diff --git a/pixi.lock b/pixi.lock
index 1154a358..828854e2 100644
--- a/pixi.lock
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-  size: 610491
-  timestamp: 1772739572046
+  size: 610723
+  timestamp: 1763746042074
 - pypi: ../autofile
   name: autofile
   version: 0.2025.0
   sha256: 1158420897d789f9aa7bc3d2053412f840d1f377d567c78ca1c1fbc98ed8faf0
   requires_python: '>=3.11'
+  editable: true
 - conda: https://conda.anaconda.org/Auto-Mech/noarch/autofile-0.2025.0-pyh4616a5c_0.conda
   sha256: 027fed4c146c65bb3d55a237c331ff4a4534964e9771c09e7220bce99a208a3d
   md5: b7bfb6a4fcf15eb0d4ec20dc69dc9f58
@@ -1347,12 +1339,13 @@ packages:
   timestamp: 1763748110716
 - pypi: ../autoio
   name: autoio
-  version: 0.2026.0
-  sha256: b554f06265eb5e8204bc87e109b9dba5df8b8a42163ad747fe0213439cb4c49c
+  version: 0.2025.0
+  sha256: 9720401e7f430caa3b97ef6d736d056eed1eeb9fc08ab5e04d3b132882a216af
   requires_python: '>=3.11'
-- conda: https://conda.anaconda.org/Auto-Mech/noarch/autoio-0.2026.0-pyh4616a5c_0.conda
-  sha256: 0dd0d28a368b55cf775b231e7710e1309491b1db79bcad5b334056afe636f6a6
-  md5: 8f97347f404687644c579ac99bae3f7d
+  editable: true
+- conda: https://conda.anaconda.org/Auto-Mech/noarch/autoio-0.2025.0-pyh4616a5c_0.conda
+  sha256: 38f151908a4e4595df7a90bc16d41f71549220ceb3ecd2a1fd7afe121266dbf5
+  md5: e8117f81ed6caf696bdc033fed6e9d93
   depends:
   - mako >=1.3.10
   - more-itertools >=10.8.0
@@ -1364,8 +1357,8 @@ packages:
   - autochem >=0.2025.0,<2.0.0
   - python >=3.11
   - python *
-  size: 5284910
-  timestamp: 1772762271687
+  size: 5285348
+  timestamp: 1763747126180
 - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.2.0-h41a2e66_0.conda
   sha256: 33239a07f7685917cac25646dd33798ee93e61f83504a0c938d86c507e05d7c9
   md5: 4ddfd44e473c676cb8e80548ba4aa704
@@ -3196,12 +3189,13 @@ packages:
   timestamp: 1733255681319
 - pypi: ../mechanalyzer
   name: mechanalyzer
-  version: 0.2026.0
-  sha256: 363ca1cad51d90753262a652999083d551e70f20286cea794df088877ee219da
+  version: 0.2025.0
+  sha256: ae648c05f2a528eeda61f591dee818e43aad5e046148c2b7a9bb070da1b801a8
   requires_python: '>=3.11'
-- conda: https://conda.anaconda.org/Auto-Mech/noarch/mechanalyzer-0.2026.0-pyh4616a5c_0.conda
-  sha256: 19a62baba6c137f47e7538511ce00682e9102be412ddd548e4750837f93eedb6
-  md5: 0670a4dc8844b832866fc5e4a3dac4e2
+  editable: true
+- conda: https://conda.anaconda.org/Auto-Mech/noarch/mechanalyzer-0.2025.0-pyh4616a5c_0.conda
+  sha256: dddf3523678cbc77b69c03521e04698ad543fd2077d587b4d1f1c66bb054d57c
+  md5: 10d551318ec5f7adb4ac58d347bcc9e9
   depends:
   - click >=8.2.1
   - mako >=1.3.10
@@ -3217,20 +3211,21 @@ packages:
   - autofile >=0.2025.0,<2.0.0
   - python >=3.11
   - python *
-  size: 2731032
-  timestamp: 1772765088653
-- pypi: ./
+  size: 2729114
+  timestamp: 1763750488901
+- pypi: .
   name: mechdriver
-  version: 0.2026.0
-  sha256: 6465daa62798154ea96b63386a443487dc2fa16f2da184281659a7430b02bb87
+  version: 0.2025.0
+  sha256: f422c33102fca7daa75628e4454feed87b8c8809e44e42e5408bdb799df10f4f
   requires_dist:
   - hyperqueue
   requires_python: '>=3.11,<3.14'
-- conda: https://conda.anaconda.org/Auto-Mech/noarch/mess-static-2026.2.4-h4616a5c_0.conda
-  sha256: 73cf524ed5a9f5a34f5c68e0309de084c9dcad833bdfcb3c7f288b48f45ac22d
-  md5: 962375844fd512acf2d0305a46fcd8f3
-  size: 42835440
-  timestamp: 1770225035248
+  editable: true
+- conda: https://conda.anaconda.org/Auto-Mech/noarch/mess-static-2025.9.0-h4616a5c_0.conda
+  sha256: bf49bc57d60cbcda20f57e6a6e63edbb6204396946703224f9ecd9e49c78e50f
+  md5: d7dee2b3a30813504691abd00da40943
+  size: 42798128
+  timestamp: 1758816360707
 - conda: https://conda.anaconda.org/conda-forge/noarch/more-itertools-10.8.0-pyhd8ed1ab_0.conda
   sha256: fabe81c8f8f3e1d0ef227fc1306526c76189b3f1175f12302c707e0972dd707c
   md5: d7620a15dc400b448e1c88a981b23ddd
diff --git a/pyproject.toml b/pyproject.toml
index c21d89cc..163ce8f4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -105,11 +105,11 @@ autoio = { path = "../autoio", editable = true }
 autofile = { path = "../autofile", editable = true }
 mechanalyzer = { path = "../mechanalyzer", editable = true }
 
-[tool.pixi.feature.dev.pypi-options.dependency-overrides]
-autochem = { path = "../autochem", editable = true }
-autoio = { path = "../autoio", editable = true }
-autofile = { path = "../autofile", editable = true }
-mechanalyzer = { path = "../mechanalyzer", editable = true }
+# [tool.pixi.feature.dev.pypi-options.dependency-overrides]
+# autochem = { path = "../autochem", editable = true }
+# autoio = { path = "../autoio", editable = true }
+# autofile = { path = "../autofile", editable = true }
+# mechanalyzer = { path = "../mechanalyzer", editable = true }
 
 [tool.pixi.system-requirements]
 linux = "3.10"
diff --git a/src/mechdriver/drivers/ktpdriver.py b/src/mechdriver/drivers/ktpdriver.py
index 420425ca..6d814fb4 100644
--- a/src/mechdriver/drivers/ktpdriver.py
+++ b/src/mechdriver/drivers/ktpdriver.py
@@ -55,7 +55,11 @@ def run(pes_rlst, pes_grp_dct,
     run_fit_tsk = parser.run.extract_task('run_fits', ktp_tsk_lst)
 
     # Group the PESs into lists
-    pes_grps_rlst = parser.rlst.pes_groups(pes_rlst, pes_grp_dct)
+    if pes_rlst is None:
+        print('No channels requested by user, check input.')
+        pes_grps_rlst = []
+    else:
+        pes_grps_rlst = parser.rlst.pes_groups(pes_rlst, pes_grp_dct)
 
     # --------------------------------------- #
     # LOOP OVER ALL OF THE SUBPES in PES_RLST #
diff --git a/src/mechlib/amech_io/parser/models.py b/src/mechlib/amech_io/parser/models.py
index a2499584..18aff25c 100644
--- a/src/mechlib/amech_io/parser/models.py
+++ b/src/mechlib/amech_io/parser/models.py
@@ -161,12 +161,11 @@ def _format_lvl(lvl_val):
         """ format weird energy calls
         """
         if isinstance(lvl_val, str):
-            lvl_val = lvl_val.replace(',','*').split('*')
+            lvl_val = lvl_val.replace(',','*').replace(' ','').split('*')
         if len(lvl_val) > 1:
             val_inf = (float(lvl_val[0]), tinfo.from_dct(thy_dct.get(lvl_val[1])))
         else:
             val_inf = (1.00, tinfo.from_dct(thy_dct.get(lvl_val[0])))
-
         return val_inf
 
     new_dct2 = {}
@@ -180,7 +179,6 @@ def _format_lvl(lvl_val):
                 _new_dct[key2] = val2
 
         new_dct2[key1] = _new_dct
-
     return new_dct2
 
 
diff --git a/src/mechlib/filesys/mincnf.py b/src/mechlib/filesys/mincnf.py
index 65454c09..647efb46 100644
--- a/src/mechlib/filesys/mincnf.py
+++ b/src/mechlib/filesys/mincnf.py
@@ -19,7 +19,8 @@
 
 
 def min_energy_conformer_locators(
-        cnf_save_fs, mod_thy_info, hbond_cutoffs=None, nprocs=1):
+        cnf_save_fs, mod_thy_info, hbond_cutoffs=None, nprocs=1,
+        print_level=1):
     """ Obtain the (ring-id, tors-id) filesystem locator pair and
         path for the conformer of a species with the lowest energy
         for the specified electronic structure method that currently
@@ -37,7 +38,8 @@ def min_energy_conformer_locators(
 
     locs, paths = conformer_locators(
         cnf_save_fs, mod_thy_info,
-        cnf_range='min', hbond_cutoffs=hbond_cutoffs, nprocs=nprocs)
+        cnf_range='min', hbond_cutoffs=hbond_cutoffs, nprocs=nprocs,
+        print_level=print_level)
     if locs and paths:
         ret = locs[0], paths[0]
     else:
@@ -48,7 +50,7 @@ def min_energy_conformer_locators(
 
 def conformer_locators(
         cnf_save_fs, mod_thy_info,
-        cnf_range='min', sort_info_lst=None, print_enes=False,
+        cnf_range='min', sort_info_lst=None, print_level=1,
         hbond_cutoffs=None, nprocs=1):
     """ Obtain the (ring-id, tors-id) filesystem locator pair and
         path for all conformers meeting
@@ -79,7 +81,7 @@ def _conformer_locators(
             cnf_save_fs, mod_thy_info, cnf_range='min',
             only_hbnds=True, only_nonhbnds=True,
             freq_info=None, sp_info=None, sort_prop_dct=None,
-            print_enes=False, already_counted_locs_lst=(), hbond_cutoffs=None,
+            print_level=1, already_counted_locs_lst=(), hbond_cutoffs=None,
             nprocs=1):
 
         fin_locs_lst, fin_paths_lst = (), ()
@@ -117,7 +119,7 @@ def _conformer_locators(
             for idx, locs in enumerate(fin_locs_lst):
                 fin_paths_lst += (cnf_save_fs[-1].path(locs),)
 
-            if print_enes:
+            if print_level == 2:
                 header = '\nConformer Ordering'
                 if only_hbnds:
                     header += ' for only hydrogen bonded conformers'
@@ -136,7 +138,7 @@ def _conformer_locators(
                         mark = ''
                     print(f'{locs[0]:<16}{locs[1]:<16}{_ene:<6.2f}{mark:<3}')
                 print()
-        else:
+        elif print_level > 0:
             print(f'No conformers located in {cnf_save_fs[0].path()}')
 
         return fin_locs_lst, fin_paths_lst
@@ -154,7 +156,7 @@ def _conformer_locators(
             only_hbnds=True, only_nonhbnds=False,
             freq_info=freq_info, sp_info=sp_info,
             sort_prop_dct=sort_prop_dct,
-            print_enes=print_enes,
+            print_level=print_level,
             already_counted_locs_lst=union_locs_lst,
             hbond_cutoffs=hbond_cutoffs,
             nprocs=nprocs)
@@ -166,7 +168,7 @@ def _conformer_locators(
             only_hbnds=False, only_nonhbnds=True,
             freq_info=freq_info, sp_info=sp_info,
             sort_prop_dct=sort_prop_dct,
-            print_enes=print_enes,
+            print_level=print_level,
             already_counted_locs_lst=union_locs_lst,
             hbond_cutoffs=hbond_cutoffs,
             nprocs=nprocs)
@@ -179,7 +181,7 @@ def _conformer_locators(
             only_hbnds=False, only_nonhbnds=False,
             freq_info=freq_info, sp_info=sp_info,
             sort_prop_dct=sort_prop_dct,
-            print_enes=print_enes,
+            print_level=print_level,
             already_counted_locs_lst=union_locs_lst,
             hbond_cutoffs=hbond_cutoffs,
             nprocs=nprocs)
@@ -455,7 +457,8 @@ def traj_sort(save_fs, mod_thy_info, rid=None):
 
     locs_lst = save_fs[-1].existing()
     if locs_lst:
-        # Update the trajectory file in the CONFS/rid level for rings
+        # Update the trajectory file in the CONFS/conf.t.xyz level for
+        # lowest torsional configurations of all puckering configurations
         enes = []
         for locs in locs_lst:
             cnf_path = save_fs[-1].path(locs)
@@ -464,10 +467,15 @@ def traj_sort(save_fs, mod_thy_info, rid=None):
                 sp_fs[-1].file.energy.read(mod_thy_info[1:4]))
         geos = [save_fs[-1].file.geometry.read(locs)
                 for locs in locs_lst]
-        traj = []
         traj_sort_data = sorted(zip(enes, geos, locs_lst), key=lambda x: x[0])
+        traj = []
+        used_rids = []
         for ene, geo, locs in traj_sort_data:
-            comment = f'energy: {ene:<15.10f} \t {locs[0]}'
+            trid, _ = locs
+            if trid in used_rids:
+                continue
+            used_rids.append(trid)
+            comment = f'energy: {ene:<15.10f} \t {trid}'
             traj.append((geo, comment))
         traj_path = save_fs[0].file.trajectory.path()
 
@@ -475,6 +483,8 @@ def traj_sort(save_fs, mod_thy_info, rid=None):
         save_fs[0].file.trajectory.write(traj)
 
         if rid is not None:
+            # Update the trajectory file in the CONFS/rid/conf.t.xyz for the
+            # torsional configurations of a puckering configuration
             locs_lst = save_fs[-1].existing()
             if locs_lst:
                 enes, geos = [], []
@@ -899,10 +909,10 @@ def fs_confs_dict(cnf_save_fs, cnf_save_locs_lst,
     if saddle:
         dist_tol = 0.25
     for ini_locs in ini_cnf_save_locs_lst:
-
         match_dct[tuple(ini_locs)] = None
         # Loop over structs in cnf_save, see if they match the current struct
-        # inigeo = ini_cnf_save_fs[-1].file.geometry.read(ini_locs)
+        ##
+        inigeos = [ini_cnf_save_fs[-1].file.geometry.read(ini_locs)]
         # inizma = automol.geom.zmatrix(inigeo)
         # inizma =  ini_cnf_save_fs[-1].file.zmatrix.read(ini_locs)
         ini_cnf_save_path = ini_cnf_save_fs[-1].path(ini_locs)
@@ -913,14 +923,18 @@ def fs_confs_dict(cnf_save_fs, cnf_save_locs_lst,
         dtt = automol.zmat.conversion_info(inizmas[0])
         for sym_locs in ini_sym_fs[-1].existing():
             geo = ini_sym_fs[-1].file.geometry.read(sym_locs)
+            ##
+            inigeos.append(geo)
             geo_wdummy = automol.geom.apply_zmatrix_conversion(geo, dtt)
             try:
                 inizmas.append(automol.zmat.from_geometry(inizmas[0], geo_wdummy))
             except:
                 print('some structures have a different zmatrix')
-        for inizma in inizmas:
+        for idx, inizma in enumerate(inizmas):
             for locs in cnf_save_locs_lst:
-                # geo = cnf_save_fs[-1].file.geometry.read(locs)
+                print('checking against run', cnf_save_fs[-1].path(locs))
+                ##
+                geo = cnf_save_fs[-1].file.geometry.read(locs)
                 # zma = automol.geom.zmatrix(geo)
                 zma_save_fs = autofile.fs.zmatrix(cnf_save_fs[-1].path(locs))
                 zma = zma_save_fs[-1].file.zmatrix.read((0,))
@@ -932,6 +946,12 @@ def fs_confs_dict(cnf_save_fs, cnf_save_locs_lst,
                     #     f'- Similar structure found at {cnf_save_path}')
                     match_dct[tuple(ini_locs)] = tuple(locs)
                     break
+                _, sym_idx = automol.geom.is_unique(
+                    geo, [inigeos[idx]], check_dct={'coulomb': 1e-2})
+                if sym_idx is not None:
+                    print(' - Structure is not symmetrically unique.')
+                    match_dct[tuple(ini_locs)] = tuple(locs)
+ 
                 else:
                     sym_fs = autofile.fs.symmetry(cnf_save_fs[-1].path(locs))
                     dtt = automol.zmat.conversion_info(zma)
diff --git a/src/mechlib/filesys/models.py b/src/mechlib/filesys/models.py
index 9b1e8c58..5d0e2594 100644
--- a/src/mechlib/filesys/models.py
+++ b/src/mechlib/filesys/models.py
@@ -250,7 +250,7 @@ def get_spc_locs_lst(
         hbond_cutoffs = spc_dct_i['hbond_cutoffs']
         min_locs_lst, _ = conformer_locators(
             cnf_save_fs, levelp, cnf_range=cnf_range,
-            sort_info_lst=mod_info_lst, print_enes=True,
+            sort_info_lst=mod_info_lst, print_level=2,
             hbond_cutoffs=hbond_cutoffs, nprocs=nprocs)
         for min_locs in min_locs_lst:
             cnf_run_fs[-1].create(min_locs)
diff --git a/src/mechlib/filesys/read.py b/src/mechlib/filesys/read.py
index c81554eb..9e30c7a5 100644
--- a/src/mechlib/filesys/read.py
+++ b/src/mechlib/filesys/read.py
@@ -362,16 +362,14 @@ def instability_transformation(spc_dct, spc_name, thy_info, save_prefix,
 
     # Check if any locs exist first?
     # hbond_cutoffs = spc_dct[spc_name]['hbond_cutoffs']
-    #ini_loc_info = min_energy_conformer_locators(
+    # ini_loc_info = min_energy_conformer_locators(
     #    cnf_save_fs, mod_thy_info, hbond_cutoffs=hbond_cutoffs, nprocs=nprocs)
     ini_loc_lst = cnf_save_fs[-1].existing()
-    if len(ini_loc_lst) > 0:
-        min_cnf_path  = cnf_save_fs[-1].path(ini_loc_lst[0])
-
-    else:
-        min_cnf_path = None
+    if len(ini_loc_lst) < 1:
+        return None, None
+    
+    min_cnf_path  = cnf_save_fs[-1].path(ini_loc_lst[0])
     zma_save_fs = autofile.fs.zmatrix(min_cnf_path)
-
     # Check if the instability files exist
     if zma_save_fs[-1].file.instability.exists(zma_locs):
         instab_trans = zma_save_fs[-1].file.instability.read(zma_locs)
diff --git a/src/mechlib/filesys/save.py b/src/mechlib/filesys/save.py
index 506b645b..6883bb68 100644
--- a/src/mechlib/filesys/save.py
+++ b/src/mechlib/filesys/save.py
@@ -291,7 +291,6 @@ def read_zma_from_geo(init_zma, geo):
     """
     zma = None
     if init_zma is not None:
-        print('Resetting ZMA coords using opt geoms...')
         zma = rebuild_zma_from_opt_geo(init_zma, geo)
     return zma
 
@@ -405,7 +404,6 @@ def _save_zmatrix(ret, zma_fs, zma_locs, init_zma=None):
     inf_obj, inp_str, out_str, prog, _ = _unpack_ret(ret)
     zma = None
     if init_zma is not None:
-        print('using opt geo fro zma')
         geo = elstruct.reader.opt_geometry(prog, out_str)
         zma = read_zma_from_geo(init_zma, geo)
     if zma is None:
diff --git a/src/mechroutines/es/_routines/conformer.py b/src/mechroutines/es/_routines/conformer.py
index 117e2462..4d0fadf0 100644
--- a/src/mechroutines/es/_routines/conformer.py
+++ b/src/mechroutines/es/_routines/conformer.py
@@ -3,7 +3,6 @@
 
 import shutil
 import time
-import random
 import subprocess
 import os
 import numpy
@@ -25,104 +24,103 @@
 from phydat import phycon
 
 # Initial conformer
-def initial_conformer(spc_dct_i, spc_info, ini_method_dct, method_dct,
-                      ini_cnf_save_fs, cnf_run_fs, cnf_save_fs,
-                      es_keyword_dct):
-    """ Assess if a conformer layer with a geometry exists in the save
-        filesys for the given species.
-        If not, attempt to generate some guess structure using InChI strings
-        or input geom from user.
-        and optimize
-        it with input method. Then assess if the optimized structure
-        corresponds to genuine minimum on the PES via a frequency calculation.
-        If a minimum is found, save the conformer geometry, zmatrix, energy,
+def initial_conformer(
+        spc_dct_i: dict,
+        spc_info: tuple,
+        ini_method_dct: dict,
+        method_dct: dict,
+        ini_cnf_save_fs: object,
+        cnf_run_fs: object,
+        cnf_save_fs: object,
+        es_keyword_dct: dict):
+    """ Create and optimize the first conformer for a species and method (init_geom).
+        - Ensure no conformer exists in the save filesys for the given species
+        at the run-LoT.
+        - Generate a guess structure with priority on input geometry from user
+        (inp/geomA.xyz) and then using RDKit geometries from InChI strings
+        - Optimize guess structure with the run-LoT
+        - Ensure optimized geometry is a minimum on the PES via a frequency calculation
+        (if imaginary frequencies are found, loop through kickoff/reoptimization procedure).
+        - If a minimum is found, save the conformer geometry, zmatrix, energy, 
         and torsions to the save filesys.
-        Also, the function assessess if the species is unstable and will
+        - Also, the function assessess if the species is unstable and will
         save the appropriate information.
+        :param spc_dct_i: Species dictionary for species i
+        :type spc_dct_i: dict
+        :param spc_info: Species info (InChI, charge, multiplicity)
+        :type spc_info: tuple
+        :param ini_method_dct: Initial method dictionary
+        :type ini_method_dct: dict
+        :param method_dct: Run Method dictionary
+        :type method_dct: dict
+        :param ini_cnf_save_fs: Initial conformer save filesystem
+        :type ini_cnf_save_fs: autofile.fs.conformer
+        :param cnf_run_fs: Conformer run filesystem
+        :type cnf_run_fs: autofile.fs.conformer
+        :param cnf_save_fs: Conformer save filesystem
+        :type cnf_save_fs: autofile.fs.conformer
+        :param es_keyword_dct: Electronic structure keyword dictionary
+        :type es_keyword_dct: dict
+        :returns: bool indicating if conformer was found
     """
-    ini_thy_info = tinfo.from_dct(ini_method_dct)
-    thy_info = tinfo.from_dct(method_dct)
-    mod_thy_info = tinfo.modify_orb_label(
-        thy_info, spc_info)
-    mod_ini_thy_info = tinfo.modify_orb_label(
-        ini_thy_info, spc_info)
-    [kickoff_size, kickoff_backward] = spc_dct_i['kickoff']
-
-    _, cnf_path = filesys.mincnf.min_energy_conformer_locators(
-        cnf_save_fs, mod_thy_info)
+    # check run and save filesystems for existing jobs
+    mod_thy_info = tinfo.modify_orb_label(tinfo.from_dct(method_dct), spc_info)
     overwrite = es_keyword_dct['overwrite']
-    if not cnf_path:
-        info_message(
-            'No conformer found in save filesys. Checking for running jobs...')
-        if _init_geom_is_running(cnf_run_fs) and not overwrite:
-            _run = False
-        else:
-            info_message(
-                'No conformers are running in run filesys.' +
-                'Proceeding with optimization...')
-            _run = True
-    elif overwrite:
-        info_message(
-            'User specified to overwrite energy with new run...')
-        _run = True
-    else:
-        _run = False
-
-    if _run:
-        info_message('Obtaining some initial guess geometry.')
-        geo_init = _obtain_ini_geom(spc_dct_i, ini_cnf_save_fs,
-                                    mod_ini_thy_info,
-                                    overwrite)
-
-        if geo_init is not None:
-            info_message(
-                'Assessing if there are any functional groups',
-                'that cause instability')
+    if not _init_geom_is_needed(
+            cnf_save_fs, cnf_run_fs, mod_thy_info, overwrite):
+        return True
 
