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);
    Vector3d GKappa_t = getThermalHelfand();
    stat[Stats::THERMAL_HELFANDMOMENT_X] = GKappa_t.x();
    stat[Stats::THERMAL_HELFANDMOMENT_Y] = GKappa_t.y();
    stat[Stats::THERMAL_HELFANDMOMENT_Z] = GKappa_t.z();

    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;
  }

 Vector3d Thermo::getThermalHelfand() {
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    SimInfo::MoleculeIterator miter;
    std::vector<Atom*>::iterator aiter;
    Molecule* mol;
    Atom* atom;
    RealType mass;
    Vector3d velocity;
    Vector3d x_a;
    RealType kinetic;
    RealType potential;
    RealType eatom;
    RealType AvgE_a_ = 0;
    Vector3d GKappa_t = V3Zero;
    Vector3d ThermalHelfandMoment;

    for (mol = info_->beginMolecule(miter); mol != NULL;
         mol = info_->nextMolecule(miter)) {

      for (atom = mol->beginAtom(aiter); atom != NULL;
           atom = mol->nextAtom(aiter)) {

        mass = atom->getMass();
        velocity = atom->getVel();
        kinetic = mass * (velocity[0]*velocity[0] + velocity[1]*velocity[1] +
                                   velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
        potential =  atom->getParticlePot();
        eatom += (kinetic + potential)/2.0;
      }
    }

   int natoms = info_->getNGlobalAtoms();
#ifdef IS_MPI

    MPI_Allreduce(&eatom, &AvgE_a_, 1, MPI_REALTYPE, MPI_SUM,
                  MPI_COMM_WORLD);
#else
    AvgE_a_ = eatom;
#endif
    AvgE_a_ = AvgE_a_/RealType(natoms);

    for (mol = info_->beginMolecule(miter); mol != NULL;
         mol = info_->nextMolecule(miter)) {

      for (atom = mol->beginAtom(aiter); atom != NULL;
           atom = mol->nextAtom(aiter)) {

        /* We think that x_a is relative to the total box and should be a wrapped coordinate */
        x_a = atom->getPos();
        currSnapshot->wrapVector(x_a);
        potential =  atom->getParticlePot();
        velocity = atom->getVel();
        kinetic = mass * (velocity[0]*velocity[0] + velocity[1]*velocity[1] +
                           velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
        eatom += (kinetic + potential)/2.0;
        GKappa_t += x_a*(eatom-AvgE_a_);
        }
      }
#ifdef IS_MPI
     MPI_Allreduce(GKappa_t.getArrayPointer(), ThermalHelfandMoment.getArrayPointer(), 3,
                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
#else
     ThermalHelfandMoment = GKappa_t;
#endif
     return ThermalHelfandMoment;

 }


} //end namespace OpenMD
Revision:	1667
Committed:	Wed Dec 14 20:24:39 2011 UTC (13 years, 10 months ago) by chuckv
File size:	16040 byte(s)
Log Message:	Fixed typo in thermo.
#	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	Vector3d GKappa_t = getThermalHelfand();
241	stat[Stats::THERMAL_HELFANDMOMENT_X] = GKappa_t.x();
242	stat[Stats::THERMAL_HELFANDMOMENT_Y] = GKappa_t.y();
243	stat[Stats::THERMAL_HELFANDMOMENT_Z] = GKappa_t.z();
244
245	Globals* simParams = info_->getSimParams();
246
247	if (simParams->haveTaggedAtomPair() &&
248	simParams->havePrintTaggedPairDistance()) {
249	if ( simParams->getPrintTaggedPairDistance()) {
250
251	std::pair<int, int> tap = simParams->getTaggedAtomPair();
252	Vector3d pos1, pos2, rab;
253
254	#ifdef IS_MPI
255	std::cerr << "tap = " << tap.first << " " << tap.second << std::endl;
256
257	int mol1 = info_->getGlobalMolMembership(tap.first);
258	int mol2 = info_->getGlobalMolMembership(tap.second);
259	std::cerr << "mols = " << mol1 << " " << mol2 << std::endl;
260
261	int proc1 = info_->getMolToProc(mol1);
262	int proc2 = info_->getMolToProc(mol2);
263
264	std::cerr << " procs = " << proc1 << " " <<proc2 <<std::endl;
265
266	RealType data[3];
267	if (proc1 == worldRank) {
268	StuntDouble* sd1 = info_->getIOIndexToIntegrableObject(tap.first);
269	std::cerr << " on proc " << proc1 << ", sd1 has global index= " << sd1->getGlobalIndex() << std::endl;
270	pos1 = sd1->getPos();
271	data[0] = pos1.x();
272	data[1] = pos1.y();
273	data[2] = pos1.z();
274	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
275	} else {
276	MPI_Bcast(data, 3, MPI_REALTYPE, proc1, MPI_COMM_WORLD);
277	pos1 = Vector3d(data);
278	}
279
280
281	if (proc2 == worldRank) {
282	StuntDouble* sd2 = info_->getIOIndexToIntegrableObject(tap.second);
283	std::cerr << " on proc " << proc2 << ", sd2 has global index= " << sd2->getGlobalIndex() << std::endl;
284	pos2 = sd2->getPos();
285	data[0] = pos2.x();
286	data[1] = pos2.y();
287	data[2] = pos2.z();
288	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
289	} else {
290	MPI_Bcast(data, 3, MPI_REALTYPE, proc2, MPI_COMM_WORLD);
291	pos2 = Vector3d(data);
292	}
293	#else
294	StuntDouble* at1 = info_->getIOIndexToIntegrableObject(tap.first);
295	StuntDouble* at2 = info_->getIOIndexToIntegrableObject(tap.second);
296	pos1 = at1->getPos();
297	pos2 = at2->getPos();
298	#endif
299	rab = pos2 - pos1;
300	currSnapshot->wrapVector(rab);
301	stat[Stats::TAGGED_PAIR_DISTANCE] = rab.length();
302	}
303	}
304
305	/*@todo need refactorying/
306	//Conserved Quantity is set by integrator and time is set by setTime
307
308	}
309
310
311
312	Vector3d Thermo::getBoxDipole() {
313	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
314	SimInfo::MoleculeIterator miter;
315	std::vector<Atom*>::iterator aiter;
316	Molecule* mol;
317	Atom* atom;
318	RealType charge;
319	RealType moment(0.0);
320	Vector3d ri(0.0);
321	Vector3d dipoleVector(0.0);
322	Vector3d nPos(0.0);
323	Vector3d pPos(0.0);
324	RealType nChg(0.0);
325	RealType pChg(0.0);
326	int nCount = 0;
327	int pCount = 0;
328
329	RealType chargeToC = 1.60217733e-19;
330	RealType angstromToM = 1.0e-10; RealType debyeToCm = 3.33564095198e-30;
331
332	for (mol = info_->beginMolecule(miter); mol != NULL;
333	mol = info_->nextMolecule(miter)) {
334
335	for (atom = mol->beginAtom(aiter); atom != NULL;
336	atom = mol->nextAtom(aiter)) {
337
338	if (atom->isCharge() ) {
339	charge = 0.0;
340	GenericData* data = atom->getAtomType()->getPropertyByName("Charge");
341	if (data != NULL) {
342
343	charge = (dynamic_cast<DoubleGenericData*>(data))->getData();
344	charge *= chargeToC;
345
346	ri = atom->getPos();
347	currSnapshot->wrapVector(ri);
348	ri *= angstromToM;
349
350	if (charge < 0.0) {
351	nPos += ri;
352	nChg -= charge;
353	nCount++;
354	} else if (charge > 0.0) {
355	pPos += ri;
356	pChg += charge;
357	pCount++;
358	}
359	}
360	}
361
362	if (atom->isDipole() ) {
363	Vector3d u_i = atom->getElectroFrame().getColumn(2);
364	GenericData* data = dynamic_cast<DirectionalAtomType*>(atom->getAtomType())->getPropertyByName("Dipole");
365	if (data != NULL) {
366	moment = (dynamic_cast<DoubleGenericData*>(data))->getData();
367
368	moment *= debyeToCm;
369	dipoleVector += u_i * moment;
370	}
371	}
372	}
373	}
374
375
376	#ifdef IS_MPI
377	RealType pChg_global, nChg_global;
378	int pCount_global, nCount_global;
379	Vector3d pPos_global, nPos_global, dipVec_global;
380
381	MPI_Allreduce(&pChg, &pChg_global, 1, MPI_REALTYPE, MPI_SUM,
382	MPI_COMM_WORLD);
383	pChg = pChg_global;
384	MPI_Allreduce(&nChg, &nChg_global, 1, MPI_REALTYPE, MPI_SUM,
385	MPI_COMM_WORLD);
386	nChg = nChg_global;
387	MPI_Allreduce(&pCount, &pCount_global, 1, MPI_INTEGER, MPI_SUM,
388	MPI_COMM_WORLD);
389	pCount = pCount_global;
390	MPI_Allreduce(&nCount, &nCount_global, 1, MPI_INTEGER, MPI_SUM,
391	MPI_COMM_WORLD);
392	nCount = nCount_global;
393	MPI_Allreduce(pPos.getArrayPointer(), pPos_global.getArrayPointer(), 3,
394	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
395	pPos = pPos_global;
396	MPI_Allreduce(nPos.getArrayPointer(), nPos_global.getArrayPointer(), 3,
397	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
398	nPos = nPos_global;
399	MPI_Allreduce(dipoleVector.getArrayPointer(),
400	dipVec_global.getArrayPointer(), 3,
401	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
402	dipoleVector = dipVec_global;
403	#endif //is_mpi
404
405	// first load the accumulated dipole moment (if dipoles were present)
406	Vector3d boxDipole = dipoleVector;
407	// now include the dipole moment due to charges
408	// use the lesser of the positive and negative charge totals
409	RealType chg_value = nChg <= pChg ? nChg : pChg;
410
411	// find the average positions
412	if (pCount > 0 && nCount > 0 ) {
413	pPos /= pCount;
414	nPos /= nCount;
415	}
416
417	// dipole is from the negative to the positive (physics notation)
418	boxDipole += (pPos - nPos) * chg_value;
419
420	return boxDipole;
421	}
422
423	Vector3d Thermo::getThermalHelfand() {
424	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
425	SimInfo::MoleculeIterator miter;
426	std::vector<Atom*>::iterator aiter;
427	Molecule* mol;
428	Atom* atom;
429	RealType mass;
430	Vector3d velocity;
431	Vector3d x_a;
432	RealType kinetic;
433	RealType potential;
434	RealType eatom;
435	RealType AvgE_a_ = 0;
436	Vector3d GKappa_t = V3Zero;
437	Vector3d ThermalHelfandMoment;
438
439	for (mol = info_->beginMolecule(miter); mol != NULL;
440	mol = info_->nextMolecule(miter)) {
441
442	for (atom = mol->beginAtom(aiter); atom != NULL;
443	atom = mol->nextAtom(aiter)) {
444
445	mass = atom->getMass();
446	velocity = atom->getVel();
447	kinetic = mass * (velocity[0]velocity[0] + velocity[1]velocity[1] +
448	velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
449	potential = atom->getParticlePot();
450	eatom += (kinetic + potential)/2.0;
451	}
452	}
453
454	int natoms = info_->getNGlobalAtoms();
455	#ifdef IS_MPI
456
457	MPI_Allreduce(&eatom, &AvgE_a_, 1, MPI_REALTYPE, MPI_SUM,
458	MPI_COMM_WORLD);
459	#else
460	AvgE_a_ = eatom;
461	#endif
462	AvgE_a_ = AvgE_a_/RealType(natoms);
463
464	for (mol = info_->beginMolecule(miter); mol != NULL;
465	mol = info_->nextMolecule(miter)) {
466
467	for (atom = mol->beginAtom(aiter); atom != NULL;
468	atom = mol->nextAtom(aiter)) {
469
470	/* We think that x_a is relative to the total box and should be a wrapped coordinate */
471	x_a = atom->getPos();
472	currSnapshot->wrapVector(x_a);
473	potential = atom->getParticlePot();
474	velocity = atom->getVel();
475	kinetic = mass * (velocity[0]velocity[0] + velocity[1]velocity[1] +
476	velocity[2]*velocity[2]) / PhysicalConstants::energyConvert;
477	eatom += (kinetic + potential)/2.0;
478	GKappa_t += x_a*(eatom-AvgE_a_);
479	}
480	}
481	#ifdef IS_MPI
482	MPI_Allreduce(GKappa_t.getArrayPointer(), ThermalHelfandMoment.getArrayPointer(), 3,
483	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
484	#else
485	ThermalHelfandMoment = GKappa_t;
486	#endif
487	return ThermalHelfandMoment;
488
489	}
490
491
492
493	} //end namespace OpenMD