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root/group/trunk/OOPSE/utils/bilayerSys.cpp
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Comparing trunk/OOPSE/utils/bilayerSys.cpp (file contents):
Revision 537 by mmeineke, Fri May 16 21:37:56 2003 UTC vs.
Revision 573 by mmeineke, Thu Jul 3 19:41:26 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;
51 >  const double water_padding = 6.0;
52 >  const double lipid_spaceing = 8.0;
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 218 | Line 224 | int buildRandomBilayer( void ){
224    
225    int targetWaters = nWaters + n_deleted * nLipids;
226  
227 +  targetWaters = (int) ( targetWaters * 1.2 );
228 +
229    // find the best box size for the sim
230  
231    int testTot;
# Line 297 | Line 305 | int buildRandomBilayer( void ){
305      done = 0;
306      while( !done ){
307        
308 <      lipidSite[i].pos[0] = drand48() * box_x;
309 <      lipidSite[i].pos[1] = drand48() * box_y;
310 <      lipidSite[i].pos[2] = drand48() * box_z;
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        
312 <      getRandomRot( lipidSite[i].rot );
312 >      getRandomRot( lipidSites[i].rot );
313        
314        ndx = i * lipidNatoms;
315  
316 <      lipidLocate->placeMol( lipidSite[i].pos, lipidSite[i].rot, atoms, ndx );
316 >      lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
317 >                             ndx );
318        
319        reject = 0;
320        for( j=0; !reject && j<i; j++){
# Line 354 | Line 363 | int buildRandomBilayer( void ){
363    for(i=0; ( (i<newWaters) && isActive[i] ); i++){
364      for(j=0; ( (j<nAtoms) && isActive[i] ); j++){
365  
366 <      dx = waterSite[i].pos[0] - rsaAtoms[j]->getX();
367 <      dy = waterSite[i].pos[1] - rsaAtoms[j]->getY();
368 <      dz = waterSite[i].pos[2] - rsaAtoms[j]->getZ();
366 >      dx = waterSites[i].pos[0] - atoms[j]->getX();
367 >      dy = waterSites[i].pos[1] - atoms[j]->getY();
368 >      dz = waterSites[i].pos[2] - atoms[j]->getZ();
369  
370        map( dx, dy, dz, box_x, box_y, box_z );
371  
# Line 414 | Line 423 | int buildRandomBilayer( void ){
423    
424    nAtoms = 0;
425    molIndex = 0;
417 –  locate = new MoLocator*[2];
418 –  molSeq = new int[nLipids + nWaters];
426    molStart = new int[nLipids + nWaters];  
427    
421 –  locate[0] = lipidLocate;
428    for(j=0; j<nLipids; j++){
423 –    molSeq[molIndex] = 0;
429      molStart[molIndex] = nAtoms;
430      molIndex++;
431      nAtoms += lipidNatoms;
432    }
433  
434 <  locate[1] = waterLocate;
430 <  for(j=0; j<nLipids; j++){
431 <    molSeq[molIndex] = 1;
434 >  for(j=0; j<nWaters; j++){
435      molStart[molIndex] = nAtoms;
436      molIndex++;
437      nAtoms += waterNatoms;
# Line 441 | Line 444 | int buildRandomBilayer( void ){
444    
445    // initialize lipid positions
446  
447 <  
448 <  
449 <  
447 >  molIndex = 0;
448 >  for(i=0; i<nLipids; i++ ){
449 >    lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
450 >                           molStart[molIndex] );
451 >    molIndex++;
452 >  }
453 >
454 >  // initialize the water positions
455 >
456 >  for(i=0; i<newWaters; i++){
457 >    
458 >    if( isActive[i] ){
459 >      
460 >      getRandomRot( waterSites[i].rot );
461 >      waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms,
462 >                             molStart[molIndex] );
463 >      molIndex++;
464 >    }
465 >  }  
466  
467    // set up the SimInfo object
468    
# Line 451 | Line 470 | int buildRandomBilayer( void ){
470    bsInfo.boxY = box_y;
471    bsInfo.boxZ = box_z;
472    
473 +  double boxVector[3];
474    simnfo = new SimInfo();
475    simnfo->n_atoms = nAtoms;
476 <  simnfo->box_x = bsInfo.boxX;
477 <  simnfo->box_y = bsInfo.boxY;
478 <  simnfo->box_z = bsInfo.boxZ;
479 <  
476 >  boxVector[0] = bsInfo.boxX;
477 >  boxVector[1] = bsInfo.boxY;
478 >  boxVector[2] = bsInfo.boxZ;
479 >  simnfo->setBox( boxVector );
480 >
481    sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
482    sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );
483  
# Line 465 | Line 486 | int buildRandomBilayer( void ){
486    // set up the writer and write out
487    
488    writer = new DumpWriter( simnfo );
489 <  writer->writeFinal();
489 >  writer->writeFinal( 0.0 );
490      
491    // clean up the memory
492    
493 <  if( molMap != NULL )   delete[] molMap;
494 <  if( cardDeck != NULL ) delete[] cardDeck;
495 <  if( locate != NULL ){
496 <    for(i=0; i<bsInfo.nComponents; i++){
497 <      delete locate[i];
498 <    }
499 <    delete[] locate;
500 <  }
501 <  if( atoms != NULL ){
502 <    for(i=0; i<nAtoms; i++){
503 <      delete atoms[i];
504 <    }
505 <    Atom::destroyArrays();
506 <    delete[] atoms;
507 <  }
508 <  if( molSeq != NULL ) delete[] molSeq;
509 <  if( simnfo != NULL ) delete simnfo;
510 <  if( writer != NULL ) delete writer;
493 > //   if( molMap != NULL )   delete[] molMap;
494 > //   if( cardDeck != NULL ) delete[] cardDeck;
495 > //   if( locate != NULL ){
496 > //     for(i=0; i<bsInfo.nComponents; i++){
497 > //       delete locate[i];
498 > //     }
499 > //     delete[] locate;
500 > //   }
501 > //   if( atoms != NULL ){
502 > //     for(i=0; i<nAtoms; i++){
503 > //       delete atoms[i];
504 > //     }
505 > //     Atom::destroyArrays();
506 > //     delete[] atoms;
507 > //   }
508 > //   if( molSeq != NULL ) delete[] molSeq;
509 > //   if( simnfo != NULL ) delete simnfo;
510 > //   if( writer != NULL ) delete writer;
511  
512    return 1;
513   }
514  
515    
516  
496 –
497 – }
498 –
499 –
500 –
517   int Old_buildRandomBilayer( void ){
518  
519    int i,j,k;
# Line 658 | Line 674 | int Old_buildRandomBilayer( void ){
674    bsInfo.boxY = nCells * cell;
675    bsInfo.boxZ = nCells * cell;
676    
677 +  double boxVector[3];
678    simnfo = new SimInfo();
679    simnfo->n_atoms = nAtoms;
680 <  simnfo->box_x = bsInfo.boxX;
681 <  simnfo->box_y = bsInfo.boxY;
682 <  simnfo->box_z = bsInfo.boxZ;
683 <  
680 >  boxVector[0] = bsInfo.boxX;
681 >  boxVector[1] = bsInfo.boxY;
682 >  boxVector[2] = bsInfo.boxZ;
683 >  simnfo->setBox( boxVector );
684 >
685    sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
686    sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );
687  
# Line 672 | Line 690 | int Old_buildRandomBilayer( void ){
690    // set up the writer and write out
691    
692    writer = new DumpWriter( simnfo );
693 <  writer->writeFinal();
693 >  writer->writeFinal(0.0);
694      
695    // clean up the memory
696    

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