OOPSE/libmdtools/Integrator.cpp

#include <iostream>
#include <stdlib.h>
#include <math.h>

#ifdef IS_MPI
#include "mpiSimulation.hpp"
#include <unistd.h>
#endif //is_mpi

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

#include "Integrator.hpp"
#include "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;

  // 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 balanceing 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 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();

  // initialize the forces before the first step

  calcForce(1, 1);

  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){
    if ((info->getTime() + dt) >= currStatus){
      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
  }

  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

  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){
  int i, j;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3];
  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;

      this->rotationPropagation( dAtom, ji );

      dAtom->setJ(ji);
    }
  }

  if (nConstrained){
    constrainA();
  }
}


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

  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
( DirectionalAtom* dAtom, double ji[3] ){

  double angle;
  double A[3][3], I[3][3];

  // 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->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:	929
Committed:	Tue Jan 13 15:46:49 2004 UTC (20 years, 5 months ago) by tim
File size:	17326 byte(s)
Log Message:	Merge the code of writeFinal and writeDump; Adding sortingIndex into DumpWriter; Fix a bug of writing last frame twice in integrator
#	User	Rev	Content
1	mmeineke	558	#include <iostream>
2	gezelter	829	#include <stdlib.h>
3			#include <math.h>
4	mmeineke	558
5			#ifdef IS_MPI
6			#include "mpiSimulation.hpp"
7			#include <unistd.h>
8			#endif //is_mpi
9
10	chuckv	892	#ifdef PROFILE
11			#include "mdProfile.hpp"
12			#endif // profile
13
14	mmeineke	558	#include "Integrator.hpp"
15			#include "simError.h"
16
17
18	tim	725	template<typename T> Integrator<T>::Integrator(SimInfo* theInfo,
19			ForceFields* the_ff){
20	mmeineke	558	info = theInfo;
21			myFF = the_ff;
22			isFirst = 1;
23
24			molecules = info->molecules;
25			nMols = info->n_mol;
26
27			// give a little love back to the SimInfo object
28	tim	725
29			if (info->the_integrator != NULL){
30			delete info->the_integrator;
31			}
32	tim	837
33	mmeineke	558	nAtoms = info->n_atoms;
34
35			// check for constraints
36	tim	725
37			constrainedA = NULL;
38			constrainedB = NULL;
39	mmeineke	558	constrainedDsqr = NULL;
40	tim	725	moving = NULL;
41			moved = NULL;
42			oldPos = NULL;
43
44	mmeineke	558	nConstrained = 0;
45
46			checkConstraints();
47			}
48
49	tim	725	template<typename T> Integrator<T>::~Integrator(){
50			if (nConstrained){
51	mmeineke	558	delete[] constrainedA;
52			delete[] constrainedB;
53			delete[] constrainedDsqr;
54			delete[] moving;
55			delete[] moved;
56	mmeineke	561	delete[] oldPos;
57	mmeineke	558	}
58			}
59
60	tim	725	template<typename T> void Integrator<T>::checkConstraints(void){
61	mmeineke	558	isConstrained = 0;
62
63	tim	725	Constraint* temp_con;
64			Constraint* dummy_plug;
65	mmeineke	558	temp_con = new Constraint[info->n_SRI];
66			nConstrained = 0;
67			int constrained = 0;
68	tim	725
69	mmeineke	558	SRI** theArray;
70	tim	725	for (int i = 0; i < nMols; i++){
71			theArray = (SRI * *) molecules[i].getMyBonds();
72			for (int j = 0; j < molecules[i].getNBonds(); j++){
73	mmeineke	558	constrained = theArray[j]->is_constrained();
74	mmeineke	594
75	tim	725	if (constrained){
76			dummy_plug = theArray[j]->get_constraint();
77			temp_con[nConstrained].set_a(dummy_plug->get_a());
78			temp_con[nConstrained].set_b(dummy_plug->get_b());
79			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
80	mmeineke	594
81	tim	725	nConstrained++;
82			constrained = 0;
83			}
84	mmeineke	558	}
85
86	tim	725	theArray = (SRI * *) molecules[i].getMyBends();
87			for (int j = 0; j < molecules[i].getNBends(); j++){
88	mmeineke	558	constrained = theArray[j]->is_constrained();
89	tim	725
90			if (constrained){
91			dummy_plug = theArray[j]->get_constraint();
92			temp_con[nConstrained].set_a(dummy_plug->get_a());
93			temp_con[nConstrained].set_b(dummy_plug->get_b());
94			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
95
96			nConstrained++;
97			constrained = 0;
98	mmeineke	558	}
99			}
100
101	tim	725	theArray = (SRI * *) molecules[i].getMyTorsions();
102			for (int j = 0; j < molecules[i].getNTorsions(); j++){
103	mmeineke	558	constrained = theArray[j]->is_constrained();
104	tim	725
105			if (constrained){
106			dummy_plug = theArray[j]->get_constraint();
107			temp_con[nConstrained].set_a(dummy_plug->get_a());
108			temp_con[nConstrained].set_b(dummy_plug->get_b());
109			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
110
111			nConstrained++;
112			constrained = 0;
113	mmeineke	558	}
114			}
115			}
116
117	tim	725	if (nConstrained > 0){
118	mmeineke	558	isConstrained = 1;
119
120	tim	725	if (constrainedA != NULL)
121			delete[] constrainedA;
122			if (constrainedB != NULL)
123			delete[] constrainedB;
124			if (constrainedDsqr != NULL)
125			delete[] constrainedDsqr;
126	mmeineke	558
127	tim	725	constrainedA = new int[nConstrained];
128			constrainedB = new int[nConstrained];
129	mmeineke	558	constrainedDsqr = new double[nConstrained];
130	tim	725
131			for (int i = 0; i < nConstrained; i++){
132	mmeineke	558	constrainedA[i] = temp_con[i].get_a();
133			constrainedB[i] = temp_con[i].get_b();
134			constrainedDsqr[i] = temp_con[i].get_dsqr();
135			}
136
137	tim	725
138	mmeineke	558	// save oldAtoms to check for lode balanceing later on.
139	tim	725
140	mmeineke	558	oldAtoms = nAtoms;
141	tim	725
142	mmeineke	558	moving = new int[nAtoms];
143	tim	725	moved = new int[nAtoms];
144	mmeineke	558
145	tim	725	oldPos = new double[nAtoms * 3];
146	mmeineke	558	}
147	tim	725
148	mmeineke	558	delete[] temp_con;
149			}
150
151
152	tim	725	template<typename T> void Integrator<T>::integrate(void){
153	mmeineke	558
154	tim	725	double runTime = info->run_time;
155			double sampleTime = info->sampleTime;
156			double statusTime = info->statusTime;
157	mmeineke	558	double thermalTime = info->thermalTime;
158	mmeineke	746	double resetTime = info->resetTime;
159	mmeineke	558
160	mmeineke	746
161	mmeineke	558	double currSample;
162			double currThermal;
163			double currStatus;
164	mmeineke	746	double currReset;
165	tim	837
166	mmeineke	558	int calcPot, calcStress;
167
168	tim	725	tStats = new Thermo(info);
169			statOut = new StatWriter(info);
170			dumpOut = new DumpWriter(info);
171	mmeineke	558
172	mmeineke	561	atoms = info->atoms;
173
174			dt = info->dt;
175	mmeineke	558	dt2 = 0.5 * dt;
176
177	mmeineke	784	readyCheck();
178
179	mmeineke	558	// initialize the forces before the first step
180
181	tim	677	calcForce(1, 1);
182	tim	781
183			if (nConstrained){
184			preMove();
185			constrainA();
186	tim	837	calcForce(1, 1);
187	tim	781	constrainB();
188			}
189	mmeineke	843
190	tim	725	if (info->setTemp){
191	tim	677	thermalize();
192	mmeineke	558	}
193	tim	725
194	mmeineke	558	calcPot = 0;
195			calcStress = 0;
196	mmeineke	711	currSample = sampleTime + info->getTime();
197			currThermal = thermalTime+ info->getTime();
198			currStatus = statusTime + info->getTime();
199	mmeineke	746	currReset = resetTime + info->getTime();
200	mmeineke	558
201	tim	725	dumpOut->writeDump(info->getTime());
202			statOut->writeStat(info->getTime());
203	mmeineke	559
204
205			#ifdef IS_MPI
206	tim	725	strcpy(checkPointMsg, "The integrator is ready to go.");
207	mmeineke	559	MPIcheckPoint();
208			#endif // is_mpi
209
210	tim	725	while (info->getTime() < runTime){
211			if ((info->getTime() + dt) >= currStatus){
212	mmeineke	558	calcPot = 1;
213			calcStress = 1;
214			}
215	mmeineke	561
216	chuckv	892	#ifdef PROFILE
217			startProfile( pro1 );
218			#endif
219
220	tim	725	integrateStep(calcPot, calcStress);
221
222	chuckv	892	#ifdef PROFILE
223			endProfile( pro1 );
224
225			startProfile( pro2 );
226			#endif // profile
227
228	mmeineke	643	info->incrTime(dt);
229	mmeineke	558
230	tim	725	if (info->setTemp){
231			if (info->getTime() >= currThermal){
232			thermalize();
233			currThermal += thermalTime;
234	mmeineke	558	}
235			}
236
237	tim	725	if (info->getTime() >= currSample){
238			dumpOut->writeDump(info->getTime());
239	mmeineke	558	currSample += sampleTime;
240			}
241
242	tim	725	if (info->getTime() >= currStatus){
243	tim	837	statOut->writeStat(info->getTime());
244			calcPot = 0;
245	mmeineke	558	calcStress = 0;
246			currStatus += statusTime;
247	tim	837	}
248	mmeineke	559
249	mmeineke	746	if (info->resetIntegrator){
250			if (info->getTime() >= currReset){
251			this->resetIntegrator();
252			currReset += resetTime;
253			}
254			}
255	chuckv	892
256			#ifdef PROFILE
257			endProfile( pro2 );
258			#endif //profile
259	mmeineke	746
260	mmeineke	559	#ifdef IS_MPI
261	tim	725	strcpy(checkPointMsg, "successfully took a time step.");
262	mmeineke	559	MPIcheckPoint();
263			#endif // is_mpi
264	mmeineke	558	}
265
266	mmeineke	561	delete dumpOut;
267			delete statOut;
268	mmeineke	558	}
269
270	tim	725	template<typename T> void Integrator<T>::integrateStep(int calcPot,
271			int calcStress){
272	mmeineke	558	// Position full step, and velocity half step
273	chuckv	892
274			#ifdef PROFILE
275			startProfile(pro3);
276			#endif //profile
277
278	tim	725	preMove();
279	mmeineke	558
280	chuckv	892	#ifdef PROFILE
281			endProfile(pro3);
282
283			startProfile(pro4);
284			#endif // profile
285
286	mmeineke	558	moveA();
287
288	chuckv	892	#ifdef PROFILE
289			endProfile(pro4);
290
291			startProfile(pro5);
292			#endif//profile
293	tim	725
294
295	mmeineke	614	#ifdef IS_MPI
296	tim	725	strcpy(checkPointMsg, "Succesful moveA\n");
297	mmeineke	614	MPIcheckPoint();
298			#endif // is_mpi
299
300	tim	725
301	mmeineke	558	// calc forces
302
303	tim	725	calcForce(calcPot, calcStress);
304	mmeineke	558
305	mmeineke	614	#ifdef IS_MPI
306	tim	725	strcpy(checkPointMsg, "Succesful doForces\n");
307	mmeineke	614	MPIcheckPoint();
308			#endif // is_mpi
309
310	chuckv	892	#ifdef PROFILE
311			endProfile( pro5 );
312	tim	725
313	chuckv	892	startProfile( pro6 );
314			#endif //profile
315
316	mmeineke	558	// finish the velocity half step
317	tim	725
318	mmeineke	558	moveB();
319	tim	725
320	chuckv	892	#ifdef PROFILE
321			endProfile(pro6);
322			#endif // profile
323	tim	725
324	mmeineke	614	#ifdef IS_MPI
325	tim	725	strcpy(checkPointMsg, "Succesful moveB\n");
326	mmeineke	614	MPIcheckPoint();
327			#endif // is_mpi
328	mmeineke	558	}
329
330
331	tim	725	template<typename T> void Integrator<T>::moveA(void){
332	gezelter	600	int i, j;
333	mmeineke	558	DirectionalAtom* dAtom;
334	gezelter	600	double Tb[3], ji[3];
335			double vel[3], pos[3], frc[3];
336			double mass;
337	mmeineke	558
338	tim	725	for (i = 0; i < nAtoms; i++){
339			atoms[i]->getVel(vel);
340			atoms[i]->getPos(pos);
341			atoms[i]->getFrc(frc);
342	mmeineke	567
343	gezelter	600	mass = atoms[i]->getMass();
344	mmeineke	594
345	tim	725	for (j = 0; j < 3; j++){
346	gezelter	600	// velocity half step
347	tim	725	vel[j] += (dt2 * frc[j] / mass) * eConvert;
348	gezelter	600	// position whole step
349			pos[j] += dt * vel[j];
350			}
351	mmeineke	594
352	tim	725	atoms[i]->setVel(vel);
353			atoms[i]->setPos(pos);
354	gezelter	600
355	tim	725	if (atoms[i]->isDirectional()){
356			dAtom = (DirectionalAtom *) atoms[i];
357	mmeineke	558
358			// get and convert the torque to body frame
359	mmeineke	597
360	tim	725	dAtom->getTrq(Tb);
361			dAtom->lab2Body(Tb);
362
363	mmeineke	558	// get the angular momentum, and propagate a half step
364	gezelter	600
365	tim	725	dAtom->getJ(ji);
366	gezelter	600
367	tim	725	for (j = 0; j < 3; j++)
368	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
369	tim	725
370	mmeineke	778	this->rotationPropagation( dAtom, ji );
371	gezelter	600
372	tim	725	dAtom->setJ(ji);
373			}
374	mmeineke	558	}
375	mmeineke	768
376			if (nConstrained){
377			constrainA();
378			}
379	mmeineke	558	}
380
381
382	tim	725	template<typename T> void Integrator<T>::moveB(void){
383	gezelter	600	int i, j;
384	mmeineke	558	DirectionalAtom* dAtom;
385	gezelter	600	double Tb[3], ji[3];
386			double vel[3], frc[3];
387			double mass;
388	mmeineke	558
389	tim	725	for (i = 0; i < nAtoms; i++){
390			atoms[i]->getVel(vel);
391			atoms[i]->getFrc(frc);
392	mmeineke	558
393	gezelter	600	mass = atoms[i]->getMass();
394
395	mmeineke	558	// velocity half step
396	tim	725	for (j = 0; j < 3; j++)
397			vel[j] += (dt2 * frc[j] / mass) * eConvert;
398	gezelter	600
399	tim	725	atoms[i]->setVel(vel);
400	mmeineke	597
401	tim	725	if (atoms[i]->isDirectional()){
402			dAtom = (DirectionalAtom *) atoms[i];
403
404	tim	837	// get and convert the torque to body frame
405	gezelter	600
406	tim	725	dAtom->getTrq(Tb);
407			dAtom->lab2Body(Tb);
408	gezelter	600
409			// get the angular momentum, and propagate a half step
410
411	tim	725	dAtom->getJ(ji);
412	gezelter	600
413	tim	725	for (j = 0; j < 3; j++)
414	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
415	mmeineke	597
416	tim	725
417			dAtom->setJ(ji);
418	mmeineke	558	}
419			}
420	mmeineke	768
421			if (nConstrained){
422			constrainB();
423			}
424	mmeineke	558	}
425
426	tim	725	template<typename T> void Integrator<T>::preMove(void){
427	gezelter	600	int i, j;
428			double pos[3];
429	mmeineke	558
430	tim	725	if (nConstrained){
431			for (i = 0; i < nAtoms; i++){
432			atoms[i]->getPos(pos);
433	mmeineke	561
434	tim	725	for (j = 0; j < 3; j++){
435			oldPos[3 * i + j] = pos[j];
436	gezelter	600	}
437			}
438	tim	725	}
439	gezelter	600	}
440
441	tim	645	template<typename T> void Integrator<T>::constrainA(){
442	mmeineke	787	int i, j;
443	mmeineke	558	int done;
444	gezelter	600	double posA[3], posB[3];
445			double velA[3], velB[3];
446	mmeineke	572	double pab[3];
447			double rab[3];
448	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
449	mmeineke	558	double rma, rmb;
450			double dx, dy, dz;
451	mmeineke	561	double rpab;
452	mmeineke	558	double rabsq, pabsq, rpabsq;
453			double diffsq;
454			double gab;
455			int iteration;
456
457	tim	725	for (i = 0; i < nAtoms; i++){
458	mmeineke	558	moving[i] = 0;
459	tim	725	moved[i] = 1;
460	mmeineke	558	}
461	mmeineke	567
462	mmeineke	558	iteration = 0;
463			done = 0;
464	tim	725	while (!done && (iteration < maxIteration)){
465	mmeineke	558	done = 1;
466	tim	725	for (i = 0; i < nConstrained; i++){
467	mmeineke	558	a = constrainedA[i];
468			b = constrainedB[i];
469	mmeineke	563
470	tim	725	ax = (a * 3) + 0;
471			ay = (a * 3) + 1;
472			az = (a * 3) + 2;
473	mmeineke	563
474	tim	725	bx = (b * 3) + 0;
475			by = (b * 3) + 1;
476			bz = (b * 3) + 2;
477
478			if (moved[a] \|\| moved[b]){
479			atoms[a]->getPos(posA);
480			atoms[b]->getPos(posB);
481
482			for (j = 0; j < 3; j++)
483	gezelter	600	pab[j] = posA[j] - posB[j];
484	mmeineke	567
485	tim	725	//periodic boundary condition
486	mmeineke	567
487	tim	725	info->wrapVector(pab);
488	mmeineke	572
489	tim	725	pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
490	mmeineke	558
491	tim	725	rabsq = constrainedDsqr[i];
492			diffsq = rabsq - pabsq;
493	mmeineke	567
494	tim	725	// the original rattle code from alan tidesley
495			if (fabs(diffsq) > (tol * rabsq * 2)){
496			rab[0] = oldPos[ax] - oldPos[bx];
497			rab[1] = oldPos[ay] - oldPos[by];
498			rab[2] = oldPos[az] - oldPos[bz];
499	mmeineke	558
500	tim	725	info->wrapVector(rab);
501	mmeineke	567
502	tim	725	rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
503	mmeineke	558
504	tim	725	rpabsq = rpab * rpab;
505	mmeineke	558
506	mmeineke	563
507	tim	725	if (rpabsq < (rabsq * -diffsq)){
508	mmeineke	558	#ifdef IS_MPI
509	tim	725	a = atoms[a]->getGlobalIndex();
510			b = atoms[b]->getGlobalIndex();
511	mmeineke	558	#endif //is_mpi
512	tim	725	sprintf(painCave.errMsg,
513			"Constraint failure in constrainA at atom %d and %d.\n", a,
514			b);
515			painCave.isFatal = 1;
516			simError();
517			}
518	mmeineke	558
519	tim	725	rma = 1.0 / atoms[a]->getMass();
520			rmb = 1.0 / atoms[b]->getMass();
521	mmeineke	567
522	tim	725	gab = diffsq / (2.0 * (rma + rmb) * rpab);
523	mmeineke	567
524	mmeineke	572	dx = rab[0] * gab;
525			dy = rab[1] * gab;
526			dz = rab[2] * gab;
527	mmeineke	558
528	tim	725	posA[0] += rma * dx;
529			posA[1] += rma * dy;
530			posA[2] += rma * dz;
531	mmeineke	558
532	tim	725	atoms[a]->setPos(posA);
533	mmeineke	558
534	tim	725	posB[0] -= rmb * dx;
535			posB[1] -= rmb * dy;
536			posB[2] -= rmb * dz;
537	gezelter	600
538	tim	725	atoms[b]->setPos(posB);
539	gezelter	600
540	mmeineke	558	dx = dx / dt;
541			dy = dy / dt;
542			dz = dz / dt;
543
544	tim	725	atoms[a]->getVel(velA);
545	mmeineke	558
546	tim	725	velA[0] += rma * dx;
547			velA[1] += rma * dy;
548			velA[2] += rma * dz;
549	mmeineke	558
550	tim	725	atoms[a]->setVel(velA);
551	gezelter	600
552	tim	725	atoms[b]->getVel(velB);
553	gezelter	600
554	tim	725	velB[0] -= rmb * dx;
555			velB[1] -= rmb * dy;
556			velB[2] -= rmb * dz;
557	gezelter	600
558	tim	725	atoms[b]->setVel(velB);
559	gezelter	600
560	tim	725	moving[a] = 1;
561			moving[b] = 1;
562			done = 0;
563			}
564	mmeineke	558	}
565			}
566	tim	725
567			for (i = 0; i < nAtoms; i++){
568	mmeineke	558	moved[i] = moving[i];
569			moving[i] = 0;
570			}
571
572			iteration++;
573			}
574
575	tim	725	if (!done){
576			sprintf(painCave.errMsg,
577			"Constraint failure in constrainA, too many iterations: %d\n",
578			iteration);
579	mmeineke	558	painCave.isFatal = 1;
580			simError();
581			}
582	mmeineke	768
583	mmeineke	558	}
584
585	tim	725	template<typename T> void Integrator<T>::constrainB(void){
586	mmeineke	787	int i, j;
587	mmeineke	558	int done;
588	gezelter	600	double posA[3], posB[3];
589			double velA[3], velB[3];
590	mmeineke	558	double vxab, vyab, vzab;
591	mmeineke	572	double rab[3];
592	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
593	mmeineke	558	double rma, rmb;
594			double dx, dy, dz;
595	mmeineke	787	double rvab;
596	mmeineke	558	double gab;
597			int iteration;
598
599	tim	725	for (i = 0; i < nAtoms; i++){
600	mmeineke	558	moving[i] = 0;
601			moved[i] = 1;
602			}
603
604			done = 0;
605	mmeineke	561	iteration = 0;
606	tim	725	while (!done && (iteration < maxIteration)){
607	mmeineke	567	done = 1;
608
609	tim	725	for (i = 0; i < nConstrained; i++){
610	mmeineke	558	a = constrainedA[i];
611			b = constrainedB[i];
612
613	tim	725	ax = (a * 3) + 0;
614			ay = (a * 3) + 1;
615			az = (a * 3) + 2;
616	mmeineke	563
617	tim	725	bx = (b * 3) + 0;
618			by = (b * 3) + 1;
619			bz = (b * 3) + 2;
620	mmeineke	563
621	tim	725	if (moved[a] \|\| moved[b]){
622			atoms[a]->getVel(velA);
623			atoms[b]->getVel(velB);
624	mmeineke	558
625	tim	725	vxab = velA[0] - velB[0];
626			vyab = velA[1] - velB[1];
627			vzab = velA[2] - velB[2];
628	gezelter	600
629	tim	725	atoms[a]->getPos(posA);
630			atoms[b]->getPos(posB);
631	gezelter	600
632	tim	725	for (j = 0; j < 3; j++)
633	gezelter	600	rab[j] = posA[j] - posB[j];
634	mmeineke	558
635	tim	725	info->wrapVector(rab);
636	mmeineke	558
637	tim	725	rma = 1.0 / atoms[a]->getMass();
638			rmb = 1.0 / atoms[b]->getMass();
639	mmeineke	558
640	tim	725	rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
641	gezelter	600
642	tim	725	gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
643	gezelter	600
644	tim	725	if (fabs(gab) > tol){
645			dx = rab[0] * gab;
646			dy = rab[1] * gab;
647			dz = rab[2] * gab;
648
649			velA[0] += rma * dx;
650			velA[1] += rma * dy;
651			velA[2] += rma * dz;
652
653			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
661			moving[a] = 1;
662			moving[b] = 1;
663			done = 0;
664			}
665	mmeineke	558	}
666			}
667
668	tim	725	for (i = 0; i < nAtoms; i++){
669	mmeineke	558	moved[i] = moving[i];
670			moving[i] = 0;
671			}
672	tim	725
673	mmeineke	558	iteration++;
674			}
675
676	tim	725	if (!done){
677			sprintf(painCave.errMsg,
678			"Constraint failure in constrainB, too many iterations: %d\n",
679			iteration);
680	mmeineke	558	painCave.isFatal = 1;
681			simError();
682	tim	725	}
683	mmeineke	558	}
684
685	mmeineke	778	template<typename T> void Integrator<T>::rotationPropagation
686			( DirectionalAtom* dAtom, double ji[3] ){
687
688			double angle;
689			double A[3][3], I[3][3];
690
691			// use the angular velocities to propagate the rotation matrix a
692			// full time step
693
694			dAtom->getA(A);
695			dAtom->getI(I);
696	tim	837
697			// rotate about the x-axis
698	mmeineke	778	angle = dt2 * ji[0] / I[0][0];
699	tim	837	this->rotate( 1, 2, angle, ji, A );
700
701	mmeineke	778	// rotate about the y-axis
702			angle = dt2 * ji[1] / I[1][1];
703			this->rotate( 2, 0, angle, ji, A );
704	tim	837
705	mmeineke	778	// rotate about the z-axis
706			angle = dt * ji[2] / I[2][2];
707			this->rotate( 0, 1, angle, ji, A);
708	tim	837
709	mmeineke	778	// rotate about the y-axis
710			angle = dt2 * ji[1] / I[1][1];
711			this->rotate( 2, 0, angle, ji, A );
712	tim	837
713	mmeineke	778	// rotate about the x-axis
714			angle = dt2 * ji[0] / I[0][0];
715			this->rotate( 1, 2, angle, ji, A );
716	tim	837
717			dAtom->setA( A );
718	mmeineke	778	}
719
720	tim	725	template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
721			double angle, double ji[3],
722			double A[3][3]){
723			int i, j, k;
724	mmeineke	558	double sinAngle;
725			double cosAngle;
726			double angleSqr;
727			double angleSqrOver4;
728			double top, bottom;
729			double rot[3][3];
730			double tempA[3][3];
731			double tempJ[3];
732
733			// initialize the tempA
734
735	tim	725	for (i = 0; i < 3; i++){
736			for (j = 0; j < 3; j++){
737	gezelter	600	tempA[j][i] = A[i][j];
738	mmeineke	558	}
739			}
740
741			// initialize the tempJ
742
743	tim	725	for (i = 0; i < 3; i++)
744			tempJ[i] = ji[i];
745
746	mmeineke	558	// initalize rot as a unit matrix
747
748			rot[0][0] = 1.0;
749			rot[0][1] = 0.0;
750			rot[0][2] = 0.0;
751
752			rot[1][0] = 0.0;
753			rot[1][1] = 1.0;
754			rot[1][2] = 0.0;
755	tim	725
756	mmeineke	558	rot[2][0] = 0.0;
757			rot[2][1] = 0.0;
758			rot[2][2] = 1.0;
759	tim	725
760	mmeineke	558	// use a small angle aproximation for sin and cosine
761
762	tim	725	angleSqr = angle * angle;
763	mmeineke	558	angleSqrOver4 = angleSqr / 4.0;
764			top = 1.0 - angleSqrOver4;
765			bottom = 1.0 + angleSqrOver4;
766
767			cosAngle = top / bottom;
768			sinAngle = angle / bottom;
769
770			rot[axes1][axes1] = cosAngle;
771			rot[axes2][axes2] = cosAngle;
772
773			rot[axes1][axes2] = sinAngle;
774			rot[axes2][axes1] = -sinAngle;
775	tim	725
776	mmeineke	558	// rotate the momentum acoording to: ji[] = rot[][] * ji[]
777	tim	725
778			for (i = 0; i < 3; i++){
779	mmeineke	558	ji[i] = 0.0;
780	tim	725	for (k = 0; k < 3; k++){
781	mmeineke	558	ji[i] += rot[i][k] * tempJ[k];
782			}
783			}
784
785	tim	837	// rotate the Rotation matrix acording to:
786	mmeineke	558	// A[][] = A[][] * transpose(rot[][])
787
788
789	mmeineke	561	// NOte for as yet unknown reason, we are performing the
790	mmeineke	558	// calculation as:
791			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
792
793	tim	725	for (i = 0; i < 3; i++){
794			for (j = 0; j < 3; j++){
795	gezelter	600	A[j][i] = 0.0;
796	tim	725	for (k = 0; k < 3; k++){
797			A[j][i] += tempA[i][k] * rot[j][k];
798	mmeineke	558	}
799			}
800			}
801			}
802	tim	677
803	tim	725	template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
804			myFF->doForces(calcPot, calcStress);
805	tim	677	}
806
807			template<typename T> void Integrator<T>::thermalize(){
808	tim	725	tStats->velocitize();
809	tim	677	}
810	tim	763
811			template<typename T> double Integrator<T>::getConservedQuantity(void){
812			return tStats->getTotalE();
813	mmeineke	768	}
814	tim	837	template<typename T> string Integrator<T>::getAdditionalParameters(void){
815			//By default, return a null string
816			//The reason we use string instead of char* is that if we use char*, we will
817			//return a pointer point to local variable which might cause problem
818			return string();
819			}