mdkits 0.1.4__tar.gz → 0.1.6__tar.gz

{mdkits-0.1.4 → mdkits-0.1.6}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.4
-Summary: tools for md or dft
+Version: 0.1.6
+Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
 Author: jxxcr
@@ -13,6 +13,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: Cp2kData (>=0.7.2,<0.8.0)
 Requires-Dist: MDAnalysis (>=2.8.0,<3.0.0)
 Requires-Dist: ase (>=3.22.1,<4.0.0)
 Requires-Dist: click (>=8.1.3,<9.0.0)
@@ -98,8 +99,10 @@ 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
+`build`为界面的工具, 其中包含多个建模工具
+
 ### 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:
+`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
 ```
@@ -116,6 +119,20 @@ mdkits build_bulk CsCl cesiumchloride -a 4.123
 mdkits build_bulk BaF2 fluorite -a 6.196
 ```
 
+### 构建表面模型
+`surface`用于构建常见的表面模型, 骑用法为:
+```bash
+mdkits build surface [ELEMENT] [SURFACE_TYPE] [SIZE]
+```
+如构建`Pt`的`fcc111`表面模型:
+```bash
+mdkits build surface Pt fcc111 2 2 3 --vacuum 15
+```
+构建石墨烯表面:
+```bash
+mdkits build surface C2 graphene 3 3 1 --vacuum 15
+```
+
 ## 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-0.1.4 → mdkits-0.1.6}/README.md

@@ -73,8 +73,10 @@ 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
+`build`为界面的工具, 其中包含多个建模工具
+
 ### 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:
+`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
 ```
@@ -91,6 +93,20 @@ mdkits build_bulk CsCl cesiumchloride -a 4.123
 mdkits build_bulk BaF2 fluorite -a 6.196
 ```
 
+### 构建表面模型
+`surface`用于构建常见的表面模型, 骑用法为:
+```bash
+mdkits build surface [ELEMENT] [SURFACE_TYPE] [SIZE]
+```
+如构建`Pt`的`fcc111`表面模型:
+```bash
+mdkits build surface Pt fcc111 2 2 3 --vacuum 15
+```
+构建石墨烯表面:
+```bash
+mdkits build surface C2 graphene 3 3 1 --vacuum 15
+```
+
 ## 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-0.1.4 → mdkits-0.1.6}/pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.1.4"
-description = "tools for md or dft"
+version = "0.1.6"
+description = "kits for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]
 license = "MIT"
@@ -20,6 +20,7 @@ MDAnalysis = "^2.8.0"
 ase = "^3.22.1"
 matplotlib = "^3.9.0"
 pyyaml = "^6.0.1"
+Cp2kData = "^0.7.2"
 numpy = "^1.26.4"
 
 [tool.poetry.group.dev.dependencies]

{mdkits-0.1.4 → mdkits-0.1.6}/src/mdkits/cli/adsorbate.py

@@ -34,6 +34,10 @@ def parse_argument():
 
     return parser.parse_args()
 
+@click.option('--adsorbate', type=arg_type.Molecule, help='add adsorbate on surface')
+@click.option('--site', type=click.Choice(['ontop', 'hollow','fcc', 'hcp', 'bridge', 'shortbridge', 'longbridge']))
+@click.option('--height', type=float, help='height above the surface')
+@click.option('--rotate', type=click.Tuple([float, float, float]), help='rotate adsorbate molcule around x, y, z axis', default=(0, 0, 0))
 def main():
     args = parse_argument()
     atoms = encapsulated_ase.atoms_read_with_cell(args.filename, cell=args.cell, coord_mode=args.coord)
@@ -47,6 +51,11 @@ def main():
         if atom.index in args.index:
             position_list.append(np.copy(atom.position[0:2])+offset)
 
+        molecule = build.molecule(adsorbate)
+        molecule.rotate(rotate[0], 'x')
+        molecule.rotate(rotate[1], 'y')
+        molecule.rotate(rotate[2], 'z')
+        build.add_adsorbate(atoms, molecule, position=site, height=height)
     if args.m in g2.names:
         molecule = build.molecule(args.m)
         if args.x:

{mdkits-0.1.4 → mdkits-0.1.6}/src/mdkits/cli/build_bulk.py

@@ -5,7 +5,7 @@ from ase.build import bulk
 import numpy as np
 
 
-@click.command(name='build_bulk')
+@click.command(name='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')

mdkits-0.1.6/src/mdkits/cli/build_cli.py

@@ -0,0 +1,19 @@
+import click
+from mdkits.cli import (
+    build_bulk,
+    build_surface,
+)
+
+
+@click.group(name='build')
+@click.pass_context
+def cli_build(ctx):
+    """kits for building"""
+    pass
+
+
+cli_build.add_command(build_bulk.main)
+cli_build.add_command(build_surface.main)
+
+if __name__ == '__main__':
+    cli_build()

mdkits-0.1.6/src/mdkits/cli/build_surface.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python3
+
+import click
+from ase import build
+import numpy as np
+
+
+def surface_check(obj, surface_type):
+    if hasattr(obj, surface_type):
+        return getattr(obj, surface_type)
+
+
+@click.command(name='surface')
+@click.argument('symbol', type=str)
+@click.argument('surface', type=click.Choice(['fcc100', 'fcc110', 'fcc111', 'fcc211', 'bcc100', 'bcc110', 'bcc111', 'hcp0001', 'hcp10m10', 'diamond100', 'diamond111', 'mx2', 'graphene']))
+@click.argument('size', type=click.Tuple([int, int, int]))
+@click.option('--kind', type=click.Choice(['2H', '1T']), help='designate the kind of MX2 surface')
+@click.option('-a', type=float, help='the lattice constant. if specified, it overrides the expermental lattice constant of the element. must be specified if setting up a crystal structure different from the one found in nature')
+@click.option('-c', type=float, help='extra hcp lattice constant. if specified, it overrides the expermental lattice constant of the element. Default is ideal ratio: sqrt(8/3)', default=np.sqrt(8/3), show_default=True)
+@click.option('--thickness', type=float, help='Thickness of the layer, for mx2 and graphene')
+@click.option('--orth', is_flag=True, help='if specified and true, forces the creation of a unit cell with orthogonal basis vectors. if the default is such a unit cell, this argument is not supported')
+@click.option('--vacuum', type=float, help='designate vacuum of surface, default is None', default=0.0)
+def main(symbol, surface, size, kind, a, c, thickness, orth, vacuum, adsorbate):
+    #if args.primitive:
+    #    a = args.a * 0.7071 * 2
+    #else:
+    #    a = args.a
+
+    vacuum = vacuum / 2
+    build_surface = surface_check(build, surface)
+    out_filename = f"{symbol}_{surface}_{size[0]}{size[1]}{size[2]}_{adsorbate}.cif"
+
+    if surface in ['hcp0001', 'hcp10m10']:
+        atoms = build_surface(symbol, size, a=a, c=c, vacuum=vacuum, orthogonal=orth)
+    elif surface in ['mx2']:
+        if thickness is None:
+            atoms = build_surface(symbol, size, kind=kind, a=a, vacuum=vacuum)
+        else:
+            atoms = build_surface(symbol, size, kind=kind, a=a, vacuum=vacuum, thickness=thickness)
+    elif surface in ['graphene']:
+        if a is None:
+            a = 2.46
+
+        if thickness is None:
+            atoms = build_surface(formula=symbol, size=size, a=a, vacuum=vacuum)
+        else:
+            atoms = build_surface(formula=symbol, size=size, thickness=thickness, a=a, vacuum=vacuum)
+    else:
+        atoms = build_surface(symbol, size, a=a, vacuum=vacuum, orthogonal=orth)
+    
+    atoms.write(out_filename)
+
+
+if __name__ == '__main__':
+    main()
+

{mdkits-0.1.4 → mdkits-0.1.6}/src/mdkits/mdkits.py

@@ -8,7 +8,7 @@ from mdkits.cli import (
     density,
     cube,
     pdos,
-    build_bulk,
+    build_cli,
 )
 
 
@@ -16,7 +16,7 @@ from mdkits.cli import (
 @click.pass_context
 @click.version_option()
 def cli(ctx):
-    """tools for md or dft"""
+    """kits for md or dft"""
     pass
 
 
@@ -28,7 +28,7 @@ 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)
+cli.add_command(build_cli.cli_build)
 
 
 if __name__ == '__main__':

{mdkits-0.1.4 → mdkits-0.1.6}/src/mdkits/util/arg_type.py

@@ -37,5 +37,16 @@ class FrameRangeType(click.ParamType):
                 self.fail(f"{value} is not a valid frame range", param, ctx)
 
 
+from ase.collections import g2
+class MoleculeType(click.Choice):
+    name = "mocular type"
+    def __init__(self):
+        super().__init__(self)
+        g2.names.append(click.Path(exists=True))
+        self.choices = tuple(g2.names)
+
+
+
 Cell = CellType()
 FrameRange = FrameRangeType()
+Molecule = MoleculeType()

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

@@ -1,134 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse, sys
-from ase import build
-from ase.geometry import cell_to_cellpar
-from ase.io import write
-import numpy as np
-
-
-
-def parse_size(s):
-    if s == None:
-        return None
-    return [int(x) for x in s.replace(',', ' ').split()]
-
-
-def surface_check(obj, surface_type):
-    if hasattr(obj, surface_type):
-        return getattr(obj, surface_type)
-    else:
-        print(f'dont have face named {surface_type}')
-        exit()
-
-
-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('--face', type=str, help='designate the face of surface')
-    parser.add_argument('-a', type=float, help='designate a lattice constant', default=None)
-    parser.add_argument('--primitive', help='designate a lattice constant of real', action='store_true')
-    parser.add_argument('--size', type=parse_size, help='designate surface size(a,b,c)')
-    parser.add_argument('--vacuum', type=float, help='designate vacuum of surface, default is None', default=0.0)
-    parser.add_argument('--adsorbate', type=str, help='add adsorbate on surface', default=None)
-    parser.add_argument('--position', type=str, help='position of adsorbate', default='ontop')
-    parser.add_argument('--offset', type=str, help='offset')
-    parser.add_argument('--height', type=float, help='position of adsorbate', default=1)
-    parser.add_argument('-o', type=str, help='output structure name', default='surface.xyz')
-    parser.add_argument('-c', help='output coord.xyz and cell.inc', action='store_true')
-    parser.add_argument('-k', type=parse_size, help='output kpoint.inc(a,b,c)', default=None)
-    parser.add_argument('--autok',  help='output kpoint.inc', action='store_true')
-    parser.add_argument('--orth',  help='orth cell', action='store_true')
-    parser.add_argument('--coverh',  type=int, help='cover H atom', default=0)
-
-    return parser.parse_args()
-
-
-def main():
-    args = parse_argument()
-    if args.primitive:
-        a = args.a * 0.7071 * 2
-    else:
-        a = args.a
-
-    vacuum = args.vacuum / 2
-
-    build_surface = surface_check(build, args.face)
-
-    if args.orth:
-        atoms = build_surface(args.symbol, args.size, a=a, vacuum=vacuum, orthogonal=args.orth)
-    else:
-        atoms = build_surface(args.symbol, args.size, a=a, vacuum=vacuum)
-
-    # add adsorbate
-    if args.adsorbate != None:
-        ## add H2Oa and OH
-        if args.adsorbate in ['H2Oa', 'OH']:
-            if args.adsorbate in ['OH']:
-                h2o = build.molecule(args.adsorbate)
-                h2o.rotate(90, 'y')
-                build.add_adsorbate(atoms, h2o, args.height, position=args.position, offset=args.offset)
-            else:
-                h2o = build.molecule('H2O')
-                h2o.rotate(90, 'y')
-                build.add_adsorbate(atoms, h2o, args.height, position=args.position, offset=args.offset)
-        ## add H2Ob
-        elif args.adsorbate in  ['H2Ob']:
-            h2o = build.molecule('H2O')
-            h2o.rotate(90, 'z')
-            h2o.rotate(45, 'y')
-            build.add_adsorbate(atoms, h2o, args.height, position=args.position, offset=args.offset)
-        ## add default something
-        else:
-            build.add_adsorbate(atoms, args.adsorbate, args.height, position=args.position, offset=args.offset)
-
-    # add h with coverage
-    if args.coverh != 0:
-        ## get atom position at surface
-        surface_positions_dict = {}
-        for atom in atoms:
-            if atom.tag == 1:
-                surface_positions_dict[atom.index] = atom.position
-        ## error checking
-        if site_number := len(surface_positions_dict) < args.coverh:
-            print(f"coverh is too big, please less then {site_number}")
-            sys.exit()
-        ## get random site
-        random_site_list = np.random.choice(list(surface_positions_dict.keys()), args.coverh, replace=False)
-        random_site_list = np.unique(random_site_list)
-        ## add H atom at hollow site
-        for site in random_site_list:
-            site_position = surface_positions_dict[site][0:2]
-            build.add_adsorbate(atoms, 'H', 2, position=site_position, offset=(0.3, 0.3))
-
-    # control output format
-    ## output with coord.xyz(cp2k format)
-    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')
-            ## output kpoint file with specific number
-            if args.k != None:
-                if True: #judge M or G
-                    with open('kpoint.inc', 'w') as f:
-                        f.write(f"SCHEME MONKHORST-PACK {args.k[0]} {args.k[1]} {args.k[2]}" + "\n")
-            ## output kpoint file autoly
-            if args.autok:
-                if True: # judge matel or semi or else
-                    if True: # judge M or G
-                        with open('kpoint.inc', 'w') as f:
-                            f.write(f"SCHEME MONKHORST-PACK {int(round(30/cell[0]))} {int(round(30/cell[1]))} {int(round(30/cell[2]))}" + "\n")
-    ## output default format or specific xyz file
-    else:
-        atoms.write(args.o)
-
-
-if __name__ == '__main__':
-    main()
-