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Parameters

Pressing the Dynamic Coherent Structure Factor button will pop up the dialog shown on figure 4.50

Figure 4.50: The dialog from where the DCSF analysis will be set up and run.

The following input fields controls the parameters for the Dynamic Coherent Structure Factor (DCSF) 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.

- Q shell width (in nm-1)
  Format: strictly positive float
  Default: 1.0
  Description: this widget allows to define the tolerance dq on the q-modulii. So, for each q-shell of modulus q, nMOLDYN will accept a q-vector to belong to that shell if its modulus falls in the range [q-dq/2,q+dq/2]. This parameter fix the q-resolution.

- Q vectors per shell
  Format: strictly positive integer
  Default: 50
  Description: this widget allows to specify the number of q-vectors , to generate for each q-shell. Indeed, when generating q-vectors, nMOLDYN will try to generate q-vectors for each q-shell in order to carry out the averages of Eq. 4.151. For a given q-shell, if nMOLDYN could generate less q-vectors than , it will only use the number of generated q-vectors instead of and if nMOLDYN could generate more q-vectors than , it will pick up randomly q-vectors among the generated q-vectors. The higher this parameter is the smoother will be the computed intermediate scattering function but at the cost of a slower analysis.

- Q vectors generator
  Format: string equal to 3D isotropic, 2D isotropic or anisotropic
  Default: 3D isotropic
  Description: this option allows to specify how the q-vectors should be generated:
  - 3D isotropic the q-vectors are generated randomly on concentric spheres.
  - 2D isotropic the q-vectors are generated randomly on concentric rings in a given plane.
  - anisotropic the q-vectors are generated randomly on one or several defined directions.

- Q vectors direction
  Format: string
  Default: no
  Description: this widget allows to specify one or several preferential directions along which the q-vectors have to be generated. Depening on the q-vectors generation type, the entered value will take different values:
  - 3D isotropic the default value no must be used.

  - 2D isotropic a string of the form
    where and are respectively the x,y,z components of q-vector q1 and q2, (q1,q2) defining the plane on which the q-vectors will be generated.

  - anisotropic a string of the form
    where , ...are respectively the x,y,z components of q-vector q1, q2 ..., the q-vector generation being performed along each defined direction.

- 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: coherent
  Description: this widget allows the selection of the weighting scheme to apply on each atomic contribution to the DCSF. See Section 4.2.1 for more details.

- DCSF output file
  Format: string
  Default: DCSF_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 DCSF analysis. A CDL version of the NetCDF output file is also automatically created with DCSF_traj_file.cdl name.

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