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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 "LRI.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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|
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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 ){ |
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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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|
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c_natoms = info.n_atoms; |
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c_atoms = info.atoms; |
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c_sr_interactions = info.sr_interactions; |
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longRange = info.longRange; |
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c_n_SRI = info.n_SRI; |
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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[c_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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|
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for(int i = 0; i < c_n_SRI; i++){ |
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|
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constrained = c_sr_interactions[i]->is_constrained(); |
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|
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if(constrained){ |
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|
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dummy_plug = c_sr_interactions[i]->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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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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|
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void Verlet::integrate_b( double time_length, double dt, |
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int n_bond_0, int n_bond_f, |
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int n_bend_0, int n_bend_f, |
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int n_torsion_0, int n_torsion_f, |
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bool do_bonds, bool do_bends, bool do_torsions, |
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bool do_LRI ){ |
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|
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// double percent_tolerance = 0.001; |
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// int max_iterations = 10000; |
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|
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int i, j; /* loop counters */ |
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double n_loops = time_length / dt; |
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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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if(is_first){ |
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is_first = 0; |
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|
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for(i = 0; i < c_natoms; i++){ |
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c_atoms[i]->zeroForces(); |
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} |
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|
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if( do_bonds ){ |
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for(i = n_bond_0; i <= n_bond_f; i++){ |
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c_sr_interactions[i]->calc_forces(); |
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} |
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} |
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|
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if( do_bends ){ |
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for(i = n_bend_0; i <= n_bend_f; i++){ |
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c_sr_interactions[i]->calc_forces(); |
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} |
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} |
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|
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if( do_torsions ){ |
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for(i = n_torsion_0; i <= n_torsion_f; i++){ |
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c_sr_interactions[i]->calc_forces(); |
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} |
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} |
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|
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if( do_LRI ) longRange->calc_forces(); |
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} |
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|
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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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for(j = 0; j < c_natoms; j++){ |
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c_atoms[j]->zeroForces(); |
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} |
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|
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|
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if( do_bonds ){ |
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for(i = n_bond_0; i <= n_bond_f; i++){ |
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c_sr_interactions[i]->calc_forces(); |
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} |
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} |
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|
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if( do_bends ){ |
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for(i = n_bend_0; i <= n_bend_f; i++){ |
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c_sr_interactions[i]->calc_forces(); |
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} |
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} |
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|
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if( do_torsions ){ |
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for(i = n_torsion_0; i <= n_torsion_f; i++){ |
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c_sr_interactions[i]->calc_forces(); |
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} |
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} |
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|
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if( do_LRI ) longRange->calc_forces(); |
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|
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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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} |
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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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|
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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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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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for(i = 0; i < c_natoms; i++){ |
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c_atoms[i]->zeroForces(); |
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} |
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|
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for(i = 0; i < c_n_SRI; i++){ |
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c_sr_interactions[i]->calc_forces(); |
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} |
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|
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longRange->calc_forces(); |
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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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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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for(j = 0; j < c_natoms; j++){ |
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c_atoms[j]->zeroForces(); |
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} |
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|
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for(j = 0; j < c_n_SRI; j++){ |
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c_sr_interactions[j]->calc_forces(); |
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} |
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|
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longRange->calc_forces(); |
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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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if( entry_plug->setTemp ){ |
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if( !(i % vel_n) ) tStats->velocitize(); |
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} |
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if( !(i % sample_n) ) dump_out->writeDump( i * dt ); |
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if( !(i % status_n) ) e_out->writeStat( i * dt ); |
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|
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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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for(j = 0; j < c_natoms; j++){ |
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c_atoms[j]->zeroForces(); |
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} |
| 362 |
|
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for(j = 0; j < c_n_SRI; j++){ |
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c_sr_interactions[j]->calc_forces(); |
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} |
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|
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longRange->calc_forces(); |
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|
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// complete the verlet move |
| 370 |
|
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move_b( dt ); |
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|
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if( entry_plug->setTemp ){ |
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if( !(i % vel_n) ) tStats->velocitize(); |
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} |
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if( !(i % sample_n) ) dump_out->writeDump( i * dt ); |
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if( !(i % status_n) ) e_out->writeStat( i * dt ); |
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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; |
| 384 |
delete e_out; |
| 385 |
|
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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 |
| 392 |
|
| 393 |
double qx, qy, qz; |
| 394 |
double vx, vy, vz; |
| 395 |
int ma; |
| 396 |
double h_dt = 0.5 * dt; |
| 397 |
double h_dt2 = h_dt * dt; |
| 398 |
|
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for( ma = 0; ma < c_natoms; ma++){ |
| 400 |
|
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qx = c_atoms[ma]->getX() + dt * c_atoms[ma]->get_vx() + |
| 402 |
h_dt2 * c_atoms[ma]->getFx() * e_convert / c_atoms[ma]->getMass(); |
| 403 |
qy = c_atoms[ma]->getY() + dt * c_atoms[ma]->get_vy() + |
| 404 |
h_dt2 * c_atoms[ma]->getFy() * e_convert / c_atoms[ma]->getMass(); |
| 405 |
qz = c_atoms[ma]->getZ() + dt * c_atoms[ma]->get_vz() + |
| 406 |
h_dt2 * c_atoms[ma]->getFz() * e_convert / c_atoms[ma]->getMass(); |
| 407 |
|
| 408 |
vx = c_atoms[ma]->get_vx() + |
| 409 |
h_dt * c_atoms[ma]->getFx() * e_convert / c_atoms[ma]->getMass(); |
| 410 |
vy = c_atoms[ma]->get_vy() + |
| 411 |
h_dt * c_atoms[ma]->getFy() * e_convert / c_atoms[ma]->getMass(); |
| 412 |
vz = c_atoms[ma]->get_vz() + |
| 413 |
h_dt * c_atoms[ma]->getFz() * e_convert / c_atoms[ma]->getMass(); |
| 414 |
|
| 415 |
c_atoms[ma]->setX(qx); |
| 416 |
c_atoms[ma]->setY(qy); |
| 417 |
c_atoms[ma]->setZ(qz); |
| 418 |
|
| 419 |
c_atoms[ma]->set_vx(vx); |
| 420 |
c_atoms[ma]->set_vy(vy); |
| 421 |
c_atoms[ma]->set_vz(vz); |
| 422 |
} |
| 423 |
} |
| 424 |
|
| 425 |
void Verlet::move_b( double dt ){ |
| 426 |
|
| 427 |
const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
| 428 |
|
| 429 |
double vx, vy, vz; |
| 430 |
double v_sqr; |
| 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 |
} |
