Cppcheck report - MOAB: test/mesquite/unit/PatchDataTest.cpp

/* *****************************************************************
    MESQUITE -- The Mesh Quality Improvement Toolkit

    Copyright 2004 Sandia Corporation and Argonne National
    Laboratory.  Under the terms of Contract DE-AC04-94AL85000
    with Sandia Corporation, the U.S. Government retains certain
    rights in this software.

    This library is free software; you can 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.

    This library is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
    Lesser General Public License for more details.

    You should have received a copy of the GNU Lesser General Public License
    (lgpl.txt) along with this library; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

    [email protected], [email protected], [email protected],
    [email protected], [email protected], [email protected]

  ***************************************************************** */
//
//    AUTHOR: Thomas Leurent <[email protected]>
//       ORG: Argonne National Laboratory
//    E-MAIL: [email protected]
//
// ORIG-DATE: 13-Nov-02 at 18:05:56
//  LAST-MOD:  9-Jun-04 at 14:50:51 by Thomas Leurent
//
// DESCRIPTION:
// ============
/*! \file PatchDataTest.cpp

Unit testing of various functions in the PatchData class.

 */
// DESCRIP-END.
//

#include "Mesquite.hpp"
#include "PatchData.hpp"
#include "PatchDataInstances.hpp"
#include "UnitUtil.hpp"
#include "Settings.hpp"
#include "Instruction.hpp"

#include "ArrayMesh.hpp"
#include "DomainClassifier.hpp"
#include "PlanarDomain.hpp"
#include "MeshDomain1D.hpp"
#include "MeshDecorator.hpp"

//#include "TriLagrangeShape.hpp"

#include "cppunit/extensions/HelperMacros.h"

#include <algorithm>
#include <set>
#include <map>

using namespace MBMesquite;

using std::cerr;
using std::cout;
using std::endl;

class PatchDataTest : public CppUnit::TestFixture
{
  private:
    CPPUNIT_TEST_SUITE( PatchDataTest );
    CPPUNIT_TEST( test_num_corners );
    CPPUNIT_TEST( test_get_element_vertex_indices );
    CPPUNIT_TEST( test_get_vertex_element_indices );
    CPPUNIT_TEST( test_get_element_vertex_coordinates );
    CPPUNIT_TEST( test_move_free_vertices_constrained );
    CPPUNIT_TEST( test_movement_function );
    CPPUNIT_TEST( test_get_adj_elems_2d );
    CPPUNIT_TEST( test_get_minmax_element_area );
    CPPUNIT_TEST( test_sub_patch );
    CPPUNIT_TEST( test_fill );
    CPPUNIT_TEST( test_reorder );
    CPPUNIT_TEST( test_update_slave_node_coords );
    CPPUNIT_TEST( test_patch_data_fill_slaved_ho_nodes );
    CPPUNIT_TEST( test_patch_reorder_ho_nodes );
    CPPUNIT_TEST( test_patch_data_fill_free_ho_nodes );
    CPPUNIT_TEST( test_patch_data_mesh_slaved_ho_nodes );
    CPPUNIT_TEST( test_patch_data_mesh_free_ho_nodes );
    CPPUNIT_TEST( test_patch_data_mesh_calcualted_ho_nodes );
    CPPUNIT_TEST( test_patch_data_mesh_flagged_ho_nodes );
    CPPUNIT_TEST( test_vertex_verts_fixed );
    CPPUNIT_TEST( test_curve_verts_fixed );
    CPPUNIT_TEST( test_surf_verts_fixed );
    CPPUNIT_TEST_SUITE_END();

  private:
    MsqVertex vtx_0_0;
    MsqVertex vtx_0_1;
    MsqVertex vtx_1_0;
    MsqVertex vtx_1_1;
    MsqVertex vtx_2_0;
    MsqVertex vtx_2_1;

    MsqMeshEntity tri1;
    MsqMeshEntity tri2;
    MsqMeshEntity quad1;

    PatchData mPatch2D;

    void test_quad8_patch( bool reorder, bool ho_nodes_slaved );
    void get_quad8_mesh( Mesh*& mesh_out );
    void get_quad8_mesh_and_domain( Mesh*& mesh_out, MeshDomain*& domain_out );
    void get_higher_order_vertices( Mesh* mesh,
                                    std::map< Mesh::VertexHandle, bool >& ho_verts,
                                    bool initial_value  = false,
                                    bool non_fixed_only = true );
    void check_higher_order_vertices_slaved( Mesh* mesh,
                                             Settings::HigherOrderSlaveMode mode,
                                             const std::map< Mesh::VertexHandle, bool >& expected );

  public:
    void setUp()
    {
        MsqPrintError err( cout );

        /* our 2D set up: 2 triangles and one quad are available
          1___3___5
           |\1|   |
           |0\| 2 |
          0---2---4
        */
        vtx_0_0.set( 0, 0, 0 );
        vtx_0_1.set( 0, 1, 0 );
        vtx_1_0.set( 1, 0, 0 );
        vtx_1_1.set( 1, 1, 0 );
        vtx_2_0.set( 2, 0, 0 );
        vtx_2_1.set( 2, 1, 0 );

        double coords[] = { 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 1, 0, 2, 0, 0, 2, 1, 0 };

        EntityTopology types[] = { TRIANGLE, TRIANGLE, QUADRILATERAL };

        size_t connectivity[] = { 0, 2, 1, 1, 2, 3, 3, 2, 4, 5 };

        size_t counts[] = { 3, 3, 4 };

        mPatch2D.fill( 6, coords, 3, types, counts, connectivity, 0, err );
    }

    void tearDown() {}

  public:
    PatchDataTest() {}

    void test_num_corners()
    {
        MsqPrintError err( cout );
        size_t n = mPatch2D.num_corners();
        CPPUNIT_ASSERT( n == 10 );
    }

    void test_get_element_vertex_indices()
    {

        MsqPrintError err( cout );

        std::vector< size_t > vtx_ind;
        std::vector< size_t > res;

        // test we get the right vertices for element 1 (tri)
        mPatch2D.get_element_vertex_indices( 1, vtx_ind, err );
        CPPUNIT_ASSERT( !err );
        res.push_back( 1 );
        res.push_back( 2 );
        res.push_back( 3 );
        CPPUNIT_ASSERT( vtx_ind == res );

        // test we get the right vertices for element 2 (quad)
        vtx_ind.clear();
        res.clear();
        mPatch2D.get_element_vertex_indices( 2, vtx_ind, err );
        CPPUNIT_ASSERT( !err );
        res.push_back( 3 );
        res.push_back( 2 );
        res.push_back( 4 );
        res.push_back( 5 );
        CPPUNIT_ASSERT( vtx_ind == res );
    }

    void test_get_vertex_element_indices()
    {
        /*  1___3___5
            |\1|   |
            |0\| 2 |
            0---2---4   */
        MsqPrintError err( cout );

        std::vector< size_t > elem_ind;
        std::vector< size_t > res;

        mPatch2D.generate_vertex_to_element_data();

        // test we get the elements contiguous to vertex 3
        mPatch2D.get_vertex_element_indices( 3, elem_ind, err );
        CPPUNIT_ASSERT( !err );
        res.push_back( 2 );
        res.push_back( 1 );
        CPPUNIT_ASSERT( res == elem_ind );

        // test we get the elements contiguous to vertex 2
        elem_ind.clear();
        res.clear();
        mPatch2D.get_vertex_element_indices( 2, elem_ind, err );
        CPPUNIT_ASSERT( !err );
        res.push_back( 2 );
        res.push_back( 1 );
        res.push_back( 0 );
        CPPUNIT_ASSERT( res == elem_ind );
    }

    void test_get_element_vertex_coordinates()
    {
        MsqPrintError err( cout );

        std::vector< Vector3D > coords;
        mPatch2D.get_element_vertex_coordinates( 1, coords, err );
        CPPUNIT_ASSERT( !err );

        CPPUNIT_ASSERT( coords[0] == vtx_0_1 );
        CPPUNIT_ASSERT( coords[1] == vtx_1_0 );
        CPPUNIT_ASSERT( coords[2] == vtx_1_1 );
    }

    /* This tests the move_vertices() function as well as the
       PatchDataCoordsMemento functionality
       */
    void test_move_free_vertices_constrained()
    {
        MsqPrintError err( cout );

        // gets a memento of the patch coordinates.
        PatchDataVerticesMemento* coords_mem = mPatch2D.create_vertices_memento( err );
        CPPUNIT_ASSERT( !err );

        // Move the two first vertices in direction dk by step size s;
        Vector3D dk[6];
        dk[0].set( -1, -2, 0 );
        dk[1].set( -1, 2, 0 );
        double s = 0.3;
        mPatch2D.move_free_vertices_constrained( dk, 6, s, err );
        CPPUNIT_ASSERT( !err );

        // gets the new coordinates and  checks the vertices were displaced as expected.
        std::vector< Vector3D > coords;
        mPatch2D.get_element_vertex_coordinates( 0, coords, err );
        Vector3D new_vtx_0_0 = vtx_0_0 + s * dk[0];
        Vector3D new_vtx_0_1 = vtx_0_1 + s * dk[1];
        CPPUNIT_ASSERT( coords[0] == new_vtx_0_0 );
        CPPUNIT_ASSERT( coords[2] == new_vtx_0_1 );

        // restore the PatchData to previous coords.
        mPatch2D.set_to_vertices_memento( coords_mem, err );
        CPPUNIT_ASSERT( !err );

        // gets the new coordinates and  checks the vertices are back to original.
        coords.clear();
        mPatch2D.get_element_vertex_coordinates( 0, coords, err );
        CPPUNIT_ASSERT( coords[0] == vtx_0_0 );
        CPPUNIT_ASSERT( coords[2] == vtx_0_1 );

        delete coords_mem;
    }

    void test_movement_function()
    {
        MsqPrintError err( cout );
        // gets a memento of the patch coordinates.
        PatchDataVerticesMemento* coords_mem = mPatch2D.create_vertices_memento( err );
        CPPUNIT_ASSERT( !err );

        // Move the two first vertices in direction dk by step size s;
        Vector3D dk[6];
        dk[0].set( 0, -2, 0 );
        dk[1].set( -1, 0, 0 );
        double s = 1;
        mPatch2D.move_free_vertices_constrained( dk, 6, 1, err );
        CPPUNIT_ASSERT( !err );
        // gets the new coordinates and  checks the vertices were displaced as expected.
        std::vector< Vector3D > coords;
        mPatch2D.get_element_vertex_coordinates( 0, coords, err );
        Vector3D new_vtx_0_0 = vtx_0_0 + s * dk[0];
        Vector3D new_vtx_0_1 = vtx_0_1 + s * dk[1];
        CPPUNIT_ASSERT( coords[0] == new_vtx_0_0 );
        CPPUNIT_ASSERT( coords[2] == new_vtx_0_1 );
        double m_dist = mPatch2D.get_max_vertex_movement_squared( coords_mem, err );
        CPPUNIT_ASSERT( m_dist == 4.0 );
        // restore the PatchData to previous coords.
        mPatch2D.set_to_vertices_memento( coords_mem, err );
        CPPUNIT_ASSERT( !err );
        // gets the new coordinates and  checks the vertices are back to original.
        coords.clear();
        mPatch2D.get_element_vertex_coordinates( 0, coords, err );
        CPPUNIT_ASSERT( coords[0] == vtx_0_0 );
        CPPUNIT_ASSERT( coords[2] == vtx_0_1 );

        delete coords_mem;
    }

    /*Tests the function PatchData::get_adjacent_entities_via_n_dim()
      which finds the elements adjacent to a given element.  If 'n'
      equals 0 the elements must share a vertex; if 'n' equals 1 the
      elements must share an edge; and if 'n' equals 2 the elements
      must share a face.*/
    void test_get_adj_elems_2d()
    {
        MsqPrintError err( cout );
        std::vector< size_t > elems_0;
        // find elements sharing an edge with oth elem (should be 1)
        mPatch2D.get_adjacent_entities_via_n_dim( 1, 0, elems_0, err );
        CPPUNIT_ASSERT( !err );
        CPPUNIT_ASSERT( elems_0.back() == 1 );
        std::vector< size_t > elems_1;
        // find elements sharing an edge with 1st elem (should be 0 and 2)
        mPatch2D.get_adjacent_entities_via_n_dim( 1, 1, elems_1, err );
        CPPUNIT_ASSERT( !err );
        CPPUNIT_ASSERT( elems_1.size() == 2 );
        std::vector< size_t > elems_2;
        // find elements sharing an vert with 0th elem (should be 1 and 2).
        mPatch2D.get_adjacent_entities_via_n_dim( 0, 0, elems_2, err );
        CPPUNIT_ASSERT( !err );
        CPPUNIT_ASSERT( elems_2.size() == 2 );
        std::vector< size_t > elems_3;
        // find elements sharing an face with 0th elem (should be empty).
        mPatch2D.get_adjacent_entities_via_n_dim( 2, 0, elems_3, err );
        CPPUNIT_ASSERT( !err );
        CPPUNIT_ASSERT( elems_3.size() == 0 );
    }

    void test_get_minmax_element_area()
    {
        MsqPrintError err( cout );
        double min, max;
        mPatch2D.get_minmax_element_unsigned_area( min, max, err );
        CPPUNIT_ASSERT( !err );

        CPPUNIT_ASSERT_DOUBLES_EQUAL( 0.5, min, 0.0001 );
        CPPUNIT_ASSERT_DOUBLES_EQUAL( 1.0, max, 0.0001 );
    }

    void check_sub_patch( unsigned vtx, unsigned layers, PatchData& pd, PatchData& sub );

    void test_sub_patch();

    void test_patch_contents( bool reorder );

    void test_fill()
    {
        test_patch_contents( false );
    }
    void test_reorder()
    {
        test_patch_contents( true );
    }

    void test_update_slave_node_coords();
    void test_patch_data_fill_slaved_ho_nodes()
    {
        test_quad8_patch( false, true );
    }
    void test_patch_reorder_ho_nodes()
    {
        test_quad8_patch( true, true );
    }
    void test_patch_data_fill_free_ho_nodes()
    {
        test_quad8_patch( false, false );
    }

    void test_patch_data_mesh_slaved_ho_nodes();
    void test_patch_data_mesh_free_ho_nodes();
    void test_patch_data_mesh_calcualted_ho_nodes();
    void test_patch_data_mesh_flagged_ho_nodes();

    void test_fixed_by_geom_dim( unsigned dim );
    void test_vertex_verts_fixed()
    {
        test_fixed_by_geom_dim( 0 );
    }
    void test_curve_verts_fixed()
    {
        test_fixed_by_geom_dim( 1 );
    }
    void test_surf_verts_fixed()
    {
        test_fixed_by_geom_dim( 2 );
    }
};

CPPUNIT_TEST_SUITE_NAMED_REGISTRATION( PatchDataTest, "PatchDataTest" );
CPPUNIT_TEST_SUITE_NAMED_REGISTRATION( PatchDataTest, "Unit" );

void PatchDataTest::check_sub_patch( unsigned vtx, unsigned layers, PatchData& pd, PatchData& sub )
{
    unsigned i, j;
    std::set< size_t > seen;
    std::vector< size_t > vtx_map, elem_map;

    // test vertex list consistency
    vtx_map.resize( sub.num_nodes() );
    for( i = 0; i < sub.num_nodes(); ++i )
    {
        // get index in old patch for this vertex
        Mesh::VertexHandle h    = sub.get_vertex_handles_array()[i];
        Mesh::VertexHandle* end = pd.get_vertex_handles_array() + pd.num_nodes();
        Mesh::VertexHandle* ptr = std::find( pd.get_vertex_handles_array(), end, h );
        CPPUNIT_ASSERT( ptr != end );
        size_t idx = ptr - pd.get_vertex_handles_array();
        CPPUNIT_ASSERT( idx < pd.num_nodes() );
        // put handle in map
        vtx_map[i] = idx;
        // make sure we don't have duplicates of vertices
        CPPUNIT_ASSERT( seen.insert( idx ).second );
        // make sure vertices have same coords
        CPPUNIT_ASSERT_VECTORS_EQUAL( pd.vertex_by_index( idx ), sub.vertex_by_index( i ), 1e-12 );
    }

    // test element list consistency
    seen.clear();
    elem_map.resize( sub.num_elements() );
    for( i = 0; i < sub.num_elements(); ++i )
    {
        // get index in old patch for element
        Mesh::ElementHandle h    = sub.get_element_handles_array()[i];
        Mesh::ElementHandle* end = pd.get_element_handles_array() + pd.num_nodes();
        Mesh::ElementHandle* ptr = std::find( pd.get_element_handles_array(), end, h );
        CPPUNIT_ASSERT( ptr != end );
        size_t idx = ptr - pd.get_element_handles_array();
        CPPUNIT_ASSERT( idx < pd.num_elements() );
        // put handle in map
        elem_map[i] = idx;
        // make sure we don't have duplicate elements
        CPPUNIT_ASSERT( seen.insert( idx ).second );
        // get elements
        MsqMeshEntity& elem1 = pd.element_by_index( idx );
        MsqMeshEntity& elem2 = sub.element_by_index( i );
        // compare element data
        CPPUNIT_ASSERT_EQUAL( elem1.get_element_type(), elem2.get_element_type() );
        CPPUNIT_ASSERT_EQUAL( elem1.node_count(), elem2.node_count() );
        // get connectivity for elements
        std::vector< size_t > vtx1, vtx2;
        elem1.get_node_indices( vtx1 );
        elem2.get_node_indices( vtx2 );
        CPPUNIT_ASSERT_EQUAL( vtx1.size(), vtx2.size() );
        // compare connectivity
        for( j = 0; j < vtx1.size(); ++j )
        {
            CPPUNIT_ASSERT( vtx1[j] < pd.num_nodes() );
            CPPUNIT_ASSERT( vtx2[j] < sub.num_nodes() );
            CPPUNIT_ASSERT_EQUAL( vtx1[j], vtx_map[vtx2[j]] );
        }
    }

    // test that the subpatch has the elements adjacent to the specified
    // vertex.

    // first get list of adjacent elements in original patch
    seen.clear();
    for( i = 0; i < pd.num_elements(); ++i )
    {
        std::vector< size_t > vtx_list;
        pd.element_by_index( i ).get_node_indices( vtx_list );
        if( std::find( vtx_list.begin(), vtx_list.end(), vtx ) != vtx_list.end() ) seen.insert( i );
    }

    // if 1 layer, then should match element count
    if( layers == 1 )
    {
        CPPUNIT_ASSERT_EQUAL( seen.size(), sub.num_elements() );
    }

    // remove from the set each element in the subpatch
    for( i = 0; i < sub.num_elements(); ++i )
    {
        size_t idx                      = elem_map[i];
        std::set< size_t >::iterator it = seen.find( idx );
        if( it != seen.end() )
        {
            seen.erase( it );
        }
        else
        {
            CPPUNIT_ASSERT( layers > 1 );
        }
    }
    CPPUNIT_ASSERT( seen.empty() );
}

void PatchDataTest::test_sub_patch()
{
    MsqPrintError err( std::cout );
    PatchData pd, sub;
    create_twelve_hex_patch( pd, err );
    CPPUNIT_ASSERT( !err );

    for( unsigned i = 0; i < pd.num_free_vertices(); ++i )
    {
        unsigned layers = i % 2 ? 2 : 1;
<--- Clarify calculation precedence for '%' and '?'. [+]
Suspicious calculation. Please use parentheses to clarify the code. The code ''a%b?c:d'' should be written as either ''(a%b)?c:d'' or ''a%(b?c:d)''.
        pd.get_subpatch( i, layers, sub, err );
        CPPUNIT_ASSERT( !err );

        check_sub_patch( i, layers, pd, sub );
    }
}

void PatchDataTest::test_patch_contents( bool reorder )
{
    const unsigned NUM_VERTEX  = 15;
    const unsigned NUM_ELEMENT = 9;

    // Mesh data used to populate patch
    // Use a relatively randomized order for verices
    // so patch reordering will result in a changed
    // vertex ordering.
    double coords[3 * NUM_VERTEX]     = { 6, 6, 3,                                      // 0
                                      0, 0, 0, 0, 6, 3, 4, 2, 2, 2, 4, 2, 4, 4, 2,  // 5
                                      0, 6, 3, 2, 2, 1, 2, 6, 3, 4, 0, 2, 6, 3, 3,  // 10
                                      0, 4, 2, 2, 0, 1, 6, 2, 2, 0, 2, 1 };         // 14
    size_t conn[]                     = { 3, 5,  4, 7, 7,  4,  11, 14, 5, 0,  8, 11, 5, 8,  13, 3, 9,
                      6, 10, 5, 3, 13, 12, 7,  14, 1, 10, 0, 5,  7, 12, 9,  3 };
    size_t conn_len[NUM_ELEMENT]      = { 4, 4, 3, 3, 4, 4, 4, 3, 4 };
    EntityTopology types[NUM_ELEMENT] = { QUADRILATERAL, QUADRILATERAL, TRIANGLE, TRIANGLE,     QUADRILATERAL,
                                          QUADRILATERAL, QUADRILATERAL, TRIANGLE, QUADRILATERAL };
    // mark vertices along X and Y axis as fixed
    bool fixed[NUM_VERTEX] = { false, true, true,  false, false, false, true, false,<--- Shadow variable
                               false, true, false, true,  true,  false, false };

    // populate patch data
    PatchData pd;
    MsqPrintError err( std::cout );
    pd.fill( NUM_VERTEX, coords, NUM_ELEMENT, types, conn_len, conn, fixed, err );
    CPPUNIT_ASSERT( !MSQ_CHKERR( err ) );

    if( reorder ) pd.reorder();

    // count free vertices
    unsigned i, j;<--- Shadowed declaration
    size_t num_free = 0;
    for( i = 0; i < NUM_VERTEX; ++i )
        if( !fixed[i] ) ++num_free;
    CPPUNIT_ASSERT_EQUAL( num_free, pd.num_free_vertices() );

    // NOTE: PatchData will reorder contents either because reorder()
    //       was called or to group vertices by fixed/free status.
    //       We will assume that the handles arrays for vertices and
    //       elements contain the initial positions in the input
    //       arrays used to populate the patch data.

    // Test vertex handles
    std::vector< bool > seen( NUM_VERTEX, false );
    for( i = 0; i < pd.num_nodes(); ++i )
    {
        size_t h = (size_t)( pd.get_vertex_handles_array()[i] );
        CPPUNIT_ASSERT( h < NUM_VERTEX );
        CPPUNIT_ASSERT( !seen[h] );
        seen[h] = true;
    }

    // Test vertex coordinates
    for( i = 0; i < pd.num_nodes(); ++i )
    {
        size_t h      = (size_t)( pd.get_vertex_handles_array()[i] );
        MsqVertex vtx = pd.vertex_by_index( i );
        CPPUNIT_ASSERT_DOUBLES_EQUAL( vtx[0], coords[3 * h], DBL_EPSILON );
        CPPUNIT_ASSERT_DOUBLES_EQUAL( vtx[1], coords[3 * h + 1], DBL_EPSILON );
        CPPUNIT_ASSERT_DOUBLES_EQUAL( vtx[2], coords[3 * h + 2], DBL_EPSILON );
    }

    // Test vertex fixed flags
    for( i = 0; i < pd.num_nodes(); ++i )
    {
        size_t h = (size_t)( pd.get_vertex_handles_array()[i] );
        if( fixed[h] )
        {
            CPPUNIT_ASSERT( i >= pd.num_free_vertices() );
            CPPUNIT_ASSERT( !pd.vertex_by_index( i ).is_free_vertex() );
        }
        else
        {
            CPPUNIT_ASSERT( i < pd.num_free_vertices() );
            CPPUNIT_ASSERT( pd.vertex_by_index( i ).is_free_vertex() );
        }
    }

    // Test element handles
    seen.clear();
    seen.resize( NUM_ELEMENT, false );
    for( i = 0; i < pd.num_elements(); ++i )
    {
        size_t h = (size_t)( pd.get_element_handles_array()[i] );
        CPPUNIT_ASSERT( h < NUM_ELEMENT );
        CPPUNIT_ASSERT( !seen[h] );
        seen[h] = true;
    }

    // Test element types
    for( i = 0; i < pd.num_elements(); ++i )
    {
        size_t h = (size_t)( pd.get_element_handles_array()[i] );
        CPPUNIT_ASSERT_EQUAL( types[h], pd.element_by_index( i ).get_element_type() );
    }

    // Test element connectivity
    for( i = 0; i < pd.num_elements(); ++i )
    {
        size_t h            = (size_t)( pd.get_element_handles_array()[i] );
        MsqMeshEntity& elem = pd.element_by_index( i );
        CPPUNIT_ASSERT_EQUAL( conn_len[h], elem.vertex_count() );
        CPPUNIT_ASSERT_EQUAL( conn_len[h], elem.node_count() );

        // calculate offset in input list for element connectivity
        unsigned conn_pos = 0;
        for( j = 0; j < h; ++j )
            conn_pos += conn_len[j];

        const size_t* elem_conn = elem.get_vertex_index_array();
        for( unsigned j = 0; j < elem.vertex_count(); ++j )<--- Shadow variable
        {
            size_t vh = (size_t)( pd.get_vertex_handles_array()[elem_conn[j]] );
            CPPUNIT_ASSERT_EQUAL( vh, conn[conn_pos] );
            ++conn_pos;
        }
    }
}

void PatchDataTest::test_update_slave_node_coords()
{
    MsqPrintError err( std::cerr );

    // create a patch containing a single 6-node triangle
    // with a) two mid-edge nodes marked as slave vertices and
    // b) with all mid-edge nodes moved away from the center
    // of their corresponding edge.
    const double coords[]    = { 0, 0, 0, 1, 0, 0, 0, 1, 0, 0.5, -0.1, -0.1, 0.6, 0.6, 0.1, -0.1, 0.5, 0.0 };
    const size_t init_conn[] = { 0, 1, 2, 3, 4, 5 };
    const bool fixed[]       = { false, false, false, false, true, false };<--- Shadow variable
    PatchData pd;
    EntityTopology type = TRIANGLE;
    size_t node_per_tri = 6;
    pd.fill( 6, coords, 1, &type, &node_per_tri, init_conn, fixed, err );
    ASSERT_NO_ERROR( err );

    // update_slave_node_coords requires a mapping function
    Settings settings;
    //  TriLagrangeShape tri_func;
    //  settings.set_mapping_function( &tri_func );
    pd.attach_settings( &settings );

    // call the function we're trying to test.
    pd.update_slave_node_coordinates( err );
    ASSERT_NO_ERROR( err );

    // get vertex coordinates in the same order that we passed them in
    MsqMeshEntity elem = pd.element_by_index( 0 );
    const size_t* conn = elem.get_vertex_index_array();
    Vector3D vtx_coords[6];
    for( size_t i = 0; i < 6; ++i )
        vtx_coords[i] = pd.vertex_by_index( conn[i] );

    // check that corner vertex coordinates are unchanged
    CPPUNIT_ASSERT_VECTORS_EQUAL( Vector3D( coords ), vtx_coords[0], 1e-12 );
    CPPUNIT_ASSERT_VECTORS_EQUAL( Vector3D( coords + 3 ), vtx_coords[1], 1e-12 );
    CPPUNIT_ASSERT_VECTORS_EQUAL( Vector3D( coords + 6 ), vtx_coords[2], 1e-12 );
    // check that fixed HO node is unchanged
    CPPUNIT_ASSERT_VECTORS_EQUAL( Vector3D( coords + 12 ), vtx_coords[4], 1e-12 );
    // check that slave HO nodes were updated
    const Vector3D mid1 = 0.5 * ( Vector3D( coords ) + Vector3D( coords + 3 ) );
    const Vector3D mid2 = 0.5 * ( Vector3D( coords ) + Vector3D( coords + 6 ) );
    CPPUNIT_ASSERT_VECTORS_EQUAL( mid1, vtx_coords[3], 1e-6 );
    CPPUNIT_ASSERT_VECTORS_EQUAL( mid2, vtx_coords[5], 1e-6 );
}

/* This is the input mesh topology
     (0)------(16)-----(1)------(17)-----(2)------(18)-----(3)
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
     (19)      0       (20)      1       (21)      2       (22)
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
     (4)------(23)-----(5)------(24)-----(6)------(25)-----(7)
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
     (26)      3       (27)      4       (28)      5       (29)
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
     (8)------(30)-----(9)------(31)-----(10)-----(32)-----(11)
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
     (33)      6       (34)      7       (35)      8       (36)
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
      |                 |                 |                 |
     (12)-----(37)-----(13)-----(38)-----(14)-----(39)-----(15)
*/
// input mesh definition
const int NUM_VTX = 40, NUM_ELEM = 9, NUM_CORNER = 16;
const double input_coords[3 * NUM_VTX] = { -3.0, 3.0,  0, -1.0, 3.0,  0, 1.0,  3.0,  0, 3.0,  3.0,  0, -3.0, 1.0,  0,
                                           -1.0, 1.0,  0, 1.0,  1.0,  0, 3.0,  1.0,  0, -3.0, -1.0, 0, -1.0, -1.0, 0,
                                           1.0,  -1.0, 0, 3.0,  -1.0, 0, -3.0, -3.0, 0, -1.0, -3.0, 0, 1.0,  -3.0, 0,
                                           3.0,  -3.0, 0, -2.0, 3.0,  0, 0.0,  3.0,  0, 2.0,  3.0,  0, -3.0, 2.0,  0,
                                           -1.0, 2.0,  0, 1.0,  2.0,  0, 3.0,  2.0,  0, -2.0, 1.0,  0, 0.0,  1.0,  0,
                                           2.0,  1.0,  0, -3.0, 0.0,  0, -1.0, 0.0,  0, 1.0,  0.0,  0, 3.0,  0.0,  0,
                                           -2.0, -1.0, 0, 0.0,  -1.0, 0, 2.0,  -1.0, 0, -3.0, -2.0, 0, -1.0, -2.0, 0,
                                           1.0,  -2.0, 0, 3.0,  -2.0, 0, -2.0, -3.0, 0, 0.0,  -3.0, 0, 2.0,  -3.0, 0 };
const bool fixed[NUM_VTX] = { true, true,  true,  true, true,  false, false, true,  true,  false, false, true,  true,<--- Shadowed declaration<--- Shadowed declaration<--- Shadowed declaration
                              true, true,  true,  true, true,  true,  true,  false, false, true,  false, false, false,
                              true, false, false, true, false, false, false, true,  false, false, true };
const size_t input_conn[8 * NUM_ELEM] = { 1,  0,  4,  5,  16, 19, 23, 20, 2,  1,  5,  6,  17, 20, 24, 21, 3,  2,
                                          6,  7,  18, 21, 25, 22, 5,  4,  8,  9,  23, 26, 30, 27, 6,  5,  9,  10,
                                          24, 27, 31, 28, 7,  6,  10, 11, 25, 28, 32, 29, 9,  8,  12, 13, 30, 33,
                                          37, 34, 10, 9,  13, 14, 31, 34, 38, 35, 11, 10, 14, 15, 32, 35, 39, 36 };

const size_t node_per_elem[NUM_ELEM]      = { 8, 8, 8, 8, 8, 8, 8, 8, 8 };
const EntityTopology elem_types[NUM_ELEM] = { QUADRILATERAL, QUADRILATERAL, QUADRILATERAL, QUADRILATERAL, QUADRILATERAL,
                                              QUADRILATERAL, QUADRILATERAL, QUADRILATERAL, QUADRILATERAL };

void PatchDataTest::test_quad8_patch( bool reorder, bool slaved )
{
    // create PatchData
    MsqPrintError err( std::cerr );
    PatchData pd;
    Settings settings;
    settings.set_slaved_ho_node_mode( Settings::SLAVE_NONE );
    if( !slaved )  // default is slaved, so only change settings if no slaved
        pd.attach_settings( &settings );
    pd.fill( NUM_VTX, input_coords, NUM_ELEM, elem_types, node_per_elem, input_conn, fixed, err );
    ASSERT_NO_ERROR( err );

    // reorder if testing that
    if( reorder ) pd.reorder();

    // Check sizes.  Assume that all non-fixed HO nodes are slave vertices
    // unless 'slaved' is false.

    CPPUNIT_ASSERT_EQUAL( NUM_VTX, (int)pd.num_nodes() );
    CPPUNIT_ASSERT_EQUAL( NUM_ELEM, (int)pd.num_elements() );
    int num_free = 0, num_slave = 0, num_fixed = 0;
    for( int i = 0; i < NUM_VTX; ++i )
    {
        if( fixed[i] )
            ++num_fixed;
        else if( i < NUM_CORNER )
            ++num_free;
        else if( slaved )
            ++num_slave;
        else
            ++num_free;
    }
    CPPUNIT_ASSERT_EQUAL( num_free, (int)pd.num_free_vertices() );
    CPPUNIT_ASSERT_EQUAL( num_slave, (int)pd.num_slave_vertices() );
    CPPUNIT_ASSERT_EQUAL( num_fixed, (int)pd.num_fixed_vertices() );

    // Check that vertex handles and vertex coords are correct.
    // Assume that handles array contains input vertex indices.

    for( int i = 0; i < NUM_VTX; ++i )
    {
        const MsqVertex& vtx   = pd.vertex_by_index( i );
        Mesh::VertexHandle hdl = pd.get_vertex_handles_array()[i];
        size_t idx             = (size_t)hdl;
        Vector3D exp_coords( input_coords + 3 * idx );
        if( ( exp_coords - vtx ).length_squared() > 1e-16 )
        {
            std::cerr << "Input Index: " << idx << std::endl;
            std::cerr << "Patch Index: " << i << std::endl;
        }
        CPPUNIT_ASSERT_VECTORS_EQUAL( exp_coords, vtx, 1e-16 );
    }

    // Check that vertex flags are correct.
    // Assume all non-fixed HO noes are slave vertices unless 'slaved' is false.
    // Assume that handles array contains input vertex indices.

    for( int i = 0; i < NUM_VTX; ++i )
    {
        const MsqVertex& vtx   = pd.vertex_by_index( i );
        Mesh::VertexHandle hdl = pd.get_vertex_handles_array()[i];
        size_t idx             = (size_t)hdl;
        if( fixed[idx] )
        {
            CPPUNIT_ASSERT( vtx.is_flag_set( MsqVertex::MSQ_HARD_FIXED ) );
        }
        else if( slaved && idx >= (size_t)NUM_CORNER )
        {
            CPPUNIT_ASSERT( vtx.is_flag_set( MsqVertex::MSQ_DEPENDENT ) );
        }
        else
        {
            CPPUNIT_ASSERT( !vtx.is_flag_set( MsqVertex::MSQ_HARD_FIXED ) );
            CPPUNIT_ASSERT( !vtx.is_flag_set( MsqVertex::MSQ_DEPENDENT ) );
        }
    }

    // Check that element connectivity is correct.
    // Assume that handles array contains input vertex and element indices.

    for( int i = 0; i < NUM_ELEM; ++i )
    {
        MsqMeshEntity& elem = pd.element_by_index( i );
        CPPUNIT_ASSERT_EQUAL( QUADRILATERAL, elem.get_element_type() );
        CPPUNIT_ASSERT_EQUAL( (size_t)4, elem.vertex_count() );
        CPPUNIT_ASSERT_EQUAL( (size_t)8, elem.node_count() );
        CPPUNIT_ASSERT_EQUAL( (size_t)4, elem.corner_count() );
        std::vector< std::size_t > conn;
        elem.get_node_indices( conn );
        CPPUNIT_ASSERT_EQUAL( elem.node_count(), conn.size() );
        for( int j = 0; j < 8; ++j )
            conn[j] = (size_t)pd.get_vertex_handles_array()[conn[j]];
        size_t idx = (size_t)pd.get_element_handles_array()[i];
        ASSERT_ARRAYS_EQUAL( input_conn + 8 * idx, arrptr( conn ), 8 );
    }
}

void PatchDataTest::get_quad8_mesh( Mesh*& mesh_out )
{
    static std::vector< int > fixed_flags( fixed, fixed + NUM_VTX );
    static std::vector< double > coords( input_coords, input_coords + 3 * NUM_VTX );
    static std::vector< unsigned long > conn( input_conn, input_conn + 8 * NUM_ELEM );
    mesh_out = new ArrayMesh( 3, NUM_VTX, arrptr( coords ), arrptr( fixed_flags ), NUM_ELEM, QUADRILATERAL,
                              arrptr( conn ), false, 8 );
}

void PatchDataTest::get_quad8_mesh_and_domain( Mesh*& mesh_out, MeshDomain*& domain_out )
{
    MsqPrintError err( std::cerr );

    get_quad8_mesh( mesh_out );
    DomainClassifier geom;
    Vector3D corners[4]   = { Vector3D( -3, 3, 0 ), Vector3D( 3, 3, 0 ), Vector3D( -3, -3, 0 ), Vector3D( 3, -3, 0 ) };
    MeshDomain* geomarr[] = { new PointDomain( corners[0] ),
                              new PointDomain( corners[1] ),
                              new PointDomain( corners[2] ),
                              new PointDomain( corners[3] ),
                              new LineDomain( corners[0], corners[1] - corners[0] ),
                              new LineDomain( corners[1], corners[2] - corners[1] ),
                              new LineDomain( corners[2], corners[3] - corners[2] ),
                              new LineDomain( corners[3], corners[0] - corners[3] ),
                              new PlanarDomain( PlanarDomain::XY ) };
    int dimarr[]          = { 0, 0, 0, 0, 1, 1, 1, 1, 2 };

    DomainClassifier* domain;
    domain_out = domain = new DomainClassifier;
    DomainClassifier::classify_geometrically( *domain, mesh_out, 1e-6, geomarr, dimarr, 9, err );
    domain->delete_sub_domains( true );
    ASSERT_NO_ERROR( err );
}

void PatchDataTest::test_fixed_by_geom_dim( unsigned dim )
{
    MsqPrintError err( std::cerr );

    Settings settings;
    switch( dim )
    {
        case 0:
            settings.set_fixed_vertex_mode( Settings::FIXED_VERTEX );
            break;
        case 1:
            settings.set_fixed_vertex_mode( Settings::FIXED_CURVE );
            break;
        case 2:
            settings.set_fixed_vertex_mode( Settings::FIXED_SURFACE );
            break;
        default:
            CPPUNIT_ASSERT( false );
    }

    Mesh* mesh         = 0;
    MeshDomain* domain = 0;
    get_quad8_mesh_and_domain( mesh, domain );
    MeshDomainAssoc mesh_and_domain = MeshDomainAssoc( mesh, domain );
    Instruction::initialize_vertex_byte( &mesh_and_domain, &settings, err );
    ASSERT_NO_ERROR( err );

    PatchData pd;
    pd.attach_settings( &settings );
    pd.set_mesh( mesh );
    pd.set_domain( domain );

    std::vector< Mesh::ElementHandle > elems;
    std::vector< Mesh::VertexHandle > verts;
    mesh->get_all_elements( elems, err );
    ASSERT_NO_ERROR( err );
    mesh->get_all_vertices( verts, err );
    ASSERT_NO_ERROR( err );
    pd.set_mesh_entities( elems, verts, err );
    ASSERT_NO_ERROR( err );
    CPPUNIT_ASSERT( !elems.empty() );

    std::vector< unsigned short > dims( verts.size() );
    domain->domain_DoF( arrptr( verts ), arrptr( dims ), verts.size(), err );
    ASSERT_NO_ERROR( err );

    for( size_t i = 0; i < pd.num_free_vertices(); ++i )
    {
        Mesh::VertexHandle handle = pd.get_vertex_handles_array()[i];
        unsigned short d;
        domain->domain_DoF( &handle, &d, 1, err );
        ASSERT_NO_ERROR( err );
        CPPUNIT_ASSERT( d > dim );
    }
    for( size_t i = 0; i < pd.num_fixed_vertices(); ++i )
    {
        size_t j                  = i + pd.num_free_vertices() + pd.num_slave_vertices();
        Mesh::VertexHandle handle = pd.get_vertex_handles_array()[j];
        unsigned short d;
        domain->domain_DoF( &handle, &d, 1, err );
        ASSERT_NO_ERROR( err );
        CPPUNIT_ASSERT( d <= dim );
    }

    delete mesh;
    delete domain;
}

void PatchDataTest::get_higher_order_vertices( Mesh* mesh,
                                               std::map< Mesh::VertexHandle, bool >& ho_verts,
                                               bool initial_value,
                                               bool non_fixed_only )
{
    // get mesh data
    MsqPrintError err( std::cerr );
    std::vector< Mesh::ElementHandle > elems;
    std::vector< Mesh::VertexHandle > verts;
    std::vector< size_t > offsets;
    mesh->get_all_elements( elems, err );
    ASSERT_NO_ERROR( err );
    CPPUNIT_ASSERT( !elems.empty() );
    mesh->elements_get_attached_vertices( arrptr( elems ), elems.size(), verts, offsets, err );
    CPPUNIT_ASSERT_EQUAL( elems.size() + 1, offsets.size() );
    ASSERT_NO_ERROR( err );
    std::vector< EntityTopology > types( elems.size() );
    mesh->elements_get_topologies( arrptr( elems ), arrptr( types ), elems.size(), err );
    ASSERT_NO_ERROR( err );

    // clear initial state
    ho_verts.clear();

    // for each element, add ho nodes
    for( size_t i = 0; i < elems.size(); ++i )
        for( size_t j = offsets[i] + TopologyInfo::corners( types[i] ); j < offsets[i + 1]; ++j )
            ho_verts[verts[j]] = initial_value;

    if( non_fixed_only )
    {
        std::map< Mesh::VertexHandle, bool >::iterator p;
        std::sort( verts.begin(), verts.end() );
        verts.erase( std::unique( verts.begin(), verts.end() ), verts.end() );
        std::vector< bool > fixed;<--- Shadow variable
        mesh->vertices_get_fixed_flag( arrptr( verts ), fixed, verts.size(), err );
        ASSERT_NO_ERROR( err );
        for( size_t i = 0; i < verts.size(); ++i )
        {
            if( fixed[i] )
            {
                p = ho_verts.find( verts[i] );
                if( p != ho_verts.end() ) ho_verts.erase( p );
            }
        }
    }
}

void PatchDataTest::check_higher_order_vertices_slaved( Mesh* mesh,
                                                        Settings::HigherOrderSlaveMode mode,
                                                        const std::map< Mesh::VertexHandle, bool >& expected )
{
    MsqPrintError err( std::cerr );

    Settings settings;
    settings.set_slaved_ho_node_mode( mode );
    MeshDomainAssoc mesh_and_domain = MeshDomainAssoc( mesh, 0 );
    Instruction::initialize_vertex_byte( &mesh_and_domain, &settings, err );
    ASSERT_NO_ERROR( err );

    PatchData pd;
    pd.attach_settings( &settings );
    pd.set_mesh( mesh );

    std::vector< Mesh::ElementHandle > elements;
    std::vector< Mesh::VertexHandle > vertices;
    mesh->get_all_elements( elements, err );
    ASSERT_NO_ERROR( err );
    pd.set_mesh_entities( elements, vertices, err );
    ASSERT_NO_ERROR( err );

    std::map< Mesh::VertexHandle, bool >::const_iterator p;
    for( size_t i = 0; i < pd.num_nodes(); ++i )
    {
        p          = expected.find( pd.get_vertex_handles_array()[i] );
        bool found = ( p != expected.end() );
        bool exp   = found && p->second;
        bool act   = pd.vertex_by_index( i ).is_flag_set( MsqVertex::MSQ_DEPENDENT );
        CPPUNIT_ASSERT_EQUAL( exp, act );
    }
}

void PatchDataTest::test_patch_data_mesh_slaved_ho_nodes()
{
    Mesh* mesh = 0;
    get_quad8_mesh( mesh );

    std::map< Mesh::VertexHandle, bool > ho_verts;
    get_higher_order_vertices( mesh, ho_verts, true, false );

    check_higher_order_vertices_slaved( mesh, Settings::SLAVE_ALL, ho_verts );
    delete mesh;
}

void PatchDataTest::test_patch_data_mesh_free_ho_nodes()
{
    Mesh* mesh = 0;
    get_quad8_mesh( mesh );

    std::map< Mesh::VertexHandle, bool > ho_verts;
    get_higher_order_vertices( mesh, ho_verts, false );

    check_higher_order_vertices_slaved( mesh, Settings::SLAVE_NONE, ho_verts );
    delete mesh;
}

void PatchDataTest::test_patch_data_mesh_calcualted_ho_nodes()
{
    Mesh* mesh = 0;
    get_quad8_mesh( mesh );

    std::map< Mesh::VertexHandle, bool > ho_verts;
    get_higher_order_vertices( mesh, ho_verts, false );

    // set bit on every other higher-order vertex
    std::map< Mesh::VertexHandle, bool >::iterator i = ho_verts.end();
    std::vector< Mesh::VertexHandle > slaved;
    std::vector< unsigned char > bytes;
    while( i != ho_verts.end() )
    {
        slaved.push_back( i->first );
        bytes.push_back( MsqVertex::MSQ_DEPENDENT );
        i->second = true;
        if( ++i == ho_verts.end() )
            ;
        break;
        ++i;<--- Statements following return, break, continue, goto or throw will never be executed.
    }

    if( !slaved.empty() )
    {
        MsqPrintError err( std::cerr );
        mesh->vertices_set_byte( arrptr( slaved ), arrptr( bytes ), slaved.size(), err );
        ASSERT_NO_ERROR( err );
    }

    check_higher_order_vertices_slaved( mesh, Settings::SLAVE_CALCULATED, ho_verts );
    delete mesh;
}

//! create a wrapper around the real mesh that returns what we
//! want from vertices_get_slaved_flag.
class HoSlavedMesh : public MeshDecorator
{
  public:
    typedef std::map< Mesh::VertexHandle, bool > SMap;
    HoSlavedMesh( Mesh* real_mesh, SMap& slaved ) : MeshDecorator( real_mesh ), slavedVerts( slaved ) {}

    virtual void vertices_get_slaved_flag( const VertexHandle vert_array[],
                                           std::vector< bool >& slaved_flag_array,
                                           size_t num_vtx,
                                           MsqError& err );

  private:
    SMap slavedVerts;
};
void HoSlavedMesh::vertices_get_slaved_flag( const VertexHandle vert_array[],
                                             std::vector< bool >& slaved_flag_array,
                                             size_t num_vtx,
                                             MsqError& err )
{
    slaved_flag_array.resize( num_vtx );
    for( size_t i = 0; i < num_vtx; ++i )
    {
        SMap::iterator j     = slavedVerts.find( vert_array[i] );
        slaved_flag_array[i] = ( j != slavedVerts.end() ) && j->second;
    }
}

void PatchDataTest::test_patch_data_mesh_flagged_ho_nodes()
{
    Mesh* mesh = 0;
    get_quad8_mesh( mesh );

    std::map< Mesh::VertexHandle, bool > ho_verts;
    get_higher_order_vertices( mesh, ho_verts, false );

    // set every other higher-order vertex as slaved
    std::map< Mesh::VertexHandle, bool >::iterator i = ho_verts.end();
    while( i != ho_verts.end() )
    {
        if( ++i == ho_verts.end() )
            ;
        break;
        i->second = true;<--- Statements following return, break, continue, goto or throw will never be executed.
        ++i;
    }

    // create a wrapper mesh that returns what we want
    // from vertices_get_slaved_flag
    HoSlavedMesh wrapper( mesh, ho_verts );

    check_higher_order_vertices_slaved( &wrapper, Settings::SLAVE_FLAG, ho_verts );
    delete mesh;
}