Merge pull request #54 from WMD-group/differentialAS

First version with differential absorption spectra functionality.
WMD-group · Oct 20, 2023 · 0e20cae · 0e20cae
2 parents e4dee3c + f0c7866
commit 0e20cae
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diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml
@@ -12,15 +12,15 @@ on:
   workflow_dispatch:
 
 jobs:
-  build-linux:
-    runs-on: ubuntu-latest
+  build:
     strategy:
-      max-parallel: 5
+      fail-fast: false
 
       matrix:
         python-version: ['3.8', '3.9','3.10']
+        os: [ ubuntu-latest,macos-latest,windows-latest ]
 
-    name: Python ${{ matrix.python-version }} Test Pop
+    runs-on: ${{matrix.os}}
 
     steps:
       - uses: actions/checkout@v3
@@ -36,10 +36,12 @@ jobs:
           pip install numpy
           pip install -e .
           pip install -e .[tests]
+
       - name: Check package versions
         run: |
           pip show -V pymatgen
           pip show -V pytest
+
       - name: Test
         run:  |
           pytest tests/test_generator.py  # test generator
@@ -49,14 +51,16 @@ jobs:
           # to run the following image comparison tests and see relative differences, use the CLI
           # pytest --mpl --mpl-generate-summary=html tests/test_plotter.py
 
-      # Download test plots
-      # - name: Archive test plots
-      #   uses: actions/upload-artifact@v3
-      #   with:
-      #     name: output-plots
-      #     path: tests/remote_baseline
-
-      # - name: Download a single artifact
-      #   uses: actions/download-artifact@v3
-      #   with:
-      #     name: output-plots
+      - name: Generate GH Actions test plots
+        if: always()  # always generate the plots, even if the tests fail
+        run: |
+          # Generate the test plots in case there were any failures:
+          pytest --mpl-generate-path=tests/remote_baseline_plots tests/test_plotter.py
+
+      # Upload test plots
+      - name: Archive test plots
+        if: always()
+        uses: actions/upload-artifact@v3
+        with:
+          name: output-plots
+          path: tests/remote_baseline_plots
diff --git a/.github/workflows/pip_install_test.yml b/.github/workflows/pip_install_test.yml
@@ -8,16 +8,17 @@ on:
       - completed  # only test when new release has been deployed to PyPI
 
 jobs:
-  build-linux:
-    runs-on: ubuntu-latest
+  build:
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
+
     strategy:
-      max-parallel: 5
+      fail-fast: false
 
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: [ '3.8', '3.9','3.10' ]
+        os: [ ubuntu-latest,macos-latest,windows-latest ]
 
-    name: Python ${{ matrix.python-version }} pip install
+    runs-on: ${{matrix.os}}
 
     steps:
       - uses: actions/checkout@v2

diff --git a/.gitignore b/.gitignore
@@ -84,6 +84,7 @@ ENV/
 
 # Spyder project settings
 .spyderproject
+.spyproject
 
 # Rope project settings
 .ropeproject

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,10 @@
 Change log
 ==========
 
