Merge branch 'master' into incar-multiline-str

Author: shyuep

dev_scripts/periodic_table_resources/_periodic_table.yaml

@@ -1143,7 +1143,7 @@ Common oxidation states:
     Li: [1]
     Be: [2]
     B: [3]
-    C: [-4, 4]
+    C: [-4, -3, -2, -1, 0, 1, 2, 3, 4]
     N: [-3, 3, 5]
     O: [-2]
     F: [-1]
@@ -1170,7 +1170,8 @@ Common oxidation states:
     Ge: [-4, 2, 4]
     As: [-3, 3, 5]
     Se: [-2, 2, 4, 6]
-    Br: [-1, 1, 3, 5, 7]
+    Br: [-1, 1, 3, 5]
+    Kr: [2]
     Rb: [1]
     Sr: [2]
     Y: [3]
@@ -1188,6 +1189,7 @@ Common oxidation states:
     Sb: [-3, 3, 5]
     Te: [-2, 2, 4, 6]
     I: [-1, 1, 3, 5, 7]
+    Xe: [2, 4, 6]
     Cs: [1]
     Ba: [2]
     La: [3]
@@ -1208,7 +1210,7 @@ Common oxidation states:
     Hf: [4]
     Ta: [5]
     W: [4, 6]
-    Re: [4]
+    Re: [4, 7]
     Os: [4]
     Ir: [3, 4]
     Pt: [2, 4]
@@ -1236,13 +1238,15 @@ Common oxidation states:
     Md: [3]
     No: [3]
     Lr: [3]
+    Rf: [4]
 Critical temperature:
   unit: K
   reference:
     https://en.wikipedia.org/wiki/Critical_points_of_the_elements_(data_page)
-  data: {H: 33, He: 5.19, Li: 3223, N: 126.2, O: 154.6, F: 144, Ne: 44.4, Na:
-      2573, P: 994, S: 1314, Cl: 417, Ar: 150.8, K: 2223, As: 1700, Se: 1766, Br:
-      586, Kr: 209.4, Rb: 2093, I: 819, Xe: 289.7, Cs: 1938, Hg: 1750, Rn: 377}
+  data: {H: 32.97, He: 5.19, Li: 3223, N: 126.21, O: 154.59, F: 144.13, Ne: 44.4,
+    Na: 2573, P: 994, S: 1314, Cl: 416.9, Ar: 150.87, K: 2223, As: 1673, Se:
+      1766, Br: 588, Kr: 209.41, Rb: 2093, I: 819, Xe: 289.77, Cs: 1938, Hg:
+      1750, Rn: 377}
 Density of solid:
   unit: kg m^-3
   reference: https://en.wikipedia.org/wiki/Densities_of_the_elements_(data_page)
@@ -1262,20 +1266,22 @@ Electrical resistivity:
   unit: ohm m
   reference:
     https://en.wikipedia.org/wiki/Electrical_resistivities_of_the_elements_(data_page)
-  data: {Li: 9.5e-08, Be: 3.8e-08, B: 15000.0, C: 1e-05, Na: 4.9e-08, Mg:
-      4.4e-08, Al: 2.7e-08, Si: 0.001, P: 1e-07, S: 2000000000000000.0, Cl: 10.0,
-    K: 7.5e-08, Ca: 3.4e-08, Sc: 5.5e-07, Ti: 4e-07, V: 2e-07, Cr: 1.27e-07, Mn:
-      1.44e-06, Fe: 1e-07, Co: 6e-08, Ni: 7.2e-08, Cu: 1.72e-08, Zn: 6e-08, Ga:
-      1.4e-07, Ge: 0.0005, As: 3.3e-07, Br: 78000000000.0, Rb: 1.33e-07, Sr:
-      1.35e-07, Y: 6e-07, Zr: 4.33e-07, Nb: 1.52e-07, Mo: 5.5e-08, Tc: 2.2e-07,
-      Ru: 7.1e-08, Rh: 4.3e-08, Pd: 1.08e-07, Ag: 1.63e-08, Cd: 7e-08, In: 8e-08,
-    Sn: 1.15e-07, Sb: 4e-07, Te: 0.0001, I: 13000000.0, Cs: 2.1e-07, Ba: 3.4e-07,
-    La: 6.15e-07, Ce: 7.4e-07, Pr: 7e-07, Nd: 6.43e-07, Pm: 7.5e-07, Sm: 9.4e-07,
-    Eu: 9e-07, Gd: 1.31e-06, Tb: 1.15e-06, Dy: 9.26e-07, Ho: 8.14e-07, Er:
-      8.6e-07, Tm: 6.76e-07, Yb: 2.5e-07, Lu: 5.8e-07, Hf: 3.4e-07, Ta: 1.35e-07,
-    W: 5.4e-08, Re: 1.8e-07, Os: 8.1e-08, Ir: 4.7e-08, Pt: 1.06e-07, Au: 2.2e-08,
-    Hg: 9.6e-07, Tl: 1.5e-07, Pb: 2.1e-07, Bi: 1.3e-06, Po: 4e-07, Ra: 1e-06, Th:
-      1.5e-07, Pa: 1.8e-07, U: 2.8e-07, Np: 1.2e-06, Pu: 1.5e-06}
+  data: {Li: 9.28e-08, Be: 3.56e-08, B: 15000.0, C: 1e-05, Na: 4.77e-08, Mg:
+      4.39e-08, Al: 2.65e-08, Si: 0.001, P: 1e-07, S: 2000000000000000.0, Cl:
+      10.0, K: 7.2e-08, Ca: 3.36e-08, Sc: 5.62e-07, Ti: 4.2e-07, V: 1.97e-07, Cr:
+      1.25e-07, Mn: 1.44e-06, Fe: 9.61e-08, Co: 6.24e-08, Ni: 6.93e-08, Cu:
+      1.678e-08, Zn: 5.9e-08, Ga: 1.4e-07, Ge: 0.0005, As: 3.33e-07, Br:
+      78000000000.0, Rb: 1.28e-07, Sr: 1.32e-07, Y: 5.96e-07, Zr: 4.21e-07, Nb:
+      1.52e-07, Mo: 5.34e-08, Tc: 2e-07, Ru: 7.1e-08, Rh: 4.33e-08, Pd:
+      1.054e-07, Ag: 1.587e-08, Cd: 7.27e-08, In: 8.37e-08, Sn: 1.1e-07, Sb:
+      4.17e-07, Te: 0.0001, I: 13000000.0, Cs: 2.05e-07, Ba: 3.32e-07, La:
+      6.15e-07, Ce: 7.44e-07, Pr: 7e-07, Nd: 6.43e-07, Pm: 7.5e-07, Sm: 9.4e-07,
+      Eu: 9e-07, Gd: 1.31e-06, Tb: 1.15e-06, Dy: 9.26e-07, Ho: 8.14e-07, Er:
+      8.6e-07, Tm: 6.76e-07, Yb: 2.5e-07, Lu: 5.82e-07, Hf: 3.31e-07, Ta:
+      1.31e-07, W: 5.28e-08, Re: 1.93e-07, Os: 8.12e-08, Ir: 4.71e-08, Pt:
+      1.05e-07, Au: 2.214e-08, Hg: 9.61e-07, Tl: 1.8e-07, Pb: 2.08e-07, Bi:
+      1.29e-06, Po: 4e-07, Ra: 1e-06, Th: 1.54e-07, Pa: 1.91e-07, U: 2.8e-07, Np:
+      1.22e-06, Pu: 1.5e-06, Am: 6.89e-07, Cm: 1.25e-06}
 Electron affinity:
   unit: eV
   reference: https://en.wikipedia.org/wiki/Electron_affinity_(data_page)
@@ -1673,6 +1679,8 @@ Electronic structure:
     Lr:
       '0': '[Rn].5f14.7s2.7p1'
       '3': '[Rn].5f14'
+    Rf:
+      '0': '[Rn].5f14.6d2.7s2'
 Ground level:
   reference:
     https://physics.nist.gov/cgi-bin/ASD/ie.pl?spectra=H-DS+i&units=1&at_num_out=on&el_name_out=on&shells_out=on&level_out=on&e_out=0&unc_out=on&biblio=on

dev_scripts/periodic_table_resources/elemental_properties.yaml

@@ -1560,8 +1560,6 @@ Coefficient of linear thermal expansion:
     Zn: 30.2
     Zr: 5.7
 Common oxidation states:
-  # TODO: the source is very likely from wikipedia but our data need to be updated,
-  # for example the data for carbon shouldn't be only -4 or 4
   reference: "https://en.wikipedia.org/wiki/Template:List_of_oxidation_states_of_the_elements"
   data:
     Ac: [3]
@@ -1576,8 +1574,8 @@ Common oxidation states:
     Be: [2]
     Bi: [3]
     Bk: [3]
-    Br: [-1, 1, 3, 5, 7]
-    C: [-4, 4]
+    Br: [-1, 1, 3, 5]
+    C: [-4, -3, -2, -1, 0, 1, 2, 3, 4]
     Ca: [2]
     Cd: [2]
     Ce: [3, 4]
@@ -1607,6 +1605,7 @@ Common oxidation states:
     In: [3]
     Ir: [3, 4]
     K: [1]
+    Kr: [2]
     La: [3]
     Li: [1]
     Lr: [3]
@@ -1635,7 +1634,8 @@ Common oxidation states:
     Pu: [4]
     Ra: [2]
     Rb: [1]
-    Re: [4]
+    Re: [4, 7]
+    Rf: [4]
     Rh: [3]
     Ru: [3, 4]
     S: [-2, 2, 4, 6]
@@ -1657,40 +1657,40 @@ Common oxidation states:
     U: [6]
     V: [5]
     W: [4, 6]
+    Xe: [2, 4, 6]
     Y: [3]
     Yb: [3]
     Zn: [2]
     Zr: [4]
     D: [-1, 1]
     T: [-1, 1]
 Critical temperature:
-  # TODO: need to update with wikipedia
   reference: "https://en.wikipedia.org/wiki/Critical_points_of_the_elements_(data_page)"
   unit: K
   data:
-    Ar: 150.8
-    As: 1700
-    Br: 586
-    Cl: 417
+    Ar: 150.87
+    As: 1673
+    Br: 588
+    Cl: 416.9
     Cs: 1938
-    F: 144
-    H: 33
+    F: 144.13
+    H: 32.97
     He: 5.19
     Hg: 1750
     I: 819
     K: 2223
-    Kr: 209.4
+    Kr: 209.41
     Li: 3223
-    N: 126.2
+    N: 126.21
     Na: 2573
     Ne: 44.4
-    O: 154.6
+    O: 154.59
     P: 994
     Rb: 2093
     Rn: 377
     S: 1314
     Se: 1766
-    Xe: 289.7
+    Xe: 289.77
 Density of solid:
   reference: "https://en.wikipedia.org/wiki/Densities_of_the_elements_(data_page)" # WEL
   unit: kg m^-3
@@ -1777,91 +1777,94 @@ Density of solid:
     Yb: 6570
     Zn: 7140
     Zr: 6511
-Electrical resistivity: # TODO: need validate/update
+Electrical resistivity:
   reference: "https://en.wikipedia.org/wiki/Electrical_resistivities_of_the_elements_(data_page)"
   unit: ohm m
   factor: 1e-8
   data: # 293 K (20 °C)
-    Ag: 1.63
-    Al: 2.7
-    As: 33
-    Au: 2.2
+    Ag: 1.587
+    Al: 2.65
+    Am: 68.9 # room temperature
+    As: 33.3
+    Au: 2.214
     B: 1.5e12
-    Ba: 34
-    Be: 3.8
-    Bi: 130
+    Ba: 33.2
+    Be: 3.56
+    Bi: 129
     Br: 7.8e18
-    C: 1000 # direction dependent
-    Ca: 3.4
-    Cd: 7
-    Ce: 74
-    Cl: 1e9
-    Co: 6
-    Cr: 12.7
-    Cs: 21
-    Cu: 1.72
-    Dy: 92.6
-    Er: 86.0
-    Eu: 90
-    Fe: 10
+    C: 1000 # graphite (direction dependent)
+    Ca: 3.36
+    Cd: 7.27 # 22 °C
+    Ce: 74.4 # gamma, polycrystalline
+    Cl: 1e9 # > 1e9
+    Cm: 125 # room temperature
+    Co: 6.24
+    Cr: 12.5
+    Cs: 20.5
+    Cu: 1.678
+    Dy: 92.6 # alpha, polycrystalline
+    Er: 86.0 # polycrystalline
+    Eu: 90 # polycrystalline
+    Fe: 9.61
     Ga: 14
-    Gd: 131
-    Ge: 50000
-    Hf: 34
-    Hg: 96
-    Ho: 81.4
-    I: 1.3e15
-    In: 8
-    Ir: 4.7
-    K: 7.5
-    La: 61.5
-    Li: 9.5
-    Lu: 58
-    Mg: 4.4
+    Gd: 131 # alpha, polycrystalline
+    Ge: 50000 # about
+    Hf: 33.1
+    Hg: 96.1 # 25 °C
+    Ho: 81.4 # polycrystalline
+    I: 1.3e15 # 0 °C
+    In: 8.37
+    Ir: 4.71
+    K: 7.2
+    La: 61.5 # alpha, polycrystalline
+    Li: 9.28
+    Lu: 58.2 # polycrystalline
+    Mg: 4.39
     Mn: 144
-    Mo: 5.5
-    Na: 4.9
+    Mo: 5.34
+    Na: 4.77
     Nb: 15.2
-    Nd: 64.3
-    Ni: 7.2
-    Np: 120
-    Os: 8.1
+    Nd: 64.3 # alpha, polycrystalline
+    Ni: 6.93
+    Np: 122 # 22 °C
+    Os: 8.12 # 0 °C
     P: 10
-    Pa: 18
-    Pb: 21
-    Pd: 10.8
-    Pm: 75
-    Po: 40
-    Pr: 70
-    Pt: 10.6
+    Pa: 19.1 # 22 °C
+    Pb: 20.8
+    Pd: 10.54
+    Pm: 75 # alpha, polycrystalline (estimated)
+    Po: 40 # 0 °C
+    Pr: 70 # alpha, polycrystalline
+    Pt: 10.5
     Pu: 150
     Ra: 100
-    Rb: 13.3
-    Re: 18
-    Rh: 4.3
+    Rb: 12.8
+    Re: 19.3
+    Rh: 4.33
     Ru: 7.1
-    S: 2e23
-    Sb: 40
-    Sc: 55
-    Si: 100000
-    Sm: 94
-    Sn: 11.5
-    Sr: 13.5
-    Ta: 13.5
-    Tb: 115
-    Tc: 22
-    Te: 10000
-    Th: 15
-    Ti: 40
-    Tl: 15
-    Tm: 67.6
+    S: 2e23 # amorphous
+    Sb: 41.7
+    Sc: 56.2
+    # Se: "high"
+    Si: 100000 # about
+    Sm: 94 # alpha, polycrystalline
+    Sn: 11
+    Sr: 13.2
+    Ta: 13.1
+    Tb: 115 # alpha, polycrystalline
+    Tc: 20
+    Te: 10000 # about
+    Th: 15.4 # 22 °C
+    Ti: 42
+    Tl: 18
+    Tm: 67.6 # polycrystalline
     U: 28
-    V: 20
-    W: 5.4
-    Y: 60
-    Yb: 25.0
-    Zn: 6.0
-    Zr: 43.3
+    V: 19.7
+    W: 5.28
+    Y: 59.6
+    Yb: 25.0 # beta, polycrystalline
+    Zn: 5.9
+    Zr: 42.1
 Electronic structure:
   reference: "Kramida, A., Ralchenko, Yu., Reader, J., and NIST ASD Team (2023). NIST Atomic Spectra Database (ver. 5.11). https://physics.nist.gov/asd [2024, June 3]. National Institute of Standards and Technology, Gaithersburg, MD. DOI: https://doi.org/10.18434/T4W30F"
   data:
@@ -2133,6 +2136,8 @@ Electronic structure:
     Re:
       "0": "[Xe].4f14.5d5.6s2"
       "4": "[Xe].4f14.5d3"
+    Rf:
+      "0": "[Rn].5f14.6d2.7s2"
     Rh:
       "0": "[Kr].4d8.5s1"
       "3": "[Kr].4d6"

src/pymatgen/analysis/bond_valence.py

@@ -478,7 +478,7 @@ def add_oxidation_state_by_site_fraction(structure: Structure, oxidation_states:
             for j, (el, occu) in enumerate(get_z_ordered_elmap(site.species)):
                 specie = Species(el.symbol, oxidation_states[idx][j])
                 new_sp[specie] += occu
-            structure[idx] = new_sp
+            structure[idx] = new_sp  # type:ignore[assignment]
         return structure
     except IndexError:
         raise ValueError("Oxidation state of all sites must be specified in the list.")

src/pymatgen/analysis/local_env.py

@@ -682,7 +682,7 @@ def get_local_order_parameters(self, structure: Structure, n: int):
                 params.append(tmp)
             lsops = LocalStructOrderParams(types, parameters=params)
             sites = [structure[n], *self.get_nn(structure, n)]
-            lostop_vals = lsops.get_order_parameters(sites, 0, indices_neighs=list(range(1, cn + 1)))
+            lostop_vals = lsops.get_order_parameters(sites, 0, indices_neighs=list(range(1, cn + 1)))  # type:ignore[arg-type]
             dct = {}
             for idx, lsop in enumerate(lostop_vals):
                 dct[names[idx]] = lsop

src/pymatgen/analysis/magnetism/analyzer.py

@@ -983,7 +983,8 @@ def _add_structures(ordered_structures, ordered_structures_origins, structures_t
 
         for origin, trans in self.transformations.items():
             structures_to_add = trans.apply_transformation(
-                self.sanitized_structure, return_ranked_list=self.num_orderings
+                self.sanitized_structure,
+                return_ranked_list=self.num_orderings,  # type:ignore[arg-type]
             )
             ordered_structures, ordered_structures_origins = _add_structures(
                 ordered_structures,