usnistgov · knc6 · Aug 11, 2023 · Jun 20, 2021 · Jun 20, 2021 · Jun 20, 2021
diff --git a/.github/workflows/NISTtheDocs2Death.yml b/.github/workflows/NISTtheDocs2Death.yml
@@ -0,0 +1,14 @@
+name: "Build Documentation"
+
+on: [push, pull_request, delete]
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: usnistgov/NISTtheDocs2Death@0.3
+        with:
+          docs-folder: docs/
+          formats: |-
+            epub
+            pdf
diff --git a/.github/workflows/action_build.yml b/.github/workflows/action_build.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8,3.9]
+        python-version: [3.9]
     steps:
     - uses: actions/checkout@v2
     - name: Setup Python ${{ matrix.python-version }}

diff --git a/.github/workflows/action_lint.yml b/.github/workflows/action_lint.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.7]
+        python-version: [3.9]
 
     steps:
     - uses: actions/checkout@v1

diff --git a/.github/workflows/deploy_nist_pages.yml b/.github/workflows/deploy_nist_pages.yml
@@ -0,0 +1,75 @@
+#
+# This is a working example of using GitHub Actions to publish the docs
+# to the GitHub Pages (gh_pages) branch.
+#
+# Remember to have a requirements.txt file with the required dependencies.
+# This template ships with one by default.
+#
+# It is also recommendet to also copy the template with all branches, to
+# have the gh-pages branch pre-made. This prevents possible errors.
+#
+name: Deploy Site
+
+# on: [push, pull_request]
+
+on:
+  push:
+    branches:
+      - master
+
+permissions:
+  contents: write
+
+# on:
+#   push:
+#     paths:
+#     - 'docs/**'
+#     - 'mkdocs.yml'
+#     - 'theme/**'
+#     branches:
+#     - master
+#     #
+#     # If your repository would have releases should you uncomment the below lines
+#     # in order to ignore pushes caused by newly created releases.
+#     #
+#     #tags-ignore:
+#     #- '**'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        python setup.py develop
+        #python -m pip install -r requirements.txt
+
+    - name: Deploy Files
+      run: |
+        git config user.name "github-actions[bot]"
+        git config user.email "actions@github.com"
+        # python jarvis_leaderboard/rebuild.py
+        mkdocs build
+        #rm -r /tmp/site
+        cp -r site /tmp
+        git fetch
+        git checkout nist-pages --force
+        rm -r *
+        cp -r /tmp/site/* .
+
+        echo 'listing'
+        ls
+        echo 'listing tmp'
+        ls /tmp
+        git add * */*
+        git commit -m 'Adding files.'
+        git push origin nist-pages -f
+        #git commit -a -m "Move"
+        #git push -f origin nist-pages1
+        #mkdocs gh-deploy  
diff --git a/README.md b/README.md
@@ -0,0 +1,26 @@
+[![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)
+[![image](https://ci.appveyor.com/api/projects/status/d8na8vyfm7ulya9p/branch/master?svg=true)](https://ci.appveyor.com/project/knc6/jarvis-63tl9)
+[![image](https://github.com/usnistgov/jarvis/workflows/JARVIS-Tools%20github%20action/badge.svg)](https://github.com/usnistgov/jarvis)
+[![image](https://github.com/usnistgov/jarvis/workflows/JARVIS-Tools%20linting/badge.svg)](https://github.com/usnistgov/jarvis)
+[![image](https://img.shields.io/codecov/c/github/knc6/jarvis)](https://codecov.io/gh/knc6/jarvis)
+[![image](https://img.shields.io/pypi/dm/jarvis-tools.svg)](https://img.shields.io/pypi/dm/jarvis-tools.svg)
+[![image](https://pepy.tech/badge/jarvis-tools)](https://pepy.tech/badge/jarvis-tools)
+[![image](https://zenodo.org/badge/DOI/10.5281/zenodo.3903515.svg)](https://doi.org/10.5281/zenodo.3903515)
+[![image](https://img.shields.io/github/commit-activity/y/usnistgov/jarvis)](https://github.com/usnistgov/jarvis)
+[![image](https://img.shields.io/github/repo-size/usnistgov/jarvis)](https://github.com/usnistgov/jarvis)
+[![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/
diff --git a/README.rst b/README.rst
@@ -82,9 +82,9 @@ Installation
 
       bash Miniconda3-latest-Linux-x86_64.sh (for linux)
       bash Miniconda3-latest-MacOSX-x86_64.sh (for Mac)
-      Download 32/64 bit python 3.8 miniconda exe and install (for windows)
+      Download 32/64 bit python 3.9 miniconda exe and install (for windows)
       Now, let's make a conda environment just for JARVIS::
-      conda create --name my_jarvis python=3.8
+      conda create --name my_jarvis python=3.9
       source activate my_jarvis
 
