OOPSE/libmdtools/Symplectic.cpp

#include <iostream>
#include <cstdlib>

#include "Integrator.hpp"
#include "Thermo.hpp"
#include "ReadWrite.hpp"
#include "ForceFields.hpp"
#include "ExtendedSystem.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, ForceFields* the_ff,
                        ExtendedSystem* the_es ){
  entry_plug = the_entry_plug;
  myFF = the_ff;
  myES = the_es;
  isFirst = 1;

  molecules = entry_plug->molecules;
  nMols = entry_plug->n_mol;

  // 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[entry_plug->n_SRI];
  n_constrained = 0;
  int constrained = 0;
  
  SRI** theArray;
  for(int i = 0; i < nMols; i++){
    
    theArray = (SRI**) molecules[i].getMyBonds();
    for(int j=0; j<molecules[i].getNBonds(); j++){
      
      constrained = theArray[j]->is_constrained();
      
      if(constrained){
        
        dummy_plug = theArray[j]->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;
      }
    }

    theArray = (SRI**) molecules[i].getMyBends();
    for(int j=0; j<molecules[i].getNBends(); j++){
      
      constrained = theArray[j]->is_constrained();
      
      if(constrained){
        
        dummy_plug = theArray[j]->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;
      }
    }

    theArray = (SRI**) molecules[i].getMyTorsions();
    for(int j=0; j<molecules[i].getNTorsions(); j++){
      
      constrained = theArray[j]->is_constrained();
      
      if(constrained){
        
        dummy_plug = theArray[j]->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 );

  int calcPot;

   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

  myFF->doForces(1,0);
  
  if( entry_plug->setTemp ){
    
    tStats->velocitize();
  }
  
  dump_out->writeDump( 0.0 );
  e_out->writeStat( 0.0 );
  
  calcPot = 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
      
      myFF->doForces(calcPot, 0);
      
      // 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+1) % status_n) ) calcPot = 1;
      if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; }
    }
  }
  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
      
      myFF->doForces(calcPot,0);
      
      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+1) % status_n) ) calcPot = 1;
      if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; }
    }
  }

