added options for RNEMD
Bug fixes in the SelectionEvaluator and SelectionCompiler Added print option in Restraints
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
More attempts to get SMIPD to themostat properly
General bug-fixes and other changes to make particle pots work with the Helfand Energy correlation function
Returned old LD forces to SMIPDForceManager.
A few simple mods to remove gcc compile warnings
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.
Inversion fixes and amber mostly working
more changes for 1-2, 1-3, 1-4 interactions plus some initialization-ordering fixes to make gcc -Wall happier.
Many fixes
Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
Changes required for Inversions and Base Atom types. This will break OOPSE badly for a few days or so...
Adding infrastructure for Amber force field.
Adding Trappe torsion types and fixing Opls types
Code work on thiols and TraPPE torsions.
Removed accidental print lines.
Fixed typo in LJinteraction types. LJ-metal appears to work now.
Fixed a bug in BlockSnapshotManager.
A bunch of minor changes to make MPI compilation faster than the double compilation we do now...
Changing functional form
Changes to MAW. New form of the potential and cleanup.
updating configure process
Nothing important
Many fixes for Charmm-type torsions.
More changes to MnM.
Non-bonded interactions added.
Structural change to how spohr atoms will be parsed. Will be more like bonds.
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...
Changes to add thetacorr to dynamic props and fixes to radial rcorr.
Adding the ability to compute Center of Mass properties on reading in a dump file. DumpReader must be told if it needs to do this, however.
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
fixed a DumpReader bug, took out extra printing statements in residentMem and BlockSnapshotManager
adding NgammaT integrator
fixed TI MPI bug
fixed some bugs in DumpWriter, eliminated some extra printing of debugging information
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.
testing commit logger
removed printing of GBN and GBM from previous debugging
Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
more efficient file reading for thermodynamic integration, and fixed some formatting
MPI thermodynamic integration works now.
fixes for mpi thermodynamic integration, close to fully working...
Fixed a spelling error and a bug in MPI Thermodynamic Integration on file read-in
fixed some typos
testing GB, removing CM drift in Langevin Dynamics, fixing a memory leak, adding a visitor
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).
Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)
Last bug showed up in 2 places, fixed the other one.
Fix a bug of printing empty line in DumpWriter
Adding single precision capabilities to c++ side
Adding spherical boundary conditions to LD integrator
NPrT might work now
remove a unknown method
refactor Hydrodynamics module.
LangevinDynamics in progress
Removed MixingRule from Globals. Handled by forceField now.
Added NPAT to Globals integrators.
Changed formating.
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.
Added energy scaling to section parsers.
replace isType<int> with isInteger
More Sutton-Chen bug fixes.
More changes to forcefield options.
Force option changes.
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.
added copyright
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
Added forceOptions to section parser
Overloaded interface for dumpwriter.
Fix parsing error in OptionSectionParser
Adding handler for CLAY force field
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
parsing by filepp
Adding ParamConstraint.cpp
adding ForceFieldOptions
OptionSectionParser get compiled
ForceField optional parameters....
Missed makefile for sutton-chen.
Sutton-Chen almost done. Just need to fix do_forces to use Sutton-Chen.
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
Another bug fix
fix some namespace issues in Globals
changing GB architecture
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
Adding Parameter Constraint class
added default restraint spring constants into Globals
rewrite Globals
tracking down quaternion bug
Added support for skinThickness keyword to Globals.
fix a typo in DumpReader
DumpReader using pure c++ io
adding zlib support for DumpWriter
adding zipstream.hpp
Added keywords for compressed dump files.
some fixes but even more breaking (cutting out the old way to do reaction field)
Fix a bug in DumpReader in case readFrame is called without calling getNFrames
changes to include the coulombicCorrection selector
adding c-side interface to change cutoff Policy
made some changes for implementing the wolf potential
replace c++ style comment in c files
working version of DensityPlot
adding keyword printPressureTensor
NPrT in progress
NPAT is working
fix bug in NPAT and NPrT
adding NPAT and NPrT integrators
help
added gb
Fixed build issues under ifc7.
OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it...
Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
Working on the shapes parser...
xemacs has been drafted to perform our indentation services
fix one more warning message in make_nodes
more memory leak are fixed
avoid multiple inherit in basic_ifstrstream
reinitialize buffer_stack_ptr in BASS parser
fix a typo in MultipoleAtomTypesSectionParser
fixed a bug in MPI restraints
LinkedList removal project starts now
using map to replace link list
Oops... MPI now builds...
minor change
First commit of the new restraints code
fix a bug in SectionParser (lineNo is not updated)
adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
Dunno
Fixing a bug in BitSet.cpp
avoid using const char*(hope can fixed the missing atom type problem)
adding MersenneTwister random number generator
adding soft potential to LJ Module
adding basic_teebuf which can operate on multiple stream simutaneously.
adding LipidTransVisitor, GofXyz is working now
dynamicProps get built
adding dynamicProps
fix a bug in SimInfo, use number of cutoff stamp as counter to loop over rigidbody stamp
(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
moved Package variable into subdirectory makefiles to speed up the building process
using c library to do conversion instead of using iostream due to a bug in libstdc++(GCC 3.2)
port to SGI platform
remove useless debug info
merging new_design branch into OOPSE-2.0
improved restraints - mpi should work fine
Improvements to restraints
replace old GebericData with new GenericData
fix some bugs in Quaternion class
fix a bunch of bugs
change const_cast to statc_const
fix a bug in basic_ifstrstream.hpp
fix include
add checkFilename Option
adding basic_ifstrstream
FileReader in progress
define DEV_ROOT as relative path
change Makefile to relative path
add yacc and lex rules
change the #include in source files
Import of OOPSE v. 2.0