# [FLASH-USERS] FLASH 4.5 Release

Klaus Weide klaus at flash.uchicago.edu
Fri Dec 8 20:48:41 EST 2017

Dear Users,

The Flash Center Code Group announces the release of an updated version of
the FLASH code, version 4.5.

This update has a moderate amount of changes from FLASH 4.5, and a
number of new features. We are also announcing ancillary software
(FLASH Interface, a GUI for configuring FLASH), as well a standalone
Python code (PRaLine, a tool for linear reconstruction of magnetic
fields from proton radiographs); see the Release Notes for more
information.

The release is available as a tarball FLASH4.5.tar.gz, in the usual
location on the Flash Center Web site at http://flash.uchicago.edu/.
The updated RELEASE-NOTES file is attached.

Best,
-- the Flash Center Code Group
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!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!  New in FLASH 4.5 (since FLASH 4.4) - December 2017  !!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

* New implementation for synthetic Thomson scattering simulated diagnostic.

* A new 1D simulation of a 2-temperature Supernova evolution using the flux-
limiter-aware hydro treatment of radiation, and related code changes.

* A new timestep limiter, which ensures that a given list
of variables remains positive-definite during hydrodynamic advection.
This can be used as an alternative to lowering the Hydro unit's CFL
runtime parameter, and has been shown useful for 3T simulations in
particular, where non-conservative equations are considered. This will
obviate negative temperature errors when using 3T Hydro and MHD.
See the Driver section of User's Guide for more information.

* Expanded the Sedov simulation to be initialized from a quasi-
analytical profile, and added diagnostic variables to keep
track of various simulation error measures.

* New flux limiter "vanLeeer1.5" for unsplit Hydro and MHD.

* Fixed an issue in which PARAMESH block distribution failed to settle down
because of message delay, reported for some machines. This is done
by inserting sleep(1.) calls in extreme cases.

* Implement saving of laser irradiation (to "lase" variable) for 2DCyl3D ray
tracing, too. Previously was 3D only.

* Ray tracing fixes: avoid stalls; improved randomness; correct
an error in ray weights and beam power in 2D cylindrical rays with
statistical1D grids.

* Unsplit Hydro fixes for, rarely used, 2D POLAR geometry.

* FLASH now works correctly with HDF5 versions 1.10.x.

* FLASH now assumes by default that it is being compiled against MPI
version 2 or higher. If you must compile against an MPI-1 library,
define the preprocessor symbol FLASH_MPI1 for your Fortran compiler.

* More conservative defaults in header file FortranLangFeatures.fh.

* We have included detailed instructions that outline how to easily
install FLASH on Windows, Mac OS, and Linux distributions, using Docker.
See the "Quick Start" section in the User's Guide.

OTHER:

* FLASH Interface is a new graphical interface (GUI) for managing parameter files.
and is now available for download. The code was developed by Christopher Walker
(cnwalker at uchicago.edu). It currently supports:
- Configuring and editing existing flash.par files;
- Generating new flash.par files by choosing among the full set of
possible parameters;
- Filtering the full set of possible FLASH parameters (found in
setup_params) via categories;
- Searching for FLASH params by name, and viewing full descriptions of
each parameter's role and function.
The source code, along with download and build instructions can be found at
https://github.com/cnwalker/FLASH-Interface
Compiled executables for a number of operating systems can be found at
http://flash.uchicago.edu/site/flashcode/FLASH-Interface/

* The PRaLine code for Proton Radiography Linear reconstruction is now included
with the FLASH code tarball and is available for download at
https://github.com/flash-center/PRaLine
This standalone Python code was originally developed for the magnetic field
reconstruction method using proton radiography, discussed
in Graziani et al. 2017 (in press), https://arxiv.org/abs/1603.08617
Alemayehu Solomon Bogale (alemsolobog at uchicago.edu) restructured the code and

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!  New in FLASH 4.4 (since FLASH 4.3) - October 2016  !!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

* The default Hydro implementation has changed from split PPM to
unsplit Hydro. The setup shortcuts +uhd, +unsplitHydro, +usm,
+uhd3t, etc. should all work as before (although +uhd or
+unsplitHydro can now be omitted). A new shortcut +splitHydro
can be used to request a split Hydro implementation.
Simulations that previously did not specify a Hydro implementation
will now need to use the new shortcut +splitHydro to reproduce
previous behavior.

* The default Riemann solver of unsplit Hydro implementations was
changed from "Roe" to "HLLC".

* Updated values of many physical constants to 2014 CODATA values.
This may cause differences from previously obtained results. The
previous values of constants provided by the PhysicalConstants unit
can be restored by replacing the file PhysicalCosntants_init.F90
with an older version; the version from FLASH4.3 is included as
PhysicalConstants_init.F90.flash43. This should only be done to
reproduce previous simulation results to bit accuracy.

* An improved Newton-Raphson search in the 3T Multi-type Eos
implemention (MTMMMT, including Eos based on IONMIX tables) can
prevent some cases of convergence failure by bounding the search.
This implementation follows original improvements made to the
Helmholtz Eos implementation by Dean Townsley.

* The optimized code variant ("orrery avoidance") implemented in our
adapted Paramesh4dev code is now always enabled by default when
Paramesh4dev is used, not just when +pm4dev is explicitly specified
in setup.

* Added new Poisson solvers (Martin-Cartwright Geometric Multigrid [1]
and BiPCGStab [2], which uses multigrid as preconditioner).
Combinations of homogeneous Dirichlet, Neumann, and periodic boundary
conditions are supported (although not yet "isolated" boundaries for
self-gravity).
[1] D. Martin, K. Cartwright. Technical Report No. UCB/ERL M96/66 1996.
[2] H. Van Der Vorst. SIAM J. Sci. and Stat. Comput. 1992; 13:2, pp631???644.

* Added the IncompNS physics unit, which provides a solver for
incompressible flow problems on rectangular domains. Multistep and
Runge-Kutta explicit projection schemes are used for time integration.
These methods are described in [3]-[5]. Implementations on staggered
grid arrangement for both uniform grid (UG) and adaptive mesh
refinement (AMR) are provided. The new Poisson solvers are employed
for AMR cases, whereas the homogeneous trigonometric solver + PFFT can
be used in UG. Typical velocity boundary conditions for this problem
are implemented.
[3] S. Armfield, R. Street. Int. J. Numer. Meth. Fluids 2002; 38, pp255-282.
[4] J. Yang, E. Balaras. J. Comput. Phys. 2006; 215:1, pp12-40.
[5] M. Vanella, P. Rabenold, E. Balaras. J. Comput. Phys. 2010; 229:18, pp6427-6449.

* The ProtonImaging diagnostics code has been improved. Time resolved
proton imaging is now possible, where protons are traced through
the domain during several time steps. The original version (tracing
of protons during one time step with fixed domain) is still available.

* The code for Radiation-Fluxlimiter-Aware Hydro has been updated.
Smoothing of the flux-limiter function within the enhanced Hydro
implementation has been implemented and  has been shown effective
in increasing stability in 1D simulations.

* Tweaks in handling some of the geometric terms in curvilinear
coordinates in unsplit Hydro and MHD.

* New Opacity implementations: BremsstrahlungAndThomson and OPAL.
These are for gray opacities.

* In addition to the new FLASH release, the publicly available Python
module opacplot2 has received significant development (credit to
JT Laune). It can assist in handling EoS/opacity tables, and
includes command line tools to convert various table formats to
IONMIX and to compare between different tables. More information
can be found in the Flash Center's GitHub repository at <URL:
https://github.com/flash-center/opacplot2>.

* Some auxiliary units: PlasmaState. See online documentation.

* Some new (or changed) API routines (see online API documentation):
Grid_smoothVar, Grid_subcellGeometry

* The code includes stubs for several new code units for which
implementations may be added in future releases
(diagnostics/ProtonEmission, diagnostics/ThomsonScattering)

* Fixes for various errors, reported and unreported

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!  New in FLASH 4.3 (since FLASH 4.2.2) - July 2015  !!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

* Flux-limited-diffusion for radiation (implemented in
RadTransMain/MGD) is now available for astrophysical
problem setups:

