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38 /*! \libinternal \file
41 * Declares functions to calculate both essential dynamics constraints
42 * as well as flooding potentials and forces.
44 * \authors Bert de Groot <bgroot@gwdg.de>, Oliver Lange <oliver.lange@tum.de>,
45 * Carsten Kutzner <ckutzne@gwdg.de>
49 #ifndef GMX_ESSENTIALDYNAMICS_EDSAM_H
50 #define GMX_ESSENTIALDYNAMICS_EDSAM_H
54 #include "gromacs/math/vectypes.h"
56 /*! \brief Abstract type for essential dynamics
58 * The main type is defined only in edsam.cpp
63 struct gmx_output_env_t;
64 struct ObservablesHistory;
72 enum class StartingBehavior;
77 class EssentialDynamics
83 /*! \brief Getter for working data
85 * This is needed while the module is still under
87 gmx_edsam* getLegacyED();
92 std::unique_ptr<Impl> impl_;
97 /*! \brief Applies essential dynamics constrains as defined in the .edi input file.
99 * \param ir MD input parameter record.
100 * \param step Number of the time step.
101 * \param cr Data needed for MPI communication.
102 * \param coords The local positions on this processor.
103 * \param velocities The local velocities.
104 * \param box The simulation box.
105 * \param ed The essential dynamics data.
107 void do_edsam(const t_inputrec* ir,
110 gmx::ArrayRef<gmx::RVec> coords,
111 gmx::ArrayRef<gmx::RVec> velocities,
116 /*! \brief Initializes the essential dynamics and flooding module.
118 * \param mdlog Logger.
119 * \param ediFileName Essential dynamics input file.
120 * \param edoFileName Output file for essential dynamics data.
121 * \param mtop Molecular topology.
122 * \param ir MD input parameter record.
123 * \param cr Data needed for MPI communication.
124 * \param constr Data structure keeping the constraint information.
125 * \param globalState The global state, only used on the master rank.
126 * \param oh The observables history container.
127 * \param oenv The output environment information.
128 * \param startingBehavior Describes whether this is a restart appending to output files
130 * \returns A pointer to the ED data structure.
132 std::unique_ptr<gmx::EssentialDynamics> init_edsam(const gmx::MDLogger& mdlog,
133 const char* ediFileName,
134 const char* edoFileName,
135 const gmx_mtop_t& mtop,
136 const t_inputrec& ir,
138 gmx::Constraints* constr,
139 const t_state* globalState,
140 ObservablesHistory* oh,
141 const gmx_output_env_t* oenv,
142 gmx::StartingBehavior startingBehavior);
144 /*! \brief Make a selection of the home atoms for the ED groups.
146 * Should be called at every domain decomposition.
148 * \param dd Domain decomposition data.
149 * \param ed Essential dynamics and flooding data.
151 void dd_make_local_ed_indices(gmx_domdec_t* dd, gmx_edsam* ed);
154 /*! \brief Evaluate the flooding potential(s) and forces as requested in the .edi input file.
156 * \param cr Data needed for MPI communication.
157 * \param ir MD input parameter record.
158 * \param coords Positions on the local processor.
159 * \param force Forcefield forces to which the flooding forces are added.
160 * \param ed The essential dynamics data.
161 * \param box The simulation box.
162 * \param step Number of the time step.
163 * \param bNS Are we in a neighbor searching step?
165 void do_flood(const t_commrec* cr,
166 const t_inputrec& ir,
167 gmx::ArrayRef<const gmx::RVec> coords,
168 gmx::ArrayRef<gmx::RVec> force,