digichem-core 6.0.0rc1__py3-none-any.whl → 6.0.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- digichem/__init__.py +2 -2
- digichem/config/base.py +2 -2
- digichem/data/batoms/batoms-renderer.py +11 -2
- digichem/file/prattle.py +20 -16
- digichem/input/digichem_input.py +1 -1
- digichem/result/atom.py +3 -3
- digichem/result/metadata.py +3 -0
- digichem/test/test_translate.py +1 -1
- digichem/translate.py +7 -7
- {digichem_core-6.0.0rc1.dist-info → digichem_core-6.0.1.dist-info}/METADATA +6 -2
- {digichem_core-6.0.0rc1.dist-info → digichem_core-6.0.1.dist-info}/RECORD +14 -14
- {digichem_core-6.0.0rc1.dist-info → digichem_core-6.0.1.dist-info}/WHEEL +1 -1
- {digichem_core-6.0.0rc1.dist-info → digichem_core-6.0.1.dist-info}/licenses/COPYING.md +0 -0
- {digichem_core-6.0.0rc1.dist-info → digichem_core-6.0.1.dist-info}/licenses/LICENSE +0 -0
digichem/__init__.py
CHANGED
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@@ -20,7 +20,7 @@ from digichem.datas import get_resource
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# development = prerelease is not None
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# # The full version number of this package.
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# __version__ = "{}.{}.{}{}".format(major_version, minor_version, revision, "-pre.{}".format(prerelease) if development else "")
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-
__version__ = "6.0.
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+
__version__ = "6.0.1"
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_v_parts = __version__.split("-")[0].split(".")
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major_version = int(_v_parts[0])
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minor_version = int(_v_parts[1])
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@@ -39,7 +39,7 @@ __author__ = [
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]
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# Program date (when we were last updated). This is changed automatically.
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_last_updated_string = "
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_last_updated_string = "01/08/2024"
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last_updated = datetime.strptime(_last_updated_string, "%d/%m/%Y")
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# The sys attribute 'frozen' is our flag, '_MEIPASS' is the dir location.
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digichem/config/base.py
CHANGED
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@@ -72,7 +72,7 @@ Possible options are:
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batoms = Options(help = "Beautiful Atoms/Blender specific options (only applies if engine == 'batoms'",
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blender = Option(help = "Path to the blender executable, in which beautiful atoms should be installed", default = None),
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cpus = Option(help = "The number of CPUs/threads to use. This option is overridden if running in a calculation environemnt (where it uses the same number of CPUs as the calculation did)", type = int, default = 1),
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render_samples = Option(help = "The number of render samples (or passes) to use. Higher values result in higher image quality and greater render times", type = int, default =
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render_samples = Option(help = "The number of render samples (or passes) to use. Higher values result in higher image quality and greater render times", type = int, default = 64),
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perspective = Option(help = "The perspective mode", choices = ["orthographic", "perspective"], default = "orthographic")
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# TODO: Colour options.
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),
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@@ -318,4 +318,4 @@ To disable the maximum width, set to null.""", type = int, default = 1500),
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except FileNotFoundError as e:
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# We lost the race, give up.
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raise Exception("Failed to write settings to file '{}'; one of the parent directories does not exist".format(path)) from e
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-
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+
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@@ -210,8 +210,8 @@ def main():
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parser.add_argument("--isovalues", help = "List of isovalues to render", nargs = "*", type = float, default = [])
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parser.add_argument("--isotype", help = "Whether to render positive, negative or both isosurfaces for each isovalue", choices = ["positive", "negative", "both"], default = "both")
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parser.add_argument("--isocolor", help = "The colouring method to use for isosurfaces", choices = ["sign", "cube"], default = "sign")
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parser.add_argument("--primary-color", help = "RGBA for one of the colors to use for isosurfaces", type = float, nargs = 4, default = [0.1, 0.1, 0.9, 0.
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parser.add_argument("--secondary-color", help = "RGBA for the other color to use for isosurfaces", type = float, nargs = 4, default = [1, 0.058, 0.0, 0.
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parser.add_argument("--primary-color", help = "RGBA for one of the colors to use for isosurfaces", type = float, nargs = 4, default = [0.1, 0.1, 0.9, 0.65])
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parser.add_argument("--secondary-color", help = "RGBA for the other color to use for isosurfaces", type = float, nargs = 4, default = [1, 0.058, 0.0, 0.65])
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parser.add_argument("--style", help = "Material style for isosurfaces", choices = ('default', 'metallic', 'plastic', 'ceramic', 'mirror'), default = "default")
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parser.add_argument("--cpus", help = "Number of parallel CPUs to use for rendering", type = int, default = 1)
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parser.add_argument("--use-gpu", help = "Whether to enable GPU rendering", action = "store_true")
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@@ -243,6 +243,10 @@ def main():
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if args.rotations is not None:
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rotations = [yaml.safe_load(rotation) for rotation in args.rotations]
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# Remove the starting cube object.
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bpy.ops.object.select_all(action='SELECT')
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bpy.ops.object.delete()
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# Load the input data.
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mol = add_molecule(
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args.cube_file,
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# Enable to add an outline.
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#bpy.context.scene.render.use_freestyle = True
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# We have plenty of memory to play with, use one tile.
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bpy.context.scene.cycles.tile_x = args.resolution
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bpy.context.scene.cycles.tile_y = args.resolution
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bpy.context.scene.cycles.tile_size = args.resolution
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# Performance options.
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bpy.context.scene.render.threads_mode = 'FIXED'
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bpy.context.scene.render.threads = args.cpus
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digichem/file/prattle.py
CHANGED
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@@ -155,22 +155,20 @@ class Openprattle_converter():
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inputs = self.input_file
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# GO.
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check = True,
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)
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except CalledProcessError as e:
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self.handle_logging(e.stderr)
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raise
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done_process = subprocess.run(
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sig,
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input = inputs,
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stdout = subprocess.PIPE,
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stderr = subprocess.PIPE,
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# TODO: Using universal newlines is probably not safe here; some formats are binary (.cdx etc...)
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universal_newlines = True,
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)
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# This can throw exceptions.
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self.handle_logging(done_process.stderr)
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if done_process.returncode != 0:
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raise Digichem_exception("prattle subprocess returned code {}".format(done_process.returncode))
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# Return our output.
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return done_process.stdout if output_file is None else None
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def handle_logging(self, raw_output):
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"""
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"""
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exceptions = []
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for raw_message in raw_output.split("\n"):
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if raw_message == "":
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# Nothing returned, nothing to do.
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-
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continue
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# Each message should be in JSON, but check.
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try:
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message = json.loads(raw_message)
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message_text = message['message']
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if message['exception']:
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exceptions.append(Exception(message['exception']))
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continue
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#message_text += "\n" + message['exception']
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digichem.log.get_logger().log(
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message['levelno'],
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message_text
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except Exception:
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digichem.log.get_logger().error("Unexpected output from oprattle: '{}'".format(raw_message), exc_info=False)
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if len(exceptions) > 0:
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raise exceptions[0]
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digichem/input/digichem_input.py
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return Digichem_coords.from_com(com_file, file_name = file_name, **kwargs)
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except:
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raise ValueError("Could not parse
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raise ValueError("Could not parse coordinates from '{}'".format(file_name))
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digichem/result/atom.py
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# Then coordinates.
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# No effort is made here to truncate coordinates to a certain precision.
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for atom in self:
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xyz += "{} {:f} {:f} {:f}\n".format(atom.element.symbol, atom.coords[0], atom.coords[1], atom.coords[2])
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xyz += "{} {:f} {:f} {:f}\n".format(atom.element.symbol, float(atom.coords[0]), float(atom.coords[1]), float(atom.coords[2]))
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return xyz
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:param data: The data to parse.
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:param result_set: The partially constructed result set which is being populated.
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"""
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return [self(atom_dict.get('index', index +1), atom_dict['element'], (atom_dict['coords']['x']['value'], atom_dict['coords']['y']['value'], atom_dict['coords']['z']['value']), atom_dict['mass']['value']) for index, atom_dict in enumerate(data)]
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return [self(atom_dict.get('index', index +1), atom_dict['element'], (float(atom_dict['coords']['x']['value']), float(atom_dict['coords']['y']['value']), float(atom_dict['coords']['z']['value'])), atom_dict['mass']['value']) for index, atom_dict in enumerate(data)]
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@classmethod
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def list_from_parser(self, parser):
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zip_data = zip_longest(atomnos, atomcoords, atommasses, fillvalue = None)
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# Loop through and rebuild our objects.
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return [self(index+1, atomic_number,
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return [self(index+1, atomic_number, (float(coords[0]), float(coords[1]), float(coords[2])), mass) for index, (atomic_number, coords, mass) in enumerate(zip_data)]
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@classmethod
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def list_from_coords(self, coords):
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digichem/result/metadata.py
CHANGED
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pressure = None,
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orbital_spin_type = None,
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digichem_version = None,
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silico_version = None,
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solvent = None,
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num_cpu = None,
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memory_available = None,
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self.pressure = pressure
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self.orbital_spin_type = orbital_spin_type
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# TOOD: Ideally this would be parsed from the calculation output somehow, but this is fine for now.
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if silico_version:
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self.digichem_version = silico_version
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self.digichem_version = digichem.__version__ if digichem_version is None else digichem_version
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self.solvent = solvent
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self.num_cpu = num_cpu
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digichem/test/test_translate.py
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assert default.translate("gaussian") == 0
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assert default.translate("orca") == 100
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assert default.translate("turbomole") ==
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assert default.translate("turbomole") == "m3"
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# Check the named values.
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for name, value in [("Tiny", 25), ("Small", 50), ("Medium", 100), ("Large", 200), ("Huge", 500)]:
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digichem/translate.py
CHANGED
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basis_set["turbomole"] = basis_set['name'][:-5] + "**"
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# Gaussian has a strange, contracted style naming scheme for Karlsruhe,
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# and a misleading/incorrect name for def2-
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# and a misleading/incorrect name for def2-SV(P).
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#print(basis_set['name'])
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if basis_set['name'] == "def2-SV(P)":
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basis_set['gaussian'] = "def2SVPP"
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"""A class for converting between cube grid sizes."""
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table = [
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{"name": "Default", "points": 100, "gaussian": 0, "turbomole":
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{"name": "Tiny", "points": 25},
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{"name": "Small", "points": 50},
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{"name": "Medium", "points": 100},
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{"name": "Large", "points": 200},
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{"name": "Huge", "points": 500},
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{"name": "Default", "points": 100, "gaussian": 0, "turbomole": "m3", "orca": 100}, # Default depends on the calc program. Gaussian uses a special value of 'zero' to select a default algorithm.
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{"name": "Tiny", "points": 25, "turbomole": "1", },
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{"name": "Small", "points": 50, "turbomole": "2", },
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{"name": "Medium", "points": 100, "turbomole": "3", },
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{"name": "Large", "points": 200, "turbomole": "4", },
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{"name": "Huge", "points": 500, "turbomole": "5", },
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]
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Metadata-Version: 2.3
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Name: digichem-core
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Version: 6.0.
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Version: 6.0.1
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Summary: Open-source library for Digichem core components
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Project-URL: Homepage, https://github.com/Digichem-Project/digichem-core
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Project-URL: Documentation, https://doc.digi-chem.co.uk
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- Alternatively, if you are looking for the full Digichem program, try [Build-boy](https://github.com/Digichem-Project/build-boy)
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- If you'd like more information on the Digichem project, check out the [website](https://www.digi-chem.co.uk)
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## Documentation
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Please refer to the main Digichem [documentation](https://doc.digi-chem.co.uk) for further reading.
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## Dependencies
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- adjustText
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Digichem-core is licensed under the BSD-3-Clause license, but some files are licensed separately. See [COPYING.md](COPYING.md) for full details.
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The Digichem logo and branding is Copyright Digichem 2024, you may not use them in any way (although you are welcome to look at them).
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The Digichem logo and branding is Copyright Digichem 2024, you may not use them in any way (although you are welcome to look at them).
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digichem/__init__.py,sha256=
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digichem/__init__.py,sha256=xLNrL0eRkW97U0pkYCRbIk1AM-LDn8Jh02duTrdNxeg,2287
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digichem/basis.py,sha256=PDcfA8LuboEqLwMX4cktewdchxFJ5fMPdzR9-Ui16K4,4851
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digichem/datas.py,sha256=t2PuQFvPb55WO_qVF3Xz67XNodQDimqYD26VkRPEWLA,433
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digichem/log.py,sha256=tjl8Er16HUsAibBZGZMu8KyT0w53YM3u0Neh_l2jD9Q,6166
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digichem/memory.py,sha256=jfeb1AYMOdm22vSKMHf01IDzRJCCoDnowh_OB38VVNM,5375
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digichem/translate.py,sha256=
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digichem/translate.py,sha256=YKm7wko13A17zQJW8qOT52rzp9wDmR0GDzOepuzr75I,21326
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digichem/config/README,sha256=0y5sxYPAmpD3XNzgJrr-U8xmiQbheC8bz8lvnNmsNtc,180
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digichem/config/__init__.py,sha256=wXnmk1fuNZeHOKz06wBfTUkM8-XuW08F2H8QiHyS8Xs,227
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digichem/config/base.py,sha256=
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digichem/config/base.py,sha256=dd6ApHjM9UbkQ2wTDeMHaMwQkHlqvf35mdnb5HFLmcY,24585
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digichem/config/locations.py,sha256=Jlvql0KJrJEIO_2U6BRS5bjHelKjGGIETR9hOuNe0K0,584
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digichem/config/parse.py,sha256=amJx89JXkkEyMMSYr5GvLFnLZO3hWahuZtNlx0F0PhA,2667
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digichem/config/util.py,sha256=i5NgxLPcLx1RM4bArog77hsHxkQmwlqyzJbDtrozBG0,4613
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@@ -17,7 +17,7 @@ digichem/data/batoms/COPYING,sha256=cZepDmXS1dlBlf2hQ8Ez4mYUp1JkXhSISULqFMaU3-Y,
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digichem/data/batoms/LICENSE,sha256=ixuiBLtpoK3iv89l7ylKkg9rs2GzF9ukPH7ynZYzK5s,35148
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digichem/data/batoms/README,sha256=WqRkTUFuvleDNkwra2vPwuiHYy9YoRNcT82oke4MftM,224
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digichem/data/batoms/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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digichem/data/batoms/batoms-renderer.py,sha256=
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digichem/data/batoms/batoms-renderer.py,sha256=BPgxBH4BlBaKzH6UYU933hR60YNGWr5sT-a4FXXiOpw,14168
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digichem/data/config/digichem.yaml,sha256=UhPTEvVssN2FVNCakkwGxrUeD9hXLVO1urSmGdfDjn4,30360
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digichem/data/tachyon/COPYING.md,sha256=GRiBuwmAHaIlamBpWxTsyn_p04chI28RiRTAT3m8aXg,202
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digichem/data/tachyon/LICENSE,sha256=pZ-1ttB2_3CeqjwekQHX6jlPIeFvX32KbyLFNoUJMhc,1532
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@@ -36,7 +36,7 @@ digichem/file/__init__.py,sha256=vcDfoYlL0YbFcCyw-3D4SiGtA-hxkFKUtP30DO-JvqE,62
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digichem/file/base.py,sha256=841-v2GWdba-o7BP0ZtLMFNyfEMDM2HvBTYiozuV_fI,17342
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digichem/file/cube.py,sha256=kvNnyKHs0c0L-7LnYggvil-ciDEwNWAhOZT2-KgyP5s,13759
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digichem/file/fchk.py,sha256=tWhp0daZPMlYmqkGkidUFwVHTA-8wCUf6Py6CNeT7tk,4035
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digichem/file/prattle.py,sha256=
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digichem/file/prattle.py,sha256=LDayqA7TZVMJKekyl4laHePOCesfBcQ36ul0516OEfo,9927
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digichem/file/types.py,sha256=PoaCBL1fmyufduWSgBkIwnZhGPVTc06ru5YFvuvk4Ug,3533
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digichem/image/__init__.py,sha256=T9fN41dV0oZ7dT_MES7iYaFdPgzZM5R5hhIvvhlY8U4,133
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digichem/image/base.py,sha256=6LGIYK2zB7lQxFhV5t2ZJPcpNMOqRv-JzrBJEeTF9Wg,5193
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@@ -49,7 +49,7 @@ digichem/image/structure.py,sha256=gxgX5cXA3BaqBh5K7UPcVGWX-yG5kc6Robf5sWT1IYM,4
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digichem/image/vmd.py,sha256=OqZJO08dpZWdqVav2-1GNxvxRmw6RdpF-jCvGS6wUpQ,39011
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digichem/input/__init__.py,sha256=SxCeQkUNOalYu9oxhPGHQHX6s5CqBlSVuMUt7n-ywFw,165
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digichem/input/base.py,sha256=9nxut3IlvKSYCjRUzpi7SdlaO_4MU8KWAecV-z3T1jo,3082
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digichem/input/digichem_input.py,sha256
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digichem/input/digichem_input.py,sha256=dHpapTmDbAk93ve7UcgmiXZzC2PShhcYMJ9BBQF1ces,19664
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digichem/input/gaussian.py,sha256=ZwfCA0jgHcY8JVcyyKmnchU-OyQ26-8ynQJdeYtNT7A,5651
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digichem/misc/__init__.py,sha256=gRlflbkXYyKvqeQ2KTnNAdJ00S6Vhmk-tzSVCBSiWgk,162
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digichem/misc/argparse.py,sha256=AG33L7MCi-ftb4XnvndQb4hKcorzJxESAVB0HIZRlcw,1371
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@@ -68,14 +68,14 @@ digichem/parse/turbomole.py,sha256=3DJjXcfYw2RHL6bYbw9VUspYJ_dpVEiUVAartLAHlcI,9
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digichem/parse/util.py,sha256=ndeE3R_F-HlbI-dCXPEa7v_n7iVwwB7_aMoOju4tOxg,25097
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digichem/result/__init__.py,sha256=FUNL2pc2bP3XNVFRrlyrTppVWEsPRHcThLiVytpsH84,222
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digichem/result/angle.py,sha256=jehU0dRN4nALvUFzIdkh4GGQORq4lgXre8ZfFQMzB94,5043
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digichem/result/atom.py,sha256=
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digichem/result/atom.py,sha256=1eYBrZnE8jwycwt39vg8qhn3ShEPqhXwY7VCDrooVLw,27637
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digichem/result/base.py,sha256=SH4GAZt-6GsHihAUWLUXjnIhhp_jSmpebx2yJQkIr9M,9630
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digichem/result/dipole_moment.py,sha256=Pbx9o3j7ZQB5vtZlvt5yhLrvKTXpC69EGlhTXj00HT4,11075
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digichem/result/emission.py,sha256=0OPXNR1ZX9ALpjD0Ie5OkrOHNDDz6FsK3pK_0GyqqLI,19754
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digichem/result/energy.py,sha256=53Dm2kHA-x8KtDY3Wq52cPbpE5E01W1lQTNaLe0goZE,10851
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digichem/result/excited_state.py,sha256=gBPQsOxfdflyq8zJLKKyGgux01qS4O16GeW-Yjv8u_M,33930
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digichem/result/ground_state.py,sha256=JMRBQ-MC2Ak8Ur-TXGzNkJtSVykkhswHPTOnttZFujE,3790
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digichem/result/metadata.py,sha256=
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digichem/result/metadata.py,sha256=ZfmXzXL6WFSFxe62TYlF5GEwzN3vWhD5iWorC3eZLV8,26890
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digichem/result/multi.py,sha256=IzupKHMcXTf6AReeUCjY9Szy2b4TdOHVtC2Tlb9xg0o,4330
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digichem/result/nmr.py,sha256=u3qXZRrTBvUnfJexrtEHZLIyQ4dq_zFDXwcC2PoEGqQ,47263
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digichem/result/orbital.py,sha256=6BX4GfnLJRj_AZs75FWPLFX6r0z9OL0OSh1v8EOHqws,28271
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@@ -102,10 +102,10 @@ digichem/test/test_input.py,sha256=TLGFxsSYGKTUSO5fxjZN2VqzDZFP3AHlbrE2JGmnq8g,1
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digichem/test/test_parsing.py,sha256=OAK3QJfHEehhhLF4Z75o5Fj-hKakfhrXtt5PRPnDY6c,3197
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digichem/test/test_prattle.py,sha256=x-CeVX3Gbs5BHGndBGrtseGZwgUm3jamxstFijmKB5w,1033
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digichem/test/test_result.py,sha256=BPo9-weVCBL_0dgcETDdWkQ20msCSDTStZ7tPB1t55o,24328
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digichem/test/test_translate.py,sha256=
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digichem/test/test_translate.py,sha256=_3FkYottqHZGxMSTJkbcE8dQXhQlrNlVS0FjMopIwl4,3575
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digichem/test/util.py,sha256=R4lE1pg0SzpTbJIQnFh_ffeNb9jAnfFIhp-6F-_fX7Q,8576
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digichem_core-6.0.
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digichem_core-6.0.1.dist-info/METADATA,sha256=wu-J74dMb0yQKcdNRZy1C7peWg2ZgjT09fv-9n8qPrM,4050
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digichem_core-6.0.1.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
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digichem_core-6.0.1.dist-info/licenses/COPYING.md,sha256=d-yG6IJrlqLkuiuoOFe331YKzMRS05pnmk4e98gu9pQ,900
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digichem_core-6.0.1.dist-info/licenses/LICENSE,sha256=ZLlePQN2WLgdvmIGLEjjHtgIoneUGR2MgE9yjMg1JiY,1457
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digichem_core-6.0.1.dist-info/RECORD,,
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File without changes
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File without changes
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