This commit was manufactured by cvs2svn to create branch 'stable-05'.

Updated the Makefile to contain all of the new fortran

deprecated the ssd forcefield in C++

fixed some bugs in BendStamp from when Ghost Bend was implemented.

Minor alterations to the layout

spellchecked it.

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 made som e revisions to the application.

just working on some changes to the application.

Fixed some more compile bugs in do_Forces.F90.

Stick a fork in it.  It's rare.

bye bye forceGlobals (part 1)

Massive rewrite

bunch of fixes

added the force parameter files into the distribution

rearranging source files

Bug fixes

Changes to vector_class and removed all traces of linked list.

Did a bunch of match/find routines

finished adding the ghostBend into the TraPPE_Ex force Field

Massive rewrite underway.  This way be dragons.

Changed names of calculation modules for do_Forces.

some cleanup

added the ghost bend bend type.

GhostBend addition

implemented the new fortran force interface

Dan Goes Crazy

Split force loop into subroutines. Moved wrap out of simulation module.

cleaning up all of the function wrapping

overhauled TraPPE_Ex forcfield in C++

added randomSPRNG.hpp to the package (oops, should have beenthere to begin with.)

added ssdFF++.cpp to the makefile

fixed some changes to the Globals in libBASS

Added some files to the Makefile and added ssdFF++.cpp to the C++ side of things

OOPSE has been braought up to date with the mdtools devfelopment tree. mdtools should no longer be used. All development should take place in the OOPSE tree.

Added simulation struct...

Changes they are a comming....

incremented the version to 0.6

oopse compiles and links!

libmdCode builds.

added some checks for libmpich and got single processor to build in libmdCode

working on getting this distribution working

libBASS and libmpiBASS are completely self encapsulated.

Successfully added all the source for libBASS

Initial commit of ssd force module.

Changed to single version.
No change.

We have working code today... MPI bug fixes to DumpWriter.

MPI is Brooooooken...

MPI is Broooooken. Saving poor state so I know where to begin with.

Changes in mpiBass.

Added a generic util code directory and moved Linux_ifc_machdep to it.
MPI changes to compile MPI modules.

Add print lines to simBASS and fixed Makefile to link w/ icc.

For some unknown reason the Single processor builds. Has not been tested!

added generic atypes

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modified the box vairable on setSimulation to be a length 3 array

More changes to lj_ff. Force loop almost ready.

added some stuf to implement thefortran interface in LJ_FF

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tarted some additions to wrap LJ down to fortran. INCOMPLETE!

starting down the crooked path of the fornographer.

just some initial fiddling

This commit was generated by cvs2svn to compensate for changes in r226,
which included commits to RCS files with non-trunk default branches.

fixed up the LJ_FF implementation. It is now the standard for building a force routine.

More codeing on fortran force backend.

Added more code to randomSPRNG classes.

Changed thermo getKinetic and getPotential for MPI.
Added header for SPRNG random number generator class.

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Added mpi to InitializeFromFile read in.

Finished updating mpiSimulation to work with c++.

added the pareDumpLine routine to the Initialize from File class

Initial mpi io conversion.

fixed typo with #ifdef.

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Working on the clean removal of key Molecule stamps from the Hash table.
stamps will be moved into a persitient linked list.

First addition of mpiDivideLabor to split mpi simulation among processors.

added files to divide the molecules among the processes.

some quick optimizations to the indexing in the storage arrays

made some finishing changes before begining to work on the io

if the libMPImdtools is working this should be the code to run it.

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initial modifications

This commit was generated by cvs2svn to compensate for changes in r179,
which included commits to RCS files with non-trunk default branches.

overhauled the makefiles to be more elegant with regard to builds.

ie. now the name of the library will change when you select single or mpi
    build in the Makefile.inc compilers and flags will also be updated

Fixed the whole lot to be simError safe, ands compiles. Not yet tested however

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the BASS event loop has finished converiosn to simError. However, it as yet untested.

MPI Force rewrite in progress...

First commit of mpi force code.

working on the conversion of the BASS inititialization to be parrallel safe

adding simError into the mpiBASS Event loop

finished updates on the easy simError change overs.

still working on conversion over to simError

adding in simError

finished work on the error handling struct and functions

started work on a global error handling scheme

making further modifications to make FOrceField objects mpi aware

more tinkering with the forcefield event loop

more minor changes to the mpi structs

finished adding the static storage arrays to the atom class

Changing internal storage of positions, torqes, forces, velocities, etc.

adding ForceField mpi awareness


adding mpi FOrceField awareness

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Fixed double inclusion of mpiBASSEventType with define in
header file.

Clean up with icc debug flags...

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quick bug fix to bassDiag

added stamp and template diagnostic features

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changed dirs...

Initial mpi support

First stab at passing base events to mpi....

fixed allot of warnings, and adde the molecule

starting work on the molecule class

starting to add in the molecule class

the final copy went out this morning. YAYYYYYYYYY!!!!!!!!!!!!!!!

added a bunch of igures

finished the revisions of the first draft

now only lacks a complete results section, and a future Directions section

added command line arguments, and a time smoother

fixed a cosCorr and GofR flag bug, as well as the GofR scaling bug.

made some changes to the Makefile, and added the sections I think I should write

additions to the lipid model

added the ssd figure

just writing, not much editing yet

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added a utility to output what time of each frame

added the capability to specify a start and end frame for cosCorr and GofR

spell checked

fixed some figures almost done with slides

added figures fixed more of the graphs

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flexible atom selection

fixed the citations. continueing to clean up the slides.

added a crapload of crap that may or may norbe neccassary. Time will tell. Also, got footnote references working.

This commit was generated by cvs2svn to compensate for changes in r58, which
included commits to RCS files with non-trunk default branches.

fixed the Makefile

getting there. Most everything but the motivation slide has been filled out. Lacks only pictures and Diagrams.

made some changes

This commit was generated by cvs2svn to compensate for changes in r47, which
included commits to RCS files with non-trunk default branches.

got the GofR code working, and slimmed down the memory usage.

finished working on the command line options, and started working on the GofR

made a header directory, and fixed the Makefile to work with it

This commit was generated by cvs2svn to compensate for changes in r38, which
included commits to RCS files with non-trunk default branches.

moved the actual routine into a seperate source from the main. This allows the routine to
be used in other applications.

cleaned up the output a little

fixed a bug in getA( double the_A[3][3] );

adding the routines to the proogram
`

fixed some bugs in the Makefile

fixed a precision error in the calculation of the temperature.
Also fixed the order that dump file are written.

This commit was generated by cvs2svn to compensate for changes in r22, which
included commits to RCS files with non-trunk default branches.

This commit was generated by cvs2svn to compensate for changes in r18, which
included commits to RCS files with non-trunk default branches.

This commit was generated by cvs2svn to compensate for changes in r14, which
included commits to RCS files with non-trunk default branches.

This commit was generated by cvs2svn to compensate for changes in r10, which
included commits to RCS files with non-trunk default branches.

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Import Root

initial checkin