Moving some functions to custom_data

.gitignore

@@ -170,6 +170,8 @@ src/*/custom_functions.c
 src/*/custom_functions_BACKUP.c
 src/*/custom_functions.h
 
+bsbash/find_functions_with_mpi.sh
+
 .cache/
 .ccls-cache/
 

example_configs/introduction_to_monoalg3d/plot_ecg.py

@@ -24,13 +24,18 @@ def read_ecg_readings (input_file):
 
 def plot_ecg_readings (t, currents, nleads):
 
-	fig, axs = plt.subplots(nleads, 1, sharex=True, sharey=False)
+	# Plot 3 signals => 1 = Lead A, 2 = Lead B, 3 = (Lead B + Lead A)
+	fig, axs = plt.subplots(nleads+1, 1, sharex=True, sharey=False)
 	fig.text(0.5, 0.04, 'Time (ms)', ha='center', fontsize=10)
 	fig.text(0.02, 0.5, 'Current (mA)', va='center', rotation='vertical', fontsize=10)
+	# Signals 1 and 2
 	for i in range(nleads):
 		axs[i].plot(t, currents[:,i], label="lead_%d" % (i), c="black", linewidth=2.0)
-		axs[i].set_title("ECG reading - Lead %d" % (i),fontsize=14)
-
+		axs[i].set_title("ECG reading - Lead %d" % (i),fontsize=10)
+	# Signal 3
+	axs[nleads].plot(t, currents[:,1]+currents[:,0], label="lead_%d" % (nleads), c="black", linewidth=2.0)
+	axs[nleads].set_title("ECG reading - Lead %d" % (nleads),fontsize=10)
+
 	#plt.show()
 	#plt.savefig("ecg.pdf")
 	plt.savefig("ecg.png", dpi=300)

src/matrix_assembly_library/matrix_assembly.c

@@ -1220,79 +1220,3 @@ ASSEMBLY_MATRIX(anisotropic_sigma_assembly_matrix_with_fast_endocardium_layer) {
     free(s);
     free(n);
 }
-
-// Albert`s code
-ASSEMBLY_MATRIX(anisotropic_sigma_assembly_matrix_with_scaling) {
-
-    uint32_t num_active_cells = the_grid->num_active_cells;
-    struct cell_node **ac = the_grid->active_cells;
-
-    initialize_diagonal_elements(the_solver, the_grid);
-
-    real_cpu D[3][3];
-    int i;
-
-    real_cpu sigma_l = 0.0;
-    real_cpu sigma_t = 0.0;
-    real_cpu sigma_n = 0.0;
-
-    char *fiber_file = NULL;
-    GET_PARAMETER_STRING_VALUE_OR_USE_DEFAULT(fiber_file, config, "fibers_file");
-
-    struct fiber_coords_scale *fibers = NULL;
-    struct fiber_coords *fibers2 = NULL;
-
-    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, sigma_l, config, "sigma_l");
-    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, sigma_t, config, "sigma_t");
-    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(real_cpu, sigma_n, config, "sigma_n");
-
-    real_cpu *f = NULL;
-    real_cpu *s = NULL;
-    real_cpu *n = NULL;
-    real_cpu *x = NULL;
-
-    if(fiber_file) {
-        log_info("Loading mesh fibers\n");
-        fibers = read_fibers_scale(fiber_file);
-        fibers2 = read_fibers(fiber_file, false);
-    }
-    else {
-        log_error_and_exit("Fibers file not provided");
-    }
-
-    OMP(parallel for private(D))
-    for(i = 0; i < num_active_cells; i++) {
-
-        int fiber_index = ac[i]->original_position_in_file;
-
-        if(fiber_index == -1) {
-            log_error_and_exit("fiber_index should not be -1, but it is for cell in index %d - %lf, %lf, %lf\n", i, ac[i]->center.x, ac[i]->center.y, ac[i]->center.z);
-        }
-
-        if(sigma_t == sigma_n) {
-            calc_tensor2(D, fibers[fiber_index].f, sigma_l*fibers[fiber_index].x[0], sigma_t*fibers[fiber_index].x[1]);
-        }
-        else {
-            calc_tensor(D, fibers[fiber_index].f, fibers[fiber_index].s, fibers[fiber_index].n, sigma_l*fibers[fiber_index].x[0], sigma_t*fibers[fiber_index].x[1], sigma_n*fibers[fiber_index].x[2]);
-        }
-        ac[i]->sigma.fibers = fibers2[fiber_index];
-
-        ac[i]->sigma.x = D[0][0];
-        ac[i]->sigma.y = D[1][1];
-        ac[i]->sigma.z = D[2][2];
-
-        ac[i]->sigma.xy = D[0][1];
-        ac[i]->sigma.xz = D[0][2];
-        ac[i]->sigma.yz = D[1][2];
-    }
-
-    OMP(parallel for)
-    for(i = 0; i < num_active_cells; i++) {
-        fill_discretization_matrix_elements_aniso(ac[i]);
-    }
-
-    free(f);
-    free(s);
-    free(n);
-    free(x);
-}