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
Many fixes for Charmm-type torsions.
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.
Fixed pot in parallel.
forgot the if (do_stress) condition on the previous commit
fixed a bug where the pressure tensor wouldn't update for atoms in the switching region when # of atoms in a group = 1
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
Removed MixingRule from Globals. Handled by forceField now.
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.
Fixed SC bug with SIM_uses_SC
remove extra forceFieldOptions from SC_FF
Sutton-Chen no longer segfaults or produces 0 potential, but rather produces Inf for the potential. Progress....
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;
Sutton-Chen bug fixes. Almost there...
Fixed issue with symbol naming and added call to set force options in SimCreator.
Force options passed to fortran.
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
fixed a cutoff bug
made some minor changes to allow compilation with the portland group compilers
added info printout
Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers.
This should really break things.... Started adding support for ForceOptions to section parsers.
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Removed geometric distance mixing from individual modules and now use force options to detemine what the deal is.
Further fixes for compiler issues.
Fixed ifc public-private issue.
Added support for fortran force options.
Changes to SC.
Adding handler for CLAY force field
Cutoff mixing fixes have been made.
OptionSectionParser get compiled
ForceField optional parameters....
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
debug stuff for rf removed
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
reaction field looks to be working now
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
Breaky, Breaky: c-fortran interface now expects an array for pot.
More Change goodness for calculation of potential.
More changes to MPI potential calculations.
Breaky Breaky: Add Support for seperating potential contributions.
Free some variables that weren't freed before.
Bug fix, undeclared local variable in MPI.
Fixed MPI bug with Row and Column indexing of groupToGtype. We now have two seperate maps groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer that is set to groupToGtypeRow in the single processor version.
maybe some work on wolf
just some random changes when testing
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
Fixed "dum-dum" where we ignore the skin thickness and hardcode listSkin to be 1.0. We now get listskin from skin. This will get fixed to where we can manually set skin thickness.
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...
xlf found a bug that ifc missed...
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
forgot to add a header
Fixed bug where gtypeMaxCutoff was not initialized after creation. When maxval(gtypeMaxCutoff) was called, the largest random garbage value was returned from the array.
added in the undamped wolf, in the process of doing the damped wolf
some changes to activate the coulombicCorrection selector
EAM now uses eamlist to lookup eamAtypes instead of assuming a 1-1 correspondence to atypes.
fix to put back calculation of r in do_prepair
fixed a bug in the createMixingMap routine. It should now set doShift correctly
Added nGroupsInRow for mpi build.
Added access to mpi logical variables
bugfix on the grouptype finding algorithm
adding c-side interface to change cutoff Policy
Some bug hunting
Added allocation for gtypeCutoffmap etc..
initialized atomTypeMaxCutoff(i) to zero
wrote createGtypeCutoffMap
made some changes for implementing the wolf potential
updated getEAMCut
added some probably nonfunctional get*cut routines
Added eamType map to atid map.
fixing some of the problems in the interactionHash and gtypeCutoff routines
added fCutoffPolicy.h
breakage in progress
Complete rewrite of Lennard Jones module
Breaky Breaky BREAKY breaky breaky
In process of re-write for group based cutoff....
fixes in progress
fix a bug which does not update me_i and me_j correctly
Changed cutoffs... Segfaults nicely now...
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.
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More breaking and destruction of force code. Does not build at this point...
Breaky breaky!
Removed balance from the Darkside (files)
Removed balance from doForces
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...
axed because file causes havoc on Mac (capitalization confusion of filenames)
Working on the shapes parser...
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
no real changes here, maybe added a space by accident
destory atom type in fortran side
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
using map to replace link list
added fortran-side support for split dipoles
fixing restraints
fix a bug in SectionParser (lineNo is not updated)
adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
new electrostatic module
removed #include lines for outdated charge and dipole interfaces
electrostatic unification project fixed an uninitialized variable in Lennard Jones mixing map
electrostatic unification project
fix compilation problem for g++ 3.4
adding soft potential to LJ Module
reactionfield get fixed
corrected filename collision for EAM on operating systems which are not case sensitive (aka Mac OS X)
remove WATER.cpp
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
port to SGI platform
merging new_design branch into OOPSE-2.0
fix another bug in WATER.cpp
fix a bug in WATER.cpp when initializing the new Charge AtomType
Improvements to restraints
Fixed a mixing list bug that slowed down the force loop
Got rid of some write statements
current status of the debugging process
added new classes in progress
Breaky Breaky
fixed useXXX in the entry_plug so that it only is set if the atoms really are in the simulation
Shapes looks like it's working
still debugging
shapes rcut calculator added
fix of setDipoles
forgot to advance lines in the shapeFile
fixed duplicate declaration foo
bug fix
subclass foo
more char* -> string conversion
char* -> string
forcefield refactoring for shapes
Changes to help advance shapes
Changes to Shapes force field reader
Dear god! It runs and conserves energy!
fixey fixey the breakey breakey
fixey fixey
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 continues
Fortran/C++ interface de-obfuscation project (It is a very long story)
fixed include
Fortran name cleanup continues
fixing some broken fortran stuff
name sanity on the fortran side
Added correct prototypes for C-fortran interface functions.
Added correct prototypes for C-fortran interface functions.
Added new files for fortran interface.
regressing
working on shapes for portability
working on shapes
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
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change the #include in source files
Import of OOPSE v. 2.0