ASE is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
To install ASE we need to install package manager conda
Installing the conda package manager
To install the library we need to install the anaconda which includes conda package manager, python3.9 version and Jupyter Notebook used for scientific computing and data science.
* Download Anaconda installer for Linux.
* Verify your installer hashes
sha256sum Anaconda3-2021.11-Linux-x86_64.sh
* .Run
/abinitio> chmod +x Anaconda3-2021.11-Linux-x86_64.sh
/abinitio> ./Anaconda3-2021.11-Linux-x86_64.sh
accept the default choices
We get the following
==> For changes to take effect, close and re-open your current shell. <==
If you'd prefer that conda's base environment not be activated on startup,
set the auto_activate_base parameter to false:
conda config --set auto_activate_base false
Thank you for installing Anaconda3!
===========================================================================
Working with Python and Jupyter notebooks is a breeze with PyCharm Pro,
designed to be used with Anaconda. Download now and have the best data
tools at your fingertips.
PyCharm Pro for Anaconda is available at: https://www.anaconda.com/pycharm
* Source the ~/.bashrc file
source ~/.bashrc
How to avoid conda to activate base environment?
By default conda init will add to your .bashrc file for the base environment, which will slow down your terminal.
You can remove them in your .bashrc file or answer no to that question in the last step of your anaconda installation.
And then add the following to your .bashrc file. If you changed the default installation directory, change ~/anaconda3/ to that directory.
source ~/anaconda3/etc/profile.d/conda.sh
if [[ -z ${CONDA_PREFIX+x} ]]; then
export PATH="~/conda/bin:$PATH"
fiTo test it, open a new terminal tab or run source .bashrc. Run conda activate base, then you should see (base) in front of your Bash prompt.
Now you can create another environment and activate it using Anaconda. If you frequently use one environment, you can also add conda activate [env] to your .bashrc file.
NB: You can install miniconda packae which is a minimal free Conda installer. It’s a thin, bootstrap version that
contains just conda, Python, the packages they depend on, and a limited
range of other helpful modules like pip, zlib, and a few others.
Update conda
vasp-ase-tutorials> conda update -n base -c defaults conda
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/algerien1970/anaconda3
added / updated specs:
- conda
The following packages will be downloaded:
package | build
---------------------------|-----------------
conda-4.13.0 | py39h06a4308_0 895 KB
conda-pack-0.7.0 | pyh6c4a22f_0 30 KB conda-forge
conda-package-handling-1.8.1| py39h7f8727e_0 889 KB
pyjwt-2.4.0 | py39h06a4308_0 34 KB
xmltodict-0.13.0 | pyhd8ed1ab_0 13 KB conda-forge
------------------------------------------------------------
Total: 1.8 MB
The following packages will be UPDATED:
conda 4.10.3-py39h06a4308_0 --> 4.13.0-py39h06a4308_0
conda-pack pkgs/main::conda-pack-0.6.0-pyhd3eb1b~ --> conda-forge::conda-pack-0.7.0-pyh6c4a22f_0
conda-package-han~ 1.7.3-py39h27cfd23_1 --> 1.8.1-py39h7f8727e_0
pyjwt 2.1.0-py39h06a4308_0 --> 2.4.0-py39h06a4308_0
xmltodict pkgs/main::xmltodict-0.12.0-pyhd3eb1b~ --> conda-forge::xmltodict-0.13.0-pyhd8ed1ab_0
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conda-package-handli
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conda-4.13.0 | 895 KB |
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xmltodict-0.13.0 | 13 KB |
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pyjwt-2.4.0 | 34 KB |
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conda-pack-0.7.0 | 30 KB |
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Create a virtual enironment independent from the root environment and name it ase
/vasp-ase-tutorials/mg-hcp> conda create --name ase
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/algerien1970/anaconda3/envs/ase
Proceed ([y]/n)? y
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#
# To activate this environment, use
#
# $ conda activate ase
#
# To deactivate an active environment, use
#
# $ conda deactivate
Activate ase environment
/vasp-ase-tutorials/mg-hcp> conda activate ase
(ase) algerien1970@linux-kq57:~/abinitio/vasp-ase-tutorials>
Install ase package: conda will install all the necessary packages for the working of ASE interface
(ase) algerien1970/vasp-ase-tutorials> conda install -c conda-forge ase
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/algerien1970/anaconda3/envs/ase
added / updated specs:
- ase
