Adjustments to the protocols/generator for Fleur code (#265)

* Delete 'serial' key from default SCF wf parameters

The interface has changed, the default is False, so it is not needed.
In general for flexibility we might have to change some of the other
queue parameters through, since over the common workflow the default scf
cannot be changed.

* Ignore `kpoints_distance` input if a `kpt` specification comes from the parameters of the reference workchain

* Turn off writing of atom ids in get_parameters

* Adjust protocols, parse the protocol to inpgen, use fleur protocols

* Fix that protocol name was not given to inpgen

* Decouple protocol name in common workflows with profile/protocol used in
the inpgen of fleur

* Add oxides_validation protocol

* Add oxides_validation protocol also to the FleurCommonRelaxInputGenerator

* Fix wrong name of gamma option in fleur protocol

* Make sure that the gamma option is set for all relax workchains not just for the reference workchain

* Fix for last commit

* Add oxides_validation to valid type for the protocol input

* Incorporate Gregor's changes

* Add remote_folder output to FleurCommonRelaxWorkChain

* Move valid protocols to fleur workchain

* Add `verification-pbe-v1` protocol

* Add missing description

* Update aiida-fleur dependency to make sure the common workflows have everything they need

* Add extractor for TS contribution for FleurCommonRelaxWorkChain

* Add fallback solution for extracting the TS contribution directly from the out.xml

For calculations that do not already extract this information in the main fleur parser

Co-authored-by: Jens Bröder <j.broeder@fz-juelich.de>
Co-authored-by: Jens Broeder <broeder-j@users.noreply.github.com>

aiida_common_workflows/workflows/relax/fleur/extractors.py

@@ -0,0 +1,51 @@
+# -*- coding: utf-8 -*-
+"""
+Collects some functions to postprocess a `FleurCommonRelaxWorkChain`.
+"""
+
+
+def get_ts_energy(common_relax_workchain):
+    """
+    Return the TS value of a concluded FleurCommonRelaxWorkChain.
+
+    T the fictitious temperature due to the presence of a smearing and S is
+    the entropy. The units must be eV.
+    In Fleur this contribution is directly available in the output parameters
+    of the Fleur calculation
+    """
+    from aiida.common import LinkType
+    from aiida.orm import WorkChainNode
+    from aiida.plugins import WorkflowFactory
+    from masci_tools.io.io_fleurxml import load_outxml
+    from masci_tools.util.constants import HTR_TO_EV
+    from masci_tools.util.schema_dict_util import evaluate_attribute
+
+    if not isinstance(common_relax_workchain, WorkChainNode):
+        return ValueError('The input is not a workchain (instance of `WorkChainNode`)')
+    if common_relax_workchain.process_class != WorkflowFactory('common_workflows.relax.fleur'):
+        return ValueError('The input workchain is not a `FleurCommonRelaxWorkChain`')
+
+    fleur_relax_wc = common_relax_workchain.get_outgoing(link_type=LinkType.CALL_WORK).one().node
+    fleur_calc_out = fleur_relax_wc.outputs.last_scf.last_calc
+
+    output_parameters = fleur_calc_out.output_parameters
+    ts = None  #pylint: disable=invalid-name
+    if 'ts_energy' in output_parameters.keys():
+        ts = output_parameters['ts_energy']  #pylint: disable=invalid-name
+    elif fleur_relax_wc.is_finished_ok:
+        #This check makes sure that the parsing worked before so we don't get
+        #nasty surprises in load_outxml
+
+        with fleur_calc_out.retrieved.open('out.xml', 'rb') as file:
+            xmltree, schema_dict = load_outxml(file)
+        try:
+            ts_all = evaluate_attribute(
+                xmltree, schema_dict, 'value', tag_name='tkbtimesentropy', iteration_path=True, list_return=True
+            )
+        except ValueError:
+            pass
+        else:
+            if ts_all:
+                ts = ts_all[-1] * HTR_TO_EV  #pylint: disable=invalid-name
+
+    return ts

aiida_common_workflows/workflows/relax/fleur/generator.py

@@ -31,6 +31,12 @@ class FleurCommonRelaxInputGenerator(CommonRelaxInputGenerator):
         },
         'precise': {
             'description': 'high level of accuracy'
+        },
+        'oxides_validation': {
+            'description': 'high level of accuracy. Used for validating oxide results for common-workflows'
+        },
+        'verification-pbe-v1': {
+            'description': 'high level of accuracy. Used for validating oxide results for common-workflows'
         }
     }
 
@@ -54,6 +60,9 @@ def define(cls, spec):
         spec.inputs['spin_type'].valid_type = ChoiceType((SpinType.NONE, SpinType.COLLINEAR))
         spec.inputs['relax_type'].valid_type = ChoiceType((RelaxType.NONE, RelaxType.POSITIONS))
         spec.inputs['electronic_type'].valid_type = ChoiceType((ElectronicType.METAL, ElectronicType.INSULATOR))
+        spec.inputs['protocol'].valid_type = ChoiceType(
+            ('fast', 'moderate', 'precise', 'oxides_validation', 'verification-pbe-v1')
+        )
         spec.input('engines.inpgen.code', valid_type=orm.Code, serializer=orm.load_code)
         spec.input('engines.inpgen.options', valid_type=dict, required=False)
         spec.inputs['engines']['relax']['code'].valid_type = CodeType('fleur.fleur')
@@ -138,8 +147,15 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
             raise ValueError(f'relaxation type `{relax_type.value}` is not supported')
 
         # We reduce the number of sigfigs for the cell and atom positions accounts for less
-        #  numerical inpgen errors during relaxation and accuracy is still enough for this purpose
-        settings = orm.Dict(dict={'significant_figures_cell': 9, 'significant_figures_position': 9})
+        # numerical inpgen errors during relaxation and accuracy is still enough for this purpose
+        # We also currently assume that all common-workflow protocols exist in fleur
+        settings = orm.Dict(
+            dict={
+                'significant_figures_cell': 9,
+                'significant_figures_position': 9,
+                'profile': protocol['inpgen-protocol']
+            }
+        )
 
         wf_para = orm.Dict(dict=wf_para_dict)
 
@@ -153,24 +169,30 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
                 'forcemix': 'straight'
             },
             'use_relax_xml': True,
-            'serial': False,
             'mode': relaxation_mode,
         }
         protocol_scf_para = protocol.get('scf', {})
-        kmax = protocol_scf_para.pop('k_max_cutoff', None)
+        kmax = protocol_scf_para.pop('k_max_cutoff', None)  # for now always None, later consider clean up
 
         if molecule:  # We want to use only one kpoint, can be overwritten by user input
             protocol_scf_para['kpoints_distance'] = 100000000
             # In addition we might want to use a different basis APW+LO?
 
         wf_para_scf_dict = recursive_merge(default_scf, protocol_scf_para)
-        wf_para_scf = orm.Dict(dict=wf_para_scf_dict)
 
         if reference_workchain is not None:
             parameters = get_parameters(reference_workchain)
+            if 'kpt' in parameters.get_dict():
+                wf_para_scf_dict.pop('kpoints_distance', None)
+                if protocol_scf_para.get('kpoints_force_gamma', False):
+                    parameters = parameters.get_dict()
+                    parameters['kpt']['gamma'] = True
+                    parameters = orm.Dict(dict=parameters)
+
+        wf_para_scf = orm.Dict(dict=wf_para_scf_dict)
 
         # User specification overrides previous workchain!
-        if 'calc_parameters' in kwargs.keys():
+        if 'calc_parameters' in kwargs:
             parameters = kwargs.pop('calc_parameters')
 
         parameters, structure = prepare_calc_parameters(parameters, spin_type, magnetization_per_site, structure, kmax)
@@ -298,7 +320,7 @@ def get_parameters(reference_workchain):
     # Be aware that this parameter node is incomplete. LOs and econfig is
     # currently missing for example, also we do not reuse the same kpoints.
     # the density is likely the same, but the set may vary.
-    parameters = fleurinp.get_parameterdata_ncf()  # This is not a calcfunction!
+    parameters = fleurinp.get_parameterdata_ncf(write_ids=False)  # This is not a calcfunction!
 
     return parameters
 

aiida_common_workflows/workflows/relax/fleur/protocol.yml

@@ -1,14 +1,13 @@
 moderate:
     name: 'moderate'
-    description: 'Protocol to relax a structure with normal precision at moderate computational cost.'
+    inpgen-protocol: 'moderate'
+    description: 'Protocol to relax a structure with normal precision at moderate computational cost. This relies on the "moderate" protocol of the fleur code.'
     relax:
         relax_iter: 5
         change_mixing_criterion: 0.025
         run_final_scf: true
     scf:
-        density_converged: 0.00002
         kpoints_distance: 0.2
-        k_max_cutoff: 4.0
         fleur_runmax: 2
         itmax_per_run: 120
         force_dict:
@@ -18,14 +17,13 @@ moderate:
 
 precise:
     name: 'precise'
-    description: 'Protocol to relax a structure with high precision at higher computational cost.'
+    inpgen-protocol: 'precise'
+    description: 'Protocol to relax a structure with high precision at higher computational cost. This relies on the "precise" protocol of the fleur code.'
     relax:
         relax_iter: 10
         change_mixing_criterion: 0.025
         run_final_scf: true
     scf:
-        density_converged: 0.000002
-        k_max_cutoff: 5.0
         kpoints_distance: 0.1
         fleur_runmax: 3
         itmax_per_run: 120
@@ -36,19 +34,53 @@ precise:
 
 fast:
     name: 'fast'
-    description: 'Protocol to relax a structure with low precision at minimal computational cost for testing purposes.'
+    inpgen-protocol: 'fast'
+    description: 'Protocol to relax a structure with low precision at minimal computational cost for testing purposes. This relies on the "fast" protocol of the fleur code.'
     relax:
         relax_iter: 3
         change_mixing_criterion: 0.025
         run_final_scf: true
     scf:
         fleur_runmax: 2
         itmax_per_run: 120
-        force_converged: 0.001
-        density_converged: 0.0002
-        k_max_cutoff: 3.2
         kpoints_distance: 0.4
         force_dict:
             qfix: 2
             forcealpha: 1.0
             forcemix: 'straight'
+
+oxides_validation:
+    name: 'oxides_validation'
+    inpgen-protocol: 'oxides_validation'
+    description: 'Protocol to relax a structure with high precision at higher computational cost. This relies on the "precise" protocol of the fleur code.'
+    relax:
+        relax_iter: 10
+        change_mixing_criterion: 0.025
+        run_final_scf: true
+    scf:
+        kpoints_distance: 0.1
+        kpoints_force_gamma: true
+        fleur_runmax: 3
+        itmax_per_run: 120
+        force_dict:
+            qfix: 2
+            forcealpha: 0.50
+            forcemix: 'straight'
+
+verification-pbe-v1:
+    name: 'verification-pbe-v1'
+    inpgen-protocol: 'oxides_validation'
+    description: 'Protocol to relax a structure with high precision at higher computational cost. This relies on the "oxides_validation" protocol of the fleur code.'
+    relax:
+        relax_iter: 10
+        change_mixing_criterion: 0.025
+        run_final_scf: true
+    scf:
+        kpoints_distance: 0.06
+        kpoints_force_gamma: true
+        fleur_runmax: 3
+        itmax_per_run: 120
+        force_dict:
+            qfix: 2
+            forcealpha: 0.50
+            forcemix: 'straight'

aiida_common_workflows/workflows/relax/fleur/workchain.py

@@ -47,6 +47,9 @@ def convert_outputs(self):
         if 'optimized_structure' in outputs:
             self.out('relaxed_structure', outputs.optimized_structure)
 
+        if 'last_scf' in outputs:
+            self.out('remote_folder', outputs.last_scf.last_calc.remote_folder)
+
         output_parameters = outputs.output_relax_wc_para
         out_para_dict = output_parameters.get_dict()
         if 'total_magnetic_moment_cell' in out_para_dict:

setup.json

@@ -21,7 +21,7 @@
         "aiida-castep>=1.2.0a5",
         "aiida-core[atomic_tools]~=1.6",
         "aiida-cp2k~=1.3",
-        "aiida-fleur>=1.1.4",
+        "aiida-fleur>=1.3.0",
         "aiida-gaussian",
         "aiida-nwchem>=2.1.0",
         "aiida-orca",
@@ -32,7 +32,8 @@
         "pymatgen<=2021.3.3",
         "sqlalchemy<1.4",
         "ase!=3.20.*",
-        "pint~=0.16"
+        "pint~=0.16",
+        "masci-tools~=0.9"
     ],
     "extras_require": {
         "docs": [