| 1 |
/* |
| 2 |
* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
| 3 |
* |
| 4 |
* Contact: oopse@oopse.org |
| 5 |
* |
| 6 |
* This program is free software; you can redistribute it and/or |
| 7 |
* modify it under the terms of the GNU Lesser General Public License |
| 8 |
* as published by the Free Software Foundation; either version 2.1 |
| 9 |
* of the License, or (at your option) any later version. |
| 10 |
* All we ask is that proper credit is given for our work, which includes |
| 11 |
* - but is not limited to - adding the above copyright notice to the beginning |
| 12 |
* of your source code files, and to any copyright notice that you may distribute |
| 13 |
* with programs based on this work. |
| 14 |
* |
| 15 |
* This program is distributed in the hope that it will be useful, |
| 16 |
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 17 |
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 18 |
* GNU Lesser General Public License for more details. |
| 19 |
* |
| 20 |
* You should have received a copy of the GNU Lesser General Public License |
| 21 |
* along with this program; if not, write to the Free Software |
| 22 |
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
| 23 |
* |
| 24 |
*/ |
| 25 |
|
| 26 |
#include "integrators/Velocitizer.hpp" |
| 27 |
#include "math/SquareMatrix3.hpp" |
| 28 |
#include "primitives/Molecule.hpp" |
| 29 |
#include "primitives/StuntDouble.hpp" |
| 30 |
#include "math/randomSPRNG.hpp" |
| 31 |
|
| 32 |
namespace oopse { |
| 33 |
|
| 34 |
void Velocitizer::velocitize(double temperature) { |
| 35 |
Vector3d aVel; |
| 36 |
Vector3d aJ; |
| 37 |
Mat3x3d I; |
| 38 |
int l; |
| 39 |
int m; |
| 40 |
int n; |
| 41 |
Vector3d vdrift; |
| 42 |
double vbar; |
| 43 |
/**@todo refactory kb */ |
| 44 |
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 45 |
double av2; |
| 46 |
double kebar; |
| 47 |
|
| 48 |
SimInfo::MoleculeIterator i; |
| 49 |
Molecule::IntegrableObjectIterator j; |
| 50 |
Molecule * mol; |
| 51 |
StuntDouble * integrableObject; |
| 52 |
gaussianSPRNG gaussStream(info_->getSeed()); |
| 53 |
|
| 54 |
kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf()); |
| 55 |
|
| 56 |
for( mol = info_->beginMolecule(i); mol != NULL; |
| 57 |
mol = info_->nextMolecule(i) ) { |
| 58 |
for( integrableObject = mol->beginIntegrableObject(j); |
| 59 |
integrableObject != NULL; |
| 60 |
integrableObject = mol->nextIntegrableObject(j) ) { |
| 61 |
|
| 62 |
// uses equipartition theory to solve for vbar in angstrom/fs |
| 63 |
|
| 64 |
av2 = 2.0 * kebar / integrableObject->getMass(); |
| 65 |
vbar = sqrt(av2); |
| 66 |
|
| 67 |
// picks random velocities from a gaussian distribution |
| 68 |
// centered on vbar |
| 69 |
|
| 70 |
for( int k = 0; k < 3; k++ ) { |
| 71 |
aVel[k] = vbar * gaussStream.getGaussian(); |
| 72 |
} |
| 73 |
|
| 74 |
integrableObject->setVel(aVel); |
| 75 |
|
| 76 |
if (integrableObject->isDirectional()) { |
| 77 |
I = integrableObject->getI(); |
| 78 |
|
| 79 |
if (integrableObject->isLinear()) { |
| 80 |
l = integrableObject->linearAxis(); |
| 81 |
m = (l + 1) % 3; |
| 82 |
n = (l + 2) % 3; |
| 83 |
|
| 84 |
aJ[l] = 0.0; |
| 85 |
vbar = sqrt(2.0 * kebar * I(m, m)); |
| 86 |
aJ[m] = vbar * gaussStream.getGaussian(); |
| 87 |
vbar = sqrt(2.0 * kebar * I(n, n)); |
| 88 |
aJ[n] = vbar * gaussStream.getGaussian(); |
| 89 |
} else { |
| 90 |
for( int k = 0; k < 3; k++ ) { |
| 91 |
vbar = sqrt(2.0 * kebar * I(k, k)); |
| 92 |
aJ[k] = vbar * gaussStream.getGaussian(); |
| 93 |
} |
| 94 |
} // else isLinear |
| 95 |
|
| 96 |
integrableObject->setJ(aJ); |
| 97 |
} //isDirectional |
| 98 |
} |
| 99 |
} //end for (mol = beginMolecule(i); ...) |
| 100 |
|
| 101 |
|
| 102 |
|
| 103 |
removeComDrift(); |
| 104 |
|
| 105 |
} |
| 106 |
|
| 107 |
|
| 108 |
|
| 109 |
void Velocitizer::removeComDrift() { |
| 110 |
// Get the Center of Mass drift velocity. |
| 111 |
Vector3d vdrift = info_->getComVel(); |
| 112 |
|
| 113 |
SimInfo::MoleculeIterator i; |
| 114 |
Molecule::IntegrableObjectIterator j; |
| 115 |
Molecule * mol; |
| 116 |
StuntDouble * integrableObject; |
| 117 |
|
| 118 |
// Corrects for the center of mass drift. |
| 119 |
// sums all the momentum and divides by total mass. |
| 120 |
for( mol = info_->beginMolecule(i); mol != NULL; |
| 121 |
mol = info_->nextMolecule(i) ) { |
| 122 |
for( integrableObject = mol->beginIntegrableObject(j); |
| 123 |
integrableObject != NULL; |
| 124 |
integrableObject = mol->nextIntegrableObject(j) ) { |
| 125 |
integrableObject->setVel(integrableObject->getVel() - vdrift); |
| 126 |
} |
| 127 |
} |
| 128 |
|
| 129 |
} |
| 130 |
|
| 131 |
} |
