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Fixed energy logging for multiple molecules #386

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merged 1 commit into from
Feb 10, 2022
Merged

Fixed energy logging for multiple molecules #386

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2 changes: 1 addition & 1 deletion src/schnetpack/md/data/hdf5_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@ def _load_molecule_data(self):

# Extract energies
entry_start = 0
entry_stop = 1
entry_stop = self.n_molecules
self.properties[f"{properties.energy}_system"] = raw_positions[
:, :, entry_start:entry_stop
].reshape(self.entries, self.n_replicas, self.n_molecules)
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6 changes: 4 additions & 2 deletions src/schnetpack/md/simulation_hooks/callback_hooks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -218,7 +218,9 @@ def _init_data_stream(self, simulator: Simulator):
simulator (schnetpack.md.Simulator): Simulator class used in the molecular dynamics simulation.
"""
# Account for potential energy and positions
data_dimension = 1 + simulator.system.total_n_atoms * 3
data_dimension = (
simulator.system.n_molecules + simulator.system.total_n_atoms * 3
)

# If requested, also store velocities
if self.store_velocities:
Expand Down Expand Up @@ -267,7 +269,7 @@ def update_buffer(self, buffer_position: int, simulator: Simulator):

# Store energies
start = 0
stop = 1
stop = simulator.system.n_molecules
self.buffer[
buffer_position : buffer_position + 1, :, start:stop
] = simulator.system.energy.view(simulator.system.n_replicas, -1).detach()
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