mdkits 0.2.2__tar.gz → 1.0.0__tar.gz

{mdkits-0.2.2 → mdkits-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.2.2
+Version: 1.0.0
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -121,6 +121,13 @@ mdkits md wrap [FILENAME] --cell 10,10,10
 ```
 默认的`[FILENAME]`为`*-pos-1.xyz`
 
+### 振动态密度(VDOS)
+`vac`用于分析轨迹的速度自相关函数, 同时计算速度自相关函数的傅里叶变换, 即振动动态密度(VDOS), 如分析体系中的VDOS:
+```bash
+mdkits md vac h2o-vel-1.xyz
+```
+默认的`[FILENAME]`为`*-vel-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
@@ -235,7 +242,7 @@ mdkits build supercell Li3PO4.cif 2 2 2
 ```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):
+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`frames_-1.xyz`(`extract`的默认行为):
 ```bash
 mdkits extract
 ```
@@ -243,6 +250,10 @@ mdkits extract
 ```bash
 mdkits extract -cr ::50
 ```
+提取部分元素的位置, 如提取`O`元素和`H`元素的位置:
+```bash
+mdkits extract --select "name O or name H"
+```
 
 ### 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`:

{mdkits-0.2.2 → mdkits-1.0.0}/README.md

@@ -94,6 +94,13 @@ mdkits md wrap [FILENAME] --cell 10,10,10
 ```
 默认的`[FILENAME]`为`*-pos-1.xyz`
 
+### 振动态密度(VDOS)
+`vac`用于分析轨迹的速度自相关函数, 同时计算速度自相关函数的傅里叶变换, 即振动动态密度(VDOS), 如分析体系中的VDOS:
+```bash
+mdkits md vac h2o-vel-1.xyz
+```
+默认的`[FILENAME]`为`*-vel-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
@@ -208,7 +215,7 @@ mdkits build supercell Li3PO4.cif 2 2 2
 ```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):
+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`frames_-1.xyz`(`extract`的默认行为):
 ```bash
 mdkits extract
 ```
@@ -216,6 +223,10 @@ mdkits extract
 ```bash
 mdkits extract -cr ::50
 ```
+提取部分元素的位置, 如提取`O`元素和`H`元素的位置:
+```bash
+mdkits extract --select "name O or name H"
+```
 
 ### 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`:

{mdkits-0.2.2 → mdkits-1.0.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.2.2"
+version = "1.0.0"
 description = "kits for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

{mdkits-0.2.2 → mdkits-1.0.0}/src/mdkits/dft_cli/pdos.py

@@ -12,6 +12,7 @@ from mdkits.util import os_operation
 @click.option('-t', '--type', type=str, default='total', show_default=True)
 @click.option('-c', '--clos', type=tuple)
 def main(filename, type, clos):
+    """analysis cp2k pdos file"""
     if type == 'total':
         dos_obj = Cp2kPdos(filename[0])
         dos, ener = dos_obj.get_raw_dos(dos_type=type)

{mdkits-0.2.2 → mdkits-1.0.0}/src/mdkits/md_cli/angle.py

@@ -63,7 +63,7 @@ class Angle_distribution(AnalysisBase):
     def _single_frame(self):
         surface = numpy_geo.find_surface(self.surface_group.positions[:, 2])
 
-        if len(surface) == 1:
+        if surface[1] == 0:
             o_group = self.atomgroup.select_atoms(f"name O and prop z < {surface[0]+self.water_height}", updating=True)
         else:
             o_group = self.atomgroup.select_atoms(f"name O and (prop z < {surface[0]+self.water_height} or prop z > {surface[1]-self.water_height})", updating=True)

{mdkits-0.2.2 → mdkits-1.0.0}/src/mdkits/md_cli/dipole.py

@@ -89,7 +89,11 @@ class Dipole_distribution(AnalysisBase):
             bins_z = np.arange(len(average_dipole)) * self.bin_size
 
             if self.surface:
-                lower_z, upper_z = self.surface_pos / self.frame_count
+                lower_z = self.surface_pos[0] / self.frame_count
+                if self.surface_pos[1] == 0:
+                    upper_z = np.inf
+                else:
+                    upper_z = self.surface_pos[1] / self.frame_count
 
                 mask = (bins_z >= lower_z) & (bins_z <= upper_z)
                 filtered_bins_z = bins_z[mask] - lower_z

{mdkits-0.2.2 → mdkits-1.0.0}/src/mdkits/md_cli/hb_distribution.py

@@ -123,8 +123,7 @@ class Hb_distribution(AnalysisBase):
         if self.surface_group:
             surface = numpy_geo.find_surface(self.surface_group.positions[:, 2])
             self.surface_pos[0] += surface[0]
-            if len(surface) > 1:
-                self.surface_pos[1] += surface[1]
+            self.surface_pos[1] += surface[1]
 
         self.frame_count += 1
 
@@ -138,10 +137,12 @@ class Hb_distribution(AnalysisBase):
             bins_z = np.arange(len(self.donor)) * self.bin_size
 
             if self.surface:
-                surface = self.surface_pos/self.frame_count
-                lower_z = surface[0]
-                if surface[1] ==0:
+                lower_z = self.surface_pos[0] / self.frame_count
+                if self.surface_pos[1] == 0:
                     upper_z = np.inf
+                else:
+                    upper_z = self.surface_pos[1] / self.frame_count
+
                 mask = (bins_z >= lower_z) & (bins_z <= upper_z)
                 filtered_bins_z = bins_z[mask] - lower_z
                 filtered_average_accepter = average_accepter[mask]

{mdkits-0.2.2 → mdkits-1.0.0}/src/mdkits/md_cli/vac.py

@@ -33,17 +33,15 @@ class Velocity_AutoCorrelation(AnalysisBase):
         self.cvv = np.array(self.cvv)
 
         sf = self.cvv.shape[0]
-        f = np.abs(np.fft.fft(self.cvv))
+        fftraj = np.fft.rfft(self.cvv)
+        fdos = np.abs(fftraj)
 
-        faxis = np.fft.fftfreq(sf, d=1/sf)
-        pf = np.where(faxis>0)
-        faxis = faxis[pf]
-        f = f[pf]
+        faxis = np.fft.rfftfreq(sf, d=1/sf)
 
         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')
+        np.savetxt('freq.dat', np.column_stack((faxis, fdos)), fmt='%.5f', header="freq\tabundance")
 
 
 @click.command(name="vac")
@@ -51,7 +49,7 @@ class Velocity_AutoCorrelation(AnalysisBase):
 @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"""
+    """analysis velocity autocorrelation function and frequency"""
     a = Velocity_AutoCorrelation(filename, select)
 
     if r is not None: