mdkits 0.1.7__py3-none-any.whl → 0.1.8__py3-none-any.whl

mdkits/{cli → build_cli}/adsorbate.py

@@ -5,18 +5,23 @@ import os
 import click
 import numpy as np
 import MDAnalysis
-from mdkits.util import arg_type, encapsulated_ase
+from mdkits.util import arg_type, encapsulated_ase, out_err
 
 
 @click.command(name='adsorbate')
 @click.argument('atoms', type=arg_type.Structure)
 @click.argument('adsorbate', type=arg_type.Molecule)
+@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')
 @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):
+def main(atoms, adsorbate, cell, select, height, rotate, offset, cover):
+    if height is None:
+        raise ValueError("height is required")
+
+    out_err.check_cell(atoms, cell)
     offset = np.array(offset)
     u = encapsulated_ase.atoms_to_u(atoms)
 

mdkits/{cli → build_cli}/build_cli.py

@@ -1,8 +1,14 @@
 import click
-from mdkits.cli import (
+#from mdkits.cli.build import (
+#    build_bulk,
+#    build_surface,
+#    adsorbate,
+#)
+from mdkits.build_cli import (
     build_bulk,
     build_surface,
     adsorbate,
+    build_solution,
 )
 
 
@@ -16,6 +22,7 @@ def cli_build(ctx):
 cli_build.add_command(build_bulk.main)
 cli_build.add_command(build_surface.main)
 cli_build.add_command(adsorbate.main)
+cli_build.add_command(build_solution.main)
 
 if __name__ == '__main__':
     cli_build()

mdkits/build_cli/build_solution.py

@@ -0,0 +1,84 @@
+import click, os
+from julia import Pkg, Main
+from mdkits.util import arg_type
+from importlib import resources
+import tempfile
+
+
+@click.command(name="solution")
+@click.argument("filename", type=click.Path(exists=True), nargs=-1)
+@click.option('--infile', is_flag=True, help="read input mode")
+@click.option('--install', is_flag=True, help="install julia and packmol")
+@click.option('--water_number', type=int, help="number of water molecules", default=0, show_default=True)
+@click.option('-n', type=int, multiple=True, help="number of molecules")
+@click.option('--tolerance', type=float, help="tolerance of solution", default=3.5, show_default=True)
+@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")
+@click.option('--gap', type=float, help="gap between solution and cell", default=1, show_default=True)
+def main(filename, infile, install, water_number, n, tolerance, cell, gap):
+    """
+    build solution model
+    """
+    if install:
+        import julia
+        julia.install()
+        Pkg.activate("Packmol", shared=True)
+        Pkg.add("Packmol")
+        Main.exit()
+
+    if cell is None:
+        raise ValueError("cell should be provided")
+
+    if len(filename) == 0 and water_number == 0:
+        raise ValueError("at least one file should be provided, or water_number should be greater than 0")
+
+    while True:
+        try:
+            Main.using("Packmol")
+            break
+        except Exception:
+            pass
+
+    if infile:
+        for file in filename:
+            Main.run_packmol(file)
+    else:
+        if len(n) != len(filename):
+            raise ValueError("number of -n should be equal to number of files")
+
+        temp_file = tempfile.NamedTemporaryFile(mode='w+t', delete=False)
+        backslash = "\\"
+
+        structure_input = {}
+        output_filenames = []
+        if len(filename) > 0:
+            for index, file in enumerate(filename):
+                structure_input[file] = f"structure {os.path.join(os.getcwd(), file.replace(backslash, '/').replace('./', ''))}\n  number {n[index]}\n  inside box {gap} {gap} {gap} {cell[0]-gap} {cell[1]-gap} {cell[2]-gap}\nend structure\n"
+
+                output_filenames.append(f"{file.replace(backslash, '/').split('.')[-2].split('/')[-1]}_{n[index]}")
+
+        if water_number > 0:
+            water_path = resources.files('mdkits.build_cli').joinpath('water.xyz')
+
+            structure_input["water"] = f"structure {water_path}\n  number {water_number}\n  inside box {gap} {gap} {gap} {cell[0]-gap} {cell[1]-gap} {cell[2]-gap}\nend structure\n"
+
+            output_filenames.append(f"{str(water_path).replace(backslash, '/').split('.')[-2].split('/')[-1]}_{water_number}")
+
+        output_filename = "-".join(output_filenames) + ".xyz"
+        head_input = f"tolerance {tolerance}\nfiletype xyz\noutput {os.path.join(os.getcwd(), output_filename)}\npbc {cell[0]} {cell[1]} {cell[2]}\n"
+
+        total_input = head_input + "\n".join(structure_input.values())
+    
+        temp_file.write(total_input)
+        temp_file.flush()
+        temp_file.close()
+
+        Main.run_packmol(temp_file.name)
+
+        if os.path.exists(temp_file.name):
+            os.remove(temp_file.name)
+
+    Main.exit()
+
+
+if __name__ == "__main__":
+    main()

mdkits/build_cli/water.xyz

@@ -0,0 +1,5 @@
+3
+ water
+ O           10.203012       7.603800      12.673000
+ H            9.625597       8.420323      12.673000
+ H            9.625597       6.787278      12.673000

mdkits/cli/convert.py

@@ -3,7 +3,7 @@
 from ase.io import write
 import click
 import os
-from mdkits.util import encapsulated_ase, arg_type
+from mdkits.util import out_err, arg_type
 
 
 @click.command(name='convert')
@@ -15,12 +15,14 @@ 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')
-@click.option('-o', type=str, help='specify the output file name without suffix', default='out', show_default=True)
-def main(atoms, c, x, d, v, coord, cp2k, center, cell, o):
+@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, c, x, d, v, coord, cp2k, center, cell):
     """
     convet structure file in some formats
     """
+    out_err.check_cell(atoms, cell)
+    o = atoms.filename.split('.')[-2]
+
 
     if center:
         atoms.center()

mdkits/mdkits.py

@@ -1,4 +1,5 @@
 import click
+from mdkits.build_cli import build_cli
 from mdkits.cli import (
     convert,
     wrap,
@@ -8,7 +9,6 @@ from mdkits.cli import (
     density,
     cube,
     pdos,
-    build_cli,
 )
 
 

mdkits/util/arg_type.py

@@ -10,21 +10,17 @@ class CellType(click.ParamType):
 
     def convert(self, value, param, ctx):
         if isinstance(value, str):
-            if ',' not in value:
-                cell = cp2k_input_parsing.parse_cell()
+            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:
-                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)
+                self.fail(f"{value} is not a valid cell parameter", param, ctx)
 
 
 class FrameRangeType(click.ParamType):

mdkits/util/cp2k_input_parsing.py

@@ -33,7 +33,7 @@ def parse_cell():
                 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")
+            return [0., 0., 0., 90., 90., 90.]
 
 
 #def get_cell(cp2k_input_file, cell=None):

mdkits/util/out_err.py

@@ -2,7 +2,16 @@
 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")

{mdkits-0.1.7.dist-info → mdkits-0.1.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.7
+Version: 0.1.8
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory
@@ -18,6 +18,7 @@ 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)
 Requires-Dist: pyyaml (>=6.0.1,<7.0.0)

{mdkits-0.1.7.dist-info → mdkits-0.1.8.dist-info}/RECORD

@@ -1,13 +1,16 @@
 mdkits/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mdkits/build_cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mdkits/build_cli/adsorbate.py,sha256=Zp21i-miFv5zQlYjZnZuVpMxvNVT-6RtdlaoWDMwaOg,1900
+mdkits/build_cli/build_bulk.py,sha256=mOjoHHBui5fTYASabD96l6zBoKlQukT-LOyR2FZNzM4,1549
+mdkits/build_cli/build_cli.py,sha256=pH9g6OonxxEpLTJCVwk_EwhLtFrmrL51jjyCjmIXU2o,544
+mdkits/build_cli/build_interface.py,sha256=i1YE5iwazKVsTdQ_DXalNYeA8oflORWFePgJin1AJM4,3537
+mdkits/build_cli/build_solution.py,sha256=jqbrrLopBn9LaTO7UELQTqxu0NTcg1PYkf5cdT1qZnc,3359
+mdkits/build_cli/build_surface.py,sha256=LZtE3DMNgriOUb_sfPGbpYfZEf9b7sRWeKooaETsp2M,2663
+mdkits/build_cli/cut_surface.py,sha256=D1naCWj0QJE3AiInzy3SeGO37butothE3BS1rZsZ5MU,1425
+mdkits/build_cli/water.xyz,sha256=ByLDz-rYhw_wLPBU78lIQHe4s4Xf5Ckjft-Dus3czIc,171
 "mdkits/cli/,hb_distribution_down.py",sha256=i3NguzGebqCgy4uuVBeFajZRZnXtjhsJBPDGDdumlWA,4733
-mdkits/cli/adsorbate.py,sha256=rTj0oXkiUOboaxkfpbBoUicguMsB4-G-hJslsoUlbq0,1669
-mdkits/cli/build_bulk.py,sha256=mOjoHHBui5fTYASabD96l6zBoKlQukT-LOyR2FZNzM4,1549
-mdkits/cli/build_cli.py,sha256=5fFuq4VoW5sqbqKzRb5pWbNBlXBtuzHP68ur63o8WNo,380
-mdkits/cli/build_interface.py,sha256=i1YE5iwazKVsTdQ_DXalNYeA8oflORWFePgJin1AJM4,3537
-mdkits/cli/build_surface.py,sha256=LZtE3DMNgriOUb_sfPGbpYfZEf9b7sRWeKooaETsp2M,2663
-mdkits/cli/convert.py,sha256=yAMgxPvgKSB94W0PNnjIhXHwAxE8wynPdfnwjG7Fb4U,1871
+mdkits/cli/convert.py,sha256=OmQ-7hmw0imgfgCJaWFEy3ePixsU7VKf0mGuJ6jRpn0,1795
 mdkits/cli/cube.py,sha256=G-QNup8W6J1-LCcEl1EHsV3nstd23byePDOcE_95t18,1176
-mdkits/cli/cut_surface.py,sha256=D1naCWj0QJE3AiInzy3SeGO37butothE3BS1rZsZ5MU,1425
 mdkits/cli/data.py,sha256=FGA4S9Cfo6WUJBSPWKOJrrZXHo_Qza-jNG1P_Dw7yi4,3262
 mdkits/cli/density.py,sha256=Y4grT8p7CsxggGYo_nGE9z_wlkJeQS5eYWKJQcoA014,5559
 mdkits/cli/extract.py,sha256=bqqJBmSaVyPYyEseGpUJcMBufIfDLTNRdmUfJ0txE5E,2498
@@ -22,19 +25,19 @@ mdkits/cli/supercell.py,sha256=r5iddLw1NNzj7NTFlR2j_jpD1AMfrsxhA08bPwQvVvg,2059
 mdkits/cli/wrap.py,sha256=AUxGISuiCfEjdMYl-TKc2VMCPHSybWKrMIOTn_6kSp0,1043
 mdkits/config/__init__.py,sha256=ZSwmnPK02LxJLMgcYmNb-tIOk8fEuHf5jpqD3SDHWLg,1039
 mdkits/config/settings.yml,sha256=PY7u0PbFLuxSnd54H5tI9oMjUf-mzyADqSZtm99BwG0,71
-mdkits/mdkits.py,sha256=ASOEhY94G_P902ojOobvqPYu1L3AOFTS_Ooh5LJAjX0,603
+mdkits/mdkits.py,sha256=7yZHo13dn_Nn5K7BNIrEXFN44WoZoWD_MqgRQGhTJEU,627
 mdkits/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mdkits/util/arg_type.py,sha256=AbjQpv4CEjJJVV2J34jRHOtUYcvwr0lyy5EI9Su7T0s,2728
-mdkits/util/cp2k_input_parsing.py,sha256=Hnp8QEMs3bGID2qusJX1OjXVq6cdVL-d24aAUIMji_U,1290
+mdkits/util/arg_type.py,sha256=r744Q-Rau3F6BDRrS2Naygb4pLsOwcoSbVrAKIME6qc,2550
+mdkits/util/cp2k_input_parsing.py,sha256=7NMVOYEGycarokLJlhLoWWilciM7sd8MWp5FVTF7hqI,1223
 mdkits/util/encapsulated_ase.py,sha256=uhqIhsALxzwJYuFrfOYGGC6U0QLm_dcZNridvfl_XGc,4339
 mdkits/util/encapsulated_mda.py,sha256=td3H24u3eHOIS2nwPucfIaMxeaVxI77oFI8nnNhw7vo,2217
 mdkits/util/fig_operation.py,sha256=FwffNUtXorMl6qE04FipgzcVljEQii7wrNJUCJMyY3E,1045
 mdkits/util/numpy_geo.py,sha256=1Op8THoQeyqybSZAi7hVxohYCr4SzY6ndZC8_gAGXDA,3619
 mdkits/util/os_operation.py,sha256=ErN2ExjX9vZRfPe3ypsj4eyoQTEePqzlEX0Xm1N4lL4,980
-mdkits/util/out_err.py,sha256=5ckrO2_wP5QObBeJ5SJ58u6OtvMii5NsXB6-plHrmpg,207
+mdkits/util/out_err.py,sha256=K_vKJAfshamAeHIXcy3_mWYsuP5-DRjUO1ADeTn2D9Q,491
 mdkits/util/structure_parsing.py,sha256=mRPMJeih3O-ST7HeETDvBEkfV-1psT-XgxyYgDadV0U,4152
-mdkits-0.1.7.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
-mdkits-0.1.7.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
-mdkits-0.1.7.dist-info/METADATA,sha256=2g49Gv9xK-pjNm6S9xCormq10ppXLQQTaCl59y2uY0o,6910
-mdkits-0.1.7.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-mdkits-0.1.7.dist-info/RECORD,,
+mdkits-0.1.8.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
+mdkits-0.1.8.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
+mdkits-0.1.8.dist-info/METADATA,sha256=gpFmw5LOizLVQjlzU12d2--EF0gkvJxIQVJyKrhJ3n8,6948
+mdkits-0.1.8.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+mdkits-0.1.8.dist-info/RECORD,,