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 currSample;
  double currThermal;
  double currStatus;

  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;
  currThermal = thermalTime;
  currStatus = statusTime;
  
  calcPot     = 0;
  calcStress  = 0;
  currSample  = sampleTime + info->getTime();
  currThermal = thermalTime+ info->getTime();
  currStatus  = statusTime + 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;
    } 

#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:	733
Committed:	Wed Aug 27 19:23:29 2003 UTC (22 years, 2 months ago) by tim
Original Path:	*trunk/OOPSE/libmdtools/Integrator.cpp*
File size:	16232 byte(s)
Log Message:	fix bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we turn on the optimization flag, it causes a seg fault
#	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
157			double currSample;
158			double currThermal;
159			double currStatus;
160
161			int calcPot, calcStress;
162			int isError;
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	mmeineke	558	DirectionalAtom* dAtom;
170	mmeineke	561
171			dt = info->dt;
172	mmeineke	558	dt2 = 0.5 * dt;
173
174			// initialize the forces before the first step
175
176	tim	677	calcForce(1, 1);
177	tim	733
178	tim	725	if (info->setTemp){
179	tim	677	thermalize();
180	mmeineke	558	}
181	tim	725
182			calcPot = 0;
183			calcStress = 0;
184			currSample = sampleTime;
185			currThermal = thermalTime;
186			currStatus = statusTime;
187	mmeineke	558
188			calcPot = 0;
189			calcStress = 0;
190	mmeineke	711	currSample = sampleTime + info->getTime();
191			currThermal = thermalTime+ info->getTime();
192			currStatus = statusTime + info->getTime();
193	mmeineke	558
194	tim	725	dumpOut->writeDump(info->getTime());
195			statOut->writeStat(info->getTime());
196	mmeineke	559
197			readyCheck();
198
199			#ifdef IS_MPI
200	tim	725	strcpy(checkPointMsg, "The integrator is ready to go.");
201	mmeineke	559	MPIcheckPoint();
202			#endif // is_mpi
203
204	tim	725	while (info->getTime() < runTime){
205			if ((info->getTime() + dt) >= currStatus){
206	mmeineke	558	calcPot = 1;
207			calcStress = 1;
208			}
209	mmeineke	561
210	tim	725	integrateStep(calcPot, calcStress);
211
212	mmeineke	643	info->incrTime(dt);
213	mmeineke	558
214	tim	725	if (info->setTemp){
215			if (info->getTime() >= currThermal){
216			thermalize();
217			currThermal += thermalTime;
218	mmeineke	558	}
219			}
220
221	tim	725	if (info->getTime() >= currSample){
222			dumpOut->writeDump(info->getTime());
223	mmeineke	558	currSample += sampleTime;
224			}
225
226	tim	725	if (info->getTime() >= currStatus){
227			statOut->writeStat(info->getTime());
228	mmeineke	558	calcPot = 0;
229			calcStress = 0;
230			currStatus += statusTime;
231			}
232	mmeineke	559
233			#ifdef IS_MPI
234	tim	725	strcpy(checkPointMsg, "successfully took a time step.");
235	mmeineke	559	MPIcheckPoint();
236			#endif // is_mpi
237	mmeineke	558	}
238
239	mmeineke	643	dumpOut->writeFinal(info->getTime());
240	mmeineke	558
241	mmeineke	561	delete dumpOut;
242			delete statOut;
243	mmeineke	558	}
244
245	tim	725	template<typename T> void Integrator<T>::integrateStep(int calcPot,
246			int calcStress){
247	mmeineke	558	// Position full step, and velocity half step
248	tim	725	preMove();
249	mmeineke	558
250			moveA();
251
252	tim	725	if (nConstrained){
253			constrainA();
254			}
255
256
257	mmeineke	614	#ifdef IS_MPI
258	tim	725	strcpy(checkPointMsg, "Succesful moveA\n");
259	mmeineke	614	MPIcheckPoint();
260			#endif // is_mpi
261
262	tim	725
263	mmeineke	558	// calc forces
264
265	tim	725	calcForce(calcPot, calcStress);
266	mmeineke	558
267	mmeineke	614	#ifdef IS_MPI
268	tim	725	strcpy(checkPointMsg, "Succesful doForces\n");
269	mmeineke	614	MPIcheckPoint();
270			#endif // is_mpi
271
272	tim	725
273	mmeineke	558	// finish the velocity half step
274	tim	725
275	mmeineke	558	moveB();
276	tim	725
277			if (nConstrained){
278			constrainB();
279			}
280
281	mmeineke	614	#ifdef IS_MPI
282	tim	725	strcpy(checkPointMsg, "Succesful moveB\n");
283	mmeineke	614	MPIcheckPoint();
284			#endif // is_mpi
285	mmeineke	558	}
286
287
288	tim	725	template<typename T> void Integrator<T>::moveA(void){
289	gezelter	600	int i, j;
290	mmeineke	558	DirectionalAtom* dAtom;
291	gezelter	600	double Tb[3], ji[3];
292			double A[3][3], I[3][3];
293	mmeineke	561	double angle;
294	gezelter	600	double vel[3], pos[3], frc[3];
295			double mass;
296	mmeineke	558
297	tim	725	for (i = 0; i < nAtoms; i++){
298			atoms[i]->getVel(vel);
299			atoms[i]->getPos(pos);
300			atoms[i]->getFrc(frc);
301	mmeineke	567
302	gezelter	600	mass = atoms[i]->getMass();
303	mmeineke	594
304	tim	725	for (j = 0; j < 3; j++){
305	gezelter	600	// velocity half step
306	tim	725	vel[j] += (dt2 * frc[j] / mass) * eConvert;
307	gezelter	600	// position whole step
308			pos[j] += dt * vel[j];
309			}
310	mmeineke	594
311	tim	725	atoms[i]->setVel(vel);
312			atoms[i]->setPos(pos);
313	gezelter	600
314	tim	725	if (atoms[i]->isDirectional()){
315			dAtom = (DirectionalAtom *) atoms[i];
316	mmeineke	558
317			// get and convert the torque to body frame
318	mmeineke	597
319	tim	725	dAtom->getTrq(Tb);
320			dAtom->lab2Body(Tb);
321
322	mmeineke	558	// get the angular momentum, and propagate a half step
323	gezelter	600
324	tim	725	dAtom->getJ(ji);
325	gezelter	600
326	tim	725	for (j = 0; j < 3; j++)
327	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
328	tim	725
329	mmeineke	558	// use the angular velocities to propagate the rotation matrix a
330			// full time step
331	gezelter	600
332			dAtom->getA(A);
333			dAtom->getI(I);
334	tim	725
335	mmeineke	558	// rotate about the x-axis
336	gezelter	600	angle = dt2 * ji[0] / I[0][0];
337	tim	725	this->rotate(1, 2, angle, ji, A);
338	mmeineke	597
339	mmeineke	558	// rotate about the y-axis
340	gezelter	600	angle = dt2 * ji[1] / I[1][1];
341	tim	725	this->rotate(2, 0, angle, ji, A);
342
343	mmeineke	558	// rotate about the z-axis
344	gezelter	600	angle = dt * ji[2] / I[2][2];
345	tim	725	this->rotate(0, 1, angle, ji, A);
346
347	mmeineke	558	// rotate about the y-axis
348	gezelter	600	angle = dt2 * ji[1] / I[1][1];
349	tim	725	this->rotate(2, 0, angle, ji, A);
350
351			// rotate about the x-axis
352	gezelter	600	angle = dt2 * ji[0] / I[0][0];
353	tim	725	this->rotate(1, 2, angle, ji, A);
354	mmeineke	597
355	tim	725
356			dAtom->setJ(ji);
357			dAtom->setA(A);
358			}
359	mmeineke	558	}
360			}
361
362
363	tim	725	template<typename T> void Integrator<T>::moveB(void){
364	gezelter	600	int i, j;
365	mmeineke	558	DirectionalAtom* dAtom;
366	gezelter	600	double Tb[3], ji[3];
367			double vel[3], frc[3];
368			double mass;
369	mmeineke	558
370	tim	725	for (i = 0; i < nAtoms; i++){
371			atoms[i]->getVel(vel);
372			atoms[i]->getFrc(frc);
373	mmeineke	558
374	gezelter	600	mass = atoms[i]->getMass();
375
376	mmeineke	558	// velocity half step
377	tim	725	for (j = 0; j < 3; j++)
378			vel[j] += (dt2 * frc[j] / mass) * eConvert;
379	gezelter	600
380	tim	725	atoms[i]->setVel(vel);
381	mmeineke	597
382	tim	725	if (atoms[i]->isDirectional()){
383			dAtom = (DirectionalAtom *) atoms[i];
384
385	gezelter	600	// get and convert the torque to body frame
386
387	tim	725	dAtom->getTrq(Tb);
388			dAtom->lab2Body(Tb);
389	gezelter	600
390			// get the angular momentum, and propagate a half step
391
392	tim	725	dAtom->getJ(ji);
393	gezelter	600
394	tim	725	for (j = 0; j < 3; j++)
395	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
396	mmeineke	597
397	tim	725
398			dAtom->setJ(ji);
399	mmeineke	558	}
400			}
401			}
402
403	tim	725	template<typename T> void Integrator<T>::preMove(void){
404	gezelter	600	int i, j;
405			double pos[3];
406	mmeineke	558
407	tim	725	if (nConstrained){
408			for (i = 0; i < nAtoms; i++){
409			atoms[i]->getPos(pos);
410	mmeineke	561
411	tim	725	for (j = 0; j < 3; j++){
412			oldPos[3 * i + j] = pos[j];
413	gezelter	600	}
414			}
415	tim	725	}
416	gezelter	600	}
417
418	tim	645	template<typename T> void Integrator<T>::constrainA(){
419	tim	725	int i, j, k;
420	mmeineke	558	int done;
421	gezelter	600	double posA[3], posB[3];
422			double velA[3], velB[3];
423	mmeineke	572	double pab[3];
424			double rab[3];
425	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
426	mmeineke	558	double rma, rmb;
427			double dx, dy, dz;
428	mmeineke	561	double rpab;
429	mmeineke	558	double rabsq, pabsq, rpabsq;
430			double diffsq;
431			double gab;
432			int iteration;
433
434	tim	725	for (i = 0; i < nAtoms; i++){
435	mmeineke	558	moving[i] = 0;
436	tim	725	moved[i] = 1;
437	mmeineke	558	}
438	mmeineke	567
439	mmeineke	558	iteration = 0;
440			done = 0;
441	tim	725	while (!done && (iteration < maxIteration)){
442	mmeineke	558	done = 1;
443	tim	725	for (i = 0; i < nConstrained; i++){
444	mmeineke	558	a = constrainedA[i];
445			b = constrainedB[i];
446	mmeineke	563
447	tim	725	ax = (a * 3) + 0;
448			ay = (a * 3) + 1;
449			az = (a * 3) + 2;
450	mmeineke	563
451	tim	725	bx = (b * 3) + 0;
452			by = (b * 3) + 1;
453			bz = (b * 3) + 2;
454
455			if (moved[a] \|\| moved[b]){
456			atoms[a]->getPos(posA);
457			atoms[b]->getPos(posB);
458
459			for (j = 0; j < 3; j++)
460	gezelter	600	pab[j] = posA[j] - posB[j];
461	mmeineke	567
462	tim	725	//periodic boundary condition
463	mmeineke	567
464	tim	725	info->wrapVector(pab);
465	mmeineke	572
466	tim	725	pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
467	mmeineke	558
468	tim	725	rabsq = constrainedDsqr[i];
469			diffsq = rabsq - pabsq;
470	mmeineke	567
471	tim	725	// the original rattle code from alan tidesley
472			if (fabs(diffsq) > (tol * rabsq * 2)){
473			rab[0] = oldPos[ax] - oldPos[bx];
474			rab[1] = oldPos[ay] - oldPos[by];
475			rab[2] = oldPos[az] - oldPos[bz];
476	mmeineke	558
477	tim	725	info->wrapVector(rab);
478	mmeineke	567
479	tim	725	rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
480	mmeineke	558
481	tim	725	rpabsq = rpab * rpab;
482	mmeineke	558
483	mmeineke	563
484	tim	725	if (rpabsq < (rabsq * -diffsq)){
485	mmeineke	558	#ifdef IS_MPI
486	tim	725	a = atoms[a]->getGlobalIndex();
487			b = atoms[b]->getGlobalIndex();
488	mmeineke	558	#endif //is_mpi
489	tim	725	sprintf(painCave.errMsg,
490			"Constraint failure in constrainA at atom %d and %d.\n", a,
491			b);
492			painCave.isFatal = 1;
493			simError();
494			}
495	mmeineke	558
496	tim	725	rma = 1.0 / atoms[a]->getMass();
497			rmb = 1.0 / atoms[b]->getMass();
498	mmeineke	567
499	tim	725	gab = diffsq / (2.0 * (rma + rmb) * rpab);
500	mmeineke	567
501	mmeineke	572	dx = rab[0] * gab;
502			dy = rab[1] * gab;
503			dz = rab[2] * gab;
504	mmeineke	558
505	tim	725	posA[0] += rma * dx;
506			posA[1] += rma * dy;
507			posA[2] += rma * dz;
508	mmeineke	558
509	tim	725	atoms[a]->setPos(posA);
510	mmeineke	558
511	tim	725	posB[0] -= rmb * dx;
512			posB[1] -= rmb * dy;
513			posB[2] -= rmb * dz;
514	gezelter	600
515	tim	725	atoms[b]->setPos(posB);
516	gezelter	600
517	mmeineke	558	dx = dx / dt;
518			dy = dy / dt;
519			dz = dz / dt;
520
521	tim	725	atoms[a]->getVel(velA);
522	mmeineke	558
523	tim	725	velA[0] += rma * dx;
524			velA[1] += rma * dy;
525			velA[2] += rma * dz;
526	mmeineke	558
527	tim	725	atoms[a]->setVel(velA);
528	gezelter	600
529	tim	725	atoms[b]->getVel(velB);
530	gezelter	600
531	tim	725	velB[0] -= rmb * dx;
532			velB[1] -= rmb * dy;
533			velB[2] -= rmb * dz;
534	gezelter	600
535	tim	725	atoms[b]->setVel(velB);
536	gezelter	600
537	tim	725	moving[a] = 1;
538			moving[b] = 1;
539			done = 0;
540			}
541	mmeineke	558	}
542			}
543	tim	725
544			for (i = 0; i < nAtoms; i++){
545	mmeineke	558	moved[i] = moving[i];
546			moving[i] = 0;
547			}
548
549			iteration++;
550			}
551
552	tim	725	if (!done){
553			sprintf(painCave.errMsg,
554			"Constraint failure in constrainA, too many iterations: %d\n",
555			iteration);
556	mmeineke	558	painCave.isFatal = 1;
557			simError();
558			}
559			}
560
561	tim	725	template<typename T> void Integrator<T>::constrainB(void){
562			int i, j, k;
563	mmeineke	558	int done;
564	gezelter	600	double posA[3], posB[3];
565			double velA[3], velB[3];
566	mmeineke	558	double vxab, vyab, vzab;
567	mmeineke	572	double rab[3];
568	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
569	mmeineke	558	double rma, rmb;
570			double dx, dy, dz;
571			double rabsq, pabsq, rvab;
572			double diffsq;
573			double gab;
574			int iteration;
575
576	tim	725	for (i = 0; i < nAtoms; i++){
577	mmeineke	558	moving[i] = 0;
578			moved[i] = 1;
579			}
580
581			done = 0;
582	mmeineke	561	iteration = 0;
583	tim	725	while (!done && (iteration < maxIteration)){
584	mmeineke	567	done = 1;
585
586	tim	725	for (i = 0; i < nConstrained; i++){
587	mmeineke	558	a = constrainedA[i];
588			b = constrainedB[i];
589
590	tim	725	ax = (a * 3) + 0;
591			ay = (a * 3) + 1;
592			az = (a * 3) + 2;
593	mmeineke	563
594	tim	725	bx = (b * 3) + 0;
595			by = (b * 3) + 1;
596			bz = (b * 3) + 2;
597	mmeineke	563
598	tim	725	if (moved[a] \|\| moved[b]){
599			atoms[a]->getVel(velA);
600			atoms[b]->getVel(velB);
601	mmeineke	558
602	tim	725	vxab = velA[0] - velB[0];
603			vyab = velA[1] - velB[1];
604			vzab = velA[2] - velB[2];
605	gezelter	600
606	tim	725	atoms[a]->getPos(posA);
607			atoms[b]->getPos(posB);
608	gezelter	600
609	tim	725	for (j = 0; j < 3; j++)
610	gezelter	600	rab[j] = posA[j] - posB[j];
611	mmeineke	558
612	tim	725	info->wrapVector(rab);
613	mmeineke	558
614	tim	725	rma = 1.0 / atoms[a]->getMass();
615			rmb = 1.0 / atoms[b]->getMass();
616	mmeineke	558
617	tim	725	rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
