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Fix errors to make gromacs approach compilable so far

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
2022-01-25 12:19:28 +01:00
parent 6291709ae7
commit cbe42b8149
4 changed files with 26 additions and 28 deletions
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1
gromacs/includes/atom.h
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@@ -52,6 +52,7 @@ typedef struct {
MD_FLOAT *cutforcesq;
MD_FLOAT *cutneighsq;
Cluster *clusters;
int *PBCx, *PBCy, *PBCz;
} Atom;
extern void initAtom(Atom*);

4
gromacs/main.c
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@@ -101,7 +101,7 @@ double setup(
if(param->input_file == NULL) { adjustThermo(param, atom); }
setupPbc(atom, param);
updatePbc(atom, param);
buildNeighbor(atom, neighbor);
buildNeighbor(param, atom, neighbor);
E = getTimeStamp();
return E-S;
@@ -120,7 +120,7 @@ double reneighbour(
setupPbc(atom, param);
updatePbc(atom, param);
//sortAtom(atom);
buildNeighbor(atom, neighbor);
buildNeighbor(param, atom, neighbor);
LIKWID_MARKER_STOP("reneighbour");
E = getTimeStamp();

10
gromacs/neighbor.c
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@@ -54,8 +54,6 @@ static MD_FLOAT binsizex, binsizey;
static int coord2bin(MD_FLOAT, MD_FLOAT);
static MD_FLOAT bindist(int, int);
extern int *PBCx, *PBCy, *PBCz;
/* exported subroutines */
void initNeighbor(Neighbor *neighbor, Parameter *param)
{
@@ -510,10 +508,10 @@ void binGhostClusters(Parameter *param, Atom *atom) {
coord2bin2D(xtmp, ytmp, &nix, &niy);
// Always put the cluster on the bin of its innermost atom so
// the cluster should be closer to local clusters
if(PBCx[ci] > 0 && ix > nix) { ix = nix; }
if(PBCx[ci] < 0 && ix < nix) { ix = nix; }
if(PBCy[ci] > 0 && iy > niy) { iy = niy; }
if(PBCy[ci] < 0 && iy < niy) { iy = niy; }
if(atom->PBCx[ci] > 0 && ix > nix) { ix = nix; }
if(atom->PBCx[ci] < 0 && ix < nix) { ix = nix; }
if(atom->PBCy[ci] > 0 && iy > niy) { iy = niy; }
if(atom->PBCy[ci] < 0 && iy < niy) { iy = niy; }
}
int bin = iy * mbinx + ix + 1;

39
gromacs/pbc.c
View File

@@ -30,7 +30,6 @@
#define DELTA 20000
static int NmaxGhost;
static int *PBCx, *PBCy, *PBCz;
static void growPbc(Atom*);
@@ -38,7 +37,7 @@ static void growPbc(Atom*);
void initPbc(Atom* atom) {
NmaxGhost = 0;
atom->border_map = NULL;
PBCx = NULL; PBCy = NULL; PBCz = NULL;
atom->PBCx = NULL; atom->PBCy = NULL; atom->PBCz = NULL;
}
/* update coordinates of ghost atoms */
@@ -55,9 +54,9 @@ void updatePbc(Atom *atom, Parameter *param) {
MD_FLOAT *bmap_cptr = cluster_ptr(border_map[ci]);
for(int cii = 0; cii < atom->clusters[ci].natoms; cii++) {
cluster_x(cptr, cii) = cluster_x(bmap_cptr, cii) + PBCx[ci] * xprd;
cluster_y(cptr, cii) = cluster_y(bmap_cptr, cii) + PBCy[ci] * yprd;
cluster_z(cptr, cii) = cluster_z(bmap_cptr, cii) + PBCz[ci] * zprd;
cluster_x(cptr, cii) = cluster_x(bmap_cptr, cii) + atom->PBCx[ci] * xprd;
cluster_y(cptr, cii) = cluster_y(bmap_cptr, cii) + atom->PBCy[ci] * yprd;
cluster_z(cptr, cii) = cluster_z(bmap_cptr, cii) + atom->PBCz[ci] * zprd;
}
}
}
@@ -74,6 +73,7 @@ void updateAtomsPbc(Atom *atom, Parameter *param) {
atom_x(i) += xprd;
} else if(atom_x(i) >= xprd) {
atom_x(i) -= xprd;
}
if(atom_y(i) < 0.0) {
atom_y(i) += yprd;
@@ -96,9 +96,9 @@ void updateAtomsPbc(Atom *atom, Parameter *param) {
#define ADDGHOST(dx,dy,dz) \
Nghost++; \
border_map[Nghost] = ci; \
PBCx[Nghost] = dx; \
PBCy[Nghost] = dy; \
PBCz[Nghost] = dz; \
atom->PBCx[Nghost] = dx; \
atom->PBCy[Nghost] = dy; \
atom->PBCz[Nghost] = dz; \
copy_cluster_types(atom, atom->Nclusters_local + Nghost, ci)
void copy_cluster_types(Atom *atom, int dest, int src) {
@@ -107,6 +107,17 @@ void copy_cluster_types(Atom *atom, int dest, int src) {
}
}
/* internal subroutines */
void growPbc(Atom* atom) {
int nold = NmaxGhost;
NmaxGhost += DELTA;
atom->border_map = (int*) reallocate(atom->border_map, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
atom->PBCx = (int*) reallocate(atom->PBCx, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
atom->PBCy = (int*) reallocate(atom->PBCy, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
atom->PBCz = (int*) reallocate(atom->PBCz, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
}
void setupPbc(Atom *atom, Parameter *param) {
int *border_map = atom->border_map;
MD_FLOAT xprd = param->xprd;
@@ -131,7 +142,6 @@ void setupPbc(Atom *atom, Parameter *param) {
MD_FLOAT bbmaxy = atom->clusters[ci].bbmaxy;
MD_FLOAT bbminz = atom->clusters[ci].bbminz;
MD_FLOAT bbmaxz = atom->clusters[ci].bbmaxz;
/* Setup ghost atoms */
/* 6 planes */
if (bbminx < Cutneigh) { ADDGHOST(+1,0,0); }
@@ -168,14 +178,3 @@ void setupPbc(Atom *atom, Parameter *param) {
atom->Nclusters_ghost = Nghost + 1;
atom->Nclusters = atom->Nclusters_local + Nghost + 1;
}
/* internal subroutines */
void growPbc(Atom* atom) {
int nold = NmaxGhost;
NmaxGhost += DELTA;
atom->border_map = (int*) reallocate(atom->border_map, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCx = (int*) reallocate(PBCx, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCy = (int*) reallocate(PBCy, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
PBCz = (int*) reallocate(PBCz, ALIGNMENT, NmaxGhost * sizeof(int), nold * sizeof(int));
}