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mmeineke |
377 |
#include <iostream> |
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#include <cstdlib> |
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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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#include "ForceFields.hpp" |
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gezelter |
466 |
#include "ExtendedSystem.hpp" |
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mmeineke |
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#include "simError.h" |
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extern "C"{ |
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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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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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gezelter |
466 |
Symplectic::Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff, |
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ExtendedSystem* the_es ){ |
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mmeineke |
377 |
entry_plug = the_entry_plug; |
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myFF = the_ff; |
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myES = the_es; |
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mmeineke |
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isFirst = 1; |
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mmeineke |
423 |
molecules = entry_plug->molecules; |
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nMols = entry_plug->n_mol; |
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mmeineke |
377 |
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// give a little love back to the SimInfo object |
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if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator; |
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entry_plug->the_integrator = this; |
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// grab the masses |
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mass = new double[entry_plug->n_atoms]; |
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for(int i = 0; i < entry_plug->n_atoms; i++){ |
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mass[i] = entry_plug->atoms[i]->getMass(); |
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gezelter |
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} |
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mmeineke |
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// check for constraints |
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is_constrained = 0; |
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Constraint *temp_con; |
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Constraint *dummy_plug; |
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mmeineke |
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temp_con = new Constraint[entry_plug->n_SRI]; |
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mmeineke |
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n_constrained = 0; |
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int constrained = 0; |
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mmeineke |
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SRI** theArray; |
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for(int i = 0; i < nMols; i++){ |
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mmeineke |
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mmeineke |
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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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mmeineke |
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mmeineke |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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mmeineke |
428 |
temp_con[n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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mmeineke |
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mmeineke |
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n_constrained++; |
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mmeineke |
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constrained = 0; |
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} |
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} |
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mmeineke |
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mmeineke |
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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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mmeineke |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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mmeineke |
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temp_con[n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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mmeineke |
423 |
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mmeineke |
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n_constrained++; |
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mmeineke |
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constrained = 0; |
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} |
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mmeineke |
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} |
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mmeineke |
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mmeineke |
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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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mmeineke |
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constrained = theArray[j]->is_constrained(); |
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if(constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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mmeineke |
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temp_con[n_constrained].set_a( dummy_plug->get_a() ); |
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temp_con[n_constrained].set_b( dummy_plug->get_b() ); |
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temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() ); |
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mmeineke |
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mmeineke |
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n_constrained++; |
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mmeineke |
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constrained = 0; |
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} |
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} |
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mmeineke |
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} |
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if(n_constrained > 0){ |
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is_constrained = 1; |
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constrained_i = new int[n_constrained]; |
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constrained_j = new int[n_constrained]; |
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constrained_dsqr = new double[n_constrained]; |
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for( int i = 0; i < n_constrained; i++){ |
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/* add 1 to the index for the fortran arrays. */ |
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constrained_i[i] = temp_con[i].get_a() + 1; |
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constrained_j[i] = temp_con[i].get_b() + 1; |
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constrained_dsqr[i] = temp_con[i].get_dsqr(); |
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} |
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} |
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delete[] temp_con; |
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} |
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Symplectic::~Symplectic() { |
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if( n_constrained ){ |
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delete[] constrained_i; |
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delete[] constrained_j; |
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delete[] constrained_dsqr; |
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} |
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} |
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void Symplectic::integrate( void ){ |
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const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2 |
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int i, j; // loop counters |
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int nAtoms = entry_plug->n_atoms; // the number of atoms |
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double kE = 0.0; // the kinetic energy |
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double rot_kE; |
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double trans_kE; |
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int tl; // the time loop conter |
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double dt2; // half the dt |
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double vx, vy, vz; // the velocities |
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chuckv |
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double vx2, vy2, vz2; // the square of the velocities |
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mmeineke |
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double rx, ry, rz; // the postitions |
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double ji[3]; // the body frame angular momentum |
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double jx2, jy2, jz2; // the square of the angular momentums |
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double Tb[3]; // torque in the body frame |
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double angle; // the angle through which to rotate the rotation matrix |
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double A[3][3]; // the rotation matrix |
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gezelter |
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double press[9]; |
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mmeineke |
377 |
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int time; |
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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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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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gezelter |
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int calcPot, calcStress; |
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mmeineke |
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mmeineke |
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Thermo *tStats; |
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StatWriter* e_out; |
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DumpWriter* dump_out; |
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mmeineke |
377 |
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mmeineke |
469 |
tStats = new Thermo( entry_plug ); |
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e_out = new StatWriter( entry_plug ); |
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dump_out = new DumpWriter( entry_plug ); |
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mmeineke |
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Atom** atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
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dt2 = 0.5 * dt; |
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// initialize the forces the before the first step |
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gezelter |
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myFF->doForces(1,1); |
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mmeineke |
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if( entry_plug->setTemp ){ |
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tStats->velocitize(); |
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} |
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dump_out->writeDump( 0.0 ); |
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e_out->writeStat( 0.0 ); |
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calcPot = 0; |
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gezelter |
475 |
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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mmeineke |
377 |
if( n_constrained ){ |
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double *Rx = new double[nAtoms]; |
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double *Ry = new double[nAtoms]; |
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double *Rz = new double[nAtoms]; |
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double *Vx = new double[nAtoms]; |
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double *Vy = new double[nAtoms]; |
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double *Vz = new double[nAtoms]; |
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double *Fx = new double[nAtoms]; |
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double *Fy = new double[nAtoms]; |
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double *Fz = new double[nAtoms]; |
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for( tl=0; tl < n_loops; tl++ ){ |
238 |
gezelter |
475 |
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if (!strcasecmp( entry_plug->ensemble, "NVT")) |
240 |
gezelter |
477 |
myES->NoseHooverNVT( dt / 2.0 , tStats->getKinetic() ); |
241 |
mmeineke |
377 |
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for( j=0; j<nAtoms; j++ ){ |
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Rx[j] = atoms[j]->getX(); |
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Ry[j] = atoms[j]->getY(); |
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Rz[j] = atoms[j]->getZ(); |
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Vx[j] = atoms[j]->get_vx(); |
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Vy[j] = atoms[j]->get_vy(); |
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Vz[j] = atoms[j]->get_vz(); |
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Fx[j] = atoms[j]->getFx(); |
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Fy[j] = atoms[j]->getFy(); |
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Fz[j] = atoms[j]->getFz(); |
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} |
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v_constrain_a_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
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Fx, Fy, Fz, |
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n_constrained, constrained_dsqr, |
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constrained_i, constrained_j, |
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entry_plug->box_x, |
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entry_plug->box_y, |
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entry_plug->box_z ); |
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for( j=0; j<nAtoms; j++ ){ |
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atoms[j]->setX(Rx[j]); |
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atoms[j]->setY(Ry[j]); |
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atoms[j]->setZ(Rz[j]); |
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atoms[j]->set_vx(Vx[j]); |
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atoms[j]->set_vy(Vy[j]); |
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atoms[j]->set_vz(Vz[j]); |
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} |
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278 |
chuckv |
482 |
for( i=0; i<nAtoms; i++ ){ |
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if( atoms[i]->isDirectional() ){ |
280 |
mmeineke |
377 |
|
281 |
chuckv |
482 |
dAtom = (DirectionalAtom *)atoms[i]; |
282 |
mmeineke |
377 |
|
283 |
chuckv |
482 |
// get and convert the torque to body frame |
284 |
mmeineke |
377 |
|
285 |
chuckv |
482 |
Tb[0] = dAtom->getTx(); |
286 |
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Tb[1] = dAtom->getTy(); |
287 |
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Tb[2] = dAtom->getTz(); |
288 |
mmeineke |
377 |
|
289 |
chuckv |
482 |
dAtom->lab2Body( Tb ); |
290 |
mmeineke |
377 |
|
291 |
chuckv |
482 |
// get the angular momentum, and propagate a half step |
292 |
mmeineke |
377 |
|
293 |
chuckv |
482 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
294 |
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ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
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ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
296 |
mmeineke |
377 |
|
297 |
chuckv |
482 |
// get the atom's rotation matrix |
298 |
mmeineke |
377 |
|
299 |
chuckv |
482 |
A[0][0] = dAtom->getAxx(); |
300 |
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A[0][1] = dAtom->getAxy(); |
301 |
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A[0][2] = dAtom->getAxz(); |
302 |
mmeineke |
377 |
|
303 |
chuckv |
482 |
A[1][0] = dAtom->getAyx(); |
304 |
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A[1][1] = dAtom->getAyy(); |
305 |
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A[1][2] = dAtom->getAyz(); |
306 |
mmeineke |
377 |
|
307 |
chuckv |
482 |
A[2][0] = dAtom->getAzx(); |
308 |
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A[2][1] = dAtom->getAzy(); |
309 |
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A[2][2] = dAtom->getAzz(); |
310 |
mmeineke |
377 |
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311 |
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312 |
chuckv |
482 |
// use the angular velocities to propagate the rotation matrix a |
313 |
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// full time step |
314 |
mmeineke |
377 |
|
315 |
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316 |
chuckv |
482 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
317 |
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this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
318 |
mmeineke |
377 |
|
319 |
chuckv |
482 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
320 |
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this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
321 |
mmeineke |
377 |
|
322 |
chuckv |
482 |
angle = dt * ji[2] / dAtom->getIzz(); |
323 |
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this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
324 |
mmeineke |
377 |
|
325 |
chuckv |
482 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
326 |
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this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
327 |
mmeineke |
377 |
|
328 |
chuckv |
482 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
329 |
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this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
330 |
mmeineke |
377 |
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331 |
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332 |
chuckv |
482 |
dAtom->setA( A ); |
333 |
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dAtom->setJx( ji[0] ); |
334 |
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dAtom->setJy( ji[1] ); |
335 |
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dAtom->setJz( ji[2] ); |
336 |
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} |
337 |
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} |
338 |
mmeineke |
377 |
|
339 |
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// calculate the forces |
340 |
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|
341 |
gezelter |
468 |
myFF->doForces(calcPot, calcStress); |
342 |
mmeineke |
377 |
|
343 |
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// move b |
344 |
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345 |
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for( j=0; j<nAtoms; j++ ){ |
346 |
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347 |
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Rx[j] = atoms[j]->getX(); |
348 |
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Ry[j] = atoms[j]->getY(); |
349 |
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Rz[j] = atoms[j]->getZ(); |
350 |
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351 |
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Vx[j] = atoms[j]->get_vx(); |
352 |
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Vy[j] = atoms[j]->get_vy(); |
353 |
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Vz[j] = atoms[j]->get_vz(); |
354 |
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355 |
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Fx[j] = atoms[j]->getFx(); |
356 |
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Fy[j] = atoms[j]->getFy(); |
357 |
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Fz[j] = atoms[j]->getFz(); |
358 |
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} |
359 |
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360 |
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v_constrain_b_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, |
361 |
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Fx, Fy, Fz, |
362 |
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kE, n_constrained, constrained_dsqr, |
363 |
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constrained_i, constrained_j, |
364 |
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entry_plug->box_x, |
365 |
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entry_plug->box_y, |
366 |
|
|
entry_plug->box_z ); |
367 |
|
|
|
368 |
|
|
for( j=0; j<nAtoms; j++ ){ |
369 |
|
|
|
370 |
|
|
atoms[j]->setX(Rx[j]); |
371 |
|
|
atoms[j]->setY(Ry[j]); |
372 |
|
|
atoms[j]->setZ(Rz[j]); |
373 |
|
|
|
374 |
|
|
atoms[j]->set_vx(Vx[j]); |
375 |
|
|
atoms[j]->set_vy(Vy[j]); |
376 |
|
|
atoms[j]->set_vz(Vz[j]); |
377 |
|
|
} |
378 |
|
|
|
379 |
chuckv |
482 |
for( i=0; i< nAtoms; i++ ){ |
380 |
mmeineke |
377 |
|
381 |
chuckv |
482 |
if( atoms[i]->isDirectional() ){ |
382 |
mmeineke |
377 |
|
383 |
chuckv |
482 |
dAtom = (DirectionalAtom *)atoms[i]; |
384 |
mmeineke |
377 |
|
385 |
chuckv |
482 |
// get and convert the torque to body frame |
386 |
mmeineke |
377 |
|
387 |
chuckv |
482 |
Tb[0] = dAtom->getTx(); |
388 |
|
|
Tb[1] = dAtom->getTy(); |
389 |
|
|
Tb[2] = dAtom->getTz(); |
390 |
mmeineke |
377 |
|
391 |
chuckv |
482 |
dAtom->lab2Body( Tb ); |
392 |
mmeineke |
377 |
|
393 |
chuckv |
482 |
// get the angular momentum, and complete the angular momentum |
394 |
|
|
// half step |
395 |
mmeineke |
377 |
|
396 |
chuckv |
482 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
397 |
|
|
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
398 |
|
|
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
399 |
mmeineke |
377 |
|
400 |
chuckv |
482 |
dAtom->setJx( ji[0] ); |
401 |
|
|
dAtom->setJy( ji[1] ); |
402 |
|
|
dAtom->setJz( ji[2] ); |
403 |
|
|
} |
404 |
|
|
} |
405 |
mmeineke |
377 |
|
406 |
gezelter |
475 |
|
407 |
|
|
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
408 |
gezelter |
477 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
409 |
gezelter |
475 |
|
410 |
gezelter |
483 |
if (!strcasecmp( entry_plug->ensemble, "NPT") ) { |
411 |
|
|
tStats->getPressureTensor(press); |
412 |
gezelter |
475 |
myES->NoseHooverAndersonNPT( dt, |
413 |
|
|
tStats->getKinetic(), |
414 |
gezelter |
483 |
press); |
415 |
|
|
} |
416 |
gezelter |
475 |
|
417 |
mmeineke |
377 |
time = tl + 1; |
418 |
|
|
|
419 |
|
|
if( entry_plug->setTemp ){ |
420 |
|
|
if( !(time % vel_n) ) tStats->velocitize(); |
421 |
|
|
} |
422 |
|
|
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
423 |
gezelter |
468 |
if( !((time+1) % status_n) ) { |
424 |
|
|
calcPot = 1; |
425 |
gezelter |
475 |
// bitwise masking in case we need it for NPT |
426 |
|
|
calcStress = (!strcasecmp(entry_plug->ensemble,"NPT")) && 1; |
427 |
gezelter |
468 |
} |
428 |
|
|
if( !(time % status_n) ){ |
429 |
|
|
e_out->writeStat( time * dt ); |
430 |
|
|
calcPot = 0; |
431 |
gezelter |
475 |
// bitwise masking in case we need it for NPT |
432 |
|
|
calcStress = (!strcasecmp(entry_plug->ensemble,"NPT")) && 0; |
433 |
gezelter |
468 |
} |
434 |
mmeineke |
377 |
} |
435 |
|
|
} |
436 |
|
|
else{ |
437 |
|
|
|
438 |
|
|
for( tl=0; tl<n_loops; tl++ ){ |
439 |
|
|
|
440 |
|
|
kE = 0.0; |
441 |
|
|
rot_kE= 0.0; |
442 |
|
|
trans_kE = 0.0; |
443 |
gezelter |
475 |
|
444 |
|
|
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
445 |
gezelter |
477 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
446 |
mmeineke |
377 |
|
447 |
|
|
for( i=0; i<nAtoms; i++ ){ |
448 |
|
|
|
449 |
|
|
// velocity half step |
450 |
|
|
|
451 |
|
|
vx = atoms[i]->get_vx() + |
452 |
|
|
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
453 |
|
|
vy = atoms[i]->get_vy() + |
454 |
|
|
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
455 |
|
|
vz = atoms[i]->get_vz() + |
456 |
|
|
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
457 |
|
|
|
458 |
|
|
// position whole step |
459 |
|
|
|
460 |
|
|
rx = atoms[i]->getX() + dt * vx; |
461 |
|
|
ry = atoms[i]->getY() + dt * vy; |
462 |
|
|
rz = atoms[i]->getZ() + dt * vz; |
463 |
|
|
|
464 |
|
|
atoms[i]->setX( rx ); |
465 |
|
|
atoms[i]->setY( ry ); |
466 |
|
|
atoms[i]->setZ( rz ); |
467 |
|
|
|
468 |
|
|
atoms[i]->set_vx( vx ); |
469 |
|
|
atoms[i]->set_vy( vy ); |
470 |
|
|
atoms[i]->set_vz( vz ); |
471 |
|
|
|
472 |
chuckv |
482 |
if( atoms[i]->isDirectional() ){ |
473 |
mmeineke |
377 |
|
474 |
chuckv |
482 |
dAtom = (DirectionalAtom *)atoms[i]; |
475 |
mmeineke |
377 |
|
476 |
chuckv |
482 |
// get and convert the torque to body frame |
477 |
mmeineke |
377 |
|
478 |
chuckv |
482 |
Tb[0] = dAtom->getTx(); |
479 |
|
|
Tb[1] = dAtom->getTy(); |
480 |
|
|
Tb[2] = dAtom->getTz(); |
481 |
mmeineke |
377 |
|
482 |
chuckv |
482 |
dAtom->lab2Body( Tb ); |
483 |
mmeineke |
377 |
|
484 |
chuckv |
482 |
// get the angular momentum, and propagate a half step |
485 |
mmeineke |
377 |
|
486 |
chuckv |
482 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
487 |
|
|
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
488 |
|
|
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
489 |
mmeineke |
377 |
|
490 |
chuckv |
482 |
// get the atom's rotation matrix |
491 |
mmeineke |
377 |
|
492 |
chuckv |
482 |
A[0][0] = dAtom->getAxx(); |
493 |
|
|
A[0][1] = dAtom->getAxy(); |
494 |
|
|
A[0][2] = dAtom->getAxz(); |
495 |
mmeineke |
377 |
|
496 |
chuckv |
482 |
A[1][0] = dAtom->getAyx(); |
497 |
|
|
A[1][1] = dAtom->getAyy(); |
498 |
|
|
A[1][2] = dAtom->getAyz(); |
499 |
mmeineke |
377 |
|
500 |
chuckv |
482 |
A[2][0] = dAtom->getAzx(); |
501 |
|
|
A[2][1] = dAtom->getAzy(); |
502 |
|
|
A[2][2] = dAtom->getAzz(); |
503 |
mmeineke |
377 |
|
504 |
|
|
|
505 |
chuckv |
482 |
// use the angular velocities to propagate the rotation matrix a |
506 |
|
|
// full time step |
507 |
mmeineke |
377 |
|
508 |
|
|
|
509 |
chuckv |
482 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
510 |
|
|
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
511 |
mmeineke |
377 |
|
512 |
chuckv |
482 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
513 |
|
|
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
514 |
mmeineke |
377 |
|
515 |
chuckv |
482 |
angle = dt * ji[2] / dAtom->getIzz(); |
516 |
|
|
this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis |
517 |
mmeineke |
377 |
|
518 |
chuckv |
482 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
519 |
|
|
this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis |
520 |
mmeineke |
377 |
|
521 |
chuckv |
482 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
522 |
|
|
this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis |
523 |
mmeineke |
377 |
|
524 |
|
|
|
525 |
chuckv |
482 |
dAtom->setA( A ); |
526 |
|
|
dAtom->setJx( ji[0] ); |
527 |
|
|
dAtom->setJy( ji[1] ); |
528 |
|
|
dAtom->setJz( ji[2] ); |
529 |
|
|
} |
530 |
mmeineke |
377 |
} |
531 |
|
|
|
532 |
|
|
// calculate the forces |
533 |
|
|
|
534 |
gezelter |
468 |
myFF->doForces(calcPot,calcStress); |
535 |
mmeineke |
377 |
|
536 |
|
|
for( i=0; i< nAtoms; i++ ){ |
537 |
|
|
|
538 |
|
|
// complete the velocity half step |
539 |
|
|
|
540 |
|
|
vx = atoms[i]->get_vx() + |
541 |
|
|
( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert; |
542 |
|
|
vy = atoms[i]->get_vy() + |
543 |
|
|
( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert; |
544 |
|
|
vz = atoms[i]->get_vz() + |
545 |
|
|
( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert; |
546 |
|
|
|
547 |
|
|
atoms[i]->set_vx( vx ); |
548 |
|
|
atoms[i]->set_vy( vy ); |
549 |
|
|
atoms[i]->set_vz( vz ); |
550 |
|
|
|
551 |
chuckv |
482 |
vx2 = vx * vx; |
552 |
|
|
vy2 = vy * vy; |
553 |
|
|
vz2 = vz * vz; |
554 |
mmeineke |
377 |
|
555 |
chuckv |
482 |
if( atoms[i]->isDirectional() ){ |
556 |
mmeineke |
377 |
|
557 |
chuckv |
482 |
dAtom = (DirectionalAtom *)atoms[i]; |
558 |
mmeineke |
377 |
|
559 |
chuckv |
482 |
