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cudaMemcpy of Atom and other properties, first draft implementation of CUDA kernel

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This commit is contained in:
Maximilian Gaul 2021-11-09 16:40:25 +01:00
parent bfa6c581c3
commit 3f7fb7f22a
1 changed files with 56 additions and 33 deletions
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89
src/force.c
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@ -78,51 +78,44 @@ double computeForce(
atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
atom->type = (int *) reallocate(atom->type, ALIGNMENT, atom->Nmax * sizeof(int), nold * sizeof(int));
*/
MD_FLOAT *c_xtmp;
cudaMalloc((void**)&c_xtmp, sizeof(MD_FLOAT));
cudaMemcpy(c_xtmp, &xtmp, sizeof(MD_FLOAT), cudaMemcpyHostToDevice);
Atom *c_atom;
cudaMalloc((void**)&c_atom, sizeof(Atom));
cudaMemcpy(c_atom, atom, sizeof(Atom), cudaMemcpyHostToDevice);
MD_FLOAT *c_ytmp;
cudaMalloc((void**)&c_ytmp, sizeof(MD_FLOAT));
cudaMemcpy(c_ytmp, &ytmp, sizeof(MD_FLOAT), cudaMemcpyHostToDevice);
cudaMalloc((void**)&c_atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3);
cudaMemcpy(c_atom->x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice);
MD_FLOAT *c_ztmp;
cudaMalloc((void**)&c_ztmp, sizeof(MD_FLOAT));
cudaMemcpy(c_ztmp, &ztmp, sizeof(MD_FLOAT), cudaMemcpyHostToDevice);
cudaMalloc((void**)&c_atom->y, sizeof(MD_FLOAT) * atom->Nmax * 3);
cudaMemcpy(c_atom->y, atom->y, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice);
int *c_atom_ntypes;
cudaMalloc((void**)&c_atom_ntypes, sizeof(int));
cudaMemcpy(c_atom_ntypes, &(atom->ntypes), sizeof(int), cudaMemcpyHostToDevice);
cudaMalloc((void**)&c_atom->z, sizeof(MD_FLOAT) * atom->Nmax * 3);
cudaMemcpy(c_atom->z, atom->z, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice);
int *c_neighbors;
cudaMalloc((void**)&c_neighbors, sizeof(int) * numneighs);
cudaMemcpy(c_neighbors, neighs, sizeof(int) * numneighs, cudaMemcpyHostToDevice);
cudaMalloc((void**)&c_atom->type, sizeof(int) * atom->Nmax);
cudaMemcpy(c_atom->type, atom->type, sizeof(int) * atom->Nmax, cudaMemcpyHostToDevice);
MD_FLOAT *c_atom_x;
cudaMalloc((void**)&c_atom_x, sizeof(MD_FLOAT) * atom->Nmax * 3);
cudaMemcpy(c_atom_x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice);
cudaMalloc((void**)&c_atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes);
cudaMemcpy(c_atom->epsilon, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice);
MD_FLOAT *c_atom_y;
cudaMalloc((void**)&c_atom_y, sizeof(MD_FLOAT) * atom->Nmax * 3);
cudaMemcpy(c_atom_y, atom->y, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice);
cudaMalloc((void**)&c_atom->sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes);
cudaMemcpy(c_atom->sigma6, atom->sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice);
MD_FLOAT *c_atom_z;
cudaMalloc((void**)&c_atom_z, sizeof(MD_FLOAT) * atom->Nmax * 3);
cudaMemcpy(c_atom_z, atom->z, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice);
cudaMalloc((void**)&c_atom->cutforcesq, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes);
cudaMemcpy(c_atom->cutforcesq, atom->cutforcesq, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice);
MD_FLOAT *c_atom_epsilon;
cudaMalloc((void**)&c_atom_epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes);
cudaMemcpy(c_atom_epsilon, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice);
int *c_neighs;
cudaMalloc((void**)&c_neighs, sizeof(int) * numneighs);
cudaMemcpy(c_neighs, neighs, sizeof(int) * numneighs, cudaMemcpyHostToDevice);
MD_FLOAT *c_sigma6;
cudaMalloc((void**)&c_sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes);
cudaMemcpy(c_sigma6, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice);
const int num_elems = numneighs;
MD_FLOAT *c_cutforcesq;
cudaMalloc((void**)&c_cutforcesq, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes);
cudaMemcpy(c_cutforcesq, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice);
MD_FLOAT *c_fix, *c_fiy, *c_fiz;
cudaMalloc((void**)&c_fix, sizeof(MD_FLOAT) * num_elems);
cudaMalloc((void**)&c_fiy, sizeof(MD_FLOAT) * num_elems);
cudaMalloc((void**)&c_fiz, sizeof(MD_FLOAT) * num_elems);
for(int k = 0; k < numneighs; k++) {
int j = neighs[k];
@ -159,3 +152,33 @@ double computeForce(
return E-S;
}
// cuda kernel
__global__ void calc_force(
Atom *atom,
MD_FLOAT xtmp, MD_FLOAT ytmp, MD_FLOAT ztmp,
MD_FLOAT *fix, MD_FLOAT *fiy, MD_FLOAT *fiz,
int i, int k, int *neighs) {
int j = neighs[k];
MD_FLOAT delx = xtmp - atom_x(j);
MD_FLOAT dely = ytmp - atom_y(j);
MD_FLOAT delz = ztmp - atom_z(j);
MD_FLOAT rsq = delx * delx + dely * dely + delz * delz;
const int type_i = atom->type[i];
const int type_j = atom->type[j];
const int type_ij = type_i * atom->ntypes + type_j;
const MD_FLOAT cutforcesq = atom->cutforcesq[type_ij];
const MD_FLOAT sigma6 = atom->sigma6[type_ij];
const MD_FLOAT epsilon = atom->epsilon[type_ij];
if(rsq < cutforcesq) {
MD_FLOAT sr2 = 1.0 / rsq;
MD_FLOAT sr6 = sr2 * sr2 * sr2 * sigma6;
MD_FLOAT force = 48.0 * sr6 * (sr6 - 0.5) * sr2 * epsilon;
fix[j] += delx * force;
fiy[j] += dely * force;
fiz[j] += delz * force;
}
}