diff --git a/pyproject.toml b/pyproject.toml index db6f4b52ee6..cc7ff402087 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -107,7 +107,7 @@ optional = [ "hiphive>=1.3.1", "jarvis-tools>=2020.7.14", "matplotlib>=3.8", - "phonopy>=2.23", + "phonopy>=2.33.3", "seekpath>=2.0.1", ] # tblite only support Python 3.12+ through conda-forge diff --git a/src/pymatgen/command_line/OxideTersoffPotentials b/src/pymatgen/command_line/OxideTersoffPotentials deleted file mode 100644 index 8f3b1522751..00000000000 --- a/src/pymatgen/command_line/OxideTersoffPotentials +++ /dev/null @@ -1,132 +0,0 @@ -H(1) O H 1.8858 2.188184 1.12768 10.0000 -Li(1) O Li 0.98816 1.937984 1.94001 10.0000 -Be(2) O Be 2.76882 1.848429 1.52217 10.0000 -B(3) O B 2.38924 2.597403 1.34003 10.0000 -C(4) O C 4.79187 2.237136 1.20089 10.0000 -C(2) O C 2.40553 2.409639 1.03098 10.0000 -N(5) O N 6.27677 2.222222 1.16142 10.0000 -N(3) O N 3.81089 2.232143 1.13758 10.0000 -NH4(1) O NH4 0.40537 2.262443 2.45364 10.0000 -Na(1) O Na 0.57523 2.074689 2.37433 10.0000 -Mg(2) O Mg 1.57554 1.953125 1.95627 10.0000 -Al(3) O Al 1.80346 2.358491 1.75806 10.0000 -Si(4) O Si 2.8572 2.314815 1.53594 10.0000 -P(5) O P 3.89635 2.28833 1.44066 10.0000 -P(3) O P 2.02062 2.487562 1.41051 10.0000 -S(6) O S 4.96726 2.267574 1.38102 10.0000 -S(4) O S 3.03672 2.34192 1.41188 10.0000 -Cl(7) O Cl 5.991 2.257336 1.34801 10.0000 -Cl(5) O Cl 4.29089 2.247191 1.35653 10.0000 -Cl(3) O Cl 3.07119 2.03666 1.38441 10.0000 -K(1) O K 0.34985 2.293578 2.76636 10.0000 -Ca(2) O Ca 0.99429 2.10084 2.32032 10.0000 -Sc(3) O Sc 2.1561 2.024291 1.99615 10.0000 -Ti(4) O Ti 2.81333 1.988072 1.83144 10.0000 -Ti(3) O Ti 1.97851 2.173913 1.88619 10.0000 -V(5) O V 3.69533 1.960784 1.60258 10.0000 -V(4) O V 2.08047 2.347418 1.77638 10.0000 -V(3) O V 1.82936 2.277904 1.85797 10.0000 -Cr(6) O Cr 3.68751 2.10084 1.53251 10.0000 -Cr(5) O Cr 2.36551 2.487562 1.55546 10.0000 -Cr(4) O Cr 1.93329 2.444988 1.76209 10.0000 -Cr(3) O Cr 1.77335 2.325581 1.83887 10.0000 -Mn(7) O Mn 4.9163 1.923077 1.48171 10.0000 -Mn(6) O Mn 2.82236 2.403846 1.52931 10.0000 -Mn(5) O Mn 2.46456 2.421308 1.57577 10.0000 -Mn(4) O Mn 1.85886 2.487562 1.77045 10.0000 -Mn(3) O Mn 1.81283 2.28833 1.85786 10.0000 -Mn(2) O Mn 1.64143 2.079002 2.02969 10.0000 -Fe(4) O Fe 1.87285 2.439024 1.82786 10.0000 -Fe(3) O Fe 1.66681 2.380952 1.86647 10.0000 -Fe(2) O Fe 1.69269 2.083333 1.96005 10.0000 -Ni(3) O Ni 1.66191 2.415459 1.81887 10.0000 -Ni(2) O Ni 1.46841 2.257336 1.92452 10.0000 -Co(3) O Co 1.87024 2.304147 1.7762 10.0000 -Co(2) O Co 1.51476 2.217295 1.93362 10.0000 -Cu(3) O Cu 1.88242 2.34192 1.70823 10.0000 -Cu(2) O Cu 1.85341 2.227171 1.56633 10.0000 -Cu(1) O Cu 0.66417 2.932551 1.78269 10.0000 -Zn(2) O Zn 1.24031 2.48139 1.88557 10.0000 -Ga(3) O Ga 1.18456 2.680965 1.79391 10.0000 -Ge(4) O Ge 1.91375 2.525253 1.66872 10.0000 -As(5) O As 2.71934 2.43309 1.58127 10.0000 -As(3) O As 1.51493 2.475248 1.64554 10.0000 -Se(6) O Se 3.44865 2.403846 1.53287 10.0000 -Se(4) O Se 2.38082 2.34192 1.55957 10.0000 -Br(7) O Br 4.24339 2.364066 1.50274 10.0000 -Rb(1) O Rb 0.26813 2.421308 2.89683 10.0000 -Sr(2) O Sr 0.74351 2.197802 2.53589 10.0000 -Y(3) O Y 1.62701 2.09205 2.21523 10.0000 -Zr(4) O Zr 2.19103 2.040816 1.99602 10.0000 -Nb(5) O Nb 2.72326 2.008032 1.85459 10.0000 -Nb(4) O Nb 2.7096 1.901141 1.85989 10.0000 -Nb(3) O Nb 2.02848 1.996008 1.9519 10.0000 -Mo(6) O Mo 1.9915 2.557545 1.71254 10.0000 -Mo(5) O Mo 2.64802 2.074689 1.7867 10.0000 -Mo(4) O Mo 3.10807 1.779359 1.85099 10.0000 -Mo(3) O Mo 1.42826 2.392344 1.92974 10.0000 -Ru(6) O Ru 2.42109 2.352941 1.66431 10.0000 -Ru(5) O Ru 2.13208 2.293578 1.81571 10.0000 -Ru(4) O Ru 1.99513 2.227171 1.84053 10.0000 -Rh(4) O Rh 1.62725 2.48139 1.81793 10.0000 -Rh(3) O Rh 1.92826 2.09205 1.86915 10.0000 -Pd(4) O Pd 2.04218 2.227171 1.79813 10.0000 -Pd(2) O Pd 1.7391 2.008032 1.83671 10.0000 -Ag(1) O Ag 0.63519 2.538071 2.22578 10.0000 -Cd(2) O Cd 0.98346 2.457002 2.1694 10.0000 -Ta(4) O Ta 2.75655 1.831502 1.79826 10.0000 -In(3) O In 0.84076 2.832861 2.02471 10.0000 -Sn(4) O Sn 1.35268 2.638522 1.93422 10.0000 -Sn(2) O Sn 0.97261 2.183406 1.9642 10.0000 -Sb(5) O Sb 1.95523 2.5 1.86318 10.0000 -Sb(3) O Sb 1.17786 2.364066 2.07526 10.0000 -I(7) O I 3.21424 2.386635 1.74105 10.0000 -I(5) O I 2.48947 2.358491 1.64421 10.0000 -Te(6) O Te 2.56406 2.427184 1.80876 10.0000 -Te(4) O Te 1.67169 2.493766 1.75208 10.0000 -Cs(1) O Cs 0.23307 2.386635 3.13121 10.0000 -Ba(2) O Ba 0.57994 2.28833 2.73769 10.0000 -La(3) O La 1.18587 2.217295 2.46989 10.0000 -Ce(4) O Ce 1.48412 2.257336 2.19872 10.0000 -Ce(3) O Ce 1.22048 2.227171 2.37861 10.0000 -Pr(3) O Pr 1.17041 2.277904 2.37113 10.0000 -Nd(3) O Nd 1.13205 2.336449 2.33016 10.0000 -Sm(3) O Sm 1.17622 2.309469 2.29536 10.0000 -Eu(3) O Eu 1.19545 2.304147 2.26888 10.0000 -Eu(2) O Eu 1.13032 2.024291 2.53846 10.0000 -Gd(3) O Gd 1.09161 2.409639 2.2719 10.0000 -Tb(4) O Tb 1.70132 2.024291 2.38506 10.0000 -Tb(3) O Tb 1.20764 2.309469 2.23563 10.0000 -Dy(3) O Dy 1.1735 2.347418 2.22689 10.0000 -Ho(3) O Ho 1.12157 2.409639 2.21122 10.0000 -Er(3) O Er 1.12394 2.427184 2.17477 10.0000 -Tm(3) O Tm 1.18138 2.375297 2.16042 10.0000 -Yb(3) O Yb 1.21989 2.347418 2.1422 10.0000 -Lu(3) O Lu 1.19488 2.375297 2.136 10.0000 -Hf(4) O Hf 1.89992 2.09205 1.99964 10.0000 -Ta(5) O Ta 2.36669 2.057613 1.85532 10.0000 -W(6) O W 1.84267 2.493766 1.77713 10.0000 -W(5) O W 2.6157 2.008032 1.76261 10.0000 -W(4) O W 2.47114 1.923077 1.81945 10.0000 -Re(7) O Re 3.55593 1.968504 1.59634 10.0000 -Re(6) O Re 2.95099 2.008032 1.71147 10.0000 -Re(5) O Re 2.41099 2.087683 1.76914 10.0000 -Re(3) O Re 0.81067 2.493766 2.33218 10.0000 -Os(8) O Os 3.71019 1.953125 1.66146 10.0000 -Os(7) O Os 2.91948 2.087683 1.72869 10.0000 -Os(6) O Os 2.44871 2.159827 1.7828 10.0000 -Os(4) O Os 2.27524 2.008032 1.81244 10.0000 -Ir(5) O Ir 2.32476 2.087683 1.83476 10.0000 -Ir(4) O Ir 1.68667 2.293578 1.87402 10.0000 -Pt(4) O Pt 2.03825 2.087683 1.87174 10.0000 -Pt(2) O Pt 2.14999 1.74216 1.80179 10.0000 -Au(3) O Au 1.96967 2.008032 1.81312 10.0000 -Au(1) O Au 0.85304 2.267574 1.89543 10.0000 -Hg(2) O Hg 1.12852 2.150538 2.25275 10.0000 -Hg(1) O Hg 0.73931 2.150538 2.43155 10.0000 -Tl(3) O Tl 0.67637 2.95858 2.10642 10.0000 -Tl(1) O Tl 0.34999 2.070393 2.77086 10.0000 -Pb(4) O Pb 1.02719 2.824859 2.02857 10.0000 -Pb(2) O Pb 0.63833 2.309469 2.44191 10.0000 -Bi(5) O Bi 1.4405 2.695418 1.98599 10.0000 -Bi(3) O Bi 0.97904 2.415459 2.18321 10.0000 diff --git a/src/pymatgen/command_line/bush.lib b/src/pymatgen/command_line/bush.lib deleted file mode 100644 index 1d9ef873bc8..00000000000 --- a/src/pymatgen/command_line/bush.lib +++ /dev/null @@ -1,79 +0,0 @@ -# -# BUSH -library of potentials for GULP -# -# from T.S.Bush, J.D.Gale, C.R.A.Catlow and P.D. Battle -# J. Mater Chem., 4, 831-837 (1994) -# -species -Li core 1.000 -Na core 1.000 -K core 1.000 -Mg core 1.580 -Mg shel 0.420 -Ca core 0.719 -Ca shel 1.281 -Sr core 0.169 -Sr shel 1.831 -Ba core 0.169 -Ba shel 1.831 -Fe core 1.971 -Fe shel 1.029 -Ti core 2.332 -Ti shel 1.668 -Al core 0.043 -Al shel 2.957 -Ga core 3.000 -Y core 3.000 -La core 5.149 -La shel -2.149 -Pr core 1.678 -Pr shel 1.322 -Nd core 1.678 -Nd shel 1.322 -Gd core -0.973 -Gd shel 3.973 -Eu core -0.991 -Eu shel 3.991 -Tb core -0.972 -Tb shel 3.972 -Yb core -0.278 -Yb shel 3.278 -O core 0.513 -O shel -2.513 -buckingham -Li core O shel 426.480 0.3000 0.00 0.0 10.0 -Na core O shel 1271.504 0.3000 0.00 0.0 10.0 -K core O shel 3587.570 0.3000 0.00 0.0 10.0 -Mg shel O shel 2457.243 0.2610 0.00 0.0 10.0 -Ca shel O shel 2272.741 0.2986 0.00 0.0 10.0 -Sr shel O shel 1956.702 0.3252 0.00 0.0 10.0 -Ba shel O shel 4818.416 0.3067 0.00 0.0 10.0 -Fe shel O shel 3219.335 0.2641 0.00 0.0 10.0 -Ti shel O shel 2088.107 0.2888 0.00 0.0 10.0 -Al shel O shel 2409.505 0.2649 0.00 0.0 10.0 -Ga core O shel 2339.776 0.2742 0.00 0.0 10.0 -Y core O shel 1519.279 0.3291 0.00 0.0 10.0 -La shel O shel 5436.827 0.2939 0.00 0.0 10.0 -Pr shel O shel 13431.118 0.2557 0.00 0.0 10.0 -Nd shel O shel 13084.217 0.2550 0.00 0.0 10.0 -Gd shel O shel 866.339 0.3770 0.00 0.0 10.0 -Eu shel O shel 847.868 0.3791 0.00 0.0 10.0 -Tb shel O shel 845.137 0.3750 0.00 0.0 10.0 -Yb shel O shel 991.029 0.3515 0.00 0.0 10.0 -O shel O shel 25.410 0.6937 32.32 0.0 12.0 -spring -Mg 349.95 -Ca 34.05 -Sr 21.53 -Ba 34.05 -Fe 179.58 -Ti 253.60 -Al 403.98 -La 173.90 -Pr 302.36 -Nd 302.35 -Gd 299.96 -Eu 304.92 -Tb 299.98 -Yb 308.91 -O 20.53 diff --git a/src/pymatgen/command_line/critic2_caller.py b/src/pymatgen/command_line/critic2_caller.py index 4769e715860..2e57258300b 100644 --- a/src/pymatgen/command_line/critic2_caller.py +++ b/src/pymatgen/command_line/critic2_caller.py @@ -766,7 +766,7 @@ def get_volume_and_charge(nonequiv_idx): def _parse_stdout(self, stdout): warnings.warn( "Parsing critic2 standard output is deprecated and will not be maintained, " - "please use the native JSON output in future.", + "please use the native JSON output in the future.", DeprecationWarning, stacklevel=2, ) diff --git a/src/pymatgen/command_line/gulp_caller.py b/src/pymatgen/command_line/gulp_caller.py index 4d7bb3b17e0..eeeed9b0bc2 100644 --- a/src/pymatgen/command_line/gulp_caller.py +++ b/src/pymatgen/command_line/gulp_caller.py @@ -23,10 +23,8 @@ __status__ = "Production" __date__ = "Jun 22, 2013M" -MODULE_DIR = os.path.dirname(os.path.abspath(__file__)) - -_anions = set(map(Element, ["O", "S", "F", "Cl", "Br", "N", "P"])) -_cations = set( +_ANIONS = set(map(Element, ["O", "S", "F", "Cl", "Br", "N", "P"])) +_CATIONS = set( map( Element, [ @@ -92,144 +90,6 @@ ], ) ) -_gulp_kw = { - # Control of calculation type - "angle", - "bond", - "cosmo", - "cosmic", - "cost", - "defect", - "distance", - "eem", - "efg", - "fit", - "free_energy", - "gasteiger", - "genetic", - "gradients", - "md", - "montecarlo", - "noautobond", - "noenergy", - "optimise", - "pot", - "predict", - "preserve_Q", - "property", - "phonon", - "qeq", - "qbond", - "single", - "sm", - "static_first", - "torsion", - "transition_state", - # Geometric variable specification - "breathe", - "bulk_noopt", - "cellonly", - "conp", - "conv", - "isotropic", - "orthorhombic", - "nobreathe", - "noflgs", - "shell", - "unfix", - # Algorithm - "c6", - "dipole", - "fbfgs", - "fix_molecule", - "full", - "hill", - "kfull", - "marvinSE", - "madelung", - "minimum_image", - "molecule", - "molmec", - "molq", - "newda", - "noanisotropic_2b", - "nod2sym", - "nodsymmetry", - "noelectrostatics", - "noexclude", - "nofcentral", - "nofirst_point", - "noksymmetry", - "nolist_md", - "nomcediff", - "nonanal", - "noquicksearch", - "noreal", - "norecip", - "norepulsive", - "nosasinitevery", - "nosderv", - "nozeropt", - "numerical", - "qiter", - "qok", - "spatial", - "storevectors", - "nomolecularinternalke", - "voigt", - "zsisa", - # Optimization method - "conjugate", - "dfp", - "lbfgs", - "numdiag", - "positive", - "rfo", - "unit", - # Output control - "average", - "broaden_dos", - "cartesian", - "compare", - "conserved", - "dcharge", - "dynamical_matrix", - "eigenvectors", - "global", - "hessian", - "hexagonal", - "intensity", - "linmin", - "meanke", - "nodensity_out", - "nodpsym", - "nofrequency", - "nokpoints", - "operators", - "outcon", - "prt_eam", - "prt_two", - "prt_regi_before", - "qsas", - "restore", - "save", - "terse", - # Structure control - "lower_symmetry", - "nosymmetry", - # PDF control - "PDF", - "PDFcut", - "PDFbelow", - "PDFkeep", - "coreinfo", - "nowidth", - "nopartial", - # Miscellaneous - "nomodcoord", - "oldunits", - "zero_potential", -} class GulpIO: @@ -243,8 +103,6 @@ def keyword_line(*args): Args: args: 1st line keywords """ - # if len(list(filter(lambda x: x in _gulp_kw, args))) != len(args): - # raise GulpError("Wrong keywords given") gin = " ".join(args) gin += "\n" return gin @@ -300,7 +158,7 @@ def structure_lines( specie = site.specie core_site_desc = f"{specie.symbol} core {' '.join(coord)}\n" gin += core_site_desc - if (specie in _anions and anion_shell_flg) or (specie in _cations and cation_shell_flg): + if (specie in _ANIONS and anion_shell_flg) or (specie in _CATIONS and cation_shell_flg): shel_site_desc = f"{specie.symbol} shel {' '.join(coord)}\n" gin += shel_site_desc else: @@ -785,7 +643,7 @@ def __str__(self): class BuckinghamPotential: - """Generate the Buckingham Potential Table from the bush.lib and lewis.lib. + """Generate the Buckingham Potential Table from the bush.lib or lewis.lib. Ref: T.S.Bush, J.D.Gale, C.R.A.Catlow and P.D. Battle, J. Mater Chem., @@ -794,15 +652,16 @@ class BuckinghamPotential: 1149-1161 (1985) """ - def __init__(self, bush_lewis_flag): + def __init__(self, bush_lewis_flag, pot_file): """ Args: bush_lewis_flag (str): Flag for using Bush or Lewis potential. + pot_file: The potential file, either bush.lib or lewis.lib. """ if bush_lewis_flag not in {"bush", "lewis"}: raise ValueError(f"bush_lewis_flag should be bush or lewis, got {bush_lewis_flag}") - pot_file = "bush.lib" if bush_lewis_flag == "bush" else "lewis.lib" - with open(os.path.join(os.environ["GULP_LIB"], pot_file)) as file: + + with open(pot_file) as file: # In lewis.lib there is no shell for cation species_dict, pot_dict, spring_dict = {}, {}, {} sp_flg, pot_flg, spring_flg = False, False, False @@ -867,9 +726,9 @@ def __init__(self, bush_lewis_flag): class TersoffPotential: """Generate Tersoff Potential Table from "OxideTersoffPotentialentials" file.""" - def __init__(self): + def __init__(self, pot_file): """Init TersoffPotential.""" - with open(f"{MODULE_DIR}/OxideTersoffPotentials") as file: + with open(pot_file) as file: data = {} for row in file: metaloxi = row.split()[0] diff --git a/src/pymatgen/command_line/lewis.lib b/src/pymatgen/command_line/lewis.lib deleted file mode 100644 index 4bc13293b90..00000000000 --- a/src/pymatgen/command_line/lewis.lib +++ /dev/null @@ -1,86 +0,0 @@ -# -# LEWIS library - collection of potentials based -# around the Catlow oxygen-oxygen potential -# -# Taken from Tables 1 and 2 of Lewis and Catlow. -# Potentials derived using method (a) Extrapolation -# for systems with limited data - fit rho as being -# common to all related oxides and only fit A for -# each system (b) fitting of both A and rho where -# structures are of low symmetry. -# -# Reference: -# (1) G.V. Lewis and C.R.A. Catlow, J. Phys. C: Solid -# State Phys., 18, 1149-1161 (1985) -# -species -# Table 1 species -Ca_2+ core 2.00000 -Sc_2+ core 2.00000 -Ti_2+ core 2.00000 -V_2+ core 2.00000 -Cr_2+ core 2.00000 -Mn_2+ core 2.00000 -Fe_2+ core 2.00000 -Co_2+ core 2.00000 -Ni_2+ core 2.00000 -Zn_2+ core 2.00000 -Zr_4+ core 4.00000 -Cd_2+ core 2.00000 -Hf_4+ core 4.00000 -Ce_4+ core 4.00000 -Eu_2+ core 2.00000 -Tb_4+ core 4.00000 -Th_4+ core 4.00000 -U_4+ core 4.00000 -# Table 2 species -Sc_3+ core 3.00000 -Mn_3+ core 3.00000 -Y_3+ core 3.00000 -La_3+ core 3.00000 -Nd_3+ core 3.00000 -Eu_3+ core 3.00000 -Gd_3+ core 3.00000 -Ho_3+ core 3.00000 -Yb_3+ core 3.00000 -Lu_3+ core 3.00000 -Pu_3+ core 3.00000 -# Oxygen -O core 0.86902 -O shel -2.86902 -buckingham -# Table 1 potentials -Ca_2+ core O shel 1227.7 0.33720 0.00000 0.0 10.0 -Sc_2+ core O shel 838.6 0.33720 0.00000 0.0 10.0 -Ti_2+ core O shel 633.3 0.33720 0.00000 0.0 10.0 -V_2+ core O shel 557.8 0.33720 0.00000 0.0 10.0 -Cr_2+ core O shel 619.8 0.33720 0.00000 0.0 10.0 -Mn_2+ core O shel 832.7 0.33720 0.00000 0.0 10.0 -Fe_2+ core O shel 725.7 0.33720 0.00000 0.0 10.0 -Co_2+ core O shel 684.9 0.33720 0.00000 0.0 10.0 -Ni_2+ core O shel 641.2 0.33720 0.00000 0.0 10.0 -Zn_2+ core O shel 700.3 0.33720 0.00000 0.0 10.0 -Zr_4+ core O shel 1453.8 0.35000 0.00000 0.0 10.0 -Cd_2+ core O shel 868.3 0.35000 0.00000 0.0 10.0 -Hf_4+ core O shel 1454.6 0.35000 0.00000 0.0 10.0 -Ce_4+ core O shel 1017.4 0.39490 0.00000 0.0 10.0 -Eu_2+ core O shel 665.2 0.39490 0.00000 0.0 10.0 -Tb_4+ core O shel 905.3 0.39490 0.00000 0.0 10.0 -Th_4+ core O shel 1144.6 0.39490 0.00000 0.0 10.0 -U_4+ core O shel 1055.0 0.39490 0.00000 0.0 10.0 -# Table 1 potentials -Sc_3+ core O shel 1299.4 0.33120 0.00000 0.0 10.0 -Mn_3+ core O shel 1257.9 0.32140 0.00000 0.0 10.0 -Y_3+ core O shel 1345.1 0.34910 0.00000 0.0 10.0 -La_3+ core O shel 1439.7 0.36510 0.00000 0.0 10.0 -Nd_3+ core O shel 1379.9 0.36010 0.00000 0.0 10.0 -Eu_3+ core O shel 1358.0 0.35560 0.00000 0.0 10.0 -Gd_3+ core O shel 1336.8 0.35510 0.00000 0.0 10.0 -Ho_3+ core O shel 1350.2 0.34870 0.00000 0.0 10.0 -Yb_3+ core O shel 1309.6 0.34620 0.00000 0.0 10.0 -Lu_3+ core O shel 1347.1 0.34300 0.00000 0.0 10.0 -Pu_3+ core O shel 1376.2 0.35930 0.00000 0.0 10.0 -# Oxygen-oxygen potential -O shel O shel 22764.0 0.14900 27.87900 0.0 12.0 -spring -O 74.92 diff --git a/src/pymatgen/entries/compatibility.py b/src/pymatgen/entries/compatibility.py index 09770153e15..6833dd0e15b 100644 --- a/src/pymatgen/entries/compatibility.py +++ b/src/pymatgen/entries/compatibility.py @@ -913,7 +913,6 @@ def __init__( correct_peroxide: Specify whether peroxide/superoxide/ozonide corrections are to be applied or not. check_potcar_hash (bool): Use potcar hash to verify potcars are correct. - silence_deprecation (bool): Silence deprecation warning. Defaults to False. """ self.compat_type = compat_type self.correct_peroxide = correct_peroxide diff --git a/src/pymatgen/io/feff/inputs.py b/src/pymatgen/io/feff/inputs.py index d9365c25499..f56a0577057 100644 --- a/src/pymatgen/io/feff/inputs.py +++ b/src/pymatgen/io/feff/inputs.py @@ -190,8 +190,8 @@ def __init__( self.periodic = True sym = SpacegroupAnalyzer(struct, **self.spacegroup_analyzer_settings) data = sym.get_symmetry_dataset() - self.space_number = data.get("number") - self.space_group = data.get("international") + self.space_number = data.number + self.space_group = data.international # for Molecule, skip the symmetry check elif isinstance(self.struct, Molecule): self.periodic = False diff --git a/src/pymatgen/io/vasp/outputs.py b/src/pymatgen/io/vasp/outputs.py index 4694183b8c5..2bb73cd89ac 100644 --- a/src/pymatgen/io/vasp/outputs.py +++ b/src/pymatgen/io/vasp/outputs.py @@ -1631,10 +1631,13 @@ def _parse_dos(elem: XML_Element) -> tuple[Dos, Dos, list[dict]]: tdensities = {} idensities = {} + soc_run = len(elem.find("total").find("array").find("set").findall("set")) > 2 # type: ignore[union-attr] for s in elem.find("total").find("array").find("set").findall("set"): # type: ignore[union-attr] data = np.array(_parse_vasp_array(s)) energies = data[:, 0] spin = Spin.up if s.attrib["comment"] == "spin 1" else Spin.down + if spin != Spin.up and soc_run: # other 'spins' are x,y,z SOC projections + continue tdensities[spin] = data[:, 1] idensities[spin] = data[:, 2] @@ -1649,6 +1652,8 @@ def _parse_dos(elem: XML_Element) -> tuple[Dos, Dos, list[dict]]: for ss in s.findall("set"): spin = Spin.up if ss.attrib["comment"] == "spin 1" else Spin.down + if spin != Spin.up and soc_run: # other 'spins' are x,y,z SOC projections + continue data = np.array(_parse_vasp_array(ss)) _n_row, n_col = data.shape for col_idx in range(1, n_col): diff --git a/src/pymatgen/transformations/standard_transformations.py b/src/pymatgen/transformations/standard_transformations.py index 8d8e231b8ca..ea5cd933fc8 100644 --- a/src/pymatgen/transformations/standard_transformations.py +++ b/src/pymatgen/transformations/standard_transformations.py @@ -23,6 +23,7 @@ from pymatgen.transformations.transformation_abc import AbstractTransformation if TYPE_CHECKING: + from numpy.random import Generator from typing_extensions import Self from pymatgen.core.sites import PeriodicSite @@ -451,6 +452,7 @@ class OrderDisorderedStructureTransformation(AbstractTransformation): ALGO_FAST = 0 ALGO_COMPLETE = 1 ALGO_BEST_FIRST = 2 + ALGO_RANDOM = -1 def __init__(self, algo=ALGO_FAST, symmetrized_structures=False, no_oxi_states=False): """ @@ -467,7 +469,9 @@ def __init__(self, algo=ALGO_FAST, symmetrized_structures=False, no_oxi_states=F self.no_oxi_states = no_oxi_states self.symmetrized_structures = symmetrized_structures - def apply_transformation(self, structure: Structure, return_ranked_list: bool | int = False) -> Structure: + def apply_transformation( + self, structure: Structure, return_ranked_list: bool | int = False, occ_tol=0.25 + ) -> Structure: """For this transformation, the apply_transformation method will return only the ordered structure with the lowest Ewald energy, to be consistent with the method signature of the other transformations. @@ -478,6 +482,9 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool | structure: Oxidation state decorated disordered structure to order return_ranked_list (bool | int, optional): If return_ranked_list is int, that number of structures is returned. If False, only the single lowest energy structure is returned. Defaults to False. + occ_tol (float): Occupancy tolerance. If the total occupancy of a group is within this value + of an integer, it will be rounded to that integer otherwise raise a ValueError. + Defaults to 0.25. Returns: Depending on returned_ranked list, either a transformed structure @@ -529,6 +536,17 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool | # generate the list of manipulations and input structure struct = Structure.from_sites(structure) + # We will first create an initial ordered structure by filling all sites + # with the species that has the highest oxidation state (initial_sp) + # replacing all other species on a given site. + # then, we process a list of manipulations to get the final structure. + # The manipulations are of the format: + # [oxi_ratio, 1, [0,1,2,3], Li+] + # which means -- Place 1 Li+ in any of these 4 sites + # the oxi_ratio is the ratio of the oxidation state of the species to + # the initial species. This is used to determine the energy of the + # manipulation in the EwaldMinimizer, but is not used in the purely random + # algorithm. manipulations = [] for group in equivalent_sites: total_occupancy = dict( @@ -536,7 +554,7 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool | ) # round total occupancy to possible values for key, val in total_occupancy.items(): - if abs(val - round(val)) > 0.25: + if abs(val - round(val)) > occ_tol: raise ValueError("Occupancy fractions not consistent with size of unit cell") total_occupancy[key] = round(val) # start with an ordered structure @@ -555,6 +573,16 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool | if empty > 0.5: manipulations.append([0, empty, list(group), None]) + if self.algo == self.ALGO_RANDOM: + rand_structures = get_randomly_manipulated_structures( + struct=struct, manipulations=manipulations, n_return=n_to_return + ) + if return_ranked_list: + return [ + {"energy": 0.0, "energy_above_minimum": 0.0, "structure": s} for s in rand_structures[:n_to_return] + ] + return rand_structures[0] + matrix = EwaldSummation(struct).total_energy_matrix ewald_m = EwaldMinimizer(matrix, manipulations, n_to_return, self.algo) @@ -891,3 +919,82 @@ def apply_transformation(self, structure): def __repr__(self): return "ScaleToRelaxedTransformation" + + +def _sample_random_manipulation(manipulation, rng, manipulated) -> list[tuple[int, SpeciesLike]]: + """Sample a single random manipulation. + + Each manipulation is given in the form of a tuple + `(oxi_ratio, nsites, indices, sp)` where: + Which means choose nsites from the list of indices and replace them + With the species `sp`. + """ + _, nsites, indices, sp = manipulation + maniped_indices = [i for i, _ in manipulated] + allowed_sites = [i for i in indices if i not in maniped_indices] + if len(allowed_sites) < nsites: + raise RuntimeError( + "No valid manipulations possible. " + f" You have already applied a manipulation to each site in this group {indices}" + ) + sampled_sites = rng.choice(allowed_sites, nsites, replace=False).tolist() + sampled_sites.sort() + return [(i, sp) for i in sampled_sites] + + +def _get_manipulation(manipulations: list, rng: Generator, max_attempts, seen: set[tuple]) -> tuple: + """Apply each manipulation.""" + for _ in range(max_attempts): + manipulated: list[tuple] = [] + for manip_ in manipulations: + new_manips = _sample_random_manipulation(manip_, rng, manipulated) + manipulated += new_manips + tm_ = tuple(manipulated) + if tm_ not in seen: + return tm_ + raise RuntimeError( + "Could not apply manipulations to structure" + "this is likely because you have already applied all the possible manipulations" + ) + + +def _apply_manip(struct, manipulations) -> Structure: + """Apply manipulations to a structure.""" + struct_copy = struct.copy() + rm_indices = [] + for manip in manipulations: + idx, sp = manip + if sp is None: + rm_indices.append(idx) + else: + struct_copy.replace(idx, sp) + struct_copy.remove_sites(rm_indices) + return struct_copy + + +def get_randomly_manipulated_structures( + struct: Structure, manipulations: list, seed=None, n_return: int = 1 +) -> list[Structure]: + """Get a structure with random manipulations applied. + + Args: + struct: Input structure + manipulations: List of manipulations to apply + seed: Seed for random number generator + n_return: Number of structures to return + + Returns: + List of structures with manipulations applied. + """ + rng = np.random.default_rng(seed) + seen: set[tuple] = set() + sampled_manips = [] + + for _ in range(n_return): + manip_ = _get_manipulation(manipulations, rng, 1000, seen) + seen.add(manip_) + sampled_manips.append(manip_) + output_structs = [] + for manip_ in sampled_manips: + output_structs.append(_apply_manip(struct, manip_)) + return output_structs diff --git a/tests/electronic_structure/test_boltztrap2.py b/tests/electronic_structure/test_boltztrap2.py index cdb75a24532..b68c94e1cc4 100644 --- a/tests/electronic_structure/test_boltztrap2.py +++ b/tests/electronic_structure/test_boltztrap2.py @@ -80,6 +80,7 @@ def test_get_volume(self): assert self.loader.get_volume() == approx(477.6256714925874, abs=1e-5) +@pytest.mark.filterwarnings("ignore:BandstructureLoader is deprecated:DeprecationWarning") class TestBandstructureLoader(TestCase): def setUp(self): self.loader = BandstructureLoader(BAND_STRUCT, VASP_RUN.structures[-1]) @@ -107,6 +108,7 @@ def test_set_upper_lower_bands(self): assert self.loader_sp_dn.ebands.shape == (14, 198) +@pytest.mark.filterwarnings("ignore:VasprunLoader is deprecated:DeprecationWarning") class TestVasprunLoader(TestCase): def setUp(self): self.loader = VasprunLoader(VASP_RUN) diff --git a/tests/entries/test_computed_entries.py b/tests/entries/test_computed_entries.py index 9cf63caca6f..98f6b006867 100644 --- a/tests/entries/test_computed_entries.py +++ b/tests/entries/test_computed_entries.py @@ -470,11 +470,11 @@ def setUp(self): for temp in self.temps } - with open(f"{TEST_DIR}/Mn-O_entries.json") as file: - data = json.load(file) with open(f"{TEST_DIR}/structure_CO2.json") as file: self.co2_struct = MontyDecoder().process_decoded(json.load(file)) + with open(f"{TEST_DIR}/Mn-O_entries.json") as file: + data = json.load(file) self.mp_entries = [MontyDecoder().process_decoded(d) for d in data] def test_gf_sisso(self): diff --git a/tests/ext/test_matproj.py b/tests/ext/test_matproj.py index 18558a41525..8c043f61f4a 100644 --- a/tests/ext/test_matproj.py +++ b/tests/ext/test_matproj.py @@ -908,7 +908,7 @@ def test_parity_with_mp_api(self): pytest.skip("mp_api.client.MPRester cannot be imported for this test.") mpr_mp_api = MpApi(PMG_MAPI_KEY) # Test summary - mp_data = mpr_mp_api.summary.search(formula="Al2O3") + mp_data = mpr_mp_api.materials.search(formula="Al2O3") pmg_data = self.rester.get_summary({"formula": "Al2O3"}) assert len(mp_data) == len(pmg_data) diff --git a/tests/files/entries/Mn-O_entries.json b/tests/files/entries/Mn-O_entries.json index 8276418e3c1..6f69a54a958 100644 --- a/tests/files/entries/Mn-O_entries.json +++ b/tests/files/entries/Mn-O_entries.json @@ -1 +1 @@ -[{"@module": "pymatgen.entries.computed_entries", "@class": "ComputedStructureEntry", "energy": -31.42682858, "composition": {"Mn": 2.0, "O": 2.0}, "energy_adjustments": [{"@module": "pymatgen.entries.computed_entries", "@class": "ConstantEnergyAdjustment", "@version": "2020.8.3", "value": 0, "name": "MPRelaxSet Potcar Correction", "cls": {"@module": "pymatgen.entries.compatibility", "@class": "MaterialsProjectCompatibility", "@version": "2020.8.3", "compat_type": "Advanced", "correct_peroxide": true, "check_potcar_hash": false}, "description": "Constant energy adjustment (0.000 eV)"}, {"@module": "pymatgen.entries.computed_entries", "@class": "ConstantEnergyAdjustment", "@version": "2020.8.3", "value": 0, "name": "MP Gas Correction", "cls": {"@module": "pymatgen.entries.compatibility", "@class": "MaterialsProjectCompatibility", "@version": "2020.8.3", "compat_type": "Advanced", "correct_peroxide": true, "check_potcar_hash": false}, "description": "Constant energy adjustment (0.000 eV)"}, {"@module": "pymatgen.entries.computed_entries", "@class": "ConstantEnergyAdjustment", "@version": "2020.8.3", "value": -1.40458, "name": "MP Anion Correction", "cls": {"@module": "pymatgen.entries.compatibility", "@class": "MaterialsProjectCompatibility", "@version": "2020.8.3", "compat_type": "Advanced", "correct_peroxide": true, "check_potcar_hash": false}, "description": "Constant energy adjustment (-1.405 eV)"}, {"@module": "pymatgen.entries.computed_entries", "@class": "ConstantEnergyAdjustment", "@version": "2020.8.3", "value": -3.36170030192, "name": "MP Advanced Correction", "cls": {"@module": "pymatgen.entries.compatibility", "@class": "MaterialsProjectCompatibility", "@version": "2020.8.3", "compat_type": "Advanced", "correct_peroxide": true, "check_potcar_hash": false}, "description": "Constant energy adjustment (-3.362 eV)"}], "parameters": {"run_type": "GGA+U", "is_hubbard": true, "pseudo_potential": {"functional": "PBE", "labels": ["Mn_pv", "O"], "pot_type": "paw"}, "hubbards": {"Mn": 3.9, "O": 0.0}, "potcar_symbols": ["PBE Mn_pv", "PBE O"], "oxide_type": "oxide"}, "data": {"oxide_type": "oxide"}, "entry_id": "mp-19006", "correction": -4.76628030192, "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": null, "lattice": {"matrix": [[2.768974, 5e-05, 1.598707], [0.923025, 2.610708, 1.59873], [-0.878246, -2.578988, 4.71854]], "a": 3.1973553269890105, "b": 3.1974535219122417, "c": 5.448588337565979, "alpha": 89.99985583138601, "beta": 72.93751790695626, "gamma": 59.998925238391344, "volume": 45.386638186518894}, "sites": [{"species": [{"element": "Mn", "occu": 1}], "abc": [0.0, 0.0, 0.0], "xyz": [0.0, 0.0, 0.0], "label": "Mn", "properties": {"magmom": 4.591}}, {"species": [{"element": "Mn", "occu": 1}], "abc": [0.0, 0.5, 0.5], "xyz": [0.022389500000000007, 0.015859999999999985, 3.158635], "label": "Mn", "properties": {"magmom": -4.591}}, {"species": [{"element": "O", "occu": 1}], "abc": [0.499999, 0.750001, 0.250001], "xyz": [1.8571915258050005, 1.3133090316699998, 3.178040718563], "label": "O", "properties": {"magmom": 0.0}}, {"species": [{"element": "O", "occu": 1}], "abc": [0.500001, 0.249999, 0.749999], "xyz": [0.9565614741950001, -1.28153903167, 4.737936281436999], "label": "O", "properties": {"magmom": 0.0}}]}}, {"@module": "pymatgen.entries.computed_entries", "@class": "ComputedStructureEntry", "energy": -85.73370849, "composition": {"Mn": 4.0, "O": 8.0}, "energy_adjustments": [{"@module": "pymatgen.entries.computed_entries", "@class": "ConstantEnergyAdjustment", "@version": "2020.8.3", "value": 0, "name": "MPRelaxSet Potcar Correction", "cls": {"@module": "pymatgen.entries.compatibility", "@class": "MaterialsProjectCompatibility", "@version": "2020.8.3", "compat_type": "Advanced", "correct_peroxide": true, "check_potcar_hash": false}, "description": "Constant energy adjustment (0.000 eV)"}, {"@module": "pymatgen.entries.computed_entries", "@class": "ConstantEnergyAdjustment", "@version": "2020.8.3", "value": 0, "name": "MP Gas Correction", "cls": {"@module": "pymatgen.entries.compatibility", "@class": "MaterialsProjectCompatibility", "@version": "2020.8.3", "compat_type": "Advanced", "correct_peroxide": true, "check_potcar_hash": false}, "description": "Constant energy adjustment (0.000 eV)"}, {"@module": "pymatgen.entries.computed_entries", "@class": "ConstantEnergyAdjustment", "@version": "2020.8.3", "value": -5.61832, "name": "MP Anion Correction", "cls": {"@module": "pymatgen.entries.compatibility", "@class": "MaterialsProjectCompatibility", "@version": "2020.8.3", "compat_type": "Advanced", "correct_peroxide": true, "check_potcar_hash": false}, "description": "Constant energy adjustment (-5.618 eV)"}, {"@module": "pymatgen.entries.computed_entries", "@class": "ConstantEnergyAdjustment", "@version": "2020.8.3", "value": -6.72340060384, "name": "MP Advanced Correction", "cls": {"@module": "pymatgen.entries.compatibility", "@class": "MaterialsProjectCompatibility", "@version": "2020.8.3", "compat_type": "Advanced", "correct_peroxide": true, "check_potcar_hash": false}, "description": "Constant energy adjustment (-6.723 eV)"}], "parameters": {"run_type": "GGA+U", "is_hubbard": true, "pseudo_potential": {"functional": "PBE", "labels": ["Mn_pv", "O"], "pot_type": "paw"}, "hubbards": {"Mn": 3.9, "O": 0.0}, "potcar_symbols": ["PBE Mn_pv", "PBE O"], "oxide_type": "oxide"}, "data": {"oxide_type": "oxide"}, "entry_id": "mp-19395", "correction": -12.341720603839999, "structure": {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": null, "lattice": {"matrix": [[2.865569, -0.000728, 0.587157], [1.430411, 7.014927, 0.296261], [0.022098, 0.002584, 7.16407]], "a": 2.9251050521979547, "b": 7.1654062707128485, "c": 7.164104547224308, "alpha": 87.57482286635624, "beta": 78.24361041871992, "gamma": 78.25127452159832, "volume": 143.92681011884497}, "sites": [{"species": [{"element": "Mn", "occu": 1}], "abc": [0.65172, 0.183104, 0.516697], "xyz": [2.1408805747299997, 1.2853218862959999, 4.138562010974], "label": "Mn", "properties": {"magmom": 3.201}}, {"species": [{"element": "Mn", "occu": 1}], "abc": [0.16706, 0.48647, 0.183322], "xyz": [1.178625045866, 3.4129036220580002, 1.5555441776299999], "label": "Mn", "properties": {"magmom": 3.2}}, {"species": [{"element": "Mn", "occu": 1}], "abc": [0.834099, 0.516327, 0.819773], "xyz": [3.1468434014819997, 3.623507282489, 6.515625776], "label": "Mn", "properties": {"magmom": 3.202}}, {"species": [{"element": "Mn", "occu": 1}], "abc": [0.34942, 0.819682, 0.486093], "xyz": [2.1845109523960002, 5.751011079766, 3.930408486452], "label": "Mn", "properties": {"magmom": 3.201}}, {"species": 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a/tests/io/test_phonopy.py b/tests/io/test_phonopy.py index 0f20d54e474..14848c11bbb 100644 --- a/tests/io/test_phonopy.py +++ b/tests/io/test_phonopy.py @@ -1,7 +1,6 @@ from __future__ import annotations import os -import platform from pathlib import Path from unittest import TestCase @@ -124,10 +123,6 @@ def test_structure_conversion(self): assert struct_pmg_round_trip.site_properties["magmom"] == struct_pmg.site_properties["magmom"] -@pytest.mark.skipif( - platform.system() == "Windows" and int(np.__version__[0]) >= 2, - reason="cannot run NP2 on windows, see PR 4224", -) @pytest.mark.skipif(Phonopy is None, reason="Phonopy not present") class TestGetDisplacedStructures(PymatgenTest): def test_get_displaced_structures(self): @@ -160,10 +155,6 @@ def test_get_displaced_structures(self): assert os.path.isfile("test.yaml") -@pytest.mark.skipif( - platform.system() == "Windows" and int(np.__version__[0]) >= 2, - reason="cannot run NP2 on windows, see PR 4224", -) @pytest.mark.skipif(Phonopy is None, reason="Phonopy not present") class TestPhonopyFromForceConstants(TestCase): def setUp(self) -> None: diff --git a/tests/io/vasp/test_outputs.py b/tests/io/vasp/test_outputs.py index 837884c22f0..17916375dae 100644 --- a/tests/io/vasp/test_outputs.py +++ b/tests/io/vasp/test_outputs.py @@ -54,6 +54,18 @@ class TestVasprun(PymatgenTest): + def test_vasprun_soc(self): + # Test that SOC vaspruns are parsed appropriately, giving just Spin.Up tdos, idos and pdos + vasp_run = Vasprun(f"{VASP_OUT_DIR}/vasprun.int_Te_SOC.xml.gz") + dos_density_dicts_to_check = [vasp_run.complete_dos.densities, vasp_run.tdos.densities, vasp_run.idos.densities] + dos_density_dicts_to_check += [ + densities for orbital_dict in vasp_run.complete_dos.pdos.values() for densities in orbital_dict.values() + ] + for i, dos_density_dict in enumerate(dos_density_dicts_to_check): + assert set(dos_density_dict.keys()) == {Spin.up}, f"Failed spin keys check for {i}th dos obj!" + + assert vasp_run.complete_dos.spin_polarization is None + def test_vasprun_ml(self): # Test for ML MD simulation # The trajectory data is stored in md_data @@ -79,7 +91,6 @@ def test_vasprun_md(self): def test_vasprun_ediffg_set_to_0(self): # Test for case where EDIFFG is set to 0. This should pass if all ionic steps # complete and are electronically converged. - print(list(os.walk(VASP_OUT_DIR))) vasp_run = Vasprun(f"{VASP_OUT_DIR}/vasprun.ediffg_set_to_0.xml.gz") assert len(vasp_run.ionic_steps) == 3 assert vasp_run.final_energy == approx(-34.60164204) diff --git a/tests/transformations/test_standard_transformations.py b/tests/transformations/test_standard_transformations.py index 0074eece962..d9ce0da09d8 100644 --- a/tests/transformations/test_standard_transformations.py +++ b/tests/transformations/test_standard_transformations.py @@ -401,6 +401,32 @@ def test_best_first(self): output = trafo.apply_transformation(struct, return_ranked_list=3) assert output[0]["energy"] == approx(-234.57813667648315, abs=1e-4) + def test_random_sample(self): + struc_str = ( + "3.333573 0.000000 1.924639\n" + "1.111191 3.142924 1.924639\n" + "0.000000 0.000000 3.849278\n" + "1.0 0.0 0.0\n" + "0.0 1.0 0.0\n" + "0.0 0.0 1.0\n" + "0.875000 0.875000 0.875000 Si=1\n" + "0.125000 0.125000 0.125000 Si=1" + ) + si = Structure.from_str(struc_str, fmt="mcsqs") + struct = si * [3, 2, 1] + struct.replace(0, {"Fe": 0.5, "Ni": 0.5}) + struct.replace(1, {"Fe": 0.5, "Ni": 0.5}) + trafo = OrderDisorderedStructureTransformation( + algo=OrderDisorderedStructureTransformation.ALGO_RANDOM, no_oxi_states=True + ) + output = trafo.apply_transformation(struct * [2, 2, 2], return_ranked_list=3) + assert len(output) == 3 + for entry in output: + assert set(entry.keys()) == {"structure", "energy", "energy_above_minimum"} + + output = trafo.apply_transformation(struct * [2, 2, 2], return_ranked_list=False) + assert output.composition.reduced_formula == struct.composition.reduced_formula + class TestPrimitiveCellTransformation: def test_apply_transformation(self): diff --git a/tests/util/test_typing.py b/tests/util/test_typing.py index 2fe5592605c..c0dd731fb55 100644 --- a/tests/util/test_typing.py +++ b/tests/util/test_typing.py @@ -2,13 +2,10 @@ from __future__ import annotations -import sys from pathlib import Path from types import GenericAlias from typing import TYPE_CHECKING, get_args -import pytest - from pymatgen.core import Composition, DummySpecies, Element, Species from pymatgen.entries import Entry from pymatgen.util.typing import CompositionLike, EntryLike, PathLike, PbcLike, SpeciesLike @@ -20,8 +17,6 @@ __date__ = "2022-10-20" __email__ = "janosh@lbl.gov" -skip_below_py310 = pytest.mark.skipif(sys.version_info < (3, 10), reason="requires python 3.10 or higher") - def _type_str(some_type: Any) -> str: return str(some_type).replace("typing.", "").replace("pymatgen.core.periodic_table.", "") @@ -48,7 +43,6 @@ def test_entry_like(): assert Entry.__name__ in str(EntryLike) -@skip_below_py310 def test_species_like(): assert isinstance("H", SpeciesLike) assert isinstance(Element("H"), SpeciesLike) @@ -56,7 +50,6 @@ def test_species_like(): assert isinstance(DummySpecies("X"), SpeciesLike) -@skip_below_py310 def test_composition_like(): assert isinstance("H", CompositionLike) assert isinstance(Element("H"), CompositionLike) @@ -71,7 +64,6 @@ def test_pbc_like(): assert get_args(PbcLike) == (bool, bool, bool) -@skip_below_py310 def test_pathlike(): assert isinstance("path/to/file", PathLike) assert isinstance(Path("path/to/file"), PathLike)