mdkits 1.0.0__py3-none-any.whl → 1.0.2__py3-none-any.whl

mdkits/cli/extract.py

@@ -47,7 +47,7 @@ def write_to_xyz_s(u, frames, select, cut=None):
 @click.argument('input_file_name', type=click.Path(exists=True), default=os_operation.default_file_name('*-pos-1.xyz', last=True))
 @click.option('-r', type=arg_type.FrameRange, help='frame range to slice', default='-1', show_default=True)
 @click.option('-c', help='output a coord.xyz', is_flag=True)
-@click.option("--select", type=str, help="select atoms to extract")
+@click.option("--select", type=str, help="select atoms to extract", default="all", show_default=True)
 def main(input_file_name, r, c, select):
     """
     extract frames in trajectory file

mdkits/util/cp2k_input_parsing.py

@@ -30,7 +30,11 @@ def parse_cell():
                 if len(cell) == 3:
                     cell.extend([90.0, 90.0, 90.0])
 
-                out_err.cell_output(cell)
+                if len(cell) == 0:
+                    print("parse failed")
+                    return [0., 0., 0., 90., 90., 90.]
+                else:
+                    print(f"parsed cell: x = {cell[0]}, y = {cell[1]}, z = {cell[2]}, a = {cell[3]}\u00B0, b = {cell[4]}\u00B0, c = {cell[5]}\u00B0")
                 return cell
         except FileNotFoundError:
             return [0., 0., 0., 90., 90., 90.]

mdkits-1.0.2.dist-info/METADATA

@@ -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-1.0.0.dist-info → mdkits-1.0.2.dist-info}/RECORD

@@ -11,7 +11,7 @@ mdkits/build_cli/supercell.py,sha256=3iTTt3DHaERWDFonhBRS0oqWhjFh6pbS5SpIR-O1gYg
 mdkits/build_cli/water.xyz,sha256=ByLDz-rYhw_wLPBU78lIQHe4s4Xf5Ckjft-Dus3czIc,171
 mdkits/cli/convert.py,sha256=OmQ-7hmw0imgfgCJaWFEy3ePixsU7VKf0mGuJ6jRpn0,1795
 mdkits/cli/data.py,sha256=FGA4S9Cfo6WUJBSPWKOJrrZXHo_Qza-jNG1P_Dw7yi4,3262
-mdkits/cli/extract.py,sha256=JUDqASPcI0PJy6h0tyOBA1vL1AIgFo5ldpoIsYNU2M8,2910
+mdkits/cli/extract.py,sha256=dNf05CZuir98Z0EOjE33JrYK5_YBYLzuOauIt2Lwoh0,2944
 mdkits/cli/plot.py,sha256=1yh5dq5jnQDuyWlxV_9g5ztsnuFHVu4ouYQ9VJYSrUU,8938
 mdkits/config/__init__.py,sha256=ZSwmnPK02LxJLMgcYmNb-tIOk8fEuHf5jpqD3SDHWLg,1039
 mdkits/config/settings.yml,sha256=PY7u0PbFLuxSnd54H5tI9oMjUf-mzyADqSZtm99BwG0,71
@@ -33,7 +33,7 @@ mdkits/mdkits.py,sha256=EiAt7dxGTaHuuj7bCNxgAqZbX0i3sldO0mBxOG-aMnY,595
 mdkits/util/.fig_operation.py.swp,sha256=iZYqdYMj4UKS1rmbXv8Ve2FcVBcNljX7Y43-neMdPSk,12288
 mdkits/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mdkits/util/arg_type.py,sha256=_WmcFKUeOvG5LmQwzcL8-xBQgdwIxUP3gMqEqU7FYNU,2428
-mdkits/util/cp2k_input_parsing.py,sha256=7NMVOYEGycarokLJlhLoWWilciM7sd8MWp5FVTF7hqI,1223
+mdkits/util/cp2k_input_parsing.py,sha256=IAZ2fF-s_atiqdrePRkKG1_EQYB195TFdxHUuB3uYtE,1485
 mdkits/util/encapsulated_ase.py,sha256=uhqIhsALxzwJYuFrfOYGGC6U0QLm_dcZNridvfl_XGc,4339
 mdkits/util/encapsulated_mda.py,sha256=m3i-XrcscMcM5V7JzLnor3JtAOfuDx3LLMl0tZt0n-w,2325
 mdkits/util/fig_operation.py,sha256=FwffNUtXorMl6qE04FipgzcVljEQii7wrNJUCJMyY3E,1045
@@ -41,8 +41,8 @@ mdkits/util/numpy_geo.py,sha256=B2QVADl1M8iixZrIOre2UUhHqvAeghvM8Q2woEQsH3Q,3880
 mdkits/util/os_operation.py,sha256=ErN2ExjX9vZRfPe3ypsj4eyoQTEePqzlEX0Xm1N4lL4,980
 mdkits/util/out_err.py,sha256=7vGDI7wVoJWe1S0BDbcq-UC2KAhblCzg-NAYZKBZ4lo,900
 mdkits/util/structure_parsing.py,sha256=mRPMJeih3O-ST7HeETDvBEkfV-1psT-XgxyYgDadV0U,4152
-mdkits-1.0.0.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
-mdkits-1.0.0.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
-mdkits-1.0.0.dist-info/METADATA,sha256=Z2GyGDkAg9qgs7DmgDwA2mcgkA6aXOZHAiHlIFwRcSs,11351
-mdkits-1.0.0.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-mdkits-1.0.0.dist-info/RECORD,,
+mdkits-1.0.2.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
+mdkits-1.0.2.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
+mdkits-1.0.2.dist-info/METADATA,sha256=NoNCXVMUI1qGY6aXW6Hs9h2QKEIoLb6NLI-pUsGwcLM,13539
+mdkits-1.0.2.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+mdkits-1.0.2.dist-info/RECORD,,

mdkits-1.0.0.dist-info/METADATA

@@ -1,333 +0,0 @@
-Metadata-Version: 2.3
-Name: mdkits
-Version: 1.0.0
-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
-`mdkits` 提供了多种工具, 安装脚本:
-```bash
-pip install mdkits --upgrade
-```
-## 通用的选项参数类型
-1. `CELL TYPE`: 指定晶胞参数, 如`10,10,10`, `10,10,10,90,90,90`等
-2. `FRAME RANGE`: 指定帧范围, 如`1`, `1:10:2`等
-3. `--group`和`--surface`: 按[选择语言](https://userguide.mdanalysis.org/stable/selections.html)选取分析对象
-4. `--update_water`, `--distance` 和 `--angle`: 在分析轨迹的过程中开启动态更新水分子的功能
-
-## 轨迹文件处理脚本
-`md`为轨迹文件处理工具, 其中包含多个处理工具
-### 密度分布
-`density`用于分析体系中的某种元素沿z轴的密度分布, 如分析体系中的`O`元素沿z轴的密度分布:
-```bash
-mdkits md density [FILENAME] --group="name H" --cell [FILENAME]
-```
-这样会输出一个文件名为`density_name_H.dat`的文件, 第一列为z轴坐标, 第二列为浓度分布, 单位为 mol/L. 如果想输出为单位为 $g/cm^3$ 的密度分布, 可以指定`--atomic_mass` 选项, 如:
-```bash
-mdkits md density [FILENAME] --group="name H" --cell [FILENAME] --atomic_mass=1.00784
-```
-则输出单位为 $g/cm^3$ 的密度分布. 可以指定表面原子来将密度分布归一化到表面, 如:
-```bash
-mdkits md density [FILENAME] --group="name O" --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
-```
-这样会将密度分布归一化到表面, 同时以O原子的位置作为水分子的位置分析处理水分子的密度分布. 对于体系中存在 $OH^-$ 离子的体系可以使用`--update_water`的选项在每一帧更新水分子的位置, 不需要额外指定元素, 如:
-```bash
-mdkits md density [FILENAME] --update_water --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
-```
-输出的文件名为`density_water.dat`.
-
-### 氢键
-`hb`用于分析体系中的氢键, 如分析体系中的氢键在z轴上的分布:
-```bash
-mdkits md hb [FILENAME] --cell 10,10,40 --surface "prop z < 10" --update_water
-```
-或分析单个水分子的氢键:
-```bash
-mdkits md hb [FILENAME] --cell 10,10,40 --index 15
-```
-
-### 角度
-`angel`用于分析水分子中的二分向量和OH向量与表面法向量的夹角的丰度分布, 如分析距离表面 5 Å 的水分子的角度丰度分布:
-```bash
-mdkits md angle [FILENAME] --cell 10,10,40 --surface "name Pt" --water_height 5
-```
-
-### 偶极分布
-`diople`用于分析体系中的偶极($\cos \phi \rho_{H_2 O}$)分布, 如分析体系中的 $\cos \phi \rho_{H_2 O}$ 分布:
-```bash
-mdkits md diople [FILENAME] --cell 10,10,40 --surface "name Pt"
-```
-
-### 径向分布函数(RDF)
-`rdf`用于分析两个`group`之间的径向分布函数, 如分析体系中的`O`元素与`H`元素之间的径向分布函数:
-```bash
-mdkits md rdf [FILENAME] --group "name O" "name H" --cell 10,10,40 --range 0.1 5
-```
-
-### 均方位移(MSD)
-`msd`用于分析体系中某些原子的均方位移, 如分析体系中`Li`原子在z轴上的均方位移:
-```bash
-mdkits md msd [FILENAME] z "name Li"
-```
-
-### 监控
-`monitor`用于监控体系中原子高度, 键长和键角的变化, 如监控`index`为0的原子的高度:
-```bash
-mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 0
-```
