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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC vs.
Revision 690 by mmeineke, Tue Aug 12 21:44:06 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
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 14 | Line 17
17
18		// some defines for ensemble and Forcefield  cases
19
20	<	#define NVE_ENS   0
21	<	#define NVT_ENS   1
22	<	#define NPTi_ENS  2
23	<	#define NPTf_ENS  3
24	<	#define NPTim_ENS 4
25	<	#define NPTfm_ENS 5
20	>	#define NVE_ENS        0
21	>	#define NVT_ENS        1
22	>	#define NPTi_ENS       2
23	>	#define NPTf_ENS       3
24	>	#define NPTim_ENS      4
25	>	#define NPTfm_ENS      5
26
24	–
27		#define FF_DUFF 0
28		#define FF_LJ   1
29	+	#define FF_EAM  2
30
31	+	using namespace std;
32
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 41 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 76 | 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 89 | 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();
98	<
113	>	if( !isInfoArray ) initSystemCoords();
114
115		// make the output filenames
116
#	Line 120 | 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 144 | Line 160 | void SimSetup::makeMolecules( void ){
160
161		double ux, uy, uz, u, uSqr;
162
163	<	atomOffset = 0;
148	<	excludeOffset = 0;
149	<	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++){
172	<
173	<	currentAtom = comp_stamps[stampID]->getAtom( j );
174	<	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;
236	<
237	<	//make the bends
238	<	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
255	–	case 0:
256	–	theBends[j].ghost =
257	–	current_extra->getInt() + atomOffset;
258	–	theBends[j].isGhost = 1;
259	–	break;
260	–
261	–	case 1:
262	–	theBends[j].ghost =
263	–	(int)current_extra->getDouble() + atomOffset;
264	–	theBends[j].isGhost = 1;
265	–	break;
266	–
267	–	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		}
276	–	}
277	–
278	–	else{
310
311	<	sprintf( painCave.errMsg,
281	<	"SimSetup Error: unhandled bend assignment:\n"
282	<	"    -->%s in Bend[%d] in %s\n",
283	<	current_extra->getlhs(),
284	<	j, comp_stamps[stampID]->getID() );
285	<	painCave.isFatal = 1;
286	<	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;
296	<	exJ = theBends[j].c;
297	<	}
298	<	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
311	<	tempEx = exI;
312	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
313	<	tempEx = exJ;
314	<	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;
322	<
323	<	for(j=0; j<molInfo.nTorsions; j++){
372	>	}
373	>	excludeOffset += molInfo.nTorsions;
374
325	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
326	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
327	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
328	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
329	–	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
334	–	// exclude_I must always be the smaller of the pair
335	–	if( exI > exJ ){
336	–	tempEx = exI;
337	–	exI = exJ;
338	–	exJ = tempEx;
339	–	}
340	–	#ifdef IS_MPI
341	–	tempEx = exI;
342	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
343	–	tempEx = exJ;
344	–	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		}
351	–	excludeOffset += molInfo.nTorsions;
352	–
353	–
354	–	// send the arrays off to the forceField for init.
355	–
356	–	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
357	–	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
358	–	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
359	–	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
360	–
361	–
362	–	the_molecules[i].initialize( molInfo );
363	–
364	–
365	–	atomOffset += molInfo.nAtoms;
366	–	delete[] theBonds;
367	–	delete[] theBends;
368	–	delete[] theTorsions;
392		}
393	<
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 389 | 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 398 | 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 415 | 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 496 | Line 525 | void SimSetup::initFromBass( void ){
525		}
526		}
527
528	<
529	<	for( i=0; i<info->n_atoms; i++ ){
501	<	info->atoms[i]->set_vx( 0.0 );
502	<	info->atoms[i]->set_vy( 0.0 );
503	<	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 510 | 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 525 | 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() );
530	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
531	<	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
535	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
536	–
566		rotMat[0][0] = 1.0;
567		rotMat[0][1] = 0.0;
568		rotMat[0][2] = 0.0;
#	Line 569 | Line 598 | void SimSetup::gatherInfo( void ){
598		ensembleCase = -1;
599		ffCase = -1;
600
572	–	// get the stamps and globals;
573	–	stamps = stamps;
574	–	globals = globals;
575	–
601		// set the easy ones first
602	<	info->target_temp = globals->getTargetTemp();
603	<	info->dt = globals->getDt();
604	<	info->run_time = globals->getRunTime();
602	>
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 586 | Line 614 | void SimSetup::gatherInfo( void ){
614
615		if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616		else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618		else{
619		sprintf( painCave.errMsg,
620		"SimSetup Error. Unrecognized force field -> %s\n",
#	Line 615 | 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 662 | Line 694 | void SimSetup::gatherInfo( void ){
694
695		// set the status, sample, and thermal kick times
696
697	<	if( globals->haveSampleTime() ){
666	<	info->sampleTime = globals->getSampleTime();
667	<	info->statusTime = info->sampleTime;
668	<	info->thermalTime = info->sampleTime;
669	<	}
670	<	else{
671	<	info->sampleTime = globals->getRunTime();
672	<	info->statusTime = info->sampleTime;
673	<	info->thermalTime = info->sampleTime;
674	<	}
697	>	for(i=0; i<nInfo; i++){
698
699	<	if( globals->haveStatusTime() ){
700	<	info->statusTime = globals->getStatusTime();
701	<	}
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	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712	>	}
713	>
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716	>	}
717
718	<	if( globals->haveThermalTime() ){
681	<	info->thermalTime = globals->getThermalTime();
682	<	}
718	>	// check for the temperature set flag
719
720	<	// check for the temperature set flag
685	<
686	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
687	<
688	<	// get some of the tricky things that may still be in the globals
689	<
690	<	double boxVector[3];
691	<	if( globals->haveBox() ){
692	<	boxVector[0] = globals->getBox();
693	<	boxVector[1] = globals->getBox();
694	<	boxVector[2] = globals->getBox();
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721
722	<	info->setBox( boxVector );
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 if( globals->haveDensity() ){
743	<
744	<	double vol;
745	<	vol = (double)tot_nmol / globals->getDensity();
746	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
747	<	boxVector[1] = boxVector[0];
748	<	boxVector[2] = boxVector[0];
749	<
750	<	info->setBox( boxVector );
751	<	}
752	<	else{
753	<	if( !globals->haveBoxX() ){
754	<	sprintf( painCave.errMsg,
755	<	"SimSetup error, no periodic BoxX size given.\n" );
756	<	painCave.isFatal = 1;
757	<	simError();
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		}
715	–	boxVector[0] = globals->getBoxX();
769
717	–	if( !globals->haveBoxY() ){
718	–	sprintf( painCave.errMsg,
719	–	"SimSetup error, no periodic BoxY size given.\n" );
720	–	painCave.isFatal = 1;
721	–	simError();
722	–	}
723	–	boxVector[1] = globals->getBoxY();
724	–
725	–	if( !globals->haveBoxZ() ){
726	–	sprintf( painCave.errMsg,
727	–	"SimSetup error, no periodic BoxZ size given.\n" );
728	–	painCave.isFatal = 1;
729	–	simError();
730	–	}
731	–	boxVector[2] = globals->getBoxZ();
732	–
733	–	info->setBox( boxVector );
770		}
735	–
736	–
771
772		#ifdef IS_MPI
773		strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
#	Line 746 | 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	<
787	<	index = 0;
788	<	usesDipoles = 0;
789	<	while( (index < info->n_atoms) && !usesDipoles ){
790	<	usesDipoles = ((info->atoms)[index])->hasDipole();
791	<	index++;
792	<	}
793	<
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787	>
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793	>	}
794	>
795		#ifdef IS_MPI
796	<	int myUse = usesDipoles;
797	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
796	>	int myUse = usesDipoles;
797	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798		#endif //is_mpi
764	–
765	–	double theEcr, theEst;
766	–
767	–	if (globals->getUseRF() ) {
768	–	info->useReactionField = 1;
799
800	<	if( !globals->haveECR() ){
801	<	sprintf( painCave.errMsg,
802	<	"SimSetup Warning: using default value of 1/2 the smallest "
803	<	"box length for the electrostaticCutoffRadius.\n"
774	<	"I hope you have a very fast processor!\n");
775	<	painCave.isFatal = 0;
776	<	simError();
777	<	double smallest;
778	<	smallest = info->boxL[0];
779	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
780	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
781	<	theEcr = 0.5 * smallest;
782	<	} else {
783	<	theEcr = globals->getECR();
784	<	}
785	<
786	<	if( !globals->haveEST() ){
787	<	sprintf( painCave.errMsg,
788	<	"SimSetup Warning: using default value of 0.05 * the "
789	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
790	<	);
791	<	painCave.isFatal = 0;
792	<	simError();
793	<	theEst = 0.05 * theEcr;
794	<	} else {
795	<	theEst= globals->getEST();
796	<	}
797	<
798	<	info->setEcr( theEcr, theEst );
799	<
800	<	if(!globals->haveDielectric() ){
801	<	sprintf( painCave.errMsg,
802	<	"SimSetup Error: You are trying to use Reaction Field without"
803	<	"setting a dielectric constant!\n"
804	<	);
805	<	painCave.isFatal = 1;
806	<	simError();
807	<	}
808	<	info->dielectric = globals->getDielectric();
809	<	}
810	<	else {
811	<	if (usesDipoles) {
800	>	double theEcr, theEst;
801	>
802	>	if (globals->getUseRF() ) {
