(WIP) Adding override parameters for the structure dimension and boun…

…dary conditions when creating structure inputs.

src/aiida_lammps/parsers/inputfile.py

@@ -14,7 +14,7 @@
 import json
 import os
 import re
-from typing import Union
+from typing import Any, Dict, Optional, Union
 
 from aiida import orm
 import numpy as np
@@ -24,15 +24,15 @@
 
 
 def generate_input_file(
-    parameters: dict,
+    parameters: Dict[str, Any],
     potential: LammpsPotentialData,
     structure: orm.StructureData,
     trajectory_filename: str = "aiida_lammps.trajectory.dump",
     restart_filename: str = "lammps.restart",
     potential_filename: str = "potential.dat",
     structure_filename: str = "structure.dat",
     variables_filename: str = "aiida_lammps.yaml",
-    read_restart_filename: str = None,
+    read_restart_filename: Optional[str] = None,
 ) -> str:
     """
     Generate the text for the lammps input file.
@@ -271,7 +271,7 @@ def write_potential_block(
 
 
 def write_structure_block(
-    parameters_structure: dict,
+    parameters_structure: Dict[str, Any],
     structure: orm.StructureData,
     structure_filename: str,
 ) -> Union[str, list]:
@@ -305,12 +305,21 @@ def write_structure_block(
     structure_block = generate_header("Start of the Structure information")
     structure_block += f'box tilt {parameters_structure.get("box_tilt", "small")}\n'
 
-    structure_block += f'dimension {structure.get_dimensionality()["dim"]}\n'
-    structure_block += "boundary "
-    for _bound in ["pbc1", "pbc2", "pbc3"]:
-        structure_block += f'{"p" if structure.base.attributes.all[_bound] else "f"} '
-    structure_block += "\n"
+    # Set the dimensions of the structure
+    if "dimension" in parameters_structure:
+        structure_block += f"dimension {parameters_structure['dimension']}\n"
+    else:
+        structure_block += f"dimension {structure.get_dimensionality()['dim']}\n"
+
+    # Set the boundary conditions of the structure
+    if "boundary" in parameters_structure:
+        structure_block += f"boundary {' '.join(parameters_structure['boundary'])} \n"
+    else:
+        structure_block += f"boundary {' '.join(['p' if entry else 'f' for entry in structure.pbc])} \n"
+
+    # Set the atom style for the structure
     structure_block += f'atom_style {parameters_structure["atom_style"]}\n'
+    # Write the command to read the structure from a file
     structure_block += f"read_data {structure_filename}\n"
     # Set the groups which will be used for the calculations
     if "groups" in parameters_structure:

src/aiida_lammps/parsers/utils.py

@@ -1,7 +1,8 @@
 """Utility functions for the handling of the input files"""
 from collections.abc import Iterable
-from typing import Union
+from typing import Dict, Optional, Union
 
+from aiida import orm
 import numpy as np
 
 
@@ -34,10 +35,10 @@ def _transform_cell(cell) -> Union[np.array, np.array]:
 
 
 def generate_lammps_structure(
-    structure,
+    structure: orm.StructureData,
     atom_style: str = "atomic",
-    charge_dict: dict = None,
-    round_dp: float = None,
+    charge_dict: Optional[Dict[str, float]] = None,
+    round_dp: Optional[float] = None,
     docstring: str = "generated by aiida_lammps",
 ) -> Union[str, np.array]:
     """Creation of the structure file content.
@@ -155,7 +156,7 @@ def flatten(full_list: list) -> list:
             yield element
 
 
-def convert_to_str(value):
+def convert_to_str(value) -> str:
     """convert True/False to yes/no and all values to strings"""
     if isinstance(value, bool):
         if value:
@@ -164,13 +165,13 @@ def convert_to_str(value):
     return str(value)
 
 
-def _convert_values(value):
+def _convert_values(value) -> str:
     if isinstance(value, (tuple, list)):
         return " ".join([convert_to_str(v) for v in value])
     return convert_to_str(value)
 
 
-def join_keywords(dct, ignore=None):
+def join_keywords(dct, ignore=None) -> str:
     """join a dict of {keyword: value, ...} into a string 'keyword value ...'
 
     value can be a single value or a list/tuple of values

src/aiida_lammps/validation/schemas/lammps_schema.json

@@ -122,6 +122,53 @@
                         "large"
                     ]
                 }
+            },
+            "dimension":{
+                "type": "integer",
+                "propertyNames":{
+                    "enum": [1,2,3]
+                }
+            },
+            "boundary":{
+                "type": "array",
+                "minItems": 3,
+                "maxItems": 3,
+                "items": [
+                    {
+                        "description": "boundary conditions along the a-direction",
+                        "type": "string",
+                        "enum": [
+                            "p",
+                            "f",
+                            "s",
+                            "m",
+                            "pp",
+                            "pf",
+                            "ps",
+                            "pm",
+                            "fp",
+                            "ff",
+                            "fs",
+                            "fm",
+                            "sp",
+                            "sf",
+                            "ss",
+                            "sm",
+                            "mp",
+                            "mf",
+                            "ms",
+                            "mm"
+                        ]
+                    },
+                    {
+                        "description": "boundary conditions along the b-direction",
+                        "type": "string"
+                    },
+                    {
+                        "description": "boundary conditions along the c-direction",
+                        "type": "string"
+                    }
+                ]
             }
         }
     },