Add elasticity calculation (#621)

Co-authored-by: Elliott Kasoar <45317199+ElliottKasoar@users.noreply.github.com>

Author: harveydevereux

README.md

@@ -115,6 +115,7 @@ Current and planned features include:
   - MACE
 - [x] Rare events simulations
   - PLUMED
+- [x] Elasticity
 
 
 ## Python interface
@@ -154,6 +155,7 @@ directory. This currently includes examples for:
 
 - [Nudged Elastic Band](docs/source/tutorials/python/neb.ipynb) [![badge](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/python/neb.ipynb)
 
+- [Elasticity](docs/source/tutorials/python/elasticity.ipynb) [![badge](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/python/elasticity.ipynb)
 
 ### Calculation outputs
 
@@ -221,6 +223,7 @@ janus neb
 janus train
 janus descriptors
 janus preprocess
+janus elasticity
 ```
 
 For example, a single point calcuation (using the [MACE-MP](https://github.com/ACEsuit/mace-mp) "small" force-field) can be performed by running:
@@ -321,7 +324,7 @@ This currently includes examples for:
 
 - [Nudged Elastic Band](docs/source/tutorials/cli/neb.ipynb) [![badge](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/cli/neb.ipynb)
 
-
+- [Elasticity](docs/source/tutorials/cli/elasticity.ipynb) [![badge](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/cli/elasticity.ipynb)
 
 ### Using configuration files
 

docs/source/apidoc/janus_core.rst

@@ -44,6 +44,16 @@ janus\_core.calculations.eos module
    :undoc-members:
    :show-inheritance:
 
+janus\_core.calculations.elasticity module
+------------------------------------------
+
+.. automodule:: janus_core.calculations.elasticity
+   :members:
+   :special-members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
+
 janus\_core.calculations.geom\_opt module
 -----------------------------------------
 
@@ -117,6 +127,17 @@ janus\_core.cli.eos module
    :undoc-members:
    :show-inheritance:
 
+janus\_core.cli.elasticity module
+---------------------------------
+
+.. automodule:: janus_core.cli.elasticity
+   :members:
+   :special-members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
+
+
 janus\_core.cli.geomopt module
 ------------------------------
 

docs/source/conf.py

@@ -57,6 +57,7 @@
     "torch": ("https://pytorch.org/docs/stable", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
     "rich": ("https://rich.readthedocs.io/en/stable/", None),
+    "pymatgen": ("https://pymatgen.org",None),
 }
 
 # Add any paths that contain templates here, relative to this directory.
@@ -244,4 +245,5 @@
     ("py:class", "ProgressBar"),
     ("py:class", "typer.models.CallbackParam"),
     ("py:class", "SumCalculator"),
+    ("py:class", "ElasticTensor"),
 ]

docs/source/examples/elasticity.rst

@@ -0,0 +1,11 @@
+==========
+Elasticity
+==========
+
+A minimal example configuration file for ``janus elasticity`` is:
+
+.. literalinclude:: minimal/elasticity.yml
+
+An example configuration file with all parameters set for ``janus elasticity`` is:
+
+.. literalinclude:: full/elasticity.yml

docs/source/examples/full/elasticity.yml

@@ -0,0 +1,30 @@
+arch: mace_mp
+device: cpu
+model: "tests/models/mace_mp_small.model"
+calc_kwargs:
+  dispersion: True
+
+struct: "tests/data/NaCl.cif"
+fmax: 0.1
+log: null
+minimize: true
+minimize_all: true
+minimize_kwargs:
+  filter_kwargs:
+    constant_volume: True
+
+n_strains: 2
+normal_magnitude: 0.01
+shear_magnitude: 0.1
+
+file_prefix: NaCl
+write_structures: true
+write_voigt: true
+read_kwargs:
+  index: "0"
+write_kwargs:
+  invalidate_calc: True
+
+log: elasticity-log.yml
+summary: elasticity-summary.yml
+tracker: False

docs/source/examples/index.rst

@@ -12,3 +12,4 @@ Example configurations
     eos
     neb
     descriptors
+    elasticity

docs/source/examples/minimal/elasticity.yml

@@ -0,0 +1,3 @@
+arch: mace_mp
+
+struct: "tests/data/NaCl.cif"