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.
#	Content
1	/*
2	* 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	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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	*/
41
42	#include <math.h>
43	#include <iostream>
44
45	#ifdef IS_MPI
46	#include <mpi.h>
47	#endif //is_mpi
48
49	#include "brains/Thermo.hpp"
50	#include "primitives/Molecule.hpp"
51	#include "utils/simError.h"
52	#include "utils/PhysicalConstants.hpp"
53
54	namespace OpenMD {
55
56	RealType Thermo::getKinetic() {
57	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	RealType mass;
68	RealType kinetic = 0.0;
69	RealType kinetic_global = 0.0;
70
71	for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
72	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
73	integrableObject = mol->nextIntegrableObject(iiter)) {
74
75	mass = integrableObject->getMass();
76	vel = integrableObject->getVel();
77
78	kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
79
80	if (integrableObject->isDirectional()) {
81	angMom = integrableObject->getJ();
82	I = integrableObject->getI();
83
84	if (integrableObject->isLinear()) {
85	i = integrableObject->linearAxis();
86	j = (i + 1) % 3;
87	k = (i + 2) % 3;
88	kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
89	} else {
90	kinetic += angMom[0]angMom[0]/I(0, 0) + angMom[1]angMom[1]/I(1, 1)
91	+ angMom[2]*angMom[2]/I(2, 2);
92	}
93	}
94
95	}
96	}
97
98	#ifdef IS_MPI
99
100	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
101	MPI_COMM_WORLD);
102	kinetic = kinetic_global;
103
104	#endif //is_mpi
105
106	kinetic = kinetic * 0.5 / PhysicalConstants::energyConvert;
107
108	return kinetic;
109	}
110
111	RealType Thermo::getPotential() {
112	RealType potential = 0.0;
113	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114	RealType shortRangePot_local = curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
115
116	// Get total potential for entire system from MPI.
117
118	#ifdef IS_MPI
119
120	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
121	MPI_COMM_WORLD);
122	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
123
124	#else
125
126	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
127
128	#endif // is_mpi
129
130	return potential;
131	}
132
133	RealType Thermo::getTotalE() {
134	RealType total;
135
136	total = this->getKinetic() + this->getPotential();
137	return total;
138	}
139
140	RealType Thermo::getTemperature() {
141
142	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* PhysicalConstants::kb );
143	return temperature;
144	}
145
146	RealType Thermo::getVolume() {
147	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148	return curSnapshot->getVolume();
149	}
150
151	RealType Thermo::getPressure() {
152
153	// Relies on the calculation of the full molecular pressure tensor
154
155
156	Mat3x3d tensor;
157	RealType pressure;
158
159	tensor = getPressureTensor();
160
161	pressure = PhysicalConstants::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
162
163	return pressure;
164	}
165
166	RealType Thermo::getPressure(int direction) {
167
168	// Relies on the calculation of the full molecular pressure tensor
169
170
171	Mat3x3d tensor;
172	RealType pressure;
173
174	tensor = getPressureTensor();
175
176	pressure = PhysicalConstants::pressureConvert * tensor(direction, direction);
177
178	return pressure;
179	}
180
181	Mat3x3d Thermo::getPressureTensor() {
182	// 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
189	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	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195	integrableObject = mol->nextIntegrableObject(j)) {
196
197	RealType mass = integrableObject->getMass();
198	Vector3d vcom = integrableObject->getVel();
199	p_local += mass * outProduct(vcom, vcom);
200	}
201	}
202
203	#ifdef IS_MPI
204	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
205	#else
206	p_global = p_local;
207	#endif // is_mpi
208
209	RealType volume = this->getVolume();
210	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
211	Mat3x3d tau = curSnapshot->statData.getTau();
212
213	pressureTensor = (p_global + PhysicalConstants::energyConvert* tau)/volume;
214
215	return pressureTensor;
216	}
217
218
219	void Thermo::saveStat(){
220	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
221	Stats& stat = currSnapshot->statData;
222
223	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
230	Mat3x3d tensor =getPressureTensor();
231	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
241	// 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
249	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	std::cerr << "tap = " << tap.first << " " << tap.second << std::endl;
260
261	int mol1 = info_->getGlobalMolMembership(tap.first);
262	int mol2 = info_->getGlobalMolMembership(tap.second);
263	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
264
265	int proc1 = info_->getMolToProc(mol1);
266	int proc2 = info_->getMolToProc(mol2);
267
268	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
269
270	RealType data[3];
271	if (proc1 == worldRank) {
272	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
273	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
274	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
284
285	if (proc2 == worldRank) {
286	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
287	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
288	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	/*@todo need refactorying/
310	//Conserved Quantity is set by integrator and time is set by setTime
311
312	}
313
314
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	} //end namespace OpenMD