ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/utils/bilayerSys.cpp
(Generate patch)

Comparing trunk/OOPSE/utils/bilayerSys.cpp (file contents):
Revision 537 by mmeineke, Fri May 16 21:37:56 2003 UTC vs.
Revision 538 by mmeineke, Sat May 17 16:57:08 2003 UTC

# Line 45 | Line 45 | int buildRandomBilayer( void ){
45  
46  
47    const double waterRho = 0.0334; // number density per cubic angstrom
48 <  const double waterVol = 4.0 / water_rho; // volume occupied by 4 waters
48 >  const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters
49    const double waterCell = 4.929; // fcc unit cell length
50  
51    const double water_padding = 2.5;
52    const double lipid_spaceing = 5.0;
53  
54  
55 <  int i,j,k;
55 >  int i,j,k, l;
56    int nAtoms, atomIndex, molIndex, molID;
57    int* molSeq;
58    int* molMap;
# Line 65 | Line 65 | int buildRandomBilayer( void ){
65    
66    coord testSite;
67  
68 +  Atom** atoms;
69 +  SimInfo* simnfo;
70 +  DumpWriter* writer;
71 +
72    MoleculeStamp* lipidStamp;
73    MoleculeStamp* waterStamp;  
74    MoLocator *lipidLocate;
75 <  MoLocator *waterLocate
75 >  MoLocator *waterLocate;
76    int foundLipid, foundWater;
77 <  int nLipids, lipiNatoms, nWaters, waterNatoms;
77 >  int nLipids, lipidNatoms, nWaters, waterNatoms;
78    double testBox, maxLength;
79    
80    srand48( RAND_SEED );
# Line 79 | Line 83 | int buildRandomBilayer( void ){
83    // set the the lipidStamp
84  
85    foundLipid = 0;
86 +  foundWater = 0;
87    for(i=0; i<bsInfo.nComponents; i++){
88      if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){
89        
90 <      foundlipid = 1;
90 >      foundLipid = 1;
91        lipidStamp = bsInfo.compStamps[i];
92        nLipids = bsInfo.componentsNmol[i];
93      }
94      if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){
95        
96        foundWater = 1;
97 +      
98        waterStamp = bsInfo.compStamps[i];
99        nWaters = bsInfo.componentsNmol[i];
100      }
# Line 115 | Line 121 | int buildRandomBilayer( void ){
121    maxLength = lipidLocate->getMaxLength();
122  
123    waterLocate = new MoLocator( waterStamp );
124 <  waterNatoms = waterStamp->getNatoms();
124 >  waterNatoms = waterStamp->getNAtoms();
125    
126    nAtoms = nLipids * lipidNatoms;
127  
# Line 125 | Line 131 | int buildRandomBilayer( void ){
131    // create the test box for initial water displacement
132  
133    testBox = maxLength + waterCell * 4.0; // pad with 4 cells
134 <  int nCells = (int)( testBox / waterCell + 1.0 );
134 >  nCells = (int)( testBox / waterCell + 1.0 );
135    int testWaters = 4 * nCells * nCells * nCells;
136    
137    double* waterX = new double[testWaters];
138 <  double* waterX = new double[testWaters];
139 <  double* waterX = new double[testWaters];
138 >  double* waterY = new double[testWaters];
139 >  double* waterZ = new double[testWaters];
140    
141    double x0 = 0.0 - ( testBox * 0.5 );
142    double y0 = 0.0 - ( testBox * 0.5 );
# Line 297 | Line 303 | int buildRandomBilayer( void ){
303      done = 0;
304      while( !done ){
305        
306 <      lipidSite[i].pos[0] = drand48() * box_x;
307 <      lipidSite[i].pos[1] = drand48() * box_y;
308 <      lipidSite[i].pos[2] = drand48() * box_z;
306 >      lipidSites[i].pos[0] = drand48() * box_x;
307 >      lipidSites[i].pos[1] = drand48() * box_y;
308 >      lipidSites[i].pos[2] = drand48() * box_z;
309        
310 <      getRandomRot( lipidSite[i].rot );
310 >      getRandomRot( lipidSites[i].rot );
311        
312        ndx = i * lipidNatoms;
313  
314 <      lipidLocate->placeMol( lipidSite[i].pos, lipidSite[i].rot, atoms, ndx );
314 >      lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
315 >                             ndx );
316        
317        reject = 0;
318        for( j=0; !reject && j<i; j++){
# Line 354 | Line 361 | int buildRandomBilayer( void ){
361    for(i=0; ( (i<newWaters) && isActive[i] ); i++){
362      for(j=0; ( (j<nAtoms) && isActive[i] ); j++){
363  
364 <      dx = waterSite[i].pos[0] - rsaAtoms[j]->getX();
365 <      dy = waterSite[i].pos[1] - rsaAtoms[j]->getY();
366 <      dz = waterSite[i].pos[2] - rsaAtoms[j]->getZ();
364 >      dx = waterSites[i].pos[0] - atoms[j]->getX();
365 >      dy = waterSites[i].pos[1] - atoms[j]->getY();
366 >      dz = waterSites[i].pos[2] - atoms[j]->getZ();
367  
368        map( dx, dy, dz, box_x, box_y, box_z );
369  
# Line 414 | Line 421 | int buildRandomBilayer( void ){
421    
422    nAtoms = 0;
423    molIndex = 0;
417 –  locate = new MoLocator*[2];
418 –  molSeq = new int[nLipids + nWaters];
424    molStart = new int[nLipids + nWaters];  
425    
421 –  locate[0] = lipidLocate;
426    for(j=0; j<nLipids; j++){
423 –    molSeq[molIndex] = 0;
427      molStart[molIndex] = nAtoms;
428      molIndex++;
429      nAtoms += lipidNatoms;
430    }
431  
432 <  locate[1] = waterLocate;
430 <  for(j=0; j<nLipids; j++){
431 <    molSeq[molIndex] = 1;
432 >  for(j=0; j<nWaters; j++){
433      molStart[molIndex] = nAtoms;
434      molIndex++;
435      nAtoms += waterNatoms;
# Line 441 | Line 442 | int buildRandomBilayer( void ){
442    
443    // initialize lipid positions
444  
445 <  
446 <  
447 <  
445 >  molIndex = 0;
446 >  for(i=0; i<nLipids; i++ ){
447 >    lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
448 >                           molStart[molIndex] );
449 >    molIndex++;
450 >  }
451  
452 +  // initialize the water positions
453 +
454 +  for(i=0; i<newWaters; i++){
455 +    
456 +    if( isActive[i] ){
457 +      
458 +      getRandomRot( waterSites[i].rot );
459 +      waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms,
460 +                             molStart[molIndex] );
461 +      molIndex++;
462 +    }
463 +  }  
464 +
465    // set up the SimInfo object
466    
467    bsInfo.boxX = box_x;
# Line 469 | Line 486 | int buildRandomBilayer( void ){
486      
487    // clean up the memory
488    
489 <  if( molMap != NULL )   delete[] molMap;
490 <  if( cardDeck != NULL ) delete[] cardDeck;
491 <  if( locate != NULL ){
492 <    for(i=0; i<bsInfo.nComponents; i++){
493 <      delete locate[i];
494 <    }
495 <    delete[] locate;
496 <  }
497 <  if( atoms != NULL ){
498 <    for(i=0; i<nAtoms; i++){
499 <      delete atoms[i];
500 <    }
501 <    Atom::destroyArrays();
502 <    delete[] atoms;
503 <  }
504 <  if( molSeq != NULL ) delete[] molSeq;
505 <  if( simnfo != NULL ) delete simnfo;
506 <  if( writer != NULL ) delete writer;
489 > //   if( molMap != NULL )   delete[] molMap;
490 > //   if( cardDeck != NULL ) delete[] cardDeck;
491 > //   if( locate != NULL ){
492 > //     for(i=0; i<bsInfo.nComponents; i++){
493 > //       delete locate[i];
494 > //     }
495 > //     delete[] locate;
496 > //   }
497 > //   if( atoms != NULL ){
498 > //     for(i=0; i<nAtoms; i++){
499 > //       delete atoms[i];
500 > //     }
501 > //     Atom::destroyArrays();
502 > //     delete[] atoms;
503 > //   }
504 > //   if( molSeq != NULL ) delete[] molSeq;
505 > //   if( simnfo != NULL ) delete simnfo;
506 > //   if( writer != NULL ) delete writer;
507  
508    return 1;
509   }
510  
511    
512  
496 –
497 – }
498 –
499 –
500 –
513   int Old_buildRandomBilayer( void ){
514  
515    int i,j,k;

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines