+
+ +
+

pymatgen.io.jdftx package

+
+

Submodules

+
+
+

pymatgen.io.jdftx.generic_tags module

+

Module for class objects for containing JDFTx tags.

+

This module contains class objects for containing JDFTx tags. These class objects +are used to validate the type of the value for the tag, read the value string for +the tag, write the tag and its value as a string, and get the token length of the tag.

+

@mkhorton - This file is ready to review.

+
+
+class AbstractTag(multiline_tag: bool = False, can_repeat: bool = False, write_tagname: bool = True, write_value: bool = True, optional: bool = True, defer_until_struc: bool = False, is_tag_container: bool = False, allow_list_representation: bool = False)[source]
+

Bases: ClassPrintFormatter, ABC

+

Abstract base class for all tags.

+
+
+allow_list_representation: bool = False[source]
+
+ +
+
+can_repeat: bool = False[source]
+
+ +
+
+defer_until_struc: bool = False[source]
+
+ +
+
+get_dict_representation(tag: str, value: Any) → dict | list[dict][source]
+

Convert the value to a dict representation.

+
+
Parameters:
+
    +

  • tag (str) – The tag to convert the value to a dict representation for.

    • +

  • value (Any) – The value to convert to a dict representation.

    • +
+
+
Returns:
+

The value converted to a dict representation.

+
+
Return type:
+

dict | list[dict]

+
+
+
+ +
+
+get_list_representation(tag: str, value: Any) → list | list[list][source]
+

Convert the value to a list representation.

+
+
Parameters:
+
    +

  • tag (str) – The tag to convert the value to a list representation for.

    • +

  • value (Any) – The value to convert to a list representation.

    • +
+
+
Returns:
+

The value converted to a list representation.

+
+
Return type:
+

list | list[list]

+
+
+
+ +
+
+abstract get_token_len() → int[source]
+

Get the token length of the tag.

+
+
Returns:
+

The token length of the tag.

+
+
Return type:
+

int

+
+
+
+ +
+
+is_tag_container: bool = False[source]
+
+ +
+
+multiline_tag: bool = False[source]
+
+ +
+
+optional: bool = True[source]
+
+ +
+
+abstract read(tag: str, value_str: str) → Any[source]
+

Read and parse the value string for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to read the value string for.

    • +

  • value_str (str) – The value string to read.

    • +
+
+
Returns:
+

The parsed value.

+
+
Return type:
+

Any

+
+
+
+ +
+
+abstract validate_value_type(tag: str, value: Any, try_auto_type_fix: bool = False) → tuple[str, bool, Any][source]
+

Validate the type of the value for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to validate the type of the value for.

    • +

  • value (Any) – The value to validate the type of.

    • +

  • try_auto_type_fix (bool, optional) – Whether to try to automatically fix the type of the value.

    • +

  • False. (Defaults to)

    • +
+
+
Returns:
+

The tag, whether the value is of the correct type, and the possibly fixed value.

+
+
Return type:
+

tuple[str, bool, Any]

+
+
+
+ +
+
+abstract write(tag: str, value: Any) → str[source]
+

Write the tag and its value as a string.

+
+
Parameters:
+
    +

  • tag (str) – The tag to write.

    • +

  • value (Any) – The value to write.

    • +
+
+
Returns:
+

The tag and its value as a string.

+
+
Return type:
+

str

+
+
+
+ +
+
+write_tagname: bool = True[source]
+
+ +
+
+write_value: bool = True[source]
+
+ +
+ +
+
+class BoolTag(multiline_tag: bool = False, can_repeat: bool = False, write_tagname: bool = True, write_value: bool = True, optional: bool = True, defer_until_struc: bool = False, is_tag_container: bool = False, allow_list_representation: bool = False, _TF_read_options: dict[str, bool] = <factory>, _TF_write_options: dict[bool, str] = <factory>)[source]
+

Bases: AbstractTag

+

Tag for boolean values in JDFTx input files.

+

Tag for boolean values in JDFTx input files.

+
+
+get_token_len() → int[source]
+

Get the token length of the tag.

+
+
Returns:
+

The token length of the tag.

+
+
Return type:
+

int

+
+
+
+ +
+
+raise_value_error(tag: str, value: str) → None[source]
+

Raise a ValueError for the value string.

+
+
Parameters:
+
    +

  • tag (str) – The tag to raise the ValueError for.

    • +

  • value (str) – The value string to raise the ValueError for.

    • +
+
+
+
+ +
+
+read(tag: str, value: str) → bool[source]
+

Read the value string for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to read the value string for.

    • +

  • value (str) – The value string to read.

    • +
+
+
Returns:
+

The parsed boolean value.

+
+
Return type:
+

bool

+
+
+
+ +
+
+validate_value_type(tag: str, value: Any, try_auto_type_fix: bool = False) → tuple[str, bool, Any][source]
+

Validate the type of the value for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to validate the type of the value for.

    • +

  • value (Any) – The value to validate the type of.

    • +

  • try_auto_type_fix (bool, optional) – Whether to try to automatically fix the type of the value.

    • +

  • False. (Defaults to)

    • +
+
+
Returns:
+

The tag, whether the value is of the correct type, and the possibly fixed value.

+
+
Return type:
+

tuple[str, bool, Any]

+
+
+
+ +
+
+write(tag: str, value: Any) → str[source]
+

Write the tag and its value as a string.

+
+
Parameters:
+
    +

  • tag (str) – The tag to write.

    • +

  • value (Any) – The value to write.

    • +
+
+
Returns:
+

The tag and its value as a string.

+
+
Return type:
+

str

+
+
+
+ +
+ +
+
+class BoolTagContainer(multiline_tag: bool = False, can_repeat: bool = False, write_tagname: bool = True, write_value: bool = True, optional: bool = True, defer_until_struc: bool = False, is_tag_container: bool = True, allow_list_representation: bool = False, linebreak_nth_entry: int | None = None, subtags: dict[str, ~pymatgen.io.jdftx.generic_tags.AbstractTag] = <factory>)[source]
+

Bases: TagContainer

+

BoolTagContainer class for handling the subtags to the “dump” tag.

+

This class is used to handle the subtags to the “dump” tag. All subtags are freqs for dump, and all values for these +tags are boolean values that are read given the existence of their “var” name.

+
+
+read(tag: str, value_str: str) → dict[source]
+

Read the value string for this tag.

+

This method reads the value string for this tag. It is used to parse the value string for the tag and return the +parsed value.

+
+
Parameters:
+
    +

  • tag (str) – The tag to read the value string for.

    • +

  • value_str (str) – The value string to read.

    • +
+
+
Returns:
+

The parsed value.

+
+
Return type:
+

dict

+
+
+
+ +
+ +
+
+class ClassPrintFormatter[source]
+

Bases: object

+

Generic class for printing to command line in readable format.

+

Generic class for printing to command line in readable format.

+
+ +
+
+class DumpTagContainer(multiline_tag: bool = False, can_repeat: bool = False, write_tagname: bool = True, write_value: bool = True, optional: bool = True, defer_until_struc: bool = False, is_tag_container: bool = True, allow_list_representation: bool = False, linebreak_nth_entry: int | None = None, subtags: dict[str, ~pymatgen.io.jdftx.generic_tags.AbstractTag] = <factory>)[source]
+

Bases: TagContainer

+

DumpTagContainer class for handling the “dump” tag.

+

This class is used to handle the “dump” tag.

+
+
+read(tag: str, value_str: str) → dict[source]
+

Read the value string for this tag.

+

This method reads the value string for this tag. It is used to parse the value string for the tag and return the +parsed value.

+
+
Parameters:
+
    +

  • tag (str) – The tag to read the value string for.

    • +

  • value_str (str) – The value string to read.

    • +
+
+
Returns:
+

The parsed value.

+
+
Return type:
+

dict

+
+
+
+ +
+ +
+
+class FloatTag(multiline_tag: bool = False, can_repeat: bool = False, write_tagname: bool = True, write_value: bool = True, optional: bool = True, defer_until_struc: bool = False, is_tag_container: bool = False, allow_list_representation: bool = False, prec: int | None = None)[source]
+

Bases: AbstractTag

+

Tag for float values in JDFTx input files.

+

Tag for float values in JDFTx input files.

+
+
+get_token_len() → int[source]
+

Get the token length of the tag.

+
+
Returns:
+

The token length of the tag.

+
+
Return type:
+

int

+
+
+
+ +
+
+prec: int | None = None[source]
+
+ +
+
+read(tag: str, value: str) → float[source]
+

Read the value string for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to read the value string for.

    • +

  • value (str) – The value string to read.

    • +
+
+
Returns:
+

The parsed float value.

+
+
Return type:
+

float

+
+
+
+ +
+
+validate_value_type(tag: str, value: Any, try_auto_type_fix: bool = False) → tuple[str, bool, Any][source]
+

Validate the type of the value for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to validate the type of the value for.

    • +

  • value (Any) – The value to validate the type of.

    • +

  • try_auto_type_fix (bool, optional) – Whether to try to automatically fix the type of the value, by default +False.

    • +
+
+
Returns:
+

The tag, whether the value is of the correct type, and the possibly fixed value.

+
+
Return type:
+

tuple[str, bool, Any]

+
+
+
+ +
+
+write(tag: str, value: Any) → str[source]
+

Write the tag and its value as a string.

+
+
Parameters:
+
    +

  • tag (str) – The tag to write.

    • +

  • value (Any) – The value to write.

    • +
+
+
Returns:
+

The tag and its value as a string.

+
+
Return type:
+

str

+
+
+
+ +
+ +
+
+class InitMagMomTag(multiline_tag: bool = False, can_repeat: bool = False, write_tagname: bool = True, write_value: bool = True, optional: bool = True, defer_until_struc: bool = False, is_tag_container: bool = False, allow_list_representation: bool = False)[source]
+

Bases: AbstractTag

+

Tag for initial-magnetic-moments tag in JDFTx input files.

+

Tag for initial-magnetic-moments tag in JDFTx input files.

+
+
+get_token_len() → int[source]
+

Get the token length of the tag.

+
+
Returns:
+

The token length of the tag.

+
+
Return type:
+

int

+
+
+
+ +
+
+read(tag: str, value: str) → str[source]
+

Read the value string for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to read the value string for.

    • +

  • value (str) – The value string to read.

    • +
+
+
Returns:
+

The parsed string value.

+
+
Return type:
+

str

+
+
+
+ +
+
+validate_value_type(tag: str, value: Any, try_auto_type_fix: bool = False) → tuple[str, bool, Any][source]
+

Validate the type of the value for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to validate the type of the value for.

    • +

  • value (Any) – The value to validate the type of.

    • +

  • try_auto_type_fix (bool, optional) – Whether to try to automatically fix the type of the value, by default +False.

    • +
+
+
Returns:
+

The tag, whether the value is of the correct type, and the possibly fixed value.

+
+
Return type:
+

tuple[str, bool, Any]

+
+
+
+ +
+
+write(tag: str, value: Any) → str[source]
+

Write the tag and its value as a string.

+
+
Parameters:
+
    +

  • tag (str) – The tag to write.

    • +

  • value (Any) – The value to write.

    • +
+
+
Returns:
+

The tag and its value as a string.

+
+
Return type:
+

str

+
+
+
+ +
+ +
+
+class IntTag(multiline_tag: bool = False, can_repeat: bool = False, write_tagname: bool = True, write_value: bool = True, optional: bool = True, defer_until_struc: bool = False, is_tag_container: bool = False, allow_list_representation: bool = False)[source]
+

Bases: AbstractTag

+

Tag for integer values in JDFTx input files.

+

Tag for integer values in JDFTx input files.

+
+
+get_token_len() → int[source]
+

Get the token length of the tag.

+
+
Returns:
+

The token length of the tag.

+
+
Return type:
+

int

+
+
+
+ +
+
+read(tag: str, value: str) → int[source]
+

Read the value string for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to read the value string for.

    • +

  • value (str) – The value string to read.

    • +
+
+
Returns:
+

The parsed integer value.

+
+
Return type:
+

int

+
+
+
+ +
+
+validate_value_type(tag: str, value: Any, try_auto_type_fix: bool = False) → tuple[str, bool, Any][source]
+

Validate the type of the value for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to validate the type of the value for.

    • +

  • value (Any) – The value to validate the type of.

    • +

  • try_auto_type_fix (bool, optional) – Whether to try to automatically fix the type of the value, by default +False.

    • +
+
+
Returns:
+

The tag, whether the value is of the correct type, and the possibly fixed value.

+
+
Return type:
+

tuple[str, bool, Any]

+
+
+
+ +
+
+write(tag: str, value: Any) → str[source]
+

Write the tag and its value as a string.

+
+
Parameters:
+
    +

  • tag (str) – The tag to write.

    • +

  • value (Any) – The value to write.

    • +
+
+
Returns:
+

The tag and its value as a string.

+
+
Return type:
+

str

+
+
+
+ +
+ +
+
+class MultiformatTag(multiline_tag: bool = False, can_repeat: bool = False, write_tagname: bool = True, write_value: bool = True, optional: bool = True, defer_until_struc: bool = False, is_tag_container: bool = False, allow_list_representation: bool = False, format_options: list[~pymatgen.io.jdftx.generic_tags.AbstractTag] = <factory>)[source]
+

Bases: AbstractTag

+

Class for tags with multiple format options.

+

Class for tags that could have different types of input values given to them or tags where different subtag options +directly impact how many expected arguments are provided e.g. the coulomb-truncation or van-der-waals tags.

