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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 661 by tim, Fri Aug 1 16:18:13 2003 UTC vs.
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC

#	Line 3 | Line 3
3		#include <iostream>
4		#include <cmath>
5		#include <string>
6	+	#include <sys/time.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 22 | Line 24
24		#define NPTf_ENS       3
25		#define NPTim_ENS      4
26		#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
27
28		#define FF_DUFF 0
29		#define FF_LJ   1
#	Line 59 | Line 55 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
55		info = the_info;
56		nInfo = theNinfo;
57		isInfoArray = 1;
58	<	}
58	>	}
59
60
61		void SimSetup::parseFile( char* fileName ){
#	Line 97 | Line 93 | void SimSetup::receiveParse(void){
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
98		int i, j, k, globalAtomIndex;
99
100		// gather all of the information from the Bass file
101	<
101	>
102		gatherInfo();
103
104		// creation of complex system objects
#	Line 110 | Line 106 | void SimSetup::createSim( void ){
106		sysObjectsCreation();
107
108		// check on the post processing info
109	<
109	>
110		finalInfoCheck();
111
112		// initialize the system coordinates
113
114	<	initSystemCoords();
119	<
114	>	if( !isInfoArray ) initSystemCoords();
115
116		// make the output filenames
117
#	Line 141 | Line 136 | void SimSetup::makeMolecules( void ){
136
137		void SimSetup::makeMolecules( void ){
138
139	+	int k,l;
140		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
141		molInit molInfo;
142		DirectionalAtom* dAtom;
#	Line 165 | Line 161 | void SimSetup::makeMolecules( void ){
161
162		double ux, uy, uz, u, uSqr;
163
164	<	atomOffset = 0;
169	<	excludeOffset = 0;
170	<	for(i=0; i<info->n_mol; i++){
164	>	for(k=0; k<nInfo; k++){
165
166	<	stampID = the_molecules[i].getStampID();
166	>	the_ff->setSimInfo( &(info[k]) );
167
168	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
169	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
170	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
171	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
172	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
168	>	atomOffset = 0;
169	>	excludeOffset = 0;
170	>	for(i=0; i<info[k].n_mol; i++){
171	>
172	>	stampID = info[k].molecules[i].getStampID();
173
174	<	molInfo.myAtoms = &the_atoms[atomOffset];
175	<	molInfo.myExcludes = &the_excludes[excludeOffset];
176	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
177	<	molInfo.myBends = new Bend*[molInfo.nBends];
178	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
174	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
175	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
176	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
177	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
178	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
179	>
180	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
181	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
182	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
183	>	molInfo.myBends = new Bend*[molInfo.nBends];
184	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
185
186	<	theBonds = new bond_pair[molInfo.nBonds];
187	<	theBends = new bend_set[molInfo.nBends];
188	<	theTorsions = new torsion_set[molInfo.nTorsions];
186	>	theBonds = new bond_pair[molInfo.nBonds];
187	>	theBends = new bend_set[molInfo.nBends];
188	>	theTorsions = new torsion_set[molInfo.nTorsions];
189
190	<	// make the Atoms
190	>	// make the Atoms
191
192	<	for(j=0; j<molInfo.nAtoms; j++){
193	<
194	<	currentAtom = comp_stamps[stampID]->getAtom( j );
195	<	if( currentAtom->haveOrientation() ){
196	<
197	<	dAtom = new DirectionalAtom(j + atomOffset);
198	<	info->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	<	}
219	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
192	>	for(j=0; j<molInfo.nAtoms; j++){
193	>
194	>	currentAtom = comp_stamps[stampID]->getAtom( j );
195	>	if( currentAtom->haveOrientation() ){
196
197	+	dAtom = new DirectionalAtom( (j + atomOffset),
198	+	info[k].getConfiguration() );
199	+	info[k].n_oriented++;
200	+	molInfo.myAtoms[j] = dAtom;
201	+
202	+	ux = currentAtom->getOrntX();
203	+	uy = currentAtom->getOrntY();
204	+	uz = currentAtom->getOrntZ();
205	+
206	+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
207	+
208	+	u = sqrt( uSqr );
209	+	ux = ux / u;
210	+	uy = uy / u;
211	+	uz = uz / u;
212	+
213	+	dAtom->setSUx( ux );
214	+	dAtom->setSUy( uy );
215	+	dAtom->setSUz( uz );
216	+	}
217	+	else{
218	+	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
219	+	info[k].getConfiguration() );
220	+	}
221	+	molInfo.myAtoms[j]->setType( currentAtom->getType() );
222	+
223		#ifdef IS_MPI
224
225	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
226
227		#endif // is_mpi
228	<	}
228	>	}
229
230		// make the bonds
231	<	for(j=0; j<molInfo.nBonds; j++){
231	>	for(j=0; j<molInfo.nBonds; j++){
232
233	<	currentBond = comp_stamps[stampID]->getBond( j );
234	<	theBonds[j].a = currentBond->getA() + atomOffset;
235	<	theBonds[j].b = currentBond->getB() + atomOffset;
236	<
237	<	exI = theBonds[j].a;
238	<	exJ = theBonds[j].b;
239	<
240	<	// exclude_I must always be the smaller of the pair
241	<	if( exI > exJ ){
242	<	tempEx = exI;
243	<	exI = exJ;
244	<	exJ = tempEx;
245	<	}
246	<	#ifdef IS_MPI
247	<	tempEx = exI;
248	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
249	<	tempEx = exJ;
250	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
251	<
252	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
253	<	#else  // isn't MPI
254	<
255	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
233	>	currentBond = comp_stamps[stampID]->getBond( j );
234	>	theBonds[j].a = currentBond->getA() + atomOffset;
235	>	theBonds[j].b = currentBond->getB() + atomOffset;
236	>
237	>	exI = theBonds[j].a;
238	>	exJ = theBonds[j].b;
239	>
240	>	// exclude_I must always be the smaller of the pair
241	>	if( exI > exJ ){
242	>	tempEx = exI;
243	>	exI = exJ;
244	>	exJ = tempEx;
245	>	}
246	>	#ifdef IS_MPI
247	>	tempEx = exI;
248	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>	tempEx = exJ;
250	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
251	>
252	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
253	>	#else  // isn't MPI
254	>
255	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
256		#endif  //is_mpi
255	–	}
256	–	excludeOffset += molInfo.nBonds;
257	–
258	–	//make the bends
259	–	for(j=0; j<molInfo.nBends; j++){
260	–
261	–	currentBend = comp_stamps[stampID]->getBend( j );
262	–	theBends[j].a = currentBend->getA() + atomOffset;
263	–	theBends[j].b = currentBend->getB() + atomOffset;
264	–	theBends[j].c = currentBend->getC() + atomOffset;
265	–
266	–	if( currentBend->haveExtras() ){
267	–
268	–	extras = currentBend->getExtras();
269	–	current_extra = extras;
270	–
271	–	while( current_extra != NULL ){
272	–	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273	–
274	–	switch( current_extra->getType() ){
275	–
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:
289	–	sprintf( painCave.errMsg,
290	–	"SimSetup Error: ghostVectorSource was neither a "
291	–	"double nor an int.\n"
292	–	"-->Bend[%d] in %s\n",
293	–	j, comp_stamps[stampID]->getID() );
294	–	painCave.isFatal = 1;
295	–	simError();
296	–	}
297	–	}
298	–
299	–	else{
300	–
301	–	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();
308	–	}
309	–
310	–	current_extra = current_extra->getNext();
311	–	}
257		}
258	<
314	<	if( !theBends[j].isGhost ){
315	<
316	<	exI = theBends[j].a;
317	<	exJ = theBends[j].c;
318	<	}
319	<	else{
320	<
321	<	exI = theBends[j].a;
322	<	exJ = theBends[j].b;
323	<	}
258	>	excludeOffset += molInfo.nBonds;
259
260	<	// exclude_I must always be the smaller of the pair
261	<	if( exI > exJ ){
262	<	tempEx = exI;
263	<	exI = exJ;
264	<	exJ = tempEx;
260	>	//make the bends
261	>	for(j=0; j<molInfo.nBends; j++){
262	>
263	>	currentBend = comp_stamps[stampID]->getBend( j );
264	>	theBends[j].a = currentBend->getA() + atomOffset;
265	>	theBends[j].b = currentBend->getB() + atomOffset;
266	>	theBends[j].c = currentBend->getC() + atomOffset;
267	>
268	>	if( currentBend->haveExtras() ){
269	>
270	>	extras = currentBend->getExtras();
271	>	current_extra = extras;
272	>
273	>	while( current_extra != NULL ){
274	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
275	>
276	>	switch( current_extra->getType() ){
277	>
278	>	case 0:
279	>	theBends[j].ghost =
280	>	current_extra->getInt() + atomOffset;
281	>	theBends[j].isGhost = 1;
282	>	break;
283	>
284	>	case 1:
285	>	theBends[j].ghost =
286	>	(int)current_extra->getDouble() + atomOffset;
287	>	theBends[j].isGhost = 1;
288	>	break;
289	>
290	>	default:
291	>	sprintf( painCave.errMsg,
292	>	"SimSetup Error: ghostVectorSource was neither a "
293	>	"double nor an int.\n"
294	>	"-->Bend[%d] in %s\n",
295	>	j, comp_stamps[stampID]->getID() );
296	>	painCave.isFatal = 1;
297	>	simError();
298	>	}
299		}
331	–	#ifdef IS_MPI
332	–	tempEx = exI;
333	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
334	–	tempEx = exJ;
335	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
300
301	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
302	<	#else  // isn't MPI
303	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
304	<	#endif  //is_mpi
301	>	else{
302	>
303	>	sprintf( painCave.errMsg,
304	>	"SimSetup Error: unhandled bend assignment:\n"
305	>	"    -->%s in Bend[%d] in %s\n",
306	>	current_extra->getlhs(),
307	>	j, comp_stamps[stampID]->getID() );
308	>	painCave.isFatal = 1;
309	>	simError();
310	>	}
311	>
312	>	current_extra = current_extra->getNext();
313		}
314	<	excludeOffset += molInfo.nBends;
315	<
316	<	for(j=0; j<molInfo.nTorsions; j++){
314	>	}
315	>
316	>	if( !theBends[j].isGhost ){
317	>
318	>	exI = theBends[j].a;
319	>	exJ = theBends[j].c;
320	>	}
321	>	else{
322	>
323	>	exI = theBends[j].a;
324	>	exJ = theBends[j].b;
325	>	}
326	>
327	>	// exclude_I must always be the smaller of the pair
328	>	if( exI > exJ ){
329	>	tempEx = exI;
330	>	exI = exJ;
331	>	exJ = tempEx;
332	>	}
333	>	#ifdef IS_MPI
334	>	tempEx = exI;
335	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>	tempEx = exJ;
337	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
338
339	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
340	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
341	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
342	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	<
352	<	exI = theTorsions[j].a;
353	<	exJ = theTorsions[j].d;
354	<
355	<	// exclude_I must always be the smaller of the pair
356	<	if( exI > exJ ){
357	<	tempEx = exI;
358	<	exI = exJ;
359	<	exJ = tempEx;
339	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
340	>	#else  // isn't MPI
341	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
342	>	#endif  //is_mpi
343		}
344	<	#ifdef IS_MPI
362	<	tempEx = exI;
363	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
364	<	tempEx = exJ;
365	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
344	>	excludeOffset += molInfo.nBends;
345
346	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
346	>	for(j=0; j<molInfo.nTorsions; j++){
347	>
348	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
349	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
350	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
351	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
352	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
353	>
354	>	exI = theTorsions[j].a;
355	>	exJ = theTorsions[j].d;
356	>
357	>	// exclude_I must always be the smaller of the pair
358	>	if( exI > exJ ){
359	>	tempEx = exI;
360	>	exI = exJ;
361	>	exJ = tempEx;
362	>	}
363	>	#ifdef IS_MPI
364	>	tempEx = exI;
365	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	>	tempEx = exJ;
367	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
368	>
369	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
370		#else  // isn't MPI
371	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
372		#endif  //is_mpi
373	<	}
374	<	excludeOffset += molInfo.nTorsions;
373	>	}
374	>	excludeOffset += molInfo.nTorsions;
375	>
376	>
377	>	// send the arrays off to the forceField for init.
378	>
379	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
380	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
381	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
382	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
383	>
384	>
385	>	info[k].molecules[i].initialize( molInfo );
386
387	<
388	<	// send the arrays off to the forceField for init.
389	<
390	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
391	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
392	<	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;
387	>
388	>	atomOffset += molInfo.nAtoms;
389	>	delete[] theBonds;
390	>	delete[] theBends;
391	>	delete[] theTorsions;
392	>	}
393		}
394	<
394	>
395		#ifdef IS_MPI
396		sprintf( checkPointMsg, "all molecules initialized succesfully" );
397		MPIcheckPoint();
398		#endif // is_mpi
399	<
399	>
400		// clean up the forcefield
401	+
402		the_ff->calcRcut();
403		the_ff->cleanMe();
404	<
404	>
405		}
406
407		void SimSetup::initFromBass( void ){
#	Line 410 | Line 414 | void SimSetup::initFromBass( void ){
414		int n_extra;
415		int have_extra, done;
416
417	+	double vel[3];
418	+	vel[0] = 0.0;
419	+	vel[1] = 0.0;
420	+	vel[2] = 0.0;
421	+
422		temp1 = (double)tot_nmol / 4.0;
423		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
424		temp3 = ceil( temp2 );
#	Line 419 | Line 428 | void SimSetup::initFromBass( void ){
428		have_extra =1;
429
430		n_cells = (int)temp3 - 1;
431	<	cellx = info->boxL[0] / temp3;
432	<	celly = info->boxL[1] / temp3;
433	<	cellz = info->boxL[2] / temp3;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
435		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
436		n_per_extra = (int)ceil( temp1 );
437
438		if( n_per_extra > 4){
439		sprintf( painCave.errMsg,
440	<	"SimSetup error. There has been an error in constructing"
441	<	" the non-complete lattice.\n" );
440	>	"SimSetup error. There has been an error in constructing"
441	>	" the non-complete lattice.\n" );
442		painCave.isFatal = 1;
443		simError();
444		}
445		}
446		else{
447		n_cells = (int)temp3;
448	<	cellx = info->boxL[0] / temp3;
449	<	celly = info->boxL[1] / temp3;
450	<	cellz = info->boxL[2] / temp3;
448	>	cellx = info[0].boxL[0] / temp3;
449	>	celly = info[0].boxL[1] / temp3;
450	>	cellz = info[0].boxL[2] / temp3;
451		}
452
453		current_mol = 0;
#	Line 450 | Line 459 | void SimSetup::initFromBass( void ){
459		for( j=0; j < n_cells; j++ ){
460		for( k=0; k < n_cells; k++ ){
461
462	<	makeElement( i * cellx,
463	<	j * celly,
464	<	k * cellz );
462	>	makeElement( i * cellx,
463	>	j * celly,
464	>	k * cellz );
465
466	<	makeElement( i * cellx + 0.5 * cellx,
467	<	j * celly + 0.5 * celly,
468	<	k * cellz );
466	>	makeElement( i * cellx + 0.5 * cellx,
467	>	j * celly + 0.5 * celly,
468	>	k * cellz );
469
470	<	makeElement( i * cellx,
471	<	j * celly + 0.5 * celly,
472	<	k * cellz + 0.5 * cellz );
470	>	makeElement( i * cellx,
471	>	j * celly + 0.5 * celly,
472	>	k * cellz + 0.5 * cellz );
473
474	<	makeElement( i * cellx + 0.5 * cellx,
475	<	j * celly,
476	<	k * cellz + 0.5 * cellz );
474	>	makeElement( i * cellx + 0.5 * cellx,
475	>	j * celly,
476	>	k * cellz + 0.5 * cellz );
477		}
478		}
479		}
#	Line 476 | Line 485 | void SimSetup::initFromBass( void ){
485		for( i=0; i < (n_cells+1) && !done; i++ ){
486		for( j=0; j < (n_cells+1) && !done; j++ ){
487
488	<	if( i < n_cells ){
488	>	if( i < n_cells ){
489
490	<	if( j < n_cells ){
491	<	start_ndx = n_cells;
492	<	}
493	<	else start_ndx = 0;
494	<	}
495	<	else start_ndx = 0;
490	>	if( j < n_cells ){
491	>	start_ndx = n_cells;
492	>	}
493	>	else start_ndx = 0;
494	>	}
495	>	else start_ndx = 0;
496
497	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
498
499	<	makeElement( i * cellx,
500	<	j * celly,
501	<	k * cellz );
502	<	done = ( current_mol >= tot_nmol );
499	>	makeElement( i * cellx,
500	>	j * celly,
501	>	k * cellz );
502	>	done = ( current_mol >= tot_nmol );
503
504	<	if( !done && n_per_extra > 1 ){
505	<	makeElement( i * cellx + 0.5 * cellx,
506	<	j * celly + 0.5 * celly,
507	<	k * cellz );
508	<	done = ( current_mol >= tot_nmol );
509	<	}
504	>	if( !done && n_per_extra > 1 ){
505	>	makeElement( i * cellx + 0.5 * cellx,
506	>	j * celly + 0.5 * celly,
507	>	k * cellz );
508	>	done = ( current_mol >= tot_nmol );
509	>	}
510
511	<	if( !done && n_per_extra > 2){
512	<	makeElement( i * cellx,
513	<	j * celly + 0.5 * celly,
514	<	k * cellz + 0.5 * cellz );
515	<	done = ( current_mol >= tot_nmol );
516	<	}
511	>	if( !done && n_per_extra > 2){
512	>	makeElement( i * cellx,
513	>	j * celly + 0.5 * celly,
514	>	k * cellz + 0.5 * cellz );
515	>	done = ( current_mol >= tot_nmol );
516	>	}
517
518	<	if( !done && n_per_extra > 3){
519	<	makeElement( i * cellx + 0.5 * cellx,
520	<	j * celly,
521	<	k * cellz + 0.5 * cellz );
522	<	done = ( current_mol >= tot_nmol );
523	<	}
524	<	}
518	>	if( !done && n_per_extra > 3){
519	>	makeElement( i * cellx + 0.5 * cellx,
520	>	j * celly,
521	>	k * cellz + 0.5 * cellz );
522	>	done = ( current_mol >= tot_nmol );
523	>	}
524	>	}
525		}
526		}
527		}
528
529	<
530	<	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 );
529	>	for( i=0; i<info[0].n_atoms; i++ ){
530	>	info[0].atoms[i]->setVel( vel );
531		}
532		}
533
#	Line 531 | Line 537 | void SimSetup::makeElement( double x, double y, double
537		AtomStamp* current_atom;
538		DirectionalAtom* dAtom;
539		double rotMat[3][3];
540	+	double pos[3];
541
542		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
543
544		current_atom = comp_stamps[current_comp]->getAtom( k );
545		if( !current_atom->havePosition() ){
546		sprintf( painCave.errMsg,
547	<	"SimSetup:initFromBass error.\n"
548	<	"\tComponent %s, atom %s does not have a position specified.\n"
549	<	"\tThe initialization routine is unable to give a start"
550	<	" position.\n",
551	<	comp_stamps[current_comp]->getID(),
552	<	current_atom->getType() );
547	>	"SimSetup:initFromBass error.\n"
548	>	"\tComponent %s, atom %s does not have a position specified.\n"
549	>	"\tThe initialization routine is unable to give a start"
550	>	" position.\n",
551	>	comp_stamps[current_comp]->getID(),
552	>	current_atom->getType() );
553		painCave.isFatal = 1;
554		simError();
555		}
556	+
557	+	pos[0] = x + current_atom->getPosX();
558	+	pos[1] = y + current_atom->getPosY();
559	+	pos[2] = z + current_atom->getPosZ();
560	+
561	+	info[0].atoms[current_atom_ndx]->setPos( pos );
562
563	<	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() );
563	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
564
565	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
565	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
566
556	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
557	–
567		rotMat[0][0] = 1.0;
568		rotMat[0][1] = 0.0;
569		rotMat[0][2] = 0.0;
#	Line 590 | Line 599 | void SimSetup::gatherInfo( void ){
599		ensembleCase = -1;
600		ffCase = -1;
601
593	–	// get the stamps and globals;
594	–	stamps = stamps;
595	–	globals = globals;
596	–
602		// set the easy ones first
603	<	info->target_temp = globals->getTargetTemp();
604	<	info->dt = globals->getDt();
605	<	info->run_time = globals->getRunTime();
603	>
604	>	for( i=0; i<nInfo; i++){
605	>	info[i].target_temp = globals->getTargetTemp();
606	>	info[i].dt = globals->getDt();
607	>	info[i].run_time = globals->getRunTime();
608	>	}
609		n_components = globals->getNComponents();
610
611
#	Line 610 | Line 618 | void SimSetup::gatherInfo( void ){
618		else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
619		else{
620		sprintf( painCave.errMsg,
621	<	"SimSetup Error. Unrecognized force field -> %s\n",
622	<	force_field );
621	>	"SimSetup Error. Unrecognized force field -> %s\n",
622	>	force_field );
623		painCave.isFatal = 1;
624		simError();
625		}
#	Line 627 | Line 635 | void SimSetup::gatherInfo( void ){
635		else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
636		else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
637		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, "NPTZCONS"))
634	–	ensembleCase = NPTiZCONS_ENS;
635	–	else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
636	–	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637	–	else if( !strcasecmp( ensemble, "NPTfmZCONS"))  ensembleCase = NPTfmZCONS_ENS;
638	–
638		else{
639		sprintf( painCave.errMsg,
