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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC vs.
Revision 1104 by gezelter, Tue Apr 13 16:26:03 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 "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 14 | Line 20
20
21		// some defines for ensemble and Forcefield  cases
22
23	<	#define NVE_ENS  0
24	<	#define NVT_ENS  1
25	<	#define NPTi_ENS 2
26	<	#define NPTf_ENS 3
23	>	#define NVE_ENS        0
24	>	#define NVT_ENS        1
25	>	#define NPTi_ENS       2
26	>	#define NPTf_ENS       3
27	>	#define NPTxyz_ENS     4
28
29
30	<	#define FF_DUFF 0
31	<	#define FF_LJ   1
30	>	#define FF_DUFF  0
31	>	#define FF_LJ    1
32	>	#define FF_EAM   2
33	>	#define FF_H2O   3
34
35	+	using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 39 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
71	<	mpiEventLoop();
72	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
126	<	MakeStamps *the_stamps;
80	<	Globals* the_globals;
81	<	int i, j, k, globalAtomIndex;
82	<
83	<	int ensembleCase;
84	<	int ffCase;
85	<
86	<	ensembleCase = -1;
87	<	ffCase = -1;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
90	<	the_stamps = stamps;
91	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
94	<	simnfo->target_temp = the_globals->getTargetTemp();
95	<	simnfo->dt = the_globals->getDt();
96	<	simnfo->run_time = the_globals->getRunTime();
130	>	// creation of complex system objects
131
132	<	// get the ones we know are there, yet still may need some work.
99	<	n_components = the_globals->getNComponents();
100	<	strcpy( force_field, the_globals->getForceField() );
132	>	sysObjectsCreation();
133
134	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
103	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
104	<	else{
105	<	sprintf( painCave.errMsg,
106	<	"SimSetup Error. Unrecognized force field -> %s\n",
107	<	force_field );
108	<	painCave.isFatal = 1;
109	<	simError();
110	<	}
134	>	// check on the post processing info
135
136	<	// get the ensemble:
113	<	strcpy( ensemble, the_globals->getEnsemble() );
136	>	finalInfoCheck();
137
138	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
139	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
140	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
141	<	ensembleCase = NPTi_ENS;
142	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
143	<	else{
144	<	sprintf( painCave.errMsg,
122	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
123	<	"reverting to NVE for this simulation.\n",
124	<	ensemble );
125	<	painCave.isFatal = 0;
126	<	simError();
127	<	strcpy( ensemble, "NVE" );
128	<	ensembleCase = NVE_ENS;
138	>	// initialize the system coordinates
139	>
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142	>
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145		}
130	–	strcpy( simnfo->ensemble, ensemble );
146
147	+	// make the output filenames
148
149	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
134	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
135	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
136	<	//     if (the_globals->haveTargetPressure())
137	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
138	<	//     else {
139	<	//       sprintf( painCave.errMsg,
140	<	//                "SimSetup error: If you use the constant pressure\n"
141	<	//                "    ensemble, you must set targetPressure.\n"
142	<	//                "    This was found in the BASS file.\n");
143	<	//       painCave.isFatal = 1;
144	<	//       simError();
145	<	//     }
149	>	makeOutNames();
150
151	<	//     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;
157	<	//       simError();
158	<	//     }
151	>	if (globals->haveMinimizer())
152	>	// make minimizer
153	>	makeMinimizer();
154	>	else
155	>	// make the integrator
156	>	makeIntegrator();
157	>
158	>	#ifdef IS_MPI
159	>	mpiSim->mpiRefresh();
160	>	#endif
161
162	<	//     if (the_globals->haveTauBarostat())
161	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
162	<	//     else {
163	<	//       sprintf( painCave.errMsg,
164	<	//                "SimSetup error: If you use the constant pressure\n"
165	<	//                "    ensemble, you must set tauBarostat.\n"
166	<	//                "    This was found in the BASS file.\n");
167	<	//       painCave.isFatal = 1;
168	<	//       simError();
169	<	//     }
162	>	// initialize the Fortran
163
164	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
165	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
173	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
164	>	initFortran();
165	>	}
166
175	–	//     if (the_globals->haveTauThermostat())
176	–	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
177	–	//     else if (the_globals->haveQmass())
178	–	//       the_extendedsystem->setQmass(the_globals->getQmass());
179	–	//     else {
180	–	//       sprintf( painCave.errMsg,
181	–	//                "SimSetup error: If you use one of the constant temperature\n"
182	–	//                "    ensembles, you must set either tauThermostat or qMass.\n"
183	–	//                "    Neither of these was found in the BASS file.\n");
184	–	//       painCave.isFatal = 1;
185	–	//       simError();
186	–	//     }
167
168	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
169	<	simnfo->usePBC = the_globals->getPBC();
170	<
171	<	int usesDipoles = 0;
172	<	switch( ffCase ){
168	>	void SimSetup::makeMolecules(void){
169	>	int i, j, k;
170	>	int exI, exJ, exK, exL, slI, slJ;
171	>	int tempI, tempJ, tempK, tempL;
172	>	int molI;
173	>	int stampID, atomOffset, rbOffset;
174	>	molInit molInfo;
175	>	DirectionalAtom* dAtom;
176	>	RigidBody* myRB;
177	>	StuntDouble* mySD;
178	>	LinkedAssign* extras;
179	>	LinkedAssign* current_extra;
180	>	AtomStamp* currentAtom;
181	>	BondStamp* currentBond;
182	>	BendStamp* currentBend;
183	>	TorsionStamp* currentTorsion;
184	>	RigidBodyStamp* currentRigidBody;
185
186	<	case FF_DUFF:
187	<	the_ff = new DUFF();
188	<	usesDipoles = 1;
197	<	break;
186	>	bond_pair* theBonds;
187	>	bend_set* theBends;
188	>	torsion_set* theTorsions;
189
190	<	case FF_LJ:
200	<	the_ff = new LJFF();
201	<	break;
190	>	set<int> skipList;
191
192	<	default:
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup Error. Unrecognized force field in case statement.\n");
206	<	painCave.isFatal = 1;
207	<	simError();
208	<	}
192	>	double phi, theta, psi;
193
194	<	#ifdef IS_MPI
211	<	strcpy( checkPointMsg, "ForceField creation successful" );
212	<	MPIcheckPoint();
213	<	#endif // is_mpi
194	>	//init the forceField paramters
195
196	<	// get the components and calculate the tot_nMol and indvidual n_mol
216	<	the_components = the_globals->getComponents();
217	<	components_nmol = new int[n_components];
218	<	comp_stamps = new MoleculeStamp*[n_components];
196	>	the_ff->readParams();
197
198	<	if( !the_globals->haveNMol() ){
221	<	// we don't have the total number of molecules, so we assume it is
222	<	// given in each component
198	>	// init the atoms
199
200	<	tot_nmol = 0;
225	<	for( i=0; i<n_components; i++ ){
200	>	int nMembers, nNew, rb1, rb2;
201
202	<	if( !the_components[i]->haveNMol() ){
203	<	// we have a problem
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup Error. No global NMol or component NMol"
206	<	" given. Cannot calculate the number of atoms.\n" );
207	<	painCave.isFatal = 1;
208	<	simError();
209	<	}
202	>	for (k = 0; k < nInfo; k++){
203	>	the_ff->setSimInfo(&(info[k]));
204	>
205	>	atomOffset = 0;
206	>
207	>	for (i = 0; i < info[k].n_mol; i++){
208	>	stampID = info[k].molecules[i].getStampID();
209	>
210	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
211	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
212	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
213	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
214	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
215	>
216	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
217
218	<	tot_nmol += the_components[i]->getNMol();
219	<	components_nmol[i] = the_components[i]->getNMol();
220	<	}
221	<	}
240	<	else{
241	<	sprintf( painCave.errMsg,
242	<	"SimSetup error.\n"
243	<	"\tSorry, the ability to specify total"
244	<	" nMols and then give molfractions in the components\n"
245	<	"\tis not currently supported."
246	<	" Please give nMol in the components.\n" );
247	<	painCave.isFatal = 1;
248	<	simError();
249	<
250	<
251	<	//     tot_nmol = the_globals->getNMol();
252	<
253	<	//   //we have the total number of molecules, now we check for molfractions
254	<	//     for( i=0; i<n_components; i++ ){
255	<
256	<	//       if( !the_components[i]->haveMolFraction() ){
257	<
258	<	//  if( !the_components[i]->haveNMol() ){
259	<	//    //we have a problem
260	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
261	<	//              << " nMol was given in component
262	<
263	<	}
218	>	if (molInfo.nBonds > 0)
219	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
220	>	else
221	>	molInfo.myBonds = NULL;
222
223	<	#ifdef IS_MPI
224	<	strcpy( checkPointMsg, "Have the number of components" );
225	<	MPIcheckPoint();
226	<	#endif // is_mpi
223	>	if (molInfo.nBends > 0)
224	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
225	>	else
226	>	molInfo.myBends = NULL;
227
228	<	// make an array of molecule stamps that match the components used.
229	<	// also extract the used stamps out into a separate linked list
228	>	if (molInfo.nTorsions > 0)
229	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
230	>	else
231	>	molInfo.myTorsions = NULL;
232
233	<	simnfo->nComponents = n_components;
234	<	simnfo->componentsNmol = components_nmol;
235	<	simnfo->compStamps = comp_stamps;
276	<	simnfo->headStamp = new LinkedMolStamp();
277	<
278	<	char* id;
279	<	LinkedMolStamp* headStamp = simnfo->headStamp;
280	<	LinkedMolStamp* currentStamp = NULL;
281	<	for( i=0; i<n_components; i++ ){
282	<
283	<	id = the_components[i]->getType();
284	<	comp_stamps[i] = NULL;
285	<
286	<	// check to make sure the component isn't already in the list
287	<
288	<	comp_stamps[i] = headStamp->match( id );
289	<	if( comp_stamps[i] == NULL ){
233	>	theBonds = new bond_pair[molInfo.nBonds];
234	>	theBends = new bend_set[molInfo.nBends];
235	>	theTorsions = new torsion_set[molInfo.nTorsions];
236
237	<	// extract the component from the list;
292	<
293	<	currentStamp = the_stamps->extractMolStamp( id );
294	<	if( currentStamp == NULL ){
295	<	sprintf( painCave.errMsg,
296	<	"SimSetup error: Component \"%s\" was not found in the "
297	<	"list of declared molecules\n",
298	<	id );
299	<	painCave.isFatal = 1;
300	<	simError();
301	<	}
302	<
303	<	headStamp->add( currentStamp );
304	<	comp_stamps[i] = headStamp->match( id );
305	<	}
306	<	}
237	>	// make the Atoms
238
239	<	#ifdef IS_MPI
240	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
310	<	MPIcheckPoint();
311	<	#endif // is_mpi
312	<
239	>	for (j = 0; j < molInfo.nAtoms; j++){
240	>	currentAtom = comp_stamps[stampID]->getAtom(j);
241
242	+	if (currentAtom->haveOrientation()){
243	+	dAtom = new DirectionalAtom((j + atomOffset),
244	+	info[k].getConfiguration());
245	+	info[k].n_oriented++;
246	+	molInfo.myAtoms[j] = dAtom;
247
248	+	// Directional Atoms have standard unit vectors which are oriented
249	+	// in space using the three Euler angles.  We assume the standard
250	+	// unit vector was originally along the z axis below.
251
252	<	// caclulate the number of atoms, bonds, bends and torsions
252	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
253	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
254	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
255
256	<	tot_atoms = 0;
257	<	tot_bonds = 0;
258	<	tot_bends = 0;
259	<	tot_torsions = 0;
322	<	for( i=0; i<n_components; i++ ){
323	<
324	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
325	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
326	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
327	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
328	<	}
256	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
257	>
258	>	}
259	>	else{
260
261	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
261	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
262	>	}
263
264	<	simnfo->n_atoms = tot_atoms;
333	<	simnfo->n_bonds = tot_bonds;
334	<	simnfo->n_bends = tot_bends;
335	<	simnfo->n_torsions = tot_torsions;
336	<	simnfo->n_SRI = tot_SRI;
337	<	simnfo->n_mol = tot_nmol;
338	<
339	<	simnfo->molMembershipArray = new int[tot_atoms];
264	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
265
266		#ifdef IS_MPI
267
268	<	// divide the molecules among processors here.
