fixed rebasing issues in lammps parser (sec_system definition was acc…

…identally deleted)
nomad-coe · Oct 30, 2023 · 7b38d7f · 7b38d7f
1 parent 0c54406
commit 7b38d7f
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/atomisticparsers/gromacs/parser.py b/atomisticparsers/gromacs/parser.py
@@ -42,7 +42,7 @@
 from nomad.datamodel.metainfo.simulation.workflow import (
     GeometryOptimization, GeometryOptimizationMethod, GeometryOptimizationResults
 )
-from .metainfo.gromacs import x_gromacs_section_control_parameters, x_gromacs_section_input_output_files, CalcEntry
+from .metainfo.gromacs import x_gromacs_section_control_parameters, x_gromacs_section_input_output_files
 from atomisticparsers.utils import MDAnalysisParser, MDParser
 from nomad.atomutils import get_bond_list_from_model_contributions
 

diff --git a/atomisticparsers/lammps/parser.py b/atomisticparsers/lammps/parser.py
@@ -969,12 +969,16 @@ def get_composition(children_names):
                 }
             })
 
+        if not sec_run.system:
+            return
+
         # add the bond list to system 0
         sec_atoms = sec_run.system[0].atoms
         bond_list = get_bond_list_from_model_contributions(sec_run, method_index=-1, model_index=-1)
         if bond_list != []:
             setattr(sec_atoms, 'bond_list', bond_list)
 
+        sec_system = sec_run.system[-1]
         # parse atomsgroup (moltypes --> molecules --> residues)
         atoms_info = self._mdanalysistraj_parser.get('atoms_info', None)
         if atoms_info is None: