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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 567 by mmeineke, Wed Jun 25 21:12:14 2003 UTC vs.
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 14 | Line 17
17
18		// some defines for ensemble and Forcefield  cases
19
20	<	#define NVE_ENS 0
21	<	#define NVT_ENS 1
22	<	#define NPT_ENS 2
20	>	#define NVE_ENS        0
21	>	#define NVT_ENS        1
22	>	#define NPTi_ENS       2
23	>	#define NPTf_ENS       3
24	>	#define NPTim_ENS      4
25	>	#define NPTfm_ENS      5
26
27		#define FF_DUFF 0
28		#define FF_LJ   1
29	+	#define FF_EAM  2
30
31	+	using namespace std;
32
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 37 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 72 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
77	–	MakeStamps *the_stamps;
78	–	Globals* the_globals;
97		int i, j, k, globalAtomIndex;
98
99	<	int ensembleCase;
100	<	int ffCase;
99	>	// gather all of the information from the Bass file
100	>
101	>	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
87	–	// get the stamps and globals;
88	–	the_stamps = stamps;
89	–	the_globals = globals;
90	–
601		// 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();
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 107 | Line 623 | void SimSetup::createSim( void ){
623		simError();
624		}
625
626	<	// get the ensemble:
111	<	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, "NPT" )) ensembleCase = NPT_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 123 | 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 );
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();
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656		}
657	<
206	<	#ifdef IS_MPI
207	<	strcpy( checkPointMsg, "ForceField creation successful" );
208	<	MPIcheckPoint();
209	<	#endif // is_mpi
210	<
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];
214	–	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 242 | Line 690 | void SimSetup::createSim( void ){
690		" Please give nMol in the components.\n" );
691		painCave.isFatal = 1;
692		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	–
693		}
694
695	<	#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();
695	>	// set the status, sample, and thermal kick times
696
697	<	char* id;
275	<	LinkedMolStamp* headStamp = simnfo->headStamp;
276	<	LinkedMolStamp* currentStamp = NULL;
277	<	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 "
293	<	"list of declared molecules\n",
294	<	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		}
302	–	}
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
308	–
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;
316	<	tot_bends = 0;
317	<	tot_torsions = 0;
318	<	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;
333	<	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.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
887	>	}
888
889	<	// set up the local variables
889	>	void SimSetup::initSystemCoords( void ){
890	>	int i;
891
892	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
892	>	char* inName;
893
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;
894
895	<
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;
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	>	double* tempDouble = new double[1000000];
907	>	fileInit = new InitializeFromFile( inName );
908	>	#ifdef IS_MPI
909	>	}else fileInit = new InitializeFromFile( NULL );
910	>	#endif
911	>	fileInit->readInit( info ); // default velocities on
912	>
913	>	delete fileInit;
914	>	}
915	>	else{
916	>
917	>	#ifdef IS_MPI
918	>
919	>	// no init from bass
920	>
921		sprintf( painCave.errMsg,
922	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
923	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
922	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923	>	painCave.isFatal;
924		simError();
925	+
926	+	#else
927	+
928	+	initFromBass();
929	+
930	+
931	+	#endif
932		}
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();
933
934	<
934	>	#ifdef IS_MPI
935	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
936	>	MPIcheckPoint();
937		#endif // is_mpi
938
939	+	}
940
409	–	// create the atom and short range interaction arrays
941
942	<	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
942	>	void SimSetup::makeOutNames( void ){
943
944	+	int k;
945
421	–	molIndex = 0;
422	–	for(i=0; i<mpiSim->getTotNmol(); i++){
423	–
424	–	if(mol2proc[i] == worldRank ){
425	–	the_molecules[molIndex].setStampID( molCompType[i] );
426	–	the_molecules[molIndex].setMyIndex( molIndex );
427	–	the_molecules[molIndex].setGlobalIndex( i );
428	–	molIndex++;
429	–	}
430	–	}
431	–
432	–	#else // is_mpi
946
947	<	molIndex = 0;
948	<	globalAtomIndex = 0;
949	<	for(i=0; i<n_components; i++){
950	<	for(j=0; j<components_nmol[i]; j++ ){
951	<	the_molecules[molIndex].setStampID( i );
952	<	the_molecules[molIndex].setMyIndex( molIndex );
953	<	the_molecules[molIndex].setGlobalIndex( molIndex );
954	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443	<	globalAtomIndex++;
947	>	for(k=0; k<nInfo; k++){
948	>
949	>	#ifdef IS_MPI
950	>	if( worldRank == 0 ){
951	>	#endif // is_mpi
952	>
953	>	if( globals->haveFinalConfig() ){
954	>	strcpy( info[k].finalName, globals->getFinalConfig() );
955		}
956	<	molIndex++;
956	>	else{
957	>	strcpy( info[k].finalName, inFileName );
958	>	char* endTest;
959	>	int nameLength = strlen( info[k].finalName );
960	>	endTest = &(info[k].finalName[nameLength - 5]);
961	>	if( !strcmp( endTest, ".bass" ) ){
962	>	strcpy( endTest, ".eor" );
963	>	}
964	>	else if( !strcmp( endTest, ".BASS" ) ){
965	>	strcpy( endTest, ".eor" );
966	>	}
967	>	else{
968	>	endTest = &(info[k].finalName[nameLength - 4]);
969	>	if( !strcmp( endTest, ".bss" ) ){
970	>	strcpy( endTest, ".eor" );
971	>	}
972	>	else if( !strcmp( endTest, ".mdl" ) ){
973	>	strcpy( endTest, ".eor" );
974	>	}
975	>	else{
976	>	strcat( info[k].finalName, ".eor" );
977	>	}
978	>	}
979	>	}
980	>
981	>	// make the sample and status out names
982	>
983	>	strcpy( info[k].sampleName, inFileName );
984	>	char* endTest;
985	>	int nameLength = strlen( info[k].sampleName );
986	>	endTest = &(info[k].sampleName[nameLength - 5]);
987	>	if( !strcmp( endTest, ".bass" ) ){
988	>	strcpy( endTest, ".dump" );
989	>	}
990	>	else if( !strcmp( endTest, ".BASS" ) ){
991	>	strcpy( endTest, ".dump" );
992	>	}
993	>	else{
994	>	endTest = &(info[k].sampleName[nameLength - 4]);
995	>	if( !strcmp( endTest, ".bss" ) ){
996	>	strcpy( endTest, ".dump" );
997	>	}
998	>	else if( !strcmp( endTest, ".mdl" ) ){
999	>	strcpy( endTest, ".dump" );
1000	>	}
1001	>	else{
1002	>	strcat( info[k].sampleName, ".dump" );
1003	>	}
1004	>	}
1005	>
1006	>	strcpy( info[k].statusName, inFileName );
1007	>	nameLength = strlen( info[k].statusName );
1008	>	endTest = &(info[k].statusName[nameLength - 5]);
1009	>	if( !strcmp( endTest, ".bass" ) ){
1010	>	strcpy( endTest, ".stat" );
1011	>	}
1012	>	else if( !strcmp( endTest, ".BASS" ) ){
1013	>	strcpy( endTest, ".stat" );
1014	>	}
1015	>	else{
1016	>	endTest = &(info[k].statusName[nameLength - 4]);
1017	>	if( !strcmp( endTest, ".bss" ) ){
1018	>	strcpy( endTest, ".stat" );
1019	>	}
1020	>	else if( !strcmp( endTest, ".mdl" ) ){
1021	>	strcpy( endTest, ".stat" );
1022	>	}
1023	>	else{
1024	>	strcat( info[k].statusName, ".stat" );
1025	>	}
1026	>	}
1027	>
1028	>	#ifdef IS_MPI
1029		}
1030	+	#endif // is_mpi
1031		}
1032	<
1032	>	}
1033
450	–	#endif // is_mpi
1034
1035	+	void SimSetup::sysObjectsCreation( void ){
1036	+
1037	+	int i,k;
1038	+
1039	+	// create the forceField
1040
1041	<	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	<	}
1041	>	createFF();
1042
1043	<	// set the arrays into the SimInfo object
1043	>	// extract componentList
1044
1045	<	simnfo->atoms = the_atoms;
475	<	simnfo->molecules = the_molecules;
476	<	simnfo->nGlobalExcludes = 0;
477	<	simnfo->excludes = the_excludes;
1045	>	compList();
1046
1047	+	// calc the number of atoms, bond, bends, and torsions
1048
1049	<	// get some of the tricky things that may still be in the globals
1049	>	calcSysValues();
1050
1051	+	#ifdef IS_MPI
1052	+	// divide the molecules among the processors
1053
1054	<	if( the_globals->haveBox() ){
1055	<	simnfo->box_x = the_globals->getBox();
1056	<	simnfo->box_y = the_globals->getBox();
1057	<	simnfo->box_z = the_globals->getBox();
1058	<	}
1059	<	else if( the_globals->haveDensity() ){
1054	>	mpiMolDivide();
1055	>	#endif //is_mpi
1056	>
1057	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1058	>
1059	>	makeSysArrays();
1060
1061	<	double vol;
1062	<	vol = (double)tot_nmol / the_globals->getDensity();
1063	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
1064	<	simnfo->box_y = simnfo->box_x;
1065	<	simnfo->box_z = simnfo->box_x;
1066	<	}
1067	<	else{
1068	<	if( !the_globals->haveBoxX() ){
498	<	sprintf( painCave.errMsg,
499	<	"SimSetup error, no periodic BoxX size given.\n" );
500	<	painCave.isFatal = 1;
501	<	simError();
1061	>	// make and initialize the molecules (all but atomic coordinates)
1062	>
1063	>	makeMolecules();
1064	>
1065	>	for(k=0; k<nInfo; k++){
1066	>	info[k].identArray = new int[info[k].n_atoms];
1067	>	for(i=0; i<info[k].n_atoms; i++){
1068	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1069		}
1070	<	simnfo->box_x = the_globals->getBoxX();
1070	>	}
1071	>	}
1072
505	–	if( !the_globals->haveBoxY() ){
506	–	sprintf( painCave.errMsg,
507	–	"SimSetup error, no periodic BoxY size given.\n" );
508	–	painCave.isFatal = 1;
509	–	simError();
510	–	}
511	–	simnfo->box_y = the_globals->getBoxY();
1073
1074	<	if( !the_globals->haveBoxZ() ){
1075	<	sprintf( painCave.errMsg,
1076	<	"SimSetup error, no periodic BoxZ size given.\n" );
1077	<	painCave.isFatal = 1;
1078	<	simError();
1079	<	}
1080	<	simnfo->box_z = the_globals->getBoxZ();
1074	>	void SimSetup::createFF( void ){
1075	>
1076	>	switch( ffCase ){
1077	>
1078	>	case FF_DUFF:
1079	>	the_ff = new DUFF();
1080	>	break;
1081	>
1082	>	case FF_LJ:
1083	>	the_ff = new LJFF();
1084	>	break;
1085	>
1086	>	case FF_EAM:
1087	>	the_ff = new EAM_FF();
1088	>	break;
1089	>
1090	>	default:
1091	>	sprintf( painCave.errMsg,
1092	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	>	painCave.isFatal = 1;
1094	>	simError();
1095		}
1096
1097		#ifdef IS_MPI
1098	<	strcpy( checkPointMsg, "Box size set up" );
1098	>	strcpy( checkPointMsg, "ForceField creation successful" );
1099		MPIcheckPoint();
1100		#endif // is_mpi
1101
1102	+	}
1103
528	–	// initialize the arrays
1104
1105	<	the_ff->setSimInfo( simnfo );
1105	>	void SimSetup::compList( void ){
1106
1107	<	makeMolecules();
1108	<	simnfo->identArray = new int[simnfo->n_atoms];
1109	<	for(i=0; i<simnfo->n_atoms; i++){
1110	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
1111	<	}
1107	>	int i;
1108	>	char* id;
1109	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1110	>	LinkedMolStamp* currentStamp = NULL;
1111	>	comp_stamps = new MoleculeStamp*[n_components];
1112
1113	<	if (the_globals->getUseRF() ) {
1114	<	simnfo->useReactionField = 1;
1113	>	// make an array of molecule stamps that match the components used.
1114	>	// also extract the used stamps out into a separate linked list
1115
1116	<	if( !the_globals->haveECR() ){
1117	<	sprintf( painCave.errMsg,
1118	<	"SimSetup Warning: using default value of 1/2 the smallest "
1119	<	"box length for the electrostaticCutoffRadius.\n"
1120	<	"I hope you have a very fast processor!\n");
1121	<	painCave.isFatal = 0;
1122	<	simError();
548	<	double smallest;
549	<	smallest = simnfo->box_x;
550	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
551	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
552	<	simnfo->ecr = 0.5 * smallest;
553	<	} else {
554	<	simnfo->ecr        = the_globals->getECR();
555	<	}
1116	>	for(i=0; i<nInfo; i++){
1117	>	info[i].nComponents = n_components;
1118	>	info[i].componentsNmol = components_nmol;
1119	>	info[i].compStamps = comp_stamps;
1120	>	info[i].headStamp = headStamp;
1121	>	}
1122	>
1123
1124	<	if( !the_globals->haveEST() ){
1125	<	sprintf( painCave.errMsg,
1126	<	"SimSetup Warning: using default value of 0.05 * the "
1127	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
561	<	);
562	<	painCave.isFatal = 0;
563	<	simError();
564	<	simnfo->est = 0.05 * simnfo->ecr;
565	<	} else {
566	<	simnfo->est        = the_globals->getEST();
567	<	}
1124	>	for( i=0; i<n_components; i++ ){
1125	>
1126	>	id = the_components[i]->getType();
1127	>	comp_stamps[i] = NULL;
1128
1129	<	if(!the_globals->haveDielectric() ){
1130	<	sprintf( painCave.errMsg,
1131	<	"SimSetup Error: You are trying to use Reaction Field without"
1132	<	"setting a dielectric constant!\n"
573	<	);
574	<	painCave.isFatal = 1;
575	<	simError();
576	<	}
577	<	simnfo->dielectric = the_globals->getDielectric();
578	<	} else {
579	<	if (usesDipoles) {
1129	>	// check to make sure the component isn't already in the list
1130	>
1131	>	comp_stamps[i] = headStamp->match( id );
1132	>	if( comp_stamps[i] == NULL ){
1133
1134	<	if( !the_globals->haveECR() ){
582	<	sprintf( painCave.errMsg,
583	<	"SimSetup Warning: using default value of 1/2 the smallest "
584	<	"box length for the electrostaticCutoffRadius.\n"
585	<	"I hope you have a very fast processor!\n");
586	<	painCave.isFatal = 0;
587	<	simError();
588	<	double smallest;
589	<	smallest = simnfo->box_x;
590	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
591	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
592	<	simnfo->ecr = 0.5 * smallest;
593	<	} else {
594	<	simnfo->ecr        = the_globals->getECR();
595	<	}
1134	>	// extract the component from the list;
1135
1136	<	if( !the_globals->haveEST() ){
1137	<	sprintf( painCave.errMsg,
1138	<	"SimSetup Warning: using default value of 5%% of the "
1139	<	"electrostaticCutoffRadius for the "
1140	<	"electrostaticSkinThickness\n"
1141	<	);
1142	<	painCave.isFatal = 0;
1143	<	simError();
605	<	simnfo->est = 0.05 * simnfo->ecr;
606	<	} else {
607	<	simnfo->est        = the_globals->getEST();
1136	>	currentStamp = stamps->extractMolStamp( id );
1137	>	if( currentStamp == NULL ){
1138	>	sprintf( painCave.errMsg,
1139	>	"SimSetup error: Component \"%s\" was not found in the "
1140	>	"list of declared molecules\n",
1141	>	id );
1142	>	painCave.isFatal = 1;
1143	>	simError();
1144		}
1145	+
1146	+	headStamp->add( currentStamp );
1147	+	comp_stamps[i] = headStamp->match( id );
1148		}
1149	<	}
1149	>	}
1150
1151		#ifdef IS_MPI
1152	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
1152	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1153		MPIcheckPoint();
1154		#endif // is_mpi
1155
617	–	if( the_globals->haveInitialConfig() ){
618	–
619	–	InitializeFromFile* fileInit;
620	–	#ifdef IS_MPI // is_mpi
621	–	if( worldRank == 0 ){
622	–	#endif //is_mpi
623	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
624	–	#ifdef IS_MPI
625	–	}else fileInit = new InitializeFromFile( NULL );
626	–	#endif
627	–	fileInit->read_xyz( simnfo ); // default velocities on
1156
1157	<	delete fileInit;
630	<	}
631	<	else{
1157	>	}
1158
1159	<	#ifdef IS_MPI
1160	<
635	<	// no init from bass
1159	>	void SimSetup::calcSysValues( void ){
1160	>	int i, j, k;
1161
1162	<	sprintf( painCave.errMsg,
638	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
639	<	painCave.isFatal;
640	<	simError();
1162	>	int *molMembershipArray;
1163
1164	<	#else
1165	<
1166	<	initFromBass();
1167	<
1168	<
1169	<	#endif
1170	<	}
1164	>	tot_atoms = 0;
1165	>	tot_bonds = 0;
1166	>	tot_bends = 0;
1167	>	tot_torsions = 0;
1168	>	for( i=0; i<n_components; i++ ){
1169	>
1170	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1172	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1173	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174	>	}
1175	>
1176	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	>	molMembershipArray = new int[tot_atoms];
1178	>
1179	>	for(i=0; i<nInfo; i++){
1180	>	info[i].n_atoms = tot_atoms;
1181	>	info[i].n_bonds = tot_bonds;
1182	>	info[i].n_bends = tot_bends;
1183	>	info[i].n_torsions = tot_torsions;
1184	>	info[i].n_SRI = tot_SRI;
1185	>	info[i].n_mol = tot_nmol;
1186	>
1187	>	info[i].molMembershipArray = molMembershipArray;
1188	>	}
1189	>	}
1190
1191		#ifdef IS_MPI
1192	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1192	>
1193	>	void SimSetup::mpiMolDivide( void ){
1194	>
1195	>	int i, j, k;
1196	>	int localMol, allMol;
1197	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1198	>
1199	>	mpiSim = new mpiSimulation( info );
1200	>
1201	>	globalIndex = mpiSim->divideLabor();
1202	>
1203	>	// set up the local variables
1204	>
1205	>	mol2proc = mpiSim->getMolToProcMap();
1206	>	molCompType = mpiSim->getMolComponentType();
1207	>
1208	>	allMol = 0;
1209	>	localMol = 0;
1210	>	local_atoms = 0;
1211	>	local_bonds = 0;
1212	>	local_bends = 0;
1213	>	local_torsions = 0;
1214	>	globalAtomIndex = 0;
1215	>
1216	>
1217	>	for( i=0; i<n_components; i++ ){
1218	>
1219	>	for( j=0; j<components_nmol[i]; j++ ){
1220	>
1221	>	if( mol2proc[allMol] == worldRank ){
1222	>
1223	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1224	>	local_bonds +=    comp_stamps[i]->getNBonds();
