DOI: 10.5281/zenodo.5907663
title: Supplementary material: Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules

description: <strong>Supplementary material to the manuscript <em>"Picosecond pulse-shaping for strong three-dimensional field-free alignment of generic asymmetric-top molecules"</em> by Terry Mullins, Evangelos T. Karamatskos, Joss Wiese, Jolijn Onvlee, Arnaud Rouzée, Andrey Yachmenev, Sebastian Trippel, and Jochen Küpper, <em>Nat. Commun</em>, 2022</strong> <em><strong>simulations_part.z*</strong> </em>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. <strong><em>rawdata_part.z*</em></strong> is split zip archive containing raw experimental data. <strong><em>analysis_codes.zip</em></strong> is zip archive containing experimental analysis codes. <strong>The <em>simulations_part.zip</em> contains the following files and folders:</strong> <em><strong>prob_density_euler_angles</strong></em> contains files <em>rotdens_av_&lt;time&gt;.gz</em> with simulated state-averaged rotational probability density distributions in terms of Euler angles for different times &lt;time&gt;, ranging from the beginning of the alignment laser pulse at \(t=0\) up to \(t=1500\) ps with a time step of 1 ps.<br> Calculations of probability density distributions were done using Richmol program.<br> The gzipped ASCII data files <em>rotdens_av_&lt;time&gt;.gz</em> contain in columns the values of the Euler angles \(\phi,\theta,\chi\) followed by the normalized probability density value. <em><strong>prob_density_atoms_xyz</strong></em> contains files <em>monte_carlo_av_&lt;time&gt;.h5</em> with state-averaged rotational probability density distributions of all atoms in the indole molecule in terms of their Cartesian coordinates, for different times &lt;time&gt;, ranging from the beginning of the alignment pulse at \(t=0\) up to \(t=1500\) ps with a time step of 1 ps.<br> Structure of <em>monte_carlo_av_&lt;time&gt;.h5</em> HDF5 files:<br> Key Description<br> ----- ----------------<br> 'C10' - Cartesian coordinates of carbon atom no. 10<br> 'C11' - Cartesian coordinates of carbon atom no. 11<br> 'C12' - ...<br> 'C14' - ...<br> 'C3' - ...<br> 'C6' - ...<br> 'C7' - ...<br> 'C9' - ...<br> 'N4' - ...<br> 'H1-C3' - Cartesian coordinates of a vector pointing from carbon atom no. 3 to hydrogen atom no. 1<br> 'H13-C11' - ...<br> 'H15-C12' - ...<br> 'H16-C14' - ...<br> 'H2-N4' - ...<br> 'H5-C7' - ...<br> 'H8-C9' - ...<br> 'ref_vectors' - reference molecular-frame Cartesian coordinates of all atoms<br> 'x' - coordinates of the x-axis of Principal Axes of Inertia Frame<br> 'y' - coordinates of the y-axis of Principal Axes of Inertia Frame<br> 'z' - coordinates of the z-axis of Principal Axes of Inertia Frame<br> 'pol_x' - coordinates of the x-axis of Principal Axes of Polarizability Frame<br> 'pol_y' - coordinates of the y-axis of Principal Axes of Polarizability Frame<br> 'pol_z' - coordinates of the z-axis of Principal Axes of Polarizability Frame <em><strong>indole_deflected_states.txt</strong></em> ASCII file contains initial populations of rotational states of indole in the deflected beam.<br> The following data is arranged in columns: <em>m, J</em>, <em>id</em>, <em>energy</em>, <em>normalized population</em>. The <em>J</em> and <em>m</em> are rotational quantum numbers of the total angular momentum and its <em>Z</em>-projection, the <em>id</em> number refers to the state's index in file <em>indole_energies_j0_j20.txt</em> listing rotational states of indole. <em><strong>indole_data.py</strong></em> Python module provides basic functions to extract information from HDF5 data files <em>monte_carlo_av_&lt;time&gt;.h5</em>. It can also be used to compute alignment and orientation. <em><strong>example_cos.py</strong></em> and <em><strong>example_dens.py</strong></em> Python scripts that demonstrate how to use <em>indole_data.py</em> module for computing and plotting alignment traces and a 2D projection of the probability density distribution, respectively. <em><strong>monte_carlo.py</strong></em> Python script that was used to compute through Monte-Carlo sampling probability density distributions for Cartesian positions of atoms in indole (<em>monte_carlo_av_&lt;time&gt;.h5</em> files) using probability density distribution functions in Euler angles (outputs of Richmol program <em>rotdens_av_&lt;time&gt;.gz</em>). <strong>The <em>analysis_codes.zip</em> contains the following files and folders:</strong> <strong><em>H_Plus</em></strong> folder contains codes relevant for the analysis of H<sup>+</sup> ion data. <strong><em>analyse_full_alignment_scans.m</em></strong>: subtracts background and combines delay scan data sets together, takes account of errors. <em><strong>calculate_resamped_df.m</strong></em>: called by <em>analyse_full_alignment_scans.m</em> to calculate the frequency sampling. <em><strong>unique_mean.m</strong></em>: called by <em>analyse_full_alignment_scans.m</em> when combining data sets. Combines non-unique data points into a single data point. <em><strong>C_Plus2</strong></em> folder contains codes for the analysis of C<sup>2+</sup> ion data. The file descriptions are identical to those in the <em>H_Plus</em> directory. <em><strong>intensity/calculate_intensity.m</strong></em>: calculates peak intensity of the laser pulse from measured parameters as well as statistical error. <em><strong>intensity/compare_exp_sim.m</strong></em>: fits experimental and theoretical tomography and delay-dependent 2D projection values. <em><strong>intensity/nir2hdf5_kHz.py</strong></em>: converts raw data files (from <em>rawdata_part.z*</em> archive<em>)</em> into hdf5 files.