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#include <iostream> |
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#include <stdlib.h> |
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|
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#include "Atom.hpp" |
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#include "SRI.hpp" |
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#include "Integrator.hpp" |
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#include "SimInfo.hpp" |
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#include "Thermo.hpp" |
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#include "ReadWrite.hpp" |
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#include "ExtendedSystem.hpp" |
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|
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extern "C"{ |
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|
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void v_constrain_a_( double &dt, int &n_atoms, double* mass, |
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double* Rx, double* Ry, double* Rz, |
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double* Vx, double* Vy, double* Vz, |
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double* Fx, double* Fy, double* Fz, |
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int &n_constrained, double *constr_sqr, |
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int* constr_i, int* constr_j, |
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double &box_x, double &box_y, double &box_z ); |
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|
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void v_constrain_b_( double &dt, int &n_atoms, double* mass, |
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double* Rx, double* Ry, double* Rz, |
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double* Vx, double* Vy, double* Vz, |
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double* Fx, double* Fy, double* Fz, |
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double &Kinetic, |
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int &n_constrained, double *constr_sqr, |
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int* constr_i, int* constr_j, |
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double &box_x, double &box_y, double &box_z ); |
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} |
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|
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|
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Verlet::Verlet( SimInfo &info, ForceFields* the_ff, ExtendedSystem* the_es ){ |
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|
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// get what information we need from the SimInfo object |
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|
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entry_plug = &info; |
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myFF = the_ff; |
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myES = the_es; |
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|
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c_natoms = info.n_atoms; |
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c_atoms = info.atoms; |
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nMols = info.n_mol; |
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molecules = info.molecules; |
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c_is_constrained = 0; |
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c_box_x = info.box_x; |
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c_box_y = info.box_y; |
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c_box_z = info.box_z; |
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|
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// give a little love back to the SimInfo object |
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|
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if( info.the_integrator != NULL ) delete info.the_integrator; |
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info.the_integrator = this; |
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|
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// the rest are initialization issues |
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|
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is_first = 1; // let the integrate method know when the first call is |
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|
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// mass array setup |
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|
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c_mass = new double[c_natoms]; |
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|
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for(int i = 0; i < c_natoms; i++){ |
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c_mass[i] = c_atoms[i]->getMass(); |
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} |
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|
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// check for constraints |
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|
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Constraint *temp_con; |
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Constraint *dummy_plug; |
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temp_con = new Constraint[info.n_SRI]; |
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|
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c_n_constrained = 0; |
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int constrained = 0; |
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SRI** theArray; |
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for(int i = 0; i < nMols; i++){ |
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|
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theArray = (SRI**) molecules[i].getMyBonds(); |
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for(int j=0; j<molecules[i].getNBonds(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
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|
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if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
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c_n_constrained++; |
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constrained = 0; |
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} |
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} |
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|
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theArray = (SRI**) molecules[i].getMyBends(); |
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for(int j=0; j<molecules[i].getNBends(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
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|
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if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
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c_n_constrained++; |
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constrained = 0; |
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} |
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} |
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|
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theArray = (SRI**) molecules[i].getMyTorsions(); |
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for(int j=0; j<molecules[i].getNTorsions(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
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|
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if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[c_n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[c_n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[c_n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
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c_n_constrained++; |
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constrained = 0; |
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} |
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} |
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|
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|
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} |
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|
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if(c_n_constrained > 0){ |
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|
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c_is_constrained = 1; |
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c_constrained_i = new int[c_n_constrained]; |
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c_constrained_j = new int[c_n_constrained]; |
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c_constrained_dsqr = new double[c_n_constrained]; |
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|
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for( int i = 0; i < c_n_constrained; i++){ |
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|
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/* add 1 to the index for the fortran arrays. */ |
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|
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c_constrained_i[i] = temp_con[i].get_a() + 1; |
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c_constrained_j[i] = temp_con[i].get_b() + 1; |
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c_constrained_dsqr[i] = temp_con[i].get_dsqr(); |
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} |
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} |
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|
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delete[] temp_con; |
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} |
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|
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|
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Verlet::~Verlet(){ |
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|
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if( c_is_constrained ){ |
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|
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delete[] c_constrained_i; |
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delete[] c_constrained_j; |
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delete[] c_constrained_dsqr; |
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} |
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|
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delete[] c_mass; |
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c_mass = 0; |
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} |
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|
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|
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void Verlet::integrate( void ){ |
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|
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int i, j; /* loop counters */ |
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int calcPot; |
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|
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double kE; |
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|
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double *Rx = new double[c_natoms]; |
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double *Ry = new double[c_natoms]; |
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double *Rz = new double[c_natoms]; |
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|
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double *Vx = new double[c_natoms]; |
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double *Vy = new double[c_natoms]; |
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double *Vz = new double[c_natoms]; |
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|
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double *Fx = new double[c_natoms]; |
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double *Fy = new double[c_natoms]; |
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double *Fz = new double[c_natoms]; |
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|
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int time; |
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|
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double dt = entry_plug->dt; |
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double runTime = entry_plug->run_time; |
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double sampleTime = entry_plug->sampleTime; |
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double statusTime = entry_plug->statusTime; |
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double thermalTime = entry_plug->thermalTime; |
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|
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int n_loops = (int)( runTime / dt ); |
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int sample_n = (int)( sampleTime / dt ); |
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int status_n = (int)( statusTime / dt ); |
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int vel_n = (int)( thermalTime / dt ); |
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|
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Thermo *tStats = new Thermo( entry_plug ); |
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|
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StatWriter* e_out = new StatWriter( entry_plug ); |
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DumpWriter* dump_out = new DumpWriter( entry_plug ); |
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|
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// the first time integrate is called, the forces need to be initialized |
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|
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|
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myFF->doForces(1,0); |
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|
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if( entry_plug->setTemp ){ |
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tStats->velocitize(); |
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} |
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|
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dump_out->writeDump( 0.0 ); |
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|
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e_out->writeStat( 0.0 ); |
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|
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calcPot = 0; |
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|
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if( c_is_constrained ){ |
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for(i = 0; i < n_loops; i++){ |
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|
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// fill R, V, and F arrays and RATTLE in fortran |
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|
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for( j=0; j<c_natoms; j++ ){ |
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|
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Rx[j] = c_atoms[j]->getX(); |
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Ry[j] = c_atoms[j]->getY(); |
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Rz[j] = c_atoms[j]->getZ(); |
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|
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Vx[j] = c_atoms[j]->get_vx(); |
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Vy[j] = c_atoms[j]->get_vy(); |
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Vz[j] = c_atoms[j]->get_vz(); |
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|
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Fx[j] = c_atoms[j]->getFx(); |
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Fy[j] = c_atoms[j]->getFy(); |
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Fz[j] = c_atoms[j]->getFz(); |
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|
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} |
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|
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v_constrain_a_( dt, c_natoms, c_mass, Rx, Ry, Rz, Vx, Vy, Vz, |
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Fx, Fy, Fz, |
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c_n_constrained, c_constrained_dsqr, |
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c_constrained_i, c_constrained_j, |
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c_box_x, c_box_y, c_box_z ); |
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|
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for( j=0; j<c_natoms; j++ ){ |
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|
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c_atoms[j]->setX(Rx[j]); |
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c_atoms[j]->setY(Ry[j]); |
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c_atoms[j]->setZ(Rz[j]); |
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|
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c_atoms[j]->set_vx(Vx[j]); |
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c_atoms[j]->set_vy(Vy[j]); |
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c_atoms[j]->set_vz(Vz[j]); |
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} |
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|
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// calculate the forces |
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|
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myFF->doForces(calcPot,0); |
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|
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// finish the constrain move ( same as above. ) |
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|
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for( j=0; j<c_natoms; j++ ){ |
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|
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Rx[j] = c_atoms[j]->getX(); |
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Ry[j] = c_atoms[j]->getY(); |
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Rz[j] = c_atoms[j]->getZ(); |
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|
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Vx[j] = c_atoms[j]->get_vx(); |
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Vy[j] = c_atoms[j]->get_vy(); |
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Vz[j] = c_atoms[j]->get_vz(); |
