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توضیحات

Command-Line Interface for Materials Simulations

ویژگی	مقدار
سیستم عامل	-
نام فایل	clims-0.4.4
نام	clims
نسخه کتابخانه	0.4.4
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	FHI-aims developers
ایمیل نویسنده	-
آدرس صفحه اصلی	https://gitlab.com/FHI-aims-club/utilities/clims
آدرس اینترنتی	https://pypi.org/project/clims/
مجوز	LGPLv2.1+

# Table of Contents [[_TOC_]] # clims Command-line interface for materials simulations. Basically pulls together usefull python packages of the materials simulation community: * [ASE](https://wiki.fysik.dtu.dk/ase/index.html) * [spglib](https://spglib.github.io/spglib/) (cyrstal symmetry properties) * [phonopy](https://phonopy.github.io/phonopy/) (phonon properties from finite-differences) This package is tailored for the needs of FHI-aims. ## System requirements A python 3 installation with a version `python>=3.7` is required. To check your python version type: ``` python --version ``` In the following instructions on some systems it may be needed to use `python3` and `pip3`. On a computer with such an installation, the below commands will install a number of other useful community packages for atomistic simulations as prerequisites, most importantly, `ASE`, `spglib`, `phonopy`, as well as several others. Please also see the troubleshooting notes below in case you encounter a particular, missing prerequisite during the installation process. ## How to install It is best to install `clims` in a virtual environment. May not always true, e.g. on computing clusters. ### Install/Activate virtualenv (optional) Make sure that `virtualenv` is installed: ``` pip show virtualenv ``` If not installed, install it: ``` pip install --user virtualenv ``` Go into the root directory of clims. Initialize the virtual environment: ``` python -m venv env ``` Activate the virtual environment: ``` source env/bin/activate ``` You should now see `(env)` in at the beginning of your command line. ### Install clims Install clims (make sure that you are in the root director of clims (where this README is)) with: ``` pip install --user . ``` If all goes well, you will have a working clims installation after this step. If something does not work (for instance, if a particular installation prerequisite that should be part of python is missing), unfortunately the error messages written by `pip` can be somewhat cryptic. As an approximate rule, the final line of a python error message often identifies the piece that was missing. To test your installation you can run: ``` pytest -vv ``` ### Troubleshooting **Installation under CentOS**: In order for this installation to work, we noticed that the `_ctypes` module is required. This only works if the library `libffi` (including development headers - sometimes called `libffi-dev` or `libffi-devel`) is also required and the computer's python version must have been built with support for `libffi-dev` (or `libffi-devel`). If support for `libffi` headers is not present, then someone will unfortunately have to rebuild and reinstall the python >= 3.7 installation on the computer you are using from scratch. ## How to configure clims The most important thing to set is the path to the FHI-aims species defaults: ``` clims-configure --species-path <your/path/to/FHIaims/species_defaults> ``` ## Features After successful installation the following commands should be available in the terminal: | clims command | description | | ------ | ------ | | `clims-unit-cell-info` | Get brief overview of input structure, if periodic: generate primitive or conventional unit cell. | | `clims-supercell` | Generate supercell. | | `clims-real2frac`,`clims-frac2real`| Convert atomic coordinates of periodic structure from Cartesian to real and vice versa. | | `clims-phonopy-initialize`, `clims-phonopy-postprocess` | Generate supercell structures with displaced atoms (initialize) and read forces after FHI-aims calculation to plot phonon DOS (postprocess). | | `clims-wigner-seitz-cluster` | Constructs a Cluster of the shape of the Wigner-Seitz cell. | | `clims-aimsplot` | Famous aimsplot script for plotting band structure and DOS from FHI-aims. | | `clims-xyplot` | Simple X-Y plot of data files. | | `clims-prepare-run` | Create `control.in` template based on a `geometry.in` file. If requested a submission file is provided, too. | | `clims-configure` | Configure Path to exectutable and species defaults directory, mpi run command, submission header. Needed e.g. for `clims-prepare-run` | | `clims-testsuite` | Create a testsuite of all defined input parameter combinations. |

نیازمندی

مقدار	نام
>=3.21.1	ase
>=1.16.1	spglib
>=2.9.3	phonopy
>=3.4.1	matplotlib
>=7.1.2	click
>=6.2.3	pytest

زبان مورد نیاز

مقدار	نام
>=3.7	Python

نحوه نصب

نصب پکیج whl clims-0.4.4:

pip install clims-0.4.4.whl

نصب پکیج tar.gz clims-0.4.4:

pip install clims-0.4.4.tar.gz