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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 605 by gezelter, Tue Jul 15 03:27:24 2003 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 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 NPTi_ENS  2
28	<	#define NPTf_ENS  3
29	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
25	>	#define NVE_ENS        0
26	>	#define NVT_ENS        1
27	>	#define NPTi_ENS       2
28	>	#define NPTf_ENS       3
29	>	#define NPTxyz_ENS     4
30
31
32	<	#define FF_DUFF 0
33	<	#define FF_LJ   1
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 41 | 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();
73	<	mpiEventLoop();
74	<
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;
82	<	Globals* the_globals;
83	<	int i, j, k, globalAtomIndex;
84	<
85	<	int ensembleCase;
86	<	int ffCase;
87	<
88	<	ensembleCase = -1;
89	<	ffCase = -1;
128	>	// gather all of the information from the Bass file
129
130	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
130	>	gatherInfo();
131
132	<	// set the easy ones first
96	<	simnfo->target_temp = the_globals->getTargetTemp();
97	<	simnfo->dt = the_globals->getDt();
98	<	simnfo->run_time = the_globals->getRunTime();
132	>	// creation of complex system objects
133
134	<	// get the ones we know are there, yet still may need some work.
101	<	n_components = the_globals->getNComponents();
102	<	strcpy( force_field, the_globals->getForceField() );
134	>	sysObjectsCreation();
135
136	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106	<	else{
107	<	sprintf( painCave.errMsg,
108	<	"SimSetup Error. Unrecognized force field -> %s\n",
109	<	force_field );
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
136	>	// check on the post processing info
137
138	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
138	>	finalInfoCheck();
139
140	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
118	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
119	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
120	<	ensembleCase = NPTi_ENS;
121	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
122	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
123	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124	<	else{
125	<	sprintf( painCave.errMsg,
126	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
127	<	"reverting to NVE for this simulation.\n",
128	<	ensemble );
129	<	painCave.isFatal = 0;
130	<	simError();
131	<	strcpy( ensemble, "NVE" );
132	<	ensembleCase = NVE_ENS;
133	<	}
134	<	strcpy( simnfo->ensemble, ensemble );
140	>	// initialize the system coordinates
141
142	+	if ( !initSuspend ){
143	+	initSystemCoords();
144
145	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
146	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
147	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140	<	//     if (the_globals->haveTargetPressure())
141	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142	<	//     else {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "SimSetup error: If you use the constant pressure\n"
145	<	//                "    ensemble, you must set targetPressure.\n"
146	<	//                "    This was found in the BASS file.\n");
147	<	//       painCave.isFatal = 1;
148	<	//       simError();
149	<	//     }
145	>	if( !(globals->getUseInitTime()) )
146	>	info[0].currentTime = 0.0;
147	>	}
148
149	<	//     if (the_globals->haveTauThermostat())
152	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153	<	//     else if (the_globals->haveQmass())
154	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
155	<	//     else {
156	<	//       sprintf( painCave.errMsg,
157	<	//                "SimSetup error: If you use one of the constant temperature\n"
158	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
159	<	//                "    Neither of these was found in the BASS file.\n");
160	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
149	>	// make the output filenames
150
151	<	//     if (the_globals->haveTauBarostat())
152	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
153	<	//     else {
154	<	//       sprintf( painCave.errMsg,
155	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
151	>	makeOutNames();
152	>
153	>	#ifdef IS_MPI
154	>	mpiSim->mpiRefresh();
155	>	#endif
156
157	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
176	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
177	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
157	>	// initialize the Fortran
158
159	<	//     if (the_globals->haveTauThermostat())
180	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181	<	//     else if (the_globals->haveQmass())
182	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
183	<	//     else {
184	<	//       sprintf( painCave.errMsg,
185	<	//                "SimSetup error: If you use one of the constant temperature\n"
186	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
187	<	//                "    Neither of these was found in the BASS file.\n");
188	<	//       painCave.isFatal = 1;
189	<	//       simError();
190	<	//     }
159	>	initFortran();
160
161	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
162	<	simnfo->usePBC = the_globals->getPBC();
163	<
195	<	int usesDipoles = 0;
196	<	switch( ffCase ){
161	>	//creat constraint manager
162	>	for(int i = 0; i < nInfo; i++)
163	>	info[i].consMan = new ConstraintManager(&info[i]);
164
165	<	case FF_DUFF:
166	<	the_ff = new DUFF();
167	<	usesDipoles = 1;
168	<	break;
165	>	if (globals->haveMinimizer())
166	>	// make minimizer
167	>	makeMinimizer();
168	>	else
169	>	// make the integrator
170	>	makeIntegrator();
171
172	<	case FF_LJ:
204	<	the_ff = new LJFF();
205	<	break;
172	>	}
173
207	–	default:
208	–	sprintf( painCave.errMsg,
209	–	"SimSetup Error. Unrecognized force field in case statement.\n");
210	–	painCave.isFatal = 1;
211	–	simError();
212	–	}
174
175	<	#ifdef IS_MPI
176	<	strcpy( checkPointMsg, "ForceField creation successful" );
177	<	MPIcheckPoint();
178	<	#endif // is_mpi
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	<	// get the components and calculate the tot_nMol and indvidual n_mol
198	<	the_components = the_globals->getComponents();
199	<	components_nmol = new int[n_components];
222	<	comp_stamps = new MoleculeStamp*[n_components];
197	>	bond_pair* theBonds;
198	>	bend_set* theBends;
199	>	torsion_set* theTorsions;
200
201	<	if( !the_globals->haveNMol() ){
225	<	// we don't have the total number of molecules, so we assume it is
226	<	// given in each component
201	>	set<int> skipList;
202
203	<	tot_nmol = 0;
204	<	for( i=0; i<n_components; i++ ){
203	>	double phi, theta, psi;
204	>	char* molName;
205	>	char rbName[100];
206
207	<	if( !the_components[i]->haveNMol() ){
208	<	// we have a problem
209	<	sprintf( painCave.errMsg,
210	<	"SimSetup Error. No global NMol or component NMol"
211	<	" given. Cannot calculate the number of atoms.\n" );
212	<	painCave.isFatal = 1;
213	<	simError();
214	<	}
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 += the_components[i]->getNMol();
241	<	components_nmol[i] = the_components[i]->getNMol();
242	<	}
243	<	}
244	<	else{
245	<	sprintf( painCave.errMsg,
246	<	"SimSetup error.\n"
247	<	"\tSorry, the ability to specify total"
248	<	" nMols and then give molfractions in the components\n"
249	<	"\tis not currently supported."
250	<	" Please give nMol in the components.\n" );
251	<	painCave.isFatal = 1;
252	<	simError();
253	<
254	<
255	<	//     tot_nmol = the_globals->getNMol();
256	<
257	<	//   //we have the total number of molecules, now we check for molfractions
258	<	//     for( i=0; i<n_components; i++ ){
259	<
260	<	//       if( !the_components[i]->haveMolFraction() ){
261	<
262	<	//  if( !the_components[i]->haveNMol() ){
263	<	//    //we have a problem
264	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
265	<	//              << " nMol was given in component
266	<
267	<	}
216	>	the_ff->readParams();
217
218	<	#ifdef IS_MPI
270	<	strcpy( checkPointMsg, "Have the number of components" );
271	<	MPIcheckPoint();
272	<	#endif // is_mpi
218	>	// init the atoms
219
220	<	// make an array of molecule stamps that match the components used.
275	<	// also extract the used stamps out into a separate linked list
220	>	int nMembers, nNew, rb1, rb2;
221
222	<	simnfo->nComponents = n_components;
223	<	simnfo->componentsNmol = components_nmol;
279	<	simnfo->compStamps = comp_stamps;
280	<	simnfo->headStamp = new LinkedMolStamp();
281	<
282	<	char* id;
283	<	LinkedMolStamp* headStamp = simnfo->headStamp;
284	<	LinkedMolStamp* currentStamp = NULL;
285	<	for( i=0; i<n_components; i++ ){
222	>	for (k = 0; k < nInfo; k++){
223	>	the_ff->setSimInfo(&(info[k]));
224
287	–	id = the_components[i]->getType();
288	–	comp_stamps[i] = NULL;
289	–
290	–	// check to make sure the component isn't already in the list
291	–
292	–	comp_stamps[i] = headStamp->match( id );
293	–	if( comp_stamps[i] == NULL ){
294	–
295	–	// extract the component from the list;
296	–
297	–	currentStamp = the_stamps->extractMolStamp( id );
298	–	if( currentStamp == NULL ){
299	–	sprintf( painCave.errMsg,
300	–	"SimSetup error: Component \"%s\" was not found in the "
301	–	"list of declared molecules\n",
302	–	id );
303	–	painCave.isFatal = 1;
304	–	simError();
305	–	}
306	–
307	–	headStamp->add( currentStamp );
308	–	comp_stamps[i] = headStamp->match( id );
309	–	}
310	–	}
311	–
225		#ifdef IS_MPI
226	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
227	<	MPIcheckPoint();
228	<	#endif // is_mpi
229	<
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	+	atomOffset = 0;
236	+	groupOffset = 0;
237
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	<	// caclulate the number of atoms, bonds, bends and torsions
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	<	tot_atoms = 0;
249	<	tot_bonds = 0;
250	<	tot_bends = 0;
325	<	tot_torsions = 0;
326	<	for( i=0; i<n_components; i++ ){
327	<
328	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
329	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
330	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
331	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
332	<	}
248	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
249	>
250	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
251
252	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
252	>	if (molInfo.nBonds > 0)
253	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
254	>	else
255	>	molInfo.myBonds = NULL;
256
257	<	simnfo->n_atoms = tot_atoms;
258	<	simnfo->n_bonds = tot_bonds;
259	<	simnfo->n_bends = tot_bends;
260	<	simnfo->n_torsions = tot_torsions;
340	<	simnfo->n_SRI = tot_SRI;
341	<	simnfo->n_mol = tot_nmol;
342	<
343	<	simnfo->molMembershipArray = new int[tot_atoms];
257	>	if (molInfo.nBends > 0)
258	>	molInfo.myBends = new Bend*[molInfo.nBends];
259	>	else
260	>	molInfo.myBends = NULL;
261
262	<	#ifdef IS_MPI
262	>	if (molInfo.nTorsions > 0)
263	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
264	>	else
265	>	molInfo.myTorsions = NULL;
266
267	<	// divide the molecules among processors here.
