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Extend Formula for AtomicPositionsCard & PWInput #194

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merged 3 commits into from
Mar 5, 2023
Merged

Extend Formula for AtomicPositionsCard & PWInput #194

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5469068
Format .jl files
singularitti Feb 24, 2023
593420f
Add ChemicalFormula.jl to deps
singularitti Mar 5, 2023
73bd51c
Extend `Formula` for `AtomicPositionsCard` & `PWInput`
singularitti Mar 5, 2023
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1 change: 1 addition & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ version = "0.8.0"

[deps]
AbInitioSoftwareBase = "df5135bc-470e-46c6-b451-292e27ca5b84"
ChemicalFormula = "069161ab-964a-4228-89a0-7a676f2e1f46"
ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
CrystallographyBase = "93b1d1cd-a8ea-4aa5-adb1-b2407ea0ba8d"
Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
Expand Down
13 changes: 5 additions & 8 deletions docs/make.jl
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Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
using QuantumESPRESSOBase
using Documenter

DocMeta.setdocmeta!(QuantumESPRESSOBase, :DocTestSetup, :(using QuantumESPRESSOBase); recursive=true)
DocMeta.setdocmeta!(
QuantumESPRESSOBase, :DocTestSetup, :(using QuantumESPRESSOBase); recursive=true
)

makedocs(;
modules=[QuantumESPRESSOBase],
Expand All @@ -16,9 +18,7 @@ makedocs(;
),
pages=[
"Home" => "index.md",
"Manual" => [
"Installation Guide" => "installation.md",
],
"Manual" => ["Installation Guide" => "installation.md"],
"Public API" => [
"`QuantumESPRESSOBase` module" => "api/api.md",
"`Inputs` module" => "api/Inputs/Inputs.md",
Expand All @@ -34,7 +34,4 @@ makedocs(;
],
)

deploydocs(;
repo="github.com/MineralsCloud/QuantumESPRESSOBase.jl",
devbranch="main",
)
deploydocs(; repo="github.com/MineralsCloud/QuantumESPRESSOBase.jl", devbranch="main")
11 changes: 11 additions & 0 deletions src/Inputs/PWscf/crystallography.jl
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@@ -1,10 +1,12 @@
using ChemicalFormula: sumformula
using CrystallographyBase: CartesianFromFractional
using LinearAlgebra: det
using Spglib: get_dataset

using ..Inputs: Ibrav

import CrystallographyBase: Cell, crystaldensity
import ChemicalFormula: Formula

export find_symmetry

Expand Down Expand Up @@ -148,3 +150,12 @@ function find_symmetry(input::PWInput, symprec=1e-5)
dataset = get_dataset(cell, symprec)
return dataset
end

function Formula(card::AtomicPositionsCard)
atoms = map(card.data) do position
filter(isletter, position.atom)
end
str = join(symbol^count(atom == symbol for atom in atoms) for symbol in unique(atoms))
return Formula(sumformula(Formula(str)))
end
Formula(input::PWInput) = Formula(input.atomic_positions)