From d5ba6f70f2dcced16282f084c8fb27f88ad8a91f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 20 Feb 2023 12:48:39 -0500 Subject: [PATCH] enable and apply clang-format --- src/ML-IAP/mliap_data.cpp | 123 +++++++++++++++++--------------------- 1 file changed, 55 insertions(+), 68 deletions(-) diff --git a/src/ML-IAP/mliap_data.cpp b/src/ML-IAP/mliap_data.cpp index 1dee9167e8..1c817bd3bd 100644 --- a/src/ML-IAP/mliap_data.cpp +++ b/src/ML-IAP/mliap_data.cpp @@ -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; } -