| Name | ben-sci-tools JSON |
| Version |
1.1.6
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| home_page | None |
| Summary | useful python tools that I use to streamline my work. |
| upload_time | 2025-01-23 19:06:14 |
| maintainer | None |
| docs_url | None |
| author | Ben Payton |
| requires_python | None |
| license | None |
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# 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"
Raw data
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"description": "# Project Description\n\nben-science-tools (bst) is meant to contain tools that Ben uses to streamline some of his porcesses while working on computaional chemistry.\nThe 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\n\n# Documentation\n\n## process_data\n\n### Functions\n\n`statp`\ntakes a file patern and returns the number of stationary points in each file that fits that pattern.\n\n Parameters\n ----------\n file_patern (str) : a string that matches a certain string\n\n Returns\n -------\n a string that gives nomber of occurences and line numbers of stationary points\n \n`rxn_coord_list_format`\nrxn_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.\n\n Parameters\n ----------\n reaction_list (list[float]) : a list of floating point numbers representing energies or enthalpies\n\n Returns\n -------\n a list of floating point numbers with each value duplicated for better plotting of reaction coordinates\n\n### Classes\n\n`out_file_scraper`\nThis is a parent file scraper class meant to be altered or used for scraping log files for computations. \n \n Attributes\n ----------\n path : str\n a path to an output file\n \n file_list : list\n a list of strings where each item is the corrsponding line in the file.\n\n Methods\n -------\n `read_in_file()`\n Reads in a file and retruns a list where each line is an item in the list\n\n Parameters\n ----------\n file_name : str\n a path to an output file\n Returns\n -------\n None\n assignes self.file_list a list of all the lines in a file where each item in the list is an item.\n `set_flag_function()`\n Create the flag_functions dictionary mapping flag strings to the subparsing functions\n\n Parameters\n ----------\n flag : str\n this is the flag you plan to add to the flag_functions dictionary\n function_string : str\n this is the method you plan to call if the flag is found\n \n Returns\n -------\n None\n Adds to the self.flag_functions dictionary\n \n`g16_scraper`\nThis is a child class of out_file_scraper. To be a general scraper for Gaussian 16 output files\n\n Attributes\n ----------\n\n input_line : str\n this is the input line used in the original gjf file\n\n checkpoint_line : str\n The \"%chk=\" in the original gjf file\n\n nproc_line : str\n The \"%nproc=\" in the original gjf file\n\n memory_line : str\n The \"%mem=\" line in the original gjf file\n\n charge : int\n Represents the charge of the system in the original gjf file\n\n mult : int\n represents the multiplicity of the system in the original gjf file\n\n start_geometry: list[str]\n the starting geometry of the sytem in the original gjf file\n\n Methods\n -------\n `get_input_lines()`\n Extracts the input information of the gaussian file \n\n Parameters\n ----------\n self\n index : int\n The index of the line this parsing function's flag is found in the file_list\n Returns\n -------\n None\n assigns respective values to:\n checkpoint_line : str\n nproc_line : str\n memory_line : str\n input_line : str\n charge : int\n multiplicity : int\n start_geometry : list[str]\n \n `recreate_gjf()`\n Recreates the most basic starting gjf file (does not inclued anything after the starting geometry)\n\n Parameters\n ----------\n self\n\n Returns\n -------\n str\n a formatted string of a gjf file from the start of the run\n\n`g16_optfreq`\nChild of the g16_scraper. Meant to serve as a file scraper for Gaussian16 frequency calculations\n\n Attributes\n ----------\n zero_point_correction : float\n unit: hartrees/particle\n gives the gaussian calculated floating point number.\n \n thermal_correction_to_energy : float\n unit: hartrees/particle\n gives the gaussian calculated floating point number.\n \n thermal_correction_to_enthalpy : float\n unit: hartrees/particle\n gives the gaussian calculated floating point number.\n \n thermal_correction_to_gibbs_free_energy : float\n unit: hartrees/particle\n gives the gaussian calculated floating point number.\n \n sum_of_electronic_and_zero_point_energies : float\n unit: hartrees/particle\n gives the gaussian calculated floating point number.\n \n sum_of_electronic_and_thermal_enthalpies : float\n unit: hartrees/particle\n gives the gaussian calculated floating point number.\n \n sum_of_electronic_and_thermal_energies : float\n unit: hartrees/particle\n gives the gaussian calculated floating point number.\n\n sum_of_electronic_and_thermal_free_energies : float\n unit: hartrees/particle\n gives the gaussian calculated floating point number.\n\n zero_point_energy :float\n unit: hartrees/particle\n gives the zero point energy of the system\n \n vibrational_thermal_contributions : dict {str : tuple(str,float)}\n keys:\n \"Thermal_Energy\"\n unit : kcal/mol\n 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\n \"CV\" (specific Heat)\n unit : cal/(mol * kelvin)\n 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\n \"S\" (Entropy)\n unit : cal/(mol * kelvin)\n 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\n \n Methods\n -------\n `get_thermochemistry_properties()`\n Assigns the thermochemistry properties\n \n Parameters\n ----------\n index : int\n The index of the starting line for the thermochemistry section in an opt freq gaussian job\n\n Returns\n -------\n None\n Assigns values to the following attributes:\n zero_point_correction : float\n thermal_correction_to_energy : float\n thermal_correction_to_enthalpy : float\n thermal_correction_to_gibbs_free_energy : float\n sum_of_electronic_and_zero_point_energies : float\n sum_of_electronic_and_thermal_energies : float\n sum_of_electronic_and_thermal_enthalpies : float\n sum_of_electronic_and_thermal_free_energies : float\n zero_point_energy : float\n vibrational_thermal_contributions \n\n## input_file_maker\n\n### Functions\n\n### Classes\n\n`xyz_atom`\nan atom with x, y, and z coordinates\n\n Attributes\n ----------\n x_val : float\n x postion\n y_val : float\n y postion\n z_val : float\n z postion\n atom_type : str\n the atomic coded for an atom i.e. C for carbon\n\n Methods\n -------\n\n `as_string()`\n returns a formatted string of atom type and xyz data\n\n Parameters\n ----------\n None\n\n Returns\n -------\n A formatted string of atom type and xyz data\n\n`xyz_molecule`\na list of xyz_atoms\n\n Attributes\n ----------\n atom_list : list[xyz_atom]\n\n Methods\n -------\n \n `as_string()`\n returns a formatted string of atom type and xyz data\n\n Parameters\n ----------\n None\n\n Returns\n -------\n A formatted string of atom type and xyz data for each atom in the molecule on a new line\n \"\"\"\n \n `add_atom()`\n adds an atom to the atom list\n \n Parameters\n ----------\n new_atom (xyz_atom)\n\n Returns\n -------\n None\n\n`g16_input`\nA formatting object for g16_inputs\n\n Attributes\n ----------\n\n checkpoint : str\n The name of the checkpoint file\n file_name : str\n The name of the associated input file\n geometry : xyz_molecule\n The systems geometry information \n mem : int\n The memory usage of the calculation in GB. default is 1\n nproc : int\n the number of processors used in the cacluation the default is 36\n input_line : str\n The input line of the input file\n extra : str\n Any information that may come after the geometry section\n title_card : str\n The Title card of the input file\n charge : charge\n The charge of the system\n spin_mult : int\n The spin multiplicity of the system\n\n## colors\ncolors contains color pallets. in the form of a dictionary where keys are the name of the color and values are hex representations.\n\n`mines_primary`\n\n\"dark_blue\":\"#21314d\",\n\"blaster_blue\" : \"#09396C\",\n\"light_blue\" : \"#879EC3\" ,\n\"colorado_red\" : \"#CC4628\",\n\"pale_blue\" : \"#CFDCE9\"\n\n`mines_neutral`\n\n\"white\" : \"#FFFFFF\",\n\"light_gray\" : \"#AEB3B8\",\n\"silver\" : \"#81848A\",\n\"dark_gray\" : \"#75757D\"\n\n`mines_accecnt`\n\n\"earth_blue\" : \"#0272DE\",\n\"muted_blue\" : \"#57A2BD\",\n\"energy_yellow\" : \"#F0F600\",\n\"golden_tech\" : \"#F1B91A\",\n\"environment_green\" : \"#80C342\",\n\"red_flannel\" : \"#B42024\"\n",
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