Merge pull request #41 from ProjectTorreyPines/omas_imas

Final switch to IMASDD

Project.toml

@@ -9,7 +9,6 @@ ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
 IMASDD = "06b86afa-9f21-11ec-2ef8-e51b8960cfc5"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
-OMAS = "91cfaa06-6526-4804-8666-b540b3feef2f"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

examples/plotting.ipynb

@@ -48,9 +48,9 @@
          "metadata": {},
          "outputs": [],
          "source": [
-            "dd = IMASDD.json2imas(\"../samples/time_dep_edge_profiles_last_step_only.json\")\n",
-            "grid_ggd = dd.edge_profiles.grid_ggd[1]\n",
-            "space = grid_ggd.space[1]"
+            "dd = IMASDD.json2imas(\"../samples/time_dep_edge_profiles_last_step_only.json\");\n",
+            "grid_ggd = dd.edge_profiles.grid_ggd[1];\n",
+            "space = grid_ggd.space[1];"
          ]
       },
       {
@@ -146,18 +146,18 @@
    ],
    "metadata": {
       "kernelspec": {
-         "display_name": "Julia 1.9.4",
+         "display_name": "Julia 1.9.2",
          "language": "julia",
-         "name": "julia-1.10"
+         "name": "julia-1.9"
       },
       "language_info": {
          "file_extension": ".jl",
          "mimetype": "application/julia",
          "name": "julia",
-         "version": "1.9.4"
+         "version": "1.9.2"
       },
       "orig_nbformat": 4
    },
    "nbformat": 4,
    "nbformat_minor": 2
-}
+}

examples/plotting_interferometer.ipynb

@@ -53,9 +53,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ids = IMASDD.json2imas(\"$(@__DIR__)/../samples/time_dep_edge_profiles_with_interferometer.json\")\n",
-    "grid_ggd = ids.edge_profiles.grid_ggd[1]\n",
-    "space = grid_ggd.space[1]"
+    "ids = IMASDD.json2imas(\"$(@__DIR__)/../samples/time_dep_edge_profiles_with_interferometer.json\");\n",
+    "grid_ggd = ids.edge_profiles.grid_ggd[1];\n",
+    "space = grid_ggd.space[1];"
    ]
   },
   {
@@ -226,15 +226,15 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Julia 1.9.4",
+   "display_name": "Julia 1.9.2",
    "language": "julia",
    "name": "julia-1.9"
   },
   "language_info": {
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.9.4"
+   "version": "1.9.2"
   },
   "orig_nbformat": 4
  },

makefile

@@ -14,16 +14,15 @@ env_with_cloned_repo r:
 	@echo "Cloning the repositories and generating Manifest.toml"
 	-dn=$(shell dirname $(shell pwd)); \
 	if [[ "$${dn:(-10)}" == ".julia/dev" ]]; then ext="" ; else ext=".jl";fi; \
-	git clone "[email protected]:ProjectTorreyPines/OMAS.jl.git" ../OMAS$${ext}; \
 	git clone "[email protected]:ProjectTorreyPines/IMASDD.jl.git" ../IMASDD$${ext}; \
-	julia --project=. -e 'using Pkg; Pkg.rm(["OMAS", "IMASDD"]); Pkg.develop(path="../OMAS'$${ext}'"); Pkg.develop(path="../IMASDD'$${ext}'"); Pkg.instantiate()'
+	julia --project=. -e 'using Pkg; Pkg.rm(["IMASDD"]); Pkg.develop(path="../IMASDD'$${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"]); Pkg.add(url="[email protected]:ProjectTorreyPines/OMAS.jl.git", rev="master"); Pkg.add(url="[email protected]:ProjectTorreyPines/IMASDD.jl.git", rev="master"); Pkg.instantiate()'
+	julia --project=. -e 'using Pkg; Pkg.rm(["IMASDD"]); Pkg.add(url="[email protected]:ProjectTorreyPines/IMASDD.jl.git", rev="master"); Pkg.instantiate()'
 
 clean:
 	@echo "Deleting Manifest.toml"

src/GGDUtils.jl

@@ -1,6 +1,6 @@
 module GGDUtils
 
-import OMAS as IMASDD
+using IMASDD: IMASDD
 
 const inv_16pi = 1.0 / (16π)
 

src/subset_tools.jl

@@ -364,6 +364,76 @@ function project_prop_on_subset!(prop_arr::AbstractVector{T},
     end
 end
 
+function deepcopy_subset(subset::IMASDD.edge_profiles__grid_ggd___grid_subset)
+    new_subset = IMASDD.edge_profiles__grid_ggd___grid_subset()
+
+    base = getfield(subset, :base)
+    new_base = getfield(new_subset, :base)
+    resize!(new_base, length(base))
+    for (ii, b) ∈ enumerate(base)
+        if !IMASDD.ismissing(b, :jacobian)
+            new_base[ii].jacobian = deepcopy(getfield(b, :jacobian))
+        end
+        if !IMASDD.ismissing(b, :tensor_contravariant)
+            new_base[ii].tensor_contravariant =
+                deepcopy(getfield(b, :tensor_contravariant))
+        end
+        if !IMASDD.ismissing(b, :tensor_covariant)
+            new_base[ii].tensor_covariant = deepcopy(getfield(b, :tensor_covariant))
+        end
+    end
+
+    if !IMASDD.ismissing(subset, :dimension)
+        new_subset.dimension = deepcopy(getfield(subset, :dimension))
+    end
+
+    element = getfield(subset, :element)
+    new_element = getfield(new_subset, :element)
+    resize!(new_element, length(element))
+    for (ii, ele) ∈ enumerate(element)
+        object = getfield(ele, :object)
+        new_object = getfield(new_element[ii], :object)
+        resize!(new_object, length(object))
+        for (jj, obj) ∈ enumerate(object)
+            if !IMASDD.ismissing(obj, :dimension)
+                new_object[jj].dimension = deepcopy(getfield(obj, :dimension))
+            end
+            if !IMASDD.ismissing(obj, :index)
+                new_object[jj].index = deepcopy(getfield(obj, :index))
+            end
+            if !IMASDD.ismissing(obj, :space)
+                new_object[jj].space = deepcopy(getfield(obj, :space))
+            end
+        end
+    end
+
+    identifier = getfield(subset, :identifier)
+    new_identifier = getfield(new_subset, :identifier)
+    if !IMASDD.ismissing(identifier, :index)
+        new_identifier.index = deepcopy(getfield(identifier, :index))
+    end
+    if !IMASDD.ismissing(identifier, :name)
+        new_identifier.name = deepcopy(getfield(identifier, :name))
+    end
+    if !IMASDD.ismissing(identifier, :description)
+        new_identifier.description = deepcopy(getfield(identifier, :description))
+    end
+
+    metric = getfield(subset, :metric)
+    new_metric = getfield(new_subset, :metric)
+    if !IMASDD.ismissing(metric, :jacobian)
+        new_metric.jacobian = deepcopy(getfield(metric, :jacobian))
+    end
+    if !IMASDD.ismissing(metric, :tensor_contravariant)
+        new_metric.tensor_contravariant =
+            deepcopy(getfield(metric, :tensor_contravariant))
+    end
+    if !IMASDD.ismissing(metric, :tensor_covariant)
+        new_metric.tensor_covariant = deepcopy(getfield(metric, :tensor_covariant))
+    end
+    return new_subset
+end
+
 """
     Base.:∈(
     point::Tuple{Real, Real},
@@ -391,17 +461,18 @@ function Base.:∈(
 )
     r, z = point
     subset, space = subset_of_space
-    dim = subset.element[1].object[1].dimension
-    nodes = space.objects_per_dimension[1].object
-    edges = space.objects_per_dimension[2].object
+    dim = getfield(getfield(getfield(subset, :element)[1], :object)[1], :dimension)
+    opd = getfield(space, :objects_per_dimension)
+    nodes = getfield(opd[1], :object)
+    edges = getfield(opd[2], :object)
     if dim == 3
         subset_bnd = IMASDD.edge_profiles__grid_ggd___grid_subset()
         subset_bnd.element = get_subset_boundary(space, subset)
     elseif dim == 2
         subset_bnd = subset
     elseif dim == 1
-        for ele ∈ subset.element
-            node = nodes[ele.object[1].index]
+        for ele ∈ getfield(subset, :element)
+            node = nodes[getfield(getfield(ele, :object)[1], :index)]
             if node.geometry[1] == r && node.geometry[2] == z
                 return true
             end
@@ -412,12 +483,18 @@ function Base.:∈(
     end
     # Count number of times an upward going ray from (r,z) intersects the boundary
     count = 0
-    for ele ∈ subset_bnd.element
-        edge = edges[ele.object[1].index]
-        r_max = maximum(nodes[node].geometry[1] for node ∈ edge.nodes)
-        r_min = minimum(nodes[node].geometry[1] for node ∈ edge.nodes)
+    for ele ∈ getfield(subset_bnd, :element)
+        edge = edges[getfield(getfield(ele, :object)[1], :index)]
+        edge_nodes_r = zeros(2)
+        edge_nodes_z = zeros(2)
+        for (ii, node) ∈ enumerate(getfield(edge, :nodes))
+            edge_nodes_r[ii] = getfield(nodes[node], :geometry)[1]
+            edge_nodes_z[ii] = getfield(nodes[node], :geometry)[2]
+        end
+        r_max = maximum(edge_nodes_r)
+        r_min = minimum(edge_nodes_r)
         if r_min <= r < r_max
-            z_max = maximum(nodes[node].geometry[2] for node ∈ edge.nodes)
+            z_max = maximum(edge_nodes_z)
             if z < z_max
                 count += 1
             end

test/runtests.jl

@@ -1,5 +1,5 @@
 import GGDUtils: interp, get_kdtree, project_prop_on_subset!, get_grid_subset
-import OMAS as IMASDD
+using IMASDD: IMASDD
 import Statistics: mean
 using Test
 using ArgParse: ArgParse

test/speedtest.jl

@@ -0,0 +1,83 @@
+import GGDUtils: interp, get_kdtree, project_prop_on_subset!, get_grid_subset, IMASDD
+
+println("-----------------------------------------------------------------------------")
+print("json2imas() time with compilation: ")
+@time ids = IMASDD.json2imas(
+    "$(@__DIR__)/../samples/time_dep_edge_profiles_last_step_only.json",
+)
+print("json2imas() time (true runtime): ")
+@time ids = IMASDD.json2imas(
+    "$(@__DIR__)/../samples/time_dep_edge_profiles_last_step_only.json",
+)
+
+println("-----------------------------------------------------------------------------")
+n_e = ids.edge_profiles.ggd[1].electrons.density[1];
+grid_ggd = ids.edge_profiles.grid_ggd[1];
+space = grid_ggd.space[1]
+print("interp(prop, grid_ggd) time with compilation: ")
+@time get_n_e = interp(n_e, grid_ggd)
+print("interp(prop, grid_ggd) (true runtime): ")
+@time get_n_e = interp(n_e, grid_ggd)
+
+println("-----------------------------------------------------------------------------")
+subset = get_grid_subset(grid_ggd, 5)
+
+print("interp(prop_arr, space, subset) time with compilation: ")
+@time get_n_e = interp(ids.edge_profiles.ggd[1].electrons.density, space, subset)
+print("interp(prop_arr, space, subset) time (true runtime): ")
+@time get_n_e = interp(ids.edge_profiles.ggd[1].electrons.density, space, subset)
+
+println("-----------------------------------------------------------------------------")
+print("interp(prop_arr, grid_ggd, grid_subset_index) time with compilation: ")
+@time get_n_e = interp(ids.edge_profiles.ggd[1].electrons.density, grid_ggd, 5)
+print("interp(prop_arr, grid_ggd, grid_subset_index) time (true runtime): ")
+@time get_n_e = interp(ids.edge_profiles.ggd[1].electrons.density, grid_ggd, 5)
+
+println("-----------------------------------------------------------------------------")
+kdtree = get_kdtree(space)
+print("interp(prop_arr, kdtree) time with compilation: ")
+@time get_T_e = interp(ids.edge_profiles.ggd[1].electrons.temperature[1].values, kdtree)
+print("interp(prop_arr, kdtree) time (true runtime): ")
+@time get_T_e = interp(ids.edge_profiles.ggd[1].electrons.temperature[1].values, kdtree)
+
+println("-----------------------------------------------------------------------------")
+prop = ids.edge_profiles.ggd[1].electrons.density
+# All cells
+from_subset = get_grid_subset(ids.edge_profiles.grid_ggd[1], 5)
+# separatix
+to_subset = get_grid_subset(ids.edge_profiles.grid_ggd[1], 16)
+print(
+    "project_prop_on_subset!(prop, from_subset, to_subset, space) time with compilation: ",
+)
+@time separatix_centers, values_at_separatix =
+    project_prop_on_subset!(prop, from_subset, to_subset, space)
+print(
+    "project_prop_on_subset!(prop, from_subset, to_subset, space) time (true runtime): ",
+)
+@time separatix_centers, values_at_separatix =
+    project_prop_on_subset!(prop, from_subset, to_subset, space)
+
+println("-----------------------------------------------------------------------------")
+subset_core =
+    get_grid_subset(ids.edge_profiles.grid_ggd[1], 22)
+print("project_prop_on_subset!(prop, from_subset, subset_core) time with compilation: ")
+@time core_element_inds, values_at_core =
+    project_prop_on_subset!(prop, from_subset, subset_core)
+print("project_prop_on_subset!(prop, from_subset, subset_core) time (true runtime): ")
+@time core_element_inds, values_at_core =
+    project_prop_on_subset!(prop, from_subset, subset_core)
+
+println("-----------------------------------------------------------------------------")
+subset_corebnd = get_grid_subset(grid_ggd, 15)
+subset_sol = get_grid_subset(grid_ggd, 23)
+subset_odr = get_grid_subset(grid_ggd, 24)
+
+print("test ∈ (edges) time with compilation: ")
+@time (6.0, 0.0) ∈ (subset_corebnd, space)
+print("test ∈ (edges) time (true runtime): ")
+@time (6.0, 0.0) ∈ (subset_corebnd, space)
+
+print("test ∈ (cells) time with compilation: ")
+@time (6.0, 4.0) ∈ (subset_sol, space)
+print("test ∈ (cells) time (true runtime): ")
+@time (6.0, 4.0) ∈ (subset_sol, space)