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.. _post-processing-howto:
***********************
Post-processing How-To
***********************
This is a list of FAQs about the usage of the AbiPy scripts.
Feel free to suggest new entries!
.. contents::
:backlinks: top
Preliminary considerations
---------------------------
The AbiPy scripts detect the file type by looking at the file extension
so **don't change the file extension**.
Also, remember that it is possible to get the documentation by just adding
the ``--help`` option to the command line.
For example:
.. code-block:: shell
abistruct.py --help
gives the documentation and usage examples for the abistruct.py_ script while:
.. code-block:: shell
abistruct.py COMMAND --help
prints the documentation and the options supported by ``COMMAND``
Get information about a generic ``FILE``
----------------------------------------
Use::
abiopen.py FILE --print
to print information about a file inside the terminal or
abiopen.py FILE --expose
to generate multiple matplotlib figures depending on FILE.
Use ``--verbose`` or ``-v`` to increase verbosity level.
The option can be can be supplied multiple times e.g. ``-vv``.
Get all file extensions supported by ``abiopen.py``
---------------------------------------------------
Use::
abiopen.py --help
.. command-output:: abiopen.py --help
Convert the structure stored in ``FILE`` to a different format
--------------------------------------------------------------
Use::
abistruct.py convert FILE
to read the structure from ``FILE`` and generate a CIF_ file (default behaviour).
The majority of the netcdf_ files produced by Abinit contain structural information
so this command can be used with netcdf output files as well as Abinit input/output
files and all the other formats supported by pymatgen e.g. POSCAR files.
Other formats can be specified with the ``-f`` option.
For example::
abistruct.py convert FILE -f abivars
gives the Abinit input variables while::
abistruct.py convert FILE -f xsf > out.xsf
exports the structure to the ``xsf`` format (xcrysden_) and save it to file.
Use::
abistruct.py convert --help
to list the formats supported.
Check if my Abinit input file is OK
-----------------------------------
First of all, one can use::
abiopen.py ../abipy/data/refs/si_ebands/run.abi -p
to print the crystalline structure and find the space group with the spglib_ library.
If the structure looks good, use the abinp.py_ script with the ``validate`` command as in::
abinp.py validate run.abi
to validate the input file with Abinit (requires ``manager.yml`` and, obviously, Abinit).
The script provides other options to invoke Abinit
to get space group information, the list of k-points in the IBZ.
the list of atomic perturbations for phonons or the list of autoparal configurations.
See ``abinp.py --help`` for further info.
Print the warnings in the log file
----------------------------------
Use::
abiopen.py run.log -p
to get::
Events found in /Users/gmatteo/git_repos/abipy/abipy/examples/flows/develop/flow_from_files/w0/t0/run.log
[1] <AbinitWarning at m_nctk.F90:568>
netcdf lib does not support MPI-IO and: NetCDF: Parallel operation on file opened for non-parallel access
[2] <AbinitWarning at m_nctk.F90:588>
The netcdf library does not support parallel IO, see message above
Abinit won't be able to produce files in parallel e.g. when paral_kgb==1 is used.
Action: install a netcdf4+HDF5 library with MPI-IO support.
[3] <AbinitWarning at m_hdr.F90:4258>
input kptrlatt= 0 0 0 0 0 0 0 0 0 /= disk file kptrlatt=8 0 0 0 8 0 0 0 8
[4] <AbinitWarning at m_hdr.F90:4261>
input kptopt= -2 /= disk file kptopt= 1
num_errors: 0, num_warnings: 4, num_comments: 0, completed: True
A similar interface is also available via::
abiview.py log run.log
Get a quick look to a file
--------------------------
The abiview.py_ script is especially designed for this task.
The syntax is ``abiview.py COMMAND FILE`` where ``COMMAND`` is either
the Abinit file extension (without ``.nc``, if any) or the AbiPy object we want to visualize.
To get a quick look at the DDB file, use::
abiview.py ddb out_DDB
This command invokes anaddb to compute phonon bands and DOS from the DDB and produces matplotlib_ plots.
If ``FILE`` contains electronic band energies, use e.g.::
abiview.py ebands out_GSR.nc
to plot the KS eigenvalues (the same command works for other files such as ``WFK.nc``, ``DEN.nc`` etc.
Note that abiview.py_ uses a predefined logic to visualize the data.
There are options to tune some parameters and/or export data in different formats
but exposing the AbiPy API from the command line is not easy.
For a more flexible interface, we suggest to use::
abiopen.py FILE
to start an ipython_ shell that will allow you to interact with the python object directly.
If you have installed jupyter_ on your machine/cluster and you have a web browser, use::
abiopen.py FILE -nb
to generate automatically a predefined jupyter notebook associated to the file type.
Visualize a structure
---------------------
The visualization of the structure is delegated to external graphical applications
that must be installed on your machine.
AbiPy will extract the structure from ``FILE``, convert it to one of the formats
supported by the graphical application and finally invoke the executable.
If you have vesta_ installed in one of the standard
locations of your machine, you can simply execute::
abistruct.py visualize FILE
inside the terminal.
Other applications can be specified with the ``--application`` option.
At present, AbiPy supports vesta_, ovito_, xcrysden_, avogadro_, and v_sim_.
To visualize the crystalline structure inside the jupyter_ notebook, you may want to
try the nbjsmol_ jupyter extension.
Get a high-symmetry kpath for a given structure
-----------------------------------------------
Use the `kpath` command and pass a FILE providing structural info::
abistruct.py kpath FILE
to generate a template with the input variables defining the k-path
.. code-block:: shell
# Abinit Structure
natom 2
ntypat 1
typat 1 1
znucl 14
xred
0.0000000000 0.0000000000 0.0000000000
0.2500000000 0.2500000000 0.2500000000
acell 1.0 1.0 1.0
rprim
0.0000000000 5.1085000000 5.1085000000
5.1085000000 0.0000000000 5.1085000000
5.1085000000 5.1085000000 0.0000000000
# K-path in reduced coordinates:
# tolwfr 1e-20 iscf -2 getden ??
ndivsm 10
kptopt -11
kptbounds
+0.00000 +0.00000 +0.00000 # $\Gamma$
+0.50000 +0.00000 +0.50000 # X
+0.50000 +0.25000 +0.75000 # W
+0.37500 +0.37500 +0.75000 # K
+0.00000 +0.00000 +0.00000 # $\Gamma$
+0.50000 +0.50000 +0.50000 # L
+0.62500 +0.25000 +0.62500 # U
+0.50000 +0.25000 +0.75000 # W
+0.50000 +0.50000 +0.50000 # L
+0.37500 +0.37500 +0.75000 # K
+0.62500 +0.25000 +0.62500 # U
+0.50000 +0.00000 +0.50000 # X
Re-symmetrize a structure when Abinit reports less symmetries than expected
---------------------------------------------------------------------------
Crystalline structures saved in text format (e.g. CIF files downloaded from
the Materials Project websites) may not have enough significant digits
and Abinit may not find the same spacegroup as the one reported by the source
as the default tolerance for symmetry detection in Abinit is tight (tolsym = 1e-8).
In this case, one can use the `abispg` option of abistruct.py to compute the spacegroup
with Abinit and a tolerance larger that the default value::
abistruct.py abispg problematic.cif --tolsym=1e-6
Hopefully, the code will detect the correct spacegroup, will re-symmetrize
the initial lattice vectors and atomic positions and print the new symmetrized structure to terminal.
Get neighbors for each atom in the unit cell out to a distance radius
---------------------------------------------------------------------
If we are interested in the environment/nearest neighbours of the atoms in the unit cell,
we can analyze the different coordinations with::
abistruct.py neighbors sic_relax_HIST.nc
.. code-block:: shell
Finding neighbors for each atom in the unit cell, out to a distance 2 [Angstrom]
[0] site PeriodicSite: C (0.0000, -0.0000, 0.0000) [-0.0000, 0.0000, -0.0000] has 4 neighbors:
PeriodicSite: Si (1.0836, -1.0836, -1.0836) [-0.7500, 0.2500, 0.2500] at distance 1.8767766107
PeriodicSite: Si (-1.0836, 1.0836, -1.0836) [0.2500, -0.7500, 0.2500] at distance 1.8767766107
PeriodicSite: Si (-1.0836, -1.0836, 1.0836) [0.2500, 0.2500, -0.7500] at distance 1.8767766107
PeriodicSite: Si (1.0836, 1.0836, 1.0836) [0.2500, 0.2500, 0.2500] at distance 1.8767766107
[1] site PeriodicSite: Si (1.0836, 1.0836, 1.0836) [0.2500, 0.2500, 0.2500] has 4 neighbors:
PeriodicSite: C (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000] at distance 1.8767766107
PeriodicSite: C (2.1671, 2.1671, 0.0000) [0.0000, 0.0000, 1.0000] at distance 1.8767766107
PeriodicSite: C (2.1671, 0.0000, 2.1671) [0.0000, 1.0000, 0.0000] at distance 1.8767766107
PeriodicSite: C (0.0000, 2.1671, 2.1671) [1.0000, 0.0000, 0.0000] at distance 1.8767766107
Search on the Materials Project database for structures
-------------------------------------------------------
Use::
abistruct.py mp_search LiF
to search on the `materials project`_ database for structures corresponding to a
chemical system or formula e.g. ``Fe2O3`` or ``Li-Fe-O`` or
``Ir-O-*`` for wildcard pattern matching.
The script prints the results to terminal in tabular form:
.. code-block:: bash
# Found 2 structures in materials project database (use `verbose` to get full info)
pretty_formula e_above_hull energy_per_atom \
mp-1138 LiF 0.000000 -4.845142
mp-1009009 LiF 0.273111 -4.572031
formation_energy_per_atom nsites volume spacegroup.symbol \
mp-1138 -3.180439 2 17.022154 Fm-3m
mp-1009009 -2.907328 2 16.768040 Pm-3m
spacegroup.number band_gap total_magnetization material_id
mp-1138 225 8.7161 0.0 mp-1138
mp-1009009 221 7.5046 -0.0 mp-1009009
.. important::
The script will try to connect to the materials project server.
You need a ``~/.pmgrc.yaml`` configuration file inside your home directory
with the authentication token **PMG_MAPI_KEY**.
For further info please refer to the
`pymatgen documentation <http://pymatgen.org/usage.html#pymatgen-matproj-rest-integration-with-the-materials-project-rest-api>`_
The script provides other commands to get (experimental) structures from the COD_ database,
find matching structures on the `materials project`_ website and generate phase diagrams.
See ``abistruct.py --help`` for more examples.
Compare my structure with the Materials Project database
--------------------------------------------------------
Let's assume we have performed a structural relaxation and we want
to compare our results with the Materials Project data.
One can use the abicomp.py_ structure to extract the structure from the HIST.nc_
file and compare the data with the database::
abicomp.py mp_structure ../abipy/data/refs/sic_relax_HIST.nc
It's also possible to select only the structures with the same space group number as the input structure with::
abicomp.py mp_structure ../abipy/data/refs/sic_relax_HIST.nc --same-spgnum
that produces
.. code-block:: ipython
Lattice parameters:
formula natom angle0 angle1 angle2 a b c \
mp-8062 Si1 C1 2 60.0 60.0 60.0 3.096817 3.096817 3.096817
this Si1 C1 2 60.0 60.0 60.0 3.064763 3.064763 3.064763
volume abispg_num spglib_symb spglib_num
mp-8062 21.000596 None F-43m 216
this 20.355222 None F-43m 216
Use --verbose to print atomic positions.
Note that one can replace the HIST.nc_ file with any other file providing a structure object.
.. important::
The structures of the materials project have been obtained with the GGA-PBE functional
and they might include the U term in the Hamiltonian.
One should take into account these different settings when comparing structural relaxations.
Visualize the iterations of the SCF cycle
-----------------------------------------
Use::
abiview.py abo run.abo
to plot the SCF iterations or the steps of the structural relaxations or the DFPT SCF cycles
(depending on the content of run.abo).
Note that one can also use::
abiview.py log run.log
to print the warnings/comments/errors reported in the Abinit log file ``run.log``.
Export bands to xmgrace format
------------------------------
Both |ElectronBands| and |PhononBands| provide a ``to_xmgrace`` method to produce xmgrace_ files.
To export the data to xmgrace, use abiview.py_ with the ``--xmgrace`` option.
For electrons, use::
abiview.py ebands out_GSR.nc --xmgrace
and::
abiview.py phbands out_PHBST.nc -xmgrace
for phonons.
Visualize the Fermi surface
---------------------------
Use::
abiview.py ebands out_GSR.nc --bxsf
to export a set of band energies in BXSF format
suitable for the visualization of the Fermi surface with xcrysden_.
Then use::
xcrysden --bxsf BXSF_FILE
to visualize the Fermi surface with xcrysden_
.. code-block:: ipython
abifile.ebands.to_bxsf("mgb2.bxsf")
.. important::
This option requires k-points in the irreducible wedge and a gamma-centered k-mesh.
