src/brains/Thermo.cpp

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

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

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

namespace OpenMD {

  RealType Thermo::getKinetic() {
    SimInfo::MoleculeIterator miter;
    std::vector<StuntDouble*>::iterator iiter;
    Molecule* mol;
    StuntDouble* integrableObject;    
    Vector3d vel;
    Vector3d angMom;
    Mat3x3d I;
    int i;
    int j;
    int k;
    RealType mass;
    RealType kinetic = 0.0;
    RealType kinetic_global = 0.0;
    
    for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
      for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL; 
           integrableObject = mol->nextIntegrableObject(iiter)) {
        
        mass = integrableObject->getMass();
        vel = integrableObject->getVel();
        
        kinetic += mass * (vel[0]*vel[0] + vel[1]*vel[1] + vel[2]*vel[2]);
        
        if (integrableObject->isDirectional()) {
          angMom = integrableObject->getJ();
          I = integrableObject->getI();

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

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

#endif //is_mpi

    kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;

    return kinetic;
  }

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

    // Get total potential for entire system from MPI.

#ifdef IS_MPI

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

#else

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

#endif // is_mpi

    return potential;
  }

  RealType Thermo::getTotalE() {
    RealType total;

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

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

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

  RealType Thermo::getPressure() {

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


    Mat3x3d tensor;
    RealType pressure;

    tensor = getPressureTensor();

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

    return pressure;
  }

  RealType Thermo::getPressure(int direction) {

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

          
    Mat3x3d tensor;
    RealType pressure;

    tensor = getPressureTensor();

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

    return pressure;
  }

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

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

        RealType mass = integrableObject->getMass();
        Vector3d vcom = integrableObject->getVel();
        p_local += mass * outProduct(vcom, vcom);         
      }
    }
    
#ifdef IS_MPI
    MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
#else
    p_global = p_local;
#endif // is_mpi

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

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


  void Thermo::saveStat(){
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    Stats& stat = currSnapshot->statData;
    
    stat[Stats::KINETIC_ENERGY] = getKinetic();
    stat[Stats::POTENTIAL_ENERGY] = getPotential();
    stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY]  + stat[Stats::POTENTIAL_ENERGY] ;
    stat[Stats::TEMPERATURE] = getTemperature();
    stat[Stats::PRESSURE] = getPressure();
    stat[Stats::VOLUME] = getVolume();      

    Mat3x3d tensor =getPressureTensor();
    stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);      
    stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);      
    stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);      
    stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);      
    stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);      
    stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);      
    stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);      
    stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);      
    stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);      

    // 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:	1503
Committed:	Sat Oct 2 19:54:41 2010 UTC (14 years, 7 months ago) by gezelter
File size:	14345 byte(s)
Log Message:	Changes to remove more of the low level stuff from the fortran side.
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42	gezelter	2	#include <math.h>
43			#include <iostream>
44
45			#ifdef IS_MPI
46			#include <mpi.h>
47			#endif //is_mpi
48
49	tim	3	#include "brains/Thermo.hpp"
50	gezelter	246	#include "primitives/Molecule.hpp"
51	tim	3	#include "utils/simError.h"
52	gezelter	1390	#include "utils/PhysicalConstants.hpp"
53	gezelter	2
54	gezelter	1390	namespace OpenMD {
55	gezelter	2
56	tim	963	RealType Thermo::getKinetic() {
57	gezelter	246	SimInfo::MoleculeIterator miter;
58			std::vector<StuntDouble*>::iterator iiter;
59			Molecule* mol;
60			StuntDouble* integrableObject;
61			Vector3d vel;
62			Vector3d angMom;
63			Mat3x3d I;
64			int i;
65			int j;
66			int k;
67	chrisfen	998	RealType mass;
68	tim	963	RealType kinetic = 0.0;
69			RealType kinetic_global = 0.0;
70	gezelter	246
71			for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
72	gezelter	507	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
73			integrableObject = mol->nextIntegrableObject(iiter)) {
74	gezelter	945
75	chrisfen	998	mass = integrableObject->getMass();
76			vel = integrableObject->getVel();
77	gezelter	945
78	gezelter	507	kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
79	gezelter	945
80	gezelter	507	if (integrableObject->isDirectional()) {
81			angMom = integrableObject->getJ();
82			I = integrableObject->getI();
83	gezelter	2
84	gezelter	507	if (integrableObject->isLinear()) {
85			i = integrableObject->linearAxis();
86			j = (i + 1) % 3;
87			k = (i + 2) % 3;
88			kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
89			} else {
90			kinetic += angMom[0]angMom[0]/I(0, 0) + angMom[1]angMom[1]/I(1, 1)
91			+ angMom[2]*angMom[2]/I(2, 2);
92			}
93			}
94	gezelter	246
95	gezelter	507	}
96	gezelter	246	}
97
98			#ifdef IS_MPI
99	gezelter	2
100	tim	963	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
101	gezelter	246	MPI_COMM_WORLD);
102			kinetic = kinetic_global;
103	gezelter	2
104	gezelter	246	#endif //is_mpi
105	gezelter	2
106	gezelter	1390	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
107	gezelter	2
108	gezelter	246	return kinetic;
109	gezelter	507	}
110	gezelter	2
111	tim	963	RealType Thermo::getPotential() {
112			RealType potential = 0.0;
113	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114	tim	963	RealType shortRangePot_local = curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
115	gezelter	2
116	gezelter	246	// Get total potential for entire system from MPI.
117	gezelter	2
118	gezelter	246	#ifdef IS_MPI
119	gezelter	2
120	tim	963	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
121	gezelter	246	MPI_COMM_WORLD);
122	tim	833	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
123	gezelter	2
124	gezelter	246	#else
125	gezelter	2
126	tim	833	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
127	gezelter	2
128			#endif // is_mpi
129
130	gezelter	246	return potential;
131	gezelter	507	}
132	gezelter	2
133	tim	963	RealType Thermo::getTotalE() {
134			RealType total;
135	gezelter	2
136	gezelter	246	total = this->getKinetic() + this->getPotential();
137			return total;
138	gezelter	507	}
139	gezelter	2
140	tim	963	RealType Thermo::getTemperature() {
141	gezelter	246
142	gezelter	1390	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
143	gezelter	246	return temperature;
144	gezelter	507	}
145	gezelter	2
146	tim	963	RealType Thermo::getVolume() {
147	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148			return curSnapshot->getVolume();
149	gezelter	507	}
150	gezelter	2
151	tim	963	RealType Thermo::getPressure() {
152	gezelter	2
153	gezelter	246	// Relies on the calculation of the full molecular pressure tensor
154	gezelter	2
155
156	gezelter	246	Mat3x3d tensor;
157	tim	963	RealType pressure;
158	gezelter	2
159	gezelter	246	tensor = getPressureTensor();
160	gezelter	2
161	gezelter	1390	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
162	gezelter	2
163	gezelter	246	return pressure;
164	gezelter	507	}
165	gezelter	2
166	tim	963	RealType Thermo::getPressure(int direction) {
167	tim	538
168			// Relies on the calculation of the full molecular pressure tensor
169
170
171			Mat3x3d tensor;
172	tim	963	RealType pressure;
173	tim	538
174			tensor = getPressureTensor();
175
176	gezelter	1390	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
177	tim	538
178			return pressure;
179			}
180
181	gezelter	507	Mat3x3d Thermo::getPressureTensor() {
182	gezelter	246	// returns pressure tensor in units amufs^-2Ang^-1
183			// routine derived via viral theorem description in:
184			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
185			Mat3x3d pressureTensor;
186			Mat3x3d p_local(0.0);
187			Mat3x3d p_global(0.0);
188	gezelter	2
189	gezelter	246	SimInfo::MoleculeIterator i;
190			std::vector<StuntDouble*>::iterator j;
191			Molecule* mol;
192			StuntDouble* integrableObject;
193			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
194	gezelter	507	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195			integrableObject = mol->nextIntegrableObject(j)) {
196	gezelter	2
197	tim	963	RealType mass = integrableObject->getMass();
198	gezelter	507	Vector3d vcom = integrableObject->getVel();
199			p_local += mass * outProduct(vcom, vcom);
200			}
201	gezelter	246	}
202	gezelter	2
203			#ifdef IS_MPI
204	tim	963	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
205	gezelter	2	#else
206	gezelter	246	p_global = p_local;
207	gezelter	2	#endif // is_mpi
208
209	tim	963	RealType volume = this->getVolume();
210	gezelter	246	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
211			Mat3x3d tau = curSnapshot->statData.getTau();
212	gezelter	1126
213	gezelter	1390	pressureTensor = (p_global + PhysicalConstants::energyConvert* tau)/volume;
214	chrisfen	998
215	gezelter	246	return pressureTensor;
216	gezelter	507	}
217	gezelter	2
218	chrisfen	998
219	gezelter	507	void Thermo::saveStat(){
220	gezelter	246	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
221			Stats& stat = currSnapshot->statData;
222	gezelter	2
223	gezelter	246	stat[Stats::KINETIC_ENERGY] = getKinetic();
224			stat[Stats::POTENTIAL_ENERGY] = getPotential();
225			stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ;
226			stat[Stats::TEMPERATURE] = getTemperature();
227			stat[Stats::PRESSURE] = getPressure();
228			stat[Stats::VOLUME] = getVolume();
229	gezelter	2
230	tim	541	Mat3x3d tensor =getPressureTensor();
231	gezelter	1126	stat[Stats::PRESSURE_TENSOR_XX] = tensor(0, 0);
232			stat[Stats::PRESSURE_TENSOR_XY] = tensor(0, 1);
233			stat[Stats::PRESSURE_TENSOR_XZ] = tensor(0, 2);
234			stat[Stats::PRESSURE_TENSOR_YX] = tensor(1, 0);
235			stat[Stats::PRESSURE_TENSOR_YY] = tensor(1, 1);
236			stat[Stats::PRESSURE_TENSOR_YZ] = tensor(1, 2);
237			stat[Stats::PRESSURE_TENSOR_ZX] = tensor(2, 0);
238			stat[Stats::PRESSURE_TENSOR_ZY] = tensor(2, 1);
239			stat[Stats::PRESSURE_TENSOR_ZZ] = tensor(2, 2);
240	tim	541
241	gezelter	1503	// grab the simulation box dipole moment if specified
242			if (info_->getCalcBoxDipole()){
243			Vector3d totalDipole = getBoxDipole();
244			stat[Stats::BOX_DIPOLE_X] = totalDipole(0);
245			stat[Stats::BOX_DIPOLE_Y] = totalDipole(1);
246			stat[Stats::BOX_DIPOLE_Z] = totalDipole(2);
247			}
248	tim	541
249	gezelter	1291	Globals* simParams = info_->getSimParams();
250
251			if (simParams->haveTaggedAtomPair() &&
252			simParams->havePrintTaggedPairDistance()) {
253			if ( simParams->getPrintTaggedPairDistance()) {
254
255			std::pair<int, int> tap = simParams->getTaggedAtomPair();
256			Vector3d pos1, pos2, rab;
257
258			#ifdef IS_MPI
259	gezelter	1313	std::cerr << "tap = " << tap.first << " " << tap.second << std::endl;
260	gezelter	1291
261	chuckv	1292	int mol1 = info_->getGlobalMolMembership(tap.first);
262			int mol2 = info_->getGlobalMolMembership(tap.second);
263	gezelter	1313	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
264
265	gezelter	1291	int proc1 = info_->getMolToProc(mol1);
266			int proc2 = info_->getMolToProc(mol2);
267
268	gezelter	1313	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
269
270	chuckv	1292	RealType data[3];
271	gezelter	1291	if (proc1 == worldRank) {
272			StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
273	gezelter	1313	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
274	gezelter	1291	pos1 = sd1->getPos();
275			data[0] = pos1.x();
276			data[1] = pos1.y();
277			data[2] = pos1.z();
278			MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
279			} else {
280			MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
281			pos1 = Vector3d(data);
282			}
283	chuckv	1292
284
285	gezelter	1291	if (proc2 == worldRank) {
286			StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
287	gezelter	1313	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
288	gezelter	1291	pos2 = sd2->getPos();
289			data[0] = pos2.x();
290			data[1] = pos2.y();
291			data[2] = pos2.z();
292			MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
293			} else {
294			MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
295			pos2 = Vector3d(data);
296			}
297			#else
298			StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
299			StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
300			pos1 = at1->getPos();
301			pos2 = at2->getPos();
302			#endif
303			rab = pos2 - pos1;
304			currSnapshot->wrapVector(rab);
305			stat[Stats::TAGGED_PAIR_DISTANCE] = rab.length();
306			}
307			}
308
309	gezelter	246	/*@todo need refactorying/
310			//Conserved Quantity is set by integrator and time is set by setTime
311	gezelter	2
312	gezelter	507	}
313	gezelter	2
314	gezelter	1503
315			Vector3d Thermo::getBoxDipole() {
316			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
317			SimInfo::MoleculeIterator miter;
318			std::vector<Atom*>::iterator aiter;
319			Molecule* mol;
320			Atom* atom;
321			RealType charge;
322			RealType moment(0.0);
323			Vector3d ri(0.0);
324			Vector3d dipoleVector(0.0);
325			Vector3d nPos(0.0);
326			Vector3d pPos(0.0);
327			RealType nChg(0.0);
328			RealType pChg(0.0);
329			int nCount = 0;
330			int pCount = 0;
331
332			RealType chargeToC = 1.60217733e-19;
333			RealType angstromToM = 1.0e-10;
334			RealType debyeToCm = 3.33564095198e-30;
335
336			for (mol = info_->beginMolecule(miter); mol != NULL;
337			mol = info_->nextMolecule(miter)) {
338
339			for (atom = mol->beginAtom(aiter); atom != NULL;
340			atom = mol->nextAtom(aiter)) {
341
342			if (atom->isCharge() ) {
343			charge = 0.0;
344			GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
345			if (data != NULL) {
346
347			charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
348			charge *= chargeToC;
349
350			ri = atom->getPos();
351			currSnapshot->wrapVector(ri);
352			ri *= angstromToM;
353
354			if (charge < 0.0) {
355			nPos += ri;
356			nChg -= charge;
357			nCount++;
358			} else if (charge > 0.0) {
359			pPos += ri;
360			pChg += charge;
361			pCount++;
362			}
363			}
364			}
365
366			if (atom->isDipole() ) {
367			Vector3d u_i = atom->getElectroFrame().getColumn(2);
368			GenericData* data = dynamic_cast<DirectionalAtomType*>(atom->getAtomType())->getPropertyByName("Dipole");
369			if (data != NULL) {
370			moment = (dynamic_cast<DoubleGenericData*>(data))->getData();
371
372			moment *= debyeToCm;
373			dipoleVector += u_i * moment;
374			}
375			}
376			}
377			}
378
379
380			#ifdef IS_MPI
381			RealType pChg_global, nChg_global;
382			int pCount_global, nCount_global;
383			Vector3d pPos_global, nPos_global, dipVec_global;
384
385			MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
386			MPI_COMM_WORLD);
387			pChg = pChg_global;
388			MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
389			MPI_COMM_WORLD);
390			nChg = nChg_global;
391			MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
392			MPI_COMM_WORLD);
393			pCount = pCount_global;
394			MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
395			MPI_COMM_WORLD);
396			nCount = nCount_global;
397			MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
398			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
399			pPos = pPos_global;
400			MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
401			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
402			nPos = nPos_global;
403			MPI_Allreduce(dipoleVector.getArrayPointer(),
404			dipVec_global.getArrayPointer(), 3,
405			MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
406			dipoleVector = dipVec_global;
407			#endif //is_mpi
408
409			// first load the accumulated dipole moment (if dipoles were present)
410			Vector3d boxDipole = dipoleVector;
411			// now include the dipole moment due to charges
412			// use the lesser of the positive and negative charge totals
413			RealType chg_value = nChg <= pChg ? nChg : pChg;
414
415			// find the average positions
416			if (pCount > 0 && nCount > 0 ) {
417			pPos /= pCount;
418			nPos /= nCount;
419			}
420
421			// dipole is from the negative to the positive (physics notation)
422			boxDipole += (pPos - nPos) * chg_value;
423
424			return boxDipole;
425			}
426	gezelter	1390	} //end namespace OpenMD