refactor BaseLammpsCalculation, by moving _generate_input_function in…

…to class

Also:

- store potential input lines with {kind_symbols} placeholder, rather than specifying upfront.
  This allows the EmpiricalPotential nodes to be more reusable for multiple structures, with different atom types.
- add allowed_element_names to potential data
- improve reaxff_convert.write_lammps_format handling of X species

aiida_lammps/calculations/lammps/__init__.py

@@ -217,16 +217,30 @@ def validate_parameters(self, param_data, potential_object):
     def prepare_extra_files(self, tempfolder, potential_object):
         return True
 
+    def create_main_input_content(
+        self,
+        parameter_data,
+        potential_data,
+        kind_symbols,
+        structure_filename,
+        trajectory_filename,
+        info_filename,
+        restart_filename,
+        add_thermo_keywords,
+        version_date,
+    ):
+        raise NotImplementedError
+
     def prepare_for_submission(self, tempfolder):
         """Create the input files from the input nodes passed to this instance of the `CalcJob`.
 
         :param tempfolder: an `aiida.common.folders.Folder` to temporarily write files on disk
         :return: `aiida.common.CalcInfo` instance
         """
         # assert that the potential and structure have the same kind elements
-        if [
+        if self.inputs.potential.allowed_element_names is not None and not set(
             k.symbol for k in self.inputs.structure.kinds
-        ] != self.inputs.potential.kind_elements:
+        ).issubset(self.inputs.potential.allowed_element_names):
             raise ValidationError(
                 "the structure and potential are not compatible (different kind elements)"
             )
@@ -251,9 +265,10 @@ def prepare_for_submission(self, tempfolder):
         lammps_date = convert_date_string(pdict.get("lammps_version", "11 Aug 2017"))
 
         # Setup input parameters
-        input_txt = self._generate_input_function(
-            parameters=parameters,
-            potential_obj=self.inputs.potential,
+        input_txt = self.create_main_input_content(
+            parameter_data=parameters,
+            potential_data=self.inputs.potential,
+            kind_symbols=[kind.symbol for kind in self.inputs.structure.kinds],
             structure_filename=self._INPUT_STRUCTURE,
             trajectory_filename=self.options.trajectory_name,
             info_filename=self.options.info_filename,

aiida_lammps/calculations/lammps/combinate.py

@@ -42,39 +42,6 @@ def generate_dynaphopy_input(
     return input_file
 
 
-def generate_LAMMPS_input(
-    parameters, potential_obj, structure_file="potential.pot", trajectory_file=None
-):
-
-    random_number = np.random.randint(10000000)
-
-    # names_str = " ".join(potential_obj._names)
-
-    lammps_input_file = "units           {0}\n".format(potential_obj.default_units)
-    lammps_input_file += "boundary        p p p\n"
-    lammps_input_file += "box tilt large\n"
-    lammps_input_file += "atom_style      {0}\n".format(potential_obj.atom_style)
-    lammps_input_file += "read_data       {}\n".format(structure_file)
-
-    lammps_input_file += potential_obj.get_input_potential_lines()
-
-    lammps_input_file += "neighbor        0.3 bin\n"
-    lammps_input_file += "neigh_modify    every 1 delay 0 check no\n"
-
-    lammps_input_file += "velocity        all create {0} {1} dist gaussian mom yes\n".format(
-        parameters.dict.temperature, random_number
-    )
-    lammps_input_file += "velocity        all scale {}\n".format(
-        parameters.dict.temperature
-    )
-
-    lammps_input_file += "fix             int all nvt temp {0} {0} {1}\n".format(
-        parameters.dict.temperature, parameters.dict.thermostat_variable
-    )
-
-    return lammps_input_file
-
-
 class CombinateCalculation(BaseLammpsCalculation):
 
     _POSCAR_NAME = "POSCAR"
@@ -84,7 +51,6 @@ class CombinateCalculation(BaseLammpsCalculation):
     _OUTPUT_FORCE_CONSTANTS = "FORCE_CONSTANTS_OUT"
     _OUTPUT_QUASIPARTICLES = "quasiparticles_data.yaml"
     _OUTPUT_FILE_NAME = "OUTPUT"
-    _generate_input_function = generate_LAMMPS_input
 
     # self._retrieve_list = [self._OUTPUT_QUASIPARTICLES, self._OUTPUT_FORCE_CONSTANTS, self._OUTPUT_FILE_NAME]
 
@@ -104,6 +70,45 @@ def define(cls, spec):
 
         # spec.input('settings', valid_type=six.string_types, default='lammps.optimize')
 
+    def create_main_input_content(
+        self,
+        parameter_data,
+        potential_data,
+        structure_data,
+        structure_filename,
+        trajectory_filename,
+        info_filename,
+        restart_filename,
+        add_thermo_keywords,
+        version_date,
+    ):
+
+        random_number = np.random.randint(10000000)
+
+        lammps_input_file = "units           {0}\n".format(potential_data.default_units)
+        lammps_input_file += "boundary        p p p\n"
+        lammps_input_file += "box tilt large\n"
+        lammps_input_file += "atom_style      {0}\n".format(potential_data.atom_style)
+        lammps_input_file += "read_data       {}\n".format(structure_filename)
+
+        lammps_input_file += potential_data.get_input_lines(structure_data)
+
+        lammps_input_file += "neighbor        0.3 bin\n"
+        lammps_input_file += "neigh_modify    every 1 delay 0 check no\n"
+
+        lammps_input_file += "velocity        all create {0} {1} dist gaussian mom yes\n".format(
+            parameter_data.dict.temperature, random_number
+        )
+        lammps_input_file += "velocity        all scale {}\n".format(
+            parameter_data.dict.temperature
+        )
+
+        lammps_input_file += "fix             int all nvt temp {0} {0} {1}\n".format(
+            parameter_data.dict.temperature, parameter_data.dict.thermostat_variable
+        )
+
+        return lammps_input_file
+
     def prepare_extra_files(self, tempfolder, potential_object):
 
         if "fore_constants" in self.inputs:

aiida_lammps/calculations/lammps/force.py

@@ -5,81 +5,7 @@
 import six
 
 
-def generate_lammps_input(
-    calc,
-    parameters,
-    potential_obj,
-    structure_filename,
-    trajectory_filename,
-    add_thermo_keywords,
-    version_date="11 Aug 2017",
-    **kwargs
-):
-
-    lammps_input_file = "units          {0}\n".format(potential_obj.default_units)
-    lammps_input_file += "boundary        p p p\n"
-    lammps_input_file += "box tilt large\n"
-    lammps_input_file += "atom_style      {0}\n".format(potential_obj.atom_style)
-
-    lammps_input_file += "read_data       {}\n".format(structure_filename)
-
-    lammps_input_file += potential_obj.get_input_potential_lines()
-
-    lammps_input_file += "neighbor        0.3 bin\n"
-    lammps_input_file += "neigh_modify    every 1 delay 0 check no\n"
-
-    thermo_keywords = ["step", "temp", "epair", "emol", "etotal", "press"]
-    for kwd in add_thermo_keywords:
-        if kwd not in thermo_keywords:
-            thermo_keywords.append(kwd)
-    lammps_input_file += "thermo_style custom {}\n".format(" ".join(thermo_keywords))
-
-    if potential_obj.atom_style == "charge":
-        dump_variables = "element x y z fx fy fz q"
-        dump_format = "%4s  %16.10f %16.10f %16.10f  %16.10f %16.10f %16.10f %16.10f"
-    else:
-        dump_variables = "element x y z fx fy fz"
-        dump_format = "%4s  %16.10f %16.10f %16.10f  %16.10f %16.10f %16.10f"
-
-    lammps_input_file += "dump            aiida all custom 1 {0} {1}\n".format(
-        trajectory_filename, dump_variables
-    )
-
-    # TODO find exact version when changes were made
-    if version_date <= convert_date_string("10 Feb 2015"):
-        dump_mod_cmnd = "format"
-    else:
-        dump_mod_cmnd = "format line"
-
-    lammps_input_file += 'dump_modify     aiida {0} "{1}"\n'.format(
-        dump_mod_cmnd, dump_format
-    )
-
-    lammps_input_file += "dump_modify     aiida sort id\n"
-    lammps_input_file += "dump_modify     aiida element {}\n".format(
-        " ".join(potential_obj.kind_elements)
-    )
-
-    lammps_input_file += "run             0\n"
-
-    variables = parameters.get_attribute("output_variables", [])
-    for var in variables:
-        var_alias = var.replace("[", "_").replace("]", "_")
-        lammps_input_file += "variable {0} equal {1}\n".format(var_alias, var)
-        lammps_input_file += 'print "final_variable: {0} = ${{{0}}}"\n'.format(
-            var_alias
-        )
-
-    lammps_input_file += "variable final_energy equal etotal\n"
-    lammps_input_file += 'print "final_energy: ${final_energy}"\n'
-
-    return lammps_input_file
-
-
 class ForceCalculation(BaseLammpsCalculation):
-
-    _generate_input_function = generate_lammps_input
-
     @classmethod
     def define(cls, spec):
         super(ForceCalculation, cls).define(spec)
@@ -99,6 +25,82 @@ def define(cls, spec):
             help="force data per atom",
         )
 
+    def create_main_input_content(
+        self,
+        parameter_data,
+        potential_data,
+        kind_symbols,
+        structure_filename,
+        trajectory_filename,
+        info_filename,
+        restart_filename,
+        add_thermo_keywords,
+        version_date,
+    ):
+
+        lammps_input_file = "units          {0}\n".format(potential_data.default_units)
+        lammps_input_file += "boundary        p p p\n"
+        lammps_input_file += "box tilt large\n"
+        lammps_input_file += "atom_style      {0}\n".format(potential_data.atom_style)
+
+        lammps_input_file += "read_data       {}\n".format(structure_filename)
+
+        lammps_input_file += potential_data.get_input_lines(kind_symbols)
+
+        lammps_input_file += "neighbor        0.3 bin\n"
+        lammps_input_file += "neigh_modify    every 1 delay 0 check no\n"
+
+        thermo_keywords = ["step", "temp", "epair", "emol", "etotal", "press"]
+        for kwd in add_thermo_keywords:
+            if kwd not in thermo_keywords:
+                thermo_keywords.append(kwd)
+        lammps_input_file += "thermo_style custom {}\n".format(
+            " ".join(thermo_keywords)
+        )
+
+        if potential_data.atom_style == "charge":
+            dump_variables = "element x y z fx fy fz q"
+            dump_format = (
+                "%4s  %16.10f %16.10f %16.10f  %16.10f %16.10f %16.10f %16.10f"
+            )
+        else:
+            dump_variables = "element x y z fx fy fz"
+            dump_format = "%4s  %16.10f %16.10f %16.10f  %16.10f %16.10f %16.10f"
+
+        lammps_input_file += "dump            aiida all custom 1 {0} {1}\n".format(
+            trajectory_filename, dump_variables
+        )
+
+        # TODO find exact version when changes were made
+        if version_date <= convert_date_string("10 Feb 2015"):
+            dump_mod_cmnd = "format"
+        else:
+            dump_mod_cmnd = "format line"
+
+        lammps_input_file += 'dump_modify     aiida {0} "{1}"\n'.format(
+            dump_mod_cmnd, dump_format
+        )
+
+        lammps_input_file += "dump_modify     aiida sort id\n"
+        lammps_input_file += "dump_modify     aiida element {}\n".format(
+            " ".join(kind_symbols)
+        )
+
+        lammps_input_file += "run             0\n"
+
+        variables = parameter_data.get_attribute("output_variables", [])
+        for var in variables:
+            var_alias = var.replace("[", "_").replace("]", "_")
+            lammps_input_file += "variable {0} equal {1}\n".format(var_alias, var)
+            lammps_input_file += 'print "final_variable: {0} = ${{{0}}}"\n'.format(
+                var_alias
+            )
+
+        lammps_input_file += "variable final_energy equal etotal\n"
+        lammps_input_file += 'print "final_energy: ${final_energy}"\n'
+
+        return lammps_input_file
+
     def validate_parameters(self, param_data, potential_object):
         if param_data is not None:
             validate_against_schema(param_data.get_dict(), "force.schema.json")