This commit was manufactured by cvs2svn to create branch 'stable-05'.
mostly compiles. interface twixt c and fortran is broken. (c needs to be brought up to date with fortran.)
Updated the Makefile to contain all of the new fortran
vector class tests correctly.
deprecated the ssd forcefield in C++
Bug fixes in vector_class.
fixed some bugs in BendStamp from when Ghost Bend was implemented.
last minute changes
Minor alterations to the layout
changed the font
spellchecked it.
A near final product
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Setting up my CV.
made som e revisions to the application.
fixes for the exclude lists
just working on some changes to the application.
initialization routines, bug fixes, exclude lists
Fixed some more compile bugs in do_Forces.F90.
forceGlobals is gone (part3)
Stick a fork in it. It's rare.
bye bye atypeGlobals (part2)
bye bye forceGlobals (part 1)
fixes for major rewrite
Massive rewrite
MPI bug fix
bunch of fixes
Massive sticky rewrite
added the force parameter files into the distribution
Fixed mixing list to work with new atypes using vector class.
rearranging source files
Added allocation of module arrays.
Bug fixes
Fixed bugs, added logical routines
Changes to vector_class and removed all traces of linked list.
Fixed a bug
Did a bunch of match/find routines
Bunch o' stuff, particularly the vector_class.F90 module
finished adding the ghostBend into the TraPPE_Ex force Field
Changed generic lists so they work correctly
Massive rewrite underway. This way be dragons.
Added ghostBend into SimSetup. only need to add awareness to TraPPE_Ex
Changed names of calculation modules for do_Forces.
More changes to code. Hopefully these will commit smoothly.
some cleanup
Removed extra copy of dipole dipole
added the ghost bend bend type.
Added stuff for Dipole/Dipole and ReactionField
GhostBend addition
added fortranWrappers and Forcefield.cpp to the makefile
implemented the new fortran force interface
More code clean-up.
Dan Goes Crazy
dded more static arrays to the Atom class;
Split force loop into subroutines. Moved wrap out of simulation module.
finished conversion of all function wrapping into fortranWrappers.cpp and .hpp respectively
cleaning up all of the function wrapping
Changed code to use one generic force loop. Only one super atype that has all information is now used.
overhauled TraPPE_Ex forcfield in C++
Made changes to lj_FF.cpp to pass stress tensor.
added randomSPRNG.hpp to the package (oops, should have beenthere to begin with.) added ssdFF++.cpp to the makefile
Changed lj_FF to use new neighbor list module.
fixed some changes to the Globals in libBASS Added some files to the Makefile and added ssdFF++.cpp to the C++ side of things
fixed some changes to the Globals in libBASS
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 neighbor list module that auto expands...
Added simulation struct...
Changes...
Changes they are a comming....
added changelog and NEws info
incremented the version to 0.6
oose and oopse build and distribute!
oopse compiles and links!
oose builds and links oopse builds but can't find mpich++
libmdCode builds.
added mpi for libmdCode (still working out the kinks)
added some checks for libmpich and got single processor to build in libmdCode
dded some stuff
working on getting this distribution working
added libmdCode and a couple help scripts
libBASS and libmpiBASS are completely self encapsulated.
added mpiBASS.c and .h for the mpi libraries
Successfully added all the source for libBASS
Added SSD atypes.
Initial commit of ssd force module.
Fixed bug with pot energy.
Changed to single version. No change.
Changed to single version.
We have working code today... MPI bug fixes to DumpWriter.
Fixed some bugs, made some more.
MPI is Brooooooken...
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MPI is Broooooken. Saving poor state so I know where to begin with.
fixed a bug in the final eor file.
Changes in mpiBass.
Bug fixes for mpi version of code
Added a generic util code directory and moved Linux_ifc_machdep to it. MPI changes to compile MPI modules.
Force loops seems to work, velocitize never being called....
Add print lines to simBASS and fixed Makefile to link w/ icc.
More bug fixes... Forgot to build sprng
For some unknown reason the Single processor builds. Has not been tested!
final version before the single processor build
added generic atypes
lj_FF.F90 and simulation_module now compile. Logical bug still exists in lj_FF.F90 lj_atypes_list.
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added the fortran function wrapping to the mpiSim class
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added wrapping of fortran to a private function of SimInfo
modified the box vairable on setSimulation to be a length 3 array
Added init function to c++ force module.
More changes to lj_ff. Force loop almost ready.
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added some stuf to implement thefortran interface in LJ_FF
this completes the addition of fvortran function wrapping into the LJ_FF class.
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started some additions to wrap LJ down to fortran. INCOMPLETE!
tarted some additions to wrap LJ down to fortran. INCOMPLETE!
A few more changes to force loop.
starting down the crooked path of the fornographer.
More changes to lj_FF.
just some initial fiddling
removed a ps file that should not be backed up
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
fixed up the LJ_FF implementation. It is now the standard for building a force routine.
Finished thermo and randomSPRNG classes.
More codeing on fortran force backend.
Thermo now can use SPRNG or rand48 (if not MPI). Finished up work on randomSPRNG. Still need to fix access to MPISimulation.
Added more code to randomSPRNG classes.
Added classes to handle random number generation.
Changed thermo getKinetic and getPotential for MPI. Added header for SPRNG random number generator class.
Added SPRNG header file.
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+ added lennard-jones force module and corresponding class. + created forceFactory directory.
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finishing work on making DumpWriter parrallel
Added mpi to InitializeFromFile read in.
Added replan of gather-scatter routines for future load balancing.
Finished updating mpiSimulation to work with c++.
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added the pareDumpLine routine to the Initialize from File class
Changed name of mpi_force_module to mpiSimulation to match with C++ code.
Initial mpi io conversion.
finished adding in the code to divide and set up the atoms and such across all of the processors.
fixed typo with #ifdef.
Added mpiComponentPlan.h a dual fortran c header file defining mpi simulation parameters for both c and fortran.
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made some shanges to streamline the setup in SimSetup
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cleaned up the divideLabour interface to use the information about Moleculestamps in the entryPlug.
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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.
Working on the clean removal of key Molecule stamps from the Hash table. stamps will be moved into a persitient linked list.
Added divideLabor.
First addition of mpiDivideLabor to split mpi simulation among processors.
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added files to divide the molecules among the processes.
Addition of c wrapper header for for fortran module proceedures.
some quick optimizations to the indexing in the storage arrays
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made some finishing changes before begining to work on the io
This will run the single processor version of libmdtools
if the libMPImdtools is working this should be the code to run it.
Initial commit of wrappers for fortran module proceedures.
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The simulation can run successfully on parrallel computers!! Now all that is need is the parrallel io routines, and parrallel forces
initial modifications
added simError.h to the makefile
This commit was generated by cvs2svn to compensate for changes in r179, which included commits to RCS files with non-trunk default branches.
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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
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Fixed the whole lot to be simError safe, ands compiles. Not yet tested however
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Bass shopuld be simError safe
the BASS event loop has finished converiosn to simError. However, it as yet untested.
continuing to refine the error checking in the BASS processing
MPI Force rewrite in progress...
Initial commit of mpi routines for force decomposition.
First commit of mpi force code.
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working on the conversion of the BASS inititialization to be parrallel safe
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adding simError into the mpiBASS Event loop
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finished updates on the easy simError change overs.
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still working on conversion over to simError
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adding in simError
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finished work on the error handling struct and functions
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started work on a global error handling scheme
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making further modifications to make FOrceField objects mpi aware
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more tinkering with the forcefield event loop
minor revisions
more minor changes to the mpi structs
finished adding in the extra structures needed to pass info through mpi. Still need to add the implementation.
finished adding the static storage arrays to the atom class
Changing internal storage of positions, torqes, forces, velocities, etc. not sure here, still working
Changing internal storage of positions, torqes, forces, velocities, etc.
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adding ForceField mpi awareness adding mpi FOrceField awareness
adding ForceField mpi awareness
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changed mpiInterface.c and .h -> mpiBASS.c and .h for clarity of purpose
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Added lhs of assignments..
Fixed double inclusion of mpiBASSEventType with define in header file.
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Clean up with icc debug flags...
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Include makefile
quick bug fix to bassDiag
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added stamp and template diagnostic features
Added make include.
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changed dirs...
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Initial mpi support
Addition of mpiInterface to code base.
First stab at passing base events to mpi....
begin the pain that is MPI. abandon all hope ye who check out this branch.. P.S. we've added consistent BASS error checking
fixed allot of warnings, and adde the molecule
starting work on the molecule class starting to add in the molecule class adding in the molecule class
starting work on the molecule class starting to add in the molecule class
starting work on the molecule class
the final copy went out this morning. YAYYYYYYYYY!!!!!!!!!!!!!!!
made some final revisions, and started to add some figures
added a bunch of igures
text is finished YAY!!!
finished the revisions of the first draft now only lacks a complete results section, and a future Directions section
revisions to the first draft halfway complete. completed the introduction.
added command line arguments, and a time smoother
fixed a little seen output bug. (Tarega is not always default)
fixed a cosCorr and GofR flag bug, as well as the GofR scaling bug.
running into some problemsd with the figures.
made some changes to the Makefile, and added the sections I think I should write
did a little more typing
additions to the lipid model
got the water SSD model section "done"
added the ssd figure
added some equations and other misc stuff. needs lots of work.
just writing, not much editing yet
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.
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fixed somebugs with start frame
added a utility to output what time of each frame
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added the capability to specify a start and end frame for cosCorr and GofR
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spell checked
I think I have most of it the way I like it, just need to change the correlation functions, and the final pictures
fixed some figures almost done with slides
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added figures fixed more of the graphs
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changed some of the figures, and put some more polish on the intro
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flexible atom selection
made a new figure. trying to add it to the slide
fixed the citations. continueing to clean up the slides.
switched in Chuck's magic slide enviroment
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 r60, which included commits to RCS files with non-trunk default branches.
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
added all of the pictures. And gave a practice talk based on this version. Now begins the process of cleanup and additions of citations.
getting there. Most everything but the motivation slide has been filled out. Lacks only pictures and Diagrams.
Skeletons of most every slide
made some changes
This commit was generated by cvs2svn to compensate for changes in r49, which included commits to RCS files with non-trunk default branches.
This commit was generated by cvs2svn to compensate for changes in r47, which included commits to RCS files with non-trunk default branches.
added the cos correlation function
got the GofR code working, and slimmed down the memory usage.
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
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 the new header dir
made a header directory, and fixed the Makefile to work with it
took out a reference file
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
moved the actual routine into a seperate source from the main. This allows the routine to be used in other applications.
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 makeRandom to set up a correct simulation
fixed a bug in getA( double the_A[3][3] );
added the getA( double the_A[3][3] ) routine to the Directional Atom Class, to facilitate easier RotMat aquisition
adding the routines to the proogram `
adding a program to make a lipid configuration with random dispersion of lipids.
fixed some bugs in the Makefile
removed xLate.cpp which was part of a seperate project
fixed a precision error in the calculation of the temperature. Also fixed the order that dump file are written.
removed a misc file
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 r20, 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 r16, 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 r12, 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.
nose hoover chains added
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Import Root
initial checkin
initial checkin
Standard project directories initialized by cvs2svn.