mdkits 0.1a1__tar.gz

mdkits-0.1a1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 jxxcr
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

mdkits-0.1a1/PKG-INFO

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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
+```

mdkits-0.1a1/README.md

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+# 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
+```

mdkits-0.1a1/pyproject.toml

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+[tool.poetry]
+name = "mdkits"
+version = "0.1.a1"
+description = "tools for md or dft"
+readme = "README.md"
+authors = ["jxxcr <jixxcr@qq.com>"]
+license = "MIT"
+keywords = ["molecular dynamics", "density functional theory"]
+classifiers = [
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3.11",
+]
+repository = "https://github.com/jxxcr/mdkits"
+
+[tool.poetry.dependencies]
+python = "^3.11"
+dynaconf = "^3.1.12"
+click = "^8.1.3"
+MDAnalysis = "^2.8.0"
+ase = "^3.22.1"
+matplotlib = "^3.9.0"
+pyyaml = "^6.0.1"
+numpy = "^1.26.4"
+
+[tool.poetry.group.dev.dependencies]
+pylint = "^2.17.4"
+isort = "^5.12.0"
+pytest = "^7.3.1"
+tox = "^4.5.2"
+mkdocs = "^1.4.3"
+mkdocs-material = "^8.5.11"
+pytest-pylint = "^0.19.0"
+pre-commit = "^3.3.2"
+
+[tool.poetry.scripts]
+mdkits = "mdkits.mdkits:cli"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+[tool.pytest.ini_options]
+testpaths = "tests"
+python_files = "tests.py test_*.py *_tests.py"
+
+[tool.pylint.design]
+max-line-length = 120

mdkits-0.1a1/src/mdkits/cli/,hb_distribution.py

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+#!/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.accepter = np.zeros(bin_num, dtype=np.float64)
+        self.donor = np.zeros(bin_num, dtype=np.float64)
+
+    def _append(self, hb_d, hb_a):
+        bins_d = np.floor(hb_d / self.bin_size).astype(int) + 1
+        bins_a = np.floor(hb_a / self.bin_size).astype(int) + 1
+
+        bins_d = bins_d[bins_d < len(self.donor)]
+        bins_a = bins_a[bins_a < len(self.accepter)]
+
+        np.add.at(self.donor, bins_d, 1)
+        np.add.at(self.accepter, bins_a, 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]
+        o1h1 = self.atomgroup[o1.indices + 1]
+        o1h2 = self.atomgroup[o1.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)
+        )
+        angle_o1h1_o1_o0 = np.degrees(
+            MDAnalysis.lib.distances.calc_angles(o1h1.positions, o1.positions, o0.positions, box=self.u.dimensions)
+        )
+        angle_o1h2_o1_o0 = np.degrees(
+            MDAnalysis.lib.distances.calc_angles(o1h2.positions, o1.positions, o0.positions, box=self.u.dimensions)
+        )
+
+        condition_d = (angle_o0h1_o0_o1 < self.hb_angle) | (angle_o0h2_o0_o1 < self.hb_angle)
+        condition_a = (angle_o1h1_o1_o0 < self.hb_angle) | (angle_o1h2_o1_o0 < self.hb_angle)
+
+        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, hb_a)
+
+    def _conclude(self):
+        if self.frame_count > 0:
+            average_donor = self.donor / self.frame_count
+            average_accepter = self.accepter / self.frame_count
+            average_sum = average_donor + average_accepter
+
+        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_accepter = average_accepter[mask]
+        filtered_average_donor = average_donor[mask]
+        filtered_average_sum = average_sum[mask]
+
+        combined_data = np.column_stack((filtered_bins_z, filtered_average_accepter, filtered_average_donor, filtered_average_sum))
+
+        np.savetxt("hb_distribution.dat", combined_data, header="Z\tAccepter\tDonor\tAccepter+Donor", 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-0.1a1/src/mdkits/cli/,hb_distribution_down.py

@@ -0,0 +1,114 @@
+#!/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-0.1a1/src/mdkits/cli/adsorbate.py

@@ -0,0 +1,84 @@
+#!/usr/bin/env python3
+
+from ase import io, build
+from ase.collections import g2
+import argparse, os
+import numpy as np
+from util import encapsulated_ase
+
+
+def parse_size(s):
+    if s == None:
+        return None
+    return [float(x) for x in s.replace(',', ' ').split()]
+
+
+def parse_index(s):
+    return [int(x)-1 for x in s.replace(',', ' ').split()]
+
+
+def parse_argument():
+    parser = argparse.ArgumentParser(description='add some adsorbate')
+    parser.add_argument('filename', type=str, help='init structure filename')
+    parser.add_argument('-m', type=str, help='atom or molecule to add')
+    parser.add_argument('--index', type=parse_index, help='index(list) of atom to add atom(top site)')
+    parser.add_argument('--offset', type=parse_size, help='adjust site, default is 0,0', default='0,0')
+    parser.add_argument('--height', type=float, help='designate vacuum of surface, default is None', default=0.0)
+    parser.add_argument('-x', type=float, help='rotate axis and angle')
+    parser.add_argument('-y', type=float, help='rotate axis and angle')
+    parser.add_argument('-z', type=float, help='rotate axis and angle')
+    parser.add_argument('-o', type=str, help='specify the output file name without suffix, default is "adsorbated.cif"', default='adsorbated.cif')
+    parser.add_argument('--coord', help='coord format', action='store_true')
+    parser.add_argument('--cell', type=parse_size, help='set xyz file cell, --cell x,y,z,a,b,c')
+    parser.add_argument('--cp2k', help='output cp2k format', action='store_true')
+
+    return parser.parse_args()
+
+def main():
+    args = parse_argument()
+    atoms = encapsulated_ase.atoms_read_with_cell(args.filename, cell=args.cell, coord_mode=args.coord)
+
+    if len(args.offset) < 2:
+        args.offset.append(0)
+    offset = np.array(args.offset)
+
+    position_list = []
+    for atom in atoms:
+        if atom.index in args.index:
+            position_list.append(np.copy(atom.position[0:2])+offset)
+
+    if args.m in g2.names:
+        molecule = build.molecule(args.m)
+        if args.x:
+            molecule.rotate(args.x, 'x')
+        if args.y:
+            molecule.rotate(args.y, 'y')
+        if args.z:
+            molecule.rotate(args.z, 'z')
+        for position in position_list:
+            build.add_adsorbate(atoms, molecule, args.height, position=position)
+    else:
+        for position in position_list:
+            build.add_adsorbate(atoms, args.m, args.height, position=position)
+
+
+    if args.cp2k:
+        args.o = 'coord.xyz'
+        atoms.write(args.o, format='xyz')
+        with open(args.o, 'r') as f:
+            lines = f.readlines()
+        with open(args.o, 'w') as f:
+            f.writelines(lines[2:])
+        with open('cell.inc', 'w') as f:
+            cell = atoms.get_cell().cellpar()
+            f.write('ABC [angstrom] ' + str(cell[0]) + ' ' + str(cell[1]) + ' ' + str(cell[2]) + ' ' + '\n')
+            f.write('ALPHA_BETA_GAMMA ' + str(cell[3]) + ' ' + str(cell[4]) + ' ' + str(cell[5]) + '\n')
+    else:
+        atoms.write(args.o, format='cif')
+
+    print(os.path.abspath(args.o))
+
+
+if __name__ == '__main__':
+    main()
+