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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 604 by gezelter, Tue Jul 15 03:08:00 2003 UTC vs.
Revision 701 by tim, Wed Aug 20 14:34:04 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 14 | Line 17
17
18		// some defines for ensemble and Forcefield  cases
19
20	<	#define NVE_ENS   0
21	<	#define NVT_ENS   1
22	<	#define NPTi_ENS  2
23	<	#define NPTf_ENS  3
24	<	#define NPTim_ENS 4
25	<	#define NPTfm_ENS 5
20	>	#define NVE_ENS        0
21	>	#define NVT_ENS        1
22	>	#define NPTi_ENS       2
23	>	#define NPTf_ENS       3
24	>	#define NPTim_ENS      4
25	>	#define NPTfm_ENS      5
26
24	–
27		#define FF_DUFF 0
28		#define FF_LJ   1
29	+	#define FF_EAM  2
30
31	+	using namespace std;
32
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 41 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 76 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
81	–	MakeStamps *the_stamps;
82	–	Globals* the_globals;
97		int i, j, k, globalAtomIndex;
98
99	<	int ensembleCase;
86	<	int ffCase;
87	<
88	<	ensembleCase = -1;
89	<	ffCase = -1;
99	>	// gather all of the information from the Bass file
100
101	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
101	>	gatherInfo();
102
103	<	// set the easy ones first
96	<	simnfo->target_temp = the_globals->getTargetTemp();
97	<	simnfo->dt = the_globals->getDt();
98	<	simnfo->run_time = the_globals->getRunTime();
103	>	// creation of complex system objects
104
105	<	// get the ones we know are there, yet still may need some work.
101	<	n_components = the_globals->getNComponents();
102	<	strcpy( force_field, the_globals->getForceField() );
105	>	sysObjectsCreation();
106
107	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106	<	else{
107	<	sprintf( painCave.errMsg,
108	<	"SimSetup Error. Unrecognized force field -> %s\n",
109	<	force_field );
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
107	>	// check on the post processing info
108
109	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
109	>	finalInfoCheck();
110
111	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
118	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
119	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
120	<	ensembleCase = NPTi_ENS;
121	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
122	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
123	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124	<	else{
125	<	sprintf( painCave.errMsg,
126	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
127	<	"reverting to NVE for this simulation.\n",
128	<	ensemble );
129	<	painCave.isFatal = 0;
130	<	simError();
131	<	strcpy( ensemble, "NVE" );
132	<	ensembleCase = NVE_ENS;
133	<	}
134	<	strcpy( simnfo->ensemble, ensemble );
111	>	// initialize the system coordinates
112
113	+	if( !isInfoArray ) initSystemCoords();
114
115	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
138	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
139	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140	<	//     if (the_globals->haveTargetPressure())
141	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142	<	//     else {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "SimSetup error: If you use the constant pressure\n"
145	<	//                "    ensemble, you must set targetPressure.\n"
146	<	//                "    This was found in the BASS file.\n");
147	<	//       painCave.isFatal = 1;
148	<	//       simError();
149	<	//     }
115	>	// make the output filenames
116
117	<	//     if (the_globals->haveTauThermostat())
118	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
119	<	//     else if (the_globals->haveQmass())
120	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
121	<	//     else {
122	<	//       sprintf( painCave.errMsg,
123	<	//                "SimSetup error: If you use one of the constant temperature\n"
124	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
125	<	//                "    Neither of these was found in the BASS file.\n");
160	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
117	>	makeOutNames();
118	>
119	>	// make the integrator
120	>
121	>	makeIntegrator();
122	>
123	>	#ifdef IS_MPI
124	>	mpiSim->mpiRefresh();
125	>	#endif
126
127	<	//     if (the_globals->haveTauBarostat())
165	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166	<	//     else {
167	<	//       sprintf( painCave.errMsg,
168	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
127	>	// initialize the Fortran
128
129	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
176	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
177	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
129	>	initFortran();
130
179	–	//     if (the_globals->haveTauThermostat())
180	–	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181	–	//     else if (the_globals->haveQmass())
182	–	//       the_extendedsystem->setQmass(the_globals->getQmass());
183	–	//     else {
184	–	//       sprintf( painCave.errMsg,
185	–	//                "SimSetup error: If you use one of the constant temperature\n"
186	–	//                "    ensembles, you must set either tauThermostat or qMass.\n"
187	–	//                "    Neither of these was found in the BASS file.\n");
188	–	//       painCave.isFatal = 1;
189	–	//       simError();
190	–	//     }
131
192	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
193	–	simnfo->usePBC = the_globals->getPBC();
194	–
195	–	int usesDipoles = 0;
196	–	switch( ffCase ){
132
133	<	case FF_DUFF:
199	<	the_ff = new DUFF();
200	<	usesDipoles = 1;
201	<	break;
133	>	}
134
203	–	case FF_LJ:
204	–	the_ff = new LJFF();
205	–	break;
135
136	<	default:
208	<	sprintf( painCave.errMsg,
209	<	"SimSetup Error. Unrecognized force field in case statement.\n");
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
136	>	void SimSetup::makeMolecules( void ){
137
138	<	#ifdef IS_MPI
139	<	strcpy( checkPointMsg, "ForceField creation successful" );
140	<	MPIcheckPoint();
141	<	#endif // is_mpi
138	>	int k,l;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	// get the components and calculate the tot_nMol and indvidual n_mol
150	<	the_components = the_globals->getComponents();
151	<	components_nmol = new int[n_components];
222	<	comp_stamps = new MoleculeStamp*[n_components];
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
153	<	if( !the_globals->haveNMol() ){
154	<	// we don't have the total number of molecules, so we assume it is
226	<	// given in each component
153	>
154	>	//init the forceField paramters
155
156	<	tot_nmol = 0;
229	<	for( i=0; i<n_components; i++ ){
156	>	the_ff->readParams();
157
158	<	if( !the_components[i]->haveNMol() ){
159	<	// we have a problem
233	<	sprintf( painCave.errMsg,
234	<	"SimSetup Error. No global NMol or component NMol"
235	<	" given. Cannot calculate the number of atoms.\n" );
236	<	painCave.isFatal = 1;
237	<	simError();
238	<	}
158	>
159	>	// init the atoms
160
161	<	tot_nmol += the_components[i]->getNMol();
162	<	components_nmol[i] = the_components[i]->getNMol();
163	<	}
243	<	}
244	<	else{
245	<	sprintf( painCave.errMsg,
246	<	"SimSetup error.\n"
247	<	"\tSorry, the ability to specify total"
248	<	" nMols and then give molfractions in the components\n"
249	<	"\tis not currently supported."
250	<	" Please give nMol in the components.\n" );
251	<	painCave.isFatal = 1;
252	<	simError();
161	>	double ux, uy, uz, u, uSqr;
162	>
163	>	for(k=0; k<nInfo; k++){
164
165	+	the_ff->setSimInfo( &(info[k]) );
166	+
167	+	atomOffset = 0;
168	+	excludeOffset = 0;
169	+	for(i=0; i<info[k].n_mol; i++){
170
171	<	//     tot_nmol = the_globals->getNMol();
171	>	stampID = info[k].molecules[i].getStampID();
172	>
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178	>
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184	>
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188
189	<	//   //we have the total number of molecules, now we check for molfractions
258	<	//     for( i=0; i<n_components; i++ ){
189	>	// make the Atoms
190
191	<	//       if( !the_components[i]->haveMolFraction() ){
191	>	for(j=0; j<molInfo.nAtoms; j++){
192	>
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195
196	<	//  if( !the_components[i]->haveNMol() ){
197	<	//    //we have a problem
198	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
199	<	//              << " nMol was given in component
196	>	dAtom = new DirectionalAtom( (j + atomOffset),
197	>	info[k].getConfiguration() );
198	>	info[k].n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200
201	<	}
202	<
203	<	#ifdef IS_MPI
270	<	strcpy( checkPointMsg, "Have the number of components" );
271	<	MPIcheckPoint();
272	<	#endif // is_mpi
273	<
274	<	// make an array of molecule stamps that match the components used.
275	<	// also extract the used stamps out into a separate linked list
276	<
277	<	simnfo->nComponents = n_components;
278	<	simnfo->componentsNmol = components_nmol;
279	<	simnfo->compStamps = comp_stamps;
280	<	simnfo->headStamp = new LinkedMolStamp();
281	<
282	<	char* id;
283	<	LinkedMolStamp* headStamp = simnfo->headStamp;
284	<	LinkedMolStamp* currentStamp = NULL;
285	<	for( i=0; i<n_components; i++ ){
286	<
287	<	id = the_components[i]->getType();
288	<	comp_stamps[i] = NULL;
201	>	ux = currentAtom->getOrntX();
202	>	uy = currentAtom->getOrntY();
203	>	uz = currentAtom->getOrntZ();
204
205	<	// check to make sure the component isn't already in the list
206	<
207	<	comp_stamps[i] = headStamp->match( id );
208	<	if( comp_stamps[i] == NULL ){
209	<
210	<	// extract the component from the list;
211	<
212	<	currentStamp = the_stamps->extractMolStamp( id );
213	<	if( currentStamp == NULL ){
214	<	sprintf( painCave.errMsg,
300	<	"SimSetup error: Component \"%s\" was not found in the "
301	<	"list of declared molecules\n",
302	<	id );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<
307	<	headStamp->add( currentStamp );
308	<	comp_stamps[i] = headStamp->match( id );
309	<	}
205	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	>
207	>	u = sqrt( uSqr );
208	>	ux = ux / u;
209	>	uy = uy / u;
210	>	uz = uz / u;
211	>
212	>	dAtom->setSUx( ux );
213	>	dAtom->setSUy( uy );
214	>	dAtom->setSUz( uz );
215		}
216	<
216	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	>	info[k].getConfiguration() );
219	>	}
220	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	>
222		#ifdef IS_MPI
223	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
224	<	MPIcheckPoint();
223	>
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	>
226		#endif // is_mpi
227	<
317	<
318	<
319	<
320	<	// caclulate the number of atoms, bonds, bends and torsions
321	<
322	<	tot_atoms = 0;
323	<	tot_bonds = 0;
324	<	tot_bends = 0;
325	<	tot_torsions = 0;
326	<	for( i=0; i<n_components; i++ ){
227	>	}
228
229	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
230	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
231	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
232	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
233	<	}
234	<
334	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
335	<
336	<	simnfo->n_atoms = tot_atoms;
337	<	simnfo->n_bonds = tot_bonds;
338	<	simnfo->n_bends = tot_bends;
339	<	simnfo->n_torsions = tot_torsions;
340	<	simnfo->n_SRI = tot_SRI;
341	<	simnfo->n_mol = tot_nmol;
229	>	// make the bonds
230	>	for(j=0; j<molInfo.nBonds; j++){
231	>
232	>	currentBond = comp_stamps[stampID]->getBond( j );
233	>	theBonds[j].a = currentBond->getA() + atomOffset;
234	>	theBonds[j].b = currentBond->getB() + atomOffset;
235
236	<	simnfo->molMembershipArray = new int[tot_atoms];
237	<
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244	>	}
245		#ifdef IS_MPI
246	<
247	<	// divide the molecules among processors here.
246	>	tempEx = exI;
247	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	>	tempEx = exJ;
249	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250
251	<	mpiSim = new mpiSimulation( simnfo );
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252	>	#else  // isn't MPI
253
254	<	globalIndex = mpiSim->divideLabor();
255	<
256	<	// set up the local variables
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	>	#endif  //is_mpi
256	>	}
257	>	excludeOffset += molInfo.nBonds;
258	>
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261
262	<	int localMol, allMol;
263	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
264	<
265	<	int* mol2proc = mpiSim->getMolToProcMap();
359	<	int* molCompType = mpiSim->getMolComponentType();
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266
267	<	allMol = 0;
268	<	localMol = 0;
269	<	local_atoms = 0;
270	<	local_bonds = 0;
271	<	local_bends = 0;
272	<	local_torsions = 0;
273	<	globalAtomIndex = 0;
274	<
275	<
276	<	for( i=0; i<n_components; i++ ){
277	<
278	<	for( j=0; j<components_nmol[i]; j++ ){
267	>	if( currentBend->haveExtras() ){
268	>
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276	>
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290	>	sprintf( painCave.errMsg,
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298	>	}
299
300	<	if( mol2proc[allMol] == worldRank ){
301	<
302	<	local_atoms +=    comp_stamps[i]->getNAtoms();
303	<	local_bonds +=    comp_stamps[i]->getNBonds();
304	<	local_bends +=    comp_stamps[i]->getNBends();
305	<	local_torsions += comp_stamps[i]->getNTorsions();
306	<	localMol++;
307	<	}
308	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
384	<	globalAtomIndex++;
300	>	else{
301	>
302	>	sprintf( painCave.errMsg,
303	>	"SimSetup Error: unhandled bend assignment:\n"
304	>	"    -->%s in Bend[%d] in %s\n",
305	>	current_extra->getlhs(),
306	>	j, comp_stamps[stampID]->getID() );
307	>	painCave.isFatal = 1;
308	>	simError();
309		}
310	<
311	<	allMol++;
310	>
311	>	current_extra = current_extra->getNext();
312		}
313		}
390	–	local_SRI = local_bonds + local_bends + local_torsions;
314
315	<	simnfo->n_atoms = mpiSim->getMyNlocal();
315	>	if( !theBends[j].isGhost ){
316	>
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].c;
319	>	}
320	>	else{
321	>
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].b;
324	>	}
325
326	<	if( local_atoms != simnfo->n_atoms ){
327	<	sprintf( painCave.errMsg,
328	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
329	<	" localAtom (%d) are not equal.\n",
330	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
401	<	simError();
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331		}
332	<
333	<	simnfo->n_bonds = local_bonds;
334	<	simnfo->n_bends = local_bends;
335	<	simnfo->n_torsions = local_torsions;
336	<	simnfo->n_SRI = local_SRI;
337	<	simnfo->n_mol = localMol;
338	<
339	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
340	<	MPIcheckPoint();
332	>	#ifdef IS_MPI
333	>	tempEx = exI;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	>
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	#else  // isn't MPI
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	#endif  //is_mpi
342	>	}
343	>	excludeOffset += molInfo.nBends;
344	>
345	>	for(j=0; j<molInfo.nTorsions; j++){
346
347	+	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352
353	<	#endif // is_mpi
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355
356	<
357	<	// create the atom and short range interaction arrays
358	<
359	<	Atom::createArrays(simnfo->n_atoms);
360	<	the_atoms = new Atom*[simnfo->n_atoms];
361	<	the_molecules = new Molecule[simnfo->n_mol];
422	<	int molIndex;
423	<
424	<	// initialize the molecule's stampID's
425	<
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361	>	}
362		#ifdef IS_MPI
363	+	tempEx = exI;
364	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	+	tempEx = exJ;
366	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367
368	<
369	<	molIndex = 0;
370	<	for(i=0; i<mpiSim->getTotNmol(); i++){
371	<
432	<	if(mol2proc[i] == worldRank ){
433	<	the_molecules[molIndex].setStampID( molCompType[i] );
434	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
439	<
440	<	#else // is_mpi
441	<
442	<	molIndex = 0;
443	<	globalAtomIndex = 0;
444	<	for(i=0; i<n_components; i++){
445	<	for(j=0; j<components_nmol[i]; j++ ){
446	<	the_molecules[molIndex].setStampID( i );
447	<	the_molecules[molIndex].setMyIndex( molIndex );
448	<	the_molecules[molIndex].setGlobalIndex( molIndex );
449	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
450	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
451	<	globalAtomIndex++;
368	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369	>	#else  // isn't MPI
370	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371	>	#endif  //is_mpi
372		}
373	<	molIndex++;
373	>	excludeOffset += molInfo.nTorsions;
374	>
375	>
376	>	// send the arrays off to the forceField for init.
377	>
378	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	>
383	>
384	>	info[k].molecules[i].initialize( molInfo );
385	>
386	>
387	>	atomOffset += molInfo.nAtoms;
388	>	delete[] theBonds;
389	>	delete[] theBends;
390	>	delete[] theTorsions;
391		}
392		}
393	<
394	<
393	>
394	>	#ifdef IS_MPI
395	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
396	>	MPIcheckPoint();
397		#endif // is_mpi
398	+
399	+	// clean up the forcefield
400
401	+	the_ff->calcRcut();
402	+	the_ff->cleanMe();
403	+
404	+	}
405
406	<	if( simnfo->n_SRI ){
462	<
463	<	Exclude::createArray(simnfo->n_SRI);
464	<	the_excludes = new Exclude*[simnfo->n_SRI];
465	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
466	<	simnfo->globalExcludes = new int;
467	<	simnfo->n_exclude = simnfo->n_SRI;
468	<	}
469	<	else{
470	<
471	<	Exclude::createArray( 1 );
472	<	the_excludes = new Exclude*;
473	<	the_excludes[0] = new Exclude(0);
474	<	the_excludes[0]->setPair( 0,0 );
475	<	simnfo->globalExcludes = new int;
476	<	simnfo->globalExcludes[0] = 0;
477	<	simnfo->n_exclude = 0;
478	<	}
406	>	void SimSetup::initFromBass( void ){
407
408	<	// set the arrays into the SimInfo object
408	>	int i, j, k;
409	>	int n_cells;
410	>	double cellx, celly, cellz;
411	>	double temp1, temp2, temp3;
412	>	int n_per_extra;
413	>	int n_extra;
414	>	int have_extra, done;
415
416	<	simnfo->atoms = the_atoms;
417	<	simnfo->molecules = the_molecules;
418	<	simnfo->nGlobalExcludes = 0;
419	<	simnfo->excludes = the_excludes;
416	>	double vel[3];
417	>	vel[0] = 0.0;
418	>	vel[1] = 0.0;
419	>	vel[2] = 0.0;
420
421	+	temp1 = (double)tot_nmol / 4.0;
422	+	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423	+	temp3 = ceil( temp2 );
424
425	<	// get some of the tricky things that may still be in the globals
425	>	have_extra =0;
426	>	if( temp2 < temp3 ){ // we have a non-complete lattice
427	>	have_extra =1;
428
429	<	double boxVector[3];
430	<	if( the_globals->haveBox() ){
431	<	boxVector[0] = the_globals->getBox();
432	<	boxVector[1] = the_globals->getBox();
433	<	boxVector[2] = the_globals->getBox();
434	<
435	<	simnfo->setBox( boxVector );
497	<	}
498	<	else if( the_globals->haveDensity() ){
429	>	n_cells = (int)temp3 - 1;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435	>	n_per_extra = (int)ceil( temp1 );
436
437	<	double vol;
501	<	vol = (double)tot_nmol / the_globals->getDensity();
502	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
503	<	boxVector[1] = boxVector[0];
504	<	boxVector[2] = boxVector[0];
505	<
506	<	simnfo->setBox( boxVector );
507	<	}
508	<	else{
509	<	if( !the_globals->haveBoxX() ){
437	>	if( n_per_extra > 4){
438		sprintf( painCave.errMsg,
439	<	"SimSetup error, no periodic BoxX size given.\n" );
439	>	"SimSetup error. There has been an error in constructing"
440	>	" the non-complete lattice.\n" );
441		painCave.isFatal = 1;
442		simError();
443		}
444	<	boxVector[0] = the_globals->getBoxX();
444	>	}
445	>	else{
446	>	n_cells = (int)temp3;
447	>	cellx = info[0].boxL[0] / temp3;
448	>	celly = info[0].boxL[1] / temp3;
449	>	cellz = info[0].boxL[2] / temp3;
450	>	}
451
452	<	if( !the_globals->haveBoxY() ){
453	<	sprintf( painCave.errMsg,
454	<	"SimSetup error, no periodic BoxY size given.\n" );
455	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	boxVector[1] = the_globals->getBoxY();
452	>	current_mol = 0;
453	>	current_comp_mol = 0;
454	>	current_comp = 0;
455	>	current_atom_ndx = 0;
456
457	<	if( !the_globals->haveBoxZ() ){
458	<	sprintf( painCave.errMsg,
459	<	"SimSetup error, no periodic BoxZ size given.\n" );
460	<	painCave.isFatal = 1;
461	<	simError();
457	>	for( i=0; i < n_cells ; i++ ){
458	>	for( j=0; j < n_cells; j++ ){
459	>	for( k=0; k < n_cells; k++ ){
460	>
461	>	makeElement( i * cellx,
462	>	j * celly,
463	>	k * cellz );
464	>
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly + 0.5 * celly,
467	>	k * cellz );
468	>
469	>	makeElement( i * cellx,
470	>	j * celly + 0.5 * celly,
471	>	k * cellz + 0.5 * cellz );
472	>
473	>	makeElement( i * cellx + 0.5 * cellx,
474	>	j * celly,
475	>	k * cellz + 0.5 * cellz );
476	>	}
477		}
478	<	boxVector[2] = the_globals->getBoxZ();
478	>	}
479
480	<	simnfo->setBox( boxVector );
480	>	if( have_extra ){
481	>	done = 0;
482	>
483	>	int start_ndx;
484	>	for( i=0; i < (n_cells+1) && !done; i++ ){
485	>	for( j=0; j < (n_cells+1) && !done; j++ ){
486	>
487	>	if( i < n_cells ){
488	>
489	>	if( j < n_cells ){
490	>	start_ndx = n_cells;
491	>	}
492	>	else start_ndx = 0;
493		}
494	+	else start_ndx = 0;
495
496	<	#ifdef IS_MPI
537	<	strcpy( checkPointMsg, "Box size set up" );
538	<	MPIcheckPoint();
539	<	#endif // is_mpi
496	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497
498	+	makeElement( i * cellx,
499	+	j * celly,
500	+	k * cellz );
501	+	done = ( current_mol >= tot_nmol );
502
503	<	// initialize the arrays
503	>	if( !done && n_per_extra > 1 ){
504	>	makeElement( i * cellx + 0.5 * cellx,
505	>	j * celly + 0.5 * celly,
506	>	k * cellz );
507	>	done = ( current_mol >= tot_nmol );
508	>	}
509
510	<	the_ff->setSimInfo( simnfo );
510	>	if( !done && n_per_extra > 2){
511	>	makeElement( i * cellx,
512	>	j * celly + 0.5 * celly,
513	>	k * cellz + 0.5 * cellz );
514	>	done = ( current_mol >= tot_nmol );
515	>	}
516
517	<	makeMolecules();
518	<	simnfo->identArray = new int[simnfo->n_atoms];
519	<	for(i=0; i<simnfo->n_atoms; i++){
520	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
517	>	if( !done && n_per_extra > 3){
518	>	makeElement( i * cellx + 0.5 * cellx,
519	>	j * celly,
520	>	k * cellz + 0.5 * cellz );
521	>	done = ( current_mol >= tot_nmol );
522	>	}
523		}
524	<
552	<	if (the_globals->getUseRF() ) {
553	<	simnfo->useReactionField = 1;
554	<
555	<	if( !the_globals->haveECR() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 1/2 the smallest "
558	<	"box length for the electrostaticCutoffRadius.\n"
559	<	"I hope you have a very fast processor!\n");
560	<	painCave.isFatal = 0;
561	<	simError();
562	<	double smallest;
563	<	smallest = simnfo->boxLx;
564	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566	<	simnfo->ecr = 0.5 * smallest;
567	<	} else {
568	<	simnfo->ecr        = the_globals->getECR();
524	>	}
525		}
526	+	}
527
528	<	if( !the_globals->haveEST() ){
529	<	sprintf( painCave.errMsg,
530	<	"SimSetup Warning: using default value of 0.05 * the "
531	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
532	<	);
533	<	painCave.isFatal = 0;
534	<	simError();
535	<	simnfo->est = 0.05 * simnfo->ecr;
536	<	} else {
537	<	simnfo->est        = the_globals->getEST();
538	<	}
539	<
540	<	if(!the_globals->haveDielectric() ){
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530	>	}
531	>	}
532	>
533	>	void SimSetup::makeElement( double x, double y, double z ){
534	>
535	>	int k;
536	>	AtomStamp* current_atom;
537	>	DirectionalAtom* dAtom;
538	>	double rotMat[3][3];
539	>	double pos[3];
540	>
541	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542	>
543	>	current_atom = comp_stamps[current_comp]->getAtom( k );
544	>	if( !current_atom->havePosition() ){
545		sprintf( painCave.errMsg,
546	<	"SimSetup Error: You are trying to use Reaction Field without"
547	<	"setting a dielectric constant!\n"
548	<	);
546	>	"SimSetup:initFromBass error.\n"
547	>	"\tComponent %s, atom %s does not have a position specified.\n"
548	>	"\tThe initialization routine is unable to give a start"
549	>	" position.\n",
550	>	comp_stamps[current_comp]->getID(),
551	>	current_atom->getType() );
552		painCave.isFatal = 1;
553		simError();
554		}
555	<	simnfo->dielectric = the_globals->getDielectric();
556	<	} else {
557	<	if (usesDipoles) {
558	<
559	<	if( !the_globals->haveECR() ){
560	<	sprintf( painCave.errMsg,
561	<	"SimSetup Warning: using default value of 1/2 the smallest "
562	<	"box length for the electrostaticCutoffRadius.\n"
563	<	"I hope you have a very fast processor!\n");
564	<	painCave.isFatal = 0;
565	<	simError();
566	<	double smallest;
567	<	smallest = simnfo->boxLx;
568	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
569	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
570	<	simnfo->ecr = 0.5 * smallest;
571	<	} else {
572	<	simnfo->ecr        = the_globals->getECR();
573	<	}
574	<
575	<	if( !the_globals->haveEST() ){
576	<	sprintf( painCave.errMsg,
577	<	"SimSetup Warning: using default value of 5%% of the "
578	<	"electrostaticCutoffRadius for the "
615	<	"electrostaticSkinThickness\n"
616	<	);
617	<	painCave.isFatal = 0;
618	<	simError();
619	<	simnfo->est = 0.05 * simnfo->ecr;
620	<	} else {
621	<	simnfo->est        = the_globals->getEST();
622	<	}
555	>
556	>	pos[0] = x + current_atom->getPosX();
557	>	pos[1] = y + current_atom->getPosY();
558	>	pos[2] = z + current_atom->getPosZ();
559	>
560	>	info[0].atoms[current_atom_ndx]->setPos( pos );
561	>
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563	>
564	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565	>
566	>	rotMat[0][0] = 1.0;
567	>	rotMat[0][1] = 0.0;
568	>	rotMat[0][2] = 0.0;
569	>
570	>	rotMat[1][0] = 0.0;
571	>	rotMat[1][1] = 1.0;
572	>	rotMat[1][2] = 0.0;
573	>
574	>	rotMat[2][0] = 0.0;
575	>	rotMat[2][1] = 0.0;
576	>	rotMat[2][2] = 1.0;
577	>
578	>	dAtom->setA( rotMat );
579		}
624	–	}
580
581	<	#ifdef IS_MPI
582	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
628	<	MPIcheckPoint();
629	<	#endif // is_mpi
581	>	current_atom_ndx++;
582	>	}
583
584	<	if( the_globals->haveInitialConfig() ){
585	<
633	<	InitializeFromFile* fileInit;
634	<	#ifdef IS_MPI // is_mpi
635	<	if( worldRank == 0 ){
636	<	#endif //is_mpi
637	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
638	<	#ifdef IS_MPI
639	<	}else fileInit = new InitializeFromFile( NULL );
640	<	#endif
641	<	fileInit->read_xyz( simnfo ); // default velocities on
584	>	current_mol++;
585	>	current_comp_mol++;
586
587	<	delete fileInit;
644	<	}
645	<	else{
587	>	if( current_comp_mol >= components_nmol[current_comp] ){
588
589	<	#ifdef IS_MPI
589	>	current_comp_mol = 0;
590	>	current_comp++;
591	>	}
592	>	}
593
594	<	// no init from bass
594	>
595	>	void SimSetup::gatherInfo( void ){
596	>	int i,j,k;
597	>
598	>	ensembleCase = -1;
599	>	ffCase = -1;
600	>
601	>	// set the easy ones first
602	>
603	>	for( i=0; i<nInfo; i++){
604	>	info[i].target_temp = globals->getTargetTemp();
605	>	info[i].dt = globals->getDt();
606	>	info[i].run_time = globals->getRunTime();
607	>	}
608	>	n_components = globals->getNComponents();
609	>
610	>
611	>	// get the forceField
612	>
613	>	strcpy( force_field, globals->getForceField() );
614	>
615	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618	>	else{
619	>	sprintf( painCave.errMsg,
620	>	"SimSetup Error. Unrecognized force field -> %s\n",
621	>	force_field );
622	>	painCave.isFatal = 1;
623	>	simError();
624	>	}
625	>
626	>	// get the ensemble
627	>
628	>	strcpy( ensemble, globals->getEnsemble() );
629	>
630	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633	>	ensembleCase = NPTi_ENS;
634	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637	>	else{
638	>	sprintf( painCave.errMsg,
639	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	>	"reverting to NVE for this simulation.\n",
641	>	ensemble );
642	>	painCave.isFatal = 0;
643	>	simError();
644	>	strcpy( ensemble, "NVE" );
645	>	ensembleCase = NVE_ENS;
646	>	}
647
648	<	sprintf( painCave.errMsg,
649	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
650	<	painCave.isFatal;
651	<	simError();
648	>	for(i=0; i<nInfo; i++){
649	>
650	>	strcpy( info[i].ensemble, ensemble );
651	>
652	>	// get the mixing rule
653	>
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657
658	<	#else
658	>	// get the components and calculate the tot_nMol and indvidual n_mol
659	>
660	>	the_components = globals->getComponents();
661	>	components_nmol = new int[n_components];
662
658	–	initFromBass();
663
664	+	if( !globals->haveNMol() ){
665	+	// we don't have the total number of molecules, so we assume it is
666	+	// given in each component
667
668	<	#endif
669	<	}
668	>	tot_nmol = 0;
669	>	for( i=0; i<n_components; i++ ){
670
671	<	#ifdef IS_MPI
672	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
673	<	MPIcheckPoint();
674	<	#endif // is_mpi
671	>	if( !the_components[i]->haveNMol() ){
672	>	// we have a problem
673	>	sprintf( painCave.errMsg,
674	>	"SimSetup Error. No global NMol or component NMol"
675	>	" given. Cannot calculate the number of atoms.\n" );
676	>	painCave.isFatal = 1;
677	>	simError();
678	>	}
679
680	+	tot_nmol += the_components[i]->getNMol();
681	+	components_nmol[i] = the_components[i]->getNMol();
682	+	}
683	+	}
684	+	else{
685	+	sprintf( painCave.errMsg,
686	+	"SimSetup error.\n"
687	+	"\tSorry, the ability to specify total"
688	+	" nMols and then give molfractions in the components\n"
689	+	"\tis not currently supported."
