Cleaning up the running of tests

.gitignore

@@ -6,6 +6,10 @@ simulations/input/screenlog.0
 simulations/output*
 simulations/Joyce_Nov6_10x10x1mm-forPaper/output/*
 # Tests
+tests/mesh_type_1_tests/output_*
+tests/mesh_type_1_tests/screen*
+tests/mesh_type_1_tests/*log
+
 tests/s1-s2-test/output/*
 tests/s2-only-test/output/*
 tests/s1-only-test/output/*
@@ -16,3 +20,4 @@ tests/s1-s2-test-bisection-distributed/output/*
 *.log
 *.sif 
 environment_setup/openCARP
+

tests/README.md

+This folder contains some tests:
+
+Each folder is tests based off a specific mesh and contains the following subfolders:
+ - `mesh`: Contains the files that define the openCARP mesh
+ - `opencarp-params`: Contains the openCARP stimulus parameters
+ 
+right now mesh_type_1 is a small mesh that does not take long at all to compute.
\ No newline at end of file

tests/mesh_type_1_tests/config_test_s1_only.toml

+[actors]
+# global parameters
+output_dir = "/code/openCARP-Actors/tests/mesh_type_1_tests/output_test_s1_only/"
+results_file = "/code/openCARP-Actors/tests/mesh_type_1_tests/output_test_s1_only/results.csv"
+tolerance = 1
+priority = "bisection"
+
+# s1 parameters
+s1_args = ['openCARP', '+F', '/code/openCARP-Actors/tests/mesh_type_1_tests/opencarp-params/s1.par']
+s1_min = 1.0
+s1_max = 50.0
\ No newline at end of file

tests/mesh_type_1_tests/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/mesh_type_1_tests/opencarp-params/s1.par

+# ----------------------------------------
+# Output Folder Name
+# ----------------------------------------
+
+simID = output
+
+# ----------------------------------------
+# Meshname
+# ----------------------------------------
+
+meshname = /code/openCARP-Actors/tests/mesh_type_1_tests/mesh/block
+
+# ----------------------------------------
+# Definition of physics region
+# ----------------------------------------
+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
+
+# ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ---------------
+# Definition of ionic model and plugins (IMP) for each unique tagged
+# region in the mesh
+# ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ------ ----- ----
+num_imp_regions = 1 
+
+imp_region[0].im = DrouhardRoberge
+
+
+# --------------------
+# Definition of stimuli
+# --------------------
+
+num_stim = 1
+stimulus[0].name = S1
+stimulus[0].stimtype = 0 
+stimulus[0].strength = 34.0 
+stimulus[0].duration = 2.0
+stimulus[0].x0 = -50.0
+stimulus[0].xd = 2100.0
+stimulus[0].y0 = -50.0
+stimulus[0].yd = 400.0
+stimulus[0].z0 = -50.0
+stimulus[0].zd = 300.0
+
+
+# -------------------------------
+# Definition of general parameters
+# -------------------------------
+tend = 20.0 # t_end - end of simulation
+spacedt = 1.0 # Interval to output data to files
+timedt  = 1.0 # Interval to print progress to sceen
+vofile = "vm.igb" # Output filename: Prevents invalid read when defined
+
+# --------------------------------------------------
+# Definition of solving problem and numerical methods
+# --------------------------------------------------
+bidomain = 0 
+dt = 25
+parab_options_file = /root/.local/lib/python3.8/site-packages/carputils/resources/petsc_options/ilu_cg_opts
+ellip_options_file = /root/.local/lib/python3.8/site-packages/carputils/resources/petsc_options/gamg_cg_opts
+parab_solve = 1
+ellip_use_pt = 0
+parab_use_pt = 0
+

tests/mesh_type_1_tests/opencarp-params/s2.par

+# ----------------------------------------
+# Output Folder Name
+# ----------------------------------------
+
+simID = output/
+
+# ----------------------------------------
+# Meshname
+# ----------------------------------------
+
+meshname = /code/openCARP-Actors/tests/mesh_type_1_tests/mesh/block
+
+
+# ----------------------------------------
+# Definition of physics region
+# ----------------------------------------
+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
+
+# ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ---------------
+# Definition of ionic model and plugins (IMP) for each unique tagged
+# region in the mesh
+# ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ------ ----- ----
+num_imp_regions = 1 
+
+imp_region[0].im = DrouhardRoberge
+
+
+# --------------------
+# Definition of stimuli
+# --------------------
+
+num_stim = 2, 
+stimulus[0].name = S1
+stimulus[0].stimtype = 0 
+stimulus[0].strength = 172.0 
+stimulus[0].duration = 2.0
+stimulus[0].x0 = -50.0
+stimulus[0].xd = 2100.0
+stimulus[0].y0 = -50.0
+stimulus[0].yd = 400.0
+stimulus[0].z0 = -50.0
+stimulus[0].zd = 300.0
+
+stimulus[1].name = S2 
+stimulus[1].stimtype = 0
+stimulus[1].strength = 200.0 
+stimulus[1].duration = 2.0 
+stimulus[1].start = 150.0 
+
+
+# -------------------------------
+# Definition of general parameters
+# -------------------------------
+tend = 300.0  # t_end - end of simulation
+spacedt = 1.0 # Interval to output data to files
+timedt  = 1.0 # Interval to print progress to sceen
+vofile = "vm.igb" # Output filename: Prevents invalid read when defined
+
+
+# --------------------------------------------------
+# Definition of solving problem and numerical methods
+# --------------------------------------------------
+bidomain = 0 
+dt = 25
+parab_options_file = /root/.local/lib/python3.8/site-packages/carputils/resources/petsc_options/ilu_cg_opts
+ellip_options_file = /root/.local/lib/python3.8/site-packages/carputils/resources/petsc_options/gamg_cg_opts
+parab_solve = 1
+ellip_use_pt = 0
+parab_use_pt = 0
+

tests/mesh_type_1_tests/run_tests_local.sh

+#! /bin/bash
+
+openCARP=/code/openCARP-Actors/environment_setup/openCARP/_build/bin/openCARP
+MESH_TYPE_TEST_PATH=/code/openCARP-Actors/tests/mesh_type_1_tests
+
+# Specify the test you want to run (this is the name of the config file without "config_" and ".toml")
+TEST=test_s1_only
+
+CONFIG=config_$TEST.toml
+LOG_DIR_NAME=${TEST}_log
+LOG_DIR=$MESH_TYPE_TEST_PATH/$LOG_DIR_NAME
+
+echo "LOG_DIR: $LOG_DIR"
+
+mkdir -p screen-logs
+mkdir -p $LOG_DIR
+export OMP_NUM_THREADS=1
+screen -L -dmS server -Logfile screen-logs/server.log \
+  $openCARP -c $CONFIG -o $LOG_DIR/ -s -p 4444
+
+# echo "Started Server"                   
+# sleep 1
+# N=3
+# for (( i=1; i<=N; i++ ))
+# do
+# screen -L -dmS client$i -Logfile client$i.log \
+#               $openCARP -a -H "localhost" -p 4444 -o $LOG_DIR/
+
+# done

tests/run_tests_local.sh

@@ -13,16 +13,17 @@ CONFIG=$CONTAINER_DIR/$TEST/config_test.toml
 rm client*.log
 rm server.log
 
-export OMP_NUM_THREADS=1
-screen -L -dmS server -Logfile server.log \
-              $openCARP -c $CONFIG -o $LOG_DIR/ -s -p 4444
+tmux new-session -d -s server 'export OMP_NUM_THREADS=1; $openCARP -c $CONFIG -o $LOG_DIR/ -s -p 4444' \; pipe-pane -o "cat >server.log"
+# export OMP_NUM_THREADS=1
+# screen -L -dmS server -Logfile server.log \
+#               $openCARP -c $CONFIG -o $LOG_DIR/ -s -p 4444
 
-echo "Started Server"                   
-sleep 1
-N=3
-for (( i=1; i<=N; i++ ))
-do
-screen -L -dmS client$i -Logfile client$i.log \
-              $openCARP -a -H "localhost" -p 4444 -o $LOG_DIR/
+# echo "Started Server"                   
+# sleep 1
+# N=3
+# for (( i=1; i<=N; i++ ))
+# do
+# screen -L -dmS client$i -Logfile client$i.log \
+#               $openCARP -a -H "localhost" -p 4444 -o $LOG_DIR/
 
-done
+# done

tests/s1-only-test/input/s1.par

@@ -2,7 +2,7 @@
 # Output Folder Name
 # ----------------------------------------
 
-simID = Test_Output/34
+simID = output
 
 # ----------------------------------------
 # Meshname