From 9cba3bbbd89dc72b2a14556089d30caa032533aa Mon Sep 17 00:00:00 2001
From: martinachondo <acho.martin@gmail.com>
Date: Mon, 10 Jun 2024 19:50:33 -0400
Subject: [PATCH] update post template

---
 xppbe/Post/Post_Template.ipynb | 45 ++++++++++++++++++++++++++++------
 1 file changed, 37 insertions(+), 8 deletions(-)

diff --git a/xppbe/Post/Post_Template.ipynb b/xppbe/Post/Post_Template.ipynb
index 793c2fb..f11bc1d 100644
--- a/xppbe/Post/Post_Template.ipynb
+++ b/xppbe/Post/Post_Template.ipynb
@@ -7,7 +7,6 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import json\n",
     "import numpy as np"
    ]
   },
@@ -31,12 +30,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from xppbe.Simulation import Simulation\n",
+    "from xppbe import Simulation\n",
     "from xppbe import xppbe_path\n",
     "\n",
     "simulation_name = os.path.basename(os.getcwd())\n",
     "\n",
-    "simulation = Simulation(f'{simulation_name}.yaml', results_path=xppbe_path, load_results=True)\n",
+    "simulation = Simulation(f'{simulation_name}.yaml', results_path=xppbe_path)\n",
     "\n",
     "simulation.create_simulation()\n",
     "print(simulation.domain_properties)"
@@ -55,8 +54,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Iter = 5\n",
-    "simulation.load_model(Iter, save=False)\n",
+    "Iter = 20000\n",
+    "simulation.load_model_for_Post(Iter, save=False)\n",
     "Post = simulation.Post"
    ]
   },
@@ -82,7 +81,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Post.plot_aprox_analytic(N=8000,zoom=True, lims_zoom=[[0.95,1.05],None], value='react')"
+    "Post.plot_G_solv_history(known=True, method='PBJ');"
    ]
   },
   {
@@ -91,7 +90,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Post.plot_line_interface()"
+    "Post.plot_phi_line_aprox_known('PBJ', value='react', theta=0, phi=np.pi/2, N=600);"
    ]
   },
   {
@@ -100,7 +99,37 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Post.plot_phi_contour(n=np.array([1,1,1]))"
+    "Post.plot_phi_line_aprox_known('PBJ', value='react', theta=np.pi/2, N=400);"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Post.plot_phi_line_aprox_known('PBJ', value='react', theta=np.pi/2, phi=np.pi, N=300);"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Post.plot_interface_3D(jupyter=True);"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vertices = Post.mesh.mol_verts.astype(np.float32)\n",
+    "elements = Post.mesh.mol_faces.astype(np.float32)\n",
+    "phi_known = Post.phi_known('APBS','phi', vertices,'')\n",
+    "Post.plot_interface_3D_known(phi_known, vertices, elements, jupyter=True);"
    ]
   }
  ],