Add new md workchain.

examples/workchains/example_base_md_restart.py

@@ -0,0 +1,158 @@
+###############################################################################
+# Copyright (c), The AiiDA-CP2K authors.                                      #
+# SPDX-License-Identifier: MIT                                                #
+# AiiDA-CP2K is hosted on GitHub at https://github.com/aiidateam/aiida-cp2k   #
+# For further information on the license, see the LICENSE.txt file.           #
+###############################################################################
+"""An example testing the restart calculation handler for geo_opt run in CP2K."""
+
+import os
+import sys
+
+import ase.io
+import click
+from aiida.common import NotExistent
+from aiida.engine import run
+from aiida.orm import Dict, SinglefileData, load_code
+from aiida.plugins import DataFactory, WorkflowFactory
+
+Cp2kBaseWorkChain = WorkflowFactory("cp2k.base")
+StructureData = DataFactory("core.structure")
+
+
+def example_base(cp2k_code):
+    """Run simple DFT calculation through a workchain."""
+
+    thisdir = os.path.dirname(os.path.realpath(__file__))
+
+    print("Testing CP2K ENERGY on H2O (DFT) through a workchain...")
+
+    # Basis set.
+    basis_file = SinglefileData(
+        file=os.path.join(thisdir, "..", "files", "BASIS_MOLOPT")
+    )
+
+    # Pseudopotentials.
+    pseudo_file = SinglefileData(
+        file=os.path.join(thisdir, "..", "files", "GTH_POTENTIALS")
+    )
+
+    # Structure.
+    structure = StructureData(
+        ase=ase.io.read(os.path.join(thisdir, "..", "files", "h2o.xyz"))
+    )
+
+    # Parameters.
+    parameters = Dict(
+        {
+            "GLOBAL": {
+                "RUN_TYPE": "MD",
+                "WALLTIME": "00:00:50",  # too short
+            },
+            "FORCE_EVAL": {
+                "METHOD": "Quickstep",
+                "STRESS_TENSOR": "analytical",
+                "DFT": {
+                    "BASIS_SET_FILE_NAME": "BASIS_MOLOPT",
+                    "POTENTIAL_FILE_NAME": "GTH_POTENTIALS",
+                    "QS": {
+                        "EPS_DEFAULT": 1.0e-12,
+                        "WF_INTERPOLATION": "ps",
+                        "EXTRAPOLATION_ORDER": 3,
+                    },
+                    "MGRID": {
+                        "NGRIDS": 4,
+                        "CUTOFF": 280,
+                        "REL_CUTOFF": 30,
+                    },
+                    "XC": {
+                        "XC_FUNCTIONAL": {
+                            "_": "LDA",
+                        },
+                    },
+                    "POISSON": {
+                        "PERIODIC": "none",
+                        "PSOLVER": "MT",
+                    },
+                    "SCF": {"PRINT": {"RESTART": {"_": "ON"}}},
+                },
+                "SUBSYS": {
+                    "KIND": [
+                        {
+                            "_": "O",
+                            "BASIS_SET": "DZVP-MOLOPT-SR-GTH",
+                            "POTENTIAL": "GTH-LDA-q6",
+                        },
+                        {
+                            "_": "H",
+                            "BASIS_SET": "DZVP-MOLOPT-SR-GTH",
+                            "POTENTIAL": "GTH-LDA-q1",
+                        },
+                    ],
+                },
+            },
+
+            "MOTION": {
+                "CONSTRAINT": {},
+                "MD": {
+                    "THERMOSTAT": {"CSVR": {}, "TYPE": "csvr"},
+                    "BAROSTAT": {},
+                    "STEPS": 10,
+                    "ENSEMBLE": "npt_f",
+                    "TEMPERATURE": 300.0,
+                },
+                "PRINT": {
+                    "RESTART": {"EACH": {"MD": 1}},
+                },
+            },
+        }
+    )
+
+    # Construct process builder.
+    builder = Cp2kBaseWorkChain.get_builder()
+
+    # Switch on resubmit_unconverged_geometry disabled by default.
+    builder.handler_overrides = Dict(
+        {"restart_incomplete_calculation": {"enabled": True}}
+    )
+
+    # Input structure.
+    builder.cp2k.structure = structure
+    builder.cp2k.parameters = parameters
+    builder.cp2k.code = cp2k_code
+    builder.cp2k.file = {
+        "basis": basis_file,
+        "pseudo": pseudo_file,
+    }
+    builder.cp2k.metadata.options.resources = {
+        "num_machines": 1,
+        "num_mpiprocs_per_machine": 1,
+    }
+    builder.cp2k.metadata.options.max_wallclock_seconds = 1 * 3 * 60
+
+    print("Submitted calculation...")
+    calc = run(builder)
+
+    if "EXT_RESTART" in calc["final_input_parameters"].dict:
+        print("OK, EXT_RESTART section is present in the final_input_parameters.")
+    else:
+        print(
+            "ERROR, EXT_RESTART section is NOT present in the final_input_parameters."
+        )
+        sys.exit(3)
+
+
+@click.command("cli")
+@click.argument("codelabel")
+def cli(codelabel):
+    """Click interface."""
+    try:
+        code = load_code(codelabel)
+    except NotExistent:
+        print(f"The code '{codelabel}' does not exist")
+        sys.exit(1)
+    example_base(code)
+
+
+if __name__ == "__main__":
+    cli()