+ MatRad3 (matter+rad [2T] stored in three components)
implementations for several Eos types: Gamma, Multigamma,
and (experimentally) Helmholtz/SpeciesBased.
+ Implemented additional terms in FLD Rad-Hydro equations
to handle streaming and transition-to-streaming regimes
better - including radiation pressure.
This is currently available as a variant of the unsplit Hydro
solver code, under HydroMain/unsplit_rad .
We call this RADFLAH - Radiation Flux-Limiter Aware Hydro.
Setup with shortcut +uhd3tR instead of +uhd3t .
This has had limited testing, mostly in 1D spherical geometry.
+ New test setups under Simulation/SimulationMain/radflaHD:
+ Various fixes in Eos implementations.
+ New "outstream" diffusion solver boundary condition for
streaming limit. (currently 1D spherical only)
+ Added Levermore-Pomraning flux limiter.
+ More flexible setup combinations are now easily possible -
can combine, e.g., species declared on setup command line
with SPECIES in Config files and initialized with
Simulation_initSpecies, by setup with ManualSpeciesDirectives=True .
+ Created an "Immediate" HeatExchange implementation.
+ EXPERIMENTAL: More accurate implementation of flux limiting
(and evaluation of diffusion coeffs): apply limiter to
face values, not cell centered values.
+ EXPERIMENTAL: ExpRelax variant of RadTrans diffusion solver,
implements the algorithm described in Gittings et al (2008)
for the RAGE code, good for handling strong matter-radiation
coupling; for one group (grey) only.
+ EXPERIMENTAL: Unified variant of RadTrans diffusion solver,
for handling several coupled scalar equations with HYPRE.
+ EXPERIMENTAL: More accurate implementation of flux limiting
(and evaluation of diffusion coeffs): apply limiter to
face values, not cell centered values.

* New unit ProtonImaging: The new unit is a simulated
diagnostic of the Proton Radiography used in HEDP experiments.

* Gravity can now be used in 3T simulations.

* Laser Energy Deposition:
New ray tracing options added based on cubic interpolation techniques.
Two variants: 1) Piecewise Parabolic Ray Tracing (PPRT) and 2) Runge
Kutta (RK) ray tracing.

* Introduction of new numerical tool units: 1) Interpolate: currently
contains the routines to set up and perform cubic interpolations
on rectangular 1D,2D,3D grids, 2) Roots: (will) contain all routines
that solve f(x)=0 (currently contains quadratic, cubic and quartic
polynomial root solvers, 3) Runge Kutta: sets up and performs Runge
Kutta integration of arbitrary functions (passed as arguments).

* Unsplit Hydro/MHD: Local CFL factor using CFL_VAR.
(Declare a "VARIABLE cfl" and initialize it appropriately.)

* Unsplit Hydro/MHD: Significant reorganization.
+ reorganized definition and use of scratch data. Memory savings.
+ use hy_memAllocScratch and friends.
+ hy_fullRiemannStateArrays (~ instead of FLASH_UHD_NEED_SCRATCHVARS)
+ New runtime parameter hy_fullSpecMsFluxHandling, default TRUE.
resulting in flux-corrected handling for species and
mass scalars, including USM.
+ Use shockLowerCFL instead of shockDetect runtime parameter.
+ Revived EOSforRiemann option.
+ More accurate handling of geometric effects close to the origin
in 1D spherical geometry.

From External Contributors:

* Sink particle update by Christoph Federrath.
Major changes: removed call to fill guardcell
in Particles_sinkCreateAccrete.F90. Merged
Particles_sinkAccelGasOnSinks.F90 and
Particles_sinkAccelSinksOnGas.F90 into a new routine called
Particles_sinkAccelGasOnSinksAndSinksOnGas.F90, which computes sinks
-> gas and gas -> sinks gravitational interactions in one go/loop
for performance enhancement. Added support for off-domain sink
particles, i.e., if the user switches on the runtime parameter
sink_offDomainSupport, then sink particles remain active when they
cross a domain boundary in case of outflow boundary conditions,
i.e., they are not deleted. This can be useful for some special
applications. The gravity between sinks and between gas and sinks
remains active and I/O of sink particles outside the domain also
remains active.

* Updates to Barnes-Hut-Tree and related code from Richard Wunsch.
TreeCol dummy unit has been replace by TreeRay, which includes
an implementation.

* Placeholders fo UserDefined Gravity and Simulation_freeUserArrays stub
(John ZuHone)

* Updates for using spherical with split (PPM) hydro solver.
(Rodrigo Fernandez - not tested by us)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!  New in FLASH 4.2.2 (since the FLASH 4.2.1 patch)  !!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

* Eliminated unnecessary reconstruction calls for some guard cells
in unsplit Hydro and staggered mesh MHD. This affects all unsplit
Hydro and MHD calls and can result in a significant speedup,
most noticeable for 3D PPM Hydro with small block sizes.

* New implementations for Lee & More (Phys. Fluids 1984, 27, 1273)
electron conductivity and heat exchange, contributed by Chris Orban.
These implementations can be used instead of their equivalent
SpitzerHighZ and Spitzer options and should return more accurate
results at low temperatures in 3T simulations.

* Changes in MagneticResistivity unit: uses calls that pass the
full state. Resistive fluxes are now calculated by central
differencing. The resistive coefficient is no longer upwinded.
Support for cylindrical geometry added to unsplit Hydro
implementation.

* Fixed bug where abundances could become negative for 3T setups.

* Updates to sink particle code contributed by C. Federrath.

* Improved time stepping for unsplit Hydro (or MHD) in connection
with self-gravity and massive (including sink) particles.
In this as in previous releases, the unsplit Hydro invocation
calls the gravity solver at the end to apply gravitational
accelerations in a time-centered manner; now, the code
avoids updating the state of the global "gpot" variable
in the course of this gravity solve, if such updating
might interfere with the assumptions of Particles_advance.
Also, the unsplit Driver_evolveFlash routine now avoids
calling the gravity solver again at the end of each time
step if the global "gpot" has already been updated earlier
in the time step.
New optional arguments have been added to the
Gravity_potentialListOfBlocks and Gravity_accelOneRow
API to support the improved behavior.

* Fixed allocated size of yCenter(:) in unsplit Hydro code for
non-Cartesian coordinates.
Fixed allocated size of xcent(:) in Noh_unitTest.

* Avoid access to invalid cells when BDRY_VAR is defined.
Use stencil large enough for computing velocity divergence
if use_hybridOrder is set and for computing flattening
coefficients is use_flattening is set. All these changes
can affect unsplit Hydro and staggered mesh MHD.

* Improvements to WENO reconstruction in unsplit Hydro and staggered
mesh MHD. Introduced new runtime parameter, wenoMethod, that takes
wenoMethod = "weno5" (default) or "wenoz".  The WENOZ method is a new
reconstruction algorithm based on R. Borges et al., JCP, 227 (2008)
3101-3211 and Don & Borges, JCP, 250 (2013) 347-372. Moreover, WENO
now works with the usual 4 layers of guard cells and does not require
increasing NGUARD to 6.

* Fixed beavior of staggered mesh MHD with the E_upwind flag enabled.
Upwinding for the electric field is now always based on the previous
time cell-centered state and simulation restarts work
transparently.

* Globally reduce CFL factors from different MPI tasks before
computing the time step for unsplit Hydro and staggered mesh MHD.
This may affect simulations where one of the following applies:
(a) RiemannSolver = "HYBRID", (b) use_hybridOrder = .TRUE.;
time steps will now be independent of the number of tasks.

* Some array size optimizations for saved fluxes in unsplit Hydro
(reduced memory footprint).

* Avoid problems with large (double precision) constants in
Config files. Now the forms 1.d99 and 1.e99 can both be used
for runtime parameter default values with large exponents.

* Eliminated some unnecessary "include" calls to speed up recompilations.
Tweaks to speed up recompilation on MacOS-like file systems.

* Documentation fixes and updates in various source files.
Eliminated unused variables in some files and similar cleanup.

* Protect against obscure failure when zmin = zmax in 2.5D simulations.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!  New in FLASH 4.2.1 (since the FLASH 4.2 release)  !!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

* Fix of Gravity problem in unsplit Hydro / MHD:
Do not call Eos in auxiliary invocation of guard cell filling.

* Fix of problems in WENO reconstruction in unsplit Hydro / MHD.

* Minor changes to prevent compilation failures in some
environments.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!  New in FLASH 4.2  (since the FLASH 4.0.1 patch)   !!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Added CCSN physics from Sean Couch:
* Complete nuclear EOS routines (physics/Eos/EosMain/Nuclear)
* Local neutrino heating/cooling (physics/sourceTerms/Heat/HeatMain/Neutrino)
* Multidimensional Core-Collapse supernova test problem
(Simulation/SimulationMain/CCSN)

Contributed by Dean Townsley, with code developed by Aaron Jackson and
Alan Calder:
* physics/sourceTerms/Flame unit
* physics/sourceTerms/Turb unit

* Updates to Barnes Hut tree gravity solver contributed by Richard Wunsch,
developed in collaboration with Frantisek Dinnbier (responsible for periodic
and mixed boundary conditions) and Stefanie Walch.

Contributed by Christoph Federrath:
* Significant updates for Sink Particles
* New 'FromFile' implementation of Stir unit, now sitting beside the older
'Generate' implementation

Two new optimizations of the unsplit solvers, Hydro_Unsplit and MHD_StaggeredMesh,
in source/physics/Hydro/HydroMain/unsplit. These new optimized unsplit solvers
are the default implementations of the unsplit hydrodynamics and MHD solvers
in FLASH 4.2. The old version of the unsplit solvers are now found in
source/phycis/Hydro/HydroMain/unsplit_old.

Capabilities for 3T magnetohydrodynamics, for the first time.

New magnetic resistivity implementation, Spitzer HighZ, for HEDP problems.
Extended support for resistivity in cylindrical geometry in the unsplit solver.

Laser - Async communication (experimental), some reorganization.
New feature - can run EnergyDeposition once every n time steps.

Updates to HYPRE solver coupling - avoid communicator leak with 2.0.9b.
Some changes in MGD code for increased correctness.

Threading for unsplit MHD is now available. Both strategies are supported by the new code.

New, improved multipole Poisson solver, implementing the algorithmic
refinements described in Couch, S.M., Graziani, C., and Flocke, N., ApJ 778,
181 (2013), http://dx.doi.org/10.1088/0004-637X/778/2/181,
http://arxiv.org/abs/1307.3135.  Specifically:
* Potential calculated at cell faces and averaged to produce cell-centered
values, rather than directly at cell centers, so as to eliminate a convergence
failure due to cell self-gravity
* Expansion center located at "square-density-weighted center-of-mass", to
minimize angular power at high multipoles

(smaller changes:)
* The code includes stubs for several additional code units for which
we do not include implementations in this release (TreeCol, NSE,
SolidMechanics, IncompNS, ImBound). Implementations may be available
separately from their authors, and / or may be included in a future
FLASH release.
* Hydro codes avoid unnecessary Eos calls on guard cells, this uses skipSrl
flag to Eos_guardCells routine.
* Improved HLLD solver on MHD degeneracy.
* PARAMESH's facevariable handling for divergence-free magnetic field
enforcement now uses gr_pmrpForceConsistency=.true. and
gr_pmrpDivergenceFree=.true. by default.
* New Grid_bcApplyToRegionMixedGds API allows users to implement boundary
conditions that take several types of solution variables (CENTER, FACE)
into account.

Caveats, Limitations
--------------------

Simulations results obtained with this version of FLASH should not be
expected to match exactly with results from previous versions.
Differences can be due to algorithmic changes in solvers, in particular
the unsplit Hydro and MHD implementations. Results from simulations that
use the HYPRE library for Diffusion and/or RadTrans operators may be
slightly different because we invoke HYPRE with slightly different
parameters (based on suggestions from HYPRE authors).
Another source of unexpected differences is a change in how we compute
block boundary coordinates when an AMR Grid starts with more than one
root block (i.e. any of NBlockX,NBlockY,NBlockZ > 1), leading to
a difference in rounding errors under some scenarios.

Several code units have provisions for being threaded (OpenMP directives),
but these have not been recently tested and may require some adaptation.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!  Fixes to FLASH 4.0 included in FLASH 4.0.1 patch  !!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

*** HYPRE Fix ***

* A non-symmetric matrix could be generated by our AMR HYPRE adapter
in certain situations, leading to failure to converge in PCG solver.
The constructed matrix was not symmetric, because there was a
mismatch between the order in which graph edges where created and
given values for some cells.  This only affected coarse cells that
have finer neighboring cells across more than one cell face.

Only changed file: source/Grid/GridSolvers/HYPRE/paramesh/gr_hypreSetupGrid.F90
r18739

*** PFFT Fixes ***

* PFFT fixes for unusual pencil grid configurations.
We have found errors when the global number of grid points along a
particular dimension is not a multiple of the number of MPI ranks in
the PFFT MPI cartesian communicator in the same dimension.  This
situation did not always cause problems, but errors could be
introduced in particular when using PFFT in combination with
Multigrid ("Hybrid Multigrid") as a Poisson solver and when
there was
* a small number of Paramesh blocks per pencil process, and/or
* a prime number of pencil processes which own Paramesh blocks at
the refinement level of the PFFT grid.
Fixes apply to DirectSolver and HomBcTrigSolver.
Bug reported by: Mateusz Ruszkowski 2013-01-21

* Only MPI ranks which are part of the pencil process grid should
access certain arrays.  In the previous implementation there are
accesses to unallocated arrays by the MPI ranks which are not part
of the PFFT process grid.  The patch avoids undefined behavior.

* Use the correct communicator, pfft_comm(IAXIS) instead of gr_meshComm.
Avoids possible hang with DirectSolver.

* Change in gr_pfftInitMetaData.F90 addresses a problem with
DirectSolver/SecondOrder_FD3p (not normally used). Added some lines
of diagnostic output.

r18725,r18735,r18736,r18949,r18970,r18972

NOTE: For Hybrid Multigrid configurations, we now recommend using
the HomBcTrigSolver variant of PFFT. To do this, eliminate explict
references to "DirectSolver" and use "PfftSolver=HomBcTrigSolver"
on the setup command line.

*** Barnes-Hut Tree Solver Fixes ***
* Several bug fixes of the BHTree solver. The bugs could lead to
code crashes in case of non-cubic computational domains.
Corrected some size calculations.
Grid_solvePoisson now uses the poisfact argument.
Generalized BHTree code to not assume in some places that the
source variable is DENS_VAR.
Contributed by: Richard Wunsch, John ZuHone
r17970,r18021,r18825,r19041,r19097

*** Active Particles Time Advancement Fix ***
* Fixed a long-standing bug in active particle time advancement, where
the old timestep was being used to advance the particle positions
instead of the current one. This only affects active particles with
mass that are being advanced using the leapfrog time advancement
routine (without cosmology).
Contributed by: John ZuHone
Only changed file: ../ParticlesMain/active/massive/Leapfrog/pt_advanceLeapfrog.F90
r18678

*** Misc Fixes related to Hydro / MHD ***

* Fixes in explicit viscosity for split (PPM) Hydro.
Bug reported by: Elke Roediger 2012-11-07
Only changed file: source/physics/Diffuse/DiffuseFluxBased/Diffuse_visc.F90
r18212

* Indexing error in guard cell filling for face variables (3D Staggered Mesh MHD).
Bug reported by: Mateusz Ruszkowski 2012-11-07
Only changed file: .../Paramesh4dev/PM4_package/source/amr_1blk_guardcell_srl.F90
r18220

* Modified current calculation when adding resistive fluxes for Staggered Mesh MHD.
Only changed file: .../unsplit/MHD_StaggeredMesh/hy_uhd_addResistiveFluxes.F90
r18170

*** Misc Infrastructure Fixes ***

* Fix for inexact block boundaries.
When runtime parameters nBlockX, nBlockY, or nBlockZ are different
from 1, rightmost block boundaries are computed in a way that may
make their values differ slightly from rightmost domain
boundaries. The preferred change (to be included in a future FLASH
release) is to change the way block boundaries are computed, but
that can introduce unexpected differences in checkpoint files; here
we just modify some code to use comparison with a tolerance, instead
of testing for exact equality, when detecting boundaries.
r18053

* Avoid accessing optional logical dummy arguments when they are not
present.  One must not assume short-circuit evaluation of logical
expressions in Fortran.
Only changed file: source/Grid/GridMain/paramesh/Grid_getListOfBlocks.F90
r18896

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!  Original RELEASE-NOTES file for FLASH 4.0 follows  !!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
The Flash Center is pleased to announce the release of the next
version of the FLASH code, version 4.0. FLASH 4.0 closely follows
the architecture of FLASH3. The major 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 major capabilities contributed by our
external users.

The major new capabalities in FLASH4 that were not included in FLASH 3
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 \item Cylindrical geometry support in the unsplit
staggered mesh MHD solver on UG and AMR. A couple of MHD
simulation setups using cylindrical geometry.

* Conduction

* Heat exchange.

* Multi-Temperature Multi-Material Multi-Table Eos

* Opacities, ability to use hot and cold opacities.

* The laser drive 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 many 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 Initialization.
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 in FLASH 4.0:

* 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 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

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.  An important feature
of FLASH 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-supported Flash Center for Computational Science
at the University of Chicago."

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