working on a system builder

added Ghost bends to the TraPPE_Ex forceField

fixed a memory bug in Fortran, where molMembershipArray was declared nLocal instead of nGlobal.

 added a globalIndex counter to Molecule

fixed a n mpi init bug in SimSetup. caused a miscalculation of nLocal.

added pentane to the alkane model file

fixes for NPT and NVT

Fixes for NPT / NVT

fixes for NVT

dt/2 fix in nvt

Changes to integrate the NVT and NPT ensembles

fixed a sign error in the radial portion of SSD.

Working on NVT

bug fixes

Fixed a bug caused by my experimentation

Added targetPressure to BASS

Bug fixes for simulation module rewrites

bug fixes to fortran wrappers

fixed a memory read bug in neighborlist

Fixes for ExtendedSystem

Added extended system header

renamed nvt to extendedsystem

fixed a possible call before initialize bug.

a few fixes to simError.h
also some fixes to Molecule.hpp

fixed some small things with simError.h

Added NVT file (very broken for now)

dipoles mostly work, but there is a memory leak somewhere.

more bug fixes....

Fixed bug with pot_local not zeroed.

bug fix in DumpWriter.cpp

fixed a bug where the Excludes were not being created properly

fixed long range interactions in Trappe

fixed a bug where excludes were not being initialized

Fixed a single processor segfault bug.

fixed a few more bugs.

 fixed the makefile

I have implemeted Molecules everywhere I could remember to.
will now attempt to compile.

finished conversion of TraPPE_ExFF to use Molecule

fixes for local->global atom numbering in MPI

Fixes to fileio for MPI

Making DumpWriter less dependent on sequence of atoms on the other
processors.  Node 0 now fires potatoes at other processors to get them
to send french fries back.

fixed a couple of the "static" bugs in  Atom and Exclude

Added Atom.cpp and Exclude.cpp

Make Atom.cpp able to add and delete ranges of atoms

I'm overhauling the molecule class to contain it's own bonds, bends, and torsions.

may god have mercy on my soul.

MPI stuff for passing out molecules

Fixes for Parallel thermalization

Fixed bugs with calculation of potential energy and temperature.

added dummy files to keep the build deirectories from being pruned.

moved tests to samples

Added makefiles in tests directories

little bug fixes here and there

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fixed bug where short range interactions were not being calculated.

removed some debug print statements

added links to the makefile in forceFields

Makefile fixes, directory re-org, autoconf fixes

Fixed makefile

Readme changes

Makefile fixes for depends

Bug fixes in TraPPE.
calc_LJ_FF.F90: Removed print lines.
TraPPE_ExFF.cpp: Fixed so idents are being set.

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Working on the Makefile

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Fixed bugs. Single version now runs w/o segfault. Still a conservation of energy bug.
do_Forces.F90: Fixed pot not being passed to do_pair.
neighborLists.F90: Fixed bugs in checkNeighborLists
atype_module.F90: Fixed bug with allocating atypes on each new_atype call.Now checks to see if atypes is null, then calles initialize(16).
vector_class.F90: Fixed some bugs with how MatchList was being allocated.

compiles and links. And promptly segfaults.

added GB

shed implementation of the Fortran interfaces.

brought force_globals back from the dead to fix circular references

bug fixes for new fForceField.h

fortran-side fixes to play nice with C

merged  stable-0_5 into the main trunk

mostly compiles. interface twixt c and fortran is broken. (c needs to be brought up to date with fortran.)

vector class tests correctly.

Bug fixes in vector_class.

last minute changes

changed the font

A near final product

Setting up my CV.

fixes for the exclude lists

initialization routines, bug fixes, exclude lists

forceGlobals is gone (part3)

bye bye atypeGlobals (part2)

fixes for major rewrite

MPI bug fix

Massive sticky rewrite

Fixed mixing list to work with new atypes using vector class.

Added allocation of module arrays.

Fixed bugs, added logical routines

Fixed a bug

Bunch o' stuff, particularly the vector_class.F90 module

Changed generic lists so they work correctly

Added ghostBend into SimSetup. only need to add awareness to TraPPE_Ex

More changes to code. Hopefully these will commit smoothly.

Removed extra copy of dipole dipole

Added stuff for Dipole/Dipole and ReactionField

added fortranWrappers and Forcefield.cpp to the makefile

More code clean-up.

dded more static arrays to the Atom class;

finished conversion of all function wrapping into fortranWrappers.cpp and .hpp respectively

Changed code to use one generic force loop. Only one super atype that
has all information is now used.

Made changes to lj_FF.cpp to pass stress tensor.

Changed lj_FF to use new neighbor list module.

fixed some changes to the Globals in libBASS

Added neighbor list module that auto expands...

Changes...

added changelog and NEws info

oose and oopse build and distribute!

oose builds and links
oopse builds but can't find mpich++

added mpi for libmdCode (still working out the kinks)

dded some stuff

added libmdCode and a couple help scripts

added mpiBASS.c and .h for the mpi libraries

Added SSD atypes.

Fixed bug with pot energy.

Changed to single version.

Fixed some bugs, made some more.

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fixed a bug in the final eor file.

Bug fixes for mpi version of code

Force loops seems to work, velocitize never being called....

More bug fixes... Forgot to build sprng

final version before the single processor build

lj_FF.F90 and simulation_module now compile. Logical bug still
exists in lj_FF.F90 lj_atypes_list.

added the fortran function wrapping to the mpiSim class

added wrapping of fortran to a private function of SimInfo

Added init function to c++ force module.

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this  completes the addition of fvortran function wrapping into the LJ_FF class.

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

A few more changes to force loop.

More changes to lj_FF.

removed a ps file that should not be backed up

fixed up LJ_FF

Finished thermo and randomSPRNG classes.

Thermo now can use SPRNG or rand48 (if not MPI).
Finished up work on randomSPRNG. Still need to fix
access to MPISimulation.

Added classes to handle random number generation.

Added SPRNG header file.

+ added lennard-jones force module and corresponding class.
+ created forceFactory directory.

finishing work on making DumpWriter parrallel

Added replan of gather-scatter routines for future load balancing.

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Changed name of mpi_force_module to mpiSimulation to match with C++ code.

finished adding in the code to divide and set up the atoms and such across all of the processors.

Added mpiComponentPlan.h a dual fortran c header file defining mpi
simulation parameters for both c and fortran.

 made some shanges to streamline the setup in SimSetup

cleaned up the divideLabour interface to use the information about Moleculestamps in the entryPlug.

added the extraction routines so that the moleculeStamps corresponding to the actual components used in the simulation
are now persistent throughout, and accessable through the SimInfo object.

Added divideLabor.

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Addition of c wrapper header for for fortran module proceedures.

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This will run the single processor version of libmdtools

Initial commit of wrappers for fortran module proceedures.

The simulation can run successfully on parrallel computers!! Now all that is need is the parrallel io routines, and parrallel forces

added simError.h to the makefile

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Bass shopuld be simError safe

continuing to refine the error checking in the BASS processing

Initial commit of mpi routines for force decomposition.

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minor revisions

finished adding in the extra structures needed to pass info through mpi. Still need to add the implementation.

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

not sure here, still working

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adding ForceField mpi awareness

changed mpiInterface.c and .h -> mpiBASS.c and .h for clarity of purpose

Added lhs of assignments..

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Include makefile

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Added make include.

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Addition of mpiInterface to code base.

begin the pain that is MPI.

abandon all hope ye who check out this branch..

P.S. we've added consistent BASS error checking

starting work on the molecule class

starting to add in the molecule class


adding in the molecule class

starting work on the molecule class

made some final revisions, and started to add some figures

text is finished YAY!!!

revisions to the first draft halfway complete.

completed the introduction.

fixed a little seen output bug. (Tarega is not always default)

running into some problemsd with the figures.

did a little more typing

got the water SSD model section "done"

added some equations and other misc stuff. needs lots of work.

This commit was generated by cvs2svn to compensate for changes in r93, which
included commits to RCS files with non-trunk default branches.

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VS: ----------------------------------------------------------------------
added more figures, and fixed the slides. GFave a practice talk 6-16-02 with this.

fixed somebugs with start frame

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I think I have most of it the way I like it, just need to change the correlation functions, and the final pictures

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changed some of the figures, and put some more polish on the intro

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made a new figure. trying to add it to the slide

switched in Chuck's magic slide enviroment

This commit was generated by cvs2svn to compensate for changes in r60, which
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This commit was generated by cvs2svn to compensate for changes in r56, which
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added all of the pictures. And gave a practice talk based on this version. Now begins the process of cleanup and additions
of citations.

Skeletons of most every slide

This commit was generated by cvs2svn to compensate for changes in r49, which
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added the cos correlation function

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

added the GofR header, and moved the strructure definitions to the madProps.h

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

the new header dir

took out a reference file

fixed the ordering on the end of file test

This commit was generated by cvs2svn to compensate for changes in r34, which
included commits to RCS files with non-trunk default branches.

fixed makeRandom to set up a correct simulation

added the getA( double the_A[3][3] ) routine to the Directional Atom Class, to facilitate easier RotMat aquisition

adding a program to make a lipid configuration with random dispersion of lipids.

removed xLate.cpp which was part of a seperate project

removed a misc file

This commit was generated by cvs2svn to compensate for changes in r20, which
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This commit was generated by cvs2svn to compensate for changes in r16, which
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This commit was generated by cvs2svn to compensate for changes in r12, which
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nose hoover chains added

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initial checkin

Standard project directories initialized by cvs2svn.