[doc] Add 3D visualization of WFs

docs/src/tutorials_src/4-realspace.jl

@@ -48,7 +48,7 @@ The [`disentangle`](@ref) function
 will disentangle and maximally localize the spread
 functional, and returns the gauge matrices `A`,
 =#
-A = disentangle(model)
+A = disentangle(model);
 
 # The initial spread is
 omega(model)
@@ -99,6 +99,32 @@ visualizer, e.g., `vesta`, to have a look at the WFs!
 
 =#
 
+using JSServe  # hide
+Page(; exportable=true, offline=true)  # hide
+#=
+We also provide a simple plotting package
+[`WannierPlots.jl`](https://github.com/qiaojunfeng/WannierPlots.jl)
+for quick Visualization of band structure, real space WFs, etc.
+
+First, load the plotting packages
+=#
+using WGLMakie
+set_theme!(; resolution=(800, 800))
+using WannierPlots
+#=
+!!! tip
+
+    Here we want to show the WFs in this web page, so we first load `WGLMakie`.
+    When you use the `WannierPlots` package in REPL, you can first load `GLMakie`,
+    then the WFs will be shown in a standalone window.
+=#
+# Read the 1st WF
+xsf = read_xsf("$CUR_DIR/wjl_00001.xsf");
+# Visualize with `WannierPlots.jl`,
+pos = inv(xsf.primvec) * xsf.atom_positions  # to fractional coordinates
+atom_numbers = parse.(Int, xsf.atoms)  # to integer atomic numbers
+plot_wf(xsf.rgrid, xsf.W, xsf.primvec, pos, atom_numbers)
+
 #=
 ## Compute WF centers in realspace
 

docs/src/tutorials_src/5-parallel_transport.jl

@@ -216,9 +216,32 @@ Also, you can try to plot the WFs, by first truncating the `unk`
 Wannier.truncate_unk(CUR_DIR, [7], "$CUR_DIR/truncate")
 # the new `unk`s are stored in a subfolder `truncate`,
 # now write the realspace WF
-write_realspace_wf("$CUR_DIR/wjl", model_top; unkdir="$CUR_DIR/truncate")
+write_realspace_wf(
+    "$CUR_DIR/wjl", model_top; n_supercells=[3, 3, 2], unkdir="$CUR_DIR/truncate"
+)
 # and visualize with your favorite tool.
 
+# As a reference, here is the real space WFs visualized with [`WannierPlots.jl`].
+using JSServe  # hide
+Page(; exportable=true, offline=true)  # hide
+# First, load the plotting packages
+using WGLMakie
+set_theme!(; resolution=(800, 800))
+using WannierPlots
+#=
+!!! tip
+
+    Here we want to show the WFs in this web page, so we first load `WGLMakie`.
+    When you use the `WannierPlots` package in REPL, you can first load `GLMakie`,
+    then the WFs will be shown in a standalone window.
+=#
+# Read the 1st WF
+xsf = read_xsf("$CUR_DIR/wjl_00001.xsf");
+# Visualize with `WannierPlots.jl`,
+pos = inv(xsf.primvec) * xsf.atom_positions  # to fractional coordinates
+atom_numbers = parse.(Int, xsf.atoms)  # to integer atomic numbers
+plot_wf(xsf.rgrid, xsf.W, xsf.primvec, pos, atom_numbers)
+
 #=
 Now we have automated Wannierization of the valence manifold,
 and the top valence band of MoS2, without any initial projection!

src/io/xsf.jl

@@ -95,21 +95,14 @@ function read_xsf(filename::AbstractString)
         n_x, n_y, n_z = size(W)
         # fractional w.r.t. span_vectors
         O = inv(span_vectors) * origin
-        X = range(0, 1, n_x) .- O[1]
-        Y = range(0, 1, n_y) .- O[2]
-        Z = range(0, 1, n_z) .- O[3]
+        X = range(0, 1, n_x) .+ O[1]
+        Y = range(0, 1, n_y) .+ O[2]
+        Z = range(0, 1, n_z) .+ O[3]
         Xg, Yg, Zg = ndgrid(X, Y, Z)
         rgrid = RGrid(span_vectors, Xg, Yg, Zg)
     end
 
-    return (
-        primvec=primvec,
-        convvec=convvec,
-        atoms=atoms,
-        atom_positions=atom_positions,
-        rgrid=rgrid,
-        W=W,
-    )
+    return (; primvec, convvec, atoms, atom_positions, rgrid, W)
 end
 
 """