	<	strcpy( simnfo->sampleName, inFileName );
602	<	char* endTest;
603	<	int nameLength = strlen( simnfo->sampleName );
604	<	endTest = &(simnfo->sampleName[nameLength - 5]);
605	<	if( !strcmp( endTest, ".bass" ) ){
606	<	strcpy( endTest, ".dump" );
607	<	}
608	<	else if( !strcmp( endTest, ".BASS" ) ){
609	<	strcpy( endTest, ".dump" );
610	<	}
611	<	else{
612	<	endTest = &(simnfo->sampleName[nameLength - 4]);
613	<	if( !strcmp( endTest, ".bss" ) ){
614	<	strcpy( endTest, ".dump" );
615	<	}
616	<	else if( !strcmp( endTest, ".mdl" ) ){
617	<	strcpy( endTest, ".dump" );
618	<	}
619	<	else{
620	<	strcat( simnfo->sampleName, ".dump" );
621	<	}
622	<	}
623	<
624	<	strcpy( simnfo->statusName, inFileName );
625	<	nameLength = strlen( simnfo->statusName );
626	<	endTest = &(simnfo->statusName[nameLength - 5]);
627	<	if( !strcmp( endTest, ".bass" ) ){
628	<	strcpy( endTest, ".stat" );
629	<	}
630	<	else if( !strcmp( endTest, ".BASS" ) ){
631	<	strcpy( endTest, ".stat" );
632	<	}
633	<	else{
634	<	endTest = &(simnfo->statusName[nameLength - 4]);
635	<	if( !strcmp( endTest, ".bss" ) ){
636	<	strcpy( endTest, ".stat" );
637	<	}
638	<	else if( !strcmp( endTest, ".mdl" ) ){
639	<	strcpy( endTest, ".stat" );
640	<	}
641	<	else{
642	<	strcat( simnfo->statusName, ".stat" );
643	<	}
644	<	}
645	<
646	<	#ifdef IS_MPI
647	<	}
648	<	#endif // is_mpi
649	<
650	<	// set the status, sample, and themal kick times
651	<
652	<	if( the_globals->haveSampleTime() ){
653	<	simnfo->sampleTime = the_globals->getSampleTime();
654	<	simnfo->statusTime = simnfo->sampleTime;
655	<	simnfo->thermalTime = simnfo->sampleTime;
656	<	}
657	<	else{
658	<	simnfo->sampleTime = the_globals->getRunTime();
659	<	simnfo->statusTime = simnfo->sampleTime;
660	<	simnfo->thermalTime = simnfo->sampleTime;
661	<	}
514	>	cutoffAtomSet.clear();
515	>	molInfo.myCutoffGroups.clear();
516	>
517	>	for (j = 0; j < nCutoffGroups; j++){
518
519	<	if( the_globals->haveStatusTime() ){
520	<	simnfo->statusTime = the_globals->getStatusTime();
665	<	}
519	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
520	>	nMembers = currentCutoffGroup->getNMembers();
521
522	<	if( the_globals->haveThermalTime() ){
523	<	simnfo->thermalTime = the_globals->getThermalTime();
524	<	}
522	>	myCutoffGroup = new CutoffGroup();
523	>
524	>	#ifdef IS_MPI
525	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
526	>	#else
527	>	myCutoffGroup->setGlobalIndex(groupOffset);
528	>	#endif
529	>
530	>	for (int cg = 0; cg < nMembers; cg++) {
531
532	<	// check for the temperature set flag
532	>	// molI is atom numbering inside this molecule
533	>	molI = currentCutoffGroup->getMember(cg);
534
535	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
535	>	// tempI is atom numbering on local processor
536	>	tempI = molI + atomOffset;
537
538	+	#ifdef IS_MPI
539	+	globalID = info[k].atoms[tempI]->getGlobalIndex();
540	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
541	+	#else
542	+	globalID = info[k].atoms[tempI]->getIndex();
543	+	info[k].globalGroupMembership[globalID] = groupOffset;
544	+	#endif
545	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
546	+	cutoffAtomSet.insert(tempI);
547	+	}
548	+
549	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
550	+	groupOffset++;
551
552	<	//   // make the longe range forces and the integrator
552	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
553	>
554	>
555	>	// create a cutoff group for every atom in current molecule which
556	>	// does not belong to cutoffgroup defined at mdl file
557	>
558	>	for(j = 0; j < molInfo.nAtoms; j++){
559	>
560	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
561	>	myCutoffGroup = new CutoffGroup();
562	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
563	>
564	>	#ifdef IS_MPI
565	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
566	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
567	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
568	>	#else
569	>	myCutoffGroup->setGlobalIndex(groupOffset);
570	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
571	>	info[k].globalGroupMembership[globalID] = groupOffset;
572	>	#endif
573	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
574	>	groupOffset++;
575	>	}
576	>	}
577
578	<	//   new AllLong( simnfo );
578	>	// After this is all set up, scan through the atoms to
579	>	// see if they can be added to the integrableObjects:
580
581	+	molInfo.myIntegrableObjects.clear();
582	+
583
584	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
585	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
683	<	std::cerr << "called new Symplecic\n";
684	<	fprintf( stderr, "called new Symplectic. stderr\n" );
685	<	}
686	<	else if( !strcmp( force_field, "LJ" ) ){
687	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
688	<	std::cerr << "called new Verlet\n";
689	<	fprintf( stderr, "called new Verlet. stderr\n" );
690	<	}
691	<	else {
692	<	std::cerr << "I'm a bug.\n";
693	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
694	<	}
584	>	for (j = 0; j < molInfo.nAtoms; j++){
585	>
586		#ifdef IS_MPI
587	<	mpiSim->mpiRefresh();
587	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
588	>	#else
589	>	slJ = j+atomOffset;
590		#endif
591
592	<	// initialize the Fortran
592	>	// if they aren't on the skip list, then they can be integrated
593
594	<
595	<	simnfo->refreshSim();
596	<
597	<	if( !strcmp( simnfo->mixingRule, "standard") ){
598	<	the_ff->initForceField( LB_MIXING_RULE );
599	<	}
707	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
708	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
709	<	}
710	<	else{
711	<	sprintf( painCave.errMsg,
712	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
713	<	simnfo->mixingRule );
714	<	painCave.isFatal = 1;
715	<	simError();
716	<	}
594	>	if (skipList.find(slJ) == skipList.end()) {
595	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
596	>	info[k].integrableObjects.push_back(mySD);
597	>	molInfo.myIntegrableObjects.push_back(mySD);
598	>	}
599	>	}
600
601	+	// all rigid bodies are integrated:
602
603	<	#ifdef IS_MPI
604	<	strcpy( checkPointMsg,
605	<	"Successfully intialized the mixingRule for Fortran." );
606	<	MPIcheckPoint();
607	<	#endif // is_mpi
608	<	}
603	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
604	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
605	>	info[k].integrableObjects.push_back(mySD);
606	>	molInfo.myIntegrableObjects.push_back(mySD);
607	>	}
608	>
609	>	// send the arrays off to the forceField for init.
610	>
611	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
612	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
613	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
614	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
615	>	theTorsions);
616
617
618	<	void SimSetup::makeMolecules( void ){
618	>	//creat ConstraintPair.
