Next: Output Up: Coordination number Previous: Theory and implementation Contents

####
Parameters

Pressing the Coordination Number button will pop up the dialog shown on figure 4.59

Figure 4.59: The dialog from where the CN analysis will be set up and run.

The following input fields controls the parameters for the CN 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.

- Distances (in nm)
  Format: string
  Default: 0.0:1.0:0.1.
  Description: this widget allows to select distances in nm at which the CN will be computed. This must be a string of the form:
  In this way, the CN will be calculated for discrete r defined as where is the smallest r , is the distance between two consecutive r values and with m running from 0 to where is the number of selected r values defined as where is the radius of the biggest r value .

  For example,

  - 0:10:1 will compute PDF for r = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 nm.
  - 3:7:1.2 will compute PDF for r = 3, 4.2, 5.4, 6.6 nm.
- Group selection
  Format: group selection string
  Default: all
  Description: this widget allows the selection of the groups of atoms whose centers of gravity will be used to compute the CN (see Section 4.2.6.2). See Section 4.2.2.3 for more details about group selection.

- Subset selection
  Format: subset selection string
  Default: all
  Description: this widget allows the selection of a subset of the system for the analysis. Only the atoms of this subset will be considered when looking around the centers of gravity of the selected groups of atoms. See Section 4.2.2.1 for more details about subset selection.

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

- CN output file
  Format: string
  Default: CN_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 CN analysis. A CDL version of the NetCDF output file is also automatically created with CN_traj_file.cdl name.

Next: Output Up: Coordination number Previous: Theory and implementation Contents