OOPSE/libmdtools/Integrator.cpp

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

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

#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;
    }

    integrateStep(calcPot, calcStress);

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


  // write the last frame
  dumpOut->writeDump(info->getTime());

  delete dumpOut;
  delete statOut;
}

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

  moveA();


#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


  // finish the velocity  half step

  moveB();


#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:	843
Committed:	Wed Oct 29 20:41:39 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	16796 byte(s)
Log Message:	fixed a stdlib.h include error in bass.l fixed a little bug in the first time step, regarding the setting of ecr and est in fortran
#	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			#include "Integrator.hpp"
11			#include "simError.h"
12
13
14	tim	725	template<typename T> Integrator<T>::Integrator(SimInfo* theInfo,
15			ForceFields* the_ff){
16	mmeineke	558	info = theInfo;
17			myFF = the_ff;
18			isFirst = 1;
19
20			molecules = info->molecules;
21			nMols = info->n_mol;
22
23			// give a little love back to the SimInfo object
24	tim	725
25			if (info->the_integrator != NULL){
26			delete info->the_integrator;
27			}
28	tim	837
29	mmeineke	558	nAtoms = info->n_atoms;
30
31			// check for constraints
32	tim	725
33			constrainedA = NULL;
34			constrainedB = NULL;
35	mmeineke	558	constrainedDsqr = NULL;
36	tim	725	moving = NULL;
37			moved = NULL;
38			oldPos = NULL;
39
40	mmeineke	558	nConstrained = 0;
41
42			checkConstraints();
43			}
44
45	tim	725	template<typename T> Integrator<T>::~Integrator(){
46			if (nConstrained){
47	mmeineke	558	delete[] constrainedA;
48			delete[] constrainedB;
49			delete[] constrainedDsqr;
50			delete[] moving;
51			delete[] moved;
52	mmeineke	561	delete[] oldPos;
53	mmeineke	558	}
54			}
55
56	tim	725	template<typename T> void Integrator<T>::checkConstraints(void){
57	mmeineke	558	isConstrained = 0;
58
59	tim	725	Constraint* temp_con;
60			Constraint* dummy_plug;
61	mmeineke	558	temp_con = new Constraint[info->n_SRI];
62			nConstrained = 0;
63			int constrained = 0;
64	tim	725
65	mmeineke	558	SRI** theArray;
66	tim	725	for (int i = 0; i < nMols; i++){
67			theArray = (SRI * *) molecules[i].getMyBonds();
68			for (int j = 0; j < molecules[i].getNBonds(); j++){
69	mmeineke	558	constrained = theArray[j]->is_constrained();
70	mmeineke	594
71	tim	725	if (constrained){
72			dummy_plug = theArray[j]->get_constraint();
73			temp_con[nConstrained].set_a(dummy_plug->get_a());
74			temp_con[nConstrained].set_b(dummy_plug->get_b());
75			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
76	mmeineke	594
77	tim	725	nConstrained++;
78			constrained = 0;
79			}
80	mmeineke	558	}
81
82	tim	725	theArray = (SRI * *) molecules[i].getMyBends();
83			for (int j = 0; j < molecules[i].getNBends(); j++){
84	mmeineke	558	constrained = theArray[j]->is_constrained();
85	tim	725
86			if (constrained){
87			dummy_plug = theArray[j]->get_constraint();
88			temp_con[nConstrained].set_a(dummy_plug->get_a());
89			temp_con[nConstrained].set_b(dummy_plug->get_b());
90			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
91
92			nConstrained++;
93			constrained = 0;
94	mmeineke	558	}
95			}
96
97	tim	725	theArray = (SRI * *) molecules[i].getMyTorsions();
98			for (int j = 0; j < molecules[i].getNTorsions(); j++){
99	mmeineke	558	constrained = theArray[j]->is_constrained();
100	tim	725
101			if (constrained){
102			dummy_plug = theArray[j]->get_constraint();
103			temp_con[nConstrained].set_a(dummy_plug->get_a());
104			temp_con[nConstrained].set_b(dummy_plug->get_b());
105			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
106
107			nConstrained++;
108			constrained = 0;
109	mmeineke	558	}
110			}
111			}
112
113	tim	725	if (nConstrained > 0){
114	mmeineke	558	isConstrained = 1;
115
116	tim	725	if (constrainedA != NULL)
117			delete[] constrainedA;
118			if (constrainedB != NULL)
119			delete[] constrainedB;
120			if (constrainedDsqr != NULL)
121			delete[] constrainedDsqr;
122	mmeineke	558
123	tim	725	constrainedA = new int[nConstrained];
124			constrainedB = new int[nConstrained];
125	mmeineke	558	constrainedDsqr = new double[nConstrained];
126	tim	725
127			for (int i = 0; i < nConstrained; i++){
128	mmeineke	558	constrainedA[i] = temp_con[i].get_a();
129			constrainedB[i] = temp_con[i].get_b();
130			constrainedDsqr[i] = temp_con[i].get_dsqr();
131			}
132
133	tim	725
134	mmeineke	558	// save oldAtoms to check for lode balanceing later on.
135	tim	725
136	mmeineke	558	oldAtoms = nAtoms;
137	tim	725
138	mmeineke	558	moving = new int[nAtoms];
139	tim	725	moved = new int[nAtoms];
140	mmeineke	558
141	tim	725	oldPos = new double[nAtoms * 3];
142	mmeineke	558	}
143	tim	725
144	mmeineke	558	delete[] temp_con;
145			}
146
147
148	tim	725	template<typename T> void Integrator<T>::integrate(void){
149	mmeineke	558
150	tim	725	double runTime = info->run_time;
151			double sampleTime = info->sampleTime;
152			double statusTime = info->statusTime;
153	mmeineke	558	double thermalTime = info->thermalTime;
154	mmeineke	746	double resetTime = info->resetTime;
155	mmeineke	558
156	mmeineke	746
157	mmeineke	558	double currSample;
158			double currThermal;
159			double currStatus;
160	mmeineke	746	double currReset;
161	tim	837
162	mmeineke	558	int calcPot, calcStress;
163
164	tim	725	tStats = new Thermo(info);
165			statOut = new StatWriter(info);
166			dumpOut = new DumpWriter(info);
167	mmeineke	558
168	mmeineke	561	atoms = info->atoms;
169
170			dt = info->dt;
171	mmeineke	558	dt2 = 0.5 * dt;
172
173	mmeineke	784	readyCheck();
174
175	mmeineke	558	// initialize the forces before the first step
176
177	tim	677	calcForce(1, 1);
178	tim	781
179			if (nConstrained){
180			preMove();
181			constrainA();
182	tim	837	calcForce(1, 1);
183	tim	781	constrainB();
184			}
185	mmeineke	843
186	tim	725	if (info->setTemp){
187	tim	677	thermalize();
188	mmeineke	558	}
189	tim	725
190	mmeineke	558	calcPot = 0;
191			calcStress = 0;
192	mmeineke	711	currSample = sampleTime + info->getTime();
193			currThermal = thermalTime+ info->getTime();
194			currStatus = statusTime + info->getTime();
195	mmeineke	746	currReset = resetTime + info->getTime();
196	mmeineke	558
197	tim	725	dumpOut->writeDump(info->getTime());
198			statOut->writeStat(info->getTime());
199	mmeineke	559
200
201			#ifdef IS_MPI
202	tim	725	strcpy(checkPointMsg, "The integrator is ready to go.");
203	mmeineke	559	MPIcheckPoint();
204			#endif // is_mpi
205
206	tim	725	while (info->getTime() < runTime){
207			if ((info->getTime() + dt) >= currStatus){
208	mmeineke	558	calcPot = 1;
209			calcStress = 1;
210			}
211	mmeineke	561
212	tim	725	integrateStep(calcPot, calcStress);
213
214	mmeineke	643	info->incrTime(dt);
215	mmeineke	558
216	tim	725	if (info->setTemp){
217			if (info->getTime() >= currThermal){
218			thermalize();
219			currThermal += thermalTime;
220	mmeineke	558	}
221			}
222
223	tim	725	if (info->getTime() >= currSample){
224			dumpOut->writeDump(info->getTime());
225	mmeineke	558	currSample += sampleTime;
226			}
227
228	tim	725	if (info->getTime() >= currStatus){
229	tim	837	statOut->writeStat(info->getTime());
230			calcPot = 0;
231	mmeineke	558	calcStress = 0;
232			currStatus += statusTime;
233	tim	837	}
234	mmeineke	559
235	mmeineke	746	if (info->resetIntegrator){
236			if (info->getTime() >= currReset){
237			this->resetIntegrator();
238			currReset += resetTime;
239			}
240			}
241
242	mmeineke	559	#ifdef IS_MPI
243	tim	725	strcpy(checkPointMsg, "successfully took a time step.");
244	mmeineke	559	MPIcheckPoint();
245			#endif // is_mpi
246	mmeineke	558	}
247
248
249	mmeineke	804	// write the last frame
250			dumpOut->writeDump(info->getTime());
251
252	mmeineke	561	delete dumpOut;
253			delete statOut;
254	mmeineke	558	}
255
256	tim	725	template<typename T> void Integrator<T>::integrateStep(int calcPot,
257			int calcStress){
258	mmeineke	558	// Position full step, and velocity half step
259	tim	725	preMove();
260	mmeineke	558
261			moveA();
262
263	tim	725
264
265	mmeineke	768
266	mmeineke	614	#ifdef IS_MPI
267	tim	725	strcpy(checkPointMsg, "Succesful moveA\n");
268	mmeineke	614	MPIcheckPoint();
269			#endif // is_mpi
270
271	tim	725
272	mmeineke	558	// calc forces
273
274	tim	725	calcForce(calcPot, calcStress);
275	mmeineke	558
276	mmeineke	614	#ifdef IS_MPI
277	tim	725	strcpy(checkPointMsg, "Succesful doForces\n");
278	mmeineke	614	MPIcheckPoint();
279			#endif // is_mpi
280
281	tim	725
282	mmeineke	558	// finish the velocity half step
283	tim	725
284	mmeineke	558	moveB();
285	tim	725
286
287	mmeineke	768
288	mmeineke	614	#ifdef IS_MPI
289	tim	725	strcpy(checkPointMsg, "Succesful moveB\n");
290	mmeineke	614	MPIcheckPoint();
291			#endif // is_mpi
292	mmeineke	558	}
293
294
295	tim	725	template<typename T> void Integrator<T>::moveA(void){
296	gezelter	600	int i, j;
297	mmeineke	558	DirectionalAtom* dAtom;
298	gezelter	600	double Tb[3], ji[3];
299			double vel[3], pos[3], frc[3];
300			double mass;
301	mmeineke	558
302	tim	725	for (i = 0; i < nAtoms; i++){
303			atoms[i]->getVel(vel);
304			atoms[i]->getPos(pos);
305			atoms[i]->getFrc(frc);
306	mmeineke	567
307	gezelter	600	mass = atoms[i]->getMass();
308	mmeineke	594
309	tim	725	for (j = 0; j < 3; j++){
310	gezelter	600	// velocity half step
311	tim	725	vel[j] += (dt2 * frc[j] / mass) * eConvert;
312	gezelter	600	// position whole step
313			pos[j] += dt * vel[j];
314			}
315	mmeineke	594
316	tim	725	atoms[i]->setVel(vel);
317			atoms[i]->setPos(pos);
318	gezelter	600
319	tim	725	if (atoms[i]->isDirectional()){
320			dAtom = (DirectionalAtom *) atoms[i];
321	mmeineke	558
322			// get and convert the torque to body frame
323	mmeineke	597
324	tim	725	dAtom->getTrq(Tb);
325			dAtom->lab2Body(Tb);
326
327	mmeineke	558	// get the angular momentum, and propagate a half step
328	gezelter	600
329	tim	725	dAtom->getJ(ji);
330	gezelter	600
331	tim	725	for (j = 0; j < 3; j++)
332	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
333	tim	725
334	mmeineke	778	this->rotationPropagation( dAtom, ji );
335	gezelter	600
336	tim	725	dAtom->setJ(ji);
337			}
338	mmeineke	558	}
339	mmeineke	768
340			if (nConstrained){
341			constrainA();
342			}
343	mmeineke	558	}
344
345
346	tim	725	template<typename T> void Integrator<T>::moveB(void){
347	gezelter	600	int i, j;
348	mmeineke	558	DirectionalAtom* dAtom;
349	gezelter	600	double Tb[3], ji[3];
350			double vel[3], frc[3];
351			double mass;
352	mmeineke	558
353	tim	725	for (i = 0; i < nAtoms; i++){
354			atoms[i]->getVel(vel);
355			atoms[i]->getFrc(frc);
356	mmeineke	558
357	gezelter	600	mass = atoms[i]->getMass();
358
359	mmeineke	558	// velocity half step
360	tim	725	for (j = 0; j < 3; j++)
361			vel[j] += (dt2 * frc[j] / mass) * eConvert;
362	gezelter	600
363	tim	725	atoms[i]->setVel(vel);
364	mmeineke	597
365	tim	725	if (atoms[i]->isDirectional()){
366			dAtom = (DirectionalAtom *) atoms[i];
367
368	tim	837	// get and convert the torque to body frame
369	gezelter	600
370	tim	725	dAtom->getTrq(Tb);
371			dAtom->lab2Body(Tb);
372	gezelter	600
373			// get the angular momentum, and propagate a half step
374
375	tim	725	dAtom->getJ(ji);
376	gezelter	600
377	tim	725	for (j = 0; j < 3; j++)
378	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
379	mmeineke	597
380	tim	725
381			dAtom->setJ(ji);
382	mmeineke	558	}
383			}
384	mmeineke	768
385			if (nConstrained){
386			constrainB();
387			}
388	mmeineke	558	}
389
390	tim	725	template<typename T> void Integrator<T>::preMove(void){
391	gezelter	600	int i, j;
392			double pos[3];
393	mmeineke	558
394	tim	725	if (nConstrained){
395			for (i = 0; i < nAtoms; i++){
396			atoms[i]->getPos(pos);
397	mmeineke	561
398	tim	725	for (j = 0; j < 3; j++){
399			oldPos[3 * i + j] = pos[j];
400	gezelter	600	}
401			}
402	tim	725	}
403	gezelter	600	}
404
405	tim	645	template<typename T> void Integrator<T>::constrainA(){
406	mmeineke	787	int i, j;
407	mmeineke	558	int done;
408	gezelter	600	double posA[3], posB[3];
409			double velA[3], velB[3];
410	mmeineke	572	double pab[3];
411			double rab[3];
412	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
413	mmeineke	558	double rma, rmb;
414			double dx, dy, dz;
415	mmeineke	561	double rpab;
416	mmeineke	558	double rabsq, pabsq, rpabsq;
417			double diffsq;
418			double gab;
419			int iteration;
420
421	tim	725	for (i = 0; i < nAtoms; i++){
422	mmeineke	558	moving[i] = 0;
423	tim	725	moved[i] = 1;
424	mmeineke	558	}
425	mmeineke	567
426	mmeineke	558	iteration = 0;
427			done = 0;
428	tim	725	while (!done && (iteration < maxIteration)){
429	mmeineke	558	done = 1;
430	tim	725	for (i = 0; i < nConstrained; i++){
431	mmeineke	558	a = constrainedA[i];
432			b = constrainedB[i];
433	mmeineke	563
434	tim	725	ax = (a * 3) + 0;
435			ay = (a * 3) + 1;
436			az = (a * 3) + 2;
437	mmeineke	563
438	tim	725	bx = (b * 3) + 0;
439			by = (b * 3) + 1;
440			bz = (b * 3) + 2;
441
442			if (moved[a] \|\| moved[b]){
443			atoms[a]->getPos(posA);
444			atoms[b]->getPos(posB);
445
446			for (j = 0; j < 3; j++)
447	gezelter	600	pab[j] = posA[j] - posB[j];
448	mmeineke	567
449	tim	725	//periodic boundary condition
450	mmeineke	567
451	tim	725	info->wrapVector(pab);
452	mmeineke	572
453	tim	725	pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
454	mmeineke	558
455	tim	725	rabsq = constrainedDsqr[i];
456			diffsq = rabsq - pabsq;
457	mmeineke	567
458	tim	725	// the original rattle code from alan tidesley
459			if (fabs(diffsq) > (tol * rabsq * 2)){
460			rab[0] = oldPos[ax] - oldPos[bx];
461			rab[1] = oldPos[ay] - oldPos[by];
462			rab[2] = oldPos[az] - oldPos[bz];
463	mmeineke	558
464	tim	725	info->wrapVector(rab);
465	mmeineke	567
466	tim	725	rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
467	mmeineke	558
468	tim	725	rpabsq = rpab * rpab;
469	mmeineke	558
470	mmeineke	563
471	tim	725	if (rpabsq < (rabsq * -diffsq)){
472	mmeineke	558	#ifdef IS_MPI
473	tim	725	a = atoms[a]->getGlobalIndex();
474			b = atoms[b]->getGlobalIndex();
475	mmeineke	558	#endif //is_mpi
476	tim	725	sprintf(painCave.errMsg,
477			"Constraint failure in constrainA at atom %d and %d.\n", a,
478			b);
479			painCave.isFatal = 1;
480			simError();
481			}
482	mmeineke	558
483	tim	725	rma = 1.0 / atoms[a]->getMass();
484			rmb = 1.0 / atoms[b]->getMass();
485	mmeineke	567
486	tim	725	gab = diffsq / (2.0 * (rma + rmb) * rpab);
487	mmeineke	567
488	mmeineke	572	dx = rab[0] * gab;
489			dy = rab[1] * gab;
490			dz = rab[2] * gab;
491	mmeineke	558
492	tim	725	posA[0] += rma * dx;
493			posA[1] += rma * dy;
494			posA[2] += rma * dz;
495	mmeineke	558
496	tim	725	atoms[a]->setPos(posA);
497	mmeineke	558
498	tim	725	posB[0] -= rmb * dx;
499			posB[1] -= rmb * dy;
500			posB[2] -= rmb * dz;
501	gezelter	600
502	tim	725	atoms[b]->setPos(posB);
503	gezelter	600
504	mmeineke	558	dx = dx / dt;
505			dy = dy / dt;
506			dz = dz / dt;
507
508	tim	725	atoms[a]->getVel(velA);
509	mmeineke	558
510	tim	725	velA[0] += rma * dx;
511			velA[1] += rma * dy;
512			velA[2] += rma * dz;
513	mmeineke	558
514	tim	725	atoms[a]->setVel(velA);
515	gezelter	600
516	tim	725	atoms[b]->getVel(velB);
517	gezelter	600
518	tim	725	velB[0] -= rmb * dx;
519			velB[1] -= rmb * dy;
520			velB[2] -= rmb * dz;
521	gezelter	600
522	tim	725	atoms[b]->setVel(velB);
523	gezelter	600
524	tim	725	moving[a] = 1;
525			moving[b] = 1;
526			done = 0;
527			}
528	mmeineke	558	}
529			}
530	tim	725
531			for (i = 0; i < nAtoms; i++){
532	mmeineke	558	moved[i] = moving[i];
533			moving[i] = 0;
534			}
535
536			iteration++;
537			}
538
539	tim	725	if (!done){
540			sprintf(painCave.errMsg,
541			"Constraint failure in constrainA, too many iterations: %d\n",
542			iteration);
543	mmeineke	558	painCave.isFatal = 1;
544			simError();
545			}
546	mmeineke	768
547	mmeineke	558	}
548
549	tim	725	template<typename T> void Integrator<T>::constrainB(void){
550	mmeineke	787	int i, j;
551	mmeineke	558	int done;
552	gezelter	600	double posA[3], posB[3];
553			double velA[3], velB[3];
554	mmeineke	558	double vxab, vyab, vzab;
555	mmeineke	572	double rab[3];
556	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
557	mmeineke	558	double rma, rmb;
558			double dx, dy, dz;
559	mmeineke	787	double rvab;
560	mmeineke	558	double gab;
561			int iteration;
562
563	tim	725	for (i = 0; i < nAtoms; i++){
564	mmeineke	558	moving[i] = 0;
565			moved[i] = 1;
566			}
567
568			done = 0;
569	mmeineke	561	iteration = 0;
570	tim	725	while (!done && (iteration < maxIteration)){
571	mmeineke	567	done = 1;
572
573	tim	725	for (i = 0; i < nConstrained; i++){
574	mmeineke	558	a = constrainedA[i];
575			b = constrainedB[i];
576
577	tim	725	ax = (a * 3) + 0;
578			ay = (a * 3) + 1;
579			az = (a * 3) + 2;
580	mmeineke	563
581	tim	725	bx = (b * 3) + 0;
582			by = (b * 3) + 1;
583			bz = (b * 3) + 2;
584	mmeineke	563
585	tim	725	if (moved[a] \|\| moved[b]){
586			atoms[a]->getVel(velA);
587			atoms[b]->getVel(velB);
588	mmeineke	558
589	tim	725	vxab = velA[0] - velB[0];
590			vyab = velA[1] - velB[1];
591			vzab = velA[2] - velB[2];
592	gezelter	600
593	tim	725	atoms[a]->getPos(posA);
594			atoms[b]->getPos(posB);
595	gezelter	600
596	tim	725	for (j = 0; j < 3; j++)
597	gezelter	600	rab[j] = posA[j] - posB[j];
598	mmeineke	558
599	tim	725	info->wrapVector(rab);
600	mmeineke	558
601	tim	725	rma = 1.0 / atoms[a]->getMass();
602			rmb = 1.0 / atoms[b]->getMass();
603	mmeineke	558
604	tim	725	rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
605	gezelter	600
606	tim	725	gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
607	gezelter	600
608	tim	725	if (fabs(gab) > tol){
609			dx = rab[0] * gab;
610			dy = rab[1] * gab;
611			dz = rab[2] * gab;
612
613			velA[0] += rma * dx;
614			velA[1] += rma * dy;
615			velA[2] += rma * dz;
616
617			atoms[a]->setVel(velA);
618
619			velB[0] -= rmb * dx;
620			velB[1] -= rmb * dy;
621			velB[2] -= rmb * dz;
622
623			atoms[b]->setVel(velB);
624
625			moving[a] = 1;
626			moving[b] = 1;
627			done = 0;
628			}
629	mmeineke	558	}
630			}
631
632	tim	725	for (i = 0; i < nAtoms; i++){
633	mmeineke	558	moved[i] = moving[i];
634			moving[i] = 0;
635			}
636	tim	725
637	mmeineke	558	iteration++;
638			}
639
640	tim	725	if (!done){
641			sprintf(painCave.errMsg,
642			"Constraint failure in constrainB, too many iterations: %d\n",
643			iteration);
644	mmeineke	558	painCave.isFatal = 1;
645			simError();
646	tim	725	}
647	mmeineke	558	}
648
649	mmeineke	778	template<typename T> void Integrator<T>::rotationPropagation
650			( DirectionalAtom* dAtom, double ji[3] ){
651
652			double angle;
653			double A[3][3], I[3][3];
654
655			// use the angular velocities to propagate the rotation matrix a
656			// full time step
657
658			dAtom->getA(A);
659			dAtom->getI(I);
660	tim	837
661			// rotate about the x-axis
662	mmeineke	778	angle = dt2 * ji[0] / I[0][0];
663	tim	837	this->rotate( 1, 2, angle, ji, A );
664
665	mmeineke	778	// rotate about the y-axis
666			angle = dt2 * ji[1] / I[1][1];
667			this->rotate( 2, 0, angle, ji, A );
668	tim	837
669	mmeineke	778	// rotate about the z-axis
670			angle = dt * ji[2] / I[2][2];
671			this->rotate( 0, 1, angle, ji, A);
672	tim	837
673	mmeineke	778	// rotate about the y-axis
674			angle = dt2 * ji[1] / I[1][1];
675			this->rotate( 2, 0, angle, ji, A );
676	tim	837
677	mmeineke	778	// rotate about the x-axis
678			angle = dt2 * ji[0] / I[0][0];
679			this->rotate( 1, 2, angle, ji, A );
680	tim	837
681			dAtom->setA( A );
682	mmeineke	778	}
683
684	tim	725	template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
685			double angle, double ji[3],
686			double A[3][3]){
687			int i, j, k;
688	mmeineke	558	double sinAngle;
689			double cosAngle;
690			double angleSqr;
691			double angleSqrOver4;
692			double top, bottom;
693			double rot[3][3];
694			double tempA[3][3];
695			double tempJ[3];
696
697			// initialize the tempA
698
699	tim	725	for (i = 0; i < 3; i++){
700			for (j = 0; j < 3; j++){
701	gezelter	600	tempA[j][i] = A[i][j];
702	mmeineke	558	}
703			}
704
705			// initialize the tempJ
706
707	tim	725	for (i = 0; i < 3; i++)
708			tempJ[i] = ji[i];
709
710	mmeineke	558	// initalize rot as a unit matrix
711
712			rot[0][0] = 1.0;
713			rot[0][1] = 0.0;
714			rot[0][2] = 0.0;
715
716			rot[1][0] = 0.0;
717			rot[1][1] = 1.0;
718			rot[1][2] = 0.0;
719	tim	725
720	mmeineke	558	rot[2][0] = 0.0;
721			rot[2][1] = 0.0;
722			rot[2][2] = 1.0;
723	tim	725
724	mmeineke	558	// use a small angle aproximation for sin and cosine
725
726	tim	725	angleSqr = angle * angle;
727	mmeineke	558	angleSqrOver4 = angleSqr / 4.0;
728			top = 1.0 - angleSqrOver4;
729			bottom = 1.0 + angleSqrOver4;
730
731			cosAngle = top / bottom;
732			sinAngle = angle / bottom;
733
734			rot[axes1][axes1] = cosAngle;
735			rot[axes2][axes2] = cosAngle;
736
737			rot[axes1][axes2] = sinAngle;
738			rot[axes2][axes1] = -sinAngle;
739	tim	725
740	mmeineke	558	// rotate the momentum acoording to: ji[] = rot[][] * ji[]
741	tim	725
742			for (i = 0; i < 3; i++){
743	mmeineke	558	ji[i] = 0.0;
744	tim	725	for (k = 0; k < 3; k++){
745	mmeineke	558	ji[i] += rot[i][k] * tempJ[k];
746			}
747			}
748
749	tim	837	// rotate the Rotation matrix acording to:
750	mmeineke	558	// A[][] = A[][] * transpose(rot[][])
751
752
753	mmeineke	561	// NOte for as yet unknown reason, we are performing the
754	mmeineke	558	// calculation as:
755			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
756
757	tim	725	for (i = 0; i < 3; i++){
758			for (j = 0; j < 3; j++){
759	gezelter	600	A[j][i] = 0.0;
760	tim	725	for (k = 0; k < 3; k++){
761			A[j][i] += tempA[i][k] * rot[j][k];
762	mmeineke	558	}
763			}
764			}
765			}
766	tim	677
767	tim	725	template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
768			myFF->doForces(calcPot, calcStress);
769	tim	677	}
770
771			template<typename T> void Integrator<T>::thermalize(){
772	tim	725	tStats->velocitize();
773	tim	677	}
774	tim	763
775			template<typename T> double Integrator<T>::getConservedQuantity(void){
776			return tStats->getTotalE();
777	mmeineke	768	}
778	tim	837	template<typename T> string Integrator<T>::getAdditionalParameters(void){
779			//By default, return a null string
780			//The reason we use string instead of char* is that if we use char*, we will
781			//return a pointer point to local variable which might cause problem
782			return string();
783			}