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Add files via upload #1

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71 changes: 44 additions & 27 deletions Flat_Mesh_Ref.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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"
]
},
{
Expand Down Expand Up @@ -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",
Expand Down