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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 682 by tim, Tue Aug 12 17:51:33 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8		#include "parse_me.h"
#	Line 14 | Line 16
16
17		// some defines for ensemble and Forcefield  cases
18
19	<	#define NVE_ENS 0
20	<	#define NVT_ENS 1
21	<	#define NPT_ENS 2
19	>	#define NVE_ENS        0
20	>	#define NVT_ENS        1
21	>	#define NPTi_ENS       2
22	>	#define NPTf_ENS       3
23	>	#define NPTim_ENS      4
24	>	#define NPTfm_ENS      5
25
26		#define FF_DUFF 0
27		#define FF_LJ   1
28	+	#define FF_EAM  2
29
30	+	using namespace std;
31
32		SimSetup::SimSetup(){
33	+
34	+	isInfoArray = 0;
35	+	nInfo = 1;
36	+
37		stamps = new MakeStamps();
38		globals = new Globals();
39
40	+
41		#ifdef IS_MPI
42		strcpy( checkPointMsg, "SimSetup creation successful" );
43		MPIcheckPoint();
#	Line 37 | Line 49 | void SimSetup::parseFile( char* fileName ){
49		delete globals;
50		}
51
52	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
53	+	info = the_info;
54	+	nInfo = theNinfo;
55	+	isInfoArray = 1;
56	+	}
57	+
58	+
59		void SimSetup::parseFile( char* fileName ){
60
61		#ifdef IS_MPI
#	Line 72 | Line 91 | void SimSetup::createSim( void ){
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
94	>	void SimSetup::createSim(void){
95
77	–	MakeStamps *the_stamps;
78	–	Globals* the_globals;
96		int i, j, k, globalAtomIndex;
97
98	<	int ensembleCase;
82	<	int ffCase;
98	>	// gather all of the information from the Bass file
99
100	<	ensembleCase = -1;
85	<	ffCase = -1;
100	>	gatherInfo();
101
102	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
102	>	// creation of complex system objects
103
104	<	// 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();
104	>	sysObjectsCreation();
105
106	<	// get the ones we know are there, yet still may need some work.
107	<	n_components = the_globals->getNComponents();
108	<	strcpy( force_field, the_globals->getForceField() );
106	>	// check on the post processing info
107	>
108	>	finalInfoCheck();
109	>
110	>	// initialize the system coordinates
111	>
112	>	if( !isInfoArray ) initSystemCoords();
113	>
114	>	// make the output filenames
115	>
116	>	makeOutNames();
117	>
118	>	// make the integrator
119	>
120	>	makeIntegrator();
121	>
122	>	#ifdef IS_MPI
123	>	mpiSim->mpiRefresh();
124	>	#endif
125	>
126	>	// initialize the Fortran
127	>
128	>	initFortran();
129	>
130	>
131	>
132	>	}
133	>
134	>
135	>	void SimSetup::makeMolecules( void ){
136	>
137	>	int k,l;
138	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
139	>	molInit molInfo;
140	>	DirectionalAtom* dAtom;
141	>	LinkedAssign* extras;
142	>	LinkedAssign* current_extra;
143	>	AtomStamp* currentAtom;
144	>	BondStamp* currentBond;
145	>	BendStamp* currentBend;
146	>	TorsionStamp* currentTorsion;
147	>
148	>	bond_pair* theBonds;
149	>	bend_set* theBends;
150	>	torsion_set* theTorsions;
151	>
152	>
153	>	//init the forceField paramters
154	>
155	>	the_ff->readParams();
156	>
157	>
158	>	// init the atoms
159	>
160	>	double ux, uy, uz, u, uSqr;
161	>
162	>	for(k=0; k<nInfo; k++){
163	>
164	>	the_ff->setSimInfo( &(info[k]) );
165	>
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for(i=0; i<info[k].n_mol; i++){
169	>
170	>	stampID = info[k].molecules[i].getStampID();
171	>
172	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
173	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
174	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
175	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
177	>
178	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	>	molInfo.myBends = new Bend*[molInfo.nBends];
182	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
183	>
184	>	theBonds = new bond_pair[molInfo.nBonds];
185	>	theBends = new bend_set[molInfo.nBends];
186	>	theTorsions = new torsion_set[molInfo.nTorsions];
187	>
188	>	// make the Atoms
189	>
190	>	for(j=0; j<molInfo.nAtoms; j++){
191	>
192	>	currentAtom = comp_stamps[stampID]->getAtom( j );
193	>	if( currentAtom->haveOrientation() ){
194	>
195	>	dAtom = new DirectionalAtom( (j + atomOffset),
196	>	info[k].getConfiguration() );
197	>	info[k].n_oriented++;
198	>	molInfo.myAtoms[j] = dAtom;
199	>
200	>	ux = currentAtom->getOrntX();
201	>	uy = currentAtom->getOrntY();
202	>	uz = currentAtom->getOrntZ();
203	>
204	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
205	>
206	>	u = sqrt( uSqr );
207	>	ux = ux / u;
208	>	uy = uy / u;
209	>	uz = uz / u;
210	>
211	>	dAtom->setSUx( ux );
212	>	dAtom->setSUy( uy );
213	>	dAtom->setSUz( uz );
214	>	}
215	>	else{
216	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
217	>	info[k].getConfiguration() );
218	>	}
219	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220	>
221	>	#ifdef IS_MPI
222	>
223	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>
225	>	#endif // is_mpi
226	>	}
227	>
228	>	// make the bonds
229	>	for(j=0; j<molInfo.nBonds; j++){
230	>
231	>	currentBond = comp_stamps[stampID]->getBond( j );
232	>	theBonds[j].a = currentBond->getA() + atomOffset;
233	>	theBonds[j].b = currentBond->getB() + atomOffset;
234	>
235	>	exI = theBonds[j].a;
236	>	exJ = theBonds[j].b;
237	>
238	>	// exclude_I must always be the smaller of the pair
239	>	if( exI > exJ ){
240	>	tempEx = exI;
241	>	exI = exJ;
242	>	exJ = tempEx;
243	>	}
244	>	#ifdef IS_MPI
245	>	tempEx = exI;
246	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
247	>	tempEx = exJ;
248	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>
250	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
251	>	#else  // isn't MPI
252	>
253	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	>	#endif  //is_mpi
255	>	}
256	>	excludeOffset += molInfo.nBonds;
257	>
258	>	//make the bends
259	>	for(j=0; j<molInfo.nBends; j++){
260	>
261	>	currentBend = comp_stamps[stampID]->getBend( j );
262	>	theBends[j].a = currentBend->getA() + atomOffset;
263	>	theBends[j].b = currentBend->getB() + atomOffset;
264	>	theBends[j].c = currentBend->getC() + atomOffset;
265	>
266	>	if( currentBend->haveExtras() ){
267	>
268	>	extras = currentBend->getExtras();
269	>	current_extra = extras;
270	>
271	>	while( current_extra != NULL ){
272	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273	>
274	>	switch( current_extra->getType() ){
275	>
276	>	case 0:
277	>	theBends[j].ghost =
278	>	current_extra->getInt() + atomOffset;
279	>	theBends[j].isGhost = 1;
280	>	break;
281	>
282	>	case 1:
283	>	theBends[j].ghost =
284	>	(int)current_extra->getDouble() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	default:
289	>	sprintf( painCave.errMsg,
290	>	"SimSetup Error: ghostVectorSource was neither a "
291	>	"double nor an int.\n"
292	>	"-->Bend[%d] in %s\n",
293	>	j, comp_stamps[stampID]->getID() );
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	}
298	>
299	>	else{
300	>
301	>	sprintf( painCave.errMsg,
302	>	"SimSetup Error: unhandled bend assignment:\n"
303	>	"    -->%s in Bend[%d] in %s\n",
304	>	current_extra->getlhs(),
305	>	j, comp_stamps[stampID]->getID() );
306	>	painCave.isFatal = 1;
307	>	simError();
308	>	}
309	>
310	>	current_extra = current_extra->getNext();
311	>	}
312	>	}
313	>
314	>	if( !theBends[j].isGhost ){
315	>
316	>	exI = theBends[j].a;
317	>	exJ = theBends[j].c;
318	>	}
319	>	else{
320	>
321	>	exI = theBends[j].a;
322	>	exJ = theBends[j].b;
323	>	}
324	>
325	>	// exclude_I must always be the smaller of the pair
326	>	if( exI > exJ ){
327	>	tempEx = exI;
328	>	exI = exJ;
329	>	exJ = tempEx;
330	>	}
331	>	#ifdef IS_MPI
332	>	tempEx = exI;
333	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exJ;
335	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>
337	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
338	>	#else  // isn't MPI
339	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340	>	#endif  //is_mpi
341	>	}
342	>	excludeOffset += molInfo.nBends;
343	>
344	>	for(j=0; j<molInfo.nTorsions; j++){
345	>
346	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	>
352	>	exI = theTorsions[j].a;
353	>	exJ = theTorsions[j].d;
354	>
355	>	// exclude_I must always be the smaller of the pair
356	>	if( exI > exJ ){
357	>	tempEx = exI;
358	>	exI = exJ;
359	>	exJ = tempEx;
360	>	}
361	>	#ifdef IS_MPI
362	>	tempEx = exI;
363	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
364	>	tempEx = exJ;
365	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	>
367	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
368	>	#else  // isn't MPI
369	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370	>	#endif  //is_mpi
371	>	}
372	>	excludeOffset += molInfo.nTorsions;
373	>
374	>
375	>	// send the arrays off to the forceField for init.
376	>
377	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381	>
382	>
383	>	info[k].molecules[i].initialize( molInfo );
384
385	+
386	+	atomOffset += molInfo.nAtoms;
387	+	delete[] theBonds;
388	+	delete[] theBends;
389	+	delete[] theTorsions;
390	+	}
391	+	}
392	+
393	+	#ifdef IS_MPI
394	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
395	+	MPIcheckPoint();
396	+	#endif // is_mpi
397	+
398	+	// clean up the forcefield
399	+
400	+	the_ff->calcRcut();
401	+	the_ff->cleanMe();
402	+
403	+	}
404	+
405	+	void SimSetup::initFromBass( void ){
406	+
407	+	int i, j, k;
408	+	int n_cells;
409	+	double cellx, celly, cellz;
410	+	double temp1, temp2, temp3;
411	+	int n_per_extra;
412	+	int n_extra;
413	+	int have_extra, done;
414	+
415	+	double vel[3];
416	+	vel[0] = 0.0;
417	+	vel[1] = 0.0;
418	+	vel[2] = 0.0;
419	+
420	+	temp1 = (double)tot_nmol / 4.0;
421	+	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
422	+	temp3 = ceil( temp2 );
423	+
424	+	have_extra =0;
425	+	if( temp2 < temp3 ){ // we have a non-complete lattice
426	+	have_extra =1;
427	+
428	+	n_cells = (int)temp3 - 1;
429	+	cellx = info[0].boxL[0] / temp3;
430	+	celly = info[0].boxL[1] / temp3;
431	+	cellz = info[0].boxL[2] / temp3;
432	+	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
433	+	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
434	+	n_per_extra = (int)ceil( temp1 );
435	+
436	+	if( n_per_extra > 4){
437	+	sprintf( painCave.errMsg,
438	+	"SimSetup error. There has been an error in constructing"
439	+	" the non-complete lattice.\n" );
440	+	painCave.isFatal = 1;
441	+	simError();
442	+	}
443	+	}
444	+	else{
445	+	n_cells = (int)temp3;
446	+	cellx = info[0].boxL[0] / temp3;
447	+	celly = info[0].boxL[1] / temp3;
448	+	cellz = info[0].boxL[2] / temp3;
449	+	}
450	+
451	+	current_mol = 0;
452	+	current_comp_mol = 0;
453	+	current_comp = 0;
454	+	current_atom_ndx = 0;
455	+
456	+	for( i=0; i < n_cells ; i++ ){
457	+	for( j=0; j < n_cells; j++ ){
458	+	for( k=0; k < n_cells; k++ ){
459	+
460	+	makeElement( i * cellx,
461	+	j * celly,
462	+	k * cellz );
463	+
464	+	makeElement( i * cellx + 0.5 * cellx,
465	+	j * celly + 0.5 * celly,
466	+	k * cellz );
467	+
468	+	makeElement( i * cellx,
469	+	j * celly + 0.5 * celly,
470	+	k * cellz + 0.5 * cellz );
471	+
472	+	makeElement( i * cellx + 0.5 * cellx,
473	+	j * celly,
474	+	k * cellz + 0.5 * cellz );
475	+	}
476	+	}
477	+	}
478	+
479	+	if( have_extra ){
480	+	done = 0;
481	+
482	+	int start_ndx;
483	+	for( i=0; i < (n_cells+1) && !done; i++ ){
484	+	for( j=0; j < (n_cells+1) && !done; j++ ){
485	+
486	+	if( i < n_cells ){
487	+
488	+	if( j < n_cells ){
489	+	start_ndx = n_cells;
490	+	}
491	+	else start_ndx = 0;
492	+	}
493	+	else start_ndx = 0;
494	+
495	+	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
496	+
497	+	makeElement( i * cellx,
498	+	j * celly,
499	+	k * cellz );
500	+	done = ( current_mol >= tot_nmol );
501	+
502	+	if( !done && n_per_extra > 1 ){
503	+	makeElement( i * cellx + 0.5 * cellx,
504	+	j * celly + 0.5 * celly,
505	+	k * cellz );
506	+	done = ( current_mol >= tot_nmol );
507	+	}
508	+
509	+	if( !done && n_per_extra > 2){
510	+	makeElement( i * cellx,
511	+	j * celly + 0.5 * celly,
512	+	k * cellz + 0.5 * cellz );
513	+	done = ( current_mol >= tot_nmol );
514	+	}
515	+
516	+	if( !done && n_per_extra > 3){
517	+	makeElement( i * cellx + 0.5 * cellx,
518	+	j * celly,
519	+	k * cellz + 0.5 * cellz );
520	+	done = ( current_mol >= tot_nmol );
521	+	}
522	+	}
523	+	}
524	+	}
525	+	}
526	+
527	+	for( i=0; i<info[0].n_atoms; i++ ){
528	+	info[0].atoms[i]->setVel( vel );
529	+	}
530	+	}
531	+
532	+	void SimSetup::makeElement( double x, double y, double z ){
533	+
534	+	int k;
535	+	AtomStamp* current_atom;
536	+	DirectionalAtom* dAtom;
537	+	double rotMat[3][3];
538	+	double pos[3];
539	+
540	+	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
541	+
542	+	current_atom = comp_stamps[current_comp]->getAtom( k );
543	+	if( !current_atom->havePosition() ){
544	+	sprintf( painCave.errMsg,
545	+	"SimSetup:initFromBass error.\n"
546	+	"\tComponent %s, atom %s does not have a position specified.\n"
547	+	"\tThe initialization routine is unable to give a start"
548	+	" position.\n",
549	+	comp_stamps[current_comp]->getID(),
550	+	current_atom->getType() );
551	+	painCave.isFatal = 1;
552	+	simError();
553	+	}
554	+
555	+	pos[0] = x + current_atom->getPosX();
556	+	pos[1] = y + current_atom->getPosY();
557	+	pos[2] = z + current_atom->getPosZ();
558	+
559	+	info[0].atoms[current_atom_ndx]->setPos( pos );
560	+
561	+	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
562	+
563	+	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
564	+
565	+	rotMat[0][0] = 1.0;
566	+	rotMat[0][1] = 0.0;
567	+	rotMat[0][2] = 0.0;
568	+
569	+	rotMat[1][0] = 0.0;
570	+	rotMat[1][1] = 1.0;
571	+	rotMat[1][2] = 0.0;
572	+
573	+	rotMat[2][0] = 0.0;
574	+	rotMat[2][1] = 0.0;
575	+	rotMat[2][2] = 1.0;
576	+
577	+	dAtom->setA( rotMat );
578	+	}
579	+
580	+	current_atom_ndx++;
581	+	}
582	+
583	+	current_mol++;
584	+	current_comp_mol++;
585	+
586	+	if( current_comp_mol >= components_nmol[current_comp] ){
587	+
588	+	current_comp_mol = 0;
589	+	current_comp++;
590	+	}
591	+	}
592	+
593	+
594	+	void SimSetup::gatherInfo( void ){
595	+	int i,j,k;
596	+
597	+	ensembleCase = -1;
598	+	ffCase = -1;
599	+
600	+	// set the easy ones first
601	+
602	+	for( i=0; i<nInfo; i++){
603	+	info[i].target_temp = globals->getTargetTemp();
604	+	info[i].dt = globals->getDt();
605	+	info[i].run_time = globals->getRunTime();
606	+	}
607	+	n_components = globals->getNComponents();
608	+
609	+
610	+	// get the forceField
611	+
612	+	strcpy( force_field, globals->getForceField() );
613	+
614		if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
615		else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
616	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
617		else{
618		sprintf( painCave.errMsg,
619		"SimSetup Error. Unrecognized force field -> %s\n",
#	Line 107 | Line 622 | void SimSetup::createSim( void ){
622		simError();
623		}
624
625	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
625	>	// get the ensemble
626
627	+	strcpy( ensemble, globals->getEnsemble() );
628	+
629		if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
630		else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
631	<	else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS;
631	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
632	>	ensembleCase = NPTi_ENS;
633	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
634	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
635	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
636		else{
637		sprintf( painCave.errMsg,
638		"SimSetup Warning. Unrecognized Ensemble -> %s, "
#	Line 123 | Line 643 | void SimSetup::createSim( void ){
643		strcpy( ensemble, "NVE" );
644		ensembleCase = NVE_ENS;
645		}
646	<	strcpy( simnfo->ensemble, ensemble );
646	>
647	>	for(i=0; i<nInfo; i++){
648	>
649	>	strcpy( info[i].ensemble, ensemble );
650
651	+	// get the mixing rule
652
653	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
654	<	//     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();
653	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
654	>	info[i].usePBC = globals->getPBC();
655		}
656	<
206	<	#ifdef IS_MPI
207	<	strcpy( checkPointMsg, "ForceField creation successful" );
208	<	MPIcheckPoint();
209	<	#endif // is_mpi
210	<
656	>
657		// get the components and calculate the tot_nMol and indvidual n_mol
658	<	the_components = the_globals->getComponents();
658	>
659	>	the_components = globals->getComponents();
660		components_nmol = new int[n_components];
214	–	comp_stamps = new MoleculeStamp*[n_components];
661
662	<	if( !the_globals->haveNMol() ){
662	>
663	>	if( !globals->haveNMol() ){
664		// we don't have the total number of molecules, so we assume it is
665		// given in each component
666
#	Line 242 | Line 689 | void SimSetup::createSim( void ){
689		" Please give nMol in the components.\n" );
690		painCave.isFatal = 1;
691		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	–
692		}
693
694	<	#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
694	>	// set the status, sample, and thermal kick times
695
696	+	for(i=0; i<nInfo; i++){
697
698	<	molIndex = 0;
699	<	for(i=0; i<mpiSim->getTotNmol(); i++){
700	<
701	<	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++;
698	>	if( globals->haveSampleTime() ){
699	>	info[i].sampleTime = globals->getSampleTime();
700	>	info[i].statusTime = info[i].sampleTime;
701	>	info[i].thermalTime = info[i].sampleTime;
702		}
430	–	}
431	–
432	–	#else // is_mpi
433	–
434	–	molIndex = 0;
435	–	globalAtomIndex = 0;
436	–	for(i=0; i<n_components; i++){
437	–	for(j=0; j<components_nmol[i]; j++ ){
438	–	the_molecules[molIndex].setStampID( i );
439	–	the_molecules[molIndex].setMyIndex( molIndex );
440	–	the_molecules[molIndex].setGlobalIndex( molIndex );
441	–	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442	–	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443	–	globalAtomIndex++;
444	–	}
445	–	molIndex++;
446	–	}
447	–	}
448	–
449	–
450	–	#endif // is_mpi
451	–
452	–
453	–	if( simnfo->n_SRI ){
454	–
455	–	Exclude::createArray(simnfo->n_SRI);
456	–	the_excludes = new Exclude*[simnfo->n_SRI];
457	–	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
458	–	simnfo->globalExcludes = new int;
459	–	simnfo->n_exclude = simnfo->n_SRI;
460	–	}
461	–	else{
462	–
463	–	Exclude::createArray( 1 );
464	–	the_excludes = new Exclude*;
465	–	the_excludes[0] = new Exclude(0);
466	–	the_excludes[0]->setPair( 0,0 );
467	–	simnfo->globalExcludes = new int;
468	–	simnfo->globalExcludes[0] = 0;
469	–	simnfo->n_exclude = 0;
470	–	}
471	–
472	–	// set the arrays into the SimInfo object
473	–
474	–	simnfo->atoms = the_atoms;
475	–	simnfo->molecules = the_molecules;
476	–	simnfo->nGlobalExcludes = 0;
477	–	simnfo->excludes = the_excludes;
478	–
479	–
480	–	// get some of the tricky things that may still be in the globals
481	–
482	–	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();
506	–	}
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	–	}
703		else{
704	<	strcpy( simnfo->finalName, inFileName );
705	<	char* endTest;
706	<	int nameLength = strlen( simnfo->finalName );
678	<	endTest = &(simnfo->finalName[nameLength - 5]);
679	<	if( !strcmp( endTest, ".bass" ) ){
680	<	strcpy( endTest, ".eor" );
681	<	}
682	<	else if( !strcmp( endTest, ".BASS" ) ){
683	<	strcpy( endTest, ".eor" );
684	<	}
685	<	else{
686	<	endTest = &(simnfo->finalName[nameLength - 4]);
687	<	if( !strcmp( endTest, ".bss" ) ){
688	<	strcpy( endTest, ".eor" );
689	<	}
690	<	else if( !strcmp( endTest, ".mdl" ) ){
691	<	strcpy( endTest, ".eor" );
692	<	}
693	<	else{
694	<	strcat( simnfo->finalName, ".eor" );
695	<	}
696	<	}
704	>	info[i].sampleTime = globals->getRunTime();
705	>	info[i].statusTime = info[i].sampleTime;
706	>	info[i].thermalTime = info[i].sampleTime;
707		}
708
709	<	// make the sample and status out names
709	>	if( globals->haveStatusTime() ){
710	>	info[i].statusTime = globals->getStatusTime();
711	>	}
712
713	<	strcpy( simnfo->sampleName, inFileName );
714	<	char* endTest;
703	<	int nameLength = strlen( simnfo->sampleName );
704	<	endTest = &(simnfo->sampleName[nameLength - 5]);
705	<	if( !strcmp( endTest, ".bass" ) ){
706	<	strcpy( endTest, ".dump" );
713	>	if( globals->haveThermalTime() ){
714	>	info[i].thermalTime = globals->getThermalTime();
715		}
716	<	else if( !strcmp( endTest, ".BASS" ) ){
717	<	strcpy( endTest, ".dump" );
716	>
717	>	// check for the temperature set flag
718	>
719	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
720	>
721	>	// get some of the tricky things that may still be in the globals
722	>
723	>	double boxVector[3];
724	>	if( globals->haveBox() ){
725	>	boxVector[0] = globals->getBox();
726	>	boxVector[1] = globals->getBox();
727	>	boxVector[2] = globals->getBox();
728	>
729	>	info[i].setBox( boxVector );
730		}
731	+	else if( globals->haveDensity() ){
732	+
733	+	double vol;
