Merge 618e6dc into 962b1dd

pymatgen/entries/MP2020Compatibility.yaml

@@ -6,75 +6,75 @@ Corrections:
     # and fluorides to make GGA and GGA+U energies compatible
     # when compat_type = "Advanced" (default)
     O:
-      V: -1.602
-      Cr: -1.893
-      Mn: -1.588
-      Fe: -2.182
-      Co: -1.535
-      Ni: -2.504
-      W: -4.57
-      Mo: -3.058
+      V: -1.666
+      Cr: -1.967
+      Mn: -1.635
+      Fe: -2.224
+      Co: -1.556
+      Ni: -2.545
+      W: -4.647
+      Mo: -3.098
     F:
-      V: -1.602
-      Cr: -1.893
-      Mn: -1.588
-      Fe: -2.182
-      Co: -1.535
-      Ni: -2.504
-      W: -4.57
-      Mo: -3.058
+      V: -1.666
+      Cr: -1.967
+      Mn: -1.635
+      Fe: -2.224
+      Co: -1.556
+      Ni: -2.545
+      W: -4.647
+      Mo: -3.098
   CompositionCorrections:
     # Composition-based corrections applied to any compound containing
     # these species as anions
-    oxide: -0.74
-    peroxide: -0.466
-    superoxide: -0.16
-    S: -0.639
-    F: -0.485
-    Cl: -0.593
-    Br: -0.538
-    I: -0.377
-    N: -0.344
-    Se: -0.473
-    Si: -0.406
+    oxide: -0.706
+    peroxide: -0.464
+    superoxide: -0.168
+    S: -0.592
+    F: -0.404
+    Cl: -0.55
+    Br: -0.473
+    I: -0.275
+    N: -0.408
+    Se: -0.472
+    Si: -0.225
     Sb: -0.192
-    Te: -0.419
-    H: -0.178
+    Te: -0.406
+    H: -0.144
     ozonide: 0
 Uncertainties:
   # Uncertainties corresponding to each energy correction (eV/atom)
   GGAUMixingCorrections:
     O:
-      V: 0.006
-      Cr: 0.0093
-      Mn: 0.0051
-      Fe: 0.009
-      Co: 0.0059
-      Ni: 0.0105
-      W: 0.0181
-      Mo: 0.0085
+      V: 0.0141
+      Cr: 0.0113
+      Mn: 0.0057
+      Fe: 0.0106
+      Co: 0.0163
+      Ni: 0.0106
+      W: 0.0188
+      Mo: 0.0202
     F:
-      V: 0.006
-      Cr: 0.0093
-      Mn: 0.0051
-      Fe: 0.009
-      Co: 0.0059
-      Ni: 0.0105
-      W: 0.0181
-      Mo: 0.0085
+      V: 0.0141
+      Cr: 0.0113
+      Mn: 0.0057
+      Fe: 0.0106
+      Co: 0.0163
+      Ni: 0.0106
+      W: 0.0188
+      Mo: 0.0202
   CompositionCorrections:
-    oxide: 0.0017
-    peroxide: 0.0186
-    superoxide: 0.0075
-    S: 0.0121
-    F: 0.0025
-    Cl: 0.0016
-    Br: 0.0022
-    I: 0.0059
-    N: 0.0084
+    oxide: 0.0025
+    peroxide: 0.0198
+    superoxide: 0.0096
+    S: 0.0113
+    F: 0.0049
+    Cl: 0.0055
+    Br: 0.0044
+    I: 0.0108
+    N: 0.0217
     Se: 0.0341
-    Si: 0.0621
+    Si: 0.0435
     Sb: 0.0089
-    Te: 0.024
-    H: 0.0013
+    Te: 0.0276
+    H: 0.002
     ozonide: 0

pymatgen/entries/compatibility.py

@@ -10,7 +10,7 @@
 import os
 import warnings
 from collections import defaultdict
-from typing import List, Optional, Sequence, Union
+from typing import Optional, Sequence, Union, List, Type
 
 import numpy as np
 from monty.design_patterns import cached_class
@@ -176,7 +176,7 @@ class GasCorrection(Correction):
     """
     Correct gas energies to obtain the right formation energies. Note that
     this depends on calculations being run within the same input set.
-    For old MaterialsProjectCompatibility and MITCompatibility.
+    Used by legacy MaterialsProjectCompatibility and MITCompatibility.
     """
 
     def __init__(self, config_file):
@@ -215,7 +215,7 @@ class AnionCorrection(Correction):
     Correct anion energies to obtain the right formation energies. Note that
     this depends on calculations being run within the same input set.
 
-    For old MaterialsProjectCompatibility and MITCompatibility.
+    Used by legacy MaterialsProjectCompatibility and MITCompatibility.
     """
 
     def __init__(self, config_file, correct_peroxide=True):
@@ -306,6 +306,8 @@ class AqueousCorrection(Correction):
     """
     This class implements aqueous phase compound corrections for elements
     and H2O.
+
+    Used only by MITAqueousCompatibility.
     """
 
     def __init__(self, config_file, error_file=None):
@@ -820,6 +822,7 @@ def __init__(
         compat_type="Advanced",
         correct_peroxide=True,
         check_potcar_hash=False,
+        config_file=None,
     ):
         """
         Args:
@@ -848,6 +851,9 @@ def __init__(
             check_potcar_hash (bool): Use potcar hash to verify POTCAR settings are
                 consistent with MPRelaxSet. If False, only the POTCAR symbols will
                 be used. (Default: False)
+            config_file (Path): Path to the selected compatibility.yaml config file.
+                If None, defaults to `MP2020Compatibility.yaml` distributed with
+                pymatgen.
 
         References:
             Wang, A., et al. A framework for quantifying uncertainty in DFT energy corrections.
@@ -864,7 +870,10 @@ def __init__(
         self.check_potcar_hash = check_potcar_hash
 
         # load corrections and uncertainties
-        self.config_file = os.path.join(MODULE_DIR, "MP2020Compatibility.yaml")
+        if config_file:
+            self.config_file = config_file
+        else:
+            self.config_file = os.path.join(MODULE_DIR, "MP2020Compatibility.yaml")
         c = loadfn(self.config_file)
         self.name = c["Name"]
         self.comp_correction = c["Corrections"].get("CompositionCorrections", defaultdict(float))
@@ -1158,7 +1167,7 @@ class MaterialsProjectAqueousCompatibility(Compatibility):
 
     def __init__(
         self,
-        solid_compat: Optional[Compatibility] = MaterialsProjectCompatibility,
+        solid_compat: Optional[Type[Compatibility]] = MaterialsProjectCompatibility,
         o2_energy: Optional[float] = None,
         h2o_energy: Optional[float] = None,
         h2o_adjustments: Optional[float] = None,
@@ -1186,10 +1195,10 @@ def __init__(
                 If not set, this value will be determined from any H2O entries passed to process_entries.
                 Default: None
         """
-        self.solid_compat = solid_compat
-        if self.solid_compat:
-            if not isinstance(self.solid_compat, Compatibility):  # check whether solid_compat has been instantiated
-                self.solid_compat = solid_compat()
+        self.solid_compat = None
+        # check whether solid_compat has been instantiated
+        if solid_compat and not isinstance(solid_compat, Compatibility):
+            self.solid_compat = solid_compat()
 
         self.o2_energy = o2_energy
         self.h2o_energy = h2o_energy

pymatgen/entries/correction_calculator.py

@@ -3,9 +3,10 @@
 entries given to the CorrectionCalculator constructor.
 """
 
+import os
 import warnings
 from collections import OrderedDict
-from typing import Dict, List, Tuple, Union, Sequence
+from typing import Dict, List, Tuple, Union, Sequence, Optional
 
 try:
     import ruamel.yaml as yaml
@@ -306,6 +307,11 @@ def compute_corrections(self, exp_entries: list, calc_entries: dict) -> dict:
                 round(self.corrections[i], 3),
                 round(self.corrections_std_error[i], 4),
             )
+
+        # set ozonide correction to 0 so that this species does not recieve a correction
+        # while other oxide types do
+        self.corrections_dict["ozonide"] = (0, 0)
+
         return self.corrections_dict
 
     def graph_residual_error(self) -> go.Figure:
@@ -414,14 +420,16 @@ def graph_residual_error_per_species(self, specie: str) -> go.Figure:
 
         return fig
 
-    def make_yaml(self, name: str = "MP2020") -> None:
+    def make_yaml(self, name: str = "MP2020", dir: Optional[str] = None) -> None:
         """
         Creates the _name_Compatibility.yaml that stores corrections as well as _name_CompatibilityUncertainties.yaml
         for correction uncertainties.
 
         Args:
             name: str, alternate name for the created .yaml file.
-            Default: "MP2020"
+                Default: "MP2020"
+            dir: str, directory in which to save the file. Pass None (default) to
+                save the file in the current working directory.
         """
 
         if len(self.corrections) == 0:
@@ -438,7 +446,7 @@ def make_yaml(self, name: str = "MP2020") -> None:
         o_error: "OrderedDict[str, float]" = OrderedDict()
         f_error: "OrderedDict[str, float]" = OrderedDict()
 
-        for specie in self.species:
+        for specie in list(self.species) + ["ozonide"]:
             if specie in ggaucorrection_species:
                 o[specie] = self.corrections_dict[specie][0]
                 f[specie] = self.corrections_dict[specie][0]
@@ -450,9 +458,6 @@ def make_yaml(self, name: str = "MP2020") -> None:
                 comp_corr[specie] = self.corrections_dict[specie][0]
                 comp_corr_error[specie] = self.corrections_dict[specie][1]
 
-        comp_corr["ozonide"] = 0  # do i need this??
-        comp_corr_error["ozonide"] = 0
-
         outline = """\
         Name:
         Corrections:
@@ -466,9 +471,13 @@ def make_yaml(self, name: str = "MP2020") -> None:
                 F:
             CompositionCorrections:
         """
-
         fn = name + "Compatibility.yaml"
-        file = open(fn, "w")
+        if dir:
+            path = os.path.join(dir, fn)
+        else:
+            path = fn
+
+        file = open(path, "w")
         yml = yaml.YAML()
         yml.Representer.add_representer(OrderedDict, yml.Representer.represent_dict)
         yml.default_flow_style = False
@@ -498,5 +507,5 @@ def make_yaml(self, name: str = "MP2020") -> None:
             "Uncertainties corresponding to each energy correction (eV/atom)", indent=2
         )
 
-        yaml.dump(contents, file)
+        yml.dump(contents, file)
         file.close()