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Fix d2k function (#3932)
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* Fix d2k function

Need to use the transpose of the inverse matrix for recipmatrix

* breaking: snake_case method args kpt_density and recip_cell (better to do early while user base small)

* d2k_recip_cell fix kpt_density type anno and doc str

* Add test for aims density conversions

* Fix mypy errors

* Add print line to see what the actual errors look like

All tests pass locally

* for supercell round coords

should fix error in tests

* remove extra print line

* refactor test_static_si_no_kgrid

---------

Co-authored-by: Janosh Riebesell <[email protected]>
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@tpurcell90 @janosh
tpurcell90 and janosh authored Aug 6, 2024
1 parent 7a01f3c commit 252efa7
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Showing 6 changed files with 49 additions and 40 deletions.
64 changes: 30 additions & 34 deletions src/pymatgen/io/aims/sets/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@
import copy
import json
import logging
from collections.abc import Iterable
from dataclasses import dataclass, field
from typing import TYPE_CHECKING, Any
from warnings import warn
Expand All @@ -19,7 +18,7 @@
from pymatgen.io.core import InputFile, InputGenerator, InputSet

if TYPE_CHECKING:
from collections.abc import Sequence
from collections.abc import Iterable, Sequence

from pymatgen.util.typing import PathLike

Expand Down Expand Up @@ -234,7 +233,7 @@ def _read_previous(
prev_dir (str or Path): The previous directory for the calculation
"""
prev_structure: Structure | Molecule | None = None
prev_parameters = {}
prev_params = {}
prev_results: dict[str, Any] = {}

if prev_dir:
Expand All @@ -243,7 +242,7 @@ def _read_previous(
# jobflow_remote)
split_prev_dir = str(prev_dir).split(":")[-1]
with open(f"{split_prev_dir}/parameters.json") as param_file:
prev_parameters = json.load(param_file, cls=MontyDecoder)
prev_params = json.load(param_file, cls=MontyDecoder)

try:
aims_output: Sequence[Structure | Molecule] = read_aims_output(
Expand All @@ -256,7 +255,7 @@ def _read_previous(
except (IndexError, AimsParseError):
pass

return prev_structure, prev_parameters, prev_results
return prev_structure, prev_params, prev_results

@staticmethod
def _get_properties(
Expand Down Expand Up @@ -308,12 +307,9 @@ def _get_input_parameters(
Returns:
dict: The input object
"""
# Get the default configuration
# FHI-aims recommends using their defaults so bare-bones default parameters
parameters: dict[str, Any] = {
"xc": "pbe",
"relativistic": "atomic_zora scalar",
}
# Get the default config
# FHI-aims recommends using their defaults so bare-bones default params
params: dict[str, Any] = {"xc": "pbe", "relativistic": "atomic_zora scalar"}

# Override default parameters with previous parameters
prev_parameters = {} if prev_parameters is None else copy.deepcopy(prev_parameters)
Expand All @@ -327,25 +323,25 @@ def _get_input_parameters(
kpt_settings["density"] = density

parameter_updates = self.get_parameter_updates(structure, prev_parameters)
parameters = recursive_update(parameters, parameter_updates)
params = recursive_update(params, parameter_updates)

# Override default parameters with user_params
parameters = recursive_update(parameters, self.user_params)
if ("k_grid" in parameters) and ("density" in kpt_settings):
params = recursive_update(params, self.user_params)
if ("k_grid" in params) and ("density" in kpt_settings):
warn(
"WARNING: the k_grid is set in user_params and in the kpt_settings,"
" using the one passed in user_params.",
stacklevel=1,
)
elif isinstance(structure, Structure) and ("k_grid" not in parameters):
elif isinstance(structure, Structure) and ("k_grid" not in params):
density = kpt_settings.get("density", 5.0)
even = kpt_settings.get("even", True)
parameters["k_grid"] = self.d2k(structure, density, even)
elif isinstance(structure, Molecule) and "k_grid" in parameters:
params["k_grid"] = self.d2k(structure, density, even)
elif isinstance(structure, Molecule) and "k_grid" in params:
warn("WARNING: removing unnecessary k_grid information", stacklevel=1)
del parameters["k_grid"]
del params["k_grid"]

return parameters
return params

def get_parameter_updates(
self,
Expand All @@ -366,7 +362,7 @@ def get_parameter_updates(
def d2k(
self,
structure: Structure,
kptdensity: float | list[float] = 5.0,
kpt_density: float | tuple[float, float, float] = 5.0,
even: bool = True,
) -> Iterable[float]:
"""Convert k-point density to Monkhorst-Pack grid size.
Expand All @@ -376,15 +372,15 @@ def d2k(
Args:
structure (Structure): Contains unit cell and
information about boundary conditions.
kptdensity (float | list[float]): Required k-point
kpt_density (float | list[float]): Required k-point
density. Default value is 5.0 point per Ang^-1.
even (bool): Round up to even numbers.
Returns:
dict: Monkhorst-Pack grid size in all directions
"""
recipcell = structure.lattice.inv_matrix
return self.d2k_recipcell(recipcell, structure.lattice.pbc, kptdensity, even)
recip_cell = structure.lattice.inv_matrix.transpose()
return self.d2k_recip_cell(recip_cell, structure.lattice.pbc, kpt_density, even)

def k2d(self, structure: Structure, k_grid: np.ndarray[int]):
"""Generate the kpoint density in each direction from given k_grid.
Expand All @@ -398,36 +394,36 @@ def k2d(self, structure: Structure, k_grid: np.ndarray[int]):
Returns:
dict: Density of kpoints in each direction. result.mean() computes average density
"""
recipcell = structure.lattice.inv_matrix
densities = k_grid / (2 * np.pi * np.sqrt((recipcell**2).sum(axis=1)))
recip_cell = structure.lattice.inv_matrix.transpose()
densities = k_grid / (2 * np.pi * np.sqrt((recip_cell**2).sum(axis=1)))
return np.array(densities)

@staticmethod
def d2k_recipcell(
recipcell: np.ndarray,
def d2k_recip_cell(
recip_cell: np.ndarray,
pbc: Sequence[bool],
kptdensity: float | Sequence[float] = 5.0,
kpt_density: float | tuple[float, float, float] = 5.0,
even: bool = True,
) -> Sequence[int]:
"""Convert k-point density to Monkhorst-Pack grid size.
Args:
recipcell (Cell): The reciprocal cell
recip_cell (Cell): The reciprocal cell
pbc (Sequence[bool]): If element of pbc is True
then system is periodic in that direction
kptdensity (float or list[floats]): Required k-point
density. Default value is 3.5 point per Ang^-1.
kpt_density (float or list[floats]): Required k-point
density. Default value is 5 points per Ang^-1.
even(bool): Round up to even numbers.
Returns:
dict: Monkhorst-Pack grid size in all directions
"""
if not isinstance(kptdensity, Iterable):
kptdensity = 3 * [float(kptdensity)]
if isinstance(kpt_density, float):
kpt_density = (kpt_density, kpt_density, kpt_density)
kpts: list[int] = []
for i in range(3):
if pbc[i]:
k = 2 * np.pi * np.sqrt((recipcell[i] ** 2).sum()) * float(kptdensity[i])
k = 2 * np.pi * np.sqrt((recip_cell[i] ** 2).sum()) * float(kpt_density[i])
if even:
kpts.append(2 * int(np.ceil(k / 2)))
else:
Expand Down
15 changes: 12 additions & 3 deletions src/pymatgen/util/testing/aims.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,7 @@ def comp_system(
generator_cls: type,
properties: list[str] | None = None,
prev_dir: str | None | Path = None,
user_kpt_settings: dict[str, Any] | None = None,
) -> None:
"""Compare files generated by tests with ones in reference directories.
Expand All @@ -96,16 +97,24 @@ def comp_system(
generator_cls (type): The class of the generator
properties (list[str] | None): The list of properties to calculate
prev_dir (str | Path | None): The previous directory to pull outputs from
user_kpt_settings (dict[str, Any] | None): settings for k-point density in FHI-aims
Raises:
AssertionError: If the input files are not the same
"""
if user_kpt_settings is None:
user_kpt_settings = {}

k_point_density = user_params.pop("k_point_density", 20)

try:
generator = generator_cls(user_params=user_params, k_point_density=k_point_density)
generator = generator_cls(
user_params=user_params,
k_point_density=k_point_density,
user_kpoints_settings=user_kpt_settings,
)
except TypeError:
generator = generator_cls(user_params=user_params)
generator = generator_cls(user_params=user_params, user_kpoints_settings=user_kpt_settings)

input_set = generator.get_input_set(structure, prev_dir, properties)
input_set.write_input(work_dir / test_name)
Expand All @@ -117,7 +126,7 @@ def compare_single_files(ref_file: str | Path, test_file: str | Path) -> None:
"""Compare single files generated by tests with ones in reference directories.
Args:
ref_file (str | Path): The reference file to cmpare against
ref_file (str | Path): The reference file to compare against
test_file (str | Path): The file to compare against the reference
Raises:
Expand Down
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4 changes: 2 additions & 2 deletions tests/io/aims/aims_input_generator_ref/static-no-kgrid-si/parameters.json
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
"species_dir": "/home/tpurcell/git/atomate2/tests/aims/species_dir/light",
"k_grid": [
12,
12,
12
6,
4
]
}
6 changes: 5 additions & 1 deletion tests/io/aims/test_sets/test_static_generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,11 @@ def test_static_si(tmp_path):

def test_static_si_no_kgrid(tmp_path):
parameters = {"species_dir": "light"}
comp_system(Si, parameters, "static-no-kgrid-si", tmp_path, ref_path, StaticSetGenerator)
Si_supercell = Si.make_supercell([1, 2, 3], in_place=False)
for site in Si_supercell:
# round site.coords to ignore floating point errors
site.coords = [round(x, 15) for x in site.coords]
comp_system(Si_supercell, parameters, "static-no-kgrid-si", tmp_path, ref_path, StaticSetGenerator)


def test_static_o2(tmp_path):
Expand Down

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