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;
  }
  
  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;

  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
  }

  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();


#ifdef IS_MPI
  strcpy(checkPointMsg, "Succesful moveA\n");
  MPIcheckPoint();
#endif // is_mpi


  // calc forces

  calcForce(calcPot, calcStress);

#ifdef IS_MPI
  strcpy(checkPointMsg, "Succesful doForces\n");
  MPIcheckPoint();
#endif // is_mpi


  // finish the velocity  half step

  moveB();


#ifdef IS_MPI
  strcpy(checkPointMsg, "Succesful moveB\n");
  MPIcheckPoint();
#endif // is_mpi
}


template<typename T> void Integrator<T>::moveA(void){
  int i, j;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3];
  double vel[3], pos[3], frc[3];
  double mass;

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

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

    for (j = 0; j < 3; j++){
      // velocity half step
      vel[j] += (dt2 * frc[j] / mass) * eConvert;
      // position whole step
      pos[j] += dt * vel[j];
    }

    atoms[i]->setVel(vel);
    atoms[i]->setPos(pos);

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

      // get and convert the torque to body frame

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

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

      dAtom->getJ(ji);

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

      this->rotationPropagation( dAtom, ji );

      dAtom->setJ(ji);
    }
  }

  if (nConstrained){
    constrainA();
  }
}


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

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

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

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

    atoms[i]->setVel(vel);

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

      // get and convert the torque to body frame      

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

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

      dAtom->getJ(ji);

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


      dAtom->setJ(ji);
    }
  }

  if (nConstrained){
    constrainB();
  }
}

template<typename T> void Integrator<T>::preMove(void){
  int i, j;
  double pos[3];

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

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

template<typename T> void Integrator<T>::constrainA(){
  int i, j, 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>::rotationPropagation
( DirectionalAtom* dAtom, double ji[3] ){

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

  // use the angular velocities to propagate the rotation matrix a
  // full time step

  dAtom->getA(A);
  dAtom->getI(I);
  
  // rotate about the x-axis      
  angle = dt2 * ji[0] / I[0][0];
  this->rotate( 1, 2, angle, ji, A ); 
  
  // rotate about the y-axis
  angle = dt2 * ji[1] / I[1][1];
  this->rotate( 2, 0, angle, ji, A );
  
  // rotate about the z-axis
  angle = dt * ji[2] / I[2][2];
  this->rotate( 0, 1, angle, ji, A);
  
  // rotate about the y-axis
  angle = dt2 * ji[1] / I[1][1];
  this->rotate( 2, 0, angle, ji, A );
  
  // rotate about the x-axis
  angle = dt2 * ji[0] / I[0][0];
  this->rotate( 1, 2, angle, ji, A );
  
  dAtom->setA( A  );    
}

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

  // initialize the tempA

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

  // initialize the tempJ

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

  // initalize rot as a unit matrix

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

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

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

  // use a small angle aproximation for sin and cosine

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

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

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

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

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

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

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


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

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

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

template<typename T> void Integrator<T>::thermalize(){
  tStats->velocitize();
}

template<typename T> double Integrator<T>::getConservedQuantity(void){
  return tStats->getTotalE();
}
Revision:	784
Committed:	Wed Sep 24 19:34:39 2003 UTC (20 years, 9 months ago) by mmeineke
File size:	16659 byte(s)
Log Message:	moved readyCheck in the integrator so that it is called before the first Statistics are written.
#	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	782
29	mmeineke	558	nAtoms = info->n_atoms;
30
31			// check for constraints
32	tim	725
33			constrainedA = NULL;
34			constrainedB = NULL;
35	mmeineke	558	constrainedDsqr = NULL;
36	tim	725	moving = NULL;
37			moved = NULL;
38			oldPos = NULL;
39
40	mmeineke	558	nConstrained = 0;
41
42			checkConstraints();
43			}
44
45	tim	725	template<typename T> Integrator<T>::~Integrator(){
46			if (nConstrained){
47	mmeineke	558	delete[] constrainedA;
48			delete[] constrainedB;
49			delete[] constrainedDsqr;
50			delete[] moving;
51			delete[] moved;
52	mmeineke	561	delete[] oldPos;
53	mmeineke	558	}
54			}
55
56	tim	725	template<typename T> void Integrator<T>::checkConstraints(void){
57	mmeineke	558	isConstrained = 0;
58
59	tim	725	Constraint* temp_con;
60			Constraint* dummy_plug;
61	mmeineke	558	temp_con = new Constraint[info->n_SRI];
62			nConstrained = 0;
63			int constrained = 0;
64	tim	725
65	mmeineke	558	SRI** theArray;
66	tim	725	for (int i = 0; i < nMols; i++){
67			theArray = (SRI * *) molecules[i].getMyBonds();
68			for (int j = 0; j < molecules[i].getNBonds(); j++){
69	mmeineke	558	constrained = theArray[j]->is_constrained();
70	mmeineke	594
71	tim	725	if (constrained){
72			dummy_plug = theArray[j]->get_constraint();
73			temp_con[nConstrained].set_a(dummy_plug->get_a());
74			temp_con[nConstrained].set_b(dummy_plug->get_b());
75			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
76	mmeineke	594
77	tim	725	nConstrained++;
78			constrained = 0;
79			}
80	mmeineke	558	}
81
82	tim	725	theArray = (SRI * *) molecules[i].getMyBends();
83			for (int j = 0; j < molecules[i].getNBends(); j++){
84	mmeineke	558	constrained = theArray[j]->is_constrained();
85	tim	725
86			if (constrained){
87			dummy_plug = theArray[j]->get_constraint();
88			temp_con[nConstrained].set_a(dummy_plug->get_a());
89			temp_con[nConstrained].set_b(dummy_plug->get_b());
90			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
91
92			nConstrained++;
93			constrained = 0;
94	mmeineke	558	}
95			}
96
97	tim	725	theArray = (SRI * *) molecules[i].getMyTorsions();
98			for (int j = 0; j < molecules[i].getNTorsions(); j++){
99	mmeineke	558	constrained = theArray[j]->is_constrained();
100	tim	725
101			if (constrained){
102			dummy_plug = theArray[j]->get_constraint();
103			temp_con[nConstrained].set_a(dummy_plug->get_a());
104			temp_con[nConstrained].set_b(dummy_plug->get_b());
105			temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
106
107			nConstrained++;
108			constrained = 0;
109	mmeineke	558	}
110			}
111			}
112
113	tim	725	if (nConstrained > 0){
114	mmeineke	558	isConstrained = 1;
115
116	tim	725	if (constrainedA != NULL)
117			delete[] constrainedA;
118			if (constrainedB != NULL)
119			delete[] constrainedB;
120			if (constrainedDsqr != NULL)
121			delete[] constrainedDsqr;
122	mmeineke	558
123	tim	725	constrainedA = new int[nConstrained];
124			constrainedB = new int[nConstrained];
125	mmeineke	558	constrainedDsqr = new double[nConstrained];
126	tim	725
127			for (int i = 0; i < nConstrained; i++){
128	mmeineke	558	constrainedA[i] = temp_con[i].get_a();
129			constrainedB[i] = temp_con[i].get_b();
130			constrainedDsqr[i] = temp_con[i].get_dsqr();
131			}
132
133	tim	725
134	mmeineke	558	// save oldAtoms to check for lode balanceing later on.
135	tim	725
136	mmeineke	558	oldAtoms = nAtoms;
137	tim	725
138	mmeineke	558	moving = new int[nAtoms];
139	tim	725	moved = new int[nAtoms];
140	mmeineke	558
141	tim	725	oldPos = new double[nAtoms * 3];
142	mmeineke	558	}
143	tim	725
144	mmeineke	558	delete[] temp_con;
145			}
146
147
148	tim	725	template<typename T> void Integrator<T>::integrate(void){
149	mmeineke	558	int i, j; // loop counters
150
151	tim	725	double runTime = info->run_time;
152			double sampleTime = info->sampleTime;
153			double statusTime = info->statusTime;
154	mmeineke	558	double thermalTime = info->thermalTime;
155	mmeineke	746	double resetTime = info->resetTime;
156	mmeineke	558
157	mmeineke	746
158	mmeineke	558	double currSample;
159			double currThermal;
160			double currStatus;
161	mmeineke	746	double currReset;
162
163	mmeineke	558	int calcPot, calcStress;
164			int isError;
165
166	tim	725	tStats = new Thermo(info);
167			statOut = new StatWriter(info);
168			dumpOut = new DumpWriter(info);
169	mmeineke	558
170	mmeineke	561	atoms = info->atoms;
171	mmeineke	558	DirectionalAtom* dAtom;
172	mmeineke	561
173			dt = info->dt;
174	mmeineke	558	dt2 = 0.5 * dt;
175
176	mmeineke	784	readyCheck();
177
178	mmeineke	558	// initialize the forces before the first step
179
180	tim	677	calcForce(1, 1);
181	tim	781
182			if (nConstrained){
183			preMove();
184			constrainA();
185			calcForce(1, 1);
186			constrainB();
187			}
188	tim	733
189	tim	725	if (info->setTemp){
190	tim	677	thermalize();
191	mmeineke	558	}
192	tim	725
193	mmeineke	558	calcPot = 0;
194			calcStress = 0;
195	mmeineke	711	currSample = sampleTime + info->getTime();
196			currThermal = thermalTime+ info->getTime();
197			currStatus = statusTime + info->getTime();
198	mmeineke	746	currReset = resetTime + info->getTime();
199	mmeineke	558
200	tim	725	dumpOut->writeDump(info->getTime());
201			statOut->writeStat(info->getTime());
202	mmeineke	559
203
204	mmeineke	784
205	mmeineke	559	#ifdef IS_MPI
206	tim	725	strcpy(checkPointMsg, "The integrator is ready to go.");
207	mmeineke	559	MPIcheckPoint();
208			#endif // is_mpi
209
210	tim	725	while (info->getTime() < runTime){
211			if ((info->getTime() + dt) >= currStatus){
212	mmeineke	558	calcPot = 1;
213			calcStress = 1;
214			}
215	mmeineke	561
216	tim	725	integrateStep(calcPot, calcStress);
217
218	mmeineke	643	info->incrTime(dt);
219	mmeineke	558
220	tim	725	if (info->setTemp){
221			if (info->getTime() >= currThermal){
222			thermalize();
223			currThermal += thermalTime;
224	mmeineke	558	}
225			}
226
227	tim	725	if (info->getTime() >= currSample){
228			dumpOut->writeDump(info->getTime());
229	mmeineke	558	currSample += sampleTime;
230			}
231
232	tim	725	if (info->getTime() >= currStatus){
233			statOut->writeStat(info->getTime());
234	mmeineke	558	calcPot = 0;
235			calcStress = 0;
236			currStatus += statusTime;
237			}
238	mmeineke	559
239	mmeineke	746	if (info->resetIntegrator){
240			if (info->getTime() >= currReset){
241			this->resetIntegrator();
242			currReset += resetTime;
243			}
244			}
245
246	mmeineke	559	#ifdef IS_MPI
247	tim	725	strcpy(checkPointMsg, "successfully took a time step.");
248	mmeineke	559	MPIcheckPoint();
249			#endif // is_mpi
250	mmeineke	558	}
251
252	mmeineke	643	dumpOut->writeFinal(info->getTime());
253	mmeineke	558
254	mmeineke	561	delete dumpOut;
255			delete statOut;
256	mmeineke	558	}
257
258	tim	725	template<typename T> void Integrator<T>::integrateStep(int calcPot,
259			int calcStress){
260	mmeineke	558	// Position full step, and velocity half step
261	tim	725	preMove();
262	mmeineke	558
263			moveA();
264
265	tim	725
266
267	mmeineke	768
268	mmeineke	614	#ifdef IS_MPI
269	tim	725	strcpy(checkPointMsg, "Succesful moveA\n");
270	mmeineke	614	MPIcheckPoint();
271			#endif // is_mpi
272
273	tim	725
274	mmeineke	558	// calc forces
275
276	tim	725	calcForce(calcPot, calcStress);
277	mmeineke	558
278	mmeineke	614	#ifdef IS_MPI
279	tim	725	strcpy(checkPointMsg, "Succesful doForces\n");
280	mmeineke	614	MPIcheckPoint();
281			#endif // is_mpi
282
283	tim	725
284	mmeineke	558	// finish the velocity half step
285	tim	725
286	mmeineke	558	moveB();
287	tim	725
288
289	mmeineke	768
290	mmeineke	614	#ifdef IS_MPI
291	tim	725	strcpy(checkPointMsg, "Succesful moveB\n");
292	mmeineke	614	MPIcheckPoint();
293			#endif // is_mpi
294	mmeineke	558	}
295
296
297	tim	725	template<typename T> void Integrator<T>::moveA(void){
298	gezelter	600	int i, j;
299	mmeineke	558	DirectionalAtom* dAtom;
300	gezelter	600	double Tb[3], ji[3];
301			double vel[3], pos[3], frc[3];
302			double mass;
303	mmeineke	558
304	tim	725	for (i = 0; i < nAtoms; i++){
305			atoms[i]->getVel(vel);
306			atoms[i]->getPos(pos);
307			atoms[i]->getFrc(frc);
308	mmeineke	567
309	gezelter	600	mass = atoms[i]->getMass();
310	mmeineke	594
311	tim	725	for (j = 0; j < 3; j++){
312	gezelter	600	// velocity half step
313	tim	725	vel[j] += (dt2 * frc[j] / mass) * eConvert;
314	gezelter	600	// position whole step
315			pos[j] += dt * vel[j];
316			}
317	mmeineke	594
318	tim	725	atoms[i]->setVel(vel);
319			atoms[i]->setPos(pos);
320	gezelter	600
321	tim	725	if (atoms[i]->isDirectional()){
322			dAtom = (DirectionalAtom *) atoms[i];
323	mmeineke	558
324			// get and convert the torque to body frame
325	mmeineke	597
326	tim	725	dAtom->getTrq(Tb);
327			dAtom->lab2Body(Tb);
328
329	mmeineke	558	// get the angular momentum, and propagate a half step
330	gezelter	600
331	tim	725	dAtom->getJ(ji);
332	gezelter	600
333	tim	725	for (j = 0; j < 3; j++)
334	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
335	tim	725
336	mmeineke	778	this->rotationPropagation( dAtom, ji );
337	gezelter	600
338	tim	725	dAtom->setJ(ji);
339			}
340	mmeineke	558	}
341	mmeineke	768
342			if (nConstrained){
343			constrainA();
344			}
345	mmeineke	558	}
346
347
348	tim	725	template<typename T> void Integrator<T>::moveB(void){
349	gezelter	600	int i, j;
350	mmeineke	558	DirectionalAtom* dAtom;
351	gezelter	600	double Tb[3], ji[3];
352			double vel[3], frc[3];
353			double mass;
354	mmeineke	558
355	tim	725	for (i = 0; i < nAtoms; i++){
356			atoms[i]->getVel(vel);
357			atoms[i]->getFrc(frc);
358	mmeineke	558
359	gezelter	600	mass = atoms[i]->getMass();
360
361	mmeineke	558	// velocity half step
362	tim	725	for (j = 0; j < 3; j++)
363			vel[j] += (dt2 * frc[j] / mass) * eConvert;
364	gezelter	600
365	tim	725	atoms[i]->setVel(vel);
366	mmeineke	597
367	tim	725	if (atoms[i]->isDirectional()){
368			dAtom = (DirectionalAtom *) atoms[i];
369
370	gezelter	600	// get and convert the torque to body frame
371
372	tim	725	dAtom->getTrq(Tb);
373			dAtom->lab2Body(Tb);
374	gezelter	600
375			// get the angular momentum, and propagate a half step
376
377	tim	725	dAtom->getJ(ji);
378	gezelter	600
379	tim	725	for (j = 0; j < 3; j++)
380	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
381	mmeineke	597
382	tim	725
383			dAtom->setJ(ji);
384	mmeineke	558	}
385			}
386	mmeineke	768
387			if (nConstrained){
388			constrainB();
389			}
390	mmeineke	558	}
391
392	tim	725	template<typename T> void Integrator<T>::preMove(void){
393	gezelter	600	int i, j;
394			double pos[3];
395	mmeineke	558
396	tim	725	if (nConstrained){
397			for (i = 0; i < nAtoms; i++){
398			atoms[i]->getPos(pos);
399	mmeineke	561
400	tim	725	for (j = 0; j < 3; j++){
401			oldPos[3 * i + j] = pos[j];
402	gezelter	600	}
403			}
404	tim	725	}
405	gezelter	600	}
406
407	tim	645	template<typename T> void Integrator<T>::constrainA(){
408	tim	725	int i, j, k;
409	mmeineke	558	int done;
410	gezelter	600	double posA[3], posB[3];
411			double velA[3], velB[3];
412	mmeineke	572	double pab[3];
413			double rab[3];
414	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
415	mmeineke	558	double rma, rmb;
416			double dx, dy, dz;
417	mmeineke	561	double rpab;
418	mmeineke	558	double rabsq, pabsq, rpabsq;
419			double diffsq;
420			double gab;
421			int iteration;
422
423	tim	725	for (i = 0; i < nAtoms; i++){
424	mmeineke	558	moving[i] = 0;
425	tim	725	moved[i] = 1;
426	mmeineke	558	}
427	mmeineke	567
428	mmeineke	558	iteration = 0;
429			done = 0;
430	tim	725	while (!done && (iteration < maxIteration)){
431	mmeineke	558	done = 1;
432	tim	725	for (i = 0; i < nConstrained; i++){
433	mmeineke	558	a = constrainedA[i];
434			b = constrainedB[i];
435	mmeineke	563
436	tim	725	ax = (a * 3) + 0;
437			ay = (a * 3) + 1;
438			az = (a * 3) + 2;
439	mmeineke	563
440	tim	725	bx = (b * 3) + 0;
441			by = (b * 3) + 1;
442			bz = (b * 3) + 2;
443
444			if (moved[a] \|\| moved[b]){
445			atoms[a]->getPos(posA);
446			atoms[b]->getPos(posB);
447
448			for (j = 0; j < 3; j++)
449	gezelter	600	pab[j] = posA[j] - posB[j];
450	mmeineke	567
451	tim	725	//periodic boundary condition
452	mmeineke	567
453	tim	725	info->wrapVector(pab);
454	mmeineke	572
455	tim	725	pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
456	mmeineke	558
457	tim	725	rabsq = constrainedDsqr[i];
458			diffsq = rabsq - pabsq;
459	mmeineke	567
460	tim	725	// the original rattle code from alan tidesley
461			if (fabs(diffsq) > (tol * rabsq * 2)){
462			rab[0] = oldPos[ax] - oldPos[bx];
463			rab[1] = oldPos[ay] - oldPos[by];
464			rab[2] = oldPos[az] - oldPos[bz];
465	mmeineke	558
466	tim	725	info->wrapVector(rab);
467	mmeineke	567
468	tim	725	rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
469	mmeineke	558
470	tim	725	rpabsq = rpab * rpab;
471	mmeineke	558
472	mmeineke	563
473	tim	725	if (rpabsq < (rabsq * -diffsq)){
474	mmeineke	558	#ifdef IS_MPI
475	tim	725	a = atoms[a]->getGlobalIndex();
476			b = atoms[b]->getGlobalIndex();
477	mmeineke	558	#endif //is_mpi
478	tim	725	sprintf(painCave.errMsg,
479			"Constraint failure in constrainA at atom %d and %d.\n", a,
480			b);
481			painCave.isFatal = 1;
482			simError();
483			}
484	mmeineke	558
485	tim	725	rma = 1.0 / atoms[a]->getMass();
486			rmb = 1.0 / atoms[b]->getMass();
487	mmeineke	567
488	tim	725	gab = diffsq / (2.0 * (rma + rmb) * rpab);
489	mmeineke	567
490	mmeineke	572	dx = rab[0] * gab;
491			dy = rab[1] * gab;
492			dz = rab[2] * gab;
493	mmeineke	558
494	tim	725	posA[0] += rma * dx;
495			posA[1] += rma * dy;
496			posA[2] += rma * dz;
497	mmeineke	558
498	tim	725	atoms[a]->setPos(posA);
499	mmeineke	558
500	tim	725	posB[0] -= rmb * dx;
501			posB[1] -= rmb * dy;
502			posB[2] -= rmb * dz;
503	gezelter	600
504	tim	725	atoms[b]->setPos(posB);
505	gezelter	600
506	mmeineke	558	dx = dx / dt;
507			dy = dy / dt;
508			dz = dz / dt;
509
510	tim	725	atoms[a]->getVel(velA);
511	mmeineke	558
512	tim	725	velA[0] += rma * dx;
513			velA[1] += rma * dy;
514			velA[2] += rma * dz;
515	mmeineke	558
516	tim	725	atoms[a]->setVel(velA);
517	gezelter	600
518	tim	725	atoms[b]->getVel(velB);
519	gezelter	600
520	tim	725	velB[0] -= rmb * dx;
521			velB[1] -= rmb * dy;
522			velB[2] -= rmb * dz;
523	gezelter	600
524	tim	725	atoms[b]->setVel(velB);
525	gezelter	600
526	tim	725	moving[a] = 1;
527			moving[b] = 1;
528			done = 0;
529			}
530	mmeineke	558	}
531			}
532	tim	725
533			for (i = 0; i < nAtoms; i++){
534	mmeineke	558	moved[i] = moving[i];
535			moving[i] = 0;
536			}
537
538			iteration++;
539			}
540
541	tim	725	if (!done){
542			sprintf(painCave.errMsg,
543			"Constraint failure in constrainA, too many iterations: %d\n",
544			iteration);
545	mmeineke	558	painCave.isFatal = 1;
546			simError();
547			}
548	mmeineke	768
549	mmeineke	558	}
550
551	tim	725	template<typename T> void Integrator<T>::constrainB(void){
552			int i, j, k;
553	mmeineke	558	int done;
554	gezelter	600	double posA[3], posB[3];
555			double velA[3], velB[3];
556	mmeineke	558	double vxab, vyab, vzab;
557	mmeineke	572	double rab[3];
558	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
559	mmeineke	558	double rma, rmb;
560			double dx, dy, dz;
561			double rabsq, pabsq, rvab;
562			double diffsq;
563			double gab;
564			int iteration;
565
566	tim	725	for (i = 0; i < nAtoms; i++){
567	mmeineke	558	moving[i] = 0;
568			moved[i] = 1;
569			}
570
571			done = 0;
572	mmeineke	561	iteration = 0;
573	tim	725	while (!done && (iteration < maxIteration)){
574	mmeineke	567	done = 1;
575
576	tim	725	for (i = 0; i < nConstrained; i++){
577	mmeineke	558	a = constrainedA[i];
578			b = constrainedB[i];
579
580	tim	725	ax = (a * 3) + 0;
581			ay = (a * 3) + 1;
582			az = (a * 3) + 2;
583	mmeineke	563
584	tim	725	bx = (b * 3) + 0;
585			by = (b * 3) + 1;
586			bz = (b * 3) + 2;
587	mmeineke	563
588	tim	725	if (moved[a] \|\| moved[b]){
589			atoms[a]->getVel(velA);
590			atoms[b]->getVel(velB);
591	mmeineke	558
592	tim	725	vxab = velA[0] - velB[0];
593			vyab = velA[1] - velB[1];
594			vzab = velA[2] - velB[2];
595	gezelter	600
596	tim	725	atoms[a]->getPos(posA);
597			atoms[b]->getPos(posB);
598	gezelter	600
599	tim	725	for (j = 0; j < 3; j++)
600	gezelter	600	rab[j] = posA[j] - posB[j];
601	mmeineke	558
602	tim	725	info->wrapVector(rab);
603	mmeineke	558
604	tim	725	rma = 1.0 / atoms[a]->getMass();
605			rmb = 1.0 / atoms[b]->getMass();
606	mmeineke	558
607	tim	725	rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
608	gezelter	600
609	tim	725	gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
610	gezelter	600
611	tim	725	if (fabs(gab) > tol){
612			dx = rab[0] * gab;
613			dy = rab[1] * gab;
614			dz = rab[2] * gab;
615
616			velA[0] += rma * dx;
617			velA[1] += rma * dy;
618			velA[2] += rma * dz;
619
620			atoms[a]->setVel(velA);
621
622			velB[0] -= rmb * dx;
623			velB[1] -= rmb * dy;
624			velB[2] -= rmb * dz;
625
626			atoms[b]->setVel(velB);
627
628			moving[a] = 1;
629			moving[b] = 1;
630			done = 0;
631			}
632	mmeineke	558	}
633			}
634
635	tim	725	for (i = 0; i < nAtoms; i++){
636	mmeineke	558	moved[i] = moving[i];
637			moving[i] = 0;
638			}
639	tim	725
640	mmeineke	558	iteration++;
641			}
642
643	tim	725	if (!done){
644			sprintf(painCave.errMsg,
645			"Constraint failure in constrainB, too many iterations: %d\n",
646			iteration);
647	mmeineke	558	painCave.isFatal = 1;
648			simError();
649	tim	725	}
650	mmeineke	558	}
651
652	mmeineke	778	template<typename T> void Integrator<T>::rotationPropagation
653			( DirectionalAtom* dAtom, double ji[3] ){
654
655			double angle;
656			double A[3][3], I[3][3];
657
658			// use the angular velocities to propagate the rotation matrix a
659			// full time step
660
661			dAtom->getA(A);
662			dAtom->getI(I);
663
664			// rotate about the x-axis
665			angle = dt2 * ji[0] / I[0][0];
666			this->rotate( 1, 2, angle, ji, A );
667
668			// rotate about the y-axis
669			angle = dt2 * ji[1] / I[1][1];
670			this->rotate( 2, 0, angle, ji, A );
671
672			// rotate about the z-axis
673			angle = dt * ji[2] / I[2][2];
674			this->rotate( 0, 1, angle, ji, A);
675
676			// rotate about the y-axis
677			angle = dt2 * ji[1] / I[1][1];
678			this->rotate( 2, 0, angle, ji, A );
679
680			// rotate about the x-axis
681			angle = dt2 * ji[0] / I[0][0];
682			this->rotate( 1, 2, angle, ji, A );
683
684			dAtom->setA( A );
685			}
686
687	tim	725	template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
688			double angle, double ji[3],
689			double A[3][3]){
690			int i, j, k;
691	mmeineke	558	double sinAngle;
692			double cosAngle;
693			double angleSqr;
694			double angleSqrOver4;
695			double top, bottom;
696			double rot[3][3];
697			double tempA[3][3];
698			double tempJ[3];
699
700			// initialize the tempA
701
702	tim	725	for (i = 0; i < 3; i++){
703			for (j = 0; j < 3; j++){
704	gezelter	600	tempA[j][i] = A[i][j];
705	mmeineke	558	}
706			}
707
708			// initialize the tempJ
709
710	tim	725	for (i = 0; i < 3; i++)
711			tempJ[i] = ji[i];
712
713	mmeineke	558	// initalize rot as a unit matrix
714
715			rot[0][0] = 1.0;
716			rot[0][1] = 0.0;
717			rot[0][2] = 0.0;
718
719			rot[1][0] = 0.0;
720			rot[1][1] = 1.0;
721			rot[1][2] = 0.0;
722	tim	725
723	mmeineke	558	rot[2][0] = 0.0;
724			rot[2][1] = 0.0;
725			rot[2][2] = 1.0;
726	tim	725
727	mmeineke	558	// use a small angle aproximation for sin and cosine
728
729	tim	725	angleSqr = angle * angle;
730	mmeineke	558	angleSqrOver4 = angleSqr / 4.0;
731			top = 1.0 - angleSqrOver4;
732			bottom = 1.0 + angleSqrOver4;
733
734			cosAngle = top / bottom;
735			sinAngle = angle / bottom;
736
737			rot[axes1][axes1] = cosAngle;
738			rot[axes2][axes2] = cosAngle;
739
740			rot[axes1][axes2] = sinAngle;
741			rot[axes2][axes1] = -sinAngle;
742	tim	725
743	mmeineke	558	// rotate the momentum acoording to: ji[] = rot[][] * ji[]
744	tim	725
745			for (i = 0; i < 3; i++){
746	mmeineke	558	ji[i] = 0.0;
747	tim	725	for (k = 0; k < 3; k++){
748	mmeineke	558	ji[i] += rot[i][k] * tempJ[k];
749			}
750			}
751
752			// rotate the Rotation matrix acording to:
753			// A[][] = A[][] * transpose(rot[][])
754
755
756	mmeineke	561	// NOte for as yet unknown reason, we are performing the
757	mmeineke	558	// calculation as:
758			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
759
760	tim	725	for (i = 0; i < 3; i++){
761			for (j = 0; j < 3; j++){
762	gezelter	600	A[j][i] = 0.0;
763	tim	725	for (k = 0; k < 3; k++){
764			A[j][i] += tempA[i][k] * rot[j][k];
765	mmeineke	558	}
766			}
767			}
768			}
769	tim	677
770	tim	725	template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
771			myFF->doForces(calcPot, calcStress);
772	tim	677	}
773
774			template<typename T> void Integrator<T>::thermalize(){
775	tim	725	tStats->velocitize();
776	tim	677	}
777	tim	763
778			template<typename T> double Integrator<T>::getConservedQuantity(void){
779			return tStats->getTotalE();
780	mmeineke	768	}