From 2174abd8cd8b918d7ffb84b63a3d2cde03e62162 Mon Sep 17 00:00:00 2001
From: Yangxing Wang <alopexcanis@gmail.com>
Date: Sat, 8 Aug 2026 02:24:07 +0800
Subject: [PATCH] Add keyword for user defined polarization groups

---
 .gitignore                  | 1 +
 PoltypeModules/multipole.py | 9 ++++++++-
 PoltypeModules/poltype.py   | 3 +++
 README/README_HELP.MD       | 1 +
 4 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 7a75863a..cdd07fd2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 __pycache__/
 __init__.py
+.vscode/
\ No newline at end of file
diff --git a/PoltypeModules/multipole.py b/PoltypeModules/multipole.py
index 12a38609..b80b6cb2 100644
--- a/PoltypeModules/multipole.py
+++ b/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")
 
diff --git a/PoltypeModules/poltype.py b/PoltypeModules/poltype.py
index b219e71a..5a484edb 100644
--- a/PoltypeModules/poltype.py
+++ b/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:
diff --git a/README/README_HELP.MD b/README/README_HELP.MD
index 32ee0cff..7996dffe 100644
--- a/README/README_HELP.MD
+++ b/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.