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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 582 by mmeineke, Wed Jul 9 15:33:46 2003 UTC vs.
Revision 690 by mmeineke, Tue Aug 12 21:44:06 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 NPTi_ENS 2
23	<	#define NPTf_ENS 3
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
22	–
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 39 | 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 74 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
79	–	MakeStamps *the_stamps;
80	–	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	>	gatherInfo();
102	>
103	>	// creation of complex system objects
104	>
105	>	sysObjectsCreation();
106	>
107	>	// check on the post processing info
108	>
109	>	finalInfoCheck();
110	>
111	>	// initialize the system coordinates
112	>
113	>	if( !isInfoArray ) initSystemCoords();
114	>
115	>	// make the output filenames
116	>
117	>	makeOutNames();
118	>
119	>	// make the integrator
120	>
121	>	makeIntegrator();
122	>
123	>	#ifdef IS_MPI
124	>	mpiSim->mpiRefresh();
125	>	#endif
126	>
127	>	// initialize the Fortran
128	>
129	>	initFortran();
130	>
131	>
132	>
133	>	}
134	>
135	>
136	>	void SimSetup::makeMolecules( void ){
137	>
138	>	int k,l;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148	>
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152	>
153	>
154	>	//init the forceField paramters
155	>
156	>	the_ff->readParams();
157	>
158	>
159	>	// init the atoms
160	>
161	>	double ux, uy, uz, u, uSqr;
162	>
163	>	for(k=0; k<nInfo; k++){
164	>
165	>	the_ff->setSimInfo( &(info[k]) );
166	>
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for(i=0; i<info[k].n_mol; i++){
170	>
171	>	stampID = info[k].molecules[i].getStampID();
172	>
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178	>
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184	>
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188	>
189	>	// make the Atoms
190	>
191	>	for(j=0; j<molInfo.nAtoms; j++){
192	>
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195	>
196	>	dAtom = new DirectionalAtom( (j + atomOffset),
197	>	info[k].getConfiguration() );
198	>	info[k].n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200	>
201	>	ux = currentAtom->getOrntX();
202	>	uy = currentAtom->getOrntY();
203	>	uz = currentAtom->getOrntZ();
204	>
205	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	>
207	>	u = sqrt( uSqr );
208	>	ux = ux / u;
209	>	uy = uy / u;
210	>	uz = uz / u;
211	>
212	>	dAtom->setSUx( ux );
213	>	dAtom->setSUy( uy );
214	>	dAtom->setSUz( uz );
215	>	}
216	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	>	info[k].getConfiguration() );
219	>	}
220	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	>
222	>	#ifdef IS_MPI
223	>
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	>
226	>	#endif // is_mpi
227	>	}
228	>
229	>	// make the bonds
230	>	for(j=0; j<molInfo.nBonds; j++){
231	>
232	>	currentBond = comp_stamps[stampID]->getBond( j );
233	>	theBonds[j].a = currentBond->getA() + atomOffset;
234	>	theBonds[j].b = currentBond->getB() + atomOffset;
235	>
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244	>	}
245	>	#ifdef IS_MPI
246	>	tempEx = exI;
247	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	>	tempEx = exJ;
249	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	>
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252	>	#else  // isn't MPI
253	>
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	>	#endif  //is_mpi
256	>	}
257	>	excludeOffset += molInfo.nBonds;
258	>
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261	>
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266	>
267	>	if( currentBend->haveExtras() ){
268	>
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276	>
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290	>	sprintf( painCave.errMsg,
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298	>	}
299	>
300	>	else{
301	>
302	>	sprintf( painCave.errMsg,
303	>	"SimSetup Error: unhandled bend assignment:\n"
304	>	"    -->%s in Bend[%d] in %s\n",
305	>	current_extra->getlhs(),
306	>	j, comp_stamps[stampID]->getID() );
307	>	painCave.isFatal = 1;
308	>	simError();
309	>	}
310	>
311	>	current_extra = current_extra->getNext();
312	>	}
313	>	}
314	>
315	>	if( !theBends[j].isGhost ){
316	>
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].c;
319	>	}
320	>	else{
321	>
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].b;
324	>	}
325	>
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331	>	}
332	>	#ifdef IS_MPI
333	>	tempEx = exI;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	>
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	#else  // isn't MPI
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	#endif  //is_mpi
342	>	}
343	>	excludeOffset += molInfo.nBends;
344	>
345	>	for(j=0; j<molInfo.nTorsions; j++){
346	>
347	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352	>
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355	>
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361	>	}
362	>	#ifdef IS_MPI
363	>	tempEx = exI;
364	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	>	tempEx = exJ;
366	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	>
368	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369	>	#else  // isn't MPI
370	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371	>	#endif  //is_mpi
372	>	}
373	>	excludeOffset += molInfo.nTorsions;
374	>
375	>
376	>	// send the arrays off to the forceField for init.
377	>
378	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	>
383	>
384	>	info[k].molecules[i].initialize( molInfo );
385	>
386	>
387	>	atomOffset += molInfo.nAtoms;
388	>	delete[] theBonds;
389	>	delete[] theBends;
390	>	delete[] theTorsions;
391	>	}
392	>	}
393
394	+	#ifdef IS_MPI
395	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
396	+	MPIcheckPoint();
397	+	#endif // is_mpi
398	+
399	+	// clean up the forcefield
400	+
401	+	the_ff->calcRcut();
402	+	the_ff->cleanMe();
403	+
404	+	}
405	+
406	+	void SimSetup::initFromBass( void ){
407	+
408	+	int i, j, k;
409	+	int n_cells;
410	+	double cellx, celly, cellz;
411	+	double temp1, temp2, temp3;
412	+	int n_per_extra;
413	+	int n_extra;
414	+	int have_extra, done;
415	+
416	+	double vel[3];
417	+	vel[0] = 0.0;
418	+	vel[1] = 0.0;
419	+	vel[2] = 0.0;
420	+
421	+	temp1 = (double)tot_nmol / 4.0;
422	+	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423	+	temp3 = ceil( temp2 );
424	+
425	+	have_extra =0;
426	+	if( temp2 < temp3 ){ // we have a non-complete lattice
427	+	have_extra =1;
428	+
429	+	n_cells = (int)temp3 - 1;
430	+	cellx = info[0].boxL[0] / temp3;
431	+	celly = info[0].boxL[1] / temp3;
432	+	cellz = info[0].boxL[2] / temp3;
433	+	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434	+	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435	+	n_per_extra = (int)ceil( temp1 );
436	+
437	+	if( n_per_extra > 4){
438	+	sprintf( painCave.errMsg,
439	+	"SimSetup error. There has been an error in constructing"
440	+	" the non-complete lattice.\n" );
441	+	painCave.isFatal = 1;
442	+	simError();
443	+	}
444	+	}
445	+	else{
446	+	n_cells = (int)temp3;
447	+	cellx = info[0].boxL[0] / temp3;
448	+	celly = info[0].boxL[1] / temp3;
449	+	cellz = info[0].boxL[2] / temp3;
450	+	}
451	+
452	+	current_mol = 0;
453	+	current_comp_mol = 0;
454	+	current_comp = 0;
455	+	current_atom_ndx = 0;
456	+
457	+	for( i=0; i < n_cells ; i++ ){
458	+	for( j=0; j < n_cells; j++ ){
459	+	for( k=0; k < n_cells; k++ ){
460	+
461	+	makeElement( i * cellx,
462	+	j * celly,
463	+	k * cellz );
464	+
465	+	makeElement( i * cellx + 0.5 * cellx,
466	+	j * celly + 0.5 * celly,
467	+	k * cellz );
468	+
469	+	makeElement( i * cellx,
470	+	j * celly + 0.5 * celly,
471	+	k * cellz + 0.5 * cellz );
472	+
473	+	makeElement( i * cellx + 0.5 * cellx,
474	+	j * celly,
475	+	k * cellz + 0.5 * cellz );
476	+	}
477	+	}
478	+	}
479	+
480	+	if( have_extra ){
481	+	done = 0;
482	+
483	+	int start_ndx;
484	+	for( i=0; i < (n_cells+1) && !done; i++ ){
485	+	for( j=0; j < (n_cells+1) && !done; j++ ){
486	+
487	+	if( i < n_cells ){
488	+
489	+	if( j < n_cells ){
490	+	start_ndx = n_cells;
491	+	}
492	+	else start_ndx = 0;
493	+	}
494	+	else start_ndx = 0;
495	+
496	+	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497	+
498	+	makeElement( i * cellx,
499	+	j * celly,
500	+	k * cellz );
501	+	done = ( current_mol >= tot_nmol );
502	+
503	+	if( !done && n_per_extra > 1 ){
504	+	makeElement( i * cellx + 0.5 * cellx,
505	+	j * celly + 0.5 * celly,
506	+	k * cellz );
507	+	done = ( current_mol >= tot_nmol );
508	+	}
509	+
510	+	if( !done && n_per_extra > 2){
511	+	makeElement( i * cellx,
512	+	j * celly + 0.5 * celly,
513	+	k * cellz + 0.5 * cellz );
514	+	done = ( current_mol >= tot_nmol );
515	+	}
516	+
517	+	if( !done && n_per_extra > 3){
518	+	makeElement( i * cellx + 0.5 * cellx,
519	+	j * celly,
520	+	k * cellz + 0.5 * cellz );
521	+	done = ( current_mol >= tot_nmol );
522	+	}
523	+	}
524	+	}
525	+	}
526	+	}
527	+
528	+	for( i=0; i<info[0].n_atoms; i++ ){
529	+	info[0].atoms[i]->setVel( vel );
530	+	}
531	+	}
532	+
533	+	void SimSetup::makeElement( double x, double y, double z ){
534	+
535	+	int k;
536	+	AtomStamp* current_atom;
537	+	DirectionalAtom* dAtom;
538	+	double rotMat[3][3];
539	+	double pos[3];
540	+
541	+	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542	+
543	+	current_atom = comp_stamps[current_comp]->getAtom( k );
544	+	if( !current_atom->havePosition() ){
545	+	sprintf( painCave.errMsg,
546	+	"SimSetup:initFromBass error.\n"
547	+	"\tComponent %s, atom %s does not have a position specified.\n"
548	+	"\tThe initialization routine is unable to give a start"
549	+	" position.\n",
550	+	comp_stamps[current_comp]->getID(),
551	+	current_atom->getType() );
552	+	painCave.isFatal = 1;
553	+	simError();
554	+	}
555	+
556	+	pos[0] = x + current_atom->getPosX();
557	+	pos[1] = y + current_atom->getPosY();
558	+	pos[2] = z + current_atom->getPosZ();
559	+
560	+	info[0].atoms[current_atom_ndx]->setPos( pos );
561	+
562	+	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563	+
564	+	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565	+
566	+	rotMat[0][0] = 1.0;
567	+	rotMat[0][1] = 0.0;
568	+	rotMat[0][2] = 0.0;
569	+
570	+	rotMat[1][0] = 0.0;
571	+	rotMat[1][1] = 1.0;
572	+	rotMat[1][2] = 0.0;
573	+
574	+	rotMat[2][0] = 0.0;
575	+	rotMat[2][1] = 0.0;
576	+	rotMat[2][2] = 1.0;
577	+
578	+	dAtom->setA( rotMat );
579	+	}
580	+
581	+	current_atom_ndx++;
582	+	}
583	+
584	+	current_mol++;
585	+	current_comp_mol++;
586	+
587	+	if( current_comp_mol >= components_nmol[current_comp] ){
588	+
589	+	current_comp_mol = 0;
590	+	current_comp++;
591	+	}
592	+	}
593	+
594	+
595	+	void SimSetup::gatherInfo( void ){
596	+	int i,j,k;
597	+
598		ensembleCase = -1;
599		ffCase = -1;
600
89	–	// get the stamps and globals;
90	–	the_stamps = stamps;
91	–	the_globals = globals;
92	–
601		// set the easy ones first
94	–	simnfo->target_temp = the_globals->getTargetTemp();
95	–	simnfo->dt = the_globals->getDt();
96	–	simnfo->run_time = the_globals->getRunTime();
602
603	<	// get the ones we know are there, yet still may need some work.
604	<	n_components = the_globals->getNComponents();
605	<	strcpy( force_field, the_globals->getForceField() );
603	>	for( i=0; i<nInfo; i++){
604	>	info[i].target_temp = globals->getTargetTemp();
605	>	info[i].dt = globals->getDt();
606	>	info[i].run_time = globals->getRunTime();
607	>	}
608	>	n_components = globals->getNComponents();
609
610	+
611	+	// get the forceField
612	+
613	+	strcpy( force_field, globals->getForceField() );
614	+
615		if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616		else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618		else{
619		sprintf( painCave.errMsg,
620		"SimSetup Error. Unrecognized force field -> %s\n",
#	Line 109 | Line 623 | void SimSetup::createSim( void ){
623		simError();
624		}
625
626	<	// get the ensemble:
113	<	strcpy( ensemble, the_globals->getEnsemble() );
626	>	// get the ensemble
627
628	+	strcpy( ensemble, globals->getEnsemble() );
629	+
630		if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631		else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632		else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633		ensembleCase = NPTi_ENS;
634		else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637		else{
638		sprintf( painCave.errMsg,
639		"SimSetup Warning. Unrecognized Ensemble -> %s, "
#	Line 127 | Line 644 | void SimSetup::createSim( void ){
644		strcpy( ensemble, "NVE" );
645		ensembleCase = NVE_ENS;
646		}
647	<	strcpy( simnfo->ensemble, ensemble );
647	>
648	>	for(i=0; i<nInfo; i++){
649	>
650	>	strcpy( info[i].ensemble, ensemble );
651
652	+	// get the mixing rule
653
654	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
655	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
135	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
136	<	//     if (the_globals->haveTargetPressure())
137	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
138	<	//     else {
139	<	//       sprintf( painCave.errMsg,
140	<	//                "SimSetup error: If you use the constant pressure\n"
141	<	//                "    ensemble, you must set targetPressure.\n"
142	<	//                "    This was found in the BASS file.\n");
143	<	//       painCave.isFatal = 1;
144	<	//       simError();
145	<	//     }
146	<
147	<	//     if (the_globals->haveTauThermostat())
148	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
149	<	//     else if (the_globals->haveQmass())
150	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
151	<	//     else {
152	<	//       sprintf( painCave.errMsg,
153	<	//                "SimSetup error: If you use one of the constant temperature\n"
154	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
155	<	//                "    Neither of these was found in the BASS file.\n");
156	<	//       painCave.isFatal = 1;
157	<	//       simError();
158	<	//     }
159	<
160	<	//     if (the_globals->haveTauBarostat())
161	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
162	<	//     else {
163	<	//       sprintf( painCave.errMsg,
164	<	//                "SimSetup error: If you use the constant pressure\n"
165	<	//                "    ensemble, you must set tauBarostat.\n"
166	<	//                "    This was found in the BASS file.\n");
167	<	//       painCave.isFatal = 1;
168	<	//       simError();
169	<	//     }
170	<
171	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
172	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
173	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
174	<
175	<	//     if (the_globals->haveTauThermostat())
176	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
177	<	//     else if (the_globals->haveQmass())
178	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
179	<	//     else {
180	<	//       sprintf( painCave.errMsg,
181	<	//                "SimSetup error: If you use one of the constant temperature\n"
182	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
183	<	//                "    Neither of these was found in the BASS file.\n");
184	<	//       painCave.isFatal = 1;
185	<	//       simError();
186	<	//     }
187	<
188	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
189	<	simnfo->usePBC = the_globals->getPBC();
190	<
191	<	int usesDipoles = 0;
192	<	switch( ffCase ){
193	<
194	<	case FF_DUFF:
195	<	the_ff = new DUFF();
196	<	usesDipoles = 1;
197	<	break;
198	<
199	<	case FF_LJ:
200	<	the_ff = new LJFF();
201	<	break;
202	<
203	<	default:
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup Error. Unrecognized force field in case statement.\n");
206	<	painCave.isFatal = 1;
207	<	simError();
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656		}
657	<
210	<	#ifdef IS_MPI
211	<	strcpy( checkPointMsg, "ForceField creation successful" );
212	<	MPIcheckPoint();
213	<	#endif // is_mpi
214	<
657	>
658		// get the components and calculate the tot_nMol and indvidual n_mol
659	<	the_components = the_globals->getComponents();
659	>
660	>	the_components = globals->getComponents();
661		components_nmol = new int[n_components];
218	–	comp_stamps = new MoleculeStamp*[n_components];
662
663	<	if( !the_globals->haveNMol() ){
663	>
664	>	if( !globals->haveNMol() ){
665		// we don't have the total number of molecules, so we assume it is
666		// given in each component
667
#	Line 246 | Line 690 | void SimSetup::createSim( void ){
690		" Please give nMol in the components.\n" );
691		painCave.isFatal = 1;
692		simError();
249	–
250	–
251	–	//     tot_nmol = the_globals->getNMol();
252	–
253	–	//   //we have the total number of molecules, now we check for molfractions
254	–	//     for( i=0; i<n_components; i++ ){
255	–
256	–	//       if( !the_components[i]->haveMolFraction() ){
257	–
258	–	//  if( !the_components[i]->haveNMol() ){
259	–	//    //we have a problem
260	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
261	–	//              << " nMol was given in component
262	–
693		}
694
695	<	#ifdef IS_MPI
266	<	strcpy( checkPointMsg, "Have the number of components" );
267	<	MPIcheckPoint();
268	<	#endif // is_mpi
269	<
270	<	// make an array of molecule stamps that match the components used.
271	<	// also extract the used stamps out into a separate linked list
272	<
273	<	simnfo->nComponents = n_components;
274	<	simnfo->componentsNmol = components_nmol;
275	<	simnfo->compStamps = comp_stamps;
276	<	simnfo->headStamp = new LinkedMolStamp();
695	>	// set the status, sample, and thermal kick times
696
697	<	char* id;
279	<	LinkedMolStamp* headStamp = simnfo->headStamp;
280	<	LinkedMolStamp* currentStamp = NULL;
281	<	for( i=0; i<n_components; i++ ){
697	>	for(i=0; i<nInfo; i++){
698
699	<	id = the_components[i]->getType();
700	<	comp_stamps[i] = NULL;
699	>	if( globals->haveSampleTime() ){
700	>	info[i].sampleTime = globals->getSampleTime();
701	>	info[i].statusTime = info[i].sampleTime;
702	>	info[i].thermalTime = info[i].sampleTime;
703	>	}
704	>	else{
705	>	info[i].sampleTime = globals->getRunTime();
706	>	info[i].statusTime = info[i].sampleTime;
707	>	info[i].thermalTime = info[i].sampleTime;
708	>	}
709
710	<	// check to make sure the component isn't already in the list
710	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712	>	}
713	>
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716	>	}
717
718	<	comp_stamps[i] = headStamp->match( id );
719	<	if( comp_stamps[i] == NULL ){
718	>	// check for the temperature set flag
719	>
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721	>
722	>	// get some of the tricky things that may still be in the globals
723	>
724	>	double boxVector[3];
725	>	if( globals->haveBox() ){
726	>	boxVector[0] = globals->getBox();
727	>	boxVector[1] = globals->getBox();
728	>	boxVector[2] = globals->getBox();
729
730	<	// extract the component from the list;
730	>	info[i].setBox( boxVector );
731	>	}
732	>	else if( globals->haveDensity() ){
733
734	<	currentStamp = the_stamps->extractMolStamp( id );
735	<	if( currentStamp == NULL ){
734	>	double vol;
735	>	vol = (double)tot_nmol / globals->getDensity();
736	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	>	boxVector[1] = boxVector[0];
738	>	boxVector[2] = boxVector[0];
739	>
740	>	info[i].setBox( boxVector );
741	>	}
742	>	else{
743	>	if( !globals->haveBoxX() ){
744		sprintf( painCave.errMsg,
745	<	"SimSetup error: Component \"%s\" was not found in the "
297	<	"list of declared molecules\n",
298	<	id );
745	>	"SimSetup error, no periodic BoxX size given.\n" );
746		painCave.isFatal = 1;
747		simError();
748		}
749	+	boxVector[0] = globals->getBoxX();
750
751	<	headStamp->add( currentStamp );
752	<	comp_stamps[i] = headStamp->match( id );
751	>	if( !globals->haveBoxY() ){
752	>	sprintf( painCave.errMsg,
753	>	"SimSetup error, no periodic BoxY size given.\n" );
754	>	painCave.isFatal = 1;
755	>	simError();
756	>	}
757	>	boxVector[1] = globals->getBoxY();
758	>
759	>	if( !globals->haveBoxZ() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxZ size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764	>	}
765	>	boxVector[2] = globals->getBoxZ();
766	>
767	>	info[i].setBox( boxVector );
768		}
306	–	}
769
770	+	}
771	+
772		#ifdef IS_MPI
773	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
773	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
774		MPIcheckPoint();
775		#endif // is_mpi
312	–
776
777	+	}
778
779
780	<	// caclulate the number of atoms, bonds, bends and torsions
780	>	void SimSetup::finalInfoCheck( void ){
781	>	int index;
782	>	int usesDipoles;
783	>	int i;
784
785	<	tot_atoms = 0;
786	<	tot_bonds = 0;
320	<	tot_bends = 0;
321	<	tot_torsions = 0;
322	<	for( i=0; i<n_components; i++ ){
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787
788	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
789	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
790	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
791	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
792	<	}
793	<
794	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
795	<
796	<	simnfo->n_atoms = tot_atoms;
797	<	simnfo->n_bonds = tot_bonds;
798	<	simnfo->n_bends = tot_bends;
799	<	simnfo->n_torsions = tot_torsions;
800	<	simnfo->n_SRI = tot_SRI;
337	<	simnfo->n_mol = tot_nmol;
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793	>	}
794	>
795	>	#ifdef IS_MPI
796	>	int myUse = usesDipoles;
797	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798	>	#endif //is_mpi
799	>
800	>	double theEcr, theEst;
801
802	<	simnfo->molMembershipArray = new int[tot_atoms];
802	>	if (globals->getUseRF() ) {
803	>	info[i].useReactionField = 1;
804	>
805	>	if( !globals->haveECR() ){
806	>	sprintf( painCave.errMsg,
807	>	"SimSetup Warning: using default value of 1/2 the smallest "
808	>	"box length for the electrostaticCutoffRadius.\n"
809	>	"I hope you have a very fast processor!\n");
810	>	painCave.isFatal = 0;
811	>	simError();
812	>	double smallest;
813	>	smallest = info[i].boxL[0];
814	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	>	theEcr = 0.5 * smallest;
817	>	} else {
818	>	theEcr = globals->getECR();
819	>	}
820	>
821	>	if( !globals->haveEST() ){
822	>	sprintf( painCave.errMsg,
823	>	"SimSetup Warning: using default value of 0.05 * the "
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	>	);
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	theEst = 0.05 * theEcr;
829	>	} else {
830	>	theEst= globals->getEST();
831	>	}
832	>
833	>	info[i].setEcr( theEcr, theEst );
834	>
835	>	if(!globals->haveDielectric() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Error: You are trying to use Reaction Field without"
838	>	"setting a dielectric constant!\n"
839	>	);
840	>	painCave.isFatal = 1;
841	>	simError();
842	>	}
843	>	info[i].dielectric = globals->getDielectric();
844	>	}
845	>	else {
846	>	if (usesDipoles) {
847	>
848	>	if( !globals->haveECR() ){
849	>	sprintf( painCave.errMsg,
850	>	"SimSetup Warning: using default value of 1/2 the smallest "
851	>	"box length for the electrostaticCutoffRadius.\n"
852	>	"I hope you have a very fast processor!\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	double smallest;
856	>	smallest = info[i].boxL[0];
857	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	>	theEcr = 0.5 * smallest;
860	>	} else {
861	>	theEcr = globals->getECR();
862	>	}
863	>
864	>	if( !globals->haveEST() ){
865	>	sprintf( painCave.errMsg,
866	>	"SimSetup Warning: using default value of 0.05 * the "
867	>	"electrostaticCutoffRadius for the "
868	>	"electrostaticSkinThickness\n"
869	>	);
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	theEst = 0.05 * theEcr;
873	>	} else {
874	>	theEst= globals->getEST();
875	>	}
876	>
877	>	info[i].setEcr( theEcr, theEst );
878	>	}
879	>	}
880	>	}
881
882		#ifdef IS_MPI
883	+	strcpy( checkPointMsg, "post processing checks out" );
884	+	MPIcheckPoint();
885	+	#endif // is_mpi
886
887	<	// divide the molecules among processors here.
344	<
345	<	mpiSim = new mpiSimulation( simnfo );
346	<
347	<	globalIndex = mpiSim->divideLabor();
887	>	}
888
889	<	// set up the local variables
889	>	void SimSetup::initSystemCoords( void ){
890	>	int i;
891
892	<	int localMol, allMol;
352	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
892	>	char* inName;
893
354	–	int* mol2proc = mpiSim->getMolToProcMap();
355	–	int* molCompType = mpiSim->getMolComponentType();
356	–
357	–	allMol = 0;
358	–	localMol = 0;
359	–	local_atoms = 0;
360	–	local_bonds = 0;
361	–	local_bends = 0;
362	–	local_torsions = 0;
363	–	globalAtomIndex = 0;
894
895	<
366	<	for( i=0; i<n_components; i++ ){
367	<
368	<	for( j=0; j<components_nmol[i]; j++ ){
369	<
370	<	if( mol2proc[allMol] == worldRank ){
371	<
372	<	local_atoms +=    comp_stamps[i]->getNAtoms();
373	<	local_bonds +=    comp_stamps[i]->getNBonds();
374	<	local_bends +=    comp_stamps[i]->getNBends();
375	<	local_torsions += comp_stamps[i]->getNTorsions();
376	<	localMol++;
377	<	}
378	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
379	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
380	<	globalAtomIndex++;
381	<	}
382	<
383	<	allMol++;
384	<	}
385	<	}
386	<	local_SRI = local_bonds + local_bends + local_torsions;
895	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
896
897	<	simnfo->n_atoms = mpiSim->getMyNlocal();
897	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
898
899	<	if( local_atoms != simnfo->n_atoms ){
899	>	if( globals->haveInitialConfig() ){
900	>
901	>	InitializeFromFile* fileInit;
902	>	#ifdef IS_MPI // is_mpi
903	>	if( worldRank == 0 ){
904	>	#endif //is_mpi
905	>	inName = globals->getInitialConfig();
906	>	fileInit = new InitializeFromFile( inName );
907	>	#ifdef IS_MPI
908	>	}else fileInit = new InitializeFromFile( NULL );
909	>	#endif
910	>	fileInit->readInit( info ); // default velocities on
911	>
912	>	delete fileInit;
913	>	}
914	>	else{
915	>
916	>	#ifdef IS_MPI
917	>
918	>	// no init from bass
919	>
920		sprintf( painCave.errMsg,
921	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
922	<	" localAtom (%d) are not equal.\n",
394	<	simnfo->n_atoms,
395	<	local_atoms );
396	<	painCave.isFatal = 1;
921	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
922	>	painCave.isFatal;
923		simError();
924	+
925	+	#else
926	+
927	+	initFromBass();
928	+
929	+
930	+	#endif
931		}
399	–
400	–	simnfo->n_bonds = local_bonds;
401	–	simnfo->n_bends = local_bends;
402	–	simnfo->n_torsions = local_torsions;
403	–	simnfo->n_SRI = local_SRI;
404	–	simnfo->n_mol = localMol;
405	–
406	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
407	–	MPIcheckPoint();
932
933	<
933	>	#ifdef IS_MPI
934	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
935	>	MPIcheckPoint();
936		#endif // is_mpi
937
938	+	}
939
413	–	// create the atom and short range interaction arrays
940
941	<	Atom::createArrays(simnfo->n_atoms);
416	<	the_atoms = new Atom*[simnfo->n_atoms];
417	<	the_molecules = new Molecule[simnfo->n_mol];
418	<	int molIndex;
419	<
420	<	// initialize the molecule's stampID's
421	<
422	<	#ifdef IS_MPI
941	>	void SimSetup::makeOutNames( void ){
942
943	+	int k;
944
425	–	molIndex = 0;
426	–	for(i=0; i<mpiSim->getTotNmol(); i++){
427	–
428	–	if(mol2proc[i] == worldRank ){
429	–	the_molecules[molIndex].setStampID( molCompType[i] );
430	–	the_molecules[molIndex].setMyIndex( molIndex );
431	–	the_molecules[molIndex].setGlobalIndex( i );
432	–	molIndex++;
433	–	}
434	–	}
435	–
436	–	#else // is_mpi
945
946	<	molIndex = 0;
439	<	globalAtomIndex = 0;
440	<	for(i=0; i<n_components; i++){
441	<	for(j=0; j<components_nmol[i]; j++ ){
442	<	the_molecules[molIndex].setStampID( i );
443	<	the_molecules[molIndex].setMyIndex( molIndex );
444	<	the_molecules[molIndex].setGlobalIndex( molIndex );
445	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
446	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
447	<	globalAtomIndex++;
448	<	}
449	<	molIndex++;
450	<	}
451	<	}
452	<
946	>	for(k=0; k<nInfo; k++){
947
948	+	#ifdef IS_MPI
949	+	if( worldRank == 0 ){
950		#endif // is_mpi
951	+
952	+	if( globals->haveFinalConfig() ){
953	+	strcpy( info[k].finalName, globals->getFinalConfig() );
954	+	}
955	+	else{
956	+	strcpy( info[k].finalName, inFileName );
957	+	char* endTest;
958	+	int nameLength = strlen( info[k].finalName );
959	+	endTest = &(info[k].finalName[nameLength - 5]);
960	+	if( !strcmp( endTest, ".bass" ) ){
961	+	strcpy( endTest, ".eor" );
962	+	}
963	+	else if( !strcmp( endTest, ".BASS" ) ){
964	+	strcpy( endTest, ".eor" );
965	+	}
966	+	else{
967	+	endTest = &(info[k].finalName[nameLength - 4]);
968	+	if( !strcmp( endTest, ".bss" ) ){
969	+	strcpy( endTest, ".eor" );
970	+	}
971	+	else if( !strcmp( endTest, ".mdl" ) ){
972	+	strcpy( endTest, ".eor" );
973	+	}
974	+	else{
975	+	strcat( info[k].finalName, ".eor" );
976	+	}
977	+	}
978	+	}
979	+
980	+	// make the sample and status out names
981	+
982	+	strcpy( info[k].sampleName, inFileName );
983	+	char* endTest;
984	+	int nameLength = strlen( info[k].sampleName );
985	+	endTest = &(info[k].sampleName[nameLength - 5]);
986	+	if( !strcmp( endTest, ".bass" ) ){
987	+	strcpy( endTest, ".dump" );
988	+	}
989	+	else if( !strcmp( endTest, ".BASS" ) ){
990	+	strcpy( endTest, ".dump" );
991	+	}
992	+	else{
993	+	endTest = &(info[k].sampleName[nameLength - 4]);
994	+	if( !strcmp( endTest, ".bss" ) ){
995	+	strcpy( endTest, ".dump" );
996	+	}
997	+	else if( !strcmp( endTest, ".mdl" ) ){
998	+	strcpy( endTest, ".dump" );
999	+	}
1000	+	else{
1001	+	strcat( info[k].sampleName, ".dump" );
1002	+	}
1003	+	}
1004	+
1005	+	strcpy( info[k].statusName, inFileName );
1006	+	nameLength = strlen( info[k].statusName );
1007	+	endTest = &(info[k].statusName[nameLength - 5]);
1008	+	if( !strcmp( endTest, ".bass" ) ){
1009	+	strcpy( endTest, ".stat" );
1010	+	}
1011	+	else if( !strcmp( endTest, ".BASS" ) ){
1012	+	strcpy( endTest, ".stat" );
1013	+	}
1014	+	else{
1015	+	endTest = &(info[k].statusName[nameLength - 4]);
1016	+	if( !strcmp( endTest, ".bss" ) ){
1017	+	strcpy( endTest, ".stat" );
1018	+	}
1019	+	else if( !strcmp( endTest, ".mdl" ) ){
1020	+	strcpy( endTest, ".stat" );
1021	+	}
1022	+	else{
1023	+	strcat( info[k].statusName, ".stat" );
1024	+	}
1025	+	}
1026	+
1027	+	#ifdef IS_MPI
1028	+	}
1029	+	#endif // is_mpi
1030	+	}
1031	+	}
1032
1033
1034	<	if( simnfo->n_SRI ){
1035	<
1036	<	Exclude::createArray(simnfo->n_SRI);
1037	<	the_excludes = new Exclude*[simnfo->n_SRI];
1038	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
462	<	simnfo->globalExcludes = new int;
463	<	simnfo->n_exclude = simnfo->n_SRI;
464	<	}
465	<	else{
466	<
467	<	Exclude::createArray( 1 );
468	<	the_excludes = new Exclude*;
469	<	the_excludes[0] = new Exclude(0);
470	<	the_excludes[0]->setPair( 0,0 );
471	<	simnfo->globalExcludes = new int;
472	<	simnfo->globalExcludes[0] = 0;
473	<	simnfo->n_exclude = 0;
474	<	}
1034	>	void SimSetup::sysObjectsCreation( void ){
1035	>
1036	>	int i,k;
1037	>
1038	>	// create the forceField
1039
1040	<	// set the arrays into the SimInfo object
1040	>	createFF();
1041
1042	<	simnfo->atoms = the_atoms;
479	<	simnfo->molecules = the_molecules;
480	<	simnfo->nGlobalExcludes = 0;
481	<	simnfo->excludes = the_excludes;
1042	>	// extract componentList
1043
1044	+	compList();
1045
1046	<	// get some of the tricky things that may still be in the globals
1046	>	// calc the number of atoms, bond, bends, and torsions
1047
1048	<	double boxVector[3];
487	<	if( the_globals->haveBox() ){
488	<	boxVector[0] = the_globals->getBox();
489	<	boxVector[1] = the_globals->getBox();
490	<	boxVector[2] = the_globals->getBox();
491	<
492	<	simnfo->setBox( boxVector );
493	<	}
494	<	else if( the_globals->haveDensity() ){
1048	>	calcSysValues();
1049
1050	<	double vol;
1051	<	vol = (double)tot_nmol / the_globals->getDensity();
1052	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
1053	<	boxVector[1] = boxVector[0];
1054	<	boxVector[2] = boxVector[0];
1050	>	#ifdef IS_MPI
1051	>	// divide the molecules among the processors
1052	>
1053	>	mpiMolDivide();
1054	>	#endif //is_mpi
1055	>
1056	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1057	>
1058	>	makeSysArrays();
1059
1060	<	simnfo->setBox( boxVector );
1061	<	}
1062	<	else{
1063	<	if( !the_globals->haveBoxX() ){
1064	<	sprintf( painCave.errMsg,
1065	<	"SimSetup error, no periodic BoxX size given.\n" );
1066	<	painCave.isFatal = 1;
1067	<	simError();
1060	>	// make and initialize the molecules (all but atomic coordinates)
1061	>
1062	>	makeMolecules();
1063	>
1064	>	for(k=0; k<nInfo; k++){
1065	>	info[k].identArray = new int[info[k].n_atoms];
1066	>	for(i=0; i<info[k].n_atoms; i++){
1067	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1068		}
1069	<	boxVector[0] = the_globals->getBoxX();
1069	>	}
1070	>	}
1071
513	–	if( !the_globals->haveBoxY() ){
514	–	sprintf( painCave.errMsg,
515	–	"SimSetup error, no periodic BoxY size given.\n" );
516	–	painCave.isFatal = 1;
517	–	simError();
518	–	}
519	–	boxVector[1] = the_globals->getBoxY();
1072
1073	<	if( !the_globals->haveBoxZ() ){
522	<	sprintf( painCave.errMsg,
523	<	"SimSetup error, no periodic BoxZ size given.\n" );
524	<	painCave.isFatal = 1;
525	<	simError();
526	<	}
527	<	boxVector[2] = the_globals->getBoxZ();
1073	>	void SimSetup::createFF( void ){
1074
1075	<	simnfo->setBox( boxVector );
1075	>	switch( ffCase ){
1076	>
1077	>	case FF_DUFF:
1078	>	the_ff = new DUFF();
1079	>	break;
1080	>
1081	>	case FF_LJ:
1082	>	the_ff = new LJFF();
1083	>	break;
1084	>
1085	>	case FF_EAM:
1086	>	the_ff = new EAM_FF();
1087	>	break;
1088	>
1089	>	default:
1090	>	sprintf( painCave.errMsg,
1091	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	>	painCave.isFatal = 1;
1093	>	simError();
1094		}
1095
1096		#ifdef IS_MPI
1097	<	strcpy( checkPointMsg, "Box size set up" );
1097	>	strcpy( checkPointMsg, "ForceField creation successful" );
1098		MPIcheckPoint();
1099		#endif // is_mpi
1100
1101	+	}
1102
538	–	// initialize the arrays
1103
1104	<	the_ff->setSimInfo( simnfo );
1104	>	void SimSetup::compList( void ){
1105
1106	<	makeMolecules();
1107	<	simnfo->identArray = new int[simnfo->n_atoms];
1108	<	for(i=0; i<simnfo->n_atoms; i++){
1109	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
1110	<	}
1106	>	int i;
1107	>	char* id;
1108	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1109	>	LinkedMolStamp* currentStamp = NULL;
1110	>	comp_stamps = new MoleculeStamp*[n_components];
1111
1112	<	if (the_globals->getUseRF() ) {
1113	<	simnfo->useReactionField = 1;
1112	>	// make an array of molecule stamps that match the components used.
1113	>	// also extract the used stamps out into a separate linked list
1114
1115	<	if( !the_globals->haveECR() ){
1116	<	sprintf( painCave.errMsg,
1117	<	"SimSetup Warning: using default value of 1/2 the smallest "
1118	<	"box length for the electrostaticCutoffRadius.\n"
1119	<	"I hope you have a very fast processor!\n");
1120	<	painCave.isFatal = 0;
1121	<	simError();
558	<	double smallest;
559	<	smallest = simnfo->boxLx;
560	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
561	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
562	<	simnfo->ecr = 0.5 * smallest;
563	<	} else {
564	<	simnfo->ecr        = the_globals->getECR();
565	<	}
1115	>	for(i=0; i<nInfo; i++){
1116	>	info[i].nComponents = n_components;
1117	>	info[i].componentsNmol = components_nmol;
1118	>	info[i].compStamps = comp_stamps;
1119	>	info[i].headStamp = headStamp;
1120	>	}
1121	>
1122
1123	<	if( !the_globals->haveEST() ){
1124	<	sprintf( painCave.errMsg,
1125	<	"SimSetup Warning: using default value of 0.05 * the "
1126	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
571	<	);
572	<	painCave.isFatal = 0;
573	<	simError();
574	<	simnfo->est = 0.05 * simnfo->ecr;
575	<	} else {
576	<	simnfo->est        = the_globals->getEST();
577	<	}
1123	>	for( i=0; i<n_components; i++ ){
1124	>
1125	>	id = the_components[i]->getType();
1126	>	comp_stamps[i] = NULL;
1127
1128	<	if(!the_globals->haveDielectric() ){
1129	<	sprintf( painCave.errMsg,
1130	<	"SimSetup Error: You are trying to use Reaction Field without"
1131	<	"setting a dielectric constant!\n"
583	<	);
584	<	painCave.isFatal = 1;
585	<	simError();
586	<	}
587	<	simnfo->dielectric = the_globals->getDielectric();
588	<	} else {
589	<	if (usesDipoles) {
1128	>	// check to make sure the component isn't already in the list
1129	>
1130	>	comp_stamps[i] = headStamp->match( id );
1131	>	if( comp_stamps[i] == NULL ){
1132
1133	<	if( !the_globals->haveECR() ){
592	<	sprintf( painCave.errMsg,
593	<	"SimSetup Warning: using default value of 1/2 the smallest "
594	<	"box length for the electrostaticCutoffRadius.\n"
595	<	"I hope you have a very fast processor!\n");
596	<	painCave.isFatal = 0;
597	<	simError();
598	<	double smallest;
599	<	smallest = simnfo->boxLx;
600	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
601	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
602	<	simnfo->ecr = 0.5 * smallest;
603	<	} else {
604	<	simnfo->ecr        = the_globals->getECR();
605	<	}
1133	>	// extract the component from the list;
1134
1135	<	if( !the_globals->haveEST() ){
1136	<	sprintf( painCave.errMsg,
1137	<	"SimSetup Warning: using default value of 5%% of the "
1138	<	"electrostaticCutoffRadius for the "
1139	<	"electrostaticSkinThickness\n"
1140	<	);
1141	<	painCave.isFatal = 0;
1142	<	simError();
615	<	simnfo->est = 0.05 * simnfo->ecr;
616	<	} else {
617	<	simnfo->est        = the_globals->getEST();
1135	>	currentStamp = stamps->extractMolStamp( id );
1136	>	if( currentStamp == NULL ){
1137	>	sprintf( painCave.errMsg,
1138	>	"SimSetup error: Component \"%s\" was not found in the "
1139	>	"list of declared molecules\n",
1140	>	id );
1141	>	painCave.isFatal = 1;
1142	>	simError();
1143		}
1144	+
1145	+	headStamp->add( currentStamp );
1146	+	comp_stamps[i] = headStamp->match( id );
1147		}
1148	<	}
1148	>	}
1149
1150		#ifdef IS_MPI
1151	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
1151	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1152		MPIcheckPoint();
1153		#endif // is_mpi
1154
627	–	if( the_globals->haveInitialConfig() ){
628	–
629	–	InitializeFromFile* fileInit;
630	–	#ifdef IS_MPI // is_mpi
631	–	if( worldRank == 0 ){
632	–	#endif //is_mpi
633	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
634	–	#ifdef IS_MPI
635	–	}else fileInit = new InitializeFromFile( NULL );
636	–	#endif
637	–	fileInit->read_xyz( simnfo ); // default velocities on
1155
1156	<	delete fileInit;
640	<	}
641	<	else{
1156	>	}
1157
1158	<	#ifdef IS_MPI
1159	<
645	<	// no init from bass
1158	>	void SimSetup::calcSysValues( void ){
1159	>	int i, j, k;
1160
1161	<	sprintf( painCave.errMsg,
648	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
649	<	painCave.isFatal;
650	<	simError();
1161	>	int *molMembershipArray;
1162
1163	<	#else
1164	<
1165	<	initFromBass();
1166	<
1167	<
1168	<	#endif
1169	<	}
1163	>	tot_atoms = 0;
1164	>	tot_bonds = 0;
1165	>	tot_bends = 0;
1166	>	tot_torsions = 0;
1167	>	for( i=0; i<n_components; i++ ){
1168	>
1169	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1170	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1171	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1172	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1173	>	}
1174	>
1175	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1176	>	molMembershipArray = new int[tot_atoms];
1177	>
1178	>	for(i=0; i<nInfo; i++){
1179	>	info[i].n_atoms = tot_atoms;
1180	>	info[i].n_bonds = tot_bonds;
1181	>	info[i].n_bends = tot_bends;
1182	>	info[i].n_torsions = tot_torsions;
1183	>	info[i].n_SRI = tot_SRI;
1184	>	info[i].n_mol = tot_nmol;
1185	>
1186	>	info[i].molMembershipArray = molMembershipArray;
1187	>	}
1188	>	}
1189
1190		#ifdef IS_MPI
1191	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1191	>
1192	>	void SimSetup::mpiMolDivide( void ){
1193	>
1194	>	int i, j, k;
1195	>	int localMol, allMol;
1196	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1197	>
1198	>	mpiSim = new mpiSimulation( info );
1199	>
1200	>	globalIndex = mpiSim->divideLabor();
1201	>
1202	>	// set up the local variables
1203	>
1204	>	mol2proc = mpiSim->getMolToProcMap();
1205	>	molCompType = mpiSim->getMolComponentType();
1206	>
1207	>	allMol = 0;
1208	>	localMol = 0;
1209	>	local_atoms = 0;
1210	>	local_bonds = 0;
1211	>	local_bends = 0;
1212	>	local_torsions = 0;
1213	>	globalAtomIndex = 0;
1214	>
1215	>
1216	>	for( i=0; i<n_components; i++ ){
1217	>
1218	>	for( j=0; j<components_nmol[i]; j++ ){
1219	>
1220	>	if( mol2proc[allMol] == worldRank ){
1221	>
1222	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1223	>	local_bonds +=    comp_stamps[i]->getNBonds();
1224	>	local_bends +=    comp_stamps[i]->getNBends();
1225	>	local_torsions += comp_stamps[i]->getNTorsions();
1226	>	localMol++;
1227	>	}
1228	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1229	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1230	>	globalAtomIndex++;
1231	>	}
1232	>
1233	>	allMol++;
1234	>	}
1235	>	}
1236	>	local_SRI = local_bonds + local_bends + local_torsions;
1237	>
1238	>	info[0].n_atoms = mpiSim->getMyNlocal();
1239	>
1240	>	if( local_atoms != info[0].n_atoms ){
1241	>	sprintf( painCave.errMsg,
1242	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1243	>	" localAtom (%d) are not equal.\n",
1244	>	info[0].n_atoms,
1245	>	local_atoms );
1246	>	painCave.isFatal = 1;
1247	>	simError();
1248	>	}
1249	>
1250	>	info[0].n_bonds = local_bonds;
1251	>	info[0].n_bends = local_bends;
1252	>	info[0].n_torsions = local_torsions;
1253	>	info[0].n_SRI = local_SRI;
1254	>	info[0].n_mol = localMol;
1255	>
1256	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1257		MPIcheckPoint();
1258	+	}
1259	+
1260		#endif // is_mpi
1261
1262
1263	<
1264	<
668	<
1263	>	void SimSetup::makeSysArrays( void ){
1264	>	int i, j, k, l;
1265
1266	+	Atom** the_atoms;
1267	+	Molecule* the_molecules;
1268	+	Exclude** the_excludes;
1269	+
1270
1271	+	for(l=0; l<nInfo; l++){
1272	+
1273	+	// create the atom and short range interaction arrays
1274	+
1275	+	the_atoms = new Atom*[info[l].n_atoms];
1276	+	the_molecules = new Molecule[info[l].n_mol];
1277	+	int molIndex;
1278	+
1279	+	// initialize the molecule's stampID's
1280	+
1281		#ifdef IS_MPI
672	–	if( worldRank == 0 ){
673	–	#endif // is_mpi
1282
1283	<	if( the_globals->haveFinalConfig() ){
1284	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
1285	<	}
1286	<	else{
1287	<	strcpy( simnfo->finalName, inFileName );
1288	<	char* endTest;
1289	<	int nameLength = strlen( simnfo->finalName );
1290	<	endTest = &(simnfo->finalName[nameLength - 5]);
1291	<	if( !strcmp( endTest, ".bass" ) ){
684	<	strcpy( endTest, ".eor" );
1283	>
1284	>	molIndex = 0;
1285	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1286	>
1287	>	if(mol2proc[i] == worldRank ){
1288	>	the_molecules[molIndex].setStampID( molCompType[i] );
1289	>	the_molecules[molIndex].setMyIndex( molIndex );
1290	>	the_molecules[molIndex].setGlobalIndex( i );
1291	>	molIndex++;
1292		}
686	–	else if( !strcmp( endTest, ".BASS" ) ){
687	–	strcpy( endTest, ".eor" );
688	–	}
689	–	else{
690	–	endTest = &(simnfo->finalName[nameLength - 4]);
691	–	if( !strcmp( endTest, ".bss" ) ){
692	–	strcpy( endTest, ".eor" );
693	–	}
694	–	else if( !strcmp( endTest, ".mdl" ) ){
695	–	strcpy( endTest, ".eor" );
696	–	}
697	–	else{
698	–	strcat( simnfo->finalName, ".eor" );
699	–	}
700	–	}
1293		}
1294
1295	<	// make the sample and status out names
1295	>	#else // is_mpi
1296
1297	<	strcpy( simnfo->sampleName, inFileName );
1298	<	char* endTest;
1299	<	int nameLength = strlen( simnfo->sampleName );
1300	<	endTest = &(simnfo->sampleName[nameLength - 5]);
1301	<	if( !strcmp( endTest, ".bass" ) ){
1302	<	strcpy( endTest, ".dump" );
1303	<	}
1304	<	else if( !strcmp( endTest, ".BASS" ) ){
1305	<	strcpy( endTest, ".dump" );
1306	<	}
1307	<	else{
1308	<	endTest = &(simnfo->sampleName[nameLength - 4]);
717	<	if( !strcmp( endTest, ".bss" ) ){
718	<	strcpy( endTest, ".dump" );
1297	>	molIndex = 0;
1298	>	globalAtomIndex = 0;
1299	>	for(i=0; i<n_components; i++){
1300	>	for(j=0; j<components_nmol[i]; j++ ){
1301	>	the_molecules[molIndex].setStampID( i );
1302	>	the_molecules[molIndex].setMyIndex( molIndex );
1303	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1304	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1305	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1306	>	globalAtomIndex++;
1307	>	}
1308	>	molIndex++;
1309		}
720	–	else if( !strcmp( endTest, ".mdl" ) ){
721	–	strcpy( endTest, ".dump" );
722	–	}
723	–	else{
724	–	strcat( simnfo->sampleName, ".dump" );
725	–	}
1310		}
1311
1312	<	strcpy( simnfo->statusName, inFileName );
1313	<	nameLength = strlen( simnfo->statusName );
1314	<	endTest = &(simnfo->statusName[nameLength - 5]);
1315	<	if( !strcmp( endTest, ".bass" ) ){
1316	<	strcpy( endTest, ".stat" );
1317	<	}
1318	<	else if( !strcmp( endTest, ".BASS" ) ){
1319	<	strcpy( endTest, ".stat" );
1320	<	}
1321	<	else{
738	<	endTest = &(simnfo->statusName[nameLength - 4]);
739	<	if( !strcmp( endTest, ".bss" ) ){
740	<	strcpy( endTest, ".stat" );
1312	>
1313	>	#endif // is_mpi
1314	>
1315	>
1316	>	if( info[l].n_SRI ){
1317	>
1318	>	Exclude::createArray(info[l].n_SRI);
1319	>	the_excludes = new Exclude*[info[l].n_SRI];
1320	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1321	>	the_excludes[ex] = new Exclude(ex);
1322		}
1323	<	else if( !strcmp( endTest, ".mdl" ) ){
1324	<	strcpy( endTest, ".stat" );
744	<	}
745	<	else{
746	<	strcat( simnfo->statusName, ".stat" );
747	<	}
1323	>	info[l].globalExcludes = new int;
1324	>	info[l].n_exclude = info[l].n_SRI;
1325		}
1326	+	else{
1327
1328	<	#ifdef IS_MPI
1329	<	}
1330	<	#endif // is_mpi
1331	<
1332	<	// set the status, sample, and themal kick times
1333	<
1334	<	if( the_globals->haveSampleTime() ){
1335	<	simnfo->sampleTime = the_globals->getSampleTime();
758	<	simnfo->statusTime = simnfo->sampleTime;
759	<	simnfo->thermalTime = simnfo->sampleTime;
760	<	}
761	<	else{
762	<	simnfo->sampleTime = the_globals->getRunTime();
763	<	simnfo->statusTime = simnfo->sampleTime;
764	<	simnfo->thermalTime = simnfo->sampleTime;
765	<	}
1328	>	Exclude::createArray( 1 );
1329	>	the_excludes = new Exclude*;
1330	>	the_excludes[0] = new Exclude(0);
1331	>	the_excludes[0]->setPair( 0,0 );
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].globalExcludes[0] = 0;
1334	>	info[l].n_exclude = 0;
1335	>	}
1336
1337	<	if( the_globals->haveStatusTime() ){
768	<	simnfo->statusTime = the_globals->getStatusTime();
769	<	}
1337	>	// set the arrays into the SimInfo object
1338
1339	<	if( the_globals->haveThermalTime() ){
1340	<	simnfo->thermalTime = the_globals->getThermalTime();
1339	>	info[l].atoms = the_atoms;
1340	>	info[l].molecules = the_molecules;
1341	>	info[l].nGlobalExcludes = 0;
1342	>	info[l].excludes = the_excludes;
1343	>
1344	>	the_ff->setSimInfo( info );
1345	>
1346		}
1347	+	}
1348
1349	<	// check for the temperature set flag
1349	>	void SimSetup::makeIntegrator( void ){
1350
1351	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1351	>	int k;
1352
1353	+	NVT<RealIntegrator>*  myNVT = NULL;
1354	+	NPTi<RealIntegrator>* myNPTi = NULL;
1355	+	NPTf<RealIntegrator>* myNPTf = NULL;
1356	+	NPTim<RealIntegrator>* myNPTim = NULL;
1357	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1358	+
1359	+	for(k=0; k<nInfo; k++){
1360	+
1361	+	switch( ensembleCase ){
1362	+
1363	+	case NVE_ENS:
1364	+	if (globals->haveZconstraints()){
1365	+	setupZConstraint(info[k]);
1366	+	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1367	+	}
1368
1369	<	// make the integrator
1370	<
1371	<
1372	<	NVT* myNVT = NULL;
1373	<	switch( ensembleCase ){
1369	>	else
1370	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1371	>	break;
1372	>
1373	>	case NVT_ENS:
1374	>	if (globals->haveZconstraints()){
1375	>	setupZConstraint(info[k]);
1376	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377	>	}
1378	>	else
1379	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1380
1381	<	case NVE_ENS:
1382	<	new NVE( simnfo, the_ff );
1383	<	break;
1381	>	myNVT->setTargetTemp(globals->getTargetTemp());
1382	>
1383	>	if (globals->haveTauThermostat())
1384	>	myNVT->setTauThermostat(globals->getTauThermostat());
1385	>
1386	>	else {
1387	>	sprintf( painCave.errMsg,
1388	>	"SimSetup error: If you use the NVT\n"
1389	>	"    ensemble, you must set tauThermostat.\n");
1390	>	painCave.isFatal = 1;
1391	>	simError();
1392	>	}
1393	>	break;
1394	>
1395	>	case NPTi_ENS:
1396	>	if (globals->haveZconstraints()){
1397	>	setupZConstraint(info[k]);
1398	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399	>	}
1400	>	else
1401	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1402
1403	<	case NVT_ENS:
1404	<	myNVT = new NVT( simnfo, the_ff );
1405	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
1406	<
1407	<	if (the_globals->haveTauThermostat())
1408	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
1409	<	//     else if (the_globals->haveQmass())
1410	<	//       myNVT->setQmass(the_globals->getQmass());
1411	<	else {
1403	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	>	else {
1408	>	sprintf( painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413	>	}
1414	>
1415	>	if( globals->haveTauThermostat() )
1416	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	>	else{
1418	>	sprintf( painCave.errMsg,
1419	>	"SimSetup error: If you use an NPT\n"
1420	>	"    ensemble, you must set tauThermostat.\n");
1421	>	painCave.isFatal = 1;
1422	>	simError();
1423	>	}
1424	>
1425	>	if( globals->haveTauBarostat() )
1426	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	>	else{
1428	>	sprintf( painCave.errMsg,
1429	>	"SimSetup error: If you use an NPT\n"
1430	>	"    ensemble, you must set tauBarostat.\n");
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433	>	}
1434	>	break;
1435	>
1436	>	case NPTf_ENS:
1437	>	if (globals->haveZconstraints()){
1438	>	setupZConstraint(info[k]);
1439	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440	>	}
1441	>	else
1442	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1443	>
1444	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1445	>
1446	>	if (globals->haveTargetPressure())
1447	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1448	>	else {
1449	>	sprintf( painCave.errMsg,
1450	>	"SimSetup error: If you use a constant pressure\n"
1451	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1452	>	painCave.isFatal = 1;
1453	>	simError();
1454	>	}
1455	>
1456	>	if( globals->haveTauThermostat() )
1457	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1458	>	else{
1459	>	sprintf( painCave.errMsg,
1460	>	"SimSetup error: If you use an NPT\n"
1461	>	"    ensemble, you must set tauThermostat.\n");
1462	>	painCave.isFatal = 1;
1463	>	simError();
1464	>	}
1465	>
1466	>	if( globals->haveTauBarostat() )
1467	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1468	>	else{
1469	>	sprintf( painCave.errMsg,
1470	>	"SimSetup error: If you use an NPT\n"
1471	>	"    ensemble, you must set tauBarostat.\n");
1472	>	painCave.isFatal = 1;
1473	>	simError();
1474	>	}
1475	>	break;
1476	>
1477	>	case NPTim_ENS:
1478	>	if (globals->haveZconstraints()){
1479	>	setupZConstraint(info[k]);
1480	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481	>	}
1482	>	else
1483	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1484	>
1485	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1486	>
1487	>	if (globals->haveTargetPressure())
1488	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1489	>	else {
1490	>	sprintf( painCave.errMsg,
1491	>	"SimSetup error: If you use a constant pressure\n"
1492	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1493	>	painCave.isFatal = 1;
1494	>	simError();
1495	>	}
1496	>
1497	>	if( globals->haveTauThermostat() )
1498	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1499	>	else{
1500	>	sprintf( painCave.errMsg,
1501	>	"SimSetup error: If you use an NPT\n"
1502	>	"    ensemble, you must set tauThermostat.\n");
1503	>	painCave.isFatal = 1;
1504	>	simError();
1505	>	}
1506	>
1507	>	if( globals->haveTauBarostat() )
1508	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509	>	else{
1510		sprintf( painCave.errMsg,
1511	<	"SimSetup error: If you use the NVT\n"
1512	<	"    ensemble, you must set either tauThermostat or qMass.\n"
802	<	"    Neither of these was found in the BASS file.\n");
1511	>	"SimSetup error: If you use an NPT\n"
1512	>	"    ensemble, you must set tauBarostat.\n");
1513		painCave.isFatal = 1;
1514		simError();
1515	<	}
1516	<	break;
1515	>	}
1516	>	break;
1517	>
1518	>	case NPTfm_ENS:
1519	>	if (globals->haveZconstraints()){
1520	>	setupZConstraint(info[k]);
1521	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522	>	}
1523	>	else
1524	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1525
1526	<	default:
1527	<	sprintf( painCave.errMsg,
1528	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1529	<	painCave.isFatal = 1;
1530	<	simError();
1526	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1527	>
1528	>	if (globals->haveTargetPressure())
1529	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1530	>	else {
1531	>	sprintf( painCave.errMsg,
1532	>	"SimSetup error: If you use a constant pressure\n"
1533	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1534	>	painCave.isFatal = 1;
1535	>	simError();
1536	>	}
1537	>
1538	>	if( globals->haveTauThermostat() )
1539	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1540	>	else{
1541	>	sprintf( painCave.errMsg,
1542	>	"SimSetup error: If you use an NPT\n"
1543	>	"    ensemble, you must set tauThermostat.\n");
1544	>	painCave.isFatal = 1;
1545	>	simError();
1546	>	}
1547	>
1548	>	if( globals->haveTauBarostat() )
1549	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1550	>	else{
1551	>	sprintf( painCave.errMsg,
1552	>	"SimSetup error: If you use an NPT\n"
1553	>	"    ensemble, you must set tauBarostat.\n");
1554	>	painCave.isFatal = 1;
1555	>	simError();
1556	>	}
1557	>	break;
1558	>
1559	>	default:
1560	>	sprintf( painCave.errMsg,
1561	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1562	>	painCave.isFatal = 1;
1563	>	simError();
1564	>	}
1565		}
1566	+	}
1567
1568	+	void SimSetup::initFortran( void ){
1569
1570	<	#ifdef IS_MPI
817	<	mpiSim->mpiRefresh();
818	<	#endif
819	<
820	<	// initialize the Fortran
821	<
822	<
823	<	simnfo->refreshSim();
1570	>	info[0].refreshSim();
1571
1572	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1572	>	if( !strcmp( info[0].mixingRule, "standard") ){
1573		the_ff->initForceField( LB_MIXING_RULE );
1574		}
1575	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
1575	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1576		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1577		}
1578		else{
1579		sprintf( painCave.errMsg,
1580		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	<	simnfo->mixingRule );
1581	>	info[0].mixingRule );
1582		painCave.isFatal = 1;
1583		simError();
1584		}
#	Line 842 | Line 1589 | void SimSetup::createSim( void ){
1589		"Successfully intialized the mixingRule for Fortran." );
1590		MPIcheckPoint();
1591		#endif // is_mpi
1592	+
1593		}
1594
1595	+	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596	+	{
1597	+	int nZConstraints;
1598	+	ZconStamp** zconStamp;
1599	+
1600	+	if(globals->haveZconstraintTime()){
1601	+
1602	+	//add sample time of z-constraint  into SimInfo's property list
1603	+	DoubleData* zconsTimeProp = new DoubleData();
1604	+	zconsTimeProp->setID(ZCONSTIME_ID);
1605	+	zconsTimeProp->setData(globals->getZconsTime());
1606	+	theInfo.addProperty(zconsTimeProp);
1607	+	}
1608	+	else{
1609	+	sprintf( painCave.errMsg,
1610	+	"ZConstraint error: If you use an ZConstraint\n"
1611	+	" , you must set sample time.\n");
1612	+	painCave.isFatal = 1;
1613	+	simError();
1614	+	}
1615
1616	<	void SimSetup::makeMolecules( void ){
1616	>	//
1617	>	nZConstraints = globals->getNzConstraints();
1618	>	zconStamp = globals->getZconStamp();
1619	>	ZConsParaItem tempParaItem;
1620
1621	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
1622	<	molInit info;
1623	<	DirectionalAtom* dAtom;
1624	<	LinkedAssign* extras;
1625	<	LinkedAssign* current_extra;
1626	<	AtomStamp* currentAtom;
1627	<	BondStamp* currentBond;
1628	<	BendStamp* currentBend;
858	<	TorsionStamp* currentTorsion;
1621	>	ZConsParaData* zconsParaData = new ZConsParaData();
1622	>	zconsParaData->setID(ZCONSPARADATA_ID);
1623	>
1624	>	for(int i = 0; i < nZConstraints; i++){
1625	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1626	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1627	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1628	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1629
1630	<	bond_pair* theBonds;
1631	<	bend_set* theBends;
862	<	torsion_set* theTorsions;
1630	>	zconsParaData->addItem(tempParaItem);
1631	>	}
1632
1633	<
1634	<	//init the forceField paramters
1633	>	//sort the parameters by index of molecules
1634	>	zconsParaData->sortByIndex();
1635	>
1636	>	//push data into siminfo, therefore, we can retrieve later
1637	>	theInfo.addProperty(zconsParaData);
1638
1639	<	the_ff->readParams();
1639	>	//push zconsTol into siminfo, if user does not specify
1640	>	//value for zconsTol, a default value will be used
1641	>	DoubleData* zconsTol = new DoubleData();
1642	>	zconsTol->setID(ZCONSTOL_ID);
1643	>	if(globals->haveZconsTol()){
1644	>	zconsTol->setData(globals->getZconsTol());
1645	>	}
1646	>	else{
1647	>	double defaultZConsTol = 1E-6;
1648	>	sprintf( painCave.errMsg,
1649	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1650	>	" , default value %f is used.\n", defaultZConsTol);
1651	>	painCave.isFatal = 0;
1652	>	simError();
1653
1654	<
1655	<	// init the atoms
1656	<
1657	<	double ux, uy, uz, u, uSqr;
1658	<
1659	<	atomOffset = 0;
1660	<	excludeOffset = 0;
876	<	for(i=0; i<simnfo->n_mol; i++){
1654	>	zconsTol->setData(defaultZConsTol);
1655	>	}
1656	>	theInfo.addProperty(zconsTol);
1657	>
1658	>	//Determine the name of ouput file and add it into SimInfo's property list
1659	>	//Be careful, do not use inFileName, since it is a pointer which
1660	>	//point to a string at master node, and slave nodes do not contain that string
1661
1662	<	stampID = the_molecules[i].getStampID();
879	<
880	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
881	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
882	<	info.nBends    = comp_stamps[stampID]->getNBends();
883	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
884	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
885	<
886	<	info.myAtoms = &the_atoms[atomOffset];
887	<	info.myExcludes = &the_excludes[excludeOffset];
888	<	info.myBonds = new Bond*[info.nBonds];
889	<	info.myBends = new Bend*[info.nBends];
890	<	info.myTorsions = new Torsion*[info.nTorsions];
891	<
892	<	theBonds = new bond_pair[info.nBonds];
893	<	theBends = new bend_set[info.nBends];
894	<	theTorsions = new torsion_set[info.nTorsions];
1662	>	string zconsOutput(theInfo.finalName);
1663
1664	<	// make the Atoms
1664	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1665
1666	<	for(j=0; j<info.nAtoms; j++){
1667	<
1668	<	currentAtom = comp_stamps[stampID]->getAtom( j );
901	<	if( currentAtom->haveOrientation() ){
902	<
903	<	dAtom = new DirectionalAtom(j + atomOffset);
904	<	simnfo->n_oriented++;
905	<	info.myAtoms[j] = dAtom;
906	<
907	<	ux = currentAtom->getOrntX();
908	<	uy = currentAtom->getOrntY();
909	<	uz = currentAtom->getOrntZ();
910	<
911	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
912	<
913	<	u = sqrt( uSqr );
914	<	ux = ux / u;
915	<	uy = uy / u;
916	<	uz = uz / u;
917	<
918	<	dAtom->setSUx( ux );
919	<	dAtom->setSUy( uy );
920	<	dAtom->setSUz( uz );
921	<	}
922	<	else{
923	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
924	<	}
925	<	info.myAtoms[j]->setType( currentAtom->getType() );
1666	>	StringData* zconsFilename = new StringData();
1667	>	zconsFilename->setID(ZCONSFILENAME_ID);
1668	>	zconsFilename->setData(zconsOutput);
1669
1670	<	#ifdef IS_MPI
928	<
929	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
930	<
931	<	#endif // is_mpi
932	<	}
933	<
934	<	// make the bonds
935	<	for(j=0; j<info.nBonds; j++){
936	<
937	<	currentBond = comp_stamps[stampID]->getBond( j );
938	<	theBonds[j].a = currentBond->getA() + atomOffset;
939	<	theBonds[j].b = currentBond->getB() + atomOffset;
940	<
941	<	exI = theBonds[j].a;
942	<	exJ = theBonds[j].b;
943	<
944	<	// exclude_I must always be the smaller of the pair
945	<	if( exI > exJ ){
946	<	tempEx = exI;
947	<	exI = exJ;
948	<	exJ = tempEx;
949	<	}
950	<	#ifdef IS_MPI
951	<	tempEx = exI;
952	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
953	<	tempEx = exJ;
954	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
955	<
956	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
957	<	#else  // isn't MPI
958	<
959	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
960	<	#endif  //is_mpi
961	<	}
962	<	excludeOffset += info.nBonds;
963	<
964	<	//make the bends
965	<	for(j=0; j<info.nBends; j++){
966	<
967	<	currentBend = comp_stamps[stampID]->getBend( j );
968	<	theBends[j].a = currentBend->getA() + atomOffset;
969	<	theBends[j].b = currentBend->getB() + atomOffset;
970	<	theBends[j].c = currentBend->getC() + atomOffset;
971	<
972	<	if( currentBend->haveExtras() ){
973	<
974	<	extras = currentBend->getExtras();
975	<	current_extra = extras;
976	<
977	<	while( current_extra != NULL ){
978	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
979	<
980	<	switch( current_extra->getType() ){
981	<
982	<	case 0:
983	<	theBends[j].ghost =
984	<	current_extra->getInt() + atomOffset;
985	<	theBends[j].isGhost = 1;
986	<	break;
987	<
988	<	case 1:
989	<	theBends[j].ghost =
990	<	(int)current_extra->getDouble() + atomOffset;
991	<	theBends[j].isGhost = 1;
992	<	break;
993	<
994	<	default:
995	<	sprintf( painCave.errMsg,
996	<	"SimSetup Error: ghostVectorSource was neither a "
997	<	"double nor an int.\n"
998	<	"-->Bend[%d] in %s\n",
999	<	j, comp_stamps[stampID]->getID() );
1000	<	painCave.isFatal = 1;
1001	<	simError();
1002	<	}
1003	<	}
1004	<
1005	<	else{
1006	<
1007	<	sprintf( painCave.errMsg,
1008	<	"SimSetup Error: unhandled bend assignment:\n"
1009	<	"    -->%s in Bend[%d] in %s\n",
1010	<	current_extra->getlhs(),
1011	<	j, comp_stamps[stampID]->getID() );
1012	<	painCave.isFatal = 1;
1013	<	simError();
1014	<	}
1015	<
1016	<	current_extra = current_extra->getNext();
1017	<	}
1018	<	}
1019	<
1020	<	if( !theBends[j].isGhost ){
1021	<
1022	<	exI = theBends[j].a;
1023	<	exJ = theBends[j].c;
1024	<	}
1025	<	else{
1026	<
1027	<	exI = theBends[j].a;
1028	<	exJ = theBends[j].b;
1029	<	}
1030	<
1031	<	// exclude_I must always be the smaller of the pair
1032	<	if( exI > exJ ){
1033	<	tempEx = exI;
1034	<	exI = exJ;
1035	<	exJ = tempEx;
1036	<	}
1037	<	#ifdef IS_MPI
1038	<	tempEx = exI;
1039	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1040	<	tempEx = exJ;
1041	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1042	<
1043	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1044	<	#else  // isn't MPI
1045	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1046	<	#endif  //is_mpi
1047	<	}
1048	<	excludeOffset += info.nBends;
1049	<
1050	<	for(j=0; j<info.nTorsions; j++){
1051	<
1052	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1053	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1054	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1055	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1056	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1057	<
1058	<	exI = theTorsions[j].a;
1059	<	exJ = theTorsions[j].d;
1060	<
1061	<	// exclude_I must always be the smaller of the pair
1062	<	if( exI > exJ ){
1063	<	tempEx = exI;
1064	<	exI = exJ;
1065	<	exJ = tempEx;
1066	<	}
1067	<	#ifdef IS_MPI
1068	<	tempEx = exI;
1069	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1070	<	tempEx = exJ;
1071	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1072	<
1073	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1074	<	#else  // isn't MPI
1075	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1076	<	#endif  //is_mpi
1077	<	}
1078	<	excludeOffset += info.nTorsions;
1079	<
1080	<
1081	<	// send the arrays off to the forceField for init.
1082	<
1083	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1084	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1085	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1086	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1087	<
1088	<
1089	<	the_molecules[i].initialize( info );
1090	<
1091	<
1092	<	atomOffset += info.nAtoms;
1093	<	delete[] theBonds;
1094	<	delete[] theBends;
1095	<	delete[] theTorsions;
1096	<	}
1097	<
1098	<	#ifdef IS_MPI
1099	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1100	<	MPIcheckPoint();
1101	<	#endif // is_mpi
1102	<
1103	<	// clean up the forcefield
1104	<	the_ff->calcRcut();
1105	<	the_ff->cleanMe();
1106	<
1670	>	theInfo.addProperty(zconsFilename);
1671		}
1108	–
1109	–	void SimSetup::initFromBass( void ){
1110	–
1111	–	int i, j, k;
1112	–	int n_cells;
1113	–	double cellx, celly, cellz;
1114	–	double temp1, temp2, temp3;
1115	–	int n_per_extra;
1116	–	int n_extra;
1117	–	int have_extra, done;
1118	–
1119	–	temp1 = (double)tot_nmol / 4.0;
1120	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1121	–	temp3 = ceil( temp2 );
1122	–
1123	–	have_extra =0;
1124	–	if( temp2 < temp3 ){ // we have a non-complete lattice
1125	–	have_extra =1;
1126	–
1127	–	n_cells = (int)temp3 - 1;
1128	–	cellx = simnfo->boxLx / temp3;
1129	–	celly = simnfo->boxLy / temp3;
1130	–	cellz = simnfo->boxLz / temp3;
1131	–	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1132	–	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1133	–	n_per_extra = (int)ceil( temp1 );
1134	–
1135	–	if( n_per_extra > 4){
1136	–	sprintf( painCave.errMsg,
1137	–	"SimSetup error. There has been an error in constructing"
1138	–	" the non-complete lattice.\n" );
1139	–	painCave.isFatal = 1;
1140	–	simError();
1141	–	}
1142	–	}
1143	–	else{
1144	–	n_cells = (int)temp3;
1145	–	cellx = simnfo->boxLx / temp3;
1146	–	celly = simnfo->boxLy / temp3;
1147	–	cellz = simnfo->boxLz / temp3;
1148	–	}
1149	–
1150	–	current_mol = 0;
1151	–	current_comp_mol = 0;
1152	–	current_comp = 0;
1153	–	current_atom_ndx = 0;
1154	–
1155	–	for( i=0; i < n_cells ; i++ ){
1156	–	for( j=0; j < n_cells; j++ ){
1157	–	for( k=0; k < n_cells; k++ ){
1158	–
1159	–	makeElement( i * cellx,
1160	–	j * celly,
1161	–	k * cellz );
1162	–
1163	–	makeElement( i * cellx + 0.5 * cellx,
1164	–	j * celly + 0.5 * celly,
1165	–	k * cellz );
1166	–
1167	–	makeElement( i * cellx,
1168	–	j * celly + 0.5 * celly,
1169	–	k * cellz + 0.5 * cellz );
1170	–
1171	–	makeElement( i * cellx + 0.5 * cellx,
1172	–	j * celly,
1173	–	k * cellz + 0.5 * cellz );
1174	–	}
1175	–	}
1176	–	}
1177	–
1178	–	if( have_extra ){
1179	–	done = 0;
1180	–
1181	–	int start_ndx;
1182	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1183	–	for( j=0; j < (n_cells+1) && !done; j++ ){
1184	–
1185	–	if( i < n_cells ){
1186	–
1187	–	if( j < n_cells ){
1188	–	start_ndx = n_cells;
1189	–	}
1190	–	else start_ndx = 0;
1191	–	}
1192	–	else start_ndx = 0;
1193	–
1194	–	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1195	–
1196	–	makeElement( i * cellx,
1197	–	j * celly,
1198	–	k * cellz );
1199	–	done = ( current_mol >= tot_nmol );
1200	–
1201	–	if( !done && n_per_extra > 1 ){
1202	–	makeElement( i * cellx + 0.5 * cellx,
1203	–	j * celly + 0.5 * celly,
1204	–	k * cellz );
1205	–	done = ( current_mol >= tot_nmol );
1206	–	}
1207	–
1208	–	if( !done && n_per_extra > 2){
1209	–	makeElement( i * cellx,
1210	–	j * celly + 0.5 * celly,
1211	–	k * cellz + 0.5 * cellz );
1212	–	done = ( current_mol >= tot_nmol );
1213	–	}
1214	–
1215	–	if( !done && n_per_extra > 3){
1216	–	makeElement( i * cellx + 0.5 * cellx,
1217	–	j * celly,
1218	–	k * cellz + 0.5 * cellz );
1219	–	done = ( current_mol >= tot_nmol );
1220	–	}
1221	–	}
1222	–	}
1223	–	}
1224	–	}
1225	–
1226	–
1227	–	for( i=0; i<simnfo->n_atoms; i++ ){
1228	–	simnfo->atoms[i]->set_vx( 0.0 );
1229	–	simnfo->atoms[i]->set_vy( 0.0 );
1230	–	simnfo->atoms[i]->set_vz( 0.0 );
1231	–	}
1232	–	}
1233	–
1234	–	void SimSetup::makeElement( double x, double y, double z ){
1235	–
1236	–	int k;
1237	–	AtomStamp* current_atom;
1238	–	DirectionalAtom* dAtom;
1239	–	double rotMat[3][3];
1240	–
1241	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1242	–
1243	–	current_atom = comp_stamps[current_comp]->getAtom( k );
1244	–	if( !current_atom->havePosition() ){
1245	–	sprintf( painCave.errMsg,
1246	–	"SimSetup:initFromBass error.\n"
1247	–	"\tComponent %s, atom %s does not have a position specified.\n"
1248	–	"\tThe initialization routine is unable to give a start"
1249	–	" position.\n",
1250	–	comp_stamps[current_comp]->getID(),
1251	–	current_atom->getType() );
1252	–	painCave.isFatal = 1;
1253	–	simError();
1254	–	}
1255	–
1256	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1257	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1258	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1259	–
1260	–	if( the_atoms[current_atom_ndx]->isDirectional() ){
1261	–
1262	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1263	–
1264	–	rotMat[0][0] = 1.0;
1265	–	rotMat[0][1] = 0.0;
1266	–	rotMat[0][2] = 0.0;
1267	–
1268	–	rotMat[1][0] = 0.0;
1269	–	rotMat[1][1] = 1.0;
1270	–	rotMat[1][2] = 0.0;
1271	–
1272	–	rotMat[2][0] = 0.0;
1273	–	rotMat[2][1] = 0.0;
1274	–	rotMat[2][2] = 1.0;
1275	–
1276	–	dAtom->setA( rotMat );
1277	–	}
1278	–
1279	–	current_atom_ndx++;
1280	–	}
1281	–
1282	–	current_mol++;
1283	–	current_comp_mol++;
1284	–
1285	–	if( current_comp_mol >= components_nmol[current_comp] ){
1286	–
1287	–	current_comp_mol = 0;
1288	–	current_comp++;
1289	–	}
1290	–	}

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