schnetpack.md
This module contains all functionality for performing various molecular dynamics simulations using SchNetPack.
System
Container for all properties associated with the simulated molecular system (masses, positions, momenta, ...). |
Initial Conditions
Basic initializer class template. |
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Initializes the system momenta according to a Maxwell--Boltzmann distribution at the given temperature. |
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Initializes the system momenta according to a uniform distribution scaled to the given temperature. |
Integrators
Integrators for NVE and NVT simulations:
Basic integrator class template. |
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Standard velocity Verlet integrator for non ring-polymer simulations. |
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Integrator for ring polymer molecular dynamics, as e.g. |
Integrators for NPT simulations:
Verlet integrator for constant pressure dynamics (NPT). |
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Ring polymer integrator for constant pressure dynamics (NPT). |
Calculators
Basic calculators:
Base MDCalculator class for computing and updating the forces of the simulated system, as well as other properties predicted by the model. |
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Basic calculator for interfacing quantum chemistry codes with SchNetPack molecular dynamics. |
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Mixin for creating ensemble calculators from the standard schnetpack.md.calculators classes. |
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Lennard Jones potential calculator. |
Neural network potentials and ORCA calculators:
MD calculator for schnetpack models. |
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Ensemble calculator using schnetpack models. |
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Calculator for interfacing the ORCA code package [#orca1]_ with SchNetPack molecular dynamics. |
Neighbor List
Wrapper for neighbor list transforms to make them suitable for molecular dynamics simulations. |
Simulator
Main driver of the molecular dynamics simulation. |
Simulation hooks
Basic hooks:
Basic class for simulator hooks |
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Periodically remove motions of the center of mass from the system. |
Thermostats:
Basic thermostat hook for simulator class. |
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Berendsen velocity rescaling thermostat, as described in [#berendsen1]_. |
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Basic stochastic Langevin thermostat, see e.g. |
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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]_. |
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Stochastic generalized Langevin colored noise thermostat by Ceriotti et. |
Thermostats for ring-polymer MD:
Langevin thermostat for ring polymer molecular dynamics as introduced in [#stochastic_thermostats2]_. |
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Global variant of the ring polymer Langevin thermostat as suggested in [#stochastic_thermostats3]_. |
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Thermostatted ring polymer molecular dynamics thermostat variant of the local PILE thermostat as introduced in [#trpmd_thermostat1]_. |
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Stochastic generalized Langevin colored noise thermostat for RPMD by Ceriotti et. |
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Efficient generalized Langevin equation stochastic thermostat for ring polymer dynamics simulations, see [#piglet_thermostat1]_ for a detailed description. |
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Nose-Hoover chain thermostat for ring polymer molecular dynamics simulations as e.g. |
Barostats:
Basic barostat hook for simulator class. |
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Nose Hoover chain thermostat/barostat for isotropic cell fluctuations. |
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Nose Hoover chain thermostat/barostat for anisotropic cell fluctuations. |
Barostats for ring-polymer MD:
Barostat for ring polymer molecular dynamics simulations. |
Logging and callback
Hook for writing out checkpoint files containing the state_dict of the simulator. |
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Basic DataStream class to be used with the FileLogger. |
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DataStream for logging atom types, positions and velocities to the group 'molecules' of the main hdf5 dataset. |
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Main routine for logging the properties predicted by the calculator to the group 'properties' of hdf5 dataset. |
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Class for monitoring the simulation and storing the resulting data to a hfd5 dataset. |
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Base class for logging scalar information of the system replicas and molecules collected during the simulation to TensorBoard. |
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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:
Class for loading HDF5 datasets written by the FileLogger. |
Vibrational spectra:
Base class for computing vibrational spectra from HDF5 datasets using autocorrelation functions and fast fourier transforms. |
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Compute power spectra from a molecular dynamics HDF5 dataset. |
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Compute infrared spectra from a molecular dynamics HDF5 dataset. |
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Compute Raman spectra from a molecular dynamics HDF5 dataset. |
ORCA output parsing
Main parsers utility for ORCA output files. |
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Basic ORCA output parser class. |
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Format raw ORCA data collected by an |
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Basic property parser for ORCA output files. |
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Predefined |
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Predefined |
MD utilities
Class for transforming between bead and normal mode representation of the ring polymer, used e.g. |
Utilities for thermostats
Weights for Yoshida-Suzuki integration used in propagating the Nose-Hoover chain thermostats. |
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General parser for GLE thermostat files. |
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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. |
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McLaurin series of sinh(x)/x around zero to avoid numerical instabilities |