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Made module references more uniform

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This commit is contained in:
Karl Hammond
2022-10-21 10:58:05 -05:00
parent ed7d608919
commit 337d3f0760
1 changed files with 16 additions and 12 deletions
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doc/src/Fortran.rst
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@ -369,10 +369,10 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
.. note::
The ``MPI_F08`` module, which defines Fortran 2008 bindings for MPI,
The :f:mod:`MPI_F08` module, which defines Fortran 2008 bindings for MPI,
is not directly supported by this interface due to the complexities of
supporting both the ``MPI_F08`` and ``MPI`` modules at the same time.
However, you should be able to use the ``MPI_VAL`` member of the
supporting both the :f:mod:`MPI_F08` and :f:mod:`MPI` modules at the same
time. However, you should be able to use the ``MPI_VAL`` member of the
``MPI_comm`` derived type to access the integer value of the
communicator, such as in
@ -581,7 +581,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
.. note::
The ``MPI_F08`` module, which defines Fortran 2008 bindings for MPI,
The :f:mod:`MPI_F08` module, which defines Fortran 2008 bindings for MPI,
is not directly supported by this function. However, you should be
able to convert between the two using the `MPI_VAL` member of the
communicator. For example,
@ -595,7 +595,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
! ... [commands to set up LAMMPS/etc.]
comm%MPI_VAL = lmp%get_mpi_comm()
should assign an ``MPI_F08`` communicator properly.
should assign an :f:mod:`MPI_F08` communicator properly.
--------
@ -718,10 +718,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
``INTEGER(c_int64_t), DIMENSION(:)`` for "tag" if LAMMPS was compiled
with the ``-DLAMMPS_BIGBIG`` flag; ``REAL(c_double), DIMENSION(:,:)`` for
"x", "v", or "f"; and so forth). The pointer being associated with LAMMPS
data is type-, kind-, and rank-checked at run-time. Pointers returned by
this function are generally persistent; therefore, it is not necessary to
call the function again unless the underlying LAMMPS data are destroyed,
such as through the :doc:`clear` command.
data is type-, kind-, and rank-checked at run-time.
:p character(len=\*) name: string with the name of the property to extract
:r polymorphic: pointer to LAMMPS data. The left-hand side of the assignment
@ -730,6 +727,13 @@ Procedures Bound to the :f:type:`lammps` Derived Type
property. If expecting vector data, the pointer should have dimension ":";
if expecting matrix data, the pointer should have dimension ":,:".
.. warning::
Pointers returned by this function are generally not persistent, as
per-atom data may be redistributed, reallocated, and reordered at every
re-neighboring operation. It is advisable to re-bind pointers using
:f:func:`extract_atom` between runs.
.. admonition:: Array index order
Two-dimensional arrays returned from :f:func:`extract_atom` will be
@ -1720,9 +1724,9 @@ Procedures Bound to the :f:type:`lammps` Derived Type
:p integer(c_int) ix: image flag in :math:`x`-direction
:p integer(c_int) iy: image flag in :math:`y`-direction
:p integer(c_int) iz: image flag in :math:`z`-direction
:r integer(\*): encoded image flag. \*Kind parameter is ``c_int`` unless
LAMMPS was built with ``-DLAMMPS_BIGBIG``, in which case it is
``c_int64_t``.
:r integer(kind=\*): encoded image flag. \*The ``KIND`` parameter is
``c_int`` unless LAMMPS was built with ``-DLAMMPS_BIGBIG``, in which case
it is ``c_int64_t``.
.. note::