diff --git a/.gitignore b/.gitignore
index ce4825bef7e29737b9b90a911afd7dd9cfdac113..c424aedc3b5e413cdceada7a8e5499140b6225d3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,3 +8,4 @@ output8.txt
simulations/logs/*
.DS_Store
s1_s2_simulation
+output/
diff --git a/config.toml b/config.toml
index 31ef4ab6dfefadaff5d2432c590476287c5f7617..7b07744f8eb7346f4dfe3ca4180db9138f031222 100644
--- a/config.toml
+++ b/config.toml
@@ -5,19 +5,19 @@ results_file = "results.csv"
tolerance = 1
# s1 parameters
-s1_min = 30
-s1_max = 34
+s1_min = 1.0e7
+s1_max = 3.0e7
# s2 parameters
-s2_args = ['openCARP', '+F', '/code/openCARP-Actors/simulations/input/s1_s2.par']
-s2_min = 100
-s2_max = 500
-s2_interval_min = 250
-s2_interval_max = 250
-s2_interval_increment = 5
+s2_args = ['openCARP', '+F', '/code/simulations/input/s2.par']
+s2_min = 1.0e8
+s2_max = 3.0e8
+s2_interval_min = 185
+s2_interval_max = 205
+s2_interval_increment = 1
[petsc]
[openCARP]
-args = ['openCARP', '+F', '/code/openCARP-Actors/simulations/input/new_basic.par']
\ No newline at end of file
+args = ['openCARP', '+F', '/code/simulations/input/s1.par']
\ No newline at end of file
diff --git a/config.yaml b/config.yaml
deleted file mode 100644
index 0bb9447013d747ccecb45bc4a77b301f27301e6a..0000000000000000000000000000000000000000
--- a/config.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-# Configuration File for openCARP-Actors
-# This file helps assemble the openCARP command line arguments
-
-
-some_val:
- - 1
- - 2
\ No newline at end of file
diff --git a/environment_setup/Dockerfile b/environment_setup/Dockerfile
index 0eb6ef63c24e1fa2d1d94977add13ee237a0893d..d488dc3fdac53e9709bbc02ac8fc4ea3efb94c60 100755
--- a/environment_setup/Dockerfile
+++ b/environment_setup/Dockerfile
@@ -59,10 +59,16 @@ RUN cmake ..
RUN make
RUN make install
+# Install TOML
+WORKDIR /opt
+RUN git clone https://github.com/marzer/tomlplusplus.git
+
+
# Install OpenCARP From Numerical Simulations
WORKDIR /opt
RUN git clone https://git.cs.usask.ca/numerical_simulations_lab/cardiac/openCARP.git
WORKDIR /opt/openCARP
+RUN git checkout develop
RUN cmake -S. -B_build -DDLOPEN=ON -DCMAKE_BUILD_TYPE=Debug
RUN cmake --build _build
@@ -78,21 +84,6 @@ ENV PATH=$PATH:/opt/openCARP/_build/bin
RUN python3 ./bin/cusettings $HOME/.config/carputils/settings.yaml
ADD settings.yaml /root/.config/carputils/
-# Install YAML
-# WORKDIR /opt
-# RUN git clone https://github.com/jbeder/yaml-cpp.git
-# WORKDIR /opt/yaml-cpp
-# RUN mkdir build
-# WORKDIR /opt/yaml-cpp/build
-# RUN cmake ..
-# RUN make
-# RUN make install
-
-# Install TOML
-WORKDIR /opt
-RUN git clone https://github.com/marzer/tomlplusplus.git
-
-
# Set entrypoint
WORKDIR /code
diff --git a/find_s1.py b/legacy_scripts/find_s1.py
similarity index 100%
rename from find_s1.py
rename to legacy_scripts/find_s1.py
diff --git a/find_s2.py b/legacy_scripts/find_s2.py
similarity index 50%
rename from find_s2.py
rename to legacy_scripts/find_s2.py
index 2d774741ceb7aa2a4a917767c33cff664fb64adb..ec303782b9fe7c1535c112eb831caaf4171d5222 100644
--- a/find_s2.py
+++ b/legacy_scripts/find_s2.py
@@ -62,7 +62,7 @@ def run(args, job):
#===========================================
# Create a block with a thin z dimension
- x = 10.0 #(mm)
+ x = 1.0 #(mm)
y = 1.0 #(mm)
z = 0.2 #(mm)
geom = mesh.Block(size=(x,y,z))
@@ -73,61 +73,61 @@ def run(args, job):
# Finilaize the creation of the mesh
meshname = mesh.generate(geom)
- #===========================================
- # 2: Define the ionic models & conductivities
- #===========================================
-
- # Query for element labels
- _, etags, _ = txt.read(meshname + '.elem')
- etags = np.unique(etags)
-
- IntraTags = etags[etags != 0].tolist()
- ExtraTags = etags.tolist().copy()
-
- #===========================================
- # 3: Configure the simulation
- #===========================================
-
- # Define the geometry of the stimulus at one end of the block
- # Units are um
- stim = ['-num_stim', 2,
- '-stimulus[0].name', 'S1', #index 0 because only one type of electrode
- '-stimulus[0].stimtype', 0, #0 means intracellular stim
- '-stimulus[0].strength', args.S1_strength, #uA/Cm^2
- '-stimulus[0].duration', args.S1_dur,
- '-stimulus[0].start', args.S1_start,
- '-stimulus[1].name', 'S2',
- '-stimulus[1].stimtype', 0,
- '-stimulus[1].strength', args.S2_strength,
- '-stimulus[1].duration', args.S2_dur,
- '-stimulus[1].start', args.S2_start]
-
- #electrode = mesh.block_boundary_condition(geom, 'stimulus', 0, 'x', True) #True refers to a BC between tissue and bath
- E1_lower_bound = nplist([ 0.0, 0.0, 0.0])
- E1_upper_bound = nplist([ 2.0, 0.3, 0.2])
- electrode = mesh.block_region(geom, 'stimulus', 0, E1_lower_bound, E1_upper_bound, False) # introudce a stimulus in the region defined by the lower and upper bounds
-
- #electrode = mesh.block_boundary_condition(geom, 'stimulus', 0, 'x', True) #True refers to a BC between tissue and bath
- E1_lower_bound = nplist([ 0.0, 0.0, 0.0])
- E1_upper_bound = nplist([ 2.0, 0.3, 0.2])
- electrode = mesh.block_region(geom, 'stimulus', 0, E1_lower_bound, E1_upper_bound, False) # introudce a stimulus in the region defined by the lower and upper bounds
-
- #===========================================
- # 4: Defining simulator options:
- #===========================================
-
- # Get basic command line, including solver options
- cmd = tools.carp_cmd(os.path.join('simulations/input/basic.par')) #cmd is a carp command
-
- cmd += ['-simID', job.ID,
- '-meshname', meshname,
- '-dt', 25,
- '-tend', args.duration]
- cmd += tools.gen_physics_opts(ExtraTags=ExtraTags, IntraTags=IntraTags)
- cmd += stim + electrode
-
- # Run simulation
- print(cmd)
- job.carp(cmd) #cmd includes the params
+ # #===========================================
+ # # 2: Define the ionic models & conductivities
+ # #===========================================
+
+ # # Query for element labels
+ # _, etags, _ = txt.read(meshname + '.elem')
+ # etags = np.unique(etags)
+
+ # IntraTags = etags[etags != 0].tolist()
+ # ExtraTags = etags.tolist().copy()
+
+ # #===========================================
+ # # 3: Configure the simulation
+ # #===========================================
+
+ # # Define the geometry of the stimulus at one end of the block
+ # # Units are um
+ # stim = ['-num_stim', 2,
+ # '-stimulus[0].name', 'S1', #index 0 because only one type of electrode
+ # '-stimulus[0].stimtype', 0, #0 means intracellular stim
+ # '-stimulus[0].strength', args.S1_strength, #uA/Cm^2
+ # '-stimulus[0].duration', args.S1_dur,
+ # '-stimulus[0].start', args.S1_start,
+ # '-stimulus[1].name', 'S2',
+ # '-stimulus[1].stimtype', 0,
+ # '-stimulus[1].strength', args.S2_strength,
+ # '-stimulus[1].duration', args.S2_dur,
+ # '-stimulus[1].start', args.S2_start]
+
+ # #electrode = mesh.block_boundary_condition(geom, 'stimulus', 0, 'x', True) #True refers to a BC between tissue and bath
+ # E1_lower_bound = nplist([ 0.0, 0.0, 0.0])
+ # E1_upper_bound = nplist([ 2.0, 0.3, 0.2])
+ # electrode = mesh.block_region(geom, 'stimulus', 0, E1_lower_bound, E1_upper_bound, False) # introudce a stimulus in the region defined by the lower and upper bounds
+
+ # #electrode = mesh.block_boundary_condition(geom, 'stimulus', 0, 'x', True) #True refers to a BC between tissue and bath
+ # E1_lower_bound = nplist([ 0.0, 0.0, 0.0])
+ # E1_upper_bound = nplist([ 2.0, 0.3, 0.2])
+ # electrode = mesh.block_region(geom, 'stimulus', 0, E1_lower_bound, E1_upper_bound, False) # introudce a stimulus in the region defined by the lower and upper bounds
+
+ # #===========================================
+ # # 4: Defining simulator options:
+ # #===========================================
+
+ # # Get basic command line, including solver options
+ # cmd = tools.carp_cmd(os.path.join('simulations/input/basic.par')) #cmd is a carp command
+
+ # cmd += ['-simID', job.ID,
+ # '-meshname', meshname,
+ # '-dt', 25,
+ # '-tend', args.duration]
+ # cmd += tools.gen_physics_opts(ExtraTags=ExtraTags, IntraTags=IntraTags)
+ # cmd += stim + electrode
+
+ # # Run simulation
+ # print(cmd)
+ # job.carp(cmd) #cmd includes the params
run()
\ No newline at end of file
diff --git a/main.cpp b/legacy_scripts/main.cpp
similarity index 100%
rename from main.cpp
rename to legacy_scripts/main.cpp
diff --git a/src/main.cpp b/legacy_scripts/src/main.cpp
similarity index 100%
rename from src/main.cpp
rename to legacy_scripts/src/main.cpp
diff --git a/results.csv b/results.csv
new file mode 100644
index 0000000000000000000000000000000000000000..5499adf4df0ad2f6f17dc334cb47af9324f377fb
--- /dev/null
+++ b/results.csv
@@ -0,0 +1 @@
+s1_strength,s2_sim_time,s2_strength
diff --git a/simulations/input/basic.par b/simulations/input/basic.par
deleted file mode 100644
index f10318b3925646ca5cce1f36054ed79649041543..0000000000000000000000000000000000000000
--- a/simulations/input/basic.par
+++ /dev/null
@@ -1,18 +0,0 @@
-# ionic setup
-num_imp_regions = 1
-
-imp_region[0].im = DrouhardRoberge
-
-#electrical setup
-num_stim = 1
-
-stimulus[0].name = "S1"
-stimulus[0].stimtype = 0
-stimulus[0].strength = 250.0
-stimulus[0].duration = 2.
-stimulus[0].start = 0.
-
-bidomain = 0
-spacedt = 1.
-timedt = 1.
-parab_solve = 1
diff --git a/simulations/input/generate_mesh.py b/simulations/input/generate_mesh.py
new file mode 100644
index 0000000000000000000000000000000000000000..ce56306f2ab31be586895c2cc0453a15199f92f9
--- /dev/null
+++ b/simulations/input/generate_mesh.py
@@ -0,0 +1,138 @@
+#!/usr/bin/env python
+
+"""
+This is the setup for the S1S2 Actors study.
+
+"""
+import os
+EXAMPLE_DESCRIPTIVE_NAME = 'S1-S2 Actors Simulation'
+EXAMPLE_AUTHOR = 'Joyce Reimer <joyce.reimer@usask.ca>'
+EXAMPLE_DIR = os.path.dirname(__file__)
+GUIinclude = True
+
+import sys
+from datetime import date
+
+from carputils import settings
+from carputils import tools
+from carputils import mesh
+import numpy as np
+from numpy import array as nplist
+
+def parser():
+ parser = tools.standard_parser()
+ group = parser.add_argument_group('experiment specific options')
+ group.add_argument('--duration',
+ type = float,
+ default = 300.,
+ help = 'Duration of simulation in [ms]')
+ group.add_argument('--S1-strength',
+ type = float,
+ default = 0.,
+ help = 'pick S1 extracellular current stimulus strength in [uA/cm^3]')
+ group.add_argument('--S1-dur',
+ type = float,
+ default = 2.,
+ help = 'pick S1 current stimulus duration in [ms] (default: 2.)')
+ group.add_argument('--S1-start',
+ type = float,
+ default = 0.0,
+ help = 'pick S1 start time')
+ group.add_argument('--S2-strength',
+ type = float,
+ default = 0.,
+ help = 'pick S2 extracellular current stimulus strength in [uA/cm^3]')
+ group.add_argument('--S2-dur',
+ type = float,
+ default = 2.,
+ help = 'pick S2 current stimulus duration in [ms] (default: 2.)')
+ group.add_argument('--S2-start',
+ type = float,
+ default = 235.0,
+ help = 'pick S2 start time')
+
+ return parser
+
+def jobID(args):
+ """
+ Generate name of top level output directory.
+ """
+ today = date.today()
+ return '{}_XCstim_{}_np{}'.format(today.isoformat(),
+ args.flv, args.np)
+
+@tools.carpexample(parser, jobID)
+def run(args, job):
+
+ # Generate mesh
+ # Block which is thin in z direction
+ geom = mesh.Block(size=(10.0, 10.0, 2.0)) #in mm
+ #geom = mesh.Block(size=(1.0, 1.0, 2.0)) #in mm
+ # Set fibre angle to 0, sheet angle to 0
+ geom.set_fibres(0, 0, 90, 90)
+ geom.corner_at_origin()
+ # Generate and return base name
+ meshname = mesh.generate(geom)
+
+ # # define electrode locations
+ # #Test electrode is in bottom left corner. Has the same area as our experimental data
+ # # and has a z-thickness the size of dx.
+
+ # E1_lower_bound = nplist([ 0.0, 0.0, 2.0]) #in mm
+ # E2_lower_bound = nplist([ 0.0, 0.0, 2.0])
+ # # Last number should always be z thickness; first two numbers should be 0 if corner at origin.
+
+ # E1_upper_bound = nplist([ 0.175, 0.175, 2.0]) #in mm
+ # E2_upper_bound = nplist([ 0.175, 0.175, 2.0]) #in mm
+ # #With these dimensions and default resolution of 0.1mm, we get electrode area = .225 x .225 = 0.05 mm^2.
+ # #Last number should always be z thickness.
+
+ # #S1 and S2 electrodes:
+ # lstm = mesh.block_region(geom, 'stimulus', 0, E1_lower_bound, E1_upper_bound, False)
+ # lstm2 = mesh.block_region(geom, 'stimulus', 1, E2_lower_bound, E2_upper_bound, False)
+
+
+ # #Reference/ground electrode is behind domain.
+ # rstm = mesh.block_boundary_condition(geom, 'stimulus', 2, 'z', lower=True, verbose=not args.silent)
+
+
+ # del geom
+
+ # #astm = []
+ # #mod = []
+
+ # # tags generated with the above command
+ # IntraTags = [1]
+ # ExtraTags = [1]
+
+ # lstm += ['-stimulus[0].stimtype', '1',
+ # '-stimulus[0].strength', args.S1_strength, #3e7 uA/cm^3 worked
+ # '-stimulus[0].duration', args.S1_dur,
+ # '-stimulus[0].start', args.S1_start]
+ # lstm2 +=['-stimulus[1].stimtype', '1',
+ # '-stimulus[1].strength', args.S2_strength,
+ # '-stimulus[1].duration', args.S2_dur,
+ # '-stimulus[1].start', args.S2_start]
+
+
+ # # Add all the non-general arguments
+ # cmd = tools.carp_cmd(os.path.join(EXAMPLE_DIR, 'stimtest-og.par'))
+
+ # cmd += ['-meshname', meshname,
+ # '-simID', job.ID,
+ # '-tend', args.duration]
+ # cmd += tools.gen_physics_opts(ExtraTags=ExtraTags, IntraTags=IntraTags)
+
+ # # add PDE solver options
+ # cmd += lstm + lstm2 + rstm
+
+ # if args.visualize:
+ # cmd += ['-gridout_i', 3,
+ # '-gridout_e', 3]
+
+ # # Run simulations
+ # job.carp(cmd)
+
+
+if __name__ == '__main__':
+ run()
\ No newline at end of file
diff --git a/simulations/input/s1.par b/simulations/input/s1.par
new file mode 100644
index 0000000000000000000000000000000000000000..5ee6d4d5025a9ed14dada07a6f876a4e76ca05d3
--- /dev/null
+++ b/simulations/input/s1.par
@@ -0,0 +1,77 @@
+#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/simulations/input/meshes/2023-08-15_XAOClJVdTF/block
+#physical regions
+num_phys_regions = 2
+phys_region[0].name = "Intracellular domain"
+phys_region[0].ptype = 0
+phys_region[0].num_IDs = 1
+phys_region[0].ID[0] = 1
+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
+num_imp_regions = 1
+imp_region[0].im = Shannon
+#stimulus setup
+num_stim = 3
+stimulus[0].name = "S1"
+stimulus[0].stimtype = 1
+stimulus[0].duration = 2.
+stimulus[0].start = 0.
+stimulus[0].npls = 1
+stimulus[0].x0 = -50.0 #in um
+stimulus[0].xd = 275.0 #thickness in um
+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
+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,
+# 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)
+# 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
diff --git a/simulations/input/s2.par b/simulations/input/s2.par
new file mode 100644
index 0000000000000000000000000000000000000000..df80dc275f8981578873e3a80eae320bcfd9bcaf
--- /dev/null
+++ b/simulations/input/s2.par
@@ -0,0 +1,78 @@
+#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/simulations/input/meshes/2023-08-15_XAOClJVdTF/block
+#physical regions
+num_phys_regions = 2
+phys_region[0].name = "Intracellular domain"
+phys_region[0].ptype = 0
+phys_region[0].num_IDs = 1
+phys_region[0].ID[0] = 1
+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
+num_imp_regions = 1
+imp_region[0].im = Shannon
+#stimulus setup
+num_stim = 3
+stimulus[0].name = "S1"
+stimulus[0].stimtype = 1
+stimulus[0].duration = 2.
+stimulus[0].start = 0.
+stimulus[0].npls = 1
+stimulus[0].x0 = -50.0 #in um
+stimulus[0].xd = 275.0 #thickness in um
+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
+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,
+# 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)
+# 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
diff --git a/simulations/input/new_basic.par b/simulations/input/tests/new_basic.par
similarity index 96%
rename from simulations/input/new_basic.par
rename to simulations/input/tests/new_basic.par
index 37f789c1e4490c12a8de0638923aae3b300f1d08..9a47479eb5ca479dc54429c4e1f1d88273b6b750 100644
--- a/simulations/input/new_basic.par
+++ b/simulations/input/tests/new_basic.par
@@ -8,7 +8,7 @@ simID = Test_Output/34
# Meshname
# ----------------------------------------
-meshname = /code/openCARP-Actors/meshes/2023-06-30_TgWObjAUlq/block
+meshname = /code/meshes/2023-08-15_yqZkjFbniY/block
# ----------------------------------------
# Definition of physics region
diff --git a/simulations/input/s1_s2.par b/simulations/input/tests/s1_s2.par
similarity index 96%
rename from simulations/input/s1_s2.par
rename to simulations/input/tests/s1_s2.par
index cd75de6ffb7b3b0def8afa3366d08504232f9a0f..9a47230142690dbe233e2fecb5325e48f3d6c5a3 100644
--- a/simulations/input/s1_s2.par
+++ b/simulations/input/tests/s1_s2.par
@@ -8,7 +8,7 @@ simID = output/
# Meshname
# ----------------------------------------
-meshname = /code/openCARP-Actors/meshes/2023-06-30_TgWObjAUlq/block
+meshname = /code/meshes/2023-08-15_yqZkjFbniY/block
# ----------------------------------------
# Definition of physics region
diff --git a/yaml-cpp b/yaml-cpp
deleted file mode 160000
index b8882652fcbeba4c00dec019a39da91e702e474e..0000000000000000000000000000000000000000
--- a/yaml-cpp
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit b8882652fcbeba4c00dec019a39da91e702e474e