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debugging
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jrudz committed May 15, 2024
1 parent fb51c80 commit ff415cf
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Showing 2 changed files with 90 additions and 40 deletions.
1 change: 1 addition & 0 deletions atomisticparsers/gromacs/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1061,6 +1061,7 @@ def parse_method(self):
self.logger.error("Error parsing interactions.")

interactions = self.traj_parser.get_interactions()
print(interactions)
self.parse_interactions(interactions, sec_model)

input_parameters = self.input_parameters
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129 changes: 89 additions & 40 deletions atomisticparsers/utils/parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -182,50 +182,99 @@ def parse_interactions(self, interactions: List[Dict], sec_model: MSection) -> N
if not interactions:
return

def write_interaction_values(values):
## OLD ##
interaction_dict = {}
for interaction_key in Interaction.m_def.all_quantities.keys():
interaction_dict[interaction_key] = np.array(
[interaction.get(interaction_key) for interaction in interactions],
dtype=object,
)
interaction_dict = {key: val for key, val in interaction_dict.items()}
interaction_types = (
np.unique(interaction_dict["type"])
if interaction_dict.get("type") is not None
else []
)
for interaction_type in interaction_types:
sec_interaction = Interaction()
sec_model.contributions.append(sec_interaction)
sec_interaction.type = current_type
sec_interaction.n_atoms = max(
[len(v) for v in values.get("atom_indices", [[0]])]
)
for key, val in values.items():
# TODO tempory fix: atom_labels, atom_indices not homogeneous
# fill in missing atom label with 'X', atom index with -1
if key in ["atom_indices", "atom_labels"]:
val = [
(
v
+ [-1 if key == "atom_indices" else "X"]
* sec_interaction.n_atoms
)[: sec_interaction.n_atoms]
for v in val
]
quantity_def = sec_interaction.m_def.all_quantities.get(key)
if quantity_def:
try:
sec_interaction.m_set(quantity_def, val)
except Exception:
self.logger.error("Error setting metadata.", data={"key": key})

interactions.sort(key=lambda x: x.get("type"))
current_type = interactions[0].get("type")
interaction_values: Dict[str, Any] = {}
for interaction in interactions:
interaction_type = interaction.get("type")
if current_type and current_type != interaction_type:
write_interaction_values(interaction_values)
current_type = interaction_type
interaction_values = {}
interaction_values.setdefault("n_interactions", 0)
interaction_values["n_interactions"] += 1
for key, val in interaction.items():
interaction_indices = np.where(
interaction_dict["type"] == interaction_type
)[0]
sec_interaction.type = interaction_type
sec_interaction.n_interactions = len(interaction_indices)
sec_interaction.n_atoms
for key, val in interaction_dict.items():
if key == "type":
continue
interaction_values.setdefault(key, [])
interaction_values[key].append(val)
if interaction_values:
write_interaction_values(interaction_values)
interaction_vals = val[interaction_indices]
if type(interaction_vals[0]).__name__ == "ndarray":
interaction_vals = np.array(
[vals.tolist() for vals in interaction_vals], dtype=object
)
if interaction_vals.all() is None:
continue
if key == "parameters":
interaction_vals = interaction_vals.tolist()
elif key == "n_atoms":
interaction_vals = interaction_vals[0]
if hasattr(sec_interaction, key):
sec_interaction.m_set(
sec_interaction.m_get_quantity_definition(key), interaction_vals
)

if not sec_interaction.n_atoms:
sec_interaction.n_atoms = (
len(sec_interaction.get("atom_indices")[0])
if sec_interaction.get("atom_indices") is not None
else None
)
## NEW ##
# def write_interaction_values(values):
# sec_interaction = Interaction()
# sec_model.contributions.append(sec_interaction)
# sec_interaction.type = current_type
# sec_interaction.n_atoms = max(
# [len(v) for v in values.get("atom_indices", [[0]])]
# )
# for key, val in values.items():
# # TODO tempory fix: atom_labels, atom_indices not homogeneous
# # fill in missing atom label with 'X', atom index with -1
# # if key in ["atom_indices", "atom_labels"]:
# # val = [
# # (
# # v
# # + [-1 if key == "atom_indices" else "X"]
# # * sec_interaction.n_atoms
# # )[: sec_interaction.n_atoms]
# # for v in val
# # ]
# quantity_def = sec_interaction.m_def.all_quantities.get(key)
# if quantity_def:
# try:
# sec_interaction.m_set(quantity_def, val)
# except Exception:
# self.logger.error("Error setting metadata.", data={"key": key})

# interactions.sort(key=lambda x: x.get("type"))
# print(interactions)
# current_type = interactions[0].get("type")
# interaction_values: Dict[str, Any] = {}
# for interaction in interactions:
# interaction_type = interaction.get("type")
# if current_type and current_type != interaction_type:
# write_interaction_values(interaction_values)
# current_type = interaction_type
# interaction_values = {}
# interaction_values.setdefault("n_interactions", 0)
# interaction_values["n_interactions"] += 1
# for key, val in interaction.items():
# if key == "type":
# continue
# interaction_values.setdefault(key, [])
# interaction_values[key].append(val)
# if interaction_values:
# write_interaction_values(interaction_values)

def parse_interactions_by_type(
self, interactions_by_type: List[Dict], sec_model: Model
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