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root/group/trunk/OOPSE/utils/sysbuilder/bilayerSys.cpp
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Comparing trunk/OOPSE/utils/sysbuilder/bilayerSys.cpp (file contents):
Revision 678 by chuckv, Mon Aug 11 22:12:31 2003 UTC vs.
Revision 700 by chuckv, Mon Aug 18 20:59:47 2003 UTC

# Line 12 | Line 12
12   #include "sysBuild.hpp"
13   #include "bilayerSys.hpp"
14  
15 + #include "latticeBuilder.hpp"
16  
16 –
17   void buildMap( double &x, double &y, double &z,
18 <          double boxX, double boxY, double boxZ );
18 >               double boxX, double boxY, double boxZ );
19  
20   int buildRandomBilayer( void );
21  
# Line 44 | Line 44 | int buildRandomBilayer( void ){
44    } coord;
45  
46  
47 +
48    const double waterRho = 0.0334; // number density per cubic angstrom
49    const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters
50    const double waterCell = 4.929; // fcc unit cell length
51  
52 +  Lattice myFCC( FCC_LATTICE_TYPE, waterCell );
53 +  double *posX, *posY, *posZ;
54 +  double pos[3], posA[3], posB[3];
55 +
56    const double water_padding = 6.0;
57    const double lipid_spaceing = 8.0;
58  
59  
60 <  int i,j,k, l;
60 >  int i,j,k, l, m;
61    int nAtoms, atomIndex, molIndex, molID;
62    int* molSeq;
63    int* molMap;
# Line 67 | Line 72 | int buildRandomBilayer( void ){
72  
73    Atom** atoms;
74    SimInfo* simnfo;
75 +  SimState* theConfig;
76    DumpWriter* writer;
77  
78    MoleculeStamp* lipidStamp;
# Line 91 | Line 97 | int buildRandomBilayer( void ){
97    foundWater = 0;
98    for(i=0; i<bsInfo.nComponents; i++){
99      if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){
100 <      
100 >          
101        foundLipid = 1;
102        lipidStamp = bsInfo.compStamps[i];
103        nLipids = bsInfo.componentsNmol[i];
104      }
105      if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){
106 <      
106 >          
107        foundWater = 1;
108 <      
108 >          
109        waterStamp = bsInfo.compStamps[i];
110        nWaters = bsInfo.componentsNmol[i];
111      }
# Line 112 | Line 118 | int buildRandomBilayer( void ){
118      simError();
119    }
120    if( !foundWater ){
121 <        sprintf(painCave.errMsg,
122 <                "Could not find solvent \"%s\" in the bass file.\n",
121 >    sprintf(painCave.errMsg,
122 >            "Could not find solvent \"%s\" in the bass file.\n",
123              bsInfo.waterName );
124      painCave.isFatal = 1;
125      simError();
# Line 128 | Line 134 | int buildRandomBilayer( void ){
134    waterLocate = new MoLocator( waterStamp );
135    waterNatoms = waterStamp->getNAtoms();
136    
137 <  nAtoms = nLipids * lipidNatoms;
137 >  nAtoms = lipidNatoms;
138  
139 < simnfo[0].n_atoms = nAtoms;
140 < simnfo[0].atoms=new Atom*[nAtoms];
139 >  simnfo[0].n_atoms = nAtoms;
140 >  simnfo[0].atoms=new Atom*[nAtoms];
141  
142 < (simnfo[0]->getConfiguration())->createArrays( simnfo[0].n_atoms );
143 < for(i=0; i<simnfo[0].n_atoms; i++) simnfo[0].atoms[i]->setCoords();
142 >  theConfig = simnfo[0].getConfiguration();
143 >  theConfig->createArrays( simnfo[0].n_atoms );
144  
145 < atoms=simnfo[0].atoms;
145 >  atoms=simnfo[0].atoms;
146          
147  
148    // create the test box for initial water displacement
# Line 160 | Line 166 | int buildRandomBilayer( void ){
166    for( i=0; i < nCells; i++ ){
167      for( j=0; j < nCells; j++ ){
168        for( k=0; k < nCells; k++ ){
169 <        
170 <        waterX[ndx] = i * waterCell + x0;
171 <        waterY[ndx] = j * waterCell + y0;
172 <        waterZ[ndx] = k * waterCell + z0;
173 <        ndx++;
174 <        
175 <        waterX[ndx] = i * waterCell + 0.5 * waterCell + x0;
176 <        waterY[ndx] = j * waterCell + 0.5 * waterCell + y0;
171 <        waterZ[ndx] = k * waterCell + z0;
172 <        ndx++;
173 <        
174 <        waterX[ndx] = i * waterCell + x0;
175 <        waterY[ndx] = j * waterCell + 0.5 * waterCell + y0;
