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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 690 by mmeineke, Tue Aug 12 21:44:06 2003 UTC vs.
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC

#	Line 3 | Line 3
3		#include <iostream>
4		#include <cmath>
5		#include <string>
6	+	#include <sys/time.h>
7
8		#include "SimSetup.hpp"
9		#include "ReadWrite.hpp"
#	Line 189 | Line 190 | void SimSetup::makeMolecules( void ){
190		// make the Atoms
191
192		for(j=0; j<molInfo.nAtoms; j++){
193	<
194	<	currentAtom = comp_stamps[stampID]->getAtom( j );
195	<	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() );
193	>
194	>	currentAtom = comp_stamps[stampID]->getAtom( j );
195	>	if( currentAtom->haveOrientation() ){
196
197	+	dAtom = new DirectionalAtom( (j + atomOffset),
198	+	info[k].getConfiguration() );
199	+	info[k].n_oriented++;
200	+	molInfo.myAtoms[j] = dAtom;
201	+
202	+	ux = currentAtom->getOrntX();
203	+	uy = currentAtom->getOrntY();
204	+	uz = currentAtom->getOrntZ();
205	+
206	+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
207	+
208	+	u = sqrt( uSqr );
209	+	ux = ux / u;
210	+	uy = uy / u;
211	+	uz = uz / u;
212	+
213	+	dAtom->setSUx( ux );
214	+	dAtom->setSUy( uy );
215	+	dAtom->setSUz( uz );
216	+	}
217	+	else{
218	+	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
219	+	info[k].getConfiguration() );
220	+	}
221	+	molInfo.myAtoms[j]->setType( currentAtom->getType() );
222	+
223		#ifdef IS_MPI
224
225	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
226
227		#endif // is_mpi
228		}
#	Line 229 | Line 230 | void SimSetup::makeMolecules( void ){
230		// make the bonds
231		for(j=0; j<molInfo.nBonds; j++){
232
233	<	currentBond = comp_stamps[stampID]->getBond( j );
234	<	theBonds[j].a = currentBond->getA() + atomOffset;
235	<	theBonds[j].b = currentBond->getB() + atomOffset;
236	<
237	<	exI = theBonds[j].a;
238	<	exJ = theBonds[j].b;
239	<
240	<	// exclude_I must always be the smaller of the pair
241	<	if( exI > exJ ){
242	<	tempEx = exI;
243	<	exI = exJ;
244	<	exJ = tempEx;
245	<	}
246	<	#ifdef IS_MPI
247	<	tempEx = exI;
248	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	<	tempEx = exJ;
250	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
251	<
252	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
233	>	currentBond = comp_stamps[stampID]->getBond( j );
234	>	theBonds[j].a = currentBond->getA() + atomOffset;
235	>	theBonds[j].b = currentBond->getB() + atomOffset;
236	>
237	>	exI = theBonds[j].a;
238	>	exJ = theBonds[j].b;
239	>
240	>	// exclude_I must always be the smaller of the pair
241	>	if( exI > exJ ){
242	>	tempEx = exI;
243	>	exI = exJ;
244	>	exJ = tempEx;
245	>	}
246	>	#ifdef IS_MPI
247	>	tempEx = exI;
248	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>	tempEx = exJ;
250	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
251	>
252	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
253		#else  // isn't MPI
254	<
255	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	>
255	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
256		#endif  //is_mpi
257		}
258		excludeOffset += molInfo.nBonds;
259
260		//make the bends
261		for(j=0; j<molInfo.nBends; j++){
262	<
263	<	currentBend = comp_stamps[stampID]->getBend( j );
264	<	theBends[j].a = currentBend->getA() + atomOffset;
265	<	theBends[j].b = currentBend->getB() + atomOffset;
266	<	theBends[j].c = currentBend->getC() + atomOffset;
267	<
268	<	if( currentBend->haveExtras() ){
269	<
270	<	extras = currentBend->getExtras();
271	<	current_extra = extras;
272	<
273	<	while( current_extra != NULL ){
274	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
275	<
276	<	switch( current_extra->getType() ){
277	<
278	<	case 0:
279	<	theBends[j].ghost =
280	<	current_extra->getInt() + atomOffset;
281	<	theBends[j].isGhost = 1;
282	<	break;
283	<
284	<	case 1:
285	<	theBends[j].ghost =
286	<	(int)current_extra->getDouble() + atomOffset;
287	<	theBends[j].isGhost = 1;
288	<	break;
289	<
290	<	default:
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup Error: ghostVectorSource was neither a "
293	<	"double nor an int.\n"
294	<	"-->Bend[%d] in %s\n",
295	<	j, comp_stamps[stampID]->getID() );
296	<	painCave.isFatal = 1;
297	<	simError();
298	<	}
299	<	}
300	<
301	<	else{
302	<
303	<	sprintf( painCave.errMsg,
304	<	"SimSetup Error: unhandled bend assignment:\n"
305	<	"    -->%s in Bend[%d] in %s\n",
306	<	current_extra->getlhs(),
307	<	j, comp_stamps[stampID]->getID() );
308	<	painCave.isFatal = 1;
309	<	simError();
310	<	}
311	<
312	<	current_extra = current_extra->getNext();
313	<	}
314	<	}
315	<
316	<	if( !theBends[j].isGhost ){
317	<
318	<	exI = theBends[j].a;
319	<	exJ = theBends[j].c;
320	<	}
321	<	else{
322	<
323	<	exI = theBends[j].a;
324	<	exJ = theBends[j].b;
325	<	}
326	<
327	<	// exclude_I must always be the smaller of the pair
328	<	if( exI > exJ ){
329	<	tempEx = exI;
330	<	exI = exJ;
331	<	exJ = tempEx;
332	<	}
262	>
263	>	currentBend = comp_stamps[stampID]->getBend( j );
264	>	theBends[j].a = currentBend->getA() + atomOffset;
265	>	theBends[j].b = currentBend->getB() + atomOffset;
266	>	theBends[j].c = currentBend->getC() + atomOffset;
267	>
268	>	if( currentBend->haveExtras() ){
269	>
270	>	extras = currentBend->getExtras();
271	>	current_extra = extras;
272	>
273	>	while( current_extra != NULL ){
274	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
275	>
276	>	switch( current_extra->getType() ){
277	>
278	>	case 0:
279	>	theBends[j].ghost =
280	>	current_extra->getInt() + atomOffset;
281	>	theBends[j].isGhost = 1;
282	>	break;
283	>
284	>	case 1:
285	>	theBends[j].ghost =
286	>	(int)current_extra->getDouble() + atomOffset;
287	>	theBends[j].isGhost = 1;
288	>	break;
289	>
290	>	default:
291	>	sprintf( painCave.errMsg,
292	>	"SimSetup Error: ghostVectorSource was neither a "
293	>	"double nor an int.\n"
294	>	"-->Bend[%d] in %s\n",
295	>	j, comp_stamps[stampID]->getID() );
296	>	painCave.isFatal = 1;
297	>	simError();
298	>	}
299	>	}
300	>
301	>	else{
302	>
303	>	sprintf( painCave.errMsg,
304	>	"SimSetup Error: unhandled bend assignment:\n"
305	>	"    -->%s in Bend[%d] in %s\n",
306	>	current_extra->getlhs(),
307	>	j, comp_stamps[stampID]->getID() );
308	>	painCave.isFatal = 1;
309	>	simError();
310	>	}
311	>
312	>	current_extra = current_extra->getNext();
313	>	}
314	>	}
315	>
316	>	if( !theBends[j].isGhost ){
317	>
318	>	exI = theBends[j].a;
319	>	exJ = theBends[j].c;
320	>	}
321	>	else{
322	>
323	>	exI = theBends[j].a;
324	>	exJ = theBends[j].b;
325	>	}
326	>
327	>	// exclude_I must always be the smaller of the pair
328	>	if( exI > exJ ){
329	>	tempEx = exI;
330	>	exI = exJ;
331	>	exJ = tempEx;
332	>	}
333		#ifdef IS_MPI
334	<	tempEx = exI;
335	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	<	tempEx = exJ;
337	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exI;
335	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>	tempEx = exJ;
337	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
338
339	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
340		#else  // isn't MPI
341	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
342		#endif  //is_mpi
343		}
344		excludeOffset += molInfo.nBends;
345
346		for(j=0; j<molInfo.nTorsions; j++){
347	<
348	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
349	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
350	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
351	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
352	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
353	<
354	<	exI = theTorsions[j].a;
355	<	exJ = theTorsions[j].d;
356	<
357	<	// exclude_I must always be the smaller of the pair
358	<	if( exI > exJ ){
359	<	tempEx = exI;
360	<	exI = exJ;
361	<	exJ = tempEx;
362	<	}
347	>
348	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
349	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
350	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
351	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
352	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
353	>
354	>	exI = theTorsions[j].a;
355	>	exJ = theTorsions[j].d;
356	>
357	>	// exclude_I must always be the smaller of the pair
358	>	if( exI > exJ ){
359	>	tempEx = exI;
360	>	exI = exJ;
361	>	exJ = tempEx;
362	>	}
363		#ifdef IS_MPI
364	<	tempEx = exI;
365	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	<	tempEx = exJ;
367	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
368	<
369	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
364	>	tempEx = exI;
365	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	>	tempEx = exJ;
367	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
368	>
369	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
370		#else  // isn't MPI
371	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
372		#endif  //is_mpi
373		}
374		excludeOffset += molInfo.nTorsions;
#	Line 436 | Line 437 | void SimSetup::initFromBass( void ){
437
438		if( n_per_extra > 4){
439		sprintf( painCave.errMsg,
440	<	"SimSetup error. There has been an error in constructing"
441	<	" the non-complete lattice.\n" );
440	>	"SimSetup error. There has been an error in constructing"
441	>	" the non-complete lattice.\n" );
442		painCave.isFatal = 1;
443		simError();
444		}
#	Line 458 | Line 459 | void SimSetup::initFromBass( void ){
459		for( j=0; j < n_cells; j++ ){
460		for( k=0; k < n_cells; k++ ){
461
462	<	makeElement( i * cellx,
463	<	j * celly,
464	<	k * cellz );
462	>	makeElement( i * cellx,
463	>	j * celly,
464	>	k * cellz );
465
466	<	makeElement( i * cellx + 0.5 * cellx,
467	<	j * celly + 0.5 * celly,
468	<	k * cellz );
466	>	makeElement( i * cellx + 0.5 * cellx,
467	>	j * celly + 0.5 * celly,
468	>	k * cellz );
469
470	<	makeElement( i * cellx,
471	<	j * celly + 0.5 * celly,
472	<	k * cellz + 0.5 * cellz );
470	>	makeElement( i * cellx,
471	>	j * celly + 0.5 * celly,
472	>	k * cellz + 0.5 * cellz );
473
474	<	makeElement( i * cellx + 0.5 * cellx,
475	<	j * celly,
476	<	k * cellz + 0.5 * cellz );
474	>	makeElement( i * cellx + 0.5 * cellx,
475	>	j * celly,
476	>	k * cellz + 0.5 * cellz );
477		}
478		}
479		}
#	Line 484 | Line 485 | void SimSetup::initFromBass( void ){
485		for( i=0; i < (n_cells+1) && !done; i++ ){
486		for( j=0; j < (n_cells+1) && !done; j++ ){
487
488	<	if( i < n_cells ){
488	>	if( i < n_cells ){
489
490	<	if( j < n_cells ){
491	<	start_ndx = n_cells;
492	<	}
493	<	else start_ndx = 0;
494	<	}
495	<	else start_ndx = 0;
490	>	if( j < n_cells ){
491	>	start_ndx = n_cells;
492	>	}
493	>	else start_ndx = 0;
494	>	}
495	>	else start_ndx = 0;
496
497	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
498
499	<	makeElement( i * cellx,
500	<	j * celly,
501	<	k * cellz );
502	<	done = ( current_mol >= tot_nmol );
499	>	makeElement( i * cellx,
500	>	j * celly,
501	>	k * cellz );
502	>	done = ( current_mol >= tot_nmol );
503
504	<	if( !done && n_per_extra > 1 ){
505	<	makeElement( i * cellx + 0.5 * cellx,
506	<	j * celly + 0.5 * celly,
507	<	k * cellz );
508	<	done = ( current_mol >= tot_nmol );
509	<	}
504	>	if( !done && n_per_extra > 1 ){
505	>	makeElement( i * cellx + 0.5 * cellx,
506	>	j * celly + 0.5 * celly,
507	>	k * cellz );
508	>	done = ( current_mol >= tot_nmol );
509	>	}
510
511	<	if( !done && n_per_extra > 2){
512	<	makeElement( i * cellx,
513	<	j * celly + 0.5 * celly,
514	<	k * cellz + 0.5 * cellz );
515	<	done = ( current_mol >= tot_nmol );
516	<	}
511	>	if( !done && n_per_extra > 2){
512	>	makeElement( i * cellx,
513	>	j * celly + 0.5 * celly,
514	>	k * cellz + 0.5 * cellz );
515	>	done = ( current_mol >= tot_nmol );
516	>	}
517
518	<	if( !done && n_per_extra > 3){
519	<	makeElement( i * cellx + 0.5 * cellx,
520	<	j * celly,
521	<	k * cellz + 0.5 * cellz );
522	<	done = ( current_mol >= tot_nmol );
523	<	}
524	<	}
518	>	if( !done && n_per_extra > 3){
519	>	makeElement( i * cellx + 0.5 * cellx,
520	>	j * celly,
521	>	k * cellz + 0.5 * cellz );
522	>	done = ( current_mol >= tot_nmol );
523	>	}
524	>	}
525		}
526		}
527		}
#	Line 543 | Line 544 | void SimSetup::makeElement( double x, double y, double
544		current_atom = comp_stamps[current_comp]->getAtom( k );
545		if( !current_atom->havePosition() ){
546		sprintf( painCave.errMsg,
547	<	"SimSetup:initFromBass error.\n"
548	<	"\tComponent %s, atom %s does not have a position specified.\n"
549	<	"\tThe initialization routine is unable to give a start"
550	<	" position.\n",
551	<	comp_stamps[current_comp]->getID(),
552	<	current_atom->getType() );
547	>	"SimSetup:initFromBass error.\n"
548	>	"\tComponent %s, atom %s does not have a position specified.\n"
549	>	"\tThe initialization routine is unable to give a start"
550	>	" position.\n",
551	>	comp_stamps[current_comp]->getID(),
552	>	current_atom->getType() );
553		painCave.isFatal = 1;
554		simError();
555		}
#	Line 617 | Line 618 | void SimSetup::gatherInfo( void ){
618		else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
619		else{
620		sprintf( painCave.errMsg,
621	<	"SimSetup Error. Unrecognized force field -> %s\n",
622	<	force_field );
621	>	"SimSetup Error. Unrecognized force field -> %s\n",
622	>	force_field );
623		painCave.isFatal = 1;
624		simError();
625		}
#	Line 636 | Line 637 | void SimSetup::gatherInfo( void ){
637		else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
638		else{
639		sprintf( painCave.errMsg,
640	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641		"reverting to NVE for this simulation.\n",
642	<	ensemble );
642	>	ensemble );
643		painCave.isFatal = 0;
644		simError();
645		strcpy( ensemble, "NVE" );
#	Line 669 | Line 670 | void SimSetup::gatherInfo( void ){
670		for( i=0; i<n_components; i++ ){
671
672		if( !the_components[i]->haveNMol() ){
673	<	// we have a problem
674	<	sprintf( painCave.errMsg,
675	<	"SimSetup Error. No global NMol or component NMol"
676	<	" given. Cannot calculate the number of atoms.\n" );
677	<	painCave.isFatal = 1;
678	<	simError();
673	>	// we have a problem
674	>	sprintf( painCave.errMsg,
675	>	"SimSetup Error. No global NMol or component NMol"
676	>	" given. Cannot calculate the number of atoms.\n" );
677	>	painCave.isFatal = 1;
678	>	simError();
679		}
680
681		tot_nmol += the_components[i]->getNMol();
#	Line 683 | Line 684 | void SimSetup::gatherInfo( void ){
684		}
685		else{
686		sprintf( painCave.errMsg,
687	<	"SimSetup error.\n"
688	<	"\tSorry, the ability to specify total"
689	<	" nMols and then give molfractions in the components\n"
690	<	"\tis not currently supported."
691	<	" Please give nMol in the components.\n" );
687	>	"SimSetup error.\n"
688	>	"\tSorry, the ability to specify total"
689	>	" nMols and then give molfractions in the components\n"
690	>	"\tis not currently supported."
691	>	" Please give nMol in the components.\n" );
692		painCave.isFatal = 1;
693		simError();
694		}
#	Line 741 | Line 742 | void SimSetup::gatherInfo( void ){
742		}
743		else{
744		if( !globals->haveBoxX() ){
745	<	sprintf( painCave.errMsg,
746	<	"SimSetup error, no periodic BoxX size given.\n" );
747	<	painCave.isFatal = 1;
748	<	simError();
745	>	sprintf( painCave.errMsg,
746	>	"SimSetup error, no periodic BoxX size given.\n" );
747	>	painCave.isFatal = 1;
748	>	simError();
749		}
750		boxVector[0] = globals->getBoxX();
751
752		if( !globals->haveBoxY() ){
753	<	sprintf( painCave.errMsg,
754	<	"SimSetup error, no periodic BoxY size given.\n" );
755	<	painCave.isFatal = 1;
756	<	simError();
753	>	sprintf( painCave.errMsg,
754	>	"SimSetup error, no periodic BoxY size given.\n" );
755	>	painCave.isFatal = 1;
756	>	simError();
757		}
758		boxVector[1] = globals->getBoxY();
759
760		if( !globals->haveBoxZ() ){
761	<	sprintf( painCave.errMsg,
762	<	"SimSetup error, no periodic BoxZ size given.\n" );
763	<	painCave.isFatal = 1;
764	<	simError();
761	>	sprintf( painCave.errMsg,
762	>	"SimSetup error, no periodic BoxZ size given.\n" );
763	>	painCave.isFatal = 1;
764	>	simError();
765		}
766		boxVector[2] = globals->getBoxZ();
767
768		info[i].setBox( boxVector );
769		}
770	+	}
771
772	+	int seedValue;
773	+	struct timeval now_time_val;
774	+	struct timezone time_zone;
775	+
776	+	if(globals->haveSeed()){
777	+	seedValue = globals->getSeed();
778		}
779	<
779	>	else{
780	>	#ifndef IS_MPI
781	>	gettimeofday(&now_time_val, &time_zone);  // get the time now
782	>	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
783	>	#else
784	>	if(worldRank == 0){
785	>	gettimeofday(&now_time_val, &time_zone);  // get the time now
786	>	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
787	>	}
788	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
789	>	#endif
790	>	}
791	>
792	>	for(int i = 0; i < nInfo; i++){
793	>	info[i].setSeed(seedValue);
794	>	}
795	>
796		#ifdef IS_MPI
797		strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
798		MPIcheckPoint();
#	Line 803 | Line 827 | void SimSetup::finalInfoCheck( void ){
827		info[i].useReactionField = 1;
828
829		if( !globals->haveECR() ){
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Warning: using default value of 1/2 the smallest "
832	<	"box length for the electrostaticCutoffRadius.\n"
833	<	"I hope you have a very fast processor!\n");
834	<	painCave.isFatal = 0;
835	<	simError();
836	<	double smallest;
837	<	smallest = info[i].boxL[0];
838	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
839	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
840	<	theEcr = 0.5 * smallest;
830	>	sprintf( painCave.errMsg,
831	>	"SimSetup Warning: using default value of 1/2 the smallest "
832	>	"box length for the electrostaticCutoffRadius.\n"
833	>	"I hope you have a very fast processor!\n");
834	>	painCave.isFatal = 0;
835	>	simError();
836	>	double smallest;
837	>	smallest = info[i].boxL[0];
838	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
839	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
840	>	theEcr = 0.5 * smallest;
841		} else {
842	<	theEcr = globals->getECR();
842	>	theEcr = globals->getECR();
843		}
844
845		if( !globals->haveEST() ){
846	<	sprintf( painCave.errMsg,
847	<	"SimSetup Warning: using default value of 0.05 * the "
848	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
849	<	);
850	<	painCave.isFatal = 0;
851	<	simError();
852	<	theEst = 0.05 * theEcr;
846	>	sprintf( painCave.errMsg,
847	>	"SimSetup Warning: using default value of 0.05 * the "
848	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
849	>	);
850	>	painCave.isFatal = 0;
851	>	simError();
852	>	theEst = 0.05 * theEcr;
853		} else {
854	<	theEst= globals->getEST();
854	>	theEst= globals->getEST();
855		}
856
857		info[i].setEcr( theEcr, theEst );
858
859		if(!globals->haveDielectric() ){
860	<	sprintf( painCave.errMsg,
861	<	"SimSetup Error: You are trying to use Reaction Field without"
862	<	"setting a dielectric constant!\n"
863	<	);
864	<	painCave.isFatal = 1;
865	<	simError();
860	>	sprintf( painCave.errMsg,
861	>	"SimSetup Error: You are trying to use Reaction Field without"
862	>	"setting a dielectric constant!\n"
863	>	);
864	>	painCave.isFatal = 1;
865	>	simError();
866		}
867		info[i].dielectric = globals->getDielectric();
868		}
869		else {
870		if (usesDipoles) {
871	<
872	<	if( !globals->haveECR() ){
873	<	sprintf( painCave.errMsg,
874	<	"SimSetup Warning: using default value of 1/2 the smallest "
875	<	"box length for the electrostaticCutoffRadius.\n"
876	<	"I hope you have a very fast processor!\n");
877	<	painCave.isFatal = 0;
878	<	simError();
879	<	double smallest;
880	<	smallest = info[i].boxL[0];
881	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
882	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
883	<	theEcr = 0.5 * smallest;
884	<	} else {
885	<	theEcr = globals->getECR();
886	<	}
887	<
888	<	if( !globals->haveEST() ){
889	<	sprintf( painCave.errMsg,
890	<	"SimSetup Warning: using default value of 0.05 * the "
891	<	"electrostaticCutoffRadius for the "
892	<	"electrostaticSkinThickness\n"
893	<	);
894	<	painCave.isFatal = 0;
895	<	simError();
896	<	theEst = 0.05 * theEcr;
897	<	} else {
898	<	theEst= globals->getEST();
899	<	}
900	<
901	<	info[i].setEcr( theEcr, theEst );
871	>
872	>	if( !globals->haveECR() ){
873	>	sprintf( painCave.errMsg,
874	>	"SimSetup Warning: using default value of 1/2 the smallest "
875	>	"box length for the electrostaticCutoffRadius.\n"
876	>	"I hope you have a very fast processor!\n");
877	>	painCave.isFatal = 0;
878	>	simError();
879	>	double smallest;
880	>	smallest = info[i].boxL[0];
881	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
882	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
883	>	theEcr = 0.5 * smallest;
884	>	} else {
885	>	theEcr = globals->getECR();
886	>	}
887	>
888	>	if( !globals->haveEST() ){
889	>	sprintf( painCave.errMsg,
890	>	"SimSetup Warning: using default value of 0.05 * the "
891	>	"electrostaticCutoffRadius for the "
892	>	"electrostaticSkinThickness\n"
893	>	);
894	>	painCave.isFatal = 0;
895	>	simError();
896	>	theEst = 0.05 * theEcr;
897	>	} else {
898	>	theEst= globals->getEST();
899	>	}
900	>
901	>	info[i].setEcr( theEcr, theEst );
902		}
903		}
904		}
#	Line 891 | Line 915 | void SimSetup::initSystemCoords( void ){
915
916		char* inName;
917
894	–
918		(info[0].getConfiguration())->createArrays( info[0].n_atoms );
919	<
919	>
920		for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
921
922		if( globals->haveInitialConfig() ){
#	Line 903 | Line 926 | void SimSetup::initSystemCoords( void ){
926		if( worldRank == 0 ){
927		#endif //is_mpi
928		inName = globals->getInitialConfig();
929	+	double* tempDouble = new double[1000000];
930		fileInit = new InitializeFromFile( inName );
931		#ifdef IS_MPI
932		}else fileInit = new InitializeFromFile( NULL );
#	Line 918 | Line 942 | void SimSetup::initSystemCoords( void ){
942		// no init from bass
943
944		sprintf( painCave.errMsg,
945	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
945	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
946		painCave.isFatal;
947		simError();
948
#	Line 950 | Line 974 | void SimSetup::makeOutNames( void ){
974		#endif // is_mpi
975
976		if( globals->haveFinalConfig() ){
977	<	strcpy( info[k].finalName, globals->getFinalConfig() );
977	>	strcpy( info[k].finalName, globals->getFinalConfig() );
978		}
979		else{
980	<	strcpy( info[k].finalName, inFileName );
981	<	char* endTest;
982	<	int nameLength = strlen( info[k].finalName );
983	<	endTest = &(info[k].finalName[nameLength - 5]);
984	<	if( !strcmp( endTest, ".bass" ) ){
985	<	strcpy( endTest, ".eor" );
986	<	}
987	<	else if( !strcmp( endTest, ".BASS" ) ){
988	<	strcpy( endTest, ".eor" );
989	<	}
990	<	else{
991	<	endTest = &(info[k].finalName[nameLength - 4]);
992	<	if( !strcmp( endTest, ".bss" ) ){
993	<	strcpy( endTest, ".eor" );
994	<	}
995	<	else if( !strcmp( endTest, ".mdl" ) ){
996	<	strcpy( endTest, ".eor" );
997	<	}
998	<	else{
999	<	strcat( info[k].finalName, ".eor" );
1000	<	}
1001	<	}
980	>	strcpy( info[k].finalName, inFileName );
981	>	char* endTest;
982	>	int nameLength = strlen( info[k].finalName );
983	>	endTest = &(info[k].finalName[nameLength - 5]);
984	>	if( !strcmp( endTest, ".bass" ) ){
985	>	strcpy( endTest, ".eor" );
986	>	}
987	>	else if( !strcmp( endTest, ".BASS" ) ){
988	>	strcpy( endTest, ".eor" );
989	>	}
990	>	else{
991	>	endTest = &(info[k].finalName[nameLength - 4]);
992	>	if( !strcmp( endTest, ".bss" ) ){
993	>	strcpy( endTest, ".eor" );
994	>	}
995	>	else if( !strcmp( endTest, ".mdl" ) ){
996	>	strcpy( endTest, ".eor" );
997	>	}
998	>	else{
999	>	strcat( info[k].finalName, ".eor" );
1000	>	}
1001	>	}
1002		}
1003
1004		// make the sample and status out names
#	Line 984 | Line 1008 | void SimSetup::makeOutNames( void ){
1008		int nameLength = strlen( info[k].sampleName );
1009		endTest = &(info[k].sampleName[nameLength - 5]);
1010		if( !strcmp( endTest, ".bass" ) ){
1011	<	strcpy( endTest, ".dump" );
1011	>	strcpy( endTest, ".dump" );
1012		}
1013		else if( !strcmp( endTest, ".BASS" ) ){
1014	<	strcpy( endTest, ".dump" );
1014	>	strcpy( endTest, ".dump" );
1015		}
1016		else{
1017	<	endTest = &(info[k].sampleName[nameLength - 4]);
1018	<	if( !strcmp( endTest, ".bss" ) ){
1019	<	strcpy( endTest, ".dump" );
1020	<	}
1021	<	else if( !strcmp( endTest, ".mdl" ) ){
1022	<	strcpy( endTest, ".dump" );
1023	<	}
1024	<	else{
1025	<	strcat( info[k].sampleName, ".dump" );
1026	<	}
1017	>	endTest = &(info[k].sampleName[nameLength - 4]);
1018	>	if( !strcmp( endTest, ".bss" ) ){
1019	>	strcpy( endTest, ".dump" );
1020	>	}
1021	>	else if( !strcmp( endTest, ".mdl" ) ){
1022	>	strcpy( endTest, ".dump" );
1023	>	}
1024	>	else{
1025	>	strcat( info[k].sampleName, ".dump" );
1026	>	}
1027		}
1028
1029		strcpy( info[k].statusName, inFileName );
1030		nameLength = strlen( info[k].statusName );
1031		endTest = &(info[k].statusName[nameLength - 5]);
1032		if( !strcmp( endTest, ".bass" ) ){
1033	<	strcpy( endTest, ".stat" );
1033	>	strcpy( endTest, ".stat" );
1034		}
1035		else if( !strcmp( endTest, ".BASS" ) ){
1036	<	strcpy( endTest, ".stat" );
1036	>	strcpy( endTest, ".stat" );
1037		}
1038		else{
1039	<	endTest = &(info[k].statusName[nameLength - 4]);
1040	<	if( !strcmp( endTest, ".bss" ) ){
1041	<	strcpy( endTest, ".stat" );
1042	<	}
1043	<	else if( !strcmp( endTest, ".mdl" ) ){
1044	<	strcpy( endTest, ".stat" );
1045	<	}
1046	<	else{
1047	<	strcat( info[k].statusName, ".stat" );
1048	<	}
1039	>	endTest = &(info[k].statusName[nameLength - 4]);
1040	>	if( !strcmp( endTest, ".bss" ) ){
1041	>	strcpy( endTest, ".stat" );
1042	>	}
1043	>	else if( !strcmp( endTest, ".mdl" ) ){
1044	>	strcpy( endTest, ".stat" );
1045	>	}
1046	>	else{
1047	>	strcat( info[k].statusName, ".stat" );
1048	>	}
1049		}
1050
1051		#ifdef IS_MPI
#	Line 1088 | Line 1112 | void SimSetup::createFF( void ){
1112
1113		default:
1114		sprintf( painCave.errMsg,
1115	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1115	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1116		painCave.isFatal = 1;
1117		simError();
1118		}
#	Line 1134 | Line 1158 | void SimSetup::compList( void ){
1158
1159		currentStamp = stamps->extractMolStamp( id );
1160		if( currentStamp == NULL ){
1161	<	sprintf( painCave.errMsg,
1162	<	"SimSetup error: Component \"%s\" was not found in the "
1163	<	"list of declared molecules\n",
1164	<	id );
1165	<	painCave.isFatal = 1;
1166	<	simError();
1161	>	sprintf( painCave.errMsg,
1162	>	"SimSetup error: Component \"%s\" was not found in the "
1163	>	"list of declared molecules\n",
1164	>	id );
1165	>	painCave.isFatal = 1;
1166	>	simError();
1167		}
1168
1169		headStamp->add( currentStamp );
#	Line 1218 | Line 1242 | void SimSetup::mpiMolDivide( void ){
1242		for( j=0; j<components_nmol[i]; j++ ){
1243
1244		if( mol2proc[allMol] == worldRank ){
1245	<
1246	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1247	<	local_bonds +=    comp_stamps[i]->getNBonds();
1248	<	local_bends +=    comp_stamps[i]->getNBends();
1249	<	local_torsions += comp_stamps[i]->getNTorsions();
1250	<	localMol++;
1245	>
1246	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1247	>	local_bonds +=    comp_stamps[i]->getNBonds();
1248	>	local_bends +=    comp_stamps[i]->getNBends();
1249	>	local_torsions += comp_stamps[i]->getNTorsions();
1250	>	localMol++;
1251		}
1252		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1253		info[0].molMembershipArray[globalAtomIndex] = allMol;
#	Line 1239 | Line 1263 | void SimSetup::mpiMolDivide( void ){
1263
1264		if( local_atoms != info[0].n_atoms ){
1265		sprintf( painCave.errMsg,
1266	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1267	<	" localAtom (%d) are not equal.\n",
1268	<	info[0].n_atoms,
1269	<	local_atoms );
1266	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1267	>	" localAtom (%d) are not equal.\n",
1268	>	info[0].n_atoms,
1269	>	local_atoms );
1270		painCave.isFatal = 1;
1271		simError();
1272		}
#	Line 1285 | Line 1309 | void SimSetup::makeSysArrays( void ){
1309		for(i=0; i<mpiSim->getTotNmol(); i++){
1310
1311		if(mol2proc[i] == worldRank ){
1312	<	the_molecules[molIndex].setStampID( molCompType[i] );
1313	<	the_molecules[molIndex].setMyIndex( molIndex );
1314	<	the_molecules[molIndex].setGlobalIndex( i );
1315	<	molIndex++;
1312	>	the_molecules[molIndex].setStampID( molCompType[i] );
1313	>	the_molecules[molIndex].setMyIndex( molIndex );
1314	>	the_molecules[molIndex].setGlobalIndex( i );
1315	>	molIndex++;
1316		}
1317		}
1318
#	Line 1298 | Line 1322 | void SimSetup::makeSysArrays( void ){
1322		globalAtomIndex = 0;
1323		for(i=0; i<n_components; i++){
1324		for(j=0; j<components_nmol[i]; j++ ){
1325	<	the_molecules[molIndex].setStampID( i );
1326	<	the_molecules[molIndex].setMyIndex( molIndex );
1327	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1328	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1329	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1330	<	globalAtomIndex++;
1331	<	}
1332	<	molIndex++;
1325	>	the_molecules[molIndex].setStampID( i );
1326	>	the_molecules[molIndex].setMyIndex( molIndex );
1327	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1328	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1329	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1330	>	globalAtomIndex++;
1331	>	}
1332	>	molIndex++;
1333		}
1334		}
1335
#	Line 1318 | Line 1342 | void SimSetup::makeSysArrays( void ){
1342		Exclude::createArray(info[l].n_SRI);
