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
Adding options to RNEMD for selecting particular StuntDoubles
Added keywords for RNEMD
General bug-fixes and other changes to make particle pots work with the Helfand Energy correlation function
Returned old LD forces to SMIPDForceManager.
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
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.
Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
Adding single precision capabilities to c++ side
Adding spherical boundary conditions to LD integrator
remove a unknown method
refactor Hydrodynamics module.
LangevinDynamics in progress
Removed MixingRule from Globals. Handled by forceField now.
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
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
fix some namespace issues in Globals
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
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
NPAT is working
adding NPAT and NPrT integrators
xemacs has been drafted to perform our indentation services
LinkedList removal project starts now
using map to replace link list
First commit of the new restraints code
(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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