690	+	" Please give nMol in the components.\n" );
691	+	painCave.isFatal = 1;
692	+	simError();
693	+	}
694
695	<
671	<
695	>	// set the status, sample, and thermal kick times
696
697	+	for(i=0; i<nInfo; i++){
698
699	<
700	<	#ifdef IS_MPI
701	<	if( worldRank == 0 ){
702	<	#endif // is_mpi
678	<
679	<	if( the_globals->haveFinalConfig() ){
680	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
699	>	if( globals->haveSampleTime() ){
700	>	info[i].sampleTime = globals->getSampleTime();
701	>	info[i].statusTime = info[i].sampleTime;
702	>	info[i].thermalTime = info[i].sampleTime;
703		}
704		else{
705	<	strcpy( simnfo->finalName, inFileName );
706	<	char* endTest;
707	<	int nameLength = strlen( simnfo->finalName );
686	<	endTest = &(simnfo->finalName[nameLength - 5]);
687	<	if( !strcmp( endTest, ".bass" ) ){
688	<	strcpy( endTest, ".eor" );
689	<	}
690	<	else if( !strcmp( endTest, ".BASS" ) ){
691	<	strcpy( endTest, ".eor" );
692	<	}
693	<	else{
694	<	endTest = &(simnfo->finalName[nameLength - 4]);
695	<	if( !strcmp( endTest, ".bss" ) ){
696	<	strcpy( endTest, ".eor" );
697	<	}
698	<	else if( !strcmp( endTest, ".mdl" ) ){
699	<	strcpy( endTest, ".eor" );
700	<	}
701	<	else{
702	<	strcat( simnfo->finalName, ".eor" );
703	<	}
704	<	}
705	>	info[i].sampleTime = globals->getRunTime();
706	>	info[i].statusTime = info[i].sampleTime;
707	>	info[i].thermalTime = info[i].sampleTime;
708		}
709
710	<	// make the sample and status out names
710	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712	>	}
713
714	<	strcpy( simnfo->sampleName, inFileName );
715	<	char* endTest;
711	<	int nameLength = strlen( simnfo->sampleName );
712	<	endTest = &(simnfo->sampleName[nameLength - 5]);
713	<	if( !strcmp( endTest, ".bass" ) ){
714	<	strcpy( endTest, ".dump" );
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716		}
717	<	else if( !strcmp( endTest, ".BASS" ) ){
718	<	strcpy( endTest, ".dump" );
717	>
718	>	// check for the temperature set flag
719	>
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721	>
722	>	// get some of the tricky things that may still be in the globals
723	>
724	>	double boxVector[3];
725	>	if( globals->haveBox() ){
726	>	boxVector[0] = globals->getBox();
727	>	boxVector[1] = globals->getBox();
728	>	boxVector[2] = globals->getBox();
729	>
730	>	info[i].setBox( boxVector );
731		}
732	+	else if( globals->haveDensity() ){
733	+
734	+	double vol;
735	+	vol = (double)tot_nmol / globals->getDensity();
736	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	+	boxVector[1] = boxVector[0];
738	+	boxVector[2] = boxVector[0];
739	+
740	+	info[i].setBox( boxVector );
741	+	}
742		else{
743	<	endTest = &(simnfo->sampleName[nameLength - 4]);
744	<	if( !strcmp( endTest, ".bss" ) ){
745	<	strcpy( endTest, ".dump" );
743	>	if( !globals->haveBoxX() ){
744	>	sprintf( painCave.errMsg,
745	>	"SimSetup error, no periodic BoxX size given.\n" );
746	>	painCave.isFatal = 1;
747	>	simError();
748		}
749	<	else if( !strcmp( endTest, ".mdl" ) ){
750	<	strcpy( endTest, ".dump" );
749	>	boxVector[0] = globals->getBoxX();
750	>
751	>	if( !globals->haveBoxY() ){
752	>	sprintf( painCave.errMsg,
753	>	"SimSetup error, no periodic BoxY size given.\n" );
754	>	painCave.isFatal = 1;
755	>	simError();
756		}
757	<	else{
758	<	strcat( simnfo->sampleName, ".dump" );
757	>	boxVector[1] = globals->getBoxY();
758	>
759	>	if( !globals->haveBoxZ() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxZ size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764		}
765	+	boxVector[2] = globals->getBoxZ();
766	+
767	+	info[i].setBox( boxVector );
768		}
769	+
770	+	}
771
772	<	strcpy( simnfo->statusName, inFileName );
773	<	nameLength = strlen( simnfo->statusName );
774	<	endTest = &(simnfo->statusName[nameLength - 5]);
775	<	if( !strcmp( endTest, ".bass" ) ){
776	<	strcpy( endTest, ".stat" );
772	>	#ifdef IS_MPI
773	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
774	>	MPIcheckPoint();
775	>	#endif // is_mpi
776	>
777	>	}
778	>
779	>
780	>	void SimSetup::finalInfoCheck( void ){
781	>	int index;
782	>	int usesDipoles;
783	>	int i;
784	>
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787	>
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793		}
794	<	else if( !strcmp( endTest, ".BASS" ) ){
795	<	strcpy( endTest, ".stat" );
796	<	}
797	<	else{
798	<	endTest = &(simnfo->statusName[nameLength - 4]);
799	<	if( !strcmp( endTest, ".bss" ) ){
800	<	strcpy( endTest, ".stat" );
794	>
795	>	#ifdef IS_MPI
796	>	int myUse = usesDipoles;
797	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798	>	#endif //is_mpi
799	>
800	>	double theEcr, theEst;
801	>
802	>	if (globals->getUseRF() ) {
803	>	info[i].useReactionField = 1;
804	>
805	>	if( !globals->haveECR() ){
806	>	sprintf( painCave.errMsg,
807	>	"SimSetup Warning: using default value of 1/2 the smallest "
808	>	"box length for the electrostaticCutoffRadius.\n"
809	>	"I hope you have a very fast processor!\n");
810	>	painCave.isFatal = 0;
811	>	simError();
812	>	double smallest;
813	>	smallest = info[i].boxL[0];
814	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	>	theEcr = 0.5 * smallest;
817	>	} else {
818	>	theEcr = globals->getECR();
819		}
820	<	else if( !strcmp( endTest, ".mdl" ) ){
821	<	strcpy( endTest, ".stat" );
820	>
821	>	if( !globals->haveEST() ){
822	>	sprintf( painCave.errMsg,
823	>	"SimSetup Warning: using default value of 0.05 * the "
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	>	);
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	theEst = 0.05 * theEcr;
829	>	} else {
830	>	theEst= globals->getEST();
831		}
832	<	else{
833	<	strcat( simnfo->statusName, ".stat" );
832	>
833	>	info[i].setEcr( theEcr, theEst );
834	>
835	>	if(!globals->haveDielectric() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Error: You are trying to use Reaction Field without"
838	>	"setting a dielectric constant!\n"
839	>	);
840	>	painCave.isFatal = 1;
841	>	simError();
842		}
843	<	}
843	>	info[i].dielectric = globals->getDielectric();
844	>	}
845	>	else {
846	>	if (usesDipoles) {
847	>
848	>	if( !globals->haveECR() ){
849	>	sprintf( painCave.errMsg,
850	>	"SimSetup Warning: using default value of 1/2 the smallest "
851	>	"box length for the electrostaticCutoffRadius.\n"
852	>	"I hope you have a very fast processor!\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	double smallest;
856	>	smallest = info[i].boxL[0];
857	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	>	theEcr = 0.5 * smallest;
860	>	} else {
861	>	theEcr = globals->getECR();
862	>	}
863	>
864	>	if( !globals->haveEST() ){
865	>	sprintf( painCave.errMsg,
866	>	"SimSetup Warning: using default value of 0.05 * the "
867	>	"electrostaticCutoffRadius for the "
868	>	"electrostaticSkinThickness\n"
869	>	);
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	theEst = 0.05 * theEcr;
873	>	} else {
874	>	theEst= globals->getEST();
875	>	}
876	>
877	>	info[i].setEcr( theEcr, theEst );
878	>	}
879	>	}
880	>	}
881	>
882	>	#ifdef IS_MPI
883	>	strcpy( checkPointMsg, "post processing checks out" );
884	>	MPIcheckPoint();
885	>	#endif // is_mpi
886	>
887	>	}
888	>
889	>	void SimSetup::initSystemCoords( void ){
890	>	int i;
891	>
892	>	char* inName;
893	>
894	>
895	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
896	>
897	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
898	>
899	>	if( globals->haveInitialConfig() ){
900
901	+	InitializeFromFile* fileInit;
902	+	#ifdef IS_MPI // is_mpi
903	+	if( worldRank == 0 ){
904	+	#endif //is_mpi
905	+	inName = globals->getInitialConfig();
906	+	double* tempDouble = new double[1000000];
907	+	fileInit = new InitializeFromFile( inName );
908		#ifdef IS_MPI
909	+	}else fileInit = new InitializeFromFile( NULL );
910	+	#endif
911	+	fileInit->readInit( info ); // default velocities on
912	+
913	+	delete fileInit;
914		}
915	+	else{
916	+
917	+	#ifdef IS_MPI
918	+
919	+	// no init from bass
920	+
921	+	sprintf( painCave.errMsg,
922	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923	+	painCave.isFatal;
924	+	simError();
925	+
926	+	#else
927	+
928	+	initFromBass();
929	+
930	+
931	+	#endif
932	+	}
933	+
934	+	#ifdef IS_MPI
935	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
936	+	MPIcheckPoint();
937		#endif // is_mpi
938
939	<	// set the status, sample, and themal kick times
939	>	}
940	>
941	>
942	>	void SimSetup::makeOutNames( void ){
943
944	<	if( the_globals->haveSampleTime() ){
945	<	simnfo->sampleTime = the_globals->getSampleTime();
946	<	simnfo->statusTime = simnfo->sampleTime;
947	<	simnfo->thermalTime = simnfo->sampleTime;
944	>	int k;
945	>
946	>
947	>	for(k=0; k<nInfo; k++){
948	>
949	>	#ifdef IS_MPI
950	>	if( worldRank == 0 ){
951	>	#endif // is_mpi
952	>
953	>	if( globals->haveFinalConfig() ){
954	>	strcpy( info[k].finalName, globals->getFinalConfig() );
955	>	}
956	>	else{
957	>	strcpy( info[k].finalName, inFileName );
958	>	char* endTest;
959	>	int nameLength = strlen( info[k].finalName );
960	>	endTest = &(info[k].finalName[nameLength - 5]);
961	>	if( !strcmp( endTest, ".bass" ) ){
962	>	strcpy( endTest, ".eor" );
963		}
964	+	else if( !strcmp( endTest, ".BASS" ) ){
965	+	strcpy( endTest, ".eor" );
966	+	}
967		else{
968	<	simnfo->sampleTime = the_globals->getRunTime();
969	<	simnfo->statusTime = simnfo->sampleTime;
970	<	simnfo->thermalTime = simnfo->sampleTime;
968	>	endTest = &(info[k].finalName[nameLength - 4]);
969	>	if( !strcmp( endTest, ".bss" ) ){
970	>	strcpy( endTest, ".eor" );
971	>	}
972	>	else if( !strcmp( endTest, ".mdl" ) ){
973	>	strcpy( endTest, ".eor" );
974	>	}
975	>	else{
976	>	strcat( info[k].finalName, ".eor" );
977	>	}
978		}
979	<
980	<	if( the_globals->haveStatusTime() ){
981	<	simnfo->statusTime = the_globals->getStatusTime();
979	>	}
980	>
981	>	// make the sample and status out names
982	>
983	>	strcpy( info[k].sampleName, inFileName );
984	>	char* endTest;
985	>	int nameLength = strlen( info[k].sampleName );
986	>	endTest = &(info[k].sampleName[nameLength - 5]);
987	>	if( !strcmp( endTest, ".bass" ) ){
988	>	strcpy( endTest, ".dump" );
989	>	}
990	>	else if( !strcmp( endTest, ".BASS" ) ){
991	>	strcpy( endTest, ".dump" );
992	>	}
993	>	else{
994	>	endTest = &(info[k].sampleName[nameLength - 4]);
995	>	if( !strcmp( endTest, ".bss" ) ){
996	>	strcpy( endTest, ".dump" );
997		}
998	<
999	<	if( the_globals->haveThermalTime() ){
776	<	simnfo->thermalTime = the_globals->getThermalTime();
998	>	else if( !strcmp( endTest, ".mdl" ) ){
999	>	strcpy( endTest, ".dump" );
1000		}
1001	+	else{
1002	+	strcat( info[k].sampleName, ".dump" );
1003	+	}
1004	+	}
1005	+
1006	+	strcpy( info[k].statusName, inFileName );
1007	+	nameLength = strlen( info[k].statusName );
1008	+	endTest = &(info[k].statusName[nameLength - 5]);
1009	+	if( !strcmp( endTest, ".bass" ) ){
1010	+	strcpy( endTest, ".stat" );
1011	+	}
1012	+	else if( !strcmp( endTest, ".BASS" ) ){
1013	+	strcpy( endTest, ".stat" );
1014	+	}
1015	+	else{
1016	+	endTest = &(info[k].statusName[nameLength - 4]);
1017	+	if( !strcmp( endTest, ".bss" ) ){
1018	+	strcpy( endTest, ".stat" );
1019	+	}
1020	+	else if( !strcmp( endTest, ".mdl" ) ){
1021	+	strcpy( endTest, ".stat" );
1022	+	}
1023	+	else{
1024	+	strcat( info[k].statusName, ".stat" );
1025	+	}
1026	+	}
1027	+
1028	+	#ifdef IS_MPI
1029	+	}
1030	+	#endif // is_mpi
1031	+	}
1032	+	}
1033
779	–	// check for the temperature set flag
1034
1035	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
782	<
783	<
784	<	// make the integrator
1035	>	void SimSetup::sysObjectsCreation( void ){
1036
1037	+	int i,k;
1038
1039	<	NVT*  myNVT = NULL;
788	<	NPTi* myNPTi = NULL;
789	<	NPTf* myNPTf = NULL;
790	<	NPTim* myNPTim = NULL;
1039	>	// create the forceField
1040
1041	<	switch( ensembleCase ){
1041	>	createFF();
1042
1043	<	case NVE_ENS:
795	<	new NVE( simnfo, the_ff );
796	<	break;
1043	>	// extract componentList
1044
1045	<	case NVT_ENS:
799	<	myNVT = new NVT( simnfo, the_ff );
800	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
1045	>	compList();
1046
1047	<	if (the_globals->haveTauThermostat())
803	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
1047	>	// calc the number of atoms, bond, bends, and torsions
1048
1049	<	else {
1050	<	sprintf( painCave.errMsg,
1051	<	"SimSetup error: If you use the NVT\n"
1052	<	"    ensemble, you must set tauThermostat.\n");
1053	<	painCave.isFatal = 1;
1054	<	simError();
1055	<	}
1056	<	break;
1049	>	calcSysValues();
1050	>
1051	>	#ifdef IS_MPI
1052	>	// divide the molecules among the processors
1053	>
1054	>	mpiMolDivide();
1055	>	#endif //is_mpi
1056	>
1057	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1058	>
1059	>	makeSysArrays();
1060
1061	<	case NPTi_ENS:
1062	<	myNPTi = new NPTi( simnfo, the_ff );
1063	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
1064	<
1065	<	if (the_globals->haveTargetPressure())
1066	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
1067	<	else {
1068	<	sprintf( painCave.errMsg,
822	<	"SimSetup error: If you use a constant pressure\n"
823	<	"    ensemble, you must set targetPressure in the BASS file.\n");
824	<	painCave.isFatal = 1;
825	<	simError();
1061	>	// make and initialize the molecules (all but atomic coordinates)
1062	>
1063	>	makeMolecules();
1064	>
1065	>	for(k=0; k<nInfo; k++){
1066	>	info[k].identArray = new int[info[k].n_atoms];
1067	>	for(i=0; i<info[k].n_atoms; i++){
1068	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1069		}
1070	<
1071	<	if( the_globals->haveTauThermostat() )
829	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
830	<	else{
831	<	sprintf( painCave.errMsg,
832	<	"SimSetup error: If you use an NPT\n"
833	<	"    ensemble, you must set tauThermostat.\n");
834	<	painCave.isFatal = 1;
835	<	simError();
836	<	}
1070	>	}
1071	>	}
1072
838	–	if( the_globals->haveTauBarostat() )
839	–	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
840	–	else{
841	–	sprintf( painCave.errMsg,
842	–	"SimSetup error: If you use an NPT\n"
843	–	"    ensemble, you must set tauBarostat.\n");
844	–	painCave.isFatal = 1;
845	–	simError();
846	–	}
847	–	break;
1073
1074	<	case NPTf_ENS:
850	<	myNPTf = new NPTf( simnfo, the_ff );
851	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
1074	>	void SimSetup::createFF( void ){
1075
1076	<	if (the_globals->haveTargetPressure())
854	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
855	<	else {
856	<	sprintf( painCave.errMsg,
857	<	"SimSetup error: If you use a constant pressure\n"
858	<	"    ensemble, you must set targetPressure in the BASS file.\n");
859	<	painCave.isFatal = 1;
860	<	simError();
861	<	}
1076	>	switch( ffCase ){
1077
1078	<	if( the_globals->haveTauThermostat() )
1079	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
1080	<	else{
866	<	sprintf( painCave.errMsg,
867	<	"SimSetup error: If you use an NPT\n"
868	<	"    ensemble, you must set tauThermostat.\n");
869	<	painCave.isFatal = 1;
870	<	simError();
871	<	}
1078	>	case FF_DUFF:
1079	>	the_ff = new DUFF();
1080	>	break;
1081
1082	<	if( the_globals->haveTauBarostat() )
1083	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
875	<	else{
876	<	sprintf( painCave.errMsg,
877	<	"SimSetup error: If you use an NPT\n"
878	<	"    ensemble, you must set tauBarostat.\n");
879	<	painCave.isFatal = 1;
880	<	simError();
881	<	}
1082	>	case FF_LJ:
1083	>	the_ff = new LJFF();
1084		break;
883	–
884	–	case NPTim_ENS:
885	–	myNPTim = new NPTim( simnfo, the_ff );
886	–	myNPTim->setTargetTemp( the_globals->getTargetTemp());
1085
1086	<	if (the_globals->haveTargetPressure())
1087	<	myNPTim->setTargetPressure(the_globals->getTargetPressure());
890	<	else {
891	<	sprintf( painCave.errMsg,
892	<	"SimSetup error: If you use a constant pressure\n"
893	<	"    ensemble, you must set targetPressure in the BASS file.\n");
894	<	painCave.isFatal = 1;
895	<	simError();
896	<	}
897	<
898	<	if( the_globals->haveTauThermostat() )
899	<	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
900	<	else{
901	<	sprintf( painCave.errMsg,
902	<	"SimSetup error: If you use an NPT\n"
903	<	"    ensemble, you must set tauThermostat.\n");
904	<	painCave.isFatal = 1;
905	<	simError();
906	<	}
907	<
908	<	if( the_globals->haveTauBarostat() )
909	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
910	<	else{
911	<	sprintf( painCave.errMsg,
912	<	"SimSetup error: If you use an NPT\n"
913	<	"    ensemble, you must set tauBarostat.\n");
914	<	painCave.isFatal = 1;
915	<	simError();
916	<	}
1086	>	case FF_EAM:
1087	>	the_ff = new EAM_FF();
1088		break;
1089
919	–
920	–
1090		default:
1091		sprintf( painCave.errMsg,
1092	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1092	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1093		painCave.isFatal = 1;
1094		simError();
1095		}
1096
928	–
1097		#ifdef IS_MPI
1098	<	mpiSim->mpiRefresh();
1099	<	#endif
1098	>	strcpy( checkPointMsg, "ForceField creation successful" );
1099	>	MPIcheckPoint();
1100	>	#endif // is_mpi
1101
1102	<	// initialize the Fortran
1102	>	}
1103
1104
1105	<	simnfo->refreshSim();
1105	>	void SimSetup::compList( void ){
1106	>
1107	>	int i;
1108	>	char* id;
1109	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1110	>	LinkedMolStamp* currentStamp = NULL;
1111	>	comp_stamps = new MoleculeStamp*[n_components];
1112
1113	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1114	<	the_ff->initForceField( LB_MIXING_RULE );
1113	>	// make an array of molecule stamps that match the components used.
1114	>	// also extract the used stamps out into a separate linked list
1115	>
1116	>	for(i=0; i<nInfo; i++){
1117	>	info[i].nComponents = n_components;
1118	>	info[i].componentsNmol = components_nmol;
1119	>	info[i].compStamps = comp_stamps;
1120	>	info[i].headStamp = headStamp;
1121		}
1122	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
942	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
943	<	}
944	<	else{
945	<	sprintf( painCave.errMsg,
946	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
947	<	simnfo->mixingRule );
948	<	painCave.isFatal = 1;
949	<	simError();
950	<	}
1122	>
1123
1124	+	for( i=0; i<n_components; i++ ){
1125
1126	+	id = the_components[i]->getType();
1127	+	comp_stamps[i] = NULL;
1128	+
1129	+	// check to make sure the component isn't already in the list
1130	+
1131	+	comp_stamps[i] = headStamp->match( id );
1132	+	if( comp_stamps[i] == NULL ){
1133	+
1134	+	// extract the component from the list;
1135	+
1136	+	currentStamp = stamps->extractMolStamp( id );
1137	+	if( currentStamp == NULL ){
1138	+	sprintf( painCave.errMsg,
1139	+	"SimSetup error: Component \"%s\" was not found in the "
1140	+	"list of declared molecules\n",
1141	+	id );
1142	+	painCave.isFatal = 1;
1143	+	simError();
1144	+	}
1145	+
1146	+	headStamp->add( currentStamp );
1147	+	comp_stamps[i] = headStamp->match( id );
1148	+	}
1149	+	}
1150	+
1151		#ifdef IS_MPI
1152	<	strcpy( checkPointMsg,
955	<	"Successfully intialized the mixingRule for Fortran." );
1152	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1153		MPIcheckPoint();
1154		#endif // is_mpi
1155	+
1156	+
1157		}
1158
1159	+	void SimSetup::calcSysValues( void ){
1160	+	int i, j, k;
1161	+
1162	+	int *molMembershipArray;
1163	+
1164	+	tot_atoms = 0;
1165	+	tot_bonds = 0;
1166	+	tot_bends = 0;
1167	+	tot_torsions = 0;
1168	+	for( i=0; i<n_components; i++ ){
1169	+
1170	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1172	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1173	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174	+	}
1175	+
1176	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	+	molMembershipArray = new int[tot_atoms];
1178	+
1179	+	for(i=0; i<nInfo; i++){
1180	+	info[i].n_atoms = tot_atoms;
1181	+	info[i].n_bonds = tot_bonds;
1182	+	info[i].n_bends = tot_bends;
1183	+	info[i].n_torsions = tot_torsions;
1184	+	info[i].n_SRI = tot_SRI;
1185	+	info[i].n_mol = tot_nmol;
1186	+
1187	+	info[i].molMembershipArray = molMembershipArray;
1188	+	}
1189	+	}
1190
1191	<	void SimSetup::makeMolecules( void ){
1191	>	#ifdef IS_MPI
1192
1193	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
1194	<	molInit info;
1195	<	DirectionalAtom* dAtom;
1196	<	LinkedAssign* extras;
1197	<	LinkedAssign* current_extra;
968	<	AtomStamp* currentAtom;
969	<	BondStamp* currentBond;
970	<	BendStamp* currentBend;
971	<	TorsionStamp* currentTorsion;
1193	>	void SimSetup::mpiMolDivide( void ){
1194	>
1195	>	int i, j, k;
1196	>	int localMol, allMol;
1197	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1198
1199	<	bond_pair* theBonds;
1200	<	bend_set* theBends;
1201	<	torsion_set* theTorsions;
1199	>	mpiSim = new mpiSimulation( info );
1200	>
1201	>	globalIndex = mpiSim->divideLabor();
1202
1203	+	// set up the local variables
1204
1205	<	//init the forceField paramters
1205	>	mol2proc = mpiSim->getMolToProcMap();
1206	>	molCompType = mpiSim->getMolComponentType();
1207	>
1208	>	allMol = 0;
1209	>	localMol = 0;
1210	>	local_atoms = 0;
1211	>	local_bonds = 0;
1212	>	local_bends = 0;
1213	>	local_torsions = 0;
1214	>	globalAtomIndex = 0;
1215
980	–	the_ff->readParams();
1216
1217	+	for( i=0; i<n_components; i++ ){
1218	+
1219	+	for( j=0; j<components_nmol[i]; j++ ){
1220	+
1221	+	if( mol2proc[allMol] == worldRank ){
1222
1223	<	// init the atoms
1223	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1224	>	local_bonds +=    comp_stamps[i]->getNBonds();
1225	>	local_bends +=    comp_stamps[i]->getNBends();
1226	>	local_torsions += comp_stamps[i]->getNTorsions();
1227	>	localMol++;
1228	>	}
1229	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1230	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1231	>	globalAtomIndex++;
1232	>	}
1233
1234	<	double ux, uy, uz, u, uSqr;
1234	>	allMol++;
1235	>	}
1236	>	}
1237	>	local_SRI = local_bonds + local_bends + local_torsions;
1238
1239	<	atomOffset = 0;
1240	<	excludeOffset = 0;
1241	<	for(i=0; i<simnfo->n_mol; i++){
1242	<
1243	<	stampID = the_molecules[i].getStampID();
1239	>	info[0].n_atoms = mpiSim->getMyNlocal();
1240	>
1241	>	if( local_atoms != info[0].n_atoms ){
1242	>	sprintf( painCave.errMsg,
1243	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244	>	" localAtom (%d) are not equal.\n",
1245	>	info[0].n_atoms,
1246	>	local_atoms );
1247	>	painCave.isFatal = 1;
1248	>	simError();
1249	>	}
1250
1251	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
1252	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
1253	<	info.nBends    = comp_stamps[stampID]->getNBends();
1254	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
1255	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
1251	>	info[0].n_bonds = local_bonds;
1252	>	info[0].n_bends = local_bends;
1253	>	info[0].n_torsions = local_torsions;
1254	>	info[0].n_SRI = local_SRI;
1255	>	info[0].n_mol = localMol;
1256
1257	<	info.myAtoms = &the_atoms[atomOffset];
1258	<	info.myExcludes = &the_excludes[excludeOffset];
1259	<	info.myBonds = new Bond*[info.nBonds];
1260	<	info.myBends = new Bend*[info.nBends];
1261	<	info.myTorsions = new Torsion*[info.nTorsions];
1257	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1258	>	MPIcheckPoint();
1259	>	}
1260	>
1261	>	#endif // is_mpi
1262
1263	<	theBonds = new bond_pair[info.nBonds];
1264	<	theBends = new bend_set[info.nBends];
1265	<	theTorsions = new torsion_set[info.nTorsions];
1263	>
1264	>	void SimSetup::makeSysArrays( void ){
1265	>	int i, j, k, l;
1266	>
1267	>	Atom** the_atoms;
1268	>	Molecule* the_molecules;
1269	>	Exclude** the_excludes;
1270	>
1271	>
1272	>	for(l=0; l<nInfo; l++){
1273
1274	<	// make the Atoms
1274	>	// create the atom and short range interaction arrays
1275
1276	<	for(j=0; j<info.nAtoms; j++){
1277	<
1278	<	currentAtom = comp_stamps[stampID]->getAtom( j );
1279	<	if( currentAtom->haveOrientation() ){
1280	<
1281	<	dAtom = new DirectionalAtom(j + atomOffset);
1282	<	simnfo->n_oriented++;
1283	<	info.myAtoms[j] = dAtom;
1284	<
1285	<	ux = currentAtom->getOrntX();
1286	<	uy = currentAtom->getOrntY();
1287	<	uz = currentAtom->getOrntZ();
1288	<
1289	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1290	<
1291	<	u = sqrt( uSqr );
1292	<	ux = ux / u;
1293	<	uy = uy / u;
1294	<	uz = uz / u;
1295	<
1296	<	dAtom->setSUx( ux );
1297	<	dAtom->setSUy( uy );
1298	<	dAtom->setSUz( uz );
1276	>	the_atoms = new Atom*[info[l].n_atoms];
1277	>	the_molecules = new Molecule[info[l].n_mol];
1278	>	int molIndex;
1279	>
1280	>	// initialize the molecule's stampID's
1281	>
1282	>	#ifdef IS_MPI
1283	>
1284	>
1285	>	molIndex = 0;
1286	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1287	>
1288	>	if(mol2proc[i] == worldRank ){
1289	>	the_molecules[molIndex].setStampID( molCompType[i] );
1290	>	the_molecules[molIndex].setMyIndex( molIndex );
1291	>	the_molecules[molIndex].setGlobalIndex( i );
1292	>	molIndex++;
1293	>	}
1294	>	}
1295	>
1296	>	#else // is_mpi
1297	>
1298	>	molIndex = 0;
1299	>	globalAtomIndex = 0;
1300	>	for(i=0; i<n_components; i++){
1301	>	for(j=0; j<components_nmol[i]; j++ ){
1302	>	the_molecules[molIndex].setStampID( i );
1303	>	the_molecules[molIndex].setMyIndex( molIndex );
1304	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1305	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1306	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1307	>	globalAtomIndex++;
1308	>	}
1309	>	molIndex++;
1310		}
1311	<	else{
1036	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
1037	<	}
1038	<	info.myAtoms[j]->setType( currentAtom->getType() );
1311	>	}
1312
1040	–	#ifdef IS_MPI
1041	–
1042	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1043	–
1044	–	#endif // is_mpi
1045	–	}
1313
1314	<	// make the bonds
1048	<	for(j=0; j<info.nBonds; j++){
1049	<
1050	<	currentBond = comp_stamps[stampID]->getBond( j );
1051	<	theBonds[j].a = currentBond->getA() + atomOffset;
1052	<	theBonds[j].b = currentBond->getB() + atomOffset;
1314	>	#endif // is_mpi
1315
1054	–	exI = theBonds[j].a;
1055	–	exJ = theBonds[j].b;
1316
1317	<	// exclude_I must always be the smaller of the pair
1318	<	if( exI > exJ ){
