aiida-chemshell 0.2.0__tar.gz → 0.2.1__tar.gz

{aiida_chemshell-0.2.0/src/aiida_chemshell.egg-info → aiida_chemshell-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiida-chemshell
-Version: 0.2.0
+Version: 0.2.1
 Summary: AiiDA workflow plugin for the ChemShell chemical modelling software package
 Author-email: "Dr. Benjamin T. Speake" <benjamin.speake@stfc.ac.uk>
 License: BSD 3-Clause License
@@ -62,9 +62,10 @@ Dynamic: license-file
 [![Pipeline Status](https://github.com/stfc/aiida-chemshell/actions/workflows/ci-testing.yml/badge.svg?branch=main)](https://github.com/stfc/aiida-chemshell/actions)
 [![Coverage Status]( https://coveralls.io/repos/github/stfc/aiida-chemshell/badge.svg?branch=main)](https://coveralls.io/github/stfc/aiida-chemshell?branch=main)
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18392782.svg)](https://doi.org/10.5281/zenodo.18392782)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.18392782-blue.svg)](https://doi.org/10.5281/zenodo.18392782)
 
-# aiida-chemshell
+
+# AiiDA ChemShell
 
 An [AiiDA](https://www.aiida.net) plugin for the [ChemShell](https://chemshell.org/) multiscale 
 computational chemistry software package. 
@@ -110,6 +111,13 @@ verdi code create core.code.installed --config chemshell.yml -n
 
 If successful this will have created a code with the label `chemsh` which can then be used to run ChemShell jobs within the AiiDA workflow. 
 
+### ChemShell with MPI
+
+It is important to note that the configuration of an MPI enabled ChemShell code differs slightly depending on whether the code instance uses 
+the `chemsh` or `chemsh.x` executable. If you have a parallel (MPI enabled) build of ChemShell but are using the `chemsh` wrapper executable
+please set `with_mpi: false` as the underlying plugin will handle how to call the mpi runtime. If you are calling the `chemsh.x` executable
+directly then `with_mpi: true` is required to run parallel jobs. 
+
 ## Examples 
 
 ### QM Based Single Point Energy 

{aiida_chemshell-0.2.0 → aiida_chemshell-0.2.1}/README.md

@@ -5,9 +5,10 @@
 [![Pipeline Status](https://github.com/stfc/aiida-chemshell/actions/workflows/ci-testing.yml/badge.svg?branch=main)](https://github.com/stfc/aiida-chemshell/actions)
 [![Coverage Status]( https://coveralls.io/repos/github/stfc/aiida-chemshell/badge.svg?branch=main)](https://coveralls.io/github/stfc/aiida-chemshell?branch=main)
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18392782.svg)](https://doi.org/10.5281/zenodo.18392782)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.18392782-blue.svg)](https://doi.org/10.5281/zenodo.18392782)
 
-# aiida-chemshell
+
+# AiiDA ChemShell
 
 An [AiiDA](https://www.aiida.net) plugin for the [ChemShell](https://chemshell.org/) multiscale 
 computational chemistry software package. 
@@ -53,6 +54,13 @@ verdi code create core.code.installed --config chemshell.yml -n
 
 If successful this will have created a code with the label `chemsh` which can then be used to run ChemShell jobs within the AiiDA workflow. 
 
+### ChemShell with MPI
+
+It is important to note that the configuration of an MPI enabled ChemShell code differs slightly depending on whether the code instance uses 
+the `chemsh` or `chemsh.x` executable. If you have a parallel (MPI enabled) build of ChemShell but are using the `chemsh` wrapper executable
+please set `with_mpi: false` as the underlying plugin will handle how to call the mpi runtime. If you are calling the `chemsh.x` executable
+directly then `with_mpi: true` is required to run parallel jobs. 
+
 ## Examples 
 
 ### QM Based Single Point Energy 

{aiida_chemshell-0.2.0 → aiida_chemshell-0.2.1}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
 [project]
-version = "0.2.0"
+version = "0.2.1"
 name = "aiida-chemshell"
 description = "AiiDA workflow plugin for the ChemShell chemical modelling software package"
 authors = [
@@ -27,15 +27,16 @@ Source = "https://github.com/stfc/aiida-chemshell"
 
 [project.entry-points."aiida.calculations"]
 "chemshell" = "aiida_chemshell.calculations.base:ChemShellCalculation"
-"chemshell.file_conversion.mlip_training" = "aiida_chemshell.calculations.file_conversion:CreateJanusTrainingInputsCalcJob"
+
 
 [project.entry-points."aiida.parsers"]
 "chemshell" = "aiida_chemshell.parsers.base:ChemShellParser"
-"chemshell.file_conversion.mlip_training" = "aiida_chemshell.parsers.file_conversion:CreateJanusTrainingInputsParser"
+
 
 [project.entry-points."aiida.workflows"]
 "chemshell.opt" = "aiida_chemshell.workflows.optimisation:GeometryOptimisationWorkChain"
 "chemshell.atomic_energies" = "aiida_chemshell.workflows.isolated_atoms:IsolatedAtomicEnergiesWorkChain"
+"chemshell.batch" = "aiida_chemshell.workflows.batch_calculation:BatchProcessWorkChain"
 
 [tool.setuptools.packages.find]
 where = ["src"]

{aiida_chemshell-0.2.0 → aiida_chemshell-0.2.1}/src/aiida_chemshell/calculations/base.py

@@ -203,17 +203,17 @@ class ChemShellCalculation(CalcJob):
 
         spec.output(
             "trajectory_path",
-            valid_type=SinglefileData,
+            valid_type=TrajectoryData,
             required=False,
-            help="XYZ trajectory file for the geometry optimisation",
+            help="Trajectory with the path taken for a geometry optimisation.",
         )
         spec.output(
             "trajectory_force",
             valid_type=SinglefileData,
             required=False,
             help=(
-                "XYZ trajectory containing forces at each step of a geometry "
-                "optimisation"
+                "XYZ style trajectory file containing forces at each step of a geometry"
+                " optimisation."
             ),
         )
 
@@ -435,7 +435,7 @@ class ChemShellCalculation(CalcJob):
         return None
 
     @classmethod
-    def get_valid_qm_paramater_keys(cls) -> dict[str:type]:
+    def get_valid_qm_parameter_keys(cls) -> dict:
         """
         Return a tuple of valid parameter keys for the ChemShell calculation.
 
@@ -455,7 +455,7 @@ class ChemShellCalculation(CalcJob):
             "damping": bool,
             "diis": bool,
             "direct": bool,
-            "guess": str,  # TODO: file???
+            # "guess": str,  # TODO: file???
             "maxiter": int,
             "path": str,
             "pseudopotential": str | dict,
@@ -488,7 +488,7 @@ class ChemShellCalculation(CalcJob):
                 "ChemShell theory interface within the AiiDA-ChemShell workflow."
             )
 
-        valid_keys = cls.get_valid_qm_paramater_keys()
+        valid_keys = cls.get_valid_qm_parameter_keys()
 
         # Check for valid parameter keys
         invalid_keys = set(value.keys()).difference(set(valid_keys.keys()))
@@ -527,7 +527,7 @@ class ChemShellCalculation(CalcJob):
         return None
 
     @classmethod
-    def get_valid_mm_paramater_keys(cls, theory: str = "") -> dict[str:type]:
+    def get_valid_mm_parameter_keys(cls, theory: str = "") -> dict[str:type]:
         """
         Return a tuple of valid parameter keys for the ChemShell MM interface.
 
@@ -539,8 +539,8 @@ class ChemShellCalculation(CalcJob):
         if theory == "DL_POLY":
             valid_keys = {
                 "theory": str,
-                "input": str | tuple[str],
-                "output": str,
+                # "input": str | tuple[str],
+                # "output": str,
                 # general keys -> TODO: these are files which are not supported
                 # by as AiiDA nodes if in a Dict object
                 "berendsen": float,
@@ -564,8 +564,8 @@ class ChemShellCalculation(CalcJob):
         elif theory == "GULP":
             valid_keys = {
                 "theory": str,
-                "input": str,
-                "output": str,
+                # "input": str,
+                # "output": str,
                 # general keys -> TODO: these are files which are not supported
                 # by as AiiDA nodes if in a Dict object
                 "molecule": bool,
@@ -574,8 +574,8 @@ class ChemShellCalculation(CalcJob):
         elif theory == "NAMD":
             valid_keys = {
                 "theory": str,
-                "input": str,
-                "output": str,
+                # "input": str,
+                # "output": str,
                 # general keys -> TODO: these are files which are not supported
                 # by as AiiDA nodes if in a Dict object
                 "binary": bool,
@@ -615,7 +615,9 @@ class ChemShellCalculation(CalcJob):
                 "wrap_water": bool,
             }
         else:
-            valid_keys = {"theory": str, "input": str, "output": str}
+            valid_keys = {
+                "theory": str,
+            }
         return valid_keys
 
     @classmethod
@@ -642,7 +644,7 @@ class ChemShellCalculation(CalcJob):
                 "valid ChemShell MM interface within the AiiDA-ChemShell workflow."
             )
 
-        valid_keys = cls.get_valid_mm_paramater_keys(theory)
+        valid_keys = cls.get_valid_mm_parameter_keys(theory)
         invalid_keys = set(value.keys()).difference(set(valid_keys.keys()))
         if invalid_keys:
             # Checks for invalid parameter keys
@@ -974,11 +976,12 @@ class ChemShellCalculation(CalcJob):
         # Setup the calculation information object
         calc_info = CalcInfo()
         calc_info.codes_info = [code_info]
-        calc_info.retrieve_temporary_list = []
+        calc_info.retrieve_temporary_list = [
+            ChemShellCalculation.FILE_RESULTS,
+        ]
         calc_info.provenance_exclude_list = []
         calc_info.retrieve_list = [
             ChemShellCalculation.FILE_STDOUT,
-            ChemShellCalculation.FILE_RESULTS,
         ]
         calc_info.local_copy_list = []
 
@@ -1033,12 +1036,14 @@ class ChemShellCalculation(CalcJob):
                 "frozen",
                 "perpendicular",
             ]:
-                calc_info.retrieve_list.append(ChemShellCalculation.FILE_DLFIND)
+                calc_info.retrieve_temporary_list.append(
+                    ChemShellCalculation.FILE_DLFIND
+                )
             if self.inputs.optimisation_parameters.get("save_path", False):
-                calc_info.retrieve_list.append(
+                calc_info.retrieve_temporary_list.append(
                     "_dl_find/" + ChemShellCalculation.FILE_TRJPTH
                 )
-                calc_info.retrieve_list.append(
+                calc_info.retrieve_temporary_list.append(
                     "_dl_find/" + ChemShellCalculation.FILE_TRJFRC
                 )
             if self.inputs.optimisation_parameters.get("neb", "no") in [

{aiida_chemshell-0.2.0 → aiida_chemshell-0.2.1}/src/aiida_chemshell/parsers/base.py

@@ -17,17 +17,17 @@ class ChemShellParser(Parser):
 
     def parse(self, **kwargs):
         """Parse the output of a ChemShell calculation."""
-        retrieved_tmp_folder = kwargs.get("retrieved_temporary_folder", None)
+        retrieved_tmp_folder = Path(kwargs.get("retrieved_temporary_folder", ""))
 
         if ChemShellCalculation.FILE_STDOUT not in self.retrieved.list_object_names():
             return self.exit_codes.ERROR_STDOUT_NOT_FOUND
-        if ChemShellCalculation.FILE_RESULTS not in self.retrieved.list_object_names():
+        results_path = retrieved_tmp_folder / ChemShellCalculation.FILE_RESULTS
+        if not (results_path).exists():
             return self.exit_codes.ERROR_RESULTS_FILE_NOT_FOUND
 
         # Read the 'json' formatted results file
-        results = json.loads(
-            self.retrieved.get_object_content(ChemShellCalculation.FILE_RESULTS, "rb")
-        )
+        with open(results_path, "rb") as f:
+            results = json.loads(f.read())
 
         # Extract the final energy
         try:
@@ -70,6 +70,7 @@ class ChemShellParser(Parser):
 
         # If the calculation was a geometry optimisation, store the optimised structure
         if "optimisation_parameters" in self.node.inputs:
+            dl_find_path = retrieved_tmp_folder / ChemShellCalculation.FILE_DLFIND
             if self.node.inputs.optimisation_parameters.get("thermal", False):
                 self.parse_vibrational_analysis(
                     self.retrieved.get_object_content(
@@ -81,9 +82,9 @@ class ChemShellParser(Parser):
                 "frozen",
                 "perpendicular",
             ]:
-                self.parse_neb_path(Path(retrieved_tmp_folder) / "nebpath.xyz")
-                self.parse_neb_info(Path(retrieved_tmp_folder) / "nebinfo")
-            elif ChemShellCalculation.FILE_DLFIND in self.retrieved.list_object_names():
+                self.parse_xyz_path(retrieved_tmp_folder / "nebpath.xyz", "neb_path")
+                self.parse_neb_info(retrieved_tmp_folder / "nebinfo")
+            elif dl_find_path.exists():
                 descrip = "Optimised structure from a ChemShell optimisation"
                 input_pk = self.node.inputs.structure.pk
                 descrip += f" of node {input_pk}"
@@ -91,7 +92,7 @@ class ChemShellParser(Parser):
                     input_fname = self.node.inputs.structure.filename
                     descrip += f" ({input_fname})"
                 # Store the optimised structure file
-                with self.retrieved.open(ChemShellCalculation.FILE_DLFIND, "rb") as f:
+                with open(dl_find_path, "rb") as f:
                     self.out(
                         "optimised_structure",
                         SinglefileData(
@@ -110,26 +111,11 @@ class ChemShellParser(Parser):
                 return self.exit_codes.ERROR_MISSING_OPTIMISED_STRUCTURE_FILE
 
             if self.node.inputs.optimisation_parameters.get("save_path", False):
-                if (
-                    ChemShellCalculation.FILE_TRJPTH
-                    in self.retrieved.list_object_names()
-                ):
-                    with self.retrieved.open(
-                        ChemShellCalculation.FILE_TRJPTH, "r"
-                    ) as f:
-                        self.out(
-                            "trajectory_path",
-                            SinglefileData(
-                                file=f,
-                                filename=ChemShellCalculation.FILE_TRJPTH.replace(
-                                    "/", "_"
-                                ),
-                                label="ChemShell optimisation trajectory.",
-                            ),
-                        )
-                    with self.retrieved.open(
-                        ChemShellCalculation.FILE_TRJFRC, "r"
-                    ) as f:
+                trj_path = retrieved_tmp_folder / ChemShellCalculation.FILE_TRJPTH
+                trj_frc_path = retrieved_tmp_folder / ChemShellCalculation.FILE_TRJFRC
+                if trj_path.exists():
+                    self.parse_xyz_path(trj_path, "trajectory_path")
+                    with open(trj_frc_path, "rb") as f:
                         self.out(
                             "trajectory_force",
                             SinglefileData(
@@ -200,7 +186,7 @@ class ChemShellParser(Parser):
         self.out("optimisation_path", results)
         return
 
-    def parse_neb_path(self, file_path: Path) -> None:
+    def parse_xyz_path(self, file_path: Path, output_link: str) -> None:
         """Parse the NEB pathway into an AiiDA TrajectoryData node."""
         with open(file_path) as f:
             lines = f.readlines()
@@ -223,7 +209,9 @@ class ChemShellParser(Parser):
             i += natoms + 2
         path = TrajectoryData()
         path.set_trajectory(symbols=symbols, positions=numpy.asarray(positions))
-        self.out("neb_path", path)
+        path.label = "ChemShell (DL_FIND) optimisation path."
+        path.description = "Path taken for a ChemShell Optimisation or NEB calculation."
+        self.out(output_link, path)
         return
 
     def parse_neb_info(self, file_path: Path) -> None:

{aiida_chemshell-0.2.0 → aiida_chemshell-0.2.1}/src/aiida_chemshell/workflows/batch_calculation.py

@@ -17,9 +17,14 @@ class BatchProcessWorkChain(WorkChain):
         """Define the AiiDA process specification."""
         super().define(spec)
 
-        # Expose Chemshell inputs
+        # Expose Chemshell inputs in the top level namespace
         spec.expose_inputs(ChemShellCalculation, exclude=("structure", "metadata"))
 
