CHANGES

CURRENT RELEASE: 4.3 (June 2018)
**********************************************************
*           CHANGES from 4.2
**********************************************************

Major Changes / Addition:
=========================

- The Grid structure has been changed from an array of structures to a structure
  of arrays. 
  All arrays must be changed as
  
  grid[IDIR].x    must be chnaged to   grid->x[IDIR]

  and so on.
  Areas and volumes are now fully three-dimensional arrays containing the
  full expression rather than just the reduced one
  (i.e., Ar = R*dphi*dz and not just R).
- Log files are now always dumped to screen (in serial mode) or to different
  log files (in parallel, one per processor). It is possible to write log files
  into a separate directory using "log_dir" in your pluto.ini;
  In addition, print1 statement has been removed (only print is used).
- The "Frequently Used Options" (meaning the additional switches at the end of
  definitions.h) have been completely removed and reabsorbed into the more
  general "User-defined Constants", see the user-guide.
  Default values are used when not explicitly set.
- Added Particles modules (CR + LP), see documentation.
- Added forced turbulence module (see doc).
- Added RK_LEGENDRE option to integrate parabolic terms.
- The Asynchrounous I/O option has been removed.
- Python setup is compatible with Python 2.7.x and 3.x
- Magnetic field variable names have been changed 
  from "bx1", "bx2", "bx3" to "Bx1", "Bx2", "Bx3"
- In the userdef_output.c, ChangeDumpVar() --> ChangeOutputVar()
                           SetDumpVar()    --> SetOutputVar()
- A new function, InitDomain(), has been introduced to assign initial conditions
  in a more global way. This does *NOT* replace the old Init() function. 
- A more efficient InputData() module to assign initial conditions from
  external binary files;
- Added different pseudo random number generators (PRNG);
- The --show-dec options has been removed (now every processor
  log print its own domain);
- IDL can now read user-defined variables (see documentation);
- Time_Step structure name changed into timeStep (respect naming conventions!);



Bug Fixes:
==========

- Fixed a bug when writing VTK file header using mpich
- Fixed a memory problem for large VTK dataset.
- Changed size of (restart): this will make restarting from 
  PLUTO 4.2 (and previous) data files impossible (sorry about that).
- Binary data files (.dbl, .flt and .vtk) are deleted before writing 
  in parallel mode to avoid partial writing over pre-existing larger files.
- Added and changed I/O routine names contained in bin_io.c
  (e.g. OpenBinaryFile()   --> FileOpen(),
        CloseBinaryFile()  --> FileClose(),
        WriteBinaryArray() --> FileWriteData(), etc..)
- Tagcells & RBox structures: 
  changed names from ib --> ibeg, ie --> iend, and so forth

**********************************************************
*           CHANGES from 4.1
**********************************************************

Version 4.2 contains some small addition and a whole lot of bug fixes.

Structural Changes:
===================

- User defined constants have been removed from the python script and
  can now be added manually by editing a dedicated section in definitions.h.

- The old array indexing style using a two-letter index (e.g. DN, PR, VX,...)
  is no longer supported. Use RHO, PRS, VX1, ... instead.

- The macro STS_nu has been changed to STS_NU, it has been removed from the
  python script and it can be inserted manually in the user-defined
  constant section of definitions.h

- ENTROPY_SWITCH does not take the value YES/NO anymore but it has more
  options, see the documentation.

- The Shearing Box module has been changed:
  o It works with FARGO+IDEAL EoS.
  o The functions BodyForceVector() and BodyForcePotential() are slightly
    different from before (check Test_Problems/MHD/Shearing_Box/init.c).
  o The shear parameter and orbital frequency are no longer assigned by the
    global variables sb_q and qb_Omega but using the macros SB_Q and SB_OMEGA
    which, by default, take the values 1.5 and 1.0.
    
- Userguide has been re-organized.

- Added the MeanMolecularWeight() function and gas composition, see userguide.

- The global variable g_stepNumber now works with PLUTO-Chombo.

- Chombo HDF5 files can be written by specifying the output interval in
  clock time (hours/minutes/seconds) as well as the output directory. 

- Added GLM_ALPHA to the list of user-defined constants;

- Runtime structure renamed to Restart;

- Input structure renamed to Runtime  and setup.c renamed to runtime_setup.c;

- Suppressed / replaced constant names:
  
  o ARTIFICIAL_VISCOSITY --> ARTIFICIAL_VISC (see appendix in the userguide) 
  o CHOMBO_EN_SWITCH      (suppressed, replaced by the new ENTROPY_SWITCH)
  o CH_TRACING_REF_STATE --> CHTR_REF_STATE
  o DN, PR  are no longer supported --> use RHO and PRS instead
  o EGLM                 --> GLM_EXTENDED
  o INTERPOLATION        --> RECONSTRUCTION
  o MHD_FORMULATION      --> DIVB_CONTROL
  o RESISTIVE_MHD        --> RESISTIVITY
  o STS_nu               --> STS_NU
  o USE_FOUR_VELOCITY    --> RECONSTRUCT_4VEL (works for both RHD and RMHD)

- RHD primitive variables always contain the 3 velocity although 4-vel can
  be reconstructed by enabling the RECONSTRUCT_4VEL switch.

- Src/Cooling/Tab changed to  Src/Cooling/TABULATED

- The HD/ and MHD/ modules share the same RightHandSide() function inside
  MHD/rhs.c. Likewise, source terms have been separately implemented in
  MHD/rhs_source.c

- Runtime information can now be accessed from anywhere in the code
  using the RuntimeGet() function which gives access to a copy of
  the runtime structure, e.g., RuntimeGet()->cfl.

- RMHD module allows faster computation of eigenvalues using approximate
  expressions (RMHD_FAST_EIGENVALUES).

- Added the macro RECONSTRUCT_4VEL (YES/NO) which allows to reconstruct
  the 4-velocity rather than the 3-velocity. It works for for RHD and RMHD.

Fixed Bugs:
===========

- IDL pload function with var=".." now works also for multiple files;
- Fixed a number of minor bugs in H2_COOL module and improved
  CompEquil() function;
- PPM method works correctly for non-uniform grid in any coordinate system;
- FlagShock now called when using chombo (MULTID shock flattening and
  ENTROPY_SWITCH)
- PLUTO-Chombo now writes plotfiles correctly when restarting from a
  checkpoint file (changed AMR.cpp in library) 
- GLM complained with Background field splitting: print removed;
- Resistivity + background can be used (removed QUIT statement from
  MHD/bckgrnd_file.c);
- PathCTU.1D has been removed and all 1D AMR computations are done
  with PatchCTU.cpp or PatchEuler.cpp;
- VTK files can now be visualized with PARAVIEW;
- PVTE_LAW now uses cubic spline interpolation rather than linear 
  along the temperature axis;
- Chombo "LevelPluto::step: alpha < 0" crash has been partially solved.
- Tabulated cooling takes into account the mean molecular weight.





**********************************************************
*           CHANGES from 4.0
**********************************************************

Version 4.1 contains several bug fixes as well several additions:

Structural Changes:
==================

- Changed naming convention for ions in cooling modules, e.g. FNEUT -> X_HI.
- changed convention for global grid indices:
  (*g_i) -> g_i, (*g_j) -> g_j, (*g_k) -> g_k.
- Diffusion coefficient name of functions:
  o   --> Resistive_eta()
  o   --> TC_kappa()
  o   --> Viscous_nu()
- some global variables have been replaced by constants:
  o UNIT_DENSITY, UNIT_LENGTH, UNIT_VELOCITY

Fixed Bugs:
==========

- compilation error with ASYNC_IO
- Vector components in VTK + spherical coordinates
- Shearing box, flux symmetrization
- Background field bugs

Additions:
==========

- Added a general purpose PVTE_LAW equation of state

- Background field splitting has been extended to more Riemann solvers 
  as well as to GLM
  
- Added a new OSPRE limiter

- Added the "little" or "big" endian keyword to InputData()

- Additional features in I/O and visualization:
  o set output directory name from pluto.ini
  o VTK_LOAD procedure for IDL
  o VTK format now support time information 
  o writing of .vtk and .flt in cgs units 
  o New gnuplot scripts
  o HDF5 support writing of supplementary variables
  o pyPLUTO capabilities extended to VTK and Chombo HDF5 
  o enabled writing of .flt and .vtk files in CGS units
 
- Completely re-designed treatment of parabolic (diffusion) terms and added
  more support for entropy 
  o improved treatment of resistivity in constrained-transport 
    MHD. Now it also works with STS 
  o Entropy equation now compatible with viscosity, TC and resistivity and also
    works with STS

- New: math tools: small internal library of numerical/mathematical routines for 
  various purposes:
  o Numerical quadrature of simple functions
  o ODE solvers
  o Root finders
  o Lookup table routines
  o Miscellaneous

- Python setup:
  o added user-def constants in definitions.h
  o automatic python update with ./python setup --auto-update
  o pluto.ini allows commend to be added (starting with #)

- New H2_COOL cooling module including molecular and atomic cooling

- AMR: 
  o Added support for polar and spherical coordinates with Chombo.
    (Chombo 3.2 required)
  

**********************************************************
*           CHANGES from 3.1.1
**********************************************************

   PLUTO 4.0 contains several major improvements over previous releases:

1. Structural Changes

     * The naming syntax of the code has been slightly changed in order to
       make it more standard and to avoid confusion between MACROS and
       Functions. While macro names conserve the traditional
       "ALL_UPPER_CASE" syntax, function names have been replaced by using
       "CamelCase" letter, where compound words are joined without spaces
       or underscore and have initial capital letter, e.g. MAKE_GEOMETRY()
       –> MakeGeometry(). See section 0.6 of the User's Guide.

     * Doxygen is now used as standard documentation system for PLUTO and,
       although far from being complete, it is meant to replace the old
       Developer's guide. Please refer to Doc/Doxygen/html/index.hml.

     * ArrayLib is no longer necessary and has been replaced by a compact,
       largely debugged subset of functions directly incorporated into the
       code. Parallel executables are compiled by choosing an appropriate
       makefile from the Config/ directory. Several bugs have been fixed
       in porting PLUTO to several thousand processor architectures.

     * PLUTO 4 is now compatible with Chombo 3.1 for AMR applications.

     * Staggered arrays now contain one more point in the direction of
       staggering and span from -1...NX_TOT-1 in the staggered dir.

     * Limiter names have been changed to upper case:
          + minmod_lim –> MINMOD_LIM
          + vanleer_lin –> VANLEER_LIM

     * Makefile build has changed to a more flexible structure.

2. I/O Changes

     * VTK files are now correctly written using node-centered rather than
       cell-centered coordinates. This will produce more accurate
       visualization with VisIt or Paraview.

     * Asynchrounous binary I/O of single-precision files.

     * HDF5 output format is now available also with the static grid
       version of the code using single- or double-precision datafiles
       (*.dbl.h5, *flt.h5). Double precision HDF5 can also be used for
       restart.

     * Output interval may be given in wallclock time.

3. AMR

     * RK2 time-stepping is now supported with Chombo;
     * Bug fix: support for entropy switch;
     * Bug fix: Internal boundary + AMR.

4. (Major) Physics Addition

     * New FARGO-MHD module is available for Cartesian/polar and spherical
       geometries and it is completely parallel in all 3 directions.

     * New INCLUDE_ROTATION flag allows to solve the HD/MHD equations in a
       rotating frame of reference using a fully conservative formulation.

     * Isothermal EoS has been added to the HD module. The implementation
       has been further extended to support a spatially-varying sound
       speed.

     * ShearingBox module extended to adiabatic EoS and fully parallel in
       all 3 directions.

     * Body forces have been re-implemented using simpler functions that
       prescribe either the vector components or the gravitational
       potential.

     * Entropy Switch for RHD/RMHD modules

5. Extras

     * A new more flexible algorithm to assign initial conditions by
       interpolating (external) input data files is available.

     * Parallel decomposition may be used-defined using the -dec n1 [n2]
       [n3] command line argument.

     * Improved handling of "internal boundary" regions inside the
       computational domain.

6. Visualization

     * New pyPLUTO visualization tool for quick visualization of PLUTO
       binary files.
     * IDL: improved getT() function to compute the temperature;
     * IDL: new ptools() functions for computing averages in 3D datasets;
     * IDL: improved pload procedure to read also HDF5 files from
       thestatic grid version of the code.
     * GNUPLOT: support for reading single or multiple data files
     * VisIt/Paraview: can now read HDF5 Chombo data files and .h5 PLUTO
       new format files.

**********************************************************
*           CHANGES from 3.1.0
**********************************************************

Version 3.1.1 contains some new improvements and a number
of minor bug fixes.
Here's a list of the most important changes:

- time step computation has been revised carefully (in a 
  genuine multi-D way) for UNSPLIT Runge-Kutta schemes and 
  when including parabolic terms (both explicit and Super 
  Time Stepping).
  The resulting formulation yields time steps that are 
  larger than before for a given CFL number. 
  See the UserGuide for a more technical explanation.
  This should also fix some unstable behavior seen with 
  STS at large CFL numbers.
- dissipative processes can now be incorporated, at the 
  explicit level, with Chombo-AMR;
- FARGO scheme has been extended to spherical geometry
- introduced the -no-write runtime switch for Chombo;
- Bug fix: Viscosity/Thermal Conduction (HD module)
- Bug fix: multiple calling of diffusion terms with 
  STS should now work properly.


**********************************************************
*           CHANGES from 3.0.1
**********************************************************

Version 3.1.0 provides several improvements/optimizations
together with a few bug fixes.
Briefly:

- Improved AMR support and compatibility with the latest
  Chombo release (Chombo 3.0):

  * added support for 1D AMR (replacing the obsolete amr-1D module);
  * HDF5 files now contains primitive variables (instead of conservative ones);
  * improved GLM-MHD / CTU integration;
  * explicit integration of parabolic terms 
    (conduction, viscosity, resisistivity);
  * improved reading and visualization routines with IDL
    (see pload, hdf5load and oplotbox);

- ArrayLib should be recompiled in order to allow large number 
  of processors (> 16,000); 
- introduced the -xres command flag;
- introduced the x1jet, x2jet, x3jet for jet propagating
  in any direction and dimension (replacing the old -jet switch);
- introduced the new SHEARINGBOX module;
- introduced the new FINITE_DIFFERENCE module;
- improved IDL DISPLAY routine with lft,rgt, bot and top;
- improved IDL PLOAD routine for reading large datasets;
- FLUX_CT has been changed to "CONSTRAINED_TRANSPORT".
  This is automatically corrected by running python setup.py.
- improved GLM_MHD/CTU and finite difference (FD) implementation.
- Cooling: cooling function names have been changed 
  from RAYMOND, NEQ  to   SNEq, MINEq;
- VECTOR potential: CT_VEC_POT_INIT changed into USE_VECTOR_POTENTIAL
  and also generalized to cell-centered MHD;
- time step computation has been modified by replacing
  min(dx)/max(lambda) --> min(dx/lambda). This yields
  larger time step on curvilinear grids;
- Improved Gnuplot visualization capabilities;
- introduced new reconstruction schemes (LimO3 and WENO3) in 
  the finite volume formulation (FV);
- Bug fixes and optimizations in the Thermal Conduction module;
- Viscosity is now compatible with STS integration.
- improved portability when restarting from .dbl files.
  WARNING: restarting from files written with previous versions
           of PLUTO will no longer work due to a change in the size 
           of the INPUT and RUNTIME structures. 

**********************************************************
*           CHANGES from 3.0
**********************************************************

Version 3.01 contains a number of minor improvements
and a few bug fixes:

- 1-D AMR extended to cylindrical and spherical coordinates;
- Entropy switch is available again for the MHD module;
- improved efficiency and accuracy of the GLM-MHD module;
- improved characteristic interpolation;
- CTU integrator is less memory consuming;
- Improved pload function (for IDL users) for large data sets.
- Bug fix in 3-D polar coordinates: 
  the centrifugal term is now correctly included.
- Bug fix in 3-D Cartesian/MHD/FLUX_CT + UCT_CONTACT:
  the dEy_dxm derivative was added to Ez instead of Ey.
- Bug fix in time step computation for viscous term: a division 
  by density was missing.
- Bug fix in the vector potential in 2D Cylindrical coordinates:
  the \phi component of the EMF must flip sign before updating A_\phi.


**********************************************************
*           CHANGES from 2.07.7                          *
**********************************************************

It contains major changes and several improvements 
with respect to previous 2.xx.x versions.
See also the Quickstart chapter in the userguide.pdf:

- 2 and 3D adaptive mesh refinement via the Chombo 
  library, please consult PLUTO/Doc/userguide.pdf, Chapt 7.
- New syntax for ANALYSIS, USERDEF_BOUNDARY, GRAVITY;
- New syntax for pluto.ini;
- New syntax for gravity and/or body forces;
- Completely redesigned I/O interface with new output 
  formats (dbl/flt/vtk/png/ppm/tab);
- output is the same for both parallel/serial mode;
- New ArrayLib (please recompile !!!!);
- thermal conduction module;
- viscosity module; 
- computations are promoted to double precision (always);
- new cooling modules;
- possibility to assign initial conditions from external files;
- new Upwind Constrained transport for MHD / RMHD;
- hyperbolic/parabolic divergence cleaning for MHD and RMHD;
- improved Super-Time-Stepping module;
- advanced Non-Equilibrium Cooling function;
- new command line arguments;
- several Bug fixes;
- simpler and more efficient IDL routines;