619	>	molInfo.myConstraintPairs.clear();
620	>
621	>	for (j = 0; j < molInfo.nBonds; j++){
622
623	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
624	<	molInit info;
731	<	DirectionalAtom* dAtom;
732	<	LinkedAssign* extras;
733	<	LinkedAssign* current_extra;
734	<	AtomStamp* currentAtom;
735	<	BondStamp* currentBond;
736	<	BendStamp* currentBend;
737	<	TorsionStamp* currentTorsion;
623	>	//if bond is constrained bond, add it into constraint pair
624	>	if(molInfo.myBonds[j]->is_constrained()){
625
626	<	bond_pair* theBonds;
627	<	bend_set* theBends;
628	<	torsion_set* theTorsions;
626	>	//if both atoms are in the same rigid body, just skip it
627	>	currentBond = comp_stamps[stampID]->getBond(j);
628	>
629	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
630
631	<
632	<	//init the forceField paramters
631	>	tempI = currentBond->getA() + atomOffset;
632	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
633	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
634	>	else
635	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
636
637	<	the_ff->readParams();
637	>	tempJ =  currentBond->getB() + atomOffset;
638	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
639	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
640	>	else
641	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
642
643	<
644	<	// init the atoms
643	>	bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr();
644	>	consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2);
645
646	<	double ux, uy, uz, u, uSqr;
647	<
648	<	atomOffset = 0;
649	<	excludeOffset = 0;
650	<	for(i=0; i<simnfo->n_mol; i++){
651	<
652	<	stampID = the_molecules[i].getStampID();
646	>	molInfo.myConstraintPairs.push_back(consPair);
647	>	}
648	>	}//end if(molInfo.myBonds[j]->is_constrained())
649	>	}
650	>
651	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair
652	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
653	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
654	>
655	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
656
657	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
658	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
659	<	info.nBends    = comp_stamps[stampID]->getNBends();
762	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
763	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
657	>	for(size_t m = 0; m < jointAtoms.size(); m++){
658	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
659	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
660
661	<	info.myAtoms = &the_atoms[atomOffset];
662	<	info.myExcludes = &the_excludes[excludeOffset];
663	<	info.myBonds = new Bond*[info.nBonds];
768	<	info.myBends = new Bend*[info.nBends];
769	<	info.myTorsions = new Torsion*[info.nTorsions];
661	>	consPair = new JointConstraintPair(consElement1, consElement2);
662	>	molInfo.myConstraintPairs.push_back(consPair);
663	>	}
664
665	<	theBonds = new bond_pair[info.nBonds];
772	<	theBends = new bend_set[info.nBends];
773	<	theTorsions = new torsion_set[info.nTorsions];
774	<
775	<	// make the Atoms
776	<
777	<	for(j=0; j<info.nAtoms; j++){
778	<
779	<	currentAtom = comp_stamps[stampID]->getAtom( j );
780	<	if( currentAtom->haveOrientation() ){
781	<
782	<	dAtom = new DirectionalAtom(j + atomOffset);
783	<	simnfo->n_oriented++;
784	<	info.myAtoms[j] = dAtom;
785	<
786	<	ux = currentAtom->getOrntX();
787	<	uy = currentAtom->getOrntY();
788	<	uz = currentAtom->getOrntZ();
789	<
790	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
791	<
792	<	u = sqrt( uSqr );
793	<	ux = ux / u;
794	<	uy = uy / u;
795	<	uz = uz / u;
796	<
797	<	dAtom->setSUx( ux );
798	<	dAtom->setSUy( uy );
799	<	dAtom->setSUz( uz );
665	>	}
666		}
801	–	else{
802	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
803	–	}
804	–	info.myAtoms[j]->setType( currentAtom->getType() );
805	–
806	–	#ifdef IS_MPI
667
668	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
668	>
669	>	info[k].molecules[i].initialize(molInfo);
670
810	–	#endif // is_mpi
811	–	}
812	–
813	–	// make the bonds
814	–	for(j=0; j<info.nBonds; j++){
671
672	<	currentBond = comp_stamps[stampID]->getBond( j );
673	<	theBonds[j].a = currentBond->getA() + atomOffset;
674	<	theBonds[j].b = currentBond->getB() + atomOffset;
672	>	atomOffset += molInfo.nAtoms;
673	>	delete[] theBonds;
674	>	delete[] theBends;
675	>	delete[] theTorsions;
676	>	}
677
820	–	exI = theBonds[j].a;
821	–	exJ = theBonds[j].b;
678
823	–	// exclude_I must always be the smaller of the pair
824	–	if( exI > exJ ){
825	–	tempEx = exI;
826	–	exI = exJ;
827	–	exJ = tempEx;
828	–	}
829	–	#ifdef IS_MPI
830	–	tempEx = exI;
831	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
832	–	tempEx = exJ;
833	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
834	–
835	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
836	–	#else  // isn't MPI
679
680	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
681	<	#endif  //is_mpi
682	<	}
683	<	excludeOffset += info.nBonds;
680	>	#ifdef IS_MPI
681	>	// Since the globalGroupMembership has been zero filled and we've only
682	>	// poked values into the atoms we know, we can do an Allreduce
683	>	// to get the full globalGroupMembership array (We think).
684	>	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
685	>	// docs said we could.
686
687	<	//make the bends
844	<	for(j=0; j<info.nBends; j++){
845	<
846	<	currentBend = comp_stamps[stampID]->getBend( j );
847	<	theBends[j].a = currentBend->getA() + atomOffset;
848	<	theBends[j].b = currentBend->getB() + atomOffset;
849	<	theBends[j].c = currentBend->getC() + atomOffset;
850	<
851	<	if( currentBend->haveExtras() ){
852	<
853	<	extras = currentBend->getExtras();
854	<	current_extra = extras;
855	<
856	<	while( current_extra != NULL ){
857	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
858	<
859	<	switch( current_extra->getType() ){
860	<
861	<	case 0:
862	<	theBends[j].ghost =
863	<	current_extra->getInt() + atomOffset;
864	<	theBends[j].isGhost = 1;
865	<	break;
866	<
867	<	case 1:
868	<	theBends[j].ghost =
869	<	(int)current_extra->getDouble() + atomOffset;
870	<	theBends[j].isGhost = 1;
871	<	break;
872	<
873	<	default:
874	<	sprintf( painCave.errMsg,
875	<	"SimSetup Error: ghostVectorSource was neither a "
876	<	"double nor an int.\n"
877	<	"-->Bend[%d] in %s\n",
878	<	j, comp_stamps[stampID]->getID() );
879	<	painCave.isFatal = 1;
880	<	simError();
881	<	}
882	<	}
883	<
884	<	else{
885	<
886	<	sprintf( painCave.errMsg,
887	<	"SimSetup Error: unhandled bend assignment:\n"
888	<	"    -->%s in Bend[%d] in %s\n",
889	<	current_extra->getlhs(),
890	<	j, comp_stamps[stampID]->getID() );
891	<	painCave.isFatal = 1;
892	<	simError();
893	<	}
894	<
895	<	current_extra = current_extra->getNext();
896	<	}
897	<	}
898	<
899	<	if( !theBends[j].isGhost ){
900	<
901	<	exI = theBends[j].a;
902	<	exJ = theBends[j].c;
903	<	}
904	<	else{
905	<
906	<	exI = theBends[j].a;
907	<	exJ = theBends[j].b;
908	<	}
909	<
910	<	// exclude_I must always be the smaller of the pair
911	<	if( exI > exJ ){
912	<	tempEx = exI;
913	<	exI = exJ;
914	<	exJ = tempEx;
915	<	}
916	<	#ifdef IS_MPI
917	<	tempEx = exI;
918	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
919	<	tempEx = exJ;
920	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
921	<
922	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
923	<	#else  // isn't MPI
924	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
925	<	#endif  //is_mpi
926	<	}
927	<	excludeOffset += info.nBends;
687	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
688
689	<	for(j=0; j<info.nTorsions; j++){
690	<
691	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
692	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
933	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
934	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
935	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
936	<
937	<	exI = theTorsions[j].a;
938	<	exJ = theTorsions[j].d;
689	>	MPI_Allreduce(info[k].globalGroupMembership,
690	>	ggMjunk,
691	>	mpiSim->getNAtomsGlobal(),
692	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
693
694	<	// exclude_I must always be the smaller of the pair
695	<	if( exI > exJ ){
942	<	tempEx = exI;
943	<	exI = exJ;
944	<	exJ = tempEx;
945	<	}
946	<	#ifdef IS_MPI
947	<	tempEx = exI;
948	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
949	<	tempEx = exJ;
950	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
951	<
952	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
953	<	#else  // isn't MPI
954	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
955	<	#endif  //is_mpi
956	<	}
957	<	excludeOffset += info.nTorsions;
694	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
695	>	info[k].globalGroupMembership[i] = ggMjunk[i];
696
697	+	delete[] ggMjunk;
698
699	<	// send the arrays off to the forceField for init.
699	>	#endif
700
962	–	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
963	–	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
964	–	the_ff->initializeBends( info.nBends, info.myBends, theBends );
965	–	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
701
702
968	–	the_molecules[i].initialize( info );
969	–
970	–
971	–	atomOffset += info.nAtoms;
972	–	delete[] theBonds;
973	–	delete[] theBends;
974	–	delete[] theTorsions;
703		}
704
705		#ifdef IS_MPI
706	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
706	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
707		MPIcheckPoint();
708		#endif // is_mpi
709
982	–	// clean up the forcefield
983	–	the_ff->calcRcut();
984	–	the_ff->cleanMe();
985	–
710		}
711
712	<	void SimSetup::initFromBass( void ){
989	<
712	>	void SimSetup::initFromBass(void){
713		int i, j, k;
714		int n_cells;
715		double cellx, celly, cellz;
#	Line 995 | Line 718 | void SimSetup::initFromBass( void ){
718		int n_extra;
719		int have_extra, done;
720
721	<	temp1 = (double)tot_nmol / 4.0;
722	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
723	<	temp3 = ceil( temp2 );
721	>	double vel[3];
722	>	vel[0] = 0.0;
723	>	vel[1] = 0.0;
724	>	vel[2] = 0.0;
725
726	<	have_extra =0;
727	<	if( temp2 < temp3 ){ // we have a non-complete lattice
728	<	have_extra =1;
726	>	temp1 = (double) tot_nmol / 4.0;
727	>	temp2 = pow(temp1, (1.0 / 3.0));
728	>	temp3 = ceil(temp2);
729
730	<	n_cells = (int)temp3 - 1;
731	<	cellx = simnfo->box_x / temp3;
732	<	celly = simnfo->box_y / temp3;
733	<	cellz = simnfo->box_z / temp3;
1010	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1011	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1012	<	n_per_extra = (int)ceil( temp1 );
730	>	have_extra = 0;
731	>	if (temp2 < temp3){
732	>	// we have a non-complete lattice
733	>	have_extra = 1;
734
735	<	if( n_per_extra > 4){
736	<	sprintf( painCave.errMsg,
737	<	"SimSetup error. There has been an error in constructing"
738	<	" the non-complete lattice.\n" );
735	>	n_cells = (int) temp3 - 1;
736	>	cellx = info[0].boxL[0] / temp3;
737	>	celly = info[0].boxL[1] / temp3;
738	>	cellz = info[0].boxL[2] / temp3;
739	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
740	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
741	>	n_per_extra = (int) ceil(temp1);
742	>
743	>	if (n_per_extra > 4){
744	>	sprintf(painCave.errMsg,
745	>	"SimSetup error. There has been an error in constructing"
746	>	" the non-complete lattice.\n");
747		painCave.isFatal = 1;
748		simError();
749		}
750		}
751		else{
752	<	n_cells = (int)temp3;
753	<	cellx = simnfo->box_x / temp3;
754	<	celly = simnfo->box_y / temp3;
755	<	cellz = simnfo->box_z / temp3;
752	>	n_cells = (int) temp3;
753	>	cellx = info[0].boxL[0] / temp3;
754	>	celly = info[0].boxL[1] / temp3;
755	>	cellz = info[0].boxL[2] / temp3;
756		}
757
758		current_mol = 0;
#	Line 1031 | Line 760 | void SimSetup::initFromBass( void ){
760		current_comp = 0;
761		current_atom_ndx = 0;
762
763	<	for( i=0; i < n_cells ; i++ ){
764	<	for( j=0; j < n_cells; j++ ){
765	<	for( k=0; k < n_cells; k++ ){
763	>	for (i = 0; i < n_cells ; i++){
764	>	for (j = 0; j < n_cells; j++){
765	>	for (k = 0; k < n_cells; k++){
766	>	makeElement(i * cellx, j * celly, k * cellz);
767
768	<	makeElement( i * cellx,
1039	<	j * celly,
1040	<	k * cellz );
768	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
769
770	<	makeElement( i * cellx + 0.5 * cellx,
1043	<	j * celly + 0.5 * celly,
1044	<	k * cellz );
770	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
771
772	<	makeElement( i * cellx,
1047	<	j * celly + 0.5 * celly,
1048	<	k * cellz + 0.5 * cellz );
1049	<
1050	<	makeElement( i * cellx + 0.5 * cellx,
1051	<	j * celly,
1052	<	k * cellz + 0.5 * cellz );
772	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
773		}
774		}
775		}
776
777	<	if( have_extra ){
777	>	if (have_extra){
778		done = 0;
779
780		int start_ndx;
781	<	for( i=0; i < (n_cells+1) && !done; i++ ){
782	<	for( j=0; j < (n_cells+1) && !done; j++ ){
781	>	for (i = 0; i < (n_cells + 1) && !done; i++){
782	>	for (j = 0; j < (n_cells + 1) && !done; j++){
783	>	if (i < n_cells){
784	>	if (j < n_cells){
785	>	start_ndx = n_cells;
786	>	}
787	>	else
788	>	start_ndx = 0;
789	>	}
790	>	else
791	>	start_ndx = 0;
792
793	<	if( i < n_cells ){
793	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
794	>	makeElement(i * cellx, j * celly, k * cellz);
795	>	done = (current_mol >= tot_nmol);
796
797	<	if( j < n_cells ){
798	<	start_ndx = n_cells;
799	<	}
800	<	else start_ndx = 0;
801	<	}
1071	<	else start_ndx = 0;
797	>	if (!done && n_per_extra > 1){
798	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
799	>	k * cellz);
800	>	done = (current_mol >= tot_nmol);
801	>	}
802
803	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
803	>	if (!done && n_per_extra > 2){
804	>	makeElement(i * cellx, j * celly + 0.5 * celly,
805	>	k * cellz + 0.5 * cellz);
806	>	done = (current_mol >= tot_nmol);
807	>	}
808
809	<	makeElement( i * cellx,
810	<	j * celly,
811	<	k * cellz );
812	<	done = ( current_mol >= tot_nmol );
813	<
814	<	if( !done && n_per_extra > 1 ){
1081	<	makeElement( i * cellx + 0.5 * cellx,
1082	<	j * celly + 0.5 * celly,
1083	<	k * cellz );
1084	<	done = ( current_mol >= tot_nmol );
1085	<	}
1086	<
1087	<	if( !done && n_per_extra > 2){
1088	<	makeElement( i * cellx,
1089	<	j * celly + 0.5 * celly,
1090	<	k * cellz + 0.5 * cellz );
1091	<	done = ( current_mol >= tot_nmol );
1092	<	}
1093	<
1094	<	if( !done && n_per_extra > 3){
1095	<	makeElement( i * cellx + 0.5 * cellx,
1096	<	j * celly,
1097	<	k * cellz + 0.5 * cellz );
1098	<	done = ( current_mol >= tot_nmol );
1099	<	}
1100	<	}
809	>	if (!done && n_per_extra > 3){
810	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
811	>	k * cellz + 0.5 * cellz);
812	>	done = (current_mol >= tot_nmol);
813	>	}
814	>	}
815		}
816		}
817		}
818
819	<
820	<	for( i=0; i<simnfo->n_atoms; i++ ){
1107	<	simnfo->atoms[i]->set_vx( 0.0 );
1108	<	simnfo->atoms[i]->set_vy( 0.0 );
1109	<	simnfo->atoms[i]->set_vz( 0.0 );
819	>	for (i = 0; i < info[0].n_atoms; i++){
820	>	info[0].atoms[i]->setVel(vel);
821		}
822		}
823
824	<	void SimSetup::makeElement( double x, double y, double z ){
1114	<
824	>	void SimSetup::makeElement(double x, double y, double z){
825		int k;
826		AtomStamp* current_atom;
827		DirectionalAtom* dAtom;
828		double rotMat[3][3];
829	+	double pos[3];
830
831	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
832	<
833	<	current_atom = comp_stamps[current_comp]->getAtom( k );
834	<	if( !current_atom->havePosition() ){
835	<	sprintf( painCave.errMsg,
836	<	"SimSetup:initFromBass error.\n"
837	<	"\tComponent %s, atom %s does not have a position specified.\n"
838	<	"\tThe initialization routine is unable to give a start"
839	<	" position.\n",
1129	<	comp_stamps[current_comp]->getID(),
1130	<	current_atom->getType() );
831	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
832	>	current_atom = comp_stamps[current_comp]->getAtom(k);
833	>	if (!current_atom->havePosition()){
834	>	sprintf(painCave.errMsg,
835	>	"SimSetup:initFromBass error.\n"
836	>	"\tComponent %s, atom %s does not have a position specified.\n"
837	>	"\tThe initialization routine is unable to give a start"
838	>	" position.\n",
839	>	comp_stamps[current_comp]->getID(), current_atom->getType());
840		painCave.isFatal = 1;
841		simError();
842		}
843
844	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
845	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
846	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
844	>	pos[0] = x + current_atom->getPosX();
845	>	pos[1] = y + current_atom->getPosY();
846	>	pos[2] = z + current_atom->getPosZ();
847
848	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
848	>	info[0].atoms[current_atom_ndx]->setPos(pos);
849
850	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
850	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
851	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
852
853		rotMat[0][0] = 1.0;
854		rotMat[0][1] = 0.0;
#	Line 1152 | Line 862 | void SimSetup::makeElement( double x, double y, double
862		rotMat[2][1] = 0.0;
863		rotMat[2][2] = 1.0;
864
865	<	dAtom->setA( rotMat );
865	>	dAtom->setA(rotMat);
866		}
867
868		current_atom_ndx++;
#	Line 1161 | Line 871 | void SimSetup::makeElement( double x, double y, double
871		current_mol++;
872		current_comp_mol++;
873
874	<	if( current_comp_mol >= components_nmol[current_comp] ){
1165	<
874	>	if (current_comp_mol >= components_nmol[current_comp]){
875		current_comp_mol = 0;
876		current_comp++;
877	+	}
878	+	}
879	+
880	+
881	+	void SimSetup::gatherInfo(void){
882	+	int i;
883	+
884	+	ensembleCase = -1;
885	+	ffCase = -1;
886	+
887	+	// set the easy ones first
888	+
889	+	for (i = 0; i < nInfo; i++){
890	+	info[i].target_temp = globals->getTargetTemp();
891	+	info[i].dt = globals->getDt();
892	+	info[i].run_time = globals->getRunTime();
893	+	}
894	+	n_components = globals->getNComponents();
895	+
896	+
897	+	// get the forceField
898	+
899	+	strcpy(force_field, globals->getForceField());
900	+
901	+	if (!strcasecmp(force_field, "DUFF")){
902	+	ffCase = FF_DUFF;
903	+	}
904	+	else if (!strcasecmp(force_field, "LJ")){
905	+	ffCase = FF_LJ;
906	+	}
907	+	else if (!strcasecmp(force_field, "EAM")){
908	+	ffCase = FF_EAM;
909	+	}
910	+	else if (!strcasecmp(force_field, "WATER")){
911	+	ffCase = FF_H2O;
912	+	}
913	+	else{
914	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
915	+	force_field);
916	+	painCave.isFatal = 1;
917	+	simError();
918	+	}
919	+	if (globals->haveForceFieldVariant()) {
920	+	strcpy(forcefield_variant, globals->getForceFieldVariant());
921	+	has_forcefield_variant = 1;
922	+	}
923	+
924	+	// get the ensemble
925	+
926	+	strcpy(ensemble, globals->getEnsemble());
927	+
928	+	if (!strcasecmp(ensemble, "NVE")){
929	+	ensembleCase = NVE_ENS;
930	+	}
931	+	else if (!strcasecmp(ensemble, "NVT")){
932	+	ensembleCase = NVT_ENS;
933	+	}
934	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
935	+	ensembleCase = NPTi_ENS;
936	+	}
937	+	else if (!strcasecmp(ensemble, "NPTf")){
938	+	ensembleCase = NPTf_ENS;
939	+	}
940	+	else if (!strcasecmp(ensemble, "NPTxyz")){
941	+	ensembleCase = NPTxyz_ENS;
942	+	}
943	+	else{
944	+	sprintf(painCave.errMsg,
945	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
946	+	"\treverting to NVE for this simulation.\n",
947	+	ensemble);
948	+	painCave.isFatal = 0;
949	+	simError();
950	+	strcpy(ensemble, "NVE");
951	+	ensembleCase = NVE_ENS;
952	+	}
953	+
954	+	for (i = 0; i < nInfo; i++){
955	+	strcpy(info[i].ensemble, ensemble);
956	+
957	+	// get the mixing rule
958	+
959	+	strcpy(info[i].mixingRule, globals->getMixingRule());
960	+	info[i].usePBC = globals->getPBC();
961	+	}
962	+
963	+	// get the components and calculate the tot_nMol and indvidual n_mol
964	+
965	+	the_components = globals->getComponents();
966	+	components_nmol = new int[n_components];
967	+
968	+
969	+	if (!globals->haveNMol()){
970	+	// we don't have the total number of molecules, so we assume it is
971	+	// given in each component
972	+
973	+	tot_nmol = 0;
974	+	for (i = 0; i < n_components; i++){
975	+	if (!the_components[i]->haveNMol()){
976	+	// we have a problem
977	+	sprintf(painCave.errMsg,
978	+	"SimSetup Error. No global NMol or component NMol given.\n"
979	+	"\tCannot calculate the number of atoms.\n");
980	+	painCave.isFatal = 1;
981	+	simError();
982	+	}
983	+
984	+	tot_nmol += the_components[i]->getNMol();
985	+	components_nmol[i] = the_components[i]->getNMol();
986	+	}
987	+	}
988	+	else{
989	+	sprintf(painCave.errMsg,
990	+	"SimSetup error.\n"
991	+	"\tSorry, the ability to specify total"
992	+	" nMols and then give molfractions in the components\n"
993	+	"\tis not currently supported."
994	+	" Please give nMol in the components.\n");
995	+	painCave.isFatal = 1;
996	+	simError();
997	+	}
998	+
999	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
1000	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
1001	+	sprintf(painCave.errMsg,
1002	+	"Sample time is not divisible by dt.\n"
1003	+	"\tThis will result in samples that are not uniformly\n"
1004	+	"\tdistributed in time.  If this is a problem, change\n"
1005	+	"\tyour sampleTime variable.\n");
1006	+	painCave.isFatal = 0;
1007	+	simError();
1008	+	}
1009	+
1010	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
1011	+	sprintf(painCave.errMsg,
1012	+	"Status time is not divisible by dt.\n"
1013	+	"\tThis will result in status reports that are not uniformly\n"
1014	+	"\tdistributed in time.  If this is a problem, change \n"
1015	+	"\tyour statusTime variable.\n");
1016	+	painCave.isFatal = 0;
1017	+	simError();
1018	+	}
1019	+
1020	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1021	+	sprintf(painCave.errMsg,
1022	+	"Thermal time is not divisible by dt.\n"
1023	+	"\tThis will result in thermalizations that are not uniformly\n"
1024	+	"\tdistributed in time.  If this is a problem, change \n"
1025	+	"\tyour thermalTime variable.\n");
1026	+	painCave.isFatal = 0;
1027	+	simError();
1028	+	}
1029	+
1030	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1031	+	sprintf(painCave.errMsg,
1032	+	"Reset time is not divisible by dt.\n"
1033	+	"\tThis will result in integrator resets that are not uniformly\n"
1034	+	"\tdistributed in time.  If this is a problem, change\n"
1035	+	"\tyour resetTime variable.\n");
1036	+	painCave.isFatal = 0;
1037	+	simError();
1038	+	}
1039	+
1040	+	// set the status, sample, and thermal kick times
1041	+
1042	+	for (i = 0; i < nInfo; i++){
1043	+	if (globals->haveSampleTime()){
1044	+	info[i].sampleTime = globals->getSampleTime();
1045	+	info[i].statusTime = info[i].sampleTime;
1046	+	}
1047	+	else{
1048	+	info[i].sampleTime = globals->getRunTime();
1049	+	info[i].statusTime = info[i].sampleTime;
1050	+	}
1051	+
1052	+	if (globals->haveStatusTime()){
1053	+	info[i].statusTime = globals->getStatusTime();
1054	+	}
1055	+
1056	+	if (globals->haveThermalTime()){
1057	+	info[i].thermalTime = globals->getThermalTime();
1058	+	} else {
1059	+	info[i].thermalTime = globals->getRunTime();
1060	+	}
1061	+
1062	+	info[i].resetIntegrator = 0;
1063	+	if( globals->haveResetTime() ){
1064	+	info[i].resetTime = globals->getResetTime();
1065	+	info[i].resetIntegrator = 1;
1066	+	}
1067	+
1068	+	// check for the temperature set flag
1069	+
1070	+	if (globals->haveTempSet())
1071	+	info[i].setTemp = globals->getTempSet();
1072	+
1073	+	// check for the extended State init
1074	+
1075	+	info[i].useInitXSstate = globals->getUseInitXSstate();
1076	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1077	+
1078	+	// check for thermodynamic integration
1079	+	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1080	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1081	+	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1082	+	info[i].thermIntLambda = globals->getThermIntLambda();
1083	+	info[i].thermIntK = globals->getThermIntK();
1084	+
1085	+	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1086	+	info[i].restraint = myRestraint;
1087	+	}
1088	+	else {
1089	+	sprintf(painCave.errMsg,
1090	+	"SimSetup Error:\n"
1091	+	"\tKeyword useSolidThermInt was set to 'true' but\n"
1092	+	"\tthermodynamicIntegrationLambda (and/or\n"
1093	+	"\tthermodynamicIntegrationK) was not specified.\n"
1094	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1095	+	painCave.isFatal = 1;
1096	+	simError();
1097	+	}
1098	+	}
1099	+	else if(globals->getUseLiquidThermInt()) {
1100	+	if (globals->getUseSolidThermInt()) {
1101	+	sprintf( painCave.errMsg,
1102	+	"SimSetup Warning: It appears that you have both solid and\n"
1103	+	"\tliquid thermodynamic integration activated in your .bass\n"
1104	+	"\tfile. To avoid confusion, specify only one technique in\n"
1105	+	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1106	+	"\twill be assumed for the current simulation. If this is not\n"
1107	+	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1108	+	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1109	+	painCave.isFatal = 0;
1110	+	simError();
1111	+	}
1112	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1113	+	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1114	+	info[i].thermIntLambda = globals->getThermIntLambda();
1115	+	info[i].thermIntK = globals->getThermIntK();
1116	+	}
1117	+	else {
1118	+	sprintf(painCave.errMsg,
1119	+	"SimSetup Error:\n"
1120	+	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1121	+	"\tthermodynamicIntegrationLambda (and/or\n"
1122	+	"\tthermodynamicIntegrationK) was not specified.\n"
1123	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1124	+	painCave.isFatal = 1;
1125	+	simError();
1126	+	}
1127	+	}
1128	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1129	+	sprintf(painCave.errMsg,
1130	+	"SimSetup Warning: If you want to use Thermodynamic\n"
1131	+	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1132	+	"\t'true' in your .bass file.  These keywords are set to\n"
1133	+	"\t'false' by default, so your lambda and/or k values are\n"
1134	+	"\tbeing ignored.\n");
1135	+	painCave.isFatal = 0;
1136	+	simError();
1137	+	}
1138	+	}
1139	+
1140	+	//setup seed for random number generator
1141	+	int seedValue;
1142	+
1143	+	if (globals->haveSeed()){
1144	+	seedValue = globals->getSeed();
1145	+
1146	+	if(seedValue / 1E9 == 0){
1147	+	sprintf(painCave.errMsg,
1148	+	"Seed for sprng library should contain at least 9 digits\n"
1149	+	"OOPSE will generate a seed for user\n");
1150	+	painCave.isFatal = 0;
1151	+	simError();
1152	+
1153	+	//using seed generated by system instead of invalid seed set by user
1154	+	#ifndef IS_MPI
1155	+	seedValue = make_sprng_seed();
1156	+	#else
1157	+	if (worldRank == 0){
1158	+	seedValue = make_sprng_seed();
1159	+	}
1160	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1161	+	#endif
1162	+	}
1163	+	}//end of if branch of globals->haveSeed()
1164	+	else{
1165	+
1166	+	#ifndef IS_MPI
1167	+	seedValue = make_sprng_seed();
1168	+	#else
1169	+	if (worldRank == 0){
1170	+	seedValue = make_sprng_seed();
1171	+	}
1172	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1173	+	#endif
1174	+	}//end of globals->haveSeed()
1175	+
1176	+	for (int i = 0; i < nInfo; i++){
1177	+	info[i].setSeed(seedValue);
1178	+	}
1179	+
1180	+	#ifdef IS_MPI
1181	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1182	+	MPIcheckPoint();
1183	+	#endif // is_mpi
1184	+	}
1185	+
1186	+
1187	+	void SimSetup::finalInfoCheck(void){
1188	+	int index;
1189	+	int usesDipoles;
1190	+	int usesCharges;
1191	+	int i;
1192	+
1193	+	for (i = 0; i < nInfo; i++){
1194	+	// check electrostatic parameters
1195	+
1196	+	index = 0;
1197	+	usesDipoles = 0;
1198	+	while ((index < info[i].n_atoms) && !usesDipoles){
1199	+	usesDipoles = (info[i].atoms[index])->hasDipole();
1200	+	index++;
1201	+	}
1202	+	index = 0;
1203	+	usesCharges = 0;
1204	+	while ((index < info[i].n_atoms) && !usesCharges){
1205	+	usesCharges= (info[i].atoms[index])->hasCharge();
1206	+	index++;
1207	+	}
1208	+	#ifdef IS_MPI
1209	+	int myUse = usesDipoles;
1210	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1211	+	#endif //is_mpi
1212	+
1213	+	double theRcut, theRsw;
1214	+
1215	+	if (globals->haveRcut()) {
1216	+	theRcut = globals->getRcut();
1217	+
1218	+	if (globals->haveRsw())
1219	+	theRsw = globals->getRsw();
1220	+	else
1221	+	theRsw = theRcut;
1222	+
1223	+	info[i].setDefaultRcut(theRcut, theRsw);
1224	+
1225	+	} else {
1226	+
1227	+	the_ff->calcRcut();
1228	+	theRcut = info[i].getRcut();
1229	+
1230	+	if (globals->haveRsw())
1231	+	theRsw = globals->getRsw();
1232	+	else
1233	+	theRsw = theRcut;
1234	+
1235	+	info[i].setDefaultRcut(theRcut, theRsw);
1236	+	}
1237	+
1238	+	if (globals->getUseRF()){
1239	+	info[i].useReactionField = 1;
1240	+
1241	+	if (!globals->haveRcut()){
1242	+	sprintf(painCave.errMsg,
1243	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1244	+	"\tOOPSE will use a default value of 15.0 angstroms"
1245	+	"\tfor the cutoffRadius.\n");
1246	+	painCave.isFatal = 0;
1247	+	simError();
1248	+	theRcut = 15.0;
1249	+	}
1250	+	else{
1251	+	theRcut = globals->getRcut();
1252	+	}
1253	+
1254	+	if (!globals->haveRsw()){
1255	+	sprintf(painCave.errMsg,
1256	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1257	+	"\tOOPSE will use a default value of\n"
1258	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1259	+	painCave.isFatal = 0;
1260	+	simError();
1261	+	theRsw = 0.95 * theRcut;
1262	+	}
1263	+	else{
1264	+	theRsw = globals->getRsw();
1265	+	}
1266	+
1267	+	info[i].setDefaultRcut(theRcut, theRsw);
1268	+
1269	+	if (!globals->haveDielectric()){
1270	+	sprintf(painCave.errMsg,
1271	+	"SimSetup Error: No Dielectric constant was set.\n"
1272	+	"\tYou are trying to use Reaction Field without"
1273	+	"\tsetting a dielectric constant!\n");
1274	+	painCave.isFatal = 1;
1275	+	simError();
1276	+	}
1277	+	info[i].dielectric = globals->getDielectric();
1278	+	}
1279	+	else{
1280	+	if (usesDipoles || usesCharges){
1281	+
1282	+	if (!globals->haveRcut()){
1283	+	sprintf(painCave.errMsg,
1284	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1285	+	"\tOOPSE will use a default value of 15.0 angstroms"
1286	+	"\tfor the cutoffRadius.\n");
1287	+	painCave.isFatal = 0;
1288	+	simError();
1289	+	theRcut = 15.0;
1290	+	}
1291	+	else{
1292	+	theRcut = globals->getRcut();
1293	+	}
1294	+
1295	+	if (!globals->haveRsw()){
1296	+	sprintf(painCave.errMsg,
1297	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1298	+	"\tOOPSE will use a default value of\n"
1299	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1300	+	painCave.isFatal = 0;
1301	+	simError();
1302	+	theRsw = 0.95 * theRcut;
1303	+	}
1304	+	else{
1305	+	theRsw = globals->getRsw();
1306	+	}
1307	+
1308	+	info[i].setDefaultRcut(theRcut, theRsw);
1309	+
1310	+	}
1311	+	}
1312	+	}
1313	+	#ifdef IS_MPI
1314	+	strcpy(checkPointMsg, "post processing checks out");
1315	+	MPIcheckPoint();
1316	+	#endif // is_mpi
1317	+
1318	+	// clean up the forcefield
1319	+	the_ff->cleanMe();
1320	+	}
1321	+
1322	+	void SimSetup::initSystemCoords(void){
1323	+	int i;
1324	+
1325	+	char* inName;
1326	+
1327	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1328	+
1329	+	for (i = 0; i < info[0].n_atoms; i++)
1330	+	info[0].atoms[i]->setCoords();
1331	+
1332	+	if (globals->haveInitialConfig()){
1333	+	InitializeFromFile* fileInit;
1334	+	#ifdef IS_MPI // is_mpi
1335	+	if (worldRank == 0){
1336	+	#endif //is_mpi
1337	+	inName = globals->getInitialConfig();
1338	+	fileInit = new InitializeFromFile(inName);
1339	+	#ifdef IS_MPI
1340	+	}
1341	+	else
1342	+	fileInit = new InitializeFromFile(NULL);
1343	+	#endif
1344	+	fileInit->readInit(info); // default velocities on
1345	+
1346	+	delete fileInit;
1347	+	}
1348	+	else{
1349	+
1350	+	// no init from bass
1351	+
1352	+	sprintf(painCave.errMsg,
1353	+	"Cannot intialize a simulation without an initial configuration file.\n");
1354	+	painCave.isFatal = 1;;
1355	+	simError();
1356	+
1357	+	}
1358	+
1359	+	#ifdef IS_MPI
1360	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1361	+	MPIcheckPoint();
1362	+	#endif // is_mpi
1363	+	}
1364	+
1365	+
1366	+	void SimSetup::makeOutNames(void){
1367	+	int k;
1368	+
1369	+
1370	+	for (k = 0; k < nInfo; k++){
1371	+	#ifdef IS_MPI
1372	+	if (worldRank == 0){
1373	+	#endif // is_mpi
1374	+
1375	+	if (globals->haveFinalConfig()){
1376	+	strcpy(info[k].finalName, globals->getFinalConfig());
1377	+	}
1378	+	else{
1379	+	strcpy(info[k].finalName, inFileName);
1380	+	char* endTest;
1381	+	int nameLength = strlen(info[k].finalName);
1382	+	endTest = &(info[k].finalName[nameLength - 5]);
1383	+	if (!strcmp(endTest, ".bass")){
1384	+	strcpy(endTest, ".eor");
1385	+	}
1386	+	else if (!strcmp(endTest, ".BASS")){
1387	+	strcpy(endTest, ".eor");
1388	+	}
1389	+	else{
1390	+	endTest = &(info[k].finalName[nameLength - 4]);
1391	+	if (!strcmp(endTest, ".bss")){
1392	+	strcpy(endTest, ".eor");
1393	+	}
1394	+	else if (!strcmp(endTest, ".mdl")){
1395	+	strcpy(endTest, ".eor");
1396	+	}
1397	+	else{
1398	+	strcat(info[k].finalName, ".eor");
1399	+	}
1400	+	}
1401	+	}
1402	+
1403	+	// make the sample and status out names
1404	+
1405	+	strcpy(info[k].sampleName, inFileName);
1406	+	char* endTest;
1407	+	int nameLength = strlen(info[k].sampleName);
1408	+	endTest = &(info[k].sampleName[nameLength - 5]);
1409	+	if (!strcmp(endTest, ".bass")){
1410	+	strcpy(endTest, ".dump");
1411	+	}
1412	+	else if (!strcmp(endTest, ".BASS")){
1413	+	strcpy(endTest, ".dump");
1414	+	}
1415	+	else{
1416	+	endTest = &(info[k].sampleName[nameLength - 4]);
1417	+	if (!strcmp(endTest, ".bss")){
1418	+	strcpy(endTest, ".dump");
1419	+	}
1420	+	else if (!strcmp(endTest, ".mdl")){
1421	+	strcpy(endTest, ".dump");
1422	+	}
1423	+	else{
1424	+	strcat(info[k].sampleName, ".dump");
1425	+	}
1426	+	}
1427	+
1428	+	strcpy(info[k].statusName, inFileName);
1429	+	nameLength = strlen(info[k].statusName);
1430	+	endTest = &(info[k].statusName[nameLength - 5]);
1431	+	if (!strcmp(endTest, ".bass")){
1432	+	strcpy(endTest, ".stat");
1433	+	}
1434	+	else if (!strcmp(endTest, ".BASS")){
1435	+	strcpy(endTest, ".stat");
1436	+	}
1437	+	else{
1438	+	endTest = &(info[k].statusName[nameLength - 4]);
1439	+	if (!strcmp(endTest, ".bss")){
1440	+	strcpy(endTest, ".stat");
1441	+	}
1442	+	else if (!strcmp(endTest, ".mdl")){
1443	+	strcpy(endTest, ".stat");
1444	+	}
1445	+	else{
1446	+	strcat(info[k].statusName, ".stat");
1447	+	}
1448	+	}
1449	+
1450	+	strcpy(info[k].rawPotName, inFileName);
1451	+	nameLength = strlen(info[k].rawPotName);
1452	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1453	+	if (!strcmp(endTest, ".bass")){
1454	+	strcpy(endTest, ".raw");
1455	+	}
1456	+	else if (!strcmp(endTest, ".BASS")){
1457	+	strcpy(endTest, ".raw");
1458	+	}
1459	+	else{
1460	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1461	+	if (!strcmp(endTest, ".bss")){
1462	+	strcpy(endTest, ".raw");
1463	+	}
1464	+	else if (!strcmp(endTest, ".mdl")){
1465	+	strcpy(endTest, ".raw");
1466	+	}
1467	+	else{
1468	+	strcat(info[k].rawPotName, ".raw");
1469	+	}
1470	+	}
1471	+
1472	+	#ifdef IS_MPI
1473	+
1474	+	}
1475	+	#endif // is_mpi
1476	+	}
1477	+	}
1478	+
1479	+
1480	+	void SimSetup::sysObjectsCreation(void){
1481	+	int i, k;
1482	+
1483	+	// create the forceField
1484	+
1485	+	createFF();
1486	+
1487	+	// extract componentList
1488	+
1489	+	compList();
1490	+
1491	+	// calc the number of atoms, bond, bends, and torsions
1492	+
1493	+	calcSysValues();
1494	+
1495	+	#ifdef IS_MPI
1496	+	// divide the molecules among the processors
1497	+
1498	+	mpiMolDivide();
1499	+	#endif //is_mpi
1500	+
1501	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1502	+
1503	+	makeSysArrays();
1504	+
1505	+	// make and initialize the molecules (all but atomic coordinates)
1506	+
1507	+	makeMolecules();
1508	+
1509	+	for (k = 0; k < nInfo; k++){
1510	+	info[k].identArray = new int[info[k].n_atoms];
1511	+	for (i = 0; i < info[k].n_atoms; i++){
1512	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1513	+	}
1514	+	}
1515	+	}
1516	+
1517	+
1518	+	void SimSetup::createFF(void){
1519	+	switch (ffCase){
1520	+	case FF_DUFF:
1521	+	the_ff = new DUFF();
1522	+	break;
1523	+
1524	+	case FF_LJ:
1525	+	the_ff = new LJFF();
1526	+	break;
1527	+
1528	+	case FF_EAM:
1529	+	if (has_forcefield_variant)
1530	+	the_ff = new EAM_FF(forcefield_variant);
1531	+	else
1532	+	the_ff = new EAM_FF();
1533	+	break;
1534	+
1535	+	case FF_H2O:
1536	+	the_ff = new WATER();
1537	+	break;
1538	+
1539	+	default:
1540	+	sprintf(painCave.errMsg,
1541	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1542	+	painCave.isFatal = 1;
1543	+	simError();
1544	+	}
1545	+
1546	+
1547	+	#ifdef IS_MPI
1548	+	strcpy(checkPointMsg, "ForceField creation successful");
1549	+	MPIcheckPoint();
1550	+	#endif // is_mpi
1551	+	}
1552	+
1553	+
1554	+	void SimSetup::compList(void){
1555	+	int i;
1556	+	char* id;
1557	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1558	+	LinkedMolStamp* currentStamp = NULL;
1559	+	comp_stamps = new MoleculeStamp * [n_components];
1560	+	bool haveCutoffGroups;
1561	+
1562	+	haveCutoffGroups = false;
1563	+
1564	+	// make an array of molecule stamps that match the components used.
1565	+	// also extract the used stamps out into a separate linked list
1566	+
1567	+	for (i = 0; i < nInfo; i++){
1568	+	info[i].nComponents = n_components;
1569	+	info[i].componentsNmol = components_nmol;
1570	+	info[i].compStamps = comp_stamps;
1571	+	info[i].headStamp = headStamp;
1572	+	}
1573	+
1574	+
1575	+	for (i = 0; i < n_components; i++){
1576	+	id = the_components[i]->getType();
1577	+	comp_stamps[i] = NULL;
1578	+
1579	+	// check to make sure the component isn't already in the list
1580	+
1581	+	comp_stamps[i] = headStamp->match(id);
1582	+	if (comp_stamps[i] == NULL){
1583	+	// extract the component from the list;
1584	+
1585	+	currentStamp = stamps->extractMolStamp(id);
1586	+	if (currentStamp == NULL){
1587	+	sprintf(painCave.errMsg,
1588	+	"SimSetup error: Component \"%s\" was not found in the "
1589	+	"list of declared molecules\n",
1590	+	id);
1591	+	painCave.isFatal = 1;
1592	+	simError();
1593	+	}
1594	+
1595	+	headStamp->add(currentStamp);
1596	+	comp_stamps[i] = headStamp->match(id);
1597	+	}
1598	+
1599	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1600	+	haveCutoffGroups = true;
1601	+	}
1602	+
1603	+	for (i = 0; i < nInfo; i++)
1604	+	info[i].haveCutoffGroups = haveCutoffGroups;
1605	+
1606	+	#ifdef IS_MPI
1607	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1608	+	MPIcheckPoint();
1609	+	#endif // is_mpi
1610	+	}
1611	+
1612	+	void SimSetup::calcSysValues(void){
1613	+	int i, j;
1614	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1615	+
1616	+	int* molMembershipArray;
1617	+	CutoffGroupStamp* cg;
1618	+
1619	+	tot_atoms = 0;
1620	+	tot_bonds = 0;
1621	+	tot_bends = 0;
1622	+	tot_torsions = 0;
1623	+	tot_rigid = 0;
1624	+	tot_groups = 0;
1625	+	for (i = 0; i < n_components; i++){
1626	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1627	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1628	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1629	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1630	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1631	+
1632	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1633	+	atomsingroups = 0;
1634	+	for (j=0; j < ncutgroups; j++) {
1635	+	cg = comp_stamps[i]->getCutoffGroup(j);
1636	+	atomsingroups += cg->getNMembers();
1637	+	}
1638	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1639	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1640	+	}
1641	+
1642	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1643	+	molMembershipArray = new int[tot_atoms];
1644	+
1645	+	for (i = 0; i < nInfo; i++){
1646	+	info[i].n_atoms = tot_atoms;
1647	+	info[i].n_bonds = tot_bonds;
1648	+	info[i].n_bends = tot_bends;
1649	+	info[i].n_torsions = tot_torsions;
1650	+	info[i].n_SRI = tot_SRI;
1651	+	info[i].n_mol = tot_nmol;
1652	+	info[i].ngroup = tot_groups;
1653	+	info[i].molMembershipArray = molMembershipArray;
1654	+	}
1655	+	}
1656	+
1657	+	#ifdef IS_MPI
1658	+
1659	+	void SimSetup::mpiMolDivide(void){
1660	+	int i, j, k;
1661	+	int localMol, allMol;
1662	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1663	+	int local_rigid, local_groups;
1664	+	vector<int> globalMolIndex;
1665	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1666	+	CutoffGroupStamp* cg;
1667	+
1668	+	mpiSim = new mpiSimulation(info);
1669	+
1670	+	mpiSim->divideLabor();
1671	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1672	+	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1673	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1674	+
1675	+	// set up the local variables
1676	+
1677	+	mol2proc = mpiSim->getMolToProcMap();
1678	+	molCompType = mpiSim->getMolComponentType();
1679	+
1680	+	allMol = 0;
1681	+	localMol = 0;
1682	+	local_atoms = 0;
1683	+	local_bonds = 0;
1684	+	local_bends = 0;
1685	+	local_torsions = 0;
1686	+	local_rigid = 0;
1687	+	local_groups = 0;
1688	+	globalAtomCounter = 0;
1689	+
1690	+	for (i = 0; i < n_components; i++){
1691	+	for (j = 0; j < components_nmol[i]; j++){
1692	+	if (mol2proc[allMol] == worldRank){
1693	+	local_atoms += comp_stamps[i]->getNAtoms();
1694	+	local_bonds += comp_stamps[i]->getNBonds();
1695	+	local_bends += comp_stamps[i]->getNBends();
1696	+	local_torsions += comp_stamps[i]->getNTorsions();
1697	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1698	+
1699	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1700	+	atomsingroups = 0;
1701	+	for (k=0; k < ncutgroups; k++) {
1702	+	cg = comp_stamps[i]->getCutoffGroup(k);
1703	+	atomsingroups += cg->getNMembers();
1704	+	}
1705	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1706	+	ncutgroups;
1707	+	local_groups += ngroupsinstamp;
1708	+
1709	+	localMol++;
1710	+	}
1711	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1712	+	info[0].molMembershipArray[globalAtomCounter] = allMol;
1713	+	globalAtomCounter++;
1714	+	}
1715	+
1716	+	allMol++;
1717	+	}
1718	+	}
1719	+	local_SRI = local_bonds + local_bends + local_torsions;
1720	+
1721	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1722	+
1723	+	if (local_atoms != info[0].n_atoms){
1724	+	sprintf(painCave.errMsg,
1725	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1726	+	"\tlocalAtom (%d) are not equal.\n",
1727	+	info[0].n_atoms, local_atoms);
1728	+	painCave.isFatal = 1;
1729	+	simError();
1730	+	}
1731	+
1732	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1733	+	if (local_groups != info[0].ngroup){
1734	+	sprintf(painCave.errMsg,
1735	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1736	+	"\tlocalGroups (%d) are not equal.\n",
1737	+	info[0].ngroup, local_groups);
1738	+	painCave.isFatal = 1;
1739	+	simError();
1740	+	}
1741	+
1742	+	info[0].n_bonds = local_bonds;
1743	+	info[0].n_bends = local_bends;
1744	+	info[0].n_torsions = local_torsions;
1745	+	info[0].n_SRI = local_SRI;
1746	+	info[0].n_mol = localMol;
1747	+
1748	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1749	+	MPIcheckPoint();
1750	+	}
1751	+
1752	+	#endif // is_mpi
1753	+
1754	+
1755	+	void SimSetup::makeSysArrays(void){
1756	+
1757	+	#ifndef IS_MPI
1758	+	int k, j;
1759	+	#endif // is_mpi
1760	+	int i, l;
1761	+
1762	+	Atom** the_atoms;
1763	+	Molecule* the_molecules;
1764	+
1765	+	for (l = 0; l < nInfo; l++){
1766	+	// create the atom and short range interaction arrays
1767	+
1768	+	the_atoms = new Atom * [info[l].n_atoms];
1769	+	the_molecules = new Molecule[info[l].n_mol];
1770	+	int molIndex;
1771	+
1772	+	// initialize the molecule's stampID's
1773	+
1774	+	#ifdef IS_MPI
1775	+
1776	+
1777	+	molIndex = 0;
1778	+	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1779	+	if (mol2proc[i] == worldRank){
1780	+	the_molecules[molIndex].setStampID(molCompType[i]);
1781	+	the_molecules[molIndex].setMyIndex(molIndex);
1782	+	the_molecules[molIndex].setGlobalIndex(i);
1783	+	molIndex++;
1784	+	}
1785	+	}
1786	+
1787	+	#else // is_mpi
1788	+
1789	+	molIndex = 0;
1790	+	globalAtomCounter = 0;
1791	+	for (i = 0; i < n_components; i++){
1792	+	for (j = 0; j < components_nmol[i]; j++){
1793	+	the_molecules[molIndex].setStampID(i);
1794	+	the_molecules[molIndex].setMyIndex(molIndex);
1795	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1796	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1797	+	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1798	+	globalAtomCounter++;
1799	+	}
1800	+	molIndex++;
1801	+	}
1802	+	}
1803	+
1804	+
1805	+	#endif // is_mpi
1806	+
1807	+	info[l].globalExcludes = new int;
1808	+	info[l].globalExcludes[0] = 0;
1809	+
1810	+	// set the arrays into the SimInfo object
1811	+
1812	+	info[l].atoms = the_atoms;
1813	+	info[l].molecules = the_molecules;
1814	+	info[l].nGlobalExcludes = 0;
1815	+
1816	+	the_ff->setSimInfo(info);
1817		}
1818		}
1819	+
1820	+	void SimSetup::makeIntegrator(void){
1821	+	int k;
1822	+
1823	+	NVE<Integrator<BaseIntegrator> >* myNVE = NULL;
1824	+	NVT<Integrator<BaseIntegrator> >* myNVT = NULL;
1825	+	NPTi<NPT<Integrator<BaseIntegrator> > >* myNPTi = NULL;
1826	+	NPTf<NPT<Integrator<BaseIntegrator> > >* myNPTf = NULL;
1827	+	NPTxyz<NPT<Integrator<BaseIntegrator> > >* myNPTxyz = NULL;
1828	+
1829	+	for (k = 0; k < nInfo; k++){
1830	+	switch (ensembleCase){
1831	+	case NVE_ENS:
1832	+	if (globals->haveZconstraints()){
1833	+	setupZConstraint(info[k]);
1834	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1835	+	}
1836	+	else{
1837	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1838	+	}
1839	+
1840	+	info->the_integrator = myNVE;
1841	+	break;
1842	+
1843	+	case NVT_ENS:
1844	+	if (globals->haveZconstraints()){
1845	+	setupZConstraint(info[k]);
1846	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1847	+	}
1848	+	else
1849	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1850	+
1851	+	myNVT->setTargetTemp(globals->getTargetTemp());
1852	+
1853	+	if (globals->haveTauThermostat())
1854	+	myNVT->setTauThermostat(globals->getTauThermostat());
1855	+	else{
1856	+	sprintf(painCave.errMsg,
1857	+	"SimSetup error: If you use the NVT\n"
1858	+	"\tensemble, you must set tauThermostat.\n");
1859	+	painCave.isFatal = 1;
1860	+	simError();
1861	+	}
1862	+
1863	+	info->the_integrator = myNVT;
1864	+	break;
1865	+
1866	+	case NPTi_ENS:
1867	+	if (globals->haveZconstraints()){
1868	+	setupZConstraint(info[k]);
1869	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1870	+	}
1871	+	else
1872	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1873	+
1874	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1875	+
1876	+	if (globals->haveTargetPressure())
1877	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1878	+	else{
1879	+	sprintf(painCave.errMsg,
1880	+	"SimSetup error: If you use a constant pressure\n"
1881	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1882	+	painCave.isFatal = 1;
1883	+	simError();
1884	+	}
1885	+
1886	+	if (globals->haveTauThermostat())
1887	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1888	+	else{
1889	+	sprintf(painCave.errMsg,
1890	+	"SimSetup error: If you use an NPT\n"
1891	+	"\tensemble, you must set tauThermostat.\n");
1892	+	painCave.isFatal = 1;
1893	+	simError();
1894	+	}
1895	+
1896	+	if (globals->haveTauBarostat())
1897	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1898	+	else{
1899	+	sprintf(painCave.errMsg,
1900	+	"SimSetup error: If you use an NPT\n"
1901	+	"\tensemble, you must set tauBarostat.\n");
1902	+	painCave.isFatal = 1;
1903	+	simError();
1904	+	}
1905	+
1906	+	info->the_integrator = myNPTi;
1907	+	break;
1908	+
1909	+	case NPTf_ENS:
1910	+	if (globals->haveZconstraints()){
1911	+	setupZConstraint(info[k]);
1912	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1913	+	}
1914	+	else
1915	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1916	+
1917	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1918	+
1919	+	if (globals->haveTargetPressure())
1920	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1921	+	else{
1922	+	sprintf(painCave.errMsg,
1923	+	"SimSetup error: If you use a constant pressure\n"
1924	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1925	+	painCave.isFatal = 1;
1926	+	simError();
1927	+	}
1928	+
1929	+	if (globals->haveTauThermostat())
1930	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1931	+
1932	+	else{
1933	+	sprintf(painCave.errMsg,
1934	+	"SimSetup error: If you use an NPT\n"
1935	+	"\tensemble, you must set tauThermostat.\n");
1936	+	painCave.isFatal = 1;
1937	+	simError();
1938	+	}
1939	+
1940	+	if (globals->haveTauBarostat())
1941	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1942	+
1943	+	else{
1944	+	sprintf(painCave.errMsg,
1945	+	"SimSetup error: If you use an NPT\n"
1946	+	"\tensemble, you must set tauBarostat.\n");
1947	+	painCave.isFatal = 1;
1948	+	simError();
1949	+	}
1950	+
1951	+	info->the_integrator = myNPTf;
1952	+	break;
1953	+
1954	+	case NPTxyz_ENS:
1955	+	if (globals->haveZconstraints()){
1956	+	setupZConstraint(info[k]);
1957	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1958	+	}
1959	+	else
1960	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1961	+
1962	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1963	+
1964	+	if (globals->haveTargetPressure())
1965	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1966	+	else{
1967	+	sprintf(painCave.errMsg,
1968	+	"SimSetup error: If you use a constant pressure\n"
1969	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1970	+	painCave.isFatal = 1;
1971	+	simError();
1972	+	}
1973	+
1974	+	if (globals->haveTauThermostat())
1975	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1976	+	else{
