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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 567 by mmeineke, Wed Jun 25 21:12:14 2003 UTC vs.
Revision 656 by mmeineke, Tue Jul 29 16:32:37 2003 UTC

#	Line 14 | Line 14
14
15		// some defines for ensemble and Forcefield  cases
16
17	<	#define NVE_ENS 0
18	<	#define NVT_ENS 1
19	<	#define NPT_ENS 2
17	>	#define NVE_ENS   0
18	>	#define NVT_ENS   1
19	>	#define NPTi_ENS  2
20	>	#define NPTf_ENS  3
21	>	#define NPTim_ENS 4
22	>	#define NPTfm_ENS 5
23
24	+
25		#define FF_DUFF 0
26		#define FF_LJ   1
27	+	#define FF_EAM  2
28
24	–
29		SimSetup::SimSetup(){
30	+
31	+	isInfoArray = 0;
32	+	nInfo = 1;
33	+
34		stamps = new MakeStamps();
35		globals = new Globals();
36
37	+
38		#ifdef IS_MPI
39		strcpy( checkPointMsg, "SimSetup creation successful" );
40		MPIcheckPoint();
#	Line 37 | Line 46 | void SimSetup::parseFile( char* fileName ){
46		delete globals;
47		}
48
49	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
50	+	info = the_info;
51	+	nInfo = theNinfo;
52	+	isInfoArray = 1;
53	+	}
54	+
55	+
56		void SimSetup::parseFile( char* fileName ){
57
58		#ifdef IS_MPI
#	Line 74 | Line 90 | void SimSetup::createSim( void ){
90
91		void SimSetup::createSim( void ){
92
77	–	MakeStamps *the_stamps;
78	–	Globals* the_globals;
93		int i, j, k, globalAtomIndex;
94
95	<	int ensembleCase;
82	<	int ffCase;
95	>	// gather all of the information from the Bass file
96
97	<	ensembleCase = -1;
85	<	ffCase = -1;
97	>	gatherInfo();
98
99	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
99	>	// creation of complex system objects
100
101	<	// 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();
101	>	sysObjectsCreation();
102
103	<	// 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() );
99	<
100	<	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	<	}
109	<
110	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
112	<
113	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
114	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
115	<	else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = 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 );
127	<
128	<
129	<	//   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	<	//     }
142	<
143	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
155	<
156	<	//     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	<	//     }
166	<
167	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
168	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
169	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
170	<
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	<	//     }
183	<
184	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185	<	simnfo->usePBC = the_globals->getPBC();
186	<
187	<	int usesDipoles = 0;
188	<	switch( ffCase ){
189	<
190	<	case FF_DUFF:
191	<	the_ff = new DUFF();
192	<	usesDipoles = 1;
193	<	break;
194	<
195	<	case FF_LJ:
196	<	the_ff = new LJFF();
197	<	break;
198	<
199	<	default:
200	<	sprintf( painCave.errMsg,
201	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
205	<
206	<	#ifdef IS_MPI
207	<	strcpy( checkPointMsg, "ForceField creation successful" );
208	<	MPIcheckPoint();
209	<	#endif // is_mpi
210	<
211	<	// get the components and calculate the tot_nMol and indvidual n_mol
212	<	the_components = the_globals->getComponents();
213	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
215	<
216	<	if( !the_globals->haveNMol() ){
217	<	// we don't have the total number of molecules, so we assume it is
218	<	// given in each component
219	<
220	<	tot_nmol = 0;
221	<	for( i=0; i<n_components; i++ ){
222	<
223	<	if( !the_components[i]->haveNMol() ){
224	<	// 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	<	}
231	<
232	<	tot_nmol += the_components[i]->getNMol();
233	<	components_nmol[i] = the_components[i]->getNMol();
234	<	}
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();
245	<
246	<
247	<	//     tot_nmol = the_globals->getNMol();
248	<
249	<	//   //we have the total number of molecules, now we check for molfractions
250	<	//     for( i=0; i<n_components; i++ ){
251	<
252	<	//       if( !the_components[i]->haveMolFraction() ){
253	<
254	<	//  if( !the_components[i]->haveNMol() ){
255	<	//    //we have a problem
256	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	<	//              << " nMol was given in component
258	<
259	<	}
260	<
261	<	#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();
103	>	// check on the post processing info
104
105	<	char* id;
275	<	LinkedMolStamp* headStamp = simnfo->headStamp;
276	<	LinkedMolStamp* currentStamp = NULL;
277	<	for( i=0; i<n_components; i++ ){
105	>	finalInfoCheck();
106
107	<	id = the_components[i]->getType();
280	<	comp_stamps[i] = NULL;
281	<
282	<	// check to make sure the component isn't already in the list
107	>	// initialize the system coordinates
108
109	<	comp_stamps[i] = headStamp->match( id );
285	<	if( comp_stamps[i] == NULL ){
286	<
287	<	// extract the component from the list;
288	<
289	<	currentStamp = the_stamps->extractMolStamp( id );
290	<	if( currentStamp == NULL ){
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup error: Component \"%s\" was not found in the "
293	<	"list of declared molecules\n",
294	<	id );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	headStamp->add( currentStamp );
300	<	comp_stamps[i] = headStamp->match( id );
301	<	}
302	<	}
303	<
304	<	#ifdef IS_MPI
305	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
306	<	MPIcheckPoint();
307	<	#endif // is_mpi
109	>	initSystemCoords();
110
111
112	+	// make the output filenames
113
114	<
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++ ){
319	<
320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	<	}
325	<
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;
334	<
335	<	simnfo->molMembershipArray = new int[tot_atoms];
336	<
337	<	#ifdef IS_MPI
338	<
339	<	// divide the molecules among processors here.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
344	<
345	<	// set up the local variables
346	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
349	<
350	<	int* mol2proc = mpiSim->getMolToProcMap();
351	<	int* molCompType = mpiSim->getMolComponentType();
352	<
353	<	allMol = 0;
354	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
360	<
361	<
362	<	for( i=0; i<n_components; i++ ){
363	<
364	<	for( j=0; j<components_nmol[i]; j++ ){
365	<
366	<	if( mol2proc[allMol] == worldRank ){
367	<
368	<	local_atoms +=    comp_stamps[i]->getNAtoms();
369	<	local_bonds +=    comp_stamps[i]->getNBonds();
370	<	local_bends +=    comp_stamps[i]->getNBends();
371	<	local_torsions += comp_stamps[i]->getNTorsions();
372	<	localMol++;
373	<	}
374	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
377	<	}
378	<
379	<	allMol++;
380	<	}
381	<	}
382	<	local_SRI = local_bonds + local_bends + local_torsions;
383	<
384	<	simnfo->n_atoms = mpiSim->getMyNlocal();
385	<
386	<	if( local_atoms != simnfo->n_atoms ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
395	<
396	<	simnfo->n_bonds = local_bonds;
397	<	simnfo->n_bends = local_bends;
398	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
401	<
402	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
403	<	MPIcheckPoint();
404	<
405	<
406	<	#endif // is_mpi
407	<
408	<
409	<	// create the atom and short range interaction arrays
410	<
411	<	Atom::createArrays(simnfo->n_atoms);
412	<	the_atoms = new Atom*[simnfo->n_atoms];
413	<	the_molecules = new Molecule[simnfo->n_mol];
414	<	int molIndex;
415	<
416	<	// initialize the molecule's stampID's
417	<
418	<	#ifdef IS_MPI
419	<
420	<
421	<	molIndex = 0;
422	<	for(i=0; i<mpiSim->getTotNmol(); i++){
423	<
424	<	if(mol2proc[i] == worldRank ){
425	<	the_molecules[molIndex].setStampID( molCompType[i] );
426	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
429	<	}
430	<	}
431	<
432	<	#else // is_mpi
433	<
434	<	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	<
449	<
450	<	#endif // is_mpi
451	<
452	<
453	<	if( simnfo->n_SRI ){
454	<
455	<	Exclude::createArray(simnfo->n_SRI);
456	<	the_excludes = new Exclude*[simnfo->n_SRI];
457	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
458	<	simnfo->globalExcludes = new int;
459	<	simnfo->n_exclude = simnfo->n_SRI;
460	<	}
461	<	else{
462	<
463	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
471	<
472	<	// set the arrays into the SimInfo object
473	<
474	<	simnfo->atoms = the_atoms;
475	<	simnfo->molecules = the_molecules;
476	<	simnfo->nGlobalExcludes = 0;
477	<	simnfo->excludes = the_excludes;
478	<
479	<
480	<	// get some of the tricky things that may still be in the globals
481	<
482	<
483	<	if( the_globals->haveBox() ){
484	<	simnfo->box_x = the_globals->getBox();
485	<	simnfo->box_y = the_globals->getBox();
486	<	simnfo->box_z = the_globals->getBox();
487	<	}
488	<	else if( the_globals->haveDensity() ){
489	<
490	<	double vol;
491	<	vol = (double)tot_nmol / the_globals->getDensity();
492	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
493	<	simnfo->box_y = simnfo->box_x;
494	<	simnfo->box_z = simnfo->box_x;
495	<	}
496	<	else{
497	<	if( !the_globals->haveBoxX() ){
498	<	sprintf( painCave.errMsg,
499	<	"SimSetup error, no periodic BoxX size given.\n" );
500	<	painCave.isFatal = 1;
501	<	simError();
502	<	}
503	<	simnfo->box_x = the_globals->getBoxX();
504	<
505	<	if( !the_globals->haveBoxY() ){
506	<	sprintf( painCave.errMsg,
507	<	"SimSetup error, no periodic BoxY size given.\n" );
508	<	painCave.isFatal = 1;
509	<	simError();
510	<	}
511	<	simnfo->box_y = the_globals->getBoxY();
512	<
513	<	if( !the_globals->haveBoxZ() ){
514	<	sprintf( painCave.errMsg,
515	<	"SimSetup error, no periodic BoxZ size given.\n" );
516	<	painCave.isFatal = 1;
517	<	simError();
518	<	}
519	<	simnfo->box_z = the_globals->getBoxZ();
520	<	}
521	<
522	<	#ifdef IS_MPI
523	<	strcpy( checkPointMsg, "Box size set up" );
524	<	MPIcheckPoint();
525	<	#endif // is_mpi
526	<
527	<
528	<	// initialize the arrays
529	<
530	<	the_ff->setSimInfo( simnfo );
531	<
532	<	makeMolecules();
533	<	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() ){
542	<	sprintf( painCave.errMsg,
543	<	"SimSetup Warning: using default value of 1/2 the smallest "
544	<	"box length for the electrostaticCutoffRadius.\n"
545	<	"I hope you have a very fast processor!\n");
546	<	painCave.isFatal = 0;
547	<	simError();
548	<	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	<	);
574	<	painCave.isFatal = 1;
575	<	simError();
576	<	}
577	<	simnfo->dielectric = the_globals->getDielectric();
578	<	} else {
579	<	if (usesDipoles) {
580	<
581	<	if( !the_globals->haveECR() ){
582	<	sprintf( painCave.errMsg,
583	<	"SimSetup Warning: using default value of 1/2 the smallest "
584	<	"box length for the electrostaticCutoffRadius.\n"
585	<	"I hope you have a very fast processor!\n");
586	<	painCave.isFatal = 0;
587	<	simError();
588	<	double smallest;
589	<	smallest = simnfo->box_x;
590	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
591	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
592	<	simnfo->ecr = 0.5 * smallest;
593	<	} else {
594	<	simnfo->ecr        = the_globals->getECR();
595	<	}
596	<
597	<	if( !the_globals->haveEST() ){
598	<	sprintf( painCave.errMsg,
599	<	"SimSetup Warning: using default value of 5%% of the "
600	<	"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	<	}
609	<	}
610	<	}
611	<
612	<	#ifdef IS_MPI
613	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
614	<	MPIcheckPoint();
615	<	#endif // is_mpi
616	<
617	<	if( the_globals->haveInitialConfig() ){
618	<
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
628	<
629	<	delete fileInit;
630	<	}
631	<	else{
632	<
633	<	#ifdef IS_MPI
634	<
635	<	// no init from bass
636	<
637	<	sprintf( painCave.errMsg,
638	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
639	<	painCave.isFatal;
640	<	simError();
641	<
642	<	#else
643	<
644	<	initFromBass();
645	<
646	<
647	<	#endif
648	<	}
649	<
650	<	#ifdef IS_MPI
651	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
652	<	MPIcheckPoint();
653	<	#endif // is_mpi
654	<
655	<
114	>	makeOutNames();
115
657	–
658	–
659	–
660	–
661	–	#ifdef IS_MPI
662	–	if( worldRank == 0 ){
663	–	#endif // is_mpi
664	–
665	–	if( the_globals->haveFinalConfig() ){
666	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
667	–	}
668	–	else{
669	–	strcpy( simnfo->finalName, inFileName );
670	–	char* endTest;
671	–	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	–	}
691	–	}
692	–
693	–	// make the sample and status out names
694	–
695	–	strcpy( simnfo->sampleName, inFileName );
696	–	char* endTest;
697	–	int nameLength = strlen( simnfo->sampleName );
698	–	endTest = &(simnfo->sampleName[nameLength - 5]);
699	–	if( !strcmp( endTest, ".bass" ) ){
700	–	strcpy( endTest, ".dump" );
701	–	}
702	–	else if( !strcmp( endTest, ".BASS" ) ){
703	–	strcpy( endTest, ".dump" );
704	–	}
705	–	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	–	}
717	–
718	–	strcpy( simnfo->statusName, inFileName );
719	–	nameLength = strlen( simnfo->statusName );
720	–	endTest = &(simnfo->statusName[nameLength - 5]);
721	–	if( !strcmp( endTest, ".bass" ) ){
722	–	strcpy( endTest, ".stat" );
723	–	}
724	–	else if( !strcmp( endTest, ".BASS" ) ){
725	–	strcpy( endTest, ".stat" );
726	–	}
727	–	else{
728	–	endTest = &(simnfo->statusName[nameLength - 4]);
729	–	if( !strcmp( endTest, ".bss" ) ){
730	–	strcpy( endTest, ".stat" );
731	–	}
732	–	else if( !strcmp( endTest, ".mdl" ) ){
733	–	strcpy( endTest, ".stat" );
734	–	}
735	–	else{
736	–	strcat( simnfo->statusName, ".stat" );
737	–	}
738	–	}
739	–
740	–	#ifdef IS_MPI
741	–	}
742	–	#endif // is_mpi
