Supplementary material: Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules

Supplementary material to the manuscript "Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules" by Terry Mullins, Evangelos T. Karamatskos, Joss Wiese, Jolijn Onvlee, Arnaud Rouzée, Andrey Yachmenev, Sebastian Trippel, and Jochen Küpper, Nat. Commun, 2022  simulations_part.z* is split zip archive containing simulations data for indole molecule, such as files with rotational probability density distributions computed at different times (t=0..1500) ps during the laser pulse and field-free evolution, and example python scripts for data retrieval ... TBA   The simulations data contain the following files and folders: prob_density_euler_angles contains files rotdens_av_.gz with simulated state-averaged rotational probability density distributions in terms of Euler angles for different times , ranging from the beginning of the alignment laser pulse at (t=0) up to (t=1500) ps with a time step of 1 ps. Calculations of probability density distributions were done using Richmol program. The gzipped ASCII data files rotdens_av_.gz contain in columns the values of the Euler angles (\phi,\theta,\chi) followed by the normalized probability density value. prob_density_atoms_xyz contains files monte_carlo_av_.h5 with state-averaged rotational probability density distributions of all atoms in the indole molecule in terms of their Cartesian coordinates, for different times , ranging from the beginning of the alignment pulse at (t=0) up to (t=1500) ps with a time step of 1 ps. Structure of monte_carlo_av_.h5 HDF5 files: Key        Description -----        --------------- 'C10'     - Cartesian coordinates of carbon atom no. 10 'C11'     - Cartesian coordinates of carbon atom no. 11 'C12'     - ... 'C14'     - ... 'C3'      - ... 'C6'      - ... 'C7'      - ... 'C9'      - ... 'N4'      - ... 'H1-C3'   - Cartesian coordinates of a vector pointing from carbon atom no. 3 to hydrogen atom no. 1 'H13-C11' - ... 'H15-C12' - ... 'H16-C14' - ... 'H2-N4'   - ... 'H5-C7'   - ... 'H8-C9'   - ... 'ref_vectors' - reference molecular-frame Cartesian coordinates of all atoms 'x'       - coordinates of the x-axis of Principal Axes of Inertia Frame 'y'       - coordinates of the y-axis of Principal Axes of Inertia Frame 'z'       - coordinates of the z-axis of Principal Axes of Inertia Frame 'pol_x'   - coordinates of the x-axis of Principal Axes of Polarizability Frame 'pol_y'   - coordinates of the y-axis of Principal Axes of Polarizability Frame 'pol_z'   - coordinates of the z-axis of Principal Axes of Polarizability Frame indole_deflected_states.txt ASCII file contains initial populations of rotational states of indole in the deflected beam. The following data is arranged in columns: m, J, id, energy, normalized population. The J and m are rotational quantum numbers of the total angular momentum and its Z-projection, the id number refers to the state's index in file indole_energies_j0_j20.txt listing rotational states of indole. indole_data.py Python module provides basic functions to extract information from HDF5 data files monte_carlo_av_.h5. It can also be used to compute alignment and orientation. example_cos.py and example_dens.py Python scripts that demonstrate how to use indole_data.py module for computing and plotting alignment traces and a 2D projection of the probability density distribution, respectively. monte_carlo.py Python script that was used to compute through Monte-Carlo sampling probability density distributions for Cartesian positions of atoms in indole (monte_carlo_av_.h5 files) using probability density distribution functions in Euler angles (outputs of Richmol program rotdens_av_.gz)