Track spacegroup setting

docs/make.jl

@@ -1,5 +1,4 @@
-# To build docs, execute `julia --project=@. make.jl`. The JuliaHub build
-# environment additionally uses `--compiled-modules=no`.
+# julia --project=@. --compiled-modules=existing make.jl
 
 isdraft = false # set `true` to disable cell evaluation
 

docs/src/versions.md

@@ -9,6 +9,11 @@
   polynomial order according to an error tolerance.
 * Rename mode `:dipole_large_S` to `:dipole_uncorrected` to emphasize that
   corrections are missing.
+* The [`Crystal`](@ref) constructor, by default, interprets a spacegroup number
+  in its ITA standard setting, e.g., as used by the [Bilbao crystallographic
+  server](https://www.cryst.ehu.es/cryst/get_wp.html). The keyword argument
+  `setting` becomes `choice`, and can typically be omitted.
+* Rename `primitive_cell_shape` to [`primitive_cell`](@ref).
 
 ## v0.7.2
 (Sep 11, 2024)

examples/01_LSWT_CoRh2O4.jl

@@ -47,13 +47,12 @@ units = Units(:meV, :angstrom);
 a = 8.5031 # (Å)
 latvecs = lattice_vectors(a, a, a, 90, 90, 90)
 
-# Construct the [`Crystal`](@ref) cell from the spacegroup number 227 and one
-# representative atom of each occupied Wyckoff. In the standard setting of
-# spacegroup 227, position `[0, 0, 0]` belongs to Wyckoff 8a, which is the
-# diamond cubic crystal.
+# Construct a [`Crystal`](@ref) cell from spacegroup 227 in the ITA standard
+# setting. Cobalt atoms belong to Wyckoff 8a, which is the diamond cubic
+# lattice.
 
-positions = [[0, 0, 0]]
-cryst = Crystal(latvecs, positions, 227; types=["Co"], setting="1")
+positions = [[1/8, 1/8, 1/8]]
+cryst = Crystal(latvecs, positions, 227; types=["Co"])
 
 # [`view_crystal`](@ref) launches an interface for interactive inspection and
 # symmetry analysis.
@@ -80,7 +79,7 @@ sys = System(cryst, [1 => Moment(s=3/2, g=2)], :dipole)
 # the antiferromagnetic Heisenberg interactions as blue polkadot spheres.
 
 J = +0.63 # (meV)
-set_exchange!(sys, J, Bond(1, 3, [0, 0, 0]))
+set_exchange!(sys, J, Bond(2, 3, [0, 0, 0]))
 view_crystal(sys)
 
 # ### Optimizing spins
@@ -104,16 +103,15 @@ plot_spins(sys; color=[S[3] for S in sys.dipoles])
 
 # ### Reshaping the magnetic cell
 
-# The most compact magnetic cell for this Néel order is a primitive unit cell.
-# Reduce the magnetic cell size using [`reshape_supercell`](@ref), where columns
-# of the `shape` matrix are primitive lattice vectors as multiples of the
-# conventional cubic lattice vectors ``(𝐚_1, 𝐚_2, 𝐚_3)``. One could
-# alternatively use `shape = cryst.latvecs \ cryst.prim_latvecs`. Verify that
+# The most compact magnetic cell for this Néel order is the primitive unit cell.
+# Columns of the [`primitive_cell`](@ref) matrix provide the primitive lattice
+# vectors as multiples of the conventional cubic lattice vectors.
+
+shape = primitive_cell(cryst)
+
+# Reduce the magnetic cell size using [`reshape_supercell`](@ref). Verify that
 # the energy per site is unchanged after the reshaping the supercell.
 
-shape = [0 1 1;
-         1 0 1;
-         1 1 0] / 2
 sys_prim = reshape_supercell(sys, shape)
 @assert energy_per_site(sys_prim) ≈ -2J*(3/2)^2
 

examples/02_LLD_CoRh2O4.jl

@@ -18,11 +18,11 @@ using Sunny, GLMakie
 units = Units(:meV, :angstrom)
 a = 8.5031 # (Å)
 latvecs = lattice_vectors(a, a, a, 90, 90, 90)
-cryst = Crystal(latvecs, [[0,0,0]], 227, setting="1")
+cryst = Crystal(latvecs, [[1/8, 1/8, 1/8]], 227)
 
 sys = System(cryst, [1 => Moment(s=3/2, g=2)], :dipole)
 J = 0.63 # (meV)
-set_exchange!(sys, J, Bond(1, 3, [0,0,0]))
+set_exchange!(sys, J, Bond(2, 3, [0,0,0]))
 randomize_spins!(sys)
 minimize_energy!(sys)
 plot_spins(sys; color=[S[3] for S in sys.dipoles])

examples/07_Dipole_Dipole.jl

@@ -8,20 +8,19 @@
 
 using Sunny, GLMakie
 
-# Create a pyrochlore crystal from spacegroup 227.
+# Create a pyrochlore crystal from Wyckoff 16c for spacegroup 227.
 
 units = Units(:K, :angstrom)
 latvecs = lattice_vectors(10.19, 10.19, 10.19, 90, 90, 90)
-positions = [[1/8, 1/8, 1/8]]
-cryst = Crystal(latvecs, positions, 227, setting="1")
+positions = [[0, 0, 0]]
+cryst = Crystal(latvecs, positions, 227)
 view_crystal(cryst)
 
 # Create a system and reshape to the primitive cell, which contains four atoms.
 # Add antiferromagnetic nearest neighbor exchange interactions.
 
-primitive_cell = [1/2 1/2 0; 0 1/2 1/2; 1/2 0 1/2]
 sys = System(cryst, [1 => Moment(s=7/2, g=2)], :dipole; seed=0)
-sys = reshape_supercell(sys, primitive_cell)
+sys = reshape_supercell(sys, primitive_cell(cryst))
 J1 = 0.304 # (K)
 set_exchange!(sys, J1, Bond(1, 2, [0,0,0]))
 

examples/spinw_tutorials/SW13_LiNiPO4.jl

@@ -8,8 +8,8 @@
 
 using Sunny, GLMakie
 
-# Build an orthorhombic lattice and populate the Ni atoms according to
-# spacegroup 62 (Pnma).
+# Build an orthorhombic lattice and populate the Ni atoms according to Wyckoff
+# 4c of spacegroup 62.
 
 units = Units(:meV, :angstrom)
 a = 10.02
@@ -18,7 +18,7 @@ c = 4.68
 latvecs = lattice_vectors(a, b, c, 90, 90, 90)
 positions = [[1/4, 1/4, 0]]
 types = ["Ni"]
-cryst = Crystal(latvecs, positions, 62, setting=""; types)
+cryst = Crystal(latvecs, positions, 62; types)
 view_crystal(cryst)
 
 # Create a system with exchange parameters taken from [T. Jensen, et al., PRB

examples/spinw_tutorials/SW15_Ba3NbFe3Si2O14.jl

@@ -37,8 +37,8 @@ set_exchange!(sys, J₁, Bond(3, 2, [1,1,0]))
 set_exchange!(sys, J₄, Bond(1, 1, [0,0,1]))
 set_exchange!(sys, J₂, Bond(1, 3, [0,0,0]))
 
-# The final two exchanges are setting according to the desired chirality ``ϵ_T``
-# of the magnetic structure.
+# The final two exchanges are set according to the desired chirality ``ϵ_T`` of
+# the magnetic structure.
 
 ϵT = -1
 if ϵT == -1

examples/spinw_tutorials/SW18_Distorted_kagome.jl

@@ -13,13 +13,13 @@
 
 using Sunny, GLMakie
 
-# Build the distorted kagome crystal, with spacegroup 12.
+# Build the distorted kagome crystal, with spacegroup 12 ("C 1 2/m 1" setting).
 
 units = Units(:meV, :angstrom)
 latvecs = lattice_vectors(10.2, 5.94, 7.81, 90, 117.7, 90)
 positions = [[0, 0, 0], [1/4, 1/4, 0]]
 types = ["Cu1", "Cu2"]
-cryst = Crystal(latvecs, positions, 12; types, setting="b1")
+cryst = Crystal(latvecs, positions, "C 1 2/m 1"; types)
 view_crystal(cryst)
 
 # Define the interactions.

ext/PlottingExt.jl

@@ -312,7 +312,7 @@ function reference_bonds_upto(cryst, nbonds, ndims)
 end
 
 function propagate_reference_bond_for_cell(cryst, b_ref)
-    symops = Sunny.canonical_group_order(cryst.symops)
+    symops = Sunny.canonical_group_order(cryst.sg.symops)
 
     found = map(_ -> Bond[], cryst.positions)
     for s in symops

src/FormFactor.jl

@@ -96,14 +96,14 @@ Two special, ``𝐪``-independent form factor values are available:
 as a perfect point particle, while the second zeros all contributions from the
 magnetic ion.
 
-References:
-
- 1. [P. J. Brown, The Neutron Data Booklet, 2nd ed., Sec. 2.5 Magnetic Form
-    Factors (2003)](https://www.ill.eu/sites/ccsl/ffacts/ffachtml.html)
- 2. Coefficient tables in [McPhase
-    documentation](https://www2.cpfs.mpg.de/~rotter/homepage_mcphase/manual/node137.html)
- 3. [K. Kobayashi, T. Nagao, M. Ito, Acta Cryst. A, 67 pp 473–480
-    (2011)](https://doi.org/10.1107/S010876731102633X)
+## References:
+
+1. [P. J. Brown, The Neutron Data Booklet, 2nd ed., Sec. 2.5 Magnetic Form
+   Factors (2003)](https://www.ill.eu/sites/ccsl/ffacts/ffachtml.html)
+2. Coefficient tables in [McPhase
+   documentation](https://www2.cpfs.mpg.de/~rotter/homepage_mcphase/manual/node137.html)
+3. [K. Kobayashi, T. Nagao, M. Ito, Acta Cryst. A, 67 pp 473–480
+   (2011)](https://doi.org/10.1107/S010876731102633X)
 """
 function FormFactor(ion::String; g_lande=2)
     if !haskey(radial_integral_coefficients, ion)

src/Integrators.jl

@@ -45,7 +45,7 @@ the dipole in analogy to the vector cross product ``S × 𝐁``. The coupling to
 the thermal bath maps as ``λ̃ = |𝐒| λ``. Note, therefore, that the scaling of
 the `damping` parameter varies subtly between `:dipole` and `:SUN` modes.
 
-References:
+## References:
 
 1. [D. Dahlbom et al., Phys. Rev. B 106, 235154
    (2022)](https://arxiv.org/abs/2209.01265).
@@ -99,7 +99,7 @@ or its generalization to SU(_N_) coherent states [1]. One call to the
 This integration scheme is exactly symplectic and eliminates energy drift over
 arbitrarily long simulation trajectories.
 
-References:
+## References:
 
 1. [H. Zhang and C. D. Batista, Phys. Rev. B 104, 104409
    (2021)](https://arxiv.org/abs/2106.14125).

src/KPM/SpinWaveTheoryKPM.jl

@@ -22,10 +22,10 @@ Reasonable starting points are `1e-1` (more speed) or `1e-2` (more accuracy).
   particular, KPM may mask intensities that arise near the Goldstone modes of an
   ordered state with continuous symmetry.
 
-References:
+## References:
 
- 1. H. Lane et al., Kernel Polynomial Method for Linear Spin Wave Theory (2023)
-    [[arXiv:2312.08349v3](https://arxiv.org/abs/2312.08349)].
+1. H. Lane et al., Kernel Polynomial Method for Linear Spin Wave Theory (2023)
+   [[arXiv:2312.08349v3](https://arxiv.org/abs/2312.08349)].
 """
 struct SpinWaveTheoryKPM
     swt :: SpinWaveTheory

src/MCIF.jl

@@ -23,12 +23,14 @@ function set_dipoles_from_mcif!(sys::System, filename::AbstractString)
         tol = 0.1 * sys.crystal.symprec # Tolerance might need tuning
         orig_cryst = orig_crystal(sys)
 
-        primvecs = @something orig_cryst.prim_latvecs orig_cryst.latvecs
+        primcell = @something primitive_cell(orig_cryst) Mat3(I)
+        primvecs = orig_cryst.latvecs * primcell
 
         suggestion = if all(isinteger.(rationalize.(primvecs \ supervecs2; tol)))
             suggested_shape = rationalize.(orig_cryst.latvecs \ supervecs2; tol)
             suggestion = if isdiag(suggested_shape)
-                sz = fractional_vec3_to_string(diag(suggested_shape))
+                diag_strs = number_to_math_string.(diag(suggested_shape))
+                sz = "("*join(diag_strs, ", ")*")"
                 error("Use `resize_supercell(sys, $sz)` to get compatible system")
             else
                 shp = fractional_mat3_to_string(suggested_shape)

src/Reshaping.jl

@@ -18,14 +18,13 @@ function reshape_supercell(sys::System, shape)
 
     orig = orig_crystal(sys)
     check_shape_commensurate(orig, shape)
-
-    primvecs = @something orig.prim_latvecs orig.latvecs
-    prim_shape = primvecs \ orig.latvecs * shape
-    prim_shape′ = round.(Int, prim_shape)
-    @assert prim_shape′ ≈ prim_shape
+    prim_cell = @something primitive_cell(orig) Mat3(I)
+    shape_in_prim = prim_cell \ shape
+    @assert all_integer(shape_in_prim; orig.symprec)
+    shape_in_prim = round.(Int, shape_in_prim)
 
     # Unit cell for new system, in units of original unit cell.
-    new_dims = NTuple{3, Int}(gcd.(eachcol(prim_shape′)))
+    new_dims = NTuple{3, Int}(gcd.(eachcol(shape_in_prim)))
     new_shape = Mat3(shape * diagm(collect(inv.(new_dims))))
     new_cryst = reshape_crystal(orig_crystal(sys), new_shape)
 

src/Sunny.jl

@@ -31,14 +31,16 @@ export spin_matrices, stevens_matrices, to_product_space, rotate_operator, print
 include("Symmetry/LatticeUtils.jl")
 include("Symmetry/SymOp.jl")
 include("Symmetry/MSymOp.jl")
+include("Symmetry/SpacegroupData.jl")
+include("Symmetry/WyckoffData.jl")
 include("Symmetry/Crystal.jl")
 include("Symmetry/Bond.jl")
 include("Symmetry/SymmetryAnalysis.jl")
 include("Symmetry/AllowedCouplings.jl")
 include("Symmetry/AllowedAnisotropy.jl")
 include("Symmetry/Parsing.jl")
 include("Symmetry/Printing.jl")
-export Crystal, subcrystal, standardize, lattice_vectors, lattice_params, primitive_cell_shape, Bond,
+export Crystal, subcrystal, standardize, lattice_vectors, lattice_params, primitive_cell, Bond,
     reference_bonds, print_site, print_bond, print_symmetry_table, print_suggested_frame
 
 include("Units.jl")
@@ -174,7 +176,7 @@ PT.@setup_workload begin
     PT.@compile_workload begin
         # Crystal loading
         latvecs = lattice_vectors(1, 1, 1, 90, 90, 90)
-        cryst = Crystal(latvecs, [[0,0,0]], 227, setting="1")
+        cryst = Crystal(latvecs, [[1,1,1]/8], 227)
         repr("text/plain", cryst)
         print_symmetry_table(cryst, 0.8; io=devnull)
     end