mdkits 0.1a1__py3-none-any.whl

mdkits-0.1a1.dist-info/METADATA

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+Metadata-Version: 2.3
+Name: mdkits
+Version: 0.1a1
+Summary: tools 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: 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: dynaconf (>=3.1.12,<4.0.0)
+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)
+Project-URL: Repository, https://github.com/jxxcr/mdkits
+Description-Content-Type: text/markdown
+
+# MD 轨迹分析脚本
+`mdtool` 提供了多种工具, 安装脚本:
+```bash
+pip install mdtool --upgrade
+```
+### 密度分布
+
+### 氢键
+
+#### 单个水分子
+
+#### 氢键分布
+
+### 角度
+
+#### 与表面法向量夹角分布
+
+#### ion - O - ion 夹角分布
+
+#### $\cos \phi \rho_{H_2 O}$ 分布
+
+### RDF
+
+### 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
+mdtool wrap [FILENAME] 
+```
+或指定`cp2k`的输入文件:
+```bash
+mdtool wrap [FILENAME] --cp2k_input_file setting.inp
+```
+或指定晶胞参数:
+```bash
+mdtool wrap [FILENAME] --cell 10,10,10
+```
+默认的`[FILENAME]`为`*-pos-1.xyz`
+
+## DFT 性质分析脚本
+### PDOS
+
+### 静电势
+
+### 电荷差分
+
+## 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
+mdtool 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`extracted.xyz`(`extract`的默认行为):
+```bash
+mdtool 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
+mdtool extract -cr ::50
+```
+
+### 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
+mdtool convert -c structure.xyz --cell 10,10,10
+```
+将`structure.cif`转换为`POSCAR`:
+```bash
+mdtool convert -v structure.cif
+```
+将`structure.cif`转换为`structure_xyz.xyz`:
+```bash
+mdtool 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
+mdtool plot *.yaml
+```
+和:
+```bash
+mdtool plot *.yaml --error
+```

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mdkits-0.1a1.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: poetry-core 2.1.1
+Root-Is-Purelib: true
+Tag: py3-none-any

mdkits-0.1a1.dist-info/entry_points.txt

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+[console_scripts]
+mdkits=mdkits.mdkits:cli
+