src/gromacs/mdlib/mdatoms.h

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  38 #ifndef GMX_MDLIB_MDATOMS_H
  39 #define GMX_MDLIB_MDATOMS_H
  40
  41 #include <cstdio>
  42
  43 #include <memory>
  44 #include <vector>
  45
  46 #include "gromacs/gpu_utils/hostallocator.h"
  47 #include "gromacs/mdtypes/mdatom.h"
  48 #include "gromacs/utility/basedefinitions.h"
  49 #include "gromacs/utility/real.h"
  50 #include "gromacs/utility/unique_cptr.h"
  51
  52 struct gmx_mtop_t;
  53 struct t_inputrec;
  54
  55 namespace gmx
  56 {
  57
  58 /*! \libinternal
  59  * \brief Contains a C-style t_mdatoms while managing some of its
  60  * memory with C++ vectors with allocators.
  61  *
  62  * \todo The group-scheme kernels needed a plain C-style t_mdatoms, so
  63  * this type combines that with the memory management needed for
  64  * efficient PME on GPU transfers. The mdatoms_ member should be
  65  * removed. */
  66 class MDAtoms
  67 {
  68     //! C-style mdatoms struct.
  69     unique_cptr<t_mdatoms> mdatoms_;
  70     //! Memory for chargeA that can be set up for efficient GPU transfer.
  71     gmx::PaddedHostVector<real> chargeA_;
  72
  73 public:
  74     // TODO make this private
  75     MDAtoms();
  76     ~MDAtoms();
  77     //! Getter.
  78     t_mdatoms* mdatoms() { return mdatoms_.get(); }
  79     //! Const getter.
  80     const t_mdatoms* mdatoms() const { return mdatoms_.get(); }
  81     /*! \brief Resizes memory.
  82      *
  83      * \throws std::bad_alloc  If out of memory.
  84      */
  85     void resize(int newSize);
  86     /*! \brief Reserves memory.
  87      *
  88      * \throws std::bad_alloc  If out of memory.
  89      */
  90     void reserve(int newCapacity);
  91     //! Builder function.
  92     friend std::unique_ptr<MDAtoms>
  93     makeMDAtoms(FILE* fp, const gmx_mtop_t& mtop, const t_inputrec& ir, bool rankHasPmeGpuTask);
  94 };
  95
  96 //! Builder function for MdAtomsWrapper.
  97 std::unique_ptr<MDAtoms> makeMDAtoms(FILE* fp, const gmx_mtop_t& mtop, const t_inputrec& ir, bool useGpuForPme);
  98
  99 } // namespace gmx
 100
 101 void atoms2md(const gmx_mtop_t* mtop,
 102               const t_inputrec* ir,
 103               int               nindex,
 104               const int*        index,
 105               int               homenr,
 106               gmx::MDAtoms*     mdAtoms);
 107 /* This routine copies the atoms->atom struct into md.
 108  * If index!=NULL only the indexed atoms are copied.
 109  * For the masses the A-state (lambda=0) mass is used.
 110  * Sets md->lambda = 0.
 111  * In free-energy runs, update_mdatoms() should be called after atoms2md()
 112  * to set the masses corresponding to the value of lambda at each step.
 113  */
 114
 115 void update_mdatoms(t_mdatoms* md, real lambda);
 116 /* When necessary, sets all the mass parameters to values corresponding
 117  * to the free-energy parameter lambda.
 118  * Sets md->lambda = lambda.
 119  */
 120
 121 #endif