Anharmonicity Quantification workflow (#901)

* Generated displaced structures

* Implemented sigma_A oneshot calculations

* Added some needed object attributes

* Added some object attributes

* Added pieces to flow to utilize PhononBSDOSDoc

* Added a prefactor method to find dynamical matrix

* Fixed issue with prefactor method

* Made creation of dynamical matrix indep of phonon

* Added helper function to make Phonopy objects

* Finished writing flow

* Made all functions independent of passing Phonopy

* Code for anharmonicity code and starter for test

* o
Debug sigma^A calculations

1) Temperature needs to be in eV (kB / e)
2) Consistent supercells: phonopy and pymatgen use different standards
3) Use a BasePhononMaker instead of copy/paste

* Update anharmonicity tests

* Use pymatgen.core.units.kb

remove hard-coded constants

* Fixed assert statement

* The phonon supercell now determined to from phonon document

If relaxation changes structure it must be read from phonon doc

* Modification for mock_aims to work

* Add the test data for mock aims

Tests should now work outside of socket calcs

* Add an aims only workflow and generalize the common one

similar to what is done with the phonon workflow

* Add functionality to create an anharmonicity flow from a PhononBSDOSDoc

Default is still to start from phonons for consistency between anharmonic and phonon calcs

* Actually add Aims workflow for anharm

* Made to work with anharmonicity schema doc

* Added function to make anharmonicity doc

* Cleaned up anharmonicity flow test

* Wrote tests for anharm schema

* Added fields to anharm schema

* Added flag and function for full sigma^A

* Added files for mock_aims

* Added test for full sigma A with mock_aims

* Added capability to pass a seed for rng

* Added files for mock aims

* Added pytest fixture for NaCl structure

* Added atom-resolved sigma A calculation and test

* Fixed bug when atom_resolved was False

* Added mock_aims files for mode_resolved sigma^A

* Added mode resolved sigma^A test w/ mock_aims

* Implemented mode resolved sigma^A calcs

* Made tests work with sigma_dict

* Returns a dictionary with computed sigma values

* Cleaned up code with pre-commit

* Fixed bug in test_anharmonicity.py

* Fixed anharm quant one-shot socket test

* Fixed typo in docstring

* Added return info to docstrings

* Refactored code to make cleaner

* Fix lint errors in tests

* Remove typing.Self call

Tested on python 3.11

* Fixed lint and typing errors.

* Fixed tests to pass on github.

* Update src/atomate2/aims/flows/anharmonicity.py

Co-authored-by: J. George <JaGeo@users.noreply.github.com>

* Changed omega_to_THz to be imported from atomate2

* Made separate eigenvec/val solver for dynamical matrix and added clean_dir to tests

* Fixed torchdata version

* Re-implemented get_phonon_supercell

* Added mode-resolved sigma^A calculation

* Fixed linting issues

* Add @4kevinbeck5 to contributors.md file

* remove dict initalisation

* test if pip on torch data is really needed

---------

Co-authored-by: Tom Purcell <purcellt@arizona.edu>
Co-authored-by: J. George <JaGeo@users.noreply.github.com>
Co-authored-by: JaGeo <janinegeorge.ulfen@gmail.com>

docs/about/contributors.md

@@ -129,3 +129,11 @@ Hobbyist Contributor
 
 [comprhys]: https://github.com/comprhys
 [0000-0002-6589-1700]: https://orcid.org/0000-0002-6589-1700
+
+
+**Kevin Beck** [![gh]][4kevinbeck5] [![orc]][0009-0006-5620-1292] \
+PhD student in Applied Mathematics \
+University of Arizona
+
+[4kevinbeck5]: https://github.com/4kevinbeck5
+[0009-0006-5620-1292]: https://orcid.org/0009-0006-5620-1292

src/atomate2/aims/flows/anharmonicity.py

@@ -0,0 +1,44 @@
+"""Defines the anharmonicity quantification workflows for FHI-aims."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from typing import TYPE_CHECKING
+
+from atomate2.common.flows.anharmonicity import BaseAnharmonicityMaker
+
+if TYPE_CHECKING:
+    from atomate2.aims.flows.phonons import PhononMaker
+
+
+@dataclass
+class AnharmonicityMaker(BaseAnharmonicityMaker):
+    """
+    Maker to calculate the anharmonicity score of a material.
+
+    Calculate sigma^A as defined in doi.org/10.1103/PhysRevMaterials.4.083809, by
+    first calculating the phonons for a material and then generating the one-shot
+    sample and calculating the DFT and harmonic forces.
+
+    Parameters
+    ----------
+    name : str
+        Name of the flows produced by this maker.
+    phonon_maker: BasePhononMaker
+        The maker to generate the phonon model
+    """
+
+    name: str = "anharmonicity"
+    phonon_maker: PhononMaker = None
+
+    @property
+    def prev_calc_dir_argname(self) -> str:
+        """Name of argument informing static maker of previous calculation directory.
+
+        As this differs between different DFT codes (e.g., VASP, CP2K), it
+        has been left as a property to be implemented by the inheriting class.
+
+        Note: this is only applicable if a relax_maker is specified; i.e., two
+        calculations are performed for each ordering (relax -> static)
+        """
+        return "prev_dir"

src/atomate2/aims/run.py

@@ -92,17 +92,29 @@ def run_aims_socket(
     aims_cmd: str
         The aims command to use (defaults to SETTINGS.AIMS_CMD).
     """
+    if aims_cmd is None:
+        aims_cmd = SETTINGS.AIMS_CMD
+
     ase_adaptor = AseAtomsAdaptor()
     atoms_to_calculate = [
         ase_adaptor.get_atoms(structure) for structure in structures_to_calculate
     ]
 
     with open("parameters.json") as param_file:
         parameters = json.load(param_file, cls=MontyDecoder)
+
+    del_keys = []
+    for key, val in parameters.items():
+        if val is None:
+            del_keys.append(key)
+
+    for key in del_keys:
+        parameters.pop(key)
+
     if aims_cmd:
-        parameters["aims_command"] = aims_cmd
-    elif "aims_command" not in parameters:
-        parameters["aims_command"] = SETTINGS.AIMS_CMD
+        parameters["command"] = aims_cmd
+    elif "command" not in parameters:
+        parameters["command"] = SETTINGS.AIMS_CMD
 
     calculator = Aims(**parameters)
     port = parameters["use_pimd_wrapper"][1]

src/atomate2/common/flows/anharmonicity.py

@@ -0,0 +1,281 @@
+"""A workflow to evaluate the anharmonicity of a material with sigma^A.
+
+For details see: doi.org/10.1103/PhysRevMaterials.4.083809
+"""
+
+from __future__ import annotations
+
+from abc import ABC, abstractmethod
+from dataclasses import dataclass
+from typing import TYPE_CHECKING
+from warnings import warn
+
+from jobflow import Flow, Maker
+
+from atomate2.common.jobs.anharmonicity import (
+    displace_structure,
+    get_forces,
+    get_phonon_supercell,
+    get_sigmas,
+    run_displacements,
+    store_results,
+)
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+    from emmet.core.math import Matrix3D
+    from pymatgen.core.structure import Structure
+
+    from atomate2.common.flows.phonons import BasePhononMaker
+    from atomate2.common.schemas.phonons import PhononBSDOSDoc
+
+SUPPORTED_CODES = ["aims"]
+
+
+@dataclass
+class BaseAnharmonicityMaker(Maker, ABC):
+    """
+    Maker to calculate the anharmonicity score of a material.
+
+    Calculate sigma^A as defined in doi.org/10.1103/PhysRevMaterials.4.083809, by
+    first calculating the phonons for a material and then generating the one-shot
+    sample and calculating the DFT and harmonic forces.
+
+    Parameters
+    ----------
+    name: str
+        Name of the flows produced by this maker.
+    phonon_maker: BasePhononMaker
+        The maker to generate the phonon model
+    """
+
+    name: str = "anharmonicity"
+    phonon_maker: BasePhononMaker = None
+
+    def make(
+        self,
+        structure: Structure,
+        prev_dir: str | Path | None = None,
+        born: list[Matrix3D] | None = None,
+        epsilon_static: Matrix3D | None = None,
+        total_dft_energy_per_formula_unit: float | None = None,
+        supercell_matrix: Matrix3D | None = None,
+        temperature: float = 300,
+        one_shot_approx: bool = True,
+        seed: int | None = None,
+        element_resolved: bool = False,
+        mode_resolved: bool = False,
+        site_resolved: bool = False,
+        n_samples: int = 1,
+    ) -> Flow:
+        """Make the anharmonicity calculation flow.
+
+        Parameters
+        ----------
+        structure: Structure
+            A pymatgen structure object. Please start with a structure
+            that is nearly fully optimized as the internal optimizers
+            have very strict settings!
+        prev_dir: Optional[str | Path]
+            A previous calculation directory to use for copying outputs.
+            Default is None.
+        born: Optional[list[Matrix3D]]
+            Instead of recomputing born charges and epsilon, these values can also be
+            provided manually. If born and epsilon_static are provided, the born run
+            will be skipped it can be provided in the VASP convention with information
+            for every atom in unit cell. Please be careful when converting structures
+            within in this workflow as this could lead to errors. The default for this
+            field is None.
+        epsilon_static: Optional[Matrix3D]
+            The high-frequency dielectric constant to use instead of recomputing born
+            charges and epsilon. If born, epsilon_static are provided, the born run
+            will be skipped. The default for this field is None.
+        total_dft_energy_per_formula_unit: Optional[float]
+            It has to be given per formula unit (as a result in corresponding Doc).
+            Instead of recomputing the energy of the bulk structure every time, this
+            value can also be provided in eV. If it is provided, the static run will be
+            skipped. This energy is the typical output dft energy of the dft workflow.
+            No conversion needed. It is set to 0 by default.
+        supercell_matrix: Optional[Matrix3D]
+            Instead of min_length, also a supercell_matrix can be given, e.g.
+            [[1.0,0.0,0.0],[0.0,1.0,0.0],[0.0,0.0,1.0]]. By default, this matrix is
+            set to None.
+        temperature: float
+            The temperature for the anharmonicity calculation. The default temp is 300.
+        one_shot_approx: bool
+            If true, finds the one shot approximation of sigma^A and if false, finds
+            the full sigma^A. The default is True.
+        seed: Optional[int]
+            Seed to use for the random number generator
+            (only used if one_shot_approx == False). Set to None by default.
+        element_resolved: bool
+            If true, calculate the atom-resolved sigma^A. This is false by default.
+        mode_resolved: bool
+            If true, calculate the mode-resolved sigma^A. This is false by default.
+        site_resolved: bool
+            If true, resolve sigma^A to the different sites.
+            Default is false.
+        n_samples: int
+            Number of times displaced structures are sampled.
+            Must be >= 1 and cannot be used when one_shot_approx == True.
+            It is set to 1 by default.
+
+        Returns
+        -------
+        Flow
+            The workflow for the anharmonicity calculations
+        """
+        phonon_flow = self.phonon_maker.make(
+            structure,
+            prev_dir,
