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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 660 by tim, Thu Jul 31 19:59:34 2003 UTC vs.
Revision 689 by tim, Tue Aug 12 19:56:49 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 59 | Line 54 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
54		info = the_info;
55		nInfo = theNinfo;
56		isInfoArray = 1;
57	<	}
57	>	}
58
59
60		void SimSetup::parseFile( char* fileName ){
#	Line 97 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
97		int i, j, k, globalAtomIndex;
98
99		// gather all of the information from the Bass file
100	<
100	>
101	>	std::cerr << "gathering info\n";
102	>
103		gatherInfo();
104
105		// creation of complex system objects
106
107	+	std::cerr << "creating system objects\n";
108	+
109		sysObjectsCreation();
110
111		// check on the post processing info
112
113	+	std::cerr << "performing final info check.\n";
114	+
115		finalInfoCheck();
116
117		// initialize the system coordinates
118
119	<	initSystemCoords();
119	<
119	>	std::cerr << "about to init coords\n";
120
121	+	if( !isInfoArray ) initSystemCoords();
122	+
123		// make the output filenames
124
125		makeOutNames();
#	Line 141 | Line 143 | void SimSetup::makeMolecules( void ){
143
144		void SimSetup::makeMolecules( void ){
145
146	+	int k,l;
147		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
148		molInit molInfo;
149		DirectionalAtom* dAtom;
#	Line 165 | Line 168 | void SimSetup::makeMolecules( void ){
168
169		double ux, uy, uz, u, uSqr;
170
171	<	atomOffset = 0;
169	<	excludeOffset = 0;
170	<	for(i=0; i<info->n_mol; i++){
171	>	for(k=0; k<nInfo; k++){
172
173	<	stampID = the_molecules[i].getStampID();
173	>	the_ff->setSimInfo( &(info[k]) );
174
175	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
176	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
177	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
178	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
179	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
175	>	atomOffset = 0;
176	>	excludeOffset = 0;
177	>	for(i=0; i<info[k].n_mol; i++){
178	>
179	>	stampID = info[k].molecules[i].getStampID();
180
181	<	molInfo.myAtoms = &the_atoms[atomOffset];
182	<	molInfo.myExcludes = &the_excludes[excludeOffset];
183	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
184	<	molInfo.myBends = new Bend*[molInfo.nBends];
185	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
181	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
182	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
183	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
184	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
185	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
186	>
187	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
188	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
189	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
190	>	molInfo.myBends = new Bend*[molInfo.nBends];
191	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
192
193	<	theBonds = new bond_pair[molInfo.nBonds];
194	<	theBends = new bend_set[molInfo.nBends];
195	<	theTorsions = new torsion_set[molInfo.nTorsions];
193	>	theBonds = new bond_pair[molInfo.nBonds];
194	>	theBends = new bend_set[molInfo.nBends];
195	>	theTorsions = new torsion_set[molInfo.nTorsions];
196
197	<	// make the Atoms
197	>	// make the Atoms
198
199	<	for(j=0; j<molInfo.nAtoms; j++){
193	<
194	<	currentAtom = comp_stamps[stampID]->getAtom( j );
195	<	if( currentAtom->haveOrientation() ){
199	>	for(j=0; j<molInfo.nAtoms; j++){
200
201	<	dAtom = new DirectionalAtom(j + atomOffset);
202	<	info->n_oriented++;
203	<	molInfo.myAtoms[j] = dAtom;
204	<
205	<	ux = currentAtom->getOrntX();
206	<	uy = currentAtom->getOrntY();
207	<	uz = currentAtom->getOrntZ();
208	<
209	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
210	<
211	<	u = sqrt( uSqr );
212	<	ux = ux / u;
213	<	uy = uy / u;
214	<	uz = uz / u;
215	<
216	<	dAtom->setSUx( ux );
217	<	dAtom->setSUy( uy );
218	<	dAtom->setSUz( uz );
219	<	}
220	<	else{
221	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
222	<	}
223	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
201	>	currentAtom = comp_stamps[stampID]->getAtom( j );
202	>	if( currentAtom->haveOrientation() ){
203	>
204	>	dAtom = new DirectionalAtom( (j + atomOffset),
205	>	info[k].getConfiguration() );
206	>	info[k].n_oriented++;
207	>	molInfo.myAtoms[j] = dAtom;
208	>
209	>	ux = currentAtom->getOrntX();
210	>	uy = currentAtom->getOrntY();
211	>	uz = currentAtom->getOrntZ();
212	>
213	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
214	>
215	>	u = sqrt( uSqr );
216	>	ux = ux / u;
217	>	uy = uy / u;
218	>	uz = uz / u;
219	>
220	>	dAtom->setSUx( ux );
221	>	dAtom->setSUy( uy );
222	>	dAtom->setSUz( uz );
223	>	}
224	>	else{
225	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
226	>	info[k].getConfiguration() );
227	>	}
228	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
229
230		#ifdef IS_MPI
231
232	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
232	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
233
234		#endif // is_mpi
235	<	}
235	>	}
236
237		// make the bonds
238	<	for(j=0; j<molInfo.nBonds; j++){
238	>	for(j=0; j<molInfo.nBonds; j++){
239
240	<	currentBond = comp_stamps[stampID]->getBond( j );
241	<	theBonds[j].a = currentBond->getA() + atomOffset;
242	<	theBonds[j].b = currentBond->getB() + atomOffset;
243	<
244	<	exI = theBonds[j].a;
245	<	exJ = theBonds[j].b;
246	<
247	<	// exclude_I must always be the smaller of the pair
248	<	if( exI > exJ ){
249	<	tempEx = exI;
250	<	exI = exJ;
251	<	exJ = tempEx;
252	<	}
240	>	currentBond = comp_stamps[stampID]->getBond( j );
241	>	theBonds[j].a = currentBond->getA() + atomOffset;
242	>	theBonds[j].b = currentBond->getB() + atomOffset;
243	>
244	>	exI = theBonds[j].a;
245	>	exJ = theBonds[j].b;
246	>
247	>	// exclude_I must always be the smaller of the pair
248	>	if( exI > exJ ){
249	>	tempEx = exI;
250	>	exI = exJ;
251	>	exJ = tempEx;
252	>	}
253		#ifdef IS_MPI
254	<	tempEx = exI;
255	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
256	<	tempEx = exJ;
257	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
258	<
259	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
254	>	tempEx = exI;
255	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
256	>	tempEx = exJ;
257	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
258	>
259	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
260		#else  // isn't MPI
261	<
262	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
261	>
262	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
263		#endif  //is_mpi
264	<	}
265	<	excludeOffset += molInfo.nBonds;
257	<
258	<	//make the bends
259	<	for(j=0; j<molInfo.nBends; j++){
264	>	}
265	>	excludeOffset += molInfo.nBonds;
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;
267	>	//make the bends
268	>	for(j=0; j<molInfo.nBends; j++){
269	>
270	>	currentBend = comp_stamps[stampID]->getBend( j );
271	>	theBends[j].a = currentBend->getA() + atomOffset;
272	>	theBends[j].b = currentBend->getB() + atomOffset;
273	>	theBends[j].c = currentBend->getC() + atomOffset;
274	>
275	>	if( currentBend->haveExtras() ){
276
277	<	if( currentBend->haveExtras() ){
278	<
279	<	extras = currentBend->getExtras();
280	<	current_extra = extras;
281	<
282	<	while( current_extra != NULL ){
283	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
277	>	extras = currentBend->getExtras();
278	>	current_extra = extras;
279	>
280	>	while( current_extra != NULL ){
281	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
282	>
283	>	switch( current_extra->getType() ){
284
285	<	switch( current_extra->getType() ){
285	>	case 0:
286	>	theBends[j].ghost =
287	>	current_extra->getInt() + atomOffset;
288	>	theBends[j].isGhost = 1;
289	>	break;
290	>
291	>	case 1:
292	>	theBends[j].ghost =
293	>	(int)current_extra->getDouble() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296	>
297	>	default:
298	>	sprintf( painCave.errMsg,
299	>	"SimSetup Error: ghostVectorSource was neither a "
300	>	"double nor an int.\n"
301	>	"-->Bend[%d] in %s\n",
302	>	j, comp_stamps[stampID]->getID() );
303	>	painCave.isFatal = 1;
304	>	simError();
305	>	}
306	>	}
307	>
308	>	else{
309
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:
310		sprintf( painCave.errMsg,
311	<	"SimSetup Error: ghostVectorSource was neither a "
312	<	"double nor an int.\n"
313	<	"-->Bend[%d] in %s\n",
311	>	"SimSetup Error: unhandled bend assignment:\n"
312	>	"    -->%s in Bend[%d] in %s\n",
313	>	current_extra->getlhs(),
314		j, comp_stamps[stampID]->getID() );
315		painCave.isFatal = 1;
316		simError();
317		}
297	–	}
298	–
299	–	else{
318
319	<	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();
319	>	current_extra = current_extra->getNext();
320		}
321	+	}
322	+
323	+	if( !theBends[j].isGhost ){
324
325	<	current_extra = current_extra->getNext();
325	>	exI = theBends[j].a;
326	>	exJ = theBends[j].c;
327		}
328	<	}
328	>	else{
329
330	<	if( !theBends[j].isGhost ){
331	<
332	<	exI = theBends[j].a;
317	<	exJ = theBends[j].c;
318	<	}
319	<	else{
330	>	exI = theBends[j].a;
331	>	exJ = theBends[j].b;
332	>	}
333
334	<	exI = theBends[j].a;
335	<	exJ = theBends[j].b;
336	<	}
337	<
338	<	// exclude_I must always be the smaller of the pair
339	<	if( exI > exJ ){
334	>	// exclude_I must always be the smaller of the pair
335	>	if( exI > exJ ){
336	>	tempEx = exI;
337	>	exI = exJ;
338	>	exJ = tempEx;
339	>	}
340	>	#ifdef IS_MPI
341		tempEx = exI;
342	<	exI = exJ;
343	<	exJ = tempEx;
342	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	>	tempEx = exJ;
344	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>
346	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
347	>	#else  // isn't MPI
348	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349	>	#endif  //is_mpi
350		}
351	<	#ifdef IS_MPI
332	<	tempEx = exI;
333	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
334	<	tempEx = exJ;
335	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
351	>	excludeOffset += molInfo.nBends;
352
353	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
353	>	for(j=0; j<molInfo.nTorsions; j++){
354	>
355	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360	>
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363	>
364	>	// exclude_I must always be the smaller of the pair
365	>	if( exI > exJ ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370	>	#ifdef IS_MPI
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>
376	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
377		#else  // isn't MPI
378	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
378	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
379		#endif  //is_mpi
380	<	}
381	<	excludeOffset += molInfo.nBends;
343	<
344	<	for(j=0; j<molInfo.nTorsions; j++){
380	>	}
381	>	excludeOffset += molInfo.nTorsions;
382
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;
383
384	<	exI = theTorsions[j].a;
385	<	exJ = theTorsions[j].d;
384	>	// send the arrays off to the forceField for init.
385	>
386	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
387	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
388	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
389	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
390	>
391	>
392	>	info[k].molecules[i].initialize( molInfo );
393
355	–	// exclude_I must always be the smaller of the pair
356	–	if( exI > exJ ){
357	–	tempEx = exI;
358	–	exI = exJ;
359	–	exJ = tempEx;
360	–	}
361	–	#ifdef IS_MPI
362	–	tempEx = exI;
363	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
364	–	tempEx = exJ;
365	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
394
395	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
396	<	#else  // isn't MPI
397	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
398	<	#endif  //is_mpi
395	>	atomOffset += molInfo.nAtoms;
396	>	delete[] theBonds;
397	>	delete[] theBends;
398	>	delete[] theTorsions;
399		}
400	<	excludeOffset += molInfo.nTorsions;
401	<
374	<
375	<	// send the arrays off to the forceField for init.
376	<
377	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	<	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;
390	<	}
391	<
400	>	}
401	>
402		#ifdef IS_MPI
403		sprintf( checkPointMsg, "all molecules initialized succesfully" );
404		MPIcheckPoint();
405		#endif // is_mpi
406	<
406	>
407		// clean up the forcefield
408	+
409		the_ff->calcRcut();
410		the_ff->cleanMe();
411	<
411	>
412		}
413
414		void SimSetup::initFromBass( void ){
#	Line 410 | Line 421 | void SimSetup::initFromBass( void ){
421		int n_extra;
422		int have_extra, done;
423
424	+	double vel[3];
425	+	vel[0] = 0.0;
426	+	vel[1] = 0.0;
427	+	vel[2] = 0.0;
428	+
429		temp1 = (double)tot_nmol / 4.0;
430		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
431		temp3 = ceil( temp2 );
#	Line 419 | Line 435 | void SimSetup::initFromBass( void ){
435		have_extra =1;
436
437		n_cells = (int)temp3 - 1;
438	<	cellx = info->boxL[0] / temp3;
439	<	celly = info->boxL[1] / temp3;
440	<	cellz = info->boxL[2] / temp3;
438	>	cellx = info[0].boxL[0] / temp3;
439	>	celly = info[0].boxL[1] / temp3;
440	>	cellz = info[0].boxL[2] / temp3;
441		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
442		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
443		n_per_extra = (int)ceil( temp1 );
#	Line 436 | Line 452 | void SimSetup::initFromBass( void ){
452		}
453		else{
454		n_cells = (int)temp3;
455	<	cellx = info->boxL[0] / temp3;
456	<	celly = info->boxL[1] / temp3;
457	<	cellz = info->boxL[2] / temp3;
455	>	cellx = info[0].boxL[0] / temp3;
456	>	celly = info[0].boxL[1] / temp3;
457	>	cellz = info[0].boxL[2] / temp3;
458		}
459
460		current_mol = 0;
#	Line 517 | Line 533 | void SimSetup::initFromBass( void ){
533		}
534		}
535
536	<
537	<	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 );
536	>	for( i=0; i<info[0].n_atoms; i++ ){
537	>	info[0].atoms[i]->setVel( vel );
538		}
539		}
540
#	Line 531 | Line 544 | void SimSetup::makeElement( double x, double y, double
544		AtomStamp* current_atom;
545		DirectionalAtom* dAtom;
546		double rotMat[3][3];
547	+	double pos[3];
548
549		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
550
#	Line 546 | Line 560 | void SimSetup::makeElement( double x, double y, double
560		painCave.isFatal = 1;
561		simError();
562		}
563	+
564	+	pos[0] = x + current_atom->getPosX();
565	+	pos[1] = y + current_atom->getPosY();
566	+	pos[2] = z + current_atom->getPosZ();
567	+
568	+	info[0].atoms[current_atom_ndx]->setPos( pos );
569
570	<	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() );
553	<
554	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
570	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
571
572	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
572	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
573
574		rotMat[0][0] = 1.0;
575		rotMat[0][1] = 0.0;
#	Line 590 | Line 606 | void SimSetup::gatherInfo( void ){
606		ensembleCase = -1;
607		ffCase = -1;
608
593	–	// get the stamps and globals;
594	–	stamps = stamps;
595	–	globals = globals;
596	–
609		// set the easy ones first
610	<	info->target_temp = globals->getTargetTemp();
611	<	info->dt = globals->getDt();
612	<	info->run_time = globals->getRunTime();
610	>
611	>	for( i=0; i<nInfo; i++){
612	>	info[i].target_temp = globals->getTargetTemp();
613	>	info[i].dt = globals->getDt();
614	>	info[i].run_time = globals->getRunTime();
615	>	}
616		n_components = globals->getNComponents();
617
618
#	Line 627 | Line 642 | void SimSetup::gatherInfo( void ){
642		else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
643		else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
644		else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
630	–
631	–	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
632	–	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
633	–	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT"))
634	–	ensembleCase = NPTiZCONS_ENS;
635	–	else if( !strcasecmp( ensemble, "NPTfCONS"))  ensembleCase = NPTfZCONS_ENS;
636	–	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637	–	else if( !strcasecmp( ensemble, "NPTfmCONS"))  ensembleCase = NPTfmZCONS_ENS;
638	–
645		else{
646		sprintf( painCave.errMsg,
647		"SimSetup Warning. Unrecognized Ensemble -> %s, "
#	Line 646 | Line 652 | void SimSetup::gatherInfo( void ){
652		strcpy( ensemble, "NVE" );
653		ensembleCase = NVE_ENS;
654		}
655	<	strcpy( info->ensemble, ensemble );
655	>
656	>	for(i=0; i<nInfo; i++){
657	>
658	>	strcpy( info[i].ensemble, ensemble );
659
660	<	// get the mixing rule
660	>	// get the mixing rule
661
662	<	strcpy( info->mixingRule, globals->getMixingRule() );
663	<	info->usePBC = globals->getPBC();
664	<
662	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
663	>	info[i].usePBC = globals->getPBC();
664	>	}
665
666		// get the components and calculate the tot_nMol and indvidual n_mol
667
#	Line 693 | Line 702 | void SimSetup::gatherInfo( void ){
702
703		// set the status, sample, and thermal kick times
704
705	<	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	<	}
706	<
707	<	if( globals->haveStatusTime() ){
708	<	info->statusTime = globals->getStatusTime();
709	<	}
705	>	for(i=0; i<nInfo; i++){
706
707	<	if( globals->haveThermalTime() ){
708	<	info->thermalTime = globals->getThermalTime();
709	<	}
710	<
711	<	// check for the temperature set flag
712	<
713	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
714	<
715	<	// get some of the tricky things that may still be in the globals
716	<
721	<	double boxVector[3];
722	<	if( globals->haveBox() ){
723	<	boxVector[0] = globals->getBox();
724	<	boxVector[1] = globals->getBox();
725	<	boxVector[2] = globals->getBox();
707	>	if( globals->haveSampleTime() ){
708	>	info[i].sampleTime = globals->getSampleTime();
709	>	info[i].statusTime = info[i].sampleTime;
710	>	info[i].thermalTime = info[i].sampleTime;
711	>	}
712	>	else{
713	>	info[i].sampleTime = globals->getRunTime();
714	>	info[i].statusTime = info[i].sampleTime;
715	>	info[i].thermalTime = info[i].sampleTime;
716	>	}
717
718	<	info->setBox( boxVector );
719	<	}
729	<	else if( globals->haveDensity() ){
730	<
731	<	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];
736	<
737	<	info->setBox( boxVector );
738	<	}
739	<	else{
740	<	if( !globals->haveBoxX() ){
741	<	sprintf( painCave.errMsg,
742	<	"SimSetup error, no periodic BoxX size given.\n" );
743	<	painCave.isFatal = 1;
744	<	simError();
718	>	if( globals->haveStatusTime() ){
719	>	info[i].statusTime = globals->getStatusTime();
720		}
721	<	boxVector[0] = globals->getBoxX();
722	<
723	<	if( !globals->haveBoxY() ){
749	<	sprintf( painCave.errMsg,
750	<	"SimSetup error, no periodic BoxY size given.\n" );
751	<	painCave.isFatal = 1;
752	<	simError();
721	>
722	>	if( globals->haveThermalTime() ){
723	>	info[i].thermalTime = globals->getThermalTime();
724		}
754	–	boxVector[1] = globals->getBoxY();
725
726	<	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();
726	>	// check for the temperature set flag
727
728	<	info->setBox( boxVector );
728	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
729	>
730	>	// get some of the tricky things that may still be in the globals
731	>
732	>	double boxVector[3];
733	>	if( globals->haveBox() ){
734	>	boxVector[0] = globals->getBox();
735	>	boxVector[1] = globals->getBox();
736	>	boxVector[2] = globals->getBox();
737	>
738	>	info[i].setBox( boxVector );
739	>	}
740	>	else if( globals->haveDensity() ){
741	>
742	>	double vol;
743	>	vol = (double)tot_nmol / globals->getDensity();
744	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
745	>	boxVector[1] = boxVector[0];
746	>	boxVector[2] = boxVector[0];
747	>
748	>	info[i].setBox( boxVector );
749		}
750	+	else{
751	+	if( !globals->haveBoxX() ){
752	+	sprintf( painCave.errMsg,
753	+	"SimSetup error, no periodic BoxX size given.\n" );
754	+	painCave.isFatal = 1;
755	+	simError();
756	+	}
757	+	boxVector[0] = globals->getBoxX();
758	+
759	+	if( !globals->haveBoxY() ){
760	+	sprintf( painCave.errMsg,
761	+	"SimSetup error, no periodic BoxY size given.\n" );
762	+	painCave.isFatal = 1;
763	+	simError();
764	+	}
765	+	boxVector[1] = globals->getBoxY();
766	+
767	+	if( !globals->haveBoxZ() ){
768	+	sprintf( painCave.errMsg,
769	+	"SimSetup error, no periodic BoxZ size given.\n" );
770	+	painCave.isFatal = 1;
771	+	simError();
772	+	}
773	+	boxVector[2] = globals->getBoxZ();
774	+
775	+	info[i].setBox( boxVector );
776	+	}
777
778	<
778	>	}
779
780		#ifdef IS_MPI
781		strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
#	Line 777 | Line 788 | void SimSetup::finalInfoCheck( void ){
788		void SimSetup::finalInfoCheck( void ){
789		int index;
790		int usesDipoles;
791	<
791	>	int i;
792
793	<	// check electrostatic parameters
794	<
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;
793	>	for(i=0; i<nInfo; i++){
794	>	// check electrostatic parameters
795
796	<	if( !globals->haveECR() ){
797	<	sprintf( painCave.errMsg,
798	<	"SimSetup Warning: using default value of 1/2 the smallest "
799	<	"box length for the electrostaticCutoffRadius.\n"
800	<	"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();
796	>	index = 0;
797	>	usesDipoles = 0;
798	>	while( (index < info[i].n_atoms) && !usesDipoles ){
799	>	usesDipoles = (info[i].atoms[index])->hasDipole();
800	>	index++;
801		}
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 );
802
803	<	if(!globals->haveDielectric() ){
804	<	sprintf( painCave.errMsg,
805	<	"SimSetup Error: You are trying to use Reaction Field without"
806	<	"setting a dielectric constant!\n"
807	<	);
808	<	painCave.isFatal = 1;
809	<	simError();
810	<	}
811	<	info->dielectric = globals->getDielectric();
840	<	}
841	<	else {
842	<	if (usesDipoles) {
803	>	#ifdef IS_MPI
804	>	int myUse = usesDipoles;
805	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
806	>	#endif //is_mpi
807	>
808	>	double theEcr, theEst;
809	>
810	>	if (globals->getUseRF() ) {
811	>	info[i].useReactionField = 1;
812
813		if( !globals->haveECR() ){
814		sprintf( painCave.errMsg,
#	Line 849 | Line 818 | void SimSetup::finalInfoCheck( void ){
818		painCave.isFatal = 0;
819		simError();
820		double smallest;
821	<	smallest = info->boxL[0];
822	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
823	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
821	>	smallest = info[i].boxL[0];
822	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
823	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
824		theEcr = 0.5 * smallest;
825		} else {
826		theEcr = globals->getECR();
#	Line 860 | Line 829 | void SimSetup::finalInfoCheck( void ){
829		if( !globals->haveEST() ){
830		sprintf( painCave.errMsg,
831		"SimSetup Warning: using default value of 0.05 * the "
832	<	"electrostaticCutoffRadius for the "
864	<	"electrostaticSkinThickness\n"
832	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
833		);
834		painCave.isFatal = 0;
835		simError();
#	Line 869 | Line 837 | void SimSetup::finalInfoCheck( void ){
837		} else {
838		theEst= globals->getEST();
839		}
840	<
841	<	info->setEcr( theEcr, theEst );
842	<	}
843	<	}
840	>
841	>	info[i].setEcr( theEcr, theEst );
842	>
843	>	if(!globals->haveDielectric() ){
844	>	sprintf( painCave.errMsg,
845	>	"SimSetup Error: You are trying to use Reaction Field without"
846	>	"setting a dielectric constant!\n"
847	>	);
848	>	painCave.isFatal = 1;
849	>	simError();
850	>	}
851	>	info[i].dielectric = globals->getDielectric();
852	>	}
853	>	else {
854	>	if (usesDipoles) {
855	>
856	>	if( !globals->haveECR() ){
857	>	sprintf( painCave.errMsg,
858	>	"SimSetup Warning: using default value of 1/2 the smallest "
859	>	"box length for the electrostaticCutoffRadius.\n"
860	>	"I hope you have a very fast processor!\n");
861	>	painCave.isFatal = 0;
862	>	simError();
863	>	double smallest;
864	>	smallest = info[i].boxL[0];
865	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
866	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
867	>	theEcr = 0.5 * smallest;
868	>	} else {
869	>	theEcr = globals->getECR();
870	>	}
871	>
872	>	if( !globals->haveEST() ){
873	>	sprintf( painCave.errMsg,
874	>	"SimSetup Warning: using default value of 0.05 * the "
875	>	"electrostaticCutoffRadius for the "
876	>	"electrostaticSkinThickness\n"
877	>	);
878	>	painCave.isFatal = 0;
879	>	simError();
880	>	theEst = 0.05 * theEcr;
881	>	} else {
882	>	theEst= globals->getEST();
883	>	}
884	>
885	>	info[i].setEcr( theEcr, theEst );
886	>	}
887	>	}
888	>	}
889
890		#ifdef IS_MPI
891		strcpy( checkPointMsg, "post processing checks out" );
#	Line 882 | Line 895 | void SimSetup::initSystemCoords( void ){
895		}
896
897		void SimSetup::initSystemCoords( void ){
898	+	int i;
899	+
900	+	char* inName;
901
902	<	if( globals->haveInitialConfig() ){
903	<
904	<	InitializeFromFile* fileInit;
902	>	std::cerr << "Setting atom Coords\n";
903	>
904	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
905	>
906	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
907	>
908	>	if( globals->haveInitialConfig() ){
909	>
910	>	InitializeFromFile* fileInit;
911		#ifdef IS_MPI // is_mpi
912	<	if( worldRank == 0 ){
912	>	if( worldRank == 0 ){
913		#endif //is_mpi
914	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
914	>	inName = globals->getInitialConfig();
915	>	fileInit = new InitializeFromFile( inName );
916		#ifdef IS_MPI
917	<	}else fileInit = new InitializeFromFile( NULL );
917	>	}else fileInit = new InitializeFromFile( NULL );
918		#endif
919	<	fileInit->readInit( info ); // default velocities on
920	<
921	<	delete fileInit;
922	<	}
923	<	else{
924	<
919	>	fileInit->readInit( info ); // default velocities on
920	>
921	>	delete fileInit;
922	>	}
923	>	else{
924	>
925		#ifdef IS_MPI
926	<
927	<	// no init from bass
928	<
929	<	sprintf( painCave.errMsg,
930	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
931	<	painCave.isFatal;
932	<	simError();
933	<
926	>
927	>	// no init from bass
928	>
929	>	sprintf( painCave.errMsg,
930	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
931	>	painCave.isFatal;
932	>	simError();
933	>
934		#else
935	<
936	<	initFromBass();
937	<
938	<
935	>
936	>	initFromBass();
937	>
938	>
939		#endif
940	<	}
941	<
940	>	}
941	>
942		#ifdef IS_MPI
943		strcpy( checkPointMsg, "Successfully read in the initial configuration" );
944		MPIcheckPoint();
945		#endif // is_mpi
946	<
946	>
947		}
948
949
950		void SimSetup::makeOutNames( void ){
951	+
952	+	int k;
953
954	+
955	+	for(k=0; k<nInfo; k++){
956	+
957		#ifdef IS_MPI
958	<	if( worldRank == 0 ){
958	>	if( worldRank == 0 ){
959		#endif // is_mpi
960	<
961	<	if( globals->haveFinalConfig() ){
962	<	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" );
960	>
961	>	if( globals->haveFinalConfig() ){
962	>	strcpy( info[k].finalName, globals->getFinalConfig() );
963		}
944	–	else if( !strcmp( endTest, ".BASS" ) ){
945	–	strcpy( endTest, ".eor" );
946	–	}
964		else{
965	<	endTest = &(info->finalName[nameLength - 4]);
966	<	if( !strcmp( endTest, ".bss" ) ){
965	>	strcpy( info[k].finalName, inFileName );
966	>	char* endTest;
967	>	int nameLength = strlen( info[k].finalName );
968	>	endTest = &(info[k].finalName[nameLength - 5]);
969	>	if( !strcmp( endTest, ".bass" ) ){
970		strcpy( endTest, ".eor" );
971		}
972	<	else if( !strcmp( endTest, ".mdl" ) ){
972	>	else if( !strcmp( endTest, ".BASS" ) ){
973		strcpy( endTest, ".eor" );
974		}
975		else{
976	<	strcat( info->finalName, ".eor" );
976	>	endTest = &(info[k].finalName[nameLength - 4]);
977	>	if( !strcmp( endTest, ".bss" ) ){
978	>	strcpy( endTest, ".eor" );
979	>	}
980	>	else if( !strcmp( endTest, ".mdl" ) ){
981	>	strcpy( endTest, ".eor" );
982	>	}
983	>	else{
984	>	strcat( info[k].finalName, ".eor" );
985	>	}
986		}
987		}
988	<	}
989	<
990	<	// make the sample and status out names
991	<
992	<	strcpy( info->sampleName, inFileName );
993	<	char* endTest;
994	<	int nameLength = strlen( info->sampleName );
995	<	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" ) ){
988	>
989	>	// make the sample and status out names
990	>
991	>	strcpy( info[k].sampleName, inFileName );
992	>	char* endTest;
993	>	int nameLength = strlen( info[k].sampleName );
994	>	endTest = &(info[k].sampleName[nameLength - 5]);
995	>	if( !strcmp( endTest, ".bass" ) ){
996		strcpy( endTest, ".dump" );
997		}
998	<	else if( !strcmp( endTest, ".mdl" ) ){
998	>	else if( !strcmp( endTest, ".BASS" ) ){
999		strcpy( endTest, ".dump" );
1000		}
1001		else{
1002	<	strcat( info->sampleName, ".dump" );
1002	>	endTest = &(info[k].sampleName[nameLength - 4]);
1003	>	if( !strcmp( endTest, ".bss" ) ){
1004	>	strcpy( endTest, ".dump" );
1005	>	}
1006	>	else if( !strcmp( endTest, ".mdl" ) ){
1007	>	strcpy( endTest, ".dump" );
1008	>	}
1009	>	else{
1010	>	strcat( info[k].sampleName, ".dump" );
1011	>	}
1012		}
1013	<	}
1014	<
1015	<	strcpy( info->statusName, inFileName );
1016	<	nameLength = strlen( info->statusName );
1017	<	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" ) ){
1013	>
1014	>	strcpy( info[k].statusName, inFileName );
1015	>	nameLength = strlen( info[k].statusName );
1016	>	endTest = &(info[k].statusName[nameLength - 5]);
1017	>	if( !strcmp( endTest, ".bass" ) ){
1018		strcpy( endTest, ".stat" );
1019		}
1020	<	else if( !strcmp( endTest, ".mdl" ) ){
1020	>	else if( !strcmp( endTest, ".BASS" ) ){
1021		strcpy( endTest, ".stat" );
1022		}
1023		else{
1024	<	strcat( info->statusName, ".stat" );
1024	>	endTest = &(info[k].statusName[nameLength - 4]);
1025	>	if( !strcmp( endTest, ".bss" ) ){
1026	>	strcpy( endTest, ".stat" );
1027	>	}
1028	>	else if( !strcmp( endTest, ".mdl" ) ){
1029	>	strcpy( endTest, ".stat" );
1030	>	}
1031	>	else{
1032	>	strcat( info[k].statusName, ".stat" );
1033	>	}
1034		}
1035	<	}
1007	<
1035	>
1036		#ifdef IS_MPI
1037	<	}
1037	>	}
1038		#endif // is_mpi
1039	<
1039	>	}
1040		}
1041
1042
1043		void SimSetup::sysObjectsCreation( void ){
1044	<
1045	<	int i;
1046	<
1044	>
1045	>	int i,k;
1046	>
1047		// create the forceField
1048
1049		createFF();
#	Line 1035 | Line 1063 | void SimSetup::sysObjectsCreation( void ){
1063		#endif //is_mpi
1064
1065		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1066	<
1066	>
1067		makeSysArrays();
1068
1069		// make and initialize the molecules (all but atomic coordinates)
1070	<
1070	>
1071		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	–	}
1072
1073	<
1074	<
1073	>	for(k=0; k<nInfo; k++){
1074	>	info[k].identArray = new int[info[k].n_atoms];
1075	>	for(i=0; i<info[k].n_atoms; i++){
1076	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1077	>	}
1078	>	}
1079		}
1080
1081
#	Line 1085 | Line 1113 | void SimSetup::compList( void ){
1113		void SimSetup::compList( void ){
1114
1115		int i;
1116	<
1116	>	char* id;
1117	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1118	>	LinkedMolStamp* currentStamp = NULL;
1119		comp_stamps = new MoleculeStamp*[n_components];
1120	<
1120	>
1121		// make an array of molecule stamps that match the components used.
1122		// 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();
1123
1124	<	char* id;
1125	<	LinkedMolStamp* headStamp = info->headStamp;
1126	<	LinkedMolStamp* currentStamp = NULL;
1124	>	for(i=0; i<nInfo; i++){
1125	>	info[i].nComponents = n_components;
1126	>	info[i].componentsNmol = components_nmol;
1127	>	info[i].compStamps = comp_stamps;
1128	>	info[i].headStamp = headStamp;
1129	>	}
1130	>
1131	>
1132		for( i=0; i<n_components; i++ ){
1133
1134		id = the_components[i]->getType();
#	Line 1136 | Line 1166 | void SimSetup::calcSysValues( void ){
1166
1167		void SimSetup::calcSysValues( void ){
1168		int i, j, k;
1169	<
1170	<
1169	>
1170	>	int *molMembershipArray;
1171	>
1172		tot_atoms = 0;
1173		tot_bonds = 0;
1174		tot_bends = 0;
#	Line 1149 | Line 1180 | void SimSetup::calcSysValues( void ){
1180		tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1181		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182		}
1183	<
1183	>
1184		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	<
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;
1185	>	molMembershipArray = new int[tot_atoms];
1186
1187	<	info->molMembershipArray = new int[tot_atoms];
1187	>	for(i=0; i<nInfo; i++){
1188	>	info[i].n_atoms = tot_atoms;
1189	>	info[i].n_bonds = tot_bonds;
1190	>	info[i].n_bends = tot_bends;
1191	>	info[i].n_torsions = tot_torsions;
1192	>	info[i].n_SRI = tot_SRI;
1193	>	info[i].n_mol = tot_nmol;
1194	>
1195	>	info[i].molMembershipArray = molMembershipArray;
1196	>	}
1197		}
1198
1165	–
1199		#ifdef IS_MPI
1200
1201		void SimSetup::mpiMolDivide( void ){
#	Line 1202 | Line 1235 | void SimSetup::mpiMolDivide( void ){
1235		localMol++;
1236		}
1237		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1238	<	info->molMembershipArray[globalAtomIndex] = allMol;
1238	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1239		globalAtomIndex++;
1240		}
1241
#	Line 1211 | Line 1244 | void SimSetup::mpiMolDivide( void ){
1244		}
1245		local_SRI = local_bonds + local_bends + local_torsions;
1246
1247	<	info->n_atoms = mpiSim->getMyNlocal();
1247	>	info[0].n_atoms = mpiSim->getMyNlocal();
1248
1249	<	if( local_atoms != info->n_atoms ){
1249	>	if( local_atoms != info[0].n_atoms ){
1250		sprintf( painCave.errMsg,
1251		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1252		" localAtom (%d) are not equal.\n",
1253	<	info->n_atoms,
1253	>	info[0].n_atoms,
1254		local_atoms );
1255		painCave.isFatal = 1;
1256		simError();
1257		}
1258
1259	<	info->n_bonds = local_bonds;
1260	<	info->n_bends = local_bends;
1261	<	info->n_torsions = local_torsions;
1262	<	info->n_SRI = local_SRI;
1263	<	info->n_mol = localMol;
1259	>	info[0].n_bonds = local_bonds;
1260	>	info[0].n_bends = local_bends;
1261	>	info[0].n_torsions = local_torsions;
1262	>	info[0].n_SRI = local_SRI;
1263	>	info[0].n_mol = localMol;
1264
1265		strcpy( checkPointMsg, "Passed nlocal consistency check." );
1266		MPIcheckPoint();
1267		}
1268	<
1268	>
1269		#endif // is_mpi
1270
1271
1272		void SimSetup::makeSysArrays( void ){
1273	<	int i, j, k;
1273	>	int i, j, k, l;
1274
1275	+	Atom** the_atoms;
1276	+	Molecule* the_molecules;
1277	+	Exclude** the_excludes;
1278
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
1279
1280	<
1255	<	molIndex = 0;
1256	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1280	>	for(l=0; l<nInfo; l++){
1281
1282	<	if(mol2proc[i] == worldRank ){
1259	<	the_molecules[molIndex].setStampID( molCompType[i] );
1260	<	the_molecules[molIndex].setMyIndex( molIndex );
1261	<	the_molecules[molIndex].setGlobalIndex( i );
1262	<	molIndex++;
1263	<	}
1264	<	}
1265	<
1266	<	#else // is_mpi
1267	<
1268	<	molIndex = 0;
1269	<	globalAtomIndex = 0;
1270	<	for(i=0; i<n_components; i++){
1271	<	for(j=0; j<components_nmol[i]; j++ ){
1272	<	the_molecules[molIndex].setStampID( i );
1273	<	the_molecules[molIndex].setMyIndex( molIndex );
1274	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1275	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1276	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1277	<	globalAtomIndex++;
1278	<	}
1279	<	molIndex++;
1280	<	}
1281	<	}
1282	>	// create the atom and short range interaction arrays
1283
1284	+	the_atoms = new Atom*[info[l].n_atoms];
1285	+	the_molecules = new Molecule[info[l].n_mol];
1286	+	int molIndex;
1287
1288	+	// initialize the molecule's stampID's
1289	+
1290	+	#ifdef IS_MPI
1291	+
1292	+
1293	+	molIndex = 0;
1294	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1295	+
1296	+	if(mol2proc[i] == worldRank ){
1297	+	the_molecules[molIndex].setStampID( molCompType[i] );
1298	+	the_molecules[molIndex].setMyIndex( molIndex );
1299	+	the_molecules[molIndex].setGlobalIndex( i );
1300	+	molIndex++;
1301	+	}
1302	+	}
1303	+
1304	+	#else // is_mpi
1305	+
1306	+	molIndex = 0;
1307	+	globalAtomIndex = 0;
1308	+	for(i=0; i<n_components; i++){
1309	+	for(j=0; j<components_nmol[i]; j++ ){
1310	+	the_molecules[molIndex].setStampID( i );
1311	+	the_molecules[molIndex].setMyIndex( molIndex );
1312	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1313	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1314	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1315	+	globalAtomIndex++;
1316	+	}
1317	+	molIndex++;
1318	+	}
1319	+	}
1320	+
1321	+
1322		#endif // is_mpi
1323
1324
1325	<	if( info->n_SRI ){
1325	>	if( info[l].n_SRI ){
1326
1327	<	Exclude::createArray(info->n_SRI);
1328	<	the_excludes = new Exclude*[info->n_SRI];
1329	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1330	<	info->globalExcludes = new int;
1331	<	info->n_exclude = info->n_SRI;
1332	<	}
1333	<	else{
1327	>	Exclude::createArray(info[l].n_SRI);
1328	>	the_excludes = new Exclude*[info[l].n_SRI];
1329	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1330	>	the_excludes[ex] = new Exclude(ex);
1331	>	}
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].n_exclude = info[l].n_SRI;
1334	>	}
1335	>	else{
1336
1337	<	Exclude::createArray( 1 );
1338	<	the_excludes = new Exclude*;
1339	<	the_excludes[0] = new Exclude(0);
1340	<	the_excludes[0]->setPair( 0,0 );
1341	<	info->globalExcludes = new int;
1342	<	info->globalExcludes[0] = 0;
1343	<	info->n_exclude = 0;
1344	<	}
1337	>	Exclude::createArray( 1 );
1338	>	the_excludes = new Exclude*;
1339	>	the_excludes[0] = new Exclude(0);
1340	>	the_excludes[0]->setPair( 0,0 );
1341	>	info[l].globalExcludes = new int;
1342	>	info[l].globalExcludes[0] = 0;
1343	>	info[l].n_exclude = 0;
1344	>	}
1345
1346	<	// set the arrays into the SimInfo object
1346	>	// set the arrays into the SimInfo object
1347
1348	<	info->atoms = the_atoms;
1349	<	info->molecules = the_molecules;
1350	<	info->nGlobalExcludes = 0;
1351	<	info->excludes = the_excludes;
1348	>	info[l].atoms = the_atoms;
1349	>	info[l].molecules = the_molecules;
1350	>	info[l].nGlobalExcludes = 0;
1351	>	info[l].excludes = the_excludes;
1352
1353	<	the_ff->setSimInfo( info );
1354	<
1353	>	the_ff->setSimInfo( info );
1354	>
1355	>	}
1356		}
1357
1358		void SimSetup::makeIntegrator( void ){
1359
1360	+	int k;
1361	+
1362		NVT<RealIntegrator>*  myNVT = NULL;
1363		NPTi<RealIntegrator>* myNPTi = NULL;
1364		NPTf<RealIntegrator>* myNPTf = NULL;
1365		NPTim<RealIntegrator>* myNPTim = NULL;
1366		NPTfm<RealIntegrator>* myNPTfm = NULL;
1367	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1368	<	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1369	<	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1370	<	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1328	<	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1329	<	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1367	>
1368	>	for(k=0; k<nInfo; k++){
1369	>
1370	>	switch( ensembleCase ){
1371
1372	<	cerr << "setting integrator" <<endl;
1373	<
1374	<	switch( ensembleCase ){
1372	>	case NVE_ENS:
1373	>	if (globals->haveZconstraints()){
1374	>	setupZConstraint(info[k]);
1375	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1376	>	}
1377
1378	<	case NVE_ENS:
1379	<	new NVE<RealIntegrator>( info, the_ff );
1380	<	break;
1378	>	else
1379	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1380	>	break;
1381	>
1382	>	case NVT_ENS:
1383	>	if (globals->haveZconstraints()){
1384	>	setupZConstraint(info[k]);
1385	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1386	>	}
1387	>	else
1388	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1389
1390	<	case NVT_ENS:
1391	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1392	<	myNVT->setTargetTemp(globals->getTargetTemp());
1390	>	myNVT->setTargetTemp(globals->getTargetTemp());
1391	>
1392	>	if (globals->haveTauThermostat())
1393	>	myNVT->setTauThermostat(globals->getTauThermostat());
1394	>
1395	>	else {
1396	>	sprintf( painCave.errMsg,
1397	>	"SimSetup error: If you use the NVT\n"
1398	>	"    ensemble, you must set tauThermostat.\n");
1399	>	painCave.isFatal = 1;
1400	>	simError();
1401	>	}
1402	>	break;
1403	>
1404	>	case NPTi_ENS:
1405	>	if (globals->haveZconstraints()){
1406	>	setupZConstraint(info[k]);
1407	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1408	>	}
1409	>	else
1410	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1411
1412	<	if (globals->haveTauThermostat())
1413	<	myNVT->setTauThermostat(globals->getTauThermostat());
1412	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1413	>
1414	>	if (globals->haveTargetPressure())
1415	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1416	>	else {
1417	>	sprintf( painCave.errMsg,
1418	>	"SimSetup error: If you use a constant pressure\n"
1419	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1420	>	painCave.isFatal = 1;
1421	>	simError();
1422	>	}
1423	>
1424	>	if( globals->haveTauThermostat() )
1425	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1426	>	else{
1427	>	sprintf( painCave.errMsg,
1428	>	"SimSetup error: If you use an NPT\n"
1429	>	"    ensemble, you must set tauThermostat.\n");
1430	>	painCave.isFatal = 1;
1431	>	simError();
1432	>	}
1433	>
1434	>	if( globals->haveTauBarostat() )
1435	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1436	>	else{
1437	>	sprintf( painCave.errMsg,
1438	>	"SimSetup error: If you use an NPT\n"
1439	>	"    ensemble, you must set tauBarostat.\n");
1440	>	painCave.isFatal = 1;
1441	>	simError();
1442	>	}
1443	>	break;
1444	>
1445	>	case NPTf_ENS:
1446	>	if (globals->haveZconstraints()){
1447	>	setupZConstraint(info[k]);
1448	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1449	>	}
1450	>	else
1451	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1452
1453	<	else {
1454	<	sprintf( painCave.errMsg,
1455	<	"SimSetup error: If you use the NVT\n"
1453	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1454	>
1455	>	if (globals->haveTargetPressure())
1456	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1457	>	else {
1458	>	sprintf( painCave.errMsg,
1459	>	"SimSetup error: If you use a constant pressure\n"
1460	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1461	>	painCave.isFatal = 1;
1462	>	simError();
1463	>	}
1464	>
1465	>	if( globals->haveTauThermostat() )
1466	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1467	>	else{
1468	>	sprintf( painCave.errMsg,
1469	>	"SimSetup error: If you use an NPT\n"
1470		"    ensemble, you must set tauThermostat.\n");
1471	<	painCave.isFatal = 1;
1472	<	simError();
1473	<	}
1474	<	break;
1471	>	painCave.isFatal = 1;
1472	>	simError();
1473	>	}
1474	>
1475	>	if( globals->haveTauBarostat() )
1476	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1477	>	else{
1478	>	sprintf( painCave.errMsg,
1479	>	"SimSetup error: If you use an NPT\n"
1480	>	"    ensemble, you must set tauBarostat.\n");
1481	>	painCave.isFatal = 1;
1482	>	simError();
1483	>	}
1484	>	break;
1485	>
1486	>	case NPTim_ENS:
1487	>	if (globals->haveZconstraints()){
1488	>	setupZConstraint(info[k]);
1489	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1490	>	}
1491	>	else
1492	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1493
1494	<	case NPTi_ENS:
1495	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1496	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1497	<
1498	<	if (globals->haveTargetPressure())
1499	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1500	<	else {
1494	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1495	>
1496	>	if (globals->haveTargetPressure())
1497	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1498	>	else {
1499	>	sprintf( painCave.errMsg,
1500	>	"SimSetup error: If you use a constant pressure\n"
1501	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1502	>	painCave.isFatal = 1;
1503	>	simError();
1504	>	}
1505	>
1506	>	if( globals->haveTauThermostat() )
1507	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1508	>	else{
1509	>	sprintf( painCave.errMsg,
1510	>	"SimSetup error: If you use an NPT\n"
1511	>	"    ensemble, you must set tauThermostat.\n");
1512	>	painCave.isFatal = 1;
1513	>	simError();
1514	>	}
1515	>
1516	>	if( globals->haveTauBarostat() )
1517	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1518	>	else{
1519		sprintf( painCave.errMsg,
1363	–	"SimSetup error: If you use a constant pressure\n"
1364	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1365	–	painCave.isFatal = 1;
1366	–	simError();
1367	–	}
1368	–
1369	–	if( globals->haveTauThermostat() )
1370	–	myNPTi->setTauThermostat( globals->getTauThermostat() );
1371	–	else{
1372	–	sprintf( painCave.errMsg,
1520		"SimSetup error: If you use an NPT\n"
1374	–	"    ensemble, you must set tauThermostat.\n");
1375	–	painCave.isFatal = 1;
1376	–	simError();
1377	–	}
1378	–
1379	–	if( globals->haveTauBarostat() )
1380	–	myNPTi->setTauBarostat( globals->getTauBarostat() );
1381	–	else{
1382	–	sprintf( painCave.errMsg,
1383	–	"SimSetup error: If you use an NPT\n"
1521		"    ensemble, you must set tauBarostat.\n");
1522		painCave.isFatal = 1;
1523		simError();
1524	<	}
1525	<	break;
1524	>	}
1525	>	break;
1526	>
1527	>	case NPTfm_ENS:
1528	>	if (globals->haveZconstraints()){
1529	>	setupZConstraint(info[k]);
1530	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1531	>	}
1532	>	else
1533	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1534
1535	<	case NPTf_ENS:
1536	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1537	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1538	<
1539	<	if (globals->haveTargetPressure())
1540	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1541	<	else {
1542	<	sprintf( painCave.errMsg,
1543	<	"SimSetup error: If you use a constant pressure\n"
1544	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1545	<	painCave.isFatal = 1;
1401	<	simError();
1402	<	}
1403	<
1404	<	if( globals->haveTauThermostat() )
1405	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1406	<	else{
1407	<	sprintf( painCave.errMsg,
1408	<	"SimSetup error: If you use an NPT\n"
1409	<	"    ensemble, you must set tauThermostat.\n");
1410	<	painCave.isFatal = 1;
1411	<	simError();
1412	<	}
1413	<
1414	<	if( globals->haveTauBarostat() )
1415	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1416	<	else{
1417	<	sprintf( painCave.errMsg,
1418	<	"SimSetup error: If you use an NPT\n"
1419	<	"    ensemble, you must set tauBarostat.\n");
1420	<	painCave.isFatal = 1;
1421	<	simError();
1422	<	}
1423	<	break;
1424	<
1425	<	case NPTim_ENS:
1426	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1427	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1428	<
1429	<	if (globals->haveTargetPressure())
1430	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1431	<	else {
1432	<	sprintf( painCave.errMsg,
1433	<	"SimSetup error: If you use a constant pressure\n"
1434	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	<	painCave.isFatal = 1;
1436	<	simError();
1437	<	}
1438	<
1439	<	if( globals->haveTauThermostat() )
1440	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1441	<	else{
1442	<	sprintf( painCave.errMsg,
1443	<	"SimSetup error: If you use an NPT\n"
1444	<	"    ensemble, you must set tauThermostat.\n");
1445	<	painCave.isFatal = 1;
1446	<	simError();
1447	<	}
1448	<
1449	<	if( globals->haveTauBarostat() )
1450	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1451	<	else{
1452	<	sprintf( painCave.errMsg,
1453	<	"SimSetup error: If you use an NPT\n"
1454	<	"    ensemble, you must set tauBarostat.\n");
1455	<	painCave.isFatal = 1;
1456	<	simError();
1457	<	}
1458	<	break;
1459	<
1460	<	case NPTfm_ENS:
1461	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1462	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1463	<
1464	<	if (globals->haveTargetPressure())
1465	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1466	<	else {
1467	<	sprintf( painCave.errMsg,
1468	<	"SimSetup error: If you use a constant pressure\n"
1469	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1470	<	painCave.isFatal = 1;
1471	<	simError();
1472	<	}
1473	<
1474	<	if( globals->haveTauThermostat() )
1475	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1476	<	else{
1477	<	sprintf( painCave.errMsg,
1478	<	"SimSetup error: If you use an NPT\n"
1479	<	"    ensemble, you must set tauThermostat.\n");
1480	<	painCave.isFatal = 1;
1481	<	simError();
1482	<	}
1483	<
1484	<	if( globals->haveTauBarostat() )
1485	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1486	<	else{
1487	<	sprintf( painCave.errMsg,
1488	<	"SimSetup error: If you use an NPT\n"
1489	<	"    ensemble, you must set tauBarostat.\n");
1490	<	painCave.isFatal = 1;
1491	<	simError();
1492	<	}
1493	<	break;
1494	<
1495	<	case NVEZCONS_ENS:
1496	<
1497	<
1498	<	//setup index of z-constraint molecules, z-constraint sampel time
1499	<	//and z-constraint force output name. These parameter should be known
1500	<	//before constructing the z-constraint integrator
1501	<	setupZConstraint();
1535	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1536	>
1537	>	if (globals->haveTargetPressure())
1538	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1539	>	else {
1540	>	sprintf( painCave.errMsg,
1541	>	"SimSetup error: If you use a constant pressure\n"
1542	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1543	>	painCave.isFatal = 1;
1544	>	simError();
1545	>	}
1546
1547	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1548	<
1549	<	break;
1550	<
1551	<
1552	<	case NVTZCONS_ENS:
1553	<
1554	<	setupZConstraint();
1555	<
1512	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1513	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1514	<
1515	<	if (globals->haveTauThermostat())
1516	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1517	<
1518	<	else {
1519	<	sprintf( painCave.errMsg,
1520	<	"SimSetup error: If you use the NVT\n"
1521	<	"    ensemble, you must set tauThermostat.\n");
1522	<	painCave.isFatal = 1;
1523	<	simError();
1524	<	}
1525	<	break;
1526	<
1527	<	case NPTiZCONS_ENS:
1528	<
1529	<	setupZConstraint();
1530	<
1531	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1532	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1533	<
1534	<	if (globals->haveTargetPressure())
1535	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1536	<	else {
1537	<	sprintf( painCave.errMsg,
1538	<	"SimSetup error: If you use a constant pressure\n"
1539	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1540	<	painCave.isFatal = 1;
1541	<	simError();
1542	<	}
1543	<
1544	<	if( globals->haveTauThermostat() )
1545	<	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1546	<	else{
1547	<	sprintf( painCave.errMsg,
1548	<	"SimSetup error: If you use an NPT\n"
1549	<	"    ensemble, you must set tauThermostat.\n");
1550	<	painCave.isFatal = 1;
1551	<	simError();
1552	<	}
1553	<
1554	<	if( globals->haveTauBarostat() )
1555	<	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1556	<	else{
1557	<	sprintf( painCave.errMsg,
1558	<	"SimSetup error: If you use an NPT\n"
1559	<	"    ensemble, you must set tauBarostat.\n");
1560	<	painCave.isFatal = 1;
1561	<	simError();
1562	<	}
1563	<
1564	<	break;
1565	<
1566	<	case NPTfZCONS_ENS:
1567	<
1568	<	setupZConstraint();
1569	<
1570	<	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1571	<	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1572	<
1573	<	if (globals->haveTargetPressure())
1574	<	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1575	<	else {
1576	<	sprintf( painCave.errMsg,
1577	<	"SimSetup error: If you use a constant pressure\n"
1578	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1579	<	painCave.isFatal = 1;
1580	<	simError();
1581	<	}
1582	<
1583	<	if( globals->haveTauThermostat() )
1584	<	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1585	<	else{
1586	<	sprintf( painCave.errMsg,
1587	<	"SimSetup error: If you use an NPT\n"
1588	<	"    ensemble, you must set tauThermostat.\n");
1589	<	painCave.isFatal = 1;
1590	<	simError();
1591	<	}
1592	<
1593	<	if( globals->haveTauBarostat() )
1594	<	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1595	<	else{
1596	<	sprintf( painCave.errMsg,
1597	<	"SimSetup error: If you use an NPT\n"
1598	<	"    ensemble, you must set tauBarostat.\n");
1599	<	painCave.isFatal = 1;
1600	<	simError();
1601	<	}
1602	<
1603	<	break;
1547	>	if( globals->haveTauThermostat() )
1548	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1549	>	else{
1550	>	sprintf( painCave.errMsg,
1551	>	"SimSetup error: If you use an NPT\n"
1552	>	"    ensemble, you must set tauThermostat.\n");
1553	>	painCave.isFatal = 1;
1554	>	simError();
1555	>	}
1556
1557	<	case NPTimZCONS_ENS:
1558	<
1559	<	setupZConstraint();
1560	<
1561	<	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1562	<	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1563	<
1564	<	if (globals->haveTargetPressure())
1565	<	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1566	<	else {
1557	>	if( globals->haveTauBarostat() )
1558	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1559	>	else{
1560	>	sprintf( painCave.errMsg,
1561	>	"SimSetup error: If you use an NPT\n"
1562	>	"    ensemble, you must set tauBarostat.\n");
1563	>	painCave.isFatal = 1;
1564	>	simError();
1565	>	}
1566	>	break;
1567	>
1568	>	default:
1569		sprintf( painCave.errMsg,
1570	<	"SimSetup error: If you use a constant pressure\n"
1617	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1570	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1571		painCave.isFatal = 1;
1572		simError();
1573		}
1621	–
1622	–	if( globals->haveTauThermostat() )
1623	–	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1624	–	else{
1625	–	sprintf( painCave.errMsg,
1626	–	"SimSetup error: If you use an NPT\n"
1627	–	"    ensemble, you must set tauThermostat.\n");
1628	–	painCave.isFatal = 1;
1629	–	simError();
1630	–	}
1631	–
1632	–	if( globals->haveTauBarostat() )
1633	–	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1634	–	else{
1635	–	sprintf( painCave.errMsg,
1636	–	"SimSetup error: If you use an NPT\n"
1637	–	"    ensemble, you must set tauBarostat.\n");
1638	–	painCave.isFatal = 1;
1639	–	simError();
1640	–	}
1641	–
1642	–	break;
1643	–
1644	–	case NPTfmZCONS_ENS:
1645	–
1646	–	setupZConstraint();
1647	–
1648	–	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1649	–	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1650	–
1651	–	if (globals->haveTargetPressure())
1652	–	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1653	–	else {
1654	–	sprintf( painCave.errMsg,
1655	–	"SimSetup error: If you use a constant pressure\n"
1656	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1657	–	painCave.isFatal = 1;
1658	–	simError();
1659	–	}
1660	–
1661	–	if( globals->haveTauThermostat() )
1662	–	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1663	–	else{
1664	–	sprintf( painCave.errMsg,
1665	–	"SimSetup error: If you use an NPT\n"
1666	–	"    ensemble, you must set tauThermostat.\n");
1667	–	painCave.isFatal = 1;
1668	–	simError();
1669	–	}
1670	–
1671	–	if( globals->haveTauBarostat() )
1672	–	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1673	–	else{
1674	–	sprintf( painCave.errMsg,
1675	–	"SimSetup error: If you use an NPT\n"
1676	–	"    ensemble, you must set tauBarostat.\n");
1677	–	painCave.isFatal = 1;
1678	–	simError();
1679	–	}
1680	–	break;
1681	–
1682	–
1683	–
1684	–	default:
1685	–	sprintf( painCave.errMsg,
1686	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1687	–	painCave.isFatal = 1;
1688	–	simError();
1574		}
1690	–
1575		}
1576
1577		void SimSetup::initFortran( void ){
1578
1579	<	info->refreshSim();
1579	>	info[0].refreshSim();
1580
1581	<	if( !strcmp( info->mixingRule, "standard") ){
1581	>	if( !strcmp( info[0].mixingRule, "standard") ){
1582		the_ff->initForceField( LB_MIXING_RULE );
1583		}
1584	<	else if( !strcmp( info->mixingRule, "explicit") ){
1584	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1585		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1586		}
1587		else{
1588		sprintf( painCave.errMsg,
1589		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1590	<	info->mixingRule );
1590	>	info[0].mixingRule );
1591		painCave.isFatal = 1;
1592		simError();
1593		}
#	Line 1717 | Line 1601 | void SimSetup::setupZConstraint()
1601
1602		}
1603
1604	<	void SimSetup::setupZConstraint()
1604	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1605		{
1606	<	if(globals->haveZConsTime()){
1607	<
1724	<	//add sample time of z-constraint  into SimInfo's property list
1725	<	DoubleData* zconsTimeProp = new DoubleData();
1726	<	zconsTimeProp->setID("zconstime");
1727	<	zconsTimeProp->setData(globals->getZConsTime());
1728	<	info->addProperty(zconsTimeProp);
1729	<	}
1730	<	else{
1731	<	sprintf( painCave.errMsg,
1732	<	"ZConstraint error: If you use an ZConstraint\n"
1733	<	" , you must set sample time.\n");
1734	<	painCave.isFatal = 1;
1735	<	simError();
1736	<	}
1737	<
1738	<	if(globals->haveIndexOfAllZConsMols()){
1739	<
1740	<	//add index of z-constraint molecules into SimInfo's property list
1741	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1606	>	int nZConstraints;
1607	>	ZconStamp** zconStamp;
1608
1609	<	//sort the index
1744	<	sort(tempIndex.begin(), tempIndex.end());
1745	<
1746	<	IndexData* zconsIndex = new IndexData();
1747	<	zconsIndex->setID("zconsindex");
1748	<	zconsIndex->setIndexData(tempIndex);
1749	<	info->addProperty(zconsIndex);
1750	<	}
1751	<	else{
1752	<	sprintf( painCave.errMsg,
1753	<	"SimSetup error: If you use an ZConstraint\n"
1754	<	" , you must set index of z-constraint molecules.\n");
1755	<	painCave.isFatal = 1;
1756	<	simError();
1609	>	if(globals->haveZconstraintTime()){
1610
1611	<	}
1611	>	//add sample time of z-constraint  into SimInfo's property list
1612	>	DoubleData* zconsTimeProp = new DoubleData();
1613	>	zconsTimeProp->setID(ZCONSTIME_ID);
1614	>	zconsTimeProp->setData(globals->getZconsTime());
1615	>	theInfo.addProperty(zconsTimeProp);
1616	>	}
1617	>	else{
1618	>	sprintf( painCave.errMsg,
1619	>	"ZConstraint error: If you use an ZConstraint\n"
1620	>	" , you must set sample time.\n");
1621	>	painCave.isFatal = 1;
1622	>	simError();
1623	>	}
1624
1625	<	//Determine the name of ouput file and add it into SimInfo's property list
1626	<	//Be careful, do not use inFileName, since it is a pointer which
1627	<	//point to a string at master node, and slave nodes do not contain that string
1628	<
1764	<	string zconsOutput(info->finalName);
1765	<
1766	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1767	<
1768	<	StringData* zconsFilename = new StringData();
1769	<	zconsFilename->setID("zconsfilename");
1770	<	zconsFilename->setData(zconsOutput);
1625	>	//
1626	>	nZConstraints = globals->getNzConstraints();
1627	>	zconStamp = globals->getZconStamp();
1628	>	ZConsParaItem tempParaItem;
1629
1630	<	info->addProperty(zconsFilename);
1630	>	ZConsParaData* zconsParaData = new ZConsParaData();
1631	>	zconsParaData->setID(ZCONSPARADATA_ID);
1632	>
1633	>	for(int i = 0; i < nZConstraints; i++){
1634	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1635	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1636	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1637	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1638
1639	+	zconsParaData->addItem(tempParaItem);
1640	+	}
1641	+
1642	+	//sort the parameters by index of molecules
1643	+	zconsParaData->sortByIndex();
1644	+
1645	+	//push data into siminfo, therefore, we can retrieve later
1646	+	theInfo.addProperty(zconsParaData);
1647	+
1648	+	//push zconsTol into siminfo, if user does not specify
1649	+	//value for zconsTol, a default value will be used
1650	+	DoubleData* zconsTol = new DoubleData();
1651	+	zconsTol->setID(ZCONSTOL_ID);
1652	+	if(globals->haveZconsTol()){
1653	+	zconsTol->setData(globals->getZconsTol());
1654	+	}
1655	+	else{
1656	+	double defaultZConsTol = 1E-6;
1657	+	sprintf( painCave.errMsg,
1658	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1659	+	" , default value %f is used.\n", defaultZConsTol);
1660	+	painCave.isFatal = 0;
1661	+	simError();
1662	+
1663	+	zconsTol->setData(defaultZConsTol);
1664	+	}
1665	+	theInfo.addProperty(zconsTol);
1666	+
1667	+	//Determine the name of ouput file and add it into SimInfo's property list
1668	+	//Be careful, do not use inFileName, since it is a pointer which
1669	+	//point to a string at master node, and slave nodes do not contain that string
1670	+
1671	+	string zconsOutput(theInfo.finalName);
1672	+
1673	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1674	+
1675	+	StringData* zconsFilename = new StringData();
1676	+	zconsFilename->setID(ZCONSFILENAME_ID);
1677	+	zconsFilename->setData(zconsOutput);
1678	+
1679	+	theInfo.addProperty(zconsFilename);
1680		}

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