Update tutorial for version 2.1 of meshio

Author: nicoguaro

docs/tutorials/brazilian_test.rst

@@ -3,7 +3,7 @@ Geometry in Gmsh and solution with SolidsPy
 ==========================================================================
 
 :Author: Nicolás Guarín-Zapata
-:Date: April, 208
+:Date: September, 2018
 
 This document is a tutorial on how to generate a (specific) geometry
 using Gmsh [Gmsh2009]_ and its subsequent processing for the generation
@@ -206,13 +206,14 @@ Run the finite element program in Python.
 
 .. code-block:: python
 
-  from __future__ import division, print_function
   import meshio
   import numpy as np
 
-
-  points, cells, point_data, cell_data, field_data = \
-      meshio.read("Prueba_brasilera.msh")
+  mesh = meshio.read("Prueba_brasilera.msh")
+  points = mesh.points
+  cells = mesh.cells
+  point_data = mesh.point_data
+  cell_data = mesh.cell_data
 
   # Element data
   eles = cells["triangle"]
@@ -277,13 +278,15 @@ same directory as the Python file that will process it.
 
 .. code:: python
 
-  from __future__ import division, print_function
   import meshio
   import numpy as np
 
 
-  points, cells, point_data, cell_data, field_data = \
-    meshio.read("Prueba_brasilera.msh")
+  mesh = meshio.read("Prueba_brasilera.msh")
+  points = mesh.points
+  cells = mesh.cells
+  point_data = mesh.point_data
+  cell_data = mesh.cell_data
 
 Element data
 ------------

docs/tutorials/template_input.py

@@ -1,52 +1,54 @@
 # -*- coding: utf-8 -*-
 """
-Template to generate the input files for the FEM code solids_ISO.
-The script uses module meshio.py to read a GMSH mesh and produce
+Template to generate the input files for the FEM code SolidsPy.
+The script uses meshio to read a GMSH mesh and produce
 text files nodes.txt, eles.txt , mater.txt and loads.txt
 
 @authors: Juan Gomez
          Nicolas Guarin-Zapata
 """
-from __future__ import division, print_function
 import meshio
 import numpy as np
 #
 # Read the GMSH file using meshio
 #
-points, cells, point_data, cell_data, field_data = \
-    meshio.read("template.msh")
-#
+mesh = meshio.read("template.msh")
+points = mesh.points
+cells = mesh.cells
+point_data = mesh.point_data
+cell_data = mesh.cell_data
+
+
 # Process element data. In this case we have used 3-noded triangles.
-# (In solids_ISO 1 stands for quad; 2 for triangle6; 3 for triangle)
-#
+# (In SolidsPy 1 stands for quad; 2 for triangle6; 3 for triangle)
 eles = cells["triangle"]
 els_array = np.zeros([eles.shape[0], 6], dtype=int)
-els_array[:, 0] = range(eles.shape[0])              # Asigns element id
-els_array[:, 1] = 3                                 # Assigns element type according to solids_ISO.py
-els_array[:, 3::] = eles                            # Assign element connectivities
-#
+# Asigns element id
+els_array[:, 0] = range(eles.shape[0])
+# Assigns element type according to SolidsPy
+els_array[:, 1] = 3
+# Assign element connectivities
+els_array[:, 3::] = eles
+# Creates the materials array and assigns a profile (either 0 or 1) to
+# each element according to the physical surface
 mater_array = np.array([[1.0, 0.30],
-                        [5.0, 0.30]])              # Creates the materials array and assigns a profile (either 0 or 1) to
-                                                   # each element according to the physical surface 
-maters = cell_data["triangle"]["physical"]
+                        [5.0, 0.30]])
+maters = cell_data["triangle"]["gmsh:physical"]
 els_array[:, 2]  = [0 if mater == 100 else 1 for mater in maters]
-#
+
 # Process nodal data
-#
 nodes_array = np.zeros([points.shape[0], 5])
-nodes_array[:, 0] = range(points.shape[0])          # Assigns nodal id
-nodes_array[:, 1:3] = points[:, :2]                 # Assigns space coordinates
-#
+nodes_array[:, 0] = range(points.shape[0])  # Assigns nodal id
+nodes_array[:, 1:3] = points[:, :2]  # Assigns space coordinates
+
 # Process physical lines to assign displacement boundary conditions
 # and nodal point loads
 #
 # Displacement boundary conditions
-#
 lines = cells["line"]
-bounds = cell_data["line"]["physical"]              # Bounds contains data corresponding to the physical line.
-#
+# Bounds contains data corresponding to the physical line.
+bounds = cell_data["line"]["gmsh:physical"]
 # (-1 means a restraint degree of freedom)
-#
 id_frontera_lat = [cont for cont in range(len(bounds)) if bounds[cont] == 300]
 nodes_frontera_lat = lines[id_frontera_lat]
 nodes_frontera_lat = nodes_frontera_lat.flatten()
@@ -57,9 +59,7 @@
 nodes_frontera_abajo = nodes_frontera_abajo.flatten()
 nodes_frontera_abajo = list(set(nodes_frontera_abajo))
 nodes_array[nodes_frontera_abajo, 4] = -1
-#
 # Nodal point loads
-#
 id_carga = [cont for cont in range(len(bounds)) if bounds[cont] == 500]
 nodes_carga = lines[id_carga]
 nodes_carga = nodes_carga.flatten()
@@ -69,10 +69,9 @@
 cargas = np.zeros((ncargas, 3))
 cargas[:, 0] = nodes_carga
 cargas[:, 2] = carga_total/ncargas
-#
+
 # Write the model .txt files
-#
 np.savetxt("eles.txt" , els_array   , fmt="%d")
 np.savetxt("loads.txt", cargas, fmt=("%d", "%.6f", "%.6f"))
 np.savetxt("nodes.txt", nodes_array , fmt=("%d", "%.4f", "%.4f", "%d", "%d"))
-np.savetxt("mater.txt", mater_array , fmt="%.6f")
+np.savetxt("mater.txt", mater_array , fmt="%.6f")

examples/simple_truss/simple_truss.ipynb

@@ -0,0 +1,33 @@
+@book{bathe,
+  title={Finite element procedures},
+  author={Bathe, Klaus-J{\"u}rgen},
+  year={2006},
+  publisher={Klaus-Jurgen Bathe}
+}
+
+@article{gmsh,
+  title={Gmsh: A 3-D finite element mesh generator with built-in pre-and post-processing facilities},
+  author={Geuzaine, Christophe and Remacle, Jean-Fran{\c{c}}ois},
+  journal={International journal for numerical methods in engineering},
+  volume={79},
+  number={11},
+  pages={1309--1331},
+  year={2009},
+  publisher={Wiley Online Library}
+}
+
+@Misc{scipy,
+  author =    {Eric Jones and Travis Oliphant and Pearu Peterson and others},
+  title =     {{SciPy}: Open source scientific tools for {Python}},
+  year =      {2001--},
+  url = "http://www.scipy.org/",
+  note = {[Online; accessed June 12, 2018]}
+}
+
+@Misc{meshio,
+  author =    {Nico Schlömer et al.},
+  title =     {{meshio v1.11.7. Zenodo. http://doi.org/10.5281/zenodo.1173116}},
+  year =      {2016--},
+  url = "https://github.com/nschloe/meshio",
+  note = {[Online; accessed June 12, 2018]}
+}

paper/paper.bib

@@ -0,0 +1,54 @@
+---
+title: 'SolidsPy: 2D-Finite Element Analysis with Python'
+tags:
+  - Python
+  - finite elements
+  - computational mechanics
+  - scientific computing
+authors:
+  - name: Nicolás Guarín-Zapata
+    orcid: 0000-0002-9435-1914
+    affiliation: 1
+  - name: Juan D. Gómez
+    orcid: 0000-0000-0000-0000
+    affiliation: 1
+affiliations:
+ - name: Departamento de Ingeniería Civil, Universidad EAFIT, Medellín-Colombia
+   index: 1
+date: 12 June 2018
+bibliography: paper.bib
+---
+
+# Summary
+
+
+JOSS welcomes submissions from broadly diverse research areas. For this reason, we request that authors include in the paper some sentences that would explain the software functionality and domain of use to a non-specialist reader. Your submission should probably be somewhere between 250-1000 words.
+
+   A list of the authors of the software and their affiliations
+   A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience
+   A clear statement of need that illustrates the purpose of the software
+   A list of key references including a link to the software archive
+   Mentions (if applicable) of any ongoing research projects using the software or recent scholarly publications enabled by it
+
+
+![Displacement and von Mises stress for a wrench under bending.](wrench.png)
+
+The Finite Element Method is a numerical method for the solution of  problems in engineering and physics [@bathe]. These problems are commonly written as boundary value problems and involve partial differential equations.
+
+``SolidsPy`` is a simple finite element analysis code for 2D elasticity problems and was designed to be used by researchers in computational mechanics and by
+students in courses on Computational modeling. It has also been used in graduate
+courses on Introduction to the Finite Element Method. It uses as input simple-to-create text files defining a model in terms of nodal, element, material and load data. Some feature of ``SolidsPy`` are:
+- It is based on an open-source environment.
+- It is easy to use.
+- The code allows to find displacement, strain and stress solutions for arbitrary two-dimensional domains discretized into finite elements and subject to point loads.
+- The code is organized in independent modules for pre-processing, assembly and post-processing allowing the user to easily modify it or add features like new elements or analyses pipelines.
+
+``SolidsPy`` uses SciPy [@scipy] for matrix (sparse/dense) storage and solution of systems of equations. For the creation of complex meshes it is suggested to utilize ``Gmsh`` [@gmsh] and then take advantage of ``meshio`` [@meshio] as interface to Gmsh.
+
+
+# Acknowledgements
+
+We acknowledge contributions from Edward Villegas.
+
+
+# References