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Fix CP2K 2025 stress parsing in bar #100

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Fix CP2K 2025 stress parsing in bar #100

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9 changes: 7 additions & 2 deletions cp2kdata/block_parser/stress.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,11 @@
import regex as re
import numpy as np

BAR_TO_GPA = 1e-4

STRESS_RE = re.compile(
r"""
(\sSTRESS\sTENSOR\s\[GPa\]
(\sSTRESS\sTENSOR\s\[(?P<unit>GPa|bar)\]
\n
\s+X\s+Y\s+Z\s*\n
\s+X
Expand All @@ -19,7 +21,7 @@
\s+(?P<zy>[\s-]\d+\.\d+)
\s+(?P<zz>[\s-]\d+\.\d+)\n
|# or another pattern used in v8.1
\s+STRESS\|\sAnalytical\sstress\stensor\s\[GPa\]\s*\n
\s+STRESS\|\sAnalytical\sstress\stensor\s\[(?P<unit>GPa|bar)\]\s*\n
\s+STRESS\|\s+x\s+y\s+z\s*\n
\s+STRESS\|\s+x
\s+(?P<xx>[\s-]\d+\.\d+E[\+\-]\d\d)
Expand Down Expand Up @@ -47,6 +49,9 @@ def parse_stress_tensor_list(output_file):
[match["yx"], match["yy"], match["yz"]],
[match["zx"], match["zy"], match["zz"]]
]
if match["unit"] == "bar":
stress_tensor = np.asarray(stress_tensor, dtype=float)
stress_tensor *= BAR_TO_GPA
stress_tensor_list.append(stress_tensor)
if stress_tensor_list:
return np.array(stress_tensor_list, dtype=float)
Expand Down
31 changes: 31 additions & 0 deletions tests/test_stress.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
import numpy as np

from cp2kdata.block_parser.stress import parse_stress_tensor_list


def test_parse_cp2k_2025_stress_in_bar():
output = """
STRESS| Analytical stress tensor [GPa]
STRESS| x y z
STRESS| x -1.00000000000E+00 2.00000000000E+00 3.00000000000E+00
STRESS| y 4.00000000000E+00 -5.00000000000E+00 6.00000000000E+00
STRESS| z 7.00000000000E+00 8.00000000000E+00 -9.00000000000E+00
STRESS| Analytical stress tensor [bar]
STRESS| x y z
STRESS| x -1.00000000000E+04 2.00000000000E+04 3.00000000000E+04
STRESS| y 4.00000000000E+04 -5.00000000000E+04 6.00000000000E+04
STRESS| z 7.00000000000E+04 8.00000000000E+04 -9.00000000000E+04
"""
expected = np.array(
[
[-1.0, 2.0, 3.0],
[4.0, -5.0, 6.0],
[7.0, 8.0, -9.0],
]
)

stresses = parse_stress_tensor_list(output)

assert stresses.shape == (2, 3, 3)
np.testing.assert_allclose(stresses[0], expected)
np.testing.assert_allclose(stresses[1], expected)