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();


#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:	778
Committed:	Fri Sep 19 20:00:27 2003 UTC (20 years, 9 months ago) by mmeineke
File size:	16584 byte(s)
Log Message:	added NPT base class. NPTi is up to date. NPTf is not.
#	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
258
259	mmeineke	768
260	mmeineke	614	#ifdef IS_MPI
261	tim	725	strcpy(checkPointMsg, "Succesful moveA\n");
262	mmeineke	614	MPIcheckPoint();
263			#endif // is_mpi
264
265	tim	725
266	mmeineke	558	// calc forces
267
268	tim	725	calcForce(calcPot, calcStress);
269	mmeineke	558
270	mmeineke	614	#ifdef IS_MPI
271	tim	725	strcpy(checkPointMsg, "Succesful doForces\n");
272	mmeineke	614	MPIcheckPoint();
273			#endif // is_mpi
274
275	tim	725
276	mmeineke	558	// finish the velocity half step
277	tim	725
278	mmeineke	558	moveB();
279	tim	725
280
281	mmeineke	768
282	mmeineke	614	#ifdef IS_MPI
283	tim	725	strcpy(checkPointMsg, "Succesful moveB\n");
284	mmeineke	614	MPIcheckPoint();
285			#endif // is_mpi
286	mmeineke	558	}
287
288
289	tim	725	template<typename T> void Integrator<T>::moveA(void){
290	gezelter	600	int i, j;
291	mmeineke	558	DirectionalAtom* dAtom;
292	gezelter	600	double Tb[3], ji[3];
293			double vel[3], pos[3], frc[3];
294			double mass;
295	mmeineke	558
296	tim	725	for (i = 0; i < nAtoms; i++){
297			atoms[i]->getVel(vel);
298			atoms[i]->getPos(pos);
299			atoms[i]->getFrc(frc);
300	mmeineke	567
301	gezelter	600	mass = atoms[i]->getMass();
302	mmeineke	594
303	tim	725	for (j = 0; j < 3; j++){
304	gezelter	600	// velocity half step
305	tim	725	vel[j] += (dt2 * frc[j] / mass) * eConvert;
306	gezelter	600	// position whole step
307			pos[j] += dt * vel[j];
308			}
309	mmeineke	594
310	tim	725	atoms[i]->setVel(vel);
311			atoms[i]->setPos(pos);
312	gezelter	600
313	tim	725	if (atoms[i]->isDirectional()){
314			dAtom = (DirectionalAtom *) atoms[i];
315	mmeineke	558
316			// get and convert the torque to body frame
317	mmeineke	597
318	tim	725	dAtom->getTrq(Tb);
319			dAtom->lab2Body(Tb);
320
321	mmeineke	558	// get the angular momentum, and propagate a half step
322	gezelter	600
323	tim	725	dAtom->getJ(ji);
324	gezelter	600
325	tim	725	for (j = 0; j < 3; j++)
326	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
327	tim	725
328	mmeineke	778	this->rotationPropagation( dAtom, ji );
329	gezelter	600
330	tim	725	dAtom->setJ(ji);
331			}
332	mmeineke	558	}
333	mmeineke	768
334			if (nConstrained){
335			constrainA();
336			}
337	mmeineke	558	}
338
339
340	tim	725	template<typename T> void Integrator<T>::moveB(void){
341	gezelter	600	int i, j;
342	mmeineke	558	DirectionalAtom* dAtom;
343	gezelter	600	double Tb[3], ji[3];
344			double vel[3], frc[3];
345			double mass;
346	mmeineke	558
347	tim	725	for (i = 0; i < nAtoms; i++){
348			atoms[i]->getVel(vel);
349			atoms[i]->getFrc(frc);
350	mmeineke	558
351	gezelter	600	mass = atoms[i]->getMass();
352
353	mmeineke	558	// velocity half step
354	tim	725	for (j = 0; j < 3; j++)
355			vel[j] += (dt2 * frc[j] / mass) * eConvert;
356	gezelter	600
357	tim	725	atoms[i]->setVel(vel);
358	mmeineke	597
359	tim	725	if (atoms[i]->isDirectional()){
360			dAtom = (DirectionalAtom *) atoms[i];
361
362	gezelter	600	// get and convert the torque to body frame
363
364	tim	725	dAtom->getTrq(Tb);
365			dAtom->lab2Body(Tb);
366	gezelter	600
367			// get the angular momentum, and propagate a half step
368
369	tim	725	dAtom->getJ(ji);
370	gezelter	600
371	tim	725	for (j = 0; j < 3; j++)
372	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
373	mmeineke	597
374	tim	725
375			dAtom->setJ(ji);
376	mmeineke	558	}
377			}
378	mmeineke	768
379			if (nConstrained){
380			constrainB();
381			}
382	mmeineke	558	}
383
384	tim	725	template<typename T> void Integrator<T>::preMove(void){
385	gezelter	600	int i, j;
386			double pos[3];
387	mmeineke	558
388	tim	725	if (nConstrained){
389			for (i = 0; i < nAtoms; i++){
390			atoms[i]->getPos(pos);
391	mmeineke	561
392	tim	725	for (j = 0; j < 3; j++){
393			oldPos[3 * i + j] = pos[j];
394	gezelter	600	}
395			}
396	tim	725	}
397	gezelter	600	}
398
399	tim	645	template<typename T> void Integrator<T>::constrainA(){
400	tim	725	int i, j, k;
401	mmeineke	558	int done;
402	gezelter	600	double posA[3], posB[3];
403			double velA[3], velB[3];
404	mmeineke	572	double pab[3];
405			double rab[3];
406	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
407	mmeineke	558	double rma, rmb;
408			double dx, dy, dz;
409	mmeineke	561	double rpab;
410	mmeineke	558	double rabsq, pabsq, rpabsq;
411			double diffsq;
412			double gab;
413			int iteration;
414
415	tim	725	for (i = 0; i < nAtoms; i++){
416	mmeineke	558	moving[i] = 0;
417	tim	725	moved[i] = 1;
418	mmeineke	558	}
419	mmeineke	567
420	mmeineke	558	iteration = 0;
421			done = 0;
422	tim	725	while (!done && (iteration < maxIteration)){
423	mmeineke	558	done = 1;
424	tim	725	for (i = 0; i < nConstrained; i++){
425	mmeineke	558	a = constrainedA[i];
426			b = constrainedB[i];
427	mmeineke	563
428	tim	725	ax = (a * 3) + 0;
429			ay = (a * 3) + 1;
430			az = (a * 3) + 2;
431	mmeineke	563
432	tim	725	bx = (b * 3) + 0;
433			by = (b * 3) + 1;
434			bz = (b * 3) + 2;
435
436			if (moved[a] \|\| moved[b]){
437			atoms[a]->getPos(posA);
438			atoms[b]->getPos(posB);
439
440			for (j = 0; j < 3; j++)
441	gezelter	600	pab[j] = posA[j] - posB[j];
442	mmeineke	567
443	tim	725	//periodic boundary condition
444	mmeineke	567
445	tim	725	info->wrapVector(pab);
446	mmeineke	572
447	tim	725	pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
448	mmeineke	558
449	tim	725	rabsq = constrainedDsqr[i];
450			diffsq = rabsq - pabsq;
451	mmeineke	567
452	tim	725	// the original rattle code from alan tidesley
453			if (fabs(diffsq) > (tol * rabsq * 2)){
454			rab[0] = oldPos[ax] - oldPos[bx];
455			rab[1] = oldPos[ay] - oldPos[by];
456			rab[2] = oldPos[az] - oldPos[bz];
457	mmeineke	558
458	tim	725	info->wrapVector(rab);
459	mmeineke	567
460	tim	725	rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
461	mmeineke	558
462	tim	725	rpabsq = rpab * rpab;
463	mmeineke	558
464	mmeineke	563
465	tim	725	if (rpabsq < (rabsq * -diffsq)){
466	mmeineke	558	#ifdef IS_MPI
467	tim	725	a = atoms[a]->getGlobalIndex();
468			b = atoms[b]->getGlobalIndex();
469	mmeineke	558	#endif //is_mpi
470	tim	725	sprintf(painCave.errMsg,
471			"Constraint failure in constrainA at atom %d and %d.\n", a,
472			b);
473			painCave.isFatal = 1;
474			simError();
475			}
476	mmeineke	558
477	tim	725	rma = 1.0 / atoms[a]->getMass();
478			rmb = 1.0 / atoms[b]->getMass();
479	mmeineke	567
480	tim	725	gab = diffsq / (2.0 * (rma + rmb) * rpab);
481	mmeineke	567
482	mmeineke	572	dx = rab[0] * gab;
483			dy = rab[1] * gab;
484			dz = rab[2] * gab;
485	mmeineke	558
486	tim	725	posA[0] += rma * dx;
487			posA[1] += rma * dy;
488			posA[2] += rma * dz;
489	mmeineke	558
490	tim	725	atoms[a]->setPos(posA);
491	mmeineke	558
492	tim	725	posB[0] -= rmb * dx;
493			posB[1] -= rmb * dy;
494			posB[2] -= rmb * dz;
495	gezelter	600
496	tim	725	atoms[b]->setPos(posB);
497	gezelter	600
498	mmeineke	558	dx = dx / dt;
499			dy = dy / dt;
500			dz = dz / dt;
501
502	tim	725	atoms[a]->getVel(velA);
503	mmeineke	558
504	tim	725	velA[0] += rma * dx;
505			velA[1] += rma * dy;
506			velA[2] += rma * dz;
507	mmeineke	558
508	tim	725	atoms[a]->setVel(velA);
509	gezelter	600
510	tim	725	atoms[b]->getVel(velB);
511	gezelter	600
512	tim	725	velB[0] -= rmb * dx;
513			velB[1] -= rmb * dy;
514			velB[2] -= rmb * dz;
515	gezelter	600
516	tim	725	atoms[b]->setVel(velB);
517	gezelter	600
518	tim	725	moving[a] = 1;
519			moving[b] = 1;
520			done = 0;
521			}
522	mmeineke	558	}
523			}
524	tim	725
525			for (i = 0; i < nAtoms; i++){
526	mmeineke	558	moved[i] = moving[i];
527			moving[i] = 0;
528			}
529
530			iteration++;
531			}
532
533	tim	725	if (!done){
534			sprintf(painCave.errMsg,
535			"Constraint failure in constrainA, too many iterations: %d\n",
536			iteration);
537	mmeineke	558	painCave.isFatal = 1;
538			simError();
539			}
540	mmeineke	768
541	mmeineke	558	}
542
543	tim	725	template<typename T> void Integrator<T>::constrainB(void){
544			int i, j, k;
545	mmeineke	558	int done;
546	gezelter	600	double posA[3], posB[3];
547			double velA[3], velB[3];
548	mmeineke	558	double vxab, vyab, vzab;
549	mmeineke	572	double rab[3];
550	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
551	mmeineke	558	double rma, rmb;
552			double dx, dy, dz;
553			double rabsq, pabsq, rvab;
554			double diffsq;
555			double gab;
556			int iteration;
557
558	tim	725	for (i = 0; i < nAtoms; i++){
559	mmeineke	558	moving[i] = 0;
560			moved[i] = 1;
561			}
562
563			done = 0;
564	mmeineke	561	iteration = 0;
565	tim	725	while (!done && (iteration < maxIteration)){
566	mmeineke	567	done = 1;
567
568	tim	725	for (i = 0; i < nConstrained; i++){
569	mmeineke	558	a = constrainedA[i];
570			b = constrainedB[i];
571
572	tim	725	ax = (a * 3) + 0;
573			ay = (a * 3) + 1;
574			az = (a * 3) + 2;
575	mmeineke	563
576	tim	725	bx = (b * 3) + 0;
577			by = (b * 3) + 1;
578			bz = (b * 3) + 2;
579	mmeineke	563
580	tim	725	if (moved[a] \|\| moved[b]){
581			atoms[a]->getVel(velA);
582			atoms[b]->getVel(velB);
583	mmeineke	558
584	tim	725	vxab = velA[0] - velB[0];
585			vyab = velA[1] - velB[1];
586			vzab = velA[2] - velB[2];
587	gezelter	600
588	tim	725	atoms[a]->getPos(posA);
589			atoms[b]->getPos(posB);
590	gezelter	600
591	tim	725	for (j = 0; j < 3; j++)
592	gezelter	600	rab[j] = posA[j] - posB[j];
593	mmeineke	558
594	tim	725	info->wrapVector(rab);
595	mmeineke	558
596	tim	725	rma = 1.0 / atoms[a]->getMass();
597			rmb = 1.0 / atoms[b]->getMass();
598	mmeineke	558
599	tim	725	rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
600	gezelter	600
601	tim	725	gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
602	gezelter	600
603	tim	725	if (fabs(gab) > tol){
604			dx = rab[0] * gab;
605			dy = rab[1] * gab;
606			dz = rab[2] * gab;
607
608			velA[0] += rma * dx;
609			velA[1] += rma * dy;
610			velA[2] += rma * dz;
611
612			atoms[a]->setVel(velA);
613
614			velB[0] -= rmb * dx;
615			velB[1] -= rmb * dy;
616			velB[2] -= rmb * dz;
617
618			atoms[b]->setVel(velB);
619
620			moving[a] = 1;
621			moving[b] = 1;
622			done = 0;
623			}
624	mmeineke	558	}
625			}
626
627	tim	725	for (i = 0; i < nAtoms; i++){
628	mmeineke	558	moved[i] = moving[i];
629			moving[i] = 0;
630			}
631	tim	725
632	mmeineke	558	iteration++;
633			}
634
635	tim	725	if (!done){
636			sprintf(painCave.errMsg,
637			"Constraint failure in constrainB, too many iterations: %d\n",
638			iteration);
639	mmeineke	558	painCave.isFatal = 1;
640			simError();
641	tim	725	}
642	mmeineke	558	}
643
644	mmeineke	778	template<typename T> void Integrator<T>::rotationPropagation
645			( DirectionalAtom* dAtom, double ji[3] ){
646
647			double angle;
648			double A[3][3], I[3][3];
649
650			// use the angular velocities to propagate the rotation matrix a
651			// full time step
652
653			dAtom->getA(A);
654			dAtom->getI(I);
655
656			// rotate about the x-axis
657			angle = dt2 * ji[0] / I[0][0];
658			this->rotate( 1, 2, angle, ji, A );
659
660			// rotate about the y-axis
661			angle = dt2 * ji[1] / I[1][1];
662			this->rotate( 2, 0, angle, ji, A );
663
664			// rotate about the z-axis
665			angle = dt * ji[2] / I[2][2];
666			this->rotate( 0, 1, 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 x-axis
673			angle = dt2 * ji[0] / I[0][0];
674			this->rotate( 1, 2, angle, ji, A );
675
676			dAtom->setA( A );
677			}
678
679	tim	725	template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
680			double angle, double ji[3],
681			double A[3][3]){
682			int i, j, k;
683	mmeineke	558	double sinAngle;
684			double cosAngle;
685			double angleSqr;
686			double angleSqrOver4;
687			double top, bottom;
688			double rot[3][3];
689			double tempA[3][3];
690			double tempJ[3];
691
692			// initialize the tempA
693
694	tim	725	for (i = 0; i < 3; i++){
695			for (j = 0; j < 3; j++){
696	gezelter	600	tempA[j][i] = A[i][j];
697	mmeineke	558	}
698			}
699
700			// initialize the tempJ
701
702	tim	725	for (i = 0; i < 3; i++)
703			tempJ[i] = ji[i];
704
705	mmeineke	558	// initalize rot as a unit matrix
706
707			rot[0][0] = 1.0;
708			rot[0][1] = 0.0;
709			rot[0][2] = 0.0;
710
711			rot[1][0] = 0.0;
712			rot[1][1] = 1.0;
713			rot[1][2] = 0.0;
714	tim	725
715	mmeineke	558	rot[2][0] = 0.0;
716			rot[2][1] = 0.0;
717			rot[2][2] = 1.0;
718	tim	725
719	mmeineke	558	// use a small angle aproximation for sin and cosine
720
721	tim	725	angleSqr = angle * angle;
722	mmeineke	558	angleSqrOver4 = angleSqr / 4.0;
723			top = 1.0 - angleSqrOver4;
724			bottom = 1.0 + angleSqrOver4;
725
726			cosAngle = top / bottom;
727			sinAngle = angle / bottom;
728
729			rot[axes1][axes1] = cosAngle;
730			rot[axes2][axes2] = cosAngle;
731
732			rot[axes1][axes2] = sinAngle;
733			rot[axes2][axes1] = -sinAngle;
734	tim	725
735	mmeineke	558	// rotate the momentum acoording to: ji[] = rot[][] * ji[]
736	tim	725
737			for (i = 0; i < 3; i++){
738	mmeineke	558	ji[i] = 0.0;
739	tim	725	for (k = 0; k < 3; k++){
740	mmeineke	558	ji[i] += rot[i][k] * tempJ[k];
741			}
742			}
743
744			// rotate the Rotation matrix acording to:
745			// A[][] = A[][] * transpose(rot[][])
746
747
748	mmeineke	561	// NOte for as yet unknown reason, we are performing the
749	mmeineke	558	// calculation as:
750			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
751
752	tim	725	for (i = 0; i < 3; i++){
753			for (j = 0; j < 3; j++){
754	gezelter	600	A[j][i] = 0.0;
755	tim	725	for (k = 0; k < 3; k++){
756			A[j][i] += tempA[i][k] * rot[j][k];
757	mmeineke	558	}
758			}
759			}
760			}
761	tim	677
762	tim	725	template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
763			myFF->doForces(calcPot, calcStress);
764	tim	677	}
765
766			template<typename T> void Integrator<T>::thermalize(){
767	tim	725	tStats->velocitize();
768	tim	677	}
769	tim	763
770			template<typename T> double Integrator<T>::getConservedQuantity(void){
771			return tStats->getTotalE();
772	mmeineke	768	}