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#include <iostream> |
| 2 |
#include <stdlib.h> |
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|
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#include "Atom.hpp" |
| 5 |
#include "SRI.hpp" |
| 6 |
#include "Integrator.hpp" |
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#include "SimInfo.hpp" |
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#include "Thermo.hpp" |
| 9 |
#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, |
| 15 |
double* Rx, double* Ry, double* Rz, |
| 16 |
double* Vx, double* Vy, double* Vz, |
| 17 |
double* Fx, double* Fy, double* Fz, |
| 18 |
int &n_constrained, double *constr_sqr, |
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int* constr_i, int* constr_j, |
| 20 |
double &box_x, double &box_y, double &box_z ); |
| 21 |
|
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void v_constrain_b_( double &dt, int &n_atoms, double* mass, |
| 23 |
double* Rx, double* Ry, double* Rz, |
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double* Vx, double* Vy, double* Vz, |
| 25 |
double* Fx, double* Fy, double* Fz, |
| 26 |
double &Kinetic, |
| 27 |
int &n_constrained, double *constr_sqr, |
| 28 |
int* constr_i, int* constr_j, |
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double &box_x, double &box_y, double &box_z ); |
| 30 |
} |
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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, calcStress; |
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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 press[9]; |
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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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myFF->doForces(1,1); |
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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 (!strcasecmp( entry_plug->ensemble, "NPT")) { |
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calcStress = 1; |
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} else { |
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calcStress = 0; |
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} |
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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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|
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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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if (!strcasecmp( entry_plug->ensemble, "NVT")) |
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myES->NoseHooverNVT( dt / 2.0 , tStats->getKinetic() ); |
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|
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// calculate the forces |
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|
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myFF->doForces(calcPot,calcStress); |
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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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|
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v_constrain_b_( dt, c_natoms, c_mass, Rx, Ry, Rz, Vx, Vy, Vz, |
| 291 |
Fx, Fy, Fz, |
| 292 |
kE, c_n_constrained, c_constrained_dsqr, |
| 293 |
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++ ){ |
| 297 |
|
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c_atoms[j]->setX(Rx[j]); |
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c_atoms[j]->setY(Ry[j]); |
| 300 |
c_atoms[j]->setZ(Rz[j]); |
| 301 |
|
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c_atoms[j]->set_vx(Vx[j]); |
| 303 |
c_atoms[j]->set_vy(Vy[j]); |
| 304 |
c_atoms[j]->set_vz(Vz[j]); |
| 305 |
} |
| 306 |
|
| 307 |
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
| 308 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
| 309 |
|
| 310 |
if (!strcasecmp( entry_plug->ensemble, "NPT") ) { |
| 311 |
tStats->getPressureTensor(press); |
| 312 |
myES->NoseHooverAndersonNPT( dt, |
| 313 |
tStats->getKinetic(), |
| 314 |
press); |
| 315 |
} |
| 316 |
|
| 317 |
time = i + 1; |
| 318 |
|
| 319 |
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 ); |
| 323 |
|
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if( !((time+1) % status_n) ) { |
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calcPot = 1; |
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calcStress = 1; |
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} |
| 328 |
if( !(time % status_n) ){ |
| 329 |
e_out->writeStat( time * dt ); |
| 330 |
calcPot = 0; |
| 331 |
if (!strcasecmp(entry_plug->ensemble, "NPT")) calcStress = 1; |
| 332 |
else calcStress = 0; |
| 333 |
} |
| 334 |
} |
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} |
| 336 |
else{ |
| 337 |
for(i = 0; i < n_loops; i++){ |
| 338 |
|
| 339 |
|
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move_a( dt ); |
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|
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if (!strcasecmp( entry_plug->ensemble, "NVT")) |
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myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
| 344 |
|
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// calculate the forces |
| 346 |
|
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myFF->doForces(calcPot,calcStress); |
| 348 |
|
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// complete the verlet move |
| 350 |
|
| 351 |
move_b( dt ); |
| 352 |
|
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if (!strcasecmp( entry_plug->ensemble, "NVT")) |
| 354 |
myES->NoseHooverNVT( dt / 2.0 , tStats->getKinetic() ); |
| 355 |
|
| 356 |
if (!strcasecmp( entry_plug->ensemble, "NPT") ) { |
| 357 |
tStats->getPressureTensor(press); |
| 358 |
myES->NoseHooverAndersonNPT( dt, |
| 359 |
tStats->getKinetic(), |
| 360 |
press); |
| 361 |
} |
| 362 |
|
| 363 |
time = i + 1; |
| 364 |
|
| 365 |
if( entry_plug->setTemp ){ |
| 366 |
if( !(time % vel_n) ) tStats->velocitize(); |
| 367 |
} |
| 368 |
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
| 369 |
if( !((time+1) % status_n) ) { |
| 370 |
calcPot = 1; |
| 371 |
calcStress = 1; |
| 372 |
} |
| 373 |
if( !(time % status_n) ){ |
| 374 |
e_out->writeStat( time * dt ); |
| 375 |
calcPot = 0; |
| 376 |
if (!strcasecmp(entry_plug->ensemble, "NPT")) calcStress = 1; |
| 377 |
else calcStress = 0; |
| 378 |
} |
| 379 |
} |
| 380 |
} |
| 381 |
|
| 382 |
dump_out->writeFinal(); |
| 383 |
|
| 384 |
delete dump_out; |
| 385 |
delete e_out; |
| 386 |
|
| 387 |
} |
| 388 |
|
| 389 |
|
| 390 |
void Verlet::move_a(double dt){ |
| 391 |
|
| 392 |
const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
| 393 |
|
| 394 |
double qx, qy, qz; |
| 395 |
double vx, vy, vz; |
| 396 |
int ma; |
| 397 |
double h_dt = 0.5 * dt; |
| 398 |
double h_dt2 = h_dt * dt; |
| 399 |
|
| 400 |
for( ma = 0; ma < c_natoms; ma++){ |
| 401 |
|
| 402 |
qx = c_atoms[ma]->getX() + dt * c_atoms[ma]->get_vx() + |
| 403 |
h_dt2 * c_atoms[ma]->getFx() * e_convert / c_atoms[ma]->getMass(); |
| 404 |
qy = c_atoms[ma]->getY() + dt * c_atoms[ma]->get_vy() + |
| 405 |
h_dt2 * c_atoms[ma]->getFy() * e_convert / c_atoms[ma]->getMass(); |
| 406 |
qz = c_atoms[ma]->getZ() + dt * c_atoms[ma]->get_vz() + |
| 407 |
h_dt2 * c_atoms[ma]->getFz() * e_convert / c_atoms[ma]->getMass(); |
| 408 |
|
| 409 |
vx = c_atoms[ma]->get_vx() + |
| 410 |
h_dt * c_atoms[ma]->getFx() * e_convert / c_atoms[ma]->getMass(); |
| 411 |
vy = c_atoms[ma]->get_vy() + |
| 412 |
h_dt * c_atoms[ma]->getFy() * e_convert / c_atoms[ma]->getMass(); |
| 413 |
vz = c_atoms[ma]->get_vz() + |
| 414 |
h_dt * c_atoms[ma]->getFz() * e_convert / c_atoms[ma]->getMass(); |
| 415 |
|
| 416 |
c_atoms[ma]->setX(qx); |
| 417 |
c_atoms[ma]->setY(qy); |
| 418 |
c_atoms[ma]->setZ(qz); |
| 419 |
|
| 420 |
c_atoms[ma]->set_vx(vx); |
| 421 |
c_atoms[ma]->set_vy(vy); |
| 422 |
c_atoms[ma]->set_vz(vz); |
| 423 |
} |
| 424 |
} |
| 425 |
|
| 426 |
void Verlet::move_b( double dt ){ |
| 427 |
|
| 428 |
const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
| 429 |
|
| 430 |
double vx, vy, vz; |
| 431 |
int mb; |
| 432 |
double h_dt = 0.5 * dt; |
| 433 |
|
| 434 |
|
| 435 |
for( mb = 0; mb < c_natoms; mb++){ |
| 436 |
|
| 437 |
vx = c_atoms[mb]->get_vx() + |
| 438 |
h_dt * c_atoms[mb]->getFx() * e_convert / c_atoms[mb]->getMass(); |
| 439 |
vy = c_atoms[mb]->get_vy() + |
| 440 |
h_dt * c_atoms[mb]->getFy() * e_convert / c_atoms[mb]->getMass(); |
| 441 |
vz = c_atoms[mb]->get_vz() + |
| 442 |
h_dt * c_atoms[mb]->getFz() * e_convert / c_atoms[mb]->getMass(); |
| 443 |
|
| 444 |
c_atoms[mb]->set_vx(vx); |
| 445 |
c_atoms[mb]->set_vy(vy); |
| 446 |
c_atoms[mb]->set_vz(vz); |
| 447 |
} |
| 448 |
} |
