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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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#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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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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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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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 = 4.0; |
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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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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<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 /= 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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for( j=0; j < n_cellY; j++ ){ |
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for( k=0; k < n_cellZ; k++ ){ |
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waterX[index] = i * water_cell + x0; |
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waterY[index] = j * water_cell + y0; |
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waterZ[index] = k * water_cell + z0; |
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index++; |
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waterX[index] = i * water_cell + 0.5 * water_cell + x0; |
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waterY[index] = j * water_cell + 0.5 * water_cell + y0; |
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waterZ[index] = k * water_cell + z0; |
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index++; |
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waterX[index] = i * water_cell + x0; |
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waterY[index] = j * water_cell + 0.5 * water_cell + y0; |
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waterZ[index] = k * water_cell + 0.5 * water_cell + z0; |
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index++; |
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waterX[index] = i * water_cell + 0.5 * water_cell + x0; |
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waterY[index] = j * water_cell + y0; |
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waterZ[index] = k * water_cell + 0.5 * water_cell + z0; |
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index++; |
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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 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_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<lipidNAtoms) && isActive[i] ); j++){ |
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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_deleted++; |
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} |
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} |
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} |
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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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int test_diff; |
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int n_limit = n_z; |
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n_z = n_cellZ; |
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for( i=n_generated; i<=n_limit; i++ ){ |
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for( j=i; j<=n_limit; j++ ){ |
248 |
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for( k=j; k<=n_limit; k++ ){ |
249 |
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250 |
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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 ){ |
257 |
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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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mmeineke |
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int new_nAtoms = group_nAtoms + n_active; |
285 |
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Atom** new_atoms = new Atom*[new_nAtoms]; |
286 |
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287 |
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index = 0; |
288 |
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for(i=0; i<group_nAtoms; i++ ){ |
289 |
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290 |
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if( group_atoms[i]->isDirectional() ){ |
291 |
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dAtom = (DirectionalAtom *)group_atoms[i]; |
292 |
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293 |
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dAtomNew = new DirectionalAtom(); |
294 |
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dAtomNew->setSUx( dAtom->getSUx() ); |
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dAtomNew->setSUx( dAtom->getSUx() ); |
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dAtomNew->setSUx( dAtom->getSUx() ); |
297 |
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298 |
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dAtomNew->setA( rotMat ); |
299 |
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300 |
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new_atoms[index] = dAtomNew; |
301 |
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} |
302 |
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else{ |
303 |
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304 |
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new_atoms[index] = new GeneralAtom(); |
305 |
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} |
306 |
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307 |
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new_atoms[index]->setType( group_atoms[i]->getType() ); |
308 |
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309 |
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new_atoms[index]->setX( group_atoms[i]->getX() ); |
310 |
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new_atoms[index]->setY( group_atoms[i]->getY() ); |
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new_atoms[index]->setZ( group_atoms[i]->getZ() ); |
312 |
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313 |
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new_atoms[index]->set_vx( 0.0 ); |
314 |
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new_atoms[index]->set_vy( 0.0 ); |
315 |
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new_atoms[index]->set_vz( 0.0 ); |
316 |
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317 |
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index++; |
318 |
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} |
319 |
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320 |
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321 |
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322 |
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323 |
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for(i=0; i<n_water; i++){ |
324 |
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if(isActive[i]){ |
325 |
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326 |
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new_atoms[index] = new DirectionalAtom(); |
327 |
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new_atoms[index]->setType( "SSD" ); |
328 |
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329 |
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new_atoms[index]->setX( waterX[i] ); |
330 |
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new_atoms[index]->setY( waterY[i] ); |
331 |
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new_atoms[index]->setZ( waterZ[i] ); |
332 |
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333 |
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new_atoms[index]->set_vx( 0.0 ); |
334 |
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new_atoms[index]->set_vy( 0.0 ); |
335 |
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new_atoms[index]->set_vz( 0.0 ); |
336 |
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337 |
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dAtom = (DirectionalAtom *) new_atoms[index]; |
338 |
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339 |
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dAtom->setSUx( 0.0 ); |
340 |
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dAtom->setSUy( 0.0 ); |
341 |
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dAtom->setSUz( 1.0 ); |
342 |
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343 |
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dAtom->setA( rotMat ); |
344 |
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345 |
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index++; |
346 |
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} |
347 |
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} |
348 |
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349 |
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entry_plug->n_atoms = new_nAtoms; |
350 |
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entry_plug->atoms = new_atoms; |
351 |
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352 |
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entry_plug->box_x = box_x; |
353 |
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entry_plug->box_y = box_y; |
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entry_plug->box_z = box_z; |
355 |
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356 |
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DumpWriter* xyz_out = new DumpWriter( entry_plug ); |
357 |
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xyz_out->writeFinal(); |
358 |
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delete xyz_out; |
359 |
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360 |
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FILE* out_file; |
361 |
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362 |
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out_file = fopen( out_name, "w" ); |
363 |
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364 |
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fprintf(out_file, |
365 |
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"#include \"water.mdl\"\n" |
366 |
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"#include \"lipid.mdl\"\n" |
367 |
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"\n" |
368 |
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"nComponents = 2;\n" |
369 |
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"component{\n" |
370 |
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" type = \"theLipid\";\n" |
371 |
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" nMol = %d;\n" |
372 |
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"}\n" |
373 |
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"\n" |
374 |
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"component{\n" |
375 |
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" type = \"SSD_water\";\n" |
376 |
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" nMol = %d;\n" |
377 |
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"}\n" |
378 |
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"\n" |
379 |
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"initialConfig = \"%s\";\n" |
380 |
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"\n" |
381 |
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"boxX = %lf;\n" |
382 |
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"boxY = %lf;\n" |
383 |
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"boxZ = %lf;\n", |
384 |
|
|
n_lipids, n_active, entry_plug->finalName, |
385 |
|
|
box_x, box_y, box_z ); |
386 |
|
|
|
387 |
|
|
fclose( out_file ); |
388 |
|
|
|
389 |
|
|
return 0; |
390 |
|
|
} |
391 |
mmeineke |
29 |
|
392 |
|
|
|
393 |
|
|
void map( x, y, z, centerX, centerY, centerZ, boxX, boxY, boxZ ) |
394 |
|
|
double *x, *y, *z; |
395 |
|
|
double centerX, centerY, centerZ; |
396 |
|
|
double boxX, boxY, boxZ; |
397 |
|
|
{ |
398 |
|
|
|
399 |
|
|
*x -= centerX; |
400 |
|
|
*y -= centerY; |
401 |
|
|
*z -= centerZ; |
402 |
|
|
|
403 |
|
|
if(*x < 0) *x -= boxX * (double)( (int)( (*x / boxX) - 0.5 ) ); |
404 |
|
|
else *x -= boxX * (double)( (int)( (*x / boxX ) + 0.5)); |
405 |
|
|
|
406 |
|
|
if(*y < 0) *y -= boxY * (double)( (int)( (*y / boxY) - 0.5 ) ); |
407 |
|
|
else *y -= boxY * (double)( (int)( (*y / boxY ) + 0.5)); |
408 |
|
|
|
409 |
|
|
if(*z < 0) *z -= boxZ * (double)( (int)( (*z / boxZ) - 0.5 ) ); |
410 |
|
|
else *z -= boxZ * (double)( (int)( (*z / boxZ ) + 0.5)); |
411 |
|
|
} |