utils/sysbuilder/randomBilayer.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 buildBilayer( int isRandom ){
  
  if( isRandom ){
    return buildRandomBilayer();
  }
  else{

    std::cerr << "unsupported feature\n";
    return 0;
  }
}


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;
}

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:	876
Committed:	Wed Dec 10 16:52:46 2003 UTC (20 years, 7 months ago) by mmeineke
File size:	12623 byte(s)
Log Message:	edited the makefile to add randomBilayer to the build. Also move the random bilayer builder from bilayerSys to randomBilayer
#	User	Rev	Content
1	mmeineke	876
2			#include <iostream>
3			#include <vector>
4			#include <algorithm>
5
6			#include <cstdlib>
7			#include <cstring>
8			#include <cmath>
9
10
11			#include "simError.h"
12			#include "SimInfo.hpp"
13			#include "ReadWrite.hpp"
14
15			#include "MoLocator.hpp"
16			#include "sysBuild.hpp"
17			#include "bilayerSys.hpp"
18
19			#include "latticeBuilder.hpp"
20
21			class SortCond{
22
23			public:
24			bool operator()(const pair<int, double>& p1, const pair<int, double>& p2){
25			return p1.second < p2.second;
26			}
27
28
29			};
30
31
32			void buildMap( double &x, double &y, double &z,
33			double boxX, double boxY, double boxZ );
34
35			int buildRandomBilayer( void );
36
37			int buildBilayer( int isRandom ){
38
39			if( isRandom ){
40			return buildRandomBilayer();
41			}
42			else{
43
44			std::cerr << "unsupported feature\n";
45			return 0;
46			}
47			}
48
49
50			int buildRandomBilayer( void ){
51
52			typedef struct{
53			double rot[3][3];
54			double pos[3];
55			} coord;
56
57
58
59			const double waterRho = 0.0334; // number density per cubic angstrom
60			const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters
61			const double waterCell = 4.929; // fcc unit cell length
62
63			Lattice myFCC( FCC_LATTICE_TYPE, waterCell );
64			double posX, posY, *posZ;
65			double pos[3], posA[3], posB[3];
66
67			const double water_padding = 6.0;
68			const double lipid_spaceing = 8.0;
69
70
71			int i,j,k, l, m;
72			int nAtoms, atomIndex, molIndex, molID;
73			int* molSeq;
74			int* molMap;
75			int* molStart;
76			int* cardDeck;
77			int deckSize;
78			int rSite, rCard;
79			double cell;
80			int nCells, nSites, siteIndex;
81
82			coord testSite;
83
84			Atom** atoms;
85			SimInfo* simnfo;
86			SimState* theConfig;
87			DumpWriter* writer;
88
89			MoleculeStamp* lipidStamp;
90			MoleculeStamp* waterStamp;
91			MoLocator *lipidLocate;
92			MoLocator *waterLocate;
93			int foundLipid, foundWater;
94			int nLipids, lipidNatoms, nWaters, waterNatoms;
95			double testBox, maxLength;
96
97			srand48( RAND_SEED );
98
99
100			// create the simInfo objects
101
102			simnfo = new SimInfo[3];
103
104
105			// set the the lipidStamp
106
107			foundLipid = 0;
108			foundWater = 0;
109			for(i=0; i<bsInfo.nComponents; i++){
110			if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){
111
112			foundLipid = 1;
113			lipidStamp = bsInfo.compStamps[i];
114			nLipids = bsInfo.componentsNmol[i];
115			}
116			if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){
117
118			foundWater = 1;
119
120			waterStamp = bsInfo.compStamps[i];
121			nWaters = bsInfo.componentsNmol[i];
122			}
123			}
124			if( !foundLipid ){
125			sprintf(painCave.errMsg,
126			"Could not find lipid \"%s\" in the bass file.\n",
127			bsInfo.lipidName );
128			painCave.isFatal = 1;
129			simError();
130			}
131			if( !foundWater ){
132			sprintf(painCave.errMsg,
133			"Could not find solvent \"%s\" in the bass file.\n",
134			bsInfo.waterName );
135			painCave.isFatal = 1;
136			simError();
137			}
138
139			//create the temp Molocator and atom Arrays
140
141			lipidLocate = new MoLocator( lipidStamp );
142			lipidNatoms = lipidStamp->getNAtoms();
143			maxLength = lipidLocate->getMaxLength();
144
145			waterLocate = new MoLocator( waterStamp );
146			waterNatoms = waterStamp->getNAtoms();
147
148			nAtoms = lipidNatoms;
149
150			simnfo[0].n_atoms = nAtoms;
151			simnfo[0].atoms=new Atom*[nAtoms];
152
153			theConfig = simnfo[0].getConfiguration();
154			theConfig->createArrays( simnfo[0].n_atoms );
155
156			atoms=simnfo[0].atoms;
157
158
159			// create the test box for initial water displacement
160
161			testBox = maxLength + waterCell * 4.0; // pad with 4 cells
162			nCells = (int)( testBox / waterCell + 1.0 );
163			int testWaters = 4 * nCells * nCells * nCells;
164
165			double* waterX = new double[testWaters];
166			double* waterY = new double[testWaters];
167			double* waterZ = new double[testWaters];
168
169			double x0 = 0.0 - ( testBox * 0.5 );
170			double y0 = 0.0 - ( testBox * 0.5 );
171			double z0 = 0.0 - ( testBox * 0.5 );
172
173
174			// create an fcc lattice in the water box.
175
176			int ndx = 0;
177			for( i=0; i < nCells; i++ ){
178			for( j=0; j < nCells; j++ ){
179			for( k=0; k < nCells; k++ ){
180
181			myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k);
182			for(l=0; l<4; l++){
183			waterX[ndx]=posX[l];
184			waterY[ndx]=posY[l];
185			waterZ[ndx]=posZ[l];
186			ndx++;
187			}
188			}
189			}
190			}
191
192			// calculate the number of water's displaced by our lipid.
193
194			testSite.rot[0][0] = 1.0;
195			testSite.rot[0][1] = 0.0;
196			testSite.rot[0][2] = 0.0;
197
198			testSite.rot[1][0] = 0.0;
199			testSite.rot[1][1] = 1.0;
200			testSite.rot[1][2] = 0.0;
201
202			testSite.rot[2][0] = 0.0;
203			testSite.rot[2][1] = 0.0;
204			testSite.rot[2][2] = 1.0;
205
206			testSite.pos[0] = 0.0;
207			testSite.pos[1] = 0.0;
208			testSite.pos[2] = 0.0;
209
210			lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0, theConfig );
211
212			int *isActive = new int[testWaters];
213			for(i=0; i<testWaters; i++) isActive[i] = 1;
214
215			int n_deleted = 0;
216			double dx, dy, dz;
217			double dx2, dy2, dz2, dSqr;
218			double rCutSqr = water_padding * water_padding;
219
220			for(i=0; ( (i<testWaters) && isActive[i] ); i++){
221			for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){
222
223			atoms[j]->getPos( pos );
224
225			dx = waterX[i] - pos[0];
226			dy = waterY[i] - pos[1];
227			dz = waterZ[i] - pos[2];
228
229			buildMap( dx, dy, dz, testBox, testBox, testBox );
230
231			dx2 = dx * dx;
232			dy2 = dy * dy;
233			dz2 = dz * dz;
234
235			dSqr = dx2 + dy2 + dz2;
236			if( dSqr < rCutSqr ){
237			isActive[i] = 0;
238			n_deleted++;
239			}
240			}
241			}
242
243			int targetWaters = nWaters + n_deleted * nLipids;
244
245			targetWaters = (int) ( targetWaters * 1.2 );
246
247			// find the best box size for the sim
248
249			int nCellsX, nCellsY, nCellsZ;
250
251			const double boxTargetX = 66.22752;
252			const double boxTargetY = 60.53088;
253
254			nCellsX = (int)ceil(boxTargetX / waterCell);
255			nCellsY = (int)ceil(boxTargetY / waterCell);
256
257			int testTot;
258			int done = 0;
259			nCellsZ = 0;
260			while( !done ){
261
262			nCellsZ++;
263			testTot = 4 * nCellsX * nCellsY * nCellsZ;
264
265			if( testTot >= targetWaters ) done = 1;
266			}
267
268			// create the new water box to the new specifications
269
270			int newWaters = nCellsX * nCellsY * nCellsZ * 4;
271
272			delete[] waterX;
273			delete[] waterY;
274			delete[] waterZ;
275
276			coord* waterSites = new coord[newWaters];
277
278			double box_x = waterCell * nCellsX;
279			double box_y = waterCell * nCellsY;
280			double box_z = waterCell * nCellsZ;
281
282			// create an fcc lattice in the water box.
283
284			ndx = 0;
285			for( i=0; i < nCellsX; i++ ){
286			for( j=0; j < nCellsY; j++ ){
287			for( k=0; k < nCellsZ; k++ ){
288
289			myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k);
290			for(l=0; l<4; l++){
291			waterSites[ndx].pos[0] = posX[l];
292			waterSites[ndx].pos[1] = posY[l];
293			waterSites[ndx].pos[2] = posZ[l];
294			ndx++;
295			}
296			}
297			}
298			}
299
300			coord* lipidSites = new coord[nLipids];
301
302			// start a 3D RSA for the for the lipid placements
303
304
305			int reject;
306			int testDX, acceptedDX;
307
308			nAtoms = nLipids * lipidNatoms;
309
310			simnfo[1].n_atoms = nAtoms;
311			simnfo[1].atoms=new Atom*[nAtoms];
312
313			theConfig = simnfo[1].getConfiguration();
314			theConfig->createArrays( simnfo[1].n_atoms );
315
316			atoms=simnfo[1].atoms;
317
318			rCutSqr = lipid_spaceing * lipid_spaceing;
319
320			for(i=0; i<nLipids; i++ ){
321			done = 0;
322			while( !done ){
323
324			lipidSites[i].pos[0] = drand48() * box_x;
325			lipidSites[i].pos[1] = drand48() * box_y;
326			lipidSites[i].pos[2] = drand48() * box_z;
327
328			getRandomRot( lipidSites[i].rot );
329
330			ndx = i * lipidNatoms;
331
332			lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
333			ndx, theConfig );
334
335			reject = 0;
336			for( j=0; !reject && j<i; j++){
337			for(k=0; !reject && k<lipidNatoms; k++){
338
339			acceptedDX = j*lipidNatoms + k;
340			for(l=0; !reject && l<lipidNatoms; l++){
341
342			testDX = ndx + l;
343
344			atoms[testDX]->getPos( posA );
345			atoms[acceptedDX]->getPos( posB );
346
347			dx = posA[0] - posB[0];
348			dy = posA[1] - posB[1];
349			dz = posA[2] - posB[2];
350
351			buildMap( dx, dy, dz, box_x, box_y, box_z );
352
353			dx2 = dx * dx;
354			dy2 = dy * dy;
355			dz2 = dz * dz;
356
357			dSqr = dx2 + dy2 + dz2;
358			if( dSqr < rCutSqr ) reject = 1;
359			}
360			}
361			}
362
363			if( reject ){
364
365			for(j=0; j< lipidNatoms; j++) delete atoms[ndx+j];
366			}
367			else{
368			done = 1;
369			std::cout << (i+1) << " has been accepted\n";
370			}
371			}
372			}
373
374
375			// zSort of the lipid positions
376
377
378			vector< pair<int,double> >zSortArray;
379			for(i=0;i<nLipids;i++)
380			zSortArray.push_back( make_pair(i, lipidSites[i].pos[2]) );
381
382			sort(zSortArray.begin(),zSortArray.end(),SortCond());
383
384			ofstream outFile( "./zipper.bass", ios::app);
385
386			for(i=0; i<nLipids; i++){
387			outFile << "zConstraint[" << i << "]{\n"
388			<< " molIndex = " << zSortArray[i].first << ";\n"
389			<< " zPos = ";
390
391			if(i<32) outFile << "60.0;\n";
392			else outFile << "100.0;\n";
393
394			outFile << " kRatio = 0.5;\n"
395			<< "}\n";
396			}
397
398			outFile.close();
399
400
401			// cut out the waters that overlap with the lipids.
402
403
404			delete[] isActive;
405			isActive = new int[newWaters];
406			for(i=0; i<newWaters; i++) isActive[i] = 1;
407			int n_active = newWaters;
408			rCutSqr = water_padding * water_padding;
409
410			for(i=0; ( (i<newWaters) && isActive[i] ); i++){
411			for(j=0; ( (j<nAtoms) && isActive[i] ); j++){
412
413			atoms[j]->getPos( pos );
414
415			dx = waterSites[i].pos[0] - pos[0];
416			dy = waterSites[i].pos[1] - pos[1];
417			dz = waterSites[i].pos[2] - pos[2];
418
419			buildMap( dx, dy, dz, box_x, box_y, box_z );
420
421			dx2 = dx * dx;
422			dy2 = dy * dy;
423			dz2 = dz * dz;
424
425			dSqr = dx2 + dy2 + dz2;
426			if( dSqr < rCutSqr ){
427			isActive[i] = 0;
428			n_active--;
429
430
431			}
432			}
433			}
434
435
436
437
438			if( n_active < nWaters ){
439
440			sprintf( painCave.errMsg,
441			"Too many waters were removed, edit code and try again.\n" );
442
443			painCave.isFatal = 1;
444			simError();
445			}
446
447			int quickKill;
448			while( n_active > nWaters ){
449
450			quickKill = (int)(drand48()*newWaters);
451
452			if( isActive[quickKill] ){
453			isActive[quickKill] = 0;
454			n_active--;
455
456			}
457			}
458
459			if( n_active != nWaters ){
460
461			sprintf( painCave.errMsg,
462			"QuickKill didn't work right. n_active = %d, and nWaters = %d\n",
463			n_active, nWaters );
464			painCave.isFatal = 1;
465			simError();
466			}
467
468			// clean up our messes before building the final system.
469
470			simnfo[0].getConfiguration()->destroyArrays();
471			simnfo[1].getConfiguration()->destroyArrays();
472
473			// create the real Atom arrays
474
475			nAtoms = 0;
476			molIndex = 0;
477			molStart = new int[nLipids + nWaters];
478
479			for(j=0; j<nLipids; j++){
480			molStart[molIndex] = nAtoms;
481			molIndex++;
482			nAtoms += lipidNatoms;
483			}
484
485			for(j=0; j<nWaters; j++){
486			molStart[molIndex] = nAtoms;
487			molIndex++;
488			nAtoms += waterNatoms;
489			}
490
491			theConfig = simnfo[2].getConfiguration();
492			theConfig->createArrays( nAtoms );
493			simnfo[2].atoms = new Atom*[nAtoms];
494			atoms = simnfo[2].atoms;
495			simnfo[2].n_atoms = nAtoms;
496
497			// initialize lipid positions
498
499			molIndex = 0;
500			for(i=0; i<nLipids; i++ ){
501			lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
502			molStart[molIndex], theConfig );
503			molIndex++;
504			}
505
506			// initialize the water positions
507
508			for(i=0; i<newWaters; i++){
509
510			if( isActive[i] ){
511
512			getRandomRot( waterSites[i].rot );
513			waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms,
514			molStart[molIndex], theConfig );
515			molIndex++;
516			}
517			}
518
519			// set up the SimInfo object
520
521			double Hmat[3][3];
522
523			Hmat[0][0] = box_x;
524			Hmat[0][1] = 0.0;
525			Hmat[0][2] = 0.0;
526
527			Hmat[1][0] = 0.0;
528			Hmat[1][1] = box_y;
529			Hmat[1][2] = 0.0;
530
531			Hmat[2][0] = 0.0;
532			Hmat[2][1] = 0.0;
533			Hmat[2][2] = box_z;
534
535
536			bsInfo.boxX = box_x;
537			bsInfo.boxY = box_y;
538			bsInfo.boxZ = box_z;
539
540			simnfo[2].setBoxM( Hmat );
541
542			sprintf( simnfo[2].sampleName, "%s.dump", bsInfo.outPrefix );
543			sprintf( simnfo[2].finalName, "%s.init", bsInfo.outPrefix );
544
545			// set up the writer and write out
546
547			writer = new DumpWriter( &simnfo[2] );
548			writer->writeFinal( 0.0 );
549
550			// clean up the memory
551
552			// if( molMap != NULL ) delete[] molMap;
553			// if( cardDeck != NULL ) delete[] cardDeck;
554			// if( locate != NULL ){
555			// for(i=0; i<bsInfo.nComponents; i++){
556			// delete locate[i];
557			// }
558			// delete[] locate;
559			// }
560			// if( atoms != NULL ){
561			// for(i=0; i<nAtoms; i++){
562			// delete atoms[i];
563			// }
564			// Atom::destroyArrays();
565			// delete[] atoms;
566			// }
567			// if( molSeq != NULL ) delete[] molSeq;
568			// if( simnfo != NULL ) delete simnfo;
569			// if( writer != NULL ) delete writer;
570
571			return 1;
572			}
573
574			void buildMap( double &x, double &y, double &z,
575			double boxX, double boxY, double boxZ ){
576
577			if(x < 0) x -= boxX * (double)( (int)( (x / boxX) - 0.5 ) );
578			else x -= boxX * (double)( (int)( (x / boxX ) + 0.5));
579
580			if(y < 0) y -= boxY * (double)( (int)( (y / boxY) - 0.5 ) );
581			else y -= boxY * (double)( (int)( (y / boxY ) + 0.5));
582
583			if(z < 0) z -= boxZ * (double)( (int)( (z / boxZ) - 0.5 ) );
584			else z -= boxZ * (double)( (int)( (z / boxZ ) + 0.5));
585			}