Possibly fixed the rigid body global indexing issue. Reformatted
comments. Started work on the FrameData section of Snapshot.
Individual ForceField classes have been removed (they were essentially all duplicates anyway). ForceField has moved to brains, and since only one force field is in play at any time, the ForceFieldFactory and Register methods have been removed.
Bug fixes for heat flux import
Adding more support structure for Fluctuating Charges.
Added ability to read / write dump files with fluctuating charges and electric fields.
Some fixes for DataStorage issues. Removed outdated zangle stuff that has been replaced by the more modern restraints.
Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
updated copyright notices
Splitting out ifstrstream into a header and an implementation. This means that much of the code that depends on it can be compiled only once and the parallel I/O is concentrated into a few files. To do this, a number of files that relied on basic_ifstrstream to load the mpi header had to be modified to manage their own headers.
Fixed a parallel bug in computing exclude lists. Added file versioning information in MD files. Still tracking down cutoff group bugs.
removed spurious prints, fixed one bug, but there's still a parallel problem
Completing the Fortran removal project. Fixes for compilation with clang / llvm, debugging, removing code that we'd never used.
Debugging mainly
test
bug fixes
changes for new parallel architecture
Well, it compiles and builds, but still has a bus error at runtime.
attempts at c++->fortran linkage. Still busticated.
Creating busticated version of OpenMD
Adding property set to svn entries
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
General bug-fixes and other changes to make particle pots work with the Helfand Energy correlation function
more changes for 1-2, 1-3, 1-4 interactions plus some initialization-ordering fixes to make gcc -Wall happier.
Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
A bunch of minor changes to make MPI compilation faster than the double compilation we do now...
Removed debug message from simcreator.
fixing bond order parameter code
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.
Adding single precision capabilities to c++ side
Adding spherical boundary conditions to LD integrator
instead of printing to std::cout, throwing an exception when error is found.
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.
End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
OptionSectionParser get compiled
rewrite Globals
Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
more memory leak are fixed
fix a typo in MultipoleAtomTypesSectionParser
First commit of the new restraints code
Using OOPSE_itoa and checking a NULL left over from the LinkedList days
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
replace SPRNG by MTRand
adding OOPSERandNumGen
adding MersenneTwister random number generator
fix a bug in determing the global index for rigidbodies
remove some useless files
(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
This form allows you to request diffs between any two revisions of this file. For each of the two "sides" of the diff, enter a numeric revision.