| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
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|
|
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|
#include "integrators/Velocitizer.hpp" |
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#include "math/ParallelRandNumGen.hpp" |
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#endif |
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|
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< |
/* Remove me after testing*/ |
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< |
/* |
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< |
#include <cstdio> |
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< |
#include <iostream> |
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< |
*/ |
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/*End remove me*/ |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
|
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< |
Velocitizer::Velocitizer(SimInfo* info) : info_(info) { |
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> |
Velocitizer::Velocitizer(SimInfo* info) : info_(info), thermo(info) { |
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|
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< |
int seedValue; |
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> |
|
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Globals * simParams = info->getSimParams(); |
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|
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#ifndef IS_MPI |
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if (simParams->haveSeed()) { |
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< |
seedValue = simParams->getSeed(); |
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> |
int seedValue = simParams->getSeed(); |
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randNumGen_ = new SeqRandNumGen(seedValue); |
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}else { |
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randNumGen_ = new SeqRandNumGen(); |
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} |
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#else |
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if (simParams->haveSeed()) { |
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< |
seedValue = simParams->getSeed(); |
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> |
int seedValue = simParams->getSeed(); |
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randNumGen_ = new ParallelRandNumGen(seedValue); |
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}else { |
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randNumGen_ = new ParallelRandNumGen(); |
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Vector3d aVel; |
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Vector3d aJ; |
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Mat3x3d I; |
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int l; |
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< |
int m; |
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int n; |
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> |
int l, m, n; |
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Vector3d vdrift; |
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RealType vbar; |
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< |
/**@todo refactory kb */ |
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> |
/**@todo refactor kb */ |
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const RealType kb = 8.31451e-7; // kb in amu, angstroms, fs, etc. |
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RealType av2; |
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RealType kebar; |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule * mol; |
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< |
StuntDouble * integrableObject; |
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> |
StuntDouble * sd; |
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|
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kebar = kb * temperature * info_->getNdfRaw() / (2.0 * info_->getNdf()); |
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+ |
|
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for( mol = info_->beginMolecule(i); mol != NULL; |
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mol = info_->nextMolecule(i) ) { |
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< |
for( integrableObject = mol->beginIntegrableObject(j); |
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< |
integrableObject != NULL; |
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< |
integrableObject = mol->nextIntegrableObject(j) ) { |
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> |
|
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> |
for( sd = mol->beginIntegrableObject(j); sd != NULL; |
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> |
sd = mol->nextIntegrableObject(j) ) { |
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|
|
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// uses equipartition theory to solve for vbar in angstrom/fs |
| 110 |
|
|
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< |
av2 = 2.0 * kebar / integrableObject->getMass(); |
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> |
av2 = 2.0 * kebar / sd->getMass(); |
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vbar = sqrt(av2); |
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|
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// picks random velocities from a gaussian distribution |
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for( int k = 0; k < 3; k++ ) { |
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aVel[k] = vbar * randNumGen_->randNorm(0.0, 1.0); |
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} |
| 120 |
< |
integrableObject->setVel(aVel); |
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> |
sd->setVel(aVel); |
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|
|
| 122 |
< |
if (integrableObject->isDirectional()) { |
| 123 |
< |
I = integrableObject->getI(); |
| 122 |
> |
if (sd->isDirectional()) { |
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> |
I = sd->getI(); |
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|
|
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< |
if (integrableObject->isLinear()) { |
| 126 |
< |
l = integrableObject->linearAxis(); |
| 125 |
> |
if (sd->isLinear()) { |
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> |
l = sd->linearAxis(); |
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|
m = (l + 1) % 3; |
| 128 |
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n = (l + 2) % 3; |
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|
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vbar = sqrt(2.0 * kebar * I(k, k)); |
| 138 |
|
aJ[k] = vbar *randNumGen_->randNorm(0.0, 1.0); |
| 139 |
|
} |
| 140 |
< |
} // else isLinear |
| 140 |
> |
} |
| 141 |
|
|
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< |
integrableObject->setJ(aJ); |
| 143 |
< |
} //isDirectional |
| 142 |
> |
sd->setJ(aJ); |
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> |
} |
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} |
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< |
} //end for (mol = beginMolecule(i); ...) |
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< |
|
| 154 |
< |
|
| 155 |
< |
|
| 145 |
> |
} |
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> |
|
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|
removeComDrift(); |
| 148 |
< |
// Remove angular drift if we are not using periodic boundary conditions. |
| 149 |
< |
if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift(); |
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< |
|
| 148 |
> |
|
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> |
// Remove angular drift if we are not using periodic boundary |
| 150 |
> |
// conditions: |
| 151 |
> |
|
| 152 |
> |
if(!simParams->getUsePeriodicBoundaryConditions()) removeAngularDrift(); |
| 153 |
|
} |
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< |
|
| 162 |
< |
|
| 163 |
< |
|
| 154 |
> |
|
| 155 |
|
void Velocitizer::removeComDrift() { |
| 156 |
|
// Get the Center of Mass drift velocity. |
| 157 |
< |
Vector3d vdrift = info_->getComVel(); |
| 157 |
> |
Vector3d vdrift = thermo.getComVel(); |
| 158 |
|
|
| 159 |
|
SimInfo::MoleculeIterator i; |
| 160 |
|
Molecule::IntegrableObjectIterator j; |
| 161 |
|
Molecule * mol; |
| 162 |
< |
StuntDouble * integrableObject; |
| 162 |
> |
StuntDouble * sd; |
| 163 |
|
|
| 164 |
|
// Corrects for the center of mass drift. |
| 165 |
|
// sums all the momentum and divides by total mass. |
| 166 |
|
for( mol = info_->beginMolecule(i); mol != NULL; |
| 167 |
< |
mol = info_->nextMolecule(i) ) { |
| 168 |
< |
for( integrableObject = mol->beginIntegrableObject(j); |
| 169 |
< |
integrableObject != NULL; |
| 170 |
< |
integrableObject = mol->nextIntegrableObject(j) ) { |
| 171 |
< |
integrableObject->setVel(integrableObject->getVel() - vdrift); |
| 167 |
> |
mol = info_->nextMolecule(i) ) { |
| 168 |
> |
|
| 169 |
> |
for( sd = mol->beginIntegrableObject(j); sd != NULL; |
| 170 |
> |
sd = mol->nextIntegrableObject(j) ) { |
| 171 |
> |
|
| 172 |
> |
sd->setVel(sd->getVel() - vdrift); |
| 173 |
> |
|
| 174 |
|
} |
| 175 |
< |
} |
| 183 |
< |
|
| 175 |
> |
} |
| 176 |
|
} |
| 177 |
< |
|
| 186 |
< |
|
| 177 |
> |
|
| 178 |
|
void Velocitizer::removeAngularDrift() { |
| 179 |
|
// Get the Center of Mass drift velocity. |
| 180 |
|
|
| 181 |
|
Vector3d vdrift; |
| 182 |
|
Vector3d com; |
| 183 |
|
|
| 184 |
< |
info_->getComAll(com,vdrift); |
| 184 |
> |
thermo.getComAll(com, vdrift); |
| 185 |
|
|
| 186 |
|
Mat3x3d inertiaTensor; |
| 187 |
|
Vector3d angularMomentum; |
| 188 |
|
Vector3d omega; |
| 189 |
< |
|
| 190 |
< |
|
| 191 |
< |
|
| 201 |
< |
info_->getInertiaTensor(inertiaTensor,angularMomentum); |
| 189 |
> |
|
| 190 |
> |
thermo.getInertiaTensor(inertiaTensor, angularMomentum); |
| 191 |
> |
|
| 192 |
|
// We now need the inverse of the inertia tensor. |
| 193 |
< |
/* |
| 194 |
< |
std::cerr << "Angular Momentum before is " |
| 195 |
< |
<< angularMomentum << std::endl; |
| 206 |
< |
std::cerr << "Inertia Tensor before is " |
| 207 |
< |
<< inertiaTensor << std::endl; |
| 208 |
< |
*/ |
| 209 |
< |
inertiaTensor =inertiaTensor.inverse(); |
| 210 |
< |
/* |
| 211 |
< |
std::cerr << "Inertia Tensor after inverse is " |
| 212 |
< |
<< inertiaTensor << std::endl; |
| 213 |
< |
*/ |
| 214 |
< |
omega = inertiaTensor*angularMomentum; |
| 215 |
< |
|
| 193 |
> |
inertiaTensor = inertiaTensor.inverse(); |
| 194 |
> |
omega = inertiaTensor * angularMomentum; |
| 195 |
> |
|
| 196 |
|
SimInfo::MoleculeIterator i; |
| 197 |
|
Molecule::IntegrableObjectIterator j; |
| 198 |
< |
Molecule * mol; |
| 199 |
< |
StuntDouble * integrableObject; |
| 198 |
> |
Molecule* mol; |
| 199 |
> |
StuntDouble* sd; |
| 200 |
|
Vector3d tempComPos; |
| 201 |
< |
|
| 202 |
< |
// Corrects for the center of mass angular drift. |
| 203 |
< |
// sums all the angular momentum and divides by total mass. |
| 201 |
> |
|
| 202 |
> |
// Corrects for the center of mass angular drift by summing all |
| 203 |
> |
// the angular momentum and dividing by the total mass. |
| 204 |
> |
|
| 205 |
|
for( mol = info_->beginMolecule(i); mol != NULL; |
| 206 |
|
mol = info_->nextMolecule(i) ) { |
| 207 |
< |
for( integrableObject = mol->beginIntegrableObject(j); |
| 208 |
< |
integrableObject != NULL; |
| 209 |
< |
integrableObject = mol->nextIntegrableObject(j) ) { |
| 210 |
< |
tempComPos = integrableObject->getPos()-com; |
| 211 |
< |
integrableObject->setVel((integrableObject->getVel() - vdrift)-cross(omega,tempComPos)); |
| 207 |
> |
|
| 208 |
> |
for( sd = mol->beginIntegrableObject(j); sd != NULL; |
| 209 |
> |
sd = mol->nextIntegrableObject(j) ) { |
| 210 |
> |
|
| 211 |
> |
tempComPos = sd->getPos() - com; |
| 212 |
> |
sd->setVel((sd->getVel() - vdrift) - cross(omega, tempComPos)); |
| 213 |
> |
|
| 214 |
|
} |
| 215 |
< |
} |
| 216 |
< |
|
| 234 |
< |
angularMomentum = info_->getAngularMomentum(); |
| 235 |
< |
/* |
| 236 |
< |
std::cerr << "Angular Momentum after is " |
| 237 |
< |
<< angularMomentum << std::endl; |
| 238 |
< |
*/ |
| 239 |
< |
} |
| 240 |
< |
|
| 241 |
< |
|
| 242 |
< |
|
| 243 |
< |
|
| 215 |
> |
} |
| 216 |
> |
} |
| 217 |
|
} |
