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mmeineke |
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#include <iostream> |
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#include <cstdlib> |
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#include <cstring> |
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#include <cstdio> |
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mmeineke |
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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 "Atom.hpp" |
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#include "Integrator.hpp" |
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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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mmeineke |
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void map( double &x, double &y, double &z, |
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double boxX, double boxY, double boxZ ); |
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mmeineke |
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mmeineke |
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void rotate( double &x, double &y, double &z, |
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double theta, double phi, double psi ); |
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char* program_name; |
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using namespace std; |
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int main(int argc,char* argv[]){ |
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int i, j, k, l; |
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unsigned int n_atoms, eo, xo; |
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char* in_name; |
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SimSetup* startMe; |
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SimInfo* entry_plug; |
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Thermo* tStats; |
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int lipidNAtoms; |
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Atom** lipidAtoms; |
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int tot_Natoms; |
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Atom** totAtoms; |
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const double water_rho = 0.0334; // number density per cubic angstrom |
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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_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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mmeineke |
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std::cerr << "n_lipids = " << n_lipids << "\n"; |
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double water_shell = 10.0; |
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double water_padding = 2.5; |
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double lipid_spaceing = 2.5; |
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srand48( 1337 ); // initialize the random number generator. |
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program_name = argv[0]; /*save the program name in case we need it*/ |
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if( argc < 3 ){ |
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cerr<< "Error, input and output bass files are needed to run.\n" |
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<< program_name << " <input.bass> <output.bass>\n"; |
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exit(8); |
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} |
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in_name = argv[1]; |
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char* out_name = argv[2]; |
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entry_plug = new SimInfo; |
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startMe = new SimSetup; |
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startMe->setSimInfo( entry_plug ); |
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startMe->parseFile( in_name ); |
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startMe->createSim(); |
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delete startMe; |
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lipidAtoms = entry_plug->atoms; |
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lipidNAtoms = entry_plug->n_atoms; |
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// find the width, height, and length of the molecule |
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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 = 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<lipidNAtoms; i++){ |
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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 < min_z ) min_z = test_z; |
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if( test_x > max_x ) max_x = test_x; |
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if( test_y > max_y ) max_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 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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// 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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int n_water = n_cellX * n_cellY * n_cellZ * 4; |
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double *waterX = new double[n_water]; |
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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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mmeineke |
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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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mmeineke |
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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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mmeineke |
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} |
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mmeineke |
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cx /= lipidNAtoms; |
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cy /= lipidNAtoms; |
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cz /= lipidNAtoms; |
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mmeineke |
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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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mmeineke |
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// create an fcc lattice in the water box. |
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mmeineke |
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mmeineke |
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int ndx = 0; |
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mmeineke |
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for( i=0; i < n_cellX; i++ ){ |
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for( j=0; j < n_cellY; j++ ){ |
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for( k=0; k < n_cellZ; k++ ){ |
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mmeineke |
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waterX[ndx] = i * water_cell + x0; |
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waterY[ndx] = j * water_cell + y0; |
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waterZ[ndx] = k * water_cell + z0; |
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ndx++; |
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mmeineke |
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mmeineke |
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waterX[ndx] = i * water_cell + 0.5 * water_cell + x0; |
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waterY[ndx] = j * water_cell + 0.5 * water_cell + y0; |
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waterZ[ndx] = k * water_cell + z0; |
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ndx++; |
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mmeineke |
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mmeineke |
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waterX[ndx] = i * water_cell + x0; |
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waterY[ndx] = j * water_cell + 0.5 * water_cell + y0; |
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waterZ[ndx] = k * water_cell + 0.5 * water_cell + z0; |
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ndx++; |
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mmeineke |
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mmeineke |
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waterX[ndx] = i * water_cell + 0.5 * water_cell + x0; |
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waterY[ndx] = j * water_cell + y0; |
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waterZ[ndx] = k * water_cell + 0.5 * water_cell + z0; |
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ndx++; |
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mmeineke |
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} |
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} |
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} |
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mmeineke |
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// calculate the number of water's displaced by our molecule. |
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mmeineke |
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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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mmeineke |
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int n_deleted = 0; |
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mmeineke |
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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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mmeineke |
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for(j=0; ( (j<lipidNAtoms) && isActive[i] ); j++){ |
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mmeineke |
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mmeineke |
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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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mmeineke |
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mmeineke |
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map( dx, dy, dz, box_x, box_y, box_z ); |
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mmeineke |
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mmeineke |
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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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mmeineke |
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n_deleted++; |
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mmeineke |
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} |
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} |
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} |
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mmeineke |
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mmeineke |
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n_h2o_target += n_deleted * n_lipids; |
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mmeineke |
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mmeineke |
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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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mmeineke |
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if( n_water < n_h2o_target ){ |
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mmeineke |
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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; |
229 |
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ny = n_cellY; |
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nz = n_cellZ; |
231 |
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232 |
mmeineke |
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n_test = 4 * nx * ny * nz; |
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mmeineke |
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while( n_test < n_h2o_target ){ |
235 |
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236 |
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nz++; |
237 |
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n_test = 4 * nx * ny * nz; |
238 |
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} |
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int n_diff, goodX, goodY, goodZ; |
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mmeineke |
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n_diff = n_test - n_h2o_target; |
243 |
mmeineke |
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goodX = nx; |
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goodY = ny; |
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goodZ = nz; |
246 |
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int test_diff; |
248 |
mmeineke |
32 |
int n_limit = nz; |
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nz = n_cellZ; |
250 |
mmeineke |
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for( i=n_generated; i<=n_limit; i++ ){ |
252 |
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for( j=i; j<=n_limit; j++ ){ |
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for( k=j; k<=n_limit; k++ ){ |
254 |
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255 |
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n_test = 4 * i * j * k; |
256 |
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if( n_test > n_h2o_target ){ |
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test_diff = n_test - n_h2o_target; |
260 |
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261 |
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if( test_diff < n_diff ){ |
262 |
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n_diff = test_diff; |
264 |
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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; |
274 |
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n_cellY = goodY; |
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n_cellZ = goodZ; |
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} |
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278 |
mmeineke |
32 |
// we now have the best box size for the simulation. Next we |
279 |
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// recreate the water box to the new specifications. |
280 |
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281 |
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n_water = n_cellX * n_cellY * n_cellZ * 4; |
282 |
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283 |
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delete[] waterX; |
284 |
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delete[] waterY; |
285 |
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delete[] waterZ; |
286 |
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287 |
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waterX = new double[n_water]; |
288 |
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waterY = new double[n_water]; |
289 |
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waterZ = new double[n_water]; |
290 |
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291 |
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box_x = water_cell * n_cellX; |
292 |
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box_y = water_cell * n_cellY; |
293 |
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box_z = water_cell * n_cellZ; |
294 |
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295 |
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x0 = 0.0; |
296 |
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y0 = 0.0; |
297 |
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z0 = 0.0; |
298 |
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299 |
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cx = ( box_x * 0.5 ); |
300 |
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cy = ( box_y * 0.5 ); |
301 |
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cz = ( box_z * 0.5 ); |
302 |
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303 |
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// create an fcc lattice in the water box. |
304 |
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305 |
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ndx = 0; |
306 |
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for( i=0; i < n_cellX; i++ ){ |
307 |
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for( j=0; j < n_cellY; j++ ){ |
308 |
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for( k=0; k < n_cellZ; k++ ){ |
309 |
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310 |
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waterX[ndx] = i * water_cell + x0; |
311 |
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waterY[ndx] = j * water_cell + y0; |
312 |
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waterZ[ndx] = k * water_cell + z0; |
313 |
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ndx++; |
314 |
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315 |
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waterX[ndx] = i * water_cell + 0.5 * water_cell + x0; |
316 |
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waterY[ndx] = j * water_cell + 0.5 * water_cell + y0; |
317 |
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waterZ[ndx] = k * water_cell + z0; |
318 |
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ndx++; |
319 |
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320 |
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waterX[ndx] = i * water_cell + x0; |
321 |
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waterY[ndx] = j * water_cell + 0.5 * water_cell + y0; |
322 |
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waterZ[ndx] = k * water_cell + 0.5 * water_cell + z0; |
323 |
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ndx++; |
324 |
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325 |
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waterX[ndx] = i * water_cell + 0.5 * water_cell + x0; |
326 |
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waterY[ndx] = j * water_cell + y0; |
327 |
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waterZ[ndx] = k * water_cell + 0.5 * water_cell + z0; |
328 |
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ndx++; |
329 |
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} |
330 |
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} |
331 |
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} |
332 |
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333 |
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// ************************************************************** |
334 |
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335 |
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336 |
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337 |
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// start a 3D RSA for the for the lipid placements |
338 |
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339 |
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srand48( 1337 ); |
340 |
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341 |
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int rsaNAtoms = n_lipids * lipidNAtoms; |
342 |
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Atom** rsaAtoms = new Atom*[rsaNAtoms]; |
343 |
mmeineke |
29 |
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344 |
mmeineke |
32 |
DirectionalAtom* dAtom; |
345 |
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DirectionalAtom* dAtomNew; |
346 |
mmeineke |
29 |
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347 |
mmeineke |
32 |
double rotMat[3][3]; |
348 |
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double unitRotMat[3][3]; |
349 |
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350 |
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unitRotMat[0][0] = 1.0; |
351 |
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unitRotMat[0][1] = 0.0; |
352 |
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unitRotMat[0][2] = 0.0; |
353 |
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unitRotMat[1][0] = 0.0; |
355 |
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unitRotMat[1][1] = 1.0; |
356 |
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unitRotMat[1][2] = 0.0; |
357 |
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358 |
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unitRotMat[2][0] = 0.0; |
359 |
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unitRotMat[2][1] = 0.0; |
360 |
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unitRotMat[2][2] = 1.0; |
361 |
mmeineke |
29 |
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362 |
mmeineke |
32 |
ndx = 0; |
363 |
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for(i=0; i<n_lipids; i++ ){ |
364 |
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for(j=0; j<lipidNAtoms; j++){ |
365 |
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366 |
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if( lipidAtoms[j]->isDirectional() ){ |
367 |
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dAtom = (DirectionalAtom *)lipidAtoms[j]; |
368 |
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369 |
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dAtomNew = new DirectionalAtom(); |
370 |
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dAtomNew->setSUx( dAtom->getSUx() ); |
371 |
|
|
dAtomNew->setSUx( dAtom->getSUx() ); |
372 |
|
|
dAtomNew->setSUx( dAtom->getSUx() ); |
373 |
|
|
|
374 |
|
|
dAtom->getA( rotMat ); |
375 |
|
|
dAtomNew->setA( rotMat ); |
376 |
|
|
|
377 |
|
|
rsaAtoms[ndx] = dAtomNew; |
378 |
|
|
} |
379 |
|
|
else{ |
380 |
|
|
|
381 |
|
|
rsaAtoms[ndx] = new GeneralAtom(); |
382 |
|
|
} |
383 |
|
|
|
384 |
|
|
rsaAtoms[ndx]->setType( lipidAtoms[j]->getType() ); |
385 |
|
|
|
386 |
|
|
ndx++; |
387 |
|
|
} |
388 |
|
|
} |
389 |
|
|
|
390 |
|
|
double testX, testY, testZ; |
391 |
|
|
double theta, phi, psi; |
392 |
|
|
double tempX, tempY, tempZ; |
393 |
|
|
int reject; |
394 |
|
|
int testDX, acceptedDX; |
395 |
|
|
|
396 |
|
|
rCutSqr = lipid_spaceing * lipid_spaceing; |
397 |
|
|
|
398 |
|
|
for(i=0; i<n_lipids; i++ ){ |
399 |
|
|
done = 0; |
400 |
|
|
while( !done ){ |
401 |
|
|
|
402 |
|
|
testX = drand48() * box_x; |
403 |
|
|
testY = drand48() * box_y; |
404 |
|
|
testZ = drand48() * box_z; |
405 |
|
|
|
406 |
|
|
theta = drand48() * 2.0 * M_PI; |
407 |
|
|
phi = drand48() * 2.0 * M_PI; |
408 |
|
|
psi = drand48() * 2.0 * M_PI; |
409 |
|
|
|
410 |
|
|
ndx = i * lipidNAtoms; |
411 |
|
|
for(j=0; j<lipidNAtoms; j++){ |
412 |
|
|
|
413 |
|
|
tempX = lipidAtoms[j]->getX(); |
414 |
|
|
tempY = lipidAtoms[j]->getY(); |
415 |
|
|
tempZ = lipidAtoms[j]->getZ(); |
416 |
mmeineke |
29 |
|
417 |
mmeineke |
32 |
rotate( tempX, tempY, tempZ, theta, phi, psi ); |
418 |
|
|
|
419 |
|
|
rsaAtoms[ndx + j]->setX( tempX + testX ); |
420 |
|
|
rsaAtoms[ndx + j]->setY( tempY + testY ); |
421 |
|
|
rsaAtoms[ndx + j]->setZ( tempZ + testZ ); |
422 |
|
|
} |
423 |
|
|
|
424 |
|
|
reject = 0; |
425 |
|
|
for( j=0; !reject && j<i; j++){ |
426 |
|
|
for(k=0; !reject && k<lipidNAtoms; k++){ |
427 |
|
|
|
428 |
|
|
acceptedDX = j*lipidNAtoms + k; |
429 |
|
|
for(l=0; !reject && l<lipidNAtoms; l++){ |
430 |
|
|
|
431 |
|
|
testDX = ndx + l; |
432 |
mmeineke |
29 |
|
433 |
mmeineke |
32 |
dx = rsaAtoms[testDX]->getX() - rsaAtoms[acceptedDX]->getX(); |
434 |
|
|
dy = rsaAtoms[testDX]->getY() - rsaAtoms[acceptedDX]->getY(); |
435 |
|
|
dz = rsaAtoms[testDX]->getZ() - rsaAtoms[acceptedDX]->getZ(); |
436 |
|
|
|
437 |
|
|
map( dx, dy, dz, box_x, box_y, box_z ); |
438 |
|
|
|
439 |
|
|
dx2 = dx * dx; |
440 |
|
|
dy2 = dy * dy; |
441 |
|
|
dz2 = dz * dz; |
442 |
|
|
|
443 |
|
|
dSqr = dx2 + dy2 + dz2; |
444 |
|
|
if( dSqr < rCutSqr ) reject = 1; |
445 |
|
|
} |
446 |
|
|
} |
447 |
|
|
} |
448 |
mmeineke |
29 |
|
449 |
mmeineke |
32 |
if( !reject ){ |
450 |
|
|
done = 1; |
451 |
|
|
std::cerr << i << " has been accepted\n"; |
452 |
|
|
} |
453 |
|
|
} |
454 |
|
|
} |
455 |
|
|
|
456 |
|
|
// cut out the waters that overlap with the lipids. |
457 |
|
|
|
458 |
|
|
delete[] isActive; |
459 |
|
|
isActive = new int[n_water]; |
460 |
|
|
for(i=0; i<n_water; i++) isActive[i] = 1; |
461 |
|
|
int n_active = n_water; |
462 |
|
|
rCutSqr = water_padding * water_padding; |
463 |
|
|
|
464 |
|
|
for(i=0; ( (i<n_water) && isActive[i] ); i++){ |
465 |
|
|
for(j=0; ( (j<rsaNAtoms) && isActive[i] ); j++){ |
466 |
mmeineke |
29 |
|
467 |
mmeineke |
32 |
dx = waterX[i] - rsaAtoms[j]->getX(); |
468 |
|
|
dy = waterY[i] - rsaAtoms[j]->getY(); |
469 |
|
|
dz = waterZ[i] - rsaAtoms[j]->getZ(); |
470 |
mmeineke |
29 |
|
471 |
mmeineke |
32 |
map( dx, dy, dz, box_x, box_y, box_z ); |
472 |
|
|
|
473 |
|
|
dx2 = dx * dx; |
474 |
|
|
dy2 = dy * dy; |
475 |
|
|
dz2 = dz * dz; |
476 |
|
|
|
477 |
|
|
dSqr = dx2 + dy2 + dz2; |
478 |
|
|
if( dSqr < rCutSqr ){ |
479 |
|
|
isActive[i] = 0; |
480 |
|
|
n_active--; |
481 |
|
|
} |
482 |
|
|
} |
483 |
|
|
} |
484 |
|
|
|
485 |
|
|
std::cerr << "final n_waters = " << n_active << "\n"; |
486 |
|
|
|
487 |
|
|
// place all of the waters and lipids into one new array |
488 |
|
|
|
489 |
|
|
int new_nAtoms = rsaNAtoms + n_active; |
490 |
mmeineke |
28 |
Atom** new_atoms = new Atom*[new_nAtoms]; |
491 |
|
|