734	+	vol = (double)tot_nmol / globals->getDensity();
735	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
736	+	boxVector[1] = boxVector[0];
737	+	boxVector[2] = boxVector[0];
738	+
739	+	info[i].setBox( boxVector );
740	+	}
741		else{
742	<	endTest = &(simnfo->sampleName[nameLength - 4]);
743	<	if( !strcmp( endTest, ".bss" ) ){
744	<	strcpy( endTest, ".dump" );
742	>	if( !globals->haveBoxX() ){
743	>	sprintf( painCave.errMsg,
744	>	"SimSetup error, no periodic BoxX size given.\n" );
745	>	painCave.isFatal = 1;
746	>	simError();
747		}
748	<	else if( !strcmp( endTest, ".mdl" ) ){
749	<	strcpy( endTest, ".dump" );
748	>	boxVector[0] = globals->getBoxX();
749	>
750	>	if( !globals->haveBoxY() ){
751	>	sprintf( painCave.errMsg,
752	>	"SimSetup error, no periodic BoxY size given.\n" );
753	>	painCave.isFatal = 1;
754	>	simError();
755		}
756	<	else{
757	<	strcat( simnfo->sampleName, ".dump" );
756	>	boxVector[1] = globals->getBoxY();
757	>
758	>	if( !globals->haveBoxZ() ){
759	>	sprintf( painCave.errMsg,
760	>	"SimSetup error, no periodic BoxZ size given.\n" );
761	>	painCave.isFatal = 1;
762	>	simError();
763		}
764	+	boxVector[2] = globals->getBoxZ();
765	+
766	+	info[i].setBox( boxVector );
767		}
768	+
769	+	}
770
771	<	strcpy( simnfo->statusName, inFileName );
772	<	nameLength = strlen( simnfo->statusName );
773	<	endTest = &(simnfo->statusName[nameLength - 5]);
774	<	if( !strcmp( endTest, ".bass" ) ){
775	<	strcpy( endTest, ".stat" );
771	>	#ifdef IS_MPI
772	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
773	>	MPIcheckPoint();
774	>	#endif // is_mpi
775	>
776	>	}
777	>
778	>
779	>	void SimSetup::finalInfoCheck( void ){
780	>	int index;
781	>	int usesDipoles;
782	>	int i;
783	>
784	>	for(i=0; i<nInfo; i++){
785	>	// check electrostatic parameters
786	>
787	>	index = 0;
788	>	usesDipoles = 0;
789	>	while( (index < info[i].n_atoms) && !usesDipoles ){
790	>	usesDipoles = (info[i].atoms[index])->hasDipole();
791	>	index++;
792		}
793	<	else if( !strcmp( endTest, ".BASS" ) ){
794	<	strcpy( endTest, ".stat" );
795	<	}
796	<	else{
797	<	endTest = &(simnfo->statusName[nameLength - 4]);
798	<	if( !strcmp( endTest, ".bss" ) ){
799	<	strcpy( endTest, ".stat" );
793	>
794	>	#ifdef IS_MPI
795	>	int myUse = usesDipoles;
796	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
797	>	#endif //is_mpi
798	>
799	>	double theEcr, theEst;
800	>
801	>	if (globals->getUseRF() ) {
802	>	info[i].useReactionField = 1;
803	>
804	>	if( !globals->haveECR() ){
805	>	sprintf( painCave.errMsg,
806	>	"SimSetup Warning: using default value of 1/2 the smallest "
807	>	"box length for the electrostaticCutoffRadius.\n"
808	>	"I hope you have a very fast processor!\n");
809	>	painCave.isFatal = 0;
810	>	simError();
811	>	double smallest;
812	>	smallest = info[i].boxL[0];
813	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
814	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
815	>	theEcr = 0.5 * smallest;
816	>	} else {
817	>	theEcr = globals->getECR();
818		}
819	<	else if( !strcmp( endTest, ".mdl" ) ){
820	<	strcpy( endTest, ".stat" );
819	>
820	>	if( !globals->haveEST() ){
821	>	sprintf( painCave.errMsg,
822	>	"SimSetup Warning: using default value of 0.05 * the "
823	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
824	>	);
825	>	painCave.isFatal = 0;
826	>	simError();
827	>	theEst = 0.05 * theEcr;
828	>	} else {
829	>	theEst= globals->getEST();
830		}
831	<	else{
832	<	strcat( simnfo->statusName, ".stat" );
831	>
832	>	info[i].setEcr( theEcr, theEst );
833	>
834	>	if(!globals->haveDielectric() ){
835	>	sprintf( painCave.errMsg,
836	>	"SimSetup Error: You are trying to use Reaction Field without"
837	>	"setting a dielectric constant!\n"
838	>	);
839	>	painCave.isFatal = 1;
840	>	simError();
841		}
842	<	}
843	<
844	<	#ifdef IS_MPI
842	>	info[i].dielectric = globals->getDielectric();
843	>	}
844	>	else {
845	>	if (usesDipoles) {
846	>
847	>	if( !globals->haveECR() ){
848	>	sprintf( painCave.errMsg,
849	>	"SimSetup Warning: using default value of 1/2 the smallest "
850	>	"box length for the electrostaticCutoffRadius.\n"
851	>	"I hope you have a very fast processor!\n");
852	>	painCave.isFatal = 0;
853	>	simError();
854	>	double smallest;
855	>	smallest = info[i].boxL[0];
856	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
857	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
858	>	theEcr = 0.5 * smallest;
859	>	} else {
860	>	theEcr = globals->getECR();
861	>	}
862	>
863	>	if( !globals->haveEST() ){
864	>	sprintf( painCave.errMsg,
865	>	"SimSetup Warning: using default value of 0.05 * the "
866	>	"electrostaticCutoffRadius for the "
867	>	"electrostaticSkinThickness\n"
868	>	);
869	>	painCave.isFatal = 0;
870	>	simError();
871	>	theEst = 0.05 * theEcr;
872	>	} else {
873	>	theEst= globals->getEST();
874	>	}
875	>
876	>	info[i].setEcr( theEcr, theEst );
877	>	}
878	>	}
879		}
880	+
881	+	#ifdef IS_MPI
882	+	strcpy( checkPointMsg, "post processing checks out" );
883	+	MPIcheckPoint();
884		#endif // is_mpi
885	+
886	+	}
887	+
888	+	void SimSetup::initSystemCoords( void ){
889	+	int i;
890
891	<	// set the status, sample, and themal kick times
891	>	std::cerr << "Setting atom Coords\n";
892	>
893	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
894
895	<	if( the_globals->haveSampleTime() ){
896	<	simnfo->sampleTime = the_globals->getSampleTime();
897	<	simnfo->statusTime = simnfo->sampleTime;
898	<	simnfo->thermalTime = simnfo->sampleTime;
895	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
896	>
897	>	if( globals->haveInitialConfig() ){
898	>
899	>	InitializeFromFile* fileInit;
900	>	#ifdef IS_MPI // is_mpi
901	>	if( worldRank == 0 ){
902	>	#endif //is_mpi
903	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
904	>	#ifdef IS_MPI
905	>	}else fileInit = new InitializeFromFile( NULL );
906	>	#endif
907	>	fileInit->readInit( info ); // default velocities on
908	>
909	>	delete fileInit;
910		}
911		else{
912	<	simnfo->sampleTime = the_globals->getRunTime();
913	<	simnfo->statusTime = simnfo->sampleTime;
914	<	simnfo->thermalTime = simnfo->sampleTime;
912	>
913	>	#ifdef IS_MPI
914	>
915	>	// no init from bass
916	>
917	>	sprintf( painCave.errMsg,
918	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
919	>	painCave.isFatal;
920	>	simError();
921	>
922	>	#else
923	>
924	>	initFromBass();
925	>
926	>
927	>	#endif
928		}
929	+
930	+	#ifdef IS_MPI
931	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
932	+	MPIcheckPoint();
933	+	#endif // is_mpi
934	+
935	+	}
936
763	–	if( the_globals->haveStatusTime() ){
764	–	simnfo->statusTime = the_globals->getStatusTime();
765	–	}
937
938	<	if( the_globals->haveThermalTime() ){
939	<	simnfo->thermalTime = the_globals->getThermalTime();
940	<	}
938	>	void SimSetup::makeOutNames( void ){
939	>
940	>	int k;
941
942	<	// check for the temperature set flag
942	>
943	>	for(k=0; k<nInfo; k++){
944
945	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
945	>	#ifdef IS_MPI
946	>	if( worldRank == 0 ){
947	>	#endif // is_mpi
948	>
949	>	if( globals->haveFinalConfig() ){
950	>	strcpy( info[k].finalName, globals->getFinalConfig() );
951	>	}
952	>	else{
953	>	strcpy( info[k].finalName, inFileName );
954	>	char* endTest;
955	>	int nameLength = strlen( info[k].finalName );
956	>	endTest = &(info[k].finalName[nameLength - 5]);
957	>	if( !strcmp( endTest, ".bass" ) ){
958	>	strcpy( endTest, ".eor" );
959	>	}
960	>	else if( !strcmp( endTest, ".BASS" ) ){
961	>	strcpy( endTest, ".eor" );
962	>	}
963	>	else{
964	>	endTest = &(info[k].finalName[nameLength - 4]);
965	>	if( !strcmp( endTest, ".bss" ) ){
966	>	strcpy( endTest, ".eor" );
967	>	}
968	>	else if( !strcmp( endTest, ".mdl" ) ){
969	>	strcpy( endTest, ".eor" );
970	>	}
971	>	else{
972	>	strcat( info[k].finalName, ".eor" );
973	>	}
974	>	}
975	>	}
976	>
977	>	// make the sample and status out names
978	>
979	>	strcpy( info[k].sampleName, inFileName );
980	>	char* endTest;
981	>	int nameLength = strlen( info[k].sampleName );
982	>	endTest = &(info[k].sampleName[nameLength - 5]);
983	>	if( !strcmp( endTest, ".bass" ) ){
984	>	strcpy( endTest, ".dump" );
985	>	}
986	>	else if( !strcmp( endTest, ".BASS" ) ){
987	>	strcpy( endTest, ".dump" );
988	>	}
989	>	else{
990	>	endTest = &(info[k].sampleName[nameLength - 4]);
991	>	if( !strcmp( endTest, ".bss" ) ){
992	>	strcpy( endTest, ".dump" );
993	>	}
994	>	else if( !strcmp( endTest, ".mdl" ) ){
995	>	strcpy( endTest, ".dump" );
996	>	}
997	>	else{
998	>	strcat( info[k].sampleName, ".dump" );
999	>	}
1000	>	}
1001	>
1002	>	strcpy( info[k].statusName, inFileName );
1003	>	nameLength = strlen( info[k].statusName );
1004	>	endTest = &(info[k].statusName[nameLength - 5]);
1005	>	if( !strcmp( endTest, ".bass" ) ){
1006	>	strcpy( endTest, ".stat" );
1007	>	}
1008	>	else if( !strcmp( endTest, ".BASS" ) ){
1009	>	strcpy( endTest, ".stat" );
1010	>	}
1011	>	else{
1012	>	endTest = &(info[k].statusName[nameLength - 4]);
1013	>	if( !strcmp( endTest, ".bss" ) ){
1014	>	strcpy( endTest, ".stat" );
1015	>	}
1016	>	else if( !strcmp( endTest, ".mdl" ) ){
1017	>	strcpy( endTest, ".stat" );
1018	>	}
1019	>	else{
1020	>	strcat( info[k].statusName, ".stat" );
1021	>	}
1022	>	}
1023	>
1024	>	#ifdef IS_MPI
1025	>	}
1026	>	#endif // is_mpi
1027	>	}
1028	>	}
1029
1030
1031	<	// make the integrator
1031	>	void SimSetup::sysObjectsCreation( void ){
1032
1033	+	int i,k;
1034
1035	<	NVT* myNVT = NULL;
1036	<	switch( ensembleCase ){
1035	>	// create the forceField
1036	>
1037	>	createFF();
1038
1039	<	case NVE_ENS:
783	<	new NVE( simnfo, the_ff );
784	<	break;
1039	>	// extract componentList
1040
1041	<	case NVT_ENS:
787	<	myNVT = new NVT( simnfo, the_ff );
788	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
1041	>	compList();
1042
1043	<	if (the_globals->haveTauThermostat())
1044	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
1045	<	//     else if (the_globals->haveQmass())
1046	<	//       myNVT->setQmass(the_globals->getQmass());
1047	<	else {
1048	<	sprintf( painCave.errMsg,
1049	<	"SimSetup error: If you use the NVT\n"
1050	<	"    ensemble, you must set either tauThermostat or qMass.\n"
1051	<	"    Neither of these was found in the BASS file.\n");
1052	<	painCave.isFatal = 1;
1053	<	simError();
1043	>	// calc the number of atoms, bond, bends, and torsions
1044	>
1045	>	calcSysValues();
1046	>
1047	>	#ifdef IS_MPI
1048	>	// divide the molecules among the processors
1049	>
1050	>	mpiMolDivide();
1051	>	#endif //is_mpi
1052	>
1053	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1054	>
1055	>	makeSysArrays();
1056	>
1057	>	// make and initialize the molecules (all but atomic coordinates)
1058	>
1059	>	makeMolecules();
1060	>
1061	>	for(k=0; k<nInfo; k++){
1062	>	info[k].identArray = new int[info[k].n_atoms];
1063	>	for(i=0; i<info[k].n_atoms; i++){
1064	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1065		}
1066	+	}
1067	+	}
1068	+
1069	+
1070	+	void SimSetup::createFF( void ){
1071	+
1072	+	switch( ffCase ){
1073	+
1074	+	case FF_DUFF:
1075	+	the_ff = new DUFF();
1076		break;
1077
1078	+	case FF_LJ:
1079	+	the_ff = new LJFF();
1080	+	break;
1081	+
1082	+	case FF_EAM:
1083	+	the_ff = new EAM_FF();
1084	+	break;
1085	+
1086		default:
1087		sprintf( painCave.errMsg,
1088	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1088	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1089		painCave.isFatal = 1;
1090		simError();
1091		}
1092
811	–
1093		#ifdef IS_MPI
1094	<	mpiSim->mpiRefresh();
1095	<	#endif
1094	>	strcpy( checkPointMsg, "ForceField creation successful" );
1095	>	MPIcheckPoint();
1096	>	#endif // is_mpi
1097
1098	<	// initialize the Fortran
1098	>	}
1099
1100
1101	<	simnfo->refreshSim();
1101	>	void SimSetup::compList( void ){
1102	>
1103	>	int i;
1104	>	char* id;
1105	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1106	>	LinkedMolStamp* currentStamp = NULL;
1107	>	comp_stamps = new MoleculeStamp*[n_components];
1108
1109	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1110	<	the_ff->initForceField( LB_MIXING_RULE );
1109	>	// make an array of molecule stamps that match the components used.
1110	>	// also extract the used stamps out into a separate linked list
1111	>
1112	>	for(i=0; i<nInfo; i++){
1113	>	info[i].nComponents = n_components;
1114	>	info[i].componentsNmol = components_nmol;
1115	>	info[i].compStamps = comp_stamps;
1116	>	info[i].headStamp = headStamp;
1117		}
1118	<	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	<	}
1118	>
1119
1120	+	for( i=0; i<n_components; i++ ){
1121
1122	+	id = the_components[i]->getType();
1123	+	comp_stamps[i] = NULL;
1124	+
1125	+	// check to make sure the component isn't already in the list
1126	+
1127	+	comp_stamps[i] = headStamp->match( id );
1128	+	if( comp_stamps[i] == NULL ){
1129	+
1130	+	// extract the component from the list;
1131	+
1132	+	currentStamp = stamps->extractMolStamp( id );
1133	+	if( currentStamp == NULL ){
1134	+	sprintf( painCave.errMsg,
1135	+	"SimSetup error: Component \"%s\" was not found in the "
1136	+	"list of declared molecules\n",
1137	+	id );
1138	+	painCave.isFatal = 1;
1139	+	simError();
1140	+	}
1141	+
1142	+	headStamp->add( currentStamp );
1143	+	comp_stamps[i] = headStamp->match( id );
1144	+	}
1145	+	}
1146	+
1147		#ifdef IS_MPI
1148	<	strcpy( checkPointMsg,
838	<	"Successfully intialized the mixingRule for Fortran." );
1148	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1149		MPIcheckPoint();
1150		#endif // is_mpi
841	–	}
1151
1152
1153	<	void SimSetup::makeMolecules( void ){
1153	>	}
1154
1155	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
1156	<	molInit info;
1157	<	DirectionalAtom* dAtom;
1158	<	LinkedAssign* extras;
1159	<	LinkedAssign* current_extra;
1160	<	AtomStamp* currentAtom;
1161	<	BondStamp* currentBond;
1162	<	BendStamp* currentBend;
1163	<	TorsionStamp* currentTorsion;
1155	>	void SimSetup::calcSysValues( void ){
1156	>	int i, j, k;
1157	>
1158	>	int *molMembershipArray;
1159	>
1160	>	tot_atoms = 0;
1161	>	tot_bonds = 0;
1162	>	tot_bends = 0;
1163	>	tot_torsions = 0;
1164	>	for( i=0; i<n_components; i++ ){
1165	>
1166	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1167	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1168	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1169	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1170	>	}
1171	>
1172	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1173	>	molMembershipArray = new int[tot_atoms];
1174	>
1175	>	for(i=0; i<nInfo; i++){
1176	>	info[i].n_atoms = tot_atoms;
1177	>	info[i].n_bonds = tot_bonds;
1178	>	info[i].n_bends = tot_bends;
1179	>	info[i].n_torsions = tot_torsions;
1180	>	info[i].n_SRI = tot_SRI;
1181	>	info[i].n_mol = tot_nmol;
1182	>
1183	>	info[i].molMembershipArray = molMembershipArray;
1184	>	}
1185	>	}
1186
1187	<	bond_pair* theBonds;
857	<	bend_set* theBends;
858	<	torsion_set* theTorsions;
1187	>	#ifdef IS_MPI
1188
1189	+	void SimSetup::mpiMolDivide( void ){
1190
1191	<	//init the forceField paramters
1191	>	int i, j, k;
1192	>	int localMol, allMol;
1193	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1194
1195	<	the_ff->readParams();
864	<
1195	>	mpiSim = new mpiSimulation( info );
1196
1197	<	// init the atoms
1197	>	globalIndex = mpiSim->divideLabor();
1198
1199	<	double ux, uy, uz, u, uSqr;
1199	>	// set up the local variables
1200
1201	<	atomOffset = 0;
1202	<	excludeOffset = 0;
1203	<	for(i=0; i<simnfo->n_mol; i++){
1204	<
1205	<	stampID = the_molecules[i].getStampID();
1201	>	mol2proc = mpiSim->getMolToProcMap();
1202	>	molCompType = mpiSim->getMolComponentType();
1203	>
1204	>	allMol = 0;
1205	>	localMol = 0;
1206	>	local_atoms = 0;
1207	>	local_bonds = 0;
1208	>	local_bends = 0;
1209	>	local_torsions = 0;
1210	>	globalAtomIndex = 0;
1211
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;
1212
1213	<	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];
1213	>	for( i=0; i<n_components; i++ ){
1214
1215	<	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++){
1215	>	for( j=0; j<components_nmol[i]; j++ ){
1216
1217	<	currentAtom = comp_stamps[stampID]->getAtom( j );
897	<	if( currentAtom->haveOrientation() ){
1217	>	if( mol2proc[allMol] == worldRank ){
1218
1219	<	dAtom = new DirectionalAtom(j + atomOffset);
1220	<	simnfo->n_oriented++;
1221	<	info.myAtoms[j] = dAtom;
1222	<
1223	<	ux = currentAtom->getOrntX();
1224	<	uy = currentAtom->getOrntY();
1225	<	uz = currentAtom->getOrntZ();
1226	<
1227	<	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 );
1219	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1220	>	local_bonds +=    comp_stamps[i]->getNBonds();
1221	>	local_bends +=    comp_stamps[i]->getNBends();
1222	>	local_torsions += comp_stamps[i]->getNTorsions();
1223	>	localMol++;
1224	>	}
1225	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1226	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1227	>	globalAtomIndex++;
1228		}
1229	<	else{
1230	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
1231	<	}
1232	<	info.myAtoms[j]->setType( currentAtom->getType() );
1233	<
1234	<	#ifdef IS_MPI
1235	<
1236	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1237	<
1229	>
1230	>	allMol++;
1231	>	}
1232	>	}
1233	>	local_SRI = local_bonds + local_bends + local_torsions;
1234	>
1235	>	info[0].n_atoms = mpiSim->getMyNlocal();
1236	>
1237	>	if( local_atoms != info[0].n_atoms ){
1238	>	sprintf( painCave.errMsg,
1239	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	>	" localAtom (%d) are not equal.\n",
1241	>	info[0].n_atoms,
1242	>	local_atoms );
1243	>	painCave.isFatal = 1;
1244	>	simError();
1245	>	}
1246	>
1247	>	info[0].n_bonds = local_bonds;
1248	>	info[0].n_bends = local_bends;
1249	>	info[0].n_torsions = local_torsions;
1250	>	info[0].n_SRI = local_SRI;
1251	>	info[0].n_mol = localMol;
1252	>
1253	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1254	>	MPIcheckPoint();
1255	>	}
1256	>
1257		#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;
1258
937	–	exI = theBonds[j].a;
938	–	exJ = theBonds[j].b;
1259
1260	<	// exclude_I must always be the smaller of the pair
1261	<	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
1260	>	void SimSetup::makeSysArrays( void ){
1261	>	int i, j, k, l;
1262
1263	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1264	<	#endif  //is_mpi
1265	<	}
958	<	excludeOffset += info.nBonds;
1263	>	Atom** the_atoms;
1264	>	Molecule* the_molecules;
1265	>	Exclude** the_excludes;
1266
1267	<	//make the bends
1268	<	for(j=0; j<info.nBends; j++){
1269	<
1270	<	currentBend = comp_stamps[stampID]->getBend( j );
1271	<	theBends[j].a = currentBend->getA() + atomOffset;
1272	<	theBends[j].b = currentBend->getB() + atomOffset;
1273	<	theBends[j].c = currentBend->getC() + atomOffset;
1274	<
1275	<	if( currentBend->haveExtras() ){
1276	<
1277	<	extras = currentBend->getExtras();
1278	<	current_extra = extras;
1279	<
1280	<	while( current_extra != NULL ){
1281	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1282	<
1283	<	switch( current_extra->getType() ){
1284	<
1285	<	case 0:
1286	<	theBends[j].ghost =
1287	<	current_extra->getInt() + atomOffset;
1288	<	theBends[j].isGhost = 1;
1289	<	break;
1290	<
1291	<	case 1:
1292	<	theBends[j].ghost =
1293	<	(int)current_extra->getDouble() + atomOffset;
1294	<	theBends[j].isGhost = 1;
1295	<	break;
1296	<
1297	<	default:
1298	<	sprintf( painCave.errMsg,
1299	<	"SimSetup Error: ghostVectorSource was neither a "
1300	<	"double nor an int.\n"
1301	<	"-->Bend[%d] in %s\n",
1302	<	j, comp_stamps[stampID]->getID() );
1303	<	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();
1267	>
1268	>	for(l=0; l<nInfo; l++){
1269	>
1270	>	// create the atom and short range interaction arrays
1271	>
1272	>	the_atoms = new Atom*[info[l].n_atoms];
1273	>	the_molecules = new Molecule[info[l].n_mol];
1274	>	int molIndex;
1275	>
1276	>	// initialize the molecule's stampID's
1277	>
1278	>	#ifdef IS_MPI
1279	>
1280	>
1281	>	molIndex = 0;
1282	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1283	>
1284	>	if(mol2proc[i] == worldRank ){
1285	>	the_molecules[molIndex].setStampID( molCompType[i] );
1286	>	the_molecules[molIndex].setMyIndex( molIndex );
1287	>	the_molecules[molIndex].setGlobalIndex( i );
1288	>	molIndex++;
1289	>	}
1290	>	}
1291	>
1292	>	#else // is_mpi
1293	>
1294	>	molIndex = 0;
1295	>	globalAtomIndex = 0;
1296	>	for(i=0; i<n_components; i++){
1297	>	for(j=0; j<components_nmol[i]; j++ ){
1298	>	the_molecules[molIndex].setStampID( i );
1299	>	the_molecules[molIndex].setMyIndex( molIndex );
1300	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1301	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1302	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1303	>	globalAtomIndex++;
1304		}
1305	+	molIndex++;
1306		}
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
1307		}
1308	<	excludeOffset += info.nBends;
1308	>
1309	>
1310	>	#endif // is_mpi
1311
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;
1312
1313	<	// exclude_I must always be the smaller of the pair
1314	<	if( exI > exJ ){
1315	<	tempEx = exI;
1316	<	exI = exJ;
1317	<	exJ = tempEx;
1313	>	if( info[l].n_SRI ){
1314	>
1315	>	Exclude::createArray(info[l].n_SRI);
1316	>	the_excludes = new Exclude*[info[l].n_SRI];
1317	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1318	>	the_excludes[ex] = new Exclude(ex);
1319		}
1320	<	#ifdef IS_MPI
1321	<	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
1320	>	info[l].globalExcludes = new int;
1321	>	info[l].n_exclude = info[l].n_SRI;
1322		}
1323	<	excludeOffset += info.nTorsions;
1075	<
1323	>	else{
1324
1325	<	// send the arrays off to the forceField for init.
1325	>	Exclude::createArray( 1 );
1326	>	the_excludes = new Exclude*;
1327	>	the_excludes[0] = new Exclude(0);
1328	>	the_excludes[0]->setPair( 0,0 );
1329	>	info[l].globalExcludes = new int;
1330	>	info[l].globalExcludes[0] = 0;
1331	>	info[l].n_exclude = 0;
1332	>	}
1333
1334	<	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 );
1334	>	// set the arrays into the SimInfo object
1335
1336	+	info[l].atoms = the_atoms;
1337	+	info[l].molecules = the_molecules;
1338	+	info[l].nGlobalExcludes = 0;
1339	+	info[l].excludes = the_excludes;
1340
1341	<	the_molecules[i].initialize( info );
1342	<
1087	<
1088	<	atomOffset += info.nAtoms;
1089	<	delete[] theBonds;
1090	<	delete[] theBends;
1091	<	delete[] theTorsions;
1341	>	the_ff->setSimInfo( info );
1342	>
1343		}
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	–
1344		}
1345
1346	<	void SimSetup::initFromBass( void ){
1346	>	void SimSetup::makeIntegrator( void ){
1347
1348	<	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;
1348	>	int k;
1349
1350	<	temp1 = (double)tot_nmol / 4.0;
1351	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1352	<	temp3 = ceil( temp2 );
1350	>	NVT<RealIntegrator>*  myNVT = NULL;
1351	>	NPTi<RealIntegrator>* myNPTi = NULL;
1352	>	NPTf<RealIntegrator>* myNPTf = NULL;
1353	>	NPTim<RealIntegrator>* myNPTim = NULL;
1354	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1355	>
1356	>	for(k=0; k<nInfo; k++){
1357	>
1358	>	switch( ensembleCase ){
1359	>
1360	>	case NVE_ENS:
1361	>	if (globals->haveZconstraints()){
1362	>	setupZConstraint(info[k]);
1363	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1364	>	}
1365
1366	<	have_extra =0;
1367	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1368	<	have_extra =1;
1366	>	else
1367	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1368	>	break;
1369	>
1370	>	case NVT_ENS:
1371	>	if (globals->haveZconstraints()){
1372	>	setupZConstraint(info[k]);
1373	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1374	>	}
1375	>	else
1376	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1377
1378	<	n_cells = (int)temp3 - 1;
1379	<	cellx = simnfo->boxLx / temp3;
1380	<	celly = simnfo->boxLy / temp3;
1381	<	cellz = simnfo->boxLz / temp3;
1382	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1383	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1384	<	n_per_extra = (int)ceil( temp1 );
1378	>	myNVT->setTargetTemp(globals->getTargetTemp());
1379	>
1380	>	if (globals->haveTauThermostat())
1381	>	myNVT->setTauThermostat(globals->getTauThermostat());
1382	>
1383	>	else {
1384	>	sprintf( painCave.errMsg,
1385	>	"SimSetup error: If you use the NVT\n"
1386	>	"    ensemble, you must set tauThermostat.\n");
1387	>	painCave.isFatal = 1;
1388	>	simError();
1389	>	}
1390	>	break;
1391	>
1392	>	case NPTi_ENS:
1393	>	if (globals->haveZconstraints()){
1394	>	setupZConstraint(info[k]);
1395	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1396	>	}
1397	>	else
1398	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1399
1400	<	if( n_per_extra > 4){
1400	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1401	>
1402	>	if (globals->haveTargetPressure())
1403	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1404	>	else {
1405	>	sprintf( painCave.errMsg,
1406	>	"SimSetup error: If you use a constant pressure\n"
1407	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1408	>	painCave.isFatal = 1;
1409	>	simError();
1410	>	}
1411	>
1412	>	if( globals->haveTauThermostat() )
1413	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1414	>	else{
1415	>	sprintf( painCave.errMsg,
1416	>	"SimSetup error: If you use an NPT\n"
1417	>	"    ensemble, you must set tauThermostat.\n");
1418	>	painCave.isFatal = 1;
1419	>	simError();
1420	>	}
1421	>
1422	>	if( globals->haveTauBarostat() )
1423	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1424	>	else{
1425	>	sprintf( painCave.errMsg,
1426	>	"SimSetup error: If you use an NPT\n"
1427	>	"    ensemble, you must set tauBarostat.\n");
1428	>	painCave.isFatal = 1;
1429	>	simError();
1430	>	}
1431	>	break;
1432	>
1433	>	case NPTf_ENS:
1434	>	if (globals->haveZconstraints()){
1435	>	setupZConstraint(info[k]);
1436	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1437	>	}
1438	>	else
1439	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1440	>
1441	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1442	>
1443	>	if (globals->haveTargetPressure())
1444	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1445	>	else {
1446	>	sprintf( painCave.errMsg,
1447	>	"SimSetup error: If you use a constant pressure\n"
1448	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	>	painCave.isFatal = 1;
1450	>	simError();
1451	>	}
1452	>
1453	>	if( globals->haveTauThermostat() )
1454	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1455	>	else{
1456	>	sprintf( painCave.errMsg,
1457	>	"SimSetup error: If you use an NPT\n"
1458	>	"    ensemble, you must set tauThermostat.\n");
1459	>	painCave.isFatal = 1;
1460	>	simError();
1461	>	}
1462	>
1463	>	if( globals->haveTauBarostat() )
1464	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1465	>	else{
1466	>	sprintf( painCave.errMsg,
1467	>	"SimSetup error: If you use an NPT\n"
1468	>	"    ensemble, you must set tauBarostat.\n");
1469	>	painCave.isFatal = 1;
1470	>	simError();
1471	>	}
1472	>	break;
1473	>
1474	>	case NPTim_ENS:
1475	>	if (globals->haveZconstraints()){
1476	>	setupZConstraint(info[k]);
1477	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1478	>	}
1479	>	else
1480	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1481	>
1482	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1483	>
1484	>	if (globals->haveTargetPressure())
1485	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1486	>	else {
1487	>	sprintf( painCave.errMsg,
1488	>	"SimSetup error: If you use a constant pressure\n"
1489	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1490	>	painCave.isFatal = 1;
1491	>	simError();
1492	>	}
1493	>
1494	>	if( globals->haveTauThermostat() )
1495	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1496	>	else{
1497	>	sprintf( painCave.errMsg,
1498	>	"SimSetup error: If you use an NPT\n"
1499	>	"    ensemble, you must set tauThermostat.\n");
1500	>	painCave.isFatal = 1;
1501	>	simError();
1502	>	}
1503	>
1504	>	if( globals->haveTauBarostat() )
1505	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1506	>	else{
1507		sprintf( painCave.errMsg,
1508	<	"SimSetup error. There has been an error in constructing"
1509	<	" the non-complete lattice.\n" );
1508	>	"SimSetup error: If you use an NPT\n"
1509	>	"    ensemble, you must set tauBarostat.\n");
1510		painCave.isFatal = 1;
1511		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 );
1512		}
1513	<	}
1514	<	}
1515	<
1516	<	if( have_extra ){
1517	<	done = 0;
1518	<
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;
1513	>	break;
1514	>
1515	>	case NPTfm_ENS:
1516	>	if (globals->haveZconstraints()){
1517	>	setupZConstraint(info[k]);
1518	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1519		}
1520	<	else start_ndx = 0;
1520	>	else
1521	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1522
1523	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1524	<
1525	<	makeElement( i * cellx,
1526	<	j * celly,
1527	<	k * cellz );
1528	<	done = ( current_mol >= tot_nmol );
1529	<
1530	<	if( !done && n_per_extra > 1 ){
1531	<	makeElement( i * cellx + 0.5 * cellx,
1532	<	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	<	}
1523	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1524	>
1525	>	if (globals->haveTargetPressure())
1526	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1527	>	else {
1528	>	sprintf( painCave.errMsg,
1529	>	"SimSetup error: If you use a constant pressure\n"
1530	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1531	>	painCave.isFatal = 1;
1532	>	simError();
1533		}
1534	+
1535	+	if( globals->haveTauThermostat() )
1536	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1537	+	else{
1538	+	sprintf( painCave.errMsg,
1539	+	"SimSetup error: If you use an NPT\n"
1540	+	"    ensemble, you must set tauThermostat.\n");
1541	+	painCave.isFatal = 1;
1542	+	simError();
1543	+	}
1544	+
1545	+	if( globals->haveTauBarostat() )
1546	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1547	+	else{
1548	+	sprintf( painCave.errMsg,
1549	+	"SimSetup error: If you use an NPT\n"
1550	+	"    ensemble, you must set tauBarostat.\n");
1551	+	painCave.isFatal = 1;
1552	+	simError();
1553	+	}
1554	+	break;
1555	+
1556	+	default:
1557	+	sprintf( painCave.errMsg,
1558	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1559	+	painCave.isFatal = 1;
1560	+	simError();
1561		}
1562		}
1563	+	}
1564
1565	+	void SimSetup::initFortran( void ){
1566
1567	<	for( i=0; i<simnfo->n_atoms; i++ ){
1568	<	simnfo->atoms[i]->set_vx( 0.0 );
1569	<	simnfo->atoms[i]->set_vy( 0.0 );
1570	<	simnfo->atoms[i]->set_vz( 0.0 );
1567	>	info[0].refreshSim();
1568	>
1569	>	if( !strcmp( info[0].mixingRule, "standard") ){
1570	>	the_ff->initForceField( LB_MIXING_RULE );
1571		}
1572	<	}
1572	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1573	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1574	>	}
1575	>	else{
1576	>	sprintf( painCave.errMsg,
1577	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1578	>	info[0].mixingRule );
1579	>	painCave.isFatal = 1;
1580	>	simError();
1581	>	}
1582
1230	–	void SimSetup::makeElement( double x, double y, double z ){
1583
1584	<	int k;
1585	<	AtomStamp* current_atom;
1586	<	DirectionalAtom* dAtom;
1587	<	double rotMat[3][3];
1584	>	#ifdef IS_MPI
1585	>	strcpy( checkPointMsg,
1586	>	"Successfully intialized the mixingRule for Fortran." );
1587	>	MPIcheckPoint();
1588	>	#endif // is_mpi
1589
1590	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1590	>	}
1591
1592	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1593	<	if( !current_atom->havePosition() ){
1592	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1593	>	{
1594	>	int nZConstraints;
1595	>	ZconStamp** zconStamp;
1596	>
1597	>	if(globals->haveZconstraintTime()){
1598	>
1599	>	//add sample time of z-constraint  into SimInfo's property list
1600	>	DoubleData* zconsTimeProp = new DoubleData();
1601	>	zconsTimeProp->setID(ZCONSTIME_ID);
1602	>	zconsTimeProp->setData(globals->getZconsTime());
1603	>	theInfo.addProperty(zconsTimeProp);
1604	>	}
1605	>	else{
1606		sprintf( painCave.errMsg,
1607	<	"SimSetup:initFromBass error.\n"
1608	<	"\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() );
1607	>	"ZConstraint error: If you use an ZConstraint\n"
1608	>	" , you must set sample time.\n");
1609		painCave.isFatal = 1;
1610	<	simError();
1610	>	simError();
1611		}
1612
1613	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1614	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1615	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1613	>	//
1614	>	nZConstraints = globals->getNzConstraints();
1615	>	zconStamp = globals->getZconStamp();
1616	>	ZConsParaItem tempParaItem;
1617
1618	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1618	>	ZConsParaData* zconsParaData = new ZConsParaData();
1619	>	zconsParaData->setID(ZCONSPARADATA_ID);
1620	>
1621	>	for(int i = 0; i < nZConstraints; i++){
1622	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1623	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1624	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1625	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1626
1627	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1627	>	zconsParaData->addItem(tempParaItem);
1628	>	}
1629
1630	<	rotMat[0][0] = 1.0;
1631	<	rotMat[0][1] = 0.0;
1632	<	rotMat[0][2] = 0.0;
1630	>	//sort the parameters by index of molecules
1631	>	zconsParaData->sortByIndex();
1632	>
1633	>	//push data into siminfo, therefore, we can retrieve later
1634	>	theInfo.addProperty(zconsParaData);
1635
1636	<	rotMat[1][0] = 0.0;
1637	<	rotMat[1][1] = 1.0;
1638	<	rotMat[1][2] = 0.0;
1639	<
1640	<	rotMat[2][0] = 0.0;
1641	<	rotMat[2][1] = 0.0;
1270	<	rotMat[2][2] = 1.0;
1271	<
1272	<	dAtom->setA( rotMat );
1636	>	//push zconsTol into siminfo, if user does not specify
1637	>	//value for zconsTol, a default value will be used
1638	>	DoubleData* zconsTol = new DoubleData();
1639	>	zconsTol->setID(ZCONSTOL_ID);
1640	>	if(globals->haveZconsTol()){
1641	>	zconsTol->setData(globals->getZconsTol());
1642		}
1643	+	else{
1644	+	double defaultZConsTol = 1E-6;
1645	+	sprintf( painCave.errMsg,
1646	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1647	+	" , default value %f is used.\n", defaultZConsTol);
1648	+	painCave.isFatal = 0;
1649	+	simError();
1650
1651	<	current_atom_ndx++;
1652	<	}
1653	<
1654	<	current_mol++;
1655	<	current_comp_mol++;
1656	<
1657	<	if( current_comp_mol >= components_nmol[current_comp] ){
1658	<
1659	<	current_comp_mol = 0;
1660	<	current_comp++;
1661	<	}
1651	>	zconsTol->setData(defaultZConsTol);
1652	>	}
1653	>	theInfo.addProperty(zconsTol);
1654	>
1655	>	//Determine the name of ouput file and add it into SimInfo's property list
1656	>	//Be careful, do not use inFileName, since it is a pointer which
1657	>	//point to a string at master node, and slave nodes do not contain that string
1658	>
1659	>	string zconsOutput(theInfo.finalName);
1660	>
1661	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1662	>
1663	>	StringData* zconsFilename = new StringData();
1664	>	zconsFilename->setID(ZCONSFILENAME_ID);
1665	>	zconsFilename->setData(zconsOutput);
1666	>
1667	>	theInfo.addProperty(zconsFilename);
1668		}

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