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reformat with clang-format

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This commit is contained in:
Axel Kohlmeyer
2021-07-29 13:29:56 -04:00
parent 508798ab2b
commit 2a1177fa92
1 changed files with 109 additions and 161 deletions
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270
src/SCAFACOS/scafacos.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
@ -25,10 +24,8 @@
#include "force.h"
#include "memory.h"
#include <cstring>
#include <cstdlib>
#include <string>
#include <sstream>
#include <cstring>
// ScaFaCoS library
@ -54,25 +51,24 @@ Scafacos::Scafacos(LAMMPS *lmp) : KSpace(lmp)
void Scafacos::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal scafacos command");
if (narg != 2) error->all(FLERR, "Illegal scafacos command");
method = utils::strdup(arg[0]);
tolerance = utils::numeric(FLERR,arg[1],false,lmp);
tolerance = utils::numeric(FLERR, arg[1], false, lmp);
// optional ScaFaCoS library setting defaults
// choose the correct default tolerance type for chosen method
// throw an error if a not yet supported solver is chosen
if (strcmp(method,"fmm") == 0) {
if (strcmp(method, "fmm") == 0) {
tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
fmm_tuning_flag = 0;
} else if (strcmp(method,"p3m") == 0 ||
strcmp(method,"p2nfft") == 0 ||
strcmp(method,"ewald") == 0) {
} else if (strcmp(method, "p3m") == 0 || strcmp(method, "p2nfft") == 0 ||
strcmp(method, "ewald") == 0) {
tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
} else if (strcmp(method,"direct") == 0) {
; // direct summation has no tolerance type
} else if (strcmp(method, "direct") == 0) {
; // direct summation has no tolerance type
} else {
error->all(FLERR,"Unsupported ScaFaCoS method");
error->all(FLERR, "Unsupported ScaFaCoS method");
}
}
@ -87,7 +83,7 @@ Scafacos::~Scafacos()
memory->destroy(efield);
// clean up of the ScaFaCoS handle and internal arrays
fcs_destroy((FCS)fcs);
fcs_destroy((FCS) fcs);
}
/* ---------------------------------------------------------------------- */
@ -96,26 +92,23 @@ void Scafacos::init()
{
// error checks
if (me == 0) {
utils::logmesg(lmp,"Setting up ScaFaCoS with solver {} ...\n",method);
utils::logmesg(lmp, "Setting up ScaFaCoS with solver {} ...\n", method);
if (strcmp(method,"p3m") == 0)
error->warning(FLERR,"Virial computation for P3M not available");
if (strcmp(method, "p3m") == 0)
error->warning(FLERR, "Virial computation for P3M not available");
if (strcmp(method,"ewald") == 0)
error->warning(FLERR,"Virial computation for Ewald not available");
if (strcmp(method, "ewald") == 0)
error->warning(FLERR, "Virial computation for Ewald not available");
}
if (!atom->q_flag)
error->all(FLERR,"Kspace style requires atom attribute q");
if (!atom->q_flag) error->all(FLERR, "Kspace style requires atom attribute q");
if (domain->dimension == 2)
error->all(FLERR,"Cannot use ScaFaCoS with 2d simulation");
if (domain->dimension == 2) error->all(FLERR, "Cannot use ScaFaCoS with 2d simulation");
if (domain->triclinic)
error->all(FLERR,"Cannot use ScaFaCoS with triclinic domain yet");
if (domain->triclinic) error->all(FLERR, "Cannot use ScaFaCoS with triclinic domain yet");
if (atom->natoms > INT_MAX && sizeof(int) != 8)
error->all(FLERR,"Scafacos atom count exceeds 2B");
error->all(FLERR, "Scafacos atom count exceeds 2B");
if (atom->molecular != Atom::ATOMIC)
error->all(FLERR, "Cannot use Scafacos with molecular charged systems yet");
@ -127,47 +120,44 @@ void Scafacos::init()
qqrd2e = force->qqrd2e;
if (!initialized) {
result = fcs_init((FCS*)&fcs,method,world);
check_result((void*)&result);
result = fcs_init((FCS *) &fcs, method, world);
check_result((void *) &result);
setup_handle();
// using other methods lead to termination of the program,
// since they have no tolerance tuning methods
if ( strcmp(method,"fmm") == 0 ||
strcmp(method,"p3m") == 0 ||
strcmp(method,"p2nfft") == 0 ||
strcmp(method,"ewald") == 0)
{
result = fcs_set_tolerance((FCS)fcs,tolerance_type,tolerance);
check_result((void*)&result);
if (strcmp(method, "fmm") == 0 || strcmp(method, "p3m") == 0 || strcmp(method, "p2nfft") == 0 ||
strcmp(method, "ewald") == 0) {
result = fcs_set_tolerance((FCS) fcs, tolerance_type, tolerance);
check_result((void *) &result);
}
double **x = atom->x;
double *q = atom->q;
int nlocal = atom->nlocal;
if (strcmp(method,"fmm") == 0) {
if (strcmp(method, "fmm") == 0) {
if (fmm_tuning_flag == 1)
fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_INHOMOGENOUS_SYSTEM);
fcs_fmm_set_internal_tuning((FCS) fcs, FCS_FMM_INHOMOGENOUS_SYSTEM);
else
fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_HOMOGENOUS_SYSTEM);
fcs_fmm_set_internal_tuning((FCS) fcs, FCS_FMM_HOMOGENOUS_SYSTEM);
}
// for the FMM at least one particle is required per process
if (strcmp(method,"fmm") == 0) {
int empty = (nlocal==0)?1:0;
MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world);
if (strcmp(method, "fmm") == 0) {
int empty = (nlocal == 0) ? 1 : 0;
MPI_Allreduce(MPI_IN_PLACE, &empty, 1, MPI_INT, MPI_SUM, world);
if (empty > 0)
fcs_set_redistribute((FCS)fcs,1);
fcs_set_redistribute((FCS) fcs, 1);
else
fcs_set_redistribute((FCS)fcs,0);
fcs_set_redistribute((FCS) fcs, 0);
}
result = fcs_tune((FCS)fcs,nlocal,&x[0][0],q);
check_result((void*)&result);
result = fcs_tune((FCS) fcs, nlocal, &x[0][0], q);
check_result((void *) &result);
// more useful here, since the parameters should be tuned now
if (me == 0) fcs_print_parameters((FCS)fcs);
if (me == 0) fcs_print_parameters((FCS) fcs);
}
initialized = 1;
@ -185,17 +175,16 @@ void Scafacos::compute(int eflag, int vflag)
FCSResult result;
// for the FMM at least one particle is required per process
if (strcmp(method,"fmm"))
{
int empty = (nlocal==0)?1:0;
MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world);
if (strcmp(method, "fmm")) {
int empty = (nlocal == 0) ? 1 : 0;
MPI_Allreduce(MPI_IN_PLACE, &empty, 1, MPI_INT, MPI_SUM, world);
if (empty > 0)
fcs_set_redistribute((FCS)fcs,1);
fcs_set_redistribute((FCS) fcs, 1);
else
fcs_set_redistribute((FCS)fcs,0);
fcs_set_redistribute((FCS) fcs, 0);
}
ev_init(eflag,vflag);
ev_init(eflag, vflag);
// grow xpbc, epot, efield if necessary
@ -204,28 +193,26 @@ void Scafacos::compute(int eflag, int vflag)
memory->destroy(epot);
memory->destroy(efield);
maxatom = atom->nmax;
memory->create(xpbc,3*maxatom,"scafacos:xpbc");
memory->create(epot,maxatom,"scafacos:epot");
memory->create(efield,maxatom,3,"scafacos:efield");
memory->create(xpbc, 3 * maxatom, "scafacos:xpbc");
memory->create(epot, maxatom, "scafacos:epot");
memory->create(efield, maxatom, 3, "scafacos:efield");
}
if (vflag_global) {
// for P3M or Ewald we cannot compute the virial. skip it.
if ((strcmp(method,"p3m") != 0)
&& (strcmp(method,"ewald") != 0)) {
result = fcs_set_compute_virial((FCS)fcs,1);
check_result((void*)&result);
if ((strcmp(method, "p3m") != 0) && (strcmp(method, "ewald") != 0)) {
result = fcs_set_compute_virial((FCS) fcs, 1);
check_result((void *) &result);
}
}
// pack coords into xpbc and apply PBC
memcpy(xpbc,&x[0][0],3*nlocal*sizeof(double));
memcpy(xpbc, &x[0][0], 3 * nlocal * sizeof(double));
if (domain->xperiodic || domain -> yperiodic || domain -> zperiodic) {
int j = 0;
if (domain->xperiodic || domain->yperiodic || domain->zperiodic) {
int j = 0;
for (int i = 0; i < nlocal; i++) {
domain->remap(&xpbc[j]);
j += 3;
@ -236,14 +223,14 @@ void Scafacos::compute(int eflag, int vflag)
if (box_has_changed()) {
setup_handle();
result = fcs_tune((FCS)fcs,nlocal,xpbc,q);
check_result((void*)&result);
result = fcs_tune((FCS) fcs, nlocal, xpbc, q);
check_result((void *) &result);
}
// invoke ScaFaCoS solver
result = fcs_run((FCS)fcs,nlocal,xpbc,q,&efield[0][0],epot);
check_result((void*)&result);
result = fcs_run((FCS) fcs, nlocal, xpbc, q, &efield[0][0], epot);
check_result((void *) &result);
// extract virial
@ -251,10 +238,9 @@ void Scafacos::compute(int eflag, int vflag)
// for P3M or Ewald we cannot compute the virial. skip it.
if ((strcmp(method,"p3m") != 0)
&& (strcmp(method,"ewald") != 0)) {
result = fcs_get_virial((FCS)fcs,virial_int);
check_result((void*)&result);
if ((strcmp(method, "p3m") != 0) && (strcmp(method, "ewald") != 0)) {
result = fcs_get_virial((FCS) fcs, virial_int);
check_result((void *) &result);
virial[0] = virial_int[0];
virial[1] = virial_int[1];
@ -282,11 +268,10 @@ void Scafacos::compute(int eflag, int vflag)
}
if (eflag_atom) {
for (int i = 0; i < nlocal; i++)
eatom[i] = 0.5 * qscale * q[i] * epot[i];
for (int i = 0; i < nlocal; i++) eatom[i] = 0.5 * qscale * q[i] * epot[i];
}
MPI_Allreduce(&myeng,&energy,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&myeng, &energy, 1, MPI_DOUBLE, MPI_SUM, world);
}
/* ---------------------------------------------------------------------- */
@ -299,55 +284,34 @@ int Scafacos::modify_param(int narg, char **arg)
// value1 = energy, energy_rel, etc
// everyone of these should have a default, so user doesn't need to set
if (strcmp(arg[0],"scafacos") != 0) return 0;
if (strcmp(arg[0], "scafacos") != 0) return 0;
if (strcmp(arg[1],"tolerance") == 0) {
if (narg < 3) error->all(FLERR,
"Illegal kspace_modify command (tolerance)");
if (strcmp(arg[2],"energy") == 0)
if (strcmp(arg[1], "tolerance") == 0) {
if (narg < 3) error->all(FLERR, "Illegal kspace_modify command (tolerance)");
if (strcmp(arg[2], "energy") == 0)
tolerance_type = FCS_TOLERANCE_TYPE_ENERGY;
else if (strcmp(arg[2],"energy_rel") == 0)
else if (strcmp(arg[2], "energy_rel") == 0)
tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL;
else if (strcmp(arg[2],"field") == 0)
else if (strcmp(arg[2], "field") == 0)
tolerance_type = FCS_TOLERANCE_TYPE_FIELD;
else if (strcmp(arg[2],"field_rel") == 0)
else if (strcmp(arg[2], "field_rel") == 0)
tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL;
else if (strcmp(arg[2],"potential") == 0)
else if (strcmp(arg[2], "potential") == 0)
tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL;
else if (strcmp(arg[2],"potential_rel") == 0)
else if (strcmp(arg[2], "potential_rel") == 0)
tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL;
else error->all(FLERR,
"Illegal kspace_modify command (tolerance argument)");
else
error->all(FLERR, "Illegal kspace_modify command (tolerance argument)");
// check if method is compatatible to chosen tolerance type
if (
(
strcmp(method,"fmm") == 0 &&
(
tolerance_type != FCS_TOLERANCE_TYPE_ENERGY &&
tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL
)
) ||
(
strcmp(method,"p2nfft") == 0 &&
(
tolerance_type != FCS_TOLERANCE_TYPE_FIELD &&
tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL
)
) ||
(
strcmp(method,"p3m") == 0 &&
(
tolerance_type != FCS_TOLERANCE_TYPE_FIELD
)
) ||
(
strcmp(method,"ewald") == 0 &&
(
tolerance_type != FCS_TOLERANCE_TYPE_FIELD
)
)
)
error->all(FLERR,"Illegal kspace_modify command \
if ((strcmp(method, "fmm") == 0 &&
(tolerance_type != FCS_TOLERANCE_TYPE_ENERGY &&
tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL)) ||
(strcmp(method, "p2nfft") == 0 &&
(tolerance_type != FCS_TOLERANCE_TYPE_FIELD &&
tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL)) ||
(strcmp(method, "p3m") == 0 && (tolerance_type != FCS_TOLERANCE_TYPE_FIELD)) ||
(strcmp(method, "ewald") == 0 && (tolerance_type != FCS_TOLERANCE_TYPE_FIELD)))
error->all(FLERR, "Illegal kspace_modify command \
(invalid tolerance / method combination)");
return 3;
}
@ -356,13 +320,11 @@ int Scafacos::modify_param(int narg, char **arg)
// value1 = 0, 1
// 0 -> homogenous system (default)
// 1 -> inhomogenous system (more internal tuning is provided (sequential!))
if (strcmp(arg[1],"fmm_tuning") == 0) {
if (me == 0)
utils::logmesg(lmp, "ScaFaCoS setting fmm inhomogen tuning ...\n");
if (strcmp(arg[1], "fmm_tuning") == 0) {
if (me == 0) utils::logmesg(lmp, "ScaFaCoS setting fmm inhomogen tuning ...\n");
if (narg < 3) error->all(FLERR,
"Illegal kspace_modify command (fmm_tuning)");
fmm_tuning_flag = utils::inumeric(FLERR, arg[2], false, tmp);
if (narg < 3) error->all(FLERR, "Illegal kspace_modify command (fmm_tuning)");
fmm_tuning_flag = utils::inumeric(FLERR, arg[2], false, lmp);
return 3;
}
@ -376,8 +338,8 @@ int Scafacos::modify_param(int narg, char **arg)
double Scafacos::memory_usage()
{
double bytes = 0.0;
bytes += (double)maxatom * sizeof(double);
bytes += (double)3*maxatom * sizeof(double);
bytes += (double) maxatom * sizeof(double);
bytes += (double) 3 * maxatom * sizeof(double);
return bytes;
}
@ -413,23 +375,23 @@ void Scafacos::setup_handle()
old_natoms = atom->natoms;
// store parameters to ScaFaCoS handle
result = fcs_set_box_a((FCS)fcs,old_box_x);
check_result((void*)&result);
result = fcs_set_box_a((FCS) fcs, old_box_x);
check_result((void *) &result);
result = fcs_set_box_b((FCS)fcs,old_box_y);
check_result((void*)&result);
result = fcs_set_box_b((FCS) fcs, old_box_y);
check_result((void *) &result);
result = fcs_set_box_c((FCS)fcs,old_box_z);
check_result((void*)&result);
result = fcs_set_box_c((FCS) fcs, old_box_z);
check_result((void *) &result);
result = fcs_set_box_origin((FCS)fcs,old_origin);
check_result((void*)&result);
result = fcs_set_box_origin((FCS) fcs, old_origin);
check_result((void *) &result);
result = fcs_set_periodicity((FCS)fcs,old_periodicity);
check_result((void*)&result);
result = fcs_set_periodicity((FCS) fcs, old_periodicity);
check_result((void *) &result);
result = fcs_set_total_particles((FCS)fcs,old_natoms);
check_result((void*)&result);
result = fcs_set_total_particles((FCS) fcs, old_natoms);
check_result((void *) &result);
// allow ScaFaCoS to calculate the near field computations for now
// TODO: allow the delegation of the near field computations
@ -437,8 +399,8 @@ void Scafacos::setup_handle()
// (near_field_flag = 1 -> enables the internal near field calcs
// 0 -> disables the internal near field calcs
int near_field_flag = 1;
result = fcs_set_near_field_flag((FCS)fcs,near_field_flag);
check_result((void*)&result);
result = fcs_set_near_field_flag((FCS) fcs, near_field_flag);
check_result((void *) &result);
}
/* ----------------------------------------------------------------------
@ -450,17 +412,11 @@ bool Scafacos::box_has_changed()
int *periodicity = domain->periodicity;
double *prd = domain->prd;
bool changed =
(periodicity[0] != old_periodicity[0]) ||
(periodicity[1] != old_periodicity[1]) ||
(periodicity[2] != old_periodicity[2]) ||
(domain->boundary[0][0] != old_origin[0]) ||
(domain->boundary[1][0] != old_origin[1]) ||
(domain->boundary[2][0] != old_origin[2]) ||
(prd[0] != old_box_x[0]) ||
(prd[1] != old_box_y[1]) ||
(prd[2] != old_box_z[2]) ||
(atom->natoms != old_natoms);
bool changed = (periodicity[0] != old_periodicity[0]) || (periodicity[1] != old_periodicity[1]) ||
(periodicity[2] != old_periodicity[2]) || (domain->boundary[0][0] != old_origin[0]) ||
(domain->boundary[1][0] != old_origin[1]) || (domain->boundary[2][0] != old_origin[2]) ||
(prd[0] != old_box_x[0]) || (prd[1] != old_box_y[1]) || (prd[2] != old_box_z[2]) ||
(atom->natoms != old_natoms);
return changed;
}
@ -469,19 +425,11 @@ bool Scafacos::box_has_changed()
check ScaFaCoS result for error condition
------------------------------------------------------------------------- */
void Scafacos::check_result(void* result_p)
void Scafacos::check_result(void *result_p)
{
FCSResult result = *(FCSResult*)result_p;
FCSResult result = *(FCSResult *) result_p;
if (!result) return;
std::stringstream ss;
ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n"
<< fcs_result_get_message(result) << "\n";
fcs_result_destroy(result);
std::string err_msg = ss.str();
const char *str = err_msg.c_str();
error->one(FLERR,str);
error->one(FLERR, "ScaFaCoS: {}\n{}\n", fcs_result_get_function(result),
fcs_result_get_message(result));
}