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36 #ifndef GMX_MDLIB_CALC_VERLETBUF_H
37 #define GMX_MDLIB_CALC_VERLETBUF_H
39 #include "gromacs/utility/arrayref.h"
40 #include "gromacs/utility/basedefinitions.h"
41 #include "gromacs/utility/real.h"
48 class RangePartitioning;
51 struct VerletbufListSetup
53 int cluster_size_i; /* Cluster pair-list i-cluster size atom count */
54 int cluster_size_j; /* Cluster pair-list j-cluster size atom count */
58 /* Add a 5% and 10% rlist buffer for simulations without dynamics (EM, NM, ...)
59 * and NVE simulations with zero initial temperature, respectively.
60 * 10% should be enough for any NVE simulation with PME and nstlist=10,
61 * for other settings it might not be enough, but then it's difficult
62 * to come up with any reasonable (not crazily expensive) value
63 * and grompp will notify the user when using the 10% buffer.
65 static const real verlet_buffer_ratio_nodynamics = 0.05;
66 static const real verlet_buffer_ratio_NVE_T0 = 0.10;
69 /* Returns the pair-list setup for the given nbnxn kernel type.
71 VerletbufListSetup verletbufGetListSetup(int nbnxnKernelType);
73 /* Enum for choosing the list type for verletbufGetSafeListSetup() */
74 enum class ListSetupType
76 CpuNoSimd, /* CPU Plain-C 4x4 list */
77 CpuSimdWhenSupported, /* CPU 4xN list, where N=4 when the binary doesn't support SIMD or the smallest N supported by SIMD in this binary */
78 Gpu /* GPU (8x2x)8x4 list */
81 /* Returns the pair-list setup assumed for the current Gromacs configuration.
82 * The setup with smallest cluster sizes is returned, such that the Verlet
83 * buffer size estimated with this setup will be conservative.
85 VerletbufListSetup verletbufGetSafeListSetup(ListSetupType listType);
87 /* Calculate the non-bonded pair-list buffer size for the Verlet list
88 * based on the particle masses, temperature, LJ types, charges
89 * and constraints as well as the non-bonded force behavior at the cut-off.
90 * The pair list update frequency and the list lifetime, which is nstlist-1
91 * for normal pair-list buffering, are passed separately, as in some cases
92 * we want an estimate for different values than the ones set in the inputrec.
93 * If reference_temperature < 0, the maximum coupling temperature will be used.
94 * The target is a maximum average energy jump per atom of
95 * ir->verletbuf_tol*nstlist*ir->delta_t over the lifetime of the list.
96 * Returns the number of non-linear virtual sites. For these it's difficult
97 * to determine their contribution to the drift exaclty, so we approximate.
98 * Returns the pair-list cut-off.
100 void calc_verlet_buffer_size(const gmx_mtop_t *mtop, real boxvol,
101 const t_inputrec *ir,
104 real reference_temperature,
105 const VerletbufListSetup *list_setup,
109 /* Convenience type */
110 using PartitioningPerMoltype = gmx::ArrayRef<const gmx::RangePartitioning>;
112 /* Determines the mininum cell size based on atom displacement
114 * The value returned is the minimum size for which the chance that
115 * an atom or update group crosses to non nearest-neighbor cells
116 * is <= chanceRequested within ir.nstlist steps.
117 * Update groups are used when !updateGrouping.empty().
118 * Without T-coupling, SD or BD, we can not estimate atom displacements
119 * and fall back to the, crude, estimate of using the pairlist buffer size.
121 * Note: Like the Verlet buffer estimate, this estimate is based on
122 * non-interacting atoms and constrained atom-pairs. Therefore for
123 * any system that is not an ideal gas, this will be an overestimate.
125 * Note: This size increases (very slowly) with system size.
128 minCellSizeForAtomDisplacement(const gmx_mtop_t &mtop,
129 const t_inputrec &ir,
130 PartitioningPerMoltype updateGrouping,
131 real chanceRequested);
133 /* Struct for unique atom type for calculating the energy drift.
134 * The atom displacement depends on mass and constraints.
135 * The energy jump for given distance depend on LJ type and q.
137 struct atom_nonbonded_kinetic_prop_t
139 real mass = 0; /* mass */
140 int type = 0; /* type (used for LJ parameters) */
141 real q = 0; /* charge */
142 bool bConstr = false; /* constrained, if TRUE, use #DOF=2 iso 3 */
143 real con_mass = 0; /* mass of heaviest atom connected by constraints */
144 real con_len = 0; /* constraint length to the heaviest atom */
147 /* This function computes two components of the estimate of the variance
148 * in the displacement of one atom in a system of two constrained atoms.
149 * Returns in sigma2_2d the variance due to rotation of the constrained
150 * atom around the atom to which it constrained.
151 * Returns in sigma2_3d the variance due to displacement of the COM
152 * of the whole system of the two constrained atoms.
154 * Only exposed here for testing purposes.
156 void constrained_atom_sigma2(real kT_fac,
157 const atom_nonbonded_kinetic_prop_t *prop,