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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 700 by tim, Fri Aug 15 19:24:13 2003 UTC vs.
Revision 701 by tim, Wed Aug 20 14:34:04 2003 UTC

#	Line 189 | Line 189 | void SimSetup::makeMolecules( void ){
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() );
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] );
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225
226		#endif // is_mpi
227		}
#	Line 229 | Line 229 | void SimSetup::makeMolecules( void ){
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 );
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) );
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	<	}
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;
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 );
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) );
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	<	}
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 );
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) );
370	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371		#endif  //is_mpi
372		}
373		excludeOffset += molInfo.nTorsions;
#	Line 436 | Line 436 | void SimSetup::initFromBass( void ){
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" );
439	>	"SimSetup error. There has been an error in constructing"
440	>	" the non-complete lattice.\n" );
441		painCave.isFatal = 1;
442		simError();
443		}
#	Line 458 | Line 458 | void SimSetup::initFromBass( void ){
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 );
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 );
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 );
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 );
473	>	makeElement( i * cellx + 0.5 * cellx,
474	>	j * celly,
475	>	k * cellz + 0.5 * cellz );
476		}
477		}
478		}
#	Line 484 | Line 484 | void SimSetup::initFromBass( void ){
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 ){
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;
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++ ){
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 );
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	<	}
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	<	}
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	<	}
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		}
#	Line 543 | Line 543 | void SimSetup::makeElement( double x, double y, double
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() );
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		}
#	Line 617 | Line 617 | void SimSetup::gatherInfo( void ){
617		else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618		else{
619		sprintf( painCave.errMsg,
620	<	"SimSetup Error. Unrecognized force field -> %s\n",
621	<	force_field );
620	>	"SimSetup Error. Unrecognized force field -> %s\n",
621	>	force_field );
622		painCave.isFatal = 1;
623		simError();
624		}
#	Line 636 | Line 636 | void SimSetup::gatherInfo( void ){
636		else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637		else{
638		sprintf( painCave.errMsg,
639	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
639	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640		"reverting to NVE for this simulation.\n",
641	<	ensemble );
641	>	ensemble );
642		painCave.isFatal = 0;
643		simError();
644		strcpy( ensemble, "NVE" );
#	Line 669 | Line 669 | void SimSetup::gatherInfo( void ){
669		for( i=0; i<n_components; i++ ){
670
671		if( !the_components[i]->haveNMol() ){
672	<	// we have a problem
673	<	sprintf( painCave.errMsg,
674	<	"SimSetup Error. No global NMol or component NMol"
675	<	" given. Cannot calculate the number of atoms.\n" );
676	<	painCave.isFatal = 1;
677	<	simError();
672	>	// we have a problem
673	>	sprintf( painCave.errMsg,
674	>	"SimSetup Error. No global NMol or component NMol"
675	>	" given. Cannot calculate the number of atoms.\n" );
676	>	painCave.isFatal = 1;
677	>	simError();
678		}
679
680		tot_nmol += the_components[i]->getNMol();
#	Line 683 | Line 683 | void SimSetup::gatherInfo( void ){
683		}
684		else{
685		sprintf( painCave.errMsg,
686	<	"SimSetup error.\n"
687	<	"\tSorry, the ability to specify total"
688	<	" nMols and then give molfractions in the components\n"
689	<	"\tis not currently supported."
690	<	" Please give nMol in the components.\n" );
686	>	"SimSetup error.\n"
687	>	"\tSorry, the ability to specify total"
688	>	" nMols and then give molfractions in the components\n"
689	>	"\tis not currently supported."
690	>	" Please give nMol in the components.\n" );
691		painCave.isFatal = 1;
692		simError();
693		}
#	Line 741 | Line 741 | void SimSetup::gatherInfo( void ){
741		}
742		else{
743		if( !globals->haveBoxX() ){
744	<	sprintf( painCave.errMsg,
745	<	"SimSetup error, no periodic BoxX size given.\n" );
746	<	painCave.isFatal = 1;
747	<	simError();
744	>	sprintf( painCave.errMsg,
745	>	"SimSetup error, no periodic BoxX size given.\n" );
746	>	painCave.isFatal = 1;
747	>	simError();
748		}
749		boxVector[0] = globals->getBoxX();
750
751		if( !globals->haveBoxY() ){
752	<	sprintf( painCave.errMsg,
753	<	"SimSetup error, no periodic BoxY size given.\n" );
754	<	painCave.isFatal = 1;
755	<	simError();
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();
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
#	Line 803 | Line 803 | void SimSetup::finalInfoCheck( void ){
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;
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();
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;
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();
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();
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 );
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		}
#	Line 919 | Line 919 | void SimSetup::initSystemCoords( void ){
919		// no init from bass
920
921		sprintf( painCave.errMsg,
922	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
922	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923		painCave.isFatal;
924		simError();
925
#	Line 951 | Line 951 | void SimSetup::makeOutNames( void ){
951		#endif // is_mpi
952
953		if( globals->haveFinalConfig() ){
954	<	strcpy( info[k].finalName, globals->getFinalConfig() );
954	>	strcpy( info[k].finalName, globals->getFinalConfig() );
955		}
956		else{
957	<	strcpy( info[k].finalName, inFileName );
958	<	char* endTest;
959	<	int nameLength = strlen( info[k].finalName );
960	<	endTest = &(info[k].finalName[nameLength - 5]);
961	<	if( !strcmp( endTest, ".bass" ) ){
962	<	strcpy( endTest, ".eor" );
963	<	}
964	<	else if( !strcmp( endTest, ".BASS" ) ){
965	<	strcpy( endTest, ".eor" );
966	<	}
967	<	else{
968	<	endTest = &(info[k].finalName[nameLength - 4]);
969	<	if( !strcmp( endTest, ".bss" ) ){
970	<	strcpy( endTest, ".eor" );
971	<	}
972	<	else if( !strcmp( endTest, ".mdl" ) ){
973	<	strcpy( endTest, ".eor" );
974	<	}
975	<	else{
976	<	strcat( info[k].finalName, ".eor" );
977	<	}
978	<	}
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
#	Line 985 | Line 985 | void SimSetup::makeOutNames( void ){
985		int nameLength = strlen( info[k].sampleName );
986		endTest = &(info[k].sampleName[nameLength - 5]);
987		if( !strcmp( endTest, ".bass" ) ){
988	<	strcpy( endTest, ".dump" );
988	>	strcpy( endTest, ".dump" );
989		}
990		else if( !strcmp( endTest, ".BASS" ) ){
991	<	strcpy( endTest, ".dump" );
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	<	}
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" );
1010	>	strcpy( endTest, ".stat" );
1011		}
1012		else if( !strcmp( endTest, ".BASS" ) ){
1013	<	strcpy( endTest, ".stat" );
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	<	}
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
#	Line 1089 | Line 1089 | void SimSetup::createFF( void ){
1089
1090		default:
1091		sprintf( painCave.errMsg,
1092	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1093		painCave.isFatal = 1;
1094		simError();
1095		}
#	Line 1135 | Line 1135 | void SimSetup::compList( void ){
1135
1136		currentStamp = stamps->extractMolStamp( id );
1137		if( currentStamp == NULL ){
1138	<	sprintf( painCave.errMsg,
1139	<	"SimSetup error: Component \"%s\" was not found in the "
1140	<	"list of declared molecules\n",
1141	<	id );
1142	<	painCave.isFatal = 1;
1143	<	simError();
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 );
#	Line 1219 | Line 1219 | void SimSetup::mpiMolDivide( void ){
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++;
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;
#	Line 1240 | Line 1240 | void SimSetup::mpiMolDivide( void ){
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 );
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		}
#	Line 1286 | Line 1286 | void SimSetup::makeSysArrays( void ){
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++;
1289	>	the_molecules[molIndex].setStampID( molCompType[i] );
1290	>	the_molecules[molIndex].setMyIndex( molIndex );
1291	>	the_molecules[molIndex].setGlobalIndex( i );
1292	>	molIndex++;
1293		}
1294		}
1295
#	Line 1299 | Line 1299 | void SimSetup::makeSysArrays( void ){
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++;
1302	>	the_molecules[molIndex].setStampID( i );
1303	>	the_molecules[molIndex].setMyIndex( molIndex );
1304	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1305	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1306	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1307	>	globalAtomIndex++;
1308	>	}
1309	>	molIndex++;
1310		}
1311		}
1312
#	Line 1319 | Line 1319 | void SimSetup::makeSysArrays( void ){
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);
1322	>	the_excludes[ex] = new Exclude(ex);
1323		}
1324		info[l].globalExcludes = new int;
1325		info[l].n_exclude = info[l].n_SRI;
#	Line 1362 | Line 1362 | void SimSetup::makeIntegrator( void ){
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	<	}
1365	>	if (globals->haveZconstraints()){
1366	>	setupZConstraint(info[k]);
1367	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1368	>	}
1369
1370	<	else
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
1375	>	if (globals->haveZconstraints()){
1376	>	setupZConstraint(info[k]);
1377	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	>	}
1379	>	else
1380		myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1381
1382	<	myNVT->setTargetTemp(globals->getTargetTemp());
1382	>	myNVT->setTargetTemp(globals->getTargetTemp());
1383
1384	<	if (globals->haveTauThermostat())
1385	<	myNVT->setTauThermostat(globals->getTauThermostat());
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;
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
1397	>	if (globals->haveZconstraints()){
1398	>	setupZConstraint(info[k]);
1399	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	>	}
1401	>	else
1402		myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403
1404	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	<
1404	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	>
1406		if (globals->haveTargetPressure())
1407	<	myNPTi->setTargetPressure(globals->getTargetPressure());
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();
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	<
1415	>
1416		if( globals->haveTauThermostat() )
1417	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
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();
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	<
1425	>
1426		if( globals->haveTauBarostat() )
1427	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
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;
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
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	<
1446	>
1447		if (globals->haveTargetPressure())
1448	<	myNPTf->setTargetPressure(globals->getTargetPressure());
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();
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	<
1456	>
1457		if( globals->haveTauThermostat() )
1458	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
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();
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	<
1466	>
1467		if( globals->haveTauBarostat() )
1468	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
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();
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
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	<
1486	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1487	>
1488		if (globals->haveTargetPressure())
1489	<	myNPTim->setTargetPressure(globals->getTargetPressure());
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();
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	<
1497	>
1498		if( globals->haveTauThermostat() )
1499	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
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();
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	<
1507	>
1508		if( globals->haveTauBarostat() )
1509	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510		else{
1511	<	sprintf( painCave.errMsg,
1512	<	"SimSetup error: If you use an NPT\n"
1513	<	"    ensemble, you must set tauBarostat.\n");
1514	<	painCave.isFatal = 1;
1515	<	simError();
1511	>	sprintf( painCave.errMsg,
1512	>	"SimSetup error: If you use an NPT\n"
1513	>	"    ensemble, you must set tauBarostat.\n");
1514	>	painCave.isFatal = 1;
1515	>	simError();
1516		}
1517		break;
1518
1519		case NPTfm_ENS:
1520	<	if (globals->haveZconstraints()){
1521	<	setupZConstraint(info[k]);
1522	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	<	}
1524	<	else
1520	>	if (globals->haveZconstraints()){
1521	>	setupZConstraint(info[k]);
1522	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	>	}
1524	>	else
1525		myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1526
1527	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1528	<
1527	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1528	>
1529		if (globals->haveTargetPressure())
1530	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
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();
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	<
1538	>
1539		if( globals->haveTauThermostat() )
1540	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
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();
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	<
1548	>
1549		if( globals->haveTauBarostat() )
1550	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
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();
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");
1562	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1563		painCave.isFatal = 1;
1564		simError();
1565		}
#	Line 1578 | Line 1578 | void SimSetup::initFortran( void ){
1578		}
1579		else{
1580		sprintf( painCave.errMsg,
1581	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	info[0].mixingRule );
1581	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	>	info[0].mixingRule );
1583		painCave.isFatal = 1;
1584		simError();
1585		}
#	Line 1587 | Line 1587 | void SimSetup::initFortran( void ){
1587
1588		#ifdef IS_MPI
1589		strcpy( checkPointMsg,
1590	<	"Successfully intialized the mixingRule for Fortran." );
1590	>	"Successfully intialized the mixingRule for Fortran." );
1591		MPIcheckPoint();
1592		#endif // is_mpi
1593
#	Line 1595 | Line 1595 | void SimSetup::setupZConstraint(SimInfo& theInfo)
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	<	}
1598	>	int nZConstraints;
1599	>	ZconStamp** zconStamp;
1600
1601	<	//push zconsTol into siminfo, if user does not specify
1602	<	//value for zconsTol, a default value will be used
1603	<	DoubleData* zconsTol = new DoubleData();
1604	<	zconsTol->setID(ZCONSTOL_ID);
1605	<	if(globals->haveZconsTol()){
1606	<	zconsTol->setData(globals->getZconsTol());
1607	<	}
1608	<	else{
1609	<	double defaultZConsTol = 0.01;
1610	<	sprintf( painCave.errMsg,
1611	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1612	<	" , default value %f is used.\n", defaultZConsTol);
1613	<	painCave.isFatal = 0;
1614	<	simError();
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	<	zconsTol->setData(defaultZConsTol);
1618	<	}
1619	<	theInfo.addProperty(zconsTol);
1617	>	//push zconsTol into siminfo, if user does not specify
1618	>	//value for zconsTol, a default value will be used
1619	>	DoubleData* zconsTol = new DoubleData();
1620	>	zconsTol->setID(ZCONSTOL_ID);
1621	>	if(globals->haveZconsTol()){
1622	>	zconsTol->setData(globals->getZconsTol());
1623	>	}
1624	>	else{
1625	>	double defaultZConsTol = 0.01;
1626	>	sprintf( painCave.errMsg,
1627	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628	>	" , default value %f is used.\n", defaultZConsTol);
1629	>	painCave.isFatal = 0;
1630	>	simError();
1631
1632	<	//set Force Substraction Policy
1633	<	StringData* zconsForcePolicy =  new StringData();
1634	<	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	<
1640	<	if(globals->haveZconsForcePolicy()){
1641	<	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	<	}
1643	<	else{
1644	<	sprintf( painCave.errMsg,
1645	<	"ZConstraint Warning: User does not set force substraction policy, "
1646	<	"average force substraction policy is used\n");
1647	<	painCave.isFatal = 0;
1648	<	simError();
1649	<	zconsForcePolicy->setData("BYNUMBER");
1650	<	}
1651	<
1652	<	theInfo.addProperty(zconsForcePolicy);
1653	<
1654	<	//Determine the name of ouput file and add it into SimInfo's property list
1655	<	//Be careful, do not use inFileName, since it is a pointer which
1656	<	//point to a string at master node, and slave nodes do not contain that string
1657	<
1658	<	string zconsOutput(theInfo.finalName);
1659	<
1660	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	<
1662	<	StringData* zconsFilename = new StringData();
1663	<	zconsFilename->setID(ZCONSFILENAME_ID);
1664	<	zconsFilename->setData(zconsOutput);
1665	<
1666	<	theInfo.addProperty(zconsFilename);
1667	<
1668	<	//setup index, pos and other parameters of z-constraint molecules
1669	<	nZConstraints = globals->getNzConstraints();
1670	<	theInfo.nZconstraints = nZConstraints;
1671	<
1672	<	zconStamp = globals->getZconStamp();
1673	<	ZConsParaItem tempParaItem;
1632	>	zconsTol->setData(defaultZConsTol);
1633	>	}
1634	>	theInfo.addProperty(zconsTol);
1635
1636	<	ZConsParaData* zconsParaData = new ZConsParaData();
1637	<	zconsParaData->setID(ZCONSPARADATA_ID);
1638	<
1639	<	for(int i = 0; i < nZConstraints; i++){
1636	>	//set Force Substraction Policy
1637	>	StringData* zconsForcePolicy =  new StringData();
1638	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	>
1640	>	if(globals->haveZconsForcePolicy()){
1641	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	>	}
1643	>	else{
1644	>	sprintf( painCave.errMsg,
1645	>	"ZConstraint Warning: User does not set force substraction policy, "
1646	>	"average force substraction policy is used\n");
1647	>	painCave.isFatal = 0;
1648	>	simError();
1649	>	zconsForcePolicy->setData("BYNUMBER");
1650	>	}
1651	>
1652	>	theInfo.addProperty(zconsForcePolicy);
1653	>
1654	>	//Determine the name of ouput file and add it into SimInfo's property list
1655	>	//Be careful, do not use inFileName, since it is a pointer which
1656	>	//point to a string at master node, and slave nodes do not contain that string
1657	>
1658	>	string zconsOutput(theInfo.finalName);
1659	>
1660	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	>
1662	>	StringData* zconsFilename = new StringData();
1663	>	zconsFilename->setID(ZCONSFILENAME_ID);
1664	>	zconsFilename->setData(zconsOutput);
1665	>
1666	>	theInfo.addProperty(zconsFilename);
1667	>
1668	>	//setup index, pos and other parameters of z-constraint molecules
1669	>	nZConstraints = globals->getNzConstraints();
1670	>	theInfo.nZconstraints = nZConstraints;
1671	>
1672	>	zconStamp = globals->getZconStamp();
1673	>	ZConsParaItem tempParaItem;
1674	>
1675	>	ZConsParaData* zconsParaData = new ZConsParaData();
1676	>	zconsParaData->setID(ZCONSPARADATA_ID);
1677	>
1678	>	for(int i = 0; i < nZConstraints; i++){
1679		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680		tempParaItem.zPos = zconStamp[i]->getZpos();
1681		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682		tempParaItem.kRatio = zconStamp[i]->getKratio();
1683
1684		zconsParaData->addItem(tempParaItem);
1685	<	}
1685	>	}
1686
1687	<	//sort the parameters by index of molecules
1688	<	zconsParaData->sortByIndex();
1689	<
1690	<	//push data into siminfo, therefore, we can retrieve later
1691	<	theInfo.addProperty(zconsParaData);
1687	>	//sort the parameters by index of molecules
1688	>	zconsParaData->sortByIndex();
1689	>
1690	>	//push data into siminfo, therefore, we can retrieve later
1691	>	theInfo.addProperty(zconsParaData);
1692
1693		}

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