Adding property set to svn entries
more on the minimizer Frq -> Freq conversion
Added preliminary code for Alpha Hull calculation using qhull. Added preliminary support to SMIPD to support Alpha Hull. Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. Preliminary changes for shadow hamiltonian integrator. Chages to md files so they will work in openMD.
Parallel bugfix in RestraintForceManager Reverted back to hydrodynamics on triangular plates for SMIPDForceManager Removed thermalLength and thermalConductivity keywords from Globals. Bug tracking in openmdformat (not yet resolved).
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
added options for RNEMD
Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
Latest version of SMIPD with gamma set to thermal conductivity
Adding restraint keywords to Globals
Bug fixes and sanity checks for RNEMD (nBins should be even), check to make sure we aren't selecting inappropriate numbers of integrable Objects
Adding options to RNEMD for selecting particular StuntDoubles
Added keywords for RNEMD
Returned old LD forces to SMIPDForceManager.
Added large quantities of code for convex hull and constant pressure langevin dynamics.
Added some logic to print out a special pair distance as a column in the stat file. To use this feature, use taggedAtomPair = "0, 10" and printTaggedPairDistance = "true" in the md file. Then, the distance between integrableObjects 0 and 10 will be computed and printed in the stat file on each statWrite.
Addition of section parser for Spohr water-metal potential.
Massive update to do virials (both atomic and cutoff-group) correctly. The rigid body constraint contributions had been missing and this was masked by the use of cutoff groups...
Added interface to change number of neighbors in calculating neighbor list.
fixing a wrapVector problem in staticProps, also making Shifted force and electrostatic damping the default behavior
refined the reaction field dielectric passing
fixed the half self term for wolf electrostatics and OOPSE now chooses a cutoff radius dependent alpha for damped electrostatics
adding NgammaT integrator
Massive changes preparing for release of OOPSE-4: The main difference is that the new MD file format (.md, .dump, .eor) now contains meta-data information along with the configuration information.
change the globals.cpp to make sure we can set targetPressure and surfaceTension to be negative.
Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)
Adding spherical boundary conditions to LD integrator
NPrT might work now
refactor Hydrodynamics module.
LangevinDynamics in progress
Removed MixingRule from Globals. Handled by forceField now.
Added NPAT to Globals integrators.
filepp can not handle multiple line macro, just convert multiple line macro into single line macro.
Made some changes to electrostatics for shifted-potential and shifted-force with mono and multipoles
instead of printing to std::cout, throwing an exception when error is found.
the standard library came with SUN compiler does not have a conforming std::use_facet, define a macro to handle it. Adding exception handling to SimCreator.
Fix parsing error in OptionSectionParser
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
parsing by filepp
OptionSectionParser get compiled
ForceField optional parameters....
added in a 5th order polynomial switching function option
Added a keyword and ability to output forces and torques
improvements in shifted-force
changing how we deal with summation and screening methods
fixed a capitalization problem with NPT integrator initialization
Customized StatWriter is working
fix a seg fault when try copy a string to event's err_msg, there are still tons of memory leaking problem in Globals
Change error message in Globals
Constraints for parameters are working now
added default restraint spring constants into Globals
rewrite Globals
Added support for skinThickness keyword to Globals.
Added keywords for compressed dump files.
some fixes but even more breaking (cutting out the old way to do reaction field)
changes to include the coulombicCorrection selector
adding c-side interface to change cutoff Policy
made some changes for implementing the wolf potential
adding keyword printPressureTensor
NPrT in progress
NPAT is working
fix bug in NPAT and NPrT
adding NPAT and NPrT integrators
xemacs has been drafted to perform our indentation services
using map to replace link list
First commit of the new restraints code
Dunno
(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
merging new_design branch into OOPSE-2.0
change the #include in source files
Import of OOPSE v. 2.0
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