utils/sysbuilder/bilayerSys.cpp


#include <iostream>
#include <vector>
#include <algorithm>

#include <cstdlib>
#include <cstring>
#include <cmath>


#include "simError.h"
#include "SimInfo.hpp"
#include "ReadWrite.hpp"

#include "MoLocator.hpp"
#include "sysBuild.hpp"
#include "bilayerSys.hpp"

#include "latticeBuilder.hpp"

class SortCond{
  
public:
  bool operator()(const pair<int, double>& p1, const pair<int, double>& p2){
    return p1.second < p2.second;
  }
  
  
};


void buildMap( double &x, double &y, double &z,
               double boxX, double boxY, double boxZ );

int buildRandomBilayer( void );
int buildLatticeBilayer( int isHexLattice,
                         double hexSpacing, 
                         double aLat, 
                         double bLat, 
                         int targetNlipid, 
                         double targetWaterLipidRatio,
                         double leafSpacing);

void getRandomRot( double rot[3][3] );
void getEulerRot( double theta, double phi, double psi, double rot[3][3] );
void getUnitRot( double unit[3], double rot[3][3] );

int buildBilayer( int isRandom ){
  
  if( isRandom ){
    return buildRandomBilayer();
  }
  else{

    
    return buildLatticeBilayer();
  }
}


int buildRandomBilayer( void ){

  typedef struct{
    double rot[3][3];
    double pos[3];
  } coord;


  const double waterRho = 0.0334; // number density per cubic angstrom
  const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters
  const double waterCell = 4.929; // fcc unit cell length

  Lattice myFCC( FCC_LATTICE_TYPE, waterCell );
  double *posX, *posY, *posZ;
  double pos[3], posA[3], posB[3];

  const double water_padding = 6.0;
  const double lipid_spaceing = 8.0;


  int i,j,k, l, m;
  int nAtoms, atomIndex, molIndex, molID;
  int* molSeq;
  int* molMap;
  int* molStart;
  int* cardDeck;
  int deckSize;
  int rSite, rCard;
  double cell;
  int nCells, nSites, siteIndex;
  
  coord testSite;

  Atom** atoms;
  SimInfo* simnfo;
  SimState* theConfig;
  DumpWriter* writer;

  MoleculeStamp* lipidStamp;
  MoleculeStamp* waterStamp;  
  MoLocator *lipidLocate;
  MoLocator *waterLocate;
  int foundLipid, foundWater;
  int nLipids, lipidNatoms, nWaters, waterNatoms;
  double testBox, maxLength;
  
  srand48( RAND_SEED );


  // create the simInfo objects

  simnfo = new SimInfo[3];


  // set the the lipidStamp

  foundLipid = 0;
  foundWater = 0;
  for(i=0; i<bsInfo.nComponents; i++){
    if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){
          
      foundLipid = 1;
      lipidStamp = bsInfo.compStamps[i];
      nLipids = bsInfo.componentsNmol[i];
    }
    if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){
          
      foundWater = 1;
          
      waterStamp = bsInfo.compStamps[i];
      nWaters = bsInfo.componentsNmol[i];
    }
  }
  if( !foundLipid ){
    sprintf(painCave.errMsg,
            "Could not find lipid \"%s\" in the bass file.\n",
            bsInfo.lipidName );
    painCave.isFatal = 1;
    simError();
  }
  if( !foundWater ){
    sprintf(painCave.errMsg,
            "Could not find solvent \"%s\" in the bass file.\n",
            bsInfo.waterName );
    painCave.isFatal = 1;
    simError();
  }
  
  //create the temp Molocator and atom Arrays
  
  lipidLocate = new MoLocator( lipidStamp );
  lipidNatoms = lipidStamp->getNAtoms();
  maxLength = lipidLocate->getMaxLength();

  waterLocate = new MoLocator( waterStamp );
  waterNatoms = waterStamp->getNAtoms();
  
  nAtoms = lipidNatoms;

  simnfo[0].n_atoms = nAtoms;
  simnfo[0].atoms=new Atom*[nAtoms];
 
  theConfig = simnfo[0].getConfiguration();
  theConfig->createArrays( simnfo[0].n_atoms );

  atoms=simnfo[0].atoms;
        

  // create the test box for initial water displacement

  testBox = maxLength + waterCell * 4.0; // pad with 4 cells
  nCells = (int)( testBox / waterCell + 1.0 );
  int testWaters = 4 * nCells * nCells * nCells;
  
  double* waterX = new double[testWaters];
  double* waterY = new double[testWaters];
  double* waterZ = new double[testWaters];
  
  double x0 = 0.0 - ( testBox * 0.5 );
  double y0 = 0.0 - ( testBox * 0.5 );
  double z0 = 0.0 - ( testBox * 0.5 );


  // create an fcc lattice in the water box.

  int ndx = 0;
  for( i=0; i < nCells; i++ ){
    for( j=0; j < nCells; j++ ){
      for( k=0; k < nCells; k++ ){

        myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k);
        for(l=0; l<4; l++){
          waterX[ndx]=posX[l];
          waterY[ndx]=posY[l];
          waterZ[ndx]=posZ[l];
          ndx++;
        }
      }
    }
  }

  // calculate the number of water's displaced by our lipid.

  testSite.rot[0][0] = 1.0;
  testSite.rot[0][1] = 0.0;
  testSite.rot[0][2] = 0.0;

  testSite.rot[1][0] = 0.0;
  testSite.rot[1][1] = 1.0;
  testSite.rot[1][2] = 0.0;

  testSite.rot[2][0] = 0.0;
  testSite.rot[2][1] = 0.0;
  testSite.rot[2][2] = 1.0;
  
  testSite.pos[0] = 0.0;
  testSite.pos[1] = 0.0;
  testSite.pos[2] = 0.0;

  lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0, theConfig );

  int *isActive = new int[testWaters];
  for(i=0; i<testWaters; i++) isActive[i] = 1;
  
  int n_deleted = 0;
  double dx, dy, dz;
  double dx2, dy2, dz2, dSqr;
  double rCutSqr = water_padding * water_padding;
  
  for(i=0; ( (i<testWaters) && isActive[i] ); i++){
    for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){
      
      atoms[j]->getPos( pos );

      dx = waterX[i] - pos[0];
      dy = waterY[i] - pos[1];
      dz = waterZ[i] - pos[2];

      buildMap( dx, dy, dz, testBox, testBox, testBox );

      dx2 = dx * dx;
      dy2 = dy * dy;
      dz2 = dz * dz;
          
      dSqr = dx2 + dy2 + dz2;
      if( dSqr < rCutSqr ){
        isActive[i] = 0;
        n_deleted++;
      }
    }
  }
  
  int targetWaters = nWaters + n_deleted * nLipids;

  targetWaters = (int) ( targetWaters * 1.2 );

  // find the best box size for the sim

  int nCellsX, nCellsY, nCellsZ;

  const double boxTargetX = 66.22752;
  const double boxTargetY = 60.53088;

  nCellsX = (int)ceil(boxTargetX / waterCell);
  nCellsY = (int)ceil(boxTargetY / waterCell);
  
  int testTot;
  int done = 0;
  nCellsZ = 0;
  while( !done ){
        
    nCellsZ++;
    testTot = 4 * nCellsX * nCellsY * nCellsZ;
        
    if( testTot >= targetWaters ) done = 1;
  }

  // create the new water box to the new specifications
  
  int newWaters = nCellsX * nCellsY * nCellsZ * 4;
  
  delete[] waterX;
  delete[] waterY;
  delete[] waterZ;
  
  coord* waterSites = new coord[newWaters];
  
  double box_x = waterCell * nCellsX;
  double box_y = waterCell * nCellsY;
  double box_z = waterCell * nCellsZ;
         
  // create an fcc lattice in the water box.
  
  ndx = 0;
  for( i=0; i < nCellsX; i++ ){
    for( j=0; j < nCellsY; j++ ){
      for( k=0; k < nCellsZ; k++ ){

        myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k);
        for(l=0; l<4; l++){
          waterSites[ndx].pos[0] = posX[l];
          waterSites[ndx].pos[1] = posY[l];
          waterSites[ndx].pos[2] = posZ[l];
          ndx++;
        }
      }
    }
  }  

  coord* lipidSites = new coord[nLipids];

  // start a 3D RSA for the for the lipid placements
  
  
  int reject;
  int testDX, acceptedDX;

  nAtoms = nLipids * lipidNatoms;

  simnfo[1].n_atoms = nAtoms;
  simnfo[1].atoms=new Atom*[nAtoms];
 
  theConfig = simnfo[1].getConfiguration();
  theConfig->createArrays( simnfo[1].n_atoms );

  atoms=simnfo[1].atoms;

  rCutSqr = lipid_spaceing * lipid_spaceing;

  for(i=0; i<nLipids; i++ ){
    done = 0;
    while( !done ){
          
      lipidSites[i].pos[0] = drand48() * box_x;
      lipidSites[i].pos[1] = drand48() * box_y;
      lipidSites[i].pos[2] = drand48() * box_z;
          
      getRandomRot( lipidSites[i].rot );
          
      ndx = i * lipidNatoms;

      lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, 
                             ndx, theConfig );
          
      reject = 0;
      for( j=0; !reject && j<i; j++){
        for(k=0; !reject && k<lipidNatoms; k++){
          
          acceptedDX = j*lipidNatoms + k;
          for(l=0; !reject && l<lipidNatoms; l++){
                
            testDX = ndx + l;

            atoms[testDX]->getPos( posA );
            atoms[acceptedDX]->getPos( posB );
            
            dx = posA[0] - posB[0];
            dy = posA[1] - posB[1];
            dz = posA[2] - posB[2];
                
            buildMap( dx, dy, dz, box_x, box_y, box_z );
                
            dx2 = dx * dx;
            dy2 = dy * dy;
            dz2 = dz * dz;
                
            dSqr = dx2 + dy2 + dz2;
            if( dSqr < rCutSqr ) reject = 1;
          }
        }
      }

      if( reject ){

        for(j=0; j< lipidNatoms; j++) delete atoms[ndx+j];
      }
      else{
        done = 1;
        std::cout << (i+1) << " has been accepted\n";
      }
    }
  }
        

  // zSort of the lipid positions


  vector< pair<int,double> >zSortArray;
  for(i=0;i<nLipids;i++) 
    zSortArray.push_back( make_pair(i, lipidSites[i].pos[2]) );

  sort(zSortArray.begin(),zSortArray.end(),SortCond());

  ofstream outFile( "./zipper.bass", ios::app);

  for(i=0; i<nLipids; i++){
    outFile << "zConstraint[" << i << "]{\n"
            << "  molIndex = " << zSortArray[i].first <<  ";\n"
            << "  zPos = ";

    if(i<32) outFile << "60.0;\n";
    else outFile << "100.0;\n";

    outFile << "  kRatio = 0.5;\n"
            << "}\n";
  }
  
  outFile.close();


  // cut out the waters that overlap with the lipids.
  

  delete[] isActive;
  isActive = new int[newWaters];
  for(i=0; i<newWaters; i++) isActive[i] = 1;
  int n_active = newWaters;
  rCutSqr = water_padding * water_padding;
  
  for(i=0; ( (i<newWaters) && isActive[i] ); i++){
    for(j=0; ( (j<nAtoms) && isActive[i] ); j++){

      atoms[j]->getPos( pos );

      dx = waterSites[i].pos[0] - pos[0];
      dy = waterSites[i].pos[1] - pos[1];
      dz = waterSites[i].pos[2] - pos[2];

      buildMap( dx, dy, dz, box_x, box_y, box_z );

      dx2 = dx * dx;
      dy2 = dy * dy;
      dz2 = dz * dz;
          
      dSqr = dx2 + dy2 + dz2;
      if( dSqr < rCutSqr ){
        isActive[i] = 0;
        n_active--;


      }
    }
  }


  if( n_active < nWaters ){
        
    sprintf( painCave.errMsg,
             "Too many waters were removed, edit code and try again.\n" );
        
    painCave.isFatal = 1;
    simError();
  }

  int quickKill;
  while( n_active > nWaters ){

    quickKill = (int)(drand48()*newWaters);

    if( isActive[quickKill] ){
      isActive[quickKill] = 0;
      n_active--;

    }
  }

  if( n_active != nWaters ){
        
    sprintf( painCave.errMsg,
             "QuickKill didn't work right. n_active = %d, and nWaters = %d\n",
             n_active, nWaters );
    painCave.isFatal = 1;
    simError();
  }

  // clean up our messes before building the final system.

  simnfo[0].getConfiguration()->destroyArrays();
  simnfo[1].getConfiguration()->destroyArrays();

  // create the real Atom arrays
  
  nAtoms = 0;
  molIndex = 0;
  molStart = new int[nLipids + nWaters];  
  
  for(j=0; j<nLipids; j++){
    molStart[molIndex] = nAtoms;
    molIndex++;
    nAtoms += lipidNatoms;
  }

  for(j=0; j<nWaters; j++){
    molStart[molIndex] = nAtoms;
    molIndex++;
    nAtoms += waterNatoms;
  }
  
  theConfig = simnfo[2].getConfiguration();
  theConfig->createArrays( nAtoms );
  simnfo[2].atoms = new Atom*[nAtoms];
  atoms = simnfo[2].atoms;
  simnfo[2].n_atoms = nAtoms;
  
  // initialize lipid positions

  molIndex = 0;
  for(i=0; i<nLipids; i++ ){
    lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
                           molStart[molIndex], theConfig );
    molIndex++;
  }

  // initialize the water positions

  for(i=0; i<newWaters; i++){
        
    if( isActive[i] ){
          
      getRandomRot( waterSites[i].rot );
      waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms,
                             molStart[molIndex], theConfig );
      molIndex++;
    }
  }  

  // set up the SimInfo object
  
  double Hmat[3][3];

  Hmat[0][0] = box_x;
  Hmat[0][1] = 0.0;
  Hmat[0][2] = 0.0;

  Hmat[1][0] = 0.0;
  Hmat[1][1] = box_y;
  Hmat[1][2] = 0.0;

  Hmat[2][0] = 0.0;
  Hmat[2][1] = 0.0;
  Hmat[2][2] = box_z;
  

  bsInfo.boxX = box_x;
  bsInfo.boxY = box_y;
  bsInfo.boxZ = box_z;
  
  simnfo[2].setBoxM( Hmat );

  sprintf( simnfo[2].sampleName, "%s.dump", bsInfo.outPrefix );
  sprintf( simnfo[2].finalName, "%s.init", bsInfo.outPrefix );

  // set up the writer and write out
  
  writer = new DumpWriter( &simnfo[2] );
  writer->writeFinal( 0.0 );
        
  // clean up the memory
  
  //     if( molMap != NULL )   delete[] molMap;
  //     if( cardDeck != NULL ) delete[] cardDeck;
  //     if( locate != NULL ){
  //       for(i=0; i<bsInfo.nComponents; i++){
  //             delete locate[i];
  //       }
  //       delete[] locate;
  //     }
  //     if( atoms != NULL ){
  //       for(i=0; i<nAtoms; i++){
  //             delete atoms[i];
  //       }
  //       Atom::destroyArrays();
  //       delete[] atoms;
  //     }
  //     if( molSeq != NULL ) delete[] molSeq;
  //     if( simnfo != NULL ) delete simnfo;
  //     if( writer != NULL ) delete writer;

  return 1;
}

int buildLatticeBilayer(int isHexLattice,
                        double hexSpacing, 
                        double aLat, 
                        double bLat, 
                        int targetNlipid, 
                        double targetWaterLipidRatio,
                        double leafSpacing){

  typedef struct{
    double rot[3][3];
    double pos[3];
  } coord;

  const double waterRho = 0.0334; // number density per cubic angstrom
  const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters
  
  double waterCell[3];

  double *posX, *posY, *posZ;
  double pos[3], posA[3], posB[3];

  const double waterFudge = 5.0;

  int i,j,k,l;
  int nAtoms, atomIndex, molIndex, molID;
  int* molSeq;
  int* molMap;
  int* molStart;
  int testTot, done;
  int nCells, nCellsX, nCellsY, nCellsZ; 
  int nx, ny;
  double boxX, boxY, boxZ;
  double unitVector[3];
  int which;
  int targetWaters;
  
  
  coord testSite;

  Atom** atoms;
  SimInfo* simnfo;
  SimState* theConfig;
  DumpWriter* writer;

  MoleculeStamp* lipidStamp;
  MoleculeStamp* waterStamp;  
  MoLocator *lipidLocate;
  MoLocator *waterLocate;
  int foundLipid, foundWater;
  int nLipids, lipidNatoms, nWaters, waterNatoms;
   
  srand48( RAND_SEED );

  // create the simInfo objects

  simnfo = new SimInfo;

  // set the the lipidStamp

  foundLipid = 0;
  foundWater = 0;
  for(i=0; i<bsInfo.nComponents; i++){
    if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){
          
      foundLipid = 1;
      lipidStamp = bsInfo.compStamps[i];
      nLipids = bsInfo.componentsNmol[i];
      lipidNatoms = lipidStamp->getNAtoms();
    }
    if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){
          
      foundWater = 1;
          
      waterStamp = bsInfo.compStamps[i];
      nWaters = bsInfo.componentsNmol[i];
      waterNatoms = waterStamp->getNAtoms();
    }
  }
  if( !foundLipid ){
    sprintf(painCave.errMsg,
            "Could not find lipid \"%s\" in the bass file.\n",
            bsInfo.lipidName );
    painCave.isFatal = 1;
    simError();
  }
  if( !foundWater ){
    sprintf(painCave.errMsg,
            "Could not find solvent \"%s\" in the bass file.\n",
            bsInfo.waterName );
    painCave.isFatal = 1;
    simError();
  }
  
  //create the Molocator arrays
  
  lipidLocate = new MoLocator( lipidStamp );
  waterLocate = new MoLocator( waterStamp );


  // set up the bilayer leaves
  
  if (isHexLattice) {
    aLat = sqrt(3.0)*hexSpacing;
    bLat = hexSpacing;
  } 

  nCells = (int) sqrt( (double)targetNlipid * bLat / (4.0 * aLat) );

  nx = nCells;
  ny = (int) ((double)nCells  * aLat / bLat);

  boxX = nx * aLat;
  boxY = ny * bLat;  

  nLipids = 4 * nx * ny;
  coord* lipidSites = new coord[nLipids];

  unitVector[0] = 0.0;
  unitVector[1] = 0.0;

  which = 0;

  for (i = 0; i < nx; i++) {
    for (j = 0; j < ny; j++ ) {
      for (k = 0; k < 2; k++) {
        
        lipidSites[which].pos[0] = (double)i * aLat;
        lipidSites[which].pos[1] = (double)j * bLat;
        lipidSites[which].pos[2] = ((double)k - 0.5) * (leafSpacing / 2.0);
        
        unitVector[2] = 2.0 * (double)k  - 1.0;
        
        getUnitRot( unitVector, lipidSites[which].rot );

        which++;

        lipidSites[which].pos[0] = aLat * ((double)i + 0.5);
        lipidSites[which].pos[1] = bLat * ((double)j + 0.5);
        lipidSites[which].pos[2] = ((double)k - 0.5) * (leafSpacing / 2.0);
        
        unitVector[2] = 2.0 * (double)k  - 1.0;
        
        getUnitRot( unitVector, lipidSites[which].rot );
        
        which++;
      }
    }
  }
 
  targetWaters = targetWaterLipidRatio * nLipids;

  // guess the size of the water box
  
  
  nCellsX = (int)ceil(boxX / pow(waterVol, ( 1.0 / 3.0 )) );
  nCellsY = (int)ceil(boxY / pow(waterVol, ( 1.0 / 3.0 )) );

  done = 0;
  nCellsZ = 0;
  while( !done ){
        
    nCellsZ++;
    testTot = 4 * nCellsX * nCellsY * nCellsZ;
        
    if( testTot >= targetWaters ) done = 1;
  }
  
  nWaters = nCellsX * nCellsY * nCellsZ * 4;
  
  coord* waterSites = new coord[nWaters];

  waterCell[0] = boxX / nCellsX;
  waterCell[1] = boxY / nCellsY;
  waterCell[2] = 4.0 / (waterRho * waterCell[0] * waterCell[1]);

  Lattice *myORTHO;
  myORTHO = new Lattice( ORTHORHOMBIC_LATTICE_TYPE, waterCell);
  myORTHO->setStartZ( leafSpacing / 2.0 + waterFudge);

  boxZ = waterCell[2] * nCellsZ;
         
  // create an fcc lattice in the water box.
  
  which = 0;
  for( i=0; i < nCellsX; i++ ){
    for( j=0; j < nCellsY; j++ ){
      for( k=0; k < nCellsZ; k++ ){

        myORTHO->getLatticePoints(&posX, &posY, &posZ, i, j, k);
        for(l=0; l<4; l++){
          waterSites[which].pos[0] = posX[l];
          waterSites[which].pos[1] = posY[l];
          waterSites[which].pos[2] = posZ[l];
          which++;
        }
      }
    }
  }  

  // create the real Atom arrays
  
  nAtoms = 0;
  molIndex = 0;
  molStart = new int[nLipids + nWaters];  
  
  for(j=0; j<nLipids; j++){
    molStart[molIndex] = nAtoms;
    molIndex++;
    nAtoms += lipidNatoms;
  }

  for(j=0; j<nWaters; j++){
    molStart[molIndex] = nAtoms;
    molIndex++;
    nAtoms += waterNatoms;
  }
  
  theConfig = simnfo->getConfiguration();
  theConfig->createArrays( nAtoms );
  simnfo->atoms = new Atom*[nAtoms];
  atoms = simnfo->atoms;

  // initialize lipid positions

  molIndex = 0;
  for(i=0; i<nLipids; i++ ){
    lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
                           molStart[molIndex], theConfig );
    molIndex++;
  }

  // initialize the water positions

  for(i=0; i<nWaters; i++){
    
    getRandomRot( waterSites[i].rot );
    waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms,
                           molStart[molIndex], theConfig );
    molIndex++;
  }

  // set up the SimInfo object
  
  double Hmat[3][3];

  Hmat[0][0] = boxX;
  Hmat[0][1] = 0.0;
  Hmat[0][2] = 0.0;

  Hmat[1][0] = 0.0;
  Hmat[1][1] = boxY;
  Hmat[1][2] = 0.0;

  Hmat[2][0] = 0.0;
  Hmat[2][1] = 0.0;
  Hmat[2][2] = boxZ;
  

  bsInfo.boxX = boxX;
  bsInfo.boxY = boxY;
  bsInfo.boxZ = boxZ;
  
  simnfo->setBoxM( Hmat );

  sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
  sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );

  // set up the writer and write out
  
  writer = new DumpWriter( simnfo );
  writer->writeFinal( 0.0 );

  return 1;
}


void getRandomRot( double rot[3][3] ){

  double theta, phi, psi;
  double cosTheta;

  // select random phi, psi, and cosTheta

  phi = 2.0 * M_PI * drand48();
  psi = 2.0 * M_PI * drand48();
  cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1

  theta = acos( cosTheta );

  getEulerRot( theta, phi, psi, rot );
}


void getEulerRot( double theta, double phi, double psi, double rot[3][3] ){

  rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
  rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
  rot[0][2] = sin(theta) * sin(psi);
  
  rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
  rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
  rot[1][2] = sin(theta) * cos(psi);

  rot[2][0] = sin(phi) * sin(theta);
  rot[2][1] = -cos(phi) * sin(theta);
  rot[2][2] = cos(theta);  
}


void getUnitRot( double u[3], double rot[3][3] ){

  double theta, phi, psi;

  theta = acos(u[2]);
  phi = atan(u[1] / u[0]);
  psi = 0.0;

  getEulerRot( theta, phi, psi, rot );
}
                        

void buildMap( double &x, double &y, double &z, 
               double boxX, double boxY, double boxZ ){ 
  
  if(x < 0) x -= boxX * (double)( (int)( (x / boxX)  - 0.5 ) );
  else x -= boxX * (double)( (int)( (x / boxX ) + 0.5));

  if(y < 0) y -= boxY * (double)( (int)( (y / boxY)  - 0.5 ) );
  else y -= boxY * (double)( (int)( (y / boxY ) + 0.5));
  
  if(z < 0) z -= boxZ * (double)( (int)( (z / boxZ)  - 0.5 ) );
  else z -= boxZ * (double)( (int)( (z / boxZ ) + 0.5));
}
Revision:	817
Committed:	Fri Oct 24 17:36:18 2003 UTC (21 years, 6 months ago) by gezelter
File size:	20442 byte(s)
Log Message:	work on bilayer builder