803	>	info[i].useReactionField = 1;
804
805		if( !globals->haveECR() ){
806		sprintf( painCave.errMsg,
#	Line 818 | 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 829 | 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 "
833	<	"electrostaticSkinThickness\n"
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825		);
826		painCave.isFatal = 0;
827		simError();
#	Line 838 | Line 829 | void SimSetup::finalInfoCheck( void ){
829		} else {
830		theEst= globals->getEST();
831		}
832	+
833	+	info[i].setEcr( theEcr, theEst );
834	+
835	+	if(!globals->haveDielectric() ){
836	+	sprintf( painCave.errMsg,
837	+	"SimSetup Error: You are trying to use Reaction Field without"
838	+	"setting a dielectric constant!\n"
839	+	);
840	+	painCave.isFatal = 1;
841	+	simError();
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
842	–	info->setEcr( theEcr, theEst );
843	–	}
844	–	}
845	–
882		#ifdef IS_MPI
883		strcpy( checkPointMsg, "post processing checks out" );
884		MPIcheckPoint();
#	Line 851 | 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	>	fileInit = new InitializeFromFile( inName );
907		#ifdef IS_MPI
908	<	}else fileInit = new InitializeFromFile( NULL );
908	>	}else fileInit = new InitializeFromFile( NULL );
909		#endif
910	<	fileInit->read_xyz( info ); // default velocities on
911	<
912	<	delete fileInit;
913	<	}
914	<	else{
915	<
910	>	fileInit->readInit( info ); // default velocities on
911	>
912	>	delete fileInit;
913	>	}
914	>	else{
915	>
916		#ifdef IS_MPI
917	<
918	<	// no init from bass
919	<
920	<	sprintf( painCave.errMsg,
921	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
922	<	painCave.isFatal;
923	<	simError();
924	<
917	>
918	>	// no init from bass
919	>
920	>	sprintf( painCave.errMsg,
921	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
922	>	painCave.isFatal;
923	>	simError();
924	>
925		#else
926	<
927	<	initFromBass();
928	<
929	<
926	>
927	>	initFromBass();
928	>
929	>
930		#endif
931	<	}
932	<
931	>	}
932	>
933		#ifdef IS_MPI
934		strcpy( checkPointMsg, "Successfully read in the initial configuration" );
935		MPIcheckPoint();
936		#endif // is_mpi
937	<
937	>
938		}
939
940
941		void SimSetup::makeOutNames( void ){
942	+
943	+	int k;
944
945	+
946	+	for(k=0; k<nInfo; k++){
947	+
948		#ifdef IS_MPI
949	<	if( worldRank == 0 ){
949	>	if( worldRank == 0 ){
950		#endif // is_mpi
951	<
952	<	if( globals->haveFinalConfig() ){
953	<	strcpy( info->finalName, globals->getFinalConfig() );
904	<	}
905	<	else{
906	<	strcpy( info->finalName, inFileName );
907	<	char* endTest;
908	<	int nameLength = strlen( info->finalName );
909	<	endTest = &(info->finalName[nameLength - 5]);
910	<	if( !strcmp( endTest, ".bass" ) ){
911	<	strcpy( endTest, ".eor" );
951	>
952	>	if( globals->haveFinalConfig() ){
953	>	strcpy( info[k].finalName, globals->getFinalConfig() );
954		}
913	–	else if( !strcmp( endTest, ".BASS" ) ){
914	–	strcpy( endTest, ".eor" );
915	–	}
955		else{
956	<	endTest = &(info->finalName[nameLength - 4]);
957	<	if( !strcmp( endTest, ".bss" ) ){
956	>	strcpy( info[k].finalName, inFileName );
957	>	char* endTest;
958	>	int nameLength = strlen( info[k].finalName );
959	>	endTest = &(info[k].finalName[nameLength - 5]);
960	>	if( !strcmp( endTest, ".bass" ) ){
961		strcpy( endTest, ".eor" );
962		}
963	<	else if( !strcmp( endTest, ".mdl" ) ){
963	>	else if( !strcmp( endTest, ".BASS" ) ){
964		strcpy( endTest, ".eor" );
965		}
966		else{
967	<	strcat( info->finalName, ".eor" );
967	>	endTest = &(info[k].finalName[nameLength - 4]);
968	>	if( !strcmp( endTest, ".bss" ) ){
969	>	strcpy( endTest, ".eor" );
970	>	}
971	>	else if( !strcmp( endTest, ".mdl" ) ){
972	>	strcpy( endTest, ".eor" );
973	>	}
974	>	else{
975	>	strcat( info[k].finalName, ".eor" );
976	>	}
977		}
978		}
979	<	}
980	<
981	<	// make the sample and status out names
982	<
983	<	strcpy( info->sampleName, inFileName );
984	<	char* endTest;
985	<	int nameLength = strlen( info->sampleName );
986	<	endTest = &(info->sampleName[nameLength - 5]);
936	<	if( !strcmp( endTest, ".bass" ) ){
937	<	strcpy( endTest, ".dump" );
938	<	}
939	<	else if( !strcmp( endTest, ".BASS" ) ){
940	<	strcpy( endTest, ".dump" );
941	<	}
942	<	else{
943	<	endTest = &(info->sampleName[nameLength - 4]);
944	<	if( !strcmp( endTest, ".bss" ) ){
979	>
980	>	// make the sample and status out names
981	>
982	>	strcpy( info[k].sampleName, inFileName );
983	>	char* endTest;
984	>	int nameLength = strlen( info[k].sampleName );
985	>	endTest = &(info[k].sampleName[nameLength - 5]);
986	>	if( !strcmp( endTest, ".bass" ) ){
987		strcpy( endTest, ".dump" );
988		}
989	<	else if( !strcmp( endTest, ".mdl" ) ){
989	>	else if( !strcmp( endTest, ".BASS" ) ){
990		strcpy( endTest, ".dump" );
991		}
992		else{
993	<	strcat( info->sampleName, ".dump" );
993	>	endTest = &(info[k].sampleName[nameLength - 4]);
994	>	if( !strcmp( endTest, ".bss" ) ){
995	>	strcpy( endTest, ".dump" );
996	>	}
997	>	else if( !strcmp( endTest, ".mdl" ) ){
998	>	strcpy( endTest, ".dump" );
999	>	}
1000	>	else{
1001	>	strcat( info[k].sampleName, ".dump" );
1002	>	}
1003		}
1004	<	}
1005	<
1006	<	strcpy( info->statusName, inFileName );
1007	<	nameLength = strlen( info->statusName );
1008	<	endTest = &(info->statusName[nameLength - 5]);
958	<	if( !strcmp( endTest, ".bass" ) ){
959	<	strcpy( endTest, ".stat" );
960	<	}
961	<	else if( !strcmp( endTest, ".BASS" ) ){
962	<	strcpy( endTest, ".stat" );
963	<	}
964	<	else{
965	<	endTest = &(info->statusName[nameLength - 4]);
966	<	if( !strcmp( endTest, ".bss" ) ){
1004	>
1005	>	strcpy( info[k].statusName, inFileName );
1006	>	nameLength = strlen( info[k].statusName );
1007	>	endTest = &(info[k].statusName[nameLength - 5]);
1008	>	if( !strcmp( endTest, ".bass" ) ){
1009		strcpy( endTest, ".stat" );
1010		}
1011	<	else if( !strcmp( endTest, ".mdl" ) ){
1011	>	else if( !strcmp( endTest, ".BASS" ) ){
1012		strcpy( endTest, ".stat" );
1013		}
1014		else{
1015	<	strcat( info->statusName, ".stat" );
1015	>	endTest = &(info[k].statusName[nameLength - 4]);
1016	>	if( !strcmp( endTest, ".bss" ) ){
1017	>	strcpy( endTest, ".stat" );
1018	>	}
1019	>	else if( !strcmp( endTest, ".mdl" ) ){
1020	>	strcpy( endTest, ".stat" );
1021	>	}
1022	>	else{
1023	>	strcat( info[k].statusName, ".stat" );
1024	>	}
1025		}
1026	<	}
976	<
1026	>
1027		#ifdef IS_MPI
1028	<	}
1028	>	}
1029		#endif // is_mpi
1030	<
1030	>	}
1031		}
1032
1033
1034		void SimSetup::sysObjectsCreation( void ){
1035	<
1036	<	int i;
1037	<
1035	>
1036	>	int i,k;
1037	>
1038		// create the forceField
1039
1040		createFF();
#	Line 1004 | Line 1054 | void SimSetup::sysObjectsCreation( void ){
1054		#endif //is_mpi
1055
1056		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1057	<
1057	>
1058		makeSysArrays();
1059
1060		// make and initialize the molecules (all but atomic coordinates)
1061	<
1061	>
1062		makeMolecules();
1013	–	info->identArray = new int[info->n_atoms];
1014	–	for(i=0; i<info->n_atoms; i++){
1015	–	info->identArray[i] = the_atoms[i]->getIdent();
1016	–	}
1063
1064	<
1065	<
1064	>	for(k=0; k<nInfo; k++){
1065	>	info[k].identArray = new int[info[k].n_atoms];
1066	>	for(i=0; i<info[k].n_atoms; i++){
1067	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1068	>	}
1069	>	}
1070		}
1071
1072
#	Line 1032 | Line 1082 | void SimSetup::createFF( void ){
1082		the_ff = new LJFF();
1083		break;
1084
1085	+	case FF_EAM:
1086	+	the_ff = new EAM_FF();
1087	+	break;
1088	+
1089		default:
1090		sprintf( painCave.errMsg,
1091		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1050 | Line 1104 | void SimSetup::compList( void ){
1104		void SimSetup::compList( void ){
1105
1106		int i;
1107	<
1107	>	char* id;
1108	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1109	>	LinkedMolStamp* currentStamp = NULL;
1110		comp_stamps = new MoleculeStamp*[n_components];
1111	<
1111	>
1112		// make an array of molecule stamps that match the components used.
1113		// also extract the used stamps out into a separate linked list
1058	–
1059	–	info->nComponents = n_components;
1060	–	info->componentsNmol = components_nmol;
1061	–	info->compStamps = comp_stamps;
1062	–	info->headStamp = new LinkedMolStamp();
1114
1115	<	char* id;
1116	<	LinkedMolStamp* headStamp = info->headStamp;
1117	<	LinkedMolStamp* currentStamp = NULL;
1115	>	for(i=0; i<nInfo; i++){
1116	>	info[i].nComponents = n_components;
1117	>	info[i].componentsNmol = components_nmol;
1118	>	info[i].compStamps = comp_stamps;
1119	>	info[i].headStamp = headStamp;
1120	>	}
1121	>
1122	>
1123		for( i=0; i<n_components; i++ ){
1124
1125		id = the_components[i]->getType();
#	Line 1101 | Line 1157 | void SimSetup::calcSysValues( void ){
1157
1158		void SimSetup::calcSysValues( void ){
1159		int i, j, k;
1160	<
1161	<
1160	>
1161	>	int *molMembershipArray;
1162	>
1163		tot_atoms = 0;
1164		tot_bonds = 0;
1165		tot_bends = 0;
#	Line 1114 | Line 1171 | void SimSetup::calcSysValues( void ){
1171		tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1172		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1173		}
1174	<
1174	>
1175		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1176	<
1120	<	info->n_atoms = tot_atoms;
1121	<	info->n_bonds = tot_bonds;
1122	<	info->n_bends = tot_bends;
1123	<	info->n_torsions = tot_torsions;
1124	<	info->n_SRI = tot_SRI;
1125	<	info->n_mol = tot_nmol;
1176	>	molMembershipArray = new int[tot_atoms];
1177
1178	<	info->molMembershipArray = new int[tot_atoms];
1178	>	for(i=0; i<nInfo; i++){
1179	>	info[i].n_atoms = tot_atoms;
1180	>	info[i].n_bonds = tot_bonds;
1181	>	info[i].n_bends = tot_bends;
1182	>	info[i].n_torsions = tot_torsions;
1183	>	info[i].n_SRI = tot_SRI;
1184	>	info[i].n_mol = tot_nmol;
1185	>
1186	>	info[i].molMembershipArray = molMembershipArray;
1187	>	}
1188		}
1189
1130	–
1190		#ifdef IS_MPI
1191
1192		void SimSetup::mpiMolDivide( void ){
#	Line 1167 | Line 1226 | void SimSetup::mpiMolDivide( void ){
1226		localMol++;
1227		}
1228		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1229	<	info->molMembershipArray[globalAtomIndex] = allMol;
1229	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1230		globalAtomIndex++;
1231		}
1232
#	Line 1176 | Line 1235 | void SimSetup::mpiMolDivide( void ){
1235		}
1236		local_SRI = local_bonds + local_bends + local_torsions;
1237
1238	<	info->n_atoms = mpiSim->getMyNlocal();
1238	>	info[0].n_atoms = mpiSim->getMyNlocal();
1239
1240	<	if( local_atoms != info->n_atoms ){
1240	>	if( local_atoms != info[0].n_atoms ){
1241		sprintf( painCave.errMsg,
1242		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1243		" localAtom (%d) are not equal.\n",
1244	<	info->n_atoms,
1244	>	info[0].n_atoms,
1245		local_atoms );
1246		painCave.isFatal = 1;
1247		simError();
1248		}
1249
1250	<	info->n_bonds = local_bonds;
1251	<	info->n_bends = local_bends;
1252	<	info->n_torsions = local_torsions;
1253	<	info->n_SRI = local_SRI;
1254	<	info->n_mol = localMol;
1250	>	info[0].n_bonds = local_bonds;
1251	>	info[0].n_bends = local_bends;
1252	>	info[0].n_torsions = local_torsions;
1253	>	info[0].n_SRI = local_SRI;
1254	>	info[0].n_mol = localMol;
1255
1256		strcpy( checkPointMsg, "Passed nlocal consistency check." );
1257		MPIcheckPoint();
1258		}
1259	<
1259	>
1260		#endif // is_mpi
1261
1262
1263		void SimSetup::makeSysArrays( void ){
1264	<	int i, j, k;
1264	>	int i, j, k, l;
1265
1266	+	Atom** the_atoms;
1267	+	Molecule* the_molecules;
1268	+	Exclude** the_excludes;
1269
1270	<	// create the atom and short range interaction arrays
1270	>
1271	>	for(l=0; l<nInfo; l++){
1272	>
1273	>	// create the atom and short range interaction arrays
1274	>
1275	>	the_atoms = new Atom*[info[l].n_atoms];
1276	>	the_molecules = new Molecule[info[l].n_mol];
1277	>	int molIndex;
1278
1279	<	Atom::createArrays(info->n_atoms);
1280	<	the_atoms = new Atom*[info->n_atoms];
1212	<	the_molecules = new Molecule[info->n_mol];
1213	<	int molIndex;
1214	<
1215	<	// initialize the molecule's stampID's
1216	<
1279	>	// initialize the molecule's stampID's
1280	>
1281		#ifdef IS_MPI
1218	–
1219	–
1220	–	molIndex = 0;
1221	–	for(i=0; i<mpiSim->getTotNmol(); i++){
1282
1283	<	if(mol2proc[i] == worldRank ){
1284	<	the_molecules[molIndex].setStampID( molCompType[i] );
1285	<	the_molecules[molIndex].setMyIndex( molIndex );
1286	<	the_molecules[molIndex].setGlobalIndex( i );
1287	<	molIndex++;
1283	>
1284	>	molIndex = 0;
1285	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1286	>
1287	>	if(mol2proc[i] == worldRank ){
1288	>	the_molecules[molIndex].setStampID( molCompType[i] );
1289	>	the_molecules[molIndex].setMyIndex( molIndex );
1290	>	the_molecules[molIndex].setGlobalIndex( i );
1291	>	molIndex++;
1292	>	}
1293		}
1294	<	}
1230	<
1294	>
1295		#else // is_mpi
1296	<
1297	<	molIndex = 0;
1298	<	globalAtomIndex = 0;
1299	<	for(i=0; i<n_components; i++){
1300	<	for(j=0; j<components_nmol[i]; j++ ){
1301	<	the_molecules[molIndex].setStampID( i );
1302	<	the_molecules[molIndex].setMyIndex( molIndex );
1303	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1304	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1305	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1306	<	globalAtomIndex++;
1296	>
1297	>	molIndex = 0;
1298	>	globalAtomIndex = 0;
1299	>	for(i=0; i<n_components; i++){
1300	>	for(j=0; j<components_nmol[i]; j++ ){
1301	>	the_molecules[molIndex].setStampID( i );
1302	>	the_molecules[molIndex].setMyIndex( molIndex );
1303	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1304	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1305	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1306	>	globalAtomIndex++;
1307	>	}
1308	>	molIndex++;
1309		}
1244	–	molIndex++;
1310		}
1246	–	}
1311
1312	<
1312	>
1313		#endif // is_mpi
1314
1315
1316	<	if( info->n_SRI ){
1316	>	if( info[l].n_SRI ){
1317
1318	<	Exclude::createArray(info->n_SRI);
1319	<	the_excludes = new Exclude*[info->n_SRI];
1320	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1321	<	info->globalExcludes = new int;
1322	<	info->n_exclude = info->n_SRI;
1323	<	}
1324	<	else{
1318	>	Exclude::createArray(info[l].n_SRI);
1319	>	the_excludes = new Exclude*[info[l].n_SRI];
1320	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1321	>	the_excludes[ex] = new Exclude(ex);
1322	>	}
1323	>	info[l].globalExcludes = new int;
1324	>	info[l].n_exclude = info[l].n_SRI;
1325	>	}
1326	>	else{
1327
1328	<	Exclude::createArray( 1 );
1329	<	the_excludes = new Exclude*;
1330	<	the_excludes[0] = new Exclude(0);
1331	<	the_excludes[0]->setPair( 0,0 );
1332	<	info->globalExcludes = new int;
1333	<	info->globalExcludes[0] = 0;
1334	<	info->n_exclude = 0;
1335	<	}
1328	>	Exclude::createArray( 1 );
1329	>	the_excludes = new Exclude*;
1330	>	the_excludes[0] = new Exclude(0);
1331	>	the_excludes[0]->setPair( 0,0 );
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].globalExcludes[0] = 0;
1334	>	info[l].n_exclude = 0;
1335	>	}
1336
1337	<	// set the arrays into the SimInfo object
1337	>	// set the arrays into the SimInfo object
1338
1339	<	info->atoms = the_atoms;
1340	<	info->molecules = the_molecules;
1341	<	info->nGlobalExcludes = 0;
1342	<	info->excludes = the_excludes;
1339	>	info[l].atoms = the_atoms;
1340	>	info[l].molecules = the_molecules;
1341	>	info[l].nGlobalExcludes = 0;
1342	>	info[l].excludes = the_excludes;
1343
1344	<	the_ff->setSimInfo( info );
1345	<
1344	>	the_ff->setSimInfo( info );
1345	>
1346	>	}
1347		}
1348
1349		void SimSetup::makeIntegrator( void ){
1350
1351	<	NVT*  myNVT = NULL;
1285	<	NPTi* myNPTi = NULL;
1286	<	NPTf* myNPTf = NULL;
1287	<	NPTim* myNPTim = NULL;
1288	<	NPTfm* myNPTfm = NULL;
1351	>	int k;
1352
1353	<	switch( ensembleCase ){
1353	>	NVT<RealIntegrator>*  myNVT = NULL;
1354	>	NPTi<RealIntegrator>* myNPTi = NULL;
1355	>	NPTf<RealIntegrator>* myNPTf = NULL;
1356	>	NPTim<RealIntegrator>* myNPTim = NULL;
1357	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1358	>
1359	>	for(k=0; k<nInfo; k++){
1360	>
1361	>	switch( ensembleCase ){
1362	>
1363	>	case NVE_ENS:
1364	>	if (globals->haveZconstraints()){
1365	>	setupZConstraint(info[k]);
1366	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1367	>	}
1368
1369	<	case NVE_ENS:
1370	<	new NVE( info, the_ff );
1371	<	break;
1369	>	else
1370	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1371	>	break;
1372	>
1373	>	case NVT_ENS:
1374	>	if (globals->haveZconstraints()){
1375	>	setupZConstraint(info[k]);
1376	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377	>	}
1378	>	else
1379	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1380
1381	<	case NVT_ENS:
1382	<	myNVT = new NVT( info, the_ff );
1383	<	myNVT->setTargetTemp(globals->getTargetTemp());
1381	>	myNVT->setTargetTemp(globals->getTargetTemp());
1382	>
1383	>	if (globals->haveTauThermostat())
1384	>	myNVT->setTauThermostat(globals->getTauThermostat());
1385	>
1386	>	else {
1387	>	sprintf( painCave.errMsg,
1388	>	"SimSetup error: If you use the NVT\n"
1389	>	"    ensemble, you must set tauThermostat.\n");
1390	>	painCave.isFatal = 1;
1391	>	simError();
1392	>	}
1393	>	break;
1394	>
1395	>	case NPTi_ENS:
1396	>	if (globals->haveZconstraints()){
1397	>	setupZConstraint(info[k]);
1398	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399	>	}
1400	>	else
1401	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1402
1403	<	if (globals->haveTauThermostat())
1404	<	myNVT->setTauThermostat(globals->getTauThermostat());
1403	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	>	else {
1408	>	sprintf( painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413	>	}
1414	>
1415	>	if( globals->haveTauThermostat() )
1416	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	>	else{
1418	>	sprintf( painCave.errMsg,
1419	>	"SimSetup error: If you use an NPT\n"
1420	>	"    ensemble, you must set tauThermostat.\n");
1421	>	painCave.isFatal = 1;
1422	>	simError();
1423	>	}
1424	>
1425	>	if( globals->haveTauBarostat() )
1426	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	>	else{
1428	>	sprintf( painCave.errMsg,
1429	>	"SimSetup error: If you use an NPT\n"
1430	>	"    ensemble, you must set tauBarostat.\n");
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433	>	}
1434	>	break;
1435	>
1436	>	case NPTf_ENS:
1437	>	if (globals->haveZconstraints()){
1438	>	setupZConstraint(info[k]);
1439	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440	>	}
1441	>	else
1442	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1443
1444	<	else {
1445	<	sprintf( painCave.errMsg,
1446	<	"SimSetup error: If you use the NVT\n"
1444	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1445	>
1446	>	if (globals->haveTargetPressure())
1447	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1448	>	else {
1449	>	sprintf( painCave.errMsg,
1450	>	"SimSetup error: If you use a constant pressure\n"
1451	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1452	>	painCave.isFatal = 1;
1453	>	simError();
1454	>	}
1455	>
1456	>	if( globals->haveTauThermostat() )
1457	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1458	>	else{
1459	>	sprintf( painCave.errMsg,
1460	>	"SimSetup error: If you use an NPT\n"
1461		"    ensemble, you must set tauThermostat.\n");
1462	<	painCave.isFatal = 1;
1463	<	simError();
1464	<	}
1465	<	break;
1462	>	painCave.isFatal = 1;
1463	>	simError();
1464	>	}
1465	>
1466	>	if( globals->haveTauBarostat() )
1467	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1468	>	else{
1469	>	sprintf( painCave.errMsg,
1470	>	"SimSetup error: If you use an NPT\n"
1471	>	"    ensemble, you must set tauBarostat.\n");
1472	>	painCave.isFatal = 1;
1473	>	simError();
1474	>	}
1475	>	break;
1476	>
1477	>	case NPTim_ENS:
1478	>	if (globals->haveZconstraints()){
1479	>	setupZConstraint(info[k]);
1480	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481	>	}
1482	>	else
1483	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1484
1485	<	case NPTi_ENS:
1486	<	myNPTi = new NPTi( info, the_ff );
1487	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1488	<
1489	<	if (globals->haveTargetPressure())
1490	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1491	<	else {
1485	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1486	>
1487	>	if (globals->haveTargetPressure())
1488	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1489	>	else {
1490	>	sprintf( painCave.errMsg,
1491	>	"SimSetup error: If you use a constant pressure\n"
1492	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1493	>	painCave.isFatal = 1;
1494	>	simError();
1495	>	}
1496	>
1497	>	if( globals->haveTauThermostat() )
1498	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1499	>	else{
1500	>	sprintf( painCave.errMsg,
1501	>	"SimSetup error: If you use an NPT\n"
1502	>	"    ensemble, you must set tauThermostat.\n");
1503	>	painCave.isFatal = 1;
1504	>	simError();
1505	>	}
1506	>
1507	>	if( globals->haveTauBarostat() )
1508	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509	>	else{
1510		sprintf( painCave.errMsg,
1320	–	"SimSetup error: If you use a constant pressure\n"
1321	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1322	–	painCave.isFatal = 1;
1323	–	simError();
1324	–	}
1325	–
1326	–	if( globals->haveTauThermostat() )
1327	–	myNPTi->setTauThermostat( globals->getTauThermostat() );
1328	–	else{
1329	–	sprintf( painCave.errMsg,
1511		"SimSetup error: If you use an NPT\n"
1331	–	"    ensemble, you must set tauThermostat.\n");
1332	–	painCave.isFatal = 1;
1333	–	simError();
1334	–	}
1335	–
1336	–	if( globals->haveTauBarostat() )
1337	–	myNPTi->setTauBarostat( globals->getTauBarostat() );
1338	–	else{
1339	–	sprintf( painCave.errMsg,
1340	–	"SimSetup error: If you use an NPT\n"
1512		"    ensemble, you must set tauBarostat.\n");
1513		painCave.isFatal = 1;
1514		simError();
1515	<	}
1516	<	break;
1515	>	}
1516	>	break;
1517	>
1518	>	case NPTfm_ENS:
1519	>	if (globals->haveZconstraints()){
1520	>	setupZConstraint(info[k]);
1521	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522	>	}
1523	>	else
1524	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1525
1526	<	case NPTf_ENS:
1527	<	myNPTf = new NPTf( info, the_ff );
1528	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1529	<
1530	<	if (globals->haveTargetPressure())
1531	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1532	<	else {
1526	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1527	>
1528	>	if (globals->haveTargetPressure())
1529	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1530	>	else {
1531	>	sprintf( painCave.errMsg,
1532	>	"SimSetup error: If you use a constant pressure\n"
1533	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1534	>	painCave.isFatal = 1;
1535	>	simError();
1536	>	}
1537	>
1538	>	if( globals->haveTauThermostat() )
1539	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1540	>	else{
1541	>	sprintf( painCave.errMsg,
1542	>	"SimSetup error: If you use an NPT\n"
1543	>	"    ensemble, you must set tauThermostat.\n");
1544	>	painCave.isFatal = 1;
1545	>	simError();
1546	>	}
1547	>
1548	>	if( globals->haveTauBarostat() )
1549	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1550	>	else{
1551	>	sprintf( painCave.errMsg,
1552	>	"SimSetup error: If you use an NPT\n"
1553	>	"    ensemble, you must set tauBarostat.\n");
1554	>	painCave.isFatal = 1;
1555	>	simError();
1556	>	}
1557	>	break;
1558	>
1559	>	default:
1560		sprintf( painCave.errMsg,
1561	<	"SimSetup error: If you use a constant pressure\n"
1356	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1561	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1562		painCave.isFatal = 1;
1563		simError();
1359	–	}
1360	–
1361	–	if( globals->haveTauThermostat() )
1362	–	myNPTf->setTauThermostat( globals->getTauThermostat() );
1363	–	else{
1364	–	sprintf( painCave.errMsg,
1365	–	"SimSetup error: If you use an NPT\n"
1366	–	"    ensemble, you must set tauThermostat.\n");
1367	–	painCave.isFatal = 1;
1368	–	simError();
1564		}
1370	–
1371	–	if( globals->haveTauBarostat() )
1372	–	myNPTf->setTauBarostat( globals->getTauBarostat() );
1373	–	else{
1374	–	sprintf( painCave.errMsg,
1375	–	"SimSetup error: If you use an NPT\n"
1376	–	"    ensemble, you must set tauBarostat.\n");
1377	–	painCave.isFatal = 1;
1378	–	simError();
1379	–	}
1380	–	break;
1381	–
1382	–	case NPTim_ENS:
1383	–	myNPTim = new NPTim( info, the_ff );
1384	–	myNPTim->setTargetTemp( globals->getTargetTemp());
1385	–
1386	–	if (globals->haveTargetPressure())
1387	–	myNPTim->setTargetPressure(globals->getTargetPressure());
1388	–	else {
1389	–	sprintf( painCave.errMsg,
1390	–	"SimSetup error: If you use a constant pressure\n"
1391	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1392	–	painCave.isFatal = 1;
1393	–	simError();
1394	–	}
1395	–
1396	–	if( globals->haveTauThermostat() )
1397	–	myNPTim->setTauThermostat( globals->getTauThermostat() );
1398	–	else{
1399	–	sprintf( painCave.errMsg,
1400	–	"SimSetup error: If you use an NPT\n"
1401	–	"    ensemble, you must set tauThermostat.\n");
1402	–	painCave.isFatal = 1;
1403	–	simError();
1404	–	}
1405	–
1406	–	if( globals->haveTauBarostat() )
1407	–	myNPTim->setTauBarostat( globals->getTauBarostat() );
1408	–	else{
1409	–	sprintf( painCave.errMsg,
1410	–	"SimSetup error: If you use an NPT\n"
1411	–	"    ensemble, you must set tauBarostat.\n");
1412	–	painCave.isFatal = 1;
1413	–	simError();
1414	–	}
1415	–	break;
1416	–
1417	–	case NPTfm_ENS:
1418	–	myNPTfm = new NPTfm( info, the_ff );
1419	–	myNPTfm->setTargetTemp( globals->getTargetTemp());
1420	–
1421	–	if (globals->haveTargetPressure())
1422	–	myNPTfm->setTargetPressure(globals->getTargetPressure());
1423	–	else {
1424	–	sprintf( painCave.errMsg,
1425	–	"SimSetup error: If you use a constant pressure\n"
1426	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1427	–	painCave.isFatal = 1;
1428	–	simError();
1429	–	}
1430	–
1431	–	if( globals->haveTauThermostat() )
1432	–	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1433	–	else{
1434	–	sprintf( painCave.errMsg,
1435	–	"SimSetup error: If you use an NPT\n"
1436	–	"    ensemble, you must set tauThermostat.\n");
1437	–	painCave.isFatal = 1;
1438	–	simError();
1439	–	}
1440	–
1441	–	if( globals->haveTauBarostat() )
1442	–	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1443	–	else{
1444	–	sprintf( painCave.errMsg,
1445	–	"SimSetup error: If you use an NPT\n"
1446	–	"    ensemble, you must set tauBarostat.\n");
1447	–	painCave.isFatal = 1;
1448	–	simError();
1449	–	}
1450	–	break;
1451	–
1452	–	default:
1453	–	sprintf( painCave.errMsg,
1454	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1455	–	painCave.isFatal = 1;
1456	–	simError();
1565		}
1458	–
1566		}
1567
1568		void SimSetup::initFortran( void ){
1569
1570	<	info->refreshSim();
1570	>	info[0].refreshSim();
1571
1572	<	if( !strcmp( info->mixingRule, "standard") ){
1572	>	if( !strcmp( info[0].mixingRule, "standard") ){
1573		the_ff->initForceField( LB_MIXING_RULE );
1574		}
1575	<	else if( !strcmp( info->mixingRule, "explicit") ){
1575	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1576		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1577		}
1578		else{
1579		sprintf( painCave.errMsg,
1580		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	<	info->mixingRule );
1581	>	info[0].mixingRule );
1582		painCave.isFatal = 1;
1583		simError();
1584		}
#	Line 1484 | Line 1591 | void SimSetup::initFortran( void ){
1591		#endif // is_mpi
1592
1593		}
1594	+
1595	+	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596	+	{
1597	+	int nZConstraints;
1598	+	ZconStamp** zconStamp;
1599	+
1600	+	if(globals->haveZconstraintTime()){
1601	+
1602	+	//add sample time of z-constraint  into SimInfo's property list
1603	+	DoubleData* zconsTimeProp = new DoubleData();
1604	+	zconsTimeProp->setID(ZCONSTIME_ID);
1605	+	zconsTimeProp->setData(globals->getZconsTime());
1606	+	theInfo.addProperty(zconsTimeProp);
1607	+	}
1608	+	else{
1609	+	sprintf( painCave.errMsg,
1610	+	"ZConstraint error: If you use an ZConstraint\n"
1611	+	" , you must set sample time.\n");
1612	+	painCave.isFatal = 1;
1613	+	simError();
1614	+	}
1615	+
1616	+	//
1617	+	nZConstraints = globals->getNzConstraints();
1618	+	zconStamp = globals->getZconStamp();
1619	+	ZConsParaItem tempParaItem;
1620	+
1621	+	ZConsParaData* zconsParaData = new ZConsParaData();
1622	+	zconsParaData->setID(ZCONSPARADATA_ID);
1623	+
1624	+	for(int i = 0; i < nZConstraints; i++){
1625	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1626	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1627	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1628	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1629	+
1630	+	zconsParaData->addItem(tempParaItem);
1631	+	}
1632	+
1633	+	//sort the parameters by index of molecules
1634	+	zconsParaData->sortByIndex();
1635	+
1636	+	//push data into siminfo, therefore, we can retrieve later
1637	+	theInfo.addProperty(zconsParaData);
1638	+
1639	+	//push zconsTol into siminfo, if user does not specify
1640	+	//value for zconsTol, a default value will be used
1641	+	DoubleData* zconsTol = new DoubleData();
1642	+	zconsTol->setID(ZCONSTOL_ID);
1643	+	if(globals->haveZconsTol()){
1644	+	zconsTol->setData(globals->getZconsTol());
1645	+	}
1646	+	else{
1647	+	double defaultZConsTol = 1E-6;
1648	+	sprintf( painCave.errMsg,
1649	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1650	+	" , default value %f is used.\n", defaultZConsTol);
1651	+	painCave.isFatal = 0;
1652	+	simError();
1653	+
1654	+	zconsTol->setData(defaultZConsTol);
1655	+	}
1656	+	theInfo.addProperty(zconsTol);
1657	+
1658	+	//Determine the name of ouput file and add it into SimInfo's property list
1659	+	//Be careful, do not use inFileName, since it is a pointer which
1660	+	//point to a string at master node, and slave nodes do not contain that string
1661	+
1662	+	string zconsOutput(theInfo.finalName);
1663	+
1664	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1665	+
1666	+	StringData* zconsFilename = new StringData();
1667	+	zconsFilename->setID(ZCONSFILENAME_ID);
1668	+	zconsFilename->setData(zconsOutput);
1669	+
1670	+	theInfo.addProperty(zconsFilename);
1671	+	}

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