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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 491 by mmeineke, Fri Apr 11 18:46:37 2003 UTC vs.
Revision 660 by tim, Thu Jul 31 19:59:34 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	+	#define NVTZCONS_ENS   7
27	+	#define NPTiZCONS_ENS  8
28	+	#define NPTfZCONS_ENS  9
29	+	#define NPTimZCONS_ENS 10
30	+	#define NPTfmZCONS_ENS 11
31	+
32	+	#define FF_DUFF 0
33	+	#define FF_LJ   1
34	+	#define FF_EAM  2
35	+
36	+	using namespace std;
37	+
38		SimSetup::SimSetup(){
39	+
40	+	isInfoArray = 0;
41	+	nInfo = 1;
42	+
43		stamps = new MakeStamps();
44		globals = new Globals();
45
46	+
47		#ifdef IS_MPI
48		strcpy( checkPointMsg, "SimSetup creation successful" );
49		MPIcheckPoint();
#	Line 27 | Line 55 | void SimSetup::parseFile( char* fileName ){
55		delete globals;
56		}
57
58	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
59	+	info = the_info;
60	+	nInfo = theNinfo;
61	+	isInfoArray = 1;
62	+	}
63	+
64	+
65		void SimSetup::parseFile( char* fileName ){
66
67		#ifdef IS_MPI
#	Line 64 | Line 99 | void SimSetup::createSim( void ){
99
100		void SimSetup::createSim( void ){
101
67	–	MakeStamps *the_stamps;
68	–	Globals* the_globals;
69	–	ExtendedSystem* the_extendedsystem;
102		int i, j, k, globalAtomIndex;
71	–
72	–	// get the stamps and globals;
73	–	the_stamps = stamps;
74	–	the_globals = globals;
75	–
76	–	// set the easy ones first
77	–	simnfo->target_temp = the_globals->getTargetTemp();
78	–	simnfo->dt = the_globals->getDt();
79	–	simnfo->run_time = the_globals->getRunTime();
80	–
81	–	// get the ones we know are there, yet still may need some work.
82	–	n_components = the_globals->getNComponents();
83	–	strcpy( force_field, the_globals->getForceField() );
84	–
85	–	// get the ensemble and set up an extended system if we need it:
86	–	strcpy( ensemble, the_globals->getEnsemble() );
87	–	if( !strcasecmp( ensemble, "NPT" ) ) {
88	–	the_extendedsystem = new ExtendedSystem( simnfo );
89	–	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	–	if (the_globals->haveTargetPressure())
91	–	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92	–	else {
93	–	sprintf( painCave.errMsg,
94	–	"SimSetup error: If you use the constant pressure\n"
95	–	"    ensemble, you must set targetPressure.\n"
96	–	"    This was found in the BASS file.\n");
97	–	painCave.isFatal = 1;
98	–	simError();
99	–	}
100	–
101	–	if (the_globals->haveTauThermostat())
102	–	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103	–	else if (the_globals->haveQmass())
104	–	the_extendedsystem->setQmass(the_globals->getQmass());
105	–	else {
106	–	sprintf( painCave.errMsg,
107	–	"SimSetup error: If you use one of the constant temperature\n"
108	–	"    ensembles, you must set either tauThermostat or qMass.\n"
109	–	"    Neither of these was found in the BASS file.\n");
110	–	painCave.isFatal = 1;
111	–	simError();
112	–	}
113	–
114	–	if (the_globals->haveTauBarostat())
115	–	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116	–	else {
117	–	sprintf( painCave.errMsg,
118	–	"SimSetup error: If you use the constant pressure\n"
119	–	"    ensemble, you must set tauBarostat.\n"
120	–	"    This was found in the BASS file.\n");
121	–	painCave.isFatal = 1;
122	–	simError();
123	–	}
124	–
125	–	} else if ( !strcasecmp( ensemble, "NVT") ) {
126	–	the_extendedsystem = new ExtendedSystem( simnfo );
127	–	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
128	–
129	–	if (the_globals->haveTauThermostat())
130	–	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131	–	else if (the_globals->haveQmass())
132	–	the_extendedsystem->setQmass(the_globals->getQmass());
133	–	else {
134	–	sprintf( painCave.errMsg,
135	–	"SimSetup error: If you use one of the constant temperature\n"
136	–	"    ensembles, you must set either tauThermostat or qMass.\n"
137	–	"    Neither of these was found in the BASS file.\n");
138	–	painCave.isFatal = 1;
139	–	simError();
140	–	}
141	–
142	–	} else if ( !strcasecmp( ensemble, "NVE") ) {
143	–	} else {
144	–	sprintf( painCave.errMsg,
145	–	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	–	"reverting to NVE for this simulation.\n",
147	–	ensemble );
148	–	painCave.isFatal = 0;
149	–	simError();
150	–	strcpy( ensemble, "NVE" );
151	–	}
152	–	strcpy( simnfo->ensemble, ensemble );
153	–
154	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155	–	simnfo->usePBC = the_globals->getPBC();
156	–
157	–	int usesDipoles = 0;
158	–	if( !strcmp( force_field, "TraPPE_Ex" ) ){
159	–	the_ff = new TraPPE_ExFF();
160	–	usesDipoles = 1;
161	–	}
162	–	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163	–	else{
164	–	sprintf( painCave.errMsg,
165	–	"SimSetup Error. Unrecognized force field -> %s\n",
166	–	force_field );
167	–	painCave.isFatal = 1;
168	–	simError();
169	–	}
170	–
171	–	#ifdef IS_MPI
172	–	strcpy( checkPointMsg, "ForceField creation successful" );
173	–	MPIcheckPoint();
174	–	#endif // is_mpi
175	–
103
104	<
178	<	// get the components and calculate the tot_nMol and indvidual n_mol
179	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
182	<
183	<	if( !the_globals->haveNMol() ){
184	<	// we don't have the total number of molecules, so we assume it is
185	<	// given in each component
186	<
187	<	tot_nmol = 0;
188	<	for( i=0; i<n_components; i++ ){
189	<
190	<	if( !the_components[i]->haveNMol() ){
191	<	// we have a problem
192	<	sprintf( painCave.errMsg,
193	<	"SimSetup Error. No global NMol or component NMol"
194	<	" given. Cannot calculate the number of atoms.\n" );
195	<	painCave.isFatal = 1;
196	<	simError();
197	<	}
198	<
199	<	tot_nmol += the_components[i]->getNMol();
200	<	components_nmol[i] = the_components[i]->getNMol();
201	<	}
202	<	}
203	<	else{
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup error.\n"
206	<	"\tSorry, the ability to specify total"
207	<	" nMols and then give molfractions in the components\n"
208	<	"\tis not currently supported."
209	<	" Please give nMol in the components.\n" );
210	<	painCave.isFatal = 1;
211	<	simError();
212	<
213	<
214	<	//     tot_nmol = the_globals->getNMol();
215	<
216	<	//   //we have the total number of molecules, now we check for molfractions
217	<	//     for( i=0; i<n_components; i++ ){
218	<
219	<	//       if( !the_components[i]->haveMolFraction() ){
220	<
221	<	//  if( !the_components[i]->haveNMol() ){
222	<	//    //we have a problem
223	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	<	//              << " nMol was given in component
225	<
226	<	}
227	<
228	<	#ifdef IS_MPI
229	<	strcpy( checkPointMsg, "Have the number of components" );
230	<	MPIcheckPoint();
231	<	#endif // is_mpi
232	<
233	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
235	<
236	<	simnfo->nComponents = n_components;
237	<	simnfo->componentsNmol = components_nmol;
238	<	simnfo->compStamps = comp_stamps;
239	<	simnfo->headStamp = new LinkedMolStamp();
104	>	// gather all of the information from the Bass file
105
106	<	char* id;
242	<	LinkedMolStamp* headStamp = simnfo->headStamp;
243	<	LinkedMolStamp* currentStamp = NULL;
244	<	for( i=0; i<n_components; i++ ){
106	>	gatherInfo();
107
108	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
108	>	// creation of complex system objects
109
110	<	comp_stamps[i] = headStamp->match( id );
252	<	if( comp_stamps[i] == NULL ){
253	<
254	<	// extract the component from the list;
255	<
256	<	currentStamp = the_stamps->extractMolStamp( id );
257	<	if( currentStamp == NULL ){
258	<	sprintf( painCave.errMsg,
259	<	"SimSetup error: Component \"%s\" was not found in the "
260	<	"list of declared molecules\n",
261	<	id );
262	<	painCave.isFatal = 1;
263	<	simError();
264	<	}
265	<
266	<	headStamp->add( currentStamp );
267	<	comp_stamps[i] = headStamp->match( id );
268	<	}
269	<	}
110	>	sysObjectsCreation();
111
112	<	#ifdef IS_MPI
272	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	<	MPIcheckPoint();
274	<	#endif // is_mpi
112	>	// check on the post processing info
113
114	+	finalInfoCheck();
115
116	+	// initialize the system coordinates
117
118	<
279	<	// caclulate the number of atoms, bonds, bends and torsions
280	<
281	<	tot_atoms = 0;
282	<	tot_bonds = 0;
283	<	tot_bends = 0;
284	<	tot_torsions = 0;
285	<	for( i=0; i<n_components; i++ ){
286	<
287	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
288	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
289	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
290	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
291	<	}
292	<
293	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
294	<
295	<	simnfo->n_atoms = tot_atoms;
296	<	simnfo->n_bonds = tot_bonds;
297	<	simnfo->n_bends = tot_bends;
298	<	simnfo->n_torsions = tot_torsions;
299	<	simnfo->n_SRI = tot_SRI;
300	<	simnfo->n_mol = tot_nmol;
118	>	initSystemCoords();
119
302	–	simnfo->molMembershipArray = new int[tot_atoms];
120
121	<	#ifdef IS_MPI
121	>	// make the output filenames
122
123	<	// divide the molecules among processors here.
