| 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. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
* documentation and/or other materials provided with the |
| 15 |
* distribution. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 28 |
* arising out of the use of or inability to use software, even if the |
| 29 |
* University of Notre Dame has been advised of the possibility of |
| 30 |
* such damages. |
| 31 |
* |
| 32 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
* research, please cite the appropriate papers when you publish your |
| 34 |
* work. Good starting points are: |
| 35 |
* |
| 36 |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
*/ |
| 42 |
|
| 43 |
/** |
| 44 |
* @file LangevinDynamics.cpp |
| 45 |
* @author tlin |
| 46 |
* @date 11/08/2004 |
| 47 |
* @time 15:13am |
| 48 |
* @version 1.0 |
| 49 |
*/ |
| 50 |
|
| 51 |
#include "integrators/LangevinHullDynamics.hpp" |
| 52 |
#include "primitives/Molecule.hpp" |
| 53 |
#include "utils/PhysicalConstants.hpp" |
| 54 |
#include "integrators/LangevinHullForceManager.hpp" |
| 55 |
namespace OpenMD { |
| 56 |
|
| 57 |
LangevinHullDynamics::LangevinHullDynamics(SimInfo* info) : VelocityVerletIntegrator(info){ |
| 58 |
setForceManager(new LangevinHullForceManager(info)); |
| 59 |
} |
| 60 |
|
| 61 |
void LangevinHullDynamics::moveA(){ |
| 62 |
SimInfo::MoleculeIterator i; |
| 63 |
Molecule::IntegrableObjectIterator j; |
| 64 |
Molecule* mol; |
| 65 |
StuntDouble* sd; |
| 66 |
Vector3d vel; |
| 67 |
Vector3d pos; |
| 68 |
Vector3d frc; |
| 69 |
Vector3d Tb; |
| 70 |
Vector3d ji; |
| 71 |
RealType mass; |
| 72 |
|
| 73 |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 74 |
mol = info_->nextMolecule(i)) { |
| 75 |
|
| 76 |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 77 |
sd = mol->nextIntegrableObject(j)) { |
| 78 |
|
| 79 |
vel = sd->getVel(); |
| 80 |
pos = sd->getPos(); |
| 81 |
frc = sd->getFrc(); |
| 82 |
mass = sd->getMass(); |
| 83 |
|
| 84 |
// velocity half step |
| 85 |
vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; |
| 86 |
|
| 87 |
// position whole step |
| 88 |
pos += dt * vel; |
| 89 |
|
| 90 |
sd->setVel(vel); |
| 91 |
sd->setPos(pos); |
| 92 |
|
| 93 |
if (sd->isDirectional()){ |
| 94 |
|
| 95 |
// get and convert the torque to body frame |
| 96 |
|
| 97 |
Tb = sd->lab2Body(sd->getTrq()); |
| 98 |
|
| 99 |
// get the angular momentum, and propagate a half step |
| 100 |
|
| 101 |
ji = sd->getJ(); |
| 102 |
|
| 103 |
ji += (dt2 * PhysicalConstants::energyConvert) * Tb; |
| 104 |
|
| 105 |
rotAlgo_->rotate(sd, ji, dt); |
| 106 |
|
| 107 |
sd->setJ(ji); |
| 108 |
} |
| 109 |
|
| 110 |
|
| 111 |
} |
| 112 |
} //end for(mol = info_->beginMolecule(i)) |
| 113 |
|
| 114 |
flucQ_->moveA(); |
| 115 |
rattle_->constraintA(); |
| 116 |
|
| 117 |
} |
| 118 |
|
| 119 |
void LangevinHullDynamics::moveB(){ |
| 120 |
SimInfo::MoleculeIterator i; |
| 121 |
Molecule::IntegrableObjectIterator j; |
| 122 |
Molecule* mol; |
| 123 |
StuntDouble* sd; |
| 124 |
Vector3d vel; |
| 125 |
Vector3d frc; |
| 126 |
Vector3d Tb; |
| 127 |
Vector3d ji; |
| 128 |
RealType mass; |
| 129 |
|
| 130 |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 131 |
mol = info_->nextMolecule(i)) { |
| 132 |
|
| 133 |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 134 |
sd = mol->nextIntegrableObject(j)) { |
| 135 |
|
| 136 |
vel = sd->getVel(); |
| 137 |
frc = sd->getFrc(); |
| 138 |
mass = sd->getMass(); |
| 139 |
|
| 140 |
// velocity half step |
| 141 |
vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc; |
| 142 |
|
| 143 |
sd->setVel(vel); |
| 144 |
|
| 145 |
if (sd->isDirectional()){ |
| 146 |
|
| 147 |
// get and convert the torque to body frame |
| 148 |
|
| 149 |
Tb = sd->lab2Body(sd->getTrq()); |
| 150 |
|
| 151 |
// get the angular momentum, and propagate a half step |
| 152 |
|
| 153 |
ji = sd->getJ(); |
| 154 |
|
| 155 |
ji += (dt2 * PhysicalConstants::energyConvert) * Tb; |
| 156 |
|
| 157 |
sd->setJ(ji); |
| 158 |
} |
| 159 |
|
| 160 |
|
| 161 |
} |
| 162 |
} //end for(mol = info_->beginMolecule(i)) |
| 163 |
|
| 164 |
flucQ_->moveB(); |
| 165 |
rattle_->constraintB(); |
| 166 |
} |
| 167 |
|
| 168 |
|
| 169 |
RealType LangevinHullDynamics::calcConservedQuantity() { |
| 170 |
return 0.0; |
| 171 |
} |
| 172 |
|
| 173 |
} //end namespace OpenMD |
| 174 |
|
