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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
46 #include "gromacs/legacyheaders/types/forcerec.h"
47 #include "gromacs/math/vectypes.h"
48 #include "gromacs/topology/idef.h"
49 #include "gromacs/utility/bitmask.h"
51 /*! \internal \brief struct with output for bonded forces, used per thread */
54 rvec *f; /**< Force array */
55 int f_nalloc; /**< Allocation size of f */
56 gmx_bitmask_t red_mask; /**< Mask for marking which parts of f are filled */
57 rvec *fshift; /**< Shift force array, size SHIFTS */
58 real ener[F_NRE]; /**< Energy array */
59 gmx_grppairener_t grpp; /**< Group pair energy data for pairs */
60 real dvdl[efptNR]; /**< Free-energy dV/dl output */
64 /*! \internal \brief struct contain all data for bonded force threading */
65 struct bonded_threading_t
67 /* Thread local force and energy data */
68 int nthreads; /**< Number of threads to be used for bondeds */
69 int red_ashift; /**< Size of force reduction blocks in bits */
70 int red_nblock; /**< The number of force blocks to reduce */
71 f_thread_t *f_t; /**< Force/enegry data per thread, size nthreads */
73 /* There are two different ways to distribute the bonded force calculation
74 * over the threads. We dedice which to use based on the number of threads.
76 int bonded_max_nthread_uniform; /**< Maximum thread count for uniform distribution of bondeds over threads */
80 /*! \brief Returns the global topology atom number belonging to local
83 * This function is intended for writing ascii output and returns atom
84 * numbers starting at 1. When global_atom_index=NULL returns i+1.
87 glatnr(int *global_atom_index, int i);