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

Comparing:
branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 658 by tim, Thu Jul 31 15:35:07 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 "parse_me.h"
#	Line 12 | Line 14 | SimSetup::SimSetup(){
14		#include "mpiSimulation.hpp"
15		#endif
16
17	+	// some defines for ensemble and Forcefield  cases
18	+
19	+	#define NVE_ENS   0
20	+	#define NVT_ENS   1
21	+	#define NPTi_ENS  2
22	+	#define NPTf_ENS  3
23	+	#define NPTim_ENS 4
24	+	#define NPTfm_ENS 5
25	+	#define NVEZCONS_ENS 6
26	+
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 27 | 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 64 | Line 95 | void SimSetup::createSim( void ){
95
96		void SimSetup::createSim( void ){
97
98	<	MakeStamps *the_stamps;
99	<	Globals* the_globals;
100	<	int i, j;
98	>	int i, j, k, globalAtomIndex;
99	>
100	>	// gather all of the information from the Bass file
101	>
102	>	gatherInfo();
103
104	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
104	>	// creation of complex system objects
105
106	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
106	>	sysObjectsCreation();
107
108	<	// get the ones we know are there, yet still may need some work.
109	<	n_components = the_globals->getNComponents();
110	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
108	>	// check on the post processing info
109	>
110	>	finalInfoCheck();
111
112	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
112	>	// initialize the system coordinates
113
114	+	initSystemCoords();
115	+
116
117	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
117	>	// make the output filenames
118
119	+	makeOutNames();
120	+
121	+	// make the integrator
122	+
123	+	makeIntegrator();
124	+
125		#ifdef IS_MPI
126	<	strcpy( checkPointMsg, "ForceField creation successful" );
127	<	MPIcheckPoint();
106	<	#endif // is_mpi
126	>	mpiSim->mpiRefresh();
127	>	#endif
128
129	+	// initialize the Fortran
130	+
131	+	initFortran();
132	+
133	+
134	+
135	+	}
136	+
137	+
138	+	void SimSetup::makeMolecules( void ){
139	+
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	+	bond_pair* theBonds;
151	+	bend_set* theBends;
152	+	torsion_set* theTorsions;
153	+
154
155	+	//init the forceField paramters
156
157	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
157	>	the_ff->readParams();
158
159	<	if( !the_globals->haveNMol() ){
160	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
159	>
160	>	// init the atoms
161
162	<	tot_nmol = 0;
163	<	for( i=0; i<n_components; i++ ){
162	>	double ux, uy, uz, u, uSqr;
163	>
164	>	atomOffset = 0;
165	>	excludeOffset = 0;
166	>	for(i=0; i<info->n_mol; i++){
167	>
168	>	stampID = the_molecules[i].getStampID();
169
170	<	if( !the_components[i]->haveNMol() ){
171	<	// we have a problem
172	<	sprintf( painCave.errMsg,
173	<	"SimSetup Error. No global NMol or component NMol"
174	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
170	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
171	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
172	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
173	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
174	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
175
176	<	tot_nmol += the_components[i]->getNMol();
177	<	components_nmol[i] = the_components[i]->getNMol();
178	<	}
179	<	}
180	<	else{
181	<	sprintf( painCave.errMsg,
182	<	"SimSetup error.\n"
183	<	"\tSorry, the ability to specify total"
184	<	" nMols and then give molfractions in the components\n"
140	<	"\tis not currently supported."
141	<	" Please give nMol in the components.\n" );
142	<	painCave.isFatal = 1;
143	<	simError();
176	>	molInfo.myAtoms = &the_atoms[atomOffset];
177	>	molInfo.myExcludes = &the_excludes[excludeOffset];
178	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
179	>	molInfo.myBends = new Bend*[molInfo.nBends];
180	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
181	>
182	>	theBonds = new bond_pair[molInfo.nBonds];
183	>	theBends = new bend_set[molInfo.nBends];
184	>	theTorsions = new torsion_set[molInfo.nTorsions];
185
186	+	// make the Atoms
187
188	<	//     tot_nmol = the_globals->getNMol();
188	>	for(j=0; j<molInfo.nAtoms; j++){
189	>
190	>	currentAtom = comp_stamps[stampID]->getAtom( j );
191	>	if( currentAtom->haveOrientation() ){
192	>
193	>	dAtom = new DirectionalAtom(j + atomOffset);
194	>	info->n_oriented++;
195	>	molInfo.myAtoms[j] = dAtom;
196	>
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200	>
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	>
203	>	u = sqrt( uSqr );
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207	>
208	>	dAtom->setSUx( ux );
209	>	dAtom->setSUy( uy );
210	>	dAtom->setSUz( uz );
211	>	}
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
214	>	}
215	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
216
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
159	–
217		#ifdef IS_MPI
218	<	strcpy( checkPointMsg, "Have the number of components" );
219	<	MPIcheckPoint();
218	>
219	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
220	>
221		#endif // is_mpi
222	+	}
223	+
224	+	// make the bonds
225	+	for(j=0; j<molInfo.nBonds; j++){
226	+
227	+	currentBond = comp_stamps[stampID]->getBond( j );
228	+	theBonds[j].a = currentBond->getA() + atomOffset;
229	+	theBonds[j].b = currentBond->getB() + atomOffset;
230
231	<	// make an array of molecule stamps that match the components used.
232	<	// also extract the used stamps out into a separate linked list
231	>	exI = theBonds[j].a;
232	>	exJ = theBonds[j].b;
233
234	<	simnfo->nComponents = n_components;
235	<	simnfo->componentsNmol = components_nmol;
236	<	simnfo->compStamps = comp_stamps;
237	<	simnfo->headStamp = new LinkedMolStamp();
238	<
239	<	char* id;
240	<	LinkedMolStamp* headStamp = simnfo->headStamp;
241	<	LinkedMolStamp* currentStamp = NULL;
242	<	for( i=0; i<n_components; i++ ){
234	>	// exclude_I must always be the smaller of the pair
235	>	if( exI > exJ ){
236	>	tempEx = exI;
237	>	exI = exJ;
238	>	exJ = tempEx;
239	>	}
240	>	#ifdef IS_MPI
241	>	tempEx = exI;
242	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
245	>
246	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
247	>	#else  // isn't MPI
248
249	<	id = the_components[i]->getType();
250	<	comp_stamps[i] = NULL;
251	<
252	<	// check to make sure the component isn't already in the list
249	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
250	>	#endif  //is_mpi
251	>	}
252	>	excludeOffset += molInfo.nBonds;
253
254	<	comp_stamps[i] = headStamp->match( id );
255	<	if( comp_stamps[i] == NULL ){
254	>	//make the bends
255	>	for(j=0; j<molInfo.nBends; j++){
256
257	<	// extract the component from the list;
257	>	currentBend = comp_stamps[stampID]->getBend( j );
258	>	theBends[j].a = currentBend->getA() + atomOffset;
259	>	theBends[j].b = currentBend->getB() + atomOffset;
260	>	theBends[j].c = currentBend->getC() + atomOffset;
261	>
262	>	if( currentBend->haveExtras() ){
263	>
264	>	extras = currentBend->getExtras();
265	>	current_extra = extras;
266	>
267	>	while( current_extra != NULL ){
268	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
269	>
270	>	switch( current_extra->getType() ){
271	>
272	>	case 0:
273	>	theBends[j].ghost =
274	>	current_extra->getInt() + atomOffset;
275	>	theBends[j].isGhost = 1;
276	>	break;
277	>
278	>	case 1:
279	>	theBends[j].ghost =
280	>	(int)current_extra->getDouble() + atomOffset;
281	>	theBends[j].isGhost = 1;
282	>	break;
283	>
284	>	default:
285	>	sprintf( painCave.errMsg,
286	>	"SimSetup Error: ghostVectorSource was neither a "
287	>	"double nor an int.\n"
288	>	"-->Bend[%d] in %s\n",
289	>	j, comp_stamps[stampID]->getID() );
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293	>	}
294	>
295	>	else{
296	>
297	>	sprintf( painCave.errMsg,
298	>	"SimSetup Error: unhandled bend assignment:\n"
299	>	"    -->%s in Bend[%d] in %s\n",
300	>	current_extra->getlhs(),
301	>	j, comp_stamps[stampID]->getID() );
302	>	painCave.isFatal = 1;
303	>	simError();
304	>	}
305	>
306	>	current_extra = current_extra->getNext();
307	>	}
308	>	}
309	>
310	>	if( !theBends[j].isGhost ){
311	>
312	>	exI = theBends[j].a;
313	>	exJ = theBends[j].c;
314	>	}
315	>	else{
316	>
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].b;
319	>	}
320
321	<	currentStamp = the_stamps->extractMolStamp( id );
322	<	if( currentStamp == NULL ){
323	<	sprintf( painCave.errMsg,
324	<	"SimSetup error: Component \"%s\" was not found in the "
325	<	"list of declared molecules\n",
193	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
321	>	// exclude_I must always be the smaller of the pair
322	>	if( exI > exJ ){
323	>	tempEx = exI;
324	>	exI = exJ;
325	>	exJ = tempEx;
326		}
327	+	#ifdef IS_MPI
328	+	tempEx = exI;
329	+	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
330	+	tempEx = exJ;
331	+	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
332
333	<	headStamp->add( currentStamp );
334	<	comp_stamps[i] = headStamp->match( id );
333	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
334	>	#else  // isn't MPI
335	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
336	>	#endif  //is_mpi
337		}
338	<	}
338	>	excludeOffset += molInfo.nBends;
339
340	+	for(j=0; j<molInfo.nTorsions; j++){
341	+
342	+	currentTorsion = comp_stamps[stampID]->getTorsion( j );
343	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
344	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
345	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
346	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
347	+
348	+	exI = theTorsions[j].a;
349	+	exJ = theTorsions[j].d;
350	+
351	+	// exclude_I must always be the smaller of the pair
352	+	if( exI > exJ ){
353	+	tempEx = exI;
354	+	exI = exJ;
355	+	exJ = tempEx;
356	+	}
357		#ifdef IS_MPI
358	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
359	<	MPIcheckPoint();
360	<	#endif // is_mpi
361	<
358	>	tempEx = exI;
359	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
360	>	tempEx = exJ;
361	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
362	>
363	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
364	>	#else  // isn't MPI
365	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
366	>	#endif  //is_mpi
367	>	}
368	>	excludeOffset += molInfo.nTorsions;
369
209	–
210	–
211	–	// caclulate the number of atoms, bonds, bends and torsions
212	–
213	–	tot_atoms = 0;
214	–	tot_bonds = 0;
215	–	tot_bends = 0;
216	–	tot_torsions = 0;
217	–	for( i=0; i<n_components; i++ ){
370
371	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
371	>	// send the arrays off to the forceField for init.
372
373	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
373	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
374	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
375	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
376	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
377
227	–	simnfo->n_atoms = tot_atoms;
228	–	simnfo->n_bonds = tot_bonds;
229	–	simnfo->n_bends = tot_bends;
230	–	simnfo->n_torsions = tot_torsions;
231	–	simnfo->n_SRI = tot_SRI;
232	–	simnfo->n_mol = tot_nmol;
378
379	<
235	<	#ifdef IS_MPI
379	>	the_molecules[i].initialize( molInfo );
380
237	–	// divide the molecules among processors here.
238	–
239	–	mpiSim = new mpiSimulation( simnfo );
240	–
241	–
381
382	<	globalIndex = mpiSim->divideLabor();
383	<
384	<
385	<
247	<	// set up the local variables
248	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
259	<
260	<	for( j=0; j<components_nmol[i]; j++ ){
261	<
262	<	if( mpiSim->getMyMolStart() <= allMol &&
263	<	allMol <= mpiSim->getMyMolEnd() ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
382	>	atomOffset += molInfo.nAtoms;
383	>	delete[] theBonds;
384	>	delete[] theBends;
385	>	delete[] theTorsions;
386		}
274	–	local_SRI = local_bonds + local_bends + local_torsions;
275	–
387
388	<	simnfo->n_atoms = mpiSim->getMyNlocal();
389	<
279	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
288	<
289	<	simnfo->n_bonds = local_bonds;
290	<	simnfo->n_bends = local_bends;
291	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
294	<
295	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
388	>	#ifdef IS_MPI
389	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
390		MPIcheckPoint();
297	–
298	–
391		#endif // is_mpi
300	–
392
393	<	// create the atom and short range interaction arrays
393	>	// clean up the forcefield
394	>	the_ff->calcRcut();
395	>	the_ff->cleanMe();
396
397	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
397	>	}
398
399	+	void SimSetup::initFromBass( void ){
400
401	<	if( simnfo->n_SRI ){
402	<	the_sris = new SRI*[simnfo->n_SRI];
403	<	the_excludes = new int[2 * simnfo->n_SRI];
404	<	simnfo->globalExcludes = new int;
405	<	simnfo->n_exclude = tot_SRI;
406	<	}
407	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
401	>	int i, j, k;
402	>	int n_cells;
403	>	double cellx, celly, cellz;
404	>	double temp1, temp2, temp3;
405	>	int n_per_extra;
406	>	int n_extra;
407	>	int have_extra, done;
408
409	<	simnfo->n_exclude = 1;
410	<	}
409	>	temp1 = (double)tot_nmol / 4.0;
410	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
411	>	temp3 = ceil( temp2 );
412
413	<	// set the arrays into the SimInfo object
413	>	have_extra =0;
414	>	if( temp2 < temp3 ){ // we have a non-complete lattice
415	>	have_extra =1;
416
417	<	simnfo->atoms = the_atoms;
418	<	simnfo->sr_interactions = the_sris;
419	<	simnfo->nGlobalExcludes = 0;
420	<	simnfo->excludes = the_excludes;
417	>	n_cells = (int)temp3 - 1;
418	>	cellx = info->boxL[0] / temp3;
419	>	celly = info->boxL[1] / temp3;
420	>	cellz = info->boxL[2] / temp3;
421	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
422	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
423	>	n_per_extra = (int)ceil( temp1 );
424
425	<
334	<	// get some of the tricky things that may still be in the globals
335	<
336	<	if( simnfo->n_dipoles ){
337	<
338	<	if( !the_globals->haveRRF() ){
425	>	if( n_per_extra > 4){
426		sprintf( painCave.errMsg,
427	<	"SimSetup Error, system has dipoles, but no rRF was set.\n");
427	>	"SimSetup error. There has been an error in constructing"
428	>	" the non-complete lattice.\n" );
429		painCave.isFatal = 1;
430		simError();
431		}
432	<	if( !the_globals->haveDielectric() ){
432	>	}
433	>	else{
434	>	n_cells = (int)temp3;
435	>	cellx = info->boxL[0] / temp3;
436	>	celly = info->boxL[1] / temp3;
437	>	cellz = info->boxL[2] / temp3;
438	>	}
439	>
440	>	current_mol = 0;
441	>	current_comp_mol = 0;
442	>	current_comp = 0;
443	>	current_atom_ndx = 0;
444	>
445	>	for( i=0; i < n_cells ; i++ ){
446	>	for( j=0; j < n_cells; j++ ){
447	>	for( k=0; k < n_cells; k++ ){
448	>
449	>	makeElement( i * cellx,
450	>	j * celly,
451	>	k * cellz );
452	>
453	>	makeElement( i * cellx + 0.5 * cellx,
454	>	j * celly + 0.5 * celly,
455	>	k * cellz );
456	>
457	>	makeElement( i * cellx,
458	>	j * celly + 0.5 * celly,
459	>	k * cellz + 0.5 * cellz );
460	>
461	>	makeElement( i * cellx + 0.5 * cellx,
462	>	j * celly,
463	>	k * cellz + 0.5 * cellz );
464	>	}
465	>	}
466	>	}
467	>
468	>	if( have_extra ){
469	>	done = 0;
470	>
471	>	int start_ndx;
472	>	for( i=0; i < (n_cells+1) && !done; i++ ){
473	>	for( j=0; j < (n_cells+1) && !done; j++ ){
474	>
475	>	if( i < n_cells ){
476	>
477	>	if( j < n_cells ){
478	>	start_ndx = n_cells;
479	>	}
480	>	else start_ndx = 0;
481	>	}
482	>	else start_ndx = 0;
483	>
484	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
485	>
486	>	makeElement( i * cellx,
487	>	j * celly,
488	>	k * cellz );
489	>	done = ( current_mol >= tot_nmol );
490	>
491	>	if( !done && n_per_extra > 1 ){
492	>	makeElement( i * cellx + 0.5 * cellx,
493	>	j * celly + 0.5 * celly,
494	>	k * cellz );
495	>	done = ( current_mol >= tot_nmol );
496	>	}
497	>
498	>	if( !done && n_per_extra > 2){
499	>	makeElement( i * cellx,
500	>	j * celly + 0.5 * celly,
501	>	k * cellz + 0.5 * cellz );
502	>	done = ( current_mol >= tot_nmol );
503	>	}
504	>
505	>	if( !done && n_per_extra > 3){
506	>	makeElement( i * cellx + 0.5 * cellx,
507	>	j * celly,
508	>	k * cellz + 0.5 * cellz );
509	>	done = ( current_mol >= tot_nmol );
510	>	}
511	>	}
512	>	}
513	>	}
514	>	}
515	>
516	>
517	>	for( i=0; i<info->n_atoms; i++ ){
518	>	info->atoms[i]->set_vx( 0.0 );
519	>	info->atoms[i]->set_vy( 0.0 );
520	>	info->atoms[i]->set_vz( 0.0 );
521	>	}
522	>	}
523	>
524	>	void SimSetup::makeElement( double x, double y, double z ){
525	>
526	>	int k;
527	>	AtomStamp* current_atom;
528	>	DirectionalAtom* dAtom;
529	>	double rotMat[3][3];
530	>
531	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
532	>
533	>	current_atom = comp_stamps[current_comp]->getAtom( k );
534	>	if( !current_atom->havePosition() ){
535		sprintf( painCave.errMsg,
536	<	"SimSetup Error, system has dipoles, but no"
537	<	" dielectric was set.\n" );
536	>	"SimSetup:initFromBass error.\n"
537	>	"\tComponent %s, atom %s does not have a position specified.\n"
538	>	"\tThe initialization routine is unable to give a start"
539	>	" position.\n",
540	>	comp_stamps[current_comp]->getID(),
541	>	current_atom->getType() );
542		painCave.isFatal = 1;
543		simError();
544		}
545
546	<	simnfo->rRF        = the_globals->getRRF();
547	<	simnfo->dielectric = the_globals->getDielectric();
546	>	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
547	>	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
548	>	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
549	>
550	>	if( the_atoms[current_atom_ndx]->isDirectional() ){
551	>
552	>	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
553	>
554	>	rotMat[0][0] = 1.0;
555	>	rotMat[0][1] = 0.0;
556	>	rotMat[0][2] = 0.0;
557	>
558	>	rotMat[1][0] = 0.0;
559	>	rotMat[1][1] = 1.0;
560	>	rotMat[1][2] = 0.0;
561	>
562	>	rotMat[2][0] = 0.0;
563	>	rotMat[2][1] = 0.0;
564	>	rotMat[2][2] = 1.0;
565	>
566	>	dAtom->setA( rotMat );
567	>	}
568	>
569	>	current_atom_ndx++;
570		}
571
572	<	#ifdef IS_MPI
573	<	strcpy( checkPointMsg, "rRf and dielectric check out" );
574	<	MPIcheckPoint();
575	<	#endif // is_mpi
572	>	current_mol++;
573	>	current_comp_mol++;
574	>
575	>	if( current_comp_mol >= components_nmol[current_comp] ){
576	>
577	>	current_comp_mol = 0;
578	>	current_comp++;
579	>	}
580	>	}
581	>
582	>
583	>	void SimSetup::gatherInfo( void ){
584	>	int i,j,k;
585	>
586	>	ensembleCase = -1;
587	>	ffCase = -1;
588	>
589	>	// get the stamps and globals;
590	>	stamps = stamps;
591	>	globals = globals;
592	>
593	>	// set the easy ones first
594	>	info->target_temp = globals->getTargetTemp();
595	>	info->dt = globals->getDt();
596	>	info->run_time = globals->getRunTime();
597	>	n_components = globals->getNComponents();
598	>
599	>
600	>	// get the forceField
601	>
602	>	strcpy( force_field, globals->getForceField() );
603	>
604	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
605	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
606	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
607	>	else{
608	>	sprintf( painCave.errMsg,
609	>	"SimSetup Error. Unrecognized force field -> %s\n",
610	>	force_field );
611	>	painCave.isFatal = 1;
612	>	simError();
613	>	}
614	>
615	>	// get the ensemble
616	>
617	>	strcpy( ensemble, globals->getEnsemble() );
618	>
619	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
620	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
621	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
622	>	ensembleCase = NPTi_ENS;
623	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
624	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
625	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
626	>	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
627	>	else{
628	>	sprintf( painCave.errMsg,
629	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
630	>	"reverting to NVE for this simulation.\n",
631	>	ensemble );
632	>	painCave.isFatal = 0;
633	>	simError();
634	>	strcpy( ensemble, "NVE" );
635	>	ensembleCase = NVE_ENS;
636	>	}
637	>	strcpy( info->ensemble, ensemble );
638	>
639	>	// get the mixing rule
640	>
641	>	strcpy( info->mixingRule, globals->getMixingRule() );
642	>	info->usePBC = globals->getPBC();
643	>
644
645	<	if( the_globals->haveBox() ){
646	<	simnfo->box_x = the_globals->getBox();
647	<	simnfo->box_y = the_globals->getBox();
648	<	simnfo->box_z = the_globals->getBox();
645	>	// get the components and calculate the tot_nMol and indvidual n_mol
646	>
647	>	the_components = globals->getComponents();
648	>	components_nmol = new int[n_components];
649	>
650	>
651	>	if( !globals->haveNMol() ){
652	>	// we don't have the total number of molecules, so we assume it is
653	>	// given in each component
654	>
655	>	tot_nmol = 0;
656	>	for( i=0; i<n_components; i++ ){
657	>
658	>	if( !the_components[i]->haveNMol() ){
659	>	// we have a problem
660	>	sprintf( painCave.errMsg,
661	>	"SimSetup Error. No global NMol or component NMol"
662	>	" given. Cannot calculate the number of atoms.\n" );
663	>	painCave.isFatal = 1;
664	>	simError();
665	>	}
666	>
667	>	tot_nmol += the_components[i]->getNMol();
668	>	components_nmol[i] = the_components[i]->getNMol();
669	>	}
670		}
671	<	else if( the_globals->haveDensity() ){
671	>	else{
672	>	sprintf( painCave.errMsg,
673	>	"SimSetup error.\n"
674	>	"\tSorry, the ability to specify total"
675	>	" nMols and then give molfractions in the components\n"
676	>	"\tis not currently supported."
677	>	" Please give nMol in the components.\n" );
678	>	painCave.isFatal = 1;
679	>	simError();
680	>	}
681
682	+	// set the status, sample, and thermal kick times
683	+
684	+	if( globals->haveSampleTime() ){
685	+	info->sampleTime = globals->getSampleTime();
686	+	info->statusTime = info->sampleTime;
687	+	info->thermalTime = info->sampleTime;
688	+	}
689	+	else{
690	+	info->sampleTime = globals->getRunTime();
691	+	info->statusTime = info->sampleTime;
692	+	info->thermalTime = info->sampleTime;
693	+	}
694	+
695	+	if( globals->haveStatusTime() ){
696	+	info->statusTime = globals->getStatusTime();
697	+	}
698	+
699	+	if( globals->haveThermalTime() ){
700	+	info->thermalTime = globals->getThermalTime();
701	+	}
702	+
703	+	// check for the temperature set flag
704	+
705	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
706	+
707	+	// get some of the tricky things that may still be in the globals
708	+
709	+	double boxVector[3];
710	+	if( globals->haveBox() ){
711	+	boxVector[0] = globals->getBox();
712	+	boxVector[1] = globals->getBox();
713	+	boxVector[2] = globals->getBox();
714	+
715	+	info->setBox( boxVector );
716	+	}
717	+	else if( globals->haveDensity() ){
718	+
719		double vol;
720	<	vol = (double)tot_nmol / the_globals->getDensity();
721	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
722	<	simnfo->box_y = simnfo->box_x;
723	<	simnfo->box_z = simnfo->box_x;
720	>	vol = (double)tot_nmol / globals->getDensity();
721	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
722	>	boxVector[1] = boxVector[0];
723	>	boxVector[2] = boxVector[0];
724	>
725	>	info->setBox( boxVector );
726		}
727		else{
728	<	if( !the_globals->haveBoxX() ){
728	>	if( !globals->haveBoxX() ){
729		sprintf( painCave.errMsg,
730		"SimSetup error, no periodic BoxX size given.\n" );
731		painCave.isFatal = 1;
732		simError();
733		}
734	<	simnfo->box_x = the_globals->getBoxX();
734	>	boxVector[0] = globals->getBoxX();
735
736	<	if( !the_globals->haveBoxY() ){
736	>	if( !globals->haveBoxY() ){
737		sprintf( painCave.errMsg,
738		"SimSetup error, no periodic BoxY size given.\n" );
739		painCave.isFatal = 1;
740		simError();
741		}
742	<	simnfo->box_y = the_globals->getBoxY();
742	>	boxVector[1] = globals->getBoxY();
743
744	<	if( !the_globals->haveBoxZ() ){
744	>	if( !globals->haveBoxZ() ){
745		sprintf( painCave.errMsg,
746		"SimSetup error, no periodic BoxZ size given.\n" );
747		painCave.isFatal = 1;
748		simError();
749		}
750	<	simnfo->box_z = the_globals->getBoxZ();
750	>	boxVector[2] = globals->getBoxZ();
751	>
752	>	info->setBox( boxVector );
753		}
754
755	+
756	+
757		#ifdef IS_MPI
758	<	strcpy( checkPointMsg, "Box size set up" );
758	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
759		MPIcheckPoint();
760		#endif // is_mpi
761
762	+	}
763
406	–	// initialize the arrays
764
765	<	the_ff->setSimInfo( simnfo );
765	>	void SimSetup::finalInfoCheck( void ){
766	>	int index;
767	>	int usesDipoles;
768	>
769
770	<	makeAtoms();
411	<	simnfo->identArray = new int[simnfo->n_atoms];
412	<	for(i=0; i<simnfo->n_atoms; i++){
413	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
414	<	}
770	>	// check electrostatic parameters
771
772	<	if( tot_bonds ){
773	<	makeBonds();
772	>	index = 0;
773	>	usesDipoles = 0;
774	>	while( (index < info->n_atoms) && !usesDipoles ){
775	>	usesDipoles = ((info->atoms)[index])->hasDipole();
776	>	index++;
777		}
778	+
779	+	#ifdef IS_MPI
780	+	int myUse = usesDipoles;
781	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
782	+	#endif //is_mpi
783
784	<	if( tot_bends ){
421	<	makeBends();
422	<	}
784	>	double theEcr, theEst;
785
786	<	if( tot_torsions ){
787	<	makeTorsions();
788	<	}
786	>	if (globals->getUseRF() ) {
787	>	info->useReactionField = 1;
788	>
789	>	if( !globals->haveECR() ){
790	>	sprintf( painCave.errMsg,
791	>	"SimSetup Warning: using default value of 1/2 the smallest "
792	>	"box length for the electrostaticCutoffRadius.\n"
793	>	"I hope you have a very fast processor!\n");
794	>	painCave.isFatal = 0;
795	>	simError();
796	>	double smallest;
797	>	smallest = info->boxL[0];
798	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
799	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
800	>	theEcr = 0.5 * smallest;
801	>	} else {
802	>	theEcr = globals->getECR();
803	>	}
804
805	+	if( !globals->haveEST() ){
806	+	sprintf( painCave.errMsg,
807	+	"SimSetup Warning: using default value of 0.05 * the "
808	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
809	+	);
810	+	painCave.isFatal = 0;
811	+	simError();
812	+	theEst = 0.05 * theEcr;
813	+	} else {
814	+	theEst= globals->getEST();
815	+	}
816
817	+	info->setEcr( theEcr, theEst );
818	+
819	+	if(!globals->haveDielectric() ){
820	+	sprintf( painCave.errMsg,
821	+	"SimSetup Error: You are trying to use Reaction Field without"
822	+	"setting a dielectric constant!\n"
823	+	);
824	+	painCave.isFatal = 1;
825	+	simError();
826	+	}
827	+	info->dielectric = globals->getDielectric();
828	+	}
829	+	else {
830	+	if (usesDipoles) {
831	+
832	+	if( !globals->haveECR() ){
833	+	sprintf( painCave.errMsg,
834	+	"SimSetup Warning: using default value of 1/2 the smallest "
835	+	"box length for the electrostaticCutoffRadius.\n"
836	+	"I hope you have a very fast processor!\n");
837	+	painCave.isFatal = 0;
838	+	simError();
839	+	double smallest;
840	+	smallest = info->boxL[0];
841	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
842	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
843	+	theEcr = 0.5 * smallest;
844	+	} else {
845	+	theEcr = globals->getECR();
846	+	}
847	+
848	+	if( !globals->haveEST() ){
849	+	sprintf( painCave.errMsg,
850	+	"SimSetup Warning: using default value of 0.05 * the "
851	+	"electrostaticCutoffRadius for the "
852	+	"electrostaticSkinThickness\n"
853	+	);
854	+	painCave.isFatal = 0;
855	+	simError();
856	+	theEst = 0.05 * theEcr;
857	+	} else {
858	+	theEst= globals->getEST();
859	+	}
860
861	+	info->setEcr( theEcr, theEst );
862	+	}
863	+	}
864
865	+	#ifdef IS_MPI
866	+	strcpy( checkPointMsg, "post processing checks out" );
867	+	MPIcheckPoint();
868	+	#endif // is_mpi
869
870	+	}
871
872	<	if( the_globals->haveInitialConfig() ){
872	>	void SimSetup::initSystemCoords( void ){
873	>
874	>	if( globals->haveInitialConfig() ){
875
876		InitializeFromFile* fileInit;
877		#ifdef IS_MPI // is_mpi
878		if( worldRank == 0 ){
879		#endif //is_mpi
880	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
880	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
881		#ifdef IS_MPI
882		}else fileInit = new InitializeFromFile( NULL );
883		#endif
884	<	fileInit->read_xyz( simnfo ); // default velocities on
884	>	fileInit->readInit( info ); // default velocities on
885
886		delete fileInit;
887		}
#	Line 468 | Line 909 | void SimSetup::createSim( void ){
909		MPIcheckPoint();
910		#endif // is_mpi
911
912	+	}
913
472	–
473	–
474	–
914
915	<
915	>	void SimSetup::makeOutNames( void ){
916	>
917		#ifdef IS_MPI
918		if( worldRank == 0 ){
919		#endif // is_mpi
920
921	<	if( the_globals->haveFinalConfig() ){
922	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
921	>	if( globals->haveFinalConfig() ){
922	>	strcpy( info->finalName, globals->getFinalConfig() );
923		}
924		else{
925	<	strcpy( simnfo->finalName, inFileName );
925	>	strcpy( info->finalName, inFileName );
926		char* endTest;
927	<	int nameLength = strlen( simnfo->finalName );
928	<	endTest = &(simnfo->finalName[nameLength - 5]);
927	>	int nameLength = strlen( info->finalName );
928	>	endTest = &(info->finalName[nameLength - 5]);
929		if( !strcmp( endTest, ".bass" ) ){
930		strcpy( endTest, ".eor" );
931		}
#	Line 493 | Line 933 | void SimSetup::createSim( void ){
933		strcpy( endTest, ".eor" );
934		}
935		else{
936	<	endTest = &(simnfo->finalName[nameLength - 4]);
936	>	endTest = &(info->finalName[nameLength - 4]);
937		if( !strcmp( endTest, ".bss" ) ){
938		strcpy( endTest, ".eor" );
939		}
#	Line 501 | Line 941 | void SimSetup::createSim( void ){
941		strcpy( endTest, ".eor" );
942		}
943		else{
944	<	strcat( simnfo->finalName, ".eor" );
944	>	strcat( info->finalName, ".eor" );
945		}
946		}
947		}
948
949		// make the sample and status out names
950
951	<	strcpy( simnfo->sampleName, inFileName );
951	>	strcpy( info->sampleName, inFileName );
952		char* endTest;
953	<	int nameLength = strlen( simnfo->sampleName );
954	<	endTest = &(simnfo->sampleName[nameLength - 5]);
953	>	int nameLength = strlen( info->sampleName );
954	>	endTest = &(info->sampleName[nameLength - 5]);
955		if( !strcmp( endTest, ".bass" ) ){
956		strcpy( endTest, ".dump" );
957		}
#	Line 519 | Line 959 | void SimSetup::createSim( void ){
959		strcpy( endTest, ".dump" );
960		}
961		else{
962	<	endTest = &(simnfo->sampleName[nameLength - 4]);
962	>	endTest = &(info->sampleName[nameLength - 4]);
963		if( !strcmp( endTest, ".bss" ) ){
964		strcpy( endTest, ".dump" );
965		}
#	Line 527 | Line 967 | void SimSetup::createSim( void ){
967		strcpy( endTest, ".dump" );
968		}
969		else{
970	<	strcat( simnfo->sampleName, ".dump" );
970	>	strcat( info->sampleName, ".dump" );
971		}
972		}
973
974	<	strcpy( simnfo->statusName, inFileName );
975	<	nameLength = strlen( simnfo->statusName );
976	<	endTest = &(simnfo->statusName[nameLength - 5]);
974	>	strcpy( info->statusName, inFileName );
975	>	nameLength = strlen( info->statusName );
976	>	endTest = &(info->statusName[nameLength - 5]);
977		if( !strcmp( endTest, ".bass" ) ){
978		strcpy( endTest, ".stat" );
979		}
#	Line 541 | Line 981 | void SimSetup::createSim( void ){
981		strcpy( endTest, ".stat" );
982		}
983		else{
984	<	endTest = &(simnfo->statusName[nameLength - 4]);
984	>	endTest = &(info->statusName[nameLength - 4]);
985		if( !strcmp( endTest, ".bss" ) ){
986		strcpy( endTest, ".stat" );
987		}
#	Line 549 | Line 989 | void SimSetup::createSim( void ){
989		strcpy( endTest, ".stat" );
990		}
991		else{
992	<	strcat( simnfo->statusName, ".stat" );
992	>	strcat( info->statusName, ".stat" );
993		}
994		}
995
996		#ifdef IS_MPI
997		}
998		#endif // is_mpi
559	–
560	–	// set the status, sample, and themal kick times
561	–
562	–	if( the_globals->haveSampleTime() ){
563	–	simnfo->sampleTime = the_globals->getSampleTime();
564	–	simnfo->statusTime = simnfo->sampleTime;
565	–	simnfo->thermalTime = simnfo->sampleTime;
566	–	}
567	–	else{
568	–	simnfo->sampleTime = the_globals->getRunTime();
569	–	simnfo->statusTime = simnfo->sampleTime;
570	–	simnfo->thermalTime = simnfo->sampleTime;
571	–	}
999
1000	<	if( the_globals->haveStatusTime() ){
574	<	simnfo->statusTime = the_globals->getStatusTime();
575	<	}
1000	>	}
1001
577	–	if( the_globals->haveThermalTime() ){
578	–	simnfo->thermalTime = the_globals->getThermalTime();
579	–	}
1002
1003	<	// check for the temperature set flag
1003	>	void SimSetup::sysObjectsCreation( void ){
1004
1005	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1005	>	int i;
