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enable and apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2022-05-22 03:29:33 -04:00
parent b407b2f239
commit 9a973e67fa
23 changed files with 196 additions and 267 deletions
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159
src/compute_stress_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
@ -33,15 +32,14 @@
using namespace LAMMPS_NS;
enum{NOBIAS,BIAS};
enum { NOBIAS, BIAS };
/* ---------------------------------------------------------------------- */
ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
id_temp(nullptr), stress(nullptr)
Compute(lmp, narg, arg), id_temp(nullptr), stress(nullptr)
{
if (narg < 4) error->all(FLERR,"Illegal compute stress/atom command");
if (narg < 4) error->all(FLERR, "Illegal compute stress/atom command");
peratom_flag = 1;
size_peratom_cols = 6;
@ -52,17 +50,15 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
// store temperature ID used by stress computation
// insure it is valid for temperature computation
if (strcmp(arg[3],"NULL") == 0) id_temp = nullptr;
if (strcmp(arg[3], "NULL") == 0)
id_temp = nullptr;
else {
id_temp = utils::strdup(arg[3]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Could not find compute stress/atom temperature ID");
if (icompute < 0) error->all(FLERR, "Could not find compute stress/atom temperature ID");
if (modify->compute[icompute]->tempflag == 0)
error->all(FLERR,
"Compute stress/atom temperature ID does not "
"compute temperature");
error->all(FLERR, "Compute stress/atom temperature ID does not compute temperature");
}
// process optional args
@ -81,19 +77,28 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
fixflag = 0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
else if (strcmp(arg[iarg],"virial") == 0) {
if (strcmp(arg[iarg], "ke") == 0)
keflag = 1;
else if (strcmp(arg[iarg], "pair") == 0)
pairflag = 1;
else if (strcmp(arg[iarg], "bond") == 0)
bondflag = 1;
else if (strcmp(arg[iarg], "angle") == 0)
angleflag = 1;
else if (strcmp(arg[iarg], "dihedral") == 0)
dihedralflag = 1;
else if (strcmp(arg[iarg], "improper") == 0)
improperflag = 1;
else if (strcmp(arg[iarg], "kspace") == 0)
kspaceflag = 1;
else if (strcmp(arg[iarg], "fix") == 0)
fixflag = 1;
else if (strcmp(arg[iarg], "virial") == 0) {
pairflag = 1;
bondflag = angleflag = dihedralflag = improperflag = 1;
kspaceflag = fixflag = 1;
} else error->all(FLERR,"Illegal compute stress/atom command");
} else
error->all(FLERR, "Illegal compute stress/atom command");
iarg++;
}
}
@ -105,7 +110,7 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
ComputeStressAtom::~ComputeStressAtom()
{
delete [] id_temp;
delete[] id_temp;
memory->destroy(stress);
}
@ -118,24 +123,26 @@ void ComputeStressAtom::init()
if (id_temp) {
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Could not find compute stress/atom temperature ID");
if (icompute < 0) error->all(FLERR, "Could not find compute stress/atom temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempbias) biasflag = BIAS;
else biasflag = NOBIAS;
} else biasflag = NOBIAS;
if (temperature->tempbias)
biasflag = BIAS;
else
biasflag = NOBIAS;
} else
biasflag = NOBIAS;
}
/* ---------------------------------------------------------------------- */
void ComputeStressAtom::compute_peratom()
{
int i,j;
int i, j;
double onemass;
invoked_peratom = update->ntimestep;
if (update->vflag_atom != invoked_peratom)
error->all(FLERR,"Per-atom virial was not tallied on needed timestep");
error->all(FLERR, "Per-atom virial was not tallied on needed timestep");
// grow local stress array if necessary
// needs to be atom->nmax in length
@ -143,7 +150,7 @@ void ComputeStressAtom::compute_peratom()
if (atom->nmax > nmax) {
memory->destroy(stress);
nmax = atom->nmax;
memory->create(stress,nmax,6,"stress/atom:stress");
memory->create(stress, nmax, 6, "stress/atom:stress");
array_atom = stress;
}
@ -166,51 +173,44 @@ void ComputeStressAtom::compute_peratom()
// clear local stress array
for (i = 0; i < ntotal; i++)
for (j = 0; j < 6; j++)
stress[i][j] = 0.0;
for (j = 0; j < 6; j++) stress[i][j] = 0.0;
// add in per-atom contributions from each force
if (pairflag && force->pair && force->pair->compute_flag) {
double **vatom = force->pair->vatom;
for (i = 0; i < npair; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
}
if (bondflag && force->bond) {
double **vatom = force->bond->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
}
if (angleflag && force->angle) {
double **vatom = force->angle->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
}
if (dihedralflag && force->dihedral) {
double **vatom = force->dihedral->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
}
if (improperflag && force->improper) {
double **vatom = force->improper->vatom;
for (i = 0; i < nbond; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
}
if (kspaceflag && force->kspace && force->kspace->compute_flag) {
double **vatom = force->kspace->vatom;
for (i = 0; i < nkspace; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
}
// add in per-atom contributions from relevant fixes
@ -225,15 +225,13 @@ void ComputeStressAtom::compute_peratom()
double **vatom = ifix->vatom;
if (vatom)
for (i = 0; i < nlocal; i++)
for (j = 0; j < 6; j++)
stress[i][j] += vatom[i][j];
for (j = 0; j < 6; j++) stress[i][j] += vatom[i][j];
}
}
// communicate ghost virials between neighbor procs
if (force->newton || (force->kspace && force->kspace->tip4pflag))
comm->reverse_comm(this);
if (force->newton || (force->kspace && force->kspace->tip4pflag)) comm->reverse_comm(this);
// zero virial of atoms not in group
// only do this after comm since ghost contributions must be included
@ -266,24 +264,24 @@ void ComputeStressAtom::compute_peratom()
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
onemass = mvv2e * rmass[i];
stress[i][0] += onemass*v[i][0]*v[i][0];
stress[i][1] += onemass*v[i][1]*v[i][1];
stress[i][2] += onemass*v[i][2]*v[i][2];
stress[i][3] += onemass*v[i][0]*v[i][1];
stress[i][4] += onemass*v[i][0]*v[i][2];
stress[i][5] += onemass*v[i][1]*v[i][2];
stress[i][0] += onemass * v[i][0] * v[i][0];
stress[i][1] += onemass * v[i][1] * v[i][1];
stress[i][2] += onemass * v[i][2] * v[i][2];
stress[i][3] += onemass * v[i][0] * v[i][1];
stress[i][4] += onemass * v[i][0] * v[i][2];
stress[i][5] += onemass * v[i][1] * v[i][2];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
onemass = mvv2e * mass[type[i]];
stress[i][0] += onemass*v[i][0]*v[i][0];
stress[i][1] += onemass*v[i][1]*v[i][1];
stress[i][2] += onemass*v[i][2]*v[i][2];
stress[i][3] += onemass*v[i][0]*v[i][1];
stress[i][4] += onemass*v[i][0]*v[i][2];
stress[i][5] += onemass*v[i][1]*v[i][2];
stress[i][0] += onemass * v[i][0] * v[i][0];
stress[i][1] += onemass * v[i][1] * v[i][1];
stress[i][2] += onemass * v[i][2] * v[i][2];
stress[i][3] += onemass * v[i][0] * v[i][1];
stress[i][4] += onemass * v[i][0] * v[i][2];
stress[i][5] += onemass * v[i][1] * v[i][2];
}
}
@ -292,35 +290,34 @@ void ComputeStressAtom::compute_peratom()
// invoke temperature if it hasn't been already
// this insures bias factor is pre-computed
if (keflag && temperature->invoked_scalar != update->ntimestep)
temperature->compute_scalar();
if (keflag && temperature->invoked_scalar != update->ntimestep) temperature->compute_scalar();
if (rmass) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
temperature->remove_bias(i, v[i]);
onemass = mvv2e * rmass[i];
stress[i][0] += onemass*v[i][0]*v[i][0];
stress[i][1] += onemass*v[i][1]*v[i][1];
stress[i][2] += onemass*v[i][2]*v[i][2];
stress[i][3] += onemass*v[i][0]*v[i][1];
stress[i][4] += onemass*v[i][0]*v[i][2];
stress[i][5] += onemass*v[i][1]*v[i][2];
temperature->restore_bias(i,v[i]);
stress[i][0] += onemass * v[i][0] * v[i][0];
stress[i][1] += onemass * v[i][1] * v[i][1];
stress[i][2] += onemass * v[i][2] * v[i][2];
stress[i][3] += onemass * v[i][0] * v[i][1];
stress[i][4] += onemass * v[i][0] * v[i][2];
stress[i][5] += onemass * v[i][1] * v[i][2];
temperature->restore_bias(i, v[i]);
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
temperature->remove_bias(i, v[i]);
onemass = mvv2e * mass[type[i]];
stress[i][0] += onemass*v[i][0]*v[i][0];
stress[i][1] += onemass*v[i][1]*v[i][1];
stress[i][2] += onemass*v[i][2]*v[i][2];
stress[i][3] += onemass*v[i][0]*v[i][1];
stress[i][4] += onemass*v[i][0]*v[i][2];
stress[i][5] += onemass*v[i][1]*v[i][2];
temperature->restore_bias(i,v[i]);
stress[i][0] += onemass * v[i][0] * v[i][0];
stress[i][1] += onemass * v[i][1] * v[i][1];
stress[i][2] += onemass * v[i][2] * v[i][2];
stress[i][3] += onemass * v[i][0] * v[i][1];
stress[i][4] += onemass * v[i][0] * v[i][2];
stress[i][5] += onemass * v[i][1] * v[i][2];
temperature->restore_bias(i, v[i]);
}
}
}
@ -344,7 +341,7 @@ void ComputeStressAtom::compute_peratom()
int ComputeStressAtom::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
int i, m, last;
m = 0;
last = first + n;
@ -363,7 +360,7 @@ int ComputeStressAtom::pack_reverse_comm(int n, int first, double *buf)
void ComputeStressAtom::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++) {
@ -383,6 +380,6 @@ void ComputeStressAtom::unpack_reverse_comm(int n, int *list, double *buf)
double ComputeStressAtom::memory_usage()
{
double bytes = (double)nmax*6 * sizeof(double);
double bytes = (double) nmax * 6 * sizeof(double);
return bytes;
}