1977	+	sprintf(painCave.errMsg,
1978	+	"SimSetup error: If you use an NPT\n"
1979	+	"\tensemble, you must set tauThermostat.\n");
1980	+	painCave.isFatal = 1;
1981	+	simError();
1982	+	}
1983	+
1984	+	if (globals->haveTauBarostat())
1985	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1986	+	else{
1987	+	sprintf(painCave.errMsg,
1988	+	"SimSetup error: If you use an NPT\n"
1989	+	"\tensemble, you must set tauBarostat.\n");
1990	+	painCave.isFatal = 1;
1991	+	simError();
1992	+	}
1993	+
1994	+	info->the_integrator = myNPTxyz;
1995	+	break;
1996	+
1997	+	default:
1998	+	sprintf(painCave.errMsg,
1999	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
2000	+	painCave.isFatal = 1;
2001	+	simError();
2002	+	}
2003	+	}
2004	+	}
2005	+
2006	+	void SimSetup::initFortran(void){
2007	+	info[0].refreshSim();
2008	+
2009	+	if (!strcmp(info[0].mixingRule, "standard")){
2010	+	the_ff->initForceField(LB_MIXING_RULE);
2011	+	}
2012	+	else if (!strcmp(info[0].mixingRule, "explicit")){
2013	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
2014	+	}
2015	+	else{
2016	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
2017	+	info[0].mixingRule);
2018	+	painCave.isFatal = 1;
2019	+	simError();
2020	+	}
2021	+
2022	+
2023	+	#ifdef IS_MPI
2024	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2025	+	MPIcheckPoint();
2026	+	#endif // is_mpi
2027	+	}
2028	+
2029	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
2030	+	int nZConstraints;
2031	+	ZconStamp** zconStamp;
2032	+
2033	+	if (globals->haveZconstraintTime()){
2034	+	//add sample time of z-constraint  into SimInfo's property list
2035	+	DoubleData* zconsTimeProp = new DoubleData();
2036	+	zconsTimeProp->setID(ZCONSTIME_ID);
2037	+	zconsTimeProp->setData(globals->getZconsTime());
2038	+	theInfo.addProperty(zconsTimeProp);
2039	+	}
2040	+	else{
2041	+	sprintf(painCave.errMsg,
2042	+	"ZConstraint error: If you use a ZConstraint,\n"
2043	+	"\tyou must set zconsTime.\n");
2044	+	painCave.isFatal = 1;
2045	+	simError();
2046	+	}
2047	+
2048	+	//push zconsTol into siminfo, if user does not specify
2049	+	//value for zconsTol, a default value will be used
2050	+	DoubleData* zconsTol = new DoubleData();
2051	+	zconsTol->setID(ZCONSTOL_ID);
2052	+	if (globals->haveZconsTol()){
2053	+	zconsTol->setData(globals->getZconsTol());
2054	+	}
2055	+	else{
2056	+	double defaultZConsTol = 0.01;
2057	+	sprintf(painCave.errMsg,
2058	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2059	+	"\tOOPSE will use a default value of %f.\n"
2060	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2061	+	defaultZConsTol);
2062	+	painCave.isFatal = 0;
2063	+	simError();
2064	+
2065	+	zconsTol->setData(defaultZConsTol);
2066	+	}
2067	+	theInfo.addProperty(zconsTol);
2068	+
2069	+	//set Force Subtraction Policy
2070	+	StringData* zconsForcePolicy = new StringData();
2071	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2072	+
2073	+	if (globals->haveZconsForcePolicy()){
2074	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2075	+	}
2076	+	else{
2077	+	sprintf(painCave.errMsg,
2078	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2079	+	"\tOOPSE will use PolicyByMass.\n"
2080	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2081	+	painCave.isFatal = 0;
2082	+	simError();
2083	+	zconsForcePolicy->setData("BYMASS");
2084	+	}
2085	+
2086	+	theInfo.addProperty(zconsForcePolicy);
2087	+
2088	+	//set zcons gap
2089	+	DoubleData* zconsGap = new DoubleData();
2090	+	zconsGap->setID(ZCONSGAP_ID);
2091	+
2092	+	if (globals->haveZConsGap()){
2093	+	zconsGap->setData(globals->getZconsGap());
2094	+	theInfo.addProperty(zconsGap);
2095	+	}
2096	+
2097	+	//set zcons fixtime
2098	+	DoubleData* zconsFixtime = new DoubleData();
2099	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2100	+
2101	+	if (globals->haveZConsFixTime()){
2102	+	zconsFixtime->setData(globals->getZconsFixtime());
2103	+	theInfo.addProperty(zconsFixtime);
2104	+	}
2105	+
2106	+	//set zconsUsingSMD
2107	+	IntData* zconsUsingSMD = new IntData();
2108	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2109	+
2110	+	if (globals->haveZConsUsingSMD()){
2111	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2112	+	theInfo.addProperty(zconsUsingSMD);
2113	+	}
2114	+
2115	+	//Determine the name of ouput file and add it into SimInfo's property list
2116	+	//Be careful, do not use inFileName, since it is a pointer which
2117	+	//point to a string at master node, and slave nodes do not contain that string
2118	+
2119	+	string zconsOutput(theInfo.finalName);
2120	+
2121	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2122	+
2123	+	StringData* zconsFilename = new StringData();
2124	+	zconsFilename->setID(ZCONSFILENAME_ID);
2125	+	zconsFilename->setData(zconsOutput);
2126	+
2127	+	theInfo.addProperty(zconsFilename);
2128	+
2129	+	//setup index, pos and other parameters of z-constraint molecules
2130	+	nZConstraints = globals->getNzConstraints();
2131	+	theInfo.nZconstraints = nZConstraints;
2132	+
2133	+	zconStamp = globals->getZconStamp();
2134	+	ZConsParaItem tempParaItem;
2135	+
2136	+	ZConsParaData* zconsParaData = new ZConsParaData();
2137	+	zconsParaData->setID(ZCONSPARADATA_ID);
2138	+
2139	+	for (int i = 0; i < nZConstraints; i++){
2140	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2141	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2142	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2143	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2144	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2145	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2146	+	zconsParaData->addItem(tempParaItem);
2147	+	}
2148	+
2149	+	//check the uniqueness of index
2150	+	if(!zconsParaData->isIndexUnique()){
2151	+	sprintf(painCave.errMsg,
2152	+	"ZConstraint Error: molIndex is not unique!\n");
2153	+	painCave.isFatal = 1;
2154	+	simError();
2155	+	}
2156	+
2157	+	//sort the parameters by index of molecules
2158	+	zconsParaData->sortByIndex();
2159	+
2160	+	//push data into siminfo, therefore, we can retrieve later
2161	+	theInfo.addProperty(zconsParaData);
2162	+	}
2163	+
2164	+	void SimSetup::makeMinimizer(){
2165	+
2166	+	OOPSEMinimizer* myOOPSEMinimizer;
2167	+	MinimizerParameterSet* param;
2168	+	char minimizerName[100];
2169	+
2170	+	for (int i = 0; i < nInfo; i++){
2171	+
2172	+	//prepare parameter set for minimizer
2173	+	param = new MinimizerParameterSet();
2174	+	param->setDefaultParameter();
2175	+
2176	+	if (globals->haveMinimizer()){
2177	+	param->setFTol(globals->getMinFTol());
2178	+	}
2179	+
2180	+	if (globals->haveMinGTol()){
2181	+	param->setGTol(globals->getMinGTol());
2182	+	}
2183	+
2184	+	if (globals->haveMinMaxIter()){
2185	+	param->setMaxIteration(globals->getMinMaxIter());
2186	+	}
2187	+
2188	+	if (globals->haveMinWriteFrq()){
2189	+	param->setMaxIteration(globals->getMinMaxIter());
2190	+	}
2191	+
2192	+	if (globals->haveMinWriteFrq()){
2193	+	param->setWriteFrq(globals->getMinWriteFrq());
2194	+	}
2195	+
2196	+	if (globals->haveMinStepSize()){
2197	+	param->setStepSize(globals->getMinStepSize());
2198	+	}
2199	+
2200	+	if (globals->haveMinLSMaxIter()){
2201	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2202	+	}
2203	+
2204	+	if (globals->haveMinLSTol()){
2205	+	param->setLineSearchTol(globals->getMinLSTol());
2206	+	}
2207	+
2208	+	strcpy(minimizerName, globals->getMinimizer());
2209	+
2210	+	if (!strcasecmp(minimizerName, "CG")){
2211	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2212	+	}
2213	+	else if (!strcasecmp(minimizerName, "SD")){
2214	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2215	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2216	+	}
2217	+	else{
2218	+	sprintf(painCave.errMsg,
2219	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2220	+	painCave.isFatal = 0;
2221	+	simError();
2222	+
2223	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2224	+	}
2225	+	info[i].the_integrator = myOOPSEMinimizer;
2226	+
2227	+	//store the minimizer into simInfo
2228	+	info[i].the_minimizer = myOOPSEMinimizer;
2229	+	info[i].has_minimizer = true;
2230	+	}
2231	+
2232	+	}

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