618	gezelter	600
619	tim	725	gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
620	gezelter	600
621	tim	725	if (fabs(gab) > tol){
622			dx = rab[0] * gab;
623			dy = rab[1] * gab;
624			dz = rab[2] * gab;
625
626			velA[0] += rma * dx;
627			velA[1] += rma * dy;
628			velA[2] += rma * dz;
629
630			atoms[a]->setVel(velA);
631
632			velB[0] -= rmb * dx;
633			velB[1] -= rmb * dy;
634			velB[2] -= rmb * dz;
635
636			atoms[b]->setVel(velB);
637
638			moving[a] = 1;
639			moving[b] = 1;
640			done = 0;
641			}
642	mmeineke	558	}
643			}
644
645	tim	725	for (i = 0; i < nAtoms; i++){
646	mmeineke	558	moved[i] = moving[i];
647			moving[i] = 0;
648			}
649	tim	725
650	mmeineke	558	iteration++;
651			}
652
653	tim	725	if (!done){
654			sprintf(painCave.errMsg,
655			"Constraint failure in constrainB, too many iterations: %d\n",
656			iteration);
657	mmeineke	558	painCave.isFatal = 1;
658			simError();
659	tim	725	}
660	mmeineke	558	}
661
662	tim	725	template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
663			double angle, double ji[3],
664			double A[3][3]){
665			int i, j, k;
666	mmeineke	558	double sinAngle;
667			double cosAngle;
668			double angleSqr;
669			double angleSqrOver4;
670			double top, bottom;
671			double rot[3][3];
672			double tempA[3][3];
673			double tempJ[3];
674
675			// initialize the tempA
676
677	tim	725	for (i = 0; i < 3; i++){
678			for (j = 0; j < 3; j++){
679	gezelter	600	tempA[j][i] = A[i][j];
680	mmeineke	558	}
681			}
682
683			// initialize the tempJ
684
685	tim	725	for (i = 0; i < 3; i++)
686			tempJ[i] = ji[i];
687
688	mmeineke	558	// initalize rot as a unit matrix
689
690			rot[0][0] = 1.0;
691			rot[0][1] = 0.0;
692			rot[0][2] = 0.0;
693
694			rot[1][0] = 0.0;
695			rot[1][1] = 1.0;
696			rot[1][2] = 0.0;
697	tim	725
698	mmeineke	558	rot[2][0] = 0.0;
699			rot[2][1] = 0.0;
700			rot[2][2] = 1.0;
701	tim	725
702	mmeineke	558	// use a small angle aproximation for sin and cosine
703
704	tim	725	angleSqr = angle * angle;
705	mmeineke	558	angleSqrOver4 = angleSqr / 4.0;
706			top = 1.0 - angleSqrOver4;
707			bottom = 1.0 + angleSqrOver4;
708
709			cosAngle = top / bottom;
710			sinAngle = angle / bottom;
711
712			rot[axes1][axes1] = cosAngle;
713			rot[axes2][axes2] = cosAngle;
714
715			rot[axes1][axes2] = sinAngle;
716			rot[axes2][axes1] = -sinAngle;
717	tim	725
718	mmeineke	558	// rotate the momentum acoording to: ji[] = rot[][] * ji[]
719	tim	725
720			for (i = 0; i < 3; i++){
721	mmeineke	558	ji[i] = 0.0;
722	tim	725	for (k = 0; k < 3; k++){
723	mmeineke	558	ji[i] += rot[i][k] * tempJ[k];
724			}
725			}
726
727			// rotate the Rotation matrix acording to:
728			// A[][] = A[][] * transpose(rot[][])
729
730
731	mmeineke	561	// NOte for as yet unknown reason, we are performing the
732	mmeineke	558	// calculation as:
733			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
734
735	tim	725	for (i = 0; i < 3; i++){
736			for (j = 0; j < 3; j++){
737	gezelter	600	A[j][i] = 0.0;
738	tim	725	for (k = 0; k < 3; k++){
739			A[j][i] += tempA[i][k] * rot[j][k];
740	mmeineke	558	}
741			}
742			}
743			}
744	tim	677
745	tim	725	template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
746			myFF->doForces(calcPot, calcStress);
747	tim	677	}
748
749			template<typename T> void Integrator<T>::thermalize(){
750	tim	725	tStats->velocitize();
751	tim	677	}