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/*! \libinternal \file
*
* \brief Declares the routine running the inetgrators.
*
* \author David van der Spoel <david.vanderspoel@icm.uu.se>
* \ingroup module_mdlib
*/
#ifndef GMX_MDLIB_RUNNER_H
#define GMX_MDLIB_RUNNER_H
#include <cstdio>
#include <array>
#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/hardware/hw_info.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
#include "repl_ex.h"
struct gmx_output_env_t;
struct ReplicaExchangeParameters;
struct t_commrec;
namespace gmx
{
/*! \libinternal \brief Runner object for supporting setup and execution of mdrun.
*
* This class has responsibility for the lifetime of data structures
* that exist for the life of the simulation, e.g. for logging and
* communication.
*
* \todo Most of the attributes should be declared by specific modules
* as command-line options. Accordingly, they do not conform to the
* naming scheme, because that would make for a lot of noise in the
* diff, only to have it change again when the options move to their
* modules.
*
* \todo Preparing logging and MPI contexts could probably be a
* higher-level responsibility, so that an Mdrunner would get made
* without needing to re-initialize these components (as currently
* happens always for the master rank, and differently for the spawned
* ranks with thread-MPI).
*/
class Mdrunner
{
private:
//! Parallelism-related user options.
gmx_hw_opt_t hw_opt;
//! Filenames and properties from command-line argument values.
std::array<t_filenm, 35> filenames =
{{{ efTPR, nullptr, nullptr, ffREAD },
{ efTRN, "-o", nullptr, ffWRITE },
{ efCOMPRESSED, "-x", nullptr, ffOPTWR },
{ efCPT, "-cpi", nullptr, ffOPTRD | ffALLOW_MISSING },
{ efCPT, "-cpo", nullptr, ffOPTWR },
{ efSTO, "-c", "confout", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
{ efLOG, "-g", "md", ffWRITE },
{ efXVG, "-dhdl", "dhdl", ffOPTWR },
{ efXVG, "-field", "field", ffOPTWR },
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
{ efXVG, "-tableb", "table", ffOPTRDMULT },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
{ efEDI, "-ei", "sam", ffOPTRD },
{ efXVG, "-eo", "edsam", ffOPTWR },
{ efXVG, "-devout", "deviatie", ffOPTWR },
{ efXVG, "-runav", "runaver", ffOPTWR },
{ efXVG, "-px", "pullx", ffOPTWR },
{ efXVG, "-pf", "pullf", ffOPTWR },
{ efXVG, "-ro", "rotation", ffOPTWR },
{ efLOG, "-ra", "rotangles", ffOPTWR },
{ efLOG, "-rs", "rotslabs", ffOPTWR },
{ efLOG, "-rt", "rottorque", ffOPTWR },
{ efMTX, "-mtx", "nm", ffOPTWR },
{ efRND, "-multidir", nullptr, ffOPTRDMULT},
{ efDAT, "-plumed", "plumed", ffOPTRD }, /* PLUMED */
{ efXVG, "-awh", "awhinit", ffOPTRD },
{ efDAT, "-membed", "membed", ffOPTRD },
{ efTOP, "-mp", "membed", ffOPTRD },
{ efNDX, "-mn", "membed", ffOPTRD },
{ efXVG, "-if", "imdforces", ffOPTWR },
{ efXVG, "-swap", "swapions", ffOPTWR }}};
/*! \brief Filename arguments.
*
* Provided for compatibility with old C-style code accessing
* command-line arguments that are file names. */
t_filenm *fnm = filenames.data();
/*! \brief Number of filename argument values.
*
* Provided for compatibility with old C-style code accessing
* command-line arguments that are file names. */
int nfile = filenames.size();
//! Output context for writing text files
gmx_output_env_t *oenv = nullptr;
//! Ongoing collection of mdrun options
MdrunOptions mdrunOptions;
//! Options for the domain decomposition.
DomdecOptions domdecOptions;
//! Target short-range interations for "cpu", "gpu", or "auto". Default is "auto".
const char *nbpu_opt = nullptr;
//! Target long-range interactions for "cpu", "gpu", or "auto". Default is "auto".
const char *pme_opt = nullptr;
//! Target long-range interactions FFT/solve stages for "cpu", "gpu", or "auto". Default is "auto".
const char *pme_fft_opt = nullptr;
//! Command-line override for the duration of a neighbor list with the Verlet scheme.
int nstlist_cmdline = 0;
//! Number of simulations in multi-simulation set.
int nmultisim = 0;
//! Parameters for replica-exchange simulations.
ReplicaExchangeParameters replExParams;
//! Print a warning if any force is larger than this (in kJ/mol nm).
real pforce = -1;
//! Handle to file used for logging.
FILE *fplog;
//! Handle to communication data structure.
t_commrec *cr;
public:
/*! \brief Defaulted constructor.
*
* Note that when member variables are not present in the constructor
* member initialization list (which is true for the default constructor),
* then they are initialized with any default member initializer specified
* when they were declared, or default initialized. */
Mdrunner() = default;
//! Start running mdrun by calling its C-style main function.
int mainFunction(int argc, char *argv[]);
/*! \brief Driver routine, that calls the different simulation methods. */
int mdrunner();
//! Called when thread-MPI spawns threads.
t_commrec *spawnThreads(int numThreadsToLaunch);
/*! \brief Re-initializes the object after threads spawn.
*
* \todo Can this be refactored so that the Mdrunner on a spawned thread is
* constructed ready to use? */
void reinitializeOnSpawnedThread();
};
} // namespace gmx
#endif // GMX_MDLIB_RUNNER_H