remove references to Fortran in the docs (#433)

sphinx_docs/source/addproblem.rst

@@ -110,10 +110,11 @@ By default, some of the runtime parameters are listed in
 
     PROBIN_PARAMETER_DIRS := .
 
-They are parsed at compile time and the file ``extern.F90``
-is written and compiled. This is a Fortran module that holds the values of
-the runtime parameters and makes them available to any routine via
-``probin_module``.
+These are combined with the runtime parameters specified by Microphysics
+and parsed at compile time.  A C++ header and source file is written
+(``extern_parameters.cpp`` and ``extern_parameters.H``) that define
+the parameters and their defaults.
+
 
 The final line in the GNUmakefile includes the rules to actually
 build the executable.
@@ -148,15 +149,14 @@ Each line in the ``_cpp_parameters`` file has the form::
 
   *parameter*    *data-type*    *value*    *need in Fortran?*
 
-where *parameter* is the name of the runtime parameter,
-*data-type* is one of {string, Real, int, bool},
-the *value* specifies the default value for the runtime parameter,
-and *need in Fortran?* is marked *y* only if that parameter is
-used in Fortran. Comments are indicated by a ‘#’ character and are
+where *parameter* is the name of the runtime parameter, *data-type* is
+one of {string, Real, int, bool}, the *value* specifies the default
+value for the runtime parameter.  A fourth column, *need in Fortran?*,
+is no longer used.  Comments are indicated by a ‘#’ character and are
 used to produce documentation about the available runtime parameters.
-For the documentation, runtime parameters are grouped together
-in the ``_cpp_parameters`` file into categories. The category headings
-are defined by comments in the ``_cpp_parameters`` file and any comments
+For the documentation, runtime parameters are grouped together in the
+``_cpp_parameters`` file into categories. The category headings are
+defined by comments in the ``_cpp_parameters`` file and any comments
 following that heading are placed into that category.
 
 At runtime, the default values for the parameters can be overridden

sphinx_docs/source/faq.rst

@@ -5,18 +5,9 @@ Frequently Asked Questions
 Compiling
 =========
 
-#. *What version of the Fortran standard is needed?*
-
-   Some features of Fortran 2003 are used, in particular, the
-   ISO_C_BINDING feature of Fortran 2003 is needed to define a long
-   integer type for some MPI operations in Fortran. This is supported
-   by most Fortran compilers even if they don’t support the entire
-   Fortran 2003 standard.
-
-   We also rely on the Fortran 95 standard that specifies that any
-   local allocated arrays are automatically deallocated when a
-   subroutine ends. Fortran 90 does not do this. Most
-   MAESTROeX routines rely on this Fortran 95 feature.
+#. *What version of the C++ is needed?*
+
+   We use C++17.  Most modern compilers support the features we need.
 
 
 #. *The code doesn’t compile, but complains right away that there

sphinx_docs/source/getting_started.rst

@@ -9,12 +9,11 @@ and how to look at the output.
 Requirements
 ============
 
-MAESTROeX requires a C++ compiler that supports the C++17 standard, a
-Fortran compiler that supports the Fortran 2003 standard, and a C compiler
-that supports the C99 standard. Several compiler suites are supported,
-including GNU, Intel, PGI and Cray. GNU Make (>= 3.82) is also required,
-as is Python (>= 3.6) and standard tools available in any Unix-like
-environments (e.g., Perl and ``sed``).
+MAESTROeX requires a C++ compiler that supports the C++17 standard and
+a C compiler that supports the C99 standard. Several compiler suites
+are supported, including GNU, Intel, LLVM and Cray. GNU Make (>= 3.82)
+is also required, as is Python (>= 3.9) and standard tools available
+in any Unix-like environments (e.g., Perl and ``sed``).
 
 For running in parallel, an MPI library and/or OpenMP is required.
 For running on GPUs, CUDA 11 or later is required (see :ref:`sec:gpu` for
@@ -154,7 +153,7 @@ paper 3.
 
    -  ``COMP := gnu``
 
-      This option specifies the gnu compiler suite (g++/gfortran).
+      This option specifies the gnu compiler suite (e.g., g++).
       We will use gnu, which is the preferred compiler suite for MAESTROeX.
       Specifying this compiler will automatically pull in the compiler
       settings as specified in ``AMREX_HOME/Tools/GNUMake/Make.defs``.
@@ -307,19 +306,10 @@ related development packages (e.g. libXpm-devel).
 AmrPostprocessing scripts
 -------------------------
 
-Several useful analysis scripts (written in Fortran 90) can be found
-in ``amrex/Tools/Postprocessing/F_Src/``.  The ``GNUmakefile`` there
-needs to be edited to indicate which of the tools to build. For
-example, to extract the density along a line from the center of a
-plotfile, ``plt00200``, in the :math:`y`-direction::
+Several useful analysis scripts can be found
+in the ``amrex-astro-diag`` project:
 
-    fextract.Linux.gfortran.exe -d 2 -v "density" -p plt00200
-
-These routines are described in § :ref:`sec:analysis`.
-
-There is also a python visualization method in
-``AmrPostprocessing/python``. This is described
-in § :ref:`sec:vis:python`.
+https://github.com/amrex-astro/amrex-astro-diag
 
 VisIt
 -----

sphinx_docs/source/gpu.rst

@@ -12,9 +12,8 @@ Note that currently MAESTROeX only supports NVIDIA GPUs.
 Requirements
 ============
 
-Since MAESTROeX uses primarily CUDA C++ and CUDA Fortran,
-it requires a recent version of CUDA (e.g., >= 9) and the device
-must have compute capability of >= 6.
+MAESTROeX has only been tested with NVIDIA/CUDA.  In theory AMD/HIP
+should work.
 
 .. _sec:gpubuild:
 
@@ -33,17 +32,6 @@ not compatible with building with CUDA.
 ``USE_CUDA = TRUE`` and ``USE_OMP = TRUE`` will fail to compile.
 However, you may use MPI with CUDA for additional parallelization.
 
-Only the IBM and PGI compilers support CUDA Fortran, so the compiler should be set as:
-
-::
-
-      COMP := pgi
-
-The integrator used by the Microphysics library must be set to ``VODE90``:
-
-::
-
-    INTEGRATOR_DIR   := VODE90
 
 Depending on which system you are running on, it may be necessary to specify
 the CUDA Capability using the ``CUDA_ARCH`` flag. The CUDA Capability will
@@ -61,179 +49,6 @@ capability 6.x, the flag should be set to:
 
 .. _sec:gpuporting:
 
-Offloading a routine to GPU
-===========================
-
-In order to offload a routine to the GPU, we insert a ``#pragma gpu``
-statement on the line before the call. This tells the preprocessor to
-generate a CUDA device version of the function, with all the
-additional CUDA GPU management. In addition to this, there are a few
-other modifications required to ensure the function operates correctly
-on the GPU. We summarize these below.
-
-C++
----
-
-- Make sure that the box ``lo`` and ``hi`` are the first two arguments
-  and use ``AMREX_INT_ANYD`` as the macro wrapping ``bx.loVect()`` and
-  ``bx.hiVect()``
-
-- Likewise, inplace of ``AMREX_ZFILL()``, use ``AMREX_REAL_ANYD``
-
-- Scalars must be passed by value to Fortran functions (not by
-  reference)
-
-- Make sure that you change the variable definitions in the Fortran
-  code to include value so that the Fortran knows the variables are
-  being passed by value rather than by reference. If you don’t do
-  this, the code is liable to segfault
-
-- FArrayBox functions like ``setVal()`` and ``saxpy()`` are not on the
-  GPU, so you should explicitly write out these operations in C++.
-  The MultiFab counterparts are on the GPU.
-
-- Use ``BL_TO_FORTRAN_ANYD()`` to wrap MultiFab arguments (and in the header file wrap with ``BL_FORT_FAB_ARG_3D``)
-
-To illustrate these modifications, consider the function ``mk_sponge``. To call the function on the CPU, we would write
-
-.. code-block:: c++
-
-    for (MFIter mfi(sponge_mf, true); mfi.isValid(); ++mfi) {
-
-        const Box& tileBox = mfi.tilebox();
-
-        mk_sponge(AMREX_ARLIM_3D(tileBox.loVect()), AMREX_ARLIM_3D(tileBox.hiVect()),
-                  BL_TO_FORTRAN_3D(sponge_mf[mfi]),
-          AMREX_ZFILL(dx), &dt);
-     }
-
-Implementing the changes described above to offload this to GPU, this becomes
-
-.. code-block:: c++
-
-    for (MFIter mfi(sponge_mf, true); mfi.isValid(); ++mfi) {
-
-        const Box& tileBox = mfi.tilebox();
-
-    #pragma gpu box(tileBox)
-        mk_sponge(AMREX_INT_ANYD(tileBox.loVect()), AMREX_INT_ANYD(tileBox.hiVect()),
-                  BL_TO_FORTRAN_ANYD(sponge_mf[mfi]),
-          AMREX_REAL_ANYD(dx), dt);
-     }
-
-Fortran
--------
-
-- The routine must only operate on a single zone in ``lo:hi``.
-
-  - Even for temporary arrays, you cannot write to an ``i+1`` zone
-    (e.g. when doing limiting) -- this will cause a race condition.
-    If necessary, do extra computation to avoid the temporary arrays.
-
-- Mark the routine with ``!$gpu``
-
-- If a module defines its own variables, these variables need to be
-  ``allocatable`` (even if they are scalars) and marked as
-  ``attributes(managed)``. Additional routines may be needed to
-  allocate these variables before they’re used and deallocate them
-  when they’re no longer needed.
-
-  - Examples of this can be seen for the sponge parameters. These are
-    marked as ``allocatable`` and ``attributes(managed)`` in
-    ``sponge.F90``, and therefore must be allocated (by ``init_sponge``).
-
-- Temporary variables must be defined outside of function calls. E.g. if a
-  function call contains ``foo(x(a:b)/y)``, you need to define a new variable
-  ``z = x(a:b)/y`` then pass this into the function as ``foo(z)``.
-
-  - If you don’t do this, you may see the error ``Array reshaping is
-    not supported for device subprogram calls``
-
-- If importing a function from another module, make sure to put the
-  import within the function/subroutine, and put ``! function`` at the
-  end of the line, e.g.
-
-.. code-block:: fortran
-
-   use my_module, only: my_func ! function
-
-- Individual functions should be imported individually (so not ``use
-  my_module, only: func1, func2 ! function``) and there must be a
-  space either side of the ``!``
-
-- Make sure the fortran file is ``.F90`` rather than ``.f90`` (and
-  remember to update the ``Make.xx`` file to reflect this). If you
-  don’t do this, you will see the error ``Label field of continuation
-  line is not blank``
-
-  - This is required as we use the convention that ``.F90`` files are
-    processed by the preprocessor, and ``.f90`` files are not. The
-    preprocessor will therefore only generate the required device
-    function if the file has the correct extension.
-
-We can see some of the above modifications by looking at the
-subroutine ``estdt`` in ``compute_dt.F90``:
-
-.. code-block:: fortran
-
-   subroutine estdt(lev, dt, umax, lo, hi, dx, &
-                    scal,  s_lo, s_hi, nc_s, &
-            u,     u_lo, u_hi, nc_u, &
-            force, f_lo, f_hi, nc_f, &
-            divu,  d_lo, d_hi, &
-            dSdt,  t_lo, t_hi, &
-            w0_cart, w_lo, w_hi, &
-            p0_cart, p_lo, p_hi, &
-            gamma1bar_cart, g_lo, g_hi) bind (C,name="estdt")
-
-      use amrex_constants_module, only: HALF
-      use amrex_fort_module, only: amrex_min ! function
-      use amrex_fort_module, only: amrex_max ! function
-
-      ! input parameters
-      integer  , value, intent(in   ) :: lev
-      double precision, intent(inout) :: dt, umax
-      integer         , intent(in   ) :: lo(3), hi(3)
-      ...
-
-      ! local variables
-      double precision :: spdx, spdy, spdz, spdr, rho_min
-      double precision :: fx, fy, fz, dt_temp
-      double precision :: eps,denom,gradp0
-      double precision :: a, b, c
-      integer          :: i,j,k
-
-      !$gpu
-
-      rho_min = 1.d-20
-      ...
-
-      do k = lo(3), hi(3)
-         do j = lo(2), hi(2)
-            do i = lo(1), hi(1)
-           spdx = max(spdx ,abs(u(i,j,k,1)))
-
-      ...
-
-   end subroutine estdt
-
-- Here, we can see that ``amrex_min`` and ``amrex_max`` functions from the
-  ``amrex_fort_module`` are marked separately as ``! function``, which tells
-  the preprocessor to generate a device version of this function.
-
-- The scalar ``lev`` is passed in by value.
-
-- The ``!$gpu`` directive has been inserted after the definition of
-  all the variables passed into the routine and all the local
-  variables, but before the main body of the function.
-
-- The routine only operates on values in a single zone of ``lo:hi``.
-
-
-.. To be documented
-.. ----------------
-..
-.. when do we need to mark stuff as attributes(managed)?
 
 
 .. _sec:gpuprofile:

sphinx_docs/source/initial_models.rst

@@ -45,10 +45,10 @@ problem:
    {\tt wdconvect} & \rightarrow & {\tt model\_6.e8.raw} \nonumber \\
    {\tt spherical\_heat} & \rightarrow & \mathrm{none-it~ is~ generated~ analytically} \nonumber \\\end{aligned}
 
-We use a fortran subroutine
+We use a C++ program
 to interpolate the raw data, yielding the model data, :math:`\rho^{\model},
-T^{\model}, p^{\model}`, and :math:`X^{\model}`. The fortran subroutine
-then uses an iterative procedure to modify the model data so that it
+T^{\model}, p^{\model}`, and :math:`X^{\model}`.  These initial model
+routines generally uses an iterative procedure to modify the model data so that it
 is thermodynamically consistent with the MAESTROeX equation of
 state (EOS), and also satisfies our chosen hydrostatic equilibrium
 (HSE) discretization,

sphinx_docs/source/introduction.rst

@@ -11,7 +11,7 @@ MAESTROeX models the evolution of low Mach number astrophysical
 flows that are in hydrostatic equilibrium.  The name MAESTROeX itself
 derives from MAESTRO, the original (pure Fortran) low Mach number
 stellar hydrodynamics code.  MAESTROeX began as a rewrite MAESTRO
-in the C++/Fortran framework of AMReX, and has since then gained
+in the C++ framework of AMReX, and has since then gained
 additional algorithmic capabilities.  Henceforth, we will refer
 only to MAESTROeX, although many of the ideas originated in
 MAESTRO before the change to MAESTROeX.

sphinx_docs/source/makefiles.rst

@@ -54,11 +54,9 @@ lines of the form:
 ::
 
     CEXE_sources += file.cpp
-    F90EXE_sources += file.F90
 
-where ``file.cpp`` is a C++ source file and ``file.F90`` is a Fortran
-source file that should be built when this directory is added to the
-list of build directories.
+where ``file.cpp`` is a C++ source file that should be built when this
+directory is added to the list of build directories.
 
 The AMReX build system relies on the ``vpath`` functionality of
 make. In a makefile, the ``vpath`` variable holds search path used to
@@ -74,7 +72,7 @@ Dependencies
 ------------
 
 There is no need to explicitly define the dependencies between the
-source files for Fortran modules. Scripts in
+source files.  Scripts in
 AMReX are run at the start of the build
 process and parse all the source files and make an explicit list of
 the dependency pairs.
@@ -264,7 +262,7 @@ track down memory issues, uninitialized variables, NaNs, etc.
    ``GNUmakefile`` generates an executable with debugging information
    included in the executable (e.g., to be interpreted by the
    debugger, gdb). This will usually add -g to the compile line and
-   also lower the optimization. For gfortran it will add several
+   also lower the optimization. This will add several
    options to catch uninitialize variables, bounds errors, etc.
    The resulting executable will have ``DEBUG`` in its name.
 
@@ -309,7 +307,7 @@ track down memory issues, uninitialized variables, NaNs, etc.
 
 -  ``FSANITIZER``
 
-   For gfortran, gcc, g++, setting ``FSANITIZER=TRUE``
+   For gcc/g++, setting ``FSANITIZER=TRUE``
    in ``GNUmakefile`` will enable the
    address sanitizer support built into GCC. This is enabled through
    integration with https://github.com/google/sanitizers in GCC.

sphinx_docs/source/mg.rst

@@ -32,6 +32,11 @@ Support for :math:`\Delta x \ne \Delta y \ne \Delta z`
 Data Structures
 ---------------
 
+.. note::
+
+   This information is outdated
+
+
 mg_tower
 ~~~~~~~~