added bond list

nomad-coe · Oct 30, 2023 · e43f8ae · e43f8ae
1 parent 33ae2ef
commit e43f8ae
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Showing 2 changed files with 13 additions and 2 deletions.
diff --git a/atomisticparsers/gromacs/parser.py b/atomisticparsers/gromacs/parser.py
@@ -44,6 +44,7 @@
 )
 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
 
 re_float = r'[-+]?\d+\.*\d*(?:[Ee][-+]\d+)?'
 re_n = r'[\n\r]'
@@ -704,14 +705,19 @@ def get_composition(children_names):
             if positions is None:
                 continue
 
+            bond_list = []
+            if n == 0:  # TODO add references to the bond list for other steps
+                bond_list = get_bond_list_from_model_contributions(sec_run, method_index=-1, model_index=-1)
+
             self.parse_trajectory_step({
                 'atoms': {
                     'n_atoms': self.traj_parser.get_n_atoms(n),
                     'periodic': pbc,
                     'lattice_vectors': self.traj_parser.get_lattice_vectors(n),
                     'labels': self.traj_parser.get_atom_labels(n),
                     'positions': positions,
-                    'velocities': self.traj_parser.get_velocities(n)
+                    'velocities': self.traj_parser.get_velocities(n),
+                    'bond_list': bond_list
                 }
             })
 

diff --git a/atomisticparsers/lammps/parser.py b/atomisticparsers/lammps/parser.py
@@ -36,6 +36,7 @@
 )
 from .metainfo.lammps import x_lammps_section_input_output_files, x_lammps_section_control_parameters
 from atomisticparsers.utils import MDAnalysisParser, MDParser
+from nomad.atomutils import get_bond_list_from_model_contributions
 
 
 re_float = r'[-+]?\d+\.*\d*(?:[Ee][-+]\d+)?'
@@ -958,14 +959,18 @@ def get_composition(children_names):
             velocities = self.traj_parsers.eval('get_velocities', traj_n)
             if velocities is not None:
                 velocities = apply_unit(velocities, 'velocity')
+            bond_list = []
+            if traj_n == 0:  # TODO add references to the bond list for other steps
+                bond_list = get_bond_list_from_model_contributions(sec_run, method_index=-1, model_index=-1)
             self.parse_trajectory_step({
                 'atoms': {
                     'n_atoms': self.traj_parsers.eval('get_n_atoms', traj_n),
                     'lattice_vectors': lattice_vectors,
                     'periodic': self.traj_parsers.eval('get_pbc', traj_n),
                     'positions': apply_unit(self.traj_parsers.eval('get_positions', traj_n), 'distance'),
                     'labels': self.traj_parsers.eval('get_atom_labels', traj_n),
-                    'velocities': velocities
+                    'velocities': velocities,
+                    'bond_list': bond_list
                 }
             })