Adding base fix and atom style
This commit is contained in:
jtclemm
365
src/RHEO/fix_rheo.cpp
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365
src/RHEO/fix_rheo.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "fix_rheo.h"
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#include "atom.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_kernel.h"
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#include "compute_rheo_rhosum.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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#include "force.h"
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#include "modify.h"
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#include "update.h"
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#include "utils.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg), compute_grad(nullptr), compute_kernel(nullptr),
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compute_interface(nullptr), compute_rhosum(nullptr), compute_vshift(nullptr)
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{
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thermal_flag = 0;
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rhosum_flag = 0;
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shift_flag = 0;
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solid_flag = 0;
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rho0 = 1.0;
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csq = 1.0;
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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->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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error->all(FLERR,"Insufficient arguments for fix rheo command");
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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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} else if (strcmp(arg[4],"CRK0") == 0) {
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kernel_style = CRK0;
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} else if (strcmp(arg[4],"CRK1") == 0) {
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kernel_style = CRK1;
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} else if (strcmp(arg[4],"CRK2") == 0) {
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kernel_style = CRK2;
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} else 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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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],"rhosum") == 0) {
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rhosum_flag = 1;
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if(iarg + 1 >= narg) error->all(FLERR,"Illegal rhosum option in fix rheo");
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zmin_rhosum = utils::inumeric(FLERR,arg[iarg + 1],false,lmp);
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iarg += 1;
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} else if (strcmp(arg[iarg],"rho0") == 0) {
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if(iarg + 1 >= narg) error->all(FLERR,"Illegal rho0 option in fix rheo");
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rho0 = utils::numeric(FLERR,arg[iarg + 1],false,lmp);
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iarg += 1;
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} else if (strcmp(arg[iarg],"csq") == 0) {
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if(iarg+1 >= narg) error->all(FLERR,"Illegal csq option in fix rheo");
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csq = utils::numeric(FLERR,arg[iarg + 1],false,lmp);
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iarg += 1;
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} else {
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error->all(FLERR, "Illegal fix rheo command: {}", arg[iarg]);
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}
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iarg += 1;
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}
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time_integrate = 1;
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thermal_fix_defined = 0;
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viscosity_fix_defined = 0;
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pressure_fix_defined = 0;
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}
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/* ---------------------------------------------------------------------- */
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FixRHEO::~FixRHEO()
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{
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if (compute_kernel) modify->delete_compute("rheo_kernel");
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if (compute_grad) modify->delete_compute("rheo_grad");
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if (compute_interface) modify->delete_compute("rheo_interface");
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if (compute_rhosum) modify->delete_compute("rheo_rhosum");
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if (compute_vshift) modify->delete_compute("rheo_vshift");
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}
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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(fmt::format("rheo_kernel all rheo/kernel {} {} {}", kernel_style, zmin_kernel, cut)));
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if (thermal_flag)
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compute_grad = dynamic_cast<ComputeRHEOGrad *>(modify->add_compute(fmt::format("rheo_grad all rheo/grad {} velocity rho viscosity temprature", cut)));
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else
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compute_grad = dynamic_cast<ComputeRHEOGrad *>(modify->add_compute(fmt::format("rheo_grad all rheo/grad {} velocity rho viscosity", cut)));
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compute_interface = dynamic_cast<ComputeRHEOInterface *>(modify->add_compute(fmt::format("rheo_interface all rheo/interface {}", cut)));
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if (rhosum_flag)
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compute_rhosum = dynamic_cast<ComputeRHEORhoSum *>(modify->add_compute(fmt::format("rheo_rhosum all rheo/rho/sum {} {}", cut, zmin_rhosum)));
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if (shift_flag)
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compute_vshift = dynamic_cast<ComputeRHEOVShift *>(modify->add_compute(fmt::format("rheo_vshift all rheo/vshift {}", cut)));
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}
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/* ---------------------------------------------------------------------- */
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int FixRHEO::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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mask |= FINAL_INTEGRATE;
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mask |= PRE_FORCE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixRHEO::init()
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{
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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}
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/* ---------------------------------------------------------------------- */
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void FixRHEO::setup_pre_force(int /*vflag*/)
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{
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// Check to confirm all accessory fixes are defined
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if(!thermal_fix_defined && thermal_flag)
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error->all(FLERR, "Missing fix rheo/thermal");
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if (!viscosity_fix_defined)
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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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// Reset to zero for next run
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thermal_fix_defined = 0;
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viscosity_fix_defined = 0;
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pressure_fix_defined = 0;
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pre_force(0);
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}
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/* ---------------------------------------------------------------------- */
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void FixRHEO::initial_integrate(int /*vflag*/)
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{
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// update v and x and rho of atoms in group
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int i, a, b;
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double dtfm, divu;
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int dim = domain->dimension;
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int *status = atom->status;
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double *rho = atom->rho;
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double *drho = atom->drho;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int rmass_flag = atom->rmass_flag;
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double **gradr = compute_grad->gradr;
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double **gradv = compute_grad->gradv;
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double **vshift = compute_vshift->array_atom;
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int *type = atom->type;
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int *mask = atom->mask;
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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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//Density Half-step
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for (i = 0; i < nlocal; i++) {
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if (status[i] & STATUS_NO_FORCE) continue;
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if (mask[i] & groupbit) {
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if (rmass_flag) {
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dtfm = dtf / rmass[i];
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} else {
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dtfm = dtf / mass[type[i]];
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}
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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}
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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_interface->store_forces(); // Need to save, wiped in exchange
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compute_interface->compute_peratom();
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compute_grad->compute_peratom();
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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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}
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}
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// Update density using div(u)
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if (!rhosum_flag) {
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (status[i] & STATUS_NO_FORCE) continue;
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if (!(status[i] & STATUS_FLUID)) 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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rho[i] += dtf * (drho[i] - rho[i] * divu);
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}
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}
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}
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// Shifting atoms
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if (shift_flag) {
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compute_vshift->correct_surfaces();
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for (i = 0; i < nlocal; i++) {
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if (!(status[i] & STATUS_SHIFT)) continue;
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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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}
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if (!rhosum_flag) {
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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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}
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixRHEO::pre_force(int /*vflag*/)
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{
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if (rhosum_flag)
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compute_rhosum->compute_peratom();
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compute_grad->forward_fields(); // also forwards v and rho for chi
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compute_kernel->compute_peratom();
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compute_interface->compute_peratom();
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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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// Remove extra shifting/no force options options
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int *status = atom->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] &= ~STATUS_NO_FORCE;
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if (status[i] & STATUS_FLUID)
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status[i] &= ~STATUS_SHIFT;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixRHEO::final_integrate() {
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int *status = atom->status;
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double **gradv = compute_grad->gradv;
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double *rho = atom->rho;
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double *drho = atom->drho;
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int *type = atom->type;
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int *mask = atom->mask;
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double *mass = atom->mass;
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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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double dtfm, divu;
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double *rmass = atom->rmass;
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int rmass_flag = atom->rmass_flag;
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int i, a;
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int dim = domain->dimension;
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// Update velocity
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (status[i] & STATUS_NO_FORCE) continue;
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if (rmass_flag) {
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dtfm = dtf / rmass[i];
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} else {
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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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}
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}
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// Update density using divu
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if (!rhosum_flag) {
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for (i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (status[i] & STATUS_NO_FORCE) continue;
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if (!(status[i] & STATUS_FLUID)) 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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rho[i] += dtf * (drho[i] - rho[i] * divu);
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixRHEO::reset_dt()
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{
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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}
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