743	–
744	–	// set the status, sample, and themal kick times
745	–
746	–	if( the_globals->haveSampleTime() ){
747	–	simnfo->sampleTime = the_globals->getSampleTime();
748	–	simnfo->statusTime = simnfo->sampleTime;
749	–	simnfo->thermalTime = simnfo->sampleTime;
750	–	}
751	–	else{
752	–	simnfo->sampleTime = the_globals->getRunTime();
753	–	simnfo->statusTime = simnfo->sampleTime;
754	–	simnfo->thermalTime = simnfo->sampleTime;
755	–	}
756	–
757	–	if( the_globals->haveStatusTime() ){
758	–	simnfo->statusTime = the_globals->getStatusTime();
759	–	}
760	–
761	–	if( the_globals->haveThermalTime() ){
762	–	simnfo->thermalTime = the_globals->getThermalTime();
763	–	}
764	–
765	–	// check for the temperature set flag
766	–
767	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
768	–
769	–
116		// make the integrator
117
118	+	makeIntegrator();
119
773	–	NVT* myNVT = NULL;
774	–	switch( ensembleCase ){
775	–
776	–	case NVE_ENS:
777	–	new NVE( simnfo, the_ff );
778	–	break;
779	–
780	–	case NVT_ENS:
781	–	myNVT = new NVT( simnfo, the_ff );
782	–	myNVT->setTargetTemp(the_globals->getTargetTemp());
783	–
784	–	if (the_globals->haveTauThermostat())
785	–	myNVT->setTauThermostat(the_globals->getTauThermostat());
786	–	//     else if (the_globals->haveQmass())
787	–	//       myNVT->setQmass(the_globals->getQmass());
788	–	else {
789	–	sprintf( painCave.errMsg,
790	–	"SimSetup error: If you use the NVT\n"
791	–	"    ensemble, you must set either tauThermostat or qMass.\n"
792	–	"    Neither of these was found in the BASS file.\n");
793	–	painCave.isFatal = 1;
794	–	simError();
795	–	}
796	–	break;
797	–
798	–	default:
799	–	sprintf( painCave.errMsg,
800	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
801	–	painCave.isFatal = 1;
802	–	simError();
803	–	}
804	–
805	–
120		#ifdef IS_MPI
121		mpiSim->mpiRefresh();
122		#endif
123
124		// initialize the Fortran
125
126	+	initFortran();
127
813	–	simnfo->refreshSim();
814	–
815	–	if( !strcmp( simnfo->mixingRule, "standard") ){
816	–	the_ff->initForceField( LB_MIXING_RULE );
817	–	}
818	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
819	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
820	–	}
821	–	else{
822	–	sprintf( painCave.errMsg,
823	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
824	–	simnfo->mixingRule );
825	–	painCave.isFatal = 1;
826	–	simError();
827	–	}
128
129
830	–	#ifdef IS_MPI
831	–	strcpy( checkPointMsg,
832	–	"Successfully intialized the mixingRule for Fortran." );
833	–	MPIcheckPoint();
834	–	#endif // is_mpi
130		}
131
132
133		void SimSetup::makeMolecules( void ){
134
135		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136	<	molInit info;
136	>	molInit molInfo;
137		DirectionalAtom* dAtom;
138		LinkedAssign* extras;
139		LinkedAssign* current_extra;
#	Line 863 | Line 158 | void SimSetup::makeMolecules( void ){
158
159		atomOffset = 0;
160		excludeOffset = 0;
161	<	for(i=0; i<simnfo->n_mol; i++){
161	>	for(i=0; i<info->n_mol; i++){
162
163		stampID = the_molecules[i].getStampID();
164
165	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
166	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
167	<	info.nBends    = comp_stamps[stampID]->getNBends();
168	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
169	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
875	<
876	<	info.myAtoms = &the_atoms[atomOffset];
877	<	info.myExcludes = &the_excludes[excludeOffset];
878	<	info.myBonds = new Bond*[info.nBonds];
879	<	info.myBends = new Bend*[info.nBends];
880	<	info.myTorsions = new Torsion*[info.nTorsions];
165	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
166	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
167	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
168	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
169	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
170
171	<	theBonds = new bond_pair[info.nBonds];
172	<	theBends = new bend_set[info.nBends];
173	<	theTorsions = new torsion_set[info.nTorsions];
171	>	molInfo.myAtoms = &the_atoms[atomOffset];
172	>	molInfo.myExcludes = &the_excludes[excludeOffset];
173	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
174	>	molInfo.myBends = new Bend*[molInfo.nBends];
175	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
176	>
177	>	theBonds = new bond_pair[molInfo.nBonds];
178	>	theBends = new bend_set[molInfo.nBends];
179	>	theTorsions = new torsion_set[molInfo.nTorsions];
180
181		// make the Atoms
182
183	<	for(j=0; j<info.nAtoms; j++){
183	>	for(j=0; j<molInfo.nAtoms; j++){
184
185		currentAtom = comp_stamps[stampID]->getAtom( j );
186		if( currentAtom->haveOrientation() ){
187
188		dAtom = new DirectionalAtom(j + atomOffset);
189	<	simnfo->n_oriented++;
190	<	info.myAtoms[j] = dAtom;
189	>	info->n_oriented++;
190	>	molInfo.myAtoms[j] = dAtom;
191
192		ux = currentAtom->getOrntX();
193		uy = currentAtom->getOrntY();
#	Line 910 | Line 205 | void SimSetup::makeMolecules( void ){
205		dAtom->setSUz( uz );
206		}
207		else{
208	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
208	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
209		}
210	<	info.myAtoms[j]->setType( currentAtom->getType() );
210	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
211
212		#ifdef IS_MPI
213
214	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
214	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
215
216		#endif // is_mpi
217		}
218
219		// make the bonds
220	<	for(j=0; j<info.nBonds; j++){
220	>	for(j=0; j<molInfo.nBonds; j++){
221
222		currentBond = comp_stamps[stampID]->getBond( j );
223		theBonds[j].a = currentBond->getA() + atomOffset;
#	Line 949 | Line 244 | void SimSetup::makeMolecules( void ){
244		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
245		#endif  //is_mpi
246		}
247	<	excludeOffset += info.nBonds;
247	>	excludeOffset += molInfo.nBonds;
248
249		//make the bends
250	<	for(j=0; j<info.nBends; j++){
250	>	for(j=0; j<molInfo.nBends; j++){
251
252		currentBend = comp_stamps[stampID]->getBend( j );
253		theBends[j].a = currentBend->getA() + atomOffset;
#	Line 1035 | Line 330 | void SimSetup::makeMolecules( void ){
330		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
331		#endif  //is_mpi
332		}
333	<	excludeOffset += info.nBends;
333	>	excludeOffset += molInfo.nBends;
334
335	<	for(j=0; j<info.nTorsions; j++){
335	>	for(j=0; j<molInfo.nTorsions; j++){
336
337		currentTorsion = comp_stamps[stampID]->getTorsion( j );
338		theTorsions[j].a = currentTorsion->getA() + atomOffset;
#	Line 1065 | Line 360 | void SimSetup::makeMolecules( void ){
360		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
361		#endif  //is_mpi
362		}
363	<	excludeOffset += info.nTorsions;
363	>	excludeOffset += molInfo.nTorsions;
364
365
366		// send the arrays off to the forceField for init.
