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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 699 by tim, Fri Aug 15 19:24:13 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		gatherInfo();
102
103		// creation of complex system objects
#	Line 110 | Line 105 | void SimSetup::createSim( void ){
105		sysObjectsCreation();
106
107		// check on the post processing info
108	<
108	>
109		finalInfoCheck();
110
111		// initialize the system coordinates
112
113	<	initSystemCoords();
119	<
113	>	if( !isInfoArray ) initSystemCoords();
114
115		// make the output filenames
116
#	Line 141 | Line 135 | void SimSetup::makeMolecules( void ){
135
136		void SimSetup::makeMolecules( void ){
137
138	+	int k,l;
139		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140		molInit molInfo;
141		DirectionalAtom* dAtom;
#	Line 165 | Line 160 | void SimSetup::makeMolecules( void ){
160
161		double ux, uy, uz, u, uSqr;
162
163	<	atomOffset = 0;
169	<	excludeOffset = 0;
170	<	for(i=0; i<info->n_mol; i++){
163	>	for(k=0; k<nInfo; k++){
164
165	<	stampID = the_molecules[i].getStampID();
165	>	the_ff->setSimInfo( &(info[k]) );
166
167	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
168	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
169	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
170	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
171	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for(i=0; i<info[k].n_mol; i++){
170	>
171	>	stampID = info[k].molecules[i].getStampID();
172
173	<	molInfo.myAtoms = &the_atoms[atomOffset];
174	<	molInfo.myExcludes = &the_excludes[excludeOffset];
175	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
176	<	molInfo.myBends = new Bend*[molInfo.nBends];
177	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178	>
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184
185	<	theBonds = new bond_pair[molInfo.nBonds];
186	<	theBends = new bend_set[molInfo.nBends];
187	<	theTorsions = new torsion_set[molInfo.nTorsions];
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188
189	<	// make the Atoms
189	>	// make the Atoms
190
191	<	for(j=0; j<molInfo.nAtoms; j++){
193	<
194	<	currentAtom = comp_stamps[stampID]->getAtom( j );
195	<	if( currentAtom->haveOrientation() ){
191	>	for(j=0; j<molInfo.nAtoms; j++){
192
193	<	dAtom = new DirectionalAtom(j + atomOffset);
194	<	info->n_oriented++;
195	<	molInfo.myAtoms[j] = dAtom;
196	<
197	<	ux = currentAtom->getOrntX();
198	<	uy = currentAtom->getOrntY();
199	<	uz = currentAtom->getOrntZ();
200	<
201	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	<
203	<	u = sqrt( uSqr );
204	<	ux = ux / u;
205	<	uy = uy / u;
206	<	uz = uz / u;
207	<
208	<	dAtom->setSUx( ux );
209	<	dAtom->setSUy( uy );
210	<	dAtom->setSUz( uz );
211	<	}
212	<	else{
213	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
214	<	}
215	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195	>
196	>	dAtom = new DirectionalAtom( (j + atomOffset),
197	>	info[k].getConfiguration() );
198	>	info[k].n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200	>
201	>	ux = currentAtom->getOrntX();
202	>	uy = currentAtom->getOrntY();
203	>	uz = currentAtom->getOrntZ();
204	>
205	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	>
207	>	u = sqrt( uSqr );
208	>	ux = ux / u;
209	>	uy = uy / u;
210	>	uz = uz / u;
211	>
212	>	dAtom->setSUx( ux );
213	>	dAtom->setSUy( uy );
214	>	dAtom->setSUz( uz );
215	>	}
216	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	>	info[k].getConfiguration() );
219	>	}
220	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221
222		#ifdef IS_MPI
223
224	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225
226		#endif // is_mpi
227	<	}
227	>	}
228
229		// make the bonds
230	<	for(j=0; j<molInfo.nBonds; j++){
230	>	for(j=0; j<molInfo.nBonds; j++){
231
232	<	currentBond = comp_stamps[stampID]->getBond( j );
233	<	theBonds[j].a = currentBond->getA() + atomOffset;
234	<	theBonds[j].b = currentBond->getB() + atomOffset;
235	<
236	<	exI = theBonds[j].a;
237	<	exJ = theBonds[j].b;
238	<
239	<	// exclude_I must always be the smaller of the pair
240	<	if( exI > exJ ){
241	<	tempEx = exI;
242	<	exI = exJ;
243	<	exJ = tempEx;
244	<	}
232	>	currentBond = comp_stamps[stampID]->getBond( j );
233	>	theBonds[j].a = currentBond->getA() + atomOffset;
234	>	theBonds[j].b = currentBond->getB() + atomOffset;
235	>
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244	>	}
245		#ifdef IS_MPI
246	<	tempEx = exI;
247	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
248	<	tempEx = exJ;
249	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
250	<
251	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
246	>	tempEx = exI;
247	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	>	tempEx = exJ;
249	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	>
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252		#else  // isn't MPI
253	<
254	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
253	>
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255		#endif  //is_mpi
256	<	}
257	<	excludeOffset += molInfo.nBonds;
257	<
258	<	//make the bends
259	<	for(j=0; j<molInfo.nBends; j++){
256	>	}
257	>	excludeOffset += molInfo.nBonds;
258
259	<	currentBend = comp_stamps[stampID]->getBend( j );
260	<	theBends[j].a = currentBend->getA() + atomOffset;
261	<	theBends[j].b = currentBend->getB() + atomOffset;
262	<	theBends[j].c = currentBend->getC() + atomOffset;
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261	>
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266	>
267	>	if( currentBend->haveExtras() ){
268
269	<	if( currentBend->haveExtras() ){
270	<
271	<	extras = currentBend->getExtras();
272	<	current_extra = extras;
273	<
274	<	while( current_extra != NULL ){
275	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276
277	<	switch( current_extra->getType() ){
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290	>	sprintf( painCave.errMsg,
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298	>	}
299	>
300	>	else{
301
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:
302		sprintf( painCave.errMsg,
303	<	"SimSetup Error: ghostVectorSource was neither a "
304	<	"double nor an int.\n"
305	<	"-->Bend[%d] in %s\n",
303	>	"SimSetup Error: unhandled bend assignment:\n"
304	>	"    -->%s in Bend[%d] in %s\n",
305	>	current_extra->getlhs(),
306		j, comp_stamps[stampID]->getID() );
307		painCave.isFatal = 1;
308		simError();
309		}
297	–	}
298	–
299	–	else{
310
311	<	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();
311	>	current_extra = current_extra->getNext();
312		}
313	+	}
314	+
315	+	if( !theBends[j].isGhost ){
316
317	<	current_extra = current_extra->getNext();
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].c;
319		}
320	<	}
320	>	else{
321
322	<	if( !theBends[j].isGhost ){
323	<
324	<	exI = theBends[j].a;
317	<	exJ = theBends[j].c;
318	<	}
319	<	else{
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].b;
324	>	}
325
326	<	exI = theBends[j].a;
327	<	exJ = theBends[j].b;
328	<	}
329	<
330	<	// exclude_I must always be the smaller of the pair
331	<	if( exI > exJ ){
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331	>	}
332	>	#ifdef IS_MPI
333		tempEx = exI;
334	<	exI = exJ;
335	<	exJ = tempEx;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	>
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	#else  // isn't MPI
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	#endif  //is_mpi
342		}
343	<	#ifdef IS_MPI
332	<	tempEx = exI;
333	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
334	<	tempEx = exJ;
335	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
343	>	excludeOffset += molInfo.nBends;
344
345	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
345	>	for(j=0; j<molInfo.nTorsions; j++){
346	>
347	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352	>
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355	>
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361	>	}
362	>	#ifdef IS_MPI
363	>	tempEx = exI;
364	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	>	tempEx = exJ;
366	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	>
368	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369		#else  // isn't MPI
370	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371		#endif  //is_mpi
372	<	}
373	<	excludeOffset += molInfo.nBends;
343	<
344	<	for(j=0; j<molInfo.nTorsions; j++){
372	>	}
373	>	excludeOffset += molInfo.nTorsions;
374
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;
375
376	<	exI = theTorsions[j].a;
377	<	exJ = theTorsions[j].d;
376	>	// send the arrays off to the forceField for init.
377	>
378	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	>
383	>
384	>	info[k].molecules[i].initialize( molInfo );
385
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;
386
387	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
388	<	#else  // isn't MPI
389	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
390	<	#endif  //is_mpi
387	>	atomOffset += molInfo.nAtoms;
388	>	delete[] theBonds;
389	>	delete[] theBends;
390	>	delete[] theTorsions;
391		}
392	<	excludeOffset += molInfo.nTorsions;
393	<
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	<
392	>	}
393	>
394		#ifdef IS_MPI
395		sprintf( checkPointMsg, "all molecules initialized succesfully" );
396		MPIcheckPoint();
397		#endif // is_mpi
398	<
398	>
399		// clean up the forcefield
400	+
401		the_ff->calcRcut();
402		the_ff->cleanMe();
403	<
403	>
404		}
405
406		void SimSetup::initFromBass( void ){
#	Line 410 | Line 413 | void SimSetup::initFromBass( void ){
413		int n_extra;
414		int have_extra, done;
415
416	+	double vel[3];
417	+	vel[0] = 0.0;
418	+	vel[1] = 0.0;
419	+	vel[2] = 0.0;
420	+
421		temp1 = (double)tot_nmol / 4.0;
422		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423		temp3 = ceil( temp2 );
#	Line 419 | Line 427 | void SimSetup::initFromBass( void ){
427		have_extra =1;
428
429		n_cells = (int)temp3 - 1;
430	<	cellx = info->boxL[0] / temp3;
431	<	celly = info->boxL[1] / temp3;
432	<	cellz = info->boxL[2] / temp3;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435		n_per_extra = (int)ceil( temp1 );
#	Line 436 | Line 444 | void SimSetup::initFromBass( void ){
444		}
445		else{
446		n_cells = (int)temp3;
447	<	cellx = info->boxL[0] / temp3;
448	<	celly = info->boxL[1] / temp3;
449	<	cellz = info->boxL[2] / temp3;
447	>	cellx = info[0].boxL[0] / temp3;
448	>	celly = info[0].boxL[1] / temp3;
449	>	cellz = info[0].boxL[2] / temp3;
450		}
451
452		current_mol = 0;
#	Line 517 | Line 525 | void SimSetup::initFromBass( void ){
525		}
526		}
527
528	<
529	<	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 );
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530		}
531		}
532
#	Line 531 | Line 536 | void SimSetup::makeElement( double x, double y, double
536		AtomStamp* current_atom;
537		DirectionalAtom* dAtom;
538		double rotMat[3][3];
539	+	double pos[3];
540
541		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542
#	Line 546 | Line 552 | void SimSetup::makeElement( double x, double y, double
552		painCave.isFatal = 1;
553		simError();
554		}
555	+
556	+	pos[0] = x + current_atom->getPosX();
557	+	pos[1] = y + current_atom->getPosY();
558	+	pos[2] = z + current_atom->getPosZ();
559	+
560	+	info[0].atoms[current_atom_ndx]->setPos( pos );
561
562	<	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() );
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563
564	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
564	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565
556	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
557	–
566		rotMat[0][0] = 1.0;
567		rotMat[0][1] = 0.0;
568		rotMat[0][2] = 0.0;
#	Line 590 | Line 598 | void SimSetup::gatherInfo( void ){
598		ensembleCase = -1;
599		ffCase = -1;
600
601	<	// get the stamps and globals;
594	<	stamps = stamps;
595	<	globals = globals;
601	>	// set the easy ones first
602
603	<	// set the easy ones first
604	<	info->target_temp = globals->getTargetTemp();
605	<	info->dt = globals->getDt();
606	<	info->run_time = globals->getRunTime();
603	>	for( i=0; i<nInfo; i++){
604	>	info[i].target_temp = globals->getTargetTemp();
605	>	info[i].dt = globals->getDt();
606	>	info[i].run_time = globals->getRunTime();
607	>	}
608		n_components = globals->getNComponents();
609
610
#	Line 627 | Line 634 | void SimSetup::gatherInfo( void ){
634		else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635		else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636		else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
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	–
637		else{
638		sprintf( painCave.errMsg,
639		"SimSetup Warning. Unrecognized Ensemble -> %s, "
#	Line 646 | Line 644 | void SimSetup::gatherInfo( void ){
644		strcpy( ensemble, "NVE" );
645		ensembleCase = NVE_ENS;
646		}
647	<	strcpy( info->ensemble, ensemble );
647	>
648	>	for(i=0; i<nInfo; i++){
649	>
650	>	strcpy( info[i].ensemble, ensemble );
651
652	<	// get the mixing rule
652	>	// get the mixing rule
653
654	<	strcpy( info->mixingRule, globals->getMixingRule() );
655	<	info->usePBC = globals->getPBC();
656	<
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657
658		// get the components and calculate the tot_nMol and indvidual n_mol
659
#	Line 693 | Line 694 | void SimSetup::gatherInfo( void ){
694
695		// set the status, sample, and thermal kick times
696
697	<	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	<	}
697	>	for(i=0; i<nInfo; i++){
698
699	<	if( globals->haveStatusTime() ){
700	<	info->statusTime = globals->getStatusTime();
701	<	}
702	<
703	<	if( globals->haveThermalTime() ){
704	<	info->thermalTime = globals->getThermalTime();
705	<	}
706	<
707	<	// check for the temperature set flag
708	<
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();
699	>	if( globals->haveSampleTime() ){
700	>	info[i].sampleTime = globals->getSampleTime();
701	>	info[i].statusTime = info[i].sampleTime;
702	>	info[i].thermalTime = info[i].sampleTime;
703	>	}
704	>	else{
705	>	info[i].sampleTime = globals->getRunTime();
706	>	info[i].statusTime = info[i].sampleTime;
707	>	info[i].thermalTime = info[i].sampleTime;
708	>	}
709
710	<	info->setBox( boxVector );
711	<	}
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();
710	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712		}
713	<	boxVector[0] = globals->getBoxX();
714	<
715	<	if( !globals->haveBoxY() ){
749	<	sprintf( painCave.errMsg,
750	<	"SimSetup error, no periodic BoxY size given.\n" );
751	<	painCave.isFatal = 1;
752	<	simError();
713	>
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716		}
754	–	boxVector[1] = globals->getBoxY();
717
718	<	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();
718	>	// check for the temperature set flag
719
720	<	info->setBox( boxVector );
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721	>
722	>	// get some of the tricky things that may still be in the globals
723	>
724	>	double boxVector[3];
725	>	if( globals->haveBox() ){
726	>	boxVector[0] = globals->getBox();
727	>	boxVector[1] = globals->getBox();
728	>	boxVector[2] = globals->getBox();
729	>
730	>	info[i].setBox( boxVector );
731	>	}
732	>	else if( globals->haveDensity() ){
733	>
734	>	double vol;
735	>	vol = (double)tot_nmol / globals->getDensity();
736	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	>	boxVector[1] = boxVector[0];
738	>	boxVector[2] = boxVector[0];
739	>
740	>	info[i].setBox( boxVector );
741		}
742	+	else{
743	+	if( !globals->haveBoxX() ){
744	+	sprintf( painCave.errMsg,
745	+	"SimSetup error, no periodic BoxX size given.\n" );
746	+	painCave.isFatal = 1;
747	+	simError();
748	+	}
749	+	boxVector[0] = globals->getBoxX();
750	+
751	+	if( !globals->haveBoxY() ){
752	+	sprintf( painCave.errMsg,
753	+	"SimSetup error, no periodic BoxY size given.\n" );
754	+	painCave.isFatal = 1;
755	+	simError();
756	+	}
757	+	boxVector[1] = globals->getBoxY();
758	+
759	+	if( !globals->haveBoxZ() ){
760	+	sprintf( painCave.errMsg,
761	+	"SimSetup error, no periodic BoxZ size given.\n" );
762	+	painCave.isFatal = 1;
763	+	simError();
764	+	}
765	+	boxVector[2] = globals->getBoxZ();
766	+
767	+	info[i].setBox( boxVector );
768	+	}
769
770	<
770	>	}
771
772		#ifdef IS_MPI
773		strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
#	Line 777 | Line 780 | void SimSetup::finalInfoCheck( void ){
780		void SimSetup::finalInfoCheck( void ){
781		int index;
782		int usesDipoles;
783	<
783	>	int i;
784
785	<	// check electrostatic parameters
786	<
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;
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787
788	<	if( !globals->haveECR() ){
789	<	sprintf( painCave.errMsg,
790	<	"SimSetup Warning: using default value of 1/2 the smallest "
791	<	"box length for the electrostaticCutoffRadius.\n"
792	<	"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();
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793		}
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 );
794
795	<	if(!globals->haveDielectric() ){
796	<	sprintf( painCave.errMsg,
797	<	"SimSetup Error: You are trying to use Reaction Field without"
798	<	"setting a dielectric constant!\n"
799	<	);
800	<	painCave.isFatal = 1;
801	<	simError();
802	<	}
803	<	info->dielectric = globals->getDielectric();
840	<	}
841	<	else {
842	<	if (usesDipoles) {
795	>	#ifdef IS_MPI
796	>	int myUse = usesDipoles;
797	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798	>	#endif //is_mpi
799	>
800	>	double theEcr, theEst;
801	>
802	>	if (globals->getUseRF() ) {
803	>	info[i].useReactionField = 1;
804
805		if( !globals->haveECR() ){
806		sprintf( painCave.errMsg,
#	Line 849 | Line 810 | void SimSetup::finalInfoCheck( void ){
810		painCave.isFatal = 0;
811		simError();
812		double smallest;
813	<	smallest = info->boxL[0];
814	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
815	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
813	>	smallest = info[i].boxL[0];
814	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816		theEcr = 0.5 * smallest;
817		} else {
818		theEcr = globals->getECR();
#	Line 860 | Line 821 | void SimSetup::finalInfoCheck( void ){
821		if( !globals->haveEST() ){
822		sprintf( painCave.errMsg,
823		"SimSetup Warning: using default value of 0.05 * the "
824	<	"electrostaticCutoffRadius for the "
864	<	"electrostaticSkinThickness\n"
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825		);
826		painCave.isFatal = 0;
827		simError();
#	Line 869 | Line 829 | void SimSetup::finalInfoCheck( void ){
829		} else {
830		theEst= globals->getEST();
831		}
832	<
833	<	info->setEcr( theEcr, theEst );
834	<	}
835	<	}
832	>
833	>	info[i].setEcr( theEcr, theEst );
834	>
835	>	if(!globals->haveDielectric() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Error: You are trying to use Reaction Field without"
838	>	"setting a dielectric constant!\n"
839	>	);
840	>	painCave.isFatal = 1;
841	>	simError();
842	>	}
843	>	info[i].dielectric = globals->getDielectric();
844	>	}
845	>	else {
846	>	if (usesDipoles) {
847	>
848	>	if( !globals->haveECR() ){
849	>	sprintf( painCave.errMsg,
850	>	"SimSetup Warning: using default value of 1/2 the smallest "
851	>	"box length for the electrostaticCutoffRadius.\n"
852	>	"I hope you have a very fast processor!\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	double smallest;
856	>	smallest = info[i].boxL[0];
857	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	>	theEcr = 0.5 * smallest;
860	>	} else {
861	>	theEcr = globals->getECR();
862	>	}
863	>
864	>	if( !globals->haveEST() ){
865	>	sprintf( painCave.errMsg,
866	>	"SimSetup Warning: using default value of 0.05 * the "
867	>	"electrostaticCutoffRadius for the "
868	>	"electrostaticSkinThickness\n"
869	>	);
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	theEst = 0.05 * theEcr;
873	>	} else {
874	>	theEst= globals->getEST();
875	>	}
876	>
877	>	info[i].setEcr( theEcr, theEst );
878	>	}
879	>	}
880	>	}
881
882		#ifdef IS_MPI
883		strcpy( checkPointMsg, "post processing checks out" );
#	Line 882 | Line 887 | void SimSetup::initSystemCoords( void ){
887		}
888
889		void SimSetup::initSystemCoords( void ){
890	+	int i;
891	+
892	+	char* inName;
893
894	<	if( globals->haveInitialConfig() ){
895	<
896	<	InitializeFromFile* fileInit;
894	>
895	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
896	>
897	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
898	>
899	>	if( globals->haveInitialConfig() ){
900	>
901	>	InitializeFromFile* fileInit;
902		#ifdef IS_MPI // is_mpi
903	<	if( worldRank == 0 ){
903	>	if( worldRank == 0 ){
904		#endif //is_mpi
905	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
905	>	inName = globals->getInitialConfig();
906	>	double* tempDouble = new double[1000000];
907	>	fileInit = new InitializeFromFile( inName );
908		#ifdef IS_MPI
909	<	}else fileInit = new InitializeFromFile( NULL );
909	>	}else fileInit = new InitializeFromFile( NULL );
910		#endif
911	<	fileInit->readInit( info ); // default velocities on
912	<
913	<	delete fileInit;
914	<	}
915	<	else{
916	<
911	>	fileInit->readInit( info ); // default velocities on
912	>
913	>	delete fileInit;
914	>	}
915	>	else{
916	>
917		#ifdef IS_MPI
918	<
919	<	// no init from bass
920	<
921	<	sprintf( painCave.errMsg,
922	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923	<	painCave.isFatal;
924	<	simError();
925	<
918	>
919	>	// no init from bass
920	>
921	>	sprintf( painCave.errMsg,
922	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923	>	painCave.isFatal;
924	>	simError();
925	>
926		#else
927	<
928	<	initFromBass();
929	<
930	<
927	>
928	>	initFromBass();
929	>
930	>
931		#endif
932	<	}
933	<
932	>	}
933	>
934		#ifdef IS_MPI
935		strcpy( checkPointMsg, "Successfully read in the initial configuration" );
936		MPIcheckPoint();
937		#endif // is_mpi
938	<
938	>
939		}
940
941
942		void SimSetup::makeOutNames( void ){
943	+
944	+	int k;
945
946	+
947	+	for(k=0; k<nInfo; k++){
948	+
949		#ifdef IS_MPI
950	<	if( worldRank == 0 ){
950	>	if( worldRank == 0 ){
951		#endif // is_mpi
952	<
953	<	if( globals->haveFinalConfig() ){
954	<	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" );
952	>
953	>	if( globals->haveFinalConfig() ){
954	>	strcpy( info[k].finalName, globals->getFinalConfig() );
955		}
944	–	else if( !strcmp( endTest, ".BASS" ) ){
945	–	strcpy( endTest, ".eor" );
946	–	}
956		else{
957	<	endTest = &(info->finalName[nameLength - 4]);
958	<	if( !strcmp( endTest, ".bss" ) ){
957	>	strcpy( info[k].finalName, inFileName );
958	>	char* endTest;
959	>	int nameLength = strlen( info[k].finalName );
960	>	endTest = &(info[k].finalName[nameLength - 5]);
961	>	if( !strcmp( endTest, ".bass" ) ){
962		strcpy( endTest, ".eor" );
963		}
964	<	else if( !strcmp( endTest, ".mdl" ) ){
964	>	else if( !strcmp( endTest, ".BASS" ) ){
965		strcpy( endTest, ".eor" );
966		}
967		else{
968	<	strcat( info->finalName, ".eor" );
968	>	endTest = &(info[k].finalName[nameLength - 4]);
969	>	if( !strcmp( endTest, ".bss" ) ){
970	>	strcpy( endTest, ".eor" );
971	>	}
972	>	else if( !strcmp( endTest, ".mdl" ) ){
973	>	strcpy( endTest, ".eor" );
974	>	}
975	>	else{
976	>	strcat( info[k].finalName, ".eor" );
977	>	}
978		}
979		}
980	<	}
981	<
982	<	// make the sample and status out names
983	<
984	<	strcpy( info->sampleName, inFileName );
985	<	char* endTest;
986	<	int nameLength = strlen( info->sampleName );
987	<	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" ) ){
980	>
981	>	// make the sample and status out names
982	>
983	>	strcpy( info[k].sampleName, inFileName );
984	>	char* endTest;
985	>	int nameLength = strlen( info[k].sampleName );
986	>	endTest = &(info[k].sampleName[nameLength - 5]);
987	>	if( !strcmp( endTest, ".bass" ) ){
988		strcpy( endTest, ".dump" );
989		}
990	<	else if( !strcmp( endTest, ".mdl" ) ){
990	>	else if( !strcmp( endTest, ".BASS" ) ){
991		strcpy( endTest, ".dump" );
992		}
993		else{
994	<	strcat( info->sampleName, ".dump" );
994	>	endTest = &(info[k].sampleName[nameLength - 4]);
995	>	if( !strcmp( endTest, ".bss" ) ){
996	>	strcpy( endTest, ".dump" );
997	>	}
998	>	else if( !strcmp( endTest, ".mdl" ) ){
999	>	strcpy( endTest, ".dump" );
1000	>	}
1001	>	else{
1002	>	strcat( info[k].sampleName, ".dump" );
1003	>	}
1004		}
1005	<	}
1006	<
1007	<	strcpy( info->statusName, inFileName );
1008	<	nameLength = strlen( info->statusName );
1009	<	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" ) ){
1005	>
1006	>	strcpy( info[k].statusName, inFileName );
1007	>	nameLength = strlen( info[k].statusName );
1008	>	endTest = &(info[k].statusName[nameLength - 5]);
1009	>	if( !strcmp( endTest, ".bass" ) ){
1010		strcpy( endTest, ".stat" );
1011		}
1012	<	else if( !strcmp( endTest, ".mdl" ) ){
1012	>	else if( !strcmp( endTest, ".BASS" ) ){
1013		strcpy( endTest, ".stat" );
1014		}
1015		else{
1016	<	strcat( info->statusName, ".stat" );
1016	>	endTest = &(info[k].statusName[nameLength - 4]);
1017	>	if( !strcmp( endTest, ".bss" ) ){
1018	>	strcpy( endTest, ".stat" );
1019	>	}
1020	>	else if( !strcmp( endTest, ".mdl" ) ){
1021	>	strcpy( endTest, ".stat" );
1022	>	}
1023	>	else{
1024	>	strcat( info[k].statusName, ".stat" );
1025	>	}
1026		}
1027	<	}
1007	<
1027	>
1028		#ifdef IS_MPI
1029	<	}
1029	>	}
1030		#endif // is_mpi
1031	<
1031	>	}
1032		}
1033
1034
1035		void SimSetup::sysObjectsCreation( void ){
1036	<
1037	<	int i;
1038	<
1036	>
1037	>	int i,k;
1038	>
1039		// create the forceField
1040
1041		createFF();
#	Line 1035 | Line 1055 | void SimSetup::sysObjectsCreation( void ){
1055		#endif //is_mpi
1056
1057		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1058	<
1058	>
1059		makeSysArrays();
1060
1061		// make and initialize the molecules (all but atomic coordinates)
1062	<
1062	>
1063		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	–	}
1064
1065	<
1066	<
1065	>	for(k=0; k<nInfo; k++){
1066	>	info[k].identArray = new int[info[k].n_atoms];
1067	>	for(i=0; i<info[k].n_atoms; i++){
1068	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1069	>	}
1070	>	}
1071		}
1072
1073
#	Line 1085 | Line 1105 | void SimSetup::compList( void ){
1105		void SimSetup::compList( void ){
1106
1107		int i;
1108	<
1108	>	char* id;
1109	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1110	>	LinkedMolStamp* currentStamp = NULL;
1111		comp_stamps = new MoleculeStamp*[n_components];
1112	<
1112	>
1113		// make an array of molecule stamps that match the components used.
1114		// 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();
1115
1116	<	char* id;
1117	<	LinkedMolStamp* headStamp = info->headStamp;
1118	<	LinkedMolStamp* currentStamp = NULL;
1116	>	for(i=0; i<nInfo; i++){
1117	>	info[i].nComponents = n_components;
1118	>	info[i].componentsNmol = components_nmol;
1119	>	info[i].compStamps = comp_stamps;
1120	>	info[i].headStamp = headStamp;
1121	>	}
1122	>
1123	>
1124		for( i=0; i<n_components; i++ ){
1125
1126		id = the_components[i]->getType();
#	Line 1136 | Line 1158 | void SimSetup::calcSysValues( void ){
1158
1159		void SimSetup::calcSysValues( void ){
1160		int i, j, k;
1161	<
1162	<
1161	>
1162	>	int *molMembershipArray;
1163	>
1164		tot_atoms = 0;
1165		tot_bonds = 0;
1166		tot_bends = 0;
#	Line 1149 | Line 1172 | void SimSetup::calcSysValues( void ){
1172		tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1173		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174		}
1175	<
1175	>
1176		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	<
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;
1177	>	molMembershipArray = new int[tot_atoms];
1178
1179	<	info->molMembershipArray = new int[tot_atoms];
1179	>	for(i=0; i<nInfo; i++){
1180	>	info[i].n_atoms = tot_atoms;
1181	>	info[i].n_bonds = tot_bonds;
1182	>	info[i].n_bends = tot_bends;
1183	>	info[i].n_torsions = tot_torsions;
1184	>	info[i].n_SRI = tot_SRI;
1185	>	info[i].n_mol = tot_nmol;
1186	>
1187	>	info[i].molMembershipArray = molMembershipArray;
1188	>	}
1189		}
1190
1165	–
1191		#ifdef IS_MPI
1192
1193		void SimSetup::mpiMolDivide( void ){
#	Line 1202 | Line 1227 | void SimSetup::mpiMolDivide( void ){
1227		localMol++;
1228		}
1229		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1230	<	info->molMembershipArray[globalAtomIndex] = allMol;
1230	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1231		globalAtomIndex++;
1232		}
1233
#	Line 1211 | Line 1236 | void SimSetup::mpiMolDivide( void ){
1236		}
1237		local_SRI = local_bonds + local_bends + local_torsions;
1238
1239	<	info->n_atoms = mpiSim->getMyNlocal();
1239	>	info[0].n_atoms = mpiSim->getMyNlocal();
1240
1241	<	if( local_atoms != info->n_atoms ){
1241	>	if( local_atoms != info[0].n_atoms ){
1242		sprintf( painCave.errMsg,
1243		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244		" localAtom (%d) are not equal.\n",
1245	<	info->n_atoms,
1245	>	info[0].n_atoms,
1246		local_atoms );
1247		painCave.isFatal = 1;
1248		simError();
1249		}
1250
1251	<	info->n_bonds = local_bonds;
1252	<	info->n_bends = local_bends;
1253	<	info->n_torsions = local_torsions;
1254	<	info->n_SRI = local_SRI;
1255	<	info->n_mol = localMol;
1251	>	info[0].n_bonds = local_bonds;
1252	>	info[0].n_bends = local_bends;
1253	>	info[0].n_torsions = local_torsions;
1254	>	info[0].n_SRI = local_SRI;
1255	>	info[0].n_mol = localMol;
1256
1257		strcpy( checkPointMsg, "Passed nlocal consistency check." );
1258		MPIcheckPoint();
1259		}
1260	<
1260	>
1261		#endif // is_mpi
1262
1263
1264		void SimSetup::makeSysArrays( void ){
1265	<	int i, j, k;
1265	>	int i, j, k, l;
1266
1267	+	Atom** the_atoms;
1268	+	Molecule* the_molecules;
1269	+	Exclude** the_excludes;
1270
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
1271
1272	<
1255	<	molIndex = 0;
1256	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1272	>	for(l=0; l<nInfo; l++){
1273
1274	<	if(mol2proc[i] == worldRank ){
1275	<	the_molecules[molIndex].setStampID( molCompType[i] );
1276	<	the_molecules[molIndex].setMyIndex( molIndex );
1277	<	the_molecules[molIndex].setGlobalIndex( i );
1278	<	molIndex++;
1263	<	}
1264	<	}
1274	>	// create the atom and short range interaction arrays
1275	>
1276	>	the_atoms = new Atom*[info[l].n_atoms];
1277	>	the_molecules = new Molecule[info[l].n_mol];
1278	>	int molIndex;
1279
1280	<	#else // is_mpi
1281	<
1282	<	molIndex = 0;
1283	<	globalAtomIndex = 0;
1284	<	for(i=0; i<n_components; i++){
1285	<	for(j=0; j<components_nmol[i]; j++ ){
1286	<	the_molecules[molIndex].setStampID( i );
1287	<	the_molecules[molIndex].setMyIndex( molIndex );
1288	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1289	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1290	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1291	<	globalAtomIndex++;
1292	<	}
1293	<	molIndex++;
1280	>	// initialize the molecule's stampID's
1281	>
1282	>	#ifdef IS_MPI
1283	>
1284	>
1285	>	molIndex = 0;
1286	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1287	>
1288	>	if(mol2proc[i] == worldRank ){
1289	>	the_molecules[molIndex].setStampID( molCompType[i] );
1290	>	the_molecules[molIndex].setMyIndex( molIndex );
1291	>	the_molecules[molIndex].setGlobalIndex( i );
1292	>	molIndex++;
1293	>	}
1294		}
1281	–	}
1295
1296	<
1296	>	#else // is_mpi
1297	>
1298	>	molIndex = 0;
1299	>	globalAtomIndex = 0;
1300	>	for(i=0; i<n_components; i++){
1301	>	for(j=0; j<components_nmol[i]; j++ ){
1302	>	the_molecules[molIndex].setStampID( i );
1303	>	the_molecules[molIndex].setMyIndex( molIndex );
1304	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1305	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1306	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1307	>	globalAtomIndex++;
1308	>	}
1309	>	molIndex++;
1310	>	}
1311	>	}
1312	>
1313	>
1314		#endif // is_mpi
1315
1316
1317	<	if( info->n_SRI ){
1317	>	if( info[l].n_SRI ){
1318
1319	<	Exclude::createArray(info->n_SRI);
1320	<	the_excludes = new Exclude*[info->n_SRI];
1321	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1322	<	info->globalExcludes = new int;
1323	<	info->n_exclude = info->n_SRI;
1324	<	}
1325	<	else{
1319	>	Exclude::createArray(info[l].n_SRI);
1320	>	the_excludes = new Exclude*[info[l].n_SRI];
1321	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	>	the_excludes[ex] = new Exclude(ex);
1323	>	}
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].n_exclude = info[l].n_SRI;
1326	>	}
1327	>	else{
1328
1329	<	Exclude::createArray( 1 );
1330	<	the_excludes = new Exclude*;
1331	<	the_excludes[0] = new Exclude(0);
1332	<	the_excludes[0]->setPair( 0,0 );
1333	<	info->globalExcludes = new int;
1334	<	info->globalExcludes[0] = 0;
1335	<	info->n_exclude = 0;
1336	<	}
1329	>	Exclude::createArray( 1 );
1330	>	the_excludes = new Exclude*;
1331	>	the_excludes[0] = new Exclude(0);
1332	>	the_excludes[0]->setPair( 0,0 );
1333	>	info[l].globalExcludes = new int;
1334	>	info[l].globalExcludes[0] = 0;
1335	>	info[l].n_exclude = 0;
1336	>	}
1337
1338	<	// set the arrays into the SimInfo object
1338	>	// set the arrays into the SimInfo object
1339
1340	<	info->atoms = the_atoms;
1341	<	info->molecules = the_molecules;
1342	<	info->nGlobalExcludes = 0;
1343	<	info->excludes = the_excludes;
1340	>	info[l].atoms = the_atoms;
1341	>	info[l].molecules = the_molecules;
1342	>	info[l].nGlobalExcludes = 0;
1343	>	info[l].excludes = the_excludes;
1344
1345	<	the_ff->setSimInfo( info );
1346	<
1345	>	the_ff->setSimInfo( info );
1346	>
1347	>	}
1348		}
1349
1350		void SimSetup::makeIntegrator( void ){
1351
1352	+	int k;
1353	+
1354		NVT<RealIntegrator>*  myNVT = NULL;
1355		NPTi<RealIntegrator>* myNPTi = NULL;
1356		NPTf<RealIntegrator>* myNPTf = NULL;
1357		NPTim<RealIntegrator>* myNPTim = NULL;
1358		NPTfm<RealIntegrator>* myNPTfm = NULL;
1359	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1360	<	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1361	<	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1362	<	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1328	<	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1329	<	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1359	>
1360	>	for(k=0; k<nInfo; k++){
1361	>
1362	>	switch( ensembleCase ){
1363
1364	<	cerr << "setting integrator" <<endl;
1365	<
1366	<	switch( ensembleCase ){
1364	>	case NVE_ENS:
1365	>	if (globals->haveZconstraints()){
1366	>	setupZConstraint(info[k]);
1367	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1368	>	}
1369
1370	<	case NVE_ENS:
1371	<	new NVE<RealIntegrator>( info, the_ff );
1372	<	break;
1370	>	else
1371	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1372	>	break;
1373	>
1374	>	case NVT_ENS:
1375	>	if (globals->haveZconstraints()){
1376	>	setupZConstraint(info[k]);
1377	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	>	}
1379	>	else
1380	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1381
1382	<	case NVT_ENS:
1383	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1384	<	myNVT->setTargetTemp(globals->getTargetTemp());
1382	>	myNVT->setTargetTemp(globals->getTargetTemp());
1383	>
1384	>	if (globals->haveTauThermostat())
1385	>	myNVT->setTauThermostat(globals->getTauThermostat());
1386	>
1387	>	else {
1388	>	sprintf( painCave.errMsg,
1389	>	"SimSetup error: If you use the NVT\n"
1390	>	"    ensemble, you must set tauThermostat.\n");
1391	>	painCave.isFatal = 1;
1392	>	simError();
1393	>	}
1394	>	break;
1395	>
1396	>	case NPTi_ENS:
1397	>	if (globals->haveZconstraints()){
1398	>	setupZConstraint(info[k]);
1399	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	>	}
1401	>	else
1402	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403
1404	<	if (globals->haveTauThermostat())
1405	<	myNVT->setTauThermostat(globals->getTauThermostat());
1404	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	>
1406	>	if (globals->haveTargetPressure())
1407	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	>	else {
1409	>	sprintf( painCave.errMsg,
1410	>	"SimSetup error: If you use a constant pressure\n"
1411	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	>	painCave.isFatal = 1;
1413	>	simError();
1414	>	}
1415	>
1416	>	if( globals->haveTauThermostat() )
1417	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	>	else{
1419	>	sprintf( painCave.errMsg,
1420	>	"SimSetup error: If you use an NPT\n"
1421	>	"    ensemble, you must set tauThermostat.\n");
1422	>	painCave.isFatal = 1;
1423	>	simError();
1424	>	}
1425	>
1426	>	if( globals->haveTauBarostat() )
1427	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	>	else{
1429	>	sprintf( painCave.errMsg,
1430	>	"SimSetup error: If you use an NPT\n"
1431	>	"    ensemble, you must set tauBarostat.\n");
1432	>	painCave.isFatal = 1;
1433	>	simError();
1434	>	}
1435	>	break;
1436	>
1437	>	case NPTf_ENS:
1438	>	if (globals->haveZconstraints()){
1439	>	setupZConstraint(info[k]);
1440	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	>	}
1442	>	else
1443	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1444
1445	<	else {
1446	<	sprintf( painCave.errMsg,
1447	<	"SimSetup error: If you use the NVT\n"
1445	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1446	>
1447	>	if (globals->haveTargetPressure())
1448	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	>	else {
1450	>	sprintf( painCave.errMsg,
1451	>	"SimSetup error: If you use a constant pressure\n"
1452	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	>	painCave.isFatal = 1;
1454	>	simError();
1455	>	}
1456	>
1457	>	if( globals->haveTauThermostat() )
1458	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	>	else{
1460	>	sprintf( painCave.errMsg,
1461	>	"SimSetup error: If you use an NPT\n"
1462		"    ensemble, you must set tauThermostat.\n");
1463	<	painCave.isFatal = 1;
1464	<	simError();
1465	<	}
1466	<	break;
1463	>	painCave.isFatal = 1;
1464	>	simError();
1465	>	}
1466	>
1467	>	if( globals->haveTauBarostat() )
1468	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	>	else{
1470	>	sprintf( painCave.errMsg,
1471	>	"SimSetup error: If you use an NPT\n"
1472	>	"    ensemble, you must set tauBarostat.\n");
1473	>	painCave.isFatal = 1;
1474	>	simError();
1475	>	}
1476	>	break;
1477	>
1478	>	case NPTim_ENS:
1479	>	if (globals->haveZconstraints()){
1480	>	setupZConstraint(info[k]);
1481	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	>	}
1483	>	else
1484	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1485
1486	<	case NPTi_ENS:
1487	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1488	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1489	<
1490	<	if (globals->haveTargetPressure())
1491	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1492	<	else {
1486	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1487	>
1488	>	if (globals->haveTargetPressure())
1489	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	>	else {
1491	>	sprintf( painCave.errMsg,
1492	>	"SimSetup error: If you use a constant pressure\n"
1493	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	>	painCave.isFatal = 1;
1495	>	simError();
1496	>	}
1497	>
1498	>	if( globals->haveTauThermostat() )
1499	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	>	else{
1501	>	sprintf( painCave.errMsg,
1502	>	"SimSetup error: If you use an NPT\n"
1503	>	"    ensemble, you must set tauThermostat.\n");
1504	>	painCave.isFatal = 1;
1505	>	simError();
1506	>	}
1507	>
1508	>	if( globals->haveTauBarostat() )
1509	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	>	else{
1511		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,
1512		"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"
1513		"    ensemble, you must set tauBarostat.\n");
1514		painCave.isFatal = 1;
1515		simError();
1516	<	}
1517	<	break;
1516	>	}
1517	>	break;
1518	>
1519	>	case NPTfm_ENS:
1520	>	if (globals->haveZconstraints()){
1521	>	setupZConstraint(info[k]);
1522	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	>	}
1524	>	else
1525	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1526
1527	<	case NPTf_ENS:
1528	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1529	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1530	<
1531	<	if (globals->haveTargetPressure())
1532	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1533	<	else {
1534	<	sprintf( painCave.errMsg,
1535	<	"SimSetup error: If you use a constant pressure\n"
1536	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1537	<	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();
1527	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1528	>
1529	>	if (globals->haveTargetPressure())
1530	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1531	>	else {
1532	>	sprintf( painCave.errMsg,
1533	>	"SimSetup error: If you use a constant pressure\n"
1534	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1535	>	painCave.isFatal = 1;
1536	>	simError();
1537	>	}
1538
1539	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1540	<
1541	<	break;
1542	<
1543	<
1544	<	case NVTZCONS_ENS:
1545	<
1546	<	setupZConstraint();
1547	<
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;
1539	>	if( globals->haveTauThermostat() )
1540	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1541	>	else{
1542	>	sprintf( painCave.errMsg,
1543	>	"SimSetup error: If you use an NPT\n"
1544	>	"    ensemble, you must set tauThermostat.\n");
1545	>	painCave.isFatal = 1;
1546	>	simError();
1547	>	}
1548
1549	<	case NPTimZCONS_ENS:
1550	<
1551	<	setupZConstraint();
1552	<
1553	<	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1554	<	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1555	<
1556	<	if (globals->haveTargetPressure())
1557	<	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1558	<	else {
1549	>	if( globals->haveTauBarostat() )
1550	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1551	>	else{
1552	>	sprintf( painCave.errMsg,
1553	>	"SimSetup error: If you use an NPT\n"
1554	>	"    ensemble, you must set tauBarostat.\n");
1555	>	painCave.isFatal = 1;
1556	>	simError();
1557	>	}
1558	>	break;
1559	>
1560	>	default:
1561		sprintf( painCave.errMsg,
1562	<	"SimSetup error: If you use a constant pressure\n"
1617	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1562	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1563		painCave.isFatal = 1;
1564		simError();
1565		}
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();
1566		}
1690	–
1567		}
1568
1569		void SimSetup::initFortran( void ){
1570
1571	<	info->refreshSim();
1571	>	info[0].refreshSim();
1572
1573	<	if( !strcmp( info->mixingRule, "standard") ){
1573	>	if( !strcmp( info[0].mixingRule, "standard") ){
1574		the_ff->initForceField( LB_MIXING_RULE );
1575		}
1576	<	else if( !strcmp( info->mixingRule, "explicit") ){
1576	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1577		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1578		}
1579		else{
1580		sprintf( painCave.errMsg,
1581		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	info->mixingRule );
1582	>	info[0].mixingRule );
1583		painCave.isFatal = 1;
1584		simError();
1585		}
#	Line 1717 | Line 1593 | void SimSetup::setupZConstraint()
1593
1594		}
1595
1596	<	void SimSetup::setupZConstraint()
1596	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1597		{
1598	<	if(globals->haveZConsTime()){
1599	<
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();
1598	>	int nZConstraints;
1599	>	ZconStamp** zconStamp;
1600
1601	<	//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();
1601	>	if(globals->haveZconstraintTime()){
1602
1603	<	}
1603	>	//add sample time of z-constraint  into SimInfo's property list
1604	>	DoubleData* zconsTimeProp = new DoubleData();
1605	>	zconsTimeProp->setID(ZCONSTIME_ID);
1606	>	zconsTimeProp->setData(globals->getZconsTime());
1607	>	theInfo.addProperty(zconsTimeProp);
1608	>	}
1609	>	else{
1610	>	sprintf( painCave.errMsg,
1611	>	"ZConstraint error: If you use an ZConstraint\n"
1612	>	" , you must set sample time.\n");
1613	>	painCave.isFatal = 1;
1614	>	simError();
1615	>	}
1616
1617	<	//Determine the name of ouput file and add it into SimInfo's property list
1618	<	//Be careful, do not use inFileName, since it is a pointer which
1619	<	//point to a string at master node, and slave nodes do not contain that string
1620	<
1621	<	string zconsOutput(info->finalName);
1622	<
1623	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1624	<
1625	<	StringData* zconsFilename = new StringData();
1626	<	zconsFilename->setID("zconsfilename");
1627	<	zconsFilename->setData(zconsOutput);
1617	>	//push zconsTol into siminfo, if user does not specify
1618	>	//value for zconsTol, a default value will be used
1619	>	DoubleData* zconsTol = new DoubleData();
1620	>	zconsTol->setID(ZCONSTOL_ID);
1621	>	if(globals->haveZconsTol()){
1622	>	zconsTol->setData(globals->getZconsTol());
1623	>	}
1624	>	else{
1625	>	double defaultZConsTol = 0.01;
1626	>	sprintf( painCave.errMsg,
1627	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628	>	" , default value %f is used.\n", defaultZConsTol);
1629	>	painCave.isFatal = 0;
1630	>	simError();
1631
1632	<	info->addProperty(zconsFilename);
1632	>	zconsTol->setData(defaultZConsTol);
1633	>	}
1634	>	theInfo.addProperty(zconsTol);
1635
1636	+	//set Force Substraction Policy
1637	+	StringData* zconsForcePolicy =  new StringData();
1638	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	+
1640	+	if(globals->haveZconsForcePolicy()){
1641	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	+	}
1643	+	else{
1644	+	sprintf( painCave.errMsg,
1645	+	"ZConstraint Warning: User does not set force substraction policy, "
1646	+	"average force substraction policy is used\n");
1647	+	painCave.isFatal = 0;
1648	+	simError();
1649	+	zconsForcePolicy->setData("BYNUMBER");
1650	+	}
1651	+
1652	+	theInfo.addProperty(zconsForcePolicy);
1653	+
1654	+	//Determine the name of ouput file and add it into SimInfo's property list
1655	+	//Be careful, do not use inFileName, since it is a pointer which
1656	+	//point to a string at master node, and slave nodes do not contain that string
1657	+
1658	+	string zconsOutput(theInfo.finalName);
1659	+
1660	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	+
1662	+	StringData* zconsFilename = new StringData();
1663	+	zconsFilename->setID(ZCONSFILENAME_ID);
1664	+	zconsFilename->setData(zconsOutput);
1665	+
1666	+	theInfo.addProperty(zconsFilename);
1667	+
1668	+	//setup index, pos and other parameters of z-constraint molecules
1669	+	nZConstraints = globals->getNzConstraints();
1670	+	theInfo.nZconstraints = nZConstraints;
1671	+
1672	+	zconStamp = globals->getZconStamp();
1673	+	ZConsParaItem tempParaItem;
1674	+
1675	+	ZConsParaData* zconsParaData = new ZConsParaData();
1676	+	zconsParaData->setID(ZCONSPARADATA_ID);
1677	+
1678	+	for(int i = 0; i < nZConstraints; i++){
1679	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1683	+
1684	+	zconsParaData->addItem(tempParaItem);
1685	+	}
1686	+
1687	+	//sort the parameters by index of molecules
1688	+	zconsParaData->sortByIndex();
1689	+
1690	+	//push data into siminfo, therefore, we can retrieve later
1691	+	theInfo.addProperty(zconsParaData);
1692	+
1693		}

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