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37 /*! \libinternal \file
40 * Declares functions to calculate both essential dynamics constraints
41 * as well as flooding potentials and forces.
43 * \authors Bert de Groot <bgroot@gwdg.de>, Oliver Lange <oliver.lange@tum.de>,
44 * Carsten Kutzner <ckutzne@gwdg.de>
48 #ifndef GMX_ESSENTIALDYNAMICS_EDSAM_H
49 #define GMX_ESSENTIALDYNAMICS_EDSAM_H
52 #include "gromacs/fileio/filenm.h"
58 /*! \brief Applies essential dynamics constrains as defined in the .edi input file.
60 * \param ir MD input parameter record.
61 * \param step Number of the time step.
62 * \param cr Data needed for MPI communication.
63 * \param xs The local positions on this processor.
64 * \param v The local velocities.
65 * \param box The simulation box.
66 * \param ed The essential dynamics data.
68 void do_edsam(t_inputrec *ir, gmx_int64_t step,
69 t_commrec *cr, rvec xs[], rvec v[], matrix box, gmx_edsam_t ed);
72 /*! \brief Reads in the .edi file containing the essential dynamics and flooding data.
74 * This function opens the ED input and output files, reads in all datasets it finds
75 * in the input file, and cross-checks whether the .edi file information is consistent
76 * with the essential dynamics data found in the checkpoint file (if present).
77 * gmx make_edi can be used to create an .edi input file.
79 * \param natoms Number of atoms of the whole MD system.
80 * \param EDstate Essential dynamics and flooding data stored in the checkpoint file.
81 * \param nfile Number of entries (files) in the fnm structure.
82 * \param fnm The filenames struct; it contains also the names of the
83 * essential dynamics and flooding in + output files.
84 * \param Flags Flags passed over from main, used to determine
85 * whether we are appending.
86 * \param oenv Needed to open the output xvgr file.
87 * \param cr Data needed for MPI communication.
88 * \returns Pointer to the initialized essential dynamics / flooding data.
90 gmx_edsam_t ed_open(int natoms, edsamstate_t *EDstate, int nfile, const t_filenm fnm[],
91 unsigned long Flags, const output_env_t oenv, t_commrec *cr);
94 /*! \brief Initializes the essential dynamics and flooding module.
96 * \param mtop Molecular topology.
97 * \param ir MD input parameter record.
98 * \param cr Data needed for MPI communication.
99 * \param ed The essential dynamics data.
100 * \param x Positions of the whole MD system.
101 * \param box The simulation box.
102 * \param EDstate ED data stored in the checkpoint file.
104 void init_edsam(gmx_mtop_t *mtop, t_inputrec *ir, t_commrec *cr,
105 gmx_edsam_t ed, rvec x[], matrix box, edsamstate_t *EDstate);
108 /*! \brief Make a selection of the home atoms for the ED groups.
110 * Should be called at every domain decomposition.
112 * \param dd Domain decomposition data.
113 * \param ed Essential dynamics and flooding data.
115 void dd_make_local_ed_indices(gmx_domdec_t *dd, gmx_edsam_t ed);
118 /*! \brief Evaluate the flooding potential(s) and forces as requested in the .edi input file.
120 * \param cr Data needed for MPI communication.
121 * \param ir MD input parameter record.
122 * \param x Positions on the local processor.
123 * \param force Forcefield forces to which the flooding forces are added.
124 * \param ed The essential dynamics data.
125 * \param box The simulation box.
126 * \param step Number of the time step.
127 * \param bNS Are we in a neighbor searching step?
129 void do_flood(t_commrec *cr, t_inputrec *ir, rvec x[], rvec force[], gmx_edsam_t ed,
130 matrix box, gmx_int64_t step, gmx_bool bNS);