OOPSE/libmdtools/Integrator.cpp

#include <iostream>
#include <cstdlib>
#include <cmath>

#ifdef IS_MPI
#include "mpiSimulation.hpp"
#include <unistd.h>
#endif //is_mpi

#include "Integrator.hpp"
#include "simError.h"


Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){
  
  info = theInfo;
  myFF = the_ff;
  isFirst = 1;

  molecules = info->molecules;
  nMols = info->n_mol;

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

  nAtoms = info->n_atoms;

  std::cerr << "integ nAtoms = "  << nAtoms << "\n";

  // check for constraints
  
  constrainedA    = NULL;
  constrainedB    = NULL;
  constrainedDsqr = NULL;
  moving          = NULL;
  moved           = NULL;
  oldPos          = NULL;
  
  nConstrained = 0;

  checkConstraints();
}

Integrator::~Integrator() {
  
  if( nConstrained ){
    delete[] constrainedA;
    delete[] constrainedB;
    delete[] constrainedDsqr;
    delete[] moving;
    delete[] moved;
    delete[] oldPos;
  }
  
}

void Integrator::checkConstraints( void ){


  isConstrained = 0;

  Constraint *temp_con;
  Constraint *dummy_plug;
  temp_con = new Constraint[info->n_SRI];
  nConstrained = 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();

      std::cerr << "Is the folowing bond constrained \n";
      theArray[j]->printMe();
      
      if(constrained){
        
        std::cerr << "Yes\n";

        dummy_plug = theArray[j]->get_constraint();
        temp_con[nConstrained].set_a( dummy_plug->get_a() );
        temp_con[nConstrained].set_b( dummy_plug->get_b() );
        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
        
        nConstrained++;
        constrained = 0;
      } 
      else std::cerr << "No.\n";
    }

    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[nConstrained].set_a( dummy_plug->get_a() );
        temp_con[nConstrained].set_b( dummy_plug->get_b() );
        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
        
        nConstrained++;
        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[nConstrained].set_a( dummy_plug->get_a() );
        temp_con[nConstrained].set_b( dummy_plug->get_b() );
        temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
        
        nConstrained++;
        constrained = 0;
      }
    }
  }

  if(nConstrained > 0){
    
    isConstrained = 1;

    if(constrainedA != NULL )    delete[] constrainedA;
    if(constrainedB != NULL )    delete[] constrainedB;
    if(constrainedDsqr != NULL ) delete[] constrainedDsqr;

    constrainedA =    new int[nConstrained];
    constrainedB =    new int[nConstrained];
    constrainedDsqr = new double[nConstrained];
    
    for( int i = 0; i < nConstrained; i++){
      
      constrainedA[i] = temp_con[i].get_a();
      constrainedB[i] = temp_con[i].get_b();
      constrainedDsqr[i] = temp_con[i].get_dsqr();

    }

    
    // save oldAtoms to check for lode balanceing later on.
    
    oldAtoms = nAtoms;
    
    moving = new int[nAtoms];
    moved  = new int[nAtoms];

    oldPos = new double[nAtoms*3];
  }
  
  delete[] temp_con;
}


void Integrator::integrate( void ){

  int i, j;                         // loop counters

  double runTime     = info->run_time;
  double sampleTime  = info->sampleTime;
  double statusTime  = info->statusTime;
  double thermalTime = info->thermalTime;

  double currSample;
  double currThermal;
  double currStatus;
  double currTime;

  int calcPot, calcStress;
  int isError;


  tStats   = new Thermo( info );
  statOut  = new StatWriter( info );
  dumpOut  = new DumpWriter( info );

  atoms = info->atoms;
  DirectionalAtom* dAtom;

  dt = info->dt;
  dt2 = 0.5 * dt;

  // initialize the forces before the first step

  myFF->doForces(1,1);
  
  if( info->setTemp ){
    
    tStats->velocitize();
  }
  
  dumpOut->writeDump( 0.0 );
  statOut->writeStat( 0.0 );
  
  calcPot     = 0;
  calcStress  = 0;
  currSample  = sampleTime;
  currThermal = thermalTime;
  currStatus  = statusTime;
  currTime    = 0.0;;


  readyCheck();

#ifdef IS_MPI
  strcpy( checkPointMsg, 
          "The integrator is ready to go." );
  MPIcheckPoint();
#endif // is_mpi


  pos  = Atom::getPosArray();
  vel  = Atom::getVelArray();
  frc  = Atom::getFrcArray();

  while( currTime < runTime ){

    if( (currTime+dt) >= currStatus ){
      calcPot = 1;
      calcStress = 1;
    }

    std::cerr << currTime << "\n";

    integrateStep( calcPot, calcStress );
      
    currTime += dt;

    if( info->setTemp ){
      if( currTime >= currThermal ){
        tStats->velocitize();
        currThermal += thermalTime;
      }
    }

    if( currTime >= currSample ){
      dumpOut->writeDump( currTime );
      currSample += sampleTime;
    }

    if( currTime >= currStatus ){ 
      statOut->writeStat( currTime ); 
      calcPot = 0; 
      calcStress = 0;
      currStatus += statusTime;
    } 

#ifdef IS_MPI
    strcpy( checkPointMsg, 
            "successfully took a time step." );
    MPIcheckPoint();
#endif // is_mpi

  }

  dumpOut->writeFinal(currTime);

  delete dumpOut;
  delete statOut;
}

void Integrator::integrateStep( int calcPot, int calcStress ){


  // Position full step, and velocity half step

  preMove();
  moveA();
  //if( nConstrained ) constrainA();

  // calc forces

  myFF->doForces(calcPot,calcStress);

  // finish the velocity  half step
  
  moveB();
  if( nConstrained ) constrainB();
   
}


void Integrator::moveA( void ){
  
  int i,j,k;
  int atomIndex, aMatIndex;
  DirectionalAtom* dAtom;
  double Tb[3];
  double ji[3];
  double angle;
  double A[3][3], At[3][3];


  for( i=0; i<nAtoms; i++ ){
    atomIndex = i * 3;
    aMatIndex = i * 9;

    // velocity half step
    for( j=atomIndex; j<(atomIndex+3); j++ )
      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;


    // position whole step    
    for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j];
    

    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] ) * eConvert;
      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
      
      // use the angular velocities to propagate the rotation matrix a
      // full time step
      
      // rotate about the x-axis      
      angle = dt2 * ji[0] / dAtom->getIxx();
      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); 

      // rotate about the y-axis
      angle = dt2 * ji[1] / dAtom->getIyy();
      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
      
      // rotate about the z-axis
      angle = dt * ji[2] / dAtom->getIzz();
      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
      
      // rotate about the y-axis
      angle = dt2 * ji[1] / dAtom->getIyy();
      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
      
       // rotate about the x-axis
      angle = dt2 * ji[0] / dAtom->getIxx();
      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
      
      dAtom->setJx( ji[0] );
      dAtom->setJy( ji[1] );
      dAtom->setJz( ji[2] );

      std::cerr << "Amat[" << i << "]\n";
      info->printMat9( &Amat[aMatIndex] );
          
      std::cerr << "ji[" << i << "]\t"
                << ji[0] << "\t"
                << ji[1] << "\t"
                << ji[2] << "\n";
          
    }
    
  }
}


void Integrator::moveB( void ){
  int i,j,k;
  int atomIndex, aMatIndex;
  DirectionalAtom* dAtom;
  double Tb[3];
  double ji[3];

  for( i=0; i<nAtoms; i++ ){
    atomIndex = i * 3;
    aMatIndex = i * 9;

    // velocity half step
    for( j=atomIndex; j<(atomIndex+3); j++ )
      vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;

 
    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();
      
      std::cerr << "TrqB[" << i << "]\t"
                << Tb[0] << "\t"
                << Tb[1] << "\t"
                << Tb[2] << "\n";

      dAtom->lab2Body( Tb );
      
      // get the angular momentum, and complete the angular momentum
      // half step
      
      ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
      ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
      ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
      
      dAtom->setJx( ji[0] );
      dAtom->setJy( ji[1] );
      dAtom->setJz( ji[2] );


      std::cerr << "Amat[" << i << "]\n";
      info->printMat9( &Amat[aMatIndex] );
          
      std::cerr << "ji[" << i << "]\t"
                << ji[0] << "\t"
                << ji[1] << "\t"
                << ji[2] << "\n";
    }
  }

}

void Integrator::preMove( void ){
  int i;

  if( nConstrained ){

    for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i];
  }
}  

void Integrator::constrainA(){

  int i,j,k;
  int done;
  double pab[3];
  double rab[3];
  int a, b, ax, ay, az, bx, by, bz;
  double rma, rmb;
  double dx, dy, dz;
  double rpab;
  double rabsq, pabsq, rpabsq;
  double diffsq;
  double gab;
  int iteration;

  for( i=0; i<nAtoms; i++){
    
    moving[i] = 0;
    moved[i]  = 1;
  }

  iteration = 0;
  done = 0;
  while( !done && (iteration < maxIteration )){

    done = 1;
    for(i=0; i<nConstrained; i++){

      a = constrainedA[i];
      b = constrainedB[i];
      
      ax = (a*3) + 0;
      ay = (a*3) + 1;
      az = (a*3) + 2;

      bx = (b*3) + 0;
      by = (b*3) + 1;
      bz = (b*3) + 2;

      if( moved[a] || moved[b] ){
        
        pab[0] = pos[ax] - pos[bx];
        pab[1] = pos[ay] - pos[by];
        pab[2] = pos[az] - pos[bz];

        //periodic boundary condition

        info->wrapVector( pab );

        pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];

        rabsq = constrainedDsqr[i];
        diffsq = rabsq - pabsq;

        // the original rattle code from alan tidesley
        if (fabs(diffsq) > (tol*rabsq*2)) {
          rab[0] = oldPos[ax] - oldPos[bx];
          rab[1] = oldPos[ay] - oldPos[by];
          rab[2] = oldPos[az] - oldPos[bz];

          info->wrapVector( rab );

          rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];

          rpabsq = rpab * rpab;


          if (rpabsq < (rabsq * -diffsq)){

#ifdef IS_MPI
            a = atoms[a]->getGlobalIndex();
            b = atoms[b]->getGlobalIndex();
#endif //is_mpi
            sprintf( painCave.errMsg,
                     "Constraint failure in constrainA at atom %d and %d.\n",
                     a, b );
            painCave.isFatal = 1;
            simError();
          }

          rma = 1.0 / atoms[a]->getMass();
          rmb = 1.0 / atoms[b]->getMass();

          gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );

          dx = rab[0] * gab;
          dy = rab[1] * gab;
          dz = rab[2] * gab;

          pos[ax] += rma * dx;
          pos[ay] += rma * dy;
          pos[az] += rma * dz;

          pos[bx] -= rmb * dx;
          pos[by] -= rmb * dy;
          pos[bz] -= rmb * dz;

          dx = dx / dt;
          dy = dy / dt;
          dz = dz / dt;

          vel[ax] += rma * dx;
          vel[ay] += rma * dy;
          vel[az] += rma * dz;

          vel[bx] -= rmb * dx;
          vel[by] -= rmb * dy;
          vel[bz] -= rmb * dz;

          moving[a] = 1;
          moving[b] = 1;
          done = 0;
        }
      }
    }
    
    for(i=0; i<nAtoms; i++){
      
      moved[i] = moving[i];
      moving[i] = 0;
    }

    iteration++;
  }

  if( !done ){

    sprintf( painCave.errMsg,
             "Constraint failure in constrainA, too many iterations: %d\n",
             iteration );
    painCave.isFatal = 1;
    simError();
  }

}

void Integrator::constrainB( void ){
  
  int i,j,k;
  int done;
  double vxab, vyab, vzab;
  double rab[3];
  int a, b, ax, ay, az, bx, by, bz;
  double rma, rmb;
  double dx, dy, dz;
  double rabsq, pabsq, rvab;
  double diffsq;
  double gab;
  int iteration;

  for(i=0; i<nAtoms; i++){
    moving[i] = 0;
    moved[i] = 1;
  }

  done = 0;
  iteration = 0;
  while( !done && (iteration < maxIteration ) ){

    done = 1;

    for(i=0; i<nConstrained; i++){
      
      a = constrainedA[i];
      b = constrainedB[i];

      ax = (a*3) + 0;
      ay = (a*3) + 1;
      az = (a*3) + 2;

      bx = (b*3) + 0;
      by = (b*3) + 1;
      bz = (b*3) + 2;

      if( moved[a] || moved[b] ){
        
        vxab = vel[ax] - vel[bx];
        vyab = vel[ay] - vel[by];
        vzab = vel[az] - vel[bz];

        rab[0] = pos[ax] - pos[bx];
        rab[1] = pos[ay] - pos[by];
        rab[2] = pos[az] - pos[bz];
        
        info->wrapVector( rab );
        
        rma = 1.0 / atoms[a]->getMass();
        rmb = 1.0 / atoms[b]->getMass();

        rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
          
        gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );

        if (fabs(gab) > tol) {
          
          dx = rab[0] * gab;
          dy = rab[1] * gab;
          dz = rab[2] * gab;
          
          vel[ax] += rma * dx;
          vel[ay] += rma * dy;
          vel[az] += rma * dz;

          vel[bx] -= rmb * dx;
          vel[by] -= rmb * dy;
          vel[bz] -= rmb * dz;
          
          moving[a] = 1;
          moving[b] = 1;
          done = 0;
        }
      }
    }

    for(i=0; i<nAtoms; i++){
      moved[i] = moving[i];
      moving[i] = 0;
    }
    
    iteration++;
  }

  if( !done ){

   
    sprintf( painCave.errMsg,
             "Constraint failure in constrainB, too many iterations: %d\n",
             iteration );
    painCave.isFatal = 1;
    simError();
  } 

}


void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], 
                         double A[9] ){

  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[3*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 performing the
  // calculation as:
  //                transpose(A[][]) = transpose(A[][]) * transpose(rot[][])

  for(i=0; i<3; i++){
    for(j=0; j<3; j++){
      A[3*j+i] = 0.0;
      for(k=0; k<3; k++){
        A[3*j+i] += tempA[i][k] * rot[j][k];
      }
    }
  }
}
Revision:	597
Committed:	Mon Jul 14 21:28:54 2003 UTC (20 years, 11 months ago) by mmeineke
File size:	15329 byte(s)
Log Message:	found a bug. Unit vectors were not being updated
#	User	Rev	Content
1	mmeineke	558	#include <iostream>
2			#include <cstdlib>
3	mmeineke	561	#include <cmath>
4	mmeineke	558
5			#ifdef IS_MPI
6			#include "mpiSimulation.hpp"
7			#include <unistd.h>
8			#endif //is_mpi
9
10			#include "Integrator.hpp"
11			#include "simError.h"
12
13
14	mmeineke	561	Integrator::Integrator( SimInfo theInfo, ForceFields the_ff ){
15	mmeineke	558
16			info = theInfo;
17			myFF = the_ff;
18			isFirst = 1;
19
20			molecules = info->molecules;
21			nMols = info->n_mol;
22
23			// give a little love back to the SimInfo object
24
25			if( info->the_integrator != NULL ) delete info->the_integrator;
26			info->the_integrator = this;
27
28			nAtoms = info->n_atoms;
29
30	mmeineke	594	std::cerr << "integ nAtoms = " << nAtoms << "\n";
31
32	mmeineke	558	// check for constraints
33
34			constrainedA = NULL;
35			constrainedB = NULL;
36			constrainedDsqr = NULL;
37			moving = NULL;
38			moved = NULL;
39	mmeineke	561	oldPos = NULL;
40	mmeineke	558
41			nConstrained = 0;
42
43			checkConstraints();
44			}
45
46			Integrator::~Integrator() {
47
48			if( nConstrained ){
49			delete[] constrainedA;
50			delete[] constrainedB;
51			delete[] constrainedDsqr;
52			delete[] moving;
53			delete[] moved;
54	mmeineke	561	delete[] oldPos;
55	mmeineke	558	}
56
57			}
58
59			void Integrator::checkConstraints( void ){
60
61
62			isConstrained = 0;
63
64			Constraint *temp_con;
65			Constraint *dummy_plug;
66			temp_con = new Constraint[info->n_SRI];
67			nConstrained = 0;
68			int constrained = 0;
69
70			SRI** theArray;
71			for(int i = 0; i < nMols; i++){
72
73			theArray = (SRI**) molecules[i].getMyBonds();
74			for(int j=0; j<molecules[i].getNBonds(); j++){
75
76			constrained = theArray[j]->is_constrained();
77	mmeineke	594
78			std::cerr << "Is the folowing bond constrained \n";
79			theArray[j]->printMe();
80	mmeineke	558
81			if(constrained){
82
83	mmeineke	594	std::cerr << "Yes\n";
84
85	mmeineke	558	dummy_plug = theArray[j]->get_constraint();
86			temp_con[nConstrained].set_a( dummy_plug->get_a() );
87			temp_con[nConstrained].set_b( dummy_plug->get_b() );
88			temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
89
90			nConstrained++;
91			constrained = 0;
92	mmeineke	594	}
93			else std::cerr << "No.\n";
94	mmeineke	558	}
95
96			theArray = (SRI**) molecules[i].getMyBends();
97			for(int j=0; j<molecules[i].getNBends(); j++){
98
99			constrained = theArray[j]->is_constrained();
100
101			if(constrained){
102
103			dummy_plug = theArray[j]->get_constraint();
104			temp_con[nConstrained].set_a( dummy_plug->get_a() );
105			temp_con[nConstrained].set_b( dummy_plug->get_b() );
106			temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
107
108			nConstrained++;
109			constrained = 0;
110			}
111			}
112
113			theArray = (SRI**) molecules[i].getMyTorsions();
114			for(int j=0; j<molecules[i].getNTorsions(); j++){
115
116			constrained = theArray[j]->is_constrained();
117
118			if(constrained){
119
120			dummy_plug = theArray[j]->get_constraint();
121			temp_con[nConstrained].set_a( dummy_plug->get_a() );
122			temp_con[nConstrained].set_b( dummy_plug->get_b() );
123			temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
124
125			nConstrained++;
126			constrained = 0;
127			}
128			}
129			}
130
131			if(nConstrained > 0){
132
133			isConstrained = 1;
134
135			if(constrainedA != NULL ) delete[] constrainedA;
136			if(constrainedB != NULL ) delete[] constrainedB;
137			if(constrainedDsqr != NULL ) delete[] constrainedDsqr;
138
139			constrainedA = new int[nConstrained];
140			constrainedB = new int[nConstrained];
141			constrainedDsqr = new double[nConstrained];
142
143			for( int i = 0; i < nConstrained; i++){
144
145			constrainedA[i] = temp_con[i].get_a();
146			constrainedB[i] = temp_con[i].get_b();
147			constrainedDsqr[i] = temp_con[i].get_dsqr();
148	mmeineke	563
149	mmeineke	558	}
150
151
152			// save oldAtoms to check for lode balanceing later on.
153
154			oldAtoms = nAtoms;
155
156			moving = new int[nAtoms];
157			moved = new int[nAtoms];
158
159	mmeineke	561	oldPos = new double[nAtoms*3];
160	mmeineke	558	}
161
162			delete[] temp_con;
163			}
164
165
166			void Integrator::integrate( void ){
167
168			int i, j; // loop counters
169
170			double runTime = info->run_time;
171			double sampleTime = info->sampleTime;
172			double statusTime = info->statusTime;
173			double thermalTime = info->thermalTime;
174
175			double currSample;
176			double currThermal;
177			double currStatus;
178			double currTime;
179
180			int calcPot, calcStress;
181			int isError;
182
183	mmeineke	561
184
185	mmeineke	558	tStats = new Thermo( info );
186	mmeineke	561	statOut = new StatWriter( info );
187			dumpOut = new DumpWriter( info );
188	mmeineke	558
189	mmeineke	561	atoms = info->atoms;
190	mmeineke	558	DirectionalAtom* dAtom;
191	mmeineke	561
192			dt = info->dt;
193	mmeineke	558	dt2 = 0.5 * dt;
194
195			// initialize the forces before the first step
196
197			myFF->doForces(1,1);
198
199			if( info->setTemp ){
200
201			tStats->velocitize();
202			}
203
204	mmeineke	561	dumpOut->writeDump( 0.0 );
205			statOut->writeStat( 0.0 );
206	mmeineke	558
207			calcPot = 0;
208			calcStress = 0;
209			currSample = sampleTime;
210			currThermal = thermalTime;
211			currStatus = statusTime;
212			currTime = 0.0;;
213
214	mmeineke	559
215			readyCheck();
216
217			#ifdef IS_MPI
218			strcpy( checkPointMsg,
219			"The integrator is ready to go." );
220			MPIcheckPoint();
221			#endif // is_mpi
222
223	mmeineke	561
224			pos = Atom::getPosArray();
225			vel = Atom::getVelArray();
226			frc = Atom::getFrcArray();
227
228	mmeineke	558	while( currTime < runTime ){
229
230			if( (currTime+dt) >= currStatus ){
231			calcPot = 1;
232			calcStress = 1;
233			}
234	mmeineke	561
235	mmeineke	597	std::cerr << currTime << "\n";
236	mmeineke	594
237	mmeineke	558	integrateStep( calcPot, calcStress );
238
239			currTime += dt;
240
241			if( info->setTemp ){
242			if( currTime >= currThermal ){
243			tStats->velocitize();
244			currThermal += thermalTime;
245			}
246			}
247
248			if( currTime >= currSample ){
249	mmeineke	561	dumpOut->writeDump( currTime );
250	mmeineke	558	currSample += sampleTime;
251			}
252
253			if( currTime >= currStatus ){
254	mmeineke	561	statOut->writeStat( currTime );
255	mmeineke	558	calcPot = 0;
256			calcStress = 0;
257			currStatus += statusTime;
258			}
259	mmeineke	559
260			#ifdef IS_MPI
261			strcpy( checkPointMsg,
262			"successfully took a time step." );
263			MPIcheckPoint();
264			#endif // is_mpi
265
266	mmeineke	558	}
267
268	mmeineke	572	dumpOut->writeFinal(currTime);
269	mmeineke	558
270	mmeineke	561	delete dumpOut;
271			delete statOut;
272	mmeineke	558	}
273
274			void Integrator::integrateStep( int calcPot, int calcStress ){
275
276	mmeineke	561
277
278	mmeineke	558	// Position full step, and velocity half step
279
280	mmeineke	561	preMove();
281	mmeineke	558	moveA();
282	mmeineke	597	//if( nConstrained ) constrainA();
283	mmeineke	558
284			// calc forces
285
286			myFF->doForces(calcPot,calcStress);
287
288			// finish the velocity half step
289
290			moveB();
291			if( nConstrained ) constrainB();
292
293			}
294
295
296			void Integrator::moveA( void ){
297
298			int i,j,k;
299			int atomIndex, aMatIndex;
300			DirectionalAtom* dAtom;
301			double Tb[3];
302			double ji[3];
303	mmeineke	561	double angle;
304	mmeineke	597	double A[3][3], At[3][3];
305	mmeineke	558
306	mmeineke	567
307	mmeineke	558	for( i=0; i<nAtoms; i++ ){
308			atomIndex = i * 3;
309			aMatIndex = i * 9;
310	mmeineke	567
311	mmeineke	558	// velocity half step
312			for( j=atomIndex; j<(atomIndex+3); j++ )
313			vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
314
315	mmeineke	594
316	mmeineke	558	// position whole step
317	mmeineke	567	for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j];
318
319	mmeineke	594
320	mmeineke	558	if( atoms[i]->isDirectional() ){
321
322			dAtom = (DirectionalAtom *)atoms[i];
323
324			// get and convert the torque to body frame
325
326			Tb[0] = dAtom->getTx();
327			Tb[1] = dAtom->getTy();
328			Tb[2] = dAtom->getTz();
329	mmeineke	597
330	mmeineke	558	dAtom->lab2Body( Tb );
331	mmeineke	597
332	mmeineke	558	// get the angular momentum, and propagate a half step
333
334			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
335			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
336			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
337
338			// use the angular velocities to propagate the rotation matrix a
339			// full time step
340
341			// rotate about the x-axis
342			angle = dt2 * ji[0] / dAtom->getIxx();
343	mmeineke	597	this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
344
345	mmeineke	558	// rotate about the y-axis
346			angle = dt2 * ji[1] / dAtom->getIyy();
347	mmeineke	597	this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
348	mmeineke	558
349			// rotate about the z-axis
350			angle = dt * ji[2] / dAtom->getIzz();
351	mmeineke	597	this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
352	mmeineke	558
353			// rotate about the y-axis
354			angle = dt2 * ji[1] / dAtom->getIyy();
355	mmeineke	597	this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
356	mmeineke	558
357			// rotate about the x-axis
358			angle = dt2 * ji[0] / dAtom->getIxx();
359	mmeineke	597	this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
360	mmeineke	558
361			dAtom->setJx( ji[0] );
362			dAtom->setJy( ji[1] );
363			dAtom->setJz( ji[2] );
364	mmeineke	597
365			std::cerr << "Amat[" << i << "]\n";
366			info->printMat9( &Amat[aMatIndex] );
367
368			std::cerr << "ji[" << i << "]\t"
369			<< ji[0] << "\t"
370			<< ji[1] << "\t"
371			<< ji[2] << "\n";
372
373	mmeineke	558	}
374
375			}
376			}
377
378
379			void Integrator::moveB( void ){
380			int i,j,k;
381	mmeineke	597	int atomIndex, aMatIndex;
382	mmeineke	558	DirectionalAtom* dAtom;
383			double Tb[3];
384			double ji[3];
385
386			for( i=0; i<nAtoms; i++ ){
387			atomIndex = i * 3;
388	mmeineke	597	aMatIndex = i * 9;
389	mmeineke	558
390			// velocity half step
391			for( j=atomIndex; j<(atomIndex+3); j++ )
392			vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
393
394	mmeineke	597
395	mmeineke	558	if( atoms[i]->isDirectional() ){
396
397			dAtom = (DirectionalAtom *)atoms[i];
398
399			// get and convert the torque to body frame
400
401			Tb[0] = dAtom->getTx();
402			Tb[1] = dAtom->getTy();
403			Tb[2] = dAtom->getTz();
404
405	mmeineke	597	std::cerr << "TrqB[" << i << "]\t"
406			<< Tb[0] << "\t"
407			<< Tb[1] << "\t"
408			<< Tb[2] << "\n";
409
410	mmeineke	558	dAtom->lab2Body( Tb );
411
412			// get the angular momentum, and complete the angular momentum
413			// half step
414
415			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
416			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
417			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
418
419			dAtom->setJx( ji[0] );
420			dAtom->setJy( ji[1] );
421			dAtom->setJz( ji[2] );
422	mmeineke	597
423
424			std::cerr << "Amat[" << i << "]\n";
425			info->printMat9( &Amat[aMatIndex] );
426
427			std::cerr << "ji[" << i << "]\t"
428			<< ji[0] << "\t"
429			<< ji[1] << "\t"
430			<< ji[2] << "\n";
431	mmeineke	558	}
432			}
433
434			}
435
436			void Integrator::preMove( void ){
437			int i;
438
