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37 * \defgroup module_imd Interactive molecular dynamics (IMD)
38 * \ingroup group_mdrun
41 * Allows mdrun to interface with VMD via the interactive molecular dynamics
44 * \author Martin Hoefling, Carsten Kutzner <ckutzne@gwdg.de>
48 /*! \libinternal \file
51 * This file contains datatypes and function declarations necessary for mdrun
52 * to interface with VMD via the interactive molecular dynamics protocol.
54 * \author Martin Hoefling, Carsten Kutzner <ckutzne@gwdg.de>
64 #include "../fileio/filenm.h"
65 #include "../timing/wallcycle.h"
67 #ifdef GMX_NATIVE_WINDOWS
77 static const char IMDstr[] = "IMD:"; /**< Tag output from the IMD module with this string. */
80 /*! \brief Writes out the group of atoms selected for interactive manipulation.
83 * The resulting file has to be read in by VMD if one wants it to connect to mdrun.
85 * \param bIMD Only springs into action if bIMD is TRUE. Otherwise returns directly.
86 * \param ir Structure containing MD input parameters, among those
87 * the IMD data structure.
88 * \param state The current state of the MD system.
89 * \param sys The global, complete system topology.
90 * \param nfile Number of files.
91 * \param fnm Filename struct.
93 extern void write_IMDgroup_to_file(gmx_bool bIMD, t_inputrec *ir, t_state *state,
94 gmx_mtop_t *sys, int nfile, const t_filenm fnm[]);
97 /*! \brief Make a selection of the home atoms for the IMD group.
99 * Should be called at every domain decomposition.
100 * Each node checks which of the atoms from "ind" are local and puts its local
101 * atom numbers into the "ind_local" array. Furthermore, in "xa_ind" it is
102 * stored at which position each local atom belongs in the assembled/collective
103 * array, so that on the master node all positions can be merged into the
104 * assembled array correctly.
106 * \param bIMD Only springs into action if bIMD is TRUE. Otherwise returns directly.
107 * \param dd Structure containing domain decomposition data.
108 * \param imd The IMD group of atoms.
110 extern void dd_make_local_IMD_atoms(gmx_bool bIMD, gmx_domdec_t *dd, t_IMD *imd);
113 /*! \brief Initializes (or disables) IMD.
115 * This function is called before the main MD loop over time steps,
116 * and it must be called prior to any call to dd_partition_system if in parallel.
118 * \param ir The inputrec structure containing the MD input parameters
119 * including a pointer to the IMD data structure.
120 * \param cr Information structure for MPI communication.
121 * \param top_global The topology of the whole system.
122 * \param fplog General output file, normally md.log.
123 * \param defnstimd Default IMD update (=communication) frequency.
124 * \param x The starting positions of the atoms.
125 * \param nfile Number of files.
126 * \param fnm Struct containing file names etc.
127 * \param oenv Output options.
128 * \param imdport Port to use for IMD connections.
129 * \param Flags Flags passed over from main, used to determine
130 * whether or not we are appending.
132 extern void init_IMD(t_inputrec *ir, t_commrec *cr, gmx_mtop_t *top_global,
133 FILE *fplog, int defnstimd, rvec x[],
134 int nfile, const t_filenm fnm[], output_env_t oenv,
135 int imdport, unsigned long Flags);
138 /*! \brief IMD required in this time step?
139 * Also checks for new IMD connection and syncs the nodes.
141 * \param bIMD Only springs into action if bIMD is TRUE. Otherwise returns directly.
142 * \param step The time step.
143 * \param cr Information structure for MPI communication.
144 * \param bNS Is this a neighbor searching step?
145 * \param box The simulation box.
146 * \param x The local atomic positions on this node.
147 * \param ir The inputrec structure containing the MD input parameters
148 * including a pointer to the IMD data structure.
150 * \param wcycle Count wallcycles of IMD routines for diagnostic output.
152 * \returns Whether or not we have to do IMD communication at this step.
154 extern gmx_bool do_IMD(gmx_bool bIMD, gmx_int64_t step, t_commrec *cr, gmx_bool bNS,
155 matrix box, rvec x[], t_inputrec *ir, double t,
156 gmx_wallcycle_t wcycle);
159 /*! \brief Get the IMD update frequency.
161 * \param IMDsetup Opaque pointer to IMD private data.
163 * \returns The current IMD update/communication frequency
165 extern int IMD_get_step(t_gmx_IMD IMDsetup);
168 /*! \brief Add external forces from a running interactive molecular dynamics session.
170 * \param bIMD Returns directly if bIMD is FALSE.
171 * \param imd The IMD data structure.
172 * \param cr Information structure for MPI communication.
173 * \param f The forces.
174 * \param wcycle Count wallcycles of IMD routines for diagnostic output.
176 extern void IMD_apply_forces(gmx_bool bIMD, t_IMD *imd, t_commrec *cr, rvec *f,
177 gmx_wallcycle_t wcycle);
180 /*! \brief Copy energies and convert to float from enerdata to the IMD energy record.
182 * We do no conversion, so units in client are SI!
184 * \param bIMD Only springs into action if bIMD is TRUE. Otherwise returns directly.
185 * \param imd The IMD data structure.
186 * \param enerd Contains the GROMACS energies for the different interaction types.
187 * \param step The time step.
188 * \param bHaveNewEnergies Only copy energies if we have done global summing of them before.
191 extern void IMD_fill_energy_record(gmx_bool bIMD, t_IMD *imd, gmx_enerdata_t *enerd,
192 gmx_int64_t step, gmx_bool bHaveNewEnergies);
195 /*! \brief Send positions and energies to the client.
197 * \param imd The IMD data structure.
199 extern void IMD_send_positions(t_IMD *imd);
202 /*! \brief Calls IMD_prepare_energies() and then IMD_send_positions().
204 * \param bIMD Returns directly if bIMD is FALSE.
205 * \param bIMDstep If true, transfer the positions. Otherwise just update the time step and potentially the energy record.
206 * \param imd The IMD data structure.
207 * \param enerd Contains the GROMACS energies for the different interaction types.
208 * \param step The time step.
209 * \param bHaveNewEnergies Only update the energy record if we have done global summing of the energies.
210 * \param wcycle Count wallcycles of IMD routines for diagnostic output.
213 extern void IMD_prep_energies_send_positions(gmx_bool bIMD, gmx_bool bIMDstep,
214 t_IMD *imd, gmx_enerdata_t *enerd,
215 gmx_int64_t step, gmx_bool bHaveNewEnergies,
216 gmx_wallcycle_t wcycle);
218 /*! \brief Finalize IMD and do some cleaning up.
220 * Currently, IMD finalize closes the force output file.
222 * \param bIMD Returns directly if bIMD is FALSE.
223 * \param imd The IMD data structure.
225 extern void IMD_finalize(gmx_bool bIMD, t_IMD *imd);