LAMMPS XML maker update. (#119)

* LAMMPS XML bug fix. * LAMMPS XML bug fix.
usnistgov · Sep 21, 2020 · 6bec37f · 6bec37f
1 parent 9e49ce2
commit 6bec37f
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/jarvis/db/lammps_to_xml.py b/jarvis/db/lammps_to_xml.py
@@ -189,8 +189,10 @@ def write_xml(data={}, filename="temp.xml"):
 """
 if __name__ == "__main__":
     from jarvis.io.lammps.outputs import parse_material_calculation_folder
-    fold = '/rk2/knc6/JARVIS-FF/ALLOY8/\
-    Mishin-Ni-Al-2009.eam.alloy_nist/bulk@mp-23_fold'
+
+    # fold = '/rk2/knc6/JARVIS-FF/ALLOY8/\
+    # Mishin-Ni-Al-2009.eam.alloy_nist/bulk@mp-23_fold'
+    fold = "/rk2/knc6/JARVIS-FF/COMB/ffield.TiON.comb3_nist/bulk@mp-25433_fold"
     x = parse_material_calculation_folder(fold)
     write_xml(x)
 """
diff --git a/jarvis/io/lammps/outputs.py b/jarvis/io/lammps/outputs.py
@@ -271,8 +271,12 @@ def parse_material_calculation_folder(path="bulk@mp-1487_fold", jid="x"):
     # Each element has energy_per_atom,
     # system_pressure,elastic_tensor,final_str,initial_str
     print("Found", len(info.keys()), "folders")
-    chem_pot = get_chem_pot(info)
-    info["chem_pot"] = chem_pot
+    try:
+        chem_pot = get_chem_pot(info)
+        info["chem_pot"] = chem_pot
+    except Exception:
+        print("Seems like didnt run vacancy calcs.")
+        pass
     # print (chem_pot)
     vacancy_info = []
     surface_info = []