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style: enforce LF line ending (#661)
Try to fix #657 automatically
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‎.github/workflows/test_import.yml‎

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@@ -1,18 +1,18 @@
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name: test Python import
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on:
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- push
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- pull_request
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: '3.9'
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architecture: 'x64'
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- run: python -m pip install uv
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- run: python -m uv pip install --system .
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- run: python -c 'import dpdata'
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name: test Python import
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on:
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- push
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- pull_request
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: '3.9'
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architecture: 'x64'
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- run: python -m pip install uv
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- run: python -m uv pip install --system .
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- run: python -c 'import dpdata'

‎.pre-commit-config.yaml‎

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@@ -16,6 +16,8 @@ repos:
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- id: check-merge-conflict
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- id: check-symlinks
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- id: check-toml
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- id: mixed-line-ending
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args: ["--fix=lf"]
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# Python
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- repo: https://github.com/astral-sh/ruff-pre-commit
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# Ruff version.

‎docs/credits.rst‎

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@@ -1,4 +1,4 @@
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Authors
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=======
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Authors
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=======
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.. git-shortlog-authors::

‎dpdata/orca/output.py‎

Lines changed: 64 additions & 64 deletions
Original file line numberDiff line numberDiff line change
@@ -1,64 +1,64 @@
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from __future__ import annotations
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import numpy as np
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def read_orca_sp_output(fn: str) -> tuple[np.ndarray, np.ndarray, float, np.ndarray]:
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"""Read from ORCA output.
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Note that both the energy and the gradient should be printed.
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Parameters
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----------
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fn : str
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file name
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Returns
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-------
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np.ndarray
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atomic symbols
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np.ndarray
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atomic coordinates
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float
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total potential energy
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np.ndarray
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atomic forces
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"""
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coord = None
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symbols = None
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forces = None
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energy = None
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with open(fn) as f:
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flag = 0
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for line in f:
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if flag in (1, 3, 4):
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flag += 1
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elif flag == 2:
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s = line.split()
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if not len(s):
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flag = 0
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else:
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symbols.append(s[0].capitalize())
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coord.append([float(s[1]), float(s[2]), float(s[3])])
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elif flag == 5:
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s = line.split()
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if not len(s):
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flag = 0
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else:
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forces.append([float(s[3]), float(s[4]), float(s[5])])
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elif line.startswith("CARTESIAN COORDINATES (ANGSTROEM)"):
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# coord
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flag = 1
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coord = []
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symbols = []
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elif line.startswith("CARTESIAN GRADIENT"):
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flag = 3
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forces = []
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elif line.startswith("FINAL SINGLE POINT ENERGY"):
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energy = float(line.split()[-1])
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symbols = np.array(symbols)
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forces = -np.array(forces)
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coord = np.array(coord)
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assert coord.shape == forces.shape
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return symbols, coord, energy, forces
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from __future__ import annotations
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3+
import numpy as np
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5+
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def read_orca_sp_output(fn: str) -> tuple[np.ndarray, np.ndarray, float, np.ndarray]:
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"""Read from ORCA output.
8+
9+
Note that both the energy and the gradient should be printed.
10+
11+
Parameters
12+
----------
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fn : str
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file name
15+
16+
Returns
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-------
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np.ndarray
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atomic symbols
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np.ndarray
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atomic coordinates
22+
float
23+
total potential energy
24+
np.ndarray
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atomic forces
26+
"""
27+
coord = None
28+
symbols = None
29+
forces = None
30+
energy = None
31+
with open(fn) as f:
32+
flag = 0
33+
for line in f:
34+
if flag in (1, 3, 4):
35+
flag += 1
36+
elif flag == 2:
37+
s = line.split()
38+
if not len(s):
39+
flag = 0
40+
else:
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symbols.append(s[0].capitalize())
42+
coord.append([float(s[1]), float(s[2]), float(s[3])])
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elif flag == 5:
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s = line.split()
45+
if not len(s):
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flag = 0
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else:
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forces.append([float(s[3]), float(s[4]), float(s[5])])
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elif line.startswith("CARTESIAN COORDINATES (ANGSTROEM)"):
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# coord
51+
flag = 1
52+
coord = []
53+
symbols = []
54+
elif line.startswith("CARTESIAN GRADIENT"):
55+
flag = 3
56+
forces = []
57+
elif line.startswith("FINAL SINGLE POINT ENERGY"):
58+
energy = float(line.split()[-1])
59+
symbols = np.array(symbols)
60+
forces = -np.array(forces)
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coord = np.array(coord)
62+
assert coord.shape == forces.shape
63+
64+
return symbols, coord, energy, forces

‎dpdata/plugins/orca.py‎

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Original file line numberDiff line numberDiff line change
@@ -1,53 +1,53 @@
1-
from __future__ import annotations
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import numpy as np
4-
5-
from dpdata.format import Format
6-
from dpdata.orca.output import read_orca_sp_output
7-
from dpdata.unit import EnergyConversion, ForceConversion
8-
9-
energy_convert = EnergyConversion("hartree", "eV").value()
10-
force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value()
11-
12-
13-
@Format.register("orca/spout")
14-
class ORCASPOutFormat(Format):
15-
"""ORCA single point energy output.
16-
17-
Note that both the energy and the gradient should be
18-
printed into the output file.
19-
"""
20-
21-
def from_labeled_system(self, file_name: str, **kwargs) -> dict:
22-
"""Read from ORCA single point energy output.
23-
24-
Parameters
25-
----------
26-
file_name : str
27-
file name
28-
**kwargs
29-
keyword arguments
30-
31-
Returns
32-
-------
33-
dict
34-
system data
35-
"""
36-
symbols, coord, energy, forces = read_orca_sp_output(file_name)
37-
38-
atom_names, atom_types, atom_numbs = np.unique(
39-
symbols, return_inverse=True, return_counts=True
40-
)
41-
natoms = coord.shape[0]
42-
43-
return {
44-
"atom_types": atom_types,
45-
"atom_names": list(atom_names),
46-
"atom_numbs": list(atom_numbs),
47-
"coords": coord.reshape((1, natoms, 3)),
48-
"energies": np.array([energy * energy_convert]),
49-
"forces": (forces * force_convert).reshape((1, natoms, 3)),
50-
"cells": np.zeros((1, 3, 3)),
51-
"orig": np.zeros(3),
52-
"nopbc": True,
53-
}
1+
from __future__ import annotations
2+
3+
import numpy as np
4+
5+
from dpdata.format import Format
6+
from dpdata.orca.output import read_orca_sp_output
7+
from dpdata.unit import EnergyConversion, ForceConversion
8+
9+
energy_convert = EnergyConversion("hartree", "eV").value()
10+
force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value()
11+
12+
13+
@Format.register("orca/spout")
14+
class ORCASPOutFormat(Format):
15+
"""ORCA single point energy output.
16+
17+
Note that both the energy and the gradient should be
18+
printed into the output file.
19+
"""
20+
21+
def from_labeled_system(self, file_name: str, **kwargs) -> dict:
22+
"""Read from ORCA single point energy output.
23+
24+
Parameters
25+
----------
26+
file_name : str
27+
file name
28+
**kwargs
29+
keyword arguments
30+
31+
Returns
32+
-------
33+
dict
34+
system data
35+
"""
36+
symbols, coord, energy, forces = read_orca_sp_output(file_name)
37+
38+
atom_names, atom_types, atom_numbs = np.unique(
39+
symbols, return_inverse=True, return_counts=True
40+
)
41+
natoms = coord.shape[0]
42+
43+
return {
44+
"atom_types": atom_types,
45+
"atom_names": list(atom_names),
46+
"atom_numbs": list(atom_numbs),
47+
"coords": coord.reshape((1, natoms, 3)),
48+
"energies": np.array([energy * energy_convert]),
49+
"forces": (forces * force_convert).reshape((1, natoms, 3)),
50+
"cells": np.zeros((1, 3, 3)),
51+
"orig": np.zeros(3),
52+
"nopbc": True,
53+
}

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