+

This class should not be used for tags with simply some combination of mandatory and optional args because the +TagContainer class can handle those cases by itself.

+
+
+format_options: list[AbstractTag][source]
+
+ +
+
+get_format_index_for_str_value(tag: str, value: str) → int[source]
+

Get the format index from string representation of value.

+
+
Parameters:
+
    +

  • tag (str) – The tag to read the value string for.

    • +

  • value (str) – The value string to read.

    • +
+
+
Returns:
+

The index of the format option for the value of this tag.

+
+
Return type:
+

int

+
+
Raises:
+

ValueError – If no valid read format is found for the tag.

+
+
+
+ +
+
+get_token_len() → int[source]
+

Get the token length of the tag.

+
+
Returns:
+

The token length of the tag.

+
+
Return type:
+

int

+
+
Raises:
+

NotImplementedError – If the method is called directly on MultiformatTag objects.

+
+
+
+ +
+
+raise_invalid_format_option_error(tag: str, i: int) → None[source]
+

Raise an error for an invalid format option.

+
+
Parameters:
+
    +

  • tag (str) – The tag to raise the error for.

    • +

  • i (int) – The index of the format option to raise the error for.

    • +
+
+
Raises:
+

ValueError – If the format option is invalid.

+
+
+
+ +
+
+read(tag: str, value: str) → None[source]
+

Read the value string for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to read the value string for.

    • +

  • value (str) – The value string to read.

    • +
+
+
Raises:
+

RuntimeError – If the method is called directly on MultiformatTag.

+
+
+
+ +
+
+validate_value_type(tag: str, value: Any, try_auto_type_fix: bool = False) → tuple[str, bool, Any][source]
+

Validate the type of the value for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to validate the value type for.

    • +

  • value (Any) – The value to validate the type of.

    • +

  • try_auto_type_fix (bool, optional) – Whether to try to automatically fix the type of the value. Defaults to +False.

    • +
+
+
Returns:
+

The tag, whether the value is of the correct type, and the possibly fixed value.

+
+
Return type:
+

tuple[str, bool, Any]

+
+
+
+ +
+
+write(tag: str, value: Any) → str[source]
+

Write the tag and its value as a string.

+
+
Parameters:
+
    +

  • tag (str) – The tag to write.

    • +

  • value (Any) – The value to write.

    • +
+
+
Returns:
+

The tag and its value as a string.

+
+
Return type:
+

str

+
+
Raises:
+

RuntimeError – If the method is called directly on MultiformatTag.

+
+
+
+ +
+ +
+
+class StrTag(multiline_tag: bool = False, can_repeat: bool = False, write_tagname: bool = True, write_value: bool = True, optional: bool = True, defer_until_struc: bool = False, is_tag_container: bool = False, allow_list_representation: bool = False, options: list | None = None)[source]
+

Bases: AbstractTag

+

Tag for string values in JDFTx input files.

+

Tag for string values in JDFTx input files.

+
+
+get_token_len() → int[source]
+

Get the token length of the tag.

+
+
Returns:
+

The token length of the tag.

+
+
Return type:
+

int

+
+
+
+ +
+
+options: list | None = None[source]
+
+ +
+
+read(tag: str, value: str) → str[source]
+

Read the value string for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to read the value string for.

    • +

  • value (str) – The value string to read.

    • +
+
+
Returns:
+

The parsed string value.

+
+
Return type:
+

str

+
+
+
+ +
+
+validate_value_type(tag: str, value: Any, try_auto_type_fix: bool = False) → tuple[str, bool, Any][source]
+

Validate the type of the value for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to validate the type of the value for.

    • +

  • value (Any) – The value to validate the type of.

    • +

  • try_auto_type_fix (bool, optional) – Whether to try to automatically fix the type of the value. Defaults to +False.

    • +
+
+
Returns:
+

The tag, whether the value is of the correct type, and the possibly fixed value.

+
+
Return type:
+

tuple[str, bool, Any]

+
+
+
+ +
+
+write(tag: str, value: Any) → str[source]
+

Write the tag and its value as a string.

+
+
Parameters:
+
    +

  • tag (str) – The tag to write.

    • +

  • value (Any) – The value to write.

    • +
+
+
Returns:
+

The tag and its value as a string.

+
+
Return type:
+

str

+
+
+
+ +
+ +
+
+class TagContainer(multiline_tag: bool = False, can_repeat: bool = False, write_tagname: bool = True, write_value: bool = True, optional: bool = True, defer_until_struc: bool = False, is_tag_container: bool = True, allow_list_representation: bool = False, linebreak_nth_entry: int | None = None, subtags: dict[str, ~pymatgen.io.jdftx.generic_tags.AbstractTag] = <factory>)[source]
+

Bases: AbstractTag

+

TagContainer class for handling tags that contain other tags.

+

This class is used to handle tags that contain other tags. It is used to validate the type of the value for the tag, +read the value string for the tag, write the tag and its value as a string, and get the token length of the tag.

+

Note: When constructing a TagContainer, all subtags must be able to return the correct token length without any +information about the value. +# TODO: Remove this assumption by changing the signature of get_token_len to take the value as an argument.

+
+
+get_dict_representation(tag: str, value: list) → dict | list[dict][source]
+

Convert the value to a dict representation.

+
+
Parameters:
+
    +

  • tag (str) – The tag to convert the value to a dict representation for.

    • +

  • value (list) – The value to convert to a dict representation.

    • +
+
+
Returns:
+

The value converted to a dict representation.

+
+
Return type:
+

dict | list[dict]

+
+
+
+ +
+
+get_list_representation(tag: str, value: Any) → list[source]
+

Convert the value to a list representation.

+
+
Parameters:
+
    +

  • tag (str) – The tag to convert the value to a list representation for.

    • +

  • value (Any) – The value to convert to a list representation.

    • +
+
+
Returns:
+

The value converted to a list representation.

+
+
Return type:
+

list

+
+
+
+ +
+
+get_token_len() → int[source]
+

Get the token length of the tag.

+
+
Returns:
+

The token length of the tag.

+
+
Return type:
+

int

+
+
+
+ +
+
+is_tag_container: bool = True[source]
+
+ +
+
+linebreak_nth_entry: int | None = None[source]
+
+ +
+
+read(tag: str, value: str) → dict[source]
+

Read the value string for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to read the value string for.

    • +

  • value (str) – The value string to read.

    • +
+
+
Returns:
+

The parsed value.

+
+
Return type:
+

dict

+
+
+
+ +
+
+subtags: dict[str, AbstractTag][source]
+
+ +
+
+validate_value_type(tag: str, value: Any, try_auto_type_fix: bool = False) → tuple[str, bool, Any][source]
+

Validate the type of the value for this tag.

+
+
Parameters:
+
    +

  • tag (str) – The tag to validate the type of the value for.

    • +

  • value (Any) – The value to validate the type of.

    • +

  • try_auto_type_fix (bool, optional) – Whether to try to automatically fix the type of the value, by default +False.

    • +
+
+
Returns:
+

The tag, whether the value is of the correct type, and the possibly fixed value.

+
+
Return type:
+

tuple[str, bool, Any]

+
+
+
+ +
+
+write(tag: str, value: Any) → str[source]
+

Write the tag and its value as a string.

+
+
Parameters:
+
    +

  • tag (str) – The tag to write.

    • +

  • value (Any) – The value to write.

    • +
+
+
Returns:
+

The tag and its value as a string.

+
+
Return type:
+

str

+
+
+
+ +
+ +
+
+

pymatgen.io.jdftx.inputs module

+

Classes for reading/manipulating/writing JDFTx input files.

+

Classes for reading/manipulating/writing JDFTx input files.

+

Note: JDFTXInfile will be moved back to its own module once a more broad inputs +class is written.

+

@mkhorton - This file is ready to review.

+
+
+class JDFTXInfile(params: dict[str, Any] | None = None)[source]
+

Bases: dict, MSONable

+

Class for reading/writing JDFtx input files.

+

JDFTxInfile object for reading and writing JDFTx input files. +Essentially a dictionary with some helper functions.

+

Create a JDFTXInfile object.

+
+
Parameters:
+

params (dict) – Input parameters as a dictionary.

+
+
+
+
+append_tag(tag: str, value: Any) → None[source]
+

Append a value to a tag.

+

Append a value to a tag. Use this method instead of directly appending the list contained in the tag, such that +the value is properly processed.

+
+
Parameters:
+
    +

  • tag (str) – Tag to append to.

    • +

  • value (Any) – Value to append.

    • +
+
+
+
+ +
+
+as_dict(sort_tags: bool = True, skip_module_keys: bool = False) → dict[source]
+

Return JDFTXInfile as MSONable dict.

+
+
Parameters:
+
    +

  • sort_tags (bool, optional) – Whether to sort the tags. Defaults to True.

    • +

  • skip_module_keys (bool, optional) – Whether to skip the module keys. Defaults to False.

    • +
+
+
Returns:
+

JDFTXInfile as MSONable dict.

+
+
Return type:
+

dict

+
+
+
+ +
+
+copy() → JDFTXInfile[source]
+

Return a copy of the JDFTXInfile object.

+
+
Returns:
+

Copy of the JDFTXInfile object.

+
+
Return type:
+

JDFTXInfile

+
+
+
+ +
+
+classmethod from_dict(d: dict[str, Any]) → JDFTXInfile[source]
+

Create JDFTXInfile from a dictionary.

+
+
Parameters:
+

d (dict) – Dictionary to create JDFTXInfile from.

+
+
Returns:
+

The created JDFTXInfile object.

+
+
Return type:
+

JDFTXInfile

+
+
+
+ +
+
+classmethod from_file(filename: PathLike, dont_require_structure: bool = False, sort_tags: bool = True, assign_path_parent: bool = True) → Self[source]
+

Read a JDFTXInfile object from a file.

+
+
Parameters:
+
    +

  • filename (PathLike) – Filename to read from.

    • +

  • dont_require_structure (bool, optional) – Whether to require structure tags. Defaults to False.

    • +

  • sort_tags (bool, optional) – Whether to sort the tags. Defaults to True.

    • +

  • assign_path_parent (bool, optional) – Whether to assign the parent directory of the input file for include +tags. Defaults to True.

    • +
+
+
Returns:
+

The created JDFTXInfile object.

+
+
Return type:
+

JDFTXInfile

+
+
+
+ +
+
+classmethod from_jdftxstructure(jdftxstructure: JDFTXStructure) → JDFTXInfile[source]
+

Create a JDFTXInfile object from a JDFTXStructure object.

+
+
Parameters:
+

jdftxstructure (JDFTXStructure) – JDFTXStructure object to convert.

+
+
Returns:
+

The created JDFTXInfile object.

+
+
Return type:
+

JDFTXInfile

+
+
+
+ +
+
+classmethod from_str(string: str, dont_require_structure: bool = False, sort_tags: bool = True, path_parent: Path | None = None) → JDFTXInfile[source]
+

Read a JDFTXInfile object from a string.

+
+
Parameters:
+
    +

  • string (str) – String to read from.

    • +

  • dont_require_structure (bool, optional) – Whether to require structure tags. Defaults to False.

    • +

  • sort_tags (bool, optional) – Whether to sort the tags. Defaults to True.

    • +

  • path_parent (Path, optional) – Path to the parent directory of the input file for include tags. +Defaults to None.

    • +
+
+
Returns:
+

The created JDFTXInfile object.

+
+
Return type:
+

JDFTXInfile

+
+
+
+ +
+
+classmethod from_structure(structure: Structure, selective_dynamics: ArrayLike | None = None, write_cart_coords: bool = False) → JDFTXInfile[source]
+

Create a JDFTXInfile object from a pymatgen Structure.

+
+
Parameters:
+
    +

  • structure (Structure) – Structure to convert.

    • +

  • selective_dynamics (ArrayLike, optional) – Selective dynamics attribute for each site if available. +Shape Nx1, by default None.

    • +
+
+
Returns:
+

The created JDFTXInfile object.

+
+
Return type:
+

JDFTXInfile

+
+
+
+ +
+
+classmethod get_dict_representation(jdftxinfile: JDFTXInfile) → JDFTXInfile[source]
+

Convert JDFTXInfile object properties into dict representation.

+
+
Parameters:
+

jdftxinfile (JDFTXInfile) – JDFTXInfile object to convert.

+
+
+
+ +
+
+classmethod get_list_representation(jdftxinfile: JDFTXInfile) → JDFTXInfile[source]
+

Convert JDFTXInfile object properties into list representation.

+
+
Parameters:
+

jdftxinfile (JDFTXInfile) – JDFTXInfile object to convert.

+
+
+
+ +
+
+get_text_list() → list[str][source]
+

Get a list of strings representation of the JDFTXInfile.

+
+
Returns:
+

List of strings representation of the JDFTXInfile.

+
+
Return type:
+

list[str]

+
+
+
+ +
+
+path_parent: str | None = None[source]
+
+ +
+
+property structure: Structure[source]
+

Return a pymatgen Structure object.

+
+
Returns:
+

Pymatgen structure object.

+
+
Return type:
+

Structure

+
+
+
+ +
+
+classmethod to_jdftxstructure(jdftxinfile: JDFTXInfile, sort_structure: bool = False) → JDFTXStructure[source]
+

Convert JDFTXInfile to JDFTXStructure object.

+

Converts JDFTx lattice, lattice-scale, ion tags into JDFTXStructure, with Pymatgen structure as attribute.

+
+
Parameters:
+
    +

  • jdftxinfile (JDFTXInfile) – JDFTXInfile object to convert.

    • +

  • sort_structure (bool, optional) – Whether to sort the structure. Useful if species are not grouped properly +together. Defaults to False.

    • +
+
+
+
+ +
+
+classmethod to_pmg_structure(jdftxinfile: JDFTXInfile, sort_structure: bool = False) → Structure[source]
+

Convert JDFTXInfile to pymatgen Structure object.

+

Converts JDFTx lattice, lattice-scale, ion tags into pymatgen Structure.

+
+
Parameters:
+
    +

  • jdftxinfile (JDFTXInfile) – JDFTXInfile object to convert.

    • +

  • sort_structure (bool, optional) – Whether to sort the structure. Useful if species are not grouped properly +together. Defaults to False.

    • +
+
+
Returns:
+

The created pymatgen Structure object.

+
+
Return type:
+

Structure

+
+
+
+ +
+
+validate_tags(try_auto_type_fix: bool = False, error_on_failed_fix: bool = True, return_list_rep: bool = False) → None[source]
+

Validate the tags in the JDFTXInfile.

+

Validate the tags in the JDFTXInfile. If try_auto_type_fix is True, will attempt to fix the tags. If +error_on_failed_fix is True, will raise an error if the tags cannot be fixed. If return_list_rep is True, will +return the tags in list representation.

+
+
Parameters:
+
    +

  • try_auto_type_fix (bool, optional) – Whether to attempt to fix the tags. Defaults to False.

    • +

  • error_on_failed_fix (bool, optional) – Whether to raise an error if the tags cannot be fixed. +Defaults to True.

    • +

  • return_list_rep (bool, optional) – Whether to return the tags in list representation. Defaults to False.

    • +
+
+
+
+ +
+
+write_file(filename: PathLike) → None[source]
+

Write JDFTXInfile to an in file.

+
+
Parameters:
+

filename (PathLike) – Filename to write to.

+
+
+
+ +
+ +
+
+class JDFTXStructure(structure: Structure = None, selective_dynamics: ArrayLike | None = None, sort_structure: bool = False, write_cart_coords: bool = False)[source]
+

Bases: MSONable

+

Object for representing the data in JDFTXStructure tags.

+
+
+structure[source]
+

Associated Structure.

+
+
Type:
+

Structure

+
+
+
+ +
+
+selective_dynamics[source]
+

Selective dynamics attribute for each site if available. Shape Nx1.

+
+
Type:
+

ArrayLike

+
+
+
+ +
+
+sort_structure[source]
+

Whether to sort the structure. Useful if species are not grouped properly together. +Defaults to False.

+
+
Type:
+

bool

+
+
+
+ +
+
+as_dict() → dict[source]
+

MSONable dict.

+
+
Returns:
+

MSONable dictionary representation of the JDFTXStructure.

+
+
Return type:
+

dict

+
+
+
+ +
+
+classmethod from_dict(params: dict) → Self[source]
+

Get JDFTXStructure from dict.

+
+
Parameters:
+

params (dict) – Serialized JDFTXStructure.

+
+
Returns:
+

The created JDFTXStructure object.

+
+
Return type:
+

JDFTXStructure

+
+
+
+ +
+
+classmethod from_file(filename: str) → JDFTXStructure[source]
+

Read JDFTXStructure from file.

+
+
Parameters:
+

filename (str) – Filename to read from.

+
+
Returns:
+

The created JDFTXStructure object.

+
+
Return type:
+

JDFTXStructure

+
+
+
+ +
+
+classmethod from_jdftxinfile(jdftxinfile: JDFTXInfile, sort_structure: bool = False) → JDFTXStructure[source]
+

Get JDFTXStructure from JDFTXInfile.

+
+
Parameters:
+
    +

  • jdftxinfile (JDFTXInfile) – JDFTXInfile object.

    • +

  • sort_structure (bool, optional) – Whether to sort the structure. Useful if species are not grouped properly +together as JDFTx output will have species sorted.

    • +
+
+
Returns:
+

The created JDFTXStructure object.

+
+
Return type:
+

JDFTXStructure

+
+
+
+ +
+
+classmethod from_str(data: str) → JDFTXStructure[source]
+

Read JDFTXStructure from string.

+
+
Parameters:
+

data (str) – String to read from.

+
+
Returns:
+

The created JDFTXStructure object.

+
+
Return type:
+

JDFTXStructure

+
+
+
+ +
+
+get_str(in_cart_coords: bool | None = None) → str[source]
+

Return a string to be written as JDFTXInfile tags.

+

Allows extra options as compared to calling str(JDFTXStructure) directly.

+
+
Parameters:
+

in_cart_coords (bool, optional) – Whether coordinates are output in direct or Cartesian.

+
+
Returns:
+

Representation of JDFTXInfile structure tags.

+
+
Return type:
+

str

+
+
+
+ +
+
+property natoms: int[source]
+

Return number of atoms.

+
+
Returns:
+

Number of sites.

+
+
Return type:
+

int

+
+
+
+ +
+
+selective_dynamics: ArrayLike | None = None[source]
+
+ +
+
+sort_structure: bool = False[source]
+
+ +
+
+structure: Structure = None[source]
+
+ +
+
+write_cart_coords: bool = False[source]
+
+ +
+
+write_file(filename: PathLike, **kwargs) → None[source]
+

Write JDFTXStructure to a file.

+

The supported kwargs are the same as those for the JDFTXStructure.get_str method and are passed through +directly.

+
+
Parameters:
+
    +

  • filename (PathLike) – Filename to write to.

    • +

  • **kwargs – Kwargs to pass to JDFTXStructure.get_str.

    • +
+
+
+
+ +
+ +
+
+

pymatgen.io.jdftx.jdftxinfile_master_format module

+

Master list of AbstractTag-type objects for JDFTx input file generation.

+

This module contains; +- MASTER_TAG_LIST: a dictionary mapping tag categories to dictionaries mapping

+
+

tag names to AbstractTag-type objects.

+
+
    +
  • +
    get_tag_object: a function that returns an AbstractTag-type object from

    MASTER_TAG_LIST given a tag name.

    +
    +
    +
    • +
+

@mkhorton - this file is ready to review.

+
+
+get_dump_tag_container() → DumpTagContainer[source]
+

Initialize a dump tag container.

+
+
Returns:
+

The dump tag container.

+
+
Return type:
+

DumpTagContainer

+
+
+
+ +
+
+get_tag_object(tag: str) → AbstractTag[source]
+

Get the tag object for a given tag name.

+
+
Parameters:
+

tag (str) – The tag name.

+
+
Returns:
+

The tag object.

+
+
Return type:
+

AbstractTag

+
+
+
+ +
+
+

pymatgen.io.jdftx.jdftxinfile_ref_options module

+

Module for containing reference data for JDFTx tags.

+

This module contains reference data for JDFTx tags, such as valid options for +functionals, pseudopotentials, etc.

+

@mkhorton - this file is ready to review.

+
+
+

pymatgen.io.jdftx.jdftxoutfileslice module

+

JDFTx Outfile Slice Class.

+

This module defines the JDFTxOutfileSlice class, which is used to read and +process a JDFTx out file.

+
+
+class JDFTXOutfileSlice(prefix: str | None = None, jstrucs: JOutStructures | None = None, jsettings_fluid: JMinSettings | None = None, jsettings_electronic: JMinSettings | None = None, jsettings_lattice: JMinSettings | None = None, jsettings_ionic: JMinSettings | None = None, constant_lattice: bool | None = None, xc_func: str | None = None, lattice_initial: np.ndarray | None = None, lattice_final: np.ndarray | None = None, lattice: np.ndarray | None = None, a: float | None = None, b: float | None = None, c: float | None = None, fftgrid: list[int] | None = None, geom_opt: bool | None = None, geom_opt_type: str | None = None, efermi: float | None = None, egap: float | None = None, emin: float | None = None, emax: float | None = None, homo: float | None = None, lumo: float | None = None, homo_filling: float | None = None, lumo_filling: float | None = None, is_metal: bool | None = None, etype: str | None = None, broadening_type: str | None = None, broadening: float | None = None, kgrid: list | None = None, truncation_type: str | None = None, truncation_radius: float | None = None, pwcut: float | None = None, rhocut: float | None = None, pp_type: str | None = None, semicore_electrons: int | None = None, valence_electrons: float | None = None, total_electrons_uncharged: int | None = None, semicore_electrons_uncharged: int | None = None, valence_electrons_uncharged: int | None = None, nbands: int | None = None, atom_elements: list | None = None, atom_elements_int: list | None = None, atom_types: list | None = None, spintype: str | None = None, nspin: int | None = None, nat: int | None = None, atom_coords_initial: list[list[float]] | None = None, atom_coords_final: list[list[float]] | None = None, atom_coords: list[list[float]] | None = None, has_solvation: bool = False, fluid: str | None = None, is_gc: bool | None = None, is_bgw: bool = False, has_eigstats: bool = False, has_parsable_pseudo: bool = False, _total_electrons_backup: int | None = None, total_electrons: float | None = None, _mu_backup: int | None = None, t_s: float | None = None, converged: bool | None = None, structure: Structure | None = None, trajectory: Trajectory | None = None, electronic_output: dict | None = None, eopt_type: str | None = None, elecmindata: JElSteps | None = None, stress: np.ndarray | None = None, strain: np.ndarray | None = None, forces: np.ndarray | None = None, nstep: int | None = None, e: float | None = None, grad_k: float | None = None, alpha: float | None = None, linmin: float | None = None, abs_magneticmoment: float | None = None, tot_magneticmoment: float | None = None, mu: float | None = None, elec_nstep: int | None = None, elec_e: float | None = None, elec_grad_k: float | None = None, elec_alpha: float | None = None, elec_linmin: float | None = None)[source]
+

Bases: object

+

A class to read and process a slice of a JDFTx out file.

+

A class to read and process a slice of a JDFTx out file, where a “slice” is a segment of an out file corresponding +to a single call of JDFTx.

+
+
+from_out_slice(text
+

list[str]): Read slice of out file into a JDFTXOutfileSlice instance.

+
+ +
+
+prefix[source]
+

Prefix of dump files for JDFTx calculation.

+
+
Type:
+

str | None

+
+
+
+ +
+
+jstrucs[source]
+

JOutStructures instance containing intermediate structures. Holds a “slices” +attribute, which is a list of JOutStructure instances. (A JOutStructure instance functions as a Structure +object, along with a JElSteps instance (stored as elecmindata) and other JDFTx-calculation-specific data.)

+
+
Type:
+

JOutStructures | None

+
+
+
+ +
+
+jsettings_fluid[source]
+

JMinSettings instance containing fluid optimization settings.

+
+
Type:
+

JMinSettings | None

+
+
+
+ +
+
+jsettings_electronic[source]
+

JMinSettings instance containing electronic optimization settings.

+
+
Type:
+

JMinSettings | None

+
+
+
+ +
+
+jsettings_lattice[source]
+

JMinSettings instance containing lattice optimization settings.

+
+
Type:
+

JMinSettings | None

+
+
+
+ +
+
+jsettings_ionic[source]
+

JMinSettings instance containing ionic optimization settings.

+
+
Type:
+

JMinSettings | None

+
+
+
+ +
+
+xc_func[source]
+

Exchange-correlation functional used in the calculation.

+
+
Type:
+

str | None

+
+
+
+ +
+
+lattice_initial[source]
+

Initial lattice matrix in Angstroms.

+
+
Type:
+

np.ndarray | None

+
+
+
+ +
+
+lattice_final[source]
+

Final lattice matrix in Angstroms.

+
+
Type:
+

np.ndarray | None

+
+
+
+ +
+
+lattice[source]
+

Current lattice matrix in Angstroms.

+
+
Type:
+

np.ndarray | None

+
+
+
+ +
+
+a[source]
+

Lattice parameter a in Angstroms.

+
+
Type:
+

float | None

+
+
+
+ +
+
+b[source]
+

Lattice parameter b in Angstroms.

+
+
Type:
+

float | None

+
+
+
+ +
+
+c[source]
+

Lattice parameter c in Angstroms.

+
+
Type:
+

float | None

+
+
+
+ +
+
+fftgrid[source]
+

Shape of FFT grid used in calculation (3 integers).

+
+
Type:
+

list[int] | None

+
+
+
+ +
+
+geom_opt[source]
+

True if geometric (lattice or ionic) optimization was performed.

+
+
Type:
+

bool | None

+
+
+
+ +
+
+geom_opt_type[source]
+

Type of geometric optimization performed (lattice or ionic, where lattice implies +ionic as well unless geometry was given in direct coordinates).

+
+
Type:
+

str | None

+
+
+
+ +
+
+efermi[source]
+

Fermi energy in eV (may be None if eigstats are not dumped).

+
+
Type:
+

float | None

+
+
+
+ +
+
+egap[source]
+

Band gap in eV (None if eigstats are not dumped).

+
+
Type:
+

float | None

+
+
+
+ +
+
+emin[source]
+

Minimum energy in eV (None if eigstats are not dumped).

+
+
Type:
+

float | None

+
+
+
+ +
+
+emax[source]
+

Maximum energy in eV (None if eigstats are not dumped).

+
+
Type:
+

float | None

+
+
+
+ +
+
+homo[source]
+

Energy of last band-state before Fermi level (acronym for Highest Occupied Molecular +Orbital, even though these are not molecular orbitals and this state may not be entirely occupied) +(None if eigstats are not dumped).

+
+
Type:
+

float | None

+
+
+
+ +
+
+lumo[source]
+

Energy of first band-state after Fermi level (acronym for Lowest Unoccupied Molecular +Orbital, even though these are not molecular orbitals, and this state may not be entirely unoccupied) +(None if eigstats are not dumped).

+
+
Type:
+

float | None

+
+
+
+ +
+
+homo_filling[source]
+

Filling of “homo” band-state as calculated within this class object from the homo +energy, Fermi level, electronic broadening type and electronic broadening parameter. (None if eigstats are +not dumped).

+
+
Type:
+

float | None

+
+
+
+ +
+
+lumo_filling[source]
+

Filling of “lumo” band-state as calculated within this class object from the homo +energy, Fermi level, electronic broadening type and electronic broadening parameter. (None if eigstats are +not dumped).

+
+
Type:
+

float | None

+
+
+
+ +
+
+is_metal[source]
+

True if fillings of homo and lumo band-states are off-set by 1 and 0 by at least an +arbitrary tolerance of 0.01 (ie 1 - 0.015 and 0.012 for homo/lumo fillings would be metallic, while 1-0.001 +and 0 would not be). (Only available if eigstats was dumped).

+
+
Type:
+

bool | None

+
+
+
+ +
+
+etype[source]
+

String representation of total energy-type of system. Commonly “G” (grand-canonical +potential) for GC calculations, and “F” for canonical (fixed electron count) calculations.

+
+
Type:
+

str | None

+
+
+
+ +
+
+broadening_type[source]
+

Type of broadening for electronic filling about Fermi-level requested. Either “Fermi”, +“Cold”, “MP1”, or “Gauss”.

+
+
Type:
+

str

+
+
+
+ +
+
+broadening[source]
+

Magnitude of broadening for electronic filling.

+
+
Type:
+

float

+
+
+
+ +
+
+kgrid[source]
+

Shape of k-point grid used in calculation. (equivalent to k-point folding).

+
+
Type:
+

list[int]

+
+
+
+ +
+
+truncation_type[source]
+

Type of coulomb truncation used to prevent interaction between periodic images along +certain directions. “periodic” means no coulomb truncation was used.

+
+
Type:
+

str

+
+
+
+ +
+
+truncation_radius[source]
+

If spherical truncation_type, this is the radius of the coulomb truncation +sphere.

+
+
Type:
+

float | None

+
+
+
+ +
+
+pwcut[source]
+

The plane-wave cutoff energy in Hartrees used in the most recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
+rhocut[source]
+

The density cutoff energy in Hartrees used in the most recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
+pp_type[source]
+

The pseudopotential library used in the most recent JDFTx call. Currently only “GBRV” and “SG15” +are supported by this output parser.

+
+
Type:
+

str

+
+
+
+ +
+
+total_electrons[source]
+

The total number of electrons in the most recent JDFTx call (redundant to nelectrons).

+
+
Type:
+

float

+
+
+
+ +
+
+semicore_electrons[source]
+

The number of semicore electrons in the most recent JDFTx call.

+
+
Type:
+

int

+
+
+
+ +
+
+valence_electrons[source]
+

The number of valence electrons in the most recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
+total_electrons_uncharged[source]
+

The total number of electrons in the most recent JDFTx call, uncorrected for +charge. (ie total_electrons + charge).

+
+
Type:
+

int

+
+
+
+ +
+
+semicore_electrons_uncharged[source]
+

The number of semicore electrons in the most recent JDFTx call, uncorrected +for charge. (ie semicore_electrons + charge).

+
+
Type:
+

int

+
+
+
+ +
+
+valence_electrons_uncharged[source]
+

The number of valence electrons in the most recent JDFTx call, uncorrected +for charge. (ie valence_electrons + charge).

+
+
Type:
+

int

+
+
+
+ +
+
+nbands[source]
+

The number of bands used in the most recent JDFTx call.

+
+
Type:
+

int

+
+
+
+ +
+
+atom_elements[source]
+

The list of each ion’s element symbol in the most recent JDFTx call.

+
+
Type:
+

list[str]

+
+
+
+ +
+
+atom_elements_int[source]
+

The list of ion’s atomic numbers in the most recent JDFTx call.

+
+
Type:
+

list[int]

+
+
+
+ +
+
+atom_types[source]
+

Non-repeating list of each ion’s element symbol in the most recent JDFTx call.

+
+
Type:
+

list[str]

+
+
+
+ +
+
+spintype[source]
+

The spin type used in the most recent JDFTx call. Options are “none”, “collinear”.

+
+
Type:
+

str

+
+
+
+ +
+
+nspin[source]
+

The number of spins used in the most recent JDFTx call.

+
+
Type:
+

int

+
+
+
+ +
+
+nat[source]
+

The number of atoms in the most recent JDFTx call.

+
+
Type:
+

int

+
+
+
+ +
+
+atom_coords_initial[source]
+

The initial atomic coordinates of the most recent JDFTx call.

+
+
Type:
+

list[list[float]]

+
+
+
+ +
+
+atom_coords_final[source]
+

The final atomic coordinates of the most recent JDFTx call.

+
+
Type:
+

list[list[float]]

+
+
+
+ +
+
+atom_coords[source]
+

The atomic coordinates of the most recent JDFTx call.

+
+
Type:
+

list[list[float]]

+
+
+
+ +
+
+has_solvation[source]
+

True if the most recent JDFTx call included a solvation calculation.

+
+
Type:
+

bool

+
+
+
+ +
+
+fluid[source]
+

The fluid used in the most recent JDFTx call.

+
+
Type:
+

str

+
+
+
+ +
+
+is_gc[source]
+

True if the most recent slice is a grand canonical calculation.

+
+
Type:
+

bool

+
+
+
+ +
+
+is_bgw[source]
+

True if data must be usable for a BerkeleyGW calculation (user-set).

+
+
Type:
+

bool

+
+
+
+ +
+
+has_eigstats[source]
+

True if eigstats were dumped in the most recent JDFTx call.

+
+
Type:
+

bool

+
+
+
+ +
+
+has_parsable_pseudo[source]
+

True if the most recent JDFTx call used a pseudopotential that can be parsed by this +output parser. Options are currently “GBRV” and “SG15”.

+
+
Type:
+

bool

+
+
+
+ +
+
Properties:

t_s (float | None): The total time in seconds for the calculation. +converged (bool | None): True if calculation converged. +trajectory (Trajectory): pymatgen Trajectory object containing intermediate Structure’s of outfile slice

+
+

calculation.

+
+

electronic_output (dict): Dictionary with all relevant electronic information dumped from an eigstats log. +structure (Structure): Calculation result as pymatgen Structure. +eopt_type (str | None): eopt_type from most recent JOutStructure. +elecmindata (JElSteps): elecmindata from most recent JOutStructure. +stress (np.ndarray | None): Stress tensor from most recent JOutStructure in units eV/Ang^3. +strain (np.ndarray | None): Strain tensor from most recent JOutStructure (unitless). +nstep (int | None): (geometric) nstep from most recent JOutStructure. +e (float | None): Energy of system “etype” from most recent JOutStructure. +grad_k (float): The final norm of the preconditioned gradient for geometric optimization of the most recent

+
+

JDFTx call (evaluated as dot(g, Kg), where g is the gradient and Kg is the preconditioned gradient). +(written as “|grad|_K” in JDFTx output).

+
+

alpha (float): The step size of the final geometric step in the most recent JDFTx call. +linmin (float): The final normalized projection of the geometric step direction onto the gradient for the most

+
+

recent JDFTx call.

+
+

abs_magneticmoment (float | None): The absolute magnetic moment of the most recent JDFTx call. +tot_magneticmoment (float | None): The total magnetic moment of the most recent JDFTx call. +mu (float): The Fermi energy of the most recent JDFTx call. +elec_e (float): The final energy of the most recent electronic optimization step. +elec_nstep (int): The number of electronic optimization steps in the most recent JDFTx call. +elec_grad_k (float): The final norm of the preconditioned gradient for electronic optimization of the most

+
+

recent JDFTx call (evaluated as dot(g, Kg), where g is the gradient and Kg is the preconditioned gradient). +(written as “|grad|_K” in JDFTx output).

+
+

elec_alpha (float): The step size of the final electronic step in the most recent JDFTx call. +elec_linmin (float): The final normalized projection of the electronic step direction onto the gradient for the

+
+

most recent JDFTx call.

+
+
+
Magic Methods:
+
__getattr__(name: str) -> Any: Overwrite of default __getattr__ method to allow for reference of un-defined

attributes to the “jstrucs” class field. This referring behavior is ideally never used as (currently) all +referrable attributes are defined properties, but is included to prevent errors in the case of future +changes.

+
+
+

__str__() -> str: Return a string representation of the class instance using pprint module. +__repr__() -> str: Create string representation of the class instance. Overwritten from default behavior for

+
+

dataclass so that properties are included in the string, and verbose attributes with redundant information +are trimmed.

+
+
+
+
+
+a: float | None = None[source]
+
+ +
+
+abs_magneticmoment: float | None = None[source]
+
+ +
+
+alpha: float | None = None[source]
+
+ +
+
+atom_coords: list[list[float]] | None = None[source]
+
+ +
+
+atom_coords_final: list[list[float]] | None = None[source]
+
+ +
+
+atom_coords_initial: list[list[float]] | None = None[source]
+
+ +
+
+atom_elements: list | None = None[source]
+
+ +
+
+atom_elements_int: list | None = None[source]
+
+ +
+
+atom_types: list | None = None[source]
+
+ +
+
+b: float | None = None[source]
+
+ +
+
+broadening: float | None = None[source]
+
+ +
+
+broadening_type: str | None = None[source]
+
+ +
+
+c: float | None = None[source]
+
+ +
+
+constant_lattice: bool | None = None[source]
+
+ +
+
+converged: bool | None = None[source]
+
+ +
+
+determine_is_metal() → bool | None[source]
+

Determine if the system is a metal based on the fillings of homo and lumo.

+
+
Returns:
+

True if system is metallic.

+
+
Return type:
+

bool

+
+
+
+ +
+
+e: float | None = None[source]
+
+ +
+
+efermi: float | None = None[source]
+
+ +
+
+egap: float | None = None[source]
+
+ +
+
+elec_alpha: float | None = None[source]
+
+ +
+
+elec_e: float | None = None[source]
+
+ +
+
+elec_grad_k: float | None = None[source]
+
+ +
+
+elec_linmin: float | None = None[source]
+
+ +
+
+elec_nstep: int | None = None[source]
+
+ +
+
+elecmindata: JElSteps | None = None[source]
+
+ +
+
+electronic_output: dict | None = None[source]
+
+ +
+
+emax: float | None = None[source]
+
+ +
+
+emin: float | None = None[source]
+
+ +
+
+eopt_type: str | None = None[source]
+
+ +
+
+etype: str | None = None[source]
+
+ +
+
+fftgrid: list[int] | None = None[source]
+
+ +
+
+fluid: str | None = None[source]
+
+ +
+
+forces: np.ndarray | None = None[source]
+
+ +
+
+geom_opt: bool | None = None[source]
+
+ +
+
+geom_opt_type: str | None = None[source]
+
+ +
+
+grad_k: float | None = None[source]
+
+ +
+
+has_eigstats: bool = False[source]
+
+ +
+
+has_parsable_pseudo: bool = False[source]
+
+ +
+
+has_solvation: bool = False[source]
+
+ +
+
+homo: float | None = None[source]
+
+ +
+
+homo_filling: float | None = None[source]
+
+ +
+
+is_bgw: bool = False[source]
+
+ +
+
+is_gc: bool | None = None[source]
+
+ +
+
+is_metal: bool | None = None[source]
+
+ +
+
+jsettings_electronic: JMinSettings | None = None[source]
+
+ +
+
+jsettings_fluid: JMinSettings | None = None[source]
+
+ +
+
+jsettings_ionic: JMinSettings | None = None[source]
+
+ +
+
+jsettings_lattice: JMinSettings | None = None[source]
+
+ +
+
+jstrucs: JOutStructures | None = None[source]
+
+ +
+
+kgrid: list | None = None[source]
+
+ +
+
+lattice: np.ndarray | None = None[source]
+
+ +
+
+lattice_final: np.ndarray | None = None[source]
+
+ +
+
+lattice_initial: np.ndarray | None = None[source]
+
+ +
+
+linmin: float | None = None[source]
+
+ +
+
+lumo: float | None = None[source]
+
+ +
+
+lumo_filling: float | None = None[source]
+
+ +
+
+mu: float | None = None[source]
+
+ +
+
+nat: int | None = None[source]
+
+ +
+
+nbands: int | None = None[source]
+
+ +
+
+nspin: int | None = None[source]
+
+ +
+
+nstep: int | None = None[source]
+
+ +
+
+parsable_pseudos: ClassVar[list[str]] = ['GBRV', 'SG15'][source]
+
+ +
+
+pp_type: str | None = None[source]
+
+ +
+
+prefix: str | None = None[source]
+
+ +
+
+pwcut: float | None = None[source]
+
+ +
+
+rhocut: float | None = None[source]
+
+ +
+
+semicore_electrons: int | None = None[source]
+
+ +
+
+semicore_electrons_uncharged: int | None = None[source]
+
+ +
+
+spintype: str | None = None[source]
+
+ +
+
+strain: np.ndarray | None = None[source]
+
+ +
+
+stress: np.ndarray | None = None[source]
+
+ +
+
+structure: Structure | None = None[source]
+
+ +
+
+t_s: float | None = None[source]
+
+ +
+
+to_dict() → dict[source]
+

Convert dataclass to dictionary representation.

+
+
Returns:
+

JDFTXOutfileSlice in dictionary format.

+
+
Return type:
+

dict

+
+
+
+ +
+
+tot_magneticmoment: float | None = None[source]
+
+ +
+
+total_electrons: float | None = None[source]
+
+ +
+
+total_electrons_uncharged: int | None = None[source]
+
+ +
+
+trajectory: Trajectory | None = None[source]
+
+ +
+
+truncation_radius: float | None = None[source]
+
+ +
+
+truncation_type: str | None = None[source]
+
+ +
+
+valence_electrons: float | None = None[source]
+
+ +
+
+valence_electrons_uncharged: int | None = None[source]
+
+ +
+
+write() → None[source]
+

Return an error.

+
+
Raises:
+

NotImplementedError – There is no need to write a JDFTx out file.

+
+
+
+ +
+
+xc_func: str | None = None[source]
+
+ +
+ +
+
+get_pseudo_read_section_bounds(text: list[str]) → list[list[int]][source]
+

Get the boundary line numbers for the pseudopotential read section.

+
+
Parameters:
+

text (list[str]) – Output of read_file for out file.

+
+
Returns:
+

List of line numbers for the pseudopotential read sections.

+
+
Return type:
+

list[list[int]]

+
+
+
+ +
+
+

pymatgen.io.jdftx.jelstep module

+

Module for parsing single SCF step from JDFTx.

+

This module contains the JElStep class for parsing single SCF step from a JDFTx out file.

+
+
+class JElStep(opt_type: str | None = None, etype: str | None = None, nstep: int | None = None, e: float | None = None, grad_k: float | None = None, alpha: float | None = None, linmin: float | None = None, t_s: float | None = None, mu: float | None = None, nelectrons: float | None = None, abs_magneticmoment: float | None = None, tot_magneticmoment: float | None = None, subspacerotationadjust: float | None = None, converged: bool = False, converged_reason: str | None = None)[source]
+

Bases: object

+

Electronic minimization data for a single SCF step.

+

Class object for storing logged electronic minimization data for a single +SCF step.

+
+
+opt_type[source]
+

The type of electronic minimization step +(almost always ElecMinimize).

+
+
Type:
+

str | None

+
+
+
+ +
+
+etype[source]
+

The type of energy component (G, F, or Etot).

+
+
Type:
+

str | None

+
+
+
+ +
+
+nstep[source]
+

The SCF step number.

+
+
Type:
+

int | None

+
+
+
+ +
+
+e[source]
+

The total electronic energy in eV.

+
+
Type:
+

float | None

+
+
+
+ +
+
+grad_k[source]
+

The gradient of the Kohn-Sham energy (along the +line minimization direction).

+
+
Type:
+

float | None

+
+
+
+ +
+
+alpha[source]
+

The step length.

+
+
Type:
+

float | None

+
+
+
+ +
+
+linmin[source]
+

Normalized line minimization direction / energy +gradient projection (-1 for perfectly opposite, 1 for perfectly aligned).

+
+
Type:
+

float | None

+
+
+
+ +
+
+t_s[source]
+

Time elapsed from beginning of JDFTx calculation.

+
+
Type:
+

float | None

+
+
+
+ +
+
+mu[source]
+

The chemical potential in eV.

+
+
Type:
+

float | None

+
+
+
+ +
+
+nelectrons[source]
+

The number of electrons.

+
+
Type:
+

float | None

+
+
+
+ +
+
+abs_magneticmoment[source]
+

The absolute magnetic moment.

+
+
Type:
+

float | None

+
+
+
+ +
+
+tot_magneticmoment[source]
+

The total magnetic moment.

+
+
Type:
+

float | None

+
+
+
+ +
+
+subspacerotationadjust[source]
+

The subspace rotation adjustment factor.

+
+
Type:
+

float | None

+
+
+
+ +
+
+abs_magneticmoment: float | None = None[source]
+
+ +
+
+alpha: float | None = None[source]
+
+ +
+
+converged: bool = False[source]
+
+ +
+
+converged_reason: str | None = None[source]
+
+ +
+
+e: float | None = None[source]
+
+ +
+
+etype: str | None = None[source]
+
+ +
+
+grad_k: float | None = None[source]
+
+ +
+
+linmin: float | None = None[source]
+
+ +
+
+mu: float | None = None[source]
+
+ +
+
+nelectrons: float | None = None[source]
+
+ +
+
+nstep: int | None = None[source]
+
+ +
+
+opt_type: str | None = None[source]
+
+ +
+
+subspacerotationadjust: float | None = None[source]
+
+ +
+
+t_s: float | None = None[source]
+
+ +
+
+to_dict() → dict[source]
+

Return dictionary representation of JElStep object.

+
+
Returns:
+

Dictionary representation of JElStep object.

+
+
Return type:
+

dict

+
+
+
+ +
+
+tot_magneticmoment: float | None = None[source]
+
+ +
+ +
+
+class JElSteps(opt_type: str | None = None, etype: str | None = None, iter_flag: str | None = None, converged: bool | None = None, converged_reason: str | None = None, slices: list[~pymatgen.io.jdftx.jelstep.JElStep] = <factory>)[source]
+

Bases: object

+

Class object for series of SCF steps.

+

Class object for collecting and storing a series of SCF steps done between +geometric optimization steps.

+
+
+opt_type[source]
+

The type of electronic minimization step.

+
+
Type:
+

str | None

+
+
+
+ +
+
+etype[source]
+

The type of energy component.

+
+
Type:
+

str | None

+
+
+
+ +
+
+iter_flag[source]
+

The flag that indicates the start of a log message for a JDFTx optimization step.

+
+
Type:
+

str | None

+
+
+
+ +
+
+converged[source]
+

True if the SCF steps converged.

+
+
Type:
+

bool

+
+
+
+ +
+
+converged_reason[source]
+

The reason for convergence.

+
+
Type:
+

str | None

+
+
+
+ +
+
+slices[source]
+

A list of JElStep objects.

+
+
Type:
+

list[JElStep]

+
+
+
+ +
+
+e[source]
+

The total electronic energy in eV.

+
+
Type:
+

float | None

+
+
+
+ +
+
+grad_k[source]
+

The gradient of the Kohn-Sham energy (along the +line minimization direction).

+
+
Type:
+

float | None

+
+
+
+ +
+
+alpha[source]
+

The step length.

+
+
Type:
+

float | None

+
+
+
+ +
+
+linmin[source]
+

Normalized line minimization direction / energy +gradient projection (-1 for perfectly opposite, 1 for perfectly aligned).

+
+
Type:
+

float | None

+
+
+
+ +
+
+t_s[source]
+

Time elapsed from beginning of JDFTx calculation.

+
+
Type:
+

float | None

+
+
+
+ +
+
+mu[source]
+

The chemical potential in eV.

+
+
Type:
+

float | None

+
+
+
+ +
+
+nelectrons[source]
+

The number of electrons.

+
+
Type:
+

float | None

+
+
+
+ +
+
+abs_magneticmoment[source]
+

The absolute magnetic moment.

+
+
Type:
+

float | None

+
+
+
+ +
+
+tot_magneticmoment[source]
+

The total magnetic moment.

+
+
Type:
+

float | None

+
+
+
+ +
+
+subspacerotationadjust[source]
+

The subspace rotation adjustment factor.

+
+
Type:
+

float | None

+
+
+
+ +
+
+nstep[source]
+

The SCF step number.

+
+
Type:
+

int | None

+
+
+
+ +
+
+abs_magneticmoment: float | None = None[source]
+
+ +
+
+alpha: float | None = None[source]
+
+ +
+
+converged: bool | None = None[source]
+
+ +
+
+converged_reason: str | None = None[source]
+
+ +
+
+e: float | None = None[source]
+
+ +
+
+etype: str | None = None[source]
+
+ +
+
+grad_k: float | None = None[source]
+
+ +
+
+iter_flag: str | None = None[source]
+
+ +
+
+linmin: float | None = None[source]
+
+ +
+
+mu: float | None = None[source]
+
+ +
+
+nelectrons: float | None = None[source]
+
+ +
+
+nstep: int | None = None[source]
+
+ +
+
+opt_type: str | None = None[source]
+
+ +
+
+slices: list[JElStep][source]
+
+ +
+
+subspacerotationadjust: float | None = None[source]
+
+ +
+
+t_s: float | None = None[source]
+
+ +
+
+to_dict() → dict[str, Any][source]
+

Return dictionary representation of JElSteps object.

+
+
Returns:
+

Dictionary representation of JElSteps object.

+
+
Return type:
+

dict

+
+
+
+ +
+
+tot_magneticmoment: float | None = None[source]
+
+ +
+ +
+
+

pymatgen.io.jdftx.jminsettings module

+

Store generic minimization settings read from a JDFTx out file.

+

This module contains the JMinSettings class for storing generic minimization +and mutants for storing specific minimization settings read from a JDFTx out +file.

+

@mkhorton - this file is ready to review.

+
+
+class JMinSettings(params: dict[str, Any] | None = None)[source]
+

Bases: object

+

Store generic minimization settings read from a JDFTx out file.

+

Store generic minimization settings read from a JDFTx out file.

+

Initialize a generic JMinSettings class.

+
+
Parameters:
+

params (dict[str, Any] | None) – A dictionary of minimization settings.

+
+
+
+
+params: dict[str, Any] | None = None[source]
+
+ +
+ +
+
+class JMinSettingsElectronic(params: dict[str, Any] | None = None)[source]
+

Bases: JMinSettings

+

JMInSettings mutant for electronic minimization settings.

+

A class for storing electronic minimization settings read from a JDFTx out file.

+

Initialize a generic JMinSettings class.

+
+
Parameters:
+

params (dict[str, Any] | None) – A dictionary of minimization settings.

+
+
+
+
+start_flag: str = 'electronic-minimize'[source]
+
+ +
+ +
+
+class JMinSettingsFluid(params: dict[str, Any] | None = None)[source]
+

Bases: JMinSettings

+

JMInSettings mutant for fluid minimization settings.

+

A class for storing fluid minimization settings read from a JDFTx out file.

+

Initialize a generic JMinSettings class.

+
+
Parameters:
+

params (dict[str, Any] | None) – A dictionary of minimization settings.

+
+
+
+
+start_flag: str = 'fluid-minimize'[source]
+
+ +
+ +
+
+class JMinSettingsIonic(params: dict[str, Any] | None = None)[source]
+

Bases: JMinSettings

+

JMInSettings mutant for ionic minimization settings.

+

A class for storing ionic minimization settings read from a JDFTx out file.

+

Initialize a generic JMinSettings class.

+
+
Parameters:
+

params (dict[str, Any] | None) – A dictionary of minimization settings.

+
+
+
+
+start_flag: str = 'ionic-minimize'[source]
+
+ +
+ +
+
+class JMinSettingsLattice(params: dict[str, Any] | None = None)[source]
+

Bases: JMinSettings

+

JMInSettings mutant for lattice minimization settings.

+

A class for storing lattice minimization settings read from a JDFTx out file.

+

Initialize a generic JMinSettings class.

+
+
Parameters:
+

params (dict[str, Any] | None) – A dictionary of minimization settings.

+
+
+
+
+start_flag: str = 'lattice-minimize'[source]
+
+ +
+ +
+
+

pymatgen.io.jdftx.joutstructure module

+

Class object for storing a single JDFTx geometric optimization step.

+

A mutant of the pymatgen Structure class for flexibility in holding JDFTx.

+
+
+class JOutStructure(lattice: ndarray, species: list[str], coords: list[ndarray], site_properties: dict[str, list], **kwargs)[source]
+

Bases: Structure

+

Class object for storing a single JDFTx optimization step.

+

A mutant of the pymatgen Structure class for flexibility in holding JDFTx +optimization data.

+
+
Properties:

charges (np.ndarray | None): The Lowdin charges of the atoms in the system. +magnetic_moments (np.ndarray | None): The magnetic moments of the atoms in the system.

+
+
+
+
+opt_type[source]
+

The type of optimization step.

+
+
Type:
+

str | None

+
+
+
+ +
+
+etype[source]
+

The type of energy from the electronic minimization data.

+
+
Type:
+

str | None

+
+
+
+ +
+
+eopt_type[source]
+

The type of electronic minimization step.

+
+
Type:
+

str | None

+
+
+
+ +
+
+emin_flag[source]
+

The flag that indicates the start of a log message for a JDFTx optimization step.

+
+
Type:
+

str | None

+
+
+
+ +
+
+ecomponents[source]
+

The energy components of the system.

+
+
Type:
+

dict | None

+
+
+
+ +
+
+elecmindata[source]
+

The electronic minimization data.

+
+
Type:
+

JElSteps | None

+
+
+
+ +
+
+stress[source]
+

The stress tensor.

+
+
Type:
+

np.ndarray | None

+
+
+
+ +
+
+strain[source]
+

The strain tensor.

+
+
Type:
+

np.ndarray | None

+
+
+
+ +
+
+nstep[source]
+

The most recent step number.

+
+
Type:
+

int | None

+
+
+
+ +
+
+e[source]
+

The total energy of the system.

+
+
Type:
+

float | None

+
+
+
+ +
+
+grad_k[source]
+

The gradient of the electronic density along the most recent line minimization.

+
+
Type:
+

float | None

+
+
+
+ +
+
+alpha[source]
+

The step size of the most recent SCF step along the line minimization.

+
+
Type:
+

float | None

+
+
+
+ +
+
+linmin[source]
+

The normalized alignment projection of the electronic energy gradient to the line +minimization direction.

+
+
Type:
+

float | None

+
+
+
+ +
+
+t_s[source]
+

The time in seconds for the optimization step.

+
+
Type:
+

float | None

+
+
+
+ +
+
+geom_converged[source]
+

Whether the geometry optimization has converged.

+
+
Type:
+

bool

+
+
+
+ +
+
+geom_converged_reason[source]
+

The reason for geometry optimization convergence.

+
+
Type:
+

str | None

+
+
+
+ +
+
+line_types[source]
+

The types of lines in a JDFTx out file.

+
+
Type:
+

ClassVar[list[str]]

+
+
+
+ +
+
+selective_dynamics[source]
+

The selective dynamics flags for the atoms in the system.

+
+
Type:
+

list[int] | None

+
+
+
+ +
+
+mu[source]
+

The chemical potential (Fermi level) in eV.

+
+
Type:
+

float | None

+
+
+
+ +
+
+nelectrons[source]
+

The total number of electrons in the electron density.

+
+
Type:
+

float | None

+
+
+
+ +
+
+abs_magneticmoment[source]
+

The absolute magnetic moment of the electron density.

+
+
Type:
+

float | None

+
+
+
+ +
+
+tot_magneticmoment[source]
+

The total magnetic moment of the electron density.

+
+
Type:
+

float | None

+
+
+
+ +
+
+elec_nstep[source]
+

The most recent electronic step number.

+
+
Type:
+

int | None

+
+
+
+ +
+
+elec_e[source]
+

The most recent electronic energy.

+
+
Type:
+

float | None

+
+
+
+ +
+
+elec_grad_k[source]
+

The most recent electronic grad_k.

+
+
Type:
+

float | None

+
+
+
+ +
+
+elec_alpha[source]
+

The most recent electronic alpha.

+
+
Type:
+

float | None

+
+
+
+ +
+
+elec_linmin[source]
+

The most recent electronic linmin.

+
+
Type:
+

float | None

+
+
+
+ +
+
+structure[source]
+

The Structure object of the system. (helpful for uses where the JOutStructure +metadata causes issues)

+
+
Type:
+

Structure | None

+
+
+
+ +

Create a periodic structure.

+
+
Parameters:
+
    +

  • lattice – The lattice, either as a pymatgen.core.Lattice or +simply as any 2D array. Each row should correspond to a lattice +vector. e.g. [[10,0,0], [20,10,0], [0,0,30]] specifies a +lattice with lattice vectors [10,0,0], [20,10,0] and [0,0,30].

    • +

  • species –

    List of species on each site. Can take in flexible input, +including:

    +
      +

    1. A sequence of element / species specified either as string +symbols, e.g. [“Li”, “Fe2+”, “P”, …] or atomic numbers, +e.g. (3, 56, …) or actual Element or Species objects.

      2. +

    2. List of dict of elements/species and occupancies, e.g. +[{“Fe” : 0.5, “Mn”:0.5}, …]. This allows the setup of +disordered structures.

      3. +
    +

    • +

  • coords (Nx3 array) – list of fractional/cartesian coordinates of +each species.

    • +

  • charge (float) – overall charge of the structure. Defaults to behavior +in SiteCollection where total charge is the sum of the oxidation +states.

    • +

  • validate_proximity (bool) – Whether to check if there are sites +that are less than 0.01 Ang apart. Defaults to False.

    • +

  • to_unit_cell (bool) – Whether to map all sites into the unit cell, +i.e., fractional coords between 0 and 1. Defaults to False.

    • +

  • coords_are_cartesian (bool) – Set to True if you are providing +coordinates in Cartesian coordinates. Defaults to False.

    • +

  • site_properties (dict) – Properties associated with the sites as a +dict of sequences, e.g. {“magmom”:[5,5,5,5]}. The sequences +have to be the same length as the atomic species and +fractional_coords. Defaults to None for no properties.

    • +

  • labels (list[str]) – Labels associated with the sites as a +list of strings, e.g. [‘Li1’, ‘Li2’]. Must have the same +length as the species and fractional coords. Defaults to +None for no labels.

    • +

  • properties (dict) – Properties associated with the whole structure. +Will be serialized when writing the structure to JSON or YAML but is +lost when converting to other formats.

    • +
+
+
+
+
+abs_magneticmoment: float | None = None[source]
+
+ +
+
+alpha: float | None = None[source]
+
+ +
+
+property charges: ndarray | None[source]
+

Return the Lowdin charges.

+
+
Returns:
+

The Lowdin charges of the atoms in the system.

+
+
Return type:
+

np.ndarray

+
+
+
+ +
+
+e: float | None = None[source]
+
+ +
+
+ecomponents: dict | None = None[source]
+
+ +
+
+elec_alpha: float | None = None[source]
+
+ +
+
+elec_e: float | None = None[source]
+
+ +
+
+elec_grad_k: float | None = None[source]
+
+ +
+
+elec_linmin: float | None = None[source]
+
+ +
+
+elec_nstep: int | None = None[source]
+
+ +
+
+elecmindata: JElSteps | None = None[source]
+
+ +
+
+emin_flag: str | None = None[source]
+
+ +
+
+eopt_type: str | None = None[source]
+
+ +
+
+etype: str | None = None[source]
+
+ +
+
+forces: np.ndarray | None = None[source]
+
+ +
+
+geom_converged: bool = False[source]
+
+ +
+
+geom_converged_reason: str | None = None[source]
+
+ +
+
+grad_k: float | None = None[source]
+
+ +
+
+line_types: ClassVar[list[str]] = ['emin', 'lattice', 'strain', 'stress', 'posns', 'forces', 'ecomp', 'lowdin', 'opt'][source]
+
+ +
+
+linmin: float | None = None[source]
+
+ +
+
+property magnetic_moments: ndarray | None[source]
+

Return the magnetic moments.

+
+
Returns:
+

The magnetic moments of the atoms in the system.

+
+
Return type:
+

np.ndarray

+
+
+
+ +
+
+mu: float | None = None[source]
+
+ +
+
+nelectrons: float | None = None[source]
+
+ +
+
+nstep: int | None = None[source]
+
+ +
+
+opt_type: str | None = None[source]
+
+ +
+
+selective_dynamics: list[int] | None = None[source]
+
+ +
+
+strain: np.ndarray | None = None[source]
+
+ +
+
+stress: np.ndarray | None = None[source]
+
+ +
+
+structure: Structure | None = None[source]
+
+ +
+
+t_s: float | None = None[source]
+
+ +
+
+to_dict() → dict[source]
+

Convert the JOutStructure object to a dictionary.

+
+
Returns:
+

A dictionary representation of the JOutStructure object.

+
+
Return type:
+

dict

+
+
+
+ +
+
+tot_magneticmoment: float | None = None[source]
+
+ +
+ +
+
+

pymatgen.io.jdftx.joutstructures module

+

Module for JOutStructures class.

+

This module contains the JOutStructures class for storing a series of +JOutStructure.

+
+
+class JOutStructures(opt_type: str | None = None, geom_converged: bool = False, geom_converged_reason: str | None = None, elec_converged: bool = False, elec_converged_reason: str | None = None, _t_s: float | None = None, slices: list[JOutStructure] = <factory>, eopt_type: str | None = None, etype: str | None = None, emin_flag: str | None = None, ecomponents: list[str] | None = None, elecmindata: JElSteps = None, stress: np.ndarray | None = None, strain: np.ndarray | None = None, forces: np.ndarray | None = None, nstep: int | None = None, e: float | None = None, grad_k: float | None = None, alpha: float | None = None, linmin: float | None = None, nelectrons: float | None = None, abs_magneticmoment: float | None = None, tot_magneticmoment: float | None = None, mu: float | None = None, elec_nstep: int | None = None, elec_e: float | None = None, elec_grad_k: float | None = None, elec_alpha: float | None = None, elec_linmin: float | None = None, charges: np.ndarray[float] | None = None, magnetic_moments: np.ndarray[float] | None = None, selective_dynamics: list[int] | None = None, structure: Structure | None = None)[source]
+

Bases: object

+

Class for storing a series of JStructure objects.

+

A class for storing a series of JStructure objects.

+
+
+out_slice_start_flag[source]
+

The string that marks the beginning of the portion of an out file slice +that contains data for a JOutStructures object.

+
+
Type:
+

str

+
+
+
+ +
+
+opt_type[source]
+

The type of optimization performed on the structures in the JOutStructures object.

+
+
Type:
+

str | None

+
+
+
+ +
+
+geom_converged[source]
+

Whether the geometry of the last structure in the list has converged.

+
+
Type:
+

bool

+
+
+
+ +
+
+geom_converged_reason[source]
+

The reason the geometry of the last structure in the list has converged.

+
+
Type:
+

str | None

+
+
+
+ +
+
+elec_converged[source]
+

Whether the electronic density of the last structure in the list has converged.

+
+
Type:
+

bool

+
+
+
+ +
+
+elec_converged_reason[source]
+

The reason the electronic density of the last structure in the list has +converged.

+
+
Type:
+

str | None

+
+
+
+ +
+
+slices[source]
+

A list of JOutStructure objects.

+
+
Type:
+

list[JOutStructure]

+
+
+
+ +
+
+eopt_type[source]
+

The type of electronic optimization performed on the last structure in the list.

+
+
Type:
+

str | None

+
+
+
+ +
+
+etype[source]
+

String representation of total energy-type of system. Commonly “G”

+
+
Type:
+

str | None

+
+
+
+ +
+
+(grand-canonical potential) for GC calculations, and "F" for canonical
+
+
Type:
+

fixed electron count

+
+
+
+ +
+
+emin_flag[source]
+

The flag for the electronic minimization.

+
+
Type:
+

str | None

+
+
+
+ +
+
+ecomponents[source]
+

The components of the electronic minimization.

+
+
Type:
+

list[str] | None

+
+
+
+ +
+
+elecmindata[source]
+

The electronic minimization data.

+
+
Type:
+

JElSteps

+
+
+
+ +
+
+stress[source]
+

The stress tensor.

+
+
Type:
+

np.ndarray | None

+
+
+
+ +
+
+strain[source]
+

The strain tensor.

+
+
Type:
+

np.ndarray | None

+
+
+
+ +
+
+nstep[source]
+

The number of steps in the optimization.

+
+
Type:
+

int | None

+
+
+
+ +
+
+e[source]
+

The total energy.

+
+
Type:
+

float | None

+
+
+
+ +
+
+grad_k[source]
+

The final norm of the preconditioned gradient for geometric optimization of the most +recent JDFTx call (evaluated as dot(g, Kg), where g is the gradient and Kg is the preconditioned gradient). +(written as “|grad|_K” in JDFTx output).

+
+
Type:
+

float | None

+
+
+
+ +
+
+alpha[source]
+

The step size of the final geometric step in the most recent JDFTx call.

+
+
Type:
+

float | None

+
+
+
+ +
+
+linmin[source]
+

The final normalized projection of the geometric step direction onto the gradient for +the most recent JDFTx call.

+
+
Type:
+

float | None

+
+
+
+ +
+
+abs_magneticmoment[source]
+

The absolute magnetic moment of the most recent JDFTx call.

+
+
Type:
+

float | None

+
+
+
+ +
+
+tot_magneticmoment[source]
+

The total magnetic moment of the most recent JDFTx call.

+
+
Type:
+

float | None

+
+
+
+ +
+
+mu[source]
+

The Fermi energy of the most recent JDFTx call.

+
+
Type:
+

float | None

+
+
+
+ +
+
+elec_e[source]
+

The final energy of the most recent electronic optimization step.

+
+
Type:
+

float

+
+
+
+ +
+
+elec_nstep[source]
+

The number of electronic optimization steps in the most recent JDFTx call.

+
+
Type:
+

int

+
+
+
+ +
+
+elec_grad_k[source]
+

The final norm of the preconditioned gradient for electronic optimization of the +most recent JDFTx call (evaluated as dot(g, Kg), where g is the gradient and Kg is the preconditioned +gradient). (written as “|grad|_K” in JDFTx output).

+
+
Type:
+

float | None

+
+
+
+ +
+
+elec_alpha[source]
+

The step size of the final electronic step in the most recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
+elec_linmin[source]
+

The final normalized projection of the electronic step direction onto the gradient +for the most recent JDFTx call.

+
+
Type:
+

float | None

+
+
+
+ +
+
+charges[source]
+

The most recent Lowdin-charges.

+
+
Type:
+

np.ndarray[float] | None

+
+
+
+ +
+
+magnetic_moments[source]
+

The most recent Lowdin-magnetic moments.

+
+
Type:
+

np.ndarray[float] | None

+
+
+
+ +
+
+selective_dynamics[source]
+

The selective dynamics flags for the most recent JDFTx call.

+
+
Type:
+

list[int] | None

+
+
+
+ +
+
+structure[source]
+

Cleaned pymatgen Structure object of final JOutStructure

+
+
Type:
+

Structure | None

+
+
+
+ +
+
+abs_magneticmoment: float | None = None[source]
+
+ +
+
+alpha: float | None = None[source]
+
+ +
+
+charges: np.ndarray[float] | None = None[source]
+
+ +
+
+e: float | None = None[source]
+
+ +
+
+ecomponents: list[str] | None = None[source]
+
+ +
+
+elec_alpha: float | None = None[source]
+
+ +
+
+elec_converged: bool = False[source]
+
+ +
+
+elec_converged_reason: str | None = None[source]
+
+ +
+
+elec_e: float | None = None[source]
+
+ +
+
+elec_grad_k: float | None = None[source]
+
+ +
+
+elec_linmin: float | None = None[source]
+
+ +
+
+elec_nstep: int | None = None[source]
+
+ +
+
+elecmindata: JElSteps = None[source]
+
+ +
+
+emin_flag: str | None = None[source]
+
+ +
+
+eopt_type: str | None = None[source]
+
+ +
+
+etype: str | None = None[source]
+
+ +
+
+forces: np.ndarray | None = None[source]
+
+ +
+
+geom_converged: bool = False[source]
+
+ +
+
+geom_converged_reason: str | None = None[source]
+
+ +
+
+grad_k: float | None = None[source]
+
+ +
+
+linmin: float | None = None[source]
+
+ +
+
+magnetic_moments: np.ndarray[float] | None = None[source]
+
+ +
+
+mu: float | None = None[source]
+
+ +
+
+nelectrons: float | None = None[source]
+
+ +
+
+nstep: int | None = None[source]
+
+ +
+
+opt_type: str | None = None[source]
+
+ +
+
+out_slice_start_flag = '-------- Electronic minimization -----------'[source]
+
+ +
+
+selective_dynamics: list[int] | None = None[source]
+
+ +
+
+slices: list[JOutStructure][source]
+
+ +
+
+strain: np.ndarray | None = None[source]
+
+ +
+
+stress: np.ndarray | None = None[source]
+
+ +
+
+structure: Structure | None = None[source]
+
+ +
+
+to_dict() → dict[source]
+

Convert the JOutStructures object to a dictionary.

+
+
Returns:
+

A dictionary representation of the JOutStructures object.

+
+
Return type:
+

dict

+
+
+
+ +
+
+tot_magneticmoment: float | None = None[source]
+
+ +
+ +
+
+

pymatgen.io.jdftx.outputs module

+

JDFTx outputs parsing module.

+

Module for parsing outputs of JDFTx.

+

Note: JDFTXOutfile will be moved back to its own module once a more broad outputs +class is written.

+
+
+class JDFTXOutfile(slices: list[~pymatgen.io.jdftx.jdftxoutfileslice.JDFTXOutfileSlice] = <factory>)[source]
+

Bases: object

+

JDFTx out file parsing class.

+

A class to read and process a JDFTx out file.

+
+
+from_file(file_path
+

str | Path) -> JDFTXOutfile: +Return JDFTXOutfile object from the path to a JDFTx out file.

+
+ +
+
+slices[source]
+

A list of JDFTXOutfileSlice objects. Each slice corresponds to an individual +call of the JDFTx executable. Subsequent JDFTx calls within the same directory and prefix will append +outputs to the same out file. More than one slice may correspond to restarted calculations, geom + single +point calculations, or optimizations done with 3rd-party wrappers like ASE.

+
+
Type:
+

list[JDFTXOutfileSlice]

+
+
+
+ +
+
+prefix[source]
+

The prefix of the most recent JDFTx call.

+
+
Type:
+

str

+
+
+
+ +
+
+jstrucs[source]
+

The JOutStructures object from the most recent JDFTx call. This object contains a +series of JOutStructure objects in its ‘slices’ attribute, each corresponding to a single structure +(multiple iff performing a geometric optimization) as well as convergence data for the structures as a +series.

+
+
Type:
+

JOutStructures

+
+
+
+ +
+
+jsettings_fluid[source]
+

The JMinSettingsFluid object from the most recent JDFTx call. This object +contains only a ‘params’ attribute, which is a dictionary of the input parameters for the fluid +optimization.

+
+
Type:
+

JMinSettingsFluid

+
+
+
+ +
+
+jsettings_electronic[source]
+

The JMinSettingsElectronic object from the most recent JDFTx +call. This object contains only a ‘params’ attribute, which is a dictionary of the input parameters for the +electronic optimization.

+
+
Type:
+

JMinSettingsElectronic

+
+
+
+ +
+
+jsettings_lattice[source]
+

The JMinSettingsLattice object from the most recent JDFTx call. This +object contains only a ‘params’ attribute, which is a dictionary of the input parameters for the lattice +optimization.

+
+
Type:
+

JMinSettingsLattice

+
+
+
+ +
+
+jsettings_ionic[source]
+

The JMinSettingsIonic object from the most recent JDFTx call. This object +contains only a ‘params’ attribute, which is a dictionary of the input parameters for the ionic +optimization.

+
+
Type:
+

JMinSettingsIonic

+
+
+
+ +
+
+xc_func[source]
+

The exchange-correlation functional used in the most recent JDFTx call. See documentation for +JDFTx online for a list of available exchange-correlation functionals.

+
+
Type:
+

str

+
+
+
+ +
+
+lattice_initial[source]
+

The initial lattice vectors of the most recent JDFTx call as a 3x3 numpy array. +In units of Angstroms.

+
+
Type:
+

np.ndarray

+
+
+
+ +
+
+lattice_final[source]
+

The final lattice vectors of the most recent JDFTx call as a 3x3 numpy array. In +units of Angstroms.

+
+
Type:
+

np.ndarray

+
+
+
+ +
+
+lattice[source]
+

The lattice vectors of the most recent JDFTx call as a 3x3 numpy array (redundant to +lattice_final).

+
+
Type:
+

np.ndarray

+
+
+
+ +
+
+a[source]
+

Length of the first lattice vector. In units of Angstroms.

+
+
Type:
+

float

+
+
+
+ +
+
+b[source]
+

Length of the second lattice vector. In units of Angstroms.

+
+
Type:
+

float

+
+
+
+ +
+
+c[source]
+

Length of the third lattice vector. In units of Angstroms.

+
+
Type:
+

float

+
+
+
+ +
+
+fftgrid[source]
+

The FFT grid shape used in the most recent JDFTx call. Can be used to properly shape +densities dumped as binary files.

+
+
Type:
+

list[int]

+
+
+
+ +
+
+geom_opt[source]
+

True if the most recent JDFTx call was a geometry optimization (lattice or ionic).

+
+
Type:
+

bool

+
+
+
+ +
+
+geom_opt_type[source]
+

The type of geometry optimization performed in the most recent JDFTx call. Options are +‘lattice’ or ‘ionic’ if geom_opt, else “single point”. (‘lattice’ optimizations perform ionic optimizations +as well unless ion positions are given in direct coordinates).

+
+
Type:
+

str

+
+
+
+ +
+
+ecomponents[source]
+

The components of the total energy in eV of the most recent JDFTx call.

+
+
Type:
+

dict

+
+
+
+ +
+
+efermi[source]
+

The Fermi energy in eV of the most recent JDFTx call. Equivalent to “mu”.

+
+
Type:
+

float

+
+
+
+ +
+
+egap[source]
+

The band gap in eV of the most recent JDFTx call. (Only available if eigstats was dumped).

+
+
Type:
+

float

+
+
+
+ +
+
+emin[source]
+

The minimum energy in eV (smallest Kohn-Sham eigenvalue) of the most recent JDFTx call. (Only +available if eigstats was dumped).

+
+
Type:
+

float

+
+
+
+ +
+
+emax[source]
+

The maximum energy in eV (largest Kohn-Sham eigenvalue) of the most recent JDFTx call. (Only +available if eigstats was dumped).

+
+
Type:
+

float

+
+
+
+ +
+
+homo[source]
+

The energy in eV of the band-gap lower bound (Highest Occupied Molecular Orbital) (Only available +if eigstats was dumped).

+
+
Type:
+

float

+
+
+
+ +
+
+lumo[source]
+

The energy in eV of the band-gap upper bound (Lowest Unoccupied Molecular Orbital) (Only +available if eigstats was dumped).

+
+
Type:
+

float

+
+
+
+ +
+
+homo_filling[source]
+

The electron filling at the homo band-state. (Only available if eigstats was dumped).

+
+
Type:
+

float

+
+
+
+ +
+
+lumo_filling[source]
+

The electron filling at the lumo band-state. (Only available if eigstats was dumped).

+
+
Type:
+

float

+
+
+
+ +
+
+is_metal[source]
+

True if fillings of homo and lumo band-states are off-set by 1 and 0 by at least an arbitrary +tolerance of 0.01 (ie 1 - 0.015 and 0.012 for homo/lumo fillings would be metallic, while 1-0.001 and 0 +would not be). (Only available if eigstats was dumped).

+
+
Type:
+

bool

+
+
+
+ +
+
+converged[source]
+

True if most recent SCF cycle converged (and geom forces converged is calc is geom_opt)

+
+
Type:
+

bool

+
+
+
+ +
+
+etype[source]
+

String representation of total energy-type of system. Commonly “G” (grand-canonical potential) for +GC calculations, and “F” for canonical (fixed electron count) calculations.

+
+
Type:
+

str

+
+
+
+ +
+
+broadening_type[source]
+

Type of broadening for electronic filling about Fermi-level requested. Either “Fermi”, +“Cold”, “MP1”, or “Gauss”.

+
+
Type:
+

str

+
+
+
+ +
+
+broadening[source]
+

Magnitude of broadening for electronic filling.

+
+
Type:
+

float

+
+
+
+ +
+
+kgrid[source]
+

Shape of k-point grid used in calculation. (equivalent to k-point folding)

+
+
Type:
+

list[int]

+
+
+
+ +
+
+truncation_type[source]
+

Type of coulomb truncation used to prevent interaction between periodic images along +certain directions. “periodic” means no coulomb truncation was used.

+
+
Type:
+

str

+
+
+
+ +
+
+truncation_radius[source]
+

If spherical truncation_type, this is the radius of the coulomb truncation +sphere.

+
+
Type:
+

float | None

+
+
+
+ +
+
+pwcut[source]
+

The plane-wave cutoff energy in Hartrees used in the most recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
+rhocut[source]
+

The density cutoff energy in Hartrees used in the most recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
+pp_type[source]
+

The pseudopotential library used in the most recent JDFTx call. Currently only “GBRV” and “SG15” +are supported by this output parser.

+
+
Type:
+

str

+
+
+
+ +
+
+total_electrons[source]
+

The total number of electrons in the most recent JDFTx call (redundant to nelectrons).

+
+
Type:
+

float

+
+
+
+ +
+
+semicore_electrons[source]
+

The number of semicore electrons in the most recent JDFTx call.

+
+
Type:
+

int

+
+
+
+ +
+
+valence_electrons[source]
+

The number of valence electrons in the most recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
+total_electrons_uncharged[source]
+

The total number of electrons in the most recent JDFTx call, uncorrected for +charge. (ie total_electrons + charge)

+
+
Type:
+

int

+
+
+
+ +
+
+semicore_electrons_uncharged[source]
+

The number of semicore electrons in the most recent JDFTx call, uncorrected +for charge. (ie semicore_electrons + charge)

+
+
Type:
+

int

+
+
+
+ +
+
+valence_electrons_uncharged[source]
+

The number of valence electrons in the most recent JDFTx call, uncorrected +for charge. (ie valence_electrons + charge)

+
+
Type:
+

int

+
+
+
+ +
+
+nbands[source]
+

The number of bands used in the most recent JDFTx call.

+
+
Type:
+

int

+
+
+
+ +
+
+atom_elements[source]
+

The list of each ion’s element symbol in the most recent JDFTx call.

+
+
Type:
+

list[str]

+
+
+
+ +
+
+atom_elements_int[source]
+

The list of ion’s atomic numbers in the most recent JDFTx call.

+
+
Type:
+

list[int]

+
+
+
+ +
+
+atom_types[source]
+

Non-repeating list of each ion’s element symbol in the most recent JDFTx call.

+
+
Type:
+

list[str]

+
+
+
+ +
+
+spintype[source]
+

The spin type used in the most recent JDFTx call. Options are “none”, “collinear”,

+
+
Type:
+

str

+
+
+
+ +
+
+nspin[source]
+

The number of spins used in the most recent JDFTx call.

+
+
Type:
+

int

+
+
+
+ +
+
+nat[source]
+

The number of atoms in the most recent JDFTx call.

+
+
Type:
+

int

+
+
+
+ +
+
+atom_coords_initial[source]
+

The initial atomic coordinates of the most recent JDFTx call.

+
+
Type:
+

list[list[float]]

+
+
+
+ +
+
+atom_coords_final[source]
+

The final atomic coordinates of the most recent JDFTx call.

+
+
Type:
+

list[list[float]]

+
+
+
+ +
+
+atom_coords[source]
+

The atomic coordinates of the most recent JDFTx call.

+
+
Type:
+

list[list[float]]

+
+
+
+ +
+
+structure[source]
+

The updated pymatgen Structure object of the most recent JDFTx call.

+
+
Type:
+

Structure

+
+
+
+ +
+
+trajectory[source]
+

The Trajectory object of the most recent JDFTx call.

+
+
Type:
+

Trajectory

+
+
+
+ +
+
+has_solvation[source]
+

True if the most recent JDFTx call included a solvation calculation.

+
+
Type:
+

bool

+
+
+
+ +
+
+fluid[source]
+

The fluid used in the most recent JDFTx call.

+
+
Type:
+

str

+
+
+
+ +
+
+is_gc[source]
+

True if the most recent slice is a grand canonical calculation.

+
+
Type:
+

bool

+
+
+
+ +
+
+eopt_type[source]
+

The type of energy iteration used in the most recent JDFTx call.

+
+
Type:
+

str

+
+
+
+ +
+
+elecmindata[source]
+

The JElSteps object from the most recent JDFTx call. This object contains a series of +JElStep objects in its ‘steps’ attribute, each corresponding to a single energy iteration.

+
+
Type:
+

JElSteps

+
+
+
+ +
+
+stress[source]
+

The stress tensor of the most recent JDFTx call as a 3x3 numpy array. In units of +eV/Angstrom^3.

+
+
Type:
+

np.ndarray

+
+
+
+ +
+
+strain[source]
+

The strain tensor of the most recent JDFTx call as a 3x3 numpy array.

+
+
Type:
+

np.ndarray

+
+
+
+ +
+
+nstep[source]
+

The number of geometric optimization steps in the most recent JDFTx call.

+
+
Type:
+

int

+
+
+
+ +
+
+e[source]
+

The final energy in eV of the most recent JDFTx call (equivalent to the call’s etype).

+
+
Type:
+

float

+
+
+
+ +
+
+grad_k[source]
+

The final norm of the preconditioned gradient for geometric optimization of the most recent +JDFTx call (evaluated as dot(g, Kg), where g is the gradient and Kg is the preconditioned gradient). +(written as “|grad|_K” in JDFTx output).

+
+
Type:
+

float

+
+
+
+ +
+
+alpha[source]
+

The step size of the final geometric step in the most recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
+linmin[source]
+

The final normalized projection of the geometric step direction onto the gradient for the most +recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
+abs_magneticmoment[source]
+

The absolute magnetic moment of the most recent JDFTx call.

+
+
Type:
+

float | None

+
+
+
+ +
+
+tot_magneticmoment[source]
+

The total magnetic moment of the most recent JDFTx call.

+
+
Type:
+

float | None

+
+
+
+ +
+
+mu[source]
+

The Fermi energy in eV of the most recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
+elec_e[source]
+

The final energy in eV of the most recent electronic optimization step.

+
+
Type:
+

float

+
+
+
+ +
+
+elec_nstep[source]
+

The number of electronic optimization steps in the most recent JDFTx call.

+
+
Type:
+

int

+
+
+
+ +
+
+elec_grad_k[source]
+

The final norm of the preconditioned gradient for electronic optimization of the most +recent JDFTx call (evaluated as dot(g, Kg), where g is the gradient and Kg is the preconditioned gradient). +(written as “|grad|_K” in JDFTx output).

+
+
Type:
+

float

+
+
+
+ +
+
+elec_alpha[source]
+

The step size of the final electronic step in the most recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
+elec_linmin[source]
+

The final normalized projection of the electronic step direction onto the gradient for the +most recent JDFTx call.

+
+
Type:
+

float

+
+
+
+ +
+
Magic Methods:
+
__getitem__(key: str | int) -> Any: Decides behavior of how JDFTXOutfile objects are indexed. If the key is a

string, it will return the value of the property with the same name. If the key is an integer, it will +return the slice of the JDFTXOutfile object at that index.

+
+
+

__len__() -> int: Returns the number of slices in the JDFTXOutfile object. +__getattr__(name: str) -> Any: Returns the value of the property with the same name as the input string. +__str__() -> str: Returns a string representation of the JDFTXOutfile object.

+
+
+
+
+a: float[source]
+
+ +
+
+abs_magneticmoment: float[source]
+
+ +
+
+alpha: float[source]
+
+ +
+
+atom_coords: list[list[float]][source]
+
+ +
+
+atom_coords_final: list[list[float]][source]
+
+ +
+
+atom_coords_initial: list[list[float]][source]
+
+ +
+
+atom_elements: list[str][source]
+
+ +
+
+atom_elements_int: list[int][source]
+
+ +
+
+atom_types: list[str][source]
+
+ +
+
+b: float[source]
+
+ +
+
+broadening: float[source]
+
+ +
+
+broadening_type: str[source]
+
+ +
+
+c: float[source]
+
+ +
+
+converged: bool[source]
+
+ +
+
+e: float[source]
+
+ +
+
+efermi: float[source]
+
+ +
+
+egap: float[source]
+
+ +
+
+elec_alpha: float[source]
+
+ +
+
+elec_e: float[source]
+
+ +
+
+elec_grad_k: float[source]
+
+ +
+
+elec_linmin: float[source]
+
+ +
+
+elec_nstep: int[source]
+
+ +
+
+elecmindata: JElSteps[source]
+
+ +
+
+electronic_output: float[source]
+
+ +
+
+emax: float[source]
+
+ +
+
+emin: float[source]
+
+ +
+
+eopt_type: str[source]
+
+ +
+
+etype: str[source]
+
+ +
+
+fftgrid: list[int][source]
+
+ +
+
+fluid: str[source]
+
+ +
+
+forces: np.ndarray[source]
+
+ +
+
+classmethod from_calc_dir(calc_dir: str | Path, is_bgw: bool = False, none_slice_on_error: bool = False) → JDFTXOutfile[source]
+

Create a JDFTXOutfile object from a directory containing JDFTx out files.

+
+
Parameters:
+
    +

  • calc_dir (str | Path) – The path to the directory containing the JDFTx out files.

    • +

  • is_bgw (bool) – Mark True if data must be usable for BGW calculations. This will change the behavior of the +parser to be stricter with certain criteria.

    • +

  • none_slice_on_error (bool) – If True, will return None if an error occurs while parsing a slice instead of +halting the parsing process. This can be useful for parsing files with multiple slices where some slices +may be incomplete or corrupted.

    • +
+
+
Returns:
+

The JDFTXOutfile object.

+
+
Return type:
+

JDFTXOutfile

+
+
+
+ +
+
+classmethod from_file(file_path: str | Path, is_bgw: bool = False, none_slice_on_error: bool | None = None) → JDFTXOutfile[source]
+

Create a JDFTXOutfile object from a JDFTx out file.

+
+
Parameters:
+
    +

  • file_path (str | Path) – The path to the JDFTx out file.

    • +

  • is_bgw (bool) – Mark True if data must be usable for BGW calculations. This will change the behavior of the +parser to be stricter with certain criteria.

    • +

  • none_slice_on_error (bool | None) – If True, will return None if an error occurs while parsing a slice +instead of halting the parsing process. This can be useful for parsing files with multiple slices where +some slices may be incomplete or corrupted. If False, all slices may raise errors. If None, only the +final slice can raise an error upon parsing (default behavior)

    • +
+
+
Returns:
+

The JDFTXOutfile object.

+
+
Return type:
+

JDFTXOutfile

+
+
+
+ +
+
+geom_opt: bool[source]
+
+ +
+
+geom_opt_type: str[source]
+
+ +
+
+grad_k: float[source]
+
+ +
+
+has_solvation: bool[source]
+
+ +
+
+homo: float[source]
+
+ +
+
+homo_filling: float[source]
+
+ +
+
+is_gc: bool[source]
+
+ +
+
+is_metal: bool[source]
+
+ +
+
+jsettings_electronic: JMinSettingsElectronic[source]
+
+ +
+
+jsettings_fluid: JMinSettingsFluid[source]
+
+ +
+
+jsettings_ionic: JMinSettingsIonic[source]
+
+ +
+
+jsettings_lattice: JMinSettingsLattice[source]
+
+ +
+
+jstrucs: JOutStructures[source]
+
+ +
+
+kgrid: list[int][source]
+
+ +
+
+lattice: np.ndarray[source]
+
+ +
+
+lattice_final: np.ndarray[source]
+
+ +
+
+lattice_initial: np.ndarray[source]
+
+ +
+
+linmin: float[source]
+
+ +
+
+lumo: float[source]
+
+ +
+
+lumo_filling: float[source]
+
+ +
+
+mu: float[source]
+
+ +
+
+nat: int[source]
+
+ +
+
+nbands: int[source]
+
+ +
+
+nspin: int[source]
+
+ +
+
+nstep: int[source]
+
+ +
+
+pp_type: str[source]
+
+ +
+
+prefix: str[source]
+
+ +
+
+pwcut: float[source]
+
+ +
+
+rhocut: float[source]
+
+ +
+
+semicore_electrons: int[source]
+
+ +
+
+semicore_electrons_uncharged: int[source]
+
+ +
+
+slices: list[JDFTXOutfileSlice][source]
+
+ +
+
+spintype: str[source]
+
+ +
+
+strain: np.ndarray[source]
+
+ +
+
+stress: np.ndarray[source]
+
+ +
+
+structure: Structure[source]
+
+ +
+
+to_dict() → dict[source]
+

Convert the JDFTXOutfile object to a dictionary.

+
+
Returns:
+

A dictionary representation of the JDFTXOutfile object.

+
+
Return type:
+

dict

+
+
+
+ +
+
+tot_magneticmoment: float[source]
+
+ +
+
+total_electrons: float[source]
+
+ +
+
+total_electrons_uncharged: int[source]
+
+ +
+
+trajectory: Trajectory[source]
+
+ +
+
+truncation_radius: float[source]
+
+ +
+
+truncation_type: str[source]
+
+ +
+
+valence_electrons: float[source]
+
+ +
+
+valence_electrons_uncharged: int[source]
+
+ +
+
+xc_func: str[source]
+
+ +
+ +
+
+class JDFTXOutputs(calc_dir: str | ~pathlib.Path, outfile_name: str | ~pathlib.Path | None, store_vars: list[str] = <factory>)[source]
+

Bases: object

+

JDFTx outputs parsing class.

+

A class to read and process JDFTx outputs.

+
+
+from_calc_dir(calc_dir
+

str | Path, store_vars: list[str] = None) -> JDFTXOutputs: +Return JDFTXOutputs object from the path to a directory containing JDFTx out files.

+
+ +
+
+calc_dir[source]
+

The path to the directory containing the JDFTx output files.

+
+
Type:
+

str | Path

+
+
+
+ +
+
+store_vars[source]
+

A list of the names of dump files to read and store.

+
+
Type:
+

list[str]

+
+
+
+ +
+
+paths[source]
+

A dictionary of the paths to the dump files.

+
+
Type:
+

dict[str, Path]

+
+
+
+ +
+
+outfile[source]
+

The JDFTXOutfile object for the out file.

+
+
Type:
+

JDFTXOutfile

+
+
+
+ +
+
+bandProjections[source]
+

The band projections. Stored in shape (nstates, nbands, nproj) where nstates +is nspin*nkpts (nkpts may not equal prod(kfolding) if symmetry reduction occurred), nbands is the number of +bands, and nproj is the number of projections. This shape is chosen instead of the pymatgen convention of +(nspin, nkpt, nbands, nion, nionproj) to save on memory as nonionproj is different depending on the ion +type. This array may also be complex if specified in ‘band-projections-params’ in the JDFTx input, allowing +for pCOHP analysis.

+
+
Type:
+

np.ndarray

+
+
+
+ +
+
+eigenvals[source]
+

The eigenvalues. Stored in shape (nstates, nbands) where nstates is nspin*nkpts (nkpts +may not equal prod(kfolding) if symmetry reduction occurred) and nbands is the number of bands.

+
+
Type:
+

np.ndarray

+
+
+
+ +
+
+orb_label_list[source]
+

A tuple of the orbital labels for the bandProjections file, where the i’th +element describes the i’th orbital. Orbital labels are formatted as “<ion>#<ion-number>(<orbital>)”, +where <ion> is the element symbol of the ion, <ion-number> is the 1-based index of the ion-type in the +structure (ie C#2 would be the second carbon atom, but not necessarily the second ion in the structure), +and <orbital> is a string describing “l” and “ml” quantum numbers (ie “p_x” or “d_yz”). Note that while “z” +corresponds to the “z” axis, “x” and “y” are arbitrary and may not correspond to the actual x and y axes of +the structure. In the case where multiple shells of a given “l” are available within the projections, a +0-based index will appear mimicking a principle quantum number (ie “0px” for first shell and “1px” for +second shell). The actual principal quantum number is not stored in the JDFTx output files and must be +inferred by the user.

+
+
Type:
+

tuple[str, …]

+
+
+
+ +
+
+bandProjections: ndarray | None[source]
+
+ +
+
+calc_dir: str | Path[source]
+
+ +
+
+eigenvals: ndarray | None[source]
+
+ +
+
+classmethod from_calc_dir(calc_dir: str | Path, store_vars: list[str] | None = None, outfile_name: str | Path | None = None) → JDFTXOutputs[source]
+

Create a JDFTXOutputs object from a directory containing JDFTx out files.

+
+
Parameters:
+
    +

  • calc_dir (str | Path) – The path to the directory containing the JDFTx out files.

    • +

  • is_bgw (bool) – Mark True if data must be usable for BGW calculations. This will change the behavior of the +parser to be stricter with certain criteria.

    • +

  • none_slice_on_error (bool) – If True, will return None if an error occurs while parsing a slice instead of +halting the parsing process. This can be useful for parsing files with multiple slices where some slices +may be incomplete or corrupted.

    • +

  • outfile_name (str | Path) – The name of the outfile to use. If None, will search for the outfile in the +calc_dir. If provided, will concatenate with calc_dir as the outfile path. Use this if the calc_dir +contains multiple files that may be mistaken for the outfile (ie multiple files with the ‘.out’ suffix).

    • +
+
+
Returns:
+

The JDFTXOutputs object.

+
+
Return type:
+

JDFTXOutputs

+
+
+
+ +
+
+orb_label_list: tuple[str, ...] | None[source]
+
+ +
+
+outfile: JDFTXOutfile[source]
+
+ +
+
+outfile_name: str | Path | None[source]
+
+ +
+
+paths: dict[str, Path][source]
+
+ +
+
+store_vars: list[str][source]
+
+ +
+ +
+
+ + +
+