Removed older version of openbabel from our code. We now have a configure check to see if openbabel is installed and then we link to the stuff we need. Conversion to OOPSE's md format is handled by only one application (atom2md), so most of the work went on there. ElementsTable still needs some work to function in parallel.
Changes to do hydrodynamics modeling and to explain a diff file
Bug fixes for non-declared objects
removed extra file in Hydro.cpp
Massive changes for GB code with multiple ellipsoid types (a la Cleaver's paper). Also, changes in hydrodynamics code to make HydroProp a somewhat smarter class (rather than just a struct).
Fix a type promotion problem
replace double with RealType
fixes for Hydrodynamics
Adding single precision capabilities to c++ side
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adding a gay-berne switch to Dump2XYZ
Using OpenBabel element table to pick vdw radii for hydrodynamics if the LJ sigma can't be found.
Adding spherical boundary conditions to LD integrator
Added EAM atom types to Hydro models
Many performance improvements
(1) RoughShell Model is working; (20)Adding a new option into Hydro which allows user to generate the beads only
update writeBeads method
fix a bug in calculating hydrodynamics tensor when the radius of beads are not the same
Fix a bug in friction calculation for ellipsoid
Verify the correctness of Ellipsoid's hydrodynamics properties
New version of Hydro is working now.
refactor Hydrodynamics module.
LagevinDynamics is working?
fixed a const problem
unit conversion for diffusion tensor is wrong
change the epsilon of numeric_limit
correcting the unit in HydrodynamicsModel
Adding RoughShell and BeadModel
adding hydrodynamics module into build system
LangevinDynamics in progress
fix bugs in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out product of Rij
Bead Model is working
Adding Hydrodynamics Module