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|
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Fx[j] = c_atoms[j]->getFx(); |
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Fy[j] = c_atoms[j]->getFy(); |
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Fz[j] = c_atoms[j]->getFz(); |
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} |
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|
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v_constrain_b_( dt, c_natoms, c_mass, Rx, Ry, Rz, Vx, Vy, Vz, |
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Fx, Fy, Fz, |
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kE, c_n_constrained, c_constrained_dsqr, |
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c_constrained_i, c_constrained_j, |
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c_box_x, c_box_y, c_box_z ); |
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|
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for( j=0; j<c_natoms; j++ ){ |
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|
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c_atoms[j]->setX(Rx[j]); |
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c_atoms[j]->setY(Ry[j]); |
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c_atoms[j]->setZ(Rz[j]); |
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|
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c_atoms[j]->set_vx(Vx[j]); |
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c_atoms[j]->set_vy(Vy[j]); |
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c_atoms[j]->set_vz(Vz[j]); |
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} |
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|
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time = i + 1; |
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|
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if( entry_plug->setTemp ){ |
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if( !(time % vel_n) ) tStats->velocitize(); |
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} |
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if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
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if( !((time+1) % status_n) ) calcPot = 1; |
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if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; } |
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} |
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} |
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else{ |
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for(i = 0; i < n_loops; i++){ |
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|
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move_a( dt ); |
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|
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// calculate the forces |
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|
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myFF->doForces(calcPot,0); |
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|
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// complete the verlet move |
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|
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move_b( dt ); |
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|
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time = i + 1; |
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|
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if( entry_plug->setTemp ){ |
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if( !(time % vel_n) ) tStats->velocitize(); |
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} |
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if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
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if( !((time+1) % status_n) ) calcPot = 1; |
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if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; } |
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} |
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} |
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|
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dump_out->writeFinal(); |
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|
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delete dump_out; |
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delete e_out; |
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|
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} |
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|
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|
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void Verlet::move_a(double dt){ |
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|
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const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
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|
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double qx, qy, qz; |
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double vx, vy, vz; |
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int ma; |
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double h_dt = 0.5 * dt; |
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double h_dt2 = h_dt * dt; |
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|
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for( ma = 0; ma < c_natoms; ma++){ |
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|
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qx = c_atoms[ma]->getX() + dt * c_atoms[ma]->get_vx() + |
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h_dt2 * c_atoms[ma]->getFx() * e_convert / c_atoms[ma]->getMass(); |
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qy = c_atoms[ma]->getY() + dt * c_atoms[ma]->get_vy() + |
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h_dt2 * c_atoms[ma]->getFy() * e_convert / c_atoms[ma]->getMass(); |
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qz = c_atoms[ma]->getZ() + dt * c_atoms[ma]->get_vz() + |
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h_dt2 * c_atoms[ma]->getFz() * e_convert / c_atoms[ma]->getMass(); |
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|
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vx = c_atoms[ma]->get_vx() + |
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h_dt * c_atoms[ma]->getFx() * e_convert / c_atoms[ma]->getMass(); |
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vy = c_atoms[ma]->get_vy() + |
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h_dt * c_atoms[ma]->getFy() * e_convert / c_atoms[ma]->getMass(); |
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vz = c_atoms[ma]->get_vz() + |
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h_dt * c_atoms[ma]->getFz() * e_convert / c_atoms[ma]->getMass(); |
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|
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c_atoms[ma]->setX(qx); |
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c_atoms[ma]->setY(qy); |
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c_atoms[ma]->setZ(qz); |
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|
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c_atoms[ma]->set_vx(vx); |
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c_atoms[ma]->set_vy(vy); |
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c_atoms[ma]->set_vz(vz); |
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} |
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} |
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|
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void Verlet::move_b( double dt ){ |
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|
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const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
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|
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double vx, vy, vz; |
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int mb; |
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double h_dt = 0.5 * dt; |
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|
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|
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for( mb = 0; mb < c_natoms; mb++){ |
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|
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vx = c_atoms[mb]->get_vx() + |
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h_dt * c_atoms[mb]->getFx() * e_convert / c_atoms[mb]->getMass(); |
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vy = c_atoms[mb]->get_vy() + |
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h_dt * c_atoms[mb]->getFy() * e_convert / c_atoms[mb]->getMass(); |
| 388 |
vz = c_atoms[mb]->get_vz() + |
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h_dt * c_atoms[mb]->getFz() * e_convert / c_atoms[mb]->getMass(); |
| 390 |
|
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c_atoms[mb]->set_vx(vx); |
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c_atoms[mb]->set_vy(vy); |
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c_atoms[mb]->set_vz(vz); |
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} |
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} |
