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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC vs.
Revision 1174 by gezelter, Wed May 12 20:54:10 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 NPT_ENS 2
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
21	–	#define FF_DUFF 0
22	–	#define FF_LJ   1
29
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 37 | 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();
69	<	mpiEventLoop();
70	<
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;
78	<	Globals* the_globals;
79	<	int i, j, k, globalAtomIndex;
80	<
81	<	int ensembleCase;
82	<	int ffCase;
83	<
84	<	ensembleCase = -1;
85	<	ffCase = -1;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
92	<	simnfo->target_temp = the_globals->getTargetTemp();
93	<	simnfo->dt = the_globals->getDt();
94	<	simnfo->run_time = the_globals->getRunTime();
130	>	// creation of complex system objects
131
132	<	// get the ones we know are there, yet still may need some work.
97	<	n_components = the_globals->getNComponents();
98	<	strcpy( force_field, the_globals->getForceField() );
132	>	sysObjectsCreation();
133
134	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
101	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102	<	else{
103	<	sprintf( painCave.errMsg,
104	<	"SimSetup Error. Unrecognized force field -> %s\n",
105	<	force_field );
106	<	painCave.isFatal = 1;
107	<	simError();
108	<	}
134	>	// check on the post processing info
135
136	<	// get the ensemble:
111	<	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, "NPT" )) ensembleCase = NPT_ENS;
141	<	else{
142	<	sprintf( painCave.errMsg,
143	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
144	<	"reverting to NVE for this simulation.\n",
120	<	ensemble );
121	<	painCave.isFatal = 0;
122	<	simError();
123	<	strcpy( ensemble, "NVE" );
124	<	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		}
126	–	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());
134	<	//     else {
135	<	//       sprintf( painCave.errMsg,
136	<	//                "SimSetup error: If you use the constant pressure\n"
137	<	//                "    ensemble, you must set targetPressure.\n"
138	<	//                "    This was found in the BASS file.\n");
139	<	//       painCave.isFatal = 1;
140	<	//       simError();
141	<	//     }
149	>	makeOutNames();
150	>
151	>	#ifdef IS_MPI
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
155	>	// initialize the Fortran
156
157	<	//     if (the_globals->haveTauBarostat())
157	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158	<	//     else {
159	<	//       sprintf( painCave.errMsg,
160	<	//                "SimSetup error: If you use the constant pressure\n"
161	<	//                "    ensemble, you must set tauBarostat.\n"
162	<	//                "    This was found in the BASS file.\n");
163	<	//       painCave.isFatal = 1;
164	<	//       simError();
165	<	//     }
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())
172	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173	<	//     else if (the_globals->haveQmass())
174	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
175	<	//     else {
176	<	//       sprintf( painCave.errMsg,
177	<	//                "SimSetup error: If you use one of the constant temperature\n"
178	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
179	<	//                "    Neither of these was found in the BASS file.\n");
180	<	//       painCave.isFatal = 1;
181	<	//       simError();
182	<	//     }
166	>	}
167
184	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185	–	simnfo->usePBC = the_globals->getPBC();
186	–
187	–	int usesDipoles = 0;
188	–	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	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191	<	case FF_LJ:
192	<	the_ff = new LJFF();
193	<	break;
191	>	bond_pair* theBonds;
192	>	bend_set* theBends;
193	>	torsion_set* theTorsions;
194
195	<	default:
200	<	sprintf( painCave.errMsg,
201	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
195	>	set<int> skipList;
196
197	<	#ifdef IS_MPI
198	<	strcpy( checkPointMsg, "ForceField creation successful" );
199	<	MPIcheckPoint();
209	<	#endif // is_mpi
197	>	double phi, theta, psi;
198	>	char* molName;
199	>	char rbName[100];
200
201	<	// get the components and calculate the tot_nMol and indvidual n_mol
212	<	the_components = the_globals->getComponents();
213	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
201	>	//init the forceField paramters
202
203	<	if( !the_globals->haveNMol() ){
217	<	// we don't have the total number of molecules, so we assume it is
218	<	// given in each component
203	>	the_ff->readParams();
204
205	<	tot_nmol = 0;
221	<	for( i=0; i<n_components; i++ ){
205	>	// init the atoms
206
207	<	if( !the_components[i]->haveNMol() ){
208	<	// we have a problem
209	<	sprintf( painCave.errMsg,
210	<	"SimSetup Error. No global NMol or component NMol"
211	<	" given. Cannot calculate the number of atoms.\n" );
212	<	painCave.isFatal = 1;
213	<	simError();
214	<	}
207	>	int nMembers, nNew, rb1, rb2;
208	>
209	>	for (k = 0; k < nInfo; k++){
210	>	the_ff->setSimInfo(&(info[k]));
211	>
212	>	atomOffset = 0;
213	>
214	>	for (i = 0; i < info[k].n_mol; i++){
215	>	stampID = info[k].molecules[i].getStampID();
216	>	molName = comp_stamps[stampID]->getID();
217
218	<	tot_nmol += the_components[i]->getNMol();
219	<	components_nmol[i] = the_components[i]->getNMol();
220	<	}
221	<	}
222	<	else{
237	<	sprintf( painCave.errMsg,
238	<	"SimSetup error.\n"
239	<	"\tSorry, the ability to specify total"
240	<	" nMols and then give molfractions in the components\n"
241	<	"\tis not currently supported."
242	<	" Please give nMol in the components.\n" );
243	<	painCave.isFatal = 1;
244	<	simError();
245	<
246	<
247	<	//     tot_nmol = the_globals->getNMol();
248	<
249	<	//   //we have the total number of molecules, now we check for molfractions
250	<	//     for( i=0; i<n_components; i++ ){
251	<
252	<	//       if( !the_components[i]->haveMolFraction() ){
253	<
254	<	//  if( !the_components[i]->haveNMol() ){
255	<	//    //we have a problem
256	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	<	//              << " nMol was given in component
258	<
259	<	}
218	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
221	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223
224	<	#ifdef IS_MPI
225	<	strcpy( checkPointMsg, "Have the number of components" );
226	<	MPIcheckPoint();
264	<	#endif // is_mpi
224	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225	>
226	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
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.nBonds > 0)
229	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	>	else
231	>	molInfo.myBonds = NULL;
232
233	<	simnfo->nComponents = n_components;
234	<	simnfo->componentsNmol = components_nmol;
235	<	simnfo->compStamps = comp_stamps;
236	<	simnfo->headStamp = new LinkedMolStamp();
273	<
274	<	char* id;
275	<	LinkedMolStamp* headStamp = simnfo->headStamp;
276	<	LinkedMolStamp* currentStamp = NULL;
277	<	for( i=0; i<n_components; i++ ){
233	>	if (molInfo.nBends > 0)
234	>	molInfo.myBends = new Bend*[molInfo.nBends];
235	>	else
236	>	molInfo.myBends = NULL;
237
238	<	id = the_components[i]->getType();
239	<	comp_stamps[i] = NULL;
240	<
241	<	// check to make sure the component isn't already in the list
238	>	if (molInfo.nTorsions > 0)
239	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	>	else
241	>	molInfo.myTorsions = NULL;
242
243	<	comp_stamps[i] = headStamp->match( id );
244	<	if( comp_stamps[i] == NULL ){
243	>	theBonds = new bond_pair[molInfo.nBonds];
244	>	theBends = new bend_set[molInfo.nBends];
245	>	theTorsions = new torsion_set[molInfo.nTorsions];
246
247	<	// extract the component from the list;
288	<
289	<	currentStamp = the_stamps->extractMolStamp( id );
290	<	if( currentStamp == NULL ){
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup error: Component \"%s\" was not found in the "
293	<	"list of declared molecules\n",
294	<	id );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	headStamp->add( currentStamp );
300	<	comp_stamps[i] = headStamp->match( id );
301	<	}
302	<	}
247	>	// make the Atoms
248
249	<	#ifdef IS_MPI
250	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
306	<	MPIcheckPoint();
307	<	#endif // is_mpi
308	<
249	>	for (j = 0; j < molInfo.nAtoms; j++){
250	>	currentAtom = comp_stamps[stampID]->getAtom(j);
251
252	+	if (currentAtom->haveOrientation()){
253	+	dAtom = new DirectionalAtom((j + atomOffset),
254	+	info[k].getConfiguration());
255	+	info[k].n_oriented++;
256	+	molInfo.myAtoms[j] = dAtom;
257
258	+	// Directional Atoms have standard unit vectors which are oriented
259	+	// in space using the three Euler angles.  We assume the standard
260	+	// unit vector was originally along the z axis below.
261
262	<	// caclulate the number of atoms, bonds, bends and torsions
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265
266	<	tot_atoms = 0;
267	<	tot_bonds = 0;
268	<	tot_bends = 0;
269	<	tot_torsions = 0;
318	<	for( i=0; i<n_components; i++ ){
319	<
320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	<	}
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268	>	}
269	>	else{
270
271	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272
273	<	simnfo->n_atoms = tot_atoms;
329	<	simnfo->n_bonds = tot_bonds;
330	<	simnfo->n_bends = tot_bends;
331	<	simnfo->n_torsions = tot_torsions;
332	<	simnfo->n_SRI = tot_SRI;
333	<	simnfo->n_mol = tot_nmol;
334	<
335	<	simnfo->molMembershipArray = new int[tot_atoms];
273	>	}
274
275	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
277
278	<	// divide the molecules among processors here.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279
280	<	// set up the local variables
281	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
280	>	#endif // is_mpi
281	>	}
282
283	<	int* mol2proc = mpiSim->getMolToProcMap();
284	<	int* molCompType = mpiSim->getMolComponentType();
285	<
286	<	allMol = 0;
287	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
283	>	// make the bonds
284	>	for (j = 0; j < molInfo.nBonds; j++){
285	>	currentBond = comp_stamps[stampID]->getBond(j);
286	>	theBonds[j].a = currentBond->getA() + atomOffset;
287	>	theBonds[j].b = currentBond->getB() + atomOffset;
288
289	+	tempI = theBonds[j].a;
290	+	tempJ = theBonds[j].b;
291
292	<	for( i=0; i<n_components; i++ ){
292	>	#ifdef IS_MPI
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299
300	<	for( j=0; j<components_nmol[i]; j++ ){
365	<
366	<	if( mol2proc[allMol] == worldRank ){
367	<
368	<	local_atoms +=    comp_stamps[i]->getNAtoms();
369	<	local_bonds +=    comp_stamps[i]->getNBonds();
370	<	local_bends +=    comp_stamps[i]->getNBends();
371	<	local_torsions += comp_stamps[i]->getNTorsions();
372	<	localMol++;
373	<	}
374	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
300	>	info[k].excludes->addPair(exI, exJ);
301		}
302
303	<	allMol++;
304	<	}
305	<	}
306	<	local_SRI = local_bonds + local_bends + local_torsions;
307	<
308	<	simnfo->n_atoms = mpiSim->getMyNlocal();
385	<
386	<	if( local_atoms != simnfo->n_atoms ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
303	>	//make the bends
304	>	for (j = 0; j < molInfo.nBends; j++){
305	>	currentBend = comp_stamps[stampID]->getBend(j);
306	>	theBends[j].a = currentBend->getA() + atomOffset;
307	>	theBends[j].b = currentBend->getB() + atomOffset;
308	>	theBends[j].c = currentBend->getC() + atomOffset;
309
310	<	simnfo->n_bonds = local_bonds;
311	<	simnfo->n_bends = local_bends;
312	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
310	>	if (currentBend->haveExtras()){
311	>	extras = currentBend->getExtras();
312	>	current_extra = extras;
313
314	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
315	<	MPIcheckPoint();
316	<
317	<
318	<	#endif // is_mpi
319	<
314	>	while (current_extra != NULL){
315	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
316	>	switch (current_extra->getType()){
317	>	case 0:
318	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	// create the atom and short range interaction arrays
322	>	case 1:
323	>	theBends[j].ghost = (int) current_extra->getDouble() +
324	>	atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327
328	<	Atom::createArrays(simnfo->n_atoms);
329	<	the_atoms = new Atom*[simnfo->n_atoms];
330	<	the_molecules = new Molecule[simnfo->n_mol];
331	<	int molIndex;
332	<
333	<	// initialize the molecule's stampID's
328	>	default:
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: ghostVectorSource was neither a "
331	>	"double nor an int.\n"
332	>	"-->Bend[%d] in %s\n",
333	>	j, comp_stamps[stampID]->getID());
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338	>	else{
339	>	sprintf(painCave.errMsg,
340	>	"SimSetup Error: unhandled bend assignment:\n"
341	>	"    -->%s in Bend[%d] in %s\n",
342	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
343	>	painCave.isFatal = 1;
344	>	simError();
345	>	}
346
347	+	current_extra = current_extra->getNext();
348	+	}
349	+	}
350	+
351	+	if (theBends[j].isGhost) {
352	+
353	+	tempI = theBends[j].a;
354	+	tempJ = theBends[j].b;
355	+
356		#ifdef IS_MPI
357	<
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364
365	<	molIndex = 0;
422	<	for(i=0; i<mpiSim->getTotNmol(); i++){
423	<
424	<	if(mol2proc[i] == worldRank ){
425	<	the_molecules[molIndex].setStampID( molCompType[i] );
426	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
429	<	}
430	<	}
365	>	} else {
366
367	<	#else // is_mpi
368	<
369	<	molIndex = 0;
370	<	globalAtomIndex = 0;
371	<	for(i=0; i<n_components; i++){
372	<	for(j=0; j<components_nmol[i]; j++ ){
373	<	the_molecules[molIndex].setStampID( i );
374	<	the_molecules[molIndex].setMyIndex( molIndex );
375	<	the_molecules[molIndex].setGlobalIndex( molIndex );
376	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
377	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
378	<	globalAtomIndex++;
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371	>	#ifdef IS_MPI
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385		}
445	–	molIndex++;
446	–	}
447	–	}
448	–
386
387	<	#endif // is_mpi
387	>	for (j = 0; j < molInfo.nTorsions; j++){
388	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
389	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
390	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
391	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
392	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
393
394	+	tempI = theTorsions[j].a;
395	+	tempJ = theTorsions[j].b;
396	+	tempK = theTorsions[j].c;
397	+	tempL = theTorsions[j].d;
398
399	<	if( simnfo->n_SRI ){
400	<
401	<	Exclude::createArray(simnfo->n_SRI);
402	<	the_excludes = new Exclude*[simnfo->n_SRI];
403	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
404	<	simnfo->globalExcludes = new int;
405	<	simnfo->n_exclude = simnfo->n_SRI;
406	<	}
407	<	else{
408	<
409	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
399	>	#ifdef IS_MPI
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409	>	#endif
410
411	<	// set the arrays into the SimInfo object
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417	>	}
418
419	<	simnfo->atoms = the_atoms;
420	<	simnfo->molecules = the_molecules;
421	<	simnfo->nGlobalExcludes = 0;
422	<	simnfo->excludes = the_excludes;
419	>
420	>	molInfo.myRigidBodies.clear();
421	>
422	>	for (j = 0; j < molInfo.nRigidBodies; j++){
423
424	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	+	nMembers = currentRigidBody->getNMembers();
426
427	<	// get some of the tricky things that may still be in the globals
427	>	// Create the Rigid Body:
428
429	<	double boxVector[3];
483	<	if( the_globals->haveBox() ){
484	<	boxVector[0] = the_globals->getBox();
485	<	boxVector[1] = the_globals->getBox();
486	<	boxVector[2] = the_globals->getBox();
487	<
488	<	simnfo->setBox( boxVector );
489	<	}
490	<	else if( the_globals->haveDensity() ){
429	>	myRB = new RigidBody();
430
431	<	double vol;
432	<	vol = (double)tot_nmol / the_globals->getDensity();
433	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
434	<	boxVector[1] = boxVector[0];
496	<	boxVector[2] = boxVector[0];
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435
436	<	simnfo->setBox( boxVector );
437	<	}
500	<	else{
501	<	if( !the_globals->haveBoxX() ){
502	<	sprintf( painCave.errMsg,
503	<	"SimSetup error, no periodic BoxX size given.\n" );
504	<	painCave.isFatal = 1;
505	<	simError();
506	<	}
507	<	boxVector[0] = the_globals->getBoxX();
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438
439	<	if( !the_globals->haveBoxY() ){
440	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxY size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[1] = the_globals->getBoxY();
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441
442	<	if( !the_globals->haveBoxZ() ){
443	<	sprintf( painCave.errMsg,
444	<	"SimSetup error, no periodic BoxZ size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	boxVector[2] = the_globals->getBoxZ();
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445
446	<	simnfo->setBox( boxVector );
447	<	}
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448
449	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	+
451	+	// Add this atom to the Skip List for the integrators
452		#ifdef IS_MPI
453	<	strcpy( checkPointMsg, "Box size set up" );
454	<	MPIcheckPoint();
455	<	#endif // is_mpi
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472	>	#ifdef IS_MPI
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484
485	+	molInfo.myRigidBodies.push_back(myRB);
486	+	info[k].rigidBodies.push_back(myRB);
487	+	}
488	+
489
490	<	// initialize the arrays
490	>	//create cutoff group for molecule
491
492	<	the_ff->setSimInfo( simnfo );
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
495	>	for (j = 0; j < nCutoffGroups; j++){
496
497	<	makeMolecules();
498	<	simnfo->identArray = new int[simnfo->n_atoms];
540	<	for(i=0; i<simnfo->n_atoms; i++){
541	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
542	<	}
543	<
544	<	if (the_globals->getUseRF() ) {
545	<	simnfo->useReactionField = 1;
546	<
547	<	if( !the_globals->haveECR() ){
548	<	sprintf( painCave.errMsg,
549	<	"SimSetup Warning: using default value of 1/2 the smallest "
550	<	"box length for the electrostaticCutoffRadius.\n"
551	<	"I hope you have a very fast processor!\n");
552	<	painCave.isFatal = 0;
553	<	simError();
554	<	double smallest;
555	<	smallest = simnfo->boxLx;
556	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
557	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
558	<	simnfo->ecr = 0.5 * smallest;
559	<	} else {
560	<	simnfo->ecr        = the_globals->getECR();
561	<	}
497	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	>	nMembers = currentCutoffGroup->getNMembers();
499
500	<	if( !the_globals->haveEST() ){
501	<	sprintf( painCave.errMsg,
502	<	"SimSetup Warning: using default value of 0.05 * the "
503	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
504	<	);
505	<	painCave.isFatal = 0;
506	<	simError();
507	<	simnfo->est = 0.05 * simnfo->ecr;
508	<	} else {
509	<	simnfo->est        = the_globals->getEST();
510	<	}
511	<
512	<	if(!the_globals->haveDielectric() ){
513	<	sprintf( painCave.errMsg,
514	<	"SimSetup Error: You are trying to use Reaction Field without"
515	<	"setting a dielectric constant!\n"
516	<	);
517	<	painCave.isFatal = 1;
518	<	simError();
519	<	}
520	<	simnfo->dielectric = the_globals->getDielectric();
521	<	} else {
522	<	if (usesDipoles) {
523	<
524	<	if( !the_globals->haveECR() ){
525	<	sprintf( painCave.errMsg,
526	<	"SimSetup Warning: using default value of 1/2 the smallest "
527	<	"box length for the electrostaticCutoffRadius.\n"
591	<	"I hope you have a very fast processor!\n");
592	<	painCave.isFatal = 0;
593	<	simError();
594	<	double smallest;
595	<	smallest = simnfo->boxLx;
596	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
597	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
598	<	simnfo->ecr = 0.5 * smallest;
599	<	} else {
600	<	simnfo->ecr        = the_globals->getECR();
500	>	myCutoffGroup = new CutoffGroup();
501	>
502	>	for (int cg = 0; cg < nMembers; cg++) {
503	>
504	>	// molI is atom numbering inside this molecule
505	>	molI = currentCutoffGroup->getMember(cg);
506	>
507	>	// tempI is atom numbering on local processor
508	>	tempI = molI + atomOffset;
509	>
510	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511	>
512	>	cutoffAtomSet.insert(tempI);
513	>	}
514	>
515	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517	>
518	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519	>
520	>	for(j = 0; j < molInfo.nAtoms; j++){
521	>
522	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	>	myCutoffGroup = new CutoffGroup();
524	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	>	}
527	>
528		}
529	+
530	+
531	+
532	+
533	+	// After this is all set up, scan through the atoms to
534	+	// see if they can be added to the integrableObjects:
535	+
536	+	molInfo.myIntegrableObjects.clear();
537
603	–	if( !the_globals->haveEST() ){
604	–	sprintf( painCave.errMsg,
605	–	"SimSetup Warning: using default value of 5%% of the "
606	–	"electrostaticCutoffRadius for the "
607	–	"electrostaticSkinThickness\n"
608	–	);
609	–	painCave.isFatal = 0;
610	–	simError();
611	–	simnfo->est = 0.05 * simnfo->ecr;
612	–	} else {
613	–	simnfo->est        = the_globals->getEST();
614	–	}
615	–	}
616	–	}
538
539	<	#ifdef IS_MPI
619	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
620	<	MPIcheckPoint();
621	<	#endif // is_mpi
539	>	for (j = 0; j < molInfo.nAtoms; j++){
540
623	–	if( the_globals->haveInitialConfig() ){
624	–
625	–	InitializeFromFile* fileInit;
626	–	#ifdef IS_MPI // is_mpi
627	–	if( worldRank == 0 ){
628	–	#endif //is_mpi
629	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
541		#ifdef IS_MPI
542	<	}else fileInit = new InitializeFromFile( NULL );
542	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	>	#else
544	>	slJ = j+atomOffset;
545		#endif
633	–	fileInit->read_xyz( simnfo ); // default velocities on
546
547	<	delete fileInit;
636	<	}
637	<	else{
547	>	// if they aren't on the skip list, then they can be integrated
548
549	<	#ifdef IS_MPI
549	>	if (skipList.find(slJ) == skipList.end()) {
550	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	>	info[k].integrableObjects.push_back(mySD);
552	>	molInfo.myIntegrableObjects.push_back(mySD);
553	>	}
554	>	}
555
556	<	// no init from bass
642	<
643	<	sprintf( painCave.errMsg,
644	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
645	<	painCave.isFatal;
646	<	simError();
647	<
648	<	#else
556	>	// all rigid bodies are integrated:
557
558	<	initFromBass();
558	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	>	info[k].integrableObjects.push_back(mySD);
561	>	molInfo.myIntegrableObjects.push_back(mySD);
562	>	}
563	>
564	>
565	>	// send the arrays off to the forceField for init.
