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Merge branch 'develop' into collected-small-changes

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Axel Kohlmeyer
2023-01-04 07:28:03 -05:00
parent 2e74813155 e902b7a8f1
commit 5cbe303af4
39 changed files with 548 additions and 724 deletions
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62
doc/src/Fortran.rst
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@ -5,46 +5,58 @@ The :f:mod:`LIBLAMMPS` module provides an interface to call LAMMPS from
Fortran. It is based on the LAMMPS C library interface and requires a
fully Fortran 2003-compatible compiler to be compiled. It is designed
to be self-contained and not require any support functions written in C,
C++, or Fortran other than those in the C library interface and the module
itself.
C++, or Fortran other than those in the C library interface and the
LAMMPS Fortran module itself.
While C libraries have a defined binary interface (ABI) and can thus be
used from multiple compiler versions from different vendors as long
as they are compatible with the hosting operating system, the same is
not true for Fortran programs. Thus, the LAMMPS Fortran module needs to be
used from multiple compiler versions from different vendors as long as
they are compatible with the hosting operating system, the same is not
true for Fortran programs. Thus, the LAMMPS Fortran module needs to be
compiled alongside the code using it from the source code in
``fortran/lammps.f90``. When linking, you also need to
:doc:`link to the LAMMPS library <Build_link>`. A typical command line
for a simple program using the Fortran interface would be:
``fortran/lammps.f90`` *and* with the same compiler used to build the
rest of the Fortran code that interfaces to LAMMPS. When linking, you
also need to :doc:`link to the LAMMPS library <Build_link>`. A typical
command line for a simple program using the Fortran interface would be:
.. code-block:: bash
mpifort -o testlib.x lammps.f90 testlib.f90 -L. -llammps
Please note that the MPI compiler wrapper is only required when the
calling the library from an MPI-parallelized program. Otherwise, using
the plain Fortran compiler (gfortran, ifort, flang, etc.) will suffice.
It may be necessary to link to additional libraries, depending on how
LAMMPS was configured and whether the LAMMPS library :doc:`was compiled
as a static or dynamic library <Build_link>`.
calling the library *from* an MPI-parallelized program. Otherwise,
using the plain Fortran compiler (gfortran, ifort, flang, etc.) will
suffice, since there are no direct references to MPI library features,
definitions and subroutine calls; MPI communicators are referred to by
their integer index representation as required by the Fortran MPI
interface. It may be necessary to link to additional libraries,
depending on how LAMMPS was configured and whether the LAMMPS library
:doc:`was compiled as a static or dynamic library <Build_link>`.
If the LAMMPS library itself has been compiled with MPI support, the
resulting executable will still be able to run LAMMPS in parallel with
``mpirun``, ``mpiexec``, or equivalent. Please also note that the order
of the source files matters: the ``lammps.f90`` file needs to be
compiled first, since it provides the :f:mod:`LIBLAMMPS` module that is
imported by the Fortran code that uses the interface. A working example
can be found together with equivalent examples in C and C++ in the
``examples/COUPLE/simple`` folder of the LAMMPS distribution.
resulting executable will be able to run LAMMPS in parallel with
``mpirun``, ``mpiexec``, or equivalent. This may be either on the
"world" communicator or a sub-communicator created by the calling
Fortran code. If, on the other hand, the LAMMPS library has been
compiled **without** MPI support, each LAMMPS instance will run
independently using just one processor.
.. versionadded:: 9Oct2020
Please also note that the order of the source files matters: the
``lammps.f90`` file needs to be compiled first, since it provides the
:f:mod:`LIBLAMMPS` module that would need to be imported by the calling
Fortran code in order to uses the Fortran interface.
A working example can be found together with equivalent examples in C and
C++ in the ``examples/COUPLE/simple`` folder of the LAMMPS distribution.
.. versionchanged:: TBD
.. note::
A contributed Fortran interface that more closely resembles the C library
interface is available in the ``examples/COUPLE/fortran2`` folder. Please
see the ``README`` file in that folder for more information about it and how
to contact its author and maintainer.
A contributed Fortran interface interface is available in the
``examples/COUPLE/fortran2`` folder. However, since the completion
of the :f:mod:`LIBLAMMPS` module, this interface is now deprecated,
no longer actively maintained and will likely be removed in the
future. Please see the ``README`` file in that folder for more
information about it and how to contact its author and maintainer.
----------

6
doc/src/fix_sgcmc.rst
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@ -131,7 +131,7 @@ the parameter *window_moves* (see Sect. III.B in :ref:`Sadigh1
------------
Restart, fix_modify, output, run start/stop, minimize info
==========================================================
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to restart files.
@ -149,7 +149,7 @@ components of the vector represent the following quantities:
* N+2: The current global concentration of species *X* (= number of atoms of type *N* / total number of atoms)
Restrictions
============
""""""""""""
This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
@ -169,7 +169,7 @@ execution i.e. it only works with a single MPI process.
------------
Default
=======
"""""""
The optional parameters default to the following values: