Cp2k 2.0

.pre-commit-config.yaml

@@ -62,7 +62,7 @@ repos:
       - id: codespell
         stages: [commit, commit-msg]
         exclude_types: [html]
-        args: [--ignore-words-list, 'titel,titels,reson,rute,pres,kno']
+        args: [--ignore-words-list, 'titel,titels,reson,rute,pres,kno,coo']
 
   - repo: https://github.com/PyCQA/pydocstyle
     rev: 6.1.1

pymatgen/cli/pmg.py

@@ -132,6 +132,16 @@ def main():
         nargs="+",
         help="Variables to add in the form of space separated key value pairs. E.g., PMG_VASP_PSP_DIR ~/psps",
     )
+
+    groups.add_argument(
+        "--cp2k",
+        dest="cp2k_data_dirs",
+        metavar="dir_name",
+        nargs=2,
+        help="Initial directory where the CP2K data is located and the output directory where the "
+        "CP2K yaml data files will be written",
+    )
+
     parser_config.add_argument(
         "-b",
         "--backup",

pymatgen/cli/pmg_config.py

@@ -22,16 +22,105 @@
 from pymatgen.core import OLD_SETTINGS_FILE, SETTINGS_FILE
 
 
+def setup_cp2k_data(cp2k_data_dirs: list[str]) -> None:
+    """Setup CP2K basis and potential data directory"""
+    data_dir, target_dir = (os.path.abspath(dir) for dir in cp2k_data_dirs)
+    try:
+        os.mkdir(target_dir)
+    except OSError:
+        reply = input("Destination directory exists. Continue (y/n)?")
+        if reply != "y":
+            print("Exiting ...")
+            raise SystemExit(0)
+    print("Generating pymatgen resource directory for CP2K...")
+
+    import glob
+
+    from monty.json import jsanitize
+    from ruamel import yaml
+
+    from pymatgen.core import Element
+    from pymatgen.io.cp2k.inputs import GaussianTypeOrbitalBasisSet, GthPotential
+    from pymatgen.io.cp2k.utils import chunk
+
+    basis_files = glob.glob(os.path.join(data_dir, "*BASIS*"))
+    potential_files = glob.glob(os.path.join(data_dir, "*POTENTIAL*"))
+
+    settings: dict[str, dict] = {str(el): {"potentials": {}, "basis_sets": {}} for el in Element}
+
+    for potential_file in potential_files:
+        print(f"Processing... {potential_file}")
+        with open(potential_file) as file:
+            try:
+                chunks = chunk(file.read())
+            except IndexError:
+                continue
+        for chk in chunks:
+            try:
+                potential = GthPotential.from_string(chk)
+                potential.filename = os.path.basename(potential_file)
+                potential.version = None
+                settings[potential.element.symbol]["potentials"][potential.get_hash()] = jsanitize(
+                    potential, strict=True
+                )
+            except ValueError:
+                # Chunk was readable, but the element is not pmg recognized
+                continue
+            except IndexError:
+                # Chunk was readable, but invalid. Mostly likely "N/A" for this potential
+                continue
+
+    for basis_file in basis_files:
+        print(f"Processing... {basis_file}")
+        with open(basis_file) as file:
+            try:
+                chunks = chunk(file.read())
+            except IndexError:
+                continue
+        for chk in chunks:
+            try:
+                basis = GaussianTypeOrbitalBasisSet.from_string(chk)
+                basis.filename = os.path.basename(basis_file)
+                settings[basis.element.symbol]["basis_sets"][basis.get_hash()] = jsanitize(  # type: ignore
+                    basis, strict=True
+                )
+            except ValueError:
+                # Chunk was readable, but the element is not pmg recognized
+                continue
+            except IndexError:
+                # Chunk was readable, but invalid. Mostly likely "N/A" for this potential
+                continue
+
+    print("Done processing cp2k data files")
+
+    for el in settings:
+        print(f"Writing {el} settings file")
+        with open(os.path.join(target_dir, el), "w") as file:
+            yaml.dump(settings.get(el), file, default_flow_style=False)
+
+    print(
+        "\n CP2K resource directory generated. It is recommended that you run:"
+        f"\n  'pmg config --add PMG_CP2K_DATA_DIR {os.path.abspath(target_dir)}' "
+    )
+    print(
+        "\n It is also recommended that you set the following (with example values):"
+        "\n  'pmg config --add PMG_DEFAULT_CP2K_FUNCTIONAL PBE' "
+        "\n  'pmg config --add PMG_DEFAULT_CP2K_BASIS_TYPE TZVP-MOLOPT' "
+        "\n  'pmg config --add PMG_DEFAULT_CP2K_AUX_BASIS_TYPE pFIT' "
+    )
+    print("\n Start a new terminal to ensure that your environment variables are properly set.")
+
+
 def setup_potcars(potcar_dirs: list[str]):
     """Setup POTCAR directories."""
-    pspdir, targetdir = (os.path.abspath(d) for d in potcar_dirs)
+    psp_dir, target_dir = (os.path.abspath(d) for d in potcar_dirs)
     try:
-        os.makedirs(targetdir)
+        os.makedirs(target_dir)
     except OSError:
-        r = input("Destination directory exists. Continue (y/n)? ")
-        if r != "y":
+        reply = input("Destination directory exists. Continue (y/n)? ")
+        if reply != "y":
             print("Exiting ...")
-            sys.exit(0)
+            raise SystemExit(0)
 
     print("Generating pymatgen resources directory...")
 
@@ -51,18 +140,18 @@ def setup_potcars(potcar_dirs: list[str]):
         "potUSPP_GGA": "POT_GGA_US_PW91",
     }
 
-    for parent, subdirs, _files in os.walk(pspdir):
+    for parent, subdirs, _files in os.walk(psp_dir):
         basename = os.path.basename(parent)
         basename = name_mappings.get(basename, basename)
         for subdir in subdirs:
             filenames = glob.glob(os.path.join(parent, subdir, "POTCAR*"))
             if len(filenames) > 0:
                 try:
-                    basedir = os.path.join(targetdir, basename)
-                    if not os.path.exists(basedir):
-                        os.makedirs(basedir)
+                    base_dir = os.path.join(target_dir, basename)
+                    if not os.path.exists(base_dir):
+                        os.makedirs(base_dir)
                     fname = filenames[0]
-                    dest = os.path.join(basedir, os.path.basename(fname))
+                    dest = os.path.join(base_dir, os.path.basename(fname))
                     shutil.copy(fname, dest)
                     ext = fname.split(".")[-1]
                     if ext.upper() in ["Z", "GZ"]:
@@ -73,16 +162,16 @@ def setup_potcars(potcar_dirs: list[str]):
                             p.communicate()
                     if subdir == "Osmium":
                         subdir = "Os"
-                    dest = os.path.join(basedir, f"POTCAR.{subdir}")
-                    shutil.move(os.path.join(basedir, "POTCAR"), dest)
+                    dest = os.path.join(base_dir, f"POTCAR.{subdir}")
+                    shutil.move(os.path.join(base_dir, "POTCAR"), dest)
                     with subprocess.Popen(["gzip", "-f", dest]) as p:
                         p.communicate()
                 except Exception as ex:
                     print(f"An error has occurred. Message is {str(ex)}. Trying to continue... ")
 
     print(
         "\nPSP resources directory generated. It is recommended that you "
-        f"run 'pmg config --add PMG_VASP_PSP_DIR {os.path.abspath(targetdir)}'"
+        f"run 'pmg config --add PMG_VASP_PSP_DIR {os.path.abspath(target_dir)}'"
     )
     print("Start a new terminal to ensure that your environment variables are properly set.")
 
@@ -209,3 +298,5 @@ def configure_pmg(args: Namespace):
         install_software(args.install)
     elif args.var_spec:
         add_config_var(args.var_spec, args.backup)
+    elif args.cp2k_data_dirs:
+        setup_cp2k_data(args.cp2k_data_dirs)

pymatgen/entries/compatibility.py

@@ -938,8 +938,9 @@ def get_adjustments(self, entry: AnyComputedEntry) -> list[EnergyAdjustment]:
 
         # check the POTCAR symbols
         # this should return ufloat(0, 0) or raise a CompatibilityError or ValueError
-        pc = PotcarCorrection(MPRelaxSet, check_hash=self.check_potcar_hash)
-        pc.get_correction(entry)
+        if entry.parameters.get("software", "vasp") == "vasp":
+            pc = PotcarCorrection(MPRelaxSet, check_hash=self.check_potcar_hash)
+            pc.get_correction(entry)
 
         # apply energy adjustments
         adjustments: list[CompositionEnergyAdjustment] = []