Bump euphonic version, support .yml input to Abins

Testing/Data/UnitTest/Ge-force_constants.hdf5.md5

@@ -0,0 +1 @@
+ce75e1d1d4e693a320349b2e996f6d4a

Testing/Data/UnitTest/Ge-phonopy.yml.md5

@@ -0,0 +1 @@
+5e3f4a778792461cfa47d5b5d1003309

Testing/SystemTests/tests/framework/AbinsTest.py

@@ -103,7 +103,7 @@ class AbinsCRYSTALTestT(AbinsTestingMixin, systemtesting.MantidSystemTest):
     parameters are identical across calculations. In the third run the required
     data /should/ be read from the hdf file.
 
-    We only check that here that the results are correct, we cannot tell if the
+    We only check here that the results are correct, we cannot tell if the
     cache was used.
     """
 

conda/recipes/conda_build_config.yaml

@@ -164,7 +164,7 @@ libopenblas:
 # which does not require future https://github.com/conda-forge/seekpath-feedstock/pull/15/
 # please remove this comment and the pins in those recipes when euphonic and seekpath release new versions
 euphonic:
-  - '>=1.4.3,<2.0'
+  - '>=1.4.5,<2.0'
 
 librdkafka:
   - '>=1.6.0'

docs/source/algorithms/Abins-v1.rst

@@ -23,7 +23,7 @@ scattering spectra (INS).
 
 Abins requires data from existing lattice dynamics calculations to determine the phonon mode frequencies and displacements. These are used to compute INS intensities; higher-order phonons may be approximated as combinations of fundamental modes.
 Several file formats are supported for frequency and displacement data at given :math:`\mathbf{q}`-points. Alternatively, force-constants data can be provided and a fine :math:`\mathbf{q}`-point mesh will be sampled automatically.
-Supported codes include CASTEP (.phonon), CRYSTAL (.out), DMOL3 (.outmol), GAUSSIAN (.log), PHONOPY (.yaml), VASP (.xml) as well as some pre-processed JSON (.json) formats. For more information about the files, features and quirks of these codes see :ref:`AbinsDataFormats`.
+Supported codes include CASTEP (.phonon), CRYSTAL (.out), DMOL3 (.outmol), GAUSSIAN (.log), PHONOPY (.yaml, .yml), VASP (.xml) as well as some pre-processed JSON (.json) formats. For more information about the files, features and quirks of these codes see :ref:`AbinsDataFormats`.
 
 The user may also provide an experimental file with measured dynamical structure factor S in order to directly
 compare theoretical and experimental spectra.

docs/source/algorithms/Abins2D-v1.rst

@@ -26,7 +26,7 @@ Abins requires data from existing lattice dynamics calculations to determine the
 
 Several file formats are supported for frequency and displacement data at given :math:`\mathbf{q}`-points. Alternatively, force-constants data can be provided and a fine :math:`\mathbf{q}`-point mesh will be sampled automatically.
 
-Supported codes include CASTEP (.phonon), CRYSTAL (.out), DMOL3 (.outmol), GAUSSIAN (.log), PHONOPY (.yaml), VASP (.xml) as well as some pre-processed JSON (.json) formats. For more information about the files, features and quirks of theskee codes see :ref:`AbinsDataFormats`.
+Supported codes include CASTEP (.phonon), CRYSTAL (.out), DMOL3 (.outmol), GAUSSIAN (.log), PHONOPY (.yaml, .yml), VASP (.xml) as well as some pre-processed JSON (.json) formats. For more information about the files, features and quirks of theskee codes see :ref:`AbinsDataFormats`.
 
 For VASP XML inputs, it is also permitted to use a "selective dynamics" in which some atoms are frozen.
 In this case, data is only available for the moving atoms and contributions from the other atoms are omitted from the calculated spectrum.

docs/source/concepts/AbinsDataFormats.rst

@@ -91,6 +91,9 @@ It is also permitted to use a phonopy YAML file which does not contain the force
 We recommend using the *force_constants.hdf5* file where practical as the read/write performance is significantly better.
 (With the power and flexibility of *.yaml* comes a lot of computational overhead to read simple arrays!)
 
+Machine-learned interatomic potential calculations with `janus-core <https://stfc.github.io/janus-core/>`_ can use Phonopy to produce phonon outputs with filenames *PREFIX-phonopy.yml* and *PREFIX-force_constants.hdf5*.
+This filename convention can be used with Abins: again, the force constants file should be in the same directory as the YAML file.
+
 VASP
 ----
 Abins can read the frequencies and displacements from Gamma-point vibration calculations performed with the ``IBRION=5,6,7,8`` tags.

docs/source/release/v6.14.0/Indirect/Algorithms/Bugfixes/39881.rst

@@ -0,0 +1,6 @@
+- Euphonic dependency is updated to 1.4.5. Notably, this includes a
+  bugfix when importing force constants with dipole-dipole corrections
+  from Phonopy: if the supercell matrix was non-symmetric, the long-range
+  subtraction was done incorrectly. Calculations with "diagonal"
+  supercells (e.g. 2×3×4) are unaffected, and primitive-FCC or
+  primitive-BCC transformations should also use a symmetric matrix.

docs/source/release/v6.14.0/Indirect/Algorithms/New_features/39881.rst

@@ -0,0 +1,5 @@
+- *<prefix>-phonopy.yml* and *<prefix>-force_constants.hdf5* files
+  from `janus-core <https://stfc.github.io/janus-core>`_ are now
+  supported as input to Abins/Abins2D Algorithms. Use the
+  FORCE_CONSTANTS "AbInitioProgram" as for regular *phonopy.yaml*
+  files.

scripts/abins/abinsalgorithm.py

@@ -840,27 +840,45 @@ def _validate_euphonic_input_file(cls, filename_full_path: str) -> dict:
 
         if (suffix := path.suffix) == ".castep_bin":
             # Assume any .castep_bin file is valid choice
-            pass
-
-        elif suffix == ".yaml":
-            # Check .yaml files have expected keys for Phonopy force constants
-            with open(filename_full_path, "r") as yaml_file:
-                phonon_data = yaml.load(yaml_file, Loader=SafeLoader)
-
-            if {"phonopy", "force_constants"}.issubset(phonon_data):
-                pass
-
-            elif "phonopy" in phonon_data:
-                # Phonon file without force constants included: they could be in
-                # a FORCE_CONSTANTS or force_constants.hdf5 file so check if one exists
-                fc_filenames = ("FORCE_CONSTANTS", "force_constants.hdf5")
-                if not any(map(lambda fc_filename: (path.parent / fc_filename).is_file(), fc_filenames)):
-                    return dict(
-                        Invalid=True,
-                        Comment=f"Could not find force constants in {filename_full_path}, or find data file {' or '.join(fc_filenames)}",
-                    )
+            return dict(Invalid=False, Comment="")
+
+        if suffix not in (".yaml", ".yml"):
+            return dict(Invalid=True, Comment="Invalid extension: FORCECONSTANTS requires .castep_bin, .yaml or .yml")
+
+        # Check .yaml files have expected keys for Phonopy force constants
+        with open(filename_full_path, "r") as yaml_file:
+            phonon_data = yaml.load(yaml_file, Loader=SafeLoader)
+
+        if {"phonopy", "force_constants"}.issubset(phonon_data):
+            # Force constants are in the yaml file: good
+            return dict(Invalid=False, Comment="")
+
+        if "phonopy" not in phonon_data:
+            # Not a Phonopy file: can't use this
+            return dict(Invalid=True, Comment=f"No 'phonopy' section found in {filename_full_path}")
+
+        # Phonopy file without force constants: they must be in another file
+
+        # Check if following janus conventions:
+        # /parent/seedname-phonopy.yml -> /parent/seedname-force_constants.hdf5
+        janus_phonopy_re = "(?P<seedname>.+)-phonopy.yml"
+        fc_filenames = ("FORCE_CONSTANTS", "force_constants.hdf5")
+        if re_match := re.match(janus_phonopy_re, path.name):
+            fc_file = path.parent / f"{re_match['seedname']}-force_constants.hdf5"
+            if not fc_file.is_file():
+                return dict(
+                    Invalid=True,
+                    Comment=f"Could not find force constants in {filename_full_path}, or find data file {fc_file}",
+                )
+
+        # Otherwise FC could be in a FORCE_CONSTANTS or force_constants.hdf5 file
+        elif not any(map(lambda fc_filename: (path.parent / fc_filename).is_file(), fc_filenames)):
+            return dict(
+                Invalid=True,
+                Comment=f"Could not find force constants in {filename_full_path}, or find data file {' or '.join(fc_filenames)}",
+            )
 
-        # Did not return already: No problems found
+        # Phonopy YAML with available force constants
         return dict(Invalid=False, Comment="")
 
     @classmethod

scripts/abins/constants.py

@@ -270,7 +270,7 @@
 MAX_ORDER = 4  # max quantum order event
 
 ALL_SUPPORTED_AB_INITIO_PROGRAMS = ["CRYSTAL", "CASTEP", "DMOL3", "GAUSSIAN", "VASP"]
-AB_INITIO_FILE_EXTENSIONS = ["castep_bin", "hdf5", "json", "out", "outmol", "phonon", "log", "LOG", "mol", "yaml", "xml"]
+AB_INITIO_FILE_EXTENSIONS = ["castep_bin", "hdf5", "json", "out", "outmol", "phonon", "log", "LOG", "mol", "yaml", "yml", "xml"]
 
 
 ONE_DIMENSIONAL_INSTRUMENTS = ["TOSCA", "Lagrange"]

scripts/test/Abins/AbinsAlgorithmTest.py

@@ -42,6 +42,30 @@ def test_bad_atom_info(self):
             species.neutron_data
 
 
+class AbinsAlgorithmValidatorsTest(unittest.TestCase):
+    """Test input validators"""
+
+    def test_validate_euphonic_yml(self):
+        """Check that force constants are located for .yml input"""
+        # with open(abins.test_helpers.find_file(seedname + "_data.txt")) as data_file:
+        # def _validate_euphonic_input_file(cls, filename_full_path: str) -> dict:
+        from abins.test_helpers import find_file
+
+        issues = AbinsAlgorithm._validate_euphonic_input_file(find_file("Al_LoadPhonopy.yaml"))
+        self.assertEqual(issues, {"Invalid": False, "Comment": ""})
+
+        issues = AbinsAlgorithm._validate_euphonic_input_file(find_file("Ge-phonopy.yml"))
+        self.assertEqual(issues, {"Invalid": False, "Comment": ""})
+
+        issues = AbinsAlgorithm._validate_euphonic_input_file(find_file("Si2-phonon_LoadCASTEP.phonon"))
+        self.assertEqual(issues, {"Invalid": True, "Comment": "Invalid extension: FORCECONSTANTS requires .castep_bin, .yaml or .yml"})
+
+        # Non-phonopy yaml from another test
+        wrong_yaml = find_file("ISISPowderRunDetailsTestCallable.yaml")
+        issues = AbinsAlgorithm._validate_euphonic_input_file(wrong_yaml)
+        self.assertEqual(issues, {"Invalid": True, "Comment": f"No 'phonopy' section found in {wrong_yaml}"})
+
+
 class AbinsAlgorithmMethodsTest(unittest.TestCase):
     """Test static methods on AbinsAlgorithm"""