mdkits 1.0.0__tar.gz → 1.0.2__tar.gz

mdkits-1.0.2/PKG-INFO

@@ -0,0 +1,365 @@
+Metadata-Version: 2.3
+Name: mdkits
+Version: 1.0.2
+Summary: kits for md or dft
+License: MIT
+Keywords: molecular dynamics,density functional theory
+Author: jxxcr
+Author-email: jixxcr@qq.com
+Requires-Python: >=3.11,<4.0
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: Cp2kData (>=0.7.2,<0.8.0)
+Requires-Dist: MDAnalysis (>=2.8.0,<3.0.0)
+Requires-Dist: ase (>=3.22.1,<4.0.0)
+Requires-Dist: click (>=8.1.3,<9.0.0)
+Requires-Dist: julia (>=0.6.2,<0.7.0)
+Requires-Dist: matplotlib (>=3.9.0,<4.0.0)
+Requires-Dist: numpy (>=1.26.4,<2.0.0)
+Requires-Dist: pyyaml (>=6.0.1,<7.0.0)
+Requires-Dist: tidynamics (>=1.1.2,<2.0.0)
+Project-URL: Repository, https://github.com/jxxcr/mdkits
+Description-Content-Type: text/markdown
+
+# mdkits
+[中文文档](README_zh.md)
+
+`mdkits` provides a variety of tools. Installation script:
+```bash
+pip install mdkits --upgrade
+```
+
+## General Option Parameter Types
+
+1.  `CELL TYPE`: Specifies lattice cell parameters, e.g., `10,10,10`, `10,10,10,90,90,90`, etc.
+2.  `FRAME RANGE`: Specifies the frame range, e.g., `1`, `1:10:2`, etc.
+3.  `--group` and `--surface`: Select analysis objects using [selection language](https://userguide.mdanalysis.org/stable/selections.html).
+4.  `--update_water`, `--distance`, and `--angle`: Enable dynamic update of water molecule positions during trajectory analysis.
+
+## Trajectory File Processing Scripts
+
+`md` is the trajectory file processing tool, which includes several processing utilities.
+
+### Density Distribution
+
+`density` is used to analyze the density distribution of a specific element along the z-axis in a system. For example, to analyze the density distribution of the `O` element along the z-axis:
+```bash
+mdkits md density [FILENAME] --group="name H" --cell [FILENAME]
+```
+This will output a file named `density_name_H.dat`, where the first column is the z-axis coordinate and the second column is the density distribution in units of mol/L. To output the density distribution in units of $g/cm^3$, you can specify the `--atomic_mass` option, for example:
+```bash
+mdkits md density [FILENAME] --group="name H" --cell [FILENAME] --atomic_mass=1.00784
+```
+This will output the density distribution in units of $g/cm^3$. You can specify surface atoms to normalize the density distribution to the surface, for example:
+```bash
+mdkits md density [FILENAME] --group="name O" --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+```
+This will normalize the density distribution to the surface and analyze the density distribution of water molecules using the positions of O atoms as the reference for water molecules. For systems with $OH^-$ ions, you can use the `--update_water` option to update the positions of water molecules in each frame, without needing to specify an element explicitly, for example:
+```bash
+mdkits md density [FILENAME] --update_water --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+```
+The output file will be named `density_water.dat`.