176 <        waterZ[ndx] = k * waterCell + 0.5 * waterCell + z0;
177 <        ndx++;
178 <        
179 <        waterX[ndx] = i * waterCell + 0.5 * waterCell + x0;
180 <        waterY[ndx] = j * waterCell + y0;
181 <        waterZ[ndx] = k * waterCell + 0.5 * waterCell + z0;
182 <        ndx++;
169 >
170 >        myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k);
171 >        for(l=0; l<4; l++){
172 >          waterX[ndx]=posX[l];
173 >          waterY[ndx]=posY[l];
174 >          waterZ[ndx]=posZ[l];
175 >          ndx++;
176 >        }
177        }
178      }
179    }
# Line 202 | Line 196 | int buildRandomBilayer( void ){
196    testSite.pos[1] = 0.0;
197    testSite.pos[2] = 0.0;
198  
199 <  lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0 );
199 >  lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0, theConfig );
200  
201    int *isActive = new int[testWaters];
202    for(i=0; i<testWaters; i++) isActive[i] = 1;
# Line 214 | Line 208 | int buildRandomBilayer( void ){
208    
209    for(i=0; ( (i<testWaters) && isActive[i] ); i++){
210      for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){
211 +      
212 +      atoms[j]->getPos( pos );
213  
214 <      dx = waterX[i] - atoms[j]->getX();
215 <      dy = waterY[i] - atoms[j]->getY();
216 <      dz = waterZ[i] - atoms[j]->getZ();
214 >      dx = waterX[i] - pos[0];
215 >      dy = waterY[i] - pos[1];
216 >      dz = waterZ[i] - pos[2];
217  
218        buildMap( dx, dy, dz, testBox, testBox, testBox );
219  
220        dx2 = dx * dx;
221        dy2 = dy * dy;
222        dz2 = dz * dz;
223 <      
223 >          
224        dSqr = dx2 + dy2 + dz2;
225        if( dSqr < rCutSqr ){
226          isActive[i] = 0;
# Line 243 | Line 239 | int buildRandomBilayer( void ){
239    int done = 0;
240    ndx = 0;
241    while( !done ){
242 <    
242 >        
243      ndx++;
244      testTot = 4 * ndx * ndx * ndx;
245 <    
245 >        
246      if( testTot >= targetWaters ) done = 1;
247    }
248  
249    nCells = ndx;
250 <    
251 <    
250 >        
251 >        
252    // create the new water box to the new specifications
253    
254    int newWaters = nCells * nCells * nCells * 4;
# Line 266 | Line 262 | int buildRandomBilayer( void ){
262    double box_x = waterCell * nCells;
263    double box_y = waterCell * nCells;
264    double box_z = waterCell * nCells;
265 <    
265 >        
266    // create an fcc lattice in the water box.
267    
268    ndx = 0;
269    for( i=0; i < nCells; i++ ){
270      for( j=0; j < nCells; j++ ){
271        for( k=0; k < nCells; k++ ){
272 <        
273 <        waterSites[ndx].pos[0] = i * waterCell;
274 <        waterSites[ndx].pos[1] = j * waterCell;
275 <        waterSites[ndx].pos[2] = k * waterCell;
276 <        ndx++;
277 <        
278 <        waterSites[ndx].pos[0] = i * waterCell + 0.5 * waterCell;
279 <        waterSites[ndx].pos[1] = j * waterCell + 0.5 * waterCell;
284 <        waterSites[ndx].pos[2] = k * waterCell;
285 <        ndx++;
286 <        
287 <        waterSites[ndx].pos[0] = i * waterCell;
288 <        waterSites[ndx].pos[1] = j * waterCell + 0.5 * waterCell;
289 <        waterSites[ndx].pos[2] = k * waterCell + 0.5 * waterCell;
290 <        ndx++;
291 <        
292 <        waterSites[ndx].pos[0] = i * waterCell + 0.5 * waterCell;
293 <        waterSites[ndx].pos[1] = j * waterCell;
294 <        waterSites[ndx].pos[2] = k * waterCell + 0.5 * waterCell;
295 <        ndx++;
272 >
273 >        myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k);
274 >        for(l=0; l<4; l++){
275 >          waterSites[ndx].pos[0] = posX[l];
276 >          waterSites[ndx].pos[1] = posY[l];
277 >          waterSites[ndx].pos[2] = posZ[l];
278 >          ndx++;
279 >        }
280        }
281      }
282    }  
# Line 305 | Line 289 | int buildRandomBilayer( void ){
289    int reject;
290    int testDX, acceptedDX;
291  
292 +  nAtoms = nLipids * lipidNatoms;
293 +
294 +  simnfo[1].n_atoms = nAtoms;
295 +  simnfo[1].atoms=new Atom*[nAtoms];
296 +
297 +  theConfig = simnfo[1].getConfiguration();
298 +  theConfig->createArrays( simnfo[1].n_atoms );
299 +
300 +  atoms=simnfo[1].atoms;
301 +
302    rCutSqr = lipid_spaceing * lipid_spaceing;
303  
304    for(i=0; i<nLipids; i++ ){
305      done = 0;
306      while( !done ){
307 <      
307 >          
308        lipidSites[i].pos[0] = drand48() * box_x;
309        lipidSites[i].pos[1] = drand48() * box_y;
310        lipidSites[i].pos[2] = drand48() * box_z;
311 <      
311 >          
312        getRandomRot( lipidSites[i].rot );
313 <      
313 >          
314        ndx = i * lipidNatoms;
315  
316        lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
317 <                             ndx );
318 <      
317 >                             ndx, theConfig );
318 >          
319        reject = 0;
320        for( j=0; !reject && j<i; j++){
321          for(k=0; !reject && k<lipidNatoms; k++){
322            
323            acceptedDX = j*lipidNatoms + k;
324            for(l=0; !reject && l<lipidNatoms; l++){
325 <            
325 >                
326              testDX = ndx + l;
327  
328 <            dx = atoms[testDX]->getX() - atoms[acceptedDX]->getX();
329 <            dy = atoms[testDX]->getY() - atoms[acceptedDX]->getY();
336 <            dz = atoms[testDX]->getZ() - atoms[acceptedDX]->getZ();
328 >            atoms[testDX]->getPos( posA );
329 >            atoms[acceptedDX]->getPos( posB );
330              
331 +            dx = posA[0] - posB[0];
332 +            dy = posA[1] - posB[1];
333 +            dz = posA[2] - posB[2];
334 +                
335              buildMap( dx, dy, dz, box_x, box_y, box_z );
336 <            
336 >                
337              dx2 = dx * dx;
338              dy2 = dy * dy;
339              dz2 = dz * dz;
340 <            
340 >                
341              dSqr = dx2 + dy2 + dz2;
342              if( dSqr < rCutSqr ) reject = 1;
343            }
# Line 353 | Line 350 | int buildRandomBilayer( void ){
350        }
351        else{
352          done = 1;
353 <        std::cout << i << " has been accepted\n";
353 >        std::cout << (i+1) << " has been accepted\n";
354        }
355      }
356    }
357          
358    // cut out the waters that overlap with the lipids.
359    
360 +
361    delete[] isActive;
362    isActive = new int[newWaters];
363    for(i=0; i<newWaters; i++) isActive[i] = 1;
# Line 369 | Line 367 | int buildRandomBilayer( void ){
367    for(i=0; ( (i<newWaters) && isActive[i] ); i++){
368      for(j=0; ( (j<nAtoms) && isActive[i] ); j++){
369  
370 <      dx = waterSites[i].pos[0] - atoms[j]->getX();
373 <      dy = waterSites[i].pos[1] - atoms[j]->getY();
374 <      dz = waterSites[i].pos[2] - atoms[j]->getZ();
370 >      atoms[j]->getPos( pos );
371  
372 +      dx = waterSites[i].pos[0] - pos[0];
373 +      dy = waterSites[i].pos[1] - pos[1];
374 +      dz = waterSites[i].pos[2] - pos[2];
375 +
376        buildMap( dx, dy, dz, box_x, box_y, box_z );
377  
378        dx2 = dx * dx;
379        dy2 = dy * dy;
380        dz2 = dz * dz;
381 <      
381 >          
382        dSqr = dx2 + dy2 + dz2;
383        if( dSqr < rCutSqr ){
384          isActive[i] = 0;
385          n_active--;
386 +
387 +
388        }
389      }
390    }
391  
392 +
393 +
394 +
395    if( n_active < nWaters ){
396 <    
396 >        
397      sprintf( painCave.errMsg,
398               "Too many waters were removed, edit code and try again.\n" );
399 <    
399 >        
400      painCave.isFatal = 1;
401      simError();
402    }
# Line 404 | Line 409 | int buildRandomBilayer( void ){
409      if( isActive[quickKill] ){
410        isActive[quickKill] = 0;
411        n_active--;
412 +
413      }
414    }
415  
416    if( n_active != nWaters ){
417 <    
417 >        
418      sprintf( painCave.errMsg,
419               "QuickKill didn't work right. n_active = %d, and nWaters = %d\n",
420               n_active, nWaters );
# Line 418 | Line 424 | int buildRandomBilayer( void ){
424  
425    // clean up our messes before building the final system.
