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Add support for PseudoDojo PAW pseudos (alternative) #42

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merged 4 commits into from
Jan 13, 2021
Merged

Add support for PseudoDojo PAW pseudos (alternative) #42

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99e3a66
Add support for PseudoDojo PAW pseudos (alternative)
zooks97 Dec 17, 2020
a672dc7
Set unknown cutoffs to 2 * max(cutoffs) of the stringency
zooks97 Dec 18, 2020
699a49d
Restrict checks to PAW configurations, check only , modify warning me…
zooks97 Dec 18, 2020
0ce2390
Set missing wfc cutoffs in PD PAW families to 1.5 * the maximum cutof…
zooks97 Jan 13, 2021
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32 changes: 32 additions & 0 deletions aiida_pseudo/cli/install.py
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Original file line number Diff line number Diff line change
Expand Up @@ -180,6 +180,15 @@ def cmd_install_pseudo_dojo(version, functional, relativistic, protocol, pseudo_
'upf': UpfData,
}

# yapf: disable
paw_configurations = (
PseudoDojoConfiguration('1.0', 'PBE', 'SR', 'standard', 'jthxml'),
PseudoDojoConfiguration('1.0', 'PBE', 'SR', 'stringent', 'jthxml'),
PseudoDojoConfiguration('1.0', 'LDA', 'SR', 'standard', 'jthxml'),
PseudoDojoConfiguration('1.0', 'LDA', 'SR', 'stringent', 'jthxml')
)
# yapf: enable

try:
pseudo_type = pseudo_type_mapping[pseudo_format]
except KeyError:
Expand Down Expand Up @@ -231,6 +240,29 @@ def cmd_install_pseudo_dojo(version, functional, relativistic, protocol, pseudo_
msg = f'md5 of pseudo for element {element} does not match that of the metadata {md5}'
echo.echo_critical(msg)

# The PAW configurations have missing cutoffs for the Lanthanides, which have ben replaced with a placeholder
# value of `-1`. We replace these with the 1.5 * the maximum cutoff from the same stringency so that these
# potentials are still usable, but this should be taken as a _rough_ approximation.
# We check only the `cutoff_wfc` because `cutoff_rho` is not provided by PseudoDojo and is therefore
# locally calculated in `PseudoDojoFamily.parse_djrepos_from_archive` as `2.0 * cutoff_wfc` for PAW.
if configuration in paw_configurations:
adjusted_cutoffs = {}
for stringency, str_cutoffs in cutoffs.items():
adjusted_cutoffs[stringency] = []
max_cutoff_wfc = max([str_cutoffs[element]['cutoff_wfc'] for element in str_cutoffs])
filler_cutoff_wfc = max_cutoff_wfc * 1.5
for element, cutoff in str_cutoffs.items():
if cutoff['cutoff_wfc'] <= 0:
cutoffs[stringency][element]['cutoff_wfc'] = filler_cutoff_wfc
cutoffs[stringency][element]['cutoff_rho'] = 2.0 * filler_cutoff_wfc
adjusted_cutoffs[stringency].append(element)

for stringency, elements in adjusted_cutoffs.items():
msg = f'stringency `{stringency}` has missing recommended cutoffs for elements ' \
f'{", ".join(elements)}: as a substitute, 1.5 * the maximum cutoff of the stringency ' \
'was set for these elements. USE WITH CAUTION!'
echo.echo_warning(msg)

family.description = description
family.set_cutoffs(cutoffs, default_stringency=default_stringency)

Expand Down
10 changes: 5 additions & 5 deletions aiida_pseudo/groups/family/pseudo_dojo.py
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Expand Up @@ -66,10 +66,10 @@ class PseudoDojoFamily(RecommendedCutoffMixin, PseudoPotentialFamily):
PseudoDojoConfiguration('0.4', 'PBE', 'FR', 'stringent', 'psml'),
PseudoDojoConfiguration('0.4', 'PBEsol', 'FR', 'standard', 'psml'),
PseudoDojoConfiguration('0.4', 'PBEsol', 'FR', 'stringent', 'psml'),
# PseudoDojoConfiguration('1.0', 'PBE', 'SR', 'standard', 'jthxml'), # paw families have placeholder cutoffs
# PseudoDojoConfiguration('1.0', 'PBE', 'SR', 'stringent', 'jthxml'),
# PseudoDojoConfiguration('1.0', 'LDA', 'SR', 'standard', 'jthxml'),
# PseudoDojoConfiguration('1.0', 'LDA', 'SR', 'stringent', 'jthxml')
PseudoDojoConfiguration('1.0', 'PBE', 'SR', 'standard', 'jthxml'),
PseudoDojoConfiguration('1.0', 'PBE', 'SR', 'stringent', 'jthxml'),
PseudoDojoConfiguration('1.0', 'LDA', 'SR', 'standard', 'jthxml'),
PseudoDojoConfiguration('1.0', 'LDA', 'SR', 'stringent', 'jthxml')
)
# yapf: enable

Expand Down Expand Up @@ -206,7 +206,7 @@ def get_cutoffs_from_djrepo(cls, djrepo, pseudo_type):
:returns: cutoffs dictionary (in eV) where keys are stringency levels and values are
{'cutoff_wfc': ..., 'cutoff_rho': ...}
"""
dual_mapping = {UpfData: 8.0, Psp8Data: 8.0, PsmlData: 8.0, JthXmlData: 2.0}
dual_mapping = {UpfData: 4.0, Psp8Data: 4.0, PsmlData: 4.0, JthXmlData: 2.0}

try:
dual = dual_mapping[pseudo_type]
Expand Down