mdkits 0.1a3__tar.gz → 0.1a6__tar.gz

{mdkits-0.1a3 → mdkits-0.1a6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1a3
+Version: 0.1a6
 Summary: tools for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -24,9 +24,9 @@ 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:
+`mdkits` 提供了多种工具, 安装脚本:
 ```bash
-pip install mdtool --upgrade
+pip install mdkits --upgrade
 ```
 ### 密度分布
 
@@ -49,15 +49,15 @@ pip install mdtool --upgrade
 ### 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] 
+mdkits wrap [FILENAME] 
 ```
 或指定`cp2k`的输入文件:
 ```bash
-mdtool wrap [FILENAME] --cp2k_input_file setting.inp
+mdkits wrap [FILENAME] --cp2k_input_file setting.inp
 ```
 或指定晶胞参数:
 ```bash
-mdtool wrap [FILENAME] --cell 10,10,10
+mdkits wrap [FILENAME] --cell 10,10,10
 ```
 默认的`[FILENAME]`为`*-pos-1.xyz`
 
@@ -72,29 +72,29 @@ mdtool wrap [FILENAME] --cell 10,10,10
 ### 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
+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
-mdtool extract
+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
-mdtool extract -cr ::50
+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
-mdtool convert -c structure.xyz --cell 10,10,10
+mdkits convert -c structure.xyz --cell 10,10,10
 ```
 将`structure.cif`转换为`POSCAR`:
 ```bash
-mdtool convert -v structure.cif
+mdkits convert -v structure.cif
 ```
 将`structure.cif`转换为`structure_xyz.xyz`:
 ```bash
-mdtool convert -c structure.cif -o structure_xyz
+mdkits convert -c structure.cif -o structure_xyz
 ```
 
 ### 数据处理
@@ -153,9 +153,9 @@ figure2:
 
 `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
+mdkits plot *.yaml
 ```
 和:
 ```bash
-mdtool plot *.yaml --error
+mdkits plot *.yaml --error
 ```

{mdkits-0.1a3 → mdkits-0.1a6}/README.md

@@ -1,7 +1,7 @@
 # MD 轨迹分析脚本
-`mdtool` 提供了多种工具, 安装脚本:
+`mdkits` 提供了多种工具, 安装脚本:
 ```bash
-pip install mdtool --upgrade
+pip install mdkits --upgrade
 ```
 ### 密度分布
 
@@ -24,15 +24,15 @@ pip install mdtool --upgrade
 ### 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] 
+mdkits wrap [FILENAME] 
 ```
 或指定`cp2k`的输入文件:
 ```bash
-mdtool wrap [FILENAME] --cp2k_input_file setting.inp
+mdkits wrap [FILENAME] --cp2k_input_file setting.inp
 ```
 或指定晶胞参数:
 ```bash
-mdtool wrap [FILENAME] --cell 10,10,10
+mdkits wrap [FILENAME] --cell 10,10,10
 ```
 默认的`[FILENAME]`为`*-pos-1.xyz`
 
@@ -47,29 +47,29 @@ mdtool wrap [FILENAME] --cell 10,10,10
 ### 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
+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
-mdtool extract
+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
-mdtool extract -cr ::50
+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
-mdtool convert -c structure.xyz --cell 10,10,10
+mdkits convert -c structure.xyz --cell 10,10,10
 ```
 将`structure.cif`转换为`POSCAR`:
 ```bash
-mdtool convert -v structure.cif
+mdkits convert -v structure.cif
 ```
 将`structure.cif`转换为`structure_xyz.xyz`:
 ```bash
-mdtool convert -c structure.cif -o structure_xyz
+mdkits convert -c structure.cif -o structure_xyz
 ```
 
 ### 数据处理
@@ -128,9 +128,9 @@ figure2:
 
 `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
+mdkits plot *.yaml
 ```
 和:
 ```bash
-mdtool plot *.yaml --error
+mdkits plot *.yaml --error
 ```

{mdkits-0.1a3 → mdkits-0.1a6}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.1.a3"
+version = "0.1.a6"
 description = "tools for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

{mdkits-0.1a3 → mdkits-0.1a6}/src/mdkits/cli/cmdline.py

@@ -2,9 +2,9 @@
 import click
 from click import Context
 
-from mdtool import __version__
-from mdtool.config import settings
-from mdtool.log import init_log
+from mdkits import __version__
+from mdkits.config import settings
+from mdkits.log import init_log
 
 
 @click.group(invoke_without_command=True)

{mdkits-0.1a3 → mdkits-0.1a6}/src/mdkits/cli/convert.py

@@ -3,7 +3,7 @@
 from ase.io import write
 import click
 import os
-from mdtool.util import encapsulated_ase, arg_type
+from mdkits.util import encapsulated_ase, arg_type
 
 
 @click.command(name='convert')

{mdkits-0.1a3 → mdkits-0.1a6}/src/mdkits/cli/density.py

@@ -5,13 +5,18 @@ import click
 import MDAnalysis
 from MDAnalysis import Universe
 from MDAnalysis.analysis.base import AnalysisBase
-from mdtool.util import cp2k_input_parsing, numpy_geo, encapsulated_mda
+from mdkits.util import (
+    arg_type,
+    numpy_geo,
+    encapsulated_mda,
+    os_operation,
+)
 import warnings
 warnings.filterwarnings("ignore")
 
 
 class Density_distribution(AnalysisBase):
-    def __init__(self, filename, cell, o, distance_judg, angle_judg, dt=0.001, bin_size=0.2, return_index=False):
+    def __init__(self, filename, cell, o, element, density, update_water, distance_judg, angle_judg, surface, dt=0.001, bin_size=0.2, return_index=False):
         u = Universe(filename)
         u.trajectory.ts.dt = dt
         u.dimensions = cell
@@ -25,21 +30,31 @@ class Density_distribution(AnalysisBase):
         self.bin_size = bin_size
         self.frame_count = 0
         self.return_index = return_index
+        self.surface = surface
+        self.element = element
+        self.density = density
+        self.update_water = update_water
+
+        if surface is not None:
+            self.surface_group = self.atomgroup.select_atoms(f"{surface}")
+        else:
+            self.surface_group = False
 
         super(Density_distribution, self).__init__(self.atomgroup.universe.trajectory, verbose=True)
 
     def _prepare(self):
         self.bin_num = int(self.u.dimensions[2] / self.bin_size) + 2
         self.density_distribution = np.zeros(self.bin_num, dtype=np.float64)
-        if self.surface:
-            self.surface_pos = ()
+        if self.surface_group:
+            self.surface_pos = np.zeros(2)
 
     def _append(self, z):
         bins = np.floor(z / self.bin_size).astype(int) + 1
         np.add.at(self.density_distribution, bins, 1)
 
+
     def _single_frame(self):
-        if self.water:
+        if self.update_water:
             o_group = self.atomgroup.select_atoms("name O")
             h_group = self.atomgroup.select_atoms("name H")
 
@@ -48,40 +63,58 @@ class Density_distribution(AnalysisBase):
             self._append(o.positions[:, 2])
 
         else:
-            group = self.atomgroup.select_atoms(f"name {self.element}")
+            group = self.atomgroup.select_atoms(f"{self.element}")
             self._append(group.positions[:, 2])
 
-        self.
+        if self.surface_group:
+            lower_z, upper_z = numpy_geo.find_surface(self.surface_group.positions[:, 2], layer_tolerance=1, surface_tolerance=5)
+            self.surface_pos[0] += lower_z
+            self.surface_pos[1] += upper_z
+
         self.frame_count += 1
 
     def _conclude(self):
         if self.frame_count > 0:
             V = self.u.dimensions[0] * self.u.dimensions[1] * self.bin_size
 
-            if self.water:
-                density_distribution = (self.density_distribution * (15.999+1.008*2) * 1.660539 / V) / self.frame_count
+            if self.density:
+                density_distribution = (self.density_distribution * self.density * 1.660539 / V) / self.frame_count
             else:
                 density_distribution = (self.density_distribution * (10000/6.02) / V) / self.frame_count
 
             bins_z = np.arange(len(self.density_distribution)) * self.bin_size
 
-            surface = self.find_surface(self.atomgroup.select_atoms("name Pt"))
+            if self.surface:
+                lower_z = self.surface_pos[0] / self.frame_count
+                upper_z = self.surface_pos[1] / self.frame_count
 
-            lower_z, upper_z = surface
-            mask = (bins_z >= lower_z) & (bins_z <= upper_z)
-            filtered_bins_z = bins_z[mask] - lower_z
-            filtered_density_distribution = density_distribution[mask]
-            conbined_data = np.column_stack((filtered_bins_z, filtered_density_distribution))
+                mask = (bins_z >= lower_z) & (bins_z <= upper_z)
+                filtered_bins_z = bins_z[mask] - lower_z
+                filtered_density_distribution = density_distribution[mask]
+
+                conbined_data = np.column_stack((filtered_bins_z, filtered_density_distribution))
+            else:
+                conbined_data = np.column_stack((bins_z, density_distribution))
 
             np.savetxt(self.o, conbined_data, header="Z\tdensity", fmt='%.5f', delimiter='\t')
 
 @click.command(name='density')
 @click.argument('filename', type=click.Path(exists=True), default=os_operation.default_file_name('*-pos-1.xyz', last=True))
-@click.option('--cell', type=arg_type.Cell, help='set xyz file cell, --cell x,y,z,a,b,c')
 @click.option('--cell', type=arg_type.Cell, help='set cell from cp2k input file or a list of lattice: --cell x,y,z or x,y,z,a,b,c', default='input.inp', show_default=True)
+@click.option('--element', type=str, help='element to analysis')
+@click.option('--density', type=float, help='output density unit (g/cm3), should give atomic mass of element, else is concentration unit (mol/L)')
 @click.option('-o', type=str, help='output file name', default='density.dat', show_default=True)
-def main(filename, cell, o):
-    density_dist = Density_distribution(filename, cell, o=o)
+@click.option('--update_water', is_flag=True, help='update water with distance or angle judgment')
+@click.option('--distance', type=float, help='update water distance judgment', default=1.2, show_default=True)
+@click.option('--angle', type=(float), help='update water angle judgment')
+@click.option('--surface', type=str, help='surface element')
+def main(filename, cell, o, element, density, update_water, distance, angle, surface):
+    """
+    analysis density or concentration of element in a trajectory file
+    """
+
+    density_dist = Density_distribution(filename, cell, o=o, distance_judg=distance, angle_judg=angle, element=element, density=density, update_water=update_water, surface=surface)
+
     density_dist.run()
 
 

{mdkits-0.1a3 → mdkits-0.1a6}/src/mdkits/cli/extract.py

@@ -4,7 +4,7 @@
 
 import os
 import click
-from mdtool.util import os_operation, arg_type
+from mdkits.util import os_operation, arg_type
 import MDAnalysis
 from MDAnalysis import Universe
 

{mdkits-0.1a3 → mdkits-0.1a6}/src/mdkits/cli/log.py

@@ -3,7 +3,7 @@ import logging
 import os
 from logging.config import dictConfig
 
-from mdtool.config import settings
+from mdkits.config import settings
 
 os.makedirs(settings.LOGPATH, exist_ok=True)
 

{mdkits-0.1a3 → mdkits-0.1a6}/src/mdkits/cli/plot.py

@@ -6,7 +6,7 @@ from matplotlib import pyplot as plt
 from matplotlib import rcParams
 import matplotlib.ticker as ticker
 import yaml, click
-from mdtool.util import fig_operation
+from mdkits.util import fig_operation
 
 DEFAULT_CONFIG = {
         'data': {},

{mdkits-0.1a3 → mdkits-0.1a6}/src/mdkits/cli/wrap.py

@@ -3,7 +3,7 @@
 import os
 from MDAnalysis import Universe
 import MDAnalysis, click
-from mdtool.util import (
+from mdkits.util import (
     arg_type,
     os_operation,
     cp2k_input_parsing

{mdkits-0.1a3 → mdkits-0.1a6}/src/mdkits/config/__init__.py

@@ -18,17 +18,17 @@ _settings_files = [
 
 # User configuration. It will be created automatically by the pip installer .
 _external_files = [
-    Path(sys.prefix, 'etc', 'mdtool', 'settings.yml')
+    Path(sys.prefix, 'etc', 'mdkits', 'settings.yml')
 ]
 
 
 settings = Dynaconf(
-    # Set env `MDTOOL_FOO='bar'`，use `settings.FOO` .
-    envvar_prefix='MDTOOL',
+    # Set env `mdkits_FOO='bar'`，use `settings.FOO` .
+    envvar_prefix='mdkits',
     settings_files=_settings_files,  # load user configuration.
     # environments=True,  # Enable multi-level configuration，eg: default, development, production
     load_dotenv=True,  # Enable load .env
-    # env_switcher='MDTOOL_ENV',
+    # env_switcher='mdkits_ENV',
     lowercase_read=False,  # If true, can't use `settings.foo`, but can only use `settings.FOO`
     includes=_external_files,  # Customs settings.
     base_dir=_base_dir,  # `settings.BASE_DIR`

{mdkits-0.1a3 → mdkits-0.1a6}/src/mdkits/config/settings.yml

@@ -1,4 +1,4 @@
 verbose: false
 debug: false
 loglevel: warning
-logpath: /tmp/mdtool
+logpath: /tmp/mdkits

{mdkits-0.1a3 → mdkits-0.1a6}/src/mdkits/mdkits.py

@@ -5,6 +5,7 @@ from mdkits.cli import (
     extract,
     data,
     plot,
+    density
 )
 
 
@@ -12,7 +13,6 @@ from mdkits.cli import (
 @click.pass_context
 @click.version_option()
 def cli(ctx):
-    print(ctx)
     """tools for md or dft"""
     pass
 
@@ -22,6 +22,7 @@ cli.add_command(wrap.main)
 cli.add_command(extract.main)
 cli.add_command(data.main)
 cli.add_command(plot.main)
+cli.add_command(density.main)
 
 
 if __name__ == '__main__':

{mdkits-0.1a3 → mdkits-0.1a6}/src/mdkits/util/numpy_geo.py

@@ -97,7 +97,7 @@ def unwrap(atom1, atom2, coefficients, max=0, total=False):
 
 
 def find_surface(surface_group:np.ndarray, layer_tolerance=1, surface_tolerance=5):
-    sort_group = surface_group.sort()
+    sort_group = np.sort(surface_group)
     layer_mean = []
     current_layer = [sort_group[0]]
     for i in range(1, len(sort_group)):
@@ -106,6 +106,7 @@ def find_surface(surface_group:np.ndarray, layer_tolerance=1, surface_tolerance=
         else:
             layer_mean.append(np.mean(current_layer))
             current_layer = [sort_group[i]]
+        layer_mean.append(np.mean(current_layer))
     
     if len(current_layer) == 1:
         return layer_mean[0]
@@ -115,4 +116,4 @@ def find_surface(surface_group:np.ndarray, layer_tolerance=1, surface_tolerance=
         index = np.argmax(diff > 5)
         return (layer_mean[index], layer_mean[index + 1])
     else:
-        return layer_mean[-1]
+        return (layer_mean[-1], layer_mean[0])