diff --git a/.gitignore b/.gitignore
index 7ca8f23bc..44dcf1033 100644
--- a/.gitignore
+++ b/.gitignore
@@ -30,3 +30,8 @@ site/
 
 src/Core/_version
 .DS_Store
+
+# Files related to Python scripts #
+#############
+*.egg*
+__pycache__
diff --git a/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/minas_inlet_2m.reg b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/minas_inlet_2m.reg
new file mode 100644
index 000000000..0850aac38
--- /dev/null
+++ b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/minas_inlet_2m.reg
@@ -0,0 +1,12 @@
+Region written by ACE/gredit
+1
+9 1
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+-64.401771 45.298463
diff --git a/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence1.reg b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence1.reg
new file mode 100644
index 000000000..b2ed6f3f1
--- /dev/null
+++ b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence1.reg
@@ -0,0 +1,48 @@
+Region written by ACE/gredit
+1
+45 1
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diff --git a/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence2.reg b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence2.reg
new file mode 100644
index 000000000..2feda88a4
--- /dev/null
+++ b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence2.reg
@@ -0,0 +1,27 @@
+Region written by ACE/gredit
+1
+24 1
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+-67.970558 49.665844
diff --git a/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence3.reg b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence3.reg
new file mode 100644
index 000000000..a37e7df78
--- /dev/null
+++ b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence3.reg
@@ -0,0 +1,27 @@
+Region written by ACE/gredit
+1
+24 1
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+-54.454654 50.402194
+-55.132660 51.698171
diff --git a/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Gr3/Nudge_gr3/gen_nudge_gr3.py b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Gr3/Nudge_gr3/gen_nudge_gr3.py
new file mode 100644
index 000000000..c61d2c017
--- /dev/null
+++ b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Gr3/Nudge_gr3/gen_nudge_gr3.py
@@ -0,0 +1,83 @@
+from pylib_essentials.schism_file import schism_grid
+
+def gen_nudge(hgrid:schism_grid, outdir, rlmax = 1.5, rnu_day=0.25):
+        """
+        schism_grid (from pylib) must be in lon/lat coordinates
+        set up nudge zone within rlmax distance from the ocean boundary;
+        modify the nudging zone width rlmax.
+        rlmax can be a uniform value, e.g., rl_max = 1.5,
+        or a 2D array of the same size as the hgrid's number of nodes,
+        e.g., rl_max = np.zeros(NP) with further tuning of the nudging zone width.
+        """
+
+        rnu_max = 1.0 / rnu_day / 86400.0
+
+        #get nudge zone
+        lon = hgrid.x
+        lat = hgrid.y
+        nudge_coeff = np.zeros(hgrid.x.shape, dtype=float)
+
+        global_idxs = {}
+
+        t0 = time()
+
+        nudge_coeff = np.array([0.0]*NP, dtype=float)
+
+        for i in self.ocean_bnd_ids:
+            print(f'boundary {i}')
+            bnd_idxs = gdf.iloc[i].indexes
+
+            dis = abs((lon + 1j*lat)[:, None] - (lon[bnd_idxs] + 1j*lat[bnd_idxs])[None, :]).min(axis=1)
+
+            out = (1-dis/rlmax)*rnu_max
+            out[out<0] = 0
+            out[out>rnu_max] = rnu_max
+            fp = out>0
+            nudge_coeff[fp] = np.maximum(out[fp], nudge_coeff[fp])
+
+            idxs_nudge=np.zeros(NP, dtype=int)
+            idxs=np.where(out > 0)[0]
+            idxs_nudge[idxs]=1
+  
+            #expand nudging marker to neighbor nodes
+            i34 = self.hgrid.elements.i34
+            fp = i34==3
+            idxs=np.where(np.max(out[elnode[fp, 0:3]], axis=1) > 0)[0]
+            idxs_nudge[elnode[fp,0:3][idxs,:]]=1
+            idxs=np.where(np.max(out[elnode[~fp, :]], axis=1) > 0)[0]
+            idxs_nudge[elnode[~fp,:][idxs,:]]=1
+
+            idxs=np.where(idxs_nudge == 1)[0]
+            global_idxs[i] = idxs
+
+
+        #logger.info(f'len of nudge idxs is {len(idxs)}')
+        logger.info(f'It took {time() -t0} sencods to calcuate nudge coefficient')
+
+        nudge = [f"rlmax={rlmax}, rnu_day={rnu_day}"]
+        nudge.extend("\n")
+        nudge.append(f"{NE} {NP}")
+        nudge.extend("\n")
+        hgrid = self.hgrid.to_dict()
+        nodes = hgrid['nodes']
+        elements = hgrid['elements']
+        for idn, (coords, values) in nodes.items():
+            line = [f"{idn}"]
+            line.extend([f"{x:<.7e}" for x in coords])
+            line.extend([f"{nudge_coeff[int(idn)-1]:<.7e}"])
+            line.extend("\n")
+            nudge.append(" ".join(line))
+
+        for id, element in elements.items():
+            line = [f"{id}"]
+            line.append(f"{len(element)}")
+            line.extend([f"{e}" for e in element])
+            line.extend("\n")
+            nudge.append(" ".join(line))
+
+        with open(outdir / 'TEM_nudge.gr3','w+') as fid:
+            fid.writelines(nudge)
+
+        shutil.copy2(outdir / 'TEM_nudge.gr3', outdir / 'SAL_nudge.gr3')
+
+        return global_idxs
\ No newline at end of file
diff --git a/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Nudge/gen_nudge2.py b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Nudge/gen_nudge2.py
new file mode 100755
index 000000000..a40a7bcc2
--- /dev/null
+++ b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Nudge/gen_nudge2.py
@@ -0,0 +1,21 @@
+#! /usr/bin/env python
+from datetime import datetime, timedelta
+import logging
+
+from pyschism.mesh import Hgrid, Vgrid
+from pyschism.forcing.hycom.hycom2schism import Nudge
+
+
+logging.basicConfig(level=logging.INFO, force=True)
+
+
+if __name__ == '__main__':
+
+    hgrid=Hgrid.open('./hgrid.gr3', crs='epsg:4326')
+    vgrid='./vgrid.in'
+    outdir='./'
+    start_date = datetime(2022, 1, 1)
+    rnday=171
+
+    nudge=Nudge()
+    nudge.fetch_data(outdir, hgrid, vgrid, start_date, rnday)
diff --git a/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/setup.py b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/setup.py
deleted file mode 100644
index 02a3ed261..000000000
--- a/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/setup.py
+++ /dev/null
@@ -1,29 +0,0 @@
-import setuptools
-import io
-
-with io.open('README.md','r', encoding='utf8') as fh:
-  long_description = fh.read()
-
-  setuptools.setup(
-  name='stofs3d_atlantic_preproc',
-  version='0.0.1',
-  description='Python tools for generating inputs for STOFS3D-ATL',
-  long_description=long_description,
-  long_description_content_type="text/markdown",
-  url='',
-  project_urls = {
-    "Issues": ""
-  },
-  license='MIT',
-  packages=[
-    '',
-  ],
-  package_data={},
-  install_requires=[
-    'numpy',
-    'pandas',
-    'gdal>=3.6.0',
-    'shapely>=2.0.0',
-    'geopandas>=0.12.0',
-  ],
-)
diff --git a/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/__pycache__/__init__.cpython-39.pyc b/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/__pycache__/__init__.cpython-39.pyc
deleted file mode 100644
index fa4b8f243..000000000
Binary files a/src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/__pycache__/__init__.cpython-39.pyc and /dev/null differ