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"

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);      

    // 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();

    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;
  }
} //end namespace OpenMD
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	14411 byte(s)
Log Message:	updated copyright notices
#	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	2
55	gezelter	1390	namespace OpenMD {
56	gezelter	2
57	tim	963	RealType Thermo::getKinetic() {
58	gezelter	246	SimInfo::MoleculeIterator miter;
59			std::vector<StuntDouble*>::iterator iiter;
60			Molecule* mol;
61			StuntDouble* integrableObject;
62			Vector3d vel;
63			Vector3d angMom;
64			Mat3x3d I;
65			int i;
66			int j;
67			int k;
68	chrisfen	998	RealType mass;
69	tim	963	RealType kinetic = 0.0;
70			RealType kinetic_global = 0.0;
71	gezelter	246
72			for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
73	gezelter	507	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
74			integrableObject = mol->nextIntegrableObject(iiter)) {
75	gezelter	945
76	chrisfen	998	mass = integrableObject->getMass();
77			vel = integrableObject->getVel();
78	gezelter	945
79	gezelter	507	kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
80	gezelter	945
81	gezelter	507	if (integrableObject->isDirectional()) {
82			angMom = integrableObject->getJ();
83			I = integrableObject->getI();
84	gezelter	2
85	gezelter	507	if (integrableObject->isLinear()) {
86			i = integrableObject->linearAxis();
87			j = (i + 1) % 3;
88			k = (i + 2) % 3;
89			kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
90			} else {
91			kinetic += angMom[0]angMom[0]/I(0, 0) + angMom[1]angMom[1]/I(1, 1)
92			+ angMom[2]*angMom[2]/I(2, 2);
93			}
94			}
95	gezelter	246
96	gezelter	507	}
97	gezelter	246	}
98
99			#ifdef IS_MPI
100	gezelter	2
101	tim	963	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
102	gezelter	246	MPI_COMM_WORLD);
103			kinetic = kinetic_global;
104	gezelter	2
105	gezelter	246	#endif //is_mpi
106	gezelter	2
107	gezelter	1390	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
108	gezelter	2
109	gezelter	246	return kinetic;
110	gezelter	507	}
111	gezelter	2
112	tim	963	RealType Thermo::getPotential() {
113			RealType potential = 0.0;
114	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
115	tim	963	RealType shortRangePot_local = curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
116	gezelter	2
117	gezelter	246	// Get total potential for entire system from MPI.
118	gezelter	2
119	gezelter	246	#ifdef IS_MPI
120	gezelter	2
121	tim	963	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
122	gezelter	246	MPI_COMM_WORLD);
123	tim	833	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
124	gezelter	2
125	gezelter	246	#else
126	gezelter	2
127	tim	833	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
128	gezelter	2
129			#endif // is_mpi
130
131	gezelter	246	return potential;
132	gezelter	507	}
133	gezelter	2
134	tim	963	RealType Thermo::getTotalE() {
135			RealType total;
136	gezelter	2
137	gezelter	246	total = this->getKinetic() + this->getPotential();
138			return total;
139	gezelter	507	}
140	gezelter	2
141	tim	963	RealType Thermo::getTemperature() {
142	gezelter	246
143	gezelter	1390	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
144	gezelter	246	return temperature;
145	gezelter	507	}
146	gezelter	2
147	tim	963	RealType Thermo::getVolume() {
148	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
149			return curSnapshot->getVolume();
150	gezelter	507	}
151	gezelter	2
152	tim	963	RealType Thermo::getPressure() {
153	gezelter	2
154	gezelter	246	// Relies on the calculation of the full molecular pressure tensor
155	gezelter	2
156
157	gezelter	246	Mat3x3d tensor;
158	tim	963	RealType pressure;
159	gezelter	2
160	gezelter	246	tensor = getPressureTensor();
161	gezelter	2
162	gezelter	1390	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
163	gezelter	2
164	gezelter	246	return pressure;
165	gezelter	507	}
166	gezelter	2
167	tim	963	RealType Thermo::getPressure(int direction) {
168	tim	538
169			// Relies on the calculation of the full molecular pressure tensor
170
171
172			Mat3x3d tensor;
173	tim	963	RealType pressure;
174	tim	538
175			tensor = getPressureTensor();
176
177	gezelter	1390	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
178	tim	538
179			return pressure;
180			}
181
182	gezelter	507	Mat3x3d Thermo::getPressureTensor() {
183	gezelter	246	// returns pressure tensor in units amufs^-2Ang^-1
184			// routine derived via viral theorem description in:
185			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
186			Mat3x3d pressureTensor;
187			Mat3x3d p_local(0.0);
188			Mat3x3d p_global(0.0);
189	gezelter	2
190	gezelter	246	SimInfo::MoleculeIterator i;
191			std::vector<StuntDouble*>::iterator j;
192			Molecule* mol;
193			StuntDouble* integrableObject;
194			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
195	gezelter	507	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
196			integrableObject = mol->nextIntegrableObject(j)) {
197	gezelter	2
198	tim	963	RealType mass = integrableObject->getMass();
199	gezelter	507	Vector3d vcom = integrableObject->getVel();
200			p_local += mass * outProduct(vcom, vcom);
201			}
202	gezelter	246	}
203	gezelter	2
204			#ifdef IS_MPI
205	tim	963	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
206	gezelter	2	#else
207	gezelter	246	p_global = p_local;
208	gezelter	2	#endif // is_mpi
209
210	tim	963	RealType volume = this->getVolume();
211	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
212			Mat3x3d tau = curSnapshot->statData.getTau();
213	gezelter	1126
214	gezelter	1390	pressureTensor = (p_global + PhysicalConstants::energyConvert* tau)/volume;
215	chrisfen	998
216	gezelter	246	return pressureTensor;
217	gezelter	507	}
218	gezelter	2
219	chrisfen	998
220	gezelter	507	void Thermo::saveStat(){
221	gezelter	246	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
222			Stats& stat = currSnapshot->statData;
223	gezelter	2
224	gezelter	246	stat[Stats::KINETIC_ENERGY] = getKinetic();
225			stat[Stats::POTENTIAL_ENERGY] = getPotential();
226			stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ;
227			stat[Stats::TEMPERATURE] = getTemperature();
228			stat[Stats::PRESSURE] = getPressure();
229			stat[Stats::VOLUME] = getVolume();
230	gezelter	2
231	tim	541	Mat3x3d tensor =getPressureTensor();
232	gezelter	1126	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
233			stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
234			stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
235			stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
236			stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
237			stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
238			stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
239			stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
240			stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
241	tim	541
242	gezelter	1503	// grab the simulation box dipole moment if specified
243			if (info_->getCalcBoxDipole()){
244			Vector3d totalDipole = getBoxDipole();
245			stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
246			stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
247			stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
248			}
249	tim	541
250	gezelter	1291	Globals* simParams = info_->getSimParams();
251
252			if (simParams->haveTaggedAtomPair() &&
253			simParams->havePrintTaggedPairDistance()) {
254			if ( simParams->getPrintTaggedPairDistance()) {
255
256			std::pair<int, int> tap = simParams->getTaggedAtomPair();
257			Vector3d pos1, pos2, rab;
258
259			#ifdef IS_MPI
260	gezelter	1313	std::cerr << "tap = " << tap.first << " " << tap.second << std::endl;
261	gezelter	1291
262	chuckv	1292	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	1292	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			data[2] = pos1.z();
279			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			data[2] = pos2.z();
293			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			#endif
304			rab = pos2 - pos1;
305			currSnapshot->wrapVector(rab);
306			stat[Stats::TAGGED_PAIR_DISTANCE] = rab.length();
307			}
308			}
309
310	gezelter	246	/*@todo need refactorying/
311			//Conserved Quantity is set by integrator and time is set by setTime
312	gezelter	2
313	gezelter	507	}
314	gezelter	2
315	gezelter	1503
316			Vector3d Thermo::getBoxDipole() {
317			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
318			SimInfo::MoleculeIterator miter;
319			std::vector<Atom*>::iterator aiter;
320			Molecule* mol;
321			Atom* atom;
322			RealType charge;
323			RealType moment(0.0);
324			Vector3d ri(0.0);
325			Vector3d dipoleVector(0.0);
326			Vector3d nPos(0.0);
327			Vector3d pPos(0.0);
328			RealType nChg(0.0);
329			RealType pChg(0.0);
330			int nCount = 0;
331			int pCount = 0;
332
333			RealType chargeToC = 1.60217733e-19;
334			RealType angstromToM = 1.0e-10;
335			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	gezelter	1390	} //end namespace OpenMD