123	>	makeOutNames();
124	>
125	>	// make the integrator
126
127	<	mpiSim = new mpiSimulation( simnfo );
309	<
310	<	globalIndex = mpiSim->divideLabor();
311	<
312	<	// set up the local variables
313	<
314	<	int localMol, allMol;
315	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
316	<
317	<	int* mol2proc = mpiSim->getMolToProcMap();
318	<	int* molCompType = mpiSim->getMolComponentType();
319	<
320	<	allMol = 0;
321	<	localMol = 0;
322	<	local_atoms = 0;
323	<	local_bonds = 0;
324	<	local_bends = 0;
325	<	local_torsions = 0;
326	<	globalAtomIndex = 0;
327	<
328	<
329	<	for( i=0; i<n_components; i++ ){
330	<
331	<	for( j=0; j<components_nmol[i]; j++ ){
332	<
333	<	if( mol2proc[allMol] == worldRank ){
334	<
335	<	local_atoms +=    comp_stamps[i]->getNAtoms();
336	<	local_bonds +=    comp_stamps[i]->getNBonds();
337	<	local_bends +=    comp_stamps[i]->getNBends();
338	<	local_torsions += comp_stamps[i]->getNTorsions();
339	<	localMol++;
340	<	}
341	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
342	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
343	<	globalAtomIndex++;
344	<	}
345	<
346	<	allMol++;
347	<	}
348	<	}
349	<	local_SRI = local_bonds + local_bends + local_torsions;
350	<
351	<	simnfo->n_atoms = mpiSim->getMyNlocal();
352	<
353	<	if( local_atoms != simnfo->n_atoms ){
354	<	sprintf( painCave.errMsg,
355	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
356	<	" localAtom (%d) are not equal.\n",
357	<	simnfo->n_atoms,
358	<	local_atoms );
359	<	painCave.isFatal = 1;
360	<	simError();
361	<	}
362	<
363	<	simnfo->n_bonds = local_bonds;
364	<	simnfo->n_bends = local_bends;
365	<	simnfo->n_torsions = local_torsions;
366	<	simnfo->n_SRI = local_SRI;
367	<	simnfo->n_mol = localMol;
368	<
369	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
370	<	MPIcheckPoint();
371	<
372	<
373	<	#endif // is_mpi
374	<
375	<
376	<	// create the atom and short range interaction arrays
377	<
378	<	Atom::createArrays(simnfo->n_atoms);
379	<	the_atoms = new Atom*[simnfo->n_atoms];
380	<	the_molecules = new Molecule[simnfo->n_mol];
381	<	int molIndex;
382	<
383	<	// initialize the molecule's stampID's
384	<
385	<	#ifdef IS_MPI
386	<
387	<
388	<	molIndex = 0;
389	<	for(i=0; i<mpiSim->getTotNmol(); i++){
390	<
391	<	if(mol2proc[i] == worldRank ){
392	<	the_molecules[molIndex].setStampID( molCompType[i] );
393	<	the_molecules[molIndex].setMyIndex( molIndex );
394	<	the_molecules[molIndex].setGlobalIndex( i );
395	<	molIndex++;
396	<	}
397	<	}
398	<
399	<	#else // is_mpi
400	<
401	<	molIndex = 0;
402	<	globalAtomIndex = 0;
403	<	for(i=0; i<n_components; i++){
404	<	for(j=0; j<components_nmol[i]; j++ ){
405	<	the_molecules[molIndex].setStampID( i );
406	<	the_molecules[molIndex].setMyIndex( molIndex );
407	<	the_molecules[molIndex].setGlobalIndex( molIndex );
408	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
409	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
410	<	globalAtomIndex++;
411	<	}
412	<	molIndex++;
413	<	}
414	<	}
415	<
416	<
417	<	#endif // is_mpi
418	<
419	<
420	<	if( simnfo->n_SRI ){
421	<
422	<	Exclude::createArray(simnfo->n_SRI);
423	<	the_excludes = new Exclude*[simnfo->n_SRI];
424	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
425	<	simnfo->globalExcludes = new int;
426	<	simnfo->n_exclude = simnfo->n_SRI;
427	<	}
428	<	else{
429	<
430	<	Exclude::createArray( 1 );
431	<	the_excludes = new Exclude*;
432	<	the_excludes[0] = new Exclude(0);
433	<	the_excludes[0]->setPair( 0,0 );
434	<	simnfo->globalExcludes = new int;
435	<	simnfo->globalExcludes[0] = 0;
436	<	simnfo->n_exclude = 0;
437	<	}
438	<
439	<	// set the arrays into the SimInfo object
440	<
441	<	simnfo->atoms = the_atoms;
442	<	simnfo->molecules = the_molecules;
443	<	simnfo->nGlobalExcludes = 0;
444	<	simnfo->excludes = the_excludes;
445	<
446	<
447	<	// get some of the tricky things that may still be in the globals
448	<
449	<
450	<	if( the_globals->haveBox() ){
451	<	simnfo->box_x = the_globals->getBox();
452	<	simnfo->box_y = the_globals->getBox();
453	<	simnfo->box_z = the_globals->getBox();
454	<	}
455	<	else if( the_globals->haveDensity() ){
456	<
457	<	double vol;
458	<	vol = (double)tot_nmol / the_globals->getDensity();
459	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
460	<	simnfo->box_y = simnfo->box_x;
461	<	simnfo->box_z = simnfo->box_x;
462	<	}
463	<	else{
464	<	if( !the_globals->haveBoxX() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup error, no periodic BoxX size given.\n" );
467	<	painCave.isFatal = 1;
468	<	simError();
469	<	}
470	<	simnfo->box_x = the_globals->getBoxX();
471	<
472	<	if( !the_globals->haveBoxY() ){
473	<	sprintf( painCave.errMsg,
474	<	"SimSetup error, no periodic BoxY size given.\n" );
475	<	painCave.isFatal = 1;
476	<	simError();
477	<	}
478	<	simnfo->box_y = the_globals->getBoxY();
479	<
480	<	if( !the_globals->haveBoxZ() ){
481	<	sprintf( painCave.errMsg,
482	<	"SimSetup error, no periodic BoxZ size given.\n" );
483	<	painCave.isFatal = 1;
484	<	simError();
485	<	}
486	<	simnfo->box_z = the_globals->getBoxZ();
487	<	}
488	<
489	<	#ifdef IS_MPI
490	<	strcpy( checkPointMsg, "Box size set up" );
491	<	MPIcheckPoint();
492	<	#endif // is_mpi
493	<
494	<
495	<	// initialize the arrays
496	<
497	<	the_ff->setSimInfo( simnfo );
498	<
499	<	makeMolecules();
500	<	simnfo->identArray = new int[simnfo->n_atoms];
501	<	for(i=0; i<simnfo->n_atoms; i++){
502	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
503	<	}
504	<
505	<	if (the_globals->getUseRF() ) {
506	<	simnfo->useReactionField = 1;
507	<
508	<	if( !the_globals->haveECR() ){
509	<	sprintf( painCave.errMsg,
510	<	"SimSetup Warning: using default value of 1/2 the smallest "
511	<	"box length for the electrostaticCutoffRadius.\n"
512	<	"I hope you have a very fast processor!\n");
513	<	painCave.isFatal = 0;
514	<	simError();
515	<	double smallest;
516	<	smallest = simnfo->box_x;
517	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
518	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
519	<	simnfo->ecr = 0.5 * smallest;
520	<	} else {
521	<	simnfo->ecr        = the_globals->getECR();
522	<	}
523	<
524	<	if( !the_globals->haveEST() ){
525	<	sprintf( painCave.errMsg,
526	<	"SimSetup Warning: using default value of 0.05 * the "
527	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
528	<	);
529	<	painCave.isFatal = 0;
530	<	simError();
531	<	simnfo->est = 0.05 * simnfo->ecr;
532	<	} else {
533	<	simnfo->est        = the_globals->getEST();
534	<	}
535	<
536	<	if(!the_globals->haveDielectric() ){
537	<	sprintf( painCave.errMsg,
538	<	"SimSetup Error: You are trying to use Reaction Field without"
539	<	"setting a dielectric constant!\n"
540	<	);
541	<	painCave.isFatal = 1;
542	<	simError();
543	<	}
544	<	simnfo->dielectric = the_globals->getDielectric();
545	<	} else {
546	<	if (usesDipoles) {
547	<
548	<	if( !the_globals->haveECR() ){
549	<	sprintf( painCave.errMsg,
550	<	"SimSetup Warning: using default value of 1/2 the smallest "
551	<	"box length for the electrostaticCutoffRadius.\n"
552	<	"I hope you have a very fast processor!\n");
553	<	painCave.isFatal = 0;
554	<	simError();
555	<	double smallest;
556	<	smallest = simnfo->box_x;
557	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
558	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
559	<	simnfo->ecr = 0.5 * smallest;
560	<	} else {
561	<	simnfo->ecr        = the_globals->getECR();
562	<	}
563	<
564	<	if( !the_globals->haveEST() ){
565	<	sprintf( painCave.errMsg,
566	<	"SimSetup Warning: using default value of 5%% of the "
567	<	"electrostaticCutoffRadius for the "
568	<	"electrostaticSkinThickness\n"
569	<	);
570	<	painCave.isFatal = 0;
571	<	simError();
572	<	simnfo->est = 0.05 * simnfo->ecr;
573	<	} else {
574	<	simnfo->est        = the_globals->getEST();
575	<	}
576	<	}
577	<	}
578	<
579	<	#ifdef IS_MPI
580	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
581	<	MPIcheckPoint();
582	<	#endif // is_mpi
583	<
584	<	if( the_globals->haveInitialConfig() ){
585	<
586	<	InitializeFromFile* fileInit;
587	<	#ifdef IS_MPI // is_mpi
588	<	if( worldRank == 0 ){
589	<	#endif //is_mpi
590	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
591	<	#ifdef IS_MPI
592	<	}else fileInit = new InitializeFromFile( NULL );
593	<	#endif
594	<	fileInit->read_xyz( simnfo ); // default velocities on
595	<
596	<	delete fileInit;
597	<	}
598	<	else{
599	<
600	<	#ifdef IS_MPI
601	<
602	<	// no init from bass
127	>	makeIntegrator();
128
604	–	sprintf( painCave.errMsg,
605	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
606	–	painCave.isFatal;
607	–	simError();
608	–
609	–	#else
610	–
611	–	initFromBass();
612	–
613	–
614	–	#endif
615	–	}
616	–
129		#ifdef IS_MPI
618	–	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
619	–	MPIcheckPoint();
620	–	#endif // is_mpi
621	–
622	–
623	–
624	–
625	–
626	–
627	–
628	–	#ifdef IS_MPI
629	–	if( worldRank == 0 ){
630	–	#endif // is_mpi
631	–
632	–	if( the_globals->haveFinalConfig() ){
633	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
634	–	}
635	–	else{
636	–	strcpy( simnfo->finalName, inFileName );
637	–	char* endTest;
638	–	int nameLength = strlen( simnfo->finalName );
639	–	endTest = &(simnfo->finalName[nameLength - 5]);
640	–	if( !strcmp( endTest, ".bass" ) ){
641	–	strcpy( endTest, ".eor" );
642	–	}
643	–	else if( !strcmp( endTest, ".BASS" ) ){
644	–	strcpy( endTest, ".eor" );
645	–	}
646	–	else{
647	–	endTest = &(simnfo->finalName[nameLength - 4]);
648	–	if( !strcmp( endTest, ".bss" ) ){
649	–	strcpy( endTest, ".eor" );
650	–	}
651	–	else if( !strcmp( endTest, ".mdl" ) ){
652	–	strcpy( endTest, ".eor" );
653	–	}
654	–	else{
655	–	strcat( simnfo->finalName, ".eor" );
656	–	}
657	–	}
658	–	}
659	–
660	–	// make the sample and status out names
661	–
662	–	strcpy( simnfo->sampleName, inFileName );
663	–	char* endTest;
664	–	int nameLength = strlen( simnfo->sampleName );
665	–	endTest = &(simnfo->sampleName[nameLength - 5]);
666	–	if( !strcmp( endTest, ".bass" ) ){
667	–	strcpy( endTest, ".dump" );
668	–	}
669	–	else if( !strcmp( endTest, ".BASS" ) ){
670	–	strcpy( endTest, ".dump" );
671	–	}
672	–	else{
673	–	endTest = &(simnfo->sampleName[nameLength - 4]);
674	–	if( !strcmp( endTest, ".bss" ) ){
675	–	strcpy( endTest, ".dump" );
676	–	}
677	–	else if( !strcmp( endTest, ".mdl" ) ){
678	–	strcpy( endTest, ".dump" );
679	–	}
680	–	else{
681	–	strcat( simnfo->sampleName, ".dump" );
682	–	}
683	–	}
684	–
685	–	strcpy( simnfo->statusName, inFileName );
686	–	nameLength = strlen( simnfo->statusName );
687	–	endTest = &(simnfo->statusName[nameLength - 5]);
688	–	if( !strcmp( endTest, ".bass" ) ){
689	–	strcpy( endTest, ".stat" );
690	–	}
691	–	else if( !strcmp( endTest, ".BASS" ) ){
692	–	strcpy( endTest, ".stat" );
693	–	}
694	–	else{
695	–	endTest = &(simnfo->statusName[nameLength - 4]);
696	–	if( !strcmp( endTest, ".bss" ) ){
697	–	strcpy( endTest, ".stat" );
698	–	}
699	–	else if( !strcmp( endTest, ".mdl" ) ){
700	–	strcpy( endTest, ".stat" );
701	–	}
702	–	else{
703	–	strcat( simnfo->statusName, ".stat" );
704	–	}
705	–	}
706	–
707	–	#ifdef IS_MPI
708	–	}
709	–	#endif // is_mpi
710	–
711	–	// set the status, sample, and themal kick times
712	–
713	–	if( the_globals->haveSampleTime() ){
714	–	simnfo->sampleTime = the_globals->getSampleTime();
715	–	simnfo->statusTime = simnfo->sampleTime;
716	–	simnfo->thermalTime = simnfo->sampleTime;
717	–	}
718	–	else{
719	–	simnfo->sampleTime = the_globals->getRunTime();
720	–	simnfo->statusTime = simnfo->sampleTime;
721	–	simnfo->thermalTime = simnfo->sampleTime;
722	–	}
723	–
724	–	if( the_globals->haveStatusTime() ){
725	–	simnfo->statusTime = the_globals->getStatusTime();
726	–	}
727	–
728	–	if( the_globals->haveThermalTime() ){
729	–	simnfo->thermalTime = the_globals->getThermalTime();
730	–	}
731	–
732	–	// check for the temperature set flag
733	–
734	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
735	–
736	–
737	–	//   // make the longe range forces and the integrator
738	–
739	–	//   new AllLong( simnfo );
740	–
741	–
742	–	if( !strcmp( force_field, "TraPPE_Ex" ) ){
743	–	new Symplectic(simnfo, the_ff, the_extendedsystem);
744	–	}
745	–	else if( !strcmp( force_field, "LJ" ) ){
746	–	new Verlet( *simnfo, the_ff, the_extendedsystem );
747	–	}
748	–	else {
749	–	std::cerr << "I'm a bug.\n";
750	–	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
751	–	}
752	–	#ifdef IS_MPI
130		mpiSim->mpiRefresh();
131		#endif
132
133		// initialize the Fortran
134
135	+	initFortran();
136
759	–	simnfo->refreshSim();
760	–
761	–	if( !strcmp( simnfo->mixingRule, "standard") ){
762	–	the_ff->initForceField( LB_MIXING_RULE );
763	–	}
764	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
765	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
766	–	}
767	–	else{
768	–	sprintf( painCave.errMsg,
769	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
770	–	simnfo->mixingRule );
771	–	painCave.isFatal = 1;
772	–	simError();
773	–	}
137
138
776	–	#ifdef IS_MPI
777	–	strcpy( checkPointMsg,
778	–	"Successfully intialized the mixingRule for Fortran." );
779	–	MPIcheckPoint();
780	–	#endif // is_mpi
139		}
140
141
142		void SimSetup::makeMolecules( void ){
143
144		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
145	<	molInit info;
145	>	molInit molInfo;
146		DirectionalAtom* dAtom;
147		LinkedAssign* extras;
148		LinkedAssign* current_extra;
#	Line 809 | Line 167 | void SimSetup::makeMolecules( void ){
167
168		atomOffset = 0;
169		excludeOffset = 0;
170	<	for(i=0; i<simnfo->n_mol; i++){
170	>	for(i=0; i<info->n_mol; i++){
171
172		stampID = the_molecules[i].getStampID();
173
174	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
175	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
176	<	info.nBends    = comp_stamps[stampID]->getNBends();
177	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
178	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
174	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
175	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
176	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
177	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
178	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
179
180	<	info.myAtoms = &the_atoms[atomOffset];
181	<	info.myExcludes = &the_excludes[excludeOffset];
182	<	info.myBonds = new Bond*[info.nBonds];
183	<	info.myBends = new Bend*[info.nBends];
184	<	info.myTorsions = new Torsion*[info.nTorsions];
180	>	molInfo.myAtoms = &the_atoms[atomOffset];
181	>	molInfo.myExcludes = &the_excludes[excludeOffset];
182	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
183	>	molInfo.myBends = new Bend*[molInfo.nBends];
184	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
185
186	<	theBonds = new bond_pair[info.nBonds];
187	<	theBends = new bend_set[info.nBends];
188	<	theTorsions = new torsion_set[info.nTorsions];
186	>	theBonds = new bond_pair[molInfo.nBonds];
187	>	theBends = new bend_set[molInfo.nBends];
188	>	theTorsions = new torsion_set[molInfo.nTorsions];
189
190		// make the Atoms
191
192	<	for(j=0; j<info.nAtoms; j++){
192	>	for(j=0; j<molInfo.nAtoms; j++){
193
194		currentAtom = comp_stamps[stampID]->getAtom( j );
195		if( currentAtom->haveOrientation() ){
196
197		dAtom = new DirectionalAtom(j + atomOffset);
198	<	simnfo->n_oriented++;
199	<	info.myAtoms[j] = dAtom;
198	>	info->n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200
201		ux = currentAtom->getOrntX();
202		uy = currentAtom->getOrntY();
#	Line 856 | Line 214 | void SimSetup::makeMolecules( void ){
214		dAtom->setSUz( uz );
215		}
216		else{
217	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
217	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
218		}
219	<	info.myAtoms[j]->setType( currentAtom->getType() );
219	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220
221		#ifdef IS_MPI
222
223	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
223	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224
225		#endif // is_mpi
226		}
227
228		// make the bonds
229	<	for(j=0; j<info.nBonds; j++){
229	>	for(j=0; j<molInfo.nBonds; j++){
230
231		currentBond = comp_stamps[stampID]->getBond( j );
232		theBonds[j].a = currentBond->getA() + atomOffset;
#	Line 895 | Line 253 | void SimSetup::makeMolecules( void ){
253		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254		#endif  //is_mpi
255		}
256	<	excludeOffset += info.nBonds;
256	>	excludeOffset += molInfo.nBonds;
257
258		//make the bends
259	<	for(j=0; j<info.nBends; j++){
259	>	for(j=0; j<molInfo.nBends; j++){
260
261		currentBend = comp_stamps[stampID]->getBend( j );
262		theBends[j].a = currentBend->getA() + atomOffset;
#	Line 981 | Line 339 | void SimSetup::makeMolecules( void ){
339		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340		#endif  //is_mpi
341		}
342	<	excludeOffset += info.nBends;
342	>	excludeOffset += molInfo.nBends;
343
344	<	for(j=0; j<info.nTorsions; j++){
344	>	for(j=0; j<molInfo.nTorsions; j++){
345
346		currentTorsion = comp_stamps[stampID]->getTorsion( j );
347		theTorsions[j].a = currentTorsion->getA() + atomOffset;
#	Line 1011 | Line 369 | void SimSetup::makeMolecules( void ){
369		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370		#endif  //is_mpi
371		}
372	<	excludeOffset += info.nTorsions;
372	>	excludeOffset += molInfo.nTorsions;
373
374
375		// send the arrays off to the forceField for init.
376
377	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
378	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
379	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
380	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
377	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381
382
383	<	the_molecules[i].initialize( info );
383	>	the_molecules[i].initialize( molInfo );
384
385
386	<	atomOffset += info.nAtoms;
386	>	atomOffset += molInfo.nAtoms;
387		delete[] theBonds;
388		delete[] theBends;
389		delete[] theTorsions;
#	Line 1061 | Line 419 | void SimSetup::initFromBass( void ){
419		have_extra =1;
420
421		n_cells = (int)temp3 - 1;
422	<	cellx = simnfo->box_x / temp3;
423	<	celly = simnfo->box_y / temp3;
424	<	cellz = simnfo->box_z / temp3;
422	>	cellx = info->boxL[0] / temp3;
423	>	celly = info->boxL[1] / temp3;
424	>	cellz = info->boxL[2] / temp3;
425		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
426		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
427		n_per_extra = (int)ceil( temp1 );
#	Line 1078 | Line 436 | void SimSetup::initFromBass( void ){
436		}
437		else{
438		n_cells = (int)temp3;
439	<	cellx = simnfo->box_x / temp3;
440	<	celly = simnfo->box_y / temp3;
441	<	cellz = simnfo->box_z / temp3;
439	>	cellx = info->boxL[0] / temp3;
440	>	celly = info->boxL[1] / temp3;
441	>	cellz = info->boxL[2] / temp3;
442		}
443
444		current_mol = 0;
#	Line 1160 | Line 518 | void SimSetup::initFromBass( void ){
518		}
519
520
521	<	for( i=0; i<simnfo->n_atoms; i++ ){
522	<	simnfo->atoms[i]->set_vx( 0.0 );
523	<	simnfo->atoms[i]->set_vy( 0.0 );
524	<	simnfo->atoms[i]->set_vz( 0.0 );
521	>	for( i=0; i<info->n_atoms; i++ ){
522	>	info->atoms[i]->set_vx( 0.0 );
523	>	info->atoms[i]->set_vy( 0.0 );
524	>	info->atoms[i]->set_vz( 0.0 );
525		}
526		}
527
#	Line 1222 | Line 580 | void SimSetup::makeElement( double x, double y, double
580
581		current_comp_mol = 0;
582		current_comp++;
583	+	}
584	+	}
585	+
586	+
587	+	void SimSetup::gatherInfo( void ){
588	+	int i,j,k;
589	+
590	+	ensembleCase = -1;
591	+	ffCase = -1;
592	+
593	+	// get the stamps and globals;
594	+	stamps = stamps;
595	+	globals = globals;
596	+
597	+	// set the easy ones first
598	+	info->target_temp = globals->getTargetTemp();
599	+	info->dt = globals->getDt();
600	+	info->run_time = globals->getRunTime();
601	+	n_components = globals->getNComponents();
602	+
603	+
604	+	// get the forceField
605	+
606	+	strcpy( force_field, globals->getForceField() );
607	+
608	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
609	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
610	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
611	+	else{
612	+	sprintf( painCave.errMsg,
613	+	"SimSetup Error. Unrecognized force field -> %s\n",
614	+	force_field );
615	+	painCave.isFatal = 1;
616	+	simError();
617	+	}
618	+
619	+	// get the ensemble
620	+
621	+	strcpy( ensemble, globals->getEnsemble() );
622	+
623	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
624	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
625	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
626	+	ensembleCase = NPTi_ENS;
627	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
628	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
629	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
630	+
631	+	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
632	+	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
633	+	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT"))
634	+	ensembleCase = NPTiZCONS_ENS;
635	+	else if( !strcasecmp( ensemble, "NPTfCONS"))  ensembleCase = NPTfZCONS_ENS;
636	+	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637	+	else if( !strcasecmp( ensemble, "NPTfmCONS"))  ensembleCase = NPTfmZCONS_ENS;
638	+
639	+	else{
640	+	sprintf( painCave.errMsg,
641	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
642	+	"reverting to NVE for this simulation.\n",
643	+	ensemble );
644	+	painCave.isFatal = 0;
645	+	simError();
646	+	strcpy( ensemble, "NVE" );
647	+	ensembleCase = NVE_ENS;
648	+	}
649	+	strcpy( info->ensemble, ensemble );
650	+
651	+	// get the mixing rule
652	+
653	+	strcpy( info->mixingRule, globals->getMixingRule() );
654	+	info->usePBC = globals->getPBC();
655	+
656	+
657	+	// get the components and calculate the tot_nMol and indvidual n_mol
658	+
659	+	the_components = globals->getComponents();
660	+	components_nmol = new int[n_components];
661	+
662	+
663	+	if( !globals->haveNMol() ){
664	+	// we don't have the total number of molecules, so we assume it is
665	+	// given in each component
666	+
667	+	tot_nmol = 0;
668	+	for( i=0; i<n_components; i++ ){
669	+
670	+	if( !the_components[i]->haveNMol() ){
671	+	// we have a problem
672	+	sprintf( painCave.errMsg,
673	+	"SimSetup Error. No global NMol or component NMol"
674	+	" given. Cannot calculate the number of atoms.\n" );
675	+	painCave.isFatal = 1;
676	+	simError();
677	+	}
678	+
679	+	tot_nmol += the_components[i]->getNMol();
680	+	components_nmol[i] = the_components[i]->getNMol();
681	+	}
682	+	}
683	+	else{
684	+	sprintf( painCave.errMsg,
685	+	"SimSetup error.\n"
686	+	"\tSorry, the ability to specify total"
687	+	" nMols and then give molfractions in the components\n"
688	+	"\tis not currently supported."