268	<
269	<	mpiSim = new mpiSimulation( simnfo );
270	<
271	<	globalIndex = mpiSim->divideLabor();
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	<	// set up the local variables
274	<
355	<	int localMol, allMol;
356	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
273	>	for (j = 0; j < molInfo.nAtoms; j++){
274	>	currentAtom = comp_stamps[stampID]->getAtom(j);
275
276	<	int* mol2proc = mpiSim->getMolToProcMap();
277	<	int* molCompType = mpiSim->getMolComponentType();
278	<
279	<	allMol = 0;
280	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
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	+	// 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	<	for( i=0; i<n_components; i++ ){
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	<	for( j=0; j<components_nmol[i]; j++ ){
291	<
292	<	if( mol2proc[allMol] == worldRank ){
293	<
376	<	local_atoms +=    comp_stamps[i]->getNAtoms();
377	<	local_bonds +=    comp_stamps[i]->getNBonds();
378	<	local_bends +=    comp_stamps[i]->getNBends();
379	<	local_torsions += comp_stamps[i]->getNTorsions();
380	<	localMol++;
381	<	}
382	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
384	<	globalAtomIndex++;
385	<	}
290	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
291	>
292	>	}
293	>	else{
294
295	<	allMol++;
388	<	}
389	<	}
390	<	local_SRI = local_bonds + local_bends + local_torsions;
391	<
392	<	simnfo->n_atoms = mpiSim->getMyNlocal();
393	<
394	<	if( local_atoms != simnfo->n_atoms ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
397	<	" localAtom (%d) are not equal.\n",
398	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
295	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
296
297	<	simnfo->n_bonds = local_bonds;
405	<	simnfo->n_bends = local_bends;
406	<	simnfo->n_torsions = local_torsions;
407	<	simnfo->n_SRI = local_SRI;
408	<	simnfo->n_mol = localMol;
297	>	}
298
299	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
300	<	MPIcheckPoint();
301	<
413	<
299	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
300	>	#ifdef IS_MPI
301	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
302		#endif // is_mpi
303	<
303	>	}
304
305	<	// create the atom and short range interaction arrays
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	<	Atom::createArrays(simnfo->n_atoms);
312	<	the_atoms = new Atom*[simnfo->n_atoms];
421	<	the_molecules = new Molecule[simnfo->n_mol];
422	<	int molIndex;
311	>	tempI = theBonds[j].a;
312	>	tempJ = theBonds[j].b;
313
424	–	// initialize the molecule's stampID's
425	–
314		#ifdef IS_MPI
315	<
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	<	molIndex = 0;
430	<	for(i=0; i<mpiSim->getTotNmol(); i++){
431	<
432	<	if(mol2proc[i] == worldRank ){
433	<	the_molecules[molIndex].setStampID( molCompType[i] );
434	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
439	<
440	<	#else // is_mpi
441	<
442	<	molIndex = 0;
443	<	globalAtomIndex = 0;
444	<	for(i=0; i<n_components; i++){
445	<	for(j=0; j<components_nmol[i]; j++ ){
446	<	the_molecules[molIndex].setStampID( i );
447	<	the_molecules[molIndex].setMyIndex( molIndex );
448	<	the_molecules[molIndex].setGlobalIndex( molIndex );
449	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
450	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
451	<	globalAtomIndex++;
322	>	info[k].excludes->addPair(exI, exJ);
323		}
453	–	molIndex++;
454	–	}
455	–	}
456	–
324
325	<	#endif // is_mpi
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	+	if (currentBend->haveExtras()){
333	+	extras = currentBend->getExtras();
334	+	current_extra = extras;
335
336	<	if( simnfo->n_SRI ){
337	<
338	<	Exclude::createArray(simnfo->n_SRI);
339	<	the_excludes = new Exclude*[simnfo->n_SRI];
340	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
341	<	simnfo->globalExcludes = new int;
342	<	simnfo->n_exclude = simnfo->n_SRI;
468	<	}
469	<	else{
470	<
471	<	Exclude::createArray( 1 );
472	<	the_excludes = new Exclude*;
473	<	the_excludes[0] = new Exclude(0);
474	<	the_excludes[0]->setPair( 0,0 );
475	<	simnfo->globalExcludes = new int;
476	<	simnfo->globalExcludes[0] = 0;
477	<	simnfo->n_exclude = 0;
478	<	}
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	<	// set the arrays into the SimInfo object
344	>	case 1:
345	>	theBends[j].ghost = (int) current_extra->getDouble() +
346	>	atomOffset;
347	>	theBends[j].isGhost = 1;
348	>	break;
349
350	<	simnfo->atoms = the_atoms;
351	<	simnfo->molecules = the_molecules;
352	<	simnfo->nGlobalExcludes = 0;
353	<	simnfo->excludes = the_excludes;
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	<	// get some of the tricky things that may still be in the globals
373	>	if (theBends[j].isGhost) {
374	>
375	>	tempI = theBends[j].a;
376	>	tempJ = theBends[j].b;
377	>
378	>	#ifdef IS_MPI
379	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
380	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
381	>	#else
382	>	exI = tempI + 1;
383	>	exJ = tempJ + 1;
384	>	#endif
385	>	info[k].excludes->addPair(exI, exJ);
386
387	<	double boxVector[3];
491	<	if( the_globals->haveBox() ){
492	<	boxVector[0] = the_globals->getBox();
493	<	boxVector[1] = the_globals->getBox();
494	<	boxVector[2] = the_globals->getBox();
495	<
496	<	simnfo->setBox( boxVector );
497	<	}
498	<	else if( the_globals->haveDensity() ){
387	>	} else {
388
389	<	double vol;
390	<	vol = (double)tot_nmol / the_globals->getDensity();
391	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
392	<	boxVector[1] = boxVector[0];
393	<	boxVector[2] = boxVector[0];
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	>	}
408
409	<	simnfo->setBox( boxVector );
410	<	}
411	<	else{
412	<	if( !the_globals->haveBoxX() ){
413	<	sprintf( painCave.errMsg,
414	<	"SimSetup error, no periodic BoxX size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[0] = the_globals->getBoxX();
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	<	if( !the_globals->haveBoxY() ){
417	<	sprintf( painCave.errMsg,
418	<	"SimSetup error, no periodic BoxY size given.\n" );
419	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	boxVector[1] = the_globals->getBoxY();
416	>	tempI = theTorsions[j].a;
417	>	tempJ = theTorsions[j].b;
418	>	tempK = theTorsions[j].c;
419	>	tempL = theTorsions[j].d;
420
421	<	if( !the_globals->haveBoxZ() ){
422	<	sprintf( painCave.errMsg,
423	<	"SimSetup error, no periodic BoxZ size given.\n" );
424	<	painCave.isFatal = 1;
425	<	simError();
426	<	}
427	<	boxVector[2] = the_globals->getBoxZ();
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	<	simnfo->setBox( boxVector );
434	<	}
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	<	#ifdef IS_MPI
442	<	strcpy( checkPointMsg, "Box size set up" );
443	<	MPIcheckPoint();
444	<	#endif // is_mpi
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	<	// initialize the arrays
449	>	// Create the Rigid Body:
450
451	<	the_ff->setSimInfo( simnfo );
451	>	myRB = new RigidBody();
452
453	<	makeMolecules();
454	<	simnfo->identArray = new int[simnfo->n_atoms];
455	<	for(i=0; i<simnfo->n_atoms; i++){
456	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
550	<	}
551	<
552	<	if (the_globals->getUseRF() ) {
553	<	simnfo->useReactionField = 1;
554	<
555	<	if( !the_globals->haveECR() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 1/2 the smallest "
558	<	"box length for the electrostaticCutoffRadius.\n"
559	<	"I hope you have a very fast processor!\n");
560	<	painCave.isFatal = 0;
561	<	simError();
562	<	double smallest;
563	<	smallest = simnfo->boxLx;
564	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566	<	simnfo->ecr = 0.5 * smallest;
567	<	} else {
568	<	simnfo->ecr        = the_globals->getECR();
569	<	}
453	>	sprintf(rbName,"%s_RB_%d", molName, j);
454	>	myRB->setType(rbName);
455	>
456	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
457
458	<	if( !the_globals->haveEST() ){
459	<	sprintf( painCave.errMsg,
460	<	"SimSetup Warning: using default value of 0.05 * the "
461	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
462	<	);
463	<	painCave.isFatal = 0;
464	<	simError();
465	<	simnfo->est = 0.05 * simnfo->ecr;
466	<	} else {
467	<	simnfo->est        = the_globals->getEST();
468	<	}
469	<
470	<	if(!the_globals->haveDielectric() ){
471	<	sprintf( painCave.errMsg,
472	<	"SimSetup Error: You are trying to use Reaction Field without"
473	<	"setting a dielectric constant!\n"
474	<	);
475	<	painCave.isFatal = 1;
476	<	simError();
477	<	}
478	<	simnfo->dielectric = the_globals->getDielectric();
479	<	} else {
480	<	if (usesDipoles) {
481	<
482	<	if( !the_globals->haveECR() ){
483	<	sprintf( painCave.errMsg,
484	<	"SimSetup Warning: using default value of 1/2 the smallest "
485	<	"box length for the electrostaticCutoffRadius.\n"
486	<	"I hope you have a very fast processor!\n");
487	<	painCave.isFatal = 0;
488	<	simError();
489	<	double smallest;
490	<	smallest = simnfo->boxLx;
491	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
492	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
493	<	simnfo->ecr = 0.5 * smallest;
494	<	} else {
495	<	simnfo->ecr        = the_globals->getECR();
458	>	// molI is atom numbering inside this molecule
459	>	molI = currentRigidBody->getMember(rb1);
460	>
461	>	// tempI is atom numbering on local processor
462	>	tempI = molI + atomOffset;
463	>
464	>	// currentAtom is the AtomStamp (which we need for
465	>	// rigid body reference positions)
466	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
467	>
468	>	// 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	>	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
611	–	if( !the_globals->haveEST() ){
612	–	sprintf( painCave.errMsg,
613	–	"SimSetup Warning: using default value of 5%% of the "
614	–	"electrostaticCutoffRadius for the "
615	–	"electrostaticSkinThickness\n"
616	–	);
617	–	painCave.isFatal = 0;
618	–	simError();
619	–	simnfo->est = 0.05 * simnfo->ecr;
620	–	} else {
621	–	simnfo->est        = the_globals->getEST();
622	–	}
623	–	}
624	–	}
511
512	<	#ifdef IS_MPI
627	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
628	<	MPIcheckPoint();
629	<	#endif // is_mpi
512	>	//create cutoff group for molecule
513
514	<	if( the_globals->haveInitialConfig() ){
515	<
516	<	InitializeFromFile* fileInit;
517	<	#ifdef IS_MPI // is_mpi
518	<	if( worldRank == 0 ){
519	<	#endif //is_mpi
520	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
514	>	cutoffAtomSet.clear();
515	>	molInfo.myCutoffGroups.clear();
516	>
517	>	for (j = 0; j < nCutoffGroups; j++){
518	>
519	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
520	>	nMembers = currentCutoffGroup->getNMembers();
521	>
522	>	myCutoffGroup = new CutoffGroup();
523	>
524		#ifdef IS_MPI
525	<	}else fileInit = new InitializeFromFile( NULL );
525	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
526	>	#else
527	>	myCutoffGroup->setGlobalIndex(groupOffset);
528		#endif
529	<	fileInit->read_xyz( simnfo ); // default velocities on
529	>
530	>	for (int cg = 0; cg < nMembers; cg++) {
531
532	<	delete fileInit;
533	<	}
645	<	else{
532	>	// molI is atom numbering inside this molecule
533	>	molI = currentCutoffGroup->getMember(cg);
534
535	<	#ifdef IS_MPI
535	>	// tempI is atom numbering on local processor
536	>	tempI = molI + atomOffset;
537
538	<	// no init from bass
539	<
540	<	sprintf( painCave.errMsg,
541	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
542	<	painCave.isFatal;
543	<	simError();
544	<
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	>
554	>
555	>	// create a cutoff group for every atom in current molecule which
556	>	// does not belong to cutoffgroup defined at mdl file
557	>
558	>	for(j = 0; j < molInfo.nAtoms; j++){
559	>
560	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
561	>	myCutoffGroup = new CutoffGroup();
562	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
563	>
564	>	#ifdef IS_MPI
565	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
566	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
567	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
568		#else
569	+	myCutoffGroup->setGlobalIndex(groupOffset);
570	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
571	+	info[k].globalGroupMembership[globalID] = groupOffset;
572	+	#endif
573	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
574	+	groupOffset++;
575	+	}
576	+	}
577
578	<	initFromBass();
578	>	// After this is all set up, scan through the atoms to
579	>	// see if they can be added to the integrableObjects:
580
581	+	molInfo.myIntegrableObjects.clear();
582	+
583
584	<	#endif
662	<	}
584	>	for (j = 0; j < molInfo.nAtoms; j++){
585
586		#ifdef IS_MPI
587	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
588	<	MPIcheckPoint();
589	<	#endif // is_mpi
587	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
588	>	#else
589	>	slJ = j+atomOffset;
590	>	#endif
591
592	+	// if they aren't on the skip list, then they can be integrated
593
594	<
595	<
596	<
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	<
602	<	#ifdef IS_MPI
603	<	if( worldRank == 0 ){
604	<	#endif // is_mpi
605	<
606	<	if( the_globals->haveFinalConfig() ){
607	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
608	<	}
609	<	else{
610	<	strcpy( simnfo->finalName, inFileName );
611	<	char* endTest;
612	<	int nameLength = strlen( simnfo->finalName );
613	<	endTest = &(simnfo->finalName[nameLength - 5]);
614	<	if( !strcmp( endTest, ".bass" ) ){
615	<	strcpy( endTest, ".eor" );
616	<	}
617	<	else if( !strcmp( endTest, ".BASS" ) ){
618	<	strcpy( endTest, ".eor" );
619	<	}
620	<	else{
621	<	endTest = &(simnfo->finalName[nameLength - 4]);
622	<	if( !strcmp( endTest, ".bss" ) ){
623	<	strcpy( endTest, ".eor" );
624	<	}
625	<	else if( !strcmp( endTest, ".mdl" ) ){
626	<	strcpy( endTest, ".eor" );
627	<	}
628	<	else{
629	<	strcat( simnfo->finalName, ".eor" );
630	<	}
631	<	}
632	<	}
633	<
634	<	// make the sample and status out names
635	<
636	<	strcpy( simnfo->sampleName, inFileName );
637	<	char* endTest;
638	<	int nameLength = strlen( simnfo->sampleName );
639	<	endTest = &(simnfo->sampleName[nameLength - 5]);
640	<	if( !strcmp( endTest, ".bass" ) ){
641	<	strcpy( endTest, ".dump" );
642	<	}
643	<	else if( !strcmp( endTest, ".BASS" ) ){
644	<	strcpy( endTest, ".dump" );
645	<	}
646	<	else{
647	<	endTest = &(simnfo->sampleName[nameLength - 4]);
648	<	if( !strcmp( endTest, ".bss" ) ){
649	<	strcpy( endTest, ".dump" );
650	<	}
651	<	else if( !strcmp( endTest, ".mdl" ) ){
652	<	strcpy( endTest, ".dump" );
653	<	}
654	<	else{
655	<	strcat( simnfo->sampleName, ".dump" );
656	<	}
657	<	}
658	<
659	<	strcpy( simnfo->statusName, inFileName );
660	<	nameLength = strlen( simnfo->statusName );
661	<	endTest = &(simnfo->statusName[nameLength - 5]);
662	<	if( !strcmp( endTest, ".bass" ) ){
663	<	strcpy( endTest, ".stat" );
664	<	}
665	<	else if( !strcmp( endTest, ".BASS" ) ){
666	<	strcpy( endTest, ".stat" );
667	<	}
668	<	else{
669	<	endTest = &(simnfo->statusName[nameLength - 4]);
670	<	if( !strcmp( endTest, ".bss" ) ){
671	<	strcpy( endTest, ".stat" );
672	<	}
673	<	else if( !strcmp( endTest, ".mdl" ) ){
674	<	strcpy( endTest, ".stat" );
675	<	}
676	<	else{
677	<	strcat( simnfo->statusName, ".stat" );
678	<	}
679	<	}
680	<
681	<	#ifdef IS_MPI
682	<	}
683	<	#endif // is_mpi
684	<
685	<	// set the status, sample, and themal kick times
686	<
687	<	if( the_globals->haveSampleTime() ){
688	<	simnfo->sampleTime = the_globals->getSampleTime();
689	<	simnfo->statusTime = simnfo->sampleTime;
690	<	simnfo->thermalTime = simnfo->sampleTime;
691	<	}
692	<	else{
693	<	simnfo->sampleTime = the_globals->getRunTime();
694	<	simnfo->statusTime = simnfo->sampleTime;
695	<	simnfo->thermalTime = simnfo->sampleTime;
696	<	}
697	<
698	<	if( the_globals->haveStatusTime() ){
699	<	simnfo->statusTime = the_globals->getStatusTime();
700	<	}
701	<
702	<	if( the_globals->haveThermalTime() ){
703	<	simnfo->thermalTime = the_globals->getThermalTime();
704	<	}
705	<
706	<	// check for the temperature set flag
707	<
708	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
709	<
710	<
711	<	// make the integrator
712	<
713	<
714	<	NVT*  myNVT = NULL;
715	<	NPTi* myNPTi = NULL;
716	<	NPTf* myNPTf = NULL;
717	<	NPTim* myNPTim = NULL;
718	<	NPTfm* myNPTfm = NULL;
719	<
720	<	switch( ensembleCase ){
721	<
722	<	case NVE_ENS:
723	<	new NVE( simnfo, the_ff );
724	<	break;
725	<
726	<	case NVT_ENS:
727	<	myNVT = new NVT( simnfo, the_ff );
728	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
729	<
730	<	if (the_globals->haveTauThermostat())
731	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
732	<
733	<	else {
734	<	sprintf( painCave.errMsg,
735	<	"SimSetup error: If you use the NVT\n"
736	<	"    ensemble, you must set tauThermostat.\n");
737	<	painCave.isFatal = 1;
738	<	simError();
739	<	}
740	<	break;
741	<
742	<	case NPTi_ENS:
743	<	myNPTi = new NPTi( simnfo, the_ff );
744	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
745	<
746	<	if (the_globals->haveTargetPressure())
747	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
748	<	else {
749	<	sprintf( painCave.errMsg,
750	<	"SimSetup error: If you use a constant pressure\n"
751	<	"    ensemble, you must set targetPressure in the BASS file.\n");
752	<	painCave.isFatal = 1;
753	<	simError();
754	<	}
755	<
756	<	if( the_globals->haveTauThermostat() )
757	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
758	<	else{
759	<	sprintf( painCave.errMsg,
760	<	"SimSetup error: If you use an NPT\n"
761	<	"    ensemble, you must set tauThermostat.\n");
762	<	painCave.isFatal = 1;
763	<	simError();
764	<	}
765	<
766	<	if( the_globals->haveTauBarostat() )
767	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
768	<	else{
769	<	sprintf( painCave.errMsg,
770	<	"SimSetup error: If you use an NPT\n"
771	<	"    ensemble, you must set tauBarostat.\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
775	<	break;
776	<
777	<	case NPTf_ENS:
778	<	myNPTf = new NPTf( simnfo, the_ff );
779	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
780	<
781	<	if (the_globals->haveTargetPressure())
782	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
783	<	else {
784	<	sprintf( painCave.errMsg,
785	<	"SimSetup error: If you use a constant pressure\n"
786	<	"    ensemble, you must set targetPressure in the BASS file.\n");
787	<	painCave.isFatal = 1;
788	<	simError();
789	<	}
790	<
791	<	if( the_globals->haveTauThermostat() )
792	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
793	<	else{
794	<	sprintf( painCave.errMsg,
795	<	"SimSetup error: If you use an NPT\n"
796	<	"    ensemble, you must set tauThermostat.\n");
797	<	painCave.isFatal = 1;
798	<	simError();
799	<	}
800	<
801	<	if( the_globals->haveTauBarostat() )
802	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
803	<	else{
804	<	sprintf( painCave.errMsg,
805	<	"SimSetup error: If you use an NPT\n"
806	<	"    ensemble, you must set tauBarostat.\n");
807	<	painCave.isFatal = 1;
808	<	simError();
809	<	}
810	<	break;
811	<
812	<	case NPTim_ENS:
813	<	myNPTim = new NPTim( simnfo, the_ff );
814	<	myNPTim->setTargetTemp( the_globals->getTargetTemp());
815	<
816	<	if (the_globals->haveTargetPressure())
817	<	myNPTim->setTargetPressure(the_globals->getTargetPressure());
818	<	else {
819	<	sprintf( painCave.errMsg,
820	<	"SimSetup error: If you use a constant pressure\n"
821	<	"    ensemble, you must set targetPressure in the BASS file.\n");
822	<	painCave.isFatal = 1;
823	<	simError();
824	<	}
825	<
826	<	if( the_globals->haveTauThermostat() )
827	<	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
828	<	else{
829	<	sprintf( painCave.errMsg,
830	<	"SimSetup error: If you use an NPT\n"
831	<	"    ensemble, you must set tauThermostat.\n");
832	<	painCave.isFatal = 1;
833	<	simError();
834	<	}
835	<
836	<	if( the_globals->haveTauBarostat() )
837	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
838	<	else{
839	<	sprintf( painCave.errMsg,
840	<	"SimSetup error: If you use an NPT\n"
841	<	"    ensemble, you must set tauBarostat.\n");
842	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<	break;
846	<
847	<	case NPTfm_ENS:
848	<	myNPTfm = new NPTfm( simnfo, the_ff );
849	<	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
850	<
851	<	if (the_globals->haveTargetPressure())
852	<	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
853	<	else {
854	<	sprintf( painCave.errMsg,
855	<	"SimSetup error: If you use a constant pressure\n"
856	<	"    ensemble, you must set targetPressure in the BASS file.\n");
857	<	painCave.isFatal = 1;
858	<	simError();
859	<	}
860	<
861	<	if( the_globals->haveTauThermostat() )
862	<	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
863	<	else{
864	<	sprintf( painCave.errMsg,
865	<	"SimSetup error: If you use an NPT\n"
866	<	"    ensemble, you must set tauThermostat.\n");
867	<	painCave.isFatal = 1;
868	<	simError();
869	<	}
870	<
871	<	if( the_globals->haveTauBarostat() )
872	<	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
873	<	else{
874	<	sprintf( painCave.errMsg,
875	<	"SimSetup error: If you use an NPT\n"
876	<	"    ensemble, you must set tauBarostat.\n");
877	<	painCave.isFatal = 1;
878	<	simError();
879	<	}
880	<	break;
881	<
882	<	default:
883	<	sprintf( painCave.errMsg,
884	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
885	<	painCave.isFatal = 1;
886	<	simError();
887	<	}
888	<
889	<
890	<	#ifdef IS_MPI
891	<	mpiSim->mpiRefresh();
892	<	#endif
893	<
894	<	// initialize the Fortran
895	<
896	<
897	<	simnfo->refreshSim();
898	<
899	<	if( !strcmp( simnfo->mixingRule, "standard") ){
900	<	the_ff->initForceField( LB_MIXING_RULE );
901	<	}
902	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
903	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
904	<	}
905	<	else{
906	<	sprintf( painCave.errMsg,
907	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
908	<	simnfo->mixingRule );
909	<	painCave.isFatal = 1;
910	<	simError();
911	<	}
912	<
913	<
914	<	#ifdef IS_MPI
915	<	strcpy( checkPointMsg,
916	<	"Successfully intialized the mixingRule for Fortran." );
917	<	MPIcheckPoint();
918	<	#endif // is_mpi
919	<	}
920	<
921	<
922	<	void SimSetup::makeMolecules( void ){
923	<
924	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
925	<	molInit info;
926	<	DirectionalAtom* dAtom;
927	<	LinkedAssign* extras;
928	<	LinkedAssign* current_extra;
929	<	AtomStamp* currentAtom;
930	<	BondStamp* currentBond;
931	<	BendStamp* currentBend;
932	<	TorsionStamp* currentTorsion;
933	<
934	<	bond_pair* theBonds;
935	<	bend_set* theBends;
936	<	torsion_set* theTorsions;
937	<
938	<
939	<	//init the forceField paramters
940	<
941	<	the_ff->readParams();
942	<
943	<
944	<	// init the atoms
945	<
946	<	double ux, uy, uz, u, uSqr;
947	<
948	<	atomOffset = 0;
949	<	excludeOffset = 0;
950	<	for(i=0; i<simnfo->n_mol; i++){
951	<
952	<	stampID = the_molecules[i].getStampID();
953	<
954	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
955	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
956	<	info.nBends    = comp_stamps[stampID]->getNBends();
957	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
958	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
959	<
960	<	info.myAtoms = &the_atoms[atomOffset];
961	<	info.myExcludes = &the_excludes[excludeOffset];
962	<	info.myBonds = new Bond*[info.nBonds];
963	<	info.myBends = new Bend*[info.nBends];
964	<	info.myTorsions = new Torsion*[info.nTorsions];
965	<
966	<	theBonds = new bond_pair[info.nBonds];
967	<	theBends = new bend_set[info.nBends];
968	<	theTorsions = new torsion_set[info.nTorsions];
969	<
970	<	// make the Atoms
971	<
972	<	for(j=0; j<info.nAtoms; j++){
973	<
974	<	currentAtom = comp_stamps[stampID]->getAtom( j );
975	<	if( currentAtom->haveOrientation() ){
976	<
977	<	dAtom = new DirectionalAtom(j + atomOffset);
978	<	simnfo->n_oriented++;
979	<	info.myAtoms[j] = dAtom;
980	<
981	<	ux = currentAtom->getOrntX();
982	<	uy = currentAtom->getOrntY();
983	<	uz = currentAtom->getOrntZ();
984	<
985	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
986	<
987	<	u = sqrt( uSqr );
988	<	ux = ux / u;
989	<	uy = uy / u;
990	<	uz = uz / u;
991	<
992	<	dAtom->setSUx( ux );
993	<	dAtom->setSUy( uy );
994	<	dAtom->setSUz( uz );
995	<	}
996	<	else{
997	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
998	<	}
999	<	info.myAtoms[j]->setType( currentAtom->getType() );
1000	<
1001	<	#ifdef IS_MPI
1002	<
1003	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1004	<
1005	<	#endif // is_mpi
1006	<	}
1007	<
1008	<	// make the bonds
1009	<	for(j=0; j<info.nBonds; j++){
1010	<
1011	<	currentBond = comp_stamps[stampID]->getBond( j );
1012	<	theBonds[j].a = currentBond->getA() + atomOffset;
1013	<	theBonds[j].b = currentBond->getB() + atomOffset;
1014	<
1015	<	exI = theBonds[j].a;
1016	<	exJ = theBonds[j].b;
1017	<
1018	<	// exclude_I must always be the smaller of the pair
1019	<	if( exI > exJ ){
1020	<	tempEx = exI;
1021	<	exI = exJ;
1022	<	exJ = tempEx;
1023	<	}
1024	<	#ifdef IS_MPI
1025	<	tempEx = exI;
1026	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1027	<	tempEx = exJ;
1028	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1029	<
1030	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1031	<	#else  // isn't MPI
1032	<
1033	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1034	<	#endif  //is_mpi
1035	<	}
1036	<	excludeOffset += info.nBonds;
1037	<
1038	<	//make the bends
1039	<	for(j=0; j<info.nBends; j++){
1040	<
1041	<	currentBend = comp_stamps[stampID]->getBend( j );
1042	<	theBends[j].a = currentBend->getA() + atomOffset;
1043	<	theBends[j].b = currentBend->getB() + atomOffset;
1044	<	theBends[j].c = currentBend->getC() + atomOffset;
1045	<
1046	<	if( currentBend->haveExtras() ){
1047	<
1048	<	extras = currentBend->getExtras();
1049	<	current_extra = extras;
1050	<
1051	<	while( current_extra != NULL ){
1052	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1053	<
1054	<	switch( current_extra->getType() ){
1055	<
1056	<	case 0:
1057	<	theBends[j].ghost =
1058	<	current_extra->getInt() + atomOffset;
1059	<	theBends[j].isGhost = 1;
1060	<	break;
1061	<
1062	<	case 1:
1063	<	theBends[j].ghost =
1064	<	(int)current_extra->getDouble() + atomOffset;
1065	<	theBends[j].isGhost = 1;
1066	<	break;
1067	<
1068	<	default:
1069	<	sprintf( painCave.errMsg,
1070	<	"SimSetup Error: ghostVectorSource was neither a "
1071	<	"double nor an int.\n"
1072	<	"-->Bend[%d] in %s\n",
1073	<	j, comp_stamps[stampID]->getID() );
1074	<	painCave.isFatal = 1;
1075	<	simError();
1076	<	}
1077	<	}
1078	<
1079	<	else{
1080	<
1081	<	sprintf( painCave.errMsg,
1082	<	"SimSetup Error: unhandled bend assignment:\n"
1083	<	"    -->%s in Bend[%d] in %s\n",
1084	<	current_extra->getlhs(),
1085	<	j, comp_stamps[stampID]->getID() );
1086	<	painCave.isFatal = 1;
1087	<	simError();
1088	<	}
1089	<
1090	<	current_extra = current_extra->getNext();
1091	<	}
1092	<	}
1093	<
1094	<	if( !theBends[j].isGhost ){
1095	<
1096	<	exI = theBends[j].a;
1097	<	exJ = theBends[j].c;
1098	<	}
1099	<	else{
1100	<
1101	<	exI = theBends[j].a;
1102	<	exJ = theBends[j].b;
1103	<	}
1104	<
1105	<	// exclude_I must always be the smaller of the pair
1106	<	if( exI > exJ ){
1107	<	tempEx = exI;
1108	<	exI = exJ;
1109	<	exJ = tempEx;
1110	<	}
1111	<	#ifdef IS_MPI
1112	<	tempEx = exI;
1113	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1114	<	tempEx = exJ;
1115	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1116	<
1117	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1118	<	#else  // isn't MPI
1119	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1120	<	#endif  //is_mpi
1121	<	}
1122	<	excludeOffset += info.nBends;
1123	<
1124	<	for(j=0; j<info.nTorsions; j++){
1125	<
1126	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1127	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1128	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1129	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1130	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1131	<
1132	<	exI = theTorsions[j].a;
1133	<	exJ = theTorsions[j].d;
1134	<
1135	<	// exclude_I must always be the smaller of the pair
1136	<	if( exI > exJ ){
1137	<	tempEx = exI;
1138	<	exI = exJ;
1139	<	exJ = tempEx;
1140	<	}
1141	<	#ifdef IS_MPI
1142	<	tempEx = exI;
1143	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1144	<	tempEx = exJ;
1145	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1146	<
1147	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1148	<	#else  // isn't MPI
1149	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1150	<	#endif  //is_mpi
1151	<	}
1152	<	excludeOffset += info.nTorsions;
1153	<
1154	<
1155	<	// send the arrays off to the forceField for init.
1156	<
1157	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1158	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1159	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1160	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1161	<
1162	<
1163	<	the_molecules[i].initialize( info );
1164	<
1165	<
1166	<	atomOffset += info.nAtoms;
1167	<	delete[] theBonds;
1168	<	delete[] theBends;
1169	<	delete[] theTorsions;
1170	<	}
1171	<
1172	<	#ifdef IS_MPI
1173	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1174	<	MPIcheckPoint();
1175	<	#endif // is_mpi
1176	<
1177	<	// clean up the forcefield
1178	<	the_ff->calcRcut();
1179	<	the_ff->cleanMe();
1180	<
1181	<	}
1182	<
1183	<	void SimSetup::initFromBass( void ){
1184	<
1185	<	int i, j, k;
1186	<	int n_cells;
1187	<	double cellx, celly, cellz;
1188	<	double temp1, temp2, temp3;
1189	<	int n_per_extra;
1190	<	int n_extra;
1191	<	int have_extra, done;
1192	<
1193	<	temp1 = (double)tot_nmol / 4.0;
1194	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1195	<	temp3 = ceil( temp2 );
1196	<
1197	<	have_extra =0;
1198	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1199	<	have_extra =1;
1200	<
1201	<	n_cells = (int)temp3 - 1;
1202	<	cellx = simnfo->boxLx / temp3;
1203	<	celly = simnfo->boxLy / temp3;
1204	<	cellz = simnfo->boxLz / temp3;
1205	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1206	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1207	<	n_per_extra = (int)ceil( temp1 );
1208	<
1209	<	if( n_per_extra > 4){
1210	<	sprintf( painCave.errMsg,
1211	<	"SimSetup error. There has been an error in constructing"
1212	<	" the non-complete lattice.\n" );
1213	<	painCave.isFatal = 1;
1214	<	simError();
1215	<	}
1216	<	}
1217	<	else{
1218	<	n_cells = (int)temp3;
1219	<	cellx = simnfo->boxLx / temp3;
1220	<	celly = simnfo->boxLy / temp3;
1221	<	cellz = simnfo->boxLz / temp3;
1222	<	}
1223	<
1224	<	current_mol = 0;
1225	<	current_comp_mol = 0;
1226	<	current_comp = 0;
1227	<	current_atom_ndx = 0;
1228	<
1229	<	for( i=0; i < n_cells ; i++ ){
1230	<	for( j=0; j < n_cells; j++ ){
1231	<	for( k=0; k < n_cells; k++ ){
1232	<
1233	<	makeElement( i * cellx,
1234	<	j * celly,
1235	<	k * cellz );
1236	<
1237	<	makeElement( i * cellx + 0.5 * cellx,
1238	<	j * celly + 0.5 * celly,
1239	<	k * cellz );
1240	<
1241	<	makeElement( i * cellx,
1242	<	j * celly + 0.5 * celly,
1243	<	k * cellz + 0.5 * cellz );
1244	<
1245	<	makeElement( i * cellx + 0.5 * cellx,
1246	<	j * celly,
1247	<	k * cellz + 0.5 * cellz );
1248	<	}
1249	<	}
1250	<	}
1251	<
1252	<	if( have_extra ){
1253	<	done = 0;
1254	<
1255	<	int start_ndx;
1256	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1257	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1258	<
1259	<	if( i < n_cells ){
1260	<
1261	<	if( j < n_cells ){
1262	<	start_ndx = n_cells;
1263	<	}
1264	<	else start_ndx = 0;
1265	<	}
1266	<	else start_ndx = 0;
1267	<
1268	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1269	<
1270	<	makeElement( i * cellx,
1271	<	j * celly,
1272	<	k * cellz );
1273	<	done = ( current_mol >= tot_nmol );
1274	<
1275	<	if( !done && n_per_extra > 1 ){
1276	<	makeElement( i * cellx + 0.5 * cellx,
1277	<	j * celly + 0.5 * celly,
1278	<	k * cellz );
1279	<	done = ( current_mol >= tot_nmol );
1280	<	}
1281	<
1282	<	if( !done && n_per_extra > 2){
1283	<	makeElement( i * cellx,
1284	<	j * celly + 0.5 * celly,
1285	<	k * cellz + 0.5 * cellz );
1286	<	done = ( current_mol >= tot_nmol );
1287	<	}
1288	<
1289	<	if( !done && n_per_extra > 3){
1290	<	makeElement( i * cellx + 0.5 * cellx,
1291	<	j * celly,
1292	<	k * cellz + 0.5 * cellz );
1293	<	done = ( current_mol >= tot_nmol );
1294	<	}
1295	<	}
1296	<	}
1297	<	}
1298	<	}
1299	<
1300	<
1301	<	for( i=0; i<simnfo->n_atoms; i++ ){
1302	<	simnfo->atoms[i]->set_vx( 0.0 );
1303	<	simnfo->atoms[i]->set_vy( 0.0 );
1304	<	simnfo->atoms[i]->set_vz( 0.0 );
1305	<	}
1306	<	}
1307	<
1308	<	void SimSetup::makeElement( double x, double y, double z ){
1309	<
1310	<	int k;
1311	<	AtomStamp* current_atom;
1312	<	DirectionalAtom* dAtom;
1313	<	double rotMat[3][3];
1314	<
1315	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1316	<
1317	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1318	<	if( !current_atom->havePosition() ){
1319	<	sprintf( painCave.errMsg,
1320	<	"SimSetup:initFromBass error.\n"
1321	<	"\tComponent %s, atom %s does not have a position specified.\n"
1322	<	"\tThe initialization routine is unable to give a start"
1323	<	" position.\n",
1324	<	comp_stamps[current_comp]->getID(),
1325	<	current_atom->getType() );
1326	<	painCave.isFatal = 1;
1327	<	simError();
1328	<	}
1329	<
1330	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1331	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1332	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1333	<
1334	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1335	<
1336	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1337	<
1338	<	rotMat[0][0] = 1.0;
1339	<	rotMat[0][1] = 0.0;
1340	<	rotMat[0][2] = 0.0;
1341	<
1342	<	rotMat[1][0] = 0.0;
1343	<	rotMat[1][1] = 1.0;
1344	<	rotMat[1][2] = 0.0;
1345	<
1346	<	rotMat[2][0] = 0.0;
1347	<	rotMat[2][1] = 0.0;
1348	<	rotMat[2][2] = 1.0;
1349	<
1350	<	dAtom->setA( rotMat );
1351	<	}
1352	<
1353	<	current_atom_ndx++;
1354	<	}
1355	<
1356	<	current_mol++;
1357	<	current_comp_mol++;
1358	<
1359	<	if( current_comp_mol >= components_nmol[current_comp] ){
1360	<
1361	<	current_comp_mol = 0;
1362	<	current_comp++;
1363	<	}
601	>	// all rigid bodies are integrated:
602	>
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	>	//creat ConstraintPair.
619	>	molInfo.myConstraintPairs.clear();
620	>
621	>	for (j = 0; j < molInfo.nBonds; j++){
622	>
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	>	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	>	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	>	bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr();
644	>	consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2);
645	>
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	>	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	>	consPair = new JointConstraintPair(consElement1, consElement2);
662	>	molInfo.myConstraintPairs.push_back(consPair);
663	>	}
664	>
665	>	}
666	>	}
667	>
668	>
669	>	info[k].molecules[i].initialize(molInfo);
670	>
671	>
672	>	atomOffset += molInfo.nAtoms;
673	>	delete[] theBonds;
674	>	delete[] theBends;
675	>	delete[] theTorsions;
676	>	}
677	>
678	>
679	>
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	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
688	>
689	>	MPI_Allreduce(info[k].globalGroupMembership,
690	>	ggMjunk,
691	>	mpiSim->getNAtomsGlobal(),
692	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
693	>
694	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
695	>	info[k].globalGroupMembership[i] = ggMjunk[i];
696	>
697	>	delete[] ggMjunk;
698	>
699	>	#endif
700	>
701	>
702	>
703	>	}
704	>
705	>	#ifdef IS_MPI
706	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
707	>	MPIcheckPoint();
708	>	#endif // is_mpi
709	>
710	>	}
711	>
712	>	void SimSetup::initFromBass(void){
713	>	int i, j, k;
714	>	int n_cells;
715	>	double cellx, celly, cellz;
716	>	double temp1, temp2, temp3;
717	>	int n_per_extra;
718	>	int n_extra;
719	>	int have_extra, done;
720	>
721	>	double vel[3];
722	>	vel[0] = 0.0;
723	>	vel[1] = 0.0;
724	>	vel[2] = 0.0;
725	>
726	>	temp1 = (double) tot_nmol / 4.0;
727	>	temp2 = pow(temp1, (1.0 / 3.0));
728	>	temp3 = ceil(temp2);
729	>
730	>	have_extra = 0;
731	>	if (temp2 < temp3){
732	>	// we have a non-complete lattice
733	>	have_extra = 1;
734	>
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 = 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;
759	>	current_comp_mol = 0;
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++){
766	>	makeElement(i * cellx, j * celly, k * cellz);
767	>
768	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
769	>
770	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
771	>
772	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
773	>	}
774	>	}
775	>	}
776	>
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++){
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	>	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 (!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	>	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	>	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	>	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){
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	>	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	>	pos[0] = x + current_atom->getPosX();
845	>	pos[1] = y + current_atom->getPosY();
846	>	pos[2] = z + current_atom->getPosZ();
847	>
848	>	info[0].atoms[current_atom_ndx]->setPos(pos);
849	>
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;
855	>	rotMat[0][2] = 0.0;
856	>
857	>	rotMat[1][0] = 0.0;
858	>	rotMat[1][1] = 1.0;
859	>	rotMat[1][2] = 0.0;
860	>
861	>	rotMat[2][0] = 0.0;
862	>	rotMat[2][1] = 0.0;
863	>	rotMat[2][2] = 1.0;
864	>
865	>	dAtom->setA(rotMat);
866	>	}
867	>
868	>	current_atom_ndx++;
869	>	}
870	>
871	>	current_mol++;
872	>	current_comp_mol++;
873	>
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	>
920	>	// get the ensemble
921	>
922	>	strcpy(ensemble, globals->getEnsemble());
923	>
924	>	if (!strcasecmp(ensemble, "NVE")){
925	>	ensembleCase = NVE_ENS;
926	>	}
927	>	else if (!strcasecmp(ensemble, "NVT")){
928	>	ensembleCase = NVT_ENS;
929	>	}
930	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
931	>	ensembleCase = NPTi_ENS;
932	>	}
933	>	else if (!strcasecmp(ensemble, "NPTf")){
934	>	ensembleCase = NPTf_ENS;
935	>	}
936	>	else if (!strcasecmp(ensemble, "NPTxyz")){
937	>	ensembleCase = NPTxyz_ENS;
938	>	}
939	>	else{
940	>	sprintf(painCave.errMsg,
941	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
942	>	"\treverting to NVE for this simulation.\n",
943	>	ensemble);
944	>	painCave.isFatal = 0;
945	>	simError();
946	>	strcpy(ensemble, "NVE");
947	>	ensembleCase = NVE_ENS;
948	>	}
949	>
950	>	for (i = 0; i < nInfo; i++){
951	>	strcpy(info[i].ensemble, ensemble);
952	>
953	>	// get the mixing rule
954	>
955	>	strcpy(info[i].mixingRule, globals->getMixingRule());
956	>	info[i].usePBC = globals->getPBC();
957	>	}
958	>
959	>	// get the components and calculate the tot_nMol and indvidual n_mol
960	>
961	>	the_components = globals->getComponents();
962	>	components_nmol = new int[n_components];
963	>
964	>
965	>	if (!globals->haveNMol()){
966	>	// we don't have the total number of molecules, so we assume it is
967	>	// given in each component
968	>
969	>	tot_nmol = 0;
970	>	for (i = 0; i < n_components; i++){
971	>	if (!the_components[i]->haveNMol()){
972	>	// we have a problem
973	>	sprintf(painCave.errMsg,
974	>	"SimSetup Error. No global NMol or component NMol given.\n"
975	>	"\tCannot calculate the number of atoms.\n");
976	>	painCave.isFatal = 1;
977	>	simError();
978	>	}
979	>
980	>	tot_nmol += the_components[i]->getNMol();
981	>	components_nmol[i] = the_components[i]->getNMol();
982	>	}
983	>	}
984	>	else{
985	>	sprintf(painCave.errMsg,
986	>	"SimSetup error.\n"
987	>	"\tSorry, the ability to specify total"
988	>	" nMols and then give molfractions in the components\n"
989	>	"\tis not currently supported."
990	>	" Please give nMol in the components.\n");
991	>	painCave.isFatal = 1;
992	>	simError();
993	>	}
994	>
995	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
996	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
997	>	sprintf(painCave.errMsg,
998	>	"Sample time is not divisible by dt.\n"
999	>	"\tThis will result in samples that are not uniformly\n"
1000	>	"\tdistributed in time.  If this is a problem, change\n"
1001	>	"\tyour sampleTime variable.\n");
1002	>	painCave.isFatal = 0;
1003	>	simError();
1004	>	}
1005	>
1006	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
1007	>	sprintf(painCave.errMsg,
1008	>	"Status time is not divisible by dt.\n"
1009	>	"\tThis will result in status reports that are not uniformly\n"
1010	>	"\tdistributed in time.  If this is a problem, change \n"
1011	>	"\tyour statusTime variable.\n");
1012	>	painCave.isFatal = 0;
1013	>	simError();
1014	>	}
1015	>
1016	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1017	>	sprintf(painCave.errMsg,
1018	>	"Thermal time is not divisible by dt.\n"
1019	>	"\tThis will result in thermalizations that are not uniformly\n"
1020	>	"\tdistributed in time.  If this is a problem, change \n"
1021	>	"\tyour thermalTime variable.\n");
1022	>	painCave.isFatal = 0;
1023	>	simError();
1024	>	}
1025	>
1026	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1027	>	sprintf(painCave.errMsg,
1028	>	"Reset time is not divisible by dt.\n"
1029	>	"\tThis will result in integrator resets that are not uniformly\n"
1030	>	"\tdistributed in time.  If this is a problem, change\n"
1031	>	"\tyour resetTime variable.\n");
1032	>	painCave.isFatal = 0;
1033	>	simError();
1034	>	}
1035	>
1036	>	// set the status, sample, and thermal kick times
1037	>
1038	>	for (i = 0; i < nInfo; i++){
1039	>	if (globals->haveSampleTime()){
1040	>	info[i].sampleTime = globals->getSampleTime();
1041	>	info[i].statusTime = info[i].sampleTime;
1042	>	}
1043	>	else{
1044	>	info[i].sampleTime = globals->getRunTime();
1045	>	info[i].statusTime = info[i].sampleTime;
1046	>	}
1047	>
1048	>	if (globals->haveStatusTime()){
1049	>	info[i].statusTime = globals->getStatusTime();
1050	>	}
1051	>
1052	>	if (globals->haveThermalTime()){
1053	>	info[i].thermalTime = globals->getThermalTime();
1054	>	} else {
1055	>	info[i].thermalTime = globals->getRunTime();
1056	>	}
1057	>
1058	>	info[i].resetIntegrator = 0;
1059	>	if( globals->haveResetTime() ){
1060	>	info[i].resetTime = globals->getResetTime();
1061	>	info[i].resetIntegrator = 1;
1062	>	}
1063	>
1064	>	// check for the temperature set flag
1065	>
1066	>	if (globals->haveTempSet())
1067	>	info[i].setTemp = globals->getTempSet();
1068	>
1069	>	// check for the extended State init
1070	>
1071	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1072	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1073	>
1074	>	// check for thermodynamic integration
1075	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1076	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1077	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1078	>	info[i].thermIntLambda = globals->getThermIntLambda();
1079	>	info[i].thermIntK = globals->getThermIntK();
1080	>
1081	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1082	>	info[i].restraint = myRestraint;
1083	>	}
1084	>	else {
1085	>	sprintf(painCave.errMsg,
1086	>	"SimSetup Error:\n"
1087	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1088	>	"\tthermodynamicIntegrationLambda (and/or\n"
1089	>	"\tthermodynamicIntegrationK) was not specified.\n"
1090	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1091	>	painCave.isFatal = 1;
1092	>	simError();
1093	>	}
1094	>	}
1095	>	else if(globals->getUseLiquidThermInt()) {
1096	>	if (globals->getUseSolidThermInt()) {
1097	>	sprintf( painCave.errMsg,
1098	>	"SimSetup Warning: It appears that you have both solid and\n"
1099	>	"\tliquid thermodynamic integration activated in your .bass\n"
1100	>	"\tfile. To avoid confusion, specify only one technique in\n"
1101	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1102	>	"\twill be assumed for the current simulation. If this is not\n"
1103	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1104	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1105	>	painCave.isFatal = 0;
1106	>	simError();
1107	>	}
1108	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1109	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1110	>	info[i].thermIntLambda = globals->getThermIntLambda();
1111	>	info[i].thermIntK = globals->getThermIntK();
1112	>	}
1113	>	else {
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Error:\n"
1116	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1117	>	"\tthermodynamicIntegrationLambda (and/or\n"
1118	>	"\tthermodynamicIntegrationK) was not specified.\n"
1119	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1120	>	painCave.isFatal = 1;
1121	>	simError();
1122	>	}
1123	>	}
1124	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1125	>	sprintf(painCave.errMsg,
1126	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1127	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1128	>	"\t'true' in your .bass file.  These keywords are set to\n"
1129	>	"\t'false' by default, so your lambda and/or k values are\n"
1130	>	"\tbeing ignored.\n");
1131	>	painCave.isFatal = 0;
