mdtools/md_code/Symplectic.cpp

#include <iostream>
#include <cstdlib>

#include "Integrator.hpp"
#include "Thermo.hpp"
#include "ReadWrite.hpp"
#include "ForceField.hpp"
#include "simError.h"

extern "C"{
  
  void v_constrain_a_( double &dt, int &n_atoms, double* mass, 
                       double* Rx, double* Ry, double* Rz, 
                       double* Vx, double* Vy, double* Vz, 
                       double* Fx, double* Fy, double* Fz, 
                       int &n_constrained, double *constr_sqr,
                       int* constr_i, int* constr_j, 
                       double &box_x, double &box_y, double &box_z );

  void v_constrain_b_( double &dt, int &n_atoms, double* mass, 
                       double* Rx, double* Ry, double* Rz, 
                       double* Vx, double* Vy, double* Vz, 
                       double* Fx, double* Fy, double* Fz, 
                       double &Kinetic, 
                       int &n_constrained, double *constr_sqr,
                       int* constr_i, int* constr_j, 
                       double &box_x, double &box_y, double &box_z );
}


Symplectic::Symplectic( SimInfo* the_entry_plug ){
  entry_plug = the_entry_plug;
  isFirst = 1;

  srInteractions = entry_plug->sr_interactions;
  nSRI           =           entry_plug->n_SRI;

  // give a little love back to the SimInfo object
  
  if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator;
  entry_plug->the_integrator = this;

  // grab the masses

  mass = new double[entry_plug->n_atoms];
  for(int i = 0; i < entry_plug->n_atoms; i++){
    mass[i] = entry_plug->atoms[i]->getMass();
  }

 
  // check for constraints

  is_constrained = 0;

  Constraint *temp_con;
  Constraint *dummy_plug;
  temp_con = new Constraint[nSRI];
  n_constrained = 0;
  int constrained = 0;
  
  for(int i = 0; i < nSRI; i++){
    
    constrained = srInteractions[i]->is_constrained();
    
    if(constrained){
      
      dummy_plug = srInteractions[i]->get_constraint();
      temp_con[n_constrained].set_a( dummy_plug->get_a() );
      temp_con[n_constrained].set_b( dummy_plug->get_b() );
      temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );

      n_constrained++;
      constrained = 0;
    }
  }

  if(n_constrained > 0){
    
    is_constrained = 1;
    constrained_i = new int[n_constrained];
    constrained_j = new int[n_constrained];
    constrained_dsqr = new double[n_constrained];
    
    for( int i = 0; i < n_constrained; i++){
      
      /* add 1 to the index for the fortran arrays. */

      constrained_i[i] = temp_con[i].get_a() + 1;
      constrained_j[i] = temp_con[i].get_b() + 1;
      constrained_dsqr[i] = temp_con[i].get_dsqr();
    }
  }
  
  delete[] temp_con;
}

Symplectic::~Symplectic() {
  
  if( n_constrained ){
    delete[] constrained_i;
    delete[] constrained_j;
    delete[] constrained_dsqr;
  }
  
}


void Symplectic::integrate( void ){

  const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2

  int i, j;                         // loop counters
  int nAtoms = entry_plug->n_atoms; // the number of atoms
  double kE = 0.0;                  // the kinetic energy  
  double rot_kE;
  double trans_kE;
  int tl;                        // the time loop conter
  double dt2;                       // half the dt

  double vx, vy, vz;    // the velocities
//  double vx2, vy2, vz2; // the square of the velocities
  double rx, ry, rz;    // the postitions
  
  double ji[3];   // the body frame angular momentum
  double jx2, jy2, jz2; // the square of the angular momentums
  double Tb[3];   // torque in the body frame
  double angle;   // the angle through which to rotate the rotation matrix
  double A[3][3]; // the rotation matrix

  int time;

  double dt          = entry_plug->dt;
  double runTime     = entry_plug->run_time;
  double sampleTime  = entry_plug->sampleTime;
  double statusTime  = entry_plug->statusTime;
  double thermalTime = entry_plug->thermalTime;

  int n_loops  = (int)( runTime / dt );
  int sample_n = (int)( sampleTime / dt );
  int status_n = (int)( statusTime / dt );
  int vel_n    = (int)( thermalTime / dt );

  ForceFields *ff = entry_plug->

  Thermo *tStats = new Thermo( entry_plug );

  StatWriter*  e_out    = new StatWriter( entry_plug );
  DumpWriter*  dump_out = new DumpWriter( entry_plug );

  Atom** atoms = entry_plug->atoms;
  DirectionalAtom* dAtom;
  dt2 = 0.5 * dt;

  // initialize the forces the before the first step

  
  for(i = 0; i < nAtoms; i++){
    atoms[i]->zeroForces();
  }
  
  for(i = 0; i < nSRI; i++){
    
    srInteractions[i]->calc_forces();
  }
  
  longRange->calc_forces();

  if( entry_plug->setTemp ){
    
    tStats->velocitize();
  }
  
  dump_out->writeDump( 0.0 );
  e_out->writeStat( 0.0 );

  if( n_constrained ){

    double *Rx = new double[nAtoms];
    double *Ry = new double[nAtoms];
    double *Rz = new double[nAtoms];
    
    double *Vx = new double[nAtoms];
    double *Vy = new double[nAtoms];
    double *Vz = new double[nAtoms];
    
    double *Fx = new double[nAtoms];
    double *Fy = new double[nAtoms];
    double *Fz = new double[nAtoms];
    

    for( tl=0; tl < n_loops; tl++ ){
      
      for( j=0; j<nAtoms; j++ ){

        Rx[j] = atoms[j]->getX();
        Ry[j] = atoms[j]->getY();
        Rz[j] = atoms[j]->getZ();

        Vx[j] = atoms[j]->get_vx();
        Vy[j] = atoms[j]->get_vy();
        Vz[j] = atoms[j]->get_vz();

        Fx[j] = atoms[j]->getFx();
        Fy[j] = atoms[j]->getFy();
        Fz[j] = atoms[j]->getFz();

      }
        
      v_constrain_a_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, 
                      Fx, Fy, Fz,
                      n_constrained, constrained_dsqr, 
                      constrained_i, constrained_j,
                      entry_plug->box_x, 
                      entry_plug->box_y, 
                      entry_plug->box_z );
      
      for( j=0; j<nAtoms; j++ ){

        atoms[j]->setX(Rx[j]);
        atoms[j]->setY(Ry[j]);
        atoms[j]->setZ(Rz[j]);
        
        atoms[j]->set_vx(Vx[j]);
        atoms[j]->set_vy(Vy[j]);
        atoms[j]->set_vz(Vz[j]);
      }


      for( i=0; i<nAtoms; i++ ){
        if( atoms[i]->isDirectional() ){
                  
          dAtom = (DirectionalAtom *)atoms[i];
          
          // get and convert the torque to body frame
          
          Tb[0] = dAtom->getTx();
          Tb[1] = dAtom->getTy();
          Tb[2] = dAtom->getTz();
          
          dAtom->lab2Body( Tb );
          
          // get the angular momentum, and propagate a half step
          
          ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
          ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
          ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
          
          // get the atom's rotation matrix
          
          A[0][0] = dAtom->getAxx();
          A[0][1] = dAtom->getAxy();
          A[0][2] = dAtom->getAxz();
          
          A[1][0] = dAtom->getAyx();
          A[1][1] = dAtom->getAyy();
          A[1][2] = dAtom->getAyz();
          
          A[2][0] = dAtom->getAzx();
          A[2][1] = dAtom->getAzy();
          A[2][2] = dAtom->getAzz();
          
          
          // use the angular velocities to propagate the rotation matrix a
          // full time step
          
          
          angle = dt2 * ji[0] / dAtom->getIxx();
          this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
          
          angle = dt2 * ji[1] / dAtom->getIyy();
          this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
          
          angle = dt * ji[2] / dAtom->getIzz();
          this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis
          
          angle = dt2 * ji[1] / dAtom->getIyy();
          this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
          
          angle = dt2 * ji[0] / dAtom->getIxx();
          this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
          
          
          dAtom->setA( A );
          dAtom->setJx( ji[0] );
          dAtom->setJy( ji[1] );
          dAtom->setJz( ji[2] );
        }
      }
      
      // calculate the forces
      
      for(j = 0; j < nAtoms; j++){
        atoms[j]->zeroForces();
      }
      
      for(j = 0; j < nSRI; j++){
        srInteractions[j]->calc_forces();
      }
      
      longRange->calc_forces();
      
      // move b

      for( j=0; j<nAtoms; j++ ){

        Rx[j] = atoms[j]->getX();
        Ry[j] = atoms[j]->getY();
        Rz[j] = atoms[j]->getZ();

        Vx[j] = atoms[j]->get_vx();
        Vy[j] = atoms[j]->get_vy();
        Vz[j] = atoms[j]->get_vz();

        Fx[j] = atoms[j]->getFx();
        Fy[j] = atoms[j]->getFy();
        Fz[j] = atoms[j]->getFz();
      }
        
      v_constrain_b_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz, 
                      Fx, Fy, Fz,
                      kE, n_constrained, constrained_dsqr, 
                      constrained_i, constrained_j,
                      entry_plug->box_x,
                      entry_plug->box_y, 
                      entry_plug->box_z );
      
      for( j=0; j<nAtoms; j++ ){

        atoms[j]->setX(Rx[j]);
        atoms[j]->setY(Ry[j]);
        atoms[j]->setZ(Rz[j]);

        atoms[j]->set_vx(Vx[j]);
        atoms[j]->set_vy(Vy[j]);
        atoms[j]->set_vz(Vz[j]);
      }
      
      for( i=0; i< nAtoms; i++ ){

        if( atoms[i]->isDirectional() ){

          dAtom = (DirectionalAtom *)atoms[i];
          
          // get and convert the torque to body frame
          
          Tb[0] = dAtom->getTx();
          Tb[1] = dAtom->getTy();
          Tb[2] = dAtom->getTz();
          
          dAtom->lab2Body( Tb );
          
          // get the angular momentum, and complete the angular momentum
          // half step
          
          ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
          ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
          ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
          
          dAtom->setJx( ji[0] );
          dAtom->setJy( ji[1] );
          dAtom->setJz( ji[2] );
        }
      }
     
      time = tl + 1;
      
      if( entry_plug->setTemp ){
        if( !(time % vel_n) ) tStats->velocitize();
      }
      if( !(time % sample_n) ) dump_out->writeDump( time * dt );
      if( !(time % status_n) ) e_out->writeStat( time * dt );
    }
  }
  else{

    for( tl=0; tl<n_loops; tl++ ){
      
      kE = 0.0;
      rot_kE= 0.0;
      trans_kE = 0.0;
      
      for( i=0; i<nAtoms; i++ ){
        
        // velocity half step
        
        vx = atoms[i]->get_vx() + 
          ( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert;
        vy = atoms[i]->get_vy() + 
          ( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert;
        vz = atoms[i]->get_vz() + 
          ( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert;
        
        // position whole step
        
        rx = atoms[i]->getX() + dt * vx;
        ry = atoms[i]->getY() + dt * vy;
        rz = atoms[i]->getZ() + dt * vz;
        
        atoms[i]->setX( rx );
        atoms[i]->setY( ry );
        atoms[i]->setZ( rz );
        
        atoms[i]->set_vx( vx );
        atoms[i]->set_vy( vy );
        atoms[i]->set_vz( vz );
        
        if( atoms[i]->isDirectional() ){

          dAtom = (DirectionalAtom *)atoms[i];
          
          // get and convert the torque to body frame
          
          Tb[0] = dAtom->getTx();
          Tb[1] = dAtom->getTy();
          Tb[2] = dAtom->getTz();
          
          dAtom->lab2Body( Tb );
          
          // get the angular momentum, and propagate a half step
          
          ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
          ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
          ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
          
          // get the atom's rotation matrix
          
          A[0][0] = dAtom->getAxx();
          A[0][1] = dAtom->getAxy();
          A[0][2] = dAtom->getAxz();
          
          A[1][0] = dAtom->getAyx();
          A[1][1] = dAtom->getAyy();
          A[1][2] = dAtom->getAyz();
          
          A[2][0] = dAtom->getAzx();
          A[2][1] = dAtom->getAzy();
          A[2][2] = dAtom->getAzz();
          
          
          // use the angular velocities to propagate the rotation matrix a
          // full time step
          
          
          angle = dt2 * ji[0] / dAtom->getIxx();
          this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
          
          angle = dt2 * ji[1] / dAtom->getIyy();
          this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
          
          angle = dt * ji[2] / dAtom->getIzz();
          this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis
          
          angle = dt2 * ji[1] / dAtom->getIyy();
          this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
          
          angle = dt2 * ji[0] / dAtom->getIxx();
          this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
          
          
          dAtom->setA( A );
          dAtom->setJx( ji[0] );
          dAtom->setJy( ji[1] );
          dAtom->setJz( ji[2] );
        }
      }
      
      // calculate the forces
      
      for(j = 0; j < nAtoms; j++){
        atoms[j]->zeroForces();
      }
      
      for(j = 0; j < nSRI; j++){
        srInteractions[j]->calc_forces();
      }
      
      longRange->calc_forces();
      
      for( i=0; i< nAtoms; i++ ){
        
        // complete the velocity half step
        
        vx = atoms[i]->get_vx() + 
          ( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert;
        vy = atoms[i]->get_vy() + 
          ( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert;
        vz = atoms[i]->get_vz() + 
          ( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert;
        
        atoms[i]->set_vx( vx );
        atoms[i]->set_vy( vy );
        atoms[i]->set_vz( vz );
        
//      vx2 = vx * vx;
//      vy2 = vy * vy;
//      vz2 = vz * vz;
        
        if( atoms[i]->isDirectional() ){

          dAtom = (DirectionalAtom *)atoms[i];
          
          // get and convert the torque to body frame
          
          Tb[0] = dAtom->getTx();
          Tb[1] = dAtom->getTy();
          Tb[2] = dAtom->getTz();
          
          dAtom->lab2Body( Tb );
          
          // get the angular momentum, and complete the angular momentum
          // half step
          
          ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
          ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
          ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
          
          jx2 = ji[0] * ji[0];
          jy2 = ji[1] * ji[1];
          jz2 = ji[2] * ji[2];
          
          rot_kE += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy()) 
            + (jz2 / dAtom->getIzz());
          
          dAtom->setJx( ji[0] );
          dAtom->setJy( ji[1] );
          dAtom->setJz( ji[2] );
        }
      }
      
      time = tl + 1;
      
      if( entry_plug->setTemp ){
        if( !(time % vel_n) ) tStats->velocitize();
      }
      if( !(time % sample_n) ) dump_out->writeDump( time * dt );
      if( !(time % status_n) ) e_out->writeStat( time * dt );
    }
  }

  dump_out->writeFinal();

  delete dump_out;
  delete e_out;
}

void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3], 
                         double A[3][3] ){

  int i,j,k;
  double sinAngle;
  double cosAngle;
  double angleSqr;
  double angleSqrOver4;
  double top, bottom;
  double rot[3][3];
  double tempA[3][3];
  double tempJ[3];

  // initialize the tempA

  for(i=0; i<3; i++){
    for(j=0; j<3; j++){
      tempA[i][j] = A[i][j];
    }
  }

  // initialize the tempJ

  for( i=0; i<3; i++) tempJ[i] = ji[i];
  
  // initalize rot as a unit matrix

  rot[0][0] = 1.0;
  rot[0][1] = 0.0;
  rot[0][2] = 0.0;

  rot[1][0] = 0.0;
  rot[1][1] = 1.0;
  rot[1][2] = 0.0;
  
  rot[2][0] = 0.0;
  rot[2][1] = 0.0;
  rot[2][2] = 1.0;
  
  // use a small angle aproximation for sin and cosine

  angleSqr  = angle * angle;
  angleSqrOver4 = angleSqr / 4.0;
  top = 1.0 - angleSqrOver4;
  bottom = 1.0 + angleSqrOver4;

  cosAngle = top / bottom;
  sinAngle = angle / bottom;

  rot[axes1][axes1] = cosAngle;
  rot[axes2][axes2] = cosAngle;

  rot[axes1][axes2] = sinAngle;
  rot[axes2][axes1] = -sinAngle;
  
  // rotate the momentum acoording to: ji[] = rot[][] * ji[]
  
  for(i=0; i<3; i++){
    ji[i] = 0.0;
    for(k=0; k<3; k++){
      ji[i] += rot[i][k] * tempJ[k];
    }
  }

  // rotate the Rotation matrix acording to: 
  //            A[][] = A[][] * transpose(rot[][])


  // NOte for as yet unknown reason, we are setting the performing the
  // calculation as:
  //                transpose(A[][]) = transpose(A[][]) * transpose(rot[][])

