Lattice dynamics workflow using Pheasy #1063
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Modified some parts based on Janine's comments.
…atomate2 into atomate2_jz_pheasy
…group for crystals.
src/atomate2/common/flows/pheasy.py
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| displacement_calcs = run_phonon_displacements( | ||
| displacements=displacements.output, | ||
| structure=structure, | ||
| supercell_matrix=supercell_matrix, | ||
| phonon_maker=self.phonon_displacement_maker, | ||
| socket=self.socket, | ||
| prev_dir_argname=self.prev_calc_dir_argname, | ||
| prev_dir=prev_dir, | ||
| ) |
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This is also different than in phonon.BasePhononMaker
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This is currently getting imported like this:
from atomate2.common.jobs.pheasy import (
generate_frequencies_eigenvectors,
generate_phonon_displacements,
get_supercell_size,
run_phonon_displacements,
)
This is also different than in phonon.BasePhononMaker
What should be done to fix this then?
src/atomate2/common/flows/pheasy.py
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| phonon_collect = generate_frequencies_eigenvectors( | ||
| supercell_matrix=supercell_matrix, | ||
| displacement=self.displacement, | ||
| num_displaced_supercells=self.num_displaced_supercells, | ||
| cal_anhar_fcs=self.cal_anhar_fcs, | ||
| displacement_anhar=self.displacement_anhar, | ||
| num_disp_anhar=self.num_disp_anhar, | ||
| fcs_cutoff_radius=self.fcs_cutoff_radius, | ||
| renorm_phonon=self.renorm_phonon, | ||
| renorm_temp=self.renorm_temp, | ||
| cal_ther_cond=self.cal_ther_cond, | ||
| ther_cond_mesh=self.ther_cond_mesh, | ||
| ther_cond_temp=self.ther_cond_temp, |
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Since we have many job(s) which are similar yet different in pheasy.py & phonons.py, do you think it would be a good idea to create another file for eg: core_phonons.py, and place these repeated job(s) in this file?
We can then rename phonons.py to lets say phonopy.py.
So, in that way, we will have three files in common/flows :
- core_phonons.py
- phonopy.,py
- pheasy.py
What do you think?
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This would be one option but it might be a breaking change.
…_pheasy_anharmonic
HipHive leverages Numba under the hood for its force-constant calculators, and numba only works with NumPy ≤ 2.2.
@JaGeo , can you pls check if the PR looks okay? |
tests/vasp/flows/test_pheasy.py
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| job = PhononMaker( | ||
| force_diagonal=True, | ||
| min_length=12, | ||
| mp_id="mp-149", |
| - name: Install ALA-Mode | ||
| run: | | ||
| micromamba activate a2 | ||
| micromamba install -n a2 -c conda-forge "numpy<=2.2" scipy h5py compilers “libblas=*=*mkl” spglib boost eigen cmake ipython mkl-include openmpi --yes | ||
| git clone https://github.com/ttadano/ALM.git # do I need to modify this? | ||
| cd ALM # do I need to modify this? | ||
| cd python | ||
| python setup.py build # do I need to modify this? | ||
| uv pip install -e . # do I need to modify this? | ||
|
|
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Could you add these instructions to the documentation?
| run: | | ||
| micromamba activate a2 | ||
| micromamba install -n a2 -c conda-forge "numpy<=2.2" scipy h5py compilers “libblas=*=*mkl” spglib boost eigen cmake ipython mkl-include openmpi --yes | ||
| git clone https://github.com/ttadano/ALM.git # do I need to modify this? |
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https://anaconda.org/conda-forge/alm why not installing it directly from conda? Is a different version needed?
src/atomate2/vasp/flows/pheasy.py
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| """ | ||
| Maker to calculate harmonic phonons with VASP and Phonopy. | ||
|
|
||
| Calculate the harmonic phonons of a material. Initially, a tight structural | ||
| relaxation is performed to obtain a structure without forces on the atoms. | ||
| Subsequently, supercells with one displaced atom are generated and accurate | ||
| forces are computed for these structures. With the help of phonopy, these | ||
| forces are then converted into a dynamical matrix. To correct for polarization | ||
| effects, a correction of the dynamical matrix based on BORN charges can | ||
| be performed. Finally, phonon densities of states, phonon band structures | ||
| and thermodynamic properties are computed. |
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Doc strings would need to be updated.
|
@hrushikesh-s I increased code reuse in the pheasy code. The other changes already look great! What is missing:
|
…ng/atomate2 into atomate2_jz_pheasy_anharmonic
| warnings.warn( | ||
| "Initial magnetic moments will not be considered for the determination " | ||
| "of the symmetry of the structure and thus will be removed now.", | ||
| stacklevel=1, | ||
| ) | ||
| cell = get_phonopy_structure( | ||
| structure.remove_site_property(property_name="magmom") |
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ideally, we export the common parts from the phonons and pheasy jobs into a method and reuse it? This would then also make it easier when we change anything here in the future in either of the jobs in pheasy.py or phonons.py
| # I did not directly import this job from the phonon module | ||
| # because I modified the job to pass the displaced structures | ||
| # to the output. | ||
| @job(data=["forces", "displaced_structures"]) | ||
| def run_phonon_displacements( | ||
| displacements: list[Structure], | ||
| structure: Structure, | ||
| supercell_matrix: Matrix3D, | ||
| phonon_maker: BaseVaspMaker | ForceFieldStaticMaker | BaseAimsMaker = None, | ||
| prev_dir: str | Path = None, | ||
| prev_dir_argname: str = None, | ||
| socket: bool = False, | ||
| ) -> Flow: |
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if possible, i would modify the phonons.py job instead to avoid code duplication
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