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();
    potential = curSnapshot->getShortRangePotential() + curSnapshot->getLongRangePotential();
    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;
    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:	1760
Committed:	Thu Jun 21 19:26:46 2012 UTC (12 years, 10 months ago) by gezelter
File size:	18499 byte(s)
Log Message:	Some bugfixes (CholeskyDecomposition), more work on fluctuating charges, migrating stats stuff into frameData
#	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	1760
116	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
117	gezelter	1760	potential = curSnapshot->getShortRangePotential() + curSnapshot->getLongRangePotential();
118	gezelter	246	return potential;
119	gezelter	507	}
120	gezelter	2
121	tim	963	RealType Thermo::getTotalE() {
122			RealType total;
123	gezelter	2
124	gezelter	246	total = this->getKinetic() + this->getPotential();
125			return total;
126	gezelter	507	}
127	gezelter	2
128	tim	963	RealType Thermo::getTemperature() {
129	gezelter	246
130	gezelter	1390	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
131	gezelter	246	return temperature;
132	gezelter	507	}
133	gezelter	2
134	gezelter	1715	RealType Thermo::getElectronicTemperature() {
135			SimInfo::MoleculeIterator miter;
136			std::vector<Atom*>::iterator iiter;
137			Molecule* mol;
138			Atom* atom;
139			RealType cvel;
140			RealType cmass;
141			RealType kinetic = 0.0;
142			RealType kinetic_global = 0.0;
143
144			for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
145			for (atom = mol->beginFluctuatingCharge(iiter); atom != NULL;
146			atom = mol->nextFluctuatingCharge(iiter)) {
147			cmass = atom->getChargeMass();
148			cvel = atom->getFlucQVel();
149
150			kinetic += cmass * cvel * cvel;
151
152			}
153			}
154
155			#ifdef IS_MPI
156
157			MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
158			MPI_COMM_WORLD);
159			kinetic = kinetic_global;
160
161			#endif //is_mpi
162
163	jmichalk	1733	kinetic = kinetic * 0.5;
164	gezelter	1715	return ( 2.0 * kinetic) / (info_->getNFluctuatingCharges()* PhysicalConstants::kb );
165			}
166
167
168
169
170	tim	963	RealType Thermo::getVolume() {
171	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
172			return curSnapshot->getVolume();
173	gezelter	507	}
174	gezelter	2
175	tim	963	RealType Thermo::getPressure() {
176	gezelter	2
177	gezelter	246	// Relies on the calculation of the full molecular pressure tensor
178	gezelter	2
179
180	gezelter	246	Mat3x3d tensor;
181	tim	963	RealType pressure;
182	gezelter	2
183	gezelter	246	tensor = getPressureTensor();
184	gezelter	2
185	gezelter	1390	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
186	gezelter	2
187	gezelter	246	return pressure;
188	gezelter	507	}
189	gezelter	2
190	tim	963	RealType Thermo::getPressure(int direction) {
191	tim	538
192			// Relies on the calculation of the full molecular pressure tensor
193
194
195			Mat3x3d tensor;
196	tim	963	RealType pressure;
197	tim	538
198			tensor = getPressureTensor();
199
200	gezelter	1390	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
201	tim	538
202			return pressure;
203			}
204
205	gezelter	507	Mat3x3d Thermo::getPressureTensor() {
206	gezelter	246	// returns pressure tensor in units amufs^-2Ang^-1
207			// routine derived via viral theorem description in:
208			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
209			Mat3x3d pressureTensor;
210			Mat3x3d p_local(0.0);
211			Mat3x3d p_global(0.0);
212	gezelter	2
213	gezelter	246	SimInfo::MoleculeIterator i;
214			std::vector<StuntDouble*>::iterator j;
215			Molecule* mol;
216			StuntDouble* integrableObject;
217			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
218	gezelter	507	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
219			integrableObject = mol->nextIntegrableObject(j)) {
220	gezelter	2