367
368	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
369	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
370	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
371	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
368	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
369	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
370	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
371	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
372
373
374	<	the_molecules[i].initialize( info );
374	>	the_molecules[i].initialize( molInfo );
375
376
377	<	atomOffset += info.nAtoms;
377	>	atomOffset += molInfo.nAtoms;
378		delete[] theBonds;
379		delete[] theBends;
380		delete[] theTorsions;
#	Line 1115 | Line 410 | void SimSetup::initFromBass( void ){
410		have_extra =1;
411
412		n_cells = (int)temp3 - 1;
413	<	cellx = simnfo->box_x / temp3;
414	<	celly = simnfo->box_y / temp3;
415	<	cellz = simnfo->box_z / temp3;
413	>	cellx = info->boxL[0] / temp3;
414	>	celly = info->boxL[1] / temp3;
415	>	cellz = info->boxL[2] / temp3;
416		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
417		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
418		n_per_extra = (int)ceil( temp1 );
#	Line 1132 | Line 427 | void SimSetup::initFromBass( void ){
427		}
428		else{
429		n_cells = (int)temp3;
430	<	cellx = simnfo->box_x / temp3;
431	<	celly = simnfo->box_y / temp3;
432	<	cellz = simnfo->box_z / temp3;
430	>	cellx = info->boxL[0] / temp3;
431	>	celly = info->boxL[1] / temp3;
432	>	cellz = info->boxL[2] / temp3;
433		}
434
435		current_mol = 0;
#	Line 1214 | Line 509 | void SimSetup::initFromBass( void ){
509		}
510
511
512	<	for( i=0; i<simnfo->n_atoms; i++ ){
513	<	simnfo->atoms[i]->set_vx( 0.0 );
514	<	simnfo->atoms[i]->set_vy( 0.0 );
515	<	simnfo->atoms[i]->set_vz( 0.0 );
512	>	for( i=0; i<info->n_atoms; i++ ){
513	>	info->atoms[i]->set_vx( 0.0 );
514	>	info->atoms[i]->set_vy( 0.0 );
515	>	info->atoms[i]->set_vz( 0.0 );
516		}
517		}
518
#	Line 1278 | Line 573 | void SimSetup::makeElement( double x, double y, double
573		current_comp++;
574		}
575		}
576	+
577	+
578	+	void SimSetup::gatherInfo( void ){
579	+	int i,j,k;
580	+
581	+	ensembleCase = -1;
582	+	ffCase = -1;
583	+
584	+	// get the stamps and globals;
585	+	stamps = stamps;
586	+	globals = globals;
587	+
588	+	// set the easy ones first
589	+	info->target_temp = globals->getTargetTemp();
590	+	info->dt = globals->getDt();
591	+	info->run_time = globals->getRunTime();
592	+	n_components = globals->getNComponents();
593	+
594	+
595	+	// get the forceField
596	+
597	+	strcpy( force_field, globals->getForceField() );
598	+
599	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
600	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
601	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
602	+	else{
603	+	sprintf( painCave.errMsg,
604	+	"SimSetup Error. Unrecognized force field -> %s\n",
605	+	force_field );
606	+	painCave.isFatal = 1;
607	+	simError();
608	+	}
609	+
610	+	// get the ensemble
611	+
612	+	strcpy( ensemble, globals->getEnsemble() );
613	+
614	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
615	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
616	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
617	+	ensembleCase = NPTi_ENS;
618	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
619	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
620	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
621	+	else{
622	+	sprintf( painCave.errMsg,
623	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
624	+	"reverting to NVE for this simulation.\n",
625	+	ensemble );
626	+	painCave.isFatal = 0;
627	+	simError();
628	+	strcpy( ensemble, "NVE" );
629	+	ensembleCase = NVE_ENS;
630	+	}
631	+	strcpy( info->ensemble, ensemble );
632	+
633	+	// get the mixing rule
634	+
635	+	strcpy( info->mixingRule, globals->getMixingRule() );
636	+	info->usePBC = globals->getPBC();
637	+
638	+
639	+	// get the components and calculate the tot_nMol and indvidual n_mol
640	+
641	+	the_components = globals->getComponents();
642	+	components_nmol = new int[n_components];
643	+
644	+
645	+	if( !globals->haveNMol() ){
646	+	// we don't have the total number of molecules, so we assume it is
647	+	// given in each component
648	+
649	+	tot_nmol = 0;
650	+	for( i=0; i<n_components; i++ ){
651	+
652	+	if( !the_components[i]->haveNMol() ){
653	+	// we have a problem
654	+	sprintf( painCave.errMsg,
655	+	"SimSetup Error. No global NMol or component NMol"
656	+	" given. Cannot calculate the number of atoms.\n" );
657	+	painCave.isFatal = 1;
658	+	simError();
659	+	}
660	+
661	+	tot_nmol += the_components[i]->getNMol();
662	+	components_nmol[i] = the_components[i]->getNMol();
663	+	}
664	+	}
665	+	else{
666	+	sprintf( painCave.errMsg,
667	+	"SimSetup error.\n"
668	+	"\tSorry, the ability to specify total"
669	+	" nMols and then give molfractions in the components\n"
670	+	"\tis not currently supported."