566	>
567	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571	>	theTorsions);
572
573	+	info[k].molecules[i].initialize(molInfo);
574
653	–	#endif
654	–	}
575
576	+	atomOffset += molInfo.nAtoms;
577	+	delete[] theBonds;
578	+	delete[] theBends;
579	+	delete[] theTorsions;
580	+	}
581	+	}
582	+
583		#ifdef IS_MPI
584	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
584	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
585		MPIcheckPoint();
586		#endif // is_mpi
587
588	+	}
589
590	<
591	<
592	<
590	>	void SimSetup::initFromBass(void){
591	>	int i, j, k;
592	>	int n_cells;
593	>	double cellx, celly, cellz;
594	>	double temp1, temp2, temp3;
595	>	int n_per_extra;
596	>	int n_extra;
597	>	int have_extra, done;
598
599	<
600	<	#ifdef IS_MPI
601	<	if( worldRank == 0 ){
602	<	#endif // is_mpi
603	<
604	<	if( the_globals->haveFinalConfig() ){
605	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
599	>	double vel[3];
600	>	vel[0] = 0.0;
601	>	vel[1] = 0.0;
602	>	vel[2] = 0.0;
603	>
604	>	temp1 = (double) tot_nmol / 4.0;
605	>	temp2 = pow(temp1, (1.0 / 3.0));
606	>	temp3 = ceil(temp2);
607	>
608	>	have_extra = 0;
609	>	if (temp2 < temp3){
610	>	// we have a non-complete lattice
611	>	have_extra = 1;
612	>
613	>	n_cells = (int) temp3 - 1;
614	>	cellx = info[0].boxL[0] / temp3;
615	>	celly = info[0].boxL[1] / temp3;
616	>	cellz = info[0].boxL[2] / temp3;
617	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
618	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
619	>	n_per_extra = (int) ceil(temp1);
620	>
621	>	if (n_per_extra > 4){
622	>	sprintf(painCave.errMsg,
623	>	"SimSetup error. There has been an error in constructing"
624	>	" the non-complete lattice.\n");
625	>	painCave.isFatal = 1;
626	>	simError();
627		}
674	–	else{
675	–	strcpy( simnfo->finalName, inFileName );
676	–	char* endTest;
677	–	int nameLength = strlen( simnfo->finalName );
678	–	endTest = &(simnfo->finalName[nameLength - 5]);
679	–	if( !strcmp( endTest, ".bass" ) ){
680	–	strcpy( endTest, ".eor" );
681	–	}
682	–	else if( !strcmp( endTest, ".BASS" ) ){
683	–	strcpy( endTest, ".eor" );
684	–	}
685	–	else{
686	–	endTest = &(simnfo->finalName[nameLength - 4]);
687	–	if( !strcmp( endTest, ".bss" ) ){
688	–	strcpy( endTest, ".eor" );
689	–	}
690	–	else if( !strcmp( endTest, ".mdl" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else{
694	–	strcat( simnfo->finalName, ".eor" );
695	–	}
696	–	}
697	–	}
698	–
699	–	// make the sample and status out names
700	–
701	–	strcpy( simnfo->sampleName, inFileName );
702	–	char* endTest;
703	–	int nameLength = strlen( simnfo->sampleName );
704	–	endTest = &(simnfo->sampleName[nameLength - 5]);
705	–	if( !strcmp( endTest, ".bass" ) ){
706	–	strcpy( endTest, ".dump" );
707	–	}
708	–	else if( !strcmp( endTest, ".BASS" ) ){
709	–	strcpy( endTest, ".dump" );
710	–	}
711	–	else{
712	–	endTest = &(simnfo->sampleName[nameLength - 4]);
713	–	if( !strcmp( endTest, ".bss" ) ){
714	–	strcpy( endTest, ".dump" );
715	–	}
716	–	else if( !strcmp( endTest, ".mdl" ) ){
717	–	strcpy( endTest, ".dump" );
718	–	}
719	–	else{
720	–	strcat( simnfo->sampleName, ".dump" );
721	–	}
722	–	}
723	–
724	–	strcpy( simnfo->statusName, inFileName );
725	–	nameLength = strlen( simnfo->statusName );
726	–	endTest = &(simnfo->statusName[nameLength - 5]);
727	–	if( !strcmp( endTest, ".bass" ) ){
728	–	strcpy( endTest, ".stat" );
729	–	}
730	–	else if( !strcmp( endTest, ".BASS" ) ){
731	–	strcpy( endTest, ".stat" );
732	–	}
733	–	else{
734	–	endTest = &(simnfo->statusName[nameLength - 4]);
735	–	if( !strcmp( endTest, ".bss" ) ){
736	–	strcpy( endTest, ".stat" );
737	–	}
738	–	else if( !strcmp( endTest, ".mdl" ) ){
739	–	strcpy( endTest, ".stat" );
740	–	}
741	–	else{
742	–	strcat( simnfo->statusName, ".stat" );
743	–	}
744	–	}
745	–
746	–	#ifdef IS_MPI
628		}
748	–	#endif // is_mpi
749	–
750	–	// set the status, sample, and themal kick times
751	–
752	–	if( the_globals->haveSampleTime() ){
753	–	simnfo->sampleTime = the_globals->getSampleTime();
754	–	simnfo->statusTime = simnfo->sampleTime;
755	–	simnfo->thermalTime = simnfo->sampleTime;
756	–	}
629		else{
630	<	simnfo->sampleTime = the_globals->getRunTime();
631	<	simnfo->statusTime = simnfo->sampleTime;
632	<	simnfo->thermalTime = simnfo->sampleTime;
630	>	n_cells = (int) temp3;
631	>	cellx = info[0].boxL[0] / temp3;
632	>	celly = info[0].boxL[1] / temp3;
633	>	cellz = info[0].boxL[2] / temp3;
634		}
635
636	<	if( the_globals->haveStatusTime() ){
637	<	simnfo->statusTime = the_globals->getStatusTime();
638	<	}
636	>	current_mol = 0;
637	>	current_comp_mol = 0;
638	>	current_comp = 0;
639	>	current_atom_ndx = 0;
640
641	<	if( the_globals->haveThermalTime() ){
642	<	simnfo->thermalTime = the_globals->getThermalTime();
641	>	for (i = 0; i < n_cells ; i++){
642	>	for (j = 0; j < n_cells; j++){
643	>	for (k = 0; k < n_cells; k++){
644	>	makeElement(i * cellx, j * celly, k * cellz);
645	>
646	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
647	>
648	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
649	>
650	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
651	>	}
652	>	}
653		}
654
655	<	// check for the temperature set flag
655	>	if (have_extra){
656	>	done = 0;
657
658	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
658	>	int start_ndx;
659	>	for (i = 0; i < (n_cells + 1) && !done; i++){
660	>	for (j = 0; j < (n_cells + 1) && !done; j++){
661	>	if (i < n_cells){
662	>	if (j < n_cells){
663	>	start_ndx = n_cells;
664	>	}
665	>	else
666	>	start_ndx = 0;
667	>	}
668	>	else
669	>	start_ndx = 0;
670
671	+	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
672	+	makeElement(i * cellx, j * celly, k * cellz);
673	+	done = (current_mol >= tot_nmol);
674
675	<	// make the integrator
676	<
677	<
678	<	NVT* myNVT = NULL;
679	<	switch( ensembleCase ){
675	>	if (!done && n_per_extra > 1){
676	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
677	>	k * cellz);
678	>	done = (current_mol >= tot_nmol);
679	>	}
680
681	<	case NVE_ENS:
682	<	new NVE( simnfo, the_ff );
683	<	break;
681	>	if (!done && n_per_extra > 2){
682	>	makeElement(i * cellx, j * celly + 0.5 * celly,
683	>	k * cellz + 0.5 * cellz);
684	>	done = (current_mol >= tot_nmol);
685	>	}
686
687	<	case NVT_ENS:
688	<	myNVT = new NVT( simnfo, the_ff );
689	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
687	>	if (!done && n_per_extra > 3){
688	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
689	>	k * cellz + 0.5 * cellz);
690	>	done = (current_mol >= tot_nmol);
691	>	}
692	>	}
693	>	}
694	>	}
695	>	}
696
697	<	if (the_globals->haveTauThermostat())
698	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
699	<	//     else if (the_globals->haveQmass())
700	<	//       myNVT->setQmass(the_globals->getQmass());
701	<	else {
702	<	sprintf( painCave.errMsg,
703	<	"SimSetup error: If you use the NVT\n"
704	<	"    ensemble, you must set either tauThermostat or qMass.\n"
705	<	"    Neither of these was found in the BASS file.\n");
697	>	for (i = 0; i < info[0].n_atoms; i++){
698	>	info[0].atoms[i]->setVel(vel);
699	>	}
700	>	}
701	>
702	>	void SimSetup::makeElement(double x, double y, double z){
703	>	int k;
704	>	AtomStamp* current_atom;
705	>	DirectionalAtom* dAtom;
706	>	double rotMat[3][3];
707	>	double pos[3];
708	>
709	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
710	>	current_atom = comp_stamps[current_comp]->getAtom(k);
711	>	if (!current_atom->havePosition()){
712	>	sprintf(painCave.errMsg,
713	>	"SimSetup:initFromBass error.\n"
714	>	"\tComponent %s, atom %s does not have a position specified.\n"
715	>	"\tThe initialization routine is unable to give a start"
716	>	" position.\n",
717	>	comp_stamps[current_comp]->getID(), current_atom->getType());
718		painCave.isFatal = 1;
719		simError();
720		}
802	–	break;
721
722	<	default:
723	<	sprintf( painCave.errMsg,
724	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
807	<	painCave.isFatal = 1;
808	<	simError();
809	<	}
722	>	pos[0] = x + current_atom->getPosX();
723	>	pos[1] = y + current_atom->getPosY();
724	>	pos[2] = z + current_atom->getPosZ();
725
726	+	info[0].atoms[current_atom_ndx]->setPos(pos);
727
728	<	#ifdef IS_MPI
729	<	mpiSim->mpiRefresh();
814	<	#endif
728	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
729	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
730
731	<	// initialize the Fortran
731	>	rotMat[0][0] = 1.0;
732	>	rotMat[0][1] = 0.0;
733	>	rotMat[0][2] = 0.0;
734
735	+	rotMat[1][0] = 0.0;
736	+	rotMat[1][1] = 1.0;
737	+	rotMat[1][2] = 0.0;
738
739	<	simnfo->refreshSim();
740	<
741	<	if( !strcmp( simnfo->mixingRule, "standard") ){
742	<	the_ff->initForceField( LB_MIXING_RULE );
739	>	rotMat[2][0] = 0.0;
740	>	rotMat[2][1] = 0.0;
741	>	rotMat[2][2] = 1.0;
742	>
743	>	dAtom->setA(rotMat);
744	>	}
745	>
746	>	current_atom_ndx++;
747		}
824	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
825	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
826	–	}
827	–	else{
828	–	sprintf( painCave.errMsg,
829	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
830	–	simnfo->mixingRule );
831	–	painCave.isFatal = 1;
832	–	simError();
833	–	}
748
749	+	current_mol++;
750	+	current_comp_mol++;
751
752	<	#ifdef IS_MPI
753	<	strcpy( checkPointMsg,
754	<	"Successfully intialized the mixingRule for Fortran." );
755	<	MPIcheckPoint();
840	<	#endif // is_mpi
752	>	if (current_comp_mol >= components_nmol[current_comp]){
753	>	current_comp_mol = 0;
754	>	current_comp++;
755	>	}
756		}
757
758
759	<	void SimSetup::makeMolecules( void ){
759	>	void SimSetup::gatherInfo(void){
760	>	int i;
761
762	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
763	<	molInit info;
848	<	DirectionalAtom* dAtom;
849	<	LinkedAssign* extras;
850	<	LinkedAssign* current_extra;
851	<	AtomStamp* currentAtom;
852	<	BondStamp* currentBond;
853	<	BendStamp* currentBend;
854	<	TorsionStamp* currentTorsion;
762	>	ensembleCase = -1;
763	>	ffCase = -1;
764
765	<	bond_pair* theBonds;
857	<	bend_set* theBends;
858	<	torsion_set* theTorsions;
859	<
860	<
861	<	//init the forceField paramters
765	>	// set the easy ones first
766
767	<	the_ff->readParams();
767	>	for (i = 0; i < nInfo; i++){
768	>	info[i].target_temp = globals->getTargetTemp();
769	>	info[i].dt = globals->getDt();
770	>	info[i].run_time = globals->getRunTime();
771	>	}
772	>	n_components = globals->getNComponents();
773
865	–
866	–	// init the atoms
774
775	<	double ux, uy, uz, u, uSqr;
869	<
870	<	atomOffset = 0;
871	<	excludeOffset = 0;
872	<	for(i=0; i<simnfo->n_mol; i++){
873	<
874	<	stampID = the_molecules[i].getStampID();
775	>	// get the forceField
776
777	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
877	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
878	<	info.nBends    = comp_stamps[stampID]->getNBends();
879	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
880	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
777	>	strcpy(force_field, globals->getForceField());
778
779	<	info.myAtoms = &the_atoms[atomOffset];
780	<	info.myExcludes = &the_excludes[excludeOffset];
781	<	info.myBonds = new Bond*[info.nBonds];
782	<	info.myBends = new Bend*[info.nBends];
783	<	info.myTorsions = new Torsion*[info.nTorsions];
779	>	if (!strcasecmp(force_field, "DUFF")){
780	>	ffCase = FF_DUFF;
781	>	}
782	>	else if (!strcasecmp(force_field, "LJ")){
783	>	ffCase = FF_LJ;
784	>	}
785	>	else if (!strcasecmp(force_field, "EAM")){
786	>	ffCase = FF_EAM;
787	>	}
788	>	else if (!strcasecmp(force_field, "WATER")){
789	>	ffCase = FF_H2O;
790	>	}
791	>	else{
792	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793	>	force_field);
794	>	painCave.isFatal = 1;
795	>	simError();
796	>	}
797
798	<	theBonds = new bond_pair[info.nBonds];
799	<	theBends = new bend_set[info.nBends];
800	<	theTorsions = new torsion_set[info.nTorsions];
798	>	// get the ensemble
799	>
800	>	strcpy(ensemble, globals->getEnsemble());
801	>
802	>	if (!strcasecmp(ensemble, "NVE")){
803	>	ensembleCase = NVE_ENS;
804	>	}
805	>	else if (!strcasecmp(ensemble, "NVT")){
806	>	ensembleCase = NVT_ENS;
807	>	}
808	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
809	>	ensembleCase = NPTi_ENS;
810	>	}
811	>	else if (!strcasecmp(ensemble, "NPTf")){
812	>	ensembleCase = NPTf_ENS;
813	>	}
814	>	else if (!strcasecmp(ensemble, "NPTxyz")){
815	>	ensembleCase = NPTxyz_ENS;
816	>	}
817	>	else{
818	>	sprintf(painCave.errMsg,
819	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	>	"\treverting to NVE for this simulation.\n",
821	>	ensemble);
822	>	painCave.isFatal = 0;
823	>	simError();
824	>	strcpy(ensemble, "NVE");
825	>	ensembleCase = NVE_ENS;
826	>	}
827	>
828	>	for (i = 0; i < nInfo; i++){
829	>	strcpy(info[i].ensemble, ensemble);
830	>
831	>	// get the mixing rule
832	>
833	>	strcpy(info[i].mixingRule, globals->getMixingRule());
834	>	info[i].usePBC = globals->getPBC();
835	>	}
836	>
837	>	// get the components and calculate the tot_nMol and indvidual n_mol
838	>
839	>	the_components = globals->getComponents();
840	>	components_nmol = new int[n_components];
841	>
842	>
843	>	if (!globals->haveNMol()){
844	>	// we don't have the total number of molecules, so we assume it is
845	>	// given in each component
846	>
847	>	tot_nmol = 0;
848	>	for (i = 0; i < n_components; i++){
849	>	if (!the_components[i]->haveNMol()){
850	>	// we have a problem
851	>	sprintf(painCave.errMsg,
852	>	"SimSetup Error. No global NMol or component NMol given.\n"
853	>	"\tCannot calculate the number of atoms.\n");
854	>	painCave.isFatal = 1;
855	>	simError();
856	>	}
857	>
858	>	tot_nmol += the_components[i]->getNMol();
859	>	components_nmol[i] = the_components[i]->getNMol();
860	>	}
861	>	}
862	>	else{
863	>	sprintf(painCave.errMsg,
864	>	"SimSetup error.\n"
865	>	"\tSorry, the ability to specify total"
866	>	" nMols and then give molfractions in the components\n"
867	>	"\tis not currently supported."
868	>	" Please give nMol in the components.\n");
869	>	painCave.isFatal = 1;
870	>	simError();
871	>	}
872	>
873	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	>	sprintf(painCave.errMsg,
876	>	"Sample time is not divisible by dt.\n"
877	>	"\tThis will result in samples that are not uniformly\n"
878	>	"\tdistributed in time.  If this is a problem, change\n"
879	>	"\tyour sampleTime variable.\n");
880	>	painCave.isFatal = 0;
881	>	simError();
882	>	}
883	>
884	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	>	sprintf(painCave.errMsg,
886	>	"Status time is not divisible by dt.\n"
887	>	"\tThis will result in status reports that are not uniformly\n"
888	>	"\tdistributed in time.  If this is a problem, change \n"
889	>	"\tyour statusTime variable.\n");
890	>	painCave.isFatal = 0;
891	>	simError();
892	>	}
893	>
894	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	>	sprintf(painCave.errMsg,
896	>	"Thermal time is not divisible by dt.\n"
897	>	"\tThis will result in thermalizations that are not uniformly\n"
898	>	"\tdistributed in time.  If this is a problem, change \n"
899	>	"\tyour thermalTime variable.\n");
900	>	painCave.isFatal = 0;
901	>	simError();
902	>	}
903	>
904	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	>	sprintf(painCave.errMsg,
906	>	"Reset time is not divisible by dt.\n"
907	>	"\tThis will result in integrator resets that are not uniformly\n"
908	>	"\tdistributed in time.  If this is a problem, change\n"
909	>	"\tyour resetTime variable.\n");
910	>	painCave.isFatal = 0;
911	>	simError();
912	>	}
913	>
914	>	// set the status, sample, and thermal kick times
915	>
916	>	for (i = 0; i < nInfo; i++){
917	>	if (globals->haveSampleTime()){
918	>	info[i].sampleTime = globals->getSampleTime();
919	>	info[i].statusTime = info[i].sampleTime;
920	>	}
921	>	else{
922	>	info[i].sampleTime = globals->getRunTime();
923	>	info[i].statusTime = info[i].sampleTime;
924	>	}
925	>
926	>	if (globals->haveStatusTime()){
927	>	info[i].statusTime = globals->getStatusTime();
928	>	}
929	>
930	>	if (globals->haveThermalTime()){
931	>	info[i].thermalTime = globals->getThermalTime();
932	>	} else {
933	>	info[i].thermalTime = globals->getRunTime();
934	>	}
935	>
936	>	info[i].resetIntegrator = 0;
937	>	if( globals->haveResetTime() ){
938	>	info[i].resetTime = globals->getResetTime();
939	>	info[i].resetIntegrator = 1;
940	>	}
941	>
942	>	// check for the temperature set flag
943
944	<	// make the Atoms
944	>	if (globals->haveTempSet())
945	>	info[i].setTemp = globals->getTempSet();
946	>
947	>	// check for the extended State init
948	>
949	>	info[i].useInitXSstate = globals->getUseInitXSstate();
950	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951
952	<	for(j=0; j<info.nAtoms; j++){
953	<
954	<	currentAtom = comp_stamps[stampID]->getAtom( j );
955	<	if( currentAtom->haveOrientation() ){
956	<
957	<	dAtom = new DirectionalAtom(j + atomOffset);
958	<	simnfo->n_oriented++;
959	<	info.myAtoms[j] = dAtom;
960	<
961	<	ux = currentAtom->getOrntX();
962	<	uy = currentAtom->getOrntY();
963	<	uz = currentAtom->getOrntZ();
964	<
965	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
966	<
967	<	u = sqrt( uSqr );
968	<	ux = ux / u;
969	<	uy = uy / u;
970	<	uz = uz / u;
971	<
972	<	dAtom->setSUx( ux );
973	<	dAtom->setSUy( uy );
974	<	dAtom->setSUz( uz );
975	<	}
976	<	else{
977	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
978	<	}
921	<	info.myAtoms[j]->setType( currentAtom->getType() );
952	>	}
953	>
954	>	//setup seed for random number generator
955	>	int seedValue;
956	>
957	>	if (globals->haveSeed()){
958	>	seedValue = globals->getSeed();
959	>
960	>	if(seedValue / 1E9 == 0){
961	>	sprintf(painCave.errMsg,
962	>	"Seed for sprng library should contain at least 9 digits\n"
963	>	"OOPSE will generate a seed for user\n");
964	>	painCave.isFatal = 0;
965	>	simError();
966	>
967	>	//using seed generated by system instead of invalid seed set by user
968	>	#ifndef IS_MPI
969	>	seedValue = make_sprng_seed();
970	>	#else
971	>	if (worldRank == 0){
972	>	seedValue = make_sprng_seed();
973	>	}
974	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
975	>	#endif
976	>	}
977	>	}//end of if branch of globals->haveSeed()
978	>	else{
979
980	+	#ifndef IS_MPI
981	+	seedValue = make_sprng_seed();
982	+	#else
983	+	if (worldRank == 0){
984	+	seedValue = make_sprng_seed();
985	+	}
986	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
987	+	#endif
988	+	}//end of globals->haveSeed()
989	+
990	+	for (int i = 0; i < nInfo; i++){
991	+	info[i].setSeed(seedValue);
992	+	}
993	+
994		#ifdef IS_MPI
995	<
996	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
926	<
995	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
996	>	MPIcheckPoint();
997		#endif // is_mpi
998	<	}
929	<
930	<	// make the bonds
931	<	for(j=0; j<info.nBonds; j++){
932	<
933	<	currentBond = comp_stamps[stampID]->getBond( j );
934	<	theBonds[j].a = currentBond->getA() + atomOffset;
935	<	theBonds[j].b = currentBond->getB() + atomOffset;
998	>	}
999
937	–	exI = theBonds[j].a;
938	–	exJ = theBonds[j].b;
1000
1001	<	// exclude_I must always be the smaller of the pair
1002	<	if( exI > exJ ){
1003	<	tempEx = exI;
1004	<	exI = exJ;
1005	<	exJ = tempEx;
1006	<	}
1001	>	void SimSetup::finalInfoCheck(void){
1002	>	int index;
1003	>	int usesDipoles;
1004	>	int usesCharges;
1005	>	int i;
1006	>
1007	>	for (i = 0; i < nInfo; i++){
1008	>	// check electrostatic parameters
1009	>
1010	>	index = 0;
1011	>	usesDipoles = 0;
1012	>	while ((index < info[i].n_atoms) && !usesDipoles){
1013	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1014	>	index++;
1015	>	}
1016	>	index = 0;
1017	>	usesCharges = 0;
1018	>	while ((index < info[i].n_atoms) && !usesCharges){
1019	>	usesCharges= (info[i].atoms[index])->hasCharge();
1020	>	index++;
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;
1023	>	int myUse = usesDipoles;
1024	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1025	>	#endif //is_mpi
1026	>
1027	>	double theRcut, theRsw;
1028	>
1029	>	if (globals->haveRcut()) {
1030	>	theRcut = globals->getRcut();
1031	>
1032	>	if (globals->haveRsw())
1033	>	theRsw = globals->getRsw();
1034	>	else
1035	>	theRsw = theRcut;
1036
1037	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
953	<	#else  // isn't MPI
1037	>	info[i].setDefaultRcut(theRcut, theRsw);
1038
1039	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1040	<	#endif  //is_mpi
1039	>	} else {
1040	>
1041	>	the_ff->calcRcut();
1042	>	theRcut = info[i].getRcut();
1043	>
1044	>	if (globals->haveRsw())
1045	>	theRsw = globals->getRsw();
1046	>	else
1047	>	theRsw = theRcut;
1048	>
1049	>	info[i].setDefaultRcut(theRcut, theRsw);
1050		}
958	–	excludeOffset += info.nBonds;
1051
1052	<	//make the bends
1053	<	for(j=0; j<info.nBends; j++){
1052	>	if (globals->getUseRF()){
1053	>	info[i].useReactionField = 1;
1054
1055	<	currentBend = comp_stamps[stampID]->getBend( j );
1056	<	theBends[j].a = currentBend->getA() + atomOffset;
1057	<	theBends[j].b = currentBend->getB() + atomOffset;
1058	<	theBends[j].c = currentBend->getC() + atomOffset;
1059	<
1060	<	if( currentBend->haveExtras() ){
1061	<
1062	<	extras = currentBend->getExtras();
971	<	current_extra = extras;
972	<
973	<	while( current_extra != NULL ){
974	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
975	<
976	<	switch( current_extra->getType() ){
977	<
978	<	case 0:
979	<	theBends[j].ghost =
980	<	current_extra->getInt() + atomOffset;
981	<	theBends[j].isGhost = 1;
982	<	break;
983	<
984	<	case 1:
985	<	theBends[j].ghost =
986	<	(int)current_extra->getDouble() + atomOffset;
987	<	theBends[j].isGhost = 1;
988	<	break;
989	<
990	<	default:
991	<	sprintf( painCave.errMsg,
992	<	"SimSetup Error: ghostVectorSource was neither a "
993	<	"double nor an int.\n"
994	<	"-->Bend[%d] in %s\n",
995	<	j, comp_stamps[stampID]->getID() );
996	<	painCave.isFatal = 1;
997	<	simError();
998	<	}
999	<	}
1000	<
1001	<	else{
1002	<
1003	<	sprintf( painCave.errMsg,
1004	<	"SimSetup Error: unhandled bend assignment:\n"
1005	<	"    -->%s in Bend[%d] in %s\n",
1006	<	current_extra->getlhs(),
1007	<	j, comp_stamps[stampID]->getID() );
1008	<	painCave.isFatal = 1;
1009	<	simError();
1010	<	}
1011	<
1012	<	current_extra = current_extra->getNext();
1013	<	}
1055	>	if (!globals->haveRcut()){
1056	>	sprintf(painCave.errMsg,
1057	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1058	>	"\tOOPSE will use a default value of 15.0 angstroms"
1059	>	"\tfor the cutoffRadius.\n");
1060	>	painCave.isFatal = 0;
1061	>	simError();
1062	>	theRcut = 15.0;
1063		}
1064	<
1065	<	if( !theBends[j].isGhost ){
1017	<
1018	<	exI = theBends[j].a;
1019	<	exJ = theBends[j].c;
1064	>	else{
1065	>	theRcut = globals->getRcut();
1066		}
1067	+
1068	+	if (!globals->haveRsw()){
1069	+	sprintf(painCave.errMsg,
1070	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1071	+	"\tOOPSE will use a default value of\n"
1072	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1073	+	painCave.isFatal = 0;
1074	+	simError();
1075	+	theRsw = 0.95 * theRcut;
1076	+	}
1077		else{
1078	<
1023	<	exI = theBends[j].a;
1024	<	exJ = theBends[j].b;
1078	>	theRsw = globals->getRsw();
1079		}
1080	<
1081	<	// exclude_I must always be the smaller of the pair
1082	<	if( exI > exJ ){
1083	<	tempEx = exI;
1084	<	exI = exJ;
1085	<	exJ = tempEx;
1080	>
1081	>	info[i].setDefaultRcut(theRcut, theRsw);
1082	>
1083	>	if (!globals->haveDielectric()){
1084	>	sprintf(painCave.errMsg,
1085	>	"SimSetup Error: No Dielectric constant was set.\n"
1086	>	"\tYou are trying to use Reaction Field without"
1087	>	"\tsetting a dielectric constant!\n");
1088	>	painCave.isFatal = 1;
1089	>	simError();
1090		}
1091	<	#ifdef IS_MPI
1034	<	tempEx = exI;
1035	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1036	<	tempEx = exJ;
1037	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1038	<
1039	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1040	<	#else  // isn't MPI
1041	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1042	<	#endif  //is_mpi
1091	>	info[i].dielectric = globals->getDielectric();
1092		}
1093	<	excludeOffset += info.nBends;
1093	>	else{
1094	>	if (usesDipoles || usesCharges){
1095
1096	<	for(j=0; j<info.nTorsions; j++){
1097	<
1098	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1099	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1100	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1101	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1102	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1103	<
1054	<	exI = theTorsions[j].a;
1055	<	exJ = theTorsions[j].d;
1056	<
1057	<	// exclude_I must always be the smaller of the pair
1058	<	if( exI > exJ ){
1059	<	tempEx = exI;
1060	<	exI = exJ;
1061	<	exJ = tempEx;
1096	>	if (!globals->haveRcut()){
1097	>	sprintf(painCave.errMsg,
1098	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1099	>	"\tOOPSE will use a default value of 15.0 angstroms"
1100	>	"\tfor the cutoffRadius.\n");
1101	>	painCave.isFatal = 0;
1102	>	simError();
1103	>	theRcut = 15.0;
1104		}
1105	<	#ifdef IS_MPI
1106	<	tempEx = exI;
1107	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1108	<	tempEx = exJ;
1109	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1110	<
1111	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1112	<	#else  // isn't MPI
1113	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1114	<	#endif  //is_mpi
1105	>	else{
1106	>	theRcut = globals->getRcut();
1107	>	}
1108	>
1109	>	if (!globals->haveRsw()){
1110	>	sprintf(painCave.errMsg,
1111	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1112	>	"\tOOPSE will use a default value of\n"
1113	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1114	>	painCave.isFatal = 0;
1115	>	simError();
1116	>	theRsw = 0.95 * theRcut;
1117	>	}
1118	>	else{
1119	>	theRsw = globals->getRsw();
1120	>	}
1121	>
1122	>	info[i].setDefaultRcut(theRcut, theRsw);
1123	>
1124	>	}
1125		}
1126	<	excludeOffset += info.nTorsions;
1126	>	}
1127	>	#ifdef IS_MPI
1128	>	strcpy(checkPointMsg, "post processing checks out");
1129	>	MPIcheckPoint();
1130	>	#endif // is_mpi
1131
1132	<
1133	<	// send the arrays off to the forceField for init.
1132	>	// clean up the forcefield
1133	>	the_ff->cleanMe();
1134	>	}
1135	>
1136	>	void SimSetup::initSystemCoords(void){
1137	>	int i;
1138
1139	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1080	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1081	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1082	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1139	>	char* inName;
1140
1141	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1142
1143	<	the_molecules[i].initialize( info );
1143	>	for (i = 0; i < info[0].n_atoms; i++)
1144	>	info[0].atoms[i]->setCoords();
1145
1146	+	if (globals->haveInitialConfig()){
1147	+	InitializeFromFile* fileInit;
1148	+	#ifdef IS_MPI // is_mpi
1149	+	if (worldRank == 0){
1150	+	#endif //is_mpi
1151	+	inName = globals->getInitialConfig();
1152	+	fileInit = new InitializeFromFile(inName);
1153	+	#ifdef IS_MPI
1154	+	}
1155	+	else
1156	+	fileInit = new InitializeFromFile(NULL);
1157	+	#endif
1158	+	fileInit->readInit(info); // default velocities on
1159
1160	<	atomOffset += info.nAtoms;
1089	<	delete[] theBonds;
1090	<	delete[] theBends;
1091	<	delete[] theTorsions;
1160	>	delete fileInit;
1161		}
1162	+	else{
1163	+
1164	+	// no init from bass
1165	+
1166	+	sprintf(painCave.errMsg,
1167	+	"Cannot intialize a simulation without an initial configuration file.\n");
1168	+	painCave.isFatal = 1;;
1169	+	simError();
1170	+
1171	+	}
1172
1173		#ifdef IS_MPI
1174	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1174	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1175		MPIcheckPoint();
1176		#endif // is_mpi
1177	+	}
1178
1099	–	// clean up the forcefield
1100	–	the_ff->calcRcut();
1101	–	the_ff->cleanMe();
1179
1180	<	}
1180	>	void SimSetup::makeOutNames(void){
1181	>	int k;
1182
1105	–	void SimSetup::initFromBass( void ){
1183
1184	<	int i, j, k;
1185	<	int n_cells;
1186	<	double cellx, celly, cellz;
1187	<	double temp1, temp2, temp3;
1111	<	int n_per_extra;
1112	<	int n_extra;
1113	<	int have_extra, done;
1184	>	for (k = 0; k < nInfo; k++){
1185	>	#ifdef IS_MPI
1186	>	if (worldRank == 0){
1187	>	#endif // is_mpi
1188
1189	<	temp1 = (double)tot_nmol / 4.0;
1190	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1191	<	temp3 = ceil( temp2 );
1189	>	if (globals->haveFinalConfig()){
1190	>	strcpy(info[k].finalName, globals->getFinalConfig());
1191	>	}
1192	>	else{
1193	>	strcpy(info[k].finalName, inFileName);
1194	>	char* endTest;
1195	>	int nameLength = strlen(info[k].finalName);
1196	>	endTest = &(info[k].finalName[nameLength - 5]);
1197	>	if (!strcmp(endTest, ".bass")){
1198	>	strcpy(endTest, ".eor");
1199	>	}
1200	>	else if (!strcmp(endTest, ".BASS")){
1201	>	strcpy(endTest, ".eor");
1202	>	}
1203	>	else{
1204	>	endTest = &(info[k].finalName[nameLength - 4]);
1205	>	if (!strcmp(endTest, ".bss")){
1206	>	strcpy(endTest, ".eor");
1207	>	}
1208	>	else if (!strcmp(endTest, ".mdl")){
1209	>	strcpy(endTest, ".eor");
1210	>	}
1211	>	else{
1212	>	strcat(info[k].finalName, ".eor");
1213	>	}
1214	>	}
1215	>	}
1216
1217	<	have_extra =0;
1120	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1121	<	have_extra =1;
1217	>	// make the sample and status out names
1218
1219	<	n_cells = (int)temp3 - 1;
1220	<	cellx = simnfo->boxLx / temp3;
1221	<	celly = simnfo->boxLy / temp3;
1222	<	cellz = simnfo->boxLz / temp3;
1223	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1224	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1225	<	n_per_extra = (int)ceil( temp1 );
1219	>	strcpy(info[k].sampleName, inFileName);
1220	>	char* endTest;
1221	>	int nameLength = strlen(info[k].sampleName);
1222	>	endTest = &(info[k].sampleName[nameLength - 5]);
1223	>	if (!strcmp(endTest, ".bass")){
1224	>	strcpy(endTest, ".dump");
1225	>	}
1226	>	else if (!strcmp(endTest, ".BASS")){
1227	>	strcpy(endTest, ".dump");
1228	>	}
1229	>	else{
1230	>	endTest = &(info[k].sampleName[nameLength - 4]);
1231	>	if (!strcmp(endTest, ".bss")){
1232	>	strcpy(endTest, ".dump");
1233	>	}
1234	>	else if (!strcmp(endTest, ".mdl")){
1235	>	strcpy(endTest, ".dump");
1236	>	}
1237	>	else{
1238	>	strcat(info[k].sampleName, ".dump");
1239	>	}
1240	>	}
1241
1242	<	if( n_per_extra > 4){
1243	<	sprintf( painCave.errMsg,
1244	<	"SimSetup error. There has been an error in constructing"
1245	<	" the non-complete lattice.\n" );
1246	<	painCave.isFatal = 1;
1247	<	simError();
1242	>	strcpy(info[k].statusName, inFileName);
1243	>	nameLength = strlen(info[k].statusName);
1244	>	endTest = &(info[k].statusName[nameLength - 5]);
1245	>	if (!strcmp(endTest, ".bass")){
1246	>	strcpy(endTest, ".stat");
1247	>	}
1248	>	else if (!strcmp(endTest, ".BASS")){
1249	>	strcpy(endTest, ".stat");
1250	>	}
1251	>	else{
1252	>	endTest = &(info[k].statusName[nameLength - 4]);
1253	>	if (!strcmp(endTest, ".bss")){
1254	>	strcpy(endTest, ".stat");
1255	>	}
1256	>	else if (!strcmp(endTest, ".mdl")){
1257	>	strcpy(endTest, ".stat");
1258	>	}
1259	>	else{
1260	>	strcat(info[k].statusName, ".stat");
1261	>	}
1262	>	}
1263	>
1264	>	#ifdef IS_MPI
1265	>
1266		}
1267	+	#endif // is_mpi
1268		}
1269	<	else{
1270	<	n_cells = (int)temp3;
1271	<	cellx = simnfo->boxLx / temp3;
1272	<	celly = simnfo->boxLy / temp3;
1273	<	cellz = simnfo->boxLz / temp3;
1269	>	}
1270	>
1271	>
1272	>	void SimSetup::sysObjectsCreation(void){
1273	>	int i, k;
1274	>
1275	>	// create the forceField
1276	>
1277	>	createFF();
1278	>
1279	>	// extract componentList
1280	>
1281	>	compList();
1282	>
1283	>	// calc the number of atoms, bond, bends, and torsions
1284	>
1285	>	calcSysValues();
1286	>
1287	>	#ifdef IS_MPI
1288	>	// divide the molecules among the processors
1289	>
1290	>	mpiMolDivide();
1291	>	#endif //is_mpi
1292	>
1293	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1294	>
1295	>	makeSysArrays();
1296	>
1297	>	// make and initialize the molecules (all but atomic coordinates)
1298	>
1299	>	makeMolecules();
1300	>
1301	>	for (k = 0; k < nInfo; k++){
1302	>	info[k].identArray = new int[info[k].n_atoms];
1303	>	for (i = 0; i < info[k].n_atoms; i++){
1304	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1305	>	}
1306		}
1307	+	}
1308
1146	–	current_mol = 0;
1147	–	current_comp_mol = 0;
1148	–	current_comp = 0;
1149	–	current_atom_ndx = 0;
1309
1310	<	for( i=0; i < n_cells ; i++ ){
1311	<	for( j=0; j < n_cells; j++ ){
1312	<	for( k=0; k < n_cells; k++ ){
1310	>	void SimSetup::createFF(void){
1311	>	switch (ffCase){
1312	>	case FF_DUFF:
1313	>	the_ff = new DUFF();
1314	>	break;
1315
1316	<	makeElement( i * cellx,
1317	<	j * celly,
1318	<	k * cellz );
1316	>	case FF_LJ:
1317	>	the_ff = new LJFF();
1318	>	break;
1319
1320	<	makeElement( i * cellx + 0.5 * cellx,
1321	<	j * celly + 0.5 * celly,
1322	<	k * cellz );
1320	>	case FF_EAM:
1321	>	the_ff = new EAM_FF();
1322	>	break;
1323
1324	<	makeElement( i * cellx,
1325	<	j * celly + 0.5 * celly,
1326	<	k * cellz + 0.5 * cellz );
1324	>	case FF_H2O:
1325	>	the_ff = new WATER();
1326	>	break;
1327
1328	<	makeElement( i * cellx + 0.5 * cellx,
1329	<	j * celly,
1330	<	k * cellz + 0.5 * cellz );
1328	>	default:
1329	>	sprintf(painCave.errMsg,
1330	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1331	>	painCave.isFatal = 1;
1332	>	simError();
1333	>	}
1334	>
1335	>	#ifdef IS_MPI
1336	>	strcpy(checkPointMsg, "ForceField creation successful");
1337	>	MPIcheckPoint();
1338	>	#endif // is_mpi
1339	>	}
1340	>
1341	>
1342	>	void SimSetup::compList(void){
1343	>	int i;
1344	>	char* id;
1345	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1346	>	LinkedMolStamp* currentStamp = NULL;
1347	>	comp_stamps = new MoleculeStamp * [n_components];
1348	>	bool haveCutoffGroups;
1349	>
1350	>	haveCutoffGroups = false;
1351	>
1352	>	// make an array of molecule stamps that match the components used.
1353	>	// also extract the used stamps out into a separate linked list
1354	>
1355	>	for (i = 0; i < nInfo; i++){
1356	>	info[i].nComponents = n_components;
1357	>	info[i].componentsNmol = components_nmol;
1358	>	info[i].compStamps = comp_stamps;
1359	>	info[i].headStamp = headStamp;
1360	>	}
1361	>
1362	>
1363	>	for (i = 0; i < n_components; i++){
1364	>	id = the_components[i]->getType();
1365	>	comp_stamps[i] = NULL;
1366	>
1367	>	// check to make sure the component isn't already in the list
1368	>
1369	>	comp_stamps[i] = headStamp->match(id);
1370	>	if (comp_stamps[i] == NULL){
1371	>	// extract the component from the list;
1372	>
1373	>	currentStamp = stamps->extractMolStamp(id);
1374	>	if (currentStamp == NULL){
1375	>	sprintf(painCave.errMsg,
1376	>	"SimSetup error: Component \"%s\" was not found in the "
1377	>	"list of declared molecules\n",
1378	>	id);
1379	>	painCave.isFatal = 1;
1380	>	simError();
1381		}
1382	+
1383	+	headStamp->add(currentStamp);
1384	+	comp_stamps[i] = headStamp->match(id);
1385		}
1386	+
1387	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1388	+	haveCutoffGroups = true;
1389		}
1390	+
1391	+	for (i = 0; i < nInfo; i++)
1392	+	info[i].haveCutoffGroups = haveCutoffGroups;
1393
1394	<	if( have_extra ){
1395	<	done = 0;
1394	>	#ifdef IS_MPI
1395	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1396	>	MPIcheckPoint();
1397	>	#endif // is_mpi
1398	>	}
1399
1400	<	int start_ndx;
1401	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1179	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1400	>	void SimSetup::calcSysValues(void){
1401	>	int i;
1402
1403	<	if( i < n_cells ){
1403	>	int* molMembershipArray;
1404
1405	<	if( j < n_cells ){
1406	<	start_ndx = n_cells;
1407	<	}
1408	<	else start_ndx = 0;
1409	<	}
1410	<	else start_ndx = 0;
1405	>	tot_atoms = 0;
1406	>	tot_bonds = 0;
1407	>	tot_bends = 0;
1408	>	tot_torsions = 0;
1409	>	tot_rigid = 0;
1410	>	for (i = 0; i < n_components; i++){
1411	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1412	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1413	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1414	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1415	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1416	>	}
1417	>
1418	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1419	>	molMembershipArray = new int[tot_atoms];
1420
1421	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1421	>	for (i = 0; i < nInfo; i++){
1422	>	info[i].n_atoms = tot_atoms;
1423	>	info[i].n_bonds = tot_bonds;
1424	>	info[i].n_bends = tot_bends;
1425	>	info[i].n_torsions = tot_torsions;
1426	>	info[i].n_SRI = tot_SRI;
1427	>	info[i].n_mol = tot_nmol;
1428
1429	<	makeElement( i * cellx,
1430	<	j * celly,
1431	<	k * cellz );
1195	<	done = ( current_mol >= tot_nmol );
1429	>	info[i].molMembershipArray = molMembershipArray;
1430	>	}
1431	>	}
1432
1433	<	if( !done && n_per_extra > 1 ){
1198	<	makeElement( i * cellx + 0.5 * cellx,
1199	<	j * celly + 0.5 * celly,
1200	<	k * cellz );
1201	<	done = ( current_mol >= tot_nmol );
1202	<	}
1433	>	#ifdef IS_MPI
1434
1435	<	if( !done && n_per_extra > 2){
1436	<	makeElement( i * cellx,
1437	<	j * celly + 0.5 * celly,
1438	<	k * cellz + 0.5 * cellz );
1439	<	done = ( current_mol >= tot_nmol );
1440	<	}
1435	>	void SimSetup::mpiMolDivide(void){
1436	>	int i, j, k;
1437	>	int localMol, allMol;
1438	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1439	>	int local_rigid;
1440	>	vector<int> globalMolIndex;
1441
1442	<	if( !done && n_per_extra > 3){
1443	<	makeElement( i * cellx + 0.5 * cellx,
1444	<	j * celly,
1445	<	k * cellz + 0.5 * cellz );
1446	<	done = ( current_mol >= tot_nmol );
1447	<	}
1448	<	}
1442	>	mpiSim = new mpiSimulation(info);
1443	>
1444	>	mpiSim->divideLabor();
1445	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1446	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1447	>
1448	>	// set up the local variables
1449	>
1450	>	mol2proc = mpiSim->getMolToProcMap();
1451	>	molCompType = mpiSim->getMolComponentType();
1452	>
1453	>	allMol = 0;
1454	>	localMol = 0;
1455	>	local_atoms = 0;
1456	>	local_bonds = 0;
1457	>	local_bends = 0;
1458	>	local_torsions = 0;
1459	>	local_rigid = 0;
1460	>	globalAtomCounter = 0;
1461	>
1462	>	for (i = 0; i < n_components; i++){
1463	>	for (j = 0; j < components_nmol[i]; j++){
1464	>	if (mol2proc[allMol] == worldRank){
1465	>	local_atoms += comp_stamps[i]->getNAtoms();
1466	>	local_bonds += comp_stamps[i]->getNBonds();
1467	>	local_bends += comp_stamps[i]->getNBends();
1468	>	local_torsions += comp_stamps[i]->getNTorsions();
1469	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1470	>	localMol++;
1471	>	}
1472	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1473	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1474	>	globalAtomCounter++;
1475		}
1476	+
1477	+	allMol++;
1478		}
1479		}
1480	+	local_SRI = local_bonds + local_bends + local_torsions;
1481
1482	+	info[0].n_atoms = mpiSim->getMyNlocal();
1483	+
1484
1485	<	for( i=0; i<simnfo->n_atoms; i++ ){
1486	<	simnfo->atoms[i]->set_vx( 0.0 );
1487	<	simnfo->atoms[i]->set_vy( 0.0 );
1488	<	simnfo->atoms[i]->set_vz( 0.0 );
1485	>	if (local_atoms != info[0].n_atoms){
1486	>	sprintf(painCave.errMsg,
1487	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1488	>	"\tlocalAtom (%d) are not equal.\n",
1489	>	info[0].n_atoms, local_atoms);
1490	>	painCave.isFatal = 1;
1491	>	simError();
1492		}
1493	+
1494	+	info[0].n_bonds = local_bonds;
1495	+	info[0].n_bends = local_bends;
1496	+	info[0].n_torsions = local_torsions;
1497	+	info[0].n_SRI = local_SRI;
1498	+	info[0].n_mol = localMol;
1499	+
1500	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1501	+	MPIcheckPoint();
1502		}
1503
1504	<	void SimSetup::makeElement( double x, double y, double z ){
1504	>	#endif // is_mpi
1505
1232	–	int k;
1233	–	AtomStamp* current_atom;
1234	–	DirectionalAtom* dAtom;
1235	–	double rotMat[3][3];
1506
1507	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1507	>	void SimSetup::makeSysArrays(void){
1508	>
1509	>	#ifndef IS_MPI
1510	>	int k, j;
1511	>	#endif // is_mpi
1512	>	int i, l;
1513
1514	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1515	<	if( !current_atom->havePosition() ){
1241	<	sprintf( painCave.errMsg,
1242	<	"SimSetup:initFromBass error.\n"
1243	<	"\tComponent %s, atom %s does not have a position specified.\n"
1244	<	"\tThe initialization routine is unable to give a start"
1245	<	" position.\n",
1246	<	comp_stamps[current_comp]->getID(),
1247	<	current_atom->getType() );
1248	<	painCave.isFatal = 1;
1249	<	simError();
1250	<	}
1514	>	Atom** the_atoms;
1515	>	Molecule* the_molecules;
1516
1517	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1518	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1254	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1517	>	for (l = 0; l < nInfo; l++){
1518	>	// create the atom and short range interaction arrays
1519
1520	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1520	>	the_atoms = new Atom * [info[l].n_atoms];
1521	>	the_molecules = new Molecule[info[l].n_mol];
1522	>	int molIndex;
1523
1524	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1524	>	// initialize the molecule's stampID's
1525
1526	<	rotMat[0][0] = 1.0;
1261	<	rotMat[0][1] = 0.0;
1262	<	rotMat[0][2] = 0.0;
1526	>	#ifdef IS_MPI
1527
1264	–	rotMat[1][0] = 0.0;
1265	–	rotMat[1][1] = 1.0;
1266	–	rotMat[1][2] = 0.0;
1528
1529	<	rotMat[2][0] = 0.0;
1530	<	rotMat[2][1] = 0.0;
1531	<	rotMat[2][2] = 1.0;
1529	>	molIndex = 0;
1530	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1531	>	if (mol2proc[i] == worldRank){
1532	>	the_molecules[molIndex].setStampID(molCompType[i]);
1533	>	the_molecules[molIndex].setMyIndex(molIndex);
1534	>	the_molecules[molIndex].setGlobalIndex(i);
1535	>	molIndex++;
1536	>	}
1537	>	}
1538
1539	<	dAtom->setA( rotMat );
1539	>	#else // is_mpi
1540	>
1541	>	molIndex = 0;
1542	>	globalAtomCounter = 0;
1543	>	for (i = 0; i < n_components; i++){
1544	>	for (j = 0; j < components_nmol[i]; j++){
1545	>	the_molecules[molIndex].setStampID(i);
1546	>	the_molecules[molIndex].setMyIndex(molIndex);
1547	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1548	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1549	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1550	>	globalAtomCounter++;
1551	>	}
1552	>	molIndex++;
1553	>	}
1554		}
1555
1275	–	current_atom_ndx++;
1276	–	}
1556
1557	<	current_mol++;
1279	<	current_comp_mol++;
1557	>	#endif // is_mpi
1558
1559	<	if( current_comp_mol >= components_nmol[current_comp] ){
1559	>	info[l].globalExcludes = new int;
1560	>	info[l].globalExcludes[0] = 0;
1561	>
1562	>	// set the arrays into the SimInfo object
1563
1564	<	current_comp_mol = 0;
1565	<	current_comp++;
1564	>	info[l].atoms = the_atoms;
1565	>	info[l].molecules = the_molecules;
1566	>	info[l].nGlobalExcludes = 0;
1567	>
1568	>	the_ff->setSimInfo(info);
1569	>	}
1570	>	}
1571	>
1572	>	void SimSetup::makeIntegrator(void){
1573	>	int k;
1574	>
1575	>	NVE<RealIntegrator>* myNVE = NULL;
1576	>	NVT<RealIntegrator>* myNVT = NULL;
1577	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1578	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1579	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1580	>
1581	>	for (k = 0; k < nInfo; k++){
1582	>	switch (ensembleCase){
1583	>	case NVE_ENS:
1584	>	if (globals->haveZconstraints()){
1585	>	setupZConstraint(info[k]);
1586	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1587	>	}
1588	>	else{
1589	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1590	>	}
1591	>
1592	>	info->the_integrator = myNVE;
1593	>	break;
1594	>
1595	>	case NVT_ENS:
1596	>	if (globals->haveZconstraints()){
1597	>	setupZConstraint(info[k]);
1598	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1599	>	}
1600	>	else
1601	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1602	>
1603	>	myNVT->setTargetTemp(globals->getTargetTemp());
1604	>
1605	>	if (globals->haveTauThermostat())
1606	>	myNVT->setTauThermostat(globals->getTauThermostat());
1607	>	else{
1608	>	sprintf(painCave.errMsg,
1609	>	"SimSetup error: If you use the NVT\n"
1610	>	"\tensemble, you must set tauThermostat.\n");
1611	>	painCave.isFatal = 1;
1612	>	simError();
1613	>	}
1614	>
1615	>	info->the_integrator = myNVT;
1616	>	break;
1617	>
1618	>	case NPTi_ENS:
1619	>	if (globals->haveZconstraints()){
1620	>	setupZConstraint(info[k]);
1621	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1622	>	}
1623	>	else
1624	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1625	>
1626	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1627	>
1628	>	if (globals->haveTargetPressure())
1629	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1630	>	else{
1631	>	sprintf(painCave.errMsg,
1632	>	"SimSetup error: If you use a constant pressure\n"
1633	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1634	>	painCave.isFatal = 1;
