cctk.GaussianFile

class cctk.GaussianFile(job_types=None, route_card=None, link0=None, footer=None, title='title', success=0, elapsed_time=0.0, molecule=None)

Bases: File

Class representing Gaussian input/output files.

ensemble

ConformationalEnsemble instance

Type:

ConformationalEnsemble

job_types

list of job_type` instances

Type:

list

route_card

optional, route card of .gjf file

Type:

str

link0

optional, dictionary of Link 0 commands (e.g. {“mem”: “32GB”, “nprocshared”: 16})

Type:

dict

footer

optional, footer of .gjf file

Type:

str

successful_terminations

number of successful terminations (should be 1 for an opt, 2 for opt and then freq, 1 for a single point energy, etc)

Type:

int

elapsed_time

total time for job in seconds

Type:

float

title

optional, title of .gjf file

Type:

str

__init__(job_types=None, route_card=None, link0=None, footer=None, title='title', success=0, elapsed_time=0.0, molecule=None)

Create new GaussianFile object.

Parameters:

• job_types (list) – list of job_type instances

• route_card (str) – optional, route card of .gjf file

• link0 (dict) – optional, Link 0 commands of .gjf file

• footer (str) – optional, footer of .gjf file

• title (str) – optional, title of .gjf file

• success (int) – num successful terminations

• elapsed_time (float) – total time for job in seconds

• molecule (cctk.Molecule) – molecule to initiate, if desired

Methods

__init__([job_types, route_card, link0, ...])	Create new GaussianFile object.
add_custom_basis_set(name[, ...])	Appends custom basis sets (from Basis Set Exchange) to self.footer.
append_to_file(filename, text)	Appends output text to a file.
check_has_properties()	Checks that the file has all the appropriate properties for its job types, and raises ValueError if not.
get_molecule([num, properties])	Returns the last molecule (from an optimization job) or the only molecule (from other jobs).
imaginaries()	Returns the imaginary frequencies, rounded to the nearest integer.
num_imaginaries()	Returns the number of imaginary frequencies.
read_file(filename[, return_lines, ...])	Reads a Gaussian``.out`` or .gjf file and populates the attributes accordingly.
write_ensemble_to_file(filename, ensemble, ...)	Write each structure in the specified ensemble to a single Gaussian input file by using the Link1 specification.
write_file(filename[, molecule, route_card, ...])	Write a .gjf file, using object attributes.
write_molecule_to_file(filename, molecule, ...)	Write a .gjf file using the given molecule.

add_custom_basis_set(name, add_all_elements=False, return_string=False)

Appends custom basis sets (from Basis Set Exchange) to self.footer. Should be used in combination with the gen keyword.

Parameters:

• name (str) – name of basis set (look it up on Basis Set Exchange)

• add_all_elements (bool) – whether the complete basis set should be added or just the elements of interest

• return_string (bool) – if the basis set should be appended to the footer or returned as a string (no change to self)

Returns:

nothing (if return_string is False) string of basis set definition (if return string is True)

static append_to_file(filename, text)

Appends output text to a file.

Parameters:

• filename (str) – path to file, including name (e.g. path/to/input.gjf)

• text (str) – desired contents of file

Returns:

True if write succeeded, False otherwise

check_has_properties()

Checks that the file has all the appropriate properties for its job types, and raises ValueError if not.

This only checks the last molecule in self.ensemble, for now.

get_molecule(num=None, properties=False)

Returns the last molecule (from an optimization job) or the only molecule (from other jobs).

If num is specified, returns self.ensemble.molecule_list()[num] If properties is True, returns (molecule, properties).

imaginaries()

Returns the imaginary frequencies, rounded to the nearest integer.

num_imaginaries()

Returns the number of imaginary frequencies.

classmethod read_file(filename, return_lines=False, extended_opt_info=False, fail_silently=True)

Reads a Gaussian``.out`` or .gjf file and populates the attributes accordingly. Only footers from opt=modredundant can be read automatically – genecep custom basis sets, &c must be specified manually.

Note:

Will throw ValueError if there have been no successful iterations.

Parameters:

• filename (str) – path to the out file

• return_lines (Bool) – whether the lines of the file should be returned

• extended_opt_info (Bool) – if full parameters about each opt step should be collected (by default, only rms_displacement and rms_force are collected)

• fail_silently (Bool) – if true, files that fail validation will just be omitted and parsing will continue. useful for monitoring jobs which are in-progress and may not have all properties written.

Returns:

GaussianFile object (or list of GaussianFile objects for Link1 files) (optional) the lines of the file (or list of lines of file for Link1 files) as Lines object

classmethod write_ensemble_to_file(filename, ensemble, route_card, link0={'mem': '32GB', 'nprocshared': 16}, footer=None, title='title', print_symbol=False)

Write each structure in the specified ensemble to a single Gaussian input file by using the Link1 specification.

Parameters:

• filename (str) – where to write the file

• ensemble (Ensemble) – Ensemble object to write

• route_card (str or list) – to use the same route card for every link, use a single string; otherwise, provide a list whose entries parallel the ensemble members

• link0 (dict or list of dicts) – to use the same memory/processors for every link, use a single string; otherwise, provide a list

• footer (None/str or list) – use None for no text after geometry, provide a str to specify a footer, or provide some combination of the above as a list

• title (str or list) – use a single string to provide a generic title for every link or a list as above

• print_symbol (bool or list) – whether to print atomic symbols or atomic numbers in the geometry specification; use a single bool or a list as above

write_file(filename, molecule=None, route_card=None, link0=None, footer=None, **kwargs)

Write a .gjf file, using object attributes. If no header/footer is specified, the object’s header/footer will be used.

Parameters:

• filename (str) – path to the new file

• molecule (int) – which molecule to use – passed to self.get_molecule(). Default is -1 (e.g. the last molecule), but positive integers will select from self.ensemble(1-indexed). A Molecule object can also be passed, in which case that molecule will be written to the file.

• route_card (str) – route card for new file

• link0 (dict) – dictionary of Link 0 commands (e.g. {“mem”: “32GB”, “nprocshared”: 16}

• footer (str) – footer for new file

classmethod write_molecule_to_file(filename, molecule, route_card, link0={'mem': '32GB', 'nprocshared': 16}, footer=None, title='title', append=False, print_symbol=False, point_charges=None)

Write a .gjf file using the given molecule.

Parameters:

• filename (str) – path to the new file

• molecule (Molecule) – which molecule to use – a Molecule object.

• route_card (str) – route card for new file

• link0 (dict) – dictionary of Link 0 commands

• footer (str) – footer for new file

• title (str) – title of the file, defaults to “title”

• append (Bool) – whether or not to append to file using Link1 specifications

• print_symbol (Bool) – whether to print atomic symbols (instead of atomic numbers)