check that results from merged solver match with results presented in overleaf (for local potass buffering)

Author: adajel

examples/local-astrocyte-depolarization/make_figures.py

@@ -729,35 +729,26 @@ def plot_surface_time(fname, T, dt):
                  "E": [0.0003637753007305006, 0.0003705360300998128, 0.0003625574818125377], \
                  "I": [0.0003548050620792965, 0.0003520433961759351, 0.0003739900092393671]}
 
-T = 1.5
-#fname = "results/data/EMIx-synapse_100_tort_short_4_tort_both_ICS_and_ECS/results.h5"
-#fnameout = "results/data/EMIx-synapse_100_tort_short_4_tort_both_ICS_and_ECS/"
-#plot_3D_concentration_glial(res_3D, T, dt, x_ROI, fname, fnameout)
-#plot_surface(fname, fnameout, T, dt)
-#write_to_pvd(fname, fnameout, T, dt)
+T = 10
 
-#T = 10
-#fname = "results/data/EMIx-synapse_100_tort_short_4_tort_both_ICS_and_ECS/results.h5"
-#fnameout = "results/data/EMIx-synapse_100_tort_short_4_tort_both_ICS_and_ECS/"
+fname = "results/data/EMIx-synapse_100_tort_short_4_tort_both_ICS_and_ECS/results.h5"
+fnameout = "results/data/EMIx-synapse_100_tort_short_4_tort_both_ICS_and_ECS/"
+plot_3D_concentration_glial(res_3D, T, dt, x_ROI, fname, fnameout)
+plot_surface(fname, fnameout, T, dt)
+write_to_pvd(fname, fnameout, T, dt)
 
+#fname = "results/data/EMIx-synapse_100_tort_short_2_tort_both_ICS_and_ECS/results.h5"
+#fnameout = "results/data/EMIx-synapse_100_tort_short_2_tort_both_ICS_and_ECS/"
 #plot_3D_concentration_glial(res_3D, T, dt, x_ROI, fname, fnameout)
 #plot_surface(fname, fnameout, T, dt)
 #write_to_pvd(fname, fnameout, T, dt)
 
-#fname = "results/data/EMIx-synapse_100_tort_short_2_tort_both_ICS_and_ECS/results.h5"
-#fnameout = "results/data/EMIx-synapse_100_tort_short_2_tort_both_ICS_and_ECS/"
-
+#fname = "results/data/EMIx-synapse_100_tort_short_baseline/results.h5"
+#fnameout = "results/data/EMIx-synapse_100_tort_short_baseline/"
 #plot_3D_concentration_glial(res_3D, T, dt, x_ROI, fname, fnameout)
 #plot_surface(fname, fnameout, T, dt)
 #write_to_pvd(fname, fnameout, T, dt)
 
-fname = "results/data/EMIx-synapse_100_tort_short_baseline/results.h5"
-fnameout = "results/data/EMIx-synapse_100_tort_short_baseline/"
-
-plot_3D_concentration_glial(res_3D, T, dt, x_ROI, fname, fnameout)
-plot_surface(fname, fnameout, T, dt)
-write_to_pvd(fname, fnameout, T, dt)
-
 """
 T = 0.5
 fname = "results/data/EMIx-synapse_100_tort_short_baseline_test/results.h5"

examples/local-astrocyte-depolarization/run_K_stimuli.py

@@ -79,7 +79,7 @@ def update_ode(self, ode_model):
 
     # Time variables (PDEs)
     dt = 0.1                         # global time step (ms)
-    Tstop = 1.5                      # ms
+    Tstop = 10                       # ms
 
     t = Constant(0.0)                # time constant
 
@@ -125,10 +125,10 @@ def update_ode(self, ode_model):
     t_syn = 1.2
 
     # baseline
-    lambda_i = 3.2
-    lambda_e = 1.6
-    fname = "results/data/EMIx-synapse_100_tort_short_baseline/"
-    g_syn = 200
+    #lambda_i = 3.2
+    #lambda_e = 1.6
+    #fname = "results/data/EMIx-synapse_100_tort_short_baseline/"
+    #g_syn = 200
 
     # M1: increase ECS and ICS lambda
     #lambda_i = 3.2*2
@@ -137,10 +137,10 @@ def update_ode(self, ode_model):
     #g_syn = 65
 
     # M2: increase ECS and ICS lambda
-    #lambda_i = 3.2*4
-    #lambda_e = 1.6*4
-    #fname = "results/data/EMIx-synapse_100_tort_short_4_tort_both_ICS_and_ECS/"
-    #g_syn = 26
+    lambda_i = 3.2*4
+    lambda_e = 1.6*4
+    fname = "results/data/EMIx-synapse_100_tort_short_4_tort_both_ICS_and_ECS/"
+    g_syn = 26
 
     phi_M_init_type = 'constant'