426  
427 <  for(i=0; i<nAtoms; i++){
428 <    
423 <    delete atoms[i];
424 <  }
425 <  Atom::destroyArrays();
426 <  
427 >  simnfo[0].getConfiguration()->destroyArrays();
428 >  simnfo[1].getConfiguration()->destroyArrays();
429  
430    // create the real Atom arrays
431    
# Line 443 | Line 445 | int buildRandomBilayer( void ){
445      nAtoms += waterNatoms;
446    }
447    
448 +  theConfig = simnfo[2].getConfiguration();
449 +  theConfig->createArrays( nAtoms );
450 +  simnfo[2].atoms = new Atom*[nAtoms];
451 +  atoms = simnfo[2].atoms;
452 +  simnfo[2].n_atoms = nAtoms;
453    
447 –  Atom::createArrays( nAtoms );
448 –  atoms = new Atom*[nAtoms];
449 –
450 –  
454    // initialize lipid positions
455  
456    molIndex = 0;
457    for(i=0; i<nLipids; i++ ){
458      lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
459 <                           molStart[molIndex] );
459 >                           molStart[molIndex], theConfig );
460      molIndex++;
461    }
462  
463    // initialize the water positions
464  
465    for(i=0; i<newWaters; i++){
466 <    
466 >        
467      if( isActive[i] ){
468 <      
468 >          
469        getRandomRot( waterSites[i].rot );
470        waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms,
471 <                             molStart[molIndex] );
471 >                             molStart[molIndex], theConfig );
472        molIndex++;
473      }
474    }  
475  
476    // set up the SimInfo object
477    
478 +  double Hmat[3][3];
479 +
480 +  Hmat[0][0] = box_x;
481 +  Hmat[0][1] = 0.0;
482 +  Hmat[0][2] = 0.0;
483 +
484 +  Hmat[1][0] = 0.0;
485 +  Hmat[1][1] = box_y;
486 +  Hmat[1][2] = 0.0;
487 +
488 +  Hmat[2][0] = 0.0;
489 +  Hmat[2][1] = 0.0;
490 +  Hmat[2][2] = box_z;
491 +  
492 +
493    bsInfo.boxX = box_x;
494    bsInfo.boxY = box_y;
495    bsInfo.boxZ = box_z;
496    
497 <  double boxVector[3];
480 <
481 <  boxVector[0] = bsInfo.boxX;
482 <  boxVector[1] = bsInfo.boxY;
483 <  boxVector[2] = bsInfo.boxZ;
484 <  simnfo->setBox( boxVector );
497 >  simnfo[2].setBoxM( Hmat );
498  
499 <  sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
500 <  sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );
499 >  sprintf( simnfo[2].sampleName, "%s.dump", bsInfo.outPrefix );
500 >  sprintf( simnfo[2].finalName, "%s.init", bsInfo.outPrefix );
501  
489 –  simnfo->atoms = atoms;
490 –  
502    // set up the writer and write out
503    
504 <  writer = new DumpWriter( simnfo );
504 >  writer = new DumpWriter( &simnfo[2] );
505    writer->writeFinal( 0.0 );
495 –    
496 –  // clean up the memory
497 –  
498 – //   if( molMap != NULL )   delete[] molMap;
499 – //   if( cardDeck != NULL ) delete[] cardDeck;
500 – //   if( locate != NULL ){
501 – //     for(i=0; i<bsInfo.nComponents; i++){
502 – //       delete locate[i];
503 – //     }
504 – //     delete[] locate;
505 – //   }
506 – //   if( atoms != NULL ){
507 – //     for(i=0; i<nAtoms; i++){
508 – //       delete atoms[i];
509 – //     }
510 – //     Atom::destroyArrays();
511 – //     delete[] atoms;
512 – //   }
513 – //   if( molSeq != NULL ) delete[] molSeq;
514 – //   if( simnfo != NULL ) delete simnfo;
515 – //   if( writer != NULL ) delete writer;
516 –
517 –  return 1;
518 – }
519 –
520 –  
521 –
522 – int Old_buildRandomBilayer( void ){
523 –
524 –  int i,j,k;
525 –  int nAtoms, atomIndex, molIndex, molID;
526 –  int* molSeq;
527 –  int* molMap;
528 –  int* molStart;
529 –  int* cardDeck;
530 –  int deckSize;
531 –  int rSite, rCard;
532 –  double cell;
533 –  int nCells, nSites, siteIndex;
534 –  double rot[3][3];
535 –  double pos[3];
536 –
537 –  Atom** atoms;
538 –  SimInfo* simnfo;
539 –  DumpWriter* writer;
540 –  MoLocator** locate;
541 –
542 –  // initialize functions and variables
543 –  
544 –  srand48( RAND_SEED );
545 –  molSeq = NULL;
546 –  molStart = NULL;
547 –  molMap = NULL;
548 –  cardDeck = NULL;
549 –  atoms = NULL;
550 –  locate = NULL;
551 –  simnfo = NULL;
552 –  writer = NULL;
553 –
554 –  // calculate the number of cells in the fcc box
555 –
556 –  nCells = 0;
557 –  nSites = 0;
558 –  while( nSites < bsInfo.totNmol ){
559 –    nCells++;
560 –    nSites = 4.0 * pow( (double)nCells, 3.0 );
561 –  }
562 –
563 –
564 –  // create the molMap and cardDeck arrays
565 –  
566 –  molMap = new int[nSites];
567 –  cardDeck = new int[nSites];
568 –  
569 –  for(i=0; i<nSites; i++){
570 –    molMap[i] = -1;
571 –    cardDeck[i] = i;
572 –  }
573 –
574 –  // randomly place the molecules on the sites
575 –  
576 –  deckSize = nSites;
577 –  for(i=0; i<bsInfo.totNmol; i++){
578 –    rCard = (int)( deckSize * drand48() );
579 –    rSite = cardDeck[rCard];
580 –    molMap[rSite] = i;
581 –
582 –    // book keep the card deck;
583 –    
584 –    deckSize--;
585 –    cardDeck[rCard] = cardDeck[deckSize];
586 –  }
587 –  
588 –  
589 –  // create the MoLocator and Atom arrays
590 –  
591 –  nAtoms = 0;
592 –  molIndex = 0;
593 –  locate = new MoLocator*[bsInfo.nComponents];
594 –  molSeq = new int[bsInfo.totNmol];
595 –  molStart = new int[bsInfo.totNmol];  
596 –  for(i=0; i<bsInfo.nComponents; i++){
597 –    locate[i] = new MoLocator( bsInfo.compStamps[i] );
598 –    for(j=0; j<bsInfo.componentsNmol[i]; j++){
599 –      molSeq[molIndex] = i;
600 –      molStart[molIndex] = nAtoms;
601 –      molIndex++;
602 –      nAtoms += bsInfo.compStamps[i]->getNAtoms();
603 –    }
604 –  }
605 –  
606 –  Atom::createArrays( nAtoms );
607 –  atoms = new Atom*[nAtoms];
608 –  
609 –  
610 –  // place the molecules at each FCC site
611 –  
612 –  cell = 5.0;
613 –  for(i=0; i<bsInfo.nComponents; i++){
614 –    if(cell < locate[i]->getMaxLength() ) cell = locate[i]->getMaxLength();
615 –  }
616 –  cell *= 1.2; // add a little buffer
617 –
618 –  cell *= M_SQRT2;
619 –
620 –  siteIndex = 0;
621 –  for(i=0; i<nCells; i++){
622 –    for(j=0; j<nCells; j++){
623 –      for(k=0; k<nCells; k++){
506          
625 –        if( molMap[siteIndex] >= 0 ){
626 –          pos[0] = i * cell;
627 –          pos[1] = j * cell;
628 –          pos[2] = k * cell;
629 –          
630 –          getRandomRot( rot );
631 –          molID = molSeq[molMap[siteIndex]];
632 –          atomIndex = molStart[ molMap[siteIndex] ];
633 –          locate[molID]->placeMol( pos, rot, atoms, atomIndex );
634 –        }
635 –        siteIndex++;
636 –
637 –        if( molMap[siteIndex] >= 0 ){
638 –          pos[0] = i * cell + (0.5 * cell);
639 –          pos[1] = j * cell;
640 –          pos[2] = k * cell + (0.5 * cell);
641 –
642 –          getRandomRot( rot );
643 –          molID = molSeq[molMap[siteIndex]];
644 –          atomIndex = molStart[ molMap[siteIndex] ];
645 –          locate[molID]->placeMol( pos, rot, atoms, atomIndex );
646 –        }
647 –        siteIndex++;
648 –
649 –        if( molMap[siteIndex] >= 0 ){
