### Read and write Quantum ESPRESSO input files

Source: https://github.com/atomology/quantumespressoio.jl/blob/main/README.md

Demonstrates reading a pw.in file into a dictionary-like structure and writing it back to a new file.

```julia
using QuantumEspressoIO

julia> pw = read_pw_in("pw.in")

julia> pw["atomic_positions"]["atoms"]
2-element Vector{String}:
 "Si"
 "Si"

julia> write_pw_in("pw2.in", pw)
```

--------------------------------

### Write pw.x Input Files with QuantumEspressoIO

Source: https://context7.com/atomology/quantumespressoio.jl/llms.txt

Generates Quantum ESPRESSO pw.x input files from Julia dictionaries. Use OrderedDict to maintain parameter order. Supports writing to files or IO streams.

```julia
using QuantumEspressoIO
using OrderedCollections

inputs = OrderedDict(
    "control" => OrderedDict(
        "calculation" => "scf",
        "prefix" => "SiO2",
        "outdir" => "./out",
        "pseudo_dir" => "./pseudo",
    ),
    "system" => OrderedDict(
        "ibrav" => 0,
        "nat" => 3,
        "ntyp" => 2,
        "ecutwfc" => 40.0,
        "ecutrho" => 400.0,
    ),
    "electrons" => OrderedDict(
        "conv_thr" => 1e-8,
        "mixing_beta" => 0.7,
    ),
    "atomic_species" => Dict(
        "species" => ["Si", "O"],
        "masses" => [28.0855, 15.999],
        "pseudos" => ["Si.upf", "O.upf"],
    ),
    "atomic_positions" => Dict(
        "option" => "crystal",
        "atoms" => ["Si", "O", "O"],
        "positions" => [
            [0.0, 0.0, 0.0],
            [0.25, 0.25, 0.25],
            [0.75, 0.75, 0.75],
        ],
    ),
    "cell_parameters" => Dict(
        "option" => "angstrom",
        "cell" => [
            [4.91, 0.0, 0.0],
            [0.0, 4.91, 0.0],
            [0.0, 0.0, 5.40],
        ],
    ),
    "k_points" => Dict(
        "option" => "automatic",
        "kgrid" => [6, 6, 4],
        "kgrid_shift" => [0, 0, 0],
    ),
)

# Write to file
write_pw_in("pw.in", inputs)

# Or write to stdout/IOBuffer
write_pw_in(stdout, inputs)
# Output:
# &control
#   calculation = 'scf'
#   prefix = 'SiO2'
#   outdir = './out'
#   pseudo_dir = './pseudo'
# /
# &system
#   ibrav = 0
#   nat = 3
#   ntyp = 2
#   ecutwfc = 40.0
#   ecutrho = 400.0
# /
# ... 
```

--------------------------------

### Read Projected Density of States Files

Source: https://context7.com/atomology/quantumespressoio.jl/llms.txt

Reads output files from QE's projwfc.x for projected density of states (PDOS) analysis. Supports reading projection coefficients, total PDOS, and atom-projected PDOS. The data can be used for plotting and detailed analysis of electronic states.

```julia
using QuantumEspressoIO: read_projwfc_up, read_pdos_tot, read_pdos_atm, read_projwfc_dos

# Read projwfc_up file (contains projection coefficients)
# params, orbitals, projections = read_projwfc_up("projwfc.projwfc_up")

# Read total PDOS file
# columns, header = read_pdos_tot("prefix")  # reads prefix.pdos_tot

# Read atom-projected PDOS files
# pdos_data = read_pdos_atm("prefix")

# Example: plotting PDOS
# columns, header = read_pdos_tot("silicon")
# energy = columns[:, 1]
# total_dos = columns[:, 2]
# # Use your favorite plotting library
# # plot(energy, total_dos, xlabel="Energy (eV)", ylabel="DOS")
```

--------------------------------

### Read Fortran Namelists with QuantumEspressoIO

Source: https://context7.com/atomology/quantumespressoio.jl/llms.txt

Handles generic Fortran namelist files, useful for various Quantum ESPRESSO programs. Can optionally return remaining lines after parsing namelists.

```julia
using QuantumEspressoIO
using OrderedCollections

# Reading namelists from a file
io = IOBuffer("""
&bands
    prefix = 'silicon'
    outdir = './out'
    filband = 'bands.dat'
    lsym = .true.
/
additional content here
")

# Read namelists, optionally returning remaining lines
namelists, others = read_namelists(io; all_lines=true)

println(namelists["bands"]["prefix"])   # "silicon"
println(namelists["bands"]["lsym"])     # true
println(others)                          # ["additional content here"]
```

--------------------------------

### Read and Write Namelists

Source: https://context7.com/atomology/quantumespressoio.jl/llms.txt

Demonstrates reading a single namelist from an IOBuffer and writing a structured OrderedDict of namelists to standard output. Ensure the input namelist format is correct for reading.

```julia
using QuantumEspressoIO
using DataStructures: OrderedDict

# Read a single namelist by name
io = IOBuffer("""
&input
    a = 1
    b = 2.5
    c = 'test'
    d = .true.
/
""")
params = read_namelist(io, "input")
println(params["a"])
println(params["b"])
println(params["c"])
println(params["d"])

# Writing namelists
inputs = OrderedDict(
    "control" => OrderedDict("calculation" => "scf", "prefix" => "qe"),
    "system" => OrderedDict("ecutwfc" => 30.0, "ecutrho" => 300.0),
    "electrons" => OrderedDict("mixing_beta" => 0.7),
)
write_namelists(stdout, inputs)
```

--------------------------------

### Read pw.x Input Files with QuantumEspressoIO

Source: https://context7.com/atomology/quantumespressoio.jl/llms.txt

Parses Quantum ESPRESSO pw.x input files, extracting namelists and cards. Use this function to programmatically access data from existing input files.

```julia
using QuantumEspressoIO

# Read from an IOBuffer (or use a filename string directly)
io = IOBuffer("""
    &control
        calculation = \"scf\"
        prefix = \"silicon\"
        outdir = \"./tmp\"
        pseudo_dir = \"./pseudo\"
    /
    &system
        ibrav = 0
        nat = 2
        ntyp = 1
        ecutwfc = 30.0
    /
    &electrons
        conv_thr = 1e-8
    /
    ATOMIC_SPECIES
    Si       28.0855  Si.upf
    ATOMIC_POSITIONS crystal
    Si        0.0000000000      0.0000000000      0.0000000000
    Si        0.2500000000      0.2500000000      0.2500000000
    CELL_PARAMETERS angstrom
    5.43  0.00  0.00
    0.00  5.43  0.00
    0.00  0.00  5.43
    K_POINTS automatic
    8 8 8    0 0 0
")

inputs = read_pw_in(io)

# Access parsed data
println(inputs["control"]["calculation"])  # "scf"
println(inputs["system"]["ecutwfc"])       # 30.0
println(inputs["atomic_species"]["species"])  # ["Si"]
println(inputs["atomic_positions"]["atoms"])  # ["Si", "Si"]
println(inputs["atomic_positions"]["positions"])  # [[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]]
println(inputs["cell_parameters"]["cell"])  # [[5.43, 0.0, 0.0], [0.0, 5.43, 0.0], [0.0, 0.0, 5.43]]
println(inputs["k_points"]["kgrid"])       # [8, 8, 8]
```

--------------------------------

### QuantumEspressoIO Band Structure Module

Source: https://github.com/atomology/quantumespressoio.jl/blob/main/docs/src/api/band.md

Documentation for the band structure module within the QuantumEspressoIO package.

```APIDOC
## QuantumEspressoIO Band Structure Module

### Description
This module provides functionality for handling band structure data within the QuantumEspressoIO package.

### Module
QuantumEspressoIO.band

### Usage
This module is part of the QuantumEspressoIO ecosystem and is used to parse and manipulate band structure output files from Quantum Espresso calculations.
```

--------------------------------

### Read Quantum Espresso XML Output

Source: https://context7.com/atomology/quantumespressoio.jl/llms.txt

Parses the data-file-schema.xml file generated by Quantum Espresso's pw.x. This function extracts comprehensive calculation results including lattice, atomic structure, k-points, Fermi energy, and eigenvalues. The output is a NamedTuple.

```julia
using QuantumEspressoIO: read_pw_xml

# Read XML output from pw.x calculation
# result = read_pw_xml("prefix.save/data-file-schema.xml")

# Example usage after reading:
# println("Lattice vectors (Angstrom):")
# println(result.lattice)
# println("Fermi energy: $(result.fermi_energy) eV")
# println("Number of k-points: $(length(result.kpoints))")
# println("Band energies at Gamma: $(result.eigenvalues[1])")
```

--------------------------------

### Read Quantum Espresso Binary Wavefunction Files

Source: https://context7.com/atomology/quantumespressoio.jl/llms.txt

Reads Quantum Espresso's binary wavefunction files (wfc.dat). This function returns Miller indices for G-vectors and a list of complex coefficients for each band. The output is suitable for further analysis of electronic wavefunctions.

```julia
using QuantumEspressoIO: read_wfc_dat

# Read wavefunction data from binary file
# miller, evc_list = read_wfc_dat("wfc1.dat")

# Example usage:
# println("Number of G-vectors: $(size(miller, 2))")
# println("Number of bands: $(length(evc_list))")
# println("First band coefficients: $(evc_list[1][1:5])")
```

--------------------------------

### Read Band Structure Data

Source: https://context7.com/atomology/quantumespressoio.jl/llms.txt

Reads band structure data from a string buffer or file generated by QE's bands.x. Also shows how to identify high-symmetry k-points from a given path. Ensure the input format matches the expected structure.

```julia
using QuantumEspressoIO: read_band_dat, guess_high_symmetry_kpoints

# Read band data from bands.x output
io = IOBuffer("""&plot nbnd=  4, nks=  3 /
0.0  0.0  0.0
-5.5  -1.2   3.4   5.6
0.25  0.0  0.0
-5.4  -1.1   3.5   5.7
0.5  0.0  0.0
-5.2  -0.9   3.7   5.9
""")

result = read_band_dat(io)
println(result.kpoints)
println(result.eigenvalues)

# Identify high-symmetry points in k-path
kpoints = [
    [0.0, 0.0, 0.0],    # Gamma
    [0.1, 0.0, 0.0],
    [0.2, 0.0, 0.0],
    [0.5, 0.0, 0.0],    # X (turn point)
    [0.5, 0.1, 0.0],
    [0.5, 0.5, 0.0],    # M
]
symm_indices = guess_high_symmetry_kpoints(kpoints)
println(symm_indices)
```

--------------------------------

### Parse open_grid.x Output

Source: https://context7.com/atomology/quantumespressoio.jl/llms.txt

Parses k-point grids and weights from open_grid.x output for use in Wannier90.

```julia
using QuantumEspressoIO

io = IOBuffer("""
     EXX: q-point mesh:     4    4    4
     EXX: setup a grid of 64 q-points centered on each k-point

     List to be put in the .win file of wannier90: (already in crystal/fractionary coordinates):
    0.000000000000000    0.000000000000000    0.000000000000000    0.0156250000
    0.000000000000000    0.000000000000000    0.250000000000000    0.0156250000
    0.000000000000000    0.250000000000000    0.000000000000000    0.0156250000
    0.250000000000000    0.000000000000000    0.000000000000000    0.0156250000
""")
```

--------------------------------

### Extract Relaxed Structures from pw.x

Source: https://context7.com/atomology/quantumespressoio.jl/llms.txt

Extracts cell parameters and atomic positions from pw.x relaxation or molecular dynamics output files.

```julia
using QuantumEspressoIO: read_structures
```

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