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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 707 by mmeineke, Wed Aug 20 19:42:31 2003 UTC

#	Line 5 | Line 5
5		#include <string>
6
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 22 | Line 23
23		#define NPTf_ENS       3
24		#define NPTim_ENS      4
25		#define NPTfm_ENS      5
25	–	#define NVEZCONS_ENS   6
26	–	#define NVTZCONS_ENS   7
27	–	#define NPTiZCONS_ENS  8
28	–	#define NPTfZCONS_ENS  9
29	–	#define NPTimZCONS_ENS 10
30	–	#define NPTfmZCONS_ENS 11
26
27		#define FF_DUFF 0
28		#define FF_LJ   1
#	Line 102 | Line 97 | void SimSetup::createSim(void){
97		int i, j, k, globalAtomIndex;
98
99		// gather all of the information from the Bass file
100	<
100	>
101		gatherInfo();
102
103		// creation of complex system objects
#	Line 110 | Line 105 | void SimSetup::createSim(void){
105		sysObjectsCreation();
106
107		// check on the post processing info
108	<
108	>
109		finalInfoCheck();
110
111		// initialize the system coordinates
#	Line 194 | 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() ){
200	<
201	<	dAtom = new DirectionalAtom( (j + atomOffset),
202	<	info[k].getConfiguration() );
203	<	info[k].n_oriented++;
204	<	molInfo.myAtoms[j] = dAtom;
205	<
206	<	ux = currentAtom->getOrntX();
207	<	uy = currentAtom->getOrntY();
208	<	uz = currentAtom->getOrntZ();
209	<
210	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
211	<
212	<	u = sqrt( uSqr );
213	<	ux = ux / u;
214	<	uy = uy / u;
215	<	uz = uz / u;
216	<
217	<	dAtom->setSUx( ux );
218	<	dAtom->setSUy( uy );
219	<	dAtom->setSUz( uz );
220	<	}
221	<	else{
222	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
223	<	info[k].getConfiguration() );
224	<	}
225	<	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 234 | 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	<	}
332	<	#ifdef IS_MPI
333	<	tempEx = exI;
334	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	<	tempEx = exJ;
336	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	<
338	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
261	>
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266	>
267	>	if( currentBend->haveExtras() ){
268	>
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276	>
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290	>	sprintf( painCave.errMsg,
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298	>	}
299	>
300	>	else{
301	>
302	>	sprintf( painCave.errMsg,
303	>	"SimSetup Error: unhandled bend assignment:\n"
304	>	"    -->%s in Bend[%d] in %s\n",
305	>	current_extra->getlhs(),
306	>	j, comp_stamps[stampID]->getID() );
307	>	painCave.isFatal = 1;
308	>	simError();
309	>	}
310	>
311	>	current_extra = current_extra->getNext();
312	>	}
313	>	}
314	>
315	>	if( !theBends[j].isGhost ){
316	>
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].c;
319	>	}
320	>	else{
321	>
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].b;
324	>	}
325	>
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331	>	}
332	>	#ifdef IS_MPI
333	>	tempEx = exI;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	>
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339		#else  // isn't MPI
340	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
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 441 | 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 463 | 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 489 | 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 548 | 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 622 | 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 639 | Line 634 | void SimSetup::gatherInfo( void ){
634		else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635		else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636		else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
642	–
643	–	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
644	–	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
645	–	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS"))
646	–	ensembleCase = NPTiZCONS_ENS;
647	–	else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
648	–	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
649	–	else if( !strcasecmp( ensemble, "NPTfmZCONS"))  ensembleCase = NPTfmZCONS_ENS;
650	–
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 683 | 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 697 | 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 755 | 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 817 | 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 903 | Line 889 | void SimSetup::initSystemCoords( void ){
889		void SimSetup::initSystemCoords( void ){
890		int i;
891
892	<	std::cerr << "Setting atom Coords\n";
892	>	char* inName;
893
894		(info[0].getConfiguration())->createArrays( info[0].n_atoms );
895	<
895	>
896		for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
897
898		if( globals->haveInitialConfig() ){
#	Line 915 | Line 901 | void SimSetup::initSystemCoords( void ){
901		#ifdef IS_MPI // is_mpi
902		if( worldRank == 0 ){
903		#endif //is_mpi
904	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
904	>	inName = globals->getInitialConfig();
905	>	double* tempDouble = new double[1000000];
906	>	fileInit = new InitializeFromFile( inName );
907		#ifdef IS_MPI
908		}else fileInit = new InitializeFromFile( NULL );
909		#endif
#	Line 930 | Line 918 | void SimSetup::initSystemCoords( void ){
918		// no init from bass
919
920		sprintf( painCave.errMsg,
921	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
921	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
922		painCave.isFatal;
923		simError();
924
#	Line 962 | Line 950 | void SimSetup::makeOutNames( void ){
950		#endif // is_mpi
951
952		if( globals->haveFinalConfig() ){
953	<	strcpy( info[k].finalName, globals->getFinalConfig() );
953	>	strcpy( info[k].finalName, globals->getFinalConfig() );
954		}
955		else{
956	<	strcpy( info[k].finalName, inFileName );
957	<	char* endTest;
958	<	int nameLength = strlen( info[k].finalName );
959	<	endTest = &(info[k].finalName[nameLength - 5]);
960	<	if( !strcmp( endTest, ".bass" ) ){
961	<	strcpy( endTest, ".eor" );
962	<	}
963	<	else if( !strcmp( endTest, ".BASS" ) ){
964	<	strcpy( endTest, ".eor" );
965	<	}
966	<	else{
967	<	endTest = &(info[k].finalName[nameLength - 4]);
968	<	if( !strcmp( endTest, ".bss" ) ){
969	<	strcpy( endTest, ".eor" );
970	<	}
971	<	else if( !strcmp( endTest, ".mdl" ) ){
972	<	strcpy( endTest, ".eor" );
973	<	}
974	<	else{
975	<	strcat( info[k].finalName, ".eor" );
976	<	}
977	<	}
956	>	strcpy( info[k].finalName, inFileName );
957	>	char* endTest;
958	>	int nameLength = strlen( info[k].finalName );
959	>	endTest = &(info[k].finalName[nameLength - 5]);
960	>	if( !strcmp( endTest, ".bass" ) ){
961	>	strcpy( endTest, ".eor" );
962	>	}
963	>	else if( !strcmp( endTest, ".BASS" ) ){
964	>	strcpy( endTest, ".eor" );
965	>	}
966	>	else{
967	>	endTest = &(info[k].finalName[nameLength - 4]);
968	>	if( !strcmp( endTest, ".bss" ) ){
969	>	strcpy( endTest, ".eor" );
970	>	}
971	>	else if( !strcmp( endTest, ".mdl" ) ){
972	>	strcpy( endTest, ".eor" );
973	>	}
974	>	else{
975	>	strcat( info[k].finalName, ".eor" );
976	>	}
977	>	}
978		}
979
980		// make the sample and status out names
#	Line 996 | Line 984 | void SimSetup::makeOutNames( void ){
984		int nameLength = strlen( info[k].sampleName );
985		endTest = &(info[k].sampleName[nameLength - 5]);
986		if( !strcmp( endTest, ".bass" ) ){
987	<	strcpy( endTest, ".dump" );
987	>	strcpy( endTest, ".dump" );
988		}
989		else if( !strcmp( endTest, ".BASS" ) ){
990	<	strcpy( endTest, ".dump" );
990	>	strcpy( endTest, ".dump" );
991		}
992		else{
993	<	endTest = &(info[k].sampleName[nameLength - 4]);
994	<	if( !strcmp( endTest, ".bss" ) ){
995	<	strcpy( endTest, ".dump" );
996	<	}
997	<	else if( !strcmp( endTest, ".mdl" ) ){
998	<	strcpy( endTest, ".dump" );
999	<	}
1000	<	else{
1001	<	strcat( info[k].sampleName, ".dump" );
1002	<	}
993	>	endTest = &(info[k].sampleName[nameLength - 4]);
994	>	if( !strcmp( endTest, ".bss" ) ){
995	>	strcpy( endTest, ".dump" );
996	>	}
997	>	else if( !strcmp( endTest, ".mdl" ) ){
998	>	strcpy( endTest, ".dump" );
999	>	}
1000	>	else{
1001	>	strcat( info[k].sampleName, ".dump" );
1002	>	}
1003		}
1004
1005		strcpy( info[k].statusName, inFileName );
1006		nameLength = strlen( info[k].statusName );
1007		endTest = &(info[k].statusName[nameLength - 5]);
1008		if( !strcmp( endTest, ".bass" ) ){
1009	<	strcpy( endTest, ".stat" );
1009	>	strcpy( endTest, ".stat" );
1010		}
1011		else if( !strcmp( endTest, ".BASS" ) ){
1012	<	strcpy( endTest, ".stat" );
1012	>	strcpy( endTest, ".stat" );
1013		}
1014		else{
1015	<	endTest = &(info[k].statusName[nameLength - 4]);
1016	<	if( !strcmp( endTest, ".bss" ) ){
1017	<	strcpy( endTest, ".stat" );
1018	<	}
1019	<	else if( !strcmp( endTest, ".mdl" ) ){
1020	<	strcpy( endTest, ".stat" );
1021	<	}
1022	<	else{
1023	<	strcat( info[k].statusName, ".stat" );
1024	<	}
1015	>	endTest = &(info[k].statusName[nameLength - 4]);
1016	>	if( !strcmp( endTest, ".bss" ) ){
1017	>	strcpy( endTest, ".stat" );
1018	>	}
1019	>	else if( !strcmp( endTest, ".mdl" ) ){
1020	>	strcpy( endTest, ".stat" );
1021	>	}
1022	>	else{
1023	>	strcat( info[k].statusName, ".stat" );
1024	>	}
1025		}
1026
1027		#ifdef IS_MPI
#	Line 1048 | Line 1036 | void SimSetup::sysObjectsCreation( void ){
1036		int i,k;
1037
1038		// create the forceField
1039	<
1039	>
1040		createFF();
1041
1042		// extract componentList
#	Line 1066 | Line 1054 | void SimSetup::sysObjectsCreation( void ){
1054		#endif //is_mpi
1055
1056		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1057	<
1057	>
1058		makeSysArrays();
1059
1060		// make and initialize the molecules (all but atomic coordinates)
1061	<
1061	>
1062		makeMolecules();
1063
1064		for(k=0; k<nInfo; k++){
#	Line 1100 | Line 1088 | void SimSetup::createFF( void ){
1088
1089		default:
1090		sprintf( painCave.errMsg,
1091	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1091	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1092		painCave.isFatal = 1;
1093		simError();
1094		}
#	Line 1146 | Line 1134 | void SimSetup::compList( void ){
1134
1135		currentStamp = stamps->extractMolStamp( id );
1136		if( currentStamp == NULL ){
1137	<	sprintf( painCave.errMsg,
1138	<	"SimSetup error: Component \"%s\" was not found in the "
1139	<	"list of declared molecules\n",
1140	<	id );
1141	<	painCave.isFatal = 1;
1142	<	simError();
1137	>	sprintf( painCave.errMsg,
1138	>	"SimSetup error: Component \"%s\" was not found in the "
1139	>	"list of declared molecules\n",
1140	>	id );
1141	>	painCave.isFatal = 1;
1142	>	simError();
1143		}
1144
1145		headStamp->add( currentStamp );
#	Line 1230 | Line 1218 | void SimSetup::mpiMolDivide( void ){
1218		for( j=0; j<components_nmol[i]; j++ ){
1219
1220		if( mol2proc[allMol] == worldRank ){
1221	<
1222	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1223	<	local_bonds +=    comp_stamps[i]->getNBonds();
1224	<	local_bends +=    comp_stamps[i]->getNBends();
1225	<	local_torsions += comp_stamps[i]->getNTorsions();
1226	<	localMol++;
1221	>
1222	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1223	>	local_bonds +=    comp_stamps[i]->getNBonds();
1224	>	local_bends +=    comp_stamps[i]->getNBends();
1225	>	local_torsions += comp_stamps[i]->getNTorsions();
1226	>	localMol++;
1227		}
1228		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1229		info[0].molMembershipArray[globalAtomIndex] = allMol;
#	Line 1251 | Line 1239 | void SimSetup::mpiMolDivide( void ){
1239
1240		if( local_atoms != info[0].n_atoms ){
1241		sprintf( painCave.errMsg,
1242	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1243	<	" localAtom (%d) are not equal.\n",
1244	<	info[0].n_atoms,
1245	<	local_atoms );
1242	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1243	>	" localAtom (%d) are not equal.\n",
1244	>	info[0].n_atoms,
1245	>	local_atoms );
1246		painCave.isFatal = 1;
1247		simError();
1248		}
#	Line 1297 | Line 1285 | void SimSetup::makeSysArrays( void ){
1285		for(i=0; i<mpiSim->getTotNmol(); i++){
1286
1287		if(mol2proc[i] == worldRank ){
1288	<	the_molecules[molIndex].setStampID( molCompType[i] );
1289	<	the_molecules[molIndex].setMyIndex( molIndex );
1290	<	the_molecules[molIndex].setGlobalIndex( i );
1291	<	molIndex++;
1288	>	the_molecules[molIndex].setStampID( molCompType[i] );
1289	>	the_molecules[molIndex].setMyIndex( molIndex );
1290	>	the_molecules[molIndex].setGlobalIndex( i );
1291	>	molIndex++;
1292		}
1293		}
1294
#	Line 1310 | Line 1298 | void SimSetup::makeSysArrays( void ){
1298		globalAtomIndex = 0;
1299		for(i=0; i<n_components; i++){
1300		for(j=0; j<components_nmol[i]; j++ ){
1301	<	the_molecules[molIndex].setStampID( i );
1302	<	the_molecules[molIndex].setMyIndex( molIndex );
1303	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1304	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1305	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1306	<	globalAtomIndex++;
1307	<	}
1308	<	molIndex++;
1301	>	the_molecules[molIndex].setStampID( i );
1302	>	the_molecules[molIndex].setMyIndex( molIndex );
1303	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1304	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1305	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1306	>	globalAtomIndex++;
1307	>	}
1308	>	molIndex++;
1309		}
1310		}
1311
#	Line 1330 | Line 1318 | void SimSetup::makeSysArrays( void ){
1318		Exclude::createArray(info[l].n_SRI);
1319		the_excludes = new Exclude*[info[l].n_SRI];
1320		for( int ex=0; ex<info[l].n_SRI; ex++){
1321	<	the_excludes[ex] = new Exclude(ex);
1321	>	the_excludes[ex] = new Exclude(ex);
1322		}
1323		info[l].globalExcludes = new int;
1324		info[l].n_exclude = info[l].n_SRI;
#	Line 1367 | Line 1355 | void SimSetup::makeIntegrator( void ){
1355		NPTf<RealIntegrator>* myNPTf = NULL;
1356		NPTim<RealIntegrator>* myNPTim = NULL;
1357		NPTfm<RealIntegrator>* myNPTfm = NULL;
1370	–	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1371	–	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1372	–	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1373	–	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1374	–	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1375	–	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1358
1359		for(k=0; k<nInfo; k++){
1360
1361		switch( ensembleCase ){
1362
1363		case NVE_ENS:
1364	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1364	>	if (globals->haveZconstraints()){
1365	>	setupZConstraint(info[k]);
1366	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1367	>	}
1368	>
1369	>	else
1370	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1371		break;
1372
1373		case NVT_ENS:
1374	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1375	<	myNVT->setTargetTemp(globals->getTargetTemp());
1374	>	if (globals->haveZconstraints()){
1375	>	setupZConstraint(info[k]);
1376	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377	>	}
1378	>	else
1379	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1380	>
1381	>	myNVT->setTargetTemp(globals->getTargetTemp());
1382
1383	<	if (globals->haveTauThermostat())
1384	<	myNVT->setTauThermostat(globals->getTauThermostat());
1383	>	if (globals->haveTauThermostat())
1384	>	myNVT->setTauThermostat(globals->getTauThermostat());
1385
1386	<	else {
1387	<	sprintf( painCave.errMsg,
1388	<	"SimSetup error: If you use the NVT\n"
1389	<	"    ensemble, you must set tauThermostat.\n");
1390	<	painCave.isFatal = 1;
1391	<	simError();
1392	<	}
1393	<	break;
1386	>	else {
1387	>	sprintf( painCave.errMsg,
1388	>	"SimSetup error: If you use the NVT\n"
1389	>	"    ensemble, you must set tauThermostat.\n");
1390	>	painCave.isFatal = 1;
1391	>	simError();
1392	>	}
1393	>	break;
1394
1395		case NPTi_ENS:
1396	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1396	>	if (globals->haveZconstraints()){
1397	>	setupZConstraint(info[k]);
1398	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399	>	}
1400	>	else
1401	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1402	>
1403		myNPTi->setTargetTemp( globals->getTargetTemp() );
1404	<
1404	>
1405		if (globals->haveTargetPressure())
1406	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1406	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1407		else {
1408	<	sprintf( painCave.errMsg,
1409	<	"SimSetup error: If you use a constant pressure\n"
1410	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	<	painCave.isFatal = 1;
1412	<	simError();
1408	>	sprintf( painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413		}
1414	<
1414	>
1415		if( globals->haveTauThermostat() )
1416	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1416	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417		else{
1418	<	sprintf( painCave.errMsg,
1419	<	"SimSetup error: If you use an NPT\n"
1420	<	"    ensemble, you must set tauThermostat.\n");
1421	<	painCave.isFatal = 1;
1422	<	simError();
1418	>	sprintf( painCave.errMsg,
1419	>	"SimSetup error: If you use an NPT\n"
1420	>	"    ensemble, you must set tauThermostat.\n");
1421	>	painCave.isFatal = 1;
1422	>	simError();
1423		}
1424	<
1424	>
1425		if( globals->haveTauBarostat() )
1426	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1426	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427		else{
1428	<	sprintf( painCave.errMsg,
1429	<	"SimSetup error: If you use an NPT\n"
1430	<	"    ensemble, you must set tauBarostat.\n");
1431	<	painCave.isFatal = 1;
1432	<	simError();
1433	<	}
1434	<	break;
1428	>	sprintf( painCave.errMsg,
1429	>	"SimSetup error: If you use an NPT\n"
1430	>	"    ensemble, you must set tauBarostat.\n");
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433	>	}
1434	>	break;
1435
1436		case NPTf_ENS:
1437	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1437	>	if (globals->haveZconstraints()){
1438	>	setupZConstraint(info[k]);
1439	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440	>	}
1441	>	else
1442	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1443	>
1444		myNPTf->setTargetTemp( globals->getTargetTemp());
1445	<
1445	>
1446		if (globals->haveTargetPressure())
1447	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1447	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1448		else {
1449	<	sprintf( painCave.errMsg,
1450	<	"SimSetup error: If you use a constant pressure\n"
1451	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1452	<	painCave.isFatal = 1;
1453	<	simError();
1449	>	sprintf( painCave.errMsg,
1450	>	"SimSetup error: If you use a constant pressure\n"
1451	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1452	>	painCave.isFatal = 1;
1453	>	simError();
1454		}
1455	<
1455	>
1456		if( globals->haveTauThermostat() )
1457	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1457	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1458		else{
1459	<	sprintf( painCave.errMsg,
1460	<	"SimSetup error: If you use an NPT\n"
1461	<	"    ensemble, you must set tauThermostat.\n");
1462	<	painCave.isFatal = 1;
1463	<	simError();
1459	>	sprintf( painCave.errMsg,
1460	>	"SimSetup error: If you use an NPT\n"
1461	>	"    ensemble, you must set tauThermostat.\n");
1462	>	painCave.isFatal = 1;
1463	>	simError();
1464		}
1465	<
1465	>
1466		if( globals->haveTauBarostat() )
1467	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1467	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1468		else{
1469	<	sprintf( painCave.errMsg,
1470	<	"SimSetup error: If you use an NPT\n"
1471	<	"    ensemble, you must set tauBarostat.\n");
1472	<	painCave.isFatal = 1;
1473	<	simError();
1469	>	sprintf( painCave.errMsg,
1470	>	"SimSetup error: If you use an NPT\n"
1471	>	"    ensemble, you must set tauBarostat.\n");
1472	>	painCave.isFatal = 1;
1473	>	simError();
1474		}
1475		break;
1476
1477		case NPTim_ENS:
1478	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1479	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1480	<
1478	>	if (globals->haveZconstraints()){
1479	>	setupZConstraint(info[k]);
1480	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481	>	}
1482	>	else
1483	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1484	>
1485	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1486	>
1487		if (globals->haveTargetPressure())
1488	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1488	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1489		else {
1490	<	sprintf( painCave.errMsg,
1491	<	"SimSetup error: If you use a constant pressure\n"
1492	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1493	<	painCave.isFatal = 1;
1494	<	simError();
1490	>	sprintf( painCave.errMsg,
1491	>	"SimSetup error: If you use a constant pressure\n"
1492	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1493	>	painCave.isFatal = 1;
1494	>	simError();
1495		}
1496	<
1496	>
1497		if( globals->haveTauThermostat() )
1498	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1498	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1499		else{
1500	<	sprintf( painCave.errMsg,
1501	<	"SimSetup error: If you use an NPT\n"
1502	<	"    ensemble, you must set tauThermostat.\n");
1503	<	painCave.isFatal = 1;
1504	<	simError();
1500	>	sprintf( painCave.errMsg,
1501	>	"SimSetup error: If you use an NPT\n"
1502	>	"    ensemble, you must set tauThermostat.\n");
1503	>	painCave.isFatal = 1;
1504	>	simError();
1505		}
1506	<
1506	>
1507		if( globals->haveTauBarostat() )
1508	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1508	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509		else{
1510	<	sprintf( painCave.errMsg,
1511	<	"SimSetup error: If you use an NPT\n"
1512	<	"    ensemble, you must set tauBarostat.\n");
1513	<	painCave.isFatal = 1;
1514	<	simError();
1510	>	sprintf( painCave.errMsg,
1511	>	"SimSetup error: If you use an NPT\n"
1512	>	"    ensemble, you must set tauBarostat.\n");
1513	>	painCave.isFatal = 1;
1514	>	simError();
1515		}
1516		break;
1517
1518		case NPTfm_ENS:
1519	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1519	>	if (globals->haveZconstraints()){
1520	>	setupZConstraint(info[k]);
1521	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522	>	}
1523	>	else
1524	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1525	>
1526		myNPTfm->setTargetTemp( globals->getTargetTemp());
1527	<
1527	>
1528		if (globals->haveTargetPressure())
1529	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1529	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1530		else {
1531	<	sprintf( painCave.errMsg,
1532	<	"SimSetup error: If you use a constant pressure\n"
1533	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1534	<	painCave.isFatal = 1;
1535	<	simError();
1531	>	sprintf( painCave.errMsg,
1532	>	"SimSetup error: If you use a constant pressure\n"
1533	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1534	>	painCave.isFatal = 1;
1535	>	simError();
1536		}
1537	<
1537	>
1538		if( globals->haveTauThermostat() )
1539	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1539	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1540		else{
1541	<	sprintf( painCave.errMsg,
1542	<	"SimSetup error: If you use an NPT\n"
1543	<	"    ensemble, you must set tauThermostat.\n");
1544	<	painCave.isFatal = 1;
1545	<	simError();
1541	>	sprintf( painCave.errMsg,
1542	>	"SimSetup error: If you use an NPT\n"
1543	>	"    ensemble, you must set tauThermostat.\n");
1544	>	painCave.isFatal = 1;
1545	>	simError();
1546		}
1547	<
1547	>
1548		if( globals->haveTauBarostat() )
1549	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1549	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1550		else{
1551	<	sprintf( painCave.errMsg,
1552	<	"SimSetup error: If you use an NPT\n"
1553	<	"    ensemble, you must set tauBarostat.\n");
1554	<	painCave.isFatal = 1;
1555	<	simError();
1538	<	}
1539	<	break;
1540	<
1541	<	case NVEZCONS_ENS:
1542	<
1543	<
1544	<	//setup index of z-constraint molecules, z-constraint sampel time
1545	<	//and z-constraint force output name. These parameter should be known
1546	<	//before constructing the z-constraint integrator
1547	<	setupZConstraint();
1548	<
1549	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1550	<
1551	<	break;
1552	<
1553	<
1554	<	case NVTZCONS_ENS:
1555	<
1556	<	setupZConstraint();
1557	<
1558	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1559	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1560	<
1561	<	if (globals->haveTauThermostat())
1562	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1563	<
1564	<	else {
1565	<	sprintf( painCave.errMsg,
1566	<	"SimSetup error: If you use the NVT\n"
1567	<	"    ensemble, you must set tauThermostat.\n");
1568	<	painCave.isFatal = 1;
1569	<	simError();
1570	<	}
1571	<	break;
1572	<
1573	<	case NPTiZCONS_ENS:
1574	<
1575	<	setupZConstraint();
1576	<
1577	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1578	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1579	<
1580	<	if (globals->haveTargetPressure())
1581	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1582	<	else {
1583	<	sprintf( painCave.errMsg,
1584	<	"SimSetup error: If you use a constant pressure\n"
1585	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1586	<	painCave.isFatal = 1;
1587	<	simError();
1551	>	sprintf( painCave.errMsg,
1552	>	"SimSetup error: If you use an NPT\n"
1553	>	"    ensemble, you must set tauBarostat.\n");
1554	>	painCave.isFatal = 1;
1555	>	simError();
1556		}
1589	–
1590	–	if( globals->haveTauThermostat() )
1591	–	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1592	–	else{
1593	–	sprintf( painCave.errMsg,
1594	–	"SimSetup error: If you use an NPT\n"
1595	–	"    ensemble, you must set tauThermostat.\n");
1596	–	painCave.isFatal = 1;
1597	–	simError();
1598	–	}
1599	–
1600	–	if( globals->haveTauBarostat() )
1601	–	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1602	–	else{
1603	–	sprintf( painCave.errMsg,
1604	–	"SimSetup error: If you use an NPT\n"
1605	–	"    ensemble, you must set tauBarostat.\n");
1606	–	painCave.isFatal = 1;
1607	–	simError();
1608	–	}
1609	–
1557		break;
1558
1612	–	case NPTfZCONS_ENS:
1613	–
1614	–	setupZConstraint();
1615	–
1616	–	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1617	–	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1618	–
1619	–	if (globals->haveTargetPressure())
1620	–	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1621	–	else {
1622	–	sprintf( painCave.errMsg,
1623	–	"SimSetup error: If you use a constant pressure\n"
1624	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1625	–	painCave.isFatal = 1;
1626	–	simError();
1627	–	}
1628	–
1629	–	if( globals->haveTauThermostat() )
1630	–	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1631	–	else{
1632	–	sprintf( painCave.errMsg,
1633	–	"SimSetup error: If you use an NPT\n"
1634	–	"    ensemble, you must set tauThermostat.\n");
1635	–	painCave.isFatal = 1;
1636	–	simError();
1637	–	}
1638	–
1639	–	if( globals->haveTauBarostat() )
1640	–	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1641	–	else{
1642	–	sprintf( painCave.errMsg,
1643	–	"SimSetup error: If you use an NPT\n"
1644	–	"    ensemble, you must set tauBarostat.\n");
1645	–	painCave.isFatal = 1;
1646	–	simError();
1647	–	}
1648	–
1649	–	break;
1650	–
1651	–	case NPTimZCONS_ENS:
1652	–
1653	–	setupZConstraint();
1654	–
1655	–	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1656	–	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1657	–
1658	–	if (globals->haveTargetPressure())
1659	–	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1660	–	else {
1661	–	sprintf( painCave.errMsg,
1662	–	"SimSetup error: If you use a constant pressure\n"
1663	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1664	–	painCave.isFatal = 1;
1665	–	simError();
1666	–	}
1667	–
1668	–	if( globals->haveTauThermostat() )
1669	–	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1670	–	else{
1671	–	sprintf( painCave.errMsg,
1672	–	"SimSetup error: If you use an NPT\n"
1673	–	"    ensemble, you must set tauThermostat.\n");
1674	–	painCave.isFatal = 1;
1675	–	simError();
1676	–	}
1677	–
1678	–	if( globals->haveTauBarostat() )
1679	–	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1680	–	else{
1681	–	sprintf( painCave.errMsg,
1682	–	"SimSetup error: If you use an NPT\n"
1683	–	"    ensemble, you must set tauBarostat.\n");
1684	–	painCave.isFatal = 1;
1685	–	simError();
1686	–	}
1687	–
1688	–	break;
1689	–
1690	–	case NPTfmZCONS_ENS:
1691	–
1692	–	setupZConstraint();
1693	–
1694	–	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1695	–	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1696	–
1697	–	if (globals->haveTargetPressure())
1698	–	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1699	–	else {
1700	–	sprintf( painCave.errMsg,
1701	–	"SimSetup error: If you use a constant pressure\n"
1702	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1703	–	painCave.isFatal = 1;
1704	–	simError();
1705	–	}
1706	–
1707	–	if( globals->haveTauThermostat() )
1708	–	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1709	–	else{
1710	–	sprintf( painCave.errMsg,
1711	–	"SimSetup error: If you use an NPT\n"
1712	–	"    ensemble, you must set tauThermostat.\n");
1713	–	painCave.isFatal = 1;
1714	–	simError();
1715	–	}
1716	–
1717	–	if( globals->haveTauBarostat() )
1718	–	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1719	–	else{
1720	–	sprintf( painCave.errMsg,
1721	–	"SimSetup error: If you use an NPT\n"
1722	–	"    ensemble, you must set tauBarostat.\n");
1723	–	painCave.isFatal = 1;
1724	–	simError();
1725	–	}
1726	–	break;
1727	–
1728	–
1729	–
1559		default:
1560		sprintf( painCave.errMsg,
1561	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1561	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1562		painCave.isFatal = 1;
1563		simError();
1564		}
#	Line 1748 | Line 1577 | void SimSetup::initFortran( void ){
1577		}
1578		else{
1579		sprintf( painCave.errMsg,
1580	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	<	info[0].mixingRule );
1580	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	>	info[0].mixingRule );
1582		painCave.isFatal = 1;
1583		simError();
1584		}
#	Line 1757 | Line 1586 | void SimSetup::initFortran( void ){
1586
1587		#ifdef IS_MPI
1588		strcpy( checkPointMsg,
1589	<	"Successfully intialized the mixingRule for Fortran." );
1589	>	"Successfully intialized the mixingRule for Fortran." );
1590		MPIcheckPoint();
1591		#endif // is_mpi
1592
1593		}
1594
1595	<	void SimSetup::setupZConstraint()
1595	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596		{
1597	<	int k;
1597	>	int nZConstraints;
1598	>	ZconStamp** zconStamp;
1599
1600	<	for(k=0; k<nInfo; k++){
1600	>	if(globals->haveZconstraintTime()){
1601
1602	<	if(globals->haveZConsTime()){
1603	<
1604	<	//add sample time of z-constraint  into SimInfo's property list
1605	<	DoubleData* zconsTimeProp = new DoubleData();
1606	<	zconsTimeProp->setID("zconstime");
1607	<	zconsTimeProp->setData(globals->getZConsTime());
1608	<	info[k].addProperty(zconsTimeProp);
1609	<	}
1610	<	else{
1611	<	sprintf( painCave.errMsg,
1612	<	"ZConstraint error: If you use an ZConstraint\n"
1613	<	" , you must set sample time.\n");
1614	<	painCave.isFatal = 1;
1615	<	simError();
1616	<	}
1617	<
1618	<	if(globals->haveIndexOfAllZConsMols()){