221	tim	963	RealType mass = integrableObject->getMass();
222	gezelter	507	Vector3d vcom = integrableObject->getVel();
223			p_local += mass * outProduct(vcom, vcom);
224			}
225	gezelter	246	}
226	gezelter	2
227			#ifdef IS_MPI
228	tim	963	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
229	gezelter	2	#else
230	gezelter	246	p_global = p_local;
231	gezelter	2	#endif // is_mpi
232
233	tim	963	RealType volume = this->getVolume();
234	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
235	gezelter	1723	Mat3x3d stressTensor = curSnapshot->getStressTensor();
236	gezelter	1126
237	gezelter	1723	pressureTensor = (p_global +
238			PhysicalConstants::energyConvert * stressTensor)/volume;
239	chrisfen	998
240	gezelter	246	return pressureTensor;
241	gezelter	507	}
242	gezelter	2
243	chrisfen	998
244	gezelter	507	void Thermo::saveStat(){
245	gezelter	246	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
246			Stats& stat = currSnapshot->statData;
247	gezelter	2
248	gezelter	246	stat[Stats::KINETIC_ENERGY] = getKinetic();
249			stat[Stats::POTENTIAL_ENERGY] = getPotential();
250			stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ;
251			stat[Stats::TEMPERATURE] = getTemperature();
252			stat[Stats::PRESSURE] = getPressure();
253			stat[Stats::VOLUME] = getVolume();
254	gezelter	2
255	tim	541	Mat3x3d tensor =getPressureTensor();
256	gezelter	1126	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
257			stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
258			stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
259			stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
260			stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
261			stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
262			stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
263			stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
264			stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
265	tim	541
266	gezelter	1503	// grab the simulation box dipole moment if specified
267			if (info_->getCalcBoxDipole()){
268			Vector3d totalDipole = getBoxDipole();
269			stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
270			stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
271			stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
272			}
273	tim	541
274	gezelter	1291	Globals* simParams = info_->getSimParams();
275	gezelter	1723	// grab the heat flux if desired
276			if (simParams->havePrintHeatFlux()) {
277			if (simParams->getPrintHeatFlux()){
278			Vector3d heatFlux = getHeatFlux();
279			stat[Stats::HEATFLUX_X] = heatFlux(0);
280			stat[Stats::HEATFLUX_Y] = heatFlux(1);
281			stat[Stats::HEATFLUX_Z] = heatFlux(2);
282			}
283			}
284	gezelter	1291
285			if (simParams->haveTaggedAtomPair() &&
286			simParams->havePrintTaggedPairDistance()) {
287			if ( simParams->getPrintTaggedPairDistance()) {
288
289			std::pair<int, int> tap = simParams->getTaggedAtomPair();
290			Vector3d pos1, pos2, rab;
291
292			#ifdef IS_MPI
293	gezelter	1313	std::cerr << "tap = " << tap.first << " " << tap.second << std::endl;
294	gezelter	1291
295	chuckv	1292	int mol1 = info_->getGlobalMolMembership(tap.first);
296			int mol2 = info_->getGlobalMolMembership(tap.second);
297	gezelter	1313	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
298
299	gezelter	1291	int proc1 = info_->getMolToProc(mol1);
300			int proc2 = info_->getMolToProc(mol2);
301
302	gezelter	1313	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
303
304	chuckv	1292	RealType data[3];
305	gezelter	1291	if (proc1 == worldRank) {
306			StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
307	gezelter	1313	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
308	gezelter	1291	pos1 = sd1->getPos();
309			data[0] = pos1.x();
310			data[1] = pos1.y();
311			data[2] = pos1.z();
312			MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
313			} else {
314			MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
315			pos1 = Vector3d(data);
316			}
317	chuckv	1292
318
319	gezelter	1291	if (proc2 == worldRank) {
320			StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
321	gezelter	1313	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
322	gezelter	1291	pos2 = sd2->getPos();
323			data[0] = pos2.x();
324			data[1] = pos2.y();
325			data[2] = pos2.z();
326			MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
327			} else {
328			MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
329			pos2 = Vector3d(data);
330			}
331			#else
332			StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
333			StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
334			pos1 = at1->getPos();
335			pos2 = at2->getPos();
336			#endif
337			rab = pos2 - pos1;
338			currSnapshot->wrapVector(rab);
339			stat[Stats::TAGGED_PAIR_DISTANCE] = rab.length();
340			}
341			}
342
343	gezelter	246	/*@todo need refactorying/
344			//Conserved Quantity is set by integrator and time is set by setTime
345	gezelter	2
346	gezelter	507	}
347	gezelter	2
348	gezelter	1503
349			Vector3d Thermo::getBoxDipole() {
350			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
351			SimInfo::MoleculeIterator miter;
352			std::vector<Atom*>::iterator aiter;
353			Molecule* mol;
354			Atom* atom;
355			RealType charge;
356			RealType moment(0.0);
357			Vector3d ri(0.0);
358			Vector3d dipoleVector(0.0);
359			Vector3d nPos(0.0);
360			Vector3d pPos(0.0);
361			RealType nChg(0.0);
362			RealType pChg(0.0);
363			int nCount = 0;
364			int pCount = 0;
365
366			RealType chargeToC = 1.60217733e-19;
367			RealType angstromToM = 1.0e-10;
368			RealType debyeToCm = 3.33564095198e-30;
369
370			for (mol = info_->beginMolecule(miter); mol != NULL;
371			mol = info_->nextMolecule(miter)) {
372
373			for (atom = mol->beginAtom(aiter); atom != NULL;
374			atom = mol->nextAtom(aiter)) {
375
376			if (atom->isCharge() ) {
377			charge = 0.0;
378			GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
379			if (data != NULL) {
380
381			charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
382			charge *= chargeToC;
383
384			ri = atom->getPos();
385			currSnapshot->wrapVector(ri);
386			ri *= angstromToM;
387
388			if (charge < 0.0) {
389			nPos += ri;
390			nChg -= charge;
391			nCount++;
392			} else if (charge > 0.0) {
393			pPos += ri;
394			pChg += charge;
395			pCount++;
396			}
397			}
398			}
399
400	gezelter	1710	MultipoleAdapter ma = MultipoleAdapter(atom->getAtomType());
401			if (ma.isDipole() ) {
402	gezelter	1503	Vector3d u_i = atom->getElectroFrame().getColumn(2);
403	gezelter	1710	moment = ma.getDipoleMoment();
404			moment *= debyeToCm;
405			dipoleVector += u_i * moment;
406	gezelter	1503	}
407			}
408			}
409
410
411			#ifdef IS_MPI
412			RealType pChg_global, nChg_global;
413			int pCount_global, nCount_global;
414			Vector3d pPos_global, nPos_global, dipVec_global;
415
416			MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
417			MPI_COMM_WORLD);
418			pChg = pChg_global;
419			MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
420			MPI_COMM_WORLD);
421			nChg = nChg_global;
422			MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
423			MPI_COMM_WORLD);
424			pCount = pCount_global;
425			MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
426			MPI_COMM_WORLD);
427			nCount = nCount_global;
428			MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
429			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
430			pPos = pPos_global;
431			MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
432			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
433			nPos = nPos_global;
434			MPI_Allreduce(dipoleVector.getArrayPointer(),
435			dipVec_global.getArrayPointer(), 3,
436			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
437			dipoleVector = dipVec_global;
438			#endif //is_mpi
439
440			// first load the accumulated dipole moment (if dipoles were present)
441			Vector3d boxDipole = dipoleVector;
442			// now include the dipole moment due to charges
443			// use the lesser of the positive and negative charge totals
444			RealType chg_value = nChg <= pChg ? nChg : pChg;
445
446			// find the average positions
447			if (pCount > 0 && nCount > 0 ) {
448			pPos /= pCount;
449			nPos /= nCount;
450			}
451
452			// dipole is from the negative to the positive (physics notation)
453			boxDipole += (pPos - nPos) * chg_value;
454
455			return boxDipole;
456			}
457	gezelter	1723
458			// Returns the Heat Flux Vector for the system
459			Vector3d Thermo::getHeatFlux(){
460			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
461			SimInfo::MoleculeIterator miter;
462			std::vector<StuntDouble*>::iterator iiter;
463			Molecule* mol;
464			StuntDouble* integrableObject;
465			RigidBody::AtomIterator ai;
466			Atom* atom;
467			Vector3d vel;
468			Vector3d angMom;
469			Mat3x3d I;
470			int i;
471			int j;
472			int k;
473			RealType mass;
474
475			Vector3d x_a;
476			RealType kinetic;
477			RealType potential;
478			RealType eatom;
479			RealType AvgE_a_ = 0;
480			// Convective portion of the heat flux
481			Vector3d heatFluxJc = V3Zero;
482
483			/* Calculate convective portion of the heat flux */
484			for (mol = info_->beginMolecule(miter); mol != NULL;
485			mol = info_->nextMolecule(miter)) {
486
487			for (integrableObject = mol->beginIntegrableObject(iiter);
488			integrableObject != NULL;
489			integrableObject = mol->nextIntegrableObject(iiter)) {
490
491			mass = integrableObject->getMass();
492			vel = integrableObject->getVel();
493
494			kinetic = mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
495
496			if (integrableObject->isDirectional()) {
497			angMom = integrableObject->getJ();
498			I = integrableObject->getI();
499
500			if (integrableObject->isLinear()) {
501			i = integrableObject->linearAxis();
502			j = (i + 1) % 3;
503			k = (i + 2) % 3;
504			kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
505			} else {
506			kinetic += angMom[0]angMom[0]/I(0, 0) + angMom[1]angMom[1]/I(1, 1)
507			+ angMom[2]*angMom[2]/I(2, 2);
508			}
509			}
510
511			potential = 0.0;
512
513			if (integrableObject->isRigidBody()) {
514			RigidBody* rb = dynamic_cast<RigidBody*>(integrableObject);
515			for (atom = rb->beginAtom(ai); atom != NULL;
516			atom = rb->nextAtom(ai)) {
517			potential += atom->getParticlePot();
518			}
519			} else {
520			potential = integrableObject->getParticlePot();
521			cerr << "ppot = " << potential << "\n";
522			}
523
524			potential *= PhysicalConstants::energyConvert; // amu A^2/fs^2
525			// The potential may not be a 1/2 factor
526			eatom = (kinetic + potential)/2.0; // amu A^2/fs^2
527			heatFluxJc[0] += eatom*vel[0]; // amu A^3/fs^3
528			heatFluxJc[1] += eatom*vel[1]; // amu A^3/fs^3
529			heatFluxJc[2] += eatom*vel[2]; // amu A^3/fs^3
530			}
531			}
532
533			std::cerr << "Heat flux heatFluxJc is: " << heatFluxJc << std::endl;
534
535			/* The J_v vector is reduced in fortan so everyone has the global
536			* Jv. Jc is computed over the local atoms and must be reduced
537			* among all processors.
538			*/
539			#ifdef IS_MPI
540			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &heatFluxJc[0], 3, MPI::REALTYPE,
541			MPI::SUM);
542			#endif
543
544			// (kcal/mol * A/fs) * conversion => (amu A^3)/fs^3
545
546			Vector3d heatFluxJv = currSnapshot->getConductiveHeatFlux() *
547			PhysicalConstants::energyConvert;
548
549			std::cerr << "Heat flux Jc is: " << heatFluxJc << std::endl;
550			std::cerr << "Heat flux Jv is: " << heatFluxJv << std::endl;
551
552			// Correct for the fact the flux is 1/V (Jc + Jv)
553			return (heatFluxJv + heatFluxJc) / this->getVolume(); // amu / fs^3
554			}
555	gezelter	1390	} //end namespace OpenMD