move the entries about using the Python module into its own (sub) toctree
This commit is contained in:
Axel Kohlmeyer
@ -1,16 +1,19 @@
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Extending the library and Python interface
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******************************************
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As noted above, these Python class methods correspond one-to-one with
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As noted previously, the Python class methods correspond one-to-one with
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the functions in the LAMMPS library interface in ``src/library.cpp`` and
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``library.h``. This means you can extend the Python wrapper via the
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following steps:
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``library.h``. This means you can extend the Python wrapper by
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following these steps:
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* Add a new interface function to ``src/library.cpp`` and
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``src/library.h``.
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* Rebuild LAMMPS as a shared library.
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* Add a wrapper method to ``python/lammps.py`` for this interface
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function.
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* Define the corresponding ``argtypes`` list and ``restype``
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in the ``lammps.__init__()`` function.
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* Re-install the shared library and the python module, if needed
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* You should now be able to invoke the new interface function from a
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Python script.
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@ -10,14 +10,6 @@ together.
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Python_overview
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Python_install
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Python_run
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Python_create
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Python_execute
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Python_properties
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Python_atoms
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Python_objects
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Python_scatter
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Python_neighbor
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Python_config
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Python_module
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Python_ext
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Python_call
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108
doc/src/Python_launch.rst
Normal file
108
doc/src/Python_launch.rst
Normal file
@ -0,0 +1,108 @@
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Running LAMMPS and Python in serial
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-----------------------------------
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To run a LAMMPS in serial, type these lines into Python
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interactively from the ``bench`` directory:
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.. code-block:: python
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>>> from lammps import lammps
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>>> lmp = lammps()
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>>> lmp.file("in.lj")
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Or put the same lines in the file ``test.py`` and run it as
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.. code-block:: bash
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$ python3 test.py
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Either way, you should see the results of running the ``in.lj`` benchmark
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on a single processor appear on the screen, the same as if you had
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typed something like:
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.. code-block:: bash
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lmp_serial -in in.lj
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Running LAMMPS and Python in parallel with MPI
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----------------------------------------------
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To run LAMMPS in parallel, assuming you have installed the
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`mpi4py <https://mpi4py.readthedocs.io>`_ package as discussed
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:ref:`python_install_mpi4py`, create a ``test.py`` file containing these lines:
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.. code-block:: python
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from mpi4py import MPI
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from lammps import lammps
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lmp = lammps()
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lmp.file("in.lj")
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me = MPI.COMM_WORLD.Get_rank()
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nprocs = MPI.COMM_WORLD.Get_size()
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print("Proc %d out of %d procs has" % (me,nprocs),lmp)
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MPI.Finalize()
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You can run the script in parallel as:
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.. code-block:: bash
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$ mpirun -np 4 python3 test.py
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and you should see the same output as if you had typed
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.. code-block:: bash
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$ mpirun -np 4 lmp_mpi -in in.lj
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Note that without the mpi4py specific lines from ``test.py``
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.. code-block::
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from lammps import lammps
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lmp = lammps()
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lmp.file("in.lj")
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running the script with ``mpirun`` on :math:`P` processors would lead to
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:math:`P` independent simulations to run parallel, each with a single
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processor. Therefore, if you use the mpi4py lines and you see multiple LAMMPS
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single processor outputs, mpi4py is not working correctly.
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Also note that once you import the mpi4py module, mpi4py initializes MPI
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for you, and you can use MPI calls directly in your Python script, as
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described in the mpi4py documentation. The last line of your Python
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script should be ``MPI.finalize()``, to insure MPI is shut down
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correctly.
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Running Python scripts
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----------------------
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Note that any Python script (not just for LAMMPS) can be invoked in
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one of several ways:
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.. code-block:: bash
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$ python script.py
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$ python -i script.py
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$ ./script.py
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The last command requires that the first line of the script be
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something like this:
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.. code-block:: bash
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#!/usr/bin/python
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#!/usr/bin/python -i
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where the path points to where you have Python installed, and that you
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have made the script file executable:
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.. code-block:: bash
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$ chmod +x script.py
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Without the ``-i`` flag, Python will exit when the script finishes.
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With the ``-i`` flag, you will be left in the Python interpreter when
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the script finishes, so you can type subsequent commands. As
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mentioned above, you can only run Python interactively when running
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Python on a single processor, not in parallel.
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@ -1,110 +1,23 @@
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Run LAMMPS from Python
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======================
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Running LAMMPS and Python in serial:
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-------------------------------------
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After compiling the LAMMPS shared library and making it ready to use,
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you can now write and run Python scripts that import the LAMMPS Python
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module and launch LAMMPS simulations through Python scripts.
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The following pages take you through the various steps necessary,
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what functionality is available and give some examples how to use it.
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To run a LAMMPS in serial, type these lines into Python
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interactively from the ``bench`` directory:
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------
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.. code-block:: python
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.. toctree::
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:maxdepth: 1
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>>> from lammps import lammps
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>>> lmp = lammps()
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>>> lmp.file("in.lj")
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Or put the same lines in the file ``test.py`` and run it as
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.. code-block:: bash
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$ python3 test.py
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Either way, you should see the results of running the ``in.lj`` benchmark
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on a single processor appear on the screen, the same as if you had
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typed something like:
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.. code-block:: bash
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lmp_serial -in in.lj
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Running LAMMPS and Python in parallel with MPI
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----------------------------------------------
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To run LAMMPS in parallel, assuming you have installed the
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`mpi4py <https://mpi4py.readthedocs.io>`_ package as discussed
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:ref:`python_install_mpi4py`, create a ``test.py`` file containing these lines:
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.. code-block:: python
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from mpi4py import MPI
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from lammps import lammps
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lmp = lammps()
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lmp.file("in.lj")
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me = MPI.COMM_WORLD.Get_rank()
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nprocs = MPI.COMM_WORLD.Get_size()
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print("Proc %d out of %d procs has" % (me,nprocs),lmp)
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MPI.Finalize()
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You can run the script in parallel as:
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.. code-block:: bash
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$ mpirun -np 4 python3 test.py
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and you should see the same output as if you had typed
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.. code-block:: bash
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$ mpirun -np 4 lmp_mpi -in in.lj
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Note that without the mpi4py specific lines from ``test.py``
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.. code-block::
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from lammps import lammps
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lmp = lammps()
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lmp.file("in.lj")
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running the script with ``mpirun`` on :math:`P` processors would lead to
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:math:`P` independent simulations to run parallel, each with a single
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processor. Therefore, if you use the mpi4py lines and you see multiple LAMMPS
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single processor outputs, mpi4py is not working correctly.
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|
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Also note that once you import the mpi4py module, mpi4py initializes MPI
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for you, and you can use MPI calls directly in your Python script, as
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described in the mpi4py documentation. The last line of your Python
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script should be ``MPI.finalize()``, to insure MPI is shut down
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correctly.
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Running Python scripts
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----------------------
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Note that any Python script (not just for LAMMPS) can be invoked in
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one of several ways:
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.. code-block:: bash
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$ python script.py
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$ python -i script.py
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$ ./script.py
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The last command requires that the first line of the script be
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something like this:
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.. code-block:: bash
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#!/usr/bin/python
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#!/usr/bin/python -i
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where the path points to where you have Python installed, and that you
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have made the script file executable:
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.. code-block:: bash
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$ chmod +x script.py
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Without the ``-i`` flag, Python will exit when the script finishes.
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With the ``-i`` flag, you will be left in the Python interpreter when
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the script finishes, so you can type subsequent commands. As
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mentioned above, you can only run Python interactively when running
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Python on a single processor, not in parallel.
|
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Python_launch
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Python_create
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Python_execute
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Python_properties
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Python_atoms
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Python_objects
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Python_scatter
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Python_neighbor
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Python_config
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||||
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Reference in New Issue
Block a user