Develop (#302) · usnistgov/jarvis@e43b65a

Commit

Develop (#302)

* Typo fix.

* Add names to chem descs.

* Lessen hermsolver pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* No DFT3D

* Exclude dft_3d dataset for memory issue.

* Update figshare test.

* Update figshare test.

* Exclude db from coverage.

* Exclude db from coverage.

* Add magpie.json.

* Add magpie.json.

* Wien2k bands bug fix.

* Wien2k bands bug fix.

* Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code.

* JFF update.

* Add JQE_TB3 and hMOF dataset.

* Update LAMMPS module.

* Update LAMMPS module.

* Fix elastic tensor module.

* Figshare update, docs db name update.

* Substitutions.

* Update figshare dft_3d, cfid_3d.

* Docs data update.

* Generate substitutions.

* Lint fix.

* Update DOS.

* Update DOS.

* Adding folders for nexus setup.

* Update QMOF and hMOF info.

* Fixing auto klength error.

* Adding zeopp surface area.

* Vacancy bug fix, added hmof to docs.

* vacancy update.

* QE inputs update.

* Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details.

* Update Contribution.rst

* Minor lint fix.

* Update action_build.yml

* Update action_build.yml

* Fix qiskit requirements.

* Fix phonopy requirements.

* Fix all requirements.

* Fix phonopy requirements.

* QE test.

* QE test.

* Update action_build.

* Try other python versions.

* Try other python versions.

* README updates.

* Adding nexus. (#197)

* Develop (#196)

* Image augmentation.

* Augment images.

* Augment images.

* Specie update.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Update conf.py

* Update conf.py

* Multi-output graph bacthing.

* Add EDOS dataset.

* Temp.

* Add circuit maker.

* Add circuit maker.

* NELECT update.

* Version update, more DBs added.

* Fix CHGCAR vasp.

* Added volumetric reshape for CHGCAR.

* Tmp

* Tershoff Hamman update, specie update.

* Add crop from center in STM.

* Add Fourier transfor in STM.

* Update STM pytest.

* Add DPI to STM.

* Zeo++ added, Atoms cif update, STM update, random vacancy maker added.

* Atoms tempfile fix, Potcar from atoms module added.

* Test for docs.

* C2DB link update, docs Atoms update.

* C2DB link update, docs Atoms update.

* Version update, COD DB, QM9 JCTC DB added.

* Compostion bug fix, elemental descriptor added.

* Develop (#186)

* Update outputs.py

I added the calculation of the Raman intensities inside parse_raman_dat

* Update outputs.py

* Update outputs.py

* Update outputs.py

* Update cfid.py

* Delete __init__.py

* stylecss added.

* stylecss added.

* Adding extra Makefile/

* Remove examples from docs.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Tutorials update.

* Tutorials docs update.

* Docs update,pdb reader updated.

* Update action_build.yml

* Update action_build.yml

* Remove pytraj strong dependencies.

* Update docs, Added PDBBind and HPOV datasets.

* Docs update.

* Add thcikness to surface builder.

* Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix.

* Typo fix.

* Add names to chem descs.

* Lessen hermsolver pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* No DFT3D

* Exclude dft_3d dataset for memory issue.

* Update figshare test.

* Update figshare test.

* Exclude db from coverage.

* Exclude db from coverage.

* Add magpie.json.

* Add magpie.json.

* Wien2k bands bug fix.

* Wien2k bands bug fix.

* Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code.

* JFF update.

* Add JQE_TB3 and hMOF dataset.

* Update LAMMPS module.

* Update LAMMPS module.

* Fix elastic tensor module.

* Figshare update, docs db name update.

* Substitutions.

* Update figshare dft_3d, cfid_3d.

* Docs data update.

* Generate substitutions.

* Lint fix.

* Update DOS.

* Update DOS.

Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* First input.

* added black

* Example folder.

Co-authored-by: Kamal Choudhary <writetokamal.1989@gmail.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* Revert back.

* Update .readthedocs.yaml

* Update dev-requirements.txt

* Docs requirements update.

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update atoms.py

* Fixe pbc in ase_to_Atoms.

* Add installation tests (#214)

* QE inputs, XANES, GHAction updates. (#210)

* Image augmentation.

* Augment images.

* Augment images.

* Specie update.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Update conf.py

* Update conf.py

* Multi-output graph bacthing.

* Add EDOS dataset.

* Temp.

* Add circuit maker.

* Add circuit maker.

* NELECT update.

* Version update, more DBs added.

* Fix CHGCAR vasp.

* Added volumetric reshape for CHGCAR.

* Tmp

* Tershoff Hamman update, specie update.

* Add crop from center in STM.

* Add Fourier transfor in STM.

* Update STM pytest.

* Add DPI to STM.

* Zeo++ added, Atoms cif update, STM update, random vacancy maker added.

* Atoms tempfile fix, Potcar from atoms module added.

* Test for docs.

* C2DB link update, docs Atoms update.

* C2DB link update, docs Atoms update.

* Version update, COD DB, QM9 JCTC DB added.

* Compostion bug fix, elemental descriptor added.

* Develop (#186)

* Update outputs.py

I added the calculation of the Raman intensities inside parse_raman_dat

* Update outputs.py

* Update outputs.py

* Update outputs.py

* Update cfid.py

* Delete __init__.py

* stylecss added.

* stylecss added.

* Adding extra Makefile/

* Remove examples from docs.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Tutorials update.

* Tutorials docs update.

* Docs update,pdb reader updated.

* Update action_build.yml

* Update action_build.yml

* Remove pytraj strong dependencies.

* Update docs, Added PDBBind and HPOV datasets.

* Docs update.

* Add thcikness to surface builder.

* Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix.

* Typo fix.

* Add names to chem descs.

* Lessen hermsolver pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* No DFT3D

* Exclude dft_3d dataset for memory issue.

* Update figshare test.

* Update figshare test.

* Exclude db from coverage.

* Exclude db from coverage.

* Add magpie.json.

* Add magpie.json.

* Wien2k bands bug fix.

* Wien2k bands bug fix.

* Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code.

* JFF update.

* Add JQE_TB3 and hMOF dataset.

* Update LAMMPS module.

* Update LAMMPS module.

* Fix elastic tensor module.

* Figshare update, docs db name update.

* Substitutions.

* Update figshare dft_3d, cfid_3d.

* Docs data update.

* Generate substitutions.

* Lint fix.

* Update DOS.

* Update DOS.

* Adding folders for nexus setup.

* Update QMOF and hMOF info.

* Fixing auto klength error.

* Adding zeopp surface area.

* Vacancy bug fix, added hmof to docs.

* vacancy update.

* QE inputs update.

* Pyhon 3.9 test, added QE el-ph, VASP XANES, modified hmof db details.

* Update Contribution.rst

* Minor lint fix.

* Update action_build.yml

* Update action_build.yml

* Fix qiskit requirements.

* Fix phonopy requirements.

* Fix all requirements.

* Fix phonopy requirements.

* QE test.

* QE test.

* Update action_build.

* Try other python versions.

* Try other python versions.

* README updates.

* Adding nexus. (#197)

* Develop (#196)

* Image augmentation.

* Augment images.

* Augment images.

* Specie update.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Add Latt2D, STM image (b-1) fix, image augmentation fix.

* Update conf.py

* Update conf.py

* Multi-output graph bacthing.

* Add EDOS dataset.

* Temp.

* Add circuit maker.

* Add circuit maker.

* NELECT update.

* Version update, more DBs added.

* Fix CHGCAR vasp.

* Added volumetric reshape for CHGCAR.

* Tmp

* Tershoff Hamman update, specie update.

* Add crop from center in STM.

* Add Fourier transfor in STM.

* Update STM pytest.

* Add DPI to STM.

* Zeo++ added, Atoms cif update, STM update, random vacancy maker added.

* Atoms tempfile fix, Potcar from atoms module added.

* Test for docs.

* C2DB link update, docs Atoms update.

* C2DB link update, docs Atoms update.

* Version update, COD DB, QM9 JCTC DB added.

* Compostion bug fix, elemental descriptor added.

* Develop (#186)

* Update outputs.py

I added the calculation of the Raman intensities inside parse_raman_dat

* Update outputs.py

* Update outputs.py

* Update outputs.py

* Update cfid.py

* Delete __init__.py

* stylecss added.

* stylecss added.

* Adding extra Makefile/

* Remove examples from docs.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Docs update.

* Tutorials update.

* Tutorials docs update.

* Docs update,pdb reader updated.

* Update action_build.yml

* Update action_build.yml

* Remove pytraj strong dependencies.

* Update docs, Added PDBBind and HPOV datasets.

* Docs update.

* Add thcikness to surface builder.

* Surface builder update, Chemical only magpie descriptors added, pdb_core dataset added, zeopp tempfile bugfix.

* Typo fix.

* Add names to chem descs.

* Lessen hermsolver pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* Reduced pytest.

* No DFT3D

* Exclude dft_3d dataset for memory issue.

* Update figshare test.

* Update figshare test.

* Exclude db from coverage.

* Exclude db from coverage.

* Add magpie.json.

* Add magpie.json.

* Wien2k bands bug fix.

* Wien2k bands bug fix.

* Update JARVIS-FF,Elastictensor,LAMMPS parse folder, VASP bandstructure plot code.

* JFF update.

* Add JQE_TB3 and hMOF dataset.

* Update LAMMPS module.

* Update LAMMPS module.

* Fix elastic tensor module.

* Figshare update, docs db name update.

* Substitutions.

* Update figshare dft_3d, cfid_3d.

* Docs data update.

* Generate substitutions.

* Lint fix.

* Update DOS.

* Update DOS.

Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* First input.

* added black

* Example folder.

Co-authored-by: Kamal Choudhary <writetokamal.1989@gmail.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>

* Revert back.

* Update .readthedocs.yaml

* Update dev-requirements.txt

* Docs requirements update.

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update .readthedocs.yaml

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update atoms.py

* Fixe pbc in ase_to_Atoms.

Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>
Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com>

* Add installation tests

* Fix codestyle

* Fix codestyle with black

* Add docstrings

* Fix pydocstyle error

* Update __init__.py

* Update __init__.py

Co-authored-by: Kamal Choudhary <writetokamal.1989@gmail.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>
Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com>

* Adding QE super.

* Minor changes to QE module, atoms xyz fix.

* Adding qe_tb info, and version update.

* Update __init__.py

* WIP super QE.

* Working version of ScSi.

* QE inputs and task update.

* Add master super.

* Add master super.

* Lint fix.

* Lint fix.

* Minor fix.

* ET update.

* Fix ET test.

* Update sanitize atoms.

* Additonal checks on supercond.

* Debye bug fix.

* Pressure in QE Super.

* Version fix, publication update, supercond workflow update.

* Lint fix.

* Tensorboard fix.

* Tensorboard fix.

* Tensorboard fix.

* Melting temp fix.

* Update vasp.py (#234)

* Local tetra tmp.

* Version update.

* Lint fix.

* HSE06

* Tmp.

* Vacancy update, Optimade structureand other minor lint updates.

* STEM pytest fix.

* Minor lint fix.

* Fixed selectrive dynamics issue in Poscar, force reading for single atom system in Vasprun, np.array in core.graps, num_atoms for single atom systems in core.Atoms

* Lint fix.

* Added phononDos class.

