Added neighbor list module that auto expands...
Added simulation struct...
Changes...
Changes they are a comming....
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.
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....
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.
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
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
added simError.h to the makefile
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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
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
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 r10, which included commits to RCS files with non-trunk default branches.