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"

namespace oopse {

Velocitizer::Velocitizer(SimInfo* info) {

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

#ifndef IS_MPI
    if (simParams->haveSeed()) {
        seedValue = simParams->getSeed();
        randNumGen_ = new MTRand(seedValue);
    }else {
        randNumGen_ = new MTRand();
    }    
#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:	2072
Committed:	Tue Mar 1 23:02:33 2005 UTC (19 years, 4 months ago) by tim
File size:	5944 byte(s)
Log Message:	replace SPRNG by MTRand
#	Content
1	/*
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
47	namespace oopse {
48
49	Velocitizer::Velocitizer(SimInfo* info) {
50
51	int seedValue;
52	Globals * simParams = info->getSimParams();
53
54	#ifndef IS_MPI
55	if (simParams->haveSeed()) {
56	seedValue = simParams->getSeed();
57	randNumGen_ = new MTRand(seedValue);
58	}else {
59	randNumGen_ = new MTRand();
60	}
61	#else
62	if (simParams->haveSeed()) {
63	seedValue = simParams->getSeed();
64	randNumGen_ = new ParallelRandNumGen(seedValue);
65	}else {
66	randNumGen_ = new ParallelRandNumGen();
67	}
68	#endif
69	}
70
71	Velocitizer::~Velocitizer() {
72	delete randNumGen_;
73	}
74
75	void Velocitizer::velocitize(double temperature) {
76	Vector3d aVel;
77	Vector3d aJ;
78	Mat3x3d I;
79	int l;
80	int m;
81	int n;
82	Vector3d vdrift;
83	double vbar;
84	/*@todo refactory kb /
85	const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc.
86	double av2;
87	double kebar;
88
89	SimInfo::MoleculeIterator i;
90	Molecule::IntegrableObjectIterator j;
91	Molecule * mol;
92	StuntDouble * integrableObject;
93
94
95
96	kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf());
97
98	for( mol = info_->beginMolecule(i); mol != NULL;
99	mol = info_->nextMolecule(i) ) {
100	for( integrableObject = mol->beginIntegrableObject(j);
101	integrableObject != NULL;
102	integrableObject = mol->nextIntegrableObject(j) ) {
103
104	// uses equipartition theory to solve for vbar in angstrom/fs
105
106	av2 = 2.0 * kebar / integrableObject->getMass();
107	vbar = sqrt(av2);
108
109	// picks random velocities from a gaussian distribution
110	// centered on vbar
111
112	for( int k = 0; k < 3; k++ ) {
113	aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0);
114	}
115
116	integrableObject->setVel(aVel);
117
118	if (integrableObject->isDirectional()) {
119	I = integrableObject->getI();
120
121	if (integrableObject->isLinear()) {
122	l = integrableObject->linearAxis();
123	m = (l + 1) % 3;
124	n = (l + 2) % 3;
125
126	aJ[l] = 0.0;
127	vbar = sqrt(2.0 * kebar * I(m, m));
128	aJ[m] = vbar * randNumGen_->randNorm(0.0, 1.0);
129	vbar = sqrt(2.0 * kebar * I(n, n));
130	aJ[n] = vbar * randNumGen_->randNorm(0.0, 1.0);
131	} else {
132	for( int k = 0; k < 3; k++ ) {
133	vbar = sqrt(2.0 * kebar * I(k, k));
134	aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0);
135	}
136	} // else isLinear
137
138	integrableObject->setJ(aJ);
139	} //isDirectional
140	}
141	} //end for (mol = beginMolecule(i); ...)
142
143
144
145	removeComDrift();
146
147	}
148
149
150
151	void Velocitizer::removeComDrift() {
152	// Get the Center of Mass drift velocity.
153	Vector3d vdrift = info_->getComVel();
154
155	SimInfo::MoleculeIterator i;
156	Molecule::IntegrableObjectIterator j;
157	Molecule * mol;
158	StuntDouble * integrableObject;
159
160	// Corrects for the center of mass drift.
161	// sums all the momentum and divides by total mass.
162	for( mol = info_->beginMolecule(i); mol != NULL;
163	mol = info_->nextMolecule(i) ) {
164	for( integrableObject = mol->beginIntegrableObject(j);
165	integrableObject != NULL;
166	integrableObject = mol->nextIntegrableObject(j) ) {
167	integrableObject->setVel(integrableObject->getVel() - vdrift);
168	}
169	}
170
171	}
172
173	}