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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 582 by mmeineke, Wed Jul 9 15:33:46 2003 UTC vs.
Revision 1116 by tim, Thu Apr 15 22:15:21 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" ) ) {
150	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
151	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
152	<	//     if (the_globals->haveTargetPressure())
153	<	//       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	>	#ifdef IS_MPI
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	//     if (the_globals->haveTauThermostat())
148	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
149	<	//     else if (the_globals->haveQmass())
150	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
151	<	//     else {
152	<	//       sprintf( painCave.errMsg,
153	<	//                "SimSetup error: If you use one of the constant temperature\n"
154	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
155	<	//                "    Neither of these was found in the BASS file.\n");
156	<	//       painCave.isFatal = 1;
157	<	//       simError();
158	<	//     }
155	>	// initialize the Fortran
156
157	<	//     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	<	//     }
157	>	initFortran();
158
159	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
160	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
161	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	//     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	<	//     }
166	>	}
167
188	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
189	–	simnfo->usePBC = the_globals->getPBC();
190	–
191	–	int usesDipoles = 0;
192	–	switch( ffCase ){
168
169	<	case FF_DUFF:
170	<	the_ff = new DUFF();
171	<	usesDipoles = 1;
172	<	break;
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175	>	molInit molInfo;
176	>	DirectionalAtom* dAtom;
177	>	RigidBody* myRB;
178	>	StuntDouble* mySD;
179	>	LinkedAssign* extras;
180	>	LinkedAssign* current_extra;
181	>	AtomStamp* currentAtom;
182	>	BondStamp* currentBond;
183	>	BendStamp* currentBend;
184	>	TorsionStamp* currentTorsion;
185	>	RigidBodyStamp* currentRigidBody;
186
187	<	case FF_LJ:
188	<	the_ff = new LJFF();
189	<	break;
187	>	bond_pair* theBonds;
188	>	bend_set* theBends;
189	>	torsion_set* theTorsions;
190
191	<	default:
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup Error. Unrecognized force field in case statement.\n");
206	<	painCave.isFatal = 1;
207	<	simError();
208	<	}
191	>	set<int> skipList;
192
193	<	#ifdef IS_MPI
194	<	strcpy( checkPointMsg, "ForceField creation successful" );
195	<	MPIcheckPoint();
213	<	#endif // is_mpi
193	>	double phi, theta, psi;
194	>	char* molName;
195	>	char rbName[100];
196
197	<	// 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];
197	>	//init the forceField paramters
198
199	<	if( !the_globals->haveNMol() ){
221	<	// we don't have the total number of molecules, so we assume it is
222	<	// given in each component
199	>	the_ff->readParams();
200
201	<	tot_nmol = 0;
225	<	for( i=0; i<n_components; i++ ){
201	>	// init the atoms
202
203	<	if( !the_components[i]->haveNMol() ){
204	<	// we have a problem
205	<	sprintf( painCave.errMsg,
206	<	"SimSetup Error. No global NMol or component NMol"
207	<	" given. Cannot calculate the number of atoms.\n" );
208	<	painCave.isFatal = 1;
209	<	simError();
210	<	}
203	>	int nMembers, nNew, rb1, rb2;
204	>
205	>	for (k = 0; k < nInfo; k++){
206	>	the_ff->setSimInfo(&(info[k]));
207	>
208	>	atomOffset = 0;
209	>
210	>	for (i = 0; i < info[k].n_mol; i++){
211	>	stampID = info[k].molecules[i].getStampID();
212	>	molName = comp_stamps[stampID]->getID();
213	>
214	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
217	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219	>
220	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
221
222	<	tot_nmol += the_components[i]->getNMol();
223	<	components_nmol[i] = the_components[i]->getNMol();
224	<	}
225	<	}
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	<	}
222	>	if (molInfo.nBonds > 0)
223	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	>	else
225	>	molInfo.myBonds = NULL;
226
227	<	#ifdef IS_MPI
228	<	strcpy( checkPointMsg, "Have the number of components" );
229	<	MPIcheckPoint();
230	<	#endif // is_mpi
227	>	if (molInfo.nBends > 0)
228	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	>	else
230	>	molInfo.myBends = NULL;
231
232	<	// make an array of molecule stamps that match the components used.
233	<	// also extract the used stamps out into a separate linked list
232	>	if (molInfo.nTorsions > 0)
233	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	>	else
235	>	molInfo.myTorsions = NULL;
236
237	<	simnfo->nComponents = n_components;
238	<	simnfo->componentsNmol = components_nmol;
239	<	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 ){
237	>	theBonds = new bond_pair[molInfo.nBonds];
238	>	theBends = new bend_set[molInfo.nBends];
239	>	theTorsions = new torsion_set[molInfo.nTorsions];
240
241	<	// 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	<	}
241	>	// make the Atoms
242
243	<	#ifdef IS_MPI
244	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
310	<	MPIcheckPoint();
311	<	#endif // is_mpi
312	<
243	>	for (j = 0; j < molInfo.nAtoms; j++){
244	>	currentAtom = comp_stamps[stampID]->getAtom(j);
245
246	+	if (currentAtom->haveOrientation()){
247	+	dAtom = new DirectionalAtom((j + atomOffset),
248	+	info[k].getConfiguration());
249	+	info[k].n_oriented++;
250	+	molInfo.myAtoms[j] = dAtom;
251
252	+	// Directional Atoms have standard unit vectors which are oriented
253	+	// in space using the three Euler angles.  We assume the standard
254	+	// unit vector was originally along the z axis below.
255
256	<	// caclulate the number of atoms, bonds, bends and torsions
256	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259
260	<	tot_atoms = 0;
261	<	tot_bonds = 0;
262	<	tot_bends = 0;
263	<	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	<	}
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262	>	}
263	>	else{
264
265	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
265	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266
267	<	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];
267	>	}
268
269	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
270		#ifdef IS_MPI
271
272	<	// divide the molecules among processors here.
344	<
345	<	mpiSim = new mpiSimulation( simnfo );
346	<
347	<	globalIndex = mpiSim->divideLabor();
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273
274	<	// set up the local variables
275	<
351	<	int localMol, allMol;
352	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
274	>	#endif // is_mpi
275	>	}
276
277	<	int* mol2proc = mpiSim->getMolToProcMap();
278	<	int* molCompType = mpiSim->getMolComponentType();
279	<
280	<	allMol = 0;
281	<	localMol = 0;
359	<	local_atoms = 0;
360	<	local_bonds = 0;
361	<	local_bends = 0;
362	<	local_torsions = 0;
363	<	globalAtomIndex = 0;
277	>	// make the bonds
278	>	for (j = 0; j < molInfo.nBonds; j++){
279	>	currentBond = comp_stamps[stampID]->getBond(j);
280	>	theBonds[j].a = currentBond->getA() + atomOffset;
281	>	theBonds[j].b = currentBond->getB() + atomOffset;
282
283	+	tempI = theBonds[j].a;
284	+	tempJ = theBonds[j].b;
285
286	<	for( i=0; i<n_components; i++ ){
286	>	#ifdef IS_MPI
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293
294	<	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++;
294	>	info[k].excludes->addPair(exI, exJ);
295		}
296
297	<	allMol++;
298	<	}
299	<	}
300	<	local_SRI = local_bonds + local_bends + local_torsions;
301	<
302	<	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	<	}
297	>	//make the bends
298	>	for (j = 0; j < molInfo.nBends; j++){
299	>	currentBend = comp_stamps[stampID]->getBend(j);
300	>	theBends[j].a = currentBend->getA() + atomOffset;
301	>	theBends[j].b = currentBend->getB() + atomOffset;
302	>	theBends[j].c = currentBend->getC() + atomOffset;
303
304	<	simnfo->n_bonds = local_bonds;
305	<	simnfo->n_bends = local_bends;
306	<	simnfo->n_torsions = local_torsions;
403	<	simnfo->n_SRI = local_SRI;
404	<	simnfo->n_mol = localMol;
304	>	if (currentBend->haveExtras()){
305	>	extras = currentBend->getExtras();
306	>	current_extra = extras;
307
308	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
309	<	MPIcheckPoint();
310	<
311	<
312	<	#endif // is_mpi
313	<
308	>	while (current_extra != NULL){
309	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
310	>	switch (current_extra->getType()){
311	>	case 0:
312	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
313	>	theBends[j].isGhost = 1;
314	>	break;
315
316	<	// create the atom and short range interaction arrays
316	>	case 1:
317	>	theBends[j].ghost = (int) current_extra->getDouble() +
318	>	atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	Atom::createArrays(simnfo->n_atoms);
323	<	the_atoms = new Atom*[simnfo->n_atoms];
324	<	the_molecules = new Molecule[simnfo->n_mol];
325	<	int molIndex;
326	<
327	<	// initialize the molecule's stampID's
322	>	default:
323	>	sprintf(painCave.errMsg,
324	>	"SimSetup Error: ghostVectorSource was neither a "
325	>	"double nor an int.\n"
326	>	"-->Bend[%d] in %s\n",
327	>	j, comp_stamps[stampID]->getID());
328	>	painCave.isFatal = 1;
329	>	simError();
330	>	}
331	>	}
332	>	else{
333	>	sprintf(painCave.errMsg,
334	>	"SimSetup Error: unhandled bend assignment:\n"
335	>	"    -->%s in Bend[%d] in %s\n",
336	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340
341	+	current_extra = current_extra->getNext();
342	+	}
343	+	}
344	+
345	+	if (theBends[j].isGhost) {
346	+
347	+	tempI = theBends[j].a;
348	+	tempJ = theBends[j].b;
349	+
350		#ifdef IS_MPI
351	<
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358
359	<	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	<	}
359	>	} else {
360
361	<	#else // is_mpi
362	<
363	<	molIndex = 0;
364	<	globalAtomIndex = 0;
365	<	for(i=0; i<n_components; i++){
366	<	for(j=0; j<components_nmol[i]; j++ ){
367	<	the_molecules[molIndex].setStampID( i );
368	<	the_molecules[molIndex].setMyIndex( molIndex );
369	<	the_molecules[molIndex].setGlobalIndex( molIndex );
370	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
371	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
372	<	globalAtomIndex++;
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>	tempK = theBends[j].c;
364	>
365	>	#ifdef IS_MPI
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379		}
449	–	molIndex++;
450	–	}
451	–	}
452	–
380
381	<	#endif // is_mpi
381	>	for (j = 0; j < molInfo.nTorsions; j++){
382	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
383	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
384	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
385	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
386	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
387
388	+	tempI = theTorsions[j].a;
389	+	tempJ = theTorsions[j].b;
390	+	tempK = theTorsions[j].c;
391	+	tempL = theTorsions[j].d;
392
393	<	if( simnfo->n_SRI ){
394	<
395	<	Exclude::createArray(simnfo->n_SRI);
396	<	the_excludes = new Exclude*[simnfo->n_SRI];
397	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
398	<	simnfo->globalExcludes = new int;
399	<	simnfo->n_exclude = simnfo->n_SRI;
400	<	}
401	<	else{
402	<
403	<	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	<	}
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	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403	>	#endif
404
405	<	// set the arrays into the SimInfo object
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411	>	}
412
413	<	simnfo->atoms = the_atoms;
414	<	simnfo->molecules = the_molecules;
415	<	simnfo->nGlobalExcludes = 0;
416	<	simnfo->excludes = the_excludes;
413	>
414	>	molInfo.myRigidBodies.clear();
415	>
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417
418	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	+	nMembers = currentRigidBody->getNMembers();
420
421	<	// get some of the tricky things that may still be in the globals
421	>	// Create the Rigid Body:
422
423	<	double boxVector[3];
487	<	if( the_globals->haveBox() ){
488	<	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() ){
423	>	myRB = new RigidBody();
424
425	<	double vol;
426	<	vol = (double)tot_nmol / the_globals->getDensity();
427	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
428	<	boxVector[1] = boxVector[0];
500	<	boxVector[2] = boxVector[0];
425	>	sprintf(rbName,"%s_RB_%d", molName, j);
426	>	myRB->setType(rbName);
427	>
428	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
429
430	<	simnfo->setBox( boxVector );
431	<	}
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();
430	>	// molI is atom numbering inside this molecule
431	>	molI = currentRigidBody->getMember(rb1);
432
433	<	if( !the_globals->haveBoxY() ){
434	<	sprintf( painCave.errMsg,
515	<	"SimSetup error, no periodic BoxY size given.\n" );
516	<	painCave.isFatal = 1;
517	<	simError();
518	<	}
519	<	boxVector[1] = the_globals->getBoxY();
433	>	// tempI is atom numbering on local processor
434	>	tempI = molI + atomOffset;
435
436	<	if( !the_globals->haveBoxZ() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup error, no periodic BoxZ size given.\n" );
524	<	painCave.isFatal = 1;
525	<	simError();
526	<	}
527	<	boxVector[2] = the_globals->getBoxZ();
436	>	// currentAtom is the AtomStamp (which we need for
437	>	// rigid body reference positions)
438	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
439
440	<	simnfo->setBox( boxVector );
441	<	}
440	>	// When we add to the rigid body, add the atom itself and
441	>	// the stamp info:
442
443	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	+
445	+	// Add this atom to the Skip List for the integrators
446		#ifdef IS_MPI
447	<	strcpy( checkPointMsg, "Box size set up" );
448	<	MPIcheckPoint();
449	<	#endif // is_mpi
447	>	slI = info[k].atoms[tempI]->getGlobalIndex();
448	>	#else
449	>	slI = tempI;
450	>	#endif
451	>	skipList.insert(slI);
452	>
453	>	}
454	>
455	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	>
458	>	tempI = currentRigidBody->getMember(rb1);
459	>	tempJ = currentRigidBody->getMember(rb2);
460	>
461	>	// Some explanation is required here.
462	>	// Fortran indexing starts at 1, while c indexing starts at 0
463	>	// Also, in parallel computations, the GlobalIndex is
464	>	// used for the exclude list:
465	>
466	>	#ifdef IS_MPI
467	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478
479	+	molInfo.myRigidBodies.push_back(myRB);
480	+	info[k].rigidBodies.push_back(myRB);
481	+	}
482	+
483
484	<	// initialize the arrays
484	>	// After this is all set up, scan through the atoms to
485	>	// see if they can be added to the integrableObjects:
486
487	<	the_ff->setSimInfo( simnfo );
487	>	molInfo.myIntegrableObjects.clear();
488	>
489
490	<	makeMolecules();
543	<	simnfo->identArray = new int[simnfo->n_atoms];
544	<	for(i=0; i<simnfo->n_atoms; i++){
545	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
546	<	}
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	<	}
490	>	for (j = 0; j < molInfo.nAtoms; j++){
491
492	<	if( !the_globals->haveEST() ){
493	<	sprintf( painCave.errMsg,
494	<	"SimSetup Warning: using default value of 0.05 * the "
495	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
496	<	);
497	<	painCave.isFatal = 0;
498	<	simError();
499	<	simnfo->est = 0.05 * simnfo->ecr;
500	<	} else {
501	<	simnfo->est        = the_globals->getEST();
502	<	}
492	>	#ifdef IS_MPI
493	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	>	#else
495	>	slJ = j+atomOffset;
496	>	#endif
497	>
498	>	// if they aren't on the skip list, then they can be integrated
499	>
500	>	if (skipList.find(slJ) == skipList.end()) {
501	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	>	info[k].integrableObjects.push_back(mySD);
503	>	molInfo.myIntegrableObjects.push_back(mySD);
504	>	}
505	>	}
506	>
507	>	// all rigid bodies are integrated:
508	>
509	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	>	info[k].integrableObjects.push_back(mySD);
512	>	molInfo.myIntegrableObjects.push_back(mySD);
513	>	}
514
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) {
515
516	<	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	<	}
516	>	// send the arrays off to the forceField for init.
517
518	<	if( !the_globals->haveEST() ){
519	<	sprintf( painCave.errMsg,
520	<	"SimSetup Warning: using default value of 5%% of the "
521	<	"electrostaticCutoffRadius for the "
522	<	"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	<	}
518	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522	>	theTorsions);
523
524	+	info[k].molecules[i].initialize(molInfo);
525	+
526	+
527	+	atomOffset += molInfo.nAtoms;
528	+	delete[] theBonds;
529	+	delete[] theBends;
530	+	delete[] theTorsions;
531	+	}
532	+	}
533	+
534		#ifdef IS_MPI
535	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
535	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
536		MPIcheckPoint();
537		#endif // is_mpi
538
539	<	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
539	>	// clean up the forcefield
540
541	<	delete fileInit;
640	<	}
641	<	else{
541	>	if (!globals->haveLJrcut()){
542
543	<	#ifdef IS_MPI
543	>	the_ff->calcRcut();
544
545	<	// no init from bass
546	<
547	<	sprintf( painCave.errMsg,
548	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
649	<	painCave.isFatal;
650	<	simError();
651	<
652	<	#else
545	>	} else {
546	>
547	>	the_ff->setRcut( globals->getLJrcut() );
548	>	}
549
550	<	initFromBass();
550	>	the_ff->cleanMe();
551	>	}
552
553	+	void SimSetup::initFromBass(void){
554	+	int i, j, k;
555	+	int n_cells;
556	+	double cellx, celly, cellz;
557	+	double temp1, temp2, temp3;
558	+	int n_per_extra;
559	+	int n_extra;
560	+	int have_extra, done;
561
562	<	#endif
563	<	}
562	>	double vel[3];
563	>	vel[0] = 0.0;
564	>	vel[1] = 0.0;
565	>	vel[2] = 0.0;
566
567	<	#ifdef IS_MPI
568	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
569	<	MPIcheckPoint();
663	<	#endif // is_mpi
567	>	temp1 = (double) tot_nmol / 4.0;
568	>	temp2 = pow(temp1, (1.0 / 3.0));
569	>	temp3 = ceil(temp2);
570
571	+	have_extra = 0;
572	+	if (temp2 < temp3){
573	+	// we have a non-complete lattice
574	+	have_extra = 1;
575
576	<
577	<
578	<
576	>	n_cells = (int) temp3 - 1;
577	>	cellx = info[0].boxL[0] / temp3;
578	>	celly = info[0].boxL[1] / temp3;
579	>	cellz = info[0].boxL[2] / temp3;
580	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
581	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
582	>	n_per_extra = (int) ceil(temp1);
583
584	<
585	<	#ifdef IS_MPI
586	<	if( worldRank == 0 ){
587	<	#endif // is_mpi
588	<
589	<	if( the_globals->haveFinalConfig() ){
676	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
584	>	if (n_per_extra > 4){
585	>	sprintf(painCave.errMsg,
586	>	"SimSetup error. There has been an error in constructing"
587	>	" the non-complete lattice.\n");
588	>	painCave.isFatal = 1;
589	>	simError();
590		}
591	<	else{
592	<	strcpy( simnfo->finalName, inFileName );
593	<	char* endTest;
594	<	int nameLength = strlen( simnfo->finalName );
595	<	endTest = &(simnfo->finalName[nameLength - 5]);
596	<	if( !strcmp( endTest, ".bass" ) ){
597	<	strcpy( endTest, ".eor" );
591	>	}
592	>	else{
593	>	n_cells = (int) temp3;
594	>	cellx = info[0].boxL[0] / temp3;
595	>	celly = info[0].boxL[1] / temp3;
596	>	cellz = info[0].boxL[2] / temp3;
597	>	}
598	>
599	>	current_mol = 0;
600	>	current_comp_mol = 0;
601	>	current_comp = 0;
602	>	current_atom_ndx = 0;
603	>
604	>	for (i = 0; i < n_cells ; i++){
605	>	for (j = 0; j < n_cells; j++){
606	>	for (k = 0; k < n_cells; k++){
607	>	makeElement(i * cellx, j * celly, k * cellz);
608	>
609	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
610	>
611	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
612	>
613	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
614		}
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	–	}
615		}
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
616		}
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	–	}
617
618	<	if( the_globals->haveStatusTime() ){
619	<	simnfo->statusTime = the_globals->getStatusTime();
769	<	}
618	>	if (have_extra){
619	>	done = 0;
620
621	<	if( the_globals->haveThermalTime() ){
622	<	simnfo->thermalTime = the_globals->getThermalTime();
623	<	}
621	>	int start_ndx;
622	>	for (i = 0; i < (n_cells + 1) && !done; i++){
623	>	for (j = 0; j < (n_cells + 1) && !done; j++){
624	>	if (i < n_cells){
625	>	if (j < n_cells){
626	>	start_ndx = n_cells;
627	>	}
628	>	else
629	>	start_ndx = 0;
630	>	}
631	>	else
632	>	start_ndx = 0;
633
634	<	// check for the temperature set flag
634	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
635	>	makeElement(i * cellx, j * celly, k * cellz);
636	>	done = (current_mol >= tot_nmol);
637
638	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
638	>	if (!done && n_per_extra > 1){
639	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
640	>	k * cellz);
641	>	done = (current_mol >= tot_nmol);
642	>	}
643
644	+	if (!done && n_per_extra > 2){
645	+	makeElement(i * cellx, j * celly + 0.5 * celly,
646	+	k * cellz + 0.5 * cellz);
647	+	done = (current_mol >= tot_nmol);
648	+	}
649
650	<	// make the integrator
651	<
652	<
653	<	NVT* myNVT = NULL;
654	<	switch( ensembleCase ){
650	>	if (!done && n_per_extra > 3){
651	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
652	>	k * cellz + 0.5 * cellz);
653	>	done = (current_mol >= tot_nmol);
654	>	}
655	>	}
656	>	}
657	>	}
658	>	}
659
660	<	case NVE_ENS:
661	<	new NVE( simnfo, the_ff );
662	<	break;
660	>	for (i = 0; i < info[0].n_atoms; i++){
661	>	info[0].atoms[i]->setVel(vel);
662	>	}
663	>	}
664
665	<	case NVT_ENS:
666	<	myNVT = new NVT( simnfo, the_ff );
667	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
665	>	void SimSetup::makeElement(double x, double y, double z){
666	>	int k;
667	>	AtomStamp* current_atom;
668	>	DirectionalAtom* dAtom;
669	>	double rotMat[3][3];
670	>	double pos[3];
671
672	<	if (the_globals->haveTauThermostat())
673	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
674	<	//     else if (the_globals->haveQmass())
675	<	//       myNVT->setQmass(the_globals->getQmass());
676	<	else {
677	<	sprintf( painCave.errMsg,
678	<	"SimSetup error: If you use the NVT\n"
679	<	"    ensemble, you must set either tauThermostat or qMass.\n"
680	<	"    Neither of these was found in the BASS file.\n");
672	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
673	>	current_atom = comp_stamps[current_comp]->getAtom(k);
674	>	if (!current_atom->havePosition()){
675	>	sprintf(painCave.errMsg,
676	>	"SimSetup:initFromBass error.\n"
677	>	"\tComponent %s, atom %s does not have a position specified.\n"
678	>	"\tThe initialization routine is unable to give a start"
679	>	" position.\n",
680	>	comp_stamps[current_comp]->getID(), current_atom->getType());
681		painCave.isFatal = 1;
682		simError();
683		}
806	–	break;
684
685	<	default:
686	<	sprintf( painCave.errMsg,
687	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
811	<	painCave.isFatal = 1;
812	<	simError();
813	<	}
685	>	pos[0] = x + current_atom->getPosX();
686	>	pos[1] = y + current_atom->getPosY();
687	>	pos[2] = z + current_atom->getPosZ();
688
689	+	info[0].atoms[current_atom_ndx]->setPos(pos);
690
691	<	#ifdef IS_MPI
692	<	mpiSim->mpiRefresh();
818	<	#endif
691	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
692	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
693
694	<	// initialize the Fortran
694	>	rotMat[0][0] = 1.0;
695	>	rotMat[0][1] = 0.0;
696	>	rotMat[0][2] = 0.0;
697
698	+	rotMat[1][0] = 0.0;
699	+	rotMat[1][1] = 1.0;
700	+	rotMat[1][2] = 0.0;
701
702	<	simnfo->refreshSim();
703	<
704	<	if( !strcmp( simnfo->mixingRule, "standard") ){
705	<	the_ff->initForceField( LB_MIXING_RULE );
702	>	rotMat[2][0] = 0.0;
703	>	rotMat[2][1] = 0.0;
704	>	rotMat[2][2] = 1.0;
705	>
706	>	dAtom->setA(rotMat);
707	>	}
708	>
709	>	current_atom_ndx++;
710		}
828	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
829	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
830	–	}
831	–	else{
832	–	sprintf( painCave.errMsg,
833	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
834	–	simnfo->mixingRule );
835	–	painCave.isFatal = 1;
836	–	simError();
837	–	}
711
712	+	current_mol++;
713	+	current_comp_mol++;
714
715	<	#ifdef IS_MPI
716	<	strcpy( checkPointMsg,
717	<	"Successfully intialized the mixingRule for Fortran." );
718	<	MPIcheckPoint();
844	<	#endif // is_mpi
715	>	if (current_comp_mol >= components_nmol[current_comp]){
716	>	current_comp_mol = 0;
717	>	current_comp++;
718	>	}
719		}
720
721
722	<	void SimSetup::makeMolecules( void ){
722	>	void SimSetup::gatherInfo(void){
723	>	int i;
724
725	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
726	<	molInit info;
852	<	DirectionalAtom* dAtom;
853	<	LinkedAssign* extras;
854	<	LinkedAssign* current_extra;
855	<	AtomStamp* currentAtom;
856	<	BondStamp* currentBond;
857	<	BendStamp* currentBend;
858	<	TorsionStamp* currentTorsion;
725	>	ensembleCase = -1;
726	>	ffCase = -1;
727
728	<	bond_pair* theBonds;
861	<	bend_set* theBends;
862	<	torsion_set* theTorsions;
728	>	// set the easy ones first
729
730	<
731	<	//init the forceField paramters
730	>	for (i = 0; i < nInfo; i++){
731	>	info[i].target_temp = globals->getTargetTemp();
732	>	info[i].dt = globals->getDt();
733	>	info[i].run_time = globals->getRunTime();
734	>	}
735	>	n_components = globals->getNComponents();
736
867	–	the_ff->readParams();
737
738	<
870	<	// init the atoms
738	>	// get the forceField
739
740	<	double ux, uy, uz, u, uSqr;
873	<
874	<	atomOffset = 0;
875	<	excludeOffset = 0;
876	<	for(i=0; i<simnfo->n_mol; i++){
877	<
878	<	stampID = the_molecules[i].getStampID();
740	>	strcpy(force_field, globals->getForceField());
741
742	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
743	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
744	<	info.nBends    = comp_stamps[stampID]->getNBends();
745	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
746	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
742	>	if (!strcasecmp(force_field, "DUFF")){
743	>	ffCase = FF_DUFF;
744	>	}
745	>	else if (!strcasecmp(force_field, "LJ")){
746	>	ffCase = FF_LJ;
747	>	}
748	>	else if (!strcasecmp(force_field, "EAM")){
749	>	ffCase = FF_EAM;
750	>	}
751	>	else if (!strcasecmp(force_field, "WATER")){
752	>	ffCase = FF_H2O;
753	>	}
754	>	else{
755	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756	>	force_field);
757	>	painCave.isFatal = 1;
758	>	simError();
759	>	}
760
761	<	info.myAtoms = &the_atoms[atomOffset];
887	<	info.myExcludes = &the_excludes[excludeOffset];
888	<	info.myBonds = new Bond*[info.nBonds];
889	<	info.myBends = new Bend*[info.nBends];
890	<	info.myTorsions = new Torsion*[info.nTorsions];
761	>	// get the ensemble
762
763	<	theBonds = new bond_pair[info.nBonds];
764	<	theBends = new bend_set[info.nBends];
765	<	theTorsions = new torsion_set[info.nTorsions];
763	>	strcpy(ensemble, globals->getEnsemble());
764	>
765	>	if (!strcasecmp(ensemble, "NVE")){
766	>	ensembleCase = NVE_ENS;
767	>	}
768	>	else if (!strcasecmp(ensemble, "NVT")){
769	>	ensembleCase = NVT_ENS;
770	>	}
771	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
772	>	ensembleCase = NPTi_ENS;
773	>	}
774	>	else if (!strcasecmp(ensemble, "NPTf")){
775	>	ensembleCase = NPTf_ENS;
776	>	}
777	>	else if (!strcasecmp(ensemble, "NPTxyz")){
778	>	ensembleCase = NPTxyz_ENS;
779	>	}
780	>	else{
781	>	sprintf(painCave.errMsg,
782	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
783	>	"\treverting to NVE for this simulation.\n",
784	>	ensemble);
785	>	painCave.isFatal = 0;
786	>	simError();
787	>	strcpy(ensemble, "NVE");
788	>	ensembleCase = NVE_ENS;
789	>	}
790	>
791	>	for (i = 0; i < nInfo; i++){
792	>	strcpy(info[i].ensemble, ensemble);
793	>
794	>	// get the mixing rule
795	>
796	>	strcpy(info[i].mixingRule, globals->getMixingRule());
797	>	info[i].usePBC = globals->getPBC();
798	>	}
799	>
800	>	// get the components and calculate the tot_nMol and indvidual n_mol
801	>
802	>	the_components = globals->getComponents();
803	>	components_nmol = new int[n_components];
804	>
805	>
806	>	if (!globals->haveNMol()){
807	>	// we don't have the total number of molecules, so we assume it is
808	>	// given in each component
809	>
810	>	tot_nmol = 0;
811	>	for (i = 0; i < n_components; i++){
812	>	if (!the_components[i]->haveNMol()){
813	>	// we have a problem
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Error. No global NMol or component NMol given.\n"
816	>	"\tCannot calculate the number of atoms.\n");
817	>	painCave.isFatal = 1;
818	>	simError();
819	>	}
820	>
821	>	tot_nmol += the_components[i]->getNMol();
822	>	components_nmol[i] = the_components[i]->getNMol();
823	>	}
824	>	}
825	>	else{
826	>	sprintf(painCave.errMsg,
827	>	"SimSetup error.\n"
828	>	"\tSorry, the ability to specify total"
829	>	" nMols and then give molfractions in the components\n"
830	>	"\tis not currently supported."