Visualize phonon displacements
------------------------------
AbiPy is interfaced with the phononwebsite_ project
If you have already installed the python package from `github <https://github.com/henriquemiranda/phononwebsite>`_
it's possbile to export the ``PHBST.nc`` to JSON and then load the file via the web-interface.
Alternatively, it's possible to automate the entire procedure with the abiview.py_ script.
Use::
abiview.py phbands out_PHBST.nc -web
to start a local web server and open the HTML page inside the default browser
(the browser can be changed with the ``--browser`` option).
It is also possible to visualize the phonon modes starting directly from a DDB_ file with::
abiview.py ddb -web
In this case, AbiPy will invoke anaddb to produce the ``PHBST.nc`` file on an automatically
generated q-path and then start the web server.
Visualize the results of a structural relaxation
------------------------------------------------
The quickest way is to use::
abiview hist out_HIST.nc
to plot the results with matplotlib or::
abiopen.py out_HIST.nc -p
to print the most important results to terminal.
Note that it's possible to generate a ``XDATCAR`` file with::
abiview hist out_HIST.nc --xdatcar
and visualize the crystalline structure with ovito_::
abiview hist out_HIST.nc -appname=ovito
.. important::
The XDATCAR format assumes a fixed unit cell so you won't be able
to visualize the modifications of the unit cell lattice vectors in ovito.
Plot results stored in a text file in tabular format
----------------------------------------------------
Use::
abiview.py data FILE_WITH_COLUMNS
to plot with matplotlib_ all the columns given in the file.
By default, the first column is assumed to contain the values for the x-axis
but it is possible to change this behaviour and use the row index with the `--use-index` option.
Multiple datasets i.e. multiple sets of data separated by blank lines are supported.
To compare multiple files use::
abicomp.py data FILE1 FILE2
Obviously one can use standard tools such as gnuplot_ and xmgrace_ but
the AbiPy scripts are quite handy for a quick analysis of the results.
Compare multiple files
----------------------
The abicomp.py_ script is explicitly designed for this kind of task.
It operates on multiple files (usually files with the same extension) and
either produces matplotlib_ plots or creates AbiPy robots providing methods
to analyze the results, perform convergence studies and build pandas DataFrames_.
The ``COMMAND`` defines the quantity to be compared, followed by a list of filenames.
To compare e.g. the structure given in one Abinit input file with the structure
coming from a GSR.nc_ file, use::
abicomp.py structure run.abi out_GSR.nc
.. note::
In this example, we can use files of different type because they
both have a Structure object. This philosophy can be applied to other commands as well:
everything works as long as AbiPy is able to extract the quantity of interest from the file.
To plot multiple electronic structures on a grid, use::
abicomp.py ebands *_GSR.nc out2_WFK.nc -p
Remember that it is possible to use the shell syntax ``*_GSR.nc`` to select all files with a given extension.
If you have nested directories, use unix ``find`` to scan the directory tree for files matching a given pattern
For example::
abicomp.py ebands `find . -name *_GSR.nc`
finds all ``GSR.nc`` files contained withing the current working directory.
The output of ``find`` is then passed to the abicomp.py_ script.
.. note::
Note the `backticks syntax <https://unix.stackexchange.com/questions/27428/what-does-backquote-backtick-mean-in-commands>`_
used in the command.
Profile the scripts
-------------------
All AbiPy script can be executed in profile mode by just prepending the ``prof`` keyword
to the command line arguments.
This option could be useful if the script seems to be slow and you need to understand what's happening.
Use::
abiopen.py prof FILE
or::
abistruct.py prof COMMAND FILE
if the script requires a ``COMMAND`` argument.
Get the description of a variable
---------------------------------
The abidoc.py_ script provides a simplified interface to the Abinit documentation.
Use::
abidoc.py man ecut
to print the official documentation for the ``ecut`` variable to the terminal.
To list all the variables depending on the ``natom`` dimension, use::
abidoc.py withdim natom
More options are available. See ``abidoc.py --help``.
Avoid transfering files from the cluster to localhost just to use matplotlib
----------------------------------------------------------------------------
Use `SSHFS <https://www.digitalocean.com/community/tutorials/how-to-use-sshfs-to-mount-remote-file-systems-over-ssh>`_
to mount the remote file system over SSH.
Now one can execute the AbiPy scripts in a terminal running on the local machine.
to open/visualize the files stored on the cluster.
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