Cppcheck report - MOAB: test/perf/tstt_perf_binding.cpp

/** TSTT Mesh Interface brick mesh performance test
 *
 * This program tests TSTT mesh interface functions used to create a square structured
 * mesh.  Boilerplate taken from tstt mesh interface test in MOAB and performance test in MOAB
 *
 */

// Different platforms follow different conventions for usage
#ifndef _WIN32
#include <sys/resource.h>
#endif
#ifdef SOLARIS
extern "C" int getrusage( int, struct rusage* );
#ifndef RUSAGE_SELF
#include </usr/ucbinclude/sys/rusage.h>
#endif
#endif

#include <cstdlib>
#include <cstdio>
#include <iostream>

#include <iostream>
#include <cassert>
#include "iMesh.h"

// needed to get the proper size for handles

using namespace std;

double LENGTH = 1.0;

// forward declare some functions
void query_elem_to_vert( iMesh_Instance mesh );
void query_vert_to_elem( iMesh_Instance mesh );
void print_time( const bool print_em, double& tot_time, double& utime, double& stime, long& imem, long& rmem );
void build_connect( const int nelem, const int vstart, int*& connect );
void testB( iMesh_Instance mesh, const int nelem, const double* coords, int* connect );
void testC( iMesh_Instance mesh, const int nelem, const double* coords );
void compute_edge( double* start, const int nelem, const double xint, const int stride );
void compute_face( double* a, const int nelem, const double xint, const int stride1, const int stride2 );
void build_coords( const int nelem, double*& coords );
void build_connect( const int nelem, const int vstart, int*& connect );

int main( int argc, char* argv[] )
{
    int nelem = 20;
    if( argc < 3 )
    {
        std::cout << "Usage: " << argv[0] << " <ints_per_side> <A|B|C>" << std::endl;
        return 1;
    }

    char which_test = '\0';

    sscanf( argv[1], "%d", &nelem );
    sscanf( argv[2], "%c", &which_test );

    if( which_test != 'B' && which_test != 'C' )
    {
        std::cout << "Must indicate B or C for test." << std::endl;
        return 1;
    }

    std::cout << "number of elements: " << nelem << "; test " << which_test << std::endl;

    // initialize the data in native format

    // pre-build the coords array
    double* coords;
    build_coords( nelem, coords );
    assert( NULL != coords );

    // test B: create mesh using bulk interface

    // create an implementation
    iMesh_Instance mesh;
    int result;
    iMesh_newMesh( NULL, &mesh, &result, 0 );
    int* connect = NULL;

    if( iBase_SUCCESS != result )
    {
        cerr << "Couldn't create mesh instance." << endl;
        iMesh_dtor( mesh, &result );
        return 1;
    }

    iMesh_setGeometricDimension( mesh, 3, &result );
    if( iBase_SUCCESS != result )
    {
        cerr << "Couldn't set geometric dimension." << endl;
        iMesh_dtor( mesh, &result );
        return 1;
    }

    switch( which_test )
    {
        case 'B':
            build_connect( nelem, 1, connect );

            // test B: create mesh using bulk interface
            testB( mesh, nelem, coords, connect );
            break;

        case 'C':
            // test C: create mesh using individual interface
            testC( mesh, nelem, coords );
            break;
    }

    free( coords );

    return 0;
}

void testB( iMesh_Instance mesh, const int nelem, const double* coords, int* connect )
{
    double utime, stime, ttime0, ttime1, ttime2, ttime3, ttime4;
    long imem0, rmem0, imem1, rmem1, imem2, rmem2, imem3, rmem3, imem4, rmem4;

    print_time( false, ttime0, utime, stime, imem0, rmem0 );
    int num_verts = ( nelem + 1 ) * ( nelem + 1 ) * ( nelem + 1 );
    int num_elems = nelem * nelem * nelem;

    // create vertices as a block; initialize to NULL so allocation is done in interface
    iBase_EntityHandle* vertices = NULL;
    int vertices_allocated       = 0, vertices_size;
    int result;
    iMesh_createVtxArr( mesh, num_verts, iBase_BLOCKED, coords, 3 * num_verts, &vertices, &vertices_allocated,
                        &vertices_size, &result );
    if( iBase_SUCCESS != result )
    {
        cerr << "Couldn't create vertices in bulk call" << endl;
        free( vertices );
        return;
    }

    // need to explicitly fill connectivity array, since we don't know
    // the format of entity handles
    int nconnect                     = 8 * num_elems;
    iBase_EntityHandle* sidl_connect = (iBase_EntityHandle*)malloc( nconnect * sizeof( iBase_EntityHandle ) );

    for( int i = 0; i < nconnect; i++ )
    {
        // use connect[i]-1 because we used starting vertex index (vstart) of 1
        assert( connect[i] - 1 < num_verts );
        sidl_connect[i] = vertices[connect[i] - 1];
    }

    // no longer need vertices and connect arrays, free here to reduce overall peak memory usage
    free( vertices );
    free( connect );

    // create the entities
    iBase_EntityHandle* new_hexes = NULL;
    int new_hexes_allocated       = 0, new_hexes_size;
    int* status                   = NULL;
    int status_allocated          = 0, status_size;

    iMesh_createEntArr( mesh, iMesh_HEXAHEDRON, sidl_connect, nconnect, &new_hexes, &new_hexes_allocated,
                        &new_hexes_size, &status, &status_allocated, &status_size, &result );
    if( iBase_SUCCESS != result )
    {
        cerr << "Couldn't create hex elements in bulk call" << endl;
        free( new_hexes );
        free( status );
        free( sidl_connect );
        return;
    }

    print_time( false, ttime1, utime, stime, imem1, rmem1 );

    free( status );
    free( new_hexes );
    free( sidl_connect );

    // query the mesh 2 ways
    query_elem_to_vert( mesh );

    print_time( false, ttime2, utime, stime, imem2, rmem2 );

    query_vert_to_elem( mesh );

    print_time( false, ttime3, utime, stime, imem3, rmem3 );

    iMesh_dtor( mesh, &result );

    print_time( false, ttime4, utime, stime, imem4, rmem4 );

    std::cout << "TSTTb/MOAB_ucd_blocked: nelem, construct, e_to_v, v_to_e, after_dtor = " << nelem << ", "
              << ttime1 - ttime0 << ", " << ttime2 - ttime1 << ", " << ttime3 - ttime2 << ", " << ttime4 - ttime3
              << " seconds" << std::endl;
    std::cout << "TSTTb/MOAB_ucd_blocked_memory_(rss): initial, after_construction, e-v, v-e, after_dtor:" << rmem0
              << ", " << rmem1 << ", " << rmem2 << ", " << rmem3 << ", " << rmem4 << " kb" << std::endl;
}

void testC( iMesh_Instance mesh, const int nelem, const double* coords )
{
    double utime, stime, ttime0, ttime1, ttime2, ttime3, ttime4;
    long imem0, rmem0, imem1, rmem1, imem2, rmem2, imem3, rmem3, imem4, rmem4;
    print_time( false, ttime0, utime, stime, imem0, rmem0 );

    // need some dimensions
    int numv      = nelem + 1;
    int numv_sq   = numv * numv;
    int num_verts = numv * numv * numv;
#define VINDEX( i, j, k ) ( ( i ) + ( (j)*numv ) + ( (k)*numv_sq ) )

    // array to hold vertices created individually
    iBase_EntityHandle* sidl_vertices = (iBase_EntityHandle*)malloc( num_verts * sizeof( iBase_EntityHandle ) );
    int result;

    for( int i = 0; i < num_verts; i++ )
    {
        // create the vertex
        iMesh_createVtx( mesh, coords[i], coords[i + num_verts], coords[i + 2 * num_verts], sidl_vertices + i,
                         &result );
        if( iBase_SUCCESS != result )
        {
            cerr << "Couldn't create vertex in individual call" << endl;
            return;
        }
    }

    iBase_EntityHandle tmp_conn[8], new_hex;

    for( int i = 0; i < nelem; i++ )
    {
        for( int j = 0; j < nelem; j++ )
        {
            for( int k = 0; k < nelem; k++ )
            {
                int vijk    = VINDEX( i, j, k );
                tmp_conn[0] = sidl_vertices[vijk];
                tmp_conn[1] = sidl_vertices[vijk + 1];
                tmp_conn[2] = sidl_vertices[vijk + 1 + numv];
                tmp_conn[3] = sidl_vertices[vijk + numv];
                tmp_conn[4] = sidl_vertices[vijk + numv * numv];
                tmp_conn[5] = sidl_vertices[vijk + 1 + numv * numv];
                tmp_conn[6] = sidl_vertices[vijk + 1 + numv + numv * numv];
                tmp_conn[7] = sidl_vertices[vijk + numv + numv * numv];

                // create the entity

                int status;
                iMesh_createEnt( mesh, iMesh_HEXAHEDRON, tmp_conn, 8, &new_hex, &status, &result );
                if( iBase_SUCCESS != result )
                {
                    cerr << "Couldn't create hex element in individual call" << endl;
                    // return;  do not return if errors, as we would leak memory
                }
            }
        }
    }

    print_time( false, ttime1, utime, stime, imem1, rmem1 );

    free( sidl_vertices );

    // query the mesh 2 ways
    query_elem_to_vert( mesh );

    print_time( false, ttime2, utime, stime, imem2, rmem2 );

    query_vert_to_elem( mesh );

    print_time( false, ttime3, utime, stime, imem3, rmem3 );

    iMesh_dtor( mesh, &result );

    print_time( false, ttime4, utime, stime, imem4, rmem4 );

    std::cout << "TSTTb/MOAB_ucd_indiv: nelem, construct, e_to_v, v_to_e, after_dtor = " << nelem << ", "
              << ttime1 - ttime0 << ", " << ttime2 - ttime1 << ", " << ttime3 - ttime2 << ", " << ttime4 - ttime3
              << " seconds" << std::endl;
    std::cout << "TSTTb/MOAB_ucd_indiv_memory_(rss): initial, after_construction, e-v, v-e, after_dtor:" << rmem0
              << ", " << rmem1 << ", " << rmem2 << ", " << rmem3 << ", " << rmem4 << " kb" << std::endl;
}

void query_elem_to_vert( iMesh_Instance mesh )
{
    iBase_EntityHandle* all_hexes = NULL;
    int all_hexes_size, all_hexes_allocated = 0;

    // get all the hex elements
    int success;
    iBase_EntitySetHandle root_set;
    iMesh_getRootSet( mesh, &root_set, &success );
    if( iBase_SUCCESS != success )
    {
        cerr << "Couldn't get root set." << endl;
        return;
    }

    iMesh_getEntities( mesh, root_set, iBase_REGION, iMesh_HEXAHEDRON, &all_hexes, &all_hexes_allocated,
                       &all_hexes_size, &success );
    if( iBase_SUCCESS != success )
    {
        cerr << "Couldn't get all hex elements in query_mesh" << endl;
        return;
    }

    // now loop over elements
    iBase_EntityHandle* dum_connect = NULL;
    int dum_connect_allocated       = 0, dum_connect_size;
    double* dum_coords              = NULL;
    int dum_coords_size, dum_coords_allocated = 0;
    int order;
    iMesh_getDfltStorage( mesh, &order, &success );
    if( iBase_SUCCESS != success ) return;

    for( int i = 0; i < all_hexes_size; i++ )
    {
        // get the connectivity of this element; will allocate space on 1st iteration,
        // but will have correct size on subsequent ones
        iMesh_getEntAdj( mesh, all_hexes[i], iBase_VERTEX, &dum_connect, &dum_connect_allocated, &dum_connect_size,
                         &success );

