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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 443 by mmeineke, Wed Apr 2 22:19:03 2003 UTC vs.
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTim_ENS      4
25	+	#define NPTfm_ENS      5
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 27 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 62 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
97	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
70	<
71	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
74	<
75	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
79	<
80	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
85	<
86	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
89	<
90	<
91	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
100	<
101	<	#ifdef IS_MPI
102	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#endif // is_mpi
105	<
97	>	int i, j, k, globalAtomIndex;
98
99	+	// gather all of the information from the Bass file
100
101	<	// get the components and calculate the tot_nMol and indvidual n_mol
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
101	>	gatherInfo();
102
103	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// given in each component
103	>	// creation of complex system objects
104
105	<	tot_nmol = 0;
118	<	for( i=0; i<n_components; i++ ){
105	>	sysObjectsCreation();
106
107	<	if( !the_components[i]->haveNMol() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
107	>	// check on the post processing info
108
109	<	tot_nmol += the_components[i]->getNMol();
130	<	components_nmol[i] = the_components[i]->getNMol();
131	<	}
132	<	}
133	<	else{
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error.\n"
136	<	"\tSorry, the ability to specify total"
137	<	" nMols and then give molfractions in the components\n"
138	<	"\tis not currently supported."
139	<	" Please give nMol in the components.\n" );
140	<	painCave.isFatal = 1;
141	<	simError();
142	<
143	<
144	<	//     tot_nmol = the_globals->getNMol();
145	<
146	<	//   //we have the total number of molecules, now we check for molfractions
147	<	//     for( i=0; i<n_components; i++ ){
148	<
149	<	//       if( !the_components[i]->haveMolFraction() ){
150	<
151	<	//  if( !the_components[i]->haveNMol() ){
152	<	//    //we have a problem
153	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	<	//              << " nMol was given in component
155	<
156	<	}
109	>	finalInfoCheck();
110
111	<	#ifdef IS_MPI
159	<	strcpy( checkPointMsg, "Have the number of components" );
160	<	MPIcheckPoint();
161	<	#endif // is_mpi
111	>	// initialize the system coordinates
112
113	<	// make an array of molecule stamps that match the components used.
164	<	// also extract the used stamps out into a separate linked list
113	>	if( !isInfoArray ) initSystemCoords();
114
115	<	simnfo->nComponents = n_components;
167	<	simnfo->componentsNmol = components_nmol;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
170	<
171	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
175	<
176	<	id = the_components[i]->getType();
177	<	comp_stamps[i] = NULL;
178	<
179	<	// check to make sure the component isn't already in the list
180	<
181	<	comp_stamps[i] = headStamp->match( id );
182	<	if( comp_stamps[i] == NULL ){
183	<
184	<	// extract the component from the list;
185	<
186	<	currentStamp = the_stamps->extractMolStamp( id );
187	<	if( currentStamp == NULL ){
188	<	sprintf( painCave.errMsg,
189	<	"SimSetup error: Component \"%s\" was not found in the "
190	<	"list of declared molecules\n",
191	<	id );
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	headStamp->add( currentStamp );
197	<	comp_stamps[i] = headStamp->match( id );
198	<	}
199	<	}
200	<
201	<	#ifdef IS_MPI
202	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
203	<	MPIcheckPoint();
204	<	#endif // is_mpi
205	<
206	<
207	<
208	<
209	<	// caclulate the number of atoms, bonds, bends and torsions
210	<
211	<	tot_atoms = 0;
212	<	tot_bonds = 0;
213	<	tot_bends = 0;
214	<	tot_torsions = 0;
215	<	for( i=0; i<n_components; i++ ){
216	<
217	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	<	}
222	<
223	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
224	<
225	<	simnfo->n_atoms = tot_atoms;
226	<	simnfo->n_bonds = tot_bonds;
227	<	simnfo->n_bends = tot_bends;
228	<	simnfo->n_torsions = tot_torsions;
229	<	simnfo->n_SRI = tot_SRI;
230	<	simnfo->n_mol = tot_nmol;
231	<
232	<
233	<	#ifdef IS_MPI
234	<
235	<	// divide the molecules among processors here.
236	<
237	<	mpiSim = new mpiSimulation( simnfo );
238	<
239	<
240	<
241	<	globalIndex = mpiSim->divideLabor();
242	<
243	<	// set up the local variables
244	<
245	<	int localMol, allMol;
246	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
247	<
248	<	int* mol2proc = mpiSim->getMolToProcMap();
249	<	int* molCompType = mpiSim->getMolComponentType();
250	<
251	<	allMol = 0;
252	<	localMol = 0;
253	<	local_atoms = 0;
254	<	local_bonds = 0;
255	<	local_bends = 0;
256	<	local_torsions = 0;
257	<	for( i=0; i<n_components; i++ ){
258	<
259	<	for( j=0; j<components_nmol[i]; j++ ){
260	<
261	<	if( mol2proc[j] == worldRank ){
262	<
263	<	local_atoms +=    comp_stamps[i]->getNAtoms();
264	<	local_bonds +=    comp_stamps[i]->getNBonds();
265	<	local_bends +=    comp_stamps[i]->getNBends();
266	<	local_torsions += comp_stamps[i]->getNTorsions();
267	<	localMol++;
268	<	}
269	<	allMol++;
270	<	}
271	<	}
272	<	local_SRI = local_bonds + local_bends + local_torsions;
273	<
274	<
275	<	simnfo->n_atoms = mpiSim->getMyNlocal();
276	<
277	<	if( local_atoms != simnfo->n_atoms ){
278	<	sprintf( painCave.errMsg,
279	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
280	<	" localAtom (%d) are not equal.\n",
281	<	simnfo->n_atoms,
282	<	local_atoms );
283	<	painCave.isFatal = 1;
284	<	simError();
285	<	}
286	<
287	<	simnfo->n_bonds = local_bonds;
288	<	simnfo->n_bends = local_bends;
289	<	simnfo->n_torsions = local_torsions;
290	<	simnfo->n_SRI = local_SRI;
291	<	simnfo->n_mol = localMol;
292	<
293	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
294	<	MPIcheckPoint();
295	<
296	<
297	<	#endif // is_mpi
298	<
299	<
300	<	// create the atom and short range interaction arrays
301	<
302	<	Atom::createArrays(simnfo->n_atoms);
303	<	the_atoms = new Atom*[simnfo->n_atoms];
304	<	the_molecules = new Molecule[simnfo->n_mol];
305	<	int molIndex;
115	>	// make the output filenames
116
117	<	// initialize the molecule's stampID's
308	<
309	<	#ifdef IS_MPI
310	<
311	<
312	<	molIndex = 0;
313	<	for(i=0; i<mpiSim->getTotNmol(); i++){
314	<
315	<	if(mol2proc[i] == worldRank ){
316	<	the_molecules[molIndex].setStampID( molCompType[i] );
317	<	the_molecules[molIndex].setMyIndex( molIndex );
318	<	molIndex++;
319	<	}
320	<	}
321	<
322	<	#else // is_mpi
323	<
324	<	molIndex = 0;
325	<	for(i=0; i<n_components; i++){
326	<	for(j=0; j<components_nmol[i]; j++ ){
327	<	the_molecules[molIndex].setStampID( i );
328	<	the_molecules[molIndex].setMyIndex( molIndex );
329	<	molIndex++;
330	<	}
331	<	}
332	<
333	<
334	<	#endif // is_mpi
335	<
336	<
337	<	if( simnfo->n_SRI ){
338	<
339	<	Exclude::createArray(simnfo->n_SRI);
340	<	the_excludes = new Exclude*[simnfo->n_SRI];
341	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
342	<	simnfo->globalExcludes = new int;
343	<	simnfo->n_exclude = simnfo->n_SRI;
344	<	}
345	<	else{
346	<
347	<	Exclude::createArray( 1 );
348	<	the_excludes = new Exclude*;
349	<	the_excludes[0] = new Exclude(0);
350	<	the_excludes[0]->setPair( 0,0 );
351	<	simnfo->globalExcludes = new int;
352	<	simnfo->globalExcludes[0] = 0;
353	<	simnfo->n_exclude = 0;
354	<	}
355	<
356	<	// set the arrays into the SimInfo object
357	<
358	<	simnfo->atoms = the_atoms;
359	<	simnfo->molecules = the_molecules;
360	<	simnfo->nGlobalExcludes = 0;
361	<	simnfo->excludes = the_excludes;
362	<
363	<
364	<	// get some of the tricky things that may still be in the globals
365	<
366	<
367	<	if( the_globals->haveBox() ){
368	<	simnfo->box_x = the_globals->getBox();
369	<	simnfo->box_y = the_globals->getBox();
370	<	simnfo->box_z = the_globals->getBox();
371	<	}
372	<	else if( the_globals->haveDensity() ){
373	<
374	<	double vol;
375	<	vol = (double)tot_nmol / the_globals->getDensity();
376	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
377	<	simnfo->box_y = simnfo->box_x;
378	<	simnfo->box_z = simnfo->box_x;
379	<	}
380	<	else{
381	<	if( !the_globals->haveBoxX() ){
382	<	sprintf( painCave.errMsg,
383	<	"SimSetup error, no periodic BoxX size given.\n" );
384	<	painCave.isFatal = 1;
385	<	simError();
386	<	}
387	<	simnfo->box_x = the_globals->getBoxX();
388	<
389	<	if( !the_globals->haveBoxY() ){
390	<	sprintf( painCave.errMsg,
391	<	"SimSetup error, no periodic BoxY size given.\n" );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
395	<	simnfo->box_y = the_globals->getBoxY();
396	<
397	<	if( !the_globals->haveBoxZ() ){
398	<	sprintf( painCave.errMsg,
399	<	"SimSetup error, no periodic BoxZ size given.\n" );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
403	<	simnfo->box_z = the_globals->getBoxZ();
404	<	}
405	<
406	<	#ifdef IS_MPI
407	<	strcpy( checkPointMsg, "Box size set up" );
408	<	MPIcheckPoint();
409	<	#endif // is_mpi
410	<
411	<
412	<	// initialize the arrays
413	<
414	<	the_ff->setSimInfo( simnfo );
415	<
416	<	makeMolecules();
417	<	simnfo->identArray = new int[simnfo->n_atoms];
418	<	for(i=0; i<simnfo->n_atoms; i++){
419	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
420	<	}
421	<
422	<	if (the_globals->getUseRF() ) {
423	<	simnfo->useReactionField = 1;
424	<
425	<	if( !the_globals->haveECR() ){
426	<	sprintf( painCave.errMsg,
427	<	"SimSetup Warning: using default value of 1/2 the smallest "
428	<	"box length for the electrostaticCutoffRadius.\n"
429	<	"I hope you have a very fast processor!\n");
430	<	painCave.isFatal = 0;
431	<	simError();
432	<	double smallest;
433	<	smallest = simnfo->box_x;
434	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
435	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
436	<	simnfo->ecr = 0.5 * smallest;
437	<	} else {
438	<	simnfo->ecr        = the_globals->getECR();
439	<	}
440	<
441	<	if( !the_globals->haveEST() ){
442	<	sprintf( painCave.errMsg,
443	<	"SimSetup Warning: using default value of 0.05 * the "
444	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
445	<	);
446	<	painCave.isFatal = 0;
447	<	simError();
448	<	simnfo->est = 0.05 * simnfo->ecr;
449	<	} else {
450	<	simnfo->est        = the_globals->getEST();
451	<	}
452	<
453	<	if(!the_globals->haveDielectric() ){
454	<	sprintf( painCave.errMsg,
455	<	"SimSetup Error: You are trying to use Reaction Field without"
456	<	"setting a dielectric constant!\n"
457	<	);
458	<	painCave.isFatal = 1;
459	<	simError();
460	<	}
461	<	simnfo->dielectric = the_globals->getDielectric();
462	<	} else {
463	<	if (simnfo->n_dipoles) {
464	<
465	<	if( !the_globals->haveECR() ){
466	<	sprintf( painCave.errMsg,
467	<	"SimSetup Warning: using default value of 1/2 the smallest"
468	<	"box length for the electrostaticCutoffRadius.\n"
469	<	"I hope you have a very fast processor!\n");
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	double smallest;
473	<	smallest = simnfo->box_x;
474	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
475	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
476	<	simnfo->ecr = 0.5 * smallest;
477	<	} else {
478	<	simnfo->ecr        = the_globals->getECR();
479	<	}
480	<
481	<	if( !the_globals->haveEST() ){
482	<	sprintf( painCave.errMsg,
483	<	"SimSetup Warning: using default value of 5% of the"
484	<	"electrostaticCutoffRadius for the "
485	<	"electrostaticSkinThickness\n"
486	<	);
487	<	painCave.isFatal = 0;
488	<	simError();
489	<	simnfo->est = 0.05 * simnfo->ecr;
490	<	} else {
491	<	simnfo->est        = the_globals->getEST();
492	<	}
493	<	}
494	<	}
495	<
496	<	#ifdef IS_MPI
497	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
498	<	MPIcheckPoint();
499	<	#endif // is_mpi
500	<
501	<	if( the_globals->haveInitialConfig() ){
502	<
503	<	InitializeFromFile* fileInit;
504	<	#ifdef IS_MPI // is_mpi
505	<	if( worldRank == 0 ){
506	<	#endif //is_mpi
507	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
508	<	#ifdef IS_MPI
509	<	}else fileInit = new InitializeFromFile( NULL );
510	<	#endif
511	<	fileInit->read_xyz( simnfo ); // default velocities on
512	<
513	<	delete fileInit;
514	<	}
515	<	else{
516	<
517	<	#ifdef IS_MPI
518	<
519	<	// no init from bass
520	<
521	<	sprintf( painCave.errMsg,
522	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
523	<	painCave.isFatal;
524	<	simError();
525	<
526	<	#else
527	<
528	<	initFromBass();
529	<
530	<
531	<	#endif
532	<	}
533	<
534	<	#ifdef IS_MPI
535	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
536	<	MPIcheckPoint();
537	<	#endif // is_mpi
538	<
539	<
117	>	makeOutNames();
118
119	<
119	>	// make the integrator
120
121	<
544	<
545	<	#ifdef IS_MPI
546	<	if( worldRank == 0 ){
547	<	#endif // is_mpi
548	<
549	<	if( the_globals->haveFinalConfig() ){
550	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
551	<	}
552	<	else{
553	<	strcpy( simnfo->finalName, inFileName );
554	<	char* endTest;
555	<	int nameLength = strlen( simnfo->finalName );
556	<	endTest = &(simnfo->finalName[nameLength - 5]);
557	<	if( !strcmp( endTest, ".bass" ) ){
558	<	strcpy( endTest, ".eor" );
559	<	}
560	<	else if( !strcmp( endTest, ".BASS" ) ){
561	<	strcpy( endTest, ".eor" );
562	<	}
563	<	else{
564	<	endTest = &(simnfo->finalName[nameLength - 4]);
565	<	if( !strcmp( endTest, ".bss" ) ){
566	<	strcpy( endTest, ".eor" );
567	<	}
568	<	else if( !strcmp( endTest, ".mdl" ) ){
569	<	strcpy( endTest, ".eor" );
570	<	}
571	<	else{
572	<	strcat( simnfo->finalName, ".eor" );
573	<	}
574	<	}
575	<	}
576	<
577	<	// make the sample and status out names
578	<
579	<	strcpy( simnfo->sampleName, inFileName );
580	<	char* endTest;
581	<	int nameLength = strlen( simnfo->sampleName );
582	<	endTest = &(simnfo->sampleName[nameLength - 5]);
583	<	if( !strcmp( endTest, ".bass" ) ){
584	<	strcpy( endTest, ".dump" );
585	<	}
586	<	else if( !strcmp( endTest, ".BASS" ) ){
587	<	strcpy( endTest, ".dump" );
588	<	}
589	<	else{
590	<	endTest = &(simnfo->sampleName[nameLength - 4]);
591	<	if( !strcmp( endTest, ".bss" ) ){
592	<	strcpy( endTest, ".dump" );
593	<	}
594	<	else if( !strcmp( endTest, ".mdl" ) ){
595	<	strcpy( endTest, ".dump" );
596	<	}
597	<	else{
598	<	strcat( simnfo->sampleName, ".dump" );
599	<	}
600	<	}
601	<
602	<	strcpy( simnfo->statusName, inFileName );
603	<	nameLength = strlen( simnfo->statusName );
604	<	endTest = &(simnfo->statusName[nameLength - 5]);
605	<	if( !strcmp( endTest, ".bass" ) ){
606	<	strcpy( endTest, ".stat" );
607	<	}
608	<	else if( !strcmp( endTest, ".BASS" ) ){
609	<	strcpy( endTest, ".stat" );
610	<	}
611	<	else{
612	<	endTest = &(simnfo->statusName[nameLength - 4]);
613	<	if( !strcmp( endTest, ".bss" ) ){
614	<	strcpy( endTest, ".stat" );
615	<	}
616	<	else if( !strcmp( endTest, ".mdl" ) ){
617	<	strcpy( endTest, ".stat" );
618	<	}
619	<	else{
620	<	strcat( simnfo->statusName, ".stat" );
621	<	}
622	<	}
623	<
624	<	#ifdef IS_MPI
625	<	}
626	<	#endif // is_mpi
121	>	makeIntegrator();
122
628	–	// set the status, sample, and themal kick times
629	–
630	–	if( the_globals->haveSampleTime() ){
631	–	simnfo->sampleTime = the_globals->getSampleTime();
632	–	simnfo->statusTime = simnfo->sampleTime;
633	–	simnfo->thermalTime = simnfo->sampleTime;
634	–	}
635	–	else{
636	–	simnfo->sampleTime = the_globals->getRunTime();
637	–	simnfo->statusTime = simnfo->sampleTime;
638	–	simnfo->thermalTime = simnfo->sampleTime;
639	–	}
640	–
641	–	if( the_globals->haveStatusTime() ){
642	–	simnfo->statusTime = the_globals->getStatusTime();
643	–	}
644	–
645	–	if( the_globals->haveThermalTime() ){
646	–	simnfo->thermalTime = the_globals->getThermalTime();
647	–	}
648	–
649	–	// check for the temperature set flag
650	–
651	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
652	–
653	–
654	–	//   // make the longe range forces and the integrator
655	–
656	–	//   new AllLong( simnfo );
657	–
658	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
659	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
660	–
123		#ifdef IS_MPI
124		mpiSim->mpiRefresh();
125		#endif
126
127		// initialize the Fortran
128
129	+	initFortran();
130
668	–	simnfo->refreshSim();
669	–
670	–	if( !strcmp( simnfo->mixingRule, "standard") ){
671	–	the_ff->initForceField( LB_MIXING_RULE );
672	–	}
673	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
674	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
675	–	}
676	–	else{
677	–	sprintf( painCave.errMsg,
678	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
679	–	simnfo->mixingRule );
680	–	painCave.isFatal = 1;
681	–	simError();
682	–	}
131
132
685	–	#ifdef IS_MPI
686	–	strcpy( checkPointMsg,
687	–	"Successfully intialized the mixingRule for Fortran." );
688	–	MPIcheckPoint();
689	–	#endif // is_mpi
133		}
134
135
136		void SimSetup::makeMolecules( void ){
137
138	+	int k,l;
139		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	<	molInit info;
140	>	molInit molInfo;
141		DirectionalAtom* dAtom;
142		LinkedAssign* extras;
143		LinkedAssign* current_extra;
#	Line 716 | Line 160 | void SimSetup::makeMolecules( void ){
160
161		double ux, uy, uz, u, uSqr;
162
163	<	atomOffset = 0;
720	<	excludeOffset = 0;
721	<	for(i=0; i<simnfo->n_mol; i++){
163	>	for(k=0; k<nInfo; k++){
164
165	<	stampID = the_molecules[i].getStampID();
165	>	the_ff->setSimInfo( &(info[k]) );
166
167	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
168	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
169	<	info.nBends    = comp_stamps[stampID]->getNBends();
170	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
171	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for(i=0; i<info[k].n_mol; i++){
170	>
171	>	stampID = info[k].molecules[i].getStampID();
172
173	<	info.myAtoms = &the_atoms[atomOffset];
174	<	info.myExcludes = &the_excludes[excludeOffset];
175	<	info.myBonds = new Bond*[info.nBonds];
176	<	info.myBends = new Bend*[info.nBends];
177	<	info.myTorsions = new Torsion*[info.nTorsions];
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178	>
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184
185	<	theBonds = new bond_pair[info.nBonds];
186	<	theBends = new bend_set[info.nBends];
187	<	theTorsions = new torsion_set[info.nTorsions];
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188
189	<	// make the Atoms
189	>	// make the Atoms
190
191	<	for(j=0; j<info.nAtoms; j++){
744	<
745	<	currentAtom = comp_stamps[stampID]->getAtom( j );
746	<	if( currentAtom->haveOrientation() ){
191	>	for(j=0; j<molInfo.nAtoms; j++){
192
193	<	dAtom = new DirectionalAtom(j + atomOffset);
194	<	simnfo->n_oriented++;
195	<	info.myAtoms[j] = dAtom;
196	<
197	<	ux = currentAtom->getOrntX();
198	<	uy = currentAtom->getOrntY();
199	<	uz = currentAtom->getOrntZ();
200	<
201	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	<
203	<	u = sqrt( uSqr );
204	<	ux = ux / u;
205	<	uy = uy / u;
206	<	uz = uz / u;
207	<
208	<	dAtom->setSUx( ux );
209	<	dAtom->setSUy( uy );
210	<	dAtom->setSUz( uz );
211	<	}
212	<	else{
213	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
214	<	}
215	<	info.myAtoms[j]->setType( currentAtom->getType() );
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195	>
196	>	dAtom = new DirectionalAtom( (j + atomOffset),
197	>	info[k].getConfiguration() );
198	>	info[k].n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200	>
201	>	ux = currentAtom->getOrntX();
202	>	uy = currentAtom->getOrntY();
203	>	uz = currentAtom->getOrntZ();
204	>
205	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	>
207	>	u = sqrt( uSqr );
208	>	ux = ux / u;
209	>	uy = uy / u;
210	>	uz = uz / u;
211	>
212	>	dAtom->setSUx( ux );
213	>	dAtom->setSUy( uy );
214	>	dAtom->setSUz( uz );
215	>	}
216	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	>	info[k].getConfiguration() );
219	>	}
220	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221
222		#ifdef IS_MPI
223
224	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225
226		#endif // is_mpi
227	<	}
227	>	}
228
229		// make the bonds
230	<	for(j=0; j<info.nBonds; j++){
230	>	for(j=0; j<molInfo.nBonds; j++){
231
232	<	currentBond = comp_stamps[stampID]->getBond( j );
233	<	theBonds[j].a = currentBond->getA() + atomOffset;
234	<	theBonds[j].b = currentBond->getB() + atomOffset;
235	<
236	<	exI = theBonds[j].a;
237	<	exJ = theBonds[j].b;
238	<
239	<	// exclude_I must always be the smaller of the pair
240	<	if( exI > exJ ){
241	<	tempEx = exI;
242	<	exI = exJ;
243	<	exJ = tempEx;
244	<	}
232	>	currentBond = comp_stamps[stampID]->getBond( j );
233	>	theBonds[j].a = currentBond->getA() + atomOffset;
234	>	theBonds[j].b = currentBond->getB() + atomOffset;
235	>
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244	>	}
245		#ifdef IS_MPI
246	<	tempEx = exI;
247	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
248	<	tempEx = exJ;
249	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
250	<
251	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
246	>	tempEx = exI;
247	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	>	tempEx = exJ;
249	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	>
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252		#else  // isn't MPI
253	<
254	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
253	>
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255		#endif  //is_mpi
256	<	}
257	<	excludeOffset += info.nBonds;
808	<
809	<	//make the bends
810	<	for(j=0; j<info.nBends; j++){
256	>	}
257	>	excludeOffset += molInfo.nBonds;
258
259	<	currentBend = comp_stamps[stampID]->getBend( j );
260	<	theBends[j].a = currentBend->getA() + atomOffset;
261	<	theBends[j].b = currentBend->getB() + atomOffset;
262	<	theBends[j].c = currentBend->getC() + atomOffset;
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261	>
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266	>
267	>	if( currentBend->haveExtras() ){
268
269	<	if( currentBend->haveExtras() ){
270	<
271	<	extras = currentBend->getExtras();
272	<	current_extra = extras;
273	<
274	<	while( current_extra != NULL ){
275	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276
277	<	switch( current_extra->getType() ){
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290	>	sprintf( painCave.errMsg,
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298	>	}
299	>
300	>	else{
301
827	–	case 0:
828	–	theBends[j].ghost =
829	–	current_extra->getInt() + atomOffset;
830	–	theBends[j].isGhost = 1;
831	–	break;
832	–
833	–	case 1:
834	–	theBends[j].ghost =
835	–	(int)current_extra->getDouble() + atomOffset;
836	–	theBends[j].isGhost = 1;
837	–	break;
838	–
839	–	default:
302		sprintf( painCave.errMsg,
303	<	"SimSetup Error: ghostVectorSource was neither a "
304	<	"double nor an int.\n"
305	<	"-->Bend[%d] in %s\n",
303	>	"SimSetup Error: unhandled bend assignment:\n"
304	>	"    -->%s in Bend[%d] in %s\n",
305	>	current_extra->getlhs(),
306		j, comp_stamps[stampID]->getID() );
307		painCave.isFatal = 1;
308		simError();
309		}
848	–	}
849	–
850	–	else{
310
311	<	sprintf( painCave.errMsg,
853	<	"SimSetup Error: unhandled bend assignment:\n"
854	<	"    -->%s in Bend[%d] in %s\n",
855	<	current_extra->getlhs(),
856	<	j, comp_stamps[stampID]->getID() );
857	<	painCave.isFatal = 1;
858	<	simError();
311	>	current_extra = current_extra->getNext();
312		}
313	+	}
314	+
315	+	if( !theBends[j].isGhost ){
316
317	<	current_extra = current_extra->getNext();
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].c;
319		}
320	<	}
320	>	else{
321
322	<	if( !theBends[j].isGhost ){
323	<
324	<	exI = theBends[j].a;
868	<	exJ = theBends[j].c;
869	<	}
870	<	else{
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].b;
324	>	}
325
326	<	exI = theBends[j].a;
327	<	exJ = theBends[j].b;
328	<	}
329	<
330	<	// exclude_I must always be the smaller of the pair
331	<	if( exI > exJ ){
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331	>	}
332	>	#ifdef IS_MPI
333		tempEx = exI;
334	<	exI = exJ;
335	<	exJ = tempEx;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	>
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	#else  // isn't MPI
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	#endif  //is_mpi
342		}
343	<	#ifdef IS_MPI
883	<	tempEx = exI;
884	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
885	<	tempEx = exJ;
886	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
343	>	excludeOffset += molInfo.nBends;
344
345	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
345	>	for(j=0; j<molInfo.nTorsions; j++){
346	>
347	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352	>
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355	>
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361	>	}
362	>	#ifdef IS_MPI
363	>	tempEx = exI;
364	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	>	tempEx = exJ;
366	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	>
368	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369		#else  // isn't MPI
370	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371		#endif  //is_mpi
372	<	}
373	<	excludeOffset += info.nBends;
894	<
895	<	for(j=0; j<info.nTorsions; j++){
372	>	}
373	>	excludeOffset += molInfo.nTorsions;
374
897	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
898	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
899	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
900	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
901	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
375
376	<	exI = theTorsions[j].a;
377	<	exJ = theTorsions[j].d;
376	>	// send the arrays off to the forceField for init.
377	>
378	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	>
383	>
384	>	info[k].molecules[i].initialize( molInfo );
385
906	–	// exclude_I must always be the smaller of the pair
907	–	if( exI > exJ ){
908	–	tempEx = exI;
909	–	exI = exJ;
910	–	exJ = tempEx;
911	–	}
912	–	#ifdef IS_MPI
913	–	tempEx = exI;
914	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
915	–	tempEx = exJ;
916	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
386
387	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
388	<	#else  // isn't MPI
389	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
390	<	#endif  //is_mpi
387	>	atomOffset += molInfo.nAtoms;
388	>	delete[] theBonds;
389	>	delete[] theBends;
390	>	delete[] theTorsions;
391		}
923	–	excludeOffset += info.nTorsions;
924	–
925	–
926	–	// send the arrays off to the forceField for init.
927	–
928	–	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
929	–	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
930	–	the_ff->initializeBends( info.nBends, info.myBends, theBends );
931	–	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
932	–
933	–
934	–	the_molecules[i].initialize( info );
935	–
936	–
937	–	atomOffset += info.nAtoms;
938	–	delete[] theBonds;
939	–	delete[] theBends;
940	–	delete[] theTorsions;
392		}
393	<
393	>
394		#ifdef IS_MPI
395		sprintf( checkPointMsg, "all molecules initialized succesfully" );
396		MPIcheckPoint();
397		#endif // is_mpi
398	<
398	>
399		// clean up the forcefield
400	+
401		the_ff->calcRcut();
402		the_ff->cleanMe();
403	<
403	>
404		}
405
406		void SimSetup::initFromBass( void ){
#	Line 961 | Line 413 | void SimSetup::initFromBass( void ){
413		int n_extra;
414		int have_extra, done;
415
416	<	temp1 = (double)tot_nmol / 4.0;
417	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
418	<	temp3 = ceil( temp2 );
416	>	double vel[3];
417	>	vel[0] = 0.0;
418	>	vel[1] = 0.0;
419	>	vel[2] = 0.0;
420
421	+	temp1 = (double)tot_nmol / 4.0;
422	+	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423	+	temp3 = ceil( temp2 );
424	+
425		have_extra =0;
426		if( temp2 < temp3 ){ // we have a non-complete lattice
427		have_extra =1;
428
429		n_cells = (int)temp3 - 1;
430	<	cellx = simnfo->box_x / temp3;
431	<	celly = simnfo->box_y / temp3;
432	<	cellz = simnfo->box_z / temp3;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435		n_per_extra = (int)ceil( temp1 );
#	Line 987 | Line 444 | void SimSetup::initFromBass( void ){
444		}
445		else{
446		n_cells = (int)temp3;
447	<	cellx = simnfo->box_x / temp3;
448	<	celly = simnfo->box_y / temp3;
449	<	cellz = simnfo->box_z / temp3;
447	>	cellx = info[0].boxL[0] / temp3;
448	>	celly = info[0].boxL[1] / temp3;
449	>	cellz = info[0].boxL[2] / temp3;
450		}
451
452		current_mol = 0;
#	Line 1068 | Line 525 | void SimSetup::initFromBass( void ){
525		}
526		}
527
528	<
529	<	for( i=0; i<simnfo->n_atoms; i++ ){
1073	<	simnfo->atoms[i]->set_vx( 0.0 );
1074	<	simnfo->atoms[i]->set_vy( 0.0 );
1075	<	simnfo->atoms[i]->set_vz( 0.0 );
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530		}
531		}
532
#	Line 1082 | Line 536 | void SimSetup::makeElement( double x, double y, double
536		AtomStamp* current_atom;
537		DirectionalAtom* dAtom;
538		double rotMat[3][3];
539	+	double pos[3];
540
541		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542
#	Line 1097 | Line 552 | void SimSetup::makeElement( double x, double y, double
552		painCave.isFatal = 1;
553		simError();
554		}
555	+
556	+	pos[0] = x + current_atom->getPosX();
557	+	pos[1] = y + current_atom->getPosY();
558	+	pos[2] = z + current_atom->getPosZ();
559	+
560	+	info[0].atoms[current_atom_ndx]->setPos( pos );
561
562	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1102	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1103	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563
564	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
564	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565
1107	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1108	–
566		rotMat[0][0] = 1.0;
567		rotMat[0][1] = 0.0;
568		rotMat[0][2] = 0.0;
#	Line 1133 | Line 590 | void SimSetup::makeElement( double x, double y, double
590		current_comp++;
591		}
592		}
593	+
594	+
595	+	void SimSetup::gatherInfo( void ){
596	+	int i,j,k;
597	+
598	+	ensembleCase = -1;
599	+	ffCase = -1;
600	+
601	+	// set the easy ones first
602	+
603	+	for( i=0; i<nInfo; i++){
604	+	info[i].target_temp = globals->getTargetTemp();
605	+	info[i].dt = globals->getDt();
606	+	info[i].run_time = globals->getRunTime();
607	+	}
608	+	n_components = globals->getNComponents();
609	+
610	+
611	+	// get the forceField
612	+
613	+	strcpy( force_field, globals->getForceField() );
614	+
615	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618	+	else{
619	+	sprintf( painCave.errMsg,
620	+	"SimSetup Error. Unrecognized force field -> %s\n",
621	+	force_field );
622	+	painCave.isFatal = 1;
623	+	simError();
624	+	}
625	+
626	+	// get the ensemble
627	+
628	+	strcpy( ensemble, globals->getEnsemble() );
629	+
630	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633	+	ensembleCase = NPTi_ENS;
634	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637	+	else{
638	+	sprintf( painCave.errMsg,
639	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	+	"reverting to NVE for this simulation.\n",
641	+	ensemble );
642	+	painCave.isFatal = 0;
643	+	simError();
644	+	strcpy( ensemble, "NVE" );
645	+	ensembleCase = NVE_ENS;
646	+	}
647	+
648	+	for(i=0; i<nInfo; i++){
649	+
650	+	strcpy( info[i].ensemble, ensemble );
651	+
652	+	// get the mixing rule
653	+
654	+	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	+	info[i].usePBC = globals->getPBC();
656	+	}
657	+
658	+	// get the components and calculate the tot_nMol and indvidual n_mol
659	+
660	+	the_components = globals->getComponents();
661	+	components_nmol = new int[n_components];
662	+
663	+
664	+	if( !globals->haveNMol() ){
665	+	// we don't have the total number of molecules, so we assume it is
666	+	// given in each component
667	+
668	+	tot_nmol = 0;
669	+	for( i=0; i<n_components; i++ ){
670	+
671	+	if( !the_components[i]->haveNMol() ){
672	+	// we have a problem
673	+	sprintf( painCave.errMsg,
674	+	"SimSetup Error. No global NMol or component NMol"
675	+	" given. Cannot calculate the number of atoms.\n" );
676	+	painCave.isFatal = 1;
677	+	simError();
678	+	}
679	+
680	+	tot_nmol += the_components[i]->getNMol();
681	+	components_nmol[i] = the_components[i]->getNMol();
682	+	}
683	+	}
684	+	else{
685	+	sprintf( painCave.errMsg,
686	+	"SimSetup error.\n"
687	+	"\tSorry, the ability to specify total"
688	+	" nMols and then give molfractions in the components\n"
689	+	"\tis not currently supported."
690	+	" Please give nMol in the components.\n" );
691	+	painCave.isFatal = 1;
692	+	simError();
693	+	}
694	+
695	+	// set the status, sample, and thermal kick times
696	+
697	+	for(i=0; i<nInfo; i++){
698	+
699	+	if( globals->haveSampleTime() ){
700	+	info[i].sampleTime = globals->getSampleTime();
701	+	info[i].statusTime = info[i].sampleTime;
702	+	info[i].thermalTime = info[i].sampleTime;
703	+	}
704	+	else{
705	+	info[i].sampleTime = globals->getRunTime();
706	+	info[i].statusTime = info[i].sampleTime;
707	+	info[i].thermalTime = info[i].sampleTime;
708	+	}
709	+
710	+	if( globals->haveStatusTime() ){
711	+	info[i].statusTime = globals->getStatusTime();
712	+	}
713	+
714	+	if( globals->haveThermalTime() ){
715	+	info[i].thermalTime = globals->getThermalTime();
716	+	}
717	+
718	+	// check for the temperature set flag
719	+
720	+	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721	+
722	+	// get some of the tricky things that may still be in the globals
723	+
724	+	double boxVector[3];
725	+	if( globals->haveBox() ){
726	+	boxVector[0] = globals->getBox();
727	+	boxVector[1] = globals->getBox();
728	+	boxVector[2] = globals->getBox();
729	+
730	+	info[i].setBox( boxVector );
731	+	}
732	+	else if( globals->haveDensity() ){
733	+
734	+	double vol;
735	+	vol = (double)tot_nmol / globals->getDensity();
736	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	+	boxVector[1] = boxVector[0];
738	+	boxVector[2] = boxVector[0];
739	+
740	+	info[i].setBox( boxVector );
741	+	}
742	+	else{
743	+	if( !globals->haveBoxX() ){
744	+	sprintf( painCave.errMsg,
745	+	"SimSetup error, no periodic BoxX size given.\n" );
746	+	painCave.isFatal = 1;
747	+	simError();
748	+	}
749	+	boxVector[0] = globals->getBoxX();
750	+
751	+	if( !globals->haveBoxY() ){
752	+	sprintf( painCave.errMsg,
753	+	"SimSetup error, no periodic BoxY size given.\n" );
754	+	painCave.isFatal = 1;
755	+	simError();
756	+	}
757	+	boxVector[1] = globals->getBoxY();
758	+
759	+	if( !globals->haveBoxZ() ){
760	+	sprintf( painCave.errMsg,
761	+	"SimSetup error, no periodic BoxZ size given.\n" );
762	+	painCave.isFatal = 1;
763	+	simError();
764	+	}
765	+	boxVector[2] = globals->getBoxZ();
766	+
767	+	info[i].setBox( boxVector );
768	+	}
769	+
770	+	}
771	+
772	+	#ifdef IS_MPI
773	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
774	+	MPIcheckPoint();
775	+	#endif // is_mpi
776	+
777	+	}
778	+
779	+
780	+	void SimSetup::finalInfoCheck( void ){
781	+	int index;
782	+	int usesDipoles;
783	+	int i;
784	+
785	+	for(i=0; i<nInfo; i++){
786	+	// check electrostatic parameters
787	+
788	+	index = 0;
789	+	usesDipoles = 0;
790	+	while( (index < info[i].n_atoms) && !usesDipoles ){
791	+	usesDipoles = (info[i].atoms[index])->hasDipole();
792	+	index++;
793	+	}
794	+
795	+	#ifdef IS_MPI
796	+	int myUse = usesDipoles;
797	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798	+	#endif //is_mpi
799	+
800	+	double theEcr, theEst;
801	+
802	+	if (globals->getUseRF() ) {
803	+	info[i].useReactionField = 1;
804	+
805	+	if( !globals->haveECR() ){
806	+	sprintf( painCave.errMsg,
807	+	"SimSetup Warning: using default value of 1/2 the smallest "
808	+	"box length for the electrostaticCutoffRadius.\n"
809	+	"I hope you have a very fast processor!\n");
810	+	painCave.isFatal = 0;
811	+	simError();
812	+	double smallest;
813	+	smallest = info[i].boxL[0];
814	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	+	theEcr = 0.5 * smallest;
817	+	} else {
818	+	theEcr = globals->getECR();
819	+	}
820	+
821	+	if( !globals->haveEST() ){
822	+	sprintf( painCave.errMsg,
823	+	"SimSetup Warning: using default value of 0.05 * the "
824	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	+	);
826	+	painCave.isFatal = 0;
827	+	simError();
828	+	theEst = 0.05 * theEcr;
829	+	} else {
830	+	theEst= globals->getEST();
831	+	}
832	+
833	+	info[i].setEcr( theEcr, theEst );
834	+
835	+	if(!globals->haveDielectric() ){
836	+	sprintf( painCave.errMsg,
837	+	"SimSetup Error: You are trying to use Reaction Field without"
838	+	"setting a dielectric constant!\n"
839	+	);
840	+	painCave.isFatal = 1;
841	+	simError();
842	+	}
843	+	info[i].dielectric = globals->getDielectric();
844	+	}
845	+	else {
846	+	if (usesDipoles) {
847	+
848	+	if( !globals->haveECR() ){
849	+	sprintf( painCave.errMsg,
850	+	"SimSetup Warning: using default value of 1/2 the smallest "
851	+	"box length for the electrostaticCutoffRadius.\n"
852	+	"I hope you have a very fast processor!\n");
853	+	painCave.isFatal = 0;
854	+	simError();
855	+	double smallest;
856	+	smallest = info[i].boxL[0];
857	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	+	theEcr = 0.5 * smallest;
860	+	} else {
861	+	theEcr = globals->getECR();
862	+	}
863	+
864	+	if( !globals->haveEST() ){
865	+	sprintf( painCave.errMsg,
866	+	"SimSetup Warning: using default value of 0.05 * the "
867	+	"electrostaticCutoffRadius for the "
868	+	"electrostaticSkinThickness\n"
869	+	);
870	+	painCave.isFatal = 0;
871	+	simError();
872	+	theEst = 0.05 * theEcr;
873	+	} else {
874	+	theEst= globals->getEST();
875	+	}
876	+
877	+	info[i].setEcr( theEcr, theEst );
878	+	}
879	+	}
880	+	}
881	+
882	+	#ifdef IS_MPI
883	+	strcpy( checkPointMsg, "post processing checks out" );
884	+	MPIcheckPoint();
885	+	#endif // is_mpi
886	+
887	+	}
888	+
889	+	void SimSetup::initSystemCoords( void ){
890	+	int i;
891	+
892	+	char* inName;
893	+
894	+
895	+	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
896	+
897	+	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
898	+
899	+	if( globals->haveInitialConfig() ){
900	+
901	+	InitializeFromFile* fileInit;
902	+	#ifdef IS_MPI // is_mpi
903	+	if( worldRank == 0 ){
904	+	#endif //is_mpi
905	+	inName = globals->getInitialConfig();
906	+	double* tempDouble = new double[1000000];
907	+	fileInit = new InitializeFromFile( inName );
908	+	#ifdef IS_MPI
909	+	}else fileInit = new InitializeFromFile( NULL );
910	+	#endif
911	+	fileInit->readInit( info ); // default velocities on
912	+
913	+	delete fileInit;
914	+	}
915	+	else{
916	+
917	+	#ifdef IS_MPI
918	+
919	+	// no init from bass
920	+
921	+	sprintf( painCave.errMsg,
922	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923	+	painCave.isFatal;
924	+	simError();
925	+
926	+	#else
927	+
928	+	initFromBass();
929	+
930	+
931	+	#endif
932	+	}
933	+
934	+	#ifdef IS_MPI
935	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
936	+	MPIcheckPoint();
937	+	#endif // is_mpi
938	+
939	+	}
940	+
941	+
942	+	void SimSetup::makeOutNames( void ){
943	+
944	+	int k;
945	+
946	+
947	+	for(k=0; k<nInfo; k++){
948	+
949	+	#ifdef IS_MPI
950	+	if( worldRank == 0 ){
951	+	#endif // is_mpi
952	+
953	+	if( globals->haveFinalConfig() ){
954	+	strcpy( info[k].finalName, globals->getFinalConfig() );
955	+	}
956	+	else{
957	+	strcpy( info[k].finalName, inFileName );
958	+	char* endTest;
959	+	int nameLength = strlen( info[k].finalName );
960	+	endTest = &(info[k].finalName[nameLength - 5]);
961	+	if( !strcmp( endTest, ".bass" ) ){
962	+	strcpy( endTest, ".eor" );
963	+	}
964	+	else if( !strcmp( endTest, ".BASS" ) ){
965	+	strcpy( endTest, ".eor" );
966	+	}
967	+	else{
968	+	endTest = &(info[k].finalName[nameLength - 4]);
969	+	if( !strcmp( endTest, ".bss" ) ){
970	+	strcpy( endTest, ".eor" );
971	+	}
972	+	else if( !strcmp( endTest, ".mdl" ) ){
973	+	strcpy( endTest, ".eor" );
974	+	}
975	+	else{
976	+	strcat( info[k].finalName, ".eor" );
977	+	}
978	+	}
979	+	}
980	+
981	+	// make the sample and status out names
982	+
983	+	strcpy( info[k].sampleName, inFileName );
984	+	char* endTest;
985	+	int nameLength = strlen( info[k].sampleName );
986	+	endTest = &(info[k].sampleName[nameLength - 5]);
987	+	if( !strcmp( endTest, ".bass" ) ){
988	+	strcpy( endTest, ".dump" );
989	+	}
990	+	else if( !strcmp( endTest, ".BASS" ) ){
991	+	strcpy( endTest, ".dump" );
992	+	}
993	+	else{
994	+	endTest = &(info[k].sampleName[nameLength - 4]);
995	+	if( !strcmp( endTest, ".bss" ) ){
996	+	strcpy( endTest, ".dump" );
997	+	}
998	+	else if( !strcmp( endTest, ".mdl" ) ){
999	+	strcpy( endTest, ".dump" );
1000	+	}
1001	+	else{
1002	+	strcat( info[k].sampleName, ".dump" );
1003	+	}
1004	+	}
1005	+
1006	+	strcpy( info[k].statusName, inFileName );
1007	+	nameLength = strlen( info[k].statusName );
1008	+	endTest = &(info[k].statusName[nameLength - 5]);
1009	+	if( !strcmp( endTest, ".bass" ) ){
1010	+	strcpy( endTest, ".stat" );
1011	+	}
1012	+	else if( !strcmp( endTest, ".BASS" ) ){
1013	+	strcpy( endTest, ".stat" );
1014	+	}
1015	+	else{
1016	+	endTest = &(info[k].statusName[nameLength - 4]);
1017	+	if( !strcmp( endTest, ".bss" ) ){
1018	+	strcpy( endTest, ".stat" );
1019	+	}
1020	+	else if( !strcmp( endTest, ".mdl" ) ){
1021	+	strcpy( endTest, ".stat" );
1022	+	}
1023	+	else{
1024	+	strcat( info[k].statusName, ".stat" );
1025	+	}
1026	+	}
1027	+
1028	+	#ifdef IS_MPI
1029	+	}
1030	+	#endif // is_mpi
1031	+	}
1032	+	}
1033	+
1034	+
1035	+	void SimSetup::sysObjectsCreation( void ){
1036	+
1037	+	int i,k;
1038	+
1039	+	// create the forceField
1040	+
1041	+	createFF();
1042	+
1043	+	// extract componentList
1044	+
1045	+	compList();
1046	+
1047	+	// calc the number of atoms, bond, bends, and torsions
1048	+
1049	+	calcSysValues();
1050	+
1051	+	#ifdef IS_MPI
1052	+	// divide the molecules among the processors
1053	+
1054	+	mpiMolDivide();
1055	+	#endif //is_mpi
1056	+
1057	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1058	+
1059	+	makeSysArrays();
1060	+
1061	+	// make and initialize the molecules (all but atomic coordinates)
1062	+
1063	+	makeMolecules();
1064	+
1065	+	for(k=0; k<nInfo; k++){
1066	+	info[k].identArray = new int[info[k].n_atoms];
1067	+	for(i=0; i<info[k].n_atoms; i++){
1068	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1069	+	}
1070	+	}
1071	+	}
1072	+
1073	+
1074	+	void SimSetup::createFF( void ){
1075	+
1076	+	switch( ffCase ){
1077	+
1078	+	case FF_DUFF:
1079	+	the_ff = new DUFF();
1080	+	break;
1081	+
1082	+	case FF_LJ:
1083	+	the_ff = new LJFF();
1084	+	break;
1085	+
1086	+	case FF_EAM:
1087	+	the_ff = new EAM_FF();
1088	+	break;
1089	+
1090	+	default:
1091	+	sprintf( painCave.errMsg,
1092	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	+	painCave.isFatal = 1;
1094	+	simError();
1095	+	}
1096	+
1097	+	#ifdef IS_MPI
1098	+	strcpy( checkPointMsg, "ForceField creation successful" );
1099	+	MPIcheckPoint();
1100	+	#endif // is_mpi
1101	+
1102	+	}
1103	+
1104	+
1105	+	void SimSetup::compList( void ){
1106	+
1107	+	int i;
1108	+	char* id;
1109	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1110	+	LinkedMolStamp* currentStamp = NULL;
1111	+	comp_stamps = new MoleculeStamp*[n_components];
1112	+
1113	+	// make an array of molecule stamps that match the components used.
1114	+	// also extract the used stamps out into a separate linked list
1115	+
1116	+	for(i=0; i<nInfo; i++){
1117	+	info[i].nComponents = n_components;
1118	+	info[i].componentsNmol = components_nmol;
1119	+	info[i].compStamps = comp_stamps;
1120	+	info[i].headStamp = headStamp;
1121	+	}
1122	+
1123	+
1124	+	for( i=0; i<n_components; i++ ){
1125	+
1126	+	id = the_components[i]->getType();
1127	+	comp_stamps[i] = NULL;
1128	+
1129	+	// check to make sure the component isn't already in the list
1130	+
1131	+	comp_stamps[i] = headStamp->match( id );
1132	+	if( comp_stamps[i] == NULL ){
1133	+
1134	+	// extract the component from the list;
1135	+
1136	+	currentStamp = stamps->extractMolStamp( id );
1137	+	if( currentStamp == NULL ){
1138	+	sprintf( painCave.errMsg,
1139	+	"SimSetup error: Component \"%s\" was not found in the "
1140	+	"list of declared molecules\n",
1141	+	id );
1142	+	painCave.isFatal = 1;
1143	+	simError();
1144	+	}
1145	+
1146	+	headStamp->add( currentStamp );
1147	+	comp_stamps[i] = headStamp->match( id );
1148	+	}
1149	+	}
1150	+
1151	+	#ifdef IS_MPI
1152	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1153	+	MPIcheckPoint();
1154	+	#endif // is_mpi
1155	+
1156	+
1157	+	}
1158	+
1159	+	void SimSetup::calcSysValues( void ){
1160	+	int i, j, k;
1161	+
1162	+	int *molMembershipArray;
1163	+
1164	+	tot_atoms = 0;
1165	+	tot_bonds = 0;
1166	+	tot_bends = 0;
1167	+	tot_torsions = 0;
1168	+	for( i=0; i<n_components; i++ ){
1169	+
1170	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1172	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1173	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174	+	}
1175	+
1176	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	+	molMembershipArray = new int[tot_atoms];
1178	+
1179	+	for(i=0; i<nInfo; i++){
1180	+	info[i].n_atoms = tot_atoms;
1181	+	info[i].n_bonds = tot_bonds;
1182	+	info[i].n_bends = tot_bends;
1183	+	info[i].n_torsions = tot_torsions;
1184	+	info[i].n_SRI = tot_SRI;
1185	+	info[i].n_mol = tot_nmol;
1186	+
1187	+	info[i].molMembershipArray = molMembershipArray;
1188	+	}
1189	+	}
1190	+
1191	+	#ifdef IS_MPI
1192	+
1193	+	void SimSetup::mpiMolDivide( void ){
1194	+
1195	+	int i, j, k;
1196	+	int localMol, allMol;
1197	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1198	+
1199	+	mpiSim = new mpiSimulation( info );
1200	+
1201	+	globalIndex = mpiSim->divideLabor();
1202	+
1203	+	// set up the local variables
1204	+
1205	+	mol2proc = mpiSim->getMolToProcMap();
1206	+	molCompType = mpiSim->getMolComponentType();
1207	+
1208	+	allMol = 0;
1209	+	localMol = 0;
1210	+	local_atoms = 0;
1211	+	local_bonds = 0;
1212	+	local_bends = 0;
1213	+	local_torsions = 0;
1214	+	globalAtomIndex = 0;
1215	+
1216	+
1217	+	for( i=0; i<n_components; i++ ){
1218	+
1219	+	for( j=0; j<components_nmol[i]; j++ ){
1220	+
1221	+	if( mol2proc[allMol] == worldRank ){
1222	+
1223	+	local_atoms +=    comp_stamps[i]->getNAtoms();
1224	+	local_bonds +=    comp_stamps[i]->getNBonds();
1225	+	local_bends +=    comp_stamps[i]->getNBends();
1226	+	local_torsions += comp_stamps[i]->getNTorsions();
1227	+	localMol++;
1228	+	}
1229	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1230	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1231	+	globalAtomIndex++;
1232	+	}
1233	+
1234	+	allMol++;
1235	+	}
1236	+	}
1237	+	local_SRI = local_bonds + local_bends + local_torsions;
1238	+
1239	+	info[0].n_atoms = mpiSim->getMyNlocal();
1240	+
1241	+	if( local_atoms != info[0].n_atoms ){
1242	+	sprintf( painCave.errMsg,
1243	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244	+	" localAtom (%d) are not equal.\n",
1245	+	info[0].n_atoms,
1246	+	local_atoms );
1247	+	painCave.isFatal = 1;
1248	+	simError();
1249	+	}
1250	+
1251	+	info[0].n_bonds = local_bonds;
1252	+	info[0].n_bends = local_bends;
1253	+	info[0].n_torsions = local_torsions;
1254	+	info[0].n_SRI = local_SRI;
1255	+	info[0].n_mol = localMol;
1256	+
1257	+	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1258	+	MPIcheckPoint();
1259	+	}
1260	+
1261	+	#endif // is_mpi
1262	+
1263	+
1264	+	void SimSetup::makeSysArrays( void ){
1265	+	int i, j, k, l;
1266	+
1267	+	Atom** the_atoms;
1268	+	Molecule* the_molecules;
1269	+	Exclude** the_excludes;
1270	+
1271	+
1272	+	for(l=0; l<nInfo; l++){
1273	+
1274	+	// create the atom and short range interaction arrays
1275	+
1276	+	the_atoms = new Atom*[info[l].n_atoms];
1277	+	the_molecules = new Molecule[info[l].n_mol];
1278	+	int molIndex;
1279	+
1280	+	// initialize the molecule's stampID's
1281	+
1282	+	#ifdef IS_MPI
1283	+
1284	+
1285	+	molIndex = 0;
1286	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1287	+
1288	+	if(mol2proc[i] == worldRank ){
1289	+	the_molecules[molIndex].setStampID( molCompType[i] );
1290	+	the_molecules[molIndex].setMyIndex( molIndex );
1291	+	the_molecules[molIndex].setGlobalIndex( i );
1292	+	molIndex++;
1293	+	}
1294	+	}
1295	+
1296	+	#else // is_mpi
1297	+
1298	+	molIndex = 0;
1299	+	globalAtomIndex = 0;
1300	+	for(i=0; i<n_components; i++){
1301	+	for(j=0; j<components_nmol[i]; j++ ){
1302	+	the_molecules[molIndex].setStampID( i );
1303	+	the_molecules[molIndex].setMyIndex( molIndex );
1304	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1305	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1306	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1307	+	globalAtomIndex++;
1308	+	}
1309	+	molIndex++;
1310	+	}
1311	+	}
1312	+
1313	+
1314	+	#endif // is_mpi
1315	+
1316	+
1317	+	if( info[l].n_SRI ){
1318	+
1319	+	Exclude::createArray(info[l].n_SRI);
1320	+	the_excludes = new Exclude*[info[l].n_SRI];
1321	+	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	+	the_excludes[ex] = new Exclude(ex);
1323	+	}
1324	+	info[l].globalExcludes = new int;
1325	+	info[l].n_exclude = info[l].n_SRI;
1326	+	}
1327	+	else{
1328	+
1329	+	Exclude::createArray( 1 );
1330	+	the_excludes = new Exclude*;
1331	+	the_excludes[0] = new Exclude(0);
1332	+	the_excludes[0]->setPair( 0,0 );
1333	+	info[l].globalExcludes = new int;
1334	+	info[l].globalExcludes[0] = 0;
1335	+	info[l].n_exclude = 0;
1336	+	}
1337	+
1338	+	// set the arrays into the SimInfo object
1339	+
1340	+	info[l].atoms = the_atoms;
1341	+	info[l].molecules = the_molecules;
1342	+	info[l].nGlobalExcludes = 0;
1343	+	info[l].excludes = the_excludes;
1344	+
1345	+	the_ff->setSimInfo( info );
1346	+
1347	+	}
1348	+	}
1349	+
1350	+	void SimSetup::makeIntegrator( void ){
1351	+
1352	+	int k;
1353	+
1354	+	NVT<RealIntegrator>*  myNVT = NULL;
1355	+	NPTi<RealIntegrator>* myNPTi = NULL;
1356	+	NPTf<RealIntegrator>* myNPTf = NULL;
1357	+	NPTim<RealIntegrator>* myNPTim = NULL;
1358	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1359	+
1360	+	for(k=0; k<nInfo; k++){
1361	+
1362	+	switch( ensembleCase ){
1363	+
1364	+	case NVE_ENS:
1365	+	if (globals->haveZconstraints()){
1366	+	setupZConstraint(info[k]);
1367	+	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1368	+	}
1369	+
1370	+	else
1371	+	new NVE<RealIntegrator>( &(info[k]), the_ff );
1372	+	break;
1373	+
1374	+	case NVT_ENS:
1375	+	if (globals->haveZconstraints()){
1376	+	setupZConstraint(info[k]);
1377	+	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	+	}
1379	+	else
1380	+	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1381	+
1382	+	myNVT->setTargetTemp(globals->getTargetTemp());
1383	+
1384	+	if (globals->haveTauThermostat())
1385	+	myNVT->setTauThermostat(globals->getTauThermostat());
1386	+
1387	+	else {
1388	+	sprintf( painCave.errMsg,
1389	+	"SimSetup error: If you use the NVT\n"
1390	+	"    ensemble, you must set tauThermostat.\n");
1391	+	painCave.isFatal = 1;
1392	+	simError();
1393	+	}
1394	+	break;
1395	+
1396	+	case NPTi_ENS:
1397	+	if (globals->haveZconstraints()){
1398	+	setupZConstraint(info[k]);
1399	+	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	+	}
1401	+	else
1402	+	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403	+
1404	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	+
1406	+	if (globals->haveTargetPressure())
1407	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	+	else {
1409	+	sprintf( painCave.errMsg,
1410	+	"SimSetup error: If you use a constant pressure\n"
1411	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	+	painCave.isFatal = 1;
1413	+	simError();
1414	+	}
1415	+
1416	+	if( globals->haveTauThermostat() )
1417	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	+	else{
1419	+	sprintf( painCave.errMsg,
1420	+	"SimSetup error: If you use an NPT\n"
1421	+	"    ensemble, you must set tauThermostat.\n");
1422	+	painCave.isFatal = 1;
1423	+	simError();
1424	+	}
1425	+
1426	+	if( globals->haveTauBarostat() )
1427	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	+	else{
1429	+	sprintf( painCave.errMsg,
1430	+	"SimSetup error: If you use an NPT\n"
1431	+	"    ensemble, you must set tauBarostat.\n");
1432	+	painCave.isFatal = 1;
1433	+	simError();
1434	+	}
1435	+	break;
1436	+
1437	+	case NPTf_ENS:
1438	+	if (globals->haveZconstraints()){
1439	+	setupZConstraint(info[k]);
1440	+	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	+	}
1442	+	else
1443	+	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1444	+
1445	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1446	+
1447	+	if (globals->haveTargetPressure())
1448	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	+	else {
1450	+	sprintf( painCave.errMsg,
1451	+	"SimSetup error: If you use a constant pressure\n"
1452	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	+	painCave.isFatal = 1;
1454	+	simError();
1455	+	}
1456	+
1457	+	if( globals->haveTauThermostat() )
1458	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	+	else{
1460	+	sprintf( painCave.errMsg,
1461	+	"SimSetup error: If you use an NPT\n"
1462	+	"    ensemble, you must set tauThermostat.\n");
1463	+	painCave.isFatal = 1;
1464	+	simError();
1465	+	}
1466	+
1467	+	if( globals->haveTauBarostat() )
1468	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	+	else{
1470	+	sprintf( painCave.errMsg,
1471	+	"SimSetup error: If you use an NPT\n"
1472	+	"    ensemble, you must set tauBarostat.\n");
1473	+	painCave.isFatal = 1;
1474	+	simError();
1475	+	}
1476	+	break;
1477	+
1478	+	case NPTim_ENS:
1479	+	if (globals->haveZconstraints()){
1480	+	setupZConstraint(info[k]);
1481	+	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	+	}
1483	+	else
1484	+	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1485	+
1486	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1487	+
1488	+	if (globals->haveTargetPressure())
1489	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	+	else {
1491	+	sprintf( painCave.errMsg,
1492	+	"SimSetup error: If you use a constant pressure\n"
1493	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	+	painCave.isFatal = 1;
1495	+	simError();
1496	+	}
1497	+
1498	+	if( globals->haveTauThermostat() )
1499	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	+	else{
1501	+	sprintf( painCave.errMsg,
1502	+	"SimSetup error: If you use an NPT\n"
1503	+	"    ensemble, you must set tauThermostat.\n");
1504	+	painCave.isFatal = 1;
1505	+	simError();
1506	+	}
1507	+
1508	+	if( globals->haveTauBarostat() )
1509	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	+	else{
1511	+	sprintf( painCave.errMsg,
1512	+	"SimSetup error: If you use an NPT\n"
1513	+	"    ensemble, you must set tauBarostat.\n");
1514	+	painCave.isFatal = 1;
1515	+	simError();
1516	+	}
1517	+	break;
1518	+
1519	+	case NPTfm_ENS:
1520	+	if (globals->haveZconstraints()){
1521	+	setupZConstraint(info[k]);
1522	+	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	+	}
1524	+	else
1525	+	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1526	+
1527	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1528	+
1529	+	if (globals->haveTargetPressure())
1530	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1531	+	else {
1532	+	sprintf( painCave.errMsg,
1533	+	"SimSetup error: If you use a constant pressure\n"
1534	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1535	+	painCave.isFatal = 1;
1536	+	simError();
1537	+	}
1538	+
1539	+	if( globals->haveTauThermostat() )
1540	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1541	+	else{
1542	+	sprintf( painCave.errMsg,
1543	+	"SimSetup error: If you use an NPT\n"
1544	+	"    ensemble, you must set tauThermostat.\n");
1545	+	painCave.isFatal = 1;
1546	+	simError();
1547	+	}
1548	+
1549	+	if( globals->haveTauBarostat() )
1550	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1551	+	else{
1552	+	sprintf( painCave.errMsg,
1553	+	"SimSetup error: If you use an NPT\n"
1554	+	"    ensemble, you must set tauBarostat.\n");
1555	+	painCave.isFatal = 1;
1556	+	simError();
1557	+	}
1558	+	break;
1559	+
1560	+	default:
1561	+	sprintf( painCave.errMsg,
1562	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1563	+	painCave.isFatal = 1;
1564	+	simError();
1565	+	}
1566	+	}
1567	+	}
1568	+
1569	+	void SimSetup::initFortran( void ){
1570	+
1571	+	info[0].refreshSim();
1572	+
1573	+	if( !strcmp( info[0].mixingRule, "standard") ){
1574	+	the_ff->initForceField( LB_MIXING_RULE );
1575	+	}
1576	+	else if( !strcmp( info[0].mixingRule, "explicit") ){
1577	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1578	+	}
1579	+	else{
1580	+	sprintf( painCave.errMsg,
1581	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	+	info[0].mixingRule );
1583	+	painCave.isFatal = 1;
1584	+	simError();
1585	+	}
1586	+
1587	+
1588	+	#ifdef IS_MPI
1589	+	strcpy( checkPointMsg,
1590	+	"Successfully intialized the mixingRule for Fortran." );
1591	+	MPIcheckPoint();
1592	+	#endif // is_mpi
1593	+
1594	+	}
1595	+
1596	+	void SimSetup::setupZConstraint(SimInfo& theInfo)
1597	+	{
1598	+	int nZConstraints;
1599	+	ZconStamp** zconStamp;
1600	+
1601	+	if(globals->haveZconstraintTime()){
1602	+
1603	+	//add sample time of z-constraint  into SimInfo's property list
1604	+	DoubleData* zconsTimeProp = new DoubleData();
1605	+	zconsTimeProp->setID(ZCONSTIME_ID);
1606	+	zconsTimeProp->setData(globals->getZconsTime());
1607	+	theInfo.addProperty(zconsTimeProp);
1608	+	}
1609	+	else{
1610	+	sprintf( painCave.errMsg,
1611	+	"ZConstraint error: If you use an ZConstraint\n"
1612	+	" , you must set sample time.\n");
1613	+	painCave.isFatal = 1;
1614	+	simError();
1615	+	}
1616	+
1617	+	//push zconsTol into siminfo, if user does not specify
1618	+	//value for zconsTol, a default value will be used
1619	+	DoubleData* zconsTol = new DoubleData();
1620	+	zconsTol->setID(ZCONSTOL_ID);
1621	+	if(globals->haveZconsTol()){
1622	+	zconsTol->setData(globals->getZconsTol());
1623	+	}
1624	+	else{
1625	+	double defaultZConsTol = 0.01;
1626	+	sprintf( painCave.errMsg,
1627	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628	+	" , default value %f is used.\n", defaultZConsTol);
1629	+	painCave.isFatal = 0;
1630	+	simError();
1631	+
1632	+	zconsTol->setData(defaultZConsTol);
1633	+	}
1634	+	theInfo.addProperty(zconsTol);
1635	+
1636	+	//set Force Substraction Policy
1637	+	StringData* zconsForcePolicy =  new StringData();
1638	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	+
1640	+	if(globals->haveZconsForcePolicy()){
1641	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	+	}
1643	+	else{
1644	+	sprintf( painCave.errMsg,
1645	+	"ZConstraint Warning: User does not set force substraction policy, "
1646	+	"average force substraction policy is used\n");
1647	+	painCave.isFatal = 0;
1648	+	simError();
1649	+	zconsForcePolicy->setData("BYNUMBER");
1650	+	}
1651	+
1652	+	theInfo.addProperty(zconsForcePolicy);
1653	+
1654	+	//Determine the name of ouput file and add it into SimInfo's property list
1655	+	//Be careful, do not use inFileName, since it is a pointer which
1656	+	//point to a string at master node, and slave nodes do not contain that string
1657	+
1658	+	string zconsOutput(theInfo.finalName);
1659	+
1660	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	+
1662	+	StringData* zconsFilename = new StringData();
1663	+	zconsFilename->setID(ZCONSFILENAME_ID);
1664	+	zconsFilename->setData(zconsOutput);
1665	+
1666	+	theInfo.addProperty(zconsFilename);
1667	+
1668	+	//setup index, pos and other parameters of z-constraint molecules
1669	+	nZConstraints = globals->getNzConstraints();
1670	+	theInfo.nZconstraints = nZConstraints;
1671	+
1672	+	zconStamp = globals->getZconStamp();
1673	+	ZConsParaItem tempParaItem;
1674	+
1675	+	ZConsParaData* zconsParaData = new ZConsParaData();
1676	+	zconsParaData->setID(ZCONSPARADATA_ID);
1677	+
1678	+	for(int i = 0; i < nZConstraints; i++){
1679	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1683	+
1684	+	zconsParaData->addItem(tempParaItem);
1685	+	}
1686	+
1687	+	//sort the parameters by index of molecules
1688	+	zconsParaData->sortByIndex();
1689	+
1690	+	//push data into siminfo, therefore, we can retrieve later
1691	+	theInfo.addProperty(zconsParaData);
1692	+
1693	+	}

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