Add keyword for user defined polarization groups

.gitignore

@@ -1,2 +1,3 @@
 __pycache__/
 __init__.py
+.vscode/

PoltypeModules/multipole.py

@@ -611,7 +611,14 @@ def gen_peditinfile(poltype,mol):
     f.write("\n")
     f.flush()
     os.fsync(f.fileno())
-    f.write("2\n")
+    if poltype.polgrpcutbnds:
+        f.write("3\n")
+        for b in poltype.polgrpcutbnds.strip(" ,'\"").split(","):
+            a1, a2 = b.split("/")
+            f.write(f"{a1} {a2}\n")
+        f.write("\n")
+    else:
+        f.write("2\n")
     f.write("N\n")
     f.write("Y\n")
 

PoltypeModules/poltype.py

@@ -127,6 +127,7 @@ class PolarizableTyper():
         fragmenterdebugmode:bool=False
         jobsatsametime:int=0
         usepoleditframes:bool=True
+        polgrpcutbnds:str=""
         databasematchonly:bool=False
         setupfragjobsonly:bool=False
         allowradicals:bool=False
@@ -465,6 +466,8 @@ def __post_init__(self):
 
                         elif "usepoleditframes" in newline:
                             self.usepoleditframes=self.SetDefaultBool(line,a,True)
+                        elif "polgrpcutbnds" in newline:
+                            self.polgrpcutbnds=a
                         elif "generateextendedconf" in newline:
                             self.generateextendedconf=self.SetDefaultBool(line,a,True)
                         elif "userconformation" in newline:

README/README_HELP.MD

@@ -113,6 +113,7 @@
 
 ``usepoleditframes`` specifies to use POLEDIT frames rather than poltype frame detection. Default is True.
 
+``polgrpcutbnds`` defines a custom list of bonds to cut for polarization group separation. The format is a comma-separated list of atom index pairs (e.g., "1/2,3/4,5/6"). The default is "", which means to put all atoms in one group.
 
 ``dmamethod``  specifies which quantum method to use for distributed multipole analysis (DMA). Default is MP2.