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support maxwarn (#363)
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* Update Dockerfile

New Dockerimage including:
- cp2k
- gromacs
- packmol
- apax
- ipsuite

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update docker file and others

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update build

* update dockerfile

* build docker image

* reduce number of cores adapted to github actions runner

* publish docker on release using self-hosted runner

* skip examples test

* update znh5md

* support maxwarn

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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PythonFZ and pre-commit-ci[bot] authored Dec 4, 2024
1 parent 885a2d1 commit 3bc4670
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3 changes: 3 additions & 0 deletions ipsuite/configuration_generation/gmx.py
Original file line number Diff line number Diff line change
Expand Up @@ -323,6 +323,7 @@ class Smiles2Gromacs(base.IPSNode):
tolerance: float = zntrack.params(2.0)
production_indices: list[int] = zntrack.params(None)
cleanup: bool = zntrack.params(True)
maxwarn: int = zntrack.params(0)

mdp_files: t.Sequence[str | pathlib.Path] = zntrack.deps_path(default_factory=list)
config_files: t.Sequence[str | pathlib.Path] = zntrack.params_path(
Expand Down Expand Up @@ -451,6 +452,8 @@ def _run_gmx(self):
"-o",
"box.tpr",
"-v",
"-maxwarn",
str(self.maxwarn),
]
print(f"Running {' '.join(cmd)}")
subprocess.run(cmd, check=True, cwd=self.output_dir)
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