Final switch to IMASDD

Project.toml

@@ -9,7 +9,6 @@ DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 GGDUtils = "b7b5e640-9b39-4803-84eb-376048795def"
 IMASDD = "06b86afa-9f21-11ec-2ef8-e51b8960cfc5"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
-OMAS = "91cfaa06-6526-4804-8666-b540b3feef2f"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"

makefile

@@ -14,17 +14,16 @@ env_with_cloned_repo r:
 	@echo "Cloning the repositories and generating Manifest.toml"
 	-dn=$(shell dirname $(shell pwd)); \
 	if [[ "$${dn:(-10)}" == ".julia/dev" ]]; then ext="" ; else ext=".jl";fi; \
-	git clone "git@github.com:ProjectTorreyPines/OMAS.jl.git" ../OMAS$${ext}; \
 	git clone "git@github.com:ProjectTorreyPines/IMASDD.jl.git" ../IMASDD$${ext}; \
 	git clone "git@github.com:ProjectTorreyPines/GGDUtils.jl.git" ../GGDUtils$${ext}; \
-	julia --project=. -e 'using Pkg; Pkg.rm(["OMAS", "IMASDD", "GGDUtils"]); Pkg.develop(path="../OMAS'$${ext}'"); Pkg.develop(path="../IMASDD'$${ext}'"); Pkg.develop(path="../GGDUtils'$${ext}'"); Pkg.instantiate()'
+	julia --project=. -e 'using Pkg; Pkg.rm(["IMASDD", "GGDUtils"]); Pkg.develop(path="../IMASDD'$${ext}'"); Pkg.develop(path="../GGDUtils'$${ext}'"); Pkg.instantiate()'
 
 env_with_git_url u:
 	@echo "Pulling sample files using dvc"
 	-dvc pull
 	@echo "Creating Julia environment with the git urls without creating local clones"
 	@echo "Generating Project.toml and Manifest.toml"
-	julia --project=. -e 'using Pkg; Pkg.rm(["OMAS", "IMASDD", "GGDUtils"]); Pkg.add(url="git@github.com:ProjectTorreyPines/OMAS.jl.git", rev="master"); Pkg.add(url="git@github.com:ProjectTorreyPines/IMASDD.jl.git", rev="master");  Pkg.add(url="git@github.com:ProjectTorreyPines/GGDUtils.jl.git", rev="master"); Pkg.instantiate()'
+	julia --project=. -e 'using Pkg; Pkg.rm(["IMASDD", "GGDUtils"]); Pkg.add(url="git@github.com:ProjectTorreyPines/IMASDD.jl.git", rev="master");  Pkg.add(url="git@github.com:ProjectTorreyPines/GGDUtils.jl.git", rev="master"); Pkg.instantiate()'
 
 clean:
 	@echo "Deleting Manifest.toml"

src/SOLPS2IMAS.jl

@@ -1,12 +1,12 @@
 module SOLPS2IMAS
 
 using Revise
-import OMAS as IMASDD
+using IMASDD: IMASDD
 using NCDatasets: Dataset, dimnames
 using YAML: load_file as YAML_load_file
 using DelimitedFiles: readdlm
 import GGDUtils: add_subset_element!, get_grid_subset, get_subset_boundary,
-    get_subset_space, subset_do
+    get_subset_space, subset_do, deepcopy_subset
 
 export read_b2_output
 export solps2imas
@@ -288,6 +288,9 @@ function solps2imas(
                             resize!(edges, edge_ind)
                             edges[edge_ind].nodes = edge_nodes
                             resize!(edges[edge_ind].boundary, 2)
+                            for bnd ∈ edges[edge_ind].boundary
+                                bnd.neighbours = Int64[]
+                            end
                             for (ii, edge_bnd) ∈ enumerate(edges[edge_ind].boundary)
                                 edge_bnd.index = edge_nodes[ii]
                             end
@@ -509,8 +512,9 @@ function solps2imas(
         resize!(grid_ggd.grid_subset, cur_no_subsets + 12)
         # Copy all B2.5 nodes, faces, edges, cells to grid_subset with negative indices
         for (ii, gsi) ∈ enumerate([1, 2, 5])
-            grid_ggd.grid_subset[cur_no_subsets+ii] =
-                deepcopy(get_grid_subset(grid_ggd, gsi))
+            grid_ggd.grid_subset[cur_no_subsets+ii] = deepcopy_subset(
+                get_grid_subset(grid_ggd, gsi),
+            )
             grid_ggd.grid_subset[cur_no_subsets+ii].identifier.index = -gsi
             grid_ggd.grid_subset[cur_no_subsets+ii].identifier.name *= "_B2.5"
             gsi_ch[gsi] = -gsi
@@ -596,7 +600,6 @@ function solps2imas(
             resize!(cells, length(cells) + 1)
             this_cell_ind = length(cells)
             fntri_inds[fntri] = this_cell_ind
-            resize!(cells[this_cell_ind].nodes, 3)
             cells[this_cell_ind].nodes = [
                 fnode_inds[fntriIndNodes[fntri, 2]],
                 fnode_inds[fntriIndNodes[fntri, 3]],

src/solps_mesh_tools.jl

@@ -42,8 +42,8 @@ function search_points(nodes, r, z; tol=0)
     # If an index remains at 0, it means the point in question was not found
     for j ∈ 1:n
         for i ∈ eachindex(nodes)
-            rn = nodes[i].geometry[1]
-            zn = nodes[i].geometry[2]
+            rn, zn = getfield(nodes[i], :geometry)
+            # zn = nodes[i].geometry[2]
             if abs(rn - r[j]) <= tol && abs(zn - z[j]) <= tol
                 indices[j] = i
                 break
@@ -60,10 +60,11 @@ search if an edge with nodes as edge_nodes already exists
 """
 function search_edges(edges, edge_nodes)
     for ii ∈ eachindex(edges)
-        if edge_nodes[1] == edges[ii].nodes[1] && edge_nodes[2] == edges[ii].nodes[2]
+        edges_ii_nodes = getfield(edges[ii], :nodes)
+        if edge_nodes[1] == edges_ii_nodes[1] && edge_nodes[2] == edges_ii_nodes[2]
             return ii
-        elseif edge_nodes[2] == edges[ii].nodes[1] &&
-               edge_nodes[1] == edges[ii].nodes[2]
+        elseif edge_nodes[2] == edges_ii_nodes[1] &&
+               edge_nodes[1] == edges_ii_nodes[2]
             return ii
         end
     end
@@ -169,8 +170,9 @@ function attach_neightbours(cells, edges, gmtry, it)
         for neighbour_ind ∈ get_neighbour_inds(ic, gmtry, it)
             for boundary ∈ cell.boundary
                 for neighbour_boundary ∈ cells[neighbour_ind].boundary
-                    if boundary.index == neighbour_boundary.index &&
-                       neighbour_ind ∉ boundary.neighbours
+                    if getfield(boundary, :index) ==
+                       getfield(neighbour_boundary, :index) &&
+                       neighbour_ind ∉ getfield(boundary, :neighbours)
                         append!(boundary.neighbours, neighbour_ind)
                     end
                 end
@@ -188,10 +190,11 @@ function attach_neightbours(cells, edges, gmtry, it)
             end
             setdiff!(neighbour_edge_inds, edge_ind)
             for neighbour_edge_ind ∈ neighbour_edge_inds
-                for edge_bnd ∈ edges[edge_ind].boundary
+                for edge_bnd ∈ getfield(edges[edge_ind], :boundary)
                     for neighbour_edge_bnd ∈ edges[neighbour_edge_ind].boundary
-                        if edge_bnd.index == neighbour_edge_bnd.index &&
-                           neighbour_edge_ind ∉ edge_bnd.neighbours
+                        if getfield(edge_bnd, :index) ==
+                           getfield(neighbour_edge_bnd, :index) &&
+                           neighbour_edge_ind ∉ getfield(edge_bnd, :neighbours)
                             append!(edge_bnd.neighbours, neighbour_edge_ind)
                         end
                     end

test/runtests.jl

@@ -2,7 +2,7 @@ using SOLPS2IMAS: SOLPS2IMAS
 using Test
 using YAML: load_file as YAML_load_file
 using ArgParse: ArgParse
-import OMAS as IMASDD
+using IMASDD: IMASDD
 import SOLPS2IMAS: get_grid_subset
 
 allowed_rtol = 1e-4

test/speedtest.jl

@@ -0,0 +1,14 @@
+using SOLPS2IMAS: SOLPS2IMAS
+
+println("-----------------------------------------------------------------------------")
+b2gmtry = "$(@__DIR__)/../samples/b2fgmtry"
+b2output = "$(@__DIR__)/../samples/b2time.nc"
+b2mn = "$(@__DIR__)/../samples/b2mn.dat"
+fort = (
+    "$(@__DIR__)/../samples/fort.33",
+    "$(@__DIR__)/../samples/fort.34",
+    "$(@__DIR__)/../samples/fort.35")
+print("solps2imas(b2gmtry, b2output; b2mn, fort) time with compilation: ")
+@time dd = SOLPS2IMAS.solps2imas(b2gmtry, b2output; b2mn, fort);
+print("solps2imas(b2gmtry, b2output; b2mn, fort) time (true runtime): ")
+@time dd = SOLPS2IMAS.solps2imas(b2gmtry, b2output; b2mn, fort);