src/gromacs/mdlib/md_support.h

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  38 #ifndef GMX_MDLIB_MD_SUPPORT_H
  39 #define GMX_MDLIB_MD_SUPPORT_H
  40
  41 #include "gromacs/mdlib/vcm.h"
  42 #include "gromacs/timing/wallcycle.h"
  43
  44 struct gmx_ekindata_t;
  45 struct gmx_enerdata_t;
  46 struct gmx_global_stat;
  47 struct gmx_multisim_t;
  48 struct gmx_signalling_t;
  49 struct t_extmass;
  50 struct t_forcerec;
  51 struct t_grpopts;
  52 struct t_inputrec;
  53 struct t_lambda;
  54 struct t_nrnb;
  55 class t_state;
  56 struct t_trxframe;
  57
  58 namespace gmx
  59 {
  60 template<typename T>
  61 class ArrayRef;
  62 class Constraints;
  63 class MDLogger;
  64 class SimulationSignaller;
  65 } // namespace gmx
  66
  67 /* Define a number of flags to better control the information
  68  * passed to compute_globals in md.c and global_stat.
  69  */
  70
  71 /* we are computing the kinetic energy from average velocities */
  72 #define CGLO_EKINAVEVEL (1u << 2u)
  73 /* we are removing the center of mass momenta */
  74 #define CGLO_STOPCM (1u << 3u)
  75 /* bGStat is defined in do_md */
  76 #define CGLO_GSTAT (1u << 4u)
  77 /* Sum the energy terms in global computation */
  78 #define CGLO_ENERGY (1u << 6u)
  79 /* Sum the kinetic energy terms in global computation */
  80 #define CGLO_TEMPERATURE (1u << 7u)
  81 /* Sum the kinetic energy terms in global computation */
  82 #define CGLO_PRESSURE (1u << 8u)
  83 /* Sum the constraint term in global computation */
  84 #define CGLO_CONSTRAINT (1u << 9u)
  85 /* Reading ekin from the trajectory */
  86 #define CGLO_READEKIN (1u << 10u)
  87 /* we need to reset the ekin rescaling factor here */
  88 #define CGLO_SCALEEKIN (1u << 11u)
  89 /* After a new DD partitioning, we need to set a flag to schedule
  90  * global reduction of the total number of bonded interactions that
  91  * will be computed, to check none are missing. */
  92 #define CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS (1u << 12u)
  93
  94
  95 /*! \brief Return the number of steps that will take place between
  96  * intra-simulation communications, given the constraints of the
  97  * inputrec. */
  98 int computeGlobalCommunicationPeriod(const gmx::MDLogger& mdlog, t_inputrec* ir, const t_commrec* cr);
  99
 100 /*! \brief Return true if the \p value is equal across the set of multi-simulations
 101  *
 102  * \todo This duplicates some of check_multi_int. Consolidate. */
 103 bool multisim_int_all_are_equal(const gmx_multisim_t* ms, int64_t value);
 104
 105 void rerun_parallel_comm(t_commrec* cr, t_trxframe* fr, gmx_bool* bLastStep);
 106
 107 //! \brief Allocate and initialize node-local state entries
 108 void set_state_entries(t_state* state, const t_inputrec* ir);
 109
 110 /* Set the lambda values in the global state from a frame read with rerun */
 111 void setCurrentLambdasRerun(int64_t           step,
 112                             const t_lambda*   fepvals,
 113                             const t_trxframe* rerun_fr,
 114                             const double*     lam0,
 115                             t_state*          globalState);
 116
 117 /* Set the lambda values at each step of mdrun when they change */
 118 void setCurrentLambdasLocal(int64_t             step,
 119                             const t_lambda*     fepvals,
 120                             const double*       lam0,
 121                             gmx::ArrayRef<real> lambda,
 122                             int                 currentFEPState);
 123
 124 int multisim_min(const gmx_multisim_t* ms, int nmin, int n);
 125 /* Set an appropriate value for n across the whole multi-simulation */
 126
 127
 128 /* Compute global variables during integration
 129  *
 130  * Coordinates x are needed for kinetic energy calculation with cosine accelation
 131  * and for COM removal with rotational and acceleration correction modes.
 132  * Velocities v are needed for kinetic energy calculation and for COM removal.
 133  */
 134 void compute_globals(gmx_global_stat*          gstat,
 135                      t_commrec*                cr,
 136                      const t_inputrec*         ir,
 137                      t_forcerec*               fr,
 138                      gmx_ekindata_t*           ekind,
 139                      const rvec*               x,
 140                      const rvec*               v,
 141                      const matrix              box,
 142                      real                      vdwLambda,
 143                      const t_mdatoms*          mdatoms,
 144                      t_nrnb*                   nrnb,
 145                      t_vcm*                    vcm,
 146                      gmx_wallcycle_t           wcycle,
 147                      gmx_enerdata_t*           enerd,
 148                      tensor                    force_vir,
 149                      tensor                    shake_vir,
 150                      tensor                    total_vir,
 151                      tensor                    pres,
 152                      rvec                      mu_tot,
 153                      gmx::Constraints*         constr,
 154                      gmx::SimulationSignaller* signalCoordinator,
 155                      const matrix              lastbox,
 156                      int*                      totalNumberOfBondedInteractions,
 157                      gmx_bool*                 bSumEkinhOld,
 158                      int                       flags);
 159
 160 #endif