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;

  // 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();

      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].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

  while( currTime < runTime ){

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

    integrateStep( calcPot, calcStress );
      
    currTime += dt;
    info->setTime(currTime);

    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();

  
#ifdef IS_MPI
  strcpy( checkPointMsg, "Succesful moveA\n" );
  MPIcheckPoint();
#endif // is_mpi
  

  // calc forces

  myFF->doForces(calcPot,calcStress);

#ifdef IS_MPI
  strcpy( checkPointMsg, "Succesful doForces\n" );
  MPIcheckPoint();
#endif // is_mpi
  

  // finish the velocity  half step
  
  moveB();
  if( nConstrained ) constrainB();
  
#ifdef IS_MPI
  strcpy( checkPointMsg, "Succesful moveB\n" );
  MPIcheckPoint();
#endif // is_mpi
  
 
}


void Integrator::moveA( void ){
  
  int i, j;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3];
  double A[3][3], I[3][3];
  double angle;
  double vel[3], pos[3], frc[3];
  double mass;

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

    atoms[i]->getVel( vel );
    atoms[i]->getPos( pos );
    atoms[i]->getFrc( frc );

    mass = atoms[i]->getMass();

    for (j=0; j < 3; j++) {
      // velocity half step
      vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
      // position whole step
      pos[j] += dt * vel[j];
    }

    atoms[i]->setVel( vel );
    atoms[i]->setPos( pos );

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

      dAtom = (DirectionalAtom *)atoms[i];
          
      // get and convert the torque to body frame
      
      dAtom->getTrq( Tb );
      dAtom->lab2Body( Tb );

      // get the angular momentum, and propagate a half step

      dAtom->getJ( ji );

      for (j=0; j < 3; j++) 
        ji[j] += (dt2 * Tb[j]) * eConvert;
      
      // use the angular velocities to propagate the rotation matrix a
      // full time step

      dAtom->getA(A);
      dAtom->getI(I);
    
      // rotate about the x-axis      
      angle = dt2 * ji[0] / I[0][0];
      this->rotate( 1, 2, angle, ji, A ); 

      // rotate about the y-axis
      angle = dt2 * ji[1] / I[1][1];
      this->rotate( 2, 0, angle, ji, A );
      
      // rotate about the z-axis
      angle = dt * ji[2] / I[2][2];
      this->rotate( 0, 1, angle, ji, A);
      
      // rotate about the y-axis
      angle = dt2 * ji[1] / I[1][1];
      this->rotate( 2, 0, angle, ji, A );
      
       // rotate about the x-axis
      angle = dt2 * ji[0] / I[0][0];
      this->rotate( 1, 2, angle, ji, A );
      

      dAtom->setJ( ji );
      dAtom->setA( A  );
          
    }    
  }
}


void Integrator::moveB( void ){
  int i, j;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3];
  double vel[3], frc[3];
  double mass;

  for( i=0; i<nAtoms; i++ ){
 
    atoms[i]->getVel( vel );
    atoms[i]->getFrc( frc );

    mass = atoms[i]->getMass();

    // velocity half step
    for (j=0; j < 3; j++) 
      vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
    
    atoms[i]->setVel( vel );
 
    if( atoms[i]->isDirectional() ){

      dAtom = (DirectionalAtom *)atoms[i];

      // get and convert the torque to body frame      

      dAtom->getTrq( Tb );
      dAtom->lab2Body( Tb );

      // get the angular momentum, and propagate a half step

      dAtom->getJ( ji );

      for (j=0; j < 3; j++) 
        ji[j] += (dt2 * Tb[j]) * eConvert;
      

      dAtom->setJ( ji );
    }
  }
}

void Integrator::preMove( void ){
  int i, j;
  double pos[3];

  if( nConstrained ){

    for(i=0; i < nAtoms; i++) {
 
      atoms[i]->getPos( pos );

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

    }
  }  
}

void Integrator::constrainA(){

  int i,j,k;
  int done;
  double posA[3], posB[3];
  double velA[3], velB[3];
  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] ){
        
        atoms[a]->getPos( posA );
        atoms[b]->getPos( posB );
        
        for (j = 0; j < 3; j++ ) 
          pab[j] = posA[j] - posB[j];
        
        //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;

          posA[0] += rma * dx;
          posA[1] += rma * dy;
          posA[2] += rma * dz;

          atoms[a]->setPos( posA );

          posB[0] -= rmb * dx;
          posB[1] -= rmb * dy;
          posB[2] -= rmb * dz;

          atoms[b]->setPos( posB );

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

          atoms[a]->getVel( velA );

          velA[0] += rma * dx;
          velA[1] += rma * dy;
          velA[2] += rma * dz;

          atoms[a]->setVel( velA );

          atoms[b]->getVel( velB );

          velB[0] -= rmb * dx;
          velB[1] -= rmb * dy;
          velB[2] -= rmb * dz;

          atoms[b]->setVel( velB );

          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 posA[3], posB[3];
  double velA[3], velB[3];
  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] ){

        atoms[a]->getVel( velA );
        atoms[b]->getVel( velB );
          
        vxab = velA[0] - velB[0];
        vyab = velA[1] - velB[1];
        vzab = velA[2] - velB[2];

        atoms[a]->getPos( posA );
        atoms[b]->getPos( posB );

        for (j = 0; j < 3; j++) 
          rab[j] = posA[j] - posB[j];
          
        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;
        
          velA[0] += rma * dx;
          velA[1] += rma * dy;
          velA[2] += rma * dz;

          atoms[a]->setVel( velA );

          velB[0] -= rmb * dx;
          velB[1] -= rmb * dy;
          velB[2] -= rmb * dz;

          atoms[b]->setVel( velB );
          
          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[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 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:	637
Committed:	Thu Jul 17 21:50:01 2003 UTC (20 years, 11 months ago) by gezelter
File size:	15197 byte(s)
Log Message:	Started work on a DumpReader
#	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			// check for constraints
31
32			constrainedA = NULL;
33			constrainedB = NULL;
34			constrainedDsqr = NULL;
35			moving = NULL;
36			moved = NULL;
37	mmeineke	561	oldPos = NULL;
38	mmeineke	558
39			nConstrained = 0;
40
41			checkConstraints();
42			}
43
44			Integrator::~Integrator() {
45
46			if( nConstrained ){
47			delete[] constrainedA;
48			delete[] constrainedB;
49			delete[] constrainedDsqr;
50			delete[] moving;
51			delete[] moved;
52	mmeineke	561	delete[] oldPos;
53	mmeineke	558	}
54
55			}
56
57			void Integrator::checkConstraints( void ){
58
59
60			isConstrained = 0;
61
62			Constraint *temp_con;
63			Constraint *dummy_plug;
64			temp_con = new Constraint[info->n_SRI];
65			nConstrained = 0;
66			int constrained = 0;
67
68			SRI** theArray;
69			for(int i = 0; i < nMols; i++){
70
71			theArray = (SRI**) molecules[i].getMyBonds();
72			for(int j=0; j<molecules[i].getNBonds(); j++){
73
74			constrained = theArray[j]->is_constrained();
75	mmeineke	594
76	mmeineke	558	if(constrained){
77	mmeineke	594
78	mmeineke	558	dummy_plug = theArray[j]->get_constraint();
79			temp_con[nConstrained].set_a( dummy_plug->get_a() );
80			temp_con[nConstrained].set_b( dummy_plug->get_b() );
81			temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
82
83			nConstrained++;
84			constrained = 0;
85	mmeineke	594	}
86	mmeineke	558	}
87
88			theArray = (SRI**) molecules[i].getMyBends();
89			for(int j=0; j<molecules[i].getNBends(); j++){
90
91			constrained = theArray[j]->is_constrained();
92
93			if(constrained){
94
95			dummy_plug = theArray[j]->get_constraint();
96			temp_con[nConstrained].set_a( dummy_plug->get_a() );
97			temp_con[nConstrained].set_b( dummy_plug->get_b() );
98			temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
99
100			nConstrained++;
101			constrained = 0;
102			}
103			}
104
105			theArray = (SRI**) molecules[i].getMyTorsions();
106			for(int j=0; j<molecules[i].getNTorsions(); j++){
107
108			constrained = theArray[j]->is_constrained();
109
110			if(constrained){
111
112			dummy_plug = theArray[j]->get_constraint();
113			temp_con[nConstrained].set_a( dummy_plug->get_a() );
114			temp_con[nConstrained].set_b( dummy_plug->get_b() );
115			temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() );
116
117			nConstrained++;
118			constrained = 0;
119			}
120			}
121			}
122
123			if(nConstrained > 0){
124
125			isConstrained = 1;
126
127			if(constrainedA != NULL ) delete[] constrainedA;
128			if(constrainedB != NULL ) delete[] constrainedB;
129			if(constrainedDsqr != NULL ) delete[] constrainedDsqr;
130
131			constrainedA = new int[nConstrained];
132			constrainedB = new int[nConstrained];
133			constrainedDsqr = new double[nConstrained];
134
135			for( int i = 0; i < nConstrained; i++){
136
137			constrainedA[i] = temp_con[i].get_a();
138			constrainedB[i] = temp_con[i].get_b();
139			constrainedDsqr[i] = temp_con[i].get_dsqr();
140	mmeineke	563
141	mmeineke	558	}
142
143
144			// save oldAtoms to check for lode balanceing later on.
145
146			oldAtoms = nAtoms;
147
148			moving = new int[nAtoms];
149			moved = new int[nAtoms];
150
151	mmeineke	561	oldPos = new double[nAtoms*3];
152	mmeineke	558	}
153
154			delete[] temp_con;
155			}
156
157
158			void Integrator::integrate( void ){
159
160			int i, j; // loop counters
161
162			double runTime = info->run_time;
163			double sampleTime = info->sampleTime;
164			double statusTime = info->statusTime;
