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* Fix parser for v2024.3. * Add tests for CP2K v2024.3. * Add an example run for the advanced parser. * Improve regexes for getting step info. * Simplify reading end-of-step info. * Base workchain: improve output parsing. --------- Co-authored-by: Aliaksandr Yakutovich <yakutovicha@gmail.com>
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examples/single_calculations/example_geopt_advanced_parser.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,162 @@ | ||
| ############################################################################### | ||
| # 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. # | ||
| ############################################################################### | ||
| """Run DFT geometry optimization.""" | ||
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| import os | ||
| import sys | ||
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| 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 | ||
|
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| StructureData = DataFactory("core.structure") | ||
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| def example_geopt(cp2k_code): | ||
| """Run DFT geometry optimization.""" | ||
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| print("Testing CP2K GEO_OPT on H2O (DFT)...") | ||
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| thisdir = os.path.dirname(os.path.realpath(__file__)) | ||
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| # Structure. | ||
| structure = StructureData( | ||
| ase=ase.io.read(os.path.join(thisdir, "..", "files", "h2.xyz")) | ||
| ) | ||
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| # Basis set. | ||
| basis_file = SinglefileData( | ||
| file=os.path.join(thisdir, "..", "files", "BASIS_MOLOPT") | ||
| ) | ||
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| # Pseudopotentials. | ||
| pseudo_file = SinglefileData( | ||
| file=os.path.join(thisdir, "..", "files", "GTH_POTENTIALS") | ||
| ) | ||
|
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| # Parameters. | ||
| parameters = Dict( | ||
| { | ||
| "GLOBAL": { | ||
| "RUN_TYPE": "GEO_OPT", | ||
| }, | ||
| "FORCE_EVAL": { | ||
| "METHOD": "Quickstep", | ||
| "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": { | ||
| "_": "PBE", | ||
| }, | ||
| }, | ||
| "POISSON": { | ||
| "PERIODIC": "none", | ||
| "PSOLVER": "MT", | ||
| }, | ||
| }, | ||
| "SUBSYS": { | ||
| "KIND": [ | ||
| { | ||
| "_": "O", | ||
| "BASIS_SET": "DZVP-MOLOPT-SR-GTH", | ||
| "POTENTIAL": "GTH-PBE-q6", | ||
| }, | ||
| { | ||
| "_": "H", | ||
| "BASIS_SET": "DZVP-MOLOPT-SR-GTH", | ||
| "POTENTIAL": "GTH-PBE-q1", | ||
| }, | ||
| ], | ||
| }, | ||
| }, | ||
| } | ||
| ) | ||
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| # Construct process builder. | ||
| builder = cp2k_code.get_builder() | ||
| builder.structure = structure | ||
| builder.parameters = parameters | ||
| builder.code = cp2k_code | ||
| builder.file = { | ||
| "basis": basis_file, | ||
| "pseudo": pseudo_file, | ||
| } | ||
| builder.metadata.options.resources = { | ||
| "num_machines": 1, | ||
| "num_mpiprocs_per_machine": 1, | ||
| } | ||
| builder.metadata.options.max_wallclock_seconds = 1 * 3 * 60 | ||
| builder.metadata.options.parser_name = "cp2k_advanced_parser" | ||
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| print("Submitted calculation...") | ||
| calc = run(builder) | ||
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| # Check walltime not exceeded. | ||
| assert calc["output_parameters"]["exceeded_walltime"] is False | ||
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| # Check energy. | ||
| expected_energy = -1.17212345935 | ||
| if abs(calc["output_parameters"]["energy"] - expected_energy) < 1e-10: | ||
| print("OK, energy has the expected value.") | ||
| else: | ||
| print("ERROR!") | ||
| print(f"Expected energy value: {expected_energy}") | ||
| print(f"Actual energy value: {calc['output_parameters']['energy']}") | ||
| sys.exit(3) | ||
|
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| # Check geometry. | ||
| expected_dist = 0.732594809575 | ||
| dist = calc["output_structure"].get_ase().get_distance(0, 1) | ||
| if abs(dist - expected_dist) < 1e-7: | ||
| print("OK, H-H distance has the expected value.") | ||
| else: | ||
| print("ERROR!") | ||
| print(f"Expected dist value: {expected_dist}") | ||
| print(f"Actual dist value: {dist}") | ||
| sys.exit(3) | ||
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| # Check motion step information. | ||
| assert calc["output_parameters"]["motion_step_info"]["step"] == [ | ||
| 0, | ||
| 1, | ||
| 2, | ||
| ], "ERROR: motion step info is incorrect" | ||
| assert calc["output_parameters"]["motion_step_info"]["cell_a_angs"] == [ | ||
| 4.0, | ||
| 4.0, | ||
| 4.0, | ||
| ], "ERROR: motion step info is incorrect" | ||
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| @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_geopt(code) | ||
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| if __name__ == "__main__": | ||
| cli() |
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