-            zma_init = automol.geom.zmatrix(geo_init)
-
-            rid = autofile.schema.generate_new_ring_id()
-            cid = autofile.schema.generate_new_conformer_id()
+    # obtain initial guess structure from user input or InChI
+    # info_message('Obtaining initial guess geometry.')
+    mod_ini_thy_info = tinfo.modify_orb_label(
+        tinfo.from_dct(ini_method_dct), spc_info)
+    geo_init = _obtain_ini_geom(
+        spc_dct_i, ini_cnf_save_fs, mod_ini_thy_info, overwrite)
+    if geo_init is None:
+        warning_message(
+            'Unable to obtain an initial guess geometry')
+        return False
 
-            # Determine if there is an instability, if so return prods
-            instab_zmas = automol.reac.instability_product_zmas(zma_init)
-            if not instab_zmas:
-
-                # Build a cid and a run fs
-                cnf_run_fs[-1].create((rid, cid))
-                run_fs = autofile.fs.run(cnf_run_fs[-1].path((rid, cid)))
-
-                if not automol.geom.is_atom(geo_init):
-                    geo_found = _optimize_molecule(
-                        spc_info, zma_init,
-                        method_dct,
-                        cnf_save_fs, (rid, cid),
-                        run_fs,
-                        overwrite,
-                        kickoff_size=kickoff_size,
-                        kickoff_backward=kickoff_backward)
-                else:
-                    geo_found = _optimize_atom(
-                        spc_info, zma_init,
-                        method_dct,
-                        cnf_save_fs, (rid, cid),
-                        run_fs,
-                        overwrite)
-            else:
-                info_message(
-                    'Found functional groups that cause instabilities')
-                filesys.save.instability(
-                    zma_init, instab_zmas, cnf_save_fs,
-                    rng_locs=(rid,), tors_locs=(cid,), zma_locs=(0,))
-                geo_found = True
-        else:
-            geo_found = False
-            warning_message(
-                'Unable to obtain an initial guess geometry')
+    # Assign random ring and conformer IDs
+    rid = autofile.schema.generate_new_ring_id()
+    cid = autofile.schema.generate_new_conformer_id()
+    
+    # Check for common functional groups that cause instabilities
+    # info_message(
+    #     'Assessing if there are any functional groups',
+    #     'that cause instability')
+    zma_init = automol.geom.zmatrix(geo_init)
+    instab_zmas = automol.reac.instability_product_zmas(zma_init)
+    if instab_zmas:
+        info_message(
+            'Found functional groups that cause instabilities')
+        filesys.save.instability(
+            zma_init, instab_zmas, cnf_save_fs,
+            rng_locs=(rid,), tors_locs=(cid,), zma_locs=(0,))
+        return True
+
+    # Optimize the initial geometry, including a loop through kickoffs
+    # until no imaginary frequencies remain or max attempts reached
+    cnf_run_fs[-1].create((rid, cid))
+    run_fs = autofile.fs.run(cnf_run_fs[-1].path((rid, cid)))
+    if not automol.geom.is_atom(geo_init):
+        [kickoff_size, kickoff_backward] = spc_dct_i['kickoff']
+        geo_found = _optimize_molecule(
+            spc_info, zma_init,
+            method_dct,
+            cnf_save_fs, (rid, cid),
+            run_fs,
+            overwrite,
+            kickoff_size=kickoff_size,
+            kickoff_backward=kickoff_backward)
     else:
-        existing_path('Initial geometry', cnf_path)
-        geo_found = True
-
+        geo_found = _optimize_atom(
+            spc_info, zma_init,
+            method_dct,
+            cnf_save_fs, (rid, cid),
+            run_fs,
+            overwrite)
+    
     return geo_found
 
 
@@ -130,21 +128,31 @@ def _obtain_ini_geom(spc_dct_i, ini_cnf_save_fs,
                      mod_ini_thy_info, overwrite):
     """ Obtain an initial geometry to be optimized. Checks a hieratchy
         of places to obtain the initial geom.
-            (1) Geom dict which is the input from the user
-            (2) Geom from inchi
+        (1) Geom dict which is the input from the user (the geom dict is
+            populated during input parsing from inp/<anyfilename>.xyz if it exists)
+        (2) Geom from inchi
     """
 
     geo_init = None
     # Obtain geom from thy fs or remove the conformer filesystem if needed
     if not overwrite:
         ini_min_locs, ini_path = filesys.mincnf.min_energy_conformer_locators(
-            ini_cnf_save_fs, mod_ini_thy_info)
+            ini_cnf_save_fs, mod_ini_thy_info, print_level=0)
         if ini_path:
             geo_init = ini_cnf_save_fs[-1].file.geometry.read(ini_min_locs)
             path = ini_cnf_save_fs[-1].path(ini_min_locs)
             info_message(
                 f'Getting inital geometry from inplvl at path {path}')
     else:
+        # Note: I think this print message makes no sense for what the code does
+        # I think the rmtree is fine? It's deleting anything saved in the 
+        # ini save filesystem if overwrite is True. I guess wiping the whole system
+        # would be a reasonable meaning of overwriting init_geom, but at the same
+        # time, this could wipe more than a user would expect.
+        # This was added in 2020 in a hard to track push because it was
+        # originally added to a no-longer existing geom.py file. 
+        # https://github.com/Auto-Mech/mechdriver/commit/e4c2d52c5185d940f6e8cc242430b34eeffc3879
+        # - Sarah 01/14/2026
         debug_message(
             'Removing original conformer save data for instability')
         for locs in ini_cnf_save_fs[-1].existing():
@@ -153,14 +161,13 @@ def _obtain_ini_geom(spc_dct_i, ini_cnf_save_fs,
             shutil.rmtree(cnf_save_path)
 
     if geo_init is None:
-        if 'geo' in spc_dct_i:
-            geo_init = spc_dct_i['geo']
+        geo_init = spc_dct_i.get('init_geo', None)
+        if geo_init is not None:
             info_message(
                 'Getting initial geometry from geom dictionary')
-
-    if geo_init is None:
-        geo_init = automol.chi.geometry(spc_dct_i['canon_enant_ich'])
-        info_message('Getting initial geometry from inchi')
+        else:
+            geo_init = automol.chi.geometry(spc_dct_i['canon_enant_ich'])
+            info_message('Getting initial geometry from inchi')
 
     # Check if the init geometry is connected
     if geo_init is not None:
@@ -264,10 +271,9 @@ def _optimize_molecule(spc_info, zma_init,
             if conn and proper_stereo:
                 info_message(
                     'Saving structure as the first conformer...', newline=1)
-                filesys.save.conformer(
-                    ret, None, cnf_save_fs, mod_thy_info[1:],
-                    rng_locs=(locs[0],), tors_locs=(locs[1],),
-                    init_zma=zma)
+                save_conformer(
+                    ret, run_fs, cnf_save_fs, locs, mod_thy_info,
+                    orig_ich=spc_info[0], rid_traj=True, init_zma=zma)
             else:
                 if not conn:
                     info_message('Saving disconnected species...')
@@ -288,14 +294,27 @@ def _optimize_molecule(spc_info, zma_init,
     return conf_found
 
 
-def single_conformer(zma, spc_info, mod_thy_info,
-                     cnf_run_fs, cnf_save_fs,
-                     script_str, overwrite,
-                     retryfail=True, zrxn=None,
-                     use_locs=None, resave=False,
+def single_conformer(zma, spc_info: tuple, mod_thy_info: tuple, 
+                     cnf_run_fs: tuple, cnf_save_fs: tuple,
+                     script_str: str, overwrite: bool,
+                     retryfail: bool=True, zrxn: object=None,
+                     use_locs: tuple=None, resave: bool=False,
                      **kwargs):
-    """ generate single optimized geometry to be saved into a
-        filesystem
+    """ generate single optimized geometry to be saved into a filesystem
+        from an input zmatrix
+        :param zma: tuple(zip(symbs, key_mat, name_mat, val_mat)), 
+            automol-type Z-matrix to be optimized
+        :param spc_info: tuple, Species info (InChI, charge, multiplicity)
+        :param mod_thy_info: tuple, (program, method, basis, orb_label) to run
+        :param cnf_run_fs: autofile.fs.conformer, Conformer run filesystem
+        :param cnf_save_fs: autofile.fs.conformer, Conformer save filesystem
+        :param script_str: str, Script string for electronic structure package
+        :param overwrite: bool, Whether to overwrite existing files
+        :param retryfail: bool, Whether to retry failed jobs
+        :param zrxn: automol.reac.Reaction, automol reaction if TS optimization
+        :param use_locs: tuple, (rid, cid) to use for running
+        :param resave: bool, Whether to resave all conformers from run fs
+        :returns: None
     """
     skip_job = False
 
