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"


Integrator::Integrator(SimInfo* theInfo, ForceFields* the_ff){
  
  info = theInfo;
  myFF = the_ff;
  isFirst = 1;

  molecules = info->molecules;
  nMols = info->n_mol;

  // give a little love back to the SimInfo object

  if (info->the_integrator != NULL){
    delete info->the_integrator;
  }

  nAtoms = info->n_atoms;

  // check for constraints

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

  nConstrained = 0;

  checkConstraints();
}

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

void Integrator::checkConstraints(void){
  isConstrained = 0;

  Constraint* temp_con;
  Constraint* dummy_plug;
  temp_con = new Constraint[info->n_SRI];
  nConstrained = 0;
  int constrained = 0;

  SRI** theArray;
  for (int i = 0; i < nMols; i++){
    theArray = (SRI * *) molecules[i].getMyBonds();
    for (int j = 0; j < molecules[i].getNBonds(); j++){
      constrained = theArray[j]->is_constrained();

      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;
}


void Integrator::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;
}

void Integrator::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
}


void Integrator::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();
  }
}


void Integrator::moveB(void){
  int i, j;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3];
  double vel[3], frc[3];
  double mass;

  for (i = 0; i < nAtoms; i++){
    atoms[i]->getVel(vel);
    atoms[i]->getFrc(frc);

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

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

    atoms[i]->setVel(vel);

    if (atoms[i]->isDirectional()){
      dAtom = (DirectionalAtom *) atoms[i];

      // get and convert the torque to body frame

      dAtom->getTrq(Tb);
      dAtom->lab2Body(Tb);

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

      dAtom->getJ(ji);

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


      dAtom->setJ(ji);
    }
  }

  if (nConstrained){
    constrainB();
  }
}

void Integrator::preMove(void){
  int i, j;
  double pos[3];

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

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

void Integrator::constrainA(){
  int i, j;
  int done;
  double posA[3], posB[3];
  double velA[3], velB[3];
  double pab[3];
  double rab[3];
  int a, b, ax, ay, az, bx, by, bz;
  double rma, rmb;
  double dx, dy, dz;
  double rpab;
  double rabsq, pabsq, rpabsq;
  double diffsq;
  double gab;
  int iteration;

  for (i = 0; i < nAtoms; i++){
    moving[i] = 0;
    moved[i] = 1;
  }

  iteration = 0;
  done = 0;
  while (!done && (iteration < maxIteration)){
    done = 1;
    for (i = 0; i < nConstrained; i++){
      a = constrainedA[i];
      b = constrainedB[i];

      ax = (a * 3) + 0;
      ay = (a * 3) + 1;
      az = (a * 3) + 2;

      bx = (b * 3) + 0;
      by = (b * 3) + 1;
      bz = (b * 3) + 2;

      if (moved[a] || moved[b]){
        atoms[a]->getPos(posA);
        atoms[b]->getPos(posB);

        for (j = 0; j < 3; j++)
          pab[j] = posA[j] - posB[j];

        //periodic boundary condition

        info->wrapVector(pab);

        pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];

        rabsq = constrainedDsqr[i];
        diffsq = rabsq - pabsq;

        // the original rattle code from alan tidesley
        if (fabs(diffsq) > (tol * rabsq * 2)){
          rab[0] = oldPos[ax] - oldPos[bx];
          rab[1] = oldPos[ay] - oldPos[by];
          rab[2] = oldPos[az] - oldPos[bz];

          info->wrapVector(rab);

          rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];

          rpabsq = rpab * rpab;


          if (rpabsq < (rabsq * -diffsq)){
#ifdef IS_MPI
            a = atoms[a]->getGlobalIndex();
            b = atoms[b]->getGlobalIndex();
#endif //is_mpi
            sprintf(painCave.errMsg,
                    "Constraint failure in constrainA at atom %d and %d.\n", a,
                    b);
            painCave.isFatal = 1;
            simError();
          }

          rma = 1.0 / atoms[a]->getMass();
          rmb = 1.0 / atoms[b]->getMass();

          gab = diffsq / (2.0 * (rma + rmb) * rpab);

          dx = rab[0] * gab;
          dy = rab[1] * gab;
          dz = rab[2] * gab;

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

          atoms[a]->setPos(posA);

          posB[0] -= rmb * dx;
          posB[1] -= rmb * dy;
          posB[2] -= rmb * dz;

          atoms[b]->setPos(posB);

          dx = dx / dt;
          dy = dy / dt;
          dz = dz / dt;

          atoms[a]->getVel(velA);

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

          atoms[a]->setVel(velA);

          atoms[b]->getVel(velB);

          velB[0] -= rmb * dx;
          velB[1] -= rmb * dy;
          velB[2] -= rmb * dz;

          atoms[b]->setVel(velB);

          moving[a] = 1;
          moving[b] = 1;
          done = 0;
        }
      }
    }

    for (i = 0; i < nAtoms; i++){
      moved[i] = moving[i];
      moving[i] = 0;
    }

    iteration++;
  }

  if (!done){
    sprintf(painCave.errMsg,
            "Constraint failure in constrainA, too many iterations: %d\n",
            iteration);
    painCave.isFatal = 1;
    simError();
  }

}

void Integrator::constrainB(void){
  int i, j;
  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();
  }
}

void Integrator::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  );
}

void Integrator::rotate(int axes1, int axes2,
                        double angle, double ji[3],
                        double A[3][3]){
  int i, j, k;
  double sinAngle;
  double cosAngle;
  double angleSqr;
  double angleSqrOver4;
  double top, bottom;
  double rot[3][3];
  double tempA[3][3];
  double tempJ[3];

  // initialize the tempA

  for (i = 0; i < 3; i++){
    for (j = 0; j < 3; j++){
      tempA[j][i] = A[i][j];
    }
  }

  // initialize the tempJ

  for (i = 0; i < 3; i++)
    tempJ[i] = ji[i];

  // initalize rot as a unit matrix

  rot[0][0] = 1.0;
  rot[0][1] = 0.0;
  rot[0][2] = 0.0;

  rot[1][0] = 0.0;
  rot[1][1] = 1.0;
  rot[1][2] = 0.0;

  rot[2][0] = 0.0;
  rot[2][1] = 0.0;
  rot[2][2] = 1.0;

  // use a small angle aproximation for sin and cosine

  angleSqr = angle * angle;
  angleSqrOver4 = angleSqr / 4.0;
  top = 1.0 - angleSqrOver4;
  bottom = 1.0 + angleSqrOver4;

  cosAngle = top / bottom;
  sinAngle = angle / bottom;

  rot[axes1][axes1] = cosAngle;
  rot[axes2][axes2] = cosAngle;

  rot[axes1][axes2] = sinAngle;
  rot[axes2][axes1] = -sinAngle;

  // rotate the momentum acoording to: ji[] = rot[][] * ji[]

  for (i = 0; i < 3; i++){
    ji[i] = 0.0;
    for (k = 0; k < 3; k++){
      ji[i] += rot[i][k] * tempJ[k];
    }
  }

  // rotate the Rotation matrix acording to:
  //            A[][] = A[][] * transpose(rot[][])


  // NOte for as yet unknown reason, we are performing the
  // calculation as:
  //                transpose(A[][]) = transpose(A[][]) * transpose(rot[][])

  for (i = 0; i < 3; i++){
    for (j = 0; j < 3; j++){
      A[j][i] = 0.0;
      for (k = 0; k < 3; k++){
        A[j][i] += tempA[i][k] * rot[j][k];
      }
    }
  }
}

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

void Integrator::thermalize(){
  tStats->velocitize();
}

double Integrator::getConservedQuantity(void){
  return tStats->getTotalE();
}

char* Integrator::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
  addParams[0] = '\0';
  return addParams;
}
Revision:	852
Committed:	Thu Nov 6 18:20:47 2003 UTC (21 years, 6 months ago) by mmeineke
File size:	16260 byte(s)
Log Message:	fixed the "Sudden Death" bug. The box was not switching between orthorhombic and non-orthorhombic wrapping correctly. we added a fabs() to the check.which should fix it.
#	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	mmeineke	849	Integrator::Integrator(SimInfo* theInfo, ForceFields* the_ff){
15
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	mmeineke	849	Integrator::~Integrator(){
46	tim	725	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	mmeineke	849	void Integrator::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	mmeineke	849	void Integrator::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	852
157	mmeineke	746
158	mmeineke	558	double currSample;
159			double currThermal;
160			double currStatus;
161	mmeineke	746	double currReset;
162	tim	837
163	mmeineke	558	int calcPot, calcStress;
164
165	tim	725	tStats = new Thermo(info);
166			statOut = new StatWriter(info);
167			dumpOut = new DumpWriter(info);
168	mmeineke	558
169	mmeineke	561	atoms = info->atoms;
170
171			dt = info->dt;
172	mmeineke	558	dt2 = 0.5 * dt;
173
174	mmeineke	784	readyCheck();
175
176	mmeineke	558	// initialize the forces before the first step
177
178	tim	677	calcForce(1, 1);
179	tim	781
180			if (nConstrained){
181			preMove();
182			constrainA();
183	tim	837	calcForce(1, 1);
184	tim	781	constrainB();
185			}
186	mmeineke	843
187	tim	725	if (info->setTemp){
188	tim	677	thermalize();
189	mmeineke	558	}
190	tim	725
191	mmeineke	558	calcPot = 0;
192			calcStress = 0;
193	mmeineke	711	currSample = sampleTime + info->getTime();
194			currThermal = thermalTime+ info->getTime();
195			currStatus = statusTime + info->getTime();
196	mmeineke	746	currReset = resetTime + info->getTime();
197	mmeineke	558
198	tim	725	dumpOut->writeDump(info->getTime());
199			statOut->writeStat(info->getTime());
200	mmeineke	559
201
202			#ifdef IS_MPI
203	tim	725	strcpy(checkPointMsg, "The integrator is ready to go.");
204	mmeineke	559	MPIcheckPoint();
205			#endif // is_mpi
206
207	tim	725	while (info->getTime() < runTime){
208			if ((info->getTime() + dt) >= currStatus){
209	mmeineke	558	calcPot = 1;
210			calcStress = 1;
211			}
212	mmeineke	561
213	tim	725	integrateStep(calcPot, calcStress);
214
215	mmeineke	643	info->incrTime(dt);
216	mmeineke	558
217	tim	725	if (info->setTemp){
218			if (info->getTime() >= currThermal){
219			thermalize();
220			currThermal += thermalTime;
221	mmeineke	558	}
222			}
223
224	tim	725	if (info->getTime() >= currSample){
225			dumpOut->writeDump(info->getTime());
226	mmeineke	558	currSample += sampleTime;
227			}
228
229	tim	725	if (info->getTime() >= currStatus){
230	tim	837	statOut->writeStat(info->getTime());
231			calcPot = 0;
232	mmeineke	558	calcStress = 0;
233			currStatus += statusTime;
234	tim	837	}
235	mmeineke	559
236	mmeineke	746	if (info->resetIntegrator){
237			if (info->getTime() >= currReset){
238			this->resetIntegrator();
239			currReset += resetTime;
240			}
241			}
242
243	mmeineke	559	#ifdef IS_MPI
244	tim	725	strcpy(checkPointMsg, "successfully took a time step.");
245	mmeineke	559	MPIcheckPoint();
246			#endif // is_mpi
247	mmeineke	558	}
248
249
250	mmeineke	804	// write the last frame
251			dumpOut->writeDump(info->getTime());
252
253	mmeineke	561	delete dumpOut;
254			delete statOut;
255	mmeineke	558	}
256
257	mmeineke	849	void Integrator::integrateStep(int calcPot,
258	mmeineke	852	int calcStress){
259	mmeineke	558	// Position full step, and velocity half step
260	tim	725	preMove();
261	mmeineke	558
262			moveA();
263
264	tim	725
265
266	mmeineke	768
267	mmeineke	614	#ifdef IS_MPI
268	tim	725	strcpy(checkPointMsg, "Succesful moveA\n");
269	mmeineke	614	MPIcheckPoint();
270			#endif // is_mpi
271
272	tim	725
273	mmeineke	558	// calc forces
274
275	tim	725	calcForce(calcPot, calcStress);
276	mmeineke	558
277	mmeineke	614	#ifdef IS_MPI
278	tim	725	strcpy(checkPointMsg, "Succesful doForces\n");
279	mmeineke	614	MPIcheckPoint();
280			#endif // is_mpi
281
282	tim	725
283	mmeineke	558	// finish the velocity half step
284	tim	725
285	mmeineke	558	moveB();
286	tim	725
287
288	mmeineke	768
289	mmeineke	614	#ifdef IS_MPI
290	tim	725	strcpy(checkPointMsg, "Succesful moveB\n");
291	mmeineke	614	MPIcheckPoint();
292			#endif // is_mpi
293	mmeineke	558	}
294
295
296	mmeineke	849	void Integrator::moveA(void){
297	gezelter	600	int i, j;
298	mmeineke	558	DirectionalAtom* dAtom;
299	gezelter	600	double Tb[3], ji[3];
300			double vel[3], pos[3], frc[3];
301			double mass;
302	mmeineke	558
303	tim	725	for (i = 0; i < nAtoms; i++){
304			atoms[i]->getVel(vel);
305			atoms[i]->getPos(pos);
306			atoms[i]->getFrc(frc);
307	mmeineke	567
308	gezelter	600	mass = atoms[i]->getMass();
309	mmeineke	594
310	tim	725	for (j = 0; j < 3; j++){
311	gezelter	600	// velocity half step
312	tim	725	vel[j] += (dt2 * frc[j] / mass) * eConvert;
313	gezelter	600	// position whole step
314			pos[j] += dt * vel[j];
315			}
316	mmeineke	594
317	tim	725	atoms[i]->setVel(vel);
318			atoms[i]->setPos(pos);
319	gezelter	600
320	tim	725	if (atoms[i]->isDirectional()){
321			dAtom = (DirectionalAtom *) atoms[i];
322	mmeineke	558
323			// get and convert the torque to body frame
324	mmeineke	597
325	tim	725	dAtom->getTrq(Tb);
326			dAtom->lab2Body(Tb);
327
328	mmeineke	558	// get the angular momentum, and propagate a half step
329	gezelter	600
330	tim	725	dAtom->getJ(ji);
331	gezelter	600
332	tim	725	for (j = 0; j < 3; j++)
333	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
334	tim	725
335	mmeineke	778	this->rotationPropagation( dAtom, ji );
336	gezelter	600
337	tim	725	dAtom->setJ(ji);
338			}
339	mmeineke	558	}
340	mmeineke	768
341			if (nConstrained){
342			constrainA();
343			}
344	mmeineke	558	}
345
346
347	mmeineke	849	void Integrator::moveB(void){
348	gezelter	600	int i, j;
349	mmeineke	558	DirectionalAtom* dAtom;
350	gezelter	600	double Tb[3], ji[3];
351			double vel[3], frc[3];
352			double mass;
353	mmeineke	558
354	tim	725	for (i = 0; i < nAtoms; i++){
355			atoms[i]->getVel(vel);
356			atoms[i]->getFrc(frc);
357	mmeineke	558
358	gezelter	600	mass = atoms[i]->getMass();
359
360	mmeineke	558	// velocity half step
361	tim	725	for (j = 0; j < 3; j++)
362			vel[j] += (dt2 * frc[j] / mass) * eConvert;
363	gezelter	600
364	tim	725	atoms[i]->setVel(vel);
365	mmeineke	597
366	tim	725	if (atoms[i]->isDirectional()){
367			dAtom = (DirectionalAtom *) atoms[i];
368
369	tim	837	// get and convert the torque to body frame
370	gezelter	600
371	tim	725	dAtom->getTrq(Tb);
372			dAtom->lab2Body(Tb);
373	gezelter	600
374			// get the angular momentum, and propagate a half step
375
376	tim	725	dAtom->getJ(ji);
377	gezelter	600
378	tim	725	for (j = 0; j < 3; j++)
379	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
380	mmeineke	597
381	tim	725
382			dAtom->setJ(ji);
383	mmeineke	558	}
384			}
385	mmeineke	768
386			if (nConstrained){
387			constrainB();
388			}
389	mmeineke	558	}
390
391	mmeineke	849	void Integrator::preMove(void){
392	gezelter	600	int i, j;
393			double pos[3];
394	mmeineke	558
395	tim	725	if (nConstrained){
396			for (i = 0; i < nAtoms; i++){
397			atoms[i]->getPos(pos);
398	mmeineke	561
399	tim	725	for (j = 0; j < 3; j++){
400			oldPos[3 * i + j] = pos[j];
401	gezelter	600	}
402			}
403	tim	725	}
404	gezelter	600	}
405
406	mmeineke	849	void Integrator::constrainA(){
407	mmeineke	787	int i, j;
408	mmeineke	558	int done;
409	gezelter	600	double posA[3], posB[3];
410			double velA[3], velB[3];
411	mmeineke	572	double pab[3];
412			double rab[3];
413	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
414	mmeineke	558	double rma, rmb;
415			double dx, dy, dz;
416	mmeineke	561	double rpab;
417	mmeineke	558	double rabsq, pabsq, rpabsq;
418			double diffsq;
419			double gab;
420			int iteration;
421
422	tim	725	for (i = 0; i < nAtoms; i++){
423	mmeineke	558	moving[i] = 0;
424	tim	725	moved[i] = 1;
425	mmeineke	558	}
426	mmeineke	567
427	mmeineke	558	iteration = 0;
428			done = 0;
429	tim	725	while (!done && (iteration < maxIteration)){
430	mmeineke	558	done = 1;
431	tim	725	for (i = 0; i < nConstrained; i++){
432	mmeineke	558	a = constrainedA[i];
433			b = constrainedB[i];
434	mmeineke	563
435	tim	725	ax = (a * 3) + 0;
436			ay = (a * 3) + 1;
437			az = (a * 3) + 2;
438	mmeineke	563
439	tim	725	bx = (b * 3) + 0;
440			by = (b * 3) + 1;
441			bz = (b * 3) + 2;
442
443			if (moved[a] \|\| moved[b]){
444			atoms[a]->getPos(posA);
445			atoms[b]->getPos(posB);
446
447			for (j = 0; j < 3; j++)
448	gezelter	600	pab[j] = posA[j] - posB[j];
449	mmeineke	567
450	tim	725	//periodic boundary condition
451	mmeineke	567
452	tim	725	info->wrapVector(pab);
453	mmeineke	572
454	tim	725	pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
455	mmeineke	558
456	tim	725	rabsq = constrainedDsqr[i];
457			diffsq = rabsq - pabsq;
458	mmeineke	567
459	tim	725	// the original rattle code from alan tidesley
460			if (fabs(diffsq) > (tol * rabsq * 2)){
461			rab[0] = oldPos[ax] - oldPos[bx];
462			rab[1] = oldPos[ay] - oldPos[by];
463			rab[2] = oldPos[az] - oldPos[bz];
464	mmeineke	558
465	tim	725	info->wrapVector(rab);
466	mmeineke	567
467	tim	725	rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
468	mmeineke	558
469	tim	725	rpabsq = rpab * rpab;
470	mmeineke	558
471	mmeineke	563
472	tim	725	if (rpabsq < (rabsq * -diffsq)){
473	mmeineke	558	#ifdef IS_MPI
474	tim	725	a = atoms[a]->getGlobalIndex();
475			b = atoms[b]->getGlobalIndex();
476	mmeineke	558	#endif //is_mpi
477	tim	725	sprintf(painCave.errMsg,
478			"Constraint failure in constrainA at atom %d and %d.\n", a,
479			b);
480			painCave.isFatal = 1;
481			simError();
482			}
483	mmeineke	558
484	tim	725	rma = 1.0 / atoms[a]->getMass();
485			rmb = 1.0 / atoms[b]->getMass();
486	mmeineke	567
487	tim	725	gab = diffsq / (2.0 * (rma + rmb) * rpab);
488	mmeineke	567
489	mmeineke	572	dx = rab[0] * gab;
490			dy = rab[1] * gab;
491			dz = rab[2] * gab;
492	mmeineke	558
493	tim	725	posA[0] += rma * dx;
494			posA[1] += rma * dy;
495			posA[2] += rma * dz;
496	mmeineke	558
497	tim	725	atoms[a]->setPos(posA);
498	mmeineke	558
499	tim	725	posB[0] -= rmb * dx;
500			posB[1] -= rmb * dy;
501			posB[2] -= rmb * dz;
502	gezelter	600
503	tim	725	atoms[b]->setPos(posB);
504	gezelter	600
505	mmeineke	558	dx = dx / dt;
506			dy = dy / dt;
507			dz = dz / dt;
508
509	tim	725	atoms[a]->getVel(velA);
510	mmeineke	558
511	tim	725	velA[0] += rma * dx;
512			velA[1] += rma * dy;
513			velA[2] += rma * dz;
514	mmeineke	558
515	tim	725	atoms[a]->setVel(velA);
516	gezelter	600
517	tim	725	atoms[b]->getVel(velB);
518	gezelter	600
519	tim	725	velB[0] -= rmb * dx;
520			velB[1] -= rmb * dy;
521			velB[2] -= rmb * dz;
522	gezelter	600
523	tim	725	atoms[b]->setVel(velB);
524	gezelter	600
525	tim	725	moving[a] = 1;
526			moving[b] = 1;
527			done = 0;
528			}
529	mmeineke	558	}
530			}
531	tim	725
532			for (i = 0; i < nAtoms; i++){
533	mmeineke	558	moved[i] = moving[i];
534			moving[i] = 0;
535			}
536
537			iteration++;
538			}
539
540	tim	725	if (!done){
541			sprintf(painCave.errMsg,
542			"Constraint failure in constrainA, too many iterations: %d\n",
543			iteration);
544	mmeineke	558	painCave.isFatal = 1;
545			simError();
546			}
547	mmeineke	768
548	mmeineke	558	}
549
550	mmeineke	849	void Integrator::constrainB(void){
551	mmeineke	787	int i, j;
552	mmeineke	558	int done;
553	gezelter	600	double posA[3], posB[3];
554			double velA[3], velB[3];
555	mmeineke	558	double vxab, vyab, vzab;
556	mmeineke	572	double rab[3];
557	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
558	mmeineke	558	double rma, rmb;
559			double dx, dy, dz;
560	mmeineke	787	double rvab;
561	mmeineke	558	double gab;
562			int iteration;
563
564	tim	725	for (i = 0; i < nAtoms; i++){
565	mmeineke	558	moving[i] = 0;
566			moved[i] = 1;
567			}
568
569			done = 0;
570	mmeineke	561	iteration = 0;
571	tim	725	while (!done && (iteration < maxIteration)){
572	mmeineke	567	done = 1;
573
574	tim	725	for (i = 0; i < nConstrained; i++){
575	mmeineke	558	a = constrainedA[i];
576			b = constrainedB[i];
577
578	tim	725	ax = (a * 3) + 0;
579			ay = (a * 3) + 1;
580			az = (a * 3) + 2;
581	mmeineke	563
582	tim	725	bx = (b * 3) + 0;
583			by = (b * 3) + 1;
584			bz = (b * 3) + 2;
585	mmeineke	563
586	tim	725	if (moved[a] \|\| moved[b]){
587			atoms[a]->getVel(velA);
588			atoms[b]->getVel(velB);
589	mmeineke	558
590	tim	725	vxab = velA[0] - velB[0];
591			vyab = velA[1] - velB[1];
592			vzab = velA[2] - velB[2];
593	gezelter	600
594	tim	725	atoms[a]->getPos(posA);
595			atoms[b]->getPos(posB);
596	gezelter	600
597	tim	725	for (j = 0; j < 3; j++)
598	gezelter	600	rab[j] = posA[j] - posB[j];
599	mmeineke	558
600	tim	725	info->wrapVector(rab);
601	mmeineke	558
602	tim	725	rma = 1.0 / atoms[a]->getMass();
603			rmb = 1.0 / atoms[b]->getMass();
604	mmeineke	558
605	tim	725	rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
606	gezelter	600
607	tim	725	gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
608	gezelter	600
609	tim	725	if (fabs(gab) > tol){
610			dx = rab[0] * gab;
611			dy = rab[1] * gab;
612			dz = rab[2] * gab;
613
614			velA[0] += rma * dx;
615			velA[1] += rma * dy;
616			velA[2] += rma * dz;
617
618			atoms[a]->setVel(velA);
619
620			velB[0] -= rmb * dx;
621			velB[1] -= rmb * dy;
622			velB[2] -= rmb * dz;
623
624			atoms[b]->setVel(velB);
625
626			moving[a] = 1;
627			moving[b] = 1;
628			done = 0;
629			}
630	mmeineke	558	}
631			}
632
633	tim	725	for (i = 0; i < nAtoms; i++){
634	mmeineke	558	moved[i] = moving[i];
635			moving[i] = 0;
636			}
637	tim	725
638	mmeineke	558	iteration++;
639			}
640
641	tim	725	if (!done){
642			sprintf(painCave.errMsg,
643			"Constraint failure in constrainB, too many iterations: %d\n",
644			iteration);
645	mmeineke	558	painCave.isFatal = 1;
646			simError();
647	tim	725	}
648	mmeineke	558	}
649
650	mmeineke	849	void Integrator::rotationPropagation
651	mmeineke	778	( DirectionalAtom* dAtom, double ji[3] ){
652
653			double angle;
654			double A[3][3], I[3][3];
655
656			// use the angular velocities to propagate the rotation matrix a
657			// full time step
658
659			dAtom->getA(A);
660			dAtom->getI(I);
661	tim	837
662			// rotate about the x-axis
663	mmeineke	778	angle = dt2 * ji[0] / I[0][0];
664	tim	837	this->rotate( 1, 2, angle, ji, A );
665
666	mmeineke	778	// rotate about the y-axis
667			angle = dt2 * ji[1] / I[1][1];
668			this->rotate( 2, 0, angle, ji, A );
669	tim	837
670	mmeineke	778	// rotate about the z-axis
671			angle = dt * ji[2] / I[2][2];
672			this->rotate( 0, 1, angle, ji, A);
673	tim	837
674	mmeineke	778	// rotate about the y-axis
675			angle = dt2 * ji[1] / I[1][1];
676			this->rotate( 2, 0, angle, ji, A );
677	tim	837
678	mmeineke	778	// rotate about the x-axis
679			angle = dt2 * ji[0] / I[0][0];
680			this->rotate( 1, 2, angle, ji, A );
681	tim	837
682			dAtom->setA( A );
683	mmeineke	778	}
684
685	mmeineke	849	void Integrator::rotate(int axes1, int axes2,
686			double angle, double ji[3],
687			double A[3][3]){
688	tim	725	int i, j, k;
689	mmeineke	558	double sinAngle;
690			double cosAngle;
691			double angleSqr;
692			double angleSqrOver4;
693			double top, bottom;
694			double rot[3][3];
695			double tempA[3][3];
696			double tempJ[3];
697
698			// initialize the tempA
699
700	tim	725	for (i = 0; i < 3; i++){
701			for (j = 0; j < 3; j++){
702	gezelter	600	tempA[j][i] = A[i][j];
703	mmeineke	558	}
704			}
705
706			// initialize the tempJ
707
708	tim	725	for (i = 0; i < 3; i++)
709			tempJ[i] = ji[i];
710
711	mmeineke	558	// initalize rot as a unit matrix
712
713			rot[0][0] = 1.0;
714			rot[0][1] = 0.0;
715			rot[0][2] = 0.0;
716
717			rot[1][0] = 0.0;
718			rot[1][1] = 1.0;
719			rot[1][2] = 0.0;
720	tim	725
721	mmeineke	558	rot[2][0] = 0.0;
722			rot[2][1] = 0.0;
723			rot[2][2] = 1.0;
724	tim	725
725	mmeineke	558	// use a small angle aproximation for sin and cosine
726
727	tim	725	angleSqr = angle * angle;
728	mmeineke	558	angleSqrOver4 = angleSqr / 4.0;
729			top = 1.0 - angleSqrOver4;
730			bottom = 1.0 + angleSqrOver4;
731
732			cosAngle = top / bottom;
733			sinAngle = angle / bottom;
734
735			rot[axes1][axes1] = cosAngle;
736			rot[axes2][axes2] = cosAngle;
737
738			rot[axes1][axes2] = sinAngle;
739			rot[axes2][axes1] = -sinAngle;
740	tim	725
741	mmeineke	558	// rotate the momentum acoording to: ji[] = rot[][] * ji[]
742	tim	725
743			for (i = 0; i < 3; i++){
744	mmeineke	558	ji[i] = 0.0;
745	tim	725	for (k = 0; k < 3; k++){
746	mmeineke	558	ji[i] += rot[i][k] * tempJ[k];
747			}
748			}
749
750	tim	837	// rotate the Rotation matrix acording to:
751	mmeineke	558	// A[][] = A[][] * transpose(rot[][])
752
753
754	mmeineke	561	// NOte for as yet unknown reason, we are performing the
755	mmeineke	558	// calculation as:
756			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
757
758	tim	725	for (i = 0; i < 3; i++){
759			for (j = 0; j < 3; j++){
760	gezelter	600	A[j][i] = 0.0;
761	tim	725	for (k = 0; k < 3; k++){
762			A[j][i] += tempA[i][k] * rot[j][k];
763	mmeineke	558	}
764			}
765			}
766			}
767	tim	677
768	mmeineke	849	void Integrator::calcForce(int calcPot, int calcStress){
769	tim	725	myFF->doForces(calcPot, calcStress);
770	tim	677	}
771
772	mmeineke	849	void Integrator::thermalize(){
773	tim	725	tStats->velocitize();
774	tim	677	}
775	tim	763
776	mmeineke	849	double Integrator::getConservedQuantity(void){
777	tim	763	return tStats->getTotalE();
778	mmeineke	768	}
779	mmeineke	849
780	mmeineke	851	char* Integrator::getAdditionalParameters(void){
781	tim	837	//By default, return a null string
782			//The reason we use string instead of char* is that if we use char*, we will
783			//return a pointer point to local variable which might cause problem
784	mmeineke	851	addParams[0] = '\0';
785			return addParams;
786	tim	837	}