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enable and apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2022-03-05 20:21:32 -05:00
parent de4b9a1d20
commit 8fe78e5fc4
1 changed files with 39 additions and 43 deletions
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82
src/compute_aggregate_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
@ -32,24 +31,23 @@
#include "pair.h"
#include "update.h"
#include <cstring>
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeAggregateAtom::ComputeAggregateAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
aggregateID(nullptr)
Compute(lmp, narg, arg), aggregateID(nullptr)
{
if (narg != 4) error->all(FLERR,"Illegal compute aggregate/atom command");
if (narg != 4) error->all(FLERR, "Illegal compute aggregate/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;
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Compute aggregate/atom used when bonds are not allowed");
error->all(FLERR, "Compute aggregate/atom used when bonds are not allowed");
peratom_flag = 1;
size_peratom_cols = 0;
@ -71,26 +69,24 @@ ComputeAggregateAtom::~ComputeAggregateAtom()
void ComputeAggregateAtom::init()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use compute aggregate/atom unless atoms have IDs");
error->all(FLERR, "Cannot use compute aggregate/atom unless atoms have IDs");
if (force->bond == nullptr)
error->all(FLERR,"Compute aggregate/atom requires a bond style to be defined");
error->all(FLERR, "Compute aggregate/atom requires a bond style to be defined");
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
neighbor->add_request(this,NeighConst::REQ_FULL|NeighConst::REQ_OCCASIONAL);
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,"aggregate/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute aggregate/atom");
if (strcmp(modify->compute[i]->style, "aggregate/atom") == 0) count++;
if (count > 1 && comm->me == 0) error->warning(FLERR, "More than one compute aggregate/atom");
}
/* ---------------------------------------------------------------------- */
@ -104,7 +100,7 @@ void ComputeAggregateAtom::init_list(int /*id*/, NeighList *ptr)
void ComputeAggregateAtom::compute_peratom()
{
int i,j,k;
int i, j, k;
invoked_peratom = update->ntimestep;
@ -113,15 +109,17 @@ void ComputeAggregateAtom::compute_peratom()
if (atom->nmax > nmax) {
memory->destroy(aggregateID);
nmax = atom->nmax;
memory->create(aggregateID,nmax,"aggregate/atom:aggregateID");
memory->create(aggregateID, nmax, "aggregate/atom:aggregateID");
vector_atom = aggregateID;
}
// 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);
// if group is dynamic, insure ghost atom masks are current
@ -145,8 +143,10 @@ void ComputeAggregateAtom::compute_peratom()
double **x = atom->x;
for (i = 0; i < nlocal + atom->nghost; i++)
if (mask[i] & groupbit) aggregateID[i] = tag[i];
else aggregateID[i] = 0;
if (mask[i] & groupbit)
aggregateID[i] = tag[i];
else
aggregateID[i] = 0;
// loop until no more changes on any proc:
// acquire aggregateIDs of ghost atoms
@ -159,15 +159,14 @@ void ComputeAggregateAtom::compute_peratom()
commflag = 1;
int change,done,anychange;
int change, done, anychange;
while (true) {
comm->forward_comm(this);
// reverse communication when bonds are not stored on every processor
if (force->newton_bond)
comm->reverse_comm(this);
if (force->newton_bond) comm->reverse_comm(this);
change = 0;
while (true) {
@ -182,7 +181,7 @@ void ComputeAggregateAtom::compute_peratom()
if (!(mask[k] & groupbit)) continue;
if (aggregateID[i] == aggregateID[k]) continue;
aggregateID[i] = aggregateID[k] = MIN(aggregateID[i],aggregateID[k]);
aggregateID[i] = aggregateID[k] = MIN(aggregateID[i], aggregateID[k]);
done = 0;
}
}
@ -206,10 +205,9 @@ void ComputeAggregateAtom::compute_peratom()
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
const double rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq) {
aggregateID[i] = aggregateID[j]
= MIN(aggregateID[i],aggregateID[j]);
aggregateID[i] = aggregateID[j] = MIN(aggregateID[i], aggregateID[j]);
done = 0;
}
}
@ -220,17 +218,17 @@ void ComputeAggregateAtom::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 ComputeAggregateAtom::pack_forward_comm(int n, int *list, double *buf,
int /*pbc_flag*/, int * /*pbc*/)
int ComputeAggregateAtom::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) {
@ -253,7 +251,7 @@ int ComputeAggregateAtom::pack_forward_comm(int n, int *list, double *buf,
void ComputeAggregateAtom::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
m = 0;
last = first + n;
@ -263,7 +261,7 @@ void ComputeAggregateAtom::unpack_forward_comm(int n, int first, double *buf)
// only overwrite ghost IDs with values lower than current ones
aggregateID[i] = MIN(x,aggregateID[i]);
aggregateID[i] = MIN(x, aggregateID[i]);
}
else {
int *mask = atom->mask;
@ -275,13 +273,11 @@ void ComputeAggregateAtom::unpack_forward_comm(int n, int first, double *buf)
int ComputeAggregateAtom::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = aggregateID[i];
}
for (i = first; i < last; i++) { buf[m++] = aggregateID[i]; }
return m;
}
@ -289,7 +285,7 @@ int ComputeAggregateAtom::pack_reverse_comm(int n, int first, double *buf)
void ComputeAggregateAtom::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
int i, j, m;
m = 0;
for (i = 0; i < n; i++) {
@ -298,7 +294,7 @@ void ComputeAggregateAtom::unpack_reverse_comm(int n, int *list, double *buf)
// only overwrite local IDs with values lower than current ones
aggregateID[j] = MIN(x,aggregateID[j]);
aggregateID[j] = MIN(x, aggregateID[j]);
}
}
@ -308,6 +304,6 @@ void ComputeAggregateAtom::unpack_reverse_comm(int n, int *list, double *buf)
double ComputeAggregateAtom::memory_usage()
{
double bytes = (double)nmax * sizeof(double);
double bytes = (double) nmax * sizeof(double);
return bytes;
}