set up funcs

olive004 · Oct 27, 2024 · 75805ed · 75805ed
1 parent 8d43ecb
commit 75805ed
Showing 1 changed file with 12 additions and 4 deletions.
diff --git a/notebooks/23_Monte_Carlo_adaptability_2.ipynb b/notebooks/23_Monte_Carlo_adaptability_2.ipynb
@@ -291,7 +291,15 @@
     "\n",
     "\n",
     "def mutate(circuits):\n",
-    "    return circuits\n"
+    "    return circuits\n",
+    "\n",
+    "\n",
+    "def simulate(y00, reverse_rates):\n",
+    "    sol_steady_states = jax.vmap(bioreaction_sim_dfx_expanded)(y00, reverse_rates)\n",
+    "    y01 = np.array(sol_steady_states.ys[:, -1])\n",
+    "    y01[:, np.array(idxs_signal)] = y01[:, np.array(idxs_signal)] * signal_target\n",
+    "    sol_signal = jax.vmap(bioreaction_sim_dfx_expanded)(y01, reverse_rates)\n",
+    "    return sol_steady_states, sol_signal\n"
    ]
   },
   {
@@ -300,16 +308,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "starting = reverse_rates\n",
     "\n",
     "for step in range(total_steps):\n",
     "    \n",
     "    print(f'\\n\\nStarting step {step+1} out of {total_steps}\\n\\n')\n",
     "\n",
-    "    batch = mutate(starting, evolver, algorithm=config['mutations_args']['algorithm'])\n",
-    "    batch = simulate(batch, modeller, config)\n",
+    "    batch = mutate(starting)\n",
+    "    batch = simulate(y00, batch)\n",
     "    starting, summary_data = choose_next(batch=expanded_batchs, data_writer=data_writer, distance_func=distance_func, \n",
     "                                         choose_max=choose_max, target_species=target_species, use_diversity=config.get('use_diversity', False))\n",
-    "    starting = process_for_next_run(starting, data_writer=data_writer)\n",
     "    "
    ]
   }