ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 557 by mmeineke, Thu Jun 19 19:11:53 2003 UTC vs.
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sys/time.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 14 | Line 18
18
19		// some defines for ensemble and Forcefield  cases
20
21	<	#define NVE_ENS 0
22	<	#define NVT_ENS 1
23	<	#define NPT_ENS 2
21	>	#define NVE_ENS        0
22	>	#define NVT_ENS        1
23	>	#define NPTi_ENS       2
24	>	#define NPTf_ENS       3
25	>	#define NPTim_ENS      4
26	>	#define NPTfm_ENS      5
27
28		#define FF_DUFF 0
29		#define FF_LJ   1
30	+	#define FF_EAM  2
31
32	+	using namespace std;
33
34		SimSetup::SimSetup(){
35	+
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41
42	+
43		#ifdef IS_MPI
44		strcpy( checkPointMsg, "SimSetup creation successful" );
45		MPIcheckPoint();
#	Line 37 | Line 51 | void SimSetup::parseFile( char* fileName ){
51		delete globals;
52		}
53
54	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
55	+	info = the_info;
56	+	nInfo = theNinfo;
57	+	isInfoArray = 1;
58	+	}
59	+
60	+
61		void SimSetup::parseFile( char* fileName ){
62
63		#ifdef IS_MPI
#	Line 72 | Line 93 | void SimSetup::createSim( void ){
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
77	–	MakeStamps *the_stamps;
78	–	Globals* the_globals;
98		int i, j, k, globalAtomIndex;
99
100	<	int ensembleCase;
82	<	int ffCase;
83	<
84	<	ensembleCase = -1;
85	<	ffCase = -1;
100	>	// gather all of the information from the Bass file
101
102	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
102	>	gatherInfo();
103
104	<	// 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();
104	>	// creation of complex system objects
105
106	<	// 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() );
106	>	sysObjectsCreation();
107
108	<	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	<	}
108	>	// check on the post processing info
109
110	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
110	>	finalInfoCheck();
111
112	<	if( !strcasecmp( ensemble, "NVE" ))      ffCase = NVE_ENS;
114	<	else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS;
115	<	else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS;
116	<	else{
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
119	<	"reverting to NVE for this simulation.\n",
120	<	ensemble );
121	<	painCave.isFatal = 0;
122	<	simError();
123	<	strcpy( ensemble, "NVE" );
124	<	ensembleCase = NVE_ENS;
125	<	}
126	<	strcpy( simnfo->ensemble, ensemble );
112	>	// initialize the system coordinates
113
114	+	if( !isInfoArray ) initSystemCoords();
115
116	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
130	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
131	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132	<	//     if (the_globals->haveTargetPressure())
133	<	//       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	<	//     }
116	>	// make the output filenames
117
118	<	//     if (the_globals->haveTauThermostat())
119	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
120	<	//     else if (the_globals->haveQmass())
121	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
122	<	//     else {
123	<	//       sprintf( painCave.errMsg,
124	<	//                "SimSetup error: If you use one of the constant temperature\n"
125	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
126	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
118	>	makeOutNames();
119	>
120	>	// make the integrator
121	>
122	>	makeIntegrator();
123	>
124	>	#ifdef IS_MPI
125	>	mpiSim->mpiRefresh();
126	>	#endif
127
128	<	//     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	<	//     }
128	>	// initialize the Fortran
129
130	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
168	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
169	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
130	>	initFortran();
131
171	–	//     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	–	//     }
132
184	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185	–	simnfo->usePBC = the_globals->getPBC();
186	–
187	–	int usesDipoles = 0;
188	–	switch( ffCase ){
133
134	<	case FF_DUFF:
191	<	the_ff = new DUFF();
192	<	usesDipoles = 1;
193	<	break;
134	>	}
135
195	–	case FF_LJ:
196	–	the_ff = LJFF();
197	–	break;
136
137	<	default:
200	<	sprintf( painCave.errMsg,
201	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
137	>	void SimSetup::makeMolecules( void ){
138
139	<	#ifdef IS_MPI
140	<	strcpy( checkPointMsg, "ForceField creation successful" );
141	<	MPIcheckPoint();
142	<	#endif // is_mpi
139	>	int k,l;
140	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
141	>	molInit molInfo;
142	>	DirectionalAtom* dAtom;
143	>	LinkedAssign* extras;
144	>	LinkedAssign* current_extra;
145	>	AtomStamp* currentAtom;
146	>	BondStamp* currentBond;
147	>	BendStamp* currentBend;
148	>	TorsionStamp* currentTorsion;
149
150	<	// get the components and calculate the tot_nMol and indvidual n_mol
151	<	the_components = the_globals->getComponents();
152	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
150	>	bond_pair* theBonds;
151	>	bend_set* theBends;
152	>	torsion_set* theTorsions;
153
154	<	if( !the_globals->haveNMol() ){
155	<	// we don't have the total number of molecules, so we assume it is
218	<	// given in each component
154	>
155	>	//init the forceField paramters
156
157	<	tot_nmol = 0;
221	<	for( i=0; i<n_components; i++ ){
157	>	the_ff->readParams();
158
159	<	if( !the_components[i]->haveNMol() ){
160	<	// we have a problem
225	<	sprintf( painCave.errMsg,
226	<	"SimSetup Error. No global NMol or component NMol"
227	<	" given. Cannot calculate the number of atoms.\n" );
228	<	painCave.isFatal = 1;
229	<	simError();
230	<	}
159	>
160	>	// init the atoms
161
162	<	tot_nmol += the_components[i]->getNMol();
163	<	components_nmol[i] = the_components[i]->getNMol();
164	<	}
235	<	}
236	<	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();
162	>	double ux, uy, uz, u, uSqr;
163	>
164	>	for(k=0; k<nInfo; k++){
165
166	+	the_ff->setSimInfo( &(info[k]) );
167	+
168	+	atomOffset = 0;
169	+	excludeOffset = 0;
170	+	for(i=0; i<info[k].n_mol; i++){
171
172	<	//     tot_nmol = the_globals->getNMol();
172	>	stampID = info[k].molecules[i].getStampID();
173	>
174	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
175	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
176	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
177	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
178	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
179	>
180	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
181	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
182	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
183	>	molInfo.myBends = new Bend*[molInfo.nBends];
184	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
185	>
186	>	theBonds = new bond_pair[molInfo.nBonds];
187	>	theBends = new bend_set[molInfo.nBends];
188	>	theTorsions = new torsion_set[molInfo.nTorsions];
189
190	<	//   //we have the total number of molecules, now we check for molfractions
250	<	//     for( i=0; i<n_components; i++ ){
190	>	// make the Atoms
191
192	<	//       if( !the_components[i]->haveMolFraction() ){
192	>	for(j=0; j<molInfo.nAtoms; j++){
193	>
194	>	currentAtom = comp_stamps[stampID]->getAtom( j );
195	>	if( currentAtom->haveOrientation() ){
196
197	<	//  if( !the_components[i]->haveNMol() ){
198	<	//    //we have a problem
199	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
200	<	//              << " nMol was given in component
197	>	dAtom = new DirectionalAtom( (j + atomOffset),
198	>	info[k].getConfiguration() );
199	>	info[k].n_oriented++;
200	>	molInfo.myAtoms[j] = dAtom;
201
202	<	}
203	<
204	<	#ifdef IS_MPI
262	<	strcpy( checkPointMsg, "Have the number of components" );
263	<	MPIcheckPoint();
264	<	#endif // is_mpi
265	<
266	<	// make an array of molecule stamps that match the components used.
267	<	// also extract the used stamps out into a separate linked list
268	<
269	<	simnfo->nComponents = n_components;
270	<	simnfo->componentsNmol = components_nmol;
271	<	simnfo->compStamps = comp_stamps;
272	<	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++ ){
278	<
279	<	id = the_components[i]->getType();
280	<	comp_stamps[i] = NULL;
202	>	ux = currentAtom->getOrntX();
203	>	uy = currentAtom->getOrntY();
204	>	uz = currentAtom->getOrntZ();
205
206	<	// check to make sure the component isn't already in the list
207	<
208	<	comp_stamps[i] = headStamp->match( id );
209	<	if( comp_stamps[i] == NULL ){
210	<
211	<	// extract the component from the list;
212	<
213	<	currentStamp = the_stamps->extractMolStamp( id );
214	<	if( currentStamp == NULL ){
215	<	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	<	}
206	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
207	>
208	>	u = sqrt( uSqr );
209	>	ux = ux / u;
210	>	uy = uy / u;
211	>	uz = uz / u;
212	>
213	>	dAtom->setSUx( ux );
214	>	dAtom->setSUy( uy );
215	>	dAtom->setSUz( uz );
216		}
217	<
217	>	else{
218	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
219	>	info[k].getConfiguration() );
220	>	}
221	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
222	>
223		#ifdef IS_MPI
224	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
225	<	MPIcheckPoint();
224	>
225	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
226	>
227		#endif // is_mpi
228	<
309	<
310	<
311	<
312	<	// caclulate the number of atoms, bonds, bends and torsions
313	<
314	<	tot_atoms = 0;
315	<	tot_bonds = 0;
316	<	tot_bends = 0;
317	<	tot_torsions = 0;
318	<	for( i=0; i<n_components; i++ ){
228	>	}
229
230	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
231	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
232	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
233	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
234	<	}
235	<
326	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
327	<
328	<	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;
230	>	// make the bonds
231	>	for(j=0; j<molInfo.nBonds; j++){
232	>
233	>	currentBond = comp_stamps[stampID]->getBond( j );
234	>	theBonds[j].a = currentBond->getA() + atomOffset;
235	>	theBonds[j].b = currentBond->getB() + atomOffset;
236
237	<	simnfo->molMembershipArray = new int[tot_atoms];
238	<
237	>	exI = theBonds[j].a;
238	>	exJ = theBonds[j].b;
239	>
240	>	// exclude_I must always be the smaller of the pair
241	>	if( exI > exJ ){
242	>	tempEx = exI;
243	>	exI = exJ;
244	>	exJ = tempEx;
245	>	}
246		#ifdef IS_MPI
247	<
248	<	// divide the molecules among processors here.
247	>	tempEx = exI;
248	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>	tempEx = exJ;
250	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
251
252	<	mpiSim = new mpiSimulation( simnfo );
252	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
253	>	#else  // isn't MPI
254
255	<	globalIndex = mpiSim->divideLabor();
256	<
257	<	// set up the local variables
255	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
256	>	#endif  //is_mpi
257	>	}
258	>	excludeOffset += molInfo.nBonds;
259	>
260	>	//make the bends
261	>	for(j=0; j<molInfo.nBends; j++){
262
263	<	int localMol, allMol;
264	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
265	<
266	<	int* mol2proc = mpiSim->getMolToProcMap();
351	<	int* molCompType = mpiSim->getMolComponentType();
263	>	currentBend = comp_stamps[stampID]->getBend( j );
264	>	theBends[j].a = currentBend->getA() + atomOffset;
265	>	theBends[j].b = currentBend->getB() + atomOffset;
266	>	theBends[j].c = currentBend->getC() + atomOffset;
267
268	<	allMol = 0;
269	<	localMol = 0;
270	<	local_atoms = 0;
271	<	local_bonds = 0;
272	<	local_bends = 0;
273	<	local_torsions = 0;
274	<	globalAtomIndex = 0;
275	<
276	<
277	<	for( i=0; i<n_components; i++ ){
278	<
279	<	for( j=0; j<components_nmol[i]; j++ ){
268	>	if( currentBend->haveExtras() ){
269	>
270	>	extras = currentBend->getExtras();
271	>	current_extra = extras;
272	>
273	>	while( current_extra != NULL ){
274	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
275	>
276	>	switch( current_extra->getType() ){
277	>
278	>	case 0:
279	>	theBends[j].ghost =
280	>	current_extra->getInt() + atomOffset;
281	>	theBends[j].isGhost = 1;
282	>	break;
283	>
284	>	case 1:
285	>	theBends[j].ghost =
286	>	(int)current_extra->getDouble() + atomOffset;
287	>	theBends[j].isGhost = 1;
288	>	break;
289	>
290	>	default:
291	>	sprintf( painCave.errMsg,
292	>	"SimSetup Error: ghostVectorSource was neither a "
293	>	"double nor an int.\n"
294	>	"-->Bend[%d] in %s\n",
295	>	j, comp_stamps[stampID]->getID() );
296	>	painCave.isFatal = 1;
297	>	simError();
298	>	}
299	>	}
300
301	<	if( mol2proc[allMol] == worldRank ){
302	<
303	<	local_atoms +=    comp_stamps[i]->getNAtoms();
304	<	local_bonds +=    comp_stamps[i]->getNBonds();
305	<	local_bends +=    comp_stamps[i]->getNBends();
306	<	local_torsions += comp_stamps[i]->getNTorsions();
307	<	localMol++;
308	<	}
309	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
301	>	else{
302	>
303	>	sprintf( painCave.errMsg,
304	>	"SimSetup Error: unhandled bend assignment:\n"
305	>	"    -->%s in Bend[%d] in %s\n",
306	>	current_extra->getlhs(),
307	>	j, comp_stamps[stampID]->getID() );
308	>	painCave.isFatal = 1;
309	>	simError();
310		}
311	<
312	<	allMol++;
311	>
312	>	current_extra = current_extra->getNext();
313		}
314		}
382	–	local_SRI = local_bonds + local_bends + local_torsions;
315
316	<	simnfo->n_atoms = mpiSim->getMyNlocal();
316	>	if( !theBends[j].isGhost ){
317	>
318	>	exI = theBends[j].a;
319	>	exJ = theBends[j].c;
320	>	}
321	>	else{
322	>
323	>	exI = theBends[j].a;
324	>	exJ = theBends[j].b;
325	>	}
326
327	<	if( local_atoms != simnfo->n_atoms ){
328	<	sprintf( painCave.errMsg,
329	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
330	<	" localAtom (%d) are not equal.\n",
331	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
327	>	// exclude_I must always be the smaller of the pair
328	>	if( exI > exJ ){
329	>	tempEx = exI;
330	>	exI = exJ;
331	>	exJ = tempEx;
332		}
333	<
334	<	simnfo->n_bonds = local_bonds;
335	<	simnfo->n_bends = local_bends;
336	<	simnfo->n_torsions = local_torsions;
337	<	simnfo->n_SRI = local_SRI;
338	<	simnfo->n_mol = localMol;
339	<
340	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
341	<	MPIcheckPoint();
333	>	#ifdef IS_MPI
334	>	tempEx = exI;
335	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>	tempEx = exJ;
337	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
338	>
339	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
340	>	#else  // isn't MPI
341	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
342	>	#endif  //is_mpi
343	>	}
344	>	excludeOffset += molInfo.nBends;
345	>
346	>	for(j=0; j<molInfo.nTorsions; j++){
347
348	+	currentTorsion = comp_stamps[stampID]->getTorsion( j );
349	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
350	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
351	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
352	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
353
354	<	#endif // is_mpi
354	>	exI = theTorsions[j].a;
355	>	exJ = theTorsions[j].d;
356
357	<
358	<	// create the atom and short range interaction arrays
359	<
360	<	Atom::createArrays(simnfo->n_atoms);
361	<	the_atoms = new Atom*[simnfo->n_atoms];
362	<	the_molecules = new Molecule[simnfo->n_mol];
414	<	int molIndex;
415	<
416	<	// initialize the molecule's stampID's
417	<
357	>	// exclude_I must always be the smaller of the pair
358	>	if( exI > exJ ){
359	>	tempEx = exI;
360	>	exI = exJ;
361	>	exJ = tempEx;
362	>	}
363		#ifdef IS_MPI
364	+	tempEx = exI;
365	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	+	tempEx = exJ;
367	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
368
369	+	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
370	+	#else  // isn't MPI
371	+	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
372	+	#endif  //is_mpi
373	+	}
374	+	excludeOffset += molInfo.nTorsions;
375	+
376	+
377	+	// send the arrays off to the forceField for init.
378	+
379	+	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
380	+	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
381	+	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
382	+	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
383	+
384	+
385	+	info[k].molecules[i].initialize( molInfo );
386
387	<	molIndex = 0;
388	<	for(i=0; i<mpiSim->getTotNmol(); i++){
389	<
390	<	if(mol2proc[i] == worldRank ){
391	<	the_molecules[molIndex].setStampID( molCompType[i] );
426	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
387	>
388	>	atomOffset += molInfo.nAtoms;
389	>	delete[] theBonds;
390	>	delete[] theBends;
391	>	delete[] theTorsions;
392		}
393		}
394	+
395	+	#ifdef IS_MPI
396	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
397	+	MPIcheckPoint();
398	+	#endif // is_mpi
399	+
400	+	// clean up the forcefield
401
402	<	#else // is_mpi
402	>	the_ff->calcRcut();
403	>	the_ff->cleanMe();
404
405	<	molIndex = 0;
435	<	globalAtomIndex = 0;
436	<	for(i=0; i<n_components; i++){
437	<	for(j=0; j<components_nmol[i]; j++ ){
438	<	the_molecules[molIndex].setStampID( i );
439	<	the_molecules[molIndex].setMyIndex( molIndex );
440	<	the_molecules[molIndex].setGlobalIndex( molIndex );
441	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443	<	globalAtomIndex++;
444	<	}
445	<	molIndex++;
446	<	}
447	<	}
448	<
405	>	}
406
407	<	#endif // is_mpi
407	>	void SimSetup::initFromBass( void ){
408
409	+	int i, j, k;
410	+	int n_cells;
411	+	double cellx, celly, cellz;
412	+	double temp1, temp2, temp3;
413	+	int n_per_extra;
414	+	int n_extra;
415	+	int have_extra, done;
416
417	<	if( simnfo->n_SRI ){
418	<
419	<	Exclude::createArray(simnfo->n_SRI);
420	<	the_excludes = new Exclude*[simnfo->n_SRI];
421	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
422	<	simnfo->globalExcludes = new int;
423	<	simnfo->n_exclude = simnfo->n_SRI;
417	>	double vel[3];
418	>	vel[0] = 0.0;
419	>	vel[1] = 0.0;
420	>	vel[2] = 0.0;
421	>
422	>	temp1 = (double)tot_nmol / 4.0;
423	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
424	>	temp3 = ceil( temp2 );
425	>
426	>	have_extra =0;
427	>	if( temp2 < temp3 ){ // we have a non-complete lattice
428	>	have_extra =1;
429	>
430	>	n_cells = (int)temp3 - 1;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
435	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
436	>	n_per_extra = (int)ceil( temp1 );
437	>
438	>	if( n_per_extra > 4){
439	>	sprintf( painCave.errMsg,
440	>	"SimSetup error. There has been an error in constructing"
441	>	" the non-complete lattice.\n" );
442	>	painCave.isFatal = 1;
443	>	simError();
444	>	}
445		}
446		else{
447	<
448	<	Exclude::createArray( 1 );
449	<	the_excludes = new Exclude*;
450	<	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;
447	>	n_cells = (int)temp3;
448	>	cellx = info[0].boxL[0] / temp3;
449	>	celly = info[0].boxL[1] / temp3;
450	>	cellz = info[0].boxL[2] / temp3;
451		}
452
453	<	// set the arrays into the SimInfo object
453	>	current_mol = 0;
454	>	current_comp_mol = 0;
455	>	current_comp = 0;
456	>	current_atom_ndx = 0;
457
458	<	simnfo->atoms = the_atoms;
459	<	simnfo->molecules = the_molecules;
460	<	simnfo->nGlobalExcludes = 0;
477	<	simnfo->excludes = the_excludes;
458	>	for( i=0; i < n_cells ; i++ ){
459	>	for( j=0; j < n_cells; j++ ){
460	>	for( k=0; k < n_cells; k++ ){
461
462	+	makeElement( i * cellx,
463	+	j * celly,
464	+	k * cellz );
465
466	<	// get some of the tricky things that may still be in the globals
466	>	makeElement( i * cellx + 0.5 * cellx,
467	>	j * celly + 0.5 * celly,
468	>	k * cellz );
469
470	<
471	<	if( the_globals->haveBox() ){
472	<	simnfo->box_x = the_globals->getBox();
473	<	simnfo->box_y = the_globals->getBox();
474	<	simnfo->box_z = the_globals->getBox();
470	>	makeElement( i * cellx,
471	>	j * celly + 0.5 * celly,
472	>	k * cellz + 0.5 * cellz );
473	>
474	>	makeElement( i * cellx + 0.5 * cellx,
475	>	j * celly,
476	>	k * cellz + 0.5 * cellz );
477	>	}
478	>	}
479		}
488	–	else if( the_globals->haveDensity() ){
480
481	<	double vol;
482	<	vol = (double)tot_nmol / the_globals->getDensity();
483	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
484	<	simnfo->box_y = simnfo->box_x;
485	<	simnfo->box_z = simnfo->box_x;
481	>	if( have_extra ){
482	>	done = 0;
483	>
