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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC vs.
Revision 689 by tim, Tue Aug 12 19:56:49 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 14 | Line 17
17
18		// some defines for ensemble and Forcefield  cases
19
20	<	#define NVE_ENS 0
21	<	#define NVT_ENS 1
22	<	#define NPT_ENS 2
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 37 | 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 72 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
77	–	MakeStamps *the_stamps;
78	–	Globals* the_globals;
97		int i, j, k, globalAtomIndex;
98
99	<	int ensembleCase;
100	<	int ffCase;
99	>	// gather all of the information from the Bass file
100	>
101	>	std::cerr << "gathering info\n";
102	>
103	>	gatherInfo();
104	>
105	>	// creation of complex system objects
106	>
107	>	std::cerr << "creating system objects\n";
108	>
109	>	sysObjectsCreation();
110	>
111	>	// check on the post processing info
112
113	<	ensembleCase = -1;
85	<	ffCase = -1;
113	>	std::cerr << "performing final info check.\n";
114
115	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
115	>	finalInfoCheck();
116
117	<	// set the easy ones first
92	<	simnfo->target_temp = the_globals->getTargetTemp();
93	<	simnfo->dt = the_globals->getDt();
94	<	simnfo->run_time = the_globals->getRunTime();
117	>	// initialize the system coordinates
118
119	<	// get the ones we know are there, yet still may need some work.
120	<	n_components = the_globals->getNComponents();
121	<	strcpy( force_field, the_globals->getForceField() );
119	>	std::cerr << "about to init coords\n";
120	>
121	>	if( !isInfoArray ) initSystemCoords();
122	>
123	>	// make the output filenames
124	>
125	>	makeOutNames();
126	>
127	>	// make the integrator
128	>
129	>	makeIntegrator();
130	>
131	>	#ifdef IS_MPI
132	>	mpiSim->mpiRefresh();
133	>	#endif
134	>
135	>	// initialize the Fortran
136	>
137	>	initFortran();
138	>
139	>
140	>
141	>	}
142	>
143	>
144	>	void SimSetup::makeMolecules( void ){
145	>
146	>	int k,l;
147	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
148	>	molInit molInfo;
149	>	DirectionalAtom* dAtom;
150	>	LinkedAssign* extras;
151	>	LinkedAssign* current_extra;
152	>	AtomStamp* currentAtom;
153	>	BondStamp* currentBond;
154	>	BendStamp* currentBend;
155	>	TorsionStamp* currentTorsion;
156	>
157	>	bond_pair* theBonds;
158	>	bend_set* theBends;
159	>	torsion_set* theTorsions;
160	>
161	>
162	>	//init the forceField paramters
163	>
164	>	the_ff->readParams();
165	>
166	>
167	>	// init the atoms
168	>
169	>	double ux, uy, uz, u, uSqr;
170	>
171	>	for(k=0; k<nInfo; k++){
172	>
173	>	the_ff->setSimInfo( &(info[k]) );
174	>
175	>	atomOffset = 0;
176	>	excludeOffset = 0;
177	>	for(i=0; i<info[k].n_mol; i++){
178	>
179	>	stampID = info[k].molecules[i].getStampID();
180	>
181	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
182	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
183	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
184	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
185	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
186	>
187	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
188	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
189	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
190	>	molInfo.myBends = new Bend*[molInfo.nBends];
191	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
192	>
193	>	theBonds = new bond_pair[molInfo.nBonds];
194	>	theBends = new bend_set[molInfo.nBends];
195	>	theTorsions = new torsion_set[molInfo.nTorsions];
196	>
197	>	// make the Atoms
198	>
199	>	for(j=0; j<molInfo.nAtoms; j++){
200	>
201	>	currentAtom = comp_stamps[stampID]->getAtom( j );
202	>	if( currentAtom->haveOrientation() ){
203	>
204	>	dAtom = new DirectionalAtom( (j + atomOffset),
205	>	info[k].getConfiguration() );
206	>	info[k].n_oriented++;
207	>	molInfo.myAtoms[j] = dAtom;
208	>
209	>	ux = currentAtom->getOrntX();
210	>	uy = currentAtom->getOrntY();
211	>	uz = currentAtom->getOrntZ();
212	>
213	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
214	>
215	>	u = sqrt( uSqr );
216	>	ux = ux / u;
217	>	uy = uy / u;
218	>	uz = uz / u;
219	>
220	>	dAtom->setSUx( ux );
221	>	dAtom->setSUy( uy );
222	>	dAtom->setSUz( uz );
223	>	}
224	>	else{
225	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
226	>	info[k].getConfiguration() );
227	>	}
228	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
229	>
230	>	#ifdef IS_MPI
231	>
232	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
233	>
234	>	#endif // is_mpi
235	>	}
236	>
237	>	// make the bonds
238	>	for(j=0; j<molInfo.nBonds; j++){
239	>
240	>	currentBond = comp_stamps[stampID]->getBond( j );
241	>	theBonds[j].a = currentBond->getA() + atomOffset;
242	>	theBonds[j].b = currentBond->getB() + atomOffset;
243	>
244	>	exI = theBonds[j].a;
245	>	exJ = theBonds[j].b;
246	>
247	>	// exclude_I must always be the smaller of the pair
248	>	if( exI > exJ ){
249	>	tempEx = exI;
250	>	exI = exJ;
251	>	exJ = tempEx;
252	>	}
253	>	#ifdef IS_MPI
254	>	tempEx = exI;
255	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
256	>	tempEx = exJ;
257	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
258	>
259	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
260	>	#else  // isn't MPI
261	>
262	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
263	>	#endif  //is_mpi
264	>	}
265	>	excludeOffset += molInfo.nBonds;
266	>
267	>	//make the bends
268	>	for(j=0; j<molInfo.nBends; j++){
269	>
270	>	currentBend = comp_stamps[stampID]->getBend( j );
271	>	theBends[j].a = currentBend->getA() + atomOffset;
272	>	theBends[j].b = currentBend->getB() + atomOffset;
273	>	theBends[j].c = currentBend->getC() + atomOffset;
274	>
275	>	if( currentBend->haveExtras() ){
276	>
277	>	extras = currentBend->getExtras();
278	>	current_extra = extras;
279	>
280	>	while( current_extra != NULL ){
281	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
282	>
283	>	switch( current_extra->getType() ){
284	>
285	>	case 0:
286	>	theBends[j].ghost =
287	>	current_extra->getInt() + atomOffset;
288	>	theBends[j].isGhost = 1;
289	>	break;
290	>
291	>	case 1:
292	>	theBends[j].ghost =
293	>	(int)current_extra->getDouble() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296	>
297	>	default:
298	>	sprintf( painCave.errMsg,
299	>	"SimSetup Error: ghostVectorSource was neither a "
300	>	"double nor an int.\n"
301	>	"-->Bend[%d] in %s\n",
302	>	j, comp_stamps[stampID]->getID() );
303	>	painCave.isFatal = 1;
304	>	simError();
305	>	}
306	>	}
307	>
308	>	else{
309	>
310	>	sprintf( painCave.errMsg,
311	>	"SimSetup Error: unhandled bend assignment:\n"
312	>	"    -->%s in Bend[%d] in %s\n",
313	>	current_extra->getlhs(),
314	>	j, comp_stamps[stampID]->getID() );
315	>	painCave.isFatal = 1;
316	>	simError();
317	>	}
318	>
319	>	current_extra = current_extra->getNext();
320	>	}
321	>	}
322	>
323	>	if( !theBends[j].isGhost ){
324	>
325	>	exI = theBends[j].a;
326	>	exJ = theBends[j].c;
327	>	}
328	>	else{
329	>
330	>	exI = theBends[j].a;
331	>	exJ = theBends[j].b;
332	>	}
333	>
334	>	// exclude_I must always be the smaller of the pair
335	>	if( exI > exJ ){
336	>	tempEx = exI;
337	>	exI = exJ;
338	>	exJ = tempEx;
339	>	}
340	>	#ifdef IS_MPI
341	>	tempEx = exI;
342	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	>	tempEx = exJ;
344	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>
346	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
347	>	#else  // isn't MPI
348	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349	>	#endif  //is_mpi
350	>	}
351	>	excludeOffset += molInfo.nBends;
352	>
353	>	for(j=0; j<molInfo.nTorsions; j++){
354	>
355	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360	>
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363	>
364	>	// exclude_I must always be the smaller of the pair
365	>	if( exI > exJ ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370	>	#ifdef IS_MPI
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>
376	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
377	>	#else  // isn't MPI
378	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
379	>	#endif  //is_mpi
380	>	}
381	>	excludeOffset += molInfo.nTorsions;
382	>
383	>
384	>	// send the arrays off to the forceField for init.
385	>
386	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
387	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
388	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
389	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
390	>
391	>
392	>	info[k].molecules[i].initialize( molInfo );
393
394	+
395	+	atomOffset += molInfo.nAtoms;
396	+	delete[] theBonds;
397	+	delete[] theBends;
398	+	delete[] theTorsions;
399	+	}
400	+	}
401	+
402	+	#ifdef IS_MPI
403	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
404	+	MPIcheckPoint();
405	+	#endif // is_mpi
406	+
407	+	// clean up the forcefield
408	+
409	+	the_ff->calcRcut();
410	+	the_ff->cleanMe();
411	+
412	+	}
413	+
414	+	void SimSetup::initFromBass( void ){
415	+
416	+	int i, j, k;
417	+	int n_cells;
418	+	double cellx, celly, cellz;
419	+	double temp1, temp2, temp3;
420	+	int n_per_extra;
421	+	int n_extra;
422	+	int have_extra, done;
423	+
424	+	double vel[3];
425	+	vel[0] = 0.0;
426	+	vel[1] = 0.0;
427	+	vel[2] = 0.0;
428	+
429	+	temp1 = (double)tot_nmol / 4.0;
430	+	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
431	+	temp3 = ceil( temp2 );
432	+
433	+	have_extra =0;
434	+	if( temp2 < temp3 ){ // we have a non-complete lattice
435	+	have_extra =1;
436	+
437	+	n_cells = (int)temp3 - 1;
438	+	cellx = info[0].boxL[0] / temp3;
439	+	celly = info[0].boxL[1] / temp3;
440	+	cellz = info[0].boxL[2] / temp3;
441	+	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
442	+	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
443	+	n_per_extra = (int)ceil( temp1 );
444	+
445	+	if( n_per_extra > 4){
446	+	sprintf( painCave.errMsg,
447	+	"SimSetup error. There has been an error in constructing"
448	+	" the non-complete lattice.\n" );
449	+	painCave.isFatal = 1;
450	+	simError();
451	+	}
452	+	}
453	+	else{
454	+	n_cells = (int)temp3;
455	+	cellx = info[0].boxL[0] / temp3;
456	+	celly = info[0].boxL[1] / temp3;
457	+	cellz = info[0].boxL[2] / temp3;
458	+	}
459	+
460	+	current_mol = 0;
461	+	current_comp_mol = 0;
462	+	current_comp = 0;
463	+	current_atom_ndx = 0;
464	+
465	+	for( i=0; i < n_cells ; i++ ){
466	+	for( j=0; j < n_cells; j++ ){
467	+	for( k=0; k < n_cells; k++ ){
468	+
469	+	makeElement( i * cellx,
470	+	j * celly,
471	+	k * cellz );
472	+
473	+	makeElement( i * cellx + 0.5 * cellx,
474	+	j * celly + 0.5 * celly,
475	+	k * cellz );
476	+
477	+	makeElement( i * cellx,
478	+	j * celly + 0.5 * celly,
479	+	k * cellz + 0.5 * cellz );
480	+
481	+	makeElement( i * cellx + 0.5 * cellx,
482	+	j * celly,
483	+	k * cellz + 0.5 * cellz );
484	+	}
485	+	}
486	+	}
487	+
488	+	if( have_extra ){
489	+	done = 0;
490	+
491	+	int start_ndx;
492	+	for( i=0; i < (n_cells+1) && !done; i++ ){
493	+	for( j=0; j < (n_cells+1) && !done; j++ ){
494	+
495	+	if( i < n_cells ){
496	+
497	+	if( j < n_cells ){
498	+	start_ndx = n_cells;
499	+	}
500	+	else start_ndx = 0;
501	+	}
502	+	else start_ndx = 0;
503	+
504	+	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
505	+
506	+	makeElement( i * cellx,
507	+	j * celly,
508	+	k * cellz );
509	+	done = ( current_mol >= tot_nmol );
510	+
511	+	if( !done && n_per_extra > 1 ){
512	+	makeElement( i * cellx + 0.5 * cellx,
513	+	j * celly + 0.5 * celly,
514	+	k * cellz );
515	+	done = ( current_mol >= tot_nmol );
516	+	}
517	+
518	+	if( !done && n_per_extra > 2){
519	+	makeElement( i * cellx,
520	+	j * celly + 0.5 * celly,
521	+	k * cellz + 0.5 * cellz );
522	+	done = ( current_mol >= tot_nmol );
523	+	}
524	+
525	+	if( !done && n_per_extra > 3){
526	+	makeElement( i * cellx + 0.5 * cellx,
527	+	j * celly,
528	+	k * cellz + 0.5 * cellz );
529	+	done = ( current_mol >= tot_nmol );
530	+	}
531	+	}
532	+	}
533	+	}
534	+	}
535	+
536	+	for( i=0; i<info[0].n_atoms; i++ ){
537	+	info[0].atoms[i]->setVel( vel );
538	+	}
539	+	}
540	+
541	+	void SimSetup::makeElement( double x, double y, double z ){
542	+
543	+	int k;
544	+	AtomStamp* current_atom;
545	+	DirectionalAtom* dAtom;
546	+	double rotMat[3][3];
547	+	double pos[3];
548	+
549	+	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
550	+
551	+	current_atom = comp_stamps[current_comp]->getAtom( k );
552	+	if( !current_atom->havePosition() ){
553	+	sprintf( painCave.errMsg,
554	+	"SimSetup:initFromBass error.\n"
555	+	"\tComponent %s, atom %s does not have a position specified.\n"
556	+	"\tThe initialization routine is unable to give a start"
557	+	" position.\n",
558	+	comp_stamps[current_comp]->getID(),
559	+	current_atom->getType() );
560	+	painCave.isFatal = 1;
561	+	simError();
562	+	}
563	+
564	+	pos[0] = x + current_atom->getPosX();
565	+	pos[1] = y + current_atom->getPosY();
566	+	pos[2] = z + current_atom->getPosZ();
567	+
568	+	info[0].atoms[current_atom_ndx]->setPos( pos );
569	+
570	+	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
571	+
572	+	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
573	+
574	+	rotMat[0][0] = 1.0;
575	+	rotMat[0][1] = 0.0;
576	+	rotMat[0][2] = 0.0;
577	+
578	+	rotMat[1][0] = 0.0;
579	+	rotMat[1][1] = 1.0;
580	+	rotMat[1][2] = 0.0;
581	+
582	+	rotMat[2][0] = 0.0;
583	+	rotMat[2][1] = 0.0;
584	+	rotMat[2][2] = 1.0;
585	+
586	+	dAtom->setA( rotMat );
587	+	}
588	+
589	+	current_atom_ndx++;
590	+	}
591	+
592	+	current_mol++;
593	+	current_comp_mol++;
594	+
595	+	if( current_comp_mol >= components_nmol[current_comp] ){
596	+
597	+	current_comp_mol = 0;
598	+	current_comp++;
599	+	}
600	+	}
601	+
602	+
603	+	void SimSetup::gatherInfo( void ){
604	+	int i,j,k;
605	+
606	+	ensembleCase = -1;
607	+	ffCase = -1;
608	+
609	+	// set the easy ones first
610	+
611	+	for( i=0; i<nInfo; i++){
612	+	info[i].target_temp = globals->getTargetTemp();
613	+	info[i].dt = globals->getDt();
614	+	info[i].run_time = globals->getRunTime();
615	+	}
616	+	n_components = globals->getNComponents();
617	+
618	+
619	+	// get the forceField
620	+
621	+	strcpy( force_field, globals->getForceField() );
622	+
623		if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
624		else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
625	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
626		else{
627		sprintf( painCave.errMsg,
628		"SimSetup Error. Unrecognized force field -> %s\n",
#	Line 107 | Line 631 | void SimSetup::createSim( void ){
631		simError();
632		}
633
634	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
634	>	// get the ensemble
635
636	+	strcpy( ensemble, globals->getEnsemble() );
637	+
638		if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
639		else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
640	<	else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS;
640	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
641	>	ensembleCase = NPTi_ENS;
642	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
643	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
644	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
645		else{
646		sprintf( painCave.errMsg,
647		"SimSetup Warning. Unrecognized Ensemble -> %s, "
#	Line 123 | Line 652 | void SimSetup::createSim( void ){
652		strcpy( ensemble, "NVE" );
653		ensembleCase = NVE_ENS;
654		}
655	<	strcpy( simnfo->ensemble, ensemble );
655	>
656	>	for(i=0; i<nInfo; i++){
657	>
658	>	strcpy( info[i].ensemble, ensemble );
659
660	+	// get the mixing rule
661
662	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
663	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
131	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132	<	//     if (the_globals->haveTargetPressure())
133	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134	<	//     else {
135	<	//       sprintf( painCave.errMsg,
136	<	//                "SimSetup error: If you use the constant pressure\n"
137	<	//                "    ensemble, you must set targetPressure.\n"
138	<	//                "    This was found in the BASS file.\n");
139	<	//       painCave.isFatal = 1;
140	<	//       simError();
141	<	//     }
142	<
143	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
155	<
156	<	//     if (the_globals->haveTauBarostat())
157	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158	<	//     else {
159	<	//       sprintf( painCave.errMsg,
160	<	//                "SimSetup error: If you use the constant pressure\n"
161	<	//                "    ensemble, you must set tauBarostat.\n"
162	<	//                "    This was found in the BASS file.\n");
163	<	//       painCave.isFatal = 1;
164	<	//       simError();
165	<	//     }
166	<
167	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
168	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
169	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
170	<
171	<	//     if (the_globals->haveTauThermostat())
172	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173	<	//     else if (the_globals->haveQmass())
174	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
175	<	//     else {
176	<	//       sprintf( painCave.errMsg,
177	<	//                "SimSetup error: If you use one of the constant temperature\n"
178	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
179	<	//                "    Neither of these was found in the BASS file.\n");
180	<	//       painCave.isFatal = 1;
181	<	//       simError();
182	<	//     }
183	<
184	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185	<	simnfo->usePBC = the_globals->getPBC();
186	<
187	<	int usesDipoles = 0;
188	<	switch( ffCase ){
189	<
190	<	case FF_DUFF:
191	<	the_ff = new DUFF();
192	<	usesDipoles = 1;
193	<	break;
194	<
195	<	case FF_LJ:
196	<	the_ff = new LJFF();
197	<	break;
198	<
199	<	default:
200	<	sprintf( painCave.errMsg,
201	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
662	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
663	>	info[i].usePBC = globals->getPBC();
664		}
665	<
206	<	#ifdef IS_MPI
207	<	strcpy( checkPointMsg, "ForceField creation successful" );
208	<	MPIcheckPoint();
209	<	#endif // is_mpi
210	<
665	>
666		// get the components and calculate the tot_nMol and indvidual n_mol
667	<	the_components = the_globals->getComponents();
667	>
668	>	the_components = globals->getComponents();
669		components_nmol = new int[n_components];
214	–	comp_stamps = new MoleculeStamp*[n_components];
670
671	<	if( !the_globals->haveNMol() ){
671	>
672	>	if( !globals->haveNMol() ){
673		// we don't have the total number of molecules, so we assume it is
674		// given in each component
675
#	Line 242 | Line 698 | void SimSetup::createSim( void ){
698		" Please give nMol in the components.\n" );
699		painCave.isFatal = 1;
700		simError();
245	–
246	–
247	–	//     tot_nmol = the_globals->getNMol();
248	–
249	–	//   //we have the total number of molecules, now we check for molfractions
250	–	//     for( i=0; i<n_components; i++ ){
251	–
252	–	//       if( !the_components[i]->haveMolFraction() ){
253	–
254	–	//  if( !the_components[i]->haveNMol() ){
255	–	//    //we have a problem
256	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	–	//              << " nMol was given in component
258	–
259	–	}
260	–
261	–	#ifdef IS_MPI
262	–	strcpy( checkPointMsg, "Have the number of components" );
263	–	MPIcheckPoint();
264	–	#endif // is_mpi
265	–
266	–	// make an array of molecule stamps that match the components used.
267	–	// also extract the used stamps out into a separate linked list
268	–
269	–	simnfo->nComponents = n_components;
270	–	simnfo->componentsNmol = components_nmol;
271	–	simnfo->compStamps = comp_stamps;
272	–	simnfo->headStamp = new LinkedMolStamp();
273	–
274	–	char* id;
275	–	LinkedMolStamp* headStamp = simnfo->headStamp;
276	–	LinkedMolStamp* currentStamp = NULL;
277	–	for( i=0; i<n_components; i++ ){
278	–
279	–	id = the_components[i]->getType();
280	–	comp_stamps[i] = NULL;
281	–
282	–	// check to make sure the component isn't already in the list
283	–
284	–	comp_stamps[i] = headStamp->match( id );
285	–	if( comp_stamps[i] == NULL ){
286	–
287	–	// extract the component from the list;
288	–
289	–	currentStamp = the_stamps->extractMolStamp( id );
290	–	if( currentStamp == NULL ){
291	–	sprintf( painCave.errMsg,
292	–	"SimSetup error: Component \"%s\" was not found in the "
293	–	"list of declared molecules\n",
294	–	id );
295	–	painCave.isFatal = 1;
296	–	simError();
297	–	}
298	–
299	–	headStamp->add( currentStamp );
300	–	comp_stamps[i] = headStamp->match( id );
301	–	}
302	–	}
303	–
304	–	#ifdef IS_MPI
305	–	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
306	–	MPIcheckPoint();
307	–	#endif // is_mpi
308	–
309	–
310	–
311	–
312	–	// caclulate the number of atoms, bonds, bends and torsions
313	–
314	–	tot_atoms = 0;
315	–	tot_bonds = 0;
316	–	tot_bends = 0;
317	–	tot_torsions = 0;
318	–	for( i=0; i<n_components; i++ ){
319	–
320	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	–	}
325	–
326	–	tot_SRI = tot_bonds + tot_bends + tot_torsions;
327	–
328	–	simnfo->n_atoms = tot_atoms;
329	–	simnfo->n_bonds = tot_bonds;
330	–	simnfo->n_bends = tot_bends;
331	–	simnfo->n_torsions = tot_torsions;
332	–	simnfo->n_SRI = tot_SRI;
333	–	simnfo->n_mol = tot_nmol;
334	–
335	–	simnfo->molMembershipArray = new int[tot_atoms];
336	–
337	–	#ifdef IS_MPI
338	–
339	–	// divide the molecules among processors here.
340	–
341	–	mpiSim = new mpiSimulation( simnfo );
342	–
343	–	globalIndex = mpiSim->divideLabor();
344	–
345	–	// set up the local variables
346	–
347	–	int localMol, allMol;
348	–	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
349	–
350	–	int* mol2proc = mpiSim->getMolToProcMap();
351	–	int* molCompType = mpiSim->getMolComponentType();
352	–
353	–	allMol = 0;
354	–	localMol = 0;
355	–	local_atoms = 0;
356	–	local_bonds = 0;
357	–	local_bends = 0;
358	–	local_torsions = 0;
359	–	globalAtomIndex = 0;
360	–
361	–
362	–	for( i=0; i<n_components; i++ ){
363	–
364	–	for( j=0; j<components_nmol[i]; j++ ){
365	–
366	–	if( mol2proc[allMol] == worldRank ){
367	–
368	–	local_atoms +=    comp_stamps[i]->getNAtoms();
369	–	local_bonds +=    comp_stamps[i]->getNBonds();
370	–	local_bends +=    comp_stamps[i]->getNBends();
371	–	local_torsions += comp_stamps[i]->getNTorsions();
372	–	localMol++;
373	–	}
374	–	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	–	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	–	globalAtomIndex++;
377	–	}
378	–
379	–	allMol++;
380	–	}
381	–	}
382	–	local_SRI = local_bonds + local_bends + local_torsions;
383	–
384	–	simnfo->n_atoms = mpiSim->getMyNlocal();
385	–
386	–	if( local_atoms != simnfo->n_atoms ){
387	–	sprintf( painCave.errMsg,
388	–	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	–	" localAtom (%d) are not equal.\n",
390	–	simnfo->n_atoms,
391	–	local_atoms );
392	–	painCave.isFatal = 1;
393	–	simError();
394	–	}
395	–
396	–	simnfo->n_bonds = local_bonds;
397	–	simnfo->n_bends = local_bends;
398	–	simnfo->n_torsions = local_torsions;
399	–	simnfo->n_SRI = local_SRI;
400	–	simnfo->n_mol = localMol;
401	–
402	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
403	–	MPIcheckPoint();
404	–
405	–
406	–	#endif // is_mpi
407	–
408	–
409	–	// create the atom and short range interaction arrays
410	–
411	–	Atom::createArrays(simnfo->n_atoms);
412	–	the_atoms = new Atom*[simnfo->n_atoms];
413	–	the_molecules = new Molecule[simnfo->n_mol];
414	–	int molIndex;
415	–
416	–	// initialize the molecule's stampID's
417	–
418	–	#ifdef IS_MPI
419	–
420	–
421	–	molIndex = 0;
422	–	for(i=0; i<mpiSim->getTotNmol(); i++){
423	–
424	–	if(mol2proc[i] == worldRank ){
425	–	the_molecules[molIndex].setStampID( molCompType[i] );
426	–	the_molecules[molIndex].setMyIndex( molIndex );
427	–	the_molecules[molIndex].setGlobalIndex( i );
428	–	molIndex++;
429	–	}
701		}
702
703	<	#else // is_mpi
703	>	// set the status, sample, and thermal kick times
704
705	<	molIndex = 0;
435	<	globalAtomIndex = 0;
436	<	for(i=0; i<n_components; i++){
437	<	for(j=0; j<components_nmol[i]; j++ ){
438	<	the_molecules[molIndex].setStampID( i );
439	<	the_molecules[molIndex].setMyIndex( molIndex );
440	<	the_molecules[molIndex].setGlobalIndex( molIndex );
441	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443	<	globalAtomIndex++;
444	<	}
445	<	molIndex++;
446	<	}
447	<	}
448	<
705	>	for(i=0; i<nInfo; i++){
706
707	<	#endif // is_mpi
708	<
709	<
710	<	if( simnfo->n_SRI ){
454	<
455	<	Exclude::createArray(simnfo->n_SRI);
456	<	the_excludes = new Exclude*[simnfo->n_SRI];
457	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
458	<	simnfo->globalExcludes = new int;
459	<	simnfo->n_exclude = simnfo->n_SRI;
460	<	}
461	<	else{
462	<
463	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
471	<
472	<	// set the arrays into the SimInfo object
473	<
474	<	simnfo->atoms = the_atoms;
475	<	simnfo->molecules = the_molecules;
476	<	simnfo->nGlobalExcludes = 0;
477	<	simnfo->excludes = the_excludes;
478	<
479	<
480	<	// get some of the tricky things that may still be in the globals
481	<
482	<	double boxVector[3];
483	<	if( the_globals->haveBox() ){
484	<	boxVector[0] = the_globals->getBox();
485	<	boxVector[1] = the_globals->getBox();
486	<	boxVector[2] = the_globals->getBox();
487	<
488	<	simnfo->setBox( boxVector );
489	<	}
490	<	else if( the_globals->haveDensity() ){
491	<
492	<	double vol;
493	<	vol = (double)tot_nmol / the_globals->getDensity();
494	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
495	<	boxVector[1] = boxVector[0];
496	<	boxVector[2] = boxVector[0];
497	<
498	<	simnfo->setBox( boxVector );
499	<	}
500	<	else{
501	<	if( !the_globals->haveBoxX() ){
502	<	sprintf( painCave.errMsg,
503	<	"SimSetup error, no periodic BoxX size given.\n" );
504	<	painCave.isFatal = 1;
505	<	simError();
707	>	if( globals->haveSampleTime() ){
708	>	info[i].sampleTime = globals->getSampleTime();
709	>	info[i].statusTime = info[i].sampleTime;
710	>	info[i].thermalTime = info[i].sampleTime;
711		}
507	–	boxVector[0] = the_globals->getBoxX();
508	–
509	–	if( !the_globals->haveBoxY() ){
510	–	sprintf( painCave.errMsg,
511	–	"SimSetup error, no periodic BoxY size given.\n" );
512	–	painCave.isFatal = 1;
513	–	simError();
514	–	}
515	–	boxVector[1] = the_globals->getBoxY();
516	–
517	–	if( !the_globals->haveBoxZ() ){
518	–	sprintf( painCave.errMsg,
519	–	"SimSetup error, no periodic BoxZ size given.\n" );
520	–	painCave.isFatal = 1;
521	–	simError();
522	–	}
523	–	boxVector[2] = the_globals->getBoxZ();
524	–
525	–	simnfo->setBox( boxVector );
526	–	}
527	–
528	–	#ifdef IS_MPI
529	–	strcpy( checkPointMsg, "Box size set up" );
530	–	MPIcheckPoint();
531	–	#endif // is_mpi
532	–
533	–
534	–	// initialize the arrays
535	–
536	–	the_ff->setSimInfo( simnfo );
537	–
538	–	makeMolecules();
539	–	simnfo->identArray = new int[simnfo->n_atoms];
540	–	for(i=0; i<simnfo->n_atoms; i++){
541	–	simnfo->identArray[i] = the_atoms[i]->getIdent();
542	–	}
543	–
544	–	if (the_globals->getUseRF() ) {
545	–	simnfo->useReactionField = 1;
546	–
547	–	if( !the_globals->haveECR() ){
548	–	sprintf( painCave.errMsg,
549	–	"SimSetup Warning: using default value of 1/2 the smallest "
550	–	"box length for the electrostaticCutoffRadius.\n"
551	–	"I hope you have a very fast processor!\n");
552	–	painCave.isFatal = 0;
553	–	simError();
554	–	double smallest;
555	–	smallest = simnfo->boxLx;
556	–	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
557	–	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
558	–	simnfo->ecr = 0.5 * smallest;
559	–	} else {
560	–	simnfo->ecr        = the_globals->getECR();
561	–	}
562	–
563	–	if( !the_globals->haveEST() ){
564	–	sprintf( painCave.errMsg,
565	–	"SimSetup Warning: using default value of 0.05 * the "
566	–	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
567	–	);
568	–	painCave.isFatal = 0;
569	–	simError();
570	–	simnfo->est = 0.05 * simnfo->ecr;
571	–	} else {
572	–	simnfo->est        = the_globals->getEST();
573	–	}
574	–
575	–	if(!the_globals->haveDielectric() ){
576	–	sprintf( painCave.errMsg,
577	–	"SimSetup Error: You are trying to use Reaction Field without"
578	–	"setting a dielectric constant!\n"
579	–	);
580	–	painCave.isFatal = 1;
581	–	simError();
582	–	}
583	–	simnfo->dielectric = the_globals->getDielectric();
584	–	} else {
585	–	if (usesDipoles) {
586	–
587	–	if( !the_globals->haveECR() ){
588	–	sprintf( painCave.errMsg,
589	–	"SimSetup Warning: using default value of 1/2 the smallest "
590	–	"box length for the electrostaticCutoffRadius.\n"
591	–	"I hope you have a very fast processor!\n");
592	–	painCave.isFatal = 0;
593	–	simError();
594	–	double smallest;
595	–	smallest = simnfo->boxLx;
596	–	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
597	–	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
598	–	simnfo->ecr = 0.5 * smallest;
599	–	} else {
600	–	simnfo->ecr        = the_globals->getECR();
601	–	}
602	–
603	–	if( !the_globals->haveEST() ){
604	–	sprintf( painCave.errMsg,
605	–	"SimSetup Warning: using default value of 5%% of the "
606	–	"electrostaticCutoffRadius for the "
607	–	"electrostaticSkinThickness\n"
608	–	);
609	–	painCave.isFatal = 0;
610	–	simError();
611	–	simnfo->est = 0.05 * simnfo->ecr;
612	–	} else {
613	–	simnfo->est        = the_globals->getEST();
614	–	}
615	–	}
616	–	}
617	–
618	–	#ifdef IS_MPI
619	–	strcpy( checkPointMsg, "electrostatic parameters check out" );
620	–	MPIcheckPoint();
621	–	#endif // is_mpi
622	–
623	–	if( the_globals->haveInitialConfig() ){
624	–
625	–	InitializeFromFile* fileInit;
626	–	#ifdef IS_MPI // is_mpi
627	–	if( worldRank == 0 ){
628	–	#endif //is_mpi
629	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
630	–	#ifdef IS_MPI
631	–	}else fileInit = new InitializeFromFile( NULL );
632	–	#endif
633	–	fileInit->read_xyz( simnfo ); // default velocities on
634	–
635	–	delete fileInit;
636	–	}
637	–	else{
638	–
639	–	#ifdef IS_MPI
640	–
641	–	// no init from bass
642	–
643	–	sprintf( painCave.errMsg,
644	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
645	–	painCave.isFatal;
646	–	simError();
647	–
648	–	#else
649	–
650	–	initFromBass();
651	–
652	–
653	–	#endif
654	–	}
655	–
656	–	#ifdef IS_MPI
657	–	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
658	–	MPIcheckPoint();
659	–	#endif // is_mpi
660	–
661	–
662	–
663	–
664	–
665	–
666	–
667	–	#ifdef IS_MPI
668	–	if( worldRank == 0 ){
669	–	#endif // is_mpi
670	–
671	–	if( the_globals->haveFinalConfig() ){
672	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
673	–	}
712		else{
713	<	strcpy( simnfo->finalName, inFileName );
714	<	char* endTest;
715	<	int nameLength = strlen( simnfo->finalName );
716	<	endTest = &(simnfo->finalName[nameLength - 5]);
717	<	if( !strcmp( endTest, ".bass" ) ){
718	<	strcpy( endTest, ".eor" );
713	>	info[i].sampleTime = globals->getRunTime();
714	>	info[i].statusTime = info[i].sampleTime;
715	>	info[i].thermalTime = info[i].sampleTime;
716	>	}
717	>
718	>	if( globals->haveStatusTime() ){
719	>	info[i].statusTime = globals->getStatusTime();
720	>	}
721	>
722	>	if( globals->haveThermalTime() ){
723	>	info[i].thermalTime = globals->getThermalTime();
724	>	}
725	>
726	>	// check for the temperature set flag
727	>
728	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
729	>
730	>	// get some of the tricky things that may still be in the globals
731	>
732	>	double boxVector[3];
733	>	if( globals->haveBox() ){
734	>	boxVector[0] = globals->getBox();
735	>	boxVector[1] = globals->getBox();
736	>	boxVector[2] = globals->getBox();
737	>
738	>	info[i].setBox( boxVector );
739	>	}
740	>	else if( globals->haveDensity() ){
741	>
742	>	double vol;
743	>	vol = (double)tot_nmol / globals->getDensity();
744	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
745	>	boxVector[1] = boxVector[0];
746	>	boxVector[2] = boxVector[0];
747	>
748	>	info[i].setBox( boxVector );
749	>	}
750	>	else{
751	>	if( !globals->haveBoxX() ){
752	>	sprintf( painCave.errMsg,
753	>	"SimSetup error, no periodic BoxX size given.\n" );
754	>	painCave.isFatal = 1;
755	>	simError();
756		}
757	<	else if( !strcmp( endTest, ".BASS" ) ){
758	<	strcpy( endTest, ".eor" );
757	>	boxVector[0] = globals->getBoxX();
758	>
759	>	if( !globals->haveBoxY() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxY size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764		}
765	+	boxVector[1] = globals->getBoxY();
766	+
767	+	if( !globals->haveBoxZ() ){
768	+	sprintf( painCave.errMsg,
769	+	"SimSetup error, no periodic BoxZ size given.\n" );
770	+	painCave.isFatal = 1;
771	+	simError();
772	+	}
773	+	boxVector[2] = globals->getBoxZ();
774	+
775	+	info[i].setBox( boxVector );
776	+	}
777	+
778	+	}
779	+
780	+	#ifdef IS_MPI
781	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
782	+	MPIcheckPoint();
783	+	#endif // is_mpi
784	+
785	+	}
786	+
787	+
788	+	void SimSetup::finalInfoCheck( void ){
789	+	int index;
790	+	int usesDipoles;
791	+	int i;
792	+
793	+	for(i=0; i<nInfo; i++){
794	+	// check electrostatic parameters
795	+
796	+	index = 0;
797	+	usesDipoles = 0;
798	+	while( (index < info[i].n_atoms) && !usesDipoles ){
799	+	usesDipoles = (info[i].atoms[index])->hasDipole();
800	+	index++;
801	+	}
802	+
803	+	#ifdef IS_MPI
804	+	int myUse = usesDipoles;
805	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
806	+	#endif //is_mpi
807	+
808	+	double theEcr, theEst;
809	+
810	+	if (globals->getUseRF() ) {
811	+	info[i].useReactionField = 1;
812	+
813	+	if( !globals->haveECR() ){
814	+	sprintf( painCave.errMsg,
815	+	"SimSetup Warning: using default value of 1/2 the smallest "
816	+	"box length for the electrostaticCutoffRadius.\n"
817	+	"I hope you have a very fast processor!\n");
818	+	painCave.isFatal = 0;
819	+	simError();
820	+	double smallest;
821	+	smallest = info[i].boxL[0];
822	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
823	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
824	+	theEcr = 0.5 * smallest;
825	+	} else {
826	+	theEcr = globals->getECR();
827	+	}
828	+
829	+	if( !globals->haveEST() ){
830	+	sprintf( painCave.errMsg,
831	+	"SimSetup Warning: using default value of 0.05 * the "
832	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
833	+	);
834	+	painCave.isFatal = 0;
835	+	simError();
836	+	theEst = 0.05 * theEcr;
837	+	} else {
838	+	theEst= globals->getEST();
839	+	}
840	+
841	+	info[i].setEcr( theEcr, theEst );
842	+
843	+	if(!globals->haveDielectric() ){
844	+	sprintf( painCave.errMsg,
845	+	"SimSetup Error: You are trying to use Reaction Field without"
846	+	"setting a dielectric constant!\n"
847	+	);
848	+	painCave.isFatal = 1;
849	+	simError();
850	+	}
851	+	info[i].dielectric = globals->getDielectric();
852	+	}
853	+	else {
854	+	if (usesDipoles) {
855	+
856	+	if( !globals->haveECR() ){
857	+	sprintf( painCave.errMsg,
858	+	"SimSetup Warning: using default value of 1/2 the smallest "
859	+	"box length for the electrostaticCutoffRadius.\n"
860	+	"I hope you have a very fast processor!\n");
861	+	painCave.isFatal = 0;
862	+	simError();
863	+	double smallest;
864	+	smallest = info[i].boxL[0];
865	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
866	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
867	+	theEcr = 0.5 * smallest;
868	+	} else {
869	+	theEcr = globals->getECR();
870	+	}
871	+
872	+	if( !globals->haveEST() ){
873	+	sprintf( painCave.errMsg,
874	+	"SimSetup Warning: using default value of 0.05 * the "
875	+	"electrostaticCutoffRadius for the "
876	+	"electrostaticSkinThickness\n"
877	+	);
878	+	painCave.isFatal = 0;
879	+	simError();
880	+	theEst = 0.05 * theEcr;
881	+	} else {
882	+	theEst= globals->getEST();
883	+	}
884	+
885	+	info[i].setEcr( theEcr, theEst );
886	+	}
887	+	}
888	+	}
889	+
890	+	#ifdef IS_MPI
891	+	strcpy( checkPointMsg, "post processing checks out" );
892	+	MPIcheckPoint();
893	+	#endif // is_mpi
894	+
895	+	}
896	+
897	+	void SimSetup::initSystemCoords( void ){
898	+	int i;
899	+
900	+	char* inName;
901	+
902	+	std::cerr << "Setting atom Coords\n";
903	+
904	+	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
905	+
906	+	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
907	+
908	+	if( globals->haveInitialConfig() ){
909	+
910	+	InitializeFromFile* fileInit;
911	+	#ifdef IS_MPI // is_mpi
912	+	if( worldRank == 0 ){
913	+	#endif //is_mpi
914	+	inName = globals->getInitialConfig();
915	+	fileInit = new InitializeFromFile( inName );
916	+	#ifdef IS_MPI
917	+	}else fileInit = new InitializeFromFile( NULL );
918	+	#endif
919	+	fileInit->readInit( info ); // default velocities on
920	+
921	+	delete fileInit;
922	+	}
923	+	else{
924	+
925	+	#ifdef IS_MPI
926	+
927	+	// no init from bass
928	+
929	+	sprintf( painCave.errMsg,
930	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
931	+	painCave.isFatal;
932	+	simError();
933	+
934	+	#else
935	+
936	+	initFromBass();
937	+
938	+
939	+	#endif
940	+	}
941	+
942	+	#ifdef IS_MPI
943	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
944	+	MPIcheckPoint();
945	+	#endif // is_mpi
946	+
947	+	}
948	+
949	+
950	+	void SimSetup::makeOutNames( void ){
951	+
952	+	int k;
953	+
954	+
955	+	for(k=0; k<nInfo; k++){
956	+
957	+	#ifdef IS_MPI
958	+	if( worldRank == 0 ){
959	+	#endif // is_mpi
960	+
961	+	if( globals->haveFinalConfig() ){
962	+	strcpy( info[k].finalName, globals->getFinalConfig() );
963	+	}
964		else{
965	<	endTest = &(simnfo->finalName[nameLength - 4]);
966	<	if( !strcmp( endTest, ".bss" ) ){
965	>	strcpy( info[k].finalName, inFileName );
966	>	char* endTest;
967	>	int nameLength = strlen( info[k].finalName );
968	>	endTest = &(info[k].finalName[nameLength - 5]);
969	>	if( !strcmp( endTest, ".bass" ) ){
970		strcpy( endTest, ".eor" );
971		}
972	<	else if( !strcmp( endTest, ".mdl" ) ){
972	>	else if( !strcmp( endTest, ".BASS" ) ){
973		strcpy( endTest, ".eor" );
974		}
975		else{
976	<	strcat( simnfo->finalName, ".eor" );
976	>	endTest = &(info[k].finalName[nameLength - 4]);
977	>	if( !strcmp( endTest, ".bss" ) ){
978	>	strcpy( endTest, ".eor" );
979	>	}
980	>	else if( !strcmp( endTest, ".mdl" ) ){
981	>	strcpy( endTest, ".eor" );
982	>	}
983	>	else{
984	>	strcat( info[k].finalName, ".eor" );
985	>	}
986		}
987		}
988	<	}
989	<
990	<	// make the sample and status out names
991	<
992	<	strcpy( simnfo->sampleName, inFileName );
993	<	char* endTest;
994	<	int nameLength = strlen( simnfo->sampleName );
995	<	endTest = &(simnfo->sampleName[nameLength - 5]);
705	<	if( !strcmp( endTest, ".bass" ) ){
706	<	strcpy( endTest, ".dump" );
707	<	}
708	<	else if( !strcmp( endTest, ".BASS" ) ){
709	<	strcpy( endTest, ".dump" );
710	<	}
711	<	else{
712	<	endTest = &(simnfo->sampleName[nameLength - 4]);
713	<	if( !strcmp( endTest, ".bss" ) ){
988	>
989	>	// make the sample and status out names
990	>
991	>	strcpy( info[k].sampleName, inFileName );
992	>	char* endTest;
993	>	int nameLength = strlen( info[k].sampleName );
994	>	endTest = &(info[k].sampleName[nameLength - 5]);
995	>	if( !strcmp( endTest, ".bass" ) ){
996		strcpy( endTest, ".dump" );
997		}
998	<	else if( !strcmp( endTest, ".mdl" ) ){
998	>	else if( !strcmp( endTest, ".BASS" ) ){
999		strcpy( endTest, ".dump" );
1000		}
1001		else{
1002	<	strcat( simnfo->sampleName, ".dump" );
1002	>	endTest = &(info[k].sampleName[nameLength - 4]);
1003	>	if( !strcmp( endTest, ".bss" ) ){
1004	>	strcpy( endTest, ".dump" );
1005	>	}
1006	>	else if( !strcmp( endTest, ".mdl" ) ){
1007	>	strcpy( endTest, ".dump" );
1008	>	}
1009	>	else{
1010	>	strcat( info[k].sampleName, ".dump" );
1011	>	}
1012		}
1013	<	}
1014	<
1015	<	strcpy( simnfo->statusName, inFileName );
1016	<	nameLength = strlen( simnfo->statusName );
1017	<	endTest = &(simnfo->statusName[nameLength - 5]);
727	<	if( !strcmp( endTest, ".bass" ) ){
728	<	strcpy( endTest, ".stat" );
729	<	}
730	<	else if( !strcmp( endTest, ".BASS" ) ){
731	<	strcpy( endTest, ".stat" );
732	<	}
733	<	else{
734	<	endTest = &(simnfo->statusName[nameLength - 4]);
735	<	if( !strcmp( endTest, ".bss" ) ){
1013	>
1014	>	strcpy( info[k].statusName, inFileName );
1015	>	nameLength = strlen( info[k].statusName );
1016	>	endTest = &(info[k].statusName[nameLength - 5]);
1017	>	if( !strcmp( endTest, ".bass" ) ){
1018		strcpy( endTest, ".stat" );
1019		}
1020	<	else if( !strcmp( endTest, ".mdl" ) ){
1020	>	else if( !strcmp( endTest, ".BASS" ) ){
1021		strcpy( endTest, ".stat" );
1022		}
1023		else{
1024	<	strcat( simnfo->statusName, ".stat" );
1024	>	endTest = &(info[k].statusName[nameLength - 4]);
1025	>	if( !strcmp( endTest, ".bss" ) ){
1026	>	strcpy( endTest, ".stat" );
1027	>	}
1028	>	else if( !strcmp( endTest, ".mdl" ) ){
1029	>	strcpy( endTest, ".stat" );
1030	>	}
1031	>	else{
1032	>	strcat( info[k].statusName, ".stat" );
1033	>	}
1034		}
1035	<	}
745	<
1035	>
1036		#ifdef IS_MPI
1037	<	}
1037	>	}
1038		#endif // is_mpi
1039	+	}
1040	+	}
1041	+
1042	+
1043	+	void SimSetup::sysObjectsCreation( void ){
1044
1045	<	// set the status, sample, and themal kick times
1045	>	int i,k;
1046
1047	<	if( the_globals->haveSampleTime() ){
753	<	simnfo->sampleTime = the_globals->getSampleTime();
754	<	simnfo->statusTime = simnfo->sampleTime;
755	<	simnfo->thermalTime = simnfo->sampleTime;
756	<	}
757	<	else{
758	<	simnfo->sampleTime = the_globals->getRunTime();
759	<	simnfo->statusTime = simnfo->sampleTime;
760	<	simnfo->thermalTime = simnfo->sampleTime;
761	<	}
1047	>	// create the forceField
1048
1049	<	if( the_globals->haveStatusTime() ){
764	<	simnfo->statusTime = the_globals->getStatusTime();
765	<	}
1049	>	createFF();
1050
1051	<	if( the_globals->haveThermalTime() ){
768	<	simnfo->thermalTime = the_globals->getThermalTime();
769	<	}
1051	>	// extract componentList
1052
1053	<	// check for the temperature set flag
1053	>	compList();
1054
1055	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1055	>	// calc the number of atoms, bond, bends, and torsions
1056
1057	+	calcSysValues();
1058
1059	<	// make the integrator
1059	>	#ifdef IS_MPI
1060	>	// divide the molecules among the processors
1061
1062	+	mpiMolDivide();
1063	+	#endif //is_mpi
1064
1065	<	NVT* myNVT = NULL;
1066	<	switch( ensembleCase ){
1065	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1066	>
1067	>	makeSysArrays();
1068
1069	<	case NVE_ENS:
1070	<	new NVE( simnfo, the_ff );
1069	>	// make and initialize the molecules (all but atomic coordinates)
1070	>
1071	>	makeMolecules();
1072	>
1073	>	for(k=0; k<nInfo; k++){
1074	>	info[k].identArray = new int[info[k].n_atoms];
1075	>	for(i=0; i<info[k].n_atoms; i++){
1076	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1077	>	}
1078	>	}
1079	>	}
1080	>
1081	>
1082	>	void SimSetup::createFF( void ){
1083	>
1084	>	switch( ffCase ){
1085	>
1086	>	case FF_DUFF:
1087	>	the_ff = new DUFF();
1088		break;
1089
1090	<	case NVT_ENS:
1091	<	myNVT = new NVT( simnfo, the_ff );
1092	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
1090	>	case FF_LJ:
1091	>	the_ff = new LJFF();
1092	>	break;
1093
1094	<	if (the_globals->haveTauThermostat())
1095	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
792	<	//     else if (the_globals->haveQmass())
793	<	//       myNVT->setQmass(the_globals->getQmass());
794	<	else {
795	<	sprintf( painCave.errMsg,
796	<	"SimSetup error: If you use the NVT\n"
797	<	"    ensemble, you must set either tauThermostat or qMass.\n"
798	<	"    Neither of these was found in the BASS file.\n");
799	<	painCave.isFatal = 1;
800	<	simError();
801	<	}
1094	>	case FF_EAM:
1095	>	the_ff = new EAM_FF();
1096		break;
1097
1098		default:
1099		sprintf( painCave.errMsg,
1100	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1100	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1101		painCave.isFatal = 1;
1102		simError();
1103		}
1104
811	–
1105		#ifdef IS_MPI
1106	<	mpiSim->mpiRefresh();
1107	<	#endif
1106	>	strcpy( checkPointMsg, "ForceField creation successful" );
1107	>	MPIcheckPoint();
1108	>	#endif // is_mpi
1109
1110	<	// initialize the Fortran
1110	>	}
1111
1112
1113	<	simnfo->refreshSim();
1113	>	void SimSetup::compList( void ){
1114	>
1115	>	int i;
1116	>	char* id;
1117	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1118	>	LinkedMolStamp* currentStamp = NULL;
1119	>	comp_stamps = new MoleculeStamp*[n_components];
1120
1121	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1122	<	the_ff->initForceField( LB_MIXING_RULE );
1121	>	// make an array of molecule stamps that match the components used.
1122	>	// also extract the used stamps out into a separate linked list
1123	>
1124	>	for(i=0; i<nInfo; i++){
1125	>	info[i].nComponents = n_components;
1126	>	info[i].componentsNmol = components_nmol;
1127	>	info[i].compStamps = comp_stamps;
1128	>	info[i].headStamp = headStamp;
1129		}
1130	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
825	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
826	<	}
827	<	else{
828	<	sprintf( painCave.errMsg,
829	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
830	<	simnfo->mixingRule );
831	<	painCave.isFatal = 1;
832	<	simError();
833	<	}
1130	>
1131
1132	+	for( i=0; i<n_components; i++ ){
1133
1134	+	id = the_components[i]->getType();
1135	+	comp_stamps[i] = NULL;
1136	+
1137	+	// check to make sure the component isn't already in the list
1138	+
1139	+	comp_stamps[i] = headStamp->match( id );
1140	+	if( comp_stamps[i] == NULL ){
1141	+
1142	+	// extract the component from the list;
1143	+
1144	+	currentStamp = stamps->extractMolStamp( id );
1145	+	if( currentStamp == NULL ){
1146	+	sprintf( painCave.errMsg,
1147	+	"SimSetup error: Component \"%s\" was not found in the "
1148	+	"list of declared molecules\n",
1149	+	id );
1150	+	painCave.isFatal = 1;
1151	+	simError();
1152	+	}
1153	+
1154	+	headStamp->add( currentStamp );
1155	+	comp_stamps[i] = headStamp->match( id );
1156	+	}
1157	+	}
1158	+
1159		#ifdef IS_MPI
1160	<	strcpy( checkPointMsg,
838	<	"Successfully intialized the mixingRule for Fortran." );
1160	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1161		MPIcheckPoint();
1162		#endif // is_mpi
841	–	}
1163
1164
1165	<	void SimSetup::makeMolecules( void ){
1165	>	}
1166
1167	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
1168	<	molInit info;
1169	<	DirectionalAtom* dAtom;
1170	<	LinkedAssign* extras;
1171	<	LinkedAssign* current_extra;
1172	<	AtomStamp* currentAtom;
1173	<	BondStamp* currentBond;
1174	<	BendStamp* currentBend;
1175	<	TorsionStamp* currentTorsion;
1167	>	void SimSetup::calcSysValues( void ){
1168	>	int i, j, k;
1169	>
1170	>	int *molMembershipArray;
1171	>
1172	>	tot_atoms = 0;
1173	>	tot_bonds = 0;
1174	>	tot_bends = 0;
1175	>	tot_torsions = 0;
1176	>	for( i=0; i<n_components; i++ ){
1177	>
1178	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1180	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1181	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182	>	}
1183	>
1184	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	>	molMembershipArray = new int[tot_atoms];
1186	>
1187	>	for(i=0; i<nInfo; i++){
1188	>	info[i].n_atoms = tot_atoms;
1189	>	info[i].n_bonds = tot_bonds;
1190	>	info[i].n_bends = tot_bends;
1191	>	info[i].n_torsions = tot_torsions;
1192	>	info[i].n_SRI = tot_SRI;
1193	>	info[i].n_mol = tot_nmol;
1194	>
1195	>	info[i].molMembershipArray = molMembershipArray;
1196	>	}
1197	>	}
1198
1199	<	bond_pair* theBonds;
857	<	bend_set* theBends;
858	<	torsion_set* theTorsions;
1199	>	#ifdef IS_MPI
1200
1201	+	void SimSetup::mpiMolDivide( void ){
1202
1203	<	//init the forceField paramters
1203	>	int i, j, k;
1204	>	int localMol, allMol;
1205	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1206
1207	<	the_ff->readParams();
864	<
1207	>	mpiSim = new mpiSimulation( info );
1208
1209	<	// init the atoms
1209	>	globalIndex = mpiSim->divideLabor();
1210
1211	<	double ux, uy, uz, u, uSqr;
1211	>	// set up the local variables
1212
1213	<	atomOffset = 0;
1214	<	excludeOffset = 0;
1215	<	for(i=0; i<simnfo->n_mol; i++){
1216	<
1217	<	stampID = the_molecules[i].getStampID();
1213	>	mol2proc = mpiSim->getMolToProcMap();
1214	>	molCompType = mpiSim->getMolComponentType();
1215	>
1216	>	allMol = 0;
1217	>	localMol = 0;
1218	>	local_atoms = 0;
1219	>	local_bonds = 0;
1220	>	local_bends = 0;
1221	>	local_torsions = 0;
1222	>	globalAtomIndex = 0;
1223
876	–	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
877	–	info.nBonds    = comp_stamps[stampID]->getNBonds();
878	–	info.nBends    = comp_stamps[stampID]->getNBends();
879	–	info.nTorsions = comp_stamps[stampID]->getNTorsions();
880	–	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
1224
1225	<	info.myAtoms = &the_atoms[atomOffset];
883	<	info.myExcludes = &the_excludes[excludeOffset];
884	<	info.myBonds = new Bond*[info.nBonds];
885	<	info.myBends = new Bend*[info.nBends];
886	<	info.myTorsions = new Torsion*[info.nTorsions];
1225	>	for( i=0; i<n_components; i++ ){
1226
1227	<	theBonds = new bond_pair[info.nBonds];
889	<	theBends = new bend_set[info.nBends];
890	<	theTorsions = new torsion_set[info.nTorsions];
891	<
892	<	// make the Atoms
893	<
894	<	for(j=0; j<info.nAtoms; j++){
1227	>	for( j=0; j<components_nmol[i]; j++ ){
1228
1229	<	currentAtom = comp_stamps[stampID]->getAtom( j );
897	<	if( currentAtom->haveOrientation() ){
1229	>	if( mol2proc[allMol] == worldRank ){
1230
1231	<	dAtom = new DirectionalAtom(j + atomOffset);
1232	<	simnfo->n_oriented++;
1233	<	info.myAtoms[j] = dAtom;
1234	<
1235	<	ux = currentAtom->getOrntX();
1236	<	uy = currentAtom->getOrntY();
1237	<	uz = currentAtom->getOrntZ();
1238	<
1239	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
908	<
909	<	u = sqrt( uSqr );
910	<	ux = ux / u;
911	<	uy = uy / u;
912	<	uz = uz / u;
913	<
914	<	dAtom->setSUx( ux );
915	<	dAtom->setSUy( uy );
916	<	dAtom->setSUz( uz );
1231	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1232	>	local_bonds +=    comp_stamps[i]->getNBonds();
1233	>	local_bends +=    comp_stamps[i]->getNBends();
1234	>	local_torsions += comp_stamps[i]->getNTorsions();
1235	>	localMol++;
1236	>	}
1237	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1238	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1239	>	globalAtomIndex++;
1240		}
1241	<	else{
1242	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
1243	<	}
1244	<	info.myAtoms[j]->setType( currentAtom->getType() );
1245	<
1246	<	#ifdef IS_MPI
1247	<
1248	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1249	<
1241	>
1242	>	allMol++;
1243	>	}
1244	>	}
1245	>	local_SRI = local_bonds + local_bends + local_torsions;
1246	>
1247	>	info[0].n_atoms = mpiSim->getMyNlocal();
1248	>
1249	>	if( local_atoms != info[0].n_atoms ){
1250	>	sprintf( painCave.errMsg,
1251	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1252	>	" localAtom (%d) are not equal.\n",
1253	>	info[0].n_atoms,
1254	>	local_atoms );
1255	>	painCave.isFatal = 1;
1256	>	simError();
1257	>	}
1258	>
1259	>	info[0].n_bonds = local_bonds;
1260	>	info[0].n_bends = local_bends;
1261	>	info[0].n_torsions = local_torsions;
1262	>	info[0].n_SRI = local_SRI;
1263	>	info[0].n_mol = localMol;
1264	>
1265	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1266	>	MPIcheckPoint();
1267	>	}
1268	>
1269		#endif // is_mpi
928	–	}
929	–
930	–	// make the bonds
931	–	for(j=0; j<info.nBonds; j++){
932	–
933	–	currentBond = comp_stamps[stampID]->getBond( j );
934	–	theBonds[j].a = currentBond->getA() + atomOffset;
935	–	theBonds[j].b = currentBond->getB() + atomOffset;
1270
937	–	exI = theBonds[j].a;
938	–	exJ = theBonds[j].b;
1271
1272	<	// exclude_I must always be the smaller of the pair
1273	<	if( exI > exJ ){
942	<	tempEx = exI;
943	<	exI = exJ;
944	<	exJ = tempEx;
945	<	}
946	<	#ifdef IS_MPI
947	<	tempEx = exI;
948	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
949	<	tempEx = exJ;
950	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
951	<
952	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
953	<	#else  // isn't MPI
1272	>	void SimSetup::makeSysArrays( void ){
1273	>	int i, j, k, l;
1274
1275	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1276	<	#endif  //is_mpi
1277	<	}
958	<	excludeOffset += info.nBonds;
1275	>	Atom** the_atoms;
1276	>	Molecule* the_molecules;
1277	>	Exclude** the_excludes;
1278
1279	<	//make the bends
1280	<	for(j=0; j<info.nBends; j++){
1281	<
1282	<	currentBend = comp_stamps[stampID]->getBend( j );
1283	<	theBends[j].a = currentBend->getA() + atomOffset;
1284	<	theBends[j].b = currentBend->getB() + atomOffset;
1285	<	theBends[j].c = currentBend->getC() + atomOffset;
1286	<
1287	<	if( currentBend->haveExtras() ){
1288	<
1289	<	extras = currentBend->getExtras();
1290	<	current_extra = extras;
1291	<
1292	<	while( current_extra != NULL ){
1293	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1294	<
1295	<	switch( current_extra->getType() ){
1296	<
1297	<	case 0:
1298	<	theBends[j].ghost =
1299	<	current_extra->getInt() + atomOffset;
1300	<	theBends[j].isGhost = 1;
1301	<	break;
1302	<
1303	<	case 1:
1304	<	theBends[j].ghost =
1305	<	(int)current_extra->getDouble() + atomOffset;
1306	<	theBends[j].isGhost = 1;
1307	<	break;
1308	<
1309	<	default:
1310	<	sprintf( painCave.errMsg,
1311	<	"SimSetup Error: ghostVectorSource was neither a "
1312	<	"double nor an int.\n"
1313	<	"-->Bend[%d] in %s\n",
1314	<	j, comp_stamps[stampID]->getID() );
1315	<	painCave.isFatal = 1;
997	<	simError();
998	<	}
999	<	}
1000	<
1001	<	else{
1002	<
1003	<	sprintf( painCave.errMsg,
1004	<	"SimSetup Error: unhandled bend assignment:\n"
1005	<	"    -->%s in Bend[%d] in %s\n",
1006	<	current_extra->getlhs(),
1007	<	j, comp_stamps[stampID]->getID() );
1008	<	painCave.isFatal = 1;
1009	<	simError();
1010	<	}
1011	<
1012	<	current_extra = current_extra->getNext();
1279	>
1280	>	for(l=0; l<nInfo; l++){
1281	>
1282	>	// create the atom and short range interaction arrays
1283	>
1284	>	the_atoms = new Atom*[info[l].n_atoms];
1285	>	the_molecules = new Molecule[info[l].n_mol];
1286	>	int molIndex;
1287	>
1288	>	// initialize the molecule's stampID's
1289	>
1290	>	#ifdef IS_MPI
1291	>
1292	>
1293	>	molIndex = 0;
1294	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1295	>
1296	>	if(mol2proc[i] == worldRank ){
1297	>	the_molecules[molIndex].setStampID( molCompType[i] );
1298	>	the_molecules[molIndex].setMyIndex( molIndex );
1299	>	the_molecules[molIndex].setGlobalIndex( i );
1300	>	molIndex++;
1301	>	}
1302	>	}
1303	>
1304	>	#else // is_mpi
1305	>
1306	>	molIndex = 0;
1307	>	globalAtomIndex = 0;
1308	>	for(i=0; i<n_components; i++){
1309	>	for(j=0; j<components_nmol[i]; j++ ){
1310	>	the_molecules[molIndex].setStampID( i );
1311	>	the_molecules[molIndex].setMyIndex( molIndex );
1312	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1313	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1314	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1315	>	globalAtomIndex++;
1316		}
1317	+	molIndex++;
1318		}
1015	–
1016	–	if( !theBends[j].isGhost ){
1017	–
1018	–	exI = theBends[j].a;
1019	–	exJ = theBends[j].c;
1020	–	}
1021	–	else{
1022	–
1023	–	exI = theBends[j].a;
1024	–	exJ = theBends[j].b;
1025	–	}
1026	–
1027	–	// exclude_I must always be the smaller of the pair
1028	–	if( exI > exJ ){
1029	–	tempEx = exI;
1030	–	exI = exJ;
1031	–	exJ = tempEx;
1032	–	}
1033	–	#ifdef IS_MPI
1034	–	tempEx = exI;
1035	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1036	–	tempEx = exJ;
1037	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1038	–
1039	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1040	–	#else  // isn't MPI
1041	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1042	–	#endif  //is_mpi
1319		}
1320	<	excludeOffset += info.nBends;
1320	>
1321	>
1322	>	#endif // is_mpi
1323
1046	–	for(j=0; j<info.nTorsions; j++){
1047	–
1048	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1049	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1050	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1051	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1052	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1053	–
1054	–	exI = theTorsions[j].a;
1055	–	exJ = theTorsions[j].d;
1324
1325	<	// exclude_I must always be the smaller of the pair
1326	<	if( exI > exJ ){
1327	<	tempEx = exI;
1328	<	exI = exJ;
1329	<	exJ = tempEx;
1325	>	if( info[l].n_SRI ){
1326	>
1327	>	Exclude::createArray(info[l].n_SRI);
1328	>	the_excludes = new Exclude*[info[l].n_SRI];
1329	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1330	>	the_excludes[ex] = new Exclude(ex);
1331		}
1332	<	#ifdef IS_MPI
1333	<	tempEx = exI;
1065	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1066	<	tempEx = exJ;
1067	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1068	<
1069	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1070	<	#else  // isn't MPI
1071	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1072	<	#endif  //is_mpi
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].n_exclude = info[l].n_SRI;
1334		}
1335	<	excludeOffset += info.nTorsions;
1075	<
1335	>	else{
1336
1337	<	// send the arrays off to the forceField for init.
1337	>	Exclude::createArray( 1 );
1338	>	the_excludes = new Exclude*;
1339	>	the_excludes[0] = new Exclude(0);
1340	>	the_excludes[0]->setPair( 0,0 );
1341	>	info[l].globalExcludes = new int;
1342	>	info[l].globalExcludes[0] = 0;
1343	>	info[l].n_exclude = 0;
1344	>	}
1345
1346	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1080	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1081	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1082	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1346	>	// set the arrays into the SimInfo object
1347
1348	+	info[l].atoms = the_atoms;
1349	+	info[l].molecules = the_molecules;
1350	+	info[l].nGlobalExcludes = 0;
1351	+	info[l].excludes = the_excludes;
1352
1353	<	the_molecules[i].initialize( info );
1354	<
1087	<
1088	<	atomOffset += info.nAtoms;
1089	<	delete[] theBonds;
1090	<	delete[] theBends;
1091	<	delete[] theTorsions;
1353	>	the_ff->setSimInfo( info );
1354	>
1355		}
1093	–
1094	–	#ifdef IS_MPI
1095	–	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1096	–	MPIcheckPoint();
1097	–	#endif // is_mpi
1098	–
1099	–	// clean up the forcefield
1100	–	the_ff->calcRcut();
1101	–	the_ff->cleanMe();
1102	–
1356		}
1357
1358	<	void SimSetup::initFromBass( void ){
1358	>	void SimSetup::makeIntegrator( void ){
1359
1360	<	int i, j, k;
1108	<	int n_cells;
1109	<	double cellx, celly, cellz;
1110	<	double temp1, temp2, temp3;
1111	<	int n_per_extra;
1112	<	int n_extra;
1113	<	int have_extra, done;
1360	>	int k;
1361
1362	<	temp1 = (double)tot_nmol / 4.0;
1363	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1364	<	temp3 = ceil( temp2 );
1362	>	NVT<RealIntegrator>*  myNVT = NULL;
1363	>	NPTi<RealIntegrator>* myNPTi = NULL;
1364	>	NPTf<RealIntegrator>* myNPTf = NULL;
1365	>	NPTim<RealIntegrator>* myNPTim = NULL;
1366	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1367	>
1368	>	for(k=0; k<nInfo; k++){
1369	>
1370	>	switch( ensembleCase ){
1371	>
1372	>	case NVE_ENS:
1373	>	if (globals->haveZconstraints()){
1374	>	setupZConstraint(info[k]);
1375	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1376	>	}
1377
1378	<	have_extra =0;
1379	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1380	<	have_extra =1;
1378	>	else
1379	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1380	>	break;
1381	>
1382	>	case NVT_ENS:
1383	>	if (globals->haveZconstraints()){
1384	>	setupZConstraint(info[k]);
1385	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1386	>	}
1387	>	else
1388	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1389
1390	<	n_cells = (int)temp3 - 1;
1391	<	cellx = simnfo->boxLx / temp3;
1392	<	celly = simnfo->boxLy / temp3;
1393	<	cellz = simnfo->boxLz / temp3;
1394	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1395	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1396	<	n_per_extra = (int)ceil( temp1 );
1390	>	myNVT->setTargetTemp(globals->getTargetTemp());
1391	>
1392	>	if (globals->haveTauThermostat())
1393	>	myNVT->setTauThermostat(globals->getTauThermostat());
1394	>
1395	>	else {
1396	>	sprintf( painCave.errMsg,
1397	>	"SimSetup error: If you use the NVT\n"
1398	>	"    ensemble, you must set tauThermostat.\n");
1399	>	painCave.isFatal = 1;
1400	>	simError();
1401	>	}
1402	>	break;
1403	>
1404	>	case NPTi_ENS:
1405	>	if (globals->haveZconstraints()){
1406	>	setupZConstraint(info[k]);
1407	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1408	>	}
1409	>	else
1410	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1411
1412	<	if( n_per_extra > 4){
1412	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1413	>
1414	>	if (globals->haveTargetPressure())
1415	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1416	>	else {
1417	>	sprintf( painCave.errMsg,
1418	>	"SimSetup error: If you use a constant pressure\n"
1419	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1420	>	painCave.isFatal = 1;
1421	>	simError();
1422	>	}
1423	>
1424	>	if( globals->haveTauThermostat() )
1425	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1426	>	else{
1427	>	sprintf( painCave.errMsg,
1428	>	"SimSetup error: If you use an NPT\n"
1429	>	"    ensemble, you must set tauThermostat.\n");
1430	>	painCave.isFatal = 1;
1431	>	simError();
1432	>	}
1433	>
1434	>	if( globals->haveTauBarostat() )
1435	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1436	>	else{
1437	>	sprintf( painCave.errMsg,
1438	>	"SimSetup error: If you use an NPT\n"
1439	>	"    ensemble, you must set tauBarostat.\n");
1440	>	painCave.isFatal = 1;
1441	>	simError();
1442	>	}
1443	>	break;
1444	>
1445	>	case NPTf_ENS:
1446	>	if (globals->haveZconstraints()){
1447	>	setupZConstraint(info[k]);
1448	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1449	>	}
1450	>	else
1451	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1452	>
1453	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1454	>
1455	>	if (globals->haveTargetPressure())
1456	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1457	>	else {
1458	>	sprintf( painCave.errMsg,
1459	>	"SimSetup error: If you use a constant pressure\n"
1460	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1461	>	painCave.isFatal = 1;
1462	>	simError();
1463	>	}
1464	>
1465	>	if( globals->haveTauThermostat() )
1466	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1467	>	else{
1468	>	sprintf( painCave.errMsg,
1469	>	"SimSetup error: If you use an NPT\n"
1470	>	"    ensemble, you must set tauThermostat.\n");
1471	>	painCave.isFatal = 1;
1472	>	simError();
1473	>	}
1474	>
1475	>	if( globals->haveTauBarostat() )
1476	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1477	>	else{
1478	>	sprintf( painCave.errMsg,
1479	>	"SimSetup error: If you use an NPT\n"
1480	>	"    ensemble, you must set tauBarostat.\n");
1481	>	painCave.isFatal = 1;
1482	>	simError();
1483	>	}
1484	>	break;
1485	>
1486	>	case NPTim_ENS:
1487	>	if (globals->haveZconstraints()){
1488	>	setupZConstraint(info[k]);
1489	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1490	>	}
1491	>	else
1492	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1493	>
1494	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1495	>
1496	>	if (globals->haveTargetPressure())
1497	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1498	>	else {
1499	>	sprintf( painCave.errMsg,
1500	>	"SimSetup error: If you use a constant pressure\n"
1501	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1502	>	painCave.isFatal = 1;
1503	>	simError();
1504	>	}
1505	>
1506	>	if( globals->haveTauThermostat() )
1507	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1508	>	else{
1509	>	sprintf( painCave.errMsg,
1510	>	"SimSetup error: If you use an NPT\n"
1511	>	"    ensemble, you must set tauThermostat.\n");
1512	>	painCave.isFatal = 1;
1513	>	simError();
1514	>	}
1515	>
1516	>	if( globals->haveTauBarostat() )
1517	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1518	>	else{
1519		sprintf( painCave.errMsg,
1520	<	"SimSetup error. There has been an error in constructing"
1521	<	" the non-complete lattice.\n" );
1520	>	"SimSetup error: If you use an NPT\n"
1521	>	"    ensemble, you must set tauBarostat.\n");
1522		painCave.isFatal = 1;
1523		simError();
1137	–	}
1138	–	}
1139	–	else{
1140	–	n_cells = (int)temp3;
1141	–	cellx = simnfo->boxLx / temp3;
1142	–	celly = simnfo->boxLy / temp3;
1143	–	cellz = simnfo->boxLz / temp3;
1144	–	}
1145	–
1146	–	current_mol = 0;
1147	–	current_comp_mol = 0;
1148	–	current_comp = 0;
1149	–	current_atom_ndx = 0;
1150	–
1151	–	for( i=0; i < n_cells ; i++ ){
1152	–	for( j=0; j < n_cells; j++ ){
1153	–	for( k=0; k < n_cells; k++ ){
1154	–
1155	–	makeElement( i * cellx,
1156	–	j * celly,
1157	–	k * cellz );
1158	–
1159	–	makeElement( i * cellx + 0.5 * cellx,
1160	–	j * celly + 0.5 * celly,
1161	–	k * cellz );
1162	–
1163	–	makeElement( i * cellx,
1164	–	j * celly + 0.5 * celly,
1165	–	k * cellz + 0.5 * cellz );
1166	–
1167	–	makeElement( i * cellx + 0.5 * cellx,
1168	–	j * celly,
1169	–	k * cellz + 0.5 * cellz );
1524		}
1525	<	}
1526	<	}
1527	<
1528	<	if( have_extra ){
1529	<	done = 0;
1530	<
1177	<	int start_ndx;
1178	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1179	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1180	<
1181	<	if( i < n_cells ){
1182	<
1183	<	if( j < n_cells ){
1184	<	start_ndx = n_cells;
1185	<	}
1186	<	else start_ndx = 0;
1525	>	break;
1526	>
1527	>	case NPTfm_ENS:
1528	>	if (globals->haveZconstraints()){
1529	>	setupZConstraint(info[k]);
1530	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1531		}
1532	<	else start_ndx = 0;
1532	>	else
1533	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1534
1535	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1536	<
1537	<	makeElement( i * cellx,
1538	<	j * celly,
1539	<	k * cellz );
1540	<	done = ( current_mol >= tot_nmol );
1541	<
1542	<	if( !done && n_per_extra > 1 ){
1543	<	makeElement( i * cellx + 0.5 * cellx,
1544	<	j * celly + 0.5 * celly,
1200	<	k * cellz );
1201	<	done = ( current_mol >= tot_nmol );
1202	<	}
1203	<
1204	<	if( !done && n_per_extra > 2){
1205	<	makeElement( i * cellx,
1206	<	j * celly + 0.5 * celly,
1207	<	k * cellz + 0.5 * cellz );
1208	<	done = ( current_mol >= tot_nmol );
1209	<	}
1210	<
1211	<	if( !done && n_per_extra > 3){
1212	<	makeElement( i * cellx + 0.5 * cellx,
1213	<	j * celly,
1214	<	k * cellz + 0.5 * cellz );
1215	<	done = ( current_mol >= tot_nmol );
1216	<	}
1217	<	}
1535	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1536	>
1537	>	if (globals->haveTargetPressure())
1538	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1539	>	else {
1540	>	sprintf( painCave.errMsg,
1541	>	"SimSetup error: If you use a constant pressure\n"
1542	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1543	>	painCave.isFatal = 1;
1544	>	simError();
1545		}
1546	+
1547	+	if( globals->haveTauThermostat() )
1548	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1549	+	else{
1550	+	sprintf( painCave.errMsg,
1551	+	"SimSetup error: If you use an NPT\n"
1552	+	"    ensemble, you must set tauThermostat.\n");
1553	+	painCave.isFatal = 1;
1554	+	simError();
1555	+	}
1556	+
1557	+	if( globals->haveTauBarostat() )
1558	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1559	+	else{
1560	+	sprintf( painCave.errMsg,
1561	+	"SimSetup error: If you use an NPT\n"
1562	+	"    ensemble, you must set tauBarostat.\n");
1563	+	painCave.isFatal = 1;
1564	+	simError();
1565	+	}
1566	+	break;
1567	+
1568	+	default:
1569	+	sprintf( painCave.errMsg,
1570	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1571	+	painCave.isFatal = 1;
1572	+	simError();
1573		}
1574		}
1575	+	}
1576
1577	+	void SimSetup::initFortran( void ){
1578
1579	<	for( i=0; i<simnfo->n_atoms; i++ ){
1580	<	simnfo->atoms[i]->set_vx( 0.0 );
1581	<	simnfo->atoms[i]->set_vy( 0.0 );
1582	<	simnfo->atoms[i]->set_vz( 0.0 );
1579	>	info[0].refreshSim();
1580	>
1581	>	if( !strcmp( info[0].mixingRule, "standard") ){
1582	>	the_ff->initForceField( LB_MIXING_RULE );
1583		}
1584	<	}
1584	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1585	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1586	>	}
1587	>	else{
1588	>	sprintf( painCave.errMsg,
1589	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1590	>	info[0].mixingRule );
1591	>	painCave.isFatal = 1;
1592	>	simError();
1593	>	}
1594
1230	–	void SimSetup::makeElement( double x, double y, double z ){
1595
1596	<	int k;
1597	<	AtomStamp* current_atom;
1598	<	DirectionalAtom* dAtom;
1599	<	double rotMat[3][3];
1596	>	#ifdef IS_MPI
1597	>	strcpy( checkPointMsg,
1598	>	"Successfully intialized the mixingRule for Fortran." );
1599	>	MPIcheckPoint();
1600	>	#endif // is_mpi
1601
1602	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1602	>	}
1603
1604	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1605	<	if( !current_atom->havePosition() ){
1604	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1605	>	{
1606	>	int nZConstraints;
1607	>	ZconStamp** zconStamp;
1608	>
1609	>	if(globals->haveZconstraintTime()){
1610	>
1611	>	//add sample time of z-constraint  into SimInfo's property list
1612	>	DoubleData* zconsTimeProp = new DoubleData();
1613	>	zconsTimeProp->setID(ZCONSTIME_ID);
1614	>	zconsTimeProp->setData(globals->getZconsTime());
1615	>	theInfo.addProperty(zconsTimeProp);
1616	>	}
1617	>	else{
1618		sprintf( painCave.errMsg,
1619	<	"SimSetup:initFromBass error.\n"
1620	<	"\tComponent %s, atom %s does not have a position specified.\n"
1244	<	"\tThe initialization routine is unable to give a start"
1245	<	" position.\n",
1246	<	comp_stamps[current_comp]->getID(),
1247	<	current_atom->getType() );
1619	>	"ZConstraint error: If you use an ZConstraint\n"
1620	>	" , you must set sample time.\n");
1621		painCave.isFatal = 1;
1622	<	simError();
1622	>	simError();
1623		}
1624
1625	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1626	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1627	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1625	>	//
1626	>	nZConstraints = globals->getNzConstraints();
1627	>	zconStamp = globals->getZconStamp();
1628	>	ZConsParaItem tempParaItem;
1629
1630	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1630	>	ZConsParaData* zconsParaData = new ZConsParaData();
1631	>	zconsParaData->setID(ZCONSPARADATA_ID);
1632	>
1633	>	for(int i = 0; i < nZConstraints; i++){
1634	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1635	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1636	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1637	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1638
1639	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1639	>	zconsParaData->addItem(tempParaItem);
1640	>	}
1641
1642	<	rotMat[0][0] = 1.0;
1643	<	rotMat[0][1] = 0.0;
1644	<	rotMat[0][2] = 0.0;
1642	>	//sort the parameters by index of molecules
1643	>	zconsParaData->sortByIndex();
1644	>
1645	>	//push data into siminfo, therefore, we can retrieve later
1646	>	theInfo.addProperty(zconsParaData);
1647
1648	<	rotMat[1][0] = 0.0;
1649	<	rotMat[1][1] = 1.0;
1650	<	rotMat[1][2] = 0.0;
1651	<
1652	<	rotMat[2][0] = 0.0;
1653	<	rotMat[2][1] = 0.0;
1270	<	rotMat[2][2] = 1.0;
1271	<
1272	<	dAtom->setA( rotMat );
1648	>	//push zconsTol into siminfo, if user does not specify
1649	>	//value for zconsTol, a default value will be used
1650	>	DoubleData* zconsTol = new DoubleData();
1651	>	zconsTol->setID(ZCONSTOL_ID);
1652	>	if(globals->haveZconsTol()){
1653	>	zconsTol->setData(globals->getZconsTol());
1654		}
1655	+	else{
1656	+	double defaultZConsTol = 1E-6;
1657	+	sprintf( painCave.errMsg,
1658	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1659	+	" , default value %f is used.\n", defaultZConsTol);
1660	+	painCave.isFatal = 0;
1661	+	simError();
1662
1663	<	current_atom_ndx++;
1664	<	}
1665	<
1666	<	current_mol++;
1667	<	current_comp_mol++;
1668	<
1669	<	if( current_comp_mol >= components_nmol[current_comp] ){
1670	<
1671	<	current_comp_mol = 0;
1672	<	current_comp++;
1673	<	}
1663	>	zconsTol->setData(defaultZConsTol);
1664	>	}
1665	>	theInfo.addProperty(zconsTol);
1666	>
1667	>	//Determine the name of ouput file and add it into SimInfo's property list
1668	>	//Be careful, do not use inFileName, since it is a pointer which
1669	>	//point to a string at master node, and slave nodes do not contain that string
1670	>
1671	>	string zconsOutput(theInfo.finalName);
1672	>
1673	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1674	>
1675	>	StringData* zconsFilename = new StringData();
1676	>	zconsFilename->setID(ZCONSFILENAME_ID);
1677	>	zconsFilename->setData(zconsOutput);
1678	>
1679	>	theInfo.addProperty(zconsFilename);
1680		}

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