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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC vs.
Revision 1452 by tim, Mon Aug 23 15:11:36 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	#include "OOPSEMinimizer.hpp"
14	+	#include "ConstraintElement.hpp"
15	+	#include "ConstraintPair.hpp"
16	+	#include "ConstraintManager.hpp"
17
18		#ifdef IS_MPI
19		#include "mpiBASS.h"
#	Line 14 | Line 22
22
23		// some defines for ensemble and Forcefield  cases
24
25	<	#define NVE_ENS 0
26	<	#define NVT_ENS 1
27	<	#define NPT_ENS 2
25	>	#define NVE_ENS        0
26	>	#define NVT_ENS        1
27	>	#define NPTi_ENS       2
28	>	#define NPTf_ENS       3
29	>	#define NPTxyz_ENS     4
30
21	–	#define FF_DUFF 0
22	–	#define FF_LJ   1
31
32	+	#define FF_DUFF  0
33	+	#define FF_LJ    1
34	+	#define FF_EAM   2
35	+	#define FF_H2O   3
36
37	+	using namespace std;
38	+
39	+	/**
40	+	* Check whether dividend is divisble by divisor or not
41	+	*/
42	+	bool isDivisible(double dividend, double divisor){
43	+	double tolerance = 0.000001;
44	+	double quotient;
45	+	double diff;
46	+	int intQuotient;
47	+
48	+	quotient = dividend / divisor;
49	+
50	+	if (quotient < 0)
51	+	quotient = -quotient;
52	+
53	+	intQuotient = int (quotient + tolerance);
54	+
55	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
56	+
57	+	if (diff <= tolerance)
58	+	return true;
59	+	else
60	+	return false;
61	+	}
62	+
63		SimSetup::SimSetup(){
64	+
65	+	initSuspend = false;
66	+	isInfoArray = 0;
67	+	nInfo = 1;
68	+
69		stamps = new MakeStamps();
70		globals = new Globals();
71	<
71	>
72	>
73		#ifdef IS_MPI
74	<	strcpy( checkPointMsg, "SimSetup creation successful" );
74	>	strcpy(checkPointMsg, "SimSetup creation successful");
75		MPIcheckPoint();
76		#endif // IS_MPI
77		}
#	Line 37 | Line 81 | SimSetup::~SimSetup(){
81		delete globals;
82		}
83
84	<	void SimSetup::parseFile( char* fileName ){
84	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
85	>	info = the_info;
86	>	nInfo = theNinfo;
87	>	isInfoArray = 1;
88	>	initSuspend = true;
89	>	}
90
91	+
92	+	void SimSetup::parseFile(char* fileName){
93		#ifdef IS_MPI
94	<	if( worldRank == 0 ){
94	>	if (worldRank == 0){
95		#endif // is_mpi
96	<
96	>
97		inFileName = fileName;
98	<	set_interface_stamps( stamps, globals );
99	<
98	>	set_interface_stamps(stamps, globals);
99	>
100		#ifdef IS_MPI
101		mpiEventInit();
102		#endif
103
104	<	yacc_BASS( fileName );
104	>	yacc_BASS(fileName);
105
106		#ifdef IS_MPI
107		throwMPIEvent(NULL);
108		}
109	<	else receiveParse();
109	>	else{
110	>	receiveParse();
111	>	}
112		#endif
113
114		}
115
116		#ifdef IS_MPI
117		void SimSetup::receiveParse(void){
118	<
119	<	set_interface_stamps( stamps, globals );
120	<	mpiEventInit();
121	<	MPIcheckPoint();
69	<	mpiEventLoop();
70	<
118	>	set_interface_stamps(stamps, globals);
119	>	mpiEventInit();
120	>	MPIcheckPoint();
121	>	mpiEventLoop();
122		}
123
124		#endif // is_mpi
125
126	<	void SimSetup::createSim( void ){
126	>	void SimSetup::createSim(void){
127
128	<	MakeStamps *the_stamps;
78	<	Globals* the_globals;
79	<	int i, j, k, globalAtomIndex;
80	<
81	<	int ensembleCase;
82	<	int ffCase;
83	<
84	<	ensembleCase = -1;
85	<	ffCase = -1;
128	>	// gather all of the information from the Bass file
129
130	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
130	>	gatherInfo();
131
132	<	// set the easy ones first
92	<	simnfo->target_temp = the_globals->getTargetTemp();
93	<	simnfo->dt = the_globals->getDt();
94	<	simnfo->run_time = the_globals->getRunTime();
132	>	// creation of complex system objects
133
134	<	// get the ones we know are there, yet still may need some work.
97	<	n_components = the_globals->getNComponents();
98	<	strcpy( force_field, the_globals->getForceField() );
134	>	sysObjectsCreation();
135
136	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
101	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102	<	else{
103	<	sprintf( painCave.errMsg,
104	<	"SimSetup Error. Unrecognized force field -> %s\n",
105	<	force_field );
106	<	painCave.isFatal = 1;
107	<	simError();
108	<	}
136	>	// check on the post processing info
137
138	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
138	>	finalInfoCheck();
139
140	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
141	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
142	<	else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS;
143	<	else{
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	<	"reverting to NVE for this simulation.\n",
120	<	ensemble );
121	<	painCave.isFatal = 0;
122	<	simError();
123	<	strcpy( ensemble, "NVE" );
124	<	ensembleCase = NVE_ENS;
140	>	// initialize the system coordinates
141	>
142	>	if ( !initSuspend ){
143	>	initSystemCoords();
144	>
145	>	if( !(globals->getUseInitTime()) )
146	>	info[0].currentTime = 0.0;
147		}
126	–	strcpy( simnfo->ensemble, ensemble );
148
149	+	// make the output filenames
150
151	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
152	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
153	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
154	<	//     if (the_globals->haveTargetPressure())
155	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134	<	//     else {
135	<	//       sprintf( painCave.errMsg,
136	<	//                "SimSetup error: If you use the constant pressure\n"
137	<	//                "    ensemble, you must set targetPressure.\n"
138	<	//                "    This was found in the BASS file.\n");
139	<	//       painCave.isFatal = 1;
140	<	//       simError();
141	<	//     }
151	>	makeOutNames();
152	>
153	>	#ifdef IS_MPI
154	>	mpiSim->mpiRefresh();
155	>	#endif
156
157	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
157	>	// initialize the Fortran
158
159	<	//     if (the_globals->haveTauBarostat())
157	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158	<	//     else {
159	<	//       sprintf( painCave.errMsg,
160	<	//                "SimSetup error: If you use the constant pressure\n"
161	<	//                "    ensemble, you must set tauBarostat.\n"
162	<	//                "    This was found in the BASS file.\n");
163	<	//       painCave.isFatal = 1;
164	<	//       simError();
165	<	//     }
159	>	initFortran();
160
161	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
162	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
163	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
161	>	//creat constraint manager
162	>	for(int i = 0; i < nInfo; i++)
163	>	info[i].consMan = new ConstraintManager(&info[i]);
164
165	<	//     if (the_globals->haveTauThermostat())
166	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
167	<	//     else if (the_globals->haveQmass())
168	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
169	<	//     else {
170	<	//       sprintf( painCave.errMsg,
177	<	//                "SimSetup error: If you use one of the constant temperature\n"
178	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
179	<	//                "    Neither of these was found in the BASS file.\n");
180	<	//       painCave.isFatal = 1;
181	<	//       simError();
182	<	//     }
165	>	if (globals->haveMinimizer())
166	>	// make minimizer
167	>	makeMinimizer();
168	>	else
169	>	// make the integrator
170	>	makeIntegrator();
171
172	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185	<	simnfo->usePBC = the_globals->getPBC();
186	<
187	<	int usesDipoles = 0;
188	<	switch( ffCase ){
172	>	}
173
190	–	case FF_DUFF:
191	–	the_ff = new DUFF();
192	–	usesDipoles = 1;
193	–	break;
174
175	<	case FF_LJ:
176	<	the_ff = new LJFF();
177	<	break;
175	>	void SimSetup::makeMolecules(void){
176	>	int i, j, k;
177	>	int exI, exJ, exK, exL, slI, slJ;
178	>	int tempI, tempJ, tempK, tempL;
179	>	int molI, globalID;
180	>	int stampID, atomOffset, rbOffset, groupOffset;
181	>	molInit molInfo;
182	>	DirectionalAtom* dAtom;
183	>	RigidBody* myRB;
184	>	StuntDouble* mySD;
185	>	LinkedAssign* extras;
186	>	LinkedAssign* current_extra;
187	>	AtomStamp* currentAtom;
188	>	BondStamp* currentBond;
189	>	BendStamp* currentBend;
190	>	TorsionStamp* currentTorsion;
191	>	RigidBodyStamp* currentRigidBody;
192	>	CutoffGroupStamp* currentCutoffGroup;
193	>	CutoffGroup* myCutoffGroup;
194	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
195	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
196
197	<	default:
198	<	sprintf( painCave.errMsg,
199	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
197	>	bond_pair* theBonds;
198	>	bend_set* theBends;
199	>	torsion_set* theTorsions;
200
201	<	#ifdef IS_MPI
207	<	strcpy( checkPointMsg, "ForceField creation successful" );
208	<	MPIcheckPoint();
209	<	#endif // is_mpi
201	>	set<int> skipList;
202
203	<	// get the components and calculate the tot_nMol and indvidual n_mol
204	<	the_components = the_globals->getComponents();
205	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
203	>	double phi, theta, psi;
204	>	char* molName;
205	>	char rbName[100];
206
207	<	if( !the_globals->haveNMol() ){
208	<	// we don't have the total number of molecules, so we assume it is
209	<	// given in each component
207	>	ConstraintPair* consPair; //constraint pair
208	>	ConstraintElement* consElement1;  //first element of constraint pair
209	>	ConstraintElement* consElement2;  //second element of constraint pair
210	>	int whichRigidBody;
211	>	int consAtomIndex;  //index of constraint atom in rigid body's atom array
212	>	vector<pair<int, int> > jointAtoms;
213	>	double bondLength2;
214	>	//init the forceField paramters
215
216	<	tot_nmol = 0;
221	<	for( i=0; i<n_components; i++ ){
216	>	the_ff->readParams();
217
218	<	if( !the_components[i]->haveNMol() ){
224	<	// we have a problem
225	<	sprintf( painCave.errMsg,
226	<	"SimSetup Error. No global NMol or component NMol"
227	<	" given. Cannot calculate the number of atoms.\n" );
228	<	painCave.isFatal = 1;
229	<	simError();
230	<	}
218	>	// init the atoms
219
220	<	tot_nmol += the_components[i]->getNMol();
233	<	components_nmol[i] = the_components[i]->getNMol();
234	<	}
235	<	}
236	<	else{
237	<	sprintf( painCave.errMsg,
238	<	"SimSetup error.\n"
239	<	"\tSorry, the ability to specify total"
240	<	" nMols and then give molfractions in the components\n"
241	<	"\tis not currently supported."
242	<	" Please give nMol in the components.\n" );
243	<	painCave.isFatal = 1;
244	<	simError();
245	<
246	<
247	<	//     tot_nmol = the_globals->getNMol();
248	<
249	<	//   //we have the total number of molecules, now we check for molfractions
250	<	//     for( i=0; i<n_components; i++ ){
251	<
252	<	//       if( !the_components[i]->haveMolFraction() ){
253	<
254	<	//  if( !the_components[i]->haveNMol() ){
255	<	//    //we have a problem
256	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	<	//              << " nMol was given in component
258	<
259	<	}
220	>	int nMembers, nNew, rb1, rb2;
221
222	+	for (k = 0; k < nInfo; k++){
223	+	the_ff->setSimInfo(&(info[k]));
224	+
225		#ifdef IS_MPI
226	<	strcpy( checkPointMsg, "Have the number of components" );
227	<	MPIcheckPoint();
228	<	#endif // is_mpi
226	>	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
227	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
228	>	info[k].globalGroupMembership[i] = 0;
229	>	#else
230	>	info[k].globalGroupMembership = new int[info[k].n_atoms];
231	>	for (i = 0; i < info[k].n_atoms; i++)
232	>	info[k].globalGroupMembership[i] = 0;
233	>	#endif
234
235	<	// make an array of molecule stamps that match the components used.
236	<	// also extract the used stamps out into a separate linked list
235	>	atomOffset = 0;
236	>	groupOffset = 0;
237
238	<	simnfo->nComponents = n_components;
239	<	simnfo->componentsNmol = components_nmol;
240	<	simnfo->compStamps = comp_stamps;
272	<	simnfo->headStamp = new LinkedMolStamp();
273	<
274	<	char* id;
275	<	LinkedMolStamp* headStamp = simnfo->headStamp;
276	<	LinkedMolStamp* currentStamp = NULL;
277	<	for( i=0; i<n_components; i++ ){
238	>	for (i = 0; i < info[k].n_mol; i++){
239	>	stampID = info[k].molecules[i].getStampID();
240	>	molName = comp_stamps[stampID]->getID();
241
242	<	id = the_components[i]->getType();
243	<	comp_stamps[i] = NULL;
244	<
245	<	// check to make sure the component isn't already in the list
242	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
243	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
244	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
245	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
246	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
247
248	<	comp_stamps[i] = headStamp->match( id );
285	<	if( comp_stamps[i] == NULL ){
248	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
249
250	<	// extract the component from the list;
288	<
289	<	currentStamp = the_stamps->extractMolStamp( id );
290	<	if( currentStamp == NULL ){
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup error: Component \"%s\" was not found in the "
293	<	"list of declared molecules\n",
294	<	id );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	headStamp->add( currentStamp );
300	<	comp_stamps[i] = headStamp->match( id );
301	<	}
302	<	}
250	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
251
252	<	#ifdef IS_MPI
253	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
254	<	MPIcheckPoint();
255	<	#endif // is_mpi
308	<
252	>	if (molInfo.nBonds > 0)
253	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
254	>	else
255	>	molInfo.myBonds = NULL;
256
257	+	if (molInfo.nBends > 0)
258	+	molInfo.myBends = new Bend*[molInfo.nBends];
259	+	else
260	+	molInfo.myBends = NULL;
261
262	+	if (molInfo.nTorsions > 0)
263	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
264	+	else
265	+	molInfo.myTorsions = NULL;
266
267	<	// caclulate the number of atoms, bonds, bends and torsions
267	>	theBonds = new bond_pair[molInfo.nBonds];
268	>	theBends = new bend_set[molInfo.nBends];
269	>	theTorsions = new torsion_set[molInfo.nTorsions];
270	>
271	>	// make the Atoms
272
273	<	tot_atoms = 0;
274	<	tot_bonds = 0;
316	<	tot_bends = 0;
317	<	tot_torsions = 0;
318	<	for( i=0; i<n_components; i++ ){
319	<
320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	<	}
273	>	for (j = 0; j < molInfo.nAtoms; j++){
274	>	currentAtom = comp_stamps[stampID]->getAtom(j);
275
276	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
276	>	if (currentAtom->haveOrientation()){
277	>	dAtom = new DirectionalAtom((j + atomOffset),
278	>	info[k].getConfiguration());
279	>	info[k].n_oriented++;
280	>	molInfo.myAtoms[j] = dAtom;
281
282	<	simnfo->n_atoms = tot_atoms;
283	<	simnfo->n_bonds = tot_bonds;
284	<	simnfo->n_bends = tot_bends;
331	<	simnfo->n_torsions = tot_torsions;
332	<	simnfo->n_SRI = tot_SRI;
333	<	simnfo->n_mol = tot_nmol;
334	<
335	<	simnfo->molMembershipArray = new int[tot_atoms];
282	>	// Directional Atoms have standard unit vectors which are oriented
283	>	// in space using the three Euler angles.  We assume the standard
284	>	// unit vector was originally along the z axis below.
285
286	<	#ifdef IS_MPI
286	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
287	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
288	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
289
290	<	// divide the molecules among processors here.
291	<
292	<	mpiSim = new mpiSimulation( simnfo );
293	<
343	<	globalIndex = mpiSim->divideLabor();
290	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
291	>
292	>	}
293	>	else{
294
295	<	// set up the local variables
346	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
295	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
296
297	<	int* mol2proc = mpiSim->getMolToProcMap();
351	<	int* molCompType = mpiSim->getMolComponentType();
352	<
353	<	allMol = 0;
354	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
297	>	}
298
299	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
300	+	#ifdef IS_MPI
301	+	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
302	+	#endif // is_mpi
303	+	}
304
305	<	for( i=0; i<n_components; i++ ){
305	>	// make the bonds
306	>	for (j = 0; j < molInfo.nBonds; j++){
307	>	currentBond = comp_stamps[stampID]->getBond(j);
308	>	theBonds[j].a = currentBond->getA() + atomOffset;
309	>	theBonds[j].b = currentBond->getB() + atomOffset;
310
311	<	for( j=0; j<components_nmol[i]; j++ ){
312	<
366	<	if( mol2proc[allMol] == worldRank ){
367	<
368	<	local_atoms +=    comp_stamps[i]->getNAtoms();
369	<	local_bonds +=    comp_stamps[i]->getNBonds();
370	<	local_bends +=    comp_stamps[i]->getNBends();
371	<	local_torsions += comp_stamps[i]->getNTorsions();
372	<	localMol++;
373	<	}
374	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
377	<	}
311	>	tempI = theBonds[j].a;
312	>	tempJ = theBonds[j].b;
313
314	<	allMol++;
315	<	}
316	<	}
317	<	local_SRI = local_bonds + local_bends + local_torsions;
318	<
319	<	simnfo->n_atoms = mpiSim->getMyNlocal();
320	<
386	<	if( local_atoms != simnfo->n_atoms ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
314	>	#ifdef IS_MPI
315	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
316	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
317	>	#else
318	>	exI = tempI + 1;
319	>	exJ = tempJ + 1;
320	>	#endif
321
322	<	simnfo->n_bonds = local_bonds;
323	<	simnfo->n_bends = local_bends;
398	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
322	>	info[k].excludes->addPair(exI, exJ);
323	>	}
324
325	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
326	<	MPIcheckPoint();
327	<
328	<
329	<	#endif // is_mpi
330	<
325	>	//make the bends
326	>	for (j = 0; j < molInfo.nBends; j++){
327	>	currentBend = comp_stamps[stampID]->getBend(j);
328	>	theBends[j].a = currentBend->getA() + atomOffset;
329	>	theBends[j].b = currentBend->getB() + atomOffset;
330	>	theBends[j].c = currentBend->getC() + atomOffset;
331
332	<	// create the atom and short range interaction arrays
332	>	if (currentBend->haveExtras()){
333	>	extras = currentBend->getExtras();
334	>	current_extra = extras;
335
336	<	Atom::createArrays(simnfo->n_atoms);
337	<	the_atoms = new Atom*[simnfo->n_atoms];
338	<	the_molecules = new Molecule[simnfo->n_mol];
339	<	int molIndex;
340	<
341	<	// initialize the molecule's stampID's
336	>	while (current_extra != NULL){
337	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
338	>	switch (current_extra->getType()){
339	>	case 0:
340	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
341	>	theBends[j].isGhost = 1;
342	>	break;
343
344	+	case 1:
345	+	theBends[j].ghost = (int) current_extra->getDouble() +
346	+	atomOffset;
347	+	theBends[j].isGhost = 1;
348	+	break;
349	+
350	+	default:
351	+	sprintf(painCave.errMsg,
352	+	"SimSetup Error: ghostVectorSource was neither a "
353	+	"double nor an int.\n"
354	+	"-->Bend[%d] in %s\n",
355	+	j, comp_stamps[stampID]->getID());
356	+	painCave.isFatal = 1;
357	+	simError();
358	+	}
359	+	}
360	+	else{
361	+	sprintf(painCave.errMsg,
362	+	"SimSetup Error: unhandled bend assignment:\n"
363	+	"    -->%s in Bend[%d] in %s\n",
364	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
365	+	painCave.isFatal = 1;
366	+	simError();
367	+	}
368	+
369	+	current_extra = current_extra->getNext();
370	+	}
371	+	}
372	+
373	+	if (theBends[j].isGhost) {
374	+
375	+	tempI = theBends[j].a;
376	+	tempJ = theBends[j].b;
377	+
378		#ifdef IS_MPI
379	<
379	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
380	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
381	>	#else
382	>	exI = tempI + 1;
383	>	exJ = tempJ + 1;
384	>	#endif
385	>	info[k].excludes->addPair(exI, exJ);
386
387	<	molIndex = 0;
422	<	for(i=0; i<mpiSim->getTotNmol(); i++){
423	<
424	<	if(mol2proc[i] == worldRank ){
425	<	the_molecules[molIndex].setStampID( molCompType[i] );
426	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
429	<	}
430	<	}
387	>	} else {
388
389	<	#else // is_mpi
390	<
391	<	molIndex = 0;
392	<	globalAtomIndex = 0;
393	<	for(i=0; i<n_components; i++){
394	<	for(j=0; j<components_nmol[i]; j++ ){
395	<	the_molecules[molIndex].setStampID( i );
396	<	the_molecules[molIndex].setMyIndex( molIndex );
397	<	the_molecules[molIndex].setGlobalIndex( molIndex );
398	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
399	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
400	<	globalAtomIndex++;
389	>	tempI = theBends[j].a;
390	>	tempJ = theBends[j].b;
391	>	tempK = theBends[j].c;
392	>
393	>	#ifdef IS_MPI
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	#else
398	>	exI = tempI + 1;
399	>	exJ = tempJ + 1;
400	>	exK = tempK + 1;
401	>	#endif
402	>
403	>	info[k].excludes->addPair(exI, exK);
404	>	info[k].excludes->addPair(exI, exJ);
405	>	info[k].excludes->addPair(exJ, exK);
406	>	}
407		}
445	–	molIndex++;
446	–	}
447	–	}
448	–
408
409	<	#endif // is_mpi
409	>	for (j = 0; j < molInfo.nTorsions; j++){
410	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
411	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
412	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
413	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
414	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
415
416	+	tempI = theTorsions[j].a;
417	+	tempJ = theTorsions[j].b;
418	+	tempK = theTorsions[j].c;
419	+	tempL = theTorsions[j].d;
420
421	<	if( simnfo->n_SRI ){
422	<
423	<	Exclude::createArray(simnfo->n_SRI);
424	<	the_excludes = new Exclude*[simnfo->n_SRI];
425	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
426	<	simnfo->globalExcludes = new int;
427	<	simnfo->n_exclude = simnfo->n_SRI;
428	<	}
429	<	else{
430	<
431	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
421	>	#ifdef IS_MPI
422	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
423	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
424	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
425	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
426	>	#else
427	>	exI = tempI + 1;
428	>	exJ = tempJ + 1;
429	>	exK = tempK + 1;
430	>	exL = tempL + 1;
431	>	#endif
432
433	<	// set the arrays into the SimInfo object
433	>	info[k].excludes->addPair(exI, exJ);
434	>	info[k].excludes->addPair(exI, exK);
435	>	info[k].excludes->addPair(exI, exL);
436	>	info[k].excludes->addPair(exJ, exK);
437	>	info[k].excludes->addPair(exJ, exL);
438	>	info[k].excludes->addPair(exK, exL);
439	>	}
440
441	<	simnfo->atoms = the_atoms;
442	<	simnfo->molecules = the_molecules;
443	<	simnfo->nGlobalExcludes = 0;
444	<	simnfo->excludes = the_excludes;
441	>
442	>	molInfo.myRigidBodies.clear();
443	>
444	>	for (j = 0; j < molInfo.nRigidBodies; j++){
445
446	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
447	+	nMembers = currentRigidBody->getNMembers();
448
449	<	// get some of the tricky things that may still be in the globals
449	>	// Create the Rigid Body:
450
451	<	double boxVector[3];
483	<	if( the_globals->haveBox() ){
484	<	boxVector[0] = the_globals->getBox();
485	<	boxVector[1] = the_globals->getBox();
486	<	boxVector[2] = the_globals->getBox();
487	<
488	<	simnfo->setBox( boxVector );
489	<	}
490	<	else if( the_globals->haveDensity() ){
451	>	myRB = new RigidBody();
452
453	<	double vol;
454	<	vol = (double)tot_nmol / the_globals->getDensity();
455	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
456	<	boxVector[1] = boxVector[0];
496	<	boxVector[2] = boxVector[0];
453	>	sprintf(rbName,"%s_RB_%d", molName, j);
454	>	myRB->setType(rbName);
455	>
456	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
457
458	<	simnfo->setBox( boxVector );
459	<	}
500	<	else{
501	<	if( !the_globals->haveBoxX() ){
502	<	sprintf( painCave.errMsg,
503	<	"SimSetup error, no periodic BoxX size given.\n" );
504	<	painCave.isFatal = 1;
505	<	simError();
506	<	}
507	<	boxVector[0] = the_globals->getBoxX();
458	>	// molI is atom numbering inside this molecule
459	>	molI = currentRigidBody->getMember(rb1);
460
461	<	if( !the_globals->haveBoxY() ){
462	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxY size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[1] = the_globals->getBoxY();
461	>	// tempI is atom numbering on local processor
462	>	tempI = molI + atomOffset;
463
464	<	if( !the_globals->haveBoxZ() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup error, no periodic BoxZ size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	boxVector[2] = the_globals->getBoxZ();
464	>	// currentAtom is the AtomStamp (which we need for
465	>	// rigid body reference positions)
466	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
467
468	<	simnfo->setBox( boxVector );
469	<	}
468	>	// When we add to the rigid body, add the atom itself and
469	>	// the stamp info:
470
471	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
472	+
473	+	// Add this atom to the Skip List for the integrators
474		#ifdef IS_MPI
475	<	strcpy( checkPointMsg, "Box size set up" );
476	<	MPIcheckPoint();
477	<	#endif // is_mpi
475	>	slI = info[k].atoms[tempI]->getGlobalIndex();
476	>	#else
477	>	slI = tempI;
478	>	#endif
479	>	skipList.insert(slI);
480	>
481	>	}
482	>
483	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
484	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
485	>
486	>	tempI = currentRigidBody->getMember(rb1);
487	>	tempJ = currentRigidBody->getMember(rb2);
488	>
489	>	// Some explanation is required here.
490	>	// Fortran indexing starts at 1, while c indexing starts at 0
491	>	// Also, in parallel computations, the GlobalIndex is
492	>	// used for the exclude list:
493	>
494	>	#ifdef IS_MPI
495	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
496	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
497	>	#else
498	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
499	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
500	>	#endif
501	>
502	>	info[k].excludes->addPair(exI, exJ);
503	>
504	>	}
505	>	}
506
507	+	molInfo.myRigidBodies.push_back(myRB);
508	+	info[k].rigidBodies.push_back(myRB);
509	+	}
510	+
511
512	<	// initialize the arrays
512	>	//create cutoff group for molecule
513
514	<	the_ff->setSimInfo( simnfo );
514	>	cutoffAtomSet.clear();
515	>	molInfo.myCutoffGroups.clear();
516	>
517	>	for (j = 0; j < nCutoffGroups; j++){
518
519	<	makeMolecules();
520	<	simnfo->identArray = new int[simnfo->n_atoms];
540	<	for(i=0; i<simnfo->n_atoms; i++){
541	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
542	<	}
543	<
544	<	if (the_globals->getUseRF() ) {
545	<	simnfo->useReactionField = 1;
546	<
547	<	if( !the_globals->haveECR() ){
548	<	sprintf( painCave.errMsg,
549	<	"SimSetup Warning: using default value of 1/2 the smallest "
550	<	"box length for the electrostaticCutoffRadius.\n"
551	<	"I hope you have a very fast processor!\n");
552	<	painCave.isFatal = 0;
553	<	simError();
554	<	double smallest;
555	<	smallest = simnfo->boxLx;
556	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
557	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
558	<	simnfo->ecr = 0.5 * smallest;
559	<	} else {
560	<	simnfo->ecr        = the_globals->getECR();
561	<	}
519	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
520	>	nMembers = currentCutoffGroup->getNMembers();
521
522	<	if( !the_globals->haveEST() ){
523	<	sprintf( painCave.errMsg,
524	<	"SimSetup Warning: using default value of 0.05 * the "
525	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
526	<	);
527	<	painCave.isFatal = 0;
528	<	simError();
529	<	simnfo->est = 0.05 * simnfo->ecr;
530	<	} else {
531	<	simnfo->est        = the_globals->getEST();
532	<	}
533	<
534	<	if(!the_globals->haveDielectric() ){
535	<	sprintf( painCave.errMsg,
536	<	"SimSetup Error: You are trying to use Reaction Field without"
537	<	"setting a dielectric constant!\n"
538	<	);
539	<	painCave.isFatal = 1;
540	<	simError();
541	<	}
542	<	simnfo->dielectric = the_globals->getDielectric();
543	<	} else {
544	<	if (usesDipoles) {
522	>	myCutoffGroup = new CutoffGroup();
523	>
524	>	#ifdef IS_MPI
525	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
526	>	#else
527	>	myCutoffGroup->setGlobalIndex(groupOffset);
528	>	#endif
529	>
530	>	for (int cg = 0; cg < nMembers; cg++) {
531	>
532	>	// molI is atom numbering inside this molecule
533	>	molI = currentCutoffGroup->getMember(cg);
534	>
535	>	// tempI is atom numbering on local processor
536	>	tempI = molI + atomOffset;
537	>
538	>	#ifdef IS_MPI
539	>	globalID = info[k].atoms[tempI]->getGlobalIndex();
540	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
541	>	#else
542	>	globalID = info[k].atoms[tempI]->getIndex();
543	>	info[k].globalGroupMembership[globalID] = groupOffset;
544	>	#endif
545	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
546	>	cutoffAtomSet.insert(tempI);
547	>	}
548	>
549	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
550	>	groupOffset++;
551	>
552	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
553
587	–	if( !the_globals->haveECR() ){
588	–	sprintf( painCave.errMsg,
589	–	"SimSetup Warning: using default value of 1/2 the smallest "
590	–	"box length for the electrostaticCutoffRadius.\n"
591	–	"I hope you have a very fast processor!\n");
592	–	painCave.isFatal = 0;
593	–	simError();
594	–	double smallest;
595	–	smallest = simnfo->boxLx;
596	–	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
597	–	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
598	–	simnfo->ecr = 0.5 * smallest;
599	–	} else {
600	–	simnfo->ecr        = the_globals->getECR();
601	–	}
554
555	<	if( !the_globals->haveEST() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 5%% of the "
558	<	"electrostaticCutoffRadius for the "
559	<	"electrostaticSkinThickness\n"
560	<	);
561	<	painCave.isFatal = 0;
562	<	simError();
563	<	simnfo->est = 0.05 * simnfo->ecr;
564	<	} else {
565	<	simnfo->est        = the_globals->getEST();
555	>	// create a cutoff group for every atom in current molecule which
556	>	// does not belong to cutoffgroup defined at mdl file
557	>
558	>	for(j = 0; j < molInfo.nAtoms; j++){
559	>
560	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
561	>	myCutoffGroup = new CutoffGroup();
562	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
563	>
564	>	#ifdef IS_MPI
565	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
566	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
567	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
568	>	#else
569	>	myCutoffGroup->setGlobalIndex(groupOffset);
570	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
571	>	info[k].globalGroupMembership[globalID] = groupOffset;
572	>	#endif
573	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
574	>	groupOffset++;
575	>	}
576		}
615	–	}
616	–	}
577
578	<	#ifdef IS_MPI
579	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
620	<	MPIcheckPoint();
621	<	#endif // is_mpi
578	>	// After this is all set up, scan through the atoms to
579	>	// see if they can be added to the integrableObjects:
580
581	<	if( the_globals->haveInitialConfig() ){
582	<
583	<	InitializeFromFile* fileInit;
584	<	#ifdef IS_MPI // is_mpi
585	<	if( worldRank == 0 ){
628	<	#endif //is_mpi
629	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
581	>	molInfo.myIntegrableObjects.clear();
582	>
583	>
584	>	for (j = 0; j < molInfo.nAtoms; j++){
585	>
586		#ifdef IS_MPI
587	<	}else fileInit = new InitializeFromFile( NULL );
587	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
588	>	#else
589	>	slJ = j+atomOffset;
590		#endif
633	–	fileInit->read_xyz( simnfo ); // default velocities on
591
592	<	delete fileInit;
636	<	}
637	<	else{
592	>	// if they aren't on the skip list, then they can be integrated
593
594	<	#ifdef IS_MPI
594	>	if (skipList.find(slJ) == skipList.end()) {
595	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
596	>	info[k].integrableObjects.push_back(mySD);
597	>	molInfo.myIntegrableObjects.push_back(mySD);
598	>	}
599	>	}
600
601	<	// no init from bass
642	<
643	<	sprintf( painCave.errMsg,
644	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
645	<	painCave.isFatal;
646	<	simError();
647	<
648	<	#else
601	>	// all rigid bodies are integrated:
602
603	<	initFromBass();
603	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
604	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
605	>	info[k].integrableObjects.push_back(mySD);
606	>	molInfo.myIntegrableObjects.push_back(mySD);
607	>	}
608	>
609	>	// send the arrays off to the forceField for init.
610	>
611	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
612	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
613	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
614	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
615	>	theTorsions);
616
617
618	<	#endif
619	<	}
618	>	//creat ConstraintPair.
619	>	molInfo.myConstraintPairs.clear();
620	>
621	>	for (j = 0; j < molInfo.nBonds; j++){
622
623	<	#ifdef IS_MPI
624	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
658	<	MPIcheckPoint();
659	<	#endif // is_mpi
623	>	//if bond is constrained bond, add it into constraint pair
624	>	if(molInfo.myBonds[j]->is_constrained()){
625
626	+	//if both atoms are in the same rigid body, just skip it
627	+	currentBond = comp_stamps[stampID]->getBond(j);
628	+
629	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
630
631	<
632	<
633	<
631	>	tempI = currentBond->getA() + atomOffset;
632	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
633	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
634	>	else
635	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
636
637	<
638	<	#ifdef IS_MPI
639	<	if( worldRank == 0 ){
640	<	#endif // is_mpi
641	<
671	<	if( the_globals->haveFinalConfig() ){
672	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
673	<	}
674	<	else{
675	<	strcpy( simnfo->finalName, inFileName );
676	<	char* endTest;
677	<	int nameLength = strlen( simnfo->finalName );
678	<	endTest = &(simnfo->finalName[nameLength - 5]);
679	<	if( !strcmp( endTest, ".bass" ) ){
680	<	strcpy( endTest, ".eor" );
681	<	}
682	<	else if( !strcmp( endTest, ".BASS" ) ){
683	<	strcpy( endTest, ".eor" );
684	<	}
685	<	else{
686	<	endTest = &(simnfo->finalName[nameLength - 4]);
687	<	if( !strcmp( endTest, ".bss" ) ){
688	<	strcpy( endTest, ".eor" );
689	<	}
690	<	else if( !strcmp( endTest, ".mdl" ) ){
691	<	strcpy( endTest, ".eor" );
692	<	}
693	<	else{
694	<	strcat( simnfo->finalName, ".eor" );
695	<	}
696	<	}
697	<	}
698	<
699	<	// make the sample and status out names
700	<
701	<	strcpy( simnfo->sampleName, inFileName );
702	<	char* endTest;
703	<	int nameLength = strlen( simnfo->sampleName );
704	<	endTest = &(simnfo->sampleName[nameLength - 5]);
705	<	if( !strcmp( endTest, ".bass" ) ){
706	<	strcpy( endTest, ".dump" );
707	<	}
708	<	else if( !strcmp( endTest, ".BASS" ) ){
709	<	strcpy( endTest, ".dump" );
710	<	}
711	<	else{
712	<	endTest = &(simnfo->sampleName[nameLength - 4]);
713	<	if( !strcmp( endTest, ".bss" ) ){
714	<	strcpy( endTest, ".dump" );
715	<	}
716	<	else if( !strcmp( endTest, ".mdl" ) ){
717	<	strcpy( endTest, ".dump" );
718	<	}
719	<	else{
720	<	strcat( simnfo->sampleName, ".dump" );
721	<	}
722	<	}
723	<
724	<	strcpy( simnfo->statusName, inFileName );
725	<	nameLength = strlen( simnfo->statusName );
726	<	endTest = &(simnfo->statusName[nameLength - 5]);
727	<	if( !strcmp( endTest, ".bass" ) ){
728	<	strcpy( endTest, ".stat" );
729	<	}
730	<	else if( !strcmp( endTest, ".BASS" ) ){
731	<	strcpy( endTest, ".stat" );
732	<	}
733	<	else{
734	<	endTest = &(simnfo->statusName[nameLength - 4]);
735	<	if( !strcmp( endTest, ".bss" ) ){
736	<	strcpy( endTest, ".stat" );
737	<	}
738	<	else if( !strcmp( endTest, ".mdl" ) ){
739	<	strcpy( endTest, ".stat" );
740	<	}
741	<	else{
742	<	strcat( simnfo->statusName, ".stat" );
743	<	}
744	<	}
745	<
746	<	#ifdef IS_MPI
747	<	}
748	<	#endif // is_mpi
749	<
750	<	// set the status, sample, and themal kick times
751	<
752	<	if( the_globals->haveSampleTime() ){
753	<	simnfo->sampleTime = the_globals->getSampleTime();
754	<	simnfo->statusTime = simnfo->sampleTime;
755	<	simnfo->thermalTime = simnfo->sampleTime;
756	<	}
757	<	else{
758	<	simnfo->sampleTime = the_globals->getRunTime();
759	<	simnfo->statusTime = simnfo->sampleTime;
760	<	simnfo->thermalTime = simnfo->sampleTime;
761	<	}
637	>	tempJ =  currentBond->getB() + atomOffset;
638	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
639	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
640	>	else
641	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
642
643	<	if( the_globals->haveStatusTime() ){
644	<	simnfo->statusTime = the_globals->getStatusTime();
765	<	}
643	>	bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr();
644	>	consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2);
645
646	<	if( the_globals->haveThermalTime() ){
647	<	simnfo->thermalTime = the_globals->getThermalTime();
648	<	}
646	>	molInfo.myConstraintPairs.push_back(consPair);
647	>	}
648	>	}//end if(molInfo.myBonds[j]->is_constrained())
649	>	}
650	>
651	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair
652	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
653	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
654	>
655	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
656
657	<	// check for the temperature set flag
657	>	for(size_t m = 0; m < jointAtoms.size(); m++){
658	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
659	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
660
661	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
661	>	consPair = new JointConstraintPair(consElement1, consElement2);
662	>	molInfo.myConstraintPairs.push_back(consPair);
663	>	}
664
665	+	}
666	+	}
667	+
668
669	<	// make the integrator
670	<
671	<
672	<	NVT* myNVT = NULL;
673	<	switch( ensembleCase ){
674	<
675	<	case NVE_ENS:
783	<	new NVE( simnfo, the_ff );
784	<	break;
785	<
786	<	case NVT_ENS:
787	<	myNVT = new NVT( simnfo, the_ff );
788	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
789	<
790	<	if (the_globals->haveTauThermostat())
791	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
792	<	//     else if (the_globals->haveQmass())
793	<	//       myNVT->setQmass(the_globals->getQmass());
794	<	else {
795	<	sprintf( painCave.errMsg,
796	<	"SimSetup error: If you use the NVT\n"
797	<	"    ensemble, you must set either tauThermostat or qMass.\n"
798	<	"    Neither of these was found in the BASS file.\n");
799	<	painCave.isFatal = 1;
800	<	simError();
669	>	info[k].molecules[i].initialize(molInfo);
670	>
671	>
672	>	atomOffset += molInfo.nAtoms;
673	>	delete[] theBonds;
674	>	delete[] theBends;
675	>	delete[] theTorsions;
676		}
802	–	break;
677
804	–	default:
805	–	sprintf( painCave.errMsg,
806	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
807	–	painCave.isFatal = 1;
808	–	simError();
809	–	}
678
679
680	<	#ifdef IS_MPI
681	<	mpiSim->mpiRefresh();
682	<	#endif
680	>	#ifdef IS_MPI
681	>	// Since the globalGroupMembership has been zero filled and we've only
682	>	// poked values into the atoms we know, we can do an Allreduce
683	>	// to get the full globalGroupMembership array (We think).
684	>	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
685	>	// docs said we could.
686
687	<	// initialize the Fortran
687	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
688
689	<
690	<	simnfo->refreshSim();
691	<
692	<	if( !strcmp( simnfo->mixingRule, "standard") ){
822	<	the_ff->initForceField( LB_MIXING_RULE );
823	<	}
824	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
825	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
826	<	}
827	<	else{
828	<	sprintf( painCave.errMsg,
829	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
830	<	simnfo->mixingRule );
831	<	painCave.isFatal = 1;
832	<	simError();
833	<	}
834	<
835	<
836	<	#ifdef IS_MPI
837	<	strcpy( checkPointMsg,
838	<	"Successfully intialized the mixingRule for Fortran." );
839	<	MPIcheckPoint();
840	<	#endif // is_mpi
841	<	}
842	<
843	<
844	<	void SimSetup::makeMolecules( void ){
845	<
846	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
847	<	molInit info;
848	<	DirectionalAtom* dAtom;
849	<	LinkedAssign* extras;
850	<	LinkedAssign* current_extra;
851	<	AtomStamp* currentAtom;
852	<	BondStamp* currentBond;
853	<	BendStamp* currentBend;
854	<	TorsionStamp* currentTorsion;
855	<
856	<	bond_pair* theBonds;
857	<	bend_set* theBends;
858	<	torsion_set* theTorsions;
859	<
860	<
861	<	//init the forceField paramters
862	<
863	<	the_ff->readParams();
864	<
865	<
866	<	// init the atoms
867	<
868	<	double ux, uy, uz, u, uSqr;
869	<
870	<	atomOffset = 0;
871	<	excludeOffset = 0;
872	<	for(i=0; i<simnfo->n_mol; i++){
873	<
874	<	stampID = the_molecules[i].getStampID();
875	<
876	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
877	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
878	<	info.nBends    = comp_stamps[stampID]->getNBends();
879	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
880	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
881	<
882	<	info.myAtoms = &the_atoms[atomOffset];
883	<	info.myExcludes = &the_excludes[excludeOffset];
884	<	info.myBonds = new Bond*[info.nBonds];
885	<	info.myBends = new Bend*[info.nBends];
886	<	info.myTorsions = new Torsion*[info.nTorsions];
887	<
888	<	theBonds = new bond_pair[info.nBonds];
889	<	theBends = new bend_set[info.nBends];
890	<	theTorsions = new torsion_set[info.nTorsions];
891	<
892	<	// make the Atoms
893	<
894	<	for(j=0; j<info.nAtoms; j++){
895	<
896	<	currentAtom = comp_stamps[stampID]->getAtom( j );
897	<	if( currentAtom->haveOrientation() ){
898	<
899	<	dAtom = new DirectionalAtom(j + atomOffset);
900	<	simnfo->n_oriented++;
901	<	info.myAtoms[j] = dAtom;
902	<
903	<	ux = currentAtom->getOrntX();
904	<	uy = currentAtom->getOrntY();
905	<	uz = currentAtom->getOrntZ();
906	<
907	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
908	<
909	<	u = sqrt( uSqr );
910	<	ux = ux / u;
911	<	uy = uy / u;
912	<	uz = uz / u;
913	<
914	<	dAtom->setSUx( ux );
915	<	dAtom->setSUy( uy );
916	<	dAtom->setSUz( uz );
917	<	}
918	<	else{
919	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
920	<	}
921	<	info.myAtoms[j]->setType( currentAtom->getType() );
922	<
923	<	#ifdef IS_MPI
924	<
925	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
926	<
927	<	#endif // is_mpi
928	<	}
929	<
930	<	// make the bonds
931	<	for(j=0; j<info.nBonds; j++){
932	<
933	<	currentBond = comp_stamps[stampID]->getBond( j );
934	<	theBonds[j].a = currentBond->getA() + atomOffset;
935	<	theBonds[j].b = currentBond->getB() + atomOffset;
689	>	MPI_Allreduce(info[k].globalGroupMembership,
690	>	ggMjunk,
691	>	mpiSim->getNAtomsGlobal(),
692	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
693
694	<	exI = theBonds[j].a;
695	<	exJ = theBonds[j].b;
694	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
695	>	info[k].globalGroupMembership[i] = ggMjunk[i];
696
697	<	// exclude_I must always be the smaller of the pair
941	<	if( exI > exJ ){
942	<	tempEx = exI;
943	<	exI = exJ;
944	<	exJ = tempEx;
945	<	}
946	<	#ifdef IS_MPI
947	<	tempEx = exI;
948	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
949	<	tempEx = exJ;
950	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
951	<
952	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
953	<	#else  // isn't MPI
954	<
955	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
956	<	#endif  //is_mpi
957	<	}
958	<	excludeOffset += info.nBonds;
959	<
960	<	//make the bends
961	<	for(j=0; j<info.nBends; j++){
962	<
963	<	currentBend = comp_stamps[stampID]->getBend( j );
964	<	theBends[j].a = currentBend->getA() + atomOffset;
965	<	theBends[j].b = currentBend->getB() + atomOffset;
966	<	theBends[j].c = currentBend->getC() + atomOffset;
967	<
968	<	if( currentBend->haveExtras() ){
969	<
970	<	extras = currentBend->getExtras();
971	<	current_extra = extras;
972	<
973	<	while( current_extra != NULL ){
974	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
975	<
976	<	switch( current_extra->getType() ){
977	<
978	<	case 0:
979	<	theBends[j].ghost =
980	<	current_extra->getInt() + atomOffset;
981	<	theBends[j].isGhost = 1;
982	<	break;
983	<
984	<	case 1:
985	<	theBends[j].ghost =
986	<	(int)current_extra->getDouble() + atomOffset;
987	<	theBends[j].isGhost = 1;
988	<	break;
989	<
990	<	default:
991	<	sprintf( painCave.errMsg,
992	<	"SimSetup Error: ghostVectorSource was neither a "
993	<	"double nor an int.\n"
994	<	"-->Bend[%d] in %s\n",
995	<	j, comp_stamps[stampID]->getID() );
996	<	painCave.isFatal = 1;
997	<	simError();
998	<	}
999	<	}
1000	<
1001	<	else{
1002	<
1003	<	sprintf( painCave.errMsg,
1004	<	"SimSetup Error: unhandled bend assignment:\n"
1005	<	"    -->%s in Bend[%d] in %s\n",
1006	<	current_extra->getlhs(),
1007	<	j, comp_stamps[stampID]->getID() );
1008	<	painCave.isFatal = 1;
1009	<	simError();
1010	<	}
1011	<
1012	<	current_extra = current_extra->getNext();
1013	<	}
1014	<	}
1015	<
1016	<	if( !theBends[j].isGhost ){
1017	<
1018	<	exI = theBends[j].a;
1019	<	exJ = theBends[j].c;
1020	<	}
1021	<	else{
1022	<
1023	<	exI = theBends[j].a;
1024	<	exJ = theBends[j].b;
1025	<	}
1026	<
1027	<	// exclude_I must always be the smaller of the pair
1028	<	if( exI > exJ ){
1029	<	tempEx = exI;
1030	<	exI = exJ;
1031	<	exJ = tempEx;
1032	<	}
1033	<	#ifdef IS_MPI
1034	<	tempEx = exI;
1035	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1036	<	tempEx = exJ;
1037	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1038	<
1039	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1040	<	#else  // isn't MPI
1041	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1042	<	#endif  //is_mpi
1043	<	}
1044	<	excludeOffset += info.nBends;
1045	<
1046	<	for(j=0; j<info.nTorsions; j++){
1047	<
1048	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1049	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1050	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1051	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1052	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1053	<
1054	<	exI = theTorsions[j].a;
1055	<	exJ = theTorsions[j].d;
1056	<
1057	<	// exclude_I must always be the smaller of the pair
1058	<	if( exI > exJ ){
1059	<	tempEx = exI;
1060	<	exI = exJ;
1061	<	exJ = tempEx;
1062	<	}
1063	<	#ifdef IS_MPI
1064	<	tempEx = exI;
1065	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1066	<	tempEx = exJ;
1067	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1068	<
1069	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1070	<	#else  // isn't MPI
1071	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1072	<	#endif  //is_mpi
1073	<	}
1074	<	excludeOffset += info.nTorsions;
1075	<
697	>	delete[] ggMjunk;
698
699	<	// send the arrays off to the forceField for init.
699	>	#endif
700
1079	–	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1080	–	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1081	–	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1082	–	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
701
702
1085	–	the_molecules[i].initialize( info );
1086	–
1087	–
1088	–	atomOffset += info.nAtoms;
1089	–	delete[] theBonds;
1090	–	delete[] theBends;
1091	–	delete[] theTorsions;
703		}
704
705		#ifdef IS_MPI
706	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
706	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
707		MPIcheckPoint();
708		#endif // is_mpi
709
1099	–	// clean up the forcefield
1100	–	the_ff->calcRcut();
1101	–	the_ff->cleanMe();
1102	–
710		}
711
712	<	void SimSetup::initFromBass( void ){
1106	<
712	>	void SimSetup::initFromBass(void){
713		int i, j, k;
714		int n_cells;
715		double cellx, celly, cellz;
#	Line 1112 | Line 718 | void SimSetup::initFromBass( void ){
718		int n_extra;
719		int have_extra, done;
720
721	<	temp1 = (double)tot_nmol / 4.0;
722	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
723	<	temp3 = ceil( temp2 );
721	>	double vel[3];
722	>	vel[0] = 0.0;
723	>	vel[1] = 0.0;
724	>	vel[2] = 0.0;
725
726	<	have_extra =0;
727	<	if( temp2 < temp3 ){ // we have a non-complete lattice
728	<	have_extra =1;
726	>	temp1 = (double) tot_nmol / 4.0;
727	>	temp2 = pow(temp1, (1.0 / 3.0));
728	>	temp3 = ceil(temp2);
729
730	<	n_cells = (int)temp3 - 1;
731	<	cellx = simnfo->boxLx / temp3;
732	<	celly = simnfo->boxLy / temp3;
733	<	cellz = simnfo->boxLz / temp3;
1127	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1128	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1129	<	n_per_extra = (int)ceil( temp1 );
730	>	have_extra = 0;
731	>	if (temp2 < temp3){
732	>	// we have a non-complete lattice
733	>	have_extra = 1;
734
735	<	if( n_per_extra > 4){
736	<	sprintf( painCave.errMsg,
737	<	"SimSetup error. There has been an error in constructing"
738	<	" the non-complete lattice.\n" );
735	>	n_cells = (int) temp3 - 1;
736	>	cellx = info[0].boxL[0] / temp3;
737	>	celly = info[0].boxL[1] / temp3;
738	>	cellz = info[0].boxL[2] / temp3;
739	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
740	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
741	>	n_per_extra = (int) ceil(temp1);
742	>
743	>	if (n_per_extra > 4){
744	>	sprintf(painCave.errMsg,
745	>	"SimSetup error. There has been an error in constructing"
746	>	" the non-complete lattice.\n");
747		painCave.isFatal = 1;
748		simError();
749		}
750		}
751		else{
752	<	n_cells = (int)temp3;
753	<	cellx = simnfo->boxLx / temp3;
754	<	celly = simnfo->boxLy / temp3;
755	<	cellz = simnfo->boxLz / temp3;
752	>	n_cells = (int) temp3;
753	>	cellx = info[0].boxL[0] / temp3;
754	>	celly = info[0].boxL[1] / temp3;
755	>	cellz = info[0].boxL[2] / temp3;
756		}
757
758		current_mol = 0;
#	Line 1148 | Line 760 | void SimSetup::initFromBass( void ){
760		current_comp = 0;
761		current_atom_ndx = 0;
762
763	<	for( i=0; i < n_cells ; i++ ){
764	<	for( j=0; j < n_cells; j++ ){
765	<	for( k=0; k < n_cells; k++ ){
763	>	for (i = 0; i < n_cells ; i++){
764	>	for (j = 0; j < n_cells; j++){
765	>	for (k = 0; k < n_cells; k++){
766	>	makeElement(i * cellx, j * celly, k * cellz);
767
768	<	makeElement( i * cellx,
1156	<	j * celly,
1157	<	k * cellz );
768	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
769
770	<	makeElement( i * cellx + 0.5 * cellx,
1160	<	j * celly + 0.5 * celly,
1161	<	k * cellz );
770	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
771
772	<	makeElement( i * cellx,
1164	<	j * celly + 0.5 * celly,
1165	<	k * cellz + 0.5 * cellz );
1166	<
1167	<	makeElement( i * cellx + 0.5 * cellx,
1168	<	j * celly,
1169	<	k * cellz + 0.5 * cellz );
772	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
773		}
774		}
775		}
776
777	<	if( have_extra ){
777	>	if (have_extra){
778		done = 0;
779
780		int start_ndx;
781	<	for( i=0; i < (n_cells+1) && !done; i++ ){
782	<	for( j=0; j < (n_cells+1) && !done; j++ ){
781	>	for (i = 0; i < (n_cells + 1) && !done; i++){
782	>	for (j = 0; j < (n_cells + 1) && !done; j++){
783	>	if (i < n_cells){
784	>	if (j < n_cells){
785	>	start_ndx = n_cells;
786	>	}
787	>	else
788	>	start_ndx = 0;
789	>	}
790	>	else
791	>	start_ndx = 0;
792
793	<	if( i < n_cells ){
793	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
794	>	makeElement(i * cellx, j * celly, k * cellz);
795	>	done = (current_mol >= tot_nmol);
796
797	<	if( j < n_cells ){
798	<	start_ndx = n_cells;
799	<	}
800	<	else start_ndx = 0;
801	<	}
1188	<	else start_ndx = 0;
797	>	if (!done && n_per_extra > 1){
798	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
799	>	k * cellz);
800	>	done = (current_mol >= tot_nmol);
801	>	}
802
803	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
803	>	if (!done && n_per_extra > 2){
804	>	makeElement(i * cellx, j * celly + 0.5 * celly,
805	>	k * cellz + 0.5 * cellz);
806	>	done = (current_mol >= tot_nmol);
807	>	}
808
809	<	makeElement( i * cellx,
810	<	j * celly,
811	<	k * cellz );
812	<	done = ( current_mol >= tot_nmol );
813	<
814	<	if( !done && n_per_extra > 1 ){
1198	<	makeElement( i * cellx + 0.5 * cellx,
1199	<	j * celly + 0.5 * celly,
1200	<	k * cellz );
1201	<	done = ( current_mol >= tot_nmol );
1202	<	}
1203	<
1204	<	if( !done && n_per_extra > 2){
1205	<	makeElement( i * cellx,
1206	<	j * celly + 0.5 * celly,
1207	<	k * cellz + 0.5 * cellz );
1208	<	done = ( current_mol >= tot_nmol );
1209	<	}
1210	<
1211	<	if( !done && n_per_extra > 3){
1212	<	makeElement( i * cellx + 0.5 * cellx,
1213	<	j * celly,
1214	<	k * cellz + 0.5 * cellz );
1215	<	done = ( current_mol >= tot_nmol );
1216	<	}
1217	<	}
809	>	if (!done && n_per_extra > 3){
810	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
811	>	k * cellz + 0.5 * cellz);
812	>	done = (current_mol >= tot_nmol);
813	>	}
814	>	}
815		}
816		}
817		}
818
819	<
820	<	for( i=0; i<simnfo->n_atoms; i++ ){
1224	<	simnfo->atoms[i]->set_vx( 0.0 );
1225	<	simnfo->atoms[i]->set_vy( 0.0 );
1226	<	simnfo->atoms[i]->set_vz( 0.0 );
819	>	for (i = 0; i < info[0].n_atoms; i++){
820	>	info[0].atoms[i]->setVel(vel);
821		}
822		}
823
824	<	void SimSetup::makeElement( double x, double y, double z ){
1231	<
824	>	void SimSetup::makeElement(double x, double y, double z){
825		int k;
826		AtomStamp* current_atom;
827		DirectionalAtom* dAtom;
828		double rotMat[3][3];
829	+	double pos[3];
830
831	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
832	<
833	<	current_atom = comp_stamps[current_comp]->getAtom( k );
834	<	if( !current_atom->havePosition() ){
835	<	sprintf( painCave.errMsg,
836	<	"SimSetup:initFromBass error.\n"
837	<	"\tComponent %s, atom %s does not have a position specified.\n"
838	<	"\tThe initialization routine is unable to give a start"
839	<	" position.\n",
1246	<	comp_stamps[current_comp]->getID(),
1247	<	current_atom->getType() );
831	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
832	>	current_atom = comp_stamps[current_comp]->getAtom(k);
833	>	if (!current_atom->havePosition()){
834	>	sprintf(painCave.errMsg,
835	>	"SimSetup:initFromBass error.\n"
836	>	"\tComponent %s, atom %s does not have a position specified.\n"
837	>	"\tThe initialization routine is unable to give a start"
838	>	" position.\n",
839	>	comp_stamps[current_comp]->getID(), current_atom->getType());
840		painCave.isFatal = 1;
841		simError();
842		}
843
844	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
845	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
846	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
844	>	pos[0] = x + current_atom->getPosX();
845	>	pos[1] = y + current_atom->getPosY();
846	>	pos[2] = z + current_atom->getPosZ();
847
848	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
848	>	info[0].atoms[current_atom_ndx]->setPos(pos);
849
850	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
850	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
851	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
852
853		rotMat[0][0] = 1.0;
854		rotMat[0][1] = 0.0;
#	Line 1269 | Line 862 | void SimSetup::makeElement( double x, double y, double
862		rotMat[2][1] = 0.0;
863		rotMat[2][2] = 1.0;
864
865	<	dAtom->setA( rotMat );
865	>	dAtom->setA(rotMat);
866		}
867
868		current_atom_ndx++;
#	Line 1278 | Line 871 | void SimSetup::makeElement( double x, double y, double
871		current_mol++;
872		current_comp_mol++;
873
874	<	if( current_comp_mol >= components_nmol[current_comp] ){
1282	<
874	>	if (current_comp_mol >= components_nmol[current_comp]){
875		current_comp_mol = 0;
876		current_comp++;
877	+	}
878	+	}
879	+
880	+
881	+	void SimSetup::gatherInfo(void){
882	+	int i;
883	+
884	+	ensembleCase = -1;
885	+	ffCase = -1;
886	+
887	+	// set the easy ones first
888	+
889	+	for (i = 0; i < nInfo; i++){
890	+	info[i].target_temp = globals->getTargetTemp();
891	+	info[i].dt = globals->getDt();
892	+	info[i].run_time = globals->getRunTime();
893	+	}
894	+	n_components = globals->getNComponents();
895	+
896	+
897	+	// get the forceField
898	+
899	+	strcpy(force_field, globals->getForceField());
900	+
901	+	if (!strcasecmp(force_field, "DUFF")){
902	+	ffCase = FF_DUFF;
903	+	}
904	+	else if (!strcasecmp(force_field, "LJ")){
905	+	ffCase = FF_LJ;
906	+	}
907	+	else if (!strcasecmp(force_field, "EAM")){
908	+	ffCase = FF_EAM;
909	+	}
910	+	else if (!strcasecmp(force_field, "WATER")){
911	+	ffCase = FF_H2O;
912	+	}
913	+	else{
914	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
915	+	force_field);
916	+	painCave.isFatal = 1;
917	+	simError();
918	+	}
919	+	if (globals->haveForceFieldVariant()) {
920	+	strcpy(forcefield_variant, globals->getForceFieldVariant());
921	+	has_forcefield_variant = 1;
922	+	}
923	+
924	+	// get the ensemble
925	+
926	+	strcpy(ensemble, globals->getEnsemble());
927	+
928	+	if (!strcasecmp(ensemble, "NVE")){
929	+	ensembleCase = NVE_ENS;
930	+	}
931	+	else if (!strcasecmp(ensemble, "NVT")){
932	+	ensembleCase = NVT_ENS;
933	+	}
934	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
935	+	ensembleCase = NPTi_ENS;
936	+	}
937	+	else if (!strcasecmp(ensemble, "NPTf")){
938	+	ensembleCase = NPTf_ENS;
939	+	}
940	+	else if (!strcasecmp(ensemble, "NPTxyz")){
941	+	ensembleCase = NPTxyz_ENS;
942	+	}
943	+	else{
944	+	sprintf(painCave.errMsg,
945	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
946	+	"\treverting to NVE for this simulation.\n",
947	+	ensemble);
948	+	painCave.isFatal = 0;
949	+	simError();
950	+	strcpy(ensemble, "NVE");
951	+	ensembleCase = NVE_ENS;
952	+	}
953	+
954	+	for (i = 0; i < nInfo; i++){
955	+	strcpy(info[i].ensemble, ensemble);
956	+
957	+	// get the mixing rule
958	+
959	+	strcpy(info[i].mixingRule, globals->getMixingRule());
960	+	info[i].usePBC = globals->getPBC();
961	+	}
962	+
963	+	// get the components and calculate the tot_nMol and indvidual n_mol
964	+
965	+	the_components = globals->getComponents();
966	+	components_nmol = new int[n_components];
967	+
968	+
969	+	if (!globals->haveNMol()){
970	+	// we don't have the total number of molecules, so we assume it is
971	+	// given in each component
972	+
973	+	tot_nmol = 0;
974	+	for (i = 0; i < n_components; i++){
975	+	if (!the_components[i]->haveNMol()){
976	+	// we have a problem
977	+	sprintf(painCave.errMsg,
978	+	"SimSetup Error. No global NMol or component NMol given.\n"
979	+	"\tCannot calculate the number of atoms.\n");
980	+	painCave.isFatal = 1;
981	+	simError();
982	+	}
983	+
984	+	tot_nmol += the_components[i]->getNMol();
985	+	components_nmol[i] = the_components[i]->getNMol();
986	+	}
987	+	}
988	+	else{
989	+	sprintf(painCave.errMsg,
990	+	"SimSetup error.\n"
991	+	"\tSorry, the ability to specify total"
992	+	" nMols and then give molfractions in the components\n"
993	+	"\tis not currently supported."
994	+	" Please give nMol in the components.\n");
995	+	painCave.isFatal = 1;
996	+	simError();
997	+	}
998	+
999	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
1000	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
1001	+	sprintf(painCave.errMsg,
1002	+	"Sample time is not divisible by dt.\n"
1003	+	"\tThis will result in samples that are not uniformly\n"
1004	+	"\tdistributed in time.  If this is a problem, change\n"
1005	+	"\tyour sampleTime variable.\n");
1006	+	painCave.isFatal = 0;
1007	+	simError();
1008		}
1009	+
1010	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
1011	+	sprintf(painCave.errMsg,
1012	+	"Status time is not divisible by dt.\n"
1013	+	"\tThis will result in status reports that are not uniformly\n"
1014	+	"\tdistributed in time.  If this is a problem, change \n"
1015	+	"\tyour statusTime variable.\n");
1016	+	painCave.isFatal = 0;
1017	+	simError();
1018	+	}
1019	+
1020	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1021	+	sprintf(painCave.errMsg,
1022	+	"Thermal time is not divisible by dt.\n"
1023	+	"\tThis will result in thermalizations that are not uniformly\n"
1024	+	"\tdistributed in time.  If this is a problem, change \n"
1025	+	"\tyour thermalTime variable.\n");
1026	+	painCave.isFatal = 0;
1027	+	simError();
1028	+	}
1029	+
1030	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1031	+	sprintf(painCave.errMsg,
1032	+	"Reset time is not divisible by dt.\n"
1033	+	"\tThis will result in integrator resets that are not uniformly\n"
1034	+	"\tdistributed in time.  If this is a problem, change\n"
1035	+	"\tyour resetTime variable.\n");
1036	+	painCave.isFatal = 0;
1037	+	simError();
1038	+	}
1039	+
1040	+	// set the status, sample, and thermal kick times
1041	+
1042	+	for (i = 0; i < nInfo; i++){
1043	+	if (globals->haveSampleTime()){
1044	+	info[i].sampleTime = globals->getSampleTime();
1045	+	info[i].statusTime = info[i].sampleTime;
1046	+	}
1047	+	else{
1048	+	info[i].sampleTime = globals->getRunTime();
1049	+	info[i].statusTime = info[i].sampleTime;
1050	+	}
1051	+
1052	+	if (globals->haveStatusTime()){
1053	+	info[i].statusTime = globals->getStatusTime();
1054	+	}
1055	+
1056	+	if (globals->haveThermalTime()){
1057	+	info[i].thermalTime = globals->getThermalTime();
1058	+	} else {
1059	+	info[i].thermalTime = globals->getRunTime();
1060	+	}
1061	+
1062	+	info[i].resetIntegrator = 0;
1063	+	if( globals->haveResetTime() ){
1064	+	info[i].resetTime = globals->getResetTime();
1065	+	info[i].resetIntegrator = 1;
1066	+	}
1067	+
1068	+	// check for the temperature set flag
1069	+
1070	+	if (globals->haveTempSet())
1071	+	info[i].setTemp = globals->getTempSet();
1072	+
1073	+	// check for the extended State init
1074	+
1075	+	info[i].useInitXSstate = globals->getUseInitXSstate();
1076	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1077	+
1078	+	// check for thermodynamic integration
1079	+	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1080	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1081	+	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1082	+	info[i].thermIntLambda = globals->getThermIntLambda();
1083	+	info[i].thermIntK = globals->getThermIntK();
1084	+
1085	+	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1086	+	info[i].restraint = myRestraint;
1087	+	}
1088	+	else {
1089	+	sprintf(painCave.errMsg,
1090	+	"SimSetup Error:\n"
1091	+	"\tKeyword useSolidThermInt was set to 'true' but\n"
1092	+	"\tthermodynamicIntegrationLambda (and/or\n"
1093	+	"\tthermodynamicIntegrationK) was not specified.\n"
1094	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1095	+	painCave.isFatal = 1;
1096	+	simError();
1097	+	}
1098	+	}
1099	+	else if(globals->getUseLiquidThermInt()) {
1100	+	if (globals->getUseSolidThermInt()) {
1101	+	sprintf( painCave.errMsg,
1102	+	"SimSetup Warning: It appears that you have both solid and\n"
1103	+	"\tliquid thermodynamic integration activated in your .bass\n"
1104	+	"\tfile. To avoid confusion, specify only one technique in\n"
1105	+	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1106	+	"\twill be assumed for the current simulation. If this is not\n"
1107	+	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1108	+	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1109	+	painCave.isFatal = 0;
1110	+	simError();
1111	+	}
1112	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1113	+	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1114	+	info[i].thermIntLambda = globals->getThermIntLambda();
1115	+	info[i].thermIntK = globals->getThermIntK();
1116	+	}
1117	+	else {
1118	+	sprintf(painCave.errMsg,
1119	+	"SimSetup Error:\n"
1120	+	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1121	+	"\tthermodynamicIntegrationLambda (and/or\n"
1122	+	"\tthermodynamicIntegrationK) was not specified.\n"
1123	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1124	+	painCave.isFatal = 1;
1125	+	simError();
1126	+	}
1127	+	}
1128	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1129	+	sprintf(painCave.errMsg,
1130	+	"SimSetup Warning: If you want to use Thermodynamic\n"
1131	+	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1132	+	"\t'true' in your .bass file.  These keywords are set to\n"
1133	+	"\t'false' by default, so your lambda and/or k values are\n"
1134	+	"\tbeing ignored.\n");
1135	+	painCave.isFatal = 0;
1136	+	simError();
1137	+	}
1138	+	}
1139	+
1140	+	//setup seed for random number generator
1141	+	int seedValue;
1142	+
1143	+	if (globals->haveSeed()){
1144	+	seedValue = globals->getSeed();
1145	+
1146	+	if(seedValue / 1E9 == 0){
1147	+	sprintf(painCave.errMsg,
1148	+	"Seed for sprng library should contain at least 9 digits\n"
1149	+	"OOPSE will generate a seed for user\n");
1150	+	painCave.isFatal = 0;
1151	+	simError();
1152	+
1153	+	//using seed generated by system instead of invalid seed set by user
1154	+	#ifndef IS_MPI
1155	+	seedValue = make_sprng_seed();
1156	+	#else
1157	+	if (worldRank == 0){
1158	+	seedValue = make_sprng_seed();
1159	+	}
1160	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1161	+	#endif
1162	+	}
1163	+	}//end of if branch of globals->haveSeed()
1164	+	else{
1165	+
1166	+	#ifndef IS_MPI
1167	+	seedValue = make_sprng_seed();
1168	+	#else
1169	+	if (worldRank == 0){
1170	+	seedValue = make_sprng_seed();
1171	+	}
1172	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1173	+	#endif
1174	+	}//end of globals->haveSeed()
1175	+
1176	+	for (int i = 0; i < nInfo; i++){
1177	+	info[i].setSeed(seedValue);
1178	+	}
1179	+
1180	+	#ifdef IS_MPI
1181	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1182	+	MPIcheckPoint();
1183	+	#endif // is_mpi
1184		}
1185	+
1186	+
1187	+	void SimSetup::finalInfoCheck(void){
1188	+	int index;
1189	+	int usesDipoles;
1190	+	int usesCharges;
1191	+	int i;
1192	+
1193	+	for (i = 0; i < nInfo; i++){
1194	+	// check electrostatic parameters
1195	+
1196	+	index = 0;
1197	+	usesDipoles = 0;
1198	+	while ((index < info[i].n_atoms) && !usesDipoles){
1199	+	usesDipoles = (info[i].atoms[index])->hasDipole();
1200	+	index++;
1201	+	}
1202	+	index = 0;
1203	+	usesCharges = 0;
1204	+	while ((index < info[i].n_atoms) && !usesCharges){
1205	+	usesCharges= (info[i].atoms[index])->hasCharge();
1206	+	index++;
1207	+	}
1208	+	#ifdef IS_MPI
1209	+	int myUse = usesDipoles;
1210	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1211	+	#endif //is_mpi
1212	+
1213	+	double theRcut, theRsw;
1214	+
1215	+	if (globals->haveRcut()) {
1216	+	theRcut = globals->getRcut();
1217	+
1218	+	if (globals->haveRsw())
1219	+	theRsw = globals->getRsw();
1220	+	else
1221	+	theRsw = theRcut;
1222	+
1223	+	info[i].setDefaultRcut(theRcut, theRsw);
1224	+
1225	+	} else {
1226	+
1227	+	the_ff->calcRcut();
1228	+	theRcut = info[i].getRcut();
1229	+
1230	+	if (globals->haveRsw())
1231	+	theRsw = globals->getRsw();
1232	+	else
1233	+	theRsw = theRcut;
1234	+
1235	+	info[i].setDefaultRcut(theRcut, theRsw);
1236	+	}
1237	+
1238	+	if (globals->getUseRF()){
1239	+	info[i].useReactionField = 1;
1240	+
1241	+	if (!globals->haveRcut()){
1242	+	sprintf(painCave.errMsg,
1243	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1244	+	"\tOOPSE will use a default value of 15.0 angstroms"
1245	+	"\tfor the cutoffRadius.\n");
1246	+	painCave.isFatal = 0;
1247	+	simError();
1248	+	theRcut = 15.0;
1249	+	}
1250	+	else{
1251	+	theRcut = globals->getRcut();
1252	+	}
1253	+
1254	+	if (!globals->haveRsw()){
1255	+	sprintf(painCave.errMsg,
1256	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1257	+	"\tOOPSE will use a default value of\n"
1258	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1259	+	painCave.isFatal = 0;
1260	+	simError();
1261	+	theRsw = 0.95 * theRcut;
1262	+	}
1263	+	else{
1264	+	theRsw = globals->getRsw();
1265	+	}
1266	+
1267	+	info[i].setDefaultRcut(theRcut, theRsw);
1268	+
1269	+	if (!globals->haveDielectric()){
1270	+	sprintf(painCave.errMsg,
1271	+	"SimSetup Error: No Dielectric constant was set.\n"
1272	+	"\tYou are trying to use Reaction Field without"
1273	+	"\tsetting a dielectric constant!\n");
1274	+	painCave.isFatal = 1;
1275	+	simError();
1276	+	}
1277	+	info[i].dielectric = globals->getDielectric();
1278	+	}
1279	+	else{
1280	+	if (usesDipoles || usesCharges){
1281	+
1282	+	if (!globals->haveRcut()){
1283	+	sprintf(painCave.errMsg,
1284	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1285	+	"\tOOPSE will use a default value of 15.0 angstroms"
1286	+	"\tfor the cutoffRadius.\n");
1287	+	painCave.isFatal = 0;
1288	+	simError();
1289	+	theRcut = 15.0;
1290	+	}
1291	+	else{
1292	+	theRcut = globals->getRcut();
1293	+	}
1294	+
1295	+	if (!globals->haveRsw()){
1296	+	sprintf(painCave.errMsg,
1297	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1298	+	"\tOOPSE will use a default value of\n"
1299	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1300	+	painCave.isFatal = 0;
1301	+	simError();
1302	+	theRsw = 0.95 * theRcut;
1303	+	}
1304	+	else{
1305	+	theRsw = globals->getRsw();
1306	+	}
1307	+
1308	+	info[i].setDefaultRcut(theRcut, theRsw);
1309	+
1310	+	}
1311	+	}
1312	+	}
1313	+	#ifdef IS_MPI
1314	+	strcpy(checkPointMsg, "post processing checks out");
1315	+	MPIcheckPoint();
1316	+	#endif // is_mpi
1317	+
1318	+	// clean up the forcefield
1319	+	the_ff->cleanMe();
1320	+	}
1321	+
1322	+	void SimSetup::initSystemCoords(void){
1323	+	int i;
1324	+
1325	+	char* inName;
1326	+
1327	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1328	+
1329	+	for (i = 0; i < info[0].n_atoms; i++)
1330	+	info[0].atoms[i]->setCoords();
1331	+
1332	+	if (globals->haveInitialConfig()){
1333	+	InitializeFromFile* fileInit;
1334	+	#ifdef IS_MPI // is_mpi
1335	+	if (worldRank == 0){
1336	+	#endif //is_mpi
1337	+	inName = globals->getInitialConfig();
1338	+	fileInit = new InitializeFromFile(inName);
1339	+	#ifdef IS_MPI
1340	+	}
1341	+	else
1342	+	fileInit = new InitializeFromFile(NULL);
1343	+	#endif
1344	+	fileInit->readInit(info); // default velocities on
1345	+
1346	+	delete fileInit;
1347	+	}
1348	+	else{
1349	+
1350	+	// no init from bass
1351	+
1352	+	sprintf(painCave.errMsg,
1353	+	"Cannot intialize a simulation without an initial configuration file.\n");
1354	+	painCave.isFatal = 1;;
1355	+	simError();
1356	+
1357	+	}
1358	+
1359	+	#ifdef IS_MPI
1360	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1361	+	MPIcheckPoint();
1362	+	#endif // is_mpi
1363	+	}
1364	+
1365	+
1366	+	void SimSetup::makeOutNames(void){
1367	+	int k;
1368	+
1369	+
1370	+	for (k = 0; k < nInfo; k++){
1371	+	#ifdef IS_MPI
1372	+	if (worldRank == 0){
1373	+	#endif // is_mpi
1374	+
1375	+	if (globals->haveFinalConfig()){
1376	+	strcpy(info[k].finalName, globals->getFinalConfig());
1377	+	}
1378	+	else{
1379	+	strcpy(info[k].finalName, inFileName);
1380	+	char* endTest;
1381	+	int nameLength = strlen(info[k].finalName);
1382	+	endTest = &(info[k].finalName[nameLength - 5]);
1383	+	if (!strcmp(endTest, ".bass")){
1384	+	strcpy(endTest, ".eor");
1385	+	}
1386	+	else if (!strcmp(endTest, ".BASS")){
1387	+	strcpy(endTest, ".eor");
1388	+	}
1389	+	else{
1390	+	endTest = &(info[k].finalName[nameLength - 4]);
1391	+	if (!strcmp(endTest, ".bss")){
1392	+	strcpy(endTest, ".eor");
1393	+	}
1394	+	else if (!strcmp(endTest, ".mdl")){
1395	+	strcpy(endTest, ".eor");
1396	+	}
1397	+	else{
1398	+	strcat(info[k].finalName, ".eor");
1399	+	}
1400	+	}
1401	+	}
1402	+
1403	+	// make the sample and status out names
1404	+
1405	+	strcpy(info[k].sampleName, inFileName);
1406	+	char* endTest;
1407	+	int nameLength = strlen(info[k].sampleName);
1408	+	endTest = &(info[k].sampleName[nameLength - 5]);
1409	+	if (!strcmp(endTest, ".bass")){
1410	+	strcpy(endTest, ".dump");
1411	+	}
1412	+	else if (!strcmp(endTest, ".BASS")){
1413	+	strcpy(endTest, ".dump");
1414	+	}
1415	+	else{
1416	+	endTest = &(info[k].sampleName[nameLength - 4]);
1417	+	if (!strcmp(endTest, ".bss")){
1418	+	strcpy(endTest, ".dump");
1419	+	}
1420	+	else if (!strcmp(endTest, ".mdl")){
1421	+	strcpy(endTest, ".dump");
1422	+	}
1423	+	else{
1424	+	strcat(info[k].sampleName, ".dump");
1425	+	}
1426	+	}
1427	+
1428	+	strcpy(info[k].statusName, inFileName);
1429	+	nameLength = strlen(info[k].statusName);
1430	+	endTest = &(info[k].statusName[nameLength - 5]);
1431	+	if (!strcmp(endTest, ".bass")){
1432	+	strcpy(endTest, ".stat");
1433	+	}
1434	+	else if (!strcmp(endTest, ".BASS")){
1435	+	strcpy(endTest, ".stat");
1436	+	}
1437	+	else{
1438	+	endTest = &(info[k].statusName[nameLength - 4]);
1439	+	if (!strcmp(endTest, ".bss")){
1440	+	strcpy(endTest, ".stat");
1441	+	}
1442	+	else if (!strcmp(endTest, ".mdl")){
1443	+	strcpy(endTest, ".stat");
1444	+	}
1445	+	else{
1446	+	strcat(info[k].statusName, ".stat");
1447	+	}
1448	+	}
1449	+
1450	+	strcpy(info[k].rawPotName, inFileName);
1451	+	nameLength = strlen(info[k].rawPotName);
1452	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1453	+	if (!strcmp(endTest, ".bass")){
1454	+	strcpy(endTest, ".raw");
1455	+	}
1456	+	else if (!strcmp(endTest, ".BASS")){
1457	+	strcpy(endTest, ".raw");
1458	+	}
1459	+	else{
1460	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1461	+	if (!strcmp(endTest, ".bss")){
1462	+	strcpy(endTest, ".raw");
1463	+	}
1464	+	else if (!strcmp(endTest, ".mdl")){
1465	+	strcpy(endTest, ".raw");
1466	+	}
1467	+	else{
1468	+	strcat(info[k].rawPotName, ".raw");
1469	+	}
1470	+	}
1471	+
1472	+	#ifdef IS_MPI
1473	+
1474	+	}
1475	+	#endif // is_mpi
1476	+	}
1477	+	}
1478	+
1479	+
1480	+	void SimSetup::sysObjectsCreation(void){
1481	+	int i, k;
1482	+
1483	+	// create the forceField
1484	+
1485	+	createFF();
1486	+
1487	+	// extract componentList
1488	+
1489	+	compList();
1490	+
1491	+	// calc the number of atoms, bond, bends, and torsions
1492	+
1493	+	calcSysValues();
1494	+
1495	+	#ifdef IS_MPI
1496	+	// divide the molecules among the processors
1497	+
1498	+	mpiMolDivide();
1499	+	#endif //is_mpi
1500	+
1501	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1502	+
1503	+	makeSysArrays();
1504	+
1505	+	// make and initialize the molecules (all but atomic coordinates)
1506	+
1507	+	makeMolecules();
1508	+
1509	+	for (k = 0; k < nInfo; k++){
1510	+	info[k].identArray = new int[info[k].n_atoms];
1511	+	for (i = 0; i < info[k].n_atoms; i++){
1512	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1513	+	}
1514	+	}
1515	+	}
1516	+
1517	+
1518	+	void SimSetup::createFF(void){
1519	+	switch (ffCase){
1520	+	case FF_DUFF:
1521	+	the_ff = new DUFF();
1522	+	break;
1523	+
1524	+	case FF_LJ:
1525	+	the_ff = new LJFF();
1526	+	break;
1527	+
1528	+	case FF_EAM:
1529	+	if (has_forcefield_variant)
1530	+	the_ff = new EAM_FF(forcefield_variant);
1531	+	else
1532	+	the_ff = new EAM_FF();
1533	+	break;
1534	+
1535	+	case FF_H2O:
1536	+	the_ff = new WATER();
1537	+	break;
1538	+
1539	+	default:
1540	+	sprintf(painCave.errMsg,
1541	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1542	+	painCave.isFatal = 1;
1543	+	simError();
1544	+	}
1545	+
1546	+
1547	+	#ifdef IS_MPI
1548	+	strcpy(checkPointMsg, "ForceField creation successful");
1549	+	MPIcheckPoint();
1550	+	#endif // is_mpi
1551	+	}
1552	+
1553	+
1554	+	void SimSetup::compList(void){
1555	+	int i;
1556	+	char* id;
1557	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1558	+	LinkedMolStamp* currentStamp = NULL;
1559	+	comp_stamps = new MoleculeStamp * [n_components];
1560	+	bool haveCutoffGroups;
1561	+
1562	+	haveCutoffGroups = false;
1563	+
1564	+	// make an array of molecule stamps that match the components used.
1565	+	// also extract the used stamps out into a separate linked list
1566	+
1567	+	for (i = 0; i < nInfo; i++){
1568	+	info[i].nComponents = n_components;
1569	+	info[i].componentsNmol = components_nmol;
1570	+	info[i].compStamps = comp_stamps;
1571	+	info[i].headStamp = headStamp;
1572	+	}
1573	+
1574	+
1575	+	for (i = 0; i < n_components; i++){
1576	+	id = the_components[i]->getType();
1577	+	comp_stamps[i] = NULL;
1578	+
1579	+	// check to make sure the component isn't already in the list
1580	+
1581	+	comp_stamps[i] = headStamp->match(id);
1582	+	if (comp_stamps[i] == NULL){
1583	+	// extract the component from the list;
1584	+
1585	+	currentStamp = stamps->extractMolStamp(id);
1586	+	if (currentStamp == NULL){
1587	+	sprintf(painCave.errMsg,
1588	+	"SimSetup error: Component \"%s\" was not found in the "
1589	+	"list of declared molecules\n",
1590	+	id);
1591	+	painCave.isFatal = 1;
1592	+	simError();
1593	+	}
1594	+
1595	+	headStamp->add(currentStamp);
1596	+	comp_stamps[i] = headStamp->match(id);
1597	+	}
1598	+
1599	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1600	+	haveCutoffGroups = true;
1601	+	}
1602	+
1603	+	for (i = 0; i < nInfo; i++)
1604	+	info[i].haveCutoffGroups = haveCutoffGroups;
1605	+
1606	+	#ifdef IS_MPI
1607	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1608	+	MPIcheckPoint();
1609	+	#endif // is_mpi
1610	+	}
1611	+
1612	+	void SimSetup::calcSysValues(void){
1613	+	int i, j;
1614	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1615	+
1616	+	int* molMembershipArray;
1617	+	CutoffGroupStamp* cg;
1618	+
1619	+	tot_atoms = 0;
1620	+	tot_bonds = 0;
1621	+	tot_bends = 0;
1622	+	tot_torsions = 0;
1623	+	tot_rigid = 0;
1624	+	tot_groups = 0;
1625	+	for (i = 0; i < n_components; i++){
1626	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1627	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1628	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1629	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1630	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1631	+
1632	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1633	+	atomsingroups = 0;
1634	+	for (j=0; j < ncutgroups; j++) {
1635	+	cg = comp_stamps[i]->getCutoffGroup(j);
1636	+	atomsingroups += cg->getNMembers();
1637	+	}
1638	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1639	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1640	+	}
1641	+
1642	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1643	+	molMembershipArray = new int[tot_atoms];
1644	+
1645	+	for (i = 0; i < nInfo; i++){
1646	+	info[i].n_atoms = tot_atoms;
1647	+	info[i].n_bonds = tot_bonds;
1648	+	info[i].n_bends = tot_bends;
1649	+	info[i].n_torsions = tot_torsions;
1650	+	info[i].n_SRI = tot_SRI;
1651	+	info[i].n_mol = tot_nmol;
1652	+	info[i].ngroup = tot_groups;
1653	+	info[i].molMembershipArray = molMembershipArray;
1654	+	}
1655	+	}
1656	+
1657	+	#ifdef IS_MPI
1658	+
1659	+	void SimSetup::mpiMolDivide(void){
1660	+	int i, j, k;
1661	+	int localMol, allMol;
1662	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1663	+	int local_rigid, local_groups;
1664	+	vector<int> globalMolIndex;
1665	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1666	+	CutoffGroupStamp* cg;
1667	+
1668	+	mpiSim = new mpiSimulation(info);
1669	+
1670	+	mpiSim->divideLabor();
1671	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1672	+	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1673	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1674	+
1675	+	// set up the local variables
1676	+
1677	+	mol2proc = mpiSim->getMolToProcMap();
1678	+	molCompType = mpiSim->getMolComponentType();
1679	+
1680	+	allMol = 0;
1681	+	localMol = 0;
1682	+	local_atoms = 0;
1683	+	local_bonds = 0;
1684	+	local_bends = 0;
1685	+	local_torsions = 0;
1686	+	local_rigid = 0;
1687	+	local_groups = 0;
1688	+	globalAtomCounter = 0;
1689	+
1690	+	for (i = 0; i < n_components; i++){
1691	+	for (j = 0; j < components_nmol[i]; j++){
1692	+	if (mol2proc[allMol] == worldRank){
1693	+	local_atoms += comp_stamps[i]->getNAtoms();
1694	+	local_bonds += comp_stamps[i]->getNBonds();
1695	+	local_bends += comp_stamps[i]->getNBends();
1696	+	local_torsions += comp_stamps[i]->getNTorsions();
1697	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1698	+
1699	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1700	+	atomsingroups = 0;
1701	+	for (k=0; k < ncutgroups; k++) {
1702	+	cg = comp_stamps[i]->getCutoffGroup(k);
1703	+	atomsingroups += cg->getNMembers();
1704	+	}
1705	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1706	+	ncutgroups;
1707	+	local_groups += ngroupsinstamp;
1708	+
1709	+	localMol++;
1710	+	}
1711	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1712	+	info[0].molMembershipArray[globalAtomCounter] = allMol;
1713	+	globalAtomCounter++;
1714	+	}
1715	+
1716	+	allMol++;
1717	+	}
1718	+	}
1719	+	local_SRI = local_bonds + local_bends + local_torsions;
1720	+
1721	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1722	+
1723	+	if (local_atoms != info[0].n_atoms){
1724	+	sprintf(painCave.errMsg,
1725	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1726	+	"\tlocalAtom (%d) are not equal.\n",
1727	+	info[0].n_atoms, local_atoms);
1728	+	painCave.isFatal = 1;
1729	+	simError();
1730	+	}
1731	+
1732	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1733	+	if (local_groups != info[0].ngroup){
1734	+	sprintf(painCave.errMsg,
1735	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1736	+	"\tlocalGroups (%d) are not equal.\n",
1737	+	info[0].ngroup, local_groups);
1738	+	painCave.isFatal = 1;
1739	+	simError();
1740	+	}
1741	+
1742	+	info[0].n_bonds = local_bonds;
1743	+	info[0].n_bends = local_bends;
1744	+	info[0].n_torsions = local_torsions;
1745	+	info[0].n_SRI = local_SRI;
1746	+	info[0].n_mol = localMol;
1747	+
1748	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1749	+	MPIcheckPoint();
1750	+	}
1751	+
1752	+	#endif // is_mpi
1753	+
1754	+
1755	+	void SimSetup::makeSysArrays(void){
1756	+
1757	+	#ifndef IS_MPI
1758	+	int k, j;
1759	+	#endif // is_mpi
1760	+	int i, l;
1761	+
1762	+	Atom** the_atoms;
1763	+	Molecule* the_molecules;
1764	+
1765	+	for (l = 0; l < nInfo; l++){
1766	+	// create the atom and short range interaction arrays
1767	+
1768	+	the_atoms = new Atom * [info[l].n_atoms];
1769	+	the_molecules = new Molecule[info[l].n_mol];
1770	+	int molIndex;
1771	+
1772	+	// initialize the molecule's stampID's
1773	+
1774	+	#ifdef IS_MPI
1775	+
1776	+
1777	+	molIndex = 0;
1778	+	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1779	+	if (mol2proc[i] == worldRank){
1780	+	the_molecules[molIndex].setStampID(molCompType[i]);
1781	+	the_molecules[molIndex].setMyIndex(molIndex);
1782	+	the_molecules[molIndex].setGlobalIndex(i);
1783	+	molIndex++;
1784	+	}
1785	+	}
1786	+
1787	+	#else // is_mpi
1788	+
1789	+	molIndex = 0;
1790	+	globalAtomCounter = 0;
1791	+	for (i = 0; i < n_components; i++){
1792	+	for (j = 0; j < components_nmol[i]; j++){
1793	+	the_molecules[molIndex].setStampID(i);
1794	+	the_molecules[molIndex].setMyIndex(molIndex);
1795	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1796	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1797	+	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1798	+	globalAtomCounter++;
1799	+	}
1800	+	molIndex++;
1801	+	}
1802	+	}
1803	+
1804	+
1805	+	#endif // is_mpi
1806	+
1807	+	info[l].globalExcludes = new int;
1808	+	info[l].globalExcludes[0] = 0;
1809	+
1810	+	// set the arrays into the SimInfo object
1811	+
1812	+	info[l].atoms = the_atoms;
1813	+	info[l].molecules = the_molecules;
1814	+	info[l].nGlobalExcludes = 0;
1815	+
1816	+	the_ff->setSimInfo(info);
1817	+	}
1818	+	}
1819	+
1820	+	void SimSetup::makeIntegrator(void){
1821	+	int k;
1822	+
1823	+	NVE<Integrator<BaseIntegrator> >* myNVE = NULL;
1824	+	NVT<Integrator<BaseIntegrator> >* myNVT = NULL;
1825	+	NPTi<NPT<Integrator<BaseIntegrator> > >* myNPTi = NULL;
1826	+	NPTf<NPT<Integrator<BaseIntegrator> > >* myNPTf = NULL;
1827	+	NPTxyz<NPT<Integrator<BaseIntegrator> > >* myNPTxyz = NULL;
1828	+
1829	+	for (k = 0; k < nInfo; k++){
1830	+	switch (ensembleCase){
1831	+	case NVE_ENS:
1832	+	if (globals->haveZconstraints()){
1833	+	setupZConstraint(info[k]);
1834	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1835	+	}
1836	+	else{
1837	+	if (globals->haveQuaternion()){
1838	+	if (globals->getUseQuaternion())
1839	+	info->the_integrator = new NVE<SQSIntegrator<RealIntegrator> >(&(info[k]), the_ff);
1840	+	}
1841	+	else
1842	+	info->the_integrator = new NVE<RealIntegrator>(&(info[k]), the_ff);
1843	+	break;
1844	+
1845	+	//myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1846	+	}
1847	+
1848	+	info->the_integrator = myNVE;
1849	+	break;
1850	+
1851	+	case NVT_ENS:
1852	+	if (globals->haveZconstraints()){
1853	+	setupZConstraint(info[k]);
1854	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1855	+	}
1856	+	else
1857	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1858	+
1859	+	myNVT->setTargetTemp(globals->getTargetTemp());
1860	+
1861	+	if (globals->haveTauThermostat())
1862	+	myNVT->setTauThermostat(globals->getTauThermostat());
1863	+	else{
1864	+	sprintf(painCave.errMsg,
1865	+	"SimSetup error: If you use the NVT\n"
1866	+	"\tensemble, you must set tauThermostat.\n");
1867	+	painCave.isFatal = 1;
1868	+	simError();
1869	+	}
1870	+
1871	+	info->the_integrator = myNVT;
1872	+	break;
1873	+
1874	+	case NPTi_ENS:
1875	+	if (globals->haveZconstraints()){
1876	+	setupZConstraint(info[k]);
1877	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1878	+	}
1879	+	else
1880	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1881	+
1882	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1883	+
1884	+	if (globals->haveTargetPressure())
1885	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1886	+	else{
1887	+	sprintf(painCave.errMsg,
1888	+	"SimSetup error: If you use a constant pressure\n"
1889	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1890	+	painCave.isFatal = 1;
1891	+	simError();
1892	+	}
1893	+
1894	+	if (globals->haveTauThermostat())
1895	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1896	+	else{
1897	+	sprintf(painCave.errMsg,
1898	+	"SimSetup error: If you use an NPT\n"
1899	+	"\tensemble, you must set tauThermostat.\n");
1900	+	painCave.isFatal = 1;
1901	+	simError();
1902	+	}
1903	+
1904	+	if (globals->haveTauBarostat())
1905	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1906	+	else{
1907	+	sprintf(painCave.errMsg,
1908	+	"SimSetup error: If you use an NPT\n"
1909	+	"\tensemble, you must set tauBarostat.\n");
1910	+	painCave.isFatal = 1;
1911	+	simError();
1912	+	}
1913	+
1914	+	info->the_integrator = myNPTi;
1915	+	break;
1916	+
1917	+	case NPTf_ENS:
1918	+	if (globals->haveZconstraints()){
1919	+	setupZConstraint(info[k]);
1920	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1921	+	}
1922	+	else
1923	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1924	+
1925	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1926	+
1927	+	if (globals->haveTargetPressure())
1928	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1929	+	else{
1930	+	sprintf(painCave.errMsg,
1931	+	"SimSetup error: If you use a constant pressure\n"
1932	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1933	+	painCave.isFatal = 1;
1934	+	simError();
1935	+	}
1936	+
1937	+	if (globals->haveTauThermostat())
1938	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1939	+
1940	+	else{
1941	+	sprintf(painCave.errMsg,
1942	+	"SimSetup error: If you use an NPT\n"
1943	+	"\tensemble, you must set tauThermostat.\n");
1944	+	painCave.isFatal = 1;
1945	+	simError();
1946	+	}
1947	+
1948	+	if (globals->haveTauBarostat())
1949	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1950	+
1951	+	else{
1952	+	sprintf(painCave.errMsg,
1953	+	"SimSetup error: If you use an NPT\n"
1954	+	"\tensemble, you must set tauBarostat.\n");
1955	+	painCave.isFatal = 1;
1956	+	simError();
1957	+	}
1958	+
1959	+	info->the_integrator = myNPTf;
1960	+	break;
1961	+
1962	+	case NPTxyz_ENS:
1963	+	if (globals->haveZconstraints()){
1964	+	setupZConstraint(info[k]);
1965	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1966	+	}
1967	+	else
1968	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1969	+
1970	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1971	+
1972	+	if (globals->haveTargetPressure())
1973	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1974	+	else{
1975	+	sprintf(painCave.errMsg,
1976	+	"SimSetup error: If you use a constant pressure\n"
1977	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1978	+	painCave.isFatal = 1;
1979	+	simError();
1980	+	}
1981	+
1982	+	if (globals->haveTauThermostat())
1983	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1984	+	else{
1985	+	sprintf(painCave.errMsg,
1986	+	"SimSetup error: If you use an NPT\n"
1987	+	"\tensemble, you must set tauThermostat.\n");
1988	+	painCave.isFatal = 1;
1989	+	simError();
1990	+	}
1991	+
1992	+	if (globals->haveTauBarostat())
1993	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1994	+	else{
1995	+	sprintf(painCave.errMsg,
1996	+	"SimSetup error: If you use an NPT\n"
1997	+	"\tensemble, you must set tauBarostat.\n");
1998	+	painCave.isFatal = 1;
1999	+	simError();
2000	+	}
2001	+
2002	+	info->the_integrator = myNPTxyz;
2003	+	break;
2004	+
2005	+	default:
2006	+	sprintf(painCave.errMsg,
2007	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
2008	+	painCave.isFatal = 1;
2009	+	simError();
2010	+	}
2011	+	}
2012	+	}
2013	+
2014	+	void SimSetup::initFortran(void){
2015	+	info[0].refreshSim();
2016	+
2017	+	if (!strcmp(info[0].mixingRule, "standard")){
2018	+	the_ff->initForceField(LB_MIXING_RULE);
2019	+	}
2020	+	else if (!strcmp(info[0].mixingRule, "explicit")){
2021	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
2022	+	}
2023	+	else{
2024	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
2025	+	info[0].mixingRule);
2026	+	painCave.isFatal = 1;
2027	+	simError();
2028	+	}
2029	+
2030	+
2031	+	#ifdef IS_MPI
2032	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2033	+	MPIcheckPoint();
2034	+	#endif // is_mpi
2035	+	}
2036	+
2037	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
2038	+	int nZConstraints;
2039	+	ZconStamp** zconStamp;
2040	+
2041	+	if (globals->haveZconstraintTime()){
2042	+	//add sample time of z-constraint  into SimInfo's property list
2043	+	DoubleData* zconsTimeProp = new DoubleData();
2044	+	zconsTimeProp->setID(ZCONSTIME_ID);
2045	+	zconsTimeProp->setData(globals->getZconsTime());
2046	+	theInfo.addProperty(zconsTimeProp);
2047	+	}
2048	+	else{
2049	+	sprintf(painCave.errMsg,
2050	+	"ZConstraint error: If you use a ZConstraint,\n"
2051	+	"\tyou must set zconsTime.\n");
2052	+	painCave.isFatal = 1;
2053	+	simError();
2054	+	}
2055	+
2056	+	//push zconsTol into siminfo, if user does not specify
2057	+	//value for zconsTol, a default value will be used
2058	+	DoubleData* zconsTol = new DoubleData();
2059	+	zconsTol->setID(ZCONSTOL_ID);
2060	+	if (globals->haveZconsTol()){
2061	+	zconsTol->setData(globals->getZconsTol());
2062	+	}
2063	+	else{
2064	+	double defaultZConsTol = 0.01;
2065	+	sprintf(painCave.errMsg,
2066	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2067	+	"\tOOPSE will use a default value of %f.\n"
2068	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2069	+	defaultZConsTol);
2070	+	painCave.isFatal = 0;
2071	+	simError();
2072	+
2073	+	zconsTol->setData(defaultZConsTol);
2074	+	}
2075	+	theInfo.addProperty(zconsTol);
2076	+
2077	+	//set Force Subtraction Policy
2078	+	StringData* zconsForcePolicy = new StringData();
2079	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2080	+
2081	+	if (globals->haveZconsForcePolicy()){
2082	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2083	+	}
2084	+	else{
2085	+	sprintf(painCave.errMsg,
2086	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2087	+	"\tOOPSE will use PolicyByMass.\n"
2088	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2089	+	painCave.isFatal = 0;
2090	+	simError();
2091	+	zconsForcePolicy->setData("BYMASS");
2092	+	}
2093	+
2094	+	theInfo.addProperty(zconsForcePolicy);
2095	+
2096	+	//set zcons gap
2097	+	DoubleData* zconsGap = new DoubleData();
2098	+	zconsGap->setID(ZCONSGAP_ID);
2099	+
2100	+	if (globals->haveZConsGap()){
2101	+	zconsGap->setData(globals->getZconsGap());
2102	+	theInfo.addProperty(zconsGap);
2103	+	}
2104	+
2105	+	//set zcons fixtime
2106	+	DoubleData* zconsFixtime = new DoubleData();
2107	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2108	+
2109	+	if (globals->haveZConsFixTime()){
2110	+	zconsFixtime->setData(globals->getZconsFixtime());
2111	+	theInfo.addProperty(zconsFixtime);
2112	+	}
2113	+
2114	+	//set zconsUsingSMD
2115	+	IntData* zconsUsingSMD = new IntData();
2116	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2117	+
2118	+	if (globals->haveZConsUsingSMD()){
2119	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2120	+	theInfo.addProperty(zconsUsingSMD);
2121	+	}
2122	+
2123	+	//Determine the name of ouput file and add it into SimInfo's property list
2124	+	//Be careful, do not use inFileName, since it is a pointer which
2125	+	//point to a string at master node, and slave nodes do not contain that string
2126	+
2127	+	string zconsOutput(theInfo.finalName);
2128	+
2129	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2130	+
2131	+	StringData* zconsFilename = new StringData();
2132	+	zconsFilename->setID(ZCONSFILENAME_ID);
2133	+	zconsFilename->setData(zconsOutput);
2134	+
2135	+	theInfo.addProperty(zconsFilename);
2136	+
2137	+	//setup index, pos and other parameters of z-constraint molecules
2138	+	nZConstraints = globals->getNzConstraints();
2139	+	theInfo.nZconstraints = nZConstraints;
2140	+
2141	+	zconStamp = globals->getZconStamp();
2142	+	ZConsParaItem tempParaItem;
2143	+
2144	+	ZConsParaData* zconsParaData = new ZConsParaData();
2145	+	zconsParaData->setID(ZCONSPARADATA_ID);
2146	+
2147	+	for (int i = 0; i < nZConstraints; i++){
2148	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2149	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2150	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2151	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2152	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2153	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2154	+	zconsParaData->addItem(tempParaItem);
2155	+	}
2156	+
2157	+	//check the uniqueness of index
2158	+	if(!zconsParaData->isIndexUnique()){
2159	+	sprintf(painCave.errMsg,
2160	+	"ZConstraint Error: molIndex is not unique!\n");
2161	+	painCave.isFatal = 1;
2162	+	simError();
2163	+	}
2164	+
2165	+	//sort the parameters by index of molecules
2166	+	zconsParaData->sortByIndex();
2167	+
2168	+	//push data into siminfo, therefore, we can retrieve later
2169	+	theInfo.addProperty(zconsParaData);
2170	+	}
2171	+
2172	+	void SimSetup::makeMinimizer(){
2173	+
2174	+	OOPSEMinimizer* myOOPSEMinimizer;
2175	+	MinimizerParameterSet* param;
2176	+	char minimizerName[100];
2177	+
2178	+	for (int i = 0; i < nInfo; i++){
2179	+
2180	+	//prepare parameter set for minimizer
2181	+	param = new MinimizerParameterSet();
2182	+	param->setDefaultParameter();
2183	+
2184	+	if (globals->haveMinimizer()){
2185	+	param->setFTol(globals->getMinFTol());
2186	+	}
2187	+
2188	+	if (globals->haveMinGTol()){
2189	+	param->setGTol(globals->getMinGTol());
2190	+	}
2191	+
2192	+	if (globals->haveMinMaxIter()){
2193	+	param->setMaxIteration(globals->getMinMaxIter());
2194	+	}
2195	+
2196	+	if (globals->haveMinWriteFrq()){
2197	+	param->setMaxIteration(globals->getMinMaxIter());
2198	+	}
2199	+
2200	+	if (globals->haveMinWriteFrq()){
2201	+	param->setWriteFrq(globals->getMinWriteFrq());
2202	+	}
2203	+
2204	+	if (globals->haveMinStepSize()){
2205	+	param->setStepSize(globals->getMinStepSize());
2206	+	}
2207	+
2208	+	if (globals->haveMinLSMaxIter()){
2209	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2210	+	}
2211	+
2212	+	if (globals->haveMinLSTol()){
2213	+	param->setLineSearchTol(globals->getMinLSTol());
2214	+	}
2215	+
2216	+	strcpy(minimizerName, globals->getMinimizer());
2217	+
2218	+	if (!strcasecmp(minimizerName, "CG")){
2219	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2220	+	}
2221	+	else if (!strcasecmp(minimizerName, "SD")){
2222	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2223	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2224	+	}
2225	+	else{
2226	+	sprintf(painCave.errMsg,
2227	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2228	+	painCave.isFatal = 0;
2229	+	simError();
2230	+
2231	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2232	+	}
2233	+	info[i].the_integrator = myOOPSEMinimizer;
2234	+
2235	+	//store the minimizer into simInfo
2236	+	info[i].the_minimizer = myOOPSEMinimizer;
2237	+	info[i].has_minimizer = true;
2238	+	}
2239	+
2240	+	}

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