+        # Expose the calculation metadata under a dedicated 'calc' namespace.
+        spec.expose_inputs(
+            ChemShellCalculation, namespace="calc", include=("metadata",)
+        )
+
         # Input structure series
         spec.input(
             "trajectory",
@@ -90,6 +95,10 @@ class BatchProcessWorkChain(WorkChain):
         """Extract all individual structures and submit their calculations."""
         futures: dict[str, ProcessNode] = {}
         inputs = {"code": self.inputs.code}
+        # Forward the calculation options (resources, MPI processes, wallclock, ...)
+        # to every job in the batch.
+        if "calc" in self.inputs and "options" in self.inputs.calc.metadata:
+            inputs["metadata"] = {"options": dict(self.inputs.calc.metadata.options)}
         if "qm_parameters" in self.inputs:
             inputs["qm_parameters"] = self.inputs.qm_parameters
         if "mm_parameters" in self.inputs:

{aiida_chemshell-0.2.0 → aiida_chemshell-0.2.1/src/aiida_chemshell.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiida-chemshell
-Version: 0.2.0
+Version: 0.2.1
 Summary: AiiDA workflow plugin for the ChemShell chemical modelling software package
 Author-email: "Dr. Benjamin T. Speake" <benjamin.speake@stfc.ac.uk>
 License: BSD 3-Clause License
@@ -62,9 +62,10 @@ Dynamic: license-file
 [![Pipeline Status](https://github.com/stfc/aiida-chemshell/actions/workflows/ci-testing.yml/badge.svg?branch=main)](https://github.com/stfc/aiida-chemshell/actions)
 [![Coverage Status]( https://coveralls.io/repos/github/stfc/aiida-chemshell/badge.svg?branch=main)](https://coveralls.io/github/stfc/aiida-chemshell?branch=main)
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18392782.svg)](https://doi.org/10.5281/zenodo.18392782)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.18392782-blue.svg)](https://doi.org/10.5281/zenodo.18392782)
 
-# aiida-chemshell
+
+# AiiDA ChemShell
 
 An [AiiDA](https://www.aiida.net) plugin for the [ChemShell](https://chemshell.org/) multiscale 
 computational chemistry software package. 
@@ -110,6 +111,13 @@ verdi code create core.code.installed --config chemshell.yml -n
 
 If successful this will have created a code with the label `chemsh` which can then be used to run ChemShell jobs within the AiiDA workflow. 
 
+### ChemShell with MPI
+
+It is important to note that the configuration of an MPI enabled ChemShell code differs slightly depending on whether the code instance uses 
+the `chemsh` or `chemsh.x` executable. If you have a parallel (MPI enabled) build of ChemShell but are using the `chemsh` wrapper executable
+please set `with_mpi: false` as the underlying plugin will handle how to call the mpi runtime. If you are calling the `chemsh.x` executable
+directly then `with_mpi: true` is required to run parallel jobs. 
+
 ## Examples 
 
 ### QM Based Single Point Energy 

{aiida_chemshell-0.2.0 → aiida_chemshell-0.2.1}/src/aiida_chemshell.egg-info/entry_points.txt

@@ -1,11 +1,10 @@
 [aiida.calculations]
 chemshell = aiida_chemshell.calculations.base:ChemShellCalculation
-chemshell.file_conversion.mlip_training = aiida_chemshell.calculations.file_conversion:CreateJanusTrainingInputsCalcJob
 
 [aiida.parsers]
 chemshell = aiida_chemshell.parsers.base:ChemShellParser
-chemshell.file_conversion.mlip_training = aiida_chemshell.parsers.file_conversion:CreateJanusTrainingInputsParser
 
 [aiida.workflows]
 chemshell.atomic_energies = aiida_chemshell.workflows.isolated_atoms:IsolatedAtomicEnergiesWorkChain
+chemshell.batch = aiida_chemshell.workflows.batch_calculation:BatchProcessWorkChain
 chemshell.opt = aiida_chemshell.workflows.optimisation:GeometryOptimisationWorkChain

{aiida_chemshell-0.2.0 → aiida_chemshell-0.2.1}/tests/test_batch_workcahin.py

@@ -7,6 +7,45 @@ from aiida.orm import Dict
 from aiida_chemshell.workflows.batch_calculation import BatchProcessWorkChain
 
 
+def test_batch_exposes_calculation_metadata_options():
+    """The calculation metadata options must be exposed under the 'calc' namespace.
+
+    This allows users to specify the resources (e.g. number of MPI processes) used
+    by the underlying series of ChemShell calculations, without clashing with the
+    WorkChain's own reserved 'metadata' namespace.
+    """
+    spec = BatchProcessWorkChain.spec()
+    assert "options" not in spec.inputs["metadata"], (
+        "Calculation options must not be merged into the WorkChain metadata."
+    )
+    options = spec.inputs["calc"]["metadata"]["options"]
+    assert "resources" in options, "The calculation metadata options are not exposed."
+
+
+def test_batch_forwards_metadata_options(chemsh_code, water_trajectory_object):
+    """Resources set on the WorkChain are forwarded to every sub-calculation."""
+    resources = {"num_machines": 1, "num_mpiprocs_per_machine": 2}
+    inputs = {
+        "code": chemsh_code(),
+        "trajectory": water_trajectory_object,
+        "qm_parameters": Dict(
+            {
+                "theory": "PySCF",
+                "method": "hf",
+            }
+        ),
+        "calc": {"metadata": {"options": {"resources": resources}}},
+    }
+    results, node = run_get_node(BatchProcessWorkChain, **inputs)
+
+    assert node.is_finished_ok, "WorkChain Failed"
+
+    sub_nodes = node.called
+    assert len(sub_nodes) == 3, "Incorrect number of sub processes created."
+    for sub_node in sub_nodes:
+        assert sub_node.get_option("resources") == resources
+
+
 def test_batch_from_trajectorydata(chemsh_code, water_trajectory_object):
     """DFT based single point test."""
     inputs = {

{aiida_chemshell-0.2.0 → aiida_chemshell-0.2.1}/tests/test_calculations.py

@@ -24,7 +24,7 @@ def test_sp_calculation_qm_hf(chemsh_code, get_test_data_file):
 
     ofiles = results["retrieved"].list_object_names()
     assert ChemShellCalculation.FILE_STDOUT in ofiles
-    assert ChemShellCalculation.FILE_RESULTS in ofiles
+    # assert ChemShellCalculation.FILE_RESULTS in ofiles
 
     eref = -75.585287777076
     assert abs(results.get("energy") - eref) < 1e-8, (
@@ -79,7 +79,7 @@ def test_sp_calculation_qm_dft(chemsh_code, get_test_data_file, water_structure_
 
     ofiles = results.get("retrieved").list_object_names()
     assert ChemShellCalculation.FILE_STDOUT in ofiles
-    assert ChemShellCalculation.FILE_RESULTS in ofiles
+    # assert ChemShellCalculation.FILE_RESULTS in ofiles
 
     # eref = -75.946889377347 # If using conversion to bohr
     eref = -75.946889436563
@@ -110,7 +110,7 @@ def test_sp_calculation_dlpoly(chemsh_code, get_test_data_file):
 
     ofiles = results.get("retrieved").list_object_names()
     assert ChemShellCalculation.FILE_STDOUT in ofiles
-    assert ChemShellCalculation.FILE_RESULTS in ofiles
+    # assert ChemShellCalculation.FILE_RESULTS in ofiles
 
     eref = 0.018194285557
     assert (abs(results.get("energy") - eref)) < 1e-8, (
@@ -138,7 +138,7 @@ def test_sp_calculation_qmmm(chemsh_code, get_test_data_file):
 
     ofiles = results.get("retrieved").list_object_names()
     assert ChemShellCalculation.FILE_STDOUT in ofiles
-    assert ChemShellCalculation.FILE_RESULTS in ofiles
+    # assert ChemShellCalculation.FILE_RESULTS in ofiles
 
     eref = -75.594381915214
 
@@ -164,7 +164,7 @@ def test_opt_calculation_qm_dft(chemsh_code, get_test_data_file):
 
     ofiles = results.get("retrieved").list_object_names()
     assert ChemShellCalculation.FILE_STDOUT in ofiles
-    assert ChemShellCalculation.FILE_RESULTS in ofiles
+    # assert ChemShellCalculation.FILE_RESULTS in ofiles
 
     assert (
         results.get("optimised_structure").filename == ChemShellCalculation.FILE_DLFIND
@@ -205,7 +205,7 @@ def test_opt_calculation_dlpoly(chemsh_code, get_test_data_file):
     builder.structure = get_test_data_file("butanol.cjson")
     builder.mm_parameters = Dict({"theory": "DL_POLY"})
     builder.force_field_file = get_test_data_file("butanol.ff")
-    builder.optimisation_parameters = Dict({})
+    builder.optimisation_parameters = Dict({"save_path": True})
 
     results, node = run.get_node(builder)
 
@@ -216,8 +216,6 @@ def test_opt_calculation_dlpoly(chemsh_code, get_test_data_file):
 
     ofiles = results.get("retrieved").list_object_names()
     assert ChemShellCalculation.FILE_STDOUT in ofiles
-    assert ChemShellCalculation.FILE_DLFIND in ofiles
-    assert ChemShellCalculation.FILE_RESULTS in ofiles
 
     assert (
         results.get("optimised_structure").filename == ChemShellCalculation.FILE_DLFIND
@@ -234,6 +232,10 @@ def test_opt_calculation_dlpoly(chemsh_code, get_test_data_file):
         "Incorrect energy result for DL_POLY based optimisation calculation."
     )
 
+    assert results.get("trajectory_path").numsteps == 13
+    assert results.get("trajectory_path").numsites == 15
+    assert results.get("trajectory_force").filename == ChemShellCalculation.FILE_TRJFRC
+
 
 def test_vibrational_calculation(chemsh_code, get_test_data_file):
     """MM based geometry optimisation test."""
@@ -282,7 +284,7 @@ def test_structure_from_trajectorydata(chemsh_code, water_trajectory_object):
 
     ofiles = results.get("retrieved").list_object_names()
     assert ChemShellCalculation.FILE_STDOUT in ofiles
-    assert ChemShellCalculation.FILE_RESULTS in ofiles
+    # assert ChemShellCalculation.FILE_RESULTS in ofiles
 
     # eref = -75.946889377347 # Use if inputs are in bohr
     eref = -75.946889436563
@@ -311,8 +313,8 @@ def test_neb_calculation(chemsh_code, get_test_data_file):
 
     ofiles = results.get("retrieved").list_object_names()
     assert ChemShellCalculation.FILE_STDOUT in ofiles
-    assert ChemShellCalculation.FILE_DLFIND not in ofiles
-    assert ChemShellCalculation.FILE_RESULTS in ofiles
+    # assert ChemShellCalculation.FILE_DLFIND not in ofiles
+    # assert ChemShellCalculation.FILE_RESULTS in ofiles
 
     eref = -149.56942655605
     assert abs(results.get("energy") - eref) < 1e-8

{aiida_chemshell-0.2.0 → aiida_chemshell-0.2.1}/tests/test_inputs.py

@@ -11,8 +11,8 @@ def test_defaults(generate_calcjob):
 
     assert calc_info.retrieve_list == [
         ChemShellCalculation.FILE_STDOUT,
-        ChemShellCalculation.FILE_RESULTS,
     ]
+    assert ChemShellCalculation.FILE_RESULTS in calc_info.retrieve_temporary_list
     code_info = calc_info.codes_info[0]
     assert ChemShellCalculation.FILE_SCRIPT in code_info.cmdline_params
     assert code_info.stdout_name == ChemShellCalculation.FILE_STDOUT
@@ -99,9 +99,9 @@ def test_default_qm_opt(generate_calcjob, generate_inputs):
 
     assert calc_info.retrieve_list == [
         ChemShellCalculation.FILE_STDOUT,
-        ChemShellCalculation.FILE_RESULTS,
-        ChemShellCalculation.FILE_DLFIND,
     ]
+    assert ChemShellCalculation.FILE_DLFIND in calc_info.retrieve_temporary_list
+    assert ChemShellCalculation.FILE_RESULTS in calc_info.retrieve_temporary_list
 
 
 def test_expanded_mm_parameters(generate_calcjob, generate_inputs):