Add phonons (stfc#143)

* Add phonopy dependency * Add seekpath for qpoints calculation * Update .gitignore to ignore pdf and yaml files * Allow ax as variable name * Add initial phonons * Allow list of supercell dimensions * Remove plotting for phonons * Add kwargs for phonons optimizer * Tidy phonons * Add initial phonons CLI * Fix docs * Update docstrings * Add options for phonon CLI * Add file prefix option for phonons * Separate thermal property calculation from phonons * Add default supercell value for phonons * Add structure name option for phonon CLI * Fix setting structure name for phonons * Enable setting DOS and PSDOS file prefixes * Add initial tests for phonon CLI * Add logging for optimize via phonons * Add tests for phonons * Add logging for phonons * Rename phonon params file * Update README for phonons * Add phonon CLI flags to summary * Create separate functions to write phonon results * Change hdf5 force constants to option * Fix default mesh for phonons * Refactor setting default filenames for phonons * Add hdf5 to gitignore * Tidy printing thermal properties for phonons * Change phonon supercell input to string * Add tests for supercell * Update tests/test_phonons_cli.py Co-authored-by: Jacob Wilkins <[email protected]> * Tidy supercell CLI parsing * Update janus_core/cli/phonons.py * Update janus_core/calculations/phonons.py * Update janus_core/cli/phonons.py * restructure a little bit and test the permissions * Update janus_core/cli/phonons.py Co-authored-by: Jacob Wilkins <[email protected]> * restructure a little bit and test the permissions --------- Co-authored-by: ElliottKasoar <[email protected]> Co-authored-by: Jacob Wilkins <[email protected]> Co-authored-by: Alin Marin Elena <[email protected]>
alinelena · May 24, 2024 · 3e2adb8 · 3e2adb8
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diff --git a/.gitignore b/.gitignore
@@ -8,6 +8,9 @@
 *.cif
 *.xyz
 *.yml
+*.yaml
+*.pdf
+*.hdf5
 *.traj
 ~*
 *~

diff --git a/README.md b/README.md
@@ -24,9 +24,9 @@ Tools for machine learnt interatomic potentials
   - NVT (Langevin(Eijnden/Ciccotti flavour) and Nosé-Hoover (Melchionna flavour))
   - NPT (Nosé-Hoover (Melchiona flavour))
 - [ ] Nudge Elastic Band
+- [x] Phonons
+  - Phonopy
 - [x] Equation of State
-- [ ] Phonons
-  - vibroscopy
 - [x] Training ML potentials
   - MACE
 - [x] Fine tunning MLIPs
@@ -196,6 +196,27 @@ janus eos --struct tests/data/NaCl.cif --minimize-all --fmax 0.0001
 For all options, run `janus eos --help`.
 
 
+### Phonons
+
+Calculate phonons with a 2x2x2 supercell, after geometry optimization (using the [MACE-MP](https://github.com/ACEsuit/mace-mp):
+
+```shell
+janus phonons --struct tests/data/NaCl.cif --supercell 2x2x2 --minimize --arch mace_mp --calc-kwargs "{'model' : 'small'}"
+```
+
+This will save the Phonopy parameters, including displacements and force constants, to `NaCl-params.yml`, and the calculated band structure to `NaCl-auto-band.yml`, in addition to generating a log file, `phonons.log`, and summary of inputs, `phonons_summary.yml`.
+
+Further calculations, including thermal properties, DOS, and PDOS, can also be calculated (using a 2x3x4 supercell):
+
+```shell
+janus phonons --struct tests/data/NaCl.cif --supercell 2x3x4 --dos --pdos --thermal --temp-start 0 --temp-end 300 --temp-step 50
+```
+
+This will create additional output files: `NaCl-cv.dat` for the thermal properties (heat capacity, entropy, and free energy) between 0K and 300K, `NaCl-dos.dat` for the DOS, and `NaCl-pdos.dat` for the PDOS.
+
+For all options, run `janus phonons --help`.
+
+
 ### Using configuration files
 
 Default values for all command line options may be specifed through a Yaml 1.1 formatted configuration file by adding the `--config` option. If an option is present in both the command line and configuration file, the command line value takes precedence.

diff --git a/docs/source/apidoc/janus_core.rst b/docs/source/apidoc/janus_core.rst
@@ -64,6 +64,16 @@ janus\_core.cli.train module
    :undoc-members:
    :show-inheritance:
 
+janus\_core.cli.phonons module
+------------------------------
+
+.. automodule:: janus_core.cli.phonons
+   :members:
+   :special-members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
+
 janus\_core.cli.eos module
 --------------------------
 
@@ -188,6 +198,17 @@ janus\_core.calculations.md module
    :undoc-members:
    :show-inheritance:
 
+janus\_core.calculations.phonons module
+---------------------------------------
+
+.. automodule:: janus_core.calculations.phonons
+   :members:
+   :special-members:
+   :private-members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
 janus\_core.helpers.stats
 -------------------------
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -49,6 +49,7 @@
     "python": ("https://docs.python.org/3", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "ase": ("https://wiki.fysik.dtu.dk/ase/", None),
+    "phonopy": ("https://phonopy.github.io/phonopy/", None),
 }
 
 # Add any paths that contain templates here, relative to this directory.
@@ -198,4 +199,5 @@
     ("py:class", "typer.models.Context"),
     ("py:class", "ellipsis"),
     ("py:class", "janus_core.helpers.stats.T"),
+    ("py:class", "phonopy.structure.atoms.PhonopyAtoms"),
 ]
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,6 +8,9 @@ @@
     *.cif
     *.xyz
     *.yml
+    *.yaml
+    *.pdf
+    *.hdf5
     *.traj
     ~*
     *~
@@ Expand Down @@