mdkits 0.1.1__tar.gz → 0.1.3__tar.gz

{mdkits-0.1.1 → mdkits-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.1
+Version: 0.1.3
 Summary: tools for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -81,10 +81,21 @@ mdkits wrap [FILENAME] --cell 10,10,10
 
 ## 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
+```
 
-### 静电势
-
-### 电荷差分
+### 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.
 
 ## 其他
 ### 轨迹提取

{mdkits-0.1.1 → mdkits-0.1.3}/README.md

@@ -56,10 +56,21 @@ mdkits wrap [FILENAME] --cell 10,10,10
 
 ## 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
+```
 
-### 静电势
-
-### 电荷差分
+### 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.
 
 ## 其他
 ### 轨迹提取

{mdkits-0.1.1 → mdkits-0.1.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.1.1"
+version = "0.1.3"
 description = "tools for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

mdkits-0.1.3/src/mdkits/cli/cube.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+
+import numpy as np
+import click
+from mdkits.util import encapsulated_ase, os_operation
+
+
+def ave_cube_data(cube_data, range):
+	mask = (cube_data[:,0] >= range[0]) & (cube_data[:,0] <=range[1])
+	bulk_cube_data = cube_data[mask]
+	ave_cube_data = np.mean(bulk_cube_data[:,1])
+	return ave_cube_data
+
+
+@click.command(name='cube')
+@click.argument('filename', type=click.Path(exists=True), default=os_operation.default_file_name('*.cube', last=True))
+@click.option('-b', '--bulk_range', type=(float, float), help='parameter to calculate mean value of bulk', default=None)
+@click.option('-o', type=str, help='output file name, default is "cube.out"', default='cube.out', show_default=True)
+def main(filename, bulk_range, o):
+	"""
+	analysis cube file
+	"""
+
+	cube_data = encapsulated_ase.ave_cube(filename)
+
+	## if bulk range is exit, out put a difference of cube_data
+	if bulk_range is not None:
+		bulk_cube_data = ave_cube_data(cube_data, bulk_range)
+		print(bulk_cube_data)
+		np.savetxt(o, cube_data, header=f'Z\tcube_data\t area average is: {bulk_cube_data}')
+	
+	else:
+		np.savetxt(o, cube_data, header='Z\tcube_data')
+
+	
+
+
+if __name__ == '__main__':
+	main()

mdkits-0.1.3/src/mdkits/cli/pdos.py

@@ -0,0 +1,37 @@
+#!/usr/bin/env python3
+
+from cp2kdata import Cp2kPdos
+import click
+import numpy as np
+from mdkits.util import os_operation
+
+
+# set argument
+@click.command(name='pdos')
+@click.argument('filename', type=list, default=os_operation.default_file_name('*-k*.pdos'))
+@click.option('-t', '--type', type=str, default='total', show_default=True)
+@click.option('-c', '--clos', type=tuple)
+def main(filename, type, clos):
+    if type == 'total':
+        dos_obj = Cp2kPdos(filename[0])
+        dos, ener = dos_obj.get_raw_dos(dos_type=type)
+        print(f"analysis of total dos is done")
+        np.savetxt('total.pdos', np.column_stack((ener, dos)), header='energy\tdos')
+    else:
+        if type:
+            for file in filename:
+                dos_obj = Cp2kPdos(file)
+                dos, ener = dos_obj.get_raw_dos(dos_type=type)
+                print(f"analysis of {file}'s {type} dos is done")
+                np.savetxt(f'{dos_obj.read_dos_element()}_{type}.pdos', np.column_stack((ener, dos)), header='energy\tdos')
+
+        if clos:
+            for file in filename:
+                dos_obj = Cp2kPdos(file)
+                dos, ener = dos_obj.get_raw_dos(usecols=clos)
+                print(f"analysis of {file}'s {type} dos is done")
+                np.savetxt(f'{dos_obj.read_dos_element()}_{"_".join(clos)}.pdos', np.column_stack((ener, dos)), header='energy\tdos')
+
+
+if __name__ == '__main__':
+    main()

{mdkits-0.1.1 → mdkits-0.1.3}/src/mdkits/mdkits.py

@@ -5,7 +5,9 @@ from mdkits.cli import (
     extract,
     data,
     plot,
-    density
+    density,
+    cube,
+    pdos,
 )
 
 
@@ -23,6 +25,8 @@ cli.add_command(extract.main)
 cli.add_command(data.main)
 cli.add_command(plot.main)
 cli.add_command(density.main)
+cli.add_command(cube.main)
+cli.add_command(pdos.main)
 
 
 if __name__ == '__main__':

{mdkits-0.1.1 → mdkits-0.1.3}/src/mdkits/util/encapsulated_ase.py

@@ -65,13 +65,13 @@ def rdf(chunk, cell, bin_size, name, parallel=True):
     ana.clear_cache()
 
 
-def ave_potential(filepath):
+def ave_cube(filepath):
     """
     function: average hartree file in z_coordinate
     parameter:
         filepath: hartree cube file path
     return:
-        z_potential: a list of potential alone z axes
+        z_cube_data: a list of cube data alone z axes
         z_coordinates: a list of coordinates of z axes
     """
     # read data from filepath
@@ -81,8 +81,8 @@ def ave_potential(filepath):
     step_size = atoms.cell[2, 2] / ( npoints - 1 )
     # average hartree file, and calculate z_coordinates
     z_coordinates = [i * step_size for i in range(npoints)]
-    z_potential = 27.2114 * data[:, :, :].sum(axis=(0, 1)) / ( data.shape[0] * data.shape[1] )
-    return z_potential, z_coordinates
+    z_cube_data = data[:, :, :].sum(axis=(0, 1)) / ( data.shape[0] * data.shape[1] )
+    return np.column_stack((z_coordinates, z_cube_data))
 
 
 def atoms_read_with_cell(file_name, cell=None, coord_mode=False, default_cell=np.array([0., 0., 0., 90., 90., 90.])):

mdkits-0.1.1/src/mdkits/cli/cube.py

@@ -1,59 +0,0 @@
-#!/usr/bin/env python3
-
-################################################
-# averange cp2k output(or some else file correspond to ase.io.read_cube_data) hartree.cube to z coordinate with python
-## file path is need to pay attention
-## cycle parameter is need to pay attention
-## buck range is need to pay attention
-################################################
-
-from numpy import empty, array, mean, append, concatenate
-from argparse import ArgumentParser
-from util import encapsulated_ase, os_operation
-
-
-def array_type(string):
-	number_list = string.split(',')
-	number_array = array(number_list, dtype=float)
-	return number_array
-
-
-def buck_potential(xaxe, potential, range):
-	mix = concatenate((xaxe.reshape(-1, 1), potential.reshape(-1, 1)), axis=1)
-	mask = (mix[:,0] >= range[0]) & (mix[:,0] <=range[1])
-	buck_potential = mix[mask]
-	ave_potential = mean(buck_potential[:,1])
-	return ave_potential
-
-
-# set argument
-parser = ArgumentParser(description='to handle cp2k output file hartree cube, name should be "hartree-*.cube"')
-parser.add_argument('file_name', type=str, nargs='?', help='hartree cube file', default=os_operation.default_file_name('*-v_hartree-1_*.cube', last=True))
-parser.add_argument('-b', '--buck_range', type=array_type, help='parameter to calculate mean value of buck', default=None)
-parser.add_argument('-o', type=str, help='output file name, default is "out.put"', default='hartree.out')
-
-args = parser.parse_args()
-
-
-## init output potential file's shape, and define a z axe
-init_array = encapsulated_ase.ave_potential(args.file_name)
-potential = empty((0, init_array[0].shape[0]))
-z_coordinates = array((init_array[1])).reshape(-1, 1)
-
-potential = encapsulated_ase.ave_potential(args.file_name)[0]
-
-aved = mean(potential, axis=0)
-total_potential = append(z_coordinates, potential.reshape(-1, 1), axis=1)
-
-## if buck range is exit, out put a difference of potential
-if args.buck_range is not None:
-	buck_potential = buck_potential(z_coordinates, potential, args.buck_range)
-	print(buck_potential)
-	with open('hartree_potential.dat', 'w') as f:
-		f.write(f"{buck_potential}" + '\n')
-
-## write output
-with open(args.o, 'w') as f:
-	for value in total_potential:
-		f.write(" ".join(map(str, value)) + '\n')
-

mdkits-0.1.1/src/mdkits/cli/pdos.py

@@ -1,36 +0,0 @@
-#!/usr/bin/env python3.9
-
-# caculate pdos
-
-from cp2kdata import Cp2kPdos
-import argparse
-import numpy as np
-from util import os_operation
-
-
-def to_file(filename, ener, dos):
-	to_file = np.column_stack((ener, dos))
-	np.savetxt(filename, to_file, delimiter=" ")
-
-
-# set argument
-parser = argparse.ArgumentParser(description='calculate pdos')
-parser.add_argument('filename', type=str, nargs='?', default=os_operation.default_file_name('*-k*.pdos'))
-parser.add_argument('--type', type=str, default='total')
-args = parser.parse_args()
-
-
-# pdos
-#dos_types = ['0']
-#for dos_type in dos_types:
-#	for atom_type in range(1, args.type_number+1):
-#		dos_obj = Cp2kPdos(f'{args.project_name}-k{atom_type}-1_{args.run_step}.pdos')
-#		dos, ener = dos_obj.get_raw_dos()
-#		to_file(f"{dos_obj.read_dos_element()}_{dos_type}.pdos", ener, dos)
-
-# total dos
-print(args.filename)
-for file in args.filename:
-    dos_obj = Cp2kPdos(file)
-    dos, ener = dos_obj.get_raw_dos(dos_type=args.type)
-    to_file(f'{dos_obj.read_dos_element()}_{args.type}.pdos', ener, dos)