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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 661 by tim, Fri Aug 1 16:18:13 2003 UTC vs.
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC

#	Line 59 | Line 59 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
59		info = the_info;
60		nInfo = theNinfo;
61		isInfoArray = 1;
62	<	}
62	>	}
63
64
65		void SimSetup::parseFile( char* fileName ){
#	Line 97 | Line 97 | void SimSetup::receiveParse(void){
97
98		#endif // is_mpi
99
100	<	void SimSetup::createSim( void ){
100	>	void SimSetup::createSim(void){
101
102		int i, j, k, globalAtomIndex;
103
#	Line 115 | Line 115 | void SimSetup::createSim( void ){
115
116		// initialize the system coordinates
117
118	<	initSystemCoords();
119	<
118	>	if( !isInfoArray ) initSystemCoords();
119
120		// make the output filenames
121
#	Line 141 | Line 140 | void SimSetup::makeMolecules( void ){
140
141		void SimSetup::makeMolecules( void ){
142
143	+	int k,l;
144		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
145		molInit molInfo;
146		DirectionalAtom* dAtom;
#	Line 165 | Line 165 | void SimSetup::makeMolecules( void ){
165
166		double ux, uy, uz, u, uSqr;
167
168	<	atomOffset = 0;
169	<	excludeOffset = 0;
170	<	for(i=0; i<info->n_mol; i++){
168	>	for(k=0; k<nInfo; k++){
169
170	<	stampID = the_molecules[i].getStampID();
170	>	the_ff->setSimInfo( &(info[k]) );
171
172	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
173	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
174	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
175	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
172	>	atomOffset = 0;
173	>	excludeOffset = 0;
174	>	for(i=0; i<info[k].n_mol; i++){
175	>
176	>	stampID = info[k].molecules[i].getStampID();
177
178	<	molInfo.myAtoms = &the_atoms[atomOffset];
179	<	molInfo.myExcludes = &the_excludes[excludeOffset];
180	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	<	molInfo.myBends = new Bend*[molInfo.nBends];
182	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
178	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
179	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
180	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
181	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
182	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
183	>
184	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
185	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
186	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
187	>	molInfo.myBends = new Bend*[molInfo.nBends];
188	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
189
190	<	theBonds = new bond_pair[molInfo.nBonds];
191	<	theBends = new bend_set[molInfo.nBends];
192	<	theTorsions = new torsion_set[molInfo.nTorsions];
190	>	theBonds = new bond_pair[molInfo.nBonds];
191	>	theBends = new bend_set[molInfo.nBends];
192	>	theTorsions = new torsion_set[molInfo.nTorsions];
193
194	<	// make the Atoms
194	>	// make the Atoms
195
196	<	for(j=0; j<molInfo.nAtoms; j++){
193	<
194	<	currentAtom = comp_stamps[stampID]->getAtom( j );
195	<	if( currentAtom->haveOrientation() ){
196	>	for(j=0; j<molInfo.nAtoms; j++){
197
198	<	dAtom = new DirectionalAtom(j + atomOffset);
199	<	info->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	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
198	>	currentAtom = comp_stamps[stampID]->getAtom( j );
199	>	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() );
226
227		#ifdef IS_MPI
228
229	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
229	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
230
231		#endif // is_mpi
232	<	}
232	>	}
233
234		// make the bonds
235	<	for(j=0; j<molInfo.nBonds; j++){
235	>	for(j=0; j<molInfo.nBonds; j++){
236
237	<	currentBond = comp_stamps[stampID]->getBond( j );
238	<	theBonds[j].a = currentBond->getA() + atomOffset;
239	<	theBonds[j].b = currentBond->getB() + atomOffset;
240	<
241	<	exI = theBonds[j].a;
242	<	exJ = theBonds[j].b;
243	<
244	<	// exclude_I must always be the smaller of the pair
245	<	if( exI > exJ ){
246	<	tempEx = exI;
247	<	exI = exJ;
248	<	exJ = tempEx;
249	<	}
237	>	currentBond = comp_stamps[stampID]->getBond( j );
238	>	theBonds[j].a = currentBond->getA() + atomOffset;
239	>	theBonds[j].b = currentBond->getB() + atomOffset;
240	>
241	>	exI = theBonds[j].a;
242	>	exJ = theBonds[j].b;
243	>
244	>	// exclude_I must always be the smaller of the pair
245	>	if( exI > exJ ){
246	>	tempEx = exI;
247	>	exI = exJ;
248	>	exJ = tempEx;
249	>	}
250		#ifdef IS_MPI
251	<	tempEx = exI;
252	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
253	<	tempEx = exJ;
254	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
255	<
256	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
257	<	#else  // isn't MPI
258	<
259	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
251	>	tempEx = exI;
252	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
253	>	tempEx = exJ;
254	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
255	>
256	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
257	>	#else  // isn't MPI
258	>
259	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
260		#endif  //is_mpi
261	<	}
262	<	excludeOffset += molInfo.nBonds;
257	<
258	<	//make the bends
259	<	for(j=0; j<molInfo.nBends; j++){
261	>	}
262	>	excludeOffset += molInfo.nBonds;
263
264	<	currentBend = comp_stamps[stampID]->getBend( j );
265	<	theBends[j].a = currentBend->getA() + atomOffset;
266	<	theBends[j].b = currentBend->getB() + atomOffset;
267	<	theBends[j].c = currentBend->getC() + atomOffset;
264	>	//make the bends
265	>	for(j=0; j<molInfo.nBends; j++){
266	>
267	>	currentBend = comp_stamps[stampID]->getBend( j );
268	>	theBends[j].a = currentBend->getA() + atomOffset;
269	>	theBends[j].b = currentBend->getB() + atomOffset;
270	>	theBends[j].c = currentBend->getC() + atomOffset;
271	>
272	>	if( currentBend->haveExtras() ){
273
274	<	if( currentBend->haveExtras() ){
275	<
276	<	extras = currentBend->getExtras();
277	<	current_extra = extras;
278	<
279	<	while( current_extra != NULL ){
280	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>	extras = currentBend->getExtras();
275	>	current_extra = extras;
276	>
277	>	while( current_extra != NULL ){
278	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
279	>
280	>	switch( current_extra->getType() ){
281
282	<	switch( current_extra->getType() ){
282	>	case 0:
283	>	theBends[j].ghost =
284	>	current_extra->getInt() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	case 1:
289	>	theBends[j].ghost =
290	>	(int)current_extra->getDouble() + atomOffset;
291	>	theBends[j].isGhost = 1;
292	>	break;
293	>
294	>	default:
295	>	sprintf( painCave.errMsg,
296	>	"SimSetup Error: ghostVectorSource was neither a "
297	>	"double nor an int.\n"
298	>	"-->Bend[%d] in %s\n",
299	>	j, comp_stamps[stampID]->getID() );
300	>	painCave.isFatal = 1;
301	>	simError();
302	>	}
303	>	}
304	>
305	>	else{
306
276	–	case 0:
277	–	theBends[j].ghost =
278	–	current_extra->getInt() + atomOffset;
279	–	theBends[j].isGhost = 1;
280	–	break;
281	–
282	–	case 1:
283	–	theBends[j].ghost =
284	–	(int)current_extra->getDouble() + atomOffset;
285	–	theBends[j].isGhost = 1;
286	–	break;
287	–
288	–	default:
307		sprintf( painCave.errMsg,
308	<	"SimSetup Error: ghostVectorSource was neither a "
309	<	"double nor an int.\n"
310	<	"-->Bend[%d] in %s\n",
308	>	"SimSetup Error: unhandled bend assignment:\n"
309	>	"    -->%s in Bend[%d] in %s\n",
310	>	current_extra->getlhs(),
311		j, comp_stamps[stampID]->getID() );
312		painCave.isFatal = 1;
313		simError();
314		}
297	–	}
298	–
299	–	else{
315
316	<	sprintf( painCave.errMsg,
302	<	"SimSetup Error: unhandled bend assignment:\n"
303	<	"    -->%s in Bend[%d] in %s\n",
304	<	current_extra->getlhs(),
305	<	j, comp_stamps[stampID]->getID() );
306	<	painCave.isFatal = 1;
307	<	simError();
316	>	current_extra = current_extra->getNext();
317		}
318	+	}
319	+
320	+	if( !theBends[j].isGhost ){
321
322	<	current_extra = current_extra->getNext();
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].c;
324		}
325	<	}
325	>	else{
326
327	<	if( !theBends[j].isGhost ){
328	<
329	<	exI = theBends[j].a;
317	<	exJ = theBends[j].c;
318	<	}
319	<	else{
327	>	exI = theBends[j].a;
328	>	exJ = theBends[j].b;
329	>	}
330
331	<	exI = theBends[j].a;
332	<	exJ = theBends[j].b;
333	<	}
334	<
335	<	// exclude_I must always be the smaller of the pair
336	<	if( exI > exJ ){
327	<	tempEx = exI;
328	<	exI = exJ;
329	<	exJ = tempEx;
330	<	}
331	>	// exclude_I must always be the smaller of the pair
332	>	if( exI > exJ ){
333	>	tempEx = exI;
334	>	exI = exJ;
335	>	exJ = tempEx;
336	>	}
337		#ifdef IS_MPI
338	<	tempEx = exI;
339	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
340	<	tempEx = exJ;
341	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
338	>	tempEx = exI;
339	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
340	>	tempEx = exJ;
341	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
342
343	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
343	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
344		#else  // isn't MPI
345	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
345	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
346		#endif  //is_mpi
341	–	}
342	–	excludeOffset += molInfo.nBends;
343	–
344	–	for(j=0; j<molInfo.nTorsions; j++){
345	–
346	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	–
352	–	exI = theTorsions[j].a;
353	–	exJ = theTorsions[j].d;
354	–
355	–	// exclude_I must always be the smaller of the pair
356	–	if( exI > exJ ){
357	–	tempEx = exI;
358	–	exI = exJ;
359	–	exJ = tempEx;
347		}
348	<	#ifdef IS_MPI
362	<	tempEx = exI;
363	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
364	<	tempEx = exJ;
365	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
348	>	excludeOffset += molInfo.nBends;
349
350	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
350	>	for(j=0; j<molInfo.nTorsions; j++){
351	>
352	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
353	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
354	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
355	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
356	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
357	>
358	>	exI = theTorsions[j].a;
359	>	exJ = theTorsions[j].d;
360	>
361	>	// exclude_I must always be the smaller of the pair
362	>	if( exI > exJ ){
363	>	tempEx = exI;
364	>	exI = exJ;
365	>	exJ = tempEx;
366	>	}
367	>	#ifdef IS_MPI
368	>	tempEx = exI;
369	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
370	>	tempEx = exJ;
371	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
372	>
373	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
374		#else  // isn't MPI
375	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
375	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
376		#endif  //is_mpi
377	<	}
378	<	excludeOffset += molInfo.nTorsions;
377	>	}
378	>	excludeOffset += molInfo.nTorsions;
379	>
380	>
381	>	// send the arrays off to the forceField for init.
382	>
383	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
384	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
385	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
386	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
387	>
388	>
389	>	info[k].molecules[i].initialize( molInfo );
390
391	<
392	<	// send the arrays off to the forceField for init.
393	<
394	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
395	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
396	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381	<
382	<
383	<	the_molecules[i].initialize( molInfo );
384	<
385	<
386	<	atomOffset += molInfo.nAtoms;
387	<	delete[] theBonds;
388	<	delete[] theBends;
389	<	delete[] theTorsions;
391	>
392	>	atomOffset += molInfo.nAtoms;
393	>	delete[] theBonds;
394	>	delete[] theBends;
395	>	delete[] theTorsions;
396	>	}
397		}
398	<
398	>
399		#ifdef IS_MPI
400		sprintf( checkPointMsg, "all molecules initialized succesfully" );
401		MPIcheckPoint();
402		#endif // is_mpi
403	<
403	>
404		// clean up the forcefield
405	+
406		the_ff->calcRcut();
407		the_ff->cleanMe();
408	<
408	>
409		}
410
411		void SimSetup::initFromBass( void ){
#	Line 410 | Line 418 | void SimSetup::initFromBass( void ){
418		int n_extra;
419		int have_extra, done;
420
421	+	double vel[3];
422	+	vel[0] = 0.0;
423	+	vel[1] = 0.0;
424	+	vel[2] = 0.0;
425	+
426		temp1 = (double)tot_nmol / 4.0;
427		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
428		temp3 = ceil( temp2 );
#	Line 419 | Line 432 | void SimSetup::initFromBass( void ){
432		have_extra =1;
433
434		n_cells = (int)temp3 - 1;
435	<	cellx = info->boxL[0] / temp3;
436	<	celly = info->boxL[1] / temp3;
437	<	cellz = info->boxL[2] / temp3;
435	>	cellx = info[0].boxL[0] / temp3;
436	>	celly = info[0].boxL[1] / temp3;
437	>	cellz = info[0].boxL[2] / temp3;
438		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
439		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
440		n_per_extra = (int)ceil( temp1 );
#	Line 436 | Line 449 | void SimSetup::initFromBass( void ){
449		}
450		else{
451		n_cells = (int)temp3;
452	<	cellx = info->boxL[0] / temp3;
453	<	celly = info->boxL[1] / temp3;
454	<	cellz = info->boxL[2] / temp3;
452	>	cellx = info[0].boxL[0] / temp3;
453	>	celly = info[0].boxL[1] / temp3;
454	>	cellz = info[0].boxL[2] / temp3;
455		}
456
457		current_mol = 0;
#	Line 517 | Line 530 | void SimSetup::initFromBass( void ){
530		}
531		}
532
533	<
534	<	for( i=0; i<info->n_atoms; i++ ){
522	<	info->atoms[i]->set_vx( 0.0 );
523	<	info->atoms[i]->set_vy( 0.0 );
524	<	info->atoms[i]->set_vz( 0.0 );
533	>	for( i=0; i<info[0].n_atoms; i++ ){
534	>	info[0].atoms[i]->setVel( vel );
535		}
536		}
537
#	Line 531 | Line 541 | void SimSetup::makeElement( double x, double y, double
541		AtomStamp* current_atom;
542		DirectionalAtom* dAtom;
543		double rotMat[3][3];
544	+	double pos[3];
545
546		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
547
#	Line 546 | Line 557 | void SimSetup::makeElement( double x, double y, double
557		painCave.isFatal = 1;
558		simError();
559		}
560	+
561	+	pos[0] = x + current_atom->getPosX();
562	+	pos[1] = y + current_atom->getPosY();
563	+	pos[2] = z + current_atom->getPosZ();
564	+
565	+	info[0].atoms[current_atom_ndx]->setPos( pos );
566
567	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
551	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
552	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
567	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
568
569	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
569	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
570
556	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
557	–
571		rotMat[0][0] = 1.0;
572		rotMat[0][1] = 0.0;
573		rotMat[0][2] = 0.0;
#	Line 590 | Line 603 | void SimSetup::gatherInfo( void ){
603		ensembleCase = -1;
604		ffCase = -1;
605
593	–	// get the stamps and globals;
594	–	stamps = stamps;
595	–	globals = globals;
596	–
606		// set the easy ones first
607	<	info->target_temp = globals->getTargetTemp();
608	<	info->dt = globals->getDt();
609	<	info->run_time = globals->getRunTime();
607	>
608	>	for( i=0; i<nInfo; i++){
609	>	info[i].target_temp = globals->getTargetTemp();
610	>	info[i].dt = globals->getDt();
611	>	info[i].run_time = globals->getRunTime();
612	>	}
613		n_components = globals->getNComponents();
614
615
#	Line 646 | Line 658 | void SimSetup::gatherInfo( void ){
658		strcpy( ensemble, "NVE" );
659		ensembleCase = NVE_ENS;
660		}
661	<	strcpy( info->ensemble, ensemble );
661	>
662	>	for(i=0; i<nInfo; i++){
663	>
664	>	strcpy( info[i].ensemble, ensemble );
665
666	<	// get the mixing rule
666	>	// get the mixing rule
667
668	<	strcpy( info->mixingRule, globals->getMixingRule() );
669	<	info->usePBC = globals->getPBC();
670	<
668	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
669	>	info[i].usePBC = globals->getPBC();
670	>	}
671
672		// get the components and calculate the tot_nMol and indvidual n_mol
673
#	Line 693 | Line 708 | void SimSetup::gatherInfo( void ){
708
709		// set the status, sample, and thermal kick times
710
711	<	if( globals->haveSampleTime() ){
697	<	info->sampleTime = globals->getSampleTime();
698	<	info->statusTime = info->sampleTime;
699	<	info->thermalTime = info->sampleTime;
700	<	}
701	<	else{
702	<	info->sampleTime = globals->getRunTime();
703	<	info->statusTime = info->sampleTime;
704	<	info->thermalTime = info->sampleTime;
705	<	}
711	>	for(i=0; i<nInfo; i++){
712
713	<	if( globals->haveStatusTime() ){
714	<	info->statusTime = globals->getStatusTime();
715	<	}
716	<
717	<	if( globals->haveThermalTime() ){
718	<	info->thermalTime = globals->getThermalTime();
719	<	}
720	<
721	<	// check for the temperature set flag
722	<
717	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
718	<
719	<	// get some of the tricky things that may still be in the globals
720	<
721	<	double boxVector[3];
722	<	if( globals->haveBox() ){
723	<	boxVector[0] = globals->getBox();
724	<	boxVector[1] = globals->getBox();
725	<	boxVector[2] = globals->getBox();
713	>	if( globals->haveSampleTime() ){
714	>	info[i].sampleTime = globals->getSampleTime();
715	>	info[i].statusTime = info[i].sampleTime;
716	>	info[i].thermalTime = info[i].sampleTime;
717	>	}
718	>	else{
719	>	info[i].sampleTime = globals->getRunTime();
720	>	info[i].statusTime = info[i].sampleTime;
721	>	info[i].thermalTime = info[i].sampleTime;
722	>	}
723
724	<	info->setBox( boxVector );
725	<	}
726	<	else if( globals->haveDensity() ){
724	>	if( globals->haveStatusTime() ){
725	>	info[i].statusTime = globals->getStatusTime();
726	>	}
727	>
728	>	if( globals->haveThermalTime() ){
729	>	info[i].thermalTime = globals->getThermalTime();
730	>	}
731
732	<	double vol;
732	<	vol = (double)tot_nmol / globals->getDensity();
733	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
734	<	boxVector[1] = boxVector[0];
735	<	boxVector[2] = boxVector[0];
732	>	// check for the temperature set flag
733
734	<	info->setBox( boxVector );
734	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
735	>
736	>	// get some of the tricky things that may still be in the globals
737	>
738	>	double boxVector[3];
739	>	if( globals->haveBox() ){
740	>	boxVector[0] = globals->getBox();
741	>	boxVector[1] = globals->getBox();
742	>	boxVector[2] = globals->getBox();
743	>
744	>	info[i].setBox( boxVector );
745	>	}
746	>	else if( globals->haveDensity() ){
747	>
748	>	double vol;
749	>	vol = (double)tot_nmol / globals->getDensity();
750	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
751	>	boxVector[1] = boxVector[0];
752	>	boxVector[2] = boxVector[0];
753	>
754	>	info[i].setBox( boxVector );
755		}
756	<	else{
757	<	if( !globals->haveBoxX() ){
758	<	sprintf( painCave.errMsg,
759	<	"SimSetup error, no periodic BoxX size given.\n" );
760	<	painCave.isFatal = 1;
761	<	simError();
756	>	else{
757	>	if( !globals->haveBoxX() ){
758	>	sprintf( painCave.errMsg,
759	>	"SimSetup error, no periodic BoxX size given.\n" );
760	>	painCave.isFatal = 1;
761	>	simError();
762	>	}
763	>	boxVector[0] = globals->getBoxX();
764	>
765	>	if( !globals->haveBoxY() ){
766	>	sprintf( painCave.errMsg,
767	>	"SimSetup error, no periodic BoxY size given.\n" );
768	>	painCave.isFatal = 1;
769	>	simError();
770	>	}
771	>	boxVector[1] = globals->getBoxY();
772	>
773	>	if( !globals->haveBoxZ() ){
774	>	sprintf( painCave.errMsg,
775	>	"SimSetup error, no periodic BoxZ size given.\n" );
776	>	painCave.isFatal = 1;
777	>	simError();
778	>	}
779	>	boxVector[2] = globals->getBoxZ();
780	>
781	>	info[i].setBox( boxVector );
782		}
746	–	boxVector[0] = globals->getBoxX();
783
748	–	if( !globals->haveBoxY() ){
749	–	sprintf( painCave.errMsg,
750	–	"SimSetup error, no periodic BoxY size given.\n" );
751	–	painCave.isFatal = 1;
752	–	simError();
753	–	}
754	–	boxVector[1] = globals->getBoxY();
755	–
756	–	if( !globals->haveBoxZ() ){
757	–	sprintf( painCave.errMsg,
758	–	"SimSetup error, no periodic BoxZ size given.\n" );
759	–	painCave.isFatal = 1;
760	–	simError();
761	–	}
762	–	boxVector[2] = globals->getBoxZ();
763	–
764	–	info->setBox( boxVector );
784		}
766	–
767	–
785
786		#ifdef IS_MPI
787		strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
#	Line 777 | Line 794 | void SimSetup::finalInfoCheck( void ){
794		void SimSetup::finalInfoCheck( void ){
795		int index;
796		int usesDipoles;
797	<
797	>	int i;
798
799	<	// check electrostatic parameters
800	<
784	<	index = 0;
785	<	usesDipoles = 0;
786	<	while( (index < info->n_atoms) && !usesDipoles ){
787	<	usesDipoles = ((info->atoms)[index])->hasDipole();
788	<	index++;
789	<	}
790	<
791	<	#ifdef IS_MPI
792	<	int myUse = usesDipoles;
793	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
794	<	#endif //is_mpi
795	<
796	<	double theEcr, theEst;
797	<
798	<	if (globals->getUseRF() ) {
799	<	info->useReactionField = 1;
799	>	for(i=0; i<nInfo; i++){
800	>	// check electrostatic parameters
801
802	<	if( !globals->haveECR() ){
803	<	sprintf( painCave.errMsg,
804	<	"SimSetup Warning: using default value of 1/2 the smallest "
805	<	"box length for the electrostaticCutoffRadius.\n"
806	<	"I hope you have a very fast processor!\n");
806	<	painCave.isFatal = 0;
807	<	simError();
808	<	double smallest;
809	<	smallest = info->boxL[0];
810	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
811	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
812	<	theEcr = 0.5 * smallest;
813	<	} else {
814	<	theEcr = globals->getECR();
802	>	index = 0;
803	>	usesDipoles = 0;
804	>	while( (index < info[i].n_atoms) && !usesDipoles ){
805	>	usesDipoles = (info[i].atoms[index])->hasDipole();
806	>	index++;
807		}
816	–
817	–	if( !globals->haveEST() ){
818	–	sprintf( painCave.errMsg,
819	–	"SimSetup Warning: using default value of 0.05 * the "
820	–	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
821	–	);
822	–	painCave.isFatal = 0;
823	–	simError();
824	–	theEst = 0.05 * theEcr;
825	–	} else {
826	–	theEst= globals->getEST();
827	–	}
828	–
829	–	info->setEcr( theEcr, theEst );
808
809	<	if(!globals->haveDielectric() ){
810	<	sprintf( painCave.errMsg,
811	<	"SimSetup Error: You are trying to use Reaction Field without"
812	<	"setting a dielectric constant!\n"
813	<	);
814	<	painCave.isFatal = 1;
815	<	simError();
816	<	}
817	<	info->dielectric = globals->getDielectric();
840	<	}
841	<	else {
842	<	if (usesDipoles) {
809	>	#ifdef IS_MPI
810	>	int myUse = usesDipoles;
811	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
812	>	#endif //is_mpi
813	>
814	>	double theEcr, theEst;
815	>
816	>	if (globals->getUseRF() ) {
817	>	info[i].useReactionField = 1;
818
819		if( !globals->haveECR() ){
820		sprintf( painCave.errMsg,
#	Line 849 | Line 824 | void SimSetup::finalInfoCheck( void ){
824		painCave.isFatal = 0;
825		simError();
826		double smallest;
827	<	smallest = info->boxL[0];
828	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
829	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
827	>	smallest = info[i].boxL[0];
828	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
829	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
830		theEcr = 0.5 * smallest;
831		} else {
832		theEcr = globals->getECR();
#	Line 860 | Line 835 | void SimSetup::finalInfoCheck( void ){
835		if( !globals->haveEST() ){
836		sprintf( painCave.errMsg,
837		"SimSetup Warning: using default value of 0.05 * the "
838	<	"electrostaticCutoffRadius for the "
864	<	"electrostaticSkinThickness\n"
838	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
839		);
840		painCave.isFatal = 0;
841		simError();
#	Line 869 | Line 843 | void SimSetup::finalInfoCheck( void ){
843		} else {
844		theEst= globals->getEST();
845		}
846	+
847	+	info[i].setEcr( theEcr, theEst );
848	+
849	+	if(!globals->haveDielectric() ){
850	+	sprintf( painCave.errMsg,
851	+	"SimSetup Error: You are trying to use Reaction Field without"
852	+	"setting a dielectric constant!\n"
853	+	);
854	+	painCave.isFatal = 1;
855	+	simError();
856	+	}
857	+	info[i].dielectric = globals->getDielectric();
858	+	}
859	+	else {
860	+	if (usesDipoles) {
861	+
862	+	if( !globals->haveECR() ){
863	+	sprintf( painCave.errMsg,
864	+	"SimSetup Warning: using default value of 1/2 the smallest "
865	+	"box length for the electrostaticCutoffRadius.\n"
866	+	"I hope you have a very fast processor!\n");
867	+	painCave.isFatal = 0;
868	+	simError();
869	+	double smallest;
870	+	smallest = info[i].boxL[0];
871	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
872	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
873	+	theEcr = 0.5 * smallest;
874	+	} else {
875	+	theEcr = globals->getECR();
876	+	}
877	+
878	+	if( !globals->haveEST() ){
879	+	sprintf( painCave.errMsg,
880	+	"SimSetup Warning: using default value of 0.05 * the "
881	+	"electrostaticCutoffRadius for the "
882	+	"electrostaticSkinThickness\n"
883	+	);
884	+	painCave.isFatal = 0;
885	+	simError();
886	+	theEst = 0.05 * theEcr;
887	+	} else {
888	+	theEst= globals->getEST();
889	+	}
890	+
891	+	info[i].setEcr( theEcr, theEst );
892	+	}
893	+	}
894	+	}
895
873	–	info->setEcr( theEcr, theEst );
874	–	}
875	–	}
876	–
896		#ifdef IS_MPI
897		strcpy( checkPointMsg, "post processing checks out" );
898		MPIcheckPoint();
#	Line 882 | Line 901 | void SimSetup::initSystemCoords( void ){
901		}
902
903		void SimSetup::initSystemCoords( void ){
904	+	int i;
905	+
906	+	std::cerr << "Setting atom Coords\n";
907
908	<	if( globals->haveInitialConfig() ){
909	<
910	<	InitializeFromFile* fileInit;
908	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
909	>
910	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
911	>
912	>	if( globals->haveInitialConfig() ){
913	>
914	>	InitializeFromFile* fileInit;
915		#ifdef IS_MPI // is_mpi
916	<	if( worldRank == 0 ){
916	>	if( worldRank == 0 ){
917		#endif //is_mpi
918	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
918	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
919		#ifdef IS_MPI
920	<	}else fileInit = new InitializeFromFile( NULL );
920	>	}else fileInit = new InitializeFromFile( NULL );
921		#endif
922	<	fileInit->readInit( info ); // default velocities on
923	<
924	<	delete fileInit;
925	<	}
926	<	else{
927	<
922	>	fileInit->readInit( info ); // default velocities on
923	>
924	>	delete fileInit;
925	>	}
926	>	else{
927	>
928		#ifdef IS_MPI
929	<
930	<	// no init from bass
931	<
932	<	sprintf( painCave.errMsg,
933	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
934	<	painCave.isFatal;
935	<	simError();
936	<
929	>
930	>	// no init from bass
931	>
932	>	sprintf( painCave.errMsg,
933	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
934	>	painCave.isFatal;
935	>	simError();
936	>
937		#else
938	<
939	<	initFromBass();
940	<
941	<
938	>
939	>	initFromBass();
940	>
941	>
942		#endif
943	<	}
944	<
943	>	}
944	>
945		#ifdef IS_MPI
946		strcpy( checkPointMsg, "Successfully read in the initial configuration" );
947		MPIcheckPoint();
948		#endif // is_mpi
949	<
949	>
950		}
951
952
953		void SimSetup::makeOutNames( void ){
954	+
955	+	int k;
956
957	+
958	+	for(k=0; k<nInfo; k++){
959	+
960		#ifdef IS_MPI
961	<	if( worldRank == 0 ){
961	>	if( worldRank == 0 ){
962		#endif // is_mpi
963	<
964	<	if( globals->haveFinalConfig() ){
965	<	strcpy( info->finalName, globals->getFinalConfig() );
935	<	}
936	<	else{
937	<	strcpy( info->finalName, inFileName );
938	<	char* endTest;
939	<	int nameLength = strlen( info->finalName );
940	<	endTest = &(info->finalName[nameLength - 5]);
941	<	if( !strcmp( endTest, ".bass" ) ){
942	<	strcpy( endTest, ".eor" );
963	>
964	>	if( globals->haveFinalConfig() ){
965	>	strcpy( info[k].finalName, globals->getFinalConfig() );
966		}
944	–	else if( !strcmp( endTest, ".BASS" ) ){
945	–	strcpy( endTest, ".eor" );
946	–	}
967		else{
968	<	endTest = &(info->finalName[nameLength - 4]);
969	<	if( !strcmp( endTest, ".bss" ) ){
968	>	strcpy( info[k].finalName, inFileName );
969	>	char* endTest;
970	>	int nameLength = strlen( info[k].finalName );
971	>	endTest = &(info[k].finalName[nameLength - 5]);
972	>	if( !strcmp( endTest, ".bass" ) ){
973		strcpy( endTest, ".eor" );
974		}
975	<	else if( !strcmp( endTest, ".mdl" ) ){
975	>	else if( !strcmp( endTest, ".BASS" ) ){
976		strcpy( endTest, ".eor" );
977		}
978		else{
979	<	strcat( info->finalName, ".eor" );
979	>	endTest = &(info[k].finalName[nameLength - 4]);
980	>	if( !strcmp( endTest, ".bss" ) ){
981	>	strcpy( endTest, ".eor" );
982	>	}
983	>	else if( !strcmp( endTest, ".mdl" ) ){
984	>	strcpy( endTest, ".eor" );
985	>	}
986	>	else{
987	>	strcat( info[k].finalName, ".eor" );
988	>	}
989		}
990		}
991	<	}
992	<
993	<	// make the sample and status out names
994	<
995	<	strcpy( info->sampleName, inFileName );
996	<	char* endTest;
997	<	int nameLength = strlen( info->sampleName );
998	<	endTest = &(info->sampleName[nameLength - 5]);
967	<	if( !strcmp( endTest, ".bass" ) ){
968	<	strcpy( endTest, ".dump" );
969	<	}
970	<	else if( !strcmp( endTest, ".BASS" ) ){
971	<	strcpy( endTest, ".dump" );
972	<	}
973	<	else{
974	<	endTest = &(info->sampleName[nameLength - 4]);
975	<	if( !strcmp( endTest, ".bss" ) ){
991	>
992	>	// make the sample and status out names
993	>
994	>	strcpy( info[k].sampleName, inFileName );
995	>	char* endTest;
996	>	int nameLength = strlen( info[k].sampleName );
997	>	endTest = &(info[k].sampleName[nameLength - 5]);
998	>	if( !strcmp( endTest, ".bass" ) ){
999		strcpy( endTest, ".dump" );
1000		}
1001	<	else if( !strcmp( endTest, ".mdl" ) ){
1001	>	else if( !strcmp( endTest, ".BASS" ) ){
1002		strcpy( endTest, ".dump" );
1003		}
1004		else{
1005	<	strcat( info->sampleName, ".dump" );
1005	>	endTest = &(info[k].sampleName[nameLength - 4]);
1006	>	if( !strcmp( endTest, ".bss" ) ){
1007	>	strcpy( endTest, ".dump" );
1008	>	}
1009	>	else if( !strcmp( endTest, ".mdl" ) ){
1010	>	strcpy( endTest, ".dump" );
1011	>	}
1012	>	else{
1013	>	strcat( info[k].sampleName, ".dump" );
1014	>	}
1015		}
1016	<	}
1017	<
1018	<	strcpy( info->statusName, inFileName );
1019	<	nameLength = strlen( info->statusName );
1020	<	endTest = &(info->statusName[nameLength - 5]);
