src/integrators/Integrator.cpp

#include <iostream>
#include <stdlib.h>
#include <math.h>
#ifdef IS_MPI
#include "brains/mpiSimulation.hpp"
#include <unistd.h>
#endif //is_mpi

#ifdef PROFILE
#include "profiling/mdProfile.hpp"
#endif // profile

#include "integrators/Integrator.hpp"
#include "utils/simError.h"


template<typename T> Integrator<T>::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;
  }

  nAtoms = info->n_atoms;
  integrableObjects = info->integrableObjects;


  // check for constraints

  constrainedA = NULL;
  constrainedB = NULL;
  constrainedDsqr = NULL;
  moving = NULL;
  moved = NULL;
  oldPos = NULL;

  nConstrained = 0;

  checkConstraints();

}

template<typename T> Integrator<T>::~Integrator(){

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

}


template<typename T> void Integrator<T>::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 balancing later on.

    oldAtoms = nAtoms;

    moving = new int[nAtoms];
    moved = new int[nAtoms];

    oldPos = new double[nAtoms * 3];
  }

  delete[] temp_con;
}


template<typename T> void Integrator<T>::integrate(void){

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

  double difference;
  double currSample;
  double currThermal;
  double currStatus;
  double currReset;

  int calcPot, calcStress;

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

  atoms = info->atoms;

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

  readyCheck();

  // remove center of mass drift velocity (in case we passed in a configuration
  // that was drifting
  tStats->removeCOMdrift();

  // initialize the retraints if necessary
  if (info->useSolidThermInt && !info->useLiquidThermInt) {
    myFF->initRestraints();
  }

  // initialize the forces before the first step

  calcForce(1, 1);

  //execute constraint algorithm to make sure at the very beginning the system is constrained  
  if(nConstrained){
    preMove();
    constrainA();
    calcForce(1, 1);
    constrainB();
  }

  if (info->setTemp){
    thermalize();
  }

  calcPot     = 0;
  calcStress  = 0;
  currSample  = sampleTime + info->getTime();
  currThermal = thermalTime+ info->getTime();
  currStatus  = statusTime + info->getTime();
  currReset   = resetTime  + info->getTime();

  dumpOut->writeDump(info->getTime());
  statOut->writeStat(info->getTime());


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

  while (info->getTime() < runTime && !stopIntegrator()){
    difference = info->getTime() + dt - currStatus;
    if (difference > 0 || fabs(difference) < 1e-4 ){
      calcPot = 1;
      calcStress = 1;
    }

#ifdef PROFILE
    startProfile( pro1 );
#endif
    
    integrateStep(calcPot, calcStress);

#ifdef PROFILE
    endProfile( pro1 );

    startProfile( pro2 );
#endif // profile

    info->incrTime(dt);

    if (info->setTemp){
      if (info->getTime() >= currThermal){
        thermalize();
        currThermal += thermalTime;
      }
    }

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

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

    if (info->resetIntegrator){
      if (info->getTime() >= currReset){
        this->resetIntegrator();
        currReset += resetTime;
      }
    }
    
#ifdef PROFILE
    endProfile( pro2 );
#endif //profile

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

  dumpOut->writeFinal(info->getTime());

  // dump out a file containing the omega values for the final configuration
  if (info->useSolidThermInt && !info->useLiquidThermInt)
    myFF->dumpzAngle();
  

  delete dumpOut;
  delete statOut;
}

template<typename T> void Integrator<T>::integrateStep(int calcPot,
                                                       int calcStress){
  // Position full step, and velocity half step

#ifdef PROFILE
  startProfile(pro3);
#endif //profile

  //save old state (position, velocity etc)
  preMove();
#ifdef PROFILE
  endProfile(pro3);

  startProfile(pro4);
#endif // profile

  moveA();

#ifdef PROFILE
  endProfile(pro4);
  
  startProfile(pro5);
#endif//profile


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

  // calc forces
  calcForce(calcPot, calcStress);

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

#ifdef PROFILE
  endProfile( pro5 );

  startProfile( pro6 );
#endif //profile

  // finish the velocity  half step

  moveB();

