custom_quantity

A collection of functions evaluating quantiities of trajectories. For easiest integration into chemtain, functions should be compatible with traj_util.quantity_traj. Functions provided to quantity_traj need to take the state and additional kwargs.

Common Quantities

energy_wrapper(energy_fn_template[, ...])	Wrapper around energy_fn to allow energy computation via traj_util.quantity_traj.
kinetic_energy_wrapper(state, **unused_kwargs)	Wrapper around kinetic_energy to allow kinetic energy computation via traj_util.quantity_traj.
total_energy_wrapper(energy_fn_template)	Wrapper around energy_fn to allow total energy computation via traj_util.quantity_traj.
temperature(state[, mask])	Temperature function that is consistent with quantity_traj interface.
volume(state, **kwargs)	Returns volume of a single snapshot.
density(state, **unused_kwargs)	Returns density of a single snapshot of the NPT ensemble.

Structural Quantities

Intra-Molecular

init_bond_angle_distribution(...[, ...])	Initializes a function computing a dihedral distribution.
init_bond_dihedral_distribution(...[, smoothing])	Initializes a function computing a dihedral distribution.
init_rmsd(reference_positions, ...[, idx, ...])	Initializes the root mean squared distance from a reference structure.
init_local_structure_index(displacement_fn)	Initializes function to compute the local structure index (LSI).
init_bond_length(displacement_fn, bonds[, ...])	Initializes a function that computes bond lengths for given atom pairs.
estimate_bond_constants(positions, bonds, ...)	Calculates the equlibrium harmonic bond constants from given positions.
angular_displacement(positions, ...[, degrees])	Computes the dihedral angle for all quadruple of atoms given in idxs.
dihedral_displacement(positions, ...[, degrees])	Computes the dihedral angle for all quadruple of atoms given in idxs.

Inter-Molecular

init_rdf(displacement_fn, rdf_params[, ...])	Initializes a function that computes the radial distribution function (RDF) for a single state.
init_adf_nbrs(displacement_fn, adf_params[, ...])	Initializes a function to computes the angular distribution function (ADF).
init_tcf_nbrs(displacement_fn, tcf_params[, ...])	Initializes a function to compute the triplet correlation function (TCF).
init_tetrahedral_order_parameter(displacement_fn)	Initializes a function that computes the tetrahedral order parameter q for a single state.
init_velocity_autocorrelation(num_lags)	Returns the velocity autocorrelation function (VACF).
self_diffusion_green_kubo(traj_state, ...)	Green-Kubo formulation to compute self-diffusion D via the velocity autocorrelation function (VACF).
kinetic_energy_tensor(state)	Computes the kinetic energy tensor of a single snapshot.
virial_potential_part(energy_fn, state, ...)	Interaction part of the virial pressure tensor for a single snaphot based on the formulation of Chen at al.
init_virial_stress_tensor(energy_fn_template)	Initializes a function that computes the virial stress tensor for a single state.
init_pressure(energy_fn_template[, ...])	Initializes a function that computes the pressure for a single state.
energy_under_strain(epsilon, energy_fn, ...)	Potential energy of a state after applying linear strain epsilon.
init_sigma_born(energy_fn_template[, ...])	Initialiizes a function that computes the Born contribution to the stress tensor.
init_stiffness_tensor_stress_fluctuation(...)	Initializes all functions necessary to compute the elastic stiffness tensor via the stress fluctuation method in the NVT ensemble.

States

RDFParams(reference, rdf_bin_centers, ...)	Hyperparameters to initialize the radial distribution function (RDF).
ADFParams(reference, adf_bin_centers, sigma, ...)	Hyperparameters to initialize a angular distribution function (ADF).
TCFParams(reference, sigma_tcf, volume, ...)	Hyperparameters to initialize a triplet correlation function (TFC).
BondAngleParams(reference, sigma, bonds, ...)
BondDihedralParams(reference, sigma, bonds, ...)