Merge pull request #54 from sphuber/fix/spec-parser-default

Do not recreate `parser_name` input port to change default

aiida_lammps/calculations/lammps/__init__.py

@@ -12,87 +12,6 @@
 from aiida_lammps.data.potential import EmpiricalPotential
 
 
-def get_supercell(
-    structure: orm.StructureData,
-    supercell_shape: orm.Dict,
-) -> orm.StructureData:
-    """Generate a supercell from a given StructureData
-
-    :param structure: original structure that will be used to generate the supercell
-    :type structure: orm.StructureData
-    :param supercell_shape: dictionary with the supercell information
-    :type supercell_shape: orm.Dict
-    :return: generated supercell
-    :rtype: orm.StructureData
-    """
-    symbols = np.array([site.kind_name for site in structure.sites])
-    positions = np.array([site.position for site in structure.sites])
-    cell = np.array(structure.cell)
-    supercell_shape = np.array(supercell_shape.dict.shape)
-
-    supercell_array = np.dot(cell, np.diag(supercell_shape))
-
-    supercell = orm.StructureData(cell=supercell_array)
-    for k in range(positions.shape[0]):
-        for entry in itertools.product(*[range(i) for i in supercell_shape[::-1]]):
-            position = positions[k, :] + np.dot(np.array(entry[::-1]), cell)
-            symbol = symbols[k]
-            supercell.append_atom(position=position, symbols=symbol)
-
-    return supercell
-
-
-def get_force_constants(force_constants: orm.ArrayData) -> str:
-    """Get the force constants in text format
-
-    :param force_constants: Array with the information needed for the force constants
-    :type force_constants: orm.ArrayData
-    :return: force constants in text
-    :rtype: str
-    """
-    force_constants = force_constants.get_array("force_constants")
-
-    fc_shape = force_constants.shape
-    fc_txt = "%4d\n" % (fc_shape[0])
-    for i in range(fc_shape[0]):
-        for j in range(fc_shape[1]):
-            fc_txt += "%4d%4d\n" % (i + 1, j + 1)
-            for vec in force_constants[i][j]:
-                fc_txt += ("%22.15f" * 3 + "\n") % tuple(vec)
-
-    return fc_txt
-
-
-def structure_to_poscar(structure: orm.StructureData) -> str:
-    """Write the structure into a POSCAR
-
-    :param structure: structure used for the simulation
-    :type structure: orm.StructureData
-    :return: POSCAR format for the structure
-    :rtype: str
-    """
-    atom_type_unique = np.unique(
-        [site.kind_name for site in structure.sites],
-        return_index=True,
-    )[1]
-    labels = np.diff(np.append(atom_type_unique, [len(structure.sites)]))
-
-    poscar = " ".join(np.unique([site.kind_name for site in structure.sites]))
-    poscar += "\n1.0\n"
-    cell = structure.cell
-    for row in cell:
-        poscar += f"{row[0]: 22.16f} {row[1]: 22.16f} {row[2]: 22.16f}\n"
-    poscar += " ".join(np.unique([site.kind_name for site in structure.sites])) + "\n"
-    poscar += " ".join(np.array(labels, dtype=str)) + "\n"
-    poscar += "Cartesian\n"
-    for site in structure.sites:
-        poscar += f"{site.position[0]: 22.16f} "
-        poscar += f"{site.position[1]: 22.16f} "
-        poscar += f"{site.position[2]: 22.16f}\n"
-
-    return poscar
-
-
 class BaseLammpsCalculation(CalcJob):
     """
     A basic plugin for calculating force constants using Lammps.
@@ -372,7 +291,6 @@ def prepare_for_submission(self, tempfolder):  # pylint: disable=arguments-diffe
         codeinfo = CodeInfo()
         codeinfo.cmdline_params = list(self._cmdline_params)
         codeinfo.code_uuid = self.inputs.code.uuid
-        codeinfo.withmpi = self.metadata.options.withmpi
         codeinfo.stdout_name = self._stdout_name
 
         calcinfo = CalcInfo()

aiida_lammps/calculations/lammps/base.py

@@ -101,11 +101,8 @@ def define(cls, spec):
             valid_type=str,
             default=cls._DEFAULT_RESTART_FILENAME,
         )
-        spec.input(
-            "metadata.options.parser_name",
-            valid_type=str,
-            default=cls._DEFAULT_PARSER,
-        )
+        spec.inputs["metadata"]["options"]["parser_name"].default = cls._DEFAULT_PARSER
+
         spec.output(
             "results",
             valid_type=orm.Dict,
@@ -258,8 +255,6 @@ def prepare_for_submission(self, folder):
         codeinfo.code_uuid = self.inputs.code.uuid
         # Set the name of the stdout
         codeinfo.stdout_name = _output_filename
-        # Set whether or not one is running with MPI
-        codeinfo.withmpi = self.inputs.metadata.options.withmpi
 
         # Generate the datastructure for the calculation information
         calcinfo = datastructures.CalcInfo()

aiida_lammps/calculations/lammps/force.py

@@ -14,11 +14,7 @@ class ForceCalculation(BaseLammpsCalculation):
     def define(cls, spec):
         super().define(spec)
 
-        spec.input(
-            "metadata.options.parser_name",
-            valid_type=str,
-            default="lammps.force",
-        )
+        spec.inputs["metadata"]["options"]["parser_name"].default = "lammps.force"
 
         spec.output(
             "arrays",

aiida_lammps/calculations/lammps/md.py

@@ -17,11 +17,7 @@ class MdCalculation(BaseLammpsCalculation):
     def define(cls, spec):
         super().define(spec)
 
-        spec.input(
-            "metadata.options.parser_name",
-            valid_type=str,
-            default="lammps.md",
-        )
+        spec.inputs["metadata"]["options"]["parser_name"].default = "lammps.md"
         spec.default_output_port = "results"
 
         spec.output(

aiida_lammps/calculations/lammps/md_multi.py

@@ -16,11 +16,7 @@ class MdMultiCalculation(BaseLammpsCalculation):
     def define(cls, spec):
         super().define(spec)
 
-        spec.input(
-            "metadata.options.parser_name",
-            valid_type=str,
-            default="lammps.md.multi",
-        )
+        spec.inputs["metadata"]["options"]["parser_name"].default = "lammps.md.multi"
         spec.default_output_port = "results"
 
         spec.output_namespace(

aiida_lammps/calculations/lammps/optimize.py

@@ -19,11 +19,7 @@ class OptimizeCalculation(BaseLammpsCalculation):
     def define(cls, spec):
         super().define(spec)
 
-        spec.input(
-            "metadata.options.parser_name",
-            valid_type=str,
-            default="lammps.optimize",
-        )
+        spec.inputs["metadata"]["options"]["parser_name"].default = "lammps.optimize"
 
         spec.output(
             "structure",