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#include <cstdlib> |
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#include <cstring> |
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#include <cstdio> |
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#include <cmath> |
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#include "SimSetup.hpp" |
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#include "SimInfo.hpp" |
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#include "ReadWrite.hpp" |
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void map( double *x, double *y, double *z, double centerX, double centerY, |
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double centerZ, double boxX, double boxY, double boxZ ); |
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char* program_name; |
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using namespace std; |
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const double water_vol = 4.0 / water_rho; // volume occupied by 4 waters |
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const double water_cell = 4.929; // fcc unit cell length |
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int n_lipidsX = 5; |
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int n_lipidsY = 10; |
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int n_lipids = n_lipidsX * n_lipidsY; |
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int n_lipids = 50; |
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double water_ratio = 25.0; // water to lipid ratio |
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int n_h2o_target = (int)( n_lipids * water_ratio + 0.5 ); |
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std::cerr << "n_lipids = " << n_lipids << "\n"; |
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lipidAtoms = entry_plug->atoms; |
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lipidNAtoms = entry_plug->n_atoms; |
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int group_nAtoms = n_lipids * lipidNAtoms; |
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Atom** group_atoms = new Atom*[group_nAtoms]; |
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DirectionalAtom* dAtom; |
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DirectionalAtom* dAtomNew; |
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double rotMat[3][3]; |
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rotMat[0][0] = 1.0; |
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rotMat[0][1] = 0.0; |
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rotMat[0][2] = 0.0; |
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rotMat[1][0] = 0.0; |
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rotMat[1][1] = 1.0; |
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rotMat[1][2] = 0.0; |
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rotMat[2][0] = 0.0; |
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rotMat[2][1] = 0.0; |
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rotMat[2][2] = 1.0; |
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int index =0; |
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for(i=0; i<n_lipids; i++ ){ |
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for(j=0; j<lipidNAtoms; j++){ |
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if( lipidAtoms[j]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)lipidAtoms[j]; |
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dAtomNew = new DirectionalAtom(); |
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dAtomNew->setSUx( dAtom->getSUx() ); |
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dAtomNew->setSUx( dAtom->getSUx() ); |
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dAtomNew->setSUx( dAtom->getSUx() ); |
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dAtomNew->setA( rotMat ); |
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group_atoms[index] = dAtomNew; |
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} |
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else{ |
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group_atoms[index] = new GeneralAtom(); |
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} |
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group_atoms[index]->setType( lipidAtoms[j]->getType() ); |
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index++; |
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} |
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} |
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// find the width, height, and length of the molecule |
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index = 0; |
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for(i=0; i<n_lipidsX; i++){ |
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for(j=0; j<n_lipidsY; j++){ |
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for(l=0; l<lipidNAtoms; l++){ |
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group_atoms[index]->setX( lipidAtoms[l]->getX() + |
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i*lipid_spaceing ); |
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group_atoms[index]->setY( lipidAtoms[l]->getY() + |
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j*lipid_spaceing ); |
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group_atoms[index]->setZ( lipidAtoms[l]->getZ() ); |
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index++; |
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} |
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} |
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} |
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double min_x, min_y, min_z; |
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double max_x, max_y, max_z; |
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double test_x, test_y, test_z; |
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max_x = min_x = group_atoms[0]->getX(); |
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max_y = min_y = group_atoms[0]->getY(); |
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max_z = min_z = group_atoms[0]->getZ(); |
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max_x = min_x = lipidAtoms[0]->getX(); |
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max_y = min_y = lipidAtoms[0]->getY(); |
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max_z = min_z = lipidAtoms[0]->getZ(); |
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for(i=0; i<group_nAtoms; i++){ |
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for(i=0; i<lipidNAtoms; i++){ |
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test_x = group_atoms[i]->getX(); |
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test_y = group_atoms[i]->getY(); |
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test_z = group_atoms[i]->getZ(); |
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test_x = lipidAtoms[i]->getX(); |
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test_y = lipidAtoms[i]->getY(); |
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test_z = lipidAtoms[i]->getZ(); |
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if( test_x < min_x ) min_x = test_x; |
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if( test_y < min_y ) min_y = test_y; |
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if( test_z > max_z ) max_z = test_z; |
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} |
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double box_x = max_x - min_x + 2*water_shell; |
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double box_y = max_y - min_y + 2*water_shell; |
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double box_z = max_z - min_z + 2*water_shell; |
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double ml2 = pow((max_x - min_x), 2 ) + pow((max_y - min_y), 2 ) |
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+ pow((max_x - min_x), 2 ); |
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double max_length = sqrt( ml2 ); |
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int n_cellX = (int)(box_x / water_cell + 0.5 ); |
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int n_cellY = (int)(box_y / water_cell + 0.5 ); |
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int n_cellZ = (int)(box_z / water_cell + 0.5 ); |
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// from this information, create the test box |
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double box_x; |
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double box_y; |
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double box_z; |
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box_x = box_y = box_z = max_length + water_cell * 4.0; // pad with 4 cells |
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int n_cellX = (int)(box_x / water_cell + 1.0 ); |
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int n_cellY = (int)(box_y / water_cell + 1.0 ); |
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int n_cellZ = (int)(box_z / water_cell + 1.0 ); |
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box_x = water_cell * n_cellX; |
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box_y = water_cell * n_cellY; |
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box_z = water_cell * n_cellZ; |
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double *waterY = new double[n_water]; |
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double *waterZ = new double[n_water]; |
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// find the center of the test lipid, and make it the center of our |
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// soon to be created water box. |
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double cx, cy, cz; |
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cx = 0.0; |
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cy = 0.0; |
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cz = 0.0; |
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for(i=0; i<group_nAtoms; i++){ |
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cx += group_atoms[i]->getX(); |
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cy += group_atoms[i]->getY(); |
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cz += group_atoms[i]->getZ(); |
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for(i=0; i<lipidNAtoms; i++){ |
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cx += lipidAtoms[i]->getX(); |
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cy += lipidAtoms[i]->getY(); |
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cz += lipidAtoms[i]->getZ(); |
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} |
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cx /= group_nAtoms; |
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cy /= group_nAtoms; |
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cz /= group_nAtoms; |
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cx /= lipidNAtoms; |
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cy /= lipidNAtoms; |
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cz /= lipidNAtoms; |
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double x0 = cx - ( box_x * 0.5 ); |
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double y0 = cy - ( box_y * 0.5 ); |
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double z0 = cz - ( box_z * 0.5 ); |
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// create an fcc lattice in the water box. |
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index = 0; |
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for( i=0; i < n_cellX; i++ ){ |
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} |
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} |
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// calculate the number of water's displaced by our molecule. |
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int *isActive = new int[n_water]; |
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for(i=0; i<n_water; i++) isActive[i] = 1; |
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int n_active = n_water; |
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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<n_water) && isActive[i] ); i++){ |
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for(j=0; ( (j<group_nAtoms) && isActive[i] ); j++){ |
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for(j=0; ( (j<lipidNAtoms) && isActive[i] ); j++){ |
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dx = waterX[i] - group_atoms[j]->getX(); |
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dy = waterY[i] - group_atoms[j]->getY(); |
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dz = waterZ[i] - group_atoms[j]->getZ(); |
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dx = waterX[i] - lipidAtoms[j]->getX(); |
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dy = waterY[i] - lipidAtoms[j]->getY(); |
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dz = waterZ[i] - lipidAtoms[j]->getZ(); |
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map( &dx, &dy, &dz, cx, cy, cz, box_x, box_y, box_z ); |
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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_active--; |
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n_deleted++; |
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} |
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} |
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} |
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std::cerr << "final n_waters = " << n_active << "\n"; |
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n_h2o_target += n_deleted * n_lipids; |
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// find a box size that best suits the number of waters we need. |
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int done = 0; |
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if( n_waters < n_h2o_target ){ |
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int n_generated = n_cellX; |
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int n_test, nx, ny, nz; |
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nx = n_cellX; |
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ny = n_cellY; |
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nz = n_cellZ; |
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while( n_test < n_h2o_target ){ |
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nz++; |
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n_test = 4 * nx * ny * nz; |
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} |
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int n_diff, goodX, goodY, goodZ; |
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n_diff = ntest - n_h2o_target; |
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goodX = nx; |
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goodY = ny; |
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goodZ = nz; |
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|
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int test_diff; |
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int n_limit = n_z; |
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n_z = n_cellZ; |
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|
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for( i=n_generated; i<=n_limit; i++ ){ |
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for( j=i; j<=n_limit; j++ ){ |
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for( k=j; k<=n_limit; k++ ){ |
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n_test = 4 * i * j * k; |
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if( n_test > n_h2o_target ){ |
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test_diff = n_test - n_h2o_target; |
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if( test_diff < n_diff ){ |
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n_diff = test_diff; |
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goodX = nx; |
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goodY = ny; |
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goodZ = nz; |
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} |
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} |
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} |
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} |
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} |
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n_cellX = goodX; |
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n_cellY = goodY; |
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n_cellZ = goodZ; |
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} |
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// we now have the best box size for the simulation. |
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int new_nAtoms = group_nAtoms + n_active; |
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Atom** new_atoms = new Atom*[new_nAtoms]; |
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return 0; |
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} |
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|
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void map( x, y, z, centerX, centerY, centerZ, boxX, boxY, boxZ ) |
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double *x, *y, *z; |
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double centerX, centerY, centerZ; |
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double boxX, boxY, boxZ; |
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{ |
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|
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*x -= centerX; |
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*y -= centerY; |
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*z -= centerZ; |
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|
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if(*x < 0) *x -= boxX * (double)( (int)( (*x / boxX) - 0.5 ) ); |
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else *x -= boxX * (double)( (int)( (*x / boxX ) + 0.5)); |
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|
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if(*y < 0) *y -= boxY * (double)( (int)( (*y / boxY) - 0.5 ) ); |
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else *y -= boxY * (double)( (int)( (*y / boxY ) + 0.5)); |
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|
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if(*z < 0) *z -= boxZ * (double)( (int)( (*z / boxZ) - 0.5 ) ); |
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else *z -= boxZ * (double)( (int)( (*z / boxZ ) + 0.5)); |
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} |