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Use semantikon annotation for units in a random number of functions #467

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Use semantikon annotation for units in a random number of functions #467

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5d009be
add units
samwaseda May 2, 2025
22f3489
Merge remote-tracking branch 'origin' into semantikon
samwaseda May 2, 2025
e073bdc
Use units for optimizer
samwaseda May 6, 2025
3093ba0
Add units everywhere
samwaseda May 6, 2025
32cadf8
Add semantikon to environment
samwaseda May 6, 2025
dfacb26
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 6, 2025
9d3b0ff
Add semantikon to environment-old
samwaseda May 7, 2025
ac99710
Merge branch 'semantikon' of github.com:pyiron/atomistics into semant…
samwaseda May 7, 2025
278634e
Forgot to remove print statement
samwaseda May 7, 2025
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1 change: 1 addition & 0 deletions .ci_support/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,3 +16,4 @@ dependencies:
- sphinx_parser =0.0.1
- tqdm =4.67.1
- pyiron_vasp =0.2.5
- semantikon =0.0.16
64 changes: 37 additions & 27 deletions atomistics/calculators/lammps/libcalculator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,8 @@
import pandas
from jinja2 import Template
from pylammpsmpi import LammpsASELibrary
from semantikon.converter import units
from semantikon.typing import u

from atomistics.calculators.interface import get_quantities_from_tasks
from atomistics.calculators.lammps.commands import (
Expand Down Expand Up @@ -40,12 +42,13 @@
from atomistics.calculators.interface import TaskName


@units
def optimize_positions_and_volume_with_lammpslib(
structure: Atoms,
potential_dataframe: DataFrame,
min_style: str = "cg",
etol: float = 0.0,
ftol: float = 0.0001,
ftol: u(float, units="eV/angstrom") = 0.0001,
maxiter: int = 100000,
maxeval: int = 10000000,
thermo: int = 10,
Expand Down Expand Up @@ -82,12 +85,13 @@ def optimize_positions_and_volume_with_lammpslib(
return structure_copy


@units
def optimize_positions_with_lammpslib(
structure: Atoms,
potential_dataframe: DataFrame,
min_style: str = "cg",
etol: float = 0.0,
ftol: float = 0.0001,
ftol: u(float, units="eV/angstrom") = 0.0001,
maxiter: int = 100000,
maxeval: int = 10000000,
thermo: int = 10,
Expand Down Expand Up @@ -143,15 +147,16 @@ def calc_static_with_lammpslib(
return result_dict


@units
def calc_molecular_dynamics_nvt_with_lammpslib(
structure: Atoms,
potential_dataframe: pandas.DataFrame,
Tstart: float = 100.0,
Tstop: float = 100.0,
Tdamp: float = 0.1,
Tstart: u(float, units="kelvin") = 100.0,
Tstop: u(float, units="kelvin") = 100.0,
Tdamp: u(float, units="picosecond") = 0.1,
run: int = 100,
thermo: int = 10,
timestep: float = 0.001,
timestep: u(float, units="picosecond") = 0.001,
seed: int = 4928459,
dist: str = "gaussian",
lmp=None,
Expand Down Expand Up @@ -197,18 +202,19 @@ def calc_molecular_dynamics_nvt_with_lammpslib(
return result_dict


@units
def calc_molecular_dynamics_npt_with_lammpslib(
structure: Atoms,
potential_dataframe: pandas.DataFrame,
Tstart: float = 100.0,
Tstop: float = 100.0,
Tdamp: float = 0.1,
Tstart: u(float, units="kelvin") = 100.0,
Tstop: u(float, units="kelvin") = 100.0,
Tdamp: u(float, units="picosecond") = 0.1,
run: int = 100,
thermo: int = 100,
timestep: float = 0.001,
Pstart: float = 0.0,
Pstop: float = 0.0,
Pdamp: float = 1.0,
timestep: u(float, units="picosecond") = 0.001,
Pstart: u(float, units="bar") = 0.0,
Pstop: u(float, units="bar") = 0.0,
Pdamp: u(float, units="picosecond") = 1.0,
seed: int = 4928459,
dist: str = "gaussian",
lmp=None,
Expand Down Expand Up @@ -257,16 +263,17 @@ def calc_molecular_dynamics_npt_with_lammpslib(
return result_dict


@units
def calc_molecular_dynamics_nph_with_lammpslib(
structure: Atoms,
potential_dataframe: pandas.DataFrame,
run: int = 100,
thermo: int = 100,
timestep: float = 0.001,
Tstart: float = 100.0,
Pstart: float = 0.0,
Pstop: float = 0.0,
Pdamp: float = 1.0,
Tstart: u(float, units="kelvin") = 100.0,
Pstart: u(float, units="bar") = 0.0,
Pstop: u(float, units="bar") = 0.0,
Pdamp: u(float, units="picosecond") = 1.0,
seed: int = 4928459,
dist: str = "gaussian",
lmp=None,
Expand Down Expand Up @@ -312,21 +319,23 @@ def calc_molecular_dynamics_nph_with_lammpslib(
return result_dict


@units
def calc_molecular_dynamics_langevin_with_lammpslib(
structure: Atoms,
potential_dataframe: pandas.DataFrame,
run: int = 100,
thermo: int = 100,
timestep: float = 0.001,
Tstart: float = 100.0,
Tstop: float = 100,
Tdamp: float = 0.1,
timestep: u(float, units="picosecond") = 0.001,
Tstart: u(float, units="kelvin") = 100.0,
Tstop: u(float, units="kelvin") = 100.0,
Tdamp: u(float, units="picosecond") = 0.1,
seed: int = 4928459,
dist: str = "gaussian",
lmp=None,
output_keys=OutputMolecularDynamics.keys(),
**kwargs,
):
print("Force", timestep)
init_str = (
LAMMPS_THERMO_STYLE
+ "\n"
Expand Down Expand Up @@ -368,19 +377,20 @@ def calc_molecular_dynamics_langevin_with_lammpslib(
return result_dict


@units
def calc_molecular_dynamics_thermal_expansion_with_lammpslib(
structure: Atoms,
potential_dataframe: pandas.DataFrame,
Tstart: float = 15.0,
Tstop: float = 1500.0,
Tstart: u(float, units="kelvin") = 15.0,
Tstop: u(float, units="kelvin") = 1500.0,
Tstep: int = 5,
Tdamp: float = 0.1,
Tdamp: u(float, units="picosecond") = 0.1,
run: int = 100,
thermo: int = 100,
timestep: float = 0.001,
Pstart: float = 0.0,
Pstop: float = 0.0,
Pdamp: float = 1.0,
Pstart: u(float, units="bar") = 0.0,
Pstop: u(float, units="bar") = 0.0,
Pdamp: u(float, units="picosecond") = 1.0,
seed: int = 4928459,
dist: str = "gaussian",
lmp=None,
Expand Down
5 changes: 4 additions & 1 deletion atomistics/workflows/phonons/helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@
import structuretoolkit
from ase.atoms import Atoms
from phonopy import Phonopy
from semantikon.converter import units
from semantikon.typing import u

from atomistics.shared.output import OutputPhonons, OutputThermodynamic
from atomistics.workflows.phonons.units import VaspToTHz, kJ_mol_to_eV
Expand Down Expand Up @@ -260,10 +262,11 @@ def restore_magmoms(
return structure


@units
def generate_structures_helper(
structure: Atoms,
primitive_matrix: Optional[np.ndarray] = None,
displacement: float = 0.01,
displacement: u(float, units="angstrom") = 0.01,
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@coderabbitai coderabbitai bot May 6, 2025

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💡 Verification agent

🧩 Analysis chain

Good unit specification for displacement parameter.

The displacement parameter is appropriately annotated with angstrom units, which clearly communicates its physical meaning and enables automatic unit conversion.

There is a similar function in atomistics/workflows/quasiharmonic.py that also has a displacement parameter. Consider adding unit annotations there as well for consistency:

🏁 Script executed:

#!/bin/bash
# Check if there are other similar functions that might benefit from unit annotations
grep -rn "def generate_structures_helper" --include="*.py" .

Length of output: 368

🏁 Script executed:

#!/bin/bash
# Display the signature of generate_structures_helper in each file to check for displacement unit annotations
sed -n '1,40p' atomistics/workflows/elastic/helper.py
sed -n '180,240p' atomistics/workflows/evcurve/helper.py
sed -n '357,407p' atomistics/workflows/quasiharmonic.py

Length of output: 5925

Add unit annotation for displacement in QuasiHarmonic helper

The phonons helper correctly uses

displacement: u(float, units="angstrom") = 0.01

to convey units, but the QuasiHarmonic generate_structures_helper still has a plain float:

• File: atomistics/workflows/quasiharmonic.py
• Around line 367 in the def generate_structures_helper(...) signature

Update the parameter to match the phonons helper:

-    displacement: float = 0.01,
+    displacement: u(float, units="angstrom") = 0.01,

And add the corresponding import for u if it’s not already present:

from atomistics.shared.units import u

number_of_snapshots: Optional[int] = None,
interaction_range: float = 10.0,
factor: float = VaspToTHz,
Expand Down
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