src/gromacs/essentialdynamics/edsam.h

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  37 /*! \libinternal \file
  38  *
  39  * \brief
  40  * Declares functions to calculate both essential dynamics constraints
  41  * as well as flooding potentials and forces.
  42  *
  43  * \authors Bert de Groot <bgroot@gwdg.de>, Oliver Lange <oliver.lange@tum.de>,
  44  * Carsten Kutzner <ckutzne@gwdg.de>
  45  *
  46  * \inlibraryapi
  47  */
  48 #ifndef GMX_ESSENTIALDYNAMICS_EDSAM_H
  49 #define GMX_ESSENTIALDYNAMICS_EDSAM_H
  50
  51 #include <memory>
  52
  53 #include "gromacs/math/vectypes.h"
  54 #include "gromacs/utility/basedefinitions.h"
  55 #include "gromacs/utility/classhelpers.h"
  56
  57 /*! \brief Abstract type for essential dynamics
  58  *
  59  * The main type is defined only in edsam.cpp
  60  */
  61 struct gmx_edsam;
  62 struct gmx_domdec_t;
  63 struct gmx_mtop_t;
  64 struct gmx_output_env_t;
  65 struct ObservablesHistory;
  66 struct t_commrec;
  67 struct t_filenm;
  68 struct t_inputrec;
  69 class t_state;
  70
  71 namespace gmx
  72 {
  73 class Constraints;
  74 class EssentialDynamics
  75 {
  76     public:
  77         EssentialDynamics();
  78         ~EssentialDynamics();
  79
  80         /*! \brief Getter for working data
  81          *
  82          * This is needed while the module is still under
  83          * construction. */
  84         gmx_edsam *getLegacyED();
  85     private:
  86         class Impl;
  87
  88         PrivateImplPointer<Impl> impl_;
  89 };
  90 } // namespace gmx
  91
  92 /*! \brief Applies essential dynamics constrains as defined in the .edi input file.
  93  *
  94  * \param ir                MD input parameter record.
  95  * \param step              Number of the time step.
  96  * \param cr                Data needed for MPI communication.
  97  * \param xs                The local positions on this processor.
  98  * \param v                 The local velocities.
  99  * \param box               The simulation box.
 100  * \param ed                The essential dynamics data.
 101  */
 102 void do_edsam(const t_inputrec *ir, int64_t step,
 103               const t_commrec *cr, rvec xs[], rvec v[], matrix box, gmx_edsam *ed);
 104
 105
 106 /*! \brief Initializes the essential dynamics and flooding module.
 107  *
 108  * \param ediFileName       Essential dynamics input file.
 109  * \param edoFileName       Output file for essential dynamics data.
 110  * \param mtop              Molecular topology.
 111  * \param ir                MD input parameter record.
 112  * \param cr                Data needed for MPI communication.
 113  * \param constr            Data structure keeping the constraint information.
 114  * \param globalState       The global state, only used on the master rank.
 115  * \param oh                The observables history container.
 116  * \param oenv              The output environment information.
 117  * \param bAppend           Append to existing output files?
 118  *
 119  * \returns                 A pointer to the ED data structure.
 120  */
 121 std::unique_ptr<gmx::EssentialDynamics> init_edsam(
 122         const char             *ediFileName,
 123         const char             *edoFileName,
 124         const gmx_mtop_t       *mtop,
 125         const t_inputrec       *ir,
 126         const t_commrec        *cr,
 127         gmx::Constraints       *constr,
 128         const t_state          *globalState,
 129         ObservablesHistory     *oh,
 130         const gmx_output_env_t *oenv,
 131         gmx_bool                bAppend);
 132
 133 /*! \brief Make a selection of the home atoms for the ED groups.
 134  *
 135  * Should be called at every domain decomposition.
 136  *
 137  * \param dd                Domain decomposition data.
 138  * \param ed                Essential dynamics and flooding data.
 139  */
 140 void dd_make_local_ed_indices(gmx_domdec_t *dd, gmx_edsam * ed);
 141
 142
 143 /*! \brief Evaluate the flooding potential(s) and forces as requested in the .edi input file.
 144  *
 145  * \param cr                Data needed for MPI communication.
 146  * \param ir                MD input parameter record.
 147  * \param x                 Positions on the local processor.
 148  * \param force             Forcefield forces to which the flooding forces are added.
 149  * \param ed                The essential dynamics data.
 150  * \param box               The simulation box.
 151  * \param step              Number of the time step.
 152  * \param bNS               Are we in a neighbor searching step?
 153  */
 154 void do_flood(const t_commrec  *cr,
 155               const t_inputrec *ir,
 156               const rvec        x[],
 157               rvec              force[],
 158               const gmx_edsam  *ed,
 159               matrix            box,
 160               int64_t           step,
 161               gmx_bool          bNS);
 162
 163 #endif