+v2.2.0
+~~~~~~
+- Initial version of differential absorption spectra (DAS) functionality.
+
 v2.1.4
 ~~~~~~
 - Addition of MAPI example outputs download instructions to DFT example by @youngwonwoo.

diff --git a/README.md b/README.md
@@ -11,12 +11,12 @@
 
 [Official Documentation](https://pytaser.readthedocs.io/en/latest/)
 
-PyTASER is a Python (3.9+) library for simulating differential absorption in general, and transient absorption spectroscopy (TAS) in particular, features from quantum chemical calculations of crystals. The goal of this library is to simulate spectra for comparison with and interpretation of experiments. The main features include:
+PyTASER is a Python library for simulating differential absorption spectra in compounds using quantum chemical calculations, including transient (TAS) and differential (DAS) absorption spectroscopies. The goal of this library is to simulate spectra for comparison with and interpretation of experiments. The main features include:
 
-* Spectra for insulating and semiconducting crystals
-* Components from individual band-to-band transitions
-* Spectra for different conditions: temperature and carrier concentrations
-* Consideration of non-magnetic and magnetic materials
+* Transient (TAS) and differential (DAS) absorption spectra for insulating and semiconducting crystals (using DFT or database calculations)
+* Plotting contributions from individual band-to-band transitions
+* TAS spectra for different conditions: temperature and carrier concentrations
+* Customisable plotting.
 * Capability to input calculated bandstructure and density of states inputs with support for the [Materials Project](https://materialsproject.org)
 
 # Installation
@@ -95,4 +95,4 @@ Future topics we plan to build on:
 
 # Acknowledgements
 
-The project has been developed by @savya10, @kavanase and @youngwonwoo under the supervision of @utf and @aronwalsh.
+The project has been developed by @savya10, @kavanase, @LucasGVerga and @youngwonwoo, under the supervision of @utf and @aronwalsh.
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -19,6 +19,5 @@ numpy>=1.21
 scipy
 setuptools
 monty
-deepdiff
 pytest-mpl
 pytest
diff --git a/docs/source/contributors.rst b/docs/source/contributors.rst
@@ -59,4 +59,17 @@ Additional contributions have been provided by:
    :height: 16
    :alt: GitHub commits from youngwonwoo
 
+| **Lucas Verga** |LucasGVerga| |0000-0002-7453-238X|
+| Postdoc, Imperial College London
+
+.. |0000-0002-7453-238X| image:: _static/orcid.svg
+   :target: https://orcid.org/0000-0002-7453-238X
+   :width: 16
+   :height: 16
+   :alt: ORCID profile for 0000-0002-7453-238X
+.. |LucasGVerga| image:: https://cdnjs.cloudflare.com/ajax/libs/octicons/8.5.0/svg/mark-github.svg
+   :target: https://github.com/LucasGVerga
+   :width: 16
+   :height: 16
+   :alt: GitHub profile for LucasGVerga
 
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -31,21 +31,23 @@ Welcome to PyTASER's documentation!
 Introduction
 ============
 
-``PyTASER`` is a ``Python`` (3.9+) library built for simulating transient absorption spectroscopy (TAS) features from
-DFT calculations. The goal of this library is to simulate TAS spectra for comparison with and interpretation of
-experimental spectra. The main features include:
-
-* An interactive TAS spectrum for a pristine semiconducting crystal
-* Isolated spectra for individual band transitions
-* Spectra for different conditions: temperature and carrier concentrations
-* Consideration of non-magnetic and magnetic materials
+``PyTASER`` is a ``Python`` library for simulating differential absorption spectra in compounds using
+quantum chemical calculations, including transient (TAS) and differential (DAS) absorption spectroscopies.
+The goal of this library is to simulate spectra for comparison with and interpretation of experiments.
+The main features include:
+
+* Transient (TAS) and differential (DAS) absorption spectra for insulating and semiconducting crystals
+  (using DFT or database calculations)
+* Plotting contributions from individual band-to-band transitions
+* TAS spectra for different conditions: temperature and carrier concentrations
+* Customisable plotting.
 * Capability to input calculated bandstructures and density of states inputs with support for https://materialsproject.org.
 
 ==========
 Background
 ==========
 
-TAS is a powerful pump-probe tool to characterise the excited states of materials. It can be used to understand microscopic processes in photochemical and electrochemical transformations, including phenomena such as electron trapping and carrier recombination.
+TAS is a powerful pump-probe tool to characterise the excited states of materials, while DAS can be used to represent how changes in a system affects its ground-state optical absorption spectra. These techniques can be used to understand microscopic processes in photochemical and electrochemical transformations, including phenomena such as electron trapping and carrier recombination.
 
 The drawback is that TAS spectra are difficult to interpret, especially for crystals where the specific valence and conduction band structure can give rise to complex features. Our goal here is to predict TAS features from first-principles starting from the most simple models of static excitations through to the kinetics of relaxation of the excited state back to the ground state.
 
@@ -153,7 +155,9 @@ Future topics we plan to build on:
 Acknowledgements
 ================
 
-Developed by Savyasanchi Aggarwal, Seán Kavanagh, Youngwon Woo and Alex Ganose. Aron Walsh designed and led the project. Thanks to group members for their support, especially Anahita Manchala and Liam Harnett-Caulfield.
+Developed by Savyasanchi Aggarwal, Seán Kavanagh, Lucas Verga, Youngwon Woo and Alex Ganose. Aron Walsh
+designed and led the project. Thanks to group members for their support, especially Anahita Manchala and
+Liam Harnett-Caulfield.
 
 
 .. toctree::

diff --git a/docs/source/pytaser.rst b/docs/source/pytaser.rst
@@ -9,6 +9,14 @@ pytaser.generator module
    :undoc-members:
    :show-inheritance:
 
+pytaser.das_generator module
+---------------------
+
+.. automodule:: pytaser.das_generator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pytaser.kpoints module
 -----------------------------
 
@@ -24,11 +32,5 @@ pytaser.plotter module
    :undoc-members:
    :show-inheritance:
 
-pytaser.tas module
----------------------
 
-.. automodule:: pytaser.tas
-   :members:
-   :undoc-members:
-   :show-inheritance: