mesh_tissue: initial update 2.80

1 files changed, 40 insertions, 0 deletions

diff --git a/mesh_tissue/numba_functions.py b/mesh_tissue/numba_functions.py
new file mode 100644
index 00000000..1cb8e6b8
--- /dev/null
+++ b/mesh_tissue/numba_functions.py
@@ -0,0 +1,40 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+
+from numba import jit
+import numpy as np
+
+@jit
+def numba_reaction_diffusion(n_verts, a, b, diff_a, diff_b, f, k, dt, id0, id1, time_steps):
+    for i in range(time_steps):
+        lap_a = np.zeros(n_verts)
+        lap_b = np.zeros(n_verts)
+        lap_a0 =  a[id1] -  a[id0]   # laplacian increment for first vertex of each edge
+        lap_b0 =  b[id1] -  b[id0]   # laplacian increment for first vertex of each edge
+
+        for i, j, la0, lb0 in zip(id0,id1,lap_a0,lap_b0):
+            lap_a[i] += la0
+            lap_b[i] += lb0
+            lap_a[j] -= la0
+            lap_b[j] -= lb0
+        ab2 = a*b**2
+        #a += eval("(diff_a*lap_a - ab2 + f*(1-a))*dt")
+        #b += eval("(diff_b*lap_b + ab2 - (k+f)*b)*dt")
+        a += (diff_a*lap_a - ab2 + f*(1-a))*dt
+        b += (diff_b*lap_b + ab2 - (k+f)*b)*dt
+    return a, b