schrodinger.application.matsci.mlip.adapters module

Conversions between Schrodinger structures and MLIP molecular-dynamics state.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.matsci.mlip.adapters.structure_to_md_variables(input_st, replicas=1, temperature=300.0, device='cpu', random_seed=None, charge=0, spin_multiplicity=1, recenter_to=None)

Convert a structure to batched molecular-dynamics variables.

Parameters:

  • input_st (Structure) – Input structure. It is not modified.

  • replicas (int) – Number of identical systems in the batch

  • temperature (float) – Initial velocity temperature in Kelvin

  • device (str) – PyTorch device name

  • random_seed (int or None) – Random seed for velocity initialization

  • charge (int) – Total charge of each replica

  • spin_multiplicity (int) – Spin multiplicity of each replica

  • recenter_to (str or None) – RECENTER_TO_CENTER_OF_MASS, RECENTER_TO_CENTER_OF_GEOMETRY, or None

Return type:

tuple[MDVariables, torch.Generator or None]

Returns:

Molecular-dynamics variables and the optional random generator

schrodinger.application.matsci.mlip.adapters.md_variables_to_structure_file(md_variables, output_filename)

Write the final snapshot of each replica to a structure file.

Parameters:

  • md_variables (MDVariables) – Molecular-dynamics variables containing the final state

  • output_filename (str) – MAE or MAEGZ output filename