Utility

Shared utility types and helper functions used across file-format readers, writers, and conversion pipelines.

Constants

Physical constants and package-wide defaults.

WannierIO.Bohr Constant

Bohr radius in Angstrom unit.

This is the default CODATA2006 value in W90 src/constants.F90.

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WannierIO.Bohr_QE Constant

Bohr radius in Angstrom unit.

This is the default (Physical constants, SI (NIST 2018)) value in QE Modules/constants.f90.

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Helper functions

General helpers for parsing, headers, TOML conversion, and comparisons.

WannierIO.default_header Method

Default header for writing wannier90 files.

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WannierIO.from_toml Method

I store atoms_frac and kpoint_path as Vector of StringVec3. However, TOML.print does not accept Pair (specifically, StringVec3); instead, I convert StringVec3 to Dict in write_win with toml format. On reading I convert it back.

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WannierIO.from_toml Method

Fallback to doing nothing.

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WannierIO.istoml Method

julia

istoml(io)

Return true if the input can be parsed as TOML, otherwise false.

This helper catches TOML.ParserError and returns false for invalid TOML content while rethrowing other unexpected errors.

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WannierIO.to_toml Method

julia

to_toml(x)

Convert types for TOML writing.

Examples

julia

using TOML
x = Dict(:a => (; b=1))
TOML.print(to_toml, x)

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WannierIO.write_toml Function

Write kwargs into io as a TOML file.

This is more convenient than TOML.print, in that:

Do some type conversion before writing.
Keep the order of kwargs, whereas TOML.print always requires a Dict which will change the order of keys.

Examples

julia

write_toml(stdout; b=2, a=1)

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WannierIO.format_indices Method

julia

format_indices(indices)

Convert a vector of integers to a string of comma-separated indices or range.

E.g., the exclude_bands tag of win file.

Examples

julia

julia> format_indices([1, 2, 5, 8, 9, 10])
"1-2 5 8-10"

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WannierIO.nextline Method

julia

nextline(io; comment, lower)

Read a line from the input stream, ignoring empty lines (containing only whitespace).

Returns the first non-empty line found, or empty string if EOF is reached.

Arguments

io::IO: input stream

Keyword Arguments

comment::Bool=false: if true, keep comments (starting with ! or #)
lower::Bool=false: if true, convert the returned string to lowercase

Returns

A string containing the first non-empty line, with leading and trailing whitespace removed, or empty string if EOF is reached.

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WannierIO.parse_bool Method

julia

parse_bool(s)

Parse a string as bool.

This is capable of parsing Fortran outputs, e.g., .true., .false., true, T.

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WannierIO.parse_bool Method

julia

parse_bool(i)

Parse an integer as bool.

0: false
1 or -1: true

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WannierIO.parse_float Method

julia

parse_float(s)

Parse a string as Float64.

The is capable of parsing Fortran outputs, e.g. 1.0D-10, to the ordinary 1e-10.

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WannierIO.parse_indices Method

julia

parse_indices(str)

Parse a string of comma-separated indices or range into a vector of integers.

E.g., the exclude_bands tag of win file.

Examples

julia

julia> parse_indices("1-2, 5,8 -10")
6-element Vector{Int64}:
  1
  2
  5
  8
  9
 10
julia> parse_indices("1-2 5,8 -10")

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WannierIO.parse_vector Method

julia

parse_vector(io, T, n_elements)

Parse a vector of n_elements elements of type T from io.

Arguments

io: input stream
T: type of elements
n_elements::Int: total number of elements

Examples

Suppose a file demo.txt has the following content:

julia

1  2  3  4  5  6  7  8  9  10
11 12 13 14 15 16 17 18 19 20
21 22 23

Then the following code parses the file and return a vector filled with 1 to 23:

julia

julia> vector = open("demo.txt") do io
    parse_vector(io, Int, 23)
end

The number of elements in each line can be different.

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WannierIO.strip_comment Method

julia

strip_comment(line; spaces)

Strip comments (! or #) from a line.

Arguments

line::AbstractString: input line

Keyword Arguments

spaces::Bool=false: if true, preserve leading and trailing whitespace.

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WannierIO._isapprox Method

julia

_isapprox(a, b)

Compare two (same-type) structs.

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Low-level helpers for formatted/unformatted Fortran IO.

WannierIO.isbinary Method

julia

isbinary(filename)

Check if the file is in binary format.

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WannierIO.isbinary Method

julia

isbinary(chars)

Check if a sequence of chars is binary.

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WannierIO.isbinary Method

julia

isbinary(io)

Check if the IO is in binary format.

This function preserves the stream position for seekable IO.

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File formats

Format tags used by high-level APIs for dispatch and auto-detection.

WannierIO.AbstractFileFormat Type

Abstract supertype for all explicit file format tags used by WannierIO.

These tags are lightweight dispatch objects. Pass them to functions like read_eig, write_amn, read_win, etc. when you want to choose a format explicitly instead of relying on auto detection.

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WannierIO.AbstractFortranFormat Type

Abstract supertype for Fortran-style matrix/data file formats.

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WannierIO.AbstractW90InputFormat Type

Abstract supertype for Wannier90 small input-file formats such as win and nnkp.

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WannierIO.FortranBinary Type

Fortran unformatted record-based IO.

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WannierIO.FortranBinaryStream Type

Fortran unformatted IO with stream access.

For example, file written using these Fortran code:

fortran

OPEN(UNIT=11, FILE="ustream.demo", STATUS="NEW", ACCESS="STREAM", FORM="UNFORMATTED")

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WannierIO.FortranText Type

Fortran formatted text IO.

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WannierIO.HDF5Format Type

HDF5 storage format for tight-binding data.

Requires loading the HDF5 package.

Note

The matrices written in the HDF5 is row-major (Python/C-style) order, which is different from the column-major (Julia/Fortran-style) order used throughout the rest of WannierIO. If you use the read_w90_tb and write_w90_tb functions to read/write HDF5 files, this is handled automatically. However, if you want to load them in python, be aware of this difference accordingly.

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WannierIO.JLD2Format Type

JLD2 storage format for tight-binding data.

Requires loading the JLD2 package.

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WannierIO.W90Dat Type

Native Wannier90 tight-binding text format (.dat files written by Wannier90).

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WannierIO.W90InputText Type

Plain-text format for Wannier90 win and nnkp files.

The default win and nnkp files are text files, but they are not simple tables that can be parsed with readdlm. This format tag selects the custom Wannier90 text parser used by functions such as read_win and read_nnkp.

Compared with W90InputToml, this format is for the native Wannier90 input syntax. Compared with FortranText, it is for small structured input files rather than large numeric matrix dumps such as amn, mmn, or eig.

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WannierIO.W90InputToml Type

TOML format for Wannier90 win and nnkp files.

This allows win or nnkp data to be stored in a standard TOML representation that can be parsed by generic TOML tooling.

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WannierIO.ZarrFormat Type

Zarr storage format for tight-binding data.

Requires loading the Zarr package.

Note

Similar to the HDF5 format, the matrices written in Zarr are row-major (Python/C-style) order. If you use the read_w90_tb and write_w90_tb functions to read/write Zarr files, this is handled automatically. However, if you want to load them in python, be aware of this difference accordingly.

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WannierIO.ZarrZipFormat Type

Zarr storage format for tight-binding data, zipped into a single file.

Requires loading the Zarr package.

Note

Note the row-major order of the matrices in this format, as described in the documentation of ZarrFormat.

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WannierIO.detect_fortran_format Method

julia

detect_fortran_format(file; stream=false)

Infer a Fortran-format tag from file using isbinary.

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WannierIO.detect_operator_format Method

julia

detect_operator_format(path)

Infer an operator storage format tag from the file extension of path:

.h5 / .hdf5 → HDF5Format
.jld2 → JLD2Format
.zarr → ZarrFormat
.zarr.zip → ZarrZipFormat

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WannierIO.detect_w90input_format Method

julia

detect_w90input_format(file)

Infer a win/nnkp format tag from file using istoml.

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WannierIO.format_name Method

julia

format_name(format)

Return a short human-readable name for a FileFormat tag.

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WannierIO.fortran_format Method

julia

fortran_format(; binary=false, stream=false)

Construct a Fortran-format tag.

binary=false returns FortranText
binary=true, stream=false returns FortranBinary
binary=true, stream=true returns FortranBinaryStream

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WannierIO.w90input_format Method

julia

w90input_format(; toml=false)

Construct a format tag for win/nnkp-style input files.

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Package docstring

Top-level package docstring and exported-symbol overview.

WannierIO.WannierIO Module

WannierIO.jl: a package for reading and writing Wannier90 file formats.

WannierIO.jl

A Julia package for reading/writing Wannier90 file formats.

The package is designed to be minimalistic to allow easy reuse in other packages.

Quick examples

julia

using WannierIO

amn = read_amn("silicon.amn")
write_amn("silicon_2.amn", amn.A; amn.header)

chk = read_chk("silicon.chk")
write_chk("silicon_2.chk", chk; binary=true)

Related packages

Wannier.jl: Wannierization and Wannier interpolation. The IO part of Wannier.jl was isolated and moved into this package.

Exported functions:

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Page index

WannierIO.WannierIO
WannierIO.Bohr
WannierIO.Bohr_QE
WannierIO.AbstractFileFormat
WannierIO.AbstractFortranFormat
WannierIO.AbstractW90InputFormat
WannierIO.FortranBinary
WannierIO.FortranBinaryStream
WannierIO.FortranText
WannierIO.HDF5Format
WannierIO.JLD2Format
WannierIO.W90Dat
WannierIO.W90InputText
WannierIO.W90InputToml
WannierIO.ZarrFormat
WannierIO.ZarrZipFormat
WannierIO._isapprox
WannierIO.default_header
WannierIO.detect_fortran_format
WannierIO.detect_operator_format
WannierIO.detect_w90input_format
WannierIO.format_indices
WannierIO.format_name
WannierIO.fortran_format
WannierIO.from_toml
WannierIO.from_toml
WannierIO.isbinary
WannierIO.isbinary
WannierIO.isbinary
WannierIO.istoml
WannierIO.nextline
WannierIO.parse_bool
WannierIO.parse_bool
WannierIO.parse_float
WannierIO.parse_indices
WannierIO.parse_vector
WannierIO.strip_comment
WannierIO.to_toml
WannierIO.w90input_format
WannierIO.write_toml

Utility ​

Constants ​

Helper functions ​

Fortran related ​

File formats ​

Package docstring ​

Page index ​

Utility

Constants

Helper functions

Fortran related

File formats

Package docstring

Page index