Merge pull request #286 from pyiron/cp2k

First draft of cp2k interface

.ci_support/environment.yml

@@ -16,3 +16,4 @@ dependencies:
 - randspg =0.0.1
 - boto3 =1.26.32
 - moto =4.0.12
+- pycp2k =0.2.2

pyiron_contrib/__init__.py

@@ -46,8 +46,10 @@
 JOB_CLASS_DICT['StorageJob'] = 'pyiron_contrib.RDM.storagejob'
 JOB_CLASS_DICT['PacemakerJob'] = 'pyiron_contrib.atomistics.pacemaker.job'
 JOB_CLASS_DICT['MeamFit'] = 'pyiron_contrib.atomistics.meamfit.meamfit'
+JOB_CLASS_DICT['Cp2kJob'] = 'pyiron_contrib.atomistics.cp2k.job'
+
 
 from ._version import get_versions
 
 __version__ = get_versions()["version"]
-del get_versions
+del get_versions

pyiron_contrib/atomistics/cp2k/job.py

@@ -0,0 +1,119 @@
+import os
+from pyiron_base import DataContainer, state
+from pyiron_atomistics.atomistics.structure.atoms import pyiron_to_ase, ase_to_pyiron
+from pyiron_atomistics.atomistics.job.atomistic import AtomisticGenericJob
+from pycp2k import CP2K
+
+
+pyiron_dict = {
+    "global": {
+        "run_type": "ENERGY_FORCE"
+    },
+    "force_eval": {
+        "method": "Quickstep",
+        "print_forces_section": "ON"
+    },
+    "dft": {
+        "qs": {
+            "eps": 1.0E-10
+        },
+        "mgrid": {
+            "ngrids": 4,
+            "cutoff": 300,
+            "rel_cutoff": 60
+        },
+        "xc": {
+            "functional": "PADE"
+        }
+    },
+    "scf": {
+        "scf_guess": "ATOMIC",
+        "eps": 1.0E-7,
+        "max": 300,
+        "diagonalization": {
+            "algorthim": "STANDARD"
+        },
+        "mixing": {
+            "method": "BROYDEN_MIXING",
+            "alpha": 0.4,
+            "n_broyden": 8,
+        }
+    },
+    "kind": {
+        "basis_set": "DZVP-GTH-PADE",
+        "potential": "GTH-PADE-q4"
+    }
+}
+
+
+class Cp2kJob(AtomisticGenericJob):
+    def __init__(self, project, job_name):
+        super(Cp2kJob, self).__init__(project, job_name)
+        self.__name__ = "cp2k"
+        self.input = DataContainer(pyiron_dict, table_name="control_dict")
+
+    def to_hdf(self, hdf=None, group_name=None):
+        """
+        Store the ExampleJob object in the HDF5 File
+
+        Args:
+            hdf (ProjectHDFio): HDF5 group object - optional
+            group_name (str): HDF5 subgroup name - optional
+        """
+        super(Cp2kJob, self).to_hdf(hdf=hdf, group_name=group_name)
+        self._structure_to_hdf()
+        with self.project_hdf5.open("input") as hdf5_input:
+            self.input.to_hdf(hdf5_input)
+
+    def from_hdf(self, hdf=None, group_name=None):
+        """
+        Restore the ExampleJob object in the HDF5 File
+
+        Args:
+            hdf (ProjectHDFio): HDF5 group object - optional
+            group_name (str): HDF5 subgroup name - optional
+        """
+        super(Cp2kJob, self).from_hdf(hdf=hdf, group_name=group_name)
+        self._structure_from_hdf()
+        with self.project_hdf5.open("input") as hdf5_input:
+            self.input.from_hdf(hdf5_input)
+
+    def write_input(self):
+        calc = CP2K()
+        calc.working_directory = self.working_directory
+        calc.project_name = "pyiron"
+        CP2K_INPUT = calc.CP2K_INPUT
+        GLOBAL = CP2K_INPUT.GLOBAL
+        FORCE_EVAL = CP2K_INPUT.FORCE_EVAL_add()  # Repeatable items have to be first created
+        SUBSYS = FORCE_EVAL.SUBSYS
+        DFT = FORCE_EVAL.DFT
+        SCF = DFT.SCF
+        GLOBAL.Run_type = self.input["global"]["run_type"]
+        FORCE_EVAL.Method = self.input["force_eval"]["method"]
+        FORCE_EVAL.PRINT.FORCES.Section_parameters = self.input["force_eval"]["print_forces_section"]
+        DFT.Basis_set_file_name = os.path.join(state.settings.resource_paths[0], "cp2k", "potentials", "BASIS_SET")
+        DFT.Potential_file_name = os.path.join(state.settings.resource_paths[0], "cp2k", "potentials", "GTH_POTENTIALS")
+        DFT.QS.Eps_default = self.input["dft"]["qs"]["eps"]
+        DFT.MGRID.Ngrids = self.input["dft"]["mgrid"]["ngrids"]
+        DFT.MGRID.Cutoff = self.input["dft"]["mgrid"]["cutoff"]
+        DFT.MGRID.Rel_cutoff = self.input["dft"]["mgrid"]["rel_cutoff"]
+        DFT.XC.XC_FUNCTIONAL.Section_parameters = self.input["dft"]["xc"]["functional"]
+        SCF.Scf_guess = self.input["scf"]["scf_guess"]
+        SCF.Eps_scf = self.input["scf"]["eps"]
+        SCF.Max_scf = self.input["scf"]["max"]
+        SCF.DIAGONALIZATION.Section_parameters = "ON"
+        SCF.DIAGONALIZATION.Algorithm = self.input["scf"]["diagonalization"]["algorthim"]
+        SCF.MIXING.Section_parameters = "T"
+        SCF.MIXING.Method = self.input["scf"]["mixing"]["method"]
+        SCF.MIXING.Alpha = self.input["scf"]["mixing"]["alpha"]
+        SCF.MIXING.Nbroyden = self.input["scf"]["mixing"]["n_broyden"]
+        for el in set(self.structure.get_chemical_symbols()):
+            KIND = SUBSYS.KIND_add(el)
+        KIND.Basis_set = self.input["kind"]["basis_set"]
+        KIND.Potential = self.input["kind"]["potential"]
+        calc.create_cell(SUBSYS, pyiron_to_ase(self.structure))
+        calc.create_coord(SUBSYS, pyiron_to_ase(self.structure))
+        calc.write_input_file()
+
+    def collect_output(self):
+        pass

setup.py

@@ -42,6 +42,7 @@
         'atomistic': [
             'ase==3.22.1',
             'pyiron_atomistics==0.2.61',
+            'pycp2k==0.2.2',
         ],
         'fenics': [
             'fenics==2019.1.0',