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){

  double runTime = info->run_time;
  double sampleTime = info->sampleTime;
  double statusTime = info->statusTime;
  double thermalTime = info->thermalTime;
  double resetTime = info->resetTime;


  double currSample;
  double currThermal;
  double currStatus;
  double currReset;
  
  int calcPot, calcStress;

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

  atoms = info->atoms;

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

  readyCheck();

  // initialize the forces before the first step

  calcForce(1, 1);

  if (nConstrained){
    preMove();
    constrainA();
    calcForce(1, 1);    
    constrainB();
  }
  
  if (info->setTemp){
    thermalize();
  }

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

  dumpOut->writeDump(info->getTime());
  statOut->writeStat(info->getTime());


#ifdef IS_MPI
  strcpy(checkPointMsg, "The integrator is ready to go.");
  MPIcheckPoint();
#endif // is_mpi

  while (info->getTime() < runTime){
    if ((info->getTime() + dt) >= currStatus){
      calcPot = 1;
      calcStress = 1;
    }

    integrateStep(calcPot, calcStress);

    info->incrTime(dt);

    if (info->setTemp){
      if (info->getTime() >= currThermal){
        thermalize();
        currThermal += thermalTime;
      }
    }

    if (info->getTime() >= currSample){
      dumpOut->writeDump(info->getTime());
      currSample += sampleTime;
    }

    if (info->getTime() >= currStatus){
      statOut->writeStat(info->getTime()); 
      calcPot = 0; 
      calcStress = 0;
      currStatus += statusTime;
    } 

    if (info->resetIntegrator){
      if (info->getTime() >= currReset){
        this->resetIntegrator();
        currReset += resetTime;
      }
    }

#ifdef IS_MPI
    strcpy(checkPointMsg, "successfully took a time step.");
    MPIcheckPoint();
#endif // is_mpi
  }

  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;
  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;
  int done;
  double posA[3], posB[3];
  double velA[3], velB[3];
  double vxab, vyab, vzab;
  double rab[3];
  int a, b, ax, ay, az, bx, by, bz;
  double rma, rmb;
  double dx, dy, dz;
  double rvab;
  double gab;
  int iteration;

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

  done = 0;
  iteration = 0;
  while (!done && (iteration < maxIteration)){
    done = 1;

    for (i = 0; i < nConstrained; i++){
      a = constrainedA[i];
      b = constrainedB[i];

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

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

      if (moved[a] || moved[b]){
        atoms[a]->getVel(velA);
        atoms[b]->getVel(velB);

        vxab = velA[0] - velB[0];
        vyab = velA[1] - velB[1];
        vzab = velA[2] - velB[2];

        atoms[a]->getPos(posA);
        atoms[b]->getPos(posB);

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

        info->wrapVector(rab);

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

        rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;

        gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);

        if (fabs(gab) > tol){
          dx = rab[0] * gab;
          dy = rab[1] * gab;
          dz = rab[2] * gab;

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

          atoms[a]->setVel(velA);

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

          atoms[b]->setVel(velB);

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

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

    iteration++;
  }

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

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:	787
Committed:	Thu Sep 25 19:27:15 2003 UTC (20 years, 9 months ago) by mmeineke
File size:	16528 byte(s)
Log Message:	cleaned things with gcc -Wall and g++ -Wall
#	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
150	tim	725	double runTime = info->run_time;
151			double sampleTime = info->sampleTime;
152			double statusTime = info->statusTime;
153	mmeineke	558	double thermalTime = info->thermalTime;
154	mmeineke	746	double resetTime = info->resetTime;
155	mmeineke	558
156	mmeineke	746
157	mmeineke	558	double currSample;
158			double currThermal;
159			double currStatus;
160	mmeineke	746	double currReset;
161
162	mmeineke	558	int calcPot, calcStress;
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
170			dt = info->dt;
171	mmeineke	558	dt2 = 0.5 * dt;
172
173	mmeineke	784	readyCheck();
174
175	mmeineke	558	// initialize the forces before the first step
176
177	tim	677	calcForce(1, 1);
178	tim	781
179			if (nConstrained){
180			preMove();
181			constrainA();
182			calcForce(1, 1);
183			constrainB();
184			}
185	tim	733
186	tim	725	if (info->setTemp){
187	tim	677	thermalize();
188	mmeineke	558	}
189	tim	725
190	mmeineke	558	calcPot = 0;
191			calcStress = 0;
192	mmeineke	711	currSample = sampleTime + info->getTime();
193			currThermal = thermalTime+ info->getTime();
194			currStatus = statusTime + info->getTime();
195	mmeineke	746	currReset = resetTime + info->getTime();
196	mmeineke	558
197	tim	725	dumpOut->writeDump(info->getTime());
198			statOut->writeStat(info->getTime());
199	mmeineke	559
200
201	mmeineke	784
202	mmeineke	559	#ifdef IS_MPI
203	tim	725	strcpy(checkPointMsg, "The integrator is ready to go.");
204	mmeineke	559	MPIcheckPoint();
205			#endif // is_mpi
206
207	tim	725	while (info->getTime() < runTime){
208			if ((info->getTime() + dt) >= currStatus){
209	mmeineke	558	calcPot = 1;
210			calcStress = 1;
211			}
212	mmeineke	561
213	tim	725	integrateStep(calcPot, calcStress);
214
215	mmeineke	643	info->incrTime(dt);
216	mmeineke	558
217	tim	725	if (info->setTemp){
218			if (info->getTime() >= currThermal){
219			thermalize();
220			currThermal += thermalTime;
221	mmeineke	558	}
222			}
223
224	tim	725	if (info->getTime() >= currSample){
225			dumpOut->writeDump(info->getTime());
226	mmeineke	558	currSample += sampleTime;
227			}
228
229	tim	725	if (info->getTime() >= currStatus){
230			statOut->writeStat(info->getTime());
231	mmeineke	558	calcPot = 0;
232			calcStress = 0;
233			currStatus += statusTime;
234			}
235	mmeineke	559
236	mmeineke	746	if (info->resetIntegrator){
237			if (info->getTime() >= currReset){
238			this->resetIntegrator();
239			currReset += resetTime;
240			}
241			}
242
243	mmeineke	559	#ifdef IS_MPI
244	tim	725	strcpy(checkPointMsg, "successfully took a time step.");
245	mmeineke	559	MPIcheckPoint();
246			#endif // is_mpi
247	mmeineke	558	}
248
249	mmeineke	643	dumpOut->writeFinal(info->getTime());
250	mmeineke	558
251	mmeineke	561	delete dumpOut;
252			delete statOut;
253	mmeineke	558	}
254
255	tim	725	template<typename T> void Integrator<T>::integrateStep(int calcPot,
256			int calcStress){
257	mmeineke	558	// Position full step, and velocity half step
258	tim	725	preMove();
259	mmeineke	558
260			moveA();
261