@@ -303,13 +322,6 @@ def single_conformer(zma, spc_info, mod_thy_info,
         _presamp_save(
             spc_info, cnf_run_fs, cnf_save_fs,
             mod_thy_info, zrxn=zrxn, rid=None, ref_zma=zma)
-        if use_locs is None:
-            print('getting rid')
-            rid = rng_loc_for_geo(
-                automol.zmat.geometry(zma), cnf_save_fs)
-            if rid is not None:
-                cid = autofile.schema.generate_new_conformer_id()
-                locs = (rid, cid)
 
     if this_conformer_is_running(zma, cnf_run_fs):
         skip_job = True
@@ -322,15 +334,22 @@ def single_conformer(zma, spc_info, mod_thy_info,
             skip_job = True
 
     if not skip_job:
-        # Build the filesystem
-        if use_locs is None:
-            rid = autofile.schema.generate_new_ring_id()
-            cid = autofile.schema.generate_new_conformer_id()
-            locs = (rid, cid)
+        # Build the run filesystem
+        existing_rid = rng_loc_for_geo(
+            automol.zmat.geometry(zma), cnf_save_fs)
+        if use_locs is not None:
+            rid, cid = use_locs
+            if existing_rid is not None:
+                rid = existing_rid
+            elif [rid] in cnf_save_fs[-2].existing():
+                rid = autofile.schema.generate_new_ring_id()
         else:
-            locs = use_locs
-            rid = locs[0]
-
+            cid = autofile.schema.generate_new_conformer_id()
+            if existing_rid is not None:
+                rid = existing_rid
+            else:
+                rid = autofile.schema.generate_new_ring_id()
+        locs = (rid, cid)
         cnf_run_fs[-1].create(locs)
         cnf_run_path = cnf_run_fs[-1].path(locs)
         run_fs = autofile.fs.run(cnf_run_path)
@@ -353,111 +372,84 @@ def single_conformer(zma, spc_info, mod_thy_info,
         )
 
         if success:
-            inf_obj, _, out_str = ret
-            prog = inf_obj.prog
-            method = inf_obj.method
-            ene = elstruct.reader.energy(prog, method, out_str)
-            geo = elstruct.reader.opt_geometry(prog, out_str)
-            # zma = elstruct.reader.opt_zmatrix(prog, out_str)
-            saved_locs, saved_geos, saved_enes = _saved_cnf_info(
-                cnf_save_fs, mod_thy_info)
-
-            opt_zma = None
-            if zma is not None:
-                opt_zma = filesys.save.read_zma_from_geo(zma, geo)
-            if zma is None:
-                opt_zma = filesys.save.read_job_zma(ret, init_zma=zma)
-            viable = _geo_connected(geo, zrxn)
-            if viable:
-                if zrxn:
-                    viable = _ts_geo_viable(
-                        opt_zma, zrxn, cnf_save_fs, mod_thy_info, ref_zma=zma)
-                else:
-                    viable = _inchi_are_same(spc_info[0], geo)
-
-            if viable:
-                if _geo_unique(geo, ene, saved_geos, saved_enes, zrxn=zrxn):
-                    sym_id = _sym_unique(
-                        geo, ene, saved_geos, saved_enes)
-                    if sym_id is None:
-                        if cnf_save_fs[0].file.info.exists():
-                            debug_message(
-                                'inf_obj path', cnf_save_fs[0].path())
-                            rinf_obj = cnf_save_fs[0].file.info.read()
-                            rinf = rinf_obj
-                            debug_message(
-                                'inf_obj for r', rinf)
-                            rnsampd = rinf_obj.nsamp
-                            rnsampd += 1
-                            rinf.nsamp = rnsampd
-                        else:
-                            rinf = autofile.schema.info_objects.conformer_trunk(0)
-                            rinf.nsamp = 1
-                        if cnf_save_fs[1].file.info.exists([locs[0]]):
-                            cinf_obj_s = cnf_save_fs[1].file.info.read([locs[0]])
-                            cinf = cinf_obj_s
-                            cnsampd = cinf_obj_s.nsamp
-                            cnsampd += 1
-                            cinf.nsamp = cnsampd
-                        else:
-                            cinf = autofile.schema.info_objects.conformer_branch(0)
-                            cinf.nsamp = 1
-                        cnf_save_fs[1].create([locs[0]])
-                        cnf_save_fs[0].file.info.write(rinf)
-                        cnf_save_fs[1].file.info.write(cinf, [locs[0]])
-                        filesys.save.conformer(
-                            ret, None, cnf_save_fs, mod_thy_info[1:],
-                            zrxn=zrxn, init_zma=zma,
-                            rng_locs=(locs[0],), tors_locs=(locs[1],))
-                        saved_geos.append(geo)
-                        saved_enes.append(ene)
-                        saved_locs.append(locs)
-
-                        # Update the conformer trajectory file
-                        obj('vspace')
-                        filesys.mincnf.traj_sort(
-                            cnf_save_fs, mod_thy_info)
-                        filesys.mincnf.traj_sort(
-                            cnf_save_fs, mod_thy_info, locs[0])
-                    else:
-                        sym_locs = saved_locs[sym_id]
-                        filesys.save.sym_indistinct_conformer(
-                            geo, cnf_save_fs, locs, sym_locs)
-                        if cnf_save_fs[-1].exists(locs):
-                            cnf_save_path = cnf_save_fs[-1].path(locs)
-                        if cnf_run_fs[-1].exists(locs):
-                            cnf_run_path = cnf_run_fs[-1].path(locs)
-
-
-def conformer_sampling(zma, spc_info, thy_info,
-                       cnf_run_fs, cnf_save_fs, rid,
-                       script_str, overwrite,
-                       nsamp_par=(False, 3, 3, 1, 50, 50),
-                       tors_names=(),
-                       zrxn=None, two_stage=False,
-                       retryfail=False, resave=False,
-                       repulsion_thresh=40.0, print_debug=True,
+            # Determine if the optimized ring puckering state already exists
+            inf_obj_temp, _, out_str = ret
+            prog = inf_obj_temp.prog
+            opt_geo = elstruct.reader.opt_geometry(prog, out_str)
+            existing_rid = rng_loc_for_geo(opt_geo, cnf_save_fs)
+            # increment sample count for rings and conformers,
+            # if csamp.yaml and rsamp.yaml exist 
+            # save_conformer will set these to 1 if 
+            # csamp.yaml and rsamp.yaml don't currently exist
+            if existing_rid is None:
+                if cnf_save_fs[0].file.info.exists():
+                    rinf_obj = cnf_save_fs[0].file.info.read()
+                    rsampd = util.calc_nsampd(cnf_save_fs, cnf_run_fs)
+                    rsampd += 1
+                    rinf_obj.nsamp = rsampd
+                    cnf_save_fs[0].file.info.write(rinf_obj)
+                    cnf_run_fs[0].file.info.write(rinf_obj)
+            if cnf_save_fs[1].file.info.exists([locs[0]]):
+                cinf_obj = cnf_save_fs[1].file.info.read([locs[0]])
+                csampd = util.calc_nsampd(cnf_save_fs, cnf_run_fs, locs[0])
+                csampd += 1
+                cinf_obj.nsamp = csampd
+                cnf_save_fs[1].file.info.write(cinf_obj, [locs[0]])
+                cnf_run_fs[1].file.info.write(cinf_obj, [locs[0]])
+            # use save_conformer to save the conformer if it passes
+            # viability and uniqueness checks
+            if existing_rid is not None:
+                rid = existing_rid
+            locs = [rid, cid]
+            save_conformer(
+                ret, cnf_run_fs, cnf_save_fs, locs, mod_thy_info,
+                zrxn=zrxn, orig_ich=spc_info[0], rid_traj=True, init_zma=zma, ref_zma=zma)
+
+
+def conformer_sampling(zma, spc_info: tuple, mod_thy_info: tuple,
+                       cnf_run_fs: object, cnf_save_fs: object, rid: str,
+                       script_str: str, overwrite: bool,
+                       nsamp_par: tuple=(False, 3, 3, 1, 50, 50),
+                       tors_names: tuple=(),
+                       zrxn: object=None, two_stage: bool=False,
+                       retryfail: bool=False, resave: bool=False,
+                       repulsion_thresh: float=40.0, print_debug: bool=True,
                        **kwargs):
-    """ run sampling algorithm to find conformers
+    """ Sample the torsional configurations of a specific ring-puckering state
+        :param zma: tuple(zip(symbs, key_mat, name_mat, val_mat)), 
+            automol-type Z-matrix to be optimized
+        :param spc_info: tuple, Species info (InChI, charge, multiplicity)
+        :param mod_thy_info: tuple, (program, method, basis, orb_label) to run
+        :param cnf_run_fs: autofile.fs.conformer, Conformer run filesystem
+        :param cnf_save_fs: autofile.fs.conformer, Conformer save filesystem
+        :param rid: str, Ring ID for the puckering state
+        :param script_str: str, Script string for electronic structure package
+        :param overwrite: bool, Whether to overwrite existing files
+        :param nsamp_par: tuple, Parameters to determine the number of samples
+        :param tors_names: tuple, Names of torsions to sample
+        :param zrxn: automol.reac.Reaction, automol reaction if TS
+        :param two_stage: bool, Whether to use two-stage optimization
+        :param retryfail: bool, Whether to retry failed jobs
+        :param resave: bool, Whether to resave all conformers from run fs
+        :param repulsion_thresh: float, Threshold for relative repulsion energy
+        :param print_debug: bool, Whether to print debug messages
+        :returns: None
     """
-
     # Check if any saving needs to be done before hand
     ref_rid = rid
     cnf_run_fs[1].create([rid])
+    cnf_save_fs[1].create([rid])
     if resave:
         _presamp_save(
-            spc_info, cnf_run_fs, cnf_save_fs, thy_info, zrxn=zrxn, rid=rid, ref_zma=zma)
+            spc_info, cnf_run_fs, cnf_save_fs, mod_thy_info, 
+            zrxn=zrxn, rid=rid, ref_zma=zma)
 
-    # Build filesys
-    cnf_save_fs[1].create([rid])
-    inf_obj = autofile.schema.info_objects.conformer_branch(0)
 
     # Set the samples
     nsamp, tors_range_dct = util.calc_nsamp(
         tors_names, nsamp_par, zma, zrxn=zrxn)
     nsamp0 = nsamp
     nsampd = util.calc_nsampd(cnf_save_fs, cnf_run_fs, rid)
-
     tot_samp = nsamp - nsampd
     brk_tot_samp = nsamp * 5
 
@@ -486,22 +478,23 @@ def conformer_sampling(zma, spc_info, thy_info,
                 f'Max sample num: 5*{nsamp} attempted, ending search',
                 'Run again if more samples desired.')
             break
-        print(f"Debug: new iteration, nsampd - {nsampd}")
         # Run the conformer sampling
         if nsampd > 0:
             samp_zma, = automol.zmat.samples(zma, 1, tors_range_dct)
         else:
             samp_zma = zma
 
-        info_message(
-            'Generating sample Z-Matrix that does not have',
-            'high intramolecular repulsion...')
+        info_message(f"Run {samp_idx}/{tot_samp}, Total {nsampd}/{nsamp0}")
+        info_message(' - Generating sample Z-Matrix')
         bad_geo_cnt = 0
-        while not automol.zmat.has_low_relative_repulsion_energy(samp_zma, zma) and bad_geo_cnt < 1000:
+        # the repulsion_thresh argument is not being used, it seems like this would
+        # be the place to apply it -Sarah 01/15/2026
+        while not (
+                automol.zmat.has_low_relative_repulsion_energy(samp_zma, zma) 
+                and bad_geo_cnt < 1000):
             if print_debug:
                 warning_message('Structure has high repulsion.')
-                warning_message(
-                    'Generating new sample Z-Matrix')
+                warning_message('Generating new sample Z-Matrix')
             samp_zma, = automol.zmat.samples(zma, 1, tors_range_dct)
             bad_geo_cnt += 1
 
@@ -512,9 +505,7 @@ def conformer_sampling(zma, spc_info, thy_info,
         cnf_run_path = cnf_run_fs[-1].path(locs)
         run_fs = autofile.fs.run(cnf_run_path)
 