  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[j][i] = 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[i][k] * rot[j][k];
      }
    }
  }
}
Revision:	466
Committed:	Mon Apr 7 14:30:36 2003 UTC (21 years, 3 months ago) by gezelter
File size:	15863 byte(s)
Log Message:	Added ExtendedSystem infrastructure for NPT and NVT calculations
#	User	Rev	Content
1	mmeineke	377	#include <iostream>
2			#include <cstdlib>
3
4			#include "Integrator.hpp"
5			#include "Thermo.hpp"
6			#include "ReadWrite.hpp"
7			#include "ForceFields.hpp"
8	gezelter	466	#include "ExtendedSystem.hpp"
9	mmeineke	377	#include "simError.h"
10
11			extern "C"{
12
13			void v_constrain_a_( double &dt, int &n_atoms, double* mass,
14			double* Rx, double* Ry, double* Rz,
15			double* Vx, double* Vy, double* Vz,
16			double* Fx, double* Fy, double* Fz,
17			int &n_constrained, double *constr_sqr,
18			int* constr_i, int* constr_j,
19			double &box_x, double &box_y, double &box_z );
20
21			void v_constrain_b_( double &dt, int &n_atoms, double* mass,
22			double* Rx, double* Ry, double* Rz,
23			double* Vx, double* Vy, double* Vz,
24			double* Fx, double* Fy, double* Fz,
25			double &Kinetic,
26			int &n_constrained, double *constr_sqr,
27			int* constr_i, int* constr_j,
28			double &box_x, double &box_y, double &box_z );
29			}
30
31
32
33
34	gezelter	466	Symplectic::Symplectic( SimInfo* the_entry_plug, ForceFields* the_ff,
35			ExtendedSystem* the_es ){
36	mmeineke	377	entry_plug = the_entry_plug;
37			myFF = the_ff;
38	gezelter	466	myES = the_es;
39	mmeineke	377	isFirst = 1;
40
41	mmeineke	423	molecules = entry_plug->molecules;
42			nMols = entry_plug->n_mol;
43	mmeineke	377
44			// give a little love back to the SimInfo object
45
46			if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator;
47			entry_plug->the_integrator = this;
48
49			// grab the masses
50
51			mass = new double[entry_plug->n_atoms];
52			for(int i = 0; i < entry_plug->n_atoms; i++){
53			mass[i] = entry_plug->atoms[i]->getMass();
54	gezelter	466	}
55	mmeineke	377
56			// check for constraints
57
58			is_constrained = 0;
59
60			Constraint *temp_con;
61			Constraint *dummy_plug;
62	mmeineke	423	temp_con = new Constraint[entry_plug->n_SRI];
63	mmeineke	377	n_constrained = 0;
64			int constrained = 0;
65
66	mmeineke	423	SRI** theArray;
67			for(int i = 0; i < nMols; i++){
68	mmeineke	377
69	mmeineke	428	theArray = (SRI**) molecules[i].getMyBonds();
70			for(int j=0; j<molecules[i].getNBonds(); j++){
71	mmeineke	377
72	mmeineke	423	constrained = theArray[j]->is_constrained();
73
74			if(constrained){
75
76			dummy_plug = theArray[j]->get_constraint();
77	mmeineke	428	temp_con[n_constrained].set_a( dummy_plug->get_a() );
78			temp_con[n_constrained].set_b( dummy_plug->get_b() );
79			temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
80	mmeineke	423
81	mmeineke	428	n_constrained++;
82	mmeineke	423	constrained = 0;
83			}
84			}
85	mmeineke	377
86	mmeineke	428	theArray = (SRI**) molecules[i].getMyBends();
87			for(int j=0; j<molecules[i].getNBends(); j++){
88	mmeineke	423
89			constrained = theArray[j]->is_constrained();
90
91			if(constrained){
92
93			dummy_plug = theArray[j]->get_constraint();
94	mmeineke	428	temp_con[n_constrained].set_a( dummy_plug->get_a() );
95			temp_con[n_constrained].set_b( dummy_plug->get_b() );
96			temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
97	mmeineke	423
98	mmeineke	428	n_constrained++;
99	mmeineke	423	constrained = 0;
100			}
101	mmeineke	377	}
102	mmeineke	423
103	mmeineke	428	theArray = (SRI**) molecules[i].getMyTorsions();
104			for(int j=0; j<molecules[i].getNTorsions(); j++){
105	mmeineke	423
106			constrained = theArray[j]->is_constrained();
107
108			if(constrained){
109
110			dummy_plug = theArray[j]->get_constraint();
111	mmeineke	428	temp_con[n_constrained].set_a( dummy_plug->get_a() );
112			temp_con[n_constrained].set_b( dummy_plug->get_b() );
113			temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
114	mmeineke	423
115	mmeineke	428	n_constrained++;
116	mmeineke	423	constrained = 0;
117			}
118			}
119	mmeineke	377	}
120
121			if(n_constrained > 0){
122
123			is_constrained = 1;
124			constrained_i = new int[n_constrained];
125			constrained_j = new int[n_constrained];
126			constrained_dsqr = new double[n_constrained];
127
128			for( int i = 0; i < n_constrained; i++){
129
130			/* add 1 to the index for the fortran arrays. */
131
132			constrained_i[i] = temp_con[i].get_a() + 1;
133			constrained_j[i] = temp_con[i].get_b() + 1;
134			constrained_dsqr[i] = temp_con[i].get_dsqr();
135			}
136			}
137
138			delete[] temp_con;
139			}
140
141			Symplectic::~Symplectic() {
142
143			if( n_constrained ){
144			delete[] constrained_i;
145			delete[] constrained_j;
146			delete[] constrained_dsqr;
147			}
148
149			}
150
151
152			void Symplectic::integrate( void ){
153
154			const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
155
156			int i, j; // loop counters
157			int nAtoms = entry_plug->n_atoms; // the number of atoms
158			double kE = 0.0; // the kinetic energy
159			double rot_kE;
160			double trans_kE;
161			int tl; // the time loop conter
162			double dt2; // half the dt
163
164			double vx, vy, vz; // the velocities
165			// double vx2, vy2, vz2; // the square of the velocities
166			double rx, ry, rz; // the postitions
167
168			double ji[3]; // the body frame angular momentum
169			double jx2, jy2, jz2; // the square of the angular momentums
170			double Tb[3]; // torque in the body frame
171			double angle; // the angle through which to rotate the rotation matrix
172			double A[3][3]; // the rotation matrix
173
174			int time;
175
176			double dt = entry_plug->dt;
177			double runTime = entry_plug->run_time;
178			double sampleTime = entry_plug->sampleTime;
179			double statusTime = entry_plug->statusTime;
180			double thermalTime = entry_plug->thermalTime;
181
182			int n_loops = (int)( runTime / dt );
183			int sample_n = (int)( sampleTime / dt );
184			int status_n = (int)( statusTime / dt );
185			int vel_n = (int)( thermalTime / dt );
186
187			int calcPot;
188
189			Thermo *tStats = new Thermo( entry_plug );
190
191			StatWriter* e_out = new StatWriter( entry_plug );
192			DumpWriter* dump_out = new DumpWriter( entry_plug );
193
194			Atom** atoms = entry_plug->atoms;
195			DirectionalAtom* dAtom;
196			dt2 = 0.5 * dt;
197
198			// initialize the forces the before the first step
199
200			myFF->doForces(1,0);
201
202			if( entry_plug->setTemp ){
203
204			tStats->velocitize();
205			}
206
207			dump_out->writeDump( 0.0 );
208			e_out->writeStat( 0.0 );
209
210			calcPot = 0;
211
212			if( n_constrained ){
213
214			double *Rx = new double[nAtoms];
215			double *Ry = new double[nAtoms];
216			double *Rz = new double[nAtoms];
217
218			double *Vx = new double[nAtoms];
219			double *Vy = new double[nAtoms];
220			double *Vz = new double[nAtoms];
221
222			double *Fx = new double[nAtoms];
223			double *Fy = new double[nAtoms];
224			double *Fz = new double[nAtoms];
225
226
227			for( tl=0; tl < n_loops; tl++ ){
228
229			for( j=0; j<nAtoms; j++ ){
230
231			Rx[j] = atoms[j]->getX();
232			Ry[j] = atoms[j]->getY();
233			Rz[j] = atoms[j]->getZ();
234
235			Vx[j] = atoms[j]->get_vx();
236			Vy[j] = atoms[j]->get_vy();
237			Vz[j] = atoms[j]->get_vz();
238
239			Fx[j] = atoms[j]->getFx();
240			Fy[j] = atoms[j]->getFy();
241			Fz[j] = atoms[j]->getFz();
242
243			}
244
245			v_constrain_a_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz,
246			Fx, Fy, Fz,
247			n_constrained, constrained_dsqr,
248			constrained_i, constrained_j,
249			entry_plug->box_x,
250			entry_plug->box_y,
251			entry_plug->box_z );
252
253			for( j=0; j<nAtoms; j++ ){
254
255			atoms[j]->setX(Rx[j]);
256			atoms[j]->setY(Ry[j]);
257			atoms[j]->setZ(Rz[j]);
258
259			atoms[j]->set_vx(Vx[j]);
260			atoms[j]->set_vy(Vy[j]);
261			atoms[j]->set_vz(Vz[j]);
262			}
263
264
265			for( i=0; i<nAtoms; i++ ){
266			if( atoms[i]->isDirectional() ){
267
268			dAtom = (DirectionalAtom *)atoms[i];
269
270			// get and convert the torque to body frame
271
272			Tb[0] = dAtom->getTx();
273			Tb[1] = dAtom->getTy();
274			Tb[2] = dAtom->getTz();
275
276			dAtom->lab2Body( Tb );
277
278			// get the angular momentum, and propagate a half step
279
280			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
281			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
282			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
283
284			// get the atom's rotation matrix
285
286			A[0][0] = dAtom->getAxx();
287			A[0][1] = dAtom->getAxy();
288			A[0][2] = dAtom->getAxz();
289
290			A[1][0] = dAtom->getAyx();
291			A[1][1] = dAtom->getAyy();
292			A[1][2] = dAtom->getAyz();
293
294			A[2][0] = dAtom->getAzx();
295			A[2][1] = dAtom->getAzy();
296			A[2][2] = dAtom->getAzz();
297
298
299			// use the angular velocities to propagate the rotation matrix a
300			// full time step
301
302
303			angle = dt2 * ji[0] / dAtom->getIxx();
304			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
305
306			angle = dt2 * ji[1] / dAtom->getIyy();
307			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
308
309			angle = dt * ji[2] / dAtom->getIzz();
310			this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis
311
312			angle = dt2 * ji[1] / dAtom->getIyy();
313			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
314
315			angle = dt2 * ji[0] / dAtom->getIxx();
316			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
317
318
319			dAtom->setA( A );
320			dAtom->setJx( ji[0] );
321			dAtom->setJy( ji[1] );
322			dAtom->setJz( ji[2] );
323			}
324			}
325
326			// calculate the forces
327
328			myFF->doForces(calcPot, 0);
329
330			// move b
331
332			for( j=0; j<nAtoms; j++ ){
333
334			Rx[j] = atoms[j]->getX();
335			Ry[j] = atoms[j]->getY();
336			Rz[j] = atoms[j]->getZ();
337
338			Vx[j] = atoms[j]->get_vx();
339			Vy[j] = atoms[j]->get_vy();
340			Vz[j] = atoms[j]->get_vz();
341
342			Fx[j] = atoms[j]->getFx();
343			Fy[j] = atoms[j]->getFy();
344			Fz[j] = atoms[j]->getFz();
345			}
346
347			v_constrain_b_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz,
348			Fx, Fy, Fz,
349			kE, n_constrained, constrained_dsqr,
350			constrained_i, constrained_j,
351			entry_plug->box_x,
352			entry_plug->box_y,
353			entry_plug->box_z );
354
355			for( j=0; j<nAtoms; j++ ){
356
357			atoms[j]->setX(Rx[j]);
358			atoms[j]->setY(Ry[j]);
359			atoms[j]->setZ(Rz[j]);
360
361			atoms[j]->set_vx(Vx[j]);
362			atoms[j]->set_vy(Vy[j]);
363			atoms[j]->set_vz(Vz[j]);
364			}
365
366			for( i=0; i< nAtoms; i++ ){
367
368			if( atoms[i]->isDirectional() ){
369
370			dAtom = (DirectionalAtom *)atoms[i];
371
372			// get and convert the torque to body frame
373
374			Tb[0] = dAtom->getTx();
375			Tb[1] = dAtom->getTy();
376			Tb[2] = dAtom->getTz();
377
378			dAtom->lab2Body( Tb );
379
380			// get the angular momentum, and complete the angular momentum
381			// half step
382
383			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
384			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
385			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
386
387			dAtom->setJx( ji[0] );
388			dAtom->setJy( ji[1] );
389			dAtom->setJz( ji[2] );
390			}
391			}
392
393			time = tl + 1;
394
395			if( entry_plug->setTemp ){
396			if( !(time % vel_n) ) tStats->velocitize();
397			}
398			if( !(time % sample_n) ) dump_out->writeDump( time * dt );
399			if( !((time+1) % status_n) ) calcPot = 1;
400			if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; }
401			}
402			}
403			else{
404
405			for( tl=0; tl<n_loops; tl++ ){
406
407			kE = 0.0;
408			rot_kE= 0.0;
409			trans_kE = 0.0;
410
411			for( i=0; i<nAtoms; i++ ){
412
413			// velocity half step
414
415			vx = atoms[i]->get_vx() +
416			( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert;
417			vy = atoms[i]->get_vy() +
418			( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert;
419			vz = atoms[i]->get_vz() +
420			( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert;
421
422			// position whole step
423
424			rx = atoms[i]->getX() + dt * vx;
425			ry = atoms[i]->getY() + dt * vy;
426			rz = atoms[i]->getZ() + dt * vz;
427
428			atoms[i]->setX( rx );
429			atoms[i]->setY( ry );
430			atoms[i]->setZ( rz );
431
432			atoms[i]->set_vx( vx );
433			atoms[i]->set_vy( vy );
434			atoms[i]->set_vz( vz );
435
436			if( atoms[i]->isDirectional() ){
437
438			dAtom = (DirectionalAtom *)atoms[i];
439
440			// get and convert the torque to body frame
441
442			Tb[0] = dAtom->getTx();
443			Tb[1] = dAtom->getTy();
444			Tb[2] = dAtom->getTz();
445
446			dAtom->lab2Body( Tb );
447
448			// get the angular momentum, and propagate a half step
449
450			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
451			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
452			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
453
454			// get the atom's rotation matrix
455
456			A[0][0] = dAtom->getAxx();
457			A[0][1] = dAtom->getAxy();
458			A[0][2] = dAtom->getAxz();
459
460			A[1][0] = dAtom->getAyx();
461			A[1][1] = dAtom->getAyy();
462			A[1][2] = dAtom->getAyz();
463
464			A[2][0] = dAtom->getAzx();
465			A[2][1] = dAtom->getAzy();
466			A[2][2] = dAtom->getAzz();
467
468
469			// use the angular velocities to propagate the rotation matrix a
470			// full time step
471
472
473			angle = dt2 * ji[0] / dAtom->getIxx();
474			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
475
476			angle = dt2 * ji[1] / dAtom->getIyy();
477			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
478
479			angle = dt * ji[2] / dAtom->getIzz();
480			this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis
481
482			angle = dt2 * ji[1] / dAtom->getIyy();
483			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
484
485			angle = dt2 * ji[0] / dAtom->getIxx();
486			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
487
488
489			dAtom->setA( A );
490			dAtom->setJx( ji[0] );
491			dAtom->setJy( ji[1] );
492			dAtom->setJz( ji[2] );
493			}
494			}
495
496			// calculate the forces
497
498			myFF->doForces(calcPot,0);
499
500			for( i=0; i< nAtoms; i++ ){
501
502			// complete the velocity half step
503
504			vx = atoms[i]->get_vx() +
505			( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert;
506			vy = atoms[i]->get_vy() +
507			( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert;
508			vz = atoms[i]->get_vz() +
509			( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert;
510
511			atoms[i]->set_vx( vx );
512			atoms[i]->set_vy( vy );
513			atoms[i]->set_vz( vz );
514
515			// vx2 = vx * vx;
516			// vy2 = vy * vy;
517			// vz2 = vz * vz;
518
519			if( atoms[i]->isDirectional() ){
520
521			dAtom = (DirectionalAtom *)atoms[i];
522
523			// get and convert the torque to body frame
524
525			Tb[0] = dAtom->getTx();
526			Tb[1] = dAtom->getTy();
527			Tb[2] = dAtom->getTz();
528
529			dAtom->lab2Body( Tb );
530
531			// get the angular momentum, and complete the angular momentum
532			// half step
533
534			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
535			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
536			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
537
538			jx2 = ji[0] * ji[0];
539			jy2 = ji[1] * ji[1];
540			jz2 = ji[2] * ji[2];
541
542			rot_kE += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
543			+ (jz2 / dAtom->getIzz());
544
545			dAtom->setJx( ji[0] );
546			dAtom->setJy( ji[1] );
547			dAtom->setJz( ji[2] );
548			}
549			}
550
551			time = tl + 1;
552
553			if( entry_plug->setTemp ){
554			if( !(time % vel_n) ) tStats->velocitize();
555			}
556			if( !(time % sample_n) ) dump_out->writeDump( time * dt );
557			if( !((time+1) % status_n) ) calcPot = 1;
558			if( !(time % status_n) ){ e_out->writeStat( time * dt ); calcPot = 0; }
559			}
560			}
561
562			dump_out->writeFinal();
563
564			delete dump_out;
565			delete e_out;
566			}
567
568			void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3],
569			double A[3][3] ){
570
571			int i,j,k;
572			double sinAngle;
573			double cosAngle;
574			double angleSqr;
575			double angleSqrOver4;
576			double top, bottom;
577			double rot[3][3];
578			double tempA[3][3];
579			double tempJ[3];
580
581			// initialize the tempA
582
583			for(i=0; i<3; i++){
584			for(j=0; j<3; j++){
585	mmeineke	443	tempA[j][i] = A[i][j];
586	mmeineke	377	}
587			}
588
589			// initialize the tempJ
590
591			for( i=0; i<3; i++) tempJ[i] = ji[i];
592
593			// initalize rot as a unit matrix
594
595			rot[0][0] = 1.0;
596			rot[0][1] = 0.0;
597			rot[0][2] = 0.0;
598
599			rot[1][0] = 0.0;
600			rot[1][1] = 1.0;
601			rot[1][2] = 0.0;
602
603			rot[2][0] = 0.0;
604			rot[2][1] = 0.0;
605			rot[2][2] = 1.0;
606
607			// use a small angle aproximation for sin and cosine
608
609			angleSqr = angle * angle;
610			angleSqrOver4 = angleSqr / 4.0;
611			top = 1.0 - angleSqrOver4;
612			bottom = 1.0 + angleSqrOver4;
613
614			cosAngle = top / bottom;
615			sinAngle = angle / bottom;
616
617			rot[axes1][axes1] = cosAngle;
618			rot[axes2][axes2] = cosAngle;
619
620			rot[axes1][axes2] = sinAngle;
621			rot[axes2][axes1] = -sinAngle;
622
623			// rotate the momentum acoording to: ji[] = rot[][] * ji[]
624
625			for(i=0; i<3; i++){
626			ji[i] = 0.0;
627			for(k=0; k<3; k++){
628			ji[i] += rot[i][k] * tempJ[k];
629			}
630			}
631
632			// rotate the Rotation matrix acording to:
633			// A[][] = A[][] * transpose(rot[][])
634
635
636			// NOte for as yet unknown reason, we are setting the performing the
637			// calculation as:
638			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
639
640			for(i=0; i<3; i++){
641			for(j=0; j<3; j++){
642			A[j][i] = 0.0;
643			for(k=0; k<3; k++){
644	mmeineke	443	A[j][i] += tempA[i][k] * rot[j][k];
645	mmeineke	377	}
646			}
647			}
648			}