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module UnitCells
using Random
using Printf
import ..CrystFEL: libcrystfel
export UnitCell, LatticeType, CenteringType, UniqueAxis
export TriclinicLattice, MonoclinicLattice, OrthorhombicLattice
export TetragonalLattice, HexagonalLattice, RhombohedralLattice, CubicLattice
export PrimitiveCell, ACenteredCell, BCenteredCell, CCenteredCell
export BodyCenteredCell, FaceCenteredCell, RhombohedralCell, RhombohedralCellOnHexagonalAxes
export NoUniqueAxis, UnknownUniqueAxis, UniqueAxisA, UniqueAxisB, UniqueAxisC
export rotatecell
# Represents the real C-side (opaque) structure.
mutable struct InternalUnitCell end
# The Julia-side structure, needed to house the pointer to the C structure
# Without this, we would only ever have a Ptr{DataTemplate}, not a DataTemplate.
mutable struct UnitCell
internalptr::Ptr{InternalUnitCell}
end
"""
Enumeration of the seven Bravais lattice types: `TriclinicLattice`,
`MonoclinicLattice`, `OrthorhombicLattice`, `TetragonalLattice`,
`RhombohedralLattice`, `HexagonalLattice`, `CubicLattice`.
"""
@enum LatticeType begin
TriclinicLattice
MonoclinicLattice
OrthorhombicLattice
TetragonalLattice
RhombohedralLattice
HexagonalLattice
CubicLattice
end
"""
Enumeration of unit cell centering possibilities: `PrimitiveCell`,
`ACenteredCell`, `BCenteredCell`, `CCenteredCell`, `BodyCenteredCell`
(I-centering), `FaceCenteredCell` (F-centering), and `RhombohedralCell`
(R-centering, primitive rhombohedral cell). `RhombohedralCellOnHexagonalAxes`
indicates "H-centering" as used by the protein data bank, which is different
from the "triple hexagonal cell" described in the International Tables.
"""
@enum CenteringType begin
PrimitiveCell = Int('P')
ACenteredCell = Int('A')
BCenteredCell = Int('B')
CCenteredCell = Int('C')
BodyCenteredCell = Int('I')
FaceCenteredCell = Int('F')
RhombohedralCell = Int('R')
RhombohedralCellOnHexagonalAxes = Int('H')
end
"""
Enumeration of unique axis possibilities. The possibilities are `UniqueAxisA`,
`UniqueAxisB` and `UniqueAxisC`. Alternatively, use `NoUniqueAxis` if the type
of unit cell does not have a unique axis (triclinic, orthorhombic, cubic or
rhombohedral). `UnknownUniqueAxis` means that the unique axis is not known.
"""
@enum UniqueAxis begin
NoUniqueAxis = Int('*')
UnknownUniqueAxis = Int('?')
UniqueAxisA = Int('a')
UniqueAxisB = Int('b')
UniqueAxisC = Int('c')
end
"""
UnitCell(latticetype, centering, uniqueaxis, a, b, c, α, β, γ)
Creates a CrystFEL UnitCell, in an undefined orientation, from the given
parameters. The axis lengths (a, b, c) should be in *Ångstroms*, and the
angles (α, β, γ) should be in *degrees* - note that this is different to the
equivalent function in CrystFEL's C API.
See the documentation for `LatticeType`, `CenteringType` and `UniqueAxis` for
possible values. You can also use the characters `'a'`, `'b'` and `'c'` for
`uniqueaxis`, or `'P'`, `'A'`, `'B'`, `'C'`, `'I'`, `'F'`, `'R'` and `'H`' for
`centering.
Corresponds to CrystFEL C API function `cell_new_from_parameters` with follow-up
calls to `cell_set_centering`, `cell_set_lattice_type` and `cell_set_unique_axis`.
"""
function UnitCell(latticetype, centering, uniqueaxis, a, b, c, α, β, γ)
ninety(a) = isapprox(a, 90, atol=0.1)
if latticetype == OrthorhombicLattice
if !(ninety(α) && ninety(β) && ninety(γ))
throw(ArgumentError("All angles must be 90°"))
end
elseif latticetype == TetragonalLattice
if !(ninety(α) && ninety(β) && ninety(γ))
throw(ArgumentError("All angles must be 90°"))
end
elseif latticetype == CubicLattice
if !(ninety(α) && ninety(β) && ninety(γ))
throw(ArgumentError("All angles must be 90°"))
end
elseif latticetype == HexagonalLattice
if uniqueaxis == UniqueAxisA
if !isapprox(b, c, rtol=0.01)
throw(ArgumentError("b and c lengths should be equal"))
end
elseif uniqueaxis == UniqueAxisB
if !isapprox(a, c, rtol=0.01)
throw(ArgumentError("a and c lengths should be equal"))
end
elseif uniqueaxis == UniqueAxisC
if !isapprox(a, b, rtol=0.01)
throw(ArgumentError("a and b lengths should be equal"))
end
else
throw(ArgumentError("Hexagonal cell requires a unique axis"))
end
end
out = ccall((:cell_new_from_parameters, libcrystfel),
Ptr{InternalUnitCell},
(Cdouble,Cdouble,Cdouble,Cdouble,Cdouble,Cdouble),
a/1e10, b/1e10, c/1e10, deg2rad(α), deg2rad(β), deg2rad(γ))
if out == C_NULL
throw(ArgumentError("Failed to create unit cell"))
end
ccall((:cell_set_centering, libcrystfel),
Cvoid, (Ptr{InternalUnitCell},Cchar),
out, centering)
ccall((:cell_set_unique_axis, libcrystfel),
Cvoid, (Ptr{InternalUnitCell},Cchar),
out, uniqueaxis)
ccall((:cell_set_lattice_type, libcrystfel),
Cvoid, (Ptr{InternalUnitCell},Cint),
out, latticetype)
cell = UnitCell(out)
finalizer(cell) do x
ccall((:cell_free, libcrystfel),
Cvoid, (Ptr{InternalUnitCell},), x.internalptr)
end
return cell
end
"""
UnitCell(latticetype, centering, a, b, c, α, β, γ)
A convenience constructor which attempts to determine the unique axis
automatically from the cell parameters. If the unique axis is not obvious,
an `ArgumentError` will be thrown.
"""
function UnitCell(latticetype, centering, a, b, c, α, β, γ)
notninety(a) = !isapprox(a, 90, atol=0.5)
ninety(a) = isapprox(a, 90, atol=0.1)
onetwenty(a) = isapprox(a, 120, atol=0.1)
if latticetype == TriclinicLattice
ua = NoUniqueAxis
elseif latticetype == OrthorhombicLattice
ua = NoUniqueAxis
elseif latticetype == RhombohedralLattice
ua = NoUniqueAxis
elseif latticetype == CubicLattice
ua = NoUniqueAxis
elseif latticetype == MonoclinicLattice
if notninety(α) && ninety(β) && ninety(γ)
ua = UniqueAxisA
elseif ninety(α) && notninety(β) && ninety(γ)
ua = UniqueAxisB
elseif ninety(α) && ninety(β) && notninety(γ)
ua = UniqueAxisC
else
throw(ArgumentError("Can't determine unique axis"))
end
elseif latticetype == TetragonalLattice
if isapprox(b, c, rtol=0.01) && !isapprox(a, b, rtol=0.05)
ua = UniqueAxisA
elseif isapprox(a, c, rtol=0.01) && !isapprox(a, b, rtol=0.05)
ua = UniqueAxisB
elseif isapprox(a, b, rtol=0.01) && !isapprox(c, b, rtol=0.05)
ua = UniqueAxisC
else
throw(ArgumentError("Can't determine unique axis"))
end
elseif latticetype == HexagonalLattice
if onetwenty(α) && ninety(β) && ninety(γ)
ua = UniqueAxisA
elseif ninety(α) && onetwenty(β) && ninety(γ)
ua = UniqueAxisB
elseif ninety(α) && ninety(β) && onetwenty(γ)
ua = UniqueAxisC
else
throw(ArgumentError("Can't determine unique axis"))
end
end
UnitCell(latticetype, centering, ua, a, b, c, α, β, γ)
end
"""
UnitCell(latticetype, centering, a, b, c)
Construct a `UnitCell` for an `OrthorhombicLattice`, `TetragonalLattice` or
`CubicLattice`.
"""
function UnitCell(latticetype::LatticeType, centering::CenteringType, a::Real, b::Real, c::Real)
if latticetype in (OrthorhombicLattice, TetragonalLattice, CubicLattice)
UnitCell(latticetype, centering, a, b, c, 90, 90, 90)
else
throw(ArgumentError("More parameters needed for this type of lattice"))
end
end
"""
UnitCell(CubicLattice, centering, a)
Construct a `UnitCell` for a `CubicLattice`.
"""
function UnitCell(latticetype::LatticeType, centering::CenteringType, a::Real)
if latticetype == CubicLattice
UnitCell(latticetype, centering, a, a, a, 90, 90, 90)
else
throw(ArgumentError("More parameters needed for this type of lattice"))
end
end
"""
UnitCell(RhombohedralLattice, a, α)
Construct a `UnitCell` for a `RhombohedralLattice`.
"""
function UnitCell(latticetype::LatticeType, a::Real, α::Real)
if latticetype == RhombohedralLattice
UnitCell(latticetype, RhombohedralCell, a, a, a, α, α, α)
else
throw(ArgumentError("More parameters needed for this type of lattice"))
end
end
function getlatticetype(cell)
lt = ccall((:cell_get_lattice_type, libcrystfel),
Cint, (Ptr{InternalUnitCell},), cell.internalptr)
cen = ccall((:cell_get_centering, libcrystfel),
Cchar, (Ptr{InternalUnitCell},), cell.internalptr)
ua = ccall((:cell_get_unique_axis, libcrystfel),
Cchar, (Ptr{InternalUnitCell},), cell.internalptr)
return LatticeType(lt),CenteringType(cen),UniqueAxis(ua)
end
function getcellparams(cell)
let a=Ref{Cdouble}(0),
b=Ref{Cdouble}(0),
c=Ref{Cdouble}(0),
α=Ref{Cdouble}(0),
β=Ref{Cdouble}(0),
γ=Ref{Cdouble}(0)
ccall((:cell_get_parameters, libcrystfel),
Cvoid, (Ptr{InternalUnitCell},
Ref{Cdouble},Ref{Cdouble},Ref{Cdouble},
Ref{Cdouble},Ref{Cdouble},Ref{Cdouble}),
cell.internalptr, a, b, c, α, β, γ)
return (a=a[], b=b[], c=c[], α=α[], β=β[], γ=γ[])
end
end
# Returns the direct-space basis vectors as a Julia matrix
# See matrix-notation.pdf for information. This returns an "M-matrix".
function directcartesianmatrix(uc)
ax = Ref{Cdouble}(0)
ay = Ref{Cdouble}(0)
az = Ref{Cdouble}(0)
bx = Ref{Cdouble}(0)
by = Ref{Cdouble}(0)
bz = Ref{Cdouble}(0)
cx = Ref{Cdouble}(0)
cy = Ref{Cdouble}(0)
cz = Ref{Cdouble}(0)
out = @ccall libcrystfel.cell_get_cartesian(uc.internalptr::Ptr{InternalUnitCell},
ax::Ref{Cdouble}, ay::Ref{Cdouble}, az::Ref{Cdouble},
bx::Ref{Cdouble}, by::Ref{Cdouble}, bz::Ref{Cdouble},
cx::Ref{Cdouble}, cy::Ref{Cdouble}, cz::Ref{Cdouble})::Cint
if out != 0
throw(ErrorException("Failed to convert cell parameters"))
end
return [ax[] bx[] cx[]; ay[] by[] cy[]; az[] bz[] cz[]]
end
# Returns the reciprocal-space basis vectors as a Julia matrix
# See matrix-notation.pdf for information. This returns an "R-matrix".
function reciprocalcartesianmatrix(uc)
ax = Ref{Cdouble}(0)
ay = Ref{Cdouble}(0)
az = Ref{Cdouble}(0)
bx = Ref{Cdouble}(0)
by = Ref{Cdouble}(0)
bz = Ref{Cdouble}(0)
cx = Ref{Cdouble}(0)
cy = Ref{Cdouble}(0)
cz = Ref{Cdouble}(0)
out = @ccall libcrystfel.cell_get_reciprocal(uc.internalptr::Ptr{InternalUnitCell},
ax::Ref{Cdouble}, ay::Ref{Cdouble}, az::Ref{Cdouble},
bx::Ref{Cdouble}, by::Ref{Cdouble}, bz::Ref{Cdouble},
cx::Ref{Cdouble}, cy::Ref{Cdouble}, cz::Ref{Cdouble})::Cint
if out != 0
throw(ErrorException("Failed to convert cell parameters"))
end
return [ax[] ay[] az[]; bx[] by[] bz[]; cx[] cy[] cz[]]
end
function Base.propertynames(uc::UnitCell; private=false)
(:a, :b, :c, :α, :β, :γ, :latticetype, :cellparams,
:directcartesian, :reciprocalcartesian,
:internalptr)
end
function Base.getproperty(uc::UnitCell, name::Symbol)
if name === :internalptr
getfield(uc, :internalptr)
elseif name === :cellparams
return getcellparams(uc)
elseif name === :latticetype
return getlatticetype(uc)
elseif name === :a
return getcellparams(uc).a
elseif name === :b
return getcellparams(uc).b
elseif name === :c
return getcellparams(uc).c
elseif name === :α
return getcellparams(uc).α
elseif name === :β
return getcellparams(uc).β
elseif name === :γ
return getcellparams(uc).γ
elseif name === :directcartesian
return directcartesianmatrix(uc)
elseif name === :reciprocalcartesian
return reciprocalcartesianmatrix(uc)
end
end
function Base.show(io::IO, uc::UnitCell)
write(io, "UnitCell(")
lt,cen,ua = uc.latticetype
show(io, lt); write(io, ", ")
show(io, cen); write(io, ", ")
show(io, ua); write(io, ",\n ")
@printf(io, "%.3f Å, %.3f Å, %.3f Å, %.3f°, %.3f°, %.3f°",
uc.a*1e10, uc.b*1e10, uc.c*1e10,
rad2deg(uc.α), rad2deg(uc.β), rad2deg(uc.γ))
write(io, ")")
end
# This type is for talking to libcrystfel, and is named to avoid conflicting
# with other quaternion libraries.
mutable struct CrystFELQuaternion
w::Cdouble
x::Cdouble
y::Cdouble
z::Cdouble
end
function randomquat()
r = ()->2.0*rand(Float64)-1.0
q = [r(), r(), r(), r()]
q ./ √(sum(q.^2))
end
"""
rotatecell(uc::UnitCell, quaternion)
Rotate a unit cell according to a quaternion (represented as a vector of 4 floats).
"""
function rotatecell(uc, quat)
q = CrystFELQuaternion(quat...)
out = @ccall libcrystfel.cell_rotate(uc.internalptr::Ptr{InternalUnitCell},
q::CrystFELQuaternion)::Ptr{InternalUnitCell}
if out == C_NULL
throw(ErrorException("Failed to rotate unit cell"))
end
UnitCell(out)
end
"""
rotatecell(uc::UnitCell)
Rotate a unit cell at random in three dimensions. Use this routine for
simulating serial crystallography datasets.
Equivalent to CrystFEL routine `cell_rotate(uc, random_quaternion(<rng>))`.
"""
rotatecell(uc) = rotatecell(uc, randomquat())
end # of module
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