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;

  std::cerr<< "calling symplectic constructor\n";

  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, calcStress;

  Thermo *tStats;
  StatWriter*  e_out;
  DumpWriter*  dump_out;

  std::cerr << "about to call new thermo\n";

  tStats   = new Thermo( entry_plug );
  e_out    = new StatWriter( entry_plug );

  std::cerr << "calling dumpWriter \n";
  dump_out = new DumpWriter( entry_plug );
  std::cerr << "called dumpWriter \n";

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

  // initialize the forces the before the first step

  myFF->doForces(1,1);
  
  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, calcStress);
      
      // 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;
        calcStress = 1;
      }
      if( !(time % status_n) ){ 
        e_out->writeStat( time * dt ); 
        calcPot = 0; 
        calcStress = 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,calcStress);
      
      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;
        calcStress = 1;
      }
      if( !(time % status_n) ){ 
        e_out->writeStat( time * dt ); 
        calcPot = 0; 
        calcStress = 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:	469
Committed:	Mon Apr 7 20:06:31 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	16290 byte(s)
Log Message:	bug fixes
#	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	469	std::cerr<< "calling symplectic constructor\n";
42
43	mmeineke	423	molecules = entry_plug->molecules;
44			nMols = entry_plug->n_mol;
45	mmeineke	377
46			// give a little love back to the SimInfo object
47
48			if( entry_plug->the_integrator != NULL ) delete entry_plug->the_integrator;
49			entry_plug->the_integrator = this;
50
51			// grab the masses
52
53			mass = new double[entry_plug->n_atoms];
54			for(int i = 0; i < entry_plug->n_atoms; i++){
55			mass[i] = entry_plug->atoms[i]->getMass();
56	gezelter	466	}
57	mmeineke	377
58			// check for constraints
59
60			is_constrained = 0;
61
62			Constraint *temp_con;
63			Constraint *dummy_plug;
64	mmeineke	423	temp_con = new Constraint[entry_plug->n_SRI];
65	mmeineke	377	n_constrained = 0;
66			int constrained = 0;
67
68	mmeineke	423	SRI** theArray;
69			for(int i = 0; i < nMols; i++){
70	mmeineke	377
71	mmeineke	428	theArray = (SRI**) molecules[i].getMyBonds();
72			for(int j=0; j<molecules[i].getNBonds(); j++){
73	mmeineke	377
74	mmeineke	423	constrained = theArray[j]->is_constrained();
75
76			if(constrained){
77
78			dummy_plug = theArray[j]->get_constraint();
79	mmeineke	428	temp_con[n_constrained].set_a( dummy_plug->get_a() );
80			temp_con[n_constrained].set_b( dummy_plug->get_b() );
81			temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
82	mmeineke	423
83	mmeineke	428	n_constrained++;
84	mmeineke	423	constrained = 0;
85			}
86			}
87	mmeineke	377
88	mmeineke	428	theArray = (SRI**) molecules[i].getMyBends();
89			for(int j=0; j<molecules[i].getNBends(); j++){
90	mmeineke	423
91			constrained = theArray[j]->is_constrained();
92
93			if(constrained){
94
95			dummy_plug = theArray[j]->get_constraint();
96	mmeineke	428	temp_con[n_constrained].set_a( dummy_plug->get_a() );
97			temp_con[n_constrained].set_b( dummy_plug->get_b() );
98			temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
99	mmeineke	423
100	mmeineke	428	n_constrained++;
101	mmeineke	423	constrained = 0;
102			}
103	mmeineke	377	}
104	mmeineke	423
105	mmeineke	428	theArray = (SRI**) molecules[i].getMyTorsions();
106			for(int j=0; j<molecules[i].getNTorsions(); j++){
107	mmeineke	423
108			constrained = theArray[j]->is_constrained();
109
110			if(constrained){
111
112			dummy_plug = theArray[j]->get_constraint();
113	mmeineke	428	temp_con[n_constrained].set_a( dummy_plug->get_a() );
114			temp_con[n_constrained].set_b( dummy_plug->get_b() );
115			temp_con[n_constrained].set_dsqr( dummy_plug->get_dsqr() );
116	mmeineke	423
117	mmeineke	428	n_constrained++;
118	mmeineke	423	constrained = 0;
119			}
120			}
121	mmeineke	377	}
122
123			if(n_constrained > 0){
124
125			is_constrained = 1;
126			constrained_i = new int[n_constrained];
127			constrained_j = new int[n_constrained];
128			constrained_dsqr = new double[n_constrained];
129
130			for( int i = 0; i < n_constrained; i++){
131
132			/* add 1 to the index for the fortran arrays. */
133
134			constrained_i[i] = temp_con[i].get_a() + 1;
135			constrained_j[i] = temp_con[i].get_b() + 1;
136			constrained_dsqr[i] = temp_con[i].get_dsqr();
137			}
138			}
139
140			delete[] temp_con;
141			}
142
143			Symplectic::~Symplectic() {
144
145			if( n_constrained ){
146			delete[] constrained_i;
147			delete[] constrained_j;
148			delete[] constrained_dsqr;
149			}
150
151			}
152
153
154			void Symplectic::integrate( void ){
155
156			const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
157
158			int i, j; // loop counters
159			int nAtoms = entry_plug->n_atoms; // the number of atoms
160			double kE = 0.0; // the kinetic energy
161			double rot_kE;
162			double trans_kE;
163			int tl; // the time loop conter
164			double dt2; // half the dt
165
166			double vx, vy, vz; // the velocities
167			// double vx2, vy2, vz2; // the square of the velocities
168			double rx, ry, rz; // the postitions
169
170			double ji[3]; // the body frame angular momentum
171			double jx2, jy2, jz2; // the square of the angular momentums
172			double Tb[3]; // torque in the body frame
173			double angle; // the angle through which to rotate the rotation matrix
174			double A[3][3]; // the rotation matrix
175
176			int time;
177
178			double dt = entry_plug->dt;
179			double runTime = entry_plug->run_time;
180			double sampleTime = entry_plug->sampleTime;
181			double statusTime = entry_plug->statusTime;
182			double thermalTime = entry_plug->thermalTime;
183
184			int n_loops = (int)( runTime / dt );
185			int sample_n = (int)( sampleTime / dt );
186			int status_n = (int)( statusTime / dt );
187			int vel_n = (int)( thermalTime / dt );
188
189	gezelter	468	int calcPot, calcStress;
190	mmeineke	377
191	mmeineke	469	Thermo *tStats;
192			StatWriter* e_out;
193			DumpWriter* dump_out;
194	mmeineke	377
195	mmeineke	469	std::cerr << "about to call new thermo\n";
196	mmeineke	377
197	mmeineke	469	tStats = new Thermo( entry_plug );
198			e_out = new StatWriter( entry_plug );
199
200			std::cerr << "calling dumpWriter \n";
201			dump_out = new DumpWriter( entry_plug );
202			std::cerr << "called dumpWriter \n";
203
204	mmeineke	377	Atom** atoms = entry_plug->atoms;
205			DirectionalAtom* dAtom;
206			dt2 = 0.5 * dt;
207
208			// initialize the forces the before the first step
209
210	gezelter	468	myFF->doForces(1,1);
211	mmeineke	377
212			if( entry_plug->setTemp ){
213
214			tStats->velocitize();
215			}
216
217			dump_out->writeDump( 0.0 );
218			e_out->writeStat( 0.0 );
219
220			calcPot = 0;
221
222			if( n_constrained ){
223
224			double *Rx = new double[nAtoms];
225			double *Ry = new double[nAtoms];
226			double *Rz = new double[nAtoms];
227
228			double *Vx = new double[nAtoms];
229			double *Vy = new double[nAtoms];
230			double *Vz = new double[nAtoms];
231
232			double *Fx = new double[nAtoms];
233			double *Fy = new double[nAtoms];
234			double *Fz = new double[nAtoms];
235
236
237			for( tl=0; tl < n_loops; tl++ ){
238
239			for( j=0; j<nAtoms; j++ ){
240
241			Rx[j] = atoms[j]->getX();
242			Ry[j] = atoms[j]->getY();
243			Rz[j] = atoms[j]->getZ();
244
245			Vx[j] = atoms[j]->get_vx();
246			Vy[j] = atoms[j]->get_vy();
247			Vz[j] = atoms[j]->get_vz();
248
249			Fx[j] = atoms[j]->getFx();
250			Fy[j] = atoms[j]->getFy();
251			Fz[j] = atoms[j]->getFz();
252
253			}
254
255			v_constrain_a_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz,
256			Fx, Fy, Fz,
257			n_constrained, constrained_dsqr,
258			constrained_i, constrained_j,
259			entry_plug->box_x,
260			entry_plug->box_y,
261			entry_plug->box_z );
262
263			for( j=0; j<nAtoms; j++ ){
264
265			atoms[j]->setX(Rx[j]);
266			atoms[j]->setY(Ry[j]);
267			atoms[j]->setZ(Rz[j]);
268
269			atoms[j]->set_vx(Vx[j]);
270			atoms[j]->set_vy(Vy[j]);
271			atoms[j]->set_vz(Vz[j]);
272			}
273
274
275			for( i=0; i<nAtoms; i++ ){
276			if( atoms[i]->isDirectional() ){
277
278			dAtom = (DirectionalAtom *)atoms[i];
279
280			// get and convert the torque to body frame
281
282			Tb[0] = dAtom->getTx();
283			Tb[1] = dAtom->getTy();
284			Tb[2] = dAtom->getTz();
285
286			dAtom->lab2Body( Tb );
287
288			// get the angular momentum, and propagate a half step
289
290			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
291			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
292			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
293
294			// get the atom's rotation matrix
295
296			A[0][0] = dAtom->getAxx();
297			A[0][1] = dAtom->getAxy();
298			A[0][2] = dAtom->getAxz();
299
300			A[1][0] = dAtom->getAyx();
301			A[1][1] = dAtom->getAyy();
302			A[1][2] = dAtom->getAyz();
303
304			A[2][0] = dAtom->getAzx();
305			A[2][1] = dAtom->getAzy();
306			A[2][2] = dAtom->getAzz();
307
308
309			// use the angular velocities to propagate the rotation matrix a
310			// full time step
311
312
313			angle = dt2 * ji[0] / dAtom->getIxx();
314			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
315
316			angle = dt2 * ji[1] / dAtom->getIyy();
317			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
318
319			angle = dt * ji[2] / dAtom->getIzz();
320			this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis
321
322			angle = dt2 * ji[1] / dAtom->getIyy();
323			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
324
325			angle = dt2 * ji[0] / dAtom->getIxx();
326			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
327
328
329			dAtom->setA( A );
330			dAtom->setJx( ji[0] );
331			dAtom->setJy( ji[1] );
332			dAtom->setJz( ji[2] );
333			}
334			}
335
336			// calculate the forces
337
338	gezelter	468	myFF->doForces(calcPot, calcStress);
339	mmeineke	377
340			// move b
341
342			for( j=0; j<nAtoms; j++ ){
343
344			Rx[j] = atoms[j]->getX();
345			Ry[j] = atoms[j]->getY();
346			Rz[j] = atoms[j]->getZ();
347
348			Vx[j] = atoms[j]->get_vx();
349			Vy[j] = atoms[j]->get_vy();
350			Vz[j] = atoms[j]->get_vz();
351
352			Fx[j] = atoms[j]->getFx();
353			Fy[j] = atoms[j]->getFy();
354			Fz[j] = atoms[j]->getFz();
355			}
356
357			v_constrain_b_( dt, nAtoms, mass, Rx, Ry, Rz, Vx, Vy, Vz,
358			Fx, Fy, Fz,
359			kE, n_constrained, constrained_dsqr,
360			constrained_i, constrained_j,
361			entry_plug->box_x,
362			entry_plug->box_y,
363			entry_plug->box_z );
364
365			for( j=0; j<nAtoms; j++ ){
366
367			atoms[j]->setX(Rx[j]);
368			atoms[j]->setY(Ry[j]);
369			atoms[j]->setZ(Rz[j]);
370
371			atoms[j]->set_vx(Vx[j]);
372			atoms[j]->set_vy(Vy[j]);
373			atoms[j]->set_vz(Vz[j]);
374			}
375
376			for( i=0; i< nAtoms; i++ ){
377
378			if( atoms[i]->isDirectional() ){
379
380			dAtom = (DirectionalAtom *)atoms[i];
381
382			// get and convert the torque to body frame
383
384			Tb[0] = dAtom->getTx();
385			Tb[1] = dAtom->getTy();
386			Tb[2] = dAtom->getTz();
387
388			dAtom->lab2Body( Tb );
389
390			// get the angular momentum, and complete the angular momentum
391			// half step
392
393			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
394			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
395			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
396
397			dAtom->setJx( ji[0] );
398			dAtom->setJy( ji[1] );
399			dAtom->setJz( ji[2] );
400			}
401			}
402
403			time = tl + 1;
404
405			if( entry_plug->setTemp ){
406			if( !(time % vel_n) ) tStats->velocitize();
407			}
408			if( !(time % sample_n) ) dump_out->writeDump( time * dt );
409	gezelter	468	if( !((time+1) % status_n) ) {
410			calcPot = 1;
411			calcStress = 1;
412			}
413			if( !(time % status_n) ){
414			e_out->writeStat( time * dt );
415			calcPot = 0;
416			calcStress = 0;
417			}
418	mmeineke	377	}
419			}
420			else{
421
422			for( tl=0; tl<n_loops; tl++ ){
423
424			kE = 0.0;
425			rot_kE= 0.0;
426			trans_kE = 0.0;
427
428			for( i=0; i<nAtoms; i++ ){
429
430			// velocity half step
431
432			vx = atoms[i]->get_vx() +
433			( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert;
434			vy = atoms[i]->get_vy() +
435			( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert;
436			vz = atoms[i]->get_vz() +
437			( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert;
438
439			// position whole step
440
441			rx = atoms[i]->getX() + dt * vx;
442			ry = atoms[i]->getY() + dt * vy;
443			rz = atoms[i]->getZ() + dt * vz;
444
445			atoms[i]->setX( rx );
446			atoms[i]->setY( ry );
447			atoms[i]->setZ( rz );
448
449			atoms[i]->set_vx( vx );
450			atoms[i]->set_vy( vy );
451			atoms[i]->set_vz( vz );
452
453			if( atoms[i]->isDirectional() ){
454
455			dAtom = (DirectionalAtom *)atoms[i];
456
457			// get and convert the torque to body frame
458
459			Tb[0] = dAtom->getTx();
460			Tb[1] = dAtom->getTy();
461			Tb[2] = dAtom->getTz();
462
463			dAtom->lab2Body( Tb );
464
465			// get the angular momentum, and propagate a half step
466
467			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
468			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
469			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
470
471			// get the atom's rotation matrix
472
473			A[0][0] = dAtom->getAxx();
474			A[0][1] = dAtom->getAxy();
475			A[0][2] = dAtom->getAxz();
476
477			A[1][0] = dAtom->getAyx();
478			A[1][1] = dAtom->getAyy();
479			A[1][2] = dAtom->getAyz();
480
481			A[2][0] = dAtom->getAzx();
482			A[2][1] = dAtom->getAzy();
483			A[2][2] = dAtom->getAzz();
484
485
486			// use the angular velocities to propagate the rotation matrix a
487			// full time step
488
489
490			angle = dt2 * ji[0] / dAtom->getIxx();
491			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
492
493			angle = dt2 * ji[1] / dAtom->getIyy();
494			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
495
496			angle = dt * ji[2] / dAtom->getIzz();
497			this->rotate( 0, 1, angle, ji, A ); // rotate about the z-axis
498
499			angle = dt2 * ji[1] / dAtom->getIyy();
500			this->rotate( 2, 0, angle, ji, A ); // rotate about the y-axis
501
502			angle = dt2 * ji[0] / dAtom->getIxx();
503			this->rotate( 1, 2, angle, ji, A ); // rotate about the x-axis
504
505
506			dAtom->setA( A );
507			dAtom->setJx( ji[0] );
508			dAtom->setJy( ji[1] );
509			dAtom->setJz( ji[2] );
510			}
511			}
512
513			// calculate the forces
514
515	gezelter	468	myFF->doForces(calcPot,calcStress);
516	mmeineke	377
517			for( i=0; i< nAtoms; i++ ){
518
519			// complete the velocity half step
520
521			vx = atoms[i]->get_vx() +
522			( dt2 * atoms[i]->getFx() / atoms[i]->getMass() ) * e_convert;
523			vy = atoms[i]->get_vy() +
524			( dt2 * atoms[i]->getFy() / atoms[i]->getMass() ) * e_convert;
525			vz = atoms[i]->get_vz() +
526			( dt2 * atoms[i]->getFz() / atoms[i]->getMass() ) * e_convert;
527
528			atoms[i]->set_vx( vx );
529			atoms[i]->set_vy( vy );
530			atoms[i]->set_vz( vz );
531
532			// vx2 = vx * vx;
533			// vy2 = vy * vy;
534			// vz2 = vz * vz;
535
536			if( atoms[i]->isDirectional() ){
537
538			dAtom = (DirectionalAtom *)atoms[i];
539
540			// get and convert the torque to body frame
541
542			Tb[0] = dAtom->getTx();
543			Tb[1] = dAtom->getTy();
544			Tb[2] = dAtom->getTz();
545
546			dAtom->lab2Body( Tb );
547
548			// get the angular momentum, and complete the angular momentum
549			// half step
550
551			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * e_convert;
552			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * e_convert;
553			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * e_convert;
554
555			jx2 = ji[0] * ji[0];
556			jy2 = ji[1] * ji[1];
557			jz2 = ji[2] * ji[2];
558
559			rot_kE += (jx2 / dAtom->getIxx()) + (jy2 / dAtom->getIyy())
560			+ (jz2 / dAtom->getIzz());
561
562			dAtom->setJx( ji[0] );
563			dAtom->setJy( ji[1] );
564			dAtom->setJz( ji[2] );
565			}
566			}
567
568			time = tl + 1;
569
570			if( entry_plug->setTemp ){
571			if( !(time % vel_n) ) tStats->velocitize();
572			}
573			if( !(time % sample_n) ) dump_out->writeDump( time * dt );
574	gezelter	468	if( !((time+1) % status_n) ) {
575			calcPot = 1;
576			calcStress = 1;
577			}
578			if( !(time % status_n) ){
579			e_out->writeStat( time * dt );
580			calcPot = 0;
581			calcStress = 0;
582			}
583	mmeineke	377	}
584			}
585
586			dump_out->writeFinal();
587
588			delete dump_out;
589			delete e_out;
590			}
591
592			void Symplectic::rotate( int axes1, int axes2, double angle, double ji[3],
593			double A[3][3] ){
594
595			int i,j,k;
596			double sinAngle;
597			double cosAngle;
598			double angleSqr;
599			double angleSqrOver4;
600			double top, bottom;
601			double rot[3][3];
602			double tempA[3][3];
603			double tempJ[3];
604
605			// initialize the tempA
606
607			for(i=0; i<3; i++){
608			for(j=0; j<3; j++){
609	mmeineke	443	tempA[j][i] = A[i][j];
610	mmeineke	377	}
611			}
612
613			// initialize the tempJ
614
615			for( i=0; i<3; i++) tempJ[i] = ji[i];
616
617			// initalize rot as a unit matrix
618
619			rot[0][0] = 1.0;
620			rot[0][1] = 0.0;
621			rot[0][2] = 0.0;
622
623			rot[1][0] = 0.0;
624			rot[1][1] = 1.0;
625			rot[1][2] = 0.0;
626
627			rot[2][0] = 0.0;
628			rot[2][1] = 0.0;
629			rot[2][2] = 1.0;
630
631			// use a small angle aproximation for sin and cosine
632
633			angleSqr = angle * angle;
634			angleSqrOver4 = angleSqr / 4.0;
635			top = 1.0 - angleSqrOver4;
636			bottom = 1.0 + angleSqrOver4;
637
638			cosAngle = top / bottom;
639			sinAngle = angle / bottom;
640
641			rot[axes1][axes1] = cosAngle;
642			rot[axes2][axes2] = cosAngle;
643
644			rot[axes1][axes2] = sinAngle;
645			rot[axes2][axes1] = -sinAngle;
646
647			// rotate the momentum acoording to: ji[] = rot[][] * ji[]
648
649			for(i=0; i<3; i++){
650			ji[i] = 0.0;
651			for(k=0; k<3; k++){
652			ji[i] += rot[i][k] * tempJ[k];
653			}
654			}
655
656			// rotate the Rotation matrix acording to:
657			// A[][] = A[][] * transpose(rot[][])
658
659
660			// NOte for as yet unknown reason, we are setting the performing the
661			// calculation as:
662			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
663
664			for(i=0; i<3; i++){
665			for(j=0; j<3; j++){
666			A[j][i] = 0.0;
667			for(k=0; k<3; k++){
668	mmeineke	443	A[j][i] += tempA[i][k] * rot[j][k];
669	mmeineke	377	}
670			}
671			}
672			}