src/brains/Thermo.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
 * [4]  Vardeman & Gezelter, in progress (2009).
 */

#include <math.h>
#include <iostream>

#ifdef IS_MPI
#include <mpi.h>
#endif //is_mpi

#include "brains/Thermo.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "utils/PhysicalConstants.hpp"

namespace OpenMD {

  RealType Thermo::getKinetic() {
    SimInfo::MoleculeIterator miter;
    std::vector<StuntDouble*>::iterator iiter;
    Molecule* mol;
    StuntDouble* integrableObject;
    Vector3d vel;
    Vector3d angMom;
    Mat3x3d I;
    int i;
    int j;
    int k;
    RealType mass;
    RealType kinetic = 0.0;
    RealType kinetic_global = 0.0;

    for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
     integrableObject = mol->nextIntegrableObject(iiter)) {

  mass = integrableObject->getMass();
  vel = integrableObject->getVel();

  kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);

  if (integrableObject->isDirectional()) {
    angMom = integrableObject->getJ();
    I = integrableObject->getI();

    if (integrableObject->isLinear()) {
      i = integrableObject->linearAxis();
      j = (i + 1) % 3;
      k = (i + 2) % 3;
      kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
    } else {
      kinetic += angMom[0]*angMom[0]/I(0, 0) + angMom[1]*angMom[1]/I(1, 1)
        + angMom[2]*angMom[2]/I(2, 2);
    }
  }

      }
    }

#ifdef IS_MPI

    MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
                  MPI_COMM_WORLD);
    kinetic = kinetic_global;

#endif //is_mpi

    kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;

    return kinetic;
  }

  RealType Thermo::getPotential() {
    RealType potential = 0.0;
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    RealType shortRangePot_local =  curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;

    // Get total potential for entire system from MPI.

#ifdef IS_MPI

    MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
                  MPI_COMM_WORLD);
    potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];

#else

    potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];

#endif // is_mpi

    return potential;
  }

  RealType Thermo::getTotalE() {
    RealType total;

    total = this->getKinetic() + this->getPotential();
    return total;
  }

  RealType Thermo::getTemperature() {

    RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
    return temperature;
  }

  RealType Thermo::getVolume() {
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    return curSnapshot->getVolume();
  }

  RealType Thermo::getPressure() {

    // Relies on the calculation of the full molecular pressure tensor


    Mat3x3d tensor;
    RealType pressure;

    tensor = getPressureTensor();

    pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;

    return pressure;
  }

  RealType Thermo::getPressure(int direction) {

    // Relies on the calculation of the full molecular pressure tensor


    Mat3x3d tensor;
    RealType pressure;

    tensor = getPressureTensor();

    pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);

    return pressure;
  }

  Mat3x3d Thermo::getPressureTensor() {
    // returns pressure tensor in units amu*fs^-2*Ang^-1
    // routine derived via viral theorem description in:
    // Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
    Mat3x3d pressureTensor;
    Mat3x3d p_local(0.0);
    Mat3x3d p_global(0.0);

    SimInfo::MoleculeIterator i;
    std::vector<StuntDouble*>::iterator j;
    Molecule* mol;
    StuntDouble* integrableObject;
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
      for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
     integrableObject = mol->nextIntegrableObject(j)) {

  RealType mass = integrableObject->getMass();
  Vector3d vcom = integrableObject->getVel();
  p_local += mass * outProduct(vcom, vcom);
      }
    }

#ifdef IS_MPI
    MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
#else
    p_global = p_local;
#endif // is_mpi

    RealType volume = this->getVolume();
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    Mat3x3d tau = curSnapshot->statData.getTau();

    pressureTensor =  (p_global + PhysicalConstants::energyConvert* tau)/volume;

    return pressureTensor;
  }


  void Thermo::saveStat(){
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    Stats& stat = currSnapshot->statData;

    stat[Stats::KINETIC_ENERGY] = getKinetic();
    stat[Stats::POTENTIAL_ENERGY] = getPotential();
    stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
    stat[Stats::TEMPERATURE] = getTemperature();
    stat[Stats::PRESSURE] = getPressure();
    stat[Stats::VOLUME] = getVolume();

