diff --git a/vayesta/solver/hamiltonian.py b/vayesta/solver/hamiltonian.py
index c0ccd940..3ccf4c76 100644
--- a/vayesta/solver/hamiltonian.py
+++ b/vayesta/solver/hamiltonian.py
@@ -1,3 +1,4 @@
+import os
 import dataclasses
 from typing import Optional
 
@@ -309,7 +310,11 @@ def pad(a, diag_val):
         # Copy over all output controls from original mol object.
         clusmol.verbose = self.orig_mf.mol.verbose
         if self.orig_mf.mol.output is not None:
-            clusmol.output = f"f{self._fragment.id}_{self.orig_mf.mol.output}"
+            fid = self._fragment.id
+            output = self.orig_mf.mol.output
+            dirname = os.path.dirname(output)
+            basename = os.path.basename(output)
+            clusmol.output = os.path.join(dirname, f"f{fid}_{basename}")
             self.log.debugv("Setting solver output file to %s", clusmol.output)
         # Set information as required for our cluster.
         clusmol.nelec = self.nelec