Add unit test for conceptual dictionary in LAMMPS

.ci_support/environment.yml

@@ -1,11 +1,14 @@
 channels:
   - conda-forge
 dependencies:
-  - numpy =2.3.1
+  - numpy
+  - lammps =2024.02.07=*_openmpi_*
   - setuptools >=68
   - pandas
   - python >=3.11,<3.14
+  - pyiron_atomistics =0.7.18
   - pyiron_base
+  - pyiron-data >=0.0.30
   - pybis=1.37.0
   - python-xxhash=3.5.0
   - boto3=1.35

.github/workflows/push-pull.yml

@@ -17,8 +17,8 @@ jobs:
       do-codecov: true
       # The test matrix supports up to four python versions
       python-version-alt3: 'exclude'
-      python-version-alt2: '3.11'
-      python-version-alt1: '3.13'
+      python-version-alt2: 'exclude'
+      python-version-alt1: '3.11'
       python-version: '3.12'
       # Test lower bounds:
       alternate-tests-env-files: .ci_support/lower-bounds.yml

docs/environment.yml

@@ -7,11 +7,14 @@ dependencies:
 - sphinx-gallery
 - sphinx-rtd-theme
 - versioneer
-- numpy =2.3.1
+- numpy
+- lammps =2024.02.07=*_openmpi_*
 - setuptools >=68
 - pandas
 - python >=3.11,<3.14
+- pyiron_atomistics =0.7.18
 - pyiron_base
+- pyiron-data >=0.0.30
 - pybis=1.37.0
 - python-xxhash=3.5.0
 - boto3=1.35

pyproject.toml

@@ -24,7 +24,7 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "numpy==2.3.1",
+    "numpy==1.26.4",
     "pandas==2.3.2",
     "pyiron_base==0.14.3",
     "pybis==1.37.0",

tests/unit/test_concept_dict.py

@@ -0,0 +1,171 @@
+import os
+import unittest
+
+import numpy as np
+from pyiron_atomistics import Project
+
+from pyiron_rdm.concept_dict import process_lammps_job
+
+
+class TestLammps(unittest.TestCase):
+    def setUp(self):
+        self._project = Project("test_lammps")
+
+    def tearDown(self):
+        self._project.remove_jobs(recursive=True, silently=True)
+        self._project.remove(enable=True)
+
+    def test_calc_minimize_pressure_zero(self):
+        pr = Project("test_project")
+        job = pr.create.job.Lammps("lmp")
+        job.structure = pr.create.structure.bulk("Al", cubic=True)
+        job.calc_minimize(pressure=0.0)
+        job.run()
+        job_dict = process_lammps_job(job)
+        print(job_dict)
+        self.assertEqual(job_dict["workflow_manager"]["label"], "pyiron")
+        self.assertTrue(job_dict["software"][0]["label"].startswith("LAMMPS"))
+        for item in job_dict["job_details"]:
+            if item["label"] == "job_name":
+                self.assertEqual(item["value"], job.job_name)
+            elif item["label"] == "project_name":
+                self.assertEqual(
+                    item["value"], os.path.basename(os.path.dirname(job.project.path))
+                )
+            elif item["label"] == "job_type":
+                self.assertEqual(item["value"], "Lammps")
+            elif item["label"] == "job_status":
+                self.assertEqual(item["value"], "finished")
+            elif item["label"] == "sim_coretime_hours":
+                self.assertTrue(item["value"] < 0.2)
+            elif item["label"] == "number_cores":
+                self.assertEqual(item["value"], job.server.cores)
+            else:
+                self.assertTrue(
+                    item["label"] in ["job_starttime", "job_stoptime", "host"]
+                )
+        self.assertEqual(
+            job_dict["path"],
+            os.path.abspath(os.path.join(job.working_directory, "../..", job.job_name)),
+        )
+        context_dict = {
+            "sample": "http://purls.helmholtz-metadaten.de/cmso/AtomicScaleSample",
+            "path": "http://purls.helmholtz-metadaten.de/cmso/hasPath",
+            "dof": "http://purls.helmholtz-metadaten.de/asmo/hasRelaxationDOF",
+            "inputs": "http://purls.helmholtz-metadaten.de/asmo/hasInputParameter",
+            "label": "http://www.w3.org/2000/01/rdf-schema#label",
+            "unit": "http://purls.helmholtz-metadaten.de/asmo/hasUnit",
+            "value": "http://purls.helmholtz-metadaten.de/asmo/hasValue",
+            "outputs": "http://purls.helmholtz-metadaten.de/cmso/hasCalculatedProperty",
+            "workflow_manager": "http://demo.fiz-karlsruhe.de/matwerk/E457491",
+            "molecular_dynamics": "http://purls.helmholtz-metadaten.de/asmo/MolecularDynamics",
+            "molecular_statics": "http://purls.helmholtz-metadaten.de/asmo/MolecularStatics",
+            "ensemble": "http://purls.helmholtz-metadaten.de/asmo/hasStatisticalEnsemble",
+            "job_details": "http://id-from-pmdco-pending",
+            "periodic_boundary_condition": "http://purls.helmholtz-metadaten.de/asmo/PeriodicBoundaryCondition",
+            "initial_temperature": "http://purls.helmholtz-metadaten.de/asmo/Temperature",
+            "initial_pressure": "http://purls.helmholtz-metadaten.de/asmo/Pressure",
+            "target_temperature": "http://purls.helmholtz-metadaten.de/asmo/Temperature",
+            "target_pressure": "http://purls.helmholtz-metadaten.de/asmo/Pressure",
+            "ionic_energy_tolerance": "http://purls.helmholtz-metadaten.de/asmo/InputParameter",
+            "force_tolerace": "http://purls.helmholtz-metadaten.de/asmo/InputParameter",
+            "maximum_iterations": "http://purls.helmholtz-metadaten.de/asmo/InputParameter",
+            "potential": "http://purls.helmholtz-metadaten.de/asmo/EmbeddedAtomModel",
+            "average_temperature": "http://purls.helmholtz-metadaten.de/asmo/Temperature",
+            "average_pressure": "http://purls.helmholtz-metadaten.de/asmo/Pressure",
+            "average_total_energy": "http://purls.helmholtz-metadaten.de/asmo/TotalEnergy",
+            "final_total_energy": "http://purls.helmholtz-metadaten.de/asmo/TotalEnergy",
+            "final_potential_energy": "http://purls.helmholtz-metadaten.de/asmo/PotentialEnergy",
+            "average_total_volume": "http://purls.helmholtz-metadaten.de/asmo/Volume",
+            "final_total_volume": "http://purls.helmholtz-metadaten.de/asmo/Volume",
+            "final_maximum_force": "http://purls.helmholtz-metadaten.de/asmo/Force",
+            "number_ionic_steps": "http://purls.helmholtz-metadaten.de/asmo/NumberOfIonicSteps",
+            "time_step": "http://purls.helmholtz-metadaten.de/asmo/TimeStep",
+            "simulation_time": "http://purls.helmholtz-metadaten.de/asmo/Time",
+            "LAMMPS": "http://demo.fiz-karlsruhe.de/matwerk/E447986",
+        }
+        for k, v in context_dict.items():
+            self.assertEqual(job_dict["@context"][k], v)
+        for item in job_dict["outputs"]:
+            if item["label"] == "average_total_energy":
+                self.assertEqual(item["unit"], "EV")
+                self.assertEqual(
+                    item["value"], np.round(job["output/generic/energy_tot"][-1], 2)
+                )
+            elif item["label"] == "average_total_volume":
+                self.assertEqual(item["unit"], "ANGSTROM3")
+                self.assertEqual(
+                    item["value"], np.round(job["output/generic/volume"][-1], 4)
+                )
+            elif item["label"] == "final_total_volume":
+                self.assertEqual(item["unit"], "ANGSTROM3")
+                self.assertEqual(
+                    item["value"], np.round(job["output/generic/volume"][-1], 4)
+                )
+            elif item["label"] == "final_total_energy":
+                self.assertEqual(item["unit"], "EV")
+                self.assertEqual(
+                    item["value"], np.round(job["output/generic/energy_tot"][-1], 2)
+                )
+            elif item["label"] == "final_potential_energy":
+                self.assertEqual(item["unit"], "EV")
+                self.assertEqual(
+                    item["value"], np.round(job["output/generic/energy_pot"][-1], 2)
+                )
+            elif item["label"] == "number_ionic_steps":
+                self.assertEqual(item["value"], 1)
+            elif item["label"] == "final_maximum_force":
+                self.assertEqual(item["unit"], "EV-PER-ANGSTROM")
+                self.assertEqual(item["value"], 1.4e-15)
+            else:
+                raise ValueError()
+        for item in job_dict["dof"]:
+            self.assertTrue(
+                item
+                in [
+                    "http://purls.helmholtz-metadaten.de/asmo/AtomicPositionRelaxation",
+                    "http://purls.helmholtz-metadaten.de/asmo/CellVolumeRelaxation",
+                ]
+            )
+        self.assertEqual(job_dict["molecular_statics"]["minimization_algorithm"], "cg")
+        self.assertTrue(job_dict["molecular_statics"]["periodicity_in_x"])
+        self.assertTrue(job_dict["molecular_statics"]["periodicity_in_y"])
+        self.assertTrue(job_dict["molecular_statics"]["periodicity_in_z"])
+        for item in job_dict["molecular_statics"]["inputs"]:
+            if item["label"] == "initial_temperature":
+                self.assertEqual(item["unit"], "K")
+                self.assertIsNone(item["value"])
+            elif item["label"] == "target_temperature":
+                self.assertEqual(item["unit"], "K")
+                self.assertIsNone(item["value"])
+            elif item["label"] == "initial_pressure":
+                self.assertEqual(item["unit"], "GigaPA")
+                self.assertIsNone(item["value"])
+            elif item["label"] == "target_pressure":
+                self.assertEqual(item["unit"], "GigaPA")
+                self.assertEqual(item["value"], 0.0)
+            elif item["label"] == "ionic_energy_tolerance":
+                self.assertEqual(item["unit"], "EV")
+                self.assertEqual(item["value"], 0.0)
+            elif item["label"] == "force_tolerance":
+                self.assertEqual(item["unit"], "EV-PER-ANGSTROM")
+                self.assertEqual(item["value"], 0.0001)
+            elif item["label"] == "maximum_iterations":
+                self.assertEqual(item["value"], 100000)
+            elif item["label"] == "timestep":
+                self.assertIsNone(item["value"])
+                self.assertEqual(item["unit"], "PICOSECOND")
+            elif item["label"] == "simulation_time":
+                self.assertIsNone(item["value"])
+                self.assertEqual(item["unit"], "PICOSECOND")
+            else:
+                raise ValueError()
+        self.assertIsNone(job_dict["molecular_statics"]["ensemble"])
+        self.assertEqual(
+            job_dict["molecular_statics"]["potential"]["label"],
+            "1995--Angelo-J-E--Ni-Al-H--LAMMPS--ipr1",
+        )
+        self.assertEqual(
+            job_dict["molecular_statics"]["potential"]["url"],
+            "https://doi.org/10.1088%2F0965-0393%2F3%2F3%2F001",
+        )