ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

enable and apply clang-format

Browse Source
This commit is contained in:
Axel Kohlmeyer
2025-01-23 04:54:45 -05:00
parent 4be26c3480
commit d1dc0f7efc
1 changed files with 90 additions and 87 deletions
Download Patch File Download Diff File Expand all files Collapse all files

177
src/DRUDE/compute_temp_drude.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -29,10 +28,9 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempDrude::ComputeTempDrude(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
ComputeTempDrude::ComputeTempDrude(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute temp command");
if (narg != 3) error->all(FLERR, "Illegal compute temp command");
vector_flag = 1;
scalar_flag = 1;
@ -42,7 +40,7 @@ ComputeTempDrude::ComputeTempDrude(LAMMPS *lmp, int narg, char **arg) :
extlist = new int[6];
extlist[0] = extlist[1] = 0;
extlist[2] = extlist[3] = extlist[4] = extlist[5] = 1;
tempflag = 0; // because does not compute a single temperature (scalar and vector)
tempflag = 0; // because does not compute a single temperature (scalar and vector)
vector = new double[size_vector];
fix_drude = nullptr;
@ -69,7 +67,7 @@ void ComputeTempDrude::init()
fix_drude = dynamic_cast<FixDrude *>(fixes[0]);
if (!comm->ghost_velocity)
error->all(FLERR,"compute temp/drude requires ghost velocities. Use comm_modify vel yes");
error->all(FLERR, "compute temp/drude requires ghost velocities. Use comm_modify vel yes");
}
/* ---------------------------------------------------------------------- */
@ -93,15 +91,15 @@ void ComputeTempDrude::dof_compute()
bigint dof_core_loc = 0, dof_drude_loc = 0;
for (int i = 0; i < nlocal; i++) {
if (atom->mask[i] & groupbit) {
if (drudetype[type[i]] == DRUDE_TYPE) // Non-polarizable atom
dof_drude_loc++;
if (drudetype[type[i]] == DRUDE_TYPE) // Non-polarizable atom
dof_drude_loc++;
else
dof_core_loc++;
dof_core_loc++;
}
}
dof_core_loc *= dim;
dof_drude_loc *= dim;
MPI_Allreduce(&dof_core_loc, &dof_core, 1, MPI_LMP_BIGINT, MPI_SUM, world);
MPI_Allreduce(&dof_core_loc, &dof_core, 1, MPI_LMP_BIGINT, MPI_SUM, world);
MPI_Allreduce(&dof_drude_loc, &dof_drude, 1, MPI_LMP_BIGINT, MPI_SUM, world);
dof_core -= fix_dof;
vector[2] = dof_core;
@ -112,19 +110,19 @@ void ComputeTempDrude::dof_compute()
int ComputeTempDrude::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
delete [] id_temp;
if (strcmp(arg[0], "temp") == 0) {
if (narg < 2) utils::missing_cmd_args(FLERR, "compute_modify temp", error);
delete[] id_temp;
id_temp = utils::strdup(arg[1]);
temperature = modify->get_compute_by_id(id_temp);
if (!temperature)
error->all(FLERR,"Could not find fix_modify temperature compute {}", id_temp);
error->all(FLERR, "Could not find fix_modify temperature compute {}", id_temp);
if (temperature->tempflag == 0)
error->all(FLERR, "Fix_modify temperature compute {} does not compute temperature", id_temp);
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
error->warning(FLERR, "Group for fix_modify temp != fix group");
return 2;
}
return 0;
@ -134,64 +132,39 @@ int ComputeTempDrude::modify_param(int narg, char **arg)
void ComputeTempDrude::compute_vector()
{
invoked_vector = update->ntimestep;
invoked_vector = update->ntimestep;
int nlocal = atom->nlocal;
int *mask = atom->mask;
int *type = atom->type;
double *rmass = atom->rmass, *mass = atom->mass;
double **v = atom->v;
tagint *drudeid = fix_drude->drudeid;
int *drudetype = fix_drude->drudetype;
int dim = domain->dimension;
double mvv2e = force->mvv2e, kb = force->boltz;
int nlocal = atom->nlocal;
int *mask = atom->mask;
int *type = atom->type;
double *rmass = atom->rmass, *mass = atom->mass;
double **v = atom->v;
tagint *drudeid = fix_drude->drudeid;
int *drudetype = fix_drude->drudetype;
int dim = domain->dimension;
