src/brains/Thermo.cpp

#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:	1901
Committed:	Tue Jan 4 22:18:36 2005 UTC (19 years, 6 months ago) by tim
File size:	5234 byte(s)
Log Message:	constraints in progress
#	User	Rev	Content
1	tim	1725	#include <math.h>
2			#include <iostream>
3
4
5	tim	1827
6	tim	1725	#ifdef IS_MPI
7			#include <mpi.h>
8			#endif //is_mpi
9
10			#include "brains/Thermo.hpp"
11	tim	1804	#include "primitives/Molecule.hpp"
12	tim	1725	#include "utils/simError.h"
13	tim	1804	#include "utils/OOPSEConstant.hpp"
14	tim	1725
15			namespace oopse {
16
17			double Thermo::getKinetic() {
18	tim	1804	SimInfo::MoleculeIterator miter;
19			std::vector<StuntDouble*>::iterator iiter;
20			Molecule* mol;
21			StuntDouble* integrableObject;
22			Vector3d vel;
23			Vector3d angMom;
24			Mat3x3d I;
25			int i;
26			int j;
27			int k;
28			double kinetic = 0.0;
29			double kinetic_global = 0.0;
30
31			for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
32			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
33			integrableObject = mol->nextIntegrableObject(iiter)) {
34	tim	1725
35	tim	1804	double mass = integrableObject->getMass();
36			Vector3d vel = integrableObject->getVel();
37	tim	1725
38	tim	1847	kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
39	tim	1725
40	tim	1804	if (integrableObject->isDirectional()) {
41			angMom = integrableObject->getJ();
42			I = integrableObject->getI();
43	tim	1725
44	tim	1804	if (integrableObject->isLinear()) {
45			i = integrableObject->linearAxis();
46			j = (i + 1) % 3;
47			k = (i + 2) % 3;
48			kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
49			} else {
50			kinetic += angMom[0]angMom[0]/I(0, 0) + angMom[1]angMom[1]/I(1, 1)
51			+ angMom[2]*angMom[2]/I(2, 2);
52			}
53	tim	1725	}
54	tim	1804
55	tim	1725	}
56			}
57	tim	1804
58	tim	1725	#ifdef IS_MPI
59
60			MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_DOUBLE, MPI_SUM,
61			MPI_COMM_WORLD);
62			kinetic = kinetic_global;
63
64			#endif //is_mpi
65
66	tim	1804	kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
67	tim	1725
68			return kinetic;
69			}
70
71			double Thermo::getPotential() {
72	tim	1804	double potential = 0.0;
73			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
74	tim	1901	double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] +
75			curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ;
76	tim	1725
77			// Get total potential for entire system from MPI.
78
79			#ifdef IS_MPI
80
81			MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM,
82			MPI_COMM_WORLD);
83
84			#else
85
86			potential = potential_local;
87
88			#endif // is_mpi
89
90			return potential;
91			}
92
93			double Thermo::getTotalE() {
94			double total;
95
96			total = this->getKinetic() + this->getPotential();
97			return total;
98			}
99
100			double Thermo::getTemperature() {
101	tim	1804
102			double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
103	tim	1725	return temperature;
104			}
105
106	tim	1804	double Thermo::getVolume() {
107			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
108			return curSnapshot->getVolume();
109			}
110	tim	1725
111			double Thermo::getPressure() {
112
113			// Relies on the calculation of the full molecular pressure tensor
114
115
116	tim	1804	Mat3x3d tensor;
117			double pressure;
118	tim	1725
119	tim	1822	tensor = getPressureTensor();
120	tim	1725
121	tim	1804	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
122
123	tim	1725	return pressure;
124			}
125
126	tim	1822	Mat3x3d Thermo::getPressureTensor() {
127	tim	1725	// returns pressure tensor in units amufs^-2Ang^-1
128			// routine derived via viral theorem description in:
129			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
130	tim	1822	Mat3x3d pressureTensor;
131	tim	1804	Mat3x3d p_local(0.0);
132			Mat3x3d p_global(0.0);
133	tim	1725
134	tim	1804	SimInfo::MoleculeIterator i;
135			std::vector<StuntDouble*>::iterator j;
136			Molecule* mol;
137			StuntDouble* integrableObject;
138			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
139			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
140			integrableObject = mol->nextIntegrableObject(j)) {
141	tim	1725
142	tim	1804	double mass = integrableObject->getMass();
143			Vector3d vcom = integrableObject->getVel();
144			p_local += mass * outProduct(vcom, vcom);
145			}
146	tim	1725	}
147	tim	1804
148	tim	1725	#ifdef IS_MPI
149	tim	1804	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
150	tim	1725	#else
151	tim	1804	p_global = p_local;
152	tim	1725	#endif // is_mpi
153
154	tim	1804	double volume = this->getVolume();
155			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
156			Mat3x3d tau = curSnapshot->statData.getTau();
157	tim	1725
158	tim	1854	pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume;
159	tim	1822
160			return pressureTensor;
161	tim	1804	}
162	tim	1725
163	tim	1820	void Thermo::saveStat(){
164			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
165			Stats& stat = currSnapshot->statData;
166
167			stat[Stats::KINETIC_ENERGY] = getKinetic();
168			stat[Stats::POTENTIAL_ENERGY] = getPotential();
169			stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ;
170			stat[Stats::TEMPERATURE] = getTemperature();
171			stat[Stats::PRESSURE] = getPressure();
172	tim	1822	stat[Stats::VOLUME] = getVolume();
173	tim	1820
174			/*@todo need refactorying/
175			//Conserved Quantity is set by integrator and time is set by setTime
176
177			}
178
179	tim	1725	} //end namespace oopse