gaussianclasses

One of the two core libraries of pyssian. Contains the Classes that represent Gaussian Files (input and output).

To do:

• Create a Class to represent the basis and core electronic pontentials

GaussianInFile

• Accepts a context manager usage similar to 'with open(file) as F:...'

• Does not parse ONIOM calculation inputs

• Does not parse MM calculation inputs

• Not tested for z-matrix inputs

class pyssian.GaussianInFile(file=None)

Gaussian 09/16 .in file parent class, if any special type of input requires different processing it should be a subclass of this one.

Parameters:

file (io.TextIOBase or str) -- File instance (Result of open(filename,'r')) or valid filename.

preprocessing

Dictionary in which each key corresponds to a certain Link0 keyword

Type:

dict

commandline

Dictionary that contains the information of how the calculation will be carried out.

Type:

dict

title

title of the calculation.

Type:

str

method

If it cannot be recognized in the command line it will be empty.

Type:

str

basis

If it cannot be recognized in the command line it will be empty.

Type:

str

spin

Type:

int

charge

Type:

int

geometry

It should be able to write the text block of an input file upon calling str(geometry)

Type:

str-ish

tail

List of str in which each should be separated from the others by a single blank line in the input file.

Type:

list

structure

A string holding the structure of the input file. Used to write new Input files.

Type:

str

nprocs

property to easily access and change the preprocessing['nprocshared'] value

Type:

int

mem

property to easily access and change the preprocessing['mem'] value

Type:

int

extra_printout

Controls the behaviour of the command line's "#" or "#p". If True the command line will appear with the "#p". It is True by default.

Type:

bool

solvent

When set to None the solvation is still active but no solvent has been specified. When set to 'gas' the solvation is completely removed and when set to a different string, the string is assumed to be a valid name for the solvent in gaussian.

Type:

str or None

solvent_model

This property controls the keyword scrf and has three possible values: None -> the scrf keyword is not included 'pcm' -> the 'pcm' suboption within scrf is included 'smd' -> the 'smd' suboption within the scrf is included.

Type:

str or None

add_chk(name=None)

Adds the chk to the file, with the specified name. If none is provided defaults to the file name ended in .chk

add_kwd(keyword, where=None)

Adds a keyword to the command line.

Parameters:

• keyword (str) -- keyword to add to the command line.

• where (str, optional) -- if provided it adds the keyword as a suboption of the "where" keyword i.e. add_kwd('smd',where='scrf') or add_kwd('cartesian',where='opt')

add_l0_kwd(keyword, where=None)

Adds a keyword to the preprocessing.

Parameters:

• keyword (str) -- keyword to add to the preprocessing.

• where (str, optional) -- if provided it adds the keyword as a suboption of the "where" keyword i.e. add_l0_kwd('job1.chk',where='chk') or add_kwd('40GB',where='mem')

change_basis(basis)

Changes appropiately the basis of the calculation. Running self.basis = basis makes a call to this function.

Parameters:

basis (str) -- A string representation of a valid method if specified in the command line.

Raises:

NotImplementedError -- If the basis is not within the registered basis keywords

change_method(method)

Changes appropiately the method of the calculation. Running self.method = method makes a call to this function.

Parameters:

method (str) -- A string representation of a valid method

Raises:

NotImplementedError -- If the method is not within the registered methods keywords

close()

Alias to file.close for consistency with the io.TextIOBase class

commandline_as_str()

Transforms the commandline attribute to a suitable string representation.

Returns:

string corresponding to the commandline of the input file.

Return type:

str

disable_extra_printout()

When used, the string representation of the object will not include the #p in the command line.

enable_extra_printout()

When used, the string representation of the object will include the #p in the command line.

classmethod from_str(text)

Creates a GaussianInFile object from a gaussian input file read as a string, parses it and populates the attributes of the class.

Parameters:

• text (str) --

  Contents of a Gaussian input file as a string. i.e. .. code:: python

  with open('somefile.com','r') as F:

  text = F.read()

• name (str) -- Name to represent the GaussianInFile

Returns:

A populated GaussianInFile object

Return type:

GaussianInFile

parse_commandline(lines)

Parses the lines that contain the calculation commands keywords and transforms them into a dictionary representation.

Parameters:

lines (list) -- list of strings previously stripped and split. Empty lines will be ignored.

parse_geometry(lines)

Parses each line that contains 'Atom x y z' in an appropiate form and saves it to self.geometry

Parameters:

lines (list) -- list of strings previously stripped. Should not contain empty lines

parse_preprocessing(lines)

Parses the lines that contain the Link 0 keywords and transforms them into a dictionary representation.

Parameters:

lines (list) -- list of strings previously stripped. Empty lines will be ignored.

parse_tail(lines)

Chops the set of lines into different blocks of text using as reference the emptylines/blank lines

Parameters:

lines (list) -- list of strings previously stripped.

Returns:

Description of returned object.

Return type:

type

Raises:

ExceptionName -- Why the exception is raised.

pop_chk(default=None)

Removes the chk from the file, returns 'default' if the chk was not included already

pop_kwd(keyword, where=None)

Removes a keyword from the command line and returns it.

Parameters:

• keyword (str) -- keyword to remove from the command line.

• where (str, optional) -- if provided it searches the keyword as a suboption of the "where" keyword i.e. pop_kwd('smd',where='scrf') or pop_kwd('cartesian',where='opt')

Returns:

Returns the removed keyword (or None when the keyword was not in the command line)

Return type:

str or None

pop_l0_kwd(keyword, where=None)

Removes a keyword from the preprocessing and returns it.

Parameters:

• keyword (str) -- keyword to remove from the preprocessing.

• where (str, optional) -- if provided it searches the keyword as a suboption of the "where" keyword i.e. pop_l0_kwd('job1.chk',where='oldchk')

Returns:

Returns the removed keyword (or None when the keyword was not in the preprocessing)

Return type:

str or None

preprocessing_as_str()

Transforms the preprocessing attribute to a suitable string representation.

Returns:

string corresponding to the preprocessing part of the input file.

Return type:

str

read()

Reads the file and populates the appropiate attributes.

write(filepath=None)

Writes the File object to a File. If a filepath is provided it will write to that filepath otherwise it will attempt to write to the path provided in the initialization.

Parameters:

filepath (str) -- A valid filepath.

MultiGaussianInFile

• Allows the concatenation of multiple GaussianInFile instances to create a linked (--Link1--) gaussian input.

• Provides some convenience methods to enforce same resources across each concatenated job

• It was conceived for writing gaussian input files rather than reading gaussian input files with linked calculations, so no much testing was put into this task.

class pyssian.MultiGaussianInFile(file=None)

Container class of multiple GausianInFiles linked together in a single gaussian input calculation.

Parameters:

file (io.TextIOBase or str (the default is None)) -- File instance (Result of open(filename,'r')) or valid filename.

jobs

List providing access to each one of the individual GaussianInFile objects representing each one of the linked calculations.

Type:

list

enforce_continuous_chk(basename=None)

Enforces that the chk of job i-1 is retained and a copy of it is used at the start of job i. For an example with two jobs, the first link0 section will look like:

%chk=basename_job0.chk

Then the link0 of the second job will look like:

Parameters:

basename (str, optional) -- basename of the chk to use, if none is provided it defaults to the one of the first job.

enforce_same_chk(chk=None)

Enforces the same chk file in all jobs.

Parameters:

chk (str, optional) -- filename of the chk to use, if none is provided it defaults to the one of the first job.

enforce_same_mem(mem=None)

Enforces the same memory in all jobs.

Parameters:

mem (int, optional) -- Memory to use in a calculation, if none is provided it defaults to the value of the mem of the first job.

enforce_same_method(method)

Enforces the same method in all jobs.

Parameters:

method (str, optional) -- method to use in a calculation, if none is provided it defaults to the value of the first job's method.

enforce_same_nprocs(nprocs=None)

Enforces the same nprocs in all jobs.

Parameters:

nprocs (int, optional) -- number of processors to use in a calculation, if none is provided it defaults to the value of the nprocs of the first job.

read()

Reads the file and populates the appropiate attributes.

write(filepath=None)

Writes the File object to a File. If a filepath is provided it will write to that filepath otherwise it will attempt to write to the path provided in the initialization.

Parameters:

filepath (str) -- A valid filepath.

GaussianOutFile

• Accepts a context manager usage similar to 'with open(file) as F:...'

• Will only parse a Gaussian Output File that has the "#p".

class pyssian.GaussianOutFile(file, parselist=None)

Gaussian 09/16 '.log' file parent class, if any special type of calculation requires different processing it should be a subclass of this one. Accepts a context manager usage similar to 'with open(file) as F:...' For a Gaussian .log file to be parsable it requires that its corresponding input has the additional printout enabled (#p)

Parameters:

• file (io.TextIOBase or str) -- File instance (Result of open(filename,'r')) or valid filename.

• parselist (list) -- List of integrers that represent which types of Links to parse (the default is None).

InternalJobs

List of InternalJobs done by gaussian i.e an gaussian calculation with the opt freq keywords will run first an InternalJob for the Optimization and after an InternalJob for the Frequency calculation.

clean()

Removes per each InternalJob stored all the EmptyLinkJobs.

get_links(*LinkIds)

Wrapper Method to get a list of Links with certain Ids across the different Internal Jobs.

Parameters:

*LinkIds (int) -- Integrers that correspond to the type of links to be return.

Return type:

list

print_file_structure()

Display the structure of links and internal jobs of the file.

read()

Alias of update for consistency with GaussianInFile class

update(clean=True, FinalPrint=False)

Tries to fetch new data. If it exists it parses it appropiately otherwise it fails silently.

Parameters:

• clean (Bool) -- If True removes all the EmptyLinkJobs found (the default is True).

• FinalPrint (Bool) -- If True after a normal execution has finished it will print in the console a message to notify the user (the default is False).

InternalJob

class pyssian.InternalJob(number=None)

Gaussian 09/16 InternalJob parent class, if any special type of Job requires different parsing it should be a subclass of this one.

Parameters:

number (int) -- ordinal number of the InternalJob (the default is None).

type

string identifier for the job.

Links

List of the different Links that belong to the InternalJob.

number

clean()

Removes all the Empty Link instances within Links.

get_links(*LinkIds)

Wrapper Method to get a list of Links with certain Ids.

Parameters:

*LinkIds (int) -- Integrers that correspond to the type of links to be return.

Returns:

List of Link Objects ordered by appearance in the file and filtered by Link Number.

Return type:

list

guess_info()

Guesses the number and type attributes of itself using the stored Links.