Moved FluctuatingChargeNVT to the flucq directory
Fixed the Slater overlap integral code, added dVdFq to the self interaction.
Units fix for electronic temperature, we also need to initialize dVdFq
Make fluctuating charges also charges.
Reorganized source directories, added RNEMD and flucQ blocks for options parsing.
Fixed compilation issues
resolved
resolved
Use the force directory is no longer used.
Forgot to delete the individual FF classes.
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.
DarkSide isn't needed
Bug fixes for heat flux import
Merging Shenyu's RNEMD changes from openmd-1 into the development branch.
Fixing some bugs
Fixed a few bugs in that last commit
Forgot the factorials!
Adding fluctuating charges, still a work in progress
Updating the build
Adding the propagators for FlucQ
Adding more support structure for Fluctuating Charges.
Added ability to read / write dump files with fluctuating charges and electric fields.
adding communication and parallel support for fluctuating charges and polarizability
Bugfixes (mostly related to particlePot and storageLayout).
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 Removed outdated zangle stuff that has been replaced by the more modern restraints.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.
Moving silly stuff out of Stats and into Snapshot. Most of it should go into a not-yet-implemented FrameData class.
Adding some new atom types, fixing a convex hull bug, removing silly stuff from Snapshot
Use the static version of the qhull library.
fixed an initialization bug in Dump2XYZ
Fixing some bugs in the CMakeLists file
qhull modifications for compilation
JRM Added additional section parsers to EAM_FF.cpp
Un-did some changes that weren't ready to be committed.
Added files for fcc and pentagonal nanorod builders. Updated runMe in samples/builders to include nanorod builders.
Adding a vector parsing option to the parameter Manager.
Simplifying build process
tweaking build process
Updating build process, copyright, and publications.
Doing some work to simplify cmake build process
Fixed a compilation warning for CLANG compiler
Fixed a number of force files to use new Gay Berne format
Bug fixes for GB. Now using strength parameter mixing ideas from Wu et al. [J. Chem. Phys. 135, 155104 (2011)]. This helps get the dissimilar particle mixing behavior to be the same whichever order the two particles come in. This does require that the force field file to specify explicitly the values for epsilon in the cross (X), side-by-side (S), and end-to-end (E) configurations.
Fixes for compilation under LLVM compiler Bug-fix for switching function in Gay-Berne
Bug squashes. Pre-existing bug where ppot_row and ppot_col were never zeroed. In non-metallic potentials these arrays should be zero.
Fixed bug with rigidbodies not updating velocities for heat flux calculation.
LJ.cpp has been updated to more correctly deal with nonbonded interactions (i.e. explicit interactions where the species are not necessarily defined to be lennardJones type atoms)
Debugging heat flux calculation for rigid bodies.
More bug fixes....
Bug fixes for v_j not being set correctly and accumulation error.
Changed sign of force in stress tensor J_v calculation.
Added revision to svn for Gianluca.
Fixed naming.
Batch of sample files for testing different configurations of Gay-Berne atoms. Included is a force file and test atom build for running the '.md' files.
Updated version of Gianluca's stat2thcond.
Fixed two bugs in new Gay-Berne module. Torque 2 had a sign error, and there was a subtle mixing bug for dissimilar particles in different orderings.
Fixed alignment issues
Update for energy units conversion.
Adding support for atomic heat flux. Is broken w/ group based cuttoffs. Units need to be corrected and their may be a sign error in Jv.
Adding experimental branch for calculation of the heatflux based on old version of OpenMD. This will need to be ported to the development branch later.
Some fixes for CMake and single precision builds
updated copyright notices
Modified some of the nonbonded interactions and types
Added a waterReplacer script. A bit rough around the edges, but seems to do the right thing for a slab of ice.
Adding new function to check .eor files.
Minor modifications to set environment variable.
Validation script update with logging.
Adding validation python code.
Adding bits for numerical validation of openmd results.
First few fixes for explicit interactions.
Replacing most of the C-code with C++ code, and migrating the config.h file into the PROJECT_BINARY_DIR so that we can have multiple builds on the same architecture.
fixed a compile bug for PGI
fixing compilation bugs on gcc-4.4
added an INSTALL file, using svn2cl to get the ChangeLog target
Added "doc" build target.
fixing install permissions
removed a directory
cleaning up build cruft
fixing the build system
update for cmake build and install
OK, we need these directories for the build.
removing build cruft
migrating Doxyfile to a more sensible location, removing old build cruft
removing old build cruft
cleaning up cruft
removing cruft from build system
changing build process
fixing a link order problem
fixed cmake build system for single and parallel targets
cleaning up the development branch a bit, removing cruft, etc.
indenting fix
Updated antlr, fixed a clang compilation bug, removed a warning message
cleaning up configure script & readme
cleaning up the configure script
updating gengetopt runs
Merging changes from old branch into development branch
ifstrstream in Cmake
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.
Cmake fixes and updates.
Adding RepulsivePower interaction to development branch.
Adding RepulsivePower interaction to the development branch
Build fixes for qhull 2011, fixes for compilation with PGI.
Added sample files for argon: 1000, 10000, 75000.
Fixing cutoff groups
Updated scalability of OpenMP threads.
Fixed a parallel bug in computing exclude lists. Added file versioning information in MD files. Still tracking down cutoff group bugs.
fixed an offset bug causing problems in MPI
First OpenMP version.
good bye fortran!
Fortran begone!
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.
Updated: Build neighbor list method with frequency counter. Additional parameter to md file.
Updated ordered neighbor list generation.
Debugging mainly
Adding initial OpenMP support using new neighbor lists.
Branching from main development branch to OpenMP dev version at dev branch 1593
test
test
Efficiency fix
more bug fixes
Fixing some parallel bugs
fixed one MPI bug, working on another
Fixes
bug fixes
bug fixes.
Bug squashing
Well, the potential energy values are still garbage, but the LJ sample runs.
bug fixes
Forgot Grid3d
bug fixes (not done yet)
bug fixes
migrating cutoff information from InteractionManager to ForceManager
more parallel fixes
Forgot some headers and other files
Added Atypes to new C++ force decomposition.
More fixes
A few more fixes for the missing routines
Added neighbor list check, and migrated skinThickness into ForceDecomposition (and out of the InteractionManager). Removed a spurious inline.
Fixed some busted stuff in buildNeighborList
changes for cell linked lists
For efficiency, pointers instead of objects will be passed during main force loop.
More fortran removal, and trimming out unused code
Fortran removal
More changes for parallel
more fortran removal
a few more tweaks We're getting somewhat closer to deleting fortran.
more minor changes to help build
closer to a real force loop
still busted, but much progress
More modifications for paralllel rewrite
working on communicators
changes for new parallel architecture
Starting a Parallel architecture
Adding parallel classes...
forgot one method
compiles, builds and runs, but is very slow
Well, it compiles and builds, but still has a bus error at runtime.
getting closer to compiling
One more fortran file that we don't need:
Added MAW to the C++ side, removed a whole bunch more fortran.
Moved switching functions and force options over to the C++ side, and removed them from Fortran.
fixes
Doesn't build yet, but getting much closer...
removing group-selective cutoff cruft
Less busted than it was on last check-in, but still won't completely build.
The C++ side now compiles. Moving on to doForces
Changes to remove more of the low level stuff from the fortran side.
Many changes, and we're not quite done with this phase yet.
Starting migration of Morse to C++
More fixes for cmake.
Fixed case typos in cmake.
Different version of FindOpenBabel that actually works.
Somewhat working cmake build system now. Does not yet build a parallel target. Builds all non-mpi programs.
Needed by openbabel macro.
Fixing headers. They are now .hpp files.
Removed .h files. They are .hpp files committed yesterday.
Adding exception and reporting mechanism from ProtoMol to OpenMD.
Adding debugging and tracing tools from protomol to openmd.
Adding some error reporting and debuging code to OpenMD. This code is borrowed from ProtoMol.
Migrating Sutton-Chen from Fortran over to C++
Converting Sticky over to C++
removing cruft
Added GB module to the C++ side, got rid of it on the fortran side.
Fixed a bug in EAM. Seems to work now!
fixed phi mixing
no longer segfaults
Added EAM. Still segfaults but compiles.
busticated EAM
fixed some destructor bugs dealing with the TypeContainers
Added CubicSpline class to replace our interpolation F90 module
fixing c/fortran bugs
fixing calls
Added nonbonded directory. Compiles, links, runs, but gives incorrect answer.
builds
attempts at c++->fortran linkage. Still busticated.
added nonbonded directory
well, it compiles, but still segfaults
Adding stuff for cmake
Creating busticated version of OpenMD
Standard project directories initialized by cvs2svn.