1132	>	simError();
1133	>	}
1134	>	}
1135	>
1136	>	//setup seed for random number generator
1137	>	int seedValue;
1138	>
1139	>	if (globals->haveSeed()){
1140	>	seedValue = globals->getSeed();
1141	>
1142	>	if(seedValue / 1E9 == 0){
1143	>	sprintf(painCave.errMsg,
1144	>	"Seed for sprng library should contain at least 9 digits\n"
1145	>	"OOPSE will generate a seed for user\n");
1146	>	painCave.isFatal = 0;
1147	>	simError();
1148	>
1149	>	//using seed generated by system instead of invalid seed set by user
1150	>	#ifndef IS_MPI
1151	>	seedValue = make_sprng_seed();
1152	>	#else
1153	>	if (worldRank == 0){
1154	>	seedValue = make_sprng_seed();
1155	>	}
1156	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1157	>	#endif
1158	>	}
1159	>	}//end of if branch of globals->haveSeed()
1160	>	else{
1161	>
1162	>	#ifndef IS_MPI
1163	>	seedValue = make_sprng_seed();
1164	>	#else
1165	>	if (worldRank == 0){
1166	>	seedValue = make_sprng_seed();
1167	>	}
1168	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1169	>	#endif
1170	>	}//end of globals->haveSeed()
1171	>
1172	>	for (int i = 0; i < nInfo; i++){
1173	>	info[i].setSeed(seedValue);
1174	>	}
1175	>
1176	>	#ifdef IS_MPI
1177	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1178	>	MPIcheckPoint();
1179	>	#endif // is_mpi
1180	>	}
1181	>
1182	>
1183	>	void SimSetup::finalInfoCheck(void){
1184	>	int index;
1185	>	int usesDipoles;
1186	>	int usesCharges;
1187	>	int i;
1188	>
1189	>	for (i = 0; i < nInfo; i++){
1190	>	// check electrostatic parameters
1191	>
1192	>	index = 0;
1193	>	usesDipoles = 0;
1194	>	while ((index < info[i].n_atoms) && !usesDipoles){
1195	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1196	>	index++;
1197	>	}
1198	>	index = 0;
1199	>	usesCharges = 0;
1200	>	while ((index < info[i].n_atoms) && !usesCharges){
1201	>	usesCharges= (info[i].atoms[index])->hasCharge();
1202	>	index++;
1203	>	}
1204	>	#ifdef IS_MPI
1205	>	int myUse = usesDipoles;
1206	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1207	>	#endif //is_mpi
1208	>
1209	>	double theRcut, theRsw;
1210	>
1211	>	if (globals->haveRcut()) {
1212	>	theRcut = globals->getRcut();
1213	>
1214	>	if (globals->haveRsw())
1215	>	theRsw = globals->getRsw();
1216	>	else
1217	>	theRsw = theRcut;
1218	>
1219	>	info[i].setDefaultRcut(theRcut, theRsw);
1220	>
1221	>	} else {
1222	>
1223	>	the_ff->calcRcut();
1224	>	theRcut = info[i].getRcut();
1225	>
1226	>	if (globals->haveRsw())
1227	>	theRsw = globals->getRsw();
1228	>	else
1229	>	theRsw = theRcut;
1230	>
1231	>	info[i].setDefaultRcut(theRcut, theRsw);
1232	>	}
1233	>
1234	>	if (globals->getUseRF()){
1235	>	info[i].useReactionField = 1;
1236	>
1237	>	if (!globals->haveRcut()){
1238	>	sprintf(painCave.errMsg,
1239	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1240	>	"\tOOPSE will use a default value of 15.0 angstroms"
1241	>	"\tfor the cutoffRadius.\n");
1242	>	painCave.isFatal = 0;
1243	>	simError();
1244	>	theRcut = 15.0;
1245	>	}
1246	>	else{
1247	>	theRcut = globals->getRcut();
1248	>	}
1249	>
1250	>	if (!globals->haveRsw()){
1251	>	sprintf(painCave.errMsg,
1252	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1253	>	"\tOOPSE will use a default value of\n"
1254	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1255	>	painCave.isFatal = 0;
1256	>	simError();
1257	>	theRsw = 0.95 * theRcut;
1258	>	}
1259	>	else{
1260	>	theRsw = globals->getRsw();
1261	>	}
1262	>
1263	>	info[i].setDefaultRcut(theRcut, theRsw);
1264	>
1265	>	if (!globals->haveDielectric()){
1266	>	sprintf(painCave.errMsg,
1267	>	"SimSetup Error: No Dielectric constant was set.\n"
1268	>	"\tYou are trying to use Reaction Field without"
1269	>	"\tsetting a dielectric constant!\n");
1270	>	painCave.isFatal = 1;
1271	>	simError();
1272	>	}
1273	>	info[i].dielectric = globals->getDielectric();
1274	>	}
1275	>	else{
1276	>	if (usesDipoles || usesCharges){
1277	>
1278	>	if (!globals->haveRcut()){
1279	>	sprintf(painCave.errMsg,
1280	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1281	>	"\tOOPSE will use a default value of 15.0 angstroms"
1282	>	"\tfor the cutoffRadius.\n");
1283	>	painCave.isFatal = 0;
1284	>	simError();
1285	>	theRcut = 15.0;
1286	>	}
1287	>	else{
1288	>	theRcut = globals->getRcut();
1289	>	}
1290	>
1291	>	if (!globals->haveRsw()){
1292	>	sprintf(painCave.errMsg,
1293	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1294	>	"\tOOPSE will use a default value of\n"
1295	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1296	>	painCave.isFatal = 0;
1297	>	simError();
1298	>	theRsw = 0.95 * theRcut;
1299	>	}
1300	>	else{
1301	>	theRsw = globals->getRsw();
1302	>	}
1303	>
1304	>	info[i].setDefaultRcut(theRcut, theRsw);
1305	>
1306	>	}
1307	>	}
1308	>	}
1309	>	#ifdef IS_MPI
1310	>	strcpy(checkPointMsg, "post processing checks out");
1311	>	MPIcheckPoint();
1312	>	#endif // is_mpi
1313	>
1314	>	// clean up the forcefield
1315	>	the_ff->cleanMe();
1316	>	}
1317	>
1318	>	void SimSetup::initSystemCoords(void){
1319	>	int i;
1320	>
1321	>	char* inName;
1322	>
1323	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1324	>
1325	>	for (i = 0; i < info[0].n_atoms; i++)
1326	>	info[0].atoms[i]->setCoords();
1327	>
1328	>	if (globals->haveInitialConfig()){
1329	>	InitializeFromFile* fileInit;
1330	>	#ifdef IS_MPI // is_mpi
1331	>	if (worldRank == 0){
1332	>	#endif //is_mpi
1333	>	inName = globals->getInitialConfig();
1334	>	fileInit = new InitializeFromFile(inName);
1335	>	#ifdef IS_MPI
1336	>	}
1337	>	else
1338	>	fileInit = new InitializeFromFile(NULL);
1339	>	#endif
1340	>	fileInit->readInit(info); // default velocities on
1341	>
1342	>	delete fileInit;
1343	>	}
1344	>	else{
1345	>
1346	>	// no init from bass
1347	>
1348	>	sprintf(painCave.errMsg,
1349	>	"Cannot intialize a simulation without an initial configuration file.\n");
1350	>	painCave.isFatal = 1;;
1351	>	simError();
1352	>
1353	>	}
1354	>
1355	>	#ifdef IS_MPI
1356	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1357	>	MPIcheckPoint();
1358	>	#endif // is_mpi
1359	>	}
1360	>
1361	>
1362	>	void SimSetup::makeOutNames(void){
1363	>	int k;
1364	>
1365	>
1366	>	for (k = 0; k < nInfo; k++){
1367	>	#ifdef IS_MPI
1368	>	if (worldRank == 0){
1369	>	#endif // is_mpi
1370	>
1371	>	if (globals->haveFinalConfig()){
1372	>	strcpy(info[k].finalName, globals->getFinalConfig());
1373	>	}
1374	>	else{
1375	>	strcpy(info[k].finalName, inFileName);
1376	>	char* endTest;
1377	>	int nameLength = strlen(info[k].finalName);
1378	>	endTest = &(info[k].finalName[nameLength - 5]);
1379	>	if (!strcmp(endTest, ".bass")){
1380	>	strcpy(endTest, ".eor");
1381	>	}
1382	>	else if (!strcmp(endTest, ".BASS")){
1383	>	strcpy(endTest, ".eor");
1384	>	}
1385	>	else{
1386	>	endTest = &(info[k].finalName[nameLength - 4]);
1387	>	if (!strcmp(endTest, ".bss")){
1388	>	strcpy(endTest, ".eor");
1389	>	}
1390	>	else if (!strcmp(endTest, ".mdl")){
1391	>	strcpy(endTest, ".eor");
1392	>	}
1393	>	else{
1394	>	strcat(info[k].finalName, ".eor");
1395	>	}
1396	>	}
1397	>	}
1398	>
1399	>	// make the sample and status out names
1400	>
1401	>	strcpy(info[k].sampleName, inFileName);
1402	>	char* endTest;
1403	>	int nameLength = strlen(info[k].sampleName);
1404	>	endTest = &(info[k].sampleName[nameLength - 5]);
1405	>	if (!strcmp(endTest, ".bass")){
1406	>	strcpy(endTest, ".dump");
1407	>	}
1408	>	else if (!strcmp(endTest, ".BASS")){
1409	>	strcpy(endTest, ".dump");
1410	>	}
1411	>	else{
1412	>	endTest = &(info[k].sampleName[nameLength - 4]);
1413	>	if (!strcmp(endTest, ".bss")){
1414	>	strcpy(endTest, ".dump");
1415	>	}
1416	>	else if (!strcmp(endTest, ".mdl")){
1417	>	strcpy(endTest, ".dump");
1418	>	}
1419	>	else{
1420	>	strcat(info[k].sampleName, ".dump");
1421	>	}
1422	>	}
1423	>
1424	>	strcpy(info[k].statusName, inFileName);
1425	>	nameLength = strlen(info[k].statusName);
1426	>	endTest = &(info[k].statusName[nameLength - 5]);
1427	>	if (!strcmp(endTest, ".bass")){
1428	>	strcpy(endTest, ".stat");
1429	>	}
1430	>	else if (!strcmp(endTest, ".BASS")){
1431	>	strcpy(endTest, ".stat");
1432	>	}
1433	>	else{
1434	>	endTest = &(info[k].statusName[nameLength - 4]);
1435	>	if (!strcmp(endTest, ".bss")){
1436	>	strcpy(endTest, ".stat");
1437	>	}
1438	>	else if (!strcmp(endTest, ".mdl")){
1439	>	strcpy(endTest, ".stat");
1440	>	}
1441	>	else{
1442	>	strcat(info[k].statusName, ".stat");
1443	>	}
1444	>	}
1445	>
1446	>	strcpy(info[k].rawPotName, inFileName);
1447	>	nameLength = strlen(info[k].rawPotName);
1448	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1449	>	if (!strcmp(endTest, ".bass")){
1450	>	strcpy(endTest, ".raw");
1451	>	}
1452	>	else if (!strcmp(endTest, ".BASS")){
1453	>	strcpy(endTest, ".raw");
1454	>	}
1455	>	else{
1456	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1457	>	if (!strcmp(endTest, ".bss")){
1458	>	strcpy(endTest, ".raw");
1459	>	}
1460	>	else if (!strcmp(endTest, ".mdl")){
1461	>	strcpy(endTest, ".raw");
1462	>	}
1463	>	else{
1464	>	strcat(info[k].rawPotName, ".raw");
1465	>	}
1466	>	}
1467	>
1468	>	#ifdef IS_MPI
1469	>
1470	>	}
1471	>	#endif // is_mpi
1472	>	}
1473	>	}
1474	>
1475	>
1476	>	void SimSetup::sysObjectsCreation(void){
1477	>	int i, k;
1478	>
1479	>	// create the forceField
1480	>
1481	>	createFF();
1482	>
1483	>	// extract componentList
1484	>
1485	>	compList();
1486	>
1487	>	// calc the number of atoms, bond, bends, and torsions
1488	>
1489	>	calcSysValues();
1490	>
1491	>	#ifdef IS_MPI
1492	>	// divide the molecules among the processors
1493	>
1494	>	mpiMolDivide();
1495	>	#endif //is_mpi
1496	>
1497	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1498	>
1499	>	makeSysArrays();
1500	>
1501	>	// make and initialize the molecules (all but atomic coordinates)
1502	>
1503	>	makeMolecules();
1504	>
1505	>	for (k = 0; k < nInfo; k++){
1506	>	info[k].identArray = new int[info[k].n_atoms];
1507	>	for (i = 0; i < info[k].n_atoms; i++){
1508	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1509	>	}
1510	>	}
1511	>	}
1512	>
1513	>
1514	>	void SimSetup::createFF(void){
1515	>	switch (ffCase){
1516	>	case FF_DUFF:
1517	>	the_ff = new DUFF();
1518	>	break;
1519	>
1520	>	case FF_LJ:
1521	>	the_ff = new LJFF();
1522	>	break;
1523	>
1524	>	case FF_EAM:
1525	>	the_ff = new EAM_FF();
1526	>	break;
1527	>
1528	>	case FF_H2O:
1529	>	the_ff = new WATER();
1530	>	break;
1531	>
1532	>	default:
1533	>	sprintf(painCave.errMsg,
1534	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1535	>	painCave.isFatal = 1;
1536	>	simError();
1537	>	}
1538	>
1539	>	#ifdef IS_MPI
1540	>	strcpy(checkPointMsg, "ForceField creation successful");
1541	>	MPIcheckPoint();
1542	>	#endif // is_mpi
1543	>	}
1544	>
1545	>
1546	>	void SimSetup::compList(void){
1547	>	int i;
1548	>	char* id;
1549	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1550	>	LinkedMolStamp* currentStamp = NULL;
1551	>	comp_stamps = new MoleculeStamp * [n_components];
1552	>	bool haveCutoffGroups;
1553	>
1554	>	haveCutoffGroups = false;
1555	>
1556	>	// make an array of molecule stamps that match the components used.
