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
2023-02-20 12:48:39 -05:00
parent f7aae84cf6
commit d5ba6f70f2
1 changed files with 55 additions and 68 deletions
Download Patch File Download Diff File Expand all files Collapse all files

123
src/ML-IAP/mliap_data.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
@ -27,16 +26,14 @@
using namespace LAMMPS_NS;
MLIAPData::MLIAPData(LAMMPS *lmp, int gradgradflag_in, int *map_in,
class MLIAPModel* model_in,
class MLIAPDescriptor* descriptor_in,
class PairMLIAP* pairmliap_in) :
Pointers(lmp), f(nullptr), gradforce(nullptr), betas(nullptr),
descriptors(nullptr), eatoms(nullptr), gamma(nullptr),
gamma_row_index(nullptr), gamma_col_index(nullptr), egradient(nullptr),
numneighs(nullptr), iatoms(nullptr), ielems(nullptr), pair_i(nullptr),
jatoms(nullptr), jelems(nullptr), elems(nullptr), rij(nullptr),
graddesc(nullptr), model(nullptr), descriptor(nullptr), list(nullptr)
MLIAPData::MLIAPData(LAMMPS *lmp, int gradgradflag_in, int *map_in, class MLIAPModel *model_in,
class MLIAPDescriptor *descriptor_in, class PairMLIAP *pairmliap_in) :
Pointers(lmp),
f(nullptr), gradforce(nullptr), betas(nullptr), descriptors(nullptr), eatoms(nullptr),
gamma(nullptr), gamma_row_index(nullptr), gamma_col_index(nullptr), egradient(nullptr),
numneighs(nullptr), iatoms(nullptr), ielems(nullptr), pair_i(nullptr), jatoms(nullptr),
jelems(nullptr), elems(nullptr), rij(nullptr), graddesc(nullptr), model(nullptr),
descriptor(nullptr), list(nullptr)
{
gradgradflag = gradgradflag_in;
map = map_in;
@ -51,25 +48,24 @@ MLIAPData::MLIAPData(LAMMPS *lmp, int gradgradflag_in, int *map_in,
gamma_nnz = model->get_gamma_nnz(this);
ndims_force = 3;
ndims_virial = 6;
yoffset = nparams*nelements;
zoffset = 2*yoffset;
yoffset = nparams * nelements;
zoffset = 2 * yoffset;
natoms = atom->natoms;
// must check before assigning bigint expression to regular int
if (1+ndims_force*natoms+ndims_virial > MAXSMALLINT)
error->all(FLERR,"Too many atoms for MLIAP package");
if (1 + ndims_force * natoms + ndims_virial > MAXSMALLINT)
error->all(FLERR, "Too many atoms for MLIAP package");
size_array_rows = 1+ndims_force*natoms+ndims_virial;
size_array_cols = nparams*nelements+1;
size_gradforce = ndims_force*nparams*nelements;
size_array_rows = 1 + ndims_force * natoms + ndims_virial;
size_array_cols = nparams * nelements + 1;
size_gradforce = ndims_force * nparams * nelements;
nlistatoms_max = 0;
natomneigh_max = 0;
nneigh_max = 0;
nmax = 0;
natomgamma_max = 0;
}
/* ---------------------------------------------------------------------- */
@ -100,14 +96,14 @@ MLIAPData::~MLIAPData()
void MLIAPData::init()
{
memory->create(egradient,nelements*nparams,"MLIAPData:egradient");
memory->create(egradient, nelements * nparams, "MLIAPData:egradient");
}
/* ----------------------------------------------------------------------
generate neighbor arrays
------------------------------------------------------------------------- */
void MLIAPData::generate_neighdata(NeighList* list_in, int eflag_in, int vflag_in)
void MLIAPData::generate_neighdata(NeighList *list_in, int eflag_in, int vflag_in)
{
list = list_in;
f = atom->f;
@ -125,19 +121,16 @@ void MLIAPData::generate_neighdata(NeighList* list_in, int eflag_in, int vflag_i
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->grow(elems,nmax,"MLIAPData:elems");
if (gradgradflag > -1) memory->grow(gradforce,nmax,size_gradforce,
"MLIAPData:gradforce");
memory->grow(elems, nmax, "MLIAPData:elems");
if (gradgradflag > -1) memory->grow(gradforce, nmax, size_gradforce, "MLIAPData:gradforce");
}
// clear gradforce, elems arrays
for (int i = 0; i < nall; i++) {
elems[i] = 0;
if (gradgradflag > -1){
for (int j = 0; j < size_gradforce; j++) {
gradforce[i][j] = 0.0;
}
if (gradgradflag > -1) {
for (int j = 0; j < size_gradforce; j++) { gradforce[i][j] = 0.0; }
}
}
@ -145,9 +138,9 @@ void MLIAPData::generate_neighdata(NeighList* list_in, int eflag_in, int vflag_i
nlistatoms = list->inum;
if (nlistatoms_max < nlistatoms) {
memory->grow(betas,nlistatoms,ndescriptors,"MLIAPData:betas");
memory->grow(descriptors,nlistatoms,ndescriptors,"MLIAPData:descriptors");
memory->grow(eatoms,nlistatoms,"MLIAPData:eatoms");
memory->grow(betas, nlistatoms, ndescriptors, "MLIAPData:betas");
memory->grow(descriptors, nlistatoms, ndescriptors, "MLIAPData:descriptors");
memory->grow(eatoms, nlistatoms, "MLIAPData:eatoms");
nlistatoms_max = nlistatoms;
}
@ -155,9 +148,9 @@ void MLIAPData::generate_neighdata(NeighList* list_in, int eflag_in, int vflag_i
if (gradgradflag == 1) {
if (natomgamma_max < nlistatoms) {
memory->grow(gamma_row_index,nlistatoms,gamma_nnz,"MLIAPData:gamma_row_index");
memory->grow(gamma_col_index,nlistatoms,gamma_nnz,"MLIAPData:gamma_col_index");
memory->grow(gamma,nlistatoms,gamma_nnz,"MLIAPData:gamma");
memory->grow(gamma_row_index, nlistatoms, gamma_nnz, "MLIAPData:gamma_row_index");
memory->grow(gamma_col_index, nlistatoms, gamma_nnz, "MLIAPData:gamma_col_index");
memory->grow(gamma, nlistatoms, gamma_nnz, "MLIAPData:gamma");
natomgamma_max = nlistatoms;
}
}
@ -185,7 +178,7 @@ void MLIAPData::generate_neighdata(NeighList* list_in, int eflag_in, int vflag_i
const double delx = x[j][0] - xtmp;
const double dely = x[j][1] - ytmp;
const double delz = x[j][2] - ztmp;
const double rsq = delx*delx + dely*dely + delz*delz;
const double rsq = delx * delx + dely * dely + delz * delz;
int jtype = type[j];
const int jelem = map[jtype];
@ -224,12 +217,11 @@ void MLIAPData::grow_neigharrays()
// grow neighbor atom arrays if necessary
natomneigh = list->inum;
if (list->ghost == 1)
natomneigh += list->gnum;
if (list->ghost == 1) natomneigh += list->gnum;
if (natomneigh_max < natomneigh) {
memory->grow(iatoms,natomneigh,"MLIAPData:iatoms");
memory->grow(ielems,natomneigh,"MLIAPData:ielems");
memory->grow(numneighs,natomneigh,"MLIAPData:numneighs");
memory->grow(iatoms, natomneigh, "MLIAPData:iatoms");
memory->grow(ielems, natomneigh, "MLIAPData:ielems");
memory->grow(numneighs, natomneigh, "MLIAPData:numneighs");
natomneigh_max = natomneigh;
}
@ -261,7 +253,7 @@ void MLIAPData::grow_neigharrays()
const double delx = x[j][0] - xtmp;
const double dely = x[j][1] - ytmp;
const double delz = x[j][2] - ztmp;
const double rsq = delx*delx + dely*dely + delz*delz;
const double rsq = delx * delx + dely * dely + delz * delz;
int jtype = type[j];
const int jelem = map[jtype];
if (rsq < descriptor->cutsq[ielem][jelem]) ninside++;
@ -270,12 +262,11 @@ void MLIAPData::grow_neigharrays()
}
if (nneigh_max < nneigh) {
memory->grow(pair_i,nneigh,"MLIAPData:pair_i");
memory->grow(jatoms,nneigh,"MLIAPData:jatoms");
memory->grow(jelems,nneigh,"MLIAPData:jelems");
memory->grow(rij,nneigh,3,"MLIAPData:rij");
if (gradgradflag == 0)
memory->grow(graddesc,nneigh,ndescriptors,3,"MLIAPData:graddesc");
memory->grow(pair_i, nneigh, "MLIAPData:pair_i");
memory->grow(jatoms, nneigh, "MLIAPData:jatoms");
memory->grow(jelems, nneigh, "MLIAPData:jelems");
memory->grow(rij, nneigh, 3, "MLIAPData:rij");
if (gradgradflag == 0) memory->grow(graddesc, nneigh, ndescriptors, 3, "MLIAPData:graddesc");
nneigh_max = nneigh;
}
}
@ -284,35 +275,31 @@ double MLIAPData::memory_usage()
{
double bytes = 0.0;
bytes += (double)nelements*nparams*sizeof(double); // egradient
bytes += (double)nmax*size_gradforce*sizeof(double); // gradforce
bytes += (double)nmax*sizeof(int); // elems
bytes += (double) nelements * nparams * sizeof(double); // egradient
bytes += (double) nmax * size_gradforce * sizeof(double); // gradforce
bytes += (double) nmax * sizeof(int); // elems
if (gradgradflag == 1) {
bytes += (double)natomgamma_max*
gamma_nnz*sizeof(int); //gamma_row_index
bytes += (double)natomgamma_max*
gamma_nnz*sizeof(int); // gamma_col_index
bytes += (double)natomgamma_max*
gamma_nnz*sizeof(double); // gamma
bytes += (double) natomgamma_max * gamma_nnz * sizeof(int); //gamma_row_index
bytes += (double) natomgamma_max * gamma_nnz * sizeof(int); // gamma_col_index
bytes += (double) natomgamma_max * gamma_nnz * sizeof(double); // gamma
}
bytes += (double)nlistatoms*ndescriptors*sizeof(int); // betas
bytes += (double)nlistatoms*ndescriptors*sizeof(int); // descriptors
bytes += (double)nlistatoms*sizeof(double); // eatoms
bytes += (double) nlistatoms * ndescriptors * sizeof(int); // betas
bytes += (double) nlistatoms * ndescriptors * sizeof(int); // descriptors
bytes += (double) nlistatoms * sizeof(double); // eatoms
bytes += (double)natomneigh_max*sizeof(int); // iatoms
bytes += (double)natomneigh_max*sizeof(int); // ielems
bytes += (double)natomneigh_max*sizeof(int); // numneighs
bytes += (double) natomneigh_max * sizeof(int); // iatoms
bytes += (double) natomneigh_max * sizeof(int); // ielems
bytes += (double) natomneigh_max * sizeof(int); // numneighs
bytes += (double)nneigh_max*sizeof(int); // pair_i
bytes += (double)nneigh_max*sizeof(int); // jatoms
bytes += (double)nneigh_max*sizeof(int); // jelems
bytes += (double)nneigh_max*3*sizeof(double); // rij"
bytes += (double) nneigh_max * sizeof(int); // pair_i
bytes += (double) nneigh_max * sizeof(int); // jatoms
bytes += (double) nneigh_max * sizeof(int); // jelems
bytes += (double) nneigh_max * 3 * sizeof(double); // rij"
if (gradgradflag == 0)
bytes += (double)nneigh_max*ndescriptors*3*sizeof(double);// graddesc
bytes += (double) nneigh_max * ndescriptors * 3 * sizeof(double); // graddesc
return bytes;
}