src/gromacs/listed-forces/listed-internal.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2014,2015,2016,2018,2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \internal \file
  36  *
  37  * \brief This file contains declarations for functions needed
  38  * internally by the module.
  39  *
  40  * \author Mark Abraham <mark.j.abraham@gmail.com>
  41  * \ingroup module_listed-forces
  42  */
  43 #ifndef GMX_LISTED_FORCES_LISTED_INTERNAL_H
  44 #define GMX_LISTED_FORCES_LISTED_INTERNAL_H
  45
  46 #include "gromacs/math/vectypes.h"
  47 #include "gromacs/mdtypes/enerdata.h"
  48 #include "gromacs/topology/idef.h"
  49 #include "gromacs/topology/ifunc.h"
  50 #include "gromacs/utility/bitmask.h"
  51
  52 /* We reduce the force array in blocks of 32 atoms. This is large enough
  53  * to not cause overhead and 32*sizeof(rvec) is a multiple of the cache-line
  54  * size on all systems.
  55  */
  56 static const int reduction_block_size = 32; /**< Force buffer block size in atoms*/
  57 static const int reduction_block_bits =  5; /**< log2(reduction_block_size) */
  58
  59 /*! \internal \brief struct with output for bonded forces, used per thread */
  60 typedef struct
  61 {
  62     rvec4            *f;            /**< Force array */
  63     int               f_nalloc;     /**< Allocation size of f */
  64     gmx_bitmask_t    *mask;         /**< Mask for marking which parts of f are filled, working array for constructing mask in bonded_threading_t */
  65     int               nblock_used;  /**< Number of blocks touched by our thread */
  66     int              *block_index;  /**< Index to touched blocks, size nblock_used */
  67     int               block_nalloc; /**< Allocation size of f (*reduction_block_size), mask_index, mask */
  68
  69     rvec             *fshift;       /**< Shift force array, size SHIFTS */
  70     real              ener[F_NRE];  /**< Energy array */
  71     gmx_grppairener_t grpp;         /**< Group pair energy data for pairs */
  72     real              dvdl[efptNR]; /**< Free-energy dV/dl output */
  73 }
  74 f_thread_t;
  75
  76 /*! \internal \brief struct contain all data for bonded force threading */
  77 struct bonded_threading_t
  78 {
  79     /* Thread local force and energy data */
  80     int            nthreads;     /**< Number of threads to be used for bondeds */
  81     f_thread_t    *f_t;          /**< Force/energy data per thread, size nthreads */
  82     int            nblock_used;  /**< The number of force blocks to reduce */
  83     int           *block_index;  /**< Index of size nblock_used into mask */
  84     gmx_bitmask_t *mask;         /**< 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 */
  85     int            block_nalloc; /**< Allocation size of block_index and mask */
  86
  87     bool           haveBondeds;  /**< true if we have and thus need to reduce bonded forces */
  88
  89     /* There are two different ways to distribute the bonded force calculation
  90      * over the threads. We dedice which to use based on the number of threads.
  91      */
  92     int  max_nthread_uniform;       /**< Maximum thread count for uniform distribution of bondeds over threads */
  93
  94     int *il_thread_division;        /**< Stores the division of work in the t_list over threads.
  95                                      *
  96                                      * The division of the normal bonded interactions of threads.
  97                                      * il_thread_division[ftype*(nthreads+1)+t] contains an index
  98                                      * into il[ftype].iatoms; thread th operates on t=th to t=th+1. */
  99     int  il_thread_division_nalloc; /**< Allocation size of the work division, at least F_NRE*(nthreads+1). */
 100 };
 101
 102
 103 /*! \brief Returns the global topology atom number belonging to local
 104  * atom index i.
 105  *
 106  * This function is intended for writing ascii output and returns atom
 107  * numbers starting at 1.  When global_atom_index=NULL returns i+1.
 108  */
 109 int
 110 glatnr(const int *global_atom_index, int i);
 111
 112 #endif