From d9dc6d01be6e934ba9c672334711f499f825f670 Mon Sep 17 00:00:00 2001 From: ztzkz <95387041+ztzkz@users.noreply.github.com> Date: Sat, 22 Mar 2025 09:15:07 -0700 Subject: [PATCH 1/2] Update shuffle_poscar feature in run.py numpy.random.Generator.shuffle() performs the intended operation of shuffling the order of atoms. numpy.random.Generator.permuted() permutes the elements along the given axis, which mixes the coordinates of all atoms Signed-off-by: ztzkz <95387041+ztzkz@users.noreply.github.com> --- dpgen/generator/run.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dpgen/generator/run.py b/dpgen/generator/run.py index 0f6953721..53c84b7a1 100644 --- a/dpgen/generator/run.py +++ b/dpgen/generator/run.py @@ -1305,7 +1305,7 @@ def make_model_devi(iter_index, jdata, mdata): type_map=jdata["type_map"], ) if shuffle_poscar: - system.data["coords"] = rng.permuted(system.data["coords"], axis=1) + rng.shuffle(system.data["coords"], axis=1) if jdata.get("model_devi_nopbc", False): system.remove_pbc() system.to_lammps_lmp(os.path.join(conf_path, lmp_name)) From 752ed21585bbcf918c53215fb05ef32ed5497f58 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sat, 22 Mar 2025 16:20:52 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- dpgen/generator/run.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dpgen/generator/run.py b/dpgen/generator/run.py index 53c84b7a1..0ed125c86 100644 --- a/dpgen/generator/run.py +++ b/dpgen/generator/run.py @@ -1305,7 +1305,7 @@ def make_model_devi(iter_index, jdata, mdata): type_map=jdata["type_map"], ) if shuffle_poscar: - rng.shuffle(system.data["coords"], axis=1) + rng.shuffle(system.data["coords"], axis=1) if jdata.get("model_devi_nopbc", False): system.remove_pbc() system.to_lammps_lmp(os.path.join(conf_path, lmp_name))