mdkits 0.1.8__tar.gz → 0.1.10__tar.gz

{mdkits-0.1.8 → mdkits-0.1.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.8
+Version: 0.1.10
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -17,7 +17,6 @@ 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)
-Requires-Dist: dynaconf (>=3.1.12,<4.0.0)
 Requires-Dist: julia (>=0.6.2,<0.7.0)
 Requires-Dist: matplotlib (>=3.9.0,<4.0.0)
 Requires-Dist: numpy (>=1.26.4,<2.0.0)

{mdkits-0.1.8 → mdkits-0.1.10}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.1.8"
+version = "0.1.10"
 description = "kits for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]
@@ -14,7 +14,6 @@ repository = "https://github.com/jxxcr/mdkits"
 
 [tool.poetry.dependencies]
 python = "^3.11"
-dynaconf = "^3.1.12"
 click = "^8.1.3"
 MDAnalysis = "^2.8.0"
 ase = "^3.22.1"

{mdkits-0.1.8 → mdkits-0.1.10}/src/mdkits/build_cli/build_bulk.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-import click
+import click, os
 from ase.build import bulk
 import numpy as np
 
@@ -27,7 +27,9 @@ def main(symbol, cs, a, b, c, alpha, covera, u, orth, cubic):
     #    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')
+    o = f"{symbol}_{cs}.cif"
+    atoms.write(o, format='cif')
+    print(os.path.abspath(o))
 
 
 if __name__ == '__main__':

{mdkits-0.1.8 → mdkits-0.1.10}/src/mdkits/build_cli/build_cli.py

@@ -9,6 +9,9 @@ from mdkits.build_cli import (
     build_surface,
     adsorbate,
     build_solution,
+    cut_surface,
+    supercell,
+    build_interface,
 )
 
 
@@ -23,6 +26,9 @@ cli_build.add_command(build_bulk.main)
 cli_build.add_command(build_surface.main)
 cli_build.add_command(adsorbate.main)
 cli_build.add_command(build_solution.main)
+cli_build.add_command(cut_surface.main)
+cli_build.add_command(supercell.main)
+cli_build.add_command(build_interface.main)
 
 if __name__ == '__main__':
     cli_build()

mdkits-0.1.10/src/mdkits/build_cli/build_interface.py

@@ -0,0 +1,74 @@
+import click
+from mdkits.util import arg_type, out_err
+
+
+@click.command(name="interface")
+@click.option('--slab', type=arg_type.Structure, help='surface')
+@click.option('--sol', type=arg_type.Structure, help='solution')
+@click.option('--interval', type=float, help='interval between surface and sol', default=2, show_default=True)
+@click.option('--cap', type=click.Choice(['ne', 'slab']), help='build slab interface')
+@click.option('--vacuum', type=float, help='vacuum length', default=0, show_default=True)
+def main(slab, sol, interval, cap, vacuum):
+    """build interface"""
+    out_err.check_cell(slab)
+    out_err.check_cell(sol)
+
+    o = f"{slab.filename.split('.')[-2]}_{sol.filename.split('.')[-2]}.cif"
+
+    slab.set_pbc(True)
+    slab.center()
+    slab_cell = slab.cell.cellpar()
+    init_slab_cell = slab.cell.cellpar()
+    if cap == 'slab':
+        slab_copy = slab.copy()
+
+    sol_cell = sol.cell.cellpar()
+    sol.set_pbc(True)
+    sol.center()
+    sol.positions[:, 2] += slab_cell[2] + interval
+
+    slab.extend(sol)
+    slab_cell[2] += 2 * interval + sol_cell[2]
+    slab.set_cell(slab_cell)
+    slab.center()
+
+    if cap is None:
+        slab.positions[:, 2] -= 0.5 * init_slab_cell[2]
+    elif cap == 'ne':
+        from ase import Atoms
+        ne_interval = 4
+        lenx = init_slab_cell[0]
+        leny = init_slab_cell[1]
+        ne_cell = [lenx, leny, 2, 90, 90, 90]
+        ne_position = []
+        ne_symbols = []
+        ne_site = [int(lenx//ne_interval), int(leny//ne_interval)]
+        for i in range(ne_site[0]):
+            for j in range(ne_site[1]):
+                ne_position.append((i*ne_interval, j*ne_interval, 0))
+                ne_symbols.append('Ne')
+        ne_atoms = Atoms(symbols=ne_symbols, positions=ne_position, cell=ne_cell)
+        ne_atoms.center()
+
+        slab.positions[:, 2] += -(slab_cell[2] + interval)
+        slab.extend(ne_atoms)
+        slab_cell[2] += ne_cell[2]
+        slab.set_cell(slab_cell)
+        slab.center()
+    elif cap == 'slab':
+        slab.positions[:, 2] += -(slab_cell[2] + interval)
+        slab.extend(slab_copy)
+        slab_cell[2] += slab_copy.cell.cellpar()[2]
+        slab.set_cell(slab_cell)
+        slab.center()
+    
+    if vacuum > 0:
+        slab_cell[2] += vacuum
+        slab.set_cell(slab_cell)
+
+
+    slab.write(o)
+    out_err.path_output(o)
+
+if __name__ == '__main__':
+    main()

