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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#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"
#include "types/MultipoleAdapter.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::getElectronicTemperature() {
    SimInfo::MoleculeIterator miter;
    std::vector<Atom*>::iterator iiter;
    Molecule* mol;
    Atom* atom;    
    RealType cvel;
    RealType cmass;
    RealType kinetic = 0.0;
    RealType kinetic_global = 0.0;
    
    for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
      for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL; 
           atom = mol->nextFluctuatingCharge(iiter)) {
        cmass = atom->getChargeMass();
        cvel = atom->getFlucQVel();
        
        kinetic += cmass * cvel * cvel;
        
      }
    }
    
#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 ( 2.0 * kinetic) / (info_->getNFluctuatingCharges()* PhysicalConstants::kb );    
  }


  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 stressTensor = curSnapshot->getStressTensor();

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

    // grab the simulation box dipole moment if specified
    if (info_->getCalcBoxDipole()){
      Vector3d totalDipole = getBoxDipole();
      stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
      stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
      stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
    }

    Globals* simParams = info_->getSimParams();
    // grab the heat flux if desired
    if (simParams->havePrintHeatFlux()) {
      if (simParams->getPrintHeatFlux()){
        Vector3d heatFlux = getHeatFlux();
        stat[Stats::HEATFLUX_X] = heatFlux(0);
        stat[Stats::HEATFLUX_Y] = heatFlux(1);
        stat[Stats::HEATFLUX_Z] = heatFlux(2);
      }
    }

    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++;
            }                       
          }
        }
        
        MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
        if (ma.isDipole() ) {
          Vector3d u_i = atom->getElectroFrame().getColumn(2);
          moment = ma.getDipoleMoment();
          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;
  }

  // Returns the Heat Flux Vector for the system
  Vector3d Thermo::getHeatFlux(){
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    SimInfo::MoleculeIterator miter;
    std::vector<StuntDouble*>::iterator iiter;
    Molecule* mol;
    StuntDouble* integrableObject;    
    RigidBody::AtomIterator ai; 
    Atom* atom;       
    Vector3d vel;
    Vector3d angMom;
    Mat3x3d I;
    int i;
    int j;
    int k;
    RealType mass;

    Vector3d x_a;
    RealType kinetic;
    RealType potential;
    RealType eatom;
    RealType AvgE_a_ = 0;
    // Convective portion of the heat flux
    Vector3d heatFluxJc = V3Zero;

    /* Calculate convective portion of the heat flux */
    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);
          }
        }

        potential = 0.0;

        if (integrableObject->isRigidBody()) {
          RigidBody* rb = dynamic_cast<RigidBody*>(integrableObject);
          for (atom = rb->beginAtom(ai); atom != NULL; 
               atom = rb->nextAtom(ai)) {
            potential +=  atom->getParticlePot();
          }          
        } else {
          potential = integrableObject->getParticlePot();
          cerr << "ppot = "  << potential << "\n";
        }

        potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
        // The potential may not be a 1/2 factor
        eatom = (kinetic + potential)/2.0;  // amu A^2/fs^2
        heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
        heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
        heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
      }
    }

    std::cerr << "Heat flux heatFluxJc is: " << heatFluxJc << std::endl;

    /* The J_v vector is reduced in fortan so everyone has the global
     *  Jv. Jc is computed over the local atoms and must be reduced
     *  among all processors.
     */
#ifdef IS_MPI
    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE, 
                              MPI::SUM);
#endif
    
    // (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3

    Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() * 
      PhysicalConstants::energyConvert;
    
    std::cerr << "Heat flux Jc is: " << heatFluxJc << std::endl;
    std::cerr << "Heat flux Jv is: " << heatFluxJv << std::endl;
    
    // Correct for the fact the flux is 1/V (Jc + Jv)
    return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3 
  }
} //end namespace OpenMD
Revision:	1723
Committed:	Thu May 24 20:59:54 2012 UTC (12 years, 11 months ago) by gezelter
File size:	18900 byte(s)
Log Message:	Bug fixes for heat flux import
#	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			*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	2	#include <math.h>
44			#include <iostream>
45
46			#ifdef IS_MPI
47			#include <mpi.h>
48			#endif //is_mpi
49
50	tim	3	#include "brains/Thermo.hpp"
51	gezelter	246	#include "primitives/Molecule.hpp"
52	tim	3	#include "utils/simError.h"
53	gezelter	1390	#include "utils/PhysicalConstants.hpp"
54	gezelter	1710	#include "types/MultipoleAdapter.hpp"
55	gezelter	2
56	gezelter	1390	namespace OpenMD {
57	gezelter	2
58	tim	963	RealType Thermo::getKinetic() {
59	gezelter	246	SimInfo::MoleculeIterator miter;
60			std::vector<StuntDouble*>::iterator iiter;
61			Molecule* mol;
62			StuntDouble* integrableObject;
63			Vector3d vel;
64			Vector3d angMom;
65			Mat3x3d I;
66			int i;
67			int j;
68			int k;
69	chrisfen	998	RealType mass;
70	tim	963	RealType kinetic = 0.0;
71			RealType kinetic_global = 0.0;
72	gezelter	246
73			for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
74	gezelter	507	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
75			integrableObject = mol->nextIntegrableObject(iiter)) {
76	gezelter	945
77	chrisfen	998	mass = integrableObject->getMass();
78			vel = integrableObject->getVel();
79	gezelter	945
80	gezelter	507	kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
81	gezelter	945
82	gezelter	507	if (integrableObject->isDirectional()) {
83			angMom = integrableObject->getJ();
84			I = integrableObject->getI();
85	gezelter	2
86	gezelter	507	if (integrableObject->isLinear()) {
87			i = integrableObject->linearAxis();
88			j = (i + 1) % 3;
89			k = (i + 2) % 3;
90			kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
91			} else {
92			kinetic += angMom[0]angMom[0]/I(0, 0) + angMom[1]angMom[1]/I(1, 1)
93			+ angMom[2]*angMom[2]/I(2, 2);
94			}
95			}
96	gezelter	246
97	gezelter	507	}
98	gezelter	246	}
99
100			#ifdef IS_MPI
101	gezelter	2
102	tim	963	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
103	gezelter	246	MPI_COMM_WORLD);
104			kinetic = kinetic_global;
105	gezelter	2
106	gezelter	246	#endif //is_mpi
107	gezelter	2
108	gezelter	1390	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
109	gezelter	2
110	gezelter	246	return kinetic;
111	gezelter	507	}
112	gezelter	2
113	tim	963	RealType Thermo::getPotential() {
114			RealType potential = 0.0;
115	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
116	tim	963	RealType shortRangePot_local = curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
117	gezelter	2
118	gezelter	246	// Get total potential for entire system from MPI.
119	gezelter	2
120	gezelter	246	#ifdef IS_MPI
121	gezelter	2
122	tim	963	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
123	gezelter	246	MPI_COMM_WORLD);
124	tim	833	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
125	gezelter	2
126	gezelter	246	#else
127	gezelter	2
128	tim	833	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
129	gezelter	2
130			#endif // is_mpi
131
132	gezelter	246	return potential;
133	gezelter	507	}
134	gezelter	2
135	tim	963	RealType Thermo::getTotalE() {
136			RealType total;
137	gezelter	2
138	gezelter	246	total = this->getKinetic() + this->getPotential();
139			return total;
140	gezelter	507	}
141	gezelter	2
142	tim	963	RealType Thermo::getTemperature() {
143	gezelter	246
144	gezelter	1390	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
145	gezelter	246	return temperature;
146	gezelter	507	}
147	gezelter	2
148	gezelter	1715	RealType Thermo::getElectronicTemperature() {
149			SimInfo::MoleculeIterator miter;
150			std::vector<Atom*>::iterator iiter;
151			Molecule* mol;
152			Atom* atom;
153			RealType cvel;
154			RealType cmass;
155			RealType kinetic = 0.0;
156			RealType kinetic_global = 0.0;
157
158			for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
159			for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL;
160			atom = mol->nextFluctuatingCharge(iiter)) {
161			cmass = atom->getChargeMass();
162			cvel = atom->getFlucQVel();
163
164			kinetic += cmass * cvel * cvel;
165
166			}
167			}
168
169			#ifdef IS_MPI
170
171			MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
172			MPI_COMM_WORLD);
173			kinetic = kinetic_global;
174
