[FLASH-USERS] FLASH 4.0 released

Fri Sep 14 18:28:24 EDT 2012

The Flash Center is pleased to announce the release of the new version of 
the FLASH code, version 4.0. FLASH4 closely follows the architecture of 
FLASH3. The most important changes from FLASH3 are several new 
capabilities in both physics solvers and infrastructure. A major part of 
the new physics capabilities were introduced to support simulations of 
high-energy-density physics (HEDP). FLASH4 also includes four significant 
capabilities contributed by our external users.

The major new capabilities in FLASH4 that were not included in FLASH3
are (marked with ** are the external contributions, please see the
User's Guide for references and appropriate credits): 

* 3T capabilities in the split and unsplit Hydro solvers.
  There is support for non-Cartesian geometry, and
  the unsplit solver also supports stationary rigid bodies.

* Upwind biased constrained transport (CT) scheme in the unsplit
  staggered mesh MHD solver.

* Full corner transport upwind (CTU) algorithm in the unsplit
  hydro/MHD solver.

* Cylindrical geometry support in the unsplit
  staggered mesh MHD solver on UG and AMR. A couple of MHD
  simulation setups using cylindrical geometry. 

* Radiation diffusion.

* Conduction.

* Heat exchange.

* Multi-Temperature Multi-Material Multi-Table Eos.

* Opacities, ability to use hot and cold opacities.

* EnergyDeposition unit with laser ray tracing, with threading
  for performance.

* A new multipole solver.

* Ability to replicate mesh for multigroup diffusion or other
  similar applications.

* OpenMP threading of several important solvers at both
  coarse-grain (one block per thread) and fine-grain
  (threads within a block) levels.

* Ability to add particles during evolution.

* Limited support for Chombo as an alternative AMR mesh package.

* Several new HEDP simulation setups.

* Hybrid PIC.  **

* Barnes-Hut-Tree based gravity solver.  **

* Primordial chemistry.  **

* Sink particles.  **

The release also includes several new features and resolves a number
of bugs found in previous releases up to 4-beta.

Please see the attachment for a more detailed summary,
and for download instructions.

Development of the FLASH Code was funded by the DOE-supported
ASC/Alliance Center for Astrophysical Thermonuclear Flashes,
and continues to be funded by DOE NNSA and NSF.  
We acknowledge support received from Lawrence Livermore National
Laboratory and the University of Chicago.

All publications resulting from the use of the FLASH Code must
acknowledge the Flash Center for Computational Science.
Addition of the following text to the paper acknowledgments
will be sufficient.

         "The software used in this work was in part developed by the
         DOE- and NSF-supported Flash Center for Computational Science
         at the University of Chicago."
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The Flash Center is pleased to announce the release of the new
version of the FLASH code, version 4.0. FLASH4 closely follows 
the architecture of FLASH3. The most important changes from FLASH3 are
several new capabilities in both physics solvers and infrastructure.
A major part of the new physics capabilities were introduced to
support simulations of high-energy-density physics (HEDP).
FLASH4 also includes four significant capabilities contributed by our
external users. 

The major new capabilities in FLASH4 that were not included in FLASH3
are (the ones marked with ** are external contributions, please see the
User's Guide for references and appropriate credit for these capabilities): 

* 3T capabilities in the split and unsplit Hydro solvers.
  There is support for non-Cartesian geometry, and
  the unsplit solver also supports stationary rigid bodies.

* Upwind biased constrained transport (CT) scheme in the unsplit
  staggered mesh MHD solver.

* Full corner transport upwind (CTU) algorithm in the unsplit
  hydro/MHD solver.

* Cylindrical geometry support in the unsplit
  staggered mesh MHD solver on UG and AMR. A couple of MHD
  simulation setups using cylindrical geometry. 

* Radiation diffusion.

* Conduction.

* Heat exchange.

* Multi-Temperature Multi-Material Multi-Table Eos.

* Opacities, ability to use hot and cold opacities.

* EnergyDeposition unit with laser ray tracing, with threading
  for performance.

