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Consider the presence of software in your life and how so much of what we do depends upon the works of others. This is why the freedom to share is at the core of the FSF's work. We can only truly foster free software, free documentation, and free cultural works for users around the world if we have the ability to share. Read more Join. ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei molecules and periodic solids within Density Functional Theory DFT , using pseudopotentials and a planewave basis.
ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Inside the shell, execute:. If the software stack is properly configured, the output should end with:.
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. Below is a brief description of the different directories found there:.
Scripts showing how to read data from netcdf files and produce plots with matplotlib. 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. For further information, please consult the scripts docs section. 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. As an example, if you are a Linux user, download and install miniconda on your local machine with:.
Source your. The python interpreter may raise the following exception when importing one of the pymatgen modules:. 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.
Now use conda to install the pymatgen requirements listed in requirements. If you are working on a cluster, you may want to issue:. Skip to content. Star View license. This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. The format of this info block is described in abinit.
Use abinit online using onworks. The latter is needed for different tests of abinis see below. You can also issue 'make mrgddb' to make the code that merge the derivative databases, 'make ifc' to make the code that analyze interatomic force constant, 'make aim' for the Bader analysis utility. For this purpose, issue 'make blas'. This possibility is also used for the Fujitsu machines. With a bit of luck, you will succeed to generate the executables. You are ready to perform the tests. It is possible to make the compilation execute in such a way that the result is stored in a machine-dependent subdirectory.
Prior to the compilation on one platform, issue :. For the compilation on another platform, the 'make bindir' command must be performed again, before compilation, and the binaries generated by that other compilation will be put in the corresponding directory. The abinis code has five small internal tests, that can be issued automatically, and that check themselves whether the results that have been obtained are right or wrong.
At most 3 MB of memory is required, and 1 MB of disk space. PERL must be installed on your machine for these tests to work. This means that the internal test 1 ran successfully. If you do not get this message, then the executables were not properly generated, or there is a problem with the make and scripts that drive the internal test. Note : the script detects the end of the run by using the 'ps' command following by a 'grep' command.
This can lead to strange effects if a file whose name contain 'abinis' is currently visualized, or if another job is running under a name that contains 'abinis'. So, close your files before running the tests, and also check that there are no running jobs whose name contains 'abinis'. The test 1 will be done once more, followed by the 4 other internal tests.
Again, we hope that you will get the positive diagnostics for the other tests. You might now read the new user's guide , in order to learn how to use the code. This is useful if you consider that the installation has been successful, or if you want to continue the tests.
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