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Merge branch 'collected-small-changes' into add_set_time

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This commit is contained in:
Axel Kohlmeyer
2022-05-04 15:49:14 -04:00
parent 059c84bf41 eec86c8038
commit 81bb4bfc23
29 changed files with 423 additions and 203 deletions
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1
cmake/presets/windows.cmake
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@ -18,7 +18,6 @@ set(WIN_PACKAGES
DPD-REACT
DPD-SMOOTH
DRUDE
ELECTRODE
EFF
EXTRA-COMPUTE
EXTRA-DUMP

4
doc/src/compute_tally.rst
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@ -198,7 +198,9 @@ potentials only include the pair potential portion of the EAM
interaction when used by this compute, not the embedding term. Also
bonded or Kspace interactions do not contribute to this compute.
The computes in this package are not compatible with dynamic groups.
When used with dynamic groups, a :doc:`run 0 <run>` command needs to
be inserted in order to initialize the dynamic groups before accessing
the computes.
Related commands
""""""""""""""""

5
lib/atc/LammpsInterface.cpp
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@ -519,8 +519,8 @@ double LammpsInterface::domain_yz() const { return lammps_->domain->yz; }
int LammpsInterface::domain_triclinic() const { return lammps_->domain->triclinic; }
void LammpsInterface::box_periodicity(int & xperiodic,
int & yperiodic,
int & zperiodic) const
int & yperiodic,
int & zperiodic) const
{
xperiodic = lammps_->domain->xperiodic;
yperiodic = lammps_->domain->yperiodic;
@ -546,6 +546,7 @@ bool LammpsInterface::region_bounds(const char * regionName,
double & xscale, double & yscale, double & zscale) const
{
int iRegion = region_id(regionName);
if (iRegion < 0) throw ATC_Error("Unknown region " + to_string(regionName));
xscale = region_xscale(iRegion);
yscale = region_yscale(iRegion);
zscale = region_zscale(iRegion);

4
lib/gpu/lal_device.cpp
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@ -201,9 +201,9 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int ngpu,
unsigned best_cus = gpu->cus(0);
bool type_match = (gpu->device_type(0) == type);
for (int i = 1; i < gpu->num_devices(); i++) {
if (type_match && gpu->device_type(i)!=type)
if (type_match && (gpu->device_type(i) != type))
continue;
if (type_match && gpu->device_type(i) == type) {
if (!type_match && (gpu->device_type(i) == type)) {
type_match = true;
best_cus = gpu->cus(i);
best_device = i;

2
src/ELECTRODE/pppm_electrode.cpp
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@ -670,7 +670,7 @@ void PPPMElectrode::compute_matrix(bigint *imat, double **matrix, bool timer_fla
compute(1, 0);
// fft green's function k -> r
std::vector<double> greens_real(nz_pppm * ny_pppm * nx_pppm, 0.);
std::vector<double> greens_real((std::size_t) nz_pppm * ny_pppm * nx_pppm, 0.0);
for (int i = 0, n = 0; i < nfft; i++) {
work2[n++] = greensfn[i];
work2[n++] = ZEROF;

1
src/EXTRA-FIX/fix_electron_stopping.cpp
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@ -106,6 +106,7 @@ FixElectronStopping::FixElectronStopping(LAMMPS *lmp, int narg, char **arg) :
FixElectronStopping::~FixElectronStopping()
{
delete[] idregion;
memory->destroy(elstop_ranges);
}

2
src/GRANULAR/pair_granular.cpp
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@ -188,7 +188,7 @@ void PairGranular::compute(int eflag, int vflag)
double *history,*allhistory,**firsthistory;
bool touchflag = false;
const bool historyupdate = update->setupflag != 0;
const bool historyupdate = update->setupflag == 0;
ev_init(eflag,vflag);

210
src/INTEL/pppm_disp_intel.cpp
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@ -825,8 +825,6 @@ void PPPMDispIntel::make_rho_c(IntelBuffers<flt_t,acc_t> * /*buffers*/)
// (dx,dy,dz) = distance to "lower left" grid pt
// (mx,my,mz) = global coords of moving stencil pt
//double *q = atom->q;
//double **x = atom->x;
int nlocal = atom->nlocal;
int nthr = comm->nthreads;
@ -847,7 +845,6 @@ void PPPMDispIntel::make_rho_c(IntelBuffers<flt_t,acc_t> * /*buffers*/)
const flt_t xi = delxinv;
const flt_t yi = delyinv;
const flt_t zi = delzinv;
const flt_t fshift = shift;
const flt_t fshiftone = shiftone;
const flt_t fdelvolinv = delvolinv;
@ -1011,7 +1008,6 @@ void PPPMDispIntel::make_rho_g(IntelBuffers<flt_t,acc_t> * /*buffers*/)
const flt_t xi = delxinv_6;
const flt_t yi = delyinv_6;
const flt_t zi = delzinv_6;
const flt_t fshift = shift_6;
const flt_t fshiftone = shiftone_6;
const flt_t fdelvolinv = delvolinv_6;
@ -1150,20 +1146,13 @@ void PPPMDispIntel::make_rho_a(IntelBuffers<flt_t,acc_t> * /*buffers*/)
{
// clear 3d density array
memset(&(density_brick_a0[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a1[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a2[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a3[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a4[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a5[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a6[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,
ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a0[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a1[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a2[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a3[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a4[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a5[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,ngrid_6*sizeof(FFT_SCALAR));
memset(&(density_brick_a6[nzlo_out_6][nylo_out_6][nxlo_out_6]),0,ngrid_6*sizeof(FFT_SCALAR));
// loop over my charges, add their contribution to nearby grid points
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
@ -1171,117 +1160,112 @@ void PPPMDispIntel::make_rho_a(IntelBuffers<flt_t,acc_t> * /*buffers*/)
// (mx,my,mz) = global coords of moving stencil pt
int nlocal = atom->nlocal;
double **x = atom->x;
double **x = atom->x;
const flt_t lo0 = boxlo[0];
const flt_t lo1 = boxlo[1];
const flt_t lo2 = boxlo[2];
const flt_t xi = delxinv_6;
const flt_t yi = delyinv_6;
const flt_t zi = delzinv_6;
const flt_t fshiftone = shiftone_6;
const flt_t fdelvolinv = delvolinv_6;
const int nix = nxhi_out_6 - nxlo_out_6 + 1;
const int niy = nyhi_out_6 - nylo_out_6 + 1;
for (int i = 0; i < nlocal; i++) {
const flt_t lo0 = boxlo[0];
const flt_t lo1 = boxlo[1];
const flt_t lo2 = boxlo[2];
const flt_t xi = delxinv_6;
const flt_t yi = delyinv_6;
const flt_t zi = delzinv_6;
const flt_t fshift = shift_6;
const flt_t fshiftone = shiftone_6;
const flt_t fdelvolinv = delvolinv_6;
int nx = part2grid_6[i][0];
int ny = part2grid_6[i][1];
int nz = part2grid_6[i][2];
for (int i = 0; i < nlocal; i++) {
int nxsum = nx + nlower_6;
int nysum = ny + nlower_6;
int nzsum = nz + nlower_6;
int nx = part2grid_6[i][0];
int ny = part2grid_6[i][1];
int nz = part2grid_6[i][2];
FFT_SCALAR dx = nx+fshiftone - (x[i][0]-lo0)*xi;
FFT_SCALAR dy = ny+fshiftone - (x[i][1]-lo1)*yi;
FFT_SCALAR dz = nz+fshiftone - (x[i][2]-lo2)*zi;
int nxsum = nx + nlower_6;
int nysum = ny + nlower_6;
int nzsum = nz + nlower_6;
_alignvar(flt_t rho[3][INTEL_P3M_ALIGNED_MAXORDER], 64) = {0};
FFT_SCALAR dx = nx+fshiftone - (x[i][0]-lo0)*xi;
FFT_SCALAR dy = ny+fshiftone - (x[i][1]-lo1)*yi;
FFT_SCALAR dz = nz+fshiftone - (x[i][2]-lo2)*zi;
_alignvar(flt_t rho[3][INTEL_P3M_ALIGNED_MAXORDER], 64) = {0};
if (use_table) {
dx = dx*half_rho_scale + half_rho_scale_plus;
int idx = dx;
dy = dy*half_rho_scale + half_rho_scale_plus;
int idy = dy;
dz = dz*half_rho_scale + half_rho_scale_plus;
int idz = dz;
#if defined(LMP_SIMD_COMPILER)
if (use_table) {
dx = dx*half_rho_scale + half_rho_scale_plus;
int idx = dx;
dy = dy*half_rho_scale + half_rho_scale_plus;
int idy = dy;
dz = dz*half_rho_scale + half_rho_scale_plus;
int idz = dz;
#if defined(LMP_SIMD_COMPILER)
#if defined(USE_OMP_SIMD)
#pragma omp simd
#pragma omp simd
#else
#pragma simd
#pragma simd
#endif
#endif
for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) {
rho[0][k] = rho6_lookup[idx][k];
rho[1][k] = rho6_lookup[idy][k];
rho[2][k] = rho6_lookup[idz][k];
}
} else {
#if defined(LMP_SIMD_COMPILER)
#if defined(USE_OMP_SIMD)
#pragma omp simd
#else
#pragma simd
#endif
#endif
for (int k = nlower_6; k <= nupper_6; k++) {
FFT_SCALAR r1,r2,r3;
r1 = r2 = r3 = ZEROF;
for (int l = order_6-1; l >= 0; l--) {
r1 = rho_coeff_6[l][k] + r1*dx;
r2 = rho_coeff_6[l][k] + r2*dy;
r3 = rho_coeff_6[l][k] + r3*dz;
}
rho[0][k-nlower_6] = r1;
rho[1][k-nlower_6] = r2;
rho[2][k-nlower_6] = r3;
}
for (int k = 0; k < INTEL_P3M_ALIGNED_MAXORDER; k++) {
rho[0][k] = rho6_lookup[idx][k];
rho[1][k] = rho6_lookup[idy][k];
rho[2][k] = rho6_lookup[idz][k];
}
const int type = atom->type[i];
FFT_SCALAR z0 = fdelvolinv;
#if defined(LMP_SIMD_COMPILER)
#pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7)
#endif
for (int n = 0; n < order_6; n++) {
int mz = n + nzsum;
FFT_SCALAR y0 = z0*rho[2][n];
#if defined(LMP_SIMD_COMPILER)
#pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7)
#endif
for (int m = 0; m < order_6; m++) {
int my = m + nysum;
FFT_SCALAR x0 = y0*rho[1][m];
#if defined(LMP_SIMD_COMPILER)
} else {
#if defined(LMP_SIMD_COMPILER)
#if defined(USE_OMP_SIMD)
#pragma omp simd
#pragma omp simd
#else
#pragma simd
#pragma simd
#endif
#pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7)
#endif
for (int l = 0; l < order; l++) {
int mx = l + nxsum;
FFT_SCALAR w = x0*rho[0][l];
density_brick_a0[mz][my][mx] += w*B[7*type];
density_brick_a1[mz][my][mx] += w*B[7*type+1];
density_brick_a2[mz][my][mx] += w*B[7*type+2];
density_brick_a3[mz][my][mx] += w*B[7*type+3];
density_brick_a4[mz][my][mx] += w*B[7*type+4];
density_brick_a5[mz][my][mx] += w*B[7*type+5];
density_brick_a6[mz][my][mx] += w*B[7*type+6];
}
#endif
for (int k = nlower_6; k <= nupper_6; k++) {
FFT_SCALAR r1,r2,r3;
r1 = r2 = r3 = ZEROF;
for (int l = order_6-1; l >= 0; l--) {
r1 = rho_coeff_6[l][k] + r1*dx;
r2 = rho_coeff_6[l][k] + r2*dy;
r3 = rho_coeff_6[l][k] + r3*dz;
}
rho[0][k-nlower_6] = r1;
rho[1][k-nlower_6] = r2;
rho[2][k-nlower_6] = r3;
}
}
const int type = atom->type[i];
FFT_SCALAR z0 = fdelvolinv;
#if defined(LMP_SIMD_COMPILER)
#pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7)
#endif
for (int n = 0; n < order_6; n++) {
int mz = n + nzsum;
FFT_SCALAR y0 = z0*rho[2][n];
#if defined(LMP_SIMD_COMPILER)
#pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7)
#endif
for (int m = 0; m < order_6; m++) {
int my = m + nysum;
FFT_SCALAR x0 = y0*rho[1][m];
#if defined(LMP_SIMD_COMPILER)
#if defined(USE_OMP_SIMD)
#pragma omp simd
#else
#pragma simd
#endif
#pragma loop_count min(2), max(INTEL_P3M_ALIGNED_MAXORDER), avg(7)
#endif
for (int l = 0; l < order; l++) {
int mx = l + nxsum;
FFT_SCALAR w = x0*rho[0][l];
density_brick_a0[mz][my][mx] += w*B[7*type];
density_brick_a1[mz][my][mx] += w*B[7*type+1];
density_brick_a2[mz][my][mx] += w*B[7*type+2];
density_brick_a3[mz][my][mx] += w*B[7*type+3];
density_brick_a4[mz][my][mx] += w*B[7*type+4];
density_brick_a5[mz][my][mx] += w*B[7*type+5];
density_brick_a6[mz][my][mx] += w*B[7*type+6];
}
}
}
}
}
/* ----------------------------------------------------------------------
@ -1310,7 +1294,6 @@ void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> * /*buffers*/)
shared(nthr, nlocal, global_density) if (!_use_lrt)
#endif
{
int type;
double **x = atom->x;
const int nix = nxhi_out_6 - nxlo_out_6 + 1;
@ -1322,7 +1305,6 @@ void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> * /*buffers*/)
const flt_t xi = delxinv_6;
const flt_t yi = delyinv_6;
const flt_t zi = delzinv_6;
const flt_t fshift = shift_6;
const flt_t fshiftone = shiftone_6;
const flt_t fdelvolinv = delvolinv_6;
@ -1391,7 +1373,6 @@ void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> * /*buffers*/)
}
}
type = atom->type[i];
FFT_SCALAR z0 = fdelvolinv;
#if defined(LMP_SIMD_COMPILER)
@ -1416,7 +1397,6 @@ void PPPMDispIntel::make_rho_none(IntelBuffers<flt_t,acc_t> * /*buffers*/)
#endif
for (int l = 0; l < order; l++) {
int mzyx = l + mzy;
FFT_SCALAR w0 = x0*rho[0][l];
for (int k = 0; k < nsplit; k++)
my_density[mzyx + k*ngrid_6] += x0*rho[0][l];
}

5
src/KOKKOS/verlet_kokkos.h
View File

@ -35,6 +35,7 @@ class VerletKokkos : public Verlet {
void setup(int) override;
void setup_minimal(int) override;
void run(int) override;
void force_clear() override;
KOKKOS_INLINE_FUNCTION
void operator() (const int& i) const {
@ -43,13 +44,9 @@ class VerletKokkos : public Verlet {
f(i,2) += f_merge_copy(i,2);
}
protected:
DAT::t_f_array f_merge_copy,f;
void force_clear() override;
};
}
#endif

4
src/OPENMP/pair_lubricate_poly_omp.cpp
View File

@ -38,8 +38,8 @@ enum{EDGE,CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
PairLubricatePolyOMP::PairLubricatePolyOMP(LAMMPS *lmp) :
PairLubricatePoly(lmp), ThrOMP(lmp, THR_PAIR)
PairLubricatePolyOMP::PairLubricatePolyOMP(LAMMPS *_lmp) :
PairLubricatePoly(_lmp), ThrOMP(_lmp, THR_PAIR)
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;

2
src/OPENMP/pair_lubricate_poly_omp.h
View File

@ -17,7 +17,7 @@
#ifdef PAIR_CLASS
// clang-format off
PairStyle(lubricate/poly/omp,PairLubricateOMP);
PairStyle(lubricate/poly/omp,PairLubricatePolyOMP);
// clang-format on
#else

6
src/OPENMP/respa_omp.cpp
View File

@ -117,7 +117,7 @@ void RespaOMP::setup(int flag)
ev_set(update->ntimestep);
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
force_clear(newton[ilevel]);
force_clear();
modify->setup_pre_force_respa(vflag,ilevel);
if (nhybrid_styles > 0) {
@ -211,7 +211,7 @@ void RespaOMP::setup_minimal(int flag)
ev_set(update->ntimestep);
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
force_clear(newton[ilevel]);
force_clear();
modify->setup_pre_force_respa(vflag,ilevel);
if (nhybrid_styles > 0) {
@ -343,7 +343,7 @@ void RespaOMP::recurse(int ilevel)
// so that any order dependencies are the same
// when potentials are invoked at same level
force_clear(newton[ilevel]);
force_clear();
if (modify->n_pre_force_respa) {
timer->stamp();
modify->pre_force_respa(vflag,ilevel,iloop);

2
src/OPT/pair_ilp_graphene_hbn_opt.cpp
View File

@ -64,7 +64,7 @@ static bool check_vdw(tagint itag, tagint jtag, double *xi, double *xj);
PairILPGrapheneHBNOpt::PairILPGrapheneHBNOpt(LAMMPS *lmp) :
PairILPGrapheneHBN(lmp), layered_neigh(nullptr), first_layered_neigh(nullptr),
num_intra(nullptr), num_inter(nullptr), num_vdw(nullptr), special_type(nullptr)
special_type(nullptr), num_intra(nullptr), num_inter(nullptr), num_vdw(nullptr)
{
if (lmp->citeme) lmp->citeme->add(cite_ilp_cur);

13
src/SMTBQ/pair_smatb.cpp
View File

@ -404,7 +404,7 @@ double PairSMATB::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
int PairSMATB::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
int PairSMATB::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i, j, m;
@ -465,11 +465,10 @@ void PairSMATB::write_restart_settings(FILE *fp)
void PairSMATB::read_restart_settings(FILE *fp)
{
int me = comm->me;
size_t result;
if (me == 0) {
result = fread(&offset_flag, sizeof(int), 1, fp);
result = fread(&mix_flag, sizeof(int), 1, fp);
result = fread(&tail_flag, sizeof(int), 1, fp);
utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error);
utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error);
utils::sfread(FLERR, &tail_flag, sizeof(int), 1, fp, nullptr, error);
}
MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world);
MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world);
@ -504,15 +503,13 @@ void PairSMATB::write_restart(FILE *fp)
void PairSMATB::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
size_t result;
int i, j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) { result = fread(&setflag[i][j], sizeof(int), 1, fp); }
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) {
if (me == 0) {

66
src/SMTBQ/pair_smatb_single.cpp
View File

@ -87,7 +87,6 @@ void PairSMATBSingle::compute(int eflag, int vflag)
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
@ -237,16 +236,14 @@ void PairSMATBSingle::settings(int narg, char **)
void PairSMATBSingle::allocate()
{
int n = atom->ntypes;
int natoms = atom->natoms;
int np1 = atom->ntypes + 1;
memory->create(setflag, n + 1, n + 1, "pair_smatb:setflag");
for (int i = 1; i <= n; i++) {
for (int j = i; j <= n; j++) { setflag[i][j] = 0; }
memory->create(setflag, np1, np1, "pair_smatb:setflag");
for (int i = 1; i < np1; i++) {
for (int j = i; j < np1; j++) { setflag[i][j] = 0; }
}
memory->create(cutsq, n + 1, n + 1, "pair_smatb:cutsq");
memory->create(cutsq, np1, np1, "pair_smatb:cutsq");
allocated = 1;
}
@ -299,58 +296,40 @@ void PairSMATBSingle::init_style()
double PairSMATBSingle::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
//calculating the polynomial linking to zero
double es = cutOffEnd - cutOffStart;
double es2 = es * es;
double es3 = es2 * es;
//variables for poly for p and A
double expp = A * exp(p * (1. - cutOffStart / r0));
double ap = -1. / es3;
double expp = A * exp(p * (1.0 - cutOffStart / r0));
double ap = -1.0 / es3;
double bp = p / (r0 * es2);
double cp = -(p * p) / (es * r0 * r0);
a5 = expp * (12. * ap + 6. * bp + cp) / (2. * es2);
a4 = expp * (15. * ap + 7. * bp + cp) / es;
a3 = expp * (20. * ap + 8. * bp + cp) / 2.;
a5 = expp * (12.0 * ap + 6.0 * bp + cp) / (2.0 * es2);
a4 = expp * (15.0 * ap + 7.0 * bp + cp) / es;
a3 = expp * (20.0 * ap + 8.0 * bp + cp) / 2.0;
//variables for poly for q and qsi
double expq = QSI * exp(q * (1. - cutOffStart / r0));
double expq = QSI * exp(q * (1.0 - cutOffStart / r0));
double aq = -1 / es3;
double bq = q / (es2 * r0);
double cq = -(q * q) / (es * r0 * r0);
x5 = expq * (12. * aq + 6. * bq + cq) / (2. * es2);
x4 = expq * (15. * aq + 7. * bq + cq) / es;
x3 = expq * (20. * aq + 8. * bq + cq) / 2.;
x5 = expq * (12.0 * aq + 6.0 * bq + cq) / (2.0 * es2);
x4 = expq * (15.0 * aq + 7.0 * bq + cq) / es;
x3 = expq * (20.0 * aq + 8.0 * bq + cq) / 2.0;
cutOffEnd2 = cutOffEnd * cutOffEnd;
if (i != j) {
setflag[j][i] = 1;
cutOffEnd2 = cutOffEnd2;
r0 = r0;
p = p;
q = q;
A = A;
QSI = QSI;
cutOffStart = cutOffStart;
cutOffEnd = cutOffEnd;
a3 = a3;
a4 = a4;
a5 = a5;
x3 = x3;
x4 = x4;
x5 = x5;
}
return cutOffEnd;
}
/* ---------------------------------------------------------------------- */
int PairSMATBSingle::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
int PairSMATBSingle::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/,
int * /*pbc*/)
{
int i, j, m;
@ -412,11 +391,10 @@ void PairSMATBSingle::write_restart_settings(FILE *fp)
void PairSMATBSingle::read_restart_settings(FILE *fp)
{
int me = comm->me;
size_t result;
if (me == 0) {
result = fread(&offset_flag, sizeof(int), 1, fp);
result = fread(&mix_flag, sizeof(int), 1, fp);
result = fread(&tail_flag, sizeof(int), 1, fp);
utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error);
utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error);
utils::sfread(FLERR, &tail_flag, sizeof(int), 1, fp, nullptr, error);
}
MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world);
MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world);
@ -451,15 +429,13 @@ void PairSMATBSingle::write_restart(FILE *fp)
void PairSMATBSingle::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
size_t result;
int i, j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) { result = fread(&setflag[i][j], sizeof(int), 1, fp); }
if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) {
if (me == 0) {

1
src/TALLY/compute_force_tally.cpp
View File

@ -39,7 +39,6 @@ ComputeForceTally::ComputeForceTally(LAMMPS *lmp, int narg, char **arg) : Comput
vector_flag = 0;
peratom_flag = 1;
timeflag = 1;
dynamic_group_allow = 0;
comm_reverse = size_peratom_cols = 3;
extscalar = 1;

1
src/TALLY/compute_heat_flux_tally.cpp
View File

@ -37,7 +37,6 @@ ComputeHeatFluxTally::ComputeHeatFluxTally(LAMMPS *lmp, int narg, char **arg) :
vector_flag = 1;
timeflag = 1;
dynamic_group_allow = 0;
comm_reverse = 7;
extvector = 1;

1
src/TALLY/compute_heat_flux_virial_tally.cpp
View File

@ -40,7 +40,6 @@ ComputeHeatFluxVirialTally::ComputeHeatFluxVirialTally(LAMMPS *lmp, int narg, ch
vector_flag = 0;
peratom_flag = 1;
timeflag = 1;
dynamic_group_allow = 0;
comm_reverse = size_peratom_cols = 3;
extscalar = 1;

1
src/TALLY/compute_pe_mol_tally.cpp
View File

@ -36,7 +36,6 @@ ComputePEMolTally::ComputePEMolTally(LAMMPS *lmp, int narg, char **arg) : Comput
vector_flag = 1;
size_vector = 4;
timeflag = 1;
dynamic_group_allow = 0;
extvector = 1;
peflag = 1; // we need Pair::ev_tally() to be run

1
src/TALLY/compute_pe_tally.cpp
View File

@ -38,7 +38,6 @@ ComputePETally::ComputePETally(LAMMPS *lmp, int narg, char **arg) : Compute(lmp,
vector_flag = 0;
peratom_flag = 1;
timeflag = 1;
dynamic_group_allow = 0;
comm_reverse = size_peratom_cols = 2;
extscalar = 1;

1
src/TALLY/compute_stress_tally.cpp
View File

@ -39,7 +39,6 @@ ComputeStressTally::ComputeStressTally(LAMMPS *lmp, int narg, char **arg) : Comp
vector_flag = 0;
peratom_flag = 1;
timeflag = 1;
dynamic_group_allow = 0;
comm_reverse = size_peratom_cols = 6;
extscalar = 0;

1
src/integrate.h
View File

@ -26,6 +26,7 @@ class Integrate : protected Pointers {
virtual void setup(int flag) = 0;
virtual void setup_minimal(int) = 0;
virtual void run(int) = 0;
virtual void force_clear() = 0;
virtual void cleanup() {}
virtual void reset_dt() {}
virtual double memory_usage() { return 0; }

2
src/min.h
View File

@ -34,6 +34,7 @@ class Min : protected Pointers {
virtual void setup(int flag = 1);
virtual void setup_minimal(int);
virtual void run(int);
virtual void force_clear();
void cleanup();
int request(class Pair *, int, double);
virtual double memory_usage() { return 0; }
@ -138,7 +139,6 @@ class Min : protected Pointers {
int neigh_every, neigh_delay, neigh_dist_check; // neighboring params
virtual double energy_force(int);
virtual void force_clear();
void ev_setup();
void ev_set(bigint);

2
src/region_intersect.cpp
View File

@ -117,7 +117,7 @@ void RegIntersect::init()
{
Region::init();
// re-build list of sub-regions in case other regions were deleted
// re-build list of sub-regions in case regions were changed
// error if a sub-region was deleted
for (int ilist = 0; ilist < nregion; ilist++) {

8
src/respa.cpp
View File

@ -413,7 +413,7 @@ void Respa::setup(int flag)
ev_set(update->ntimestep);
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
force_clear(newton[ilevel]);
force_clear();
modify->setup_pre_force_respa(vflag, ilevel);
if (nhybrid_styles > 0) {
@ -481,7 +481,7 @@ void Respa::setup_minimal(int flag)
ev_set(update->ntimestep);
for (int ilevel = 0; ilevel < nlevels; ilevel++) {
force_clear(newton[ilevel]);
force_clear();
modify->setup_pre_force_respa(vflag, ilevel);
if (nhybrid_styles > 0) {
@ -644,7 +644,7 @@ void Respa::recurse(int ilevel)
// so that any order dependencies are the same
// when potentials are invoked at same level
force_clear(newton[ilevel]);
force_clear();
if (modify->n_pre_force_respa) {
timer->stamp();
modify->pre_force_respa(vflag, ilevel, iloop);
@ -717,7 +717,7 @@ void Respa::recurse(int ilevel)
clear other arrays as needed
------------------------------------------------------------------------- */
void Respa::force_clear(int /*newtonflag*/)
void Respa::force_clear()
{
if (external_force_clear) return;

2
src/respa.h
View File

@ -51,6 +51,7 @@ class Respa : public Integrate {
void setup(int) override;
void setup_minimal(int) override;
void run(int) override;
void force_clear() override;
void cleanup() override;
void reset_dt() override;
@ -65,7 +66,6 @@ class Respa : public Integrate {
class FixRespa *fix_respa; // Fix to store the force level array
virtual void recurse(int);
void force_clear(int);
void sum_flevel_f();
void set_compute_flags(int ilevel);
};

4
src/verlet.h
View File

@ -27,18 +27,16 @@ namespace LAMMPS_NS {
class Verlet : public Integrate {
public:
Verlet(class LAMMPS *, int, char **);
void init() override;
void setup(int flag) override;
void setup_minimal(int) override;
void run(int) override;
void force_clear() override;
void cleanup() override;
protected:
int triclinic; // 0 if domain is orthog, 1 if triclinic
int torqueflag, extraflag;
virtual void force_clear();
};
} // namespace LAMMPS_NS

4
unittest/commands/CMakeLists.txt
View File

@ -21,6 +21,10 @@ add_executable(test_groups test_groups.cpp)
target_link_libraries(test_groups PRIVATE lammps GTest::GMock)
add_test(NAME Groups COMMAND test_groups)
add_executable(test_regions test_regions.cpp)
target_link_libraries(test_regions PRIVATE lammps GTest::GMock)
add_test(NAME Regions COMMAND test_regions)
add_executable(test_delete_atoms test_delete_atoms.cpp)
target_link_libraries(test_delete_atoms PRIVATE lammps GTest::GMock)
add_test(NAME DeleteAtoms COMMAND test_delete_atoms)

270
unittest/commands/test_regions.cpp Normal file
View File

@ -0,0 +1,270 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "lammps.h"
#include "atom.h"
#include "domain.h"
#include "group.h"
#include "info.h"
#include "input.h"
#include "region.h"
#include "../testing/core.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <cstring>
#include <vector>
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
bool verbose = false;
using LAMMPS_NS::utils::split_words;
namespace LAMMPS_NS {
using ::testing::ExitedWithCode;
using ::testing::StrEq;
class RegionTest : public LAMMPSTest {
protected:
Atom *atom;
Domain *domain;
Group *group;
void SetUp() override
{
testbinary = "RegionTest";
LAMMPSTest::SetUp();
atom = lmp->atom;
domain = lmp->domain;
group = lmp->group;
}
void atomic_system()
{
BEGIN_HIDE_OUTPUT();
command("units real");
command("lattice sc 1.0 origin 0.125 0.125 0.125");
command("region box block -10 10 -10 10 -10 10");
command("create_box 8 box");
command("create_atoms 1 box");
command("mass * 1.0");
END_HIDE_OUTPUT();
}
};
TEST_F(RegionTest, NoBox)
{
auto list = domain->get_region_list();
ASSERT_EQ(list.size(), 0);
BEGIN_HIDE_OUTPUT();
command("region reg1 block 0 1 0 1 0 1");
command("region reg2 cone x 0 0 2 1 0 1 units box");
command("region reg3 plane 0 0 0 0 0 1 side out");
command("region reg4 prism 0 1 0 1 0 1 0.1 0.2 0.3");
command("region reg5 sphere 0 0 0 1");
command("region reg6 union 3 reg1 reg2 reg3");
command("region reg7 intersect 3 reg1 reg2 reg4");
command("region reg8 ellipsoid 0 0 0 2 1 2");
END_HIDE_OUTPUT();
list = domain->get_region_list();
EXPECT_EQ(list.size(), 8);
auto reg = domain->get_region_by_id("reg1");
EXPECT_EQ(reg->interior, 1);
EXPECT_EQ(reg->scaleflag, 1);
EXPECT_EQ(reg->bboxflag, 1);
EXPECT_EQ(reg->varshape, 0);
EXPECT_EQ(reg->dynamic, 0);
EXPECT_EQ(reg->moveflag, 0);
EXPECT_EQ(reg->rotateflag, 0);
EXPECT_EQ(reg->openflag, 0);
reg = domain->get_region_by_id("reg2");
EXPECT_EQ(reg->interior, 1);
EXPECT_EQ(reg->scaleflag, 0);
EXPECT_EQ(reg->bboxflag, 1);
EXPECT_EQ(reg->varshape, 0);
EXPECT_EQ(reg->dynamic, 0);
EXPECT_EQ(reg->moveflag, 0);
EXPECT_EQ(reg->rotateflag, 0);
EXPECT_EQ(reg->openflag, 0);
reg = domain->get_region_by_id("reg3");
EXPECT_EQ(reg->interior, 0);
EXPECT_EQ(reg->scaleflag, 1);
EXPECT_EQ(reg->bboxflag, 0);
EXPECT_EQ(reg->varshape, 0);
EXPECT_EQ(reg->dynamic, 0);
EXPECT_EQ(reg->moveflag, 0);
EXPECT_EQ(reg->rotateflag, 0);
EXPECT_EQ(reg->openflag, 0);
reg = domain->get_region_by_id("reg4");
EXPECT_EQ(reg->interior, 1);
EXPECT_EQ(reg->scaleflag, 1);
EXPECT_EQ(reg->bboxflag, 1);
EXPECT_EQ(reg->varshape, 0);
EXPECT_EQ(reg->dynamic, 0);
EXPECT_EQ(reg->moveflag, 0);
EXPECT_EQ(reg->rotateflag, 0);
EXPECT_EQ(reg->openflag, 0);
reg = domain->get_region_by_id("reg5");
EXPECT_EQ(reg->interior, 1);
EXPECT_EQ(reg->scaleflag, 1);
EXPECT_EQ(reg->bboxflag, 1);
EXPECT_EQ(reg->varshape, 0);
EXPECT_EQ(reg->dynamic, 0);
EXPECT_EQ(reg->moveflag, 0);
EXPECT_EQ(reg->rotateflag, 0);
EXPECT_EQ(reg->openflag, 0);
reg = domain->get_region_by_id("reg6");
EXPECT_EQ(reg->interior, 1);
EXPECT_EQ(reg->scaleflag, 1);
EXPECT_EQ(reg->bboxflag, 0);
EXPECT_EQ(reg->varshape, 0);
EXPECT_EQ(reg->dynamic, 0);
EXPECT_EQ(reg->moveflag, 0);
EXPECT_EQ(reg->rotateflag, 0);
EXPECT_EQ(reg->openflag, 0);
reg = domain->get_region_by_id("reg7");
EXPECT_EQ(reg->interior, 1);
EXPECT_EQ(reg->scaleflag, 1);
EXPECT_EQ(reg->bboxflag, 1);
EXPECT_EQ(reg->varshape, 0);
EXPECT_EQ(reg->dynamic, 0);
EXPECT_EQ(reg->moveflag, 0);
EXPECT_EQ(reg->rotateflag, 0);
EXPECT_EQ(reg->openflag, 0);
reg = domain->get_region_by_id("reg8");
EXPECT_EQ(reg->interior, 1);
EXPECT_EQ(reg->scaleflag, 1);
EXPECT_EQ(reg->bboxflag, 1);
EXPECT_EQ(reg->varshape, 0);
EXPECT_EQ(reg->dynamic, 0);
EXPECT_EQ(reg->moveflag, 0);
EXPECT_EQ(reg->rotateflag, 0);
EXPECT_EQ(reg->openflag, 0);
BEGIN_HIDE_OUTPUT();
command("region reg3 delete");
command("region reg5 delete");
command("region reg6 delete");
command("region reg1 delete");
END_HIDE_OUTPUT();
list = domain->get_region_list();
EXPECT_EQ(list.size(), 4);
reg = domain->get_region_by_id("reg7");
TEST_FAILURE(".*ERROR: Region intersect region reg1 does not exist.*", reg->init(););
TEST_FAILURE(".*ERROR: Unrecognized region style 'xxx'.*", command("region new1 xxx"););
TEST_FAILURE(".*ERROR: Illegal region command.*", command("region new1 block 0 1"););
TEST_FAILURE(".*ERROR: Delete region reg3 does not exist.*", command("region reg3 delete"););
}
TEST_F(RegionTest, Counts)
{
atomic_system();
BEGIN_HIDE_OUTPUT();
command("region reg1 block 0 5 0 5 -5 5");
command("region reg2 cone y 0 0 10 0 -5 5 units box");
command("region reg3 plane 0 0 0 0 1 0 side out");
command("region reg4 prism -5 5 -5 5 -5 5 0.1 0.2 0.3 units box");
command("region reg5 sphere 1 0 0 6");
command("region reg6 union 3 reg1 reg2 reg3");
command("region reg7 intersect 3 reg1 reg2 reg4");
command("region reg8 ellipsoid 0 0 0 5 2 3");
command("region reg9 ellipsoid 1 0 0 6 6 6"); // same as sphere
command("region reg10 prism 0 5 0 5 -5 5 0.0 0.0 0.0"); // same as block
END_HIDE_OUTPUT();
auto x = atom->x;
auto reg1 = domain->get_region_by_id("reg1");
auto reg2 = domain->get_region_by_id("reg2");
auto reg3 = domain->get_region_by_id("reg3");
auto reg4 = domain->get_region_by_id("reg4");
auto reg5 = domain->get_region_by_id("reg5");
auto reg6 = domain->get_region_by_id("reg6");
auto reg7 = domain->get_region_by_id("reg7");
auto reg8 = domain->get_region_by_id("reg8");
auto reg9 = domain->get_region_by_id("reg9");
auto reg10 = domain->get_region_by_id("reg10");
int count1, count2, count3, count4, count5, count6, count7, count8, count9, count10;
count1 = count2 = count3 = count4 = count5 = count6 = count7 = count8 = count9 = count10 = 0;
reg1->prematch();
reg2->prematch();
reg3->prematch();
reg4->prematch();
reg5->prematch();
reg6->prematch();
reg7->prematch();
reg8->prematch();
reg9->prematch();
reg10->prematch();
for (int i = 0; i < atom->nlocal; ++i) {
if (reg1->match(x[i][0], x[i][1], x[i][2])) ++count1;
if (reg2->match(x[i][0], x[i][1], x[i][2])) ++count2;
if (reg3->match(x[i][0], x[i][1], x[i][2])) ++count3;
if (reg4->match(x[i][0], x[i][1], x[i][2])) ++count4;
if (reg5->match(x[i][0], x[i][1], x[i][2])) ++count5;
if (reg6->match(x[i][0], x[i][1], x[i][2])) ++count6;
if (reg7->match(x[i][0], x[i][1], x[i][2])) ++count7;
if (reg8->match(x[i][0], x[i][1], x[i][2])) ++count8;
if (reg9->match(x[i][0], x[i][1], x[i][2])) ++count9;
if (reg10->match(x[i][0], x[i][1], x[i][2])) ++count10;
}
EXPECT_EQ(count1, 250);
EXPECT_EQ(count2, 1132);
EXPECT_EQ(count3, 4000);
EXPECT_EQ(count4, 1000);
EXPECT_EQ(count5, 907);
EXPECT_EQ(count6, 4314);
EXPECT_EQ(count7, 86);
EXPECT_EQ(count8, 122);
EXPECT_EQ(count9, count5);
EXPECT_EQ(count10, count1);
}
} // namespace LAMMPS_NS
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
if (platform::mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions())
std::cout << "Warning: using OpenMPI without exceptions. Death tests will be skipped\n";
// handle arguments passed via environment variable
if (const char *var = getenv("TEST_ARGS")) {
std::vector<std::string> env = split_words(var);
for (auto arg : env) {
if (arg == "-v") {
verbose = true;
}
}
}
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
int rv = RUN_ALL_TESTS();
MPI_Finalize();
return rv;
}