165			double thermalTime = info->thermalTime;
166
167			double currSample;
168			double currThermal;
169			double currStatus;
170			double currTime;
171
172			int calcPot, calcStress;
173			int isError;
174
175			tStats = new Thermo( info );
176	mmeineke	561	statOut = new StatWriter( info );
177			dumpOut = new DumpWriter( info );
178	mmeineke	558
179	mmeineke	561	atoms = info->atoms;
180	mmeineke	558	DirectionalAtom* dAtom;
181	mmeineke	561
182			dt = info->dt;
183	mmeineke	558	dt2 = 0.5 * dt;
184
185			// initialize the forces before the first step
186
187			myFF->doForces(1,1);
188
189			if( info->setTemp ){
190
191			tStats->velocitize();
192			}
193
194	mmeineke	561	dumpOut->writeDump( 0.0 );
195			statOut->writeStat( 0.0 );
196	mmeineke	558
197			calcPot = 0;
198			calcStress = 0;
199			currSample = sampleTime;
200			currThermal = thermalTime;
201			currStatus = statusTime;
202			currTime = 0.0;;
203
204	mmeineke	559
205			readyCheck();
206
207			#ifdef IS_MPI
208			strcpy( checkPointMsg,
209			"The integrator is ready to go." );
210			MPIcheckPoint();
211			#endif // is_mpi
212
213	mmeineke	558	while( currTime < runTime ){
214
215			if( (currTime+dt) >= currStatus ){
216			calcPot = 1;
217			calcStress = 1;
218			}
219	mmeineke	561
220	mmeineke	558	integrateStep( calcPot, calcStress );
221
222			currTime += dt;
223	gezelter	637	info->setTime(currTime);
224	mmeineke	558
225			if( info->setTemp ){
226			if( currTime >= currThermal ){
227			tStats->velocitize();
228			currThermal += thermalTime;
229			}
230			}
231
232			if( currTime >= currSample ){
233	mmeineke	561	dumpOut->writeDump( currTime );
234	mmeineke	558	currSample += sampleTime;
235			}
236
237			if( currTime >= currStatus ){
238	mmeineke	561	statOut->writeStat( currTime );
239	mmeineke	558	calcPot = 0;
240			calcStress = 0;
241			currStatus += statusTime;
242			}
243	mmeineke	559
244			#ifdef IS_MPI
245			strcpy( checkPointMsg,
246			"successfully took a time step." );
247			MPIcheckPoint();
248			#endif // is_mpi
249
250	mmeineke	558	}
251
252	mmeineke	572	dumpOut->writeFinal(currTime);
253	mmeineke	558
254	mmeineke	561	delete dumpOut;
255			delete statOut;
256	mmeineke	558	}
257
258			void Integrator::integrateStep( int calcPot, int calcStress ){
259
260	mmeineke	561
261
262	mmeineke	558	// Position full step, and velocity half step
263
264	mmeineke	561	preMove();
265	mmeineke	558	moveA();
266	gezelter	600	if( nConstrained ) constrainA();
267	mmeineke	558
268	mmeineke	614
269			#ifdef IS_MPI
270			strcpy( checkPointMsg, "Succesful moveA\n" );
271			MPIcheckPoint();
272			#endif // is_mpi
273
274
275	mmeineke	558	// calc forces
276
277			myFF->doForces(calcPot,calcStress);
278
279	mmeineke	614	#ifdef IS_MPI
280			strcpy( checkPointMsg, "Succesful doForces\n" );
281			MPIcheckPoint();
282			#endif // is_mpi
283
284
285	mmeineke	558	// finish the velocity half step
286
287			moveB();
288			if( nConstrained ) constrainB();
289	mmeineke	614
290			#ifdef IS_MPI
291			strcpy( checkPointMsg, "Succesful moveB\n" );
292			MPIcheckPoint();
293			#endif // is_mpi
294
295
296	mmeineke	558	}
297
298
299			void Integrator::moveA( void ){
300
301	gezelter	600	int i, j;
302	mmeineke	558	DirectionalAtom* dAtom;
303	gezelter	600	double Tb[3], ji[3];
304			double A[3][3], I[3][3];
305	mmeineke	561	double angle;
306	gezelter	600	double vel[3], pos[3], frc[3];
307			double mass;
308	mmeineke	558
309			for( i=0; i<nAtoms; i++ ){
310	mmeineke	567
311	gezelter	600	atoms[i]->getVel( vel );
312			atoms[i]->getPos( pos );
313			atoms[i]->getFrc( frc );
314	mmeineke	558
315	gezelter	600	mass = atoms[i]->getMass();
316	mmeineke	594
317	gezelter	600	for (j=0; j < 3; j++) {
318			// velocity half step
319			vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
320			// position whole step
321			pos[j] += dt * vel[j];
322			}
323	mmeineke	594
324	gezelter	600	atoms[i]->setVel( vel );
325			atoms[i]->setPos( pos );
326
327	mmeineke	558	if( atoms[i]->isDirectional() ){
328
329			dAtom = (DirectionalAtom *)atoms[i];
330
331			// get and convert the torque to body frame
332
333	gezelter	600	dAtom->getTrq( Tb );
334	mmeineke	558	dAtom->lab2Body( Tb );
335	mmeineke	597
336	mmeineke	558	// get the angular momentum, and propagate a half step
337	gezelter	600
338			dAtom->getJ( ji );
339
340			for (j=0; j < 3; j++)
341			ji[j] += (dt2 * Tb[j]) * eConvert;
342	mmeineke	558
343			// use the angular velocities to propagate the rotation matrix a
344			// full time step
345	gezelter	600
346			dAtom->getA(A);
347			dAtom->getI(I);
348
349	mmeineke	558	// rotate about the x-axis
350	gezelter	600	angle = dt2 * ji[0] / I[0][0];
351			this->rotate( 1, 2, angle, ji, A );
352	mmeineke	597
353	mmeineke	558	// rotate about the y-axis
354	gezelter	600	angle = dt2 * ji[1] / I[1][1];
355			this->rotate( 2, 0, angle, ji, A );
356	mmeineke	558
357			// rotate about the z-axis
358	gezelter	600	angle = dt * ji[2] / I[2][2];
359			this->rotate( 0, 1, angle, ji, A);
360	mmeineke	558
361			// rotate about the y-axis
362	gezelter	600	angle = dt2 * ji[1] / I[1][1];
363			this->rotate( 2, 0, angle, ji, A );
364	mmeineke	558
365			// rotate about the x-axis
366	gezelter	600	angle = dt2 * ji[0] / I[0][0];
367			this->rotate( 1, 2, angle, ji, A );
368	mmeineke	558
369	mmeineke	597
370	gezelter	600	dAtom->setJ( ji );
371			dAtom->setA( A );
372	mmeineke	597
373	gezelter	600	}
374	mmeineke	558	}
375			}
376
377
378			void Integrator::moveB( void ){
379	gezelter	600	int i, j;
380	mmeineke	558	DirectionalAtom* dAtom;
381	gezelter	600	double Tb[3], ji[3];
382			double vel[3], frc[3];
383			double mass;
384	mmeineke	558
385			for( i=0; i<nAtoms; i++ ){
386	gezelter	600
387			atoms[i]->getVel( vel );
388			atoms[i]->getFrc( frc );
389	mmeineke	558
390	gezelter	600	mass = atoms[i]->getMass();
391
392	mmeineke	558	// velocity half step
393	gezelter	600	for (j=0; j < 3; j++)
394			vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
395
396			atoms[i]->setVel( vel );
397	mmeineke	597
398	mmeineke	558	if( atoms[i]->isDirectional() ){
399	gezelter	600
400	mmeineke	558	dAtom = (DirectionalAtom *)atoms[i];
401	mmeineke	597
402	gezelter	600	// get and convert the torque to body frame
403
404			dAtom->getTrq( Tb );
405	mmeineke	558	dAtom->lab2Body( Tb );
406	gezelter	600
407			// get the angular momentum, and propagate a half step
408
409			dAtom->getJ( ji );
410
411			for (j=0; j < 3; j++)
412			ji[j] += (dt2 * Tb[j]) * eConvert;
413	mmeineke	558
414	mmeineke	597
415	gezelter	600	dAtom->setJ( ji );
416	mmeineke	558	}
417			}
418			}
419
420			void Integrator::preMove( void ){
421	gezelter	600	int i, j;
422			double pos[3];
423	mmeineke	558
424			if( nConstrained ){
425	mmeineke	561
426	gezelter	600	for(i=0; i < nAtoms; i++) {
427
428			atoms[i]->getPos( pos );
429	mmeineke	558
430	gezelter	600	for (j = 0; j < 3; j++) {
431			oldPos[3*i + j] = pos[j];
432			}
433
434			}
435			}
436			}
437
438	mmeineke	558	void Integrator::constrainA(){
439
440			int i,j,k;
441			int done;
442	gezelter	600	double posA[3], posB[3];
443			double velA[3], velB[3];
444	mmeineke	572	double pab[3];
445			double rab[3];
446	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
447	mmeineke	558	double rma, rmb;
448			double dx, dy, dz;
449	mmeineke	561	double rpab;
450	mmeineke	558	double rabsq, pabsq, rpabsq;
451			double diffsq;
452			double gab;
453			int iteration;
454
455	gezelter	600	for( i=0; i<nAtoms; i++){
456	mmeineke	558	moving[i] = 0;
457			moved[i] = 1;
458			}
459	mmeineke	567
460	mmeineke	558	iteration = 0;
461			done = 0;
462			while( !done && (iteration < maxIteration )){
463
464			done = 1;
465			for(i=0; i<nConstrained; i++){
466
467			a = constrainedA[i];
468			b = constrainedB[i];
469	mmeineke	563
470			ax = (a*3) + 0;
471			ay = (a*3) + 1;
472			az = (a*3) + 2;
473
474			bx = (b*3) + 0;
475			by = (b*3) + 1;
476			bz = (b*3) + 2;
477
478	mmeineke	558	if( moved[a] \|\| moved[b] ){
479	gezelter	600
480			atoms[a]->getPos( posA );
481			atoms[b]->getPos( posB );
482
483			for (j = 0; j < 3; j++ )
484			pab[j] = posA[j] - posB[j];
485
486	mmeineke	567	//periodic boundary condition
487
488	mmeineke	572	info->wrapVector( pab );
489	mmeineke	567
490	mmeineke	572	pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
491
492	mmeineke	561	rabsq = constrainedDsqr[i];
493	mmeineke	567	diffsq = rabsq - pabsq;
494	mmeineke	558
495			// the original rattle code from alan tidesley
496	mmeineke	563	if (fabs(diffsq) > (tolrabsq2)) {
497	mmeineke	572	rab[0] = oldPos[ax] - oldPos[bx];
498			rab[1] = oldPos[ay] - oldPos[by];
499			rab[2] = oldPos[az] - oldPos[bz];
500	mmeineke	567
501	mmeineke	572	info->wrapVector( rab );
502	mmeineke	558
503	mmeineke	572	rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
504	mmeineke	567
505	mmeineke	558	rpabsq = rpab * rpab;
506
507
508			if (rpabsq < (rabsq * -diffsq)){
509	mmeineke	563
510	mmeineke	558	#ifdef IS_MPI
511			a = atoms[a]->getGlobalIndex();
512			b = atoms[b]->getGlobalIndex();
513			#endif //is_mpi
514			sprintf( painCave.errMsg,
515	mmeineke	563	"Constraint failure in constrainA at atom %d and %d.\n",
516	mmeineke	558	a, b );
517			painCave.isFatal = 1;
518			simError();
519			}
520
521			rma = 1.0 / atoms[a]->getMass();
522			rmb = 1.0 / atoms[b]->getMass();
523	mmeineke	567
524	mmeineke	558	gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );
525	mmeineke	567
526	mmeineke	572	dx = rab[0] * gab;
527			dy = rab[1] * gab;
528			dz = rab[2] * gab;
529	mmeineke	558
530	gezelter	600	posA[0] += rma * dx;
531			posA[1] += rma * dy;
532			posA[2] += rma * dz;
533	mmeineke	558
534	gezelter	600	atoms[a]->setPos( posA );
535	mmeineke	558
536	gezelter	600	posB[0] -= rmb * dx;
537			posB[1] -= rmb * dy;
538			posB[2] -= rmb * dz;
539
540			atoms[b]->setPos( posB );
541
542	mmeineke	558	dx = dx / dt;
543			dy = dy / dt;
544			dz = dz / dt;
545
546	gezelter	600	atoms[a]->getVel( velA );
547	mmeineke	558
548	gezelter	600	velA[0] += rma * dx;
549			velA[1] += rma * dy;
550			velA[2] += rma * dz;
551	mmeineke	558
552	gezelter	600	atoms[a]->setVel( velA );
553
554			atoms[b]->getVel( velB );
555
556			velB[0] -= rmb * dx;
557			velB[1] -= rmb * dy;
558			velB[2] -= rmb * dz;
559
560			atoms[b]->setVel( velB );
561
562	mmeineke	558	moving[a] = 1;
563			moving[b] = 1;
564			done = 0;
565			}
566			}
567			}
568
569			for(i=0; i<nAtoms; i++){
570
571			moved[i] = moving[i];
572			moving[i] = 0;
573			}
574
575			iteration++;
576			}
577
578			if( !done ){
579
580	mmeineke	561	sprintf( painCave.errMsg,
581	mmeineke	558	"Constraint failure in constrainA, too many iterations: %d\n",
582	mmeineke	561	iteration );
583	mmeineke	558	painCave.isFatal = 1;
584			simError();
585			}
586
587			}
588
589			void Integrator::constrainB( void ){
590
591			int i,j,k;
592			int done;
593	gezelter	600	double posA[3], posB[3];
594			double velA[3], velB[3];
595	mmeineke	558	double vxab, vyab, vzab;
596	mmeineke	572	double rab[3];
597	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
598	mmeineke	558	double rma, rmb;
599			double dx, dy, dz;
600			double rabsq, pabsq, rvab;
601			double diffsq;
602			double gab;
603			int iteration;
604
605	mmeineke	561	for(i=0; i<nAtoms; i++){
606	mmeineke	558	moving[i] = 0;
607			moved[i] = 1;
608			}
609
610			done = 0;
611	mmeineke	561	iteration = 0;
612	mmeineke	558	while( !done && (iteration < maxIteration ) ){
613
614	mmeineke	567	done = 1;
615
616	mmeineke	558	for(i=0; i<nConstrained; i++){
617
618			a = constrainedA[i];
619			b = constrainedB[i];
620
621	mmeineke	567	ax = (a*3) + 0;
622			ay = (a*3) + 1;
623			az = (a*3) + 2;
624	mmeineke	563
625	mmeineke	567	bx = (b*3) + 0;
626			by = (b*3) + 1;
627			bz = (b*3) + 2;
628	mmeineke	563
629	mmeineke	558	if( moved[a] \|\| moved[b] ){
630
631	gezelter	600	atoms[a]->getVel( velA );
632			atoms[b]->getVel( velB );
633
634			vxab = velA[0] - velB[0];
635			vyab = velA[1] - velB[1];
636			vzab = velA[2] - velB[2];
637
638			atoms[a]->getPos( posA );
639			atoms[b]->getPos( posB );
640
641			for (j = 0; j < 3; j++)
642			rab[j] = posA[j] - posB[j];
643
644	mmeineke	572	info->wrapVector( rab );
645	mmeineke	567
646	mmeineke	558	rma = 1.0 / atoms[a]->getMass();
647			rmb = 1.0 / atoms[b]->getMass();
648
649	mmeineke	572	rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
650	mmeineke	558
651	mmeineke	561	gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );
652	mmeineke	558
653			if (fabs(gab) > tol) {
654
655	mmeineke	572	dx = rab[0] * gab;
656			dy = rab[1] * gab;
657			dz = rab[2] * gab;
658	gezelter	600
659			velA[0] += rma * dx;
660			velA[1] += rma * dy;
661			velA[2] += rma * dz;
662	mmeineke	558
663	gezelter	600	atoms[a]->setVel( velA );
664
665			velB[0] -= rmb * dx;
666			velB[1] -= rmb * dy;
667			velB[2] -= rmb * dz;
668
669			atoms[b]->setVel( velB );
670	mmeineke	558
671			moving[a] = 1;
672			moving[b] = 1;
673			done = 0;
674			}
675			}
676			}
677
678			for(i=0; i<nAtoms; i++){
679			moved[i] = moving[i];
680			moving[i] = 0;
681			}
682
683			iteration++;
684			}
685	gezelter	600
686	mmeineke	558	if( !done ){
687
688
689	mmeineke	561	sprintf( painCave.errMsg,
690	mmeineke	558	"Constraint failure in constrainB, too many iterations: %d\n",
691	mmeineke	561	iteration );
692	mmeineke	558	painCave.isFatal = 1;
693			simError();
694			}
695
696			}
697
698			void Integrator::rotate( int axes1, int axes2, double angle, double ji[3],
699	gezelter	600	double A[3][3] ){
700	mmeineke	558
701			int i,j,k;
702			double sinAngle;
703			double cosAngle;
704			double angleSqr;
705			double angleSqrOver4;
706			double top, bottom;
707			double rot[3][3];
708			double tempA[3][3];
709			double tempJ[3];
710
711			// initialize the tempA
712
713			for(i=0; i<3; i++){
714			for(j=0; j<3; j++){
715	gezelter	600	tempA[j][i] = A[i][j];
716	mmeineke	558	}
717			}
718
719			// initialize the tempJ
720
721			for( i=0; i<3; i++) tempJ[i] = ji[i];
722
723			// initalize rot as a unit matrix
724
725			rot[0][0] = 1.0;
726			rot[0][1] = 0.0;
727			rot[0][2] = 0.0;
728
729			rot[1][0] = 0.0;
730			rot[1][1] = 1.0;
731			rot[1][2] = 0.0;
732
733			rot[2][0] = 0.0;
734			rot[2][1] = 0.0;
735			rot[2][2] = 1.0;
736
737			// use a small angle aproximation for sin and cosine
738
739			angleSqr = angle * angle;
740			angleSqrOver4 = angleSqr / 4.0;
741			top = 1.0 - angleSqrOver4;
742			bottom = 1.0 + angleSqrOver4;
743
744			cosAngle = top / bottom;
745			sinAngle = angle / bottom;
746
747			rot[axes1][axes1] = cosAngle;
748			rot[axes2][axes2] = cosAngle;
749
750			rot[axes1][axes2] = sinAngle;
751			rot[axes2][axes1] = -sinAngle;
752
753			// rotate the momentum acoording to: ji[] = rot[][] * ji[]
754
755			for(i=0; i<3; i++){
756			ji[i] = 0.0;
757			for(k=0; k<3; k++){
758			ji[i] += rot[i][k] * tempJ[k];
759			}
760			}
761
762			// rotate the Rotation matrix acording to:
763			// A[][] = A[][] * transpose(rot[][])
764
765
766	mmeineke	561	// NOte for as yet unknown reason, we are performing the
767	mmeineke	558	// calculation as:
768			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
769
770			for(i=0; i<3; i++){
771			for(j=0; j<3; j++){
772	gezelter	600	A[j][i] = 0.0;
773	mmeineke	558	for(k=0; k<3; k++){
774	gezelter	600	A[j][i] += tempA[i][k] * rot[j][k];
775	mmeineke	558	}
776			}
777			}
778			}