1557	>	// also extract the used stamps out into a separate linked list
1558	>
1559	>	for (i = 0; i < nInfo; i++){
1560	>	info[i].nComponents = n_components;
1561	>	info[i].componentsNmol = components_nmol;
1562	>	info[i].compStamps = comp_stamps;
1563	>	info[i].headStamp = headStamp;
1564	>	}
1565	>
1566	>
1567	>	for (i = 0; i < n_components; i++){
1568	>	id = the_components[i]->getType();
1569	>	comp_stamps[i] = NULL;
1570	>
1571	>	// check to make sure the component isn't already in the list
1572	>
1573	>	comp_stamps[i] = headStamp->match(id);
1574	>	if (comp_stamps[i] == NULL){
1575	>	// extract the component from the list;
1576	>
1577	>	currentStamp = stamps->extractMolStamp(id);
1578	>	if (currentStamp == NULL){
1579	>	sprintf(painCave.errMsg,
1580	>	"SimSetup error: Component \"%s\" was not found in the "
1581	>	"list of declared molecules\n",
1582	>	id);
1583	>	painCave.isFatal = 1;
1584	>	simError();
1585	>	}
1586	>
1587	>	headStamp->add(currentStamp);
1588	>	comp_stamps[i] = headStamp->match(id);
1589	>	}
1590	>
1591	>	if(comp_stamps[i]->getNCutoffGroups() > 0)
1592	>	haveCutoffGroups = true;
1593	>	}
1594	>
1595	>	for (i = 0; i < nInfo; i++)
1596	>	info[i].haveCutoffGroups = haveCutoffGroups;
1597	>
1598	>	#ifdef IS_MPI
1599	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1600	>	MPIcheckPoint();
1601	>	#endif // is_mpi
1602	>	}
1603	>
1604	>	void SimSetup::calcSysValues(void){
1605	>	int i, j;
1606	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1607	>
1608	>	int* molMembershipArray;
1609	>	CutoffGroupStamp* cg;
1610	>
1611	>	tot_atoms = 0;
1612	>	tot_bonds = 0;
1613	>	tot_bends = 0;
1614	>	tot_torsions = 0;
1615	>	tot_rigid = 0;
1616	>	tot_groups = 0;
1617	>	for (i = 0; i < n_components; i++){
1618	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1619	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1620	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1621	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1622	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1623	>
1624	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1625	>	atomsingroups = 0;
1626	>	for (j=0; j < ncutgroups; j++) {
1627	>	cg = comp_stamps[i]->getCutoffGroup(j);
1628	>	atomsingroups += cg->getNMembers();
1629	>	}
1630	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1631	>	tot_groups += components_nmol[i] * ngroupsinstamp;
1632	>	}
1633	>
1634	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1635	>	molMembershipArray = new int[tot_atoms];
1636	>
1637	>	for (i = 0; i < nInfo; i++){
1638	>	info[i].n_atoms = tot_atoms;
1639	>	info[i].n_bonds = tot_bonds;
1640	>	info[i].n_bends = tot_bends;
1641	>	info[i].n_torsions = tot_torsions;
1642	>	info[i].n_SRI = tot_SRI;
1643	>	info[i].n_mol = tot_nmol;
1644	>	info[i].ngroup = tot_groups;
1645	>	info[i].molMembershipArray = molMembershipArray;
1646	>	}
1647	>	}
1648	>
1649	>	#ifdef IS_MPI
1650	>
1651	>	void SimSetup::mpiMolDivide(void){
1652	>	int i, j, k;
1653	>	int localMol, allMol;
1654	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1655	>	int local_rigid, local_groups;
1656	>	vector<int> globalMolIndex;
1657	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1658	>	CutoffGroupStamp* cg;
1659	>
1660	>	mpiSim = new mpiSimulation(info);
1661	>
1662	>	mpiSim->divideLabor();
1663	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1664	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1665	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1666	>
1667	>	// set up the local variables
1668	>
1669	>	mol2proc = mpiSim->getMolToProcMap();
1670	>	molCompType = mpiSim->getMolComponentType();
1671	>
1672	>	allMol = 0;
1673	>	localMol = 0;
1674	>	local_atoms = 0;
1675	>	local_bonds = 0;
1676	>	local_bends = 0;
1677	>	local_torsions = 0;
1678	>	local_rigid = 0;
1679	>	local_groups = 0;
1680	>	globalAtomCounter = 0;
1681	>
1682	>	for (i = 0; i < n_components; i++){
1683	>	for (j = 0; j < components_nmol[i]; j++){
1684	>	if (mol2proc[allMol] == worldRank){
1685	>	local_atoms += comp_stamps[i]->getNAtoms();
1686	>	local_bonds += comp_stamps[i]->getNBonds();
1687	>	local_bends += comp_stamps[i]->getNBends();
1688	>	local_torsions += comp_stamps[i]->getNTorsions();
1689	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1690	>
1691	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1692	>	atomsingroups = 0;
1693	>	for (k=0; k < ncutgroups; k++) {
1694	>	cg = comp_stamps[i]->getCutoffGroup(k);
1695	>	atomsingroups += cg->getNMembers();
1696	>	}
1697	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1698	>	ncutgroups;
1699	>	local_groups += ngroupsinstamp;
1700	>
1701	>	localMol++;
1702	>	}
1703	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1704	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1705	>	globalAtomCounter++;
1706	>	}
1707	>
1708	>	allMol++;
1709	>	}
1710	>	}
1711	>	local_SRI = local_bonds + local_bends + local_torsions;
1712	>
1713	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1714	>
1715	>	if (local_atoms != info[0].n_atoms){
1716	>	sprintf(painCave.errMsg,
1717	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1718	>	"\tlocalAtom (%d) are not equal.\n",
1719	>	info[0].n_atoms, local_atoms);
1720	>	painCave.isFatal = 1;
1721	>	simError();
1722	>	}
1723	>
1724	>	info[0].ngroup = mpiSim->getNGroupsLocal();
1725	>	if (local_groups != info[0].ngroup){
1726	>	sprintf(painCave.errMsg,
1727	>	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1728	>	"\tlocalGroups (%d) are not equal.\n",
1729	>	info[0].ngroup, local_groups);
1730	>	painCave.isFatal = 1;
1731	>	simError();
1732	>	}
1733	>
1734	>	info[0].n_bonds = local_bonds;
1735	>	info[0].n_bends = local_bends;
1736	>	info[0].n_torsions = local_torsions;
1737	>	info[0].n_SRI = local_SRI;
1738	>	info[0].n_mol = localMol;
1739	>
1740	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1741	>	MPIcheckPoint();
1742	>	}
1743	>
1744	>	#endif // is_mpi
1745	>
1746	>
1747	>	void SimSetup::makeSysArrays(void){
1748	>
1749	>	#ifndef IS_MPI
1750	>	int k, j;
1751	>	#endif // is_mpi
1752	>	int i, l;
1753	>
1754	>	Atom** the_atoms;
1755	>	Molecule* the_molecules;
1756	>
1757	>	for (l = 0; l < nInfo; l++){
1758	>	// create the atom and short range interaction arrays
1759	>
1760	>	the_atoms = new Atom * [info[l].n_atoms];
1761	>	the_molecules = new Molecule[info[l].n_mol];
1762	>	int molIndex;
1763	>
1764	>	// initialize the molecule's stampID's
1765	>
1766	>	#ifdef IS_MPI
1767	>
1768	>
1769	>	molIndex = 0;
1770	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1771	>	if (mol2proc[i] == worldRank){
1772	>	the_molecules[molIndex].setStampID(molCompType[i]);
1773	>	the_molecules[molIndex].setMyIndex(molIndex);
1774	>	the_molecules[molIndex].setGlobalIndex(i);
1775	>	molIndex++;
1776	>	}
1777	>	}
1778	>
1779	>	#else // is_mpi
1780	>
1781	>	molIndex = 0;
1782	>	globalAtomCounter = 0;
1783	>	for (i = 0; i < n_components; i++){
1784	>	for (j = 0; j < components_nmol[i]; j++){
1785	>	the_molecules[molIndex].setStampID(i);
1786	>	the_molecules[molIndex].setMyIndex(molIndex);
1787	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1788	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1789	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1790	>	globalAtomCounter++;
1791	>	}
1792	>	molIndex++;
1793	>	}
1794	>	}
1795	>
1796	>
1797	>	#endif // is_mpi
1798	>
1799	>	info[l].globalExcludes = new int;
1800	>	info[l].globalExcludes[0] = 0;
1801	>
1802	>	// set the arrays into the SimInfo object
1803	>
1804	>	info[l].atoms = the_atoms;
1805	>	info[l].molecules = the_molecules;
1806	>	info[l].nGlobalExcludes = 0;
1807	>
1808	>	the_ff->setSimInfo(info);
1809	>	}
1810	>	}
1811	>
1812	>	void SimSetup::makeIntegrator(void){
1813	>	int k;
1814	>
1815	>	NVE<RealIntegrator>* myNVE = NULL;
1816	>	NVT<RealIntegrator>* myNVT = NULL;
1817	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1818	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1819	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1820	>
1821	>	for (k = 0; k < nInfo; k++){
1822	>	switch (ensembleCase){
1823	>	case NVE_ENS:
1824	>	if (globals->haveZconstraints()){
1825	>	setupZConstraint(info[k]);
1826	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1827	>	}
1828	>	else{
1829	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1830	>	}
1831	>
1832	>	info->the_integrator = myNVE;
1833	>	break;
1834	>
1835	>	case NVT_ENS:
1836	>	if (globals->haveZconstraints()){
1837	>	setupZConstraint(info[k]);
1838	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1839	>	}
1840	>	else
1841	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1842	>
1843	>	myNVT->setTargetTemp(globals->getTargetTemp());
1844	>
1845	>	if (globals->haveTauThermostat())
1846	>	myNVT->setTauThermostat(globals->getTauThermostat());
1847	>	else{
1848	>	sprintf(painCave.errMsg,
1849	>	"SimSetup error: If you use the NVT\n"
1850	>	"\tensemble, you must set tauThermostat.\n");
1851	>	painCave.isFatal = 1;
1852	>	simError();
1853	>	}
1854	>
1855	>	info->the_integrator = myNVT;
1856	>	break;
1857	>
1858	>	case NPTi_ENS:
1859	>	if (globals->haveZconstraints()){
1860	>	setupZConstraint(info[k]);
1861	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1862	>	}
1863	>	else
1864	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1865	>
1866	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1867	>
1868	>	if (globals->haveTargetPressure())
1869	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1870	>	else{
1871	>	sprintf(painCave.errMsg,
1872	>	"SimSetup error: If you use a constant pressure\n"
1873	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1874	>	painCave.isFatal = 1;
1875	>	simError();
1876	>	}
1877	>
1878	>	if (globals->haveTauThermostat())
1879	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1880	>	else{
1881	>	sprintf(painCave.errMsg,
1882	>	"SimSetup error: If you use an NPT\n"
1883	>	"\tensemble, you must set tauThermostat.\n");
1884	>	painCave.isFatal = 1;
1885	>	simError();
1886	>	}
1887	>
1888	>	if (globals->haveTauBarostat())
1889	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1890	>	else{
1891	>	sprintf(painCave.errMsg,
1892	>	"SimSetup error: If you use an NPT\n"
1893	>	"\tensemble, you must set tauBarostat.\n");
1894	>	painCave.isFatal = 1;
1895	>	simError();
1896	>	}
1897	>
1898	>	info->the_integrator = myNPTi;
1899	>	break;
1900	>
1901	>	case NPTf_ENS:
1902	>	if (globals->haveZconstraints()){
1903	>	setupZConstraint(info[k]);
1904	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1905	>	}
1906	>	else
1907	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1908	>
1909	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1910	>
1911	>	if (globals->haveTargetPressure())
1912	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1913	>	else{
1914	>	sprintf(painCave.errMsg,
1915	>	"SimSetup error: If you use a constant pressure\n"
1916	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1917	>	painCave.isFatal = 1;
1918	>	simError();
1919	>	}
1920	>
1921	>	if (globals->haveTauThermostat())
1922	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1923	>
1924	>	else{
1925	>	sprintf(painCave.errMsg,
1926	>	"SimSetup error: If you use an NPT\n"
1927	>	"\tensemble, you must set tauThermostat.\n");
1928	>	painCave.isFatal = 1;
1929	>	simError();
1930	>	}
1931	>
1932	>	if (globals->haveTauBarostat())
1933	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1934	>
1935	>	else{
1936	>	sprintf(painCave.errMsg,
1937	>	"SimSetup error: If you use an NPT\n"
1938	>	"\tensemble, you must set tauBarostat.\n");
1939	>	painCave.isFatal = 1;
1940	>	simError();
1941	>	}
1942	>
1943	>	info->the_integrator = myNPTf;
1944	>	break;
1945	>
1946	>	case NPTxyz_ENS:
1947	>	if (globals->haveZconstraints()){
1948	>	setupZConstraint(info[k]);
1949	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1950	>	}
1951	>	else
1952	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1953	>
1954	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1955	>
1956	>	if (globals->haveTargetPressure())
1957	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1958	>	else{
1959	>	sprintf(painCave.errMsg,
1960	>	"SimSetup error: If you use a constant pressure\n"
1961	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1962	>	painCave.isFatal = 1;
1963	>	simError();
1964	>	}
1965	>
1966	>	if (globals->haveTauThermostat())
1967	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1968	>	else{
1969	>	sprintf(painCave.errMsg,
1970	>	"SimSetup error: If you use an NPT\n"
1971	>	"\tensemble, you must set tauThermostat.\n");
1972	>	painCave.isFatal = 1;
1973	>	simError();
1974	>	}
1975	>
1976	>	if (globals->haveTauBarostat())
1977	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1978	>	else{
1979	>	sprintf(painCave.errMsg,
1980	>	"SimSetup error: If you use an NPT\n"
1981	>	"\tensemble, you must set tauBarostat.\n");
1982	>	painCave.isFatal = 1;
1983	>	simError();
1984	>	}
1985	>
1986	>	info->the_integrator = myNPTxyz;
1987	>	break;
1988	>
1989	>	default:
1990	>	sprintf(painCave.errMsg,
1991	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1992	>	painCave.isFatal = 1;
1993	>	simError();
1994	>	}
1995	>	}
1996	>	}
1997	>
1998	>	void SimSetup::initFortran(void){
1999	>	info[0].refreshSim();
2000	>
2001	>	if (!strcmp(info[0].mixingRule, "standard")){
2002	>	the_ff->initForceField(LB_MIXING_RULE);
2003	>	}
2004	>	else if (!strcmp(info[0].mixingRule, "explicit")){
2005	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
2006	>	}
2007	>	else{
2008	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
2009	>	info[0].mixingRule);
2010	>	painCave.isFatal = 1;
2011	>	simError();
2012	>	}
2013	>
2014	>
2015	>	#ifdef IS_MPI
2016	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2017	>	MPIcheckPoint();
2018	>	#endif // is_mpi
2019	>	}
2020	>
2021	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
2022	>	int nZConstraints;
2023	>	ZconStamp** zconStamp;
2024	>
2025	>	if (globals->haveZconstraintTime()){
2026	>	//add sample time of z-constraint  into SimInfo's property list
2027	>	DoubleData* zconsTimeProp = new DoubleData();
2028	>	zconsTimeProp->setID(ZCONSTIME_ID);
2029	>	zconsTimeProp->setData(globals->getZconsTime());
2030	>	theInfo.addProperty(zconsTimeProp);
2031	>	}
2032	>	else{
2033	>	sprintf(painCave.errMsg,
2034	>	"ZConstraint error: If you use a ZConstraint,\n"
2035	>	"\tyou must set zconsTime.\n");
2036	>	painCave.isFatal = 1;
2037	>	simError();
2038	>	}
2039	>
2040	>	//push zconsTol into siminfo, if user does not specify
2041	>	//value for zconsTol, a default value will be used
2042	>	DoubleData* zconsTol = new DoubleData();
2043	>	zconsTol->setID(ZCONSTOL_ID);
2044	>	if (globals->haveZconsTol()){
2045	>	zconsTol->setData(globals->getZconsTol());
2046	>	}
2047	>	else{
2048	>	double defaultZConsTol = 0.01;
2049	>	sprintf(painCave.errMsg,
2050	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2051	>	"\tOOPSE will use a default value of %f.\n"
2052	>	"\tTo set the tolerance, use the zconsTol variable.\n",
2053	>	defaultZConsTol);
2054	>	painCave.isFatal = 0;
2055	>	simError();
2056	>
2057	>	zconsTol->setData(defaultZConsTol);
2058	>	}
2059	>	theInfo.addProperty(zconsTol);
2060	>
2061	>	//set Force Subtraction Policy
2062	>	StringData* zconsForcePolicy = new StringData();
2063	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2064	>
2065	>	if (globals->haveZconsForcePolicy()){
2066	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2067	>	}
2068	>	else{
2069	>	sprintf(painCave.errMsg,
2070	>	"ZConstraint Warning: No force subtraction policy was set.\n"
2071	>	"\tOOPSE will use PolicyByMass.\n"
2072	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2073	>	painCave.isFatal = 0;
2074	>	simError();
2075	>	zconsForcePolicy->setData("BYMASS");
2076	>	}
2077	>
2078	>	theInfo.addProperty(zconsForcePolicy);
2079	>
2080	>	//set zcons gap
2081	>	DoubleData* zconsGap = new DoubleData();
2082	>	zconsGap->setID(ZCONSGAP_ID);
2083	>
2084	>	if (globals->haveZConsGap()){
2085	>	zconsGap->setData(globals->getZconsGap());
2086	>	theInfo.addProperty(zconsGap);
2087	>	}
2088	>
2089	>	//set zcons fixtime
2090	>	DoubleData* zconsFixtime = new DoubleData();
2091	>	zconsFixtime->setID(ZCONSFIXTIME_ID);
2092	>
2093	>	if (globals->haveZConsFixTime()){
2094	>	zconsFixtime->setData(globals->getZconsFixtime());
2095	>	theInfo.addProperty(zconsFixtime);
2096	>	}
2097	>
2098	>	//set zconsUsingSMD
2099	>	IntData* zconsUsingSMD = new IntData();
2100	>	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2101	>
2102	>	if (globals->haveZConsUsingSMD()){
2103	>	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2104	>	theInfo.addProperty(zconsUsingSMD);
2105	>	}
2106	>
2107	>	//Determine the name of ouput file and add it into SimInfo's property list
2108	>	//Be careful, do not use inFileName, since it is a pointer which
2109	>	//point to a string at master node, and slave nodes do not contain that string
2110	>
2111	>	string zconsOutput(theInfo.finalName);
2112	>
2113	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2114	>
2115	>	StringData* zconsFilename = new StringData();
2116	>	zconsFilename->setID(ZCONSFILENAME_ID);
2117	>	zconsFilename->setData(zconsOutput);
2118	>
2119	>	theInfo.addProperty(zconsFilename);
2120	>
2121	>	//setup index, pos and other parameters of z-constraint molecules
2122	>	nZConstraints = globals->getNzConstraints();
2123	>	theInfo.nZconstraints = nZConstraints;
2124	>
2125	>	zconStamp = globals->getZconStamp();
2126	>	ZConsParaItem tempParaItem;
2127	>
2128	>	ZConsParaData* zconsParaData = new ZConsParaData();
2129	>	zconsParaData->setID(ZCONSPARADATA_ID);
2130	>
2131	>	for (int i = 0; i < nZConstraints; i++){
2132	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2133	>	tempParaItem.zPos = zconStamp[i]->getZpos();
2134	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2135	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
2136	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2137	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2138	>	zconsParaData->addItem(tempParaItem);
2139	>	}
2140	>
2141	>	//check the uniqueness of index
2142	>	if(!zconsParaData->isIndexUnique()){
2143	>	sprintf(painCave.errMsg,
2144	>	"ZConstraint Error: molIndex is not unique!\n");
2145	>	painCave.isFatal = 1;
2146	>	simError();
2147	>	}
2148	>
2149	>	//sort the parameters by index of molecules
2150	>	zconsParaData->sortByIndex();
2151	>
2152	>	//push data into siminfo, therefore, we can retrieve later
2153	>	theInfo.addProperty(zconsParaData);
2154	>	}
2155	>
2156	>	void SimSetup::makeMinimizer(){
2157	>
2158	>	OOPSEMinimizer* myOOPSEMinimizer;
2159	>	MinimizerParameterSet* param;
2160	>	char minimizerName[100];
2161	>
2162	>	for (int i = 0; i < nInfo; i++){
2163	>
2164	>	//prepare parameter set for minimizer
2165	>	param = new MinimizerParameterSet();
2166	>	param->setDefaultParameter();
2167	>
2168	>	if (globals->haveMinimizer()){
2169	>	param->setFTol(globals->getMinFTol());
2170	>	}
2171	>
2172	>	if (globals->haveMinGTol()){
2173	>	param->setGTol(globals->getMinGTol());
2174	>	}
2175	>
2176	>	if (globals->haveMinMaxIter()){
2177	>	param->setMaxIteration(globals->getMinMaxIter());
2178	>	}
2179	>
2180	>	if (globals->haveMinWriteFrq()){
2181	>	param->setMaxIteration(globals->getMinMaxIter());
2182	>	}
2183	>
2184	>	if (globals->haveMinWriteFrq()){
2185	>	param->setWriteFrq(globals->getMinWriteFrq());
2186	>	}
2187	>
2188	>	if (globals->haveMinStepSize()){
2189	>	param->setStepSize(globals->getMinStepSize());
2190	>	}
2191	>
2192	>	if (globals->haveMinLSMaxIter()){
2193	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2194	>	}
2195	>
2196	>	if (globals->haveMinLSTol()){
2197	>	param->setLineSearchTol(globals->getMinLSTol());
2198	>	}
2199	>
2200	>	strcpy(minimizerName, globals->getMinimizer());
2201	>
2202	>	if (!strcasecmp(minimizerName, "CG")){
2203	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2204	>	}
2205	>	else if (!strcasecmp(minimizerName, "SD")){
2206	>	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2207	>	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2208	>	}
2209	>	else{
2210	>	sprintf(painCave.errMsg,
2211	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2212	>	painCave.isFatal = 0;
2213	>	simError();
2214	>
2215	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2216	>	}
2217	>	info[i].the_integrator = myOOPSEMinimizer;
2218	>
2219	>	//store the minimizer into simInfo
2220	>	info[i].the_minimizer = myOOPSEMinimizer;
2221	>	info[i].has_minimizer = true;
2222	>	}
2223	>
2224		}

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