From 8c269ce4787428a68921fcd7a11610e9cd33bd39 Mon Sep 17 00:00:00 2001
From: Ramm <ramm.vicente@gmail.com>
Date: Sat, 25 May 2019 18:18:19 -0400
Subject: [PATCH] Add files via upload

Fixed some bugs.

All files might be rebuilt in order to simplify the code and make it more general
---
 Flat_Mesh_Ref.ipynb | 71 ++++++++++++++++++++++++++++-----------------
 1 file changed, 44 insertions(+), 27 deletions(-)

diff --git a/Flat_Mesh_Ref.ipynb b/Flat_Mesh_Ref.ipynb
index 4da81ed..216a98b 100644
--- a/Flat_Mesh_Ref.ipynb
+++ b/Flat_Mesh_Ref.ipynb
@@ -2,19 +2,26 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 7,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Overwriting Mesh_Ref.py\n"
+     ]
+    }
+   ],
    "source": [
+    "%%writefile Mesh_Ref.py \n",
+    "\n",
     "import bempp.api, numpy as np\n",
     "from math import pi\n",
     "import os\n",
     "from Grid_Maker import *\n",
     "\n",
     "\n",
-    "# Se crea una función que entrega la información de los archivos\n",
-    "# .vert y .face en formato np.array\n",
-    "\n",
     "def text_to_list(mol_name , suffix , txt_format , info_type=float):\n",
     "    '''\n",
     "    Rutine which builds lists from text files that contain the vert and face info\n",
@@ -23,6 +30,8 @@
     "    txt_format : file format\n",
     "    info_type  : float or int\n",
     "    '''\n",
+    "    path = os.path.join('Molecule',mol_name)\n",
+    "    \n",
     "    list_txt = open( os.path.join(path , mol_name +suffix + txt_format) ).read().split('\\n')\n",
     "\n",
     "    listing = np.empty((0,3))\n",
@@ -73,7 +82,7 @@
     "    \n",
     "    return v_centered , new_face_array.astype(int) , new_vert_array\n",
     "\n",
-    "def mesh_flat_refinement(faces,face_array,vert_array , suffix , dens):\n",
+    "def mesh_flat_refinement(mol_name,faces,face_array,vert_array , suffix , dens):\n",
     "    '''\n",
     "    This function builds the msh file for the specified faces.\n",
     "    faces : Faces arrays to be remeshed\n",
@@ -98,7 +107,34 @@
     "    for i in random_faces:\n",
     "        refined_faces = np.vstack( (refined_faces , face_array[i]))\n",
     "        \n",
-    "    return refined_faces"
+    "    return refined_faces\n",
+    "\n",
+    "def mesh_ref(mol_name , refined_faces , input_file_suffix , output_file_suffixx , starting_density):\n",
+    "    '''\n",
+    "    Global function that refines the mesh.\n",
+    "    mol_name : Abreviated name of the molecule\n",
+    "    refined_faces : np.array((N,3)) which contains faces with respective verts positions to be refined.\n",
+    "    input_file_suffix : Suffix of the starting file\n",
+    "    output_file_suffix : Suffix of the outputfile\n",
+    "    starting_density   : Starting density (For an easy handling of files)\n",
+    "    '''\n",
+    "    mol_name = 'methanol'\n",
+    "    path = os.path.join('Molecule',mol_name)\n",
+    "\n",
+    "    starting_density = 2.0\n",
+    "\n",
+    "    suffix   = ''\n",
+    "\n",
+    "    # Information is imported\n",
+    "    face_array = text_to_list(mol_name , input_file_suffix , '.face' , info_type=int  )\n",
+    "    vert_array = text_to_list(mol_name , input_file_suffix , '.vert' , info_type=float)\n",
+    "\n",
+    "\n",
+    "    #refined_faces = random_face_list(50 , face_array) \n",
+    "\n",
+    "    mesh_flat_refinement(mol_name , refined_faces,face_array,vert_array, output_file_suffixx , dens = starting_density)\n",
+    "    \n",
+    "    return None"
    ]
   },
   {
@@ -267,26 +303,7 @@
      ]
     }
    ],
-   "source": [
-    "# Let's define main variables\n",
-    "mol_name = 'methanol'\n",
-    "path = os.path.join('Molecule',mol_name)\n",
-    "\n",
-    "starting_density = 2.0\n",
-    "\n",
-    "suffix   = ''\n",
-    "\n",
-    "# Se importa la información \n",
-    "suf = '_'+str(starting_density)+ suffix\n",
-    "face_array = text_to_list(mol_name , suf , '.face' , info_type=int  )\n",
-    "vert_array = text_to_list(mol_name , suf , '.vert' , info_type=float)\n",
-    "\n",
-    "suffix = '-1'\n",
-    "\n",
-    "refined_faces = random_face_list(50 , face_array) \n",
-    "# refined_faces should be changed for the faces containing a certain error criteria!\n",
-    "mesh_flat_refinement(refined_faces,face_array,vert_array, suffix , dens = starting_density)"
-   ]
+   "source": []
   },
   {
    "cell_type": "code",