diff --git a/docs/_build/doctrees/api/tcutility.data.atom_data_info.doctree b/docs/_build/doctrees/api/tcutility.data.atom_data_info.doctree new file mode 100644 index 00000000..c41d0d96 Binary files /dev/null and b/docs/_build/doctrees/api/tcutility.data.atom_data_info.doctree differ diff --git a/docs/_build/doctrees/api/tcutility.data.doctree b/docs/_build/doctrees/api/tcutility.data.doctree new file mode 100644 index 00000000..ceb131c1 Binary files /dev/null and b/docs/_build/doctrees/api/tcutility.data.doctree differ diff --git a/docs/_build/doctrees/api/tcutility.doctree b/docs/_build/doctrees/api/tcutility.doctree index ecf2121f..58b0369c 100644 Binary files a/docs/_build/doctrees/api/tcutility.doctree and b/docs/_build/doctrees/api/tcutility.doctree differ diff --git a/docs/_build/doctrees/api/tcutility.job.doctree b/docs/_build/doctrees/api/tcutility.job.doctree index e2537876..ff9f4ddc 100644 Binary files a/docs/_build/doctrees/api/tcutility.job.doctree and b/docs/_build/doctrees/api/tcutility.job.doctree differ diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index a2770b92..31772ad8 100644 Binary files a/docs/_build/doctrees/environment.pickle and b/docs/_build/doctrees/environment.pickle differ diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html index 7a6bbbf4..22519501 100644 --- a/docs/_build/html/_modules/index.html +++ b/docs/_build/html/_modules/index.html @@ -254,6 +254,9 @@

All modules for which code is available

  • tcutility.analysis.vdd.manager
  • tcutility.analysis.vibration.ts_vibration
  • tcutility.cache
    • +
  • tcutility.data.atom
    • +
  • tcutility.data.functionals
    • +
  • tcutility.data.molecules
  • tcutility.formula
  • tcutility.geometry
  • tcutility.job.adf
    • diff --git a/docs/_build/html/_modules/tcutility.html b/docs/_build/html/_modules/tcutility.html index 95a9e6eb..13d8f78d 100644 --- a/docs/_build/html/_modules/tcutility.html +++ b/docs/_build/html/_modules/tcutility.html @@ -271,7 +271,7 @@

    Source code for tcutility

     
 
 
-from tcutility import constants, formula, geometry, log, molecule, results, slurm, data  # noqa: F401, E402
+from tcutility import constants, formula, geometry, log, molecule, results, slurm, data, analysis, spell_check  # noqa: F401, E402
    diff --git a/docs/_build/html/_modules/tcutility/data/atom.html b/docs/_build/html/_modules/tcutility/data/atom.html new file mode 100644 index 00000000..c63f3264 --- /dev/null +++ b/docs/_build/html/_modules/tcutility/data/atom.html @@ -0,0 +1,420 @@ + + + + + + + + + + tcutility.data.atom — TCutility v0.8.5 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + +
    +
    +
    +
    + + + Ctrl+K +
    +
    + +
    +
    + + + +
    + +
    + +
    + + + TCutility + +
    + +
    + +
    + + +
    + +
    + + + +
    + + +
    + TheoCheM
    + +
    + +
    + + +
    + + +
    + + + +
    + +
    + + +
    +
    + + + + + +
    + + + +
    + + + + +
    + +
    + TheoCheM
    + +
    + +
    + + +
    +
    + + + + +
    + +
    + + +
    +
    + +
    +
    + +
    + +
    + + + + +
    + +
    + + +
    +
    + + + + + +
    + +

    Source code for tcutility.data.atom

    +import pathlib as pl
+
+
+# read data
+data_dir = pl.Path(__file__).parents[0] / "atom_data_info"
+
+with open(data_dir / "name.txt") as data:
+    lines = data.readlines()
+_element_order = [line.split(",")[1].strip() for line in lines]
+
+with open(data_dir / "symbol.txt") as data:
+    lines = data.readlines()
+_symbol_order = [line.split(",")[1].strip() for line in lines]
+
+with open(data_dir / "radius.txt") as data:
+    lines = data.readlines()
+_radii = {int(line.split(",")[0]): float(line.split(",")[1].strip()) for line in lines}
+
+with open(data_dir / "color.txt") as data:
+    lines = data.readlines()
+_colors = {int(line.split(",")[0]): [int(x.strip()) for x in line.split(",")[1:]] for line in lines}
+
+
+
    
+[docs]
+def parse_element(val):
+    """
+    Parse a str or int to an atom number.
+
+    Args:
+        val: Element name, symbol or atom number.
+
+    Returns:
+        Atom number corresponding to val.
+
+    Examples:
+
+        .. code-block:: python
+
+            parse_element('Hydrogen') == 1
+            parse_element('C') == 6
+            parse_element(23) == 23
+    """
+    # we will assume an integer value is an atom number already
+    if isinstance(val, int):
+        return val
+    # if it is not an int it should be a string
+    if val.lower() in _element_order:
+        # first try to get it in the element name list
+        return _element_order.index(val.lower()) + 1
+    if val in _symbol_order:
+        # alternatively try to get it in the symbol list
+        return _symbol_order.index(val) + 1
+    raise KeyError(f'Element "{val}" not parsable.')
    
+
+
+
+
    
+[docs]
+def radius(element):
+    '''
+    Args:
+        element: the symbol, name or atom number of the element. See :func:`parse_element`.
+    Return: 
+        The empirical covalent radius of an element in angstroms, up to element 96.
+    '''
+    num = parse_element(element)
+    return _radii.get(num)
    
+
+
+
+
    
+[docs]
+def color(element):
+    '''
+    Args:
+        element: the symbol, name or atom number of the element. See :func:`parse_element`.
+
+    Return:
+        The standard CPK colors of the elements, up to element 109.
+    '''
+    num = parse_element(element)
+    return _colors[num]
    
+
+
+
+if __name__ == "__main__":
+    print(color("carbon"))
+
    + +
    + + + + + +
    + +
    +
    +
    + +
    + + + +
    + + +
    + + +
    +
    +
    + + + + + + + + \ No newline at end of file diff --git a/docs/_build/html/_modules/tcutility/data/functionals.html b/docs/_build/html/_modules/tcutility/data/functionals.html new file mode 100644 index 00000000..c0d59be9 --- /dev/null +++ b/docs/_build/html/_modules/tcutility/data/functionals.html @@ -0,0 +1,534 @@ + + + + + + + + + + tcutility.data.functionals — TCutility v0.8.5 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + +
    +
    +
    +
    + + + Ctrl+K +
    +
    + +
    +
    + + + +
    + +
    + +
    + + + TCutility + +
    + +
    + +
    + + +
    + +
    + + + +
    + + +
    + TheoCheM
    + +
    + +
    + + +
    + + +
    + + + +
    + +
    + + +
    +
    + + + + + +
    + + + +
    + + + + +
    + +
    + TheoCheM
    + +
    + +
    + + +
    +
    + + + + +
    + +
    + + +
    +
    + +
    +
    + +
    + +
    + + + + +
    + +
    + + +
    +
    + + + + + +
    + +

    Source code for tcutility.data.functionals

    +import os
+from tcutility import results, log, spell_check
+
+
+j = os.path.join
+
+
+
    
+[docs]
+def get(functional_name: str) -> results.Result:
+    '''
+    Return information about a given functional.
+
+    Args:
+        functional_name: the name of the functional. It should exist in the :func:`get_available_functionals` keys.
+
+    Return:
+        A |Result| object containing information about the functional if it exists. Else it will return ``None``.
+    
+    .. seealso::
+        :func:`get_available_functionals` for an overview of the information returned.
+    '''
+
+    spell_check.check(functional_name, functionals.keys(), caller_level=3)
+    return functionals[functional_name]
    
+
+
+
+
    
+[docs]
+def functional_name_from_path_safe_name(path_safe_name: str) -> results.Result:
+    '''
+    Return information about a given functional given its path-safe name.
+    This can be useful when you want to know the functional from a path name.
+
+    Return:
+        A |Result| object containing information about the functional if it exists. Else it will return ``None``.
+    
+    .. seealso::
+        :func:`get_available_functionals` for an overview of the information returned.
+    '''
+    for functional, functional_info in functionals.items():
+        if path_safe_name == functional_info.path_safe_name:
+            return functional
    
