diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index 19e56fcc83..dbd6b58ce7 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -91,7 +91,7 @@ KOKKOS, o = OPENMP, t = OPT. * :doc:`ke/atom/eff ` * :doc:`ke/eff ` * :doc:`ke/rigid ` - * :doc:`local/comp/atom (k) ` + * :doc:`composition/atom (k) ` * :doc:`mliap ` * :doc:`momentum ` * :doc:`msd ` diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 317efa4f41..abc89fb663 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -245,7 +245,7 @@ The individual style names on the :doc:`Commands compute ` pag * :doc:`ke/atom/eff ` - per-atom translational and radial kinetic energy in the electron force field model * :doc:`ke/eff ` - kinetic energy of a group of nuclei and electrons in the electron force field model * :doc:`ke/rigid ` - translational kinetic energy of rigid bodies -* :doc:`local/comp/atom ` - local composition for each atom +* :doc:`composition/atom ` - local composition for each atom * :doc:`mliap ` - gradients of energy and forces with respect to model parameters and related quantities for training machine learning interatomic potentials * :doc:`momentum ` - translational momentum * :doc:`msd ` - mean-squared displacement of group of atoms diff --git a/doc/src/compute_local_comp_atom.rst b/doc/src/compute_composition_atom.rst similarity index 90% rename from doc/src/compute_local_comp_atom.rst rename to doc/src/compute_composition_atom.rst index 2d0dd8c6f2..b7890fff8b 100644 --- a/doc/src/compute_local_comp_atom.rst +++ b/doc/src/compute_composition_atom.rst @@ -1,20 +1,20 @@ -.. index:: compute local/comp/atom -.. index:: compute local/comp/atom/kk +.. index:: compute composition/atom +.. index:: compute composition/atom/kk -compute local/comp/atom command -=============================== +compute composition/atom command +================================ -Accelerator Variants: *local/comp/atom/kk* +Accelerator Variants: *composition/atom/kk* Syntax """""" .. code-block:: LAMMPS - compute ID group-ID local/comp/atom keyword values ... + compute ID group-ID composition/atom keyword values ... * ID, group-ID are documented in :doc:`compute ` command -* local/comp/atom = style name of this compute command +* composition/atom = style name of this compute command * one or more keyword/value pairs may be appended .. parsed-literal:: @@ -27,9 +27,9 @@ Examples .. code-block:: LAMMPS - compute 1 all local/comp/atom + compute 1 all composition/atom - compute 1 all local/comp/atom cutoff 9.0 + compute 1 all composition/atom cutoff 9.0 comm_modify cutoff 9.0 diff --git a/src/.gitignore b/src/.gitignore index 8c1385199a..b18ab895da 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -580,8 +580,8 @@ /compute_ke_eff.h /compute_ke_rigid.cpp /compute_ke_rigid.h -/compute_local_comp_atom.cpp -/compute_local_comp_atom.h +/compute_composition_atom.cpp +/compute_composition_atom.h /compute_meso_e_atom.cpp /compute_meso_e_atom.h /compute_meso_rho_atom.cpp diff --git a/src/EXTRA-COMPUTE/compute_local_comp_atom.cpp b/src/EXTRA-COMPUTE/compute_composition_atom.cpp similarity index 83% rename from src/EXTRA-COMPUTE/compute_local_comp_atom.cpp rename to src/EXTRA-COMPUTE/compute_composition_atom.cpp index 1da8670cd2..48aaa68dea 100644 --- a/src/EXTRA-COMPUTE/compute_local_comp_atom.cpp +++ b/src/EXTRA-COMPUTE/compute_composition_atom.cpp @@ -15,7 +15,7 @@ Contributing author: Megan McCarthy (SNL) ------------------------------------------------------------------------- */ -#include "compute_local_comp_atom.h" +#include "compute_composition_atom.h" #include "atom.h" #include "comm.h" @@ -37,22 +37,22 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -ComputeLocalCompAtom::ComputeLocalCompAtom(LAMMPS *lmp, int narg, char **arg) : +ComputeCompositionAtom::ComputeCompositionAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), list(nullptr), result(nullptr) { - if (narg < 3 || narg > 5) error->all(FLERR, "Illegal compute local/comp/atom command"); + if (narg < 3 || narg > 5) error->all(FLERR, "Illegal compute composition/atom command"); cutsq = cutoff = 0.0; int iarg = 3; while (iarg < narg) { if (strcmp(arg[iarg], "cutoff") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal compute local/comp/atom command"); + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute composition/atom command"); cutoff = utils::numeric(FLERR, arg[iarg + 1], false, lmp); - if (cutoff <= 0.0) error->all(FLERR, "Illegal compute local/comp/atom command"); + if (cutoff <= 0.0) error->all(FLERR, "Illegal compute composition/atom command"); iarg += 2; } else - error->all(FLERR, "Illegal compute local/comp/atom command"); + error->all(FLERR, "Illegal compute composition/atom command"); } peratom_flag = 1; @@ -65,7 +65,7 @@ ComputeLocalCompAtom::ComputeLocalCompAtom(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -ComputeLocalCompAtom::~ComputeLocalCompAtom() +ComputeCompositionAtom::~ComputeCompositionAtom() { if (copymode) return; @@ -74,11 +74,11 @@ ComputeLocalCompAtom::~ComputeLocalCompAtom() /* ---------------------------------------------------------------------- */ -void ComputeLocalCompAtom::init() +void ComputeCompositionAtom::init() { if (!force->pair && cutoff == 0.0) error->all(FLERR, - "Compute local/comp/atom requires a cutoff be specified " + "Compute composition/atom requires a cutoff be specified " "or a pair style be defined"); double skin = neighbor->skin; @@ -91,7 +91,7 @@ void ComputeLocalCompAtom::init() if (cutoff > cutghost) error->all(FLERR, - "Compute local/comp/atom cutoff exceeds ghost atom range - " + "Compute composition/atom cutoff exceeds ghost atom range - " "use comm_modify cutoff command"); } @@ -111,14 +111,14 @@ void ComputeLocalCompAtom::init() /* ---------------------------------------------------------------------- */ -void ComputeLocalCompAtom::init_list(int /*id*/, NeighList *ptr) +void ComputeCompositionAtom::init_list(int /*id*/, NeighList *ptr) { list = ptr; } /* ---------------------------------------------------------------------- */ -void ComputeLocalCompAtom::compute_peratom() +void ComputeCompositionAtom::compute_peratom() { int i, j, ii, jj, inum, jnum; double xtmp, ytmp, ztmp, delx, dely, delz, rsq; @@ -132,7 +132,7 @@ void ComputeLocalCompAtom::compute_peratom() if (atom->nmax > nmax) { memory->destroy(result); nmax = atom->nmax; - memory->create(result, nmax, size_peratom_cols, "local/comp/atom:result"); + memory->create(result, nmax, size_peratom_cols, "composition/atom:result"); array_atom = result; } @@ -205,7 +205,7 @@ void ComputeLocalCompAtom::compute_peratom() memory usage of local atom-based array ------------------------------------------------------------------------- */ -double ComputeLocalCompAtom::memory_usage() +double ComputeCompositionAtom::memory_usage() { double bytes = (double) 2 * nmax * sizeof(double); return bytes; diff --git a/src/EXTRA-COMPUTE/compute_local_comp_atom.h b/src/EXTRA-COMPUTE/compute_composition_atom.h similarity index 81% rename from src/EXTRA-COMPUTE/compute_local_comp_atom.h rename to src/EXTRA-COMPUTE/compute_composition_atom.h index 76d92de08d..281bceffd7 100644 --- a/src/EXTRA-COMPUTE/compute_local_comp_atom.h +++ b/src/EXTRA-COMPUTE/compute_composition_atom.h @@ -13,21 +13,21 @@ #ifdef COMPUTE_CLASS // clang-format off -ComputeStyle(local/comp/atom,ComputeLocalCompAtom); +ComputeStyle(composition/atom,ComputeCompositionAtom); // clang-format on #else -#ifndef LMP_COMPUTE_LOCAL_COMP_ATOM_H -#define LMP_COMPUTE_LOCAL_COMP_ATOM_H +#ifndef LMP_COMPUTE_COMPOSITION_ATOM_H +#define LMP_COMPUTE_COMPOSITION_ATOM_H #include "compute.h" namespace LAMMPS_NS { -class ComputeLocalCompAtom : public Compute { +class ComputeCompositionAtom : public Compute { public: - ComputeLocalCompAtom(class LAMMPS *, int, char **); - ~ComputeLocalCompAtom() override; + ComputeCompositionAtom(class LAMMPS *, int, char **); + ~ComputeCompositionAtom() override; void init() override; void init_list(int, class NeighList *) override; void compute_peratom() override; diff --git a/src/KOKKOS/compute_local_comp_atom_kokkos.cpp b/src/KOKKOS/compute_composition_atom_kokkos.cpp similarity index 85% rename from src/KOKKOS/compute_local_comp_atom_kokkos.cpp rename to src/KOKKOS/compute_composition_atom_kokkos.cpp index 356efea2f1..2b0e663011 100644 --- a/src/KOKKOS/compute_local_comp_atom_kokkos.cpp +++ b/src/KOKKOS/compute_composition_atom_kokkos.cpp @@ -15,7 +15,7 @@ Contributing author: Megan McCarthy (SNL) ------------------------------------------------------------------------- */ -#include "compute_local_comp_atom_kokkos.h" +#include "compute_composition_atom_kokkos.h" #include "atom_kokkos.h" #include "atom_masks.h" @@ -39,8 +39,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ template -ComputeLocalCompAtomKokkos::ComputeLocalCompAtomKokkos(LAMMPS *lmp, int narg, char **arg) : - ComputeLocalCompAtom(lmp, narg, arg) +ComputeCompositionAtomKokkos::ComputeCompositionAtomKokkos(LAMMPS *lmp, int narg, char **arg) : + ComputeCompositionAtom(lmp, narg, arg) { kokkosable = 1; atomKK = (AtomKokkos *) atom; @@ -52,7 +52,7 @@ ComputeLocalCompAtomKokkos::ComputeLocalCompAtomKokkos(LAMMPS *lmp, /* ---------------------------------------------------------------------- */ template -ComputeLocalCompAtomKokkos::~ComputeLocalCompAtomKokkos() +ComputeCompositionAtomKokkos::~ComputeCompositionAtomKokkos() { if (copymode) return; @@ -62,9 +62,9 @@ ComputeLocalCompAtomKokkos::~ComputeLocalCompAtomKokkos() /* ---------------------------------------------------------------------- */ template -void ComputeLocalCompAtomKokkos::init() +void ComputeCompositionAtomKokkos::init() { - ComputeLocalCompAtom::init(); + ComputeCompositionAtom::init(); // adjust neighbor list request for KOKKOS @@ -77,7 +77,7 @@ void ComputeLocalCompAtomKokkos::init() /* ---------------------------------------------------------------------- */ template -void ComputeLocalCompAtomKokkos::compute_peratom() +void ComputeCompositionAtomKokkos::compute_peratom() { invoked_peratom = update->ntimestep; @@ -87,7 +87,7 @@ void ComputeLocalCompAtomKokkos::compute_peratom() if (atom->nmax > nmax) { memoryKK->destroy_kokkos(k_result,result); nmax = atom->nmax; - memoryKK->create_kokkos(k_result,result,nmax,size_peratom_cols,"local/comp/atom:result"); + memoryKK->create_kokkos(k_result,result,nmax,size_peratom_cols,"composition/atom:result"); d_result = k_result.view(); array_atom = result; } @@ -114,7 +114,7 @@ void ComputeLocalCompAtomKokkos::compute_peratom() Kokkos::deep_copy(d_result,0.0); copymode = 1; - typename Kokkos::RangePolicy policy(0,inum); + typename Kokkos::RangePolicy policy(0,inum); Kokkos::parallel_for("ComputeLocalComp",policy,*this); copymode = 0; @@ -124,7 +124,7 @@ void ComputeLocalCompAtomKokkos::compute_peratom() template KOKKOS_INLINE_FUNCTION -void ComputeLocalCompAtomKokkos::operator()(TagComputeLocalCompAtom, const int &ii) const +void ComputeCompositionAtomKokkos::operator()(TagComputeCompositionAtom, const int &ii) const { const int i = d_ilist[ii]; @@ -173,8 +173,8 @@ void ComputeLocalCompAtomKokkos::operator()(TagComputeLocalCompAtom, } namespace LAMMPS_NS { -template class ComputeLocalCompAtomKokkos; +template class ComputeCompositionAtomKokkos; #ifdef LMP_KOKKOS_GPU -template class ComputeLocalCompAtomKokkos; +template class ComputeCompositionAtomKokkos; #endif } diff --git a/src/KOKKOS/compute_local_comp_atom_kokkos.h b/src/KOKKOS/compute_composition_atom_kokkos.h similarity index 66% rename from src/KOKKOS/compute_local_comp_atom_kokkos.h rename to src/KOKKOS/compute_composition_atom_kokkos.h index 5fb52474b2..49af2c8d5b 100644 --- a/src/KOKKOS/compute_local_comp_atom_kokkos.h +++ b/src/KOKKOS/compute_composition_atom_kokkos.h @@ -13,37 +13,37 @@ #ifdef COMPUTE_CLASS // clang-format off -ComputeStyle(local/comp/atom/kk,ComputeLocalCompAtomKokkos); -ComputeStyle(local/comp/atom/kk/device,ComputeLocalCompAtomKokkos); -ComputeStyle(local/comp/atom/kk/host,ComputeLocalCompAtomKokkos); +ComputeStyle(composition/atom/kk,ComputeCompositionAtomKokkos); +ComputeStyle(composition/atom/kk/device,ComputeCompositionAtomKokkos); +ComputeStyle(composition/atom/kk/host,ComputeCompositionAtomKokkos); // clang-format on #else -#ifndef LMP_COMPUTE_LOCAL_COMP_ATOM_KOKKOS_H -#define LMP_COMPUTE_LOCAL_COMP_ATOM_KOKKOS_H +#ifndef LMP_COMPUTE_COMPOSITION_ATOM_KOKKOS_H +#define LMP_COMPUTE_COMPOSITION_ATOM_KOKKOS_H -#include "compute_local_comp_atom.h" +#include "compute_composition_atom.h" #include "kokkos_type.h" namespace LAMMPS_NS { // clang-format off -struct TagComputeLocalCompAtom {}; +struct TagComputeCompositionAtom {}; // clang-format on -template class ComputeLocalCompAtomKokkos : public ComputeLocalCompAtom { +template class ComputeCompositionAtomKokkos : public ComputeCompositionAtom { public: typedef DeviceType device_type; typedef ArrayTypes AT; - ComputeLocalCompAtomKokkos(class LAMMPS *, int, char **); - ~ComputeLocalCompAtomKokkos() override; + ComputeCompositionAtomKokkos(class LAMMPS *, int, char **); + ~ComputeCompositionAtomKokkos() override; void init() override; void compute_peratom() override; KOKKOS_INLINE_FUNCTION - void operator()(TagComputeLocalCompAtom, const int &) const; + void operator()(TagComputeCompositionAtom, const int &) const; private: