src/gromacs/selection/sm_permute.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements the \p permute selection modifier.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_selection
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "gromacs/math/vec.h"
  45 #include "gromacs/selection/position.h"
  46 #include "gromacs/utility/arraysize.h"
  47 #include "gromacs/utility/exceptions.h"
  48 #include "gromacs/utility/smalloc.h"
  49 #include "gromacs/utility/stringutil.h"
  50
  51 #include "selmethod.h"
  52 #include "selmethod-impl.h"
  53
  54 /*! \internal \brief
  55  * Data structure for the \p permute selection modifier.
  56  */
  57 typedef struct
  58 {
  59     /** Positions to permute. */
  60     gmx_ana_pos_t    p;
  61     /** Number of elements in the permutation. */
  62     int              n;
  63     /** Array describing the permutation. */
  64     int             *perm;
  65     /** Array that has the permutation reversed. */
  66     int             *rperm;
  67 } t_methoddata_permute;
  68
  69 /*! \brief
  70  * Allocates data for the \p permute selection modifier.
  71  *
  72  * \param[in]     npar  Not used (should be 2).
  73  * \param[in,out] param Method parameters (should point to a copy of
  74  *   \ref smparams_permute).
  75  * \returns Pointer to the allocated data (\p t_methoddata_permute).
  76  *
  77  * Allocates memory for a \p t_methoddata_permute structure.
  78  */
  79 static void *
  80 init_data_permute(int npar, gmx_ana_selparam_t *param);
  81 /*! \brief
  82  * Initializes data for the \p permute selection modifier.
  83  *
  84  * \param[in] top   Not used.
  85  * \param[in] npar  Not used (should be 2).
  86  * \param[in] param Method parameters (should point to \ref smparams_permute).
  87  * \param[in] data  Should point to a \p t_methoddata_permute.
  88  * \returns   0 if the input permutation is valid, -1 on error.
  89  */
  90 static void
  91 init_permute(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
  92 /*! \brief
  93  * Initializes output for the \p permute selection modifier.
  94  *
  95  * \param[in]     top   Topology data structure.
  96  * \param[in,out] out   Pointer to output data structure.
  97  * \param[in,out] data  Should point to \c t_methoddata_permute.
  98  */
  99 static void
 100 init_output_permute(const gmx_mtop_t *top, gmx_ana_selvalue_t *out, void *data);
 101 /** Frees the memory allocated for the \p permute selection modifier. */
 102 static void
 103 free_data_permute(void *data);
 104 /*! \brief
 105  * Evaluates the \p permute selection modifier.
 106  *
 107  * \param[in]  context Not used.
 108  * \param[in]  p     Positions to permute (should point to \p data->p).
 109  * \param[out] out   Output data structure (\p out->u.p is used).
 110  * \param[in]  data  Should point to a \p t_methoddata_permute.
 111  *
 112  * Throws if the size of \p p is not divisible by the number of
 113  * elements in the permutation.
 114  */
 115 static void
 116 evaluate_permute(const gmx::SelMethodEvalContext &context,
 117                  gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
 118
 119 /** Parameters for the \p permute selection modifier. */
 120 static gmx_ana_selparam_t smparams_permute[] = {
 121     {nullptr,       {POS_VALUE, -1, {nullptr}}, nullptr, SPAR_DYNAMIC | SPAR_VARNUM},
 122     {nullptr,       {INT_VALUE, -1, {nullptr}}, nullptr, SPAR_VARNUM},
 123 };
 124
 125 /** Help text for the \p permute selection modifier. */
 126 static const char *const help_permute[] = {
 127     "::",
 128     "",
 129     "  permute P1 ... PN",
 130     "",
 131     "By default, all selections are evaluated such that the atom indices are",
 132     "returned in ascending order. This can be changed by appending",
 133     "[TT]permute P1 P2 ... PN[tt] to an expression.",
 134     "The [TT]Pi[tt] should form a permutation of the numbers 1 to N.",
 135     "This keyword permutes each N-position block in the selection such that",
 136     "the i'th position in the block becomes Pi'th.",
 137     "Note that it is the positions that are permuted, not individual atoms.",
 138     "A fatal error occurs if the size of the selection is not a multiple of n.",
 139     "It is only possible to permute the whole selection expression, not any",
 140     "subexpressions, i.e., the [TT]permute[tt] keyword should appear last in",
 141     "a selection.",
 142 };
 143
 144 /** Selection method data for the \p permute modifier. */
 145 gmx_ana_selmethod_t sm_permute = {
 146     "permute", POS_VALUE, SMETH_MODIFIER,
 147     asize(smparams_permute), smparams_permute,
 148     &init_data_permute,
 149     nullptr,
 150     &init_permute,
 151     &init_output_permute,
 152     &free_data_permute,
 153     nullptr,
 154     nullptr,
 155     &evaluate_permute,
 156     {"POSEXPR permute P1 ... PN",
 157      "Permuting selections", asize(help_permute), help_permute},
 158 };
 159
 160 static void *
 161 init_data_permute(int /* npar */, gmx_ana_selparam_t *param)
 162 {
 163     t_methoddata_permute *data = new t_methoddata_permute();
 164     data->n          = 0;
 165     data->perm       = nullptr;
 166     data->rperm      = nullptr;
 167     param[0].val.u.p = &data->p;
 168     return data;
 169 }
 170
 171 static void
 172 init_permute(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
 173 {
 174     t_methoddata_permute *d = static_cast<t_methoddata_permute *>(data);
 175     int                   i;
 176
 177     d->n    = param[1].val.nr;
 178     d->perm = param[1].val.u.i;
 179     if (d->p.count() % d->n != 0)
 180     {
 181         GMX_THROW(gmx::InconsistentInputError(
 182                           gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
 183     }
 184     snew(d->rperm, d->n);
 185     for (i = 0; i < d->n; ++i)
 186     {
 187         d->rperm[i] = -1;
 188     }
 189     for (i = 0; i < d->n; ++i)
 190     {
 191         d->perm[i]--;
 192         if (d->perm[i] < 0 || d->perm[i] >= d->n)
 193         {
 194             GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
 195         }
 196         if (d->rperm[d->perm[i]] >= 0)
 197         {
 198             GMX_THROW(gmx::InvalidInputError("Invalid permutation"));
 199         }
 200         d->rperm[d->perm[i]] = i;
 201     }
 202 }
 203
 204 static void
 205 init_output_permute(const gmx_mtop_t * /* top */, gmx_ana_selvalue_t *out, void *data)
 206 {
 207     t_methoddata_permute *d = static_cast<t_methoddata_permute *>(data);
 208     int                   i, j, b;
 209
 210     out->u.p->m.type = d->p.m.type;
 211     gmx_ana_pos_reserve_for_append(out->u.p, d->p.count(), d->p.m.b.nra,
 212                                    d->p.v != nullptr, d->p.f != nullptr);
 213     gmx_ana_pos_empty_init(out->u.p);
 214     for (i = 0; i < d->p.count(); i += d->n)
 215     {
 216         for (j = 0; j < d->n; ++j)
 217         {
 218             b = i + d->rperm[j];
 219             gmx_ana_pos_append_init(out->u.p, &d->p, b);
 220         }
 221     }
 222 }
 223
 224 /*!
 225  * \param data Data to free (should point to a \p t_methoddata_permute).
 226  *
 227  * Frees the memory allocated for \c t_methoddata_permute.
 228  */
 229 static void
 230 free_data_permute(void *data)
 231 {
 232     t_methoddata_permute *d = static_cast<t_methoddata_permute *>(data);
 233
 234     sfree(d->rperm);
 235     delete d;
 236 }
 237
 238 static void
 239 evaluate_permute(const gmx::SelMethodEvalContext & /*context*/,
 240                  gmx_ana_pos_t * /*p*/, gmx_ana_selvalue_t *out, void *data)
 241 {
 242     t_methoddata_permute *d = static_cast<t_methoddata_permute *>(data);
 243     int                   i, j, b;
 244     int                   refid;
 245
 246     if (d->p.count() % d->n != 0)
 247     {
 248         GMX_THROW(gmx::InconsistentInputError(
 249                           gmx::formatString("The number of positions to be permuted is not divisible by %d", d->n)));
 250     }
 251     gmx_ana_pos_empty(out->u.p);
 252     for (i = 0; i < d->p.count(); i += d->n)
 253     {
 254         for (j = 0; j < d->n; ++j)
 255         {
 256             b     = i + d->rperm[j];
 257             refid = d->p.m.refid[b];
 258             if (refid != -1)
 259             {
 260                 /* De-permute the reference ID */
 261                 refid = refid - (refid % d->n) + d->perm[refid % d->n];
 262             }
 263             gmx_ana_pos_append(out->u.p, &d->p, b, refid);
 264         }
 265     }
 266     gmx_ana_pos_append_finish(out->u.p);
 267 }