1225	>	local_bends +=    comp_stamps[i]->getNBends();
1226	>	local_torsions += comp_stamps[i]->getNTorsions();
1227	>	localMol++;
1228	>	}
1229	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1230	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1231	>	globalAtomIndex++;
1232	>	}
1233	>
1234	>	allMol++;
1235	>	}
1236	>	}
1237	>	local_SRI = local_bonds + local_bends + local_torsions;
1238	>
1239	>	info[0].n_atoms = mpiSim->getMyNlocal();
1240	>
1241	>	if( local_atoms != info[0].n_atoms ){
1242	>	sprintf( painCave.errMsg,
1243	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244	>	" localAtom (%d) are not equal.\n",
1245	>	info[0].n_atoms,
1246	>	local_atoms );
1247	>	painCave.isFatal = 1;
1248	>	simError();
1249	>	}
1250	>
1251	>	info[0].n_bonds = local_bonds;
1252	>	info[0].n_bends = local_bends;
1253	>	info[0].n_torsions = local_torsions;
1254	>	info[0].n_SRI = local_SRI;
1255	>	info[0].n_mol = localMol;
1256	>
1257	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1258		MPIcheckPoint();
1259	+	}
1260	+
1261		#endif // is_mpi
1262
1263
1264	<
1265	<
658	<
1264	>	void SimSetup::makeSysArrays( void ){
1265	>	int i, j, k, l;
1266
1267	+	Atom** the_atoms;
1268	+	Molecule* the_molecules;
1269	+	Exclude** the_excludes;
1270	+
1271
1272	+	for(l=0; l<nInfo; l++){
1273	+
1274	+	// create the atom and short range interaction arrays
1275	+
1276	+	the_atoms = new Atom*[info[l].n_atoms];
1277	+	the_molecules = new Molecule[info[l].n_mol];
1278	+	int molIndex;
1279	+
1280	+	// initialize the molecule's stampID's
1281	+
1282		#ifdef IS_MPI
662	–	if( worldRank == 0 ){
663	–	#endif // is_mpi
1283
1284	<	if( the_globals->haveFinalConfig() ){
1285	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
1286	<	}
1287	<	else{
1288	<	strcpy( simnfo->finalName, inFileName );
1289	<	char* endTest;
1290	<	int nameLength = strlen( simnfo->finalName );
1291	<	endTest = &(simnfo->finalName[nameLength - 5]);
1292	<	if( !strcmp( endTest, ".bass" ) ){
674	<	strcpy( endTest, ".eor" );
1284	>
1285	>	molIndex = 0;
1286	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1287	>
1288	>	if(mol2proc[i] == worldRank ){
1289	>	the_molecules[molIndex].setStampID( molCompType[i] );
1290	>	the_molecules[molIndex].setMyIndex( molIndex );
1291	>	the_molecules[molIndex].setGlobalIndex( i );
1292	>	molIndex++;
1293		}
676	–	else if( !strcmp( endTest, ".BASS" ) ){
677	–	strcpy( endTest, ".eor" );
678	–	}
679	–	else{
680	–	endTest = &(simnfo->finalName[nameLength - 4]);
681	–	if( !strcmp( endTest, ".bss" ) ){
682	–	strcpy( endTest, ".eor" );
683	–	}
684	–	else if( !strcmp( endTest, ".mdl" ) ){
685	–	strcpy( endTest, ".eor" );
686	–	}
687	–	else{
688	–	strcat( simnfo->finalName, ".eor" );
689	–	}
690	–	}
1294		}
1295
1296	<	// make the sample and status out names
1296	>	#else // is_mpi
1297
1298	<	strcpy( simnfo->sampleName, inFileName );
1299	<	char* endTest;
1300	<	int nameLength = strlen( simnfo->sampleName );
1301	<	endTest = &(simnfo->sampleName[nameLength - 5]);
1302	<	if( !strcmp( endTest, ".bass" ) ){
1303	<	strcpy( endTest, ".dump" );
1304	<	}
1305	<	else if( !strcmp( endTest, ".BASS" ) ){
1306	<	strcpy( endTest, ".dump" );
1307	<	}
1308	<	else{
1309	<	endTest = &(simnfo->sampleName[nameLength - 4]);
707	<	if( !strcmp( endTest, ".bss" ) ){
708	<	strcpy( endTest, ".dump" );
1298	>	molIndex = 0;
1299	>	globalAtomIndex = 0;
1300	>	for(i=0; i<n_components; i++){
1301	>	for(j=0; j<components_nmol[i]; j++ ){
1302	>	the_molecules[molIndex].setStampID( i );
1303	>	the_molecules[molIndex].setMyIndex( molIndex );
1304	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1305	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1306	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1307	>	globalAtomIndex++;
1308	>	}
1309	>	molIndex++;
1310		}
710	–	else if( !strcmp( endTest, ".mdl" ) ){
711	–	strcpy( endTest, ".dump" );
712	–	}
713	–	else{
714	–	strcat( simnfo->sampleName, ".dump" );
715	–	}
1311		}
1312
1313	<	strcpy( simnfo->statusName, inFileName );
1314	<	nameLength = strlen( simnfo->statusName );
1315	<	endTest = &(simnfo->statusName[nameLength - 5]);
1316	<	if( !strcmp( endTest, ".bass" ) ){
1317	<	strcpy( endTest, ".stat" );
1318	<	}
1319	<	else if( !strcmp( endTest, ".BASS" ) ){
1320	<	strcpy( endTest, ".stat" );
1321	<	}
1322	<	else{
728	<	endTest = &(simnfo->statusName[nameLength - 4]);
729	<	if( !strcmp( endTest, ".bss" ) ){
730	<	strcpy( endTest, ".stat" );
1313	>
1314	>	#endif // is_mpi
1315	>
1316	>
1317	>	if( info[l].n_SRI ){
1318	>
1319	>	Exclude::createArray(info[l].n_SRI);
1320	>	the_excludes = new Exclude*[info[l].n_SRI];
1321	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	>	the_excludes[ex] = new Exclude(ex);
1323		}
1324	<	else if( !strcmp( endTest, ".mdl" ) ){
1325	<	strcpy( endTest, ".stat" );
734	<	}
735	<	else{
736	<	strcat( simnfo->statusName, ".stat" );
737	<	}
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].n_exclude = info[l].n_SRI;
1326		}
1327	+	else{
1328
1329	<	#ifdef IS_MPI
1330	<	}
1331	<	#endif // is_mpi
1332	<
1333	<	// set the status, sample, and themal kick times
1334	<
1335	<	if( the_globals->haveSampleTime() ){
1336	<	simnfo->sampleTime = the_globals->getSampleTime();
748	<	simnfo->statusTime = simnfo->sampleTime;
749	<	simnfo->thermalTime = simnfo->sampleTime;
750	<	}
751	<	else{
752	<	simnfo->sampleTime = the_globals->getRunTime();
753	<	simnfo->statusTime = simnfo->sampleTime;
754	<	simnfo->thermalTime = simnfo->sampleTime;
755	<	}
1329	>	Exclude::createArray( 1 );
1330	>	the_excludes = new Exclude*;
1331	>	the_excludes[0] = new Exclude(0);
1332	>	the_excludes[0]->setPair( 0,0 );
1333	>	info[l].globalExcludes = new int;
1334	>	info[l].globalExcludes[0] = 0;
1335	>	info[l].n_exclude = 0;
1336	>	}
1337
1338	<	if( the_globals->haveStatusTime() ){
758	<	simnfo->statusTime = the_globals->getStatusTime();
759	<	}
1338	>	// set the arrays into the SimInfo object
1339
1340	<	if( the_globals->haveThermalTime() ){
1341	<	simnfo->thermalTime = the_globals->getThermalTime();
1340	>	info[l].atoms = the_atoms;
1341	>	info[l].molecules = the_molecules;
1342	>	info[l].nGlobalExcludes = 0;
1343	>	info[l].excludes = the_excludes;
1344	>
1345	>	the_ff->setSimInfo( info );
1346	>
1347		}
1348	+	}
1349
1350	<	// check for the temperature set flag
1350	>	void SimSetup::makeIntegrator( void ){
1351
1352	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1352	>	int k;
1353
1354	+	NVT<RealIntegrator>*  myNVT = NULL;
1355	+	NPTi<RealIntegrator>* myNPTi = NULL;
1356	+	NPTf<RealIntegrator>* myNPTf = NULL;
1357	+	NPTim<RealIntegrator>* myNPTim = NULL;
1358	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1359	+
1360	+	for(k=0; k<nInfo; k++){
1361	+
1362	+	switch( ensembleCase ){
1363	+
1364	+	case NVE_ENS:
1365	+	if (globals->haveZconstraints()){
1366	+	setupZConstraint(info[k]);
1367	+	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1368	+	}
1369
1370	<	// make the integrator
1371	<
1372	<
1373	<	NVT* myNVT = NULL;
1374	<	switch( ensembleCase ){
1370	>	else
1371	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1372	>	break;
1373	>
1374	>	case NVT_ENS:
1375	>	if (globals->haveZconstraints()){
1376	>	setupZConstraint(info[k]);
1377	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	>	}
1379	>	else
1380	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1381
1382	<	case NVE_ENS:
1383	<	new NVE( simnfo, the_ff );
1384	<	break;
1382	>	myNVT->setTargetTemp(globals->getTargetTemp());
1383	>
1384	>	if (globals->haveTauThermostat())
1385	>	myNVT->setTauThermostat(globals->getTauThermostat());
1386	>
1387	>	else {
1388	>	sprintf( painCave.errMsg,
1389	>	"SimSetup error: If you use the NVT\n"
1390	>	"    ensemble, you must set tauThermostat.\n");
1391	>	painCave.isFatal = 1;
1392	>	simError();
1393	>	}
1394	>	break;
1395	>
1396	>	case NPTi_ENS:
1397	>	if (globals->haveZconstraints()){
1398	>	setupZConstraint(info[k]);
1399	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	>	}
1401	>	else
1402	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403
1404	<	case NVT_ENS:
1405	<	myNVT = new NVT( simnfo, the_ff );
1406	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
1407	<
1408	<	if (the_globals->haveTauThermostat())
1409	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
1410	<	//     else if (the_globals->haveQmass())
1411	<	//       myNVT->setQmass(the_globals->getQmass());
1412	<	else {
1404	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	>
1406	>	if (globals->haveTargetPressure())
1407	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	>	else {
1409	>	sprintf( painCave.errMsg,
1410	>	"SimSetup error: If you use a constant pressure\n"
1411	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	>	painCave.isFatal = 1;
1413	>	simError();
1414	>	}
1415	>
1416	>	if( globals->haveTauThermostat() )
1417	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	>	else{
1419	>	sprintf( painCave.errMsg,
1420	>	"SimSetup error: If you use an NPT\n"
1421	>	"    ensemble, you must set tauThermostat.\n");
1422	>	painCave.isFatal = 1;
1423	>	simError();
1424	>	}
1425	>
1426	>	if( globals->haveTauBarostat() )
1427	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	>	else{
1429	>	sprintf( painCave.errMsg,
1430	>	"SimSetup error: If you use an NPT\n"
1431	>	"    ensemble, you must set tauBarostat.\n");
1432	>	painCave.isFatal = 1;
1433	>	simError();
1434	>	}
1435	>	break;
1436	>
1437	>	case NPTf_ENS:
1438	>	if (globals->haveZconstraints()){
1439	>	setupZConstraint(info[k]);
1440	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	>	}
1442	>	else
1443	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1444	>
1445	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1446	>
1447	>	if (globals->haveTargetPressure())
1448	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	>	else {
1450	>	sprintf( painCave.errMsg,
1451	>	"SimSetup error: If you use a constant pressure\n"
1452	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	>	painCave.isFatal = 1;
1454	>	simError();
1455	>	}
1456	>
1457	>	if( globals->haveTauThermostat() )
1458	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	>	else{
1460	>	sprintf( painCave.errMsg,
1461	>	"SimSetup error: If you use an NPT\n"
1462	>	"    ensemble, you must set tauThermostat.\n");
1463	>	painCave.isFatal = 1;
1464	>	simError();
1465	>	}
1466	>
1467	>	if( globals->haveTauBarostat() )
1468	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	>	else{
1470	>	sprintf( painCave.errMsg,
1471	>	"SimSetup error: If you use an NPT\n"
1472	>	"    ensemble, you must set tauBarostat.\n");
1473	>	painCave.isFatal = 1;
1474	>	simError();
1475	>	}
1476	>	break;
1477	>
1478	>	case NPTim_ENS:
1479	>	if (globals->haveZconstraints()){
1480	>	setupZConstraint(info[k]);
1481	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	>	}
1483	>	else
1484	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1485	>
1486	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1487	>
1488	>	if (globals->haveTargetPressure())
1489	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	>	else {
1491	>	sprintf( painCave.errMsg,
1492	>	"SimSetup error: If you use a constant pressure\n"
1493	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	>	painCave.isFatal = 1;
1495	>	simError();
1496	>	}
1497	>
1498	>	if( globals->haveTauThermostat() )
1499	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	>	else{
1501	>	sprintf( painCave.errMsg,
1502	>	"SimSetup error: If you use an NPT\n"
1503	>	"    ensemble, you must set tauThermostat.\n");
1504	>	painCave.isFatal = 1;
1505	>	simError();
1506	>	}
1507	>
1508	>	if( globals->haveTauBarostat() )
1509	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	>	else{
1511		sprintf( painCave.errMsg,
1512	<	"SimSetup error: If you use the NVT\n"
1513	<	"    ensemble, you must set either tauThermostat or qMass.\n"
792	<	"    Neither of these was found in the BASS file.\n");
1512	>	"SimSetup error: If you use an NPT\n"
1513	>	"    ensemble, you must set tauBarostat.\n");
1514		painCave.isFatal = 1;
1515		simError();
1516	<	}
1517	<	break;
1516	>	}
1517	>	break;
1518	>
1519	>	case NPTfm_ENS:
1520	>	if (globals->haveZconstraints()){
1521	>	setupZConstraint(info[k]);
1522	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	>	}
1524	>	else
1525	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1526
1527	<	default:
1528	<	sprintf( painCave.errMsg,
1529	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1530	<	painCave.isFatal = 1;
1531	<	simError();
1527	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1528	>
1529	>	if (globals->haveTargetPressure())
1530	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1531	>	else {
1532	>	sprintf( painCave.errMsg,
1533	>	"SimSetup error: If you use a constant pressure\n"
1534	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1535	>	painCave.isFatal = 1;
1536	>	simError();
1537	>	}
1538	>
1539	>	if( globals->haveTauThermostat() )
1540	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1541	>	else{
1542	>	sprintf( painCave.errMsg,
1543	>	"SimSetup error: If you use an NPT\n"
1544	>	"    ensemble, you must set tauThermostat.\n");
1545	>	painCave.isFatal = 1;
1546	>	simError();
1547	>	}
1548	>
1549	>	if( globals->haveTauBarostat() )
1550	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1551	>	else{
1552	>	sprintf( painCave.errMsg,
1553	>	"SimSetup error: If you use an NPT\n"
1554	>	"    ensemble, you must set tauBarostat.\n");
1555	>	painCave.isFatal = 1;
1556	>	simError();
1557	>	}
1558	>	break;
1559	>
1560	>	default:
1561	>	sprintf( painCave.errMsg,
1562	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1563	>	painCave.isFatal = 1;
1564	>	simError();
1565	>	}
1566		}
1567	+	}
1568
1569	+	void SimSetup::initFortran( void ){
1570
1571	<	#ifdef IS_MPI
807	<	mpiSim->mpiRefresh();
808	<	#endif
809	<
810	<	// initialize the Fortran
811	<
812	<
813	<	simnfo->refreshSim();
1571	>	info[0].refreshSim();
1572
1573	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1573	>	if( !strcmp( info[0].mixingRule, "standard") ){
1574		the_ff->initForceField( LB_MIXING_RULE );
1575		}
1576	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
1576	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1577		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1578		}
1579		else{
1580		sprintf( painCave.errMsg,
1581		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	simnfo->mixingRule );
1582	>	info[0].mixingRule );
1583		painCave.isFatal = 1;
1584		simError();
1585		}
#	Line 832 | Line 1590 | void SimSetup::createSim( void ){
1590		"Successfully intialized the mixingRule for Fortran." );
1591		MPIcheckPoint();
1592		#endif // is_mpi
1593	+
1594		}
1595
1596	+	void SimSetup::setupZConstraint(SimInfo& theInfo)
1597	+	{
1598	+	int nZConstraints;
1599	+	ZconStamp** zconStamp;
1600	+
1601	+	if(globals->haveZconstraintTime()){
1602	+
1603	+	//add sample time of z-constraint  into SimInfo's property list
1604	+	DoubleData* zconsTimeProp = new DoubleData();
1605	+	zconsTimeProp->setID(ZCONSTIME_ID);
1606	+	zconsTimeProp->setData(globals->getZconsTime());
1607	+	theInfo.addProperty(zconsTimeProp);
1608	+	}
1609	+	else{
1610	+	sprintf( painCave.errMsg,
1611	+	"ZConstraint error: If you use an ZConstraint\n"
1612	+	" , you must set sample time.\n");
1613	+	painCave.isFatal = 1;
1614	+	simError();
1615	+	}
1616
1617	<	void SimSetup::makeMolecules( void ){
1617	>	//
1618	>	nZConstraints = globals->getNzConstraints();
1619	>	theInfo.nZconstraints = nZConstraints;
1620	>
1621	>	zconStamp = globals->getZconStamp();
1622	>	ZConsParaItem tempParaItem;
1623
1624	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
1625	<	molInit info;
1626	<	DirectionalAtom* dAtom;
1627	<	LinkedAssign* extras;
1628	<	LinkedAssign* current_extra;
1629	<	AtomStamp* currentAtom;
1630	<	BondStamp* currentBond;
1631	<	BendStamp* currentBend;
848	<	TorsionStamp* currentTorsion;
1624	>	ZConsParaData* zconsParaData = new ZConsParaData();
1625	>	zconsParaData->setID(ZCONSPARADATA_ID);
1626	>
1627	>	for(int i = 0; i < nZConstraints; i++){
1628	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1629	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1630	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1631	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1632
1633	<	bond_pair* theBonds;
1634	<	bend_set* theBends;
852	<	torsion_set* theTorsions;
1633	>	zconsParaData->addItem(tempParaItem);
1634	>	}
1635
1636	<
1637	<	//init the forceField paramters
1636	>	//sort the parameters by index of molecules
1637	>	zconsParaData->sortByIndex();
1638	>
1639	>	//push data into siminfo, therefore, we can retrieve later
1640	>	theInfo.addProperty(zconsParaData);
1641
1642	<	the_ff->readParams();
1642	>	//push zconsTol into siminfo, if user does not specify
1643	>	//value for zconsTol, a default value will be used
1644	>	DoubleData* zconsTol = new DoubleData();
1645	>	zconsTol->setID(ZCONSTOL_ID);
1646	>	if(globals->haveZconsTol()){
1647	>	zconsTol->setData(globals->getZconsTol());
1648	>	}
1649	>	else{
1650	>	double defaultZConsTol = 1E-6;
1651	>	sprintf( painCave.errMsg,
1652	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1653	>	" , default value %f is used.\n", defaultZConsTol);
1654	>	painCave.isFatal = 0;
1655	>	simError();
1656
1657	<
1658	<	// init the atoms
1659	<
1660	<	double ux, uy, uz, u, uSqr;
1661	<
1662	<	atomOffset = 0;
1663	<	excludeOffset = 0;
866	<	for(i=0; i<simnfo->n_mol; i++){
1657	>	zconsTol->setData(defaultZConsTol);
1658	>	}
1659	>	theInfo.addProperty(zconsTol);
1660	>
1661	>	//Determine the name of ouput file and add it into SimInfo's property list
1662	>	//Be careful, do not use inFileName, since it is a pointer which
1663	>	//point to a string at master node, and slave nodes do not contain that string
1664
1665	<	stampID = the_molecules[i].getStampID();
869	<
870	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
871	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
872	<	info.nBends    = comp_stamps[stampID]->getNBends();
873	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
874	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
875	<
876	<	info.myAtoms = &the_atoms[atomOffset];
877	<	info.myExcludes = &the_excludes[excludeOffset];
878	<	info.myBonds = new Bond*[info.nBonds];
879	<	info.myBends = new Bend*[info.nBends];
880	<	info.myTorsions = new Torsion*[info.nTorsions];
881	<
882	<	theBonds = new bond_pair[info.nBonds];
883	<	theBends = new bend_set[info.nBends];
884	<	theTorsions = new torsion_set[info.nTorsions];
1665	>	string zconsOutput(theInfo.finalName);
1666
1667	<	// make the Atoms
1667	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1668
1669	<	for(j=0; j<info.nAtoms; j++){
1670	<
1671	<	currentAtom = comp_stamps[stampID]->getAtom( j );
891	<	if( currentAtom->haveOrientation() ){
892	<
893	<	dAtom = new DirectionalAtom(j + atomOffset);
894	<	simnfo->n_oriented++;
895	<	info.myAtoms[j] = dAtom;
896	<
897	<	ux = currentAtom->getOrntX();
898	<	uy = currentAtom->getOrntY();
899	<	uz = currentAtom->getOrntZ();
900	<
901	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
902	<
903	<	u = sqrt( uSqr );
904	<	ux = ux / u;
905	<	uy = uy / u;
906	<	uz = uz / u;
907	<
908	<	dAtom->setSUx( ux );
909	<	dAtom->setSUy( uy );
910	<	dAtom->setSUz( uz );
911	<	}
912	<	else{
913	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
914	<	}
915	<	info.myAtoms[j]->setType( currentAtom->getType() );
1669	>	StringData* zconsFilename = new StringData();
1670	>	zconsFilename->setID(ZCONSFILENAME_ID);
1671	>	zconsFilename->setData(zconsOutput);
1672
1673	<	#ifdef IS_MPI
918	<
919	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
920	<
921	<	#endif // is_mpi
922	<	}
923	<
924	<	// make the bonds
925	<	for(j=0; j<info.nBonds; j++){
926	<
927	<	currentBond = comp_stamps[stampID]->getBond( j );
928	<	theBonds[j].a = currentBond->getA() + atomOffset;
929	<	theBonds[j].b = currentBond->getB() + atomOffset;
930	<
931	<	exI = theBonds[j].a;
932	<	exJ = theBonds[j].b;
933	<
934	<	// exclude_I must always be the smaller of the pair
935	<	if( exI > exJ ){
936	<	tempEx = exI;
937	<	exI = exJ;
938	<	exJ = tempEx;
939	<	}
940	<	#ifdef IS_MPI
941	<	tempEx = exI;
942	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
943	<	tempEx = exJ;
944	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
945	<
946	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
947	<	#else  // isn't MPI
948	<
949	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
950	<	#endif  //is_mpi
951	<	}
952	<	excludeOffset += info.nBonds;
953	<
954	<	//make the bends
955	<	for(j=0; j<info.nBends; j++){
956	<
957	<	currentBend = comp_stamps[stampID]->getBend( j );
958	<	theBends[j].a = currentBend->getA() + atomOffset;
959	<	theBends[j].b = currentBend->getB() + atomOffset;
960	<	theBends[j].c = currentBend->getC() + atomOffset;
961	<
962	<	if( currentBend->haveExtras() ){
963	<
964	<	extras = currentBend->getExtras();
965	<	current_extra = extras;
966	<
967	<	while( current_extra != NULL ){
968	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
969	<
970	<	switch( current_extra->getType() ){
971	<
972	<	case 0:
973	<	theBends[j].ghost =
974	<	current_extra->getInt() + atomOffset;
975	<	theBends[j].isGhost = 1;
976	<	break;
977	<
978	<	case 1:
979	<	theBends[j].ghost =
980	<	(int)current_extra->getDouble() + atomOffset;
981	<	theBends[j].isGhost = 1;
982	<	break;
983	<
984	<	default:
985	<	sprintf( painCave.errMsg,
986	<	"SimSetup Error: ghostVectorSource was neither a "
987	<	"double nor an int.\n"
988	<	"-->Bend[%d] in %s\n",
989	<	j, comp_stamps[stampID]->getID() );
990	<	painCave.isFatal = 1;
991	<	simError();
992	<	}
993	<	}
994	<
995	<	else{
996	<
997	<	sprintf( painCave.errMsg,
998	<	"SimSetup Error: unhandled bend assignment:\n"
999	<	"    -->%s in Bend[%d] in %s\n",
1000	<	current_extra->getlhs(),
1001	<	j, comp_stamps[stampID]->getID() );
1002	<	painCave.isFatal = 1;
1003	<	simError();
1004	<	}
1005	<
1006	<	current_extra = current_extra->getNext();
1007	<	}
1008	<	}
1009	<
1010	<	if( !theBends[j].isGhost ){
1011	<
1012	<	exI = theBends[j].a;
1013	<	exJ = theBends[j].c;
1014	<	}
1015	<	else{
1016	<
1017	<	exI = theBends[j].a;
1018	<	exJ = theBends[j].b;
1019	<	}
1020	<
1021	<	// exclude_I must always be the smaller of the pair
1022	<	if( exI > exJ ){
1023	<	tempEx = exI;
1024	<	exI = exJ;
1025	<	exJ = tempEx;
1026	<	}
1027	<	#ifdef IS_MPI
1028	<	tempEx = exI;
1029	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1030	<	tempEx = exJ;
1031	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1032	<
1033	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1034	<	#else  // isn't MPI
1035	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1036	<	#endif  //is_mpi
1037	<	}
1038	<	excludeOffset += info.nBends;
1039	<
1040	<	for(j=0; j<info.nTorsions; j++){
1041	<
1042	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1043	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1044	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1045	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1046	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1047	<
1048	<	exI = theTorsions[j].a;
1049	<	exJ = theTorsions[j].d;
1050	<
1051	<	// exclude_I must always be the smaller of the pair
1052	<	if( exI > exJ ){
1053	<	tempEx = exI;
1054	<	exI = exJ;
1055	<	exJ = tempEx;
1056	<	}
1057	<	#ifdef IS_MPI
1058	<	tempEx = exI;
1059	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1060	<	tempEx = exJ;
1061	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1062	<
1063	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1064	<	#else  // isn't MPI
1065	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1066	<	#endif  //is_mpi
1067	<	}
1068	<	excludeOffset += info.nTorsions;
1069	<
1070	<
1071	<	// send the arrays off to the forceField for init.
1072	<
1073	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1074	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1075	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1076	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1077	<
1078	<
1079	<	the_molecules[i].initialize( info );
1080	<
1081	<
1082	<	atomOffset += info.nAtoms;
1083	<	delete[] theBonds;
1084	<	delete[] theBends;
1085	<	delete[] theTorsions;
1086	<	}
1087	<
1088	<	#ifdef IS_MPI
1089	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1090	<	MPIcheckPoint();
1091	<	#endif // is_mpi
1092	<
1093	<	// clean up the forcefield
1094	<	the_ff->calcRcut();
1095	<	the_ff->cleanMe();
1096	<
1673	>	theInfo.addProperty(zconsFilename);
1674		}
1098	–
1099	–	void SimSetup::initFromBass( void ){
1100	–
1101	–	int i, j, k;
1102	–	int n_cells;
1103	–	double cellx, celly, cellz;
1104	–	double temp1, temp2, temp3;
1105	–	int n_per_extra;
1106	–	int n_extra;
1107	–	int have_extra, done;
1108	–
1109	–	temp1 = (double)tot_nmol / 4.0;
1110	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1111	–	temp3 = ceil( temp2 );
1112	–
1113	–	have_extra =0;
1114	–	if( temp2 < temp3 ){ // we have a non-complete lattice
1115	–	have_extra =1;
1116	–
1117	–	n_cells = (int)temp3 - 1;
1118	–	cellx = simnfo->box_x / temp3;
1119	–	celly = simnfo->box_y / temp3;
1120	–	cellz = simnfo->box_z / temp3;
1121	–	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1122	–	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1123	–	n_per_extra = (int)ceil( temp1 );
1124	–
1125	–	if( n_per_extra > 4){
1126	–	sprintf( painCave.errMsg,
1127	–	"SimSetup error. There has been an error in constructing"
1128	–	" the non-complete lattice.\n" );
1129	–	painCave.isFatal = 1;
1130	–	simError();
1131	–	}
1132	–	}
1133	–	else{
1134	–	n_cells = (int)temp3;
1135	–	cellx = simnfo->box_x / temp3;
1136	–	celly = simnfo->box_y / temp3;
1137	–	cellz = simnfo->box_z / temp3;
1138	–	}
1139	–
1140	–	current_mol = 0;
1141	–	current_comp_mol = 0;
1142	–	current_comp = 0;
1143	–	current_atom_ndx = 0;
1144	–
1145	–	for( i=0; i < n_cells ; i++ ){
1146	–	for( j=0; j < n_cells; j++ ){
1147	–	for( k=0; k < n_cells; k++ ){
1148	–
1149	–	makeElement( i * cellx,
1150	–	j * celly,
1151	–	k * cellz );
1152	–
1153	–	makeElement( i * cellx + 0.5 * cellx,
1154	–	j * celly + 0.5 * celly,
1155	–	k * cellz );
1156	–
1157	–	makeElement( i * cellx,
1158	–	j * celly + 0.5 * celly,
1159	–	k * cellz + 0.5 * cellz );
1160	–
1161	–	makeElement( i * cellx + 0.5 * cellx,
1162	–	j * celly,
1163	–	k * cellz + 0.5 * cellz );
1164	–	}
1165	–	}
1166	–	}
1167	–
1168	–	if( have_extra ){
1169	–	done = 0;
1170	–
1171	–	int start_ndx;
1172	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1173	–	for( j=0; j < (n_cells+1) && !done; j++ ){
1174	–
1175	–	if( i < n_cells ){
1176	–
1177	–	if( j < n_cells ){
1178	–	start_ndx = n_cells;
1179	–	}
1180	–	else start_ndx = 0;
1181	–	}
1182	–	else start_ndx = 0;
1183	–
1184	–	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1185	–
1186	–	makeElement( i * cellx,
1187	–	j * celly,
1188	–	k * cellz );
1189	–	done = ( current_mol >= tot_nmol );
1190	–
1191	–	if( !done && n_per_extra > 1 ){
1192	–	makeElement( i * cellx + 0.5 * cellx,
1193	–	j * celly + 0.5 * celly,
1194	–	k * cellz );
1195	–	done = ( current_mol >= tot_nmol );
1196	–	}
1197	–
1198	–	if( !done && n_per_extra > 2){
1199	–	makeElement( i * cellx,
1200	–	j * celly + 0.5 * celly,
1201	–	k * cellz + 0.5 * cellz );
1202	–	done = ( current_mol >= tot_nmol );
1203	–	}
1204	–
1205	–	if( !done && n_per_extra > 3){
1206	–	makeElement( i * cellx + 0.5 * cellx,
1207	–	j * celly,
1208	–	k * cellz + 0.5 * cellz );
1209	–	done = ( current_mol >= tot_nmol );
1210	–	}
1211	–	}
1212	–	}
1213	–	}
1214	–	}
1215	–
1216	–
1217	–	for( i=0; i<simnfo->n_atoms; i++ ){
1218	–	simnfo->atoms[i]->set_vx( 0.0 );
1219	–	simnfo->atoms[i]->set_vy( 0.0 );
1220	–	simnfo->atoms[i]->set_vz( 0.0 );
1221	–	}
1222	–	}
1223	–
1224	–	void SimSetup::makeElement( double x, double y, double z ){
1225	–
1226	–	int k;
1227	–	AtomStamp* current_atom;
1228	–	DirectionalAtom* dAtom;
1229	–	double rotMat[3][3];
1230	–
1231	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1232	–
1233	–	current_atom = comp_stamps[current_comp]->getAtom( k );
1234	–	if( !current_atom->havePosition() ){
1235	–	sprintf( painCave.errMsg,
1236	–	"SimSetup:initFromBass error.\n"
1237	–	"\tComponent %s, atom %s does not have a position specified.\n"
1238	–	"\tThe initialization routine is unable to give a start"
1239	–	" position.\n",
1240	–	comp_stamps[current_comp]->getID(),
1241	–	current_atom->getType() );
1242	–	painCave.isFatal = 1;
1243	–	simError();
1244	–	}
1245	–
1246	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1247	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1248	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1249	–
1250	–	if( the_atoms[current_atom_ndx]->isDirectional() ){
1251	–
1252	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1253	–
1254	–	rotMat[0][0] = 1.0;
1255	–	rotMat[0][1] = 0.0;
1256	–	rotMat[0][2] = 0.0;
1257	–
1258	–	rotMat[1][0] = 0.0;
1259	–	rotMat[1][1] = 1.0;
1260	–	rotMat[1][2] = 0.0;
1261	–
1262	–	rotMat[2][0] = 0.0;
1263	–	rotMat[2][1] = 0.0;
1264	–	rotMat[2][2] = 1.0;
1265	–
1266	–	dAtom->setA( rotMat );
1267	–	}
1268	–
1269	–	current_atom_ndx++;
1270	–	}
1271	–
1272	–	current_mol++;
1273	–	current_comp_mol++;
1274	–
1275	–	if( current_comp_mol >= components_nmol[current_comp] ){
1276	–
1277	–	current_comp_mol = 0;
1278	–	current_comp++;
1279	–	}
1280	–	}

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