ben-sci-tools 0.3.13

useful python tools that I use to streamline my work.

Project Description

ben-science-tools (bst) is meant to contain tools that Ben uses to streamline some of his porcesses while working on computaional chemistry. The project currently has two main modules process_data which is used for log file or computaional chemistry output file processing and analysis, and input_file_maker which is used to generate file inputs for computational chemistry

Documentation

process_data

Functions

statp takes a file patern and returns the number of stationary points in each file that fits that pattern.

Parameters
----------
file_patern (str) :  a string that matches a certain string

Returns
-------
a string that gives nomber of occurences and line numbers of stationary points

rxn_coord_list_format rxn_coord_list_format takes a list of energies or enthalpies and returns a new list where each value is duplicated. This formatted list can be used to create a step-like reaction coordinate plot.

Parameters
----------
reaction_list (list[float]) :  a list of floating point numbers representing energies or enthalpies

Returns
-------
a list of floating point numbers with each value duplicated for better plotting of reaction coordinates

Classes

out_file_scraper This is a parent file scraper class meant to be altered or used for scraping log files for computations.

Attributes
----------
path : str
    a path to an output file

file_list : list
    a list of strings where each item is the corrsponding line in the file.

Methods
-------
`read_in_file()`
Reads in a file and retruns a list where each line is an item in the list

    Parameters
    ----------
        file_name : str
            a path to an output file
    Returns
    -------
        None
            assignes self.file_list a list of all the lines in a file where each item in the list is an item.
`set_flag_function()`
Create the flag_functions dictionary mapping flag strings to the subparsing functions

    Parameters
    ----------
        flag : str
            this is the flag you plan to add to the flag_functions dictionary
        function_string : str
            this is the method you plan to call if the flag is found
    
    Returns
    -------
        None
            Adds to the self.flag_functions dictionary

g16_scraper This is a child class of out_file_scraper. To be a general scraper for Gaussian 16 output files

Attributes
----------

input_line : str
    this is the input line used in the original gjf file

checkpoint_line : str
    The "%chk=" in the original gjf file

nproc_line : str
    The "%nproc=" in the original gjf file

memory_line : str
    The "%mem=" line in the original gjf file

charge : int
    Represents the charge of the system in the original gjf file

mult : int
    represents the multiplicity of the system in the original gjf file

start_geometry: list[str]
    the starting geometry of the sytem in the original gjf file

Methods
-------
`get_input_lines()`
Extracts the input information of the gaussian file 

    Parameters
    ----------
        self
        index : int
            The index of the line this parsing function's flag is found in the file_list
    Returns
    -------
        None
            assigns respective values to:
                checkpoint_line : str
                nproc_line :      str
                memory_line :     str
                input_line :      str
                charge :          int
                multiplicity :    int
                start_geometry :  list[str]

`recreate_gjf()`
Recreates the most basic starting gjf file (does not inclued anything after the starting geometry)

    Parameters
    ----------
        self

    Returns
    -------
        str
            a formatted string of a gjf file from the start of the run

g16_optfreq Child of the g16_scraper. Meant to serve as a file scraper for Gaussian16 frequency calculations

Attributes
----------
zero_point_correction                          : float
    unit: hartrees/particle
    gives the gaussian calculated floating point number.

thermal_correction_to_energy                   : float
    unit: hartrees/particle
    gives the gaussian calculated floating point number.

thermal_correction_to_enthalpy                 : float
    unit: hartrees/particle
    gives the gaussian calculated floating point number.

thermal_correction_to_gibbs_free_energy        : float
    unit: hartrees/particle
    gives the gaussian calculated floating point number.

sum_of_electronic_and_zero_point_energies      : float
    unit: hartrees/particle
    gives the gaussian calculated floating point number.

sum_of_electronic_and_thermal_enthalpies       : float
    unit: hartrees/particle
    gives the gaussian calculated floating point number.

sum_of_electronic_and_thermal_energies         : float
    unit: hartrees/particle
    gives the gaussian calculated floating point number.

sum_of_electronic_and_thermal_free_energies    : float
    unit: hartrees/particle
    gives the gaussian calculated floating point number.

zero_point_energy                              :float
    unit: hartrees/particle
    gives the zero point energy of the system

vibrational_thermal_contributions              : dict {str : tuple(str,float)}
    keys:
        "Thermal_Energy"
            unit : kcal/mol
            returns a list of tuples with the the name : str of the of the contribution at index 0 and the value : float at index 0
        "CV" (specific Heat)
            unit : cal/(mol * kelvin)
            returns a list of tuples with the the name : str of the of the contribution at index 0 and the value : float at index 0
        "S" (Entropy)
            unit : cal/(mol * kelvin)
            returns a list of tuples with the the name : str of the of the contribution at index 0 and the value : float at index 0
    
Methods
-------
`get_thermochemistry_properties()`
Assigns the thermochemistry properties
    
    Parameters
    ----------
        index : int
            The index of the starting line for the thermochemistry section in an opt freq gaussian job

    Returns
    -------
        None
            Assigns values to the following attributes:
            zero_point_correction                          : float
            thermal_correction_to_energy                   : float
            thermal_correction_to_enthalpy                 : float
            thermal_correction_to_gibbs_free_energy        : float
            sum_of_electronic_and_zero_point_energies      : float
            sum_of_electronic_and_thermal_energies         : float
            sum_of_electronic_and_thermal_enthalpies       : float
            sum_of_electronic_and_thermal_free_energies    : float
            zero_point_energy                              : float
            vibrational_thermal_contributions 

input_file_maker

Functions

Classes

xyz_atom an atom with x, y, and z coordinates

Attributes
----------
x_val : float
    x postion
y_val : float
    y postion
z_val : float
    z postion
atom_type : str
    the atomic coded for an atom i.e. C for carbon

Methods
-------

`as_string()`
returns a formatted string of atom type and xyz data

    Parameters
    ----------
    None

    Returns
    -------
    A formatted string of atom type and xyz data

xyz_molecule a list of xyz_atoms

Attributes
----------
    atom_list : list[xyz_atom]

Methods
-------

`as_string()`
returns a formatted string of atom type and xyz data

    Parameters
    ----------
    None

    Returns
    -------
    A formatted string of atom type and xyz data for each atom in the molecule on a new line
    """

`add_atom()`
adds an atom to the atom list
    
    Parameters
    ----------
    new_atom (xyz_atom)

    Returns
    -------
    None

g16_input A formatting object for g16_inputs

Attributes
----------

checkpoint : str
    The name of the checkpoint file
file_name : str
    The name of the associated input file
geometry : xyz_molecule
    The systems geometry information 
mem : int
    The memory usage of the calculation in GB. default is 1
nproc : int
    the number of processors used in the cacluation the default is 36
input_line : str
    The input line of the input file
extra : str
    Any information that may come after the geometry section
title_card : str
    The Title card of the input file
charge : charge
    The charge of the system
spin_mult : int
    The spin multiplicity of the system

colors

colors contains color pallets. in the form of a dictionary where keys are the name of the color and values are hex representations.

mines_primary

"dark_blue":"#21314d", "blaster_blue" : "#09396C", "light_blue" : "#879EC3" , "colorado_red" : "#CC4628", "pale_blue" : "#CFDCE9"

mines_neutral

"white" : "#FFFFFF", "light_gray" : "#AEB3B8", "silver" : "#81848A", "dark_gray" : "#75757D"

mines_accecnt

"earth_blue" : "#0272DE", "muted_blue" : "#57A2BD", "energy_yellow" : "#F0F600", "golden_tech" : "#F1B91A", "environment_green" : "#80C342", "red_flannel" : "#B42024"