344	<
345	<	mpiSim = new mpiSimulation( simnfo );
346	<
347	<	globalIndex = mpiSim->divideLabor();
268	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
269
270	<	// set up the local variables
271	<
351	<	int localMol, allMol;
352	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
270	>	#endif // is_mpi
271	>	}
272
273	<	int* mol2proc = mpiSim->getMolToProcMap();
274	<	int* molCompType = mpiSim->getMolComponentType();
275	<
276	<	allMol = 0;
277	<	localMol = 0;
359	<	local_atoms = 0;
360	<	local_bonds = 0;
361	<	local_bends = 0;
362	<	local_torsions = 0;
363	<	globalAtomIndex = 0;
273	>	// make the bonds
274	>	for (j = 0; j < molInfo.nBonds; j++){
275	>	currentBond = comp_stamps[stampID]->getBond(j);
276	>	theBonds[j].a = currentBond->getA() + atomOffset;
277	>	theBonds[j].b = currentBond->getB() + atomOffset;
278
279	+	tempI = theBonds[j].a;
280	+	tempJ = theBonds[j].b;
281
282	<	for( i=0; i<n_components; i++ ){
282	>	#ifdef IS_MPI
283	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
284	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
285	>	#else
286	>	exI = tempI + 1;
287	>	exJ = tempJ + 1;
288	>	#endif
289
290	<	for( j=0; j<components_nmol[i]; j++ ){
369	<
370	<	if( mol2proc[allMol] == worldRank ){
371	<
372	<	local_atoms +=    comp_stamps[i]->getNAtoms();
373	<	local_bonds +=    comp_stamps[i]->getNBonds();
374	<	local_bends +=    comp_stamps[i]->getNBends();
375	<	local_torsions += comp_stamps[i]->getNTorsions();
376	<	localMol++;
377	<	}
378	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
379	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
380	<	globalAtomIndex++;
290	>	info[k].excludes->addPair(exI, exJ);
291		}
292
293	<	allMol++;
294	<	}
295	<	}
296	<	local_SRI = local_bonds + local_bends + local_torsions;
297	<
298	<	simnfo->n_atoms = mpiSim->getMyNlocal();
389	<
390	<	if( local_atoms != simnfo->n_atoms ){
391	<	sprintf( painCave.errMsg,
392	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
393	<	" localAtom (%d) are not equal.\n",
394	<	simnfo->n_atoms,
395	<	local_atoms );
396	<	painCave.isFatal = 1;
397	<	simError();
398	<	}
293	>	//make the bends
294	>	for (j = 0; j < molInfo.nBends; j++){
295	>	currentBend = comp_stamps[stampID]->getBend(j);
296	>	theBends[j].a = currentBend->getA() + atomOffset;
297	>	theBends[j].b = currentBend->getB() + atomOffset;
298	>	theBends[j].c = currentBend->getC() + atomOffset;
299
300	<	simnfo->n_bonds = local_bonds;
301	<	simnfo->n_bends = local_bends;
302	<	simnfo->n_torsions = local_torsions;
403	<	simnfo->n_SRI = local_SRI;
404	<	simnfo->n_mol = localMol;
300	>	if (currentBend->haveExtras()){
301	>	extras = currentBend->getExtras();
302	>	current_extra = extras;
303
304	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
305	<	MPIcheckPoint();
306	<
307	<
308	<	#endif // is_mpi
309	<
304	>	while (current_extra != NULL){
305	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
306	>	switch (current_extra->getType()){
307	>	case 0:
308	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
309	>	theBends[j].isGhost = 1;
310	>	break;
311
312	<	// create the atom and short range interaction arrays
312	>	case 1:
313	>	theBends[j].ghost = (int) current_extra->getDouble() +
314	>	atomOffset;
315	>	theBends[j].isGhost = 1;
316	>	break;
317
318	<	Atom::createArrays(simnfo->n_atoms);
319	<	the_atoms = new Atom*[simnfo->n_atoms];
320	<	the_molecules = new Molecule[simnfo->n_mol];
321	<	int molIndex;
322	<
323	<	// initialize the molecule's stampID's
318	>	default:
319	>	sprintf(painCave.errMsg,
320	>	"SimSetup Error: ghostVectorSource was neither a "
321	>	"double nor an int.\n"
322	>	"-->Bend[%d] in %s\n",
323	>	j, comp_stamps[stampID]->getID());
324	>	painCave.isFatal = 1;
325	>	simError();
326	>	}
327	>	}
328	>	else{
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: unhandled bend assignment:\n"
331	>	"    -->%s in Bend[%d] in %s\n",
332	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
333	>	painCave.isFatal = 1;
334	>	simError();
335	>	}
336
337	+	current_extra = current_extra->getNext();
338	+	}
339	+	}
340	+
341	+	if (theBends[j].isGhost) {
342	+
343	+	tempI = theBends[j].a;
344	+	tempJ = theBends[j].b;
345	+
346		#ifdef IS_MPI
347	<
347	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
348	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
349	>	#else
350	>	exI = tempI + 1;
351	>	exJ = tempJ + 1;
352	>	#endif
353	>	info[k].excludes->addPair(exI, exJ);
354
355	<	molIndex = 0;
426	<	for(i=0; i<mpiSim->getTotNmol(); i++){
427	<
428	<	if(mol2proc[i] == worldRank ){
429	<	the_molecules[molIndex].setStampID( molCompType[i] );
430	<	the_molecules[molIndex].setMyIndex( molIndex );
431	<	the_molecules[molIndex].setGlobalIndex( i );
432	<	molIndex++;
433	<	}
434	<	}
355	>	} else {
356
357	<	#else // is_mpi
358	<
359	<	molIndex = 0;
360	<	globalAtomIndex = 0;
361	<	for(i=0; i<n_components; i++){
362	<	for(j=0; j<components_nmol[i]; j++ ){
363	<	the_molecules[molIndex].setStampID( i );
364	<	the_molecules[molIndex].setMyIndex( molIndex );
365	<	the_molecules[molIndex].setGlobalIndex( molIndex );
366	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
367	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
368	<	globalAtomIndex++;
357	>	tempI = theBends[j].a;
358	>	tempJ = theBends[j].b;
359	>	tempK = theBends[j].c;
360	>
361	>	#ifdef IS_MPI
362	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
363	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
364	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
365	>	#else
366	>	exI = tempI + 1;
367	>	exJ = tempJ + 1;
368	>	exK = tempK + 1;
369	>	#endif
370	>
371	>	info[k].excludes->addPair(exI, exK);
372	>	info[k].excludes->addPair(exI, exJ);
373	>	info[k].excludes->addPair(exJ, exK);
374	>	}
375		}
449	–	molIndex++;
450	–	}
451	–	}
452	–
376
377	<	#endif // is_mpi
377	>	for (j = 0; j < molInfo.nTorsions; j++){
378	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
379	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
380	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
381	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
382	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
383
384	+	tempI = theTorsions[j].a;
385	+	tempJ = theTorsions[j].b;
386	+	tempK = theTorsions[j].c;
387	+	tempL = theTorsions[j].d;
388
389	<	if( simnfo->n_SRI ){
390	<
391	<	Exclude::createArray(simnfo->n_SRI);
392	<	the_excludes = new Exclude*[simnfo->n_SRI];
393	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
394	<	simnfo->globalExcludes = new int;
395	<	simnfo->n_exclude = simnfo->n_SRI;
396	<	}
397	<	else{
398	<
399	<	Exclude::createArray( 1 );
468	<	the_excludes = new Exclude*;
469	<	the_excludes[0] = new Exclude(0);
470	<	the_excludes[0]->setPair( 0,0 );
471	<	simnfo->globalExcludes = new int;
472	<	simnfo->globalExcludes[0] = 0;
473	<	simnfo->n_exclude = 0;
474	<	}
389	>	#ifdef IS_MPI
390	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
391	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
392	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
393	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
394	>	#else
395	>	exI = tempI + 1;
396	>	exJ = tempJ + 1;
397	>	exK = tempK + 1;
398	>	exL = tempL + 1;
399	>	#endif
400
401	<	// set the arrays into the SimInfo object
401	>	info[k].excludes->addPair(exI, exJ);
402	>	info[k].excludes->addPair(exI, exK);
403	>	info[k].excludes->addPair(exI, exL);
404	>	info[k].excludes->addPair(exJ, exK);
405	>	info[k].excludes->addPair(exJ, exL);
406	>	info[k].excludes->addPair(exK, exL);
407	>	}
408
409	<	simnfo->atoms = the_atoms;
479	<	simnfo->molecules = the_molecules;
480	<	simnfo->nGlobalExcludes = 0;
481	<	simnfo->excludes = the_excludes;
409	>	for (j = 0; j < molInfo.nRigidBodies; j++){
410
411	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
412	+	nMembers = currentRigidBody->getNMembers();
413
414	<	// get some of the tricky things that may still be in the globals
414	>	// Create the Rigid Body:
415
416	<	double boxVector[3];
417	<	if( the_globals->haveBox() ){
418	<	boxVector[0] = the_globals->getBox();
489	<	boxVector[1] = the_globals->getBox();
490	<	boxVector[2] = the_globals->getBox();
491	<
492	<	simnfo->setBox( boxVector );
493	<	}
494	<	else if( the_globals->haveDensity() ){
416	>	myRB = new RigidBody();
417	>
418	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
419
420	<	double vol;
421	<	vol = (double)tot_nmol / the_globals->getDensity();
498	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
499	<	boxVector[1] = boxVector[0];
500	<	boxVector[2] = boxVector[0];
420	>	// molI is atom numbering inside this molecule
421	>	molI = currentRigidBody->getMember(rb1);
422
423	<	simnfo->setBox( boxVector );
424	<	}
504	<	else{
505	<	if( !the_globals->haveBoxX() ){
506	<	sprintf( painCave.errMsg,
507	<	"SimSetup error, no periodic BoxX size given.\n" );
508	<	painCave.isFatal = 1;
509	<	simError();
510	<	}
511	<	boxVector[0] = the_globals->getBoxX();
423	>	// tempI is atom numbering on local processor
424	>	tempI = molI + atomOffset;
425
426	<	if( !the_globals->haveBoxY() ){
427	<	sprintf( painCave.errMsg,
428	<	"SimSetup error, no periodic BoxY size given.\n" );
516	<	painCave.isFatal = 1;
517	<	simError();
518	<	}
519	<	boxVector[1] = the_globals->getBoxY();
426	>	// currentAtom is the AtomStamp (which we need for
427	>	// rigid body reference positions)
428	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
429
430	<	if( !the_globals->haveBoxZ() ){
431	<	sprintf( painCave.errMsg,
523	<	"SimSetup error, no periodic BoxZ size given.\n" );
524	<	painCave.isFatal = 1;
525	<	simError();
526	<	}
527	<	boxVector[2] = the_globals->getBoxZ();
430	>	// When we add to the rigid body, add the atom itself and
431	>	// the stamp info:
432
433	<	simnfo->setBox( boxVector );
434	<	}
435	<
433	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
434	>
435	>	// Add this atom to the Skip List for the integrators
436		#ifdef IS_MPI
437	<	strcpy( checkPointMsg, "Box size set up" );
438	<	MPIcheckPoint();
439	<	#endif // is_mpi
437	>	slI = info[k].atoms[tempI]->getGlobalIndex();
438	>	#else
439	>	slI = tempI;
440	>	#endif
441	>	skipList.insert(slI);
442	>
443	>	}
444	>
445	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
446	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
447	>
448	>	tempI = currentRigidBody->getMember(rb1);
449	>	tempJ = currentRigidBody->getMember(rb2);
450	>
451	>	// Some explanation is required here.
452	>	// Fortran indexing starts at 1, while c indexing starts at 0
453	>	// Also, in parallel computations, the GlobalIndex is
454	>	// used for the exclude list:
455	>
456	>	#ifdef IS_MPI
457	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
458	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
459	>	#else
460	>	exI = tempI + 1;
461	>	exJ = tempJ + 1;
462	>	#endif
463	>
464	>	info[k].excludes->addPair(exI, exJ);
465	>
466	>	}
467	>	}
468
469	+	molInfo.myRigidBodies.push_back(myRB);
470	+	info[k].rigidBodies.push_back(myRB);
471	+	}
472	+
473
474	<	// initialize the arrays
474	>	// After this is all set up, scan through the atoms to
475	>	// see if they can be added to the integrableObjects:
476
477	<	the_ff->setSimInfo( simnfo );
477	>	for (j = 0; j < molInfo.nAtoms; j++){
478
479	<	makeMolecules();
480	<	simnfo->identArray = new int[simnfo->n_atoms];
481	<	for(i=0; i<simnfo->n_atoms; i++){
482	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
483	<	}
547	<
548	<	if (the_globals->getUseRF() ) {
549	<	simnfo->useReactionField = 1;
550	<
551	<	if( !the_globals->haveECR() ){
552	<	sprintf( painCave.errMsg,
553	<	"SimSetup Warning: using default value of 1/2 the smallest "
554	<	"box length for the electrostaticCutoffRadius.\n"
555	<	"I hope you have a very fast processor!\n");
556	<	painCave.isFatal = 0;
557	<	simError();
558	<	double smallest;
559	<	smallest = simnfo->boxLx;
560	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
561	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
562	<	simnfo->ecr = 0.5 * smallest;
563	<	} else {
564	<	simnfo->ecr        = the_globals->getECR();
565	<	}
479	>	#ifdef IS_MPI
480	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
481	>	#else
482	>	slJ = j+atomOffset;
483	>	#endif
484
485	<	if( !the_globals->haveEST() ){
486	<	sprintf( painCave.errMsg,
487	<	"SimSetup Warning: using default value of 0.05 * the "
488	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
489	<	);
490	<	painCave.isFatal = 0;
491	<	simError();
492	<	simnfo->est = 0.05 * simnfo->ecr;
493	<	} else {
494	<	simnfo->est        = the_globals->getEST();
495	<	}
485	>	// if they aren't on the skip list, then they can be integrated
486	>
487	>	if (skipList.find(slJ) == skipList.end()) {
488	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
489	>	info[k].integrableObjects.push_back(mySD);
490	>	molInfo.myIntegrableObjects.push_back(mySD);
491	>	}
492	>	}
493	>
494	>	// all rigid bodies are integrated:
495	>
496	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
497	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
498	>	info[k].integrableObjects.push_back(mySD);
499	>	molInfo.myIntegrableObjects.push_back(mySD);
500	>	}
501
579	–	if(!the_globals->haveDielectric() ){
580	–	sprintf( painCave.errMsg,
581	–	"SimSetup Error: You are trying to use Reaction Field without"
582	–	"setting a dielectric constant!\n"
583	–	);
584	–	painCave.isFatal = 1;
585	–	simError();
586	–	}
587	–	simnfo->dielectric = the_globals->getDielectric();
588	–	} else {
589	–	if (usesDipoles) {
502
503	<	if( !the_globals->haveECR() ){
592	<	sprintf( painCave.errMsg,
593	<	"SimSetup Warning: using default value of 1/2 the smallest "
594	<	"box length for the electrostaticCutoffRadius.\n"
595	<	"I hope you have a very fast processor!\n");
596	<	painCave.isFatal = 0;
597	<	simError();
598	<	double smallest;
599	<	smallest = simnfo->boxLx;
600	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
601	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
602	<	simnfo->ecr = 0.5 * smallest;
603	<	} else {
604	<	simnfo->ecr        = the_globals->getECR();
605	<	}
503	>	// send the arrays off to the forceField for init.
504
505	<	if( !the_globals->haveEST() ){
506	<	sprintf( painCave.errMsg,
507	<	"SimSetup Warning: using default value of 5%% of the "
508	<	"electrostaticCutoffRadius for the "
509	<	"electrostaticSkinThickness\n"
612	<	);
613	<	painCave.isFatal = 0;
614	<	simError();
615	<	simnfo->est = 0.05 * simnfo->ecr;
616	<	} else {
617	<	simnfo->est        = the_globals->getEST();
618	<	}
619	<	}
620	<	}
505	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
506	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
507	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
508	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
509	>	theTorsions);
510
511	+	info[k].molecules[i].initialize(molInfo);
512	+
513	+
514	+	atomOffset += molInfo.nAtoms;
515	+	delete[] theBonds;
516	+	delete[] theBends;
517	+	delete[] theTorsions;
518	+	}
519	+	}
520	+
521		#ifdef IS_MPI
522	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
522	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
523		MPIcheckPoint();
524		#endif // is_mpi
525
526	<	if( the_globals->haveInitialConfig() ){
628	<
629	<	InitializeFromFile* fileInit;
630	<	#ifdef IS_MPI // is_mpi
631	<	if( worldRank == 0 ){
632	<	#endif //is_mpi
633	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
634	<	#ifdef IS_MPI
635	<	}else fileInit = new InitializeFromFile( NULL );
636	<	#endif
637	<	fileInit->read_xyz( simnfo ); // default velocities on
526	>	// clean up the forcefield
527
528	<	delete fileInit;
640	<	}
641	<	else{
528	>	if (!globals->haveLJrcut()){
529
530	<	#ifdef IS_MPI
530	>	the_ff->calcRcut();
531
532	<	// no init from bass
533	<
534	<	sprintf( painCave.errMsg,
535	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
649	<	painCave.isFatal;
650	<	simError();
651	<
652	<	#else
532	>	} else {
533	>
534	>	the_ff->setRcut( globals->getLJrcut() );
535	>	}
536
537	<	initFromBass();
537	>	the_ff->cleanMe();
538	>	}
539
540	+	void SimSetup::initFromBass(void){
541	+	int i, j, k;
542	+	int n_cells;
543	+	double cellx, celly, cellz;
544	+	double temp1, temp2, temp3;
545	+	int n_per_extra;
546	+	int n_extra;
547	+	int have_extra, done;
548
549	<	#endif
550	<	}
549	>	double vel[3];
550	>	vel[0] = 0.0;
551	>	vel[1] = 0.0;
552	>	vel[2] = 0.0;
553
554	<	#ifdef IS_MPI
555	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
556	<	MPIcheckPoint();
663	<	#endif // is_mpi
554	>	temp1 = (double) tot_nmol / 4.0;
555	>	temp2 = pow(temp1, (1.0 / 3.0));
556	>	temp3 = ceil(temp2);
557
558	+	have_extra = 0;
559	+	if (temp2 < temp3){
560	+	// we have a non-complete lattice
561	+	have_extra = 1;
562
563	<
564	<
565	<
563	>	n_cells = (int) temp3 - 1;
564	>	cellx = info[0].boxL[0] / temp3;
565	>	celly = info[0].boxL[1] / temp3;
566	>	cellz = info[0].boxL[2] / temp3;
567	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
568	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
569	>	n_per_extra = (int) ceil(temp1);
570
571	<
572	<	#ifdef IS_MPI
573	<	if( worldRank == 0 ){
574	<	#endif // is_mpi
575	<
576	<	if( the_globals->haveFinalConfig() ){
676	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
571	>	if (n_per_extra > 4){
572	>	sprintf(painCave.errMsg,
573	>	"SimSetup error. There has been an error in constructing"
574	>	" the non-complete lattice.\n");
575	>	painCave.isFatal = 1;
576	>	simError();
577		}
578	<	else{
579	<	strcpy( simnfo->finalName, inFileName );
580	<	char* endTest;
581	<	int nameLength = strlen( simnfo->finalName );
582	<	endTest = &(simnfo->finalName[nameLength - 5]);
583	<	if( !strcmp( endTest, ".bass" ) ){
584	<	strcpy( endTest, ".eor" );
578	>	}
579	>	else{
580	>	n_cells = (int) temp3;
581	>	cellx = info[0].boxL[0] / temp3;
582	>	celly = info[0].boxL[1] / temp3;
583	>	cellz = info[0].boxL[2] / temp3;
584	>	}
585	>
586	>	current_mol = 0;
587	>	current_comp_mol = 0;
588	>	current_comp = 0;
589	>	current_atom_ndx = 0;
590	>
591	>	for (i = 0; i < n_cells ; i++){
592	>	for (j = 0; j < n_cells; j++){
593	>	for (k = 0; k < n_cells; k++){
594	>	makeElement(i * cellx, j * celly, k * cellz);
595	>
596	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
597	>
598	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
599	>
600	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
601		}
686	–	else if( !strcmp( endTest, ".BASS" ) ){
687	–	strcpy( endTest, ".eor" );
688	–	}
689	–	else{
690	–	endTest = &(simnfo->finalName[nameLength - 4]);
691	–	if( !strcmp( endTest, ".bss" ) ){
692	–	strcpy( endTest, ".eor" );
693	–	}
694	–	else if( !strcmp( endTest, ".mdl" ) ){
695	–	strcpy( endTest, ".eor" );
696	–	}
697	–	else{
698	–	strcat( simnfo->finalName, ".eor" );
699	–	}
700	–	}
602		}
702	–
703	–	// make the sample and status out names
704	–
705	–	strcpy( simnfo->sampleName, inFileName );
706	–	char* endTest;
707	–	int nameLength = strlen( simnfo->sampleName );
708	–	endTest = &(simnfo->sampleName[nameLength - 5]);
709	–	if( !strcmp( endTest, ".bass" ) ){
710	–	strcpy( endTest, ".dump" );
711	–	}
712	–	else if( !strcmp( endTest, ".BASS" ) ){
713	–	strcpy( endTest, ".dump" );
714	–	}
715	–	else{
716	–	endTest = &(simnfo->sampleName[nameLength - 4]);
717	–	if( !strcmp( endTest, ".bss" ) ){
718	–	strcpy( endTest, ".dump" );
719	–	}
720	–	else if( !strcmp( endTest, ".mdl" ) ){
721	–	strcpy( endTest, ".dump" );
722	–	}
723	–	else{
724	–	strcat( simnfo->sampleName, ".dump" );
725	–	}
726	–	}
727	–
728	–	strcpy( simnfo->statusName, inFileName );
729	–	nameLength = strlen( simnfo->statusName );
730	–	endTest = &(simnfo->statusName[nameLength - 5]);
731	–	if( !strcmp( endTest, ".bass" ) ){
732	–	strcpy( endTest, ".stat" );
733	–	}
734	–	else if( !strcmp( endTest, ".BASS" ) ){
735	–	strcpy( endTest, ".stat" );
736	–	}
737	–	else{
738	–	endTest = &(simnfo->statusName[nameLength - 4]);
739	–	if( !strcmp( endTest, ".bss" ) ){
740	–	strcpy( endTest, ".stat" );
741	–	}
742	–	else if( !strcmp( endTest, ".mdl" ) ){
743	–	strcpy( endTest, ".stat" );
744	–	}
745	–	else{
746	–	strcat( simnfo->statusName, ".stat" );
747	–	}
748	–	}
749	–
750	–	#ifdef IS_MPI
603		}
752	–	#endif // is_mpi
753	–
754	–	// set the status, sample, and themal kick times
755	–
756	–	if( the_globals->haveSampleTime() ){
757	–	simnfo->sampleTime = the_globals->getSampleTime();
758	–	simnfo->statusTime = simnfo->sampleTime;
759	–	simnfo->thermalTime = simnfo->sampleTime;
760	–	}
761	–	else{
762	–	simnfo->sampleTime = the_globals->getRunTime();
763	–	simnfo->statusTime = simnfo->sampleTime;
764	–	simnfo->thermalTime = simnfo->sampleTime;
765	–	}
604
605	<	if( the_globals->haveStatusTime() ){
606	<	simnfo->statusTime = the_globals->getStatusTime();
769	<	}
605	>	if (have_extra){
606	>	done = 0;
607
608	<	if( the_globals->haveThermalTime() ){
609	<	simnfo->thermalTime = the_globals->getThermalTime();
610	<	}
608	>	int start_ndx;
609	>	for (i = 0; i < (n_cells + 1) && !done; i++){
610	>	for (j = 0; j < (n_cells + 1) && !done; j++){
611	>	if (i < n_cells){
612	>	if (j < n_cells){
613	>	start_ndx = n_cells;
614	>	}
615	>	else
616	>	start_ndx = 0;
617	>	}
618	>	else
619	>	start_ndx = 0;
620
621	<	// check for the temperature set flag
621	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
622	>	makeElement(i * cellx, j * celly, k * cellz);
623	>	done = (current_mol >= tot_nmol);
624
625	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
625	>	if (!done && n_per_extra > 1){
626	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
627	>	k * cellz);
628	>	done = (current_mol >= tot_nmol);
629	>	}
630
631	+	if (!done && n_per_extra > 2){
632	+	makeElement(i * cellx, j * celly + 0.5 * celly,
633	+	k * cellz + 0.5 * cellz);
634	+	done = (current_mol >= tot_nmol);
635	+	}
636
637	<	// make the integrator
638	<
639	<
640	<	NVT*  myNVT = NULL;
641	<	NPTi* myNPTi = NULL;
642	<	NPTf* myNPTf = NULL;
643	<	switch( ensembleCase ){
637	>	if (!done && n_per_extra > 3){
638	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
639	>	k * cellz + 0.5 * cellz);
640	>	done = (current_mol >= tot_nmol);
641	>	}
642	>	}
643	>	}
644	>	}
645	>	}
646
647	<	case NVE_ENS:
648	<	new NVE( simnfo, the_ff );
649	<	break;
647	>	for (i = 0; i < info[0].n_atoms; i++){
648	>	info[0].atoms[i]->setVel(vel);
649	>	}
650	>	}
651
652	<	case NVT_ENS:
653	<	myNVT = new NVT( simnfo, the_ff );
654	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
652	>	void SimSetup::makeElement(double x, double y, double z){
653	>	int k;
654	>	AtomStamp* current_atom;
655	>	DirectionalAtom* dAtom;
656	>	double rotMat[3][3];
657	>	double pos[3];
658
659	<	if (the_globals->haveTauThermostat())
660	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
661	<
662	<	else {
663	<	sprintf( painCave.errMsg,
664	<	"SimSetup error: If you use the NVT\n"
665	<	"    ensemble, you must set tauThermostat.\n");
659	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
660	>	current_atom = comp_stamps[current_comp]->getAtom(k);
661	>	if (!current_atom->havePosition()){
662	>	sprintf(painCave.errMsg,
663	>	"SimSetup:initFromBass error.\n"
664	>	"\tComponent %s, atom %s does not have a position specified.\n"
665	>	"\tThe initialization routine is unable to give a start"
666	>	" position.\n",
667	>	comp_stamps[current_comp]->getID(), current_atom->getType());
668		painCave.isFatal = 1;
669		simError();
670		}
806	–	break;
671
672	<	case NPTi_ENS:
673	<	myNPTi = new NPTi( simnfo, the_ff );
674	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
672	>	pos[0] = x + current_atom->getPosX();
673	>	pos[1] = y + current_atom->getPosY();
674	>	pos[2] = z + current_atom->getPosZ();
675
676	<	if (the_globals->haveTargetPressure())
813	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
814	<	else {
815	<	sprintf( painCave.errMsg,
816	<	"SimSetup error: If you use a constant pressure\n"
817	<	"    ensemble, you must set targetPressure in the BASS file.\n");
818	<	painCave.isFatal = 1;
819	<	simError();
820	<	}
821	<
822	<	if( the_globals->haveTauThermostat() )
823	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
824	<	else{
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup error: If you use an NPT\n"
827	<	"    ensemble, you must set tauThermostat.\n");
828	<	painCave.isFatal = 1;
829	<	simError();
830	<	}
676	>	info[0].atoms[current_atom_ndx]->setPos(pos);
677
678	<	if( the_globals->haveTauBarostat() )
679	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
834	<	else{
835	<	sprintf( painCave.errMsg,
836	<	"SimSetup error: If you use an NPT\n"
837	<	"    ensemble, you must set tauBarostat.\n");
838	<	painCave.isFatal = 1;
839	<	simError();
840	<	}
841	<	break;
678	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
679	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
680
681	<	case NPTf_ENS:
682	<	myNPTf = new NPTf( simnfo, the_ff );
683	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
681	>	rotMat[0][0] = 1.0;
682	>	rotMat[0][1] = 0.0;
683	>	rotMat[0][2] = 0.0;
684
685	<	if (the_globals->haveTargetPressure())
686	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
687	<	else {
850	<	sprintf( painCave.errMsg,
851	<	"SimSetup error: If you use a constant pressure\n"
852	<	"    ensemble, you must set targetPressure in the BASS file.\n");
853	<	painCave.isFatal = 1;
854	<	simError();
855	<	}
685	>	rotMat[1][0] = 0.0;
686	>	rotMat[1][1] = 1.0;
687	>	rotMat[1][2] = 0.0;
688
689	<	if( the_globals->haveTauThermostat() )
690	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
691	<	else{
860	<	sprintf( painCave.errMsg,
861	<	"SimSetup error: If you use an NPT\n"
862	<	"    ensemble, you must set tauThermostat.\n");
863	<	painCave.isFatal = 1;
864	<	simError();
865	<	}
689	>	rotMat[2][0] = 0.0;
690	>	rotMat[2][1] = 0.0;
691	>	rotMat[2][2] = 1.0;
692
693	<	if( the_globals->haveTauBarostat() )
868	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
869	<	else{
870	<	sprintf( painCave.errMsg,
871	<	"SimSetup error: If you use an NPT\n"
872	<	"    ensemble, you must set tauBarostat.\n");
873	<	painCave.isFatal = 1;
874	<	simError();
693	>	dAtom->setA(rotMat);
694		}
876	–	break;
877	–
878	–
695
696	<	default:
881	<	sprintf( painCave.errMsg,
882	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
883	<	painCave.isFatal = 1;
884	<	simError();
696	>	current_atom_ndx++;
697		}
698
699	+	current_mol++;
700	+	current_comp_mol++;
701
702	<	#ifdef IS_MPI
703	<	mpiSim->mpiRefresh();
704	<	#endif
702	>	if (current_comp_mol >= components_nmol[current_comp]){
703	>	current_comp_mol = 0;
704	>	current_comp++;
705	>	}
706	>	}
707
892	–	// initialize the Fortran
708
709	+	void SimSetup::gatherInfo(void){
710	+	int i;
711
712	<	simnfo->refreshSim();
713	<
714	<	if( !strcmp( simnfo->mixingRule, "standard") ){
715	<	the_ff->initForceField( LB_MIXING_RULE );
712	>	ensembleCase = -1;
713	>	ffCase = -1;
714	>
715	>	// set the easy ones first
716	>
717	>	for (i = 0; i < nInfo; i++){
718	>	info[i].target_temp = globals->getTargetTemp();
719	>	info[i].dt = globals->getDt();
720	>	info[i].run_time = globals->getRunTime();
721		}
722	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
723	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
722	>	n_components = globals->getNComponents();
723	>
724	>
725	>	// get the forceField
726	>
727	>	strcpy(force_field, globals->getForceField());
728	>
729	>	if (!strcasecmp(force_field, "DUFF")){
730	>	ffCase = FF_DUFF;
731		}
732	+	else if (!strcasecmp(force_field, "LJ")){
733	+	ffCase = FF_LJ;
734	+	}
735	+	else if (!strcasecmp(force_field, "EAM")){
736	+	ffCase = FF_EAM;
737	+	}
738	+	else if (!strcasecmp(force_field, "WATER")){
739	+	ffCase = FF_H2O;
740	+	}
741		else{
742	<	sprintf( painCave.errMsg,
743	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
744	<	simnfo->mixingRule );
742	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
743	>	force_field);
744	>	painCave.isFatal = 1;
745	>	simError();
746	>	}
747	>
748	>	// get the ensemble
749	>
750	>	strcpy(ensemble, globals->getEnsemble());
751	>
752	>	if (!strcasecmp(ensemble, "NVE")){
753	>	ensembleCase = NVE_ENS;
754	>	}
755	>	else if (!strcasecmp(ensemble, "NVT")){
756	>	ensembleCase = NVT_ENS;
757	>	}
758	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
759	>	ensembleCase = NPTi_ENS;
760	>	}
761	>	else if (!strcasecmp(ensemble, "NPTf")){
762	>	ensembleCase = NPTf_ENS;
763	>	}
764	>	else if (!strcasecmp(ensemble, "NPTxyz")){
765	>	ensembleCase = NPTxyz_ENS;
766	>	}
767	>	else{
768	>	sprintf(painCave.errMsg,
769	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
770	>	"\treverting to NVE for this simulation.\n",
771	>	ensemble);
772	>	painCave.isFatal = 0;
773	>	simError();
774	>	strcpy(ensemble, "NVE");
775	>	ensembleCase = NVE_ENS;
776	>	}
777	>
778	>	for (i = 0; i < nInfo; i++){
779	>	strcpy(info[i].ensemble, ensemble);
780	>
781	>	// get the mixing rule
782	>
783	>	strcpy(info[i].mixingRule, globals->getMixingRule());
784	>	info[i].usePBC = globals->getPBC();
785	>	}
786	>
787	>	// get the components and calculate the tot_nMol and indvidual n_mol
788	>
789	>	the_components = globals->getComponents();
790	>	components_nmol = new int[n_components];
791	>
792	>
793	>	if (!globals->haveNMol()){
794	>	// we don't have the total number of molecules, so we assume it is
795	>	// given in each component
796	>
797	>	tot_nmol = 0;
798	>	for (i = 0; i < n_components; i++){
799	>	if (!the_components[i]->haveNMol()){
800	>	// we have a problem
801	>	sprintf(painCave.errMsg,
802	>	"SimSetup Error. No global NMol or component NMol given.\n"
803	>	"\tCannot calculate the number of atoms.\n");
804	>	painCave.isFatal = 1;
805	>	simError();
806	>	}
807	>
808	>	tot_nmol += the_components[i]->getNMol();
809	>	components_nmol[i] = the_components[i]->getNMol();
810	>	}
811	>	}
812	>	else{
813	>	sprintf(painCave.errMsg,
814	>	"SimSetup error.\n"
815	>	"\tSorry, the ability to specify total"
816	>	" nMols and then give molfractions in the components\n"
817	>	"\tis not currently supported."