 - Method-1: Installation using pip::

diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -83,7 +83,7 @@ pyasn1-modules==0.2.8
 pybind11==2.8.1
 PyCifRW==4.4
 pycparser==2.21
-Pygments==2.10.0
+Pygments==2.14
 pyparsing==3.0.6
 pyrsistent==0.18.0
 pytest==6.2.5

diff --git a/docs/assets/css/extensions/tabbed.css b/docs/assets/css/extensions/tabbed.css
@@ -0,0 +1,41 @@
+.tabbed-set {
+  display: flex;
+  position: relative;
+  flex-wrap: wrap;
+}
+
+.tabbed-set .highlight {
+  background: #ddd;
+}
+
+.tabbed-set .tabbed-content {
+  display: none;
+  order: 99;
+  width: 100%;
+}
+
+.tabbed-set label {
+  width: auto;
+  margin: 0 0.5em;
+  padding: 0.25em;
+  font-size: 120%;
+  cursor: pointer;
+  color: #ffffff !important;
+}
+
+.tabbed-set input {
+  position: absolute;
+  opacity: 0;
+}
+
+.tabbed-set input:nth-child(n+1) {
+  color: #333333;
+}
+
+.tabbed-set input:nth-child(n+1):checked + label {
+    color: cyan !important;
+}
+
+.tabbed-set input:nth-child(n+1):checked + label + .tabbed-content {
+    display: block;
+}
diff --git a/docs/assets/css/extra.css b/docs/assets/css/extra.css
@@ -0,0 +1 @@
+@import "extensions/tabbed.css";
diff --git a/docs/databases.md b/docs/databases.md
@@ -0,0 +1,160 @@
+# Databases
+
+## [FigShare](https://figshare.com/authors/Kamal_Choudhary/4445539) based databases
+
+| Database name     | Number of data-points | Description                                                                                                                           |
+|-------------------|-----------------------|---------------------------------------------------------------------------------------------------------------------------------------|
+| `dft_3d`          | 75993                 | Various 3D materials properties in JARVIS-DFT database computed with OptB88vdW and TBmBJ methods                                      |
+| `dft_2d`          | 1109                  | Various 2D materials properties in JARVIS-DFT database computed with OptB88vdW                                                        |
+| `dft_3d_2021`     | 55723                 | Various 3D materials properties in JARVIS-DFT database computed with OptB88vdW and TBmBJ methods                                      |
+| `dft_2d_2021`     | 1079                  | Various 2D materials properties in JARVIS-DFT database computed with OptB88vdW                                                        |
+| `qe_tb`           | 829574                | Various 3D materials properties in JARVIS-QETB database                                                                               |
+| `stm`             | 1132                  | 2D materials STM images in JARVIS-STM database                                                                                        |
+| `wtbh_electron`   | 1440                  | 3D and 2D materials Wannier tight-binding Hamiltonian dtaabase for electrons with spin-orbit coupling in JARVIS-WTB (Keyword: 'WANN') |
+| `wtbh_phonon`     | 15502                 | 3D and 2D materials Wannier tight-binding Hamiltonian for phonons at Gamma with finite difference (Keyword:FD-ELAST)                  |
+| `jff`             | 2538                  | Various 3D materials properties in JARVIS-FF database computed with several force-fields                                              |
+| `alignn_ff_db`    | 307113                | Energy per atom, forces and stresses for ALIGNN-FF trainig for 75k materials.                                                         |
+| `edos_pdos`       | 48469                 | Normalized electron and phonon density of states with interpolated values and fixed number of bins                                    |
+| `megnet`          | 69239                 | Formation energy and bandgaps of 3D materials properties in Materials project database as on 2018, used in megnet                     |
+| `mp_3d_2020`      | 127k                  | CFID descriptors for materials project                                                                                                |
+| `mp_3d`           | 84k                   | CFID descriptors for 84k materials project                                                                                            |
+| `megnet2`         | 133k                  | 133k materials and their formation energy in MP                                                                                       |
+| `twod_matpd`      | 6351                  | Formation energy and bandgaps of 2D materials properties in 2DMatPedia database                                                       |
+| `c2db`            | 3514                  | Various properties in C2DB database                                                                                                   |
+| `polymer_genome`  | 1073                  | Electronic bandgap and diecltric constants of crystall ine polymer in polymer genome database                                         |
+| `qm9_std_jctc`    | 130829                | Various properties of molecules in QM9 database                                                                                       |
+| `qm9_dgl`         | 130829                | Various properties of molecules in QM9 dgl database                                                                                   |
+| `cod`             | 431778                | Atomic structures from crystallographic open database                                                                                 |
+| `oqmd_3d_no_cfid` | 817636                | Formation energies and bandgaps of 3D materials from OQMD database                                                                    |
+| `oqmd_3d`         | 460k                  | CFID descriptors for 460k materials in OQMD                                                                                           |
+| `omdb`            | 12500                 | Bandgaps for organic polymers in OMDB database                                                                                        |
+| `hopv`            | 4855                  | Various properties of molecules in HOPV15 dataset                                                                                     |
+| `pdbbind`         | 11189                 | Bio-molecular complexes database from PDBBind v2015                                                                                   |
+| `pdbbind_core`    | 195                   | Bio-molecular complexes database from PDBBind core                                                                                    |
+| `qmof`            | 20425                 | Bandgaps and total energies of metal organic frameowrks in QMOF database                                                              |
+| `hmof`            | 137651                | Hypothetical MOF database                                                                                                             |
+| `snumat`          | 10481                 | Bandgaps with hybrid functional                                                                                                       |
+| `arXiv`           | 12500                 | arXiv dataset 1.8 million title, abstract and id dataset                                                                              |
+| `ssub`            | 1726                  | SSUB formation energy for chemical formula dataset                                                                                    |
+| `mlearn`          | 1730                  | Machine learning force-field for elements datasets                                                                                    |
+| `ocp10k`          | 59886                 | Open Catalyst 10000 training, rest validation and test dataset                                                                        |
+| `ocp100k`         | 149886                | Open Catalyst 100000 training, rest validation and test dataset                                                                       |
+| `ocp_all`         | 510214                | Open Catalyst 460328 training, rest validation and test dataset                                                                       |
+| `tinnet_N`        | 329                   | TinNet Nitrogen catalyst dataset                                                                                                      |
+| `tinnet_O`        | 747                   | TinNet Oxygen catalyst dataset                                                                                                        |
+| `tinnet_OH`       | 748                   | TinNet OH group catalyst dataset                                                                                                      |
+| `AGRA_O`          | 1000                  | AGRA Oxygen catalyst dataset                                                                                                          |
+| `AGRA_OH`         | 875                   | AGRA OH catalyst dataset                                                                                                              |
+| `AGRA_CO`         | 193                   | AGRA CO catalyst dataset                                                                                                              |
+| `AGRA_CHO`        | 214                   | AGRA CHO catalyst dataset                                                                                                             |
+| `AGRA_COOH`       | 280                   | AGRA COOH catalyst dataset                                                                                                            |
+| `supercon_3d`     | 1058                  | 3D superconductor DFT dataset                                                                                                         |
+| `supercon_2d`     | 161                   | 2D superconductor DFT dataset                                                                                                         |
+| `supercon_chem`   | 16414                 | Superconductor chemical formula dataset                                                                                               |
+| `vacancydb`       | 464                   | Vacancy formation energy dataset                                                                                                      |
+| `cfid_3d`         | 55723                 | Various 3D materials properties in JARVIS-DFT database computed with OptB88vdW and TBmBJ methods with CFID                            |
+| `raw_files`       | 144895                | Figshare links to download raw calculations VASP files from JARVIS-DFT                                                                |
+
+All these datasets can be obtained using jarvis-tools as follows,
+exception to `stm`, `wtbh_electron`, `wtbh_phonon` which have their own
+modules in `jarvis.db.figshare`:
+
+``` python
+from jarvis.db.figshare import data
+d = data('dft_3d') #choose a name of dataset from above
+# See available keys
+print (d[0].keys())
+# Dataset size
+print(len(d))
+
+# Visualize an atoms object
+from jarvis.core.atoms import Atoms
+a = Atoms.from_dict(d[0]['atoms'])
+#You can visualize this in VESTA or other similar packages
+print(a)
+
+# If pandas framework needed
+import pandas as pd
+df = pd.DataFrame(d)
+print(df)
+```
+
+## JARVIS-DFT
+
+Description coming soon!
+
+### JARVIS-Formation energy and bandgap
+
+### JARVIS-2D Exfoliation energies
+
+### JARVIS-MetaGGA (dielectric function and SLME, solar cells)
+
+### JARVIS-STM and STEM
+
+### JARVIS-WannierTB
+
+### JARVIS-Elastic constants
+
+### JARVIS-Topological materials (Spin-orbit Spillage)
+
+### JARVIS-DFPT (Piezoelectric, IR, Raman, dielectric, BEC)
+
+### JARVIS-BoltzTrap (Thermoelectrics coeff, eff. mass)
+
+### JARVIS-Magnetic moments
+
+### JARVIS-DFPT (Piezoelectric, IR, dielectric)
+
+### JARVIS-EFG
+
+### JARVIS-PBE0 and HSE06
+
+### JARVIS-Heterostructure
+
+### JARVIS-EDOS-PDOS
+
+### JARVIS-Kpoint and cut-off
+
+## JARVIS-FF
+
+### Energetics
+
+### Elastic constants 
+
+### Vacancy formation energy 
+
+### Surface energy and Wulff-plots 
+
+### Phonon DOS
+
+## JARVIS-RAW Files
+
+### JARVIS-DFT structure relaxation
+
+### JARVIS-DFT Elastic constants/finite difference
+
+### JARVIS-WannierTB
+
+### JARVIS-STM and STEM
+
+## External datasets used for ML training
+
+### Materials project dataset
+
+### QM9 dataset
+
+### OQMD dataset
+
+### AFLOW dataset
+
+### Polymer genome dataset
+
+### COD dataset
+
+### OMDB dataset
+
+### QMOF dataset
+
+### C2DB dataset
+
+### HPOV dataset