IntxUtils.cpp

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/*
 * IntxUtils.cpp
 *
 * Created on: Oct 3, 2012
 */
#if defined( _MSC_VER ) || defined( WIN32 ) /* windows */
#define _USE_MATH_DEFINES // For M_PI
#endif
 
#include <cmath>
#include <cassert>
#include <iostream>
 
#include "moab/IntxMesh/IntxUtils.hpp"
// this is from mbcoupler; maybe it should be moved somewhere in moab src
// right now, add a dependency to mbcoupler
// #include "ElemUtil.hpp"
#include "moab/MergeMesh.hpp"
#include "moab/ReadUtilIface.hpp"
#include "MBTagConventions.hpp"
 
#define CHECKNEGATIVEAREA
#ifdef CHECKNEGATIVEAREA
#include <iomanip>
#endif
#include <queue>
#include <map>
 
#ifdef MOAB_HAVE_TEMPESTREMAP
#include "GridElements.h"
#endif
 
#ifdef MOAB_HAVE_EIGEN3
#define EIGEN_NO_DEBUG
#define EIGEN_MAX_CPP_VER 11
#include "Eigen/Dense"
#endif
 
namespace moab
{
/**
 * This code defines several utility functions for computing edge intersections and performing geometric operations.
 *
 * - `borderPointsOfXinY2`: Computes the border points of a set of points `X` inside another set of points `Y`.
 * - `SortAndRemoveDoubles2`: Sorts a set of points `P` according to their angles and removes duplicate points.
 * - `EdgeIntersections2`: Computes the intersections between the edges of two sets of points `blue` and `red`.
 * - `EdgeIntxRllCs`: Computes the intersections between the edges of a set of points `blue` and a set of points `red` on a specific plane.
 *
 * The code also defines some helper structs and functions used by these utility functions.
 */
 
#define CORRTAGNAME "__correspondent"
#define MAXEDGES 10
 
/**
 * Computes the border points of X in Y2.
 *
 * @param X The array of points representing X.
 * @param nX The number of points in X.
 * @param Y The array of points representing Y.
 * @param nY The number of points in Y.
 * @param P The array to store the border points of X in Y2.
 * @param side The array to store the side information for each point in X.
 * @param epsilon_area The epsilon value for area comparison.
 * @return The number of extra points found.
 */
int IntxUtils::borderPointsOfXinY2( double* X, int nX, double* Y, int nY, double* P, int* side, double epsilon_area )
{
 // 2 triangles, 3 corners, is the corner of X in Y?
 // Y must have a positive area
 /*
 */
 int extraPoint = 0;
 for( int i = 0; i < nX; i++ )
 {
 // compute double the area of all nY triangles formed by a side of Y and a corner of X; if
 // one is negative, stop (negative means it is outside; X and Y are all oriented such that
 // they are positive oriented;
 // if one area is negative, it means it is outside the convex region, for sure)
 double* A = X + 2 * i;
 
 int inside = 1;
 for( int j = 0; j < nY; j++ )
 {
 double* B = Y + 2 * j;
 int j1 = ( j + 1 ) % nY;
 double* C = Y + 2 * j1; // no copy of data
 
 double area2 = ( B[0] - A[0] ) * ( C[1] - A[1] ) - ( C[0] - A[0] ) * ( B[1] - A[1] );
 if( area2 < -epsilon_area )
 {
 inside = 0;
 break;
 }
 }
 if( inside )
 {
 side[i] = 1; // so vertex i of X is inside the convex region formed by Y
 // so side has nX dimension (first array)
 P[extraPoint * 2] = A[0];
 P[extraPoint * 2 + 1] = A[1];
 extraPoint++;
 }
 }
 return extraPoint;
}
 
// used to order according to angle, so it can remove double easily
struct angleAndIndex
{
 double angle;
 int index;
};
 
bool angleCompare( angleAndIndex lhs, angleAndIndex rhs )
{
 return lhs.angle < rhs.angle;
}
 
/**
 * Sorts and removes duplicate points in the given array.
 *
 * Note: nP might be modified too, we will remove duplicates if found
 *
 * @param P The array of points to be sorted and checked for duplicates.
 * @param nP The number of points in P.
 * @param epsilon_1 The epsilon value for distance comparison.
 * @return 0 if successful.
 */
int IntxUtils::SortAndRemoveDoubles2( double* P, int& nP, double epsilon_1 )
{
 if( nP < 2 ) return 0; // nothing to do
 
 // center of gravity for the points
 double c[2] = { 0., 0. };
 int k = 0;
 for( k = 0; k < nP; k++ )
 {
 c[0] += P[2 * k];
 c[1] += P[2 * k + 1];
 }
 c[0] /= nP;
 c[1] /= nP;
 
 // how many? we dimensioned P at MAXEDGES*10; so we imply we could have at most 5*MAXEDGES
 // intersection points
 struct angleAndIndex pairAngleIndex[5 * MAXEDGES];
 
 for( k = 0; k < nP; k++ )
 {
 double x = P[2 * k] - c[0], y = P[2 * k + 1] - c[1];
 if( x != 0. || y != 0. )
 {
 pairAngleIndex[k].angle = atan2( y, x );
 }
 else
 {
 pairAngleIndex[k].angle = 0;
 // it would mean that the cells are touching at a vertex
 }
 pairAngleIndex[k].index = k;
 }
 
 // this should be faster than the bubble sort we had before
 std::sort( pairAngleIndex, pairAngleIndex + nP, angleCompare );
 // copy now to a new double array
 double PCopy[10 * MAXEDGES]; // the same dimension as P; very conservative, but faster than
 // reallocate for a vector
 for( k = 0; k < nP; k++ ) // index will show where it should go now;
 {
 int ck = pairAngleIndex[k].index;
 PCopy[2 * k] = P[2 * ck];
 PCopy[2 * k + 1] = P[2 * ck + 1];
 }
 // now copy from PCopy over original P location
 std::copy( PCopy, PCopy + 2 * nP, P );
 
 // eliminate duplicates, finally
 
 int i = 0, j = 1; // the next one; j may advance faster than i
 // check the unit
 // double epsilon_1 = 1.e-5; // these are cm; 2 points are the same if the distance is less
 // than 1.e-5 cm
 while( j < nP )
 {
 double d2 = dist2( &P[2 * i], &P[2 * j] );
 if( d2 > epsilon_1 )
 {
 i++;
 P[2 * i] = P[2 * j];
 P[2 * i + 1] = P[2 * j + 1];
 }
 j++;
 }
 // test also the last point with the first one (index 0)
 // the first one could be at -PI; last one could be at +PI, according to atan2 span
 
 double d2 = dist2( P, &P[2 * i] ); // check the first and last points (ordered from -pi to +pi)
 if( d2 > epsilon_1 )
 {
 nP = i + 1;
 }
 else
 nP = i; // effectively delete the last point (that would have been the same with first)
 if( nP == 0 ) nP = 1; // we should be left with at least one point we already tested if nP is 0 originally
 return 0;
}
 
/**
 * Computes the edge intersections of two elements.
 *
 * @param blue The array of points representing the blue element.
 * @param nsBlue The number of points in the blue element.
 * @param red The array of points representing the red element.
 * @param nsRed The number of points in the red element.
 * @param markb The array to mark the intersecting edges of the blue element.
 * @param markr The array to mark the intersecting edges of the red element.
 * @param points The array to store the intersection points.
 * @param nPoints The number of intersection points found.
 * @return The error code.
 */
ErrorCode IntxUtils::EdgeIntersections2( double* blue,
 int nsBlue,
 double* red,
 int nsRed,
 int* markb,
 int* markr,
 double* points,
 int& nPoints )
{
 /* EDGEINTERSECTIONS computes edge intersections of two elements
 [P,n]=EdgeIntersections(X,Y) computes for the two given elements * red
 and blue ( stored column wise )
 (point coordinates are stored column-wise, in counter clock
 order) the points P where their edges intersect. In addition,
 in n the indices of which neighbors of red are also intersecting
 with blue are given.
 */
 
 // points is an array with enough slots (24 * 2 doubles)
 nPoints = 0;
 for( int i = 0; i < MAXEDGES; i++ )
 {
 markb[i] = markr[i] = 0;
 }
 
 for( int i = 0; i < nsBlue; i++ )
 {
 for( int j = 0; j < nsRed; j++ )
 {
 double b[2];
 double a[2][2]; // 2*2
 int iPlus1 = ( i + 1 ) % nsBlue;
 int jPlus1 = ( j + 1 ) % nsRed;
 for( int k = 0; k < 2; k++ )
 {
 b[k] = red[2 * j + k] - blue[2 * i + k];
 // row k of a: a(k, 0), a(k, 1)
 a[k][0] = blue[2 * iPlus1 + k] - blue[2 * i + k];
 a[k][1] = red[2 * j + k] - red[2 * jPlus1 + k];
 }
 double delta = a[0][0] * a[1][1] - a[0][1] * a[1][0];
 if( fabs( delta ) > 1.e-14 ) // this is close to machine epsilon
 {
 // not parallel
 double alfa = ( b[0] * a[1][1] - a[0][1] * b[1] ) / delta;
 double beta = ( -b[0] * a[1][0] + b[1] * a[0][0] ) / delta;
 if( 0 <= alfa && alfa <= 1. && 0 <= beta && beta <= 1. )
 {
 // the intersection is good
 for( int k = 0; k < 2; k++ )
 {
 points[2 * nPoints + k] = blue[2 * i + k] + alfa * ( blue[2 * iPlus1 + k] - blue[2 * i + k] );
 }
 markb[i] = 1; // so neighbor number i of blue will be considered too.
 markr[j] = 1; // this will be used in advancing red around blue quad
 nPoints++;
 }
 }
 // the case delta ~ 0. will be considered by the interior points logic
 }
 }
 return MB_SUCCESS;
}
 
/**
 * Computes the edge intersections between a RLL and CS quad.
 *
 * Note: Special function.
 *
 * @param blue The array of points representing the blue element.
 * @param bluec The array of Cartesian coordinates for the blue element.
 * @param blueEdgeType The array of edge types for the blue element.
 * @param nsBlue The number of points in the blue element.
 * @param red The array of points representing the red element.
 * @param redc The array of Cartesian coordinates for the red element.
 * @param nsRed The number of points in the red element.
 * @param markb The array to mark the intersecting edges of the blue element.
 * @param markr The array to mark the intersecting edges of the red element.
 * @param plane The plane of intersection.
 * @param R The radius of the sphere.
 * @param points The array to store the intersection points.
 * @param nPoints The number of intersection points found.
 * @return The error code.
 */
ErrorCode IntxUtils::EdgeIntxRllCs( double* blue,
 CartVect* bluec,
 int* blueEdgeType,
 int nsBlue,
 double* red,
 CartVect* redc,
 int nsRed,
 int* markb,
 int* markr,
 int plane,
 double R,
 double* points,
 int& nPoints )
{
 // if blue edge type is 1, intersect in 3d then project to 2d by gnomonic projection
 // everything else the same (except if there are 2 points resulting, which is rare)
 for( int i = 0; i < 4; i++ )
 { // always at most 4 , so maybe don't bother
 markb[i] = markr[i] = 0;
 }
 
 for( int i = 0; i < nsBlue; i++ )
 {
 int iPlus1 = ( i + 1 ) % nsBlue;
 if( blueEdgeType[i] == 0 ) // old style, just 2d
 {
 for( int j = 0; j < nsRed; j++ )
 {
 double b[2];
 double a[2][2]; // 2*2
 
 int jPlus1 = ( j + 1 ) % nsRed;
 for( int k = 0; k < 2; k++ )
 {
 b[k] = red[2 * j + k] - blue[2 * i + k];
 // row k of a: a(k, 0), a(k, 1)
 a[k][0] = blue[2 * iPlus1 + k] - blue[2 * i + k];
 a[k][1] = red[2 * j + k] - red[2 * jPlus1 + k];
 }
 double delta = a[0][0] * a[1][1] - a[0][1] * a[1][0];
 if( fabs( delta ) > 1.e-14 )
 {
 // not parallel
 double alfa = ( b[0] * a[1][1] - a[0][1] * b[1] ) / delta;
 double beta = ( -b[0] * a[1][0] + b[1] * a[0][0] ) / delta;
 if( 0 <= alfa && alfa <= 1. && 0 <= beta && beta <= 1. )
 {
 // the intersection is good
 for( int k = 0; k < 2; k++ )
 {
 points[2 * nPoints + k] =
 blue[2 * i + k] + alfa * ( blue[2 * iPlus1 + k] - blue[2 * i + k] );
 }
 markb[i] = 1; // so neighbor number i of blue will be considered too.
 markr[j] = 1; // this will be used in advancing red around blue quad
 nPoints++;
 }
 } // if the edges are too "parallel", skip them
 }
 }
 else // edge type is 1, so use 3d intersection
 {
 CartVect& C = bluec[i];
 CartVect& D = bluec[iPlus1];
 for( int j = 0; j < nsRed; j++ )
 {
 int jPlus1 = ( j + 1 ) % nsRed; // nsRed is just 4, forget about it, usually
 CartVect& A = redc[j];
 CartVect& B = redc[jPlus1];
 int np = 0;
 double E[9];
 intersect_great_circle_arc_with_clat_arc( A.array(), B.array(), C.array(), D.array(), R, E, np );
 if( np == 0 ) continue;
 if( np >= 2 )
 {
 std::cout << "intersection with 2 points :" << A << B << C << D << "\n";
 }
 for( int k = 0; k < np; k++ )
 {
 gnomonic_projection( CartVect( E + k * 3 ), R, plane, points[2 * nPoints],
 points[2 * nPoints + 1] );
 nPoints++;
 }
 markb[i] = 1; // so neighbor number i of blue will be considered too.
 markr[j] = 1; // this will be used in advancing red around blue quad
 }
 }
 }
 return MB_SUCCESS;
}
 
// vec utils related to gnomonic projection on a sphere
 
// vec utils
 
/*
 *
 * position on a sphere of radius R
 * if plane specified, use it; if not, return the plane, and the point in the plane
 * there are 6 planes, numbered 1 to 6
 * plane 1: x=R, plane 2: y=R, 3: x=-R, 4: y=-R, 5: z=-R, 6: z=R
 *
 * projection on the plane will preserve the orientation, such that a triangle, quad pointing
 * outside the sphere will have a positive orientation in the projection plane
 */
void IntxUtils::decide_gnomonic_plane( const CartVect& pos, int& plane )
{
 // decide plane, based on max x, y, z
 if( fabs( pos[0] ) < fabs( pos[1] ) )
 {
 if( fabs( pos[2] ) < fabs( pos[1] ) )
 {
 // pos[1] is biggest
 if( pos[1] > 0 )
 plane = 2;
 else
 plane = 4;
 }
 else
 {
 // pos[2] is biggest
 if( pos[2] < 0 )
 plane = 5;
 else
 plane = 6;
 }
 }
 else
 {
 if( fabs( pos[2] ) < fabs( pos[0] ) )
 {
 // pos[0] is the greatest
 if( pos[0] > 0 )
 plane = 1;
 else
 plane = 3;
 }
 else
 {
 // pos[2] is biggest
 if( pos[2] < 0 )
 plane = 5;
 else
 plane = 6;
 }
 }
 return;
}
 
// point on a sphere is projected on one of six planes, decided earlier
ErrorCode IntxUtils::gnomonic_projection( const CartVect& pos, double R, int plane, double& c1, double& c2 )
{
 double alfa = 1.; // the new point will be on line alfa*pos
 
 switch( plane )
 {
 case 1: {
 // the plane with x = R; x>y, x>z
 // c1->y, c2->z
 alfa = R / pos[0];
 c1 = alfa * pos[1];
 c2 = alfa * pos[2];
 break;
 }
 case 2: {
 // y = R -> zx
 alfa = R / pos[1];
 c1 = alfa * pos[2];
 c2 = alfa * pos[0];
 break;
 }
 case 3: {
 // x=-R, -> yz
 alfa = -R / pos[0];
 c1 = -alfa * pos[1]; // the sign is to preserve orientation
 c2 = alfa * pos[2];
 break;
 }
 case 4: {
 // y = -R
 alfa = -R / pos[1];
 c1 = -alfa * pos[2]; // the sign is to preserve orientation
 c2 = alfa * pos[0];
 break;
 }
 case 5: {
 // z = -R
 alfa = -R / pos[2];
 c1 = -alfa * pos[0]; // the sign is to preserve orientation
 c2 = alfa * pos[1];
 break;
 }
 case 6: {
 alfa = R / pos[2];
 c1 = alfa * pos[0];
 c2 = alfa * pos[1];
 break;
 }
 default:
 return MB_FAILURE; // error
 }
 
 return MB_SUCCESS; // no error
}
 
// given the position on plane (one out of 6), find out the position on sphere
ErrorCode IntxUtils::reverse_gnomonic_projection( const double& c1,
 const double& c2,
 double R,
 int plane,
 CartVect& pos )
{
 
 // the new point will be on line beta*pos
 double len = sqrt( c1 * c1 + c2 * c2 + R * R );
 double beta = R / len; // it is less than 1, in general
 
 switch( plane )
 {
 case 1: {
 // the plane with x = R; x>y, x>z
 // c1->y, c2->z
 pos[0] = beta * R;
 pos[1] = c1 * beta;
 pos[2] = c2 * beta;
 break;
 }
 case 2: {
 // y = R -> zx
 pos[1] = R * beta;
 pos[2] = c1 * beta;
 pos[0] = c2 * beta;
 break;
 }
 case 3: {
 // x=-R, -> yz
 pos[0] = -R * beta;
 pos[1] = -c1 * beta; // the sign is to preserve orientation
 pos[2] = c2 * beta;
 break;
 }
 case 4: {
 // y = -R
 pos[1] = -R * beta;
 pos[2] = -c1 * beta; // the sign is to preserve orientation
 pos[0] = c2 * beta;
 break;
 }
 case 5: {
 // z = -R
 pos[2] = -R * beta;
 pos[0] = -c1 * beta; // the sign is to preserve orientation
 pos[1] = c2 * beta;
 break;
 }
 case 6: {
 pos[2] = R * beta;
 pos[0] = c1 * beta;
 pos[1] = c2 * beta;
 break;
 }
 default:
 return MB_FAILURE; // error
 }
 
 return MB_SUCCESS; // no error
}
 
void IntxUtils::gnomonic_unroll( double& c1, double& c2, double R, int plane )
{
 double tmp;
 switch( plane )
 {
 case 1:
 break; // nothing
 case 2: // rotate + 90
 tmp = c1;
 c1 = -c2;
 c2 = tmp;
 c1 = c1 + 2 * R;
 break;
 case 3:
 c1 = c1 + 4 * R;
 break;
 case 4: // rotate with -90 x-> -y; y -> x
 
 tmp = c1;
 c1 = c2;
 c2 = -tmp;
 c1 = c1 - 2 * R;
 break;
 case 5: // South Pole
 // rotate 180 then move to (-2, -2)
 c1 = -c1 - 2. * R;
 c2 = -c2 - 2. * R;
 break;
 ;
 case 6: // North Pole
 c1 = c1 - 2. * R;
 c2 = c2 + 2. * R;
 break;
 }
 return;
}
// given a mesh on the sphere, project all centers in 6 gnomonic planes, or project mesh too
ErrorCode IntxUtils::global_gnomonic_projection( Interface* mb,
 EntityHandle inSet,
 double R,
 bool centers_only,
 EntityHandle& outSet )
{
 std::string parTagName( "PARALLEL_PARTITION" );
 Tag part_tag;
 Range partSets;
 ErrorCode rval = mb->tag_get_handle( parTagName.c_str(), part_tag );
 if( MB_SUCCESS == rval && part_tag != 0 )
 {
 rval = mb->get_entities_by_type_and_tag( inSet, MBENTITYSET, &part_tag, NULL, 1, partSets, Interface::UNION );MB_CHK_ERR( rval );
 }
 rval = ScaleToRadius( mb, inSet, 1.0 );MB_CHK_ERR( rval );
 // Get all entities of dimension 2
 Range inputRange; // get
 rval = mb->get_entities_by_dimension( inSet, 1, inputRange );MB_CHK_ERR( rval );
 rval = mb->get_entities_by_dimension( inSet, 2, inputRange );MB_CHK_ERR( rval );
 
 std::map< EntityHandle, int > partsAssign;
 std::map< int, EntityHandle > newPartSets;
 if( !partSets.empty() )
 {
 // get all cells, and assign parts
 for( Range::iterator setIt = partSets.begin(); setIt != partSets.end(); ++setIt )
 {
 EntityHandle pSet = *setIt;
 Range ents;
 rval = mb->get_entities_by_handle( pSet, ents );MB_CHK_ERR( rval );
 int val;
 rval = mb->tag_get_data( part_tag, &pSet, 1, &val );MB_CHK_ERR( rval );
 // create a new set with the same part id tag, in the outSet
 EntityHandle newPartSet;
 rval = mb->create_meshset( MESHSET_SET, newPartSet );MB_CHK_ERR( rval );
 rval = mb->tag_set_data( part_tag, &newPartSet, 1, &val );MB_CHK_ERR( rval );
 newPartSets[val] = newPartSet;
 rval = mb->add_entities( outSet, &newPartSet, 1 );MB_CHK_ERR( rval );
 for( Range::iterator it = ents.begin(); it != ents.end(); ++it )
 {
 partsAssign[*it] = val;
 }
 }
 }
 
 if( centers_only )
 {
 for( Range::iterator it = inputRange.begin(); it != inputRange.end(); ++it )
 {
 CartVect center;
 EntityHandle cell = *it;
 rval = mb->get_coords( &cell, 1, center.array() );MB_CHK_ERR( rval );
 int plane;
 decide_gnomonic_plane( center, plane );
 double c[3];
 c[2] = 0.;
 gnomonic_projection( center, R, plane, c[0], c[1] );
 
 gnomonic_unroll( c[0], c[1], R, plane );
 
 EntityHandle vertex;
 rval = mb->create_vertex( c, vertex );MB_CHK_ERR( rval );
 rval = mb->add_entities( outSet, &vertex, 1 );MB_CHK_ERR( rval );
 }
 }
 else
 {
 // distribute the cells to 6 planes, based on the center
 Range subranges[6];
 for( Range::iterator it = inputRange.begin(); it != inputRange.end(); ++it )
 {
 CartVect center;
 EntityHandle cell = *it;
 rval = mb->get_coords( &cell, 1, center.array() );MB_CHK_ERR( rval );
 int plane;
 decide_gnomonic_plane( center, plane );
 subranges[plane - 1].insert( cell );
 }
 for( int i = 1; i <= 6; i++ )
 {
 Range verts;
 rval = mb->get_connectivity( subranges[i - 1], verts );MB_CHK_ERR( rval );
 std::map< EntityHandle, EntityHandle > corr;
 for( Range::iterator vt = verts.begin(); vt != verts.end(); ++vt )
 {
 CartVect vect;
 EntityHandle v = *vt;
 rval = mb->get_coords( &v, 1, vect.array() );MB_CHK_ERR( rval );
 double c[3];
 c[2] = 0.;
 gnomonic_projection( vect, R, i, c[0], c[1] );
 gnomonic_unroll( c[0], c[1], R, i );
 EntityHandle vertex;
 rval = mb->create_vertex( c, vertex );MB_CHK_ERR( rval );
 corr[v] = vertex; // for new connectivity
 }
 EntityHandle new_conn[20]; // max edges in 2d ?
 for( Range::iterator eit = subranges[i - 1].begin(); eit != subranges[i - 1].end(); ++eit )
 {
 EntityHandle eh = *eit;
 const EntityHandle* conn = NULL;
 int num_nodes;
 rval = mb->get_connectivity( eh, conn, num_nodes );MB_CHK_ERR( rval );
 // build a new vertex array
 for( int j = 0; j < num_nodes; j++ )
 new_conn[j] = corr[conn[j]];
 EntityType type = mb->type_from_handle( eh );
 EntityHandle newCell;
 rval = mb->create_element( type, new_conn, num_nodes, newCell );MB_CHK_ERR( rval );
 rval = mb->add_entities( outSet, &newCell, 1 );MB_CHK_ERR( rval );
 std::map< EntityHandle, int >::iterator mit = partsAssign.find( eh );
 if( mit != partsAssign.end() )
 {
 int val = mit->second;
 rval = mb->add_entities( newPartSets[val], &newCell, 1 );MB_CHK_ERR( rval );
 }
 }
 }
 }
 
 return MB_SUCCESS;
}
void IntxUtils::transform_coordinates( double* avg_position, int projection_type )
{
 if( projection_type == 1 )
 {
 double R =
 avg_position[0] * avg_position[0] + avg_position[1] * avg_position[1] + avg_position[2] * avg_position[2];
 R = sqrt( R );
 double lat = asin( avg_position[2] / R );
 double lon = atan2( avg_position[1], avg_position[0] );
 avg_position[0] = lon;
 avg_position[1] = lat;
 avg_position[2] = R;
 }
 else if( projection_type == 2 ) // gnomonic projection
 {
 CartVect pos( avg_position );
 int gplane;
 IntxUtils::decide_gnomonic_plane( pos, gplane );
 
 IntxUtils::gnomonic_projection( pos, 1.0, gplane, avg_position[0], avg_position[1] );
 avg_position[2] = 0;
 IntxUtils::gnomonic_unroll( avg_position[0], avg_position[1], 1.0, gplane );
 }
}
/*
 *
 use physical_constants, only : dd_pi
 type(cartesian3D_t), intent(in) :: cart
 type(spherical_polar_t) :: sphere
 
 sphere%r=distance(cart)
 sphere%lat=ASIN(cart%z/sphere%r)
 sphere%lon=0
 
 ! ==========================================================
 ! enforce three facts:
 !
 ! 1) lon at poles is defined to be zero
 !
 ! 2) Grid points must be separated by about .01 Meter (on earth)
 ! from pole to be considered "not the pole".
 !
 ! 3) range of lon is { 0<= lon < 2*pi }
 !
 ! ==========================================================
 
 if (distance(cart) >= DIST_THRESHOLD) then
 sphere%lon=ATAN2(cart%y,cart%x)
 if (sphere%lon<0) then
 sphere%lon=sphere%lon+2*DD_PI
 end if
 end if
 
 end function cart_to_spherical
 */
IntxUtils::SphereCoords IntxUtils::cart_to_spherical( CartVect& cart3d )
{
 SphereCoords res;
 res.R = cart3d.length();
 if( res.R < 0 )
 {
 res.lon = res.lat = 0.;
 return res;
 }
 res.lat = asin( cart3d[2] / res.R );
 res.lon = atan2( cart3d[1], cart3d[0] );
 if( res.lon < 0 ) res.lon += 2 * M_PI; // M_PI is defined in math.h? it seems to be true, although
 // there are some defines it depends on :(
 // #if defined __USE_BSD || defined __USE_XOPEN ???
 
 return res;
}
 
/*
 * ! ===================================================================
 ! spherical_to_cart:
 ! converts spherical polar {lon,lat} to 3D cartesian {x,y,z}
 ! on unit sphere
 ! ===================================================================
 
 function spherical_to_cart(sphere) result (cart)
 
 type(spherical_polar_t), intent(in) :: sphere
 type(cartesian3D_t) :: cart
 
 cart%x=sphere%r*COS(sphere%lat)*COS(sphere%lon)
 cart%y=sphere%r*COS(sphere%lat)*SIN(sphere%lon)
 cart%z=sphere%r*SIN(sphere%lat)
 
 end function spherical_to_cart
 */
CartVect IntxUtils::spherical_to_cart( IntxUtils::SphereCoords& sc )
{
 CartVect res;
 res[0] = sc.R * cos( sc.lat ) * cos( sc.lon ); // x coordinate
 res[1] = sc.R * cos( sc.lat ) * sin( sc.lon ); // y
 res[2] = sc.R * sin( sc.lat ); // z
 return res;
}
 
ErrorCode IntxUtils::ScaleToRadius( Interface* mb, EntityHandle set, double R )
{
 Range nodes;
 ErrorCode rval = mb->get_entities_by_type( set, MBVERTEX, nodes, true ); // recursive
 if( rval != moab::MB_SUCCESS ) return rval;
 
 // one by one, get the node and project it on the sphere, with a radius given
 // the center of the sphere is at 0,0,0
 for( Range::iterator nit = nodes.begin(); nit != nodes.end(); ++nit )
 {
 EntityHandle nd = *nit;
 CartVect pos;
 rval = mb->get_coords( &nd, 1, (double*)&( pos[0] ) );
 if( rval != moab::MB_SUCCESS ) return rval;
 double len = pos.length();
 if( len == 0. ) return MB_FAILURE;
 pos = R / len * pos;
 rval = mb->set_coords( &nd, 1, (double*)&( pos[0] ) );
 if( rval != moab::MB_SUCCESS ) return rval;
 }
 return MB_SUCCESS;
}
 
// assume they are one the same sphere
double IntxAreaUtils::spherical_angle( const double* A, const double* B, const double* C, double Radius )
{
 // the angle by definition is between the planes OAB and OBC
 CartVect a( A );
 CartVect b( B );
 CartVect c( C );
 double err1 = a.length_squared() - Radius * Radius;
 if( fabs( err1 ) > 0.0001 )
 {
 std::cout << " error in input " << a << " radius: " << Radius << " error:" << err1 << "\n";
 }
 CartVect normalOAB = a * b;
 CartVect normalOCB = c * b;
 return angle( normalOAB, normalOCB );
}
 
