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

  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;
  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:	600
Committed:	Mon Jul 14 22:38:13 2003 UTC (20 years, 11 months ago) by gezelter
File size:	15099 byte(s)
Log Message:	Fixes for get and set routines in Atom and DirectionalAtom
#	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			tStats = new Thermo( info );
184	mmeineke	561	statOut = new StatWriter( info );
185			dumpOut = new DumpWriter( info );
186	mmeineke	558
187	mmeineke	561	atoms = info->atoms;
188	mmeineke	558	DirectionalAtom* dAtom;
189	mmeineke	561
190			dt = info->dt;
191	mmeineke	558	dt2 = 0.5 * dt;
192
193			// initialize the forces before the first step
194
195			myFF->doForces(1,1);
196
197			if( info->setTemp ){
198
199			tStats->velocitize();
200			}
201
202	mmeineke	561	dumpOut->writeDump( 0.0 );
203			statOut->writeStat( 0.0 );
204	mmeineke	558
205			calcPot = 0;
206			calcStress = 0;
207			currSample = sampleTime;
208			currThermal = thermalTime;
209			currStatus = statusTime;
210			currTime = 0.0;;
211
212	mmeineke	559
213			readyCheck();
214
215			#ifdef IS_MPI
216			strcpy( checkPointMsg,
217			"The integrator is ready to go." );
218			MPIcheckPoint();
219			#endif // is_mpi
220
221	mmeineke	558	while( currTime < runTime ){
222
223			if( (currTime+dt) >= currStatus ){
224			calcPot = 1;
225			calcStress = 1;
226			}
227	mmeineke	561
228	mmeineke	597	std::cerr << currTime << "\n";
229	mmeineke	594
230	mmeineke	558	integrateStep( calcPot, calcStress );
231
232			currTime += dt;
233
234			if( info->setTemp ){
235			if( currTime >= currThermal ){
236			tStats->velocitize();
237			currThermal += thermalTime;
238			}
239			}
240
241			if( currTime >= currSample ){
242	mmeineke	561	dumpOut->writeDump( currTime );
243	mmeineke	558	currSample += sampleTime;
244			}
245
246			if( currTime >= currStatus ){
247	mmeineke	561	statOut->writeStat( currTime );
248	mmeineke	558	calcPot = 0;
249			calcStress = 0;
250			currStatus += statusTime;
251			}
252	mmeineke	559
253			#ifdef IS_MPI
254			strcpy( checkPointMsg,
255			"successfully took a time step." );
256			MPIcheckPoint();
257			#endif // is_mpi
258
259	mmeineke	558	}
260
261	mmeineke	572	dumpOut->writeFinal(currTime);
262	mmeineke	558
263	mmeineke	561	delete dumpOut;
264			delete statOut;
265	mmeineke	558	}
266
267			void Integrator::integrateStep( int calcPot, int calcStress ){
268
269	mmeineke	561
270
271	mmeineke	558	// Position full step, and velocity half step
272
273	mmeineke	561	preMove();
274	mmeineke	558	moveA();
275	gezelter	600	if( nConstrained ) constrainA();
276	mmeineke	558
277			// calc forces
278
279			myFF->doForces(calcPot,calcStress);
280
281			// finish the velocity half step
282
283			moveB();
284			if( nConstrained ) constrainB();
285
286			}
287
288
289			void Integrator::moveA( void ){
290
291	gezelter	600	int i, j;
292	mmeineke	558	DirectionalAtom* dAtom;
293	gezelter	600	double Tb[3], ji[3];
294			double A[3][3], I[3][3];
295	mmeineke	561	double angle;
296	gezelter	600	double vel[3], pos[3], frc[3];
297			double mass;
298	mmeineke	558
299			for( i=0; i<nAtoms; i++ ){
300	mmeineke	567
301	gezelter	600	atoms[i]->getVel( vel );
302			atoms[i]->getPos( pos );
303			atoms[i]->getFrc( frc );
304	mmeineke	558
305	gezelter	600	mass = atoms[i]->getMass();
306	mmeineke	594
307	gezelter	600	for (j=0; j < 3; j++) {
308			// velocity half step
309			vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
310			// position whole step
311			pos[j] += dt * vel[j];
312			}
313	mmeineke	594
314	gezelter	600	atoms[i]->setVel( vel );
315			atoms[i]->setPos( pos );
316
317	mmeineke	558	if( atoms[i]->isDirectional() ){
318
319			dAtom = (DirectionalAtom *)atoms[i];
320
321			// get and convert the torque to body frame
322
323	gezelter	600	dAtom->getTrq( Tb );
324	mmeineke	558	dAtom->lab2Body( Tb );
325	mmeineke	597
326	mmeineke	558	// get the angular momentum, and propagate a half step
327	gezelter	600
328			dAtom->getJ( ji );
329
330			for (j=0; j < 3; j++)
331			ji[j] += (dt2 * Tb[j]) * eConvert;
332	mmeineke	558
333			// use the angular velocities to propagate the rotation matrix a
334			// full time step
335	gezelter	600
336			dAtom->getA(A);
337			dAtom->getI(I);
338
339	mmeineke	558	// rotate about the x-axis
340	gezelter	600	angle = dt2 * ji[0] / I[0][0];
341			this->rotate( 1, 2, angle, ji, A );
342	mmeineke	597
343	mmeineke	558	// rotate about the y-axis
344	gezelter	600	angle = dt2 * ji[1] / I[1][1];
345			this->rotate( 2, 0, angle, ji, A );
346	mmeineke	558
347			// rotate about the z-axis
348	gezelter	600	angle = dt * ji[2] / I[2][2];
349			this->rotate( 0, 1, angle, ji, A);
350	mmeineke	558
351			// rotate about the y-axis
352	gezelter	600	angle = dt2 * ji[1] / I[1][1];
353			this->rotate( 2, 0, angle, ji, A );
354	mmeineke	558
355			// rotate about the x-axis
356	gezelter	600	angle = dt2 * ji[0] / I[0][0];
357			this->rotate( 1, 2, angle, ji, A );
358	mmeineke	558
359	mmeineke	597
360	gezelter	600	dAtom->setJ( ji );
361			dAtom->setA( A );
362	mmeineke	597
363	gezelter	600	}
364	mmeineke	558	}
365			}
366
367
368			void Integrator::moveB( void ){
369	gezelter	600	int i, j;
370	mmeineke	558	DirectionalAtom* dAtom;
371	gezelter	600	double Tb[3], ji[3];
372			double vel[3], frc[3];
373			double mass;
374	mmeineke	558
375			for( i=0; i<nAtoms; i++ ){
376	gezelter	600
377			atoms[i]->getVel( vel );
378			atoms[i]->getFrc( frc );
379	mmeineke	558
380	gezelter	600	mass = atoms[i]->getMass();
381
382	mmeineke	558	// velocity half step
383	gezelter	600	for (j=0; j < 3; j++)
384			vel[j] += ( dt2 * frc[j] / mass ) * eConvert;
385
386			atoms[i]->setVel( vel );
387	mmeineke	597
388	mmeineke	558	if( atoms[i]->isDirectional() ){
389	gezelter	600
390	mmeineke	558	dAtom = (DirectionalAtom *)atoms[i];
391	mmeineke	597
392	gezelter	600	// get and convert the torque to body frame
393
394			dAtom->getTrq( Tb );
395	mmeineke	558	dAtom->lab2Body( Tb );
396	gezelter	600
397			// get the angular momentum, and propagate a half step
398
399			dAtom->getJ( ji );
400
401			for (j=0; j < 3; j++)
402			ji[j] += (dt2 * Tb[j]) * eConvert;
403	mmeineke	558
404	mmeineke	597
405	gezelter	600	dAtom->setJ( ji );
406	mmeineke	558	}
407			}
408			}
409
410			void Integrator::preMove( void ){
411	gezelter	600	int i, j;
412			double pos[3];
413	mmeineke	558
414			if( nConstrained ){
415	mmeineke	561
416	gezelter	600	for(i=0; i < nAtoms; i++) {
417
418			atoms[i]->getPos( pos );
419	mmeineke	558
420	gezelter	600	for (j = 0; j < 3; j++) {
421			oldPos[3*i + j] = pos[j];
422			}
423
424			}
425			}
426			}
427
428	mmeineke	558	void Integrator::constrainA(){
429
430			int i,j,k;
431			int done;
432	gezelter	600	double posA[3], posB[3];
433			double velA[3], velB[3];
434	mmeineke	572	double pab[3];
435			double rab[3];
436	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
437	mmeineke	558	double rma, rmb;
438			double dx, dy, dz;
439	mmeineke	561	double rpab;
440	mmeineke	558	double rabsq, pabsq, rpabsq;
441			double diffsq;
442			double gab;
443			int iteration;
444
445	gezelter	600	for( i=0; i<nAtoms; i++){
446	mmeineke	558	moving[i] = 0;
447			moved[i] = 1;
448			}
449	mmeineke	567
450	mmeineke	558	iteration = 0;
451			done = 0;
452			while( !done && (iteration < maxIteration )){
453
454			done = 1;
455			for(i=0; i<nConstrained; i++){
456
457			a = constrainedA[i];
458			b = constrainedB[i];
459	mmeineke	563
460			ax = (a*3) + 0;
461			ay = (a*3) + 1;
462			az = (a*3) + 2;
463
464			bx = (b*3) + 0;
465			by = (b*3) + 1;
466			bz = (b*3) + 2;
467
468	mmeineke	558	if( moved[a] \|\| moved[b] ){
469	gezelter	600
470			atoms[a]->getPos( posA );
471			atoms[b]->getPos( posB );
472
473			for (j = 0; j < 3; j++ )
474			pab[j] = posA[j] - posB[j];
475
476	mmeineke	567	//periodic boundary condition
477
478	mmeineke	572	info->wrapVector( pab );
479	mmeineke	567
480	mmeineke	572	pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
481
482	mmeineke	561	rabsq = constrainedDsqr[i];
483	mmeineke	567	diffsq = rabsq - pabsq;
484	mmeineke	558
485			// the original rattle code from alan tidesley
486	mmeineke	563	if (fabs(diffsq) > (tolrabsq2)) {
487	mmeineke	572	rab[0] = oldPos[ax] - oldPos[bx];
488			rab[1] = oldPos[ay] - oldPos[by];
489			rab[2] = oldPos[az] - oldPos[bz];
490	mmeineke	567
491	mmeineke	572	info->wrapVector( rab );
492	mmeineke	558
493	mmeineke	572	rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
494	mmeineke	567
495	mmeineke	558	rpabsq = rpab * rpab;
496
497
498			if (rpabsq < (rabsq * -diffsq)){
499	mmeineke	563
500	mmeineke	558	#ifdef IS_MPI
501			a = atoms[a]->getGlobalIndex();
502			b = atoms[b]->getGlobalIndex();
503			#endif //is_mpi
504			sprintf( painCave.errMsg,
505	mmeineke	563	"Constraint failure in constrainA at atom %d and %d.\n",
506	mmeineke	558	a, b );
507			painCave.isFatal = 1;
508			simError();
509			}
510
511			rma = 1.0 / atoms[a]->getMass();
512			rmb = 1.0 / atoms[b]->getMass();
513	mmeineke	567
514	mmeineke	558	gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab );
515	mmeineke	567
516	mmeineke	572	dx = rab[0] * gab;
517			dy = rab[1] * gab;
518			dz = rab[2] * gab;
519	mmeineke	558
520	gezelter	600	posA[0] += rma * dx;
521			posA[1] += rma * dy;
522			posA[2] += rma * dz;
523	mmeineke	558
524	gezelter	600	atoms[a]->setPos( posA );
525	mmeineke	558
526	gezelter	600	posB[0] -= rmb * dx;
527			posB[1] -= rmb * dy;
528			posB[2] -= rmb * dz;
529
530			atoms[b]->setPos( posB );
531
532	mmeineke	558	dx = dx / dt;
533			dy = dy / dt;
534			dz = dz / dt;
535
536	gezelter	600	atoms[a]->getVel( velA );
537	mmeineke	558
538	gezelter	600	velA[0] += rma * dx;
539			velA[1] += rma * dy;
540			velA[2] += rma * dz;
541	mmeineke	558
542	gezelter	600	atoms[a]->setVel( velA );
543
544			atoms[b]->getVel( velB );
545
546			velB[0] -= rmb * dx;
547			velB[1] -= rmb * dy;
548			velB[2] -= rmb * dz;
549
550			atoms[b]->setVel( velB );
551
552	mmeineke	558	moving[a] = 1;
553			moving[b] = 1;
554			done = 0;
555			}
556			}
557			}
558
559			for(i=0; i<nAtoms; i++){
560
561			moved[i] = moving[i];
562			moving[i] = 0;
563			}
564
565			iteration++;
566			}
567
568			if( !done ){
569
570	mmeineke	561	sprintf( painCave.errMsg,
571	mmeineke	558	"Constraint failure in constrainA, too many iterations: %d\n",
572	mmeineke	561	iteration );
573	mmeineke	558	painCave.isFatal = 1;
574			simError();
575			}
576
577			}
578
579			void Integrator::constrainB( void ){
580
581			int i,j,k;
582			int done;
583	gezelter	600	double posA[3], posB[3];
584			double velA[3], velB[3];
585	mmeineke	558	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	gezelter	600	atoms[a]->getVel( velA );
622			atoms[b]->getVel( velB );
623
624			vxab = velA[0] - velB[0];
625			vyab = velA[1] - velB[1];
626			vzab = velA[2] - velB[2];
627
628			atoms[a]->getPos( posA );
629			atoms[b]->getPos( posB );
630
631			for (j = 0; j < 3; j++)
632			rab[j] = posA[j] - posB[j];
633
634	mmeineke	572	info->wrapVector( rab );
635	mmeineke	567
636	mmeineke	558	rma = 1.0 / atoms[a]->getMass();
637			rmb = 1.0 / atoms[b]->getMass();
638
639	mmeineke	572	rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
640	mmeineke	558
641	mmeineke	561	gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] );
642	mmeineke	558
643			if (fabs(gab) > tol) {
644
645	mmeineke	572	dx = rab[0] * gab;
646			dy = rab[1] * gab;
647			dz = rab[2] * gab;
648	gezelter	600
649			velA[0] += rma * dx;
650			velA[1] += rma * dy;
651			velA[2] += rma * dz;
652	mmeineke	558
653	gezelter	600	atoms[a]->setVel( velA );
654
655			velB[0] -= rmb * dx;
656			velB[1] -= rmb * dy;
657			velB[2] -= rmb * dz;
658
659			atoms[b]->setVel( velB );
660	mmeineke	558
661			moving[a] = 1;
662			moving[b] = 1;
663			done = 0;
664			}
665			}
666			}
667
668			for(i=0; i<nAtoms; i++){
669			moved[i] = moving[i];
670			moving[i] = 0;
671			}
672
673			iteration++;
674			}
675	gezelter	600
676	mmeineke	558	if( !done ){
677
678
679	mmeineke	561	sprintf( painCave.errMsg,
680	mmeineke	558	"Constraint failure in constrainB, too many iterations: %d\n",
681	mmeineke	561	iteration );
682	mmeineke	558	painCave.isFatal = 1;
683			simError();
684			}
685
686			}
687
688			void Integrator::rotate( int axes1, int axes2, double angle, double ji[3],
689	gezelter	600	double A[3][3] ){
690	mmeineke	558
691			int i,j,k;
692			double sinAngle;
693			double cosAngle;
694			double angleSqr;
695			double angleSqrOver4;
696			double top, bottom;
697			double rot[3][3];
698			double tempA[3][3];
699			double tempJ[3];
700
701			// initialize the tempA
702
703			for(i=0; i<3; i++){
704			for(j=0; j<3; j++){
705	gezelter	600	tempA[j][i] = A[i][j];
706	mmeineke	558	}
707			}
708
709			// initialize the tempJ
710
711			for( i=0; i<3; i++) tempJ[i] = ji[i];
712
713			// initalize rot as a unit matrix
714
715			rot[0][0] = 1.0;
716			rot[0][1] = 0.0;
717			rot[0][2] = 0.0;
718
719			rot[1][0] = 0.0;
720			rot[1][1] = 1.0;
721			rot[1][2] = 0.0;
722
723			rot[2][0] = 0.0;
724			rot[2][1] = 0.0;
725			rot[2][2] = 1.0;
726
727			// use a small angle aproximation for sin and cosine
728
729			angleSqr = angle * angle;
730			angleSqrOver4 = angleSqr / 4.0;
731			top = 1.0 - angleSqrOver4;
732			bottom = 1.0 + angleSqrOver4;
733
734			cosAngle = top / bottom;
735			sinAngle = angle / bottom;
736
737			rot[axes1][axes1] = cosAngle;
738			rot[axes2][axes2] = cosAngle;
739
740			rot[axes1][axes2] = sinAngle;
741			rot[axes2][axes1] = -sinAngle;
742
743			// rotate the momentum acoording to: ji[] = rot[][] * ji[]
744
745			for(i=0; i<3; i++){
746			ji[i] = 0.0;
747			for(k=0; k<3; k++){
748			ji[i] += rot[i][k] * tempJ[k];
749			}
750			}
751
752			// rotate the Rotation matrix acording to:
753			// A[][] = A[][] * transpose(rot[][])
754
755
756	mmeineke	561	// NOte for as yet unknown reason, we are performing the
757	mmeineke	558	// calculation as:
758			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
759
760			for(i=0; i<3; i++){
761			for(j=0; j<3; j++){
762	gezelter	600	A[j][i] = 0.0;
763	mmeineke	558	for(k=0; k<3; k++){
764	gezelter	600	A[j][i] += tempA[i][k] * rot[j][k];
765	mmeineke	558	}
766			}
767			}
768			}