Adding check for the raw calculation to see if lammps has exited with…

… an error (#90)

* Adding check for the raw calculation to see if lammps has exited with an error. Addresses #87

* Adding a test for the parsing of files when lammps exits with an error.

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: Jonathan Chico <jonathan.chico@sandvik.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

aiida_lammps/calculations/base.py

@@ -198,7 +198,7 @@ def define(cls, spec):
         spec.exit_code(
             309,
             "ERROR_PARSER_DETECTED_LAMMPS_RUN_ERROR",
-            message="The parser detected the lampps error :{error}",
+            message="The parser detected the lammps error :{error}",
         )
         spec.exit_code(
             400,

aiida_lammps/calculations/raw.py

@@ -49,6 +49,11 @@ def define(cls, spec):
             required=True,
             help="The data extracted from the lammps out file",
         )
+        spec.exit_code(
+            309,
+            "ERROR_PARSER_DETECTED_LAMMPS_RUN_ERROR",
+            message="The parser detected the lammps error :{error}",
+        )
         spec.exit_code(
             351,
             "ERROR_OUTFILE_MISSING",

aiida_lammps/parsers/base.py

@@ -58,7 +58,6 @@ def parse(self, **kwargs):
             return self.exit_codes.ERROR_NO_RETRIEVED_FOLDER
 
         list_of_files = out_folder.base.repository.list_object_names()
-
         # Check the output file
         outputfile_filename = self.node.get_option("output_filename")
         if outputfile_filename not in list_of_files:
@@ -70,9 +69,11 @@ def parse(self, **kwargs):
         )
 
         if parsed_data["global"]["errors"]:
+            # Output the data for checking what was parsed
+            self.out("results", orm.Dict({"compute_variables": parsed_data["global"]}))
             for entry in parsed_data["global"]["errors"]:
                 self.logger.error(f"LAMMPS emitted the error {entry}")
-                return self.exit_codes.ERROR_PARSER_DECTECTED_LAMMPS_RUN_ERROR.format(
+                return self.exit_codes.ERROR_PARSER_DETECTED_LAMMPS_RUN_ERROR.format(
                     error=entry
                 )
 
@@ -223,11 +224,9 @@ def parse_restartfile(
             and not restart_found
             and temp_folder
         ):
-
             restartfiles = glob.glob(f"{temp_folder}/{input_restart_filename}*")
 
             if restartfiles:
-
                 _files = []
                 for entry in restartfiles:
                     try:

aiida_lammps/parsers/raw.py

@@ -26,6 +26,15 @@ def parse(self, **kwargs):
         if parsed_data is None:
             return self.exit_codes.ERROR_PARSING_OUTFILE
 
+        if parsed_data["global"]["errors"]:
+            # Output the data for checking what was parsed
+            self.out("results", orm.Dict({"compute_variables": parsed_data["global"]}))
+            for entry in parsed_data["global"]["errors"]:
+                self.logger.error(f"LAMMPS emitted the error {entry}")
+                return self.exit_codes.ERROR_PARSER_DETECTED_LAMMPS_RUN_ERROR.format(
+                    error=entry
+                )
+
         global_data = parsed_data["global"]
         results = {"compute_variables": global_data}
 

conftest.py

@@ -9,7 +9,7 @@
 import pathlib
 import shutil
 import tempfile
-from typing import Any
+from typing import Any, Optional
 
 from aiida import orm
 from aiida.common import AttributeDict, CalcInfo, LinkType, exceptions
@@ -86,7 +86,6 @@ def fixture_code(fixture_localhost):
     """Return an ``InstalledCode`` instance configured to run calculations of given entry point on localhost."""
 
     def _fixture_code(entry_point_name):
-
         label = f"test.{entry_point_name}"
 
         try:
@@ -637,12 +636,11 @@ def _generate_calc_job_node(
         if test_name is not None:
             basepath = os.path.dirname(os.path.abspath(__file__))
             filepath_folder = os.path.join(TEST_DIR, test_name)
-
         entry_point = format_entry_point_string("aiida.calculations", entry_point_name)
 
         node = orm.CalcJobNode(computer=computer, process_type=entry_point)
         node.base.attributes.set("input_filename", "input.in")
-        node.base.attributes.set("output_filename", "lammps_output")
+        node.base.attributes.set("output_filename", "lammps.out")
         node.set_option("resources", {"num_machines": 1, "num_mpiprocs_per_machine": 1})
         node.set_option("max_wallclock_seconds", 1800)
         node.set_metadata_inputs(
@@ -683,7 +681,6 @@ def _generate_calc_job_node(
         if filepath_folder:
             retrieved = orm.FolderData()
             retrieved.base.repository.put_object_from_tree(filepath_folder)
-
             # Remove files that are supposed to be only present in the retrieved temporary folder
             if retrieve_temporary:
                 for filename in filenames:
@@ -793,7 +790,6 @@ def get_structure_data():
     def _get_structure_data(pkey):
         """return test structure data"""
         if pkey == "Fe":
-
             cell = [
                 [2.848116, 0.000000, 0.000000],
                 [0.000000, 2.848116, 0.000000],
@@ -810,7 +806,6 @@ def _get_structure_data(pkey):
             names = ["Fe1", "Fe2"]
 
         elif pkey == "Ar":
-
             cell = [
                 [3.987594, 0.000000, 0.000000],
                 [-1.993797, 3.453358, 0.000000],
@@ -826,7 +821,6 @@ def _get_structure_data(pkey):
             fractional = True
 
         elif pkey == "GaN":
-
             cell = [
                 [3.1900000572, 0, 0],
                 [-1.5950000286, 2.762621076, 0],
@@ -844,7 +838,6 @@ def _get_structure_data(pkey):
             symbols = names = ["Ga", "Ga", "N", "N"]
 
         elif pkey == "pyrite":
-
             cell = [
                 [5.38, 0.000000, 0.000000],
                 [0.000000, 5.38, 0.000000],
@@ -1038,7 +1031,7 @@ def generate_singlefile_data():
     def _generate_singlefile_data(
         computer: orm.Computer,
         label: str = "restartfile",
-        entry_point_name: str = None,
+        entry_point_name: str | None = None,
     ):
         entry_point = format_entry_point_string("aiida.calculations", entry_point_name)
 
@@ -1067,7 +1060,7 @@ def generate_lammps_trajectory():
     def _generate_lammps_trajectory(
         computer: orm.Computer,
         label: str = "trajectory",
-        entry_point_name: str = None,
+        entry_point_name: str | None = None,
     ):
         entry_point = format_entry_point_string("aiida.calculations", entry_point_name)
 
@@ -1098,8 +1091,8 @@ def generate_lammps_results():
     def _generate_lammps_results(
         computer: orm.Computer,
         label: str = "results",
-        entry_point_name: str = None,
-        data: dict = None,
+        entry_point_name: str | None = None,
+        data: dict | None = None,
     ):
         entry_point = format_entry_point_string("aiida.calculations", entry_point_name)
 

tests/parsers/fixtures/base/error/lammps.out

@@ -0,0 +1,3 @@
+LAMMPS (23 Jun 2022 - Update 1)
+ERROR: Cannot open file data.rhodo: No such file or directory (src/read_data.cpp:331)
+Last command: read_data       data.rhodo

tests/parsers/fixtures/raw/error/lammps.out

@@ -0,0 +1,3 @@
+LAMMPS (23 Jun 2022 - Update 1)
+ERROR: Cannot open file data.rhodo: No such file or directory (src/read_data.cpp:331)
+Last command: read_data       data.rhodo

tests/parsers/test_raw.py

@@ -31,3 +31,17 @@ def test_alt_timing_info(generate_calc_job_node, data_regression, fixture_localh
     assert calcfunction.is_finished, calcfunction.exception
     assert calcfunction.is_finished_ok, calcfunction.exit_message
     data_regression.check({"results": results["results"].get_dict()})
+
+
+def test_raw_parser_error(generate_calc_job_node, data_regression, fixture_localhost):
+    """Test the parser when an error is found in the output file."""
+    node = generate_calc_job_node(
+        computer=fixture_localhost,
+        entry_point_name="lammps.raw",
+        test_name="parsers/fixtures/raw/error",
+    )
+    parser = ParserFactory("lammps.raw")
+    results, calcfunction = parser.parse_from_node(node, store_provenance=False)
+    assert calcfunction.is_finished, calcfunction.exception
+    assert calcfunction.exit_status == 309, calcfunction.exit_message
+    data_regression.check({"results": results["results"].get_dict()})

tests/parsers/test_raw/test_raw_parser_error.yml

@@ -0,0 +1,6 @@
+results:
+  compute_variables:
+    errors:
+    - command: 'Last command: read_data       data.rhodo'
+      message: 'ERROR: Cannot open file data.rhodo: No such file or directory (src/read_data.cpp:331)'
+    warnings: []

tests/test_calculations.py

@@ -232,13 +232,13 @@ def test_lammps_restart_generation(
     else:
         # Check that if the file was not asked to be stored that it is not stored
         assert (
-            not "restartfile" in results
+            "restartfile" not in results
         ), "The restartfile is stored even when it was not requested"
         if restart_parameters.restart.get("print_final", False):
             _msg = "The restartfile is in the retrieved folder even when it was not requested"
             assert (
-                not node.get_option("restart_filename")
-                in results["retrieved"].base.repository.list_object_names()
+                node.get_option("restart_filename")
+                not in results["retrieved"].base.repository.list_object_names()
             ), _msg
 
     # Check that the final restartfile is printed

tests/test_parsers.py

@@ -3,6 +3,8 @@
 """
 import os
 
+from aiida.plugins import ParserFactory
+
 from aiida_lammps.parsers.parse_raw import parse_final_data, parse_outputfile
 from .utils import TEST_DIR
 
@@ -39,3 +41,17 @@ def test_parse_final_variables():
 
     assert "final_step" in parsed_data, "no step information present"
     assert "final_etotal" in parsed_data, "no total energy information present"
+
+
+def test_base_parser_error(generate_calc_job_node, data_regression, fixture_localhost):
+    """Test the parser when an error is found in the output file."""
+    node = generate_calc_job_node(
+        computer=fixture_localhost,
+        entry_point_name="lammps.base",
+        test_name="parsers/fixtures/base/error",
+    )
+    parser = ParserFactory("lammps.base")
+    results, calcfunction = parser.parse_from_node(node, store_provenance=False)
+    assert calcfunction.is_finished, calcfunction.exception
+    assert calcfunction.exit_status == 309, calcfunction.exit_message
+    data_regression.check({"results": results["results"].get_dict()})

tests/test_parsers/test_base_parser_error.yml

@@ -0,0 +1,6 @@
+results:
+  compute_variables:
+    errors:
+    - command: 'Last command: read_data       data.rhodo'
+      message: 'ERROR: Cannot open file data.rhodo: No such file or directory (src/read_data.cpp:331)'
+    warnings: []