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37 #ifndef GMX_MDTYPES_NBLIST_H
38 #define GMX_MDTYPES_NBLIST_H
42 #include "gromacs/utility/alignedallocator.h"
43 #include "gromacs/utility/basedefinitions.h"
44 #include "gromacs/utility/real.h"
46 typedef unsigned long t_excl;
48 /* The interactions contained in a (possibly merged) table
49 * for computing electrostatic, VDW repulsion and/or VDW dispersion
52 enum gmx_table_interaction
54 GMX_TABLE_INTERACTION_ELEC,
55 GMX_TABLE_INTERACTION_VDWREP_VDWDISP,
56 GMX_TABLE_INTERACTION_VDWEXPREP_VDWDISP,
57 GMX_TABLE_INTERACTION_VDWDISP,
58 GMX_TABLE_INTERACTION_ELEC_VDWREP_VDWDISP,
59 GMX_TABLE_INTERACTION_ELEC_VDWEXPREP_VDWDISP,
60 GMX_TABLE_INTERACTION_ELEC_VDWDISP,
61 GMX_TABLE_INTERACTION_NR
64 /* Different formats for table data. Cubic spline tables are typically stored
65 * with the four Y,F,G,H intermediate values (check tables.c for format), which
66 * makes it easy to load with a single 4-way SIMD instruction too.
67 * Linear tables only need one value per table point, or two if both V and F
68 * are calculated. However, with SIMD instructions this makes the loads unaligned,
69 * and in that case we store the data as F, D=F(i+1)-F(i), V, and then a blank value,
70 * which again makes it possible to load as a single instruction.
74 GMX_TABLE_FORMAT_CUBICSPLINE_YFGH,
75 GMX_TABLE_FORMAT_LINEAR_VF,
76 GMX_TABLE_FORMAT_LINEAR_V,
77 GMX_TABLE_FORMAT_LINEAR_F,
78 GMX_TABLE_FORMAT_LINEAR_FDV0,
107 /* The maximum charge group size because of minimum size of t_excl
110 #define MAX_CHARGEGROUP_SIZE 32
112 /* The maximum charge group size for CG-CG nblists.
113 * The excl entry in t_nblist uses blocks of this size.
115 #define MAX_CGCGSIZE 32
117 typedef struct t_nblist
119 int igeometry; /* The type of list (atom, water, etc.) */
120 int ielec; /* Coulomb loop type index for kernels */
121 int ielecmod; /* Coulomb modifier (e.g. switch/shift) */
122 int ivdw; /* VdW loop type index for kernels */
123 int ivdwmod; /* VdW modifier (e.g. switch/shift) */
124 int type; /* Type of interaction, listed in
125 gmx_nblist_interaction_type */
127 int nri, maxnri; /* Current/max number of i particles */
128 int nrj, maxnrj; /* Current/max number of j particles */
129 int* iinr; /* The i-elements */
130 int* iinr_end; /* The end atom, only with enlistCG */
131 int* gid; /* Index in energy arrays */
132 int* shift; /* Shift vector index */
133 int* jindex; /* Index in jjnr */
134 int* jjnr; /* The j-atom list */
135 int* jjnr_end; /* The end atom, only with enltypeCG */
136 char* excl_fep; /* Exclusions for FEP with Verlet scheme */
137 t_excl* excl; /* Exclusions, only with enltypeCG */
139 /* We use separate pointers for kernels that compute both potential
140 * and force (vf suffix), only potential (v) or only force (f)
146 /* Pad the list of neighbors for each i atom with "-1" entries up to the
147 * simd_padding_width, if it is larger than 0. This is necessary for many
148 * accelerated kernels using single-instruction multiple-data operations
151 int simd_padding_width;
155 /* For atom I = nblist->iinr[N] (0 <= N < nblist->nri) there can be
156 * several neighborlists (N's), for different energy groups (gid) and
157 * different shifts (shift).
158 * For corresponding J atoms for each list start at:
160 * with nblist->jindex[N] <= JI < nblist->jindex[N+1]
162 * enlist is of the form enlistUNIT1_UNIT2:
163 * UNIT ATOM: there is one atom: iinr[N] or jjnr[JI]
164 * UNIT SPC: there are 3 atoms: iinr[N],iinr[N]+1,iinr[N]+2, jjnr analog.
165 * UNIT TIP4P: there are 4 atoms: iinr[N],...,iinr[N]+3, jjnr analog.
166 * UNIT CG: there are N atoms: iinr[N],...,iinr_end[N]-1, jjnr analog.
171 /* Structure describing the data in a single table */
174 t_forcetable(enum gmx_table_interaction interaction, enum gmx_table_format format);
178 enum gmx_table_interaction interaction; /* Types of interactions stored in this table */
179 enum gmx_table_format format; /* Interpolation type and data format */
181 real r; /* range of the table */
182 int n; /* n+1 is the number of table points */
183 real scale; /* distance (nm) between two table points */
184 std::vector<real, gmx::AlignedAllocator<real>> data; /* the actual table data */
186 /* Some information about the table layout. This can also be derived from the interpolation
187 * type and the table interactions, but it is convenient to have here for sanity checks, and it
188 * makes it much easier to access the tables in the nonbonded kernels when we can set the data
189 * from variables. It is always true that stride = formatsize*ninteractions
191 int formatsize; /* Number of fp variables for each table point (1 for F, 2 for VF, 4 for YFGH, etc.) */
192 int ninteractions; /* Number of interactions in table, 1 for coul-only, 3 for coul+rep+disp. */
193 int stride; /* Distance to next table point (number of fp variables per table point in total) */
204 gmx_bool* bExcludeAlleg;
213 /* the nblists should probably go in here */
214 gmx_bool nblist_initialized; /* has the nblist been initialized? */
215 int dump_nl; /* neighbour list dump level (from env. var. GMX_DUMP_NL)*/
218 #endif /* GMX_MDTYPES_NBLIST_H */