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];

    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:	1883
Committed:	Mon Dec 13 22:30:27 2004 UTC (19 years, 6 months ago) by tim
File size:	5329 byte(s)
Log Message:	MPI version is built
#	Content
1	#include <math.h>
2	#include <iostream>
3
4
5
6	#ifdef IS_MPI
7	#include <mpi.h>
8	#endif //is_mpi
9
10	#include "brains/Thermo.hpp"
11	#include "primitives/Molecule.hpp"
12	#include "utils/simError.h"
13	#include "utils/OOPSEConstant.hpp"
14
15	namespace oopse {
16
17	double Thermo::getKinetic() {
18	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
35	double mass = integrableObject->getMass();
36	Vector3d vel = integrableObject->getVel();
37
38	kinetic += mass * (vel[0]vel[0] + vel[1]vel[1] + vel[2]*vel[2]);
39
40	if (integrableObject->isDirectional()) {
41	angMom = integrableObject->getJ();
42	I = integrableObject->getI();
43
44	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	}
54
55	}
56	}
57
58	#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	kinetic = kinetic * 0.5 / OOPSEConstant::energyConvert;
67
68	return kinetic;
69	}
70
71	double Thermo::getPotential() {
72	double potential = 0.0;
73	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
74	double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
75
76	SimInfo::MoleculeIterator i;
77	Molecule* mol;
78	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
79	potential_local += mol->getPotential();
80	}
81
82	// Get total potential for entire system from MPI.
83
84	#ifdef IS_MPI
85
86	MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM,
87	MPI_COMM_WORLD);
88
89	#else
90
91	potential = potential_local;
92
93	#endif // is_mpi
94
95	return potential;
96	}
97
98	double Thermo::getTotalE() {
99	double total;
100
101	total = this->getKinetic() + this->getPotential();
102	return total;
103	}
104
105	double Thermo::getTemperature() {
106
107	double temperature = ( 2.0 * this->getKinetic() ) / (info_->getNdf()* OOPSEConstant::kb );
108	return temperature;
109	}
110
111	double Thermo::getVolume() {
112	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
113	return curSnapshot->getVolume();
114	}
115
116	double Thermo::getPressure() {
117
118	// Relies on the calculation of the full molecular pressure tensor
119
120
121	Mat3x3d tensor;
122	double pressure;
123
124	tensor = getPressureTensor();
125
126	pressure = OOPSEConstant::pressureConvert * (tensor(0, 0) + tensor(1, 1) + tensor(2, 2)) / 3.0;
127
128	return pressure;
129	}
130
131	Mat3x3d Thermo::getPressureTensor() {
132	// returns pressure tensor in units amufs^-2Ang^-1
133	// routine derived via viral theorem description in:
134	// Paci, E. and Marchi, M. J.Phys.Chem. 1996, 100, 4314-4322
135	Mat3x3d pressureTensor;
136	Mat3x3d p_local(0.0);
137	Mat3x3d p_global(0.0);
138
139	SimInfo::MoleculeIterator i;
140	std::vector<StuntDouble*>::iterator j;
141	Molecule* mol;
142	StuntDouble* integrableObject;
143	for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
144	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
145	integrableObject = mol->nextIntegrableObject(j)) {
146
147	double mass = integrableObject->getMass();
148	Vector3d vcom = integrableObject->getVel();
149	p_local += mass * outProduct(vcom, vcom);
150	}
151	}
152
153	#ifdef IS_MPI
154	MPI_Allreduce(p_local.getArrayPointer(), p_global.getArrayPointer(), 9, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
155	#else
156	p_global = p_local;
157	#endif // is_mpi
158
159	double volume = this->getVolume();
160	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
161	Mat3x3d tau = curSnapshot->statData.getTau();
162
163	pressureTensor = (p_global + OOPSEConstant::energyConvert* tau)/volume;
164
165	return pressureTensor;
166	}
167
168	void Thermo::saveStat(){
169	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
170	Stats& stat = currSnapshot->statData;
171
172	stat[Stats::KINETIC_ENERGY] = getKinetic();
173	stat[Stats::POTENTIAL_ENERGY] = getPotential();
174	stat[Stats::TOTAL_ENERGY] = stat[Stats::KINETIC_ENERGY] + stat[Stats::POTENTIAL_ENERGY] ;
175	stat[Stats::TEMPERATURE] = getTemperature();
176	stat[Stats::PRESSURE] = getPressure();
177	stat[Stats::VOLUME] = getVolume();
178
179	/*@todo need refactorying/
180	//Conserved Quantity is set by integrator and time is set by setTime
181
182	}
183
184	} //end namespace oopse