989	<	if( !strcmp( endTest, ".bass" ) ){
990	<	strcpy( endTest, ".stat" );
991	<	}
992	<	else if( !strcmp( endTest, ".BASS" ) ){
993	<	strcpy( endTest, ".stat" );
994	<	}
995	<	else{
996	<	endTest = &(info->statusName[nameLength - 4]);
997	<	if( !strcmp( endTest, ".bss" ) ){
1016	>
1017	>	strcpy( info[k].statusName, inFileName );
1018	>	nameLength = strlen( info[k].statusName );
1019	>	endTest = &(info[k].statusName[nameLength - 5]);
1020	>	if( !strcmp( endTest, ".bass" ) ){
1021		strcpy( endTest, ".stat" );
1022		}
1023	<	else if( !strcmp( endTest, ".mdl" ) ){
1023	>	else if( !strcmp( endTest, ".BASS" ) ){
1024		strcpy( endTest, ".stat" );
1025		}
1026		else{
1027	<	strcat( info->statusName, ".stat" );
1027	>	endTest = &(info[k].statusName[nameLength - 4]);
1028	>	if( !strcmp( endTest, ".bss" ) ){
1029	>	strcpy( endTest, ".stat" );
1030	>	}
1031	>	else if( !strcmp( endTest, ".mdl" ) ){
1032	>	strcpy( endTest, ".stat" );
1033	>	}
1034	>	else{
1035	>	strcat( info[k].statusName, ".stat" );
1036	>	}
1037		}
1038	<	}
1007	<
1038	>
1039		#ifdef IS_MPI
1040	<	}
1040	>	}
1041		#endif // is_mpi
1042	<
1042	>	}
1043		}
1044
1045
1046		void SimSetup::sysObjectsCreation( void ){
1047	<
1048	<	int i;
1049	<
1047	>
1048	>	int i,k;
1049	>
1050		// create the forceField
1051	<
1051	>
1052		createFF();
1053
1054		// extract componentList
#	Line 1041 | Line 1072 | void SimSetup::sysObjectsCreation( void ){
1072		// make and initialize the molecules (all but atomic coordinates)
1073
1074		makeMolecules();
1044	–	info->identArray = new int[info->n_atoms];
1045	–	for(i=0; i<info->n_atoms; i++){
1046	–	info->identArray[i] = the_atoms[i]->getIdent();
1047	–	}
1075
1076	<
1077	<
1076	>	for(k=0; k<nInfo; k++){
1077	>	info[k].identArray = new int[info[k].n_atoms];
1078	>	for(i=0; i<info[k].n_atoms; i++){
1079	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1080	>	}
1081	>	}
1082		}
1083
1084
#	Line 1085 | Line 1116 | void SimSetup::compList( void ){
1116		void SimSetup::compList( void ){
1117
1118		int i;
1119	<
1119	>	char* id;
1120	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1121	>	LinkedMolStamp* currentStamp = NULL;
1122		comp_stamps = new MoleculeStamp*[n_components];
1123	<
1123	>
1124		// make an array of molecule stamps that match the components used.
1125		// also extract the used stamps out into a separate linked list
1093	–
1094	–	info->nComponents = n_components;
1095	–	info->componentsNmol = components_nmol;
1096	–	info->compStamps = comp_stamps;
1097	–	info->headStamp = new LinkedMolStamp();
1126
1127	<	char* id;
1128	<	LinkedMolStamp* headStamp = info->headStamp;
1129	<	LinkedMolStamp* currentStamp = NULL;
1127	>	for(i=0; i<nInfo; i++){
1128	>	info[i].nComponents = n_components;
1129	>	info[i].componentsNmol = components_nmol;
1130	>	info[i].compStamps = comp_stamps;
1131	>	info[i].headStamp = headStamp;
1132	>	}
1133	>
1134	>
1135		for( i=0; i<n_components; i++ ){
1136
1137		id = the_components[i]->getType();
#	Line 1136 | Line 1169 | void SimSetup::calcSysValues( void ){
1169
1170		void SimSetup::calcSysValues( void ){
1171		int i, j, k;
1172	<
1173	<
1172	>
1173	>	int *molMembershipArray;
1174	>
1175		tot_atoms = 0;
1176		tot_bonds = 0;
1177		tot_bends = 0;
#	Line 1149 | Line 1183 | void SimSetup::calcSysValues( void ){
1183		tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1184		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1185		}
1186	<
1186	>
1187		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1188	<
1155	<	info->n_atoms = tot_atoms;
1156	<	info->n_bonds = tot_bonds;
1157	<	info->n_bends = tot_bends;
1158	<	info->n_torsions = tot_torsions;
1159	<	info->n_SRI = tot_SRI;
1160	<	info->n_mol = tot_nmol;
1188	>	molMembershipArray = new int[tot_atoms];
1189
1190	<	info->molMembershipArray = new int[tot_atoms];
1190	>	for(i=0; i<nInfo; i++){
1191	>	info[i].n_atoms = tot_atoms;
1192	>	info[i].n_bonds = tot_bonds;
1193	>	info[i].n_bends = tot_bends;
1194	>	info[i].n_torsions = tot_torsions;
1195	>	info[i].n_SRI = tot_SRI;
1196	>	info[i].n_mol = tot_nmol;
1197	>
1198	>	info[i].molMembershipArray = molMembershipArray;
1199	>	}
1200		}
1201
1165	–
1202		#ifdef IS_MPI
1203
1204		void SimSetup::mpiMolDivide( void ){
#	Line 1202 | Line 1238 | void SimSetup::mpiMolDivide( void ){
1238		localMol++;
1239		}
1240		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1241	<	info->molMembershipArray[globalAtomIndex] = allMol;
1241	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1242		globalAtomIndex++;
1243		}
1244
#	Line 1211 | Line 1247 | void SimSetup::mpiMolDivide( void ){
1247		}
1248		local_SRI = local_bonds + local_bends + local_torsions;
1249
1250	<	info->n_atoms = mpiSim->getMyNlocal();
1250	>	info[0].n_atoms = mpiSim->getMyNlocal();
1251
1252	<	if( local_atoms != info->n_atoms ){
1252	>	if( local_atoms != info[0].n_atoms ){
1253		sprintf( painCave.errMsg,
1254		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1255		" localAtom (%d) are not equal.\n",
1256	<	info->n_atoms,
1256	>	info[0].n_atoms,
1257		local_atoms );
1258		painCave.isFatal = 1;
1259		simError();
1260		}
1261
1262	<	info->n_bonds = local_bonds;
1263	<	info->n_bends = local_bends;
1264	<	info->n_torsions = local_torsions;
1265	<	info->n_SRI = local_SRI;
1266	<	info->n_mol = localMol;
1262	>	info[0].n_bonds = local_bonds;
1263	>	info[0].n_bends = local_bends;
1264	>	info[0].n_torsions = local_torsions;
1265	>	info[0].n_SRI = local_SRI;
1266	>	info[0].n_mol = localMol;
1267
1268		strcpy( checkPointMsg, "Passed nlocal consistency check." );
1269		MPIcheckPoint();
1270		}
1271	<
1271	>
1272		#endif // is_mpi
1273
1274
1275		void SimSetup::makeSysArrays( void ){
1276	<	int i, j, k;
1276	>	int i, j, k, l;
1277
1278	+	Atom** the_atoms;
1279	+	Molecule* the_molecules;
1280	+	Exclude** the_excludes;
1281
1243	–	// create the atom and short range interaction arrays
1244	–
1245	–	Atom::createArrays(info->n_atoms);
1246	–	the_atoms = new Atom*[info->n_atoms];
1247	–	the_molecules = new Molecule[info->n_mol];
1248	–	int molIndex;
1249	–
1250	–	// initialize the molecule's stampID's
1251	–
1252	–	#ifdef IS_MPI
1282
1283	+	for(l=0; l<nInfo; l++){
1284	+
1285	+	// create the atom and short range interaction arrays
1286	+
1287	+	the_atoms = new Atom*[info[l].n_atoms];
1288	+	the_molecules = new Molecule[info[l].n_mol];
1289	+	int molIndex;
1290
1291	<	molIndex = 0;
1256	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1291	>	// initialize the molecule's stampID's
1292
1293	<	if(mol2proc[i] == worldRank ){
1294	<	the_molecules[molIndex].setStampID( molCompType[i] );
1295	<	the_molecules[molIndex].setMyIndex( molIndex );
1296	<	the_molecules[molIndex].setGlobalIndex( i );
1297	<	molIndex++;
1293	>	#ifdef IS_MPI
1294	>
1295	>
1296	>	molIndex = 0;
1297	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1298	>
1299	>	if(mol2proc[i] == worldRank ){
1300	>	the_molecules[molIndex].setStampID( molCompType[i] );
1301	>	the_molecules[molIndex].setMyIndex( molIndex );
1302	>	the_molecules[molIndex].setGlobalIndex( i );
1303	>	molIndex++;
1304	>	}
1305		}
1306	<	}
1265	<
1306	>
1307		#else // is_mpi
1308	<
1309	<	molIndex = 0;
1310	<	globalAtomIndex = 0;
1311	<	for(i=0; i<n_components; i++){
1312	<	for(j=0; j<components_nmol[i]; j++ ){
1313	<	the_molecules[molIndex].setStampID( i );
1314	<	the_molecules[molIndex].setMyIndex( molIndex );
1315	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1316	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1317	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1318	<	globalAtomIndex++;
1308	>
1309	>	molIndex = 0;
1310	>	globalAtomIndex = 0;
1311	>	for(i=0; i<n_components; i++){
1312	>	for(j=0; j<components_nmol[i]; j++ ){
1313	>	the_molecules[molIndex].setStampID( i );
1314	>	the_molecules[molIndex].setMyIndex( molIndex );
1315	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1316	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1317	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1318	>	globalAtomIndex++;
1319	>	}
1320	>	molIndex++;
1321		}
1279	–	molIndex++;
1322		}
1281	–	}
1323
1324	<
1324	>
1325		#endif // is_mpi
1326
1327
1328	<	if( info->n_SRI ){
1328	>	if( info[l].n_SRI ){
1329
1330	<	Exclude::createArray(info->n_SRI);
1331	<	the_excludes = new Exclude*[info->n_SRI];
1332	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1333	<	info->globalExcludes = new int;
1334	<	info->n_exclude = info->n_SRI;
1335	<	}
1336	<	else{
1330	>	Exclude::createArray(info[l].n_SRI);
1331	>	the_excludes = new Exclude*[info[l].n_SRI];
1332	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1333	>	the_excludes[ex] = new Exclude(ex);
1334	>	}
1335	>	info[l].globalExcludes = new int;
1336	>	info[l].n_exclude = info[l].n_SRI;
1337	>	}
1338	>	else{
1339
1340	<	Exclude::createArray( 1 );
1341	<	the_excludes = new Exclude*;
1342	<	the_excludes[0] = new Exclude(0);
1343	<	the_excludes[0]->setPair( 0,0 );
1344	<	info->globalExcludes = new int;
1345	<	info->globalExcludes[0] = 0;
1346	<	info->n_exclude = 0;
1347	<	}
1340	>	Exclude::createArray( 1 );
1341	>	the_excludes = new Exclude*;
1342	>	the_excludes[0] = new Exclude(0);
1343	>	the_excludes[0]->setPair( 0,0 );
1344	>	info[l].globalExcludes = new int;
1345	>	info[l].globalExcludes[0] = 0;
1346	>	info[l].n_exclude = 0;
1347	>	}
1348
1349	<	// set the arrays into the SimInfo object
1349	>	// set the arrays into the SimInfo object
1350
1351	<	info->atoms = the_atoms;
1352	<	info->molecules = the_molecules;
1353	<	info->nGlobalExcludes = 0;
1354	<	info->excludes = the_excludes;
1351	>	info[l].atoms = the_atoms;
1352	>	info[l].molecules = the_molecules;
1353	>	info[l].nGlobalExcludes = 0;
1354	>	info[l].excludes = the_excludes;
1355
1356	<	the_ff->setSimInfo( info );
1357	<
1356	>	the_ff->setSimInfo( info );
1357	>
1358	>	}
1359		}
1360
1361		void SimSetup::makeIntegrator( void ){
1362
1363	+	int k;
1364	+
1365		NVT<RealIntegrator>*  myNVT = NULL;
1366		NPTi<RealIntegrator>* myNPTi = NULL;
1367		NPTf<RealIntegrator>* myNPTf = NULL;
#	Line 1328 | Line 1374 | void SimSetup::makeIntegrator( void ){
1374		ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1375		ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1376
1377	<	switch( ensembleCase ){
1332	<
1333	<	case NVE_ENS:
1334	<	new NVE<RealIntegrator>( info, the_ff );
1335	<	break;
1336	<
1337	<	case NVT_ENS:
1338	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1339	<	myNVT->setTargetTemp(globals->getTargetTemp());
1340	<
1341	<	if (globals->haveTauThermostat())
1342	<	myNVT->setTauThermostat(globals->getTauThermostat());
1343	<
1344	<	else {
1345	<	sprintf( painCave.errMsg,
1346	<	"SimSetup error: If you use the NVT\n"
1347	<	"    ensemble, you must set tauThermostat.\n");
1348	<	painCave.isFatal = 1;
1349	<	simError();
1350	<	}
1351	<	break;
1352	<
1353	<	case NPTi_ENS:
1354	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1355	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1356	<
1357	<	if (globals->haveTargetPressure())
1358	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1359	<	else {
1360	<	sprintf( painCave.errMsg,
1361	<	"SimSetup error: If you use a constant pressure\n"
1362	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1363	<	painCave.isFatal = 1;
1364	<	simError();
1365	<	}
1377	>	for(k=0; k<nInfo; k++){
1378
1379	<	if( globals->haveTauThermostat() )
1368	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1369	<	else{
1370	<	sprintf( painCave.errMsg,
1371	<	"SimSetup error: If you use an NPT\n"
1372	<	"    ensemble, you must set tauThermostat.\n");
1373	<	painCave.isFatal = 1;
1374	<	simError();
1375	<	}
1376	<
1377	<	if( globals->haveTauBarostat() )
1378	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1379	<	else{
1380	<	sprintf( painCave.errMsg,
1381	<	"SimSetup error: If you use an NPT\n"
1382	<	"    ensemble, you must set tauBarostat.\n");
1383	<	painCave.isFatal = 1;
1384	<	simError();
1385	<	}
1386	<	break;
1387	<
1388	<	case NPTf_ENS:
1389	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1390	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1391	<
1392	<	if (globals->haveTargetPressure())
1393	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1394	<	else {
1395	<	sprintf( painCave.errMsg,
1396	<	"SimSetup error: If you use a constant pressure\n"
1397	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1398	<	painCave.isFatal = 1;
1399	<	simError();
1400	<	}
1401	<
1402	<	if( globals->haveTauThermostat() )
1403	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1404	<	else{
1405	<	sprintf( painCave.errMsg,
1406	<	"SimSetup error: If you use an NPT\n"
1407	<	"    ensemble, you must set tauThermostat.\n");
1408	<	painCave.isFatal = 1;
1409	<	simError();
1410	<	}
1411	<
1412	<	if( globals->haveTauBarostat() )
1413	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1414	<	else{
1415	<	sprintf( painCave.errMsg,
1416	<	"SimSetup error: If you use an NPT\n"
1417	<	"    ensemble, you must set tauBarostat.\n");
1418	<	painCave.isFatal = 1;
1419	<	simError();
1420	<	}
1421	<	break;
1422	<
1423	<	case NPTim_ENS:
1424	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1425	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1426	<
1427	<	if (globals->haveTargetPressure())
1428	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1429	<	else {
1430	<	sprintf( painCave.errMsg,
1431	<	"SimSetup error: If you use a constant pressure\n"
1432	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1433	<	painCave.isFatal = 1;
1434	<	simError();
1435	<	}
1436	<
1437	<	if( globals->haveTauThermostat() )
1438	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1439	<	else{
1440	<	sprintf( painCave.errMsg,
1441	<	"SimSetup error: If you use an NPT\n"
1442	<	"    ensemble, you must set tauThermostat.\n");
1443	<	painCave.isFatal = 1;
1444	<	simError();
1445	<	}
1446	<
1447	<	if( globals->haveTauBarostat() )
1448	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1449	<	else{
1450	<	sprintf( painCave.errMsg,
1451	<	"SimSetup error: If you use an NPT\n"
1452	<	"    ensemble, you must set tauBarostat.\n");
1453	<	painCave.isFatal = 1;
1454	<	simError();
1455	<	}
1456	<	break;
1457	<
1458	<	case NPTfm_ENS:
1459	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1460	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1461	<
1462	<	if (globals->haveTargetPressure())
1463	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1464	<	else {
1465	<	sprintf( painCave.errMsg,
1466	<	"SimSetup error: If you use a constant pressure\n"
1467	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1468	<	painCave.isFatal = 1;
1469	<	simError();
1470	<	}
1471	<
1472	<	if( globals->haveTauThermostat() )
1473	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1474	<	else{
1475	<	sprintf( painCave.errMsg,
1476	<	"SimSetup error: If you use an NPT\n"
1477	<	"    ensemble, you must set tauThermostat.\n");
1478	<	painCave.isFatal = 1;
1479	<	simError();
1480	<	}
1481	<
1482	<	if( globals->haveTauBarostat() )
1483	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1484	<	else{
1485	<	sprintf( painCave.errMsg,
1486	<	"SimSetup error: If you use an NPT\n"
1487	<	"    ensemble, you must set tauBarostat.\n");
1488	<	painCave.isFatal = 1;
1489	<	simError();
1490	<	}
1491	<	break;
1492	<
1493	<	case NVEZCONS_ENS:
1494	<
1495	<
1496	<	//setup index of z-constraint molecules, z-constraint sampel time
1497	<	//and z-constraint force output name. These parameter should be known
1498	<	//before constructing the z-constraint integrator
1499	<	setupZConstraint();
1379	>	switch( ensembleCase ){
1380
1381	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1382	<
1383	<	break;
1504	<
1505	<
1506	<	case NVTZCONS_ENS:
1507	<
1508	<	setupZConstraint();
1509	<
1510	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1511	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1512	<
1513	<	if (globals->haveTauThermostat())
1514	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1515	<
1516	<	else {
1517	<	sprintf( painCave.errMsg,
1518	<	"SimSetup error: If you use the NVT\n"
1519	<	"    ensemble, you must set tauThermostat.\n");
1520	<	painCave.isFatal = 1;
1521	<	simError();
1522	<	}
1523	<	break;
1524	<
1525	<	case NPTiZCONS_ENS:
1526	<
1527	<	setupZConstraint();
1528	<
1529	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1530	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1531	<
1532	<	if (globals->haveTargetPressure())
1533	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1534	<	else {
1535	<	sprintf( painCave.errMsg,
1536	<	"SimSetup error: If you use a constant pressure\n"
1537	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1538	<	painCave.isFatal = 1;
1539	<	simError();
1540	<	}
1541	<
1542	<	if( globals->haveTauThermostat() )
1543	<	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1544	<	else{
1545	<	sprintf( painCave.errMsg,
1546	<	"SimSetup error: If you use an NPT\n"
1547	<	"    ensemble, you must set tauThermostat.\n");
1548	<	painCave.isFatal = 1;
1549	<	simError();
1550	<	}
1551	<
1552	<	if( globals->haveTauBarostat() )
1553	<	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1554	<	else{
1555	<	sprintf( painCave.errMsg,
1556	<	"SimSetup error: If you use an NPT\n"
1557	<	"    ensemble, you must set tauBarostat.\n");
1558	<	painCave.isFatal = 1;
1559	<	simError();
1560	<	}
1561	<
1562	<	break;
1563	<
1564	<	case NPTfZCONS_ENS:
1565	<
1566	<	setupZConstraint();
1567	<
1568	<	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1569	<	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1570	<
1571	<	if (globals->haveTargetPressure())
1572	<	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1573	<	else {
1574	<	sprintf( painCave.errMsg,
1575	<	"SimSetup error: If you use a constant pressure\n"
1576	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1577	<	painCave.isFatal = 1;
1578	<	simError();
1579	<	}
1580	<
1581	<	if( globals->haveTauThermostat() )
1582	<	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1583	<	else{
1584	<	sprintf( painCave.errMsg,
1585	<	"SimSetup error: If you use an NPT\n"
1586	<	"    ensemble, you must set tauThermostat.\n");
1587	<	painCave.isFatal = 1;
1588	<	simError();
1589	<	}
1590	<
1591	<	if( globals->haveTauBarostat() )
1592	<	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1593	<	else{
1594	<	sprintf( painCave.errMsg,
1595	<	"SimSetup error: If you use an NPT\n"
1596	<	"    ensemble, you must set tauBarostat.\n");
1597	<	painCave.isFatal = 1;
1598	<	simError();
1599	<	}
1600	<
1601	<	break;
1381	>	case NVE_ENS:
1382	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1383	>	break;
1384
1385	<	case NPTimZCONS_ENS:
1386	<
1387	<	setupZConstraint();
1388	<
1389	<	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1390	<	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1391	<
1392	<	if (globals->haveTargetPressure())
1393	<	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1394	<	else {
1395	<	sprintf( painCave.errMsg,
1396	<	"SimSetup error: If you use a constant pressure\n"
1397	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1398	<	painCave.isFatal = 1;
1399	<	simError();
1400	<	}
1401	<
1402	<	if( globals->haveTauThermostat() )
1403	<	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1404	<	else{
1405	<	sprintf( painCave.errMsg,
1406	<	"SimSetup error: If you use an NPT\n"
1385	>	case NVT_ENS:
1386	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1387	>	myNVT->setTargetTemp(globals->getTargetTemp());
1388	>
1389	>	if (globals->haveTauThermostat())
1390	>	myNVT->setTauThermostat(globals->getTauThermostat());
1391	>
1392	>	else {
1393	>	sprintf( painCave.errMsg,
1394	>	"SimSetup error: If you use the NVT\n"
1395	>	"    ensemble, you must set tauThermostat.\n");
1396	>	painCave.isFatal = 1;
1397	>	simError();
1398	>	}
1399	>	break;
1400	>
1401	>	case NPTi_ENS:
1402	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	>	else {
1408	>	sprintf( painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413	>	}
1414	>
1415	>	if( globals->haveTauThermostat() )
1416	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	>	else{
1418	>	sprintf( painCave.errMsg,
1419	>	"SimSetup error: If you use an NPT\n"
1420	>	"    ensemble, you must set tauThermostat.\n");
1421	>	painCave.isFatal = 1;
1422	>	simError();
1423	>	}
1424	>
1425	>	if( globals->haveTauBarostat() )
1426	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	>	else{
1428	>	sprintf( painCave.errMsg,
1429	>	"SimSetup error: If you use an NPT\n"
1430	>	"    ensemble, you must set tauBarostat.\n");
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433	>	}
1434	>	break;
1435	>
1436	>	case NPTf_ENS:
1437	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1438	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1439	>
1440	>	if (globals->haveTargetPressure())
1441	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	>	else {
1443	>	sprintf( painCave.errMsg,
1444	>	"SimSetup error: If you use a constant pressure\n"
1445	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1446	>	painCave.isFatal = 1;
1447	>	simError();
1448	>	}
1449	>
1450	>	if( globals->haveTauThermostat() )
1451	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1452	>	else{
1453	>	sprintf( painCave.errMsg,
1454	>	"SimSetup error: If you use an NPT\n"
1455		"    ensemble, you must set tauThermostat.\n");
1456	<	painCave.isFatal = 1;
1457	<	simError();
1458	<	}
1459	<
1460	<	if( globals->haveTauBarostat() )
1461	<	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1462	<	else{
1456	>	painCave.isFatal = 1;
1457	>	simError();
1458	>	}
1459	>
1460	>	if( globals->haveTauBarostat() )
1461	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1462	>	else{
1463	>	sprintf( painCave.errMsg,
1464	>	"SimSetup error: If you use an NPT\n"
1465	>	"    ensemble, you must set tauBarostat.\n");
1466	>	painCave.isFatal = 1;
1467	>	simError();
1468	>	}
1469	>	break;
1470	>
1471	>	case NPTim_ENS:
1472	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1473	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1474	>
1475	>	if (globals->haveTargetPressure())
1476	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1477	>	else {
1478	>	sprintf( painCave.errMsg,
1479	>	"SimSetup error: If you use a constant pressure\n"
1480	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1481	>	painCave.isFatal = 1;
1482	>	simError();
1483	>	}
1484	>
1485	>	if( globals->haveTauThermostat() )
1486	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1487	>	else{
1488	>	sprintf( painCave.errMsg,
1489	>	"SimSetup error: If you use an NPT\n"
1490	>	"    ensemble, you must set tauThermostat.\n");
1491	>	painCave.isFatal = 1;
1492	>	simError();
1493	>	}
1494	>
1495	>	if( globals->haveTauBarostat() )
1496	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1497	>	else{
1498		sprintf( painCave.errMsg,
1499		"SimSetup error: If you use an NPT\n"
1500		"    ensemble, you must set tauBarostat.\n");
1501		painCave.isFatal = 1;
1502		simError();
1503	<	}
1504	<
1505	<	break;
1506	<
1507	<	case NPTfmZCONS_ENS:
1508	<
1509	<	setupZConstraint();
1510	<
1511	<	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1512	<	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1513	<
1514	<	if (globals->haveTargetPressure())
1515	<	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1516	<	else {
1517	<	sprintf( painCave.errMsg,
1518	<	"SimSetup error: If you use a constant pressure\n"
1519	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1520	<	painCave.isFatal = 1;
1521	<	simError();
1522	<	}
1523	<
1524	<	if( globals->haveTauThermostat() )
1525	<	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1526	<	else{
1503	>	}
1504	>	break;
1505	>
1506	>	case NPTfm_ENS:
1507	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1508	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1509	>
1510	>	if (globals->haveTargetPressure())
1511	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1512	>	else {
1513	>	sprintf( painCave.errMsg,
1514	>	"SimSetup error: If you use a constant pressure\n"
1515	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1516	>	painCave.isFatal = 1;
1517	>	simError();
1518	>	}
1519	>
1520	>	if( globals->haveTauThermostat() )
1521	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1522	>	else{
1523	>	sprintf( painCave.errMsg,
1524	>	"SimSetup error: If you use an NPT\n"
1525	>	"    ensemble, you must set tauThermostat.\n");
1526	>	painCave.isFatal = 1;
1527	>	simError();
1528	>	}
1529	>
1530	>	if( globals->haveTauBarostat() )
1531	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1532	>	else{
1533	>	sprintf( painCave.errMsg,
1534	>	"SimSetup error: If you use an NPT\n"
1535	>	"    ensemble, you must set tauBarostat.\n");
1536	>	painCave.isFatal = 1;
1537	>	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();
1588	>	}
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	>
1610	>	break;
1611	>
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	>
1730	>	default:
1731		sprintf( painCave.errMsg,
1732	<	"SimSetup error: If you use an NPT\n"
1664	<	"    ensemble, you must set tauThermostat.\n");
1732	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1733		painCave.isFatal = 1;
1734		simError();
1735		}
1668	–
1669	–	if( globals->haveTauBarostat() )
1670	–	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1671	–	else{
1672	–	sprintf( painCave.errMsg,
1673	–	"SimSetup error: If you use an NPT\n"
1674	–	"    ensemble, you must set tauBarostat.\n");
1675	–	painCave.isFatal = 1;
1676	–	simError();
1677	–	}
1678	–	break;
1679	–
1680	–
1681	–
1682	–	default:
1683	–	sprintf( painCave.errMsg,
1684	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1685	–	painCave.isFatal = 1;
1686	–	simError();
1736		}
1688	–
1737		}
1738
1739		void SimSetup::initFortran( void ){
1740
1741	<	info->refreshSim();
1741	>	info[0].refreshSim();
1742
1743	<	if( !strcmp( info->mixingRule, "standard") ){
1743	>	if( !strcmp( info[0].mixingRule, "standard") ){
1744		the_ff->initForceField( LB_MIXING_RULE );
1745		}
1746	<	else if( !strcmp( info->mixingRule, "explicit") ){
1746	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1747		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1748		}
1749		else{
1750		sprintf( painCave.errMsg,
1751		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1752	<	info->mixingRule );
1752	>	info[0].mixingRule );
1753		painCave.isFatal = 1;
1754		simError();
1755		}
#	Line 1717 | Line 1765 | void SimSetup::setupZConstraint()
1765
1766		void SimSetup::setupZConstraint()
1767		{
1768	<	if(globals->haveZConsTime()){
1769	<
1770	<	//add sample time of z-constraint  into SimInfo's property list
1771	<	DoubleData* zconsTimeProp = new DoubleData();
1772	<	zconsTimeProp->setID("zconstime");
1725	<	zconsTimeProp->setData(globals->getZConsTime());
1726	<	info->addProperty(zconsTimeProp);
1727	<	}
1728	<	else{
1729	<	sprintf( painCave.errMsg,
1730	<	"ZConstraint error: If you use an ZConstraint\n"
1731	<	" , you must set sample time.\n");
1732	<	painCave.isFatal = 1;
1733	<	simError();
1734	<	}
1768	>	int k;
1769	>
1770	>	for(k=0; k<nInfo; k++){
1771	>
1772	>	if(globals->haveZConsTime()){
1773
1774	<	if(globals->haveIndexOfAllZConsMols()){
1774	>	//add sample time of z-constraint  into SimInfo's property list
1775	>	DoubleData* zconsTimeProp = new DoubleData();
1776	>	zconsTimeProp->setID("zconstime");
1777	>	zconsTimeProp->setData(globals->getZConsTime());
1778	>	info[k].addProperty(zconsTimeProp);
1779	>	}
1780	>	else{
1781	>	sprintf( painCave.errMsg,
1782	>	"ZConstraint error: If you use an ZConstraint\n"
1783	>	" , you must set sample time.\n");
1784	>	painCave.isFatal = 1;
1785	>	simError();
1786	>	}
1787	>
1788	>	if(globals->haveIndexOfAllZConsMols()){
1789
1790	<	//add index of z-constraint molecules into SimInfo's property list
1791	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1740	<
1741	<	//sort the index
1742	<	sort(tempIndex.begin(), tempIndex.end());
1743	<
1744	<	IndexData* zconsIndex = new IndexData();
1745	<	zconsIndex->setID("zconsindex");
1746	<	zconsIndex->setIndexData(tempIndex);
1747	<	info->addProperty(zconsIndex);
1748	<	}
1749	<	else{
1750	<	sprintf( painCave.errMsg,
1751	<	"SimSetup error: If you use an ZConstraint\n"
1752	<	" , you must set index of z-constraint molecules.\n");
1753	<	painCave.isFatal = 1;
1754	<	simError();
1790	>	//add index of z-constraint molecules into SimInfo's property list
1791	>	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1792
1793	+	//sort the index
1794	+	sort(tempIndex.begin(), tempIndex.end());
1795	+
1796	+	IndexData* zconsIndex = new IndexData();
1797	+	zconsIndex->setID("zconsindex");
1798	+	zconsIndex->setIndexData(tempIndex);
1799	+	info[k].addProperty(zconsIndex);
1800	+	}
1801	+	else{
1802	+	sprintf( painCave.errMsg,
1803	+	"SimSetup error: If you use an ZConstraint\n"
1804	+	" , you must set index of z-constraint molecules.\n");
1805	+	painCave.isFatal = 1;
1806	+	simError();
1807	+
1808	+	}
1809	+
1810	+	//Determine the name of ouput file and add it into SimInfo's property list
1811	+	//Be careful, do not use inFileName, since it is a pointer which
1812	+	//point to a string at master node, and slave nodes do not contain that string
1813	+
1814	+	string zconsOutput(info[k].finalName);
1815	+
1816	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1817	+
1818	+	StringData* zconsFilename = new StringData();
1819	+	zconsFilename->setID("zconsfilename");
1820	+	zconsFilename->setData(zconsOutput);
1821	+
1822	+	info[k].addProperty(zconsFilename);
1823		}
1757	–
1758	–	//Determine the name of ouput file and add it into SimInfo's property list
1759	–	//Be careful, do not use inFileName, since it is a pointer which
1760	–	//point to a string at master node, and slave nodes do not contain that string
1761	–
1762	–	string zconsOutput(info->finalName);
1763	–
1764	–	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1765	–
1766	–	StringData* zconsFilename = new StringData();
1767	–	zconsFilename->setID("zconsfilename");
1768	–	zconsFilename->setData(zconsOutput);
1769	–
1770	–	info->addProperty(zconsFilename);
1771	–
1824		}

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