src/integrators/Velocitizer.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 "integrators/Velocitizer.hpp"
#include "math/SquareMatrix3.hpp"
#include "primitives/Molecule.hpp"
#include "primitives/StuntDouble.hpp"
#include "math/randomSPRNG.hpp"

namespace oopse {

void Velocitizer::velocitize(double temperature) {
    Vector3d aVel;
    Vector3d aJ;
    Mat3x3d I;
    int l;
    int m;
    int n; 
    Vector3d vdrift;
    double vbar;
    /**@todo refactory kb */
    const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
    double av2;
    double kebar;

    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator j;
    Molecule * mol;
    StuntDouble * integrableObject;
    gaussianSPRNG gaussStream(info_->getSeed());

    kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());

    for( mol = info_->beginMolecule(i); mol != NULL;
        mol = info_->nextMolecule(i) ) {
        for( integrableObject = mol->beginIntegrableObject(j);
            integrableObject != NULL;
            integrableObject = mol->nextIntegrableObject(j) ) {

            // uses equipartition theory to solve for vbar in angstrom/fs

            av2 = 2.0 * kebar / integrableObject->getMass();
            vbar = sqrt(av2);

            // picks random velocities from a gaussian distribution
            // centered on vbar

            for( int k = 0; k < 3; k++ ) {
                aVel[k] = vbar * gaussStream.getGaussian();
            }

            integrableObject->setVel(aVel);

            if (integrableObject->isDirectional()) {
                I = integrableObject->getI();

                if (integrableObject->isLinear()) {
                    l = integrableObject->linearAxis();
                    m = (l + 1) % 3;
                    n = (l + 2) % 3;

                    aJ[l] = 0.0;
                    vbar = sqrt(2.0 * kebar * I(m, m));
                    aJ[m] = vbar * gaussStream.getGaussian();
                    vbar = sqrt(2.0 * kebar * I(n, n));
                    aJ[n] = vbar * gaussStream.getGaussian();
                } else {
                    for( int k = 0; k < 3; k++ ) {
                        vbar = sqrt(2.0 * kebar * I(k, k));
                        aJ[k] = vbar * gaussStream.getGaussian();
                    }
                } // else isLinear

                integrableObject->setJ(aJ);
            }     //isDirectional 
        }
    }             //end for (mol = beginMolecule(i); ...)


    removeComDrift();

}


void Velocitizer::removeComDrift() {
    // Get the Center of Mass drift velocity.
    Vector3d vdrift = info_->getComVel();
    
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator j;
    Molecule * mol;
    StuntDouble * integrableObject;
    
    //  Corrects for the center of mass drift.
    // sums all the momentum and divides by total mass.
    for( mol = info_->beginMolecule(i); mol != NULL;
        mol = info_->nextMolecule(i) ) {
        for( integrableObject = mol->beginIntegrableObject(j);
            integrableObject != NULL;
            integrableObject = mol->nextIntegrableObject(j) ) {
            integrableObject->setVel(integrableObject->getVel() - vdrift);
        }
    }

}

}
Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	5247 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	1930	/*
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 "integrators/Velocitizer.hpp"
43			#include "math/SquareMatrix3.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "primitives/StuntDouble.hpp"
46			#include "math/randomSPRNG.hpp"
47
48			namespace oopse {
49
50			void Velocitizer::velocitize(double temperature) {
51			Vector3d aVel;
52			Vector3d aJ;
53			Mat3x3d I;
54			int l;
55			int m;
56			int n;
57			Vector3d vdrift;
58			double vbar;
59			/*@todo refactory kb /
60			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
61			double av2;
62			double kebar;
63
64			SimInfo::MoleculeIterator i;
65			Molecule::IntegrableObjectIterator j;
66			Molecule * mol;
67			StuntDouble * integrableObject;
68			gaussianSPRNG gaussStream(info_->getSeed());
69
70			kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
71
72			for( mol = info_->beginMolecule(i); mol != NULL;
73			mol = info_->nextMolecule(i) ) {
74			for( integrableObject = mol->beginIntegrableObject(j);
75			integrableObject != NULL;
76			integrableObject = mol->nextIntegrableObject(j) ) {
77
78			// uses equipartition theory to solve for vbar in angstrom/fs
79
80			av2 = 2.0 * kebar / integrableObject->getMass();
81			vbar = sqrt(av2);
82
83			// picks random velocities from a gaussian distribution
84			// centered on vbar
85
86			for( int k = 0; k < 3; k++ ) {
87			aVel[k] = vbar * gaussStream.getGaussian();
88			}
89
90			integrableObject->setVel(aVel);
91
92			if (integrableObject->isDirectional()) {
93			I = integrableObject->getI();
94
95			if (integrableObject->isLinear()) {
96			l = integrableObject->linearAxis();
97			m = (l + 1) % 3;
98			n = (l + 2) % 3;
99
100			aJ[l] = 0.0;
101			vbar = sqrt(2.0 * kebar * I(m, m));
102			aJ[m] = vbar * gaussStream.getGaussian();
103			vbar = sqrt(2.0 * kebar * I(n, n));
104			aJ[n] = vbar * gaussStream.getGaussian();
105			} else {
106			for( int k = 0; k < 3; k++ ) {
107			vbar = sqrt(2.0 * kebar * I(k, k));
108			aJ[k] = vbar * gaussStream.getGaussian();
109			}
110			} // else isLinear
111
112			integrableObject->setJ(aJ);
113			} //isDirectional
114			}
115			} //end for (mol = beginMolecule(i); ...)
116
117
118
119			removeComDrift();
120
121			}
122
123
124
125			void Velocitizer::removeComDrift() {
126			// Get the Center of Mass drift velocity.
127			Vector3d vdrift = info_->getComVel();
128
129			SimInfo::MoleculeIterator i;
130			Molecule::IntegrableObjectIterator j;
131			Molecule * mol;
132			StuntDouble * integrableObject;
133
134			// Corrects for the center of mass drift.
135			// sums all the momentum and divides by total mass.
136			for( mol = info_->beginMolecule(i); mol != NULL;
137			mol = info_->nextMolecule(i) ) {
138			for( integrableObject = mol->beginIntegrableObject(j);
139			integrableObject != NULL;
140			integrableObject = mol->nextIntegrableObject(j) ) {
141			integrableObject->setVel(integrableObject->getVel() - vdrift);
142			}
143			}
144
145			}
146
147			}