Open-source library for analyzing the results produced by ABINIT

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About

AbiPy is a python library to analyze the results produced by Abinit, an open-source program for the ab-initio calculations of the physical properties of materials within Density Functional Theory and Many-Body perturbation theory. It also provides tools to generate input files and workflows to automate ab-initio calculations and typical convergence studies. AbiPy is interfaced with pymatgen and this allows users to benefit from the different tools and python objects available in the pymatgen ecosystem.

The official documentation is hosted on github pages. Check out our gallery of plotting scripts and the gallery of AbiPy workflows.

AbiPy can be used in conjunction with matplotlib, pandas, scipy, seaborn, ipython and jupyter notebooks thus providing a powerful and user-friendly environment for data analysis and visualization.

To learn more about the integration between jupyter and AbiPy, visit our collection of notebooks or click the Launch Binder badge to start a Docker image with Abinit, AbiPy and all the other python dependencies required to run the code inside the jupyter notebooks. The notebook will be opened in your browser after building.

AbiPy is free to use. However, we also welcome your help to improve this library by making your own contributions. Please report any bugs and issues at AbiPy's Github page.

Links to talks

This section collects links to some of the talks given by the AbiPy developers.

• The new features of AbiPy v0.9.1. 10th international ABINIT developer workshop, May 31 - June 4, 2021 (New workflows, plotly interface, etc.)
• Automating ABINIT calculations with AbiPy. Boston MA, 3 March 2019 (Introduction to AbiPy for newcomers).
• New features of AbiPy v0.7. Louvain-la-Neuve, Belgium, 20 May 2019 (How to use the AbiPy command line interface in the terminal)
• Automatize a DFT code: high-throughput workflows for Abinit

Getting AbiPy

Stable version

The version at the Python Package Index (PyPI) is always the latest stable release that can be installed in user mode with:

pip install abipy --user

Note that you may need to install some optional dependencies manually. In this case, please consult the detailed installation instructions provided by the pymatgen howto to install pymatgen and then follow the instructions in our howto.

The installation process is greatly simplified if you install the required python packages through Anaconda (or conda). See Installing conda to install conda itself. We routinely use conda to test new developments with multiple Python versions and multiple virtual environments. The anaconda distribution already provides the most critical dependencies (matplotlib, scipy, numpy, netcdf4-python) in the form of pre-compiled packages that can be easily installed with e.g.:

conda install numpy scipy netcdf4

Create a new conda environment (let's call it abienv) based on python3.6 with:

conda create --name abienv python=3.6

and activate it with:

conda activate abienv

You should see the name of the conda environment in the shell prompt.

Now add conda-forge to your conda channels with:

conda config --add channels conda-forge

This is the channel from which we will download pymatgen, abipy and abinit.

Finally, install AbiPy with:

conda install abipy

Additional information on the steps required to install AbiPy with anaconda are available in the anaconda howto.

We are also collaborating with the spack community to provide packages for AbiPy and Abinit in order to facilitate the installation on large supercomputing centers.

Developmental version

Getting the developmental version of AbiPy is easy. Clone the github repository with:

git clone https://github.com/abinit/abipy

For pip, use:

pip install -r requirements.txt
pip install -r requirements-optional.txt

If you are using conda (see Installing conda to install conda itself), create a new environment (abienv) based on python3.6 with:

conda create -n abienv python=3.6
source activate abienv

Add conda-forge, and abinit to your channels with:

conda config --add channels conda-forge
conda config --add channels abinit

and install the AbiPy dependencies with:

conda install --file ./requirements.txt
conda install --file ./requirements-optional.txt

The second command is needed for Jupyter only. Once the requirements have been installed (either with pip or conda), execute:

python setup.py install

or alternately:

python setup.py develop

to install the package in developmental mode. This is the recommended approach, especially if you are planning to implement new features.

Note, however, that the developmental version of AbiPy is kept in sync with the developmental version of pymatgen thus `python setup.py develop` may try to download new versions from the PyPi portal and then fail with e.g. the error message:

...
processing dependencies for abipy==0.6.0.dev0
error: scipy 1.0.0 is installed but scipy>=1.0.1 is required by {'pymatgen'}

due to inconsistent dependencies. To solve the problem, use conda to update scipy to a version >= 1.0.1 with:

conda install "scipy>=1.0.1"

then issue again python setup.py develop. If this fails, supposing you were upgrading abipy inside an already existing conda environment, try to restart by creating from scratch a fresh conda environment, see above.

Use:

conda info pymatgen

to display information about the installed version of pymatgen.

Also note that the BLAS/Lapack libraries provided by conda have multithreading support activated by default. Each process will try to use all of the cores on your machine, which quickly overloads things if there are multiple processes running. (Also, this is a shared machine, so it is just rude behavior in general). To disable multithreading, add these lines to your ~/.bash_profile:

export OPENBLAS_NUM_THREADS=1
export OMP_NUM_THREADS=1

and then activate these settings with:

source ~/.bash_profile

The Github version include test files for complete unit testing. To run the suite of unit tests, make sure you have pytest installed and then type:

pytest

in the AbiPy root directory. A quicker check might be obtained with:

pytest abipy/core/tests -v

Unit tests require scripttest that can be installed with:

pip install scripttest

Two tests rely on the availability of a pymatgen PMG_MAPI_KEY <http://pymatgen.org/usage.html#setting-the-pmg-mapi-key-in-the-config-file> in ~/.pmgrc.yaml.

Note that several unit tests check the integration between AbiPy and Abinit. In order to run the tests, you will need a working set of Abinit executables and a manager.yml configuration file.

Contributing to AbiPy is relatively easy. Just send us a pull request. When you send your request, make develop the destination branch on the repository AbiPy uses the Git Flow branching model. The develop branch contains the latest contributions, and master is always tagged and points to the latest stable release.

Installing Abinit

One of the big advantages of conda over pip is that conda can also install libraries and executables written in Fortran. A pre-compiled sequential version of Abinit for Linux and OSx can be installed directly from the conda-forge channel with:

conda install abinit -c conda-forge

Otherwise, follow the usual abinit installation instructions, and make sure abinit can be run with the command:

abinit --version

Configuration files for Abipy

In order to run the Abipy tests, you will need a manager.yml configuration file. For a detailed description of the syntax used in this configuration file please consult the TaskManager documentation.

At this stage, for the purpose of checking the installation, you might take the shell_nompi_manager.yml file from the abipy/data/managers directory of this repository, and copy it with new name manager.yml to your $HOME/.abinit/abipy directory. Open this file and make sure that the pre_run section contains the shell commands needed to setup the environment before launching Abinit (e.g. Abinit is in $PATH), unless it is available from the environment (e.g. conda).

To complete the configuration files for Abipy, you might also copy the simple_scheduler.yml file from the same directory, and copy it with name scheduler.yml. Modifications are needed if you are developer.

Checking the installation

Now open the python interpreter and import the following three modules to check that the python installation is OK:

import spglib
import pymatgen
from abipy import abilab

then quit the interpreter.

For general information about how to troubleshoot problems that may occur at this level, see the :ref:`troubleshooting` section.

The Abinit executables are placed inside the anaconda directory associated to the abienv environment:

which abinit
/Users/gmatteo/anaconda3/envs/abienv/bin/abinit

To perform a basic validation of the build, execute:

abinit -b

Abinit should echo miscellaneous information, starting with:

DATA TYPE INFORMATION:
REAL:      Data type name: REAL(DP)
           Kind value:      8
           Precision:      15

and ending with:

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
  --- None ---


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

If successful, one can start to use the AbiPy scripts from the command line to analyze the output results. Execute:

abicheck.py

You should see (with minor changes):

$ abicheck.py
AbiPy Manager:
[Qadapter 0]
ShellAdapter:localhost
Hardware:
   num_nodes: 2, sockets_per_node: 1, cores_per_socket: 2, mem_per_node 4096,
Qadapter selected: 0

Abinitbuild:
Abinit Build Information:
    Abinit version: 8.8.2
    MPI: True, MPI-IO: True, OpenMP: False
    Netcdf: True

Abipy Scheduler:
PyFlowScheduler, Pid: 19379
Scheduler options: {'weeks': 0, 'days': 0, 'hours': 0, 'minutes': 0, 'seconds': 5}

Installed packages:
Package         Version
--------------  ---------
system          Darwin
python_version  3.6.5
numpy           1.14.3
scipy           1.1.0
netCDF4         1.4.0
apscheduler     2.1.0
pydispatch      2.0.5
yaml            3.12
pymatgen        2018.6.11


Abipy requirements are properly configured

If the script fails with the error message:

Abinit executable does not support netcdf
Abipy requires Abinit version >= 8.0.8 but got 0.0.0

it means that your environment is not property configured or that there's a problem with the binary executable. In this case, look at the files produced in the temporary directory of the flow. The script reports the name of the directory, something like:

CRITICAL:pymatgen.io.abinit.tasks:Error while executing /var/folders/89/47k8wfdj11x035svqf8qnl4m0000gn/T/tmp28xi4dy1/job.sh

Check the job.sh script for possible typos, then search for possible error messages in run.err.

The last test consists in executing a small calculation with AbiPy and Abinit. Inside the shell, execute:

abicheck.py --with-flow

to run a GS + NSCF band structure calculation for Si. If the software stack is properly configured, the output should end with:

Work #0: 
  , Finalized=True
  Finalized works are not shown. Use verbose > 0 to force output.

all_ok reached

Submitted on: Sat Jul 28 09:14:28 2018
Completed on: Sat Jul 28 09:14:38 2018
Elapsed time: 0:00:10.030767
Flow completed successfully

Calling flow.finalize()...

Work #0: 
  
   , Finalized=True
  Finalized works are not shown. Use verbose > 0 to force output.

all_ok reached


Test flow completed successfully

  
 

Great, if you've reached this part it means that you've installed AbiPy and Abinit on your machine! We can finally start to run the scripts in this repo or use one of the AbiPy script to analyze the results.

Using AbiPy

Basic usage

There are a variety of ways to use AbiPy, and most of them are illustrated in the abipy/examples directory. Below is a brief description of the different directories found there:

• examples/plot

  Scripts showing how to read data from netcdf files and produce plots with matplotlib

• examples/flows.

  Scripts showing how to generate an AbiPy flow, run the calculation and use ipython to analyze the data.

Additional jupyter notebooks with the Abinit tutorials written with AbiPy are available in the abitutorial repository.

Users are strongly encouraged to explore the detailed API docs.

Command line tools

The following scripts can be invoked directly from the terminal:

• abiopen.py Open file inside ipython.
• abistruct.py Swiss knife to operate on structures.
• abiview.py Visualize results from file.
• abicomp.py Compare results extracted from multiple files.
• abicheck.py Validate integration between AbiPy and Abinit
• abirun.py Execute AbiPy flow from terminal.
• abidoc.py Document Abinit input variables and Abipy configuration files.
• abinp.py Build input files (simplified interface for the AbiPy factory functions).

Use SCRIPT --help to get the list of supported commands and SCRIPT COMMAND --help to get the documentation for COMMAND.

For further information, please consult the scripts docs section.

Installing conda

A brief install guide, in case you have not yet used conda ... For a more extensive description, see our Anaconda Howto.

Download the miniconda installer. Select python3.6 and the version corresponding to your operating system.

As an example, if you are a Linux user, download and install miniconda on your local machine with:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

while for MacOSx use:

curl -o https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh

Answer yes to the question:

Do you wish the installer to prepend the Miniconda3 install location
to PATH in your /home/gmatteo/.bashrc ? [yes|no]
[no] >>> yes

Source your .bashrc file to activate the changes done by miniconda to your $PATH:

source ~/.bashrc

Troubleshooting

GLIBC error

The python interpreter may raise the following exception when importing one of the pymatgen modules:

from pymatgen.util.coord import pbc_shortest_vectors
File "/python3.6/site-packages/pymatgen/util/coord.py", line 11, in 
  
from . import coord_cython as cuc
ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /python3.6/site-packages/pymatgen/util/coord_cython.cpython-36m-x86_64-linux-gnu.so)`

 

This means that the pre-compiled version of pymatgen is not compatible with the GLIBC version available on your machine. To solve the problem, we suggest to build and install pymatgen from source using the local version of GLIBC and the gcc compiler. In the example below, we use a conda environment to install most of the dependencies with the exception of pymatgen and abipy.

Let's start by creating a conda environment with:

conda create -n glibc_env python=3.6
source activate glibc_env
conda config --add channels conda-forge

Use pip to install spglib:

pip install spglib

and try to import spglib inside the python terminal.

Download the pymatgen repository from github with:

git clone https://github.com/materialsproject/pymatgen.git
cd pymatgen

If git is not installed, use conda install git

Now use conda to install the pymatgen requirements listed in requirements.txt but before that make sure that gcc is in $PATH. If you are working on a cluster, you may want to issue:

module purge

to avoid compiling C code with the intel compiler (it's possible to use icc but gcc is less problematic).

Remove the line:

enum34==1.1.6; python_version < '3.4'

from requirements.txt as this syntax is not supported by conda then issue:

conda install -y --file requirements.txt

At this point, we can build pymatgen and the C extensions:

python setup.py install

then cd to another directory (important) and test the build inside the python terminal with:

import spglib
import pymatgen

Finally, we can install Abipy from source with:

git clone https://github.com/abinit/abipy.git
cd abipy && conda install -y --file ./requirements.txt

License

AbiPy is released under the GNU GPL license. For more details see the LICENSE file.