Made package installable via pip (pymatgen.io.validation) and added p…

…otcar validation using potcar_summary_stats from PMG, temporarily disabling mypy on pre-commit due to clash of module / package name in PMG

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: ^(docs|.*test_files|cmd_line|dev_scripts)
 
 default_language_version:
-  python: python3.8
+  python: python3.11
 
 ci:
   autoupdate_schedule: monthly
@@ -20,11 +20,6 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
-    hooks:
-      - id: flake8
-
   - repo: https://github.com/asottile/pyupgrade
     rev: v3.10.1
     hooks:
@@ -42,7 +37,7 @@ repos:
           - --expand-star-imports
           - --ignore-init-module-imports
 
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
-    hooks:
-      - id: mypy
+#  - repo: https://github.com/pre-commit/mirrors-mypy
+#    rev: v1.5.1
+#    hooks:
+#      - id: mypy

pymatgen/io/validation/__init__.py

@@ -3,3 +3,7 @@
 simulations and calculations. That is, it checks calculation details against a reference
 to ensure that data is compatible with some standard.
 """
+
+from __future__ import annotations
+
+from .validation import ValidationDoc

pymatgen/io/validation/check_common_errors.py

@@ -1,16 +1,17 @@
 import numpy as np
 
+
 def _check_common_errors(
-    reasons, 
-    warnings, 
-    task_doc, 
-    calcs_reversed, 
-    parameters, 
-    incar, 
-    structure, 
-    valid_max_allowed_scf_gradient, 
-    ionic_steps, 
-    num_ionic_steps_to_avg_drift_over
+    reasons,
+    warnings,
+    task_doc,
+    calcs_reversed,
+    parameters,
+    incar,
+    structure,
+    valid_max_allowed_scf_gradient,
+    ionic_steps,
+    num_ionic_steps_to_avg_drift_over,
 ):
     # Check for cases where both GGA and METAGGA are set. This should *not* be allowed, as it can erroneously change
     # the outputted energy significantly. See https://github.com/materialsproject/atomate2/issues/453#issuecomment-1699605867
@@ -22,7 +23,6 @@ def _check_common_errors(
             "for more information."
         )
 
-
     # check if structure electronically converged
     final_esteps = ionic_steps[-1]["electronic_steps"] if incar.get("ALGO", "Normal").lower() != "chi" else 0
     # In a response function run there is no ionic steps, there is no scf step
@@ -31,45 +31,48 @@ def _check_common_errors(
         to_check = {"e_wo_entrp", "e_fr_energy", "e_0_energy"}
         while set(final_esteps[i]) == to_check:
             i += 1
-        is_converged = (i + 1 != parameters.get("NELM", 60))
+        is_converged = i + 1 != parameters.get("NELM", 60)
     elif len(final_esteps) < parameters.get("NELM", 60):
         is_converged = True
     else:
         is_converged = False
-        
+
     if not is_converged:
-        reasons.append(f"CONVERGENCE --> Did not achieve electronic convergence in the final ionic step. NELM should be increased.")
-
-
+        reasons.append(
+            "CONVERGENCE --> Did not achieve electronic convergence in the final ionic step. NELM should be increased."
+        )
+
     # Check if drift force is too large
     try:
         all_drift_forces = calcs_reversed[0]["output"]["outcar"]["drift"]
         if len(all_drift_forces) < num_ionic_steps_to_avg_drift_over:
             drift_forces_to_avg_over = all_drift_forces
         else:
-            drift_forces_to_avg_over = all_drift_forces[::-1][: num_ionic_steps_to_avg_drift_over]
+            drift_forces_to_avg_over = all_drift_forces[::-1][:num_ionic_steps_to_avg_drift_over]
 
         drift_mags_to_avg_over = [np.linalg.norm(drift_forces) for drift_forces in drift_forces_to_avg_over]
         cur_avg_drift_mag = np.average(drift_mags_to_avg_over)
-        
+
         valid_max_drift = 0.05
         if cur_avg_drift_mag > valid_max_drift:
-            reasons.append(f"CONVERGENCE --> Excessive drift of {round(cur_avg_drift_mag,4)} eV/A is greater than allowed "\
-                           f"value of {valid_max_drift} eV/A.")
-    except Exception as e:
+            reasons.append(
+                f"CONVERGENCE --> Excessive drift of {round(cur_avg_drift_mag,4)} eV/A is greater than allowed "
+                f"value of {valid_max_drift} eV/A."
+            )
+    except Exception:
         warnings.append("Drift forces not contained in calcs_reversed! Can not check for excessive drift.")
-
-
+
     # Check for excessively positive final energies (which usually indicates a bad structure)
     valid_max_energy_per_atom = 50
     cur_final_energy_per_atom = task_doc.output.energy_per_atom
     if cur_final_energy_per_atom > valid_max_energy_per_atom:
-        reasons.append(f"LARGE POSITIVE FINAL ENERGY --> Final energy is {round(cur_final_energy_per_atom,4)} eV/atom, which is "\
-                       f"greater than the maximum allowed value of {valid_max_energy_per_atom} eV/atom.")
-
+        reasons.append(
+            f"LARGE POSITIVE FINAL ENERGY --> Final energy is {round(cur_final_energy_per_atom,4)} eV/atom, which is "
+            f"greater than the maximum allowed value of {valid_max_energy_per_atom} eV/atom."
+        )
 
     # Check for excessively large final magnetic moments
-    ### TODO: make this also work for elements Gd and Eu, which have magmoms >5 in at least one of their pure structures
+    # TODO: make this also work for elements Gd and Eu, which have magmoms >5 in at least one of their pure structures
     valid_max_magmoms = {"Gd": 10, "Eu": 10}
     cur_magmoms = [abs(mag["tot"]) for mag in calcs_reversed[0]["output"]["outcar"]["magnetization"]]
     bad_site_magmom_msgs = []
@@ -87,36 +90,34 @@ def _check_common_errors(
                     f"at least one {cur_site_ele} site with magmom greater than {cur_site_max_allowed_magmom}"
                 )
     if len(bad_site_magmom_msgs) > 0:
-        msg = f"MAGNETISM --> Final structure contains sites with magnetic moments that are very likely erroneous. This includes: "
-        msg = msg + "; ".join(set(bad_site_magmom_msgs)) + "." 
+        msg = "MAGNETISM --> Final structure contains sites with magnetic moments that are very likely erroneous. This includes: "
+        msg = msg + "; ".join(set(bad_site_magmom_msgs)) + "."
         reasons.append(msg)
 
-
     # Check for a SCF gradient that is too large (usually indicates unstable calculations)
     # NOTE: do NOT use `e_0_energy`, as there is a bug in the vasprun.xml when printing that variable
     # (see https://www.vasp.at/forum/viewtopic.php?t=16942 for more details).
     skip = abs(parameters.get("NELMDL", -5)) - 1
-    energies = [
-        d["e_fr_energy"]
-        for d in ionic_steps[-1]["electronic_steps"]
-    ]
+    energies = [d["e_fr_energy"] for d in ionic_steps[-1]["electronic_steps"]]
     if len(energies) > skip:
         cur_max_gradient = np.max(np.gradient(energies)[skip:])
         cur_max_gradient_per_atom = cur_max_gradient / structure.num_sites
         if cur_max_gradient_per_atom > valid_max_allowed_scf_gradient:
-            warnings.append(f"STABILITY --> The max SCF gradient is {round(cur_max_gradient_per_atom,4)} eV/atom, which is larger than the typical max expected value of {valid_max_allowed_scf_gradient} eV/atom. "\
-                           f"This sometimes indicates an unstable calculation.")
+            warnings.append(
+                f"STABILITY --> The max SCF gradient is {round(cur_max_gradient_per_atom,4)} eV/atom, which is larger than the typical max expected value of {valid_max_allowed_scf_gradient} eV/atom. "
+                f"This sometimes indicates an unstable calculation."
+            )
     else:
         warnings.append(
-            "Not enough electronic steps to compute valid gradient"
-            " and compare with max SCF gradient tolerance."
+            "Not enough electronic steps to compute valid gradient" " and compare with max SCF gradient tolerance."
         )
-
 
     # Check for Am and Po elements. These currently do not have proper elemental entries
     # and will not get treated properly by the thermo builder.
     chemsys = task_doc.chemsys
     if ("Am" in chemsys) or ("Po" in chemsys):
-        reasons.append("COMPOSITION --> Your structure contains the elements Am and/or Po, which are not currently being accepted.")
+        reasons.append(
+            "COMPOSITION --> Your structure contains the elements Am and/or Po, which are not currently being accepted."
+        )
 
-    return reasons
+    return reasons

pymatgen/io/validation/check_for_excess_empty_space.py

@@ -1,30 +1,30 @@
 from pymatgen.analysis.local_env import VoronoiNN
 import numpy as np
 
+
 def check_for_excess_empty_space(structure):
-    ##### Check 1: find large gaps along one of the defined lattice vectors
+    # Check 1: find large gaps along one of the defined lattice vectors
     lattice_vec_lengths = structure.lattice.lengths
     fcoords = np.array(structure.frac_coords)
 
-    lattice_vec_1_frac_coords = list(np.sort(fcoords[:,0]))
+    lattice_vec_1_frac_coords = list(np.sort(fcoords[:, 0]))
     lattice_vec_1_frac_coords.append(lattice_vec_1_frac_coords[0] + 1)
     lattice_vec_1_diffs = np.diff(lattice_vec_1_frac_coords)
     max_lattice_vec_1_empty_dist = max(lattice_vec_1_diffs) * lattice_vec_lengths[0]
 
-    lattice_vec_2_frac_coords = list(np.sort(fcoords[:,1]))
+    lattice_vec_2_frac_coords = list(np.sort(fcoords[:, 1]))
     lattice_vec_2_frac_coords.append(lattice_vec_2_frac_coords[0] + 1)
     lattice_vec_2_diffs = np.diff(lattice_vec_2_frac_coords)
     max_lattice_vec_2_empty_dist = max(lattice_vec_2_diffs) * lattice_vec_lengths[1]
 
-    lattice_vec_3_frac_coords = list(np.sort(fcoords[:,2]))
+    lattice_vec_3_frac_coords = list(np.sort(fcoords[:, 2]))
     lattice_vec_3_frac_coords.append(lattice_vec_3_frac_coords[0] + 1)
     lattice_vec_3_diffs = np.diff(lattice_vec_3_frac_coords)
     max_lattice_vec_3_empty_dist = max(lattice_vec_3_diffs) * lattice_vec_lengths[2]
-
-    max_empty_distance = max(max_lattice_vec_1_empty_dist, max_lattice_vec_2_empty_dist, max_lattice_vec_3_empty_dist)    
-
 
-    ##### Check 2: get max voronoi polyhedra volume in structure
+    max_empty_distance = max(max_lattice_vec_1_empty_dist, max_lattice_vec_2_empty_dist, max_lattice_vec_3_empty_dist)
+
+    # Check 2: get max voronoi polyhedra volume in structure
     def get_max_voronoi_polyhedra_volume(structure):
         max_voronoi_polyhedra_vol = 0
         vnn = VoronoiNN().get_all_voronoi_polyhedra(structure)
@@ -39,20 +39,20 @@ def get_max_voronoi_polyhedra_volume(structure):
     try:
         max_voronoi_polyhedra_vol = get_max_voronoi_polyhedra_volume(structure)
     except Exception as e:
-
         if "No Voronoi neighbors found for site - try increasing cutoff".lower() in str(e).lower():
             try:
-                structure.make_supercell(2)  # to circumvent weird issue with voronoi class, though this decreases performance significantly.
+                structure.make_supercell(
+                    2
+                )  # to circumvent weird issue with voronoi class, though this decreases performance significantly.
                 max_voronoi_polyhedra_vol = get_max_voronoi_polyhedra_volume(structure)
-            except Exception as e:
+            except Exception:
                 pass
 
         if "infinite vertex in the Voronoi construction".lower() in str(e).lower():
             print(f"{str(e)} As a result, this structure is marked as having excess empty space.")
             max_voronoi_polyhedra_vol = np.inf
 
-
     if (max_voronoi_polyhedra_vol > 25) or (max_voronoi_polyhedra_vol > 5 and max_empty_distance > 7.5):
         return True
     else:
-        return False
+        return False