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