Cppcheck - HTML report

/* *****************************************************************
    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]

  ***************************************************************** */
// -*- Mode : c++; tab-width: 3; c-tab-always-indent: t; indent-tabs-mode: nil; c-basic-offset: 3
// -*-
//
//    AUTHOR: Todd Munson <[email protected]>
//       ORG: Argonne National Laboratory
//    E-MAIL: [email protected]
//
// ORIG-DATE:  2-Jan-03 at 11:02:19 by Thomas Leurent
//  LAST-MOD: 26-Nov-03 at 15:47:42 by Thomas Leurent
//
// DESCRIPTION:
// ============
/*! \file MsqHessian.cpp

  \author Thomas Leurent

*/

#include "MsqHessian.hpp"
#include "MsqTimer.hpp"

#include <cmath>
#include <iostream>

namespace MBMesquite
{

MsqHessian::MsqHessian()
    : mEntries( 0 ), mRowStart( 0 ), mColIndex( 0 ), mSize( 0 ), mPreconditioner( 0 ), precondArraySize( 0 ), mR( 0 ),
      mZ( 0 ), mP( 0 ), mW( 0 ), cgArraySizes( 0 ), maxCGiter( 50 )
{
}

MsqHessian::~MsqHessian()
{
    clear();
}

void MsqHessian::clear()
{
    mSize = precondArraySize = cgArraySizes = 0;

    delete[] mEntries;
    mEntries = 0;
    delete[] mRowStart;
    mRowStart = 0;
    delete[] mColIndex;
    mColIndex = 0;

    delete[] mPreconditioner;
    mPreconditioner = 0;

    delete[] mR;
    mR = 0;
    delete[] mZ;
    mZ = 0;
    delete[] mP;
    mP = 0;
    delete[] mW;
    mW = 0;
}

/*! \brief creates a sparse structure for a Hessian, based on the
  connectivity information contained in the PatchData.
  Only the upper triangular part of the Hessian is stored. */
void MsqHessian::initialize( PatchData& pd, MsqError& err )
{
    MSQ_FUNCTION_TIMER( "MsqHession::initialize" );
    delete[] mEntries;
    delete[] mRowStart;
    delete[] mColIndex;

    size_t num_vertices = pd.num_free_vertices();
    size_t num_elements = pd.num_elements();
    size_t const* vtx_list;
    size_t e, r, rs, re, c, cs, ce, nz, nnz, nve, i, j;<--- The scope of the variable 'cs' can be reduced. [+]The scope of the variable 'cs' can be reduced. Warning: Be careful when fixing this message, especially when there are inner loops. Here is an example where cppcheck will write that the scope for 'i' can be reduced:
void f(int x)
{
    int i = 0;
    if (x) {
        // it's safe to move 'int i = 0;' here
        for (int n = 0; n < 10; ++n) {
            // it is possible but not safe to move 'int i = 0;' here
            do_something(&i);
        }
    }
}
When you see this message it is always safe to reduce the variable scope 1 level.
<--- The scope of the variable 'ce' can be reduced. [+]The scope of the variable 'ce' can be reduced. Warning: Be careful when fixing this message, especially when there are inner loops. Here is an example where cppcheck will write that the scope for 'i' can be reduced:
void f(int x)
{
    int i = 0;
    if (x) {
        // it's safe to move 'int i = 0;' here
        for (int n = 0; n < 10; ++n) {
            // it is possible but not safe to move 'int i = 0;' here
            do_something(&i);
        }
    }
}
When you see this message it is always safe to reduce the variable scope 1 level.
    MsqMeshEntity* patchElemArray = pd.get_element_array( err );MSQ_CHKERR( err );

    if( num_vertices == 0 )
    {
        MSQ_SETERR( err )( "No vertices in PatchData", MsqError::INVALID_ARG );
        return;
    }

    mSize = num_vertices;

    // Calculate the offsets for a CSC representation of the accumulation
    // pattern.

    size_t* col_start = new size_t[num_vertices + 1];
    // mAccumElemStart = new size_t[num_elements+1];
    // mAccumElemStart[0] = 0;

    for( i = 0; i < num_vertices; ++i )
    {
        col_start[i] = 0;
    }

    for( e = 0; e < num_elements; ++e )
    {
        nve      = patchElemArray[e].node_count();
        vtx_list = patchElemArray[e].get_vertex_index_array();
        int nfe  = 0;

        for( i = 0; i < nve; ++i )
        {
            r = vtx_list[i];
            if( r < num_vertices ) ++nfe;

            for( j = i; j < nve; ++j )
            {
                c = vtx_list[j];

                if( r <= c )
                {
                    if( c < num_vertices ) ++col_start[c];
                }
                else
                {
                    if( r < num_vertices ) ++col_start[r];
                }
            }
        }
        // mAccumElemStart[e+1] = mAccumElemStart[e] + (nfe+1)*nfe/2;
    }

    nz = 0;
    for( i = 0; i < num_vertices; ++i )
    {
        j            = col_start[i];
        col_start[i] = nz;
        nz += j;
    }
    col_start[i] = nz;

    // Finished putting matrix into CSC representation

    int* row_instr    = new int[5 * nz];
    size_t* row_index = new size_t[nz];

    nz = 0;
    for( e = 0; e < num_elements; ++e )
    {
        nve      = patchElemArray[e].node_count();
        vtx_list = patchElemArray[e].get_vertex_index_array();

        for( i = 0; i < nve; ++i )
        {
            r = vtx_list[i];

            for( j = i; j < nve; ++j )
            {
                c = vtx_list[j];

                if( r <= c )
                {
                    if( c < num_vertices )
                    {
                        row_index[col_start[c]] = r;
                        row_instr[col_start[c]] = nz++;
                        ++col_start[c];
                    }
                }
                else
                {
                    if( r < num_vertices )
                    {
                        row_index[col_start[r]] = c;
                        // can't use -nz, but can negate row_instr[col_start[r]]
                        row_instr[col_start[r]] = nz++;
                        row_instr[col_start[r]] = -row_instr[col_start[r]];
                        ++col_start[r];
                    }
                }
            }
        }
    }

    for( i = num_vertices - 1; i > 0; --i )
    {
        col_start[i + 1] = col_start[i];
    }
    col_start[1] = col_start[0];
    col_start[0] = 0;

    //   cout << "col_start: ";
    //   for (int t=0; t<num_vertices+1; ++t)
    //     cout << col_start[t] << " ";
    //   cout << endl;
    //   cout << "row_index: ";
    //   for (int t=0; t<nz; ++t)
    //     cout << row_index[t] << " ";
    //   cout << endl;
    //   cout << "row_instr: ";
    //   for (int t=0; t<nz; ++t)
    //     cout << row_instr[t] << " ";
    //   cout << endl;

    // Convert CSC to CSR
    // First calculate the offsets in the row

    size_t* row_start = new size_t[num_vertices + 1];

    for( i = 0; i < num_vertices; ++i )
    {
        row_start[i] = 0;
    }

    for( i = 0; i < nz; ++i )
    {
        ++row_start[row_index[i]];
    }

    nz = 0;
    for( i = 0; i < num_vertices; ++i )
    {
        j            = row_start[i];
        row_start[i] = nz;
        nz += j;
    }
    row_start[i] = nz;

    // Now calculate the pattern

    size_t* col_index = new size_t[nz];
    int* col_instr    = new int[nz];

    for( i = 0; i < num_vertices; ++i )
    {
        cs = col_start[i];
        ce = col_start[i + 1];

        while( cs < ce )
        {
            r = row_index[cs];

            col_index[row_start[r]] = i;
            col_instr[row_start[r]] = row_instr[cs];

            ++row_start[r];
            ++cs;
        }
    }

    for( i = num_vertices - 1; i > 0; --i )
    {
        row_start[i + 1] = row_start[i];
    }
    row_start[1] = row_start[0];
    row_start[0] = 0;

    delete[] row_index;

    // Now that the matrix is CSR
    // Column indices for each row are sorted

    // Compaction -- count the number of nonzeros
    mRowStart = col_start;  // don't need to reallocate
    // mAccumulation = row_instr;   // don't need to reallocate
    delete[] row_instr;

    for( i = 0; i <= num_vertices; ++i )
    {
        mRowStart[i] = 0;
    }

    nnz = 0;
    for( i = 0; i < num_vertices; ++i )
    {
        rs = row_start[i];
        re = row_start[i + 1];

        c = num_vertices;
        while( rs < re )
        {
            if( c != col_index[rs] )
            {
                // This is an unseen nonzero

                c = col_index[rs];
                ++mRowStart[i];
                ++nnz;
            }

            // if (col_instr[rs] >= 0) {
            //  mAccumulation[col_instr[rs]] = nnz - 1;
            //}
            // else {
            //  mAccumulation[-col_instr[rs]] = 1 - nnz;
            //}

            ++rs;
        }
    }

    nnz = 0;
    for( i = 0; i < num_vertices; ++i )
    {
        j            = mRowStart[i];
        mRowStart[i] = nnz;
        nnz += j;
    }
    mRowStart[i] = nnz;

    delete[] col_instr;

    // Fill in the compacted hessian matrix

    mColIndex = new size_t[nnz];

    for( i = 0; i < num_vertices; ++i )
    {
        rs = row_start[i];
        re = row_start[i + 1];

        c = num_vertices;
        while( rs < re )
        {
            if( c != col_index[rs] )
            {
                // This is an unseen nonzero

                c                       = col_index[rs];
                mColIndex[mRowStart[i]] = c;
                mRowStart[i]++;
            }
            ++rs;
        }
    }

    for( i = num_vertices - 1; i > 0; --i )
    {
        mRowStart[i + 1] = mRowStart[i];
    }
    mRowStart[1] = mRowStart[0];
    mRowStart[0] = 0;

    delete[] row_start;
    delete[] col_index;

    mEntries = new Matrix3D[nnz];  // On Solaris, no initializer allowed for new of an array
    for( i = 0; i < nnz; ++i )
        mEntries[i] = 0.;  // so we initialize all entries manually.

    // origin_pd = &pd;

    return;
}

void MsqHessian::initialize( const MsqHessian& other )
{
    if( !other.mSize )
    {
        delete[] mEntries;
        delete[] mRowStart;
        delete[] mColIndex;
        mEntries  = 0;
        mRowStart = 0;
        mColIndex = 0;
        mSize     = 0;
        return;
    }

    if( mSize != other.mSize || mRowStart[mSize] != other.mRowStart[mSize] )
    {
        delete[] mEntries;
        delete[] mRowStart;
        delete[] mColIndex;

        mSize = other.mSize;

        mRowStart = new size_t[mSize + 1];
        mEntries  = new Matrix3D[other.mRowStart[mSize]];
        mColIndex = new size_t[other.mRowStart[mSize]];
    }

    memcpy( mRowStart, other.mRowStart, sizeof( size_t ) * ( mSize + 1 ) );
    memcpy( mColIndex, other.mColIndex, sizeof( size_t ) * mRowStart[mSize] );
}

void MsqHessian::add( const MsqHessian& other )
{
    assert( mSize == other.mSize );
    assert( !memcmp( mRowStart, other.mRowStart, sizeof( size_t ) * ( mSize + 1 ) ) );
    assert( !memcmp( mColIndex, other.mColIndex, sizeof( size_t ) * mRowStart[mSize] ) );
    for( unsigned i = 0; i < mRowStart[mSize]; ++i )
        mEntries[i] += other.mEntries[i];
}

/*! \param diag is an STL vector of size MsqHessian::size() . */
void MsqHessian::get_diagonal_blocks( std::vector< Matrix3D >& diag, MsqError& /*err*/ ) const<--- The function 'get_diagonal_blocks' is never used.
{
    // make sure we have enough memory, so that no reallocation is needed later.
    if( diag.size() != size() )
    {
        diag.reserve( size() );
    }

    for( size_t i = 0; i < size(); ++i )
    {
        diag[i] = mEntries[mRowStart[i]];
    }
}

/*! compute a preconditioner used in the preconditioned conjugate gradient
  algebraic solver. In fact, this computes \f$ M^{-1} \f$ .
*/
void MsqHessian::compute_preconditioner( MsqError& /*err*/ )
{
    // reallocates arrays if size of the Hessian has changed too much.
    if( mSize > precondArraySize || mSize < precondArraySize / 10 )
    {
        delete[] mPreconditioner;
        mPreconditioner = new Matrix3D[mSize];
    }

    Matrix3D* diag_block;<--- The scope of the variable 'diag_block' can be reduced. [+]The scope of the variable 'diag_block' can be reduced. Warning: Be careful when fixing this message, especially when there are inner loops. Here is an example where cppcheck will write that the scope for 'i' can be reduced:
void f(int x)
{
    int i = 0;
    if (x) {
        // it's safe to move 'int i = 0;' here
        for (int n = 0; n < 10; ++n) {
            // it is possible but not safe to move 'int i = 0;' here
            do_something(&i);
        }
    }
}
When you see this message it is always safe to reduce the variable scope 1 level.
    double sum, tmp;<--- Unused variable: tmp
    size_t m;
    // For each diagonal block, the (inverted) preconditioner is
    // the inverse of the sum of the diagonal entries.
    for( m = 0; m < mSize; ++m )
    {
        diag_block = mEntries + mRowStart[m];  // Gets block at position m,m .

#if !DIAGONAL_PRECONDITIONER
        // calculate LDL^T factorization of the diagonal block
        //  L = [1 pre[0][1] pre[0][2]]
        //      [0 1         pre[1][2]]
        //      [0 0         1        ]
        //  inv(D) = [pre[0][0] 0         0        ]
        //           [0         pre[1][1] 0        ]
        //           [0         0         pre[2][2]]

        // If the first method of calculating a preconditioner fails,
        // use the diagonal method.
        bool use_diag = false;

        if( fabs( ( *diag_block )[0][0] ) < DBL_EPSILON )
        {
            use_diag = true;
        }
        else
        {
            mPreconditioner[m][0][0] = 1.0 / ( *diag_block )[0][0];
            mPreconditioner[m][0][1] = ( *diag_block )[0][1] * mPreconditioner[m][0][0];
            mPreconditioner[m][0][2] = ( *diag_block )[0][2] * mPreconditioner[m][0][0];
            sum                      = ( ( *diag_block )[1][1] - ( *diag_block )[0][1] * mPreconditioner[m][0][1] );
            if( fabs( sum ) <= DBL_EPSILON )
                use_diag = true;
            else
            {
                mPreconditioner[m][1][1] = 1.0 / sum;

                tmp = ( *diag_block )[1][2] - ( *diag_block )[0][2] * mPreconditioner[m][0][1];

                mPreconditioner[m][1][2] = mPreconditioner[m][1][1] * tmp;

                sum = ( ( *diag_block )[2][2] - ( *diag_block )[0][2] * mPreconditioner[m][0][2] -
                        mPreconditioner[m][1][2] * tmp );

                if( fabs( sum ) <= DBL_EPSILON )
                    use_diag = true;
                else
                    mPreconditioner[m][2][2] = 1.0 / sum;
            }
        }
        if( use_diag )
#endif
        {
            // Either this is a fixed vertex or the diagonal block is not
            // invertible.  Switch to the diagonal preconditioner in this
            // case.

            sum = ( *diag_block )[0][0] + ( *diag_block )[1][1] + ( *diag_block )[2][2];
            if( fabs( sum ) > DBL_EPSILON )
                sum = 1 / sum;
            else
                sum = 0.0;

            mPreconditioner[m][0][0] = sum;
            mPreconditioner[m][0][1] = 0.0;
            mPreconditioner[m][0][2] = 0.0;
            mPreconditioner[m][1][1] = sum;
            mPreconditioner[m][1][2] = 0.0;
            mPreconditioner[m][2][2] = sum;
        }
    }
}

/*! uses the preconditionned conjugate gradient algebraic solver
  to find d in \f$ H * d = -g \f$ .
  \param x : the solution, usually the descent direction d.
  \param b : -b will be the right hand side. Usually b is the gradient.
*/
void MsqHessian::cg_solver( Vector3D x[], Vector3D b[], MsqError& err )
{
    MSQ_FUNCTION_TIMER( "MsqHessian::cg_solver" );

    // reallocates arrays if size of the Hessian has changed too much.
    if( mSize > cgArraySizes || mSize < cgArraySizes / 10 )
    {
        delete[] mR;
        delete[] mZ;
        delete[] mP;
        delete[] mW;
        mR           = new Vector3D[mSize];
        mZ           = new Vector3D[mSize];
        mP           = new Vector3D[mSize];
        mW           = new Vector3D[mSize];
        cgArraySizes = mSize;
    }

    size_t i;
    double alpha_, alpha, beta;<--- The scope of the variable 'alpha_' can be reduced. [+]The scope of the variable 'alpha_' can be reduced. Warning: Be careful when fixing this message, especially when there are inner loops. Here is an example where cppcheck will write that the scope for 'i' can be reduced:
void f(int x)
{
    int i = 0;
    if (x) {
        // it's safe to move 'int i = 0;' here
        for (int n = 0; n < 10; ++n) {
            // it is possible but not safe to move 'int i = 0;' here
            do_something(&i);
        }
    }
}
When you see this message it is always safe to reduce the variable scope 1 level.
<--- The scope of the variable 'alpha' can be reduced. [+]The scope of the variable 'alpha' can be reduced. Warning: Be careful when fixing this message, especially when there are inner loops. Here is an example where cppcheck will write that the scope for 'i' can be reduced:
void f(int x)
{
    int i = 0;
    if (x) {
        // it's safe to move 'int i = 0;' here
        for (int n = 0; n < 10; ++n) {
            // it is possible but not safe to move 'int i = 0;' here
            do_something(&i);
        }
    }
}
When you see this message it is always safe to reduce the variable scope 1 level.
<--- The scope of the variable 'beta' can be reduced. [+]The scope of the variable 'beta' can be reduced. Warning: Be careful when fixing this message, especially when there are inner loops. Here is an example where cppcheck will write that the scope for 'i' can be reduced:
void f(int x)
{
    int i = 0;
    if (x) {
        // it's safe to move 'int i = 0;' here
        for (int n = 0; n < 10; ++n) {
            // it is possible but not safe to move 'int i = 0;' here
            do_something(&i);
        }
    }
}
When you see this message it is always safe to reduce the variable scope 1 level.
    double cg_tol = 1e-2;  // 1e-2 will give a reasonably good solution (~1%).
    double norm_g = length( b, mSize );
    double norm_r = norm_g;
    double rzm1;  // r^T_{k-1} z_{k-1}
    double rzm2;  // r^T_{k-2} z_{k-2}<--- The scope of the variable 'rzm2' can be reduced. [+]The scope of the variable 'rzm2' can be reduced. Warning: Be careful when fixing this message, especially when there are inner loops. Here is an example where cppcheck will write that the scope for 'i' can be reduced:
void f(int x)
{
    int i = 0;
    if (x) {
        // it's safe to move 'int i = 0;' here
        for (int n = 0; n < 10; ++n) {
            // it is possible but not safe to move 'int i = 0;' here
            do_something(&i);
        }
    }
}
When you see this message it is always safe to reduce the variable scope 1 level.

    this->compute_preconditioner( err );MSQ_CHKERR( err );  // get M^{-1} for diagonal blocks

    for( i = 0; i < mSize; ++i )
        x[i] = 0.;
    for( i = 0; i < mSize; ++i )
        mR[i] = -b[i];  // r = -b because x_0 = 0 and we solve H*x = -b
    norm_g *= cg_tol;

    this->apply_preconditioner( mZ, mR, err );  // solve Mz = r (computes z = M^-1 r)
    for( i = 0; i < mSize; ++i )
        mP[i] = mZ[i];              // p_1 = z_0
    rzm1 = inner( mZ, mR, mSize );  // inner product r_{k-1}^T z_{k-1}

    size_t cg_iter = 0;
    while( ( norm_r > norm_g ) && ( cg_iter < maxCGiter ) )
    {
        ++cg_iter;

        axpy( mW, mSize, *this, mP, mSize, 0, 0, err );  // w = A * p_k

        alpha_ = inner( mP, mW, mSize );  // alpha_ = p_k^T A p_k
        if( alpha_ <= 0.0 )
        {
            if( 1 == cg_iter )
            {
                for( i = 0; i < mSize; ++i )
                    x[i] += mP[i];  // x_{k+1} = x_k + p_{k+1}
            }
            break;  // Newton goes on with this direction of negative curvature
        }

        alpha = rzm1 / alpha_;

        for( i = 0; i < mSize; ++i )
            x[i] += alpha * mP[i];  // x_{k+1} = x_k + alpha_{k+1} p_{k+1}
        for( i = 0; i < mSize; ++i )
            mR[i] -= alpha * mW[i];  // r_{k+1} = r_k - alpha_{k+1} A p_{k+1}
        norm_r = length( mR, mSize );

        this->apply_preconditioner( mZ, mR, err );  // solve Mz = r (computes z = M^-1 r)

        rzm2 = rzm1;
        rzm1 = inner( mZ, mR, mSize );  // inner product r_{k-1}^T z_{k-1}
        beta = rzm1 / rzm2;
        for( i = 0; i < mSize; ++i )
            mP[i] = mZ[i] + beta * mP[i];  // p_k = z_{k-1} + Beta_k * p_{k-1}
    }
}

void MsqHessian::product( Vector3D* v, const Vector3D* x ) const
{
    // zero output array
    memset( v, 0, size() * sizeof( *v ) );<--- Using memset() on class which contains a floating point number. [+]Using memset() on class which contains a floating point number. This is not portable because memset() sets each byte of a block of memory to a specific value and the actual representation of a floating-point value is implementation defined. Note: In case of an IEEE754-1985 compatible implementation setting all bits to zero results in the value 0.0.

    // for each row
    const Matrix3D* m_iter = mEntries;
    const size_t* c_iter   = mColIndex;
    for( size_t r = 0; r < size(); ++r )
    {

        // diagonal entry
        plusEqAx( v[r], *m_iter, x[r] );
        ++m_iter;
        ++c_iter;

        // off-diagonal entires
        for( size_t c = mRowStart[r] + 1; c != mRowStart[r + 1]; ++c )
        {
            plusEqAx( v[r], *m_iter, x[*c_iter] );
            plusEqTransAx( v[*c_iter], *m_iter, x[r] );
            ++m_iter;
            ++c_iter;
        }
    }
}

/* ------------------ I/O ----------------- */

//! Prints out the MsqHessian blocks.
std::ostream& operator<<( std::ostream& s, const MsqHessian& h )
{
    size_t i, j;
    s << "MsqHessian of size: " << h.mSize << "x" << h.mSize << "\n";
    for( i = 0; i < h.mSize; ++i )
    {
        s << " ROW " << i << " ------------------------\n";
        for( j = h.mRowStart[i]; j < h.mRowStart[i + 1]; ++j )
        {
            s << "   column " << h.mColIndex[j] << " ----\n";
            s << h.mEntries[j];
        }
    }
    return s;
}

}  // namespace MBMesquite
Cppcheck report - MOAB: src/mesquite/Misc/MsqHessian.cpp