439			if( nConstrained ){
440	mmeineke	561
441	mmeineke	558	for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i];
442			}
443			}
444
445			void Integrator::constrainA(){
446
447			int i,j,k;
448			int done;
449	mmeineke	572	double pab[3];
450			double rab[3];
451	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
452	mmeineke	558	double rma, rmb;
453			double dx, dy, dz;
454	mmeineke	561	double rpab;
455	mmeineke	558	double rabsq, pabsq, rpabsq;
456			double diffsq;
457			double gab;
458			int iteration;
459
460			for( i=0; i<nAtoms; i++){
461
462			moving[i] = 0;
463			moved[i] = 1;
464			}
465	mmeineke	567
466	mmeineke	558	iteration = 0;
467			done = 0;
468			while( !done && (iteration < maxIteration )){
469
470			done = 1;
471			for(i=0; i<nConstrained; i++){
472
473			a = constrainedA[i];
474			b = constrainedB[i];
475	mmeineke	563
476			ax = (a*3) + 0;
477			ay = (a*3) + 1;
478			az = (a*3) + 2;
479
480			bx = (b*3) + 0;
481			by = (b*3) + 1;
482			bz = (b*3) + 2;
483
484	mmeineke	558	if( moved[a] \|\| moved[b] ){
485
486	mmeineke	572	pab[0] = pos[ax] - pos[bx];
487			pab[1] = pos[ay] - pos[by];
488			pab[2] = pos[az] - pos[bz];
489	mmeineke	558
490	mmeineke	567	//periodic boundary condition
491
492	mmeineke	572	info->wrapVector( pab );
493	mmeineke	567
494	mmeineke	572	pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
495
496	mmeineke	561	rabsq = constrainedDsqr[i];
497	mmeineke	567	diffsq = rabsq - pabsq;
498	mmeineke	558
499			// the original rattle code from alan tidesley
500	mmeineke	563	if (fabs(diffsq) > (tolrabsq2)) {
501	mmeineke	572	rab[0] = oldPos[ax] - oldPos[bx];
502			rab[1] = oldPos[ay] - oldPos[by];
503			rab[2] = oldPos[az] - oldPos[bz];
504	mmeineke	567
505	mmeineke	572	info->wrapVector( rab );
506	mmeineke	558
507	mmeineke	572	rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
508	mmeineke	567
509	mmeineke	558	rpabsq = rpab * rpab;
510
511
512			if (rpabsq < (rabsq * -diffsq)){
513	mmeineke	563
514	mmeineke	558	#ifdef IS_MPI
515			a = atoms[a]->getGlobalIndex();
516			b = atoms[b]->getGlobalIndex();
517			#endif //is_mpi
518			sprintf( painCave.errMsg,
519	mmeineke	563	"Constraint failure in constrainA at atom %d and %d.\n",
520	mmeineke	558	a, b );
521			painCave.isFatal = 1;
522			simError();
523			}
524
525			rma = 1.0 / atoms[a]->getMass();
526			rmb = 1.0 / atoms[b]->getMass();
527	mmeineke	567
528	mmeineke	558	gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );
529	mmeineke	567
530	mmeineke	572	dx = rab[0] * gab;
531			dy = rab[1] * gab;
532			dz = rab[2] * gab;
533	mmeineke	558
534	mmeineke	563	pos[ax] += rma * dx;
535			pos[ay] += rma * dy;
536			pos[az] += rma * dz;
537	mmeineke	558
538	mmeineke	563	pos[bx] -= rmb * dx;
539			pos[by] -= rmb * dy;
540			pos[bz] -= rmb * dz;
541	mmeineke	558
542			dx = dx / dt;
543			dy = dy / dt;
544			dz = dz / dt;
545
546	mmeineke	563	vel[ax] += rma * dx;
547			vel[ay] += rma * dy;
548			vel[az] += rma * dz;
549	mmeineke	558
550	mmeineke	563	vel[bx] -= rmb * dx;
551			vel[by] -= rmb * dy;
552			vel[bz] -= rmb * dz;
553	mmeineke	558
554			moving[a] = 1;
555			moving[b] = 1;
556			done = 0;
557			}
558			}
559			}
560
561			for(i=0; i<nAtoms; i++){
562
563			moved[i] = moving[i];
564			moving[i] = 0;
565			}
566
567			iteration++;
568			}
569
570			if( !done ){
571
572	mmeineke	561	sprintf( painCave.errMsg,
573	mmeineke	558	"Constraint failure in constrainA, too many iterations: %d\n",
574	mmeineke	561	iteration );
575	mmeineke	558	painCave.isFatal = 1;
576			simError();
577			}
578
579			}
580
581			void Integrator::constrainB( void ){
582
583			int i,j,k;
584			int done;
585			double vxab, vyab, vzab;
586	mmeineke	572	double rab[3];
587	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
588	mmeineke	558	double rma, rmb;
589			double dx, dy, dz;
590			double rabsq, pabsq, rvab;
591			double diffsq;
592			double gab;
593			int iteration;
594
595	mmeineke	561	for(i=0; i<nAtoms; i++){
596	mmeineke	558	moving[i] = 0;
597			moved[i] = 1;
598			}
599
600			done = 0;
601	mmeineke	561	iteration = 0;
602	mmeineke	558	while( !done && (iteration < maxIteration ) ){
603
604	mmeineke	567	done = 1;
605
606	mmeineke	558	for(i=0; i<nConstrained; i++){
607
608			a = constrainedA[i];
609			b = constrainedB[i];
610
611	mmeineke	567	ax = (a*3) + 0;
612			ay = (a*3) + 1;
613			az = (a*3) + 2;
614	mmeineke	563
615	mmeineke	567	bx = (b*3) + 0;
616			by = (b*3) + 1;
617			bz = (b*3) + 2;
618	mmeineke	563
619	mmeineke	558	if( moved[a] \|\| moved[b] ){
620
621	mmeineke	563	vxab = vel[ax] - vel[bx];
622			vyab = vel[ay] - vel[by];
623			vzab = vel[az] - vel[bz];
624	mmeineke	558
625	mmeineke	572	rab[0] = pos[ax] - pos[bx];
626			rab[1] = pos[ay] - pos[by];
627			rab[2] = pos[az] - pos[bz];
628	mmeineke	558
629	mmeineke	572	info->wrapVector( rab );
630	mmeineke	567
631	mmeineke	558	rma = 1.0 / atoms[a]->getMass();
632			rmb = 1.0 / atoms[b]->getMass();
633
634	mmeineke	572	rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
635	mmeineke	558
636	mmeineke	561	gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );
637	mmeineke	558
638			if (fabs(gab) > tol) {
639
640	mmeineke	572	dx = rab[0] * gab;
641			dy = rab[1] * gab;
642			dz = rab[2] * gab;
643	mmeineke	558
644	mmeineke	563	vel[ax] += rma * dx;
645			vel[ay] += rma * dy;
646			vel[az] += rma * dz;
647	mmeineke	558
648	mmeineke	563	vel[bx] -= rmb * dx;
649			vel[by] -= rmb * dy;
650			vel[bz] -= rmb * dz;
651	mmeineke	558
652			moving[a] = 1;
653			moving[b] = 1;
654			done = 0;
655			}
656			}
657			}
658
659			for(i=0; i<nAtoms; i++){
660			moved[i] = moving[i];
661			moving[i] = 0;
662			}
663
664			iteration++;
665			}
666
667			if( !done ){
668
669
670	mmeineke	561	sprintf( painCave.errMsg,
671	mmeineke	558	"Constraint failure in constrainB, too many iterations: %d\n",
672	mmeineke	561	iteration );
673	mmeineke	558	painCave.isFatal = 1;
674			simError();
675			}
676
677			}
678
679
680
681
682
683
684
685			void Integrator::rotate( int axes1, int axes2, double angle, double ji[3],
686	mmeineke	597	double A[9] ){
687	mmeineke	558
688			int i,j,k;
689			double sinAngle;
690			double cosAngle;
691			double angleSqr;
692			double angleSqrOver4;
693			double top, bottom;
694			double rot[3][3];
695			double tempA[3][3];
696			double tempJ[3];
697
698	mmeineke	597
699	mmeineke	558	// initialize the tempA
700
701			for(i=0; i<3; i++){
702			for(j=0; j<3; j++){
703	mmeineke	597	tempA[j][i] = A[3*i+j];
704	mmeineke	558	}
705			}
706
707			// initialize the tempJ
708
709			for( i=0; i<3; i++) tempJ[i] = ji[i];
710
711			// initalize rot as a unit matrix
712
713			rot[0][0] = 1.0;
714			rot[0][1] = 0.0;
715			rot[0][2] = 0.0;
716
717			rot[1][0] = 0.0;
718			rot[1][1] = 1.0;
719			rot[1][2] = 0.0;
720
721			rot[2][0] = 0.0;
722			rot[2][1] = 0.0;
723			rot[2][2] = 1.0;
724
725			// use a small angle aproximation for sin and cosine
726
727			angleSqr = angle * angle;
728			angleSqrOver4 = angleSqr / 4.0;
729			top = 1.0 - angleSqrOver4;
730			bottom = 1.0 + angleSqrOver4;
731
732			cosAngle = top / bottom;
733			sinAngle = angle / bottom;
734
735			rot[axes1][axes1] = cosAngle;
736			rot[axes2][axes2] = cosAngle;
737
738			rot[axes1][axes2] = sinAngle;
739			rot[axes2][axes1] = -sinAngle;
740
741			// rotate the momentum acoording to: ji[] = rot[][] * ji[]
742
743			for(i=0; i<3; i++){
744			ji[i] = 0.0;
745			for(k=0; k<3; k++){
746			ji[i] += rot[i][k] * tempJ[k];
747			}
748			}
749
750			// rotate the Rotation matrix acording to:
751			// A[][] = A[][] * transpose(rot[][])
752
753
754	mmeineke	561	// NOte for as yet unknown reason, we are performing the
755	mmeineke	558	// calculation as:
756			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
757
758			for(i=0; i<3; i++){
759			for(j=0; j<3; j++){
760	mmeineke	597	A[3*j+i] = 0.0;
761	mmeineke	558	for(k=0; k<3; k++){
762	mmeineke	597	A[3j+i] += tempA[i][k] rot[j][k];
763	mmeineke	558	}
764			}
765			}
766			}