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convert more styles to use new neighbor list request API, apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2022-03-05 21:09:19 -05:00
parent ffb367663d
commit 54e667e491
20 changed files with 1083 additions and 1122 deletions
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70
src/compute_cluster_atom.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -22,7 +21,6 @@
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "pair.h"
#include "update.h"
@ -32,18 +30,17 @@
using namespace LAMMPS_NS;
enum{CLUSTER,MASK,COORDS};
enum { CLUSTER, MASK, COORDS };
/* ---------------------------------------------------------------------- */
ComputeClusterAtom::ComputeClusterAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
clusterID(nullptr)
Compute(lmp, narg, arg), clusterID(nullptr)
{
if (narg != 4) error->all(FLERR,"Illegal compute cluster/atom command");
if (narg != 4) error->all(FLERR, "Illegal compute cluster/atom command");
double cutoff = utils::numeric(FLERR,arg[3],false,lmp);
cutsq = cutoff*cutoff;
double cutoff = utils::numeric(FLERR, arg[3], false, lmp);
cutsq = cutoff * cutoff;
peratom_flag = 1;
size_peratom_cols = 0;
@ -64,28 +61,21 @@ ComputeClusterAtom::~ComputeClusterAtom()
void ComputeClusterAtom::init()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use compute cluster/atom unless atoms have IDs");
error->all(FLERR, "Cannot use compute cluster/atom unless atoms have IDs");
if (force->pair == nullptr)
error->all(FLERR,"Compute cluster/atom requires a pair style to be defined");
error->all(FLERR, "Compute cluster/atom requires a pair style to be defined");
if (sqrt(cutsq) > force->pair->cutforce)
error->all(FLERR,
"Compute cluster/atom cutoff is longer than pairwise cutoff");
error->all(FLERR, "Compute cluster/atom cutoff is longer than pairwise cutoff");
// need an occasional full neighbor list
// full required so that pair of atoms on 2 procs both set their clusterID
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"cluster/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute cluster/atom");
if (strcmp(modify->compute[i]->style, "cluster/atom") == 0) count++;
if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute cluster/atom");
}
/* ---------------------------------------------------------------------- */
@ -99,9 +89,9 @@ void ComputeClusterAtom::init_list(int /*id*/, NeighList *ptr)
void ComputeClusterAtom::compute_peratom()
{
int i,j,ii,jj,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
int i, j, ii, jj, inum, jnum;
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
int *ilist, *jlist, *numneigh, **firstneigh;
invoked_peratom = update->ntimestep;
@ -110,15 +100,17 @@ void ComputeClusterAtom::compute_peratom()
if (atom->nmax > nmax) {
memory->destroy(clusterID);
nmax = atom->nmax;
memory->create(clusterID,nmax,"cluster/atom:clusterID");
memory->create(clusterID, nmax, "cluster/atom:clusterID");
vector_atom = clusterID;
}
// invoke full neighbor list (will copy or build if necessary)
// on the first step of a run, set preflag to one in neighbor->build_one(...)
if (update->firststep == update->ntimestep) neighbor->build_one(list,1);
else neighbor->build_one(list);
if (update->firststep == update->ntimestep)
neighbor->build_one(list, 1);
else
neighbor->build_one(list);
inum = list->inum;
ilist = list->ilist;
@ -148,8 +140,10 @@ void ComputeClusterAtom::compute_peratom()
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) clusterID[i] = tag[i];
else clusterID[i] = 0;
if (mask[i] & groupbit)
clusterID[i] = tag[i];
else
clusterID[i] = 0;
}
// loop until no more changes on any proc:
@ -162,7 +156,7 @@ void ComputeClusterAtom::compute_peratom()
commflag = CLUSTER;
double **x = atom->x;
int change,done,anychange;
int change, done, anychange;
while (true) {
comm->forward_comm(this);
@ -189,9 +183,9 @@ void ComputeClusterAtom::compute_peratom()
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq) {
clusterID[i] = clusterID[j] = MIN(clusterID[i],clusterID[j]);
clusterID[i] = clusterID[j] = MIN(clusterID[i], clusterID[j]);
done = 0;
}
}
@ -202,17 +196,17 @@ void ComputeClusterAtom::compute_peratom()
// stop if all procs are done
MPI_Allreduce(&change,&anychange,1,MPI_INT,MPI_MAX,world);
MPI_Allreduce(&change, &anychange, 1, MPI_INT, MPI_MAX, world);
if (!anychange) break;
}
}
/* ---------------------------------------------------------------------- */
int ComputeClusterAtom::pack_forward_comm(int n, int *list, double *buf,
int /*pbc_flag*/, int * /*pbc*/)
int ComputeClusterAtom::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/,
int * /*pbc*/)
{
int i,j,m;
int i, j, m;
m = 0;
if (commflag == CLUSTER) {
@ -243,7 +237,7 @@ int ComputeClusterAtom::pack_forward_comm(int n, int *list, double *buf,
void ComputeClusterAtom::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
m = 0;
last = first + n;
@ -268,6 +262,6 @@ void ComputeClusterAtom::unpack_forward_comm(int n, int first, double *buf)
double ComputeClusterAtom::memory_usage()
{
double bytes = (double)nmax * sizeof(double);
double bytes = (double) nmax * sizeof(double);
return bytes;
}