        if( iBase_SUCCESS == success )
        {
            // get vertex coordinates; ; will allocate space on 1st iteration,
            // but will have correct size on subsequent ones
            iMesh_getVtxArrCoords( mesh, dum_connect, dum_connect_size, order, &dum_coords, &dum_coords_allocated,
                                   &dum_coords_size, &success );

            double centroid[3] = { 0.0, 0.0, 0.0 };
            if( order == iBase_BLOCKED )
            {
                for( int j = 0; j < 8; j++ )
                {
                    centroid[0] += dum_coords[j];
                    centroid[1] += dum_coords[8 + j];
                    centroid[2] += dum_coords[16 + j];
                }
            }
            else
            {
                for( int j = 0; j < 8; j++ )
                {
                    centroid[0] += dum_coords[3 * j];
                    centroid[1] += dum_coords[3 * j + 1];
                    centroid[2] += dum_coords[3 * j + 2];
                }
            }
        }

        if( iBase_SUCCESS != success )
        {
            cerr << "Problem getting connectivity or vertex coords." << endl;
            return;
        }
    }

    free( all_hexes );
    free( dum_connect );
    free( dum_coords );
}

void query_vert_to_elem( iMesh_Instance mesh )
{
    iBase_EntityHandle* all_verts = NULL;
    int all_verts_allocated       = 0, all_verts_size;

    iBase_EntitySetHandle root_set;
    int success;
    iMesh_getRootSet( mesh, &root_set, &success );
    if( iBase_SUCCESS != success )
    {
        cerr << "Couldn't get root set." << endl;
        return;
    }

    // get all the vertices elements
    iMesh_getEntities( mesh, root_set, iBase_VERTEX, iMesh_POINT, &all_verts, &all_verts_allocated, &all_verts_size,
                       &success );
    if( iBase_SUCCESS != success )
    {
        cerr << "Couldn't get all vertices in query_vert_to_elem" << endl;
        return;
    }

    // for this mesh, should never be more than 8 hexes connected to a vertex
    iBase_EntityHandle* dum_hexes = (iBase_EntityHandle*)calloc( 8, sizeof( iBase_EntityHandle ) );

    int dum_hexes_allocated = 8, dum_hexes_size;

    // now loop over vertices
    for( int i = 0; i < all_verts_size; i++ )
    {

        // get the connectivity of this element; will have to allocate space on every
        // iteration, since size can vary
        iMesh_getEntAdj( mesh, all_verts[i], iBase_REGION, &dum_hexes, &dum_hexes_allocated, &dum_hexes_size,
                         &success );
        if( iBase_SUCCESS != success )
        {
            cerr << "Problem getting connectivity or vertex coords." << endl;
            // do not return early, as we would leak memory
        }
    }

    free( dum_hexes );
    free( all_verts );
}

void print_time( const bool print_em, double& tot_time, double& utime, double& stime, long& imem, long& rmem )
{
    // Disabling this for windows
    // Different platforms follow different conventions for usage
#ifndef _WIN32  // Windows does not have rusage
    struct rusage r_usage;
    getrusage( RUSAGE_SELF, &r_usage );
    utime    = (double)r_usage.ru_utime.tv_sec + ( (double)r_usage.ru_utime.tv_usec / 1.e6 );
    stime    = (double)r_usage.ru_stime.tv_sec + ( (double)r_usage.ru_stime.tv_usec / 1.e6 );
    tot_time = utime + stime;
    if( print_em )
        std::cout << "User, system, total time = " << utime << ", " << stime << ", " << tot_time << std::endl;

#ifndef LINUX
    imem = r_usage.ru_idrss;
    rmem = r_usage.ru_maxrss;
    std::cout << "Max resident set size = " << r_usage.ru_maxrss << " kbytes" << std::endl;
    std::cout << "Int resident set size = " << r_usage.ru_idrss << " kbytes" << std::endl;
#else
    imem = rmem = 0;
    system( "ps o args,drs,rss | grep perf | grep -v grep" );  // RedHat 9.0 doesnt fill in actual
                                                               // memory data
#endif
    // delete [] hex_array;
#endif  // if not on windows
}

void compute_edge( double* start, const int nelem, const double xint, const int stride )
{
    for( int i = 1; i < nelem; i++ )
    {
        start[i * stride]                     = start[0] + i * xint;
        start[nelem + 1 + i * stride]         = start[nelem + 1] + i * xint;
        start[2 * ( nelem + 1 ) + i * stride] = start[2 * ( nelem + 1 )] + i * xint;
    }
}

void compute_face( double* a, const int nelem, const double xint, const int stride1, const int stride2 )
{
    // 2D TFI on a face starting at a, with strides stride1 in ada and stride2 in tse
    for( int j = 1; j < nelem; j++ )
    {
        double tse = j * xint;
        for( int i = 1; i < nelem; i++ )
        {
            double ada = i * xint;

            a[i * stride1 + j * stride2] =
                ( 1.0 - ada ) * a[i * stride1] + ada * a[i * stride1 + nelem * stride2] +
                ( 1.0 - tse ) * a[j * stride2] + tse * a[j * stride2 + nelem * stride1] -
                ( 1.0 - tse ) * ( 1.0 - ada ) * a[0] - ( 1.0 - tse ) * ada * a[nelem * stride1] -
                tse * ( 1.0 - ada ) * a[nelem * stride2] - tse * ada * a[nelem * ( stride1 + stride2 )];
            a[nelem + 1 + i * stride1 + j * stride2] =
                ( 1.0 - ada ) * a[nelem + 1 + i * stride1] + ada * a[nelem + 1 + i * stride1 + nelem * stride2] +
                ( 1.0 - tse ) * a[nelem + 1 + j * stride2] + tse * a[nelem + 1 + j * stride2 + nelem * stride1] -
                ( 1.0 - tse ) * ( 1.0 - ada ) * a[nelem + 1 + 0] -
                ( 1.0 - tse ) * ada * a[nelem + 1 + nelem * stride1] -
                tse * ( 1.0 - ada ) * a[nelem + 1 + nelem * stride2] -
                tse * ada * a[nelem + 1 + nelem * ( stride1 + stride2 )];
            a[2 * ( nelem + 1 ) + i * stride1 + j * stride2] =
                ( 1.0 - ada ) * a[2 * ( nelem + 1 ) + i * stride1] +
                ada * a[2 * ( nelem + 1 ) + i * stride1 + nelem * stride2] +
                ( 1.0 - tse ) * a[2 * ( nelem + 1 ) + j * stride2] +
                tse * a[2 * ( nelem + 1 ) + j * stride2 + nelem * stride1] -
                ( 1.0 - tse ) * ( 1.0 - ada ) * a[2 * ( nelem + 1 ) + 0] -
                ( 1.0 - tse ) * ada * a[2 * ( nelem + 1 ) + nelem * stride1] -
                tse * ( 1.0 - ada ) * a[2 * ( nelem + 1 ) + nelem * stride2] -
                tse * ada * a[2 * ( nelem + 1 ) + nelem * ( stride1 + stride2 )];
        }
    }
}

void build_coords( const int nelem, double*& coords )
{
    double ttime0, ttime1, utime1, stime1;
    long imem, rmem;
    print_time( false, ttime0, utime1, stime1, imem, rmem );

    // allocate the memory
    int numv     = nelem + 1;
    int numv_sq  = numv * numv;
    int tot_numv = numv * numv * numv;
    coords       = (double*)malloc( 3 * tot_numv * sizeof( double ) );

// use FORTRAN-like indexing
#define VINDEX( i, j, k ) ( ( i ) + ( (j)*numv ) + ( (k)*numv_sq ) )
    int idx;<--- Unused variable: idx
    double scale1, scale2, scale3;
    // use these to prevent optimization on 1-scale, etc (real map wouldn't have
    // all these equal)
    scale1 = LENGTH / nelem;
    scale2 = LENGTH / nelem;
    scale3 = LENGTH / nelem;

#ifdef REALTFI
    // use a real TFI xform to compute coordinates
    // compute edges
    // i (stride=1)
    compute_edge( &coords[VINDEX( 0, 0, 0 )], nelem, scale1, 1 );
    compute_edge( &coords[VINDEX( 0, nelem, 0 )], nelem, scale1, 1 );
    compute_edge( &coords[VINDEX( 0, 0, nelem )], nelem, scale1, 1 );
    compute_edge( &coords[VINDEX( 0, nelem, nelem )], nelem, scale1, 1 );
    // j (stride=numv)
    compute_edge( &coords[VINDEX( 0, 0, 0 )], nelem, scale1, numv );
    compute_edge( &coords[VINDEX( nelem, 0, 0 )], nelem, scale1, numv );
    compute_edge( &coords[VINDEX( 0, 0, nelem )], nelem, scale1, numv );
    compute_edge( &coords[VINDEX( nelem, 0, nelem )], nelem, scale1, numv );
    // k (stride=numv^2)
    compute_edge( &coords[VINDEX( 0, 0, 0 )], nelem, scale1, numv_sq );
    compute_edge( &coords[VINDEX( nelem, 0, 0 )], nelem, scale1, numv_sq );
    compute_edge( &coords[VINDEX( 0, nelem, 0 )], nelem, scale1, numv_sq );
    compute_edge( &coords[VINDEX( nelem, nelem, 0 )], nelem, scale1, numv_sq );

    // compute faces
    // i=0, nelem
    compute_face( &coords[VINDEX( 0, 0, 0 )], nelem, scale1, numv, numv_sq );
    compute_face( &coords[VINDEX( nelem, 0, 0 )], nelem, scale1, numv, numv_sq );
    // j=0, nelem
    compute_face( &coords[VINDEX( 0, 0, 0 )], nelem, scale1, 1, numv_sq );
    compute_face( &coords[VINDEX( 0, nelem, 0 )], nelem, scale1, 1, numv_sq );
    // k=0, nelem
    compute_face( &coords[VINDEX( 0, 0, 0 )], nelem, scale1, 1, numv );
    compute_face( &coords[VINDEX( 0, 0, nelem )], nelem, scale1, 1, numv );

    // initialize corner indices
    int i000 = VINDEX( 0, 0, 0 );
    int ia00 = VINDEX( nelem, 0, 0 );
    int i0t0 = VINDEX( 0, nelem, 0 );
    int iat0 = VINDEX( nelem, nelem, 0 );
    int i00g = VINDEX( 0, 0, nelem );
    int ia0g = VINDEX( nelem, 0, nelem );
    int i0tg = VINDEX( 0, nelem, nelem );
    int iatg = VINDEX( nelem, nelem, nelem );
    double cX, cY, cZ;
    int adaInts   = nelem;
    int tseInts   = nelem;
    int gammaInts = nelem;

    for( int i = 1; i < nelem; i++ )
    {
        for( int j = 1; j < nelem; j++ )
        {
            for( int k = 1; k < nelem; k++ )
            {
                // idx = VINDEX(i,j,k);
                double tse   = i * scale1;
                double ada   = j * scale2;
                double gamma = k * scale3;
                double tm1   = 1.0 - tse;
                double am1   = 1.0 - ada;
                double gm1   = 1.0 - gamma;

                cX = gm1 * ( am1 * ( tm1 * coords[i000] + tse * coords[i0t0] ) +
                             ada * ( tm1 * coords[ia00] + tse * coords[iat0] ) ) +
                     gamma * ( am1 * ( tm1 * coords[i00g] + tse * coords[i0tg] ) +
                               ada * ( tm1 * coords[ia0g] + tse * coords[iatg] ) );

                cY = gm1 * ( am1 * ( tm1 * coords[i000] + tse * coords[i0t0] ) +
                             ada * ( tm1 * coords[ia00] + tse * coords[iat0] ) ) +
                     gamma * ( am1 * ( tm1 * coords[i00g] + tse * coords[i0tg] ) +
                               ada * ( tm1 * coords[ia0g] + tse * coords[iatg] ) );

                cZ = gm1 * ( am1 * ( tm1 * coords[i000] + tse * coords[i0t0] ) +
                             ada * ( tm1 * coords[ia00] + tse * coords[iat0] ) ) +
                     gamma * ( am1 * ( tm1 * coords[i00g] + tse * coords[i0tg] ) +
                               ada * ( tm1 * coords[ia0g] + tse * coords[iatg] ) );

                double* ai0k = &coords[VINDEX( k, 0, i )];
                double* aiak = &coords[VINDEX( k, adaInts, i )];
                double* a0jk = &coords[VINDEX( k, j, 0 )];
                double* atjk = &coords[VINDEX( k, j, tseInts )];
                double* aij0 = &coords[VINDEX( 0, j, i )];
                double* aijg = &coords[VINDEX( gammaInts, j, i )];

                coords[VINDEX( i, j, k )] = ( am1 * ai0k[0] + ada * aiak[0] + tm1 * a0jk[0] + tse * atjk[0] +
                                              gm1 * aij0[0] + gamma * aijg[0] ) /
                                                2.0 -
                                            cX / 2.0;

                coords[nelem + 1 + VINDEX( i, j, k )] =
                    ( am1 * ai0k[nelem + 1] + ada * aiak[nelem + 1] + tm1 * a0jk[nelem + 1] + tse * atjk[nelem + 1] +
                      gm1 * aij0[nelem + 1] + gamma * aijg[nelem + 1] ) /
                        2.0 -
                    cY / 2.0;

                coords[2 * ( nelem + 1 ) + VINDEX( i, j, k )] =
                    ( am1 * ai0k[2 * ( nelem + 1 )] + ada * aiak[2 * ( nelem + 1 )] + tm1 * a0jk[2 * ( nelem + 1 )] +
                      tse * atjk[2 * ( nelem + 1 )] + gm1 * aij0[2 * ( nelem + 1 )] +
                      gamma * aijg[2 * ( nelem + 1 )] ) /
                        2.0 -
                    cZ / 2.0;
            }
        }
    }

#else
    for( int i = 0; i < numv; i++ )
    {
        for( int j = 0; j < numv; j++ )
        {
            for( int k = 0; k < numv; k++ )
            {
                idx = VINDEX( i, j, k );
                // blocked coordinate ordering
                coords[idx]                = i * scale1;
                coords[tot_numv + idx]     = j * scale2;
                coords[2 * tot_numv + idx] = k * scale3;
            }
        }
    }
#endif

    print_time( false, ttime1, utime1, stime1, imem, rmem );
    std::cout << "TSTTbinding/MOAB: TFI time = " << ttime1 - ttime0 << " sec" << std::endl;
}

void build_connect( const int nelem, const int vstart, int*& connect )
{
    // allocate the memory
    int nume_tot = nelem * nelem * nelem;
    connect      = (int*)malloc( 8 * nume_tot * sizeof( int ) );

    int vijk;
    int numv    = nelem + 1;
    int numv_sq = numv * numv;
    int idx     = 0;
    for( int i = 0; i < nelem; i++ )
    {
        for( int j = 0; j < nelem; j++ )
        {
            for( int k = 0; k < nelem; k++ )
            {
                vijk           = vstart + VINDEX( i, j, k );
                connect[idx++] = vijk;
                connect[idx++] = vijk + 1;
                connect[idx++] = vijk + 1 + numv;
                connect[idx++] = vijk + numv;
                connect[idx++] = vijk + numv * numv;
                connect[idx++] = vijk + 1 + numv * numv;
                connect[idx++] = vijk + 1 + numv + numv * numv;
                connect[idx++] = vijk + numv + numv * numv;
                assert( i <= numv * numv * numv );
            }
        }
    }
}