  for(i=0; i<3; i++){
    for(j=0; j<3; j++){
      A[j][i] = 0.0;
      for(k=0; k<3; k++){
        A[j][i] += tempA[k][i] * rot[j][k];
      }
    }
  }
}
Revision:	238
Committed:	Fri Jan 17 21:53:36 2003 UTC (22 years, 9 months ago) by mmeineke
File size:	15062 byte(s)
Log Message:	* empty log message *
#	User	Rev	Content
1	mmeineke	10	#include <iostream>
2			#include <cstdlib>
3
4			#include "Integrator.hpp"
5			#include "Thermo.hpp"
6			#include "ReadWrite.hpp"
7	mmeineke	238	#include "ForceField.hpp"
8	mmeineke	184	#include "simError.h"
9	mmeineke	10
10			extern "C"{
11
12			void v_constrain_a_( double &dt, int &n_atoms, double* mass,
13			double* Rx, double* Ry, double* Rz,
14			double* Vx, double* Vy, double* Vz,
15			double* Fx, double* Fy, double* Fz,
16			int &n_constrained, double *constr_sqr,
17			int* constr_i, int* constr_j,
18			double &box_x, double &box_y, double &box_z );
19
20			void v_constrain_b_( double &dt, int &n_atoms, double* mass,
21			double* Rx, double* Ry, double* Rz,
22			double* Vx, double* Vy, double* Vz,
23			double* Fx, double* Fy, double* Fz,
24			double &Kinetic,
25			int &n_constrained, double *constr_sqr,
26			int* constr_i, int* constr_j,
27			double &box_x, double &box_y, double &box_z );
28			}
29
30
31
32
33			Symplectic::Symplectic( SimInfo* the_entry_plug ){
34			entry_plug = the_entry_plug;
35			isFirst = 1;
36
37			srInteractions = entry_plug->sr_interactions;
38			nSRI = entry_plug->n_SRI;
39
40			// give a little love back to the SimInfo object
41
42			if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator;
43			entry_plug->the_integrator = this;
44
45			// grab the masses
46
47			mass = new double[entry_plug->n_atoms];
48			for(int i = 0; i < entry_plug->n_atoms; i++){
49			mass[i] = entry_plug->atoms[i]->getMass();
50			}
51
52
53			// check for constraints
54
55			is_constrained = 0;
56
57			Constraint *temp_con;
58			Constraint *dummy_plug;
59			temp_con = new Constraint[nSRI];
60			n_constrained = 0;
61			int constrained = 0;
62
63			for(int i = 0; i < nSRI; i++){
64
65			constrained = srInteractions[i]->is_constrained();
66
67			if(constrained){
68
69			dummy_plug = srInteractions[i]->get_constraint();
70			temp_con[n_constrained].set_a( dummy_plug->get_a() );
71			temp_con[n_constrained].set_b( dummy_plug->get_b() );
72			temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
73
74			n_constrained++;
75			constrained = 0;
76			}
77			}
78
79			if(n_constrained > 0){
80
81			is_constrained = 1;
82			constrained_i = new int[n_constrained];
83			constrained_j = new int[n_constrained];
84			constrained_dsqr = new double[n_constrained];
85
86			for( int i = 0; i < n_constrained; i++){
87
88			/* add 1 to the index for the fortran arrays. */
89
90			constrained_i[i] = temp_con[i].get_a() + 1;
91			constrained_j[i] = temp_con[i].get_b() + 1;
92			constrained_dsqr[i] = temp_con[i].get_dsqr();
93			}
94			}
95
96			delete[] temp_con;
97			}
98
99			Symplectic::~Symplectic() {
100
101			if( n_constrained ){
102			delete[] constrained_i;
103			delete[] constrained_j;
104			delete[] constrained_dsqr;
105			}
106
107			}
108
109
110			void Symplectic::integrate( void ){
111
112			const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
113
114			int i, j; // loop counters
115			int nAtoms = entry_plug->n_atoms; // the number of atoms
116			double kE = 0.0; // the kinetic energy
117			double rot_kE;
118			double trans_kE;
119			int tl; // the time loop conter
120			double dt2; // half the dt
121
122			double vx, vy, vz; // the velocities
123	chuckv	134	// double vx2, vy2, vz2; // the square of the velocities
124	mmeineke	10	double rx, ry, rz; // the postitions
125
126			double ji[3]; // the body frame angular momentum
127			double jx2, jy2, jz2; // the square of the angular momentums
128			double Tb[3]; // torque in the body frame
129			double angle; // the angle through which to rotate the rotation matrix
130			double A[3][3]; // the rotation matrix
131
132	mmeineke	25	int time;
133	mmeineke	10
134			double dt = entry_plug->dt;
135			double runTime = entry_plug->run_time;
136			double sampleTime = entry_plug->sampleTime;
137			double statusTime = entry_plug->statusTime;
138			double thermalTime = entry_plug->thermalTime;
139
140			int n_loops = (int)( runTime / dt );
141			int sample_n = (int)( sampleTime / dt );
142			int status_n = (int)( statusTime / dt );
143			int vel_n = (int)( thermalTime / dt );
144
145	mmeineke	238	ForceFields *ff = entry_plug->
146
147	mmeineke	10	Thermo *tStats = new Thermo( entry_plug );
148
149			StatWriter* e_out = new StatWriter( entry_plug );
150			DumpWriter* dump_out = new DumpWriter( entry_plug );
151
152			Atom** atoms = entry_plug->atoms;
153			DirectionalAtom* dAtom;
154			dt2 = 0.5 * dt;
155
156			// initialize the forces the before the first step
157
158
159	mmeineke	238
160	mmeineke	10	for(i = 0; i < nAtoms; i++){
161			atoms[i]->zeroForces();
162			}
163
164			for(i = 0; i < nSRI; i++){
165
166			srInteractions[i]->calc_forces();
167			}
168
169			longRange->calc_forces();
170
171			if( entry_plug->setTemp ){
172
173			tStats->velocitize();
174			}
175
176	mmeineke	25	dump_out->writeDump( 0.0 );
177			e_out->writeStat( 0.0 );
178
179	mmeineke	10	if( n_constrained ){
180
181			double *Rx = new double[nAtoms];
182			double *Ry = new double[nAtoms];
183			double *Rz = new double[nAtoms];
184
185			double *Vx = new double[nAtoms];
186			double *Vy = new double[nAtoms];
187			double *Vz = new double[nAtoms];
188
189			double *Fx = new double[nAtoms];
190			double *Fy = new double[nAtoms];
191			double *Fz = new double[nAtoms];
192
193
194			for( tl=0; tl < n_loops; tl++ ){
195
196			for( j=0; j<nAtoms; j++ ){
197
198			Rx[j] = atoms[j]->getX();
199			Ry[j] = atoms[j]->getY();
200			Rz[j] = atoms[j]->getZ();
201
202			Vx[j] = atoms[j]->get_vx();
203			Vy[j] = atoms[j]->get_vy();
204			Vz[j] = atoms[j]->get_vz();
205
206			Fx[j] = atoms[j]->getFx();
207			Fy[j] = atoms[j]->getFy();
208			Fz[j] = atoms[j]->getFz();
209
210			}
211
212			v_constrain_a_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz,
213			Fx, Fy, Fz,
214			n_constrained, constrained_dsqr,
215			constrained_i, constrained_j,
216			entry_plug->box_x,
217			entry_plug->box_y,
218			entry_plug->box_z );
219
220			for( j=0; j<nAtoms; j++ ){
221
222			atoms[j]->setX(Rx[j]);
223			atoms[j]->setY(Ry[j]);
224			atoms[j]->setZ(Rz[j]);
225
226			atoms[j]->set_vx(Vx[j]);
227			atoms[j]->set_vy(Vy[j]);
228			atoms[j]->set_vz(Vz[j]);
229			}
230
231
232			for( i=0; i<nAtoms; i++ ){
233			if( atoms[i]->isDirectional() ){
234
235			dAtom = (DirectionalAtom *)atoms[i];
236
237			// get and convert the torque to body frame
238
239			Tb[0] = dAtom->getTx();
240			Tb[1] = dAtom->getTy();
241			Tb[2] = dAtom->getTz();
242
243			dAtom->lab2Body( Tb );
244
245			// get the angular momentum, and propagate a half step
246
247			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
248			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
249			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
250
251			// get the atom's rotation matrix
252
253			A[0][0] = dAtom->getAxx();
254			A[0][1] = dAtom->getAxy();
255			A[0][2] = dAtom->getAxz();
256
257			A[1][0] = dAtom->getAyx();
258			A[1][1] = dAtom->getAyy();
259			A[1][2] = dAtom->getAyz();
260
261			A[2][0] = dAtom->getAzx();
262			A[2][1] = dAtom->getAzy();
263			A[2][2] = dAtom->getAzz();
264
265
266			// use the angular velocities to propagate the rotation matrix a
267			// full time step
268
269
270			angle = dt2 * ji[0] / dAtom->getIxx();
271			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
272
273			angle = dt2 * ji[1] / dAtom->getIyy();
274			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
275
276			angle = dt * ji[2] / dAtom->getIzz();
277			this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis
278
279			angle = dt2 * ji[1] / dAtom->getIyy();
280			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
281
282			angle = dt2 * ji[0] / dAtom->getIxx();
283			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
284
285
286			dAtom->setA( A );
287			dAtom->setJx( ji[0] );
288			dAtom->setJy( ji[1] );
289			dAtom->setJz( ji[2] );
290			}
291			}
292
293			// calculate the forces
294
295			for(j = 0; j < nAtoms; j++){
296			atoms[j]->zeroForces();
297			}
298
299			for(j = 0; j < nSRI; j++){
300			srInteractions[j]->calc_forces();
301			}
302
303			longRange->calc_forces();
304
305			// move b
306
307			for( j=0; j<nAtoms; j++ ){
308
309			Rx[j] = atoms[j]->getX();
310			Ry[j] = atoms[j]->getY();
311			Rz[j] = atoms[j]->getZ();
312
313			Vx[j] = atoms[j]->get_vx();
314			Vy[j] = atoms[j]->get_vy();
315			Vz[j] = atoms[j]->get_vz();
316
317			Fx[j] = atoms[j]->getFx();
318			Fy[j] = atoms[j]->getFy();
319			Fz[j] = atoms[j]->getFz();
320			}
321
322			v_constrain_b_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz,
323			Fx, Fy, Fz,
324			kE, n_constrained, constrained_dsqr,
325			constrained_i, constrained_j,
326			entry_plug->box_x,
327			entry_plug->box_y,
328			entry_plug->box_z );
329
330			for( j=0; j<nAtoms; j++ ){
331
332			atoms[j]->setX(Rx[j]);
333			atoms[j]->setY(Ry[j]);
334			atoms[j]->setZ(Rz[j]);
335
336			atoms[j]->set_vx(Vx[j]);
337			atoms[j]->set_vy(Vy[j]);
338			atoms[j]->set_vz(Vz[j]);
339			}
340
341			for( i=0; i< nAtoms; i++ ){
342
343			if( atoms[i]->isDirectional() ){
344
345			dAtom = (DirectionalAtom *)atoms[i];
346
347			// get and convert the torque to body frame
348
349			Tb[0] = dAtom->getTx();
350			Tb[1] = dAtom->getTy();
351			Tb[2] = dAtom->getTz();
352
353			dAtom->lab2Body( Tb );
354
355			// get the angular momentum, and complete the angular momentum
356			// half step
357
358			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
359			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
360			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
361
362			dAtom->setJx( ji[0] );
363			dAtom->setJy( ji[1] );
364			dAtom->setJz( ji[2] );
365			}
366			}
367	mmeineke	25
368			time = tl + 1;
369
370	mmeineke	10	if( entry_plug->setTemp ){
371	mmeineke	25	if( !(time % vel_n) ) tStats->velocitize();
372	mmeineke	10	}
373	mmeineke	25	if( !(time % sample_n) ) dump_out->writeDump( time * dt );
374			if( !(time % status_n) ) e_out->writeStat( time * dt );
375	mmeineke	10	}
376			}
377			else{
378
379			for( tl=0; tl<n_loops; tl++ ){
380
381			kE = 0.0;
382			rot_kE= 0.0;
383			trans_kE = 0.0;
384
385			for( i=0; i<nAtoms; i++ ){
386
387			// velocity half step
388
389			vx = atoms[i]->get_vx() +
390			( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert;
391			vy = atoms[i]->get_vy() +
392			( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert;
393			vz = atoms[i]->get_vz() +
394			( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert;
395
396			// position whole step
397
398			rx = atoms[i]->getX() + dt * vx;
399			ry = atoms[i]->getY() + dt * vy;
400			rz = atoms[i]->getZ() + dt * vz;
401
402			atoms[i]->setX( rx );
403			atoms[i]->setY( ry );
404			atoms[i]->setZ( rz );
405
406			atoms[i]->set_vx( vx );
407			atoms[i]->set_vy( vy );
408			atoms[i]->set_vz( vz );
409
410			if( atoms[i]->isDirectional() ){
411
412			dAtom = (DirectionalAtom *)atoms[i];
413
414			// get and convert the torque to body frame
415
416			Tb[0] = dAtom->getTx();
417			Tb[1] = dAtom->getTy();
418			Tb[2] = dAtom->getTz();
419
420			dAtom->lab2Body( Tb );
421
422			// get the angular momentum, and propagate a half step
423
424			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
425			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
426			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
427
428			// get the atom's rotation matrix
429
430			A[0][0] = dAtom->getAxx();
431			A[0][1] = dAtom->getAxy();
432			A[0][2] = dAtom->getAxz();
433
434			A[1][0] = dAtom->getAyx();
435			A[1][1] = dAtom->getAyy();
436			A[1][2] = dAtom->getAyz();
437
438			A[2][0] = dAtom->getAzx();
439			A[2][1] = dAtom->getAzy();
440			A[2][2] = dAtom->getAzz();
441
442
443			// use the angular velocities to propagate the rotation matrix a
444			// full time step
445
446
447			angle = dt2 * ji[0] / dAtom->getIxx();
448			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
449
450			angle = dt2 * ji[1] / dAtom->getIyy();
451			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
452
453			angle = dt * ji[2] / dAtom->getIzz();
454			this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis
455
456			angle = dt2 * ji[1] / dAtom->getIyy();
457			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