831	>	" Please give nMol in the components.\n");
832	>	painCave.isFatal = 1;
833	>	simError();
834	>	}
835	>
836	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
838	>	sprintf(painCave.errMsg,
839	>	"Sample time is not divisible by dt.\n"
840	>	"\tThis will result in samples that are not uniformly\n"
841	>	"\tdistributed in time.  If this is a problem, change\n"
842	>	"\tyour sampleTime variable.\n");
843	>	painCave.isFatal = 0;
844	>	simError();
845	>	}
846	>
847	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
848	>	sprintf(painCave.errMsg,
849	>	"Status time is not divisible by dt.\n"
850	>	"\tThis will result in status reports that are not uniformly\n"
851	>	"\tdistributed in time.  If this is a problem, change \n"
852	>	"\tyour statusTime variable.\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	}
856	>
857	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	>	sprintf(painCave.errMsg,
859	>	"Thermal time is not divisible by dt.\n"
860	>	"\tThis will result in thermalizations that are not uniformly\n"
861	>	"\tdistributed in time.  If this is a problem, change \n"
862	>	"\tyour thermalTime variable.\n");
863	>	painCave.isFatal = 0;
864	>	simError();
865	>	}
866	>
867	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868	>	sprintf(painCave.errMsg,
869	>	"Reset time is not divisible by dt.\n"
870	>	"\tThis will result in integrator resets that are not uniformly\n"
871	>	"\tdistributed in time.  If this is a problem, change\n"
872	>	"\tyour resetTime variable.\n");
873	>	painCave.isFatal = 0;
874	>	simError();
875	>	}
876	>
877	>	// set the status, sample, and thermal kick times
878	>
879	>	for (i = 0; i < nInfo; i++){
880	>	if (globals->haveSampleTime()){
881	>	info[i].sampleTime = globals->getSampleTime();
882	>	info[i].statusTime = info[i].sampleTime;
883	>	info[i].thermalTime = info[i].sampleTime;
884	>	}
885	>	else{
886	>	info[i].sampleTime = globals->getRunTime();
887	>	info[i].statusTime = info[i].sampleTime;
888	>	info[i].thermalTime = info[i].sampleTime;
889	>	}
890	>
891	>	if (globals->haveStatusTime()){
892	>	info[i].statusTime = globals->getStatusTime();
893	>	}
894	>
895	>	if (globals->haveThermalTime()){
896	>	info[i].thermalTime = globals->getThermalTime();
897	>	}
898	>
899	>	info[i].resetIntegrator = 0;
900	>	if( globals->haveResetTime() ){
901	>	info[i].resetTime = globals->getResetTime();
902	>	info[i].resetIntegrator = 1;
903	>	}
904	>
905	>	// check for the temperature set flag
906
907	<	// make the Atoms
907	>	if (globals->haveTempSet())
908	>	info[i].setTemp = globals->getTempSet();
909	>
910	>	// check for the extended State init
911	>
912	>	info[i].useInitXSstate = globals->getUseInitXSstate();
913	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914
915	<	for(j=0; j<info.nAtoms; j++){
916	<
917	<	currentAtom = comp_stamps[stampID]->getAtom( j );
918	<	if( currentAtom->haveOrientation() ){
919	<
920	<	dAtom = new DirectionalAtom(j + atomOffset);
921	<	simnfo->n_oriented++;
922	<	info.myAtoms[j] = dAtom;
923	<
924	<	ux = currentAtom->getOrntX();
925	<	uy = currentAtom->getOrntY();
926	<	uz = currentAtom->getOrntZ();
927	<
928	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
929	<
930	<	u = sqrt( uSqr );
931	<	ux = ux / u;
932	<	uy = uy / u;
933	<	uz = uz / u;
934	<
935	<	dAtom->setSUx( ux );
919	<	dAtom->setSUy( uy );
920	<	dAtom->setSUz( uz );
921	<	}
922	<	else{
923	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
915	>	}
916	>
917	>	//setup seed for random number generator
918	>	int seedValue;
919	>
920	>	if (globals->haveSeed()){
921	>	seedValue = globals->getSeed();
922	>
923	>	if(seedValue / 1E9 == 0){
924	>	sprintf(painCave.errMsg,
925	>	"Seed for sprng library should contain at least 9 digits\n"
926	>	"OOPSE will generate a seed for user\n");
927	>	painCave.isFatal = 0;
928	>	simError();
929	>
930	>	//using seed generated by system instead of invalid seed set by user
931	>	#ifndef IS_MPI
932	>	seedValue = make_sprng_seed();
933	>	#else
934	>	if (worldRank == 0){
935	>	seedValue = make_sprng_seed();
936		}
937	<	info.myAtoms[j]->setType( currentAtom->getType() );
937	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
938	>	#endif
939	>	}
940	>	}//end of if branch of globals->haveSeed()
941	>	else{
942
943	+	#ifndef IS_MPI
944	+	seedValue = make_sprng_seed();
945	+	#else
946	+	if (worldRank == 0){
947	+	seedValue = make_sprng_seed();
948	+	}
949	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
950	+	#endif
951	+	}//end of globals->haveSeed()
952	+
953	+	for (int i = 0; i < nInfo; i++){
954	+	info[i].setSeed(seedValue);
955	+	}
956	+
957		#ifdef IS_MPI
958	<
959	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
930	<
958	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
959	>	MPIcheckPoint();
960		#endif // is_mpi
961	<	}
933	<
934	<	// make the bonds
935	<	for(j=0; j<info.nBonds; j++){
936	<
937	<	currentBond = comp_stamps[stampID]->getBond( j );
938	<	theBonds[j].a = currentBond->getA() + atomOffset;
939	<	theBonds[j].b = currentBond->getB() + atomOffset;
961	>	}
962
941	–	exI = theBonds[j].a;
942	–	exJ = theBonds[j].b;
963
964	<	// exclude_I must always be the smaller of the pair
965	<	if( exI > exJ ){
966	<	tempEx = exI;
967	<	exI = exJ;
968	<	exJ = tempEx;
949	<	}
950	<	#ifdef IS_MPI
951	<	tempEx = exI;
952	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
953	<	tempEx = exJ;
954	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
955	<
956	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
957	<	#else  // isn't MPI
964	>	void SimSetup::finalInfoCheck(void){
965	>	int index;
966	>	int usesDipoles;
967	>	int usesCharges;
968	>	int i;
969
970	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
971	<	#endif  //is_mpi
970	>	for (i = 0; i < nInfo; i++){
971	>	// check electrostatic parameters
972	>
973	>	index = 0;
974	>	usesDipoles = 0;
975	>	while ((index < info[i].n_atoms) && !usesDipoles){
976	>	usesDipoles = (info[i].atoms[index])->hasDipole();
977	>	index++;
978		}
979	<	excludeOffset += info.nBonds;
979	>	index = 0;
980	>	usesCharges = 0;
981	>	while ((index < info[i].n_atoms) && !usesCharges){
982	>	usesCharges= (info[i].atoms[index])->hasCharge();
983	>	index++;
984	>	}
985	>	#ifdef IS_MPI
986	>	int myUse = usesDipoles;
987	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
988	>	#endif //is_mpi
989
990	<	//make the bends
991	<	for(j=0; j<info.nBends; j++){
992	<
993	<	currentBend = comp_stamps[stampID]->getBend( j );
994	<	theBends[j].a = currentBend->getA() + atomOffset;
995	<	theBends[j].b = currentBend->getB() + atomOffset;
996	<	theBends[j].c = currentBend->getC() + atomOffset;
997	<
998	<	if( currentBend->haveExtras() ){
999	<
1000	<	extras = currentBend->getExtras();
1001	<	current_extra = extras;
1002	<
977	<	while( current_extra != NULL ){
978	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
979	<
980	<	switch( current_extra->getType() ){
981	<
982	<	case 0:
983	<	theBends[j].ghost =
984	<	current_extra->getInt() + atomOffset;
985	<	theBends[j].isGhost = 1;
986	<	break;
987	<
988	<	case 1:
989	<	theBends[j].ghost =
990	<	(int)current_extra->getDouble() + atomOffset;
991	<	theBends[j].isGhost = 1;
992	<	break;
993	<
994	<	default:
995	<	sprintf( painCave.errMsg,
996	<	"SimSetup Error: ghostVectorSource was neither a "
997	<	"double nor an int.\n"
998	<	"-->Bend[%d] in %s\n",
999	<	j, comp_stamps[stampID]->getID() );
1000	<	painCave.isFatal = 1;
1001	<	simError();
1002	<	}
1003	<	}
1004	<
1005	<	else{
1006	<
1007	<	sprintf( painCave.errMsg,
1008	<	"SimSetup Error: unhandled bend assignment:\n"
1009	<	"    -->%s in Bend[%d] in %s\n",
1010	<	current_extra->getlhs(),
1011	<	j, comp_stamps[stampID]->getID() );
1012	<	painCave.isFatal = 1;
1013	<	simError();
1014	<	}
1015	<
1016	<	current_extra = current_extra->getNext();
1017	<	}
990	>	double theEcr, theEst;
991	>
992	>	if (globals->getUseRF()){
993	>	info[i].useReactionField = 1;
994	>
995	>	if (!globals->haveECR()){
996	>	sprintf(painCave.errMsg,
997	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
998	>	"\tOOPSE will use a default value of 15.0 angstroms"
999	>	"\tfor the electrostaticCutoffRadius.\n");
1000	>	painCave.isFatal = 0;
1001	>	simError();
1002	>	theEcr = 15.0;
1003		}
1019	–
1020	–	if( !theBends[j].isGhost ){
1021	–
1022	–	exI = theBends[j].a;
1023	–	exJ = theBends[j].c;
1024	–	}
1004		else{
1005	<
1027	<	exI = theBends[j].a;
1028	<	exJ = theBends[j].b;
1005	>	theEcr = globals->getECR();
1006		}
1007	<
1008	<	// exclude_I must always be the smaller of the pair
1009	<	if( exI > exJ ){
1010	<	tempEx = exI;
1011	<	exI = exJ;
1012	<	exJ = tempEx;
1007	>
1008	>	if (!globals->haveEST()){
1009	>	sprintf(painCave.errMsg,
1010	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1011	>	"\tOOPSE will use a default value of\n"
1012	>	"\t0.05 * electrostaticCutoffRadius\n"
1013	>	"\tfor the electrostaticSkinThickness\n");
1014	>	painCave.isFatal = 0;
1015	>	simError();
1016	>	theEst = 0.05 * theEcr;
1017		}
1018	<	#ifdef IS_MPI
1019	<	tempEx = exI;
1020	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1040	<	tempEx = exJ;
1041	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1042	<
1043	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1044	<	#else  // isn't MPI
1045	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1046	<	#endif  //is_mpi
1047	<	}
1048	<	excludeOffset += info.nBends;
1018	>	else{
1019	>	theEst = globals->getEST();
1020	>	}
1021
1022	<	for(j=0; j<info.nTorsions; j++){
1051	<
1052	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1053	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1054	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1055	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1056	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1057	<
1058	<	exI = theTorsions[j].a;
1059	<	exJ = theTorsions[j].d;
1022	>	info[i].setDefaultEcr(theEcr, theEst);
1023
1024	<	// exclude_I must always be the smaller of the pair
1025	<	if( exI > exJ ){
1026	<	tempEx = exI;
1027	<	exI = exJ;
1028	<	exJ = tempEx;
1024	>	if (!globals->haveDielectric()){
1025	>	sprintf(painCave.errMsg,
1026	>	"SimSetup Error: No Dielectric constant was set.\n"
1027	>	"\tYou are trying to use Reaction Field without"
1028	>	"\tsetting a dielectric constant!\n");
1029	>	painCave.isFatal = 1;
1030	>	simError();
1031		}
1032	<	#ifdef IS_MPI
1068	<	tempEx = exI;
1069	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1070	<	tempEx = exJ;
1071	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1072	<
1073	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1074	<	#else  // isn't MPI
1075	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1076	<	#endif  //is_mpi
1032	>	info[i].dielectric = globals->getDielectric();
1033		}
1034	<	excludeOffset += info.nTorsions;
1034	>	else{
1035	>	if (usesDipoles || usesCharges){
1036	>	if (!globals->haveECR()){
1037	>	sprintf(painCave.errMsg,
1038	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1039	>	"\tOOPSE will use a default value of 15.0 angstroms"
1040	>	"\tfor the electrostaticCutoffRadius.\n");
1041	>	painCave.isFatal = 0;
1042	>	simError();
1043	>	theEcr = 15.0;
1044	>	}
1045	>	else{
1046	>	theEcr = globals->getECR();
1047	>	}
1048	>
1049	>	if (!globals->haveEST()){
1050	>	sprintf(painCave.errMsg,
1051	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1052	>	"\tOOPSE will use a default value of\n"
1053	>	"\t0.05 * electrostaticCutoffRadius\n"
1054	>	"\tfor the electrostaticSkinThickness\n");
1055	>	painCave.isFatal = 0;
1056	>	simError();
1057	>	theEst = 0.05 * theEcr;
1058	>	}
1059	>	else{
1060	>	theEst = globals->getEST();
1061	>	}
1062	>
1063	>	info[i].setDefaultEcr(theEcr, theEst);
1064	>	}
1065	>	}
1066	>	}
1067	>	#ifdef IS_MPI
1068	>	strcpy(checkPointMsg, "post processing checks out");
1069	>	MPIcheckPoint();
1070	>	#endif // is_mpi
1071	>	}
1072	>
1073	>	void SimSetup::initSystemCoords(void){
1074	>	int i;
1075
1076	<
1081	<	// send the arrays off to the forceField for init.
1076	>	char* inName;
1077
1078	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1084	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1085	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1086	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1078	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1079
1080	+	for (i = 0; i < info[0].n_atoms; i++)
1081	+	info[0].atoms[i]->setCoords();
1082
1083	<	the_molecules[i].initialize( info );
1083	>	if (globals->haveInitialConfig()){
1084	>	InitializeFromFile* fileInit;
1085	>	#ifdef IS_MPI // is_mpi
1086	>	if (worldRank == 0){
1087	>	#endif //is_mpi
1088	>	inName = globals->getInitialConfig();
1089	>	fileInit = new InitializeFromFile(inName);
1090	>	#ifdef IS_MPI
1091	>	}
1092	>	else
1093	>	fileInit = new InitializeFromFile(NULL);
1094	>	#endif
1095	>	fileInit->readInit(info); // default velocities on
1096
1097	<
1092	<	atomOffset += info.nAtoms;
1093	<	delete[] theBonds;
1094	<	delete[] theBends;
1095	<	delete[] theTorsions;
1097	>	delete fileInit;
1098		}
1099	+	else{
1100	+
1101	+	// no init from bass
1102	+
1103	+	sprintf(painCave.errMsg,
1104	+	"Cannot intialize a simulation without an initial configuration file.\n");
1105	+	painCave.isFatal = 1;;
1106	+	simError();
1107	+
1108	+	}
1109
1110		#ifdef IS_MPI
1111	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1111	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1112		MPIcheckPoint();
1113		#endif // is_mpi
1114	+	}
1115
1103	–	// clean up the forcefield
1104	–	the_ff->calcRcut();
1105	–	the_ff->cleanMe();
1116
1117	<	}
1117	>	void SimSetup::makeOutNames(void){
1118	>	int k;
1119
1109	–	void SimSetup::initFromBass( void ){
1120
1121	<	int i, j, k;
1122	<	int n_cells;
1123	<	double cellx, celly, cellz;
1124	<	double temp1, temp2, temp3;
1115	<	int n_per_extra;
1116	<	int n_extra;
1117	<	int have_extra, done;
1121	>	for (k = 0; k < nInfo; k++){
1122	>	#ifdef IS_MPI
1123	>	if (worldRank == 0){
1124	>	#endif // is_mpi
1125
1126	<	temp1 = (double)tot_nmol / 4.0;
1127	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1128	<	temp3 = ceil( temp2 );
1126	>	if (globals->haveFinalConfig()){
1127	>	strcpy(info[k].finalName, globals->getFinalConfig());
1128	>	}
1129	>	else{
1130	>	strcpy(info[k].finalName, inFileName);
1131	>	char* endTest;
1132	>	int nameLength = strlen(info[k].finalName);
1133	>	endTest = &(info[k].finalName[nameLength - 5]);
1134	>	if (!strcmp(endTest, ".bass")){
1135	>	strcpy(endTest, ".eor");
1136	>	}
1137	>	else if (!strcmp(endTest, ".BASS")){
1138	>	strcpy(endTest, ".eor");
1139	>	}
1140	>	else{
1141	>	endTest = &(info[k].finalName[nameLength - 4]);
1142	>	if (!strcmp(endTest, ".bss")){
1143	>	strcpy(endTest, ".eor");
1144	>	}
1145	>	else if (!strcmp(endTest, ".mdl")){
1146	>	strcpy(endTest, ".eor");
1147	>	}
1148	>	else{
1149	>	strcat(info[k].finalName, ".eor");
1150	>	}
1151	>	}
1152	>	}
1153
1154	<	have_extra =0;
1124	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1125	<	have_extra =1;
1154	>	// make the sample and status out names
1155
1156	<	n_cells = (int)temp3 - 1;
1157	<	cellx = simnfo->boxLx / temp3;
1158	<	celly = simnfo->boxLy / temp3;
1159	<	cellz = simnfo->boxLz / temp3;
1160	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1161	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1162	<	n_per_extra = (int)ceil( temp1 );
1156	>	strcpy(info[k].sampleName, inFileName);
1157	>	char* endTest;
1158	>	int nameLength = strlen(info[k].sampleName);
1159	>	endTest = &(info[k].sampleName[nameLength - 5]);
1160	>	if (!strcmp(endTest, ".bass")){
1161	>	strcpy(endTest, ".dump");
1162	>	}
1163	>	else if (!strcmp(endTest, ".BASS")){
1164	>	strcpy(endTest, ".dump");
1165	>	}
1166	>	else{
1167	>	endTest = &(info[k].sampleName[nameLength - 4]);
1168	>	if (!strcmp(endTest, ".bss")){
1169	>	strcpy(endTest, ".dump");
1170	>	}
1171	>	else if (!strcmp(endTest, ".mdl")){
1172	>	strcpy(endTest, ".dump");
1173	>	}
1174	>	else{
1175	>	strcat(info[k].sampleName, ".dump");
1176	>	}
1177	>	}
1178
1179	<	if( n_per_extra > 4){
1180	<	sprintf( painCave.errMsg,
1181	<	"SimSetup error. There has been an error in constructing"
1182	<	" the non-complete lattice.\n" );
1183	<	painCave.isFatal = 1;
1184	<	simError();
1179	>	strcpy(info[k].statusName, inFileName);
1180	>	nameLength = strlen(info[k].statusName);
1181	>	endTest = &(info[k].statusName[nameLength - 5]);
1182	>	if (!strcmp(endTest, ".bass")){
1183	>	strcpy(endTest, ".stat");
1184	>	}
1185	>	else if (!strcmp(endTest, ".BASS")){
1186	>	strcpy(endTest, ".stat");
1187	>	}
1188	>	else{
1189	>	endTest = &(info[k].statusName[nameLength - 4]);
1190	>	if (!strcmp(endTest, ".bss")){
1191	>	strcpy(endTest, ".stat");
1192	>	}
1193	>	else if (!strcmp(endTest, ".mdl")){
1194	>	strcpy(endTest, ".stat");
1195	>	}
1196	>	else{
1197	>	strcat(info[k].statusName, ".stat");
1198	>	}
1199	>	}
1200	>
1201	>	#ifdef IS_MPI
1202	>
1203		}
1204	+	#endif // is_mpi
1205		}
1206	<	else{
1207	<	n_cells = (int)temp3;
1208	<	cellx = simnfo->boxLx / temp3;
1209	<	celly = simnfo->boxLy / temp3;
1210	<	cellz = simnfo->boxLz / temp3;
1206	>	}
1207	>
1208	>
1209	>	void SimSetup::sysObjectsCreation(void){
1210	>	int i, k;
1211	>
1212	>	// create the forceField
1213	>
1214	>	createFF();
1215	>
1216	>	// extract componentList
1217	>
1218	>	compList();
1219	>
1220	>	// calc the number of atoms, bond, bends, and torsions
1221	>
1222	>	calcSysValues();
1223	>
1224	>	#ifdef IS_MPI
1225	>	// divide the molecules among the processors
1226	>
1227	>	mpiMolDivide();
1228	>	#endif //is_mpi
1229	>
1230	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1231	>
1232	>	makeSysArrays();
1233	>
1234	>	// make and initialize the molecules (all but atomic coordinates)
1235	>
1236	>	makeMolecules();
1237	>
1238	>	for (k = 0; k < nInfo; k++){
1239	>	info[k].identArray = new int[info[k].n_atoms];
1240	>	for (i = 0; i < info[k].n_atoms; i++){
1241	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1242	>	}
1243		}
1244	+	}
1245
1150	–	current_mol = 0;
1151	–	current_comp_mol = 0;
1152	–	current_comp = 0;
1153	–	current_atom_ndx = 0;
1246
1247	<	for( i=0; i < n_cells ; i++ ){
1248	<	for( j=0; j < n_cells; j++ ){
1249	<	for( k=0; k < n_cells; k++ ){
1247	>	void SimSetup::createFF(void){
1248	>	switch (ffCase){
1249	>	case FF_DUFF:
1250	>	the_ff = new DUFF();
1251	>	break;
1252
1253	<	makeElement( i * cellx,
1254	<	j * celly,
1255	<	k * cellz );
1253	>	case FF_LJ:
1254	>	the_ff = new LJFF();
1255	>	break;
1256
1257	<	makeElement( i * cellx + 0.5 * cellx,
1258	<	j * celly + 0.5 * celly,
1259	<	k * cellz );
1257	>	case FF_EAM:
1258	>	the_ff = new EAM_FF();
1259	>	break;
1260
1261	<	makeElement( i * cellx,
1262	<	j * celly + 0.5 * celly,
1263	<	k * cellz + 0.5 * cellz );
1261	>	case FF_H2O:
1262	>	the_ff = new WATER();
1263	>	break;
1264
1265	<	makeElement( i * cellx + 0.5 * cellx,
1266	<	j * celly,
1267	<	k * cellz + 0.5 * cellz );
1265	>	default:
1266	>	sprintf(painCave.errMsg,
1267	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1268	>	painCave.isFatal = 1;
1269	>	simError();
1270	>	}
1271	>
1272	>	#ifdef IS_MPI
1273	>	strcpy(checkPointMsg, "ForceField creation successful");
1274	>	MPIcheckPoint();
1275	>	#endif // is_mpi
1276	>	}
1277	>
1278	>
1279	>	void SimSetup::compList(void){
1280	>	int i;
1281	>	char* id;
1282	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1283	>	LinkedMolStamp* currentStamp = NULL;
1284	>	comp_stamps = new MoleculeStamp * [n_components];
1285	>
1286	>	// make an array of molecule stamps that match the components used.
1287	>	// also extract the used stamps out into a separate linked list
1288	>
1289	>	for (i = 0; i < nInfo; i++){
1290	>	info[i].nComponents = n_components;
1291	>	info[i].componentsNmol = components_nmol;
1292	>	info[i].compStamps = comp_stamps;
1293	>	info[i].headStamp = headStamp;
1294	>	}
1295	>
1296	>
1297	>	for (i = 0; i < n_components; i++){
1298	>	id = the_components[i]->getType();
1299	>	comp_stamps[i] = NULL;
1300	>
1301	>	// check to make sure the component isn't already in the list
1302	>
1303	>	comp_stamps[i] = headStamp->match(id);
1304	>	if (comp_stamps[i] == NULL){
1305	>	// extract the component from the list;
1306	>
1307	>	currentStamp = stamps->extractMolStamp(id);
1308	>	if (currentStamp == NULL){
1309	>	sprintf(painCave.errMsg,
1310	>	"SimSetup error: Component \"%s\" was not found in the "
1311	>	"list of declared molecules\n",
1312	>	id);
1313	>	painCave.isFatal = 1;
1314	>	simError();
1315		}
1316	+
1317	+	headStamp->add(currentStamp);
1318	+	comp_stamps[i] = headStamp->match(id);
1319		}
1320		}
1321
1322	<	if( have_extra ){
1323	<	done = 0;
1322	>	#ifdef IS_MPI
1323	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1324	>	MPIcheckPoint();
1325	>	#endif // is_mpi
1326	>	}
1327
1328	<	int start_ndx;
1329	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1183	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1328	>	void SimSetup::calcSysValues(void){
1329	>	int i;
1330
1331	<	if( i < n_cells ){
1331	>	int* molMembershipArray;
1332
1333	<	if( j < n_cells ){
1334	<	start_ndx = n_cells;
1335	<	}
1336	<	else start_ndx = 0;
1337	<	}
1338	<	else start_ndx = 0;
1333	>	tot_atoms = 0;
1334	>	tot_bonds = 0;
1335	>	tot_bends = 0;
1336	>	tot_torsions = 0;
1337	>	tot_rigid = 0;
1338	>	for (i = 0; i < n_components; i++){
1339	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1340	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1341	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1342	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1343	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1344	>	}
1345	>
1346	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1347	>	molMembershipArray = new int[tot_atoms];
1348
1349	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1349	>	for (i = 0; i < nInfo; i++){
1350	>	info[i].n_atoms = tot_atoms;
1351	>	info[i].n_bonds = tot_bonds;
1352	>	info[i].n_bends = tot_bends;
1353	>	info[i].n_torsions = tot_torsions;
1354	>	info[i].n_SRI = tot_SRI;
1355	>	info[i].n_mol = tot_nmol;
1356
1357	<	makeElement( i * cellx,
1358	<	j * celly,
1359	<	k * cellz );
1199	<	done = ( current_mol >= tot_nmol );
1357	>	info[i].molMembershipArray = molMembershipArray;
1358	>	}
1359	>	}
1360
1361	<	if( !done && n_per_extra > 1 ){
1202	<	makeElement( i * cellx + 0.5 * cellx,
1203	<	j * celly + 0.5 * celly,
1204	<	k * cellz );
1205	<	done = ( current_mol >= tot_nmol );
1206	<	}
1361	>	#ifdef IS_MPI
1362
1363	<	if( !done && n_per_extra > 2){
1364	<	makeElement( i * cellx,
1365	<	j * celly + 0.5 * celly,
1366	<	k * cellz + 0.5 * cellz );
1367	<	done = ( current_mol >= tot_nmol );
1368	<	}
1363	>	void SimSetup::mpiMolDivide(void){
1364	>	int i, j, k;
1365	>	int localMol, allMol;
1366	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1367	>	int local_rigid;
1368	>	vector<int> globalAtomIndex;
1369	>	vector<int> globalMolIndex;
1370
1371	<	if( !done && n_per_extra > 3){
1372	<	makeElement( i * cellx + 0.5 * cellx,
1373	<	j * celly,
1374	<	k * cellz + 0.5 * cellz );
1375	<	done = ( current_mol >= tot_nmol );
1376	<	}
1377	<	}
1371	>	mpiSim = new mpiSimulation(info);
1372	>
1373	>	mpiSim->divideLabor();
1374	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1375	>	globalMolIndex = mpiSim->getGlobalMolIndex();
1376	>
1377	>	// set up the local variables
1378	>
1379	>	mol2proc = mpiSim->getMolToProcMap();
1380	>	molCompType = mpiSim->getMolComponentType();
1381	>
1382	>	allMol = 0;
1383	>	localMol = 0;
1384	>	local_atoms = 0;
1385	>	local_bonds = 0;
1386	>	local_bends = 0;
1387	>	local_torsions = 0;
1388	>	local_rigid = 0;
1389	>	globalAtomCounter = 0;
1390	>
1391	>	for (i = 0; i < n_components; i++){
1392	>	for (j = 0; j < components_nmol[i]; j++){
1393	>	if (mol2proc[allMol] == worldRank){
1394	>	local_atoms += comp_stamps[i]->getNAtoms();
1395	>	local_bonds += comp_stamps[i]->getNBonds();
1396	>	local_bends += comp_stamps[i]->getNBends();
1397	>	local_torsions += comp_stamps[i]->getNTorsions();
1398	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1399	>	localMol++;
1400	>	}
1401	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1402	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1403	>	globalAtomCounter++;
1404		}
1405	+
1406	+	allMol++;
1407		}
1408		}
1409	+	local_SRI = local_bonds + local_bends + local_torsions;
1410
1411	+	info[0].n_atoms = mpiSim->getMyNlocal();
1412	+
1413
1414	<	for( i=0; i<simnfo->n_atoms; i++ ){
1415	<	simnfo->atoms[i]->set_vx( 0.0 );
1416	<	simnfo->atoms[i]->set_vy( 0.0 );
1417	<	simnfo->atoms[i]->set_vz( 0.0 );
1414	>	if (local_atoms != info[0].n_atoms){
1415	>	sprintf(painCave.errMsg,
1416	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1417	>	"\tlocalAtom (%d) are not equal.\n",
1418	>	info[0].n_atoms, local_atoms);
1419	>	painCave.isFatal = 1;
1420	>	simError();
1421		}
1422	+
1423	+	info[0].n_bonds = local_bonds;
1424	+	info[0].n_bends = local_bends;
1425	+	info[0].n_torsions = local_torsions;
1426	+	info[0].n_SRI = local_SRI;
1427	+	info[0].n_mol = localMol;
1428	+
1429	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1430	+	MPIcheckPoint();
1431		}
1432
1433	<	void SimSetup::makeElement( double x, double y, double z ){
1433	>	#endif // is_mpi
1434
1236	–	int k;
1237	–	AtomStamp* current_atom;
1238	–	DirectionalAtom* dAtom;
1239	–	double rotMat[3][3];
1435
1436	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1436	>	void SimSetup::makeSysArrays(void){
1437	>
1438	>	#ifndef IS_MPI
1439	>	int k, j;
1440	>	#endif // is_mpi
1441	>	int i, l;
1442
1443	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1444	<	if( !current_atom->havePosition() ){
1245	<	sprintf( painCave.errMsg,
1246	<	"SimSetup:initFromBass error.\n"
1247	<	"\tComponent %s, atom %s does not have a position specified.\n"
1248	<	"\tThe initialization routine is unable to give a start"
1249	<	" position.\n",
1250	<	comp_stamps[current_comp]->getID(),
1251	<	current_atom->getType() );
1252	<	painCave.isFatal = 1;
1253	<	simError();
1254	<	}
1443	>	Atom** the_atoms;
1444	>	Molecule* the_molecules;
1445
1446	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1447	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1258	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1446	>	for (l = 0; l < nInfo; l++){
1447	>	// create the atom and short range interaction arrays
1448
1449	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1449	>	the_atoms = new Atom * [info[l].n_atoms];
1450	>	the_molecules = new Molecule[info[l].n_mol];
1451	>	int molIndex;
1452
1453	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1453	>	// initialize the molecule's stampID's
1454
1455	<	rotMat[0][0] = 1.0;
1265	<	rotMat[0][1] = 0.0;
1266	<	rotMat[0][2] = 0.0;
1455	>	#ifdef IS_MPI
1456
1268	–	rotMat[1][0] = 0.0;
1269	–	rotMat[1][1] = 1.0;
1270	–	rotMat[1][2] = 0.0;
1457
1458	<	rotMat[2][0] = 0.0;
1459	<	rotMat[2][1] = 0.0;
1460	<	rotMat[2][2] = 1.0;
1458	>	molIndex = 0;
1459	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1460	>	if (mol2proc[i] == worldRank){
1461	>	the_molecules[molIndex].setStampID(molCompType[i]);
1462	>	the_molecules[molIndex].setMyIndex(molIndex);
1463	>	the_molecules[molIndex].setGlobalIndex(i);
1464	>	molIndex++;
1465	>	}
1466	>	}
1467
1468	<	dAtom->setA( rotMat );
1468	>	#else // is_mpi
1469	>
1470	>	molIndex = 0;
1471	>	globalAtomCounter = 0;
1472	>	for (i = 0; i < n_components; i++){
1473	>	for (j = 0; j < components_nmol[i]; j++){
1474	>	the_molecules[molIndex].setStampID(i);
1475	>	the_molecules[molIndex].setMyIndex(molIndex);
1476	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1477	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1478	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1479	>	globalAtomCounter++;
1480	>	}
1481	>	molIndex++;
1482	>	}
1483		}
1484
1279	–	current_atom_ndx++;
1280	–	}
1485
1486	<	current_mol++;
1283	<	current_comp_mol++;
1486	>	#endif // is_mpi
1487
1488	<	if( current_comp_mol >= components_nmol[current_comp] ){
1488	>	info[l].globalExcludes = new int;
1489	>	info[l].globalExcludes[0] = 0;
1490	>
1491	>	// set the arrays into the SimInfo object
1492
1493	<	current_comp_mol = 0;
1494	<	current_comp++;
1493	>	info[l].atoms = the_atoms;
1494	>	info[l].molecules = the_molecules;
1495	>	info[l].nGlobalExcludes = 0;
1496	>
1497	>	the_ff->setSimInfo(info);
1498		}
1499		}
1500	+
1501	+	void SimSetup::makeIntegrator(void){
1502	+	int k;
1503	+
1504	+	NVE<RealIntegrator>* myNVE = NULL;
1505	+	NVT<RealIntegrator>* myNVT = NULL;
1506	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1507	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1508	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1509	+
1510	+	for (k = 0; k < nInfo; k++){
1511	+	switch (ensembleCase){
1512	+	case NVE_ENS:
1513	+	if (globals->haveZconstraints()){
1514	+	setupZConstraint(info[k]);
1515	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1516	+	}
1517	+	else{
1518	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1519	+	}
1520	+
1521	+	info->the_integrator = myNVE;
1522	+	break;
1523	+
1524	+	case NVT_ENS:
1525	+	if (globals->haveZconstraints()){
1526	+	setupZConstraint(info[k]);
1527	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1528	+	}
1529	+	else
1530	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1531	+
1532	+	myNVT->setTargetTemp(globals->getTargetTemp());
1533	+
1534	+	if (globals->haveTauThermostat())
1535	+	myNVT->setTauThermostat(globals->getTauThermostat());
1536	+	else{
1537	+	sprintf(painCave.errMsg,
1538	+	"SimSetup error: If you use the NVT\n"
1539	+	"\tensemble, you must set tauThermostat.\n");
1540	+	painCave.isFatal = 1;
1541	+	simError();
1542	+	}
1543	+
1544	+	info->the_integrator = myNVT;
1545	+	break;
1546	+
1547	+	case NPTi_ENS:
1548	+	if (globals->haveZconstraints()){
1549	+	setupZConstraint(info[k]);
1550	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1551	+	}
1552	+	else
1553	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1554	+
1555	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1556	+
1557	+	if (globals->haveTargetPressure())
1558	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1559	+	else{
1560	+	sprintf(painCave.errMsg,
1561	+	"SimSetup error: If you use a constant pressure\n"
1562	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1563	+	painCave.isFatal = 1;
1564	+	simError();
1565	+	}
1566	+
1567	+	if (globals->haveTauThermostat())
1568	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1569	+	else{
1570	+	sprintf(painCave.errMsg,
1571	+	"SimSetup error: If you use an NPT\n"
1572	+	"\tensemble, you must set tauThermostat.\n");
1573	+	painCave.isFatal = 1;
1574	+	simError();
1575	+	}
1576	+
1577	+	if (globals->haveTauBarostat())
1578	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1579	+	else{
1580	+	sprintf(painCave.errMsg,
1581	+	"SimSetup error: If you use an NPT\n"
1582	+	"\tensemble, you must set tauBarostat.\n");
1583	+	painCave.isFatal = 1;
1584	+	simError();
1585	+	}
1586	+
1587	+	info->the_integrator = myNPTi;
1588	+	break;
1589	+
1590	+	case NPTf_ENS:
1591	+	if (globals->haveZconstraints()){
1592	+	setupZConstraint(info[k]);
1593	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1594	+	}
1595	+	else
1596	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1597	+
1598	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1599	+
1600	+	if (globals->haveTargetPressure())
1601	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1602	+	else{
1603	+	sprintf(painCave.errMsg,
1604	+	"SimSetup error: If you use a constant pressure\n"
1605	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1606	+	painCave.isFatal = 1;
1607	+	simError();
1608	+	}
1609	+
1610	+	if (globals->haveTauThermostat())
1611	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1612	+
1613	+	else{
1614	+	sprintf(painCave.errMsg,
1615	+	"SimSetup error: If you use an NPT\n"
1616	+	"\tensemble, you must set tauThermostat.\n");
1617	+	painCave.isFatal = 1;
1618	+	simError();
1619	+	}
1620	+
1621	+	if (globals->haveTauBarostat())
1622	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1623	+
1624	+	else{
1625	+	sprintf(painCave.errMsg,
1626	+	"SimSetup error: If you use an NPT\n"
1627	+	"\tensemble, you must set tauBarostat.\n");
1628	+	painCave.isFatal = 1;
1629	+	simError();
1630	+	}
1631	+
1632	+	info->the_integrator = myNPTf;
1633	+	break;
1634	+
1635	+	case NPTxyz_ENS:
1636	+	if (globals->haveZconstraints()){
1637	+	setupZConstraint(info[k]);
1638	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1639	+	}
1640	+	else
1641	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1642	+
1643	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1644	+
1645	+	if (globals->haveTargetPressure())
1646	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1647	+	else{
1648	+	sprintf(painCave.errMsg,
1649	+	"SimSetup error: If you use a constant pressure\n"
1650	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1651	+	painCave.isFatal = 1;
1652	+	simError();
1653	+	}
1654	+
1655	+	if (globals->haveTauThermostat())
1656	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1657	+	else{
1658	+	sprintf(painCave.errMsg,
1659	+	"SimSetup error: If you use an NPT\n"
1660	+	"\tensemble, you must set tauThermostat.\n");
1661	+	painCave.isFatal = 1;
1662	+	simError();
1663	+	}
1664	+
1665	+	if (globals->haveTauBarostat())
1666	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1667	+	else{
1668	+	sprintf(painCave.errMsg,
1669	+	"SimSetup error: If you use an NPT\n"
1670	+	"\tensemble, you must set tauBarostat.\n");
1671	+	painCave.isFatal = 1;
1672	+	simError();
1673	+	}
1674	+
1675	+	info->the_integrator = myNPTxyz;
1676	+	break;
1677	+
1678	+	default:
1679	+	sprintf(painCave.errMsg,
1680	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1681	+	painCave.isFatal = 1;
1682	+	simError();
1683	+	}
1684	+	}
1685	+	}
1686	+
1687	+	void SimSetup::initFortran(void){
1688	+	info[0].refreshSim();
1689	+
1690	+	if (!strcmp(info[0].mixingRule, "standard")){
1691	+	the_ff->initForceField(LB_MIXING_RULE);
1692	+	}
1693	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1694	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1695	+	}
1696	+	else{
1697	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1698	+	info[0].mixingRule);
1699	+	painCave.isFatal = 1;
1700	+	simError();
1701	+	}
1702	+
1703	+
1704	+	#ifdef IS_MPI
1705	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1706	+	MPIcheckPoint();
1707	+	#endif // is_mpi
1708	+	}
1709	+
1710	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1711	+	int nZConstraints;
1712	+	ZconStamp** zconStamp;
1713	+
1714	+	if (globals->haveZconstraintTime()){
1715	+	//add sample time of z-constraint  into SimInfo's property list
1716	+	DoubleData* zconsTimeProp = new DoubleData();
1717	+	zconsTimeProp->setID(ZCONSTIME_ID);
1718	+	zconsTimeProp->setData(globals->getZconsTime());
1719	+	theInfo.addProperty(zconsTimeProp);
1720	+	}
1721	+	else{
1722	+	sprintf(painCave.errMsg,
1723	+	"ZConstraint error: If you use a ZConstraint,\n"
1724	+	"\tyou must set zconsTime.\n");
1725	+	painCave.isFatal = 1;
1726	+	simError();
1727	+	}
1728	+
1729	+	//push zconsTol into siminfo, if user does not specify
1730	+	//value for zconsTol, a default value will be used
1731	+	DoubleData* zconsTol = new DoubleData();
1732	+	zconsTol->setID(ZCONSTOL_ID);
1733	+	if (globals->haveZconsTol()){
1734	+	zconsTol->setData(globals->getZconsTol());
1735	+	}
1736	+	else{
1737	+	double defaultZConsTol = 0.01;
1738	+	sprintf(painCave.errMsg,
1739	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1740	+	"\tOOPSE will use a default value of %f.\n"
1741	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1742	+	defaultZConsTol);
1743	+	painCave.isFatal = 0;
1744	+	simError();
1745	+
1746	+	zconsTol->setData(defaultZConsTol);
1747	+	}
1748	+	theInfo.addProperty(zconsTol);
1749	+
1750	+	//set Force Subtraction Policy
1751	+	StringData* zconsForcePolicy = new StringData();
1752	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1753	+
1754	+	if (globals->haveZconsForcePolicy()){
1755	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1756	+	}
1757	+	else{
1758	+	sprintf(painCave.errMsg,
1759	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1760	+	"\tOOPSE will use PolicyByMass.\n"
1761	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1762	+	painCave.isFatal = 0;
1763	+	simError();
1764	+	zconsForcePolicy->setData("BYMASS");
1765	+	}
1766	+
1767	+	theInfo.addProperty(zconsForcePolicy);
1768	+
1769	+	//set zcons gap
1770	+	DoubleData* zconsGap = new DoubleData();
1771	+	zconsGap->setID(ZCONSGAP_ID);
1772	+
1773	+	if (globals->haveZConsGap()){
1774	+	zconsGap->setData(globals->getZconsGap());
1775	+	theInfo.addProperty(zconsGap);
1776	+	}
1777	+
1778	+	//set zcons fixtime
1779	+	DoubleData* zconsFixtime = new DoubleData();
1780	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1781	+
1782	+	if (globals->haveZConsFixTime()){
1783	+	zconsFixtime->setData(globals->getZconsFixtime());
1784	+	theInfo.addProperty(zconsFixtime);
1785	+	}
1786	+
1787	+	//set zconsUsingSMD
1788	+	IntData* zconsUsingSMD = new IntData();
1789	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1790	+
1791	+	if (globals->haveZConsUsingSMD()){
1792	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1793	+	theInfo.addProperty(zconsUsingSMD);
1794	+	}
1795	+
1796	+	//Determine the name of ouput file and add it into SimInfo's property list
1797	+	//Be careful, do not use inFileName, since it is a pointer which
1798	+	//point to a string at master node, and slave nodes do not contain that string
1799	+
1800	+	string zconsOutput(theInfo.finalName);
1801	+
1802	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1803	+
1804	+	StringData* zconsFilename = new StringData();
1805	+	zconsFilename->setID(ZCONSFILENAME_ID);
1806	+	zconsFilename->setData(zconsOutput);
1807	+
1808	+	theInfo.addProperty(zconsFilename);
1809	+
1810	+	//setup index, pos and other parameters of z-constraint molecules
1811	+	nZConstraints = globals->getNzConstraints();
1812	+	theInfo.nZconstraints = nZConstraints;
1813	+
1814	+	zconStamp = globals->getZconStamp();
1815	+	ZConsParaItem tempParaItem;
1816	+
1817	+	ZConsParaData* zconsParaData = new ZConsParaData();
1818	+	zconsParaData->setID(ZCONSPARADATA_ID);
1819	+
1820	+	for (int i = 0; i < nZConstraints; i++){
1821	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1822	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1823	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1824	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1825	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1826	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1827	+	zconsParaData->addItem(tempParaItem);
1828	+	}
1829	+
1830	+	//check the uniqueness of index
1831	+	if(!zconsParaData->isIndexUnique()){
1832	+	sprintf(painCave.errMsg,
1833	+	"ZConstraint Error: molIndex is not unique!\n");
1834	+	painCave.isFatal = 1;
1835	+	simError();
1836	+	}
1837	+
1838	+	//sort the parameters by index of molecules
1839	+	zconsParaData->sortByIndex();
1840	+
1841	+	//push data into siminfo, therefore, we can retrieve later
1842	+	theInfo.addProperty(zconsParaData);
1843	+	}
1844	+
1845	+	void SimSetup::makeMinimizer(){
1846	+
1847	+	OOPSEMinimizer* myOOPSEMinimizer;
1848	+	MinimizerParameterSet* param;
1849	+	char minimizerName[100];
1850	+
1851	+	for (int i = 0; i < nInfo; i++){
1852	+
1853	+	//prepare parameter set for minimizer
1854	+	param = new MinimizerParameterSet();
1855	+	param->setDefaultParameter();
1856	+
1857	+	if (globals->haveMinimizer()){
1858	+	param->setFTol(globals->getMinFTol());
1859	+	}
1860	+
1861	+	if (globals->haveMinGTol()){
1862	+	param->setGTol(globals->getMinGTol());
1863	+	}
1864	+
1865	+	if (globals->haveMinMaxIter()){
1866	+	param->setMaxIteration(globals->getMinMaxIter());
1867	+	}
1868	+
1869	+	if (globals->haveMinWriteFrq()){
1870	+	param->setMaxIteration(globals->getMinMaxIter());
1871	+	}
1872	+
1873	+	if (globals->haveMinWriteFrq()){
1874	+	param->setWriteFrq(globals->getMinWriteFrq());
1875	+	}
1876	+
1877	+	if (globals->haveMinStepSize()){
1878	+	param->setStepSize(globals->getMinStepSize());
1879	+	}
1880	+
1881	+	if (globals->haveMinLSMaxIter()){
1882	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1883	+	}
1884	+
1885	+	if (globals->haveMinLSTol()){
1886	+	param->setLineSearchTol(globals->getMinLSTol());
1887	+	}
1888	+
1889	+	strcpy(minimizerName, globals->getMinimizer());
1890	+
1891	+	if (!strcasecmp(minimizerName, "CG")){
1892	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1893	+	}
1894	+	else if (!strcasecmp(minimizerName, "SD")){
1895	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1896	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1897	+	}
1898	+	else{
1899	+	sprintf(painCave.errMsg,
1900	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1901	+	painCave.isFatal = 0;
1902	+	simError();
1903	+
1904	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1905	+	}
1906	+	info[i].the_integrator = myOOPSEMinimizer;
1907	+
1908	+	//store the minimizer into simInfo
1909	+	info[i].the_minimizer = myOOPSEMinimizer;
1910	+	info[i].has_minimizer = true;
1911	+	}
1912	+
1913	+	}

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