Merge pull request #4 from kmlefran/docs

Expand documentation significantly

docs/source/reference/api/auto/aiida_aimall/calculations/index.rst

@@ -22,7 +22,6 @@ Classes
 .. autoapisummary::
 
    aiida_aimall.calculations.AimqbCalculation
-   aiida_aimall.calculations.GaussianWFXCalculation
 
 
 
@@ -137,102 +136,3 @@ Attributes
       :param folder: an `aiida.common.folders.Folder` where the plugin should temporarily
           place all files needed by the calculation.
       :return: `aiida.common.datastructures.CalcInfo` instance
-
-
-
-.. py:class:: GaussianWFXCalculation(*args, **kwargs)
-
-
-   Bases: :py:obj:`aiida.engine.CalcJob`
-
-   AiiDA calculation plugin wrapping Gaussian. Adapted from aiida-gaussian
-          https://github.com/nanotech-empa/aiida-gaussian, Copyright (c) 2020 Kristjan Eimre.
-          Additions made to enable providing molecule input as orm.Str,
-          and wfx files are retrieved by default. We further define another input wfxgroup in which you can provide an
-          optional group to store the wfx file in and fragment_label as an optional extra to add on the output.
-
-      Args:
-          structure: StructureData for molecule to be run. Do not provide structure AND structure_str, but provide
-          at least one
-          structure_str: Str for molecule to be run. e.g. orm.Str(H 0.0 0.0 0.0
-   H -1.0 0.0 0.0)
-          Do not provide structure AND structure_str, but provide at least one
-          wfxgroup: Str of a group to add the .wfx files to
-          parameters: required: Dict of Gaussian parameters, same as from aiida-gaussian. Note that the options provided should
-          generate a wfx file. See Example
-          settings: optional, additional input parameters
-          fragment_label: Str, optional: an extra to add to the wfx file node. Involved in the controllers,
-          which check extras
-          parent_calc_folder: RemoteData, optional: the folder of a completed gaussian calculation
-
-      Example:
-      ::
-
-          builder = GaussianCalculation.get_builder()
-          builder.structure_str = orm.Str("H 0.0 0.0 0.0 -1.0 0.0 0.0") # needs newline but docs doesn't like
-          builder.parameters = orm.Dict(dict={
-              'link0_parameters': {
-                  '%chk':'aiida.chk',
-                  "%mem": "3200MB", # Currently set to use 8000 MB in .sh files
-                  "%nprocshared": 4,
-              },
-              'functional':'wb97xd',
-              'basis_set':'aug-cc-pvtz',
-              'charge': 0,
-              'multiplicity': 1,
-              'route_parameters': {'opt': None, 'Output':'WFX'},
-              "input_parameters": {"output.wfx": None},
-          })
-          builder.code = orm.load_code("g16@localhost")
-          builder.metadata.options.resources = {"num_machines": 1, "tot_num_mpiprocs": 4}
-          builder.metadata.options.max_memory_kb = int(6400 * 1.25) * 1024
-          builder.metadata.options.max_wallclock_seconds = 604800
-          submit(builder)
-
-
-
-   .. py:attribute:: INPUT_FILE
-      :value: 'aiida.inp'
-
-
-
-   .. py:attribute:: OUTPUT_FILE
-      :value: 'aiida.out'
-
-
-
-   .. py:attribute:: PARENT_FOLDER_NAME
-      :value: 'parent_calc'
-
-
-
-   .. py:attribute:: DEFAULT_PARSER
-      :value: 'aimall.gaussianwfx'
-
-
-
-   .. py:method:: define(spec)
-      :classmethod:
-
-      Define the process specification, including its inputs, outputs and known exit codes.
-
-      Ports are added to the `metadata` input namespace (inherited from the base Process),
-      and a `code` input Port, a `remote_folder` output Port and retrieved folder output Port
-      are added.
-
-      :param spec: the calculation job process spec to define.
-
-
-   .. py:method:: prepare_for_submission(folder)
-
-      This is the routine to be called when you want to create
-      the input files and related stuff with a plugin.
-
-      :param folder: a aiida.common.folders.Folder subclass where
-                         the plugin should put all its files.
-
-
-   .. py:method:: _render_input_string_from_params(parameters, structure_string)
-      :classmethod:
-
-      Generate the Gaussian input file using pymatgen.

docs/source/reference/api/auto/aiida_aimall/controllers/index.rst

@@ -434,7 +434,7 @@ Attributes
 
 
    .. py:attribute:: CALCULATION_ENTRY_POINT
-      :value: 'aimall.gaussianwfx'
+      :value: 'gaussian'
 
 
 

docs/source/reference/api/auto/aiida_aimall/parsers/index.rst

@@ -20,7 +20,6 @@ Classes
 .. autoapisummary::
 
    aiida_aimall.parsers.AimqbBaseParser
-   aiida_aimall.parsers.GaussianWFXParser
    aiida_aimall.parsers.AimqbGroupParser
 
 
@@ -90,40 +89,6 @@ Attributes
 
 
 
-.. py:class:: GaussianWFXParser(node: aiida.orm.CalcJobNode)
-
-
-   Bases: :py:obj:`aiida.parsers.parser.Parser`
-
-   Basic AiiDA parser for the output of Gaussian
-
-   Parses default cclib output as 'output_parameters' node and separates final SCF
-   energy as 'energy_ev' and output structure as 'output_structure' (if applicable)
-
-   Adapted from aiida-gaussian https://github.com/nanotech-empa/aiida-gaussian, Copyright (c) 2020 Kristjan Eimre.
-
-
-   .. py:method:: parse(**kwargs)
-
-      Receives in input a dictionary of retrieved nodes. Does all the logic here.
-
-
-   .. py:method:: _parse_log(log_file_string, inputs)
-
-
-   .. py:method:: _parse_electron_numbers(log_file_string)
-
-
-   .. py:method:: _parse_log_cclib(log_file_string)
-
-
-   .. py:method:: _set_output_structure(inputs, property_dict)
-
-
-   .. py:method:: _final_checks_on_log(log_file_string, property_dict, inputs)
-
-
-
 .. py:class:: AimqbGroupParser(node)