aiidaplugins · pre-commit-ci · Sep 21, 2026 · Sep 21, 2026
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -8,15 +8,15 @@ exclude: >
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-json
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.16.8
     hooks:
     - id: ruff
       args: [--fix]

diff --git a/conftest.py b/conftest.py
@@ -64,8 +64,8 @@ def get_work_directory(config):
 def pytest_report_header(config):
     """Add header information for pytest execution."""
     return [
-        f'LAMMPS Executable: {shutil.which(config.getoption("lammps_exec") or "lammps")}',
-        f'LAMMPS Work Directory: {config.getoption("lammps_workdir") or "<TEMP>"}',
+        f"LAMMPS Executable: {shutil.which(config.getoption('lammps_exec') or 'lammps')}",
+        f"LAMMPS Work Directory: {config.getoption('lammps_workdir') or '<TEMP>'}",
     ]
 
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -150,6 +150,6 @@
 with open("nitpick-exceptions") as handle:
     nitpick_ignore = [
         tuple(line.strip().split(None, 1))
-        for line in handle.readlines()
+        for line in handle
         if line.strip() and not line.startswith("#")
     ]
diff --git a/docs/source/getting_started/index.md b/docs/source/getting_started/index.md
@@ -99,11 +99,11 @@ from pathlib import Path
 
 # Create the node with the computer
 computer = Computer(
-    label='localhost',
-    hostname='localhost',
-    transport_type='core.local',
-    scheduler_type='core.direct',
-    workdir=Path('/home/my_username/aiida_workspace').resolve()
+    label="localhost",
+    hostname="localhost",
+    transport_type="core.local",
+    scheduler_type="core.direct",
+    workdir=Path("/home/my_username/aiida_workspace").resolve(),
 )
 # Store the node in the database
 computer.store()
@@ -143,14 +143,14 @@ To define the [InstalledCode](https://aiida.readthedocs.io/projects/aiida-core/e
 from aiida.orm import InstalledCode
 
 # Load the computer resource where LAMMPS is installed
-computer = load_computer('localhost')
+computer = load_computer("localhost")
 
 # Define the code node
 code = InstalledCode(
-    label='lammps',
+    label="lammps",
     computer=computer,
-    filepath_executable='/path/to/lammps/lmp',
-    default_calc_job_plugin='lammps.base'
+    filepath_executable="/path/to/lammps/lmp",
+    default_calc_job_plugin="lammps.base",
 )
 
 # Store the code node in the database

diff --git a/docs/source/topics/data/parameters.md b/docs/source/topics/data/parameters.md
@@ -16,35 +16,35 @@ The behavior of the {{ aiida_lammps }} calculation can be controlled by collecti
 
 ```python
 parameters = {
-    'md': {
-        'velocity': [{'group': 'all', 'create': {'temp': 300}}],
-        'integration': {
-            'style': 'npt',
-            'constraints': {'iso': [0.0, 0.0, 1000.0], 'temp': [300, 300, 100]}
+    "md": {
+        "velocity": [{"group": "all", "create": {"temp": 300}}],
+        "integration": {
+            "style": "npt",
+            "constraints": {"iso": [0.0, 0.0, 1000.0], "temp": [300, 300, 100]},
         },
-        'max_number_steps': 5000
+        "max_number_steps": 5000,
     },
-    'dump': {'dump_rate': 1000},
-    'thermo': {
-        'printing_rate': 100,
-        'thermo_printing': {
-            'ke': True,
-            'pe': True,
-            'pxx': True,
-            'pyy': True,
-            'pzz': True,
-            'step': True,
-            'press': True
-        }
+    "dump": {"dump_rate": 1000},
+    "thermo": {
+        "printing_rate": 100,
+        "thermo_printing": {
+            "ke": True,
+            "pe": True,
+            "pxx": True,
+            "pyy": True,
+            "pzz": True,
+            "step": True,
+            "press": True,
+        },
     },
-    'compute': {
-        'ke/atom': [{'type': [{'value': ' ', 'keyword': ' '}], 'group': 'all'}],
-        'pe/atom': [{'type': [{'value': ' ', 'keyword': ' '}], 'group': 'all'}],
-        'pressure': [{'type': ['thermo_temp'], 'group': 'all'}],
-        'stress/atom': [{'type': ['NULL'], 'group': 'all'}]
+    "compute": {
+        "ke/atom": [{"type": [{"value": " ", "keyword": " "}], "group": "all"}],
+        "pe/atom": [{"type": [{"value": " ", "keyword": " "}], "group": "all"}],
+        "pressure": [{"type": ["thermo_temp"], "group": "all"}],
+        "stress/atom": [{"type": ["NULL"], "group": "all"}],
     },
-    'control': {'units': 'metal', 'timestep': 1e-05},
-    'structure': {'atom_style': 'atomic'}
+    "control": {"units": "metal", "timestep": 1e-05},
+    "structure": {"atom_style": "atomic"},
 }
 ```
 

diff --git a/docs/source/topics/data/potential.md b/docs/source/topics/data/potential.md
@@ -18,47 +18,49 @@ To demonstrate how this works one can [download](https://openkim.org/id/EAM_Dyna
 
 ```python
 potential_parameters = {
-    'species': ['Fe'],  # Which species can be treated by this potential (required)
-    'atom_style': 'atomic', # Which kind of atomic style is associated with this potential (required)
-    'pair_style': 'eam/fs', # LAMMPS pair style (required)
-    'units': 'metal', # Default units of this potential (required)
-    'extra_tags': {
-        'content_origin': 'NIST IPRP: https: // www.ctcms.nist.gov/potentials/Fe.html', # Where the file was original found
-        'content_other_locations': None, # If the file can be found somewhere else
-        'data_method': 'unknown', # How was the data generated
-        'description': """
+    "species": ["Fe"],  # Which species can be treated by this potential (required)
+    "atom_style": "atomic",  # Which kind of atomic style is associated with this potential (required)
+    "pair_style": "eam/fs",  # LAMMPS pair style (required)
+    "units": "metal",  # Default units of this potential (required)
+    "extra_tags": {
+        "content_origin": "NIST IPRP: https: // www.ctcms.nist.gov/potentials/Fe.html",  # Where the file was original found
+        "content_other_locations": None,  # If the file can be found somewhere else
+        "data_method": "unknown",  # How was the data generated
+        "description": """
         This Fe EAM potential parameter file is from the NIST repository, \"Fe_2.eam.fs\" as of the March 9, 2009 update.
         It is similar to \"Fe_mm.eam.fs\" in the LAMMPS distribution dated 2007-06-11,
         but gives different results for very small interatomic distances
         (The LAMMPS potential is in fact the deprecated potential referred to in the March 9, 2009 update on the NIST repository).
         The file header includes a note from the NIST contributor:
         \"The potential was taken from v9_4_bcc (in C:\\SIMULATION.MD\\Fe\\Results\\ab_initio+Interstitials)\"
-        """, # Short description of the potential
-        'developer': ['Ronald E. Miller'], # Name of the developer that uploaded it to OpenKIM
-        'disclaimer': """
+        """,  # Short description of the potential
+        "developer": [
+            "Ronald E. Miller"
+        ],  # Name of the developer that uploaded it to OpenKIM
+        "disclaimer": """
         According to the developer Giovanni Bonny (as reported by the NIST IPRP),
         this potential was not stiffened and cannot be used in its present form for collision cascades.
-        """, # Any known issues with the potential
-        'properties': None, # If any specific properties are associated to the potential
-        'publication_year': 2018, # Year of publication to OpenKIM
-        'source_citations': [{
-            'abstract': None,
-            'author':
-            'Mendelev, MI and Han, S and Srolovitz, DJ and Ackland, GJ and Sun, DY and Asta, M',
-            'doi': '10.1080/14786430310001613264',
-            'journal': '{Phil. Mag.}',
-            'number': '{35}',
-            'pages': '{3977-3994}',
-            'recordkey': 'MO_546673549085_000a',
-            'recordprimary': 'recordprimary',
-            'recordtype': 'article',
-            'title':
-            '{Development of new interatomic potentials appropriate for crystalline and liquid iron}',
-            'volume': '{83}',
-            'year': '{2003}'
-        }],
-        'title': 'EAM potential (LAMMPS cubic hermite tabulation) for Fe developed by Mendelev et al. (2003) v000' # Title of the potential
-    }
+        """,  # Any known issues with the potential
+        "properties": None,  # If any specific properties are associated to the potential
+        "publication_year": 2018,  # Year of publication to OpenKIM
+        "source_citations": [
+            {
+                "abstract": None,
+                "author": "Mendelev, MI and Han, S and Srolovitz, DJ and Ackland, GJ and Sun, DY and Asta, M",
+                "doi": "10.1080/14786430310001613264",
+                "journal": "{Phil. Mag.}",
+                "number": "{35}",
+                "pages": "{3977-3994}",
+                "recordkey": "MO_546673549085_000a",
+                "recordprimary": "recordprimary",
+                "recordtype": "article",
+                "title": "{Development of new interatomic potentials appropriate for crystalline and liquid iron}",
+                "volume": "{83}",
+                "year": "{2003}",
+            }
+        ],
+        "title": "EAM potential (LAMMPS cubic hermite tabulation) for Fe developed by Mendelev et al. (2003) v000",  # Title of the potential
+    },
 }
 ```
 Certain tags are required, and must be provided to be able to upload the potential to the database. This is because they identify which {{ pair_style }} is associated with the potential, which atomic species can be treated with it, etc. The rest of the tags, in this example are filled so that they follow the [OpenKIM](https://openkim.org/doc/schema/kimspec/) standard as that is the place where the potential was obtained. If another database is used or if it is a homemade potential, these tags can be used to facilitate the querying of the potential.
@@ -68,10 +70,9 @@ Then the potential can be uploaded to the database
 from aiida_lamps.data.potential import LammpsPotentialData
 
 potential = LammpsPotentialData.get_or_create(
-    source='Fe_2.eam.fs', # Relative path to the potential file
-    **potential_parameters, # Parameters to tag the potential
+    source="Fe_2.eam.fs",  # Relative path to the potential file
+    **potential_parameters,  # Parameters to tag the potential
 )
-
 ```
 
 The {meth}`~aiida_lammps.data.potential.LammpsPotentialData.get_or_create` method is based on the one by [aiida-pseudo](https://github.com/aiidateam/aiida-pseudo/blob/master/aiida_pseudo/data/pseudo/pseudo.py), which will calculate the md5 sum of the file and check the database for another file with the same [md5 hash](https://en.wikipedia.org/wiki/MD5), if such entry is found, that potential is used instead. This avoids the unnecessary replication of potential data nodes whenever one tries to upload a previously uploaded potential.

diff --git a/docs/source/tutorials/first_md.md b/docs/source/tutorials/first_md.md
@@ -31,7 +31,7 @@ Then, load the code that was setup in AiiDA for `lmp` and get an instance of the
 ```python
 # Load the code configured for ``lmp``. Make sure to replace
 # this string with the label used in the code setup.
-code = load_code('lammps@localhost')
+code = load_code("lammps@localhost")
 builder = code.get_builder()
 ```
 
@@ -40,7 +40,8 @@ One can start by defining and assigning the structure to the builder:
 
 ```python
 from ase.build import bulk
-structure = StructureData(ase=bulk('Fe', 'bcc', 2.87, cubic=True))
+
+structure = StructureData(ase=bulk("Fe", "bcc", 2.87, cubic=True))
 builder.structure = structure
 ```
 
@@ -60,24 +61,28 @@ import requests
 import io
 
 # Download the potential from the repository and store it as a BytesIO object
-_stream = io.BytesIO(requests.get('https://openkim.org/files/MO_546673549085_000/Fe_2.eam.fs', timeout=20).text.encode('utf-8'))
+_stream = io.BytesIO(
+    requests.get(
+        "https://openkim.org/files/MO_546673549085_000/Fe_2.eam.fs", timeout=20
+    ).text.encode("utf-8")
+)
 
 # Set the metadata for the potential
 potential_parameters = {
-    'species': ['Fe'],
-    'atom_style': 'atomic',
-    'pair_style': 'eam/fs',
-    'units': 'metal',
-    'extra_tags': {
-        'title': 'EAM potential (LAMMPS cubic hermite tabulation) for Fe developed by Mendelev et al. (2003) v000',
-        'content_origin': 'NIST IPRP: https: // www.ctcms.nist.gov/potentials/Fe.html',
-        'developer': ['Ronald E. Miller'],
-        'publication_year': 2018,
-    }
+    "species": ["Fe"],
+    "atom_style": "atomic",
+    "pair_style": "eam/fs",
+    "units": "metal",
+    "extra_tags": {
+        "title": "EAM potential (LAMMPS cubic hermite tabulation) for Fe developed by Mendelev et al. (2003) v000",
+        "content_origin": "NIST IPRP: https: // www.ctcms.nist.gov/potentials/Fe.html",
+        "developer": ["Ronald E. Miller"],
+        "publication_year": 2018,
+    },
 }
 
 # Store the potential in an AiiDA node
-potential = LammpsPotentialData.get_or_create(source=_stream,**potential_parameters)
+potential = LammpsPotentialData.get_or_create(source=_stream, **potential_parameters)
 
 builder.potential = potential
 ```
@@ -95,45 +100,42 @@ Then one needs to define the parameters which control how the input file for the
 For a structural minimization the minimal set of parameters is the following:
 
 ```python
-
 # Parameters to control the input file generation
-parameters = Dict({
-    "control": {
-        "units": "metal",
-        "timestep": 1e-5
-    },
-    "compute":{
-        "pe/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
-        "ke/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
-        "stress/atom": [{"type": ["NULL"], "group": "all"}],
-        "pressure": [{"type": ["thermo_temp"], "group": "all"}],
-    },
-
-    "structure":{"atom_style": "atomic"},
-    "thermo":{
-        "printing_rate": 100,
-        "thermo_printing": {
-            "step": True,
-            "pe": True,
-            "ke": True,
-            "press": True,
-            "pxx": True,
-            "pyy": True,
-            "pzz": True,
-        }
-    },
-    "md":{
-        "integration": {
-            "style": "npt",
-            "constraints": {
-                "temp": [300, 300, 100],
-                "iso": [0.0, 0.0, 1000.0],
+parameters = Dict(
+    {
+        "control": {"units": "metal", "timestep": 1e-5},
+        "compute": {
+            "pe/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
+            "ke/atom": [{"type": [{"keyword": " ", "value": " "}], "group": "all"}],
+            "stress/atom": [{"type": ["NULL"], "group": "all"}],
+            "pressure": [{"type": ["thermo_temp"], "group": "all"}],
+        },
+        "structure": {"atom_style": "atomic"},
+        "thermo": {
+            "printing_rate": 100,
+            "thermo_printing": {
+                "step": True,
+                "pe": True,
+                "ke": True,
+                "press": True,
+                "pxx": True,
+                "pyy": True,
+                "pzz": True,
             },
         },
-        "max_number_steps": 5000,
-        "velocity": [{"create": {"temp": 300}, "group": "all"}],
-    },
-})
+        "md": {
+            "integration": {
+                "style": "npt",
+                "constraints": {
+                    "temp": [300, 300, 100],
+                    "iso": [0.0, 0.0, 1000.0],
+                },
+            },
+            "max_number_steps": 5000,
+            "velocity": [{"create": {"temp": 300}, "group": "all"}],
+        },
+    }
+)
 builder.parameters = parameters
 ```
 The parameters have several sections which control different behavior of the calculation:
@@ -154,11 +156,11 @@ Lastly one needs to define the computational resources needed to perform the cal
 # Run the calculation on 1 CPU and kill it if it runs longer than 1800 seconds.
 # Set ``withmpi`` to ``False`` if ``pw.x`` was compiled without MPI support.
 builder.metadata.options = {
-    'resources': {
-        'num_machines': 1,
+    "resources": {
+        "num_machines": 1,
     },
-    'max_wallclock_seconds': 1800,
-    'withmpi': False,
+    "max_wallclock_seconds": 1800,
+    "withmpi": False,
 }
 ```
 
@@ -213,5 +215,5 @@ The `time_dependent_computes` contains a series of numpy arrays each one represe
 The complete output that was written by {{ LAMMPS }} to stdout, can be retrieved as follows:
 
 ```python
-results['retrieved'].base.repository.get_object_content('aiida_lammps.out')
+results["retrieved"].base.repository.get_object_content("aiida_lammps.out")
 ```