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 );

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

int buildBilayer( int isRandom ){
  
  if( isRandom ){
    return buildRandomBilayer();
  }
  else{
    sprintf( painCave.errMsg,
             "Cannot currently create a non-random bilayer.\n" );
    painCave.isFatal = 1;
    simError();
    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 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 );

  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 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:	763
Committed:	Mon Sep 15 16:52:02 2003 UTC (20 years, 10 months ago) by tim
File size:	13521 byte(s)
Log Message:	add conserved quantity to statWriter fix bug of vector wrapping at NPTi
#	User	Rev	Content
1	mmeineke	707
2	chuckv	678	#include <iostream>
3	mmeineke	707	#include <vector>
4			#include <algorithm>
5	chuckv	678
6			#include <cstdlib>
7			#include <cstring>
8			#include <cmath>
9
10	mmeineke	707
11	chuckv	678	#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	chuckv	700	#include "latticeBuilder.hpp"
20	chuckv	678
21	mmeineke	707	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	chuckv	678	void buildMap( double &x, double &y, double &z,
33	chuckv	700	double boxX, double boxY, double boxZ );
34	chuckv	678
35			int buildRandomBilayer( void );
36
37			void getRandomRot( double rot[3][3] );
38
39			int buildBilayer( int isRandom ){
40
41			if( isRandom ){
42			return buildRandomBilayer();
43			}
44			else{
45			sprintf( painCave.errMsg,
46			"Cannot currently create a non-random bilayer.\n" );
47			painCave.isFatal = 1;
48			simError();
49			return 0;
50			}
51			}
52
53
54			int buildRandomBilayer( void ){
55
56			typedef struct{
57			double rot[3][3];
58			double pos[3];
59			} coord;
60
61
62	chuckv	700
63	chuckv	678	const double waterRho = 0.0334; // number density per cubic angstrom
64			const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters
65			const double waterCell = 4.929; // fcc unit cell length
66
67	chuckv	700	Lattice myFCC( FCC_LATTICE_TYPE, waterCell );
68			double posX, posY, *posZ;
69			double pos[3], posA[3], posB[3];
70
71	chuckv	678	const double water_padding = 6.0;
72			const double lipid_spaceing = 8.0;
73
74
75	chuckv	700	int i,j,k, l, m;
76	chuckv	678	int nAtoms, atomIndex, molIndex, molID;
77			int* molSeq;
78			int* molMap;
79			int* molStart;
80			int* cardDeck;
81			int deckSize;
82			int rSite, rCard;
83			double cell;
84			int nCells, nSites, siteIndex;
85
86			coord testSite;
87
88			Atom** atoms;
89			SimInfo* simnfo;
90	chuckv	700	SimState* theConfig;
91	chuckv	678	DumpWriter* writer;
92
93			MoleculeStamp* lipidStamp;
94			MoleculeStamp* waterStamp;
95			MoLocator *lipidLocate;
96			MoLocator *waterLocate;
97			int foundLipid, foundWater;
98			int nLipids, lipidNatoms, nWaters, waterNatoms;
99			double testBox, maxLength;
100
101			srand48( RAND_SEED );
102
103
104			// create the simInfo objects
105
106			simnfo = new SimInfo[3];
107
108
109			// set the the lipidStamp
110
111			foundLipid = 0;
112			foundWater = 0;
113			for(i=0; i<bsInfo.nComponents; i++){
114			if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){
115	chuckv	700
116	chuckv	678	foundLipid = 1;
117			lipidStamp = bsInfo.compStamps[i];
118			nLipids = bsInfo.componentsNmol[i];
119			}
120			if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){
121	chuckv	700
122	chuckv	678	foundWater = 1;
123	chuckv	700
124	chuckv	678	waterStamp = bsInfo.compStamps[i];
125			nWaters = bsInfo.componentsNmol[i];
126			}
127			}
128			if( !foundLipid ){
129			sprintf(painCave.errMsg,
130			"Could not find lipid \"%s\" in the bass file.\n",
131			bsInfo.lipidName );
132			painCave.isFatal = 1;
133			simError();
134			}
135			if( !foundWater ){
136	chuckv	700	sprintf(painCave.errMsg,
137			"Could not find solvent \"%s\" in the bass file.\n",
138	chuckv	678	bsInfo.waterName );
139			painCave.isFatal = 1;
140			simError();
141			}
142
143			//create the temp Molocator and atom Arrays
144
145			lipidLocate = new MoLocator( lipidStamp );
146			lipidNatoms = lipidStamp->getNAtoms();
147			maxLength = lipidLocate->getMaxLength();
148
149			waterLocate = new MoLocator( waterStamp );
150			waterNatoms = waterStamp->getNAtoms();
151
152	chuckv	700	nAtoms = lipidNatoms;
153	chuckv	678
154	chuckv	700	simnfo[0].n_atoms = nAtoms;
155			simnfo[0].atoms=new Atom*[nAtoms];
156	chuckv	678
157	chuckv	700	theConfig = simnfo[0].getConfiguration();
158			theConfig->createArrays( simnfo[0].n_atoms );
159	chuckv	678
160	chuckv	700	atoms=simnfo[0].atoms;
161	chuckv	678
162
163			// create the test box for initial water displacement
164
165			testBox = maxLength + waterCell * 4.0; // pad with 4 cells
166			nCells = (int)( testBox / waterCell + 1.0 );
167			int testWaters = 4 * nCells * nCells * nCells;
168
169			double* waterX = new double[testWaters];
170			double* waterY = new double[testWaters];
171			double* waterZ = new double[testWaters];
172
173			double x0 = 0.0 - ( testBox * 0.5 );
174			double y0 = 0.0 - ( testBox * 0.5 );
175			double z0 = 0.0 - ( testBox * 0.5 );
176
177
178			// create an fcc lattice in the water box.
179
180			int ndx = 0;
181			for( i=0; i < nCells; i++ ){
182			for( j=0; j < nCells; j++ ){
183			for( k=0; k < nCells; k++ ){
184	chuckv	700
185			myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k);
186			for(l=0; l<4; l++){
187			waterX[ndx]=posX[l];
188			waterY[ndx]=posY[l];
189			waterZ[ndx]=posZ[l];
190			ndx++;
191			}
192	chuckv	678	}
193			}
194			}
195
196			// calculate the number of water's displaced by our lipid.
197
198			testSite.rot[0][0] = 1.0;
199			testSite.rot[0][1] = 0.0;
200			testSite.rot[0][2] = 0.0;
201
202			testSite.rot[1][0] = 0.0;
203			testSite.rot[1][1] = 1.0;
204			testSite.rot[1][2] = 0.0;
205
206			testSite.rot[2][0] = 0.0;
207			testSite.rot[2][1] = 0.0;
208			testSite.rot[2][2] = 1.0;
209
210			testSite.pos[0] = 0.0;
211			testSite.pos[1] = 0.0;
212			testSite.pos[2] = 0.0;
213
214	chuckv	700	lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0, theConfig );
215	chuckv	678
216			int *isActive = new int[testWaters];
217			for(i=0; i<testWaters; i++) isActive[i] = 1;
218
219			int n_deleted = 0;
220			double dx, dy, dz;
221			double dx2, dy2, dz2, dSqr;
222			double rCutSqr = water_padding * water_padding;
223
224			for(i=0; ( (i<testWaters) && isActive[i] ); i++){
225			for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){
226	chuckv	700
227			atoms[j]->getPos( pos );
228	chuckv	678
229	chuckv	700	dx = waterX[i] - pos[0];
230			dy = waterY[i] - pos[1];
231			dz = waterZ[i] - pos[2];
232	chuckv	678
233			buildMap( dx, dy, dz, testBox, testBox, testBox );
234
235			dx2 = dx * dx;
236			dy2 = dy * dy;
237			dz2 = dz * dz;
238	chuckv	700
239	chuckv	678	dSqr = dx2 + dy2 + dz2;
240			if( dSqr < rCutSqr ){
241			isActive[i] = 0;
242			n_deleted++;
243			}
244			}
245			}
246
247			int targetWaters = nWaters + n_deleted * nLipids;
248
249			targetWaters = (int) ( targetWaters * 1.2 );
250
251			// find the best box size for the sim
252
253	mmeineke	707	int nCellsX, nCellsY, nCellsZ;
254
255	tim	763	const double boxTargetX = 66.22752;
256			const double boxTargetY = 60.53088;
257	mmeineke	707
258			nCellsX = (int)ceil(boxTargetX / waterCell);
259			nCellsY = (int)ceil(boxTargetY / waterCell);
260
261	chuckv	678	int testTot;
262			int done = 0;
263	mmeineke	707	nCellsZ = 0;
264	chuckv	678	while( !done ){
265	chuckv	700
266	mmeineke	707	nCellsZ++;
267			testTot = 4 * nCellsX * nCellsY * nCellsZ;
268	chuckv	700
269	chuckv	678	if( testTot >= targetWaters ) done = 1;
270			}
271
272			// create the new water box to the new specifications
273
274	mmeineke	707	int newWaters = nCellsX * nCellsY * nCellsZ * 4;
275	chuckv	678
276			delete[] waterX;
277			delete[] waterY;
278			delete[] waterZ;
279
280			coord* waterSites = new coord[newWaters];
281
282	mmeineke	707	double box_x = waterCell * nCellsX;
283			double box_y = waterCell * nCellsY;
284			double box_z = waterCell * nCellsZ;
285	chuckv	700
286	chuckv	678	// create an fcc lattice in the water box.
287
288			ndx = 0;
289	mmeineke	707	for( i=0; i < nCellsX; i++ ){
290			for( j=0; j < nCellsY; j++ ){
291			for( k=0; k < nCellsZ; k++ ){
292	chuckv	700
293			myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k);
294			for(l=0; l<4; l++){
295			waterSites[ndx].pos[0] = posX[l];
296			waterSites[ndx].pos[1] = posY[l];
297			waterSites[ndx].pos[2] = posZ[l];
298			ndx++;
299			}
300	chuckv	678	}
301			}
302			}
303
304			coord* lipidSites = new coord[nLipids];
305
306			// start a 3D RSA for the for the lipid placements
307
308
309			int reject;
310			int testDX, acceptedDX;
311
312	chuckv	700	nAtoms = nLipids * lipidNatoms;
313
314			simnfo[1].n_atoms = nAtoms;
315			simnfo[1].atoms=new Atom*[nAtoms];
316
317			theConfig = simnfo[1].getConfiguration();
318			theConfig->createArrays( simnfo[1].n_atoms );
319
320			atoms=simnfo[1].atoms;
321
322	chuckv	678	rCutSqr = lipid_spaceing * lipid_spaceing;
323
324			for(i=0; i<nLipids; i++ ){
325			done = 0;
326			while( !done ){
327	chuckv	700
328	chuckv	678	lipidSites[i].pos[0] = drand48() * box_x;
329			lipidSites[i].pos[1] = drand48() * box_y;
330			lipidSites[i].pos[2] = drand48() * box_z;
331	chuckv	700
332	chuckv	678	getRandomRot( lipidSites[i].rot );
333	chuckv	700
334	chuckv	678	ndx = i * lipidNatoms;
335
336			lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
337	chuckv	700	ndx, theConfig );
338
339	chuckv	678	reject = 0;
340			for( j=0; !reject && j<i; j++){
341			for(k=0; !reject && k<lipidNatoms; k++){
342
343			acceptedDX = j*lipidNatoms + k;
344			for(l=0; !reject && l<lipidNatoms; l++){
345	chuckv	700
346	chuckv	678	testDX = ndx + l;
347
348	chuckv	700	atoms[testDX]->getPos( posA );
349			atoms[acceptedDX]->getPos( posB );
350	chuckv	678
351	chuckv	700	dx = posA[0] - posB[0];
352			dy = posA[1] - posB[1];
353			dz = posA[2] - posB[2];
354
355	chuckv	678	buildMap( dx, dy, dz, box_x, box_y, box_z );
356	chuckv	700
357	chuckv	678	dx2 = dx * dx;
358			dy2 = dy * dy;
359			dz2 = dz * dz;
360	chuckv	700
361	chuckv	678	dSqr = dx2 + dy2 + dz2;
362			if( dSqr < rCutSqr ) reject = 1;
363			}
364			}
365			}
366
367			if( reject ){
368
369			for(j=0; j< lipidNatoms; j++) delete atoms[ndx+j];
370			}
371			else{
372			done = 1;
373	chuckv	700	std::cout << (i+1) << " has been accepted\n";
374	chuckv	678	}
375			}
376			}
377
378	mmeineke	707
379			// zSort of the lipid positions
380
381
382			vector< pair<int,double> >zSortArray;
383			for(i=0;i<nLipids;i++)
384			zSortArray.push_back( make_pair(i, lipidSites[i].pos[2]) );
385
386			sort(zSortArray.begin(),zSortArray.end(),SortCond());
387
388	mmeineke	724	ofstream outFile( "./zipper.bass", ios::app);
389	mmeineke	707
390			for(i=0; i<nLipids; i++){
391			outFile << "zConstraint[" << i << "]{\n"
392			<< " molIndex = " << zSortArray[i].first << ";\n"
393			<< " zPos = ";
394
395			if(i<32) outFile << "60.0;\n";
396			else outFile << "100.0;\n";
397
398			outFile << " kRatio = 0.5;\n"
399			<< "}\n";
400			}
401
402			outFile.close();
403
404
405	chuckv	678	// cut out the waters that overlap with the lipids.
406
407	chuckv	700
408	chuckv	678	delete[] isActive;
409			isActive = new int[newWaters];
410			for(i=0; i<newWaters; i++) isActive[i] = 1;
411			int n_active = newWaters;
412			rCutSqr = water_padding * water_padding;
413
414			for(i=0; ( (i<newWaters) && isActive[i] ); i++){
415			for(j=0; ( (j<nAtoms) && isActive[i] ); j++){
416
417	chuckv	700	atoms[j]->getPos( pos );
418	chuckv	678
419	chuckv	700	dx = waterSites[i].pos[0] - pos[0];
420			dy = waterSites[i].pos[1] - pos[1];
421			dz = waterSites[i].pos[2] - pos[2];
422
423	chuckv	678	buildMap( dx, dy, dz, box_x, box_y, box_z );
424
425			dx2 = dx * dx;
426			dy2 = dy * dy;
427			dz2 = dz * dz;
428	chuckv	700
429	chuckv	678	dSqr = dx2 + dy2 + dz2;
430			if( dSqr < rCutSqr ){
431			isActive[i] = 0;
432			n_active--;
433	chuckv	700
434
435	chuckv	678	}
436			}
437			}
438
439	chuckv	700
440
441
442	chuckv	678	if( n_active < nWaters ){
443	chuckv	700
444	chuckv	678	sprintf( painCave.errMsg,
445			"Too many waters were removed, edit code and try again.\n" );
446	chuckv	700
447	chuckv	678	painCave.isFatal = 1;
448			simError();
449			}
450
451			int quickKill;
452			while( n_active > nWaters ){
453
454			quickKill = (int)(drand48()*newWaters);
455
456			if( isActive[quickKill] ){
457			isActive[quickKill] = 0;
458			n_active--;
459	chuckv	700
460	chuckv	678	}
461			}
462
463			if( n_active != nWaters ){
464	chuckv	700
465	chuckv	678	sprintf( painCave.errMsg,
466			"QuickKill didn't work right. n_active = %d, and nWaters = %d\n",
467			n_active, nWaters );
468			painCave.isFatal = 1;
469			simError();
470			}
471
472			// clean up our messes before building the final system.
473
474	chuckv	700	simnfo[0].getConfiguration()->destroyArrays();
475			simnfo[1].getConfiguration()->destroyArrays();
476	chuckv	678
477			// create the real Atom arrays
478
479			nAtoms = 0;
480			molIndex = 0;
481			molStart = new int[nLipids + nWaters];
482
483			for(j=0; j<nLipids; j++){
484			molStart[molIndex] = nAtoms;
485			molIndex++;
486			nAtoms += lipidNatoms;
487			}
488
489			for(j=0; j<nWaters; j++){
490			molStart[molIndex] = nAtoms;
491			molIndex++;
492			nAtoms += waterNatoms;
493			}
494
495	chuckv	700	theConfig = simnfo[2].getConfiguration();
496			theConfig->createArrays( nAtoms );
497			simnfo[2].atoms = new Atom*[nAtoms];
498			atoms = simnfo[2].atoms;
499			simnfo[2].n_atoms = nAtoms;
500	chuckv	678
501			// initialize lipid positions
502
503			molIndex = 0;
504			for(i=0; i<nLipids; i++ ){
505			lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
506	chuckv	700	molStart[molIndex], theConfig );
507	chuckv	678	molIndex++;
508			}
509
510			// initialize the water positions
511
512			for(i=0; i<newWaters; i++){
513	chuckv	700
514	chuckv	678	if( isActive[i] ){
515	chuckv	700
516	chuckv	678	getRandomRot( waterSites[i].rot );
517			waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms,
518	chuckv	700	molStart[molIndex], theConfig );
519	chuckv	678	molIndex++;
520			}
521			}
522
523			// set up the SimInfo object
524
525	chuckv	700	double Hmat[3][3];
526
527			Hmat[0][0] = box_x;
528			Hmat[0][1] = 0.0;
529			Hmat[0][2] = 0.0;
530
531			Hmat[1][0] = 0.0;
532			Hmat[1][1] = box_y;
533			Hmat[1][2] = 0.0;
534
535			Hmat[2][0] = 0.0;
536			Hmat[2][1] = 0.0;
537			Hmat[2][2] = box_z;
538
539
540	chuckv	678	bsInfo.boxX = box_x;
541			bsInfo.boxY = box_y;
542			bsInfo.boxZ = box_z;
543
544	chuckv	700	simnfo[2].setBoxM( Hmat );
545	chuckv	678
546	chuckv	700	sprintf( simnfo[2].sampleName, "%s.dump", bsInfo.outPrefix );
547			sprintf( simnfo[2].finalName, "%s.init", bsInfo.outPrefix );
548	chuckv	678
549			// set up the writer and write out
550
551	chuckv	700	writer = new DumpWriter( &simnfo[2] );
552	chuckv	678	writer->writeFinal( 0.0 );
553
554			// clean up the memory
555
556	chuckv	700	// if( molMap != NULL ) delete[] molMap;
557			// if( cardDeck != NULL ) delete[] cardDeck;
558			// if( locate != NULL ){
559			// for(i=0; i<bsInfo.nComponents; i++){
560			// delete locate[i];
561			// }
562			// delete[] locate;
563			// }
564			// if( atoms != NULL ){
565			// for(i=0; i<nAtoms; i++){
566			// delete atoms[i];
567			// }
568			// Atom::destroyArrays();
569			// delete[] atoms;
570			// }
571			// if( molSeq != NULL ) delete[] molSeq;
572			// if( simnfo != NULL ) delete simnfo;
573			// if( writer != NULL ) delete writer;
574	chuckv	678
575			return 1;
576			}
577
578			void getRandomRot( double rot[3][3] ){
579
580			double theta, phi, psi;
581			double cosTheta;
582
583			// select random phi, psi, and cosTheta
584
585			phi = 2.0 * M_PI * drand48();
586			psi = 2.0 * M_PI * drand48();
587			cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1
588
589			theta = acos( cosTheta );
590
591			rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
592			rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
593			rot[0][2] = sin(theta) * sin(psi);
594
595			rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
596			rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
597			rot[1][2] = sin(theta) * cos(psi);
598
599			rot[2][0] = sin(phi) * sin(theta);
600			rot[2][1] = -cos(phi) * sin(theta);
601			rot[2][2] = cos(theta);
602			}
603
604
605
606			void buildMap( double &x, double &y, double &z,
607	chuckv	700	double boxX, double boxY, double boxZ ){
608	chuckv	678
609			if(x < 0) x -= boxX * (double)( (int)( (x / boxX) - 0.5 ) );
610			else x -= boxX * (double)( (int)( (x / boxX ) + 0.5));
611
612			if(y < 0) y -= boxY * (double)( (int)( (y / boxY) - 0.5 ) );
613			else y -= boxY * (double)( (int)( (y / boxY ) + 0.5));
614
615			if(z < 0) z -= boxZ * (double)( (int)( (z / boxZ) - 0.5 ) );
616			else z -= boxZ * (double)( (int)( (z / boxZ ) + 0.5));
617			}