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;
  }

  double Thermo::getPressure(int direction) {

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

          
    Mat3x3d tensor;
    double pressure;

    tensor = getPressureTensor();

    pressure = OOPSEConstant::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)) {

        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:	538
Committed:	Thu May 19 21:31:23 2005 UTC (20 years, 5 months ago) by tim
File size:	7321 byte(s)
Log Message:	NPAT is working
#	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. 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	#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/OOPSEConstant.hpp"
53
54	namespace oopse {
55
56	double 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	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
74	double mass = integrableObject->getMass();
75	Vector3d vel = integrableObject->getVel();
76
77	kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
78
79	if (integrableObject->isDirectional()) {
80	angMom = integrableObject->getJ();
81	I = integrableObject->getI();
82
83	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	}
93
94	}
95	}
96
97	#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	kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
106
107	return kinetic;
108	}
109
110	double Thermo::getPotential() {
111	double potential = 0.0;
112	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
113	double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] +
114	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(&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
141	double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
142	return temperature;
143	}
144
145	double Thermo::getVolume() {
146	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
147	return curSnapshot->getVolume();
148	}
149
150	double Thermo::getPressure() {
151
152	// Relies on the calculation of the full molecular pressure tensor
153
154
155	Mat3x3d tensor;
156	double pressure;
157
158	tensor = getPressureTensor();
159
160	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
161
162	return pressure;
163	}
164
165	double Thermo::getPressure(int direction) {
166
167	// Relies on the calculation of the full molecular pressure tensor
168
169
170	Mat3x3d tensor;
171	double pressure;
172
173	tensor = getPressureTensor();
174
175	pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
176
177	return pressure;
178	}
179
180
181
182	Mat3x3d Thermo::getPressureTensor() {
183	// returns pressure tensor in units amufs^-2Ang^-1
184	// routine derived via viral theorem description in:
185	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
186	Mat3x3d pressureTensor;
187	Mat3x3d p_local(0.0);
188	Mat3x3d p_global(0.0);
189
190	SimInfo::MoleculeIterator i;
191	std::vector<StuntDouble*>::iterator j;
192	Molecule* mol;
193	StuntDouble* integrableObject;
194	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
195	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
196	integrableObject = mol->nextIntegrableObject(j)) {
197
198	double mass = integrableObject->getMass();
199	Vector3d vcom = integrableObject->getVel();
200	p_local += mass * outProduct(vcom, vcom);
201	}
202	}
203
204	#ifdef IS_MPI
205	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
206	#else
207	p_global = p_local;
208	#endif // is_mpi
209
210	double volume = this->getVolume();
211	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
212	Mat3x3d tau = curSnapshot->statData.getTau();
213
214	pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume;
215
216	return pressureTensor;
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	/*@todo need refactorying/
231	//Conserved Quantity is set by integrator and time is set by setTime
232
233	}
234
235	} //end namespace oopse