src/gromacs/topology/block.h

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  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 #include "gromacs/utility/range.h"
  47
  48 namespace gmx
  49 {
  50
  51 /*! \brief Division of a range of indices into consecutive blocks
  52  *
  53  * A range of consecutive indices 0 to full.range.end() is divided
  54  * into numBlocks() consecutive blocks of consecutive indices.
  55  * Block b contains indices i for which block(b).begin() <= i < block(b).end().
  56  */
  57 class RangePartitioning
  58 {
  59     public:
  60         /*! \brief A block defined by a range of atom indices */
  61         using Block = Range<int>;
  62
  63         /*! \brief Returns the number of blocks */
  64         int numBlocks() const
  65         {
  66             return static_cast<int>(index_.size()) - 1;
  67         }
  68
  69         /*! \brief Returns the size of the block with index \p blockIndex */
  70         Block block(int blockIndex) const
  71         {
  72             return Block(index_[blockIndex], index_[blockIndex + 1]);
  73         }
  74
  75         /*! \brief Returns the full range */
  76         Block fullRange() const
  77         {
  78             return Block(index_.front(), index_.back());
  79         }
  80
  81         /*! \brief Returns a range starting at \p blockIndexBegin and ending at \p blockIndexEnd */
  82         Block subRange(int blockIndexBegin,
  83                        int blockIndexEnd) const
  84         {
  85             return Block(index_[blockIndexBegin], index_[blockIndexEnd]);
  86         }
  87
  88         /*! \brief Returns true when all blocks have size 0 or numBlocks()=0 */
  89         bool allBlocksHaveSizeOne() const
  90         {
  91             return (index_.back() == numBlocks());
  92         }
  93
  94         /*! \brief Appends a block of size \p blockSize at the end of the range
  95          *
  96          * \note blocksize has to be >= 1
  97          */
  98         void appendBlock(int blockSize)
  99         {
 100             GMX_ASSERT(blockSize > 0, "block sizes should be >= 1");
 101             index_.push_back(index_.back() + blockSize);
 102         }
 103
 104         /*! \brief Removes all blocks */
 105         void clear()
 106         {
 107             index_.resize(1);
 108         }
 109
 110         /*! \brief Reduces the number of blocks to \p newNumBlocks
 111          *
 112          * \note \p newNumBlocks should be <= numBlocks().
 113          */
 114         void reduceNumBlocks(int newNumBlocks)
 115         {
 116             GMX_ASSERT(newNumBlocks <= numBlocks(), "Can only shrink to fewer blocks");
 117             index_.resize(newNumBlocks + 1);
 118         }
 119
 120         /*! \brief Sets the partitioning to \p numBlocks blocks each of size 1 */
 121         void setAllBlocksSizeOne(int numBlocks);
 122
 123         /*! \brief Returns the raw block index array, avoid using this */
 124         std::vector<int> &rawIndex()
 125         {
 126             return index_;
 127         }
 128
 129     private:
 130         std::vector<int> index_ = { 0 }; /**< The list of block begin/end indices */
 131 };
 132
 133 }  // namespace gmx
 134
 135 /* Deprecated, C-style version of RangePartitioning */
 136 typedef struct t_block
 137 {
 138     int blockSize(int blockIndex) const
 139     {
 140         GMX_ASSERT(blockIndex < nr, "blockIndex should be in range");
 141         return index[blockIndex + 1] - index[blockIndex];
 142     }
 143
 144     int      nr;           /* The number of blocks          */
 145     int     *index;        /* Array of indices (dim: nr+1)  */
 146     int      nalloc_index; /* The allocation size for index */
 147 } t_block;
 148
 149 struct t_blocka
 150 {
 151     int      nr;    /* The number of blocks              */
 152     int     *index; /* Array of indices in a (dim: nr+1) */
 153     int      nra;   /* The number of atoms               */
 154     int     *a;     /* Array of atom numbers in each group  */
 155     /* (dim: nra)                           */
 156     /* Block i (0<=i<nr) runs from          */
 157     /* index[i] to index[i+1]-1. There will */
 158     /* allways be an extra entry in index   */
 159     /* to terminate the table               */
 160     int nalloc_index;           /* The allocation size for index        */
 161     int nalloc_a;               /* The allocation size for a            */
 162 };
 163
 164 /*! \brief
 165  * Fully initialize t_block datastructure.
 166  *
 167  * Initializes a \p block and sets up the first index to zero.
 168  *
 169  * \param[in,out] block datastructure to initialize.
 170  */
 171 void init_block(t_block *block);
 172
 173 /*! \brief
 174  * Fully initialize t_blocka datastructure.
 175  *
 176  * Initializes a \p block and sets up the first index to zero.
 177  * The atom number array is initialized to nullptr.
 178  *
 179  * \param[in,out] block datastructure to initialize.
 180  */
 181 void init_blocka(t_blocka *block);
 182
 183 /* TODO
 184  * In general all t_block datastructures should be avoided
 185  * in favour of RangePartitioning. This here is a simple cludge
 186  * to use more modern initialization while we move to the use
 187  * of RangePartitioning.
 188  */
 189
 190 /*! \brief
 191  * Minimal initialization of t_block datastructure.
 192  *
 193  * Performs the equivalent to a snew on a t_block, setting all
 194  * values to zero or nullptr. Needed for some cases where the topology
 195  * handling expects a block to be valid initialized (e.g. during domain
 196  * decomposition) but without the first block set to zero.
 197  *
 198  * \param[in,out] block datastructure to initialize.
 199  */
 200 void init_block_null(t_block *block);
 201
 202 /*! \brief
 203  * Minimal initialization of t_blocka datastructure.
 204  *
 205  * Performs the equivalent to a snew on a t_blocka, setting all
 206  * values to zero or nullptr. Needed for some cases where the topology
 207  * handling expects a block to be valid initialized (e.g. during domain
 208  * decomposition) but without the first block set to zero.
 209  *
 210  * \param[in,out] block datastructure to initialize.
 211  */
 212 void init_blocka_null(t_blocka *block);
 213
 214 t_blocka *new_blocka();
 215 /* allocate new block */
 216
 217 void done_block(t_block *block);
 218 void done_blocka(t_blocka *block);
 219
 220 void copy_blocka(const t_blocka *src, t_blocka *dest);
 221
 222 void copy_block(const t_block *src, t_block *dst);
 223
 224 void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup);
 225 /* Fill a block structure with numbers identical to the index
 226  * (0, 1, 2, .. natom-1)
 227  * If bOneIndexGroup, then all atoms are  lumped in one index group,
 228  * otherwise there is one atom per index entry
 229  */
 230
 231 void stupid_fill_blocka(t_blocka *grp, int natom);
 232 /* Fill a block structure with numbers identical to the index
 233  * (0, 1, 2, .. natom-1)
 234  * There is one atom per index entry
 235  */
 236
 237 void pr_block(FILE *fp, int indent, const char *title, const t_block *block, gmx_bool bShowNumbers);
 238 void pr_blocka(FILE *fp, int indent, const char *title, const t_blocka *block, gmx_bool bShowNumbers);
 239
 240 #endif