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Removing the unnecessary inputs due to the split between the base and raw parsers and calculations #82

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Jun 7, 2023
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Removing the unnecessary inputs due to the split between the base and raw parsers and calculations #82

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74 changes: 26 additions & 48 deletions aiida_lammps/calculations/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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."""
Expand Down Expand Up @@ -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
Expand Down
6 changes: 2 additions & 4 deletions aiida_lammps/parsers/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand All @@ -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
Expand Down
6 changes: 3 additions & 3 deletions tests/input_files/parsers/log_alt.lammps → tests/parsers/fixtures/raw/alt/lammps.log
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
14 changes: 11 additions & 3 deletions tests/parsers/test_raw.py
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Original file line number Diff line number Diff line change
@@ -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."""
Expand All @@ -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()})
15 changes: 15 additions & 0 deletions tests/parsers/test_raw/test_alt_timing_info.yml
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Original file line number Diff line number Diff line change
@@ -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
47 changes: 10 additions & 37 deletions tests/test_calculations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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}}},
}
Expand Down
70 changes: 0 additions & 70 deletions tests/test_parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down