#ifdef PROFILE
  endProfile(pro6);
#endif // profile

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


template<typename T> void Integrator<T>::moveA(void){
  size_t i, j;
  DirectionalAtom* dAtom;
  Vector3d Tb;
  Vector3d ji;
  Vector3d vel;
  Vector3d pos;
  Vector3d frc;
  double mass;
  double omega;
 
  for (i = 0; i < integrableObjects.size() ; i++){
    vel = integrableObjects[i]->getVel();
    pos = integrableObjects[i]->getPos();
    integrableObjects[i]->getFrc(frc);
    
    mass = integrableObjects[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];
    }

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

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

      // get and convert the torque to body frame

      Tb = integrableObjects[i]->getTrq();
      integrableObjects[i]->lab2Body(Tb);

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

      ji = integrableObjects[i]->getJ();

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

      this->rotationPropagation( integrableObjects[i], ji );

      integrableObjects[i]->setJ(ji);
    }
  }

  if(nConstrained)
    constrainA();
}


template<typename T> void Integrator<T>::moveB(void){
  int i, j;
  double Tb[3], ji[3];
  double vel[3], frc[3];
  double mass;

  for (i = 0; i < integrableObjects.size(); i++){
    vel = integrableObjects[i]->getVel();
    integrableObjects[i]->getFrc(frc);

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

    // velocity half step
    for (j = 0; j < 3; j++)
      vel[j] += (dt2 * frc[j] / mass) * eConvert;

    integrableObjects[i]->setVel(vel);

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

      // get and convert the torque to body frame

      Tb = integrableObjects[i]->getTrq();
      integrableObjects[i]->lab2Body(Tb);

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

      ji = integrableObjects[i]->getJ();

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


      integrableObjects[i]->setJ(ji);
    }
  }

  if(nConstrained)
    constrainB();
}


template<typename T> void Integrator<T>::preMove(void){
  int i, j;
  double pos[3];

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

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

template<typename T> void Integrator<T>::constrainA(){
  int i, j;
  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]){
        posA = atoms[a]->getPos();
        posB = atoms[b]->getPos();

        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;

          velA = atoms[a]->getVel();

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

          atoms[a]->setVel(velA);

          velB = atoms[b]->getVel();

          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();
  }

}

template<typename T> void Integrator<T>::constrainB(void){
  int i, j;
  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 rvab;
  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]){
        velA = atoms[a]->getVel();
        velB = atoms[b]->getVel();

        vxab = velA[0] - velB[0];
        vyab = velA[1] - velB[1];
        vzab = velA[2] - velB[2];

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

        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();
  }
}

template<typename T> void Integrator<T>::rotationPropagation
( StuntDouble* sd, double ji[3] ){

  double angle;
  double A[3][3], I[3][3];
  int i, j, k;

  // use the angular velocities to propagate the rotation matrix a
  // full time step

  sd->getA(A);
  sd->getI(I);

  if (sd->isLinear()) {
    i = sd->linearAxis();
    j = (i+1)%3;
    k = (i+2)%3;
    
    angle = dt2 * ji[j] / I[j][j];
    this->rotate( k, i, angle, ji, A );

    angle = dt * ji[k] / I[k][k];
    this->rotate( i, j, angle, ji, A);

    angle = dt2 * ji[j] / I[j][j];
    this->rotate( k, i, angle, ji, A );

  } else {
    // 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];
    sd->addZangle(angle);
    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 );
    
