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 {

  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 / OOPSEConstant::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()* OOPSEConstant::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 = OOPSEConstant::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 = 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)) {

        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 + 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();      

    Mat3x3d tensor =getPressureTensor();
    stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0);      
    stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1);      
    stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2);      


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

} //end namespace oopse
Revision:	2917
Committed:	Mon Jul 3 13:18:43 2006 UTC (18 years, 2 months ago) by chrisfen
File size:	7684 byte(s)
Log Message:	Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	1490	#include <math.h>
43			#include <iostream>
44
45			#ifdef IS_MPI
46			#include <mpi.h>
47			#endif //is_mpi
48
49	tim	1492	#include "brains/Thermo.hpp"
50	gezelter	1930	#include "primitives/Molecule.hpp"
51	tim	1492	#include "utils/simError.h"
52	gezelter	1930	#include "utils/OOPSEConstant.hpp"
53	gezelter	1490
54	gezelter	1930	namespace oopse {
55	gezelter	1490
56	tim	2759	RealType Thermo::getKinetic() {
57	gezelter	1930	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	2917	RealType mass;
68	tim	2759	RealType kinetic = 0.0;
69			RealType kinetic_global = 0.0;
70	gezelter	1930
71			for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
72	gezelter	2204	for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
73			integrableObject = mol->nextIntegrableObject(iiter)) {
74	gezelter	2733
75	chrisfen	2917	mass = integrableObject->getMass();
76			vel = integrableObject->getVel();
77	gezelter	2733
78	gezelter	2204	kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
79	gezelter	2733
80	gezelter	2204	if (integrableObject->isDirectional()) {
81			angMom = integrableObject->getJ();
82			I = integrableObject->getI();
83	gezelter	1490
84	gezelter	2204	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	1930
95	gezelter	2204	}
96	gezelter	1930	}
97
98			#ifdef IS_MPI
99	gezelter	1490
100	tim	2759	MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_REALTYPE, MPI_SUM,
101	gezelter	1930	MPI_COMM_WORLD);
102			kinetic = kinetic_global;
103	gezelter	1490
104	gezelter	1930	#endif //is_mpi
105	gezelter	1490
106	gezelter	1930	kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
107	gezelter	1490
108	gezelter	1930	return kinetic;
109	gezelter	2204	}
110	gezelter	1490
111	tim	2759	RealType Thermo::getPotential() {
112			RealType potential = 0.0;
113	gezelter	1930	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114	tim	2759	RealType shortRangePot_local = curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
115	gezelter	1490
116	gezelter	1930	// Get total potential for entire system from MPI.
117	gezelter	1490
118	gezelter	1930	#ifdef IS_MPI
119	gezelter	1490
120	tim	2759	MPI_Allreduce(&shortRangePot_local, &potential, 1, MPI_REALTYPE, MPI_SUM,
121	gezelter	1930	MPI_COMM_WORLD);
122	tim	2532	potential += curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
123	gezelter	1490
124	gezelter	1930	#else
125	gezelter	1490
126	tim	2532	potential = shortRangePot_local + curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
127	gezelter	1490
128			#endif // is_mpi
129
130	gezelter	1930	return potential;
131	gezelter	2204	}
132	gezelter	1490
133	tim	2759	RealType Thermo::getTotalE() {
134			RealType total;
135	gezelter	1490
136	gezelter	1930	total = this->getKinetic() + this->getPotential();
137			return total;
138	gezelter	2204	}
139	gezelter	1490
140	tim	2759	RealType Thermo::getTemperature() {
141	gezelter	1930
142	tim	2759	RealType temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
143	gezelter	1930	return temperature;
144	gezelter	2204	}
145	gezelter	1490
146	tim	2759	RealType Thermo::getVolume() {
147	gezelter	1930	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
148			return curSnapshot->getVolume();
149	gezelter	2204	}
150	gezelter	1490
151	tim	2759	RealType Thermo::getPressure() {
152	gezelter	1490
153	gezelter	1930	// Relies on the calculation of the full molecular pressure tensor
154	gezelter	1490
155
156	gezelter	1930	Mat3x3d tensor;
157	tim	2759	RealType pressure;
158	gezelter	1490
159	gezelter	1930	tensor = getPressureTensor();
160	gezelter	1490
161	gezelter	1930	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
162	gezelter	1490
163	gezelter	1930	return pressure;
164	gezelter	2204	}
165	gezelter	1490
166	tim	2759	RealType Thermo::getPressure(int direction) {
167	tim	2235
168			// Relies on the calculation of the full molecular pressure tensor
169
170
171			Mat3x3d tensor;
172	tim	2759	RealType pressure;
173	tim	2235
174			tensor = getPressureTensor();
175
176			pressure = OOPSEConstant::pressureConvert * tensor(direction, direction);
177
178			return pressure;
179			}
180
181	gezelter	2204	Mat3x3d Thermo::getPressureTensor() {
182	gezelter	1930	// 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	1490
189	gezelter	1930	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	2204	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
195			integrableObject = mol->nextIntegrableObject(j)) {
196	gezelter	1490
197	tim	2759	RealType mass = integrableObject->getMass();
198	gezelter	2204	Vector3d vcom = integrableObject->getVel();
199			p_local += mass * outProduct(vcom, vcom);
200			}
201	gezelter	1930	}
202	gezelter	1490
203			#ifdef IS_MPI
204	tim	2759	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
205	gezelter	1490	#else
206	gezelter	1930	p_global = p_local;
207	gezelter	1490	#endif // is_mpi
208
209	tim	2759	RealType volume = this->getVolume();
210	gezelter	1930	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
211			Mat3x3d tau = curSnapshot->statData.getTau();
212	chrisfen	2917
213	gezelter	1930	pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume;
214	chrisfen	2917
215	gezelter	1930	return pressureTensor;
216	gezelter	2204	}
217	gezelter	1490
218	chrisfen	2917
219	gezelter	2204	void Thermo::saveStat(){
220	gezelter	1930	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
221			Stats& stat = currSnapshot->statData;
222	gezelter	1490
223	gezelter	1930	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	1490
230	tim	2238	Mat3x3d tensor =getPressureTensor();
231			stat[Stats::PRESSURE_TENSOR_X] = tensor(0, 0);
232			stat[Stats::PRESSURE_TENSOR_Y] = tensor(1, 1);
233			stat[Stats::PRESSURE_TENSOR_Z] = tensor(2, 2);
234
235
236	gezelter	1930	/*@todo need refactorying/
237			//Conserved Quantity is set by integrator and time is set by setTime
238	gezelter	1490
239	gezelter	2204	}
240	gezelter	1490
241	gezelter	1930	} //end namespace oopse