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/utility/basedefinitions.h"
  48 #include "gromacs/utility/real.h"
  49 #include "gromacs/utility/unique_cptr.h"
  50
  51 struct gmx_mtop_t;
  52 struct t_inputrec;
  53 struct t_mdatoms;
  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     //! Memory for chargeB that can be set up for efficient GPU transfer.
  73     gmx::PaddedHostVector<real> chargeB_;
  74
  75 public:
  76     // TODO make this private
  77     MDAtoms();
  78     ~MDAtoms();
  79     //! Getter.
  80     t_mdatoms* mdatoms() { return mdatoms_.get(); }
  81     //! Const getter.
  82     const t_mdatoms* mdatoms() const { return mdatoms_.get(); }
  83     /*! \brief Resizes memory for charges of FEP state A.
  84      *
  85      * \throws std::bad_alloc  If out of memory.
  86      */
  87     void resizeChargeA(int newSize);
  88     /*! \brief Resizes memory for charges of FEP state B.
  89      *
  90      * \throws std::bad_alloc  If out of memory.
  91      */
  92     void resizeChargeB(int newSize);
  93     /*! \brief Reserves memory for charges of FEP state A.
  94      *
  95      * \throws std::bad_alloc  If out of memory.
  96      */
  97     void reserveChargeA(int newCapacity);
  98     /*! \brief Reserves memory for charges of FEP state B.
  99      *
 100      * \throws std::bad_alloc  If out of memory.
 101      */
 102     void reserveChargeB(int newCapacity);
 103     //! Builder function.
 104     friend std::unique_ptr<MDAtoms>
 105     makeMDAtoms(FILE* fp, const gmx_mtop_t& mtop, const t_inputrec& ir, bool rankHasPmeGpuTask);
 106 };
 107
 108 //! Builder function for MdAtomsWrapper.
 109 std::unique_ptr<MDAtoms> makeMDAtoms(FILE* fp, const gmx_mtop_t& mtop, const t_inputrec& ir, bool useGpuForPme);
 110
 111 } // namespace gmx
 112
 113 void atoms2md(const gmx_mtop_t*  mtop,
 114               const t_inputrec*  ir,
 115               int                nindex,
 116               gmx::ArrayRef<int> index,
 117               int                homenr,
 118               gmx::MDAtoms*      mdAtoms);
 119 /* This routine copies the atoms->atom struct into md.
 120  * If index!=NULL only the indexed atoms are copied.
 121  * For the masses the A-state (lambda=0) mass is used.
 122  * Sets md->lambda = 0.
 123  * In free-energy runs, update_mdatoms() should be called after atoms2md()
 124  * to set the masses corresponding to the value of lambda at each step.
 125  */
 126
 127 void update_mdatoms(t_mdatoms* md, real lambda);
 128 /* When necessary, sets all the mass parameters to values corresponding
 129  * to the free-energy parameter lambda.
 130  * Sets md->lambda = lambda.
 131  */
 132
 133 #endif