Experimental and simulation data from Stransky et al. "Ionization by XFEL radiation produces distinct structure in liquid water"

This deposition contains two separate gzipped tarballs:

preprocessed_diffraction_data.tar.gzpre-processed diffraction data, specifically I(q) traces for each X-ray pulse along with associated metadata

XMDYN_simulations.tar.gzsimulation trajectories produced by the XMDYN code that describe water ionization following an intense X-ray pulse

In more detail, the preprocessed_diffraction_data.tar.gz contains 36 HDF5 files, each corresponding to a single LCLS run. Each HDF5 contains the following data arrays:

ebeam Group
event_time Dataset {8674/Inf}
evr Group
fiducials Dataset {8674/Inf}
gas_detector Group
phase_cav Group
probe_energy Dataset {8674/Inf}
probe_mag Dataset {8674/Inf}
pump_energy Dataset {8674/Inf}
pump_mag Dataset {8674/Inf}
radial_profile Dataset {8674/Inf, 500}
radial_profile_qvalues Dataset {500/8192}

The X contains trajectories for 7 different simulations, each in a separate directory. These top level directories are named according to simulation parameters:

simA__

Box sizes are in [Å], probe delay is in [fs] or there is only single pulse, 1.00 is the nominal fluence.

Each of these directories contain subdirectories recording snapshots every 5 fs.

The subdirectory name is the snapshot time in attoseconds.

The simulation starts at 0 fs, the pump pulse is centered at the time 30 fs.

That means that if there is a probe pulse with delay of 110 fs, it is centered

at 140 fs.

The snapshot directories contain 6 text files:

econf.dat : list of all atomic configurations observed in the simulation snapshot, each line starts with the atomic Z, followed by the electron configuration

T.dat : the electronic configuration for each particle in the simulation, in the form of a list of indices. The n-th element of the list indicates the electronic configuration of the n-th particle in the simulation by specifying a line in econf.dat. For instance, if the 10th element is "0", it indicates the 10th simulated particle has the electronic configuration written on the first line of econf.dat

Z.dat : sequence of atomic numbers for all simulated atoms.

q.dat : charge of atoms in elementary charge units (redundant data).

r.dat : cartesian position in [m], each atom position on one line.

v.dat : velocity components in [m/s], each atom on one line.