Add UpfData input namespace (#194)

- Add aiida-pseudo dependency.
- Install SSSP/1.3/PBE/efficiency pseudo using aiida-sssp.
- Add an example run.
- Add setup_sssp_pseudos fixture.

Author: yakutovicha

aiida_cp2k/calculations/__init__.py

@@ -6,13 +6,15 @@
 ###############################################################################
 """AiiDA-CP2K input plugin."""
 
+import json
 from operator import add
 
 import numpy as np
 from aiida.common import CalcInfo, CodeInfo, InputValidationError
 from aiida.engine import CalcJob
 from aiida.orm import Dict, RemoteData, SinglefileData
 from aiida.plugins import DataFactory
+from upf_to_json import upf_to_json
 
 from ..utils import Cp2kInput
 from ..utils.datatype_helpers import (
@@ -28,6 +30,7 @@
 StructureData = DataFactory("core.structure")
 TrajectoryData = DataFactory("core.array.trajectory")
 KpointsData = DataFactory("core.array.kpoints")
+UpfData = DataFactory("pseudo.upf")
 
 
 class Cp2kCalculation(CalcJob):
@@ -118,6 +121,14 @@ def define(cls, spec):
             ),
         )
 
+        spec.input_namespace(
+            "pseudos_upf",
+            valid_type=UpfData,
+            dynamic=True,
+            required=True,
+            help="A mapping of `UpfData` nodes onto the kind name to which they should apply.",
+        )
+
         # Specify default parser.
         spec.input(
             "metadata.options.parser_name",
@@ -316,6 +327,12 @@ def prepare_for_submission(self, folder):
             )
             write_pseudos(inp, self.inputs.pseudos, folder)
 
+        if "pseudos_upf" in self.inputs:
+            for atom_kind, pseudo in self.inputs.pseudos_upf.items():
+                pseudo_dict = upf_to_json(pseudo.get_content(), atom_kind)
+                with folder.open(atom_kind + ".json", "w") as fobj:
+                    fobj.write(json.dumps(pseudo_dict, indent=2))
+
         # Kpoints.
         if "kpoints" in self.inputs:
             try:

conftest.py

@@ -1,5 +1,7 @@
 """For pytest initialise a test database and profile."""
 
+import subprocess
+
 import pytest
 
 pytest_plugins = ["aiida.manage.tests.pytest_fixtures"]
@@ -31,3 +33,21 @@ def pytest_unconfigure(config):
     import sys
 
     del sys._called_from_test
+
+
+@pytest.fixture(scope="function", autouse=True)
+def setup_sssp_pseudos(aiida_profile):
+    """Create an SSSP pseudo potential family from scratch."""
+    subprocess.run(
+        [
+            "aiida-pseudo",
+            "install",
+            "sssp",
+            "-p",
+            "efficiency",
+            "-x",
+            "PBE",
+            "-v",
+            "1.3",
+        ]
+    )

examples/files/si.xyz

@@ -0,0 +1,4 @@
+2
+Lattice="3.81196 0.0 0.0 1.9059800000000005 3.3012541982101284 0.0 1.9059800000000005 1.100418066070043 3.112452306633254" Properties=species:S:1:pos:R:3:_aiidalab_viewer_representation_default:I:1 spacegroup="P 1" unit_cell=conventional pbc="T T T"
+Si       0.00000000       0.00000000       0.00000000        0
+Si       1.90598000       1.10041807       0.77811308        0

examples/single_calculations/example_sirius.py

@@ -0,0 +1,127 @@
+###############################################################################
+# 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 simple DFT with calculation with SIRIUS."""
+
+import os
+import sys
+
+import ase.io
+import click
+from aiida import common, engine, orm, plugins
+
+StructureData = plugins.DataFactory("core.structure")
+
+
+def example_sirius(cp2k_code, setup_sssp_pseudos):
+    """Run simple DFT calculation."""
+
+    print("Testing CP2K SIRIUS ENERGY on Si (DFT)...")
+
+    thisdir = os.path.dirname(os.path.realpath(__file__))
+
+    # Structure.
+    structure = StructureData(
+        ase=ase.io.read(os.path.join(thisdir, "..", "files", "si.xyz"))
+    )
+
+    # Parameters.
+    parameters = orm.Dict(
+        {
+            "FORCE_EVAL": {
+                "METHOD": "SIRIUS",
+                "STRESS_TENSOR": "ANALYTICAL",
+                "PRINT": {
+                    "FORCES": {"FILENAME": "requested-forces", "ADD_LAST": "SYMBOLIC"}
+                },
+                "PW_DFT": {
+                    "CONTROL": {"VERBOSITY": 2},
+                    "PARAMETERS": {
+                        "ELECTRONIC_STRUCTURE_METHOD": "pseudopotential",
+                        "USE_SYMMETRY": True,
+                        "GK_CUTOFF": 5,
+                        "PW_CUTOFF": 20,
+                        "ENERGY_TOL": 0.1,
+                        "DENSITY_TOL": 0.1,
+                        "NUM_DFT_ITER": 400,
+                        "SMEARING": "FERMI_DIRAC",
+                        "SMEARING_WIDTH": 0.00225,
+                    },
+                    "ITERATIVE_SOLVER": {
+                        "ENERGY_TOLERANCE": 0.001,
+                        "NUM_STEPS": 20,
+                        "SUBSPACE_SIZE": 4,
+                        "CONVERGE_BY_ENERGY": 1,
+                    },
+                },
+                "DFT": {
+                    "XC": {
+                        "XC_FUNCTIONAL": {
+                            "GGA_X_PBE": {"_": ""},
+                            "GGA_C_PBE": {"_": ""},
+                        }
+                    },
+                    "PRINT": {
+                        "MO": {
+                            "_": "OFF",
+                            "ADD_LAST": "SYMBOLIC",
+                            "EIGENVALUES": True,
+                            "OCCUPATION_NUMBERS": True,
+                            "NDIGITS": 12,
+                            "EACH": {"CELL_OPT": 0, "GEO_OPT": 0, "MD": 0, "QS_SCF": 0},
+                        },
+                        "MULLIKEN": {
+                            "_": "ON",
+                            "ADD_LAST": "SYMBOLIC",
+                            "EACH": {"CELL_OPT": 0, "GEO_OPT": 0, "MD": 0},
+                        },
+                        "LOWDIN": {"_": "OFF"},
+                        "HIRSHFELD": {"_": "OFF"},
+                    },
+                },
+                "SUBSYS": {
+                    "KIND": [
+                        {
+                            "_": "Si",
+                            "POTENTIAL": "UPF Si.json",
+                        },
+                    ],
+                },
+            },
+        }
+    )
+
+    # Construct process builder.
+    builder = cp2k_code.get_builder()
+    builder.structure = structure
+    builder.parameters = parameters
+    builder.code = cp2k_code
+    pseudo_family = orm.load_group("SSSP/1.3/PBE/efficiency")
+    builder.pseudos_upf = pseudo_family.get_pseudos(structure=structure)
+    builder.metadata.options.resources = {
+        "num_machines": 1,
+        "num_mpiprocs_per_machine": 1,
+    }
+    builder.metadata.options.max_wallclock_seconds = 1 * 3 * 60
+
+    print("Submitted calculation...")
+    engine.run(builder)
+
+
+@click.command("cli")
+@click.argument("codelabel")
+def cli(codelabel):
+    """Click interface."""
+    try:
+        code = orm.load_code(codelabel)
+    except common.NotExistent:
+        print(f"The code '{codelabel}' does not exist.")
+        sys.exit(1)
+    example_sirius(code, setup_sssp_pseudos=None)
+
+
+if __name__ == "__main__":
+    cli()

pyproject.toml

@@ -25,6 +25,8 @@ dependencies = [
     "ase",
     "ruamel.yaml>=0.16.5",
     "cp2k-output-tools",
+    "aiida-pseudo~=1.2",
+    "upf-to-json>=0.9",
 ]
 
 [[project.authors]]