debugging globals

fixed a few references to older stuff...

Missed del of files before.

commit makefile

changed how the comment line is handled to allow greater flexibility.

added utils/sysbuilder to be built.

added method of moving zconstraint molecules to specified positions

Added zConstraint into the BASS language syntax.

EAM works...... Neighbor list also works.....

 fixed a deprcated instance of Atom::setZ and Atom::getZ in ZConstaint.

Bug fixes for eam...

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This commit was generated by cvs2svn to compensate for changes in r662,
which included commits to RCS files with non-trunk default branches.

stable version of Z-Constraint

added z-constraint parameters to the globals

More bug fixes for eam.

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Added eam to simSetup and added changecutoffeam.

rewrote the makefiles a little to install two scripts for rendering

added a '-' to the formating of the pov output file.

also removed pov2anim from the project. It will be replaced with shell scripts

added the scan function to the DumpReader. It should now save the start of each frame in a vector.

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some initial changes to Dumpwriter and friends to accomadate random file access

fixed Initializefrom file to start the simulation from the time specified in the init file.

added DUFF lipid models to the AtomTypes file

Started work on a DumpReader

Changes for SSD/E

fixed spelling issue

Added massive changes for eam....

Fixed a the centering on the Periodic Box. Also corrected the y and z switch in the box vectors

More up to date version of EAM_FF

Started work on Hmat stuff to replace box Lengths

Fixed bug in updating mixing lists

more fixes for box changes

fixed a long lived bug in do_forces. Rrf was not being used in the neighborlist correctly. rcut was conssistently being set lowere than Rrf causing the dipole cutoff region to be to small. Also led to the removal of the taper region to buffer the dipole cutoff.

Fixes for the NPT ensembles

added KMol

added more command line arguments

Fixing  pressure tensor

removed old outdated code

removing get_vx

Bugfix in NPTim, fixes for NPTfm

Broken SysBuilder

Removed some debugging write statements

added get and set routines to Atom and DirectionalAtom

found a bug. Unit vectors were not being updated

Switched the bond in the force field back to constrained, to preserve energy

Starting to worry about all the strtok() calls in our code

Fixed hmat in DumpWriter (MPI) and eor.

Added nanoBuilder and a general Lattice builder.

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starting some work for xlate

This is the dp and read file

Removed Qmass

Fixes in NPTi migrated into NPTf

fixed box scaling

 cleaned up the dependecy scripts in the makefiles

Fortran flexi-BOX

working on adding the box matrix to everything.

Changed over the bonds to Harmonic bonds in the DUFF frc file

fixed constraints.

Fixes to NVT.  Check them!

Doing some work to debug the constraint code.

Most of the integrator and NVT seem to be working now.

slowly converting to new integrator and forcefield names.

 doing some work on SimSetup to clean it up / get it to work with the new Integrator.

Added Teng's parmeters fro the ghost Bend in TraPPE_Ex

some work on the integrator. ( incomplete)

mostly final version

fixed the left alignment bug. Bugger if I know what was causing it.

nothing major just some little changes here and there.

updated the logo a little as well as some of the colors

This commit was generated by cvs2svn to compensate for changes in r544,
which included commits to RCS files with non-trunk default branches.

currently modifiying Symplectic to become the basic integrator.

bilayerSys.cpp altered for building tb3.

added some member variables for position, velocity, etc.

fixed an a mismatched Ghostbend bug.

still working on the bilayer code

This commit was manufactured by cvs2svn to create tag 'bob-5_14_03'.

Added bead lipid model to the sample directory

added the TailBead atom types to the TraPPe_Ex forceField

fixed up the TraPPE_Ex force field. there were some duplicate entries

added the utils subdirectory to the configure script

calculation of the pi

We update the Makefile.

 fleshed out all of the ideas we wanted to see in this interface.

 it is still not yet debugged.

Added binary extensions

This commit was generated by cvs2svn to compensate for changes in r516,
which included commits to RCS files with non-trunk default branches.

updated xyz2pov to put out better pov scripts. I'm begining to think pov2anim isn't as useful.
not sure if I should up date it, or just leave the rendering steps to shell scripts.

this should be the last of the random crap to toss out.

killing misc . crap that shouldn't be inb the source tree.

cleanning up the makefiles

Rearranged the source tree to be easier to distribute.
Added autoconf and automatic dependency generation

added all the files

added a new test for constraint failure

almost finished.

finished bilayerSys.cpp

sysBuild still need to write the bass file.

MoLocator.cpp is currently empty

More eam work.

Fixed ordering on NVT calculation in integrators.

 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

New OOPSE Tree

more bug fixes...

fixed a bug in the torsions.

Fixed bugs in atype_module.F90
atype_module.F90:new_atype: status was reused for force field checks, created
new variable FFcheckStatus to be result of FF checks.

fixed some bugs. LJ argon works. Error calling new atype for SSD in TraPPE_Ex.

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some initial bug fixes

 last little changes before compiling and debuging

getNlocal no longer in force_globals

adding more to the interface

working on the fortran init ForceField interface.

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this is an inital attempt to implement the new fortran interfaces

blah!

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 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

This is the mpi version of simBASS

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

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

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

my Canidacy paper

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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 r58, which
included commits to RCS files with non-trunk default branches.

This commit was generated by cvs2svn to compensate for changes in r56, 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

Matt's canidacy presentation

little utility for catting together dump files.

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.

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.

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