mdkits 0.1.5__tar.gz → 0.1.7__tar.gz

{mdkits-0.1.5 → mdkits-0.1.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.5
+Version: 0.1.7
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -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)

{mdkits-0.1.5 → mdkits-0.1.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.1.5"
+version = "0.1.7"
 description = "kits for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]
@@ -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-0.1.7/src/mdkits/cli/adsorbate.py

@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+
+from ase import build
+import os
+import click
+import numpy as np
+import MDAnalysis
+from mdkits.util import arg_type, encapsulated_ase
+
+
+@click.command(name='adsorbate')
+@click.argument('atoms', type=arg_type.Structure)
+@click.argument('adsorbate', type=arg_type.Molecule)
+@click.option('--select', type=str, help="select adsorbate position")
+@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), show_default=True)
+@click.option('--offset', type=click.Tuple([float, float]), help='adjust site', default=(0, 0), show_default=True)
+@click.option("--cover", type=int, help='cover the surface with adsorbate randomly')
+def main(atoms, adsorbate, select, height, rotate, offset, cover):
+    offset = np.array(offset)
+    u = encapsulated_ase.atoms_to_u(atoms)
+
+    molecule = build.molecule(adsorbate)
+    molecule.rotate(rotate[0], 'x')
+    molecule.rotate(rotate[1], 'y')
+    molecule.rotate(rotate[2], 'z')
+
+    output_filename = f"{atoms.filename.split('.')[0]}_{adsorbate}.cif"
+
+    s = u.select_atoms(select)
+    positions = s.positions[:, 0:2] + offset
+    if cover:
+        for index in np.random.choice(positions.shape[0], cover, replace=False):
+            build.add_adsorbate(atoms, molecule, height, position=positions[index])
+    else:
+        for position in positions:
+            build.add_adsorbate(atoms, molecule, height, position=position)
+
+
+    atoms.write(output_filename, format='cif')
+
+    print(os.path.abspath(output_filename))
+
+
+if __name__ == '__main__':
+    main()
+

{mdkits-0.1.5 → mdkits-0.1.7}/src/mdkits/cli/build_cli.py

@@ -2,6 +2,7 @@ import click
 from mdkits.cli import (
     build_bulk,
     build_surface,
+    adsorbate,
 )
 
 
@@ -14,6 +15,7 @@ def cli_build(ctx):
 
 cli_build.add_command(build_bulk.main)
 cli_build.add_command(build_surface.main)
+cli_build.add_command(adsorbate.main)
 
 if __name__ == '__main__':
     cli_build()

{mdkits-0.1.5 → mdkits-0.1.7}/src/mdkits/cli/build_surface.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-import click
+import click, os
 from ase import build
 import numpy as np
 
@@ -20,7 +20,7 @@ def surface_check(obj, surface_type):
 @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):
+def main(symbol, surface, size, kind, a, c, thickness, orth, vacuum):
     #if args.primitive:
     #    a = args.a * 0.7071 * 2
     #else:
@@ -28,7 +28,7 @@ def main(symbol, surface, size, kind, a, c, thickness, orth, vacuum, adsorbate):
 
     vacuum = vacuum / 2
     build_surface = surface_check(build, surface)
-    out_filename = f"{symbol}_{surface}_{size[0]}{size[1]}{size[2]}_{adsorbate}.cif"
+    out_filename = f"{symbol}_{surface}_{size[0]}{size[1]}{size[2]}.cif"
 
     if surface in ['hcp0001', 'hcp10m10']:
         atoms = build_surface(symbol, size, a=a, c=c, vacuum=vacuum, orthogonal=orth)
@@ -49,6 +49,7 @@ def main(symbol, surface, size, kind, a, c, thickness, orth, vacuum, adsorbate):
         atoms = build_surface(symbol, size, a=a, vacuum=vacuum, orthogonal=orth)
     
     atoms.write(out_filename)
+    print(os.path.abspath(out_filename))
 
 
 if __name__ == '__main__':

{mdkits-0.1.5 → mdkits-0.1.7}/src/mdkits/cli/convert.py

@@ -7,6 +7,7 @@ from mdkits.util import encapsulated_ase, arg_type
 
 
 @click.command(name='convert')
+@click.argument('atoms', type=arg_type.Structure)
 @click.option('-c', help='covert to cif', is_flag=True)
 @click.option('-x', help='covert to xyz', is_flag=True)
 @click.option('-d', help='covert to lammps data file', is_flag=True)
@@ -14,14 +15,12 @@ from mdkits.util import encapsulated_ase, arg_type
 @click.option('--coord', help='coord format', is_flag=True)
 @click.option('--cp2k', help='convert to cp2k format(coord + cell)', is_flag=True)
 @click.option('--center', help='center atoms', is_flag=True)
-@click.option('--cell', type=arg_type.Cell, help='set cell from cp2k input file or a list of lattice: --cell x,y,z or x,y,z,a,b,c', default='input.inp', show_default=True)
+@click.option('--cell', type=arg_type.Cell, help='set cell from cp2k input file or a list of lattice: --cell x,y,z or x,y,z,a,b,c')
 @click.option('-o', type=str, help='specify the output file name without suffix', default='out', show_default=True)
-@click.argument('file_name', type=click.Path(exists=True))
-def main(c, x, d, v, coord, cp2k, center, cell, o, file_name):
+def main(atoms, c, x, d, v, coord, cp2k, center, cell, o):
     """
     convet structure file in some formats
     """
-    atoms = encapsulated_ase.atoms_read_with_cell(file_name, cell=cell, coord_mode=coord)
 
     if center:
         atoms.center()

mdkits-0.1.7/src/mdkits/util/arg_type.py

@@ -0,0 +1,86 @@
+import click, os
+from ase.io import read
+import numpy as np
+from ase.collections import g2
+from mdkits.util import os_operation, cp2k_input_parsing, out_err
+
+
+class CellType(click.ParamType):
+    name = "pbc cell type"
+
+    def convert(self, value, param, ctx):
+        if isinstance(value, str):
+            if ',' not in value:
+                cell = cp2k_input_parsing.parse_cell()
+                return cell
+            else:
+                cell = [float(x) for x in value.split(',')]
+
+                if len(cell) == 3:
+                    cell += [90, 90, 90]
+                    out_err.cell_output(cell)
+                    return cell
+                elif len(cell) == 6:
+                    out_err.cell_output(cell)
+                    return cell
+                else:
+                    self.fail(f"{value} is not a valid cell parameter", param, ctx)
+
+
+class FrameRangeType(click.ParamType):
+    name = "frame range"
+    def convert(self, value, param, ctx):
+        if isinstance(value, str):
+            parts = value.split(':')
+
+            range_list = [int(x) if x else None for x in parts]
+
+            if len(range_list) > 0 and len(range_list) <= 3:
+                return range_list
+            else:
+                self.fail(f"{value} is not a valid frame range", param, ctx)
+
+
+class StructureType(click.ParamType):
+    name = "structure file type"
+    def convert(self, value, param, ctx):
+        no_cell=np.array([0., 0., 0., 90., 90., 90.])
+        if isinstance(value, str):
+            if os.path.exists(value):
+                try:
+                    atoms = read(value)
+                except:
+                    self.fail(f"{value} is not a valid structure file", param, ctx)
+
+                if np.array_equal(atoms.cell.cellpar(), no_cell):
+                    cell = cp2k_input_parsing.parse_cell()
+                    atoms.set_cell(cell)
+
+                atoms.filename = value.replace('./', '').replace('.\\', '')
+                return atoms
+            else:
+                self.fail(f"{value} is not exists", param, ctx)
+
+
+
+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)
+
+class AdsSiteType(click.Choice):
+    name = "adsorption site"
+    def __init__(self):
+        super().__init__(self)
+        site = ['ontop', 'hollow','fcc', 'hcp', 'bridge', 'shortbridge', 'longbridge']
+        self.choices = tuple(site)
+
+
+
+Cell = CellType()
+FrameRange = FrameRangeType()
+Molecule = MoleculeType()
+AdsSite = AdsSiteType()
+Structure = StructureType()

mdkits-0.1.7/src/mdkits/util/cp2k_input_parsing.py

@@ -0,0 +1,47 @@
+"""
+filename: cp2k_input_parsing.py
+function: prase cp2k file
+"""
+
+
+import sys
+from mdkits.util import os_operation, out_err
+
+
+def parse_cell():
+    """
+    function: parse cell information from cp2k input file
+    parameter:
+        cp2k_input_file: filename of cp2k input
+    return:
+        cell: list with 6 number
+    """
+    for file in os_operation.default_input():
+        try:
+            with open(file, 'r') as f:
+                cell = []
+                for line in f:
+                    if "ABC" in line:
+                        xyz = line.split()[-3:]
+                        cell.extend(xyz)
+                    if "ALPHA_BETA_GAMMA" in line:
+                        abc = line.split()[-3:]
+                        cell.extend(abc)
+                if len(cell) == 3:
+                    cell.extend([90.0, 90.0, 90.0])
+
+                out_err.cell_output(cell)
+                return cell
+        except FileNotFoundError:
+            sys.exit(f"cant parse cell information from {','.join(os_operation.default_input())}, assign a cell")
+
+
+#def get_cell(cp2k_input_file, cell=None):
+#    if cell is None:
+#        cell = parse_cell(cp2k_input_file)
+#    else:
+#        cell = cell
+#        if len(cell) == 3:
+#            cell.extend([90.0, 90.0, 90.0])
+#
+#    return cell

{mdkits-0.1.5 → mdkits-0.1.7}/src/mdkits/util/encapsulated_ase.py

@@ -8,6 +8,7 @@ from ase.io import iread, read
 import io
 import numpy as np
 from ase.io.cube import read_cube_data
+import MDAnalysis
 
 
 def wrap_to_cell(chunk, cell, name, big=False):
@@ -132,3 +133,14 @@ def jread(filepath):
         atom = read(filepath)
 
     return atom
+
+
+def atoms_to_u(atoms):
+    virtual_file = io.StringIO()
+    cell = atoms.cell.cellpar()
+    atoms.write(virtual_file, format='xyz')
+
+    u = MDAnalysis.Universe(virtual_file, format='xyz')
+    u.dimensions = cell
+
+    return u

{mdkits-0.1.5 → mdkits-0.1.7}/src/mdkits/util/os_operation.py

@@ -33,3 +33,8 @@ def sort_word_and_number(unsort_list):
     sorted_list = sorted(unsort_list, key=fns)
 
     return sorted_list
+
+
+def default_input():
+    default_input_name = os.environ.get("DEFAULT_INPUT", "input.inp,setup.inp,cell.inc").split(',')
+    return default_input_name

mdkits-0.1.7/src/mdkits/util/out_err.py

@@ -0,0 +1,8 @@
+"""
+output and error for cli
+"""
+
+
+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")
+

mdkits-0.1.5/src/mdkits/cli/adsorbate.py

@@ -1,93 +0,0 @@
-#!/usr/bin/env python3
-
-from ase import io, build
-from ase.collections import g2
-import argparse, os
-import numpy as np
-from util import encapsulated_ase
-
-
-def parse_size(s):
-    if s == None:
-        return None
-    return [float(x) for x in s.replace(',', ' ').split()]
-
-
-def parse_index(s):
-    return [int(x)-1 for x in s.replace(',', ' ').split()]
-
-
-def parse_argument():
-    parser = argparse.ArgumentParser(description='add some adsorbate')
-    parser.add_argument('filename', type=str, help='init structure filename')
-    parser.add_argument('-m', type=str, help='atom or molecule to add')
-    parser.add_argument('--index', type=parse_index, help='index(list) of atom to add atom(top site)')
-    parser.add_argument('--offset', type=parse_size, help='adjust site, default is 0,0', default='0,0')
-    parser.add_argument('--height', type=float, help='designate vacuum of surface, default is None', default=0.0)
-    parser.add_argument('-x', type=float, help='rotate axis and angle')
-    parser.add_argument('-y', type=float, help='rotate axis and angle')
-    parser.add_argument('-z', type=float, help='rotate axis and angle')
-    parser.add_argument('-o', type=str, help='specify the output file name without suffix, default is "adsorbated.cif"', default='adsorbated.cif')
-    parser.add_argument('--coord', help='coord format', action='store_true')
-    parser.add_argument('--cell', type=parse_size, help='set xyz file cell, --cell x,y,z,a,b,c')
-    parser.add_argument('--cp2k', help='output cp2k format', action='store_true')
-
-    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)
-
-    if len(args.offset) < 2:
-        args.offset.append(0)
-    offset = np.array(args.offset)
-
-    position_list = []
-    for atom in atoms:
-        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:
-            molecule.rotate(args.x, 'x')
-        if args.y:
-            molecule.rotate(args.y, 'y')
-        if args.z:
-            molecule.rotate(args.z, 'z')
-        for position in position_list:
-            build.add_adsorbate(atoms, molecule, args.height, position=position)
-    else:
-        for position in position_list:
-            build.add_adsorbate(atoms, args.m, args.height, position=position)
-
-
-    if args.cp2k:
-        args.o = 'coord.xyz'
-        atoms.write(args.o, format='xyz')
-        with open(args.o, 'r') as f:
-            lines = f.readlines()
-        with open(args.o, 'w') as f:
-            f.writelines(lines[2:])
-        with open('cell.inc', 'w') as f:
-            cell = atoms.get_cell().cellpar()
-            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')
-    else:
-        atoms.write(args.o, format='cif')
-
-    print(os.path.abspath(args.o))
-
-
-if __name__ == '__main__':
-    main()
-

mdkits-0.1.5/src/mdkits/util/arg_type.py

@@ -1,52 +0,0 @@
-import click, os
-from . import cp2k_input_parsing
-
-
-class CellType(click.ParamType):
-    name = "pbc cell type"
-
-    def convert(self, value, param, ctx):
-        if isinstance(value, str):
-            if ',' not in value:
-                cell = cp2k_input_parsing.parse_cell(value)
-                return cell
-            else:
-                cell = [float(x) for x in value.split(',')]
-
-                if len(cell) == 3:
-                    click.echo(f"system cell: x = {cell[0]}, y = {cell[1]}, z = {cell[2]}, a = {90}\u00B0, b = {90}\u00B0, c = {90}\u00B0")
-                    return cell + [90, 90, 90]
-                elif len(cell) == 6:
-                    click.echo(f"system cell: x = {cell[0]}, y = {cell[1]}, z = {cell[2]}, a = {cell[3]}\u00B0, b = {cell[4]}\u00B0, c = {cell[5]}\u00B0")
-                    return cell
-                else:
-                    self.fail(f"{value} is not a valid cell parameter", param, ctx)
-
-
-class FrameRangeType(click.ParamType):
-    name = "frame range"
-    def convert(self, value, param, ctx):
-        if isinstance(value, str):
-            parts = value.split(':')
-
-            range_list = [int(x) if x else None for x in parts]
-
-            if len(range_list) > 0 and len(range_list) <= 3:
-                return range_list
-            else:
-                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-0.1.5/src/mdkits/util/cp2k_input_parsing.py

@@ -1,46 +0,0 @@
-"""
-filename: cp2k_input_parsing.py
-function: prase cp2k file
-"""
-
-
-import sys
-
-
-def parse_cell(cp2k_input_file):
-    """
-    function: parse cell information from cp2k input file
-    parameter:
-        cp2k_input_file: filename of cp2k input
-    return:
-        cell: list with 6 number
-    """
-    try:
-        with open(cp2k_input_file, 'r') as f:
-            cell = []
-            for line in f:
-                if "ABC" in line:
-                    xyz = line.split()[-3:]
-                    cell.extend(xyz)
-                if "ALPHA_BETA_GAMMA" in line:
-                    abc = line.split()[-3:]
-                    cell.extend(abc)
-            if len(cell) == 3:
-                cell.extend([90.0, 90.0, 90.0])
-
-            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")
-            return cell
-    except FileNotFoundError:
-        print(f'cp2k input file name "{cp2k_input_file}" is not found, assign a cp2k input file or assign a "cell"')
-        sys.exit(1)
-
-
-#def get_cell(cp2k_input_file, cell=None):
-#    if cell is None:
-#        cell = parse_cell(cp2k_input_file)
-#    else:
-#        cell = cell
-#        if len(cell) == 3:
-#            cell.extend([90.0, 90.0, 90.0])
-#
-#    return cell