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"

#ifndef IS_MPI
#include "math/SeqRandNumGen.hpp"
#else
#include "math/ParallelRandNumGen.hpp"
#endif

namespace oopse {

Velocitizer::Velocitizer(SimInfo* info) : info_(info) {

    int seedValue;
    Globals * simParams = info->getSimParams();

#ifndef IS_MPI
    if (simParams->haveSeed()) {
        seedValue = simParams->getSeed();
        randNumGen_ = new SeqRandNumGen(seedValue);
    }else {
        randNumGen_ = new SeqRandNumGen();
    }    
#else
    if (simParams->haveSeed()) {
        seedValue = simParams->getSeed();
        randNumGen_ = new ParallelRandNumGen(seedValue);
    }else {
        randNumGen_ = new ParallelRandNumGen();
    }    
#endif 
}

Velocitizer::~Velocitizer() {
    delete randNumGen_;
}

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;


    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 * randNumGen_->randNorm(0.0, 1.0);
            }

            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 * randNumGen_->randNorm(0.0, 1.0);
                    vbar = sqrt(2.0 * kebar * I(n, n));
                    aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0);
                } else {
                    for( int k = 0; k < 3; k++ ) {
                        vbar = sqrt(2.0 * kebar * I(k, k));
                        aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0);
                    }
                } // 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:	2077
Committed:	Wed Mar 2 16:28:20 2005 UTC (19 years, 4 months ago) by tim
File size:	6080 byte(s)
Log Message:	info_ in Velocitizer is not initialized which causes a seg fault
#	User	Rev	Content
1	tim	2065	/*
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	tim	2068
47	tim	2076	#ifndef IS_MPI
48			#include "math/SeqRandNumGen.hpp"
49			#else
50			#include "math/ParallelRandNumGen.hpp"
51			#endif
52
53	tim	2065	namespace oopse {
54
55	tim	2077	Velocitizer::Velocitizer(SimInfo* info) : info_(info) {
56	tim	2068
57			int seedValue;
58			Globals * simParams = info->getSimParams();
59
60	tim	2072	#ifndef IS_MPI
61	tim	2068	if (simParams->haveSeed()) {
62			seedValue = simParams->getSeed();
63	tim	2076	randNumGen_ = new SeqRandNumGen(seedValue);
64	tim	2068	}else {
65	tim	2076	randNumGen_ = new SeqRandNumGen();
66	tim	2068	}
67	tim	2072	#else
68			if (simParams->haveSeed()) {
69			seedValue = simParams->getSeed();
70			randNumGen_ = new ParallelRandNumGen(seedValue);
71			}else {
72			randNumGen_ = new ParallelRandNumGen();
73			}
74			#endif
75	tim	2068	}
76
77			Velocitizer::~Velocitizer() {
78			delete randNumGen_;
79			}
80
81	tim	2065	void Velocitizer::velocitize(double temperature) {
82			Vector3d aVel;
83			Vector3d aJ;
84			Mat3x3d I;
85			int l;
86			int m;
87			int n;
88			Vector3d vdrift;
89			double vbar;
90			/*@todo refactory kb /
91			const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
92			double av2;
93			double kebar;
94
95			SimInfo::MoleculeIterator i;
96			Molecule::IntegrableObjectIterator j;
97			Molecule * mol;
98			StuntDouble * integrableObject;
99
100
101	tim	2068
102	tim	2065	kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
103
104			for( mol = info_->beginMolecule(i); mol != NULL;
105			mol = info_->nextMolecule(i) ) {
106			for( integrableObject = mol->beginIntegrableObject(j);
107			integrableObject != NULL;
108			integrableObject = mol->nextIntegrableObject(j) ) {
109
110			// uses equipartition theory to solve for vbar in angstrom/fs
111
112			av2 = 2.0 * kebar / integrableObject->getMass();
113			vbar = sqrt(av2);
114
115			// picks random velocities from a gaussian distribution
116			// centered on vbar
117
118			for( int k = 0; k < 3; k++ ) {
119	tim	2068	aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0);
120	tim	2065	}
121
122			integrableObject->setVel(aVel);
123
124			if (integrableObject->isDirectional()) {
125			I = integrableObject->getI();
126
127			if (integrableObject->isLinear()) {
128			l = integrableObject->linearAxis();
129			m = (l + 1) % 3;
130			n = (l + 2) % 3;
131
132			aJ[l] = 0.0;
133			vbar = sqrt(2.0 * kebar * I(m, m));
134	tim	2068	aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0);
135	tim	2065	vbar = sqrt(2.0 * kebar * I(n, n));
136	tim	2068	aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0);
137	tim	2065	} else {
138			for( int k = 0; k < 3; k++ ) {
139			vbar = sqrt(2.0 * kebar * I(k, k));
140	tim	2068	aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0);
141	tim	2065	}
142			} // else isLinear
143
144			integrableObject->setJ(aJ);
145			} //isDirectional
146			}
147			} //end for (mol = beginMolecule(i); ...)
148
149
150
151			removeComDrift();
152
153			}
154
155
156
157			void Velocitizer::removeComDrift() {
158			// Get the Center of Mass drift velocity.
159			Vector3d vdrift = info_->getComVel();
160
161			SimInfo::MoleculeIterator i;
162			Molecule::IntegrableObjectIterator j;
163			Molecule * mol;
164			StuntDouble * integrableObject;
165
166			// Corrects for the center of mass drift.
167			// sums all the momentum and divides by total mass.
168			for( mol = info_->beginMolecule(i); mol != NULL;
169			mol = info_->nextMolecule(i) ) {
170			for( integrableObject = mol->beginIntegrableObject(j);
171			integrableObject != NULL;
172			integrableObject = mol->nextIntegrableObject(j) ) {
173			integrableObject->setVel(integrableObject->getVel() - vdrift);
174			}
175			}
176
177			}
178
179			}