+
+
+
+
    
+[docs]
+def get_available_functionals():
+    '''
+    Function that returns a dictionary of all available XC-functionals.
+
+    Returns:
+        : A |Result| object containing information about all available XC-functionals.
+            The functional names are stored as the keys and the functional information is stored as the values.
+            The values contain the following information:
+
+                - ``name`` **(str)** - the name of the functional.
+                - ``path_safe_name`` **(str)** - the name of the functional made suitable for file paths. 
+                    This name is the same as the normal name, but without parentheses. Asterisks are replaced with lower-case ``s``.
+                - ``name_no_disp`` **(str)** - the name of functional without the dispersion correction.
+                - ``category`` **(str)** - the category the functional belongs to.
+                - ``dispersion`` **(str)** - the dispersion correction part of the functional name.
+                - ``dispersion_name`` **(str)** - the name of the dispersion correction as it would be written in ADF.
+                - ``includes_disp`` **(bool)** - whether the functional already includes a dispersion correction.
+                - ``use_libxc`` **(bool)** - whether the functional is from the LibXC library.
+                - ``available_in_adf`` **(bool)** - whether the functional is available in ADF.
+                - ``available_in_band`` **(bool)** - whether the functional is available in BAND.
+                - ``available_in_orca`` **(bool)** - whether the functional is available in ORCA.
+                - ``adf_settings`` **(|Result|)** - the settings that are used to select the functional in the ADF input.
+    '''
+    def set_dispersion(func):
+        disp_map = {
+            '-D4': 'GRIMME4',
+            '-D3(BJ)': 'GRIMME3 BJDAMP',
+            '-D3BJ': 'GRIMME3 BJDAMP',
+            '-D3': 'GRIMME3',
+            '-dDsC': 'dDsC',
+            '-dUFF': 'UFF',
+            '-MBD': 'MBD',
+            '-MBD@rsSC': 'MBD',
+            '-D': 'DEFAULT'
+        }
+
+        # set some default values for useful parameters
+        func.name_no_disp = func.name
+        func.dispersion = None
+        func.dispersion_name = None
+
+        # go through every dispersion correction and check if we are using it
+        for disp_suffix, disp_name in disp_map.items():
+            if func.name.endswith(disp_suffix):
+                # dispersion will be the suffix without the -
+                func.dispersion = disp_suffix[1:]
+                func.dispersion_name = disp_name
+
+                # check if the functional already includes the dispersion correction
+                if func.includes_disp:
+                    break
+
+                # else we set the name of the functional without dispersion for later
+                func.name_no_disp = func.name[:-len(disp_suffix)]
+                # get the dispersion settings for ADF. Try to get custom values if they were provided.
+                func.adf_settings.XC.Dispersion = func.disp_params or disp_name
+                break
+
+    def set_functional(func):
+        # set the functional settings for ADF
+        # first go through some special functionals that require special settings
+        if func.name_no_disp == 'BMK':
+            func.adf_settings.XC.LibXC = 'HYB_MGGA_X_BMK GGA_C_BMK'
+            return
+
+        if func.name in ['LCY-BLYP', 'LCY-BP86', 'LCY-PBE']:
+            func.adf_settings.XC.GGA = func.name.split('-')[1]
+            func.adf_settings.XC.RANGESEP = ''
+            func.adf_settings.XC.xcfun = ''
+            return
+
+        if func.name in ['CAMY-B3LYP']:
+            func.adf_settings.XC.Hybrid = 'CAMY-B3LYP'
+            func.adf_settings.XC.RANGESEP = ''
+            func.adf_settings.XC.xcfun = ''
+            return
+
+        if func.name == 'GGA:SSB-D':
+            func.adf_settings.XC.GGA = 'SSB-D'
+            return
+
+        if func.name == 'MetaGGA:SSB-D':
+            func.adf_settings.XC.MetaGGA = 'SSB-D'
+            return
+
+        if func.name_no_disp == 'HartreeFock':
+            func.adf_settings.XC.HartreeFock = ''
+            return
+
+        if func.name == 'MP2':
+            func.adf_settings.XC.MP2 = ''
+            return
+
+        if func.name in ['SOS-MP2', 'SCS-MP2']:
+            func.adf_settings.XC.MP2 = ''
+            func.adf_settings.XC.EmpiricalScaling = func.name[:-4]
+            return
+
+        # the normal functionals are defined based on their category, or selected from libxc
+        if func.use_libxc:
+            func.adf_settings.XC.LibXC = func.name_no_disp
+        else:
+            func.adf_settings.XC[func.category] = func.name_no_disp
+
+    # gather all data about available functionals
+    functionals = results.Result()  # store all info in this dict
+
+    with open(j(os.path.split(__file__)[0], 'available_functionals.txt')) as file:
+        lines = file.readlines()
+
+    for line in lines:
+        # there can be empty lines
+        if not line.strip():
+            continue
+
+        # functional names are given starting with -
+        # category names without -
+        if not line.startswith('- '):
+            curr_category = line.strip()
+            continue
+
+        # store data about the func in a dict
+        func = results.Result()
+        func.category = curr_category
+
+        # separate the functional name from the line
+        functional_name = line[2:].split('!')[0].split(',')[0].strip()
+        func.name = functional_name
+        func.path_safe_name = functional_name.replace(')', '').replace('(', '').replace('*', 's')
+
+        # check if custom params were given for dispersion
+        if 'GRIMME' in line:
+            func.disp_params = line.split('!')[0].split(',')[1].strip().strip("'")
+
+        func.use_libxc = '!libxc' in line
+        func.includes_disp = '!includesdisp' in line
+        func.available_in_adf = '!noadf' not in line
+        func.available_in_band = '!band' in line
+        func.available_in_orca = '!orca' in line
+
+        set_dispersion(func)
+        set_functional(func)
+
+        functionals[functional_name] = func
+
+    return functionals
    
+
+
+functionals = get_available_functionals()
+
+
+if __name__ == '__main__':
+    log.log(get('LYP'))
+
    + +
    + + + + + +
    + +
    +
    +
    + +
    + + + +
    + + +
    + + +
    +
    +
    + + + + + + + + \ No newline at end of file diff --git a/docs/_build/html/_modules/tcutility/data/molecules.html b/docs/_build/html/_modules/tcutility/data/molecules.html new file mode 100644 index 00000000..7e57d84d --- /dev/null +++ b/docs/_build/html/_modules/tcutility/data/molecules.html @@ -0,0 +1,365 @@ + + + + + + + + + + tcutility.data.molecules — TCutility v0.8.5 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + +
    +
    +
    +
    + + + Ctrl+K +
    +
    + +
    +
    + + + +
    + +
    + +
    + + + TCutility + +
    + +
    + +
    + + +
    + +
    + + + +
    + + +
    + TheoCheM
    + +
    + +
    + + +
    + + +
    + + + +
    + +
    + + +
    +
    + + + + + +
    + + + +
    + + + + +
    + +
    + TheoCheM
    + +
    + +
    + + +
    +
    + + + + +
    + +
    + + +
    +
    + +
    +
    + +
    + +
    + + + + +
    + +
    + + +
    +
    + + + + + +
    + +

    Source code for tcutility.data.molecules

    +from tcutility import molecule
+import os
+
+
+j = os.path.join
+
+root_dir = j(os.path.split(__file__)[0], 'molecules')
+
+
+
    
+[docs]
+def get(name):
+    p = j(root_dir, f'{name.removesuffix(".xyz")}.xyz')
+    return molecule.load(p)
    
+
+
+
+
    
+[docs]
+def get_molecules(tags=None):
+    for f in os.listdir(root_dir):
+        if not f.endswith('.xyz'):
+            continue
+            
+        mol = get(f)
+        if tags is None or any(tag in mol.flags.tags for tag in tags):
+            yield mol
    
+
+
+
+if __name__ == '__main__':
+    for mol in get_molecules():
+        print(mol, mol.flags)
+
    + +
    + + + + + +
    + +
    +
    +
    + +
    + + + +
    + + +
    + + +
    +
    +
    + + + + + + + + \ No newline at end of file diff --git a/docs/_build/html/_modules/tcutility/job/adf.html b/docs/_build/html/_modules/tcutility/job/adf.html index efd0c270..79326850 100644 --- a/docs/_build/html/_modules/tcutility/job/adf.html +++ b/docs/_build/html/_modules/tcutility/job/adf.html @@ -256,8 +256,7 @@

    Source code for tcutility.job.adf

     from scm import plams
-from tcutility import log, results, formula
-from tcutility.data import functionals
+from tcutility import log, results, formula, spell_check, data
 from tcutility.job.ams import AMSJob
 import os
 
@@ -271,11 +270,11 @@ 
    Source code for tcutility.job.adf
         def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self._functional = None
+        self.solvent('vacuum')
         self.basis_set('TZ2P')
         self.quality('Good')
         self.SCF_convergence(1e-8)
         self.single_point()
-        self.solvent('vacuum')
 
     def __str__(self):
         return f'{self._task}({self._functional}/{self._basis_set}), running in {os.path.join(os.path.abspath(self.rundir), self.name)}'
@@ -290,8 +289,16 @@ 
    Source code for tcutility.job.adf
                 typ: the type of basis-set to use. Default is TZ2P.
             core: the size of the frozen core approximation. Default is None.
 
+        Raises:
+            ValueError: if the basis-set name or core is incorrect.
+
         .. note:: If the selected functional is the r2SCAN-3c functional, then the basis-set will be set to mTZ2P.
+
+        .. seealso:: 
+            :mod:`tcutility.data.basis_sets` for an overview of the available basis-sets in ADF.
         '''
+        spell_check.check(typ, data.basis_sets.available_basis_sets['ADF'], ignore_case=True)
+        spell_check.check(core, ['None', 'Small', 'Large'], ignore_case=True)
         if self._functional == 'r2SCAN-3c' and typ != 'mTZ2P':
             log.warn(f'Basis set {typ} is not allowed with r2SCAN-3c, switching to mTZ2P.')
             typ = 'mTZ2P'
@@ -323,7 +330,7 @@ 
    Source code for tcutility.job.adf
             3) triplet
         4) ...
     
-        The multiplicity is equal to 2*S+1 for spin-polarization of S.
+        The multiplicity is equal to 2*S+1 for spin-polarization S.
         '''
         self.settings.input.adf.SpinPolarization = (val - 1)//2
         if val != 1:
@@ -347,7 +354,11 @@ 
    Source code for tcutility.job.adf
     
         Args:
             val: the numerical quality value to set to. This is the same as the ones used in the ADF GUI. Defaults to Good.
+
+        Raises:
+            ValueError: if the quality value is incorrect.
         '''
+        spell_check.check(val, ['Basic', 'Normal', 'Good', 'VeryGood', 'Excellent'], ignore_case=True)
         self.settings.input.adf.NumericalQuality = val
    
 
 
@@ -370,10 +381,16 @@ 
    Source code for tcutility.job.adf
             Set the functional to be used by the calculation. This also sets the dispersion if it is specified in the functional name.
 
         Args:
-            funtional_name: the name of the functional. The value can be the same as the ones used in the ADF GUI. For a full list of functionals please see :func:`functionals.get_available_functionals`.
+            funtional_name: the name of the functional. The value can be the same as the ones used in the ADF GUI.
             dispersion: dispersion setting to use with the functional. This is used when you want to use a functional from LibXC.
 
+        Raises:
+            ValueError: if the functional name is not recognized.
+
         .. note:: Setting the functional to r2SCAN-3c will automatically set the basis-set to mTZ2P.
+
+        .. seealso::
+            :mod:`tcutility.data.functionals` for an overview of the available functionals in ADF.
         '''
         # before adding the new functional we should clear any previous functional settings
         self.settings.input.adf.pop('XC', None)
@@ -390,11 +407,11 @@ 
    Source code for tcutility.job.adf
                 log.error('There are two functionals called SSB-D, please use "GGA:SSB-D" or "MetaGGA:SSB-D".')
             return
 
-        if not functionals.get(functional):
+        if not data.functionals.get(functional):
             log.warn(f'XC-functional {functional} not found. Please ask a TheoCheM developer to add it. Adding functional as LibXC.')
             self.settings.input.adf.XC.LibXC = functional
         else:
-            func = functionals.get(functional)
+            func = data.functionals.get(functional)
             self.settings.input.adf.update(func.adf_settings)
    
 
 
@@ -406,7 +423,11 @@ 
    Source code for tcutility.job.adf
     
         Args:
             level: the level to set. Can be the same as the values in the ADF GUI and documentation. By default it is set to Scalar.
+
+        Raises:
+            ValueError: if the relativistic correction level is not correct.
         '''
+        spell_check.check(level, ['Scalar', 'None', 'Spin-Orbit'], ignore_case=True)
         self.settings.input.adf.relativity.level = level
    
 
 
@@ -421,8 +442,15 @@ 
    Source code for tcutility.job.adf
                 eps: the dielectric constant of your solvent. You can use this in place of the solvent name if you need more control over COSMO.
             rad: the radius of the solvent molecules. You can use this in place of the solvent name if you need more control over COSMO.
             use_klamt: whether to use the klamt atomic radii. This is usually used when you have charged species (?).
+
+        Raises:
+            ValueError: if the solvent name is given, but incorrect.
+
+        .. seealso::
+            :mod:`tcutility.data.cosmo` for an overview of the available solvent names and formulas.
         '''
         if name:
+            spell_check.check(name, data.cosmo.available_solvents, ignore_case=True, insertion_cost=0.3)
             self._solvent = name
         else:
             self._solvent = f'COSMO(eps={eps} rad={rad})'
@@ -614,8 +642,10 @@ 
    Source code for tcutility.job.adf
             job.rundir = 'tmp/SN2/EDA'
         job.molecule('../../../test/fixtures/xyz/pyr.xyz')
         job.sbatch(p='tc', ntasks_per_node=15)
-        job.functional('OLYP')
-        job.basis_set('DZP')
+        job.solvent('')
+        job.basis_set('tz2p')
+        job.quality('veryGood')
+        job.functional('LYP-D3BJ')
 
    
 
                 
diff --git a/docs/_build/html/_modules/tcutility/spell_check.html b/docs/_build/html/_modules/tcutility/spell_check.html
index 42af72b1..c788ba6b 100644
--- a/docs/_build/html/_modules/tcutility/spell_check.html
+++ b/docs/_build/html/_modules/tcutility/spell_check.html
@@ -352,7 +352,7 @@ 
    Source code for tcutility.spell_check
     
 
    
 [docs]
-def get_closest(a: str, others: List[str], compare_func=wagner_fischer, ignore_case: bool = False, ignore_chars: str = '', maximum_distance: int = None) -> List[str]:
+def get_closest(a: str, others: List[str], compare_func=wagner_fischer, ignore_case: bool = False, ignore_chars: str = '', maximum_distance: int = None, **kwargs) -> List[str]:
     '''
     Return strings that are similar to an input string using the Levenshtein distance.
 
@@ -369,6 +369,7 @@ 
    Source code for tcutility.spell_check
         Returns:
         A collection of strings that have a Levenshtein distance to ``a`` below ``maximum_distance`` 
         or have the lowest distance to ``a`` if all strings have a distance greater than ``maximum_distance``.
+        If the lowest distance is ``0``, return an empty list instead.
 
     Example:
         .. code-block:: python
@@ -391,11 +392,11 @@ 
    Source code for tcutility.spell_check
             for char in ignore_chars:
             other = other.replace(char, '')
 
-        dists.append(compare_func(a, other))
+        dists.append(compare_func(a, other, **kwargs))
 
     if maximum_distance is None:
         maximum_distance = -1
-    lowest_strs = [other for dist, other in zip(dists, others) if dist <= max(maximum_distance, min(dists))]
+    lowest_strs = [other for dist, other in zip(dists, others) if 0 < dist <= max(maximum_distance, min(dists))]
     return lowest_strs
    
 
 
@@ -425,6 +426,24 @@ 
    Source code for tcutility.spell_check
         # write a warning message
     log.warn(f'Could not find "{a}". Did you mean {closest_string}?', caller_level=3)
    
 
+
+
+
    
+[docs]
+def check(a: str, others: List[str], caller_level=2, **kwargs):
+    closest = get_closest(a, others, **kwargs)
+    if len(closest) == 0:
+        return
+
+    if len(closest) > 1:
+        closest_string = " or ".join([", ".join(closest[:-1]), closest[-1]])
+    else:
+        closest_string = closest[0]
+
+    # write a warning message
+    msg = f"({log.caller_name(caller_level)}): " + f'Could not find "{a}". Did you mean {closest_string}?'
+    raise ValueError(msg)
    
+
 
    
 
                 
diff --git a/docs/_build/html/_sources/api/tcutility.data.atom_data_info.rst.txt b/docs/_build/html/_sources/api/tcutility.data.atom_data_info.rst.txt
new file mode 100644
index 00000000..7b4c05e9
--- /dev/null
+++ b/docs/_build/html/_sources/api/tcutility.data.atom_data_info.rst.txt
@@ -0,0 +1,10 @@
+tcutility.data.atom\_data\_info package
+=======================================
+
+Module contents
+---------------
+
+.. automodule:: tcutility.data.atom_data_info
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_build/html/_sources/api/tcutility.data.rst.txt b/docs/_build/html/_sources/api/tcutility.data.rst.txt
new file mode 100644
index 00000000..44b0121c
--- /dev/null
+++ b/docs/_build/html/_sources/api/tcutility.data.rst.txt
@@ -0,0 +1,61 @@
+tcutility.data package
+======================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tcutility.data.atom_data_info
+
+Submodules
+----------
+
+tcutility.data.atom module
+--------------------------
+
+.. automodule:: tcutility.data.atom
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tcutility.data.basis\_sets module
+---------------------------------
+
+.. automodule:: tcutility.data.basis_sets
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tcutility.data.cosmo module
+---------------------------
+
+.. automodule:: tcutility.data.cosmo
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tcutility.data.functionals module
+---------------------------------
+
+.. automodule:: tcutility.data.functionals
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tcutility.data.molecules module
+-------------------------------
+
+.. automodule:: tcutility.data.molecules
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tcutility.data
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_build/html/_sources/api/tcutility.rst.txt b/docs/_build/html/_sources/api/tcutility.rst.txt
index 4b98ca3c..3654fd72 100644
--- a/docs/_build/html/_sources/api/tcutility.rst.txt
+++ b/docs/_build/html/_sources/api/tcutility.rst.txt
@@ -8,6 +8,7 @@ Subpackages
    :maxdepth: 4
 
    tcutility.analysis
+   tcutility.data
    tcutility.job
    tcutility.results
    tcutility.typing
diff --git a/docs/_build/html/api/modules.html b/docs/_build/html/api/modules.html
index 26b67fcb..50755c12 100644
--- a/docs/_build/html/api/modules.html
+++ b/docs/_build/html/api/modules.html
@@ -216,7 +216,11 @@
 
  • tcutility.analysis.vibration package
    • 
 
 
-
  • tcutility.job package
 
    • 
+
  • tcutility.data package
+
    • 
 
  • tcutility.job package
 
    • 
 
  • Module contents
      
diff --git a/docs/_build/html/api/tcutility.analysis.html b/docs/_build/html/api/tcutility.analysis.html
index 2bfc01e8..9581c66e 100644
--- a/docs/_build/html/api/tcutility.analysis.html
+++ b/docs/_build/html/api/tcutility.analysis.html
@@ -216,7 +216,11 @@
 
    • tcutility.analysis.vibration package
      • 
 
    
 
    • 
-
  • tcutility.job package
 
    • 
-
  • tcutility.job package
 
    • 
-
  • tcutility.job package
      
+
    • tcutility.data package
+
      • 
+
    • tcutility.job package
 
      • 
@@ -387,11 +391,11 @@ 
      Submodules
       
      
         
      next
      
-        
      tcutility.job package
      
+        
      tcutility.data package
      
       
      
       
           
diff --git a/docs/_build/html/api/tcutility.data.atom_data_info.html b/docs/_build/html/api/tcutility.data.atom_data_info.html
new file mode 100644
index 00000000..0b43783b
--- /dev/null
+++ b/docs/_build/html/api/tcutility.data.atom_data_info.html
@@ -0,0 +1,418 @@
+
+
+
+
+
+
+  
+    
+    
+
+    tcutility.data.atom_data_info package — TCutility v0.8.5 documentation
+  
+  
+  
+  
+  
+  
+  
+
+
+
+  
+  
+  
+
+
+
+    
+    
+    
+  
+  
+  
+
+  
+
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+  
+  
+  
+  
+  
+  
+
+  
+  
+  
+  
+  
      
+  
+  
+
+  
+  
+  
+  
+  
+  
+  
+  
      
+    
      
+    
      
+
      
+  
+  
+  Ctrl+K
+
      
+  
      
+  
+    
      
+
      
+  
+  
+  
+  
      
+    
+      
      
+
+
      
+    
+        
+        TCutility
+    
+
      
+    
+  
      
+  
+  
      
+    
+    
+    
      
+      
+        
      
+          
+
+ 
+        
      
+      
+      
+        
      
+ TheoCheM
      
+      
+    
      
+    
+  
      
+  
+  
+    
      
+
+ 
+    
      
+  
+
+  
+    
+  
+
      
+
+    
      
+  
+
+  
      
+    
      
+      
+      
+      
+      
      
+        
+
+  
+  
      
+    
+    
+    
+    
+      
      
+        
+          
      
+ TheoCheM
      
+        
+      
      
+    
+  
      
+  
+    
      
+        
      
+
      
+    
      
+  
+  
+  
      
+  
      
+  
+  
+
+
+      
      
+      
+      
      
+        
+        
+          
      
+            
      
+              
+              
      
+
      
+  
+    
      
+      
+        
      
+
+
+
+
+
+
+
      
+      
+    
      
+  
+  
+
      
+
      
+              
+              
+              
+                
+
+                
      
+                  
+  
      
+
      tcutility.data.atom_data_info package#
      
+
      
+
      Module contents#
      
+
      
+
      
+
+
+                
      
+              
+              
+              
+              
+              
+                
+              
+            
      
+            
+            
+              
+                
      
+
+
+  
      
+
      
+     On this page
+  
      
+  
      
+
+  
      
+
+  
      
+    
+       Show Source
+    
+  
      
+
      
+
+
      
+              
+            
+          
      
+          
      
+            
+          
      
+        
+      
      
+    
      
+  
      
+  
+  
+  
+
+
+  
      
+
      
+  
+    
      
+      
+        
      
+
+  
      
+    
+      © Copyright 2024, TheoCheM VU Amsterdam.
+      
      
+    
+  
      
+
      
+      
+        
      
+
+  
      
+    Created using Sphinx 7.2.6.
+    
      
+  
      
+
      
+      
+    
      
+  
+  
+  
+    
      
+      
+        
      
+
      
+  Built with the PyData Sphinx Theme 0.15.2.
+
      
+      
+    
      
+  
+
      
+
+  
      
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/api/tcutility.data.html b/docs/_build/html/api/tcutility.data.html
new file mode 100644
index 00000000..45c13d0b
--- /dev/null
+++ b/docs/_build/html/api/tcutility.data.html
@@ -0,0 +1,589 @@
+
+
+
+
+
+
+  
+    
+    
+
+    tcutility.data package — TCutility v0.8.5 documentation
+  
+  
+  
+  
+  
+  
+  
+
+
+
+  
+  
+  
+
+
+
+    
+    
+    
+  
+  
+  
+
+  
+
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+  
+  
+  
+  
+  
+  
+
+  
+  
+  
+  
+  
      
+  
+  
+
+  
+  
+  
+  
+  
+  
+  
+  
      
+    
      
+    
      
+
      
+  
+  
+  Ctrl+K
+
      
+  
      
+  
+    
      
+
      
+  
+  
+  
+  
      
+    
+      
      
+
+
      
+    
+        
+        TCutility
+    
+
      
+    
+  
      
+  
+  
      
+    
+    
+    
      
+      
+        
      
+          
+
+ 
+        
      
+      
+      
+        
      
+ TheoCheM
      
+      
+    
      
+    
+  
      
+  
+  
+    
      
+
+ 
+    
      
+  
+
+  
+    
+  
+
      
+
+    
      
+  
+
+  
      
+    
      
+      
+      
+      
+      
      
+        
+
+  
+  
      
+    
+    
+    
+    
+      
      
+        
+          
      
+ TheoCheM
      
+        
+      
      
+    
+  
      
+  
+    
      
+        
      
+
      
+    
      
+  
+  
+  
      
+  
      
+  
+  
+
+
+      
      
+      
+      
      
+        
+        
+          
      
+            
      
+              
+              
      
+
      
+  
+    
      
+      
+        
      
+
+
+
+
+
      
+      
+    
      
+  
+  
+
      
+
      
+              
+              
+              
+                
+
+                
      
+                  
+  
      
+
      tcutility.data package#
      
+
      
+
      Subpackages#
      
+
      
+
+
      
+
      
+
      
+
      Submodules#
      
+
      
+
      
+
      tcutility.data.atom module#
      
+
      
+
      
+parse_element(val)[source]#
      
+
      Parse a str or int to an atom number.
      
+
      
+
      Parameters:
      
+
      val – Element name, symbol or atom number.
      
+
      
+
      Returns:
      
+
      Atom number corresponding to val.
      
+
      
+
      
+
      Examples
      
+
      parse_element('Hydrogen') == 1
+parse_element('C') == 6
+parse_element(23) == 23
+
      
+
      
+
      
+
+
      
+
      
+radius(element)[source]#
      
+
      
+
      Parameters:
      
+
      element – the symbol, name or atom number of the element. See parse_element().
      
+
      
+
      Returns:
      
+
      The empirical covalent radius of an element in angstroms, up to element 96.
      
+
      
+
      
+
      
+
+
      
+
      
+color(element)[source]#
      
+
      
+
      Parameters:
      
+
      element – the symbol, name or atom number of the element. See parse_element().
      
+
      
+
      Returns:
      
+
      The standard CPK colors of the elements, up to element 109.
      
+
      
+
      
+
      
+
+
      
+
      
+
      tcutility.data.basis_sets module#
      
+
      
+
      
+
      tcutility.data.cosmo module#
      
+
      
+
      
+
      tcutility.data.functionals module#
      
+
      
+
      
+get(functional_name: str) → Result[source]#
      
+
      Return information about a given functional.
      
+
      
+
      Parameters:
      
+
      functional_name – the name of the functional. It should exist in the get_available_functionals() keys.
      
+
      
+
      Returns:
      
+
      A |Result| object containing information about the functional if it exists. Else it will return None.
      
+
      
+
      
+
      
+
      See also
      
+
      get_available_functionals() for an overview of the information returned.
      
+
      
+
      
+
+
      
+
      
+functional_name_from_path_safe_name(path_safe_name: str) → Result[source]#
      
+
      Return information about a given functional given its path-safe name.
+This can be useful when you want to know the functional from a path name.
      
+
      
+
      Returns:
      
+
      A |Result| object containing information about the functional if it exists. Else it will return None.
      
+
      
+
      
+
      
+
      See also
      
+
      get_available_functionals() for an overview of the information returned.
      
+
      
+
      
+
+
      
+
      
+get_available_functionals()[source]#
      
+
      Function that returns a dictionary of all available XC-functionals.
      
+
      
+
      Returns:
      
+
      
+
      A |Result| object containing information about all available XC-functionals.
      The functional names are stored as the keys and the functional information is stored as the values.
+The values contain the following information:
      
+
      
+
        
+
      • name (str) - the name of the functional.
        • 
+
      • 
+
        path_safe_name (str) - the name of the functional made suitable for file paths.
        This name is the same as the normal name, but without parentheses. Asterisks are replaced with lower-case s.
        
+
        
+
        
+
        • 
+
      • name_no_disp (str) - the name of functional without the dispersion correction.
        • 
+
      • category (str) - the category the functional belongs to.
        • 
+
      • dispersion (str) - the dispersion correction part of the functional name.
        • 
+
      • dispersion_name (str) - the name of the dispersion correction as it would be written in ADF.
        • 
+
      • includes_disp (bool) - whether the functional already includes a dispersion correction.
        • 
+
      • use_libxc (bool) - whether the functional is from the LibXC library.
        • 
+
      • available_in_adf (bool) - whether the functional is available in ADF.
        • 
+
      • available_in_band (bool) - whether the functional is available in BAND.
        • 
+
      • available_in_orca (bool) - whether the functional is available in ORCA.
        • 
+
      • adf_settings (|Result|) - the settings that are used to select the functional in the ADF input.
        • 
+
      
+
      
+
      
+
      
+
      
+
      
+
      
+
      
+
+
      
+
      
+
      tcutility.data.molecules module#
      
+
      
+
      
+get(name)[source]#
      
+
      
+
+
      
+
      
+get_molecules(tags=None)[source]#
      
+
      
+
+
      
+
      
+
      Module contents#
      
+
      
+
      
+
+
+                
      
+              
+              
+              
+              
+              
+                
+              
+            
      
+            
+            
+              
+                
      
+
+
+  
      
+
      
+     On this page
+  
      
+  
      
+
+  
      
+
+  
      
+    
+       Show Source
+    
+  
      
+
      
+
+
      
+              
+            
+          
      
+          
      
+            
+          
      
+        
+      
      
+    
      
+  
      
+  
+  
+  
+
+
+  
      
+
      
+  
+    
      
+      
+        
      
+
+  
      
+    
+      © Copyright 2024, TheoCheM VU Amsterdam.
+      
      
+    
+  
      
+
      
+      
+        
      
+
+  
      
+    Created using Sphinx 7.2.6.
+    
      
+  
      
+
      
+      
+    
      
+  
+  
+  
+    
      
+      
+        
      
+
      
+  Built with the PyData Sphinx Theme 0.15.2.
+
      
+      
+    
      
+  
+
      
+
+  
      
+  
+
\ No newline at end of file
diff --git a/docs/_build/html/api/tcutility.html b/docs/_build/html/api/tcutility.html
index c5e3a3e1..0a984dcf 100644
--- a/docs/_build/html/api/tcutility.html
+++ b/docs/_build/html/api/tcutility.html
@@ -217,7 +217,11 @@
 
    • tcutility.analysis.vibration package
      • 
 
    
 
    • 
-
  • tcutility.job package
 
    • 
+
  • tcutility.data package
+
    • 
 
  • tcutility.job package
      
 
    • Subpackages
+  
-  
        
       
      • get_memory_usage() (ORCAJob method)
 
        • 
-      
      • get_molecules() (in module tcutility.results.ams)
+      
      • get_molecules() (in module tcutility.data.molecules)
 
       
        • 
@@ -629,6 +645,20 @@ 
        M
        
         
      • tcutility.cache
 
        • 
         
      • tcutility.constants
+
        • 
+        
      • tcutility.data
+
        • 
+        
      • tcutility.data.atom
+
        • 
+        
      • tcutility.data.atom_data_info
+
        • 
+        
      • tcutility.data.basis_sets
+
        • 
+        
      • tcutility.data.cosmo
+
        • 
+        
      • tcutility.data.functionals
+
        • 
+        
      • tcutility.data.molecules
 
        • 
         
      • tcutility.formula
 
        • 
@@ -753,12 +783,14 @@ 
        O
        
 
        P
        
 
        
   
   
          
+      
        • parse_str() (in module tcutility.molecule)
+
          • 
       
        • plot_vdd_charges_per_atom() (VDDChargeManager method)
 
          • 
       
        • prune() (Result method)
@@ -783,6 +815,8 @@ 
          Q
          
 
          R
          
 
+  
-  
+     
+       
+       
+     
+       
+       
+     
+       
+       
+     
+       
+       
+     
+       
+       
+     
+       
+       
+     
+       
+       
          
   
   
+  
            
       
          • 
     tcutility.job.nmr
 
@@ -1025,8 +1110,6 @@ 
            T
            
         
          • module
 
            • 
       
          
-  
            
       
          • 
     tcutility.job.postscripts.clean_workdir
 
diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv
index 350d8bc3..ead49c5b 100644
Binary files a/docs/_build/html/objects.inv and b/docs/_build/html/objects.inv differ
diff --git a/docs/_build/html/py-modindex.html b/docs/_build/html/py-modindex.html
index 37b539a1..a56d9cfd 100644
--- a/docs/_build/html/py-modindex.html
+++ b/docs/_build/html/py-modindex.html
@@ -277,6 +277,41 @@ 
            Python Module Index
            
        
          		   
        tcutility.constants
        
             
+       tcutility.data
+       
             
+       tcutility.data.atom
+       
             
+       tcutility.data.atom_data_info
+       
             
+       tcutility.data.basis_sets
+       
             
+       tcutility.data.cosmo
+       
             
+       tcutility.data.functionals
+       
             
+       tcutility.data.molecules
+       
          
      
          
        
           
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index 1018decf..47797d3a 100644
--- a/docs/_build/html/searchindex.js
+++ b/docs/_build/html/searchindex.js
@@ -1 +1 @@
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(in module tcutility.slurm)": [[4, "tcutility.slurm.workdir_info"]], "tcutility.analysis": [[5, "module-tcutility.analysis"]], "vddcharge (class in tcutility.analysis.vdd.charge)": [[6, "tcutility.analysis.vdd.charge.VDDCharge"]], "vddchargemanager (class in tcutility.analysis.vdd.manager)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager"]], "atom_index (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.atom_index"]], "atom_symbol (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.atom_symbol"]], "calc_dir (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.calc_dir"]], "change_unit() (vddcharge method)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.change_unit"]], "change_unit() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.change_unit"]], "change_unit_decorator() (in module tcutility.analysis.vdd.manager)": [[6, "tcutility.analysis.vdd.manager.change_unit_decorator"]], "charge (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.charge"]], "charge_is_conserved() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.charge_is_conserved"]], "create_vdd_charge_manager() (in module tcutility.analysis.vdd.manager)": [[6, "tcutility.analysis.vdd.manager.create_vdd_charge_manager"]], "frag_index (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.frag_index"]], "get_summed_vdd_charges() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_summed_vdd_charges"]], "get_summed_vdd_charges_dataframe() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_summed_vdd_charges_dataframe"]], "get_summed_vdd_charges_table() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_summed_vdd_charges_table"]], "get_vdd_charges() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_vdd_charges"]], "get_vdd_charges_dataframe() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_vdd_charges_dataframe"]], "get_vdd_charges_table() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_vdd_charges_table"]], "irreps (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.irreps"]], "is_fragment_calculation (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.is_fragment_calculation"]], "mol_charge (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.mol_charge"]], "name (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.name"]], "plot_vdd_charges_per_atom() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.plot_vdd_charges_per_atom"]], "tcutility.analysis.vdd": [[6, "module-tcutility.analysis.vdd"]], "tcutility.analysis.vdd.charge": [[6, "module-tcutility.analysis.vdd.charge"]], "tcutility.analysis.vdd.manager": [[6, "module-tcutility.analysis.vdd.manager"]], "unit (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.unit"]], "vdd_charges (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.vdd_charges"]], "write_to_excel() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.write_to_excel"]], "write_to_txt() (vddchargemanager static method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.write_to_txt"]], "avg_relative_bond_length_delta() (in module tcutility.analysis.vibration.ts_vibration)": [[7, "tcutility.analysis.vibration.ts_vibration.avg_relative_bond_length_delta"]], "determine_ts_reactioncoordinate() (in module tcutility.analysis.vibration.ts_vibration)": [[7, "tcutility.analysis.vibration.ts_vibration.determine_ts_reactioncoordinate"]], "tcutility.analysis.vibration": [[7, "module-tcutility.analysis.vibration"]], "tcutility.analysis.vibration.ts_vibration": [[7, "module-tcutility.analysis.vibration.ts_vibration"]], "validate_transitionstate() (in module tcutility.analysis.vibration.ts_vibration)": [[7, "tcutility.analysis.vibration.ts_vibration.validate_transitionstate"]], "adffragmentjob (class in tcutility.job.adf)": [[9, "tcutility.job.adf.ADFFragmentJob"]], "adfjob (class in tcutility.job.adf)": [[9, "tcutility.job.adf.ADFJob"]], "amsjob (class in tcutility.job.ams)": [[9, "tcutility.job.ams.AMSJob"]], "crestjob (class in tcutility.job.crest)": [[9, "tcutility.job.crest.CRESTJob"]], "dftbjob (class in tcutility.job.dftb)": [[9, "tcutility.job.dftb.DFTBJob"]], "irc() (amsjob method)": [[9, "tcutility.job.ams.AMSJob.IRC"]], "job (class in tcutility.job.generic)": [[9, "tcutility.job.generic.Job"]], "nmrjob (class in tcutility.job.nmr)": [[9, "tcutility.job.nmr.NMRJob"]], "orcajob (class in tcutility.job.orca)": [[9, "tcutility.job.orca.ORCAJob"]], "qcgjob (class in tcutility.job.crest)": [[9, "tcutility.job.crest.QCGJob"]], "scf_convergence() (adfjob method)": [[9, "tcutility.job.adf.ADFJob.SCF_convergence"]], "add_fragment() (adffragmentjob method)": [[9, "tcutility.job.adf.ADFFragmentJob.add_fragment"]], "add_nics_point() (nmrjob method)": [[9, "tcutility.job.nmr.NMRJob.add_nics_point"]], "add_postamble() (job method)": [[9, "tcutility.job.generic.Job.add_postamble"]], "add_postscript() (job method)": [[9, "tcutility.job.generic.Job.add_postscript"]], "add_preamble() (job method)": [[9, "tcutility.job.generic.Job.add_preamble"]], "alpb() (qcgjob method)": [[9, "tcutility.job.crest.QCGJob.alpb"]], "basis_set() (adfjob method)": [[9, "tcutility.job.adf.ADFJob.basis_set"]], "best_conformer_path (crestjob property)": [[9, "tcutility.job.crest.CRESTJob.best_conformer_path"]], "best_ensemble_path (qcgjob property)": [[9, "tcutility.job.crest.QCGJob.best_ensemble_path"]], "can_skip() (job method)": [[9, "tcutility.job.generic.Job.can_skip"]], "charge() (amsjob method)": [[9, "tcutility.job.ams.AMSJob.charge"]], "charge() (crestjob method)": [[9, "tcutility.job.crest.CRESTJob.charge"]], "charge() (orcajob method)": [[9, "tcutility.job.orca.ORCAJob.charge"]], "conformer_directory (crestjob property)": [[9, "tcutility.job.crest.CRESTJob.conformer_directory"]], "dependency() (job method)": [[9, "tcutility.job.generic.Job.dependency"]], "ensemble_directory (qcgjob property)": [[9, "tcutility.job.crest.QCGJob.ensemble_directory"]], "ensemble_mode() (qcgjob method)": [[9, "tcutility.job.crest.QCGJob.ensemble_mode"]], "functional() (adfjob method)": [[9, "tcutility.job.adf.ADFJob.functional"]], "geometry_convergence() (amsjob method)": [[9, "tcutility.job.ams.AMSJob.geometry_convergence"]], "get_conformer_xyz() (crestjob method)": [[9, "tcutility.job.crest.CRESTJob.get_conformer_xyz"]], "get_ensemble_xyz() (qcgjob method)": [[9, "tcutility.job.crest.QCGJob.get_ensemble_xyz"]], "get_input() (orcajob method)": [[9, "tcutility.job.orca.ORCAJob.get_input"]], "get_memory_usage() (orcajob method)": [[9, "tcutility.job.orca.ORCAJob.get_memory_usage"]], "get_rotamer_xyz() (crestjob method)": [[9, "tcutility.job.crest.CRESTJob.get_rotamer_xyz"]], "inputfile_path (job property)": [[9, "tcutility.job.generic.Job.inputfile_path"]], "kspace() (dftbjob method)": [[9, "tcutility.job.dftb.DFTBJob.kspace"]], "md_length() (crestjob method)": [[9, "tcutility.job.crest.CRESTJob.md_length"]], "md_temperature() (crestjob method)": [[9, "tcutility.job.crest.CRESTJob.md_temperature"]], "model() (dftbjob method)": [[9, "tcutility.job.dftb.DFTBJob.model"]], "molecule() (job method)": [[9, "tcutility.job.generic.Job.molecule"]], "multiplicity() (adfjob method)": [[9, "tcutility.job.adf.ADFJob.multiplicity"]], "multiplicity() (crestjob method)": [[9, "tcutility.job.crest.CRESTJob.multiplicity"]], "multiplicity() (orcajob method)": [[9, "tcutility.job.orca.ORCAJob.multiplicity"]], "nofix() (qcgjob method)": [[9, "tcutility.job.crest.QCGJob.nofix"]], "nsolv() (qcgjob method)": [[9, "tcutility.job.crest.QCGJob.nsolv"]], "optimization() (amsjob method)": [[9, "tcutility.job.ams.AMSJob.optimization"]], "optimization() (orcajob method)": [[9, "tcutility.job.orca.ORCAJob.optimization"]], "output_mol_path (amsjob property)": [[9, "tcutility.job.ams.AMSJob.output_mol_path"]], "output_mol_path (job property)": [[9, "tcutility.job.generic.Job.output_mol_path"]], "quality() (adfjob method)": [[9, "tcutility.job.adf.ADFJob.quality"]], "relativity() (adfjob method)": [[9, "tcutility.job.adf.ADFJob.relativity"]], "rotamer_directory (crestjob property)": [[9, "tcutility.job.crest.CRESTJob.rotamer_directory"]], "run() (adffragmentjob method)": [[9, "tcutility.job.adf.ADFFragmentJob.run"]], "run() (job method)": [[9, "tcutility.job.generic.Job.run"]], "runfile_path (job property)": [[9, "tcutility.job.generic.Job.runfile_path"]], "sbatch() (job method)": [[9, "tcutility.job.generic.Job.sbatch"]], "single_point() (amsjob method)": [[9, "tcutility.job.ams.AMSJob.single_point"]], "single_point() (orcajob method)": [[9, "tcutility.job.orca.ORCAJob.single_point"]], "solvent() (adfjob method)": [[9, "tcutility.job.adf.ADFJob.solvent"]], "solvent() (dftbjob method)": [[9, "tcutility.job.dftb.DFTBJob.solvent"]], "solvent() (qcgjob method)": [[9, "tcutility.job.crest.QCGJob.solvent"]], "spin_polarization() (adfjob method)": [[9, "tcutility.job.adf.ADFJob.spin_polarization"]], "spin_polarization() (crestjob method)": [[9, "tcutility.job.crest.CRESTJob.spin_polarization"]], "spin_polarization() (orcajob method)": [[9, "tcutility.job.orca.ORCAJob.spin_polarization"]], "tcutility.job": [[9, "module-tcutility.job"]], "tcutility.job.adf": [[9, "module-tcutility.job.adf"]], "tcutility.job.ams": [[9, "module-tcutility.job.ams"]], "tcutility.job.crest": [[9, "module-tcutility.job.crest"]], "tcutility.job.dftb": [[9, "module-tcutility.job.dftb"]], "tcutility.job.generic": [[9, "module-tcutility.job.generic"]], "tcutility.job.nmr": [[9, "module-tcutility.job.nmr"]], "tcutility.job.orca": [[9, "module-tcutility.job.orca"]], "transition_state() (amsjob method)": [[9, "tcutility.job.ams.AMSJob.transition_state"]], "transition_state() (orcajob method)": [[9, "tcutility.job.orca.ORCAJob.transition_state"]], "unrestricted() (adfjob method)": [[9, "tcutility.job.adf.ADFJob.unrestricted"]], "vibrations() (amsjob method)": [[9, "tcutility.job.ams.AMSJob.vibrations"]], "vibrations() (orcajob method)": [[9, "tcutility.job.orca.ORCAJob.vibrations"]], "workdir (job property)": [[9, "tcutility.job.generic.Job.workdir"]], "tcutility.job.postscripts": [[10, "module-tcutility.job.postscripts"]], "tcutility.job.postscripts.clean_workdir": [[10, "module-tcutility.job.postscripts.clean_workdir"]], "tcutility.job.postscripts.split_crest_xyz": [[10, "module-tcutility.job.postscripts.split_crest_xyz"]], "tcutility.job.postscripts.write_converged_geoms": [[10, "module-tcutility.job.postscripts.write_converged_geoms"]], "result (class in tcutility.results.result)": [[11, "tcutility.results.result.Result"]], "trackkfreader (class in tcutility.results.cache)": [[11, "tcutility.results.cache.TrackKFReader"]], "as_plams_settings() (result method)": [[11, "tcutility.results.result.Result.as_plams_settings"]], "get() (in module tcutility.results.cache)": [[11, "tcutility.results.cache.get"]], "get_ams_info() (in module tcutility.results.ams)": [[11, "tcutility.results.ams.get_ams_info"]], "get_ams_input() (in module tcutility.results.ams)": [[11, "tcutility.results.ams.get_ams_input"]], "get_ams_version() (in module tcutility.results.ams)": [[11, "tcutility.results.ams.get_ams_version"]], "get_calc_files() (in module tcutility.results.ams)": [[11, "tcutility.results.ams.get_calc_files"]], "get_calc_files() (in module tcutility.results.orca)": [[11, "tcutility.results.orca.get_calc_files"]], "get_calc_settings() (in module tcutility.results.adf)": [[11, "tcutility.results.adf.get_calc_settings"]], "get_calc_settings() (in module tcutility.results.dftb)": [[11, "tcutility.results.dftb.get_calc_settings"]], "get_calc_settings() (in module tcutility.results.orca)": [[11, "tcutility.results.orca.get_calc_settings"]], "get_calculation_status() (in module tcutility.results.ams)": [[11, "tcutility.results.ams.get_calculation_status"]], "get_calculation_status() (in module tcutility.results.orca)": [[11, "tcutility.results.orca.get_calculation_status"]], "get_history() (in module tcutility.results.ams)": [[11, "tcutility.results.ams.get_history"]], "get_info() (in module tcutility.results)": [[11, "tcutility.results.get_info"]], "get_info() (in module tcutility.results.orca)": [[11, "tcutility.results.orca.get_info"]], "get_input() (in module tcutility.results.orca)": [[11, "tcutility.results.orca.get_input"]], "get_input_blocks() (in module tcutility.results.ams)": [[11, "tcutility.results.ams.get_input_blocks"]], "get_level_of_theory() (in module tcutility.results.adf)": [[11, "tcutility.results.adf.get_level_of_theory"]], "get_level_of_theory() (in module tcutility.results.orca)": [[11, "tcutility.results.orca.get_level_of_theory"]], "get_molecules() (in module tcutility.results.ams)": [[11, "tcutility.results.ams.get_molecules"]], "get_molecules() (in module tcutility.results.orca)": [[11, "tcutility.results.orca.get_molecules"]], "get_multi_key() (result method)": [[11, "tcutility.results.result.Result.get_multi_key"]], "get_parent_tree() (result method)": [[11, "tcutility.results.result.Result.get_parent_tree"]], "get_properties() (in module tcutility.results.adf)": [[11, "tcutility.results.adf.get_properties"]], "get_properties() (in module tcutility.results.dftb)": [[11, "tcutility.results.dftb.get_properties"]], "get_properties() (in module tcutility.results.orca)": [[11, "tcutility.results.orca.get_properties"]], "get_timing() (in module tcutility.results.ams)": [[11, "tcutility.results.ams.get_timing"]], "get_version() (in module tcutility.results.orca)": [[11, "tcutility.results.orca.get_version"]], "get_vibrations() (in module tcutility.results.orca)": [[11, "tcutility.results.orca.get_vibrations"]], "items() (result method)": [[11, "tcutility.results.result.Result.items"]], "keys() (result method)": [[11, "tcutility.results.result.Result.keys"]], "prune() (result method)": [[11, "tcutility.results.result.Result.prune"]], "read() (trackkfreader method)": [[11, "tcutility.results.cache.TrackKFReader.read"]], "read() (in module tcutility.results)": [[11, "tcutility.results.read"]], "store() (in module tcutility.results.cache)": [[11, "tcutility.results.cache.store"]], "tcutility.results": [[11, "module-tcutility.results"]], "tcutility.results.adf": [[11, "module-tcutility.results.adf"]], "tcutility.results.ams": [[11, "module-tcutility.results.ams"]], "tcutility.results.cache": [[11, "module-tcutility.results.cache"]], "tcutility.results.dftb": [[11, "module-tcutility.results.dftb"]], "tcutility.results.orca": [[11, "module-tcutility.results.orca"]], "tcutility.results.result": [[11, "module-tcutility.results.result"]], "unload() (in module tcutility.results.cache)": [[11, "tcutility.results.cache.unload"]], "tcutility.typing": [[12, "module-tcutility.typing"]], "tcutility.typing.arrays": [[12, "module-tcutility.typing.arrays"]]}})
\ No newline at end of file
+Search.setIndex({"docnames": ["analysis/analysis", "analysis/transition_state_analysis", "analysis/vdd_charge_analysis", "api/modules", "api/tcutility", "api/tcutility.analysis", "api/tcutility.analysis.vdd", "api/tcutility.analysis.vibration", "api/tcutility.atom_data_info", "api/tcutility.data", "api/tcutility.data.atom_data_info", "api/tcutility.job", "api/tcutility.job.postscripts", "api/tcutility.results", "api/tcutility.typing", "examples", "index", "tcutility.constants", "tcutility.job", "tcutility.results"], "filenames": ["analysis/analysis.rst", "analysis/transition_state_analysis.rst", "analysis/vdd_charge_analysis.rst", "api/modules.rst", "api/tcutility.rst", "api/tcutility.analysis.rst", "api/tcutility.analysis.vdd.rst", "api/tcutility.analysis.vibration.rst", "api/tcutility.atom_data_info.rst", "api/tcutility.data.rst", "api/tcutility.data.atom_data_info.rst", "api/tcutility.job.rst", "api/tcutility.job.postscripts.rst", "api/tcutility.results.rst", "api/tcutility.typing.rst", "examples.rst", "index.rst", "tcutility.constants.rst", "tcutility.job.rst", "tcutility.results.rst"], "titles": ["Overview of the analysis module", "Transition State Analysis module", "VDD Charge Analysis module", "tcutility", "tcutility package", "tcutility.analysis package", "tcutility.analysis.vdd package", "tcutility.analysis.vibration package", "tcutility.atom_data_info package", "tcutility.data package", "tcutility.data.atom_data_info package", "tcutility.job package", "tcutility.job.postscripts package", "tcutility.results package", "tcutility.typing package", "Examples", "TCutility v0.8.5 documentation", "tcutility.constants package", "Setup workflows with tcutility.job", "Reading a calculation"], "terms": {"thi": [0, 1, 2, 4, 7, 9, 11, 13, 16, 18, 19], "chapter": 0, "contain": [0, 1, 2, 4, 7, 9, 11, 13, 16, 17], "descript": [0, 4], "all": [0, 4, 7, 9, 11, 18], "function": [0, 2, 3, 4, 7, 11, 13, 16, 18, 19], "includ": [0, 2, 4, 9, 13, 18, 19], 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"tcutility.log.Emojis.question"]], "random_points_in_anular_sphere() (in module tcutility.geometry)": [[4, "tcutility.geometry.random_points_in_anular_sphere"]], "random_points_on_sphere() (in module tcutility.geometry)": [[4, "tcutility.geometry.random_points_on_sphere"]], "rarrow (emojis attribute)": [[4, "tcutility.log.Emojis.rarrow"]], "receive (emojis attribute)": [[4, "tcutility.log.Emojis.receive"]], "rlarrow (emojis attribute)": [[4, "tcutility.log.Emojis.rlarrow"]], "rotate() (transform method)": [[4, "tcutility.geometry.Transform.rotate"]], "rotate() (in module tcutility.geometry)": [[4, "tcutility.geometry.rotate"]], "save() (in module tcutility.molecule)": [[4, "tcutility.molecule.save"]], "sbatch() (in module tcutility.slurm)": [[4, "tcutility.slurm.sbatch"]], "scale() (transform method)": [[4, "tcutility.geometry.Transform.scale"]], "send (emojis attribute)": [[4, "tcutility.log.Emojis.send"]], "sleep (emojis attribute)": [[4, "tcutility.log.Emojis.sleep"]], "squeeze_list() (in module tcutility)": [[4, "tcutility.squeeze_list"]], "squeue() (in module tcutility.slurm)": [[4, "tcutility.slurm.squeue"]], "table() (in module tcutility.log)": [[4, "tcutility.log.table"]], "tcutility": [[4, "module-tcutility"]], "tcutility.cache": [[4, "module-tcutility.cache"]], "tcutility.constants": [[4, "module-tcutility.constants"]], "tcutility.formula": [[4, "module-tcutility.formula"]], "tcutility.geometry": [[4, "module-tcutility.geometry"]], "tcutility.log": [[4, "module-tcutility.log"]], "tcutility.molecule": [[4, "module-tcutility.molecule"]], "tcutility.report": [[4, "module-tcutility.report"]], "tcutility.slurm": [[4, "module-tcutility.slurm"]], "tcutility.spell_check": [[4, "module-tcutility.spell_check"]], "time_stamp() (in module tcutility.log)": [[4, "tcutility.log.time_stamp"]], "timed_cache() (in module tcutility.cache)": [[4, "tcutility.cache.timed_cache"]], "translate() (transform method)": [[4, "tcutility.geometry.Transform.translate"]], "vector_align_rotmat() (in module tcutility.geometry)": [[4, "tcutility.geometry.vector_align_rotmat"]], "wagner_fischer() (in module tcutility.spell_check)": [[4, "tcutility.spell_check.wagner_fischer"]], "wait (emojis attribute)": [[4, "tcutility.log.Emojis.wait"]], "wait_for_job() (in module tcutility.slurm)": [[4, "tcutility.slurm.wait_for_job"]], "warn() (in module tcutility.log)": [[4, "tcutility.log.warn"]], "warning (emojis attribute)": [[4, "tcutility.log.Emojis.warning"]], "workdir_info() (in module tcutility.slurm)": [[4, "tcutility.slurm.workdir_info"]], "tcutility.analysis": [[5, "module-tcutility.analysis"]], "vddcharge (class in tcutility.analysis.vdd.charge)": [[6, "tcutility.analysis.vdd.charge.VDDCharge"]], "vddchargemanager (class in tcutility.analysis.vdd.manager)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager"]], "atom_index (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.atom_index"]], "atom_symbol (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.atom_symbol"]], "calc_dir (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.calc_dir"]], "change_unit() (vddcharge method)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.change_unit"]], "change_unit() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.change_unit"]], "change_unit_decorator() (in module tcutility.analysis.vdd.manager)": [[6, "tcutility.analysis.vdd.manager.change_unit_decorator"]], "charge (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.charge"]], "charge_is_conserved() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.charge_is_conserved"]], "create_vdd_charge_manager() (in module tcutility.analysis.vdd.manager)": [[6, "tcutility.analysis.vdd.manager.create_vdd_charge_manager"]], "frag_index (vddcharge attribute)": [[6, "tcutility.analysis.vdd.charge.VDDCharge.frag_index"]], "get_summed_vdd_charges() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_summed_vdd_charges"]], "get_summed_vdd_charges_dataframe() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_summed_vdd_charges_dataframe"]], "get_summed_vdd_charges_table() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_summed_vdd_charges_table"]], "get_vdd_charges() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_vdd_charges"]], "get_vdd_charges_dataframe() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_vdd_charges_dataframe"]], "get_vdd_charges_table() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.get_vdd_charges_table"]], "irreps (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.irreps"]], "is_fragment_calculation (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.is_fragment_calculation"]], "mol_charge (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.mol_charge"]], "name (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.name"]], "plot_vdd_charges_per_atom() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.plot_vdd_charges_per_atom"]], "tcutility.analysis.vdd": [[6, "module-tcutility.analysis.vdd"]], "tcutility.analysis.vdd.charge": [[6, "module-tcutility.analysis.vdd.charge"]], "tcutility.analysis.vdd.manager": [[6, "module-tcutility.analysis.vdd.manager"]], "unit (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.unit"]], "vdd_charges (vddchargemanager attribute)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.vdd_charges"]], "write_to_excel() (vddchargemanager method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.write_to_excel"]], "write_to_txt() (vddchargemanager static method)": [[6, "tcutility.analysis.vdd.manager.VDDChargeManager.write_to_txt"]], "avg_relative_bond_length_delta() (in module tcutility.analysis.vibration.ts_vibration)": [[7, "tcutility.analysis.vibration.ts_vibration.avg_relative_bond_length_delta"]], "determine_ts_reactioncoordinate() (in module tcutility.analysis.vibration.ts_vibration)": [[7, "tcutility.analysis.vibration.ts_vibration.determine_ts_reactioncoordinate"]], "tcutility.analysis.vibration": [[7, "module-tcutility.analysis.vibration"]], "tcutility.analysis.vibration.ts_vibration": [[7, "module-tcutility.analysis.vibration.ts_vibration"]], "validate_transitionstate() (in module tcutility.analysis.vibration.ts_vibration)": [[7, "tcutility.analysis.vibration.ts_vibration.validate_transitionstate"]], "color() (in module tcutility.data.atom)": [[9, "tcutility.data.atom.color"]], "functional_name_from_path_safe_name() (in module tcutility.data.functionals)": [[9, "tcutility.data.functionals.functional_name_from_path_safe_name"]], "get() (in module tcutility.data.functionals)": [[9, "tcutility.data.functionals.get"]], "get() (in module tcutility.data.molecules)": [[9, "tcutility.data.molecules.get"]], "get_available_functionals() (in module tcutility.data.functionals)": [[9, "tcutility.data.functionals.get_available_functionals"]], "get_molecules() (in module tcutility.data.molecules)": [[9, "tcutility.data.molecules.get_molecules"]], "parse_element() (in module tcutility.data.atom)": [[9, "tcutility.data.atom.parse_element"]], "radius() (in module tcutility.data.atom)": [[9, "tcutility.data.atom.radius"]], "tcutility.data": [[9, "module-tcutility.data"]], "tcutility.data.atom": [[9, "module-tcutility.data.atom"]], "tcutility.data.basis_sets": [[9, "module-tcutility.data.basis_sets"]], "tcutility.data.cosmo": [[9, "module-tcutility.data.cosmo"]], "tcutility.data.functionals": [[9, "module-tcutility.data.functionals"]], "tcutility.data.molecules": [[9, "module-tcutility.data.molecules"]], "tcutility.data.atom_data_info": [[10, "module-tcutility.data.atom_data_info"]], "adffragmentjob (class in tcutility.job.adf)": [[11, "tcutility.job.adf.ADFFragmentJob"]], "adfjob (class in tcutility.job.adf)": [[11, "tcutility.job.adf.ADFJob"]], "amsjob (class in tcutility.job.ams)": [[11, "tcutility.job.ams.AMSJob"]], "crestjob (class in tcutility.job.crest)": [[11, "tcutility.job.crest.CRESTJob"]], "dftbjob (class in tcutility.job.dftb)": [[11, "tcutility.job.dftb.DFTBJob"]], "irc() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.IRC"]], "job (class in tcutility.job.generic)": [[11, "tcutility.job.generic.Job"]], "nmrjob (class in tcutility.job.nmr)": [[11, "tcutility.job.nmr.NMRJob"]], "orcajob (class in tcutility.job.orca)": [[11, "tcutility.job.orca.ORCAJob"]], "qcgjob (class in tcutility.job.crest)": [[11, "tcutility.job.crest.QCGJob"]], "scf_convergence() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.SCF_convergence"]], "add_fragment() (adffragmentjob method)": [[11, "tcutility.job.adf.ADFFragmentJob.add_fragment"]], "add_nics_point() (nmrjob method)": [[11, "tcutility.job.nmr.NMRJob.add_nics_point"]], "add_postamble() (job method)": [[11, "tcutility.job.generic.Job.add_postamble"]], "add_postscript() (job method)": [[11, "tcutility.job.generic.Job.add_postscript"]], "add_preamble() (job method)": [[11, "tcutility.job.generic.Job.add_preamble"]], "alpb() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.alpb"]], "basis_set() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.basis_set"]], "best_conformer_path (crestjob property)": [[11, "tcutility.job.crest.CRESTJob.best_conformer_path"]], "best_ensemble_path (qcgjob property)": [[11, "tcutility.job.crest.QCGJob.best_ensemble_path"]], "can_skip() (job method)": [[11, "tcutility.job.generic.Job.can_skip"]], "charge() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.charge"]], "charge() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.charge"]], "charge() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.charge"]], "conformer_directory (crestjob property)": [[11, "tcutility.job.crest.CRESTJob.conformer_directory"]], "dependency() (job method)": [[11, "tcutility.job.generic.Job.dependency"]], "ensemble_directory (qcgjob property)": [[11, "tcutility.job.crest.QCGJob.ensemble_directory"]], "ensemble_mode() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.ensemble_mode"]], "functional() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.functional"]], "geometry_convergence() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.geometry_convergence"]], "get_conformer_xyz() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.get_conformer_xyz"]], "get_ensemble_xyz() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.get_ensemble_xyz"]], "get_input() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.get_input"]], "get_memory_usage() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.get_memory_usage"]], "get_rotamer_xyz() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.get_rotamer_xyz"]], "inputfile_path (job property)": [[11, "tcutility.job.generic.Job.inputfile_path"]], "kspace() (dftbjob method)": [[11, "tcutility.job.dftb.DFTBJob.kspace"]], "md_length() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.md_length"]], "md_temperature() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.md_temperature"]], "model() (dftbjob method)": [[11, "tcutility.job.dftb.DFTBJob.model"]], "molecule() (job method)": [[11, "tcutility.job.generic.Job.molecule"]], "multiplicity() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.multiplicity"]], "multiplicity() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.multiplicity"]], "multiplicity() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.multiplicity"]], "nofix() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.nofix"]], "nsolv() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.nsolv"]], "optimization() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.optimization"]], "optimization() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.optimization"]], "output_mol_path (amsjob property)": [[11, "tcutility.job.ams.AMSJob.output_mol_path"]], "output_mol_path (job property)": [[11, "tcutility.job.generic.Job.output_mol_path"]], "quality() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.quality"]], "relativity() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.relativity"]], "rotamer_directory (crestjob property)": [[11, "tcutility.job.crest.CRESTJob.rotamer_directory"]], "run() (adffragmentjob method)": [[11, "tcutility.job.adf.ADFFragmentJob.run"]], "run() (job method)": [[11, "tcutility.job.generic.Job.run"]], "runfile_path (job property)": [[11, "tcutility.job.generic.Job.runfile_path"]], "sbatch() (job method)": [[11, "tcutility.job.generic.Job.sbatch"]], "single_point() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.single_point"]], "single_point() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.single_point"]], "solvent() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.solvent"]], "solvent() (dftbjob method)": [[11, "tcutility.job.dftb.DFTBJob.solvent"]], "solvent() (qcgjob method)": [[11, "tcutility.job.crest.QCGJob.solvent"]], "spin_polarization() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.spin_polarization"]], "spin_polarization() (crestjob method)": [[11, "tcutility.job.crest.CRESTJob.spin_polarization"]], "spin_polarization() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.spin_polarization"]], "tcutility.job": [[11, "module-tcutility.job"]], "tcutility.job.adf": [[11, "module-tcutility.job.adf"]], "tcutility.job.ams": [[11, "module-tcutility.job.ams"]], "tcutility.job.crest": [[11, "module-tcutility.job.crest"]], "tcutility.job.dftb": [[11, "module-tcutility.job.dftb"]], "tcutility.job.generic": [[11, "module-tcutility.job.generic"]], "tcutility.job.nmr": [[11, "module-tcutility.job.nmr"]], "tcutility.job.orca": [[11, "module-tcutility.job.orca"]], "transition_state() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.transition_state"]], "transition_state() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.transition_state"]], "unrestricted() (adfjob method)": [[11, "tcutility.job.adf.ADFJob.unrestricted"]], "vibrations() (amsjob method)": [[11, "tcutility.job.ams.AMSJob.vibrations"]], "vibrations() (orcajob method)": [[11, "tcutility.job.orca.ORCAJob.vibrations"]], "workdir (job property)": [[11, "tcutility.job.generic.Job.workdir"]], "tcutility.job.postscripts": [[12, "module-tcutility.job.postscripts"]], "tcutility.job.postscripts.clean_workdir": [[12, "module-tcutility.job.postscripts.clean_workdir"]], "tcutility.job.postscripts.split_crest_xyz": [[12, "module-tcutility.job.postscripts.split_crest_xyz"]], "tcutility.job.postscripts.write_converged_geoms": [[12, "module-tcutility.job.postscripts.write_converged_geoms"]], "result (class in tcutility.results.result)": [[13, "tcutility.results.result.Result"]], "trackkfreader (class in tcutility.results.cache)": [[13, "tcutility.results.cache.TrackKFReader"]], "as_plams_settings() (result method)": [[13, "tcutility.results.result.Result.as_plams_settings"]], "get() (in module tcutility.results.cache)": [[13, "tcutility.results.cache.get"]], "get_ams_info() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_ams_info"]], "get_ams_input() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_ams_input"]], "get_ams_version() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_ams_version"]], "get_calc_files() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_calc_files"]], "get_calc_files() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_calc_files"]], "get_calc_settings() (in module tcutility.results.adf)": [[13, "tcutility.results.adf.get_calc_settings"]], "get_calc_settings() (in module tcutility.results.dftb)": [[13, "tcutility.results.dftb.get_calc_settings"]], "get_calc_settings() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_calc_settings"]], "get_calculation_status() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_calculation_status"]], "get_calculation_status() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_calculation_status"]], "get_history() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_history"]], "get_info() (in module tcutility.results)": [[13, "tcutility.results.get_info"]], "get_info() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_info"]], "get_input() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_input"]], "get_input_blocks() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_input_blocks"]], "get_level_of_theory() (in module tcutility.results.adf)": [[13, "tcutility.results.adf.get_level_of_theory"]], "get_level_of_theory() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_level_of_theory"]], "get_molecules() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_molecules"]], "get_molecules() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_molecules"]], "get_multi_key() (result method)": [[13, "tcutility.results.result.Result.get_multi_key"]], "get_parent_tree() (result method)": [[13, "tcutility.results.result.Result.get_parent_tree"]], "get_properties() (in module tcutility.results.adf)": [[13, "tcutility.results.adf.get_properties"]], "get_properties() (in module tcutility.results.dftb)": [[13, "tcutility.results.dftb.get_properties"]], "get_properties() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_properties"]], "get_timing() (in module tcutility.results.ams)": [[13, "tcutility.results.ams.get_timing"]], "get_version() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_version"]], "get_vibrations() (in module tcutility.results.orca)": [[13, "tcutility.results.orca.get_vibrations"]], "items() (result method)": [[13, "tcutility.results.result.Result.items"]], "keys() (result method)": [[13, "tcutility.results.result.Result.keys"]], "prune() (result method)": [[13, "tcutility.results.result.Result.prune"]], "read() (trackkfreader method)": [[13, "tcutility.results.cache.TrackKFReader.read"]], "read() (in module tcutility.results)": [[13, "tcutility.results.read"]], "store() (in module tcutility.results.cache)": [[13, "tcutility.results.cache.store"]], "tcutility.results": [[13, "module-tcutility.results"]], "tcutility.results.adf": [[13, "module-tcutility.results.adf"]], "tcutility.results.ams": [[13, "module-tcutility.results.ams"]], "tcutility.results.cache": [[13, "module-tcutility.results.cache"]], "tcutility.results.dftb": [[13, "module-tcutility.results.dftb"]], "tcutility.results.orca": [[13, "module-tcutility.results.orca"]], "tcutility.results.result": [[13, "module-tcutility.results.result"]], "unload() (in module tcutility.results.cache)": [[13, "tcutility.results.cache.unload"]], "tcutility.typing": [[14, "module-tcutility.typing"]], "tcutility.typing.arrays": [[14, "module-tcutility.typing.arrays"]]}})
\ No newline at end of file
diff --git a/docs/api/tcutility.data.atom_data_info.rst b/docs/api/tcutility.data.atom_data_info.rst
new file mode 100644
index 00000000..7b4c05e9
--- /dev/null
+++ b/docs/api/tcutility.data.atom_data_info.rst
@@ -0,0 +1,10 @@
+tcutility.data.atom\_data\_info package
+=======================================
+
+Module contents
+---------------
+
+.. automodule:: tcutility.data.atom_data_info
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/tcutility.data.rst b/docs/api/tcutility.data.rst
new file mode 100644
index 00000000..44b0121c
--- /dev/null
+++ b/docs/api/tcutility.data.rst
@@ -0,0 +1,61 @@
+tcutility.data package
+======================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tcutility.data.atom_data_info
+
+Submodules
+----------
+
+tcutility.data.atom module
+--------------------------
+
+.. automodule:: tcutility.data.atom
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tcutility.data.basis\_sets module
+---------------------------------
+
+.. automodule:: tcutility.data.basis_sets
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tcutility.data.cosmo module
+---------------------------
+
+.. automodule:: tcutility.data.cosmo
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tcutility.data.functionals module
+---------------------------------
+
+.. automodule:: tcutility.data.functionals
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tcutility.data.molecules module
+-------------------------------
+
+.. automodule:: tcutility.data.molecules
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tcutility.data
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/tcutility.rst b/docs/api/tcutility.rst
index 4b98ca3c..3654fd72 100644
--- a/docs/api/tcutility.rst
+++ b/docs/api/tcutility.rst
@@ -8,6 +8,7 @@ Subpackages
    :maxdepth: 4
 
    tcutility.analysis
+   tcutility.data
    tcutility.job
    tcutility.results
    tcutility.typing