From 1edd654aa0dfd9737197d30f9ec19cf7eeda1e52 Mon Sep 17 00:00:00 2001
From: Calvin Pieters <calvinpieters@gmail.com>
Date: Wed, 7 Jan 2026 16:21:19 +0200
Subject: [PATCH 1/2] Mutated conformer jobs issue

It appears when there are many conf opts for a TS and then deduplicated due to similarity, the successful_tsgs was nto made aware of the deduplicaiton (which collapses duplicates and shirnks/reorders). So when ARC finishes conf_opt and tries to write results using hte old integers, it would report out of range and fail.
---
 arc/scheduler.py | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/arc/scheduler.py b/arc/scheduler.py
index f53ee8eead..89c0a29270 100644
--- a/arc/scheduler.py
+++ b/arc/scheduler.py
@@ -1161,14 +1161,18 @@ def run_ts_conformer_jobs(self, label: str):
         successful_tsgs = [tsg for tsg in self.species_dict[label].ts_guesses if tsg.success]
         if len(successful_tsgs) > 1:
             self.job_dict[label]['conf_opt'] = dict()
-            for i, tsg in enumerate(successful_tsgs):
+            for tsg in successful_tsgs:
+                if tsg.index is None:
+                    existing_indices = [guess.index for guess in self.species_dict[label].ts_guesses
+                                        if guess.index is not None]
+                    tsg.index = max(existing_indices or [-1]) + 1
                 self.run_job(label=label,
                              xyz=tsg.initial_xyz,
                              level_of_theory=self.ts_guess_level,
                              job_type='conf_opt',
-                             conformer=i,
+                             conformer=tsg.index,
                              )
-                tsg.conformer_index = i  # Store the conformer index in the TSGuess object to match them later.
+                tsg.conformer_index = tsg.index  # Use a stable identifier for mapping back to TSGuess.
         elif len(successful_tsgs) == 1:
             if 'opt' not in self.job_dict[label].keys() and 'composite' not in self.job_dict[label].keys():
                 # proceed only if opt (/composite) not already spawned
@@ -1980,9 +1984,15 @@ def parse_conformer(self,
             xyz = parser.parse_geometry(log_file_path=job.local_path_to_output_file)
             energy = parser.parse_e_elect(log_file_path=job.local_path_to_output_file)
             if self.species_dict[label].is_ts:
-                self.species_dict[label].ts_guesses[i].energy = energy
-                self.species_dict[label].ts_guesses[i].opt_xyz = xyz
-                self.species_dict[label].ts_guesses[i].index = i
+                tsg = next((guess for guess in self.species_dict[label].ts_guesses
+                            if guess.conformer_index == i), None)
+                if tsg is None:
+                    logger.warning(f'Could not find TSGuess for conformer {i} of {label} '
+                                   f'(expected a matching conformer_index); skipping.')
+                    return False
+                tsg.energy = energy
+                tsg.opt_xyz = xyz
+                tsg.index = i
                 if energy is not None:
                     logger.debug(f'Energy for TSGuess {i} of {label} is {energy:.2f}')
                 else:

From 7d8d8618c13df0a9e6b0b75737a75c14797d08aa Mon Sep 17 00:00:00 2001
From: Calvin <56573970+calvinp0@users.noreply.github.com>
Date: Sat, 10 Jan 2026 15:35:23 +0200
Subject: [PATCH 2/2] Update arc/scheduler.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 arc/scheduler.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/arc/scheduler.py b/arc/scheduler.py
index 89c0a29270..29c139dd49 100644
--- a/arc/scheduler.py
+++ b/arc/scheduler.py
@@ -1992,7 +1992,6 @@ def parse_conformer(self,
                     return False
                 tsg.energy = energy
                 tsg.opt_xyz = xyz
-                tsg.index = i
                 if energy is not None:
                     logger.debug(f'Energy for TSGuess {i} of {label} is {energy:.2f}')
                 else: