adding NgammaT integrator
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.
starting change of file formats
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
LangevinDynamics in progress
fixed a spelling error
Missing brace caused the last commit not to build
Changes to cutoff radius setting to a more logical procedure - still may change...
unifying function name in electrostatics
instead of printing to std::cout, throwing an exception when error is found.
More Sutton-Chen bug fixes.
Long range potential return from fortran is already accumulated, it should not be accumulated again; nGroupTypesCol is not initialized; GroupMaxCutoffCol is not allocated;
In order to compile MPI version, we need to cast const char* to void* for stringstream.str(); Previous Makefile use bjects of single version to make the MPI library;
Fixed issue with symbol naming and added call to set force options in SimCreator.
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.
made some minor changes to allow compilation with the portland group compilers
Adding handler for CLAY force field
Got rid of spurious printing out of junk
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
Cutoff Mixing fixes
OptionSectionParser get compiled
register openbabel readers/writers
Sutton-Chen added to SimInfo
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 for output of forces and torques
improvements in shifted-force
again, changing how we deal with summation and screening methods
fixed a capitalization problem with NPT integrator initialization
changed the default switching radius to 85% of rcut
Still had some globals toUpper problems - these changes should fix those...
fix an index mismathcing between c and fortran
merged reaction field with electrostatics.F90
Customized StatWriter is working
rewrite Globals
Fix to forceManager to pass potential array to fortran.
fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array
fixed an annoying mass ratio bug that results in simulation failure with massless particles
Added support for skinThickness keyword to Globals.
Fixed bugs in reaction field, now it appears as though it really is working...
reaction field seems to work now, still need to do some testing...
xlf found a bug that ifc missed...
fixed a capitalization error
it builds now, but there are known issues - particularly with reaction field...
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
replace c++ style comment in c files
Changes to remove angular momentum.
Added method to remove system angular momentum to velocitizer and added method to calculate system angular momentum to siminfo.
adding keyword printPressureTensor
NPAT is working
adding NPAT and NPrT integrators
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...
xemacs has been drafted to perform our indentation services
fix some warning messages
more memory leak are fixed
refactory lattice
refactory LatticeFactory and LatticeCreator
fix a typo in MultipoleAtomTypesSectionParser
pairs inside cutoff group should not be excluded
clean up SimInfo; modify the images of SelectionExpression.html
adding exclude pairs for rigidbody and cutoff group
First commit of the new restraints code
adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
Using OOPSE_itoa and checking a NULL left over from the LinkedList days
Fixing a bug in BitSet.cpp
SPRNG eradication project
info_ in Velocitizer is not initialized which causes a seg fault
remove default parameter from MersenneTwister.hpp which causes all kinds of trouble. Refactory random number generator
fixed a file inclusion problem
replace SPRNG by MTRand
fix compilation problem for g++ 3.4
adding OOPSERandNumGen
adding MersenneTwister random number generator
Corrected filename collision for EAM on Mac OS X
The change of interface of BitSet cause a bug in SelectionEvaluation
using PhysMem - RSSMem to estimate avaliable memory
change the default bin number
fix a bug in BlockSnapshotManager
BlockSnapshotManager is using reference counting now
(1) adding #ifdef __RWSTD to make sun compiler happy (2) fix pair density calculation problem when two selections intersect with each other
cast of NULL to satisfy xlc++
fix a bug in BlockSnapshotManager.hpp
begin bug fix
fix a bug in calculating bytes per stuntdouble
fixed a bug in SimInfo::getCutoff()
maximum length defaults to the cutoff radius
dynamicProps get built
dynamicProps in progress
more work in dynamicProps
adding dynamicProps
adding one more constructor to Snapshot to create customized DataStorage
fix a bug in determing the global index for rigidbodies
adding SelectionManager into SimInfo
remove some useless files
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
no message
port to SGI platform
merging new_design branch into OOPSE-2.0
Improvements to restraints
Don't remember what I did
More work on StuntDouble, Atom, DirectionalAtom and RigidBody
char* -> string
forcefield refactoring for shapes
DataStorage passes unit test
Snaphot and SnapshotTestCase in progress
more classes get reconstructed
more work in Snapshot
fixey fixey the breakey breakey
fixey fixey
Snapshot and SnapshotManager in progress
Breaky Breaky. Fixey Fixey.
replace old GebericData with new GenericData
Fortran/C++ interface de-obfuscation project appears to be complete! Woo hoo!
Fortran/C++ interface de-obfuscation project (It is a very long story)
Snapshot and SnapshotManager in design phase
namespace problem prevented linking
fix some bugs in Quaternion class
Cleaning up a bit
define DEV_ROOT as relative path
change Makefile to relative path
move fortran files around to solve dependency problem
*** empty log message ***
change the #include in source files
Import of OOPSE v. 2.0