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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). <a href="https://doi.org/10.1038/s41467-022-28951-z">https://doi.org/10.1038/s41467-022-28951-z</a>, arXiv: <a href="https://arxiv.org/abs/2009.08157">2009.08157 </a> <ul> <li> 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.</li> <li>rawdata_part.z* is split zip archive containing raw experimental data.</li> <li>analysis_scripts.zip is zip archive containing experimental analysis codes.</li> </ul> The simulations_part.zip contains the following files and folders: <ul> <li>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 <a href="https://github.com/CFEL-CMI/richmol">Richmol</a> 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.</li> <li>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</li> <li>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.</li> <li>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.</li> <li>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.</li> <li>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).</li> </ul> The analysis_scripts.zip contains the following files and folders: <ul> <li>H_Plus folder contains codes relevant for the analysis of H+ ion data. <ul> <li>analyse_full_alignment_scans.m: subtracts background and combines delay scan data sets together, takes account of errors.</li> <li>calculate_resamped_df.m: called by analyse_full_alignment_scans.m to calculate the frequency sampling.</li> <li>unique_mean.m: called by analyse_full_alignment_scans.m when combining data sets. Combines non-unique data points into a single data point.</li> </ul> </li> <li>C_Plus2 folder contains codes for the analysis of C2+ ion data. The file descriptions are identical to those in the H_Plus directory.</li> <li>intensity/calculate_intensity.m: calculates peak intensity of the laser pulse from measured parameters as well as statistical error.</li> <li>intensity/compare_exp_sim.m: fits experimental and theoretical tomography and delay-dependent 2D projection values.</li> <li>intensity/nir2hdf5_kHz.py: converts raw data files (from rawdata_part.z* archive) into hdf5 files.</li> </ul>

ShareScore

40/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 4
Harmonization: 4
Access: 20
Reuse readiness: 8
Engagement: 4