lammps/src/RHEO/fix_rheo.cpp

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   https://www.lammps.org/, Sandia National Laboratories
   LAMMPS development team: developers@lammps.org

   Copyright (2003) Sandia Corporation.  Under the terms of Contract
   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
   certain rights in this software.  This software is distributed under
   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */

/* ----------------------------------------------------------------------
   Contributing authors:
   Joel Clemmer (SNL), Thomas O'Connor (CMU), Eric Palermo (CMU)
----------------------------------------------------------------------- */

#include "fix_rheo.h"

#include "atom.h"
#include "citeme.h"
#include "compute_rheo_grad.h"
#include "compute_rheo_interface.h"
#include "compute_rheo_kernel.h"
#include "compute_rheo_rho_sum.h"
#include "compute_rheo_surface.h"
#include "compute_rheo_vshift.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "modify.h"
#include "update.h"
#include "utils.h"

using namespace LAMMPS_NS;
using namespace RHEO_NS;
using namespace FixConst;

static const char cite_rheo[] =
    "@article{Palermo2024,\n"
    " journal = {Physics of Fluids},\n"
    " title = {Reproducing hydrodynamics and elastic objects: A hybrid mesh-free model framework for dynamic multi-phase flows},\n"
    " volume = {36},\n"
    " number = {11},\n"
    " pages = {113337},\n"
    " year = {2024},\n"
    " issn = {1070-6631},\n"
    " doi = {https://doi.org/10.1063/5.0228823},\n"
    " author = {Palermo, Eric T. and Wolf, Ki T. and Clemmer, Joel T. and O'Connor, Thomas C.},\n"
    "}\n\n";

/* ---------------------------------------------------------------------- */

FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
    Fix(lmp, narg, arg), rho0(nullptr), csq(nullptr), shift_type(nullptr),
    compute_grad(nullptr), compute_kernel(nullptr), compute_interface(nullptr),
    compute_surface(nullptr), compute_rhosum(nullptr), compute_vshift(nullptr)
{
  time_integrate = 1;

  viscosity_fix_defined = 0;
  pressure_fix_defined = 0;
  thermal_fix_defined = 0;
  oxidation_fix_defined = 0;

  thermal_flag = 0;
  rhosum_flag = 0;
  shift_flag = 0;
  interface_flag = 0;
  surface_flag = 0;
  coordination_flag = 0;

  rhosum_self_mass_flag = 0;
  shift_cross_type_flag = 0;

  int i, nlo, nhi;
  int n = atom->ntypes;
  memory->create(rho0, n + 1, "rheo:rho0");
  memory->create(csq, n + 1, "rheo:csq");
  for (i = 1; i <= n; i++) {
    rho0[i] = 1.0;
    csq[i] = 1.0;
  }

  if (igroup != 0) error->all(FLERR, "fix rheo command requires group all");

  if (atom->pressure_flag != 1)
    error->all(FLERR, "fix rheo command requires atom_style with pressure");
  if (atom->rho_flag != 1) error->all(FLERR, "fix rheo command requires atom_style with density");
  if (atom->viscosity_flag != 1)
    error->all(FLERR, "fix rheo command requires atom_style with viscosity");
  if (atom->rheo_status_flag != 1)
    error->all(FLERR, "fix rheo command requires atom_style with status");

  if (narg < 5) utils::missing_cmd_args(FLERR, "fix rheo", error);

  cut = utils::numeric(FLERR, arg[3], false, lmp);
  if (strcmp(arg[4], "quintic") == 0) {
    kernel_style = QUINTIC;
  } else if (strcmp(arg[4], "wendland/c4") == 0) {
    kernel_style = WENDLANDC4;
  } else if (strcmp(arg[4], "RK0") == 0) {
    kernel_style = RK0;
  } else if (strcmp(arg[4], "RK1") == 0) {
    kernel_style = RK1;
  } else if (strcmp(arg[4], "RK2") == 0) {
    kernel_style = RK2;
  } else
    error->all(FLERR, "Unknown kernel style {} in fix rheo", arg[4]);
  zmin_kernel = utils::numeric(FLERR, arg[5], false, lmp);

  int iarg = 6;
  while (iarg < narg) {
    if (strcmp(arg[iarg], "shift") == 0) {
      shift_flag = 1;
      memory->create(shift_type, n + 1, "rheo:shift_type");
      for (i = 1; i <= n; i++) shift_type[i] = 1;
      while (iarg < narg) {  // optional sub-arguments
        if (strcmp(arg[iarg], "scale/cross/type") == 0) {
          if (iarg + 3 >= narg) utils::missing_cmd_args(FLERR, "fix rheo shift scale/cross/type", error);
          shift_cross_type_flag = 1;
          shift_scale = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
          shift_cmin = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
          shift_wmin = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
          iarg += 3;
        } else if (strcmp(arg[iarg], "exclude/type") == 0) {
          if (iarg + 1 >= narg) utils::missing_cmd_args(FLERR, "fix rheo shift exclude/type", error);
          utils::bounds(FLERR, arg[iarg + 1], 1, n, nlo, nhi, error);
          for (i = nlo; i <= nhi; i++) shift_type[i] = 0;
          iarg += 1;
        } else {
          break;
        }
        iarg += 1;
      }
    } else if (strcmp(arg[iarg], "thermal") == 0) {
      thermal_flag = 1;
    } else if (strcmp(arg[iarg], "surface/detection") == 0) {
      surface_flag = 1;
      if (iarg + 3 >= narg) utils::missing_cmd_args(FLERR, "fix rheo surface/detection", error);
      if (strcmp(arg[iarg + 1], "coordination") == 0) {
        surface_style = COORDINATION;
        zmin_surface = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
        zmin_splash = utils::inumeric(FLERR, arg[iarg + 3], false, lmp);
      } else if (strcmp(arg[iarg + 1], "divergence") == 0) {
        surface_style = DIVR;
        divr_surface = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
        zmin_splash = utils::inumeric(FLERR, arg[iarg + 3], false, lmp);
      } else {
        error->all(FLERR, "Illegal surface/detection option in fix rheo, {}", arg[iarg + 1]);
      }
      iarg += 3;
    } else if (strcmp(arg[iarg], "interface/reconstruct") == 0) {
      interface_flag = 1;
    } else if (strcmp(arg[iarg], "rho/sum") == 0) {
      rhosum_flag = 1;
      while (iarg < narg) {  // optional sub-arguments
        if (strcmp(arg[iarg], "self/mass") == 0) {
          rhosum_self_mass_flag = 1;
        } else {
          break;
        }
        iarg += 1;
      }
    } else if (strcmp(arg[iarg], "density") == 0) {
      if (iarg + n >= narg) utils::missing_cmd_args(FLERR, "fix rheo density", error);
      for (i = 1; i <= n; i++) rho0[i] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
      iarg += n;
    } else if (strcmp(arg[iarg], "speed/sound") == 0) {
      if (iarg + n >= narg) utils::missing_cmd_args(FLERR, "fix rheo speed/sound", error);
      for (i = 1; i <= n; i++) {
        csq[i] = utils::numeric(FLERR, arg[iarg + i], false, lmp);
        csq[i] *= csq[i];
      }
      iarg += n;
    } else {
      error->all(FLERR, "Illegal fix rheo command: {}", arg[iarg]);
    }
    iarg += 1;
  }

  if (lmp->citeme) lmp->citeme->add(cite_rheo);
}

/* ---------------------------------------------------------------------- */

FixRHEO::~FixRHEO()
{
  if (compute_kernel) modify->delete_compute("rheo_kernel");
  if (compute_grad) modify->delete_compute("rheo_grad");
  if (compute_interface) modify->delete_compute("rheo_interface");
  if (compute_surface) modify->delete_compute("rheo_surface");
  if (compute_rhosum) modify->delete_compute("rheo_rhosum");
  if (compute_vshift) modify->delete_compute("rheo_vshift");

  memory->destroy(csq);
  memory->destroy(rho0);
  memory->destroy(shift_type);
}

/* ----------------------------------------------------------------------
  Create necessary internal computes
------------------------------------------------------------------------- */

void FixRHEO::post_constructor()
{
  compute_kernel = dynamic_cast<ComputeRHEOKernel *>(
      modify->add_compute(fmt::format("rheo_kernel all RHEO/KERNEL {}", kernel_style)));
  compute_kernel->fix_rheo = this;

  std::string cmd = "rheo_grad all RHEO/GRAD velocity rho viscosity";
  if (thermal_flag) cmd += " energy";
  compute_grad = dynamic_cast<ComputeRHEOGrad *>(modify->add_compute(cmd));
  compute_grad->fix_rheo = this;

  if (rhosum_flag) {
    compute_rhosum = dynamic_cast<ComputeRHEORhoSum *>(
        modify->add_compute(fmt::format("rheo_rhosum all RHEO/RHO/SUM {}", rhosum_self_mass_flag)));
    compute_rhosum->fix_rheo = this;
  }

  if (shift_flag) {
    compute_vshift =
        dynamic_cast<ComputeRHEOVShift *>(modify->add_compute("rheo_vshift all RHEO/VSHIFT"));
    compute_vshift->fix_rheo = this;
  }

  if (interface_flag) {
    compute_interface = dynamic_cast<ComputeRHEOInterface *>(
        modify->add_compute("rheo_interface all RHEO/INTERFACE"));
    compute_interface->fix_rheo = this;
  }

  if (surface_flag) {
    compute_surface =
        dynamic_cast<ComputeRHEOSurface *>(modify->add_compute("rheo_surface all RHEO/SURFACE"));
    compute_surface->fix_rheo = this;
  }
}

/* ---------------------------------------------------------------------- */

int FixRHEO::setmask()
{
  int mask = 0;
  mask |= INITIAL_INTEGRATE;
  mask |= FINAL_INTEGRATE;
  mask |= PRE_FORCE;
  return mask;
}

/* ---------------------------------------------------------------------- */

void FixRHEO::init()
{
  dtv = update->dt;
  dtf = 0.5 * update->dt * force->ftm2v;

  if (modify->get_fix_by_style("^rheo$").size() > 1)
    error->all(FLERR, "Can only specify one instance of fix rheo");

  if (atom->rheo_status_flag != 1)
    error->all(FLERR, "fix rheo command requires atom property status");
  if (atom->rho_flag != 1) error->all(FLERR, "fix rheo command requires atom property rho");
  if (atom->pressure_flag != 1)
    error->all(FLERR, "fix rheo command requires atom property pressure");
  if (atom->viscosity_flag != 1)
    error->all(FLERR, "fix rheo command requires atom property viscosity");

  if (thermal_flag) {
    if (atom->esph_flag != 1)
      error->all(FLERR, "fix rheo command requires atom property esph with thermal setting");
    if (atom->temperature_flag != 1)
      error->all(FLERR, "fix rheo command requires atom property temperature with thermal setting");
    if (atom->heatflow_flag != 1)
      error->all(FLERR, "fix rheo command requires atom property heatflow with thermal setting");
    if (atom->conductivity_flag != 1)
      error->all(FLERR,
                 "fix rheo command requires atom property conductivity with thermal setting");
  }
}

/* ---------------------------------------------------------------------- */

void FixRHEO::setup_pre_force(int /*vflag*/)
{
  // Check to confirm accessory fixes do not preceed FixRHEO
  // Note: fixes set this flag in setup_pre_force()
  if (viscosity_fix_defined || pressure_fix_defined || thermal_fix_defined || oxidation_fix_defined)
    error->all(FLERR, "Fix RHEO must be defined before all other RHEO fixes");

  // Calculate surfaces
  if (surface_flag) {
    compute_kernel->compute_coordination();
    compute_surface->compute_peratom();
  }

  pre_force(0);
}

/* ---------------------------------------------------------------------- */

void FixRHEO::setup(int /*vflag*/)
{
  // Confirm all accessory fixes are defined
  // Note: fixes set this flag in setup_pre_force()
  if (!viscosity_fix_defined) error->all(FLERR, "Missing fix rheo/viscosity");

  if (!pressure_fix_defined) error->all(FLERR, "Missing fix rheo/pressure");

  if (thermal_flag && !thermal_fix_defined) error->all(FLERR, "Missing fix rheo/thermal");

  // Reset to zero for future runs
  thermal_fix_defined = 0;
  viscosity_fix_defined = 0;
  pressure_fix_defined = 0;
  oxidation_fix_defined = 0;

  if (rhosum_flag) compute_rhosum->compute_peratom();
}

/* ---------------------------------------------------------------------- */

void FixRHEO::initial_integrate(int /*vflag*/)
{
  // update v, x and rho of atoms in group
  int i, a, b;
  double dtfm, divu;

  int *type = atom->type;
  int *mask = atom->mask;
  int *status = atom->rheo_status;
  double **x = atom->x;
  double **v = atom->v;
  double **f = atom->f;
  double *rho = atom->rho;
  double *drho = atom->drho;
  double *mass = atom->mass;
  double *rmass = atom->rmass;
  double **gradr = compute_grad->gradr;
  double **gradv = compute_grad->gradv;
  double **vshift;
  if (shift_flag) vshift = compute_vshift->vshift;

  int nlocal = atom->nlocal;
  int rmass_flag = atom->rmass_flag;
  int dim = domain->dimension;

  if (igroup == atom->firstgroup) nlocal = atom->nfirst;

  //Density Half-step
  for (i = 0; i < nlocal; i++) {
    if (status[i] & STATUS_NO_INTEGRATION) continue;

    if (mask[i] & groupbit) {
      if (rmass_flag) {
        dtfm = dtf / rmass[i];
      } else {
        dtfm = dtf / mass[type[i]];
      }

      v[i][0] += dtfm * f[i][0];
      v[i][1] += dtfm * f[i][1];
      v[i][2] += dtfm * f[i][2];
    }
  }

  // Update gradients and interpolate solid properties
  compute_grad->forward_fields();    // also forwards v and rho for chi
  if (interface_flag) {
    // Need to save, wiped in exchange
    compute_interface->store_forces();
    compute_interface->compute_peratom();
  }
  compute_grad->compute_peratom();

  // Position half-step
  for (i = 0; i < nlocal; i++) {
    if (mask[i] & groupbit) {
      for (a = 0; a < dim; a++) { x[i][a] += dtv * v[i][a]; }
    }
  }

  // Update density using div(u)
  if (!rhosum_flag) {
    for (i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) {
        if (status[i] & STATUS_NO_INTEGRATION) continue;
        if (status[i] & PHASECHECK) continue;

        divu = 0;
        for (a = 0; a < dim; a++) { divu += gradv[i][a * (1 + dim)]; }
        rho[i] += dtf * (drho[i] - rho[i] * divu);
      }
    }
  }

  // Shifting atoms
  if (shift_flag) {
    for (i = 0; i < nlocal; i++) {
      if (status[i] & STATUS_NO_SHIFT) continue;
      if (status[i] & PHASECHECK) continue;

      if (mask[i] & groupbit) {
        for (a = 0; a < dim; a++) {
          x[i][a] += dtv * vshift[i][a];
          for (b = 0; b < dim; b++) { v[i][a] += dtv * vshift[i][b] * gradv[i][a * dim + b]; }
        }

        if (!rhosum_flag) {
          if (status[i] & PHASECHECK) continue;
          for (a = 0; a < dim; a++) { rho[i] += dtv * vshift[i][a] * gradr[i][a]; }
        }
      }
    }
  }
}

/* ---------------------------------------------------------------------- */

void FixRHEO::pre_force(int /*vflag*/)
{
  compute_kernel->compute_coordination();    // Needed for rho sum

  if (rhosum_flag) compute_rhosum->compute_peratom();

  compute_kernel->compute_peratom();

  if (interface_flag) {
    // Note on first setup, have no forces for pressure to reference
    compute_interface->compute_peratom();
  }

  // No need to forward v, rho, or T for compute_grad since already done
  compute_grad->compute_peratom();
  compute_grad->forward_gradients();

  if (shift_flag) compute_vshift->compute_peratom();

  // Remove temporary options
  int *mask = atom->mask;
  int *status = atom->rheo_status;
  int nall = atom->nlocal + atom->nghost;
  for (int i = 0; i < nall; i++)
    if (mask[i] & groupbit) status[i] &= OPTIONSMASK;

  // Calculate surfaces, update status
  if (surface_flag) {
    compute_surface->compute_peratom();
    if (shift_flag) compute_vshift->correct_surfaces();
  }
}

/* ---------------------------------------------------------------------- */

void FixRHEO::final_integrate()
{
  int nlocal = atom->nlocal;
  if (igroup == atom->firstgroup) nlocal = atom->nfirst;

  double dtfm, divu;
  int i, a;

  double **v = atom->v;
  double **f = atom->f;
  double **gradv = compute_grad->gradv;
  double *rho = atom->rho;
  double *drho = atom->drho;
  double *mass = atom->mass;
  double *rmass = atom->rmass;
  int *type = atom->type;
  int *mask = atom->mask;
  int *status = atom->rheo_status;

  int dim = domain->dimension;

  // Update velocity
  for (i = 0; i < nlocal; i++) {
    if (mask[i] & groupbit) {
      if (status[i] & STATUS_NO_INTEGRATION) continue;

      if (rmass) {
        dtfm = dtf / rmass[i];
      } else {
        dtfm = dtf / mass[type[i]];
      }

      for (a = 0; a < dim; a++) { v[i][a] += dtfm * f[i][a]; }
    }
  }

  // Update density using divu
  if (!rhosum_flag) {
    for (i = 0; i < nlocal; i++) {
      if (mask[i] & groupbit) {
        if (status[i] & STATUS_NO_INTEGRATION) continue;
        if (status[i] & PHASECHECK) continue;

        divu = 0;
        for (a = 0; a < dim; a++) { divu += gradv[i][a * (1 + dim)]; }
        rho[i] += dtf * (drho[i] - rho[i] * divu);
      }
    }
  }
}

/* ---------------------------------------------------------------------- */

void FixRHEO::reset_dt()
{
  dtv = update->dt;
  dtf = 0.5 * update->dt * force->ftm2v;
}