Skip to content
Snippets Groups Projects
Commit 40ae48e5 authored by KyleKlenk's avatar KyleKlenk
Browse files

Add Test configuration

parent 47a4f0cb
No related branches found
No related tags found
No related merge requests found
.vscode/settings.json
results.csv
tests/output/*
simulations/output/*
[actors]
# global parameters
output_dir = "/code/output/"
output_dir = "/code/openCARP-Actors/simulations/output/"
results_file = "results.csv"
tolerance = 1
......
#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
#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
[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
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
-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
......@@ -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
......
......@@ -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
# ----------------------------------------
......
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
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment