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Add first draft code with GROMACS approach

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-01-25 00:43:10 +01:00
parent 72730bc27b
commit 6291709ae7
5 changed files with 368 additions and 216 deletions
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24
gromacs/includes/atom.h
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@@ -25,11 +25,25 @@
#ifndef __ATOM_H_
#define __ATOM_H_
#define CLUSTER_DIM_N 4
#define CLUSTER_DIM_M 4
typedef struct {
int bin;
int natoms;
int type[CLUSTER_DIM_N];
MD_FLOAT bbminx, bbmaxx;
MD_FLOAT bbminy, bbmaxy;
MD_FLOAT bbminz, bbmaxz;
} Cluster;
typedef struct {
int Natoms, Nlocal, Nghost, Nmax;
int Nclusters, Nclusters_local, Nclusters_ghost, Nclusters_max;
MD_FLOAT *x, *y, *z;
MD_FLOAT *vx, *vy, *vz;
MD_FLOAT *fx, *fy, *fz;
MD_FLOAT *cl_x;
int *border_map;
int *type;
int ntypes;
@@ -37,23 +51,33 @@ typedef struct {
MD_FLOAT *sigma6;
MD_FLOAT *cutforcesq;
MD_FLOAT *cutneighsq;
Cluster *clusters;
} Atom;
extern void initAtom(Atom*);
extern void createAtom(Atom*, Parameter*);
extern int readAtom(Atom*, Parameter*);
extern void growAtom(Atom*);
extern void growClusters(Atom*);
#define cluster_ptr(ci) &(atom->cl_x[ci * CLUSTER_DIM_N * 3])
#ifdef AOS
#define POS_DATA_LAYOUT "AoS"
#define atom_x(i) atom->x[(i) * 3 + 0]
#define atom_y(i) atom->x[(i) * 3 + 1]
#define atom_z(i) atom->x[(i) * 3 + 2]
#define cluster_x(cptr, i) cptr[(i) * 3 + 0]
#define cluster_y(cptr, i) cptr[(i) * 3 + 1]
#define cluster_z(cptr, i) cptr[(i) * 3 + 2]
#else
#define POS_DATA_LAYOUT "SoA"
#define atom_x(i) atom->x[i]
#define atom_y(i) atom->y[i]
#define atom_z(i) atom->z[i]
#define cluster_x(cptr, i) cptr[0 * CLUSTER_DIM_N + (i)]
#define cluster_y(cptr, i) cptr[1 * CLUSTER_DIM_N + (i)]
#define cluster_z(cptr, i) cptr[2 * CLUSTER_DIM_N + (i)]
#endif
#endif

3
gromacs/includes/neighbor.h
View File

@@ -36,6 +36,7 @@ typedef struct {
extern void initNeighbor(Neighbor*, Parameter*);
extern void setupNeighbor(Parameter*);
extern void binatoms(Atom*);
extern void buildNeighbor(Atom*, Neighbor*);
extern void buildNeighbor(Parameter*, Atom*, Neighbor*);
extern void sortAtom(Atom*);
extern void buildClusters(Parameter*, Atom*);
#endif