1602	>	//add sample time of z-constraint  into SimInfo's property list
1603	>	DoubleData* zconsTimeProp = new DoubleData();
1604	>	zconsTimeProp->setID(ZCONSTIME_ID);
1605	>	zconsTimeProp->setData(globals->getZconsTime());
1606	>	theInfo.addProperty(zconsTimeProp);
1607	>	}
1608	>	else{
1609	>	sprintf( painCave.errMsg,
1610	>	"ZConstraint error: If you use an ZConstraint\n"
1611	>	" , you must set sample time.\n");
1612	>	painCave.isFatal = 1;
1613	>	simError();
1614	>	}
1615	>
1616	>	//push zconsTol into siminfo, if user does not specify
1617	>	//value for zconsTol, a default value will be used
1618	>	DoubleData* zconsTol = new DoubleData();
1619	>	zconsTol->setID(ZCONSTOL_ID);
1620	>	if(globals->haveZconsTol()){
1621	>	zconsTol->setData(globals->getZconsTol());
1622	>	}
1623	>	else{
1624	>	double defaultZConsTol = 0.01;
1625	>	sprintf( painCave.errMsg,
1626	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1627	>	" , default value %f is used.\n", defaultZConsTol);
1628	>	painCave.isFatal = 0;
1629	>	simError();
1630	>
1631	>	zconsTol->setData(defaultZConsTol);
1632	>	}
1633	>	theInfo.addProperty(zconsTol);
1634	>
1635	>	//set Force Substraction Policy
1636	>	StringData* zconsForcePolicy =  new StringData();
1637	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1638	>
1639	>	if(globals->haveZconsForcePolicy()){
1640	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1641	>	}
1642	>	else{
1643	>	sprintf( painCave.errMsg,
1644	>	"ZConstraint Warning: User does not set force substraction policy, "
1645	>	"average force substraction policy is used\n");
1646	>	painCave.isFatal = 0;
1647	>	simError();
1648	>	zconsForcePolicy->setData("BYNUMBER");
1649	>	}
1650
1651	<	//add index of z-constraint molecules into SimInfo's property list
1652	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1653	<
1654	<	//sort the index
1655	<	sort(tempIndex.begin(), tempIndex.end());
1656	<
1657	<	IndexData* zconsIndex = new IndexData();
1658	<	zconsIndex->setID("zconsindex");
1659	<	zconsIndex->setIndexData(tempIndex);
1660	<	info[k].addProperty(zconsIndex);
1661	<	}
1662	<	else{
1663	<	sprintf( painCave.errMsg,
1664	<	"SimSetup error: If you use an ZConstraint\n"
1665	<	" , you must set index of z-constraint molecules.\n");
1666	<	painCave.isFatal = 1;
1667	<	simError();
1668	<
1669	<	}
1670	<
1671	<	//Determine the name of ouput file and add it into SimInfo's property list
1672	<	//Be careful, do not use inFileName, since it is a pointer which
1673	<	//point to a string at master node, and slave nodes do not contain that string
1674	<
1675	<	string zconsOutput(info[k].finalName);
1676	<
1677	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1678	<
1679	<	StringData* zconsFilename = new StringData();
1680	<	zconsFilename->setID("zconsfilename");
1681	<	zconsFilename->setData(zconsOutput);
1682	<
1683	<	info[k].addProperty(zconsFilename);
1651	>	theInfo.addProperty(zconsForcePolicy);
1652	>
1653	>	//Determine the name of ouput file and add it into SimInfo's property list
1654	>	//Be careful, do not use inFileName, since it is a pointer which
1655	>	//point to a string at master node, and slave nodes do not contain that string
1656	>
1657	>	string zconsOutput(theInfo.finalName);
1658	>
1659	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1660	>
1661	>	StringData* zconsFilename = new StringData();
1662	>	zconsFilename->setID(ZCONSFILENAME_ID);
1663	>	zconsFilename->setData(zconsOutput);
1664	>
1665	>	theInfo.addProperty(zconsFilename);
1666	>
1667	>	//setup index, pos and other parameters of z-constraint molecules
1668	>	nZConstraints = globals->getNzConstraints();
1669	>	theInfo.nZconstraints = nZConstraints;
1670	>
1671	>	zconStamp = globals->getZconStamp();
1672	>	ZConsParaItem tempParaItem;
1673	>
1674	>	ZConsParaData* zconsParaData = new ZConsParaData();
1675	>	zconsParaData->setID(ZCONSPARADATA_ID);
1676	>
1677	>	for(int i = 0; i < nZConstraints; i++){
1678	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1679	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1680	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1681	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1682	>
1683	>	zconsParaData->addItem(tempParaItem);
1684		}
1685	+
1686	+	//sort the parameters by index of molecules
1687	+	zconsParaData->sortByIndex();
1688	+
1689	+	//push data into siminfo, therefore, we can retrieve later
1690	+	theInfo.addProperty(zconsParaData);
1691	+
1692		}

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