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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 1229 by gezelter, Thu Jun 3 20:02:25 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	#include "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
19		#include "mpiSimulation.hpp"
20		#endif
21
22	+	// some defines for ensemble and Forcefield  cases
23	+
24	+	#define NVE_ENS        0
25	+	#define NVT_ENS        1
26	+	#define NPTi_ENS       2
27	+	#define NPTf_ENS       3
28	+	#define NPTxyz_ENS     4
29	+
30	+
31	+	#define FF_DUFF  0
32	+	#define FF_LJ    1
33	+	#define FF_EAM   2
34	+	#define FF_H2O   3
35	+
36	+	using namespace std;
37	+
38	+	/**
39	+	* Check whether dividend is divisble by divisor or not
40	+	*/
41	+	bool isDivisible(double dividend, double divisor){
42	+	double tolerance = 0.000001;
43	+	double quotient;
44	+	double diff;
45	+	int intQuotient;
46	+
47	+	quotient = dividend / divisor;
48	+
49	+	if (quotient < 0)
50	+	quotient = -quotient;
51	+
52	+	intQuotient = int (quotient + tolerance);
53	+
54	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
55	+
56	+	if (diff <= tolerance)
57	+	return true;
58	+	else
59	+	return false;
60	+	}
61	+
62		SimSetup::SimSetup(){
63	+
64	+	initSuspend = false;
65	+	isInfoArray = 0;
66	+	nInfo = 1;
67	+
68		stamps = new MakeStamps();
69		globals = new Globals();
70	<
70	>
71	>
72		#ifdef IS_MPI
73	<	strcpy( checkPointMsg, "SimSetup creation successful" );
73	>	strcpy(checkPointMsg, "SimSetup creation successful");
74		MPIcheckPoint();
75		#endif // IS_MPI
76		}
#	Line 27 | Line 80 | SimSetup::~SimSetup(){
80		delete globals;
81		}
82
83	<	void SimSetup::parseFile( char* fileName ){
83	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
84	>	info = the_info;
85	>	nInfo = theNinfo;
86	>	isInfoArray = 1;
87	>	initSuspend = true;
88	>	}
89
90	+
91	+	void SimSetup::parseFile(char* fileName){
92		#ifdef IS_MPI
93	<	if( worldRank == 0 ){
93	>	if (worldRank == 0){
94		#endif // is_mpi
95	<
95	>
96		inFileName = fileName;
97	<	set_interface_stamps( stamps, globals );
98	<
97	>	set_interface_stamps(stamps, globals);
98	>
99		#ifdef IS_MPI
100		mpiEventInit();
101		#endif
102
103	<	yacc_BASS( fileName );
103	>	yacc_BASS(fileName);
104
105		#ifdef IS_MPI
106		throwMPIEvent(NULL);
107		}
108	<	else receiveParse();
108	>	else{
109	>	receiveParse();
110	>	}
111		#endif
112
113		}
114
115		#ifdef IS_MPI
116		void SimSetup::receiveParse(void){
117	<
118	<	set_interface_stamps( stamps, globals );
119	<	mpiEventInit();
120	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
117	>	set_interface_stamps(stamps, globals);
118	>	mpiEventInit();
119	>	MPIcheckPoint();
120	>	mpiEventLoop();
121		}
122
123		#endif // is_mpi
124
125	<	void SimSetup::createSim( void ){
125	>	void SimSetup::createSim(void){
126
127	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
127	>	// gather all of the information from the Bass file
128
129	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
129	>	gatherInfo();
130
131	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
131	>	// creation of complex system objects
132
133	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
133	>	sysObjectsCreation();
134
135	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
135	>	// check on the post processing info
136
137	+	finalInfoCheck();
138
139	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
139	>	// initialize the system coordinates
140
141	<	#ifdef IS_MPI
142	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
141	>	if ( !initSuspend ){
142	>	initSystemCoords();
143
144	<
144	>	if( !(globals->getUseInitTime()) )
145	>	info[0].currentTime = 0.0;
146	>	}
147
148	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
148	>	// make the output filenames
149
150	<	if( !the_globals->haveNMol() ){
151	<	// we don't have the total number of molecules, so we assume it is
152	<	// given in each component
150	>	makeOutNames();
151	>
152	>	#ifdef IS_MPI
153	>	mpiSim->mpiRefresh();
154	>	#endif
155
156	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
156	>	// initialize the Fortran
157
158	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
158	>	initFortran();
159
160	<	tot_nmol += the_components[i]->getNMol();
161	<	components_nmol[i] = the_components[i]->getNMol();
162	<	}
163	<	}
164	<	else{
165	<	sprintf( painCave.errMsg,
137	<	"SimSetup error.\n"
138	<	"\tSorry, the ability to specify total"
139	<	" nMols and then give molfractions in the components\n"
140	<	"\tis not currently supported."
141	<	" Please give nMol in the components.\n" );
142	<	painCave.isFatal = 1;
143	<	simError();
144	<
145	<
146	<	//     tot_nmol = the_globals->getNMol();
147	<
148	<	//   //we have the total number of molecules, now we check for molfractions
149	<	//     for( i=0; i<n_components; i++ ){
150	<
151	<	//       if( !the_components[i]->haveMolFraction() ){
152	<
153	<	//  if( !the_components[i]->haveNMol() ){
154	<	//    //we have a problem
155	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	<	//              << " nMol was given in component
157	<
158	<	}
160	>	if (globals->haveMinimizer())
161	>	// make minimizer
162	>	makeMinimizer();
163	>	else
164	>	// make the integrator
165	>	makeIntegrator();
166
167	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
167	>	}
168
165	–	// make an array of molecule stamps that match the components used.
166	–	// also extract the used stamps out into a separate linked list
169
170	<	simnfo->nComponents = n_components;
171	<	simnfo->componentsNmol = components_nmol;
172	<	simnfo->compStamps = comp_stamps;
173	<	simnfo->headStamp = new LinkedMolStamp();
174	<
175	<	char* id;
176	<	LinkedMolStamp* headStamp = simnfo->headStamp;
177	<	LinkedMolStamp* currentStamp = NULL;
178	<	for( i=0; i<n_components; i++ ){
170	>	void SimSetup::makeMolecules(void){
171	>	int i, j, k;
172	>	int exI, exJ, exK, exL, slI, slJ;
173	>	int tempI, tempJ, tempK, tempL;
174	>	int molI, globalID;
175	>	int stampID, atomOffset, rbOffset, groupOffset;
176	>	molInit molInfo;
177	>	DirectionalAtom* dAtom;
178	>	RigidBody* myRB;
179	>	StuntDouble* mySD;
180	>	LinkedAssign* extras;
181	>	LinkedAssign* current_extra;
182	>	AtomStamp* currentAtom;
183	>	BondStamp* currentBond;
184	>	BendStamp* currentBend;
185	>	TorsionStamp* currentTorsion;
186	>	RigidBodyStamp* currentRigidBody;
187	>	CutoffGroupStamp* currentCutoffGroup;
188	>	CutoffGroup* myCutoffGroup;
189	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
190	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
191
192	<	id = the_components[i]->getType();
193	<	comp_stamps[i] = NULL;
194	<
181	<	// check to make sure the component isn't already in the list
192	>	bond_pair* theBonds;
193	>	bend_set* theBends;
194	>	torsion_set* theTorsions;
195
196	<	comp_stamps[i] = headStamp->match( id );
184	<	if( comp_stamps[i] == NULL ){
185	<
186	<	// extract the component from the list;
187	<
188	<	currentStamp = the_stamps->extractMolStamp( id );
189	<	if( currentStamp == NULL ){
190	<	sprintf( painCave.errMsg,
191	<	"SimSetup error: Component \"%s\" was not found in the "
192	<	"list of declared molecules\n",
193	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
196	>	set<int> skipList;
197
198	<	#ifdef IS_MPI
199	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
200	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
198	>	double phi, theta, psi;
199	>	char* molName;
200	>	char rbName[100];
201
202	+	//ConstraintPair* consPair; //constraint pair
203	+	//ConstraintElement* consElement1;  //first element of constraint pair
204	+	//ConstraintElement* consElement2;  //second element of constraint pair
205	+	//int whichRigidBody;
206	+	//int consAtomIndex;  //index of constraint atom in rigid body's atom array
207	+	//vector<pair<int, int> > jointAtoms;
208	+	//init the forceField paramters
209
210	+	the_ff->readParams();
211
212	<	// caclulate the number of atoms, bonds, bends and torsions
212	>	// init the atoms
213
214	<	tot_atoms = 0;
214	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
218	<
219	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
214	>	int nMembers, nNew, rb1, rb2;
215
216	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
216	>	for (k = 0; k < nInfo; k++){
217	>	the_ff->setSimInfo(&(info[k]));
218
227	–	simnfo->n_atoms = tot_atoms;
228	–	simnfo->n_bonds = tot_bonds;
229	–	simnfo->n_bends = tot_bends;
230	–	simnfo->n_torsions = tot_torsions;
231	–	simnfo->n_SRI = tot_SRI;
232	–	simnfo->n_mol = tot_nmol;
233	–
234	–
219		#ifdef IS_MPI
220	+	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
221	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
222	+	info[k].globalGroupMembership[i] = 0;
223	+	#else
224	+	info[k].globalGroupMembership = new int[info[k].n_atoms];
225	+	for (i = 0; i < info[k].n_atoms; i++)
226	+	info[k].globalGroupMembership[i] = 0;
227	+	#endif
228
229	<	// divide the molecules among processors here.
230	<
239	<	mpiSim = new mpiSimulation( simnfo );
240	<
241	<
229	>	atomOffset = 0;
230	>	groupOffset = 0;
231
232	<	globalIndex = mpiSim->divideLabor();
232	>	for (i = 0; i < info[k].n_mol; i++){
233	>	stampID = info[k].molecules[i].getStampID();
234	>	molName = comp_stamps[stampID]->getID();
235
236	+	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
237	+	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
238	+	molInfo.nBends = comp_stamps[stampID]->getNBends();
239	+	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
240	+	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
241
242	<
247	<	// set up the local variables
248	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
259	<
260	<	for( j=0; j<components_nmol[i]; j++ ){
242	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
243
244	<	if( mpiSim->getMyMolStart() <= allMol &&
263	<	allMol <= mpiSim->getMyMolEnd() ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
244	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
245
246	<	simnfo->n_atoms = mpiSim->getMyNlocal();
247	<
248	<	if( local_atoms != simnfo->n_atoms ){
249	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
246	>	if (molInfo.nBonds > 0)
247	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
248	>	else
249	>	molInfo.myBonds = NULL;
250
251	<	simnfo->n_bonds = local_bonds;
252	<	simnfo->n_bends = local_bends;
253	<	simnfo->n_torsions = local_torsions;
254	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
251	>	if (molInfo.nBends > 0)
252	>	molInfo.myBends = new Bend*[molInfo.nBends];
253	>	else
254	>	molInfo.myBends = NULL;
255
256	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
257	<	MPIcheckPoint();
258	<
259	<
299	<	#endif // is_mpi
300	<
256	>	if (molInfo.nTorsions > 0)
257	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
258	>	else
259	>	molInfo.myTorsions = NULL;
260
261	<	// create the atom and short range interaction arrays
261	>	theBonds = new bond_pair[molInfo.nBonds];
262	>	theBends = new bend_set[molInfo.nBends];
263	>	theTorsions = new torsion_set[molInfo.nTorsions];
264	>
265	>	// make the Atoms
266
267	<	Atom::createArrays(simnfo->n_atoms);
268	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
267	>	for (j = 0; j < molInfo.nAtoms; j++){
268	>	currentAtom = comp_stamps[stampID]->getAtom(j);
269
270	+	if (currentAtom->haveOrientation()){
271	+	dAtom = new DirectionalAtom((j + atomOffset),
272	+	info[k].getConfiguration());
273	+	info[k].n_oriented++;
274	+	molInfo.myAtoms[j] = dAtom;
275
276	<	if( simnfo->n_SRI ){
277	<	the_sris = new SRI*[simnfo->n_SRI];
278	<	the_excludes = new int[2 * simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
276	>	// Directional Atoms have standard unit vectors which are oriented
277	>	// in space using the three Euler angles.  We assume the standard
278	>	// unit vector was originally along the z axis below.
279
280	<	simnfo->n_exclude = 1;
281	<	}
280	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
281	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
282	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
283
284	<	// set the arrays into the SimInfo object
284	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
285	>
286	>	}
287	>	else{
288
289	<	simnfo->atoms = the_atoms;
329	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
289	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
290
291	+	}
292
293	<	// get some of the tricky things that may still be in the globals
335	<
336	<	if( simnfo->n_dipoles ){
337	<
338	<	if( !the_globals->haveRRF() ){
339	<	sprintf( painCave.errMsg,
340	<	"SimSetup Error, system has dipoles, but no rRF was set.\n");
341	<	painCave.isFatal = 1;
342	<	simError();
343	<	}
344	<	if( !the_globals->haveDielectric() ){
345	<	sprintf( painCave.errMsg,
346	<	"SimSetup Error, system has dipoles, but no"
347	<	" dielectric was set.\n" );
348	<	painCave.isFatal = 1;
349	<	simError();
350	<	}
351	<
352	<	simnfo->rRF        = the_globals->getRRF();
353	<	simnfo->dielectric = the_globals->getDielectric();
354	<	}
355	<
293	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
294		#ifdef IS_MPI
295	<	strcpy( checkPointMsg, "rRf and dielectric check out" );
358	<	MPIcheckPoint();
295	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
296		#endif // is_mpi
297	<
361	<	if( the_globals->haveBox() ){
362	<	simnfo->box_x = the_globals->getBox();
363	<	simnfo->box_y = the_globals->getBox();
364	<	simnfo->box_z = the_globals->getBox();
365	<	}
366	<	else if( the_globals->haveDensity() ){
297	>	}
298
299	<	double vol;
300	<	vol = (double)tot_nmol / the_globals->getDensity();
301	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
302	<	simnfo->box_y = simnfo->box_x;
303	<	simnfo->box_z = simnfo->box_x;
373	<	}
374	<	else{
375	<	if( !the_globals->haveBoxX() ){
376	<	sprintf( painCave.errMsg,
377	<	"SimSetup error, no periodic BoxX size given.\n" );
378	<	painCave.isFatal = 1;
379	<	simError();
380	<	}
381	<	simnfo->box_x = the_globals->getBoxX();
299	>	// make the bonds
300	>	for (j = 0; j < molInfo.nBonds; j++){
301	>	currentBond = comp_stamps[stampID]->getBond(j);
302	>	theBonds[j].a = currentBond->getA() + atomOffset;
303	>	theBonds[j].b = currentBond->getB() + atomOffset;
304
305	<	if( !the_globals->haveBoxY() ){
306	<	sprintf( painCave.errMsg,
385	<	"SimSetup error, no periodic BoxY size given.\n" );
386	<	painCave.isFatal = 1;
387	<	simError();
388	<	}
389	<	simnfo->box_y = the_globals->getBoxY();
305	>	tempI = theBonds[j].a;
306	>	tempJ = theBonds[j].b;
307
391	–	if( !the_globals->haveBoxZ() ){
392	–	sprintf( painCave.errMsg,
393	–	"SimSetup error, no periodic BoxZ size given.\n" );
394	–	painCave.isFatal = 1;
395	–	simError();
396	–	}
397	–	simnfo->box_z = the_globals->getBoxZ();
398	–	}
399	–
308		#ifdef IS_MPI
309	<	strcpy( checkPointMsg, "Box size set up" );
310	<	MPIcheckPoint();
311	<	#endif // is_mpi
309	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
310	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
311	>	#else
312	>	exI = tempI + 1;
313	>	exJ = tempJ + 1;
314	>	#endif
315
316	+	info[k].excludes->addPair(exI, exJ);
317	+	}
318
319	<	// initialize the arrays
319	>	//make the bends
320	>	for (j = 0; j < molInfo.nBends; j++){
321	>	currentBend = comp_stamps[stampID]->getBend(j);
322	>	theBends[j].a = currentBend->getA() + atomOffset;
323	>	theBends[j].b = currentBend->getB() + atomOffset;
324	>	theBends[j].c = currentBend->getC() + atomOffset;
325
326	<	the_ff->setSimInfo( simnfo );
327	<
328	<	makeAtoms();
411	<	simnfo->identArray = new int[simnfo->n_atoms];
412	<	for(i=0; i<simnfo->n_atoms; i++){
413	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
414	<	}
415	<
416	<	if( tot_bonds ){
417	<	makeBonds();
418	<	}
326	>	if (currentBend->haveExtras()){
327	>	extras = currentBend->getExtras();
328	>	current_extra = extras;
329
330	<	if( tot_bends ){
331	<	makeBends();
332	<	}
330	>	while (current_extra != NULL){
331	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
332	>	switch (current_extra->getType()){
333	>	case 0:
334	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
335	>	theBends[j].isGhost = 1;
336	>	break;
337
338	<	if( tot_torsions ){
339	<	makeTorsions();
340	<	}
338	>	case 1:
339	>	theBends[j].ghost = (int) current_extra->getDouble() +
340	>	atomOffset;
341	>	theBends[j].isGhost = 1;
342	>	break;
343
344	+	default:
345	+	sprintf(painCave.errMsg,
346	+	"SimSetup Error: ghostVectorSource was neither a "
347	+	"double nor an int.\n"
348	+	"-->Bend[%d] in %s\n",
349	+	j, comp_stamps[stampID]->getID());
350	+	painCave.isFatal = 1;
351	+	simError();
352	+	}
353	+	}
354	+	else{
355	+	sprintf(painCave.errMsg,
356	+	"SimSetup Error: unhandled bend assignment:\n"
357	+	"    -->%s in Bend[%d] in %s\n",
358	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
359	+	painCave.isFatal = 1;
360	+	simError();
361	+	}
362
363	+	current_extra = current_extra->getNext();
364	+	}
365	+	}
366
367	+	if (theBends[j].isGhost) {
368	+
369	+	tempI = theBends[j].a;
370	+	tempJ = theBends[j].b;
371	+
372	+	#ifdef IS_MPI
373	+	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
374	+	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
375	+	#else
376	+	exI = tempI + 1;
377	+	exJ = tempJ + 1;
378	+	#endif
379	+	info[k].excludes->addPair(exI, exJ);
380
381	+	} else {
382
383	<
384	<	if( the_globals->haveInitialConfig() ){
385	<
386	<	InitializeFromFile* fileInit;
436	<	#ifdef IS_MPI // is_mpi
437	<	if( worldRank == 0 ){
438	<	#endif //is_mpi
439	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
383	>	tempI = theBends[j].a;
384	>	tempJ = theBends[j].b;
385	>	tempK = theBends[j].c;
386	>
387		#ifdef IS_MPI
388	<	}else fileInit = new InitializeFromFile( NULL );
388	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
389	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
390	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
391	>	#else
392	>	exI = tempI + 1;
393	>	exJ = tempJ + 1;
394	>	exK = tempK + 1;
395		#endif
396	<	fileInit->read_xyz( simnfo ); // default velocities on
396	>
397	>	info[k].excludes->addPair(exI, exK);
398	>	info[k].excludes->addPair(exI, exJ);
399	>	info[k].excludes->addPair(exJ, exK);
400	>	}
401	>	}
402
403	<	delete fileInit;
404	<	}
405	<	else{
403	>	for (j = 0; j < molInfo.nTorsions; j++){
404	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
405	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
406	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
407	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
408	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
409
410	<	#ifdef IS_MPI
410	>	tempI = theTorsions[j].a;
411	>	tempJ = theTorsions[j].b;
412	>	tempK = theTorsions[j].c;
413	>	tempL = theTorsions[j].d;
414
415	<	// no init from bass
416	<
417	<	sprintf( painCave.errMsg,
418	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
419	<	painCave.isFatal;
456	<	simError();
457	<
415	>	#ifdef IS_MPI
416	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
417	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
418	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
419	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
420		#else
421	+	exI = tempI + 1;
422	+	exJ = tempJ + 1;
423	+	exK = tempK + 1;
424	+	exL = tempL + 1;
425	+	#endif
426
427	<	initFromBass();
427	>	info[k].excludes->addPair(exI, exJ);
428	>	info[k].excludes->addPair(exI, exK);
429	>	info[k].excludes->addPair(exI, exL);
430	>	info[k].excludes->addPair(exJ, exK);
431	>	info[k].excludes->addPair(exJ, exL);
432	>	info[k].excludes->addPair(exK, exL);
433	>	}
434
435	+
436	+	molInfo.myRigidBodies.clear();
437	+
438	+	for (j = 0; j < molInfo.nRigidBodies; j++){
439
440	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
441	+	nMembers = currentRigidBody->getNMembers();
442	+
443	+	// Create the Rigid Body:
444	+
445	+	myRB = new RigidBody();
446	+
447	+	sprintf(rbName,"%s_RB_%d", molName, j);
448	+	myRB->setType(rbName);
449	+
450	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
451	+
452	+	// molI is atom numbering inside this molecule
453	+	molI = currentRigidBody->getMember(rb1);
454	+
455	+	// tempI is atom numbering on local processor
456	+	tempI = molI + atomOffset;
457	+
458	+	// currentAtom is the AtomStamp (which we need for
459	+	// rigid body reference positions)
460	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
461	+
462	+	// When we add to the rigid body, add the atom itself and
463	+	// the stamp info:
464	+
465	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
466	+
467	+	// Add this atom to the Skip List for the integrators
468	+	#ifdef IS_MPI
469	+	slI = info[k].atoms[tempI]->getGlobalIndex();
470	+	#else
471	+	slI = tempI;
472		#endif
473	<	}
473	>	skipList.insert(slI);
474	>
475	>	}
476	>
477	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
478	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
479	>
480	>	tempI = currentRigidBody->getMember(rb1);
481	>	tempJ = currentRigidBody->getMember(rb2);
482	>
483	>	// Some explanation is required here.
484	>	// Fortran indexing starts at 1, while c indexing starts at 0
485	>	// Also, in parallel computations, the GlobalIndex is
486	>	// used for the exclude list:
487	>
488	>	#ifdef IS_MPI
489	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
490	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
491	>	#else
492	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
493	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
494	>	#endif
495	>
496	>	info[k].excludes->addPair(exI, exJ);
497	>
498	>	}
499	>	}
500
501	+	molInfo.myRigidBodies.push_back(myRB);
502	+	info[k].rigidBodies.push_back(myRB);
503	+	}
504	+
505	+
506	+	//create cutoff group for molecule
507	+
508	+	cutoffAtomSet.clear();
509	+	molInfo.myCutoffGroups.clear();
510	+
511	+	for (j = 0; j < nCutoffGroups; j++){
512	+
513	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
514	+	nMembers = currentCutoffGroup->getNMembers();
515	+
516	+	myCutoffGroup = new CutoffGroup();
517	+
518		#ifdef IS_MPI
519	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
520	<	MPIcheckPoint();
521	<	#endif // is_mpi
519	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
520	>	#else
521	>	myCutoffGroup->setGlobalIndex(groupOffset);
522	>	#endif
523	>
524	>	for (int cg = 0; cg < nMembers; cg++) {
525
526	+	// molI is atom numbering inside this molecule
527	+	molI = currentCutoffGroup->getMember(cg);
528
529	<
530	<
474	<
529	>	// tempI is atom numbering on local processor
530	>	tempI = molI + atomOffset;
531
476	–
532		#ifdef IS_MPI
533	<	if( worldRank == 0 ){
534	<	#endif // is_mpi
535	<
536	<	if( the_globals->haveFinalConfig() ){
537	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
538	<	}
539	<	else{
540	<	strcpy( simnfo->finalName, inFileName );
541	<	char* endTest;
542	<	int nameLength = strlen( simnfo->finalName );
543	<	endTest = &(simnfo->finalName[nameLength - 5]);
544	<	if( !strcmp( endTest, ".bass" ) ){
545	<	strcpy( endTest, ".eor" );
546	<	}
547	<	else if( !strcmp( endTest, ".BASS" ) ){
548	<	strcpy( endTest, ".eor" );
549	<	}
550	<	else{
551	<	endTest = &(simnfo->finalName[nameLength - 4]);
552	<	if( !strcmp( endTest, ".bss" ) ){
553	<	strcpy( endTest, ".eor" );
554	<	}
555	<	else if( !strcmp( endTest, ".mdl" ) ){
556	<	strcpy( endTest, ".eor" );
557	<	}
558	<	else{
559	<	strcat( simnfo->finalName, ".eor" );
560	<	}
533	>	globalID = info[k].atoms[tempI]->getGlobalIndex();
534	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
535	>	#else
536	>	globalID = info[k].atoms[tempI]->getIndex();
537	>	info[k].globalGroupMembership[globalID] = groupOffset;
538	>	#endif
539	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
540	>	cutoffAtomSet.insert(tempI);
541	>	}
542	>
543	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
544	>	groupOffset++;
545	>
546	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
547	>
548	>
549	>	// create a cutoff group for every atom in current molecule which
550	>	// does not belong to cutoffgroup defined at mdl file
551	>
552	>	for(j = 0; j < molInfo.nAtoms; j++){
553	>
554	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
555	>	myCutoffGroup = new CutoffGroup();
556	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
557	>
558	>	#ifdef IS_MPI
559	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
560	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
561	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
562	>	#else
563	>	myCutoffGroup->setGlobalIndex(groupOffset);
564	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
565	>	info[k].globalGroupMembership[globalID] = groupOffset;
566	>	#endif
567	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
568	>	groupOffset++;
569	>	}
570		}
571	<	}
572	<
573	<	// make the sample and status out names
574	<
575	<	strcpy( simnfo->sampleName, inFileName );
576	<	char* endTest;
577	<	int nameLength = strlen( simnfo->sampleName );
578	<	endTest = &(simnfo->sampleName[nameLength - 5]);
579	<	if( !strcmp( endTest, ".bass" ) ){
580	<	strcpy( endTest, ".dump" );
581	<	}
582	<	else if( !strcmp( endTest, ".BASS" ) ){
583	<	strcpy( endTest, ".dump" );
584	<	}
585	<	else{
586	<	endTest = &(simnfo->sampleName[nameLength - 4]);
587	<	if( !strcmp( endTest, ".bss" ) ){
588	<	strcpy( endTest, ".dump" );
571	>
572	>	// After this is all set up, scan through the atoms to
573	>	// see if they can be added to the integrableObjects:
574	>
575	>	molInfo.myIntegrableObjects.clear();
576	>
577	>
578	>	for (j = 0; j < molInfo.nAtoms; j++){
579	>
580	>	#ifdef IS_MPI
581	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
582	>	#else
583	>	slJ = j+atomOffset;
584	>	#endif
585	>
586	>	// if they aren't on the skip list, then they can be integrated
587	>
588	>	if (skipList.find(slJ) == skipList.end()) {
589	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
590	>	info[k].integrableObjects.push_back(mySD);
591	>	molInfo.myIntegrableObjects.push_back(mySD);
592	>	}
593		}
594	<	else if( !strcmp( endTest, ".mdl" ) ){
595	<	strcpy( endTest, ".dump" );
594	>
595	>	// all rigid bodies are integrated:
596	>
597	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
598	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
599	>	info[k].integrableObjects.push_back(mySD);
600	>	molInfo.myIntegrableObjects.push_back(mySD);
601		}
602	<	else{
603	<	strcat( simnfo->sampleName, ".dump" );
602	>
603	>
604	>	/*
605	>
606	>	//creat ConstraintPair.
607	>	molInfo.myConstraintPair.clear();
608	>
609	>	for (j = 0; j < molInfo.nBonds; j++){
610	>
611	>	//if both atoms are in the same rigid body, just skip it
612	>	currentBond = comp_stamps[stampID]->getBond(j);
613	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
614	>
615	>	tempI = currentBond->getA() + atomOffset;
616	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
617	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
618	>	else
619	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
620	>
621	>	tempJ =  currentBond->getB() + atomOffset;
622	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
623	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
624	>	else
625	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
626	>
627	>	consPair = new DistanceConstraintPair(consElement1, consElement2);
628	>	molInfo.myConstraintPairs.push_back(consPair);
629	>	}
630	>	}
631	>
632	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
633	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
634	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
635	>
636	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
637	>
638	>	for(size_t m = 0; m < jointAtoms.size(); m++){
639	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
640	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
641	>
642	>	consPair = new JointConstraintPair(consElement1, consElement2);
643	>	molInfo.myConstraintPairs.push_back(consPair);
644	>	}
645	>
646	>	}
647		}
648	+
649	+	*/
650	+	// send the arrays off to the forceField for init.
651	+
652	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
653	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
654	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
655	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
656	+	theTorsions);
657	+
658	+	info[k].molecules[i].initialize(molInfo);
659	+
660	+
661	+	atomOffset += molInfo.nAtoms;
662	+	delete[] theBonds;
663	+	delete[] theBends;
664	+	delete[] theTorsions;
665		}
533	–
534	–	strcpy( simnfo->statusName, inFileName );
535	–	nameLength = strlen( simnfo->statusName );
536	–	endTest = &(simnfo->statusName[nameLength - 5]);
537	–	if( !strcmp( endTest, ".bass" ) ){
538	–	strcpy( endTest, ".stat" );
539	–	}
540	–	else if( !strcmp( endTest, ".BASS" ) ){
541	–	strcpy( endTest, ".stat" );
542	–	}
543	–	else{
544	–	endTest = &(simnfo->statusName[nameLength - 4]);
545	–	if( !strcmp( endTest, ".bss" ) ){
546	–	strcpy( endTest, ".stat" );
547	–	}
548	–	else if( !strcmp( endTest, ".mdl" ) ){
549	–	strcpy( endTest, ".stat" );
550	–	}
551	–	else{
552	–	strcat( simnfo->statusName, ".stat" );
553	–	}
554	–	}
555	–
556	–	#ifdef IS_MPI
557	–	}
558	–	#endif // is_mpi
559	–
560	–	// set the status, sample, and themal kick times
561	–
562	–	if( the_globals->haveSampleTime() ){
563	–	simnfo->sampleTime = the_globals->getSampleTime();
564	–	simnfo->statusTime = simnfo->sampleTime;
565	–	simnfo->thermalTime = simnfo->sampleTime;
566	–	}
567	–	else{
568	–	simnfo->sampleTime = the_globals->getRunTime();
569	–	simnfo->statusTime = simnfo->sampleTime;
570	–	simnfo->thermalTime = simnfo->sampleTime;
571	–	}
666
573	–	if( the_globals->haveStatusTime() ){
574	–	simnfo->statusTime = the_globals->getStatusTime();
575	–	}
667
577	–	if( the_globals->haveThermalTime() ){
578	–	simnfo->thermalTime = the_globals->getThermalTime();
579	–	}
668
669	<	// check for the temperature set flag
669	>	#ifdef IS_MPI
670	>	// Since the globalGroupMembership has been zero filled and we've only
671	>	// poked values into the atoms we know, we can do an Allreduce
672	>	// to get the full globalGroupMembership array (We think).
673	>	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
674	>	// docs said we could.
675
676	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
676	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
677
678	+	MPI_Allreduce(info[k].globalGroupMembership,
679	+	ggMjunk,
680	+	mpiSim->getNAtomsGlobal(),
681	+	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
682
683	<	//   // make the longe range forces and the integrator
683	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
684	>	info[k].globalGroupMembership[i] = ggMjunk[i];
685
686	<	//   new AllLong( simnfo );
686	>	delete[] ggMjunk;
687	>
688	>	#endif
689
590	–	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
591	–	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
592	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
593	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
690
691
596	–
597	–	// initialize the Fortran
598	–
599	–	simnfo->refreshSim();
600	–
601	–	if( !strcmp( simnfo->mixingRule, "standard") ){
602	–	the_ff->initForceField( LB_MIXING_RULE );
692		}
604	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
605	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
606	–	}
607	–	else{
608	–	sprintf( painCave.errMsg,
609	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
610	–	simnfo->mixingRule );
611	–	painCave.isFatal = 1;
612	–	simError();
613	–	}
693
615	–
694		#ifdef IS_MPI
695	<	strcpy( checkPointMsg,
618	<	"Successfully intialized the mixingRule for Fortran." );
695	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
696		MPIcheckPoint();
697		#endif // is_mpi
698	+
699		}
700
701	<	void SimSetup::makeAtoms( void ){
624	<
625	<	int i, j, k, index;
626	<	double ux, uy, uz, uSqr, u;
627	<	AtomStamp* current_atom;
628	<
629	<	DirectionalAtom* dAtom;
630	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
631	<
632	<	lMolIndex = 0;
633	<	molIndex = 0;
634	<	index = 0;
635	<	for( i=0; i<n_components; i++ ){
636	<
637	<	for( j=0; j<components_nmol[i]; j++ ){
638	<
639	<	#ifdef IS_MPI
640	<	if( mpiSim->getMyMolStart() <= molIndex &&
641	<	molIndex <= mpiSim->getMyMolEnd() ){
642	<	#endif // is_mpi
643	<
644	<	molStart = index;
645	<	nMemb = comp_stamps[i]->getNAtoms();
646	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
647	<
648	<	current_atom = comp_stamps[i]->getAtom( k );
649	<	if( current_atom->haveOrientation() ){
650	<
651	<	dAtom = new DirectionalAtom(index);
652	<	simnfo->n_oriented++;
653	<	the_atoms[index] = dAtom;
654	<
655	<	ux = current_atom->getOrntX();
656	<	uy = current_atom->getOrntY();
657	<	uz = current_atom->getOrntZ();
658	<
659	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
660	<
661	<	u = sqrt( uSqr );
662	<	ux = ux / u;
663	<	uy = uy / u;
664	<	uz = uz / u;
665	<
666	<	dAtom->setSUx( ux );
667	<	dAtom->setSUy( uy );
668	<	dAtom->setSUz( uz );
669	<	}
670	<	else{
671	<	the_atoms[index] = new GeneralAtom(index);
672	<	}
673	<	the_atoms[index]->setType( current_atom->getType() );
674	<	the_atoms[index]->setIndex( index );
675	<
676	<	// increment the index and repeat;
677	<	index++;
678	<	}
679	<
680	<	molEnd = index -1;
681	<	the_molecules[lMolIndex].setNMembers( nMemb );
682	<	the_molecules[lMolIndex].setStartAtom( molStart );
683	<	the_molecules[lMolIndex].setEndAtom( molEnd );
684	<	the_molecules[lMolIndex].setStampID( i );
685	<	lMolIndex++;
686	<
687	<	#ifdef IS_MPI
688	<	}
689	<	#endif //is_mpi
690	<
691	<	molIndex++;
692	<	}
693	<	}
694	<
695	<	#ifdef IS_MPI
696	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
697	<
698	<	delete[] globalIndex;
699	<
700	<	mpiSim->mpiRefresh();
701	<	#endif //IS_MPI
702	<
703	<	the_ff->initializeAtoms();
704	<	}
705	<
706	<	void SimSetup::makeBonds( void ){
707	<
708	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
709	<	bond_pair* the_bonds;
710	<	BondStamp* current_bond;
711	<
712	<	the_bonds = new bond_pair[tot_bonds];
713	<	index = 0;
714	<	offset = 0;
715	<	molIndex = 0;
716	<
717	<	for( i=0; i<n_components; i++ ){
718	<
719	<	for( j=0; j<components_nmol[i]; j++ ){
720	<
721	<	#ifdef IS_MPI
722	<	if( mpiSim->getMyMolStart() <= molIndex &&
723	<	molIndex <= mpiSim->getMyMolEnd() ){
724	<	#endif // is_mpi
725	<
726	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
727	<
728	<	current_bond = comp_stamps[i]->getBond( k );
729	<	the_bonds[index].a = current_bond->getA() + offset;
730	<	the_bonds[index].b = current_bond->getB() + offset;
731	<
732	<	exI = the_bonds[index].a;
733	<	exJ = the_bonds[index].b;
734	<
735	<	// exclude_I must always be the smaller of the pair
736	<	if( exI > exJ ){
737	<	tempEx = exI;
738	<	exI = exJ;
739	<	exJ = tempEx;
740	<	}
741	<
742	<
743	<	#ifdef IS_MPI
744	<
745	<	the_excludes[index*2] =
746	<	the_atoms[exI]->getGlobalIndex() + 1;
747	<	the_excludes[index*2 + 1] =
748	<	the_atoms[exJ]->getGlobalIndex() + 1;
749	<
750	<	#else  // isn't MPI
751	<
752	<	the_excludes[index*2] =     exI + 1;
753	<	the_excludes[index*2 + 1] = exJ + 1;
754	<	// fortran index from 1 (hence the +1 in the indexing)
755	<	#endif  //is_mpi
756	<
757	<	// increment the index and repeat;
758	<	index++;
759	<	}
760	<	offset += comp_stamps[i]->getNAtoms();
761	<
762	<	#ifdef IS_MPI
763	<	}
764	<	#endif //is_mpi
765	<
766	<	molIndex++;
767	<	}
768	<	}
769	<
770	<	the_ff->initializeBonds( the_bonds );
771	<	}
772	<
773	<	void SimSetup::makeBends( void ){
774	<
775	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
776	<	bend_set* the_bends;
777	<	BendStamp* current_bend;
778	<	LinkedAssign* extras;
779	<	LinkedAssign* current_extra;
780	<
781	<
782	<	the_bends = new bend_set[tot_bends];
783	<	index = 0;
784	<	offset = 0;
785	<	molIndex = 0;
786	<	for( i=0; i<n_components; i++ ){
787	<
788	<	for( j=0; j<components_nmol[i]; j++ ){
789	<
790	<	#ifdef IS_MPI
791	<	if( mpiSim->getMyMolStart() <= molIndex &&
792	<	molIndex <= mpiSim->getMyMolEnd() ){
793	<	#endif // is_mpi
794	<
795	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
796	<
797	<	current_bend = comp_stamps[i]->getBend( k );
798	<	the_bends[index].a = current_bend->getA() + offset;
799	<	the_bends[index].b = current_bend->getB() + offset;
800	<	the_bends[index].c = current_bend->getC() + offset;
801	<
802	<	if( current_bend->haveExtras() ){
803	<
804	<	extras = current_bend->getExtras();
805	<	current_extra = extras;
806	<
807	<	while( current_extra != NULL ){
808	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
809	<
810	<	switch( current_extra->getType() ){
811	<
812	<	case 0:
813	<	the_bends[index].ghost =
814	<	current_extra->getInt() + offset;
815	<	the_bends[index].isGhost = 1;
816	<	break;
817	<
818	<	case 1:
819	<	the_bends[index].ghost =
820	<	(int)current_extra->getDouble() + offset;
821	<	the_bends[index].isGhost = 1;
822	<	break;
823	<
824	<	default:
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup Error: ghostVectorSource was neiter a "
827	<	"double nor an int.\n"
828	<	"-->Bend[%d] in %s\n",
829	<	k, comp_stamps[i]->getID() );
830	<	painCave.isFatal = 1;
831	<	simError();
832	<	}
833	<	}
834	<
835	<	else{
836	<
837	<	sprintf( painCave.errMsg,
838	<	"SimSetup Error: unhandled bend assignment:\n"
839	<	"    -->%s in Bend[%d] in %s\n",
840	<	current_extra->getlhs(),
841	<	k, comp_stamps[i]->getID() );
842	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<
846	<	current_extra = current_extra->getNext();
847	<	}
848	<	}
849	<
850	<	if( !the_bends[index].isGhost ){
851	<
852	<	exI = the_bends[index].a;
853	<	exJ = the_bends[index].c;
854	<	}
855	<	else{
856	<
857	<	exI = the_bends[index].a;
858	<	exJ = the_bends[index].b;
859	<	}
860	<
861	<	// exclude_I must always be the smaller of the pair
862	<	if( exI > exJ ){
863	<	tempEx = exI;
864	<	exI = exJ;
865	<	exJ = tempEx;
866	<	}
867	<
868	<
869	<	#ifdef IS_MPI
870	<
871	<	the_excludes[(index + tot_bonds)*2] =
872	<	the_atoms[exI]->getGlobalIndex() + 1;
873	<	the_excludes[(index + tot_bonds)*2 + 1] =
874	<	the_atoms[exJ]->getGlobalIndex() + 1;
875	<
876	<	#else  // isn't MPI
877	<
878	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
879	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
880	<	// fortran index from 1 (hence the +1 in the indexing)
881	<	#endif  //is_mpi
882	<
883	<
884	<	// increment the index and repeat;
885	<	index++;
886	<	}
887	<	offset += comp_stamps[i]->getNAtoms();
888	<
889	<	#ifdef IS_MPI
890	<	}
891	<	#endif //is_mpi
892	<
893	<	molIndex++;
894	<	}
895	<	}
896	<
897	<	#ifdef IS_MPI
898	<	sprintf( checkPointMsg,
899	<	"Successfully created the bends list.\n" );
900	<	MPIcheckPoint();
901	<	#endif // is_mpi
902	<
903	<
904	<	the_ff->initializeBends( the_bends );
905	<	}
906	<
907	<	void SimSetup::makeTorsions( void ){
908	<
909	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
910	<	torsion_set* the_torsions;
911	<	TorsionStamp* current_torsion;
912	<
913	<	the_torsions = new torsion_set[tot_torsions];
914	<	index = 0;
915	<	offset = 0;
916	<	molIndex = 0;
917	<	for( i=0; i<n_components; i++ ){
918	<
919	<	for( j=0; j<components_nmol[i]; j++ ){
920	<
921	<	#ifdef IS_MPI
922	<	if( mpiSim->getMyMolStart() <= molIndex &&
923	<	molIndex <= mpiSim->getMyMolEnd() ){
924	<	#endif // is_mpi
925	<
926	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
927	<
928	<	current_torsion = comp_stamps[i]->getTorsion( k );
929	<	the_torsions[index].a = current_torsion->getA() + offset;
930	<	the_torsions[index].b = current_torsion->getB() + offset;
931	<	the_torsions[index].c = current_torsion->getC() + offset;
932	<	the_torsions[index].d = current_torsion->getD() + offset;
933	<
934	<	exI = the_torsions[index].a;
935	<	exJ = the_torsions[index].d;
936	<
937	<
938	<	// exclude_I must always be the smaller of the pair
939	<	if( exI > exJ ){
940	<	tempEx = exI;
941	<	exI = exJ;
942	<	exJ = tempEx;
943	<	}
944	<
945	<
946	<	#ifdef IS_MPI
947	<
948	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
949	<	the_atoms[exI]->getGlobalIndex() + 1;
950	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
951	<	the_atoms[exJ]->getGlobalIndex() + 1;
952	<
953	<	#else  // isn't MPI
954	<
955	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957	<	// fortran indexes from 1 (hence the +1 in the indexing)
958	<	#endif  //is_mpi
959	<
960	<
961	<	// increment the index and repeat;
962	<	index++;
963	<	}
964	<	offset += comp_stamps[i]->getNAtoms();
965	<
966	<	#ifdef IS_MPI
967	<	}
968	<	#endif //is_mpi
969	<
970	<	molIndex++;
971	<	}
972	<	}
973	<
974	<	the_ff->initializeTorsions( the_torsions );
975	<	}
976	<
977	<	void SimSetup::initFromBass( void ){
978	<
701	>	void SimSetup::initFromBass(void){
702		int i, j, k;
703		int n_cells;
704		double cellx, celly, cellz;
#	Line 984 | Line 707 | void SimSetup::initFromBass( void ){
707		int n_extra;
708		int have_extra, done;
709
710	<	temp1 = (double)tot_nmol / 4.0;
711	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
712	<	temp3 = ceil( temp2 );
710	>	double vel[3];
711	>	vel[0] = 0.0;
712	>	vel[1] = 0.0;
713	>	vel[2] = 0.0;
714
715	<	have_extra =0;
716	<	if( temp2 < temp3 ){ // we have a non-complete lattice
717	<	have_extra =1;
715	>	temp1 = (double) tot_nmol / 4.0;
716	>	temp2 = pow(temp1, (1.0 / 3.0));
717	>	temp3 = ceil(temp2);
718
719	<	n_cells = (int)temp3 - 1;
720	<	cellx = simnfo->box_x / temp3;
721	<	celly = simnfo->box_y / temp3;
722	<	cellz = simnfo->box_z / temp3;
999	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1000	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1001	<	n_per_extra = (int)ceil( temp1 );
719	>	have_extra = 0;
720	>	if (temp2 < temp3){
721	>	// we have a non-complete lattice
722	>	have_extra = 1;
723
724	<	if( n_per_extra > 4){
725	<	sprintf( painCave.errMsg,
726	<	"SimSetup error. There has been an error in constructing"
727	<	" the non-complete lattice.\n" );
724	>	n_cells = (int) temp3 - 1;
725	>	cellx = info[0].boxL[0] / temp3;
726	>	celly = info[0].boxL[1] / temp3;
727	>	cellz = info[0].boxL[2] / temp3;
728	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
729	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
730	>	n_per_extra = (int) ceil(temp1);
731	>
732	>	if (n_per_extra > 4){
733	>	sprintf(painCave.errMsg,
734	>	"SimSetup error. There has been an error in constructing"
735	>	" the non-complete lattice.\n");
736		painCave.isFatal = 1;
737		simError();
738		}
739		}
740		else{
741	<	n_cells = (int)temp3;
742	<	cellx = simnfo->box_x / temp3;
743	<	celly = simnfo->box_y / temp3;
744	<	cellz = simnfo->box_z / temp3;
741	>	n_cells = (int) temp3;
742	>	cellx = info[0].boxL[0] / temp3;
743	>	celly = info[0].boxL[1] / temp3;
744	>	cellz = info[0].boxL[2] / temp3;
745		}
746
747		current_mol = 0;
#	Line 1020 | Line 749 | void SimSetup::initFromBass( void ){
749		current_comp = 0;
750		current_atom_ndx = 0;
751
752	<	for( i=0; i < n_cells ; i++ ){
753	<	for( j=0; j < n_cells; j++ ){
754	<	for( k=0; k < n_cells; k++ ){
752	>	for (i = 0; i < n_cells ; i++){
753	>	for (j = 0; j < n_cells; j++){
754	>	for (k = 0; k < n_cells; k++){
755	>	makeElement(i * cellx, j * celly, k * cellz);
756
757	<	makeElement( i * cellx,
1028	<	j * celly,
1029	<	k * cellz );
757	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
758
759	<	makeElement( i * cellx + 0.5 * cellx,
1032	<	j * celly + 0.5 * celly,
1033	<	k * cellz );
759	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
760
761	<	makeElement( i * cellx,
1036	<	j * celly + 0.5 * celly,
1037	<	k * cellz + 0.5 * cellz );
1038	<
1039	<	makeElement( i * cellx + 0.5 * cellx,
1040	<	j * celly,
1041	<	k * cellz + 0.5 * cellz );
761	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
762		}
763		}
764		}
765
766	<	if( have_extra ){
766	>	if (have_extra){
767		done = 0;
768
769		int start_ndx;
770	<	for( i=0; i < (n_cells+1) && !done; i++ ){
771	<	for( j=0; j < (n_cells+1) && !done; j++ ){
770	>	for (i = 0; i < (n_cells + 1) && !done; i++){
771	>	for (j = 0; j < (n_cells + 1) && !done; j++){
772	>	if (i < n_cells){
773	>	if (j < n_cells){
774	>	start_ndx = n_cells;
775	>	}
776	>	else
777	>	start_ndx = 0;
778	>	}
779	>	else
780	>	start_ndx = 0;
781
782	<	if( i < n_cells ){
782	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
783	>	makeElement(i * cellx, j * celly, k * cellz);
784	>	done = (current_mol >= tot_nmol);
785
786	<	if( j < n_cells ){
787	<	start_ndx = n_cells;
788	<	}
789	<	else start_ndx = 0;
790	<	}
1060	<	else start_ndx = 0;
786	>	if (!done && n_per_extra > 1){
787	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
788	>	k * cellz);
789	>	done = (current_mol >= tot_nmol);
790	>	}
791
792	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
792	>	if (!done && n_per_extra > 2){
793	>	makeElement(i * cellx, j * celly + 0.5 * celly,
794	>	k * cellz + 0.5 * cellz);
795	>	done = (current_mol >= tot_nmol);
796	>	}
797
798	<	makeElement( i * cellx,
799	<	j * celly,
800	<	k * cellz );
801	<	done = ( current_mol >= tot_nmol );
802	<
803	<	if( !done && n_per_extra > 1 ){
1070	<	makeElement( i * cellx + 0.5 * cellx,
1071	<	j * celly + 0.5 * celly,
1072	<	k * cellz );
1073	<	done = ( current_mol >= tot_nmol );
1074	<	}
1075	<
1076	<	if( !done && n_per_extra > 2){
1077	<	makeElement( i * cellx,
1078	<	j * celly + 0.5 * celly,
1079	<	k * cellz + 0.5 * cellz );
1080	<	done = ( current_mol >= tot_nmol );
1081	<	}
1082	<
1083	<	if( !done && n_per_extra > 3){
1084	<	makeElement( i * cellx + 0.5 * cellx,
1085	<	j * celly,
1086	<	k * cellz + 0.5 * cellz );
1087	<	done = ( current_mol >= tot_nmol );
1088	<	}
1089	<	}
798	>	if (!done && n_per_extra > 3){
799	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
800	>	k * cellz + 0.5 * cellz);
801	>	done = (current_mol >= tot_nmol);
802	>	}
803	>	}
804		}
805		}
806		}
807
808	<
809	<	for( i=0; i<simnfo->n_atoms; i++ ){
1096	<	simnfo->atoms[i]->set_vx( 0.0 );
1097	<	simnfo->atoms[i]->set_vy( 0.0 );
1098	<	simnfo->atoms[i]->set_vz( 0.0 );
808	>	for (i = 0; i < info[0].n_atoms; i++){
809	>	info[0].atoms[i]->setVel(vel);
810		}
811		}
812
813	<	void SimSetup::makeElement( double x, double y, double z ){
1103	<
813	>	void SimSetup::makeElement(double x, double y, double z){
814		int k;
815		AtomStamp* current_atom;
816		DirectionalAtom* dAtom;
817		double rotMat[3][3];
818	+	double pos[3];
819
820	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
821	<
822	<	current_atom = comp_stamps[current_comp]->getAtom( k );
823	<	if( !current_atom->havePosition() ){
824	<	sprintf( painCave.errMsg,
825	<	"SimSetup:initFromBass error.\n"
826	<	"\tComponent %s, atom %s does not have a position specified.\n"
827	<	"\tThe initialization routine is unable to give a start"
828	<	" position.\n",
1118	<	comp_stamps[current_comp]->getID(),
1119	<	current_atom->getType() );
820	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
821	>	current_atom = comp_stamps[current_comp]->getAtom(k);
822	>	if (!current_atom->havePosition()){
823	>	sprintf(painCave.errMsg,
824	>	"SimSetup:initFromBass error.\n"
825	>	"\tComponent %s, atom %s does not have a position specified.\n"
826	>	"\tThe initialization routine is unable to give a start"
827	>	" position.\n",
828	>	comp_stamps[current_comp]->getID(), current_atom->getType());
829		painCave.isFatal = 1;
830		simError();
831		}
832
833	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
834	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
835	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
833	>	pos[0] = x + current_atom->getPosX();
834	>	pos[1] = y + current_atom->getPosY();
835	>	pos[2] = z + current_atom->getPosZ();
836
837	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
837	>	info[0].atoms[current_atom_ndx]->setPos(pos);
838
839	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
839	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
840	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
841
842		rotMat[0][0] = 1.0;
843		rotMat[0][1] = 0.0;
#	Line 1141 | Line 851 | void SimSetup::makeElement( double x, double y, double
851		rotMat[2][1] = 0.0;
852		rotMat[2][2] = 1.0;
853
854	<	dAtom->setA( rotMat );
854	>	dAtom->setA(rotMat);
855		}
856
857		current_atom_ndx++;
858	+	}
859	+
860	+	current_mol++;
861	+	current_comp_mol++;
862	+
863	+	if (current_comp_mol >= components_nmol[current_comp]){
864	+	current_comp_mol = 0;
865	+	current_comp++;
866	+	}
867	+	}
868	+
869	+
870	+	void SimSetup::gatherInfo(void){
871	+	int i;
872	+
873	+	ensembleCase = -1;
874	+	ffCase = -1;
875	+
876	+	// set the easy ones first
877	+
878	+	for (i = 0; i < nInfo; i++){
879	+	info[i].target_temp = globals->getTargetTemp();
880	+	info[i].dt = globals->getDt();
881	+	info[i].run_time = globals->getRunTime();
882	+	}
883	+	n_components = globals->getNComponents();
884	+
885	+
886	+	// get the forceField
887	+
888	+	strcpy(force_field, globals->getForceField());
889	+
890	+	if (!strcasecmp(force_field, "DUFF")){
891	+	ffCase = FF_DUFF;
892	+	}
893	+	else if (!strcasecmp(force_field, "LJ")){
894	+	ffCase = FF_LJ;
895	+	}
896	+	else if (!strcasecmp(force_field, "EAM")){
897	+	ffCase = FF_EAM;
898	+	}
899	+	else if (!strcasecmp(force_field, "WATER")){
900	+	ffCase = FF_H2O;
901	+	}
902	+	else{
903	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
904	+	force_field);
905	+	painCave.isFatal = 1;
906	+	simError();
907	+	}
908	+
909	+	// get the ensemble
910	+
911	+	strcpy(ensemble, globals->getEnsemble());
912	+
913	+	if (!strcasecmp(ensemble, "NVE")){
914	+	ensembleCase = NVE_ENS;
915	+	}
916	+	else if (!strcasecmp(ensemble, "NVT")){
917	+	ensembleCase = NVT_ENS;
918	+	}
919	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
920	+	ensembleCase = NPTi_ENS;
921	+	}
922	+	else if (!strcasecmp(ensemble, "NPTf")){
923	+	ensembleCase = NPTf_ENS;
924	+	}
925	+	else if (!strcasecmp(ensemble, "NPTxyz")){
926	+	ensembleCase = NPTxyz_ENS;
927	+	}
928	+	else{
929	+	sprintf(painCave.errMsg,
930	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
931	+	"\treverting to NVE for this simulation.\n",
932	+	ensemble);
933	+	painCave.isFatal = 0;
934	+	simError();
935	+	strcpy(ensemble, "NVE");
936	+	ensembleCase = NVE_ENS;
937	+	}
938	+
939	+	for (i = 0; i < nInfo; i++){
940	+	strcpy(info[i].ensemble, ensemble);
941	+
942	+	// get the mixing rule
943	+
944	+	strcpy(info[i].mixingRule, globals->getMixingRule());
945	+	info[i].usePBC = globals->getPBC();
946	+	}
947	+
948	+	// get the components and calculate the tot_nMol and indvidual n_mol
949	+
950	+	the_components = globals->getComponents();
951	+	components_nmol = new int[n_components];
952	+
953	+
954	+	if (!globals->haveNMol()){
955	+	// we don't have the total number of molecules, so we assume it is
956	+	// given in each component
957	+
958	+	tot_nmol = 0;
959	+	for (i = 0; i < n_components; i++){
960	+	if (!the_components[i]->haveNMol()){
961	+	// we have a problem
962	+	sprintf(painCave.errMsg,
963	+	"SimSetup Error. No global NMol or component NMol given.\n"
964	+	"\tCannot calculate the number of atoms.\n");
965	+	painCave.isFatal = 1;
966	+	simError();
967	+	}
968	+
969	+	tot_nmol += the_components[i]->getNMol();
970	+	components_nmol[i] = the_components[i]->getNMol();
971	+	}
972	+	}
973	+	else{
974	+	sprintf(painCave.errMsg,
975	+	"SimSetup error.\n"
976	+	"\tSorry, the ability to specify total"
977	+	" nMols and then give molfractions in the components\n"
978	+	"\tis not currently supported."
979	+	" Please give nMol in the components.\n");
980	+	painCave.isFatal = 1;
981	+	simError();
982	+	}
983	+
984	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
985	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
986	+	sprintf(painCave.errMsg,
987	+	"Sample time is not divisible by dt.\n"
988	+	"\tThis will result in samples that are not uniformly\n"
989	+	"\tdistributed in time.  If this is a problem, change\n"
990	+	"\tyour sampleTime variable.\n");
991	+	painCave.isFatal = 0;
992	+	simError();
993	+	}
994	+
995	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
996	+	sprintf(painCave.errMsg,
997	+	"Status time is not divisible by dt.\n"
998	+	"\tThis will result in status reports that are not uniformly\n"
999	+	"\tdistributed in time.  If this is a problem, change \n"
1000	+	"\tyour statusTime variable.\n");
1001	+	painCave.isFatal = 0;
1002	+	simError();
1003	+	}
1004	+
1005	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1006	+	sprintf(painCave.errMsg,
1007	+	"Thermal time is not divisible by dt.\n"
1008	+	"\tThis will result in thermalizations that are not uniformly\n"
1009	+	"\tdistributed in time.  If this is a problem, change \n"
1010	+	"\tyour thermalTime variable.\n");
1011	+	painCave.isFatal = 0;
1012	+	simError();
1013	+	}
1014	+
1015	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1016	+	sprintf(painCave.errMsg,
1017	+	"Reset time is not divisible by dt.\n"
1018	+	"\tThis will result in integrator resets that are not uniformly\n"
1019	+	"\tdistributed in time.  If this is a problem, change\n"
1020	+	"\tyour resetTime variable.\n");
1021	+	painCave.isFatal = 0;
1022	+	simError();
1023	+	}
1024	+
1025	+	// set the status, sample, and thermal kick times
1026	+
1027	+	for (i = 0; i < nInfo; i++){
1028	+	if (globals->haveSampleTime()){
1029	+	info[i].sampleTime = globals->getSampleTime();
1030	+	info[i].statusTime = info[i].sampleTime;
1031	+	}
1032	+	else{
1033	+	info[i].sampleTime = globals->getRunTime();
1034	+	info[i].statusTime = info[i].sampleTime;
1035	+	}
1036	+
1037	+	if (globals->haveStatusTime()){
1038	+	info[i].statusTime = globals->getStatusTime();
1039	+	}
1040	+
1041	+	if (globals->haveThermalTime()){
1042	+	info[i].thermalTime = globals->getThermalTime();
1043	+	} else {
1044	+	info[i].thermalTime = globals->getRunTime();
1045	+	}
1046	+
1047	+	info[i].resetIntegrator = 0;
1048	+	if( globals->haveResetTime() ){
1049	+	info[i].resetTime = globals->getResetTime();
1050	+	info[i].resetIntegrator = 1;
1051	+	}
1052	+
1053	+	// check for the temperature set flag
1054	+
1055	+	if (globals->haveTempSet())
1056	+	info[i].setTemp = globals->getTempSet();
1057	+
1058	+	// check for the extended State init
1059	+
1060	+	info[i].useInitXSstate = globals->getUseInitXSstate();
1061	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1062	+
1063	+	// check for thermodynamic integration
1064	+	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1065	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1066	+	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1067	+	info[i].thermIntLambda = globals->getThermIntLambda();
1068	+	info[i].thermIntK = globals->getThermIntK();
1069	+
1070	+	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1071	+	info[i].restraint = myRestraint;
1072	+	}
1073	+	else {
1074	+	sprintf(painCave.errMsg,
1075	+	"SimSetup Error:\n"
1076	+	"\tKeyword useSolidThermInt was set to 'true' but\n"
1077	+	"\tthermodynamicIntegrationLambda (and/or\n"
1078	+	"\tthermodynamicIntegrationK) was not specified.\n"
1079	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1080	+	painCave.isFatal = 1;
1081	+	simError();
1082	+	}
1083	+	}
1084	+	else if(globals->getUseLiquidThermInt()) {
1085	+	if (globals->getUseSolidThermInt()) {
1086	+	sprintf( painCave.errMsg,
1087	+	"SimSetup Warning: It appears that you have both solid and\n"
1088	+	"\tliquid thermodynamic integration activated in your .bass\n"
1089	+	"\tfile. To avoid confusion, specify only one technique in\n"
1090	+	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1091	+	"\twill be assumed for the current simulation. If this is not\n"
1092	+	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1093	+	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1094	+	painCave.isFatal = 0;
1095	+	simError();
1096	+	}
1097	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1098	+	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1099	+	info[i].thermIntLambda = globals->getThermIntLambda();
1100	+	info[i].thermIntK = globals->getThermIntK();
1101	+	}
1102	+	else {
1103	+	sprintf(painCave.errMsg,
1104	+	"SimSetup Error:\n"
1105	+	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1106	+	"\tthermodynamicIntegrationLambda (and/or\n"
1107	+	"\tthermodynamicIntegrationK) was not specified.\n"
