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37 * \brief This file contains declarations for functions needed
38 * internally by the module.
40 * \author Mark Abraham <mark.j.abraham@gmail.com>
41 * \ingroup module_listed_forces
43 #ifndef GMX_LISTED_FORCES_LISTED_INTERNAL_H
44 #define GMX_LISTED_FORCES_LISTED_INTERNAL_H
48 #include "gromacs/math/vectypes.h"
49 #include "gromacs/mdtypes/enerdata.h"
50 #include "gromacs/topology/idef.h"
51 #include "gromacs/topology/ifunc.h"
52 #include "gromacs/utility/bitmask.h"
54 /* We reduce the force array in blocks of 32 atoms. This is large enough
55 * to not cause overhead and 32*sizeof(rvec) is a multiple of the cache-line
56 * size on all systems.
58 static const int reduction_block_size = 32; /**< Force buffer block size in atoms*/
59 static const int reduction_block_bits = 5; /**< log2(reduction_block_size) */
61 /*! \internal \brief The division of bonded interactions of the threads */
66 WorkDivision(int numThreads) : stride_(numThreads + 1), packedBounds_(F_NRE * stride_) {}
68 //! Sets the bound between threads \p boundIndex-1 and \p boundIndex to \p count
69 void setBound(int functionType, int boundIndex, int count)
71 packedBounds_[functionType * stride_ + boundIndex] = count;
74 //! Returns the bound between threads \p boundIndex-1 and \p boundIndex
75 int bound(int functionType, int boundIndex) const
77 return packedBounds_[functionType * stride_ + boundIndex];
80 //! Returns the last bound
81 int end(int ftype) const { return bound(ftype, stride_ - 1); }
84 //! The stride_ between and size of the entries for a function type
86 //! The bounds stored as a flat array for fast access
87 std::vector<int> packedBounds_;
90 /*! \internal \brief struct with output for bonded forces, used per thread */
94 f_thread_t(int numEnergyGroups);
98 rvec4* f = nullptr; /**< Force array */
99 int f_nalloc = 0; /**< Allocation size of f */
100 gmx_bitmask_t* mask =
101 nullptr; /**< Mask for marking which parts of f are filled, working array for constructing mask in bonded_threading_t */
102 int nblock_used; /**< Number of blocks touched by our thread */
103 int* block_index = nullptr; /**< Index to touched blocks, size nblock_used */
104 int block_nalloc = 0; /**< Allocation size of f (*reduction_block_size), mask_index, mask */
106 rvec* fshift; /**< Shift force array, size SHIFTS */
107 real ener[F_NRE]; /**< Energy array */
108 gmx_grppairener_t grpp; /**< Group pair energy data for pairs */
109 real dvdl[efptNR]; /**< Free-energy dV/dl output */
112 /*! \internal \brief struct contain all data for bonded force threading */
113 struct bonded_threading_t
116 bonded_threading_t(int numThreads, int numEnergyGroups);
118 //! Number of threads to be used for bondeds
120 //! Force/energy data per thread, size nthreads, stored in unique_ptr to allow thread local allocation
121 std::vector<std::unique_ptr<f_thread_t>> f_t;
122 //! The number of force blocks to reduce
124 //! Index of size nblock_used into mask
125 std::vector<int> block_index;
126 //! Mask array, one element corresponds to a block of reduction_block_size atoms of the force array, bit corresponding to thread indices set if a thread writes to that block
127 std::vector<gmx_bitmask_t> mask;
128 //! true if we have and thus need to reduce bonded forces
131 /* There are two different ways to distribute the bonded force calculation
132 * over the threads. We dedice which to use based on the number of threads.
134 //! Maximum thread count for uniform distribution of bondeds over threads
135 int max_nthread_uniform;
137 //! The division of work in the t_list over threads.
138 WorkDivision workDivision;
140 //! Work division for free-energy foreign lambda calculations, always uses 1 thread
141 WorkDivision foreignLambdaWorkDivision;
145 /*! \brief Returns the global topology atom number belonging to local
148 * This function is intended for writing ascii output and returns atom
149 * numbers starting at 1. When global_atom_index=NULL returns i+1.
151 int glatnr(const int* global_atom_index, int i);