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Parameters

Pressing the Dynamic Incoherent Structure Factor (Gaussian Approximation) button will pop up the dialog shown on figure 4.54

Figure 4.54: The dialog from where the DISFG analysis will be set up and run.

The following input fields controls the parameters for the Dynamic Incoherent Structure Factor using an Gaussian approximation (DISFG) analysis:

- Trajectory file
  Format: string
  Default: traj_file where traj_file is the name of the loaded trajectory
  Description: the value of this widget can not be changed. It just recalls for information purpose the name of the trajectory file loaded for the analysis.

- Frame selection
  Format: string
  Default: 1:traj_length:1 where traj_length is the number of frames of the trajectory.
  Description: this widget allows to select the trajectory frames that will be used for the analysis. This must be a string of the form:
  first:last:step
  where first is an integer specifying the first frame number to consider, last is an integer specifying the last frame number to consider and step is an integer specifying the step number between two frames.

  For example,

  - 2:10:3 will select the frames 2, 5 and 8.
  - 1:5:1 will select the frames 1, 2, 3, 4 and 5.

- Q values (in nm-1)
  Format: string
  Default: 0:100:1.
  Description: this widget allows to select the modulii of the q-vectors. This must be a string of the form:
  In this way, the intermediate scattering function will be calculated for discrete q defined as where is the radius of the smallest q-shell, is the distance between two consecutive q-shells and with m running from 0 to where is the number of selected q-shells defined as where is the radius of the biggest q-shell.

  For example,

  - 0:10:1 will generate q-shells of radii 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10.
  - 3:12:2 will generate q-shells of radii 3, 5, 7, 9, 11.

- FFT window
  Format: float in [0.0,100.0]
  Default: 10.0
  Description: this widget allows to define the width in percentage of the trajectory length of the Gaussian function to be used in the smoothing procedure for the calculation of the coherent structure factor out of the intermediate scattering function. See Appendix A for more details.

- Subset selection
  Format: subset selection string
  Default: all
  Description: this widget allows the selection of a subset of the system for the analysis. See Section 4.2.2.1 for more details.

- Deuteration selection
  Format: deuteration selection string
  Default: no
  Description: this widget allows the selection of a subset hydrogen atoms that will take the atomic parameters of deuterium. See Section 4.2.2.2 for more details.

- Weights
  Format: string equal to equal, mass, coherent, incoherent or atomicNumber
  Default: incoherent
  Description: this widget allows the selection of the weighting scheme to apply on each atomic contribution to the DISFG. See Section 4.2.1 for more details.

- DISFG output file
  Format: string
  Default: DISFG_traj_file.nc where traj_file.nc is the name of the input trajectory
  Description: this widget allows to enter the name of the NetCDF output file of the DISFG analysis. A CDL version of the NetCDF output file is also automatically created with DISFG_traj_file.cdl name.

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