640	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641		"reverting to NVE for this simulation.\n",
642	<	ensemble );
642	>	ensemble );
643		painCave.isFatal = 0;
644		simError();
645		strcpy( ensemble, "NVE" );
646		ensembleCase = NVE_ENS;
647		}
648	<	strcpy( info->ensemble, ensemble );
648	>
649	>	for(i=0; i<nInfo; i++){
650	>
651	>	strcpy( info[i].ensemble, ensemble );
652
653	<	// get the mixing rule
653	>	// get the mixing rule
654
655	<	strcpy( info->mixingRule, globals->getMixingRule() );
656	<	info->usePBC = globals->getPBC();
657	<
655	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
656	>	info[i].usePBC = globals->getPBC();
657	>	}
658
659		// get the components and calculate the tot_nMol and indvidual n_mol
660
#	Line 668 | Line 670 | void SimSetup::gatherInfo( void ){
670		for( i=0; i<n_components; i++ ){
671
672		if( !the_components[i]->haveNMol() ){
673	<	// we have a problem
674	<	sprintf( painCave.errMsg,
675	<	"SimSetup Error. No global NMol or component NMol"
676	<	" given. Cannot calculate the number of atoms.\n" );
677	<	painCave.isFatal = 1;
678	<	simError();
673	>	// we have a problem
674	>	sprintf( painCave.errMsg,
675	>	"SimSetup Error. No global NMol or component NMol"
676	>	" given. Cannot calculate the number of atoms.\n" );
677	>	painCave.isFatal = 1;
678	>	simError();
679		}
680
681		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 684 | void SimSetup::gatherInfo( void ){
684		}
685		else{
686		sprintf( painCave.errMsg,
687	<	"SimSetup error.\n"
688	<	"\tSorry, the ability to specify total"
689	<	" nMols and then give molfractions in the components\n"
690	<	"\tis not currently supported."
691	<	" Please give nMol in the components.\n" );
687	>	"SimSetup error.\n"
688	>	"\tSorry, the ability to specify total"
689	>	" nMols and then give molfractions in the components\n"
690	>	"\tis not currently supported."
691	>	" Please give nMol in the components.\n" );
692		painCave.isFatal = 1;
693		simError();
694		}
695
696		// set the status, sample, and thermal kick times
697
698	<	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	<	}
698	>	for(i=0; i<nInfo; i++){
699
700	<	if( globals->haveStatusTime() ){
701	<	info->statusTime = globals->getStatusTime();
702	<	}
700	>	if( globals->haveSampleTime() ){
701	>	info[i].sampleTime = globals->getSampleTime();
702	>	info[i].statusTime = info[i].sampleTime;
703	>	info[i].thermalTime = info[i].sampleTime;
704	>	}
705	>	else{
706	>	info[i].sampleTime = globals->getRunTime();
707	>	info[i].statusTime = info[i].sampleTime;
708	>	info[i].thermalTime = info[i].sampleTime;
709	>	}
710	>
711	>	if( globals->haveStatusTime() ){
712	>	info[i].statusTime = globals->getStatusTime();
713	>	}
714	>
715	>	if( globals->haveThermalTime() ){
716	>	info[i].thermalTime = globals->getThermalTime();
717	>	}
718
719	<	if( globals->haveThermalTime() ){
712	<	info->thermalTime = globals->getThermalTime();
713	<	}
719	>	// check for the temperature set flag
720
721	<	// check for the temperature set flag
716	<
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();
721	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
722
723	<	info->setBox( boxVector );
724	<	}
725	<	else if( globals->haveDensity() ){
723	>	// get some of the tricky things that may still be in the globals
724	>
725	>	double boxVector[3];
726	>	if( globals->haveBox() ){
727	>	boxVector[0] = globals->getBox();
728	>	boxVector[1] = globals->getBox();
729	>	boxVector[2] = globals->getBox();
730	>
731	>	info[i].setBox( boxVector );
732	>	}
733	>	else if( globals->haveDensity() ){
734	>
735	>	double vol;
736	>	vol = (double)tot_nmol / globals->getDensity();
737	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
738	>	boxVector[1] = boxVector[0];
739	>	boxVector[2] = boxVector[0];
740	>
741	>	info[i].setBox( boxVector );
742	>	}
743	>	else{
744	>	if( !globals->haveBoxX() ){
745	>	sprintf( painCave.errMsg,
746	>	"SimSetup error, no periodic BoxX size given.\n" );
747	>	painCave.isFatal = 1;
748	>	simError();
749	>	}
750	>	boxVector[0] = globals->getBoxX();
751	>
752	>	if( !globals->haveBoxY() ){
753	>	sprintf( painCave.errMsg,
754	>	"SimSetup error, no periodic BoxY size given.\n" );
755	>	painCave.isFatal = 1;
756	>	simError();
757	>	}
758	>	boxVector[1] = globals->getBoxY();
759	>
760	>	if( !globals->haveBoxZ() ){
761	>	sprintf( painCave.errMsg,
762	>	"SimSetup error, no periodic BoxZ size given.\n" );
763	>	painCave.isFatal = 1;
764	>	simError();
765	>	}
766	>	boxVector[2] = globals->getBoxZ();
767	>
768	>	info[i].setBox( boxVector );
769	>	}
770	>	}
771
772	<	double vol;
773	<	vol = (double)tot_nmol / globals->getDensity();
774	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
734	<	boxVector[1] = boxVector[0];
735	<	boxVector[2] = boxVector[0];
772	>	int seedValue;
773	>	struct timeval now_time_val;
774	>	struct timezone time_zone;
775
776	<	info->setBox( boxVector );
776	>	if(globals->haveSeed()){
777	>	seedValue = globals->getSeed();
778		}
779		else{
780	<	if( !globals->haveBoxX() ){
781	<	sprintf( painCave.errMsg,
782	<	"SimSetup error, no periodic BoxX size given.\n" );
783	<	painCave.isFatal = 1;
784	<	simError();
780	>	#ifndef IS_MPI
781	>	gettimeofday(&now_time_val, &time_zone);  // get the time now
782	>	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
783	>	#else
784	>	if(worldRank == 0){
785	>	gettimeofday(&now_time_val, &time_zone);  // get the time now
786	>	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
787		}
788	<	boxVector[0] = globals->getBoxX();
788	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
789	>	#endif
790	>	}
791
792	<	if( !globals->haveBoxY() ){
793	<	sprintf( painCave.errMsg,
750	<	"SimSetup error, no periodic BoxY size given.\n" );
751	<	painCave.isFatal = 1;
752	<	simError();
753	<	}
754	<	boxVector[1] = globals->getBoxY();
755	<
756	<	if( !globals->haveBoxZ() ){
757	<	sprintf( painCave.errMsg,
758	<	"SimSetup error, no periodic BoxZ size given.\n" );
759	<	painCave.isFatal = 1;
760	<	simError();
761	<	}
762	<	boxVector[2] = globals->getBoxZ();
763	<
764	<	info->setBox( boxVector );
792	>	for(int i = 0; i < nInfo; i++){
793	>	info[i].setSeed(seedValue);
794		}
795
767	–
768	–
796		#ifdef IS_MPI
797		strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
798		MPIcheckPoint();
#	Line 777 | Line 804 | void SimSetup::finalInfoCheck( void ){
804		void SimSetup::finalInfoCheck( void ){
805		int index;
806		int usesDipoles;
807	<
807	>	int i;
808
809	<	// check electrostatic parameters
810	<
811	<	index = 0;
812	<	usesDipoles = 0;
813	<	while( (index < info->n_atoms) && !usesDipoles ){
814	<	usesDipoles = ((info->atoms)[index])->hasDipole();
815	<	index++;
816	<	}
817	<
809	>	for(i=0; i<nInfo; i++){
810	>	// check electrostatic parameters
811	>
812	>	index = 0;
813	>	usesDipoles = 0;
814	>	while( (index < info[i].n_atoms) && !usesDipoles ){
815	>	usesDipoles = (info[i].atoms[index])->hasDipole();
816	>	index++;
817	>	}
818	>
819		#ifdef IS_MPI
820	<	int myUse = usesDipoles;
821	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
820	>	int myUse = usesDipoles;
821	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
822		#endif //is_mpi
795	–
796	–	double theEcr, theEst;
797	–
798	–	if (globals->getUseRF() ) {
799	–	info->useReactionField = 1;
823
824	<	if( !globals->haveECR() ){
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup Warning: using default value of 1/2 the smallest "
827	<	"box length for the electrostaticCutoffRadius.\n"
805	<	"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();
815	<	}
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 );
830	<
831	<	if(!globals->haveDielectric() ){
832	<	sprintf( painCave.errMsg,
833	<	"SimSetup Error: You are trying to use Reaction Field without"
834	<	"setting a dielectric constant!\n"
835	<	);
836	<	painCave.isFatal = 1;
837	<	simError();
838	<	}
839	<	info->dielectric = globals->getDielectric();
840	<	}
841	<	else {
842	<	if (usesDipoles) {
824	>	double theEcr, theEst;
825	>
826	>	if (globals->getUseRF() ) {
827	>	info[i].useReactionField = 1;
828
829		if( !globals->haveECR() ){
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Warning: using default value of 1/2 the smallest "
832	<	"box length for the electrostaticCutoffRadius.\n"
833	<	"I hope you have a very fast processor!\n");
834	<	painCave.isFatal = 0;
835	<	simError();
836	<	double smallest;
837	<	smallest = info->boxL[0];
838	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
839	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
840	<	theEcr = 0.5 * smallest;
830	>	sprintf( painCave.errMsg,
831	>	"SimSetup Warning: using default value of 1/2 the smallest "
832	>	"box length for the electrostaticCutoffRadius.\n"
833	>	"I hope you have a very fast processor!\n");
834	>	painCave.isFatal = 0;
835	>	simError();
836	>	double smallest;
837	>	smallest = info[i].boxL[0];
838	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
839	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
840	>	theEcr = 0.5 * smallest;
841		} else {
842	<	theEcr = globals->getECR();
842	>	theEcr = globals->getECR();
843		}
844
845		if( !globals->haveEST() ){
846	<	sprintf( painCave.errMsg,
847	<	"SimSetup Warning: using default value of 0.05 * the "
848	<	"electrostaticCutoffRadius for the "
849	<	"electrostaticSkinThickness\n"
850	<	);
851	<	painCave.isFatal = 0;
852	<	simError();
868	<	theEst = 0.05 * theEcr;
846	>	sprintf( painCave.errMsg,
847	>	"SimSetup Warning: using default value of 0.05 * the "
848	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
849	>	);
850	>	painCave.isFatal = 0;
851	>	simError();
852	>	theEst = 0.05 * theEcr;
853		} else {
854	<	theEst= globals->getEST();
854	>	theEst= globals->getEST();
855		}
856	+
857	+	info[i].setEcr( theEcr, theEst );
858	+
859	+	if(!globals->haveDielectric() ){
860	+	sprintf( painCave.errMsg,
861	+	"SimSetup Error: You are trying to use Reaction Field without"
862	+	"setting a dielectric constant!\n"
863	+	);
864	+	painCave.isFatal = 1;
865	+	simError();
866	+	}
867	+	info[i].dielectric = globals->getDielectric();
868	+	}
869	+	else {
870	+	if (usesDipoles) {
871	+
872	+	if( !globals->haveECR() ){
873	+	sprintf( painCave.errMsg,
874	+	"SimSetup Warning: using default value of 1/2 the smallest "
875	+	"box length for the electrostaticCutoffRadius.\n"
876	+	"I hope you have a very fast processor!\n");
877	+	painCave.isFatal = 0;
878	+	simError();
879	+	double smallest;
880	+	smallest = info[i].boxL[0];
881	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
882	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
883	+	theEcr = 0.5 * smallest;
884	+	} else {
885	+	theEcr = globals->getECR();
886	+	}
887	+
888	+	if( !globals->haveEST() ){
889	+	sprintf( painCave.errMsg,
890	+	"SimSetup Warning: using default value of 0.05 * the "
891	+	"electrostaticCutoffRadius for the "
892	+	"electrostaticSkinThickness\n"
893	+	);
894	+	painCave.isFatal = 0;
895	+	simError();
896	+	theEst = 0.05 * theEcr;
897	+	} else {
898	+	theEst= globals->getEST();
899	+	}
900	+
901	+	info[i].setEcr( theEcr, theEst );
902	+	}
903	+	}
904	+	}
905
873	–	info->setEcr( theEcr, theEst );
874	–	}
875	–	}
876	–
906		#ifdef IS_MPI
907		strcpy( checkPointMsg, "post processing checks out" );
908		MPIcheckPoint();
#	Line 882 | Line 911 | void SimSetup::initSystemCoords( void ){
911		}
912
913		void SimSetup::initSystemCoords( void ){
914	+	int i;
915	+
916	+	char* inName;
917
918	<	if( globals->haveInitialConfig() ){
919	<
920	<	InitializeFromFile* fileInit;
918	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
919	>
920	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
921	>
922	>	if( globals->haveInitialConfig() ){
923	>
924	>	InitializeFromFile* fileInit;
925		#ifdef IS_MPI // is_mpi
926	<	if( worldRank == 0 ){
926	>	if( worldRank == 0 ){
927		#endif //is_mpi
928	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
928	>	inName = globals->getInitialConfig();
929	>	double* tempDouble = new double[1000000];
930	>	fileInit = new InitializeFromFile( inName );
931		#ifdef IS_MPI
932	<	}else fileInit = new InitializeFromFile( NULL );
932	>	}else fileInit = new InitializeFromFile( NULL );
933		#endif
934	<	fileInit->readInit( info ); // default velocities on
935	<
936	<	delete fileInit;
937	<	}
938	<	else{
939	<
934	>	fileInit->readInit( info ); // default velocities on
935	>
936	>	delete fileInit;
937	>	}
938	>	else{
939	>
940		#ifdef IS_MPI
941	<
942	<	// no init from bass
943	<
944	<	sprintf( painCave.errMsg,
945	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
946	<	painCave.isFatal;
947	<	simError();
948	<
941	>
942	>	// no init from bass
943	>
944	>	sprintf( painCave.errMsg,
945	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
946	>	painCave.isFatal;
947	>	simError();
948	>
949		#else
950	<
951	<	initFromBass();
952	<
953	<
950	>
951	>	initFromBass();
952	>
953	>
954		#endif
955	<	}
956	<
955	>	}
956	>
957		#ifdef IS_MPI
958		strcpy( checkPointMsg, "Successfully read in the initial configuration" );
959		MPIcheckPoint();
960		#endif // is_mpi
961	<
961	>
962		}
963
964
965		void SimSetup::makeOutNames( void ){
966	+
967	+	int k;
968
969	+
970	+	for(k=0; k<nInfo; k++){
971	+
972		#ifdef IS_MPI
973	<	if( worldRank == 0 ){
973	>	if( worldRank == 0 ){
974		#endif // is_mpi
975	<
976	<	if( globals->haveFinalConfig() ){
977	<	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" );
975	>
976	>	if( globals->haveFinalConfig() ){
977	>	strcpy( info[k].finalName, globals->getFinalConfig() );
978		}
944	–	else if( !strcmp( endTest, ".BASS" ) ){
945	–	strcpy( endTest, ".eor" );
946	–	}
979		else{
980	<	endTest = &(info->finalName[nameLength - 4]);
981	<	if( !strcmp( endTest, ".bss" ) ){
982	<	strcpy( endTest, ".eor" );
983	<	}
984	<	else if( !strcmp( endTest, ".mdl" ) ){
985	<	strcpy( endTest, ".eor" );
986	<	}
987	<	else{
988	<	strcat( info->finalName, ".eor" );
989	<	}
990	<	}
980	>	strcpy( info[k].finalName, inFileName );
981	>	char* endTest;
982	>	int nameLength = strlen( info[k].finalName );
983	>	endTest = &(info[k].finalName[nameLength - 5]);
984	>	if( !strcmp( endTest, ".bass" ) ){
985	>	strcpy( endTest, ".eor" );
986	>	}
987	>	else if( !strcmp( endTest, ".BASS" ) ){
988	>	strcpy( endTest, ".eor" );
989	>	}
990	>	else{
991	>	endTest = &(info[k].finalName[nameLength - 4]);
992	>	if( !strcmp( endTest, ".bss" ) ){
993	>	strcpy( endTest, ".eor" );
994		}
995	<
996	<	// make the sample and status out names
962	<
963	<	strcpy( info->sampleName, inFileName );
964	<	char* endTest;
965	<	int nameLength = strlen( info->sampleName );
966	<	endTest = &(info->sampleName[nameLength - 5]);
967	<	if( !strcmp( endTest, ".bass" ) ){
968	<	strcpy( endTest, ".dump" );
995	>	else if( !strcmp( endTest, ".mdl" ) ){
996	>	strcpy( endTest, ".eor" );
997		}
970	–	else if( !strcmp( endTest, ".BASS" ) ){
971	–	strcpy( endTest, ".dump" );
972	–	}
998		else{
999	<	endTest = &(info->sampleName[nameLength - 4]);
1000	<	if( !strcmp( endTest, ".bss" ) ){
1001	<	strcpy( endTest, ".dump" );
999	>	strcat( info[k].finalName, ".eor" );
1000	>	}
1001	>	}
1002		}
1003	<	else if( !strcmp( endTest, ".mdl" ) ){
1004	<	strcpy( endTest, ".dump" );
1003	>
1004	>	// make the sample and status out names
1005	>
1006	>	strcpy( info[k].sampleName, inFileName );
1007	>	char* endTest;
1008	>	int nameLength = strlen( info[k].sampleName );
1009	>	endTest = &(info[k].sampleName[nameLength - 5]);
1010	>	if( !strcmp( endTest, ".bass" ) ){
1011	>	strcpy( endTest, ".dump" );
1012		}
1013	+	else if( !strcmp( endTest, ".BASS" ) ){
1014	+	strcpy( endTest, ".dump" );
1015	+	}
1016		else{
1017	<	strcat( info->sampleName, ".dump" );
1017	>	endTest = &(info[k].sampleName[nameLength - 4]);
1018	>	if( !strcmp( endTest, ".bss" ) ){
1019	>	strcpy( endTest, ".dump" );
1020	>	}
1021	>	else if( !strcmp( endTest, ".mdl" ) ){
1022	>	strcpy( endTest, ".dump" );
1023	>	}
1024	>	else{
1025	>	strcat( info[k].sampleName, ".dump" );
1026	>	}
1027		}
1028	<	}
1029	<
1030	<	strcpy( info->statusName, inFileName );
1031	<	nameLength = strlen( info->statusName );
1032	<	endTest = &(info->statusName[nameLength - 5]);
1033	<	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" ) ){
998	<	strcpy( endTest, ".stat" );
1028	>
1029	>	strcpy( info[k].statusName, inFileName );
1030	>	nameLength = strlen( info[k].statusName );
1031	>	endTest = &(info[k].statusName[nameLength - 5]);
1032	>	if( !strcmp( endTest, ".bass" ) ){
1033	>	strcpy( endTest, ".stat" );
1034		}
1035	<	else if( !strcmp( endTest, ".mdl" ) ){
1036	<	strcpy( endTest, ".stat" );
1035	>	else if( !strcmp( endTest, ".BASS" ) ){
1036	>	strcpy( endTest, ".stat" );
1037		}
1038		else{
1039	<	strcat( info->statusName, ".stat" );
1039	>	endTest = &(info[k].statusName[nameLength - 4]);
1040	>	if( !strcmp( endTest, ".bss" ) ){
1041	>	strcpy( endTest, ".stat" );
1042	>	}
1043	>	else if( !strcmp( endTest, ".mdl" ) ){
1044	>	strcpy( endTest, ".stat" );
1045	>	}
1046	>	else{
1047	>	strcat( info[k].statusName, ".stat" );
1048	>	}
1049		}
1050	<	}
1007	<
1050	>
1051		#ifdef IS_MPI
1052	<	}
1052	>	}
1053		#endif // is_mpi
1054	<
1054	>	}
1055		}
1056
1057
1058		void SimSetup::sysObjectsCreation( void ){
1059	<
1060	<	int i;
1061	<
1059	>
1060	>	int i,k;
1061	>
1062		// create the forceField
1063
1064		createFF();
#	Line 1035 | Line 1078 | void SimSetup::sysObjectsCreation( void ){
1078		#endif //is_mpi
1079
1080		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1081	<
1081	>
1082		makeSysArrays();
1083
1084		// make and initialize the molecules (all but atomic coordinates)
1085	<
1085	>
1086		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	–	}
1087
1088	<
1089	<
1088	>	for(k=0; k<nInfo; k++){
1089	>	info[k].identArray = new int[info[k].n_atoms];
1090	>	for(i=0; i<info[k].n_atoms; i++){
1091	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1092	>	}
1093	>	}
1094		}
1095
1096
#	Line 1069 | Line 1112 | void SimSetup::createFF( void ){
1112
1113		default:
1114		sprintf( painCave.errMsg,
1115	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1115	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1116		painCave.isFatal = 1;
1117		simError();
1118		}
#	Line 1085 | Line 1128 | void SimSetup::compList( void ){
1128		void SimSetup::compList( void ){
1129
1130		int i;
1131	<
1131	>	char* id;
1132	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1133	>	LinkedMolStamp* currentStamp = NULL;
1134		comp_stamps = new MoleculeStamp*[n_components];
1135	<
1135	>
1136		// make an array of molecule stamps that match the components used.
1137		// also extract the used stamps out into a separate linked list
1138	<
1139	<	info->nComponents = n_components;
1140	<	info->componentsNmol = components_nmol;
1141	<	info->compStamps = comp_stamps;
1142	<	info->headStamp = new LinkedMolStamp();
1138	>
1139	>	for(i=0; i<nInfo; i++){
1140	>	info[i].nComponents = n_components;
1141	>	info[i].componentsNmol = components_nmol;
1142	>	info[i].compStamps = comp_stamps;
1143	>	info[i].headStamp = headStamp;
1144	>	}
1145
1146	<	char* id;
1100	<	LinkedMolStamp* headStamp = info->headStamp;
1101	<	LinkedMolStamp* currentStamp = NULL;
1146	>
1147		for( i=0; i<n_components; i++ ){
1148
1149		id = the_components[i]->getType();
#	Line 1113 | Line 1158 | void SimSetup::compList( void ){
1158
1159		currentStamp = stamps->extractMolStamp( id );
1160		if( currentStamp == NULL ){
1161	<	sprintf( painCave.errMsg,
1162	<	"SimSetup error: Component \"%s\" was not found in the "
1163	<	"list of declared molecules\n",
1164	<	id );
1165	<	painCave.isFatal = 1;
1166	<	simError();
1161	>	sprintf( painCave.errMsg,
1162	>	"SimSetup error: Component \"%s\" was not found in the "
1163	>	"list of declared molecules\n",
1164	>	id );
1165	>	painCave.isFatal = 1;
1166	>	simError();
1167		}
1168
1169		headStamp->add( currentStamp );
#	Line 1136 | Line 1181 | void SimSetup::calcSysValues( void ){
1181
1182		void SimSetup::calcSysValues( void ){
1183		int i, j, k;
1184	<
1185	<
1184	>
1185	>	int *molMembershipArray;
1186	>
1187		tot_atoms = 0;
1188		tot_bonds = 0;
1189		tot_bends = 0;
#	Line 1149 | Line 1195 | void SimSetup::calcSysValues( void ){
1195		tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1196		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1197		}
1198	<
1198	>
1199		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1200	<
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;
1200	>	molMembershipArray = new int[tot_atoms];
1201
1202	<	info->molMembershipArray = new int[tot_atoms];
1202	>	for(i=0; i<nInfo; i++){
1203	>	info[i].n_atoms = tot_atoms;
1204	>	info[i].n_bonds = tot_bonds;
1205	>	info[i].n_bends = tot_bends;
1206	>	info[i].n_torsions = tot_torsions;
1207	>	info[i].n_SRI = tot_SRI;
1208	>	info[i].n_mol = tot_nmol;
1209	>
1210	>	info[i].molMembershipArray = molMembershipArray;
1211	>	}
1212		}
1213
1165	–
1214		#ifdef IS_MPI
1215
1216		void SimSetup::mpiMolDivide( void ){
#	Line 1194 | Line 1242 | void SimSetup::mpiMolDivide( void ){
1242		for( j=0; j<components_nmol[i]; j++ ){
1243
1244		if( mol2proc[allMol] == worldRank ){
1245	<
1246	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1247	<	local_bonds +=    comp_stamps[i]->getNBonds();
1248	<	local_bends +=    comp_stamps[i]->getNBends();
1249	<	local_torsions += comp_stamps[i]->getNTorsions();
1250	<	localMol++;
1245	>
1246	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1247	>	local_bonds +=    comp_stamps[i]->getNBonds();
1248	>	local_bends +=    comp_stamps[i]->getNBends();
1249	>	local_torsions += comp_stamps[i]->getNTorsions();
1250	>	localMol++;
1251		}
1252		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1253	<	info->molMembershipArray[globalAtomIndex] = allMol;
1253	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1254		globalAtomIndex++;
1255		}
1256
#	Line 1211 | Line 1259 | void SimSetup::mpiMolDivide( void ){
1259		}
1260		local_SRI = local_bonds + local_bends + local_torsions;
1261
1262	<	info->n_atoms = mpiSim->getMyNlocal();
1262	>	info[0].n_atoms = mpiSim->getMyNlocal();
1263
1264	<	if( local_atoms != info->n_atoms ){
1264	>	if( local_atoms != info[0].n_atoms ){
1265		sprintf( painCave.errMsg,
1266	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1267	<	" localAtom (%d) are not equal.\n",
1268	<	info->n_atoms,
1269	<	local_atoms );
1266	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1267	>	" localAtom (%d) are not equal.\n",
1268	>	info[0].n_atoms,
1269	>	local_atoms );
1270		painCave.isFatal = 1;
1271		simError();
1272		}
1273
1274	<	info->n_bonds = local_bonds;
1275	<	info->n_bends = local_bends;
1276	<	info->n_torsions = local_torsions;
1277	<	info->n_SRI = local_SRI;
1278	<	info->n_mol = localMol;
1274	>	info[0].n_bonds = local_bonds;
1275	>	info[0].n_bends = local_bends;
1276	>	info[0].n_torsions = local_torsions;
1277	>	info[0].n_SRI = local_SRI;
1278	>	info[0].n_mol = localMol;
1279
1280		strcpy( checkPointMsg, "Passed nlocal consistency check." );
1281		MPIcheckPoint();
1282		}
1283	<
1283	>
1284		#endif // is_mpi
1285
1286
1287		void SimSetup::makeSysArrays( void ){
1288	<	int i, j, k;
1288	>	int i, j, k, l;
1289
1290	+	Atom** the_atoms;
1291	+	Molecule* the_molecules;
1292	+	Exclude** the_excludes;
1293
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
1294
1295	<
1296	<	molIndex = 0;
1297	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1298	<
1299	<	if(mol2proc[i] == worldRank ){
1300	<	the_molecules[molIndex].setStampID( molCompType[i] );
1301	<	the_molecules[molIndex].setMyIndex( molIndex );
1302	<	the_molecules[molIndex].setGlobalIndex( i );
1303	<	molIndex++;
1304	<	}
1305	<	}
1306	<
1307	<	#else // is_mpi
1308	<
1309	<	molIndex = 0;
1310	<	globalAtomIndex = 0;
1311	<	for(i=0; i<n_components; i++){
1312	<	for(j=0; j<components_nmol[i]; j++ ){
1313	<	the_molecules[molIndex].setStampID( i );
1314	<	the_molecules[molIndex].setMyIndex( molIndex );
1315	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1316	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1276	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1277	<	globalAtomIndex++;
1278	<	}
1279	<	molIndex++;
1295	>	for(l=0; l<nInfo; l++){
1296	>
1297	>	// create the atom and short range interaction arrays
1298	>
1299	>	the_atoms = new Atom*[info[l].n_atoms];
1300	>	the_molecules = new Molecule[info[l].n_mol];
1301	>	int molIndex;
1302	>
1303	>	// initialize the molecule's stampID's
1304	>
1305	>	#ifdef IS_MPI
1306	>
1307	>
1308	>	molIndex = 0;
1309	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1310	>
1311	>	if(mol2proc[i] == worldRank ){
1312	>	the_molecules[molIndex].setStampID( molCompType[i] );
1313	>	the_molecules[molIndex].setMyIndex( molIndex );
1314	>	the_molecules[molIndex].setGlobalIndex( i );
1315	>	molIndex++;
1316	>	}
1317		}
1318	+
1319	+	#else // is_mpi
1320	+
1321	+	molIndex = 0;
1322	+	globalAtomIndex = 0;
1323	+	for(i=0; i<n_components; i++){
1324	+	for(j=0; j<components_nmol[i]; j++ ){
1325	+	the_molecules[molIndex].setStampID( i );
1326	+	the_molecules[molIndex].setMyIndex( molIndex );
1327	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1328	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1329	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1330	+	globalAtomIndex++;
1331		}
1332	+	molIndex++;
1333	+	}
1334	+	}
1335
1336	<
1336	>
1337		#endif // is_mpi
1338
1339
1340	<	if( info->n_SRI ){
1340	>	if( info[l].n_SRI ){
1341
1342	<	Exclude::createArray(info->n_SRI);
1343	<	the_excludes = new Exclude*[info->n_SRI];
1344	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1345	<	info->globalExcludes = new int;
1346	<	info->n_exclude = info->n_SRI;
1347	<	}
1348	<	else{
1342	>	Exclude::createArray(info[l].n_SRI);
1343	>	the_excludes = new Exclude*[info[l].n_SRI];
1344	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1345	>	the_excludes[ex] = new Exclude(ex);
1346	>	}
1347	>	info[l].globalExcludes = new int;
1348	>	info[l].n_exclude = info[l].n_SRI;
1349	>	}
1350	>	else{
1351
1352	<	Exclude::createArray( 1 );
1353	<	the_excludes = new Exclude*;
1354	<	the_excludes[0] = new Exclude(0);
1355	<	the_excludes[0]->setPair( 0,0 );
1356	<	info->globalExcludes = new int;
1357	<	info->globalExcludes[0] = 0;
1358	<	info->n_exclude = 0;
1359	<	}
1352	>	Exclude::createArray( 1 );
1353	>	the_excludes = new Exclude*;
1354	>	the_excludes[0] = new Exclude(0);
1355	>	the_excludes[0]->setPair( 0,0 );
1356	>	info[l].globalExcludes = new int;
1357	>	info[l].globalExcludes[0] = 0;
1358	>	info[l].n_exclude = 0;
1359	>	}
1360
1361	<	// set the arrays into the SimInfo object
1361	>	// set the arrays into the SimInfo object
1362
1363	<	info->atoms = the_atoms;
1364	<	info->molecules = the_molecules;
1365	<	info->nGlobalExcludes = 0;
1366	<	info->excludes = the_excludes;
1363	>	info[l].atoms = the_atoms;
1364	>	info[l].molecules = the_molecules;
1365	>	info[l].nGlobalExcludes = 0;
1366	>	info[l].excludes = the_excludes;
1367
1368	<	the_ff->setSimInfo( info );
1369	<
1368	>	the_ff->setSimInfo( info );
1369	>
1370	>	}
1371		}
1372
1373		void SimSetup::makeIntegrator( void ){
1374
1375	+	int k;
1376	+
1377		NVT<RealIntegrator>*  myNVT = NULL;
1378		NPTi<RealIntegrator>* myNPTi = NULL;
1379		NPTf<RealIntegrator>* myNPTf = NULL;
1380		NPTim<RealIntegrator>* myNPTim = NULL;
1381		NPTfm<RealIntegrator>* myNPTfm = NULL;
1324	–	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1325	–	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1326	–	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1327	–	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1328	–	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1329	–	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1382
1383	<	switch( ensembleCase ){
1332	<
1333	<	case NVE_ENS:
1334	<	new NVE<RealIntegrator>( info, the_ff );
1335	<	break;
1336	<
1337	<	case NVT_ENS:
1338	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1339	<	myNVT->setTargetTemp(globals->getTargetTemp());
1340	<
1341	<	if (globals->haveTauThermostat())
1342	<	myNVT->setTauThermostat(globals->getTauThermostat());
1343	<
1344	<	else {
1345	<	sprintf( painCave.errMsg,
1346	<	"SimSetup error: If you use the NVT\n"
1347	<	"    ensemble, you must set tauThermostat.\n");
1348	<	painCave.isFatal = 1;
1349	<	simError();
1350	<	}
1351	<	break;
1352	<
1353	<	case NPTi_ENS:
1354	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1355	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1356	<
1357	<	if (globals->haveTargetPressure())
1358	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1359	<	else {
1360	<	sprintf( painCave.errMsg,
1361	<	"SimSetup error: If you use a constant pressure\n"
1362	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1363	<	painCave.isFatal = 1;
1364	<	simError();
1365	<	}
1383	>	for(k=0; k<nInfo; k++){
1384
1385	<	if( globals->haveTauThermostat() )
1386	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1387	<	else{
1388	<	sprintf( painCave.errMsg,
1389	<	"SimSetup error: If you use an NPT\n"
1390	<	"    ensemble, you must set tauThermostat.\n");
1391	<	painCave.isFatal = 1;
1374	<	simError();
1375	<	}
1385	>	switch( ensembleCase ){
1386	>
1387	>	case NVE_ENS:
1388	>	if (globals->haveZconstraints()){
1389	>	setupZConstraint(info[k]);
1390	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1391	>	}
1392
1393	<	if( globals->haveTauBarostat() )
1394	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1395	<	else{
1396	<	sprintf( painCave.errMsg,
1397	<	"SimSetup error: If you use an NPT\n"
1398	<	"    ensemble, you must set tauBarostat.\n");
1399	<	painCave.isFatal = 1;
1400	<	simError();
1401	<	}
1402	<	break;
1393	>	else
1394	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1395	>	break;
1396	>
1397	>	case NVT_ENS:
1398	>	if (globals->haveZconstraints()){
1399	>	setupZConstraint(info[k]);
1400	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1401	>	}
1402	>	else
1403	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1404
1405	<	case NPTf_ENS:
1406	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1407	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1405	>	myNVT->setTargetTemp(globals->getTargetTemp());
1406	>
1407	>	if (globals->haveTauThermostat())
1408	>	myNVT->setTauThermostat(globals->getTauThermostat());
1409	>
1410	>	else {
1411	>	sprintf( painCave.errMsg,
1412	>	"SimSetup error: If you use the NVT\n"
1413	>	"    ensemble, you must set tauThermostat.\n");
1414	>	painCave.isFatal = 1;
1415	>	simError();
1416	>	}
1417	>	break;
1418	>
1419	>	case NPTi_ENS:
1420	>	if (globals->haveZconstraints()){
1421	>	setupZConstraint(info[k]);
1422	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1423	>	}
1424	>	else
1425	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1426
1427	<	if (globals->haveTargetPressure())
1428	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1429	<	else {
1430	<	sprintf( painCave.errMsg,
1431	<	"SimSetup error: If you use a constant pressure\n"
1432	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1433	<	painCave.isFatal = 1;
1434	<	simError();
1435	<	}
1427	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1428	>
1429	>	if (globals->haveTargetPressure())
1430	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1431	>	else {
1432	>	sprintf( painCave.errMsg,
1433	>	"SimSetup error: If you use a constant pressure\n"
1434	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	>	painCave.isFatal = 1;
1436	>	simError();
1437	>	}
1438	>
1439	>	if( globals->haveTauThermostat() )
1440	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1441	>	else{
1442	>	sprintf( painCave.errMsg,
1443	>	"SimSetup error: If you use an NPT\n"
1444	>	"    ensemble, you must set tauThermostat.\n");
1445	>	painCave.isFatal = 1;
1446	>	simError();
1447	>	}
1448	>
1449	>	if( globals->haveTauBarostat() )
1450	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1451	>	else{
1452	>	sprintf( painCave.errMsg,
1453	>	"SimSetup error: If you use an NPT\n"
1454	>	"    ensemble, you must set tauBarostat.\n");
1455	>	painCave.isFatal = 1;
1456	>	simError();
1457	>	}
1458	>	break;
1459	>
1460	>	case NPTf_ENS:
1461	>	if (globals->haveZconstraints()){
1462	>	setupZConstraint(info[k]);
1463	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1464	>	}
1465	>	else
1466	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1467
1468	<	if( globals->haveTauThermostat() )
1469	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1470	<	else{
1471	<	sprintf( painCave.errMsg,
1472	<	"SimSetup error: If you use an NPT\n"
1473	<	"    ensemble, you must set tauThermostat.\n");
1474	<	painCave.isFatal = 1;
1475	<	simError();
1476	<	}
1477	<
1478	<	if( globals->haveTauBarostat() )
1479	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1480	<	else{
1481	<	sprintf( painCave.errMsg,
1482	<	"SimSetup error: If you use an NPT\n"
1483	<	"    ensemble, you must set tauBarostat.\n");
1484	<	painCave.isFatal = 1;
1485	<	simError();
1486	<	}
1487	<	break;
1488	<
1489	<	case NPTim_ENS:
1490	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1491	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1468	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1469	>
1470	>	if (globals->haveTargetPressure())
1471	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1472	>	else {
1473	>	sprintf( painCave.errMsg,
1474	>	"SimSetup error: If you use a constant pressure\n"
1475	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1476	>	painCave.isFatal = 1;
1477	>	simError();
1478	>	}
1479	>