650 –          pos[0] = i * cell + (0.5 * cell);
651 –          pos[1] = j * cell + (0.5 * cell);
652 –          pos[2] = k * cell;
653 –          
654 –          getRandomRot( rot );
655 –          molID = molSeq[molMap[siteIndex]];
656 –          atomIndex = molStart[ molMap[siteIndex] ];
657 –          locate[molID]->placeMol( pos, rot, atoms, atomIndex );
658 –        }
659 –        siteIndex++;
660 –
661 –        if( molMap[siteIndex] >= 0 ){
662 –          pos[0] = i * cell;
663 –          pos[1] = j * cell + (0.5 * cell);
664 –          pos[2] = k * cell + (0.5 * cell);
665 –
666 –          getRandomRot( rot );
667 –          molID = molSeq[molMap[siteIndex]];
668 –          atomIndex = molStart[ molMap[siteIndex] ];
669 –          locate[molID]->placeMol( pos, rot, atoms, atomIndex );
670 –        }
671 –        siteIndex++;
672 –      }
673 –    }
674 –  }
675 –
676 –  // set up the SimInfo object
677 –  
678 –  bsInfo.boxX = nCells * cell;
679 –  bsInfo.boxY = nCells * cell;
680 –  bsInfo.boxZ = nCells * cell;
681 –  
682 –  double boxVector[3];
683 –  simnfo = new SimInfo();
684 –  simnfo->n_atoms = nAtoms;
685 –  boxVector[0] = bsInfo.boxX;
686 –  boxVector[1] = bsInfo.boxY;
687 –  boxVector[2] = bsInfo.boxZ;
688 –  simnfo->setBox( boxVector );
689 –
690 –  sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
691 –  sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );
692 –
693 –  simnfo->atoms = atoms;
694 –  
695 –  // set up the writer and write out
696 –  
697 –  writer = new DumpWriter( simnfo );
698 –  writer->writeFinal(0.0);
699 –    
507    // clean up the memory
508    
509 <  if( molMap != NULL )   delete[] molMap;
510 <  if( cardDeck != NULL ) delete[] cardDeck;
511 <  if( locate != NULL ){
512 <    for(i=0; i<bsInfo.nComponents; i++){
513 <      delete locate[i];
514 <    }
515 <    delete[] locate;
516 <  }
517 <  if( atoms != NULL ){
518 <    for(i=0; i<nAtoms; i++){
519 <      delete atoms[i];
520 <    }
521 <    Atom::destroyArrays();
522 <    delete[] atoms;
523 <  }
524 <  if( molSeq != NULL ) delete[] molSeq;
525 <  if( simnfo != NULL ) delete simnfo;
526 <  if( writer != NULL ) delete writer;
509 >  //     if( molMap != NULL )   delete[] molMap;
510 >  //     if( cardDeck != NULL ) delete[] cardDeck;
511 >  //     if( locate != NULL ){
512 >  //       for(i=0; i<bsInfo.nComponents; i++){
513 >  //             delete locate[i];
514 >  //       }
515 >  //       delete[] locate;
516 >  //     }
517 >  //     if( atoms != NULL ){
518 >  //       for(i=0; i<nAtoms; i++){
519 >  //             delete atoms[i];
520 >  //       }
521 >  //       Atom::destroyArrays();
522 >  //       delete[] atoms;
523 >  //     }
524 >  //     if( molSeq != NULL ) delete[] molSeq;
525 >  //     if( simnfo != NULL ) delete simnfo;
526 >  //     if( writer != NULL ) delete writer;
527  
528    return 1;
529   }
530  
724 –
531   void getRandomRot( double rot[3][3] ){
532  
533    double theta, phi, psi;
# Line 751 | Line 557 | void buildMap( double &x, double &y, double &z,
557  
558  
559   void buildMap( double &x, double &y, double &z,
560 <          double boxX, double boxY, double boxZ ){
560 >               double boxX, double boxY, double boxZ ){
561    
562    if(x < 0) x -= boxX * (double)( (int)( (x / boxX)  - 0.5 ) );
563    else x -= boxX * (double)( (int)( (x / boxX ) + 0.5));

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