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39 /*! \libinternal \file
42 * Declares functions to enforce rotational motion upon a group of particles.
44 * \author Carsten Kutzner <ckutzne@gwdg.de>
49 #ifndef GMX_PULLING_PULL_ROTATION_H
50 #define GMX_PULLING_PULL_ROTATION_H
56 #include "gromacs/math/vectypes.h"
61 struct gmx_output_env_t;
70 enum class StartingBehavior;
71 class LocalAtomSetManager;
76 class EnforcedRotation
82 /*! \brief Getter for working data
84 * This is needed while the module is still under
86 gmx_enfrot* getLegacyEnfrot();
91 std::unique_ptr<Impl> impl_;
96 /*! \brief Initializes the enforced rotation groups.
98 * This routine does the memory allocation for various helper arrays, opens
99 * the output files etc.
101 * \param fplog General output file, normally md.log.
102 * \param ir Struct containing MD input parameters, among those
103 * also the enforced rotation parameters.
104 * \param nfile Number of entries in the fnm structure.
105 * \param fnm The filenames struct containing also the names
106 * of the rotation output files.
107 * \param atomSets Tracks indices of atoms subject to enforced rotation for each DD rank.
108 * \param cr Pointer to MPI communication data.
109 * \param globalState The global state, only used on the master rank.
110 * \param mtop Molecular topology.
111 * \param oenv Needed to open the rotation output xvgr file.
112 * \param mdrunOptions Options for mdrun.
113 * \param startingBehavior Describes whether this is a restart appending to output files
114 * \return An enforced rotation module.
116 std::unique_ptr<gmx::EnforcedRotation> init_rot(FILE* fplog,
119 const t_filenm fnm[],
121 gmx::LocalAtomSetManager* atomSets,
122 const t_state* globalState,
123 const gmx_mtop_t& mtop,
124 const gmx_output_env_t* oenv,
125 const gmx::MdrunOptions& mdrunOptions,
126 gmx::StartingBehavior startingBehavior);
128 /*! \brief Calculates the enforced rotation potential(s).
130 * This is the main enforced rotation module which is called during every time
131 * step. Here the rotation potential as well as the resulting forces are
134 * \param cr Pointer to MPI communication data.
135 * \param er Pointer to the enforced rotation working data.
136 * \param box Simulation box, needed to make group whole.
137 * \param coords The positions of all the local particles.
139 * \param step The time step.
140 * \param bNS After domain decomposition / neighbor searching several
141 * local arrays have to be updated (masses, shifts)
143 void do_rotation(const t_commrec* cr,
146 gmx::ArrayRef<const gmx::RVec> coords,
152 /*! \brief Add the enforced rotation forces to the official force array.
154 * Adds the forces from enforced rotation potential to the local forces and
155 * sums up the contributions to the rotation potential from all the nodes. Since
156 * this needs communication, this routine should be called after the short range
157 * forces have been evaluated (in order not to spoil cycle counts).
158 * This routine also outputs data to the rotation output files (e.g.
159 * the potential, the angle of the group(s), and torques).
161 * \param er Pointer to the enforced rotation working data.
162 * \param force The local forces to which the rotational forces have
164 * \param cr Pointer to MPI communication data.
165 * \param step The time step, used for output.
166 * \param t Time, used for output.
167 * \returns The potential energy of the rotation potentials.
169 real add_rot_forces(gmx_enfrot* er, gmx::ArrayRef<gmx::RVec> force, const t_commrec* cr, int64_t step, real t);