mdkits 0.1.9__tar.gz → 0.1.10__tar.gz

{mdkits-0.1.9 → mdkits-0.1.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.9
+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-0.1.9 → mdkits-0.1.10}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.1.9"
+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-0.1.9 → mdkits-0.1.10}/src/mdkits/build_cli/build_cli.py

@@ -11,6 +11,7 @@ from mdkits.build_cli import (
     build_solution,
     cut_surface,
     supercell,
+    build_interface,
 )
 
 
@@ -27,6 +28,7 @@ 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-0.1.9 → 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-0.1.9 → 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, show_default=True)
+@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-0.1.9 → mdkits-0.1.10}/src/mdkits/util/out_err.py

@@ -3,14 +3,17 @@ output and error for cli
 """
 
 import numpy as np
-import sys
+import sys, os
 
 
-def cell_output(cell: list):
+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 check_cell(atoms, cell):
+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:

mdkits-0.1.9/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-0.1.9/src/mdkits/build_cli/cut_surface.py

@@ -1,28 +0,0 @@
-#!/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
-
-
-@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')
-def main(atoms, face, vacuum, size, cell):
-    """cut surface"""
-    out_err.check_cell(atoms, cell)
-
-    surface = build.surface(atoms, face, size[2], vacuum=vacuum/2)
-    super_surface = supercell.supercell(surface, size[0], size[1], 1)
-
-    o = f"{atoms.filename.split('.')[-2]}_{face[0]}{face[1]}{face[2]}_{size[0]}{size[1]}{size[2]}.cif"
-    super_surface.write(o)
-    print(os.path.abspath(o))
-
-
-if __name__ == '__main__':
-    main()