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Create separate structs DeviceAtom and DeviceNeighbor with device pointers

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-08-12 17:28:06 +02:00
parent 065b596074
commit 939197a785
13 changed files with 172 additions and 153 deletions
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16
lammps/includes/atom.h
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@@ -48,6 +48,18 @@
# define updateAtomsPbc updateAtomsPbc_cpu
#endif
typedef struct {
MD_FLOAT *x, *y, *z;
MD_FLOAT *vx, *vy, *vz;
MD_FLOAT *fx, *fy, *fz;
int *border_map;
int *type;
MD_FLOAT *epsilon;
MD_FLOAT *sigma6;
MD_FLOAT *cutforcesq;
MD_FLOAT *cutneighsq;
} DeviceAtom;
typedef struct {
int Natoms, Nlocal, Nghost, Nmax;
MD_FLOAT *x, *y, *z;
@@ -60,10 +72,14 @@ typedef struct {
MD_FLOAT *sigma6;
MD_FLOAT *cutforcesq;
MD_FLOAT *cutneighsq;
// DEM
MD_FLOAT *radius;
MD_FLOAT *av;
MD_FLOAT *r;
// Device data
DeviceAtom d_atom;
} Atom;
extern void initAtom(Atom*);

2
lammps/includes/cuda_atom.h
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@@ -5,7 +5,7 @@
#ifndef __CUDA_ATOM_H_
#define __CUDA_ATOM_H_
extern void initCuda(Atom*, Neighbor*, Atom*, Neighbor*);
extern void initCuda(Atom*, Neighbor*);
extern void cuda_assert(const char *msg, cudaError_t err);
extern void *allocateGPU(size_t bytesize);
extern void *reallocateGPU(void *ptr, size_t new_bytesize);

8
lammps/includes/integrate.h
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@@ -23,7 +23,7 @@
#include <parameter.h>
#include <atom.h>
void initialIntegrate_cpu(bool reneigh, Parameter *param, Atom *atom, Atom *c_atom) {
void initialIntegrate_cpu(bool reneigh, Parameter *param, Atom *atom) {
for(int i = 0; i < atom->Nlocal; i++) {
atom_vx(i) += param->dtforce * atom_fx(i);
atom_vy(i) += param->dtforce * atom_fy(i);
@@ -34,7 +34,7 @@ void initialIntegrate_cpu(bool reneigh, Parameter *param, Atom *atom, Atom *c_at
}
}
void finalIntegrate_cpu(bool reneigh, Parameter *param, Atom *atom, Atom *c_atom) {
void finalIntegrate_cpu(bool reneigh, Parameter *param, Atom *atom) {
for(int i = 0; i < atom->Nlocal; i++) {
atom_vx(i) += param->dtforce * atom_fx(i);
atom_vy(i) += param->dtforce * atom_fy(i);
@@ -43,6 +43,6 @@ void finalIntegrate_cpu(bool reneigh, Parameter *param, Atom *atom, Atom *c_atom
}
#ifdef CUDA_TARGET
void initialIntegrate_cuda(bool, Parameter*, Atom*, Atom*);
void finalIntegrate_cuda(bool, Parameter*, Atom*, Atom*);
void initialIntegrate_cuda(bool, Parameter*, Atom*);
void finalIntegrate_cuda(bool, Parameter*, Atom*);
#endif

17
lammps/includes/neighbor.h
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@@ -25,13 +25,22 @@
#ifndef __NEIGHBOR_H_
#define __NEIGHBOR_H_
typedef struct {
int *neighbors;
int *numneigh;
} DeviceNeighbor;
typedef struct {
int every;
int ncalls;
int maxneighs;
int half_neigh;
int* neighbors;
int* numneigh;
int *neighbors;
int *numneigh;
// Device data
DeviceNeighbor d_neighbor;
} Neighbor;
typedef struct {
@@ -52,11 +61,11 @@ typedef struct {
extern void initNeighbor(Neighbor*, Parameter*);
extern void setupNeighbor(Parameter*);
extern void binatoms(Atom*);
extern void buildNeighbor_cpu(Atom*, Neighbor*, Atom*, Neighbor*);
extern void buildNeighbor_cpu(Atom*, Neighbor*);
extern void sortAtom(Atom*);
#ifdef CUDA_TARGET
extern void buildNeighbor_cuda(Atom*, Neighbor*, Atom*, Neighbor*);
extern void buildNeighbor_cuda(Atom*, Neighbor*);
#endif
#endif

8
lammps/includes/pbc.h
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@@ -28,13 +28,13 @@
#ifndef __PBC_H_
#define __PBC_H_
extern void initPbc();
extern void updatePbc_cpu(Atom*, Atom*, Parameter*, bool);
extern void updateAtomsPbc_cpu(Atom*, Atom*, Parameter*);
extern void updatePbc_cpu(Atom*, Parameter*, bool);
extern void updateAtomsPbc_cpu(Atom*, Parameter*);
extern void setupPbc(Atom*, Parameter*);
#ifdef CUDA_TARGET
extern void updatePbc_cuda(Atom*, Atom*, Parameter*, bool);
extern void updateAtomsPbc_cuda(Atom*, Atom*, Parameter*);
extern void updatePbc_cuda(Atom*, Parameter*, bool);
extern void updateAtomsPbc_cuda(Atom*, Parameter*);
#endif
#endif