+
+### Hydrogen Bonds
+
+`hb` is used to analyze hydrogen bonds in a system, for example, to analyze the distribution of hydrogen bonds along the z-axis:
+```bash
+mdkits md hb [FILENAME] --cell 10,10,40 --surface "prop z < 10" --update_water
+```
+Or to analyze hydrogen bonds of a single water molecule:
+```bash
+mdkits md hb [FILENAME] --cell 10,10,40 --index 15
+```
+
+### Angle
+
+`angle` is used to analyze the abundance distribution of the angle between the bisector vector of a water molecule's OH bond and the surface normal. For example, to analyze the angle abundance distribution of water molecules within 5 Å of the surface:
+```bash
+mdkits md angle [FILENAME] --cell 10,10,40 --surface "name Pt" --water_height 5
+```
+
+### Dipole Distribution
+
+`diople` is used to analyze the dipole ($\cos \phi \rho_{H_2 O}$) distribution in a system. For example, to analyze the $\cos \phi \rho_{H_2 O}$ distribution in the system:
+```bash
+mdkits md diople [FILENAME] --cell 10,10,40 --surface "name Pt"
+```
+
+### Radial Distribution Function (RDF)
+
+`rdf` is used to analyze the radial distribution function between two `group`s. For example, to analyze the radial distribution function between `O` and `H` elements in the system:
+```bash
+mdkits md rdf [FILENAME] --group "name O" "name H" --cell 10,10,40 --range 0.1 5
+```
+
+### Mean Squared Displacement (MSD)
+
+`msd` is used to analyze the mean squared displacement of certain atoms in a system. For example, to analyze the MSD of `Li` atoms along the z-axis:
+```bash
+mdkits md msd [FILENAME] z "name Li"
+```
+
+### Monitor
+
+`monitor` is used to monitor changes in atom height, bond length, and bond angle in a system. For example, to monitor the height of the atom with `index` 0:
+```bash
+mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 0
+```
+This will output the height from the surface as a function of each frame. To monitor the bond length between atoms 0 and 1:
+```bash
+mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 0 -i 1
+```
+This will output the heights from the surface for atoms 0 and 1, and the bond length between 0 and 1 as a function of each frame. To monitor the bond angle of 1-0-2:
+```bash
+mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 1 -i 0 -i 2
+```
+This will output the heights from the surface for atoms 1, 0, and 2, the bond lengths between 1-0 and 0-2, and the bond angle 1-0-2 as a function of each frame. Note that atoms at the vertex of an angle should be placed in the middle.
+
+### Position Normalization
+
+`wrap` is used to normalize the atomic positions in a trajectory file. For example, to normalize the atomic positions in `[FILENAME]` within the unit cell and output it as `wrapped.xyz`. By default, it reads `ABC` and `ALPHA_BETA_GAMMA` information from the `cp2k` output file `input_inp` as lattice cell parameters:
+```bash
+mdkits md wrap [FILENAME]
+```
+Or specify the `cp2k` input file:
+```bash
+mdkits md wrap [FILENAME] --cp2k_input_file setting.inp
+```
+Or specify the lattice cell parameters:
+```bash
+mdkits md wrap [FILENAME] --cell 10,10,10
+```
+The default `[FILENAME]` is `*-pos-1.xyz`.
+
+### Vibrational Density of States (VDOS)
+
+`vac` is used to analyze the velocity autocorrelation function of a trajectory and compute the Fourier transform of the velocity autocorrelation function, which is the vibrational density of states (VDOS). For example, to analyze the VDOS of the system:
+```bash
+mdkits md vac h2o-vel-1.xyz
+```
+The default `[FILENAME]` is `*-vel-1.xyz`.
+
+## DFT Property Analysis Scripts
+
+`dft` is the DFT property analysis tool, which includes several analysis utilities.
+
+### PDOS
+
+`pdos` is used to analyze the PDOS of a system. To analyze the d-orbital DOS of `[FILENAME]`:
+```bash
+mdkits dft pdos [FILENAME] -t d
+```
+
+### CUBE Files
+
+`cube` is used to process files in [`cube` format](https://paulbourke.net/dataformats/cube/), averaging them along the z-axis:
+```bash
+mdkits dft cube [FILENAME]
+```
+The processed data will be output to `cube.out`. You can also calculate the average value within a specific region:
+```bash
+mdkits dft cube [FILENAME] -b 1 2
+```
+This will print the average value to the screen and also record it in the comment line of `cube.out`.
+
+## Modeling
+
+`build` is the modeling tool, which includes several modeling utilities.
+
+### Building Bulk Models
+
+`bulk` is used to build bulk models. For example, to build an `fcc` bulk model of `Pt`:
+```bash
+mdkits build bulk Pt fcc
+```
+To build as a conventional cell model:
+```bash
+mdkits build bulk Pt fcc --cubic
+```
+To build a `Caesium chloride` structure model:
+```bash
+mdkits build bulk CsCl cesiumchloride -a 4.123
+```
+To build a `fluorite` structure model:
+```bash
+mdkits build bulk BaF2 fluorite -a 6.196
+```
+
+### Building Surface Models
+
+`surface` is used to build common surface models. Usage:
+```bash
+mdkits build surface [ELEMENT] [SURFACE_TYPE] [SIZE]
+```
+For example, to build an `fcc111` surface model of `Pt`:
+```bash
+mdkits build surface Pt fcc111 2 2 3 --vacuum 15
+```
+To build a graphene surface:
+```bash
+mdkits build surface C2 graphene 3 3 1 --vacuum 15
+```
+
+### Building Surface Models from Existing Structures
+
+`cut` is used to build surface models from existing structures (the structure must be in a conventional cell). For example, to build an `fcc331` surface model from `Pt_fcc.cif`:
+```bash
+mdkits build cut Pt_fcc.cif --face 3 3 1 --size 3 3 5 --vacuum 15
+```
+
+### Adding Adsorbates to Surface Structures
+
+`adsorbate` is used to add adsorbates to surface structures. For example, to add an `H` atom to `surface.cif`:
+```bash
+mdkits build adsorbate surface.cif H --select "index 0" --height 1    
+```
+Or to add an `H` atom with a coverage of 5 to `Pt_fcc111_335.cif`:
+```bash
+mdkits build adsorbate Pt_fcc111_335.cif H --select "prop z > 16" --height 2 --cover 5
+```
+
+### Building Solution Phase Models
+
+`solution` is used to build solution phase models. When using for the first time, you should install `juliaup`:
+```bash
+mdkits build solution --install_julia
+```
+Then install `Packmol`:
+```bash
+mdkits build solution --install_packmol
+```
+After successful installation, you can use the `solution` functionality. For example, to build a water box with 32 water molecules:
+```bash
+mdkits build solution --water_number 32 --cell 9.86,9.86,9.86
+```
+Or to build a solution containing ions:
+```bash
+mdkits build solution li.xyz k.xyz --water_number 64 --tolerance 2.5 -n 25 -n 45 --cell 15,15,15
+```
+Here, the number of `-n` arguments must match the number of specified solvent molecule types, used to specify the number of solvents to add, respectively. Alternatively, build a solution phase model from `packmol` input files:
+```bash
+mdkits build solution input.pm input2.pm  --infile
+```
+
+### Building Interface Models
+
+`interface` is used to build interface models. For example, to build an interface model without vacuum:
+```bash
+mdkits build interface --slab Pt_fcc100_555.cif --sol water_160.cif
+```
+Or to build an interface with a gas phase model:
+```bash
+mdkits build interface --slab Pt_fcc100_555.cif --sol water_160.cif --cap ne --vacuum 20
+```
+
+### Building Supercell Models
+
+`supercell` is used to build supercell models:
+```bash
+mdkits build supercell Li3PO4.cif 2 2 2
+```
+
+## Others
+
+### Trajectory Extraction
+
+`extract` is used to extract specific frames from a trajectory file. For example, to extract frames from the 1000th to the 2000th frame from `frames.xyz` and output them to `1000-2000.xyz`. The parameters for the `-r` option are consistent with Python's slicing syntax:
+```bash
+mdkits extract frames.xyz -r 1000:2000 -o 1000-2000.xyz
+```
+Or to extract the last frame from the default trajectory file `*-pos-1.xyz` generated by `cp2k` and output it as `frames_-1.xyz` (which is the default behavior of `extract`):
+```bash
+mdkits extract
+```
+Or to output a structure every 50 frames into the `./coord` directory, while adjusting the output format to `cp2k`'s `@INCLUDE coord.xyz` format:
+```bash
+mdkits extract -cr ::50
+```
+To extract the positions of specific elements, for example, to extract the positions of `O` and `H` elements:
+```bash
+mdkits extract --select "name O or name H"
+```
+
+### Structure File Conversion
+
+`convert` is used to convert structure files from one format to another. For example, to convert `structure.xyz` to `out.cif` (default filename is `out`). For files that do not store periodic boundary conditions, you can use the `--cell` option to specify `PBC`:
+```bash
+mdkits convert -c structure.xyz --cell 10,10,10
+```
+To convert `structure.cif` to `POSCAR`:
+```bash
+mdkits convert -v structure.cif
+```
+To convert `structure.cif` to `structure_xyz.xyz`:
+```bash
+mdkits convert -c structure.cif -o structure_xyz
+```
+
+### Data Processing
+
+`data` is used for data processing, such as:
+1.  `--nor`: Normalizes the data.
+2.  `--gaus`: Applies Gaussian filtering to the data.
+3.  `--fold`: Folds and averages stacked data.
+4.  `--err`: Calculates error bars for the data.
+And so on.
+
+### Plotting Tool
+
+`plot` is used for plotting data. `plot` requires reading a YAML format configuration file for plotting. The YAML file format is as follows:
+```yaml
+# plot mode 1
+figure1:
+  data:
+    legend1: ./data1.dat
+    legend2: ./data2.dat
+  x:
+    0: x-axis
+  y:
+    1: y-axis
+  x_range: 
+    - 5
+    - 15
+
+# plot mode 2
+figure2:
+  data:
+    y-xais: ./data.dat
+  x:
+    0: x-axis
+  y:
+    1: legend1
+    2: legend2
+    3: legend3
+    4: legend4
+    5: legend5
+  y_range:
+    - 0.5
+    - 6
+  legend_fontsize: 12
+
+# plot mode error
+12_dp_e_error:
+  data:
+    legend: ./error.dat
+  x:
+    0: x-axis
+  y:
+    1: y-axis
+  fold: dp
+  legend_fontsize: 12
+```
+The above illustrates three plotting modes supported by `plot`: `mode 1`, `mode 2`, and `mode error`. `mode 1` is used for comparing the same column data from multiple data files, `mode 2` is used for comparing different column data from the same data file, and `mode error` is used for plotting mean squared error plots.
+
+`plot` can process multiple YAML files simultaneously. Each YAML file can contain multiple plotting configurations. Plotting configurations for `mode 1` and `mode 2` can be automatically recognized, but the `error` mode requires explicit specification, for example:
+```bash
+mdkits plot *.yaml
+```
+and:
+```bash
+mdkits plot *.yaml --error
+```

mdkits-1.0.2/README.md

@@ -0,0 +1,338 @@
+# mdkits
+[中文文档](README_zh.md)
+
+`mdkits` provides a variety of tools. Installation script:
+```bash
+pip install mdkits --upgrade
+```
+
+## General Option Parameter Types
+
+1.  `CELL TYPE`: Specifies lattice cell parameters, e.g., `10,10,10`, `10,10,10,90,90,90`, etc.
+2.  `FRAME RANGE`: Specifies the frame range, e.g., `1`, `1:10:2`, etc.
+3.  `--group` and `--surface`: Select analysis objects using [selection language](https://userguide.mdanalysis.org/stable/selections.html).
+4.  `--update_water`, `--distance`, and `--angle`: Enable dynamic update of water molecule positions during trajectory analysis.
+
+## Trajectory File Processing Scripts
+
+`md` is the trajectory file processing tool, which includes several processing utilities.
+
+### Density Distribution
+
+`density` is used to analyze the density distribution of a specific element along the z-axis in a system. For example, to analyze the density distribution of the `O` element along the z-axis:
+```bash
+mdkits md density [FILENAME] --group="name H" --cell [FILENAME]
+```
+This will output a file named `density_name_H.dat`, where the first column is the z-axis coordinate and the second column is the density distribution in units of mol/L. To output the density distribution in units of $g/cm^3$, you can specify the `--atomic_mass` option, for example:
+```bash
+mdkits md density [FILENAME] --group="name H" --cell [FILENAME] --atomic_mass=1.00784
+```
+This will output the density distribution in units of $g/cm^3$. You can specify surface atoms to normalize the density distribution to the surface, for example:
+```bash
+mdkits md density [FILENAME] --group="name O" --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+```
+This will normalize the density distribution to the surface and analyze the density distribution of water molecules using the positions of O atoms as the reference for water molecules. For systems with $OH^-$ ions, you can use the `--update_water` option to update the positions of water molecules in each frame, without needing to specify an element explicitly, for example:
+```bash
+mdkits md density [FILENAME] --update_water --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+```
+The output file will be named `density_water.dat`.
+
+### Hydrogen Bonds
+
+`hb` is used to analyze hydrogen bonds in a system, for example, to analyze the distribution of hydrogen bonds along the z-axis:
+```bash
+mdkits md hb [FILENAME] --cell 10,10,40 --surface "prop z < 10" --update_water
+```
+Or to analyze hydrogen bonds of a single water molecule:
+```bash
+mdkits md hb [FILENAME] --cell 10,10,40 --index 15
+```
+
+### Angle
+
+`angle` is used to analyze the abundance distribution of the angle between the bisector vector of a water molecule's OH bond and the surface normal. For example, to analyze the angle abundance distribution of water molecules within 5 Å of the surface:
+```bash
+mdkits md angle [FILENAME] --cell 10,10,40 --surface "name Pt" --water_height 5
+```
+
+### Dipole Distribution
+
+`diople` is used to analyze the dipole ($\cos \phi \rho_{H_2 O}$) distribution in a system. For example, to analyze the $\cos \phi \rho_{H_2 O}$ distribution in the system:
+```bash
+mdkits md diople [FILENAME] --cell 10,10,40 --surface "name Pt"
+```
+
+### Radial Distribution Function (RDF)
+
+`rdf` is used to analyze the radial distribution function between two `group`s. For example, to analyze the radial distribution function between `O` and `H` elements in the system:
+```bash
+mdkits md rdf [FILENAME] --group "name O" "name H" --cell 10,10,40 --range 0.1 5
+```
+
+### Mean Squared Displacement (MSD)
+
+`msd` is used to analyze the mean squared displacement of certain atoms in a system. For example, to analyze the MSD of `Li` atoms along the z-axis:
+```bash
+mdkits md msd [FILENAME] z "name Li"
+```
+
+### Monitor
+
+`monitor` is used to monitor changes in atom height, bond length, and bond angle in a system. For example, to monitor the height of the atom with `index` 0:
+```bash
+mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 0
+```
+This will output the height from the surface as a function of each frame. To monitor the bond length between atoms 0 and 1:
+```bash
+mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 0 -i 1
+```
+This will output the heights from the surface for atoms 0 and 1, and the bond length between 0 and 1 as a function of each frame. To monitor the bond angle of 1-0-2:
+```bash
+mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 1 -i 0 -i 2
+```
+This will output the heights from the surface for atoms 1, 0, and 2, the bond lengths between 1-0 and 0-2, and the bond angle 1-0-2 as a function of each frame. Note that atoms at the vertex of an angle should be placed in the middle.
+
+### Position Normalization
+
+`wrap` is used to normalize the atomic positions in a trajectory file. For example, to normalize the atomic positions in `[FILENAME]` within the unit cell and output it as `wrapped.xyz`. By default, it reads `ABC` and `ALPHA_BETA_GAMMA` information from the `cp2k` output file `input_inp` as lattice cell parameters:
+```bash
+mdkits md wrap [FILENAME]
+```
+Or specify the `cp2k` input file:
+```bash
+mdkits md wrap [FILENAME] --cp2k_input_file setting.inp
+```
+Or specify the lattice cell parameters:
+```bash
+mdkits md wrap [FILENAME] --cell 10,10,10
+```
+The default `[FILENAME]` is `*-pos-1.xyz`.
+
+### Vibrational Density of States (VDOS)
+
+`vac` is used to analyze the velocity autocorrelation function of a trajectory and compute the Fourier transform of the velocity autocorrelation function, which is the vibrational density of states (VDOS). For example, to analyze the VDOS of the system:
+```bash
+mdkits md vac h2o-vel-1.xyz
+```
+The default `[FILENAME]` is `*-vel-1.xyz`.
+
+## DFT Property Analysis Scripts
+
+`dft` is the DFT property analysis tool, which includes several analysis utilities.
+
+### PDOS
+
+`pdos` is used to analyze the PDOS of a system. To analyze the d-orbital DOS of `[FILENAME]`:
+```bash
+mdkits dft pdos [FILENAME] -t d
+```
+
+### CUBE Files
+
+`cube` is used to process files in [`cube` format](https://paulbourke.net/dataformats/cube/), averaging them along the z-axis:
+```bash
+mdkits dft cube [FILENAME]
+```
+The processed data will be output to `cube.out`. You can also calculate the average value within a specific region:
+```bash
+mdkits dft cube [FILENAME] -b 1 2
+```
+This will print the average value to the screen and also record it in the comment line of `cube.out`.
+
+## Modeling
+
+`build` is the modeling tool, which includes several modeling utilities.
+
+### Building Bulk Models
+
+`bulk` is used to build bulk models. For example, to build an `fcc` bulk model of `Pt`:
+```bash
+mdkits build bulk Pt fcc
+```
+To build as a conventional cell model:
+```bash
+mdkits build bulk Pt fcc --cubic
+```
+To build a `Caesium chloride` structure model:
+```bash
+mdkits build bulk CsCl cesiumchloride -a 4.123
+```
+To build a `fluorite` structure model:
+```bash
+mdkits build bulk BaF2 fluorite -a 6.196
+```
+
+### Building Surface Models
+
+`surface` is used to build common surface models. Usage:
+```bash
+mdkits build surface [ELEMENT] [SURFACE_TYPE] [SIZE]
+```
+For example, to build an `fcc111` surface model of `Pt`:
+```bash
+mdkits build surface Pt fcc111 2 2 3 --vacuum 15
+```
+To build a graphene surface:
+```bash
+mdkits build surface C2 graphene 3 3 1 --vacuum 15
+```
+
+### Building Surface Models from Existing Structures
+
+`cut` is used to build surface models from existing structures (the structure must be in a conventional cell). For example, to build an `fcc331` surface model from `Pt_fcc.cif`:
+```bash
+mdkits build cut Pt_fcc.cif --face 3 3 1 --size 3 3 5 --vacuum 15
+```
+
+### Adding Adsorbates to Surface Structures
+
+`adsorbate` is used to add adsorbates to surface structures. For example, to add an `H` atom to `surface.cif`:
+```bash
+mdkits build adsorbate surface.cif H --select "index 0" --height 1    
+```
+Or to add an `H` atom with a coverage of 5 to `Pt_fcc111_335.cif`:
+```bash
+mdkits build adsorbate Pt_fcc111_335.cif H --select "prop z > 16" --height 2 --cover 5
+```
+
+### Building Solution Phase Models
+
+`solution` is used to build solution phase models. When using for the first time, you should install `juliaup`:
+```bash
+mdkits build solution --install_julia
+```
+Then install `Packmol`:
+```bash
+mdkits build solution --install_packmol
+```
+After successful installation, you can use the `solution` functionality. For example, to build a water box with 32 water molecules:
+```bash
+mdkits build solution --water_number 32 --cell 9.86,9.86,9.86
+```
+Or to build a solution containing ions:
+```bash
+mdkits build solution li.xyz k.xyz --water_number 64 --tolerance 2.5 -n 25 -n 45 --cell 15,15,15
+```
+Here, the number of `-n` arguments must match the number of specified solvent molecule types, used to specify the number of solvents to add, respectively. Alternatively, build a solution phase model from `packmol` input files:
+```bash
+mdkits build solution input.pm input2.pm  --infile
+```
+
+### Building Interface Models
+
+`interface` is used to build interface models. For example, to build an interface model without vacuum:
+```bash
+mdkits build interface --slab Pt_fcc100_555.cif --sol water_160.cif
+```
+Or to build an interface with a gas phase model:
+```bash
+mdkits build interface --slab Pt_fcc100_555.cif --sol water_160.cif --cap ne --vacuum 20
+```
+
+### Building Supercell Models
+
+`supercell` is used to build supercell models:
+```bash
+mdkits build supercell Li3PO4.cif 2 2 2
+```
+
+## Others
+
+### Trajectory Extraction
+
+`extract` is used to extract specific frames from a trajectory file. For example, to extract frames from the 1000th to the 2000th frame from `frames.xyz` and output them to `1000-2000.xyz`. The parameters for the `-r` option are consistent with Python's slicing syntax:
+```bash
+mdkits extract frames.xyz -r 1000:2000 -o 1000-2000.xyz
+```
+Or to extract the last frame from the default trajectory file `*-pos-1.xyz` generated by `cp2k` and output it as `frames_-1.xyz` (which is the default behavior of `extract`):
+```bash
+mdkits extract
+```
+Or to output a structure every 50 frames into the `./coord` directory, while adjusting the output format to `cp2k`'s `@INCLUDE coord.xyz` format:
+```bash
+mdkits extract -cr ::50
+```
+To extract the positions of specific elements, for example, to extract the positions of `O` and `H` elements:
+```bash
+mdkits extract --select "name O or name H"
+```
+
+### Structure File Conversion
+
+`convert` is used to convert structure files from one format to another. For example, to convert `structure.xyz` to `out.cif` (default filename is `out`). For files that do not store periodic boundary conditions, you can use the `--cell` option to specify `PBC`:
+```bash
+mdkits convert -c structure.xyz --cell 10,10,10
+```
+To convert `structure.cif` to `POSCAR`:
+```bash
+mdkits convert -v structure.cif
+```
+To convert `structure.cif` to `structure_xyz.xyz`:
+```bash
+mdkits convert -c structure.cif -o structure_xyz
+```
+
+### Data Processing
+
+`data` is used for data processing, such as:
+1.  `--nor`: Normalizes the data.
+2.  `--gaus`: Applies Gaussian filtering to the data.
+3.  `--fold`: Folds and averages stacked data.
+4.  `--err`: Calculates error bars for the data.
+And so on.
+
+### Plotting Tool
+
+`plot` is used for plotting data. `plot` requires reading a YAML format configuration file for plotting. The YAML file format is as follows:
+```yaml
+# plot mode 1
+figure1:
+  data:
+    legend1: ./data1.dat
+    legend2: ./data2.dat
+  x:
+    0: x-axis
+  y:
+    1: y-axis
+  x_range: 
+    - 5
+    - 15
+
+# plot mode 2
+figure2:
+  data:
+    y-xais: ./data.dat
+  x:
+    0: x-axis
+  y:
+    1: legend1
+    2: legend2
+    3: legend3
+    4: legend4
+    5: legend5
+  y_range:
+    - 0.5
+    - 6
+  legend_fontsize: 12
+
+# plot mode error
+12_dp_e_error:
+  data:
+    legend: ./error.dat
+  x:
+    0: x-axis
+  y:
+    1: y-axis
+  fold: dp
+  legend_fontsize: 12
+```
+The above illustrates three plotting modes supported by `plot`: `mode 1`, `mode 2`, and `mode error`. `mode 1` is used for comparing the same column data from multiple data files, `mode 2` is used for comparing different column data from the same data file, and `mode error` is used for plotting mean squared error plots.
+
+`plot` can process multiple YAML files simultaneously. Each YAML file can contain multiple plotting configurations. Plotting configurations for `mode 1` and `mode 2` can be automatically recognized, but the `error` mode requires explicit specification, for example:
+```bash
+mdkits plot *.yaml
+```
+and:
+```bash
+mdkits plot *.yaml --error
+```