    Mat3x3d tensor =getPressureTensor();
    stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
    stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
    stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
    stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
    stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
    stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
    stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
    stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
    stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
    Vector3d GKappa_t = getThermalHelfand();
    stat[Stats::THERMAL_HELFANDMOMENT_X] = GKappa_t.x();
    stat[Stats::THERMAL_HELFANDMOMENT_Y] = GKappa_t.y();
    stat[Stats::THERMAL_HELFANDMOMENT_Z] = GKappa_t.z();
    Vector3d HeatFlux_J = getHeatFlux();
    stat[Stats::HEATFLUX_X] = HeatFlux_J.x();
    stat[Stats::HEATFLUX_Y] = HeatFlux_J.y();
    stat[Stats::HEATFLUX_Z] = HeatFlux_J.z();


    Globals* simParams = info_->getSimParams();

    if (simParams->haveTaggedAtomPair() &&
        simParams->havePrintTaggedPairDistance()) {
      if ( simParams->getPrintTaggedPairDistance()) {

        std::pair<int, int> tap = simParams->getTaggedAtomPair();
        Vector3d pos1, pos2, rab;

#ifdef IS_MPI
        std::cerr << "tap = " << tap.first << "  " << tap.second << std::endl;

  int mol1 = info_->getGlobalMolMembership(tap.first);
  int mol2 = info_->getGlobalMolMembership(tap.second);
        std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;

        int proc1 = info_->getMolToProc(mol1);
        int proc2 = info_->getMolToProc(mol2);

        std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;

  RealType data[3];
        if (proc1 == worldRank) {
          StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
          std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
          pos1 = sd1->getPos();
          data[0] = pos1.x();
          data[1] = pos1.y();
          data[2] = pos1.z();
          MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
        } else {
          MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
          pos1 = Vector3d(data);
        }


        if (proc2 == worldRank) {
          StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
          std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
          pos2 = sd2->getPos();
          data[0] = pos2.x();
          data[1] = pos2.y();
          data[2] = pos2.z();
          MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
        } else {
          MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
          pos2 = Vector3d(data);
        }
#else
        StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
        StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
        pos1 = at1->getPos();
        pos2 = at2->getPos();
#endif
        rab = pos2 - pos1;
        currSnapshot->wrapVector(rab);
        stat[Stats::TAGGED_PAIR_DISTANCE] =  rab.length();
      }
    }

    /**@todo need refactorying*/
    //Conserved Quantity is set by integrator and time is set by setTime

  }


 Vector3d Thermo::getBoxDipole() {
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    SimInfo::MoleculeIterator miter;
    std::vector<Atom*>::iterator aiter;
    Molecule* mol;
    Atom* atom;
    RealType charge;
    RealType moment(0.0);
    Vector3d ri(0.0);
    Vector3d dipoleVector(0.0);
    Vector3d nPos(0.0);
    Vector3d pPos(0.0);
    RealType nChg(0.0);
    RealType pChg(0.0);
    int nCount = 0;
    int pCount = 0;

    RealType chargeToC = 1.60217733e-19;
    RealType angstromToM = 1.0e-10;    RealType debyeToCm = 3.33564095198e-30;

    for (mol = info_->beginMolecule(miter); mol != NULL;
         mol = info_->nextMolecule(miter)) {

      for (atom = mol->beginAtom(aiter); atom != NULL;
           atom = mol->nextAtom(aiter)) {

        if (atom->isCharge() ) {
          charge = 0.0;
          GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
          if (data != NULL) {

            charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
            charge *= chargeToC;

            ri = atom->getPos();
            currSnapshot->wrapVector(ri);
            ri *= angstromToM;

            if (charge < 0.0) {
              nPos += ri;
              nChg -= charge;
              nCount++;
            } else if (charge > 0.0) {
              pPos += ri;
              pChg += charge;
              pCount++;
            }
          }
        }

        if (atom->isDipole() ) {
          Vector3d u_i = atom->getElectroFrame().getColumn(2);
          GenericData* data = dynamic_cast<DirectionalAtomType*>(atom->getAtomType())->getPropertyByName("Dipole");
          if (data != NULL) {
            moment = (dynamic_cast<DoubleGenericData*>(data))->getData();

            moment *= debyeToCm;
            dipoleVector += u_i * moment;
          }
        }
      }
    }


#ifdef IS_MPI
    RealType pChg_global, nChg_global;
    int pCount_global, nCount_global;
    Vector3d pPos_global, nPos_global, dipVec_global;

    MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
                  MPI_COMM_WORLD);
    pChg = pChg_global;
    MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
                  MPI_COMM_WORLD);
    nChg = nChg_global;
    MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
                  MPI_COMM_WORLD);
    pCount = pCount_global;
    MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
                  MPI_COMM_WORLD);
    nCount = nCount_global;
    MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
    pPos = pPos_global;
    MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
    nPos = nPos_global;
    MPI_Allreduce(dipoleVector.getArrayPointer(),
                  dipVec_global.getArrayPointer(), 3,
                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
    dipoleVector = dipVec_global;
#endif //is_mpi

    // first load the accumulated dipole moment (if dipoles were present)
    Vector3d boxDipole = dipoleVector;
    // now include the dipole moment due to charges
    // use the lesser of the positive and negative charge totals
    RealType chg_value = nChg <= pChg ? nChg : pChg;

    // find the average positions
    if (pCount > 0 && nCount > 0 ) {
      pPos /= pCount;
      nPos /= nCount;
    }

    // dipole is from the negative to the positive (physics notation)
    boxDipole += (pPos - nPos) * chg_value;

    return boxDipole;
  }

 Vector3d Thermo::getThermalHelfand() {
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    SimInfo::MoleculeIterator miter;
    std::vector<Atom*>::iterator aiter;
    Molecule* mol;
    Atom* atom;
    RealType mass;
    Vector3d velocity;
    Vector3d x_a;
    RealType kinetic;
    RealType potential;
    RealType eatom;
    RealType AvgE_a_ = 0;
    Vector3d GKappa_t = V3Zero;
    Vector3d ThermalHelfandMoment;

    for (mol = info_->beginMolecule(miter); mol != NULL;
         mol = info_->nextMolecule(miter)) {

      for (atom = mol->beginAtom(aiter); atom != NULL;
           atom = mol->nextAtom(aiter)) {

        mass = atom->getMass();
        velocity = atom->getVel();
        kinetic = mass * (velocity[0]*velocity[0] + velocity[1]*velocity[1] +
                                   velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
        potential =  atom->getParticlePot();
        eatom += (kinetic + potential)/2.0;
      }
    }

   int natoms = info_->getNGlobalAtoms();
#ifdef IS_MPI

    MPI_Allreduce(&eatom, &AvgE_a_, 1, MPI_REALTYPE, MPI_SUM,
                  MPI_COMM_WORLD);
#else
    AvgE_a_ = eatom;
#endif
    AvgE_a_ = AvgE_a_/RealType(natoms);

    for (mol = info_->beginMolecule(miter); mol != NULL;
         mol = info_->nextMolecule(miter)) {

      for (atom = mol->beginAtom(aiter); atom != NULL;
           atom = mol->nextAtom(aiter)) {

        /* We think that x_a is relative to the total box and should be a wrapped coordinate */
        x_a = atom->getPos();
        currSnapshot->wrapVector(x_a);
        potential =  atom->getParticlePot();
        velocity = atom->getVel();
        kinetic = mass * (velocity[0]*velocity[0] + velocity[1]*velocity[1] +
                           velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
        eatom += (kinetic + potential)/2.0;
        GKappa_t += x_a*(eatom-AvgE_a_);
        }
      }
#ifdef IS_MPI
     MPI_Allreduce(GKappa_t.getArrayPointer(), ThermalHelfandMoment.getArrayPointer(), 3,
                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
#else
     ThermalHelfandMoment = GKappa_t;
#endif
     return ThermalHelfandMoment;

 }

// Returns the Heat Flux Vector S for the system
Vector3d Thermo::getHeatFlux(){
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    SimInfo::MoleculeIterator miter;
    std::vector<Atom*>::iterator aiter;
    Molecule* mol;
    Atom* atom;
    RealType mass;
    Vector3d velocity;
    Vector3d x_a;
    RealType kinetic;
    RealType potential;
    RealType eatom;
    RealType AvgE_a_ = 0;
    // Conductive portion of the heat flux
    Vector3d heatFlux_Jc = V3Zero;
    Vector3d heatFlux_J;
    Vector3d heatFlux_J_local = V3Zero;

    /* Calculate conductive portion of the heat flux */
    for (mol = info_->beginMolecule(miter); mol != NULL;
         mol = info_->nextMolecule(miter)) {

      for (atom = mol->beginAtom(aiter); atom != NULL;
           atom = mol->nextAtom(aiter)) {

        mass = atom->getMass();
        velocity = atom->getVel();
        kinetic = mass * (velocity[0]*velocity[0] + velocity[1]*velocity[1] +
                                   velocity[2]*velocity[2]);
        potential =  atom->getParticlePot() * PhysicalConstants::energyConvert;
        // The potential may not be a 1/2 factor
        eatom += (kinetic + potential)/2.0;
        heatFlux_Jc[0] += eatom*velocity[0];
        heatFlux_Jc[1] += eatom*velocity[1];
        heatFlux_Jc[2] += eatom*velocity[2];
      }
    }
    Vector3d heatFlux_Jv = currSnapshot->statData.getJv() * PhysicalConstants::energyConvert;

    heatFlux_J_local = heatFlux_Jv/2.0 + heatFlux_Jc;
    // Correct for the fact the flux is 1/V (Jc + Jv)
    heatFlux_J_local = heatFlux_J_local/getVolume();


#ifdef IS_MPI
     MPI_Allreduce(heatFlux_J_local.getArrayPointer(), heatFlux_J.getArrayPointer(), 3,
                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
#else
     heatFlux_J = heatFlux_J_local;
#endif

    return heatFlux_J;


}


} //end namespace OpenMD
Revision:	1672
Committed:	Mon Jan 30 21:47:39 2012 UTC (13 years, 5 months ago) by chuckv
File size:	18071 byte(s)
Log Message:	Update for energy units conversion.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35	chuckv	1666	*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41	chuckv	1666
42	gezelter	2	#include <math.h>
43			#include <iostream>
44
45			#ifdef IS_MPI
46			#include <mpi.h>
47			#endif //is_mpi
48
49	tim	3	#include "brains/Thermo.hpp"
50	gezelter	246	#include "primitives/Molecule.hpp"
51	tim	3	#include "utils/simError.h"
52	gezelter	1390	#include "utils/PhysicalConstants.hpp"
53	gezelter	2
54	gezelter	1390	namespace OpenMD {
55	gezelter	2
56	tim	963	RealType Thermo::getKinetic() {
57	gezelter	246	SimInfo::MoleculeIterator miter;
58			std::vector<StuntDouble*>::iterator iiter;
59			Molecule* mol;
60	chuckv	1666	StuntDouble* integrableObject;
61	gezelter	246	Vector3d vel;
62			Vector3d angMom;
63			Mat3x3d I;
64			int i;
65			int j;
66			int k;
67	chrisfen	998	RealType mass;
68	tim	963	RealType kinetic = 0.0;
69			RealType kinetic_global = 0.0;
70	chuckv	1666
71	gezelter	246	for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
72	chuckv	1666	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
73			integrableObject = mol->nextIntegrableObject(iiter)) {
74	gezelter	2
75	chuckv	1666	mass = integrableObject->getMass();
76			vel = integrableObject->getVel();
77
78			kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
79
80			if (integrableObject->isDirectional()) {
81			angMom = integrableObject->getJ();
82			I = integrableObject->getI();
83
84			if (integrableObject->isLinear()) {
85			i = integrableObject->linearAxis();
86			j = (i + 1) % 3;
87			k = (i + 2) % 3;
88			kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
89			} else {
90			kinetic += angMom[0]angMom[0]/I(0, 0) + angMom[1]angMom[1]/I(1, 1)
91			+ angMom[2]*angMom[2]/I(2, 2);
92			}
93			}
94
95	gezelter	507	}
96	gezelter	246	}
97	chuckv	1666
98	gezelter	246	#ifdef IS_MPI
99	gezelter	2
100	tim	963	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
101	gezelter	246	MPI_COMM_WORLD);
102			kinetic = kinetic_global;
103	gezelter	2
104	gezelter	246	#endif //is_mpi
105	gezelter	2
106	gezelter	1390	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
107	gezelter	2
108	gezelter	246	return kinetic;
109	gezelter	507	}
110	gezelter	2
111	tim	963	RealType Thermo::getPotential() {
112			RealType potential = 0.0;
113	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114	tim	963	RealType shortRangePot_local = curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
115	gezelter	2
116	gezelter	246	// Get total potential for entire system from MPI.
117	gezelter	2
118	gezelter	246	#ifdef IS_MPI
119	gezelter	2
120	tim	963	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
121	gezelter	246	MPI_COMM_WORLD);
122	tim	833	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
123	gezelter	2
124	gezelter	246	#else
125	gezelter	2
126	tim	833	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
127	gezelter	2
128			#endif // is_mpi
129
130	gezelter	246	return potential;
131	gezelter	507	}
132	gezelter	2
133	tim	963	RealType Thermo::getTotalE() {
134			RealType total;
135	gezelter	2
136	gezelter	246	total = this->getKinetic() + this->getPotential();
137			return total;
138	gezelter	507	}
139	gezelter	2
140	tim	963	RealType Thermo::getTemperature() {
141	chuckv	1666
142	gezelter	1390	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
143	gezelter	246	return temperature;
144	gezelter	507	}
145	gezelter	2
146	chuckv	1666	RealType Thermo::getVolume() {
147	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148			return curSnapshot->getVolume();
149	gezelter	507	}
150	gezelter	2
151	tim	963	RealType Thermo::getPressure() {
152	gezelter	2
153	gezelter	246	// Relies on the calculation of the full molecular pressure tensor
154	gezelter	2
155
156	gezelter	246	Mat3x3d tensor;
157	tim	963	RealType pressure;
158	gezelter	2
159	gezelter	246	tensor = getPressureTensor();
160	gezelter	2
161	gezelter	1390	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
162	gezelter	2
163	gezelter	246	return pressure;
164	gezelter	507	}
165	gezelter	2
166	tim	963	RealType Thermo::getPressure(int direction) {
167	tim	538
168			// Relies on the calculation of the full molecular pressure tensor
169
170	chuckv	1666
171	tim	538	Mat3x3d tensor;
172	tim	963	RealType pressure;
173	tim	538
174			tensor = getPressureTensor();
175
176	gezelter	1390	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
177	tim	538
178			return pressure;
179			}
180
181	gezelter	507	Mat3x3d Thermo::getPressureTensor() {
182	gezelter	246	// returns pressure tensor in units amufs^-2Ang^-1
183			// routine derived via viral theorem description in:
184			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
185			Mat3x3d pressureTensor;
186			Mat3x3d p_local(0.0);
187			Mat3x3d p_global(0.0);
188	gezelter	2
189	gezelter	246	SimInfo::MoleculeIterator i;
190			std::vector<StuntDouble*>::iterator j;
191			Molecule* mol;
192	chuckv	1666	StuntDouble* integrableObject;
193	gezelter	246	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
194	chuckv	1666	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195			integrableObject = mol->nextIntegrableObject(j)) {
196	gezelter	2
197	chuckv	1666	RealType mass = integrableObject->getMass();
198			Vector3d vcom = integrableObject->getVel();
199			p_local += mass * outProduct(vcom, vcom);
200	gezelter	507	}
201	gezelter	246	}
202	chuckv	1666
203	gezelter	2	#ifdef IS_MPI
204	tim	963	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
205	gezelter	2	#else
206	gezelter	246	p_global = p_local;
207	gezelter	2	#endif // is_mpi
208
209	tim	963	RealType volume = this->getVolume();
210	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
211			Mat3x3d tau = curSnapshot->statData.getTau();
212	gezelter	1126
213	gezelter	1390	pressureTensor = (p_global + PhysicalConstants::energyConvert* tau)/volume;
214	chuckv	1666
215	gezelter	246	return pressureTensor;
216	gezelter	507	}
217	gezelter	2
218	chrisfen	998
219	gezelter	507	void Thermo::saveStat(){
220	gezelter	246	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
221			Stats& stat = currSnapshot->statData;
222	chuckv	1666
223	gezelter	246	stat[Stats::KINETIC_ENERGY] = getKinetic();
224			stat[Stats::POTENTIAL_ENERGY] = getPotential();
225			stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ;
226			stat[Stats::TEMPERATURE] = getTemperature();
227			stat[Stats::PRESSURE] = getPressure();
228	chuckv	1666	stat[Stats::VOLUME] = getVolume();
229	gezelter	2
230	tim	541	Mat3x3d tensor =getPressureTensor();
231	chuckv	1666	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
232			stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
233			stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
234			stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
235			stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
236			stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
237			stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
238			stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
239			stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
240	chuckv	1638	Vector3d GKappa_t = getThermalHelfand();
241			stat[Stats::THERMAL_HELFANDMOMENT_X] = GKappa_t.x();
242			stat[Stats::THERMAL_HELFANDMOMENT_Y] = GKappa_t.y();
243			stat[Stats::THERMAL_HELFANDMOMENT_Z] = GKappa_t.z();
244	chuckv	1671	Vector3d HeatFlux_J = getHeatFlux();
245			stat[Stats::HEATFLUX_X] = HeatFlux_J.x();
246			stat[Stats::HEATFLUX_Y] = HeatFlux_J.y();
247			stat[Stats::HEATFLUX_Z] = HeatFlux_J.z();
248	tim	541
249	chuckv	1671
250	gezelter	1291	Globals* simParams = info_->getSimParams();
251
252	chuckv	1666	if (simParams->haveTaggedAtomPair() &&
253	gezelter	1291	simParams->havePrintTaggedPairDistance()) {
254			if ( simParams->getPrintTaggedPairDistance()) {
255	chuckv	1666
256	gezelter	1291	std::pair<int, int> tap = simParams->getTaggedAtomPair();
257			Vector3d pos1, pos2, rab;
258
259	chuckv	1666	#ifdef IS_MPI
260	gezelter	1313	std::cerr << "tap = " << tap.first << " " << tap.second << std::endl;
261	gezelter	1291
262	chuckv	1666	int mol1 = info_->getGlobalMolMembership(tap.first);
263			int mol2 = info_->getGlobalMolMembership(tap.second);
264	gezelter	1313	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
265
266	gezelter	1291	int proc1 = info_->getMolToProc(mol1);
267			int proc2 = info_->getMolToProc(mol2);
268
269	gezelter	1313	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
270
271	chuckv	1666	RealType data[3];
272	gezelter	1291	if (proc1 == worldRank) {
273			StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
274	gezelter	1313	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
275	gezelter	1291	pos1 = sd1->getPos();
276			data[0] = pos1.x();
277			data[1] = pos1.y();
278	chuckv	1666	data[2] = pos1.z();
279	gezelter	1291	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
280			} else {
281			MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
282			pos1 = Vector3d(data);
283			}
284	chuckv	1292
285
286	gezelter	1291	if (proc2 == worldRank) {
287			StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
288	gezelter	1313	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
289	gezelter	1291	pos2 = sd2->getPos();
290			data[0] = pos2.x();
291			data[1] = pos2.y();
292	chuckv	1666	data[2] = pos2.z();
293	gezelter	1291	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
294			} else {
295			MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
296			pos2 = Vector3d(data);
297			}
298			#else
299			StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
300			StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
301			pos1 = at1->getPos();
302			pos2 = at2->getPos();
303	chuckv	1666	#endif
304	gezelter	1291	rab = pos2 - pos1;
305			currSnapshot->wrapVector(rab);
306			stat[Stats::TAGGED_PAIR_DISTANCE] = rab.length();
307			}
308			}
309	chuckv	1666
310	gezelter	246	/*@todo need refactorying/
311			//Conserved Quantity is set by integrator and time is set by setTime
312	chuckv	1666
313	gezelter	507	}
314	gezelter	2
315	jmichalk	1604
316
317			Vector3d Thermo::getBoxDipole() {
318			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
319			SimInfo::MoleculeIterator miter;
320			std::vector<Atom*>::iterator aiter;
321			Molecule* mol;
322			Atom* atom;
323			RealType charge;
324			RealType moment(0.0);
325			Vector3d ri(0.0);
326			Vector3d dipoleVector(0.0);
327			Vector3d nPos(0.0);
328			Vector3d pPos(0.0);
329			RealType nChg(0.0);
330			RealType pChg(0.0);
331			int nCount = 0;
332			int pCount = 0;
333
334			RealType chargeToC = 1.60217733e-19;
335			RealType angstromToM = 1.0e-10; RealType debyeToCm = 3.33564095198e-30;
336
337			for (mol = info_->beginMolecule(miter); mol != NULL;
338			mol = info_->nextMolecule(miter)) {
339
340			for (atom = mol->beginAtom(aiter); atom != NULL;
341			atom = mol->nextAtom(aiter)) {
342
343			if (atom->isCharge() ) {
344			charge = 0.0;
345			GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
346			if (data != NULL) {
347
348			charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
349			charge *= chargeToC;
350
351			ri = atom->getPos();
352			currSnapshot->wrapVector(ri);
353			ri *= angstromToM;
354
355			if (charge < 0.0) {
356			nPos += ri;
357			nChg -= charge;
358			nCount++;
359			} else if (charge > 0.0) {
360			pPos += ri;
361			pChg += charge;
362			pCount++;
363			}
364			}
365			}
366
367			if (atom->isDipole() ) {
368			Vector3d u_i = atom->getElectroFrame().getColumn(2);
369			GenericData* data = dynamic_cast<DirectionalAtomType*>(atom->getAtomType())->getPropertyByName("Dipole");
370			if (data != NULL) {
371			moment = (dynamic_cast<DoubleGenericData*>(data))->getData();
372
373			moment *= debyeToCm;
374			dipoleVector += u_i * moment;
375			}
376			}
377			}
378			}
379
380
381			#ifdef IS_MPI
382			RealType pChg_global, nChg_global;
383			int pCount_global, nCount_global;
384			Vector3d pPos_global, nPos_global, dipVec_global;
385
386			MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
387			MPI_COMM_WORLD);
388			pChg = pChg_global;
389			MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
390			MPI_COMM_WORLD);
391			nChg = nChg_global;
392			MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
393			MPI_COMM_WORLD);
394			pCount = pCount_global;
395			MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
396			MPI_COMM_WORLD);
397			nCount = nCount_global;
398			MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
399			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
400			pPos = pPos_global;
401			MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
402			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
403			nPos = nPos_global;
404			MPI_Allreduce(dipoleVector.getArrayPointer(),
405			dipVec_global.getArrayPointer(), 3,
406			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
407			dipoleVector = dipVec_global;
408			#endif //is_mpi
409
410			// first load the accumulated dipole moment (if dipoles were present)
411			Vector3d boxDipole = dipoleVector;
412			// now include the dipole moment due to charges
413			// use the lesser of the positive and negative charge totals
414			RealType chg_value = nChg <= pChg ? nChg : pChg;
415
416			// find the average positions
417			if (pCount > 0 && nCount > 0 ) {
418			pPos /= pCount;
419			nPos /= nCount;
420			}
421
422			// dipole is from the negative to the positive (physics notation)
423			boxDipole += (pPos - nPos) * chg_value;
424
425			return boxDipole;
426			}
427
428	chuckv	1638	Vector3d Thermo::getThermalHelfand() {
429			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
430			SimInfo::MoleculeIterator miter;
431			std::vector<Atom*>::iterator aiter;
432			Molecule* mol;
433			Atom* atom;
434			RealType mass;
435			Vector3d velocity;
436			Vector3d x_a;
437			RealType kinetic;
438			RealType potential;
439			RealType eatom;
440			RealType AvgE_a_ = 0;
441			Vector3d GKappa_t = V3Zero;
442			Vector3d ThermalHelfandMoment;
443	chuckv	1666
444	chuckv	1638	for (mol = info_->beginMolecule(miter); mol != NULL;
445			mol = info_->nextMolecule(miter)) {
446	jmichalk	1604
447	chuckv	1638	for (atom = mol->beginAtom(aiter); atom != NULL;
448			atom = mol->nextAtom(aiter)) {
449
450			mass = atom->getMass();
451			velocity = atom->getVel();
452	chuckv	1666	kinetic = mass * (velocity[0]velocity[0] + velocity[1]velocity[1] +
453	chuckv	1638	velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
454			potential = atom->getParticlePot();
455			eatom += (kinetic + potential)/2.0;
456			}
457			}
458
459			int natoms = info_->getNGlobalAtoms();
460			#ifdef IS_MPI
461	chuckv	1666
462	chuckv	1638	MPI_Allreduce(&eatom, &AvgE_a_, 1, MPI_REALTYPE, MPI_SUM,
463			MPI_COMM_WORLD);
464	chuckv	1666	#else
465	chuckv	1638	AvgE_a_ = eatom;
466			#endif
467			AvgE_a_ = AvgE_a_/RealType(natoms);
468	chuckv	1666
469	chuckv	1638	for (mol = info_->beginMolecule(miter); mol != NULL;
470			mol = info_->nextMolecule(miter)) {
471	chuckv	1666
472	chuckv	1638	for (atom = mol->beginAtom(aiter); atom != NULL;
473			atom = mol->nextAtom(aiter)) {
474	chuckv	1666
475	chuckv	1638	/* We think that x_a is relative to the total box and should be a wrapped coordinate */
476			x_a = atom->getPos();
477			currSnapshot->wrapVector(x_a);
478			potential = atom->getParticlePot();
479	chuckv	1666	velocity = atom->getVel();
480			kinetic = mass * (velocity[0]velocity[0] + velocity[1]velocity[1] +
481			velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
482	chuckv	1667	eatom += (kinetic + potential)/2.0;
483	chuckv	1666	GKappa_t += x_a*(eatom-AvgE_a_);
484	chuckv	1638	}
485			}
486			#ifdef IS_MPI
487			MPI_Allreduce(GKappa_t.getArrayPointer(), ThermalHelfandMoment.getArrayPointer(), 3,
488			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
489	chuckv	1666	#else
490	chuckv	1638	ThermalHelfandMoment = GKappa_t;
491	chuckv	1666	#endif
492	chuckv	1638	return ThermalHelfandMoment;
493	chuckv	1666
494	chuckv	1638	}
495
496	chuckv	1671	// Returns the Heat Flux Vector S for the system
497			Vector3d Thermo::getHeatFlux(){
498			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
499			SimInfo::MoleculeIterator miter;
500			std::vector<Atom*>::iterator aiter;
501			Molecule* mol;
502			Atom* atom;
503			RealType mass;
504			Vector3d velocity;
505			Vector3d x_a;
506			RealType kinetic;
507			RealType potential;
508			RealType eatom;
509			RealType AvgE_a_ = 0;
510			// Conductive portion of the heat flux
511			Vector3d heatFlux_Jc = V3Zero;
512			Vector3d heatFlux_J;
513			Vector3d heatFlux_J_local = V3Zero;
514	chuckv	1638
515	chuckv	1671	/* Calculate conductive portion of the heat flux */
516			for (mol = info_->beginMolecule(miter); mol != NULL;
517			mol = info_->nextMolecule(miter)) {
518	chuckv	1638
519	chuckv	1671	for (atom = mol->beginAtom(aiter); atom != NULL;
520			atom = mol->nextAtom(aiter)) {
521
522			mass = atom->getMass();
523			velocity = atom->getVel();
524			kinetic = mass * (velocity[0]velocity[0] + velocity[1]velocity[1] +
525	chuckv	1672	velocity[2]*velocity[2]);
526			potential = atom->getParticlePot() * PhysicalConstants::energyConvert;
527			// The potential may not be a 1/2 factor
528	chuckv	1671	eatom += (kinetic + potential)/2.0;
529			heatFlux_Jc[0] += eatom*velocity[0];
530			heatFlux_Jc[1] += eatom*velocity[1];
531			heatFlux_Jc[2] += eatom*velocity[2];
532			}
533			}
534	chuckv	1672	Vector3d heatFlux_Jv = currSnapshot->statData.getJv() * PhysicalConstants::energyConvert;
535	chuckv	1671
536	chuckv	1672	heatFlux_J_local = heatFlux_Jv/2.0 + heatFlux_Jc;
537			// Correct for the fact the flux is 1/V (Jc + Jv)
538			heatFlux_J_local = heatFlux_J_local/getVolume();
539	chuckv	1671
540
541			#ifdef IS_MPI
542			MPI_Allreduce(heatFlux_J_local.getArrayPointer(), heatFlux_J.getArrayPointer(), 3,
543			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
544			#else
545			heatFlux_J = heatFlux_J_local;
546			#endif
547
548			return heatFlux_J;
549
550
551			}
552
553
554
555
556	gezelter	1390	} //end namespace OpenMD