Fix undefined behavior flagged by UBSAN

[gromacs.git] / src / gromacs / selection / sm_same.cpp

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 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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/*! \internal \file
 * \brief
 * Implements the \p same selection method.
 *
 * \author Teemu Murtola <teemu.murtola@gmail.com>
 * \ingroup module_selection
 */
#include "gmxpre.h"

#include <cstdlib>
#include <cstring>

#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"

#include "keywords.h"
#include "parsetree.h"
#include "selelem.h"
#include "selmethod.h"
#include "selmethod_impl.h"

/*! \internal
 * \brief
 * Data structure for the \p same selection method.
 *
 * To avoid duplicate initialization code, the same data structure is used
 * for matching both integer and string keywords; hence the unions.
 *
 * \ingroup module_selection
 */
typedef struct
{
    /** Value for each atom to match. */
    union {
        int*   i;
        char** s;
        void*  ptr;
    } val;
    /*! \brief
     * Number of values in the \p as array.
     *
     * For string values, this is actually the number of values in the
     * \p as_s_sorted array.
     */
    int nas;
    /** Values to match against. */
    union {
        int*   i;
        char** s;
        void*  ptr;
    } as;
    /*! \brief
     * Separate array for sorted \p as.s array.
     *
     * The array of strings returned as the output value of a parameter should
     * not be messed with to avoid memory corruption (the pointers in the array
     * may be reused for several evaluations), so we keep our own copy for
     * modifications.
     */
    char** as_s_sorted;
    /** Whether simple matching can be used. */
    bool bSorted;
} t_methoddata_same;

/*! \brief
 * Allocates data for the \p same selection method.
 *
 * \param[in]     npar  Not used (should be 2).
 * \param[in,out] param Method parameters (should point to a copy of
 *      ::smparams_same_int or ::smparams_same_str).
 * \returns Pointer to the allocated data (\ref t_methoddata_same).
 */
static void* init_data_same(int npar, gmx_ana_selparam_t* param);
/*! \brief
 * Initializes the \p same selection method.
 *
 * \param   top   Not used.
 * \param   npar  Not used (should be 2).
 * \param   param Initialized method parameters (should point to a copy of
 *      ::smparams_same_int or ::smparams_same_str).
 * \param   data  Pointer to \ref t_methoddata_same to initialize.
 * \returns 0 on success, -1 on failure.
 */
static void init_same(const gmx_mtop_t* top, int npar, gmx_ana_selparam_t* param, void* data);
/** Frees the data allocated for the \p same selection method. */
static void free_data_same(void* data);
/*! \brief
 * Initializes the evaluation of the \p same selection method for a frame.
 *
 * \param[in]  context  Not used.
 * \param      data Should point to a \ref t_methoddata_same.
 *
 * Sorts the \c data->as.i array and removes identical values for faster and
 * simpler lookup.
 */
static void init_frame_same_int(const gmx::SelMethodEvalContext& context, void* data);
/** Evaluates the \p same selection method. */
static void evaluate_same_int(const gmx::SelMethodEvalContext& context,
                              gmx_ana_index_t*                 g,
                              gmx_ana_selvalue_t*              out,
                              void*                            data);
/*! \brief
 * Initializes the evaluation of the \p same selection method for a frame.
 *
 * \param[in]  context  Not used.
 * \param      data Should point to a \ref t_methoddata_same.
 *
 * Sorts the \c data->as.s array and removes identical values for faster and
 * simpler lookup.
 */
static void init_frame_same_str(const gmx::SelMethodEvalContext& context, void* data);
/** Evaluates the \p same selection method. */
static void evaluate_same_str(const gmx::SelMethodEvalContext& context,
                              gmx_ana_index_t*                 g,
                              gmx_ana_selvalue_t*              out,
                              void*                            data);

/** Parameters for the \p same selection method. */
static gmx_ana_selparam_t smparams_same_int[] = {
    { nullptr, { INT_VALUE, -1, { nullptr } }, nullptr, SPAR_DYNAMIC | SPAR_ATOMVAL },
    { "as", { INT_VALUE, -1, { nullptr } }, nullptr, SPAR_DYNAMIC | SPAR_VARNUM },
};

/** Parameters for the \p same selection method. */
static gmx_ana_selparam_t smparams_same_str[] = {
    { nullptr, { STR_VALUE, -1, { nullptr } }, nullptr, SPAR_DYNAMIC | SPAR_ATOMVAL },
    { "as", { STR_VALUE, -1, { nullptr } }, nullptr, SPAR_DYNAMIC | SPAR_VARNUM },
};

/** Help text for the \p same selection method. */
static const char* const help_same[] = {
    "::",
    "",
    "  same KEYWORD as ATOM_EXPR",
    "",

    "The keyword [TT]same[tt] can be used to select all atoms for which",
    "the given [TT]KEYWORD[tt] matches any of the atoms in [TT]ATOM_EXPR[tt].",
    "Keywords that evaluate to integer or string values are supported.",
};

/*! \internal \brief Selection method data for the \p same method. */
gmx_ana_selmethod_t sm_same = {
    "same",
    GROUP_VALUE,
    0,
    asize(smparams_same_int),
    smparams_same_int,
    &init_data_same,
    nullptr,
    &init_same,
    nullptr,
    &free_data_same,
    &init_frame_same_int,
    &evaluate_same_int,
    nullptr,
    { "same KEYWORD as ATOM_EXPR", "Extending selections", asize(help_same), help_same },
};

/*! \brief
 * Selection method data for the \p same method.
 *
 * This selection method is used for matching string keywords. The parser
 * never sees this method; _gmx_selelem_custom_init_same() replaces sm_same
 * with this method in cases where it is required.
 */
static gmx_ana_selmethod_t sm_same_str = {
    "same",
    GROUP_VALUE,
    SMETH_SINGLEVAL,
    asize(smparams_same_str),
    smparams_same_str,
    &init_data_same,
    nullptr,
    &init_same,
    nullptr,
    &free_data_same,
    &init_frame_same_str,
    &evaluate_same_str,
    nullptr,
    { nullptr, nullptr, 0, nullptr },
};

static void* init_data_same(int /* npar */, gmx_ana_selparam_t* param)
{
    t_methoddata_same* data;

    snew(data, 1);
    data->as_s_sorted = nullptr;
    param[1].nvalptr  = &data->nas;
    return data;
}

/*!
 * \param[in,out] method  The method to initialize.
 * \param[in,out] params  Pointer to the first parameter.
 * \param[in]     scanner Scanner data structure.
 *
 * If \p *method is not a \c same method, this function returns
 * immediately.
 */
void _gmx_selelem_custom_init_same(gmx_ana_selmethod_t**                           method,
                                   const gmx::SelectionParserParameterListPointer& params,
                                   void*                                           scanner)
{

    /* Do nothing if this is not a same method. */
    if (!*method || (*method)->name != sm_same.name || params->empty())
    {
        return;
    }

    const gmx::SelectionParserValueList& kwvalues = params->front().values();
    if (kwvalues.size() != 1 || !kwvalues.front().hasExpressionValue()
        || kwvalues.front().expr->type != SEL_EXPRESSION)
    {
        GMX_THROW(gmx::InvalidInputError("'same' should be followed by a single keyword"));
    }
    gmx_ana_selmethod_t* kwmethod = kwvalues.front().expr->u.expr.method;
    if (kwmethod->type == STR_VALUE)
    {
        *method = &sm_same_str;
    }

    /* We do custom processing for the "as" parameter. */
    gmx::SelectionParserParameterList::iterator asparam = ++params->begin();
    if (asparam != params->end() && asparam->name() == sm_same.param[1].name)
    {
        const gmx::SelectionParserValueList& asvalues = asparam->values();
        if (asvalues.size() != 1 || !asvalues.front().hasExpressionValue())
        {
            // TODO: Think about providing more informative context.
            GMX_THROW(gmx::InvalidInputError(
                    "'same ... as' should be followed by a single expression"));
        }
        const gmx::SelectionTreeElementPointer& child = asvalues.front().expr;
        /* Create a second keyword evaluation element for the keyword given as
         * the first parameter, evaluating the keyword in the group given by the
         * second parameter. */
        gmx::SelectionTreeElementPointer kwelem =
                _gmx_sel_init_keyword_evaluator(kwmethod, child, scanner);
        /* Replace the second parameter with one with a value from \p kwelem. */
        std::string pname = asparam->name();
        *asparam          = gmx::SelectionParserParameter::createFromExpression(pname, kwelem);
    }
}

static void init_same(const gmx_mtop_t* /* top */, int /* npar */, gmx_ana_selparam_t* param, void* data)
{
    t_methoddata_same* d = static_cast<t_methoddata_same*>(data);

    d->val.ptr = param[0].val.u.ptr;
    d->as.ptr  = param[1].val.u.ptr;
    if (param[1].val.type == STR_VALUE)
    {
        snew(d->as_s_sorted, d->nas);
    }
    if (!(param[0].flags & SPAR_ATOMVAL))
    {
        GMX_THROW(
                gmx::InvalidInputError("The 'same' selection keyword combined with a "
                                       "non-keyword does not make sense"));
    }
}

/*!
 * \param data Data to free (should point to a \ref t_methoddata_same).
 */
static void free_data_same(void* data)
{
    t_methoddata_same* d = static_cast<t_methoddata_same*>(data);

    sfree(d->as_s_sorted);
    sfree(d);
}

/*! \brief
 * Helper function for comparison of two integers.
 */
static int cmp_int(const void* a, const void* b)
{
    if (*reinterpret_cast<const int*>(a) < *reinterpret_cast<const int*>(b))
    {
        return -1;
    }
    if (*reinterpret_cast<const int*>(a) > *reinterpret_cast<const int*>(b))
    {
        return 1;
    }
    return 0;
}

static void init_frame_same_int(const gmx::SelMethodEvalContext& /*context*/, void* data)
{
    t_methoddata_same* d = static_cast<t_methoddata_same*>(data);
    int                i, j;

    /* Collapse adjacent values, and check whether the array is sorted. */
    d->bSorted = true;
    if (d->nas == 0)
    {
        return;
    }
    for (i = 1, j = 0; i < d->nas; ++i)
    {
        if (d->as.i[i] != d->as.i[j])
        {
            if (d->as.i[i] < d->as.i[j])
            {
                d->bSorted = false;
            }
            ++j;
            d->as.i[j] = d->as.i[i];
        }
    }
    d->nas = j + 1;

    if (!d->bSorted)
    {
        qsort(d->as.i, d->nas, sizeof(d->as.i[0]), &cmp_int);
        /* More identical values may become adjacent after sorting. */
        for (i = 1, j = 0; i < d->nas; ++i)
        {
            if (d->as.i[i] != d->as.i[j])
            {
                ++j;
                d->as.i[j] = d->as.i[i];
            }
        }
        d->nas = j + 1;
    }
}

/*!
 * See sel_updatefunc() for description of the parameters.
 * \p data should point to a \c t_methoddata_same.
 *
 * Calculates which values in \c data->val.i can be found in \c data->as.i
 * (assumed sorted), and writes the corresponding atoms to output.
 * If \c data->val is sorted, uses a linear scan of both arrays, otherwise a
 * binary search of \c data->as is performed for each block of values in
 * \c data->val.
 */
static void evaluate_same_int(const gmx::SelMethodEvalContext& /*context*/,
                              gmx_ana_index_t*    g,
                              gmx_ana_selvalue_t* out,
                              void*               data)
{
    t_methoddata_same* d = static_cast<t_methoddata_same*>(data);
    int                i, j;

    out->u.g->isize = 0;
    i = j = 0;
    while (j < g->isize)
    {
        if (d->bSorted)
        {
            /* If we are sorted, we can do a simple linear scan. */
            while (i < d->nas && d->as.i[i] < d->val.i[j])
            {
                ++i;
            }
        }
        else
        {
            /* If not, we must do a binary search of all the values. */
            int i1, i2;

            i1 = 0;
            i2 = d->nas;
            while (i2 - i1 > 1)
            {
                int itry = (i1 + i2) / 2;
                if (d->as.i[itry] <= d->val.i[j])
                {
                    i1 = itry;
                }
                else
                {
                    i2 = itry;
                }
            }
            i = (d->as.i[i1] == d->val.i[j] ? i1 : d->nas);
        }
        /* Check whether the value was found in the as list. */
        if (i == d->nas || d->as.i[i] != d->val.i[j])
        {
            /* If not, skip all atoms with the same value. */
            int tmpval = d->val.i[j];
            ++j;
            while (j < g->isize && d->val.i[j] == tmpval)
            {
                ++j;
            }
        }
        else
        {
            /* Copy all the atoms with this value to the output. */
            while (j < g->isize && d->val.i[j] == d->as.i[i])
            {
                out->u.g->index[out->u.g->isize++] = g->index[j];
                ++j;
            }
        }
        if (j < g->isize && d->val.i[j] < d->val.i[j - 1])
        {
            d->bSorted = false;
        }
    }
}

/*! \brief
 * Helper function for comparison of two strings.
 */
static int cmp_str(const void* a, const void* b)
{
    return strcmp(*static_cast<char* const*>(a), *static_cast<char* const*>(b));
}

static void init_frame_same_str(const gmx::SelMethodEvalContext& /*context*/, void* data)
{
    t_methoddata_same* d = static_cast<t_methoddata_same*>(data);
    int                i, j;

    /* Collapse adjacent values.
     * For strings, it's unlikely that the values would be sorted originally,
     * so set bSorted always to false. */
    d->bSorted = false;
    if (d->nas == 0)
    {
        return;
    }
    d->as_s_sorted[0] = d->as.s[0];
    for (i = 1, j = 0; i < d->nas; ++i)
    {
        if (strcmp(d->as.s[i], d->as_s_sorted[j]) != 0)
        {
            ++j;
            d->as_s_sorted[j] = d->as.s[i];
        }
    }
    d->nas = j + 1;

    qsort(d->as_s_sorted, d->nas, sizeof(d->as_s_sorted[0]), &cmp_str);
    /* More identical values may become adjacent after sorting. */
    for (i = 1, j = 0; i < d->nas; ++i)
    {
        if (strcmp(d->as_s_sorted[i], d->as_s_sorted[j]) != 0)
        {
            ++j;
            d->as_s_sorted[j] = d->as_s_sorted[i];
        }
    }
    d->nas = j + 1;
}

/*!
 * See sel_updatefunc() for description of the parameters.
 * \p data should point to a \c t_methoddata_same.
 *
 * Calculates which strings in \c data->val.s can be found in \c data->as.s
 * (assumed sorted), and writes the corresponding atoms to output.
 * A binary search of \c data->as is performed for each block of values in
 * \c data->val.
 */
static void evaluate_same_str(const gmx::SelMethodEvalContext& /*context*/,
                              gmx_ana_index_t*    g,
                              gmx_ana_selvalue_t* out,
                              void*               data)
{
    t_methoddata_same* d = static_cast<t_methoddata_same*>(data);
    int                j;

    out->u.g->isize = 0;
    j               = 0;
    while (j < g->isize)
    {
        /* Do a binary search of the strings. */
        void* ptr = nullptr;
        if (d->nas > 0)
        {
            ptr = bsearch(&d->val.s[j], d->as_s_sorted, d->nas, sizeof(d->as_s_sorted[0]), &cmp_str);
        }
        /* Check whether the value was found in the as list. */
        if (ptr == nullptr)
        {
            /* If not, skip all atoms with the same value. */
            const char* tmpval = d->val.s[j];
            ++j;
            while (j < g->isize && strcmp(d->val.s[j], tmpval) == 0)
            {
                ++j;
            }
        }
        else
        {
            const char* tmpval = d->val.s[j];
            /* Copy all the atoms with this value to the output. */
            while (j < g->isize && strcmp(d->val.s[j], tmpval) == 0)
            {
                out->u.g->index[out->u.g->isize++] = g->index[j];
                ++j;
            }
        }
    }
}