pymatgen.io.adf module

IO for ADF files.

class AdfInput(task)

Bases: object

A basic ADF input file writer.

Initialization method.

Parameters

task (AdfTask) – An ADF task.

write_file(molecule, inpfile)

Write an ADF input file.

Parameters

• molecule (Molecule) – The molecule for this task.

• inpfile (str) – The name where the input file will be saved.

exception AdfInputError

Bases: Exception

The default error class for ADF.

class AdfKey(name, options=None, subkeys=None)

Bases: monty.json.MSONable

The basic input unit for ADF. A key is a string of characters that does not contain a delimiter (blank, comma or equal sign). A key may have multiple subkeys and a set of options.

Initialization method.

Parameters

• name (str) – The name of this key.

• options (Sized) – The options for this key. Each element can be a primitive object or a tuple/list with two elements: the first is the name and the second is a primitive object.

• subkeys (Sized) – The subkeys for this key.

Raises

ValueError – If elements in subkeys are not AdfKey objects.

add_option(option)

Add a new option to this key.

Parameters

option (Sized or str or int or float) – A new option to add. This must have the same format with exsiting options.

Raises

TypeError – If the format of the given option is different.

add_subkey(subkey)

Add a new subkey to this key.

Parameters

subkey (AdfKey) – A new subkey.

Notes

Duplicate check will not be performed if this is an ‘Atoms’ block.

as_dict()

A JSON serializable dict representation of self.

block_keys = {'A1FIT', 'ANALYTICALFREQ', 'ATOMS', 'BASIS', 'CHARGE', 'EXACTDENSITY', 'GEOMETRY', 'INTEGRATION', 'OCCUPATIONS', 'RELATIVISTIC', 'SAVE', 'SCF', 'SYMMETRY', 'TITLE', 'TOTALENERGY', 'UNITS', 'UNRESTRICTED', 'XC', 'ZLMFIT'}

classmethod from_dict(d)

Construct a MSONable AdfKey object from the JSON dict.

Parameters

d (dict) – A dict of saved attributes.

Returns

adfkey – An AdfKey object recovered from the JSON dict d.

Return type

AdfKey

static from_string(string)

Construct an AdfKey object from the string.

Parameters

string (str) – A string.

Returns

adfkey – An AdfKey object recovered from the string.

Return type

AdfKey

Raises

ValueError – Currently nested subkeys are not supported. If subend was found a ValueError would be raised.

Notes

Only the first block key will be returned.

has_option(option)

Return True if the option is included in this key.

Parameters

option (str) – The option.

Returns

has – True if the option can be found. Otherwise False will be returned.

Return type

bool

has_subkey(subkey)

Return True if this AdfKey contains the given subkey.

Parameters

subkey (str or AdfKey) – A key name or an AdfKey object.

Returns

has – True if this key contains the given key. Otherwise False.

Return type

bool

is_block_key()

Return True if this key is a block key.

property key

Return the name of this key. If this is a block key, the name will be converted to upper cases.

remove_option(option)

Remove an option.

Parameters

option (str or int) – The name (str) or index (int) of the option to remove.

Raises

TypeError – If the option has a wrong type.

remove_subkey(subkey)

Remove the given subkey, if existed, from this AdfKey.

Parameters

subkey (str or AdfKey) – The subkey to remove.

sub_keys = {'AtomDepQuality'}

to_json()

Return a json string representation of the MSONable AdfKey object.

class AdfOutput(filename)

Bases: object

A basic ADF output file parser.

is_failed: bool

True is the ADF job is terminated without success. Otherwise False.

is_internal_crash: bool

True if the job is terminated with internal crash. Please read ‘TAPE13’ of the ADF manual for more detail.

error: str

The error description.

run_type: str

The RunType of this ADF job. Possible options are: ‘SinglePoint’, ‘GeometryOptimization’, ‘AnalyticalFreq’ and ‘NUmericalFreq’.

final_energy: float

The final molecule energy (a.u).

final_structure: GMolecule

The final structure of the molecule.

energies: Sized

The energy of each cycle.

structures: Sized

The structure of each cycle If geometry optimization is performed.

frequencies: array_like

The frequencies of the molecule.

normal_modes: array_like

The normal modes of the molecule.

freq_type: str

Either ‘Analytical’ or ‘Numerical’.

Initialization method.

Parameters

filename (str) – The ADF output file to parse.

exception AdfOutputError

Bases: Exception

The default error class for errors raised by AdfOutput.

class AdfTask(operation='energy', basis_set=None, xc=None, title='ADF_RUN', units=None, geo_subkeys=None, scf=None, other_directives=None)

Bases: monty.json.MSONable

Basic task for ADF. All settings in this class are independent of molecules.

Notes

Unlike other quantum chemistry packages (NWChem, Gaussian, …), ADF does not support calculating force/gradient.

Initialization method.

Parameters

• operation (str) – The target operation.

• basis_set (AdfKey) – The basis set definitions for this task. Defaults to ‘DZ/Large’.

• xc (AdfKey) – The exchange-correlation functionals. Defaults to PBE.

• title (str) – The title of this ADF task.

• units (AdfKey) – The units. Defaults to Angstroms/Degree.

• geo_subkeys (Sized) – The subkeys for the block key ‘GEOMETRY’.

• scf (AdfKey) – The scf options.

• other_directives (Sized) – User-defined directives.

as_dict()

A JSON serializable dict representation of self.

classmethod from_dict(d)

Construct a MSONable AdfTask object from the JSON dict.

Parameters

d (dict) – A dict of saved attributes.

Returns

task – An AdfTask object recovered from the JSON dict d.

Return type

AdfTask

static get_default_basis_set()

Returns: Default basis set

static get_default_geo()

Returns: ADFKey using default geometry.

static get_default_scf()

Returns: ADF using default SCF.

static get_default_units()

Returns: Default units.

static get_default_xc()

Returns: ADFKey using default XC.

operations = {'energy': 'Evaluate the single point energy.', 'freq': 'Same as frequencies.', 'frequencies': 'Compute second derivatives and print out an analysis of molecular vibrations.', 'numerical_frequencies': 'Compute molecular frequencies using numerical method.', 'optimize': 'Minimize the energy by varying the molecular structure.'}

to_json()

Return a json string representation of the MSONable AdfTask object.

is_numeric(s)

Return True is the string s is a numeric string.

Parameters

s (str) – A string.

Returns

res – If True, s is a numeric string and can be converted to an int or a float. Otherwise False will be returned.

Return type

bool

iterlines(s)

A generator form of s.split(‘n’) for reducing memory overhead.

Parameters

s (str) – A multi-line string.

Yields

line (str) – A string.