CLF-Ultra geometry optimisation workchain

pyproject.toml

@@ -1,26 +1,24 @@
 [build-system]
-requires = ["setuptools",]
+requires = ["setuptools"]
 build-backend = "setuptools.build_meta"
 
 [project]
 version = "0.1.10"
 name = "aiida-chemshell"
 description = "AiiDA workflow plugin for the ChemShell chemical modelling software package"
 authors = [
-    {name = "Dr. Benjamin T. Speake", email = "benjamin.speake@stfc.ac.uk"},
-]
-dependencies = [
-    "aiida-core >= 2.5",
+    { name = "Dr. Benjamin T. Speake", email = "benjamin.speake@stfc.ac.uk" },
 ]
+dependencies = ["aiida-core >= 2.5"]
 readme = "README.md"
-license = {file = "LICENSE"}
-keywords = ["aiida", "workflows", "chemshell", ]
+license = { file = "LICENSE" }
+keywords = ["aiida", "workflows", "chemshell"]
 classifiers = [
     "Intended Audience :: Science/Research",
     "Programming Language :: Python :: 3",
-    "Topic :: Scientific/Engineering", 
+    "Topic :: Scientific/Engineering",
     "Framework :: AiiDA",
-    "Development Status :: 5 - Production/Stable"
+    "Development Status :: 5 - Production/Stable",
 ]
 requires-python = ">=3.10"
 
@@ -29,36 +27,34 @@ 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"
 
 [tool.setuptools.packages.find]
-where = ["src",]
+where = ["src"]
 
 [project.optional-dependencies]
 dev = [
     "aiida-core>=2.6", # Required to support aiida.tools.pytest_fixtures 
-    "pytest>=8.0", 
+    "pytest>=8.0",
     "pytest-cov>=6.0",
     "ruff>=0.11.0",
-    "pre-commit"
-]
-docs = [
-    "sphinx>=8.0.2",
-    "piccolo-theme>=0.14.0",
-    "sphinx-toolbox",
-    "numpydoc",
+    "pre-commit",
 ]
+docs = ["sphinx>=8.0.2", "piccolo-theme>=0.14.0", "sphinx-toolbox", "numpydoc"]
 
 [tool.ruff]
-target-version = "py310" 
-line-length = 88 
+target-version = "py310"
+line-length = 88
 indent-width = 4
-exclude = ["conf.py",]
+exclude = ["conf.py"]
 
 [tool.ruff.lint.per-file-ignores]
 "tests/conftest.py" = ["B008"]
@@ -68,23 +64,24 @@ select = [
     # flake8-bugbear
     "B",
     # pylint
-    "C", "R",
+    "C",
+    "R",
     # pydocstyle
     "D",
     # pycodestyle
-    "E", "W",
+    "E",
+    "W",
     # Pyflakes
-    "F", "FA",
+    "F",
+    "FA",
     # isort
     "I",
     # pep8-naming
     "N",
     # pyupgrade
     "UP",
 ]
-ignore = [
-    "C901",
-]
+ignore = ["C901"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"

src/aiida_chemshell/calculations/base.py

@@ -5,6 +5,7 @@
 from aiida.engine import CalcJob, CalcJobProcessSpec, PortNamespace
 from aiida.orm import ArrayData, Dict, Float, SinglefileData, StructureData
 
+from aiida_chemshell.units import UnitsConverter
 from aiida_chemshell.utils import ChemShellMMTheory, ChemShellQMTheory
 
 
@@ -23,6 +24,8 @@ class ChemShellCalculation(CalcJob):
     FILE_DLFIND = "_dl_find.cjson"
     FILE_TMP_STRUCTURE = "input_structure.xyz"
     FILE_RESULTS = "result.json"
+    FILE_TRJPTH = "path.xyz"
+    FILE_TRJFRC = "path_force.xyz"
 
     @classmethod
     def define(cls, spec: CalcJobProcessSpec) -> None:
@@ -41,8 +44,8 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
             validator=cls.validate_structure_file,
             required=True,
             help=(
-                "The input structure for the ChemShell calculation either contained"
-                "within an '.xyz', '.pun' or '.cjson' file or as a StructureData"
+                "The input structure for the ChemShell calculation either contained "
+                "within an '.xyz', '.pun' or '.cjson' file or as a StructureData "
                 "instance."
             ),
         )
@@ -131,6 +134,14 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
                 "structure is contained within a ChemShell '.pun' file."
             ),
         )
+        spec.output(
+            "optimisation_path",
+            valid_type=ArrayData,
+            required=False,
+            help=(
+                "Values calculated at each step of an optimisation based calculation."
+            ),
+        )
         spec.output(
             "vibrational_energies",
             valid_type=Dict,
@@ -160,10 +171,26 @@ def inputs_validator_wrapper(inputs, namespace):
 
         spec.inputs.validator = inputs_validator_wrapper
 
+        spec.output(
+            "trajectory_path",
+            valid_type=SinglefileData,
+            required=False,
+            help="XYZ trajectory file for the geometry optimisation",
+        )
+        spec.output(
+            "trajectory_force",
+            valid_type=SinglefileData,
+            required=False,
+            help=(
+                "XYZ trajectory containing forces at each step of a geometry "
+                "optimisation"
+            ),
+        )
+
         ## Metadata
         spec.inputs["metadata"]["options"]["resources"].default = {
             "num_machines": 1,
-            "num_mpiprocs_per_machine": 1,
+            "num_mpiprocs_per_machine": 4,
         }
         spec.inputs["metadata"]["options"]["parser_name"].default = "chemshell"
 
@@ -327,6 +354,7 @@ def get_valid_optimisation_parameter_keys(cls) -> tuple[str]:
             "delta",
             "tsrelative",
             "thermal",
+            "save_path",
         )
 
     @classmethod
@@ -565,7 +593,7 @@ def validate_mm_parameters(cls, value: Dict | None, _) -> str | None:
         theory = value.get("theory", "").upper()
         if theory not in ChemShellMMTheory.__members__:
             return (
-                "The specified MM theory '{theory:s}' is not a "
+                f"The specified MM theory '{theory:s}' is not a "
                 "valid ChemShell MM interface within the AiiDA-ChemShell workflow."
             )
 
@@ -664,22 +692,37 @@ def _build_process_label(self) -> str:
         Defines the process label to be associated with the created ProcessNode
         stored in the AiiDA database.
 
+        Returns
+        -------
+        str
+            The process label based on what inputs have been provided.
+        """
+        return ChemShellCalculation.default_process_label(self)
+
+    @classmethod
+    def default_process_label(cls, node) -> str:
+        """
+        AiiDA Process label definition (Class Method).
+
+        Defines the process label to be associated with the created ProcessNode
+        stored in the AiiDA database.
+
         Returns
         -------
         str
             The process label based on what inputs have been provided.
         """
         theory_key = ""
-        if "qm_parameters" in self.inputs:
-            if "mm_parameters" in self.inputs:
+        if "qm_parameters" in node.inputs:
+            if "mm_parameters" in node.inputs:
                 theory_key = "_(QM/MM)"
             else:
                 theory_key = "_(QM)"
         else:
             theory_key = "_(MM)"
 
-        if "optimisation_parameters" in self.inputs:
-            if self.inputs.optimisation_parameters.get("thermal", False):
+        if "optimisation_parameters" in node.inputs:
+            if node.inputs.optimisation_parameters.get("thermal", False):
                 return "ChemShell_Vibrational_Frequencies" + theory_key
             return "ChemShell_Geometry_Optimisation" + theory_key
 
@@ -700,10 +743,19 @@ def chemsh_script_generator(self) -> str:
 
         script = "from chemsh import Fragment\n"
         if isinstance(self.inputs.structure, SinglefileData):
-            fname = self.inputs.structure.filename
+            script += (
+                f"structure = Fragment(coords='{self.inputs.structure.filename:s}')\n"
+            )
         else:
-            fname = ChemShellCalculation.FILE_TMP_STRUCTURE
-        script += f"structure = Fragment(coords='{fname:s}')\n"
+            atom_names = [site.kind_name for site in self.inputs.structure.sites]
+            coords = [
+                [UnitsConverter.angstrom_to_bohr(r) for r in site.position]
+                for site in self.inputs.structure.sites
+            ]
+            script += (
+                f"structure = Fragment(coords={str(coords):s}, names="
+                f"{str(atom_names):s})\n"
+            )
 
         ## Setup Theory objects
 
@@ -829,9 +881,21 @@ def prepare_for_submission(self, folder: Folder) -> CalcInfo:
         # Define the AiiDA code parameters
         code_info = CodeInfo()
         code_info.code_uuid = self.inputs.code.uuid
-        code_info.cmdline_params = [
-            ChemShellCalculation.FILE_SCRIPT,
-        ]
+        if "chemsh.x" in str(self.inputs.code.filepath_executable):
+            code_info.cmdline_params = [
+                ChemShellCalculation.FILE_SCRIPT,
+            ]
+        else:
+            n_machines = self.inputs.metadata.options.resources.get("num_machines")
+            n_mpi_pm = self.inputs.metadata.options.resources.get(
+                "num_mpiprocs_per_machine"
+            )
+            tot_mpi = n_machines * n_mpi_pm
+            code_info.cmdline_params = [
+                "-np",
+                self.inputs.metadata.options.resources.get("tot_num_mpiprocs", tot_mpi),
+                ChemShellCalculation.FILE_SCRIPT,
+            ]
         code_info.stdout_name = ChemShellCalculation.FILE_STDOUT
 
         # Setup the calculation information object
@@ -871,5 +935,12 @@ def prepare_for_submission(self, folder: Folder) -> CalcInfo:
         # file containing the optimised structure
         if "optimisation_parameters" in self.inputs:
             calc_info.retrieve_list.append(ChemShellCalculation.FILE_DLFIND)
+            if self.inputs.optimisation_parameters.get("save_path", False):
+                calc_info.retrieve_list.append(
+                    "_dl_find/" + ChemShellCalculation.FILE_TRJPTH
+                )
+                calc_info.retrieve_list.append(
+                    "_dl_find/" + ChemShellCalculation.FILE_TRJFRC
+                )
 
         return calc_info