Various small cleanups to RHEO package flagged by compiler warnings
The individual changes are: - remove of unused function parameters - replace non-standard variable length arrays on the stack with static ones - disable citation removed from the manual - replace #defined constants with enum or static constexpr - enable and apply clang-format
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,3 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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@ -23,9 +22,9 @@
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#include "citeme.h"
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#include "compute_rheo_grad.h"
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#include "compute_rheo_interface.h"
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#include "compute_rheo_surface.h"
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#include "compute_rheo_kernel.h"
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#include "compute_rheo_rho_sum.h"
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#include "compute_rheo_surface.h"
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#include "compute_rheo_vshift.h"
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#include "domain.h"
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#include "error.h"
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@ -39,20 +38,23 @@ using namespace LAMMPS_NS;
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using namespace RHEO_NS;
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using namespace FixConst;
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#if 0
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// publication was removed from documentation
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static const char cite_rheo[] =
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"@article{PalermoInPrep,\n"
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" journal = {in prep},\n"
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" title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},\n"
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" year = {2024},\n"
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" author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},\n"
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"}\n\n";
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"@article{PalermoInPrep,\n"
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" journal = {in prep},\n"
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" title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},\n"
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" year = {2024},\n"
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" author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},\n"
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"}\n\n";
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#endif
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/* ---------------------------------------------------------------------- */
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FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg), rho0(nullptr), csq(nullptr), compute_grad(nullptr), compute_kernel(nullptr),
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compute_interface(nullptr), compute_surface(nullptr), compute_rhosum(nullptr),
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compute_vshift(nullptr)
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Fix(lmp, narg, arg), rho0(nullptr), csq(nullptr), compute_grad(nullptr),
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compute_kernel(nullptr), compute_interface(nullptr), compute_surface(nullptr),
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compute_rhosum(nullptr), compute_vshift(nullptr)
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{
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time_integrate = 1;
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@ -78,44 +80,42 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
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csq[i] = 1.0;
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}
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if (igroup != 0)
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error->all(FLERR, "fix rheo command requires group all");
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if (igroup != 0) error->all(FLERR, "fix rheo command requires group all");
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if (atom->pressure_flag != 1)
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error->all(FLERR, "fix rheo command requires atom_style with pressure");
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if (atom->rho_flag != 1)
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error->all(FLERR, "fix rheo command requires atom_style with density");
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if (atom->rho_flag != 1) error->all(FLERR, "fix rheo command requires atom_style with density");
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if (atom->viscosity_flag != 1)
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error->all(FLERR, "fix rheo command requires atom_style with viscosity");
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if (atom->rheo_status_flag != 1)
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error->all(FLERR, "fix rheo command requires atom_style with status");
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if (narg < 5)
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utils::missing_cmd_args(FLERR, "fix rheo", error);
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if (narg < 5) utils::missing_cmd_args(FLERR, "fix rheo", error);
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cut = utils::numeric(FLERR, arg[3], false, lmp);
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if (strcmp(arg[4], "quintic") == 0) {
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kernel_style = QUINTIC;
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kernel_style = QUINTIC;
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} else if (strcmp(arg[4], "wendland/c4") == 0) {
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kernel_style = WENDLANDC4;
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kernel_style = WENDLANDC4;
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} else if (strcmp(arg[4], "RK0") == 0) {
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kernel_style = RK0;
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kernel_style = RK0;
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} else if (strcmp(arg[4], "RK1") == 0) {
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kernel_style = RK1;
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kernel_style = RK1;
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} else if (strcmp(arg[4], "RK2") == 0) {
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kernel_style = RK2;
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} else error->all(FLERR, "Unknown kernel style {} in fix rheo", arg[4]);
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kernel_style = RK2;
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} else
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error->all(FLERR, "Unknown kernel style {} in fix rheo", arg[4]);
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zmin_kernel = utils::numeric(FLERR, arg[5], false, lmp);
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int iarg = 6;
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while (iarg < narg){
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while (iarg < narg) {
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if (strcmp(arg[iarg], "shift") == 0) {
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shift_flag = 1;
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} else if (strcmp(arg[iarg], "thermal") == 0) {
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thermal_flag = 1;
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} else if (strcmp(arg[iarg], "surface/detection") == 0) {
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surface_flag = 1;
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if(iarg + 3 >= narg) utils::missing_cmd_args(FLERR, "fix rheo surface/detection", error);
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if (iarg + 3 >= narg) utils::missing_cmd_args(FLERR, "fix rheo surface/detection", error);
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if (strcmp(arg[iarg + 1], "coordination") == 0) {
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surface_style = COORDINATION;
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zmin_surface = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
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@ -137,8 +137,7 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
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self_mass_flag = 1;
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} else if (strcmp(arg[iarg], "density") == 0) {
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if (iarg + n >= narg) utils::missing_cmd_args(FLERR, "fix rheo density", error);
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for (i = 1; i <= n; i++)
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rho0[i] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
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for (i = 1; i <= n; i++) rho0[i] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
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iarg += n;
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} else if (strcmp(arg[iarg], "speed/sound") == 0) {
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if (iarg + n >= narg) utils::missing_cmd_args(FLERR, "fix rheo speed/sound", error);
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@ -156,7 +155,9 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
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if (self_mass_flag && (!rhosum_flag))
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error->all(FLERR, "Cannot use self/mass setting without rho/sum");
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#if 0
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if (lmp->citeme) lmp->citeme->add(cite_rheo);
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#endif
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}
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/* ---------------------------------------------------------------------- */
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@ -174,15 +175,14 @@ FixRHEO::~FixRHEO()
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memory->destroy(rho0);
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}
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/* ----------------------------------------------------------------------
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Create necessary internal computes
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------------------------------------------------------------------------- */
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void FixRHEO::post_constructor()
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{
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compute_kernel = dynamic_cast<ComputeRHEOKernel *>(modify->add_compute(
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fmt::format("rheo_kernel all RHEO/KERNEL {}", kernel_style)));
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compute_kernel = dynamic_cast<ComputeRHEOKernel *>(
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modify->add_compute(fmt::format("rheo_kernel all RHEO/KERNEL {}", kernel_style)));
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compute_kernel->fix_rheo = this;
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std::string cmd = "rheo_grad all RHEO/GRAD velocity rho viscosity";
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@ -191,26 +191,26 @@ void FixRHEO::post_constructor()
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compute_grad->fix_rheo = this;
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if (rhosum_flag) {
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compute_rhosum = dynamic_cast<ComputeRHEORhoSum *>(modify->add_compute(
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fmt::format("rheo_rhosum all RHEO/RHO/SUM {}", self_mass_flag)));
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compute_rhosum = dynamic_cast<ComputeRHEORhoSum *>(
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modify->add_compute(fmt::format("rheo_rhosum all RHEO/RHO/SUM {}", self_mass_flag)));
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compute_rhosum->fix_rheo = this;
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}
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if (shift_flag) {
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compute_vshift = dynamic_cast<ComputeRHEOVShift *>(modify->add_compute(
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"rheo_vshift all RHEO/VSHIFT"));
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compute_vshift =
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dynamic_cast<ComputeRHEOVShift *>(modify->add_compute("rheo_vshift all RHEO/VSHIFT"));
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compute_vshift->fix_rheo = this;
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}
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if (interface_flag) {
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compute_interface = dynamic_cast<ComputeRHEOInterface *>(modify->add_compute(
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"rheo_interface all RHEO/INTERFACE"));
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compute_interface = dynamic_cast<ComputeRHEOInterface *>(
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modify->add_compute("rheo_interface all RHEO/INTERFACE"));
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compute_interface->fix_rheo = this;
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}
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if (surface_flag) {
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compute_surface = dynamic_cast<ComputeRHEOSurface *>(modify->add_compute(
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"rheo_surface all RHEO/SURFACE"));
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compute_surface =
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dynamic_cast<ComputeRHEOSurface *>(modify->add_compute("rheo_surface all RHEO/SURFACE"));
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compute_surface->fix_rheo = this;
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}
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}
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@ -237,23 +237,23 @@ void FixRHEO::init()
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error->all(FLERR, "Can only specify one instance of fix rheo");
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if (atom->rheo_status_flag != 1)
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error->all(FLERR,"fix rheo command requires atom property status");
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if (atom->rho_flag != 1)
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error->all(FLERR,"fix rheo command requires atom property rho");
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error->all(FLERR, "fix rheo command requires atom property status");
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if (atom->rho_flag != 1) error->all(FLERR, "fix rheo command requires atom property rho");
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if (atom->pressure_flag != 1)
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error->all(FLERR,"fix rheo command requires atom property pressure");
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error->all(FLERR, "fix rheo command requires atom property pressure");
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if (atom->viscosity_flag != 1)
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error->all(FLERR,"fix rheo command requires atom property viscosity");
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error->all(FLERR, "fix rheo command requires atom property viscosity");
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if (thermal_flag) {
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if (atom->esph_flag != 1)
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error->all(FLERR,"fix rheo command requires atom property esph with thermal setting");
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error->all(FLERR, "fix rheo command requires atom property esph with thermal setting");
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if (atom->temperature_flag != 1)
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error->all(FLERR,"fix rheo command requires atom property temperature with thermal setting");
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error->all(FLERR, "fix rheo command requires atom property temperature with thermal setting");
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if (atom->heatflow_flag != 1)
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error->all(FLERR,"fix rheo command requires atom property heatflow with thermal setting");
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error->all(FLERR, "fix rheo command requires atom property heatflow with thermal setting");
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if (atom->conductivity_flag != 1)
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error->all(FLERR,"fix rheo command requires atom property conductivity with thermal setting");
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error->all(FLERR,
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"fix rheo command requires atom property conductivity with thermal setting");
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}
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}
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@ -281,14 +281,11 @@ void FixRHEO::setup(int /*vflag*/)
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{
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// Confirm all accessory fixes are defined
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// Note: fixes set this flag in setup_pre_force()
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if (!viscosity_fix_defined)
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error->all(FLERR, "Missing fix rheo/viscosity");
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if (!viscosity_fix_defined) error->all(FLERR, "Missing fix rheo/viscosity");
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if (!pressure_fix_defined)
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error->all(FLERR, "Missing fix rheo/pressure");
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if (!pressure_fix_defined) error->all(FLERR, "Missing fix rheo/pressure");
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if(thermal_flag && !thermal_fix_defined)
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error->all(FLERR, "Missing fix rheo/thermal");
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if (thermal_flag && !thermal_fix_defined) error->all(FLERR, "Missing fix rheo/thermal");
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// Reset to zero for future runs
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thermal_fix_defined = 0;
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@ -296,8 +293,7 @@ void FixRHEO::setup(int /*vflag*/)
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pressure_fix_defined = 0;
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oxidation_fix_defined = 0;
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if (rhosum_flag)
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compute_rhosum->compute_peratom();
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if (rhosum_flag) compute_rhosum->compute_peratom();
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}
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/* ---------------------------------------------------------------------- */
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@ -321,15 +317,13 @@ void FixRHEO::initial_integrate(int /*vflag*/)
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double **gradr = compute_grad->gradr;
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double **gradv = compute_grad->gradv;
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double **vshift;
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if (shift_flag)
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vshift = compute_vshift->vshift;
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if (shift_flag) vshift = compute_vshift->vshift;
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int nlocal = atom->nlocal;
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int rmass_flag = atom->rmass_flag;
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int dim = domain->dimension;
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if (igroup == atom->firstgroup)
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nlocal = atom->nfirst;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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//Density Half-step
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for (i = 0; i < nlocal; i++) {
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@ -349,7 +343,7 @@ void FixRHEO::initial_integrate(int /*vflag*/)
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}
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// Update gradients and interpolate solid properties
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compute_grad->forward_fields(); // also forwards v and rho for chi
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compute_grad->forward_fields(); // also forwards v and rho for chi
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if (interface_flag) {
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// Need to save, wiped in exchange
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compute_interface->store_forces();
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@ -360,9 +354,7 @@ void FixRHEO::initial_integrate(int /*vflag*/)
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// Position half-step
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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for (a = 0; a < dim; a++) {
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x[i][a] += dtv * v[i][a];
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}
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for (a = 0; a < dim; a++) { x[i][a] += dtv * v[i][a]; }
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}
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}
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@ -374,9 +366,7 @@ void FixRHEO::initial_integrate(int /*vflag*/)
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if (status[i] & PHASECHECK) continue;
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divu = 0;
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for (a = 0; a < dim; a++) {
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divu += gradv[i][a * (1 + dim)];
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}
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for (a = 0; a < dim; a++) { divu += gradv[i][a * (1 + dim)]; }
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rho[i] += dtf * (drho[i] - rho[i] * divu);
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}
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}
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@ -392,16 +382,12 @@ void FixRHEO::initial_integrate(int /*vflag*/)
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if (mask[i] & groupbit) {
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for (a = 0; a < dim; a++) {
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x[i][a] += dtv * vshift[i][a];
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for (b = 0; b < dim; b++) {
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v[i][a] += dtv * vshift[i][b] * gradv[i][a * dim + b];
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}
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for (b = 0; b < dim; b++) { v[i][a] += dtv * vshift[i][b] * gradv[i][a * dim + b]; }
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}
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if (!rhosum_flag) {
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if (status[i] & PHASECHECK) continue;
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for (a = 0; a < dim; a++) {
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rho[i] += dtv * vshift[i][a] * gradr[i][a];
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}
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for (a = 0; a < dim; a++) { rho[i] += dtv * vshift[i][a] * gradr[i][a]; }
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}
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}
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}
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@ -412,10 +398,9 @@ void FixRHEO::initial_integrate(int /*vflag*/)
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void FixRHEO::pre_force(int /*vflag*/)
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{
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compute_kernel->compute_coordination(); // Needed for rho sum
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compute_kernel->compute_coordination(); // Needed for rho sum
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if (rhosum_flag)
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compute_rhosum->compute_peratom();
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if (rhosum_flag) compute_rhosum->compute_peratom();
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compute_kernel->compute_peratom();
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@ -428,22 +413,19 @@ void FixRHEO::pre_force(int /*vflag*/)
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compute_grad->compute_peratom();
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compute_grad->forward_gradients();
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if (shift_flag)
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compute_vshift->compute_peratom();
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if (shift_flag) compute_vshift->compute_peratom();
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// Remove temporary options
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int *mask = atom->mask;
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int *status = atom->rheo_status;
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int nall = atom->nlocal + atom->nghost;
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for (int i = 0; i < nall; i++)
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if (mask[i] & groupbit)
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status[i] &= OPTIONSMASK;
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if (mask[i] & groupbit) status[i] &= OPTIONSMASK;
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// Calculate surfaces, update status
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if (surface_flag) {
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compute_surface->compute_peratom();
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if (shift_flag)
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compute_vshift->correct_surfaces();
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if (shift_flag) compute_vshift->correct_surfaces();
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}
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}
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@ -452,8 +434,7 @@ void FixRHEO::pre_force(int /*vflag*/)
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void FixRHEO::final_integrate()
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{
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup)
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nlocal = atom->nfirst;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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double dtfm, divu;
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int i, a;
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@ -482,9 +463,7 @@ void FixRHEO::final_integrate()
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dtfm = dtf / mass[type[i]];
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}
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for (a = 0; a < dim; a++) {
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v[i][a] += dtfm * f[i][a];
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}
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for (a = 0; a < dim; a++) { v[i][a] += dtfm * f[i][a]; }
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}
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}
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@ -496,9 +475,7 @@ void FixRHEO::final_integrate()
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if (status[i] & PHASECHECK) continue;
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divu = 0;
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for (a = 0; a < dim; a++) {
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divu += gradv[i][a * (1 + dim)];
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}
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for (a = 0; a < dim; a++) { divu += gradv[i][a * (1 + dim)]; }
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rho[i] += dtf * (drho[i] - rho[i] * divu);
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}
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}
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