262	tim	725
263
264	mmeineke	768
265	mmeineke	614	#ifdef IS_MPI
266	tim	725	strcpy(checkPointMsg, "Succesful moveA\n");
267	mmeineke	614	MPIcheckPoint();
268			#endif // is_mpi
269
270	tim	725
271	mmeineke	558	// calc forces
272
273	tim	725	calcForce(calcPot, calcStress);
274	mmeineke	558
275	mmeineke	614	#ifdef IS_MPI
276	tim	725	strcpy(checkPointMsg, "Succesful doForces\n");
277	mmeineke	614	MPIcheckPoint();
278			#endif // is_mpi
279
280	tim	725
281	mmeineke	558	// finish the velocity half step
282	tim	725
283	mmeineke	558	moveB();
284	tim	725
285
286	mmeineke	768
287	mmeineke	614	#ifdef IS_MPI
288	tim	725	strcpy(checkPointMsg, "Succesful moveB\n");
289	mmeineke	614	MPIcheckPoint();
290			#endif // is_mpi
291	mmeineke	558	}
292
293
294	tim	725	template<typename T> void Integrator<T>::moveA(void){
295	gezelter	600	int i, j;
296	mmeineke	558	DirectionalAtom* dAtom;
297	gezelter	600	double Tb[3], ji[3];
298			double vel[3], pos[3], frc[3];
299			double mass;
300	mmeineke	558
301	tim	725	for (i = 0; i < nAtoms; i++){
302			atoms[i]->getVel(vel);
303			atoms[i]->getPos(pos);
304			atoms[i]->getFrc(frc);
305	mmeineke	567
306	gezelter	600	mass = atoms[i]->getMass();
307	mmeineke	594
308	tim	725	for (j = 0; j < 3; j++){
309	gezelter	600	// velocity half step
310	tim	725	vel[j] += (dt2 * frc[j] / mass) * eConvert;
311	gezelter	600	// position whole step
312			pos[j] += dt * vel[j];
313			}
314	mmeineke	594
315	tim	725	atoms[i]->setVel(vel);
316			atoms[i]->setPos(pos);
317	gezelter	600
318	tim	725	if (atoms[i]->isDirectional()){
319			dAtom = (DirectionalAtom *) atoms[i];
320	mmeineke	558
321			// get and convert the torque to body frame
322	mmeineke	597
323	tim	725	dAtom->getTrq(Tb);
324			dAtom->lab2Body(Tb);
325
326	mmeineke	558	// get the angular momentum, and propagate a half step
327	gezelter	600
328	tim	725	dAtom->getJ(ji);
329	gezelter	600
330	tim	725	for (j = 0; j < 3; j++)
331	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
332	tim	725
333	mmeineke	778	this->rotationPropagation( dAtom, ji );
334	gezelter	600
335	tim	725	dAtom->setJ(ji);
336			}
337	mmeineke	558	}
338	mmeineke	768
339			if (nConstrained){
340			constrainA();
341			}
342	mmeineke	558	}
343
344
345	tim	725	template<typename T> void Integrator<T>::moveB(void){
346	gezelter	600	int i, j;
347	mmeineke	558	DirectionalAtom* dAtom;
348	gezelter	600	double Tb[3], ji[3];
349			double vel[3], frc[3];
350			double mass;
351	mmeineke	558
352	tim	725	for (i = 0; i < nAtoms; i++){
353			atoms[i]->getVel(vel);
354			atoms[i]->getFrc(frc);
355	mmeineke	558
356	gezelter	600	mass = atoms[i]->getMass();
357
358	mmeineke	558	// velocity half step
359	tim	725	for (j = 0; j < 3; j++)
360			vel[j] += (dt2 * frc[j] / mass) * eConvert;
361	gezelter	600
362	tim	725	atoms[i]->setVel(vel);
363	mmeineke	597
364	tim	725	if (atoms[i]->isDirectional()){
365			dAtom = (DirectionalAtom *) atoms[i];
366
367	gezelter	600	// get and convert the torque to body frame
368
369	tim	725	dAtom->getTrq(Tb);
370			dAtom->lab2Body(Tb);
371	gezelter	600
372			// get the angular momentum, and propagate a half step
373
374	tim	725	dAtom->getJ(ji);
375	gezelter	600
376	tim	725	for (j = 0; j < 3; j++)
377	gezelter	600	ji[j] += (dt2 * Tb[j]) * eConvert;
378	mmeineke	597
379	tim	725
380			dAtom->setJ(ji);
381	mmeineke	558	}
382			}
383	mmeineke	768
384			if (nConstrained){
385			constrainB();
386			}
387	mmeineke	558	}
388
389	tim	725	template<typename T> void Integrator<T>::preMove(void){
390	gezelter	600	int i, j;
391			double pos[3];
392	mmeineke	558
393	tim	725	if (nConstrained){
394			for (i = 0; i < nAtoms; i++){
395			atoms[i]->getPos(pos);
396	mmeineke	561
397	tim	725	for (j = 0; j < 3; j++){
398			oldPos[3 * i + j] = pos[j];
399	gezelter	600	}
400			}
401	tim	725	}
402	gezelter	600	}
403
404	tim	645	template<typename T> void Integrator<T>::constrainA(){
405	mmeineke	787	int i, j;
406	mmeineke	558	int done;
407	gezelter	600	double posA[3], posB[3];
408			double velA[3], velB[3];
409	mmeineke	572	double pab[3];
410			double rab[3];
411	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
412	mmeineke	558	double rma, rmb;
413			double dx, dy, dz;
414	mmeineke	561	double rpab;
415	mmeineke	558	double rabsq, pabsq, rpabsq;
416			double diffsq;
417			double gab;
418			int iteration;
419
420	tim	725	for (i = 0; i < nAtoms; i++){
421	mmeineke	558	moving[i] = 0;
422	tim	725	moved[i] = 1;
423	mmeineke	558	}
424	mmeineke	567
425	mmeineke	558	iteration = 0;
426			done = 0;
427	tim	725	while (!done && (iteration < maxIteration)){
428	mmeineke	558	done = 1;
429	tim	725	for (i = 0; i < nConstrained; i++){
430	mmeineke	558	a = constrainedA[i];
431			b = constrainedB[i];
432	mmeineke	563
433	tim	725	ax = (a * 3) + 0;
434			ay = (a * 3) + 1;
435			az = (a * 3) + 2;
436	mmeineke	563
437	tim	725	bx = (b * 3) + 0;
438			by = (b * 3) + 1;
439			bz = (b * 3) + 2;
440
441			if (moved[a] \|\| moved[b]){
442			atoms[a]->getPos(posA);
443			atoms[b]->getPos(posB);
444
445			for (j = 0; j < 3; j++)
446	gezelter	600	pab[j] = posA[j] - posB[j];
447	mmeineke	567
448	tim	725	//periodic boundary condition
449	mmeineke	567
450	tim	725	info->wrapVector(pab);
451	mmeineke	572
452	tim	725	pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
453	mmeineke	558
454	tim	725	rabsq = constrainedDsqr[i];
455			diffsq = rabsq - pabsq;
456	mmeineke	567
457	tim	725	// the original rattle code from alan tidesley
458			if (fabs(diffsq) > (tol * rabsq * 2)){
459			rab[0] = oldPos[ax] - oldPos[bx];
460			rab[1] = oldPos[ay] - oldPos[by];
461			rab[2] = oldPos[az] - oldPos[bz];
462	mmeineke	558
463	tim	725	info->wrapVector(rab);
464	mmeineke	567
465	tim	725	rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
466	mmeineke	558
467	tim	725	rpabsq = rpab * rpab;
468	mmeineke	558
469	mmeineke	563
470	tim	725	if (rpabsq < (rabsq * -diffsq)){
471	mmeineke	558	#ifdef IS_MPI
472	tim	725	a = atoms[a]->getGlobalIndex();
473			b = atoms[b]->getGlobalIndex();
474	mmeineke	558	#endif //is_mpi
475	tim	725	sprintf(painCave.errMsg,
476			"Constraint failure in constrainA at atom %d and %d.\n", a,
477			b);
478			painCave.isFatal = 1;
479			simError();
480			}
481	mmeineke	558
482	tim	725	rma = 1.0 / atoms[a]->getMass();
483			rmb = 1.0 / atoms[b]->getMass();
484	mmeineke	567
485	tim	725	gab = diffsq / (2.0 * (rma + rmb) * rpab);
486	mmeineke	567
487	mmeineke	572	dx = rab[0] * gab;
488			dy = rab[1] * gab;
489			dz = rab[2] * gab;
490	mmeineke	558
491	tim	725	posA[0] += rma * dx;
492			posA[1] += rma * dy;
493			posA[2] += rma * dz;
494	mmeineke	558
495	tim	725	atoms[a]->setPos(posA);
496	mmeineke	558
497	tim	725	posB[0] -= rmb * dx;
498			posB[1] -= rmb * dy;
499			posB[2] -= rmb * dz;
500	gezelter	600
501	tim	725	atoms[b]->setPos(posB);
502	gezelter	600
503	mmeineke	558	dx = dx / dt;
504			dy = dy / dt;
505			dz = dz / dt;
506
507	tim	725	atoms[a]->getVel(velA);
508	mmeineke	558
509	tim	725	velA[0] += rma * dx;
510			velA[1] += rma * dy;
511			velA[2] += rma * dz;
512	mmeineke	558
513	tim	725	atoms[a]->setVel(velA);
514	gezelter	600
515	tim	725	atoms[b]->getVel(velB);
516	gezelter	600
517	tim	725	velB[0] -= rmb * dx;
518			velB[1] -= rmb * dy;
519			velB[2] -= rmb * dz;
520	gezelter	600
521	tim	725	atoms[b]->setVel(velB);
522	gezelter	600
523	tim	725	moving[a] = 1;
524			moving[b] = 1;
525			done = 0;
526			}
527	mmeineke	558	}
528			}
529	tim	725
530			for (i = 0; i < nAtoms; i++){
531	mmeineke	558	moved[i] = moving[i];
532			moving[i] = 0;
533			}
534
535			iteration++;
536			}
537
538	tim	725	if (!done){
539			sprintf(painCave.errMsg,
540			"Constraint failure in constrainA, too many iterations: %d\n",
541			iteration);
542	mmeineke	558	painCave.isFatal = 1;
543			simError();
544			}
545	mmeineke	768
546	mmeineke	558	}
547
548	tim	725	template<typename T> void Integrator<T>::constrainB(void){
549	mmeineke	787	int i, j;
550	mmeineke	558	int done;
551	gezelter	600	double posA[3], posB[3];
552			double velA[3], velB[3];
553	mmeineke	558	double vxab, vyab, vzab;
554	mmeineke	572	double rab[3];
555	mmeineke	563	int a, b, ax, ay, az, bx, by, bz;
556	mmeineke	558	double rma, rmb;
557			double dx, dy, dz;
558	mmeineke	787	double rvab;
559	mmeineke	558	double gab;
560			int iteration;
561
562	tim	725	for (i = 0; i < nAtoms; i++){
563	mmeineke	558	moving[i] = 0;
564			moved[i] = 1;
565			}
566
567			done = 0;
568	mmeineke	561	iteration = 0;
569	tim	725	while (!done && (iteration < maxIteration)){
570	mmeineke	567	done = 1;
571
572	tim	725	for (i = 0; i < nConstrained; i++){
573	mmeineke	558	a = constrainedA[i];
574			b = constrainedB[i];
575
576	tim	725	ax = (a * 3) + 0;
577			ay = (a * 3) + 1;
578			az = (a * 3) + 2;
579	mmeineke	563
580	tim	725	bx = (b * 3) + 0;
581			by = (b * 3) + 1;
582			bz = (b * 3) + 2;
583	mmeineke	563
584	tim	725	if (moved[a] \|\| moved[b]){
585			atoms[a]->getVel(velA);
586			atoms[b]->getVel(velB);
587	mmeineke	558
588	tim	725	vxab = velA[0] - velB[0];
589			vyab = velA[1] - velB[1];
590			vzab = velA[2] - velB[2];
591	gezelter	600
592	tim	725	atoms[a]->getPos(posA);
593			atoms[b]->getPos(posB);
594	gezelter	600
595	tim	725	for (j = 0; j < 3; j++)
596	gezelter	600	rab[j] = posA[j] - posB[j];
597	mmeineke	558
598	tim	725	info->wrapVector(rab);
599	mmeineke	558
600	tim	725	rma = 1.0 / atoms[a]->getMass();
601			rmb = 1.0 / atoms[b]->getMass();
602	mmeineke	558
603	tim	725	rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
604	gezelter	600
605	tim	725	gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
606	gezelter	600
607	tim	725	if (fabs(gab) > tol){
608			dx = rab[0] * gab;
609			dy = rab[1] * gab;
610			dz = rab[2] * gab;
611
612			velA[0] += rma * dx;
613			velA[1] += rma * dy;
614			velA[2] += rma * dz;
615
616			atoms[a]->setVel(velA);
617
618			velB[0] -= rmb * dx;
619			velB[1] -= rmb * dy;
620			velB[2] -= rmb * dz;
621
622			atoms[b]->setVel(velB);
623
624			moving[a] = 1;
625			moving[b] = 1;
626			done = 0;
627			}
628	mmeineke	558	}
629			}
630
631	tim	725	for (i = 0; i < nAtoms; i++){
632	mmeineke	558	moved[i] = moving[i];
633			moving[i] = 0;
634			}
635	tim	725
636	mmeineke	558	iteration++;
637			}
638
639	tim	725	if (!done){
640			sprintf(painCave.errMsg,
641			"Constraint failure in constrainB, too many iterations: %d\n",
642			iteration);
643	mmeineke	558	painCave.isFatal = 1;
644			simError();
645	tim	725	}
646	mmeineke	558	}
647
648	mmeineke	778	template<typename T> void Integrator<T>::rotationPropagation
649			( DirectionalAtom* dAtom, double ji[3] ){
650
651			double angle;
652			double A[3][3], I[3][3];
653
654			// use the angular velocities to propagate the rotation matrix a
655			// full time step
656
657			dAtom->getA(A);
658			dAtom->getI(I);
659
660			// rotate about the x-axis
661			angle = dt2 * ji[0] / I[0][0];
662			this->rotate( 1, 2, angle, ji, A );
663
664			// rotate about the y-axis
665			angle = dt2 * ji[1] / I[1][1];
666			this->rotate( 2, 0, angle, ji, A );
667
668			// rotate about the z-axis
669			angle = dt * ji[2] / I[2][2];
670			this->rotate( 0, 1, angle, ji, A);
671
672			// rotate about the y-axis
673			angle = dt2 * ji[1] / I[1][1];
674			this->rotate( 2, 0, angle, ji, A );
675
676			// rotate about the x-axis
677			angle = dt2 * ji[0] / I[0][0];
678			this->rotate( 1, 2, angle, ji, A );
679
680			dAtom->setA( A );
681			}
682
683	tim	725	template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
684			double angle, double ji[3],
685			double A[3][3]){
686			int i, j, k;
687	mmeineke	558	double sinAngle;
688			double cosAngle;
689			double angleSqr;
690			double angleSqrOver4;
691			double top, bottom;
692			double rot[3][3];
693			double tempA[3][3];
694			double tempJ[3];
695
696			// initialize the tempA
697
698	tim	725	for (i = 0; i < 3; i++){
699			for (j = 0; j < 3; j++){
700	gezelter	600	tempA[j][i] = A[i][j];
701	mmeineke	558	}
702			}
703
704			// initialize the tempJ
705
706	tim	725	for (i = 0; i < 3; i++)
707			tempJ[i] = ji[i];
708
709	mmeineke	558	// initalize rot as a unit matrix
710
711			rot[0][0] = 1.0;
712			rot[0][1] = 0.0;
713			rot[0][2] = 0.0;
714
715			rot[1][0] = 0.0;
716			rot[1][1] = 1.0;
717			rot[1][2] = 0.0;
718	tim	725
719	mmeineke	558	rot[2][0] = 0.0;
720			rot[2][1] = 0.0;
721			rot[2][2] = 1.0;
722	tim	725
723	mmeineke	558	// use a small angle aproximation for sin and cosine
724
725	tim	725	angleSqr = angle * angle;
726	mmeineke	558	angleSqrOver4 = angleSqr / 4.0;
727			top = 1.0 - angleSqrOver4;
728			bottom = 1.0 + angleSqrOver4;
729
730			cosAngle = top / bottom;
731			sinAngle = angle / bottom;
732
733			rot[axes1][axes1] = cosAngle;
734			rot[axes2][axes2] = cosAngle;
735
736			rot[axes1][axes2] = sinAngle;
737			rot[axes2][axes1] = -sinAngle;
738	tim	725
739	mmeineke	558	// rotate the momentum acoording to: ji[] = rot[][] * ji[]
740	tim	725
741			for (i = 0; i < 3; i++){
742	mmeineke	558	ji[i] = 0.0;
743	tim	725	for (k = 0; k < 3; k++){
744	mmeineke	558	ji[i] += rot[i][k] * tempJ[k];
745			}
746			}
747
748			// rotate the Rotation matrix acording to:
749			// A[][] = A[][] * transpose(rot[][])
750
751
752	mmeineke	561	// NOte for as yet unknown reason, we are performing the
753	mmeineke	558	// calculation as:
754			// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
755
756	tim	725	for (i = 0; i < 3; i++){
757			for (j = 0; j < 3; j++){
758	gezelter	600	A[j][i] = 0.0;
759	tim	725	for (k = 0; k < 3; k++){
760			A[j][i] += tempA[i][k] * rot[j][k];
761	mmeineke	558	}
762			}
763			}
764			}
765	tim	677
766	tim	725	template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
767			myFF->doForces(calcPot, calcStress);
768	tim	677	}
769
770			template<typename T> void Integrator<T>::thermalize(){
771	tim	725	tStats->velocitize();
772	tim	677	}
773	tim	763
774			template<typename T> double Integrator<T>::getConservedQuantity(void){
775			return tStats->getTotalE();
776	mmeineke	768	}