* fix pytorch UserWarning in build_undirected_edgedata() (#243)

site-packages/jarvis/core/graphs.py:158: UserWarning: Creating a tensor from a list of numpy.ndarrays is extremely slow. Please consider converting the list to a single numpy.ndarray with numpy.array() before converting to a tensor.
  r = torch.tensor(r).type(torch.get_default_dtype())

* Add PhaseDiagram.

* Add PhaseDiagram.

* PhaseDiagram update.

* STM image pytest increase, requirements upgrade.

* STM image pytest increase, requirements upgrade.

* STM image pytest increase, requirements upgrade.

* Compare atoms, get spg info directly from atoms.

* Flake8 fix.

* Update publications.rst

* Update qiskit.

* Update qiskit.

* Update test_hermsolver.py

* FIix qiskit DOS.

* Update test_hermsolver.py

* Fix linting.

* Develop og (#257)

* Added isotope scattering rate to phonon DOS analysis script.

* Linting fix.

* Linting fix.

* Linting fix.

* Add QE convergence.

* Update converg.py.

* Nexus.

* Super with converg.

* Super with converg.

* SuperCon QE update.

* Figshare DB update.

* Figshare DB update.

* Update alignn ff link.

* Lint fix.

* DB docs update.

* Minor fixes: delete agg in figshare, add destination path in figshare data, dtype compatibility with new numpy.

* Lint fix.

* Supercon workflow fix.

* Add extra db entires, fix chem in cfid_chem.

* Version update.

* Add figshare datasets.

* Update databases.rst

* codecov fix.

* Version update.

* Lint fix.

* Add FigShare datasets, DOS in QE, Uncertainty.

* Add python 3.9.

* Create README.md

* Update README.

* Add README.md.

* Update action_build.yml

* Update action_lint.yml

* Allow md file, add mode databases.

* Create NISTtheDocs2Death.yml

* Allow md file, add mode databases.

* Add publications.

* Update publications.rst

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Update requirements.txt

* Create deploy_nist_pages.yml

* Add mkdocs.

* Update deploy_nist_pages.yml

* Update md.

* Update setup.py

* Update readme.

* Update setup.py

* Remove absl.

* Update dev-requirements.txt

* Update index.md

* Update deploy_nist_pages.yml

* Update index.rst

* Add redirect.

* Update action_build.yml

* Update dev-requirements.txt

* Update dev-requirements.txt

* Update setup.py

* Update dev-requirements.txt

* Fix __repr__ for Atoms.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Update requirements.

* Fix requirements.

* Fix requirements.

* Fix requirements.

* Fix requirements.

* Use poscar write as string.

* Use poscar write as string.

* Use poscar write as string.

* Update action_build.yml

* Use poscar write as string.

* Use poscar write as string.

* Update action_build.yml

* Use poscar write as string.

* Use poscar write as string.

* Delete NISTtheDocs2Death.yml

* Delete action_lint.yml

* Use poscar write as string.

* Fix phonopy.

* Update dev-requirements.txt

* Update databases.

* Add eigs.

* Add eigs.

* Add eigs.

* Fix STM test.

* Delete .travis.yml

* Update README.

* Add python docs.

* GA

* Update action_build.yml

---------

Co-authored-by: KAMAL CHOUDHARY <kamalch@login1.frontera.tacc.utexas.edu>
Co-authored-by: wines1 <74620550+wines1@users.noreply.github.com>
Co-authored-by: tavazza <tavazza@gmail.com>
Co-authored-by: knc6 <kamal.choudhary@nist.gov>
Co-authored-by: Saurav Maheshkar <sauravvmaheshkar@gmail.com>
Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
Co-authored-by: Ramya Gurunathan <ramya1006@gmail.com>

Loading branch information

8 people authored Aug 20, 2023

1 parent f5c01e0 commit e43b65a

.github/workflows/action_build.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -23,6 +23,7 @@ jobs: @@
         - name: Install requirements
           run: |
+            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
@@ Expand Down Expand Up / @@ -148,4 +149,4 @@ jobs: @@
     #             # git clone https://github.com/QEF/q-e.git
     #             # cd q-e
     #             # ./configure
-    #             # make pw
+    #             # make pw

README.md

-Original file line number
+Diff line change
@@ -1,3 +1,13 @@
+    # JARVIS-Tools
+    The JARVIS-Tools is an open-access software package for atomistic
+    data-driven materials design. JARVIS-Tools can be used for a) setting up
+    calculations, b) analysis and informatics, c) plotting, d) database
+    development and e) web-page development.
+    Detailed documentation available at: https://pages.nist.gov/jarvis/
     [![image](https://badge.fury.io/py/jarvis-tools.svg)](https://pypi.org/project/jarvis-tools/)
     [![image](https://anaconda.org/conda-forge/jarvis-tools/badges/version.svg)](https://anaconda.org/conda-forge/jarvis-tools)
     [![image](https://img.shields.io/github/v/tag/usnistgov/jarvis)](https://github.com/usnistgov/jarvis)
@@ Expand All / @@ -13,14 +23,4 @@ @@
     [![image](https://img.shields.io/badge/JARVIS-Figshare-Green.svg)](https://figshare.com/authors/Kamal_Choudhary/4445539)
     [![image](https://img.shields.io/badge/JARVIS-ToolsDocs-Green.svg)](https://pages.nist.gov/jarvis)
     [![image](https://colab.research.google.com/assets/colab-badge.svg)](https://github.com/JARVIS-Materials-Design/jarvis-tools-notebooks)
-    <!-- [![image](https://img.shields.io/travis/usnistgov/jarvis/master.svg?label=Travis%20CI)](https://travis-ci.org/usnistgov/jarvis) -->
-    ------------------------------------------------------------------------
-    # JARVIS-Tools
-    The JARVIS-Tools is an open-access software package for atomistic
-    data-driven materials design. JARVIS-Tools can be used for a) setting up
-    calculations, b) analysis and informatics, c) plotting, d) database
-    development and e) web-page development.
-    Detailed documentation available at: https://pages.nist.gov/jarvis/

docs/index.md

-Original file line number
+Diff line change
@@ Expand Up @@
     <a name="example"></a>
     ## Example function
-    ```
+    ``` python
     from jarvis.core.atoms import Atoms
     box = [[2.715, 2.715, 0], [0, 2.715, 2.715], [2.715, 0, 2.715]]
     coords = [[0, 0, 0], [0.25, 0.25, 0.25]]
@@ Expand Down @@

mkdocs.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -262,7 +262,7 @@ theme: @@
       extra:
       analytics:
         provider: google
-        property: G-0HPG8D56KJ
+        property: G-QBKG1JE5QF
       # +------------------------------------------------------------------------------------------------------+
       # |                                                                                                      |
@@ Expand Down @@

overrides/main.html

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -8,13 +8,13 @@
  
    <script async type="text/javascript" id="_fed_an_ua_tag" src="https://dap.digitalgov.gov/Universal-Federated-Analytics-Min.js?agency=NIST&subagency=github&pua=UA-66610693-1&yt=true&exts=ppsx,pps,f90,sch,rtf,wrl,txz,m1v,xlsm,msi,xsd,f,tif,eps,mpg,xml,pl,xlt,c">

    </script> -->

    <!-- <script async src="https://www.googletagmanager.com/gtag/js?id=G-1Q89M6QHG7"></script> -->

    <script async src="https://www.googletagmanager.com/gtag/js?id=G-0HPG8D56KJ"></script>

    <script async src="https://www.googletagmanager.com/gtag/js?id=G-QBKG1JE5QF"></script>

    <script>

      window.dataLayer = window.dataLayer || [];

      function gtag(){dataLayer.push(arguments);}

      gtag('js', new Date());

      gtag('config', 'G-0HPG8D56KJ');

      gtag('config', 'G-QBKG1JE5QF');

    </script>

    {% endblock %}

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