-        info_message(f"Run {samp_idx}/{tot_samp}")
-        tors_names = tuple(tors_range_dct.keys())
-        print('two_stage test:', two_stage, tors_names)
+        tors_names = tuple(tors_range_dct.keys()) if tors_range_dct else ()
         if two_stage and tors_names:
             frozen_coords_lst = (tors_names, ())
             success, ret = es_runner.multi_stage_optimization(
@@ -522,7 +513,7 @@ def conformer_sampling(zma, spc_info, thy_info,
                 run_fs=run_fs,
                 geo=samp_zma,
                 spc_info=spc_info,
-                thy_info=thy_info,
+                thy_info=mod_thy_info,
                 frozen_coords_lst=frozen_coords_lst,
                 zrxn=zrxn,
                 overwrite=overwrite,
@@ -537,7 +528,7 @@ def conformer_sampling(zma, spc_info, thy_info,
                 run_fs=run_fs,
                 geo=samp_zma,
                 spc_info=spc_info,
-                thy_info=thy_info,
+                thy_info=mod_thy_info,
                 zrxn=zrxn,
                 overwrite=overwrite,
                 saddle=bool(zrxn is not None),
@@ -556,15 +547,19 @@ def conformer_sampling(zma, spc_info, thy_info,
                 rid = autofile.schema.generate_new_ring_id()
             locs = [rid, cid]
             save_conformer(
-                ret, cnf_run_fs, cnf_save_fs, locs, thy_info,
+                ret, cnf_run_fs, cnf_save_fs, locs, mod_thy_info,
                 zrxn=zrxn, orig_ich=spc_info[0], rid_traj=True,
                 init_zma=samp_zma, ref_zma=samp_zma)
+            if cnf_save_fs[1].file.info.exists([ref_rid]): 
+                cinf_obj = cnf_save_fs[1].file.info.read([ref_rid])
+            else:
+                cinf_obj = autofile.schema.info_objects.conformer_branch(0)
             nsampd = util.calc_nsampd(cnf_save_fs, cnf_run_fs, ref_rid)
             nsampd += 1
             samp_idx += 1
-            inf_obj.nsamp = nsampd
-            cnf_save_fs[1].file.info.write(inf_obj, [ref_rid])
-            cnf_run_fs[1].file.info.write(inf_obj, [ref_rid])
+            cinf_obj.nsamp = nsampd
+            cnf_save_fs[1].file.info.write(cinf_obj, [ref_rid])
+            cnf_run_fs[1].file.info.write(cinf_obj, [ref_rid])
 
         # Increment attempt counter
         samp_attempt_idx += 1
@@ -1348,51 +1343,73 @@ def _presamp_save(spc_info, cnf_run_fs, cnf_save_fs,
             filesys.mincnf.traj_sort(cnf_save_fs, thy_info, rid=rloc[0])
 
 
-def save_conformer(ret, cnf_run_fs, cnf_save_fs, locs, thy_info, zrxn=None,
-                   orig_ich='', rid_traj=False, init_zma=None, ref_zma=None):
-    """ save the conformers that have been found so far
-          # Only go through save procedure if conf not in save
-          # may need to get geo, ene, etc; maybe make function
+def save_conformer(
+        ret: tuple, cnf_run_fs: object, cnf_save_fs: object, locs: tuple,
+        mod_thy_info: tuple, zrxn: object=None, orig_ich: str='', 
+        rid_traj: bool=False, init_zma: object=None, ref_zma: object=None):
+    """ Save a conformer into the correct location if unique and viable
+        1) Check if geometry is properly connected
+        2) Check if geometry is totally or symmetrically unique (compared to saved) 
+        3) Save conformer accordingly
+        :param ret: tuple, (inf_obj, err_msg, out_str) from es_runner.read_job
+        :param cnf_run_fs: tuple(autofile.fs), conformer run filesystem
+        :param cnf_save_fs: tuple(autofile.fs), conformer save filesystem
+        :param locs: tuple(str), (ring_id, conf_id) location of conformer
+        :param thy_info: tuple, (program, method, basis, program, orb_res) theory information
+        :param zrxn: automol.reac.Reaction, reaction object if a TS else None
+        :param orig_ich: str, InChI string of original species
+        :param rid_traj: bool, whether to update traj for ring id
+        :param init_zma: automol.zmat.ZMatrix, initial zmatrix used in optimization
+        :param ref_zma: automol.zmat.ZMatrix, reference zmatrix for TS viability check 
+            (this differs from init_zma, which is the starting point of the optimization,
+            which is a perturbed structure along reactant coordinates for a TS whereas
+            the ref_zma is zma built by automol from the reactant geometries)
+        :return: None
     """
-
-    saved_locs, saved_geos, saved_enes = _saved_cnf_info(
-        cnf_save_fs, thy_info, locs)
-
+    # Read the electronic structure optimization job output
     inf_obj, _, out_str = ret
     prog = inf_obj.prog
     method = inf_obj.method
     ene = elstruct.reader.energy(prog, method, out_str)
     geo = elstruct.reader.opt_geometry(prog, out_str)
-    zma = None
-    if init_zma is not None:
-        zma = filesys.save.read_zma_from_geo(init_zma, geo)
+    zma = filesys.save.read_zma_from_geo(init_zma, geo)
     if zma is None:
         zma = filesys.save.read_job_zma(ret, init_zma=init_zma)
+    # Gather saved conformer information to ensure uniqueness of current output 
+    saved_locs, saved_geos, saved_enes = _saved_cnf_info(
+        cnf_save_fs, mod_thy_info, locs)
 
     # Assess if geometry is properly connected
     viable = _geo_connected(geo, zrxn)
     if viable:
         if zrxn:
             viable = _ts_geo_viable(
-                zma, zrxn, cnf_save_fs, thy_info, ref_zma=ref_zma)
+                zma, zrxn, cnf_save_fs, mod_thy_info, ref_zma=ref_zma)
         else:
             viable = _inchi_are_same(orig_ich, geo)
 
     # Determine uniqueness of conformer, save if needed
     if viable:
         if _geo_unique(geo, ene, saved_geos, saved_enes, zrxn):
+            # Determine correct ring location
+            existing_rid = rng_loc_for_geo(geo, cnf_save_fs)
+            rid, cid = locs
+            if existing_rid is None:
+                if [rid] in cnf_save_fs[-2].existing():
+                    rid = autofile.schema.generate_new_ring_id()
+                    print("Generating new ring state folder RID")
+            else:
+                rid = existing_rid
+            locs = (rid, cid)
+
+            # if symmetrical to saved conformer,
+            # save under SYM/ of corresponding saved conformer
+            # otherwise save it under its own CONF/rid/cid
             sym_id = _sym_unique(
                 geo, ene, saved_geos, saved_enes)
-            # Determine correct ring location
-            rid = rng_loc_for_geo(geo, cnf_save_fs)
-            if rid is None:
-                rid = autofile.schema.generate_new_ring_id()
-                print("Generating new ring state folder RID")
-            _,cid = locs
-            locs = (rid,cid)
             if sym_id is None:
                 filesys.save.conformer(
-                    ret, None, cnf_save_fs, thy_info[1:],
+                    ret, None, cnf_save_fs, mod_thy_info[1:],
                     init_zma=init_zma,  zrxn=zrxn,
                     rng_locs=(locs[0],), tors_locs=(locs[1],))
             else:
@@ -1411,18 +1428,31 @@ def save_conformer(ret, cnf_run_fs, cnf_save_fs, locs, thy_info, zrxn=None,
                     check_dct = {'dist': 0.3, 'tors': None}
                 else:
                     check_dct = {'dist': 0.3}
-                unique, match_idx = automol.geom.is_unique(geo, sym_geos, check_dct=check_dct)
+                unique, match_idx = automol.geom.is_unique(
+                    geo, sym_geos, check_dct=check_dct)
                 if unique:
                     filesys.save.sym_indistinct_conformer(
                         geo, cnf_save_fs, locs, sym_locs, inf_obj=ret[0])
-
-            #     if cnf_save_fs[-1].exists(locs):
-            #         cnf_save_path = cnf_save_fs[-1].path(locs)
-            #         shutil.rmtree(cnf_save_path)
-            #     if cnf_run_fs[-1].exists(locs):
-            #         cnf_run_path = cnf_run_fs[-1].path(locs)
-            #         shutil.rmtree(cnf_run_path)
-        else:
+            
+            # Update the conformer trajectory files rid/conf.t.xyz and potentially also
+            # rid/cid/conf.t.xyz
+            obj('vspace')
+            if rid_traj and [rid] in cnf_save_fs[-2].existing():
+                filesys.mincnf.traj_sort(cnf_save_fs, mod_thy_info, rid=rid)
+            else:
+                filesys.mincnf.traj_sort(cnf_save_fs, mod_thy_info, rid=None)
+
+        else: 
+            # Note: this is clearing both the run and save filesystems
+            # if not unique. The save removal should always do nothing
+            # because it should not exist there if not unique.
+            # perhaps an old cleanup attempt:
+            # https://github.com/Auto-Mech/mechdriver/commit/f5f6bab75df92ba91230ee80469f86e50306767a
+            # I think removing the run is bad, because we have checks to see if
+            # a new conformer we want to optimize has already been run  
+            # but optimized into something non-unique. If we remove it here,
+            # we lose that record.
+            # - Sarah 01/15/2026
             if cnf_save_fs[-1].exists(locs):
                 cnf_save_path = cnf_save_fs[-1].path(locs)
                 shutil.rmtree(cnf_save_path)
@@ -1430,19 +1460,11 @@ def save_conformer(ret, cnf_run_fs, cnf_save_fs, locs, thy_info, zrxn=None,
                 cnf_run_path = cnf_run_fs[-1].path(locs)
                 shutil.rmtree(cnf_run_path)
 
-        # Update the conformer trajectory file
-        obj('vspace')
-        rid = None
-        if rid_traj:
-            if rid in cnf_save_fs[-1].existing():
-                rid = locs[0]
-        filesys.mincnf.traj_sort(cnf_save_fs, thy_info, rid=rid)
-
 
-def _saved_cnf_info(cnf_save_fs, mod_thy_info, orig_locs=None):
+def _saved_cnf_info(
+        cnf_save_fs: object, mod_thy_info: tuple, orig_locs: tuple=None):
     """ get the locs, geos and enes for saved conformers
     """
-
     saved_locs = list(cnf_save_fs[-1].existing())
     saved_locs = [locs for locs in saved_locs if not locs == orig_locs]
     saved_geos = [cnf_save_fs[-1].file.geometry.read(locs)
@@ -1486,45 +1508,86 @@ def _saved_cnf_info(cnf_save_fs, mod_thy_info, orig_locs=None):
     return found_saved_locs, found_saved_geos, found_saved_enes
 
 
-def _init_geom_is_running(cnf_run_fs):
+def _init_geom_is_needed(
+        cnf_save_fs: object, cnf_run_fs: object, 
+        mod_thy_info: tuple, overwrite: bool=False):
+    """ Determine if initial geometry optimization is needed
+    """
+    # Check to see if conformer already exists in the save filesys
+    _, cnf_path = filesys.mincnf.min_energy_conformer_locators(
+        cnf_save_fs, mod_thy_info)
+    if cnf_path:
+        if overwrite:
+            info_message(
+                f'Overwrite will search for new conformer'
+                f'despite existing conformer at {cnf_path}')
+            return True
+        existing_path('Initial geometry', cnf_path)
+        return False
+
+    # Check to see if it exists or is running in the run filesystem
+    info_message('Checking for running jobs...')
+    if _init_geom_is_running(cnf_run_fs) and not overwrite:
+        info_message(
+            'No conformers are running in run filesys.'
+            'Proceeding with optimization...')
+        return False
+    return True
+
+
+def _init_geom_is_running(cnf_run_fs: object):
     """ Check the RUN filesystem for currently running initial geometry submissions
     """
-    running = False
     jobs = [elstruct.Job.OPTIMIZATION, elstruct.Job.HESSIAN]
     locs = cnf_run_fs[-1].existing()
     if not locs:
-        wait_time = random.randint(10, 60)
-        print('lets wait a bit', wait_time)
+        # this gives us a random chance to desynchronize jobs that were launched
+        # at the exact same time (which means they might both check the run.yaml
+        # for existing jobs at the same time, see none, and both launch)
+        # it is not the ideal solution, but it is simple and should work most of the time
+        # Get the unique PID and current time
+        rng = numpy.random.default_rng(os.getpid())
+        wait_time = rng.uniform(2, 40)
+        print(f'Starting job in {wait_time:3.2f}s if no other submissions launch it')
         time.sleep(wait_time)
         locs = cnf_run_fs[-1].existing()
-    print('im going to check locs',  cnf_run_fs[-1].existing())
+    
+    # Check all of the conformer locations for this species/LoT in the run filesystem
+    # to make sure the desired job is not already running/just succeeded
     for locs in cnf_run_fs[-1].existing():
-        cnf_run_path = cnf_run_fs[-1].path(locs)
-        run_fs = autofile.fs.run(cnf_run_path)
-        print('im going to check here',  cnf_run_path)
+        run_fs = autofile.fs.run(cnf_run_fs[-1].path(locs))
         for job in jobs:
             if not run_fs[-1].file.info.exists([job]):
                 continue
-            print('im going to check it job',  job)
             inf_obj = run_fs[-1].file.info.read([job])
             status = inf_obj.status
-            print('its job status is', status)
+            start_time = inf_obj.utc_start_time
+            current_time = autofile.schema.utc_time()
+            elapsed_time = (current_time - start_time).total_seconds()
             if status == autofile.schema.RunStatus.RUNNING:
-                start_time = inf_obj.utc_start_time
-                current_time = autofile.schema.utc_time()
-                _time = (current_time - start_time).total_seconds()
-                print('its jtime is', _time)
-                if _time < 3000000:
+                # a month is probably long enough for any initial geometry optimization
+                # but maybe someone decides to do an init geom with CCSDTQP
+                if elapsed_time < 3000000:
                     path = cnf_run_fs[-1].path(locs)
                     info_message(
-                        'init_geom was started in the last '
-                        f'{_time/3600:3.4f} hours in {path}.')
-                    running = True
-                    break
-    return running
+                        f'An init_geom task was started by another submission '
+                        f'in the last {elapsed_time/3600:3.4f} hours in {path}.')
+                    return True
+            elif status == autofile.schema.RunStatus.SUCCESS:
+                # this time should be stricter, its should only pass if a running job
+                # finished in the middle of the running check, otherwise finished
+                # jobs that didn't make it to save mean something was wrong with the
+                # final optimized structure
+                if elapsed_time < 500:
+                    path = cnf_run_fs[-1].path(locs)
+                    info_message(
+                        f'An init_geom was successfully completed by another submission '
+                        f'in the last {elapsed_time/3600:3.4f} hours in {path}.')
+                    return True
+    return False
 
 
-def this_conformer_was_run_in_save(zma, cnf_fs):
+def this_conformer_was_run_in_save(zma, cnf_fs: object):
     """ Assess if a conformer was run in save
     """
     running = False
@@ -1564,7 +1627,7 @@ def this_conformer_was_run_in_save(zma, cnf_fs):
     return running
 
 
-def this_conformer_is_running(zma, cnf_run_fs):
+def this_conformer_is_running(zma, cnf_run_fs: object):
     """ Check the RUN filesystem for similar geometry
         submissions that are currently running
     """
@@ -1603,11 +1666,9 @@ def this_conformer_is_running(zma, cnf_run_fs):
     return running
 
 
-def _geo_connected(geo, rxn):
-    """ Assess if geometry is connected. Right now only works for
-        minima
+def _geo_connected(geo: object, rxn: object=None):
+    """ Assess if geometry is connected. Right now only works for minima
     """
-
     # Determine connectivity (only for minima)
     if rxn is None:
         gra = automol.geom.graph(geo)
@@ -1626,7 +1687,9 @@ def _geo_connected(geo, rxn):
     return connected
 
 
-def _geo_unique(geo, ene, seen_geos, seen_enes, zrxn=None):
+def _geo_unique(
+        geo: object, ene: float, 
+        seen_geos: list, seen_enes: list, zrxn: object=None):
     """ Assess if a geometry is unique to saved geos
         Need to pass the torsions
     """
@@ -1653,7 +1716,7 @@ def _geo_unique(geo, ene, seen_geos, seen_enes, zrxn=None):
     return unique
 
 
-def _inchi_are_same(orig_ich, geo):
+def _inchi_are_same(orig_ich: str, geo: object):
     """ Assess if a geometry has the same connectivity to
      saved geos evaluated in temrs of inchi
     """
@@ -1670,21 +1733,12 @@ def _inchi_are_same(orig_ich, geo):
     return same
 
 
-def _check_old_inchi(orig_ich, seen_geos, saved_locs, cnf_save_fs):
-    """
-    This assumes you already have bad geos in your save
-    """
-    for i, geoi in enumerate(seen_geos):
-        if not orig_ich == automol.geom.chi(geoi):
-            smi = automol.geom.smiles(geoi)
-            path = cnf_save_fs[-1].path(saved_locs[i])
-            error_message(
-                f'inchi do not match for {smi} at {path}')
-
-
-def _sym_unique(geo, ene, saved_geos, saved_enes, ethresh=1.0e-5):
+def _sym_unique(
+        geo: object, ene: float, saved_geos: list, 
+        saved_enes: list, ethresh: float=1.0e-5):
     """ Check if a conformer is symmetrically distinct from the
-        existing conformers in the filesystem
+        existing conformers in the filesystem, returns index of
+        the matching conformer if not symmetrically unique
     """
 
     sym_idx = None
@@ -1851,36 +1905,35 @@ def unique_fs_confs(cnf_save_fs, cnf_save_locs_lst,
     return uni_ini_cnf_save_locs
 
 
-def rng_loc_for_geo(geo, cnf_save_fs):
+def rng_loc_for_geo(geo, cnf_save_fs, ang_tol=.2):
     """ Find the ring-conf locators for a given geometry in the
         conformer save filesystem
     """
 
     rid = None
+    checked_rids = []
+    
     frag_geo = automol.geom.ring_fragments_geometry(geo)
     if frag_geo is not None:
         frag_zma = automol.geom.zmatrix(frag_geo)
-    checked_rids = []
+    
     for locs in cnf_save_fs[-1].existing():
-        print("Debug: locs", locs)        
         current_rid, _ = locs
+        if frag_geo is None:
+            rid = current_rid 
+            break
         if current_rid in checked_rids:
             continue
         checked_rids.append(current_rid)
         locs_geo = cnf_save_fs[-1].file.geometry.read(locs)
         frag_locs_geo = automol.geom.ring_fragments_geometry(locs_geo)
-        if frag_geo is None:
-            rid = locs[0]
-            break
-        else:
-            if frag_locs_geo is None:
-                continue
+        if frag_locs_geo is None:
+            continue
         frag_locs_zma = automol.geom.zmatrix(frag_locs_geo)
         
         if automol.zmat.almost_equal(frag_locs_zma, frag_zma,
-                                     dist_rtol=0.018, ang_atol=.1):
-            rid = locs[0]
-            print("Debug: Zmat similar - locs: ", locs)
+                                     dist_rtol=0.018, ang_atol=ang_tol):
+            rid = current_rid
             break
 
     return rid
diff --git a/src/mechroutines/es/runner/scan.py b/src/mechroutines/es/runner/scan.py
index fbe8c291..03e00e3f 100644
--- a/src/mechroutines/es/runner/scan.py
+++ b/src/mechroutines/es/runner/scan.py
@@ -35,8 +35,8 @@ def execute_scan(zma, spc_info, mod_thy_info,
 
     # Need a resave option
     _fin = scan_finished(
-        coord_names, coord_grids, scn_save_fs,
-        constraint_dct=constraint_dct, overwrite=overwrite)
+        coord_names, coord_grids, scn_save_fs, scn_run_fs,
+        scn_typ, constraint_dct=constraint_dct, overwrite=overwrite)
 
     if not _fin:
         run_scan(
@@ -524,8 +524,8 @@ def scan_locs(scn_save_fs, coord_names, constraint_dct=None):
     return coord_locs, scn_locs
 
 
-def scan_finished(coord_names, coord_grids, scn_save_fs,
-                   constraint_dct=None, overwrite=False):
+def scan_finished(coord_names, coord_grids, scn_save_fs, scn_run_fs,
+                   scn_typ, job=None, constraint_dct=None, overwrite=False):
     """ Assesses if the scan calculations requested by the user have been
         completed by assessing if Z-Matrices exist in the filesystem for
         all grid values of the scan coordinates.
@@ -536,6 +536,10 @@ def scan_finished(coord_names, coord_grids, scn_save_fs,
         :type coord_grids: tuple(tuple(float))
         :param scn_save_fs: SCAN/CSCAN object with save filesys prefix
         :type scn_save_fs: autofile.fs.scan or autofile.fs.cscan object
+        :param scn_run_fs: SCAN/CSCAN object with run filesys prefix
+        :type scn_run_fs: autofile.fs.scan or autofile.fs.cscan object
+        :param scn_typ: label for scan type ('relaxed' or 'rigid')
+        :type scn_typ: str
         :param constraint_dct: values of coordinates to constrain during scan
         :type constraint_dct: dict[str: float]
         :param overwrite:
@@ -544,7 +548,7 @@ def scan_finished(coord_names, coord_grids, scn_save_fs,
     """
 
     run_finished = True
-
+    job = _set_job(scn_typ)
     if not overwrite:
         grid_vals = tuple(itertools.product(*coord_grids))
         for vals in grid_vals:
@@ -555,17 +559,34 @@ def scan_finished(coord_names, coord_grids, scn_save_fs,
                 locs = [constraint_dct] + locs
 
             # Check if ZMA (other info?) exists
-            if not scn_save_fs[-1].file.zmatrix.exists(locs):
-                run_finished = False
-                break
+            if scn_save_fs[-1].file.zmatrix.exists(locs):
+                continue
+
+            # If no zma, check if the scan is suceeded or failed
+            if scn_run_fs[-1].exists(locs):
+                run_fs = autofile.fs.run(scn_run_fs[-1].path(locs))
+                if run_fs[-1].file.info.exists([job]):
+                    inf_obj = run_fs[-1].file.info.read([job])
+                    if inf_obj.status == autofile.schema.RunStatus.FAILURE:
+                        ioprinter.info_message(
+                            'Scan point dropped at ', locs)
+                        continue
+                    if inf_obj.status == autofile.schema.RunStatus.RUNNING:
+                        ioprinter.info_message(
+                            'Scan job is currently running at ',
+                            coord_names, locs)
+                        run_finished = False
+                        break
+            ioprinter.info_message(
+                'Waiting for scan point to be started at ', locs)    
+            run_finished = False
+            break
     else:
         run_finished = False
         ioprinter.message('User elected to overwrite scan')
 
     if run_finished:
         ioprinter.message(f'Scan saved previously at {scn_save_fs[0].path()}')
-    else:
-        ioprinter.message('Need to run scans')
 
     return run_finished
 
diff --git a/src/mechroutines/es/ts/_rpath.py b/src/mechroutines/es/ts/_rpath.py
index 954823ea..6ca3a950 100644
--- a/src/mechroutines/es/ts/_rpath.py
+++ b/src/mechroutines/es/ts/_rpath.py
@@ -75,6 +75,8 @@ def internal_coordinates_scan(ts_zma, zrxn,
         coord_names=coord_names,
         coord_grids=coord_grids,
         scn_save_fs=_scn_save_fs,
+        scn_run_fs=_scn_run_fs,
+        scn_typ='relaxed',
         constraint_dct=constraint_dct,
     )
     if scan_finished_ and find_max:
diff --git a/src/mechroutines/es/tsk.py b/src/mechroutines/es/tsk.py
index 53f3efcc..fd0db37d 100644
--- a/src/mechroutines/es/tsk.py
+++ b/src/mechroutines/es/tsk.py
@@ -166,20 +166,18 @@ def conformer_tsk(job, spc_dct, spc_name,
         :type save_prefix: str
     """
 
-    saddle = bool('ts_' in spc_name)
+    overwrite = es_keyword_dct['overwrite']
+    retryfail = es_keyword_dct['retryfail']
 
+    # Get species information out of dictionaries 
     spc_dct_i = spc_dct[spc_name]
-
-    # Set the spc_info
-    if not saddle:
+    zrxn = spc_dct_i.get('zrxn', None)
+    if zrxn is None:
         spc_info = sinfo.from_dct(spc_dct_i, canonical=True)
     else:
         spc_info = rinfo.ts_info(spc_dct_i['canon_rxn_info'])
-    zrxn = spc_dct_i.get('zrxn', None)
 
-    overwrite = es_keyword_dct['overwrite']
-    retryfail = es_keyword_dct['retryfail']
-    # Modify the theory
+    # Get method information out of dictionaries
     method_dct = thy_dct.get(es_keyword_dct['runlvl'])
     ini_method_dct = thy_dct.get(es_keyword_dct['inplvl'])
     thy_info = tinfo.from_dct(method_dct)
@@ -188,8 +186,12 @@ def conformer_tsk(job, spc_dct, spc_name,
     mod_ini_thy_info = tinfo.modify_orb_label(
         ini_thy_info, spc_info)
     nprocs = method_dct['nprocs']
-    # New filesystem objects
-    _root = root_locs(spc_dct_i, saddle=saddle, name=spc_name)
+    
+    # Create/locate filesystem for running/saving
+    _root = root_locs(
+        spc_dct_i, 
+        saddle=(zrxn is not None),
+        name=spc_name)
     ini_cnf_run_fs, ini_cnf_save_fs = build_fs(
         run_prefix, save_prefix, 'CONFORMER',
         thy_locs=mod_ini_thy_info[1:],
@@ -201,47 +203,52 @@ def conformer_tsk(job, spc_dct, spc_name,
 
     if job == 'samp':
 
-        # Build the ini zma filesys
+        # Determine the initial conformers to sample from
         user_conf_ids = spc_dct_i.get('conf_id')
+        all_locs, all_paths = filesys.mincnf.conformer_locators(
+            ini_cnf_save_fs, mod_ini_thy_info, cnf_range='all', nprocs=nprocs)
+        ini_confs = []
+        ### TODO give option to only sample minimum ring state
+        ### (currently done on individual case by user specifying conf_id)
         if user_conf_ids is None:
-            ini_loc_info = filesys.mincnf.min_energy_conformer_locators(
-                ini_cnf_save_fs, mod_ini_thy_info, nprocs=nprocs)
-            ini_locs, ini_min_cnf_path = ini_loc_info
-
-            all_locs,all_paths = filesys.mincnf.conformer_locators(
-            cnf_save_fs, mod_thy_info, cnf_range='all', nprocs=nprocs)
+            # Collect the minimum energy conformer of each ring state
             unique_rids = set()
-            ini_confs = []
-            for loc,loc_path in zip(all_locs,all_paths):
+            for loc, loc_path in zip(all_locs, all_paths):
                 if loc[0] not in unique_rids:
-                    ini_confs.append((loc,loc_path))
+                    ini_confs.append((loc, loc_path))
                 unique_rids.add(loc[0])
-            visited_rids = set()
-    
         else:
+            # Use only user specified conformer
             print(f'Using user specified conformer IDs: {user_conf_ids}')
-            ini_locs = user_conf_ids
+            for loc, loc_path in zip(all_locs, all_paths):
+                if loc == user_conf_ids:
+                    ini_confs.append((loc, loc_path))
 
-        if any(ini_locs):
-            ini_zma_save_fs = autofile.fs.zmatrix(ini_min_cnf_path)
+        if not any(ini_confs):
+            ioprinter.info_message(
+                'Missing conformers. Skipping task...')
 
-            # Set up the run scripts
-            script_str, kwargs = qchem_params(
-                method_dct, elstruct.Job.OPTIMIZATION)
+        # Set up the run scripts
+        script_str, kwargs = qchem_params(
+            method_dct, elstruct.Job.OPTIMIZATION)
 
-            # Set variables if it is a saddle
-            two_stage = saddle
-            mc_nsamp = spc_dct_i['mc_nsamp']
-            resave = es_keyword_dct['resave']
+        # Set variables if it is a saddle
+        two_stage = zrxn is not None
+        mc_nsamp = spc_dct_i['mc_nsamp']
+        resave = es_keyword_dct['resave']
 
-            # Read the geometry and zma from the ini file system
+        # Loop over all the initial conformers to sample from
+        for ini_locs, ini_path in ini_confs:
+
+            # Read the geometry and zma from the initial file system
+            ini_zma_save_fs = autofile.fs.zmatrix(ini_path)
             geo = ini_cnf_save_fs[-1].file.geometry.read(ini_locs)
             zma_locs = (0,)
-            if saddle:
+            if zrxn is not None:
                 zma_locs = ts_zma_locs(spc_dct, spc_name, ini_zma_save_fs)
             zma = ini_zma_save_fs[-1].file.zmatrix.read(zma_locs)
 
-            # Read the torsions from the ini file sys
+            # Read the torsions from the initial file sys
             if ini_zma_save_fs[-1].file.torsions.exists(zma_locs):
                 tors_lst = ini_zma_save_fs[-1].file.torsions.read(zma_locs)
                 rotors = automol.data.rotor.rotors_from_data(zma, tors_lst)
@@ -249,27 +256,19 @@ def conformer_tsk(job, spc_dct, spc_name,
             else:
                 tors_names = ()
 
-            geo_path = ini_cnf_save_fs[-1].path(ini_locs)
-            ioprinter.initial_geom_path('Sampling started', geo_path)
-
-            # Check runsystem for equal ring CONF make conf_fs
-            # Else make new ring conf directory
-            # Why should RID be None? I am taking stuff from filesys so it will already have a RID!
-            rid = ini_locs[0]
-            # rid = conformer.rng_loc_for_geo(geo, cnf_save_fs)
-            # print("Debug: back to tsk - rid", rid)
-
-            # if rid is None:
-            #     conformer.single_conformer(
-            #         zma, spc_info, mod_thy_info,
-            #         cnf_run_fs, cnf_save_fs,
-            #         script_str, overwrite,
-            #         retryfail=retryfail, zrxn=zrxn,
-            #         **kwargs)
+            ioprinter.initial_geom_path(
+                'Sampling started', 
+                ini_cnf_save_fs[-1].path(ini_locs))
 
-            #     rid = conformer.rng_loc_for_geo(
-            #         geo, cnf_save_fs)
 
+            rid = conformer.rng_loc_for_geo(geo, cnf_save_fs)
+            if rid is None:
+                rid = conformer.rng_loc_for_geo(geo, ini_cnf_save_fs)
+                # use the rid for the initial LoT unless it corresponds
+                # to a different puckering state at the run LoT
+                if rid is None or [rid] in cnf_save_fs[-2].existing():
+                    rid = autofile.schema.generate_new_ring_id()
+            
             # Run the sampling
             conformer.conformer_sampling(
                 zma, spc_info, mod_thy_info,
@@ -278,58 +277,10 @@ def conformer_tsk(job, spc_dct, spc_name,
                 nsamp_par=mc_nsamp,
                 tors_names=tors_names,
                 zrxn=zrxn, two_stage=two_stage,
-                retryfail=retryfail, resave=resave,
+                retryfail=retryfail, resave=False,
                 repulsion_thresh=40.0, print_debug=print_debug,
                 **kwargs)
             
-            visited_rids.add(rid)
-            if True:
-                for ini_locs,ini_path in ini_confs:
-                    if ini_locs[0] not in visited_rids:
-                        ini_zma_save_fs = autofile.fs.zmatrix(ini_path)
-                        # Set up the run scripts
-                        # script_str, kwargs = qchem_params(
-                        #     method_dct, elstruct.Job.OPTIMIZATION)
-                        # Set variables if it is a saddle
-                        # two_stage = saddle
-                        # mc_nsamp = spc_dct_i['mc_nsamp']
-                        # resave = resave
-
-                        # Read the geometry and zma from the ini file system
-                        geo = ini_cnf_save_fs[-1].file.geometry.read(ini_locs)
-                        zma_locs = (0,)
-                        if saddle:
-                            zma_locs = ts_zma_locs(spc_dct, spc_name, ini_zma_save_fs)
-                        zma = ini_zma_save_fs[-1].file.zmatrix.read(zma_locs)
-
-                        # Read the torsions from the ini file sys
-                        if ini_zma_save_fs[-1].file.torsions.exists(zma_locs):
-                            tors_lst = ini_zma_save_fs[-1].file.torsions.read(zma_locs)
-                            rotors = automol.data.rotor.rotors_from_data(zma, tors_lst)
-                            tors_names = automol.data.rotor.rotors_torsion_names(rotors, flat=True)
-                        else:
-                            tors_names = ()
-
-                        geo_path = ini_cnf_save_fs[-1].path(ini_locs)
-                        ioprinter.initial_geom_path('Sampling started', geo_path)
-                        rid = ini_locs[0]
-                        # Run the sampling
-                        conformer.conformer_sampling(
-                            zma, spc_info, mod_thy_info,
-                            cnf_run_fs, cnf_save_fs, rid,
-                            script_str, overwrite,
-                            nsamp_par=mc_nsamp,
-                            tors_names=tors_names,
-                            zrxn=zrxn, two_stage=two_stage,
-                            retryfail=retryfail, resave=False,
-                            repulsion_thresh=40.0, print_debug=print_debug,
-                            **kwargs)
-                
-
-
-        else:
-            ioprinter.info_message(
-                'Missing conformers. Skipping task...')
 
     elif job == 'pucker':
         algo = es_keyword_dct['algorithm']
@@ -341,54 +292,59 @@ def conformer_tsk(job, spc_dct, spc_name,
         ini_loc_info = filesys.mincnf.min_energy_conformer_locators(
             ini_cnf_save_fs, mod_ini_thy_info, nprocs=nprocs)
         ini_min_locs, ini_min_cnf_path = ini_loc_info
-        ini_zma_save_fs = autofile.fs.zmatrix(ini_min_cnf_path)
+        
+        if not ini_min_cnf_path:
+            ioprinter.info_message(
+                'No conformer found for starting point. Skipping task...')
+        else:
+            ini_zma_save_fs = autofile.fs.zmatrix(ini_min_cnf_path)
 
-        # Set up the run scripts
-        script_str, kwargs = qchem_params(
-            method_dct, elstruct.Job.OPTIMIZATION)
-        # Always run two stage optimization
-        two_stage = True
-        mc_nsamp = spc_dct_i['mc_nsamp']
+            # Set up the run scripts
+            script_str, kwargs = qchem_params(
+                method_dct, elstruct.Job.OPTIMIZATION)
+            # Always run two stage optimization
+            two_stage = True
+            mc_nsamp = spc_dct_i['mc_nsamp']
 
-        # Read the geometry and zma from the ini file system
-        geo = ini_cnf_save_fs[-1].file.geometry.read(ini_min_locs)
-        zma_locs = (0,)
-        if saddle:
-            zma_locs = ts_zma_locs(spc_dct, spc_name, ini_zma_save_fs)
-        zma = ini_zma_save_fs[-1].file.zmatrix.read(zma_locs)
+            # Read the geometry and zma from the ini file system
+            geo = ini_cnf_save_fs[-1].file.geometry.read(ini_min_locs)
+            zma_locs = (0,)
+            if zrxn is not None:
+                zma_locs = ts_zma_locs(spc_dct, spc_name, ini_zma_save_fs)
+            zma = ini_zma_save_fs[-1].file.zmatrix.read(zma_locs)
 
-        # Read the ring torsions from the ini file sys
-        if ini_zma_save_fs[-1].file.ring_torsions.exists(zma_locs):
-            ring_tors_dct = ini_zma_save_fs[-1].file.ring_torsions.read(zma_locs)
-        else:
-            ring_tors_dct = {}
+            # Read the ring torsions from the ini file sys
+            if ini_zma_save_fs[-1].file.ring_torsions.exists(zma_locs):
+                ring_tors_dct = ini_zma_save_fs[-1].file.ring_torsions.read(zma_locs)
+            else:
+                ring_tors_dct = {}
 
-        # Read the torsions from the ini file sys
-        if ini_zma_save_fs[-1].file.torsions.exists(zma_locs):
-            tors_lst = ini_zma_save_fs[-1].file.torsions.read(zma_locs)
-            rotors = automol.data.rotor.rotors_from_data(zma, tors_lst)
-            tors_names = automol.data.rotor.rotors_torsion_names(rotors, flat=True)
-        else:
-            tors_names = ()
-
-        geo_path = ini_cnf_save_fs[-1].path(ini_min_locs)
-        ioprinter.initial_geom_path('Sampling started', geo_path)
-
-        # Run the sampling
-        conformer.ring_conformer_sampling(
-            zma, spc_info, mod_thy_info,
-            cnf_run_fs, cnf_save_fs,
-            script_str, overwrite,
-            tors_names,
-            algorithm=algo,
-            thresholds=thresh_pucker,
-            eps=eps,
-            checks=checks,
-            rand_tors=rand_tors,
-            nsamp_par=mc_nsamp,
-            ring_tors_dct=ring_tors_dct, zrxn=zrxn,
-            two_stage=two_stage, retryfail=retryfail,
-            **kwargs)
+            # Read the torsions from the ini file sys
+            if ini_zma_save_fs[-1].file.torsions.exists(zma_locs):
+                tors_lst = ini_zma_save_fs[-1].file.torsions.read(zma_locs)
+                rotors = automol.data.rotor.rotors_from_data(zma, tors_lst)
+                tors_names = automol.data.rotor.rotors_torsion_names(rotors, flat=True)
+            else:
+                tors_names = ()
+
+            geo_path = ini_cnf_save_fs[-1].path(ini_min_locs)
+            ioprinter.initial_geom_path('Sampling started', geo_path)
+
+            # Run the sampling
+            conformer.ring_conformer_sampling(
+                zma, spc_info, mod_thy_info,
+                cnf_run_fs, cnf_save_fs,
+                script_str, overwrite,
+                tors_names,
+                algorithm=algo,
+                thresholds=thresh_pucker,
+                eps=eps,
+                checks=checks,
+                rand_tors=rand_tors,
+                nsamp_par=mc_nsamp,
+                ring_tors_dct=ring_tors_dct, zrxn=zrxn,
+                two_stage=two_stage, retryfail=retryfail,
+                **kwargs)
 
     elif job == 'opt':
 
@@ -402,24 +358,32 @@ def conformer_tsk(job, spc_dct, spc_name,
         script_str, kwargs = qchem_params(
             method_dct, elstruct.Job.OPTIMIZATION)
 
+        # collect the conformers saved at the run LoT
         rng_cnf_locs_lst, _ = filesys.mincnf.conformer_locators(
             cnf_save_fs, mod_thy_info,
-            cnf_range='all', nprocs=nprocs)
-
+            cnf_range='all', nprocs=nprocs, print_level=0)
+        
+        # choose conformers from the ini LoT to optimize at run LoT
         ini_rng_cnf_locs_lst, _ = filesys.mincnf.conformer_locators(
             ini_cnf_save_fs, mod_ini_thy_info,
             cnf_range=cnf_range, sort_info_lst=cnf_sort_info_lst,
             hbond_cutoffs=hbond_cutoffs,
-            print_enes=True, nprocs=nprocs)
+            print_level=2, nprocs=nprocs)
 
-        # Truncate the list of the ini confs
+        if not ini_rng_cnf_locs_lst:
+            ioprinter.warning_message(
+                f'No min-energy conformer found at {ini_cnf_save_fs[0].path()}')
+            if ini_cnf_save_fs[-1].existing():
+                ioprinter.warning_message(
+                     ' likely due to missing sorting criteria.'
+                )
+                print(cnf_sort_info_lst)
+
+        # Determine which of the requested conformers are unique to the ini 
+        # LoT save, and are not in the run LoT save
         uni_rng_locs_lst, uni_cnf_locs_lst = conformer.unique_fs_ring_confs(
             cnf_save_fs, rng_cnf_locs_lst,
             ini_cnf_save_fs, ini_rng_cnf_locs_lst)
-        # ioprinter.debug_message(
-        #    'uni lst that has no similar ring', uni_rng_locs_lst)
-        # ioprinter.debug_message(
-        #    'uni lst that has similar ring', uni_cnf_locs_lst)
 
         for locs in uni_rng_locs_lst + uni_cnf_locs_lst:
 
@@ -431,10 +395,11 @@ def conformer_tsk(job, spc_dct, spc_name,
                 ini_locs, rid = locs
                 cid = autofile.schema.generate_new_conformer_id()
 
+            # get the zma for the ini LoT conformer for the current locs
             ini_cnf_save_path = ini_cnf_save_fs[-1].path(ini_locs)
             ini_zma_save_fs = autofile.fs.zmatrix(ini_cnf_save_path)
             zma_locs = (0,)
-            if saddle:
+            if zrxn is not None:
                 zma_locs = ts_zma_locs(spc_dct, spc_name, ini_zma_save_fs)
             zma = ini_zma_save_fs[-1].file.zmatrix.read(zma_locs)
             
@@ -449,7 +414,7 @@ def conformer_tsk(job, spc_dct, spc_name,
                     zma, instab_zmas, cnf_save_fs,
                     rng_locs=(rid,), tors_locs=(cid,), zma_locs=(0,))
             else:
-                # Make the ring filesystem
+                # Optimize the conformer at the run LoT
                 conformer.single_conformer(
                     zma, spc_info, mod_thy_info,
                     cnf_run_fs, cnf_save_fs,
@@ -480,7 +445,7 @@ def conformer_tsk(job, spc_dct, spc_name,
                 ini_cnf_save_fs, mod_ini_thy_info,
                 cnf_range=cnf_range, sort_info_lst=cnf_sort_info_lst,
                 hbond_cutoffs=hbond_cutoffs,
-                print_enes=True, nprocs=nprocs)
+                print_level=2, nprocs=nprocs)
         else:
             print(f'Using user specified conformer IDs: {user_conf_ids}')
             ini_rng_cnf_locs_lst = (user_conf_ids,)
@@ -517,7 +482,7 @@ def conformer_tsk(job, spc_dct, spc_name,
                 ini_zma_save_fs = autofile.fs.zmatrix(geo_save_path)
                 geo = ini_cnf_save_fs[-1].file.geometry.read(ini_locs)
                 zma_locs = (0,)
-                if saddle:
+                if zrxn is not None:
                     zma_locs = ts_zma_locs(spc_dct, spc_name, ini_zma_save_fs)
                 zma = ini_zma_save_fs[-1].file.zmatrix.read(zma_locs)
 
@@ -849,7 +814,7 @@ def hr_tsk(job, spc_dct, spc_name,
             ini_cnf_save_fs, mod_ini_thy_info,
             cnf_range=cnf_range, sort_info_lst=cnf_sort_info_lst,
             hbond_cutoffs=hbond_cutoffs,
-            print_enes=True, nprocs=nprocs)
+            print_level=2, nprocs=nprocs)
     else:
         ini_min_locs_lst = (user_conf_ids,)
         ini_path_lst = (ini_cnf_save_fs[-1].path(user_conf_ids),)
diff --git a/src/mechroutines/proc/_collect.py b/src/mechroutines/proc/_collect.py
index ea6cf903..5a391930 100644
--- a/src/mechroutines/proc/_collect.py
+++ b/src/mechroutines/proc/_collect.py
@@ -337,8 +337,8 @@ def enthalpy(
     if cnf_fs[-1].file.hessian.exists(locs):
         # print(pf_filesystems)
         ene_abs = ene.read_energy(
-            spc_dct_i, pf_filesystems, spc_mod_dct_i,
-            run_prefix, spc_dct, conf=(locs, locs_path, cnf_fs),
+            spc_dct_i, pf_filesystems, spc_mod_dct_i, spc_dct,
+            run_prefix, conf=(locs, locs_path, cnf_fs),
             read_ene=True, read_zpe=True, saddle=saddle)
         hf0k, _, chn_basis_ene_dct, hbasis = basis.enthalpy_calculation(
             spc_dct, spc_name, ene_abs,
diff --git a/src/mechroutines/proc/_util.py b/src/mechroutines/proc/_util.py
index 19986beb..a1238b8b 100644
--- a/src/mechroutines/proc/_util.py
+++ b/src/mechroutines/proc/_util.py
@@ -142,7 +142,7 @@ def choose_conformers(
     rng_cnf_locs_lst, rng_cnf_locs_path = filesys.mincnf.conformer_locators(
         cnf_save_fs, mod_thy_info,
         cnf_range=cnf_range, sort_info_lst=sort_info_lst, hbond_cutoffs=hbond_cutoffs,
-        print_enes=True, nprocs=proc_keyword_dct['nprocs'])
+        print_level=2, nprocs=proc_keyword_dct['nprocs'])
     if populate_symm:
         for cnf_locs, cnf_path in zip(rng_cnf_locs_lst, rng_cnf_locs_path):
             symm_fs = autofile.fs.symmetry(cnf_path)
diff --git a/src/mechroutines/trans/_routines/_trans.py b/src/mechroutines/trans/_routines/_trans.py
index 4d40d518..b46e4ee1 100644
--- a/src/mechroutines/trans/_routines/_trans.py
+++ b/src/mechroutines/trans/_routines/_trans.py
@@ -172,7 +172,7 @@ def _etrans_fs(spc_dct, tgt_name, bath_name,
             cnf_range=etrans_keyword_dct['cnf_range'],
             sort_info_lst=cnf_sort_info_lst,
             hbond_cutoffs=spc_dct_i['hbond_cutoffs'],
-            print_enes=True,
+            print_level=2,
             nprocs=1)
         min_cnf_locs = cnf_rng_info[0][0]
 
diff --git a/tests/archive.tgz b/tests/archive.tgz
index 3e579810..198ec1bd 100644
Binary files a/tests/archive.tgz and b/tests/archive.tgz differ