mdkits 0.1.13__py3-none-any.whl → 1.2.3__py3-none-any.whl

mdkits/cli/hb.py

@@ -1,101 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse, multiprocessing, os
-import numpy as np
-from util import (
-    structure_parsing,
-    numpy_geo,
-    os_operation,
-    cp2k_input_parsing,
-    )
-
-
-def hb_count(chunk, index, cell, filename, hb_distance=3.5, hb_angle=35):
-    groups = structure_parsing.chunk_to_groups(chunk)
-    groups_hb_list = []
-    coefficients = numpy_geo.cell_to_wrap_coefficients(cell)
-    for group in groups:
-        group_hb_array = np.zeros((3, 1))
-        present_index = index
-        o_present = group[present_index].split()
-        if o_present[0] == 'O':
-            o_present = np.array(o_present[1:], dtype=np.float64)
-            group_hb_array[2, 0] += 1
-            for other_index in range(2, len(group)):
-                o_other = group[other_index].split()
-                if o_other[0] == 'O':
-                    o_other = np.array(o_other[1:], dtype=np.float64)
-                    oo_distance, o_other = numpy_geo.unwrap(o_present, o_other, coefficients, max=0)
-                    if oo_distance < hb_distance and oo_distance > 1:
-                        _, o_present_h1 = numpy_geo.unwrap(o_present, np.array(group[present_index+1].split()[1:], dtype=np.float64), coefficients)
-                        _, o_present_h2 = numpy_geo.unwrap(o_present, np.array(group[present_index+2].split()[1:], dtype=np.float64), coefficients)
-                        _, o_other_h1 = numpy_geo.unwrap(o_other, np.array(group[other_index+1].split()[1:], dtype=np.float64), coefficients)
-                        _, o_other_h2 = numpy_geo.unwrap(o_other, np.array(group[other_index+2].split()[1:], dtype=np.float64), coefficients)
-
-                        o_present_o_other_h1_angle = numpy_geo.vector_vector_angle(o_present-o_other, o_other_h1-o_other)
-                        o_present_o_other_h2_angle = numpy_geo.vector_vector_angle(o_present-o_other, o_other_h2-o_other)
-                        if o_present_o_other_h1_angle < hb_angle or o_present_o_other_h2_angle < hb_angle:
-                            group_hb_array[0, 0] += 1
-                        o_other_o_present_h1_angle = numpy_geo.vector_vector_angle(o_other-o_present, o_present_h1-o_present)
-                        o_other_o_present_h2_angle = numpy_geo.vector_vector_angle(o_other-o_present, o_present_h2-o_present)
-                        if o_other_o_present_h1_angle < hb_angle or o_other_o_present_h2_angle < hb_angle:
-                            group_hb_array[1, 0] += 1
-        groups_hb_list.append(group_hb_array)
-    groups_hb_array = np.vstack(groups_hb_list)
-    group_hb_acc_array = np.sum(groups_hb_array[0::3], axis=0).reshape(1, -1)
-    group_hb_don_array = np.sum(groups_hb_array[1::3], axis=0).reshape(1, -1)
-    group_hb_num_array = np.sum(groups_hb_array[2::3], axis=0).reshape(1, -1)
-    group_hb_array = np.vstack([group_hb_acc_array, group_hb_don_array, group_hb_num_array])
-    np.save(filename, group_hb_array)
-
-
-def parse_data(s):
-    return [float(x) for x in s.replace(',', ' ').split()]
-
-def parse_argument():
-    parser = argparse.ArgumentParser(description="analysis an O atom's hydrogen bond in water")
-    parser.add_argument('index', type=int, help='index of target atom in coord.xyz, or all of hb distribution on z')
-    parser.add_argument('input_file_name', type=str, nargs='?', help='input file name', default=os_operation.default_file_name('wraped.xyz', last=True))
-    parser.add_argument('--cp2k_input_file', type=str, help='input file name of cp2k, default is "input.inp"', default='input.inp')
-    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('--hb_param', type=parse_data, help='[hb_distance, hb_angle], default is [3.5, 35]', default=[3.5, 35])
-    parser.add_argument('--process', type=int, help='paralle process number default is 28', default=28)
-    parser.add_argument('--temp', help='keep temp file', action='store_false')
-
-    return parser.parse_args()
-
-def main():
-    args = parse_argument()
-    output = f'./hb_{args.index}.dat'
-    cell = cp2k_input_parsing.get_cell(args.cp2k_input_file, args.cell)
-    chunks = structure_parsing.xyz_to_chunks(args.input_file_name, args.process)
-    temp_dir = f'{os.environ.get("TEMP_DIR")}/{os.getpid()}'
-    os_operation.make_temp_dir(temp_dir, delete=args.temp)
-
-    for index, chunk in enumerate(chunks):
-        t = multiprocessing.Process(target=hb_count, args=[chunk, args.index, cell, f'{temp_dir}/chunk_{index}.temp'])
-        t.start()
-
-    for t in multiprocessing.active_children():
-        t.join()
-
-    chunks_array_list = []
-    for i in range(len(chunks)):
-        chunk_array = np.load(f'{temp_dir}/chunk_{i}.temp.npy')
-        chunks_array_list.append(chunk_array)
-    chunks_array = np.vstack(chunks_array_list)
-    chunks_array = np.mean(chunks_array, axis=1)
-
-    with open(output, 'w') as f:
-        f.write(f"# {args.index}\n")
-        f.write(f"accepter : {chunks_array[0]:.2f}\n")
-        f.write(f"donor    : {chunks_array[1]:.2f}\n")
-        f.write(f"total    : {chunks_array[0]+chunks_array[1]:.2f}\n")
-    print(f"# {args.index}")
-    print(f"accepter : {chunks_array[0]:.2f}")
-    print(f"donor    : {chunks_array[1]:.2f}")
-    print(f"total    : {chunks_array[0]+chunks_array[1]:.2f}")
-
-
-if __name__ == '__main__':
-    main()

mdkits/cli/hb_distribution.py

@@ -1,126 +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.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/cli/packmol_input.py

@@ -1,76 +0,0 @@
-import argparse
-
-
-def parse_cell(s):
-    return [float(x) for x in s.replace(',', ' ').split()]
-
-
-def parse_argument():
-    parser = argparse.ArgumentParser(description='generate packmol input file with give parameter')
-    parser.add_argument('--size', type=int, help='water size default is 30', default=30)
-    parser.add_argument('--cell', type=parse_cell, help='input box size(a,b,c)')
-    parser.add_argument('--addwat', type=int, help='add some additional water, default is 0', default=0)
-    parser.add_argument('--ioncon', type=float, help='concentration of sol box, default is 0.0', default=0.0)
-    parser.add_argument('--tolerance', type=float, help='tolerance of packmol, default is 2.5', default=2.5)
-    parser.add_argument('--watpath', type=str, help='water xyz file path', default='C:\\home\\.can\\temp\\packmol\\default\\water.xyz')
-    parser.add_argument('--ionpath', type=str, help='ion xyz file path')
-    parser.add_argument('-o', type=str, help='output file name, default is "input.pm"', default='input.pm')
-    parser.add_argument('--output', type=str, help='output file name of packmol, default is "solbox.xyz"', default='solbox.xyz')
-
-    return parser.parse_args()
-
-
-def get_water_number():
-    water_number = water_volume / water_size
-
-    return int(round(water_number, 0))
-
-
-def get_ion_number(concentration):
-    ion_number = ( (concentration * avogadro) / 1e+27 ) * water_volume
-
-    return int(round(ion_number, 0))
-
-
-def main():
-    global water_volume, water_size, avogadro
-    args = parse_argument()
-    water_volume = args.cell[0] * args.cell[1] * args.cell[2]
-    water_size = args.size
-    avogadro = 6.02214179e+23
-    water_number = get_water_number() + args.addwat
-    ion_number = get_ion_number(args.ioncon)
-
-    if ion_number == 0:
-        packmol_input_str = f"""
-        tolerance {args.tolerance}
-        filetype xyz
-        output {args.output}
-        pbc {args.cell[3]} {args.cell[4]} {args.cell[5]}
-        structure {args.watpath}
-          number {water_number}
-          inside box 2. 2. 2. {args.cell[0]-2} {args.cell[1]-2} {args.cell[2]-2}
-        end structure
-        """
-    else:
-        packmol_input_str = f"""
-        tolerance {args.tolerance}
-        filetype xyz
-        output {args.output}
-        pbc {args.cell[3]} {args.cell[4]} {args.cell[5]}
-        structure {args.watpath}
-          number {water_number}
-          inside box 2. 2. 2. {args.cell[0]-2} {args.cell[1]-2} {args.cell[2]-2}
-        end structure
-        structure {args.ionpath}
-          number {ion_number}
-          inside box 2. 2. 2. {args.cell[0]-2} {args.cell[1]-2} {args.cell[2]-2}
-        end structure
-        """
-
-    with open(args.o, 'w') as f:
-        f.write(packmol_input_str)
-
-
-if __name__ == '__main__':
-    main()

mdkits-0.1.13.dist-info/METADATA

@@ -1,226 +0,0 @@
-Metadata-Version: 2.3
-Name: mdkits
-Version: 0.1.13
-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)
-Project-URL: Repository, https://github.com/jxxcr/mdkits
-Description-Content-Type: text/markdown
-
-# MD 轨迹分析脚本
-`mdkits` 提供了多种工具, 安装脚本:
-```bash
-pip install mdkits --upgrade
-```
-
-### 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):
-```bash
-mdkits density [FILENAME] --element="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
-```
-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"
-```
-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"
-```
-输出的文件名为`density_water.dat`.
-
-### 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
-mdkits wrap [FILENAME] 
-```
-或指定`cp2k`的输入文件:
-```bash
-mdkits wrap [FILENAME] --cp2k_input_file setting.inp
-```
-或指定晶胞参数:
-```bash
-mdkits wrap [FILENAME] --cell 10,10,10
-```
-默认的`[FILENAME]`为`*-pos-1.xyz`
-
-## DFT 性质分析脚本
-### 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
-```
-
-### 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]
-```
-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
-```
-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
-
-### 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
-```
-
-## 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`extracted.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
-```
-
-### 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
-```

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