Ion particle fluxes

Makefile

@@ -128,8 +128,6 @@ using Pkg;\
 Pkg.activate();\
 Pkg.develop([["FUSE"] ; fuse_packages]);\
 Pkg.add(["JuliaFormatter", "Test", "Plots"]);\
-Pkg.activate(".");\
-Pkg.develop(fuse_packages);\
 '
 	@make revise
 
@@ -192,10 +190,10 @@ Pkg.activate("./docs");\
 Pkg.develop(["FUSE"; fuse_packages])'
 
 # install FUSE without using the registry
-install_no_registry: forward_compatibility registry clone_pull_all develop
+install_no_registry: registry clone_pull_all develop
 
 # install FUSE using the registry (requires registry to be up-to-date, which most likely are not! Don't use!)
-install_via_registry: forward_compatibility registry develop
+install_via_registry: registry develop
 
 # install used by CI (add packages, do not dev them)
 install_ci_add: registry https_add
@@ -206,25 +204,15 @@ install: install_no_registry
 
 # update_all, a shorthand for install and precompile
 update_all: install
-	@julia -e 'using Pkg; Pkg.resolve(); Pkg.activate("."); Pkg.resolve(); Pkg.update(); Pkg.precompile()'
+	@julia -e 'using Pkg; Pkg.resolve(); Pkg.update(); Pkg.precompile()'
 
 # update, a synonim of clone_pull and develop
-update: forward_compatibility clone_pull_all develop resolve
+update: clone_pull_all develop resolve
 
 # resolve the current environment (eg. after manually adding a new package)
 resolve:
-	@julia -e 'using Pkg; Pkg.resolve(); Pkg.activate("."); Pkg.resolve(); Pkg.precompile()'
+	@julia -e 'using Pkg; Pkg.resolve(); Pkg.precompile()'
 
-# delete local packages that have become obsolete
-forward_compatibility:
-	@julia -e '\
-using Pkg;\
-for package in ("Equilibrium", "Broker", "ZMQ", "FUSE_GA");\
-	try; Pkg.activate();    Pkg.rm(package); catch; end;\
-	try; Pkg.activate("."); Pkg.rm(package); catch; end;\
-	try; Pkg.activate("./docs"); Pkg.rm(package); catch; end;\
-end;\
-'
 # undo --single-branch clones of git repos
 undo_single_branch:
 	$(foreach package,$(FUSE_PACKAGES_MAKEFILE),cd ../$(package)/; echo `pwd`; git config remote.origin.fetch "+refs/heads/*:refs/remotes/origin/*"; git fetch origin;)
@@ -442,9 +430,11 @@ endif
 
 # run julia using the Manifest_CI.toml
 manifest_ci:
-	@TEMP_DIR=$$(mktemp -d /var/tmp/manifest_ci.XXXXXX) && echo $$TEMP_DIR &&\
+	@TEMP_DIR=$$(mktemp -d /var/tmp/manifest_ci.XXXXXX) &&\
+	echo $$TEMP_DIR &&\
 	sed "s/git@/https:\\/\\//g" Manifest_CI.toml > $$TEMP_DIR/Manifest.toml && \
-	cd $$TEMP_DIR && julia -i -e 'using Pkg; Pkg.activate("."); Pkg.instantiate()'
+	cd $$TEMP_DIR &&\
+	julia -i -e 'using Pkg; Pkg.activate("."); Pkg.instantiate()'
 
 # remove all Manifest.toml files
 rm_manifests:

Project.toml

@@ -4,29 +4,23 @@ authors = ["Orso Meneghini <[email protected]>"]
 version = "0.1.4"
 
 [deps]
-ADAS = "f4a0d185-1024-41e7-8ef7-3196bb2f6549"
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 BoundaryPlasmaModels = "2da5b0d0-c5e5-4f14-9caf-62d0020df410"
 CHEASE = "40781a8e-f1bb-11ec-24ef-0f6bc40c1567"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 ClusterManagers = "34f1f09b-3a8b-5176-ab39-66d58a4d544e"
-CoordinateConventions = "7204ce3a-f536-43d2-be4a-fbed74e90d86"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 EPEDNN = "e64856f0-3bb8-4376-b4b7-c03396503991"
-FXP = "e356478e-5a30-45f6-9775-70cc66e4fbd4"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-FiniteElementHermite = "6ce10167-d368-4c0e-af34-9787cdd175e5"
-Fortran90Namelists = "8fb689aa-71ff-4044-8071-0cffc910b57d"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 FuseUtils = "c8e4ee58-0bec-4a6a-b552-9dd24d6374ac"
 FusionMaterials = "4c86da02-02c8-4634-8460-96566129f8e0"
 GeoInterface = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
 IMAS = "13ead8c1-b7d1-41bb-a6d0-5b8b65ed587a"
-IMASDD = "06b86afa-9f21-11ec-2ef8-e51b8960cfc5"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
@@ -38,9 +32,7 @@ Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
 MXHEquilibrium = "8efa4e5a-7b9a-4eec-876e-01d13d5b5d75"
 Memoize = "c03570c3-d221-55d1-a50c-7939bbd78826"
-MeshTools = "804828d9-b4e9-4eca-b847-748d6c7bafa9"
 Metaheuristics = "bcdb8e00-2c21-11e9-3065-2b553b22f898"
-MillerExtendedHarmonic = "c82744c2-dc08-461a-8c37-87ab04d0f9b8"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 NEO = "081d0416-0f87-42c0-8034-5895805e76d8"
 NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
@@ -70,27 +62,21 @@ Weave = "44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [compat]
-ADAS = "1"
 AbstractTrees = "0.4"
 BoundaryPlasmaModels = "1.0"
 CHEASE = "1.0"
 CSV = "0.10"
 ClusterManagers = "0.4"
-CoordinateConventions = "1"
 DataFrames = "1"
 DelimitedFiles = "1"
 DifferentialEquations = "7"
 EPEDNN = "1"
-FXP = "1"
 FileIO = "1"
-FiniteElementHermite = "1"
-Fortran90Namelists = "0.1"
 ForwardDiff = "0.10"
 FuseUtils = "1.1"
 FusionMaterials = "1"
 GeoInterface = "1"
 IMAS = "1"
-IMASDD = "1"
 Interpolations = "0.15"
 JSON = "0.21"
 JpegTurbo = "0.1"
@@ -99,9 +85,7 @@ LibGEOS = "0.9"
 LoggingExtras = "1"
 MXHEquilibrium = "1"
 Memoize = "0.4"
-MeshTools = "1"
 Metaheuristics = "3"
-MillerExtendedHarmonic = "1"
 ModelingToolkit = "9"
 NEO = "1"
 NLsolve = "4"

src/actors/current/qed_actor.jl

@@ -1,5 +1,4 @@
 import QED
-import FiniteElementHermite
 
 #= ======== =#
 #  ActorQED  #

src/actors/transport/neoclassical_actor.jl

@@ -87,15 +87,15 @@ function _finalize(actor::ActorNeoclassical)
 
     if par.model == :changhinton
         model.identifier.name = "Chang-Hinton"
-        IMAS.flux_gacode_to_fuse([:ion_energy_flux], actor.flux_solutions, m1d, eqt, cp1d)
+        IMAS.flux_gacode_to_fuse((:ion_energy_flux,), actor.flux_solutions, m1d, eqt, cp1d)
 
     elseif par.model == :neo
         model.identifier.name = "NEO"
-        IMAS.flux_gacode_to_fuse([:ion_energy_flux, :electron_energy_flux, :electron_particle_flux], actor.flux_solutions, m1d, eqt, cp1d)
+        IMAS.flux_gacode_to_fuse((:electron_energy_flux, :ion_energy_flux,  :electron_particle_flux, :ion_particle_flux, :momentum_flux), actor.flux_solutions, m1d, eqt, cp1d)
 
     elseif par.model == :hirshmansigmar
         model.identifier.name = "Hirshman-Sigmar"
-        IMAS.flux_gacode_to_fuse([:ion_energy_flux, :electron_energy_flux, :electron_particle_flux], actor.flux_solutions, m1d, eqt, cp1d)
+        IMAS.flux_gacode_to_fuse((:electron_energy_flux, :ion_energy_flux,  :electron_particle_flux, :ion_particle_flux), actor.flux_solutions, m1d, eqt, cp1d)
     end
 
     return actor

src/actors/transport/qlgyro_actor.jl

@@ -107,7 +107,7 @@ function _finalize(actor::ActorQLGYRO)
     m1d = resize!(model.profiles_1d)
     m1d.grid_flux.rho_tor_norm = par.rho_transport
 
-    IMAS.flux_gacode_to_fuse([:ion_energy_flux, :electron_energy_flux, :electron_particle_flux, :momentum_flux], actor.flux_solutions, m1d, eqt, cp1d)
+    IMAS.flux_gacode_to_fuse((:electron_energy_flux, :ion_energy_flux,  :electron_particle_flux, :ion_particle_flux, :momentum_flux), actor.flux_solutions, m1d, eqt, cp1d)
 
     return actor
 end

src/actors/transport/tglf_actor.jl

@@ -115,7 +115,7 @@ function _finalize(actor::ActorTGLF)
     m1d = resize!(model.profiles_1d)
     m1d.grid_flux.rho_tor_norm = par.rho_transport
 
-    IMAS.flux_gacode_to_fuse([:ion_energy_flux, :electron_energy_flux, :electron_particle_flux, :momentum_flux], actor.flux_solutions, m1d, eqt, cp1d)
+    IMAS.flux_gacode_to_fuse((:electron_energy_flux, :ion_energy_flux,  :electron_particle_flux, :ion_particle_flux, :momentum_flux), actor.flux_solutions, m1d, eqt, cp1d)
 
     return actor
 end