818	>	" Please give nMol in the components.\n");
819		painCave.isFatal = 1;
820		simError();
821		}
822
823	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
824	+	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
825	+	sprintf(painCave.errMsg,
826	+	"Sample time is not divisible by dt.\n"
827	+	"\tThis will result in samples that are not uniformly\n"
828	+	"\tdistributed in time.  If this is a problem, change\n"
829	+	"\tyour sampleTime variable.\n");
830	+	painCave.isFatal = 0;
831	+	simError();
832	+	}
833
834	<	#ifdef IS_MPI
835	<	strcpy( checkPointMsg,
836	<	"Successfully intialized the mixingRule for Fortran." );
837	<	MPIcheckPoint();
838	<	#endif // is_mpi
839	<	}
834	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
835	>	sprintf(painCave.errMsg,
836	>	"Status time is not divisible by dt.\n"
837	>	"\tThis will result in status reports that are not uniformly\n"
838	>	"\tdistributed in time.  If this is a problem, change \n"
839	>	"\tyour statusTime variable.\n");
840	>	painCave.isFatal = 0;
841	>	simError();
842	>	}
843
844	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
845	+	sprintf(painCave.errMsg,
846	+	"Thermal time is not divisible by dt.\n"
847	+	"\tThis will result in thermalizations that are not uniformly\n"
848	+	"\tdistributed in time.  If this is a problem, change \n"
849	+	"\tyour thermalTime variable.\n");
850	+	painCave.isFatal = 0;
851	+	simError();
852	+	}
853
854	<	void SimSetup::makeMolecules( void ){
854	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
855	>	sprintf(painCave.errMsg,
856	>	"Reset time is not divisible by dt.\n"
857	>	"\tThis will result in integrator resets that are not uniformly\n"
858	>	"\tdistributed in time.  If this is a problem, change\n"
859	>	"\tyour resetTime variable.\n");
860	>	painCave.isFatal = 0;
861	>	simError();
862	>	}
863
864	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
923	<	molInit info;
924	<	DirectionalAtom* dAtom;
925	<	LinkedAssign* extras;
926	<	LinkedAssign* current_extra;
927	<	AtomStamp* currentAtom;
928	<	BondStamp* currentBond;
929	<	BendStamp* currentBend;
930	<	TorsionStamp* currentTorsion;
864	>	// set the status, sample, and thermal kick times
865
866	<	bond_pair* theBonds;
867	<	bend_set* theBends;
868	<	torsion_set* theTorsions;
866	>	for (i = 0; i < nInfo; i++){
867	>	if (globals->haveSampleTime()){
868	>	info[i].sampleTime = globals->getSampleTime();
869	>	info[i].statusTime = info[i].sampleTime;
870	>	info[i].thermalTime = info[i].sampleTime;
871	>	}
872	>	else{
873	>	info[i].sampleTime = globals->getRunTime();
874	>	info[i].statusTime = info[i].sampleTime;
875	>	info[i].thermalTime = info[i].sampleTime;
876	>	}
877
878	<
879	<	//init the forceField paramters
878	>	if (globals->haveStatusTime()){
879	>	info[i].statusTime = globals->getStatusTime();
880	>	}
881
882	<	the_ff->readParams();
882	>	if (globals->haveThermalTime()){
883	>	info[i].thermalTime = globals->getThermalTime();
884	>	}
885
886	<
887	<	// init the atoms
886	>	info[i].resetIntegrator = 0;
887	>	if( globals->haveResetTime() ){
888	>	info[i].resetTime = globals->getResetTime();
889	>	info[i].resetIntegrator = 1;
890	>	}
891
892	<	double ux, uy, uz, u, uSqr;
945	<
946	<	atomOffset = 0;
947	<	excludeOffset = 0;
948	<	for(i=0; i<simnfo->n_mol; i++){
892	>	// check for the temperature set flag
893
894	<	stampID = the_molecules[i].getStampID();
894	>	if (globals->haveTempSet())
895	>	info[i].setTemp = globals->getTempSet();
896
897	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
953	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
954	<	info.nBends    = comp_stamps[stampID]->getNBends();
955	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
956	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
897	>	// check for the extended State init
898
899	<	info.myAtoms = &the_atoms[atomOffset];
900	<	info.myExcludes = &the_excludes[excludeOffset];
960	<	info.myBonds = new Bond*[info.nBonds];
961	<	info.myBends = new Bend*[info.nBends];
962	<	info.myTorsions = new Torsion*[info.nTorsions];
963	<
964	<	theBonds = new bond_pair[info.nBonds];
965	<	theBends = new bend_set[info.nBends];
966	<	theTorsions = new torsion_set[info.nTorsions];
899	>	info[i].useInitXSstate = globals->getUseInitXSstate();
900	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
901
902	<	// make the Atoms
903	<
904	<	for(j=0; j<info.nAtoms; j++){
905	<
906	<	currentAtom = comp_stamps[stampID]->getAtom( j );
907	<	if( currentAtom->haveOrientation() ){
908	<
909	<	dAtom = new DirectionalAtom(j + atomOffset);
910	<	simnfo->n_oriented++;
911	<	info.myAtoms[j] = dAtom;
912	<
913	<	ux = currentAtom->getOrntX();
914	<	uy = currentAtom->getOrntY();
915	<	uz = currentAtom->getOrntZ();
916	<
917	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
918	<
919	<	u = sqrt( uSqr );
920	<	ux = ux / u;
921	<	uy = uy / u;
922	<	uz = uz / u;
989	<
990	<	dAtom->setSUx( ux );
991	<	dAtom->setSUy( uy );
992	<	dAtom->setSUz( uz );
902	>	}
903	>
904	>	//setup seed for random number generator
905	>	int seedValue;
906	>
907	>	if (globals->haveSeed()){
908	>	seedValue = globals->getSeed();
909	>
910	>	if(seedValue / 1E9 == 0){
911	>	sprintf(painCave.errMsg,
912	>	"Seed for sprng library should contain at least 9 digits\n"
913	>	"OOPSE will generate a seed for user\n");
914	>	painCave.isFatal = 0;
915	>	simError();
916	>
917	>	//using seed generated by system instead of invalid seed set by user
918	>	#ifndef IS_MPI
919	>	seedValue = make_sprng_seed();
920	>	#else
921	>	if (worldRank == 0){
922	>	seedValue = make_sprng_seed();
923		}
924	<	else{
925	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
926	<	}
927	<	info.myAtoms[j]->setType( currentAtom->getType() );
924	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
925	>	#endif
926	>	}
927	>	}//end of if branch of globals->haveSeed()
928	>	else{
929
930	+	#ifndef IS_MPI
931	+	seedValue = make_sprng_seed();
932	+	#else
933	+	if (worldRank == 0){
934	+	seedValue = make_sprng_seed();
935	+	}
936	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
937	+	#endif
938	+	}//end of globals->haveSeed()
939	+
940	+	for (int i = 0; i < nInfo; i++){
941	+	info[i].setSeed(seedValue);
942	+	}
943	+
944		#ifdef IS_MPI
945	<
946	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1002	<
945	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
946	>	MPIcheckPoint();
947		#endif // is_mpi
948	<	}
1005	<
1006	<	// make the bonds
1007	<	for(j=0; j<info.nBonds; j++){
1008	<
1009	<	currentBond = comp_stamps[stampID]->getBond( j );
1010	<	theBonds[j].a = currentBond->getA() + atomOffset;
1011	<	theBonds[j].b = currentBond->getB() + atomOffset;
948	>	}
949
1013	–	exI = theBonds[j].a;
1014	–	exJ = theBonds[j].b;
950
951	<	// exclude_I must always be the smaller of the pair
952	<	if( exI > exJ ){
953	<	tempEx = exI;
954	<	exI = exJ;
1020	<	exJ = tempEx;
1021	<	}
1022	<	#ifdef IS_MPI
1023	<	tempEx = exI;
1024	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1025	<	tempEx = exJ;
1026	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1027	<
1028	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1029	<	#else  // isn't MPI
951	>	void SimSetup::finalInfoCheck(void){
952	>	int index;
953	>	int usesDipoles;
954	>	int i;
955
956	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
957	<	#endif  //is_mpi
956	>	for (i = 0; i < nInfo; i++){
957	>	// check electrostatic parameters
958	>
959	>	index = 0;
960	>	usesDipoles = 0;
961	>	while ((index < info[i].n_atoms) && !usesDipoles){
962	>	usesDipoles = (info[i].atoms[index])->hasDipole();
963	>	index++;
964		}
1034	–	excludeOffset += info.nBonds;
965
966	<	//make the bends
967	<	for(j=0; j<info.nBends; j++){
968	<
969	<	currentBend = comp_stamps[stampID]->getBend( j );
970	<	theBends[j].a = currentBend->getA() + atomOffset;
971	<	theBends[j].b = currentBend->getB() + atomOffset;
972	<	theBends[j].c = currentBend->getC() + atomOffset;
973	<
974	<	if( currentBend->haveExtras() ){
975	<
976	<	extras = currentBend->getExtras();
977	<	current_extra = extras;
978	<
979	<	while( current_extra != NULL ){
980	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
981	<
982	<	switch( current_extra->getType() ){
983	<
1054	<	case 0:
1055	<	theBends[j].ghost =
1056	<	current_extra->getInt() + atomOffset;
1057	<	theBends[j].isGhost = 1;
1058	<	break;
1059	<
1060	<	case 1:
1061	<	theBends[j].ghost =
1062	<	(int)current_extra->getDouble() + atomOffset;
1063	<	theBends[j].isGhost = 1;
1064	<	break;
1065	<
1066	<	default:
1067	<	sprintf( painCave.errMsg,
1068	<	"SimSetup Error: ghostVectorSource was neither a "
1069	<	"double nor an int.\n"
1070	<	"-->Bend[%d] in %s\n",
1071	<	j, comp_stamps[stampID]->getID() );
1072	<	painCave.isFatal = 1;
1073	<	simError();
1074	<	}
1075	<	}
1076	<
1077	<	else{
1078	<
1079	<	sprintf( painCave.errMsg,
1080	<	"SimSetup Error: unhandled bend assignment:\n"
1081	<	"    -->%s in Bend[%d] in %s\n",
1082	<	current_extra->getlhs(),
1083	<	j, comp_stamps[stampID]->getID() );
1084	<	painCave.isFatal = 1;
1085	<	simError();
1086	<	}
1087	<
1088	<	current_extra = current_extra->getNext();
1089	<	}
966	>	#ifdef IS_MPI
967	>	int myUse = usesDipoles;
968	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
969	>	#endif //is_mpi
970	>
971	>	double theEcr, theEst;
972	>
973	>	if (globals->getUseRF()){
974	>	info[i].useReactionField = 1;
975	>
976	>	if (!globals->haveECR()){
977	>	sprintf(painCave.errMsg,
978	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
979	>	"\tOOPSE will use a default value of 15.0 angstroms"
980	>	"\tfor the electrostaticCutoffRadius.\n");
981	>	painCave.isFatal = 0;
982	>	simError();
983	>	theEcr = 15.0;
984		}
1091	–
1092	–	if( !theBends[j].isGhost ){
1093	–
1094	–	exI = theBends[j].a;
1095	–	exJ = theBends[j].c;
1096	–	}
985		else{
986	<
1099	<	exI = theBends[j].a;
1100	<	exJ = theBends[j].b;
986	>	theEcr = globals->getECR();
987		}
988	<
989	<	// exclude_I must always be the smaller of the pair
990	<	if( exI > exJ ){
991	<	tempEx = exI;
992	<	exI = exJ;
993	<	exJ = tempEx;
988	>
989	>	if (!globals->haveEST()){
990	>	sprintf(painCave.errMsg,
991	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
992	>	"\tOOPSE will use a default value of\n"
993	>	"\t0.05 * electrostaticCutoffRadius\n"
994	>	"\tfor the electrostaticSkinThickness\n");
995	>	painCave.isFatal = 0;
996	>	simError();
997	>	theEst = 0.05 * theEcr;
998		}
999	<	#ifdef IS_MPI
1000	<	tempEx = exI;
1001	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1112	<	tempEx = exJ;
1113	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1114	<
1115	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1116	<	#else  // isn't MPI
1117	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1118	<	#endif  //is_mpi
1119	<	}
1120	<	excludeOffset += info.nBends;
999	>	else{
1000	>	theEst = globals->getEST();
1001	>	}
1002
1003	<	for(j=0; j<info.nTorsions; j++){
1123	<
1124	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1125	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1126	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1127	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1128	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1129	<
1130	<	exI = theTorsions[j].a;
1131	<	exJ = theTorsions[j].d;
1003	>	info[i].setDefaultEcr(theEcr, theEst);
1004
1005	<	// exclude_I must always be the smaller of the pair
1006	<	if( exI > exJ ){
1007	<	tempEx = exI;
1008	<	exI = exJ;
1009	<	exJ = tempEx;
1005	>	if (!globals->haveDielectric()){
1006	>	sprintf(painCave.errMsg,
1007	>	"SimSetup Error: No Dielectric constant was set.\n"
1008	>	"\tYou are trying to use Reaction Field without"
1009	>	"\tsetting a dielectric constant!\n");
1010	>	painCave.isFatal = 1;
1011	>	simError();
1012		}
1013	<	#ifdef IS_MPI
1140	<	tempEx = exI;
1141	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1142	<	tempEx = exJ;
1143	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1144	<
1145	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1146	<	#else  // isn't MPI
1147	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1148	<	#endif  //is_mpi
1013	>	info[i].dielectric = globals->getDielectric();
1014		}
1015	<	excludeOffset += info.nTorsions;
1015	>	else{
1016	>	if (usesDipoles){
1017	>	if (!globals->haveECR()){
1018	>	sprintf(painCave.errMsg,
1019	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1020	>	"\tOOPSE will use a default value of 15.0 angstroms"
1021	>	"\tfor the electrostaticCutoffRadius.\n");
1022	>	painCave.isFatal = 0;
1023	>	simError();
1024	>	theEcr = 15.0;
1025	>	}
1026	>	else{
1027	>	theEcr = globals->getECR();
1028	>	}
1029	>
1030	>	if (!globals->haveEST()){
1031	>	sprintf(painCave.errMsg,
1032	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1033	>	"\tOOPSE will use a default value of\n"
1034	>	"\t0.05 * electrostaticCutoffRadius\n"
1035	>	"\tfor the electrostaticSkinThickness\n");
1036	>	painCave.isFatal = 0;
1037	>	simError();
1038	>	theEst = 0.05 * theEcr;
1039	>	}
1040	>	else{
1041	>	theEst = globals->getEST();
1042	>	}
1043	>
1044	>	info[i].setDefaultEcr(theEcr, theEst);
1045	>	}
1046	>	}
1047	>	}
1048	>	#ifdef IS_MPI
1049	>	strcpy(checkPointMsg, "post processing checks out");
1050	>	MPIcheckPoint();
1051	>	#endif // is_mpi
1052	>	}
1053	>
1054	>	void SimSetup::initSystemCoords(void){
1055	>	int i;
1056
1057	<
1153	<	// send the arrays off to the forceField for init.
1057	>	char* inName;
1058
1059	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1156	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1157	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1158	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1059	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1060
1061	+	for (i = 0; i < info[0].n_atoms; i++)
1062	+	info[0].atoms[i]->setCoords();
1063
1064	<	the_molecules[i].initialize( info );
1064	>	if (globals->haveInitialConfig()){
1065	>	InitializeFromFile* fileInit;
1066	>	#ifdef IS_MPI // is_mpi
1067	>	if (worldRank == 0){
1068	>	#endif //is_mpi
1069	>	inName = globals->getInitialConfig();
1070	>	fileInit = new InitializeFromFile(inName);
1071	>	#ifdef IS_MPI
1072	>	}
1073	>	else
1074	>	fileInit = new InitializeFromFile(NULL);
1075	>	#endif
1076	>	fileInit->readInit(info); // default velocities on
1077
1078	<
1164	<	atomOffset += info.nAtoms;
1165	<	delete[] theBonds;
1166	<	delete[] theBends;
1167	<	delete[] theTorsions;
1078	>	delete fileInit;
1079		}
1080	+	else{
1081	+
1082	+	// no init from bass
1083	+
1084	+	sprintf(painCave.errMsg,
1085	+	"Cannot intialize a simulation without an initial configuration file.\n");
1086	+	painCave.isFatal = 1;;
1087	+	simError();
1088	+
1089	+	}
1090
1091		#ifdef IS_MPI
1092	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1092	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1093		MPIcheckPoint();
1094		#endif // is_mpi
1095	+	}
1096
1175	–	// clean up the forcefield
1176	–	the_ff->calcRcut();
1177	–	the_ff->cleanMe();
1097
1098	<	}
1098	>	void SimSetup::makeOutNames(void){
1099	>	int k;
1100
1181	–	void SimSetup::initFromBass( void ){
1101
1102	<	int i, j, k;
1103	<	int n_cells;
1104	<	double cellx, celly, cellz;
1105	<	double temp1, temp2, temp3;
1187	<	int n_per_extra;
1188	<	int n_extra;
1189	<	int have_extra, done;
1102	>	for (k = 0; k < nInfo; k++){
1103	>	#ifdef IS_MPI
1104	>	if (worldRank == 0){
1105	>	#endif // is_mpi
1106
1107	<	temp1 = (double)tot_nmol / 4.0;
1108	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1109	<	temp3 = ceil( temp2 );
1107	>	if (globals->haveFinalConfig()){
1108	>	strcpy(info[k].finalName, globals->getFinalConfig());
1109	>	}
1110	>	else{
1111	>	strcpy(info[k].finalName, inFileName);
1112	>	char* endTest;
1113	>	int nameLength = strlen(info[k].finalName);
1114	>	endTest = &(info[k].finalName[nameLength - 5]);
1115	>	if (!strcmp(endTest, ".bass")){
1116	>	strcpy(endTest, ".eor");
1117	>	}
1118	>	else if (!strcmp(endTest, ".BASS")){
1119	>	strcpy(endTest, ".eor");
1120	>	}
1121	>	else{
1122	>	endTest = &(info[k].finalName[nameLength - 4]);
1123	>	if (!strcmp(endTest, ".bss")){
1124	>	strcpy(endTest, ".eor");
1125	>	}
1126	>	else if (!strcmp(endTest, ".mdl")){
1127	>	strcpy(endTest, ".eor");
1128	>	}
1129	>	else{
1130	>	strcat(info[k].finalName, ".eor");
1131	>	}
1132	>	}
1133	>	}
1134
1135	<	have_extra =0;
1196	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1197	<	have_extra =1;
1135	>	// make the sample and status out names
1136
1137	<	n_cells = (int)temp3 - 1;
1138	<	cellx = simnfo->boxLx / temp3;
1139	<	celly = simnfo->boxLy / temp3;
1140	<	cellz = simnfo->boxLz / temp3;
1141	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1142	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1143	<	n_per_extra = (int)ceil( temp1 );
1137	>	strcpy(info[k].sampleName, inFileName);
1138	>	char* endTest;
1139	>	int nameLength = strlen(info[k].sampleName);
1140	>	endTest = &(info[k].sampleName[nameLength - 5]);
1141	>	if (!strcmp(endTest, ".bass")){
1142	>	strcpy(endTest, ".dump");
1143	>	}
1144	>	else if (!strcmp(endTest, ".BASS")){
1145	>	strcpy(endTest, ".dump");
1146	>	}
1147	>	else{
1148	>	endTest = &(info[k].sampleName[nameLength - 4]);
1149	>	if (!strcmp(endTest, ".bss")){
1150	>	strcpy(endTest, ".dump");
1151	>	}
1152	>	else if (!strcmp(endTest, ".mdl")){
1153	>	strcpy(endTest, ".dump");
1154	>	}
1155	>	else{
1156	>	strcat(info[k].sampleName, ".dump");
1157	>	}
1158	>	}
1159
1160	<	if( n_per_extra > 4){
1161	<	sprintf( painCave.errMsg,
1162	<	"SimSetup error. There has been an error in constructing"
1163	<	" the non-complete lattice.\n" );
1164	<	painCave.isFatal = 1;
1165	<	simError();
1160	>	strcpy(info[k].statusName, inFileName);
1161	>	nameLength = strlen(info[k].statusName);
1162	>	endTest = &(info[k].statusName[nameLength - 5]);
1163	>	if (!strcmp(endTest, ".bass")){
1164	>	strcpy(endTest, ".stat");
1165	>	}
1166	>	else if (!strcmp(endTest, ".BASS")){
1167	>	strcpy(endTest, ".stat");
1168	>	}
1169	>	else{
1170	>	endTest = &(info[k].statusName[nameLength - 4]);
1171	>	if (!strcmp(endTest, ".bss")){
1172	>	strcpy(endTest, ".stat");
1173	>	}
1174	>	else if (!strcmp(endTest, ".mdl")){
1175	>	strcpy(endTest, ".stat");
1176	>	}
1177	>	else{
1178	>	strcat(info[k].statusName, ".stat");
1179	>	}
1180	>	}
1181	>
1182	>	#ifdef IS_MPI
1183	>
1184		}
1185	+	#endif // is_mpi
1186		}
1187	<	else{
1188	<	n_cells = (int)temp3;
1189	<	cellx = simnfo->boxLx / temp3;
1190	<	celly = simnfo->boxLy / temp3;
1191	<	cellz = simnfo->boxLz / temp3;
1187	>	}
1188	>
1189	>
1190	>	void SimSetup::sysObjectsCreation(void){
1191	>	int i, k;
1192	>
1193	>	// create the forceField
1194	>
1195	>	createFF();
1196	>
1197	>	// extract componentList
1198	>
1199	>	compList();
1200	>
1201	>	// calc the number of atoms, bond, bends, and torsions
1202	>
1203	>	calcSysValues();
1204	>
1205	>	#ifdef IS_MPI
1206	>	// divide the molecules among the processors
1207	>
1208	>	mpiMolDivide();
1209	>	#endif //is_mpi
1210	>
1211	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1212	>
1213	>	makeSysArrays();
1214	>
1215	>	// make and initialize the molecules (all but atomic coordinates)
1216	>
1217	>	makeMolecules();
1218	>
1219	>	for (k = 0; k < nInfo; k++){
1220	>	info[k].identArray = new int[info[k].n_atoms];
1221	>	for (i = 0; i < info[k].n_atoms; i++){
1222	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1223	>	}
1224		}
1225	+	}
1226
1222	–	current_mol = 0;
1223	–	current_comp_mol = 0;
1224	–	current_comp = 0;
1225	–	current_atom_ndx = 0;
1227
1228	<	for( i=0; i < n_cells ; i++ ){
1229	<	for( j=0; j < n_cells; j++ ){
1230	<	for( k=0; k < n_cells; k++ ){
1228	>	void SimSetup::createFF(void){
1229	>	switch (ffCase){
1230	>	case FF_DUFF:
1231	>	the_ff = new DUFF();
1232	>	break;
1233
1234	<	makeElement( i * cellx,
1235	<	j * celly,
1236	<	k * cellz );
1234	>	case FF_LJ:
1235	>	the_ff = new LJFF();
1236	>	break;
1237
1238	<	makeElement( i * cellx + 0.5 * cellx,
1239	<	j * celly + 0.5 * celly,
1240	<	k * cellz );
1238	>	case FF_EAM:
1239	>	the_ff = new EAM_FF();
1240	>	break;
1241
1242	<	makeElement( i * cellx,
1243	<	j * celly + 0.5 * celly,
1244	<	k * cellz + 0.5 * cellz );
1242	>	case FF_H2O:
1243	>	the_ff = new WATER();
1244	>	break;
1245
1246	<	makeElement( i * cellx + 0.5 * cellx,
1247	<	j * celly,
1248	<	k * cellz + 0.5 * cellz );
1246	>	default:
1247	>	sprintf(painCave.errMsg,
1248	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1249	>	painCave.isFatal = 1;
1250	>	simError();
1251	>	}
1252	>
1253	>	#ifdef IS_MPI
1254	>	strcpy(checkPointMsg, "ForceField creation successful");
1255	>	MPIcheckPoint();
1256	>	#endif // is_mpi
1257	>	}
1258	>
1259	>
1260	>	void SimSetup::compList(void){
1261	>	int i;
1262	>	char* id;
1263	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1264	>	LinkedMolStamp* currentStamp = NULL;
1265	>	comp_stamps = new MoleculeStamp * [n_components];
1266	>
1267	>	// make an array of molecule stamps that match the components used.
1268	>	// also extract the used stamps out into a separate linked list
1269	>
1270	>	for (i = 0; i < nInfo; i++){
1271	>	info[i].nComponents = n_components;
1272	>	info[i].componentsNmol = components_nmol;
1273	>	info[i].compStamps = comp_stamps;
1274	>	info[i].headStamp = headStamp;
1275	>	}
1276	>
1277	>
1278	>	for (i = 0; i < n_components; i++){
1279	>	id = the_components[i]->getType();
1280	>	comp_stamps[i] = NULL;
1281	>
1282	>	// check to make sure the component isn't already in the list
1283	>
1284	>	comp_stamps[i] = headStamp->match(id);
1285	>	if (comp_stamps[i] == NULL){
1286	>	// extract the component from the list;
1287	>
1288	>	currentStamp = stamps->extractMolStamp(id);
1289	>	if (currentStamp == NULL){
1290	>	sprintf(painCave.errMsg,
1291	>	"SimSetup error: Component \"%s\" was not found in the "
1292	>	"list of declared molecules\n",
1293	>	id);
1294	>	painCave.isFatal = 1;
1295	>	simError();
1296		}
1297	+
1298	+	headStamp->add(currentStamp);
1299	+	comp_stamps[i] = headStamp->match(id);
1300		}
1301		}
1302
1303	<	if( have_extra ){
1304	<	done = 0;
1303	>	#ifdef IS_MPI
1304	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1305	>	MPIcheckPoint();
1306	>	#endif // is_mpi
1307	>	}
1308
1309	<	int start_ndx;
1310	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1255	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1309	>	void SimSetup::calcSysValues(void){
1310	>	int i;
1311
1312	<	if( i < n_cells ){
1312	>	int* molMembershipArray;
1313
1314	<	if( j < n_cells ){
1315	<	start_ndx = n_cells;
1316	<	}
1317	<	else start_ndx = 0;
1318	<	}
1319	<	else start_ndx = 0;
1314	>	tot_atoms = 0;
1315	>	tot_bonds = 0;
1316	>	tot_bends = 0;
1317	>	tot_torsions = 0;
1318	>	tot_rigid = 0;
1319	>	for (i = 0; i < n_components; i++){
1320	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1321	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1322	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1323	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1324	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1325	>	}
1326	>
1327	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1328	>	molMembershipArray = new int[tot_atoms];
1329
1330	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1330	>	for (i = 0; i < nInfo; i++){
1331	>	info[i].n_atoms = tot_atoms;
1332	>	info[i].n_bonds = tot_bonds;
1333	>	info[i].n_bends = tot_bends;
1334	>	info[i].n_torsions = tot_torsions;
1335	>	info[i].n_SRI = tot_SRI;
1336	>	info[i].n_mol = tot_nmol;
1337
1338	<	makeElement( i * cellx,
1339	<	j * celly,
1340	<	k * cellz );
1271	<	done = ( current_mol >= tot_nmol );
1338	>	info[i].molMembershipArray = molMembershipArray;
1339	>	}
1340	>	}
1341
1342	<	if( !done && n_per_extra > 1 ){
1274	<	makeElement( i * cellx + 0.5 * cellx,
1275	<	j * celly + 0.5 * celly,
1276	<	k * cellz );
1277	<	done = ( current_mol >= tot_nmol );
1278	<	}
1342	>	#ifdef IS_MPI
1343
1344	<	if( !done && n_per_extra > 2){
1345	<	makeElement( i * cellx,
1346	<	j * celly + 0.5 * celly,
1347	<	k * cellz + 0.5 * cellz );
1348	<	done = ( current_mol >= tot_nmol );
1285	<	}
1344	>	void SimSetup::mpiMolDivide(void){
1345	>	int i, j, k;
1346	>	int localMol, allMol;
1347	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1348	>	int local_rigid;
1349
1350	<	if( !done && n_per_extra > 3){
1351	<	makeElement( i * cellx + 0.5 * cellx,
1352	<	j * celly,
1353	<	k * cellz + 0.5 * cellz );
1354	<	done = ( current_mol >= tot_nmol );
1355	<	}
1356	<	}
1350	>	mpiSim = new mpiSimulation(info);
1351	>
1352	>	globalIndex = mpiSim->divideLabor();
1353	>
1354	>	// set up the local variables
1355	>
1356	>	mol2proc = mpiSim->getMolToProcMap();
1357	>	molCompType = mpiSim->getMolComponentType();
1358	>
1359	>	allMol = 0;
1360	>	localMol = 0;
1361	>	local_atoms = 0;
1362	>	local_bonds = 0;
1363	>	local_bends = 0;
1364	>	local_torsions = 0;
1365	>	local_rigid = 0;
1366	>	globalAtomIndex = 0;
1367	>
1368	>	for (i = 0; i < n_components; i++){
1369	>	for (j = 0; j < components_nmol[i]; j++){
1370	>	if (mol2proc[allMol] == worldRank){
1371	>	local_atoms += comp_stamps[i]->getNAtoms();
1372	>	local_bonds += comp_stamps[i]->getNBonds();
1373	>	local_bends += comp_stamps[i]->getNBends();
1374	>	local_torsions += comp_stamps[i]->getNTorsions();
1375	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1376	>	localMol++;
1377	>	}
1378	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1379	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1380	>	globalAtomIndex++;
1381		}
1382	+
1383	+	allMol++;
1384		}
1385		}
1386	+	local_SRI = local_bonds + local_bends + local_torsions;
1387
1388	+	info[0].n_atoms = mpiSim->getMyNlocal();
1389	+
1390
1391	<	for( i=0; i<simnfo->n_atoms; i++ ){
1392	<	simnfo->atoms[i]->set_vx( 0.0 );
1393	<	simnfo->atoms[i]->set_vy( 0.0 );
1394	<	simnfo->atoms[i]->set_vz( 0.0 );
1391	>	if (local_atoms != info[0].n_atoms){
1392	>	sprintf(painCave.errMsg,
1393	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1394	>	"\tlocalAtom (%d) are not equal.\n",
1395	>	info[0].n_atoms, local_atoms);
1396	>	painCave.isFatal = 1;
1397	>	simError();
1398		}
1399	+
1400	+	info[0].n_bonds = local_bonds;
1401	+	info[0].n_bends = local_bends;
1402	+	info[0].n_torsions = local_torsions;
1403	+	info[0].n_SRI = local_SRI;
1404	+	info[0].n_mol = localMol;
1405	+
1406	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1407	+	MPIcheckPoint();
1408		}
1409
1410	<	void SimSetup::makeElement( double x, double y, double z ){
1410	>	#endif // is_mpi
1411
1308	–	int k;
1309	–	AtomStamp* current_atom;
1310	–	DirectionalAtom* dAtom;
1311	–	double rotMat[3][3];
1412
1413	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1413	>	void SimSetup::makeSysArrays(void){
1414	>
1415	>	#ifndef IS_MPI
1416	>	int k, j;
1417	>	#endif // is_mpi
1418	>	int i, l;
1419
1420	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1421	<	if( !current_atom->havePosition() ){
1317	<	sprintf( painCave.errMsg,
1318	<	"SimSetup:initFromBass error.\n"
1319	<	"\tComponent %s, atom %s does not have a position specified.\n"
1320	<	"\tThe initialization routine is unable to give a start"
1321	<	" position.\n",
1322	<	comp_stamps[current_comp]->getID(),
1323	<	current_atom->getType() );
1324	<	painCave.isFatal = 1;
1325	<	simError();
1326	<	}
1420	>	Atom** the_atoms;
1421	>	Molecule* the_molecules;
1422
1423	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1424	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1330	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1423	>	for (l = 0; l < nInfo; l++){
1424	>	// create the atom and short range interaction arrays
1425
1426	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1426	>	the_atoms = new Atom * [info[l].n_atoms];
1427	>	the_molecules = new Molecule[info[l].n_mol];
1428	>	int molIndex;
1429
1430	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1430	>	// initialize the molecule's stampID's
1431
1432	<	rotMat[0][0] = 1.0;
1337	<	rotMat[0][1] = 0.0;
1338	<	rotMat[0][2] = 0.0;
1432	>	#ifdef IS_MPI
1433
1340	–	rotMat[1][0] = 0.0;
1341	–	rotMat[1][1] = 1.0;
1342	–	rotMat[1][2] = 0.0;
1434
1435	<	rotMat[2][0] = 0.0;
1436	<	rotMat[2][1] = 0.0;
1437	<	rotMat[2][2] = 1.0;
1435	>	molIndex = 0;
1436	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1437	>	if (mol2proc[i] == worldRank){
1438	>	the_molecules[molIndex].setStampID(molCompType[i]);
1439	>	the_molecules[molIndex].setMyIndex(molIndex);
1440	>	the_molecules[molIndex].setGlobalIndex(i);
1441	>	molIndex++;
1442	>	}
1443	>	}
1444
1445	<	dAtom->setA( rotMat );
1445	>	#else // is_mpi
1446	>
1447	>	molIndex = 0;
1448	>	globalAtomIndex = 0;
1449	>	for (i = 0; i < n_components; i++){
1450	>	for (j = 0; j < components_nmol[i]; j++){
1451	>	the_molecules[molIndex].setStampID(i);
1452	>	the_molecules[molIndex].setMyIndex(molIndex);
1453	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1454	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1455	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1456	>	globalAtomIndex++;
1457	>	}
1458	>	molIndex++;
1459	>	}
1460		}
1461
1351	–	current_atom_ndx++;
1352	–	}
1462
1463	<	current_mol++;
1355	<	current_comp_mol++;
1463	>	#endif // is_mpi
1464
1465	<	if( current_comp_mol >= components_nmol[current_comp] ){
1465	>	info[l].globalExcludes = new int;
1466	>	info[l].globalExcludes[0] = 0;
1467	>
1468	>	// set the arrays into the SimInfo object
1469
1470	<	current_comp_mol = 0;
1471	<	current_comp++;
1470	>	info[l].atoms = the_atoms;
1471	>	info[l].molecules = the_molecules;
1472	>	info[l].nGlobalExcludes = 0;
1473	>
1474	>	the_ff->setSimInfo(info);
1475	>	}
1476	>	}
1477	>
1478	>	void SimSetup::makeIntegrator(void){
1479	>	int k;
1480	>
1481	>	NVE<RealIntegrator>* myNVE = NULL;
1482	>	NVT<RealIntegrator>* myNVT = NULL;
1483	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1484	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1485	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1486	>
1487	>	for (k = 0; k < nInfo; k++){
1488	>	switch (ensembleCase){
1489	>	case NVE_ENS:
1490	>	if (globals->haveZconstraints()){
1491	>	setupZConstraint(info[k]);
1492	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1493	>	}
1494	>	else{
1495	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1496	>	}
1497	>
1498	>	info->the_integrator = myNVE;
1499	>	break;
1500	>
1501	>	case NVT_ENS:
1502	>	if (globals->haveZconstraints()){
1503	>	setupZConstraint(info[k]);
1504	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1505	>	}
1506	>	else
1507	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1508	>
1509	>	myNVT->setTargetTemp(globals->getTargetTemp());
1510	>
1511	>	if (globals->haveTauThermostat())
1512	>	myNVT->setTauThermostat(globals->getTauThermostat());
1513	>	else{
1514	>	sprintf(painCave.errMsg,
1515	>	"SimSetup error: If you use the NVT\n"
1516	>	"\tensemble, you must set tauThermostat.\n");
1517	>	painCave.isFatal = 1;
1518	>	simError();
1519	>	}
1520	>
1521	>	info->the_integrator = myNVT;
1522	>	break;
1523	>
1524	>	case NPTi_ENS:
1525	>	if (globals->haveZconstraints()){
1526	>	setupZConstraint(info[k]);
1527	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1528	>	}
1529	>	else
1530	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1531	>
1532	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1533	>
1534	>	if (globals->haveTargetPressure())
1535	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1536	>	else{
1537	>	sprintf(painCave.errMsg,
1538	>	"SimSetup error: If you use a constant pressure\n"
1539	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1540	>	painCave.isFatal = 1;
1541	>	simError();
1542	>	}
1543	>
1544	>	if (globals->haveTauThermostat())
1545	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1546	>	else{
1547	>	sprintf(painCave.errMsg,
1548	>	"SimSetup error: If you use an NPT\n"
1549	>	"\tensemble, you must set tauThermostat.\n");
1550	>	painCave.isFatal = 1;
1551	>	simError();
1552	>	}
1553	>
1554	>	if (globals->haveTauBarostat())
1555	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1556	>	else{
1557	>	sprintf(painCave.errMsg,
1558	>	"SimSetup error: If you use an NPT\n"
1559	>	"\tensemble, you must set tauBarostat.\n");
1560	>	painCave.isFatal = 1;
1561	>	simError();
1562	>	}
1563	>
1564	>	info->the_integrator = myNPTi;
1565	>	break;
1566	>
1567	>	case NPTf_ENS:
1568	>	if (globals->haveZconstraints()){
1569	>	setupZConstraint(info[k]);
1570	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1571	>	}
1572	>	else
1573	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1574	>
1575	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1576	>
1577	>	if (globals->haveTargetPressure())
1578	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1579	>	else{
1580	>	sprintf(painCave.errMsg,
1581	>	"SimSetup error: If you use a constant pressure\n"
1582	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1583	>	painCave.isFatal = 1;
1584	>	simError();
1585	>	}
1586	>
1587	>	if (globals->haveTauThermostat())
1588	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1589	>
1590	>	else{
1591	>	sprintf(painCave.errMsg,
1592	>	"SimSetup error: If you use an NPT\n"
1593	>	"\tensemble, you must set tauThermostat.\n");
1594	>	painCave.isFatal = 1;
1595	>	simError();
1596	>	}
1597	>
1598	>	if (globals->haveTauBarostat())
1599	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1600	>
1601	>	else{
1602	>	sprintf(painCave.errMsg,
1603	>	"SimSetup error: If you use an NPT\n"
1604	>	"\tensemble, you must set tauBarostat.\n");
1605	>	painCave.isFatal = 1;
1606	>	simError();
1607	>	}
1608	>
1609	>	info->the_integrator = myNPTf;
1610	>	break;
1611	>
1612	>	case NPTxyz_ENS:
1613	>	if (globals->haveZconstraints()){
1614	>	setupZConstraint(info[k]);
1615	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1616	>	}
1617	>	else
1618	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1619	>
1620	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1621	>
1622	>	if (globals->haveTargetPressure())
1623	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1624	>	else{
1625	>	sprintf(painCave.errMsg,
1626	>	"SimSetup error: If you use a constant pressure\n"
1627	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1628	>	painCave.isFatal = 1;
1629	>	simError();
1630	>	}
1631	>
1632	>	if (globals->haveTauThermostat())
1633	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1634	>	else{
1635	>	sprintf(painCave.errMsg,
1636	>	"SimSetup error: If you use an NPT\n"
1637	>	"\tensemble, you must set tauThermostat.\n");
1638	>	painCave.isFatal = 1;
1639	>	simError();
1640	>	}
1641	>
1642	>	if (globals->haveTauBarostat())
1643	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1644	>	else{
1645	>	sprintf(painCave.errMsg,
1646	>	"SimSetup error: If you use an NPT\n"
1647	>	"\tensemble, you must set tauBarostat.\n");
1648	>	painCave.isFatal = 1;
1649	>	simError();
1650	>	}
1651	>
1652	>	info->the_integrator = myNPTxyz;
1653	>	break;
1654	>
1655	>	default:
1656	>	sprintf(painCave.errMsg,
1657	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1658	>	painCave.isFatal = 1;
1659	>	simError();
1660	>	}
1661		}
1662		}
1663	+
1664	+	void SimSetup::initFortran(void){
1665	+	info[0].refreshSim();
1666	+
1667	+	if (!strcmp(info[0].mixingRule, "standard")){
1668	+	the_ff->initForceField(LB_MIXING_RULE);
1669	+	}
1670	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1671	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1672	+	}
1673	+	else{
1674	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1675	+	info[0].mixingRule);
1676	+	painCave.isFatal = 1;
1677	+	simError();
1678	+	}
1679	+
1680	+
1681	+	#ifdef IS_MPI
1682	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1683	+	MPIcheckPoint();
1684	+	#endif // is_mpi
1685	+	}
1686	+
1687	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1688	+	int nZConstraints;
1689	+	ZconStamp** zconStamp;
1690	+
1691	+	if (globals->haveZconstraintTime()){
1692	+	//add sample time of z-constraint  into SimInfo's property list
1693	+	DoubleData* zconsTimeProp = new DoubleData();
1694	+	zconsTimeProp->setID(ZCONSTIME_ID);
1695	+	zconsTimeProp->setData(globals->getZconsTime());
1696	+	theInfo.addProperty(zconsTimeProp);
1697	+	}
1698	+	else{
1699	+	sprintf(painCave.errMsg,
1700	+	"ZConstraint error: If you use a ZConstraint,\n"
1701	+	"\tyou must set zconsTime.\n");
1702	+	painCave.isFatal = 1;
1703	+	simError();
1704	+	}
1705	+
1706	+	//push zconsTol into siminfo, if user does not specify
1707	+	//value for zconsTol, a default value will be used
1708	+	DoubleData* zconsTol = new DoubleData();
1709	+	zconsTol->setID(ZCONSTOL_ID);
1710	+	if (globals->haveZconsTol()){
1711	+	zconsTol->setData(globals->getZconsTol());
1712	+	}
1713	+	else{
1714	+	double defaultZConsTol = 0.01;
1715	+	sprintf(painCave.errMsg,
1716	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1717	+	"\tOOPSE will use a default value of %f.\n"
1718	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1719	+	defaultZConsTol);
1720	+	painCave.isFatal = 0;
1721	+	simError();
1722	+
1723	+	zconsTol->setData(defaultZConsTol);
1724	+	}
1725	+	theInfo.addProperty(zconsTol);
1726	+
1727	+	//set Force Subtraction Policy
1728	+	StringData* zconsForcePolicy = new StringData();
1729	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1730	+
1731	+	if (globals->haveZconsForcePolicy()){
1732	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1733	+	}
1734	+	else{
1735	+	sprintf(painCave.errMsg,
1736	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1737	+	"\tOOPSE will use PolicyByMass.\n"
1738	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1739	+	painCave.isFatal = 0;
1740	+	simError();
1741	+	zconsForcePolicy->setData("BYMASS");
1742	+	}
1743	+
1744	+	theInfo.addProperty(zconsForcePolicy);
1745	+
1746	+	//set zcons gap
1747	+	DoubleData* zconsGap = new DoubleData();
1748	+	zconsGap->setID(ZCONSGAP_ID);
1749	+
1750	+	if (globals->haveZConsGap()){
1751	+	zconsGap->setData(globals->getZconsGap());
1752	+	theInfo.addProperty(zconsGap);
1753	+	}
1754	+
1755	+	//set zcons fixtime
1756	+	DoubleData* zconsFixtime = new DoubleData();
1757	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1758	+
1759	+	if (globals->haveZConsFixTime()){
1760	+	zconsFixtime->setData(globals->getZconsFixtime());
1761	+	theInfo.addProperty(zconsFixtime);
1762	+	}
1763	+
1764	+	//set zconsUsingSMD
1765	+	IntData* zconsUsingSMD = new IntData();
1766	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1767	+
1768	+	if (globals->haveZConsUsingSMD()){
1769	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1770	+	theInfo.addProperty(zconsUsingSMD);
1771	+	}
1772	+
1773	+	//Determine the name of ouput file and add it into SimInfo's property list
1774	+	//Be careful, do not use inFileName, since it is a pointer which
1775	+	//point to a string at master node, and slave nodes do not contain that string
1776	+
1777	+	string zconsOutput(theInfo.finalName);
1778	+
1779	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1780	+
1781	+	StringData* zconsFilename = new StringData();
1782	+	zconsFilename->setID(ZCONSFILENAME_ID);
1783	+	zconsFilename->setData(zconsOutput);
1784	+
1785	+	theInfo.addProperty(zconsFilename);
1786	+
1787	+	//setup index, pos and other parameters of z-constraint molecules
1788	+	nZConstraints = globals->getNzConstraints();
1789	+	theInfo.nZconstraints = nZConstraints;
1790	+
1791	+	zconStamp = globals->getZconStamp();
1792	+	ZConsParaItem tempParaItem;
1793	+
1794	+	ZConsParaData* zconsParaData = new ZConsParaData();
1795	+	zconsParaData->setID(ZCONSPARADATA_ID);
1796	+
1797	+	for (int i = 0; i < nZConstraints; i++){
1798	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1799	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1800	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1801	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1802	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1803	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1804	+	zconsParaData->addItem(tempParaItem);
1805	+	}
1806	+
1807	+	//check the uniqueness of index
1808	+	if(!zconsParaData->isIndexUnique()){
1809	+	sprintf(painCave.errMsg,
1810	+	"ZConstraint Error: molIndex is not unique!\n");
1811	+	painCave.isFatal = 1;
1812	+	simError();
1813	+	}
1814	+
1815	+	//sort the parameters by index of molecules
1816	+	zconsParaData->sortByIndex();
1817	+
1818	+	//push data into siminfo, therefore, we can retrieve later
1819	+	theInfo.addProperty(zconsParaData);
1820	+	}
1821	+
1822	+	void SimSetup::makeMinimizer(){
1823	+
1824	+	OOPSEMinimizer* myOOPSEMinimizer;
1825	+	MinimizerParameterSet* param;
1826	+	char minimizerName[100];
1827	+
1828	+	for (int i = 0; i < nInfo; i++){
1829	+
1830	+	//prepare parameter set for minimizer
1831	+	param = new MinimizerParameterSet();
1832	+	param->setDefaultParameter();
1833	+
1834	+	if (globals->haveMinimizer()){
1835	+	param->setFTol(globals->getMinFTol());
1836	+	}
1837	+
1838	+	if (globals->haveMinGTol()){
1839	+	param->setGTol(globals->getMinGTol());
1840	+	}
1841	+
1842	+	if (globals->haveMinMaxIter()){
1843	+	param->setMaxIteration(globals->getMinMaxIter());
1844	+	}
1845	+
1846	+	if (globals->haveMinWriteFrq()){
1847	+	param->setMaxIteration(globals->getMinMaxIter());
1848	+	}
1849	+
1850	+	if (globals->haveMinWriteFrq()){
1851	+	param->setWriteFrq(globals->getMinWriteFrq());
1852	+	}
1853	+
1854	+	if (globals->haveMinStepSize()){
1855	+	param->setStepSize(globals->getMinStepSize());
1856	+	}
1857	+
1858	+	if (globals->haveMinLSMaxIter()){
1859	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1860	+	}
1861	+
1862	+	if (globals->haveMinLSTol()){
1863	+	param->setLineSearchTol(globals->getMinLSTol());
1864	+	}
1865	+
1866	+	strcpy(minimizerName, globals->getMinimizer());
1867	+
1868	+	if (!strcasecmp(minimizerName, "CG")){
1869	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1870	+	}
1871	+	else if (!strcasecmp(minimizerName, "SD")){
1872	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1873	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1874	+	}
1875	+	else{
1876	+	sprintf(painCave.errMsg,
1877	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1878	+	painCave.isFatal = 0;
1879	+	simError();
1880	+
1881	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1882	+	}
1883	+	info[i].the_integrator = myOOPSEMinimizer;
1884	+
1885	+	//store the minimizer into simInfo
1886	+	info[i].the_minimizer = myOOPSEMinimizer;
1887	+	info[i].has_minimizer = true;
1888	+	}
1889	+
1890	+	}

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