Update to tomek

c/tomek-2020.mmt

@@ -1,7 +1,7 @@
 [[model]]
-name: ToRORd_dyn_chloride
+name: tomek-2020
 mmt_authors: Michael Clerx
-version: 20240816
+version: 20240819
 desc: """
     The Tomek et al. "ToRORd-dynCL" model of the human ventricular action
     potential [1], based on the earlier model without dynamic chloride [2],
@@ -15,6 +15,9 @@ desc: """
     matlab code: it matched to within machine precision. After verification,
     the fixes to INaK desribed in [6] were applied.
 
+    The stimulus was set to 1Hz pacing for 0.5ms, at approximately two times
+    the minimum amplitude needed to elicit an AP.
+
     References:
 
     [1] Tomek, J., Bueno-Orovio, A., & Rodriguez, B. (2020) ToR-ORd-dynCl: an
@@ -140,7 +143,7 @@ i_ion = (
 [stimulus]
 i_stim = engine.pace * amplitude
     in [A/F]
-amplitude = -53 [A/F]
+amplitude = 2 * -53 [A/F]
     in [A/F]
 
 #
@@ -1137,11 +1140,30 @@ m = get_model()
 p = get_protocol()
 s = myokit.Simulation(m, p)
 
-# Run simulation
-d = s.run(1000)
+# Run for all three modes
+modes = {
+    0: 'Endocardial',
+    1: 'Epicardial',
+    2: 'Midmyocardial'
+}
+
+fig = plt.figure()
+ax0 = fig.add_subplot(2, 1, 1)
+ax0.set_ylabel('V (mV)')
+ax1 = fig.add_subplot(2, 1, 2)
+ax1.set_ylabel('[Ca]i (mM)')
+ax1.set_xlabel('Time (ms)')
+
+for mode, label in modes.items():
+    s.set_constant('cell.mode', mode)
+    s.reset()
+    s.pre(100 * 1000)
+    d = s.run(1000, log=['engine.time', 'membrane.V', 'calcium.Ca_i'])
+
+    ax0.plot(d.time(), d['membrane.V'], label=label)
+    ax1.plot(d.time(), d['calcium.Ca_i'])
+
+ax0.legend(loc='upper right')
 
-# Display the results
-plt.figure()
-plt.plot(d.time(), d['membrane.V'])
 plt.show()