mdkits 0.1.10__tar.gz → 0.1.12__tar.gz

{mdkits-0.1.10 → mdkits-0.1.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.10
+Version: 0.1.12
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory

{mdkits-0.1.10 → mdkits-0.1.12}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.1.10"
+version = "0.1.12"
 description = "kits for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

mdkits-0.1.12/src/mdkits/build_cli/build_solution.py

@@ -0,0 +1,90 @@
+import click, os
+from mdkits.util import arg_type
+from importlib import resources
+from mdkits.cli import convert
+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()
+    else:
+        from julia import Pkg, Main
+
+        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)
+
+        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()
+
+
+if __name__ == "__main__":
+    main()

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

@@ -1,89 +0,0 @@
-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
-
-
-@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)
-
-    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()
-
-
-if __name__ == "__main__":
-    main()