  }
  sd->setA( A  );
}

template<typename T> void Integrator<T>::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];
      }
    }
  }
}

template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
  myFF->doForces(calcPot, calcStress);
}

template<typename T> void Integrator<T>::thermalize(){
  tStats->velocitize();
}

template<typename T> double Integrator<T>::getConservedQuantity(void){
  return tStats->getTotalE();
}
template<typename T> string Integrator<T>::getAdditionalParameters(void){
  //By default, return a null string
  //The reason we use string instead of char* is that if we use char*, we will
  //return a pointer point to local variable which might cause problem
  return string();
}
Revision:	1695
Committed:	Mon Nov 1 22:52:57 2004 UTC (19 years, 9 months ago) by tim
File size:	19667 byte(s)
Log Message:	Molecule, Atom, DirectionalAtom, RigidBody and StuntDouble classes get compiled
#	User	Rev	Content
1	tim	1695	#include <iostream>
2			#include <stdlib.h>
3			#include <math.h>
4			#ifdef IS_MPI
5			#include "brains/mpiSimulation.hpp"
6			#include <unistd.h>
7			#endif //is_mpi
8
9			#ifdef PROFILE
10			#include "profiling/mdProfile.hpp"
11			#endif // profile
12
13			#include "integrators/Integrator.hpp"
14			#include "utils/simError.h"
15
16
17			template<typename T> Integrator<T>::Integrator(SimInfo* theInfo,
18			ForceFields* the_ff){
19			info = theInfo;
20			myFF = the_ff;
21			isFirst = 1;
22
23			molecules = info->molecules;
24			nMols = info->n_mol;
25
26			// give a little love back to the SimInfo object
27
28			if (info->the_integrator != NULL){
29			delete info->the_integrator;
30			}
31
32			nAtoms = info->n_atoms;
33			integrableObjects = info->integrableObjects;
34
35
36			// check for constraints
37
38			constrainedA = NULL;
39			constrainedB = NULL;
40			constrainedDsqr = NULL;
41			moving = NULL;
42			moved = NULL;
43			oldPos = NULL;
44
45			nConstrained = 0;
46
47			checkConstraints();
48
49			}
50
51			template<typename T> Integrator<T>::~Integrator(){
52
53			if (nConstrained){
54			delete[] constrainedA;
55			delete[] constrainedB;
56			delete[] constrainedDsqr;
57			delete[] moving;
58			delete[] moved;
59			delete[] oldPos;
60			}
61
62			}
63
64
65			template<typename T> void Integrator<T>::checkConstraints(void){
66			isConstrained = 0;
67
68			Constraint* temp_con;
69			Constraint* dummy_plug;
70			temp_con = new Constraint[info->n_SRI];
71			nConstrained = 0;
72			int constrained = 0;
73
74			SRI** theArray;
75			for (int i = 0; i < nMols; i++){
76
77			theArray = (SRI * *) molecules[i].getMyBonds();
78			for (int j = 0; j < molecules[i].getNBonds(); j++){
79			constrained = theArray[j]->is_constrained();
80
81			if (constrained){
82			dummy_plug = theArray[j]->get_constraint();
83			temp_con[nConstrained].set_a(dummy_plug->get_a());
84			temp_con[nConstrained].set_b(dummy_plug->get_b());
85			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
86
87			nConstrained++;
88			constrained = 0;
89			}
90			}
91
92			theArray = (SRI * *) molecules[i].getMyBends();
93			for (int j = 0; j < molecules[i].getNBends(); j++){
94			constrained = theArray[j]->is_constrained();
95
96			if (constrained){
97			dummy_plug = theArray[j]->get_constraint();
98			temp_con[nConstrained].set_a(dummy_plug->get_a());
99			temp_con[nConstrained].set_b(dummy_plug->get_b());
100			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
101
102			nConstrained++;
103			constrained = 0;
104			}
105			}
106
