src/gromacs/mdlib/mdrun.h

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  37
  38 /*! \libinternal \file
  39  *
  40  * \brief This file declares types and functions for initializing an MD run
  41  *
  42  * \author Berk Hess <hess@kth.se>
  43  * \inlibraryapi
  44  */
  45
  46 #ifndef GMX_MDLIB_MDRUN_H
  47 #define GMX_MDLIB_MDRUN_H
  48
  49 #include "gromacs/timing/wallcycle.h"
  50 #include "gromacs/utility/real.h"
  51
  52 struct gmx_mtop_t;
  53 struct t_commrec;
  54 struct t_inputrec;
  55 class t_state;
  56
  57 //! \internal \brief Options and settings for continuing from checkpoint
  58 struct ContinuationOptions
  59 {
  60     //! True if we are continuing from a checkpoint and should append output files
  61     bool appendFiles = false;
  62     //! True if the -append option was explicitly set by the user (either to true of false
  63     bool appendFilesOptionSet = false;
  64     //! True if we started from a checkpoint file
  65     bool startedFromCheckpoint = false;
  66     //! True if we read the kinetic energy from checkpoint file
  67     bool haveReadEkin = false;
  68 };
  69
  70 //! \internal \brief Options for writing checkpoint files
  71 struct CheckpointOptions
  72 {
  73     //! True means keep all checkpoint file and add the step number to the name
  74     gmx_bool keepAndNumberCheckpointFiles = FALSE;
  75     //! The period in minutes for writing checkpoint files
  76     real     period = 15;
  77 };
  78
  79 //! \internal \brief Options for timing (parts of) mdrun
  80 struct TimingOptions
  81 {
  82     //! Reset timers at the start of this MD step, -1 means do not reset
  83     int      resetStep = -1;
  84     //! If true, reset timers half-way the run
  85     gmx_bool resetHalfway = FALSE;
  86 };
  87
  88 //! \internal \brief Options for IMD
  89 struct ImdOptions
  90 {
  91     //! IMD listening port
  92     int      port = 8888;
  93     //! If true, pause the simulation while no IMD client is connected
  94     gmx_bool wait = FALSE;
  95     //! If true, allow termination of the simulation from IMD client
  96     gmx_bool terminatable = FALSE;
  97     //! If true, allow COM pulling in the simulation from IMD client
  98     gmx_bool pull = FALSE;
  99 };
 100
 101 //! \internal \brief Collection of all options of mdrun that are not processed separately
 102 struct MdrunOptions
 103 {
 104     //! Re-compute energies, and possibly forces, for frames from an input tracjectory
 105     gmx_bool            rerun = FALSE;
 106     //! Re-construct virual sites durin a rerun simulation
 107     gmx_bool            rerunConstructVsites = FALSE;
 108     //! Request to do global communication at this interval in steps, -1 is determine from inputrec
 109     int                 globalCommunicationInterval = -1;
 110     //! Try to make the simulation binary reproducible
 111     gmx_bool            reproducible = FALSE;
 112     //! Write confout.gro at the end of the run
 113     gmx_bool            writeConfout = TRUE;
 114     //! Options for continuing a simulation from a checkpoint file
 115     ContinuationOptions continuationOptions;
 116     //! Options for checkpointing th simulation
 117     CheckpointOptions   checkpointOptions;
 118     //! Number of steps to run, -2 is use inputrec, -1 is infinite
 119     int64_t             numStepsCommandline = -2;
 120     //! Maximum duration of this simulation in wall-clock hours, -1 is no limit
 121     real                maximumHoursToRun = -1;
 122     //! Options for timing the run
 123     TimingOptions       timingOptions;
 124     //! If true and supported, will tune the PP-PME load balance
 125     gmx_bool            tunePme = TRUE;
 126     //! True if the user explicitly set the -ntomp command line option
 127     gmx_bool            ntompOptionIsSet = FALSE;
 128     //! Options for IMD
 129     ImdOptions          imdOptions;
 130     //! Increase the verbosity level in the logging and/or stdout/stderr
 131     gmx_bool            verbose = FALSE;
 132     //! If verbose=true, print remaining runtime at this step interval
 133     int                 verboseStepPrintInterval = 100;
 134 };
 135
 136 //! \brief Allocate and initialize node-local state entries
 137 void set_state_entries(t_state *state, const t_inputrec *ir);
 138
 139 //! \brief Broadcast inputrec and mtop and allocate node-specific settings
 140 void init_parallel(t_commrec *cr, t_inputrec *inputrec,
 141                    gmx_mtop_t *mtop);
 142
 143 //! \brief Broadcasts the, non-dynamic, state from the master to all ranks in cr->mpi_comm_mygroup
 144 //
 145 // This is intended to be used with MPI parallelization without
 146 // domain decompostion (currently with NM and TPI).
 147 void broadcastStateWithoutDynamics(const t_commrec *cr, t_state *state);
 148
 149 #endif