Settings#
Command-line Settings for DensityMap#
The following table provides an overview of the command-line parameters available for the DensityMap script:
Parameter |
Description |
Default |
|---|---|---|
-to |
Topology file name (.gro or .data formats). XDATCAR does not require to include -to. |
topo.gro |
-tr |
Trajectory file name. |
trajectory.xtc |
-f |
Format options: XTC, TRR, LAMMPSDUMP, and XDATCAR. |
XDATCAR |
-ts |
Time interval between frames in the trajectory. |
0.1 |
-v |
Voxel side size. |
0.2 |
-a |
Atom selection: integer (index) or string (name) based on trajectory format. |
Li |
-tts |
Frames interval to print the VoxelIndices.dat. |
1 |
-clus |
Set whether clustering <d₁> of the trajectory is applied (0 = NO or 1 = YES). |
0 |
-verb |
Set verbosity level (0 = L and HM or 1 = L, M, H, and HM). |
0 |
Notes:
The frequency at which the position of each diffusive atom is recorded in terms of voxel indices can be adjusted. A value equivalent to 1 ps is suggested (i.e., -ts * -tts ≈ 1 ps) since it is in the range of a typical phonon frequency [Lim-2018, Kam-2023].
L, M, and H represent the <d₁> clusters low, medium, and high, respectively [Cortes-2024].
Command-line Settings for CrySF#
The following table provides an overview of the command-line parameters available for the CrySF script:
Parameter |
Description |
Default |
|---|---|---|
-nts |
New time interval between frames in VoxelIndices.dat. |
0.1 |
-minv |
Minimum volume condition for the site. |
0.28 |
-maxv |
Maximum volume condition for the site. |
3.05 |
-clus |
Set whether clustering <d₁> of the trajectory is used (0 = NO or 1 = YES). |
0 |
-dop |
Set whether to use a doped density map (0 = NO or 1 = YES). |
0 |
-verb |
Set verbosity level, 0 = L and HM or 1 = L, M, H, and HM. |
0 |
-deltf |
Frames intervals to calculate the simultaneous jumps. |
1 |
-scaler |
Scaler method used for site type identification: MinMaxScaler or StandardScaler. |
MinMaxScaler |
Notes:
The -nts value is an output of the DensityMap routine in the Voxel indices information (see Time interval between frames).
Further details about clustering are discussed in the <d₁> Clustering section.
Additional information about doped systems can be found in the Doped Systems section.
Given that simultaneous jumps are rare events, it is often advantageous to segment the trajectory into chunks for analysis. This setting is an alternative to -tts > 1 in DensityMap. Using -tts = 1 (all frames), you can split the trajectory into chunks and establish whether a jump occurred in each.
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Units of Measurement#
The software uses the following units of measurement:
Distance: Angstroms (Å)
Time: Picoseconds (ps)