Cp2kMobilityWorkChain

.github/workflows/ci.yml

@@ -32,7 +32,7 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -58,11 +58,11 @@ jobs:
 
   docs:
     runs-on: ubuntu-latest
-    timeout-minutes: 15
+    timeout-minutes: 30
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python 3.8
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
         python-version: 3.8
     - name: Install python dependencies
@@ -77,9 +77,9 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v2
     - name: Set up Python 3.8
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
         python-version: 3.8
     - name: Install python dependencies

aiida_lsmo/calcfunctions/__init__.py

@@ -7,3 +7,5 @@
 from .selectivity import calc_selectivity
 from .wrappers import PE_PARAMETERS_DEFAULT
 from .wrappers import calc_co2_parasitic_energy
+from .vac_vaccum import VACCalculation
+

aiida_lsmo/calcfunctions/vac_vaccum.py

@@ -0,0 +1,93 @@
+from aiida.common import datastructures
+from aiida.engine import CalcJob
+from aiida.orm import RemoteData, Float
+
+class VACCalculation(CalcJob):
+    """AiiDA calculation plugin wrapping the MOFVacLevel executable."""
+    _DEFAULT_INPUT_FILE = "vac_vacuum.py"
+    _DEFAULT_OUTPUT_FILE = "log.out"
+    _DEFAULT_PARENT_CALC_FLDR_NAME = "parent_calc/"
+    @classmethod
+    def define(cls, spec):
+        """Define inputs and outputs of the calculation."""
+        super(VACCalculation, cls).define(spec)
+
+        # new ports
+        spec.input('folder', valid_type=RemoteData, help='First file to be compared.')
+        spec.output('vac_level', valid_type=Float, help='diff between file1 and file2.')
+
+        spec.input('metadata.options.output_filename', valid_type=str, default='log.out' )
+        spec.inputs['metadata']['options']['resources'].default = {
+                                            'num_machines': 1,
+                                            'num_mpiprocs_per_machine': 1,
+                                            }
+        spec.inputs['metadata']['options']['parser_name'].default = 'lsmo.vac_vaccum_parser'
+        spec.exit_code(
+            200,
+            "ERROR_NO_RETRIEVED_FOLDER",
+            message="The retrieved folder data node could not be accessed.",
+        )
+        spec.exit_code(300, 'ERROR_MISSING_OUTPUT_FILES',
+                message='Calculation did not produce all expected output files.')
+        spec.exit_code(
+            301, "ERROR_OUTPUT_READ", message="The output file could not be read."
+        )
+        spec.exit_code(
+            302, "ERROR_OUTPUT_PARSE", message="The output file could not be parsed."
+        )
+
+
+    def prepare_for_submission(self, folder):
+        """
+        Create input files.
+
+        :param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files needed by
+            the calculation.
+        :return: `aiida.common.datastructures.CalcInfo` instance
+        """
+        #lines= ['from mof_vac_level import MOFVacLevel', 'mvl = MOFVacLevel(\'parent_calc/aiida-v_hartree-1_0.cube\')', 'value = mvl.get_vacuum_potential(res=0.4, cube_size= [25, 25, 25] )','print(value)']
+        lines = "from mof_vac_level import"
+        with folder.open("vac_vacuum.py", 'w') as fobj:
+        #with open(folder.get_abs_path(self._DEFAULT_INPUT_FILE), mode='w') as fobj:
+            #fobj.write(f'from mof_vac_level import \n  ')
+            fobj.write("from mof_vac_level import MOFVacLevel \nmvl = MOFVacLevel(\'parent_calc/aiida-v_hartree-1_0.cube\') \nvalue = mvl.get_vacuum_potential(res=0.5, cube_size= [25, 25, 25] ) \nprint(value)") 
+
+
+
+
+
+        codeinfo = datastructures.CodeInfo()
+        codeinfo.cmdline_params = [self._DEFAULT_INPUT_FILE]
+        codeinfo.stin_name = self._DEFAULT_INPUT_FILE
+        codeinfo.code_uuid = self.inputs.code.uuid
+        codeinfo.stdout_name = self._DEFAULT_OUTPUT_FILE
+
+        # Prepare a `CalcInfo` to be returned to the engine
+        calcinfo = datastructures.CalcInfo()
+        calcinfo.cmdline_params = codeinfo.cmdline_params
+        calcinfo.stdin_name = self._DEFAULT_INPUT_FILE
+        calcinfo.stdout_name = self._DEFAULT_OUTPUT_FILE
+
+        calcinfo.codes_info = [codeinfo]
+        #calcinfo.local_copy_list = [
+        #    (self.inputs.folder.uuid, self.inputs.folder.filename, self.inputs.folder.filename)
+        #]
+        calcinfo.retrieve_list = [self.metadata.options.output_filename]
+
+        #Make a link of cube_file folder 
+        calcinfo.remote_symlink_list = []
+        calcinfo.remote_copy_list = []
+
+        comp_uuid = self.inputs.folder.computer.uuid
+        remote_path = self.inputs.folder.get_remote_path()
+        copy_info = (comp_uuid, remote_path, self._DEFAULT_PARENT_CALC_FLDR_NAME)
+        # If running on the same computer - make a symlink.
+        if self.inputs.code.computer.uuid == comp_uuid:
+            calcinfo.remote_symlink_list.append(copy_info)
+        # If not - copy the folder.
+        else:
+            calcinfo.remote_copy_list.append(copy_info)
+
+        return calcinfo
+
+

aiida_lsmo/parsers/__init__.py

@@ -5,6 +5,7 @@
 from aiida.orm import Dict, BandsData
 from aiida_cp2k.parsers import Cp2kBaseParser
 from .parser_functions import parse_cp2k_output_bsse, parse_cp2k_output_advanced
+from .vac_vacuum_parser import VACCalculationParser
 
 
 class Cp2kBsseParser(Cp2kBaseParser):  # pylint: disable=too-few-public-methods

aiida_lsmo/parsers/vac_vacuum_parser.py

@@ -0,0 +1,37 @@
+from aiida.engine import ExitCode
+
+from aiida.common import exceptions
+from aiida.orm import SinglefileData, Float
+from aiida.parsers.parser import Parser
+from aiida.plugins import CalculationFactory
+
+VACCalculation = CalculationFactory('lsmo.vac_vaccum')
+
+
+class VACCalculationParser(Parser):
+
+    def parse(self, **kwargs):
+        """
+        Parse outputs, store results in database.
+        """
+
+
+
+
+        output_filename = self.node.get_option('output_filename')
+
+        files_retrieved = self.retrieved.list_object_names()
+        files_expected = [output_filename]
+        # Note: set(A) <= set(B) checks whether A is a subset of B
+        if not set(files_expected) <= set(files_retrieved):
+            self.logger.error(f"Found files '{files_retrieved}', expected to find '{files_expected}'")
+            return self.exit_codes.ERROR_MISSING_OUTPUT_FILES
+        # add output file
+        self.logger.info(f"Parsing '{output_filename}'")
+        with self.retrieved.open(output_filename, 'rb') as handle:
+            value_file = float(handle.readline())
+            output_node = Float(value_file)
+        self.out('vac_level', output_node)
+
+        return ExitCode(0)
+

aiida_lsmo/utils/cp2k_utils_master.py

@@ -0,0 +1,123 @@
+"""Utilities related to CP2K."""
+
+from aiida_lsmo.utils import HARTREE2EV
+
+# Functions to get inputs
+
+
+def get_input_multiplicity(structure, protocol_settings):
+    """ Compute the total multiplicity of the structure,
+    by summing the atomic magnetizations:
+    multiplicity = 1 + sum_i ( natoms_i * magnetization_i ), for each atom_type i
+    """
+    multiplicity = 1
+    all_atoms = structure.get_ase().get_chemical_symbols()
+    for key, value in protocol_settings['initial_magnetization'].items():
+        multiplicity += all_atoms.count(key) * value
+    multiplicity = int(round(multiplicity))
+    multiplicity_dict = {'FORCE_EVAL': {'DFT': {'MULTIPLICITY': multiplicity}}}
+    if multiplicity != 1:
+        multiplicity_dict['FORCE_EVAL']['DFT']['UKS'] = True
+    return multiplicity_dict
+
+
+def get_kinds_section(structure, protocol_settings):
+    """ Write the &KIND sections given the structure and the settings_dict"""
+    kinds = []
+    all_atoms = set(structure.get_ase().get_chemical_symbols())
+    for atom in all_atoms:
+        kinds.append({
+            '_': atom,
+            'BASIS_SET': protocol_settings['basis_set'][atom],
+            'POTENTIAL': protocol_settings['pseudopotential'][atom],
+            'MAGNETIZATION': protocol_settings['initial_magnetization'][atom],
+        })
+    return {'FORCE_EVAL': {'SUBSYS': {'KIND': kinds}}}
+
+
+def get_kinds_with_ghost_section(structure, protocol_settings):
+    """Write the &KIND sections given the structure and the settings_dict, and add also GHOST atoms"""
+    kinds = []
+    all_atoms = set(structure.get_ase().get_chemical_symbols())
+    for atom in all_atoms:
+        kinds.append({
+            '_': atom,
+            'BASIS_SET': protocol_settings['basis_set'][atom],
+            'POTENTIAL': protocol_settings['pseudopotential'][atom],
+            'MAGNETIZATION': protocol_settings['initial_magnetization'][atom],
+        })
+        kinds.append({'_': atom + "_ghost", 'BASIS_SET': protocol_settings['basis_set'][atom], 'GHOST': True})
+    return {'FORCE_EVAL': {'SUBSYS': {'KIND': kinds}}}
+
+
+def get_bsse_section(natoms_a, natoms_b, mult_a=1, mult_b=1, charge_a=0, charge_b=0):
+    """Get the &FORCE_EVAL/&BSSE section."""
+    bsse_section = {
+        'FORCE_EVAL': {
+            'BSSE' : {
+                'FRAGMENT': [{
+                'LIST': '1..{}'.format(natoms_a)
+                },
+                {
+                'LIST': '{}..{}'.format(natoms_a + 1, natoms_a + natoms_b)
+                }],
+                'CONFIGURATION': [
+                    { # A fragment with basis set A
+                        'MULTIPLICITY': mult_a,
+                        'CHARGE': charge_a,
+                        'GLB_CONF': '1 0',
+                        'SUB_CONF': '1 0',
+                        },
+                    { # B fragment with basis set B
+                        'MULTIPLICITY': mult_b,
+                        'CHARGE': charge_b,
+                        'GLB_CONF': '0 1',
+                        'SUB_CONF': '0 1',
+                        },
+                    { # A fragment with basis set A+B
+                        'MULTIPLICITY': mult_a,
+                        'CHARGE': charge_a,
+                        'GLB_CONF': '1 1',
+                        'SUB_CONF': '1 0',
+                        },
+                    { # B fragment with basis set A+B
+                        'MULTIPLICITY': mult_b,
+                        'CHARGE': charge_b,
+                        'GLB_CONF': '1 1',
+                        'SUB_CONF': '0 1',
+                        },
+                    { # A+B fragments with basis set A+B
+                        'MULTIPLICITY': mult_a + mult_b - 1,
+                        'CHARGE': charge_a + charge_b,
+                        'GLB_CONF': '1 1',
+                        'SUB_CONF': '1 1',
+                        }
+                ]
+            }
+        }
+    }
+    return bsse_section
+
+
+# Functions to parse results
+
+
+def ot_has_small_bandgap(cp2k_input, cp2k_output, bandgap_thr_ev):
+    """ Returns True if the calculation used OT and had a smaller bandgap then the guess needed for the OT.
+    (NOTE: It has been observed also negative bandgap with OT in CP2K!)
+    cp2k_input: dict
+    cp2k_output: dict
+    bandgap_thr_ev: float [eV]
+    """
+    list_true = [True, 'T', 't', '.TRUE.', 'True', 'true']  #add more?
+    try:
+        ot_settings = cp2k_input['FORCE_EVAL']['DFT']['SCF']['OT']
+        if '_' not in ot_settings.keys() or ot_settings['_'] in list_true:  #pylint: disable=simplifiable-if-statement
+            using_ot = True
+        else:
+            using_ot = False
+    except KeyError:
+        using_ot = False
+    min_bandgap_ev = min(cp2k_output["bandgap_spin1_au"], cp2k_output["bandgap_spin2_au"]) * HARTREE2EV
+    is_bandgap_small = (min_bandgap_ev < bandgap_thr_ev)
+    return using_ot and is_bandgap_small