src/gmxlib/selection/sm_permute.c

   1 /*
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  31 /*! \internal \file
  32  * \brief Implementation of the \p permute selection modifier.
  33  */
  34 #ifdef HAVE_CONFIG_H
  35 #include <config.h>
  36 #endif
  37
  38 #include <macros.h>
  39 #include <smalloc.h>
  40 #include <vec.h>
  41
  42 #include <position.h>
  43 #include <selmethod.h>
  44
  45 /*! \internal \brief
  46  * Data structure for the \p permute selection modifier.
  47  */
  48 typedef struct
  49 {
  50     /** Positions to permute. */
  51     gmx_ana_pos_t    p;
  52     /** Group to receive the output permutation. */
  53     gmx_ana_index_t  g;
  54     /** Number of elements in the permutation. */
  55     int              n;
  56     /** Array describing the permutation. */
  57     int             *perm;
  58     /** Array that has the permutation reversed. */
  59     int             *rperm;
  60 } t_methoddata_permute;
  61
  62 /** Allocates data for the \p permute selection modifier. */
  63 static void *
  64 init_data_permute(int npar, gmx_ana_selparam_t *param);
  65 /** Initializes data for the \p permute selection modifier. */
  66 static int
  67 init_permute(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
  68 /** Initializes output for the \p permute selection modifier. */
  69 static int
  70 init_output_permute(t_topology *top, gmx_ana_selvalue_t *out, void *data);
  71 /** Frees the memory allocated for the \p permute selection modifier. */
  72 static void
  73 free_data_permute(void *data);
  74 /** Evaluates the \p permute selection modifier. */
  75 static int
  76 evaluate_permute(t_topology *top, t_trxframe *fr, t_pbc *pbc,
  77                  gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
  78
  79 /** Parameters for the \p permute selection modifier. */
  80 static gmx_ana_selparam_t smparams_permute[] = {
  81     {NULL,       {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
  82     {NULL,       {INT_VALUE, -1, {NULL}}, NULL, SPAR_VARNUM},
  83 };
  84
  85 /** Help text for the \p permute selection modifier. */
  86 static const char *help_permute[] = {
  87     "PERMUTING SELECTIONS[PAR]",
  88
  89     "[TT]permute P1 ... PN[tt][PAR]",
  90
  91     "By default, all selections are evaluated such that the atom indices are",
  92     "returned in ascending order. This can be changed by appending",
  93     "[TT]permute P1 P2 ... PN[tt] to an expression.",
  94     "The [TT]Pi[tt] should form a permutation of the numbers 1 to N.",
  95     "This keyword permutes each N-position block in the selection such that",
  96     "the i'th position in the block becomes Pi'th.",
  97     "Note that it is the positions that are permuted, not individual atoms.",
  98     "A fatal error occurs if the size of the selection is not a multiple of n.",
  99     "It is only possible to permute the whole selection expression, not any",
 100     "subexpressions, i.e., the [TT]permute[tt] keyword should appear last in",
 101     "a selection.",
 102 };
 103
 104 /** \internal Selection method data for the \p permute modifier. */
 105 gmx_ana_selmethod_t sm_permute = {
 106     "permute", POS_VALUE, SMETH_MODIFIER,
 107     asize(smparams_permute), smparams_permute,
 108     &init_data_permute,
 109     NULL,
 110     &init_permute,
 111     &init_output_permute,
 112     &free_data_permute,
 113     NULL,
 114     NULL,
 115     &evaluate_permute,
 116     {"permute P1 ... PN", asize(help_permute), help_permute},
 117 };
 118
 119 /*!
 120  * \param[in]     npar  Not used (should be 2).
 121  * \param[in,out] param Method parameters (should point to a copy of
 122  *   \ref smparams_permute).
 123  * \returns Pointer to the allocated data (\p t_methoddata_permute).
 124  *
 125  * Allocates memory for a \p t_methoddata_permute structure.
 126  */
 127 static void *
 128 init_data_permute(int npar, gmx_ana_selparam_t *param)
 129 {
 130     t_methoddata_permute *data;
 131
 132     snew(data, 1);
 133     param[0].val.u.p = &data->p;
 134     return data;
 135 }
 136
 137 /*!
 138  * \param[in] top   Not used.
 139  * \param[in] npar  Not used (should be 2).
 140  * \param[in] param Method parameters (should point to \ref smparams_permute).
 141  * \param[in] data  Should point to a \p t_methoddata_permute.
 142  * \returns   0 if the input permutation is valid, -1 on error.
 143  */
 144 static int
 145 init_permute(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
 146 {
 147     t_methoddata_permute *d = (t_methoddata_permute *)data;
 148     int                   i;
 149
 150     gmx_ana_index_reserve(&d->g, d->p.g->isize);
 151     d->n    = param[1].val.nr;
 152     d->perm = param[1].val.u.i;
 153     if (d->p.nr % d->n != 0)
 154     {
 155         fprintf(stderr, "error: the number of positions to be permuted is not divisible by %d\n",
 156                 d->n);
 157         return -1;
 158     }
 159     snew(d->rperm, d->n);
 160     for (i = 0; i < d->n; ++i)
 161     {
 162         d->rperm[i] = -1;
 163     }
 164     for (i = 0; i < d->n; ++i)
 165     {
 166         d->perm[i]--;
 167         if (d->perm[i] < 0 || d->perm[i] >= d->n)
 168         {
 169             fprintf(stderr, "invalid permutation");
 170             return -1;
 171         }
 172         if (d->rperm[d->perm[i]] >= 0)
 173         {
 174             fprintf(stderr, "invalid permutation");
 175             return -1;
 176         }
 177         d->rperm[d->perm[i]] = i;
 178     }
 179     return 0;
 180 }
 181
 182 /*!
 183  * \param[in]     top   Topology data structure.
 184  * \param[in,out] out   Pointer to output data structure.
 185  * \param[in,out] data  Should point to \c t_methoddata_permute.
 186  * \returns       0 for success.
 187  */
 188 static int
 189 init_output_permute(t_topology *top, gmx_ana_selvalue_t *out, void *data)
 190 {
 191     t_methoddata_permute *d = (t_methoddata_permute *)data;
 192     int                   i, j, b, k;
 193
 194     gmx_ana_pos_copy(out->u.p, &d->p, TRUE);
 195     gmx_ana_pos_set_evalgrp(out->u.p, &d->g);
 196     d->g.isize = 0;
 197     gmx_ana_pos_empty_init(out->u.p);
 198     for (i = 0; i < d->p.nr; i += d->n)
 199     {
 200         for (j = 0; j < d->n; ++j)
 201         {
 202             b = i + d->rperm[j];
 203             gmx_ana_pos_append_init(out->u.p, &d->g, &d->p, b);
 204         }
 205     }
 206     return 0;
 207 }
 208
 209 /*!
 210  * \param data Data to free (should point to a \p t_methoddata_permute).
 211  *
 212  * Frees the memory allocated for \c t_methoddata_permute.
 213  */
 214 static void
 215 free_data_permute(void *data)
 216 {
 217     t_methoddata_permute *d = (t_methoddata_permute *)data;
 218
 219     gmx_ana_index_deinit(&d->g);
 220     sfree(d->rperm);
 221 }
 222
 223 /*!
 224  * \param[in]  top   Not used.
 225  * \param[in]  fr    Not used.
 226  * \param[in]  pbc   Not used.
 227  * \param[in]  p     Positions to permute (should point to \p data->p).
 228  * \param[out] out   Output data structure (\p out->u.p is used).
 229  * \param[in]  data  Should point to a \p t_methoddata_permute.
 230  * \returns    0 if \p p could be permuted, -1 on error.
 231  *
 232  * Returns -1 if the size of \p p is not divisible by the number of
 233  * elements in the permutation.
 234  */
 235 static int
 236 evaluate_permute(t_topology *top, t_trxframe *fr, t_pbc *pbc,
 237                  gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data)
 238 {
 239     t_methoddata_permute *d = (t_methoddata_permute *)data;
 240     int                   i, j, b, k;
 241     int                   refid;
 242
 243     if (d->p.nr % d->n != 0)
 244     {
 245         fprintf(stderr, "error: the number of positions to be permuted is not divisible by %d\n",
 246                 d->n);
 247         return -1;
 248     }
 249     d->g.isize = 0;
 250     gmx_ana_pos_empty(out->u.p);
 251     for (i = 0; i < d->p.nr; i += d->n)
 252     {
 253         for (j = 0; j < d->n; ++j)
 254         {
 255             b = i + d->rperm[j];
 256             refid = d->p.m.refid[b];
 257             if (refid != -1)
 258             {
 259                 /* De-permute the reference ID */
 260                 refid = refid - (refid % d->n) + d->perm[refid % d->n];
 261             }
 262             gmx_ana_pos_append(out->u.p, &d->g, p, b, refid);
 263         }
 264     }
 265     gmx_ana_pos_append_finish(out->u.p);
 266     return 0;
 267 }