1635	>	simError();
1636	>	}
1637	>
1638	>	if (globals->haveTauThermostat())
1639	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1640	>	else{
1641	>	sprintf(painCave.errMsg,
1642	>	"SimSetup error: If you use an NPT\n"
1643	>	"\tensemble, you must set tauThermostat.\n");
1644	>	painCave.isFatal = 1;
1645	>	simError();
1646	>	}
1647	>
1648	>	if (globals->haveTauBarostat())
1649	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1650	>	else{
1651	>	sprintf(painCave.errMsg,
1652	>	"SimSetup error: If you use an NPT\n"
1653	>	"\tensemble, you must set tauBarostat.\n");
1654	>	painCave.isFatal = 1;
1655	>	simError();
1656	>	}
1657	>
1658	>	info->the_integrator = myNPTi;
1659	>	break;
1660	>
1661	>	case NPTf_ENS:
1662	>	if (globals->haveZconstraints()){
1663	>	setupZConstraint(info[k]);
1664	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1665	>	}
1666	>	else
1667	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1668	>
1669	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1670	>
1671	>	if (globals->haveTargetPressure())
1672	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1673	>	else{
1674	>	sprintf(painCave.errMsg,
1675	>	"SimSetup error: If you use a constant pressure\n"
1676	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1677	>	painCave.isFatal = 1;
1678	>	simError();
1679	>	}
1680	>
1681	>	if (globals->haveTauThermostat())
1682	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1683	>
1684	>	else{
1685	>	sprintf(painCave.errMsg,
1686	>	"SimSetup error: If you use an NPT\n"
1687	>	"\tensemble, you must set tauThermostat.\n");
1688	>	painCave.isFatal = 1;
1689	>	simError();
1690	>	}
1691	>
1692	>	if (globals->haveTauBarostat())
1693	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1694	>
1695	>	else{
1696	>	sprintf(painCave.errMsg,
1697	>	"SimSetup error: If you use an NPT\n"
1698	>	"\tensemble, you must set tauBarostat.\n");
1699	>	painCave.isFatal = 1;
1700	>	simError();
1701	>	}
1702	>
1703	>	info->the_integrator = myNPTf;
1704	>	break;
1705	>
1706	>	case NPTxyz_ENS:
1707	>	if (globals->haveZconstraints()){
1708	>	setupZConstraint(info[k]);
1709	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1710	>	}
1711	>	else
1712	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1713	>
1714	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1715	>
1716	>	if (globals->haveTargetPressure())
1717	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1718	>	else{
1719	>	sprintf(painCave.errMsg,
1720	>	"SimSetup error: If you use a constant pressure\n"
1721	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1722	>	painCave.isFatal = 1;
1723	>	simError();
1724	>	}
1725	>
1726	>	if (globals->haveTauThermostat())
1727	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1728	>	else{
1729	>	sprintf(painCave.errMsg,
1730	>	"SimSetup error: If you use an NPT\n"
1731	>	"\tensemble, you must set tauThermostat.\n");
1732	>	painCave.isFatal = 1;
1733	>	simError();
1734	>	}
1735	>
1736	>	if (globals->haveTauBarostat())
1737	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1738	>	else{
1739	>	sprintf(painCave.errMsg,
1740	>	"SimSetup error: If you use an NPT\n"
1741	>	"\tensemble, you must set tauBarostat.\n");
1742	>	painCave.isFatal = 1;
1743	>	simError();
1744	>	}
1745	>
1746	>	info->the_integrator = myNPTxyz;
1747	>	break;
1748	>
1749	>	default:
1750	>	sprintf(painCave.errMsg,
1751	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1752	>	painCave.isFatal = 1;
1753	>	simError();
1754	>	}
1755		}
1756		}
1757	+
1758	+	void SimSetup::initFortran(void){
1759	+	info[0].refreshSim();
1760	+
1761	+	if (!strcmp(info[0].mixingRule, "standard")){
1762	+	the_ff->initForceField(LB_MIXING_RULE);
1763	+	}
1764	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1765	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1766	+	}
1767	+	else{
1768	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1769	+	info[0].mixingRule);
1770	+	painCave.isFatal = 1;
1771	+	simError();
1772	+	}
1773	+
1774	+
1775	+	#ifdef IS_MPI
1776	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1777	+	MPIcheckPoint();
1778	+	#endif // is_mpi
1779	+	}
1780	+
1781	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1782	+	int nZConstraints;
1783	+	ZconStamp** zconStamp;
1784	+
1785	+	if (globals->haveZconstraintTime()){
1786	+	//add sample time of z-constraint  into SimInfo's property list
1787	+	DoubleData* zconsTimeProp = new DoubleData();
1788	+	zconsTimeProp->setID(ZCONSTIME_ID);
1789	+	zconsTimeProp->setData(globals->getZconsTime());
1790	+	theInfo.addProperty(zconsTimeProp);
1791	+	}
1792	+	else{
1793	+	sprintf(painCave.errMsg,
1794	+	"ZConstraint error: If you use a ZConstraint,\n"
1795	+	"\tyou must set zconsTime.\n");
1796	+	painCave.isFatal = 1;
1797	+	simError();
1798	+	}
1799	+
1800	+	//push zconsTol into siminfo, if user does not specify
1801	+	//value for zconsTol, a default value will be used
1802	+	DoubleData* zconsTol = new DoubleData();
1803	+	zconsTol->setID(ZCONSTOL_ID);
1804	+	if (globals->haveZconsTol()){
1805	+	zconsTol->setData(globals->getZconsTol());
1806	+	}
1807	+	else{
1808	+	double defaultZConsTol = 0.01;
1809	+	sprintf(painCave.errMsg,
1810	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1811	+	"\tOOPSE will use a default value of %f.\n"
1812	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1813	+	defaultZConsTol);
1814	+	painCave.isFatal = 0;
1815	+	simError();
1816	+
1817	+	zconsTol->setData(defaultZConsTol);
1818	+	}
1819	+	theInfo.addProperty(zconsTol);
1820	+
1821	+	//set Force Subtraction Policy
1822	+	StringData* zconsForcePolicy = new StringData();
1823	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1824	+
1825	+	if (globals->haveZconsForcePolicy()){
1826	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1827	+	}
1828	+	else{
1829	+	sprintf(painCave.errMsg,
1830	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1831	+	"\tOOPSE will use PolicyByMass.\n"
1832	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1833	+	painCave.isFatal = 0;
1834	+	simError();
1835	+	zconsForcePolicy->setData("BYMASS");
1836	+	}
1837	+
1838	+	theInfo.addProperty(zconsForcePolicy);
1839	+
1840	+	//set zcons gap
1841	+	DoubleData* zconsGap = new DoubleData();
1842	+	zconsGap->setID(ZCONSGAP_ID);
1843	+
1844	+	if (globals->haveZConsGap()){
1845	+	zconsGap->setData(globals->getZconsGap());
1846	+	theInfo.addProperty(zconsGap);
1847	+	}
1848	+
1849	+	//set zcons fixtime
1850	+	DoubleData* zconsFixtime = new DoubleData();
1851	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1852	+
1853	+	if (globals->haveZConsFixTime()){
1854	+	zconsFixtime->setData(globals->getZconsFixtime());
1855	+	theInfo.addProperty(zconsFixtime);
1856	+	}
1857	+
1858	+	//set zconsUsingSMD
1859	+	IntData* zconsUsingSMD = new IntData();
1860	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1861	+
1862	+	if (globals->haveZConsUsingSMD()){
1863	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1864	+	theInfo.addProperty(zconsUsingSMD);
1865	+	}
1866	+
1867	+	//Determine the name of ouput file and add it into SimInfo's property list
1868	+	//Be careful, do not use inFileName, since it is a pointer which
1869	+	//point to a string at master node, and slave nodes do not contain that string
1870	+
1871	+	string zconsOutput(theInfo.finalName);
1872	+
1873	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1874	+
1875	+	StringData* zconsFilename = new StringData();
1876	+	zconsFilename->setID(ZCONSFILENAME_ID);
1877	+	zconsFilename->setData(zconsOutput);
1878	+
1879	+	theInfo.addProperty(zconsFilename);
1880	+
1881	+	//setup index, pos and other parameters of z-constraint molecules
1882	+	nZConstraints = globals->getNzConstraints();
1883	+	theInfo.nZconstraints = nZConstraints;
1884	+
1885	+	zconStamp = globals->getZconStamp();
1886	+	ZConsParaItem tempParaItem;
1887	+
1888	+	ZConsParaData* zconsParaData = new ZConsParaData();
1889	+	zconsParaData->setID(ZCONSPARADATA_ID);
1890	+
1891	+	for (int i = 0; i < nZConstraints; i++){
1892	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1893	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1894	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1895	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1896	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1897	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1898	+	zconsParaData->addItem(tempParaItem);
1899	+	}
1900	+
1901	+	//check the uniqueness of index
1902	+	if(!zconsParaData->isIndexUnique()){
1903	+	sprintf(painCave.errMsg,
1904	+	"ZConstraint Error: molIndex is not unique!\n");
1905	+	painCave.isFatal = 1;
1906	+	simError();
1907	+	}
1908	+
1909	+	//sort the parameters by index of molecules
1910	+	zconsParaData->sortByIndex();
1911	+
1912	+	//push data into siminfo, therefore, we can retrieve later
1913	+	theInfo.addProperty(zconsParaData);
1914	+	}
1915	+
1916	+	void SimSetup::makeMinimizer(){
1917	+
1918	+	OOPSEMinimizer* myOOPSEMinimizer;
1919	+	MinimizerParameterSet* param;
1920	+	char minimizerName[100];
1921	+
1922	+	for (int i = 0; i < nInfo; i++){
1923	+
1924	+	//prepare parameter set for minimizer
1925	+	param = new MinimizerParameterSet();
1926	+	param->setDefaultParameter();
1927	+
1928	+	if (globals->haveMinimizer()){
1929	+	param->setFTol(globals->getMinFTol());
1930	+	}
1931	+
1932	+	if (globals->haveMinGTol()){
1933	+	param->setGTol(globals->getMinGTol());
1934	+	}
1935	+
1936	+	if (globals->haveMinMaxIter()){
1937	+	param->setMaxIteration(globals->getMinMaxIter());
1938	+	}
1939	+
1940	+	if (globals->haveMinWriteFrq()){
1941	+	param->setMaxIteration(globals->getMinMaxIter());
1942	+	}
1943	+
1944	+	if (globals->haveMinWriteFrq()){
1945	+	param->setWriteFrq(globals->getMinWriteFrq());
1946	+	}
1947	+
1948	+	if (globals->haveMinStepSize()){
1949	+	param->setStepSize(globals->getMinStepSize());
1950	+	}
1951	+
1952	+	if (globals->haveMinLSMaxIter()){
1953	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1954	+	}
1955	+
1956	+	if (globals->haveMinLSTol()){
1957	+	param->setLineSearchTol(globals->getMinLSTol());
1958	+	}
1959	+
1960	+	strcpy(minimizerName, globals->getMinimizer());
1961	+
1962	+	if (!strcasecmp(minimizerName, "CG")){
1963	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1964	+	}
1965	+	else if (!strcasecmp(minimizerName, "SD")){
1966	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1967	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1968	+	}
1969	+	else{
1970	+	sprintf(painCave.errMsg,
1971	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1972	+	painCave.isFatal = 0;
1973	+	simError();
1974	+
1975	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1976	+	}
1977	+	info[i].the_integrator = myOOPSEMinimizer;
1978	+
1979	+	//store the minimizer into simInfo
1980	+	info[i].the_minimizer = myOOPSEMinimizer;
1981	+	info[i].has_minimizer = true;
1982	+	}
1983	+
1984	+	}

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