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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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< |
* 1. Acknowledgement of the program authors must be made in any |
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< |
* publication of scientific results based in part on use of the |
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< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
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< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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< |
* 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 |
|
* |
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< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
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+ |
* |
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+ |
* 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 |
+ |
* |
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+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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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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|
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< |
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(); |
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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, |
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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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} |
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} else { |
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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.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, "Can not find Parameters for GayBerne\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, |
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"Can not cast GenericData to LJParam\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, |
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"Could not find atom type in default element.txt\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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if (!simParams->haveTargetTemp()) { |
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sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n"); |
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painCave.isFatal = 1; |
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< |
painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
| 220 |
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simError(); |
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} |
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|
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if (!simParams->haveViscosity()) { |
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sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n"); |
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painCave.isFatal = 1; |
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< |
painCave.severity = OOPSE_ERROR; |
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> |
painCave.severity = OPENMD_ERROR; |
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simError(); |
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} |
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|
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} |
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} |
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} |
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< |
variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt(); |
| 243 |
> |
variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt(); |
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} |
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|
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std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) { |
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return props; |
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} |
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|
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< |
void LDForceManager::postCalculation(bool needStress){ |
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> |
void LDForceManager::postCalculation(){ |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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//estimate velocity at full-step using everything but friction forces: |
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|
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frc = integrableObject->getFrc(); |
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< |
Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc; |
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> |
Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc; |
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|
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Tb = integrableObject->lab2Body(integrableObject->getTrq()); |
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< |
Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb; |
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> |
Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb; |
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|
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Vector3d omegaLab; |
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Vector3d vcdLab; |
| 392 |
|
|
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// re-estimate velocities at full-step using friction forces: |
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|
|
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< |
velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab); |
| 396 |
< |
angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody); |
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> |
velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab); |
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> |
angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody); |
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|
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// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0): |
| 399 |
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|
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|
//estimate velocity at full-step using everything but friction forces: |
| 429 |
|
|
| 430 |
|
frc = integrableObject->getFrc(); |
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< |
Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc; |
| 431 |
> |
Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc; |
| 432 |
|
|
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Vector3d frictionForce(0.0); |
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Vector3d oldFF; // used to test for convergence |
| 443 |
|
|
| 444 |
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// re-estimate velocities at full-step using friction forces: |
| 445 |
|
|
| 446 |
< |
velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce); |
| 446 |
> |
velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce); |
| 447 |
|
|
| 448 |
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// check for convergence (if the vector has converged, fdot will be 1.0): |
| 449 |
|
|
| 469 |
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if(!simParams->getUsePeriodicBoundaryConditions()) |
| 470 |
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veloMunge->removeAngularDrift(); |
| 471 |
|
|
| 472 |
< |
ForceManager::postCalculation(needStress); |
| 472 |
> |
ForceManager::postCalculation(); |
| 473 |
|
} |
| 474 |
|
|
| 475 |
|
void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) { |