* A new multipole solver.

* Ability to replicate mesh for multigroup diffusion or other
  similar applications.

* OpenMP threading of several important solvers at both
  coarse-grain (one block per thread) and fine-grain
  (threads within a block) levels.

* Ability to add particles during evolution.

* Limited support for Chombo as an alternative AMR mesh package.

* Several new HEDP simulation setups.

* Hybrid PIC.  **

* Barnes-Hut-Tree based gravity solver.  **

* Primordial chemistry.  **

* Sink particles.  **

The release also includes several new features and resolves a number
of bugs found in previous releases up to 4-beta. The modifications
since the 4-beta release include 

* The HEDP capabilities of the code have been exercised more and are
  therefore more robust.

* Laser 3D in 2D ray tracing has been added. The code traces rays in a real 3D
  cylindrical domain using a computational 2D cylindrical domain and is based
  on a polygon approximation to the angular part. 

* New public interface Particles_addNew, which makes it possible to
  add particles to a simulation during evolution. (It has been
  possible to include multiple different types of particles in the
  same simulation since release FLASH 3.1.)

* Fixed reading of particles from checkpoint in -nofbs uniform grid. 

* All I/O implementations now support writing/reading 0
  particles and/or 0 blocks. 

* Support for particles and face variables in the same PnetCDF simulation.

* Optimization of Initializaton.
  Eliminated redundant calls to orrery at simulation startup.
  Ability to run the orrery in a reduced communicator in order to
  speed up FLASH initialization.  The original orrery can be restored
  by setting the parameter use_reduced_orrery to .false..  

* Ability to avoid unnecessary calls of guard cell filling.
  Ability to avoid a subsequent guard cell fill when a unit declares
  that it only reads mesh data.  It is off by default, but can be
  turned on by setting the parameter reduceGcellFills to .true..  

There are a few other changes from the beta release :

* Removed custom region code and Grid API routines. 

* PARAMESH4DEV has become the default Grid implementation.  

* PARAMESH4DEV does not need an amr_runtime_parameters file
  any more.  The corresponding parameters are now set in
  a parameter file, like other FLASH runtime parameters. 

The following features are provided on an EXPERIMENTAL basis.
They may only work in limited circumstances and/or have not
yet been tested to our satisfaction.

* New experimental configuration tool, "setup_alt".  
  Intended to be a compatible replacement for "setup" with
  a cleaner structure.

* Electron-Entropy Advection in Hydro for non-ideal Eos.  

* New cubic and quartic equation solvers have been added and
  are ready to be used. They return only real cubic and quartic roots.
  The routines are in the flashUtilites/general section and their
  names are: 'ut_cubicRealRoots' and 'ut_quarticRealRoots'. 

Known Limitations:

* The new multipole solver is missing the ability to treat
  a non-zero minimal radius for spherical geometries, and the
  ability to specify a point mass contribution to the potential.

* Usage of the Split diffusion solver in FLASH4 is only for debugging
  purposes and not generally recommended for usage.
  Split diffusion has not been tested with PARAMESH.

* Some configurations of hydrodynamic test problems with Chombo grid
  show worse than expected mass and total energy conservation.  Please
  see the Chombo section in Hydro chapter of the FLASH user guide for
  details.

* We have experienced the following abort when running
  IsentropicVortex problem with Chombo Grid:
  "MayDay: TreeIntVectSet.cpp:1995: Assertion `bxNumPts != 0' failed. !!!"
  We have been in contact with the Chombo team to resolve this
  issue.

* The Absoft compiler produces erroneous results with optimization in
  gr_markRefineDerefine routine. The results are fine without
  optimization. There may be other files with similar behavior, but
  this is the only one we are aware of.

* The PG compiler fails to compile source files which contain OpenMP
  parallel regions that reference threadprivate data.  This happens in
  the threaded versions of the Multipole solver and the within block
  threaded version of split hydro.  A workaround is to remove
  "default(none)" from the OpenMP parallel region.

* The unsplit hydro solver has an issue with preserving symmetry in 
  non-fixed block size mode in UG.

* The unsplit MHD solver doesn't support the mode "use_GravPotUpdate=.true."
  for 1D when self-gravity is utilized. The solver will still work if it
  is set to be .false. In this case the usual reconstruction schemes 
  will be used in computing the gravitational accelerations at the 
  predictor step (i.e., at the n+1/2 step) rather than calling the
  Poisson solver to compute them.

* The -index-reorder setup flag does not work in all the configurations.
  If you wish to use it please contact the FLASH team. 

The release is available at:

http://flash.uchicago.edu/site/flashcode/

A stripped-down version of FLASH3 that may be downloaded without a
license is also available at the same site. 
This version is essentially the FLASH framework without any
implementations.  The Flash Center is also providing support for
"add-ons" to the code. Please see the section on "What's new in this
release" in the first chapter of the User's Guide for details.
Also, a collection of stand-alone mini-apps are available for download
under the general FLASH license from the same site. 

Additionally, the FLASH testing software FlashTest, which became
available with the FLASH3 beta release, continues to be available for
download at:

http://flash.uchicago.edu/site/flashcode/

Many, but not all parts of FLASH4 are backwards-compatible with
FLASH2. There are no architectural changes from FLASH3 to FLASH4. The
Flash code group has written extensive documentation 
detailing how to make the transition from FLASH2 to FLASH3 as smooth
as possible.  The user should look to:

http://flash.uchicago.edu/site/flashcode/user_support/

The website also contains other documentation including
a User's Guide and a developer's section.  A new feature in FLASH3
documentation is the online description of the public interface
routines to various code units.

FLASH should be portable to most UNIX-like operating systems with a 
python interpreter, Fortran 90 compiler,  C compiler, and MPI library. 
It has been used in production mode, or undergone regular testing on            
the following platforms. 

-- IBM BlueGene/P and Power5

   compilers : FORTRAN90 : xlf90

               C         : xlc

-- CRAY-XT4 system

   compilers : FORTRAN90 : Portland Group Fortran 90

               C         : gcc

-- Linux

   compilers: FORTRAN90 : Portland Group Fortran 90

                          Lahey/Fujitsu Fortran 95 

                          Intel Fortran Compiler

                          gFortran (known to have trouble with versions
                              before 4.1.0)

                          NAGWare Fortran 95

                          Absoft 

              C         : gcc

                          Portland Group C Compiler

                          Intel C++ Compiler       

-- MAC-OSX

   compilers : FORTRAN90 : gFortran

               C         : gcc

FLASH uses libraries such as MPI for communication, Paramesh
and Chombo for AMR, HDF5 or PnetCDF for IO, and Hypre for linear
solvers. The source for Paramesh 4 is included in two variants in the 
distribution; the versions included in this release are
equivalent to Paramesh 4.0 and Paramesh 4.1, respectively.
Some earlier versions of HDF5, for example 1.6.1, have been known to
have issues with FLASH. We recommend using version 1.6.2 or higher of
the HDF5 library.

Two options are available to visualize FLASH output data. One is 
Fidlr, the IDL based visualization tool included in the
distribution. Fidlr requires IDL version 6.1 or higher to work correctly.
A more extensive option is VisIt, a visualization tool from LLNL,
available from

http://flash.uchicago.edu/site/flashcode/visit and
https://wci.llnl.gov/codes/visit

Visit supports FLASH data output Format.Information on using
Visit with FLASH is contained on the website above.

Development of the FLASH Code was funded by the DOE-supported
ASC/Alliance Center for Astrophysical Thermonuclear Flashes,
and continues to be funded by DOE NNSA and NSF.  
We acknowledge support received from Lawrence Livermore National
Laboratory and the University of Chicago.

All publications resulting from the use of the FLASH Code must
acknowledge the Flash Center for Computational Science.
  Addition of the following text to the paper acknowledgments
will be sufficient.

         "The software used in this work was in part developed by the
         DOE- and NSF-supported Flash Center for Computational Science
         at the University of Chicago."