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Parameters

Pressing the Order Parameter button will pop up the dialog shown on figure 4.62

Figure 4.62: The dialog from where the OP analysis will be set up and run.

The following input fields controls the parameters for the OP 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.

- Bond selection
  Format: string
  Default: all
  Description: this widget allows the selection of the pairs of atoms from which Eq. 4.195 will be computed. See section 4.2.2.3 for more details. Any selection that does not contain exactly two atoms will be discarded.

- Atom order
  Format: string
  Default: no
  Description: this widget allows to specify the order in which the atoms a1, a2 should be ordered. By default, the order will be defined by nMOLDYN by ranking for the atoms of each bond by their MMTK name. Otherwise, the entered value must have the following specific format:
  MMTK name for a1,MMTK name for a2

- OP output file
  Format: string
  Default: OP_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 OP analysis. A CDL version of the NetCDF output file is also automatically created with OP_traj_file.cdl name.

Next: Output Up: Order Parameter Previous: Theory and implementation Contents