fixed a missing F[\rho] error for calculating particle potentials in the many body force fields
fixed a strange compiler structure alignment problem with the intel Mac compiler (structs that cross between C and fortran appear to need 8-byte boundary alignment on this compiler).
Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
Adding infrastructure for Amber force field.
Added files to Module section.
Removed accidental print lines.
Fixed typo in LJinteraction types. LJ-metal appears to work now.
Checking in changes for Hefland moment calculations
Changes....
Changing functional form
Fixed sign error in MnM based on atid's.
MnM interaction now works.
Changes to MAW. New form of the potential and cleanup.
Changes to simparalell to remove MPI stuff.
updating configure process
added a check for non-initialized MnM_map
Changes to MetalnonMetal derivatives.
More bug fixes to Metalnonmetal.
adding MetalNonMetal interactions
Added more Morse and Lennard-Jones part of metal-nonmetal.
removed a stray is_MWM
One more to add.
Adding more missing files from metal-nonmetal interaction.
Added c-fortran interaction map.
More changes to MnM.
Bug fix to types.
Added metal-nonmetal forcefield.
Changes to allow for non-bonded interactions.
Removed debug message from simParallel.
SF Lennard-Jones was added for everyones' enjoyment. The behavior is tethered to the electrostaticSummationMethod keyword.
more changes for atomic virials and Lennard-Jones force switching
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...
Fixed conversion bug in self_self, when adding self energy to mypot, energy needs to be converted by pre11.
Fixed a bug in NeighborListNeighbors.
Added more error reporting to simParallel.
Added interface to change number of neighbors in calculating neighbor list.
returned to half self-term values
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 an ordering issue in quadrupole-charge interactions
fixed a getSigma bug
fixed d / sigma0 confusion
removed icc from C++ search lines, did some formatting work on GB module, mucked around with a GB example
Added the multipole interaction routine. It doesn't work yet, so it's not included in the build.
Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
fixed forces and torques for GB
reformulated some of the electrostatics
damping now works for charge-quadrupole and dipole-dipole
Fixed a spelling error and a bug in MPI Thermodynamic Integration on file read-in
testing GB, removing CM drift in Langevin Dynamics, fixing a memory leak, adding a visitor
Added methods to access GB_mu and GB_nu from the force field options
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).
Adding single precision capabilities to c++ side
Adding single precision capabilities to the fortran side
Getting fortran side prepped for single precision...
electrostatic refinement
Adding qpole
Adding spherical boundary conditions to LD integrator
put spline subroutines in the EAM module
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
Added interpolation module.
Added status module to simParallel for error reporting.
Fixed memory leak bug where SCList capacity was not reset to zero on destruction.
fixed a problem with cutoff radii being set larger than 1/2 the length of the shortest box dimension. added a few fortran utility routines
unifying function name in electrostatics
Made some changes to electrostatics for shifted-potential and shifted-force with mono and multipoles
autoconf modernization and cruft removal
Sutton and Chen should be working now.
Sutton-Chen no longer segfaults or produces 0 potential, but rather produces Inf for the potential. Progress....
More Sutton-Chen bug fixes.
Sutton-Chen bug fixes. Almost there...
Fixed issue with symbol naming and added call to set force options in SimCreator.
Force option changes.
changed __FUNCTION__ to __func__ to match C99 standard, and then added an autoconf test to check for __func__ usability. Changed some default compile flags for the Sun architecture
made some minor changes to allow compilation with the portland group compilers
*** empty log message ***
Removed geometric distance mixing from individual modules and now use force options to detemine what the deal is.
Further fixes for compiler issues.
Added support for fortran force options.
Cutoff mixing fixes have been made.
included shifted potential self term
removed unnecessary commented code
cleaned up the charge-charge interactions a bit...
fixed a bug in the shifted_potential case
Made preforce calc public in suttonchen.
Added Sutton-Chen to force loop...
Build Fixes for sutton-chen.
Sutton-chen stuff
Sutton-Chen almost done. Just need to fix do_forces to use Sutton-Chen.
Forgot to add some files
added in a 5th order polynomial switching function
Working on shifted_force...
removed a poorly commented section
improvements in shifted-force
More work on SC.
More work on suttonchen.
removed some test code
forgot to add the screening method header
changing how we deal with summation and screening methods
Added suppport to atypes for MEAM and sutton-chen
removed some testing code...
still fixing up wolf...
In process of adding sutton-chen forcefield.
reaction field looks to be working now - for charges and dipoles alike
added charge-dipole reaction field - don't know if it works...
streamlined reaction field for dipoles (now a good bit faster) and added reaction field for charges - still need to do charge-dipole RF
Still had some globals toUpper problems - these changes should fix those...
fixed an MPI compilation bug in GayBerne
fix an index mismathcing between c and fortran
fixed gb/lj and gb/gb torques and a rotation matrix bug
merged reaction field with electrostatics.F90
using notation from Cleaver paper
bugtracking gb
changing GB architecture
Add parts for the GayBerne LJ
simplifying long range potential array
More Change goodness for calculation of potential.
Breaky Breaky: Add Support for seperating potential contributions.
maybe some work on wolf
working on wolf
Added define for ifc 7 so derfc is external. Other compilers should treat erfc as intrinsic.
Changed erfc to derfc and declared it to be external to fix issure with ifc7. Hopefully this will not cause a problem with other compilers where derfc is an intrinsic function.
MPI fix for SimHasAtype in simulation module. We needed a seperate receive buffer.
slowdown fixed - now roughly the same speed as the old version when using dipoles energies are now exactly the same between the old version of OOPSE and this version
Bug fix: If we are not using LJ (say we are using EAM), we probably shouldn't rebuild the LJ mixing map.
Fixed a defaultCutoff bug (HEMES!)
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...
fixing some summation method issues
moved a header file around
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)
Working on adding WOLF
added in the undamped wolf, in the process of doing the damped wolf
EAM now uses eamlist to lookup eamAtypes instead of assuming a 1-1 correspondence to atypes.
fixed a bug in the createMixingMap routine. It should now set doShift correctly
Added access to mpi logical variables
made some changes for implementing the wolf potential
updated getEAMCut
added some probably nonfunctional get*cut routines
Added eamType map to atid map.
added fCutoffPolicy.h
Complete rewrite of Lennard Jones module
replace c++ style comment in c files
Added subroutine to set cuttoff for Interaction map and function in simulation.F90 to determine if a particular atype is present in a simulation.
Breaky breaky!
Removed balance from the Darkside (files)
fix bug in NPAT and NPrT
just some tap changes
Modifications to temper the dipolar strength in the first solvation shell for tap
Modifications to tap. Also correcting changes to the previous merge that were not caught
added gb
Couple of changes for TAP water. Need to parametrize.
OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it...
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...
xemacs has been drafted to perform our indentation services
Changed interface name for SGI Compiler
Added destroy methods for Fortran modules.
Added destroy method to clean up memory
cleaned up memory leak fix
Updates to deallocate object in fortran.
Changes to delete atypes...
fixing of the quadrupoles. look! it's divide by 3 like stone says!
added some stuff to clean out module files during "make clean"
quadrupole interactions should be working with a remaining question of interaction magnitude
Altered signs to fix charge-dipole interactions
Make sure electrostatic_module provides data for reaction_field
constant back to correct value
fixed three typos
first run at charge-quadrupole interactions
added some samples
settled on a unit for quadrupoles
added fortran-side support for split dipoles
new electrostatic module
electrostatic unification project fixed an uninitialized variable in Lennard Jones mixing map
adding soft potential to LJ Module
reactionfield get fixed
moved Package variable into subdirectory makefiles to speed up the building process
added dummy subroutine to avoid empty unit, synchronized this dummy routine between C and fortran
separating modules and C/Fortran interface subroutines
merging new_design branch into OOPSE-2.0
Fixed a mixing list bug that slowed down the force loop
current status of the debugging process
Breaky Breaky
Shapes looks like it's working
still debugging
forcefield refactoring for shapes
Changes to help advance shapes
Dear god! It runs and conserves energy!
Added un-busticated fortran files and c/Fortran interfaces
Breaky Breaky. Fixey Fixey.
Added newLJtype to lj module.
Added interface for fortran lj module.
fixed a fortran name problem
Fortran/C++ interface de-obfuscation project appears to be complete! Woo hoo!
Fortran/C++ interface de-obfuscation project (It is a very long story)
fixing some broken fortran stuff
name sanity on the fortran side
Added correct prototypes for C-fortran interface functions.
Added new files for fortran interface.
working on shapes for portability
move mpiSimulation_module to DarkSide
Started work merging shapes
define DEV_ROOT as relative path
change Makefile to relative path
move fortran files around to solve dependency problem
change the #include in source files
Import of OOPSE v. 2.0