Core hole calculations

doc/users/user_ref.rst

@@ -920,6 +920,15 @@ User input reference
         **Predicates**
           - ``value.lower() in ['exponential']``
 
+ :OrbitalOccupancies: Modify the default orbital occupancies in order to perform a DeltaSCF calculation. 
+
+  :red:`Keywords`
+   :occupancies: List of orbitals, i, for which the default occupancy, f, should be overwritten, written as a list in the format "i f_up f_down", where the orbitals are indexed from zero. 
+
+    **Type** ``str``
+
+    **Default** ````
+
  :Constants: Physical and mathematical constants used by MRChem
 
   :red:`Keywords`

python/mrchem/api.py

@@ -32,6 +32,7 @@
     write_scf_properties,
     write_scf_plot,
     write_rsp_calc,
+    write_scf_occupancies,
     parse_wf_method,
 )
 from .periodictable import PeriodicTable as PT, PeriodicTableByZ as PT_Z
@@ -165,6 +166,8 @@ def write_scf_calculation(user_dict, origin):
     plot_dict = write_scf_plot(user_dict)
     if len(plot_dict) > 0:
         scf_dict["plots"] = plot_dict
+
+    scf_dict["occupancies"] = write_scf_occupancies(user_dict)
 
     return scf_dict
 

python/mrchem/helpers.py

@@ -526,3 +526,99 @@ def parse_wf_method(user_dict):
         "dft_funcs": dft_funcs,
     }
     return wf_dict
+
+# Error/warning messages
+ERROR_MESSAGE_ORBITAL_OCCUPANCIES = (
+    lambda details: f"ABORT: INVALID ORBITAL OCCUPANCIES: {details}"
+)
+
+def write_scf_occupancies(user_dict):
+    """Convert orbital occupancies from JSON syntax to program syntax."""
+    # First validate the input file
+    orbitals, occupancies = validate_orbital_occupancies(user_dict)
+
+    return [
+        {"orbital": orbital, "occupancy": occupancy}
+        for orbital, occupancy in zip(orbitals, occupancies)
+    ]
+
+def validate_orbital_occupancies(user_dict):
+    """Parse the $occupancies block and ensure correct formatting."""
+    import re
+
+    # Regex components
+    line_start = r"^"
+    line_end = r"$"
+    decimal = r"[+-]?([0-9]+\.?[0-9]*|\.[0-9]+)"
+    integer = r"[0-9]+"
+    one_or_more_whitespace = r"[\s]+"
+    zero_or_more_whitespace = r"[\s]*"
+
+    # Build regex
+    restricted_occupancies = (
+        line_start
+        + zero_or_more_whitespace
+        + integer
+        + (one_or_more_whitespace + decimal)
+        + zero_or_more_whitespace
+        + line_end
+    )
+    unrestricted_occupancies = (
+        line_start
+        + zero_or_more_whitespace
+        + integer
+        + (one_or_more_whitespace + decimal) * 2
+        + zero_or_more_whitespace
+        + line_end
+    )
+
+    occ_restricted = re.compile(restricted_occupancies)
+    occ_unrestricted = re.compile(unrestricted_occupancies)
+
+    occs_raw = user_dict["OrbitalOccupancies"]["occupancies"]
+
+    lines = [x.strip() for x in occs_raw.strip().splitlines() if x != ""]
+    # Parse coordinates
+    orbitals = []
+    occupancies = []
+    bad_occupancies = []
+    for occ in lines:
+        match_restricted = occ_restricted.match(occ)
+        match_unrestricted = occ_unrestricted.match(occ)
+        if match_restricted:
+            g = match_restricted.group()
+            orbitals.append(int(g.split()[0].strip()))
+            occupancies.append([float(c.strip()) for c in g.split()[1:]])
+        elif match_unrestricted:
+            g = match_unrestricted.group()
+            orbitals.append(int(g.split()[0].strip()))
+            occupancies.append([float(c.strip()) for c in g.split()[1:]])
+        else:
+            bad_occupancies.append(occ)
+
+    if bad_occupancies:
+        newline = "\n"
+        raise RuntimeError(
+            ERROR_MESSAGE_ORBITAL_OCCUPANCIES(
+                f"One or more orbital occupancies had an invalid input format:\n{newline.join(bad_occupancies)}"
+            )
+        )
+
+    # Check that the orbital is valid - we would need the total number of orbitals to do this properly
+    # so here we just check the index isn't negative
+    fltr = filter(lambda x: x < 0, orbitals)
+    if any(list(fltr)):
+        newline = "\n"
+        raise RuntimeError(
+            self.ERROR_MESSAGE_ORBITAL_OCCUPANCIES(
+                f"One or more invalid atomic symbols:\n{newline.join(set(fltr))}"
+            )
+        )
+
+    return orbitals, occupancies
+
+
+
+
+
+

python/mrchem/input_parser/README.md

@@ -1,2 +1,2 @@
-This file was automatically generated by parselglossy on 2022-10-03
+This file was automatically generated by parselglossy on 2023-09-01
 Editing is *STRONGLY DISCOURAGED*

python/mrchem/input_parser/__init__.py

@@ -1,4 +1,4 @@
 # -*- coding: utf-8 -*-
 
-# This file was automatically generated by parselglossy on 2022-10-03
+# This file was automatically generated by parselglossy on 2023-09-01
 # Editing is *STRONGLY DISCOURAGED*

python/mrchem/input_parser/api.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# This file was automatically generated by parselglossy on 2022-10-26
+# This file was automatically generated by parselglossy on 2023-09-01
 # Editing is *STRONGLY DISCOURAGED*
 
 from copy import deepcopy
@@ -614,6 +614,10 @@ def stencil() -> JSONDict:
                                                                                   "['exponential']"],
                                                                 'type': 'str'}],
                                             'name': 'Permittivity'}]},
+                    {   'keywords': [   {   'default': '',
+                                            'name': 'occupancies',
+                                            'type': 'str'}],
+                        'name': 'OrbitalOccupancies'},
                     {   'keywords': [   {   'default': 78.9451185,
                                             'name': 'hartree2simagnetizability',
                                             'type': 'float'},

python/mrchem/input_parser/cli.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# This file was automatically generated by parselglossy on 2022-10-03
+# This file was automatically generated by parselglossy on 2023-09-01
 # Editing is *STRONGLY DISCOURAGED*
 
 import argparse

python/mrchem/input_parser/docs/user_ref.rst

@@ -920,6 +920,15 @@ User input reference
         **Predicates**
           - ``value.lower() in ['exponential']``
 
+ :OrbitalOccupancies: Modify the default orbital occupancies in order to perform a DeltaSCF calculation. 
+
+  :red:`Keywords`
+   :occupancies: List of orbitals, i, for which the default occupancy, f, should be overwritten, written as a list in the format "i f_up f_down", where the orbitals are indexed from zero. 
+
+    **Type** ``str``
+
+    **Default** ````
+
  :Constants: Physical and mathematical constants used by MRChem
 
   :red:`Keywords`

python/mrchem/input_parser/plumbing/atoms.py

@@ -34,9 +34,10 @@
 
 try:
     import pyparsing as pp
+
     if pp.__version__.split(".")[0] < "3":
-       # Import local copy
-       from . import pyparsing as pp  # type: ignore
+        # Import local copy
+        from . import pyparsing as pp  # type: ignore
 except ImportError:
     # Import local copy
     from . import pyparsing as pp  # type: ignore

python/mrchem/input_parser/plumbing/getkw.py

@@ -43,9 +43,10 @@
 
 try:
     import pyparsing as pp
+
     if pp.__version__.split(".")[0] < "3":
-       # Import local copy
-       from . import pyparsing as pp  # type: ignore
+        # Import local copy
+        from . import pyparsing as pp  # type: ignore
 except ImportError:
     # Import local copy
     from . import pyparsing as pp  # type: ignore
@@ -131,3 +132,4 @@ def parse_string_to_dict(lexer: "pp.ParserElement", s: str) -> JSONDict:
     if flatten_list(tokens_list) != flatten_list(dict_to_list(tokens_dict)):
         raise ParselglossyError("A keyword is repeated. Please check your input.")
     return tokens_dict
+

python/mrchem/input_parser/plumbing/lexer.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# This file was automatically generated by parselglossy on 2022-10-03
+# This file was automatically generated by parselglossy on 2023-09-01
 # Editing is *STRONGLY DISCOURAGED*
 
 import json