pymatgen.io.core module

This module defines the abstract interface for reading and writing calculation inputs in pymatgen. The interface comprises a 3-tiered hierarchy of clases.

  1. An InputFile object represents the contents of a single input file, e.g. the INCAR. This class standardizes file read and write operations.

  2. An InputSet is a dict-like container that maps filenames (keys) to file contents (either strings or InputFile objects). This class provides a standard write_input() method.

  3. InputGenerator classes implement a get_input_set method that, when provided with a structure, return an InputSet object with all parameters set correctly. Calculation input files can be written to disk with the write_inputs method.

If you want to implement a new InputGenerator, please take note of the following:

  1. You must implement a get_input_set method that returns an InputSet

  2. All customization of calculation parameters should be done in the __init__ method of the InputGenerator. The idea is that the generator contains the “recipe”, but nothing that is specific to a particular system. get_input_set takes system-specific information (such as structure) and applies the recipe.

  3. All InputGenerator must save all supplied args and kwargs as instance variables. E.g., self.my_arg = my_arg and self.kwargs = kwargs in the __init__. This ensures the as_dict and from_dict work correctly.

class InputFile[source]

Bases: MSONable

Abstract base class to represent a single input file. Note that use of this class is optional; it is possible create an InputSet that does not rely on underlying Inputfile objects.

All InputFile classes must implement a get_string method, which is called by write_file.

If InputFile classes implement an __init__ method, they must assign all arguments to __init__ as attributes.

classmethod from_file(path: str | Path)[source]

Creates an InputFile object from a file.

Parameters:

path – Filename to read, including path.

Returns:

InputFile

abstract classmethod from_string(contents: str)[source]

Create an InputFile object from a string

Parameters:

contents – The contents of the file as a single string

Returns:

InputFile

abstract get_string() str[source]

Return a string representation of an entire input file.

write_file(filename: str | Path) None[source]

Write the input file.

Parameters:
  • filename – The filename to output to, including path.

  • kwargs – Keyword arguments passed to get_string()

class InputGenerator[source]

Bases: MSONable

InputGenerator classes serve as generators for Input objects. They contain settings or sets of instructions for how to create Input from a set of coordinates or a previous calculation directory.

abstract get_input_set() InputSet[source]

Generate an InputSet object. Typically the first argument to this method will be a Structure or other form of atomic coordinates.

class InputSet(inputs: dict[str | Path, str | InputFile] = None, **kwargs)[source]

Bases: MSONable, MutableMapping

Abstract base class for all InputSet classes. InputSet are dict-like containers for all calculation input data.

Since InputSet inherits dict, it can be instantiated in the same manner, or a custom __init__ can be provided. Either way, self should be populated with keys that are filenames to be written, and values that are InputFile objects or strings representing the entire contents of the file.

All InputSet must implement from_directory. Implementing the validate method is optional.

Instantiate an InputSet.

Parameters:
  • inputs – The core mapping of filename: file contents that defines the InputSet data. This should be a dict where keys are filenames and values are InputFile objects or strings representing the entire contents of the file. If a value is not an InputFile object nor a str, but has a __str__ method, this str representation of the object will be written to the corresponding file. This mapping will become the .inputs attribute of the InputSet.

  • **kwargs – Any kwargs passed will be set as class attributes e.g. InputSet(inputs={}, foo=’bar’) will make InputSet.foo == ‘bar’.

classmethod from_directory(directory: str | Path)[source]

Construct an InputSet from a directory of one or more files.

Parameters:

directory – Directory to read input files from

validate() bool[source]

A place to implement basic checks to verify the validity of an input set. Can be as simple or as complex as desired.

Will raise a NotImplementedError unless overloaded by the inheriting class.

write_input(directory: str | Path, make_dir: bool = True, overwrite: bool = True, zip_inputs: bool = False)[source]

Write Inputs to one or more files

Parameters:
  • directory – Directory to write input files to

  • make_dir – Whether to create the directory if it does not already exist.

  • overwrite – Whether to overwrite an input file if it already exists.

  • generate_inputs (Additional kwargs are passed to) –

  • zip_inputs – If True, inputs will be zipped into a file with the same name as the InputSet (e.g., InputSet.zip)