pyscivr package

Subpackages

• pyscivr.coordinates package
  • Submodules
    • pyscivr.coordinates.core module
      • get_bond()
      • get_bond_angle()
      • get_dihedral_angle()
      • get_polar_angle()
      • get_azimuthal_angle()
      • quat_to_rotmat()
      • get_rotation_matrix()
      • get_euler_angles()
      • Coordinate
      • InternalCoordinates
      • QuaternionCoordinates
      • make_converters()
      • quaternion_metric()
    • pyscivr.coordinates.scan module
      • rigid_scan_1d()
  • Module contents

Submodules

• pyscivr.basis module
  • overlap_1d()
  • get_overlap()
• pyscivr.hessian module
  • eval_hess_active()
  • projected_hessian()
  • interpolate_hessian()
• pyscivr.integrators module
  • Integrator
    • Integrator.step()
    • Integrator.get_kinetic_energy()
    • Integrator.get_potential_energy()
    • Integrator.get_total_energy()
    • Integrator.run()
    • Integrator.get_trajectory()
  • Verlet
    • Verlet.step()
  • ShakeRattle
    • ShakeRattle.step()
  • ImplicitVerlet
    • ImplicitVerlet.step()
    • ImplicitVerlet.run()
    • ImplicitVerlet.get_total_energy()
    • ImplicitVerlet.get_trajectory()
• pyscivr.potentials module
  • Calculator
    • Calculator.energy_forces()
    • Calculator.energy()
    • Calculator.forces()
    • Calculator.hessian()
  • ZeroPotential
  • H2SplinePotential
  • ASEPotential
  • mace_anicc_potential()
  • DFTPotential
  • ArgonPotential
• pyscivr.save module
  • save_trajectory()
  • restore_multipliers()
  • load_trajectory()
  • save_hessian()
  • load_hessian()
• pyscivr.scivr module
  • get_action()
  • get_lagrangian()
  • get_prefactor()
  • get_ta_spectrum_naive()
  • get_ta_spectrum_fft()
• pyscivr.units module
• pyscivr.utils module
  • get_geom()
  • get_mass_center()
  • get_inertia()
• pyscivr.variations module
  • make_vari_propagator()
  • propagate_variation()
  • make_vari_propagator_implicit()
  • propagate_variation_implicit()
  • make_jacobi_func()
  • to_internal()

Module contents

PySCIVR: semiclassical initial value representation in internal coordinates.

Modules:

• coordinates: internal coordinates and coordinate conversions.

• integrators: integrators for classical trajectories.

• hessian: Hessians in the active internal coordinates.

• variations: propagation of the monodromy matrices.

• basis: coherent state overlaps for various topologies.

• scivr: semiclassical prefactors, actions and spectra.

• potentials: potential energy calculators.

• save: saving and loading of trajectories and Hessians.

• units: physical constants and unit conversion.

• utils: utilities for molecular geometries.