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chuckv |
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#include <iostream> |
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#include <cstdlib> |
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#include <cstring> |
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#include <cmath> |
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#include "simError.h" |
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#include "SimInfo.hpp" |
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#include "ReadWrite.hpp" |
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#include "MoLocator.hpp" |
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#include "sysBuild.hpp" |
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#include "bilayerSys.hpp" |
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void buildMap( double &x, double &y, double &z, |
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double boxX, double boxY, double boxZ ); |
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int buildRandomBilayer( void ); |
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void getRandomRot( double rot[3][3] ); |
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int buildBilayer( int isRandom ){ |
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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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sprintf( painCave.errMsg, |
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"Cannot currently create a non-random bilayer.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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return 0; |
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} |
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} |
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int buildRandomBilayer( void ){ |
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typedef struct{ |
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double rot[3][3]; |
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double pos[3]; |
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} coord; |
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const double waterRho = 0.0334; // number density per cubic angstrom |
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const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters |
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const double waterCell = 4.929; // fcc unit cell length |
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const double water_padding = 6.0; |
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const double lipid_spaceing = 8.0; |
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int i,j,k, l; |
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int nAtoms, atomIndex, molIndex, molID; |
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int* molSeq; |
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int* molMap; |
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int* molStart; |
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int* cardDeck; |
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int deckSize; |
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int rSite, rCard; |
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double cell; |
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int nCells, nSites, siteIndex; |
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coord testSite; |
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Atom** atoms; |
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SimInfo* simnfo; |
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DumpWriter* writer; |
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MoleculeStamp* lipidStamp; |
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MoleculeStamp* waterStamp; |
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MoLocator *lipidLocate; |
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MoLocator *waterLocate; |
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int foundLipid, foundWater; |
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int nLipids, lipidNatoms, nWaters, waterNatoms; |
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double testBox, maxLength; |
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srand48( RAND_SEED ); |
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// create the simInfo objects |
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simnfo = new SimInfo[3]; |
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// set the the lipidStamp |
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foundLipid = 0; |
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foundWater = 0; |
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for(i=0; i<bsInfo.nComponents; i++){ |
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if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){ |
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foundLipid = 1; |
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lipidStamp = bsInfo.compStamps[i]; |
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nLipids = bsInfo.componentsNmol[i]; |
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} |
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if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){ |
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foundWater = 1; |
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waterStamp = bsInfo.compStamps[i]; |
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nWaters = bsInfo.componentsNmol[i]; |
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} |
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} |
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if( !foundLipid ){ |
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sprintf(painCave.errMsg, |
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"Could not find lipid \"%s\" in the bass file.\n", |
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bsInfo.lipidName ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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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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//create the temp Molocator and atom Arrays |
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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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waterLocate = new MoLocator( waterStamp ); |
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waterNatoms = waterStamp->getNAtoms(); |
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nAtoms = nLipids * lipidNatoms; |
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simnfo[0].n_atoms = nAtoms; |
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simnfo[0].atoms=new Atom*[nAtoms]; |
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(simnfo[0]->getConfiguration())->createArrays( simnfo[0].n_atoms ); |
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for(i=0; i<simnfo[0].n_atoms; i++) simnfo[0].atoms[i]->setCoords(); |
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atoms=simnfo[0].atoms; |
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// create the test box for initial water displacement |
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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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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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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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// create an fcc lattice in the water box. |
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int ndx = 0; |
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for( i=0; i < nCells; i++ ){ |
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for( j=0; j < nCells; j++ ){ |
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for( k=0; k < nCells; k++ ){ |
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waterX[ndx] = i * waterCell + x0; |
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waterY[ndx] = j * waterCell + y0; |
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waterZ[ndx] = k * waterCell + z0; |
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ndx++; |
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waterX[ndx] = i * waterCell + 0.5 * waterCell + x0; |
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waterY[ndx] = j * waterCell + 0.5 * waterCell + y0; |
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waterZ[ndx] = k * waterCell + z0; |
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ndx++; |
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waterX[ndx] = i * waterCell + x0; |
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waterY[ndx] = j * waterCell + 0.5 * waterCell + y0; |
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waterZ[ndx] = k * waterCell + 0.5 * waterCell + z0; |
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ndx++; |
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waterX[ndx] = i * waterCell + 0.5 * waterCell + x0; |
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waterY[ndx] = j * waterCell + y0; |
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waterZ[ndx] = k * waterCell + 0.5 * waterCell + z0; |
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ndx++; |
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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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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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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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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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testSite.pos[0] = 0.0; |
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testSite.pos[1] = 0.0; |
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testSite.pos[2] = 0.0; |
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lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0 ); |
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int *isActive = new int[testWaters]; |
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for(i=0; i<testWaters; i++) isActive[i] = 1; |
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int n_deleted = 0; |
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double dx, dy, dz; |
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double dx2, dy2, dz2, dSqr; |
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double rCutSqr = water_padding * water_padding; |
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for(i=0; ( (i<testWaters) && isActive[i] ); i++){ |
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for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){ |
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dx = waterX[i] - atoms[j]->getX(); |
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dy = waterY[i] - atoms[j]->getY(); |
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dz = waterZ[i] - atoms[j]->getZ(); |
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buildMap( dx, dy, dz, testBox, testBox, testBox ); |
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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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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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int targetWaters = nWaters + n_deleted * nLipids; |
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targetWaters = (int) ( targetWaters * 1.2 ); |
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// find the best box size for the sim |
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int testTot; |
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int done = 0; |
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ndx = 0; |
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while( !done ){ |
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ndx++; |
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testTot = 4 * ndx * ndx * ndx; |
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if( testTot >= targetWaters ) done = 1; |
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} |
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nCells = ndx; |
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// create the new water box to the new specifications |
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int newWaters = nCells * nCells * nCells * 4; |
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delete[] waterX; |
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delete[] waterY; |
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delete[] waterZ; |
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coord* waterSites = new coord[newWaters]; |
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double box_x = waterCell * nCells; |
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double box_y = waterCell * nCells; |
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double box_z = waterCell * nCells; |
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// create an fcc lattice in the water box. |
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ndx = 0; |
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for( i=0; i < nCells; i++ ){ |
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for( j=0; j < nCells; j++ ){ |
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for( k=0; k < nCells; k++ ){ |
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waterSites[ndx].pos[0] = i * waterCell; |
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waterSites[ndx].pos[1] = j * waterCell; |
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waterSites[ndx].pos[2] = k * waterCell; |
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ndx++; |
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waterSites[ndx].pos[0] = i * waterCell + 0.5 * waterCell; |
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waterSites[ndx].pos[1] = j * waterCell + 0.5 * waterCell; |
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waterSites[ndx].pos[2] = k * waterCell; |
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ndx++; |
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waterSites[ndx].pos[0] = i * waterCell; |
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waterSites[ndx].pos[1] = j * waterCell + 0.5 * waterCell; |
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waterSites[ndx].pos[2] = k * waterCell + 0.5 * waterCell; |
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ndx++; |
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waterSites[ndx].pos[0] = i * waterCell + 0.5 * waterCell; |
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waterSites[ndx].pos[1] = j * waterCell; |
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waterSites[ndx].pos[2] = k * waterCell + 0.5 * waterCell; |
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ndx++; |
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} |
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} |
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} |
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coord* lipidSites = new coord[nLipids]; |
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// start a 3D RSA for the for the lipid placements |
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int reject; |
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int testDX, acceptedDX; |
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rCutSqr = lipid_spaceing * lipid_spaceing; |
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for(i=0; i<nLipids; i++ ){ |
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done = 0; |
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while( !done ){ |
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lipidSites[i].pos[0] = drand48() * box_x; |
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lipidSites[i].pos[1] = drand48() * box_y; |
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lipidSites[i].pos[2] = drand48() * box_z; |
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getRandomRot( lipidSites[i].rot ); |
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ndx = i * lipidNatoms; |
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lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
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ndx ); |
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reject = 0; |
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for( j=0; !reject && j<i; j++){ |
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for(k=0; !reject && k<lipidNatoms; k++){ |
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acceptedDX = j*lipidNatoms + k; |
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for(l=0; !reject && l<lipidNatoms; l++){ |
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testDX = ndx + l; |
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dx = atoms[testDX]->getX() - atoms[acceptedDX]->getX(); |
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dy = atoms[testDX]->getY() - atoms[acceptedDX]->getY(); |
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dz = atoms[testDX]->getZ() - atoms[acceptedDX]->getZ(); |
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buildMap( dx, dy, dz, box_x, box_y, box_z ); |
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dx2 = dx * dx; |
| 341 |
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dy2 = dy * dy; |
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dz2 = dz * dz; |
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| 344 |
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dSqr = dx2 + dy2 + dz2; |
| 345 |
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if( dSqr < rCutSqr ) reject = 1; |
| 346 |
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} |
| 347 |
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} |
| 348 |
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} |
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| 350 |
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if( reject ){ |
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for(j=0; j< lipidNatoms; j++) delete atoms[ndx+j]; |
| 353 |
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} |
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else{ |
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done = 1; |
| 356 |
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std::cout << i << " has been accepted\n"; |
| 357 |
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} |
| 358 |
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} |
| 359 |
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} |
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// cut out the waters that overlap with the lipids. |
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delete[] isActive; |
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isActive = new int[newWaters]; |
| 365 |
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for(i=0; i<newWaters; i++) isActive[i] = 1; |
| 366 |
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int n_active = newWaters; |
| 367 |
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rCutSqr = water_padding * water_padding; |
| 368 |
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| 369 |
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for(i=0; ( (i<newWaters) && isActive[i] ); i++){ |
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for(j=0; ( (j<nAtoms) && isActive[i] ); j++){ |
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| 372 |
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dx = waterSites[i].pos[0] - atoms[j]->getX(); |
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dy = waterSites[i].pos[1] - atoms[j]->getY(); |
| 374 |
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dz = waterSites[i].pos[2] - atoms[j]->getZ(); |
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|
|
|
| 376 |
|
|
buildMap( dx, dy, dz, box_x, box_y, box_z ); |
| 377 |
|
|
|
| 378 |
|
|
dx2 = dx * dx; |
| 379 |
|
|
dy2 = dy * dy; |
| 380 |
|
|
dz2 = dz * dz; |
| 381 |
|
|
|
| 382 |
|
|
dSqr = dx2 + dy2 + dz2; |
| 383 |
|
|
if( dSqr < rCutSqr ){ |
| 384 |
|
|
isActive[i] = 0; |
| 385 |
|
|
n_active--; |
| 386 |
|
|
} |
| 387 |
|
|
} |
| 388 |
|
|
} |
| 389 |
|
|
|
| 390 |
|
|
if( n_active < nWaters ){ |
| 391 |
|
|
|
| 392 |
|
|
sprintf( painCave.errMsg, |
| 393 |
|
|
"Too many waters were removed, edit code and try again.\n" ); |
| 394 |
|
|
|
| 395 |
|
|
painCave.isFatal = 1; |
| 396 |
|
|
simError(); |
| 397 |
|
|
} |
| 398 |
|
|
|
| 399 |
|
|
int quickKill; |
| 400 |
|
|
while( n_active > nWaters ){ |
| 401 |
|
|
|
| 402 |
|
|
quickKill = (int)(drand48()*newWaters); |
| 403 |
|
|
|
| 404 |
|
|
if( isActive[quickKill] ){ |
| 405 |
|
|
isActive[quickKill] = 0; |
| 406 |
|
|
n_active--; |
| 407 |
|
|
} |
| 408 |
|
|
} |
| 409 |
|
|
|
| 410 |
|
|
if( n_active != nWaters ){ |
| 411 |
|
|
|
| 412 |
|
|
sprintf( painCave.errMsg, |
| 413 |
|
|
"QuickKill didn't work right. n_active = %d, and nWaters = %d\n", |
| 414 |
|
|
n_active, nWaters ); |
| 415 |
|
|
painCave.isFatal = 1; |
| 416 |
|
|
simError(); |
| 417 |
|
|
} |
| 418 |
|
|
|
| 419 |
|
|
// clean up our messes before building the final system. |
| 420 |
|
|
|
| 421 |
|
|
for(i=0; i<nAtoms; i++){ |
| 422 |
|
|
|
| 423 |
|
|
delete atoms[i]; |
| 424 |
|
|
} |
| 425 |
|
|
Atom::destroyArrays(); |
| 426 |
|
|
|
| 427 |
|
|
|
| 428 |
|
|
// create the real Atom arrays |
| 429 |
|
|
|
| 430 |
|
|
nAtoms = 0; |
| 431 |
|
|
molIndex = 0; |
| 432 |
|
|
molStart = new int[nLipids + nWaters]; |
| 433 |
|
|
|
| 434 |
|
|
for(j=0; j<nLipids; j++){ |
| 435 |
|
|
molStart[molIndex] = nAtoms; |
| 436 |
|
|
molIndex++; |
| 437 |
|
|
nAtoms += lipidNatoms; |
| 438 |
|
|
} |
| 439 |
|
|
|
| 440 |
|
|
for(j=0; j<nWaters; j++){ |
| 441 |
|
|
molStart[molIndex] = nAtoms; |
| 442 |
|
|
molIndex++; |
| 443 |
|
|
nAtoms += waterNatoms; |
| 444 |
|
|
} |
| 445 |
|
|
|
| 446 |
|
|
|
| 447 |
|
|
Atom::createArrays( nAtoms ); |
| 448 |
|
|
atoms = new Atom*[nAtoms]; |
| 449 |
|
|
|
| 450 |
|
|
|
| 451 |
|
|
// initialize lipid positions |
| 452 |
|
|
|
| 453 |
|
|
molIndex = 0; |
| 454 |
|
|
for(i=0; i<nLipids; i++ ){ |
| 455 |
|
|
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 456 |
|
|
molStart[molIndex] ); |
| 457 |
|
|
molIndex++; |
| 458 |
|
|
} |
| 459 |
|
|
|
| 460 |
|
|
// initialize the water positions |
| 461 |
|
|
|
| 462 |
|
|
for(i=0; i<newWaters; i++){ |
| 463 |
|
|
|
| 464 |
|
|
if( isActive[i] ){ |
| 465 |
|
|
|
| 466 |
|
|
getRandomRot( waterSites[i].rot ); |
| 467 |
|
|
waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms, |
| 468 |
|
|
molStart[molIndex] ); |
| 469 |
|
|
molIndex++; |
| 470 |
|
|
} |
| 471 |
|
|
} |
| 472 |
|
|
|
| 473 |
|
|
// set up the SimInfo object |
| 474 |
|
|
|
| 475 |
|
|
bsInfo.boxX = box_x; |
| 476 |
|
|
bsInfo.boxY = box_y; |
| 477 |
|
|
bsInfo.boxZ = box_z; |
| 478 |
|
|
|
| 479 |
|
|
double boxVector[3]; |
| 480 |
|
|
|
| 481 |
|
|
boxVector[0] = bsInfo.boxX; |
| 482 |
|
|
boxVector[1] = bsInfo.boxY; |
| 483 |
|
|
boxVector[2] = bsInfo.boxZ; |
| 484 |
|
|
simnfo->setBox( boxVector ); |
| 485 |
|
|
|
| 486 |
|
|
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
| 487 |
|
|
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
| 488 |
|
|
|
| 489 |
|
|
simnfo->atoms = atoms; |
| 490 |
|
|
|
| 491 |
|
|
// set up the writer and write out |
| 492 |
|
|
|
| 493 |
|
|
writer = new DumpWriter( simnfo ); |
| 494 |
|
|
writer->writeFinal( 0.0 ); |
| 495 |
|
|
|
| 496 |
|
|
// clean up the memory |
| 497 |
|
|
|
| 498 |
|
|
// if( molMap != NULL ) delete[] molMap; |
| 499 |
|
|
// if( cardDeck != NULL ) delete[] cardDeck; |
| 500 |
|
|
// if( locate != NULL ){ |
| 501 |
|
|
// for(i=0; i<bsInfo.nComponents; i++){ |
| 502 |
|
|
// delete locate[i]; |
| 503 |
|
|
// } |
| 504 |
|
|
// delete[] locate; |
| 505 |
|
|
// } |
| 506 |
|
|
// if( atoms != NULL ){ |
| 507 |
|
|
// for(i=0; i<nAtoms; i++){ |
| 508 |
|
|
// delete atoms[i]; |
| 509 |
|
|
// } |
| 510 |
|
|
// Atom::destroyArrays(); |
| 511 |
|
|
// delete[] atoms; |
| 512 |
|
|
// } |
| 513 |
|
|
// if( molSeq != NULL ) delete[] molSeq; |
| 514 |
|
|
// if( simnfo != NULL ) delete simnfo; |
| 515 |
|
|
// if( writer != NULL ) delete writer; |
| 516 |
|
|
|
| 517 |
|
|
return 1; |
| 518 |
|
|
} |
| 519 |
|
|
|
| 520 |
|
|
|
| 521 |
|
|
|
| 522 |
|
|
int Old_buildRandomBilayer( void ){ |
| 523 |
|
|
|
| 524 |
|
|
int i,j,k; |
| 525 |
|
|
int nAtoms, atomIndex, molIndex, molID; |
| 526 |
|
|
int* molSeq; |
| 527 |
|
|
int* molMap; |
| 528 |
|
|
int* molStart; |
| 529 |
|
|
int* cardDeck; |
| 530 |
|
|
int deckSize; |
| 531 |
|
|
int rSite, rCard; |
| 532 |
|
|
double cell; |
| 533 |
|
|
int nCells, nSites, siteIndex; |
| 534 |
|
|
double rot[3][3]; |
| 535 |
|
|
double pos[3]; |
| 536 |
|
|
|
| 537 |
|
|
Atom** atoms; |
| 538 |
|
|
SimInfo* simnfo; |
| 539 |
|
|
DumpWriter* writer; |
| 540 |
|
|
MoLocator** locate; |
| 541 |
|
|
|
| 542 |
|
|
// initialize functions and variables |
| 543 |
|
|
|
| 544 |
|
|
srand48( RAND_SEED ); |
| 545 |
|
|
molSeq = NULL; |
| 546 |
|
|
molStart = NULL; |
| 547 |
|
|
molMap = NULL; |
| 548 |
|
|
cardDeck = NULL; |
| 549 |
|
|
atoms = NULL; |
| 550 |
|
|
locate = NULL; |
| 551 |
|
|
simnfo = NULL; |
| 552 |
|
|
writer = NULL; |
| 553 |
|
|
|
| 554 |
|
|
// calculate the number of cells in the fcc box |
| 555 |
|
|
|
| 556 |
|
|
nCells = 0; |
| 557 |
|
|
nSites = 0; |
| 558 |
|
|
while( nSites < bsInfo.totNmol ){ |
| 559 |
|
|
nCells++; |
| 560 |
|
|
nSites = 4.0 * pow( (double)nCells, 3.0 ); |
| 561 |
|
|
} |
| 562 |
|
|
|
| 563 |
|
|
|
| 564 |
|
|
// create the molMap and cardDeck arrays |
| 565 |
|
|
|
| 566 |
|
|
molMap = new int[nSites]; |
| 567 |
|
|
cardDeck = new int[nSites]; |
| 568 |
|
|
|
| 569 |
|
|
for(i=0; i<nSites; i++){ |
| 570 |
|
|
molMap[i] = -1; |
| 571 |
|
|
cardDeck[i] = i; |
| 572 |
|
|
} |
| 573 |
|
|
|
| 574 |
|
|
// randomly place the molecules on the sites |
| 575 |
|
|
|
| 576 |
|
|
deckSize = nSites; |
| 577 |
|
|
for(i=0; i<bsInfo.totNmol; i++){ |
| 578 |
|
|
rCard = (int)( deckSize * drand48() ); |
| 579 |
|
|
rSite = cardDeck[rCard]; |
| 580 |
|
|
molMap[rSite] = i; |
| 581 |
|
|
|
| 582 |
|
|
// book keep the card deck; |
| 583 |
|
|
|
| 584 |
|
|
deckSize--; |
| 585 |
|
|
cardDeck[rCard] = cardDeck[deckSize]; |
| 586 |
|
|
} |
| 587 |
|
|
|
| 588 |
|
|
|
| 589 |
|
|
// create the MoLocator and Atom arrays |
| 590 |
|
|
|
| 591 |
|
|
nAtoms = 0; |
| 592 |
|
|
molIndex = 0; |
| 593 |
|
|
locate = new MoLocator*[bsInfo.nComponents]; |
| 594 |
|
|
molSeq = new int[bsInfo.totNmol]; |
| 595 |
|
|
molStart = new int[bsInfo.totNmol]; |
| 596 |
|
|
for(i=0; i<bsInfo.nComponents; i++){ |
| 597 |
|
|
locate[i] = new MoLocator( bsInfo.compStamps[i] ); |
| 598 |
|
|
for(j=0; j<bsInfo.componentsNmol[i]; j++){ |
| 599 |
|
|
molSeq[molIndex] = i; |
| 600 |
|
|
molStart[molIndex] = nAtoms; |
| 601 |
|
|
molIndex++; |
| 602 |
|
|
nAtoms += bsInfo.compStamps[i]->getNAtoms(); |
| 603 |
|
|
} |
| 604 |
|
|
} |
| 605 |
|
|
|
| 606 |
|
|
Atom::createArrays( nAtoms ); |
| 607 |
|
|
atoms = new Atom*[nAtoms]; |
| 608 |
|
|
|
| 609 |
|
|
|
| 610 |
|
|
// place the molecules at each FCC site |
| 611 |
|
|
|
| 612 |
|
|
cell = 5.0; |
| 613 |
|
|
for(i=0; i<bsInfo.nComponents; i++){ |
| 614 |
|
|
if(cell < locate[i]->getMaxLength() ) cell = locate[i]->getMaxLength(); |
| 615 |
|
|
} |
| 616 |
|
|
cell *= 1.2; // add a little buffer |
| 617 |
|
|
|
| 618 |
|
|
cell *= M_SQRT2; |
| 619 |
|
|
|
| 620 |
|
|
siteIndex = 0; |
| 621 |
|
|
for(i=0; i<nCells; i++){ |
| 622 |
|
|
for(j=0; j<nCells; j++){ |
| 623 |
|
|
for(k=0; k<nCells; k++){ |
| 624 |
|
|
|
| 625 |
|
|
if( molMap[siteIndex] >= 0 ){ |
| 626 |
|
|
pos[0] = i * cell; |
| 627 |
|
|
pos[1] = j * cell; |
| 628 |
|
|
pos[2] = k * cell; |
| 629 |
|
|
|
| 630 |
|
|
getRandomRot( rot ); |
| 631 |
|
|
molID = molSeq[molMap[siteIndex]]; |
| 632 |
|
|
atomIndex = molStart[ molMap[siteIndex] ]; |
| 633 |
|
|
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 634 |
|
|
} |
| 635 |
|
|
siteIndex++; |
| 636 |
|
|
|
| 637 |
|
|
if( molMap[siteIndex] >= 0 ){ |
| 638 |
|
|
pos[0] = i * cell + (0.5 * cell); |
| 639 |
|
|
pos[1] = j * cell; |
| 640 |
|
|
pos[2] = k * cell + (0.5 * cell); |
| 641 |
|
|
|
| 642 |
|
|
getRandomRot( rot ); |
| 643 |
|
|
molID = molSeq[molMap[siteIndex]]; |
| 644 |
|
|
atomIndex = molStart[ molMap[siteIndex] ]; |
| 645 |
|
|
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 646 |
|
|
} |
| 647 |
|
|
siteIndex++; |
| 648 |
|
|
|
| 649 |
|
|
if( molMap[siteIndex] >= 0 ){ |
| 650 |
|
|
pos[0] = i * cell + (0.5 * cell); |
| 651 |
|
|
pos[1] = j * cell + (0.5 * cell); |
| 652 |
|
|
pos[2] = k * cell; |
| 653 |
|
|
|
| 654 |
|
|
getRandomRot( rot ); |
| 655 |
|
|
molID = molSeq[molMap[siteIndex]]; |
| 656 |
|
|
atomIndex = molStart[ molMap[siteIndex] ]; |
| 657 |
|
|
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 658 |
|
|
} |
| 659 |
|
|
siteIndex++; |
| 660 |
|
|
|
| 661 |
|
|
if( molMap[siteIndex] >= 0 ){ |
| 662 |
|
|
pos[0] = i * cell; |
| 663 |
|
|
pos[1] = j * cell + (0.5 * cell); |
| 664 |
|
|
pos[2] = k * cell + (0.5 * cell); |
| 665 |
|
|
|
| 666 |
|
|
getRandomRot( rot ); |
| 667 |
|
|
molID = molSeq[molMap[siteIndex]]; |
| 668 |
|
|
atomIndex = molStart[ molMap[siteIndex] ]; |
| 669 |
|
|
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 670 |
|
|
} |
| 671 |
|
|
siteIndex++; |
| 672 |
|
|
} |
| 673 |
|
|
} |
| 674 |
|
|
} |
| 675 |
|
|
|
| 676 |
|
|
// set up the SimInfo object |
| 677 |
|
|
|
| 678 |
|
|
bsInfo.boxX = nCells * cell; |
| 679 |
|
|
bsInfo.boxY = nCells * cell; |
| 680 |
|
|
bsInfo.boxZ = nCells * cell; |
| 681 |
|
|
|
| 682 |
|
|
double boxVector[3]; |
| 683 |
|
|
simnfo = new SimInfo(); |
| 684 |
|
|
simnfo->n_atoms = nAtoms; |
| 685 |
|
|
boxVector[0] = bsInfo.boxX; |
| 686 |
|
|
boxVector[1] = bsInfo.boxY; |
| 687 |
|
|
boxVector[2] = bsInfo.boxZ; |
| 688 |
|
|
simnfo->setBox( boxVector ); |
| 689 |
|
|
|
| 690 |
|
|
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
| 691 |
|
|
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
| 692 |
|
|
|
| 693 |
|
|
simnfo->atoms = atoms; |
| 694 |
|
|
|
| 695 |
|
|
// set up the writer and write out |
| 696 |
|
|
|
| 697 |
|
|
writer = new DumpWriter( simnfo ); |
| 698 |
|
|
writer->writeFinal(0.0); |
| 699 |
|
|
|
| 700 |
|
|
// clean up the memory |
| 701 |
|
|
|
| 702 |
|
|
if( molMap != NULL ) delete[] molMap; |
| 703 |
|
|
if( cardDeck != NULL ) delete[] cardDeck; |
| 704 |
|
|
if( locate != NULL ){ |
| 705 |
|
|
for(i=0; i<bsInfo.nComponents; i++){ |
| 706 |
|
|
delete locate[i]; |
| 707 |
|
|
} |
| 708 |
|
|
delete[] locate; |
| 709 |
|
|
} |
| 710 |
|
|
if( atoms != NULL ){ |
| 711 |
|
|
for(i=0; i<nAtoms; i++){ |
| 712 |
|
|
delete atoms[i]; |
| 713 |
|
|
} |
| 714 |
|
|
Atom::destroyArrays(); |
| 715 |
|
|
delete[] atoms; |
| 716 |
|
|
} |
| 717 |
|
|
if( molSeq != NULL ) delete[] molSeq; |
| 718 |
|
|
if( simnfo != NULL ) delete simnfo; |
| 719 |
|
|
if( writer != NULL ) delete writer; |
| 720 |
|
|
|
| 721 |
|
|
return 1; |
| 722 |
|
|
} |
| 723 |
|
|
|
| 724 |
|
|
|
| 725 |
|
|
void getRandomRot( double rot[3][3] ){ |
| 726 |
|
|
|
| 727 |
|
|
double theta, phi, psi; |
| 728 |
|
|
double cosTheta; |
| 729 |
|
|
|
| 730 |
|
|
// select random phi, psi, and cosTheta |
| 731 |
|
|
|
| 732 |
|
|
phi = 2.0 * M_PI * drand48(); |
| 733 |
|
|
psi = 2.0 * M_PI * drand48(); |
| 734 |
|
|
cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1 |
| 735 |
|
|
|
| 736 |
|
|
theta = acos( cosTheta ); |
| 737 |
|
|
|
| 738 |
|
|
rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 739 |
|
|
rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 740 |
|
|
rot[0][2] = sin(theta) * sin(psi); |
| 741 |
|
|
|
| 742 |
|
|
rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 743 |
|
|
rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 744 |
|
|
rot[1][2] = sin(theta) * cos(psi); |
| 745 |
|
|
|
| 746 |
|
|
rot[2][0] = sin(phi) * sin(theta); |
| 747 |
|
|
rot[2][1] = -cos(phi) * sin(theta); |
| 748 |
|
|
rot[2][2] = cos(theta); |
| 749 |
|
|
} |
| 750 |
|
|
|
| 751 |
|
|
|
| 752 |
|
|
|
| 753 |
|
|
void buildMap( double &x, double &y, double &z, |
| 754 |
|
|
double boxX, double boxY, double boxZ ){ |
| 755 |
|
|
|
| 756 |
|
|
if(x < 0) x -= boxX * (double)( (int)( (x / boxX) - 0.5 ) ); |
| 757 |
|
|
else x -= boxX * (double)( (int)( (x / boxX ) + 0.5)); |
| 758 |
|
|
|
| 759 |
|
|
if(y < 0) y -= boxY * (double)( (int)( (y / boxY) - 0.5 ) ); |
| 760 |
|
|
else y -= boxY * (double)( (int)( (y / boxY ) + 0.5)); |
| 761 |
|
|
|
| 762 |
|
|
if(z < 0) z -= boxZ * (double)( (int)( (z / boxZ) - 0.5 ) ); |
| 763 |
|
|
else z -= boxZ * (double)( (int)( (z / boxZ ) + 0.5)); |
| 764 |
|
|
} |
