first commit

- add calcfunctions birch_murnaghan_fit and calculate_delta.
- add a eos workchain which has the similar framework as eos workchain in common
workflow package.

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+source=aiida_sssp_workflow

.github/check_version.py

@@ -0,0 +1,36 @@
+"""Check that version numbers match.
+
+Check version number in setup.json and aiida_sssp_workflow/__init__.py and make sure
+they match.
+"""
+from __future__ import absolute_import
+from __future__ import print_function
+import os
+import json
+import sys
+
+this_path = os.path.split(os.path.realpath(__file__))[0]
+
+# Get content of setup.json
+setup_fname = 'setup.json'
+setup_path = os.path.join(this_path, os.pardir, setup_fname)
+with open(setup_path) as f:
+    setup_content = json.load(f)
+
+# Get version from python package
+sys.path.insert(0, os.path.join(this_path, os.pardir))
+import aiida_sssp_workflow  # pylint: disable=wrong-import-position
+version = aiida_sssp_workflow.__version__
+
+if version != setup_content['version']:
+    print("Version number mismatch detected:")
+    print("Version number in '{}': {}".format(setup_fname,
+                                              setup_content['version']))
+    print("Version number in '{}/__init__.py': {}".format(
+        'aiida_sssp_workflow', version))
+    sys.exit(1)
+
+# Overwrite version in setup.json
+#setup_content['version'] = version
+#with open(setup_path, 'w') as f:
+#	json.dump(setup_content, f, indent=4, sort_keys=True)

.github/install_aiida_github.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+git clone https://github.com/aiidateam/aiida_core ../aiida_core
+cd ../aiida_core
+git checkout $AIIDA_DEVELOP_GIT_HASH
+pip install -e .[docs,pre-commit,testing]
+cd ${TRAVIS_BUILD_DIR}

.github/workflows/ci.yml

@@ -0,0 +1,79 @@
+name: ci
+
+on: [push, pull_request]
+
+jobs:
+
+  tests:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        python-version: [3.7]
+        backend: ['django']
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install system dependencies
+      run: |
+        wget -O - "https://github.com/rabbitmq/signing-keys/releases/download/2.0/rabbitmq-release-signing-key.asc" | sudo apt-key add -
+        echo 'deb https://dl.bintray.com/rabbitmq-erlang/debian bionic erlang' | sudo tee -a /etc/apt/sources.list.d/bintray.rabbitmq.list
+        echo 'deb https://dl.bintray.com/rabbitmq/debian bionic main' | sudo tee -a /etc/apt/sources.list.d/bintray.rabbitmq.list
+        sudo rm -f /etc/apt/sources.list.d/dotnetdev.list /etc/apt/sources.list.d/microsoft-prod.list
+        sudo apt update
+        sudo apt install postgresql-10 rabbitmq-server graphviz
+        sudo systemctl status rabbitmq-server.service
+
+    - name: Install python dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -e .[testing]
+        reentry scan -r aiida
+
+    - name: Run test suite
+      env:
+        AIIDA_TEST_BACKEND: ${{ matrix.backend }}
+        # show timings of tests
+        PYTEST_ADDOPTS: "--durations=0"
+      run: py.test --cov aiida_sssp_workflow --cov-append .
+
+  docs:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install python dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -e .[docs]
+        reentry scan -r aiida
+    - name: Build docs
+      run: cd docs && make
+
+  pre-commit:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install python dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -e .[pre-commit,docs,testing]
+        reentry scan -r aiida
+    - name: Run pre-commit
+      run: |
+        pre-commit install
+        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.github/workflows/publish-on-pypi.yml

@@ -0,0 +1,40 @@
+name: Publish on PyPI
+
+on:
+  push:
+    tags:
+      # After vMajor.Minor.Patch _anything_ is allowed (without "/") !
+      - v[0-9]+.[0-9]+.[0-9]+*
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    if: github.repository == 'aiidateam/aiida-sssp-workflow' && startsWith(github.ref, 'refs/tags/v')
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+
+    - name: Upgrade setuptools and install package
+      run: |
+        python -m pip install --upgrade pip setuptools
+        python -m pip install -e .
+
+    - name: Assert package version
+      env:
+        TAG_VERSION: ${{ github.ref }}
+      run: python ./.github/check_version.py
+
+    - name: Build source distribution
+      run: python ./setup.py sdist
+
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.pypi_token }}

.gitignore

@@ -0,0 +1,15 @@
+*.pyc
+*.swo
+*.swp
+~*
+*~
+.project
+*.egg*
+.DS_Store
+.coverage
+.pytest_cache
+.vscode
+.idea/
+build/
+dist/
+pip-wheel-metadata/

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+# Install pre-commit hooks via:
+# pre-commit install
+
+# yapf = yet another python formatter
+- repo: https://github.com/pre-commit/mirrors-yapf
+  rev: v0.28.0
+  hooks:
+  - id: yapf
+    name: yapf
+    args: ["-i"]
+
+- repo: local
+  hooks:
+  # prospector: collection of linters
+  - id: prospector
+    language: system
+    types: [file, python]
+    name: prospector
+    description: "This hook runs Prospector: https://github.com/landscapeio/prospector"
+    entry: prospector
+
+  - id: version-number
+    name: Check version numbers
+    entry: python ./.github/check_version.py
+    language: system
+    files: '^(setup.json)|(aiida_sssp_workflow/__init__.py)'

.readthedocs.yml

@@ -0,0 +1,9 @@
+version: 2
+
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 The AiiDA Team.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

@@ -0,0 +1,2 @@
+include setup.json
+include LICENSE

README.md

@@ -126,3 +126,4 @@ MIT
 [email protected]
 
 # aiida-sssp-workflow
+# aiida-sssp-workflow

aiida_sssp_workflow/__init__.py

@@ -0,0 +1,7 @@
+"""
+aiida_sssp_workflow
+
+SSSP verification workflows
+"""
+
+__version__ = "0.1.0a0"

aiida_sssp_workflow/calculations/birch_murnaghan_fit.py

@@ -0,0 +1,52 @@
+# -*- coding: utf-8 -*-
+"""
+Birch-Murnaghan fit as calcfunction refactor from eosfit.py v3.1 write by Kurt Lejaeghere
+Copyright (C) 2012 Kurt Lejaeghere <[email protected]>, Center for
+Molecular Modeling (CMM), Ghent University, Ghent, Belgium
+"""
+from aiida.engine import calcfunction
+from aiida import orm
+
+@calcfunction
+def birch_murnaghan_fit(volume_energy: orm.Dict) -> orm.Dict:
+    import numpy as np
+
+    volumes = np.array(list(volume_energy['volumes'].values()))
+    energies = np.array(list(volume_energy['energies'].values()))
+    fitdata = np.polyfit(volumes ** (-2. / 3.), energies, 3, full=True)
+    ssr = fitdata[1]
+    sst = np.sum((energies - np.average(energies)) ** 2.)
+    residuals0 = ssr / sst
+    deriv0 = np.poly1d(fitdata[0])
+    deriv1 = np.polyder(deriv0, 1)
+    deriv2 = np.polyder(deriv1, 1)
+    deriv3 = np.polyder(deriv2, 1)
+
+    volume0 = 0
+    x = 0
+    for x in np.roots(deriv1):
+        if x > 0 and deriv2(x) > 0:
+            volume0 = x ** (-3. / 2.)
+            break
+
+    if volume0 == 0:
+        print('Error: No minimum could be found')
+        exit()
+
+    derivV2 = 4. / 9. * x ** 5. * deriv2(x)
+    derivV3 = (-20. / 9. * x ** (13. / 2.) * deriv2(x) -
+               8. / 27. * x ** (15. / 2.) * deriv3(x))
+    bulk_modulus0 = derivV2 / x ** (3. / 2.)
+    bulk_deriv0 = -1 - x ** (-3. / 2.) * derivV3 / derivV2
+
+    echarge = 1.60217733e-19
+    # TODO 'E0': minimum energy, per atom,
+    res = orm.Dict(dict={
+        'volume0': volume0,
+        'bulk_modulus0': bulk_modulus0 * echarge * 1.0e21,
+        'bulk_deriv0': bulk_deriv0,
+        'residuals0': residuals0[0],
+        'volume0_unit': 'A^3/atom',
+        'bulk_modulus0_unit': 'GPa',
+    })
+    return res