Merge branch 'main' of https://github.com/PeriHub/PeriLab.jl into main

PeriHub · Mar 24, 2024 · 99c74b7 · 99c74b7
2 parents e9232bf + 2c31031
commit 99c74b7
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diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml
@@ -32,9 +32,7 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          # Edit the following line to reflect the actual name of the GitHub Secret containing your private key
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
-          # ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}
+          ssh: ${{ secrets.SSH_KEY }}
   DockerHub:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
     runs-on: ubuntu-latest

diff --git a/src/IO/IO.jl b/src/IO/IO.jl
@@ -24,6 +24,8 @@ using Reexport
 @reexport using .Parameter_Handling
 export initialize_data
 export init_write_results
+export get_results_mapping
+export init_orientations
 export write_results
 export merge_exodus_files
 export show_block_summary

diff --git a/src/Support/data_manager.jl b/src/Support/data_manager.jl
@@ -377,9 +377,13 @@ Returns a list of all field keys.
 """
 function clear_data_manager()
     global field_types
+    global nsets
+    global nnsets
     global physics_options
 
     field_types = Dict()
+    nsets = Dict()
+    nnsets = 0
     physics_options = Dict("Deformed Bond Geometry" => true,
     "Deformation Gradient" => false,
     "Shape Tensor" => false,
@@ -391,13 +395,11 @@ function clear_data_manager()
     # global properties
     # global fields
     # global model_modules
-    # global nsets
     # field_array_type = Dict()
     # fields_to_synch = Dict()
     # properties = Dict()
     # fields = Dict()
     # model_modules = Dict()
-    # nsets = Dict()
 end
 
 """

diff --git a/test/unit_tests/Compute/ut_compute_field_values.jl b/test/unit_tests/Compute/ut_compute_field_values.jl
@@ -3,10 +3,11 @@
 # SPDX-License-Identifier: BSD-3-Clause
 
 using Test
-include("../../../src/Support/data_manager.jl")
+# include("../../../src/Support/data_manager.jl")
 include("../../../src/Compute/compute_field_values.jl")
 @testset "ut_get_forces_from_force_density" begin
-    test_Data_manager = Data_manager
+    test_Data_manager = PeriLab.Data_manager
+    test_Data_manager.clear_data_manager()
     test_Data_manager.set_num_controller(5)
 
     test_Data_manager.create_node_field("Forces", Float64, 3)
@@ -27,7 +28,7 @@ include("../../../src/Compute/compute_field_values.jl")
 end
 
 @testset "ut_get_partial_stresses" begin
-    test_Data_manager = Data_manager
+    test_Data_manager = PeriLab.Data_manager
     test_Data_manager.set_dof(3)
     test_Data_manager.set_num_controller(5)
     nn = test_Data_manager.create_constant_node_field("Number of Neighbors", Int64, 1)

diff --git a/test/unit_tests/Compute/ut_compute_global_values.jl b/test/unit_tests/Compute/ut_compute_global_values.jl
@@ -3,11 +3,11 @@
 # SPDX-License-Identifier: BSD-3-Clause
 
 using Test
-include("../../../src/Support/data_manager.jl")
+# include("../../../src/Support/data_manager.jl")
 include("../../../src/Compute/compute_global_values.jl")
 
 @testset "ut_global_value_sum" begin
-    test_Data_manager = Data_manager
+    test_Data_manager = PeriLab.Data_manager
     test_Data_manager.set_num_controller(4)
     nodes = Vector{Int64}(1:4)
     (forcesN, forcesNP1) = test_Data_manager.create_node_field("Forces", Float64, 3)
@@ -41,7 +41,7 @@ include("../../../src/Compute/compute_global_values.jl")
 end
 
 @testset "ut_global_value_max" begin
-    test_Data_manager = Data_manager
+    test_Data_manager = PeriLab.Data_manager
     test_Data_manager.set_num_controller(4)
     nodes = Vector{Int64}(1:4)
     (forcesN, forcesNP1) = test_Data_manager.create_node_field("Forces", Float64, 3)
@@ -76,7 +76,7 @@ end
 end
 
 @testset "ut_global_value_min" begin
-    test_Data_manager = Data_manager
+    test_Data_manager = PeriLab.Data_manager
     test_Data_manager.set_num_controller(4)
     nodes = Vector{Int64}(1:4)
     (forcesN, forcesNP1) = test_Data_manager.create_node_field("Forces", Float64, 3)
@@ -108,7 +108,7 @@ end
     @test isnothing(calculate_nodelist(test_Data_manager, "not there", 1, "Minimum", nodes))
 end
 @testset "ut_global_value_avg" begin
-    test_Data_manager = Data_manager
+    test_Data_manager = PeriLab.Data_manager
     test_Data_manager.set_num_controller(4)
     nodes = Vector{Int64}(1:4)
     (forcesN, forcesNP1) = test_Data_manager.create_node_field("Forces", Float64, 3)
@@ -141,7 +141,7 @@ end
 end
 
 @testset "ut_calculate_block" begin
-    test_Data_manager = Data_manager
+    test_Data_manager = PeriLab.Data_manager
     test_Data_manager.create_constant_node_field("Block_Id", Int64, 1)
     @test isnothing(calculate_block(test_Data_manager, "no field", 1, "sum", 1))
     @test isnothing(calculate_block(test_Data_manager, "Disp", 1, "no option", 1))

diff --git a/test/unit_tests/Core/Module_inclusion/ut_set_Modules.jl b/test/unit_tests/Core/Module_inclusion/ut_set_Modules.jl
@@ -7,7 +7,7 @@ include("../../../../src/Core/Module_inclusion/set_Modules.jl")
 
 using Test
 using Random
-using .Set_modules
+# using .Set_modules
 
 @testset "ut_find_jl_files" begin
     Random.seed!(rand(1:100000))
@@ -47,7 +47,7 @@ using .Set_modules
     io = open(folder * "/" * filename4 * ".dat", "w")
     close(io)
 
-    list = Set_modules.find_jl_files(base)
+    list = PeriLab.Solver.FEM.Set_modules.find_jl_files(base)
     folder * "/" * filename1 * ".jl" in list
     @test subfolder1 * "/" * filename2 * ".jl" in list
     @test subfolder1 * "/" * filename3 * ".jl" in list

diff --git a/test/unit_tests/Core/Solver/ut_Solver_control.jl b/test/unit_tests/Core/Solver/ut_Solver_control.jl
@@ -5,19 +5,19 @@
 using Test
 using MPI
 using TimerOutputs
-include("../../../../src/Core/Solver/Solver_control.jl")
-include("../../../../src/Support/geometry.jl")
-if !isdefined(@__MODULE__, :Data_manager)
-    include("../../../../src/Support/data_manager.jl")
-end
-include("../../../../src/Support/Parameters/parameter_handling.jl")
-using Reexport
-@reexport using .Parameter_Handling
-import .Solver
+# include("../../../../src/Core/Solver/Solver_control.jl")
+# include("../../../../src/Support/geometry.jl")
+# if !isdefined(@__MODULE__, :Data_manager)
+#     include("../../../../src/Support/data_manager.jl")
+# end
+# include("../../../../src/Support/Parameters/parameter_handling.jl")
+# using Reexport
+# @reexport using .Parameter_Handling
+# import .Solver
 
 @testset "ut_get_block_nodes" begin
     block_ids = [1, 1, 1, 2, 2, 3, 3, 3, 3, 1, 1, 2, 3, 3, 1, 1, 2]
-    block_nodes = Solver.get_block_nodes(block_ids, length(block_ids))
+    block_nodes = PeriLab.Solver.get_block_nodes(block_ids, length(block_ids))
     @test block_nodes[1] == [1, 2, 3, 10, 11, 15, 16]
     @test block_nodes[2] == [4, 5, 12, 17]
     @test block_nodes[3] == [6, 7, 8, 9, 13, 14]

diff --git a/test/unit_tests/Core/Solver/ut_Verlet.jl b/test/unit_tests/Core/Solver/ut_Verlet.jl
@@ -5,45 +5,45 @@
 using Test
 
 
-include("../../../../src/Core/BC_manager.jl")
-include("../../../../src/Core/Solver/Verlet.jl")
-include("../../../../src/Core/Solver/Solver_control.jl")
-include("../../../../src/Support/geometry.jl")
+# include("../../../../src/Core/BC_manager.jl")
+# include("../../../../src/Core/Solver/Verlet.jl")
+# include("../../../../src/Core/Solver/Solver_control.jl")
+# include("../../../../src/Support/geometry.jl")
 
-if !isdefined(@__MODULE__, :Data_manager)
-    include("../../../../src/Support/data_manager.jl")
-end
-include("../../../../src/Support/Parameters/parameter_handling.jl")
-using Reexport
-@reexport using .Parameter_Handling
-using .Data_manager
-using .Geometry
-using .Boundary_conditions
-using .Solver
-using .Verlet
+# if !isdefined(@__MODULE__, :Data_manager)
+#     include("../../../../src/Support/data_manager.jl")
+# end
+# include("../../../../src/Support/Parameters/parameter_handling.jl")
+# using Reexport
+# @reexport using .Parameter_Handling
+# using .Data_manager
+# using .Geometry
+# using .Boundary_conditions
+# using .Solver
+# using .Verlet
 using MPI
 @testset "ut_test_timestep" begin
-    @test Verlet.test_timestep(1.0, 2.0) == 1
-    @test Verlet.test_timestep(2.0, 1.1) == 1.1
-    @test Verlet.test_timestep(2.0, 2.0) == 2
+    @test PeriLab.Solver.Verlet.test_timestep(1.0, 2.0) == 1
+    @test PeriLab.Solver.Verlet.test_timestep(2.0, 1.1) == 1.1
+    @test PeriLab.Solver.Verlet.test_timestep(2.0, 2.0) == 2
 end
 
 @testset "ut_get_integration_steps" begin
-    @test isnothing(Verlet.get_integration_steps(0.0, 0.0, -1.0))
-    @test Verlet.get_integration_steps(0.0, 1.0, 1.0) == (1, 1.0)
-    @test Verlet.get_integration_steps(0.0, 2.0, 1.0) == (2, 1.0)
-    @test Verlet.get_integration_steps(0.0, 6.0, 2.0) == (3, 2.0)
-    @test Verlet.get_integration_steps(2.0, 6.0, 2.0) == (2, 2.0)
+    @test isnothing(PeriLab.Solver.Verlet.get_integration_steps(0.0, 0.0, -1.0))
+    @test PeriLab.Solver.Verlet.get_integration_steps(0.0, 1.0, 1.0) == (1, 1.0)
+    @test PeriLab.Solver.Verlet.get_integration_steps(0.0, 2.0, 1.0) == (2, 1.0)
+    @test PeriLab.Solver.Verlet.get_integration_steps(0.0, 6.0, 2.0) == (3, 2.0)
+    @test PeriLab.Solver.Verlet.get_integration_steps(2.0, 6.0, 2.0) == (2, 2.0)
 end
 
 @testset "ut_get_cs_denominator" begin
     volume = Float64[1, 2, 3]
     undeformed_bond = [1, 2, 3]
-    @test Verlet.get_cs_denominator(volume, undeformed_bond) == 3
+    @test PeriLab.Solver.Verlet.get_cs_denominator(volume, undeformed_bond) == 3
     undeformed_bond = [2, 4, 6]
-    @test Verlet.get_cs_denominator(volume, undeformed_bond) == 1.5
+    @test PeriLab.Solver.Verlet.get_cs_denominator(volume, undeformed_bond) == 1.5
     undeformed_bond = [1, 0.5, 2]
-    @test Verlet.get_cs_denominator(volume, undeformed_bond) == 6.5
+    @test PeriLab.Solver.Verlet.get_cs_denominator(volume, undeformed_bond) == 6.5
 end
 
 # nnodes = 5