1480	>	if( globals->haveTauThermostat() )
1481	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1482	>	else{
1483	>	sprintf( painCave.errMsg,
1484	>	"SimSetup error: If you use an NPT\n"
1485	>	"    ensemble, you must set tauThermostat.\n");
1486	>	painCave.isFatal = 1;
1487	>	simError();
1488	>	}
1489	>
1490	>	if( globals->haveTauBarostat() )
1491	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1492	>	else{
1493	>	sprintf( painCave.errMsg,
1494	>	"SimSetup error: If you use an NPT\n"
1495	>	"    ensemble, you must set tauBarostat.\n");
1496	>	painCave.isFatal = 1;
1497	>	simError();
1498	>	}
1499	>	break;
1500	>
1501	>	case NPTim_ENS:
1502	>	if (globals->haveZconstraints()){
1503	>	setupZConstraint(info[k]);
1504	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1505	>	}
1506	>	else
1507	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1508
1509	<	if (globals->haveTargetPressure())
1510	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1511	<	else {
1512	<	sprintf( painCave.errMsg,
1513	<	"SimSetup error: If you use a constant pressure\n"
1514	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1515	<	painCave.isFatal = 1;
1516	<	simError();
1517	<	}
1518	<
1519	<	if( globals->haveTauThermostat() )
1520	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1521	<	else{
1522	<	sprintf( painCave.errMsg,
1523	<	"SimSetup error: If you use an NPT\n"
1524	<	"    ensemble, you must set tauThermostat.\n");
1525	<	painCave.isFatal = 1;
1526	<	simError();
1527	<	}
1528	<
1529	<	if( globals->haveTauBarostat() )
1530	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1531	<	else{
1532	<	sprintf( painCave.errMsg,
1533	<	"SimSetup error: If you use an NPT\n"
1534	<	"    ensemble, you must set tauBarostat.\n");
1535	<	painCave.isFatal = 1;
1536	<	simError();
1537	<	}
1538	<	break;
1539	<
1540	<	case NPTfm_ENS:
1459	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1460	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1461	<
1462	<	if (globals->haveTargetPressure())
1463	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1464	<	else {
1465	<	sprintf( painCave.errMsg,
1466	<	"SimSetup error: If you use a constant pressure\n"
1467	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1468	<	painCave.isFatal = 1;
1469	<	simError();
1470	<	}
1471	<
1472	<	if( globals->haveTauThermostat() )
1473	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1474	<	else{
1475	<	sprintf( painCave.errMsg,
1476	<	"SimSetup error: If you use an NPT\n"
1477	<	"    ensemble, you must set tauThermostat.\n");
1478	<	painCave.isFatal = 1;
1479	<	simError();
1480	<	}
1481	<
1482	<	if( globals->haveTauBarostat() )
1483	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1484	<	else{
1485	<	sprintf( painCave.errMsg,
1486	<	"SimSetup error: If you use an NPT\n"
1487	<	"    ensemble, you must set tauBarostat.\n");
1488	<	painCave.isFatal = 1;
1489	<	simError();
1490	<	}
1491	<	break;
1492	<
1493	<	case NVEZCONS_ENS:
1494	<
1495	<
1496	<	//setup index of z-constraint molecules, z-constraint sampel time
1497	<	//and z-constraint force output name. These parameter should be known
1498	<	//before constructing the z-constraint integrator
1499	<	setupZConstraint();
1509	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1510	>
1511	>	if (globals->haveTargetPressure())
1512	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1513	>	else {
1514	>	sprintf( painCave.errMsg,
1515	>	"SimSetup error: If you use a constant pressure\n"
1516	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1517	>	painCave.isFatal = 1;
1518	>	simError();
1519	>	}
1520	>
1521	>	if( globals->haveTauThermostat() )
1522	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1523	>	else{
1524	>	sprintf( painCave.errMsg,
1525	>	"SimSetup error: If you use an NPT\n"
1526	>	"    ensemble, you must set tauThermostat.\n");
1527	>	painCave.isFatal = 1;
1528	>	simError();
1529	>	}
1530	>
1531	>	if( globals->haveTauBarostat() )
1532	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1533	>	else{
1534	>	sprintf( painCave.errMsg,
1535	>	"SimSetup error: If you use an NPT\n"
1536	>	"    ensemble, you must set tauBarostat.\n");
1537	>	painCave.isFatal = 1;
1538	>	simError();
1539	>	}
1540	>	break;
1541
1542	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1543	<
1544	<	break;
1545	<
1546	<
1547	<	case NVTZCONS_ENS:
1548	<
1508	<	setupZConstraint();
1509	<
1510	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1511	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1542	>	case NPTfm_ENS:
1543	>	if (globals->haveZconstraints()){
1544	>	setupZConstraint(info[k]);
1545	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1546	>	}
1547	>	else
1548	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1549
1550	<	if (globals->haveTauThermostat())
1514	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1550	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1551
1552	<	else {
1553	<	sprintf( painCave.errMsg,
1554	<	"SimSetup error: If you use the NVT\n"
1555	<	"    ensemble, you must set tauThermostat.\n");
1556	<	painCave.isFatal = 1;
1557	<	simError();
1558	<	}
1559	<	break;
1560	<
1525	<	case NPTiZCONS_ENS:
1526	<
1527	<	setupZConstraint();
1528	<
1529	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1530	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1552	>	if (globals->haveTargetPressure())
1553	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1554	>	else {
1555	>	sprintf( painCave.errMsg,
1556	>	"SimSetup error: If you use a constant pressure\n"
1557	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1558	>	painCave.isFatal = 1;
1559	>	simError();
1560	>	}
1561
1562	<	if (globals->haveTargetPressure())
1563	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1564	<	else {
1565	<	sprintf( painCave.errMsg,
1566	<	"SimSetup error: If you use a constant pressure\n"
1567	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1568	<	painCave.isFatal = 1;
1569	<	simError();
1570	<	}
1541	<
1542	<	if( globals->haveTauThermostat() )
1543	<	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1544	<	else{
1545	<	sprintf( painCave.errMsg,
1546	<	"SimSetup error: If you use an NPT\n"
1547	<	"    ensemble, you must set tauThermostat.\n");
1548	<	painCave.isFatal = 1;
1549	<	simError();
1550	<	}
1562	>	if( globals->haveTauThermostat() )
1563	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1564	>	else{
1565	>	sprintf( painCave.errMsg,
1566	>	"SimSetup error: If you use an NPT\n"
1567	>	"    ensemble, you must set tauThermostat.\n");
1568	>	painCave.isFatal = 1;
1569	>	simError();
1570	>	}
1571
1572	<	if( globals->haveTauBarostat() )
1573	<	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1574	<	else{
1575	<	sprintf( painCave.errMsg,
1576	<	"SimSetup error: If you use an NPT\n"
1577	<	"    ensemble, you must set tauBarostat.\n");
1578	<	painCave.isFatal = 1;
1579	<	simError();
1580	<	}
1581	<
1562	<	break;
1563	<
1564	<	case NPTfZCONS_ENS:
1565	<
1566	<	setupZConstraint();
1567	<
1568	<	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1569	<	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1570	<
1571	<	if (globals->haveTargetPressure())
1572	<	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1573	<	else {
1574	<	sprintf( painCave.errMsg,
1575	<	"SimSetup error: If you use a constant pressure\n"
1576	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1577	<	painCave.isFatal = 1;
1578	<	simError();
1579	<	}
1580	<
1581	<	if( globals->haveTauThermostat() )
1582	<	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1583	<	else{
1584	<	sprintf( painCave.errMsg,
1585	<	"SimSetup error: If you use an NPT\n"
1586	<	"    ensemble, you must set tauThermostat.\n");
1587	<	painCave.isFatal = 1;
1588	<	simError();
1589	<	}
1590	<
1591	<	if( globals->haveTauBarostat() )
1592	<	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1593	<	else{
1594	<	sprintf( painCave.errMsg,
1595	<	"SimSetup error: If you use an NPT\n"
1596	<	"    ensemble, you must set tauBarostat.\n");
1597	<	painCave.isFatal = 1;
1598	<	simError();
1599	<	}
1600	<
1601	<	break;
1572	>	if( globals->haveTauBarostat() )
1573	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1574	>	else{
1575	>	sprintf( painCave.errMsg,
1576	>	"SimSetup error: If you use an NPT\n"
1577	>	"    ensemble, you must set tauBarostat.\n");
1578	>	painCave.isFatal = 1;
1579	>	simError();
1580	>	}
1581	>	break;
1582
1583	<	case NPTimZCONS_ENS:
1604	<
1605	<	setupZConstraint();
1606	<
1607	<	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1608	<	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1609	<
1610	<	if (globals->haveTargetPressure())
1611	<	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1612	<	else {
1583	>	default:
1584		sprintf( painCave.errMsg,
1585	<	"SimSetup error: If you use a constant pressure\n"
1615	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1585	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1586		painCave.isFatal = 1;
1587		simError();
1588		}
1619	–
1620	–	if( globals->haveTauThermostat() )
1621	–	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1622	–	else{
1623	–	sprintf( painCave.errMsg,
1624	–	"SimSetup error: If you use an NPT\n"
1625	–	"    ensemble, you must set tauThermostat.\n");
1626	–	painCave.isFatal = 1;
1627	–	simError();
1628	–	}
1629	–
1630	–	if( globals->haveTauBarostat() )
1631	–	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1632	–	else{
1633	–	sprintf( painCave.errMsg,
1634	–	"SimSetup error: If you use an NPT\n"
1635	–	"    ensemble, you must set tauBarostat.\n");
1636	–	painCave.isFatal = 1;
1637	–	simError();
1638	–	}
1639	–
1640	–	break;
1641	–
1642	–	case NPTfmZCONS_ENS:
1643	–
1644	–	setupZConstraint();
1645	–
1646	–	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1647	–	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1648	–
1649	–	if (globals->haveTargetPressure())
1650	–	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1651	–	else {
1652	–	sprintf( painCave.errMsg,
1653	–	"SimSetup error: If you use a constant pressure\n"
1654	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1655	–	painCave.isFatal = 1;
1656	–	simError();
1657	–	}
1658	–
1659	–	if( globals->haveTauThermostat() )
1660	–	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1661	–	else{
1662	–	sprintf( painCave.errMsg,
1663	–	"SimSetup error: If you use an NPT\n"
1664	–	"    ensemble, you must set tauThermostat.\n");
1665	–	painCave.isFatal = 1;
1666	–	simError();
1667	–	}
1668	–
1669	–	if( globals->haveTauBarostat() )
1670	–	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1671	–	else{
1672	–	sprintf( painCave.errMsg,
1673	–	"SimSetup error: If you use an NPT\n"
1674	–	"    ensemble, you must set tauBarostat.\n");
1675	–	painCave.isFatal = 1;
1676	–	simError();
1677	–	}
1678	–	break;
1679	–
1680	–
1681	–
1682	–	default:
1683	–	sprintf( painCave.errMsg,
1684	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1685	–	painCave.isFatal = 1;
1686	–	simError();
1589		}
1688	–
1590		}
1591
1592		void SimSetup::initFortran( void ){
1593
1594	<	info->refreshSim();
1594	>	info[0].refreshSim();
1595
1596	<	if( !strcmp( info->mixingRule, "standard") ){
1596	>	if( !strcmp( info[0].mixingRule, "standard") ){
1597		the_ff->initForceField( LB_MIXING_RULE );
1598		}
1599	<	else if( !strcmp( info->mixingRule, "explicit") ){
1599	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1600		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1601		}
1602		else{
1603		sprintf( painCave.errMsg,
1604	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	<	info->mixingRule );
1604	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	>	info[0].mixingRule );
1606		painCave.isFatal = 1;
1607		simError();
1608		}
#	Line 1709 | Line 1610 | void SimSetup::initFortran( void ){
1610
1611		#ifdef IS_MPI
1612		strcpy( checkPointMsg,
1613	<	"Successfully intialized the mixingRule for Fortran." );
1613	>	"Successfully intialized the mixingRule for Fortran." );
1614		MPIcheckPoint();
1615		#endif // is_mpi
1616
1617		}
1618
1619	<	void SimSetup::setupZConstraint()
1619	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1620		{
1621	<	if(globals->haveZConsTime()){
1622	<
1623	<	//add sample time of z-constraint  into SimInfo's property list
1624	<	DoubleData* zconsTimeProp = new DoubleData();
1625	<	zconsTimeProp->setID("zconstime");
1626	<	zconsTimeProp->setData(globals->getZConsTime());
1627	<	info->addProperty(zconsTimeProp);
1621	>	int nZConstraints;
1622	>	ZconStamp** zconStamp;
1623	>
1624	>	if(globals->haveZconstraintTime()){
1625	>
1626	>	//add sample time of z-constraint  into SimInfo's property list
1627	>	DoubleData* zconsTimeProp = new DoubleData();
1628	>	zconsTimeProp->setID(ZCONSTIME_ID);
1629	>	zconsTimeProp->setData(globals->getZconsTime());
1630	>	theInfo.addProperty(zconsTimeProp);
1631		}
1632		else{
1633		sprintf( painCave.errMsg,
1634	<	"ZConstraint error: If you use an ZConstraint\n"
1635	<	" , you must set sample time.\n");
1634	>	"ZConstraint error: If you use an ZConstraint\n"
1635	>	" , you must set sample time.\n");
1636		painCave.isFatal = 1;
1637		simError();
1638		}
1639	<
1640	<	if(globals->haveIndexOfAllZConsMols()){
1641	<
1642	<	//add index of z-constraint molecules into SimInfo's property list
1643	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1644	<
1645	<	//sort the index
1742	<	sort(tempIndex.begin(), tempIndex.end());
1743	<
1744	<	IndexData* zconsIndex = new IndexData();
1745	<	zconsIndex->setID("zconsindex");
1746	<	zconsIndex->setIndexData(tempIndex);
1747	<	info->addProperty(zconsIndex);
1639	>
1640	>	//push zconsTol into siminfo, if user does not specify
1641	>	//value for zconsTol, a default value will be used
1642	>	DoubleData* zconsTol = new DoubleData();
1643	>	zconsTol->setID(ZCONSTOL_ID);
1644	>	if(globals->haveZconsTol()){
1645	>	zconsTol->setData(globals->getZconsTol());
1646		}
1647		else{
1648	+	double defaultZConsTol = 0.01;
1649		sprintf( painCave.errMsg,
1650	<	"SimSetup error: If you use an ZConstraint\n"
1651	<	" , you must set index of z-constraint molecules.\n");
1652	<	painCave.isFatal = 1;
1653	<	simError();
1654	<
1650	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1651	>	" , default value %f is used.\n", defaultZConsTol);
1652	>	painCave.isFatal = 0;
1653	>	simError();
1654	>
1655	>	zconsTol->setData(defaultZConsTol);
1656		}
1657	+	theInfo.addProperty(zconsTol);
1658
1659	+	//set Force Substraction Policy
1660	+	StringData* zconsForcePolicy =  new StringData();
1661	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1662	+
1663	+	if(globals->haveZconsForcePolicy()){
1664	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1665	+	}
1666	+	else{
1667	+	sprintf( painCave.errMsg,
1668	+	"ZConstraint Warning: User does not set force substraction policy, "
1669	+	"average force substraction policy is used\n");
1670	+	painCave.isFatal = 0;
1671	+	simError();
1672	+	zconsForcePolicy->setData("BYNUMBER");
1673	+	}
1674	+
1675	+	theInfo.addProperty(zconsForcePolicy);
1676	+
1677		//Determine the name of ouput file and add it into SimInfo's property list
1678		//Be careful, do not use inFileName, since it is a pointer which
1679		//point to a string at master node, and slave nodes do not contain that string
1680	<
1681	<	string zconsOutput(info->finalName);
1682	<
1680	>
1681	>	string zconsOutput(theInfo.finalName);
1682	>
1683		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1684	<
1684	>
1685		StringData* zconsFilename = new StringData();
1686	<	zconsFilename->setID("zconsfilename");
1686	>	zconsFilename->setID(ZCONSFILENAME_ID);
1687		zconsFilename->setData(zconsOutput);
1688	+
1689	+	theInfo.addProperty(zconsFilename);
1690	+
1691	+	//setup index, pos and other parameters of z-constraint molecules
1692	+	nZConstraints = globals->getNzConstraints();
1693	+	theInfo.nZconstraints = nZConstraints;
1694
1695	<	info->addProperty(zconsFilename);
1695	>	zconStamp = globals->getZconStamp();
1696	>	ZConsParaItem tempParaItem;
1697
1698	+	ZConsParaData* zconsParaData = new ZConsParaData();
1699	+	zconsParaData->setID(ZCONSPARADATA_ID);
1700	+
1701	+	for(int i = 0; i < nZConstraints; i++){
1702	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1703	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1704	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1705	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1706	+
1707	+	zconsParaData->addItem(tempParaItem);
1708	+	}
1709	+
1710	+	//sort the parameters by index of molecules
1711	+	zconsParaData->sortByIndex();
1712	+
1713	+	//push data into siminfo, therefore, we can retrieve later
1714	+	theInfo.addProperty(zconsParaData);
1715	+
1716		}

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