| 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 |
/** |
| 27 |
* @file VelocityVerletIntegrator.cpp |
| 28 |
* @author tlin |
| 29 |
* @date 11/09/2004 |
| 30 |
* @time 16:16am |
| 31 |
* @version 1.0 |
| 32 |
*/ |
| 33 |
|
| 34 |
#include "integrators/VelocityVerletIntegrator.hpp" |
| 35 |
|
| 36 |
namespace oopse { |
| 37 |
|
| 38 |
|
| 39 |
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo* info){ |
| 40 |
|
| 41 |
} |
| 42 |
|
| 43 |
VelocityVerletIntegrator::~VelocityVerletIntegrator() { |
| 44 |
|
| 45 |
} |
| 46 |
|
| 47 |
void VelocityVerletIntegrator::integrate() { |
| 48 |
|
| 49 |
} |
| 50 |
|
| 51 |
void VelocityVerletIntegrator::integrateStep() { |
| 52 |
|
| 53 |
} |
| 54 |
|
| 55 |
void VelocityVerletIntegrator::moveA() { |
| 56 |
|
| 57 |
} |
| 58 |
|
| 59 |
void VelocityVerletIntegrator::moveB() { |
| 60 |
|
| 61 |
} |
| 62 |
|
| 63 |
void VelocityVerletIntegrator::thermalize() { |
| 64 |
|
| 65 |
} |
| 66 |
|
| 67 |
void VelocityVerletIntegrator::velocitize() { |
| 68 |
|
| 69 |
Vector3d aVel; |
| 70 |
Vector3d aJ; |
| 71 |
Mat3x3d I; |
| 72 |
int l, m, n; // velocity randomizer loop counts |
| 73 |
Vector3d vdrift; |
| 74 |
double vbar; |
| 75 |
const double kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
| 76 |
double av2; |
| 77 |
double kebar; |
| 78 |
double temperature; |
| 79 |
|
| 80 |
std::vector<Molecule*>::iterator i; |
| 81 |
std::vector<StuntDouble*>::iterator j; |
| 82 |
Molecule* mol; |
| 83 |
StuntDouble* integrableObject; |
| 84 |
gaussianSPRNG gaussStream(info_->getSeed()); |
| 85 |
|
| 86 |
if (!info->have_target_temp) { |
| 87 |
sprintf( painCave.errMsg, |
| 88 |
"You can't resample the velocities without a targetTemp!\n" |
| 89 |
); |
| 90 |
painCave.isFatal = 1; |
| 91 |
painCave.severity = OOPSE_ERROR; |
| 92 |
simError(); |
| 93 |
return; |
| 94 |
} |
| 95 |
|
| 96 |
temperature = info_->target_temp; |
| 97 |
|
| 98 |
kebar = kb * temperature * info_->getNdfRaw() / ( 2.0 * info_->getNdf()); |
| 99 |
|
| 100 |
|
| 101 |
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 102 |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 103 |
integrableObject = mol->nextIntegrableObject(j)) { |
| 104 |
|
| 105 |
// uses equipartition theory to solve for vbar in angstrom/fs |
| 106 |
|
| 107 |
av2 = 2.0 * kebar / integrableObject->getMass(); |
| 108 |
vbar = sqrt( av2 ); |
| 109 |
|
| 110 |
// picks random velocities from a gaussian distribution |
| 111 |
// centered on vbar |
| 112 |
|
| 113 |
for (int k=0; k<3; k++) { |
| 114 |
aVel[k] = vbar * gaussStream.getGaussian(); |
| 115 |
} |
| 116 |
|
| 117 |
integrableObject->setVel( aVel ); |
| 118 |
|
| 119 |
if(integrableObject->isDirectional()){ |
| 120 |
|
| 121 |
I = integrableObject->getI(); |
| 122 |
|
| 123 |
if (integrableObject->isLinear()) { |
| 124 |
|
| 125 |
l= integrableObject->linearAxis(); |
| 126 |
m = (l+1)%3; |
| 127 |
n = (l+2)%3; |
| 128 |
|
| 129 |
aJ[l] = 0.0; |
| 130 |
vbar = sqrt( 2.0 * kebar * I(m, m) ); |
| 131 |
aJ[m] = vbar * gaussStream.getGaussian(); |
| 132 |
vbar = sqrt( 2.0 * kebar * I(n, n) ); |
| 133 |
aJ[n] = vbar * gaussStream.getGaussian(); |
| 134 |
|
| 135 |
} else { |
| 136 |
|
| 137 |
for (int k = 0 ; k < 3; k++) { |
| 138 |
vbar = sqrt( 2.0 * kebar * I(k, k) ); |
| 139 |
aJ[k] = vbar * gaussStream.getGaussian(); |
| 140 |
} |
| 141 |
|
| 142 |
} // else isLinear |
| 143 |
|
| 144 |
integrableObject->setJ( aJ ); |
| 145 |
|
| 146 |
}//isDirectional |
| 147 |
|
| 148 |
} |
| 149 |
}//end for (mol = beginMolecule(i); ...) |
| 150 |
|
| 151 |
// Get the Center of Mass drift velocity. |
| 152 |
vdrift = info_->getComVel(); |
| 153 |
|
| 154 |
// Corrects for the center of mass drift. |
| 155 |
// sums all the momentum and divides by total mass. |
| 156 |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 157 |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 158 |
integrableObject = mol->nextIntegrableObject(j)) { |
| 159 |
|
| 160 |
aVel = integrableObject->getVel(); |
| 161 |
aVel -= vdrift; |
| 162 |
integrableObject->setVel( aVel ); |
| 163 |
} |
| 164 |
} |
| 165 |
|
| 166 |
} |
| 167 |
|
| 168 |
void VelocityVerletIntegrator::calcForce(int needPotential, int needStress){ |
| 169 |
|
| 170 |
} |
| 171 |
|
| 172 |
void VelocityVerletIntegrator::velocitize() { |
| 173 |
|
| 174 |
} |
| 175 |
|
| 176 |
void removeComDrift(){ |
| 177 |
|
| 178 |
} |