|
492 |
mmeineke |
32 |
ndx = 0; |
493 |
|
|
for(i=0; i<rsaNAtoms; i++ ){ |
494 |
mmeineke |
28 |
|
495 |
mmeineke |
32 |
if( rsaAtoms[i]->isDirectional() ){ |
496 |
|
|
dAtom = (DirectionalAtom *)rsaAtoms[i]; |
497 |
mmeineke |
28 |
|
498 |
|
|
dAtomNew = new DirectionalAtom(); |
499 |
|
|
dAtomNew->setSUx( dAtom->getSUx() ); |
500 |
|
|
dAtomNew->setSUx( dAtom->getSUx() ); |
501 |
|
|
dAtomNew->setSUx( dAtom->getSUx() ); |
502 |
|
|
|
503 |
mmeineke |
32 |
dAtom->getA( rotMat ); |
504 |
mmeineke |
28 |
dAtomNew->setA( rotMat ); |
505 |
|
|
|
506 |
mmeineke |
32 |
new_atoms[ndx] = dAtomNew; |
507 |
mmeineke |
28 |
} |
508 |
|
|
else{ |
509 |
|
|
|
510 |
mmeineke |
32 |
new_atoms[ndx] = new GeneralAtom(); |
511 |
mmeineke |
28 |
} |
512 |
|
|
|
513 |
mmeineke |
32 |
new_atoms[ndx]->setType( rsaAtoms[i]->getType() ); |
514 |
mmeineke |
28 |
|
515 |
mmeineke |
32 |
new_atoms[ndx]->setX( rsaAtoms[i]->getX() ); |
516 |
|
|
new_atoms[ndx]->setY( rsaAtoms[i]->getY() ); |
517 |
|
|
new_atoms[ndx]->setZ( rsaAtoms[i]->getZ() ); |
518 |
mmeineke |
28 |
|
519 |
mmeineke |
32 |
new_atoms[ndx]->set_vx( 0.0 ); |
520 |
|
|
new_atoms[ndx]->set_vy( 0.0 ); |
521 |
|
|
new_atoms[ndx]->set_vz( 0.0 ); |
522 |
mmeineke |
28 |
|
523 |
mmeineke |
32 |
ndx++; |
524 |
mmeineke |
28 |
} |
525 |
|
|
|
526 |
|
|
for(i=0; i<n_water; i++){ |
527 |
|
|
if(isActive[i]){ |
528 |
|
|
|
529 |
mmeineke |
32 |
new_atoms[ndx] = new DirectionalAtom(); |
530 |
|
|
new_atoms[ndx]->setType( "SSD" ); |
531 |
mmeineke |
28 |
|
532 |
mmeineke |
32 |
new_atoms[ndx]->setX( waterX[i] ); |
533 |
|
|
new_atoms[ndx]->setY( waterY[i] ); |
534 |
|
|
new_atoms[ndx]->setZ( waterZ[i] ); |
535 |
mmeineke |
28 |
|
536 |
mmeineke |
32 |
new_atoms[ndx]->set_vx( 0.0 ); |
537 |
|
|
new_atoms[ndx]->set_vy( 0.0 ); |
538 |
|
|
new_atoms[ndx]->set_vz( 0.0 ); |
539 |
mmeineke |
28 |
|
540 |
mmeineke |
32 |
dAtom = (DirectionalAtom *) new_atoms[ndx]; |
541 |
mmeineke |
28 |
|
542 |
|
|
dAtom->setSUx( 0.0 ); |
543 |
|
|
dAtom->setSUy( 0.0 ); |
544 |
|
|
dAtom->setSUz( 1.0 ); |
545 |
|
|
|
546 |
mmeineke |
32 |
dAtom->setA( unitRotMat ); |
547 |
mmeineke |
28 |
|
548 |
mmeineke |
32 |
ndx++; |
549 |
mmeineke |
28 |
} |
550 |
|
|
} |
551 |
|
|
|
552 |
|
|
entry_plug->n_atoms = new_nAtoms; |
553 |
|
|
entry_plug->atoms = new_atoms; |
554 |
|
|
|
555 |
|
|
entry_plug->box_x = box_x; |
556 |
|
|
entry_plug->box_y = box_y; |
557 |
|
|
entry_plug->box_z = box_z; |
558 |
|
|
|
559 |
|
|
DumpWriter* xyz_out = new DumpWriter( entry_plug ); |
560 |
|
|
xyz_out->writeFinal(); |
561 |
|
|
delete xyz_out; |
562 |
|
|
|
563 |
|
|
FILE* out_file; |
564 |
|
|
|
565 |
|
|
out_file = fopen( out_name, "w" ); |
566 |
|
|
|
567 |
|
|
fprintf(out_file, |
568 |
|
|
"#include \"water.mdl\"\n" |
569 |
|
|
"#include \"lipid.mdl\"\n" |
570 |
|
|
"\n" |
571 |
|
|
"nComponents = 2;\n" |
572 |
|
|
"component{\n" |
573 |
|
|
" type = \"theLipid\";\n" |
574 |
|
|
" nMol = %d;\n" |
575 |
|
|
"}\n" |
576 |
|
|
"\n" |
577 |
|
|
"component{\n" |
578 |
|
|
" type = \"SSD_water\";\n" |
579 |
|
|
" nMol = %d;\n" |
580 |
|
|
"}\n" |
581 |
|
|
"\n" |
582 |
|
|
"initialConfig = \"%s\";\n" |
583 |
|
|
"\n" |
584 |
|
|
"boxX = %lf;\n" |
585 |
|
|
"boxY = %lf;\n" |
586 |
|
|
"boxZ = %lf;\n", |
587 |
|
|
n_lipids, n_active, entry_plug->finalName, |
588 |
|
|
box_x, box_y, box_z ); |
589 |
|
|
|
590 |
|
|
fclose( out_file ); |
591 |
|
|
|
592 |
|
|
return 0; |
593 |
|
|
} |
594 |
mmeineke |
29 |
|
595 |
|
|
|
596 |
mmeineke |
32 |
void map( double &x, double &y, double &z, |
597 |
|
|
double boxX, double boxY, double boxZ ){ |
598 |
|
|
|
599 |
|
|
if(x < 0) x -= boxX * (double)( (int)( (x / boxX) - 0.5 ) ); |
600 |
|
|
else x -= boxX * (double)( (int)( (x / boxX ) + 0.5)); |
601 |
mmeineke |
29 |
|
602 |
mmeineke |
32 |
if(y < 0) y -= boxY * (double)( (int)( (y / boxY) - 0.5 ) ); |
603 |
|
|
else y -= boxY * (double)( (int)( (y / boxY ) + 0.5)); |
604 |
|
|
|
605 |
|
|
if(z < 0) z -= boxZ * (double)( (int)( (z / boxZ) - 0.5 ) ); |
606 |
|
|
else z -= boxZ * (double)( (int)( (z / boxZ ) + 0.5)); |
607 |
|
|
} |
608 |
mmeineke |
29 |
|
609 |
|
|
|
610 |
mmeineke |
32 |
void rotate( double &x, double &y, double &z, |
611 |
|
|
double theta, double phi, double psi ){ |
612 |
|
|
|
613 |
|
|
double newX, newY, newZ; |
614 |
|
|
|
615 |
|
|
double A[3][3]; |
616 |
|
|
|
617 |
|
|
A[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
618 |
|
|
A[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
619 |
|
|
A[0][2] = sin(theta) * sin(psi); |
620 |
mmeineke |
29 |
|
621 |
mmeineke |
32 |
A[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
622 |
|
|
A[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
623 |
|
|
A[1][2] = sin(theta) * cos(psi); |
624 |
|
|
|
625 |
|
|
A[2][0] = sin(phi) * sin(theta); |
626 |
|
|
A[2][1] = -cos(phi) * sin(theta); |
627 |
|
|
A[2][2] = cos(theta); |
628 |
|
|
|
629 |
|
|
newX = (x * A[0][0]) + (y * A[0][1]) + (z * A[0][2]); |
630 |
|
|
newY = (x * A[1][0]) + (y * A[1][1]) + (z * A[1][2]); |
631 |
|
|
newZ = (x * A[2][0]) + (y * A[2][1]) + (z * A[2][2]); |
632 |
|
|
|
633 |
|
|
x = newX; |
634 |
|
|
y = newY; |
635 |
|
|
z = newZ; |
636 |
mmeineke |
29 |
} |