Merge pull request #177 from atomec-project/develop

Make new release 1.3.0

.github/workflows/gh-pages.yml

@@ -12,13 +12,13 @@ on:
 
 jobs:
   python-style-checks:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: '3.8'
 
@@ -36,13 +36,13 @@ jobs:
 
   build-and-deploy-pages:
     needs: python-style-checks
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: '3.8'
 

.github/workflows/mirror.yml

@@ -4,13 +4,15 @@ on: [push, delete]
 
 jobs:
   mirror-to-CASUS:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
     - name: mirror-repository
-      uses: spyoungtech/mirror-action@v0.4.0
+      uses: spyoungtech/mirror-action@v0.6.0
       with:
-        REMOTE: git@github.com:casus/atoMEC.git
+        REMOTE: 'ssh://git@github.com/casus/atoMEC.git'
         GIT_SSH_PRIVATE_KEY: ${{ secrets.GIT_SSH_KEY }}
         GIT_SSH_NO_VERIFY_HOST: "true"
         DEBUG: "true"

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

@@ -14,13 +14,13 @@ on:
 jobs:
   build-n-publish:
     name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
     - name: Check out repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.8'
 

.github/workflows/tests.yml

@@ -9,38 +9,41 @@ on:
     branches:
       - master
       - develop
-      
+
 jobs:
   run-test-suite:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     timeout-minutes: 15
     steps:
       - name: Check out repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Setup Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: '3.8'
 
       - name: Upgrade pip
         run: python3 -m pip install --upgrade pip
-        
+
       - name : Install pipenv
-        run : python -m pip install --upgrade pipenv
-  
+        run : python3 -m pip install --upgrade pipenv
+
       - id: cache-pipenv
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         with:
           path: ~/.local/share/virtualenvs
           key: ${{ runner.os }}-pipenv-${{ hashFiles('**/Pipfile.lock') }}
-     
+
       - name: Install dependencies
         if: steps.cache-pipenv.outputs.cache-hit != 'true'
-        run: pipenv install --dev
-     
+        run: pipenv --python 3.8 install --dev
+
       - name: Install atoMEC
-        run: pipenv run python -m pip install -e .
-        
+        run: pipenv run python3 -m pip install -e .
+
       - name: Run test suite
-        run: pipenv run pytest --cov=atoMEC --random-order tests/
+        run: pipenv run pytest --cov=atoMEC --cov-report=xml --random-order tests/
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3

README.md

@@ -8,6 +8,7 @@
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![PyPI version](https://badge.fury.io/py/atoMEC.svg)](https://badge.fury.io/py/atoMEC)
 [![Python 3.8](https://img.shields.io/badge/python-3.8-blue.svg)](https://www.python.org/downloads/release/python-380/)
+[![codecov](https://codecov.io/gh/atomec-project/atoMEC/branch/develop/graph/badge.svg?token=V66CJJ3KPI)](https://codecov.io/gh/atomec-project/atoMEC)
 
 atoMEC is a python-based average-atom code for simulations of high energy density phenomena such as in warm dense matter.
 It is designed as an open-source and modular python package.

atoMEC/check_inputs.py

@@ -355,7 +355,7 @@ def radius_to_dens(self, atom, radius):
         # radius in cm
         rad_cm = radius / unitconv.cm_to_bohr
         # volume in cm
-        vol_cm = (4.0 * pi * rad_cm ** 3) / 3.0
+        vol_cm = (4.0 * pi * rad_cm**3) / 3.0
         # atomic mass in g
         mass_g = config.mp_g * atom.at_mass
         # density in g cm^-3
@@ -752,10 +752,11 @@ def check_conv_params(input_params):
         conv_params : dict of floats
             dictionary of convergence parameters as follows:
             {
-            `econv` (``float``)  : convergence for total energy,
-            `nconv` (``float``)  : convergence for density,
-            `vconv` (``float``)  : convergence for electron number,
-            `eigtol` (``float``) : tolerance for eigenvalues
+            `econv` (``float``)   : convergence for total energy,
+            `nconv` (``float``)   : convergence for density,
+            `vconv` (``float``)   : convergence for electron number,
+            `eigtol` (``float``)  : tolerance for eigenvalues,
+            `bandtol` (``float``) : tolerance for n(l)max warning
             }
 
         Raises
@@ -765,7 +766,7 @@ def check_conv_params(input_params):
         """
         conv_params = {}
         # loop through the convergence parameters
-        for conv in ["econv", "nconv", "vconv", "eigtol"]:
+        for conv in ["econv", "nconv", "vconv", "eigtol", "bandtol"]:
             # assign value if not given
             try:
                 x_conv = input_params[conv]
@@ -1171,3 +1172,27 @@ def ngrid_warning(err1, err2):
             " convergence \n"
         )
         return warning
+
+    def norbs_warning(quantum_num):
+        """
+        Warn if either nmax or lmax is too low for convergence.
+
+        Parameters
+        ----------
+        quantum_num : str
+            lmax or nmax
+
+        Returns
+        -------
+        warning : str
+            full error message
+        """
+        warning = (
+            "Warning: "
+            + quantum_num
+            + " appears to be too low. Proceeding anyway, but suggest to increase "
+            + quantum_num
+            + " and restart calculation"
+        )
+
+        return warning

atoMEC/config.py

@@ -14,7 +14,13 @@
 # numerical grid for static calculations
 grid_params = {"ngrid": 1000, "x0": -12, "ngrid_coarse": 300}
 # convergence parameters for static calculations
-conv_params = {"econv": 1.0e-5, "nconv": 1.0e-4, "vconv": 1.0e-4, "eigtol": 1.0e-4}
+conv_params = {
+    "econv": 1.0e-5,
+    "nconv": 1.0e-4,
+    "vconv": 1.0e-4,
+    "eigtol": 1.0e-4,
+    "bandtol": 1.0e-3,
+}
 # scf parameters
 scf_params = {"maxscf": 50, "mixfrac": 0.3}
 # band parameters for massacrier band model

atoMEC/models.py

@@ -259,7 +259,8 @@ def CalcEnergy(
             `econv` (``float``)  : convergence for total energy,
             `nconv` (``float``)  : convergence for density,
             `vconv` (``float``)  : convergence for electron number,
-            `eigtol` (``float``) : convergence for eigenvalues
+            `eigtol` (``float``) : convergence for eigenvalues,
+            `bandtol` (``float``) : tolerance for n(l)max warning
             }
         scf_params : dict, optional
             dictionary for scf cycle parameters as follows:
@@ -458,6 +459,7 @@ def CalcPressure(
         write_info=False,
         verbosity=0,
         dR=0.01,
+        method="A",
     ):
         r"""
         Calculate the electronic pressure using the finite differences method.
@@ -523,6 +525,7 @@ def CalcPressure(
             write_info,
             verbosity,
             dR,
+            method,
         )
 
         return P_e