mdkits 0.1.2__tar.gz → 0.1.4__tar.gz

{mdkits-0.1.2 → mdkits-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.2
+Version: 0.1.4
 Summary: tools for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -81,6 +81,10 @@ 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
+```
 
 ### 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:
@@ -93,6 +97,25 @@ 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
+### 构建体相模型
+`build_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
+```
+
 ## 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:

{mdkits-0.1.2 → mdkits-0.1.4}/README.md

@@ -56,6 +56,10 @@ 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
+```
 
 ### 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:
@@ -68,6 +72,25 @@ 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
+### 构建体相模型
+`build_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
+```
+
 ## 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:

{mdkits-0.1.2 → mdkits-0.1.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.1.2"
+version = "0.1.4"
 description = "tools for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

mdkits-0.1.4/src/mdkits/cli/build_bulk.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+
+import click
+from ase.build import bulk
+import numpy as np
+
+
+@click.command(name='build_bulk')
+@click.argument('symbol', type=str)
+@click.argument('cs', type=click.Choice(['sc', 'fcc', 'bcc', 'tetragonal', 'bct', 'hcp', 'rhombohedral', 'orthorhombic', 'mcl', 'diamond', 'zincblende', 'rocksalt', 'cesiumchloride', 'fluorite', 'wurtzite']))
+@click.option('-a', type=float, help='designate lattice constant a')
+@click.option('-b', type=float, help='designate lattice constant b. if only a and b is given, b will be interpreted as c instead')
+@click.option('-c', type=float, help='designate lattice constant c')
+@click.option('--alpha', type=float, help='angle in degrees for rhombohedral lattice')
+@click.option('--covera', type=float, help='c/a ratio used for hcp. Default is ideal ratio: sqrt(8/3)', default=np.sqrt(8/3), show_default=True)
+@click.option('-u', type=float, help='internal coordinate for Wurtzite structure')
+@click.option('--orth', is_flag=True, help='construct orthorhombic unit cell instead of primitive cell which is the default')
+@click.option('--cubic', is_flag=True, help='construct cubic unit cell if possible')
+def main(symbol, cs, a, b, c, alpha, covera, u, orth, cubic):
+    """
+    build a bulk structure
+    """
+
+    #if args.primitve:
+    #    a = args.a * 0.7071 * 2
+    #else:
+    #    a = args.a
+    atoms = bulk(symbol, cs, a=a, b=b, c=c, alpha=alpha, covera=covera, u=u, orthorhombic=orth, cubic=cubic)
+
+    atoms.write(f"{symbol}_{cs}.cif", format='cif')
+
+
+if __name__ == '__main__':
+    main()
+

mdkits-0.1.4/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-0.1.2 → mdkits-0.1.4}/src/mdkits/mdkits.py

@@ -7,6 +7,8 @@ from mdkits.cli import (
     plot,
     density,
     cube,
+    pdos,
+    build_bulk,
 )
 
 
@@ -25,6 +27,8 @@ 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)
+cli.add_command(build_bulk.main)
 
 
 if __name__ == '__main__':

mdkits-0.1.2/src/mdkits/cli/build_bulk.py

@@ -1,55 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from ase.build import bulk
-from ase.geometry import cell_to_cellpar
-from ase.io import write
-
-
-def parse_size(s):
-    return [int(x) for x in s.replace(',', ' ').split()]
-
-
-def parse_argument():
-    parser = argparse.ArgumentParser(description='build a surface structure of matel')
-    parser.add_argument('symbol', type=str, help='designate the symbol of matel')
-    parser.add_argument('--crystal', type=str, help='designate the crystal of structure')
-    parser.add_argument('--orth', help='outpue orthorhombic crystal', action='store_true')
-    parser.add_argument('-a', type=float, help='designate a lattice constant')
-    parser.add_argument('--primitve', help='designate a lattice constant of real', action='store_true')
-    parser.add_argument('-o', type=str, help='output structure name', default='bulk.xyz')
-    parser.add_argument('-c', help='output coord.xyz and cell.inc', action='store_true')
-    parser.add_argument('-k', help='output kpoint.inc', action='store_true')
-
-    return parser.parse_args()
-
-
-def main():
-    args = parse_argument()
-    if args.primitve:
-        a = args.a * 0.7071 * 2
-    else:
-        a = args.a
-    atoms = bulk(args.symbol, args.crystal, a=a, orthorhombic=args.orth)
-    if args.c:
-        atoms.write('coord.xyz', format='xyz')
-        with open('coord.xyz', 'r') as f:
-            lines = f.readlines()[2:]
-        with open('coord.xyz', 'w') as f:
-            f.writelines(lines)
-        with open('cell.inc', 'w') as f:
-            cell = list(cell_to_cellpar(atoms.cell))
-            f.write('ABC [angstrom] ' + str(cell[0]) + ' ' + str(cell[1]) + ' ' + str(cell[2]) + ' ' + '\n')
-            f.write('ALPHA_BETA_GAMMA ' + str(cell[3]) + ' ' + str(cell[4]) + ' ' + str(cell[5]) + '\n')
-        if args.k:
-            with open('kpoint.inc', 'w') as f:
-                if True:
-                    if True:
-                        f.write(f"SCHEME MONKHORST-PACK {int(round(30/cell[0]))} {int(round(30/cell[1]))} {int(round(30/cell[2]))}" + "\n")
-    else:
-        atoms.write(args.o)
-
-
-if __name__ == '__main__':
-    main()
-

mdkits-0.1.2/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)