Removing the unnecessary inputs due to the split between the base and…

… raw parsers and calculations.
aiidaplugins · Jun 7, 2023 · 5a69516 · 5a69516
1 parent a796cae
commit 5a69516
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Showing 7 changed files with 67 additions and 165 deletions.
diff --git a/aiida_lammps/calculations/base.py b/aiida_lammps/calculations/base.py
@@ -47,12 +47,6 @@ class LammpsBaseCalculation(CalcJob):
     @classmethod
     def define(cls, spec):
         super().define(spec)
-        spec.input(
-            "script",
-            valid_type=orm.SinglefileData,
-            required=False,
-            help="Complete input script to use. If specified, `structure`, `potential` and `parameters` are ignored.",
-        )
         spec.input(
             "structure",
             valid_type=orm.StructureData,
@@ -126,7 +120,6 @@ def define(cls, spec):
             default=cls._DEFAULT_RESTART_FILENAME,
         )
         spec.inputs["metadata"]["options"]["parser_name"].default = cls._DEFAULT_PARSER
-        spec.inputs.validator = cls.validate_inputs
 
         spec.output(
             "results",
@@ -213,17 +206,6 @@ def define(cls, spec):
             message="error parsing the final variable file has failed.",
         )
 
-    @classmethod
-    def validate_inputs(cls, value, ctx):
-        """Validate the top-level inputs namespace."""
-        if "script" not in value and any(
-            key not in value for key in ("structure", "potential", "parameters")
-        ):
-            return (
-                "Unless `script` is specified the inputs `structure`, `potential` and "
-                "`parameters` have to be specified."
-            )
-
     @classmethod
     def validate_settings(cls, value, ctx):
         """Validate the ``settings`` input."""
@@ -299,38 +281,34 @@ def prepare_for_submission(self, folder):
         retrieve_list += restart_data.get("retrieve_list", [])
         retrieve_temporary_list += restart_data.get("retrieve_temporary_list", [])
 
-        if "script" in self.inputs:
-            input_filecontent = self.inputs.script.get_content()
-        else:
+        # Generate the content of the structure file based on the input
+        # structure
+        structure_filecontent, _ = generate_lammps_structure(
+            self.inputs.structure,
+            self.inputs.potential.atom_style,
+        )
 
-            # Generate the content of the structure file based on the input
-            # structure
-            structure_filecontent, _ = generate_lammps_structure(
-                self.inputs.structure,
-                self.inputs.potential.atom_style,
-            )
+        # Get the name of the structure file and write it to the remote folder
+        _structure_filename = self.inputs.metadata.options.structure_filename
 
-            # Get the name of the structure file and write it to the remote folder
-            _structure_filename = self.inputs.metadata.options.structure_filename
-
-            with folder.open(_structure_filename, "w") as handle:
-                handle.write(structure_filecontent)
-
-            # Write the potential to the remote folder
-            with folder.open(self._DEFAULT_POTENTIAL_FILENAME, "w") as handle:
-                handle.write(self.inputs.potential.get_content())
-
-            # Write the input file content. This function will also check the
-            # sanity of the passed parameters when comparing it to a schema
-            input_filecontent = generate_input_file(
-                potential=self.inputs.potential,
-                structure=self.inputs.structure,
-                parameters=_parameters,
-                restart_filename=_restart_filename,
-                trajectory_filename=_trajectory_filename,
-                variables_filename=_variables_filename,
-                read_restart_filename=_read_restart_filename,
-            )
+        with folder.open(_structure_filename, "w") as handle:
+            handle.write(structure_filecontent)
+
+        # Write the potential to the remote folder
+        with folder.open(self._DEFAULT_POTENTIAL_FILENAME, "w") as handle:
+            handle.write(self.inputs.potential.get_content())
+
+        # Write the input file content. This function will also check the
+        # sanity of the passed parameters when comparing it to a schema
+        input_filecontent = generate_input_file(
+            potential=self.inputs.potential,
+            structure=self.inputs.structure,
+            parameters=_parameters,
+            restart_filename=_restart_filename,
+            trajectory_filename=_trajectory_filename,
+            variables_filename=_variables_filename,
+            read_restart_filename=_read_restart_filename,
+        )
 
         # Get the name of the input file, and write it to the remote folder
         _input_filename = self.inputs.metadata.options.input_filename

diff --git a/aiida_lammps/parsers/base.py b/aiida_lammps/parsers/base.py
@@ -92,8 +92,7 @@ def parse(self, **kwargs):
         final_variables = None
         variables_filename = self.node.get_option("variables_filename")
         if variables_filename not in list_of_files:
-            if "script" not in self.node.inputs:
-                return self.exit_codes.ERROR_FINAL_VARIABLE_FILE_MISSING
+            return self.exit_codes.ERROR_FINAL_VARIABLE_FILE_MISSING
         else:
             final_variables = parse_final_data(
                 file_contents=self.node.outputs.retrieved.base.repository.get_object_content(
@@ -120,8 +119,7 @@ def parse(self, **kwargs):
         # check trajectory file
         trajectory_filename = self.node.get_option("trajectory_filename")
         if trajectory_filename not in list_of_files:
-            if "script" not in self.node.inputs:
-                return self.exit_codes.ERROR_TRAJECTORY_FILE_MISSING
+            return self.exit_codes.ERROR_TRAJECTORY_FILE_MISSING
         else:
             with self.node.outputs.retrieved.base.repository.open(
                 trajectory_filename

diff --git a/tests/input_files/parsers/log_alt.lammps → tests/parsers/fixtures/raw/alt/lammps.log b/tests/input_files/parsers/log_alt.lammps → tests/parsers/fixtures/raw/alt/lammps.log
@@ -27,9 +27,9 @@ Setting up Verlet run ...
   Current step  : 0
   Time step     : 0.005
 Per MPI rank memory allocation (min/avg/max) = 2.039 | 2.065 | 2.082 Mbytes
-   Step          Temp          E_pair         E_mol          TotEng         Press     
-         0   1.44          -6.7733681      0             -4.6133724     -5.0196717    
-      1000   0.70380068    -5.6761498      0             -4.6204508      0.70370101   
+   Step          Temp          E_pair         E_mol          TotEng         Press
+         0   1.44          -6.7733681      0             -4.6133724     -5.0196717
+      1000   0.70380068    -5.6761498      0             -4.6204508      0.70370101
 Loop time of 3.07792 on 120 procs for 1000 steps with 500000 atoms
 
 Performance: 140354.357 tau/day, 324.894 timesteps/s, 162.447 Matom-step/s

diff --git a/tests/parsers/test_raw.py b/tests/parsers/test_raw.py
@@ -1,10 +1,7 @@
 """Tests for the :mod:`aiida_lammps.parsers.raw` module."""
 # pylint: disable=redefined-outer-name
-from aiida.orm import SinglefileData
 from aiida.plugins import ParserFactory
 
-from aiida_lammps.calculations.raw import LammpsRawCalculation
-
 
 def test_default(generate_calc_job_node, data_regression):
     """Test parsing a default output case."""
@@ -15,3 +12,14 @@ def test_default(generate_calc_job_node, data_regression):
     assert calcfunction.is_finished, calcfunction.exception
     assert calcfunction.is_finished_ok, calcfunction.exit_message
     data_regression.check({"results": results["results"].get_dict()})
+
+
+def test_alt_timing_info(generate_calc_job_node, data_regression):
+    """Test parsing an alt output case."""
+    node = generate_calc_job_node("lammps.raw", "alt")
+    parser = ParserFactory("lammps.raw")
+    results, calcfunction = parser.parse_from_node(node, store_provenance=False)
+
+    assert calcfunction.is_finished, calcfunction.exception
+    assert calcfunction.is_finished_ok, calcfunction.exit_message
+    data_regression.check({"results": results["results"].get_dict()})
diff --git a/tests/parsers/test_raw/test_alt_timing_info.yml b/tests/parsers/test_raw/test_alt_timing_info.yml
@@ -0,0 +1,15 @@
+results:
+  compute_variables:
+    bin: kk/device
+    bins:
+    - 60
+    - 60
+    - 60
+    binsize: 1.4
+    ghost_atom_cutoff: 2.8
+    master_list_distance_cutoff: 2.8
+    max_neighbors_atom: 2000
+    steps_per_second: 324.894
+    total_wall_time: 0:00:03
+    total_wall_time_seconds: 3
+    units_style: lattice
diff --git a/tests/test_calculations.py b/tests/test_calculations.py
@@ -137,40 +137,6 @@ def test_lammps_base(
                 assert sub_value == _step_data[sub_key], _msg
 
 
-def test_lammps_base_script(generate_calc_job, aiida_local_code_factory):
-    """Test the ``LammpsBaseCalculation`` with the ``script`` input."""
-    from aiida_lammps.calculations.base import LammpsBaseCalculation
-
-    inputs = {
-        "code": aiida_local_code_factory("lammps.base", "bash"),
-        "metadata": {"options": {"resources": {"num_machines": 1}}},
-    }
-
-    with pytest.raises(
-        ValueError,
-        match=r"Unless `script` is specified the inputs .* have to be specified.",
-    ):
-        generate_calc_job("lammps.base", inputs)
-
-    content = textwrap.dedent(
-        """
-        "velocity      all create 1.44 87287 loop geom
-        "pair_style    lj/cut 2.5
-        "pair_coeff    1 1 1.0 1.0 2.5
-        "neighbor      0.3 bin
-        "neigh_modify  delay 0 every 20 check no
-        "fix           1 all nve
-        "run           10000
-        """
-    )
-    stream = io.StringIO(content)
-    script = orm.SinglefileData(stream)
-
-    inputs["script"] = script
-    tmp_path, calc_info = generate_calc_job("lammps.base", inputs)
-    assert (tmp_path / LammpsBaseCalculation._INPUT_FILENAME).read_text() == content
-
-
 @pytest.mark.lammps_call
 @pytest.mark.parametrize(
     "parameters,restart_parameters",
@@ -342,13 +308,20 @@ def test_lammps_base_settings_invalid(generate_calc_job, aiida_local_code_factor
         generate_calc_job("lammps.base", inputs)
 
 
-def test_lammps_base_settings(generate_calc_job, aiida_local_code_factory):
+def test_lammps_base_settings(
+    generate_calc_job,
+    aiida_local_code_factory,
+    minimize_parameters,
+    get_potential_fe_eam,
+    generate_structure,
+):
     """Test the ``LammpsBaseCalculation`` with the ``settings`` input."""
-    from aiida_lammps.calculations.base import LammpsBaseCalculation
 
     inputs = {
         "code": aiida_local_code_factory("lammps.base", "bash"),
-        "script": orm.SinglefileData(io.StringIO("")),
+        "parameters": orm.Dict(minimize_parameters),
+        "potential": get_potential_fe_eam,
+        "structure": generate_structure,
         "settings": orm.Dict({"additional_cmdline_params": ["--option", "value"]}),
         "metadata": {"options": {"resources": {"num_machines": 1}}},
     }

diff --git a/tests/test_parsers.py b/tests/test_parsers.py
@@ -47,76 +47,6 @@ def get_traj_force():
     )
 
 
-def test_lammps_base(db_test_app, data_regression):
-    """Check if the log file is produced during calculation."""
-    filename = os.path.join(
-        TEST_DIR,
-        "input_files",
-        "parsers",
-        "log.lammps",
-    )
-    retrieved = FolderData()
-    retrieved.base.repository.put_object_from_file(filename, "log.lammps")
-    retrieved.base.repository.put_object_from_filelike(
-        io.StringIO(""), "_scheduler-stdout.txt"
-    )
-    retrieved.base.repository.put_object_from_filelike(
-        io.StringIO(""), "_scheduler-stderr.txt"
-    )
-    inputs = {"script": SinglefileData(io.StringIO(""))}
-    calc_node = db_test_app.generate_calcjob_node(
-        "lammps.base", retrieved, inputs=inputs
-    )
-    parser = ParserFactory("lammps.base")
-    with db_test_app.sandbox_folder() as temp_path:
-        (
-            results,
-            calcfunction,
-        ) = parser.parse_from_node(  # pylint: disable=unused-variable
-            calc_node,
-            retrieved_temporary_folder=temp_path.abspath,
-        )
-
-    assert calcfunction.is_finished_ok
-    assert "results" in calcfunction.outputs
-    data_regression.check({"results": calcfunction.outputs.results.get_dict()})
-
-
-def test_lammps_base_timing_info(db_test_app, data_regression):
-    """Test that the timing performance is properly parsed."""
-    filename = os.path.join(
-        TEST_DIR,
-        "input_files",
-        "parsers",
-        "log_alt.lammps",
-    )
-    retrieved = FolderData()
-    retrieved.base.repository.put_object_from_file(filename, "log.lammps")
-    retrieved.base.repository.put_object_from_filelike(
-        io.StringIO(""), "_scheduler-stdout.txt"
-    )
-    retrieved.base.repository.put_object_from_filelike(
-        io.StringIO(""), "_scheduler-stderr.txt"
-    )
-    inputs = {"script": SinglefileData(io.StringIO(""))}
-    calc_node = db_test_app.generate_calcjob_node(
-        "lammps.base", retrieved, inputs=inputs
-    )
-    parser = ParserFactory("lammps.base")
-    with db_test_app.sandbox_folder() as temp_path:
-        (
-            results,
-            calcfunction,
-        ) = parser.parse_from_node(  # pylint: disable=unused-variable
-            calc_node,
-            retrieved_temporary_folder=temp_path.abspath,
-        )
-
-    assert calcfunction.is_finished_ok
-    assert "results" in calcfunction.outputs
-    data_regression.check({"results": calcfunction.outputs.results.get_dict()})
-
-
 def test_parser_log(data_regression):
     """
     Test the parser for the ``log.lammps`` file.