The following packages will be downloaded:
package | build
---------------------------|-----------------
pillow-9.2.0 | py310hace64e9_1 1.2 MB
------------------------------------------------------------
Total: 1.2 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ase conda-forge/noarch::ase-3.22.1-pyhd8ed1ab_1
brotli conda-forge/linux-64::brotli-1.0.9-h166bdaf_7
brotli-bin conda-forge/linux-64::brotli-bin-1.0.9-h166bdaf_7
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
ca-certificates conda-forge/linux-64::ca-certificates-2022.6.15-ha878542_0
certifi conda-forge/linux-64::certifi-2022.6.15-py310hff52083_0
click conda-forge/linux-64::click-8.1.3-py310hff52083_0
cycler conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab_0
flask conda-forge/noarch::flask-2.1.3-pyhd8ed1ab_0
fonttools conda-forge/linux-64::fonttools-4.34.4-py310h5764c6d_0
freetype pkgs/main/linux-64::freetype-2.11.0-h70c0345_0
giflib conda-forge/linux-64::giflib-5.2.1-h36c2ea0_2
importlib-metadata conda-forge/linux-64::importlib-metadata-4.11.4-py310hff52083_0
itsdangerous conda-forge/noarch::itsdangerous-2.1.2-pyhd8ed1ab_0
jinja2 conda-forge/noarch::jinja2-3.1.2-pyhd8ed1ab_1
jpeg conda-forge/linux-64::jpeg-9e-h166bdaf_2
kiwisolver conda-forge/linux-64::kiwisolver-1.4.4-py310hbf28c38_0
lcms2 conda-forge/linux-64::lcms2-2.12-hddcbb42_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
lerc conda-forge/linux-64::lerc-3.0-h9c3ff4c_0
libblas conda-forge/linux-64::libblas-3.9.0-15_linux64_openblas
libbrotlicommon conda-forge/linux-64::libbrotlicommon-1.0.9-h166bdaf_7
libbrotlidec conda-forge/linux-64::libbrotlidec-1.0.9-h166bdaf_7
libbrotlienc conda-forge/linux-64::libbrotlienc-1.0.9-h166bdaf_7
libcblas conda-forge/linux-64::libcblas-3.9.0-15_linux64_openblas
libdeflate conda-forge/linux-64::libdeflate-1.12-h166bdaf_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-12.1.0-h8d9b700_16
libgfortran-ng conda-forge/linux-64::libgfortran-ng-12.1.0-h69a702a_16
libgfortran5 conda-forge/linux-64::libgfortran5-12.1.0-hdcd56e2_16
libgomp conda-forge/linux-64::libgomp-12.1.0-h8d9b700_16
liblapack conda-forge/linux-64::liblapack-3.9.0-15_linux64_openblas
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libopenblas conda-forge/linux-64::libopenblas-0.3.20-pthreads_h78a6416_0
libpng conda-forge/linux-64::libpng-1.6.37-h753d276_3
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-12.1.0-ha89aaad_16
libtiff conda-forge/linux-64::libtiff-4.4.0-hc85c160_1
libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
libwebp conda-forge/linux-64::libwebp-1.2.2-h3452ae3_0
libwebp-base conda-forge/linux-64::libwebp-base-1.2.2-h7f98852_1
libzlib conda-forge/linux-64::libzlib-1.2.12-h166bdaf_2
lz4-c conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_1
markupsafe conda-forge/linux-64::markupsafe-2.1.1-py310h5764c6d_1
matplotlib-base conda-forge/linux-64::matplotlib-base-3.5.2-py310h5701ce4_0
munkres conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
numpy conda-forge/linux-64::numpy-1.23.1-py310h53a5b5f_0
openssl conda-forge/linux-64::openssl-3.0.5-h166bdaf_0
packaging conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0
pillow pkgs/main/linux-64::pillow-9.2.0-py310hace64e9_1
pip conda-forge/noarch::pip-22.1.2-pyhd8ed1ab_0
pyparsing conda-forge/noarch::pyparsing-3.0.9-pyhd8ed1ab_0
python conda-forge/linux-64::python-3.10.5-ha86cf86_0_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.10-2_cp310
readline conda-forge/linux-64::readline-8.1.2-h0f457ee_0
scipy conda-forge/linux-64::scipy-1.8.1-py310h7612f91_0
setuptools conda-forge/linux-64::setuptools-63.2.0-py310hff52083_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
sqlite conda-forge/linux-64::sqlite-3.39.1-h4ff8645_0
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
tzdata conda-forge/noarch::tzdata-2022a-h191b570_0
unicodedata2 conda-forge/linux-64::unicodedata2-14.0.0-py310h5764c6d_1
werkzeug conda-forge/noarch::werkzeug-2.1.2-pyhd8ed1ab_1
wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.5-h516909a_1
zipp conda-forge/noarch::zipp-3.8.0-pyhd8ed1ab_0
zlib conda-forge/linux-64::zlib-1.2.12-h166bdaf_2
zstd conda-forge/linux-64::zstd-1.5.2-h8a70e8d_2
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Downloading and Extracting Packages
pillow-9.2.0 | 1.2 MB | #################################################################################################################################################### | 100%
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Hello, my name is Dr Abderrahmane Reggad. I'm a 53 year old and I am a researcher in materials' sciences. 
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