458
459			angle = dt2 * ji[0] / dAtom->getIxx();
460			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
461
462
463			dAtom->setA( A );
464			dAtom->setJx( ji[0] );
465			dAtom->setJy( ji[1] );
466			dAtom->setJz( ji[2] );
467			}
468			}
469
470			// calculate the forces
471
472			for(j = 0; j < nAtoms; j++){
473			atoms[j]->zeroForces();
474			}
475
476			for(j = 0; j < nSRI; j++){
477			srInteractions[j]->calc_forces();
478			}
479
480			longRange->calc_forces();
481
482			for( i=0; i< nAtoms; i++ ){
483
484			// complete the velocity half step
485
486			vx = atoms[i]->get_vx() +
487			( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert;
488			vy = atoms[i]->get_vy() +
489			( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert;
490			vz = atoms[i]->get_vz() +
491			( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert;
492
493			atoms[i]->set_vx( vx );
494			atoms[i]->set_vy( vy );
495			atoms[i]->set_vz( vz );
496
497	chuckv	134	// vx2 = vx * vx;
498			// vy2 = vy * vy;
499			// vz2 = vz * vz;
500	mmeineke	10
501			if( atoms[i]->isDirectional() ){
502
503			dAtom = (DirectionalAtom *)atoms[i];
504
505			// get and convert the torque to body frame
506
507			Tb[0] = dAtom->getTx();
508			Tb[1] = dAtom->getTy();
509			Tb[2] = dAtom->getTz();
510
511			dAtom->lab2Body( Tb );
512
513			// get the angular momentum, and complete the angular momentum
514			// half step
515
516			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
517			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
518			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
519
520			jx2 = ji[0] * ji[0];
521			jy2 = ji[1] * ji[1];
522			jz2 = ji[2] * ji[2];
523
524			rot_kE += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
525			+ (jz2 / dAtom->getIzz());
526
527			dAtom->setJx( ji[0] );
528			dAtom->setJy( ji[1] );
529			dAtom->setJz( ji[2] );
530			}
531			}
532	mmeineke	25
533			time = tl + 1;
534
535	mmeineke	10	if( entry_plug->setTemp ){
536	mmeineke	25	if( !(time % vel_n) ) tStats->velocitize();
537	mmeineke	10	}
538	mmeineke	25	if( !(time % sample_n) ) dump_out->writeDump( time * dt );
539			if( !(time % status_n) ) e_out->writeStat( time * dt );
540	mmeineke	10	}
541			}
542
543			dump_out->writeFinal();
544
545			delete dump_out;
546			delete e_out;
547			}
548
549			void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3],
550			double A[3][3] ){
551
552			int i,j,k;
553			double sinAngle;
554			double cosAngle;
555			double angleSqr;
556			double angleSqrOver4;
557			double top, bottom;
558			double rot[3][3];
559			double tempA[3][3];
560			double tempJ[3];
561
562			// initialize the tempA
563
564			for(i=0; i<3; i++){
565			for(j=0; j<3; j++){
566			tempA[i][j] = A[i][j];
567			}
568			}
569
570			// initialize the tempJ
571
572			for( i=0; i<3; i++) tempJ[i] = ji[i];
573
574			// initalize rot as a unit matrix
575
576			rot[0][0] = 1.0;
577			rot[0][1] = 0.0;
578			rot[0][2] = 0.0;
579
580			rot[1][0] = 0.0;
581			rot[1][1] = 1.0;
582			rot[1][2] = 0.0;
583
584			rot[2][0] = 0.0;
585			rot[2][1] = 0.0;
586			rot[2][2] = 1.0;
587
588			// use a small angle aproximation for sin and cosine
589
590			angleSqr = angle * angle;
591			angleSqrOver4 = angleSqr / 4.0;
592			top = 1.0 - angleSqrOver4;
593			bottom = 1.0 + angleSqrOver4;
594
595			cosAngle = top / bottom;
596			sinAngle = angle / bottom;
597
598			rot[axes1][axes1] = cosAngle;
599			rot[axes2][axes2] = cosAngle;
600
601			rot[axes1][axes2] = sinAngle;
602			rot[axes2][axes1] = -sinAngle;
603
604			// rotate the momentum acoording to: ji[] = rot[][] * ji[]
605
606			for(i=0; i<3; i++){
607			ji[i] = 0.0;
608			for(k=0; k<3; k++){
609			ji[i] += rot[i][k] * tempJ[k];
610			}
611			}
612
613			// rotate the Rotation matrix acording to:
614			// A[][] = A[][] * transpose(rot[][])
615
616
617			// NOte for as yet unknown reason, we are setting the performing the
618			// calculation as:
619			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
620
621			for(i=0; i<3; i++){
622			for(j=0; j<3; j++){
623			A[j][i] = 0.0;
624			for(k=0; k<3; k++){
625			A[j][i] += tempA[k][i] * rot[j][k];
626			}
627			}
628			}
629			}