1108	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1109	+	painCave.isFatal = 1;
1110	+	simError();
1111	+	}
1112	+	}
1113	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1114	+	sprintf(painCave.errMsg,
1115	+	"SimSetup Warning: If you want to use Thermodynamic\n"
1116	+	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1117	+	"\t'true' in your .bass file.  These keywords are set to\n"
1118	+	"\t'false' by default, so your lambda and/or k values are\n"
1119	+	"\tbeing ignored.\n");
1120	+	painCave.isFatal = 0;
1121	+	simError();
1122	+	}
1123	+	}
1124	+
1125	+	//setup seed for random number generator
1126	+	int seedValue;
1127	+
1128	+	if (globals->haveSeed()){
1129	+	seedValue = globals->getSeed();
1130	+
1131	+	if(seedValue / 1E9 == 0){
1132	+	sprintf(painCave.errMsg,
1133	+	"Seed for sprng library should contain at least 9 digits\n"
1134	+	"OOPSE will generate a seed for user\n");
1135	+	painCave.isFatal = 0;
1136	+	simError();
1137	+
1138	+	//using seed generated by system instead of invalid seed set by user
1139	+	#ifndef IS_MPI
1140	+	seedValue = make_sprng_seed();
1141	+	#else
1142	+	if (worldRank == 0){
1143	+	seedValue = make_sprng_seed();
1144	+	}
1145	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1146	+	#endif
1147	+	}
1148	+	}//end of if branch of globals->haveSeed()
1149	+	else{
1150	+
1151	+	#ifndef IS_MPI
1152	+	seedValue = make_sprng_seed();
1153	+	#else
1154	+	if (worldRank == 0){
1155	+	seedValue = make_sprng_seed();
1156	+	}
1157	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1158	+	#endif
1159	+	}//end of globals->haveSeed()
1160	+
1161	+	for (int i = 0; i < nInfo; i++){
1162	+	info[i].setSeed(seedValue);
1163	+	}
1164	+
1165	+	#ifdef IS_MPI
1166	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1167	+	MPIcheckPoint();
1168	+	#endif // is_mpi
1169	+	}
1170	+
1171	+
1172	+	void SimSetup::finalInfoCheck(void){
1173	+	int index;
1174	+	int usesDipoles;
1175	+	int usesCharges;
1176	+	int i;
1177	+
1178	+	for (i = 0; i < nInfo; i++){
1179	+	// check electrostatic parameters
1180	+
1181	+	index = 0;
1182	+	usesDipoles = 0;
1183	+	while ((index < info[i].n_atoms) && !usesDipoles){
1184	+	usesDipoles = (info[i].atoms[index])->hasDipole();
1185	+	index++;
1186	+	}
1187	+	index = 0;
1188	+	usesCharges = 0;
1189	+	while ((index < info[i].n_atoms) && !usesCharges){
1190	+	usesCharges= (info[i].atoms[index])->hasCharge();
1191	+	index++;
1192	+	}
1193	+	#ifdef IS_MPI
1194	+	int myUse = usesDipoles;
1195	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1196	+	#endif //is_mpi
1197	+
1198	+	double theRcut, theRsw;
1199	+
1200	+	if (globals->haveRcut()) {
1201	+	theRcut = globals->getRcut();
1202	+
1203	+	if (globals->haveRsw())
1204	+	theRsw = globals->getRsw();
1205	+	else
1206	+	theRsw = theRcut;
1207	+
1208	+	info[i].setDefaultRcut(theRcut, theRsw);
1209	+
1210	+	} else {
1211	+
1212	+	the_ff->calcRcut();
1213	+	theRcut = info[i].getRcut();
1214	+
1215	+	if (globals->haveRsw())
1216	+	theRsw = globals->getRsw();
1217	+	else
1218	+	theRsw = theRcut;
1219	+
1220	+	info[i].setDefaultRcut(theRcut, theRsw);
1221	+	}
1222	+
1223	+	if (globals->getUseRF()){
1224	+	info[i].useReactionField = 1;
1225	+
1226	+	if (!globals->haveRcut()){
1227	+	sprintf(painCave.errMsg,
1228	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1229	+	"\tOOPSE will use a default value of 15.0 angstroms"
1230	+	"\tfor the cutoffRadius.\n");
1231	+	painCave.isFatal = 0;
1232	+	simError();
1233	+	theRcut = 15.0;
1234	+	}
1235	+	else{
1236	+	theRcut = globals->getRcut();
1237	+	}
1238	+
1239	+	if (!globals->haveRsw()){
1240	+	sprintf(painCave.errMsg,
1241	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1242	+	"\tOOPSE will use a default value of\n"
1243	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1244	+	painCave.isFatal = 0;
1245	+	simError();
1246	+	theRsw = 0.95 * theRcut;
1247	+	}
1248	+	else{
1249	+	theRsw = globals->getRsw();
1250	+	}
1251	+
1252	+	info[i].setDefaultRcut(theRcut, theRsw);
1253	+
1254	+	if (!globals->haveDielectric()){
1255	+	sprintf(painCave.errMsg,
1256	+	"SimSetup Error: No Dielectric constant was set.\n"
1257	+	"\tYou are trying to use Reaction Field without"
1258	+	"\tsetting a dielectric constant!\n");
1259	+	painCave.isFatal = 1;
1260	+	simError();
1261	+	}
1262	+	info[i].dielectric = globals->getDielectric();
1263	+	}
1264	+	else{
1265	+	if (usesDipoles || usesCharges){
1266	+
1267	+	if (!globals->haveRcut()){
1268	+	sprintf(painCave.errMsg,
1269	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1270	+	"\tOOPSE will use a default value of 15.0 angstroms"
1271	+	"\tfor the cutoffRadius.\n");
1272	+	painCave.isFatal = 0;
1273	+	simError();
1274	+	theRcut = 15.0;
1275	+	}
1276	+	else{
1277	+	theRcut = globals->getRcut();
1278	+	}
1279	+
1280	+	if (!globals->haveRsw()){
1281	+	sprintf(painCave.errMsg,
1282	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1283	+	"\tOOPSE will use a default value of\n"
1284	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1285	+	painCave.isFatal = 0;
1286	+	simError();
1287	+	theRsw = 0.95 * theRcut;
1288	+	}
1289	+	else{
1290	+	theRsw = globals->getRsw();
1291	+	}
1292	+
1293	+	info[i].setDefaultRcut(theRcut, theRsw);
1294	+
1295	+	}
1296	+	}
1297		}
1298	+	#ifdef IS_MPI
1299	+	strcpy(checkPointMsg, "post processing checks out");
1300	+	MPIcheckPoint();
1301	+	#endif // is_mpi
1302
1303	<	current_mol++;
1304	<	current_comp_mol++;
1303	>	// clean up the forcefield
1304	>	the_ff->cleanMe();
1305	>	}
1306	>
1307	>	void SimSetup::initSystemCoords(void){
1308	>	int i;
1309
1310	<	if( current_comp_mol >= components_nmol[current_comp] ){
1310	>	char* inName;
1311
1312	<	current_comp_mol = 0;
1313	<	current_comp++;
1312	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1313	>
1314	>	for (i = 0; i < info[0].n_atoms; i++)
1315	>	info[0].atoms[i]->setCoords();
1316	>
1317	>	if (globals->haveInitialConfig()){
1318	>	InitializeFromFile* fileInit;
1319	>	#ifdef IS_MPI // is_mpi
1320	>	if (worldRank == 0){
1321	>	#endif //is_mpi
1322	>	inName = globals->getInitialConfig();
1323	>	fileInit = new InitializeFromFile(inName);
1324	>	#ifdef IS_MPI
1325	>	}
1326	>	else
1327	>	fileInit = new InitializeFromFile(NULL);
1328	>	#endif
1329	>	fileInit->readInit(info); // default velocities on
1330	>
1331	>	delete fileInit;
1332	>	}
1333	>	else{
1334	>
1335	>	// no init from bass
1336	>
1337	>	sprintf(painCave.errMsg,
1338	>	"Cannot intialize a simulation without an initial configuration file.\n");
1339	>	painCave.isFatal = 1;;
1340	>	simError();
1341	>
1342	>	}
1343	>
1344	>	#ifdef IS_MPI
1345	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1346	>	MPIcheckPoint();
1347	>	#endif // is_mpi
1348	>	}
1349	>
1350	>
1351	>	void SimSetup::makeOutNames(void){
1352	>	int k;
1353	>
1354	>
1355	>	for (k = 0; k < nInfo; k++){
1356	>	#ifdef IS_MPI
1357	>	if (worldRank == 0){
1358	>	#endif // is_mpi
1359	>
1360	>	if (globals->haveFinalConfig()){
1361	>	strcpy(info[k].finalName, globals->getFinalConfig());
1362	>	}
1363	>	else{
1364	>	strcpy(info[k].finalName, inFileName);
1365	>	char* endTest;
1366	>	int nameLength = strlen(info[k].finalName);
1367	>	endTest = &(info[k].finalName[nameLength - 5]);
1368	>	if (!strcmp(endTest, ".bass")){
1369	>	strcpy(endTest, ".eor");
1370	>	}
1371	>	else if (!strcmp(endTest, ".BASS")){
1372	>	strcpy(endTest, ".eor");
1373	>	}
1374	>	else{
1375	>	endTest = &(info[k].finalName[nameLength - 4]);
1376	>	if (!strcmp(endTest, ".bss")){
1377	>	strcpy(endTest, ".eor");
1378	>	}
1379	>	else if (!strcmp(endTest, ".mdl")){
1380	>	strcpy(endTest, ".eor");
1381	>	}
1382	>	else{
1383	>	strcat(info[k].finalName, ".eor");
1384	>	}
1385	>	}
1386	>	}
1387	>
1388	>	// make the sample and status out names
1389	>
1390	>	strcpy(info[k].sampleName, inFileName);
1391	>	char* endTest;
1392	>	int nameLength = strlen(info[k].sampleName);
1393	>	endTest = &(info[k].sampleName[nameLength - 5]);
1394	>	if (!strcmp(endTest, ".bass")){
1395	>	strcpy(endTest, ".dump");
1396	>	}
1397	>	else if (!strcmp(endTest, ".BASS")){
1398	>	strcpy(endTest, ".dump");
1399	>	}
1400	>	else{
1401	>	endTest = &(info[k].sampleName[nameLength - 4]);
1402	>	if (!strcmp(endTest, ".bss")){
1403	>	strcpy(endTest, ".dump");
1404	>	}
1405	>	else if (!strcmp(endTest, ".mdl")){
1406	>	strcpy(endTest, ".dump");
1407	>	}
1408	>	else{
1409	>	strcat(info[k].sampleName, ".dump");
1410	>	}
1411	>	}
1412	>
1413	>	strcpy(info[k].statusName, inFileName);
1414	>	nameLength = strlen(info[k].statusName);
1415	>	endTest = &(info[k].statusName[nameLength - 5]);
1416	>	if (!strcmp(endTest, ".bass")){
1417	>	strcpy(endTest, ".stat");
1418	>	}
1419	>	else if (!strcmp(endTest, ".BASS")){
1420	>	strcpy(endTest, ".stat");
1421	>	}
1422	>	else{
1423	>	endTest = &(info[k].statusName[nameLength - 4]);
1424	>	if (!strcmp(endTest, ".bss")){
1425	>	strcpy(endTest, ".stat");
1426	>	}
1427	>	else if (!strcmp(endTest, ".mdl")){
1428	>	strcpy(endTest, ".stat");
1429	>	}
1430	>	else{
1431	>	strcat(info[k].statusName, ".stat");
1432	>	}
1433	>	}
1434	>
1435	>	strcpy(info[k].rawPotName, inFileName);
1436	>	nameLength = strlen(info[k].rawPotName);
1437	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1438	>	if (!strcmp(endTest, ".bass")){
1439	>	strcpy(endTest, ".raw");
1440	>	}
1441	>	else if (!strcmp(endTest, ".BASS")){
1442	>	strcpy(endTest, ".raw");
1443	>	}
1444	>	else{
1445	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1446	>	if (!strcmp(endTest, ".bss")){
1447	>	strcpy(endTest, ".raw");
1448	>	}
1449	>	else if (!strcmp(endTest, ".mdl")){
1450	>	strcpy(endTest, ".raw");
1451	>	}
1452	>	else{
1453	>	strcat(info[k].rawPotName, ".raw");
1454	>	}
1455	>	}
1456	>
1457	>	#ifdef IS_MPI
1458	>
1459	>	}
1460	>	#endif // is_mpi
1461	>	}
1462	>	}
1463	>
1464	>
1465	>	void SimSetup::sysObjectsCreation(void){
1466	>	int i, k;
1467	>
1468	>	// create the forceField
1469	>
1470	>	createFF();
1471	>
1472	>	// extract componentList
1473	>
1474	>	compList();
1475	>
1476	>	// calc the number of atoms, bond, bends, and torsions
1477	>
1478	>	calcSysValues();
1479	>
1480	>	#ifdef IS_MPI
1481	>	// divide the molecules among the processors
1482	>
1483	>	mpiMolDivide();
1484	>	#endif //is_mpi
1485	>
1486	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1487	>
1488	>	makeSysArrays();
1489	>
1490	>	// make and initialize the molecules (all but atomic coordinates)
1491	>
1492	>	makeMolecules();
1493	>
1494	>	for (k = 0; k < nInfo; k++){
1495	>	info[k].identArray = new int[info[k].n_atoms];
1496	>	for (i = 0; i < info[k].n_atoms; i++){
1497	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1498	>	}
1499	>	}
1500	>	}
1501	>
1502	>
1503	>	void SimSetup::createFF(void){
1504	>	switch (ffCase){
1505	>	case FF_DUFF:
1506	>	the_ff = new DUFF();
1507	>	break;
1508	>
1509	>	case FF_LJ:
1510	>	the_ff = new LJFF();
1511	>	break;
1512	>
1513	>	case FF_EAM:
1514	>	the_ff = new EAM_FF();
1515	>	break;
1516	>
1517	>	case FF_H2O:
1518	>	the_ff = new WATER();
1519	>	break;
1520	>
1521	>	default:
1522	>	sprintf(painCave.errMsg,
1523	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1524	>	painCave.isFatal = 1;
1525	>	simError();
1526	>	}
1527	>
1528	>	#ifdef IS_MPI
1529	>	strcpy(checkPointMsg, "ForceField creation successful");
1530	>	MPIcheckPoint();
1531	>	#endif // is_mpi
1532	>	}
1533	>
1534	>
1535	>	void SimSetup::compList(void){
1536	>	int i;
1537	>	char* id;
1538	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1539	>	LinkedMolStamp* currentStamp = NULL;
1540	>	comp_stamps = new MoleculeStamp * [n_components];
1541	>	bool haveCutoffGroups;
1542	>
1543	>	haveCutoffGroups = false;
1544	>
1545	>	// make an array of molecule stamps that match the components used.
1546	>	// also extract the used stamps out into a separate linked list
1547	>
1548	>	for (i = 0; i < nInfo; i++){
1549	>	info[i].nComponents = n_components;
1550	>	info[i].componentsNmol = components_nmol;
1551	>	info[i].compStamps = comp_stamps;
1552	>	info[i].headStamp = headStamp;
1553	>	}
1554	>
1555	>
1556	>	for (i = 0; i < n_components; i++){
1557	>	id = the_components[i]->getType();
1558	>	comp_stamps[i] = NULL;
1559	>
1560	>	// check to make sure the component isn't already in the list
1561	>
1562	>	comp_stamps[i] = headStamp->match(id);
1563	>	if (comp_stamps[i] == NULL){
1564	>	// extract the component from the list;
1565	>
1566	>	currentStamp = stamps->extractMolStamp(id);
1567	>	if (currentStamp == NULL){
1568	>	sprintf(painCave.errMsg,
1569	>	"SimSetup error: Component \"%s\" was not found in the "
1570	>	"list of declared molecules\n",
1571	>	id);
1572	>	painCave.isFatal = 1;
1573	>	simError();
1574	>	}
1575	>
1576	>	headStamp->add(currentStamp);
1577	>	comp_stamps[i] = headStamp->match(id);
1578	>	}
1579	>
1580	>	if(comp_stamps[i]->getNCutoffGroups() > 0)
1581	>	haveCutoffGroups = true;
1582	>	}
1583	>
1584	>	for (i = 0; i < nInfo; i++)
1585	>	info[i].haveCutoffGroups = haveCutoffGroups;
1586	>
1587	>	#ifdef IS_MPI
1588	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1589	>	MPIcheckPoint();
1590	>	#endif // is_mpi
1591	>	}
1592	>
1593	>	void SimSetup::calcSysValues(void){
1594	>	int i, j;
1595	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1596	>
1597	>	int* molMembershipArray;
1598	>	CutoffGroupStamp* cg;
1599	>
1600	>	tot_atoms = 0;
1601	>	tot_bonds = 0;
1602	>	tot_bends = 0;
1603	>	tot_torsions = 0;
1604	>	tot_rigid = 0;
1605	>	tot_groups = 0;
1606	>	for (i = 0; i < n_components; i++){
1607	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1608	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1609	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1610	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1611	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1612	>
1613	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1614	>	atomsingroups = 0;
1615	>	for (j=0; j < ncutgroups; j++) {
1616	>	cg = comp_stamps[i]->getCutoffGroup(j);
1617	>	atomsingroups += cg->getNMembers();
1618	>	}
1619	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1620	>	tot_groups += components_nmol[i] * ngroupsinstamp;
1621	>	}
1622	>
1623	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1624	>	molMembershipArray = new int[tot_atoms];
1625	>
1626	>	for (i = 0; i < nInfo; i++){
1627	>	info[i].n_atoms = tot_atoms;
1628	>	info[i].n_bonds = tot_bonds;
1629	>	info[i].n_bends = tot_bends;
1630	>	info[i].n_torsions = tot_torsions;
1631	>	info[i].n_SRI = tot_SRI;
1632	>	info[i].n_mol = tot_nmol;
1633	>	info[i].ngroup = tot_groups;
1634	>	info[i].molMembershipArray = molMembershipArray;
1635	>	}
1636	>	}
1637	>
1638	>	#ifdef IS_MPI
1639	>
1640	>	void SimSetup::mpiMolDivide(void){
1641	>	int i, j, k;
1642	>	int localMol, allMol;
1643	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1644	>	int local_rigid, local_groups;
1645	>	vector<int> globalMolIndex;
1646	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1647	>	CutoffGroupStamp* cg;
1648	>
1649	>	mpiSim = new mpiSimulation(info);
1650	>
1651	>	mpiSim->divideLabor();
1652	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1653	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1654	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1655	>
1656	>	// set up the local variables
1657	>
1658	>	mol2proc = mpiSim->getMolToProcMap();
1659	>	molCompType = mpiSim->getMolComponentType();
1660	>
1661	>	allMol = 0;
1662	>	localMol = 0;
1663	>	local_atoms = 0;
1664	>	local_bonds = 0;
1665	>	local_bends = 0;
1666	>	local_torsions = 0;
1667	>	local_rigid = 0;
1668	>	local_groups = 0;
1669	>	globalAtomCounter = 0;
1670	>
1671	>	for (i = 0; i < n_components; i++){
1672	>	for (j = 0; j < components_nmol[i]; j++){
1673	>	if (mol2proc[allMol] == worldRank){
1674	>	local_atoms += comp_stamps[i]->getNAtoms();
1675	>	local_bonds += comp_stamps[i]->getNBonds();
1676	>	local_bends += comp_stamps[i]->getNBends();
1677	>	local_torsions += comp_stamps[i]->getNTorsions();
1678	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1679	>
1680	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1681	>	atomsingroups = 0;
1682	>	for (k=0; k < ncutgroups; k++) {
1683	>	cg = comp_stamps[i]->getCutoffGroup(k);
1684	>	atomsingroups += cg->getNMembers();
1685	>	}
1686	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1687	>	ncutgroups;
1688	>	local_groups += ngroupsinstamp;
1689	>
1690	>	localMol++;
1691	>	}
1692	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1693	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1694	>	globalAtomCounter++;
1695	>	}
1696	>
1697	>	allMol++;
1698	>	}
1699	>	}
1700	>	local_SRI = local_bonds + local_bends + local_torsions;
1701	>
1702	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1703	>
1704	>	if (local_atoms != info[0].n_atoms){
1705	>	sprintf(painCave.errMsg,
1706	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1707	>	"\tlocalAtom (%d) are not equal.\n",
1708	>	info[0].n_atoms, local_atoms);
1709	>	painCave.isFatal = 1;
1710	>	simError();
1711	>	}
1712	>
1713	>	info[0].ngroup = mpiSim->getNGroupsLocal();
1714	>	if (local_groups != info[0].ngroup){
1715	>	sprintf(painCave.errMsg,
1716	>	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1717	>	"\tlocalGroups (%d) are not equal.\n",
1718	>	info[0].ngroup, local_groups);
1719	>	painCave.isFatal = 1;
1720	>	simError();
1721	>	}
1722	>
1723	>	info[0].n_bonds = local_bonds;
1724	>	info[0].n_bends = local_bends;
1725	>	info[0].n_torsions = local_torsions;
1726	>	info[0].n_SRI = local_SRI;
1727	>	info[0].n_mol = localMol;
1728	>
1729	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1730	>	MPIcheckPoint();
1731	>	}
1732	>
1733	>	#endif // is_mpi
1734	>
1735	>
1736	>	void SimSetup::makeSysArrays(void){
1737	>
1738	>	#ifndef IS_MPI
1739	>	int k, j;
1740	>	#endif // is_mpi
1741	>	int i, l;
1742	>
1743	>	Atom** the_atoms;
1744	>	Molecule* the_molecules;
1745	>
1746	>	for (l = 0; l < nInfo; l++){
1747	>	// create the atom and short range interaction arrays
1748	>
1749	>	the_atoms = new Atom * [info[l].n_atoms];
1750	>	the_molecules = new Molecule[info[l].n_mol];
1751	>	int molIndex;
1752	>
1753	>	// initialize the molecule's stampID's
1754	>
1755	>	#ifdef IS_MPI
1756	>
1757	>
1758	>	molIndex = 0;
1759	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1760	>	if (mol2proc[i] == worldRank){
1761	>	the_molecules[molIndex].setStampID(molCompType[i]);
1762	>	the_molecules[molIndex].setMyIndex(molIndex);
1763	>	the_molecules[molIndex].setGlobalIndex(i);
1764	>	molIndex++;
1765	>	}
1766	>	}
1767	>
1768	>	#else // is_mpi
1769	>
1770	>	molIndex = 0;
1771	>	globalAtomCounter = 0;
1772	>	for (i = 0; i < n_components; i++){
1773	>	for (j = 0; j < components_nmol[i]; j++){
1774	>	the_molecules[molIndex].setStampID(i);
1775	>	the_molecules[molIndex].setMyIndex(molIndex);
1776	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1777	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1778	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1779	>	globalAtomCounter++;
1780	>	}
1781	>	molIndex++;
1782	>	}
1783	>	}
1784	>
1785	>
1786	>	#endif // is_mpi
1787	>
1788	>	info[l].globalExcludes = new int;
1789	>	info[l].globalExcludes[0] = 0;
1790	>
1791	>	// set the arrays into the SimInfo object
1792	>
1793	>	info[l].atoms = the_atoms;
1794	>	info[l].molecules = the_molecules;
1795	>	info[l].nGlobalExcludes = 0;
1796	>
1797	>	the_ff->setSimInfo(info);
1798		}
1799		}
1800	+
1801	+	void SimSetup::makeIntegrator(void){
1802	+	int k;
1803	+
1804	+	NVE<RealIntegrator>* myNVE = NULL;
1805	+	NVT<RealIntegrator>* myNVT = NULL;
1806	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1807	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1808	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1809	+
1810	+	for (k = 0; k < nInfo; k++){
1811	+	switch (ensembleCase){
1812	+	case NVE_ENS:
1813	+	if (globals->haveZconstraints()){
1814	+	setupZConstraint(info[k]);
1815	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1816	+	}
1817	+	else{
1818	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1819	+	}
1820	+
1821	+	info->the_integrator = myNVE;
1822	+	break;
1823	+
1824	+	case NVT_ENS:
1825	+	if (globals->haveZconstraints()){
1826	+	setupZConstraint(info[k]);
1827	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1828	+	}
1829	+	else
1830	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1831	+
1832	+	myNVT->setTargetTemp(globals->getTargetTemp());
1833	+
1834	+	if (globals->haveTauThermostat())
1835	+	myNVT->setTauThermostat(globals->getTauThermostat());
1836	+	else{
1837	+	sprintf(painCave.errMsg,
1838	+	"SimSetup error: If you use the NVT\n"
1839	+	"\tensemble, you must set tauThermostat.\n");
1840	+	painCave.isFatal = 1;
1841	+	simError();
1842	+	}
1843	+
1844	+	info->the_integrator = myNVT;
1845	+	break;
1846	+
1847	+	case NPTi_ENS:
1848	+	if (globals->haveZconstraints()){
1849	+	setupZConstraint(info[k]);
1850	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1851	+	}
1852	+	else
1853	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1854	+
1855	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1856	+
1857	+	if (globals->haveTargetPressure())
1858	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1859	+	else{
1860	+	sprintf(painCave.errMsg,
1861	+	"SimSetup error: If you use a constant pressure\n"
1862	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1863	+	painCave.isFatal = 1;
1864	+	simError();
1865	+	}
1866	+
1867	+	if (globals->haveTauThermostat())
1868	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1869	+	else{
1870	+	sprintf(painCave.errMsg,
1871	+	"SimSetup error: If you use an NPT\n"
1872	+	"\tensemble, you must set tauThermostat.\n");
1873	+	painCave.isFatal = 1;
1874	+	simError();
1875	+	}
1876	+
1877	+	if (globals->haveTauBarostat())
1878	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1879	+	else{
1880	+	sprintf(painCave.errMsg,
1881	+	"SimSetup error: If you use an NPT\n"
1882	+	"\tensemble, you must set tauBarostat.\n");
1883	+	painCave.isFatal = 1;
1884	+	simError();
1885	+	}
1886	+
1887	+	info->the_integrator = myNPTi;
1888	+	break;
1889	+
1890	+	case NPTf_ENS:
1891	+	if (globals->haveZconstraints()){
1892	+	setupZConstraint(info[k]);
1893	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1894	+	}
1895	+	else
1896	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1897	+
1898	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1899	+
1900	+	if (globals->haveTargetPressure())
1901	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1902	+	else{
1903	+	sprintf(painCave.errMsg,
1904	+	"SimSetup error: If you use a constant pressure\n"
1905	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1906	+	painCave.isFatal = 1;
1907	+	simError();
1908	+	}
1909	+
1910	+	if (globals->haveTauThermostat())
1911	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1912	+
1913	+	else{
1914	+	sprintf(painCave.errMsg,
1915	+	"SimSetup error: If you use an NPT\n"
1916	+	"\tensemble, you must set tauThermostat.\n");
1917	+	painCave.isFatal = 1;
1918	+	simError();
1919	+	}
1920	+
1921	+	if (globals->haveTauBarostat())
1922	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1923	+
1924	+	else{
1925	+	sprintf(painCave.errMsg,
1926	+	"SimSetup error: If you use an NPT\n"
1927	+	"\tensemble, you must set tauBarostat.\n");
1928	+	painCave.isFatal = 1;
1929	+	simError();
1930	+	}
1931	+
1932	+	info->the_integrator = myNPTf;
1933	+	break;
1934	+
1935	+	case NPTxyz_ENS:
1936	+	if (globals->haveZconstraints()){
1937	+	setupZConstraint(info[k]);
1938	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1939	+	}
1940	+	else
1941	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1942	+
1943	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1944	+
1945	+	if (globals->haveTargetPressure())
1946	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1947	+	else{
1948	+	sprintf(painCave.errMsg,
1949	+	"SimSetup error: If you use a constant pressure\n"
1950	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1951	+	painCave.isFatal = 1;
1952	+	simError();
1953	+	}
1954	+
1955	+	if (globals->haveTauThermostat())
1956	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1957	+	else{
1958	+	sprintf(painCave.errMsg,
1959	+	"SimSetup error: If you use an NPT\n"
1960	+	"\tensemble, you must set tauThermostat.\n");
1961	+	painCave.isFatal = 1;
1962	+	simError();
1963	+	}
1964	+
1965	+	if (globals->haveTauBarostat())
1966	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1967	+	else{
1968	+	sprintf(painCave.errMsg,
1969	+	"SimSetup error: If you use an NPT\n"
1970	+	"\tensemble, you must set tauBarostat.\n");
1971	+	painCave.isFatal = 1;
1972	+	simError();
1973	+	}
1974	+
1975	+	info->the_integrator = myNPTxyz;
1976	+	break;
1977	+
1978	+	default:
1979	+	sprintf(painCave.errMsg,
1980	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1981	+	painCave.isFatal = 1;
1982	+	simError();
1983	+	}
1984	+	}
1985	+	}
1986	+
1987	+	void SimSetup::initFortran(void){
1988	+	info[0].refreshSim();
1989	+
1990	+	if (!strcmp(info[0].mixingRule, "standard")){
1991	+	the_ff->initForceField(LB_MIXING_RULE);
1992	+	}
1993	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1994	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1995	+	}
1996	+	else{
1997	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1998	+	info[0].mixingRule);
1999	+	painCave.isFatal = 1;
2000	+	simError();
2001	+	}
2002	+
2003	+
2004	+	#ifdef IS_MPI
2005	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2006	+	MPIcheckPoint();
2007	+	#endif // is_mpi
2008	+	}
2009	+
2010	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
2011	+	int nZConstraints;
2012	+	ZconStamp** zconStamp;
2013	+
2014	+	if (globals->haveZconstraintTime()){
2015	+	//add sample time of z-constraint  into SimInfo's property list
2016	+	DoubleData* zconsTimeProp = new DoubleData();
2017	+	zconsTimeProp->setID(ZCONSTIME_ID);
2018	+	zconsTimeProp->setData(globals->getZconsTime());
2019	+	theInfo.addProperty(zconsTimeProp);
2020	+	}
2021	+	else{
2022	+	sprintf(painCave.errMsg,
2023	+	"ZConstraint error: If you use a ZConstraint,\n"
2024	+	"\tyou must set zconsTime.\n");
2025	+	painCave.isFatal = 1;
2026	+	simError();
2027	+	}
2028	+
2029	+	//push zconsTol into siminfo, if user does not specify
2030	+	//value for zconsTol, a default value will be used
2031	+	DoubleData* zconsTol = new DoubleData();
2032	+	zconsTol->setID(ZCONSTOL_ID);
2033	+	if (globals->haveZconsTol()){
2034	+	zconsTol->setData(globals->getZconsTol());
2035	+	}
2036	+	else{
2037	+	double defaultZConsTol = 0.01;
2038	+	sprintf(painCave.errMsg,
2039	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2040	+	"\tOOPSE will use a default value of %f.\n"
2041	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2042	+	defaultZConsTol);
2043	+	painCave.isFatal = 0;
2044	+	simError();
2045	+
2046	+	zconsTol->setData(defaultZConsTol);
2047	+	}
2048	+	theInfo.addProperty(zconsTol);
2049	+
2050	+	//set Force Subtraction Policy
2051	+	StringData* zconsForcePolicy = new StringData();
2052	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2053	+
2054	+	if (globals->haveZconsForcePolicy()){
2055	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2056	+	}
2057	+	else{
2058	+	sprintf(painCave.errMsg,
2059	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2060	+	"\tOOPSE will use PolicyByMass.\n"
2061	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2062	+	painCave.isFatal = 0;
2063	+	simError();
2064	+	zconsForcePolicy->setData("BYMASS");
2065	+	}
2066	+
2067	+	theInfo.addProperty(zconsForcePolicy);
2068	+
2069	+	//set zcons gap
2070	+	DoubleData* zconsGap = new DoubleData();
2071	+	zconsGap->setID(ZCONSGAP_ID);
2072	+
2073	+	if (globals->haveZConsGap()){
2074	+	zconsGap->setData(globals->getZconsGap());
2075	+	theInfo.addProperty(zconsGap);
2076	+	}
2077	+
2078	+	//set zcons fixtime
2079	+	DoubleData* zconsFixtime = new DoubleData();
2080	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2081	+
2082	+	if (globals->haveZConsFixTime()){
2083	+	zconsFixtime->setData(globals->getZconsFixtime());
2084	+	theInfo.addProperty(zconsFixtime);
2085	+	}
2086	+
2087	+	//set zconsUsingSMD
2088	+	IntData* zconsUsingSMD = new IntData();
2089	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2090	+
2091	+	if (globals->haveZConsUsingSMD()){
2092	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2093	+	theInfo.addProperty(zconsUsingSMD);
2094	+	}
2095	+
2096	+	//Determine the name of ouput file and add it into SimInfo's property list
2097	+	//Be careful, do not use inFileName, since it is a pointer which
2098	+	//point to a string at master node, and slave nodes do not contain that string
2099	+
2100	+	string zconsOutput(theInfo.finalName);
2101	+
2102	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2103	+
2104	+	StringData* zconsFilename = new StringData();
2105	+	zconsFilename->setID(ZCONSFILENAME_ID);
2106	+	zconsFilename->setData(zconsOutput);
2107	+
2108	+	theInfo.addProperty(zconsFilename);
2109	+
2110	+	//setup index, pos and other parameters of z-constraint molecules
2111	+	nZConstraints = globals->getNzConstraints();
2112	+	theInfo.nZconstraints = nZConstraints;
2113	+
2114	+	zconStamp = globals->getZconStamp();
2115	+	ZConsParaItem tempParaItem;
2116	+
2117	+	ZConsParaData* zconsParaData = new ZConsParaData();
2118	+	zconsParaData->setID(ZCONSPARADATA_ID);
2119	+
2120	+	for (int i = 0; i < nZConstraints; i++){
2121	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2122	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2123	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2124	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2125	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2126	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2127	+	zconsParaData->addItem(tempParaItem);
2128	+	}
2129	+
2130	+	//check the uniqueness of index
2131	+	if(!zconsParaData->isIndexUnique()){
2132	+	sprintf(painCave.errMsg,
2133	+	"ZConstraint Error: molIndex is not unique!\n");
2134	+	painCave.isFatal = 1;
2135	+	simError();
2136	+	}
2137	+
2138	+	//sort the parameters by index of molecules
2139	+	zconsParaData->sortByIndex();
2140	+
2141	+	//push data into siminfo, therefore, we can retrieve later
2142	+	theInfo.addProperty(zconsParaData);
2143	+	}
2144	+
2145	+	void SimSetup::makeMinimizer(){
2146	+
2147	+	OOPSEMinimizer* myOOPSEMinimizer;
2148	+	MinimizerParameterSet* param;
2149	+	char minimizerName[100];
2150	+
2151	+	for (int i = 0; i < nInfo; i++){
2152	+
2153	+	//prepare parameter set for minimizer
2154	+	param = new MinimizerParameterSet();
2155	+	param->setDefaultParameter();
2156	+
2157	+	if (globals->haveMinimizer()){
2158	+	param->setFTol(globals->getMinFTol());
2159	+	}
2160	+
2161	+	if (globals->haveMinGTol()){
2162	+	param->setGTol(globals->getMinGTol());
2163	+	}
2164	+
2165	+	if (globals->haveMinMaxIter()){
2166	+	param->setMaxIteration(globals->getMinMaxIter());
2167	+	}
2168	+
2169	+	if (globals->haveMinWriteFrq()){
2170	+	param->setMaxIteration(globals->getMinMaxIter());
2171	+	}
2172	+
2173	+	if (globals->haveMinWriteFrq()){
2174	+	param->setWriteFrq(globals->getMinWriteFrq());
2175	+	}
2176	+
2177	+	if (globals->haveMinStepSize()){
2178	+	param->setStepSize(globals->getMinStepSize());
2179	+	}
2180	+
2181	+	if (globals->haveMinLSMaxIter()){
2182	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2183	+	}
2184	+
2185	+	if (globals->haveMinLSTol()){
2186	+	param->setLineSearchTol(globals->getMinLSTol());
2187	+	}
2188	+
2189	+	strcpy(minimizerName, globals->getMinimizer());
2190	+
2191	+	if (!strcasecmp(minimizerName, "CG")){
2192	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2193	+	}
2194	+	else if (!strcasecmp(minimizerName, "SD")){
2195	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2196	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2197	+	}
2198	+	else{
2199	+	sprintf(painCave.errMsg,
2200	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2201	+	painCave.isFatal = 0;
2202	+	simError();
2203	+
2204	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2205	+	}
2206	+	info[i].the_integrator = myOOPSEMinimizer;
2207	+
2208	+	//store the minimizer into simInfo
2209	+	info[i].the_minimizer = myOOPSEMinimizer;
2210	+	info[i].has_minimizer = true;
2211	+	}
2212	+
2213	+	}

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