Index

A

add_angle() (pyscivr.coordinates.core.InternalCoordinates method) add_azimuthal() (pyscivr.coordinates.core.InternalCoordinates method) add_bond() (pyscivr.coordinates.core.InternalCoordinates method) add_dihedral() (pyscivr.coordinates.core.InternalCoordinates method) add_eckart() (pyscivr.coordinates.core.InternalCoordinates method) add_euler() (pyscivr.coordinates.core.InternalCoordinates method) add_local() (pyscivr.coordinates.core.InternalCoordinates method)

add_normal_mode() (pyscivr.coordinates.core.InternalCoordinates method) add_polar() (pyscivr.coordinates.core.InternalCoordinates method) add_rotation() (pyscivr.coordinates.core.InternalCoordinates method) add_translation() (pyscivr.coordinates.core.InternalCoordinates method) ArgonPotential (class in pyscivr.potentials) ASEPotential (class in pyscivr.potentials) atom_indices (pyscivr.coordinates.core.Coordinate attribute)

B

build() (pyscivr.coordinates.core.InternalCoordinates method) (pyscivr.coordinates.core.QuaternionCoordinates method)

C

Calculator (class in pyscivr.potentials)

Coordinate (class in pyscivr.coordinates.core)

D

DFTPotential (class in pyscivr.potentials)

E

energy() (pyscivr.potentials.Calculator method)

energy_forces() (pyscivr.potentials.Calculator method) eval_hess_active() (in module pyscivr.hessian)

F

find_coordinate() (pyscivr.coordinates.core.InternalCoordinates method)

forces() (pyscivr.potentials.Calculator method)

G

get_action() (in module pyscivr.scivr) get_azimuthal_angle() (in module pyscivr.coordinates.core) get_bond() (in module pyscivr.coordinates.core) get_bond_angle() (in module pyscivr.coordinates.core) get_dihedral_angle() (in module pyscivr.coordinates.core) get_euler_angles() (in module pyscivr.coordinates.core) get_geom() (in module pyscivr.utils) get_inertia() (in module pyscivr.utils) get_kinetic_energy() (pyscivr.integrators.Integrator method) get_lagrangian() (in module pyscivr.scivr) get_mass_center() (in module pyscivr.utils)

get_overlap() (in module pyscivr.basis) get_polar_angle() (in module pyscivr.coordinates.core) get_potential_energy() (pyscivr.integrators.Integrator method) get_prefactor() (in module pyscivr.scivr) get_rotation_matrix() (in module pyscivr.coordinates.core) get_ta_spectrum_fft() (in module pyscivr.scivr) get_ta_spectrum_naive() (in module pyscivr.scivr) get_total_energy() (pyscivr.integrators.ImplicitVerlet method) (pyscivr.integrators.Integrator method) get_trajectory() (pyscivr.integrators.ImplicitVerlet method) (pyscivr.integrators.Integrator method)

H

H2SplinePotential (class in pyscivr.potentials)

hessian() (pyscivr.potentials.Calculator method)

I

ImplicitVerlet (class in pyscivr.integrators) Integrator (class in pyscivr.integrators)

InternalCoordinates (class in pyscivr.coordinates.core) interpolate_hessian() (in module pyscivr.hessian)

K

kind (pyscivr.coordinates.core.Coordinate attribute)

L

load_hessian() (in module pyscivr.save)

load_trajectory() (in module pyscivr.save)

M

mace_anicc_potential() (in module pyscivr.potentials) make_converters() (in module pyscivr.coordinates.core) make_jacobi_func() (in module pyscivr.variations) make_vari_propagator() (in module pyscivr.variations) make_vari_propagator_implicit() (in module pyscivr.variations) module pyscivr pyscivr.basis pyscivr.coordinates pyscivr.coordinates.core pyscivr.coordinates.scan pyscivr.hessian pyscivr.integrators pyscivr.potentials pyscivr.save pyscivr.scivr pyscivr.units pyscivr.utils pyscivr.variations

N

name (pyscivr.coordinates.core.Coordinate attribute)

O

overlap_1d() (in module pyscivr.basis)

P

projected_hessian() (in module pyscivr.hessian) propagate_variation() (in module pyscivr.variations) propagate_variation_implicit() (in module pyscivr.variations) pyscivr module pyscivr.basis module pyscivr.coordinates module pyscivr.coordinates.core module pyscivr.coordinates.scan module pyscivr.hessian module

pyscivr.integrators module pyscivr.potentials module pyscivr.save module pyscivr.scivr module pyscivr.units module pyscivr.utils module pyscivr.variations module

Q

quat_to_rotmat() (in module pyscivr.coordinates.core)

quaternion_metric() (in module pyscivr.coordinates.core) QuaternionCoordinates (class in pyscivr.coordinates.core)

R

register_kind() (pyscivr.coordinates.core.InternalCoordinates method) restore_multipliers() (in module pyscivr.save)

rigid_scan_1d() (in module pyscivr.coordinates.scan) run() (pyscivr.integrators.ImplicitVerlet method) (pyscivr.integrators.Integrator method)

S

save_hessian() (in module pyscivr.save) save_trajectory() (in module pyscivr.save) ShakeRattle (class in pyscivr.integrators)

step() (pyscivr.integrators.ImplicitVerlet method) (pyscivr.integrators.Integrator method) (pyscivr.integrators.ShakeRattle method) (pyscivr.integrators.Verlet method)

T

to_internal() (in module pyscivr.variations)

topology (pyscivr.coordinates.core.Coordinate attribute)

V

value_ref (pyscivr.coordinates.core.Coordinate attribute)

Verlet (class in pyscivr.integrators)

Z

ZeroPotential (class in pyscivr.potentials)