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@knc6
knc6 committed Mar 20, 2024
1 parent e0419b2 commit 6733a9b
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16 changes: 12 additions & 4 deletions .github/workflows/action_build.yml
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Expand Up @@ -23,17 +23,20 @@ jobs:

- name: Install requirements
run: |
find . -type f > before_test_files.txt
pip install --upgrade pip
pip install pycodestyle flake8 pydocstyle
flake8 --ignore E203,W503 --exclude=examples,tests --statistics --count --exit-zero jarvis
pycodestyle --ignore E203,W503 --exclude=examples,testfiles jarvis
pydocstyle --match-dir=core --match-dir=io --match-dir=io --match-dir=ai --match-dir=analysis --match-dir=db --match-dir=tasks --count jarvis
#python setup.py develop
#pip install --upgrade --upgrade-strategy eager -r dev-requirements.txt -e .
#conda install -c ambermd pytraj
pip install numpy scipy matplotlib
pip install -r dev-requirements.txt
conda install pandas numpy matplotlib --quiet
conda env create -f environment.yml
#pip install numpy scipy matplotlib
#pip install -r dev-requirements.txt
pip install -e .
echo 'CONDA LIST'
conda list
Expand All @@ -49,6 +52,11 @@ jobs:
coverage report -m -i
codecov
codecov --token="b61081a0-39de-44a8-8a9c-97d4be82af6d"
find . -type f > after_test_files.txt
#comm -13 <(sort before_test_files.txt) <(sort after_test_files.txt) > new_files.txt
#cat new_files.txt | xargs rm
#rm before_test_files.txt after_test_files.txt new_files.txt
# git clone https://github.com/QEF/q-e.git
# cd q-e
# ./configure
Expand Down Expand Up @@ -149,4 +157,4 @@ jobs:
# # git clone https://github.com/QEF/q-e.git
# # cd q-e
# # ./configure
# # make pw
# # make pw
274 changes: 274 additions & 0 deletions environment.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,274 @@
name: my_jarvis
channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- alsa-lib=1.2.11=hd590300_1
- archspec=0.2.2=pyhd8ed1ab_0
- attr=2.5.1=h166bdaf_1
- boltons=23.1.1=pyhd8ed1ab_0
- brotli=1.1.0=hd590300_1
- brotli-bin=1.1.0=hd590300_1
- brotli-python=1.1.0=py310hc6cd4ac_1
- bzip2=1.0.8=hd590300_5
- c-ares=1.24.0=hd590300_0
- ca-certificates=2024.2.2=hbcca054_0
- cairo=1.18.0=h3faef2a_0
- certifi=2024.2.2=pyhd8ed1ab_0
- cffi=1.16.0=py310h2fee648_0
- charset-normalizer=3.3.2=pyhd8ed1ab_0
- colorama=0.4.6=pyhd8ed1ab_0
- conda=23.11.0=py310hff52083_1
- conda-libmamba-solver=23.12.0=pyhd8ed1ab_0
- conda-package-handling=2.2.0=pyh38be061_0
- conda-package-streaming=0.9.0=pyhd8ed1ab_0
- contourpy=1.2.0=py310hd41b1e2_0
- cycler=0.12.1=pyhd8ed1ab_0
- dbus=1.13.6=h5008d03_3
- distro=1.8.0=pyhd8ed1ab_0
- expat=2.6.2=h59595ed_0
- fmt=10.1.1=h00ab1b0_1
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=h77eed37_1
- fontconfig=2.14.2=h14ed4e7_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.50.0=py310h2372a71_0
- freetype=2.12.1=h267a509_2
- gettext=0.21.1=h27087fc_0
- glib=2.80.0=hf2295e7_0
- glib-tools=2.80.0=hde27a5a_0
- graphite2=1.3.13=h58526e2_1001
- gst-plugins-base=1.22.9=h8e1006c_0
- gstreamer=1.22.9=h98fc4e7_0
- harfbuzz=8.3.0=h3d44ed6_0
- icu=73.2=h59595ed_0
- idna=3.6=pyhd8ed1ab_0
- jsonpatch=1.33=pyhd8ed1ab_0
- jsonpointer=2.4=py310hff52083_3
- keyutils=1.6.1=h166bdaf_0
- kiwisolver=1.4.5=py310hd41b1e2_1
- krb5=1.21.2=h659d440_0
- lame=3.100=h166bdaf_1003
- lcms2=2.16=hb7c19ff_0
- ld_impl_linux-64=2.40=h41732ed_0
- lerc=4.0.0=h27087fc_0
- libarchive=3.7.2=h2aa1ff5_1
- libblas=3.9.0=21_linux64_openblas
- libbrotlicommon=1.1.0=hd590300_1
- libbrotlidec=1.1.0=hd590300_1
- libbrotlienc=1.1.0=hd590300_1
- libcap=2.69=h0f662aa_0
- libcblas=3.9.0=21_linux64_openblas
- libclang=15.0.7=default_hb11cfb5_4
- libclang13=15.0.7=default_ha2b6cf4_4
- libcups=2.3.3=h4637d8d_4
- libcurl=8.5.0=hca28451_0
- libdeflate=1.19=hd590300_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=hd590300_2
- libevent=2.1.12=hf998b51_1
- libexpat=2.6.2=h59595ed_0
- libffi=3.4.2=h7f98852_5
- libflac=1.4.3=h59595ed_0
- libgcc-ng=13.2.0=h807b86a_3
- libgcrypt=1.10.3=hd590300_0
- libgfortran-ng=13.2.0=h69a702a_5
- libgfortran5=13.2.0=ha4646dd_5
- libglib=2.80.0=hf2295e7_0
- libgomp=13.2.0=h807b86a_3
- libgpg-error=1.48=h71f35ed_0
- libiconv=1.17=hd590300_2
- libjpeg-turbo=3.0.0=hd590300_1
- liblapack=3.9.0=21_linux64_openblas
- libllvm15=15.0.7=hb3ce162_4
- libmamba=1.5.5=had39da4_0
- libmambapy=1.5.5=py310h39ff949_0
- libnghttp2=1.58.0=h47da74e_1
- libnsl=2.0.1=hd590300_0
- libogg=1.3.4=h7f98852_1
- libopenblas=0.3.26=pthreads_h413a1c8_0
- libopus=1.3.1=h7f98852_1
- libpng=1.6.43=h2797004_0
- libpq=16.2=h33b98f1_1
- libsndfile=1.2.2=hc60ed4a_1
- libsolv=0.7.27=hfc55251_0
- libsqlite=3.44.2=h2797004_0
- libssh2=1.11.0=h0841786_0
- libstdcxx-ng=13.2.0=h7e041cc_3
- libsystemd0=255=h3516f8a_1
- libtiff=4.6.0=ha9c0a0a_2
- libuuid=2.38.1=h0b41bf4_0
- libvorbis=1.3.7=h9c3ff4c_0
- libwebp-base=1.3.2=hd590300_0
- libxcb=1.15=h0b41bf4_0
- libxkbcommon=1.6.0=hd429924_1
- libxml2=2.12.3=h232c23b_0
- libzlib=1.2.13=hd590300_5
- lz4-c=1.9.4=hcb278e6_0
- lzo=2.10=h516909a_1000
- mamba=1.5.5=py310h51d5547_0
- matplotlib=3.8.3=py310hff52083_0
- matplotlib-base=3.8.3=py310h62c0568_0
- menuinst=2.0.1=py310hff52083_0
- mpg123=1.32.4=h59595ed_0
- munkres=1.1.4=pyh9f0ad1d_0
- mysql-common=8.0.33=hf1915f5_6
- mysql-libs=8.0.33=hca2cd23_6
- ncurses=6.4=h59595ed_2
- nspr=4.35=h27087fc_0
- nss=3.97=h1d7d5a4_0
- openjpeg=2.5.2=h488ebb8_0
- openssl=3.2.1=hd590300_1
- packaging=23.2=pyhd8ed1ab_0
- pandas=2.2.1=py310hcc13569_0
- pcre2=10.43=hcad00b1_0
- pillow=10.2.0=py310h01dd4db_0
- pip=23.3.2=pyhd8ed1ab_0
- pixman=0.43.2=h59595ed_0
- platformdirs=4.1.0=pyhd8ed1ab_0
- ply=3.11=py_1
- pthread-stubs=0.4=h36c2ea0_1001
- pulseaudio-client=16.1=hb77b528_5
- pybind11-abi=4=hd8ed1ab_3
- pycosat=0.6.6=py310h2372a71_0
- pycparser=2.21=pyhd8ed1ab_0
- pyparsing=3.1.2=pyhd8ed1ab_0
- pyqt=5.15.9=py310h04931ad_5
- pyqt5-sip=12.12.2=py310hc6cd4ac_5
- pysocks=1.7.1=pyha2e5f31_6
- python=3.10.13=hd12c33a_0_cpython
- python-tzdata=2024.1=pyhd8ed1ab_0
- python_abi=3.10=4_cp310
- pytz=2024.1=pyhd8ed1ab_0
- qt-main=5.15.8=h450f30e_18
- readline=8.2=h8228510_1
- reproc=14.2.4.post0=hd590300_1
- reproc-cpp=14.2.4.post0=h59595ed_1
- ruamel.yaml=0.18.5=py310h2372a71_0
- ruamel.yaml.clib=0.2.7=py310h2372a71_2
- setuptools=68.2.2=pyhd8ed1ab_0
- sip=6.7.12=py310hc6cd4ac_0
- six=1.16.0=pyh6c4a22f_0
- tk=8.6.13=noxft_h4845f30_101
- toml=0.10.2=pyhd8ed1ab_0
- tomli=2.0.1=pyhd8ed1ab_0
- tornado=6.4=py310h2372a71_0
- tqdm=4.66.1=pyhd8ed1ab_0
- truststore=0.8.0=pyhd8ed1ab_0
- tzdata=2023c=h71feb2d_0
- unicodedata2=15.1.0=py310h2372a71_0
- wheel=0.42.0=pyhd8ed1ab_0
- xcb-util=0.4.0=hd590300_1
- xcb-util-image=0.4.0=h8ee46fc_1
- xcb-util-keysyms=0.4.0=h8ee46fc_1
- xcb-util-renderutil=0.3.9=hd590300_1
- xcb-util-wm=0.4.1=h8ee46fc_1
- xkeyboard-config=2.41=hd590300_0
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.1.1=hd590300_0
- xorg-libsm=1.2.4=h7391055_0
- xorg-libx11=1.8.7=h8ee46fc_0
- xorg-libxau=1.0.11=hd590300_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h0b41bf4_2
- xorg-libxrender=0.9.11=hd590300_0
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h0b41bf4_1003
- xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.6=h166bdaf_0
- yaml-cpp=0.8.0=h59595ed_0
- zlib=1.2.13=hd590300_5
- zstandard=0.22.0=py310h1275a96_0
- zstd=1.5.5=hfc55251_0
- pip:
- annotated-types==0.6.0
- appdirs==1.4.4
- autograd==1.6.2
- babel==2.14.0
- bokeh==2.4.2
- cif2cell==2.1.0
- click==8.1.7
- coverage==7.4.4
- cryptography==42.0.5
- dgl==2.1.0
- dill==0.3.8
- exceptiongroup==1.2.0
- filelock==3.13.1
- fsspec==2024.3.1
- future==1.0.0
- ghp-import==2.1.0
- h5py==3.10.0
- iniconfig==2.0.0
- jinja2==3.1.3
- joblib==1.3.2
- lightgbm==3.3.1
- markdown==3.6
- markupsafe==2.1.5
- mergedeep==1.3.4
- mkdocs==1.5.3
- mkdocs-material==9.5.14
- mkdocs-material-extensions==1.3.1
- mpmath==1.3.0
- networkx==3.2.1
- ntlm-auth==1.5.0
- numpy==1.23.5
- nvidia-cublas-cu12==12.1.3.1
- nvidia-cuda-cupti-cu12==12.1.105
- nvidia-cuda-nvrtc-cu12==12.1.105
- nvidia-cuda-runtime-cu12==12.1.105
- nvidia-cudnn-cu12==8.9.2.26
- nvidia-cufft-cu12==11.0.2.54
- nvidia-curand-cu12==10.3.2.106
- nvidia-cusolver-cu12==11.4.5.107
- nvidia-cusparse-cu12==12.1.0.106
- nvidia-nccl-cu12==2.19.3
- nvidia-nvjitlink-cu12==12.4.99
- nvidia-nvtx-cu12==12.1.105
- paginate==0.5.6
- pathspec==0.12.1
- pbr==6.0.0
- pennylane==0.14.1
- phonopy==2.10.0
- pluggy==1.4.0
- psutil==5.9.8
- pycifrw==4.4.6
- pydantic==2.6.4
- pydantic-core==2.16.3
- pygments==2.17.2
- pymdown-extensions==10.7.1
- pytest==8.1.1
- python-dateutil==2.8.2
- pyyaml==6.0.1
- pyyaml-env-tag==0.1
- qiskit==0.41.1
- qiskit-aer==0.11.2
- qiskit-ibmq-provider==0.20.1
- qiskit-terra==0.23.2
- regex==2023.12.25
- requests==2.28.2
- requests-ntlm==1.1.0
- rustworkx==0.14.2
- scikit-learn==1.4.1.post1
- scipy==1.12.0
- semantic-version==2.6.0
- spglib==2.3.1
- stevedore==5.2.0
- symengine==0.11.0
- sympy==1.12
- threadpoolctl==3.3.0
- toolz==0.12.1
- torch==2.2.1
- torchdata==0.7.1
- triton==2.2.0
- typing-extensions==4.10.0
- urllib3==1.26.18
- watchdog==4.0.0
- websocket-client==1.5.3
- websockets==10.4
- xmltodict==0.13.0
26 changes: 15 additions & 11 deletions jarvis/core/graphs.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
"""Module to generate networkx graphs."""

from jarvis.core.atoms import get_supercell_dims
from jarvis.core.specie import Specie
from jarvis.core.utils import random_colors
Expand All @@ -11,18 +12,16 @@
# from jarvis.core.atoms import Atoms
from collections import defaultdict
from typing import List, Tuple, Sequence, Optional

try:
import torch
from tqdm import tqdm
import dgl
except Exception as exp:
print("dgl/torch/tqdm is not installed.", exp)
pass
import torch
from tqdm import tqdm
import dgl


def canonize_edge(
src_id, dst_id, src_image, dst_image,
src_id,
dst_id,
src_image,
dst_image,
):
"""Compute canonical edge representation.
Expand All @@ -46,7 +45,11 @@ def canonize_edge(


def nearest_neighbor_edges(
atoms=None, cutoff=8, max_neighbors=12, id=None, use_canonize=False,
atoms=None,
cutoff=8,
max_neighbors=12,
id=None,
use_canonize=False,
):
"""Construct k-NN edge list."""
# returns List[List[Tuple[site, distance, index, image]]]
Expand Down Expand Up @@ -118,7 +121,8 @@ def nearest_neighbor_edges(


def build_undirected_edgedata(
atoms=None, edges={},
atoms=None,
edges={},
):
"""Build undirected graph data from edge set.
Expand Down
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