fix inputs prefixes from amr to mfix

MFIX-Exa also allows for the "dual grid approach", in which mesh and particle data are allocated

on different box layouts with different mappings to MPI ranks.  This option is enabled

by setting :cpp:`amr.dual_grid = 1` in the inputs file.

by setting :cpp:`mfix.dual_grid = 1` in the inputs file.

See :ref:`sec:dual_grid` for more about this approach.

When running on multicore machines with OpenMP, we can also control the distribution of

and embedded boundaries.  This particular example is

particles flowing down a cylinder.

First, edit ``path/to/mfix/benchmarks/05-cyl-fluidbed/Size0001/inputs``

so that ``mfix.write_eb_surface = true`` and ``amr.plot_int = 1``.

so that ``mfix.write_eb_surface = true`` and ``mfix.plot_int = 1``.

Then, run the example with:

.. highlight:: console

-----------------------

The solver will write plot files if one of the write frequency options is set

(``amr.plot_int``, ``amr.plot_per_exact``, or ``amr.plot_per_approx``) in

(``mfix.plot_int``, ``mfix.plot_per_exact``, or ``mfix.plot_per_approx``) in

directories that are prefixed with the prefix specified in the inputs file

(``amr.plot_file = 'plt'``). To visualize these particles in Paraview, press

(``mfix.plot_file = 'plt'``). To visualize these particles in Paraview, press

the open button. In the file dialog, browse to the simulation directory and

select the directory group corresponding to the specified prefix. In this

example, the director group is displayed as ``plt...``. If only one plot

Checkpoint/Restart

==================

The following inputs must be preceded by "amr" and control checkpoint/restart.

The following inputs must be preceded by "mfix" and control checkpoint/restart.

+-------------------------+-----------------------------------------------------------------------+-------------+-----------+

|                         | Description                                                           |   Type      | Default   |

| check_file              | Prefix to use for checkpoint output                                   |  String     | chk       |

+-------------------------+-----------------------------------------------------------------------+-------------+-----------+

| check_walltime          | Write a check point file after the specified walltime (HH:MM:SS)      |  String     | None      |

|                         | has lapsed. For example, if amr.check_waltime = 00:10:00, then a      |             |           |

|                         | has lapsed. For example, if mfix.check_walltime = 00:10:00, then a    |             |           |

|                         | checkpoint file is after a job has run for ten minutes.               |             |           |

+-------------------------+-----------------------------------------------------------------------+-------------+-----------+

| geom_chk_write          | When True, writes the EB geometry data into geom_chk_file             |  bool       | False     |

Initialization

==============

The following inputs must be preceded by "amr" and determine how we initialize a calculation:

The following inputs must be preceded by "mfix" and determine how we initialize a calculation:

+----------------------+-----------------------------------------------------------------------+-------------+--------------+

|                      | Description                                                           |   Type      | Default      |

+======================+=======================================================================+=============+==============+

| input_deck           | Read physical data from this file                                     |  String     |  mfix.dat    |

+----------------------+-----------------------------------------------------------------------+-------------+--------------+

| restart              | If set, then restart from this file rather than from scratch          |  String     |   None       |

+----------------------+-----------------------------------------------------------------------+-------------+--------------+

| repl_x               | Replicate initial data by this factor in the x-direction              |   Int       |    1         |