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 | `topo.gro` | | | require to include `-to`. | | +-------------+---------------------------------------------------------------+-------------------+ | `-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 | `Li` | | | trajectory format. | | +-------------+---------------------------------------------------------------+-------------------+ | `-tts` | Frames interval to print the `VoxelIndices.dat`. | `1` | +-------------+---------------------------------------------------------------+-------------------+ | `-clus` | Set whether clustering of the trajectory is applied | `0` | | | (0 = NO or 1 = YES). | | +-------------+---------------------------------------------------------------+-------------------+ | `-verb` | Set verbosity level (0 = L and HM or 1 = L, M, H, and HM). | `0` | +-------------+---------------------------------------------------------------+-------------------+ **Notes:** 1. 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]. 2. L, M, and H represent the 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 of the trajectory is used | `0` | | | (0 = NO or 1 = YES). | | +-------------+---------------------------------------------------------------+-------------------+ | `-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` | | | MinMaxScaler or StandardScaler. | | +-------------+---------------------------------------------------------------+-------------------+ **Notes:** 1. The `-nts` value is an output of the `DensityMap` routine in the Voxel indices information (see `Time interval between frames`). 2. Further details about clustering are discussed in the ** Clustering** section. 3. Additional information about doped systems can be found in the **Doped Systems** section. 4. 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. --- Units of Measurement -------------------- The software uses the following units of measurement: - **Distance**: Angstroms (`Å`) - **Time**: Picoseconds (`ps`)