689	+	" Please give nMol in the components.\n" );
690	+	painCave.isFatal = 1;
691	+	simError();
692	+	}
693	+
694	+	// set the status, sample, and thermal kick times
695	+
696	+	if( globals->haveSampleTime() ){
697	+	info->sampleTime = globals->getSampleTime();
698	+	info->statusTime = info->sampleTime;
699	+	info->thermalTime = info->sampleTime;
700	+	}
701	+	else{
702	+	info->sampleTime = globals->getRunTime();
703	+	info->statusTime = info->sampleTime;
704	+	info->thermalTime = info->sampleTime;
705	+	}
706	+
707	+	if( globals->haveStatusTime() ){
708	+	info->statusTime = globals->getStatusTime();
709	+	}
710	+
711	+	if( globals->haveThermalTime() ){
712	+	info->thermalTime = globals->getThermalTime();
713	+	}
714	+
715	+	// check for the temperature set flag
716	+
717	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
718	+
719	+	// get some of the tricky things that may still be in the globals
720	+
721	+	double boxVector[3];
722	+	if( globals->haveBox() ){
723	+	boxVector[0] = globals->getBox();
724	+	boxVector[1] = globals->getBox();
725	+	boxVector[2] = globals->getBox();
726	+
727	+	info->setBox( boxVector );
728	+	}
729	+	else if( globals->haveDensity() ){
730	+
731	+	double vol;
732	+	vol = (double)tot_nmol / globals->getDensity();
733	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
734	+	boxVector[1] = boxVector[0];
735	+	boxVector[2] = boxVector[0];
736	+
737	+	info->setBox( boxVector );
738	+	}
739	+	else{
740	+	if( !globals->haveBoxX() ){
741	+	sprintf( painCave.errMsg,
742	+	"SimSetup error, no periodic BoxX size given.\n" );
743	+	painCave.isFatal = 1;
744	+	simError();
745	+	}
746	+	boxVector[0] = globals->getBoxX();
747	+
748	+	if( !globals->haveBoxY() ){
749	+	sprintf( painCave.errMsg,
750	+	"SimSetup error, no periodic BoxY size given.\n" );
751	+	painCave.isFatal = 1;
752	+	simError();
753	+	}
754	+	boxVector[1] = globals->getBoxY();
755	+
756	+	if( !globals->haveBoxZ() ){
757	+	sprintf( painCave.errMsg,
758	+	"SimSetup error, no periodic BoxZ size given.\n" );
759	+	painCave.isFatal = 1;
760	+	simError();
761	+	}
762	+	boxVector[2] = globals->getBoxZ();
763	+
764	+	info->setBox( boxVector );
765	+	}
766	+
767	+
768	+
769	+	#ifdef IS_MPI
770	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
771	+	MPIcheckPoint();
772	+	#endif // is_mpi
773	+
774	+	}
775	+
776	+
777	+	void SimSetup::finalInfoCheck( void ){
778	+	int index;
779	+	int usesDipoles;
780	+
781	+
782	+	// check electrostatic parameters
783	+
784	+	index = 0;
785	+	usesDipoles = 0;
786	+	while( (index < info->n_atoms) && !usesDipoles ){
787	+	usesDipoles = ((info->atoms)[index])->hasDipole();
788	+	index++;
789	+	}
790	+
791	+	#ifdef IS_MPI
792	+	int myUse = usesDipoles;
793	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
794	+	#endif //is_mpi
795	+
796	+	double theEcr, theEst;
797	+
798	+	if (globals->getUseRF() ) {
799	+	info->useReactionField = 1;
800	+
801	+	if( !globals->haveECR() ){
802	+	sprintf( painCave.errMsg,
803	+	"SimSetup Warning: using default value of 1/2 the smallest "
804	+	"box length for the electrostaticCutoffRadius.\n"
805	+	"I hope you have a very fast processor!\n");
806	+	painCave.isFatal = 0;
807	+	simError();
808	+	double smallest;
809	+	smallest = info->boxL[0];
810	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
811	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
812	+	theEcr = 0.5 * smallest;
813	+	} else {
814	+	theEcr = globals->getECR();
815	+	}
816	+
817	+	if( !globals->haveEST() ){
818	+	sprintf( painCave.errMsg,
819	+	"SimSetup Warning: using default value of 0.05 * the "
820	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
821	+	);
822	+	painCave.isFatal = 0;
823	+	simError();
824	+	theEst = 0.05 * theEcr;
825	+	} else {
826	+	theEst= globals->getEST();
827	+	}
828	+
829	+	info->setEcr( theEcr, theEst );
830	+
831	+	if(!globals->haveDielectric() ){
832	+	sprintf( painCave.errMsg,
833	+	"SimSetup Error: You are trying to use Reaction Field without"
834	+	"setting a dielectric constant!\n"
835	+	);
836	+	painCave.isFatal = 1;
837	+	simError();
838	+	}
839	+	info->dielectric = globals->getDielectric();
840	+	}
841	+	else {
842	+	if (usesDipoles) {
843	+
844	+	if( !globals->haveECR() ){
845	+	sprintf( painCave.errMsg,
846	+	"SimSetup Warning: using default value of 1/2 the smallest "
847	+	"box length for the electrostaticCutoffRadius.\n"
848	+	"I hope you have a very fast processor!\n");
849	+	painCave.isFatal = 0;
850	+	simError();
851	+	double smallest;
852	+	smallest = info->boxL[0];
853	+	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
854	+	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
855	+	theEcr = 0.5 * smallest;
856	+	} else {
857	+	theEcr = globals->getECR();
858	+	}
859	+
860	+	if( !globals->haveEST() ){
861	+	sprintf( painCave.errMsg,
862	+	"SimSetup Warning: using default value of 0.05 * the "
863	+	"electrostaticCutoffRadius for the "
864	+	"electrostaticSkinThickness\n"
865	+	);
866	+	painCave.isFatal = 0;
867	+	simError();
868	+	theEst = 0.05 * theEcr;
869	+	} else {
870	+	theEst= globals->getEST();
871	+	}
872	+
873	+	info->setEcr( theEcr, theEst );
874	+	}
875	+	}
876	+
877	+	#ifdef IS_MPI
878	+	strcpy( checkPointMsg, "post processing checks out" );
879	+	MPIcheckPoint();
880	+	#endif // is_mpi
881	+
882	+	}
883	+
884	+	void SimSetup::initSystemCoords( void ){
885	+
886	+	if( globals->haveInitialConfig() ){
887	+
888	+	InitializeFromFile* fileInit;
889	+	#ifdef IS_MPI // is_mpi
890	+	if( worldRank == 0 ){
891	+	#endif //is_mpi
892	+	fileInit = new InitializeFromFile( globals->getInitialConfig() );
893	+	#ifdef IS_MPI
894	+	}else fileInit = new InitializeFromFile( NULL );
895	+	#endif
896	+	fileInit->readInit( info ); // default velocities on
897	+
898	+	delete fileInit;
899	+	}
900	+	else{
901	+
902	+	#ifdef IS_MPI
903	+
904	+	// no init from bass
905	+
906	+	sprintf( painCave.errMsg,
907	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
908	+	painCave.isFatal;
909	+	simError();
910	+
911	+	#else
912	+
913	+	initFromBass();
914	+
915	+
916	+	#endif
917	+	}
918	+
919	+	#ifdef IS_MPI
920	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
921	+	MPIcheckPoint();
922	+	#endif // is_mpi
923	+
924	+	}
925	+
926	+
927	+	void SimSetup::makeOutNames( void ){
928	+
929	+	#ifdef IS_MPI
930	+	if( worldRank == 0 ){
931	+	#endif // is_mpi
932	+
933	+	if( globals->haveFinalConfig() ){
934	+	strcpy( info->finalName, globals->getFinalConfig() );
935	+	}
936	+	else{
937	+	strcpy( info->finalName, inFileName );
938	+	char* endTest;
939	+	int nameLength = strlen( info->finalName );
940	+	endTest = &(info->finalName[nameLength - 5]);
941	+	if( !strcmp( endTest, ".bass" ) ){
942	+	strcpy( endTest, ".eor" );
943	+	}
944	+	else if( !strcmp( endTest, ".BASS" ) ){
945	+	strcpy( endTest, ".eor" );
946	+	}
947	+	else{
948	+	endTest = &(info->finalName[nameLength - 4]);
949	+	if( !strcmp( endTest, ".bss" ) ){
950	+	strcpy( endTest, ".eor" );
951	+	}
952	+	else if( !strcmp( endTest, ".mdl" ) ){
953	+	strcpy( endTest, ".eor" );
954	+	}
955	+	else{
956	+	strcat( info->finalName, ".eor" );
957	+	}
958	+	}
959	+	}
960	+
961	+	// make the sample and status out names
962	+
963	+	strcpy( info->sampleName, inFileName );
964	+	char* endTest;
965	+	int nameLength = strlen( info->sampleName );
966	+	endTest = &(info->sampleName[nameLength - 5]);
967	+	if( !strcmp( endTest, ".bass" ) ){
968	+	strcpy( endTest, ".dump" );
969	+	}
970	+	else if( !strcmp( endTest, ".BASS" ) ){
971	+	strcpy( endTest, ".dump" );
972	+	}
973	+	else{
974	+	endTest = &(info->sampleName[nameLength - 4]);
975	+	if( !strcmp( endTest, ".bss" ) ){
