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...
Added simulation box dipole moment accumulation for the purposes of calculating dielectric constants
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 the fortran side
Getting fortran side prepped for single precision...
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.
Complete rewrite of spline code and everything that uses it.
Many performance improvements
added a cubic spline to switcheroo
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
Fixed SC bug with SIM_uses_SC
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 a cutoff bug
added info printout
Cutoff mixing fixes have been made.
Added Sutton-Chen to force loop...
removed some test code
debug stuff for rf removed
removed some testing code...
still fixing up wolf...
reaction field looks to be working now
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...
merged reaction field with electrostatics.F90
changing GB architecture
Add parts for the GayBerne LJ
simplifying long range potential array
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.
just some random changes when testing
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.
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
Working on adding WOLF
Fixed bug where gtypeMaxCutoff was not initialized after creation. When maxval(gtypeMaxCutoff) was called, the largest random garbage value was returned from the array.
some changes to activate the coulombicCorrection selector
fix to put back calculation of r in do_prepair
Added nGroupsInRow for mpi build.
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
added some probably nonfunctional get*cut routines
fixing some of the problems in the interactionHash and gtypeCutoff routines
added fCutoffPolicy.h
breakage in progress
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...
Added subroutine to set cuttoff for Interaction map and function in simulation.F90 to determine if a particular atype is present in a simulation.
*** empty log message ***
More breaking and destruction of force code. Does not build at this point...
Breaky breaky!
Removed balance from doForces
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
OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it...
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
Make sure electrostatic_module provides data for reaction_field
electrostatic unification project
separating modules and C/Fortran interface subroutines
merging new_design branch into OOPSE-2.0
Got rid of some write statements
fixed useXXX in the entry_plug so that it only is set if the atoms really are in the simulation
shapes rcut calculator added
forcefield refactoring for shapes
fixey fixey the breakey breakey
fixey fixey
Breaky Breaky. Fixey Fixey.
Fortran name cleanup continues
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