{mdkits-0.1.8 → mdkits-0.1.10}/src/mdkits/build_cli/build_solution.py

@@ -2,6 +2,7 @@ import click, os
 from julia import Pkg, Main
 from mdkits.util import arg_type
 from importlib import resources
+from mdkits.cli import convert
 import tempfile
 
 
@@ -77,6 +78,10 @@ def main(filename, infile, install, water_number, n, tolerance, cell, gap):
         if os.path.exists(temp_file.name):
             os.remove(temp_file.name)
 
+    print("="*15)
+    print(total_input)
+    print("="*15)
+    convert.main([output_filename, "-c", "--cell", ",".join([str(a) for a in cell])], standalone_mode=False)
     Main.exit()
 
 

{mdkits-0.1.8 → mdkits-0.1.10}/src/mdkits/build_cli/build_surface.py

@@ -3,6 +3,7 @@
 import click, os
 from ase import build
 import numpy as np
+from mdkits.util import out_err
 
 
 def surface_check(obj, surface_type):
@@ -19,7 +20,7 @@ def surface_check(obj, surface_type):
 @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)
+@click.option('--vacuum', type=float, help='designate vacuum of surface, default is None', default=0.1, show_default=True)
 def main(symbol, surface, size, kind, a, c, thickness, orth, vacuum):
     #if args.primitive:
     #    a = args.a * 0.7071 * 2
@@ -29,6 +30,8 @@ def main(symbol, surface, size, kind, a, c, thickness, orth, vacuum):
     vacuum = vacuum / 2
     build_surface = surface_check(build, surface)
     out_filename = f"{symbol}_{surface}_{size[0]}{size[1]}{size[2]}.cif"
+    if surface in ['fcc100']:
+        orth = True
 
     if surface in ['hcp0001', 'hcp10m10']:
         atoms = build_surface(symbol, size, a=a, c=c, vacuum=vacuum, orthogonal=orth)
@@ -48,6 +51,7 @@ def main(symbol, surface, size, kind, a, c, thickness, orth, vacuum):
     else:
         atoms = build_surface(symbol, size, a=a, vacuum=vacuum, orthogonal=orth)
     
+    out_err.check_cell(atoms)
     atoms.write(out_filename)
     print(os.path.abspath(out_filename))
 

mdkits-0.1.10/src/mdkits/build_cli/cut_surface.py

@@ -0,0 +1,78 @@
+#!/usr/bin/env python3
+
+from ase import build
+import click, os
+from mdkits.util import arg_type, out_err
+from mdkits.build_cli import supercell
+import numpy as np
+import ase.visualize
+
+
+def find_vector(atoms):
+    position = atoms.positions
+    max_z = np.max(position[:, 2])
+    highest_points = position[position[:, 2] == max_z]
+
+    shortest_vector = None
+    min_distance = float('inf')
+    x_axis = np.array([1, 0, 0])
+
+    for i in range(len(highest_points)):
+        for j in range(i + 1, len(highest_points)):
+            point1 = highest_points[i]
+            point2 = highest_points[j]
+            vector = point2 - point1
+
+            cos_angle = np.dot(vector, x_axis) / (np.linalg.norm(vector) * np.linalg.norm(x_axis))
+            angle = np.arccos(cos_angle)
+
+            if angle <= np.pi / 2:
+                distance = np.linalg.norm(vector)
+                if distance < min_distance:
+                    min_distance = distance
+                    shortest_vector = vector
+
+    return shortest_vector
+
+
+@click.command(name='cut')
+@click.argument('atoms', type=arg_type.Structure)
+@click.option('--face', type=click.Tuple([int, int, int]), help='face index')
+@click.option('--size', type=click.Tuple([int, int, int]), help='surface size')
+@click.option('--vacuum', type=float, help='designate vacuum of surface, default is None', default=0.0, show_default=True)
+@click.option('--cell', type=arg_type.Cell, help='set xyz file cell, --cell x,y,z,a,b,c')
+@click.option('--orth', is_flag=True, help='orthogonalize cell')
+def main(atoms, face, vacuum, size, cell, orth):
+    """cut surface"""
+    out_err.check_cell(atoms, cell)
+    o = f"{atoms.filename.split('.')[-2]}_{face[0]}{face[1]}{face[2]}_{size[0]}{size[1]}{size[2]}.cif"
+
+    surface = build.surface(atoms, face, size[2], vacuum=vacuum/2)
+
+    if orth:
+        #vector = surface[-2].position - surface[-1].position
+        #vector = find_vector(surface)
+        surface_cell = surface.cell.cellpar()
+        ase.visualize.view(surface)
+        gamma = surface_cell[-1]
+        if gamma != 90:
+            a = np.sin(np.radians(gamma)) * surface_cell[0]
+            b = surface_cell[1]
+            surface_cell[1] = a
+            surface_cell[0] = b
+            surface_cell[-1] = 90
+            #surface.rotate(vector, np.array([1, 0, 0]))
+            surface.rotate(-gamma, 'z')
+            surface.set_cell(surface_cell)
+            surface.wrap()
+        o = f"{atoms.filename.split('.')[-2]}_{face[0]}{face[1]}{face[2]}_{size[0]}{size[1]}{size[2]}_orth.cif"
+
+    super_surface = supercell.supercell(surface, size[0], size[1], 1)
+
+    super_surface.write(o)
+    out_err.cell_output(super_surface.cell.cellpar())
+    out_err.path_output(o)
+
+
+if __name__ == '__main__':
+    main()

mdkits-0.1.10/src/mdkits/build_cli/supercell.py

@@ -0,0 +1,41 @@
+#!/usr/bin/env python3
+
+from ase.io import read
+import click, os
+import numpy as np
+from ase.build import make_supercell
+from mdkits.util import (
+    structure_parsing,
+    encapsulated_ase,
+    cp2k_input_parsing,
+    arg_type,
+    out_err,
+    )
+
+
+def supercell(atom, x, y, z):
+    P = [ [x, 0, 0], [0, y, 0], [0, 0, z] ]
+    super_atom = make_supercell(atom, P)
+    return super_atom
+
+
+@click.command(name='supercell')
+@click.argument('atoms', type=arg_type.Structure)
+@click.argument('super', type=click.Tuple([int, int, int]), default=(1, 1, 1))
+@click.option('--cell', type=arg_type.Cell, help='set cell, a list of lattice, --cell x,y,z or x,y,z,a,b,c')
+def main(atoms, super, cell):
+    """make a supercell"""
+
+    out_err.check_cell(atoms, cell)
+
+    atoms.set_pbc(True)
+    atoms.wrap()
+    super_atom = supercell(atoms, super[0], super[1], super[2])
+
+    o = f"{atoms.filename.split('.')[-2]}_{super[0]}{super[1]}{super[2]}.cif"
+    super_atom.write(o)
+    print(os.path.abspath(o))
+
+
+if __name__ == '__main__':
+    main()

{mdkits-0.1.8 → mdkits-0.1.10}/src/mdkits/util/arg_type.py

@@ -52,7 +52,7 @@ class StructureType(click.ParamType):
                     cell = cp2k_input_parsing.parse_cell()
                     atoms.set_cell(cell)
 
-                atoms.filename = value.replace('./', '').replace('.\\', '')
+                atoms.filename = value.replace('./', '').replace('.\\', '').split('/')[-1]
                 return atoms
             else:
                 self.fail(f"{value} is not exists", param, ctx)

mdkits-0.1.10/src/mdkits/util/out_err.py

@@ -0,0 +1,22 @@
+"""
+output and error for cli
+"""
+
+import numpy as np
+import sys, os
+
+
+def cell_output(cell):
+    print(f"system cell: x = {cell[0]}, y = {cell[1]}, z = {cell[2]}, a = {cell[3]}\u00B0, b = {cell[4]}\u00B0, c = {cell[5]}\u00B0")
+
+
+def path_output(file: str):
+    print(os.path.abspath(file))
+
+def check_cell(atoms, cell=None):
+    if not np.array_equal(atoms.cell.cellpar(), np.array([0., 0., 0., 90., 90., 90.])):
+        cell_output(atoms.cell.cellpar())
+    elif np.array_equal(atoms.cell.cellpar(), np.array([0., 0., 0., 90., 90., 90.])) and cell is not None:
+        atoms.set_cell(cell)
+    else:
+        raise ValueError("can't parse cell please use --cell set cell")

mdkits-0.1.8/src/mdkits/build_cli/build_interface.py

@@ -1,86 +0,0 @@
-from ase.io import write, read
-import argparse
-from ase.geometry import cell_to_cellpar, cellpar_to_cell
-import math
-
-
-def parse_argument():
-    parser = argparse.ArgumentParser(description='combain solbox and surface to a interface')
-    parser.add_argument('--surface', type=str, help='surface path')
-    parser.add_argument('--sol', type=str, help='solbox path')
-    parser.add_argument('--move', type=float, help='move at z, default = 0', default=0)
-    parser.add_argument('--interval', type=float, help='interval between surface to sol, default is 2', default=2)
-    parser.add_argument('--vacuum', type=float, help='vacuum of structure, default is 0', default=0)
-    parser.add_argument('--symmetry', help='two side interface, default is false', action='store_true')
-    parser.add_argument('--ne', help='two side interface, one side is Ne atom, default is false', action='store_true')
-    parser.add_argument('-o', type=str, help='output file name', default='interface')
-
-    return parser.parse_args()
-
-
-def chformat(input_filename, output_filename, format):
-    atoms = read(input_filename)
-    write(output_filename, atoms, format=format)
-
-
-def main():
-    args = parse_argument()
-    surface = read(args.surface)
-    surface.set_pbc(True)
-    surface.center()
-    sy_surface = surface.copy()
-    cell = surface.get_cell()
-    [lenx, leny, lenz, anga, angb, angc] = cell_to_cellpar(cell)
-
-    solbox = read(args.sol)
-    solbox_cell = solbox.cell.cellpar()
-    solbox.set_pbc(True)
-    solbox.center()
-    tmp_list = solbox.get_positions()
-    tmp_list[:, 2] += lenz + args.interval
-    solbox.set_positions(tmp_list)
-
-    surface.extend(solbox)
-    surface.cell = [lenx, leny, (lenz + args.interval + solbox_cell[2] + args.interval), anga, angb, angc]
-    surface.center()
-
-    if args.symmetry:
-        tmp_list = surface.get_positions()
-        tmp_list[:, 2] += -(lenz + args.interval + solbox_cell[2] + args.interval)
-        surface.set_positions(tmp_list)
-        surface.extend(sy_surface)
-        surface.cell = [lenx, leny, (lenz + args.interval + solbox_cell[2] + args.interval + lenz + args.vacuum), anga, angb, angc]
-        surface.center()
-    elif args.ne:
-        from ase import Atoms
-        ne_interval = 4 # adjust water density
-        ne_cell = [lenx, leny, 2, 90, 90, 90]
-        ne_position = []
-        ne_symbols = []
-        ne_site = [int(lenx//ne_interval), int(leny//ne_interval)]
-        for i in range(ne_site[0]):
-            for j in range(ne_site[1]):
-                ne_position.append((i*ne_interval, j*ne_interval, 0))
-                ne_symbols.append('Ne')
-        ne_atoms = Atoms(symbols=ne_symbols, positions=ne_position, cell=ne_cell)
-        ne_atoms.center()
-        tmp_list = surface.get_positions()
-        tmp_list[:, 2] += -(lenz + args.interval + solbox_cell[2])
-        surface.set_positions(tmp_list)
-        surface.extend(ne_atoms)
-        surface.cell = [lenx, leny, (lenz + args.interval + solbox_cell[2] + args.interval + 2 + args.vacuum), anga, angb, angc]
-        surface.center()
-    else:
-        surface.set_pbc(True)
-        tmp_list = surface.get_positions()
-        #tmp_list[:, 2] -= lenz
-        tmp_list[:, 2] -= args.move
-        surface.set_positions(tmp_list)
-
-
-    write(args.o + '.xyz', surface, format='extxyz')
-    write(args.o + '.cif', surface, format='cif')
-    #chformat(args.o + '.cif', args.o + '.xyz', format='xyz')
-
-if __name__ == '__main__':
-    main()

mdkits-0.1.8/src/mdkits/build_cli/cut_surface.py

@@ -1,38 +0,0 @@
-#!/usr/bin/env python3
-
-from ase import io, build
-import argparse
-from util import encapsulated_ase
-
-
-def parse_size(s):
-    return [int(x) for x in s.replace(',', ' ').split()]
-
-def parse_size1(s):
-    return [float(x) for x in s.replace(',', ' ').split()]
-
-
-def parse_argument():
-    parser = argparse.ArgumentParser(description='cut surface of structure')
-    parser.add_argument('filename', type=str, help='init structure filename')
-    parser.add_argument('--face', type=parse_size, help='face index')
-    parser.add_argument('--vacuum', type=float, help='designate vacuum of surface, default is None', default=0.0)
-    parser.add_argument('--size', type=parse_size, help='surface size')
-    parser.add_argument('--coord', help='coord format', action='store_true')
-    parser.add_argument('--cell', type=parse_size1, help='set xyz file cell, --cell x,y,z,a,b,c')
-
-    return parser.parse_args()
-
-
-def main():
-    args = parse_argument()
-    atoms = encapsulated_ase.atoms_read_with_cell(args.filename, cell=args.cell, coord_mode=args.coord)
-    surface = build.surface(atoms, args.face, args.size[2], vacuum=args.vacuum/2)
-    super_cell = [[args.size[0], 0, 0], [0, args.size[1], 0], [0, 0, 1]]
-    super_surface = build.make_supercell(surface, super_cell)
-
-    super_surface.write(f"{args.filename.split('.')[-2].split('/')[-1]}_{args.face[0]}{args.face[1]}{args.face[2]}.cif")
-
-
-if __name__ == '__main__':
-    main()

mdkits-0.1.8/src/mdkits/cli/supercell.py

@@ -1,72 +0,0 @@
-#!/usr/bin/env python3
-
-from ase.io import read
-import argparse, os
-import numpy as np
-from ase.build import make_supercell
-from util import (
-    structure_parsing,
-    encapsulated_ase,
-    cp2k_input_parsing
-    )
-
-
-def supercell(atom, x, y, z):
-    P = [ [x, 0, 0], [0, y, 0], [0, 0, z] ]
-    super_atom = make_supercell(atom, P)
-    return super_atom
-
-
-def parse_cell(s):
-    return [float(x) for x in s.replace(',', ' ').split()]
-
-
-def super_cell(s):
-    super_cell = [int(x) for x in s.replace(',', ' ').split()]
-    leng = len(super_cell)
-    if leng == 2:
-        super_cell.append(1)
-    elif leng == 3:
-        pass
-    else:
-        print('wrong super cell size')
-        exit(1)
-
-    return super_cell
-
-
-def parse_argument():
-    parser = argparse.ArgumentParser(description='make a supercell')
-
-    parser.add_argument('input_file_name', type=str, help='input file name')
-    parser.add_argument('super', type=super_cell, help='super cell size, a,b,c')
-    parser.add_argument('-o', type=str, help='output file name, default is "super.cif"', default='super.cif')
-    parser.add_argument('--cp2k_input_file', type=str, help='input file name of cp2k, default is "input.inp"', default='input.inp')
-    parser.add_argument('--coord', help='coord format', action='store_true')
-    parser.add_argument('--cell', type=parse_cell, help='set cell, a list of lattice, --cell x,y,z or x,y,z,a,b,c')
-
-    return parser.parse_args()
-
-
-def main():
-    args = parse_argument()
-    if args.input_file_name == None:
-        print('give a xyz file')
-        sys.exit()
-
-    atom = encapsulated_ase.atoms_read_with_cell(args.input_file_name, cell=args.cell, coord_mode=args.coord)
-    atom.set_pbc(True)
-    atom.wrap()
-    super_atom = supercell(atom, args.super[0], args.super[1], args.super[2])
-
-    suffix = args.o.split('.')[-1]
-    if suffix == 'data':
-        super_atom.write(f'{args.o}', format='lammps-data', atom_style='atomic')
-    else:
-        super_atom.write(f'{args.o}')
-
-    print(os.path.abspath(args.o))
-
-
-if __name__ == '__main__':
-    main()

mdkits-0.1.8/src/mdkits/util/out_err.py

@@ -1,17 +0,0 @@
-"""
-output and error for cli
-"""
-
-import numpy as np
-import sys
-
-
-def cell_output(cell: list):
-    print(f"system cell: x = {cell[0]}, y = {cell[1]}, z = {cell[2]}, a = {cell[3]}\u00B0, b = {cell[4]}\u00B0, c = {cell[5]}\u00B0")
-
-
-def check_cell(atoms, cell):
-    if np.array_equal(atoms.cell.cellpar(), np.array([0., 0., 0., 90., 90., 90.])) and cell is not None:
-        atoms.set_cell(cell)
-    else:
-        raise ValueError("can't parse cell please use --cell set cell")