builds

well, it compiles, but still segfaults

removing cruft (atom numbers, do_pot, do_stress) from many modules and
force managers

Fixed a typo in EAM, cleaned up EAM and sutton chen a bit

Fixed bug is Sutton-Chen force calculation in parallel.

removing MPI responsibilities from the lowest level force routines.  This is
in preparation for migrating these routines (LJ, electrostatic, eam, suttonchen,
gay-berne, sticky) to C++

Fixing a parallel bug in the self-self interaction.

Fixed odd bug in electrostatic for self-term forces with neutral molecules

many changes to keep track of particle potentials for both bonded and non-bonded interactions

Added support for scaled 1-2, 1-3 and 1-4 interactions.

Checking in changes for Hefland moment calculations

More changes to MnM.

forgot the if (do_stress) condition on the previous commit

SF Lennard-Jones was added for everyones' enjoyment.  The behavior is tethered to the electrostaticSummationMethod keyword.

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...

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).

Getting fortran side prepped for single precision...

Complete rewrite of spline code and everything that uses it.

added a cubic spline to switcheroo

Fixed SC bug with SIM_uses_SC

Long range potential return from fortran is already accumulated, it should not be accumulated again;
nGroupTypesCol is not initialized; GroupMaxCutoffCol is not allocated;

fixed a cutoff bug

Cutoff mixing fixes have been made.

removed some test code

removed some testing code...

reaction field looks to be working now

Still had some globals toUpper problems - these changes should fix those...

changing GB architecture

simplifying long range potential array

More changes to MPI potential calculations.

Free some variables that weren't freed before.

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.

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 bugs in reaction field, now it appears as though it really is working...

fixing some summation method issues

Fixed bug where gtypeMaxCutoff was not initialized after creation. When maxval(gtypeMaxCutoff) was called, the largest random garbage value was returned from the array.

fix to put back calculation of r in do_prepair

bugfix on the grouptype finding algorithm

Some bug hunting

initialized atomTypeMaxCutoff(i) to zero

made some changes for implementing the wolf potential

fixing some of the problems in the interactionHash and gtypeCutoff routines

breakage in progress

In process of re-write for group based cutoff....

fix a bug which does not update me_i and me_j correctly

Added subroutine to set cuttoff for Interaction map and function in simulation.F90 to determine if a particular atype is present in a simulation.

More breaking and destruction of force code. Does not build at this point...

Removed balance from doForces

Modifications to tap.  Also correcting changes to the previous merge that were not caught

OOPSE setup for TAP water.  It's not parametrized, but OOPSE will now let me run it...

xemacs has been drafted to perform our indentation services

electrostatic unification project

merging new_design branch into OOPSE-2.0

fixed useXXX in the entry_plug so that it only is
set if the atoms really are in the simulation

forcefield refactoring for shapes

fixey fixey

Fortran name cleanup continues