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Parameters

Pressing the Angular Velocity Autocorrelation Function button will pop up the dialog shown on figure 4.48

Figure 4.48: The dialog from where the AVACF analysis will be set up and run.

The following input fields controls the parameters for the Angular Velocity AutoCorrelation Function (AVACF) 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.

- Differentiation order
  Format: integer in [0,5]
  Default: 0 if velocities are stored in the trajectory file, 1 otherwise
  Description: this widget allows to specify the order of the derivation scheme used to get the velocities out of the coordinates. If your trajectory NetCDF file already contains the velocities then just select 0. However, you can still decide to get the velocities out of the coordinates. In that case, nMOLDYN performs a numerical differentiation of the input data. To do so, nMOLDYN can perform numerical differentiation from order 1 to order 5. Using order 1, the first time derivative of each point is calculated as

  | (4.128)

  where is the time step. Choosing order N with N=2,...,5, nMOLDYN calculates the first time-derivative of each point () using the N-order polynomial interpolating the N+1 points across , where belongs to this set [52].

- Project displacement on
  Format: string
  Default: no
  Description: this widget allows to specify a vector along which the AVACF will be computed. This vector does not need to be normalized as nMOLDYN will perform the normalization when processing it. The entered value must have the following format:
  vx:vy:vz
  where vx, vy and vz are floats that represent respectively the x, y and z coordinates of the vector.

- Reference frame
  Format: integer in [1,traj_length] where traj_length is the number of frames of the input trajectory
  Default: 1
  Description: this widget allows to specify which frame should be the reference for the AVACF analysis. The value entered should be an integer ranging from 1 to traj_length where traj_length is the number of rames of the input trajectory.

- Stepwise RBT
  Format: string equal to yes or no
  Default: no
  Description: if set to yes, each frame f will serve as the reference for the frame f+1 when defining the RBT canceling the value entred in Reference frame entry.

- Group selection
  Format: group selection string
  Default: all
  Description: this widget allows the selection of the groups of atoms that will be defined as rigid-bodies when performing the AVACF. See Section 4.2.2.3 for more details.

- AVACF output file
  Format: string
  Default: AVACF_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 AVACF analysis. A CDL version of the NetCDF output file is also automatically created with AVACF_traj_file.cdl name.

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