Add Test configuration

.gitignore

 .vscode/settings.json
 results.csv
+tests/output/*
+simulations/output/*

simulations/input/config_official.toml

 [actors]
 # global parameters
-output_dir = "/code/output/"
+output_dir = "/code/openCARP-Actors/simulations/output/"
 results_file = "results.csv"
 tolerance = 1
 

simulations/input/s1.par

-#Parameters file for the S1-S2 Actors Study
-#mesh parameters (these parameters get passed to mesher when the Python script is run. Hopefully 
-#                 openCARP automatically does this when only using the .par file.)
-meshname = /code/openCARP-Actors/simulations/input/meshes/large_domain/block
-#physical regions
+# Parameters file for the S1-S2 Actors Study (S1)
+# Mesh Needs to be generated first by Carputils
+
+
+meshname = /code/openCARP-Actors/tests/input/meshes/test_mesh/block
+
+
+############### physical regions ##############
 num_phys_regions     = 2
 phys_region[0].name  = "Intracellular domain"
 phys_region[0].ptype = 0 
@@ -12,10 +15,13 @@ phys_region[1].name  = "Extracellular domain"
 phys_region[1].ptype = 1
 phys_region[1].num_IDs = 1
 phys_region[1].ID[0] = 1
-# ionic setup
+
+############### ionic setup ###################
 num_imp_regions      = 1
 imp_region[0].im     = Shannon
-#stimulus setup
+
+
+############## stimulus setup #################
 num_stim             =      3
 stimulus[0].name     = "S1"
 stimulus[0].stimtype =      1 
@@ -28,50 +34,46 @@ stimulus[0].y0       = -50.0
 stimulus[0].yd       = 275.0
 stimulus[0].z0       = 1950.0
 stimulus[0].zd       = 100.0
-# stimulus[1].name     = "S2"
-# stimulus[1].stimtype =      1
-# stimulus[1].duration =      2.
-# stimulus[1].npls     =      1
-# stimulus[1].x0       = -50.0
-# stimulus[1].xd       = 275.0
-# stimulus[1].y0       = -50.0
-# stimulus[1].yd       = 275.0
-# stimulus[1].z0       = 1950.0
-# stimulus[1].zd       = 100.0
-stimulus[2].name     = "Ground"
-stimulus[2].stimtype =      3
-stimulus[2].x0       = -50.0
-stimulus[2].xd       = 10100.0
-stimulus[2].y0       = -50.0
-stimulus[2].yd       = 10100.0
-stimulus[2].z0       = -50.0
-stimulus[2].zd       = 100.0
-#Simulation parameters
+
+stimulus[1].name     = "Ground"
+stimulus[1].stimtype =      3
+stimulus[1].x0       = -50.0
+stimulus[1].xd       = 10100.0
+stimulus[1].y0       = -50.0
+stimulus[1].yd       = 10100.0
+stimulus[1].z0       = -50.0
+stimulus[1].zd       = 100.0
+
+
+################# Simulation parameters #################
 bidomain = 1 
 tend    =  300. 
 spacedt = 1.0 
 timedt = 1.0
 parab_solve = 1
-#S1-S2 script params to start with:
-#S1 min = 1.0e7
-#S1 max = 3.0e7
-#(Actual S1 threshold = 28,167,114)
-#Absolute S2 max = 3.0e8 (could go higher if needed, it depends when the solution blows up.)
-#S1S2_interval_min=185
-#S1S2_interval_max=205 (If it is still refractory here, we can extend the range. If it is not, 
+
+
+############# Notes #############
+# S1-S2 script params to start with:
+# S1 min = 1.0e7
+# S1 max = 3.0e7
+# (Actual S1 threshold = 28,167,114)
+# Absolute S2 max = 3.0e8 (could go higher if needed, it depends when the solution blows up.)
+# S1S2_interval_min=185
+# S1S2_interval_max=205 (If it is still refractory here, we can extend the range. If it is not, 
 #                       we can extend it in the other direction by lowering min.)
-#S1S2_interval_increment=1
-#This interval range is subject to change...I have it so that we find 20 data points, 
-#but I don't know what the proper min and max is for this setup yet. 
-#tol = 1 
-#So far I have tolerance at 1, but because we are working on a much larger scale, we could probably
-#increase this number quite a bit if needed.
-#Sample points - 2 in bottom left, 2 in bottom right, 2 close to centre, 4 in top left, 4 in top right.
-#E.g.:  Bottom Left = (2, 2, 0.5), (2, 2, 1.5)
-#       Bottom Right = (8, 8, 0.5), (8, 8, 1.5)
-#       Centre       = (3.5, 5, 0.5), (6.5, 5, 1.5)
-#       Top Left     = (0, 10, 0.5), (0, 10, 1.5), (0.5, 9.5, 0.25), (0.5, 9.5, 1.75)
-#       Top Right    = (10, 10, 0.5), (10, 10, 1.5), (9.5, 9.5, 0.25), (9.5, 9.5, 1.75)
+# S1S2_interval_increment=1
+# This interval range is subject to change...I have it so that we find 20 data points, 
+# but I don't know what the proper min and max is for this setup yet. 
+# tol = 1 
+# So far I have tolerance at 1, but because we are working on a much larger scale, we could probably
+# increase this number quite a bit if needed.
+# Sample points - 2 in bottom left, 2 in bottom right, 2 close to centre, 4 in top left, 4 in top right.
+# E.g.:  Bottom Left = (2, 2, 0.5), (2, 2, 1.5)
+#        Bottom Right = (8, 8, 0.5), (8, 8, 1.5)
+#        Centre       = (3.5, 5, 0.5), (6.5, 5, 1.5)
+#        Top Left     = (0, 10, 0.5), (0, 10, 1.5), (0.5, 9.5, 0.25), (0.5, 9.5, 1.75)
+#        Top Right    = (10, 10, 0.5), (10, 10, 1.5), (9.5, 9.5, 0.25), (9.5, 9.5, 1.75)
 # These are somewhat arbitrary, we will need to test these out and see how they go.
 # Also, it is unlikely that these exact coordinates are vertices. This is okay, however, in the paper,
 # we should put what the actual coordinates are.
\ No newline at end of file

simulations/input/s2.par

-#Parameters file for the S1-S2 Actors Study
-#mesh parameters (these parameters get passed to mesher when the Python script is run. Hopefully 
-#                 openCARP automatically does this when only using the .par file.)
+#Parameters file for the S1-S2 Actors Study (S2)
+# Mesh Needs to be generated first by Carputils
+
 
 meshname = /code/openCARP-Actors/simulations/input/meshes/large_domain/block
-#physical regions
+
+############### physical regions ##############
 num_phys_regions     = 2
 phys_region[0].name  = "Intracellular domain"
 phys_region[0].ptype = 0 
@@ -13,10 +14,12 @@ phys_region[1].name  = "Extracellular domain"
 phys_region[1].ptype = 1
 phys_region[1].num_IDs = 1
 phys_region[1].ID[0] = 1
-# ionic setup
+
+############### ionic setup ###################
 num_imp_regions      = 1
 imp_region[0].im     = Shannon
-#stimulus setup
+
+############## stimulus setup #################
 num_stim             =      3
 stimulus[0].name     = "S1"
 stimulus[0].stimtype =      1 
@@ -47,32 +50,36 @@ stimulus[2].y0       = -50.0
 stimulus[2].yd       = 10100.0
 stimulus[2].z0       = -50.0
 stimulus[2].zd       = 100.0
-#Simulation parameters
+
+################# Simulation parameters #################
 bidomain = 1 
 tend    =  300. 
 spacedt = 1.0 
 timedt = 1.0
 parab_solve = 1
-#S1-S2 script params to start with:
-#S1 min = 1.0e7
-#S1 max = 3.0e7
-#(Actual S1 threshold = 28,167,114)
-#Absolute S2 max = 3.0e8 (could go higher if needed, it depends when the solution blows up.)
-#S1S2_interval_min=185
-#S1S2_interval_max=205 (If it is still refractory here, we can extend the range. If it is not, 
+
+
+############# Notes #############
+# S1-S2 script params to start with:
+# S1 min = 1.0e7
+# S1 max = 3.0e7
+# (Actual S1 threshold = 28,167,114)
+# Absolute S2 max = 3.0e8 (could go higher if needed, it depends when the solution blows up.)
+# S1S2_interval_min=185
+# S1S2_interval_max=205 (If it is still refractory here, we can extend the range. If it is not, 
 #                       we can extend it in the other direction by lowering min.)
-#S1S2_interval_increment=1
-#This interval range is subject to change...I have it so that we find 20 data points, 
-#but I don't know what the proper min and max is for this setup yet. 
-#tol = 1 
-#So far I have tolerance at 1, but because we are working on a much larger scale, we could probably
-#increase this number quite a bit if needed.
-#Sample points - 2 in bottom left, 2 in bottom right, 2 close to centre, 4 in top left, 4 in top right.
-#E.g.:  Bottom Left = (2, 2, 0.5), (2, 2, 1.5)
-#       Bottom Right = (8, 8, 0.5), (8, 8, 1.5)
-#       Centre       = (3.5, 5, 0.5), (6.5, 5, 1.5)
-#       Top Left     = (0, 10, 0.5), (0, 10, 1.5), (0.5, 9.5, 0.25), (0.5, 9.5, 1.75)
-#       Top Right    = (10, 10, 0.5), (10, 10, 1.5), (9.5, 9.5, 0.25), (9.5, 9.5, 1.75)
+# S1S2_interval_increment=1
+# This interval range is subject to change...I have it so that we find 20 data points, 
+# but I don't know what the proper min and max is for this setup yet. 
+# tol = 1 
+# So far I have tolerance at 1, but because we are working on a much larger scale, we could probably
+# increase this number quite a bit if needed.
+# Sample points - 2 in bottom left, 2 in bottom right, 2 close to centre, 4 in top left, 4 in top right.
+# E.g.:  Bottom Left = (2, 2, 0.5), (2, 2, 1.5)
+#        Bottom Right = (8, 8, 0.5), (8, 8, 1.5)
+#        Centre       = (3.5, 5, 0.5), (6.5, 5, 1.5)
+#        Top Left     = (0, 10, 0.5), (0, 10, 1.5), (0.5, 9.5, 0.25), (0.5, 9.5, 1.75)
+#        Top Right    = (10, 10, 0.5), (10, 10, 1.5), (9.5, 9.5, 0.25), (9.5, 9.5, 1.75)
 # These are somewhat arbitrary, we will need to test these out and see how they go.
 # Also, it is unlikely that these exact coordinates are vertices. This is okay, however, in the paper,
 # we should put what the actual coordinates are.
\ No newline at end of file

tests/config_test.toml → tests/input/config_test.toml

 [actors]
 # global parameters
-output_dir = "/code/output/"
-results_file = "results.csv"
+output_dir = "/code/openCARP-Actors/tests/output/"
+results_file = "/code/openCARP-Actors/tests/output/results.csv"
 tolerance = 1
 
 # s1 parameters
@@ -9,15 +9,15 @@ s1_min = 1.0
 s1_max = 250.0
 
 # s2 parameters
-s2_args = ['openCARP', '+F', '/code/simulations/input/tests/s1_s2.par']
+s2_args = ['openCARP', '+F', '//code/openCARP-Actors/tests/input/s2.par']
 s2_min = 100.0
 s2_max = 500.0
 s2_interval_min = 245
 s2_interval_max = 250
-s2_interval_increment = 1
+s2_interval_increment = 5
 
 
 [petsc]
 
 [openCARP]
-args = ['openCARP', '+F', '/code/simulations/input/tests/new_basic.par']
\ No newline at end of file
+args = ['openCARP', '+F', '//code/openCARP-Actors/tests/input/s1.par']
\ No newline at end of file

tests/input/meshes/test_mesh/mesher_cmd.txt

+-size[0]
+1.0
+-size[1]
+0.1
+-size[2]
+0.02
+-bath[0]
+-0.0
+-bath[1]
+-0.0
+-bath[2]
+-0.0
+-center[0]
+0.0
+-center[1]
+0.0
+-center[2]
+0.0
+-resolution[0]
+100.0
+-resolution[1]
+100.0
+-resolution[2]
+100.0
+-mesh
+<placeholder>
+-Elem3D
+0
+-fibers.rotEndo
+0.0
+-fibers.rotEpi
+0.0
+-fibers.sheetEndo
+90.0
+-fibers.sheetEpi
+90.0
+-periodic
+0
+-periodic_tag
+1234
+-perturb
+0.0
\ No newline at end of file

tests/new_basic.par → tests/input/s1.par

@@ -8,7 +8,7 @@ simID = Test_Output/34
 # Meshname
 # ----------------------------------------
 
-meshname = /code/simulations/input/meshes/2023-08-18_kIyaoCwKin/block
+meshname = /code/openCARP-Actors/tests/input/meshes/test_mesh/block
 
 # ----------------------------------------
 # Definition of physics region

tests/s1_s2.par → tests/input/s2.par

@@ -8,7 +8,7 @@ simID = output/
 # Meshname
 # ----------------------------------------
 
-meshname = /code/simulations/input/meshes/2023-08-18_kIyaoCwKin/block
+meshname = /code/openCARP-Actors/tests/input/meshes/test_mesh/block
 
 
 # ----------------------------------------

tests/timing.txt

+Agha
+
+Run 1:
+real    3m35.834s
+user    56m32.703s
+sys     0m8.851s
+
+Run 2:
+real    3m17.573s
+user    51m49.249s
+sys     0m5.414s
+
+Run 3:
+real    3m16.245s
+user    51m29.026s
+sys     0m4.755s
+
+
+After update
+real    3m1.850s
+user    47m39.918s
+sys     0m4.916s
+
+real    3m1.776s
+user    47m39.225s
+sys     0m5.412s
\ No newline at end of file