minor fixes

adajel · Aug 26, 2024 · d68f06a · d68f06a
1 parent 05a77ff
commit d68f06a
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Showing 5 changed files with 24 additions and 27 deletions.
diff --git a/emix-simulations/make_figures_calibration.py b/emix-simulations/make_figures_calibration.py
@@ -308,14 +308,14 @@ def plot_3D_concentration_neuron(res, T, dt, fname):
     plt.title(r'Membrane potential ODE')
     plt.plot(phi_M_ODE, linewidth=3)
 
-    print("membrane potential", phi_M[-1])
-    print("membrane potential", phi_M_ODE[-1])
-    #print("Na_e", Na_e[-1])
-    #print("Na_i", Na_i[-1])
-    #print("K_i", K_i[-1])
-    #print("K_e", K_e[-1])
-    #print("Cl_i", Cl_i[-1])
-    #print("Cl_e", Cl_e[-1])
+    print("membrane potential", phi_M[0], phi_M[-1])
+    print("membrane potential", phi_M_ODE[0], phi_M_ODE[-1])
+    print("Na_e", Na_e[0], Na_e[-1])
+    print("Na_i", Na_i[0], Na_i[-1])
+    print("K_i", K_i[0], K_i[-1])
+    print("K_e", K_e[0], K_e[-1])
+    print("Cl_i", Cl_i[0], Cl_i[-1])
+    print("Cl_e", Cl_e[0], Cl_e[-1])
 
     # make pretty
     ax.axis('off')
@@ -406,14 +406,14 @@ def plot_3D_concentration_glial(res, T, dt, fname):
     plt.title(r'Membrane potential ODE')
     plt.plot(phi_M_ODE, linewidth=3)
 
-    print("membrane potential", phi_M[-1])
-    print("membrane potential", phi_M_ODE[-1])
-    #print("Na_e", Na_e[-1])
-    #print("Na_i", Na_i[-1])
-    #print("K_i", K_i[-1])
-    #print("K_e", K_e[-1])
-    #print("Cl_i", Cl_i[-1])
-    #print("Cl_e", Cl_e[-1])
+    print("membrane potential", phi_M[0], phi_M[-1])
+    print("membrane potential", phi_M_ODE[0] ,phi_M_ODE[-1])
+    print("Na_e", Na_e[0], Na_e[-1])
+    print("Na_i", Na_i[0], Na_i[-1])
+    print("K_i", K_i[0], K_i[-1])
+    print("K_e", K_e[0], K_e[-1])
+    print("Cl_i", Cl_i[0], Cl_i[-1])
+    print("Cl_e", Cl_e[0], Cl_e[-1])
 
     # make pretty
     ax.axis('off')
@@ -708,15 +708,15 @@ def get_velocity(fname, T, dt):
 # create figures
 res_3D = '0' # mesh resolution for 3D axon bundle
 dt = 0.1
-T = 10
+T = 2
 
 #fname = 'results/data/calibration_two_tags/results.h5'
 fname = 'results/data/two_tags/results.h5'
 
 #plot_surface(fname, T, dt)
 plot_3D_concentration_neuron(res_3D, T, dt, fname)
 plot_3D_concentration_glial(res_3D, T, dt, fname)
-write_to_pvd(dt, T, fname)
+#write_to_pvd(dt, T, fname)
 
 #get_velocity(fname, T, dt)
 #plot_surface_time(fname, T, dt)
diff --git a/emix-simulations/run_EMIx_simulation.py b/emix-simulations/run_EMIx_simulation.py
@@ -32,7 +32,7 @@ class bcolors:
 
     # Time variables (PDEs)
     dt = 0.1                         # global time step (s)
-    Tstop = 2                        # global end time (s)
+    Tstop = 50                       # global end time (s)
     t = Constant(0.0)                # time constant
 
     # Time variables (ODEs)
@@ -99,7 +99,7 @@ class bcolors:
     ion_list = [K, Cl, Na]
 
     # Membrane parameters
-    g_syn_bar = 0                      # synaptic conductivity (mS/cm**2)
+    g_syn_bar = 5                      # synaptic conductivity (mS/cm**2)
 
     # Set stimulus ODE
     stimulus = {'stim_amplitude': g_syn_bar}

diff --git a/emix-simulations/run_calibration_ODE.py b/emix-simulations/run_calibration_ODE.py
@@ -2,9 +2,6 @@
 import dolfin as df
 import numpy as np
 import matplotlib.pyplot as plt
-#import mm_hh_calibration_ODE as ode
-#import mm_glial_calibration_ODE as ode
-#import mm_leak_calibration_ODE as ode
 import mm_hh_glial_calibration_ODE as ode
 from knpemidg.membrane import MembraneModel
 from collections import namedtuple

diff --git a/emix-simulations/run_calibration_two_tags.py b/emix-simulations/run_calibration_two_tags.py
@@ -32,7 +32,7 @@ class bcolors:
 
         # Time variables PDEs
         dt = 0.1                       # global time step (ms)
-        Tstop = 10                     # global end time (ms)
+        Tstop = 2                      # global end time (ms)
         t = Constant(0.0)              # time constant
 
         # Time variables ODEs

diff --git a/emix-simulations/run_two_tags.py b/emix-simulations/run_two_tags.py
@@ -30,7 +30,7 @@ class bcolors:
 
     # Time variables PDEs
     dt = 0.1                       # global time step (ms)
-    Tstop = 10                     # global end time (ms)
+    Tstop = 2                      # global end time (ms)
     t = Constant(0.0)              # time constant
 
     # Time variables ODEs
@@ -114,8 +114,8 @@ class bcolors:
     ion_list = [K, Cl, Na]
 
     # Membrane parameters
-    g_syn_bar = 5.0                  # synaptic conductivity (mS/cm**2)
-    #g_syn_bar = 0.0                   # synaptic conductivity (mS/cm**2)
+    #g_syn_bar = 5.0                  # synaptic conductivity (mS/cm**2)
+    g_syn_bar = 0.0                   # synaptic conductivity (mS/cm**2)
 
     # Set stimulus ODE
     stimulus = {'stim_amplitude': g_syn_bar}