Data description

Except for the file defining the system (r.txt, Z.txt and hessian.dat), all files are in the HDF5 format.

System file

  • Z.txt: The atomic number of each atom in the system.
  • r.txt: The position of each atom in the system (one atom per line), in its equilibrium geometry, in meter.
  • hessian.dat: The Hessian matrix of the system at equilibrium, in atomic units. The Hessian is 33 x 33, the entry are ordered followin the XYZ convention (i.e. x component of 1st atom, y component of 1st atom, z component of 1st atom, x component of 2nd atom, y component of 2nd atoms, etc.)

Simulation data

The file names have the form simulation_<name>.h5.

Attributes

  • author: the author (Benoît Richard in all cases).
  • description: a short description of the data.

Datasets

Each dataset has an attribute units containing the units in which the values are expressed (they are atomic units, except for fluence).

Most datasets have the shape (N, 11, 3), which correspond to the number of trajectory (N), the number of atoms (11) and the number of dimensions (3).

The number of trajectory in each dataset is N, and can vary between datasets.

The system dataset define the order of the atom for all datasets.

  • fluence float: the total fluence in the simulation (photons/μm^2)
  • system string(11): name of each atom in the system.
  • momenta float(N, 11, 3): final momentum of each atom after 1000 fs.
  • charges int(N, 11): final charge on each after 1000 fs.

The file simulation_main.h5 has the additional datasets:

  • initial_positions float(N, 11, 3): position of each just before the first photoionization.
  • initial_momenta float(N, 11, 3): momentum of each atom just before the first photoionization.

damped_forcefield_Eph=2000_fluence=1.5e+11_q0=0.35.h5

  • Simulation results.
  • Propagated up to 200fs.
  • Contain initial states

damped_forcefield_Eph=2000_fluence=1.5e+11_q0=0.35_q=17-21.h5

  • Simulation results.
  • Propagated from 200fs to 1000fs if the total charge was in the range 17-21 at 200fs.

damped_forcefield_Eph=2000_fluence=7.5e+10_q0=0.35.h5

  • Simulation results.
  • Low fluence.
  • Propagated from 200fs to 1000fs (?)

no_zpv_damped_forcefield_Eph=2000_fluence=1.5e+11_q0=0.35_q=17-21.h5

  • Simulation results
  • Propagated from 200fs to 1000fs if the total charge was in the range 17-21 at 200fs.
  • No GSF

thermal_Eph=2000_fluence=1.5e+11_q0=0.35_FWHM=10e-15s_T=250.0.h5

  • Simulation results
  • Initial state at 250K

Reconstruction

The file names have the form reconstruction_<name>_C<coincidence_order>_M<moment_order>.h5.

Each file contains the following attributes (at the file level) and datasets.

Attributes

  • coincidence_order: the coincidence ordered considered in the reconstruction.
  • max_cumulant_order: the maximum moment order used in the reconstruction.
  • iter: the number of iteration the algorithm used.
  • units: the units of the data (atomic units in all cases).
  • author: the author (Benoît Richard in all cases).
  • description: a short description of the data.

Datasets

The datasets have shape 33 or 33 x 33, because the value for each atom is concatenated (indices 1 to 3 correspond to the first atom, 4 to 6 to the second atom, and so on).

The system dataset define the order of the atom for all datasets.

  • system string(11): name of each atom in the system.
  • mean float(33): reconstructed mean of the weighted momenta.
  • covariance float(33, 33): reconstructed covariance matrix of the weighted momenta.
  • guess_mean float(33): initial guess for the mean of the weighted momenta.
  • guess_covariance float(33, 33): initial guess for the covariance of the weighted momenta.