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Allow to switch off print of ChemEnv citation #2448

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merged 4 commits into from
Feb 24, 2022
Merged

Allow to switch off print of ChemEnv citation #2448

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8e8380c
allow to switch off ChemEnv citation
JaGeo Feb 24, 2022
817eb99
Reformat
JaGeo Feb 24, 2022
5b4c154
Change default for printing citation in ChemEnv tool
JaGeo Feb 24, 2022
1217240
Fix logic error
JaGeo Feb 24, 2022
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19 changes: 15 additions & 4 deletions pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,10 @@
"Statistical analysis of coordination environments in oxides",
Chem. Mater., 2017, 29 (19), pp 8346–8360,
DOI: 10.1021/acs.chemmater.7b02766
D. Waroquiers, J. George, M. Horton, S. Schenk, K. A. Persson, G.-M. Rignanese, X. Gonze, G. Hautier
"ChemEnv: a fast and robust coordination environment identification tool",
Acta Cryst. B 2020, 76, pp 683–695,
DOI: 10.1107/S2052520620007994
"""

__author__ = "David Waroquiers"
Expand Down Expand Up @@ -376,12 +380,18 @@ def __init__(
debug_level=None,
plane_safe_permutations=False,
only_symbols=None,
print_citation=False,
):
"""
Constructor for the LocalGeometryFinder, initializes the list of coordination geometries
:param permutations_safe_override: If set to True, all permutations are tested (very time-consuming for large

Args:
permutations_safe_override: If set to True, all permutations are tested (very time-consuming for large
coordination numbers!)
:param plane_ordering_override: If set to False, the ordering of the points in the plane is disabled
plane_ordering_override: If set to False, the ordering of the points in the plane is disabled
debug_level: decides the level of debugging
permutations_safe_override: Whether to use safe permutations.
only_symbols: Whether to restrict the list of environments to be identified.
print_citation: If True, the ChemEnv citation will be printed
"""
self.allcg = AllCoordinationGeometries(
permutations_safe_override=permutations_safe_override,
Expand All @@ -396,7 +406,8 @@ def __init__(
bva_distance_scale_factor=None,
structure_refinement=self.STRUCTURE_REFINEMENT_NONE,
)
print(chemenv_citations())
if print_citation:
print(chemenv_citations())

def setup_parameters(
self,
Expand Down
1 change: 1 addition & 0 deletions ...gen/analysis/chemenv/coordination_environments/tests/test_coordination_geometry_finder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@ def setUp(self):
centering_type="standard",
structure_refinement=self.lgf.STRUCTURE_REFINEMENT_NONE,
)
self.lgf2 = LocalGeometryFinder(print_citation=True)

# self.strategies = [SimplestChemenvStrategy(), SimpleAbundanceChemenvStrategy()]

Expand Down
9 changes: 7 additions & 2 deletions pymatgen/analysis/chemenv/utils/defs_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,16 @@
)

STATS_ENV_PAPER = (
"David Waroquiers, Xavier Gonze, Gian-Marco Rignanese, Cathrin Welker-Nieuwoudt, Frank Rosowski,\n"
"Michael Goebel, Stephan Schenk, Peter Degelmann, Rute Andre, Robert Glaum, and Geoffroy Hautier,\n"
"D. Waroquiers, X. Gonze, G.-M. Rignanese, C. Welker-Nieuwoudt, F. Rosowski,\n"
"M. Goebel, S. Schenk, P. Degelmann, R. Andre, R. Glaum, and G. Hautier,\n"
'"Statistical analysis of coordination environments in oxides",\n'
"Chem. Mater., 2017, 29 (19), pp 8346-8360,\n"
"DOI: 10.1021/acs.chemmater.7b02766\n"
"\n"
"D. Waroquiers, J. George, M. Horton, S. Schenk, K. A. Persson, G.-M. Rignanese, X. Gonze, G. Hautier,\n"
'"ChemEnv: a fast and robust coordination environment identification tool",\n'
"Acta Cryst. B 2020, 76, pp 683–695\n."
"DOI: 10.1107/S2052520620007994\n"
)


Expand Down