// get and convert the torque to body frame |
560 |
mmeineke |
377 |
|
561 |
chuckv |
482 |
Tb[0] = dAtom->getTx(); |
562 |
|
|
Tb[1] = dAtom->getTy(); |
563 |
|
|
Tb[2] = dAtom->getTz(); |
564 |
mmeineke |
377 |
|
565 |
chuckv |
482 |
dAtom->lab2Body( Tb ); |
566 |
mmeineke |
377 |
|
567 |
chuckv |
482 |
// get the angular momentum, and complete the angular momentum |
568 |
|
|
// half step |
569 |
mmeineke |
377 |
|
570 |
chuckv |
482 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert; |
571 |
|
|
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert; |
572 |
|
|
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert; |
573 |
mmeineke |
377 |
|
574 |
chuckv |
482 |
jx2 = ji[0] * ji[0]; |
575 |
|
|
jy2 = ji[1] * ji[1]; |
576 |
|
|
jz2 = ji[2] * ji[2]; |
577 |
mmeineke |
377 |
|
578 |
chuckv |
482 |
rot_kE += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) |
579 |
|
|
+ (jz2 / dAtom->getIzz()); |
580 |
mmeineke |
377 |
|
581 |
chuckv |
482 |
dAtom->setJx( ji[0] ); |
582 |
|
|
dAtom->setJy( ji[1] ); |
583 |
|
|
dAtom->setJz( ji[2] ); |
584 |
|
|
} |
585 |
mmeineke |
377 |
} |
586 |
gezelter |
475 |
|
587 |
|
|
if (!strcasecmp( entry_plug->ensemble, "NVT")) |
588 |
gezelter |
477 |
myES->NoseHooverNVT( dt / 2.0, tStats->getKinetic() ); |
589 |
gezelter |
475 |
|
590 |
gezelter |
483 |
if (!strcasecmp( entry_plug->ensemble, "NPT") ) { |
591 |
|
|
tStats->getPressureTensor(press); |
592 |
gezelter |
475 |
myES->NoseHooverAndersonNPT( dt, |
593 |
|
|
tStats->getKinetic(), |
594 |
gezelter |
483 |
press); |
595 |
|
|
} |
596 |
gezelter |
475 |
|
597 |
mmeineke |
377 |
time = tl + 1; |
598 |
|
|
|
599 |
|
|
if( entry_plug->setTemp ){ |
600 |
|
|
if( !(time % vel_n) ) tStats->velocitize(); |
601 |
|
|
} |
602 |
|
|
if( !(time % sample_n) ) dump_out->writeDump( time * dt ); |
603 |
gezelter |
468 |
if( !((time+1) % status_n) ) { |
604 |
|
|
calcPot = 1; |
605 |
gezelter |
475 |
// bitwise masking in case we need it for NPT |
606 |
|
|
calcStress = (!strcasecmp(entry_plug->ensemble,"NPT")) && 1; |
607 |
gezelter |
468 |
} |
608 |
|
|
if( !(time % status_n) ){ |
609 |
|
|
e_out->writeStat( time * dt ); |
610 |
|
|
calcPot = 0; |
611 |
gezelter |
475 |
// bitwise masking in case we need it for NPT |
612 |
|
|
calcStress = (!strcasecmp(entry_plug->ensemble,"NPT")) && 0; |
613 |
gezelter |
468 |
} |
614 |
mmeineke |
377 |
} |
615 |
|
|
} |
616 |
|
|
|
617 |
|
|
dump_out->writeFinal(); |
618 |
|
|
|
619 |
|
|
delete dump_out; |
620 |
|
|
delete e_out; |
621 |
|
|
} |
622 |
|
|
|
623 |
|
|
void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3], |
624 |
|
|
double A[3][3] ){ |
625 |
|
|
|
626 |
|
|
int i,j,k; |
627 |
|
|
double sinAngle; |
628 |
|
|
double cosAngle; |
629 |
|
|
double angleSqr; |
630 |
|
|
double angleSqrOver4; |
631 |
|
|
double top, bottom; |
632 |
|
|
double rot[3][3]; |
633 |
|
|
double tempA[3][3]; |
634 |
|
|
double tempJ[3]; |
635 |
|
|
|
636 |
|
|
// initialize the tempA |
637 |
|
|
|
638 |
|
|
for(i=0; i<3; i++){ |
639 |
|
|
for(j=0; j<3; j++){ |
640 |
mmeineke |
443 |
tempA[j][i] = A[i][j]; |
641 |
mmeineke |
377 |
} |
642 |
|
|
} |
643 |
|
|
|
644 |
|
|
// initialize the tempJ |
645 |
|
|
|
646 |
|
|
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
647 |
|
|
|
648 |
|
|
// initalize rot as a unit matrix |
649 |
|
|
|
650 |
|
|
rot[0][0] = 1.0; |
651 |
|
|
rot[0][1] = 0.0; |
652 |
|
|
rot[0][2] = 0.0; |
653 |
|
|
|
654 |
|
|
rot[1][0] = 0.0; |
655 |
|
|
rot[1][1] = 1.0; |
656 |
|
|
rot[1][2] = 0.0; |
657 |
|
|
|
658 |
|
|
rot[2][0] = 0.0; |
659 |
|
|
rot[2][1] = 0.0; |
660 |
|
|
rot[2][2] = 1.0; |
661 |
|
|
|
662 |
|
|
// use a small angle aproximation for sin and cosine |
663 |
|
|
|
664 |
|
|
angleSqr = angle * angle; |
665 |
|
|
angleSqrOver4 = angleSqr / 4.0; |
666 |
|
|
top = 1.0 - angleSqrOver4; |
667 |
|
|
bottom = 1.0 + angleSqrOver4; |
668 |
|
|
|
669 |
|
|
cosAngle = top / bottom; |
670 |
|
|
sinAngle = angle / bottom; |
671 |
|
|
|
672 |
|
|
rot[axes1][axes1] = cosAngle; |
673 |
|
|
rot[axes2][axes2] = cosAngle; |
674 |
|
|
|
675 |
|
|
rot[axes1][axes2] = sinAngle; |
676 |
|
|
rot[axes2][axes1] = -sinAngle; |
677 |
|
|
|
678 |
|
|
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
679 |
|
|
|
680 |
|
|
for(i=0; i<3; i++){ |
681 |
|
|
ji[i] = 0.0; |
682 |
|
|
for(k=0; k<3; k++){ |
683 |
|
|
ji[i] += rot[i][k] * tempJ[k]; |
684 |
|
|
} |
685 |
|
|
} |
686 |
|
|
|
687 |
|
|
// rotate the Rotation matrix acording to: |
688 |
|
|
// A[][] = A[][] * transpose(rot[][]) |
689 |
|
|
|
690 |
|
|
|
691 |
|
|
// NOte for as yet unknown reason, we are setting the performing the |
692 |
|
|
// calculation as: |
693 |
|
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
694 |
|
|
|
695 |
|
|
for(i=0; i<3; i++){ |
696 |
|
|
for(j=0; j<3; j++){ |
697 |
|
|
A[j][i] = 0.0; |
698 |
|
|
for(k=0; k<3; k++){ |
699 |
mmeineke |
443 |
A[j][i] += tempA[i][k] * rot[j][k]; |
700 |
mmeineke |
377 |
} |
701 |
|
|
} |
702 |
|
|
} |
703 |
|
|
} |