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();

      cerr << "constraint " << constrainedA[i] << " <-> " << constrainedB[i]
           << " => " << constrainedDsqr[i] << "\n";
    }

    
    // 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();
  trq  = Atom::getTrqArray();
  Amat = Atom::getAmatArray();

  while( currTime < runTime ){

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

    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();

  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;

  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] );
    }
    
  }
}


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

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

    // 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();
      
      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] );
    }
  }

}

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 pxab, pyab, pzab;
  double rxab, ryab, rzab;
  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] ){
        
        pxab = pos[ax] - pos[bx];
        pyab = pos[ay] - pos[by];
        pzab = pos[az] - pos[bz];

        //periodic boundary condition
        pxab = pxab - info->box_x * copysign(1, pxab) 
          * (int)( fabs(pxab / info->box_x) + 0.5);
        pyab = pyab - info->box_y * copysign(1, pyab) 
          * (int)( fabs(pyab / info->box_y) + 0.5);
        pzab = pzab - info->box_z * copysign(1, pzab) 
          * (int)( fabs(pzab / info->box_z) + 0.5);
      
        pabsq = pxab * pxab + pyab * pyab + pzab * pzab;
        rabsq = constrainedDsqr[i];
        diffsq = pabsq - rabsq;

        // the original rattle code from alan tidesley
        if (fabs(diffsq) > (tol*rabsq*2)) {
          rxab = oldPos[ax] - oldPos[bx];
          ryab = oldPos[ay] - oldPos[by];
          rzab = oldPos[az] - oldPos[bz];
 
          rxab = rxab - info->box_x * copysign(1, rxab) 
            * (int)( fabs(rxab / info->box_x) + 0.5);
          ryab = ryab - info->box_y * copysign(1, ryab) 
            * (int)( fabs(ryab / info->box_y) + 0.5);
          rzab = rzab - info->box_z * copysign(1, rzab) 
            * (int)( fabs(rzab / info->box_z) + 0.5);

          rpab = rxab * pxab + ryab * pyab + rzab * pzab;
          rpabsq = rpab * rpab;


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

            cerr << "rpabsq = " << rpabsq << ", rabsq = " << rabsq 
                 << ", -diffsq = " << -diffsq << "\n";

#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 = rxab * gab;
          dy = ryab * gab;
          dz = rzab * 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++;
    cerr << "iterainA = " << iteration << "\n";
  }

  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 rxab, ryab, rzab;
  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 ) ){

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

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

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

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

        rxab = pos[ax] - pos[bx];
        ryab = pos[ay] - pos[by];
        rzab = pos[az] - pos[bz];
        
        rxab = rxab - info->box_x * copysign(1, rxab) 
          * (int)( fabs(rxab / info->box_x) + 0.5);
        ryab = ryab - info->box_y * copysign(1, ryab) 
          * (int)( fabs(ryab / info->box_y) + 0.5);
        rzab = rzab - info->box_z * copysign(1, rzab) 
          * (int)( fabs(rzab / info->box_z) + 0.5);

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

        rvab = rxab * vxab + ryab * vyab + rzab * vzab;
          
        gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );

        if (fabs(gab) > tol) {
          
          dx = rxab * gab;
          dy = ryab * gab;
          dz = rzab * 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:	563
Committed:	Mon Jun 23 21:24:03 2003 UTC (21 years ago) by mmeineke
File size:	15623 byte(s)
Log Message:	Doing some work to debug the constraint code.
#	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
76			if(constrained){
77
78			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			}
86			}
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			cerr << "constraint " << constrainedA[i] << " <-> " << constrainedB[i]
142			<< " => " << constrainedDsqr[i] << "\n";
143	mmeineke	558	}
144
145
146			// save oldAtoms to check for lode balanceing later on.
147
148			oldAtoms = nAtoms;
149
150			moving = new int[nAtoms];
151			moved = new int[nAtoms];
152
153	mmeineke	561	oldPos = new double[nAtoms*3];
154	mmeineke	558	}
155
156			delete[] temp_con;
157			}
158
159
160			void Integrator::integrate( void ){
161
162			int i, j; // loop counters
163
164			double runTime = info->run_time;
165			double sampleTime = info->sampleTime;
166			double statusTime = info->statusTime;
167			double thermalTime = info->thermalTime;
168
169			double currSample;
170			double currThermal;
171			double currStatus;
172			double currTime;
173
174			int calcPot, calcStress;
175			int isError;
176
177	mmeineke	561
178
179	mmeineke	558	tStats = new Thermo( info );
180	mmeineke	561	statOut = new StatWriter( info );
181			dumpOut = new DumpWriter( info );
182	mmeineke	558
183	mmeineke	561	atoms = info->atoms;
184	mmeineke	558	DirectionalAtom* dAtom;
185	mmeineke	561
186			dt = info->dt;
187	mmeineke	558	dt2 = 0.5 * dt;
188
189			// initialize the forces before the first step
190
191			myFF->doForces(1,1);
192
193			if( info->setTemp ){
194
195			tStats->velocitize();
196			}
197
198	mmeineke	561	dumpOut->writeDump( 0.0 );
199			statOut->writeStat( 0.0 );
200	mmeineke	558
201			calcPot = 0;
202			calcStress = 0;
203			currSample = sampleTime;
204			currThermal = thermalTime;
205			currStatus = statusTime;
206			currTime = 0.0;;
207
208	mmeineke	559
209			readyCheck();
210
211			#ifdef IS_MPI
212			strcpy( checkPointMsg,
213			"The integrator is ready to go." );
214			MPIcheckPoint();
215			#endif // is_mpi
216
217	mmeineke	561
218			pos = Atom::getPosArray();
219			vel = Atom::getVelArray();
220			frc = Atom::getFrcArray();
221			trq = Atom::getTrqArray();
222			Amat = Atom::getAmatArray();
223
224	mmeineke	558	while( currTime < runTime ){
225
226			if( (currTime+dt) >= currStatus ){
227			calcPot = 1;
228			calcStress = 1;
229			}
230	mmeineke	561
231	mmeineke	558	integrateStep( calcPot, calcStress );
232
233			currTime += dt;
234
235			if( info->setTemp ){
236			if( currTime >= currThermal ){
237			tStats->velocitize();
238			currThermal += thermalTime;
239			}
240			}
241
242			if( currTime >= currSample ){
243	mmeineke	561	dumpOut->writeDump( currTime );
244	mmeineke	558	currSample += sampleTime;
245			}
246
247			if( currTime >= currStatus ){
248	mmeineke	561	statOut->writeStat( currTime );
249	mmeineke	558	calcPot = 0;
250			calcStress = 0;
251			currStatus += statusTime;
252			}
253	mmeineke	559
254			#ifdef IS_MPI
255			strcpy( checkPointMsg,
256			"successfully took a time step." );
257			MPIcheckPoint();
258			#endif // is_mpi
259
260	mmeineke	558	}
261
262	mmeineke	561	dumpOut->writeFinal();
263	mmeineke	558
264	mmeineke	561	delete dumpOut;
265			delete statOut;
266	mmeineke	558	}
267
268			void Integrator::integrateStep( int calcPot, int calcStress ){
269
270	mmeineke	561
271
272	mmeineke	558	// Position full step, and velocity half step
273
274	mmeineke	561	preMove();
275	mmeineke	558	moveA();
276			if( nConstrained ) constrainA();
277
278			// calc forces
279
280			myFF->doForces(calcPot,calcStress);
281
282			// finish the velocity half step
283
284			moveB();
285			if( nConstrained ) constrainB();
286
287			}
288
289
290			void Integrator::moveA( void ){
291
292			int i,j,k;
293			int atomIndex, aMatIndex;
294			DirectionalAtom* dAtom;
295			double Tb[3];
296			double ji[3];
297	mmeineke	561	double angle;
298	mmeineke	558
299			for( i=0; i<nAtoms; i++ ){
300			atomIndex = i * 3;
301			aMatIndex = i * 9;
302
303			// velocity half step
304			for( j=atomIndex; j<(atomIndex+3); j++ )
305			vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
306
307			// position whole step
308			for( j=atomIndex; j<(atomIndex+3); j++ )
309			pos[j] += dt * vel[j];
310
311
312			if( atoms[i]->isDirectional() ){
313
314			dAtom = (DirectionalAtom *)atoms[i];
315
316			// get and convert the torque to body frame
317
318			Tb[0] = dAtom->getTx();
319			Tb[1] = dAtom->getTy();
320			Tb[2] = dAtom->getTz();
321
322			dAtom->lab2Body( Tb );
323
324			// get the angular momentum, and propagate a half step
325
326			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
327			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
328			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
329
330			// use the angular velocities to propagate the rotation matrix a
331			// full time step
332
333			// rotate about the x-axis
334			angle = dt2 * ji[0] / dAtom->getIxx();
335	mmeineke	561	this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
336	mmeineke	558
337			// rotate about the y-axis
338			angle = dt2 * ji[1] / dAtom->getIyy();
339	mmeineke	561	this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
340	mmeineke	558
341			// rotate about the z-axis
342			angle = dt * ji[2] / dAtom->getIzz();
343	mmeineke	561	this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
344	mmeineke	558
345			// rotate about the y-axis
346			angle = dt2 * ji[1] / dAtom->getIyy();
347	mmeineke	561	this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
348	mmeineke	558
349			// rotate about the x-axis
350			angle = dt2 * ji[0] / dAtom->getIxx();
351	mmeineke	561	this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
352	mmeineke	558
353			dAtom->setJx( ji[0] );
354			dAtom->setJy( ji[1] );
355			dAtom->setJz( ji[2] );
356			}
357
358			}
359			}
360
361
362			void Integrator::moveB( void ){
363			int i,j,k;
364			int atomIndex;
365			DirectionalAtom* dAtom;
366			double Tb[3];
367			double ji[3];
368
369			for( i=0; i<nAtoms; i++ ){
370			atomIndex = i * 3;
371
372			// velocity half step
373			for( j=atomIndex; j<(atomIndex+3); j++ )
374			vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert;
375
376			if( atoms[i]->isDirectional() ){
377
378			dAtom = (DirectionalAtom *)atoms[i];
379
380			// get and convert the torque to body frame
381
382			Tb[0] = dAtom->getTx();
383			Tb[1] = dAtom->getTy();
384			Tb[2] = dAtom->getTz();
385
386			dAtom->lab2Body( Tb );
387
388			// get the angular momentum, and complete the angular momentum
389			// half step
390
391			ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert;
392			ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert;
393			ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert;
394
395			dAtom->setJx( ji[0] );
396			dAtom->setJy( ji[1] );
397			dAtom->setJz( ji[2] );
398			}
399			}
400
401			}
402
403			void Integrator::preMove( void ){
404			int i;
405
406			if( nConstrained ){
407	mmeineke	561
408	mmeineke	558	for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i];
409			}
410			}
411
412			void Integrator::constrainA(){
413
414			int i,j,k;
415			int done;
416			double pxab, pyab, pzab;
417			double rxab, ryab, rzab;
418	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
419	mmeineke	558	double rma, rmb;
420			double dx, dy, dz;
421	mmeineke	561	double rpab;
422	mmeineke	558	double rabsq, pabsq, rpabsq;
423			double diffsq;
424			double gab;
425			int iteration;
426
427
428
429			for( i=0; i<nAtoms; i++){
430
431			moving[i] = 0;
432			moved[i] = 1;
433			}
434
435
436			iteration = 0;
437			done = 0;
438			while( !done && (iteration < maxIteration )){
439
440			done = 1;
441			for(i=0; i<nConstrained; i++){
442
443			a = constrainedA[i];
444			b = constrainedB[i];
445	mmeineke	563
446			ax = (a*3) + 0;
447			ay = (a*3) + 1;
448			az = (a*3) + 2;
449
450			bx = (b*3) + 0;
451			by = (b*3) + 1;
452			bz = (b*3) + 2;
453
454
455	mmeineke	558	if( moved[a] \|\| moved[b] ){
456
457	mmeineke	563	pxab = pos[ax] - pos[bx];
458			pyab = pos[ay] - pos[by];
459			pzab = pos[az] - pos[bz];
460	mmeineke	558
461			//periodic boundary condition
462			pxab = pxab - info->box_x * copysign(1, pxab)
463	mmeineke	563	* (int)( fabs(pxab / info->box_x) + 0.5);
464	mmeineke	558	pyab = pyab - info->box_y * copysign(1, pyab)
465	mmeineke	563	* (int)( fabs(pyab / info->box_y) + 0.5);
466	mmeineke	558	pzab = pzab - info->box_z * copysign(1, pzab)
467	mmeineke	563	* (int)( fabs(pzab / info->box_z) + 0.5);
468	mmeineke	558
469			pabsq = pxab * pxab + pyab * pyab + pzab * pzab;
470	mmeineke	561	rabsq = constrainedDsqr[i];
471	mmeineke	558	diffsq = pabsq - rabsq;
472
473			// the original rattle code from alan tidesley
474	mmeineke	563	if (fabs(diffsq) > (tolrabsq2)) {
475			rxab = oldPos[ax] - oldPos[bx];
476			ryab = oldPos[ay] - oldPos[by];
477			rzab = oldPos[az] - oldPos[bz];
478	mmeineke	558
479			rxab = rxab - info->box_x * copysign(1, rxab)
480	mmeineke	563	* (int)( fabs(rxab / info->box_x) + 0.5);
481	mmeineke	558	ryab = ryab - info->box_y * copysign(1, ryab)
482	mmeineke	563	* (int)( fabs(ryab / info->box_y) + 0.5);
483	mmeineke	558	rzab = rzab - info->box_z * copysign(1, rzab)
484	mmeineke	563	* (int)( fabs(rzab / info->box_z) + 0.5);
485	mmeineke	558
486			rpab = rxab * pxab + ryab * pyab + rzab * pzab;
487			rpabsq = rpab * rpab;
488
489
490			if (rpabsq < (rabsq * -diffsq)){
491	mmeineke	563
492			cerr << "rpabsq = " << rpabsq << ", rabsq = " << rabsq
493			<< ", -diffsq = " << -diffsq << "\n";
494
495	mmeineke	558	#ifdef IS_MPI
496			a = atoms[a]->getGlobalIndex();
497			b = atoms[b]->getGlobalIndex();
498			#endif //is_mpi
499			sprintf( painCave.errMsg,
500	mmeineke	563	"Constraint failure in constrainA at atom %d and %d.\n",
501	mmeineke	558	a, b );
502			painCave.isFatal = 1;
503			simError();
504			}
505
506			rma = 1.0 / atoms[a]->getMass();
507			rmb = 1.0 / atoms[b]->getMass();
508
509			gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );
510			dx = rxab * gab;
511			dy = ryab * gab;
512			dz = rzab * gab;
513
514	mmeineke	563	pos[ax] += rma * dx;
515			pos[ay] += rma * dy;
516			pos[az] += rma * dz;
517	mmeineke	558
518	mmeineke	563	pos[bx] -= rmb * dx;
519			pos[by] -= rmb * dy;
520			pos[bz] -= rmb * dz;
521	mmeineke	558
522			dx = dx / dt;
523			dy = dy / dt;
524			dz = dz / dt;
525
526	mmeineke	563	vel[ax] += rma * dx;
527			vel[ay] += rma * dy;
528			vel[az] += rma * dz;
529	mmeineke	558
530	mmeineke	563	vel[bx] -= rmb * dx;
531			vel[by] -= rmb * dy;
532			vel[bz] -= rmb * dz;
533	mmeineke	558
534			moving[a] = 1;
535			moving[b] = 1;
536			done = 0;
537			}
538			}
539			}
540
541			for(i=0; i<nAtoms; i++){
542
543			moved[i] = moving[i];
544			moving[i] = 0;
545			}
546
547			iteration++;
548	mmeineke	563	cerr << "iterainA = " << iteration << "\n";
549	mmeineke	558	}
550
551			if( !done ){
552
553	mmeineke	561	sprintf( painCave.errMsg,
554	mmeineke	558	"Constraint failure in constrainA, too many iterations: %d\n",
555	mmeineke	561	iteration );
556	mmeineke	558	painCave.isFatal = 1;
557			simError();
558			}
559
560			}
561
562			void Integrator::constrainB( void ){
563
564			int i,j,k;
565			int done;
566			double vxab, vyab, vzab;
567			double rxab, ryab, rzab;
568	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
569	mmeineke	558	double rma, rmb;
570			double dx, dy, dz;
571			double rabsq, pabsq, rvab;
572			double diffsq;
573			double gab;
574			int iteration;
575
576	mmeineke	561	for(i=0; i<nAtoms; i++){
577	mmeineke	558	moving[i] = 0;
578			moved[i] = 1;
579			}
580
581			done = 0;
582	mmeineke	561	iteration = 0;
583	mmeineke	558	while( !done && (iteration < maxIteration ) ){
584
585			for(i=0; i<nConstrained; i++){
586
587			a = constrainedA[i];
588			b = constrainedB[i];
589
590	mmeineke	563	ax = 3*a +0;
591			ay = 3*a +1;
592			az = 3*a +2;
593
594			bx = 3*b +0;
595			by = 3*b +1;
596			bz = 3*b +2;
597
598	mmeineke	558	if( moved[a] \|\| moved[b] ){
599
600	mmeineke	563	vxab = vel[ax] - vel[bx];
601			vyab = vel[ay] - vel[by];
602			vzab = vel[az] - vel[bz];
603	mmeineke	558
604	mmeineke	563	rxab = pos[ax] - pos[bx];
605			ryab = pos[ay] - pos[by];
606			rzab = pos[az] - pos[bz];
607	mmeineke	558
608			rxab = rxab - info->box_x * copysign(1, rxab)
609	mmeineke	563	* (int)( fabs(rxab / info->box_x) + 0.5);
610	mmeineke	558	ryab = ryab - info->box_y * copysign(1, ryab)
611	mmeineke	563	* (int)( fabs(ryab / info->box_y) + 0.5);
612	mmeineke	558	rzab = rzab - info->box_z * copysign(1, rzab)
613	mmeineke	563	* (int)( fabs(rzab / info->box_z) + 0.5);
614	mmeineke	558
615			rma = 1.0 / atoms[a]->getMass();
616			rmb = 1.0 / atoms[b]->getMass();
617
618			rvab = rxab * vxab + ryab * vyab + rzab * vzab;
619
620	mmeineke	561	gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );
621	mmeineke	558
622			if (fabs(gab) > tol) {
623
624			dx = rxab * gab;
625			dy = ryab * gab;
626			dz = rzab * gab;
627
628	mmeineke	563	vel[ax] += rma * dx;
629			vel[ay] += rma * dy;
630			vel[az] += rma * dz;
631	mmeineke	558
632	mmeineke	563	vel[bx] -= rmb * dx;
633			vel[by] -= rmb * dy;
634			vel[bz] -= rmb * dz;
635	mmeineke	558
636			moving[a] = 1;
637			moving[b] = 1;
638			done = 0;
639			}
640			}
641			}
642
643			for(i=0; i<nAtoms; i++){
644			moved[i] = moving[i];
645			moving[i] = 0;
646			}
647
648			iteration++;
649			}
650
651			if( !done ){
652
653
654	mmeineke	561	sprintf( painCave.errMsg,
655	mmeineke	558	"Constraint failure in constrainB, too many iterations: %d\n",
656	mmeineke	561	iteration );
657	mmeineke	558	painCave.isFatal = 1;
658			simError();
659			}
660
661			}
662
663
664
665
666
667
668
669			void Integrator::rotate( int axes1, int axes2, double angle, double ji[3],
670	mmeineke	561	double A[9] ){
671	mmeineke	558
672			int i,j,k;
673			double sinAngle;
674			double cosAngle;
675			double angleSqr;
676			double angleSqrOver4;
677			double top, bottom;
678			double rot[3][3];
679			double tempA[3][3];
680			double tempJ[3];
681
682			// initialize the tempA
683
684			for(i=0; i<3; i++){
685			for(j=0; j<3; j++){
686	mmeineke	561	tempA[j][i] = A[3*i + j];
687	mmeineke	558	}
688			}
689
690			// initialize the tempJ
691
692			for( i=0; i<3; i++) tempJ[i] = ji[i];
693
694			// initalize rot as a unit matrix
695
696			rot[0][0] = 1.0;
697			rot[0][1] = 0.0;
698			rot[0][2] = 0.0;
699
700			rot[1][0] = 0.0;
701			rot[1][1] = 1.0;
702			rot[1][2] = 0.0;
703
704			rot[2][0] = 0.0;
705			rot[2][1] = 0.0;
706			rot[2][2] = 1.0;
707
708			// use a small angle aproximation for sin and cosine
709
710			angleSqr = angle * angle;
711			angleSqrOver4 = angleSqr / 4.0;
712			top = 1.0 - angleSqrOver4;
713			bottom = 1.0 + angleSqrOver4;
714
715			cosAngle = top / bottom;
716			sinAngle = angle / bottom;
717
718			rot[axes1][axes1] = cosAngle;
719			rot[axes2][axes2] = cosAngle;
720
721			rot[axes1][axes2] = sinAngle;
722			rot[axes2][axes1] = -sinAngle;
723
724			// rotate the momentum acoording to: ji[] = rot[][] * ji[]
725
726			for(i=0; i<3; i++){
727			ji[i] = 0.0;
728			for(k=0; k<3; k++){
729			ji[i] += rot[i][k] * tempJ[k];
730			}
731			}
732
733			// rotate the Rotation matrix acording to:
734			// A[][] = A[][] * transpose(rot[][])
735
736
737	mmeineke	561	// NOte for as yet unknown reason, we are performing the
738	mmeineke	558	// calculation as:
739			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
740
741			for(i=0; i<3; i++){
742			for(j=0; j<3; j++){
743	mmeineke	561	A[3*j + i] = 0.0;
744	mmeineke	558	for(k=0; k<3; k++){
745	mmeineke	561	A[3j + i] += tempA[i][k] rot[j][k];
746	mmeineke	558	}
747			}
748			}
749			}