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;
  double Tb[3], ji[3];
  double vel[3], pos[3], frc[3];
  double mass;
  double omega;
 
  for (i = 0; i < integrableObjects.size() ; i++){
    integrableObjects[i]->getVel(vel);
    integrableObjects[i]->getPos(pos);
    integrableObjects[i]->getFrc(frc);
    //    std::cerr << "f = " << frc[0] << "\t" << frc[1] << "\t" << frc[2] << "\n";
    
    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

      integrableObjects[i]->getTrq(Tb);

      //      std::cerr << "t = " << Tb[0] << "\t" << Tb[1] << "\t" << Tb[2] << "\n";
      integrableObjects[i]->lab2Body(Tb);

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

      integrableObjects[i]->getJ(ji);

      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++){
    integrableObjects[i]->getVel(vel);
    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

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

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

      integrableObjects[i]->getJ(ji);

      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++){
      atoms[i]->getPos(pos);

      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]){
        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();
  }

}

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]){
        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();
  }
}

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:	1730
Committed:	Thu Nov 11 21:47:05 2004 UTC (19 years, 8 months ago) by chrisfen
File size:	18907 byte(s)
Log Message:	Commented out some write statements
#	User	Rev	Content
1	gezelter	1490	#include <iostream>
2			#include <stdlib.h>
3			#include <math.h>
4			#ifdef IS_MPI
5	tim	1492	#include "brains/mpiSimulation.hpp"
6	gezelter	1490	#include <unistd.h>
7			#endif //is_mpi
8
9			#ifdef PROFILE
10	tim	1492	#include "profiling/mdProfile.hpp"
11	gezelter	1490	#endif // profile
12
13	tim	1492	#include "integrators/Integrator.hpp"
14			#include "utils/simError.h"
15	gezelter	1490
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			double Tb[3], ji[3];
358			double vel[3], pos[3], frc[3];
359			double mass;
360			double omega;
361
362			for (i = 0; i < integrableObjects.size() ; i++){
363			integrableObjects[i]->getVel(vel);
364			integrableObjects[i]->getPos(pos);
365			integrableObjects[i]->getFrc(frc);
366	chrisfen	1730	// std::cerr << "f = " << frc[0] << "\t" << frc[1] << "\t" << frc[2] << "\n";
367	gezelter	1490
368			mass = integrableObjects[i]->getMass();
369
370			for (j = 0; j < 3; j++){
371			// velocity half step
372			vel[j] += (dt2 * frc[j] / mass) * eConvert;
373			// position whole step
374			pos[j] += dt * vel[j];
375			}
376
377			integrableObjects[i]->setVel(vel);
378			integrableObjects[i]->setPos(pos);
379
380	gezelter	1708
381	gezelter	1490	if (integrableObjects[i]->isDirectional()){
382
383			// get and convert the torque to body frame
384
385			integrableObjects[i]->getTrq(Tb);
386	gezelter	1708
387	chrisfen	1730	// std::cerr << "t = " << Tb[0] << "\t" << Tb[1] << "\t" << Tb[2] << "\n";
388	gezelter	1490	integrableObjects[i]->lab2Body(Tb);
389
390			// get the angular momentum, and propagate a half step
391
392			integrableObjects[i]->getJ(ji);
393
394			for (j = 0; j < 3; j++)
395			ji[j] += (dt2 * Tb[j]) * eConvert;
396
397			this->rotationPropagation( integrableObjects[i], ji );
398
399			integrableObjects[i]->setJ(ji);
400			}
401			}
402
403			if(nConstrained)
404			constrainA();
405			}
406
407
408			template<typename T> void Integrator<T>::moveB(void){
409			int i, j;
410			double Tb[3], ji[3];
411			double vel[3], frc[3];
412			double mass;
413
414			for (i = 0; i < integrableObjects.size(); i++){
415			integrableObjects[i]->getVel(vel);
416			integrableObjects[i]->getFrc(frc);
417
418			mass = integrableObjects[i]->getMass();
419
420			// velocity half step
421			for (j = 0; j < 3; j++)
422			vel[j] += (dt2 * frc[j] / mass) * eConvert;
423
424			integrableObjects[i]->setVel(vel);
425
426			if (integrableObjects[i]->isDirectional()){
427
428			// get and convert the torque to body frame
429
430			integrableObjects[i]->getTrq(Tb);
431			integrableObjects[i]->lab2Body(Tb);
432
433			// get the angular momentum, and propagate a half step
434
435			integrableObjects[i]->getJ(ji);
436
437			for (j = 0; j < 3; j++)
438			ji[j] += (dt2 * Tb[j]) * eConvert;
439
440
441			integrableObjects[i]->setJ(ji);
442			}
443			}
444
445			if(nConstrained)
446			constrainB();
447			}
448
449
450			template<typename T> void Integrator<T>::preMove(void){
451			int i, j;
452			double pos[3];
453
454			if (nConstrained){
455			for (i = 0; i < nAtoms; i++){
456			atoms[i]->getPos(pos);
457
458			for (j = 0; j < 3; j++){
459			oldPos[3 * i + j] = pos[j];
460			}
461			}
462			}
463			}
464
465			template<typename T> void Integrator<T>::constrainA(){
466			int i, j;
467			int done;
468			double posA[3], posB[3];
469			double velA[3], velB[3];
470			double pab[3];
471			double rab[3];
472			int a, b, ax, ay, az, bx, by, bz;
473			double rma, rmb;
474			double dx, dy, dz;
475			double rpab;
476			double rabsq, pabsq, rpabsq;
477			double diffsq;
478			double gab;
479			int iteration;
480
481			for (i = 0; i < nAtoms; i++){
482			moving[i] = 0;
483			moved[i] = 1;
484			}
485
486			iteration = 0;
487			done = 0;
488			while (!done && (iteration < maxIteration)){
489			done = 1;
490			for (i = 0; i < nConstrained; i++){
491			a = constrainedA[i];
492			b = constrainedB[i];
493
494			ax = (a * 3) + 0;
495			ay = (a * 3) + 1;
496			az = (a * 3) + 2;
497
498			bx = (b * 3) + 0;
499			by = (b * 3) + 1;
500			bz = (b * 3) + 2;
501
502			if (moved[a] \|\| moved[b]){
503			atoms[a]->getPos(posA);
504			atoms[b]->getPos(posB);
505
506			for (j = 0; j < 3; j++)
507			pab[j] = posA[j] - posB[j];
508
509			//periodic boundary condition
510
511			info->wrapVector(pab);
512
513			pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
514
515			rabsq = constrainedDsqr[i];
516			diffsq = rabsq - pabsq;
517
518			// the original rattle code from alan tidesley
519			if (fabs(diffsq) > (tol * rabsq * 2)){
520			rab[0] = oldPos[ax] - oldPos[bx];
521			rab[1] = oldPos[ay] - oldPos[by];
522			rab[2] = oldPos[az] - oldPos[bz];
523
524			info->wrapVector(rab);
525
526			rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
527
528			rpabsq = rpab * rpab;
529
530
531			if (rpabsq < (rabsq * -diffsq)){
532			#ifdef IS_MPI
533			a = atoms[a]->getGlobalIndex();
534			b = atoms[b]->getGlobalIndex();
535			#endif //is_mpi
536			sprintf(painCave.errMsg,
537			"Constraint failure in constrainA at atom %d and %d.\n", a,
538			b);
539			painCave.isFatal = 1;
540			simError();
541			}
542
543			rma = 1.0 / atoms[a]->getMass();
544			rmb = 1.0 / atoms[b]->getMass();
545
546			gab = diffsq / (2.0 * (rma + rmb) * rpab);
547
548			dx = rab[0] * gab;
549			dy = rab[1] * gab;
550			dz = rab[2] * gab;
551
552			posA[0] += rma * dx;
553			posA[1] += rma * dy;
554			posA[2] += rma * dz;
555
556			atoms[a]->setPos(posA);
557
558			posB[0] -= rmb * dx;
559			posB[1] -= rmb * dy;
560			posB[2] -= rmb * dz;
561
562			atoms[b]->setPos(posB);
563
564			dx = dx / dt;
565			dy = dy / dt;
566			dz = dz / dt;
567
568			atoms[a]->getVel(velA);
569
570			velA[0] += rma * dx;
571			velA[1] += rma * dy;
572			velA[2] += rma * dz;
573
574			atoms[a]->setVel(velA);
575
576			atoms[b]->getVel(velB);
577
578			velB[0] -= rmb * dx;
579			velB[1] -= rmb * dy;
580			velB[2] -= rmb * dz;
581
582			atoms[b]->setVel(velB);
583
584			moving[a] = 1;
585			moving[b] = 1;
586			done = 0;
587			}
588			}
589			}
590
591			for (i = 0; i < nAtoms; i++){
592			moved[i] = moving[i];
593			moving[i] = 0;
594			}
595
596			iteration++;
597			}
598
599			if (!done){
600			sprintf(painCave.errMsg,
601			"Constraint failure in constrainA, too many iterations: %d\n",
602			iteration);
603			painCave.isFatal = 1;
604			simError();
605			}
606
607			}
608
609			template<typename T> void Integrator<T>::constrainB(void){
610			int i, j;
611			int done;
612			double posA[3], posB[3];
613			double velA[3], velB[3];
614			double vxab, vyab, vzab;
615			double rab[3];
616			int a, b, ax, ay, az, bx, by, bz;
617			double rma, rmb;
618			double dx, dy, dz;
619			double rvab;
620			double gab;
621			int iteration;
622
623			for (i = 0; i < nAtoms; i++){
624			moving[i] = 0;
625			moved[i] = 1;
626			}
627
628			done = 0;
629			iteration = 0;
630			while (!done && (iteration < maxIteration)){
631			done = 1;
632
633			for (i = 0; i < nConstrained; i++){
634			a = constrainedA[i];
635			b = constrainedB[i];
636
637			ax = (a * 3) + 0;
638			ay = (a * 3) + 1;
639			az = (a * 3) + 2;
640
641			bx = (b * 3) + 0;
642			by = (b * 3) + 1;
643			bz = (b * 3) + 2;
644
645			if (moved[a] \|\| moved[b]){
646			atoms[a]->getVel(velA);
647			atoms[b]->getVel(velB);
648
649			vxab = velA[0] - velB[0];
650			vyab = velA[1] - velB[1];
651			vzab = velA[2] - velB[2];
652
653			atoms[a]->getPos(posA);
654			atoms[b]->getPos(posB);
655
656			for (j = 0; j < 3; j++)
657			rab[j] = posA[j] - posB[j];
658
659			info->wrapVector(rab);
660
661			rma = 1.0 / atoms[a]->getMass();
662			rmb = 1.0 / atoms[b]->getMass();
663
664			rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
665
666			gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
667
668			if (fabs(gab) > tol){
669			dx = rab[0] * gab;
670			dy = rab[1] * gab;
671			dz = rab[2] * gab;
672
673			velA[0] += rma * dx;
674			velA[1] += rma * dy;
675			velA[2] += rma * dz;
676
677			atoms[a]->setVel(velA);
678
679			velB[0] -= rmb * dx;
680			velB[1] -= rmb * dy;
681			velB[2] -= rmb * dz;
682
683			atoms[b]->setVel(velB);
684
685			moving[a] = 1;
686			moving[b] = 1;
687			done = 0;
688			}
689			}
690			}
691
692			for (i = 0; i < nAtoms; i++){
693			moved[i] = moving[i];
694			moving[i] = 0;
695			}
696
697			iteration++;
698			}
699
700			if (!done){
701			sprintf(painCave.errMsg,
702			"Constraint failure in constrainB, too many iterations: %d\n",
703			iteration);
704			painCave.isFatal = 1;
705			simError();
706			}
707			}
708
709			template<typename T> void Integrator<T>::rotationPropagation
710			( StuntDouble* sd, double ji[3] ){
711
712			double angle;
713			double A[3][3], I[3][3];
714			int i, j, k;
715
716			// use the angular velocities to propagate the rotation matrix a
717			// full time step
718
719			sd->getA(A);
720			sd->getI(I);
721
722			if (sd->isLinear()) {
723	gezelter	1708
724	gezelter	1490	i = sd->linearAxis();
725			j = (i+1)%3;
726			k = (i+2)%3;
727	gezelter	1708
728	gezelter	1490	angle = dt2 * ji[j] / I[j][j];
729			this->rotate( k, i, angle, ji, A );
730
731			angle = dt * ji[k] / I[k][k];
732			this->rotate( i, j, angle, ji, A);
733
734			angle = dt2 * ji[j] / I[j][j];
735			this->rotate( k, i, angle, ji, A );
736
737			} else {
738			// rotate about the x-axis
739			angle = dt2 * ji[0] / I[0][0];
740			this->rotate( 1, 2, angle, ji, A );
741
742			// rotate about the y-axis
743			angle = dt2 * ji[1] / I[1][1];
744			this->rotate( 2, 0, angle, ji, A );
745
746			// rotate about the z-axis
747			angle = dt * ji[2] / I[2][2];
748			sd->addZangle(angle);
749			this->rotate( 0, 1, angle, ji, A);
750
751			// rotate about the y-axis
752			angle = dt2 * ji[1] / I[1][1];
753			this->rotate( 2, 0, angle, ji, A );
754
755			// rotate about the x-axis
756			angle = dt2 * ji[0] / I[0][0];
757			this->rotate( 1, 2, angle, ji, A );
758
759			}
760			sd->setA( A );
761			}
762
763			template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
764			double angle, double ji[3],
765			double A[3][3]){
766			int i, j, k;
767			double sinAngle;
768			double cosAngle;
769			double angleSqr;
770			double angleSqrOver4;
771			double top, bottom;
772			double rot[3][3];
773			double tempA[3][3];
774			double tempJ[3];
775
776			// initialize the tempA
777
778			for (i = 0; i < 3; i++){
779			for (j = 0; j < 3; j++){
780			tempA[j][i] = A[i][j];
781			}
782			}
783
784			// initialize the tempJ
785
786			for (i = 0; i < 3; i++)
787			tempJ[i] = ji[i];
788
789			// initalize rot as a unit matrix
790
791			rot[0][0] = 1.0;
792			rot[0][1] = 0.0;
793			rot[0][2] = 0.0;
794
795			rot[1][0] = 0.0;
796			rot[1][1] = 1.0;
797			rot[1][2] = 0.0;
798
799			rot[2][0] = 0.0;
800			rot[2][1] = 0.0;
801			rot[2][2] = 1.0;
802
803			// use a small angle aproximation for sin and cosine
804
805			angleSqr = angle * angle;
806			angleSqrOver4 = angleSqr / 4.0;
807			top = 1.0 - angleSqrOver4;
808			bottom = 1.0 + angleSqrOver4;
809
810			cosAngle = top / bottom;
811			sinAngle = angle / bottom;
812
813			rot[axes1][axes1] = cosAngle;
814			rot[axes2][axes2] = cosAngle;
815
816			rot[axes1][axes2] = sinAngle;
817			rot[axes2][axes1] = -sinAngle;
818
819			// rotate the momentum acoording to: ji[] = rot[][] * ji[]
820
821			for (i = 0; i < 3; i++){
822			ji[i] = 0.0;
823			for (k = 0; k < 3; k++){
824			ji[i] += rot[i][k] * tempJ[k];
825			}
826			}
827
828			// rotate the Rotation matrix acording to:
829			// A[][] = A[][] * transpose(rot[][])
830
831
832			// NOte for as yet unknown reason, we are performing the
833			// calculation as:
834			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
835
836			for (i = 0; i < 3; i++){
837			for (j = 0; j < 3; j++){
838			A[j][i] = 0.0;
839			for (k = 0; k < 3; k++){
840			A[j][i] += tempA[i][k] * rot[j][k];
841			}
842			}
843			}
844			}
845
846			template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
847			myFF->doForces(calcPot, calcStress);
848			}
849
850			template<typename T> void Integrator<T>::thermalize(){
851			tStats->velocitize();
852			}
853
854			template<typename T> double Integrator<T>::getConservedQuantity(void){
855			return tStats->getTotalE();
856			}
857			template<typename T> string Integrator<T>::getAdditionalParameters(void){
858			//By default, return a null string
859			//The reason we use string instead of char* is that if we use char*, we will
860			//return a pointer point to local variable which might cause problem
861			return string();
862			}