#ifndef GMX_MDLIB_COUPLING_H
#define GMX_MDLIB_COUPLING_H
-#include "gromacs/math/paddedvector.h"
+#include <cstdio>
+
+#include <array>
+#include <vector>
+
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"
-struct gmx_ekindata_t;
+class 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;
class BoxDeformation;
class Constraints;
class Update;
+template<typename>
+class ArrayRef;
}; // 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);
+void update_tcouple(int64_t step,
+ const t_inputrec* inputrec,
+ t_state* state,
+ gmx_ekindata_t* ekind,
+ const t_extmass* MassQ,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC);
/* Update Parrinello-Rahman, to be called before the coordinate update */
void update_pcouple_before_coordinates(FILE* fplog,
t_state* state,
matrix parrinellorahmanMu,
matrix M,
- gmx_bool bInitStep);
+ 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);
+void update_pcouple_after_coordinates(FILE* fplog,
+ int64_t step,
+ const t_inputrec* inputrec,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ 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);
+extern bool update_randomize_velocities(const t_inputrec* ir,
+ int64_t step,
+ const t_commrec* cr,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC,
+ gmx::ArrayRef<const real> invMass,
+ 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 andersen_tcoupl(const t_inputrec* ir,
+ int64_t step,
+ const t_commrec* cr,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC,
+ gmx::ArrayRef<const real> invMass,
+ 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[],
+ gmx::ArrayRef<double> xi,
+ gmx::ArrayRef<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);
+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,
+ int homenr,
+ gmx::ArrayRef<const unsigned short> cTC,
+ gmx::ArrayRef<const real> invMass,
+ const t_extmass* MassQ,
+ gmx::ArrayRef<std::vector<int>> trotter_seqlist,
+ TrotterSequence trotter_seqno);
-std::array<std::vector<int>, ettTSEQMAX>
-init_npt_vars(const t_inputrec* ir, t_state* state, t_extmass* Mass, gmx_bool bTrotter);
+gmx::EnumerationArray<TrotterSequence, std::vector<int>>
+init_npt_vars(const t_inputrec* ir, t_state* state, t_extmass* Mass, 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[]);
+void vrescale_tcoupl(const t_inputrec* ir,
+ int64_t step,
+ gmx_ekindata_t* ekind,
+ real dt,
+ gmx::ArrayRef<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[]);
+void rescale_velocities(const gmx_ekindata_t* ekind,
+ gmx::ArrayRef<const unsigned short> cTC,
+ int start,
+ int end,
+ gmx::ArrayRef<gmx::RVec> v);
/* Rescale the velocities with the scaling factor in ekind */
+/*!
+ * \brief Compute the new annealing temperature for a temperature group
+ *
+ * \param inputrec The input record
+ * \param temperatureGroup The temperature group
+ * \param time The current time
+ * \return The new reference temperature for the group
+ */
+real computeAnnealingTargetTemperature(const t_inputrec& inputrec, int temperatureGroup, real time);
+
//! Check whether we do simulated annealing.
bool doSimulatedAnnealing(const t_inputrec* ir);
tensor boxv,
tensor M,
matrix mu,
- gmx_bool bFirstStep);
+ bool bFirstStep);
/*! \brief Calculate the pressure coupling scaling matrix
*
* coupling algorithm.
*/
template<PressureCoupling pressureCouplingType>
-void pressureCouplingScaleBoxAndCoordinates(const t_inputrec* ir,
- const matrix mu,
- matrix box,
- matrix box_rel,
- int start,
- int nr_atoms,
- rvec x[],
- rvec v[],
- const unsigned short cFREEZE[],
- t_nrnb* nrnb,
- bool scaleCoordinates);
+void pressureCouplingScaleBoxAndCoordinates(const t_inputrec* ir,
+ const matrix mu,
+ matrix box,
+ matrix box_rel,
+ int start,
+ int nr_atoms,
+ gmx::ArrayRef<gmx::RVec> x,
+ gmx::ArrayRef<gmx::RVec> v,
+ gmx::ArrayRef<const unsigned short> cFREEZE,
+ t_nrnb* nrnb,
+ bool scaleCoordinates);
void pleaseCiteCouplingAlgorithms(FILE* fplog, const t_inputrec& ir);
* 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
+ * 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);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff