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#include <iostream> |
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#include <vector> |
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#include <algorithm> |
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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 "sysBuild.hpp" |
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#include "bilayerSys.hpp" |
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#include "latticeBuilder.hpp" |
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class SortCond{ |
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public: |
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bool operator()(const pair<int, double>& p1, const pair<int, double>& p2){ |
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return p1.second < p2.second; |
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} |
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}; |
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|
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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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double boxX, double boxY, double boxZ ); |
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int buildRandomBilayer( void ); |
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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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Lattice myFCC( FCC_LATTICE_TYPE, waterCell ); |
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double *posX, *posY, *posZ; |
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double pos[3], posA[3], posB[3]; |
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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 i,j,k, l, m; |
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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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Atom** atoms; |
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SimInfo* simnfo; |
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SimState* theConfig; |
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DumpWriter* writer; |
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MoleculeStamp* lipidStamp; |
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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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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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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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waterLocate = new MoLocator( waterStamp ); |
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waterNatoms = waterStamp->getNAtoms(); |
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nAtoms = nLipids * lipidNatoms; |
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nAtoms = 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].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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theConfig = simnfo[0].getConfiguration(); |
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theConfig->createArrays( simnfo[0].n_atoms ); |
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atoms=simnfo[0].atoms; |
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atoms=simnfo[0].atoms; |
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// create the test box for initial water displacement |
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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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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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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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lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0, theConfig ); |
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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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for(i=0; ( (i<testWaters) && isActive[i] ); i++){ |
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for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){ |
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atoms[j]->getPos( pos ); |
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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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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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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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// find the best box size for the sim |
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int nCellsX, nCellsY, nCellsZ; |
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const double boxTargetX = 20; |
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const double boxTargetY = 20; |
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|
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nCellsX = (int)ceil(boxTargetX / waterCell); |
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nCellsY = (int)ceil(boxTargetY / waterCell); |
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|
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int testTot; |
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int done = 0; |
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ndx = 0; |
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nCellsZ = 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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nCellsZ++; |
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testTot = 4 * nCellsX * nCellsY * nCellsZ; |
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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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int newWaters = nCellsX * nCellsY * nCellsZ * 4; |
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delete[] waterX; |
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delete[] waterY; |
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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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> |
double box_x = waterCell * nCellsX; |
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double box_y = waterCell * nCellsY; |
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double box_z = waterCell * nCellsZ; |
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> |
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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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< |
|
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waterSites[ndx].pos[0] = i * waterCell; |
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< |
waterSites[ndx].pos[1] = j * waterCell; |
| 297 |
< |
waterSites[ndx].pos[2] = k * waterCell; |
| 298 |
< |
ndx++; |
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< |
|
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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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< |
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< |
waterSites[ndx].pos[0] = i * waterCell; |
| 288 |
< |
waterSites[ndx].pos[1] = j * waterCell + 0.5 * waterCell; |
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< |
waterSites[ndx].pos[2] = k * waterCell + 0.5 * waterCell; |
| 290 |
< |
ndx++; |
| 291 |
< |
|
| 292 |
< |
waterSites[ndx].pos[0] = i * waterCell + 0.5 * waterCell; |
| 293 |
< |
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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> |
for( i=0; i < nCellsX; i++ ){ |
| 292 |
> |
for( j=0; j < nCellsY; j++ ){ |
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> |
for( k=0; k < nCellsZ; 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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> |
waterSites[ndx].pos[0] = posX[l]; |
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> |
waterSites[ndx].pos[1] = posY[l]; |
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> |
waterSites[ndx].pos[2] = posZ[l]; |
| 300 |
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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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int reject; |
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int testDX, acceptedDX; |
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nAtoms = nLipids * lipidNatoms; |
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|
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simnfo[1].n_atoms = nAtoms; |
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simnfo[1].atoms=new Atom*[nAtoms]; |
| 318 |
+ |
|
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theConfig = simnfo[1].getConfiguration(); |
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theConfig->createArrays( simnfo[1].n_atoms ); |
| 321 |
+ |
|
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atoms=simnfo[1].atoms; |
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|
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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; |
| 328 |
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while( !done ){ |
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< |
|
| 329 |
> |
|
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lipidSites[i].pos[0] = drand48() * box_x; |
| 331 |
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lipidSites[i].pos[1] = drand48() * box_y; |
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lipidSites[i].pos[2] = drand48() * box_z; |
| 333 |
< |
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| 333 |
> |
|
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getRandomRot( lipidSites[i].rot ); |
| 335 |
< |
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| 335 |
> |
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| 336 |
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ndx = i * lipidNatoms; |
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| 338 |
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lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 339 |
< |
ndx ); |
| 340 |
< |
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| 339 |
> |
ndx, theConfig ); |
| 340 |
> |
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| 341 |
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reject = 0; |
| 342 |
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for( j=0; !reject && j<i; j++){ |
| 343 |
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for(k=0; !reject && k<lipidNatoms; k++){ |
| 344 |
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|
| 345 |
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acceptedDX = j*lipidNatoms + k; |
| 346 |
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for(l=0; !reject && l<lipidNatoms; l++){ |
| 347 |
< |
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| 347 |
> |
|
| 348 |
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testDX = ndx + l; |
| 349 |
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|
| 350 |
< |
dx = atoms[testDX]->getX() - atoms[acceptedDX]->getX(); |
| 351 |
< |
dy = atoms[testDX]->getY() - atoms[acceptedDX]->getY(); |
| 336 |
< |
dz = atoms[testDX]->getZ() - atoms[acceptedDX]->getZ(); |
| 350 |
> |
atoms[testDX]->getPos( posA ); |
| 351 |
> |
atoms[acceptedDX]->getPos( posB ); |
| 352 |
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|
| 353 |
+ |
dx = posA[0] - posB[0]; |
| 354 |
+ |
dy = posA[1] - posB[1]; |
| 355 |
+ |
dz = posA[2] - posB[2]; |
| 356 |
+ |
|
| 357 |
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buildMap( dx, dy, dz, box_x, box_y, box_z ); |
| 358 |
< |
|
| 358 |
> |
|
| 359 |
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dx2 = dx * dx; |
| 360 |
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dy2 = dy * dy; |
| 361 |
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dz2 = dz * dz; |
| 362 |
< |
|
| 362 |
> |
|
| 363 |
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dSqr = dx2 + dy2 + dz2; |
| 364 |
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if( dSqr < rCutSqr ) reject = 1; |
| 365 |
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} |
| 372 |
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} |
| 373 |
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else{ |
| 374 |
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done = 1; |
| 375 |
< |
std::cout << i << " has been accepted\n"; |
| 375 |
> |
std::cout << (i+1) << " has been accepted\n"; |
| 376 |
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} |
| 377 |
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} |
| 378 |
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} |
| 379 |
|
|
| 380 |
+ |
|
| 381 |
+ |
// zSort of the lipid positions |
| 382 |
+ |
|
| 383 |
+ |
|
| 384 |
+ |
vector< pair<int,double> >zSortArray; |
| 385 |
+ |
for(i=0;i<nLipids;i++) |
| 386 |
+ |
zSortArray.push_back( make_pair(i, lipidSites[i].pos[2]) ); |
| 387 |
+ |
|
| 388 |
+ |
sort(zSortArray.begin(),zSortArray.end(),SortCond()); |
| 389 |
+ |
|
| 390 |
+ |
ofstream outFile( "./zipper.bass", ios::app); |
| 391 |
+ |
|
| 392 |
+ |
for(i=0; i<nLipids; i++){ |
| 393 |
+ |
outFile << "zConstraint[" << i << "]{\n" |
| 394 |
+ |
<< " molIndex = " << zSortArray[i].first << ";\n" |
| 395 |
+ |
<< " zPos = "; |
| 396 |
+ |
|
| 397 |
+ |
if(i<32) outFile << "60.0;\n"; |
| 398 |
+ |
else outFile << "100.0;\n"; |
| 399 |
+ |
|
| 400 |
+ |
outFile << " kRatio = 0.5;\n" |
| 401 |
+ |
<< "}\n"; |
| 402 |
+ |
} |
| 403 |
+ |
|
| 404 |
+ |
outFile.close(); |
| 405 |
+ |
|
| 406 |
+ |
|
| 407 |
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// cut out the waters that overlap with the lipids. |
| 408 |
|
|
| 409 |
+ |
|
| 410 |
|
delete[] isActive; |
| 411 |
|
isActive = new int[newWaters]; |
| 412 |
|
for(i=0; i<newWaters; i++) isActive[i] = 1; |
| 416 |
|
for(i=0; ( (i<newWaters) && isActive[i] ); i++){ |
| 417 |
|
for(j=0; ( (j<nAtoms) && isActive[i] ); j++){ |
| 418 |
|
|
| 419 |
< |
dx = waterSites[i].pos[0] - atoms[j]->getX(); |
| 373 |
< |
dy = waterSites[i].pos[1] - atoms[j]->getY(); |
| 374 |
< |
dz = waterSites[i].pos[2] - atoms[j]->getZ(); |
| 419 |
> |
atoms[j]->getPos( pos ); |
| 420 |
|
|
| 421 |
+ |
dx = waterSites[i].pos[0] - pos[0]; |
| 422 |
+ |
dy = waterSites[i].pos[1] - pos[1]; |
| 423 |
+ |
dz = waterSites[i].pos[2] - pos[2]; |
| 424 |
+ |
|
| 425 |
|
buildMap( dx, dy, dz, box_x, box_y, box_z ); |
| 426 |
|
|
| 427 |
|
dx2 = dx * dx; |
| 428 |
|
dy2 = dy * dy; |
| 429 |
|
dz2 = dz * dz; |
| 430 |
< |
|
| 430 |
> |
|
| 431 |
|
dSqr = dx2 + dy2 + dz2; |
| 432 |
|
if( dSqr < rCutSqr ){ |
| 433 |
|
isActive[i] = 0; |
| 434 |
|
n_active--; |
| 435 |
+ |
|
| 436 |
+ |
|
| 437 |
|
} |
| 438 |
|
} |
| 439 |
|
} |
| 440 |
|
|
| 441 |
+ |
|
| 442 |
+ |
|
| 443 |
+ |
|
| 444 |
|
if( n_active < nWaters ){ |
| 445 |
< |
|
| 445 |
> |
|
| 446 |
|
sprintf( painCave.errMsg, |
| 447 |
|
"Too many waters were removed, edit code and try again.\n" ); |
| 448 |
< |
|
| 448 |
> |
|
| 449 |
|
painCave.isFatal = 1; |
| 450 |
|
simError(); |
| 451 |
|
} |
| 458 |
|
if( isActive[quickKill] ){ |
| 459 |
|
isActive[quickKill] = 0; |
| 460 |
|
n_active--; |
| 461 |
+ |
|
| 462 |
|
} |
| 463 |
|
} |
| 464 |
|
|
| 465 |
|
if( n_active != nWaters ){ |
| 466 |
< |
|
| 466 |
> |
|
| 467 |
|
sprintf( painCave.errMsg, |
| 468 |
|
"QuickKill didn't work right. n_active = %d, and nWaters = %d\n", |
| 469 |
|
n_active, nWaters ); |
| 473 |
|
|
| 474 |
|
// clean up our messes before building the final system. |
| 475 |
|
|
| 476 |
< |
for(i=0; i<nAtoms; i++){ |
| 477 |
< |
|
| 423 |
< |
delete atoms[i]; |
| 424 |
< |
} |
| 425 |
< |
Atom::destroyArrays(); |
| 426 |
< |
|
| 476 |
> |
simnfo[0].getConfiguration()->destroyArrays(); |
| 477 |
> |
simnfo[1].getConfiguration()->destroyArrays(); |
| 478 |
|
|
| 479 |
|
// create the real Atom arrays |
| 480 |
|
|
| 494 |
|
nAtoms += waterNatoms; |
| 495 |
|
} |
| 496 |
|
|
| 497 |
+ |
theConfig = simnfo[2].getConfiguration(); |
| 498 |
+ |
theConfig->createArrays( nAtoms ); |
| 499 |
+ |
simnfo[2].atoms = new Atom*[nAtoms]; |
| 500 |
+ |
atoms = simnfo[2].atoms; |
| 501 |
+ |
simnfo[2].n_atoms = nAtoms; |
| 502 |
|
|
| 447 |
– |
Atom::createArrays( nAtoms ); |
| 448 |
– |
atoms = new Atom*[nAtoms]; |
| 449 |
– |
|
| 450 |
– |
|
| 503 |
|
// initialize lipid positions |
| 504 |
|
|
| 505 |
|
molIndex = 0; |
| 506 |
|
for(i=0; i<nLipids; i++ ){ |
| 507 |
|
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 508 |
< |
molStart[molIndex] ); |
| 508 |
> |
molStart[molIndex], theConfig ); |
| 509 |
|
molIndex++; |
| 510 |
|
} |
| 511 |
|
|
| 512 |
|
// initialize the water positions |
| 513 |
|
|
| 514 |
|
for(i=0; i<newWaters; i++){ |
| 515 |
< |
|
| 515 |
> |
|
| 516 |
|
if( isActive[i] ){ |
| 517 |
< |
|
| 517 |
> |
|
| 518 |
|
getRandomRot( waterSites[i].rot ); |
| 519 |
|
waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms, |
| 520 |
< |
molStart[molIndex] ); |
| 520 |
> |
molStart[molIndex], theConfig ); |
| 521 |
|
molIndex++; |
| 522 |
|
} |
| 523 |
|
} |
| 524 |
|
|
| 525 |
|
// set up the SimInfo object |
| 526 |
|
|
| 527 |
+ |
double Hmat[3][3]; |
| 528 |
+ |
|
| 529 |
+ |
Hmat[0][0] = box_x; |
| 530 |
+ |
Hmat[0][1] = 0.0; |
| 531 |
+ |
Hmat[0][2] = 0.0; |
| 532 |
+ |
|
| 533 |
+ |
Hmat[1][0] = 0.0; |
| 534 |
+ |
Hmat[1][1] = box_y; |
| 535 |
+ |
Hmat[1][2] = 0.0; |
| 536 |
+ |
|
| 537 |
+ |
Hmat[2][0] = 0.0; |
| 538 |
+ |
Hmat[2][1] = 0.0; |
| 539 |
+ |
Hmat[2][2] = box_z; |
| 540 |
+ |
|
| 541 |
+ |
|
| 542 |
|
bsInfo.boxX = box_x; |
| 543 |
|
bsInfo.boxY = box_y; |
| 544 |
|
bsInfo.boxZ = box_z; |
| 545 |
|
|
| 546 |
< |
double boxVector[3]; |
| 480 |
< |
|
| 481 |
< |
boxVector[0] = bsInfo.boxX; |
| 482 |
< |
boxVector[1] = bsInfo.boxY; |
| 483 |
< |
boxVector[2] = bsInfo.boxZ; |
| 484 |
< |
simnfo->setBox( boxVector ); |
| 546 |
> |
simnfo[2].setBoxM( Hmat ); |
| 547 |
|
|
| 548 |
< |
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
| 549 |
< |
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
| 548 |
> |
sprintf( simnfo[2].sampleName, "%s.dump", bsInfo.outPrefix ); |
| 549 |
> |
sprintf( simnfo[2].finalName, "%s.init", bsInfo.outPrefix ); |
| 550 |
|
|
| 489 |
– |
simnfo->atoms = atoms; |
| 490 |
– |
|
| 551 |
|
// set up the writer and write out |
| 552 |
|
|
| 553 |
< |
writer = new DumpWriter( simnfo ); |
| 553 |
> |
writer = new DumpWriter( &simnfo[2] ); |
| 554 |
|
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++){ |
| 555 |
|
|
| 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 |
– |
|
| 556 |
|
// clean up the memory |
| 557 |
|
|
| 558 |
< |
if( molMap != NULL ) delete[] molMap; |
| 559 |
< |
if( cardDeck != NULL ) delete[] cardDeck; |
| 560 |
< |
if( locate != NULL ){ |
| 561 |
< |
for(i=0; i<bsInfo.nComponents; i++){ |
| 562 |
< |
delete locate[i]; |
| 563 |
< |
} |
| 564 |
< |
delete[] locate; |
| 565 |
< |
} |
| 566 |
< |
if( atoms != NULL ){ |
| 567 |
< |
for(i=0; i<nAtoms; i++){ |
| 568 |
< |
delete atoms[i]; |
| 569 |
< |
} |
| 570 |
< |
Atom::destroyArrays(); |
| 571 |
< |
delete[] atoms; |
| 572 |
< |
} |
| 573 |
< |
if( molSeq != NULL ) delete[] molSeq; |
| 574 |
< |
if( simnfo != NULL ) delete simnfo; |
| 575 |
< |
if( writer != NULL ) delete writer; |
| 558 |
> |
// if( molMap != NULL ) delete[] molMap; |
| 559 |
> |
// if( cardDeck != NULL ) delete[] cardDeck; |
| 560 |
> |
// if( locate != NULL ){ |
| 561 |
> |
// for(i=0; i<bsInfo.nComponents; i++){ |
| 562 |
> |
// delete locate[i]; |
| 563 |
> |
// } |
| 564 |
> |
// delete[] locate; |
| 565 |
> |
// } |
| 566 |
> |
// if( atoms != NULL ){ |
| 567 |
> |
// for(i=0; i<nAtoms; i++){ |
| 568 |
> |
// delete atoms[i]; |
| 569 |
> |
// } |
| 570 |
> |
// Atom::destroyArrays(); |
| 571 |
> |
// delete[] atoms; |
| 572 |
> |
// } |
| 573 |
> |
// if( molSeq != NULL ) delete[] molSeq; |
| 574 |
> |
// if( simnfo != NULL ) delete simnfo; |
| 575 |
> |
// if( writer != NULL ) delete writer; |
| 576 |
|
|
| 577 |
|
return 1; |
| 578 |
|
} |
| 579 |
|
|
| 724 |
– |
|
| 580 |
|
void getRandomRot( double rot[3][3] ){ |
| 581 |
|
|
| 582 |
|
double theta, phi, psi; |
| 606 |
|
|
| 607 |
|
|
| 608 |
|
void buildMap( double &x, double &y, double &z, |
| 609 |
< |
double boxX, double boxY, double boxZ ){ |
| 609 |
> |
double boxX, double boxY, double boxZ ){ |
| 610 |
|
|
| 611 |
|
if(x < 0) x -= boxX * (double)( (int)( (x / boxX) - 0.5 ) ); |
| 612 |
|
else x -= boxX * (double)( (int)( (x / boxX ) + 0.5)); |