976	+	strcpy( endTest, ".dump" );
977	+	}
978	+	else if( !strcmp( endTest, ".mdl" ) ){
979	+	strcpy( endTest, ".dump" );
980	+	}
981	+	else{
982	+	strcat( info->sampleName, ".dump" );
983	+	}
984	+	}
985	+
986	+	strcpy( info->statusName, inFileName );
987	+	nameLength = strlen( info->statusName );
988	+	endTest = &(info->statusName[nameLength - 5]);
989	+	if( !strcmp( endTest, ".bass" ) ){
990	+	strcpy( endTest, ".stat" );
991	+	}
992	+	else if( !strcmp( endTest, ".BASS" ) ){
993	+	strcpy( endTest, ".stat" );
994	+	}
995	+	else{
996	+	endTest = &(info->statusName[nameLength - 4]);
997	+	if( !strcmp( endTest, ".bss" ) ){
998	+	strcpy( endTest, ".stat" );
999	+	}
1000	+	else if( !strcmp( endTest, ".mdl" ) ){
1001	+	strcpy( endTest, ".stat" );
1002	+	}
1003	+	else{
1004	+	strcat( info->statusName, ".stat" );
1005	+	}
1006	+	}
1007	+
1008	+	#ifdef IS_MPI
1009	+	}
1010	+	#endif // is_mpi
1011	+
1012	+	}
1013	+
1014	+
1015	+	void SimSetup::sysObjectsCreation( void ){
1016	+
1017	+	int i;
1018	+
1019	+	// create the forceField
1020	+
1021	+	createFF();
1022	+
1023	+	// extract componentList
1024	+
1025	+	compList();
1026	+
1027	+	// calc the number of atoms, bond, bends, and torsions
1028	+
1029	+	calcSysValues();
1030	+
1031	+	#ifdef IS_MPI
1032	+	// divide the molecules among the processors
1033	+
1034	+	mpiMolDivide();
1035	+	#endif //is_mpi
1036	+
1037	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1038	+
1039	+	makeSysArrays();
1040	+
1041	+	// make and initialize the molecules (all but atomic coordinates)
1042	+
1043	+	makeMolecules();
1044	+	info->identArray = new int[info->n_atoms];
1045	+	for(i=0; i<info->n_atoms; i++){
1046	+	info->identArray[i] = the_atoms[i]->getIdent();
1047	+	}
1048	+
1049	+
1050	+
1051	+	}
1052	+
1053	+
1054	+	void SimSetup::createFF( void ){
1055	+
1056	+	switch( ffCase ){
1057	+
1058	+	case FF_DUFF:
1059	+	the_ff = new DUFF();
1060	+	break;
1061	+
1062	+	case FF_LJ:
1063	+	the_ff = new LJFF();
1064	+	break;
1065	+
1066	+	case FF_EAM:
1067	+	the_ff = new EAM_FF();
1068	+	break;
1069	+
1070	+	default:
1071	+	sprintf( painCave.errMsg,
1072	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1073	+	painCave.isFatal = 1;
1074	+	simError();
1075	+	}
1076	+
1077	+	#ifdef IS_MPI
1078	+	strcpy( checkPointMsg, "ForceField creation successful" );
1079	+	MPIcheckPoint();
1080	+	#endif // is_mpi
1081	+
1082	+	}
1083	+
1084	+
1085	+	void SimSetup::compList( void ){
1086	+
1087	+	int i;
1088	+
1089	+	comp_stamps = new MoleculeStamp*[n_components];
1090	+
1091	+	// make an array of molecule stamps that match the components used.
1092	+	// also extract the used stamps out into a separate linked list
1093	+
1094	+	info->nComponents = n_components;
1095	+	info->componentsNmol = components_nmol;
1096	+	info->compStamps = comp_stamps;
1097	+	info->headStamp = new LinkedMolStamp();
1098	+
1099	+	char* id;
1100	+	LinkedMolStamp* headStamp = info->headStamp;
1101	+	LinkedMolStamp* currentStamp = NULL;
1102	+	for( i=0; i<n_components; i++ ){
1103	+
1104	+	id = the_components[i]->getType();
1105	+	comp_stamps[i] = NULL;
1106	+
1107	+	// check to make sure the component isn't already in the list
1108	+
1109	+	comp_stamps[i] = headStamp->match( id );
1110	+	if( comp_stamps[i] == NULL ){
1111	+
1112	+	// extract the component from the list;
1113	+
1114	+	currentStamp = stamps->extractMolStamp( id );
1115	+	if( currentStamp == NULL ){
1116	+	sprintf( painCave.errMsg,
1117	+	"SimSetup error: Component \"%s\" was not found in the "
1118	+	"list of declared molecules\n",
1119	+	id );
1120	+	painCave.isFatal = 1;
1121	+	simError();
1122	+	}
1123	+
1124	+	headStamp->add( currentStamp );
1125	+	comp_stamps[i] = headStamp->match( id );
1126	+	}
1127	+	}
1128	+
1129	+	#ifdef IS_MPI
1130	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1131	+	MPIcheckPoint();
1132	+	#endif // is_mpi
1133	+
1134	+
1135	+	}
1136	+
1137	+	void SimSetup::calcSysValues( void ){
1138	+	int i, j, k;
1139	+
1140	+
1141	+	tot_atoms = 0;
1142	+	tot_bonds = 0;
1143	+	tot_bends = 0;
1144	+	tot_torsions = 0;
1145	+	for( i=0; i<n_components; i++ ){
1146	+
1147	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1148	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1149	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1150	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1151	+	}
1152	+
1153	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1154	+
1155	+	info->n_atoms = tot_atoms;
1156	+	info->n_bonds = tot_bonds;
1157	+	info->n_bends = tot_bends;
1158	+	info->n_torsions = tot_torsions;
1159	+	info->n_SRI = tot_SRI;
1160	+	info->n_mol = tot_nmol;
1161	+
1162	+	info->molMembershipArray = new int[tot_atoms];
1163	+	}
1164	+
1165	+
1166	+	#ifdef IS_MPI
1167	+
1168	+	void SimSetup::mpiMolDivide( void ){
1169	+
1170	+	int i, j, k;
1171	+	int localMol, allMol;
1172	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1173	+
1174	+	mpiSim = new mpiSimulation( info );
1175	+
1176	+	globalIndex = mpiSim->divideLabor();
1177	+
1178	+	// set up the local variables
1179	+
1180	+	mol2proc = mpiSim->getMolToProcMap();
1181	+	molCompType = mpiSim->getMolComponentType();
1182	+
1183	+	allMol = 0;
1184	+	localMol = 0;
1185	+	local_atoms = 0;
1186	+	local_bonds = 0;
1187	+	local_bends = 0;
1188	+	local_torsions = 0;
1189	+	globalAtomIndex = 0;
1190	+
1191	+
1192	+	for( i=0; i<n_components; i++ ){
1193	+
1194	+	for( j=0; j<components_nmol[i]; j++ ){
1195	+
1196	+	if( mol2proc[allMol] == worldRank ){
1197	+
1198	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1199	+	local_bonds +=    comp_stamps[i]->getNBonds();
1200	+	local_bends +=    comp_stamps[i]->getNBends();
1201	+	local_torsions += comp_stamps[i]->getNTorsions();
1202	+	localMol++;
1203	+	}
1204	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1205	+	info->molMembershipArray[globalAtomIndex] = allMol;
1206	+	globalAtomIndex++;
1207	+	}
1208	+
1209	+	allMol++;
1210	+	}
1211	+	}
1212	+	local_SRI = local_bonds + local_bends + local_torsions;
1213	+
1214	+	info->n_atoms = mpiSim->getMyNlocal();
1215	+
1216	+	if( local_atoms != info->n_atoms ){
1217	+	sprintf( painCave.errMsg,
1218	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1219	+	" localAtom (%d) are not equal.\n",
1220	+	info->n_atoms,
1221	+	local_atoms );
1222	+	painCave.isFatal = 1;
1223	+	simError();
1224	+	}
1225	+
1226	+	info->n_bonds = local_bonds;
1227	+	info->n_bends = local_bends;
1228	+	info->n_torsions = local_torsions;
1229	+	info->n_SRI = local_SRI;
1230	+	info->n_mol = localMol;
1231	+
1232	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1233	+	MPIcheckPoint();
1234	+	}
1235	+
1236	+	#endif // is_mpi
1237	+
1238	+
1239	+	void SimSetup::makeSysArrays( void ){
1240	+	int i, j, k;
1241	+
1242	+
1243	+	// create the atom and short range interaction arrays
1244	+
1245	+	Atom::createArrays(info->n_atoms);
1246	+	the_atoms = new Atom*[info->n_atoms];
1247	+	the_molecules = new Molecule[info->n_mol];
1248	+	int molIndex;
1249	+
1250	+	// initialize the molecule's stampID's
1251	+
1252	+	#ifdef IS_MPI
1253	+
1254	+
1255	+	molIndex = 0;
1256	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1257	+
1258	+	if(mol2proc[i] == worldRank ){
1259	+	the_molecules[molIndex].setStampID( molCompType[i] );
1260	+	the_molecules[molIndex].setMyIndex( molIndex );
1261	+	the_molecules[molIndex].setGlobalIndex( i );
1262	+	molIndex++;
1263	+	}
1264	+	}
1265	+
1266	+	#else // is_mpi
1267	+
1268	+	molIndex = 0;
1269	+	globalAtomIndex = 0;
1270	+	for(i=0; i<n_components; i++){
1271	+	for(j=0; j<components_nmol[i]; j++ ){
1272	+	the_molecules[molIndex].setStampID( i );
1273	+	the_molecules[molIndex].setMyIndex( molIndex );
1274	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1275	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1276	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1277	+	globalAtomIndex++;
1278	+	}
1279	+	molIndex++;
1280	+	}
1281		}
1282	+
1283	+
1284	+	#endif // is_mpi
1285	+
1286	+
1287	+	if( info->n_SRI ){
1288	+
1289	+	Exclude::createArray(info->n_SRI);
1290	+	the_excludes = new Exclude*[info->n_SRI];
1291	+	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1292	+	info->globalExcludes = new int;
1293	+	info->n_exclude = info->n_SRI;
1294	+	}
1295	+	else{
1296	+
1297	+	Exclude::createArray( 1 );
1298	+	the_excludes = new Exclude*;
1299	+	the_excludes[0] = new Exclude(0);
1300	+	the_excludes[0]->setPair( 0,0 );
1301	+	info->globalExcludes = new int;
1302	+	info->globalExcludes[0] = 0;
1303	+	info->n_exclude = 0;
1304	+	}
1305	+
1306	+	// set the arrays into the SimInfo object
1307	+
1308	+	info->atoms = the_atoms;
1309	+	info->molecules = the_molecules;
1310	+	info->nGlobalExcludes = 0;
1311	+	info->excludes = the_excludes;
1312	+
1313	+	the_ff->setSimInfo( info );
1314	+
1315		}
1316	+
1317	+	void SimSetup::makeIntegrator( void ){
1318	+
1319	+	NVT<RealIntegrator>*  myNVT = NULL;
1320	+	NPTi<RealIntegrator>* myNPTi = NULL;
1321	+	NPTf<RealIntegrator>* myNPTf = NULL;
1322	+	NPTim<RealIntegrator>* myNPTim = NULL;
1323	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1324	+	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1325	+	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1326	+	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1327	+	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1328	+	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1329	+	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1330	+
1331	+	cerr << "setting integrator" <<endl;
1332	+
1333	+	switch( ensembleCase ){
1334	+
1335	+	case NVE_ENS:
1336	+	new NVE<RealIntegrator>( info, the_ff );
1337	+	break;
1338	+
1339	+	case NVT_ENS:
1340	+	myNVT = new NVT<RealIntegrator>( info, the_ff );
1341	+	myNVT->setTargetTemp(globals->getTargetTemp());
1342	+
1343	+	if (globals->haveTauThermostat())
1344	+	myNVT->setTauThermostat(globals->getTauThermostat());
1345	+
1346	+	else {
1347	+	sprintf( painCave.errMsg,
1348	+	"SimSetup error: If you use the NVT\n"
1349	+	"    ensemble, you must set tauThermostat.\n");
1350	+	painCave.isFatal = 1;
1351	+	simError();
1352	+	}
1353	+	break;
1354	+
1355	+	case NPTi_ENS:
1356	+	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1357	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1358	+
1359	+	if (globals->haveTargetPressure())
1360	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1361	+	else {
1362	+	sprintf( painCave.errMsg,
1363	+	"SimSetup error: If you use a constant pressure\n"
1364	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1365	+	painCave.isFatal = 1;
1366	+	simError();
1367	+	}
1368	+
1369	+	if( globals->haveTauThermostat() )
1370	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1371	+	else{
1372	+	sprintf( painCave.errMsg,
1373	+	"SimSetup error: If you use an NPT\n"
1374	+	"    ensemble, you must set tauThermostat.\n");
1375	+	painCave.isFatal = 1;
1376	+	simError();
1377	+	}
1378	+
1379	+	if( globals->haveTauBarostat() )
1380	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1381	+	else{
1382	+	sprintf( painCave.errMsg,
1383	+	"SimSetup error: If you use an NPT\n"
1384	+	"    ensemble, you must set tauBarostat.\n");
1385	+	painCave.isFatal = 1;
1386	+	simError();
1387	+	}
1388	+	break;
1389	+
1390	+	case NPTf_ENS:
1391	+	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1392	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1393	+
1394	+	if (globals->haveTargetPressure())
1395	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1396	+	else {
1397	+	sprintf( painCave.errMsg,
1398	+	"SimSetup error: If you use a constant pressure\n"
1399	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1400	+	painCave.isFatal = 1;
1401	+	simError();
1402	+	}
1403	+
1404	+	if( globals->haveTauThermostat() )
1405	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1406	+	else{
1407	+	sprintf( painCave.errMsg,
1408	+	"SimSetup error: If you use an NPT\n"
1409	+	"    ensemble, you must set tauThermostat.\n");
1410	+	painCave.isFatal = 1;
1411	+	simError();
1412	+	}
1413	+
1414	+	if( globals->haveTauBarostat() )
1415	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1416	+	else{
1417	+	sprintf( painCave.errMsg,
1418	+	"SimSetup error: If you use an NPT\n"
1419	+	"    ensemble, you must set tauBarostat.\n");
1420	+	painCave.isFatal = 1;
1421	+	simError();
1422	+	}
1423	+	break;
1424	+
1425	+	case NPTim_ENS:
1426	+	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1427	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1428	+
1429	+	if (globals->haveTargetPressure())
1430	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1431	+	else {
1432	+	sprintf( painCave.errMsg,
1433	+	"SimSetup error: If you use a constant pressure\n"
1434	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	+	painCave.isFatal = 1;
1436	+	simError();
1437	+	}
1438	+
1439	+	if( globals->haveTauThermostat() )
1440	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1441	+	else{
1442	+	sprintf( painCave.errMsg,
1443	+	"SimSetup error: If you use an NPT\n"
1444	+	"    ensemble, you must set tauThermostat.\n");
1445	+	painCave.isFatal = 1;
1446	+	simError();
1447	+	}
1448	+
1449	+	if( globals->haveTauBarostat() )
1450	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1451	+	else{
1452	+	sprintf( painCave.errMsg,
1453	+	"SimSetup error: If you use an NPT\n"
1454	+	"    ensemble, you must set tauBarostat.\n");
1455	+	painCave.isFatal = 1;
1456	+	simError();
1457	+	}
1458	+	break;
1459	+
1460	+	case NPTfm_ENS:
1461	+	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1462	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1463	+
1464	+	if (globals->haveTargetPressure())
1465	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1466	+	else {
1467	+	sprintf( painCave.errMsg,
1468	+	"SimSetup error: If you use a constant pressure\n"
1469	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1470	+	painCave.isFatal = 1;
1471	+	simError();
1472	+	}
1473	+
1474	+	if( globals->haveTauThermostat() )
1475	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1476	+	else{
1477	+	sprintf( painCave.errMsg,
1478	+	"SimSetup error: If you use an NPT\n"
1479	+	"    ensemble, you must set tauThermostat.\n");
1480	+	painCave.isFatal = 1;
1481	+	simError();
1482	+	}
1483	+
1484	+	if( globals->haveTauBarostat() )
1485	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1486	+	else{
1487	+	sprintf( painCave.errMsg,
1488	+	"SimSetup error: If you use an NPT\n"
1489	+	"    ensemble, you must set tauBarostat.\n");
1490	+	painCave.isFatal = 1;
1491	+	simError();
1492	+	}
1493	+	break;
1494	+
1495	+	case NVEZCONS_ENS:
1496	+
1497	+
1498	+	//setup index of z-constraint molecules, z-constraint sampel time
1499	+	//and z-constraint force output name. These parameter should be known
1500	+	//before constructing the z-constraint integrator
1501	+	setupZConstraint();
1502	+
1503	+	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1504	+
1505	+	break;
1506	+
1507	+
1508	+	case NVTZCONS_ENS:
1509	+
1510	+	setupZConstraint();
1511	+
1512	+	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1513	+	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1514	+
1515	+	if (globals->haveTauThermostat())
1516	+	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1517	+
1518	+	else {
1519	+	sprintf( painCave.errMsg,
1520	+	"SimSetup error: If you use the NVT\n"
1521	+	"    ensemble, you must set tauThermostat.\n");
1522	+	painCave.isFatal = 1;
1523	+	simError();
1524	+	}
1525	+	break;
1526	+
1527	+	case NPTiZCONS_ENS:
1528	+
1529	+	setupZConstraint();
1530	+
1531	+	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1532	+	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1533	+
1534	+	if (globals->haveTargetPressure())
1535	+	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1536	+	else {
1537	+	sprintf( painCave.errMsg,
1538	+	"SimSetup error: If you use a constant pressure\n"
1539	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1540	+	painCave.isFatal = 1;
1541	+	simError();
1542	+	}
1543	+
1544	+	if( globals->haveTauThermostat() )
1545	+	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1546	+	else{
1547	+	sprintf( painCave.errMsg,
1548	+	"SimSetup error: If you use an NPT\n"
1549	+	"    ensemble, you must set tauThermostat.\n");
1550	+	painCave.isFatal = 1;
1551	+	simError();
1552	+	}
1553	+
1554	+	if( globals->haveTauBarostat() )
1555	+	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1556	+	else{
1557	+	sprintf( painCave.errMsg,
1558	+	"SimSetup error: If you use an NPT\n"
1559	+	"    ensemble, you must set tauBarostat.\n");
1560	+	painCave.isFatal = 1;
1561	+	simError();
1562	+	}
1563	+
1564	+	break;
1565	+
1566	+	case NPTfZCONS_ENS:
1567	+
1568	+	setupZConstraint();
1569	+
1570	+	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1571	+	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1572	+
1573	+	if (globals->haveTargetPressure())
1574	+	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1575	+	else {
1576	+	sprintf( painCave.errMsg,
1577	+	"SimSetup error: If you use a constant pressure\n"
1578	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1579	+	painCave.isFatal = 1;
1580	+	simError();
1581	+	}
1582	+
1583	+	if( globals->haveTauThermostat() )
1584	+	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1585	+	else{
1586	+	sprintf( painCave.errMsg,
1587	+	"SimSetup error: If you use an NPT\n"
1588	+	"    ensemble, you must set tauThermostat.\n");
1589	+	painCave.isFatal = 1;
1590	+	simError();
1591	+	}
1592	+
1593	+	if( globals->haveTauBarostat() )
1594	+	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1595	+	else{
1596	+	sprintf( painCave.errMsg,
1597	+	"SimSetup error: If you use an NPT\n"
1598	+	"    ensemble, you must set tauBarostat.\n");
1599	+	painCave.isFatal = 1;
1600	+	simError();
1601	+	}
1602	+
1603	+	break;
1604	+
1605	+	case NPTimZCONS_ENS:
1606	+
1607	+	setupZConstraint();
1608	+
1609	+	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1610	+	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1611	+
1612	+	if (globals->haveTargetPressure())
1613	+	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1614	+	else {
1615	+	sprintf( painCave.errMsg,
1616	+	"SimSetup error: If you use a constant pressure\n"
1617	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1618	+	painCave.isFatal = 1;
1619	+	simError();
1620	+	}
1621	+
1622	+	if( globals->haveTauThermostat() )
1623	+	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1624	+	else{
1625	+	sprintf( painCave.errMsg,
1626	+	"SimSetup error: If you use an NPT\n"
1627	+	"    ensemble, you must set tauThermostat.\n");
1628	+	painCave.isFatal = 1;
1629	+	simError();
1630	+	}
1631	+
1632	+	if( globals->haveTauBarostat() )
1633	+	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1634	+	else{
1635	+	sprintf( painCave.errMsg,
1636	+	"SimSetup error: If you use an NPT\n"
1637	+	"    ensemble, you must set tauBarostat.\n");
1638	+	painCave.isFatal = 1;
1639	+	simError();
1640	+	}
1641	+
1642	+	break;
1643	+
1644	+	case NPTfmZCONS_ENS:
1645	+
1646	+	setupZConstraint();
1647	+
1648	+	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1649	+	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1650	+
1651	+	if (globals->haveTargetPressure())
1652	+	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1653	+	else {
1654	+	sprintf( painCave.errMsg,
1655	+	"SimSetup error: If you use a constant pressure\n"
1656	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1657	+	painCave.isFatal = 1;
1658	+	simError();
1659	+	}
1660	+
1661	+	if( globals->haveTauThermostat() )
1662	+	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1663	+	else{
1664	+	sprintf( painCave.errMsg,
1665	+	"SimSetup error: If you use an NPT\n"
1666	+	"    ensemble, you must set tauThermostat.\n");
1667	+	painCave.isFatal = 1;
1668	+	simError();
1669	+	}
1670	+
1671	+	if( globals->haveTauBarostat() )
1672	+	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1673	+	else{
1674	+	sprintf( painCave.errMsg,
1675	+	"SimSetup error: If you use an NPT\n"
1676	+	"    ensemble, you must set tauBarostat.\n");
1677	+	painCave.isFatal = 1;
1678	+	simError();
1679	+	}
1680	+	break;
1681	+
1682	+
1683	+
1684	+	default:
1685	+	sprintf( painCave.errMsg,
1686	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1687	+	painCave.isFatal = 1;
1688	+	simError();
1689	+	}
1690	+
1691	+	}
1692	+
1693	+	void SimSetup::initFortran( void ){
1694	+
1695	+	info->refreshSim();
1696	+
1697	+	if( !strcmp( info->mixingRule, "standard") ){
1698	+	the_ff->initForceField( LB_MIXING_RULE );
1699	+	}
1700	+	else if( !strcmp( info->mixingRule, "explicit") ){
1701	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1702	+	}
1703	+	else{
1704	+	sprintf( painCave.errMsg,
1705	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1706	+	info->mixingRule );
1707	+	painCave.isFatal = 1;
1708	+	simError();
1709	+	}
1710	+
1711	+
1712	+	#ifdef IS_MPI
1713	+	strcpy( checkPointMsg,
1714	+	"Successfully intialized the mixingRule for Fortran." );
1715	+	MPIcheckPoint();
1716	+	#endif // is_mpi
1717	+
1718	+	}
1719	+
1720	+	void SimSetup::setupZConstraint()
1721	+	{
1722	+	if(globals->haveZConsTime()){
1723	+
1724	+	//add sample time of z-constraint  into SimInfo's property list
1725	+	DoubleData* zconsTimeProp = new DoubleData();
1726	+	zconsTimeProp->setID("zconstime");
1727	+	zconsTimeProp->setData(globals->getZConsTime());
1728	+	info->addProperty(zconsTimeProp);
1729	+	}
1730	+	else{
1731	+	sprintf( painCave.errMsg,
1732	+	"ZConstraint error: If you use an ZConstraint\n"
1733	+	" , you must set sample time.\n");
1734	+	painCave.isFatal = 1;
1735	+	simError();
1736	+	}
1737	+
1738	+	if(globals->haveIndexOfAllZConsMols()){
1739	+
1740	+	//add index of z-constraint molecules into SimInfo's property list
1741	+	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1742	+
1743	+	//sort the index
1744	+	sort(tempIndex.begin(), tempIndex.end());
1745	+
1746	+	IndexData* zconsIndex = new IndexData();
1747	+	zconsIndex->setID("zconsindex");
1748	+	zconsIndex->setIndexData(tempIndex);
1749	+	info->addProperty(zconsIndex);
1750	+	}
1751	+	else{
1752	+	sprintf( painCave.errMsg,
1753	+	"SimSetup error: If you use an ZConstraint\n"
1754	+	" , you must set index of z-constraint molecules.\n");
1755	+	painCave.isFatal = 1;
1756	+	simError();
1757	+
1758	+	}
1759	+
1760	+	//Determine the name of ouput file and add it into SimInfo's property list
1761	+	//Be careful, do not use inFileName, since it is a pointer which
1762	+	//point to a string at master node, and slave nodes do not contain that string
1763	+
1764	+	string zconsOutput(info->finalName);
1765	+
1766	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1767	+
1768	+	StringData* zconsFilename = new StringData();
1769	+	zconsFilename->setID("zconsfilename");
1770	+	zconsFilename->setData(zconsOutput);
1771	+
1772	+	info->addProperty(zconsFilename);
1773	+
1774	+	}

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