schnetpack.md

This module contains all functionality for performing various molecular dynamics simulations using SchNetPack.

System

System

Container for all properties associated with the simulated molecular system (masses, positions, momenta, ...).

Initial Conditions

`Initializer`	Basic initializer class template.
`MaxwellBoltzmannInit`	Initializes the system momenta according to a Maxwell--Boltzmann distribution at the given temperature.
`UniformInit`	Initializes the system momenta according to a uniform distribution scaled to the given temperature.

Integrators

Integrators for NVE and NVT simulations:

`Integrator`	Basic integrator class template.
`VelocityVerlet`	Standard velocity Verlet integrator for non ring-polymer simulations.
`RingPolymer`	Integrator for ring polymer molecular dynamics, as e.g.

Integrators for NPT simulations:

`NPTVelocityVerlet`	Verlet integrator for constant pressure dynamics (NPT).
`NPTRingPolymer`	Ring polymer integrator for constant pressure dynamics (NPT).

Calculators

Basic calculators:

`MDCalculator`	Base MDCalculator class for computing and updating the forces of the simulated system, as well as other properties predicted by the model.
`QMCalculator`	Basic calculator for interfacing quantum chemistry codes with SchNetPack molecular dynamics.
`EnsembleCalculator`	Mixin for creating ensemble calculators from the standard schnetpack.md.calculators classes.
`LJCalculator`	Lennard Jones potential calculator.

Neural network potentials and ORCA calculators:

`SchNetPackCalculator`	MD calculator for schnetpack models.
`SchNetPackEnsembleCalculator`	Ensemble calculator using schnetpack models.
`OrcaCalculator`	Calculator for interfacing the ORCA code package [#orca1]_ with SchNetPack molecular dynamics.

Neighbor List

NeighborListMD

Wrapper for neighbor list transforms to make them suitable for molecular dynamics simulations.

Simulator

Simulator

Main driver of the molecular dynamics simulation.

Simulation hooks

Basic hooks:

`SimulationHook`	Basic class for simulator hooks
`RemoveCOMMotion`	Periodically remove motions of the center of mass from the system.

Thermostats:

`ThermostatHook`	Basic thermostat hook for simulator class.
`BerendsenThermostat`	Berendsen velocity rescaling thermostat, as described in [#berendsen1]_.
`LangevinThermostat`	Basic stochastic Langevin thermostat, see e.g.
`NHCThermostat`	Nose-Hover chain thermostat, which links the system to a chain of deterministic Nose-Hoover thermostats first introduced in [#nhc_thermostat1]_ and described in great detail in [#nhc_thermostat2]_.
`GLEThermostat`	Stochastic generalized Langevin colored noise thermostat by Ceriotti et.

Thermostats for ring-polymer MD:

`PILELocalThermostat`	Langevin thermostat for ring polymer molecular dynamics as introduced in [#stochastic_thermostats2]_.
`PILEGlobalThermostat`	Global variant of the ring polymer Langevin thermostat as suggested in [#stochastic_thermostats3]_.
`TRPMDThermostat`	Thermostatted ring polymer molecular dynamics thermostat variant of the local PILE thermostat as introduced in [#trpmd_thermostat1]_.
`RPMDGLEThermostat`	Stochastic generalized Langevin colored noise thermostat for RPMD by Ceriotti et.
`PIGLETThermostat`	Efficient generalized Langevin equation stochastic thermostat for ring polymer dynamics simulations, see [#piglet_thermostat1]_ for a detailed description.
`NHCRingPolymerThermostat`	Nose-Hoover chain thermostat for ring polymer molecular dynamics simulations as e.g.

Barostats:

`BarostatHook`	Basic barostat hook for simulator class.
`NHCBarostatIsotropic`	Nose Hoover chain thermostat/barostat for isotropic cell fluctuations.
`NHCBarostatAnisotropic`	Nose Hoover chain thermostat/barostat for anisotropic cell fluctuations.

Barostats for ring-polymer MD:

PILEBarostat

Barostat for ring polymer molecular dynamics simulations.

Logging and callback

`Checkpoint`	Hook for writing out checkpoint files containing the state_dict of the simulator.
`DataStream`	Basic DataStream class to be used with the FileLogger.
`MoleculeStream`	DataStream for logging atom types, positions and velocities to the group 'molecules' of the main hdf5 dataset.
`PropertyStream`	Main routine for logging the properties predicted by the calculator to the group 'properties' of hdf5 dataset.
`FileLogger`	Class for monitoring the simulation and storing the resulting data to a hfd5 dataset.
`BasicTensorboardLogger`	Base class for logging scalar information of the system replicas and molecules collected during the simulation to TensorBoard.
`TensorBoardLogger`	TensorBoard logging hook for the properties of the replicas, as well as of the corresponding centroids for each molecule in the system container.

Simulation data and postprocessing

Data loading:

HDF5Loader

Class for loading HDF5 datasets written by the FileLogger.

Vibrational spectra:

`VibrationalSpectrum`	Base class for computing vibrational spectra from HDF5 datasets using autocorrelation functions and fast fourier transforms.
`PowerSpectrum`	Compute power spectra from a molecular dynamics HDF5 dataset.
`IRSpectrum`	Compute infrared spectra from a molecular dynamics HDF5 dataset.
`RamanSpectrum`	Compute Raman spectra from a molecular dynamics HDF5 dataset.

ORCA output parsing

`OrcaParser`	Main parsers utility for ORCA output files.
`OrcaOutputParser`	Basic ORCA output parser class.
`OrcaFormatter`	Format raw ORCA data collected by an `OrcaPropertyParser`.
`OrcaPropertyParser`	Basic property parser for ORCA output files.
`OrcaMainFileParser`	Predefined `OrcaOutputParser` for extracting data from the main ORCA output file.
`OrcaHessianFileParser`	Predefined `OrcaOutputParser` for extracting data from the hessian output file written by ORCA if some higher order derivatives are requested.

MD utilities

NormalModeTransformer

Class for transforming between bead and normal mode representation of the ring polymer, used e.g.

Utilities for thermostats

`YSWeights`	Weights for Yoshida-Suzuki integration used in propagating the Nose-Hoover chain thermostats.
`GLEMatrixParser`	General parser for GLE thermostat files.
`load_gle_matrices`	Load GLE thermostat files formatted in raw format as generated via http://gle4md.org/index.html?page=matrix The generated matrices are torch tensors of the shape normal_modes x s+1 x s+1, where normal_modes is 1 except in the case of the PIGLET thermostat and s is the number of degrees of freedom added via GLE.
`StableSinhDiv`	McLaurin series of sinh(x)/x around zero to avoid numerical instabilities