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Merge main #1461

Merged
merged 16 commits into from
Jun 21, 2024
Merged
8 changes: 4 additions & 4 deletions .ci_support/environment-docs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,15 +16,15 @@ dependencies:
- numpy =1.26.4
- pandas =2.2.2
- phonopy =2.24.2
- pint =0.23
- pyiron_base =0.9.1
- pyiron_snippets =0.1.1
- pint =0.24
- pyiron_base =0.9.3
- pyiron_snippets =0.1.2
- pylammpsmpi =0.2.19
- pyscal =2.10.18
- scikit-learn =1.5.0
- scipy =1.13.1
- seekpath =2.1.0
- spglib =2.4.0
- structuretoolkit =0.0.24
- structuretoolkit =0.0.25
- pyxtal =0.6.2
- jupyter-book =1.0.0
8 changes: 4 additions & 4 deletions .ci_support/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -14,14 +14,14 @@ dependencies:
- numpy =1.26.4
- pandas =2.2.2
- phonopy =2.24.2
- pint =0.23
- pyiron_base =0.9.1
- pyiron_snippets =0.1.1
- pint =0.24
- pyiron_base =0.9.3
- pyiron_snippets =0.1.2
- pylammpsmpi =0.2.19
- pyscal =2.10.18
- scikit-learn =1.5.0
- scipy =1.13.1
- seekpath =2.1.0
- spglib =2.4.0
- structuretoolkit =0.0.24
- structuretoolkit =0.0.25
- pyxtal =0.6.2
5 changes: 0 additions & 5 deletions .github/workflows/unittests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -43,11 +43,6 @@ jobs:
label: linux-64-py-3-10
prefix: /usr/share/miniconda3/envs/my-env

- operating-system: ubuntu-latest
python-version: 3.9
label: linux-64-py-3-9
prefix: /usr/share/miniconda3/envs/my-env

steps:
- uses: actions/checkout@v2
- name: Setup Mambaforge
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7 changes: 4 additions & 3 deletions binder/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -12,15 +12,16 @@ dependencies:
- numpy =1.26.4
- pandas =2.2.2
- phonopy =2.24.2
- pint =0.23
- pyiron_base =0.9.1
- pint =0.24
- pyiron_base =0.9.3
- pyiron_snippets =0.1.2
- pylammpsmpi =0.2.19
- pyscal =2.10.18
- scikit-learn =1.5.0
- scipy =1.13.1
- seekpath =2.1.0
- spglib =2.4.0
- structuretoolkit =0.0.24
- structuretoolkit =0.0.25
- pyxtal =0.6.2
- pyiron-data >=0.0.22
- sqsgenerator
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1 change: 1 addition & 0 deletions pyiron_atomistics/lammps/base.py
Original file line number Diff line number Diff line change
Expand Up @@ -378,6 +378,7 @@ def write_input(self):
Returns:

"""
super().write_input()
if self.structure is None:
raise ValueError("Input structure not set. Use method set_structure()")
lmp_structure = self._get_lammps_structure(
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1 change: 1 addition & 0 deletions pyiron_atomistics/sphinx/base.py
Original file line number Diff line number Diff line change
Expand Up @@ -1356,6 +1356,7 @@ def write_input(self):

Automatically called by job.run()
"""
super().write_input()

# If the structure group was not modified directly by the
# user, via job.input.structure (which is likely True),
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1 change: 1 addition & 0 deletions pyiron_atomistics/vasp/base.py
Original file line number Diff line number Diff line change
Expand Up @@ -367,6 +367,7 @@ def write_input(self):
"""
Call routines that generate the INCAR, POTCAR, KPOINTS and POSCAR input files
"""
super().write_input()
if self.input.incar["SYSTEM"] == "pyiron_jobname":
self.input.incar["SYSTEM"] = self.job_name
modified_elements = {
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8 changes: 4 additions & 4 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -34,15 +34,15 @@ dependencies = [
"numpy==1.26.4",
"pandas==2.2.2",
"phonopy==2.24.2",
"pint==0.23",
"pyiron_base==0.9.1",
"pyiron_snippets==0.1.1",
"pint==0.24",
"pyiron_base==0.9.3",
"pyiron_snippets==0.1.2",
"pylammpsmpi==0.2.19",
"scipy==1.13.1",
"scikit-learn==1.5.0",
"seekpath==2.1.0",
"spglib==2.4.0",
"structuretoolkit==0.0.24",
"structuretoolkit==0.0.25",
]
dynamic = ["version"]

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