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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#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/OOPSEConstant.hpp"

namespace oopse {

double 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;
    double kinetic = 0.0;
    double 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)) {

            double mass = integrableObject->getMass();
            Vector3d 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_DOUBLE, MPI_SUM,
                  MPI_COMM_WORLD);
    kinetic = kinetic_global;

#endif //is_mpi

    kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;

    return kinetic;
}

double Thermo::getPotential() {
    double potential = 0.0;
    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] + 
                                             curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;

    // Get total potential for entire system from MPI.

#ifdef IS_MPI

    MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM,
                  MPI_COMM_WORLD);

#else

    potential = potential_local;

#endif // is_mpi

    return potential;
}

double Thermo::getTotalE() {
    double total;

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

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

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

double Thermo::getPressure() {

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


    Mat3x3d tensor;
    double pressure;

    tensor = getPressureTensor();

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

    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)) {

            double 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_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
#else
    p_global = p_local;
#endif // is_mpi

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

    pressureTensor =  (p_global + OOPSEConstant::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();      

    /**@todo need refactorying*/
    //Conserved Quantity is set by integrator and time is set by setTime
    
}

} //end namespace oopse
Revision:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (20 years, 6 months ago) by tim
File size:	7309 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	tim	1725	#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	tim	1804	#include "primitives/Molecule.hpp"
51	tim	1725	#include "utils/simError.h"
52	tim	1804	#include "utils/OOPSEConstant.hpp"
53	tim	1725
54			namespace oopse {
55
56			double Thermo::getKinetic() {
57	tim	1804	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			double kinetic = 0.0;
68			double kinetic_global = 0.0;
69
70			for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
71			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
72			integrableObject = mol->nextIntegrableObject(iiter)) {
73	tim	1725
74	tim	1804	double mass = integrableObject->getMass();
75			Vector3d vel = integrableObject->getVel();
76	tim	1725
77	tim	1847	kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
78	tim	1725
79	tim	1804	if (integrableObject->isDirectional()) {
80			angMom = integrableObject->getJ();
81			I = integrableObject->getI();
82	tim	1725
83	tim	1804	if (integrableObject->isLinear()) {
84			i = integrableObject->linearAxis();
85			j = (i + 1) % 3;
86			k = (i + 2) % 3;
87			kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
88			} else {
89			kinetic += angMom[0]angMom[0]/I(0, 0) + angMom[1]angMom[1]/I(1, 1)
90			+ angMom[2]*angMom[2]/I(2, 2);
91			}
92	tim	1725	}
93	tim	1804
94	tim	1725	}
95			}
96	tim	1804
97	tim	1725	#ifdef IS_MPI
98
99			MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_DOUBLE, MPI_SUM,
100			MPI_COMM_WORLD);
101			kinetic = kinetic_global;
102
103			#endif //is_mpi
104
105	tim	1804	kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
106	tim	1725
107			return kinetic;
108			}
109
110			double Thermo::getPotential() {
111	tim	1804	double potential = 0.0;
112			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
113	tim	1901	double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] +
114			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
115	tim	1725
116			// Get total potential for entire system from MPI.
117
118			#ifdef IS_MPI
119
120			MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM,
121			MPI_COMM_WORLD);
122
123			#else
124
125			potential = potential_local;
126
127			#endif // is_mpi
128
129			return potential;
130			}
131
132			double Thermo::getTotalE() {
133			double total;
134
135			total = this->getKinetic() + this->getPotential();
136			return total;
137			}
138
139			double Thermo::getTemperature() {
140	tim	1804
141			double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
142	tim	1725	return temperature;
143			}
144
145	tim	1804	double Thermo::getVolume() {
146			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
147			return curSnapshot->getVolume();
148			}
149	tim	1725
150			double Thermo::getPressure() {
151
152			// Relies on the calculation of the full molecular pressure tensor
153
154
155	tim	1804	Mat3x3d tensor;
156			double pressure;
157	tim	1725
158	tim	1822	tensor = getPressureTensor();
159	tim	1725
160	tim	1804	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
161
162	tim	1725	return pressure;
163			}
164
165	tim	1822	Mat3x3d Thermo::getPressureTensor() {
166	tim	1725	// returns pressure tensor in units amufs^-2Ang^-1
167			// routine derived via viral theorem description in:
168			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
169	tim	1822	Mat3x3d pressureTensor;
170	tim	1804	Mat3x3d p_local(0.0);
171			Mat3x3d p_global(0.0);
172	tim	1725
173	tim	1804	SimInfo::MoleculeIterator i;
174			std::vector<StuntDouble*>::iterator j;
175			Molecule* mol;
176			StuntDouble* integrableObject;
177			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
178			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
179			integrableObject = mol->nextIntegrableObject(j)) {
180	tim	1725
181	tim	1804	double mass = integrableObject->getMass();
182			Vector3d vcom = integrableObject->getVel();
183			p_local += mass * outProduct(vcom, vcom);
184			}
185	tim	1725	}
186	tim	1804
187	tim	1725	#ifdef IS_MPI
188	tim	1804	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
189	tim	1725	#else
190	tim	1804	p_global = p_local;
191	tim	1725	#endif // is_mpi
192
193	tim	1804	double volume = this->getVolume();
194			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
195			Mat3x3d tau = curSnapshot->statData.getTau();
196	tim	1725
197	tim	1854	pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume;
198	tim	1822
199			return pressureTensor;
200	tim	1804	}
201	tim	1725
202	tim	1820	void Thermo::saveStat(){
203			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
204			Stats& stat = currSnapshot->statData;
205
206			stat[Stats::KINETIC_ENERGY] = getKinetic();
207			stat[Stats::POTENTIAL_ENERGY] = getPotential();
208			stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ;
209			stat[Stats::TEMPERATURE] = getTemperature();
210			stat[Stats::PRESSURE] = getPressure();
211	tim	1822	stat[Stats::VOLUME] = getVolume();
212	tim	1820
213			/*@todo need refactorying/
214			//Conserved Quantity is set by integrator and time is set by setTime
215
216			}
217
218	tim	1725	} //end namespace oopse