/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, 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;
-#ifdef __cplusplus
-extern "C" {
-#endif
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+class RangePartitioning;
+} // namespace gmx
-typedef struct
+namespace Nbnxm
{
- int cluster_size_i; /* Cluster pair-list i-cluster size atom count */
- int cluster_size_j; /* Cluster pair-list j-cluster size atom count */
-} verletbuf_list_setup_t;
+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 */
+};
/* Add a 5% and 10% rlist buffer for simulations without dynamics (EM, NM, ...)
static const real verlet_buffer_ratio_NVE_T0 = 0.10;
-/* Sets the pair-list setup assumed for the current Gromacs configuration.
- * The setup with smallest cluster sizes is return, such that the Verlet
- * buffer size estimated with this setup will be conservative.
- * bSIMD tells if to take into account SIMD, when supported.
- * bGPU tells to estimate for GPU kernels (bSIMD is ignored with bGPU=TRUE)
+/* Returns the pair-list setup for the given nbnxn kernel type.
*/
-void verletbuf_get_list_setup(gmx_bool bSIMD,
- gmx_bool bGPU,
- verletbuf_list_setup_t *list_setup);
+VerletbufListSetup verletbufGetListSetup(Nbnxm::KernelType nbnxnKernelType);
+/* Enum for choosing the list type for verletbufGetSafeListSetup() */
+enum class ListSetupType
+{
+ CpuNoSimd, /* CPU Plain-C 4x4 list */
+ CpuSimdWhenSupported, /* CPU 4xN list, where N=4 when the binary doesn't support SIMD or the smallest N supported by SIMD in this binary */
+ Gpu /* GPU (8x2x)8x4 list */
+};
-/* Calculate the non-bonded pair-list buffer size for the Verlet list
+/* Returns the pair-list setup assumed for the current Gromacs configuration.
+ * The setup with smallest cluster sizes is returned, such that the Verlet
+ * buffer size estimated with this setup will be conservative.
+ */
+VerletbufListSetup verletbufGetSafeListSetup(ListSetupType listType);
+
+/* 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.
- * If reference_temperature < 0, the maximum coupling temperature will be used.
- * The target is a maximum energy drift of ir->verletbuf_tol.
- * 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.
+ * 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 referenceTemperature < 0, the maximum coupling temperature will be used.
+ * The target is a maximum average energy jump per atom of
+ * 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,
- real reference_temperature,
- const verletbuf_list_setup_t *list_setup,
- int *n_nonlin_vsite,
- real *rlist);
-
-#ifdef __cplusplus
-}
-#endif
+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 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: Like the Verlet buffer estimate, this estimate is based on
+ * non-interacting atoms and constrained atom-pairs. Therefore for
+ * any system that is not an ideal gas, this will be an overestimate.
+ *
+ * Note: This size increases (very slowly) with system size.
+ */
+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.
+ * The energy jump for given distance depend on LJ type and q.
+ */
+struct atom_nonbonded_kinetic_prop_t
+{
+ real mass = 0; /* mass */
+ int type = 0; /* type (used for LJ parameters) */
+ real q = 0; /* charge */
+ bool bConstr = false; /* constrained, if TRUE, use #DOF=2 iso 3 */
+ real con_mass = 0; /* mass of heaviest atom connected by constraints */
+ real con_len = 0; /* constraint length to the heaviest atom */
+};
+
+/* This function computes two components of the estimate of the variance
+ * in the displacement of one atom in a system of two constrained atoms.
+ * Returns in sigma2_2d the variance due to rotation of the constrained
+ * atom around the atom to which it constrained.
+ * Returns in sigma2_3d the variance due to displacement of the COM
+ * of the whole system of the two constrained atoms.
+ *
+ * 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);
#endif
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