double mvv2e = force->mvv2e, kb = force->boltz;
double mcore, mdrude;
double ecore, edrude;
double *vcore, *vdrude;
double kineng_core_loc = 0., kineng_drude_loc = 0.;
for (int i=0; i<nlocal; i++) {
if (groupbit & mask[i] && drudetype[type[i]] != DRUDE_TYPE) {
if (drudetype[type[i]] == NOPOL_TYPE) {
ecore = 0.;
vcore = v[i];
if (temperature) temperature->remove_bias(i, vcore);
for (int k=0; k<dim; k++) ecore += vcore[k]*vcore[k];
if (temperature) temperature->restore_bias(i, vcore);
if (rmass) mcore = rmass[i];
else mcore = mass[type[i]];
kineng_core_loc += mcore * ecore;
} else { // CORE_TYPE
int j = atom->map(drudeid[i]);
if (rmass) {
mcore = rmass[i];
mdrude = rmass[j];
} else {
mcore = mass[type[i]];
mdrude = mass[type[j]];
}
double mtot_inv = 1. / (mcore + mdrude);
ecore = 0.;
edrude = 0.;
vcore = v[i];
vdrude = v[j];
if (temperature) {
temperature->remove_bias(i, vcore);
temperature->remove_bias(j, vdrude);
}
for (int k=0; k<dim; k++) {
double v1 = mdrude * vdrude[k] + mcore * vcore[k];
ecore += v1 * v1;
double v2 = vdrude[k] - vcore[k];
edrude += v2 * v2;
}
if (temperature) {
temperature->restore_bias(i, vcore);
temperature->restore_bias(j, vdrude);
}
kineng_core_loc += mtot_inv * ecore;
kineng_drude_loc += mtot_inv * mcore * mdrude * edrude;
}
double mcore, mdrude;
double ecore, edrude;
double *vcore, *vdrude;
double kineng_core_loc = 0.0, kineng_drude_loc = 0.0;
for (int i = 0; i < nlocal; i++) {
vdrude = nullptr;
vcore = nullptr;
if (groupbit & mask[i] && drudetype[type[i]] != DRUDE_TYPE) {
if (drudetype[type[i]] == NOPOL_TYPE) {
ecore = 0.0;
vcore = v[i];
if (temperature) temperature->remove_bias(i, vcore);
for (int k = 0; k < dim; k++) ecore += vcore[k] * vcore[k];
if (temperature) temperature->restore_bias(i, vcore);
if (rmass)
mcore = rmass[i];
else
mcore = mass[type[i]];
kineng_core_loc += mcore * ecore;
} else { // CORE_TYPE
int j = atom->map(drudeid[i]);
if (j < 0) {
if (drudeid[i] == 0) {
error->one(FLERR, "Drude atom for core atom ID {} is not defined", atom->tag[i]);
@ -200,24 +173,54 @@ void ComputeTempDrude::compute_vector()
atom->tag[i]);
}
}
if (rmass) {
mcore = rmass[i];
mdrude = rmass[j];
} else {
mcore = mass[type[i]];
mdrude = mass[type[j]];
}
double mtot_inv = 1.0 / (mcore + mdrude);
ecore = 0.0;
edrude = 0.0;
vcore = v[i];
vdrude = v[j];
if (temperature) {
temperature->remove_bias(i, vcore);
temperature->remove_bias(j, vdrude);
}
for (int k = 0; k < dim; k++) {
double v1 = mdrude * vdrude[k] + mcore * vcore[k];
ecore += v1 * v1;
double v2 = vdrude[k] - vcore[k];
edrude += v2 * v2;
}
if (temperature) {
temperature->restore_bias(i, vcore);
temperature->restore_bias(j, vdrude);
}
kineng_core_loc += mtot_inv * ecore;
kineng_drude_loc += mtot_inv * mcore * mdrude * edrude;
}
}
}
if (dynamic) dof_compute();
kineng_core_loc *= 0.5 * mvv2e;
kineng_drude_loc *= 0.5 * mvv2e;
MPI_Allreduce(&kineng_core_loc,&kineng_core,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&kineng_drude_loc,&kineng_drude,1,MPI_DOUBLE,MPI_SUM,world);
temp_core = 2.0 * kineng_core / (dof_core * kb);
temp_drude = 2.0 * kineng_drude / (dof_drude * kb);
vector[0] = temp_core;
vector[1] = temp_drude;
vector[4] = kineng_core;
vector[5] = kineng_drude;
if (dynamic) dof_compute();
kineng_core_loc *= 0.5 * mvv2e;
kineng_drude_loc *= 0.5 * mvv2e;
MPI_Allreduce(&kineng_core_loc, &kineng_core, 1, MPI_DOUBLE, MPI_SUM, world);
MPI_Allreduce(&kineng_drude_loc, &kineng_drude, 1, MPI_DOUBLE, MPI_SUM, world);
temp_core = 2.0 * kineng_core / (dof_core * kb);
temp_drude = 2.0 * kineng_drude / (dof_drude * kb);
vector[0] = temp_core;
vector[1] = temp_drude;
vector[4] = kineng_core;
vector[5] = kineng_drude;
}
double ComputeTempDrude::compute_scalar() {
compute_vector();
scalar = vector[0];
return scalar;
double ComputeTempDrude::compute_scalar()
{
compute_vector();
scalar = vector[0];
return scalar;
}