| 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 |
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* 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 |
|
*/ |
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#include <fstream> |
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#include <iostream> |
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|
#include "integrators/LDForceManager.hpp" |
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#include "math/CholeskyDecomposition.hpp" |
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< |
#include "utils/OOPSEConstant.hpp" |
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> |
#include "utils/PhysicalConstants.hpp" |
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#include "hydrodynamics/Sphere.hpp" |
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#include "hydrodynamics/Ellipsoid.hpp" |
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#include "utils/ElementsTable.hpp" |
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+ |
#include "types/LennardJonesAdapter.hpp" |
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+ |
#include "types/GayBerneAdapter.hpp" |
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|
| 53 |
< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
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LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) { |
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simParams = info->getSimParams(); |
| 65 |
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sprintf( painCave.errMsg, |
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"langevinBufferRadius must be specified " |
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"when useSphericalBoundaryConditions is turned on.\n"); |
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< |
painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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sprintf( painCave.errMsg, |
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"frozenBufferRadius must be specified " |
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"when useSphericalBoundaryConditions is turned on.\n"); |
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< |
painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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sprintf( painCave.errMsg, |
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"frozenBufferRadius has been set smaller than the " |
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"langevinBufferRadius. This is probably an error.\n"); |
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< |
painCave.severity = OOPSE_WARNING; |
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> |
painCave.severity = OPENMD_WARNING; |
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painCave.isFatal = 0; |
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simError(); |
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} |
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"HydroPropFile must be set to a file name if Langevin Dynamics\n" |
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"\tis specified for rigidBodies which contain more than one atom\n" |
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"\tTo create a HydroPropFile, run the \"Hydro\" program.\n"); |
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< |
painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, |
| 142 |
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"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str()); |
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< |
painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
| 159 |
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if (integrableObject->isAtom()){ |
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Atom* atom = static_cast<Atom*>(integrableObject); |
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AtomType* atomType = atom->getAtomType(); |
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< |
if (atomType->isGayBerne()) { |
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DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 164 |
< |
GenericData* data = dAtomType->getPropertyByName("GayBerne"); |
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< |
if (data != NULL) { |
| 166 |
< |
GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data); |
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< |
|
| 165 |
< |
if (gayBerneData != NULL) { |
| 166 |
< |
GayBerneParam gayBerneParam = gayBerneData->getData(); |
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< |
currShape = new Ellipsoid(V3Zero, |
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< |
gayBerneParam.GB_l / 2.0, |
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< |
gayBerneParam.GB_d / 2.0, |
| 170 |
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Mat3x3d::identity()); |
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< |
} else { |
| 172 |
< |
sprintf( painCave.errMsg, |
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< |
"Can not cast GenericData to GayBerneParam\n"); |
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< |
painCave.severity = OOPSE_ERROR; |
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< |
painCave.isFatal = 1; |
| 176 |
< |
simError(); |
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< |
} |
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< |
} else { |
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< |
sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n"); |
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< |
painCave.severity = OOPSE_ERROR; |
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< |
painCave.isFatal = 1; |
| 182 |
< |
simError(); |
| 183 |
< |
} |
| 162 |
> |
GayBerneAdapter gba = GayBerneAdapter(atomType); |
| 163 |
> |
if (gba.isGayBerne()) { |
| 164 |
> |
currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0, |
| 165 |
> |
gba.getD() / 2.0, |
| 166 |
> |
Mat3x3d::identity()); |
| 167 |
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} else { |
| 168 |
< |
if (atomType->isLennardJones()){ |
| 169 |
< |
GenericData* data = atomType->getPropertyByName("LennardJones"); |
| 170 |
< |
if (data != NULL) { |
| 188 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 189 |
< |
if (ljData != NULL) { |
| 190 |
< |
LJParam ljParam = ljData->getData(); |
| 191 |
< |
currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0); |
| 192 |
< |
} else { |
| 193 |
< |
sprintf( painCave.errMsg, |
| 194 |
< |
"Can not cast GenericData to LJParam\n"); |
| 195 |
< |
painCave.severity = OOPSE_ERROR; |
| 196 |
< |
painCave.isFatal = 1; |
| 197 |
< |
simError(); |
| 198 |
< |
} |
| 199 |
< |
} |
| 168 |
> |
LennardJonesAdapter lja = LennardJonesAdapter(atomType); |
| 169 |
> |
if (lja.isLennardJones()){ |
| 170 |
> |
currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0); |
| 171 |
|
} else { |
| 172 |
|
int aNum = etab.GetAtomicNum((atom->getType()).c_str()); |
| 173 |
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if (aNum != 0) { |
| 175 |
|
} else { |
| 176 |
|
sprintf( painCave.errMsg, |
| 177 |
|
"Could not find atom type in default element.txt\n"); |
| 178 |
< |
painCave.severity = OOPSE_ERROR; |
| 178 |
> |
painCave.severity = OPENMD_ERROR; |
| 179 |
|
painCave.isFatal = 1; |
| 180 |
|
simError(); |
| 181 |
|
} |
| 182 |
|
} |
| 183 |
|
} |
| 184 |
|
} |
| 185 |
+ |
|
| 186 |
+ |
if (!simParams->haveTargetTemp()) { |
| 187 |
+ |
sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n"); |
| 188 |
+ |
painCave.isFatal = 1; |
| 189 |
+ |
painCave.severity = OPENMD_ERROR; |
| 190 |
+ |
simError(); |
| 191 |
+ |
} |
| 192 |
+ |
|
| 193 |
+ |
if (!simParams->haveViscosity()) { |
| 194 |
+ |
sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n"); |
| 195 |
+ |
painCave.isFatal = 1; |
| 196 |
+ |
painCave.severity = OPENMD_ERROR; |
| 197 |
+ |
simError(); |
| 198 |
+ |
} |
| 199 |
+ |
|
| 200 |
+ |
|
| 201 |
|
HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp()); |
| 202 |
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std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
| 203 |
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if (iter != hydroPropMap.end()) |
| 210 |
|
} |
| 211 |
|
} |
| 212 |
|
} |
| 213 |
< |
variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt(); |
| 213 |
> |
variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt(); |
| 214 |
|
} |
| 215 |
|
|
| 216 |
|
std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) { |
| 230 |
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return props; |
| 231 |
|
} |
| 232 |
|
|
| 233 |
< |
void LDForceManager::postCalculation(bool needStress){ |
| 233 |
> |
void LDForceManager::postCalculation(){ |
| 234 |
|
SimInfo::MoleculeIterator i; |
| 235 |
|
Molecule::IntegrableObjectIterator j; |
| 236 |
|
Molecule* mol; |
| 313 |
|
//estimate velocity at full-step using everything but friction forces: |
| 314 |
|
|
| 315 |
|
frc = integrableObject->getFrc(); |
| 316 |
< |
Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc; |
| 316 |
> |
Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc; |
| 317 |
|
|
| 318 |
|
Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
| 319 |
< |
Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb; |
| 319 |
> |
Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb; |
| 320 |
|
|
| 321 |
|
Vector3d omegaLab; |
| 322 |
|
Vector3d vcdLab; |
| 362 |
|
|
| 363 |
|
// re-estimate velocities at full-step using friction forces: |
| 364 |
|
|
| 365 |
< |
velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab); |
| 366 |
< |
angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody); |
| 365 |
> |
velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab); |
| 366 |
> |
angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody); |
| 367 |
|
|
| 368 |
|
// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0): |
| 369 |
|
|
| 398 |
|
//estimate velocity at full-step using everything but friction forces: |
| 399 |
|
|
| 400 |
|
frc = integrableObject->getFrc(); |
| 401 |
< |
Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc; |
| 401 |
> |
Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc; |
| 402 |
|
|
| 403 |
|
Vector3d frictionForce(0.0); |
| 404 |
|
Vector3d oldFF; // used to test for convergence |
| 413 |
|
|
| 414 |
|
// re-estimate velocities at full-step using friction forces: |
| 415 |
|
|
| 416 |
< |
velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce); |
| 416 |
> |
velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce); |
| 417 |
|
|
| 418 |
|
// check for convergence (if the vector has converged, fdot will be 1.0): |
| 419 |
|
|
| 439 |
|
if(!simParams->getUsePeriodicBoundaryConditions()) |
| 440 |
|
veloMunge->removeAngularDrift(); |
| 441 |
|
|
| 442 |
< |
ForceManager::postCalculation(needStress); |
| 442 |
> |
ForceManager::postCalculation(); |
| 443 |
|
} |
| 444 |
|
|
| 445 |
|
void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) { |
