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;    
    double mass;
    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];

    SimInfo::MoleculeIterator i;
    Molecule* mol;    
    for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
        potential_local += mol->getPotential();
    }

    // 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:	1854
Committed:	Sun Dec 5 22:02:42 2004 UTC (20 years, 10 months ago) by tim
File size:	5346 byte(s)
Log Message:	fix a bug in filling MolMembership
#	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			double mass;
23			Vector3d vel;
24			Vector3d angMom;
25			Mat3x3d I;
26			int i;
27			int j;
28			int k;
29			double kinetic = 0.0;
30			double kinetic_global = 0.0;
31
32			for (mol = info_->beginMolecule(miter); mol != NULL; mol = info_->nextMolecule(miter)) {
33			for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
34			integrableObject = mol->nextIntegrableObject(iiter)) {
35	tim	1725
36	tim	1804	double mass = integrableObject->getMass();
37			Vector3d vel = integrableObject->getVel();
38	tim	1725
39	tim	1847	kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
40	tim	1725
41	tim	1804	if (integrableObject->isDirectional()) {
42			angMom = integrableObject->getJ();
43			I = integrableObject->getI();
44	tim	1725
45	tim	1804	if (integrableObject->isLinear()) {
46			i = integrableObject->linearAxis();
47			j = (i + 1) % 3;
48			k = (i + 2) % 3;
49			kinetic += angMom[j] * angMom[j] / I(j, j) + angMom[k] * angMom[k] / I(k, k);
50			} else {
51			kinetic += angMom[0]angMom[0]/I(0, 0) + angMom[1]angMom[1]/I(1, 1)
52			+ angMom[2]*angMom[2]/I(2, 2);
53			}
54	tim	1725	}
55	tim	1804
56	tim	1725	}
57			}
58	tim	1804
59	tim	1725	#ifdef IS_MPI
60
61			MPI_Allreduce(&kinetic, &kinetic_global, 1, MPI_DOUBLE, MPI_SUM,
62			MPI_COMM_WORLD);
63			kinetic = kinetic_global;
64
65			#endif //is_mpi
66
67	tim	1804	kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
68	tim	1725
69			return kinetic;
70			}
71
72			double Thermo::getPotential() {
73	tim	1804	double potential = 0.0;
74			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
75			double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
76	tim	1725
77	tim	1804	SimInfo::MoleculeIterator i;
78			Molecule* mol;
79			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
80			potential_local += mol->getPotential();
81	tim	1725	}
82
83			// Get total potential for entire system from MPI.
84
85			#ifdef IS_MPI
86
87			MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM,
88			MPI_COMM_WORLD);
89
90			#else
91
92			potential = potential_local;
93
94			#endif // is_mpi
95
96			return potential;
97			}
98
99			double Thermo::getTotalE() {
100			double total;
101
102			total = this->getKinetic() + this->getPotential();
103			return total;
104			}
105
106			double Thermo::getTemperature() {
107	tim	1804
108			double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
109	tim	1725	return temperature;
110			}
111
112	tim	1804	double Thermo::getVolume() {
113			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
114			return curSnapshot->getVolume();
115			}
116	tim	1725
117			double Thermo::getPressure() {
118
119			// Relies on the calculation of the full molecular pressure tensor
120
121
122	tim	1804	Mat3x3d tensor;
123			double pressure;
124	tim	1725
125	tim	1822	tensor = getPressureTensor();
126	tim	1725
127	tim	1804	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
128
129	tim	1725	return pressure;
130			}
131
132	tim	1822	Mat3x3d Thermo::getPressureTensor() {
133	tim	1725	// returns pressure tensor in units amufs^-2Ang^-1
134			// routine derived via viral theorem description in:
135			// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
136	tim	1822	Mat3x3d pressureTensor;
137	tim	1804	Mat3x3d p_local(0.0);
138			Mat3x3d p_global(0.0);
139	tim	1725
140	tim	1804	SimInfo::MoleculeIterator i;
141			std::vector<StuntDouble*>::iterator j;
142			Molecule* mol;
143			StuntDouble* integrableObject;
144			for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
145			for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
146			integrableObject = mol->nextIntegrableObject(j)) {
147	tim	1725
148	tim	1804	double mass = integrableObject->getMass();
149			Vector3d vcom = integrableObject->getVel();
150			p_local += mass * outProduct(vcom, vcom);
151			}
152	tim	1725	}
153	tim	1804
154	tim	1725	#ifdef IS_MPI
155	tim	1804	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
156	tim	1725	#else
157	tim	1804	p_global = p_local;
158	tim	1725	#endif // is_mpi
159
160	tim	1804	double volume = this->getVolume();
161			Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
162			Mat3x3d tau = curSnapshot->statData.getTau();
163	tim	1725
164	tim	1854	pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume;
165	tim	1822
166			return pressureTensor;
167	tim	1804	}
168	tim	1725
169	tim	1820	void Thermo::saveStat(){
170			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
171			Stats& stat = currSnapshot->statData;
172
173			stat[Stats::KINETIC_ENERGY] = getKinetic();
174			stat[Stats::POTENTIAL_ENERGY] = getPotential();
175			stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ;
176			stat[Stats::TEMPERATURE] = getTemperature();
177			stat[Stats::PRESSURE] = getPressure();
178	tim	1822	stat[Stats::VOLUME] = getVolume();
179	tim	1820
180			/*@todo need refactorying/
181			//Conserved Quantity is set by integrator and time is set by setTime
182
183			}
184
185	tim	1725	} //end namespace oopse