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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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|
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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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|
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|
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char* program_name; |
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using namespace std; |
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|
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int main(int argc,char* argv[]){ |
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|
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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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|
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int lipidNAtoms; |
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Atom** lipidAtoms; |
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|
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int tot_Natoms; |
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Atom** totAtoms; |
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|
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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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|
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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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|
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std::cerr << "n_lipids = " << n_lipids << "\n"; |
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|
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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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|
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srand48( 1337 ); // initialize the random number generator. |
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|
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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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|
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exit(8); |
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} |
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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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|
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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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|
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delete startMe; |
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|
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lipidAtoms = entry_plug->atoms; |
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lipidNAtoms = entry_plug->n_atoms; |
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|
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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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|
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double rotMat[3][3]; |
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double unitRotMat[3][3]; |
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|
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unitRotMat[0][0] = 1.0; |
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unitRotMat[0][1] = 0.0; |
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unitRotMat[0][2] = 0.0; |
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|
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unitRotMat[1][0] = 0.0; |
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unitRotMat[1][1] = 1.0; |
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unitRotMat[1][2] = 0.0; |
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|
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unitRotMat[2][0] = 0.0; |
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unitRotMat[2][1] = 0.0; |
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unitRotMat[2][2] = 1.0; |
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|
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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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|
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if( lipidAtoms[j]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)lipidAtoms[j]; |
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|
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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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|
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dAtom->getA( rotMat ); |
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dAtomNew->setA( rotMat ); |
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|
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group_atoms[index] = dAtomNew; |
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} |
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else{ |
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|
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group_atoms[index] = new GeneralAtom(); |
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} |
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|
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group_atoms[index]->setType( lipidAtoms[j]->getType() ); |
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|
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index++; |
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} |
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} |
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|
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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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|
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group_atoms[index]->setX( lipidAtoms[l]->getX() + |
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i*lipid_spaceing ); |
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|
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group_atoms[index]->setY( lipidAtoms[l]->getY() + |
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j*lipid_spaceing ); |
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|
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group_atoms[index]->setZ( lipidAtoms[l]->getZ() ); |
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|
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index++; |
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} |
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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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|
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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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|
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for(i=0; i<group_nAtoms; i++){ |
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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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int n_water = n_cellX * n_cellY * n_cellZ * 4; |
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|
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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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|
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double cx, cy, cz; |
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|
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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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} |
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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int n_active = n_water; |
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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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|
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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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|
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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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|
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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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|
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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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} |
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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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|
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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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|
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index = 0; |
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for(i=0; i<group_nAtoms; i++ ){ |
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|
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if( group_atoms[i]->isDirectional() ){ |
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dAtom = (DirectionalAtom *)group_atoms[i]; |
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|
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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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|
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dAtom->getA(rotMat); |
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dAtomNew->setA( rotMat ); |
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|
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new_atoms[index] = dAtomNew; |
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} |
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else{ |
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|
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new_atoms[index] = new GeneralAtom(); |
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} |
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|
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new_atoms[index]->setType( group_atoms[i]->getType() ); |
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|
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new_atoms[index]->setX( group_atoms[i]->getX() ); |
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new_atoms[index]->setY( group_atoms[i]->getY() ); |
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new_atoms[index]->setZ( group_atoms[i]->getZ() ); |
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|
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new_atoms[index]->set_vx( 0.0 ); |
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new_atoms[index]->set_vy( 0.0 ); |
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new_atoms[index]->set_vz( 0.0 ); |
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|
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index++; |
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} |
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|
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|
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|
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|
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for(i=0; i<n_water; i++){ |
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if(isActive[i]){ |
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|
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new_atoms[index] = new DirectionalAtom(); |
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new_atoms[index]->setType( "SSD" ); |
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|
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new_atoms[index]->setX( waterX[i] ); |
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new_atoms[index]->setY( waterY[i] ); |
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new_atoms[index]->setZ( waterZ[i] ); |
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|
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new_atoms[index]->set_vx( 0.0 ); |
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new_atoms[index]->set_vy( 0.0 ); |
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new_atoms[index]->set_vz( 0.0 ); |
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|
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dAtom = (DirectionalAtom *) new_atoms[index]; |
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|
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dAtom->setSUx( 0.0 ); |
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dAtom->setSUy( 0.0 ); |
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dAtom->setSUz( 1.0 ); |
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|
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dAtom->setA( unitRotMat ); |
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|
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index++; |
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} |
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} |
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|
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entry_plug->n_atoms = new_nAtoms; |
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entry_plug->atoms = new_atoms; |
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|
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entry_plug->box_x = box_x; |
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entry_plug->box_y = box_y; |
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entry_plug->box_z = box_z; |
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|
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DumpWriter* xyz_out = new DumpWriter( entry_plug ); |
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xyz_out->writeFinal(); |
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delete xyz_out; |
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|
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FILE* out_file; |
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|
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out_file = fopen( out_name, "w" ); |
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|
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fprintf(out_file, |
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"#include \"water.mdl\"\n" |
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"#include \"lipid.mdl\"\n" |
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"\n" |
| 337 |
"nComponents = 2;\n" |
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"component{\n" |
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" type = \"theLipid\";\n" |
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" nMol = %d;\n" |
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"}\n" |
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"\n" |
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"component{\n" |
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" type = \"SSD_water\";\n" |
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" nMol = %d;\n" |
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"}\n" |
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"\n" |
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"initialConfig = \"%s\";\n" |
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"\n" |
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"boxX = %lf;\n" |
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"boxY = %lf;\n" |
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"boxZ = %lf;\n", |
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n_lipids, n_active, entry_plug->finalName, |
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box_x, box_y, box_z ); |
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|
| 356 |
fclose( out_file ); |
| 357 |
|
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return 0; |
| 359 |
} |
