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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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83
src/compute_temp_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
@ -28,14 +27,12 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
idregion(nullptr)
Compute(lmp, narg, arg), region(nullptr), idregion(nullptr)
{
if (narg != 4) error->all(FLERR,"Illegal compute temp/region command");
if (narg != 4) error->all(FLERR, "Illegal compute temp/region command");
iregion = domain->find_region(arg[3]);
if (iregion == -1)
error->all(FLERR,"Region ID for compute temp/region does not exist");
if (!domain->get_region_by_id(arg[3]))
error->all(FLERR, "Region {} for compute temp/region does not exist", arg[3]);
idregion = utils::strdup(arg[3]);
scalar_flag = vector_flag = 1;
@ -54,9 +51,9 @@ ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
ComputeTempRegion::~ComputeTempRegion()
{
delete [] idregion;
delete[] idregion;
memory->destroy(vbiasall);
delete [] vector;
delete[] vector;
}
/* ---------------------------------------------------------------------- */
@ -65,9 +62,8 @@ void ComputeTempRegion::init()
{
// set index and check validity of region
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for compute temp/region does not exist");
region = domain->get_region_by_id(idregion);
if (!region) error->all(FLERR, "Region {} for compute temp/region does not exist", idregion);
}
/* ---------------------------------------------------------------------- */
@ -83,7 +79,7 @@ void ComputeTempRegion::setup()
void ComputeTempRegion::dof_remove_pre()
{
domain->regions[iregion]->prematch();
region->prematch();
}
/* ---------------------------------------------------------------------- */
@ -91,7 +87,7 @@ void ComputeTempRegion::dof_remove_pre()
int ComputeTempRegion::dof_remove(int i)
{
double *x = atom->x[i];
if (domain->regions[iregion]->match(x[0],x[1],x[2])) return 0;
if (region->match(x[0], x[1], x[2])) return 0;
return 1;
}
@ -109,7 +105,6 @@ double ComputeTempRegion::compute_scalar()
int *mask = atom->mask;
int nlocal = atom->nlocal;
Region *region = domain->regions[iregion];
region->prematch();
int count = 0;
@ -117,28 +112,29 @@ double ComputeTempRegion::compute_scalar()
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) {
count++;
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
t += (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]) * rmass[i];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) {
count++;
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
t += (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]) * mass[type[i]];
}
}
double tarray[2],tarray_all[2];
double tarray[2], tarray_all[2];
tarray[0] = count;
tarray[1] = t;
MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(tarray, tarray_all, 2, MPI_DOUBLE, MPI_SUM, world);
dof = domain->dimension * tarray_all[0] - extra_dof;
if (dof < 0.0 && tarray_all[0] > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
if (dof > 0) scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz);
else scalar = 0.0;
error->all(FLERR, "Temperature compute degrees of freedom < 0");
if (dof > 0)
scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz);
else
scalar = 0.0;
return scalar;
}
@ -158,25 +154,26 @@ void ComputeTempRegion::compute_vector()
int *mask = atom->mask;
int nlocal = atom->nlocal;
Region *region = domain->regions[iregion];
region->prematch();
double massone,t[6];
double massone, t[6];
for (i = 0; i < 6; i++) t[i] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
t[0] += massone * v[i][0]*v[i][0];
t[1] += massone * v[i][1]*v[i][1];
t[2] += massone * v[i][2]*v[i][2];
t[3] += massone * v[i][0]*v[i][1];
t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2];
if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) {
if (rmass)
massone = rmass[i];
else
massone = mass[type[i]];
t[0] += massone * v[i][0] * v[i][0];
t[1] += massone * v[i][1] * v[i][1];
t[2] += massone * v[i][2] * v[i][2];
t[3] += massone * v[i][0] * v[i][1];
t[4] += massone * v[i][0] * v[i][2];
t[5] += massone * v[i][1] * v[i][2];
}
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(t, vector, 6, MPI_DOUBLE, MPI_SUM, world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
@ -187,7 +184,7 @@ void ComputeTempRegion::compute_vector()
void ComputeTempRegion::remove_bias(int i, double *v)
{
double *x = atom->x[i];
if (domain->regions[iregion]->match(x[0],x[1],x[2]))
if (region->match(x[0], x[1], x[2]))
vbias[0] = vbias[1] = vbias[2] = 0.0;
else {
vbias[0] = v[0];
@ -204,7 +201,7 @@ void ComputeTempRegion::remove_bias(int i, double *v)
void ComputeTempRegion::remove_bias_thr(int i, double *v, double *b)
{
double *x = atom->x[i];
if (domain->regions[iregion]->match(x[0],x[1],x[2]))
if (region->match(x[0], x[1], x[2]))
b[0] = b[1] = b[2] = 0.0;
else {
b[0] = v[0];
@ -228,14 +225,12 @@ void ComputeTempRegion::remove_bias_all()
if (atom->nmax > maxbias) {
memory->destroy(vbiasall);
maxbias = atom->nmax;
memory->create(vbiasall,maxbias,3,"temp/region:vbiasall");
memory->create(vbiasall, maxbias, 3, "temp/region:vbiasall");
}
Region *region = domain->regions[iregion];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region->match(x[i][0],x[i][1],x[i][2]))
if (region->match(x[i][0], x[i][1], x[i][2]))
vbiasall[i][0] = vbiasall[i][1] = vbiasall[i][2] = 0.0;
else {
vbiasall[i][0] = v[i][0];
@ -293,6 +288,6 @@ void ComputeTempRegion::restore_bias_all()
double ComputeTempRegion::memory_usage()
{
double bytes = 3*maxbias * sizeof(double);
double bytes = 3 * maxbias * sizeof(double);
return bytes;
}