CDTK.Tools.XPYDERCreator module

class CDTK.Tools.XPYDERCreator.XPYDERCreator(**opts)[source]

Bases: object

Class for creating XPYDER input files

How to use it:

read and sort for given ic
create cluster geometries for different n_QM, c_ix, embedding status

property c_ix

create_cluster_geometry()[source]

Create a cluster geometry centered around the specified molecule.

Selects QM and MM region

property gbs

get_xuvpes_targetpath()[source]: Construct the target path for XUV / PES input files

property ic

property intensity

property md_type

property molCOMs

property n_QM

property n_tot

property pbc_dims

property r_xyz

property r_xyz_MM

property r_xyz_QM

read_cp2k_trajectory()[source]: Read coordinates and velocities from a CP2K trajectory snapshot

read_gromacs_trajectory()[source]: Read coordinates and velocities from a GROMACS trajectory snapshot

read_lammps_trajectory()[source]: Read coordinates and velocities from a LAMMPS trajectory snapshot

sort_trajectory()[source]

Sort trajectory to molecules obeying periodic boundary conditions

Final order: OHH OHH …

property t

property target_dir

property thz

property traj_path

property types

property types_MM

property types_QM

property v_xyz

property v_xyz_MM

property v_xyz_QM

property water_model

write_xpyder_inputfile()[source]

Fill in the xpyder template

Atomic units throughout

write_xuvpes_inputfile()[source]

Fill in the template for XUV photoelectron spectra (XMOLECULE)

Angstrom units throughout

property yes_embed

CDTK.Tools.XPYDERCreator.el_string(a_type, gbs)[source]

Constructs the nao-style electron string

e.g. O 2s2p

Parameters: a_type - atom type gbs - gaussian basis set