GaussianCalculation: Do no limit kwargs for GaussianInput (#34)

* Tests: Automate calculation test reference generation and checking

The reference file for the single `GaussianCalculation` test was
generated manually and read manually to compare to the one created by
running the calcjob plugin. This is replaced by using the fixture
`file_regression` which not only automates this, if the reference file
needs to change due to a change in the code, it can be automatically
generated by running the tests with the `--force-regen` flag.

* `GaussianCalculation`: Do no limit kwargs for `GaussianInput`

The `GaussianCalculation` is rendering the input file from the
`parameters` input dictionary through the `GaussianInput` utility from
`pymatgen`. However, it was hard-coding which keywords could be
specified through the parameters. For example, the `gen_basis` keyword
of `GaussianInput` was ignored. Here we simply expand the entire
parameters dictionary as it is provided through the inputs, after
setting some relevant defaults.

.pre-commit-config.yaml

@@ -7,8 +7,13 @@ repos:
       rev: v4.4.0
       hooks:
           - id: end-of-file-fixer
-            exclude: ^.*data/
+            exclude: &exclude_files >
+                (?x)^(
+                    .*data/|
+                    aiida_gaussian/tests/.*.in$
+                )$
           - id: trailing-whitespace
+            exclude: *exclude_files
           - id: check-yaml
           - id: check-added-large-files
     - repo: https://github.com/pycqa/isort

aiida_gaussian/calculations/gaussian.py

@@ -1,12 +1,11 @@
 """Gaussian input plugin."""
-
-import pymatgen.io.gaussian as mgaus
 from aiida.common import CalcInfo, CodeInfo
 
 # from aiida.cmdline.utils import echo
 from aiida.engine import CalcJob
 from aiida.orm import Dict, Float, RemoteData
 from aiida.plugins import DataFactory
+from pymatgen.io.gaussian import GaussianInput
 
 StructureData = DataFactory("core.structure")
 
@@ -213,32 +212,10 @@ def prepare_for_submission(self, folder):
         return calcinfo
 
     @classmethod
-    def _render_input_string_from_params(cls, param_dict, pmg_structure):
-        """
-        Generate the Gaussian input file using pymatgen
-
-        In the following, the param_dict.get() method is used, which returns
-        `None` if the corresponding key is not specified, resulting in the
-        default value defined by the pymatgen library. For example, charge
-        and spin_multiplicity are then defined based on the pymatgen molecule
-        definition.
-        """
-
-        inp = mgaus.GaussianInput(
-            pmg_structure,
-            title="input generated by the aiida-gaussian plugin",
-            charge=param_dict.get("charge"),
-            spin_multiplicity=param_dict.get(
-                "multiplicity", param_dict.get("spin_multiplicity")
-            ),
-            functional=param_dict.get("functional"),
-            basis_set=param_dict.get("basis_set"),
-            route_parameters=param_dict.get("route_parameters"),
-            input_parameters=param_dict.get("input_parameters"),
-            link0_parameters=param_dict.get("link0_parameters"),
-            dieze_tag=param_dict.get(
-                "dieze_tag", "#N"
-            ),  # normal print level by default
-        )
-
-        return inp.to_string(cart_coords=True)
+    def _render_input_string_from_params(cls, parameters, pmg_structure):
+        """Generate the Gaussian input file using pymatgen."""
+        parameters.setdefault("dieze_tag", "#N")
+        parameters.setdefault("spin_multiplicity", parameters.pop("multiplicity", None))
+        parameters["title"] = "input generated by the aiida-gaussian plugin"
+        gaussian_input = GaussianInput(pmg_structure, **parameters)
+        return gaussian_input.to_string(cart_coords=True)

aiida_gaussian/tests/test_gaussian.py → aiida_gaussian/tests/calculations/test_gaussian.py

@@ -1,22 +1,17 @@
-""" Tests for gaussian plugin
-
-"""
-
+"""Tests for gaussian plugin."""
 import os
 
 from aiida.orm import Dict, StructureData
-from aiida.plugins import CalculationFactory
 from pymatgen.core import Molecule
 
 from aiida_gaussian import tests
+from aiida_gaussian.calculations.gaussian import GaussianCalculation
 
 
-def test_gaussian(fixture_code):
-
+def test_default(fixture_code, generate_calc_job, file_regression):
+    """Test a default calculation for :class:`aiida_gaussian.calculations.gaussian.GaussianCalculation`."""
     geometry_file = os.path.join(tests.TEST_DIR, "data", "ch4.xyz")
-    expected_inp_file = os.path.join(tests.TEST_DIR, "data", "gaussian_test.inp")
 
-    # structure
     structure = StructureData(pymatgen_molecule=Molecule.from_file(geometry_file))
 
     num_cores = 1
@@ -58,26 +53,6 @@ def test_gaussian(fixture_code):
         },
     }
 
-    # Prepare the fake calculation for submission in a "sandbox folder"
-
-    from aiida.common.folders import SandboxFolder
-    from aiida.engine.utils import instantiate_process
-    from aiida.manage.manager import get_manager
-
-    manager = get_manager()
-    runner = manager.get_runner()
-
-    process_class = CalculationFactory("gaussian")
-    process = instantiate_process(runner, process_class, **inputs)
-
-    sandbox_folder = SandboxFolder()
-
-    process.prepare_for_submission(sandbox_folder)
-
-    with sandbox_folder.open("aiida.inp") as handle:
-        input_written = handle.read()
-
-    with open(expected_inp_file) as f:
-        expected_inp = f.read()
-
-    assert input_written == expected_inp
+    tmp_path, _ = generate_calc_job(GaussianCalculation, inputs)
+    content_input_file = (tmp_path / GaussianCalculation.INPUT_FILE).read_text()
+    file_regression.check(content_input_file, encoding="utf-8", extension=".in")