/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, 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.
struct gmx_mtop_t;
struct t_inputrec;
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+class RangePartitioning;
+} // namespace gmx
+
+namespace Nbnxm
+{
+enum class KernelType;
+} // namespace Nbnxm
+
+
struct VerletbufListSetup
{
- int cluster_size_i; /* Cluster pair-list i-cluster size atom count */
- int cluster_size_j; /* Cluster pair-list j-cluster size atom count */
+ int cluster_size_i; /* Cluster pair-list i-cluster size atom count */
+ int cluster_size_j; /* Cluster pair-list j-cluster size atom count */
};
/* Returns the pair-list setup for the given nbnxn kernel type.
*/
-VerletbufListSetup verletbufGetListSetup(int nbnxnKernelType);
+VerletbufListSetup verletbufGetListSetup(Nbnxm::KernelType nbnxnKernelType);
/* Enum for choosing the list type for verletbufGetSafeListSetup() */
enum class ListSetupType
*/
VerletbufListSetup verletbufGetSafeListSetup(ListSetupType listType);
-/* Calculate the non-bonded pair-list buffer size for the Verlet list
+/* Returns the non-bonded pair-list radius including computed buffer
+ *
+ * Calculate the non-bonded pair-list buffer size for the Verlet list
* based on the particle masses, temperature, LJ types, charges
* and constraints as well as the non-bonded force behavior at the cut-off.
* The pair list update frequency and the list lifetime, which is nstlist-1
* for normal pair-list buffering, are passed separately, as in some cases
* we want an estimate for different values than the ones set in the inputrec.
- * If reference_temperature < 0, the maximum coupling temperature will be used.
+ * If referenceTemperature < 0, the maximum coupling temperature will be used.
* The target is a maximum average energy jump per atom of
- * ir->verletbuf_tol*nstlist*ir->delta_t over the lifetime of the list.
- * Returns the number of non-linear virtual sites. For these it's difficult
- * to determine their contribution to the drift exaclty, so we approximate.
- * Returns the pair-list cut-off.
+ * inputrec.verletbuf_tol*nstlist*inputrec.delta_t over the lifetime of the list.
+ *
+ * \note For non-linear virtual sites it can be problematic to determine their
+ * contribution to the drift exaclty, so we approximate.
+ *
+ * \param[in] mtop The system topology
+ * \param[in] boxVolume The volume of the unit cell
+ * \param[in] inputrec The input record
+ * \param[in] nstlist The pair list update frequency in steps (is not taken from \p inputrec)
+ * \param[in] listLifetime The lifetime of the pair-list, usually nstlist-1, but could be different
+ * for dynamic pruning
+ * \param[in] referenceTemperature The reference temperature for the ensemble
+ * \param[in] listSetup The pair-list setup
+ * \returns The computed pair-list radius including buffer
*/
-void calc_verlet_buffer_size(const gmx_mtop_t *mtop, real boxvol,
- const t_inputrec *ir,
- int nstlist,
- int list_lifetime,
- real reference_temperature,
- const VerletbufListSetup *list_setup,
- int *n_nonlin_vsite,
- real *rlist);
+real calcVerletBufferSize(const gmx_mtop_t& mtop,
+ real boxVolume,
+ const t_inputrec& inputrec,
+ int nstlist,
+ int listLifetime,
+ real referenceTemperature,
+ const VerletbufListSetup& listSetup);
+
+/* Convenience type */
+using PartitioningPerMoltype = gmx::ArrayRef<const gmx::RangePartitioning>;
/* Determines the mininum cell size based on atom displacement
*
* The value returned is the minimum size for which the chance that
- * an atom crosses to non nearest-neighbor cells is <= chanceRequested
- * within ir.nstlist steps.
+ * an atom or update group crosses to non nearest-neighbor cells
+ * is <= chanceRequested within ir.nstlist steps.
+ * Update groups are used when !updateGrouping.empty().
* Without T-coupling, SD or BD, we can not estimate atom displacements
* and fall back to the, crude, estimate of using the pairlist buffer size.
*
*
* Note: This size increases (very slowly) with system size.
*/
-real minCellSizeForAtomDisplacement(const gmx_mtop_t &mtop,
- const t_inputrec &ir,
- real chanceRequested);
+real minCellSizeForAtomDisplacement(const gmx_mtop_t& mtop,
+ const t_inputrec& ir,
+ PartitioningPerMoltype updateGrouping,
+ real chanceRequested);
/* Struct for unique atom type for calculating the energy drift.
* The atom displacement depends on mass and constraints.
*
* Only exposed here for testing purposes.
*/
-void constrained_atom_sigma2(real kT_fac,
- const atom_nonbonded_kinetic_prop_t *prop,
- real *sigma2_2d,
- real *sigma2_3d);
+void constrained_atom_sigma2(real kT_fac, const atom_nonbonded_kinetic_prop_t* prop, real* sigma2_2d, real* sigma2_3d);
#endif
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