mdkits 0.2.1__py3-none-any.whl → 1.0.0__py3-none-any.whl

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/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/md_cli/density.py

@@ -82,8 +82,7 @@ class Density_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
 
@@ -102,6 +101,8 @@ class Density_distribution(AnalysisBase):
                 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/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/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/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:

mdkits/util/numpy_geo.py

@@ -112,7 +112,7 @@ def find_surface(surface_group:np.ndarray, layer_tolerance=0.05, surface_toleran
         layer_mean.append(np.mean(current_layer))
     
     if len(layer_mean) == 1:
-        return [layer_mean[0]]
+        return [layer_mean[0], 0]
 
     diff = np.diff(layer_mean)
     if np.any(diff > surface_tolerance):
@@ -120,5 +120,5 @@ def find_surface(surface_group:np.ndarray, layer_tolerance=0.05, surface_toleran
         return (layer_mean[index], layer_mean[index + 1])
     else:
         if layer_mean[-1] > layer_mean[0]:
-            return [layer_mean[-1]]
+            return [layer_mean[-1], 0]
         return (layer_mean[-1], layer_mean[0])

{mdkits-0.2.1.dist-info → mdkits-1.0.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.2.1
+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-0.2.1.dist-info → mdkits-1.0.0.dist-info}/RECORD

@@ -17,17 +17,17 @@ mdkits/config/__init__.py,sha256=ZSwmnPK02LxJLMgcYmNb-tIOk8fEuHf5jpqD3SDHWLg,103
 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=cfhI6dsn_hIy-YXSTXemu1m1O_l2HuL_x6zx_3uL-Uw,5450
-mdkits/md_cli/density.py,sha256=BL49331ulgrIpo1w4KowZHEsnLIioO46b1ZhuqVLSms,5258
-mdkits/md_cli/dipole.py,sha256=tXTO8CZAQTVY55GwuXWJNGo7EQ4Tb2611g5IHucdlec,4836
-mdkits/md_cli/hb_distribution.py,sha256=ForMmNjfJxpXHqo1Au0OXOmwgvHxIuVR8qnpu3iS7Eg,7897
+mdkits/dft_cli/pdos.py,sha256=EjZ1oWJHHUocZAZe8dgJUu6bkLPVwgrKkggidF3yduE,1445
+mdkits/md_cli/angle.py,sha256=dS3qMreC-vIrwa5LAaZQ9lRPYuwUAe14_8ZDkntujl0,5448
+mdkits/md_cli/density.py,sha256=br8jq_qlkKwJr_wkdKGHCYbg16TmGPjasX5LI9E55yk,5312
+mdkits/md_cli/dipole.py,sha256=Q2Bp42gB00Q1mxrHgmYbhkLT1w3uVNHMmjA_93TF-V8,5007
+mdkits/md_cli/hb_distribution.py,sha256=aoB6Yk1a4agPLEravjkvJ3llNJAroZbSgQ8vNoNSex8,7930
 mdkits/md_cli/md_cli.py,sha256=2vH04o_3d5kCJsn3qEq-iUPhebKJOrS-e7HJtyiZTiQ,571
 mdkits/md_cli/monitor.py,sha256=JNEgz5RGbFn4x_E85pAiPUY1NVIyZ3b2vjpBk_d1dR8,4536
 mdkits/md_cli/msd.py,sha256=v-9TPKBGHz6ce2PUwexrekVq_9eiutIOQYaw582yN30,965
 mdkits/md_cli/rdf.py,sha256=p4HMMYZLfFRPnGx7YHQU6kZnMAfoL6vOyOVpZhfdBfM,1712
 mdkits/md_cli/setting.py,sha256=mxMTYpm6DUjMt9hOKsJbBSKwCqzMilOR0bo1azSdJP0,846
-mdkits/md_cli/vac.py,sha256=eIVRF5ADHLwWp50gv0VoAxT0UCXpzLcD57f3TQM6Hxs,2135
+mdkits/md_cli/vac.py,sha256=MJi_uftl0UUqhWvqDtcr14qtcRgYRd6X0VSg4J5MFN8,2133
 mdkits/md_cli/wrap.py,sha256=YdUpvhRyKn7bYnIAVgP39qItPdrEoTeJl55TmbS7Qqk,1044
 mdkits/mdkits.py,sha256=EiAt7dxGTaHuuj7bCNxgAqZbX0i3sldO0mBxOG-aMnY,595
 mdkits/util/.fig_operation.py.swp,sha256=iZYqdYMj4UKS1rmbXv8Ve2FcVBcNljX7Y43-neMdPSk,12288
@@ -37,12 +37,12 @@ mdkits/util/cp2k_input_parsing.py,sha256=7NMVOYEGycarokLJlhLoWWilciM7sd8MWp5FVTF
 mdkits/util/encapsulated_ase.py,sha256=uhqIhsALxzwJYuFrfOYGGC6U0QLm_dcZNridvfl_XGc,4339
 mdkits/util/encapsulated_mda.py,sha256=m3i-XrcscMcM5V7JzLnor3JtAOfuDx3LLMl0tZt0n-w,2325
 mdkits/util/fig_operation.py,sha256=FwffNUtXorMl6qE04FipgzcVljEQii7wrNJUCJMyY3E,1045
-mdkits/util/numpy_geo.py,sha256=zkh3uNC3HGHIwtHOmiDXborab5_40PmaJF54jSQ-njU,3874
+mdkits/util/numpy_geo.py,sha256=B2QVADl1M8iixZrIOre2UUhHqvAeghvM8Q2woEQsH3Q,3880
 mdkits/util/os_operation.py,sha256=ErN2ExjX9vZRfPe3ypsj4eyoQTEePqzlEX0Xm1N4lL4,980
 mdkits/util/out_err.py,sha256=7vGDI7wVoJWe1S0BDbcq-UC2KAhblCzg-NAYZKBZ4lo,900
 mdkits/util/structure_parsing.py,sha256=mRPMJeih3O-ST7HeETDvBEkfV-1psT-XgxyYgDadV0U,4152
-mdkits-0.2.1.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
-mdkits-0.2.1.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
-mdkits-0.2.1.dist-info/METADATA,sha256=9_oMWmA5-UybFknSf90G5lAkytDGKsglzXKD7dvRo3s,10963
-mdkits-0.2.1.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-mdkits-0.2.1.dist-info/RECORD,,
+mdkits-1.0.0.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
+mdkits-1.0.0.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
+mdkits-1.0.0.dist-info/METADATA,sha256=Z2GyGDkAg9qgs7DmgDwA2mcgkA6aXOZHAiHlIFwRcSs,11351
+mdkits-1.0.0.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+mdkits-1.0.0.dist-info/RECORD,,