+            born,
+            epsilon_static,
+            total_dft_energy_per_formula_unit,
+            supercell_matrix,
+        )
+
+        phonon_doc = phonon_flow.output
+        anharmon_flow = self.make_from_phonon_doc(
+            phonon_doc,
+            prev_dir,
+            temperature,
+            one_shot_approx,
+            seed,
+            element_resolved,
+            mode_resolved,
+            site_resolved,
+            n_samples,
+        )
+
+        results = store_results(
+            sigma_dict=anharmon_flow.output,
+            phonon_doc=phonon_flow.output,
+            one_shot=one_shot_approx,
+            temp=temperature,
+            n_samples=n_samples,
+            seed=seed,
+        )
+
+        jobs = [phonon_flow, anharmon_flow, results]
+        return Flow(jobs, results.output)
+
+    def make_from_phonon_doc(
+        self,
+        phonon_doc: PhononBSDOSDoc,
+        prev_dir: str | Path | None = None,
+        temperature: float = 300,
+        one_shot_approx: bool = True,
+        seed: int | None = None,
+        element_resolved: bool = False,
+        mode_resolved: bool = False,
+        site_resolved: bool = False,
+        n_samples: int = 1,
+    ) -> Flow:
+        """Create an anharmonicity workflow from a phonon calculation.
+
+        Parameters
+        ----------
+        phonon_doc: PhononBSDOSDoc
+            The document to get the anharmonicity for
+        prev_dir: Optional[str | Path]
+            A previous calculation directory to use for copying outputs.
+            Default is None.
+        temperature: float
+            The temperature for the anharmonicity calculation. Default is 300.
+        one_shot_approx: bool
+            If true, finds the one shot approximation of sigma^A and if false,
+            finds the full sigma^A. The default is True.
+        seed: Optional[int]
+            Seed to use for the random number generator
+            (only used if one_shot_approx == False). Default is None.
+        element_resolved: bool
+            If true, calculate the atom-resolved sigma^A. This is false by default.
+        mode_resolved: bool
+            If true, calculate the mode-resolved sigma^A. This is false by default.
+        site_resolved: bool
+            If true, resolve sigma^A to the different sites.
+            Default is false.
+        n_samples: int
+            Number of times displaced structures are sampled.
+            Must be >= 1 and cannot be used when one_shot_approx == True.
+            It is set to 1 by default.
+
+        Returns
+        -------
+        Flow
+            The anharmonicity quantification workflow
+        """
+        # KB: Not always an error. There could be negative acoustic modes from
+        # unconverged phonon calculations.
+        if phonon_doc.has_imaginary_modes:
+            warn(
+                "The phonon model has imaginary modes, sampling maybe incorrect.",
+                stacklevel=1,
+            )
+
+        jobs = []
+        phonon_supercell_job = get_phonon_supercell(
+            phonon_doc.structure,
+            phonon_doc.supercell_matrix,
+        )
+        jobs.append(phonon_supercell_job)
+
+        phonon_supercell = phonon_supercell_job.output
+
+        displace_supercell = displace_structure(
+            phonon_supercell=phonon_supercell,
+            force_constants=phonon_doc.force_constants,
+            temp=temperature,
+            one_shot=one_shot_approx,
+            seed=seed,
+            n_samples=n_samples,
+        )
+        jobs.append(displace_supercell)
+
+        force_eval_maker = self.phonon_maker.phonon_displacement_maker
+        displacement_calcs = run_displacements(
+            displacements=displace_supercell.output,
+            phonon_supercell=phonon_supercell,
+            force_eval_maker=force_eval_maker,
+            socket=self.phonon_maker.socket,
+            prev_dir_argname=self.prev_calc_dir_argname,
+            prev_dir=prev_dir,
+        )
+        jobs.append(displacement_calcs)
+
+        # Get DFT and harmonic forces
+        force_calcs = get_forces(
+            phonon_doc.force_constants,
+            phonon_supercell,
+            displacement_calcs.output,
+        )
+        jobs.append(force_calcs)
+
+        # Calculate all desired sigma^A types
+        sigma_calcs = get_sigmas(
+            force_calcs.output[0],
+            force_calcs.output[1],
+            phonon_doc.force_constants,
+            phonon_supercell,
+            one_shot_approx,
+            element_resolved,
+            mode_resolved,
+            site_resolved,
+        )
+        jobs.append(sigma_calcs)
+        sigma_a_vals = sigma_calcs.output
+
+        return Flow(jobs, sigma_a_vals)
+
+    @property
+    @abstractmethod
+    def prev_calc_dir_argname(self) -> str | None:
+        """Name of argument informing static maker of previous calculation directory.
+
+        As this differs between different DFT codes (e.g., VASP, CP2K), it
+        has been left as a property to be implemented by the inheriting class.
+
+        Note: this is only applicable if a relax_maker is specified; i.e., two
+        calculations are performed for each ordering (relax -> static)
+        """