// could be bigger than M_PI;
// angle at B could be bigger than M_PI, if the orientation is such that ABC points toward the
// interior
double IntxUtils::oriented_spherical_angle( const double* A, const double* B, const double* C )
{
 // assume the same radius, sphere at origin
 CartVect a( A ), b( B ), c( C );
 CartVect normalOAB = a * b;
 CartVect normalOCB = c * b;
 CartVect orient = ( c - b ) * ( a - b );
 double ang = angle( normalOAB, normalOCB ); // this is between 0 and M_PI
 if( ang != ang )
 {
 // signal of a nan
 std::cout << a << " " << b << " " << c << "\n";
 std::cout << ang << "\n";
 }
 if( orient % b < 0 ) return ( 2 * M_PI - ang ); // the other angle, supplement
 
 return ang;
}
 
double IntxAreaUtils::area_spherical_triangle( const double* A, const double* B, const double* C, double Radius )
{
 switch( m_eAreaMethod )
 {
 case Girard:
 return area_spherical_triangle_girard( A, B, C, Radius );
#ifdef MOAB_HAVE_TEMPESTREMAP
 case GaussQuadrature:
 return area_spherical_triangle_GQ( A, B, C );
#endif
 case lHuiller:
 default:
 return area_spherical_triangle_lHuiller( A, B, C, Radius );
 }
}
 
double IntxAreaUtils::area_spherical_polygon( const double* A, int N, double Radius, int* sign )
{
 switch( m_eAreaMethod )
 {
 case Girard:
 return area_spherical_polygon_girard( A, N, Radius );
#ifdef MOAB_HAVE_TEMPESTREMAP
 case GaussQuadrature:
 return area_spherical_polygon_GQ( A, N ) * Radius * Radius; //area_spherical_polygon_GQ normalizes
#endif
 case lHuiller:
 default:
 return area_spherical_polygon_lHuiller( A, N, Radius, sign );
 }
}
 
double IntxAreaUtils::area_spherical_triangle_girard( const double* A, const double* B, const double* C, double Radius )
{
 double correction = spherical_angle( A, B, C, Radius ) + spherical_angle( B, C, A, Radius ) +
 spherical_angle( C, A, B, Radius ) - M_PI;
 double area = Radius * Radius * correction;
 // now, is it negative or positive? is it pointing toward the center or outward?
 CartVect a( A ), b( B ), c( C );
 CartVect abc = ( b - a ) * ( c - a );
 if( abc % a > 0 ) // dot product positive, means ABC points out
 return area;
 else
 return -area;
}
 
double IntxAreaUtils::area_spherical_polygon_girard( const double* A, int N, double Radius )
{
 // this should work for non-convex polygons too
 // assume that the A, A+3, ..., A+3*(N-1) are the coordinates
 //
 if( N <= 2 ) return 0.;
 double sum_angles = 0.;
 for( int i = 0; i < N; i++ )
 {
 int i1 = ( i + 1 ) % N;
 int i2 = ( i + 2 ) % N;
 sum_angles += IntxUtils::oriented_spherical_angle( A + 3 * i, A + 3 * i1, A + 3 * i2 );
 }
 double correction = sum_angles - ( N - 2 ) * M_PI;
 return Radius * Radius * correction;
}
 
double IntxAreaUtils::area_spherical_polygon_lHuiller( const double* A, int N, double Radius, int* sign )
{
 // This should work for non-convex polygons too
 // In the input vector A, assume that the A, A+3, ..., A+3*(N-1) are the coordinates
 // We also assume that the orientation is positive;
 // If negative orientation, the area will be negative
 if( N <= 2 ) return 0.;
 
 int lsign = 1; // assume positive orientain
 double area = 0.;
 for( int i = 1; i < N - 1; i++ )
 {
 int i1 = i + 1;
 double areaTriangle = area_spherical_triangle_lHuiller( A, A + 3 * i, A + 3 * i1, Radius );
 if( areaTriangle < 0 )
 lsign = -1; // signal that we have at least one triangle with negative orientation ;
 // possible nonconvex polygon
 area += areaTriangle;
 }
 if( sign ) *sign = lsign;
 
 return area;
}
 
#ifdef MOAB_HAVE_TEMPESTREMAP
 
double IntxAreaUtils::area_spherical_polygon_GQ( const double* A, int N )
{
 // this should work for non-convex polygons too
 // In the input vector A, assume that the A, A+3, ..., A+3*(N-1) are the coordinates
 // We also assume that the orientation is positive;
 // If negative orientation, the area can be negative
 if( N <= 2 ) return 0.;
 
 // assume positive orientation
 double area = 0.;
 for( int i = 1; i < N - 1; i++ )
 {
 area += area_spherical_triangle_GQ( A, A + 3 * i, A + 3 * ( i + 1 ) );
 }
 return area;
}
 
template < typename Derived >
Eigen::Array< typename Derived::Scalar, Derived::RowsAtCompileTime, Derived::ColsAtCompileTime > shift(
 const Eigen::ArrayBase< Derived >& array,
 int positions )
{
 Eigen::Array< typename Derived::Scalar, Derived::RowsAtCompileTime, Derived::ColsAtCompileTime > result = array;
 if( positions > 0 )
 {
 result.segment( positions, array.size() - positions ) = array.head( array.size() - positions );
 result.head( positions ).setZero();
 }
 else if( positions < 0 )
 {
 result.head( array.size() + positions ) = array.tail( array.size() + positions );
 result.tail( -positions ).setZero();
 }
 return result;
}
 
double IntxAreaUtils::area_spherical_triangle_GQ( const double* inode1, const double* inode2, const double* inode3 )
{
#if defined( MOAB_HAVE_EIGEN3 )
 typedef Eigen::Map< const Eigen::Vector3d > V3d;
 const V3d node1( inode1 );
 const V3d node2( inode2 );
 const V3d node3( inode3 );
 const int nOrder = 6;
 
 // If we change the quadrature order, use the call: GaussQuadrature::GetPoints(nOrder, 0.0, 1.0, dG, dW);
 const double dG[6] = { 0.03376524289842397, 0.1693953067668678, 0.3806904069584016,
 0.6193095930415985, 0.8306046932331322, 0.966234757101576 };
 const double dW[6] = { 0.08566224618958521, 0.1803807865240693, 0.2339569672863455,
 0.2339569672863455, 0.1803807865240693, 0.08566224618958521 };
 
 double dFaceArea = 0.0;
 Eigen::Vector3d dF, dF2, dDaF, dDbF, dDaG, dDbG;
 double nodeCross[3];
 
 // Calculate area at quadrature node and sum it up
 for( int p = 0; p < nOrder; p++ )
 {
 for( int q = 0; q < nOrder; q++ )
 {
 
 const double dA = dG[p];
 const double dB = dG[q];
 
 // V3d dF = (1.0 - dB) * (((1.0 - dA) * node1) + (dA * node2)) + (dB * node3);
 dF = ( ( ( 1.0 - dB ) * ( 1.0 - dA ) ) * node1 ) + ( ( ( 1.0 - dB ) * dA ) * node2 ) + ( dB * node3 );
 dF2 = dF.array().square();
 
 dDaF = ( node1 - node2 );
 
 // dDbF = -( 1.0 - dA ) * node1 - dA * node2 + node3;
 dDbF = ( node3 - node1 ) + dA * dDaF;
 dDaF *= ( dB - 1.0 );
 
 const double dDenomTerm = std::pow( dF.norm(), -3.0 );
 
 // Eigen::Vector3d temp1 = dF2;
 // temp1( 2 ) += dF2( 0 ); // temp1 = [dF2(0), dF2(1), dF2(0)+dF2(2)]
 // Eigen::Vector3d temp2 = dDaF.cwiseProduct( dF ); // temp2 = [dDaF(0)*dF(0), dDaF(1)*dF(1), dDaF(2)*dF(2)]
 // dDaG = dDaF.cwiseProduct( temp1.segment( 1, 2 ) ) - temp2.segment( 1, 2 );
 // Eigen::Vector3d temp3 = dDbF.cwiseProduct( dF ); // temp3 = [dDbF(0)*dF(0), dDbF(1)*dF(1), dDbF(2)*dF(2)]
 // dDbG = dDbF.cwiseProduct( temp1.segment( 1, 2 ) ) - temp3.segment( 1, 2 );
 
 // Eigen::Vector3d dF2_shifted = dF2 + Eigen::Vector3d( dF2( 1 ), dF2( 2 ), dF2( 0 ) );
 // Eigen::Vector3d dDaF_shifted = Eigen::Vector3d( dDaF( 1 ), dDaF( 2 ), dDaF( 0 ) ).cwiseProduct( dF );
 
 // dDaG = dDaF.cwiseProduct( dF2_shifted ) - dF.cwiseProduct( dDaF_shifted );
 
 // Eigen::Vector3d dDbF_shifted = Eigen::Vector3d( dDbF( 1 ), dDbF( 2 ), dDbF( 0 ) ).cwiseProduct( dF );
 
 // dDbG = dDbF.cwiseProduct( dF2_shifted ) - dF.cwiseProduct( dDbF_shifted );
 
 dDaG( 0 ) = dDaF( 0 ) * ( dF2( 1 ) + dF2( 2 ) ) - dF( 0 ) * ( dDaF( 1 ) * dF( 1 ) + dDaF( 2 ) * dF( 2 ) );
 dDaG( 1 ) = dDaF( 1 ) * ( dF2( 0 ) + dF2( 2 ) ) - dF( 1 ) * ( dDaF( 0 ) * dF( 0 ) + dDaF( 2 ) * dF( 2 ) );
 dDaG( 2 ) = dDaF( 2 ) * ( dF2( 0 ) + dF2( 1 ) ) - dF( 2 ) * ( dDaF( 0 ) * dF( 0 ) + dDaF( 1 ) * dF( 1 ) );
 
 // dDbG = dDbF.cwiseProduct( ( dF2.array().shift( -1 ) + dF2.array().shift( -2 ) ) ) + dF.cwiseProduct( dDbF );
 dDbG( 0 ) = dDbF( 0 ) * ( dF2( 1 ) + dF2( 2 ) ) - dF( 0 ) * ( dDbF( 1 ) * dF( 1 ) + dDbF( 2 ) * dF( 2 ) );
 dDbG( 1 ) = dDbF( 1 ) * ( dF2( 0 ) + dF2( 2 ) ) - dF( 1 ) * ( dDbF( 0 ) * dF( 0 ) + dDbF( 2 ) * dF( 2 ) );
 dDbG( 2 ) = dDbF( 2 ) * ( dF2( 0 ) + dF2( 1 ) ) - dF( 2 ) * ( dDbF( 0 ) * dF( 0 ) + dDbF( 1 ) * dF( 1 ) );
 
 // Scale the vectors by the denominator
 dDaG *= dDenomTerm;
 dDbG *= dDenomTerm;
 
