OOPSE/libmdtools/Integrator.cpp

#include <iostream>
#include <cstdlib>
#include <cmath>

#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;
  }
  info->the_integrator = this;

  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){
  int i, j;                         // loop counters

  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;
  int isError;

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

  atoms = info->atoms;
  DirectionalAtom* dAtom;

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

  // initialize the forces before the first step

  calcForce(1, 1);
  
  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());

  readyCheck();

#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
  }

  dumpOut->writeFinal(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();

  if (nConstrained){
    constrainA();
  }


#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();

  if (nConstrained){
    constrainB();
  }

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

      // 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->setJ(ji);
      dAtom->setA(A);
    }
  }
}


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);
    }
  }
}

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, k;
  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, k;
  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 rabsq, pabsq, rvab;
  double diffsq;
  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>::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();
}
Revision:	746
Committed:	Thu Sep 4 21:48:35 2003 UTC (20 years, 10 months ago) by mmeineke
File size:	16373 byte(s)
Log Message:	added resetTime to the Global namespace. added ability to reset the integrators in the NVT and NPT family.
#	User	Rev	Content
1	mmeineke	558	#include <iostream>
2			#include <cstdlib>
3	mmeineke	561	#include <cmath>
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	mmeineke	558	info->the_integrator = this;
29
30			nAtoms = info->n_atoms;
31
32			// check for constraints
33	tim	725
34			constrainedA = NULL;
35			constrainedB = NULL;
36	mmeineke	558	constrainedDsqr = NULL;
37	tim	725	moving = NULL;
38			moved = NULL;
39			oldPos = NULL;
40
41	mmeineke	558	nConstrained = 0;
42
43			checkConstraints();
44			}
45
46	tim	725	template<typename T> Integrator<T>::~Integrator(){
47			if (nConstrained){
48	mmeineke	558	delete[] constrainedA;
49			delete[] constrainedB;
50			delete[] constrainedDsqr;
51			delete[] moving;
52			delete[] moved;
53	mmeineke	561	delete[] oldPos;
54	mmeineke	558	}
55			}
56
57	tim	725	template<typename T> void Integrator<T>::checkConstraints(void){
58	mmeineke	558	isConstrained = 0;
59
60	tim	725	Constraint* temp_con;
61			Constraint* dummy_plug;
62	mmeineke	558	temp_con = new Constraint[info->n_SRI];
63			nConstrained = 0;
64			int constrained = 0;
65	tim	725
66	mmeineke	558	SRI** theArray;
67	tim	725	for (int i = 0; i < nMols; i++){
68			theArray = (SRI * *) molecules[i].getMyBonds();
69			for (int j = 0; j < molecules[i].getNBonds(); j++){
70	mmeineke	558	constrained = theArray[j]->is_constrained();
71	mmeineke	594
72	tim	725	if (constrained){
73			dummy_plug = theArray[j]->get_constraint();
74			temp_con[nConstrained].set_a(dummy_plug->get_a());
75			temp_con[nConstrained].set_b(dummy_plug->get_b());
76			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
77	mmeineke	594
78	tim	725	nConstrained++;
79			constrained = 0;
80			}
81	mmeineke	558	}
82
83	tim	725	theArray = (SRI * *) molecules[i].getMyBends();
84			for (int j = 0; j < molecules[i].getNBends(); j++){
85	mmeineke	558	constrained = theArray[j]->is_constrained();
86	tim	725
87			if (constrained){
88			dummy_plug = theArray[j]->get_constraint();
89			temp_con[nConstrained].set_a(dummy_plug->get_a());
90			temp_con[nConstrained].set_b(dummy_plug->get_b());
91			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
92
93			nConstrained++;
94			constrained = 0;
95	mmeineke	558	}
96			}
97
98	tim	725	theArray = (SRI * *) molecules[i].getMyTorsions();
99			for (int j = 0; j < molecules[i].getNTorsions(); j++){
100	mmeineke	558	constrained = theArray[j]->is_constrained();
101	tim	725
102			if (constrained){
103			dummy_plug = theArray[j]->get_constraint();
104			temp_con[nConstrained].set_a(dummy_plug->get_a());
105			temp_con[nConstrained].set_b(dummy_plug->get_b());
106			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
107
108			nConstrained++;
109			constrained = 0;
110	mmeineke	558	}
111			}
112			}
113
114	tim	725	if (nConstrained > 0){
115	mmeineke	558	isConstrained = 1;
116
117	tim	725	if (constrainedA != NULL)
118			delete[] constrainedA;
119			if (constrainedB != NULL)
120			delete[] constrainedB;
121			if (constrainedDsqr != NULL)
122			delete[] constrainedDsqr;
123	mmeineke	558
124	tim	725	constrainedA = new int[nConstrained];
125			constrainedB = new int[nConstrained];
126	mmeineke	558	constrainedDsqr = new double[nConstrained];
127	tim	725
128			for (int i = 0; i < nConstrained; i++){
129	mmeineke	558	constrainedA[i] = temp_con[i].get_a();
130			constrainedB[i] = temp_con[i].get_b();
131			constrainedDsqr[i] = temp_con[i].get_dsqr();
132			}
133
134	tim	725
135	mmeineke	558	// save oldAtoms to check for lode balanceing later on.
136	tim	725
137	mmeineke	558	oldAtoms = nAtoms;
138	tim	725
139	mmeineke	558	moving = new int[nAtoms];
140	tim	725	moved = new int[nAtoms];
141	mmeineke	558
142	tim	725	oldPos = new double[nAtoms * 3];
143	mmeineke	558	}
144	tim	725
145	mmeineke	558	delete[] temp_con;
146			}
147
148
149	tim	725	template<typename T> void Integrator<T>::integrate(void){
150	mmeineke	558	int i, j; // loop counters
151
152	tim	725	double runTime = info->run_time;
153			double sampleTime = info->sampleTime;
154			double statusTime = info->statusTime;
155	mmeineke	558	double thermalTime = info->thermalTime;
156	mmeineke	746	double resetTime = info->resetTime;
157	mmeineke	558
158	mmeineke	746
159	mmeineke	558	double currSample;
160			double currThermal;
161			double currStatus;
162	mmeineke	746	double currReset;
163
164	mmeineke	558	int calcPot, calcStress;
165			int isError;
166
167	tim	725	tStats = new Thermo(info);
168			statOut = new StatWriter(info);
169			dumpOut = new DumpWriter(info);
170	mmeineke	558
171	mmeineke	561	atoms = info->atoms;
172	mmeineke	558	DirectionalAtom* dAtom;
173	mmeineke	561
174			dt = info->dt;
175	mmeineke	558	dt2 = 0.5 * dt;
176
177			// initialize the forces before the first step
178
179	tim	677	calcForce(1, 1);
180	tim	733
181	tim	725	if (info->setTemp){
182	tim	677	thermalize();
183	mmeineke	558	}
184	tim	725
185	mmeineke	558	calcPot = 0;
186			calcStress = 0;
187	mmeineke	711	currSample = sampleTime + info->getTime();
188			currThermal = thermalTime+ info->getTime();
189			currStatus = statusTime + info->getTime();
190	mmeineke	746	currReset = resetTime + info->getTime();
191	mmeineke	558
192	tim	725	dumpOut->writeDump(info->getTime());
193			statOut->writeStat(info->getTime());
194	mmeineke	559
195			readyCheck();
196
197			#ifdef IS_MPI
198	tim	725	strcpy(checkPointMsg, "The integrator is ready to go.");
199	mmeineke	559	MPIcheckPoint();
200			#endif // is_mpi
201
202	tim	725	while (info->getTime() < runTime){
203			if ((info->getTime() + dt) >= currStatus){
204	mmeineke	558	calcPot = 1;
205			calcStress = 1;
206			}
207	mmeineke	561
208	tim	725	integrateStep(calcPot, calcStress);
209
210	mmeineke	643	info->incrTime(dt);
211	mmeineke	558
212	tim	725	if (info->setTemp){
213			if (info->getTime() >= currThermal){
214			thermalize();
215			currThermal += thermalTime;
216	mmeineke	558	}
217			}
218
219	tim	725	if (info->getTime() >= currSample){
220			dumpOut->writeDump(info->getTime());
221	mmeineke	558	currSample += sampleTime;
222			}
223
224	tim	725	if (info->getTime() >= currStatus){
225			statOut->writeStat(info->getTime());
226	mmeineke	558	calcPot = 0;
227			calcStress = 0;
228			currStatus += statusTime;
229			}
230	mmeineke	559
231	mmeineke	746	if (info->resetIntegrator){
232			if (info->getTime() >= currReset){
233			this->resetIntegrator();
234			currReset += resetTime;
235			}
236			}
237
238	mmeineke	559	#ifdef IS_MPI
239	tim	725	strcpy(checkPointMsg, "successfully took a time step.");
240	mmeineke	559	MPIcheckPoint();
241			#endif // is_mpi
242	mmeineke	558	}
243
244	mmeineke	643	dumpOut->writeFinal(info->getTime());
245	mmeineke	558
246	mmeineke	561	delete dumpOut;
247			delete statOut;
248	mmeineke	558	}
249
250	tim	725	template<typename T> void Integrator<T>::integrateStep(int calcPot,
251			int calcStress){
252	mmeineke	558	// Position full step, and velocity half step
253	tim	725	preMove();
254	mmeineke	558
255			moveA();
256
257	tim	725	if (nConstrained){
258			constrainA();
259			}
260
261
262	mmeineke	614	#ifdef IS_MPI
263	tim	725	strcpy(checkPointMsg, "Succesful moveA\n");
264	mmeineke	614	MPIcheckPoint();
265			#endif // is_mpi
266
267	tim	725
268	mmeineke	558	// calc forces
269
270	tim	725	calcForce(calcPot, calcStress);
271	mmeineke	558
272	mmeineke	614	#ifdef IS_MPI
273	tim	725	strcpy(checkPointMsg, "Succesful doForces\n");
274	mmeineke	614	MPIcheckPoint();
275			#endif // is_mpi
276
277	tim	725
278	mmeineke	558	// finish the velocity half step
279	tim	725
280	mmeineke	558	moveB();
281	tim	725
282			if (nConstrained){
283			constrainB();
284			}
285
286	mmeineke	614	#ifdef IS_MPI
287	tim	725	strcpy(checkPointMsg, "Succesful moveB\n");
288	mmeineke	614	MPIcheckPoint();
289			#endif // is_mpi
290	mmeineke	558	}
291
292
293	tim	725	template<typename T> void Integrator<T>::moveA(void){
294	gezelter	600	int i, j;
295	mmeineke	558	DirectionalAtom* dAtom;
296	gezelter	600	double Tb[3], ji[3];
297			double A[3][3], I[3][3];
298	mmeineke	561	double angle;
299	gezelter	600	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	558	// use the angular velocities to propagate the rotation matrix a
335			// full time step
336	gezelter	600
337			dAtom->getA(A);
338			dAtom->getI(I);
339	tim	725
340	mmeineke	558	// rotate about the x-axis
341	gezelter	600	angle = dt2 * ji[0] / I[0][0];
342	tim	725	this->rotate(1, 2, angle, ji, A);
343	mmeineke	597
344	mmeineke	558	// rotate about the y-axis
345	gezelter	600	angle = dt2 * ji[1] / I[1][1];
346	tim	725	this->rotate(2, 0, angle, ji, A);
347
348	mmeineke	558	// rotate about the z-axis
349	gezelter	600	angle = dt * ji[2] / I[2][2];
350	tim	725	this->rotate(0, 1, angle, ji, A);
351
352	mmeineke	558	// rotate about the y-axis
353	gezelter	600	angle = dt2 * ji[1] / I[1][1];
354	tim	725	this->rotate(2, 0, angle, ji, A);
355
356			// rotate about the x-axis
357	gezelter	600	angle = dt2 * ji[0] / I[0][0];
358	tim	725	this->rotate(1, 2, angle, ji, A);
359	mmeineke	597
360	tim	725
361			dAtom->setJ(ji);
362			dAtom->setA(A);
363			}
364	mmeineke	558	}
365			}
366
367
368	tim	725	template<typename T> void Integrator<T>::moveB(void){
369	gezelter	600	int i, j;
370	mmeineke	558	DirectionalAtom* dAtom;
371	gezelter	600	double Tb[3], ji[3];
372			double vel[3], frc[3];
373			double mass;
374	mmeineke	558
375	tim	725	for (i = 0; i < nAtoms; i++){
376			atoms[i]->getVel(vel);
377			atoms[i]->getFrc(frc);
378	mmeineke	558
379	gezelter	600	mass = atoms[i]->getMass();
380
381	mmeineke	558	// velocity half step
382	tim	725	for (j = 0; j < 3; j++)
383			vel[j] += (dt2 * frc[j] / mass) * eConvert;
384	gezelter	600
385	tim	725	atoms[i]->setVel(vel);
386	mmeineke	597
387	tim	725	if (atoms[i]->isDirectional()){
388			dAtom = (DirectionalAtom *) atoms[i];
389
390	gezelter	600	// get and convert the torque to body frame
391
392	tim	725	dAtom->getTrq(Tb);
393			dAtom->lab2Body(Tb);
394	gezelter	600
395			// get the angular momentum, and propagate a half step
396
397	tim	725	dAtom->getJ(ji);
398	gezelter	600
399	tim	725	for (j = 0; j < 3; j++)
400	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
401	mmeineke	597
402	tim	725
403			dAtom->setJ(ji);
404	mmeineke	558	}
405			}
406			}
407
408	tim	725	template<typename T> void Integrator<T>::preMove(void){
409	gezelter	600	int i, j;
410			double pos[3];
411	mmeineke	558
412	tim	725	if (nConstrained){
413			for (i = 0; i < nAtoms; i++){
414			atoms[i]->getPos(pos);
415	mmeineke	561
416	tim	725	for (j = 0; j < 3; j++){
417			oldPos[3 * i + j] = pos[j];
418	gezelter	600	}
419			}
420	tim	725	}
421	gezelter	600	}
422
423	tim	645	template<typename T> void Integrator<T>::constrainA(){
424	tim	725	int i, j, k;
425	mmeineke	558	int done;
426	gezelter	600	double posA[3], posB[3];
427			double velA[3], velB[3];
428	mmeineke	572	double pab[3];
429			double rab[3];
430	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
431	mmeineke	558	double rma, rmb;
432			double dx, dy, dz;
433	mmeineke	561	double rpab;
434	mmeineke	558	double rabsq, pabsq, rpabsq;
435			double diffsq;
436			double gab;
437			int iteration;
438
439	tim	725	for (i = 0; i < nAtoms; i++){
440	mmeineke	558	moving[i] = 0;
441	tim	725	moved[i] = 1;
442	mmeineke	558	}
443	mmeineke	567
444	mmeineke	558	iteration = 0;
445			done = 0;
446	tim	725	while (!done && (iteration < maxIteration)){
447	mmeineke	558	done = 1;
448	tim	725	for (i = 0; i < nConstrained; i++){
449	mmeineke	558	a = constrainedA[i];
450			b = constrainedB[i];
451	mmeineke	563
452	tim	725	ax = (a * 3) + 0;
453			ay = (a * 3) + 1;
454			az = (a * 3) + 2;
455	mmeineke	563
456	tim	725	bx = (b * 3) + 0;
457			by = (b * 3) + 1;
458			bz = (b * 3) + 2;
459
460			if (moved[a] \|\| moved[b]){
461			atoms[a]->getPos(posA);
462			atoms[b]->getPos(posB);
463
464			for (j = 0; j < 3; j++)
465	gezelter	600	pab[j] = posA[j] - posB[j];
466	mmeineke	567
467	tim	725	//periodic boundary condition
468	mmeineke	567
469	tim	725	info->wrapVector(pab);
470	mmeineke	572
471	tim	725	pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
472	mmeineke	558
473	tim	725	rabsq = constrainedDsqr[i];
474			diffsq = rabsq - pabsq;
475	mmeineke	567
476	tim	725	// the original rattle code from alan tidesley
477			if (fabs(diffsq) > (tol * rabsq * 2)){
478			rab[0] = oldPos[ax] - oldPos[bx];
479			rab[1] = oldPos[ay] - oldPos[by];
480			rab[2] = oldPos[az] - oldPos[bz];
481	mmeineke	558
482	tim	725	info->wrapVector(rab);
483	mmeineke	567
484	tim	725	rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
485	mmeineke	558
486	tim	725	rpabsq = rpab * rpab;
487	mmeineke	558
488	mmeineke	563
489	tim	725	if (rpabsq < (rabsq * -diffsq)){
490	mmeineke	558	#ifdef IS_MPI
491	tim	725	a = atoms[a]->getGlobalIndex();
492			b = atoms[b]->getGlobalIndex();
493	mmeineke	558	#endif //is_mpi
494	tim	725	sprintf(painCave.errMsg,
495			"Constraint failure in constrainA at atom %d and %d.\n", a,
496			b);
497			painCave.isFatal = 1;
498			simError();
499			}
500	mmeineke	558
501	tim	725	rma = 1.0 / atoms[a]->getMass();
502			rmb = 1.0 / atoms[b]->getMass();
503	mmeineke	567
504	tim	725	gab = diffsq / (2.0 * (rma + rmb) * rpab);
505	mmeineke	567
506	mmeineke	572	dx = rab[0] * gab;
507			dy = rab[1] * gab;
508			dz = rab[2] * gab;
509	mmeineke	558
510	tim	725	posA[0] += rma * dx;
511			posA[1] += rma * dy;
512			posA[2] += rma * dz;
513	mmeineke	558
514	tim	725	atoms[a]->setPos(posA);
515	mmeineke	558
516	tim	725	posB[0] -= rmb * dx;
517			posB[1] -= rmb * dy;
518			posB[2] -= rmb * dz;
519	gezelter	600
520	tim	725	atoms[b]->setPos(posB);
521	gezelter	600
522	mmeineke	558	dx = dx / dt;
523			dy = dy / dt;
524			dz = dz / dt;
525
526	tim	725	atoms[a]->getVel(velA);
527	mmeineke	558
528	tim	725	velA[0] += rma * dx;
529			velA[1] += rma * dy;
530			velA[2] += rma * dz;
531	mmeineke	558
532	tim	725	atoms[a]->setVel(velA);
533	gezelter	600
534	tim	725	atoms[b]->getVel(velB);
535	gezelter	600
536	tim	725	velB[0] -= rmb * dx;
537			velB[1] -= rmb * dy;
538			velB[2] -= rmb * dz;
539	gezelter	600
540	tim	725	atoms[b]->setVel(velB);
541	gezelter	600
542	tim	725	moving[a] = 1;
543			moving[b] = 1;
544			done = 0;
545			}
546	mmeineke	558	}
547			}
548	tim	725
549			for (i = 0; i < nAtoms; i++){
550	mmeineke	558	moved[i] = moving[i];
551			moving[i] = 0;
552			}
553
554			iteration++;
555			}
556
557	tim	725	if (!done){
558			sprintf(painCave.errMsg,
559			"Constraint failure in constrainA, too many iterations: %d\n",
560			iteration);
561	mmeineke	558	painCave.isFatal = 1;
562			simError();
563			}
564			}
565
566	tim	725	template<typename T> void Integrator<T>::constrainB(void){
567			int i, j, k;
568	mmeineke	558	int done;
569	gezelter	600	double posA[3], posB[3];
570			double velA[3], velB[3];
571	mmeineke	558	double vxab, vyab, vzab;
572	mmeineke	572	double rab[3];
573	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
574	mmeineke	558	double rma, rmb;
575			double dx, dy, dz;
576			double rabsq, pabsq, rvab;
577			double diffsq;
578			double gab;
579			int iteration;
580
581	tim	725	for (i = 0; i < nAtoms; i++){
582	mmeineke	558	moving[i] = 0;
583			moved[i] = 1;
584			}
585
586			done = 0;
587	mmeineke	561	iteration = 0;
588	tim	725	while (!done && (iteration < maxIteration)){
589	mmeineke	567	done = 1;
590
591	tim	725	for (i = 0; i < nConstrained; i++){
592	mmeineke	558	a = constrainedA[i];
593			b = constrainedB[i];
594
595	tim	725	ax = (a * 3) + 0;
596			ay = (a * 3) + 1;
597			az = (a * 3) + 2;
598	mmeineke	563
599	tim	725	bx = (b * 3) + 0;
600			by = (b * 3) + 1;
601			bz = (b * 3) + 2;
602	mmeineke	563
603	tim	725	if (moved[a] \|\| moved[b]){
604			atoms[a]->getVel(velA);
605			atoms[b]->getVel(velB);
606	mmeineke	558
607	tim	725	vxab = velA[0] - velB[0];
608			vyab = velA[1] - velB[1];
609			vzab = velA[2] - velB[2];
610	gezelter	600
611	tim	725	atoms[a]->getPos(posA);
612			atoms[b]->getPos(posB);
613	gezelter	600
614	tim	725	for (j = 0; j < 3; j++)
615	gezelter	600	rab[j] = posA[j] - posB[j];
616	mmeineke	558
617	tim	725	info->wrapVector(rab);
618	mmeineke	558
619	tim	725	rma = 1.0 / atoms[a]->getMass();
620			rmb = 1.0 / atoms[b]->getMass();
621	mmeineke	558
622	tim	725	rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
623	gezelter	600
624	tim	725	gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
625	gezelter	600
626	tim	725	if (fabs(gab) > tol){
627			dx = rab[0] * gab;
628			dy = rab[1] * gab;
629			dz = rab[2] * gab;
630
631			velA[0] += rma * dx;
632			velA[1] += rma * dy;
633			velA[2] += rma * dz;
634
635			atoms[a]->setVel(velA);
636
637			velB[0] -= rmb * dx;
638			velB[1] -= rmb * dy;
639			velB[2] -= rmb * dz;
640
641			atoms[b]->setVel(velB);
642
643			moving[a] = 1;
644			moving[b] = 1;
645			done = 0;
646			}
647	mmeineke	558	}
648			}
649
650	tim	725	for (i = 0; i < nAtoms; i++){
651	mmeineke	558	moved[i] = moving[i];
652			moving[i] = 0;
653			}
654	tim	725
655	mmeineke	558	iteration++;
656			}
657
658	tim	725	if (!done){
659			sprintf(painCave.errMsg,
660			"Constraint failure in constrainB, too many iterations: %d\n",
661			iteration);
662	mmeineke	558	painCave.isFatal = 1;
663			simError();
664	tim	725	}
665	mmeineke	558	}
666
667	tim	725	template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
668			double angle, double ji[3],
669			double A[3][3]){
670			int i, j, k;
671	mmeineke	558	double sinAngle;
672			double cosAngle;
673			double angleSqr;
674			double angleSqrOver4;
675			double top, bottom;
676			double rot[3][3];
677			double tempA[3][3];
678			double tempJ[3];
679
680			// initialize the tempA
681
682	tim	725	for (i = 0; i < 3; i++){
683			for (j = 0; j < 3; j++){
684	gezelter	600	tempA[j][i] = A[i][j];
685	mmeineke	558	}
686			}
687
688			// initialize the tempJ
689
690	tim	725	for (i = 0; i < 3; i++)
691			tempJ[i] = ji[i];
692
693	mmeineke	558	// initalize rot as a unit matrix
694
695			rot[0][0] = 1.0;
696			rot[0][1] = 0.0;
697			rot[0][2] = 0.0;
698
699			rot[1][0] = 0.0;
700			rot[1][1] = 1.0;
701			rot[1][2] = 0.0;
702	tim	725
703	mmeineke	558	rot[2][0] = 0.0;
704			rot[2][1] = 0.0;
705			rot[2][2] = 1.0;
706	tim	725
707	mmeineke	558	// use a small angle aproximation for sin and cosine
708
709	tim	725	angleSqr = angle * angle;
710	mmeineke	558	angleSqrOver4 = angleSqr / 4.0;
711			top = 1.0 - angleSqrOver4;
712			bottom = 1.0 + angleSqrOver4;
713
714			cosAngle = top / bottom;
715			sinAngle = angle / bottom;
716
717			rot[axes1][axes1] = cosAngle;
718			rot[axes2][axes2] = cosAngle;
719
720			rot[axes1][axes2] = sinAngle;
721			rot[axes2][axes1] = -sinAngle;
722	tim	725
723	mmeineke	558	// rotate the momentum acoording to: ji[] = rot[][] * ji[]
724	tim	725
725			for (i = 0; i < 3; i++){
726	mmeineke	558	ji[i] = 0.0;
727	tim	725	for (k = 0; k < 3; k++){
728	mmeineke	558	ji[i] += rot[i][k] * tempJ[k];
729			}
730			}
731
732			// rotate the Rotation matrix acording to:
733			// A[][] = A[][] * transpose(rot[][])
734
735
736	mmeineke	561	// NOte for as yet unknown reason, we are performing the
737	mmeineke	558	// calculation as:
738			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
739
740	tim	725	for (i = 0; i < 3; i++){
741			for (j = 0; j < 3; j++){
742	gezelter	600	A[j][i] = 0.0;
743	tim	725	for (k = 0; k < 3; k++){
744			A[j][i] += tempA[i][k] * rot[j][k];
745	mmeineke	558	}
746			}
747			}
748			}
749	tim	677
750	tim	725	template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
751			myFF->doForces(calcPot, calcStress);
752	tim	677	}
753
754			template<typename T> void Integrator<T>::thermalize(){
755	tim	725	tStats->velocitize();
756	tim	677	}