175			#endif //is_mpi
176
177			kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
178			return ( 2.0 * kinetic) / (info_->getNFluctuatingCharges()* PhysicalConstants::kb );
179			}
180
181
182
183
184	tim	963	RealType Thermo::getVolume() {
185	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
186			return curSnapshot->getVolume();
187	gezelter	507	}
188	gezelter	2
189	tim	963	RealType Thermo::getPressure() {
190	gezelter	2
191	gezelter	246	// Relies on the calculation of the full molecular pressure tensor
192	gezelter	2
193
194	gezelter	246	Mat3x3d tensor;
195	tim	963	RealType pressure;
196	gezelter	2
197	gezelter	246	tensor = getPressureTensor();
198	gezelter	2
199	gezelter	1390	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
200	gezelter	2
201	gezelter	246	return pressure;
202	gezelter	507	}
203	gezelter	2
204	tim	963	RealType Thermo::getPressure(int direction) {
205	tim	538
206			// Relies on the calculation of the full molecular pressure tensor
207
208
209			Mat3x3d tensor;
210	tim	963	RealType pressure;
211	tim	538
212			tensor = getPressureTensor();
213
214	gezelter	1390	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
215	tim	538
216			return pressure;
217			}
218
219	gezelter	507	Mat3x3d Thermo::getPressureTensor() {
220	gezelter	246	// returns pressure tensor in units amufs^-2Ang^-1
221			// routine derived via viral theorem description in:
222			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
223			Mat3x3d pressureTensor;
224			Mat3x3d p_local(0.0);
225			Mat3x3d p_global(0.0);
226	gezelter	2
227	gezelter	246	SimInfo::MoleculeIterator i;
228			std::vector<StuntDouble*>::iterator j;
229			Molecule* mol;
230			StuntDouble* integrableObject;
231			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
232	gezelter	507	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
233			integrableObject = mol->nextIntegrableObject(j)) {
234	gezelter	2
235	tim	963	RealType mass = integrableObject->getMass();
236	gezelter	507	Vector3d vcom = integrableObject->getVel();
237			p_local += mass * outProduct(vcom, vcom);
238			}
239	gezelter	246	}
240	gezelter	2
241			#ifdef IS_MPI
242	tim	963	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
243	gezelter	2	#else
244	gezelter	246	p_global = p_local;
245	gezelter	2	#endif // is_mpi
246
247	tim	963	RealType volume = this->getVolume();
248	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
249	gezelter	1723	Mat3x3d stressTensor = curSnapshot->getStressTensor();
250	gezelter	1126
251	gezelter	1723	pressureTensor = (p_global +
252			PhysicalConstants::energyConvert * stressTensor)/volume;
253	chrisfen	998
254	gezelter	246	return pressureTensor;
255	gezelter	507	}
256	gezelter	2
257	chrisfen	998
258	gezelter	507	void Thermo::saveStat(){
259	gezelter	246	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
260			Stats& stat = currSnapshot->statData;
261	gezelter	2
262	gezelter	246	stat[Stats::KINETIC_ENERGY] = getKinetic();
263			stat[Stats::POTENTIAL_ENERGY] = getPotential();
264			stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ;
265			stat[Stats::TEMPERATURE] = getTemperature();
266			stat[Stats::PRESSURE] = getPressure();
267			stat[Stats::VOLUME] = getVolume();
268	gezelter	2
269	tim	541	Mat3x3d tensor =getPressureTensor();
270	gezelter	1126	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
271			stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
272			stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
273			stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
274			stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
275			stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
276			stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
277			stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
278			stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
279	tim	541
280	gezelter	1503	// grab the simulation box dipole moment if specified
281			if (info_->getCalcBoxDipole()){
282			Vector3d totalDipole = getBoxDipole();
283			stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
284			stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
285			stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
286			}
287	tim	541
288	gezelter	1291	Globals* simParams = info_->getSimParams();
289	gezelter	1723	// grab the heat flux if desired
290			if (simParams->havePrintHeatFlux()) {
291			if (simParams->getPrintHeatFlux()){
292			Vector3d heatFlux = getHeatFlux();
293			stat[Stats::HEATFLUX_X] = heatFlux(0);
294			stat[Stats::HEATFLUX_Y] = heatFlux(1);
295			stat[Stats::HEATFLUX_Z] = heatFlux(2);
296			}
297			}
298	gezelter	1291
299			if (simParams->haveTaggedAtomPair() &&
300			simParams->havePrintTaggedPairDistance()) {
301			if ( simParams->getPrintTaggedPairDistance()) {
302
303			std::pair<int, int> tap = simParams->getTaggedAtomPair();
304			Vector3d pos1, pos2, rab;
305
306			#ifdef IS_MPI
307	gezelter	1313	std::cerr << "tap = " << tap.first << " " << tap.second << std::endl;
308	gezelter	1291
309	chuckv	1292	int mol1 = info_->getGlobalMolMembership(tap.first);
310			int mol2 = info_->getGlobalMolMembership(tap.second);
311	gezelter	1313	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
312
313	gezelter	1291	int proc1 = info_->getMolToProc(mol1);
314			int proc2 = info_->getMolToProc(mol2);
315
316	gezelter	1313	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
317
318	chuckv	1292	RealType data[3];
319	gezelter	1291	if (proc1 == worldRank) {
320			StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
321	gezelter	1313	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
322	gezelter	1291	pos1 = sd1->getPos();
323			data[0] = pos1.x();
324			data[1] = pos1.y();
325			data[2] = pos1.z();
326			MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
327			} else {
328			MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
329			pos1 = Vector3d(data);
330			}
331	chuckv	1292
332
333	gezelter	1291	if (proc2 == worldRank) {
334			StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
335	gezelter	1313	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
336	gezelter	1291	pos2 = sd2->getPos();
337			data[0] = pos2.x();
338			data[1] = pos2.y();
339			data[2] = pos2.z();
340			MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
341			} else {
342			MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
343			pos2 = Vector3d(data);
344			}
345			#else
346			StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
347			StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
348			pos1 = at1->getPos();
349			pos2 = at2->getPos();
350			#endif
351			rab = pos2 - pos1;
352			currSnapshot->wrapVector(rab);
353			stat[Stats::TAGGED_PAIR_DISTANCE] = rab.length();
354			}
355			}
356
357	gezelter	246	/*@todo need refactorying/
358			//Conserved Quantity is set by integrator and time is set by setTime
359	gezelter	2
360	gezelter	507	}
361	gezelter	2
362	gezelter	1503
363			Vector3d Thermo::getBoxDipole() {
364			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
365			SimInfo::MoleculeIterator miter;
366			std::vector<Atom*>::iterator aiter;
367			Molecule* mol;
368			Atom* atom;
369			RealType charge;
370			RealType moment(0.0);
371			Vector3d ri(0.0);
372			Vector3d dipoleVector(0.0);
373			Vector3d nPos(0.0);
374			Vector3d pPos(0.0);
375			RealType nChg(0.0);
376			RealType pChg(0.0);
377			int nCount = 0;
378			int pCount = 0;
379
380			RealType chargeToC = 1.60217733e-19;
381			RealType angstromToM = 1.0e-10;
382			RealType debyeToCm = 3.33564095198e-30;
383
384			for (mol = info_->beginMolecule(miter); mol != NULL;
385			mol = info_->nextMolecule(miter)) {
386
387			for (atom = mol->beginAtom(aiter); atom != NULL;
388			atom = mol->nextAtom(aiter)) {
389
390			if (atom->isCharge() ) {
391			charge = 0.0;
392			GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
393			if (data != NULL) {
394
395			charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
396			charge *= chargeToC;
397
398			ri = atom->getPos();
399			currSnapshot->wrapVector(ri);
400			ri *= angstromToM;
401
402			if (charge < 0.0) {
403			nPos += ri;
404			nChg -= charge;
405			nCount++;
406			} else if (charge > 0.0) {
407			pPos += ri;
408			pChg += charge;
409			pCount++;
410			}
411			}
412			}
413
414	gezelter	1710	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
415			if (ma.isDipole() ) {
416	gezelter	1503	Vector3d u_i = atom->getElectroFrame().getColumn(2);
417	gezelter	1710	moment = ma.getDipoleMoment();
418			moment *= debyeToCm;
419			dipoleVector += u_i * moment;
420	gezelter	1503	}
421			}
422			}
423
424
425			#ifdef IS_MPI
426			RealType pChg_global, nChg_global;
427			int pCount_global, nCount_global;
428			Vector3d pPos_global, nPos_global, dipVec_global;
429
430			MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
431			MPI_COMM_WORLD);
432			pChg = pChg_global;
433			MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
434			MPI_COMM_WORLD);
435			nChg = nChg_global;
436			MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
437			MPI_COMM_WORLD);
438			pCount = pCount_global;
439			MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
440			MPI_COMM_WORLD);
441			nCount = nCount_global;
442			MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
443			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
444			pPos = pPos_global;
445			MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
446			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
447			nPos = nPos_global;
448			MPI_Allreduce(dipoleVector.getArrayPointer(),
449			dipVec_global.getArrayPointer(), 3,
450			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
451			dipoleVector = dipVec_global;
452			#endif //is_mpi
453
454			// first load the accumulated dipole moment (if dipoles were present)
455			Vector3d boxDipole = dipoleVector;
456			// now include the dipole moment due to charges
457			// use the lesser of the positive and negative charge totals
458			RealType chg_value = nChg <= pChg ? nChg : pChg;
459
460			// find the average positions
461			if (pCount > 0 && nCount > 0 ) {
462			pPos /= pCount;
463			nPos /= nCount;
464			}
465
466			// dipole is from the negative to the positive (physics notation)
467			boxDipole += (pPos - nPos) * chg_value;
468
469			return boxDipole;
470			}
471	gezelter	1723
472			// Returns the Heat Flux Vector for the system
473			Vector3d Thermo::getHeatFlux(){
474			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
475			SimInfo::MoleculeIterator miter;
476			std::vector<StuntDouble*>::iterator iiter;
477			Molecule* mol;
478			StuntDouble* integrableObject;
479			RigidBody::AtomIterator ai;
480			Atom* atom;
481			Vector3d vel;
482			Vector3d angMom;
483			Mat3x3d I;
484			int i;
485			int j;
486			int k;
487			RealType mass;
488
489			Vector3d x_a;
490			RealType kinetic;
491			RealType potential;
492			RealType eatom;
493			RealType AvgE_a_ = 0;
494			// Convective portion of the heat flux
495			Vector3d heatFluxJc = V3Zero;
496
497			/* Calculate convective portion of the heat flux */
498			for (mol = info_->beginMolecule(miter); mol != NULL;
499			mol = info_->nextMolecule(miter)) {
500
501			for (integrableObject = mol->beginIntegrableObject(iiter);
502			integrableObject != NULL;
503			integrableObject = mol->nextIntegrableObject(iiter)) {
504
505			mass = integrableObject->getMass();
506			vel = integrableObject->getVel();
507
508			kinetic = mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
509
510			if (integrableObject->isDirectional()) {
511			angMom = integrableObject->getJ();
512			I = integrableObject->getI();
513
514			if (integrableObject->isLinear()) {
515			i = integrableObject->linearAxis();
516			j = (i + 1) % 3;
517			k = (i + 2) % 3;
518			kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
519			} else {
520			kinetic += angMom[0]angMom[0]/I(0, 0) + angMom[1]angMom[1]/I(1, 1)
521			+ angMom[2]*angMom[2]/I(2, 2);
522			}
523			}
524
525			potential = 0.0;
526
527			if (integrableObject->isRigidBody()) {
528			RigidBody* rb = dynamic_cast<RigidBody*>(integrableObject);
529			for (atom = rb->beginAtom(ai); atom != NULL;
530			atom = rb->nextAtom(ai)) {
531			potential += atom->getParticlePot();
532			}
533			} else {
534			potential = integrableObject->getParticlePot();
535			cerr << "ppot = " << potential << "\n";
536			}
537
538			potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
539			// The potential may not be a 1/2 factor
540			eatom = (kinetic + potential)/2.0; // amu A^2/fs^2
541			heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
542			heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
543			heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
544			}
545			}
546
547			std::cerr << "Heat flux heatFluxJc is: " << heatFluxJc << std::endl;
548
549			/* The J_v vector is reduced in fortan so everyone has the global
550			* Jv. Jc is computed over the local atoms and must be reduced
551			* among all processors.
552			*/
553			#ifdef IS_MPI
554			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
555			MPI::SUM);
556			#endif
557
558			// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
559
560			Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
561			PhysicalConstants::energyConvert;
562
563			std::cerr << "Heat flux Jc is: " << heatFluxJc << std::endl;
564			std::cerr << "Heat flux Jv is: " << heatFluxJv << std::endl;
565
566			// Correct for the fact the flux is 1/V (Jc + Jv)
567			return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
568			}
569	gezelter	1390	} //end namespace OpenMD