121 problem with dimensionality for non periodic boundary conditions …

…in lammpsbase (aiidaplugins#122)

* (WIP) Adding override parameters for the structure dimension and boundary conditions when creating structure inputs.

* Small formatting changes to make them more consistent

* Fixing some type errors in the input generation.

* Fixing some type errors in the input generation.

Fixing a pre-commit issue

* Adding tests to check the override of structural paramters handling the boundary and dimensionality of the structure.

* Adding notes in the documentation about the possibility to override the dimension and the boundaries.

* Updating the possible dimensions so that it is compatible with the LAMMPS options.

---------

Co-authored-by: Jonathan Chico <[email protected]>

conftest.py

@@ -1,6 +1,7 @@
 """
 initialise a test database and profile
 """
+
 # pylint: disable=redefined-outer-name
 from __future__ import annotations
 
@@ -13,7 +14,7 @@
 
 from aiida import orm
 from aiida.common import AttributeDict, CalcInfo, LinkType, exceptions
-from aiida.engine import CalcJob
+from aiida.engine import CalcJob, Process
 from aiida.engine.utils import instantiate_process
 from aiida.manage.manager import get_manager
 from aiida.plugins import WorkflowFactory
@@ -67,6 +68,12 @@ def pytest_report_header(config):
     ]
 
 
+@pytest.fixture
+def structure_parameters() -> AttributeDict:
+    parameteters = AttributeDict({"dimension": 2, "boundary": ["p", "p", "f"]})
+    return parameteters
+
+
 @pytest.fixture
 def filepath_tests() -> pathlib.Path:
     """Return the path to the tests folder."""
@@ -612,7 +619,7 @@ def factory(
         entry_point_name: str,
         inputs: dict[str, Any] | None = None,
         return_process: bool = False,
-    ) -> tuple[pathlib.Path, CalcInfo] | CalcJob:
+    ) -> tuple[pathlib.Path, CalcInfo] | Process:
         """Create a :class:`aiida.engine.CalcJob` instance with the given inputs.
 
         :param entry_point_name: The entry point name of the calculation job plugin to run.

docs/source/topics/data/parameters.md

@@ -58,6 +58,8 @@ The dictionary is separated into several nested dictionaries that control differ
     * ``box_tilt``: determines how [skewed the cell](https://docs.lammps.org/box.html) is, of great importance for triclinic systems (default: ``small``).
     * ``groups``: list with the names of the groups to be added. The names of the possible groups are generated by the list of possible kind names generated by the structure (default: skip parameter).
     * ``atom_style``: how the [atoms](https://docs.lammps.org/atom_style.html) are treated by the ``LAMMPS`` simulation.
+    * ``boundary``: allows to override the [boundary](https://docs.lammps.org/boundary.html) conditions as set by the AiiDA structure as they can be incompatible with what ``LAMMPS`` expects.
+    * ``dimension``: allows to override the [dimension](https://docs.lammps.org/dimension.html) as determined by the AiiDA structure as it is determined by the boundary conditions and this is not what ``LAMMPS`` expects.
 - ``potential``: parameters related to the potential describing the system:
     * ``potential_style_options``: extra parameters related to each of the possible pair styles (default: skip parameter).
     * ``neighbor``: sets the parameters affecting the construction of the [neighbor list](https://docs.lammps.org/neighbor.html) (default: skip parameter).

src/aiida_lammps/parsers/base.py

@@ -7,7 +7,7 @@
 import glob
 import os
 import time
-from typing import Union
+from typing import Any, Dict, List, Union
 
 from aiida import orm
 from aiida.common import exceptions
@@ -178,8 +178,8 @@ def parse(self, **kwargs):
 
     def parse_restartfile(
         self,
-        parameters: dict,
-        list_of_files: list,
+        parameters: Dict[str, Any],
+        list_of_files: List[str],
         temp_folder: Union[os.PathLike, str, None],
     ) -> str:
         """
@@ -247,8 +247,8 @@ def parse_restartfile(
                 self.out("restartfile", restart_file)
         return restart_filename
 
-    def check_convergence(self, global_data: dict):
-        """Check for the convergence of the calculaiton in the case of a minimization run"""
+    def check_convergence(self, global_data: Dict[str, Any]):
+        """Check for the convergence of the calculation in the case of a minimization run"""
         _etol = global_data.get("minimization", {}).get(
             "energy_relative_difference", None
         )