671	+	" Please give nMol in the components.\n" );
672	+	painCave.isFatal = 1;
673	+	simError();
674	+	}
675	+
676	+	// set the status, sample, and thermal kick times
677	+
678	+	if( globals->haveSampleTime() ){
679	+	info->sampleTime = globals->getSampleTime();
680	+	info->statusTime = info->sampleTime;
681	+	info->thermalTime = info->sampleTime;
682	+	}
683	+	else{
684	+	info->sampleTime = globals->getRunTime();
685	+	info->statusTime = info->sampleTime;
686	+	info->thermalTime = info->sampleTime;
687	+	}
688	+
689	+	if( globals->haveStatusTime() ){
690	+	info->statusTime = globals->getStatusTime();
691	+	}
692	+
693	+	if( globals->haveThermalTime() ){
694	+	info->thermalTime = globals->getThermalTime();
695	+	}
696	+
697	+	// check for the temperature set flag
698	+
699	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
700	+
701	+	// get some of the tricky things that may still be in the globals
702	+
703	+	double boxVector[3];
704	+	if( globals->haveBox() ){
705	+	boxVector[0] = globals->getBox();
706	+	boxVector[1] = globals->getBox();
707	+	boxVector[2] = globals->getBox();
708	+
709	+	info->setBox( boxVector );
710	+	}
711	+	else if( globals->haveDensity() ){
712	+
713	+	double vol;
714	+	vol = (double)tot_nmol / globals->getDensity();
715	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
716	+	boxVector[1] = boxVector[0];
717	+	boxVector[2] = boxVector[0];
718	+
719	+	info->setBox( boxVector );
720	+	}
721	+	else{
722	+	if( !globals->haveBoxX() ){
723	+	sprintf( painCave.errMsg,
724	+	"SimSetup error, no periodic BoxX size given.\n" );
725	+	painCave.isFatal = 1;
726	+	simError();
727	+	}
728	+	boxVector[0] = globals->getBoxX();
729	+
730	+	if( !globals->haveBoxY() ){
731	+	sprintf( painCave.errMsg,
732	+	"SimSetup error, no periodic BoxY size given.\n" );
733	+	painCave.isFatal = 1;
734	+	simError();
735	+	}
736	+	boxVector[1] = globals->getBoxY();
737	+
738	+	if( !globals->haveBoxZ() ){
739	+	sprintf( painCave.errMsg,
740	+	"SimSetup error, no periodic BoxZ size given.\n" );
741	+	painCave.isFatal = 1;
742	+	simError();
743	+	}
744	+	boxVector[2] = globals->getBoxZ();
745	+
746	+	info->setBox( boxVector );
747	+	}
748	+
749	+
750	+
751	+	#ifdef IS_MPI
752	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
753	+	MPIcheckPoint();
754	+	#endif // is_mpi
755	+
756	+	}
757	+
758	+
759	+	void SimSetup::finalInfoCheck( void ){
760	+	int index;
761	+	int usesDipoles;
762	+
763	+
764	+	// check electrostatic parameters
765	+
766	+	index = 0;
767	+	usesDipoles = 0;
768	+	while( (index < info->n_atoms) && !usesDipoles ){
769	+	usesDipoles = ((info->atoms)[index])->hasDipole();
770	+	index++;
771	+	}
772	+
773	+	#ifdef IS_MPI
774	+	int myUse = usesDipoles;
775	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
776	+	#endif //is_mpi
777	+
778	+	double theEcr, theEst;
779	+
780	+	if (globals->getUseRF() ) {
781	+	info->useReactionField = 1;
782	+
783	+	if( !globals->haveECR() ){
784	+	sprintf( painCave.errMsg,
785	+	"SimSetup Warning: using default value of 1/2 the smallest "
786	+	"box length for the electrostaticCutoffRadius.\n"
787	+	"I hope you have a very fast processor!\n");
788	+	painCave.isFatal = 0;
789	+	simError();
790	+	double smallest;
791	+	smallest = info->boxL[0];
792	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
793	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
794	+	theEcr = 0.5 * smallest;
795	+	} else {
796	+	theEcr = globals->getECR();
797	+	}
798	+
799	+	if( !globals->haveEST() ){
800	+	sprintf( painCave.errMsg,
801	+	"SimSetup Warning: using default value of 0.05 * the "
802	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
803	+	);
804	+	painCave.isFatal = 0;
805	+	simError();
806	+	theEst = 0.05 * theEcr;
807	+	} else {
808	+	theEst= globals->getEST();
809	+	}
810	+
811	+	info->setEcr( theEcr, theEst );
812	+
813	+	if(!globals->haveDielectric() ){
814	+	sprintf( painCave.errMsg,
815	+	"SimSetup Error: You are trying to use Reaction Field without"
816	+	"setting a dielectric constant!\n"
817	+	);
818	+	painCave.isFatal = 1;
819	+	simError();
820	+	}
821	+	info->dielectric = globals->getDielectric();
822	+	}
823	+	else {
824	+	if (usesDipoles) {
825	+
826	+	if( !globals->haveECR() ){
827	+	sprintf( painCave.errMsg,
828	+	"SimSetup Warning: using default value of 1/2 the smallest "
829	+	"box length for the electrostaticCutoffRadius.\n"
830	+	"I hope you have a very fast processor!\n");
831	+	painCave.isFatal = 0;
832	+	simError();
833	+	double smallest;
834	+	smallest = info->boxL[0];
835	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
836	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
837	+	theEcr = 0.5 * smallest;
838	+	} else {
839	+	theEcr = globals->getECR();
840	+	}
841	+
842	+	if( !globals->haveEST() ){
843	+	sprintf( painCave.errMsg,
844	+	"SimSetup Warning: using default value of 0.05 * the "
845	+	"electrostaticCutoffRadius for the "
846	+	"electrostaticSkinThickness\n"
847	+	);
848	+	painCave.isFatal = 0;
849	+	simError();
850	+	theEst = 0.05 * theEcr;
851	+	} else {
852	+	theEst= globals->getEST();
853	+	}
854	+
855	+	info->setEcr( theEcr, theEst );
856	+	}
857	+	}
858	+
859	+	#ifdef IS_MPI
860	+	strcpy( checkPointMsg, "post processing checks out" );
861	+	MPIcheckPoint();
862	+	#endif // is_mpi
863	+
864	+	}
865	+
866	+	void SimSetup::initSystemCoords( void ){
867	+
868	+	if( globals->haveInitialConfig() ){
869	+
870	+	InitializeFromFile* fileInit;
871	+	#ifdef IS_MPI // is_mpi
872	+	if( worldRank == 0 ){
873	+	#endif //is_mpi
874	+	fileInit = new InitializeFromFile( globals->getInitialConfig() );
875	+	#ifdef IS_MPI
876	+	}else fileInit = new InitializeFromFile( NULL );
877	+	#endif
878	+	fileInit->readInit( info ); // default velocities on
879	+
880	+	delete fileInit;
881	+	}
882	+	else{
883	+
884	+	#ifdef IS_MPI
885	+
886	+	// no init from bass
887	+
888	+	sprintf( painCave.errMsg,
889	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
890	+	painCave.isFatal;
891	+	simError();
892	+
893	+	#else
894	+
895	+	initFromBass();
896	+
897	+
898	+	#endif
899	+	}
900	+
901	+	#ifdef IS_MPI
902	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
903	+	MPIcheckPoint();
904	+	#endif // is_mpi
905	+
906	+	}
907	+
908	+
909	+	void SimSetup::makeOutNames( void ){
910	+
911	+	#ifdef IS_MPI
912	+	if( worldRank == 0 ){
913	+	#endif // is_mpi
914	+
915	+	if( globals->haveFinalConfig() ){
916	+	strcpy( info->finalName, globals->getFinalConfig() );
917	+	}
918	+	else{
919	+	strcpy( info->finalName, inFileName );
920	+	char* endTest;
921	+	int nameLength = strlen( info->finalName );
922	+	endTest = &(info->finalName[nameLength - 5]);
923	+	if( !strcmp( endTest, ".bass" ) ){
924	+	strcpy( endTest, ".eor" );
925	+	}
926	+	else if( !strcmp( endTest, ".BASS" ) ){
927	+	strcpy( endTest, ".eor" );
928	+	}
929	+	else{
930	+	endTest = &(info->finalName[nameLength - 4]);
931	+	if( !strcmp( endTest, ".bss" ) ){
932	+	strcpy( endTest, ".eor" );
933	+	}
934	+	else if( !strcmp( endTest, ".mdl" ) ){
935	+	strcpy( endTest, ".eor" );
936	+	}
937	+	else{
938	+	strcat( info->finalName, ".eor" );
939	+	}
940	+	}
941	+	}
942	+
943	+	// make the sample and status out names
944	+
945	+	strcpy( info->sampleName, inFileName );
946	+	char* endTest;
947	+	int nameLength = strlen( info->sampleName );
948	+	endTest = &(info->sampleName[nameLength - 5]);
949	+	if( !strcmp( endTest, ".bass" ) ){
950	+	strcpy( endTest, ".dump" );
951	+	}
952	+	else if( !strcmp( endTest, ".BASS" ) ){
953	+	strcpy( endTest, ".dump" );
954	+	}
955	+	else{
956	+	endTest = &(info->sampleName[nameLength - 4]);
957	+	if( !strcmp( endTest, ".bss" ) ){
958	+	strcpy( endTest, ".dump" );
959	+	}
960	+	else if( !strcmp( endTest, ".mdl" ) ){
961	+	strcpy( endTest, ".dump" );
962	+	}
963	+	else{
964	+	strcat( info->sampleName, ".dump" );
965	+	}
966	+	}
967	+
968	+	strcpy( info->statusName, inFileName );
969	+	nameLength = strlen( info->statusName );
970	+	endTest = &(info->statusName[nameLength - 5]);
971	+	if( !strcmp( endTest, ".bass" ) ){
972	+	strcpy( endTest, ".stat" );
973	+	}
974	+	else if( !strcmp( endTest, ".BASS" ) ){
975	+	strcpy( endTest, ".stat" );
976	+	}
977	+	else{
978	+	endTest = &(info->statusName[nameLength - 4]);
979	+	if( !strcmp( endTest, ".bss" ) ){
980	+	strcpy( endTest, ".stat" );
981	+	}
982	+	else if( !strcmp( endTest, ".mdl" ) ){
983	+	strcpy( endTest, ".stat" );
984	+	}
985	+	else{
986	+	strcat( info->statusName, ".stat" );
987	+	}
988	+	}
989	+
990	+	#ifdef IS_MPI
991	+	}
992	+	#endif // is_mpi
993	+
994	+	}
995	+
996	+
997	+	void SimSetup::sysObjectsCreation( void ){
998	+
999	+	int i;
1000	+
1001	+	// create the forceField
1002	+
1003	+	createFF();
1004	+
1005	+	// extract componentList
1006	+
1007	+	compList();
1008	+
1009	+	// calc the number of atoms, bond, bends, and torsions
1010	+
1011	+	calcSysValues();
1012	+
1013	+	#ifdef IS_MPI
1014	+	// divide the molecules among the processors
1015	+
1016	+	mpiMolDivide();
1017	+	#endif //is_mpi
1018	+
1019	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1020	+
1021	+	makeSysArrays();
1022	+
1023	+	// make and initialize the molecules (all but atomic coordinates)
1024	+
1025	+	makeMolecules();
1026	+	info->identArray = new int[info->n_atoms];
1027	+	for(i=0; i<info->n_atoms; i++){
1028	+	info->identArray[i] = the_atoms[i]->getIdent();
1029	+	}
1030	+
1031	+
1032	+
1033	+	}
1034	+
1035	+
1036	+	void SimSetup::createFF( void ){
1037	+
1038	+	switch( ffCase ){
1039	+
1040	+	case FF_DUFF:
1041	+	the_ff = new DUFF();
1042	+	break;
1043	+
1044	+	case FF_LJ:
1045	+	the_ff = new LJFF();
1046	+	break;
1047	+
1048	+	case FF_EAM:
1049	+	the_ff = new EAM_FF();
1050	+	break;
1051	+
1052	+	default:
1053	+	sprintf( painCave.errMsg,
1054	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1055	+	painCave.isFatal = 1;
1056	+	simError();
1057	+	}
1058	+
1059	+	#ifdef IS_MPI
1060	+	strcpy( checkPointMsg, "ForceField creation successful" );
1061	+	MPIcheckPoint();
1062	+	#endif // is_mpi
1063	+
1064	+	}
1065	+
1066	+
1067	+	void SimSetup::compList( void ){
1068	+
1069	+	int i;
1070	+
1071	+	comp_stamps = new MoleculeStamp*[n_components];
1072	+
1073	+	// make an array of molecule stamps that match the components used.
1074	+	// also extract the used stamps out into a separate linked list
1075	+
1076	+	info->nComponents = n_components;
1077	+	info->componentsNmol = components_nmol;
1078	+	info->compStamps = comp_stamps;
1079	+	info->headStamp = new LinkedMolStamp();
1080	+
1081	+	char* id;
1082	+	LinkedMolStamp* headStamp = info->headStamp;
1083	+	LinkedMolStamp* currentStamp = NULL;
1084	+	for( i=0; i<n_components; i++ ){
1085	+
1086	+	id = the_components[i]->getType();
1087	+	comp_stamps[i] = NULL;
1088	+
1089	+	// check to make sure the component isn't already in the list
1090	+
1091	+	comp_stamps[i] = headStamp->match( id );
1092	+	if( comp_stamps[i] == NULL ){
1093	+
1094	+	// extract the component from the list;
1095	+
1096	+	currentStamp = stamps->extractMolStamp( id );
1097	+	if( currentStamp == NULL ){
1098	+	sprintf( painCave.errMsg,
1099	+	"SimSetup error: Component \"%s\" was not found in the "
1100	+	"list of declared molecules\n",
1101	+	id );
1102	+	painCave.isFatal = 1;
1103	+	simError();
1104	+	}
1105	+
1106	+	headStamp->add( currentStamp );
1107	+	comp_stamps[i] = headStamp->match( id );
1108	+	}
1109	+	}
1110	+
1111	+	#ifdef IS_MPI
1112	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1113	+	MPIcheckPoint();
1114	+	#endif // is_mpi
1115	+
1116	+
1117	+	}
1118	+
1119	+	void SimSetup::calcSysValues( void ){
1120	+	int i, j, k;
1121	+
1122	+
1123	+	tot_atoms = 0;
1124	+	tot_bonds = 0;
1125	+	tot_bends = 0;
1126	+	tot_torsions = 0;
1127	+	for( i=0; i<n_components; i++ ){
1128	+
1129	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1130	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1131	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1132	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1133	+	}
1134	+
1135	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1136	+
1137	+	info->n_atoms = tot_atoms;
1138	+	info->n_bonds = tot_bonds;
1139	+	info->n_bends = tot_bends;
1140	+	info->n_torsions = tot_torsions;
1141	+	info->n_SRI = tot_SRI;
1142	+	info->n_mol = tot_nmol;
1143	+
1144	+	info->molMembershipArray = new int[tot_atoms];
1145	+	}
1146	+
1147	+
1148	+	#ifdef IS_MPI
1149	+
1150	+	void SimSetup::mpiMolDivide( void ){
1151	+
1152	+	int i, j, k;
1153	+	int localMol, allMol;
1154	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1155	+
1156	+	mpiSim = new mpiSimulation( info );
1157	+
1158	+	globalIndex = mpiSim->divideLabor();
1159	+
1160	+	// set up the local variables
1161	+
1162	+	mol2proc = mpiSim->getMolToProcMap();
1163	+	molCompType = mpiSim->getMolComponentType();
1164	+
1165	+	allMol = 0;
1166	+	localMol = 0;
1167	+	local_atoms = 0;
1168	+	local_bonds = 0;
1169	+	local_bends = 0;
1170	+	local_torsions = 0;
1171	+	globalAtomIndex = 0;
1172	+
1173	+
1174	+	for( i=0; i<n_components; i++ ){
1175	+
1176	+	for( j=0; j<components_nmol[i]; j++ ){
1177	+
1178	+	if( mol2proc[allMol] == worldRank ){
1179	+
1180	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1181	+	local_bonds +=    comp_stamps[i]->getNBonds();
1182	+	local_bends +=    comp_stamps[i]->getNBends();
1183	+	local_torsions += comp_stamps[i]->getNTorsions();
1184	+	localMol++;
1185	+	}
1186	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1187	+	info->molMembershipArray[globalAtomIndex] = allMol;
1188	+	globalAtomIndex++;
1189	+	}
1190	+
1191	+	allMol++;
1192	+	}
1193	+	}
1194	+	local_SRI = local_bonds + local_bends + local_torsions;
1195	+
1196	+	info->n_atoms = mpiSim->getMyNlocal();
1197	+
1198	+	if( local_atoms != info->n_atoms ){
1199	+	sprintf( painCave.errMsg,
1200	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1201	+	" localAtom (%d) are not equal.\n",
1202	+	info->n_atoms,
1203	+	local_atoms );
1204	+	painCave.isFatal = 1;
1205	+	simError();
1206	+	}
1207	+
1208	+	info->n_bonds = local_bonds;
1209	+	info->n_bends = local_bends;
1210	+	info->n_torsions = local_torsions;
1211	+	info->n_SRI = local_SRI;
1212	+	info->n_mol = localMol;
1213	+
1214	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1215	+	MPIcheckPoint();
1216	+	}
1217	+
1218	+	#endif // is_mpi
1219	+
1220	+
1221	+	void SimSetup::makeSysArrays( void ){
1222	+	int i, j, k;
1223	+
1224	+
1225	+	// create the atom and short range interaction arrays
1226	+
1227	+	Atom::createArrays(info->n_atoms);
1228	+	the_atoms = new Atom*[info->n_atoms];
1229	+	the_molecules = new Molecule[info->n_mol];
1230	+	int molIndex;
1231	+
1232	+	// initialize the molecule's stampID's
1233	+
1234	+	#ifdef IS_MPI
1235	+
1236	+
1237	+	molIndex = 0;
1238	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1239	+
1240	+	if(mol2proc[i] == worldRank ){
1241	+	the_molecules[molIndex].setStampID( molCompType[i] );
1242	+	the_molecules[molIndex].setMyIndex( molIndex );
1243	+	the_molecules[molIndex].setGlobalIndex( i );
1244	+	molIndex++;
1245	+	}
1246	+	}
1247	+
1248	+	#else // is_mpi
1249	+
1250	+	molIndex = 0;
1251	+	globalAtomIndex = 0;
1252	+	for(i=0; i<n_components; i++){
1253	+	for(j=0; j<components_nmol[i]; j++ ){
1254	+	the_molecules[molIndex].setStampID( i );
1255	+	the_molecules[molIndex].setMyIndex( molIndex );
1256	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1257	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1258	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1259	+	globalAtomIndex++;
1260	+	}
1261	+	molIndex++;
1262	+	}
1263	+	}
1264	+
1265	+
1266	+	#endif // is_mpi
1267	+
1268	+
1269	+	if( info->n_SRI ){
1270	+
1271	+	Exclude::createArray(info->n_SRI);
1272	+	the_excludes = new Exclude*[info->n_SRI];
1273	+	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1274	+	info->globalExcludes = new int;
1275	+	info->n_exclude = info->n_SRI;
1276	+	}
1277	+	else{
1278	+
1279	+	Exclude::createArray( 1 );
1280	+	the_excludes = new Exclude*;
1281	+	the_excludes[0] = new Exclude(0);
1282	+	the_excludes[0]->setPair( 0,0 );
1283	+	info->globalExcludes = new int;
1284	+	info->globalExcludes[0] = 0;
1285	+	info->n_exclude = 0;
1286	+	}
1287	+
1288	+	// set the arrays into the SimInfo object
1289	+
1290	+	info->atoms = the_atoms;
1291	+	info->molecules = the_molecules;
1292	+	info->nGlobalExcludes = 0;
1293	+	info->excludes = the_excludes;
1294	+
1295	+	the_ff->setSimInfo( info );
1296	+
1297	+	}
1298	+
1299	+	void SimSetup::makeIntegrator( void ){
1300	+
1301	+	NVT<RealIntegrator>*  myNVT = NULL;
1302	+	NPTi<RealIntegrator>* myNPTi = NULL;
1303	+	NPTf<RealIntegrator>* myNPTf = NULL;
1304	+	NPTim<RealIntegrator>* myNPTim = NULL;
1305	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1306	+
1307	+	switch( ensembleCase ){
1308	+
1309	+	case NVE_ENS:
1310	+	new NVE<RealIntegrator>( info, the_ff );
1311	+	break;
1312	+
1313	+	case NVT_ENS:
1314	+	myNVT = new NVT<RealIntegrator>( info, the_ff );
1315	+	myNVT->setTargetTemp(globals->getTargetTemp());
1316	+
1317	+	if (globals->haveTauThermostat())
1318	+	myNVT->setTauThermostat(globals->getTauThermostat());
1319	+
1320	+	else {
1321	+	sprintf( painCave.errMsg,
1322	+	"SimSetup error: If you use the NVT\n"
1323	+	"    ensemble, you must set tauThermostat.\n");
1324	+	painCave.isFatal = 1;
1325	+	simError();
1326	+	}
1327	+	break;
1328	+
1329	+	case NPTi_ENS:
1330	+	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1331	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1332	+
1333	+	if (globals->haveTargetPressure())
1334	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1335	+	else {
1336	+	sprintf( painCave.errMsg,
1337	+	"SimSetup error: If you use a constant pressure\n"
1338	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1339	+	painCave.isFatal = 1;
1340	+	simError();
1341	+	}
1342	+
1343	+	if( globals->haveTauThermostat() )
1344	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1345	+	else{
1346	+	sprintf( painCave.errMsg,
1347	+	"SimSetup error: If you use an NPT\n"
1348	+	"    ensemble, you must set tauThermostat.\n");
1349	+	painCave.isFatal = 1;
1350	+	simError();
1351	+	}
1352	+
1353	+	if( globals->haveTauBarostat() )
1354	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1355	+	else{
1356	+	sprintf( painCave.errMsg,
1357	+	"SimSetup error: If you use an NPT\n"
1358	+	"    ensemble, you must set tauBarostat.\n");
1359	+	painCave.isFatal = 1;
1360	+	simError();
1361	+	}
1362	+	break;
1363	+
1364	+	case NPTf_ENS:
1365	+	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1366	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1367	+
1368	+	if (globals->haveTargetPressure())
1369	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1370	+	else {
1371	+	sprintf( painCave.errMsg,
1372	+	"SimSetup error: If you use a constant pressure\n"
1373	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1374	+	painCave.isFatal = 1;
1375	+	simError();
1376	+	}
1377	+
1378	+	if( globals->haveTauThermostat() )
1379	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1380	+	else{
1381	+	sprintf( painCave.errMsg,
1382	+	"SimSetup error: If you use an NPT\n"
1383	+	"    ensemble, you must set tauThermostat.\n");
1384	+	painCave.isFatal = 1;
1385	+	simError();
1386	+	}
1387	+
1388	+	if( globals->haveTauBarostat() )
1389	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1390	+	else{
1391	+	sprintf( painCave.errMsg,
1392	+	"SimSetup error: If you use an NPT\n"
1393	+	"    ensemble, you must set tauBarostat.\n");
1394	+	painCave.isFatal = 1;
1395	+	simError();
1396	+	}
1397	+	break;
1398	+
1399	+	case NPTim_ENS:
1400	+	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1401	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1402	+
1403	+	if (globals->haveTargetPressure())
1404	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1405	+	else {
1406	+	sprintf( painCave.errMsg,
1407	+	"SimSetup error: If you use a constant pressure\n"
1408	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1409	+	painCave.isFatal = 1;
1410	+	simError();
1411	+	}
1412	+
1413	+	if( globals->haveTauThermostat() )
1414	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1415	+	else{
1416	+	sprintf( painCave.errMsg,
1417	+	"SimSetup error: If you use an NPT\n"
1418	+	"    ensemble, you must set tauThermostat.\n");
1419	+	painCave.isFatal = 1;
1420	+	simError();
1421	+	}
1422	+
1423	+	if( globals->haveTauBarostat() )
1424	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1425	+	else{
1426	+	sprintf( painCave.errMsg,
1427	+	"SimSetup error: If you use an NPT\n"
1428	+	"    ensemble, you must set tauBarostat.\n");
1429	+	painCave.isFatal = 1;
1430	+	simError();
1431	+	}
1432	+	break;
1433	+
1434	+	case NPTfm_ENS:
1435	+	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1436	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1437	+
1438	+	if (globals->haveTargetPressure())
1439	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1440	+	else {
1441	+	sprintf( painCave.errMsg,
1442	+	"SimSetup error: If you use a constant pressure\n"
1443	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1444	+	painCave.isFatal = 1;
1445	+	simError();
1446	+	}
1447	+
1448	+	if( globals->haveTauThermostat() )
1449	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1450	+	else{
1451	+	sprintf( painCave.errMsg,
1452	+	"SimSetup error: If you use an NPT\n"
1453	+	"    ensemble, you must set tauThermostat.\n");
1454	+	painCave.isFatal = 1;
1455	+	simError();
1456	+	}
1457	+
1458	+	if( globals->haveTauBarostat() )
1459	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1460	+	else{
1461	+	sprintf( painCave.errMsg,
1462	+	"SimSetup error: If you use an NPT\n"
1463	+	"    ensemble, you must set tauBarostat.\n");
1464	+	painCave.isFatal = 1;
1465	+	simError();
1466	+	}
1467	+	break;
1468	+
1469	+	default:
1470	+	sprintf( painCave.errMsg,
1471	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1472	+	painCave.isFatal = 1;
1473	+	simError();
1474	+	}
1475	+
1476	+	}
1477	+
1478	+	void SimSetup::initFortran( void ){
1479	+
1480	+	info->refreshSim();
1481	+
1482	+	if( !strcmp( info->mixingRule, "standard") ){
1483	+	the_ff->initForceField( LB_MIXING_RULE );
1484	+	}
1485	+	else if( !strcmp( info->mixingRule, "explicit") ){
1486	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1487	+	}
1488	+	else{
1489	+	sprintf( painCave.errMsg,
1490	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1491	+	info->mixingRule );
1492	+	painCave.isFatal = 1;
1493	+	simError();
1494	+	}
1495	+
1496	+
1497	+	#ifdef IS_MPI
1498	+	strcpy( checkPointMsg,
1499	+	"Successfully intialized the mixingRule for Fortran." );
1500	+	MPIcheckPoint();
1501	+	#endif // is_mpi
1502	+
1503	+	}

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