1343		the_excludes = new Exclude*[info[l].n_SRI];
1344		for( int ex=0; ex<info[l].n_SRI; ex++){
1345	<	the_excludes[ex] = new Exclude(ex);
1345	>	the_excludes[ex] = new Exclude(ex);
1346		}
1347		info[l].globalExcludes = new int;
1348		info[l].n_exclude = info[l].n_SRI;
#	Line 1361 | Line 1385 | void SimSetup::makeIntegrator( void ){
1385		switch( ensembleCase ){
1386
1387		case NVE_ENS:
1388	<	if (globals->haveZconstraints()){
1389	<	setupZConstraint(info[k]);
1390	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1391	<	}
1388	>	if (globals->haveZconstraints()){
1389	>	setupZConstraint(info[k]);
1390	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1391	>	}
1392
1393	<	else
1393	>	else
1394		new NVE<RealIntegrator>( &(info[k]), the_ff );
1395		break;
1396
1397		case NVT_ENS:
1398	<	if (globals->haveZconstraints()){
1399	<	setupZConstraint(info[k]);
1400	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1401	<	}
1402	<	else
1398	>	if (globals->haveZconstraints()){
1399	>	setupZConstraint(info[k]);
1400	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1401	>	}
1402	>	else
1403		myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1404
1405	<	myNVT->setTargetTemp(globals->getTargetTemp());
1405	>	myNVT->setTargetTemp(globals->getTargetTemp());
1406
1407	<	if (globals->haveTauThermostat())
1408	<	myNVT->setTauThermostat(globals->getTauThermostat());
1407	>	if (globals->haveTauThermostat())
1408	>	myNVT->setTauThermostat(globals->getTauThermostat());
1409
1410	<	else {
1411	<	sprintf( painCave.errMsg,
1412	<	"SimSetup error: If you use the NVT\n"
1413	<	"    ensemble, you must set tauThermostat.\n");
1414	<	painCave.isFatal = 1;
1415	<	simError();
1416	<	}
1417	<	break;
1410	>	else {
1411	>	sprintf( painCave.errMsg,
1412	>	"SimSetup error: If you use the NVT\n"
1413	>	"    ensemble, you must set tauThermostat.\n");
1414	>	painCave.isFatal = 1;
1415	>	simError();
1416	>	}
1417	>	break;
1418
1419		case NPTi_ENS:
1420	<	if (globals->haveZconstraints()){
1421	<	setupZConstraint(info[k]);
1422	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1423	<	}
1424	<	else
1420	>	if (globals->haveZconstraints()){
1421	>	setupZConstraint(info[k]);
1422	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1423	>	}
1424	>	else
1425		myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1426
1427	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1428	<
1427	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1428	>
1429		if (globals->haveTargetPressure())
1430	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1430	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1431		else {
1432	<	sprintf( painCave.errMsg,
1433	<	"SimSetup error: If you use a constant pressure\n"
1434	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	<	painCave.isFatal = 1;
1436	<	simError();
1432	>	sprintf( painCave.errMsg,
1433	>	"SimSetup error: If you use a constant pressure\n"
1434	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	>	painCave.isFatal = 1;
1436	>	simError();
1437		}
1438	<
1438	>
1439		if( globals->haveTauThermostat() )
1440	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1440	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1441		else{
1442	<	sprintf( painCave.errMsg,
1443	<	"SimSetup error: If you use an NPT\n"
1444	<	"    ensemble, you must set tauThermostat.\n");
1445	<	painCave.isFatal = 1;
1446	<	simError();
1442	>	sprintf( painCave.errMsg,
1443	>	"SimSetup error: If you use an NPT\n"
1444	>	"    ensemble, you must set tauThermostat.\n");
1445	>	painCave.isFatal = 1;
1446	>	simError();
1447		}
1448	<
1448	>
1449		if( globals->haveTauBarostat() )
1450	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1450	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1451		else{
1452	<	sprintf( painCave.errMsg,
1453	<	"SimSetup error: If you use an NPT\n"
1454	<	"    ensemble, you must set tauBarostat.\n");
1455	<	painCave.isFatal = 1;
1456	<	simError();
1457	<	}
1458	<	break;
1452	>	sprintf( painCave.errMsg,
1453	>	"SimSetup error: If you use an NPT\n"
1454	>	"    ensemble, you must set tauBarostat.\n");
1455	>	painCave.isFatal = 1;
1456	>	simError();
1457	>	}
1458	>	break;
1459
1460		case NPTf_ENS:
1461	<	if (globals->haveZconstraints()){
1462	<	setupZConstraint(info[k]);
1463	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1464	<	}
1465	<	else
1461	>	if (globals->haveZconstraints()){
1462	>	setupZConstraint(info[k]);
1463	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1464	>	}
1465	>	else
1466		myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1467
1468		myNPTf->setTargetTemp( globals->getTargetTemp());
1469	<
1469	>
1470		if (globals->haveTargetPressure())
1471	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1471	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1472		else {
1473	<	sprintf( painCave.errMsg,
1474	<	"SimSetup error: If you use a constant pressure\n"
1475	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1476	<	painCave.isFatal = 1;
1477	<	simError();
1473	>	sprintf( painCave.errMsg,
1474	>	"SimSetup error: If you use a constant pressure\n"
1475	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1476	>	painCave.isFatal = 1;
1477	>	simError();
1478		}
1479	<
1479	>
1480		if( globals->haveTauThermostat() )
1481	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1481	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1482		else{
1483	<	sprintf( painCave.errMsg,
1484	<	"SimSetup error: If you use an NPT\n"
1485	<	"    ensemble, you must set tauThermostat.\n");
1486	<	painCave.isFatal = 1;
1487	<	simError();
1483	>	sprintf( painCave.errMsg,
1484	>	"SimSetup error: If you use an NPT\n"
1485	>	"    ensemble, you must set tauThermostat.\n");
1486	>	painCave.isFatal = 1;
1487	>	simError();
1488		}
1489	<
1489	>
1490		if( globals->haveTauBarostat() )
1491	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1491	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1492		else{
1493	<	sprintf( painCave.errMsg,
1494	<	"SimSetup error: If you use an NPT\n"
1495	<	"    ensemble, you must set tauBarostat.\n");
1496	<	painCave.isFatal = 1;
1497	<	simError();
1493	>	sprintf( painCave.errMsg,
1494	>	"SimSetup error: If you use an NPT\n"
1495	>	"    ensemble, you must set tauBarostat.\n");
1496	>	painCave.isFatal = 1;
1497	>	simError();
1498		}
1499		break;
1500
1501		case NPTim_ENS:
1502	<	if (globals->haveZconstraints()){
1503	<	setupZConstraint(info[k]);
1504	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1505	<	}
1506	<	else
1502	>	if (globals->haveZconstraints()){
1503	>	setupZConstraint(info[k]);
1504	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1505	>	}
1506	>	else
1507		myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1508
1509	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1510	<
1509	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1510	>
1511		if (globals->haveTargetPressure())
1512	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1512	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1513		else {
1514	<	sprintf( painCave.errMsg,
1515	<	"SimSetup error: If you use a constant pressure\n"
1516	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1517	<	painCave.isFatal = 1;
1518	<	simError();
1514	>	sprintf( painCave.errMsg,
1515	>	"SimSetup error: If you use a constant pressure\n"
1516	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1517	>	painCave.isFatal = 1;
1518	>	simError();
1519		}
1520	<
1520	>
1521		if( globals->haveTauThermostat() )
1522	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1522	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1523		else{
1524	<	sprintf( painCave.errMsg,
1525	<	"SimSetup error: If you use an NPT\n"
1526	<	"    ensemble, you must set tauThermostat.\n");
1527	<	painCave.isFatal = 1;
1528	<	simError();
1524	>	sprintf( painCave.errMsg,
1525	>	"SimSetup error: If you use an NPT\n"
1526	>	"    ensemble, you must set tauThermostat.\n");
1527	>	painCave.isFatal = 1;
1528	>	simError();
1529		}
1530	<
1530	>
1531		if( globals->haveTauBarostat() )
1532	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1532	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1533		else{
1534	<	sprintf( painCave.errMsg,
1535	<	"SimSetup error: If you use an NPT\n"
1536	<	"    ensemble, you must set tauBarostat.\n");
1537	<	painCave.isFatal = 1;
1538	<	simError();
1534	>	sprintf( painCave.errMsg,
1535	>	"SimSetup error: If you use an NPT\n"
1536	>	"    ensemble, you must set tauBarostat.\n");
1537	>	painCave.isFatal = 1;
1538	>	simError();
1539		}
1540		break;
1541
1542		case NPTfm_ENS:
1543	<	if (globals->haveZconstraints()){
1544	<	setupZConstraint(info[k]);
1545	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1546	<	}
1547	<	else
1543	>	if (globals->haveZconstraints()){
1544	>	setupZConstraint(info[k]);
1545	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1546	>	}
1547	>	else
1548		myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1549
1550	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1551	<
1550	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1551	>
1552		if (globals->haveTargetPressure())
1553	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1553	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1554		else {
1555	<	sprintf( painCave.errMsg,
1556	<	"SimSetup error: If you use a constant pressure\n"
1557	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1558	<	painCave.isFatal = 1;
1559	<	simError();
1555	>	sprintf( painCave.errMsg,
1556	>	"SimSetup error: If you use a constant pressure\n"
1557	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1558	>	painCave.isFatal = 1;
1559	>	simError();
1560		}
1561	<
1561	>
1562		if( globals->haveTauThermostat() )
1563	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1563	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1564		else{
1565	<	sprintf( painCave.errMsg,
1566	<	"SimSetup error: If you use an NPT\n"
1567	<	"    ensemble, you must set tauThermostat.\n");
1568	<	painCave.isFatal = 1;
1569	<	simError();
1565	>	sprintf( painCave.errMsg,
1566	>	"SimSetup error: If you use an NPT\n"
1567	>	"    ensemble, you must set tauThermostat.\n");
1568	>	painCave.isFatal = 1;
1569	>	simError();
1570		}
1571	<
1571	>
1572		if( globals->haveTauBarostat() )
1573	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1573	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1574		else{
1575	<	sprintf( painCave.errMsg,
1576	<	"SimSetup error: If you use an NPT\n"
1577	<	"    ensemble, you must set tauBarostat.\n");
1578	<	painCave.isFatal = 1;
1579	<	simError();
1575	>	sprintf( painCave.errMsg,
1576	>	"SimSetup error: If you use an NPT\n"
1577	>	"    ensemble, you must set tauBarostat.\n");
1578	>	painCave.isFatal = 1;
1579	>	simError();
1580		}
1581		break;
1582
1583		default:
1584		sprintf( painCave.errMsg,
1585	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1585	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1586		painCave.isFatal = 1;
1587		simError();
1588		}
#	Line 1577 | Line 1601 | void SimSetup::initFortran( void ){
1601		}
1602		else{
1603		sprintf( painCave.errMsg,
1604	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	<	info[0].mixingRule );
1604	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	>	info[0].mixingRule );
1606		painCave.isFatal = 1;
1607		simError();
1608		}
#	Line 1586 | Line 1610 | void SimSetup::initFortran( void ){
1610
1611		#ifdef IS_MPI
1612		strcpy( checkPointMsg,
1613	<	"Successfully intialized the mixingRule for Fortran." );
1613	>	"Successfully intialized the mixingRule for Fortran." );
1614		MPIcheckPoint();
1615		#endif // is_mpi
1616
#	Line 1594 | Line 1618 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1618
1619		void SimSetup::setupZConstraint(SimInfo& theInfo)
1620		{
1621	<	int nZConstraints;
1622	<	ZconStamp** zconStamp;
1599	<
1600	<	if(globals->haveZconstraintTime()){
1601	<
1602	<	//add sample time of z-constraint  into SimInfo's property list
1603	<	DoubleData* zconsTimeProp = new DoubleData();
1604	<	zconsTimeProp->setID(ZCONSTIME_ID);
1605	<	zconsTimeProp->setData(globals->getZconsTime());
1606	<	theInfo.addProperty(zconsTimeProp);
1607	<	}
1608	<	else{
1609	<	sprintf( painCave.errMsg,
1610	<	"ZConstraint error: If you use an ZConstraint\n"
1611	<	" , you must set sample time.\n");
1612	<	painCave.isFatal = 1;
1613	<	simError();
1614	<	}
1621	>	int nZConstraints;
1622	>	ZconStamp** zconStamp;
1623
1624	<	//
1625	<	nZConstraints = globals->getNzConstraints();
1626	<	zconStamp = globals->getZconStamp();
1627	<	ZConsParaItem tempParaItem;
1624	>	if(globals->haveZconstraintTime()){
1625	>
1626	>	//add sample time of z-constraint  into SimInfo's property list
1627	>	DoubleData* zconsTimeProp = new DoubleData();
1628	>	zconsTimeProp->setID(ZCONSTIME_ID);
1629	>	zconsTimeProp->setData(globals->getZconsTime());
1630	>	theInfo.addProperty(zconsTimeProp);
1631	>	}
1632	>	else{
1633	>	sprintf( painCave.errMsg,
1634	>	"ZConstraint error: If you use an ZConstraint\n"
1635	>	" , you must set sample time.\n");
1636	>	painCave.isFatal = 1;
1637	>	simError();
1638	>	}
1639
1640	<	ZConsParaData* zconsParaData = new ZConsParaData();
1641	<	zconsParaData->setID(ZCONSPARADATA_ID);
1642	<
1643	<	for(int i = 0; i < nZConstraints; i++){
1640	>	//push zconsTol into siminfo, if user does not specify
1641	>	//value for zconsTol, a default value will be used
1642	>	DoubleData* zconsTol = new DoubleData();
1643	>	zconsTol->setID(ZCONSTOL_ID);
1644	>	if(globals->haveZconsTol()){
1645	>	zconsTol->setData(globals->getZconsTol());
1646	>	}
1647	>	else{
1648	>	double defaultZConsTol = 0.01;
1649	>	sprintf( painCave.errMsg,
1650	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1651	>	" , default value %f is used.\n", defaultZConsTol);
1652	>	painCave.isFatal = 0;
1653	>	simError();
1654	>
1655	>	zconsTol->setData(defaultZConsTol);
1656	>	}
1657	>	theInfo.addProperty(zconsTol);
1658	>
1659	>	//set Force Substraction Policy
1660	>	StringData* zconsForcePolicy =  new StringData();
1661	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1662	>
1663	>	if(globals->haveZconsForcePolicy()){
1664	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1665	>	}
1666	>	else{
1667	>	sprintf( painCave.errMsg,
1668	>	"ZConstraint Warning: User does not set force substraction policy, "
1669	>	"average force substraction policy is used\n");
1670	>	painCave.isFatal = 0;
1671	>	simError();
1672	>	zconsForcePolicy->setData("BYNUMBER");
1673	>	}
1674	>
1675	>	theInfo.addProperty(zconsForcePolicy);
1676	>
1677	>	//Determine the name of ouput file and add it into SimInfo's property list
1678	>	//Be careful, do not use inFileName, since it is a pointer which
1679	>	//point to a string at master node, and slave nodes do not contain that string
1680	>
1681	>	string zconsOutput(theInfo.finalName);
1682	>
1683	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1684	>
1685	>	StringData* zconsFilename = new StringData();
1686	>	zconsFilename->setID(ZCONSFILENAME_ID);
1687	>	zconsFilename->setData(zconsOutput);
1688	>
1689	>	theInfo.addProperty(zconsFilename);
1690	>
1691	>	//setup index, pos and other parameters of z-constraint molecules
1692	>	nZConstraints = globals->getNzConstraints();
1693	>	theInfo.nZconstraints = nZConstraints;
1694	>
1695	>	zconStamp = globals->getZconStamp();
1696	>	ZConsParaItem tempParaItem;
1697	>
1698	>	ZConsParaData* zconsParaData = new ZConsParaData();
1699	>	zconsParaData->setID(ZCONSPARADATA_ID);
1700	>
1701	>	for(int i = 0; i < nZConstraints; i++){
1702		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1703		tempParaItem.zPos = zconStamp[i]->getZpos();
1704		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1705		tempParaItem.kRatio = zconStamp[i]->getKratio();
1706
1707		zconsParaData->addItem(tempParaItem);
1708	<	}
1708	>	}
1709
1710	<	//sort the parameters by index of molecules
1711	<	zconsParaData->sortByIndex();
1712	<
1713	<	//push data into siminfo, therefore, we can retrieve later
1714	<	theInfo.addProperty(zconsParaData);
1715	<
1639	<	//push zconsTol into siminfo, if user does not specify
1640	<	//value for zconsTol, a default value will be used
1641	<	DoubleData* zconsTol = new DoubleData();
1642	<	zconsTol->setID(ZCONSTOL_ID);
1643	<	if(globals->haveZconsTol()){
1644	<	zconsTol->setData(globals->getZconsTol());
1645	<	}
1646	<	else{
1647	<	double defaultZConsTol = 1E-6;
1648	<	sprintf( painCave.errMsg,
1649	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1650	<	" , default value %f is used.\n", defaultZConsTol);
1651	<	painCave.isFatal = 0;
1652	<	simError();
1653	<
1654	<	zconsTol->setData(defaultZConsTol);
1655	<	}
1656	<	theInfo.addProperty(zconsTol);
1657	<
1658	<	//Determine the name of ouput file and add it into SimInfo's property list
1659	<	//Be careful, do not use inFileName, since it is a pointer which
1660	<	//point to a string at master node, and slave nodes do not contain that string
1661	<
1662	<	string zconsOutput(theInfo.finalName);
1663	<
1664	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1665	<
1666	<	StringData* zconsFilename = new StringData();
1667	<	zconsFilename->setID(ZCONSFILENAME_ID);
1668	<	zconsFilename->setData(zconsOutput);
1669	<
1670	<	theInfo.addProperty(zconsFilename);
1710	>	//sort the parameters by index of molecules
1711	>	zconsParaData->sortByIndex();
1712	>
1713	>	//push data into siminfo, therefore, we can retrieve later
1714	>	theInfo.addProperty(zconsParaData);
1715	>
1716		}

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