1006
1007	+	// create the forceField
1008
1009	<	//   // make the longe range forces and the integrator
1009	>	createFF();
1010
1011	<	//   new AllLong( simnfo );
1011	>	// extract componentList
1012
1013	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
591	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
592	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
593	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
1013	>	compList();
1014
1015	+	// calc the number of atoms, bond, bends, and torsions
1016
1017	+	calcSysValues();
1018
1019	<	// initialize the Fortran
1019	>	#ifdef IS_MPI
1020	>	// divide the molecules among the processors
1021
1022	<	simnfo->refreshSim();
1022	>	mpiMolDivide();
1023	>	#endif //is_mpi
1024
1025	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1026	<	the_ff->initForceField( LB_MIXING_RULE );
1025	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1026	>
1027	>	makeSysArrays();
1028	>
1029	>	// make and initialize the molecules (all but atomic coordinates)
1030	>
1031	>	makeMolecules();
1032	>	info->identArray = new int[info->n_atoms];
1033	>	for(i=0; i<info->n_atoms; i++){
1034	>	info->identArray[i] = the_atoms[i]->getIdent();
1035		}
1036	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
1037	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1038	<	}
1039	<	else{
1036	>
1037	>
1038	>
1039	>	}
1040	>
1041	>
1042	>	void SimSetup::createFF( void ){
1043	>
1044	>	switch( ffCase ){
1045	>
1046	>	case FF_DUFF:
1047	>	the_ff = new DUFF();
1048	>	break;
1049	>
1050	>	case FF_LJ:
1051	>	the_ff = new LJFF();
1052	>	break;
1053	>
1054	>	case FF_EAM:
1055	>	the_ff = new EAM_FF();
1056	>	break;
1057	>
1058	>	default:
1059		sprintf( painCave.errMsg,
1060	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
610	<	simnfo->mixingRule );
1060	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1061		painCave.isFatal = 1;
1062		simError();
1063		}
1064
615	–
1065		#ifdef IS_MPI
1066	<	strcpy( checkPointMsg,
618	<	"Successfully intialized the mixingRule for Fortran." );
1066	>	strcpy( checkPointMsg, "ForceField creation successful" );
1067		MPIcheckPoint();
1068		#endif // is_mpi
1069	+
1070		}
1071
623	–	void SimSetup::makeAtoms( void ){
1072
1073	<	int i, j, k, index;
626	<	double ux, uy, uz, uSqr, u;
627	<	AtomStamp* current_atom;
1073	>	void SimSetup::compList( void ){
1074
1075	<	DirectionalAtom* dAtom;
630	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
1075	>	int i;
1076
1077	<	lMolIndex = 0;
633	<	molIndex = 0;
634	<	index = 0;
635	<	for( i=0; i<n_components; i++ ){
1077	>	comp_stamps = new MoleculeStamp*[n_components];
1078
1079	<	for( j=0; j<components_nmol[i]; j++ ){
1079	>	// make an array of molecule stamps that match the components used.
1080	>	// also extract the used stamps out into a separate linked list
1081
1082	<	#ifdef IS_MPI
1083	<	if( mpiSim->getMyMolStart() <= molIndex &&
1084	<	molIndex <= mpiSim->getMyMolEnd() ){
1085	<	#endif // is_mpi
1082	>	info->nComponents = n_components;
1083	>	info->componentsNmol = components_nmol;
1084	>	info->compStamps = comp_stamps;
1085	>	info->headStamp = new LinkedMolStamp();
1086	>
1087	>	char* id;
1088	>	LinkedMolStamp* headStamp = info->headStamp;
1089	>	LinkedMolStamp* currentStamp = NULL;
1090	>	for( i=0; i<n_components; i++ ){
1091
1092	<	molStart = index;
1093	<	nMemb = comp_stamps[i]->getNAtoms();
1094	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
1095	<
648	<	current_atom = comp_stamps[i]->getAtom( k );
649	<	if( current_atom->haveOrientation() ){
650	<
651	<	dAtom = new DirectionalAtom(index);
652	<	simnfo->n_oriented++;
653	<	the_atoms[index] = dAtom;
654	<
655	<	ux = current_atom->getOrntX();
656	<	uy = current_atom->getOrntY();
657	<	uz = current_atom->getOrntZ();
658	<
659	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
660	<
661	<	u = sqrt( uSqr );
662	<	ux = ux / u;
663	<	uy = uy / u;
664	<	uz = uz / u;
665	<
666	<	dAtom->setSUx( ux );
667	<	dAtom->setSUy( uy );
668	<	dAtom->setSUz( uz );
669	<	}
670	<	else{
671	<	the_atoms[index] = new GeneralAtom(index);
672	<	}
673	<	the_atoms[index]->setType( current_atom->getType() );
674	<	the_atoms[index]->setIndex( index );
675	<
676	<	// increment the index and repeat;
677	<	index++;
678	<	}
679	<
680	<	molEnd = index -1;
681	<	the_molecules[lMolIndex].setNMembers( nMemb );
682	<	the_molecules[lMolIndex].setStartAtom( molStart );
683	<	the_molecules[lMolIndex].setEndAtom( molEnd );
684	<	the_molecules[lMolIndex].setStampID( i );
685	<	lMolIndex++;
1092	>	id = the_components[i]->getType();
1093	>	comp_stamps[i] = NULL;
1094	>
1095	>	// check to make sure the component isn't already in the list
1096
1097	<	#ifdef IS_MPI
1097	>	comp_stamps[i] = headStamp->match( id );
1098	>	if( comp_stamps[i] == NULL ){
1099	>
1100	>	// extract the component from the list;
1101	>
1102	>	currentStamp = stamps->extractMolStamp( id );
1103	>	if( currentStamp == NULL ){
1104	>	sprintf( painCave.errMsg,
1105	>	"SimSetup error: Component \"%s\" was not found in the "
1106	>	"list of declared molecules\n",
1107	>	id );
1108	>	painCave.isFatal = 1;
1109	>	simError();
1110		}
689	–	#endif //is_mpi
1111
1112	<	molIndex++;
1112	>	headStamp->add( currentStamp );
1113	>	comp_stamps[i] = headStamp->match( id );
1114		}
1115		}
1116
1117		#ifdef IS_MPI
1118	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
1119	<
1120	<	delete[] globalIndex;
1118	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1119	>	MPIcheckPoint();
1120	>	#endif // is_mpi
1121
1122	<	mpiSim->mpiRefresh();
701	<	#endif //IS_MPI
702	<
703	<	the_ff->initializeAtoms();
1122	>
1123		}
1124
1125	<	void SimSetup::makeBonds( void ){
1125	>	void SimSetup::calcSysValues( void ){
1126	>	int i, j, k;
1127
708	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
709	–	bond_pair* the_bonds;
710	–	BondStamp* current_bond;
1128
1129	<	the_bonds = new bond_pair[tot_bonds];
1130	<	index = 0;
1131	<	offset = 0;
1132	<	molIndex = 0;
716	<
1129	>	tot_atoms = 0;
1130	>	tot_bonds = 0;
1131	>	tot_bends = 0;
1132	>	tot_torsions = 0;
1133		for( i=0; i<n_components; i++ ){
1134	+
1135	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1136	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1137	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1138	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1139	+	}
1140
1141	<	for( j=0; j<components_nmol[i]; j++ ){
1141	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1142
1143	<	#ifdef IS_MPI
1144	<	if( mpiSim->getMyMolStart() <= molIndex &&
1145	<	molIndex <= mpiSim->getMyMolEnd() ){
1146	<	#endif // is_mpi
1147	<
1148	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1149	<
1150	<	current_bond = comp_stamps[i]->getBond( k );
1151	<	the_bonds[index].a = current_bond->getA() + offset;
730	<	the_bonds[index].b = current_bond->getB() + offset;
1143	>	info->n_atoms = tot_atoms;
1144	>	info->n_bonds = tot_bonds;
1145	>	info->n_bends = tot_bends;
1146	>	info->n_torsions = tot_torsions;
1147	>	info->n_SRI = tot_SRI;
1148	>	info->n_mol = tot_nmol;
1149	>
1150	>	info->molMembershipArray = new int[tot_atoms];
1151	>	}
1152
732	–	exI = the_bonds[index].a;
733	–	exJ = the_bonds[index].b;
1153
735	–	// exclude_I must always be the smaller of the pair
736	–	if( exI > exJ ){
737	–	tempEx = exI;
738	–	exI = exJ;
739	–	exJ = tempEx;
740	–	}
741	–
742	–
1154		#ifdef IS_MPI
1155
1156	<	the_excludes[index*2] =
1157	<	the_atoms[exI]->getGlobalIndex() + 1;
1158	<	the_excludes[index*2 + 1] =
1159	<	the_atoms[exJ]->getGlobalIndex() + 1;
1156	>	void SimSetup::mpiMolDivide( void ){
1157	>
1158	>	int i, j, k;
1159	>	int localMol, allMol;
1160	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1161
1162	<	#else  // isn't MPI
1163	<
1164	<	the_excludes[index*2] =     exI + 1;
753	<	the_excludes[index*2 + 1] = exJ + 1;
754	<	// fortran index from 1 (hence the +1 in the indexing)
755	<	#endif  //is_mpi
756	<
757	<	// increment the index and repeat;
758	<	index++;
759	<	}
760	<	offset += comp_stamps[i]->getNAtoms();
761	<
762	<	#ifdef IS_MPI
763	<	}
764	<	#endif //is_mpi
765	<
766	<	molIndex++;
767	<	}
768	<	}
1162	>	mpiSim = new mpiSimulation( info );
1163	>
1164	>	globalIndex = mpiSim->divideLabor();
1165
1166	<	the_ff->initializeBonds( the_bonds );
1167	<	}
1168	<
1169	<	void SimSetup::makeBends( void ){
774	<
775	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
776	<	bend_set* the_bends;
777	<	BendStamp* current_bend;
778	<	LinkedAssign* extras;
779	<	LinkedAssign* current_extra;
1166	>	// set up the local variables
1167	>
1168	>	mol2proc = mpiSim->getMolToProcMap();
1169	>	molCompType = mpiSim->getMolComponentType();
1170
1171	+	allMol = 0;
1172	+	localMol = 0;
1173	+	local_atoms = 0;
1174	+	local_bonds = 0;
1175	+	local_bends = 0;
1176	+	local_torsions = 0;
1177	+	globalAtomIndex = 0;
1178
1179	<	the_bends = new bend_set[tot_bends];
783	<	index = 0;
784	<	offset = 0;
785	<	molIndex = 0;
1179	>
1180		for( i=0; i<n_components; i++ ){
1181
1182		for( j=0; j<components_nmol[i]; j++ ){
1183	<
1184	<	#ifdef IS_MPI
791	<	if( mpiSim->getMyMolStart() <= molIndex &&
792	<	molIndex <= mpiSim->getMyMolEnd() ){
793	<	#endif // is_mpi
794	<
795	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
796	<
797	<	current_bend = comp_stamps[i]->getBend( k );
798	<	the_bends[index].a = current_bend->getA() + offset;
799	<	the_bends[index].b = current_bend->getB() + offset;
800	<	the_bends[index].c = current_bend->getC() + offset;
801	<
802	<	if( current_bend->haveExtras() ){
803	<
804	<	extras = current_bend->getExtras();
805	<	current_extra = extras;
806	<
807	<	while( current_extra != NULL ){
808	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
809	<
810	<	switch( current_extra->getType() ){
811	<
812	<	case 0:
813	<	the_bends[index].ghost =
814	<	current_extra->getInt() + offset;
815	<	the_bends[index].isGhost = 1;
816	<	break;
817	<
818	<	case 1:
819	<	the_bends[index].ghost =
820	<	(int)current_extra->getDouble() + offset;
821	<	the_bends[index].isGhost = 1;
822	<	break;
823	<
824	<	default:
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup Error: ghostVectorSource was neiter a "
827	<	"double nor an int.\n"
828	<	"-->Bend[%d] in %s\n",
829	<	k, comp_stamps[i]->getID() );
830	<	painCave.isFatal = 1;
831	<	simError();
832	<	}
833	<	}
834	<
835	<	else{
836	<
837	<	sprintf( painCave.errMsg,
838	<	"SimSetup Error: unhandled bend assignment:\n"
839	<	"    -->%s in Bend[%d] in %s\n",
840	<	current_extra->getlhs(),
841	<	k, comp_stamps[i]->getID() );
842	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<
846	<	current_extra = current_extra->getNext();
847	<	}
848	<	}
849	<
850	<	if( !the_bends[index].isGhost ){
851	<
852	<	exI = the_bends[index].a;
853	<	exJ = the_bends[index].c;
854	<	}
855	<	else{
856	<
857	<	exI = the_bends[index].a;
858	<	exJ = the_bends[index].b;
859	<	}
860	<
861	<	// exclude_I must always be the smaller of the pair
862	<	if( exI > exJ ){
863	<	tempEx = exI;
864	<	exI = exJ;
865	<	exJ = tempEx;
866	<	}
867	<
868	<
869	<	#ifdef IS_MPI
870	<
871	<	the_excludes[(index + tot_bonds)*2] =
872	<	the_atoms[exI]->getGlobalIndex() + 1;
873	<	the_excludes[(index + tot_bonds)*2 + 1] =
874	<	the_atoms[exJ]->getGlobalIndex() + 1;
875	<
876	<	#else  // isn't MPI
877	<
878	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
879	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
880	<	// fortran index from 1 (hence the +1 in the indexing)
881	<	#endif  //is_mpi
882	<
883	<
884	<	// increment the index and repeat;
885	<	index++;
886	<	}
887	<	offset += comp_stamps[i]->getNAtoms();
1183	>
1184	>	if( mol2proc[allMol] == worldRank ){
1185
1186	<	#ifdef IS_MPI
1186	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1187	>	local_bonds +=    comp_stamps[i]->getNBonds();
1188	>	local_bends +=    comp_stamps[i]->getNBends();
1189	>	local_torsions += comp_stamps[i]->getNTorsions();
1190	>	localMol++;
1191	>	}
1192	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1193	>	info->molMembershipArray[globalAtomIndex] = allMol;
1194	>	globalAtomIndex++;
1195		}
891	–	#endif //is_mpi
1196
1197	<	molIndex++;
1197	>	allMol++;
1198		}
1199		}
1200	+	local_SRI = local_bonds + local_bends + local_torsions;
1201	+
1202	+	info->n_atoms = mpiSim->getMyNlocal();
1203	+
1204	+	if( local_atoms != info->n_atoms ){
1205	+	sprintf( painCave.errMsg,
1206	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1207	+	" localAtom (%d) are not equal.\n",
1208	+	info->n_atoms,
1209	+	local_atoms );
1210	+	painCave.isFatal = 1;
1211	+	simError();
1212	+	}
1213
1214	<	#ifdef IS_MPI
1215	<	sprintf( checkPointMsg,
1216	<	"Successfully created the bends list.\n" );
1214	>	info->n_bonds = local_bonds;
1215	>	info->n_bends = local_bends;
1216	>	info->n_torsions = local_torsions;
1217	>	info->n_SRI = local_SRI;
1218	>	info->n_mol = localMol;
1219	>
1220	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1221		MPIcheckPoint();
1222	<	#endif // is_mpi
1222	>	}
1223
1224	+	#endif // is_mpi
1225
904	–	the_ff->initializeBends( the_bends );
905	–	}
1226
1227	<	void SimSetup::makeTorsions( void ){
1227	>	void SimSetup::makeSysArrays( void ){
1228	>	int i, j, k;
1229
909	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
910	–	torsion_set* the_torsions;
911	–	TorsionStamp* current_torsion;
1230
1231	<	the_torsions = new torsion_set[tot_torsions];
914	<	index = 0;
915	<	offset = 0;
916	<	molIndex = 0;
917	<	for( i=0; i<n_components; i++ ){
1231	>	// create the atom and short range interaction arrays
1232
1233	<	for( j=0; j<components_nmol[i]; j++ ){
1233	>	Atom::createArrays(info->n_atoms);
1234	>	the_atoms = new Atom*[info->n_atoms];
1235	>	the_molecules = new Molecule[info->n_mol];
1236	>	int molIndex;
1237
1238	<	#ifdef IS_MPI
922	<	if( mpiSim->getMyMolStart() <= molIndex &&
923	<	molIndex <= mpiSim->getMyMolEnd() ){
924	<	#endif // is_mpi
1238	>	// initialize the molecule's stampID's
1239
926	–	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
927	–
928	–	current_torsion = comp_stamps[i]->getTorsion( k );
929	–	the_torsions[index].a = current_torsion->getA() + offset;
930	–	the_torsions[index].b = current_torsion->getB() + offset;
931	–	the_torsions[index].c = current_torsion->getC() + offset;
932	–	the_torsions[index].d = current_torsion->getD() + offset;
933	–
934	–	exI = the_torsions[index].a;
935	–	exJ = the_torsions[index].d;
936	–
937	–
938	–	// exclude_I must always be the smaller of the pair
939	–	if( exI > exJ ){
940	–	tempEx = exI;
941	–	exI = exJ;
942	–	exJ = tempEx;
943	–	}
944	–
945	–
1240		#ifdef IS_MPI
1241	<
948	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
949	<	the_atoms[exI]->getGlobalIndex() + 1;
950	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
951	<	the_atoms[exJ]->getGlobalIndex() + 1;
952	<
953	<	#else  // isn't MPI
954	<
955	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957	<	// fortran indexes from 1 (hence the +1 in the indexing)
958	<	#endif  //is_mpi
959	<
1241	>
1242
1243	<	// increment the index and repeat;
1244	<	index++;
1245	<	}
1246	<	offset += comp_stamps[i]->getNAtoms();
1243	>	molIndex = 0;
1244	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1245	>
1246	>	if(mol2proc[i] == worldRank ){
1247	>	the_molecules[molIndex].setStampID( molCompType[i] );
1248	>	the_molecules[molIndex].setMyIndex( molIndex );
1249	>	the_molecules[molIndex].setGlobalIndex( i );
1250	>	molIndex++;
1251	>	}
1252	>	}
1253
1254	<	#ifdef IS_MPI
1254	>	#else // is_mpi
1255	>
1256	>	molIndex = 0;
1257	>	globalAtomIndex = 0;
1258	>	for(i=0; i<n_components; i++){
1259	>	for(j=0; j<components_nmol[i]; j++ ){
1260	>	the_molecules[molIndex].setStampID( i );
1261	>	the_molecules[molIndex].setMyIndex( molIndex );
1262	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1263	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1264	>	info->molMembershipArray[globalAtomIndex] = molIndex;
1265	>	globalAtomIndex++;
1266		}
968	–	#endif //is_mpi
969	–
1267		molIndex++;
1268		}
1269		}
1270	+
1271
1272	<	the_ff->initializeTorsions( the_torsions );
975	<	}
1272	>	#endif // is_mpi
1273
977	–	void SimSetup::initFromBass( void ){
1274
1275	<	int i, j, k;
1276	<	int n_cells;
1277	<	double cellx, celly, cellz;
1278	<	double temp1, temp2, temp3;
1279	<	int n_per_extra;
1280	<	int n_extra;
1281	<	int have_extra, done;
986	<
987	<	temp1 = (double)tot_nmol / 4.0;
988	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
989	<	temp3 = ceil( temp2 );
990	<
991	<	have_extra =0;
992	<	if( temp2 < temp3 ){ // we have a non-complete lattice
993	<	have_extra =1;
994	<
995	<	n_cells = (int)temp3 - 1;
996	<	cellx = simnfo->box_x / temp3;
997	<	celly = simnfo->box_y / temp3;
998	<	cellz = simnfo->box_z / temp3;
999	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1000	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1001	<	n_per_extra = (int)ceil( temp1 );
1002	<
1003	<	if( n_per_extra > 4){
1004	<	sprintf( painCave.errMsg,
1005	<	"SimSetup error. There has been an error in constructing"
1006	<	" the non-complete lattice.\n" );
1007	<	painCave.isFatal = 1;
1008	<	simError();
1009	<	}
1275	>	if( info->n_SRI ){
1276	>
1277	>	Exclude::createArray(info->n_SRI);
1278	>	the_excludes = new Exclude*[info->n_SRI];
1279	>	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1280	>	info->globalExcludes = new int;
1281	>	info->n_exclude = info->n_SRI;
1282		}
1283		else{
1284	<	n_cells = (int)temp3;
1285	<	cellx = simnfo->box_x / temp3;
1286	<	celly = simnfo->box_y / temp3;
1287	<	cellz = simnfo->box_z / temp3;
1284	>
1285	>	Exclude::createArray( 1 );
1286	>	the_excludes = new Exclude*;
1287	>	the_excludes[0] = new Exclude(0);
1288	>	the_excludes[0]->setPair( 0,0 );
1289	>	info->globalExcludes = new int;
1290	>	info->globalExcludes[0] = 0;
1291	>	info->n_exclude = 0;
1292		}
1293
1294	<	current_mol = 0;
1019	<	current_comp_mol = 0;
1020	<	current_comp = 0;
1021	<	current_atom_ndx = 0;
1294	>	// set the arrays into the SimInfo object
1295
1296	<	for( i=0; i < n_cells ; i++ ){
1297	<	for( j=0; j < n_cells; j++ ){
1298	<	for( k=0; k < n_cells; k++ ){
1296	>	info->atoms = the_atoms;
1297	>	info->molecules = the_molecules;
1298	>	info->nGlobalExcludes = 0;
1299	>	info->excludes = the_excludes;
1300
1301	<	makeElement( i * cellx,
1028	<	j * celly,
1029	<	k * cellz );
1301	>	the_ff->setSimInfo( info );
1302
1303	<	makeElement( i * cellx + 0.5 * cellx,
1032	<	j * celly + 0.5 * celly,
1033	<	k * cellz );
1303	>	}
1304
1305	<	makeElement( i * cellx,
1036	<	j * celly + 0.5 * celly,
1037	<	k * cellz + 0.5 * cellz );
1305	>	void SimSetup::makeIntegrator( void ){
1306
1307	<	makeElement( i * cellx + 0.5 * cellx,
1308	<	j * celly,
1309	<	k * cellz + 0.5 * cellz );
1310	<	}
1311	<	}
1312	<	}
1307	>	NVT<RealIntegrator>*  myNVT = NULL;
1308	>	NPTi<RealIntegrator>* myNPTi = NULL;
1309	>	NPTf<RealIntegrator>* myNPTf = NULL;
1310	>	NPTim<RealIntegrator>* myNPTim = NULL;
1311	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1312	>	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1313	>
1314	>	cerr << "setting integrator" <<endl;
1315	>
1316	>	switch( ensembleCase ){
1317
1318	<	if( have_extra ){
1319	<	done = 0;
1318	>	case NVE_ENS:
1319	>	new NVE<RealIntegrator>( info, the_ff );
1320	>	break;
1321
1322	<	int start_ndx;
1323	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1324	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1322	>	case NVT_ENS:
1323	>	myNVT = new NVT<RealIntegrator>( info, the_ff );
1324	>	myNVT->setTargetTemp(globals->getTargetTemp());
1325
1326	<	if( i < n_cells ){
1326	>	if (globals->haveTauThermostat())
1327	>	myNVT->setTauThermostat(globals->getTauThermostat());
1328
1329	<	if( j < n_cells ){
1330	<	start_ndx = n_cells;
1331	<	}
1332	<	else start_ndx = 0;
1333	<	}
1334	<	else start_ndx = 0;
1329	>	else {
1330	>	sprintf( painCave.errMsg,
1331	>	"SimSetup error: If you use the NVT\n"
1332	>	"    ensemble, you must set tauThermostat.\n");
1333	>	painCave.isFatal = 1;
1334	>	simError();
1335	>	}
1336	>	break;
1337
1338	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1338	>	case NPTi_ENS:
1339	>	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1340	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1341
1342	<	makeElement( i * cellx,
1343	<	j * celly,
1344	<	k * cellz );
1345	<	done = ( current_mol >= tot_nmol );
1342	>	if (globals->haveTargetPressure())
1343	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1344	>	else {
1345	>	sprintf( painCave.errMsg,
1346	>	"SimSetup error: If you use a constant pressure\n"
1347	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1348	>	painCave.isFatal = 1;
1349	>	simError();
1350	>	}
1351	>
1352	>	if( globals->haveTauThermostat() )
1353	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1354	>	else{
1355	>	sprintf( painCave.errMsg,
1356	>	"SimSetup error: If you use an NPT\n"
1357	>	"    ensemble, you must set tauThermostat.\n");
1358	>	painCave.isFatal = 1;
1359	>	simError();
1360	>	}
1361
1362	<	if( !done && n_per_extra > 1 ){
1363	<	makeElement( i * cellx + 0.5 * cellx,
1364	<	j * celly + 0.5 * celly,
1365	<	k * cellz );
1366	<	done = ( current_mol >= tot_nmol );
1367	<	}
1368	<
1369	<	if( !done && n_per_extra > 2){
1077	<	makeElement( i * cellx,
1078	<	j * celly + 0.5 * celly,
1079	<	k * cellz + 0.5 * cellz );
1080	<	done = ( current_mol >= tot_nmol );
1081	<	}
1082	<
1083	<	if( !done && n_per_extra > 3){
1084	<	makeElement( i * cellx + 0.5 * cellx,
1085	<	j * celly,
1086	<	k * cellz + 0.5 * cellz );
1087	<	done = ( current_mol >= tot_nmol );
1088	<	}
1089	<	}
1090	<	}
1362	>	if( globals->haveTauBarostat() )
1363	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1364	>	else{
1365	>	sprintf( painCave.errMsg,
1366	>	"SimSetup error: If you use an NPT\n"
1367	>	"    ensemble, you must set tauBarostat.\n");
1368	>	painCave.isFatal = 1;
1369	>	simError();
1370		}
1371	<	}
1371	>	break;
1372
1373	+	case NPTf_ENS:
1374	+	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1375	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1376
1377	<	for( i=0; i<simnfo->n_atoms; i++ ){
1378	<	simnfo->atoms[i]->set_vx( 0.0 );
1379	<	simnfo->atoms[i]->set_vy( 0.0 );
1380	<	simnfo->atoms[i]->set_vz( 0.0 );
1381	<	}
1382	<	}
1383	<
1384	<	void SimSetup::makeElement( double x, double y, double z ){
1385	<
1104	<	int k;
1105	<	AtomStamp* current_atom;
1106	<	DirectionalAtom* dAtom;
1107	<	double rotMat[3][3];
1108	<
1109	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1377	>	if (globals->haveTargetPressure())
1378	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1379	>	else {
1380	>	sprintf( painCave.errMsg,
1381	>	"SimSetup error: If you use a constant pressure\n"
1382	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1383	>	painCave.isFatal = 1;
1384	>	simError();
1385	>	}
1386
1387	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1388	<	if( !current_atom->havePosition() ){
1387	>	if( globals->haveTauThermostat() )
1388	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1389	>	else{
1390		sprintf( painCave.errMsg,
1391	<	"SimSetup:initFromBass error.\n"
1392	<	"\tComponent %s, atom %s does not have a position specified.\n"
1116	<	"\tThe initialization routine is unable to give a start"
1117	<	" position.\n",
1118	<	comp_stamps[current_comp]->getID(),
1119	<	current_atom->getType() );
1391	>	"SimSetup error: If you use an NPT\n"
1392	>	"    ensemble, you must set tauThermostat.\n");
1393		painCave.isFatal = 1;
1394		simError();
1395		}
1396
1397	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1398	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1399	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1397	>	if( globals->haveTauBarostat() )
1398	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1399	>	else{
1400	>	sprintf( painCave.errMsg,
1401	>	"SimSetup error: If you use an NPT\n"
1402	>	"    ensemble, you must set tauBarostat.\n");
1403	>	painCave.isFatal = 1;
1404	>	simError();
1405	>	}
1406	>	break;
1407	>
1408	>	case NPTim_ENS:
1409	>	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1410	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1411
1412	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1412	>	if (globals->haveTargetPressure())
1413	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1414	>	else {
1415	>	sprintf( painCave.errMsg,
1416	>	"SimSetup error: If you use a constant pressure\n"
1417	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1418	>	painCave.isFatal = 1;
1419	>	simError();
1420	>	}
1421	>
1422	>	if( globals->haveTauThermostat() )
1423	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1424	>	else{
1425	>	sprintf( painCave.errMsg,
1426	>	"SimSetup error: If you use an NPT\n"
1427	>	"    ensemble, you must set tauThermostat.\n");
1428	>	painCave.isFatal = 1;
1429	>	simError();
1430	>	}
1431
1432	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1432	>	if( globals->haveTauBarostat() )
1433	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1434	>	else{
1435	>	sprintf( painCave.errMsg,
1436	>	"SimSetup error: If you use an NPT\n"
1437	>	"    ensemble, you must set tauBarostat.\n");
1438	>	painCave.isFatal = 1;
1439	>	simError();
1440	>	}
1441	>	break;
1442
1443	<	rotMat[0][0] = 1.0;
1444	<	rotMat[0][1] = 0.0;
1445	<	rotMat[0][2] = 0.0;
1443	>	case NPTfm_ENS:
1444	>	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1445	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1446
1447	<	rotMat[1][0] = 0.0;
1448	<	rotMat[1][1] = 1.0;
1449	<	rotMat[1][2] = 0.0;
1447	>	if (globals->haveTargetPressure())
1448	>	myNPTfm->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	>	myNPTfm->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
1467	<	rotMat[2][0] = 0.0;
1468	<	rotMat[2][1] = 0.0;
1469	<	rotMat[2][2] = 1.0;
1470	<
1471	<	dAtom->setA( rotMat );
1467	>	if( globals->haveTauBarostat() )
1468	>	myNPTfm->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	+	case NVEZCONS_ENS:
1479	+	{
1480
1481	<	current_atom_ndx++;
1481	>	if(globals->haveZConsTime()){
1482	>
1483	>	//add sample time of z-constraint  into SimInfo's property list
1484	>	DoubleData* zconsTimeProp = new DoubleData();
1485	>	zconsTimeProp->setID("zconstime");
1486	>	zconsTimeProp->setData(globals->getZConsTime());
1487	>	info->addProperty(zconsTimeProp);
1488	>	}
1489	>	else{
1490	>	sprintf( painCave.errMsg,
1491	>	"ZConstraint error: If you use an ZConstraint\n"
1492	>	" , you must set sample time.\n");
1493	>	painCave.isFatal = 1;
1494	>	simError();
1495	>	}
1496	>
1497	>	if(globals->haveIndexOfAllZConsMols()){
1498	>
1499	>	//add index of z-constraint molecules into SimInfo's property list
1500	>	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1501	>	sort(tempIndex.begin(), tempIndex.end());
1502	>
1503	>	IndexData* zconsIndex = new IndexData();
1504	>	zconsIndex->setID("zconsindex");
1505	>	zconsIndex->setIndexData(tempIndex);
1506	>	info->addProperty(zconsIndex);
1507	>	}
1508	>	else{
1509	>	sprintf( painCave.errMsg,
1510	>	"SimSetup error: If you use an ZConstraint\n"
1511	>	" , you must set index of z-constraint molecules.\n");
1512	>	painCave.isFatal = 1;
1513	>	simError();
1514	>
1515	>	}
1516	>
1517	>	//Determine the name of ouput file and add it into SimInfo's property list
1518	>	//Be careful, do not use inFileName, since it is a pointer which
1519	>	//point to a string at master node, and slave nodes do not contain that string
1520	>
1521	>	string zconsOutput(info->finalName);
1522	>
1523	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1524	>
1525	>	StringData* zconsFilename = new StringData();
1526	>	zconsFilename->setID("zconsfilename");
1527	>	zconsFilename->setData(zconsOutput);
1528	>
1529	>	info->addProperty(zconsFilename);
1530	>
1531	>	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1532	>
1533	>	break;
1534	>	}
1535	>
1536	>	default:
1537	>	sprintf( painCave.errMsg,
1538	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1539	>	painCave.isFatal = 1;
1540	>	simError();
1541		}
1542
1543	<	current_mol++;
1151	<	current_comp_mol++;
1543	>	}
1544
1545	<	if( current_comp_mol >= components_nmol[current_comp] ){
1545	>	void SimSetup::initFortran( void ){
1546
1547	<	current_comp_mol = 0;
1548	<	current_comp++;
1547	>	info->refreshSim();
1548	>
1549	>	if( !strcmp( info->mixingRule, "standard") ){
1550	>	the_ff->initForceField( LB_MIXING_RULE );
1551		}
1552	+	else if( !strcmp( info->mixingRule, "explicit") ){
1553	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1554	+	}
1555	+	else{
1556	+	sprintf( painCave.errMsg,
1557	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1558	+	info->mixingRule );
1559	+	painCave.isFatal = 1;
1560	+	simError();
1561	+	}
1562	+
1563	+
1564	+	#ifdef IS_MPI
1565	+	strcpy( checkPointMsg,
1566	+	"Successfully intialized the mixingRule for Fortran." );
1567	+	MPIcheckPoint();
1568	+	#endif // is_mpi
1569	+
1570		}

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