 // Cross product gives local Jacobian: dGaG x dDbG
 nodeCross[0] = dDaG( 1 ) * dDbG( 2 ) - dDaG( 2 ) * dDbG( 1 );
 nodeCross[1] = dDaG( 2 ) * dDbG( 0 ) - dDaG( 0 ) * dDbG( 2 );
 nodeCross[2] = dDaG( 0 ) * dDbG( 1 ) - dDaG( 1 ) * dDbG( 0 );
 
 const double dJacobian =
 std::sqrt( nodeCross[0] * nodeCross[0] + nodeCross[1] * nodeCross[1] + nodeCross[2] * nodeCross[2] );
 
 // dFaceArea += 2.0 * dW[p] * dW[q] * (1.0 - dG[q]) * dJacobian;
 dFaceArea += dW[p] * dW[q] * dJacobian;
 }
 }
 
 return dFaceArea;
#else
 /* compute the area by using Gauss-Quadratures; use TR interfaces directly */
 Face face( 3 );
 NodeVector nodes( 3 );
 nodes[0] = Node( inode1[0], inode1[1], inode1[2] );
 nodes[1] = Node( inode2[0], inode2[1], inode2[2] );
 nodes[2] = Node( inode3[0], inode3[1], inode3[2] );
 face.SetNode( 0, 0 );
 face.SetNode( 1, 1 );
 face.SetNode( 2, 2 );
 return CalculateFaceArea( face, nodes );
#endif
}
 
#endif
 
/*
 * l'Huiller's formula for spherical triangle
 * http://williams.best.vwh.net/avform.htm
 * a, b, c are arc measures in radians, too
 * A, B, C are angles on the sphere, for which we already have formula
 * c
 * A -------B
 * \ |
 * \ |
 * \b |a
 * \ |
 * \ |
 * \ |
 * \C|
 * \|
 *
 * (The angle at B is not necessarily a right angle)
 *
 * sin(a) sin(b) sin(c)
 * ----- = ------ = ------
 * sin(A) sin(B) sin(C)
 *
 * In terms of the sides (this is excess, as before, but numerically stable)
 *
 * E = 4*atan(sqrt(tan(s/2)*tan((s-a)/2)*tan((s-b)/2)*tan((s-c)/2)))
 */
double IntxAreaUtils::area_spherical_triangle_lHuiller( const double* ptA,
 const double* ptB,
 const double* ptC,
 double Radius )
{
 
 // now, a is angle BOC, O is origin
 CartVect vA( ptA ), vB( ptB ), vC( ptC );
 double a = angle_robust( vB, vC );
 double b = angle_robust( vC, vA );
 double c = angle_robust( vA, vB );
 int sign = 1;
 // if( fabs( ( vA * vB ) % vC ) < 1e-17 ) sign = -1;
 if( ( vA * vB ) % vC < 0 ) sign = -1;
 double s = ( a + b + c ) / 2;
 double a1 = ( s - a ) / 2;
 double b1 = ( s - b ) / 2;
 double c1 = ( s - c ) / 2;
#ifdef MOAB_HAVE_TEMPESTREMAP
 if( fabs( a1 ) < 1.e-14 || fabs( b1 ) < 1.e-14 || fabs( c1 ) < 1.e-14 )
 {
 double area = area_spherical_triangle_GQ( ptA, ptB, ptC ) * sign;
#ifdef VERBOSE
 std::cout << " very obtuse angle, use TR to compute area " << " a1:" << a1 << " b1:" << b1 << " c1:" << c1
 << "\n";
 std::cout << " area with TR: " << area << "\n";
#endif
 return area;
 }
#endif
 double tmp = tan( s / 2 ) * tan( a1 ) * tan( b1 ) * tan( c1 );
 if( tmp < 0. ) tmp = 0.;
 
 double E = 4 * atan( sqrt( tmp ) );
 if( E != E ) std::cout << " NaN at spherical triangle area \n";
 
 double area = sign * E * Radius * Radius;
 
#ifdef CHECKNEGATIVEAREA
 if( area < 0 )
 {
 std::cout << "negative area: " << area << "\n";
 std::cout << std::setprecision( 15 );
 std::cout << "vA: " << vA << "\n";
 std::cout << "vB: " << vB << "\n";
 std::cout << "vC: " << vC << "\n";
 std::cout << "sign: " << sign << "\n";
 std::cout << " a: " << a << "\n";
 std::cout << " b: " << b << "\n";
 std::cout << " c: " << c << "\n";
 }
#endif
 
 return area;
}
 
double IntxAreaUtils::area_on_sphere( Interface* mb, EntityHandle set, double R )
{
 // Get all entities of dimension 2
 Range inputRange;
 ErrorCode rval = mb->get_entities_by_dimension( set, 2, inputRange );MB_CHK_ERR_RET_VAL( rval, -1.0 );
 
 // Filter by elements that are owned by current process
 std::vector< int > ownerinfo( inputRange.size(), -1 );
 Tag intxOwnerTag;
 rval = mb->tag_get_handle( "ORIG_PROC", intxOwnerTag );
 if( MB_SUCCESS == rval )
 {
 rval = mb->tag_get_data( intxOwnerTag, inputRange, &ownerinfo[0] );MB_CHK_ERR_RET_VAL( rval, -1.0 );
 }
 
 // compare total area with 4*M_PI * R^2
 int ie = 0;
 double total_area = 0.;
 for( Range::iterator eit = inputRange.begin(); eit != inputRange.end(); ++eit )
 {
 
 // All zero/positive owner data represents ghosted elems
 if( ownerinfo[ie++] >= 0 ) continue;
 
 EntityHandle eh = *eit;
 const double elem_area = this->area_spherical_element( mb, eh, R );
 
 // check whether the area of the spherical element is positive.
 if( elem_area <= 0 )
 {
 std::cout << "Area of element " << mb->id_from_handle( eh ) << " is = " << elem_area << "\n";
 mb->list_entity( eh );
 }
 assert( elem_area > 0 );
 
 // sum up the contribution
 total_area += elem_area;
 }
 
 // return total mesh area
 return total_area;
}
 
double IntxAreaUtils::area_spherical_element( Interface* mb, EntityHandle elem, double R )
{
 // get the nodes, then the coordinates
 const EntityHandle* verts;
 int nsides;
 ErrorCode rval = mb->get_connectivity( elem, verts, nsides );MB_CHK_ERR_RET_VAL( rval, -1.0 );
 
 // account for possible padded polygons
 while( verts[nsides - 2] == verts[nsides - 1] && nsides > 3 )
 nsides--;
 
 // get coordinates
 std::vector< double > coords( 3 * nsides );
 rval = mb->get_coords( verts, nsides, &coords[0] );MB_CHK_ERR_RET_VAL( rval, -1.0 );
 
 // compute and return the area of the polygonal element
 return area_spherical_polygon( &coords[0], nsides, R );
}
 
double IntxUtils::distance_on_great_circle( CartVect& p1, CartVect& p2 )
{
 SphereCoords sph1 = cart_to_spherical( p1 );
 SphereCoords sph2 = cart_to_spherical( p2 );
 // radius should be the same
 return sph1.R *
 acos( sin( sph1.lon ) * sin( sph2.lon ) + cos( sph1.lat ) * cos( sph2.lat ) * cos( sph2.lon - sph2.lon ) );
}
 
//
/**
 * @brief Enforces convexity for a given set of polygons.
 *
 * This function checks each polygon in the input set and computes the angles of each vertex.
 * If a reflex angle is found, the polygon is broken into triangles and added back to the set.
 * This process continues until all polygons in the set are convex.
 *
 * @param mb The interface to the MOAB instance.
 * @param lset The handle of the input set containing the polygons.
 * @param my_rank The rank of the local process.
 * @return The error code indicating the success or failure of the operation.
 */
ErrorCode IntxUtils::enforce_convexity( Interface* mb, EntityHandle lset, int my_rank )
{
 Range inputRange;
 ErrorCode rval = mb->get_entities_by_dimension( lset, 2, inputRange );MB_CHK_ERR( rval );
 
 Tag corrTag = 0;
 EntityHandle dumH = 0;
 rval = mb->tag_get_handle( CORRTAGNAME, 1, MB_TYPE_HANDLE, corrTag, MB_TAG_DENSE, &dumH );
 if( rval == MB_TAG_NOT_FOUND ) corrTag = 0;
 
 Tag gidTag;
 rval = mb->tag_get_handle( "GLOBAL_ID", 1, MB_TYPE_INTEGER, gidTag, MB_TAG_DENSE );MB_CHK_ERR( rval );
 
 std::vector< double > coords;
 coords.resize( 3 * MAXEDGES ); // at most 10 vertices per polygon
 // we should create a queue with new polygons that need processing for reflex angles
 // (obtuse)
 std::queue< EntityHandle > newPolys;
 int brokenPolys = 0;
 Range::iterator eit = inputRange.begin();
 while( eit != inputRange.end() || !newPolys.empty() )
 {
 EntityHandle eh;
 if( eit != inputRange.end() )
 {
 eh = *eit;
 ++eit;
 }
 else
 {
 eh = newPolys.front();
 newPolys.pop();
 }
 // get the nodes, then the coordinates
 const EntityHandle* verts;
 int num_nodes;
 rval = mb->get_connectivity( eh, verts, num_nodes );MB_CHK_ERR( rval );
 int nsides = num_nodes;
 // account for possible padded polygons
 while( verts[nsides - 2] == verts[nsides - 1] && nsides > 3 )
 nsides--;
 EntityHandle corrHandle = 0;
 if( corrTag )
 {
 rval = mb->tag_get_data( corrTag, &eh, 1, &corrHandle );MB_CHK_ERR( rval );
 }
 int gid = 0;
 rval = mb->tag_get_data( gidTag, &eh, 1, &gid );MB_CHK_ERR( rval );
 coords.resize( 3 * nsides );
 if( nsides < 4 ) continue; // if already triangles, don't bother
 // get coordinates
 rval = mb->get_coords( verts, nsides, &coords[0] );MB_CHK_ERR( rval );
 // compute each angle
 bool alreadyBroken = false;
 
 for( int i = 0; i < nsides; i++ )
 {
 double* A = &coords[3 * i];
 double* B = &coords[3 * ( ( i + 1 ) % nsides )];
 double* C = &coords[3 * ( ( i + 2 ) % nsides )];
 double angle = IntxUtils::oriented_spherical_angle( A, B, C );
 if( angle - M_PI > 0. ) // even almost reflex is bad; break it!
 {
 if( alreadyBroken )
 {
 mb->list_entities( &eh, 1 );
 mb->list_entities( verts, nsides );
 double* D = &coords[3 * ( ( i + 3 ) % nsides )];
 std::cout << "ABC: " << angle << " \n";
 std::cout << "BCD: " << IntxUtils::oriented_spherical_angle( B, C, D ) << " \n";
 std::cout << "CDA: " << IntxUtils::oriented_spherical_angle( C, D, A ) << " \n";
 std::cout << "DAB: " << IntxUtils::oriented_spherical_angle( D, A, B ) << " \n";
 std::cout << " this cell has at least 2 angles > 180, it has serious issues\n";
 
 return MB_FAILURE;
 }
 // the bad angle is at i+1;
 // create 1 triangle and one polygon; add the polygon to the input range, so
 // it will be processed too
 // also, add both to the set :) and remove the original polygon from the set
 // break the next triangle, even though not optimal
 // so create the triangle i+1, i+2, i+3; remove i+2 from original list
 // even though not optimal in general, it is good enough.
 EntityHandle conn3[3] = { verts[( i + 1 ) % nsides], verts[( i + 2 ) % nsides],
 verts[( i + 3 ) % nsides] };
 // create a polygon with num_nodes-1 vertices, and connectivity
 // verts[i+1], verts[i+3], (all except i+2)
 std::vector< EntityHandle > conn( nsides - 1 );
 for( int j = 1; j < nsides; j++ )
 {
 conn[j - 1] = verts[( i + j + 2 ) % nsides];
 }
 EntityHandle newElement;
 rval = mb->create_element( MBTRI, conn3, 3, newElement );MB_CHK_ERR( rval );
 
 rval = mb->add_entities( lset, &newElement, 1 );MB_CHK_ERR( rval );
 if( corrTag )
 {
 rval = mb->tag_set_data( corrTag, &newElement, 1, &corrHandle );MB_CHK_ERR( rval );
 }
 rval = mb->tag_set_data( gidTag, &newElement, 1, &gid );MB_CHK_ERR( rval );
 if( nsides == 4 )
 {
 // create another triangle
 rval = mb->create_element( MBTRI, &conn[0], 3, newElement );MB_CHK_ERR( rval );
 }
 else
 {
 // create another polygon, and add it to the inputRange
 rval = mb->create_element( MBPOLYGON, &conn[0], nsides - 1, newElement );MB_CHK_ERR( rval );
 newPolys.push( newElement ); // because it has less number of edges, the
 // reverse should work to find it.
 }
 rval = mb->add_entities( lset, &newElement, 1 );MB_CHK_ERR( rval );
 if( corrTag )
 {
 rval = mb->tag_set_data( corrTag, &newElement, 1, &corrHandle );MB_CHK_ERR( rval );
 }
 rval = mb->tag_set_data( gidTag, &newElement, 1, &gid );MB_CHK_ERR( rval );
 rval = mb->remove_entities( lset, &eh, 1 );MB_CHK_ERR( rval );
 brokenPolys++;
 alreadyBroken = true; // get out of the loop, element is broken
 }
 }
 }
 if( brokenPolys > 0 )
 {
 std::cout << "on local process " << my_rank << ", " << brokenPolys
 << " concave polygons were decomposed in convex ones \n";
#ifdef VERBOSE
 std::stringstream fff;
 fff << "file_set" << mb->id_from_handle( lset ) << "rk_" << my_rank << ".h5m";
 rval = mb->write_file( fff.str().c_str(), 0, 0, &lset, 1 );MB_CHK_ERR( rval );
 std::cout << "wrote new file set: " << fff.str() << "\n";
#endif
 }
 return MB_SUCCESS;
}
 
// looking at quad connectivity, collapse to triangle if 2 nodes equal
// then delete the old quad
ErrorCode IntxUtils::fix_degenerate_quads( Interface* mb, EntityHandle set )
{
 Range quads;
 ErrorCode rval = mb->get_entities_by_type( set, MBQUAD, quads );MB_CHK_ERR( rval );
 Tag gid;
 gid = mb->globalId_tag();
 for( Range::iterator qit = quads.begin(); qit != quads.end(); ++qit )
 {
 EntityHandle quad = *qit;
 const EntityHandle* conn4 = NULL;
 int num_nodes = 0;
 rval = mb->get_connectivity( quad, conn4, num_nodes );MB_CHK_ERR( rval );
 for( int i = 0; i < num_nodes; i++ )
 {
 int next_node_index = ( i + 1 ) % num_nodes;
 if( conn4[i] == conn4[next_node_index] )
 {
 // form a triangle and delete the quad
 // first get the global id, to set it on triangle later
 int global_id = 0;
 rval = mb->tag_get_data( gid, &quad, 1, &global_id );MB_CHK_ERR( rval );
 int i2 = ( i + 2 ) % num_nodes;
 int i3 = ( i + 3 ) % num_nodes;
 EntityHandle conn3[3] = { conn4[i], conn4[i2], conn4[i3] };
 EntityHandle tri;
 rval = mb->create_element( MBTRI, conn3, 3, tri );MB_CHK_ERR( rval );
 mb->add_entities( set, &tri, 1 );
 mb->remove_entities( set, &quad, 1 );
 mb->delete_entities( &quad, 1 );
 rval = mb->tag_set_data( gid, &tri, 1, &global_id );MB_CHK_ERR( rval );
 }
 }
 }
 return MB_SUCCESS;
}
 
ErrorCode IntxAreaUtils::positive_orientation( Interface* mb, EntityHandle set, double R )
{
 Range cells2d;
 ErrorCode rval = mb->get_entities_by_dimension( set, 2, cells2d );MB_CHK_ERR( rval );
 for( Range::iterator qit = cells2d.begin(); qit != cells2d.end(); ++qit )
 {
 EntityHandle cell = *qit;
 const EntityHandle* conn = NULL;
 int num_nodes = 0;
 rval = mb->get_connectivity( cell, conn, num_nodes );MB_CHK_ERR( rval );
 if( num_nodes < 3 ) return MB_FAILURE;
 
 double coords[9];
 rval = mb->get_coords( conn, 3, coords );MB_CHK_ERR( rval );
 
 double area;
 if( R > 0 )
 area = area_spherical_triangle_lHuiller( coords, coords + 3, coords + 6, R );
 else
 area = IntxUtils::area2D( coords, coords + 3, coords + 6 );
 if( area < 0 )
 {
 // compute all area, do not revert if total area is positive
 std::vector< double > coords2( 3 * num_nodes );
 // get coordinates
 rval = mb->get_coords( conn, num_nodes, &coords2[0] );MB_CHK_ERR( rval );
 double totArea = area_spherical_polygon_lHuiller( &coords2[0], num_nodes, R );
 if( totArea < 0 )
 {
 std::vector< EntityHandle > newconn( num_nodes );
 for( int i = 0; i < num_nodes; i++ )
 {
 newconn[num_nodes - 1 - i] = conn[i];
 }
 rval = mb->set_connectivity( cell, &newconn[0], num_nodes );MB_CHK_ERR( rval );
 }
 else
 {
 std::cout << " nonconvex problem first area:" << area << " total area: " << totArea << std::endl;
 }
 }
 }
 return MB_SUCCESS;
}
 
// distance along a great circle on a sphere of radius 1
// page 4
double IntxUtils::distance_on_sphere( double la1, double te1, double la2, double te2 )
{
 return acos( sin( te1 ) * sin( te2 ) + cos( te1 ) * cos( te2 ) * cos( la1 - la2 ) );
}
 
/*
 * given 2 great circle arcs, AB and CD, compute the unique intersection point, if it exists
 * in between
 */
ErrorCode IntxUtils::intersect_great_circle_arcs( double* A, double* B, double* C, double* D, double R, double* E )
{
 // first verify A, B, C, D are on the same sphere
 double R2 = R * R;
 const double Tolerance = 1.e-12 * R2;
 
 CartVect a( A ), b( B ), c( C ), d( D );
 
 if( fabs( a.length_squared() - R2 ) + fabs( b.length_squared() - R2 ) + fabs( c.length_squared() - R2 ) +
 fabs( d.length_squared() - R2 ) >
 10 * Tolerance )
 return MB_FAILURE;
 
 CartVect n1 = a * b;
 if( n1.length_squared() < Tolerance ) return MB_FAILURE;
 
 CartVect n2 = c * d;
 if( n2.length_squared() < Tolerance ) return MB_FAILURE;
 CartVect n3 = n1 * n2;
 n3.normalize();
 
 n3 = R * n3;
 // the intersection is either n3 or -n3
 CartVect n4 = a * n3, n5 = n3 * b;
 if( n1 % n4 >= -Tolerance && n1 % n5 >= -Tolerance )
 {
 // n3 is good for ab, see if it is good for cd
 n4 = c * n3;
 n5 = n3 * d;
 if( n2 % n4 >= -Tolerance && n2 % n5 >= -Tolerance )
 {
 E[0] = n3[0];
 E[1] = n3[1];
 E[2] = n3[2];
 }
 else
 return MB_FAILURE;
 }
 else
 {
 // try -n3
 n3 = -n3;
 n4 = a * n3, n5 = n3 * b;
 if( n1 % n4 >= -Tolerance && n1 % n5 >= -Tolerance )
 {
 // n3 is good for ab, see if it is good for cd
 n4 = c * n3;
 n5 = n3 * d;
 if( n2 % n4 >= -Tolerance && n2 % n5 >= -Tolerance )
 {
 E[0] = n3[0];
 E[1] = n3[1];
 E[2] = n3[2];
 }
 else
 return MB_FAILURE;
 }
 else
 return MB_FAILURE;
 }
 
 return MB_SUCCESS;
}
 
// verify that result is in between a and b on a great circle arc, and between c and d on a constant
// latitude arc
static bool verify( CartVect a, CartVect b, CartVect c, CartVect d, double x, double y, double z )
{
 // to check, the point has to be between a and b on a great arc, and between c and d on a const
 // lat circle
 CartVect s( x, y, z );
 CartVect n1 = a * b;
 CartVect n2 = a * s;
 CartVect n3 = s * b;
 if( n1 % n2 < 0 || n1 % n3 < 0 ) return false;
 
 // do the same for c, d, s, in plane z=0
 c[2] = d[2] = s[2] = 0.; // bring everything in the same plane, z=0;
 
 n1 = c * d;
 n2 = c * s;
 n3 = s * d;
 if( n1 % n2 < 0 || n1 % n3 < 0 ) return false;
 
 return true;
}
 
ErrorCode IntxUtils::intersect_great_circle_arc_with_clat_arc( double* A,
 double* B,
 double* C,
 double* D,
 double R,
 double* E,
 int& np )
{
 const double distTol = R * 1.e-6;
 const double Tolerance = R * R * 1.e-12; // radius should be 1, usually
 np = 0; // number of points in intersection
 CartVect a( A ), b( B ), c( C ), d( D );
 // check input first
 double R2 = R * R;
 if( fabs( a.length_squared() - R2 ) + fabs( b.length_squared() - R2 ) + fabs( c.length_squared() - R2 ) +
 fabs( d.length_squared() - R2 ) >
 10 * Tolerance )
 return MB_FAILURE;
 
 if( ( a - b ).length_squared() < Tolerance ) return MB_FAILURE;
 if( ( c - d ).length_squared() < Tolerance ) // edges are too short
 return MB_FAILURE;
 
 // CD is the const latitude arc
 if( fabs( C[2] - D[2] ) > distTol ) // cd is not on the same z (constant latitude)
 return MB_FAILURE;
 
 if( fabs( R - C[2] ) < distTol || fabs( R + C[2] ) < distTol ) return MB_FAILURE; // too close to the poles
 
 // find the points on the circle P(teta) = (r*sin(teta), r*cos(teta), C[2]) that are on the
 // great circle arc AB normal to the AB circle:
 CartVect n1 = a * b; // the normal to the great circle arc (circle)
 // solve the system of equations:
 /*
 * n1%(x, y, z) = 0 // on the great circle
 * z = C[2];
 * x^2+y^2+z^2 = R^2
 */
 double z = C[2];
 if( fabs( n1[0] ) + fabs( n1[1] ) < 2 * Tolerance )
 {
 // it is the Equator; check if the const lat edge is Equator too
 if( fabs( C[2] ) > distTol )
 {
 return MB_FAILURE; // no intx, too far from Eq
 }
 else
 {
 // all points are on the equator
 //
 CartVect cd = c * d;
 // by convention, c<d, positive is from c to d
 // is a or b between c , d?
 CartVect ca = c * a;
 CartVect ad = a * d;
 CartVect cb = c * b;
 CartVect bd = b * d;
 bool agtc = ( ca % cd >= -Tolerance ); // a>c?
 bool dgta = ( ad % cd >= -Tolerance ); // d>a?
 bool bgtc = ( cb % cd >= -Tolerance ); // b>c?
 bool dgtb = ( bd % cd >= -Tolerance ); // d>b?
 if( agtc )
 {
 if( dgta )
 {
 // a is for sure a point
 E[0] = a[0];
 E[1] = a[1];
 E[2] = a[2];
 np++;
 if( bgtc )
 {
 if( dgtb )
 {
 // b is also in between c and d
 E[3] = b[0];
 E[4] = b[1];
 E[5] = b[2];
 np++;
 }
 else
 {
 // then order is c a d b, intx is ad
 E[3] = d[0];
 E[4] = d[1];
 E[5] = d[2];
 np++;
 }
 }
 else
 {
 // b is less than c, so b c a d, intx is ac
 E[3] = c[0];
 E[4] = c[1];
 E[5] = c[2];
 np++; // what if E[0] is E[3]?
 }
 }
 else // c < d < a
 {
 if( dgtb ) // d is for sure in
 {
 E[0] = d[0];
 E[1] = d[1];
 E[2] = d[2];
 np++;
 if( bgtc ) // c<b<d<a
 {
 // another point is b
 E[3] = b[0];
 E[4] = b[1];
 E[5] = b[2];
 np++;
 }
 else // b<c<d<a
 {
 // another point is c
 E[3] = c[0];
 E[4] = c[1];
 E[5] = c[2];
 np++;
 }
 }
 else
 {
 // nothing, order is c, d < a, b
 }
 }
 }
 else // a < c < d
 {
 if( bgtc )
 {
 // c is for sure in
 E[0] = c[0];
 E[1] = c[1];
 E[2] = c[2];
 np++;
 if( dgtb )
 {
 // a < c < b < d; second point is b
 E[3] = b[0];
 E[4] = b[1];
 E[5] = b[2];
 np++;
 }
 else
 {
 // a < c < d < b; second point is d
 E[3] = d[0];
 E[4] = d[1];
 E[5] = d[2];
 np++;
 }
 }
 else // a, b < c < d
 {
 // nothing
 }
 }
 }
 // for the 2 points selected, see if it is only one?
 // no problem, maybe it will be collapsed later anyway
 if( np > 0 ) return MB_SUCCESS;
 return MB_FAILURE; // no intersection
 }
 {
 if( fabs( n1[0] ) <= fabs( n1[1] ) )
 {
 // resolve eq in x: n0 * x + n1 * y +n2*z = 0; y = -n2/n1*z -n0/n1*x
 // (u+v*x)^2+x^2=R2-z^2
 // (v^2+1)*x^2 + 2*u*v *x + u^2+z^2-R^2 = 0
 // delta = 4*u^2*v^2 - 4*(v^2-1)(u^2+z^2-R^2)
 // x1,2 =
 double u = -n1[2] / n1[1] * z, v = -n1[0] / n1[1];
 double a1 = v * v + 1, b1 = 2 * u * v, c1 = u * u + z * z - R2;
 double delta = b1 * b1 - 4 * a1 * c1;
 if( delta < -Tolerance ) return MB_FAILURE; // no intersection
 if( delta > Tolerance ) // 2 solutions possible
 {
 double x1 = ( -b1 + sqrt( delta ) ) / 2 / a1;
 double x2 = ( -b1 - sqrt( delta ) ) / 2 / a1;
 double y1 = u + v * x1;
 double y2 = u + v * x2;
 if( verify( a, b, c, d, x1, y1, z ) )
 {
 E[0] = x1;
 E[1] = y1;
 E[2] = z;
 np++;
 }
 if( verify( a, b, c, d, x2, y2, z ) )
 {
 E[3 * np + 0] = x2;
 E[3 * np + 1] = y2;
 E[3 * np + 2] = z;
 np++;
 }
 }
 else
 {
 // one solution
 double x1 = -b1 / 2 / a1;
 double y1 = u + v * x1;
 if( verify( a, b, c, d, x1, y1, z ) )
 {
 E[0] = x1;
 E[1] = y1;
 E[2] = z;
 np++;
 }
 }
 }
 else
 {
 // resolve eq in y, reverse
 // n0 * x + n1 * y +n2*z = 0; x = -n2/n0*z -n1/n0*y = u+v*y
 // (u+v*y)^2+y^2 -R2+z^2 =0
 // (v^2+1)*y^2 + 2*u*v *y + u^2+z^2-R^2 = 0
 //
 // x1,2 =
 double u = -n1[2] / n1[0] * z, v = -n1[1] / n1[0];
 double a1 = v * v + 1, b1 = 2 * u * v, c1 = u * u + z * z - R2;
 double delta = b1 * b1 - 4 * a1 * c1;
 if( delta < -Tolerance ) return MB_FAILURE; // no intersection
 if( delta > Tolerance ) // 2 solutions possible
 {
 double y1 = ( -b1 + sqrt( delta ) ) / 2 / a1;
 double y2 = ( -b1 - sqrt( delta ) ) / 2 / a1;
 double x1 = u + v * y1;
 double x2 = u + v * y2;
 if( verify( a, b, c, d, x1, y1, z ) )
 {
 E[0] = x1;
 E[1] = y1;
 E[2] = z;
 np++;
 }
 if( verify( a, b, c, d, x2, y2, z ) )
 {
 E[3 * np + 0] = x2;
 E[3 * np + 1] = y2;
 E[3 * np + 2] = z;
 np++;
 }
 }
 else
 {
 // one solution
 double y1 = -b1 / 2 / a1;
 double x1 = u + v * y1;
 if( verify( a, b, c, d, x1, y1, z ) )
 {
 E[0] = x1;
 E[1] = y1;
 E[2] = z;
 np++;
 }
 }
 }
 }
 
 if( np <= 0 ) return MB_FAILURE;
 return MB_SUCCESS;
}
 
#if 0
ErrorCode set_edge_type_flag(Interface * mb, EntityHandle sf1)
{
 Range cells;
 ErrorCode rval = mb->get_entities_by_dimension(sf1, 2, cells);
 if (MB_SUCCESS!= rval)
 return rval;
 Range edges;
 rval = mb->get_adjacencies(cells, 1, true, edges, Interface::UNION);
 if (MB_SUCCESS!= rval)
 return rval;
 
 Tag edgeTypeTag;
 int default_int=0;
 rval = mb->tag_get_handle("edge_type", 1, MB_TYPE_INTEGER, edgeTypeTag,
 MB_TAG_DENSE | MB_TAG_CREAT, &default_int);
 if (MB_SUCCESS!= rval)
 return rval;
 // add edges to the set? not yet, maybe later
 // if edge horizontal, set value to 1
 int type_constant_lat=1;
 for (Range::iterator eit=edges.begin(); eit!=edges.end(); ++eit)
 {
 EntityHandle edge = *eit;
 const EntityHandle *conn=0;
 int num_n=0;
 rval = mb->get_connectivity(edge, conn, num_n );
 if (MB_SUCCESS!= rval)
 return rval;
 double coords[6];
 rval = mb->get_coords(conn, 2, coords);
 if (MB_SUCCESS!= rval)
 return rval;
 if (fabs( coords[2]-coords[5] )< 1.e-6 )
 {
 rval = mb->tag_set_data(edgeTypeTag, &edge, 1, &type_constant_lat);
 if (MB_SUCCESS!= rval)
 return rval;
 }
 }
 
 return MB_SUCCESS;
}
#endif
 
// decide in a different metric if the corners of CS quad are
// in the interior of an RLL quad
int IntxUtils::borderPointsOfCSinRLL( CartVect* redc,
 double* red2dc,
 int nsRed,
 CartVect* bluec,
 int nsBlue,
 int* blueEdgeType,
 double* P,
 int* side,
 double epsil )
{
 int extraPoints = 0;
 // first decide the blue z coordinates
 CartVect A( 0. ), B( 0. ), C( 0. ), D( 0. );
 for( int i = 0; i < nsBlue; i++ )
 {
 if( blueEdgeType[i] == 0 )
 {
 int iP1 = ( i + 1 ) % nsBlue;
 if( bluec[i][2] > bluec[iP1][2] )
 {
 A = bluec[i];
 B = bluec[iP1];
 C = bluec[( i + 2 ) % nsBlue];
 D = bluec[( i + 3 ) % nsBlue]; // it could be back to A, if triangle on top
 break;
 }
 }
 }
 if( nsBlue == 3 && B[2] < 0 )
 {
 // select D to be C
 D = C;
 C = B; // B is the south pole then
 }
 // so we have A, B, C, D, with A at the top, b going down, then C, D, D > C, A > B
 // AB is const longitude, BC and DA constant latitude
 // check now each of the red points if they are inside this rectangle
 for( int i = 0; i < nsRed; i++ )
 {
 CartVect& X = redc[i];
 if( X[2] > A[2] || X[2] < B[2] ) continue; // it is above or below the rectangle
 // now decide if it is between the planes OAB and OCD
 if( ( ( A * B ) % X >= -epsil ) && ( ( C * D ) % X >= -epsil ) )
 {
 side[i] = 1; //
 // it means point X is in the rectangle that we want , on the sphere
 // pass the coords 2d
 P[extraPoints * 2] = red2dc[2 * i];
 P[extraPoints * 2 + 1] = red2dc[2 * i + 1];
 extraPoints++;
 }
 }
 return extraPoints;
}
 
ErrorCode IntxUtils::deep_copy_set_with_quads( Interface* mb, EntityHandle source_set, EntityHandle dest_set )
{
 ReadUtilIface* read_iface;
 ErrorCode rval = mb->query_interface( read_iface );MB_CHK_ERR( rval );
 // create the handle tag for the corresponding element / vertex
 
 EntityHandle dum = 0;
 Tag corrTag = 0; // it will be created here
 rval = mb->tag_get_handle( CORRTAGNAME, 1, MB_TYPE_HANDLE, corrTag, MB_TAG_DENSE | MB_TAG_CREAT, &dum );MB_CHK_ERR( rval );
 
 // give the same global id to new verts and cells created in the lagr(departure) mesh
 Tag gid = mb->globalId_tag();
 
 Range quads;
 rval = mb->get_entities_by_type( source_set, MBQUAD, quads );MB_CHK_ERR( rval );
 
 Range connecVerts;
 rval = mb->get_connectivity( quads, connecVerts );MB_CHK_ERR( rval );
 
 std::map< EntityHandle, EntityHandle > newNodes;
 
 std::vector< double* > coords;
 EntityHandle start_vert, start_elem, *connect;
 int num_verts = connecVerts.size();
 rval = read_iface->get_node_coords( 3, num_verts, 0, start_vert, coords );
 if( MB_SUCCESS != rval ) return rval;
 // fill it up
 int i = 0;
 for( Range::iterator vit = connecVerts.begin(); vit != connecVerts.end(); ++vit, i++ )
 {
 EntityHandle oldV = *vit;
 CartVect posi;
 rval = mb->get_coords( &oldV, 1, &( posi[0] ) );MB_CHK_ERR( rval );
 
 int global_id;
 rval = mb->tag_get_data( gid, &oldV, 1, &global_id );MB_CHK_ERR( rval );
 EntityHandle new_vert = start_vert + i;
 // Cppcheck warning (false positive): variable coords is assigned a value that is never used
 coords[0][i] = posi[0];
 coords[1][i] = posi[1];
 coords[2][i] = posi[2];
 
 newNodes[oldV] = new_vert;
 // set also the correspondent tag :)
 rval = mb->tag_set_data( corrTag, &oldV, 1, &new_vert );MB_CHK_ERR( rval );
 
 // also the other side
 // need to check if we really need this; the new vertex will never need the old vertex
 // we have the global id which is the same
 rval = mb->tag_set_data( corrTag, &new_vert, 1, &oldV );MB_CHK_ERR( rval );
 // set the global id on the corresponding vertex the same as the initial vertex
 rval = mb->tag_set_data( gid, &new_vert, 1, &global_id );MB_CHK_ERR( rval );
 }
 // now create new quads in order (in a sequence)
 
 rval = read_iface->get_element_connect( quads.size(), 4, MBQUAD, 0, start_elem, connect );
 if( MB_SUCCESS != rval ) return rval;
 int ie = 0;
 for( Range::iterator it = quads.begin(); it != quads.end(); ++it, ie++ )
 {
 EntityHandle q = *it;
 int nnodes;
 const EntityHandle* conn;
 rval = mb->get_connectivity( q, conn, nnodes );MB_CHK_ERR( rval );
 int global_id;
 rval = mb->tag_get_data( gid, &q, 1, &global_id );MB_CHK_ERR( rval );
 
 for( int ii = 0; ii < nnodes; ii++ )
 {
 EntityHandle v1 = conn[ii];
 connect[4 * ie + ii] = newNodes[v1];
 }
 EntityHandle newElement = start_elem + ie;
 
 // set the corresponding tag; not sure we need this one, from old to new
 rval = mb->tag_set_data( corrTag, &q, 1, &newElement );MB_CHK_ERR( rval );
 rval = mb->tag_set_data( corrTag, &newElement, 1, &q );MB_CHK_ERR( rval );
 
 // set the global id
 rval = mb->tag_set_data( gid, &newElement, 1, &global_id );MB_CHK_ERR( rval );
 
 rval = mb->add_entities( dest_set, &newElement, 1 );MB_CHK_ERR( rval );
 }
 
 rval = read_iface->update_adjacencies( start_elem, quads.size(), 4, connect );MB_CHK_ERR( rval );
 
 return MB_SUCCESS;
}
 
ErrorCode IntxUtils::remove_duplicate_vertices( Interface* mb,
 EntityHandle file_set,
 double merge_tol,
 std::vector< Tag >& tagList )
{
 Range verts;
 ErrorCode rval = mb->get_entities_by_dimension( file_set, 0, verts );MB_CHK_ERR( rval );
 rval = mb->remove_entities( file_set, verts );MB_CHK_ERR( rval );
 
 MergeMesh mm( mb );
 
 // remove the vertices from the set, before merging
 
 rval = mm.merge_all( file_set, merge_tol );MB_CHK_ERR( rval );
 
 // now correct vertices that are repeated in polygons
 rval = remove_padded_vertices( mb, file_set, tagList );
 return MB_SUCCESS;
}
 
ErrorCode IntxUtils::remove_padded_vertices( Interface* mb, EntityHandle file_set, std::vector< Tag >& tagList )
{
 
 // now correct vertices that are repeated in polygons
 Range cells;
 ErrorCode rval = mb->get_entities_by_dimension( file_set, 2, cells );MB_CHK_ERR( rval );
 
 Range verts;
 rval = mb->get_connectivity( cells, verts );MB_CHK_ERR( rval );
 
 Range modifiedCells; // will be deleted at the end; keep the gid
 Range newCells;
 
 for( Range::iterator cit = cells.begin(); cit != cells.end(); ++cit )
 {
 EntityHandle cell = *cit;
 const EntityHandle* connec = NULL;
 int num_verts = 0;
 rval = mb->get_connectivity( cell, connec, num_verts );MB_CHK_SET_ERR( rval, "Failed to get connectivity" );
 
 std::vector< EntityHandle > newConnec;
 newConnec.push_back( connec[0] ); // at least one vertex
 int index = 0;
 int new_size = 1;
 while( index < num_verts - 2 )
 {
 int next_index = ( index + 1 );
 if( connec[next_index] != newConnec[new_size - 1] )
 {
 newConnec.push_back( connec[next_index] );
 new_size++;
 }
 index++;
 }
 // add the last one only if different from previous and first node
 if( ( connec[num_verts - 1] != connec[num_verts - 2] ) && ( connec[num_verts - 1] != connec[0] ) )
 {
 newConnec.push_back( connec[num_verts - 1] );
 new_size++;
 }
 if( new_size < num_verts )
 {
 // cout << "new cell from " << cell << " has only " << new_size << " vertices \n";
 modifiedCells.insert( cell );
 // create a new cell with type triangle, quad or polygon
 EntityType type = MBTRI;
 if( new_size == 3 )
 type = MBTRI;
 else if( new_size == 4 )
 type = MBQUAD;
 else if( new_size > 4 )
 type = MBPOLYGON;
 
 // create new cell
 EntityHandle newCell;
 rval = mb->create_element( type, &newConnec[0], new_size, newCell );MB_CHK_SET_ERR( rval, "Failed to create new cell" );
 // set the old id to the new element
 newCells.insert( newCell );
 double value; // use the same value to reset the tags, even if the tags are int (like Global ID)
 for( size_t i = 0; i < tagList.size(); i++ )
 {
 rval = mb->tag_get_data( tagList[i], &cell, 1, (void*)( &value ) );MB_CHK_SET_ERR( rval, "Failed to get tag value" );
 rval = mb->tag_set_data( tagList[i], &newCell, 1, (void*)( &value ) );MB_CHK_SET_ERR( rval, "Failed to set tag value on new cell" );
 }
 }
 }
 
 rval = mb->remove_entities( file_set, modifiedCells );MB_CHK_SET_ERR( rval, "Failed to remove old cells from file set" );
 rval = mb->delete_entities( modifiedCells );MB_CHK_SET_ERR( rval, "Failed to delete old cells" );
 rval = mb->add_entities( file_set, newCells );MB_CHK_SET_ERR( rval, "Failed to add new cells to file set" );
 rval = mb->add_entities( file_set, verts );MB_CHK_SET_ERR( rval, "Failed to add verts to the file set" );
 
 return MB_SUCCESS;
}
 
} // namespace moab