New electrostatic method, starting to do some performance tuning.
Bugs in the FQ samples, fixed for Dump2XYZ to print out charges and electric fields
Chasing down bugs in the TIP4P_FQ model.
Added a Harmonic Torsion Type, fixed some bugs in RNEMD and waterReplacer.
Fixed a bug
Fixed a bug in Matrix-Matrix cross product
New electrostatic bug fixes.
MERGE OpenMD trunk changes 1803:1811 into development branch
Merging trunk changes back to development branch
Massive multipole rewrite
Added 6, 8, 10 and 12 length alkane chains to thiols
Updated the manual to include the RNEMD stuff. Fixed a holdover bug in a sample file.
Adding a sample of the shear and scale for argon.
Tracking down a strange bug report. Fixing some output. Fixing some samples.
Adding some RNEMD interface samples
Fixed a bug in the FluctuatingChargeLangevin propagator, updated some samples.
Added Fluctuating Charge Langevin propagator, and made it the default fixed some errors on the one-center slater coulomb integrals, and some parameters in PhysicalConstants.
fixes for fluctuating charges
Adding Joseph's FlucQ samples for testing
Fixing some bugs in optimization, fixing status functions so that they dump correctly (although some things are deferred until the Stats is accumulator-based).
fixing some bugs, adding Shake
added a minimizer parsing block
test
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.
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.
Added files for fcc and pentagonal nanorod builders. Updated runMe in samples/builders to include nanorod builders.
Fixed a number of force files to use new Gay Berne format
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.
Some fixes for CMake and single precision builds
fixing the build system
removing cruft from build system
cleaning up the development branch a bit, removing cruft, etc.
Build fixes for qhull 2011, fixes for compilation with PGI.
bug fixes
bug fixes.
Bug squashing
More modifications for paralllel rewrite
fixing c/fortran bugs
Creating busticated version of OpenMD
Added svn revision number to build process, incremented minor version number, corrected a minimizer keyword
Fixing the build and install method for samples in Madelung, RNEMD, zeolite, SMIPD
Cleanup of unit normal code in Triangle.cpp SMIPD now call getUnitNormal instead of getNormal.
Install bugs, tweaks of samples
Added preliminary code for Alpha Hull calculation using qhull. Added preliminary support to SMIPD to support Alpha Hull. Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. Preliminary changes for shadow hamiltonian integrator. Chages to md files so they will work in openMD.
more changes to fix build process and divorce ourselves from CVS
removing spurious cutoffGroup lines from default water.md sample files
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
adding interface
Relaxed structure at low T to be not so high up on the PE wall.
Adding one RNEMD sample
Adding Madelung energy sample directory with explanatory notes
Adding samples for SMIPD.
doing zeolite sample
Added large quantities of code for convex hull and constant pressure langevin dynamics.
Fixes for Torsions and Inversions, Amber is mostly working now.
Code work on thiols and TraPPE torsions.
Removed accidental print lines.
Added model for thiols.
Added minimizer sample for metal.
Changes....
Added surfaces for Ni and Pd.
Added more surfaces.
Added samples for metal slabs.
Many fixes for Charmm-type torsions.
*** empty log message ***
Broken files on install
Fixed Makefile problems with the samples and added several missing makefiles.
fixed a bug where the pressure tensor wouldn't update for atoms in the switching region when # of atoms in a group = 1
Added md file for half of a icosahedron.
Adding a starter file for the secondary prism {1,1,-2,0} face.
adding new ice surface files
new ideal structures
Added a bunch of bond order parameter test cases.
more openbabel updates, also changing velocitizer to thermalizer to avoid a filename collision on case-insensitve file systems
Added velocitizer utility program, added samples of its use to the builder samples.
Adding samples for builders
fixed a few bugs
fixing missing lattice arguments, adding a builder sample
adding builder samples
Fixing the builders to prepare for OOPSE-4 release
converted samples over to the OOPSE-4 file format Fixed an MPI bug in thermodynamic integration
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 tred to sample water.md files
removed icc from C++ search lines, did some formatting work on GB module, mucked around with a GB example
added mpi compilers, demoted pg compilers after pathscale
damping now works for charge-quadrupole and dipole-dipole
testing GB, removing CM drift in Langevin Dynamics, fixing a memory leak, adding a visitor
Added TIP5P-E and fixed a bug for Thermodynamic integration (you can now have a lambda of 0)
Adding single precision capabilities to c++ side
electrostatic refinement
Removed sqrt splines and shape stuff (doesn't work, so why was it in there?). Changed some of the water samples to use shifted_force. Probably should set the defaults to use the damped version now that we sped it up.
Electrosplines added...
splined up sticky
Complete rewrite of spline code and everything that uses it.
Many performance improvements
added a cubic spline to switcheroo
Changes to cutoff radius setting to a more logical procedure - still may change...
Changes in Sutton-Chen units
Missing Makefile in this sample directory
Old makefile.in no longer required
unifying function name in electrostatics
fix make install problem for metals samples
Sutton and Chen should be working now.
Added energy scaling to section parsers.
More Sutton-Chen bug fixes.
Sutton-Chen bug fixes. Almost there...
added files for sutton-chen
More cvs changing.
More moving...
More changes to directory structure.
More Directory changes...
More changing of directory structure
Removed one parasitic argon atom which was living inside the GB particle. No alien-like ripping out of the stomach was required.
remove deprecated keywords from samples
removing deprecated nAtoms and nComponents lines
Added Gay-Berne / Argon test case for the cutoff policies
just some parameters
just playing
just playing around - we need to refresh all the samples sometime soon...
playing with switching functions again
playing with switching functions
Just testing...
mmm... damped shifted force...
added a test molecule
minor changes when testing reaction field
reaction field now works for charges
nothing
added samples for the cutoff methods that Yang Zheng has been working on
added a few GB test cases
Adding samples for gb tests
Adding .md files for GB/LJ tests
Adding some Gay Berne tests
Adding some cutoff tests
added default restraint spring constants into Globals
Testing new cutoff methods
fixing up the samples
just some random changes when testing
fixed some samples
fixing up some samples
turned rf on
fixed up some sample md files
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...
just some testing
Equilibrated the sample
Just a longer test
fixed a bug and ran a simulation
Updated tap sample
Included a tap dimer for testing purposes
added a tap example for testing purposes
Modifications to tap. Also correcting changes to the previous merge that were not caught
Couple of changes for TAP water. Need to parametrize.
Changed SHED to TAP
OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it...
Added TIP4P-Ew
Got rid of write statements and am closer to a working shapes
Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
add Makefile of samples
some samples are not installed correctly
oops... bad sample
added quadrupole sample
updating samples
messing with samples
oops... messed up a sample
changes during debug of charge-dipole
forgot a couple of makefiles
added some samples
fixed a bug in MPI restraints
messing with the split dipole test cases
adding test case of split dipole
Oops... MPI now builds...
adding test case for split dipole
fixes to restraints
fixing restraints
First commit of the new restraints code
addded a few fun charge-dipole test cases
making some cool test cases
Added ssdrf sample
fixed a sample
oops...
Back to normal... Oh... Restraints should work in parallel now
just some testing changes, I'll return to the original on next commit
working sample
Fun with ice
testing force fields
testing shapes
shorter run
forgot the orientation line
uncommented .in line
adding sample shape directory
fix Makefile under water directory
remove argon.dump and argon.eor from Makefile
Remove some Makefile.in
add Makefile to sample directory
Import of OOPSE v. 2.0