--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
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+ */
+#ifndef GMX_MDLIB_COUPLING_H
+#define GMX_MDLIB_COUPLING_H
+
+#include "gromacs/math/paddedvector.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_ekindata_t;
+struct gmx_enerdata_t;
+struct t_commrec;
+struct t_extmass;
+struct t_grpopts;
+struct t_inputrec;
+struct t_mdatoms;
+struct t_nrnb;
+class t_state;
+
+enum class PbcType;
+
+namespace gmx
+{
+class BoxDeformation;
+class Constraints;
+class Update;
+}; // namespace gmx
+
+/* Update the size of per-atom arrays (e.g. after DD re-partitioning,
+ which might increase the number of home atoms). */
+
+void update_tcouple(int64_t step,
+ const t_inputrec* inputrec,
+ t_state* state,
+ gmx_ekindata_t* ekind,
+ const t_extmass* MassQ,
+ const t_mdatoms* md);
+
+/* Update Parrinello-Rahman, to be called before the coordinate update */
+void update_pcouple_before_coordinates(FILE* fplog,
+ int64_t step,
+ const t_inputrec* inputrec,
+ t_state* state,
+ matrix parrinellorahmanMu,
+ matrix M,
+ gmx_bool bInitStep);
+
+/* Update the box, to be called after the coordinate update.
+ * For Berendsen P-coupling, also calculates the scaling factor
+ * and scales the coordinates.
+ * When the deform option is used, scales coordinates and box here.
+ */
+void update_pcouple_after_coordinates(FILE* fplog,
+ int64_t step,
+ const t_inputrec* inputrec,
+ const t_mdatoms* md,
+ const matrix pressure,
+ const matrix forceVirial,
+ const matrix constraintVirial,
+ matrix pressureCouplingMu,
+ t_state* state,
+ t_nrnb* nrnb,
+ gmx::BoxDeformation* boxDeformation,
+ bool scaleCoordinates);
+
+/* Return TRUE if OK, FALSE in case of Shake Error */
+
+extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
+ int64_t step,
+ const t_commrec* cr,
+ const t_mdatoms* md,
+ gmx::ArrayRef<gmx::RVec> v,
+ const gmx::Update* upd,
+ const gmx::Constraints* constr);
+
+void berendsen_tcoupl(const t_inputrec* ir,
+ gmx_ekindata_t* ekind,
+ real dt,
+ std::vector<double>& therm_integral); //NOLINT(google-runtime-references)
+
+void andersen_tcoupl(const t_inputrec* ir,
+ int64_t step,
+ const t_commrec* cr,
+ const t_mdatoms* md,
+ gmx::ArrayRef<gmx::RVec> v,
+ real rate,
+ const std::vector<bool>& randomize,
+ gmx::ArrayRef<const real> boltzfac);
+
+void nosehoover_tcoupl(const t_grpopts* opts,
+ const gmx_ekindata_t* ekind,
+ real dt,
+ double xi[],
+ double vxi[],
+ const t_extmass* MassQ);
+
+void trotter_update(const t_inputrec* ir,
+ int64_t step,
+ gmx_ekindata_t* ekind,
+ const gmx_enerdata_t* enerd,
+ t_state* state,
+ const tensor vir,
+ const t_mdatoms* md,
+ const t_extmass* MassQ,
+ gmx::ArrayRef<std::vector<int>> trotter_seqlist,
+ int trotter_seqno);
+
+std::array<std::vector<int>, ettTSEQMAX>
+init_npt_vars(const t_inputrec* ir, t_state* state, t_extmass* Mass, gmx_bool bTrotter);
+
+real NPT_energy(const t_inputrec* ir, const t_state* state, const t_extmass* MassQ);
+/* computes all the pressure/tempertature control energy terms to get a conserved energy */
+
+void vrescale_tcoupl(const t_inputrec* ir, int64_t step, gmx_ekindata_t* ekind, real dt, double therm_integral[]);
+/* Compute temperature scaling. For V-rescale it is done in update. */
+
+void rescale_velocities(const gmx_ekindata_t* ekind, const t_mdatoms* mdatoms, int start, int end, rvec v[]);
+/* Rescale the velocities with the scaling factor in ekind */
+
+//! Check whether we do simulated annealing.
+bool doSimulatedAnnealing(const t_inputrec* ir);
+
+//! Initialize simulated annealing.
+bool initSimulatedAnnealing(t_inputrec* ir, gmx::Update* upd);
+
+// TODO: This is the only function in update.h altering the inputrec
+void update_annealing_target_temp(t_inputrec* ir, real t, gmx::Update* upd);
+/* Set reference temp for simulated annealing at time t*/
+
+real calc_temp(real ekin, real nrdf);
+/* Calculate the temperature */
+
+real calc_pres(PbcType pbcType, int nwall, const matrix box, const tensor ekin, const tensor vir, tensor pres);
+/* Calculate the pressure tensor, returns the scalar pressure.
+ * The unit of pressure is bar.
+ */
+
+void parrinellorahman_pcoupl(FILE* fplog,
+ int64_t step,
+ const t_inputrec* ir,
+ real dt,
+ const tensor pres,
+ const tensor box,
+ tensor box_rel,
+ tensor boxv,
+ tensor M,
+ matrix mu,
+ gmx_bool bFirstStep);
+
+void berendsen_pcoupl(FILE* fplog,
+ int64_t step,
+ const t_inputrec* ir,
+ real dt,
+ const tensor pres,
+ const matrix box,
+ const matrix force_vir,
+ const matrix constraint_vir,
+ matrix mu,
+ double* baros_integral);
+
+void berendsen_pscale(const t_inputrec* ir,
+ const matrix mu,
+ matrix box,
+ matrix box_rel,
+ int start,
+ int nr_atoms,
+ rvec x[],
+ const unsigned short cFREEZE[],
+ t_nrnb* nrnb,
+ bool scaleCoordinates);
+
+void pleaseCiteCouplingAlgorithms(FILE* fplog, const t_inputrec& ir);
+
+/*! \brief Generate a new kinetic energy for the v-rescale thermostat
+ *
+ * Generates a new value for the kinetic energy, according to
+ * Bussi et al JCP (2007), Eq. (A7)
+ *
+ * This is used by update_tcoupl(), and by the VRescaleThermostat of the modular
+ * simulator.
+ * \todo Move this to the VRescaleThermostat once the modular simulator becomes
+ * the default code path.
+ *
+ * \param[in] kk present value of the kinetic energy of the atoms to be thermalized (in
+ * arbitrary units) \param[in] sigma target average value of the kinetic energy (ndeg k_b T/2) (in
+ * the same units as kk) \param[in] ndeg number of degrees of freedom of the atoms to be
+ * thermalized \param[in] taut relaxation time of the thermostat, in units of 'how often this
+ * routine is called' \param[in] step the time step this routine is called on \param[in] seed the
+ * random number generator seed \return the new kinetic energy
+ */
+real vrescale_resamplekin(real kk, real sigma, real ndeg, real taut, int64_t step, int64_t seed);
+
+#endif // GMX_MDLIB_COUPLING_H
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff