mdkits 0.1.29__py3-none-any.whl → 0.2.0__py3-none-any.whl

mdkits/md_cli/vac.py

@@ -0,0 +1,68 @@
+import numpy as np
+import click
+import MDAnalysis
+from MDAnalysis import Universe
+from MDAnalysis.analysis.base import AnalysisBase
+from mdkits.util import os_operation, arg_type
+
+
+class Velocity_AutoCorrelation(AnalysisBase):
+    def __init__(self, filename, select, dt=0.001):
+        u = Universe(filename)
+        u.trajectory.ts.dt = dt
+        self.u = u
+        self.atomgroup = u.select_atoms(select)
+
+        super(Velocity_AutoCorrelation, self).__init__(self.atomgroup.universe.trajectory, verbose=True)
+
+    def _prepare(self):
+        self.cvv = []
+        self.v0 = self.atomgroup.positions
+        self.normalize = 1/np.sum(self.v0*self.v0)
+        self.cvv.append(np.sum(self.v0*self.v0)*self.normalize)
+
+
+    def _append(self, cvv):
+        self.cvv.append(cvv*self.normalize)
+
+    def _single_frame(self):
+        cvv = np.sum(self.atomgroup.positions*self.v0)
+        self._append(cvv)
+
+    def _conclude(self):
+        self.cvv = np.array(self.cvv)
+
+        sf = self.cvv.shape[0]
+        t = 1/sf
+        f = np.fft.fft(self.cvv).real
+
+        faxis = np.fft.fftfreq(sf, d=t)
+        pf = np.where(faxis>0)
+        faxis = faxis[pf]
+        f = f[pf]
+
+        combine = np.column_stack((np.arange(len(self.cvv)), self.cvv))
+
+        np.savetxt('vac.dat', combine, fmt='%.5f', header="frame\tvac")
+        np.savetxt('f.dat', np.column_stack((faxis, f)), fmt='%.5f')
+
+
+@click.command(name="vac")
+@click.argument("filename", type=click.Path(exists=True), default=os_operation.default_file_name('*-vel-1.xyz', last=True))
+@click.option("--select", type=str, default="all", help="atom selection", show_default=True)
+@click.option('-r', type=arg_type.FrameRange, help='range of frame to analysis')
+def main(filename, select, r):
+    """analysis velocity autocorrelation function"""
+    a = Velocity_AutoCorrelation(filename, select)
+
+    if r is not None:
+        if len(r) == 2:
+            a.run(start=r[0], stop=r[1])
+        elif len(r) == 3:
+            a.run(start=r[0], stop=r[1], step=r[2])
+    else:
+        a.run()
+
+
+if __name__ == '__main__':
+    main()

mdkits/{cli → md_cli}/wrap.py

@@ -28,7 +28,7 @@ def main(filename, o, cell):
             ag.wrap()
             W.write(ag)
 
-    click.echo("\nwrap is done, output file {o} is:")
+    click.echo(f"\nwrap is done, output file {o} is:")
     click.echo(os.path.abspath(o))
 
 

mdkits/mdkits.py

@@ -4,7 +4,6 @@ from mdkits.dft_cli import dft_cli
 from mdkits.md_cli import md_cli
 from mdkits.cli import (
     convert,
-    wrap,
     extract,
     data,
     plot,
@@ -19,11 +18,10 @@ def cli(ctx):
     pass
 
 
-cli.add_command(md_cli.main)
-cli.add_command(dft_cli.main)
+cli.add_command(md_cli.cli)
 cli.add_command(build_cli.cli_build)
+cli.add_command(dft_cli.main)
 cli.add_command(convert.main)
-cli.add_command(wrap.main)
 cli.add_command(extract.main)
 cli.add_command(data.main)
 cli.add_command(plot.main)

mdkits/util/arg_type.py

@@ -6,7 +6,7 @@ from mdkits.util import os_operation, cp2k_input_parsing, out_err
 
 
 class CellType(click.ParamType):
-    name = "pbc cell type"
+    name = "cell type"
 
     def convert(self, value, param, ctx):
         if isinstance(value, str):
@@ -36,7 +36,7 @@ class FrameRangeType(click.ParamType):
 
 
 class StructureType(click.ParamType):
-    name = "structure file type"
+    name = "structure type"
     def convert(self, value, param, ctx):
         no_cell=np.array([0., 0., 0., 90., 90., 90.])
         if isinstance(value, str):

mdkits/util/numpy_geo.py

@@ -45,7 +45,10 @@ def vector_between_two_vector(vector1, vector2):
 
 
 def vector_vector_angle(vector, surface_vector):
-    cos = np.dot(vector, surface_vector) / (np.linalg.norm(vector, axis=1) * np.linalg.norm(surface_vector))
+    if len(vector.shape) == 1:
+        cos = np.dot(vector, surface_vector) / (np.linalg.norm(vector) * np.linalg.norm(surface_vector))
+    else:
+        cos = np.dot(vector, surface_vector) / (np.linalg.norm(vector, axis=1) * np.linalg.norm(surface_vector))
     vector_vector_angle = np.arccos(np.clip(cos, -1.0, 1.0))
     vector_vector_angle = np.degrees(vector_vector_angle)
     return vector_vector_angle

{mdkits-0.1.29.dist-info → mdkits-0.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.29
+Version: 0.2.0
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -21,102 +21,144 @@ 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
 
-# MD 轨迹分析脚本
+# 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, `--element`选项指定元素使用`MDAnalysis`的[选择语言](https://userguide.mdanalysis.org/stable/selections.html):
+`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 density [FILENAME] --element="name H" --cell [FILENAME]
+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 density [FILENAME] --element="name H" --cell [FILENAME] --atomic_mass=1.00784
+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 density [FILENAME] --element="name O" --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+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 density [FILENAME] --update_water --cell 10,10,10 --atomic_mass=18.01528 --surface="name Pt and name Ru"
+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
-
-#### 单个水分子
-
-#### 氢键分布
+`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
+```
 
-#### 与表面法向量夹角分布
+### 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"
+```
 
-#### ion - O - ion 夹角分布
+### 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
+```
 
-#### $\cos \phi \rho_{H_2 O}$ 分布
+### 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"
+```
 
-### RDF
+### 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 wrap [FILENAME] 
+mdkits md wrap [FILENAME] 
 ```
 或指定`cp2k`的输入文件:
 ```bash
-mdkits wrap [FILENAME] --cp2k_input_file setting.inp
+mdkits md wrap [FILENAME] --cp2k_input_file setting.inp
 ```
 或指定晶胞参数:
 ```bash
-mdkits wrap [FILENAME] --cell 10,10,10
+mdkits md wrap [FILENAME] --cell 10,10,10
 ```
 默认的`[FILENAME]`为`*-pos-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 pdos [FILENAME] -t d
+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 cube [FILENAME]
+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 cube [FILENAME] -b 1 2
+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`为界面的工具, 其中包含多个建模工具
+`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
+mdkits build bulk Pt fcc
 ```
 构建为常胞模型:
 ```bash
-mdkits build_bulk Pt fcc --cubic
+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
+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
+mdkits build bulk BaF2 fluorite -a 6.196
 ```
 
 ### 构建表面模型
@@ -133,6 +175,60 @@ mdkits build surface Pt fcc111 2 2 3 --vacuum 15
 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:

{mdkits-0.1.29.dist-info → mdkits-0.2.0.dist-info}/RECORD

@@ -1,47 +1,48 @@
 mdkits/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mdkits/build_cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mdkits/build_cli/adsorbate.py,sha256=Zp21i-miFv5zQlYjZnZuVpMxvNVT-6RtdlaoWDMwaOg,1900
+mdkits/build_cli/adsorbate.py,sha256=9D_IYpnXd30pALC6JIvVPPxuxDfpsoArgMhE2hSeOSw,1947
 mdkits/build_cli/build_bulk.py,sha256=o3SFov5Ggk-qKcy6-NBoIYKvZV24OhcH3-du1d0U6H4,1593
 mdkits/build_cli/build_cli.py,sha256=sqjnq5aHWLYLbNzN5SORkEYeYaewLagFuSvspJxyh7E,725
 mdkits/build_cli/build_interface.py,sha256=3EDxUb-vGHFuat1Ex_wojVsN8PtzHiGrnDQIEa9WZ60,2448
 mdkits/build_cli/build_solution.py,sha256=7bwaDH-vLBNRzGoYXT72bzLVXdQAZ4HXNuUDuR7AI78,5377
-mdkits/build_cli/build_surface.py,sha256=cBEQ-KR_6j-Mcsxrwvzyl6p1SiY_chIytrCu7MS3q08,2794
+mdkits/build_cli/build_surface.py,sha256=9GGpmQlCG6vxNevMyWcfI2EL_JiAAKIhxNokZyEzVLU,2739
 mdkits/build_cli/cut_surface.py,sha256=_f0t2OyBKb8ZV04b3GezfSDUN4XFd5kQM-yWbSmOofs,2742
 mdkits/build_cli/supercell.py,sha256=3iTTt3DHaERWDFonhBRS0oqWhjFh6pbS5SpIR-O1gYg,1034
 mdkits/build_cli/water.xyz,sha256=ByLDz-rYhw_wLPBU78lIQHe4s4Xf5Ckjft-Dus3czIc,171
-"mdkits/cli/,hb_distribution_down.py",sha256=i3NguzGebqCgy4uuVBeFajZRZnXtjhsJBPDGDdumlWA,4733
 mdkits/cli/convert.py,sha256=OmQ-7hmw0imgfgCJaWFEy3ePixsU7VKf0mGuJ6jRpn0,1795
 mdkits/cli/data.py,sha256=FGA4S9Cfo6WUJBSPWKOJrrZXHo_Qza-jNG1P_Dw7yi4,3262
-mdkits/cli/extract.py,sha256=bqqJBmSaVyPYyEseGpUJcMBufIfDLTNRdmUfJ0txE5E,2498
-mdkits/cli/hartree_potential.py,sha256=XcJfsJ5Y2d5MQfD45p06_gV1fTJbDSrNhCnZ3Sz2Vb0,2233
-mdkits/cli/hartree_potential_ave.py,sha256=25oy3QsgIdxrTFpTqpnGvLAheb-d6poeLMN7iuGT3Xk,3335
-mdkits/cli/hb.py,sha256=lADr4tlctbtQ3_f_UpznkLnSI0MJlAT-pknEf_dwrnU,5330
-mdkits/cli/packmol_input.py,sha256=76MjjMMRDaW2q459B5mEpXDYSSn14W-JXudOOsx-8E4,2849
+mdkits/cli/extract.py,sha256=JUDqASPcI0PJy6h0tyOBA1vL1AIgFo5ldpoIsYNU2M8,2910
 mdkits/cli/plot.py,sha256=1yh5dq5jnQDuyWlxV_9g5ztsnuFHVu4ouYQ9VJYSrUU,8938
-mdkits/cli/wrap.py,sha256=AUxGISuiCfEjdMYl-TKc2VMCPHSybWKrMIOTn_6kSp0,1043
 mdkits/config/__init__.py,sha256=ZSwmnPK02LxJLMgcYmNb-tIOk8fEuHf5jpqD3SDHWLg,1039
 mdkits/config/settings.yml,sha256=PY7u0PbFLuxSnd54H5tI9oMjUf-mzyADqSZtm99BwG0,71
 mdkits/dft_cli/cube.py,sha256=G-QNup8W6J1-LCcEl1EHsV3nstd23byePDOcE_95t18,1176
 mdkits/dft_cli/dft_cli.py,sha256=Ou9-e4uGhDJJk2Gdg7tcj6iKApkAJZFSbN1hr7SlCMc,281
 mdkits/dft_cli/pdos.py,sha256=ALAZ5uOaoT0UpCyKYleWxwmk569HMzKTTK-lMJeicM8,1411
-mdkits/md_cli/angle.py,sha256=PaqFnlVnWHy6t6eDOQdq7J0jhMpCnekIzNCjhTMpdqw,5930
-mdkits/md_cli/density.py,sha256=-o1argCiwWr9mjggeetuX0sDMxjhRSPMG25sOS3KZYU,5574
-mdkits/md_cli/hb_distribution.py,sha256=MPrYfVW0MC01G1GZTxTca58jSlD0rVRnR1g1DmvdE00,8301
-mdkits/md_cli/md_cli.py,sha256=7hefzX0NIydlL2AjqTkTwLUg6yIOMSCn3zQ1zU9pP3s,348
-mdkits/mdkits.py,sha256=UGCAbVml8MdXXG--LGo8BUm9BXofg9P3HKIEDTUbd48,635
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mdkits/cli/,hb_distribution_down.py

@@ -1,114 +0,0 @@
-#!/usr/bin/env python3
-
-import numpy as np
-import argparse
-import MDAnalysis
-from MDAnalysis import Universe
-from MDAnalysis.analysis.base import AnalysisBase
-from util import cp2k_input_parsing
-import warnings
-warnings.filterwarnings("ignore")
-
-
-class Hb_distribution(AnalysisBase):
-    def __init__(self, filename, cell, surface, dt=0.001, hb_distance=3.5, hb_angle=35, bin_size=0.2):
-        u = Universe(filename)
-        u.trajectory.ts.dt = dt
-        u.dimensions = cell
-        self.u = u
-        self.atomgroup = u.select_atoms("all")
-        self.hb_distance = hb_distance
-        self.hb_angle = hb_angle
-        self.bin_size = bin_size
-        self.surface = surface
-        self.frame_count = 0
-        super(Hb_distribution, self).__init__(self.atomgroup.universe.trajectory, verbose=True)
-
-    def _prepare(self):
-        bin_num = int(self.u.dimensions[2] / self.bin_size) + 2
-        self.donor = np.zeros(bin_num, dtype=np.float64)
-
-    def _append(self, hb_d):
-        bins_d = np.floor(hb_d / self.bin_size).astype(int) + 1
-
-        bins_d = bins_d[bins_d < len(self.donor)]
-
-        np.add.at(self.donor, bins_d, 1)
-
-        self.frame_count += 1
-
-    def _single_frame(self):
-        o_group = self.atomgroup.select_atoms("name O")
-        o_pair = MDAnalysis.lib.distances.capped_distance(o_group.positions, o_group.positions, min_cutoff=0, max_cutoff=self.hb_distance, box=self.u.dimensions, return_distances=False)
-
-        o0 = o_group[o_pair[:, 0]]
-        o1 = o_group[o_pair[:, 1]]
-
-        o0h1 = self.atomgroup[o0.indices + 1]
-        o0h2 = self.atomgroup[o0.indices + 2]
-
-        angle_o0h1_o0_o1 = np.degrees(
-            MDAnalysis.lib.distances.calc_angles(o0h1.positions, o0.positions, o1.positions, box=self.u.dimensions)
-        )
-        angle_o0h2_o0_o1 = np.degrees(
-            MDAnalysis.lib.distances.calc_angles(o0h2.positions, o0.positions, o1.positions, box=self.u.dimensions)
-        )
-
-        mid_z = (self.surface[0] + self.surface[1]) / 2
-
-        condition_d = ((angle_o0h1_o0_o1 < self.hb_angle) | (angle_o0h2_o0_o1 < self.hb_angle)) & (o0.positions[:, 2] - o1.positions[:, 2] > 0)
-        #condition_d = ((angle_o0h1_o0_o1 < self.hb_angle) | (angle_o0h2_o0_o1 < self.hb_angle)) & (((o0.positions[:, 2] < mid_z) & (o0.positions[:, 2] - o1.positions[:, 2] > 0)) | ((o0.positions[:, 2] > mid_z) & (o0.positions[:, 2] - o1.positions[:, 2] < 0)))
-        #condition_a = ((angle_o1h1_o1_o0 < self.hb_angle) | (angle_o1h2_o1_o0 < self.hb_angle)) & (((o1.positions[:, 2] < mid_z) & (o1.positions[:, 2] - o0.positions[:, 2] > 1.5)) | ((o1.positions[:, 2] > mid_z) & (o1.positions[:, 2] - o0.positions[:, 2] < -1.5)))
-
-        hb_d = (o0.positions[:, 2][condition_d] + o1.positions[:, 2][condition_d]) / 2
-        #hb_a = (o0.positions[:, 2][condition_a] + o1.positions[:, 2][condition_a]) / 2
-
-        self._append(hb_d)
-
-    def _conclude(self):
-        if self.frame_count > 0:
-            average_donor = self.donor / self.frame_count
-
-        bins_z = np.arange(len(self.donor)) * self.bin_size
-
-        lower_z, upper_z = self.surface
-        mask = (bins_z >= lower_z) & (bins_z <= upper_z)
-        filtered_bins_z = bins_z[mask] - lower_z
-        filtered_average_donor = average_donor[mask]
-
-        combined_data = np.column_stack((filtered_bins_z, filtered_average_donor))
-
-        filename = 'hb_distribution_down.dat'
-        np.savetxt(filename, combined_data, header="Z\tDonor", fmt='%.5f', delimiter='\t')
-
-
-def parse_data(s):
-    return [float(x) for x in s.replace(',', ' ').split()]
-
-
-def parse_r(s):
-    return [int(x) for x in s.replace(':', ' ').split()]
-
-
-def parse_argument():
-    parser = argparse.ArgumentParser(description="analysis hb distribution")
-    parser.add_argument('filename', type=str, help='filename to analysis')
-    parser.add_argument('--cp2k_input_file', type=str, help='input file name of cp2k, default is "input.inp"', default='input.inp')
-    parser.add_argument('-r', type=parse_r, help='range of analysis', default=[0, -1, 1])
-    parser.add_argument('--cell', type=parse_data, help='set cell, a list of lattice, --cell x,y,z or x,y,z,a,b,c')
-    parser.add_argument('--surface', type=parse_data, help='[down_surface_z, up_surface_z]')
-    parser.add_argument('--hb_param', type=parse_data, help='[hb_distance, hb_angle], default is [3.5, 35]', default=[3.5, 35])
-
-    return parser.parse_args()
-
-
-def main():
-    args = parse_argument()
-    cell = cp2k_input_parsing.get_cell(args.cp2k_input_file, args.cell)
-
-    hb_dist = Hb_distribution(args.filename, cell, args.surface, hb_distance=args.hb_param[0], hb_angle=args.hb_param[1])
-    hb_dist.run(start=args.r[0], stop=args.r[1], step=args.r[2])
-
-
-if __name__ == '__main__':
-    main()

mdkits/cli/hartree_potential.py

@@ -1,59 +0,0 @@
-#!/usr/bin/env python3
-
-################################################
-# averange cp2k output(or some else file correspond to ase.io.read_cube_data) hartree.cube to z coordinate with python
-## file path is need to pay attention
-## cycle parameter is need to pay attention
-## buck range is need to pay attention
-################################################
-
-from numpy import empty, array, mean, append, concatenate
-from argparse import ArgumentParser
-from util import encapsulated_ase, os_operation
-
-
-def array_type(string):
-	number_list = string.split(',')
-	number_array = array(number_list, dtype=float)
-	return number_array
-
-
-def buck_potential(xaxe, potential, range):
-	mix = concatenate((xaxe.reshape(-1, 1), potential.reshape(-1, 1)), axis=1)
-	mask = (mix[:,0] >= range[0]) & (mix[:,0] <=range[1])
-	buck_potential = mix[mask]
-	ave_potential = mean(buck_potential[:,1])
-	return ave_potential
-
-
-# set argument
-parser = ArgumentParser(description='to handle cp2k output file hartree cube, name should be "hartree-*.cube"')
-parser.add_argument('file_name', type=str, nargs='?', help='hartree cube file', default=os_operation.default_file_name('*-v_hartree-1_*.cube', last=True))
-parser.add_argument('-b', '--buck_range', type=array_type, help='parameter to calculate mean value of buck', default=None)
-parser.add_argument('-o', type=str, help='output file name, default is "out.put"', default='hartree.out')
-
-args = parser.parse_args()
-
-
-## init output potential file's shape, and define a z axe
-init_array = encapsulated_ase.ave_potential(args.file_name)
-potential = empty((0, init_array[0].shape[0]))
-z_coordinates = array((init_array[1])).reshape(-1, 1)
-
-potential = encapsulated_ase.ave_potential(args.file_name)[0]
-
-aved = mean(potential, axis=0)
-total_potential = append(z_coordinates, potential.reshape(-1, 1), axis=1)
-
-## if buck range is exit, out put a difference of potential
-if args.buck_range is not None:
-	buck_potential = buck_potential(z_coordinates, potential, args.buck_range)
-	print(buck_potential)
-	with open('hartree_potential.dat', 'w') as f:
-		f.write(f"{buck_potential}" + '\n')
-
-## write output
-with open(args.o, 'w') as f:
-	for value in total_potential:
-		f.write(" ".join(map(str, value)) + '\n')
-