484	>	int start_ndx;
485	>	for( i=0; i < (n_cells+1) && !done; i++ ){
486	>	for( j=0; j < (n_cells+1) && !done; j++ ){
487	>
488	>	if( i < n_cells ){
489	>
490	>	if( j < n_cells ){
491	>	start_ndx = n_cells;
492	>	}
493	>	else start_ndx = 0;
494		}
495	<	else{
496	<	if( !the_globals->haveBoxX() ){
497	<	sprintf( painCave.errMsg,
498	<	"SimSetup error, no periodic BoxX size given.\n" );
499	<	painCave.isFatal = 1;
500	<	simError();
495	>	else start_ndx = 0;
496	>
497	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
498	>
499	>	makeElement( i * cellx,
500	>	j * celly,
501	>	k * cellz );
502	>	done = ( current_mol >= tot_nmol );
503	>
504	>	if( !done && n_per_extra > 1 ){
505	>	makeElement( i * cellx + 0.5 * cellx,
506	>	j * celly + 0.5 * celly,
507	>	k * cellz );
508	>	done = ( current_mol >= tot_nmol );
509		}
503	–	simnfo->box_x = the_globals->getBoxX();
510
511	<	if( !the_globals->haveBoxY() ){
512	<	sprintf( painCave.errMsg,
513	<	"SimSetup error, no periodic BoxY size given.\n" );
514	<	painCave.isFatal = 1;
515	<	simError();
511	>	if( !done && n_per_extra > 2){
512	>	makeElement( i * cellx,
513	>	j * celly + 0.5 * celly,
514	>	k * cellz + 0.5 * cellz );
515	>	done = ( current_mol >= tot_nmol );
516		}
511	–	simnfo->box_y = the_globals->getBoxY();
517
518	<	if( !the_globals->haveBoxZ() ){
519	<	sprintf( painCave.errMsg,
520	<	"SimSetup error, no periodic BoxZ size given.\n" );
521	<	painCave.isFatal = 1;
522	<	simError();
518	>	if( !done && n_per_extra > 3){
519	>	makeElement( i * cellx + 0.5 * cellx,
520	>	j * celly,
521	>	k * cellz + 0.5 * cellz );
522	>	done = ( current_mol >= tot_nmol );
523		}
519	–	simnfo->box_z = the_globals->getBoxZ();
524		}
525	+	}
526	+	}
527	+	}
528
529	<	#ifdef IS_MPI
530	<	strcpy( checkPointMsg, "Box size set up" );
531	<	MPIcheckPoint();
532	<	#endif // is_mpi
529	>	for( i=0; i<info[0].n_atoms; i++ ){
530	>	info[0].atoms[i]->setVel( vel );
531	>	}
532	>	}
533
534	+	void SimSetup::makeElement( double x, double y, double z ){
535
536	<	// initialize the arrays
536	>	int k;
537	>	AtomStamp* current_atom;
538	>	DirectionalAtom* dAtom;
539	>	double rotMat[3][3];
540	>	double pos[3];
541
542	<	the_ff->setSimInfo( simnfo );
542	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
543
544	<	makeMolecules();
545	<	simnfo->identArray = new int[simnfo->n_atoms];
534	<	for(i=0; i<simnfo->n_atoms; i++){
535	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
536	<	}
537	<
538	<	if (the_globals->getUseRF() ) {
539	<	simnfo->useReactionField = 1;
540	<
541	<	if( !the_globals->haveECR() ){
544	>	current_atom = comp_stamps[current_comp]->getAtom( k );
545	>	if( !current_atom->havePosition() ){
546		sprintf( painCave.errMsg,
547	<	"SimSetup Warning: using default value of 1/2 the smallest "
548	<	"box length for the electrostaticCutoffRadius.\n"
549	<	"I hope you have a very fast processor!\n");
550	<	painCave.isFatal = 0;
551	<	simError();
552	<	double smallest;
549	<	smallest = simnfo->box_x;
550	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
551	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
552	<	simnfo->ecr = 0.5 * smallest;
553	<	} else {
554	<	simnfo->ecr        = the_globals->getECR();
555	<	}
556	<
557	<	if( !the_globals->haveEST() ){
558	<	sprintf( painCave.errMsg,
559	<	"SimSetup Warning: using default value of 0.05 * the "
560	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
561	<	);
562	<	painCave.isFatal = 0;
563	<	simError();
564	<	simnfo->est = 0.05 * simnfo->ecr;
565	<	} else {
566	<	simnfo->est        = the_globals->getEST();
567	<	}
568	<
569	<	if(!the_globals->haveDielectric() ){
570	<	sprintf( painCave.errMsg,
571	<	"SimSetup Error: You are trying to use Reaction Field without"
572	<	"setting a dielectric constant!\n"
573	<	);
547	>	"SimSetup:initFromBass error.\n"
548	>	"\tComponent %s, atom %s does not have a position specified.\n"
549	>	"\tThe initialization routine is unable to give a start"
550	>	" position.\n",
551	>	comp_stamps[current_comp]->getID(),
552	>	current_atom->getType() );
553		painCave.isFatal = 1;
554		simError();
555		}
556	<	simnfo->dielectric = the_globals->getDielectric();
557	<	} else {
558	<	if (usesDipoles) {
559	<
560	<	if( !the_globals->haveECR() ){
561	<	sprintf( painCave.errMsg,
562	<	"SimSetup Warning: using default value of 1/2 the smallest "
563	<	"box length for the electrostaticCutoffRadius.\n"
564	<	"I hope you have a very fast processor!\n");
565	<	painCave.isFatal = 0;
566	<	simError();
567	<	double smallest;
568	<	smallest = simnfo->box_x;
569	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
570	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
571	<	simnfo->ecr = 0.5 * smallest;
572	<	} else {
573	<	simnfo->ecr        = the_globals->getECR();
574	<	}
575	<
576	<	if( !the_globals->haveEST() ){
577	<	sprintf( painCave.errMsg,
578	<	"SimSetup Warning: using default value of 5%% of the "
579	<	"electrostaticCutoffRadius for the "
601	<	"electrostaticSkinThickness\n"
602	<	);
603	<	painCave.isFatal = 0;
604	<	simError();
605	<	simnfo->est = 0.05 * simnfo->ecr;
606	<	} else {
607	<	simnfo->est        = the_globals->getEST();
608	<	}
556	>
557	>	pos[0] = x + current_atom->getPosX();
558	>	pos[1] = y + current_atom->getPosY();
559	>	pos[2] = z + current_atom->getPosZ();
560	>
561	>	info[0].atoms[current_atom_ndx]->setPos( pos );
562	>
563	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
564	>
565	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
566	>
567	>	rotMat[0][0] = 1.0;
568	>	rotMat[0][1] = 0.0;
569	>	rotMat[0][2] = 0.0;
570	>
571	>	rotMat[1][0] = 0.0;
572	>	rotMat[1][1] = 1.0;
573	>	rotMat[1][2] = 0.0;
574	>
575	>	rotMat[2][0] = 0.0;
576	>	rotMat[2][1] = 0.0;
577	>	rotMat[2][2] = 1.0;
578	>
579	>	dAtom->setA( rotMat );
580		}
610	–	}
581
582	<	#ifdef IS_MPI
583	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
614	<	MPIcheckPoint();
615	<	#endif // is_mpi
582	>	current_atom_ndx++;
583	>	}
584
585	<	if( the_globals->haveInitialConfig() ){
586	<
619	<	InitializeFromFile* fileInit;
620	<	#ifdef IS_MPI // is_mpi
621	<	if( worldRank == 0 ){
622	<	#endif //is_mpi
623	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
624	<	#ifdef IS_MPI
625	<	}else fileInit = new InitializeFromFile( NULL );
626	<	#endif
627	<	fileInit->read_xyz( simnfo ); // default velocities on
585	>	current_mol++;
586	>	current_comp_mol++;
587
588	<	delete fileInit;
630	<	}
631	<	else{
588	>	if( current_comp_mol >= components_nmol[current_comp] ){
589
590	<	#ifdef IS_MPI
590	>	current_comp_mol = 0;
591	>	current_comp++;
592	>	}
593	>	}
594
595	<	// no init from bass
595	>
596	>	void SimSetup::gatherInfo( void ){
597	>	int i,j,k;
598	>
599	>	ensembleCase = -1;
600	>	ffCase = -1;
601	>
602	>	// set the easy ones first
603	>
604	>	for( i=0; i<nInfo; i++){
605	>	info[i].target_temp = globals->getTargetTemp();
606	>	info[i].dt = globals->getDt();
607	>	info[i].run_time = globals->getRunTime();
608	>	}
609	>	n_components = globals->getNComponents();
610	>
611	>
612	>	// get the forceField
613	>
614	>	strcpy( force_field, globals->getForceField() );
615	>
616	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
617	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
618	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
619	>	else{
620	>	sprintf( painCave.errMsg,
621	>	"SimSetup Error. Unrecognized force field -> %s\n",
622	>	force_field );
623	>	painCave.isFatal = 1;
624	>	simError();
625	>	}
626	>
627	>	// get the ensemble
628	>
629	>	strcpy( ensemble, globals->getEnsemble() );
630	>
631	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
632	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
633	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
634	>	ensembleCase = NPTi_ENS;
635	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
636	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
637	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
638	>	else{
639	>	sprintf( painCave.errMsg,
640	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641	>	"reverting to NVE for this simulation.\n",
642	>	ensemble );
643	>	painCave.isFatal = 0;
644	>	simError();
645	>	strcpy( ensemble, "NVE" );
646	>	ensembleCase = NVE_ENS;
647	>	}
648
649	<	sprintf( painCave.errMsg,
650	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
651	<	painCave.isFatal;
652	<	simError();
649	>	for(i=0; i<nInfo; i++){
650	>
651	>	strcpy( info[i].ensemble, ensemble );
652	>
653	>	// get the mixing rule
654	>
655	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
656	>	info[i].usePBC = globals->getPBC();
657	>	}
658
659	<	#else
659	>	// get the components and calculate the tot_nMol and indvidual n_mol
660	>
661	>	the_components = globals->getComponents();
662	>	components_nmol = new int[n_components];
663
644	–	initFromBass();
664
665	+	if( !globals->haveNMol() ){
666	+	// we don't have the total number of molecules, so we assume it is
667	+	// given in each component
668
669	<	#endif
670	<	}
669	>	tot_nmol = 0;
670	>	for( i=0; i<n_components; i++ ){
671
672	<	#ifdef IS_MPI
673	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
674	<	MPIcheckPoint();
675	<	#endif // is_mpi
672	>	if( !the_components[i]->haveNMol() ){
673	>	// we have a problem
674	>	sprintf( painCave.errMsg,
675	>	"SimSetup Error. No global NMol or component NMol"
676	>	" given. Cannot calculate the number of atoms.\n" );
677	>	painCave.isFatal = 1;
678	>	simError();
679	>	}
680
681	+	tot_nmol += the_components[i]->getNMol();
682	+	components_nmol[i] = the_components[i]->getNMol();
683	+	}
684	+	}
685	+	else{
686	+	sprintf( painCave.errMsg,
687	+	"SimSetup error.\n"
688	+	"\tSorry, the ability to specify total"
689	+	" nMols and then give molfractions in the components\n"
690	+	"\tis not currently supported."
691	+	" Please give nMol in the components.\n" );
692	+	painCave.isFatal = 1;
693	+	simError();
694	+	}
695
696	<
657	<
696	>	// set the status, sample, and thermal kick times
697
698	+	for(i=0; i<nInfo; i++){
699
700	<
701	<	#ifdef IS_MPI
702	<	if( worldRank == 0 ){
703	<	#endif // is_mpi
664	<
665	<	if( the_globals->haveFinalConfig() ){
666	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
700	>	if( globals->haveSampleTime() ){
701	>	info[i].sampleTime = globals->getSampleTime();
702	>	info[i].statusTime = info[i].sampleTime;
703	>	info[i].thermalTime = info[i].sampleTime;
704		}
705		else{
706	<	strcpy( simnfo->finalName, inFileName );
707	<	char* endTest;
708	<	int nameLength = strlen( simnfo->finalName );
672	<	endTest = &(simnfo->finalName[nameLength - 5]);
673	<	if( !strcmp( endTest, ".bass" ) ){
674	<	strcpy( endTest, ".eor" );
675	<	}
676	<	else if( !strcmp( endTest, ".BASS" ) ){
677	<	strcpy( endTest, ".eor" );
678	<	}
679	<	else{
680	<	endTest = &(simnfo->finalName[nameLength - 4]);
681	<	if( !strcmp( endTest, ".bss" ) ){
682	<	strcpy( endTest, ".eor" );
683	<	}
684	<	else if( !strcmp( endTest, ".mdl" ) ){
685	<	strcpy( endTest, ".eor" );
686	<	}
687	<	else{
688	<	strcat( simnfo->finalName, ".eor" );
689	<	}
690	<	}
706	>	info[i].sampleTime = globals->getRunTime();
707	>	info[i].statusTime = info[i].sampleTime;
708	>	info[i].thermalTime = info[i].sampleTime;
709		}
710
711	<	// make the sample and status out names
711	>	if( globals->haveStatusTime() ){
712	>	info[i].statusTime = globals->getStatusTime();
713	>	}
714
715	<	strcpy( simnfo->sampleName, inFileName );
716	<	char* endTest;
697	<	int nameLength = strlen( simnfo->sampleName );
698	<	endTest = &(simnfo->sampleName[nameLength - 5]);
699	<	if( !strcmp( endTest, ".bass" ) ){
700	<	strcpy( endTest, ".dump" );
715	>	if( globals->haveThermalTime() ){
716	>	info[i].thermalTime = globals->getThermalTime();
717		}
718	<	else if( !strcmp( endTest, ".BASS" ) ){
719	<	strcpy( endTest, ".dump" );
720	<	}
721	<	else{
706	<	endTest = &(simnfo->sampleName[nameLength - 4]);
707	<	if( !strcmp( endTest, ".bss" ) ){
708	<	strcpy( endTest, ".dump" );
709	<	}
710	<	else if( !strcmp( endTest, ".mdl" ) ){
711	<	strcpy( endTest, ".dump" );
712	<	}
713	<	else{
714	<	strcat( simnfo->sampleName, ".dump" );
715	<	}
716	<	}
718	>
719	>	// check for the temperature set flag
720	>
721	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
722
723	<	strcpy( simnfo->statusName, inFileName );
724	<	nameLength = strlen( simnfo->statusName );
725	<	endTest = &(simnfo->statusName[nameLength - 5]);
726	<	if( !strcmp( endTest, ".bass" ) ){
727	<	strcpy( endTest, ".stat" );
723	>	// get some of the tricky things that may still be in the globals
724	>
725	>	double boxVector[3];
726	>	if( globals->haveBox() ){
727	>	boxVector[0] = globals->getBox();
728	>	boxVector[1] = globals->getBox();
729	>	boxVector[2] = globals->getBox();
730	>
731	>	info[i].setBox( boxVector );
732		}
733	<	else if( !strcmp( endTest, ".BASS" ) ){
734	<	strcpy( endTest, ".stat" );
735	<	}
733	>	else if( globals->haveDensity() ){
734	>
735	>	double vol;
736	>	vol = (double)tot_nmol / globals->getDensity();
737	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
738	>	boxVector[1] = boxVector[0];
739	>	boxVector[2] = boxVector[0];
740	>
741	>	info[i].setBox( boxVector );
742	>	}
743		else{
744	<	endTest = &(simnfo->statusName[nameLength - 4]);
745	<	if( !strcmp( endTest, ".bss" ) ){
746	<	strcpy( endTest, ".stat" );
744	>	if( !globals->haveBoxX() ){
745	>	sprintf( painCave.errMsg,
746	>	"SimSetup error, no periodic BoxX size given.\n" );
747	>	painCave.isFatal = 1;
748	>	simError();
749		}
750	<	else if( !strcmp( endTest, ".mdl" ) ){
751	<	strcpy( endTest, ".stat" );
750	>	boxVector[0] = globals->getBoxX();
751	>
752	>	if( !globals->haveBoxY() ){
753	>	sprintf( painCave.errMsg,
754	>	"SimSetup error, no periodic BoxY size given.\n" );
755	>	painCave.isFatal = 1;
756	>	simError();
757		}
758	<	else{
759	<	strcat( simnfo->statusName, ".stat" );
758	>	boxVector[1] = globals->getBoxY();
759	>
760	>	if( !globals->haveBoxZ() ){
761	>	sprintf( painCave.errMsg,
762	>	"SimSetup error, no periodic BoxZ size given.\n" );
763	>	painCave.isFatal = 1;
764	>	simError();
765		}
766	+	boxVector[2] = globals->getBoxZ();
767	+
768	+	info[i].setBox( boxVector );
769		}
739	–
740	–	#ifdef IS_MPI
770		}
771	<	#endif // is_mpi
772	<
773	<	// set the status, sample, and themal kick times
774	<
775	<	if( the_globals->haveSampleTime() ){
776	<	simnfo->sampleTime = the_globals->getSampleTime();
777	<	simnfo->statusTime = simnfo->sampleTime;
749	<	simnfo->thermalTime = simnfo->sampleTime;
771	>
772	>	int seedValue;
773	>	struct timeval now_time_val;
774	>	struct timezone time_zone;
775	>
776	>	if(globals->haveSeed()){
777	>	seedValue = globals->getSeed();
778		}
779		else{
780	<	simnfo->sampleTime = the_globals->getRunTime();
781	<	simnfo->statusTime = simnfo->sampleTime;
782	<	simnfo->thermalTime = simnfo->sampleTime;
780	>	#ifndef IS_MPI
781	>	gettimeofday(&now_time_val, &time_zone);  // get the time now
782	>	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
783	>	#else
784	>	if(worldRank == 0){
785	>	gettimeofday(&now_time_val, &time_zone);  // get the time now
786	>	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
787	>	}
788	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
789	>	#endif
790		}
791
792	<	if( the_globals->haveStatusTime() ){
793	<	simnfo->statusTime = the_globals->getStatusTime();
792	>	for(int i = 0; i < nInfo; i++){
793	>	info[i].setSeed(seedValue);
794		}
795
796	<	if( the_globals->haveThermalTime() ){
797	<	simnfo->thermalTime = the_globals->getThermalTime();
798	<	}
796	>	#ifdef IS_MPI
797	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
798	>	MPIcheckPoint();
799	>	#endif // is_mpi
800
801	<	// check for the temperature set flag
801	>	}
802
767	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
803
804	+	void SimSetup::finalInfoCheck( void ){
805	+	int index;
806	+	int usesDipoles;
807	+	int i;
808
809	<	// make the integrator
810	<
811	<
812	<	if( !strcmp( ensemble, "TraPPE_Ex" ) ){
813	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
809	>	for(i=0; i<nInfo; i++){
810	>	// check electrostatic parameters
811	>
812	>	index = 0;
813	>	usesDipoles = 0;
814	>	while( (index < info[i].n_atoms) && !usesDipoles ){
815	>	usesDipoles = (info[i].atoms[index])->hasDipole();
816	>	index++;
817	>	}
818	>
819	>	#ifdef IS_MPI
820	>	int myUse = usesDipoles;
821	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
822	>	#endif //is_mpi
823	>
824	>	double theEcr, theEst;
825	>
826	>	if (globals->getUseRF() ) {
827	>	info[i].useReactionField = 1;
828	>
829	>	if( !globals->haveECR() ){
830	>	sprintf( painCave.errMsg,
831	>	"SimSetup Warning: using default value of 1/2 the smallest "
832	>	"box length for the electrostaticCutoffRadius.\n"
833	>	"I hope you have a very fast processor!\n");
834	>	painCave.isFatal = 0;
835	>	simError();
836	>	double smallest;
837	>	smallest = info[i].boxL[0];
838	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
839	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
840	>	theEcr = 0.5 * smallest;
841	>	} else {
842	>	theEcr = globals->getECR();
843	>	}
844	>
845	>	if( !globals->haveEST() ){
846	>	sprintf( painCave.errMsg,
847	>	"SimSetup Warning: using default value of 0.05 * the "
848	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
849	>	);
850	>	painCave.isFatal = 0;
851	>	simError();
852	>	theEst = 0.05 * theEcr;
853	>	} else {
854	>	theEst= globals->getEST();
855	>	}
856	>
857	>	info[i].setEcr( theEcr, theEst );
858	>
859	>	if(!globals->haveDielectric() ){
860	>	sprintf( painCave.errMsg,
861	>	"SimSetup Error: You are trying to use Reaction Field without"
862	>	"setting a dielectric constant!\n"
863	>	);
864	>	painCave.isFatal = 1;
865	>	simError();
866	>	}
867	>	info[i].dielectric = globals->getDielectric();
868	>	}
869	>	else {
870	>	if (usesDipoles) {
871	>
872	>	if( !globals->haveECR() ){
873	>	sprintf( painCave.errMsg,
874	>	"SimSetup Warning: using default value of 1/2 the smallest "
875	>	"box length for the electrostaticCutoffRadius.\n"
876	>	"I hope you have a very fast processor!\n");
877	>	painCave.isFatal = 0;
878	>	simError();
879	>	double smallest;
880	>	smallest = info[i].boxL[0];
881	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
882	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
883	>	theEcr = 0.5 * smallest;
884	>	} else {
885	>	theEcr = globals->getECR();
886		}
887	<	else if( !strcmp( force_field, "LJ" ) ){
888	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
887	>
888	>	if( !globals->haveEST() ){
889	>	sprintf( painCave.errMsg,
890	>	"SimSetup Warning: using default value of 0.05 * the "
891	>	"electrostaticCutoffRadius for the "
892	>	"electrostaticSkinThickness\n"
893	>	);
894	>	painCave.isFatal = 0;
895	>	simError();
896	>	theEst = 0.05 * theEcr;
897	>	} else {
898	>	theEst= globals->getEST();
899		}
900	+
901	+	info[i].setEcr( theEcr, theEst );
902	+	}
903	+	}
904	+	}
905
906		#ifdef IS_MPI
907	<	mpiSim->mpiRefresh();
908	<	#endif
907	>	strcpy( checkPointMsg, "post processing checks out" );
908	>	MPIcheckPoint();
909	>	#endif // is_mpi
910
911	<	// initialize the Fortran
911	>	}
912
913	+	void SimSetup::initSystemCoords( void ){
914	+	int i;
915	+
916	+	char* inName;
917
918	<	simnfo->refreshSim();
918	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
919	>
920	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
921
922	<	if( !strcmp( simnfo->mixingRule, "standard") ){
923	<	the_ff->initForceField( LB_MIXING_RULE );
922	>	if( globals->haveInitialConfig() ){
923	>
924	>	InitializeFromFile* fileInit;
925	>	#ifdef IS_MPI // is_mpi
926	>	if( worldRank == 0 ){
927	>	#endif //is_mpi
928	>	inName = globals->getInitialConfig();
929	>	double* tempDouble = new double[1000000];
930	>	fileInit = new InitializeFromFile( inName );
931	>	#ifdef IS_MPI
932	>	}else fileInit = new InitializeFromFile( NULL );
933	>	#endif
934	>	fileInit->readInit( info ); // default velocities on
935	>
936	>	delete fileInit;
937		}
792	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
793	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
794	–	}
938		else{
939	+
940	+	#ifdef IS_MPI
941	+
942	+	// no init from bass
943	+
944		sprintf( painCave.errMsg,
945	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
946	<	simnfo->mixingRule );
799	<	painCave.isFatal = 1;
945	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
946	>	painCave.isFatal;
947		simError();
948	+
949	+	#else
950	+
951	+	initFromBass();
952	+
953	+
954	+	#endif
955		}
956	<
803	<
956	>
957		#ifdef IS_MPI
958	<	strcpy( checkPointMsg,
806	<	"Successfully intialized the mixingRule for Fortran." );
958	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
959		MPIcheckPoint();
960		#endif // is_mpi
961	+
962		}
963
964
965	<	void SimSetup::makeMolecules( void ){
813	<
814	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
815	<	molInit info;
816	<	DirectionalAtom* dAtom;
817	<	LinkedAssign* extras;
818	<	LinkedAssign* current_extra;
819	<	AtomStamp* currentAtom;
820	<	BondStamp* currentBond;
821	<	BendStamp* currentBend;
822	<	TorsionStamp* currentTorsion;
823	<
824	<	bond_pair* theBonds;
825	<	bend_set* theBends;
826	<	torsion_set* theTorsions;
827	<
965	>	void SimSetup::makeOutNames( void ){
966
967	<	//init the forceField paramters
967	>	int k;
968
831	–	the_ff->readParams();
832	–
969
970	<	// init the atoms
970	>	for(k=0; k<nInfo; k++){
971
972	<	double ux, uy, uz, u, uSqr;
973	<
974	<	atomOffset = 0;
839	<	excludeOffset = 0;
840	<	for(i=0; i<simnfo->n_mol; i++){
841	<
842	<	stampID = the_molecules[i].getStampID();
843	<
844	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
845	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
846	<	info.nBends    = comp_stamps[stampID]->getNBends();
847	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
848	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
849	<
850	<	info.myAtoms = &the_atoms[atomOffset];
851	<	info.myExcludes = &the_excludes[excludeOffset];
852	<	info.myBonds = new Bond*[info.nBonds];
853	<	info.myBends = new Bend*[info.nBends];
854	<	info.myTorsions = new Torsion*[info.nTorsions];
855	<
856	<	theBonds = new bond_pair[info.nBonds];
857	<	theBends = new bend_set[info.nBends];
858	<	theTorsions = new torsion_set[info.nTorsions];
859	<
860	<	// make the Atoms
861	<
862	<	for(j=0; j<info.nAtoms; j++){
972	>	#ifdef IS_MPI
973	>	if( worldRank == 0 ){
974	>	#endif // is_mpi
975
976	<	currentAtom = comp_stamps[stampID]->getAtom( j );
977	<	if( currentAtom->haveOrientation() ){
866	<
867	<	dAtom = new DirectionalAtom(j + atomOffset);
868	<	simnfo->n_oriented++;
869	<	info.myAtoms[j] = dAtom;
870	<
871	<	ux = currentAtom->getOrntX();
872	<	uy = currentAtom->getOrntY();
873	<	uz = currentAtom->getOrntZ();
874	<
875	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
876	<
877	<	u = sqrt( uSqr );
878	<	ux = ux / u;
879	<	uy = uy / u;
880	<	uz = uz / u;
881	<
882	<	dAtom->setSUx( ux );
883	<	dAtom->setSUy( uy );
884	<	dAtom->setSUz( uz );
976	>	if( globals->haveFinalConfig() ){
977	>	strcpy( info[k].finalName, globals->getFinalConfig() );
978		}
979		else{
980	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
980	>	strcpy( info[k].finalName, inFileName );
981	>	char* endTest;
982	>	int nameLength = strlen( info[k].finalName );
983	>	endTest = &(info[k].finalName[nameLength - 5]);
984	>	if( !strcmp( endTest, ".bass" ) ){
985	>	strcpy( endTest, ".eor" );
986	>	}
987	>	else if( !strcmp( endTest, ".BASS" ) ){
988	>	strcpy( endTest, ".eor" );
989	>	}
990	>	else{
991	>	endTest = &(info[k].finalName[nameLength - 4]);
992	>	if( !strcmp( endTest, ".bss" ) ){
993	>	strcpy( endTest, ".eor" );
994	>	}
995	>	else if( !strcmp( endTest, ".mdl" ) ){
996	>	strcpy( endTest, ".eor" );
997	>	}
998	>	else{
999	>	strcat( info[k].finalName, ".eor" );
1000	>	}
1001	>	}
1002		}
889	–	info.myAtoms[j]->setType( currentAtom->getType() );
890	–
891	–	#ifdef IS_MPI
1003
1004	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1004	>	// make the sample and status out names
1005
1006	<	#endif // is_mpi
1007	<	}
1008	<
1009	<	// make the bonds
1010	<	for(j=0; j<info.nBonds; j++){
1011	<
901	<	currentBond = comp_stamps[stampID]->getBond( j );
902	<	theBonds[j].a = currentBond->getA() + atomOffset;
903	<	theBonds[j].b = currentBond->getB() + atomOffset;
904	<
905	<	exI = theBonds[j].a;
906	<	exJ = theBonds[j].b;
907	<
908	<	// exclude_I must always be the smaller of the pair
909	<	if( exI > exJ ){
910	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
1006	>	strcpy( info[k].sampleName, inFileName );
1007	>	char* endTest;
1008	>	int nameLength = strlen( info[k].sampleName );
1009	>	endTest = &(info[k].sampleName[nameLength - 5]);
1010	>	if( !strcmp( endTest, ".bass" ) ){
1011	>	strcpy( endTest, ".dump" );
1012		}
1013	<	#ifdef IS_MPI
1014	<	tempEx = exI;
1015	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1016	<	tempEx = exJ;
1017	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1013	>	else if( !strcmp( endTest, ".BASS" ) ){
1014	>	strcpy( endTest, ".dump" );
1015	>	}
1016	>	else{
1017	>	endTest = &(info[k].sampleName[nameLength - 4]);
1018	>	if( !strcmp( endTest, ".bss" ) ){
1019	>	strcpy( endTest, ".dump" );
1020	>	}
1021	>	else if( !strcmp( endTest, ".mdl" ) ){
1022	>	strcpy( endTest, ".dump" );
1023	>	}
1024	>	else{
1025	>	strcat( info[k].sampleName, ".dump" );
1026	>	}
1027	>	}
1028
1029	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1030	<	#else  // isn't MPI
1031	<
1032	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1033	<	#endif  //is_mpi
925	<	}
926	<	excludeOffset += info.nBonds;
927	<
928	<	//make the bends
929	<	for(j=0; j<info.nBends; j++){
930	<
931	<	currentBend = comp_stamps[stampID]->getBend( j );
932	<	theBends[j].a = currentBend->getA() + atomOffset;
933	<	theBends[j].b = currentBend->getB() + atomOffset;
934	<	theBends[j].c = currentBend->getC() + atomOffset;
935	<
936	<	if( currentBend->haveExtras() ){
937	<
938	<	extras = currentBend->getExtras();
939	<	current_extra = extras;
940	<
941	<	while( current_extra != NULL ){
942	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
943	<
944	<	switch( current_extra->getType() ){
945	<
946	<	case 0:
947	<	theBends[j].ghost =
948	<	current_extra->getInt() + atomOffset;
949	<	theBends[j].isGhost = 1;
950	<	break;
951	<
952	<	case 1:
953	<	theBends[j].ghost =
954	<	(int)current_extra->getDouble() + atomOffset;
955	<	theBends[j].isGhost = 1;
956	<	break;
957	<
958	<	default:
959	<	sprintf( painCave.errMsg,
960	<	"SimSetup Error: ghostVectorSource was neither a "
961	<	"double nor an int.\n"
962	<	"-->Bend[%d] in %s\n",
963	<	j, comp_stamps[stampID]->getID() );
964	<	painCave.isFatal = 1;
965	<	simError();
966	<	}
967	<	}
968	<
969	<	else{
970	<
971	<	sprintf( painCave.errMsg,
972	<	"SimSetup Error: unhandled bend assignment:\n"
973	<	"    -->%s in Bend[%d] in %s\n",
974	<	current_extra->getlhs(),
975	<	j, comp_stamps[stampID]->getID() );
976	<	painCave.isFatal = 1;
977	<	simError();
978	<	}
979	<
980	<	current_extra = current_extra->getNext();
981	<	}
1029	>	strcpy( info[k].statusName, inFileName );
1030	>	nameLength = strlen( info[k].statusName );
1031	>	endTest = &(info[k].statusName[nameLength - 5]);
1032	>	if( !strcmp( endTest, ".bass" ) ){
1033	>	strcpy( endTest, ".stat" );
1034		}
1035	<
1036	<	if( !theBends[j].isGhost ){
985	<
986	<	exI = theBends[j].a;
987	<	exJ = theBends[j].c;
1035	>	else if( !strcmp( endTest, ".BASS" ) ){
1036	>	strcpy( endTest, ".stat" );
1037		}
1038		else{
1039	<
1040	<	exI = theBends[j].a;
1041	<	exJ = theBends[j].b;
1039	>	endTest = &(info[k].statusName[nameLength - 4]);
1040	>	if( !strcmp( endTest, ".bss" ) ){
1041	>	strcpy( endTest, ".stat" );
1042	>	}
1043	>	else if( !strcmp( endTest, ".mdl" ) ){
1044	>	strcpy( endTest, ".stat" );
1045	>	}
1046	>	else{
1047	>	strcat( info[k].statusName, ".stat" );
1048	>	}
1049		}
1050
995	–	// exclude_I must always be the smaller of the pair
996	–	if( exI > exJ ){
997	–	tempEx = exI;
998	–	exI = exJ;
999	–	exJ = tempEx;
1000	–	}
1051		#ifdef IS_MPI
1002	–	tempEx = exI;
1003	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1004	–	tempEx = exJ;
1005	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1006	–
1007	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1008	–	#else  // isn't MPI
1009	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1010	–	#endif  //is_mpi
1052		}
1053	<	excludeOffset += info.nBends;
1053	>	#endif // is_mpi
1054	>	}
1055	>	}
1056
1014	–	for(j=0; j<info.nTorsions; j++){
1015	–
1016	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1017	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1018	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1019	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1020	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1021	–
1022	–	exI = theTorsions[j].a;
1023	–	exJ = theTorsions[j].d;
1057
1058	<	// exclude_I must always be the smaller of the pair
1059	<	if( exI > exJ ){
1060	<	tempEx = exI;
1061	<	exI = exJ;
1062	<	exJ = tempEx;
1063	<	}
1058	>	void SimSetup::sysObjectsCreation( void ){
1059	>
1060	>	int i,k;
1061	>
1062	>	// create the forceField
1063	>
1064	>	createFF();
1065	>
1066	>	// extract componentList
1067	>
1068	>	compList();
1069	>
1070	>	// calc the number of atoms, bond, bends, and torsions
1071	>
1072	>	calcSysValues();
1073	>
1074		#ifdef IS_MPI
1075	<	tempEx = exI;
1076	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1077	<	tempEx = exJ;
1078	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1079	<
1080	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1081	<	#else  // isn't MPI
1082	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1083	<	#endif  //is_mpi
1075	>	// divide the molecules among the processors
1076	>
1077	>	mpiMolDivide();
1078	>	#endif //is_mpi
1079	>
1080	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1081	>
1082	>	makeSysArrays();
1083	>
1084	>	// make and initialize the molecules (all but atomic coordinates)
1085	>
1086	>	makeMolecules();
1087	>
1088	>	for(k=0; k<nInfo; k++){
1089	>	info[k].identArray = new int[info[k].n_atoms];
1090	>	for(i=0; i<info[k].n_atoms; i++){
1091	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1092		}
1093	<	excludeOffset += info.nTorsions;
1093	>	}
1094	>	}
1095
1044	–
1045	–	// send the arrays off to the forceField for init.
1096
1097	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1048	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1049	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1050	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1097	>	void SimSetup::createFF( void ){
1098
1099	+	switch( ffCase ){
1100
1101	<	the_molecules[i].initialize( info );
1101	>	case FF_DUFF:
1102	>	the_ff = new DUFF();
1103	>	break;
1104
1105	+	case FF_LJ:
1106	+	the_ff = new LJFF();
1107	+	break;
1108
1109	<	atomOffset += info.nAtoms;
1110	<	delete[] theBonds;
1111	<	delete[] theBends;
1112	<	delete[] theTorsions;
1109	>	case FF_EAM:
1110	>	the_ff = new EAM_FF();
1111	>	break;
1112	>
1113	>	default:
1114	>	sprintf( painCave.errMsg,
1115	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1116	>	painCave.isFatal = 1;
1117	>	simError();
1118		}
1119
1120		#ifdef IS_MPI
1121	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1121	>	strcpy( checkPointMsg, "ForceField creation successful" );
1122		MPIcheckPoint();
1123		#endif // is_mpi
1124
1067	–	// clean up the forcefield
1068	–	the_ff->calcRcut();
1069	–	the_ff->cleanMe();
1070	–
1125		}
1126
1073	–	void SimSetup::initFromBass( void ){
1127
1128	<	int i, j, k;
1076	<	int n_cells;
1077	<	double cellx, celly, cellz;
1078	<	double temp1, temp2, temp3;
1079	<	int n_per_extra;
1080	<	int n_extra;
1081	<	int have_extra, done;
1128	>	void SimSetup::compList( void ){
1129
1130	<	temp1 = (double)tot_nmol / 4.0;
1131	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1132	<	temp3 = ceil( temp2 );
1133	<
1134	<	have_extra =0;
1135	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1136	<	have_extra =1;
1137	<
1138	<	n_cells = (int)temp3 - 1;
1139	<	cellx = simnfo->box_x / temp3;
1140	<	celly = simnfo->box_y / temp3;
1141	<	cellz = simnfo->box_z / temp3;
1142	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1143	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1144	<	n_per_extra = (int)ceil( temp1 );
1130	>	int i;
1131	>	char* id;
1132	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1133	>	LinkedMolStamp* currentStamp = NULL;
1134	>	comp_stamps = new MoleculeStamp*[n_components];
1135	>
1136	>	// make an array of molecule stamps that match the components used.
1137	>	// also extract the used stamps out into a separate linked list
1138	>
1139	>	for(i=0; i<nInfo; i++){
1140	>	info[i].nComponents = n_components;
1141	>	info[i].componentsNmol = components_nmol;
1142	>	info[i].compStamps = comp_stamps;
1143	>	info[i].headStamp = headStamp;
1144	>	}
1145	>
1146
1147	<	if( n_per_extra > 4){
1148	<	sprintf( painCave.errMsg,
1149	<	"SimSetup error. There has been an error in constructing"
1150	<	" the non-complete lattice.\n" );
1151	<	painCave.isFatal = 1;
1152	<	simError();
1147	>	for( i=0; i<n_components; i++ ){
1148	>
1149	>	id = the_components[i]->getType();
1150	>	comp_stamps[i] = NULL;
1151	>
1152	>	// check to make sure the component isn't already in the list
1153	>
1154	>	comp_stamps[i] = headStamp->match( id );
1155	>	if( comp_stamps[i] == NULL ){
1156	>
1157	>	// extract the component from the list;
1158	>
1159	>	currentStamp = stamps->extractMolStamp( id );
1160	>	if( currentStamp == NULL ){
1161	>	sprintf( painCave.errMsg,
1162	>	"SimSetup error: Component \"%s\" was not found in the "
1163	>	"list of declared molecules\n",
1164	>	id );
1165	>	painCave.isFatal = 1;
1166	>	simError();
1167	>	}
1168	>
1169	>	headStamp->add( currentStamp );
1170	>	comp_stamps[i] = headStamp->match( id );
1171		}
1172		}
1173	<	else{
1174	<	n_cells = (int)temp3;
1175	<	cellx = simnfo->box_x / temp3;
1176	<	celly = simnfo->box_y / temp3;
1177	<	cellz = simnfo->box_z / temp3;
1173	>
1174	>	#ifdef IS_MPI
1175	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1176	>	MPIcheckPoint();
1177	>	#endif // is_mpi
1178	>
1179	>
1180	>	}
1181	>
1182	>	void SimSetup::calcSysValues( void ){
1183	>	int i, j, k;
1184	>
1185	>	int *molMembershipArray;
1186	>
1187	>	tot_atoms = 0;
1188	>	tot_bonds = 0;
1189	>	tot_bends = 0;
1190	>	tot_torsions = 0;
1191	>	for( i=0; i<n_components; i++ ){
1192	>
1193	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1194	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1195	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1196	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1197		}
1198	+
1199	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1200	+	molMembershipArray = new int[tot_atoms];
1201	+
1202	+	for(i=0; i<nInfo; i++){
1203	+	info[i].n_atoms = tot_atoms;
1204	+	info[i].n_bonds = tot_bonds;
1205	+	info[i].n_bends = tot_bends;
1206	+	info[i].n_torsions = tot_torsions;
1207	+	info[i].n_SRI = tot_SRI;
1208	+	info[i].n_mol = tot_nmol;
1209	+
1210	+	info[i].molMembershipArray = molMembershipArray;
1211	+	}
1212	+	}
1213
1214	<	current_mol = 0;
1115	<	current_comp_mol = 0;
1116	<	current_comp = 0;
1117	<	current_atom_ndx = 0;
1214	>	#ifdef IS_MPI
1215
1216	<	for( i=0; i < n_cells ; i++ ){
1217	<	for( j=0; j < n_cells; j++ ){
1218	<	for( k=0; k < n_cells; k++ ){
1216	>	void SimSetup::mpiMolDivide( void ){
1217	>
1218	>	int i, j, k;
1219	>	int localMol, allMol;
1220	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1221
1222	<	makeElement( i * cellx,
1223	<	j * celly,
1224	<	k * cellz );
1222	>	mpiSim = new mpiSimulation( info );
1223	>
1224	>	globalIndex = mpiSim->divideLabor();
1225
1226	<	makeElement( i * cellx + 0.5 * cellx,
1227	<	j * celly + 0.5 * celly,
1228	<	k * cellz );
1226	>	// set up the local variables
1227	>
1228	>	mol2proc = mpiSim->getMolToProcMap();
1229	>	molCompType = mpiSim->getMolComponentType();
1230	>
1231	>	allMol = 0;
1232	>	localMol = 0;
1233	>	local_atoms = 0;
1234	>	local_bonds = 0;
1235	>	local_bends = 0;
1236	>	local_torsions = 0;
1237	>	globalAtomIndex = 0;
1238
1131	–	makeElement( i * cellx,
1132	–	j * celly + 0.5 * celly,
1133	–	k * cellz + 0.5 * cellz );
1239
1240	<	makeElement( i * cellx + 0.5 * cellx,
1241	<	j * celly,
1242	<	k * cellz + 0.5 * cellz );
1240	>	for( i=0; i<n_components; i++ ){
1241	>
1242	>	for( j=0; j<components_nmol[i]; j++ ){
1243	>
1244	>	if( mol2proc[allMol] == worldRank ){
1245	>
1246	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1247	>	local_bonds +=    comp_stamps[i]->getNBonds();
1248	>	local_bends +=    comp_stamps[i]->getNBends();
1249	>	local_torsions += comp_stamps[i]->getNTorsions();
1250	>	localMol++;
1251	>	}
1252	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1253	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1254	>	globalAtomIndex++;
1255		}
1256	+
1257	+	allMol++;
1258		}
1259		}
1260	+	local_SRI = local_bonds + local_bends + local_torsions;
1261	+
1262	+	info[0].n_atoms = mpiSim->getMyNlocal();
1263	+
1264	+	if( local_atoms != info[0].n_atoms ){
1265	+	sprintf( painCave.errMsg,
1266	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1267	+	" localAtom (%d) are not equal.\n",
1268	+	info[0].n_atoms,
1269	+	local_atoms );
1270	+	painCave.isFatal = 1;
1271	+	simError();
1272	+	}
1273
1274	<	if( have_extra ){
1275	<	done = 0;
1274	>	info[0].n_bonds = local_bonds;
1275	>	info[0].n_bends = local_bends;
1276	>	info[0].n_torsions = local_torsions;
1277	>	info[0].n_SRI = local_SRI;
1278	>	info[0].n_mol = localMol;
1279
1280	<	int start_ndx;
1281	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1282	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1280	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1281	>	MPIcheckPoint();
1282	>	}
1283	>
1284	>	#endif // is_mpi
1285
1149	–	if( i < n_cells ){
1286
1287	<	if( j < n_cells ){
1288	<	start_ndx = n_cells;
1153	<	}
1154	<	else start_ndx = 0;
1155	<	}
1156	<	else start_ndx = 0;
1287	>	void SimSetup::makeSysArrays( void ){
1288	>	int i, j, k, l;
1289
1290	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1290	>	Atom** the_atoms;
1291	>	Molecule* the_molecules;
1292	>	Exclude** the_excludes;
1293
1294	<	makeElement( i * cellx,
1295	<	j * celly,
1296	<	k * cellz );
1297	<	done = ( current_mol >= tot_nmol );
1294	>
1295	>	for(l=0; l<nInfo; l++){
1296	>
1297	>	// create the atom and short range interaction arrays
1298	>
1299	>	the_atoms = new Atom*[info[l].n_atoms];
1300	>	the_molecules = new Molecule[info[l].n_mol];
1301	>	int molIndex;
1302
1303	<	if( !done && n_per_extra > 1 ){
1304	<	makeElement( i * cellx + 0.5 * cellx,
1305	<	j * celly + 0.5 * celly,
1306	<	k * cellz );
1307	<	done = ( current_mol >= tot_nmol );
1308	<	}
1303	>	// initialize the molecule's stampID's
1304	>
1305	>	#ifdef IS_MPI
1306	>
1307	>
1308	>	molIndex = 0;
1309	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1310	>
1311	>	if(mol2proc[i] == worldRank ){
1312	>	the_molecules[molIndex].setStampID( molCompType[i] );
1313	>	the_molecules[molIndex].setMyIndex( molIndex );
1314	>	the_molecules[molIndex].setGlobalIndex( i );
1315	>	molIndex++;
1316	>	}
1317	>	}
1318	>
1319	>	#else // is_mpi
1320	>
1321	>	molIndex = 0;
1322	>	globalAtomIndex = 0;
1323	>	for(i=0; i<n_components; i++){
1324	>	for(j=0; j<components_nmol[i]; j++ ){
1325	>	the_molecules[molIndex].setStampID( i );
1326	>	the_molecules[molIndex].setMyIndex( molIndex );
1327	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1328	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1329	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1330	>	globalAtomIndex++;
1331	>	}
1332	>	molIndex++;
1333	>	}
1334	>	}
1335	>
1336	>
1337	>	#endif // is_mpi
1338
1172	–	if( !done && n_per_extra > 2){
1173	–	makeElement( i * cellx,
1174	–	j * celly + 0.5 * celly,
1175	–	k * cellz + 0.5 * cellz );
1176	–	done = ( current_mol >= tot_nmol );
1177	–	}
1339
1340	<	if( !done && n_per_extra > 3){
1341	<	makeElement( i * cellx + 0.5 * cellx,
1342	<	j * celly,
1343	<	k * cellz + 0.5 * cellz );
1344	<	done = ( current_mol >= tot_nmol );
1345	<	}
1185	<	}
1340	>	if( info[l].n_SRI ){
1341	>
1342	>	Exclude::createArray(info[l].n_SRI);
1343	>	the_excludes = new Exclude*[info[l].n_SRI];
1344	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1345	>	the_excludes[ex] = new Exclude(ex);
1346		}
1347	+	info[l].globalExcludes = new int;
1348	+	info[l].n_exclude = info[l].n_SRI;
1349		}
1350	<	}
1350	>	else{
1351	>
1352	>	Exclude::createArray( 1 );
1353	>	the_excludes = new Exclude*;
1354	>	the_excludes[0] = new Exclude(0);
1355	>	the_excludes[0]->setPair( 0,0 );
1356	>	info[l].globalExcludes = new int;
1357	>	info[l].globalExcludes[0] = 0;
1358	>	info[l].n_exclude = 0;
1359	>	}
1360
1361	+	// set the arrays into the SimInfo object
1362
1363	<	for( i=0; i<simnfo->n_atoms; i++ ){
1364	<	simnfo->atoms[i]->set_vx( 0.0 );
1365	<	simnfo->atoms[i]->set_vy( 0.0 );
1366	<	simnfo->atoms[i]->set_vz( 0.0 );
1363	>	info[l].atoms = the_atoms;
1364	>	info[l].molecules = the_molecules;
1365	>	info[l].nGlobalExcludes = 0;
1366	>	info[l].excludes = the_excludes;
1367	>
1368	>	the_ff->setSimInfo( info );
1369	>
1370		}
1371		}
1372
1373	<	void SimSetup::makeElement( double x, double y, double z ){
1373	>	void SimSetup::makeIntegrator( void ){
1374
1375		int k;
1201	–	AtomStamp* current_atom;
1202	–	DirectionalAtom* dAtom;
1203	–	double rotMat[3][3];
1376
1377	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1377	>	NVT<RealIntegrator>*  myNVT = NULL;
1378	>	NPTi<RealIntegrator>* myNPTi = NULL;
1379	>	NPTf<RealIntegrator>* myNPTf = NULL;
1380	>	NPTim<RealIntegrator>* myNPTim = NULL;
1381	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1382	>
1383	>	for(k=0; k<nInfo; k++){
1384	>
1385	>	switch( ensembleCase ){
1386	>
1387	>	case NVE_ENS:
1388	>	if (globals->haveZconstraints()){
1389	>	setupZConstraint(info[k]);
1390	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1391	>	}
1392
1393	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1394	<	if( !current_atom->havePosition() ){
1393	>	else
1394	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1395	>	break;
1396	>
1397	>	case NVT_ENS:
1398	>	if (globals->haveZconstraints()){
1399	>	setupZConstraint(info[k]);
1400	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1401	>	}
1402	>	else
1403	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1404	>
1405	>	myNVT->setTargetTemp(globals->getTargetTemp());
1406	>
1407	>	if (globals->haveTauThermostat())
1408	>	myNVT->setTauThermostat(globals->getTauThermostat());
1409	>
1410	>	else {
1411	>	sprintf( painCave.errMsg,
1412	>	"SimSetup error: If you use the NVT\n"
1413	>	"    ensemble, you must set tauThermostat.\n");
1414	>	painCave.isFatal = 1;
1415	>	simError();
1416	>	}
1417	>	break;
1418	>
1419	>	case NPTi_ENS:
1420	>	if (globals->haveZconstraints()){
1421	>	setupZConstraint(info[k]);
1422	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1423	>	}
1424	>	else
1425	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1426	>
1427	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1428	>
1429	>	if (globals->haveTargetPressure())
1430	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1431	>	else {
1432	>	sprintf( painCave.errMsg,
1433	>	"SimSetup error: If you use a constant pressure\n"
1434	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	>	painCave.isFatal = 1;
1436	>	simError();
1437	>	}
1438	>
1439	>	if( globals->haveTauThermostat() )
1440	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1441	>	else{
1442	>	sprintf( painCave.errMsg,
1443	>	"SimSetup error: If you use an NPT\n"
1444	>	"    ensemble, you must set tauThermostat.\n");
1445	>	painCave.isFatal = 1;
1446	>	simError();
1447	>	}
1448	>
1449	>	if( globals->haveTauBarostat() )
1450	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1451	>	else{
1452	>	sprintf( painCave.errMsg,
1453	>	"SimSetup error: If you use an NPT\n"
1454	>	"    ensemble, you must set tauBarostat.\n");
1455	>	painCave.isFatal = 1;
1456	>	simError();
1457	>	}
1458	>	break;
1459	>
1460	>	case NPTf_ENS:
1461	>	if (globals->haveZconstraints()){
1462	>	setupZConstraint(info[k]);
1463	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1464	>	}
1465	>	else
1466	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1467	>
1468	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1469	>
1470	>	if (globals->haveTargetPressure())
1471	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1472	>	else {
1473	>	sprintf( painCave.errMsg,
1474	>	"SimSetup error: If you use a constant pressure\n"
1475	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1476	>	painCave.isFatal = 1;
1477	>	simError();
1478	>	}
1479	>
1480	>	if( globals->haveTauThermostat() )
1481	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1482	>	else{
1483	>	sprintf( painCave.errMsg,
1484	>	"SimSetup error: If you use an NPT\n"
1485	>	"    ensemble, you must set tauThermostat.\n");
1486	>	painCave.isFatal = 1;
1487	>	simError();
1488	>	}
1489	>
1490	>	if( globals->haveTauBarostat() )
1491	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1492	>	else{
1493	>	sprintf( painCave.errMsg,
1494	>	"SimSetup error: If you use an NPT\n"
1495	>	"    ensemble, you must set tauBarostat.\n");
1496	>	painCave.isFatal = 1;
1497	>	simError();
1498	>	}
1499	>	break;
1500	>
1501	>	case NPTim_ENS:
1502	>	if (globals->haveZconstraints()){
1503	>	setupZConstraint(info[k]);
1504	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1505	>	}
1506	>	else
1507	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1508	>
1509	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1510	>
1511	>	if (globals->haveTargetPressure())
1512	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1513	>	else {
1514	>	sprintf( painCave.errMsg,
1515	>	"SimSetup error: If you use a constant pressure\n"
1516	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1517	>	painCave.isFatal = 1;
1518	>	simError();
1519	>	}
1520	>
1521	>	if( globals->haveTauThermostat() )
1522	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1523	>	else{
1524	>	sprintf( painCave.errMsg,
1525	>	"SimSetup error: If you use an NPT\n"
1526	>	"    ensemble, you must set tauThermostat.\n");
1527	>	painCave.isFatal = 1;
1528	>	simError();
1529	>	}
1530	>
1531	>	if( globals->haveTauBarostat() )
1532	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1533	>	else{
1534	>	sprintf( painCave.errMsg,
1535	>	"SimSetup error: If you use an NPT\n"
1536	>	"    ensemble, you must set tauBarostat.\n");
1537	>	painCave.isFatal = 1;
1538	>	simError();
1539	>	}
1540	>	break;
1541	>
1542	>	case NPTfm_ENS:
1543	>	if (globals->haveZconstraints()){
1544	>	setupZConstraint(info[k]);
1545	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1546	>	}
1547	>	else
1548	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1549	>
1550	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1551	>
1552	>	if (globals->haveTargetPressure())
1553	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1554	>	else {
1555	>	sprintf( painCave.errMsg,
1556	>	"SimSetup error: If you use a constant pressure\n"
1557	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1558	>	painCave.isFatal = 1;
1559	>	simError();
1560	>	}
1561	>
1562	>	if( globals->haveTauThermostat() )
1563	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1564	>	else{
1565	>	sprintf( painCave.errMsg,
1566	>	"SimSetup error: If you use an NPT\n"
1567	>	"    ensemble, you must set tauThermostat.\n");
1568	>	painCave.isFatal = 1;
1569	>	simError();
1570	>	}
1571	>
1572	>	if( globals->haveTauBarostat() )
1573	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1574	>	else{
1575	>	sprintf( painCave.errMsg,
1576	>	"SimSetup error: If you use an NPT\n"
1577	>	"    ensemble, you must set tauBarostat.\n");
1578	>	painCave.isFatal = 1;
1579	>	simError();
1580	>	}
1581	>	break;
1582	>
1583	>	default:
1584		sprintf( painCave.errMsg,
1585	<	"SimSetup:initFromBass error.\n"
1211	<	"\tComponent %s, atom %s does not have a position specified.\n"
1212	<	"\tThe initialization routine is unable to give a start"
1213	<	" position.\n",
1214	<	comp_stamps[current_comp]->getID(),
1215	<	current_atom->getType() );
1585	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1586		painCave.isFatal = 1;
1587		simError();
1588		}
1589	+	}
1590	+	}
1591
1592	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1221	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1222	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1592	>	void SimSetup::initFortran( void ){
1593
1594	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1594	>	info[0].refreshSim();
1595	>
1596	>	if( !strcmp( info[0].mixingRule, "standard") ){
1597	>	the_ff->initForceField( LB_MIXING_RULE );
1598	>	}
1599	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1600	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1601	>	}
1602	>	else{
1603	>	sprintf( painCave.errMsg,
1604	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	>	info[0].mixingRule );
1606	>	painCave.isFatal = 1;
1607	>	simError();
1608	>	}
1609
1226	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1610
1611	<	rotMat[0][0] = 1.0;
1612	<	rotMat[0][1] = 0.0;
1613	<	rotMat[0][2] = 0.0;
1611	>	#ifdef IS_MPI
1612	>	strcpy( checkPointMsg,
1613	>	"Successfully intialized the mixingRule for Fortran." );
1614	>	MPIcheckPoint();
1615	>	#endif // is_mpi
1616
1617	<	rotMat[1][0] = 0.0;
1233	<	rotMat[1][1] = 1.0;
1234	<	rotMat[1][2] = 0.0;
1617	>	}
1618
1619	<	rotMat[2][0] = 0.0;
1620	<	rotMat[2][1] = 0.0;
1621	<	rotMat[2][2] = 1.0;
1619	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1620	>	{
1621	>	int nZConstraints;
1622	>	ZconStamp** zconStamp;
1623
1624	<	dAtom->setA( rotMat );
1625	<	}
1624	>	if(globals->haveZconstraintTime()){
1625	>
1626	>	//add sample time of z-constraint  into SimInfo's property list
1627	>	DoubleData* zconsTimeProp = new DoubleData();
1628	>	zconsTimeProp->setID(ZCONSTIME_ID);
1629	>	zconsTimeProp->setData(globals->getZconsTime());
1630	>	theInfo.addProperty(zconsTimeProp);
1631	>	}
1632	>	else{
1633	>	sprintf( painCave.errMsg,
1634	>	"ZConstraint error: If you use an ZConstraint\n"
1635	>	" , you must set sample time.\n");
1636	>	painCave.isFatal = 1;
1637	>	simError();
1638	>	}
1639
1640	<	current_atom_ndx++;
1640	>	//push zconsTol into siminfo, if user does not specify
1641	>	//value for zconsTol, a default value will be used
1642	>	DoubleData* zconsTol = new DoubleData();
1643	>	zconsTol->setID(ZCONSTOL_ID);
1644	>	if(globals->haveZconsTol()){
1645	>	zconsTol->setData(globals->getZconsTol());
1646		}
1647	+	else{
1648	+	double defaultZConsTol = 0.01;
1649	+	sprintf( painCave.errMsg,
1650	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1651	+	" , default value %f is used.\n", defaultZConsTol);
1652	+	painCave.isFatal = 0;
1653	+	simError();
1654
1655	<	current_mol++;
1656	<	current_comp_mol++;
1655	>	zconsTol->setData(defaultZConsTol);
1656	>	}
1657	>	theInfo.addProperty(zconsTol);
1658
1659	<	if( current_comp_mol >= components_nmol[current_comp] ){
1659	>	//set Force Substraction Policy
1660	>	StringData* zconsForcePolicy =  new StringData();
1661	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1662	>
1663	>	if(globals->haveZconsForcePolicy()){
1664	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1665	>	}
1666	>	else{
1667	>	sprintf( painCave.errMsg,
1668	>	"ZConstraint Warning: User does not set force substraction policy, "
1669	>	"average force substraction policy is used\n");
1670	>	painCave.isFatal = 0;
1671	>	simError();
1672	>	zconsForcePolicy->setData("BYNUMBER");
1673	>	}
1674	>
1675	>	theInfo.addProperty(zconsForcePolicy);
1676	>
1677	>	//Determine the name of ouput file and add it into SimInfo's property list
1678	>	//Be careful, do not use inFileName, since it is a pointer which
1679	>	//point to a string at master node, and slave nodes do not contain that string
1680	>
1681	>	string zconsOutput(theInfo.finalName);
1682	>
1683	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1684	>
1685	>	StringData* zconsFilename = new StringData();
1686	>	zconsFilename->setID(ZCONSFILENAME_ID);
1687	>	zconsFilename->setData(zconsOutput);
1688	>
1689	>	theInfo.addProperty(zconsFilename);
1690	>
1691	>	//setup index, pos and other parameters of z-constraint molecules
1692	>	nZConstraints = globals->getNzConstraints();
1693	>	theInfo.nZconstraints = nZConstraints;
1694
1695	<	current_comp_mol = 0;
1696	<	current_comp++;
1695	>	zconStamp = globals->getZconStamp();
1696	>	ZConsParaItem tempParaItem;
1697	>
1698	>	ZConsParaData* zconsParaData = new ZConsParaData();
1699	>	zconsParaData->setID(ZCONSPARADATA_ID);
1700	>
1701	>	for(int i = 0; i < nZConstraints; i++){
1702	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1703	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1704	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1705	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1706	>
1707	>	zconsParaData->addItem(tempParaItem);
1708		}
1709	+
1710	+	//sort the parameters by index of molecules
1711	+	zconsParaData->sortByIndex();
1712	+
1713	+	//push data into siminfo, therefore, we can retrieve later
1714	+	theInfo.addProperty(zconsParaData);
1715	+
1716		}

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines