mdkits 0.1.11__py3-none-any.whl → 0.1.13__py3-none-any.whl

mdkits/build_cli/build_solution.py

@@ -27,63 +27,63 @@ def main(filename, infile, install, water_number, n, tolerance, cell, gap):
     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")
+        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
 
-        temp_file = tempfile.NamedTemporaryFile(mode='w+t', delete=False)
-        backslash = "\\"
+        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")
 
-        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"
+            temp_file = tempfile.NamedTemporaryFile(mode='w+t', delete=False)
+            backslash = "\\"
 
-                output_filenames.append(f"{file.replace(backslash, '/').split('.')[-2].split('/')[-1]}_{n[index]}")
+            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"
 
-        if water_number > 0:
-            water_path = resources.files('mdkits.build_cli').joinpath('water.xyz')
+                    output_filenames.append(f"{file.replace(backslash, '/').split('.')[-2].split('/')[-1]}_{n[index]}")
 
-            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"
+            if water_number > 0:
+                water_path = resources.files('mdkits.build_cli').joinpath('water.xyz')
 
-            output_filenames.append(f"{str(water_path).replace(backslash, '/').split('.')[-2].split('/')[-1]}_{water_number}")
+                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_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"
+                output_filenames.append(f"{str(water_path).replace(backslash, '/').split('.')[-2].split('/')[-1]}_{water_number}")
 
-        total_input = head_input + "\n".join(structure_input.values())
+            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()
+            temp_file.write(total_input)
+            temp_file.flush()
+            temp_file.close()
 
-        Main.run_packmol(temp_file.name)
+            Main.run_packmol(temp_file.name)
 
-        if os.path.exists(temp_file.name):
-            os.remove(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()
+        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__":

mdkits/util/arg_type.py

@@ -62,9 +62,8 @@ class StructureType(click.ParamType):
 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)
+        super().__init__(choices=tuple(g2.names))
 
 class AdsSiteType(click.Choice):
     name = "adsorption site"

{mdkits-0.1.11.dist-info → mdkits-0.1.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.1.11
+Version: 0.1.13
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory

{mdkits-0.1.11.dist-info → mdkits-0.1.13.dist-info}/RECORD

@@ -4,7 +4,7 @@ mdkits/build_cli/adsorbate.py,sha256=Zp21i-miFv5zQlYjZnZuVpMxvNVT-6RtdlaoWDMwaOg
 mdkits/build_cli/build_bulk.py,sha256=o3SFov5Ggk-qKcy6-NBoIYKvZV24OhcH3-du1d0U6H4,1593
 mdkits/build_cli/build_cli.py,sha256=sqjnq5aHWLYLbNzN5SORkEYeYaewLagFuSvspJxyh7E,725
 mdkits/build_cli/build_interface.py,sha256=3EDxUb-vGHFuat1Ex_wojVsN8PtzHiGrnDQIEa9WZ60,2448
-mdkits/build_cli/build_solution.py,sha256=dsbI_gOS8Cz89Bv-UNxy9FziDoNBOIiddqL3bKmAe60,3582
+mdkits/build_cli/build_solution.py,sha256=An-aeqB0g2LRaWJgc1p10r-5F5MfGs9WK1EAhQzZr6U,3750
 mdkits/build_cli/build_surface.py,sha256=cBEQ-KR_6j-Mcsxrwvzyl6p1SiY_chIytrCu7MS3q08,2794
 mdkits/build_cli/cut_surface.py,sha256=R0Snr-y23SYLfNhdBC5VgT4KFY1SOGn5hZlVvX5CUvw,2757
 mdkits/build_cli/supercell.py,sha256=3iTTt3DHaERWDFonhBRS0oqWhjFh6pbS5SpIR-O1gYg,1034
@@ -27,7 +27,7 @@ mdkits/config/__init__.py,sha256=ZSwmnPK02LxJLMgcYmNb-tIOk8fEuHf5jpqD3SDHWLg,103
 mdkits/config/settings.yml,sha256=PY7u0PbFLuxSnd54H5tI9oMjUf-mzyADqSZtm99BwG0,71
 mdkits/mdkits.py,sha256=7yZHo13dn_Nn5K7BNIrEXFN44WoZoWD_MqgRQGhTJEU,627
 mdkits/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mdkits/util/arg_type.py,sha256=VQS9pMYr5CmVTy-BDSAaPrRNWnzC6up-vpoW0io8jYQ,2565
+mdkits/util/arg_type.py,sha256=VVIc3PSeIiyq2-s20KMem2feU0hI2v3fX7MBKpHsolw,2544
 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
@@ -36,8 +36,8 @@ mdkits/util/numpy_geo.py,sha256=1Op8THoQeyqybSZAi7hVxohYCr4SzY6ndZC8_gAGXDA,3619
 mdkits/util/os_operation.py,sha256=ErN2ExjX9vZRfPe3ypsj4eyoQTEePqzlEX0Xm1N4lL4,980
 mdkits/util/out_err.py,sha256=b4eFz9kqqNReK9UCHak9k5tBlEj9yHAIADDTRbaNaNk,693
 mdkits/util/structure_parsing.py,sha256=mRPMJeih3O-ST7HeETDvBEkfV-1psT-XgxyYgDadV0U,4152
-mdkits-0.1.11.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
-mdkits-0.1.11.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
-mdkits-0.1.11.dist-info/METADATA,sha256=50idwtQfdNsEeSS0OZciphe82WaevI_wpsx5j-dsRSA,6907
-mdkits-0.1.11.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-mdkits-0.1.11.dist-info/RECORD,,
+mdkits-0.1.13.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
+mdkits-0.1.13.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
+mdkits-0.1.13.dist-info/METADATA,sha256=m46S3Gbvpa5H0bQdHLA_V3JfJuA2F1AKOy2KIfMkbaY,6907
+mdkits-0.1.13.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+mdkits-0.1.13.dist-info/RECORD,,