1319	<	tempEx = exI;
1320	<	exI = exJ;
1321	<	exJ = tempEx;
1317	>	if( info[l].n_SRI ){
1318	>
1319	>	Exclude::createArray(info[l].n_SRI);
1320	>	the_excludes = new Exclude*[info[l].n_SRI];
1321	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	>	the_excludes[ex] = new Exclude(ex);
1323		}
1324	<	#ifdef IS_MPI
1325	<	tempEx = exI;
1326	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1327	<	tempEx = exJ;
1328	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].n_exclude = info[l].n_SRI;
1326	>	}
1327	>	else{
1328	>
1329	>	Exclude::createArray( 1 );
1330	>	the_excludes = new Exclude*;
1331	>	the_excludes[0] = new Exclude(0);
1332	>	the_excludes[0]->setPair( 0,0 );
1333	>	info[l].globalExcludes = new int;
1334	>	info[l].globalExcludes[0] = 0;
1335	>	info[l].n_exclude = 0;
1336	>	}
1337	>
1338	>	// set the arrays into the SimInfo object
1339	>
1340	>	info[l].atoms = the_atoms;
1341	>	info[l].molecules = the_molecules;
1342	>	info[l].nGlobalExcludes = 0;
1343	>	info[l].excludes = the_excludes;
1344	>
1345	>	the_ff->setSimInfo( info );
1346	>
1347	>	}
1348	>	}
1349	>
1350	>	void SimSetup::makeIntegrator( void ){
1351	>
1352	>	int k;
1353	>
1354	>	NVT<RealIntegrator>*  myNVT = NULL;
1355	>	NPTi<RealIntegrator>* myNPTi = NULL;
1356	>	NPTf<RealIntegrator>* myNPTf = NULL;
1357	>	NPTim<RealIntegrator>* myNPTim = NULL;
1358	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1359	>
1360	>	for(k=0; k<nInfo; k++){
1361	>
1362	>	switch( ensembleCase ){
1363
1364	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1365	<	#else  // isn't MPI
1364	>	case NVE_ENS:
1365	>	if (globals->haveZconstraints()){
1366	>	setupZConstraint(info[k]);
1367	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1368	>	}
1369
1370	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1371	<	#endif  //is_mpi
1372	<	}
1373	<	excludeOffset += info.nBonds;
1370	>	else
1371	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1372	>	break;
1373	>
1374	>	case NVT_ENS:
1375	>	if (globals->haveZconstraints()){
1376	>	setupZConstraint(info[k]);
1377	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	>	}
1379	>	else
1380	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1381
1382	<	//make the bends
1078	<	for(j=0; j<info.nBends; j++){
1382	>	myNVT->setTargetTemp(globals->getTargetTemp());
1383
1384	<	currentBend = comp_stamps[stampID]->getBend( j );
1385	<	theBends[j].a = currentBend->getA() + atomOffset;
1386	<	theBends[j].b = currentBend->getB() + atomOffset;
1387	<	theBends[j].c = currentBend->getC() + atomOffset;
1388	<
1389	<	if( currentBend->haveExtras() ){
1390	<
1391	<	extras = currentBend->getExtras();
1392	<	current_extra = extras;
1393	<
1394	<	while( current_extra != NULL ){
1395	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1396	<
1397	<	switch( current_extra->getType() ){
1398	<
1399	<	case 0:
1096	<	theBends[j].ghost =
1097	<	current_extra->getInt() + atomOffset;
1098	<	theBends[j].isGhost = 1;
1099	<	break;
1100	<
1101	<	case 1:
1102	<	theBends[j].ghost =
1103	<	(int)current_extra->getDouble() + atomOffset;
1104	<	theBends[j].isGhost = 1;
1105	<	break;
1106	<
1107	<	default:
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup Error: ghostVectorSource was neither a "
1110	<	"double nor an int.\n"
1111	<	"-->Bend[%d] in %s\n",
1112	<	j, comp_stamps[stampID]->getID() );
1113	<	painCave.isFatal = 1;
1114	<	simError();
1115	<	}
1116	<	}
1117	<
1118	<	else{
1119	<
1120	<	sprintf( painCave.errMsg,
1121	<	"SimSetup Error: unhandled bend assignment:\n"
1122	<	"    -->%s in Bend[%d] in %s\n",
1123	<	current_extra->getlhs(),
1124	<	j, comp_stamps[stampID]->getID() );
1125	<	painCave.isFatal = 1;
1126	<	simError();
1127	<	}
1128	<
1129	<	current_extra = current_extra->getNext();
1130	<	}
1384	>	if (globals->haveTauThermostat())
1385	>	myNVT->setTauThermostat(globals->getTauThermostat());
1386	>
1387	>	else {
1388	>	sprintf( painCave.errMsg,
1389	>	"SimSetup error: If you use the NVT\n"
1390	>	"    ensemble, you must set tauThermostat.\n");
1391	>	painCave.isFatal = 1;
1392	>	simError();
1393	>	}
1394	>	break;
1395	>
1396	>	case NPTi_ENS:
1397	>	if (globals->haveZconstraints()){
1398	>	setupZConstraint(info[k]);
1399	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400		}
1401	<
1402	<	if( !theBends[j].isGhost ){
1403	<
1404	<	exI = theBends[j].a;
1405	<	exJ = theBends[j].c;
1401	>	else
1402	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403	>
1404	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	>
1406	>	if (globals->haveTargetPressure())
1407	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	>	else {
1409	>	sprintf( painCave.errMsg,
1410	>	"SimSetup error: If you use a constant pressure\n"
1411	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	>	painCave.isFatal = 1;
1413	>	simError();
1414		}
1415	+
1416	+	if( globals->haveTauThermostat() )
1417	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418		else{
1419	<
1420	<	exI = theBends[j].a;
1421	<	exJ = theBends[j].b;
1419	>	sprintf( painCave.errMsg,
1420	>	"SimSetup error: If you use an NPT\n"
1421	>	"    ensemble, you must set tauThermostat.\n");
1422	>	painCave.isFatal = 1;
1423	>	simError();
1424		}
1425	+
1426	+	if( globals->haveTauBarostat() )
1427	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	+	else{
1429	+	sprintf( painCave.errMsg,
1430	+	"SimSetup error: If you use an NPT\n"
1431	+	"    ensemble, you must set tauBarostat.\n");
1432	+	painCave.isFatal = 1;
1433	+	simError();
1434	+	}
1435	+	break;
1436
1437	<	// exclude_I must always be the smaller of the pair
1438	<	if( exI > exJ ){
1439	<	tempEx = exI;
1440	<	exI = exJ;
1148	<	exJ = tempEx;
1437	>	case NPTf_ENS:
1438	>	if (globals->haveZconstraints()){
1439	>	setupZConstraint(info[k]);
1440	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441		}
1442	<	#ifdef IS_MPI
1443	<	tempEx = exI;
1152	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1153	<	tempEx = exJ;
1154	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1155	<
1156	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1157	<	#else  // isn't MPI
1158	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1159	<	#endif  //is_mpi
1160	<	}
1161	<	excludeOffset += info.nBends;
1442	>	else
1443	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1444
1445	<	for(j=0; j<info.nTorsions; j++){
1446	<
1447	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1448	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1449	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1450	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1451	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1452	<
1453	<	exI = theTorsions[j].a;
1454	<	exJ = theTorsions[j].d;
1455	<
1456	<	// exclude_I must always be the smaller of the pair
1457	<	if( exI > exJ ){
1458	<	tempEx = exI;
1459	<	exI = exJ;
1460	<	exJ = tempEx;
1445	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1446	>
1447	>	if (globals->haveTargetPressure())
1448	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	>	else {
1450	>	sprintf( painCave.errMsg,
1451	>	"SimSetup error: If you use a constant pressure\n"
1452	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	>	painCave.isFatal = 1;
1454	>	simError();
1455	>	}
1456	>
1457	>	if( globals->haveTauThermostat() )
1458	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	>	else{
1460	>	sprintf( painCave.errMsg,
1461	>	"SimSetup error: If you use an NPT\n"
1462	>	"    ensemble, you must set tauThermostat.\n");
1463	>	painCave.isFatal = 1;
1464	>	simError();
1465		}
1466	<	#ifdef IS_MPI
1467	<	tempEx = exI;
1468	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1469	<	tempEx = exJ;
1470	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1466	>
1467	>	if( globals->haveTauBarostat() )
1468	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	>	else{
1470	>	sprintf( painCave.errMsg,
1471	>	"SimSetup error: If you use an NPT\n"
1472	>	"    ensemble, you must set tauBarostat.\n");
1473	>	painCave.isFatal = 1;
1474	>	simError();
1475	>	}
1476	>	break;
1477
1478	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1479	<	#else  // isn't MPI
1480	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1481	<	#endif  //is_mpi
1482	<	}
1483	<	excludeOffset += info.nTorsions;
1478	>	case NPTim_ENS:
1479	>	if (globals->haveZconstraints()){
1480	>	setupZConstraint(info[k]);
1481	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	>	}
1483	>	else
1484	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1485
1486	<
1487	<	// send the arrays off to the forceField for init.
1488	<
1489	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1490	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1491	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1492	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1486	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1487	>
1488	>	if (globals->haveTargetPressure())
1489	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	>	else {
1491	>	sprintf( painCave.errMsg,
1492	>	"SimSetup error: If you use a constant pressure\n"
1493	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	>	painCave.isFatal = 1;
1495	>	simError();
1496	>	}
1497	>
1498	>	if( globals->haveTauThermostat() )
1499	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	>	else{
1501	>	sprintf( painCave.errMsg,
1502	>	"SimSetup error: If you use an NPT\n"
1503	>	"    ensemble, you must set tauThermostat.\n");
1504	>	painCave.isFatal = 1;
1505	>	simError();
1506	>	}
1507	>
1508	>	if( globals->haveTauBarostat() )
1509	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	>	else{
1511	>	sprintf( painCave.errMsg,
1512	>	"SimSetup error: If you use an NPT\n"
1513	>	"    ensemble, you must set tauBarostat.\n");
1514	>	painCave.isFatal = 1;
1515	>	simError();
1516	>	}
1517	>	break;
1518	>
1519	>	case NPTfm_ENS:
1520	>	if (globals->haveZconstraints()){
1521	>	setupZConstraint(info[k]);
1522	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	>	}
1524	>	else
1525	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1526
1527	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1528
1529	<	the_molecules[i].initialize( info );
1529	>	if (globals->haveTargetPressure())
1530	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1531	>	else {
1532	>	sprintf( painCave.errMsg,
1533	>	"SimSetup error: If you use a constant pressure\n"
1534	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1535	>	painCave.isFatal = 1;
1536	>	simError();
1537	>	}
1538
1539	+	if( globals->haveTauThermostat() )
1540	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1541	+	else{
1542	+	sprintf( painCave.errMsg,
1543	+	"SimSetup error: If you use an NPT\n"
1544	+	"    ensemble, you must set tauThermostat.\n");
1545	+	painCave.isFatal = 1;
1546	+	simError();
1547	+	}
1548
1549	<	atomOffset += info.nAtoms;
1550	<	delete[] theBonds;
1551	<	delete[] theBends;
1552	<	delete[] theTorsions;
1553	<	}
1554	<
1555	<	#ifdef IS_MPI
1556	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1557	<	MPIcheckPoint();
1558	<	#endif // is_mpi
1559	<
1560	<	// clean up the forcefield
1217	<	the_ff->calcRcut();
1218	<	the_ff->cleanMe();
1219	<
1220	<	}
1221	<
1222	<	void SimSetup::initFromBass( void ){
1223	<
1224	<	int i, j, k;
1225	<	int n_cells;
1226	<	double cellx, celly, cellz;
1227	<	double temp1, temp2, temp3;
1228	<	int n_per_extra;
1229	<	int n_extra;
1230	<	int have_extra, done;
1231	<
1232	<	temp1 = (double)tot_nmol / 4.0;
1233	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1234	<	temp3 = ceil( temp2 );
1235	<
1236	<	have_extra =0;
1237	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1238	<	have_extra =1;
1239	<
1240	<	n_cells = (int)temp3 - 1;
1241	<	cellx = simnfo->boxLx / temp3;
1242	<	celly = simnfo->boxLy / temp3;
1243	<	cellz = simnfo->boxLz / temp3;
1244	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1245	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1246	<	n_per_extra = (int)ceil( temp1 );
1247	<
1248	<	if( n_per_extra > 4){
1549	>	if( globals->haveTauBarostat() )
1550	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1551	>	else{
1552	>	sprintf( painCave.errMsg,
1553	>	"SimSetup error: If you use an NPT\n"
1554	>	"    ensemble, you must set tauBarostat.\n");
1555	>	painCave.isFatal = 1;
1556	>	simError();
1557	>	}
1558	>	break;
1559	>
1560	>	default:
1561		sprintf( painCave.errMsg,
1562	<	"SimSetup error. There has been an error in constructing"
1251	<	" the non-complete lattice.\n" );
1562	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1563		painCave.isFatal = 1;
1564		simError();
1565		}
1566		}
1567	+	}
1568	+
1569	+	void SimSetup::initFortran( void ){
1570	+
1571	+	info[0].refreshSim();
1572	+
1573	+	if( !strcmp( info[0].mixingRule, "standard") ){
1574	+	the_ff->initForceField( LB_MIXING_RULE );
1575	+	}
1576	+	else if( !strcmp( info[0].mixingRule, "explicit") ){
1577	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1578	+	}
1579		else{
1580	<	n_cells = (int)temp3;
1581	<	cellx = simnfo->boxLx / temp3;
1582	<	celly = simnfo->boxLy / temp3;
1583	<	cellz = simnfo->boxLz / temp3;
1580	>	sprintf( painCave.errMsg,
1581	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	>	info[0].mixingRule );
1583	>	painCave.isFatal = 1;
1584	>	simError();
1585		}
1586
1263	–	current_mol = 0;
1264	–	current_comp_mol = 0;
1265	–	current_comp = 0;
1266	–	current_atom_ndx = 0;
1587
1588	<	for( i=0; i < n_cells ; i++ ){
1589	<	for( j=0; j < n_cells; j++ ){
1590	<	for( k=0; k < n_cells; k++ ){
1588	>	#ifdef IS_MPI
1589	>	strcpy( checkPointMsg,
1590	>	"Successfully intialized the mixingRule for Fortran." );
1591	>	MPIcheckPoint();
1592	>	#endif // is_mpi
1593
1594	<	makeElement( i * cellx,
1273	<	j * celly,
1274	<	k * cellz );
1594	>	}
1595
1596	<	makeElement( i * cellx + 0.5 * cellx,
1597	<	j * celly + 0.5 * celly,
1598	<	k * cellz );
1596	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1597	>	{
1598	>	int nZConstraints;
1599	>	ZconStamp** zconStamp;
1600
1601	<	makeElement( i * cellx,
1602	<	j * celly + 0.5 * celly,
1603	<	k * cellz + 0.5 * cellz );
1604	<
1605	<	makeElement( i * cellx + 0.5 * cellx,
1606	<	j * celly,
1607	<	k * cellz + 0.5 * cellz );
1287	<	}
1288	<	}
1601	>	if(globals->haveZconstraintTime()){
1602	>
1603	>	//add sample time of z-constraint  into SimInfo's property list
1604	>	DoubleData* zconsTimeProp = new DoubleData();
1605	>	zconsTimeProp->setID(ZCONSTIME_ID);
1606	>	zconsTimeProp->setData(globals->getZconsTime());
1607	>	theInfo.addProperty(zconsTimeProp);
1608		}
1609	+	else{
1610	+	sprintf( painCave.errMsg,
1611	+	"ZConstraint error: If you use an ZConstraint\n"
1612	+	" , you must set sample time.\n");
1613	+	painCave.isFatal = 1;
1614	+	simError();
1615	+	}
1616
1617	<	if( have_extra ){
1618	<	done = 0;
1619	<
1620	<	int start_ndx;
1621	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1622	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1297	<
1298	<	if( i < n_cells ){
1299	<
1300	<	if( j < n_cells ){
1301	<	start_ndx = n_cells;
1302	<	}
1303	<	else start_ndx = 0;
1304	<	}
1305	<	else start_ndx = 0;
1306	<
1307	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1308	<
1309	<	makeElement( i * cellx,
1310	<	j * celly,
1311	<	k * cellz );
1312	<	done = ( current_mol >= tot_nmol );
1313	<
1314	<	if( !done && n_per_extra > 1 ){
1315	<	makeElement( i * cellx + 0.5 * cellx,
1316	<	j * celly + 0.5 * celly,
1317	<	k * cellz );
1318	<	done = ( current_mol >= tot_nmol );
1319	<	}
1320	<
1321	<	if( !done && n_per_extra > 2){
1322	<	makeElement( i * cellx,
1323	<	j * celly + 0.5 * celly,
1324	<	k * cellz + 0.5 * cellz );
1325	<	done = ( current_mol >= tot_nmol );
1326	<	}
1327	<
1328	<	if( !done && n_per_extra > 3){
1329	<	makeElement( i * cellx + 0.5 * cellx,
1330	<	j * celly,
1331	<	k * cellz + 0.5 * cellz );
1332	<	done = ( current_mol >= tot_nmol );
1333	<	}
1334	<	}
1335	<	}
1336	<	}
1617	>	//push zconsTol into siminfo, if user does not specify
1618	>	//value for zconsTol, a default value will be used
1619	>	DoubleData* zconsTol = new DoubleData();
1620	>	zconsTol->setID(ZCONSTOL_ID);
1621	>	if(globals->haveZconsTol()){
1622	>	zconsTol->setData(globals->getZconsTol());
1623		}
1624	+	else{
1625	+	double defaultZConsTol = 0.01;
1626	+	sprintf( painCave.errMsg,
1627	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628	+	" , default value %f is used.\n", defaultZConsTol);
1629	+	painCave.isFatal = 0;
1630	+	simError();
1631
1632	<
1340	<	for( i=0; i<simnfo->n_atoms; i++ ){
1341	<	simnfo->atoms[i]->set_vx( 0.0 );
1342	<	simnfo->atoms[i]->set_vy( 0.0 );
1343	<	simnfo->atoms[i]->set_vz( 0.0 );
1632	>	zconsTol->setData(defaultZConsTol);
1633		}
1634	<	}
1634	>	theInfo.addProperty(zconsTol);
1635
1636	<	void SimSetup::makeElement( double x, double y, double z ){
1637	<
1638	<	int k;
1639	<	AtomStamp* current_atom;
1640	<	DirectionalAtom* dAtom;
1641	<	double rotMat[3][3];
1642	<
1643	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1644	<
1645	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1646	<	if( !current_atom->havePosition() ){
1647	<	sprintf( painCave.errMsg,
1648	<	"SimSetup:initFromBass error.\n"
1649	<	"\tComponent %s, atom %s does not have a position specified.\n"
1361	<	"\tThe initialization routine is unable to give a start"
1362	<	" position.\n",
1363	<	comp_stamps[current_comp]->getID(),
1364	<	current_atom->getType() );
1365	<	painCave.isFatal = 1;
1366	<	simError();
1367	<	}
1368	<
1369	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1370	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1371	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1372	<
1373	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1374	<
1375	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1376	<
1377	<	rotMat[0][0] = 1.0;
1378	<	rotMat[0][1] = 0.0;
1379	<	rotMat[0][2] = 0.0;
1380	<
1381	<	rotMat[1][0] = 0.0;
1382	<	rotMat[1][1] = 1.0;
1383	<	rotMat[1][2] = 0.0;
1384	<
1385	<	rotMat[2][0] = 0.0;
1386	<	rotMat[2][1] = 0.0;
1387	<	rotMat[2][2] = 1.0;
1388	<
1389	<	dAtom->setA( rotMat );
1390	<	}
1391	<
1392	<	current_atom_ndx++;
1636	>	//set Force Substraction Policy
1637	>	StringData* zconsForcePolicy =  new StringData();
1638	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	>
1640	>	if(globals->haveZconsForcePolicy()){
1641	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	>	}
1643	>	else{
1644	>	sprintf( painCave.errMsg,
1645	>	"ZConstraint Warning: User does not set force substraction policy, "
1646	>	"average force substraction policy is used\n");
1647	>	painCave.isFatal = 0;
1648	>	simError();
1649	>	zconsForcePolicy->setData("BYNUMBER");
1650		}
1651	+
1652	+	theInfo.addProperty(zconsForcePolicy);
1653	+
1654	+	//Determine the name of ouput file and add it into SimInfo's property list
1655	+	//Be careful, do not use inFileName, since it is a pointer which
1656	+	//point to a string at master node, and slave nodes do not contain that string
1657	+
1658	+	string zconsOutput(theInfo.finalName);
1659	+
1660	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	+
1662	+	StringData* zconsFilename = new StringData();
1663	+	zconsFilename->setID(ZCONSFILENAME_ID);
1664	+	zconsFilename->setData(zconsOutput);
1665	+
1666	+	theInfo.addProperty(zconsFilename);
1667	+
1668	+	//setup index, pos and other parameters of z-constraint molecules
1669	+	nZConstraints = globals->getNzConstraints();
1670	+	theInfo.nZconstraints = nZConstraints;
1671
1672	<	current_mol++;
1673	<	current_comp_mol++;
1672	>	zconStamp = globals->getZconStamp();
1673	>	ZConsParaItem tempParaItem;
1674
1675	<	if( current_comp_mol >= components_nmol[current_comp] ){
1675	>	ZConsParaData* zconsParaData = new ZConsParaData();
1676	>	zconsParaData->setID(ZCONSPARADATA_ID);
1677	>
1678	>	for(int i = 0; i < nZConstraints; i++){
1679	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1683
1684	<	current_comp_mol = 0;
1401	<	current_comp++;
1684	>	zconsParaData->addItem(tempParaItem);
1685		}
1686	+
1687	+	//sort the parameters by index of molecules
1688	+	zconsParaData->sortByIndex();
1689	+
1690	+	//push data into siminfo, therefore, we can retrieve later
1691	+	theInfo.addProperty(zconsParaData);
1692	+
1693		}

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