107			theArray = (SRI * *) molecules[i].getMyTorsions();
108			for (int j = 0; j < molecules[i].getNTorsions(); j++){
109			constrained = theArray[j]->is_constrained();
110
111			if (constrained){
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
124			if (nConstrained > 0){
125			isConstrained = 1;
126
127			if (constrainedA != NULL)
128			delete[] constrainedA;
129			if (constrainedB != NULL)
130			delete[] constrainedB;
131			if (constrainedDsqr != NULL)
132			delete[] constrainedDsqr;
133
134			constrainedA = new int[nConstrained];
135			constrainedB = new int[nConstrained];
136			constrainedDsqr = new double[nConstrained];
137
138			for (int i = 0; i < nConstrained; i++){
139			constrainedA[i] = temp_con[i].get_a();
140			constrainedB[i] = temp_con[i].get_b();
141			constrainedDsqr[i] = temp_con[i].get_dsqr();
142			}
143
144
145			// save oldAtoms to check for lode balancing later on.
146
147			oldAtoms = nAtoms;
148
149			moving = new int[nAtoms];
150			moved = new int[nAtoms];
151
152			oldPos = new double[nAtoms * 3];
153			}
154
155			delete[] temp_con;
156			}
157
158
159			template<typename T> void Integrator<T>::integrate(void){
160
161			double runTime = info->run_time;
162			double sampleTime = info->sampleTime;
163			double statusTime = info->statusTime;
164			double thermalTime = info->thermalTime;
165			double resetTime = info->resetTime;
166
167			double difference;
168			double currSample;
169			double currThermal;
170			double currStatus;
171			double currReset;
172
173			int calcPot, calcStress;
174
175			tStats = new Thermo(info);
176			statOut = new StatWriter(info);
177			dumpOut = new DumpWriter(info);
178
179			atoms = info->atoms;
180
181			dt = info->dt;
182			dt2 = 0.5 * dt;
183
184			readyCheck();
185
186			// remove center of mass drift velocity (in case we passed in a configuration
187			// that was drifting
188			tStats->removeCOMdrift();
189
190			// initialize the retraints if necessary
191			if (info->useSolidThermInt && !info->useLiquidThermInt) {
192			myFF->initRestraints();
193			}
194
195			// initialize the forces before the first step
196
197			calcForce(1, 1);
198
199			//execute constraint algorithm to make sure at the very beginning the system is constrained
200			if(nConstrained){
201			preMove();
202			constrainA();
203			calcForce(1, 1);
204			constrainB();
205			}
206
207			if (info->setTemp){
208			thermalize();
209			}
210
211			calcPot = 0;
212			calcStress = 0;
213			currSample = sampleTime + info->getTime();
214			currThermal = thermalTime+ info->getTime();
215			currStatus = statusTime + info->getTime();
216			currReset = resetTime + info->getTime();
217
218			dumpOut->writeDump(info->getTime());
219			statOut->writeStat(info->getTime());
220
221
222			#ifdef IS_MPI
223			strcpy(checkPointMsg, "The integrator is ready to go.");
224			MPIcheckPoint();
225			#endif // is_mpi
226
227			while (info->getTime() < runTime && !stopIntegrator()){
228			difference = info->getTime() + dt - currStatus;
229			if (difference > 0 \|\| fabs(difference) < 1e-4 ){
230			calcPot = 1;
231			calcStress = 1;
232			}
233
234			#ifdef PROFILE
235			startProfile( pro1 );
236			#endif
237
238			integrateStep(calcPot, calcStress);
239
240			#ifdef PROFILE
241			endProfile( pro1 );
242
243			startProfile( pro2 );
244			#endif // profile
245
246			info->incrTime(dt);
247
248			if (info->setTemp){
249			if (info->getTime() >= currThermal){
250			thermalize();
251			currThermal += thermalTime;
252			}
253			}
254
255			if (info->getTime() >= currSample){
256			dumpOut->writeDump(info->getTime());
257			currSample += sampleTime;
258			}
259
260			if (info->getTime() >= currStatus){
261			statOut->writeStat(info->getTime());
262			calcPot = 0;
263			calcStress = 0;
264			currStatus += statusTime;
265			}
266
267			if (info->resetIntegrator){
268			if (info->getTime() >= currReset){
269			this->resetIntegrator();
270			currReset += resetTime;
271			}
272			}
273
274			#ifdef PROFILE
275			endProfile( pro2 );
276			#endif //profile
277
278			#ifdef IS_MPI
279			strcpy(checkPointMsg, "successfully took a time step.");
280			MPIcheckPoint();
281			#endif // is_mpi
282			}
283
284			dumpOut->writeFinal(info->getTime());
285
286			// dump out a file containing the omega values for the final configuration
287			if (info->useSolidThermInt && !info->useLiquidThermInt)
288			myFF->dumpzAngle();
289
290
291			delete dumpOut;
292			delete statOut;
293			}
294
295			template<typename T> void Integrator<T>::integrateStep(int calcPot,
296			int calcStress){
297			// Position full step, and velocity half step
298
299			#ifdef PROFILE
300			startProfile(pro3);
301			#endif //profile
302
303			//save old state (position, velocity etc)
304			preMove();
305			#ifdef PROFILE
306			endProfile(pro3);
307
308			startProfile(pro4);
309			#endif // profile
310
311			moveA();
312
313			#ifdef PROFILE
314			endProfile(pro4);
315
316			startProfile(pro5);
317			#endif//profile
318
319
320			#ifdef IS_MPI
321			strcpy(checkPointMsg, "Succesful moveA\n");
322			MPIcheckPoint();
323			#endif // is_mpi
324
325			// calc forces
326			calcForce(calcPot, calcStress);
327
328			#ifdef IS_MPI
329			strcpy(checkPointMsg, "Succesful doForces\n");
330			MPIcheckPoint();
331			#endif // is_mpi
332
333			#ifdef PROFILE
334			endProfile( pro5 );
335
336			startProfile( pro6 );
337			#endif //profile
338
339			// finish the velocity half step
340
341			moveB();
342
343			#ifdef PROFILE
344			endProfile(pro6);
345			#endif // profile
346
347			#ifdef IS_MPI
348			strcpy(checkPointMsg, "Succesful moveB\n");
349			MPIcheckPoint();
350			#endif // is_mpi
351			}
352
353
354			template<typename T> void Integrator<T>::moveA(void){
355			size_t i, j;
356			DirectionalAtom* dAtom;
357			Vector3d Tb;
358			Vector3d ji;
359			Vector3d vel;
360			Vector3d pos;
361			Vector3d frc;
362			double mass;
363			double omega;
364
365			for (i = 0; i < integrableObjects.size() ; i++){
366			vel = integrableObjects[i]->getVel();
367			pos = integrableObjects[i]->getPos();
368			integrableObjects[i]->getFrc(frc);
369
370			mass = integrableObjects[i]->getMass();
371
372			for (j = 0; j < 3; j++){
373			// velocity half step
374			vel[j] += (dt2 * frc[j] / mass) * eConvert;
375			// position whole step
376			pos[j] += dt * vel[j];
377			}
378
379			integrableObjects[i]->setVel(vel);
380			integrableObjects[i]->setPos(pos);
381
382			if (integrableObjects[i]->isDirectional()){
383
384			// get and convert the torque to body frame
385
386			Tb = integrableObjects[i]->getTrq();
387			integrableObjects[i]->lab2Body(Tb);
388
389			// get the angular momentum, and propagate a half step
390
391			ji = integrableObjects[i]->getJ();
392
393			for (j = 0; j < 3; j++)
394			ji[j] += (dt2 * Tb[j]) * eConvert;
395
396			this->rotationPropagation( integrableObjects[i], ji );
397
398			integrableObjects[i]->setJ(ji);
399			}
400			}
401
402			if(nConstrained)
403			constrainA();
404			}
405
406
407			template<typename T> void Integrator<T>::moveB(void){
408			int i, j;
409			double Tb[3], ji[3];
410			double vel[3], frc[3];
411			double mass;
412
413			for (i = 0; i < integrableObjects.size(); i++){
414			vel = integrableObjects[i]->getVel();
415			integrableObjects[i]->getFrc(frc);
416
417			mass = integrableObjects[i]->getMass();
418
419			// velocity half step
420			for (j = 0; j < 3; j++)
421			vel[j] += (dt2 * frc[j] / mass) * eConvert;
422
423			integrableObjects[i]->setVel(vel);
424
425			if (integrableObjects[i]->isDirectional()){
426
427			// get and convert the torque to body frame
428
429			Tb = integrableObjects[i]->getTrq();
430			integrableObjects[i]->lab2Body(Tb);
431
432			// get the angular momentum, and propagate a half step
433
434			ji = integrableObjects[i]->getJ();
435
436			for (j = 0; j < 3; j++)
437			ji[j] += (dt2 * Tb[j]) * eConvert;
438
439
440			integrableObjects[i]->setJ(ji);
441			}
442			}
443
444			if(nConstrained)
445			constrainB();
446			}
447
448
449			template<typename T> void Integrator<T>::preMove(void){
450			int i, j;
451			double pos[3];
452
453			if (nConstrained){
454			for (i = 0; i < nAtoms; i++){
455			pos = atoms[i]->getPos();
456
457			for (j = 0; j < 3; j++){
458			oldPos[3 * i + j] = pos[j];
459			}
460			}
461			}
462			}
463
464			template<typename T> void Integrator<T>::constrainA(){
465			int i, j;
466			int done;
467			double posA[3], posB[3];
468			double velA[3], velB[3];
469			double pab[3];
470			double rab[3];
471			int a, b, ax, ay, az, bx, by, bz;
472			double rma, rmb;
473			double dx, dy, dz;
474			double rpab;
475			double rabsq, pabsq, rpabsq;
476			double diffsq;
477			double gab;
478			int iteration;
479
480			for (i = 0; i < nAtoms; i++){
481			moving[i] = 0;
482			moved[i] = 1;
483			}
484
485			iteration = 0;
486			done = 0;
487			while (!done && (iteration < maxIteration)){
488			done = 1;
489			for (i = 0; i < nConstrained; i++){
490			a = constrainedA[i];
491			b = constrainedB[i];
492
493			ax = (a * 3) + 0;
494			ay = (a * 3) + 1;
495			az = (a * 3) + 2;
496
497			bx = (b * 3) + 0;
498			by = (b * 3) + 1;
499			bz = (b * 3) + 2;
500
501			if (moved[a] \|\| moved[b]){
502			posA = atoms[a]->getPos();
503			posB = atoms[b]->getPos();
504
505			for (j = 0; j < 3; j++)
506			pab[j] = posA[j] - posB[j];
507
508			//periodic boundary condition
509
510			info->wrapVector(pab);
511
512			pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
513
514			rabsq = constrainedDsqr[i];
515			diffsq = rabsq - pabsq;
516
517			// the original rattle code from alan tidesley
518			if (fabs(diffsq) > (tol * rabsq * 2)){
519			rab[0] = oldPos[ax] - oldPos[bx];
520			rab[1] = oldPos[ay] - oldPos[by];
521			rab[2] = oldPos[az] - oldPos[bz];
522
523			info->wrapVector(rab);
524
525			rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
526
527			rpabsq = rpab * rpab;
528
529
530			if (rpabsq < (rabsq * -diffsq)){
531			#ifdef IS_MPI
532			a = atoms[a]->getGlobalIndex();
533			b = atoms[b]->getGlobalIndex();
534			#endif //is_mpi
535			sprintf(painCave.errMsg,
536			"Constraint failure in constrainA at atom %d and %d.\n", a,
537			b);
538			painCave.isFatal = 1;
539			simError();
540			}
541
542			rma = 1.0 / atoms[a]->getMass();
543			rmb = 1.0 / atoms[b]->getMass();
544
545			gab = diffsq / (2.0 * (rma + rmb) * rpab);
546
547			dx = rab[0] * gab;
548			dy = rab[1] * gab;
549			dz = rab[2] * gab;
550
551			posA[0] += rma * dx;
552			posA[1] += rma * dy;
553			posA[2] += rma * dz;
554
555			atoms[a]->setPos(posA);
556
557			posB[0] -= rmb * dx;
558			posB[1] -= rmb * dy;
559			posB[2] -= rmb * dz;
560
561			atoms[b]->setPos(posB);
562
563			dx = dx / dt;
564			dy = dy / dt;
565			dz = dz / dt;
566
567			velA = atoms[a]->getVel();
568
569			velA[0] += rma * dx;
570			velA[1] += rma * dy;
571			velA[2] += rma * dz;
572
573			atoms[a]->setVel(velA);
574
575			velB = atoms[b]->getVel();
576
577			velB[0] -= rmb * dx;
578			velB[1] -= rmb * dy;
579			velB[2] -= rmb * dz;
580
581			atoms[b]->setVel(velB);
582
583			moving[a] = 1;
584			moving[b] = 1;
585			done = 0;
586			}
587			}
588			}
589
590			for (i = 0; i < nAtoms; i++){
591			moved[i] = moving[i];
592			moving[i] = 0;
593			}
594
595			iteration++;
596			}
597
598			if (!done){
599			sprintf(painCave.errMsg,
600			"Constraint failure in constrainA, too many iterations: %d\n",
601			iteration);
602			painCave.isFatal = 1;
603			simError();
604			}
605
606			}
607
608			template<typename T> void Integrator<T>::constrainB(void){
609			int i, j;
610			int done;
611			double posA[3], posB[3];
612			double velA[3], velB[3];
613			double vxab, vyab, vzab;
614			double rab[3];
615			int a, b, ax, ay, az, bx, by, bz;
616			double rma, rmb;
617			double dx, dy, dz;
618			double rvab;
619			double gab;
620			int iteration;
621
622			for (i = 0; i < nAtoms; i++){
623			moving[i] = 0;
624			moved[i] = 1;
625			}
626
627			done = 0;
628			iteration = 0;
629			while (!done && (iteration < maxIteration)){
630			done = 1;
631
632			for (i = 0; i < nConstrained; i++){
633			a = constrainedA[i];
634			b = constrainedB[i];
635
636			ax = (a * 3) + 0;
637			ay = (a * 3) + 1;
638			az = (a * 3) + 2;
639
640			bx = (b * 3) + 0;
641			by = (b * 3) + 1;
642			bz = (b * 3) + 2;
643
644			if (moved[a] \|\| moved[b]){
645			velA = atoms[a]->getVel();
646			velB = atoms[b]->getVel();
647
648			vxab = velA[0] - velB[0];
649			vyab = velA[1] - velB[1];
650			vzab = velA[2] - velB[2];
651
652			posA = atoms[a]->getPos();
653			posB = atoms[b]->getPos();
654
655			for (j = 0; j < 3; j++)
656			rab[j] = posA[j] - posB[j];
657
658			info->wrapVector(rab);
659
660			rma = 1.0 / atoms[a]->getMass();
661			rmb = 1.0 / atoms[b]->getMass();
662
663			rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
664
665			gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
666
667			if (fabs(gab) > tol){
668			dx = rab[0] * gab;
669			dy = rab[1] * gab;
670			dz = rab[2] * gab;
671
672			velA[0] += rma * dx;
673			velA[1] += rma * dy;
674			velA[2] += rma * dz;
675
676			atoms[a]->setVel(velA);
677
678			velB[0] -= rmb * dx;
679			velB[1] -= rmb * dy;
680			velB[2] -= rmb * dz;
681
682			atoms[b]->setVel(velB);
683
684			moving[a] = 1;
685			moving[b] = 1;
686			done = 0;
687			}
688			}
689			}
690
691			for (i = 0; i < nAtoms; i++){
692			moved[i] = moving[i];
693			moving[i] = 0;
694			}
695
696			iteration++;
697			}
698
699			if (!done){
700			sprintf(painCave.errMsg,
701			"Constraint failure in constrainB, too many iterations: %d\n",
702			iteration);
703			painCave.isFatal = 1;
704			simError();
705			}
706			}
707
708			template<typename T> void Integrator<T>::rotationPropagation
709			( StuntDouble* sd, double ji[3] ){
710
711			double angle;
712			double A[3][3], I[3][3];
713			int i, j, k;
714
715			// use the angular velocities to propagate the rotation matrix a
716			// full time step
717
718			sd->getA(A);
719			sd->getI(I);
720
721			if (sd->isLinear()) {
722			i = sd->linearAxis();
723			j = (i+1)%3;
724			k = (i+2)%3;
725
726			angle = dt2 * ji[j] / I[j][j];
727			this->rotate( k, i, angle, ji, A );
728
729			angle = dt * ji[k] / I[k][k];
730			this->rotate( i, j, angle, ji, A);
731
732			angle = dt2 * ji[j] / I[j][j];
733			this->rotate( k, i, angle, ji, A );
734
735			} else {
736			// rotate about the x-axis
737			angle = dt2 * ji[0] / I[0][0];
738			this->rotate( 1, 2, angle, ji, A );
739
740			// rotate about the y-axis
741			angle = dt2 * ji[1] / I[1][1];
742			this->rotate( 2, 0, angle, ji, A );
743
744			// rotate about the z-axis
745			angle = dt * ji[2] / I[2][2];
746			sd->addZangle(angle);
747			this->rotate( 0, 1, angle, ji, A);
748
749			// rotate about the y-axis
750			angle = dt2 * ji[1] / I[1][1];
751			this->rotate( 2, 0, angle, ji, A );
752
753			// rotate about the x-axis
754			angle = dt2 * ji[0] / I[0][0];
755			this->rotate( 1, 2, angle, ji, A );
756
757			}
758			sd->setA( A );
759			}
760
761			template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
762			double angle, double ji[3],
763			double A[3][3]){
764			int i, j, k;
765			double sinAngle;
766			double cosAngle;
767			double angleSqr;
768			double angleSqrOver4;
769			double top, bottom;
770			double rot[3][3];
771			double tempA[3][3];
772			double tempJ[3];
773
774			// initialize the tempA
775
776			for (i = 0; i < 3; i++){
777			for (j = 0; j < 3; j++){
778			tempA[j][i] = A[i][j];
779			}
780			}
781
782			// initialize the tempJ
783
784			for (i = 0; i < 3; i++)
785			tempJ[i] = ji[i];
786
787			// initalize rot as a unit matrix
788
789			rot[0][0] = 1.0;
790			rot[0][1] = 0.0;
791			rot[0][2] = 0.0;
792
793			rot[1][0] = 0.0;
794			rot[1][1] = 1.0;
795			rot[1][2] = 0.0;
796
797			rot[2][0] = 0.0;
798			rot[2][1] = 0.0;
799			rot[2][2] = 1.0;
800
801			// use a small angle aproximation for sin and cosine
802
803			angleSqr = angle * angle;
804			angleSqrOver4 = angleSqr / 4.0;
805			top = 1.0 - angleSqrOver4;
806			bottom = 1.0 + angleSqrOver4;
807
808			cosAngle = top / bottom;
809			sinAngle = angle / bottom;
810
811			rot[axes1][axes1] = cosAngle;
812			rot[axes2][axes2] = cosAngle;
813
814			rot[axes1][axes2] = sinAngle;
815			rot[axes2][axes1] = -sinAngle;
816
817			// rotate the momentum acoording to: ji[] = rot[][] * ji[]
818
819			for (i = 0; i < 3; i++){
820			ji[i] = 0.0;
821			for (k = 0; k < 3; k++){
822			ji[i] += rot[i][k] * tempJ[k];
823			}
824			}
825
826			// rotate the Rotation matrix acording to:
827			// A[][] = A[][] * transpose(rot[][])
828
829
830			// NOte for as yet unknown reason, we are performing the
831			// calculation as:
832			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
833
834			for (i = 0; i < 3; i++){
835			for (j = 0; j < 3; j++){
836			A[j][i] = 0.0;
837			for (k = 0; k < 3; k++){
838			A[j][i] += tempA[i][k] * rot[j][k];
839			}
840			}
841			}
842			}
843
844			template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
845			myFF->doForces(calcPot, calcStress);
846			}
847
848			template<typename T> void Integrator<T>::thermalize(){
849			tStats->velocitize();
850			}
851
852			template<typename T> double Integrator<T>::getConservedQuantity(void){
853			return tStats->getTotalE();
854			}
855			template<typename T> string Integrator<T>::getAdditionalParameters(void){
856			//By default, return a null string
857			//The reason we use string instead of char* is that if we use char*, we will
858			//return a pointer point to local variable which might cause problem
859			return string();
860			}