-会输出0距离表面的高度随每一帧的变化, 如监控0-1的键长:
-```bash
-mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 0 -i 1
-```
-会输出0和1距离表面的高度和0-1之间的键长随每一帧的变化, 如监控1-0-2的键角:
-```bash
-mdkits md monitor [FILENAME] --cell 10,10,40 --surface "name Pt" -i 1 -i 0 -i 2
-```
-会输出1, 0, 2距离表面的高度, 1-0和0-2的键长和1-0-2的键角随每一帧的变化, 注意位于角上的原子应该放在中间
-
-### 位置归一化
-`wrap`用于将轨迹文件中的原子位置进行归一化处理, 如将`[FILENAME]`中的原子位置归一化到晶胞中, 并输出为`wrapped.xyz`, 默认从`cp2k`的输出文件`input_inp`中读取`ABC`和`ALPHA_BETA_GAMMA`信息作为晶胞参数:
-```bash
-mdkits md wrap [FILENAME] 
-```
-或指定`cp2k`的输入文件:
-```bash
-mdkits md wrap [FILENAME] --cp2k_input_file setting.inp
-```
-或指定晶胞参数:
-```bash
-mdkits md wrap [FILENAME] --cell 10,10,10
-```
-默认的`[FILENAME]`为`*-pos-1.xyz`
-
-### 振动态密度(VDOS)
-`vac`用于分析轨迹的速度自相关函数, 同时计算速度自相关函数的傅里叶变换, 即振动动态密度(VDOS), 如分析体系中的VDOS:
-```bash
-mdkits md vac h2o-vel-1.xyz
-```
-默认的`[FILENAME]`为`*-vel-1.xyz`
-
-## DFT 性质分析脚本
-`dft`为DFT性质分析工具, 其中包含多个分析工具
-### PDOS
-`pdos`用于分析体系中的pdos, 分析[FILENAME]的d轨道的dos:
-```bash
-mdkits dft pdos [FILENAME] -t d
-```
-
-### CUBE 文件
-`cube`用于处理[`cube`格式](https://paulbourke.net/dataformats/cube/)的文件, 将其在z轴上进行平均:
-```bash
-mdkits dft cube [FILENAME]
-```
-分析好的数据会输出为`cube.out`, 可以同时计算一个区域内的平均值:
-```bash
-mdkits dft cube [FILENAME] -b 1 2
-```
-会将平均值打印在屏幕上, 同时记录在`cube.out`中的注释行.
-
-## 建模
-`build`为建模的工具, 其中包含多个建模工具
-
-### 构建体相模型
-`bulk`用于构建体相模型, 如构建`Pt`的`fcc`体相模型:
-```bash
-mdkits build bulk Pt fcc
-```
-构建为常胞模型:
-```bash
-mdkits build bulk Pt fcc --cubic
-```
-构建一个`Caesium chloride`结构的模型:
-```bash
-mdkits build bulk CsCl cesiumchloride -a 4.123
-```
-构建一个`fluorite `结构的模型:
-```bash
-mdkits build bulk BaF2 fluorite -a 6.196
-```
-
-### 构建表面模型
-`surface`用于构建常见的表面模型, 骑用法为:
-```bash
-mdkits build surface [ELEMENT] [SURFACE_TYPE] [SIZE]
-```
-如构建`Pt`的`fcc111`表面模型:
-```bash
-mdkits build surface Pt fcc111 2 2 3 --vacuum 15
-```
-构建石墨烯表面:
-```bash
-mdkits build surface C2 graphene 3 3 1 --vacuum 15
-```
-
-### 从现有结构中构建表面模型
-`cut`用于从现有的结构中构建表面模型(模型必须为常胞模型), 如从`Pt_fcc.cif`中构建`fcc331`表面模型:
-```bash
-mdkits build cut Pt_fcc.cif --face 3 3 1 --size 3 3 5 --vacuum 15
-```
-
-### 在表面结构上添加吸附物
-`adsorbate`用于在表面结构上添加吸附物, 如在`surface.cif`上添加`H`原子:
-```bash
-mdkits build adsorbate surface.cif H --select "index 0" --height 1    
-```
-或在`Pt_fcc111_335.cif`上添加覆盖度为5的`H`原子:
-```bash
-mdkits build adsorbate Pt_fcc111_335.cif H --select "prop z > 16" --height 2 --cover 5
-```
-
-### 构建溶液相模型
-`solution`用于构建溶液相模型, 初次使用时应先安装`juliaup`:
-```bash
-mdkits build solution --install_julia
-```
-然后安装`Packmol`:
-```bash
-mdkits build solution --install_packmol
-```
-成功安装后就可以使用`solution`功能了, 如构建一个32个水分子的水盒子:
-```bash
-mdkits build solution --water_number 32 --cell 9.86,9.86,9.86
-```
-或构建一个含有离子的溶液:
-```bash
-mdkits build solution li.xyz k.xyz --water_number 64 --tolerance 2.5 -n 25 -n 45 --cell 15,15,15
-```
-其中`-n`的个数必须与指定的溶剂分子种类数量一致, 用于分别指定添加的溶剂的数量. 或者从`packmol`的输入文件中构建溶液相模型:
-```bash
-mdkits build solution input.pm input2.pm  --infile
-```
-
-### 构建界面模型
-`interface`用于构建界面模型, 如构建一个没有真空的界面模型:
-```bash
-mdkits build interface --slab Pt_fcc100_555.cif --sol water_160.cif
-```
-或构建一个带有气相模型的界面:
-```bash
-mdkits build interface --slab Pt_fcc100_555.cif --sol water_160.cif --cap ne --vacuum 20
-```
-
-### 构建超胞模型
-`supercell`用于构建超胞模型:
-```bash
-mdkits build supercell Li3PO4.cif 2 2 2
-```
-
-## 其他
-### 轨迹提取
-`extract`用于提取轨迹文件中的特定的帧, 如从`frames.xyz`中提取第 1000 帧到第 2000 帧的轨迹文件, 并输出为`1000-2000.xyz`, `-r`选项的参数与`Python`的切片语法一致:
-```bash
-mdkits extract frames.xyz -r 1000:2000 -o 1000-2000.xyz
-```
-或从`cp2k`的默认输出的轨迹文件`*-pos-1.xyz`文件中提取最后一帧输出为`frames_-1.xyz`(`extract`的默认行为):
-```bash
-mdkits extract
-```
-或每50帧输出一个结构到`./coord`目录中, 同时调整输出格式为`cp2k`的`@INCLUDE coord.xyz`的形式:
-```bash
-mdkits extract -cr ::50
-```
-提取部分元素的位置, 如提取`O`元素和`H`元素的位置:
-```bash
-mdkits extract --select "name O or name H"
-```
-
-### 结构文件转换
-`convert`用于将结构文件从一种格式转换为另一种格式, 如将`structure.xyz`转换为`out.cif`(默认文件名为`out`), 对于不储存周期性边界条件的文件, 可以使用`--cell`选项指定`PBC`:
-```bash
-mdkits convert -c structure.xyz --cell 10,10,10
-```
-将`structure.cif`转换为`POSCAR`:
-```bash
-mdkits convert -v structure.cif
-```
-将`structure.cif`转换为`structure_xyz.xyz`:
-```bash
-mdkits convert -c structure.cif -o structure_xyz
-```
-
-### 数据处理
-`data`用于对数据进行处理如:
-1. `--nor`: 对数据进行归一化处理
-2. `--gaus`: 对数据进行高斯过滤
-3. `--fold`: 堆数据进行折叠平均
-4. `--err`: 计算数据的误差棒   
-等
-
-### 绘图工具
-`plot`用于绘制数据图, `plot`需要读取`yaml`格式的配置文件进行绘图, `yaml`文件的形式如下:
-```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
-```
-如上`plot`支持三种绘图模式, `mode 1`, `mode 2`和`mode error`. `mode 1`用于绘制多组数据文件的同一列数据对比, `mode 2`用于绘制同一数据文件的不同列数据对比, `mode error`用于绘制均方根误差图.
-
-`plot`可以同时处理多个`yaml`文件, 每个`yaml`文件可以包含多个绘图配置, `mode 1`和`mode 2`的绘图配置可以自动识别, 但是`error`模式需要而外指定, 如:
-```bash
-mdkits plot *.yaml
-```
-和:
-```bash
-mdkits plot *.yaml --error
-```