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Ring polymer cellboundary #9

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Ring polymer cellboundary #9

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5c249ce
Add ring-polymer versions of cell boundary methods
Alexsp32 May 2, 2024
860d2e5
Update ring-polymer versions of cell boundary methods
Alexsp32 May 3, 2024
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25 changes: 20 additions & 5 deletions src/cells.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -38,11 +38,11 @@ Base.eltype(::PeriodicCell{T}) where {T} = T

function PeriodicCell(vectors::AbstractMatrix)
vectors = austrip.(vectors)
PeriodicCell{eltype(vectors)}(vectors, [true, true, true])
PeriodicCell{eltype(vectors)}(vectors, [true, true, true])
end

function PeriodicCell(vectors::AbstractMatrix{<:Integer})
PeriodicCell{Float64}(vectors, [true, true, true])
PeriodicCell{Float64}(vectors, [true, true, true])
end

function set_periodicity!(cell::PeriodicCell, periodicity::AbstractVector{Bool})
Expand All @@ -54,9 +54,15 @@ function set_vectors!(cell::PeriodicCell, vectors::AbstractMatrix)
cell.inverse .= inv(cell.vectors)
end

function apply_cell_boundaries!(cell::PeriodicCell, R::AbstractArray{T,3}) where {T}
@views for i in axes(R, 3) # beads
apply_cell_boundaries!(cell, R[:, :, i])
end
end

function apply_cell_boundaries!(cell::PeriodicCell, R::AbstractMatrix)
@views for i in axes(R, 2) # atoms
apply_cell_boundaries!(cell, R[:,i])
apply_cell_boundaries!(cell, R[:, i])
end
end
apply_cell_boundaries!(::InfiniteCell, ::AbstractArray) = nothing
Expand All @@ -71,14 +77,23 @@ function apply_cell_boundaries!(cell::PeriodicCell, R::AbstractVector)
mul!(R, cell.vectors, cell.tmp_vector1)
end

function check_atoms_in_cell(cell::PeriodicCell, R::AbstractArray{T,3}) where {T}
@views for i in axes(R, 3) # beads
if !check_atoms_in_cell(cell, R[:, :, i])
return false
end
end
return true
end

"""
check_atoms_in_cell(cell::PeriodicCell, R::AbstractMatrix)::Bool

True if all atoms are inside the cell, false otherwise.
"""
function check_atoms_in_cell(cell::PeriodicCell, R::AbstractMatrix)::Bool
@views for i in axes(R, 2) # atoms
mul!(cell.tmp_vector1, cell.inverse, R[:,i])
mul!(cell.tmp_vector1, cell.inverse, R[:, i])
@. cell.tmp_bools = (cell.tmp_vector1 > 1) | (cell.tmp_vector1 < 0)
any(cell.tmp_bools) && return false
end
Expand All @@ -89,4 +104,4 @@ function evaluate_periodic_distance(cell::PeriodicCell, r1::AbstractVector, r2::
mul!(cell.tmp_vector1, cell.inverse, r1)
mul!(cell.tmp_vector2, cell.inverse, r2)
evaluate(periodic_distance, cell.tmp_vector1, cell.tmp_vector2)
end
end
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