f! species active

ReactionMechanismGenerator · Sep 11, 2024 · 63aa794 · 63aa794
1 parent d8833f9
commit 63aa794
Showing 1 changed file with 11 additions and 7 deletions.
diff --git a/arc/species/species.py b/arc/species/species.py
@@ -184,11 +184,15 @@ class ARCSpecies(object):
         fragments (Optional[List[List[int]]]):
             Fragments represented by this species, i.e., as in a VdW well or a TS.
             Entries are atom index lists of all atoms in a fragment, each list represents a different fragment.
-        active (Tuple[int, int], optional): The number of active electrons and orbitals, usually from a molpro CCSD sp calc.
-                                            The first value is the number of active electrons, determined by the total
-                                            number of electrons minus the core electrons (2 e's per heavy atom).
-                                            The second value is the number of active orbitals, determined by the number
-                                            of closed-shell orbitals and active orbitals (w/o core orbitals).
+        active (dict, optional): The active orbitals. Possible keys are:
+                                 'occ' (List[int]): The occupied orbitals.
+                                 'closed' (List[int]): The closed-shell orbitals.
+                                 'frozen' (List[int]): The frozen orbitals.
+                                 'core' (List[int]): The core orbitals.
+                                 'e_o' (Tuple[int, int]): The number of active electrons, determined by the total number
+                                 of electrons minus the core electrons (2 e's per heavy atom), and the number of active
+                                 orbitals, determined by the number of closed-shell orbitals and active orbitals
+                                 (w/o core orbitals).
         irc_label (str, optional): The label of an original ``ARCSpecies`` object (a TS) for which an IRC job was spawned.
                                    The present species object instance represents a geometry optimization job of the IRC
                                    result in one direction.
@@ -290,7 +294,7 @@ class ARCSpecies(object):
         fragments (Optional[List[List[int]]]):
             Fragments represented by this species, i.e., as in a VdW well or a TS.
             Entries are atom index lists of all atoms in a fragment, each list represents a different fragment.
-        active (Tuple[int, int], optional): The number of active electrons and orbitals, usually from a molpro CCSD sp calc.
+        active (dict): The active orbitals.
         irc_label (str): The label of an original ``ARCSpecies`` object (a TS)  for which an IRC job was spawned.
                          The present species object instance represents a geometry optimization job of the IRC
                          result in one direction. If a species is a transition state, then this attribute contains the
@@ -301,6 +305,7 @@ class ARCSpecies(object):
     """
 
     def __init__(self,
+                 active: Optional[dict] = None,
                  adjlist: str = '',
                  bdes: Optional[list] = None,
                  bond_corrections: Optional[dict] = None,
@@ -322,7 +327,6 @@ def __init__(self,
                  multiplicity: Optional[int] = None,
                  multi_species: Optional[str] = None,
                  number_of_radicals: Optional[int] = None,
-                 active: Optional[Tuple[int, int]] = None,
                  optical_isomers: Optional[int] = None,
                  preserve_param_in_scan: Optional[list] = None,
                  rmg_species: Optional[Species] = None,