Fix GridIn::read_abaqus() for codimension 1 case.

diff --git a/doc/news/changes/minor/20180920YuxiangWangJean-PaulPelteret b/doc/news/changes/minor/20180920YuxiangWangJean-PaulPelteret
new file mode 100644 (file)
index 0000000..e2028ee
--- /dev/null
+++ b/doc/news/changes/minor/20180920YuxiangWangJean-PaulPelteret
@@ -0,0 +1,4 @@
+Fixed: The GridIn::read_abaqus() function now correctly reads in grids designed
+for the co-dimension 1 case (specifically with dim == 2 and spacedim == 3).
+<br>
+(Yuxiang Wang, Jean-Paul Pelteret, 2018/09/20)

diff --git a/source/grid/grid_in.cc b/source/grid/grid_in.cc
index fbc76f574526b3e2db5a90e4a7906db56d4ae139..a24174e4acf25896742475d63c1820e79c020bc9 100644 (file)
--- a/source/grid/grid_in.cc
+++ b/source/grid/grid_in.cc
@@ -916,7 +916,7 @@ GridIn<dim, spacedim>::read_ucd(std::istream &in,
 
 namespace
 {
-  template <int dim>
+  template <int dim, int spacedim>
   class Abaqus_to_UCD
   {
   public:
@@ -953,12 +953,18 @@ GridIn<dim, spacedim>::read_abaqus(std::istream &in,
                                    const bool apply_all_indicators_to_manifolds)
 {
   Assert(tria != nullptr, ExcNoTriangulationSelected());
-  Assert(dim == 2 || dim == 3, ExcNotImplemented());
+  // This implementation has only been verified for:
+  // - 2d grids with codimension 0
+  // - 3d grids with codimension 0
+  // - 3d grids with codimension 1
+  Assert((spacedim == 2 && dim == spacedim) ||
+           (spacedim == 3 && (dim == spacedim || dim == spacedim - 1)),
+         ExcNotImplemented());
   AssertThrow(in, ExcIO());
 
   // Read in the Abaqus file into an intermediate object
   // that is to be passed along to the UCD reader
-  Abaqus_to_UCD<dim> abaqus_to_ucd;
+  Abaqus_to_UCD<dim, spacedim> abaqus_to_ucd;
   abaqus_to_ucd.read_in_abaqus(in);
 
   std::stringstream in_ucd;
@@ -3220,12 +3226,12 @@ GridIn<dim, spacedim>::get_format_names()
 
 namespace
 {
-  template <int dim>
-  Abaqus_to_UCD<dim>::Abaqus_to_UCD()
+  template <int dim, int spacedim>
+  Abaqus_to_UCD<dim, spacedim>::Abaqus_to_UCD()
     : tolerance(5e-16) // Used to offset Cubit tolerance error when outputting
                        // value close to zero
   {
-    AssertThrow(dim == 2 || dim == 3, ExcNotImplemented());
+    AssertThrow(spacedim == 2 || spacedim == 3, ExcNotImplemented());
   }
 
   // Convert from a string to some other data type
@@ -3256,9 +3262,9 @@ namespace
     return number;
   }
 
-  template <int dim>
+  template <int dim, int spacedim>
   void
-  Abaqus_to_UCD<dim>::read_in_abaqus(std::istream &input_stream)
+  Abaqus_to_UCD<dim, spacedim>::read_in_abaqus(std::istream &input_stream)
   {
     // References:
     // http://www.egr.msu.edu/software/abaqus/Documentation/docs/v6.7/books/usb/default.htm?startat=pt01ch02.html
@@ -3298,11 +3304,11 @@ namespace
                 if (line[0] == '*')
                   goto cont;
 
-                std::vector<double> node(dim + 1);
+                std::vector<double> node(spacedim + 1);
 
                 std::istringstream iss(line);
                 char               comma;
-                for (unsigned int i = 0; i < dim + 1; ++i)
+                for (unsigned int i = 0; i < spacedim + 1; ++i)
                   iss >> node[i] >> comma;
 
                 node_list.push_back(node);
@@ -3572,10 +3578,11 @@ namespace
       }
   }
 
-  template <int dim>
+  template <int dim, int spacedim>
   std::vector<double>
-  Abaqus_to_UCD<dim>::get_global_node_numbers(const int face_cell_no,
-                                              const int face_cell_face_no) const
+  Abaqus_to_UCD<dim, spacedim>::get_global_node_numbers(
+    const int face_cell_no,
+    const int face_cell_face_no) const
   {
     std::vector<double> quad_node_list(GeometryInfo<dim>::vertices_per_face);
 
@@ -3669,9 +3676,9 @@ namespace
     return quad_node_list;
   }
 
-  template <int dim>
+  template <int dim, int spacedim>
   void
-  Abaqus_to_UCD<dim>::write_out_avs_ucd(std::ostream &output) const
+  Abaqus_to_UCD<dim, spacedim>::write_out_avs_ucd(std::ostream &output) const
   {
     // References:
     // http://www.dealii.org/developer/doxygen/deal.II/structGeometryInfo.html
@@ -3725,7 +3732,7 @@ namespace
 
         // Node coordinates
         output.setf(std::ios::scientific, std::ios::floatfield);
-        for (unsigned int jj = 1; jj < dim + 1; ++jj)
+        for (unsigned int jj = 1; jj < spacedim + 1; ++jj)
           {
             // invoke tolerance -> set points close to zero equal to zero
             if (std::abs(node_list[ii][jj]) > tolerance)
@@ -3733,7 +3740,7 @@ namespace
             else
               output << 0.0 << "\t";
           }
-        if (dim == 2)
+        if (spacedim == 2)
           output << 0.0 << "\t";
 
         output << std::endl;

diff --git a/tests/grid/grid_in_abaqus_02.cc b/tests/grid/grid_in_abaqus_02.cc
new file mode 100644 (file)
index 0000000..df1984c
--- /dev/null
+++ b/tests/grid/grid_in_abaqus_02.cc
@@ -0,0 +1,115 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2004 - 2017 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+
+// Check whether we can read in with the abaqus format
+// Specifically, this tests for the codimension 1 case; previously the
+// third dimension was being ignored, effectively projecting the mesh to
+// the XY plane.
+
+#include <deal.II/grid/grid_in.h>
+#include <deal.II/grid/grid_out.h>
+#include <deal.II/grid/tria.h>
+#include <deal.II/grid/tria_accessor.h>
+#include <deal.II/grid/tria_iterator.h>
+
+#include "../tests.h"
+
+
+
+template <int dim, int spacedim>
+void
+abaqus_grid(const std::string path_and_name,
+            const bool        output_grid  = false,
+            const std::string gridout_name = "")
+{
+  Triangulation<dim, spacedim> tria;
+  GridIn<dim, spacedim>        grid_in;
+  grid_in.attach_triangulation(tria);
+  std::ifstream input_file(path_and_name);
+  grid_in.read_abaqus(input_file);
+
+  deallog << "  " << tria.n_active_cells() << " active cells" << std::endl;
+
+  int hash  = 0;
+  int index = 0;
+  for (typename Triangulation<dim, spacedim>::active_cell_iterator c =
+         tria.begin_active();
+       c != tria.end();
+       ++c, ++index)
+    for (unsigned int i = 0; i < GeometryInfo<dim>::vertices_per_cell; ++i)
+      hash += (index * i * c->vertex_index(i)) % (tria.n_active_cells() + 1);
+  deallog << "  hash=" << hash << std::endl;
+
+  if (output_grid)
+    {
+      // Write in uncompressed VTK so that its possible to verify by eye
+      // that the last coordinate of all nodes is non-zero.
+      std::ofstream     fout_vtk(gridout_name + ".vtk");
+      GridOutFlags::Vtk flags_vtk;
+      flags_vtk.compression_level = DataOutBase::VtkFlags::no_compression;
+      GridOut gridout;
+      gridout.set_flags(flags_vtk);
+      gridout.write_vtk(tria, fout_vtk);
+    }
+}
+
+
+int
+main()
+{
+  initlog();
+
+  try
+    {
+      deallog << "codim_1-tube" << std::endl;
+      abaqus_grid<2, 3>(SOURCE_DIR "/grids/abaqus/3d/codim_1-tube.inp",
+                        false,
+                        "codim_1-tube");
+      deallog << "codim_1-jagged_surface" << std::endl;
+      abaqus_grid<2, 3>(SOURCE_DIR
+                        "/grids/abaqus/3d/codim_1-jagged_surface.inp",
+                        false,
+                        "codim_1-jagged_surface");
+    }
+  catch (std::exception &exc)
+    {
+      deallog << std::endl
+              << std::endl
+              << "----------------------------------------------------"
+              << std::endl;
+      deallog << "Exception on processing: " << std::endl
+              << exc.what() << std::endl
+              << "Aborting!" << std::endl
+              << "----------------------------------------------------"
+              << std::endl;
+      return 1;
+    }
+  catch (...)
+    {
+      deallog << std::endl
+              << std::endl
+              << "----------------------------------------------------"
+              << std::endl;
+      deallog << "Unknown exception!" << std::endl
+              << "Aborting!" << std::endl
+              << "----------------------------------------------------"
+              << std::endl;
+      return 1;
+    };
+
+  return 0;
+}

diff --git a/tests/grid/grid_in_abaqus_02.output b/tests/grid/grid_in_abaqus_02.output
new file mode 100644 (file)
index 0000000..4e455ff
--- /dev/null
+++ b/tests/grid/grid_in_abaqus_02.output
@@ -0,0 +1,7 @@
+
+DEAL::codim_1-tube
+DEAL::  96 active cells
+DEAL::  hash=13187
+DEAL::codim_1-jagged_surface
+DEAL::  394 active cells
+DEAL::  hash=233401

diff --git a/tests/grid/grids/abaqus/3d/codim_1-jagged_surface.inp b/tests/grid/grids/abaqus/3d/codim_1-jagged_surface.inp
new file mode 100644 (file)
index 0000000..e9fdd31
--- /dev/null
+++ b/tests/grid/grids/abaqus/3d/codim_1-jagged_surface.inp
@@ -0,0 +1,838 @@
+*Part, name=MESH\r
+*Node\r
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+*End Part\r
+\r

diff --git a/tests/grid/grids/abaqus/3d/codim_1-tube.inp b/tests/grid/grids/abaqus/3d/codim_1-tube.inp
new file mode 100644 (file)
index 0000000..e41fa8f
--- /dev/null
+++ b/tests/grid/grids/abaqus/3d/codim_1-tube.inp
@@ -0,0 +1,221 @@
+*Part, name=Part-1\r
+*Node\r
+      1,  -8.66025448,           5.,          10.\r
+      2,  -8.66025448,           5.,           0.\r
+      3,           0.,         -10.,           0.\r
+      4,          10.,  8.13201453e-08,           0.\r
+      5,           0.,         -10.,          10.\r
+      6,          10.,  -8.13201453e-08,          10.\r
+      7,  -8.66025352,   5.00000048,          7.5\r
+      8,  -8.66025352,   5.00000048,           5.\r
+      9,  -8.66025352,   5.00000048,          2.5\r
+     10,  -9.65925789,   2.58819032,           0.\r
+     11,         -10.,  -8.13201453e-08,           0.\r
+     12,  -9.65925789,  -2.58819032,           0.\r
+     13,  -8.66025448,          -5.,           0.\r
+     14,  -7.07106781,  -7.07106781,           0.\r
+     15,          -5.,  -8.66025448,           0.\r
+     16,  -2.58819032,  -9.65925789,           0.\r
+     17,   2.58819032,  -9.65925789,           0.\r
+     18,           5.,  -8.66025448,           0.\r
+     19,   7.07106781,  -7.07106781,           0.\r
+     20,   8.66025448,          -5.,           0.\r
+     21,   9.65925789,  -2.58819032,           0.\r
+     22,          10.,           0.,          2.5\r
+     23,          10.,           0.,           5.\r
+     24,          10.,           0.,          7.5\r
+     25,  -2.58819032,  -9.65925789,          10.\r
+     26,          -5.,  -8.66025448,          10.\r
+     27,  -7.07106781,  -7.07106781,          10.\r
+     28,  -8.66025448,          -5.,          10.\r
+     29,  -9.65925789,  -2.58819032,          10.\r
+     30,         -10.,  8.13201453e-08,          10.\r
+     31,  -9.65925789,   2.58819032,          10.\r
+     32,   9.65925789,  -2.58819032,          10.\r
+     33,   8.66025448,          -5.,          10.\r
+     34,   7.07106781,  -7.07106781,          10.\r
+     35,           5.,  -8.66025448,          10.\r
+     36,   2.58819032,  -9.65925789,          10.\r
+     37,  -7.07106781,   7.07106781,          10.\r
+     38,          -5.,   8.66025448,          10.\r
+     39,  -2.58819032,   9.65925789,          10.\r
+     40,  8.13201453e-08,          10.,          10.\r
+     41,   2.58819032,   9.65925789,          10.\r
+     42,           5.,   8.66025448,          10.\r
+     43,   7.07106781,   7.07106781,          10.\r
+     44,   8.66025448,           5.,          10.\r
+     45,   9.65925789,   2.58819032,          10.\r
+     46,   9.65925789,   2.58819032,           0.\r
+     47,   8.66025448,           5.,           0.\r
+     48,   7.07106781,   7.07106781,           0.\r
+     49,           5.,   8.66025448,           0.\r
+     50,   2.58819032,   9.65925789,           0.\r
+     51,  -8.13201453e-08,          10.,           0.\r
+     52,  -2.58819032,   9.65925789,           0.\r
+     53,          -5.,   8.66025448,           0.\r
+     54,  -7.07106781,   7.07106781,           0.\r
+     55,  -9.65925884,   2.58818913,          7.5\r
+     56,  -9.65925884,   2.58818913,           5.\r
+     57,  -9.65925884,   2.58818913,          2.5\r
+     58,         -10.,  -1.509958e-06,          7.5\r
+     59,         -10.,  -1.509958e-06,           5.\r
+     60,         -10.,  -1.509958e-06,          2.5\r
+     61,  -9.65925789,  -2.58819151,          7.5\r
+     62,  -9.65925789,  -2.58819151,           5.\r
+     63,  -9.65925789,  -2.58819151,          2.5\r
+     64,  -8.66025352,  -5.00000048,          7.5\r
+     65,  -8.66025352,  -5.00000048,           5.\r
+     66,  -8.66025352,  -5.00000048,          2.5\r
+     67,  -7.07106781,  -7.07106781,          7.5\r
+     68,  -7.07106781,  -7.07106781,           5.\r
+     69,  -7.07106781,  -7.07106781,          2.5\r
+     70,  -5.00000048,  -8.66025352,          7.5\r
+     71,  -5.00000048,  -8.66025352,           5.\r
+     72,  -5.00000048,  -8.66025352,          2.5\r
+     73,  -2.58819151,  -9.65925789,          7.5\r
+     74,  -2.58819151,  -9.65925789,           5.\r
+     75,  -2.58819151,  -9.65925789,          2.5\r
+     76,  -1.62920685e-06,         -10.,          7.5\r
+     77,  -1.62920685e-06,         -10.,           5.\r
+     78,  -1.62920685e-06,         -10.,          2.5\r
+     79,   2.58819079,  -9.65925789,          7.5\r
+     80,   2.58819079,  -9.65925789,           5.\r
+     81,   2.58819079,  -9.65925789,          2.5\r
+     82,   4.99999952,  -8.66025448,          7.5\r
+     83,   4.99999952,  -8.66025448,           5.\r
+     84,   4.99999952,  -8.66025448,          2.5\r
+     85,   7.07106781,  -7.07106781,          7.5\r
+     86,   7.07106781,  -7.07106781,           5.\r
+     87,   7.07106781,  -7.07106781,          2.5\r
+     88,   8.66025448,  -4.99999952,          7.5\r
+     89,   8.66025448,  -4.99999952,           5.\r
+     90,   8.66025352,          -5.,          2.5\r
+     91,   9.65925789,  -2.58819056,          7.5\r
+     92,   9.65925789,  -2.58819056,           5.\r
+     93,   9.65925789,  -2.58819056,          2.5\r
+     94,  -7.07106781,   7.07106781,          2.5\r
+     95,  -7.07106781,   7.07106781,           5.\r
+     96,  -7.07106781,   7.07106781,          7.5\r
+     97,  -5.00000048,   8.66025352,          2.5\r
+     98,  -5.00000048,   8.66025352,           5.\r
+     99,  -5.00000048,   8.66025352,          7.5\r
+    100,  -2.58819151,   9.65925789,          2.5\r
+    101,  -2.58819151,   9.65925789,           5.\r
+    102,  -2.58819151,   9.65925789,          7.5\r
+    103,  -1.62920685e-06,          10.,          2.5\r
+    104,  -1.62920685e-06,          10.,           5.\r
+    105,  -1.62920685e-06,          10.,          7.5\r
+    106,   2.58819079,   9.65925789,          2.5\r
+    107,   2.58819079,   9.65925789,           5.\r
+    108,   2.58819079,   9.65925789,          7.5\r
+    109,   4.99999952,   8.66025448,          2.5\r
+    110,   4.99999952,   8.66025448,           5.\r
+    111,   4.99999952,   8.66025448,          7.5\r
+    112,   7.07106781,   7.07106781,          2.5\r
+    113,   7.07106781,   7.07106781,           5.\r
+    114,   7.07106781,   7.07106781,          7.5\r
+    115,   8.66025448,   4.99999952,          2.5\r
+    116,   8.66025448,   4.99999952,           5.\r
+    117,   8.66025352,           5.,          7.5\r
+    118,   9.65925789,   2.58819056,          2.5\r
+    119,   9.65925789,   2.58819056,           5.\r
+    120,   9.65925789,   2.58819056,          7.5\r
+*Element, type=S4R\r
+ 1,   1,   7,  55,  31\r
+ 2,   7,   8,  56,  55\r
+ 3,   8,   9,  57,  56\r
+ 4,   9,   2,  10,  57\r
+ 5,  31,  55,  58,  30\r
+ 6,  55,  56,  59,  58\r
+ 7,  56,  57,  60,  59\r
+ 8,  57,  10,  11,  60\r
+ 9,  30,  58,  61,  29\r
+10,  58,  59,  62,  61\r
+11,  59,  60,  63,  62\r
+12,  60,  11,  12,  63\r
+13,  29,  61,  64,  28\r
+14,  61,  62,  65,  64\r
+15,  62,  63,  66,  65\r
+16,  63,  12,  13,  66\r
+17,  28,  64,  67,  27\r
+18,  64,  65,  68,  67\r
+19,  65,  66,  69,  68\r
+20,  66,  13,  14,  69\r
+21,  27,  67,  70,  26\r
+22,  67,  68,  71,  70\r
+23,  68,  69,  72,  71\r
+24,  69,  14,  15,  72\r
+25,  26,  70,  73,  25\r
+26,  70,  71,  74,  73\r
+27,  71,  72,  75,  74\r
+28,  72,  15,  16,  75\r
+29,  25,  73,  76,   5\r
+30,  73,  74,  77,  76\r
+31,  74,  75,  78,  77\r
+32,  75,  16,   3,  78\r
+33,   5,  76,  79,  36\r
+34,  76,  77,  80,  79\r
+35,  77,  78,  81,  80\r
+36,  78,   3,  17,  81\r
+37,  36,  79,  82,  35\r
+38,  79,  80,  83,  82\r
+39,  80,  81,  84,  83\r
+40,  81,  17,  18,  84\r
+41,  35,  82,  85,  34\r
+42,  82,  83,  86,  85\r
+43,  83,  84,  87,  86\r
+44,  84,  18,  19,  87\r
+45,  34,  85,  88,  33\r
+46,  85,  86,  89,  88\r
+47,  86,  87,  90,  89\r
+48,  87,  19,  20,  90\r
+49,  33,  88,  91,  32\r
+50,  88,  89,  92,  91\r
+51,  89,  90,  93,  92\r
+52,  90,  20,  21,  93\r
+53,  32,  91,  24,   6\r
+54,  91,  92,  23,  24\r
+55,  92,  93,  22,  23\r
+56,  93,  21,   4,  22\r
+57,   2,   9,  94,  54\r
+58,   9,   8,  95,  94\r
+59,   8,   7,  96,  95\r
+60,   7,   1,  37,  96\r
+61,  54,  94,  97,  53\r
+62,  94,  95,  98,  97\r
+63,  95,  96,  99,  98\r
+64,  96,  37,  38,  99\r
+65,  53,  97, 100,  52\r
+66,  97,  98, 101, 100\r
+67,  98,  99, 102, 101\r
+68,  99,  38,  39, 102\r
+69,  52, 100, 103,  51\r
+70, 100, 101, 104, 103\r
+71, 101, 102, 105, 104\r
+72, 102,  39,  40, 105\r
+73,  51, 103, 106,  50\r
+74, 103, 104, 107, 106\r
+75, 104, 105, 108, 107\r
+76, 105,  40,  41, 108\r
+77,  50, 106, 109,  49\r
+78, 106, 107, 110, 109\r
+79, 107, 108, 111, 110\r
+80, 108,  41,  42, 111\r
+81,  49, 109, 112,  48\r
+82, 109, 110, 113, 112\r
+83, 110, 111, 114, 113\r
+84, 111,  42,  43, 114\r
+85,  48, 112, 115,  47\r
+86, 112, 113, 116, 115\r
+87, 113, 114, 117, 116\r
+88, 114,  43,  44, 117\r
+89,  47, 115, 118,  46\r
+90, 115, 116, 119, 118\r
+91, 116, 117, 120, 119\r
+92, 117,  44,  45, 120\r
+93,  46, 118,  22,   4\r
+94, 118, 119,  23,  22\r
+95, 119, 120,  24,  23\r
+96, 120,  45,   6,  24\r
+*End Part\r
+\r