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refactor group access, enable and apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2022-04-14 22:01:48 -04:00
parent 4b400fb4a6
commit 69d9c5187e
187 changed files with 3016 additions and 2927 deletions
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130
src/compute_reduce_region.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
@ -29,12 +28,14 @@
using namespace LAMMPS_NS;
#define BIG 1.0e20
static constexpr double BIG = 1.0e20;
/* ---------------------------------------------------------------------- */
ComputeReduceRegion::ComputeReduceRegion(LAMMPS *lmp, int narg, char **arg) :
ComputeReduce(lmp, narg, arg) {}
ComputeReduce(lmp, narg, arg)
{
}
/* ----------------------------------------------------------------------
calculate reduced value for one input M and return it
@ -47,9 +48,6 @@ ComputeReduceRegion::ComputeReduceRegion(LAMMPS *lmp, int narg, char **arg) :
double ComputeReduceRegion::compute_one(int m, int flag)
{
int i;
Region *region = domain->regions[iregion];
region->prematch();
// invoke the appropriate attribute,compute,fix,variable
@ -78,26 +76,29 @@ double ComputeReduceRegion::compute_one(int m, int flag)
if (which[m] == ArgInfo::X) {
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
combine(one,x[i][j],i);
} else one = x[flag][j];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2]))
combine(one, x[i][j], i);
} else
one = x[flag][j];
} else if (which[m] == ArgInfo::V) {
double **v = atom->v;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
combine(one,v[i][j],i);
} else one = v[flag][j];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2]))
combine(one, v[i][j], i);
} else
one = v[flag][j];
} else if (which[m] == ArgInfo::F) {
double **f = atom->f;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
combine(one,f[i][j],i);
} else one = f[flag][j];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2]))
combine(one, f[i][j], i);
} else
one = f[flag][j];
// invoke compute if not previously invoked
// invoke compute if not previously invoked
} else if (which[m] == ArgInfo::COMPUTE) {
Compute *compute = modify->compute[n];
@ -111,18 +112,20 @@ double ComputeReduceRegion::compute_one(int m, int flag)
if (j == 0) {
double *compute_vector = compute->vector_atom;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
combine(one,compute_vector[i],i);
} else one = compute_vector[flag];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2]))
combine(one, compute_vector[i], i);
} else
one = compute_vector[flag];
} else {
double **compute_array = compute->array_atom;
int jm1 = j - 1;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
combine(one,compute_array[i][jm1],i);
} else one = compute_array[flag][jm1];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2]))
combine(one, compute_array[i][jm1], i);
} else
one = compute_array[flag][jm1];
}
} else if (flavor[m] == LOCAL) {
@ -134,76 +137,79 @@ double ComputeReduceRegion::compute_one(int m, int flag)
if (j == 0) {
double *compute_vector = compute->vector_local;
if (flag < 0)
for (i = 0; i < compute->size_local_rows; i++)
combine(one,compute_vector[i],i);
else one = compute_vector[flag];
for (int i = 0; i < compute->size_local_rows; i++) combine(one, compute_vector[i], i);
else
one = compute_vector[flag];
} else {
double **compute_array = compute->array_local;
int jm1 = j - 1;
if (flag < 0)
for (i = 0; i < compute->size_local_rows; i++)
combine(one,compute_array[i][jm1],i);
else one = compute_array[flag][jm1];
for (int i = 0; i < compute->size_local_rows; i++) combine(one, compute_array[i][jm1], i);
else
one = compute_array[flag][jm1];
}
}
// check if fix frequency is a match
// check if fix frequency is a match
} else if (which[m] == ArgInfo::FIX) {
if (update->ntimestep % modify->fix[n]->peratom_freq)
error->all(FLERR,"Fix used in compute reduce not computed at compatible time");
error->all(FLERR, "Fix used in compute reduce not computed at compatible time");
Fix *fix = modify->fix[n];
if (flavor[m] == PERATOM) {
if (j == 0) {
double *fix_vector = fix->vector_atom;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
combine(one,fix_vector[i],i);
} else one = fix_vector[flag];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2]))
combine(one, fix_vector[i], i);
} else
one = fix_vector[flag];
} else {
double **fix_array = fix->array_atom;
int jm1 = j - 1;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
combine(one,fix_array[i][jm1],i);
} else one = fix_array[flag][jm1];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2]))
combine(one, fix_array[i][jm1], i);
} else
one = fix_array[flag][jm1];
}
} else if (flavor[m] == LOCAL) {
if (j == 0) {
double *fix_vector = fix->vector_local;
if (flag < 0)
for (i = 0; i < fix->size_local_rows; i++)
combine(one,fix_vector[i],i);
else one = fix_vector[flag];
for (int i = 0; i < fix->size_local_rows; i++) combine(one, fix_vector[i], i);
else
one = fix_vector[flag];
} else {
double **fix_array = fix->array_local;
int jm1 = j - 1;
if (flag < 0)
for (i = 0; i < fix->size_local_rows; i++)
combine(one,fix_array[i][jm1],i);
else one = fix_array[flag][jm1];
for (int i = 0; i < fix->size_local_rows; i++) combine(one, fix_array[i][jm1], i);
else
one = fix_array[flag][jm1];
}
}
// evaluate atom-style variable
// evaluate atom-style variable
} else if (which[m] == ArgInfo::VARIABLE) {
if (atom->nmax > maxatom) {
maxatom = atom->nmax;
memory->destroy(varatom);
memory->create(varatom,maxatom,"reduce/region:varatom");
memory->create(varatom, maxatom, "reduce/region:varatom");
}
input->variable->compute_atom(n,igroup,varatom,1,0);
input->variable->compute_atom(n, igroup, varatom, 1, 0);
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
combine(one,varatom[i],i);
} else one = varatom[flag];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2]))
combine(one, varatom[i], i);
} else
one = varatom[flag];
}
return one;
@ -216,29 +222,29 @@ bigint ComputeReduceRegion::count(int m)
int n = value2index[m];
if (which[m] == ArgInfo::X || which[m] == ArgInfo::V || which[m] == ArgInfo::F)
return group->count(igroup,iregion);
return group->count(igroup, region);
else if (which[m] == ArgInfo::COMPUTE) {
Compute *compute = modify->compute[n];
if (flavor[m] == PERATOM) {
return group->count(igroup,iregion);
return group->count(igroup, region);
} else if (flavor[m] == LOCAL) {
bigint ncount = compute->size_local_rows;
bigint ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&ncount, &ncountall, 1, MPI_DOUBLE, MPI_SUM, world);
return ncountall;
}
} else if (which[m] == ArgInfo::FIX) {
Fix *fix = modify->fix[n];
if (flavor[m] == PERATOM) {
return group->count(igroup,iregion);
return group->count(igroup, region);
} else if (flavor[m] == LOCAL) {
bigint ncount = fix->size_local_rows;
bigint ncountall;
MPI_Allreduce(&ncount,&ncountall,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&ncount, &ncountall, 1, MPI_DOUBLE, MPI_SUM, world);
return ncountall;
}
} else if (which[m] == ArgInfo::VARIABLE)
return group->count(igroup,iregion);
return group->count(igroup, region);
bigint dummy = 0;
return dummy;