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|
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#include <iostream> |
| 3 |
#include <vector> |
| 4 |
#include <algorithm> |
| 5 |
|
| 6 |
#include <cstdlib> |
| 7 |
#include <cstring> |
| 8 |
#include <cmath> |
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|
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|
| 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 |
|
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public: |
| 24 |
bool operator()(const pair<int, double>& p1, const pair<int, double>& p2){ |
| 25 |
return p1.second < p2.second; |
| 26 |
} |
| 27 |
|
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|
| 29 |
}; |
| 30 |
|
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|
| 32 |
void buildMap( double &x, double &y, double &z, |
| 33 |
double boxX, double boxY, double boxZ ); |
| 34 |
|
| 35 |
int buildRandomBilayer( void ); |
| 36 |
|
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int buildBilayer( int isRandom ){ |
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|
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if( isRandom ){ |
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return buildRandomBilayer(); |
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} |
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else{ |
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|
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std::cerr << "unsupported feature\n"; |
| 45 |
return 0; |
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} |
| 47 |
} |
| 48 |
|
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|
| 50 |
int buildRandomBilayer( void ){ |
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|
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typedef struct{ |
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double rot[3][3]; |
| 54 |
double pos[3]; |
| 55 |
} coord; |
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|
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|
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|
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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; |
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|
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|
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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 |
|
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coord testSite; |
| 83 |
|
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Atom** atoms; |
| 85 |
SimInfo* simnfo; |
| 86 |
SimState* theConfig; |
| 87 |
DumpWriter* writer; |
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|
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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; |
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|
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srand48( RAND_SEED ); |
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|
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|
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// create the simInfo objects |
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|
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simnfo = new SimInfo[3]; |
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|
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|
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// set the the lipidStamp |
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|
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foundLipid = 0; |
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foundWater = 0; |
| 109 |
for(i=0; i<bsInfo.nComponents; i++){ |
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if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){ |
| 111 |
|
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foundLipid = 1; |
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lipidStamp = bsInfo.compStamps[i]; |
| 114 |
nLipids = bsInfo.componentsNmol[i]; |
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} |
| 116 |
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){ |
| 117 |
|
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foundWater = 1; |
| 119 |
|
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waterStamp = bsInfo.compStamps[i]; |
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nWaters = bsInfo.componentsNmol[i]; |
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} |
| 123 |
} |
| 124 |
if( !foundLipid ){ |
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sprintf(painCave.errMsg, |
| 126 |
"Could not find lipid \"%s\" in the bass file.\n", |
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bsInfo.lipidName ); |
| 128 |
painCave.isFatal = 1; |
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simError(); |
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} |
| 131 |
if( !foundWater ){ |
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sprintf(painCave.errMsg, |
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"Could not find solvent \"%s\" in the bass file.\n", |
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bsInfo.waterName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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//create the temp Molocator and atom Arrays |
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|
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lipidLocate = new MoLocator( lipidStamp ); |
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lipidNatoms = lipidStamp->getNAtoms(); |
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maxLength = lipidLocate->getMaxLength(); |
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|
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waterLocate = new MoLocator( waterStamp ); |
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waterNatoms = waterStamp->getNAtoms(); |
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|
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nAtoms = lipidNatoms; |
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|
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simnfo[0].n_atoms = nAtoms; |
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simnfo[0].atoms=new Atom*[nAtoms]; |
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|
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theConfig = simnfo[0].getConfiguration(); |
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theConfig->createArrays( simnfo[0].n_atoms ); |
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|
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atoms=simnfo[0].atoms; |
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|
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|
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// create the test box for initial water displacement |
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|
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testBox = maxLength + waterCell * 4.0; // pad with 4 cells |
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nCells = (int)( testBox / waterCell + 1.0 ); |
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int testWaters = 4 * nCells * nCells * nCells; |
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|
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double* waterX = new double[testWaters]; |
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double* waterY = new double[testWaters]; |
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double* waterZ = new double[testWaters]; |
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|
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double x0 = 0.0 - ( testBox * 0.5 ); |
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double y0 = 0.0 - ( testBox * 0.5 ); |
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double z0 = 0.0 - ( testBox * 0.5 ); |
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|
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|
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// create an fcc lattice in the water box. |
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|
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int ndx = 0; |
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for( i=0; i < nCells; i++ ){ |
| 178 |
for( j=0; j < nCells; j++ ){ |
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for( k=0; k < nCells; k++ ){ |
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|
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myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k); |
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for(l=0; l<4; l++){ |
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waterX[ndx]=posX[l]; |
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waterY[ndx]=posY[l]; |
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waterZ[ndx]=posZ[l]; |
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ndx++; |
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} |
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} |
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} |
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} |
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|
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// calculate the number of water's displaced by our lipid. |
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|
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testSite.rot[0][0] = 1.0; |
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testSite.rot[0][1] = 0.0; |
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testSite.rot[0][2] = 0.0; |
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|
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testSite.rot[1][0] = 0.0; |
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testSite.rot[1][1] = 1.0; |
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testSite.rot[1][2] = 0.0; |
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|
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testSite.rot[2][0] = 0.0; |
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testSite.rot[2][1] = 0.0; |
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testSite.rot[2][2] = 1.0; |
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|
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testSite.pos[0] = 0.0; |
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testSite.pos[1] = 0.0; |
| 208 |
testSite.pos[2] = 0.0; |
| 209 |
|
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lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0, theConfig ); |
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|
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int *isActive = new int[testWaters]; |
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for(i=0; i<testWaters; i++) isActive[i] = 1; |
| 214 |
|
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int n_deleted = 0; |
| 216 |
double dx, dy, dz; |
| 217 |
double dx2, dy2, dz2, dSqr; |
| 218 |
double rCutSqr = water_padding * water_padding; |
| 219 |
|
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for(i=0; ( (i<testWaters) && isActive[i] ); i++){ |
| 221 |
for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){ |
| 222 |
|
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atoms[j]->getPos( pos ); |
| 224 |
|
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dx = waterX[i] - pos[0]; |
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dy = waterY[i] - pos[1]; |
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dz = waterZ[i] - pos[2]; |
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|
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buildMap( dx, dy, dz, testBox, testBox, testBox ); |
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|
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dx2 = dx * dx; |
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dy2 = dy * dy; |
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dz2 = dz * dz; |
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|
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dSqr = dx2 + dy2 + dz2; |
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if( dSqr < rCutSqr ){ |
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isActive[i] = 0; |
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n_deleted++; |
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} |
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} |
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} |
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|
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int targetWaters = nWaters + n_deleted * nLipids; |
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|
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targetWaters = (int) ( targetWaters * 1.2 ); |
| 246 |
|
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// find the best box size for the sim |
| 248 |
|
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int nCellsX, nCellsY, nCellsZ; |
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|
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const double boxTargetX = 66.22752; |
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const double boxTargetY = 60.53088; |
| 253 |
|
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nCellsX = (int)ceil(boxTargetX / waterCell); |
| 255 |
nCellsY = (int)ceil(boxTargetY / waterCell); |
| 256 |
|
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int testTot; |
| 258 |
int done = 0; |
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nCellsZ = 0; |
| 260 |
while( !done ){ |
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|
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nCellsZ++; |
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testTot = 4 * nCellsX * nCellsY * nCellsZ; |
| 264 |
|
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if( testTot >= targetWaters ) done = 1; |
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} |
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|
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// create the new water box to the new specifications |
| 269 |
|
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int newWaters = nCellsX * nCellsY * nCellsZ * 4; |
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|
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delete[] waterX; |
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delete[] waterY; |
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delete[] waterZ; |
| 275 |
|
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coord* waterSites = new coord[newWaters]; |
| 277 |
|
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double box_x = waterCell * nCellsX; |
| 279 |
double box_y = waterCell * nCellsY; |
| 280 |
double box_z = waterCell * nCellsZ; |
| 281 |
|
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// create an fcc lattice in the water box. |
| 283 |
|
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ndx = 0; |
| 285 |
for( i=0; i < nCellsX; i++ ){ |
| 286 |
for( j=0; j < nCellsY; j++ ){ |
| 287 |
for( k=0; k < nCellsZ; k++ ){ |
| 288 |
|
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myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k); |
| 290 |
for(l=0; l<4; l++){ |
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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 |
|
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// 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 |
} |
