src/gromacs/topology/block.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2010,2014,2015,2018,2019, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #ifndef GMX_TOPOLOGY_BLOCK_H
  38 #define GMX_TOPOLOGY_BLOCK_H
  39
  40 #include <stdio.h>
  41
  42 #include <vector>
  43
  44 #include "gromacs/utility/basedefinitions.h"
  45 #include "gromacs/utility/gmxassert.h"
  46
  47 namespace gmx
  48 {
  49
  50 /*! \brief Division of a range of indices into consecutive blocks
  51  *
  52  * A range of consecutive indices 0 to full.range.end() is divided
  53  * into numBlocks() consecutive blocks of consecutive indices.
  54  * Block b contains indices i for which block(b).begin() <= i < block(b).end().
  55  */
  56 class RangePartitioning
  57 {
  58     public:
  59         /*! \brief Struct for returning the range of a block.
  60          *
  61          * Can be used in a range loop.
  62          */
  63         struct Block
  64         {
  65             public:
  66                 /*! \brief An iterator that loops over integers */
  67                 struct iterator
  68                 {
  69                     //! Constructor
  70                     iterator(int value) : value_(value) {}
  71                     //! Value
  72                     operator int () const { return value_; }
  73                     //! Reference
  74                     operator int &()      { return value_; }
  75                     //! Pointer
  76                     int operator* () const { return value_; }
  77                     //! Inequality comparison
  78                     bool operator!= (const iterator other) { return value_ != other; }
  79                     //! Increment operator
  80                     iterator &operator++() { ++value_; return *this; }
  81                     //! Increment operator
  82                     iterator operator++(int) { iterator tmp(*this); ++value_; return tmp; }
  83                     //! The actual value
  84                     int value_;
  85                 };
  86
  87                 /*! \brief Constructor, constructs a range starting at 0 with 0 blocks */
  88                 Block(int begin,
  89                       int end) :
  90                     begin_(begin),
  91                     end_(end)
  92                 {
  93                 }
  94
  95                 /*! \brief Begin iterator/value */
  96                 iterator begin() const { return begin_; }
  97                 /*! \brief End iterator/value */
  98                 iterator end() const { return end_; }
  99
 100                 /*! \brief The number of items in the block */
 101                 int size() const
 102                 {
 103                     return end_ - begin_;
 104                 }
 105
 106                 /*! \brief Returns whether \p index is within range of the block */
 107                 bool inRange(int index) const
 108                 {
 109                     return (begin_ <= index && index < end_);
 110                 }
 111
 112             private:
 113                 const int begin_; /**< The start index of the block */
 114                 const int end_;   /**< The end index of the block */
 115         };
 116
 117         /*! \brief Returns the number of blocks */
 118         int numBlocks() const
 119         {
 120             return static_cast<int>(index_.size()) - 1;
 121         }
 122
 123         /*! \brief Returns the size of the block with index \p blockIndex */
 124         Block block(int blockIndex) const
 125         {
 126             return Block(index_[blockIndex], index_[blockIndex + 1]);
 127         }
 128
 129         /*! \brief Returns the full range */
 130         Block fullRange() const
 131         {
 132             return Block(index_.front(), index_.back());
 133         }
 134
 135         /*! \brief Returns a range starting at \p blockIndexBegin and ending at \p blockIndexEnd */
 136         Block subRange(int blockIndexBegin,
 137                        int blockIndexEnd) const
 138         {
 139             return Block(index_[blockIndexBegin], index_[blockIndexEnd]);
 140         }
 141
 142         /*! \brief Returns true when all blocks have size 0 or numBlocks()=0 */
 143         bool allBlocksHaveSizeOne() const
 144         {
 145             return (index_.back() == numBlocks());
 146         }
 147
 148         /*! \brief Appends a block of size \p blockSize at the end of the range
 149          *
 150          * \note blocksize has to be >= 1
 151          */
 152         void appendBlock(int blockSize)
 153         {
 154             GMX_ASSERT(blockSize > 0, "block sizes should be >= 1");
 155             index_.push_back(index_.back() + blockSize);
 156         }
 157
 158         /*! \brief Removes all blocks */
 159         void clear()
 160         {
 161             index_.resize(1);
 162         }
 163
 164         /*! \brief Reduces the number of blocks to \p newNumBlocks
 165          *
 166          * \note \p newNumBlocks should be <= numBlocks().
 167          */
 168         void reduceNumBlocks(int newNumBlocks)
 169         {
 170             GMX_ASSERT(newNumBlocks <= numBlocks(), "Can only shrink to fewer blocks");
 171             index_.resize(newNumBlocks + 1);
 172         }
 173
 174         /*! \brief Sets the partitioning to \p numBlocks blocks each of size 1 */
 175         void setAllBlocksSizeOne(int numBlocks);
 176
 177         /*! \brief Returns the raw block index array, avoid using this */
 178         std::vector<int> &rawIndex()
 179         {
 180             return index_;
 181         }
 182
 183     private:
 184         std::vector<int> index_ = { 0 }; /**< The list of block begin/end indices */
 185 };
 186
 187 }  // namespace gmx
 188
 189 /* Deprecated, C-style version of RangePartitioning */
 190 typedef struct t_block
 191 {
 192     int blockSize(int blockIndex) const
 193     {
 194         GMX_ASSERT(blockIndex < nr, "blockIndex should be in range");
 195         return index[blockIndex + 1] - index[blockIndex];
 196     }
 197
 198     int      nr;           /* The number of blocks          */
 199     int     *index;        /* Array of indices (dim: nr+1)  */
 200     int      nalloc_index; /* The allocation size for index */
 201 } t_block;
 202
 203 struct t_blocka
 204 {
 205     int      nr;    /* The number of blocks              */
 206     int     *index; /* Array of indices in a (dim: nr+1) */
 207     int      nra;   /* The number of atoms               */
 208     int     *a;     /* Array of atom numbers in each group  */
 209     /* (dim: nra)                           */
 210     /* Block i (0<=i<nr) runs from          */
 211     /* index[i] to index[i+1]-1. There will */
 212     /* allways be an extra entry in index   */
 213     /* to terminate the table               */
 214     int nalloc_index;           /* The allocation size for index        */
 215     int nalloc_a;               /* The allocation size for a            */
 216 };
 217
 218 /*! \brief
 219  * Fully initialize t_block datastructure.
 220  *
 221  * Initializes a \p block and sets up the first index to zero.
 222  *
 223  * \param[in,out] block datastructure to initialize.
 224  */
 225 void init_block(t_block *block);
 226
 227 /*! \brief
 228  * Fully initialize t_blocka datastructure.
 229  *
 230  * Initializes a \p block and sets up the first index to zero.
 231  * The atom number array is initialized to nullptr.
 232  *
 233  * \param[in,out] block datastructure to initialize.
 234  */
 235 void init_blocka(t_blocka *block);
 236
 237 /* TODO
 238  * In general all t_block datastructures should be avoided
 239  * in favour of RangePartitioning. This here is a simple cludge
 240  * to use more modern initialization while we move to the use
 241  * of RangePartitioning.
 242  */
 243
 244 /*! \brief
 245  * Minimal initialization of t_block datastructure.
 246  *
 247  * Performs the equivalent to a snew on a t_block, setting all
 248  * values to zero or nullptr. Needed for some cases where the topology
 249  * handling expects a block to be valid initialized (e.g. during domain
 250  * decomposition) but without the first block set to zero.
 251  *
 252  * \param[in,out] block datastructure to initialize.
 253  */
 254 void init_block_null(t_block *block);
 255
 256 /*! \brief
 257  * Minimal initialization of t_blocka datastructure.
 258  *
 259  * Performs the equivalent to a snew on a t_blocka, setting all
 260  * values to zero or nullptr. Needed for some cases where the topology
 261  * handling expects a block to be valid initialized (e.g. during domain
 262  * decomposition) but without the first block set to zero.
 263  *
 264  * \param[in,out] block datastructure to initialize.
 265  */
 266 void init_blocka_null(t_blocka *block);
 267
 268 t_blocka *new_blocka();
 269 /* allocate new block */
 270
 271 void done_block(t_block *block);
 272 void done_blocka(t_blocka *block);
 273
 274 void copy_blocka(const t_blocka *src, t_blocka *dest);
 275
 276 void copy_block(const t_block *src, t_block *dst);
 277
 278 void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup);
 279 /* Fill a block structure with numbers identical to the index
 280  * (0, 1, 2, .. natom-1)
 281  * If bOneIndexGroup, then all atoms are  lumped in one index group,
 282  * otherwise there is one atom per index entry
 283  */
 284
 285 void stupid_fill_blocka(t_blocka *grp, int natom);
 286 /* Fill a block structure with numbers identical to the index
 287  * (0, 1, 2, .. natom-1)
 288  * There is one atom per index entry
 289  */
 290
 291 void pr_block(FILE *fp, int indent, const char *title, const t_block *block, gmx_bool bShowNumbers);
 292 void pr_blocka(FILE *fp, int indent, const char *title, const t_blocka *block, gmx_bool bShowNumbers);
 293
 294 #endif