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 13, 1431 (2022). https://doi.org/10.1038/s41467-022-28951-z, arXiv: 2009.08157

•  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.
• rawdata_part.z* is split zip archive containing raw experimental data.
• analysis_scripts.zip is zip archive containing experimental analysis codes.

The simulations_part.zip contains the following files and folders:

• prob_density_euler_angles contains files rotdens_av_<time>.gz with simulated state-averaged rotational probability density distributions in terms of Euler angles for different times <time>, 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_<time>.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_<time>.h5 with state-averaged rotational probability density distributions of all atoms in the indole molecule in terms of their Cartesian coordinates, for different times <time>, 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_<time>.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_<time>.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_<time>.h5 files) using probability density distribution functions in Euler angles (outputs of Richmol program rotdens_av_<time>.gz).

The analysis_scripts.zip contains the following files and folders:

• H_Plus folder contains codes relevant for the analysis of H⁺ ion data.
  • analyse_full_alignment_scans.m: subtracts background and combines delay scan data sets together, takes account of errors.
  • calculate_resamped_df.m: called by analyse_full_alignment_scans.m to calculate the frequency sampling.
  • unique_mean.m: called by analyse_full_alignment_scans.m when combining data sets. Combines non-unique data points into a single data point.
• C_Plus2 folder contains codes for the analysis of C²⁺ ion data. The file descriptions are identical to those in the H_Plus directory.
• intensity/calculate_intensity.m: calculates peak intensity of the laser pulse from measured parameters as well as statistical error.
• intensity/compare_exp_sim.m: fits experimental and theoretical tomography and delay-dependent 2D projection values.
• intensity/nir2hdf5_kHz.py: converts raw data files (from rawdata_part.z* archive) into hdf5 files.