Bug in rheo, cleaning up old files

src/RHEO/fix_rheo.cpp

@@ -94,11 +94,11 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
     } else if (strcmp(arg[iarg],"surface/detection") == 0) {
       surface_flag = 1;
       if(iarg + 2 >= narg) error->all(FLERR,"Illegal surface/detection option in fix rheo");
-      if (strcmp(arg[iarg + 1], "coordination")) {
+      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")) {
+      } 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);

src/atom_vec_rheo_thermal.cpp

@@ -1,200 +0,0 @@
-/* ----------------------------------------------------------------------
- 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 "atom_vec_rheo_thermal.h"
-
-#include "atom.h"
-
-#include <cstring>
-
-using namespace LAMMPS_NS;
-
-/* ---------------------------------------------------------------------- */
-
-AtomVecRHEOThermal::AtomVecRHEOThermal(LAMMPS *lmp) : AtomVec(lmp)
-{
-  molecular = Atom::ATOMIC;
-  mass_type = PER_TYPE;
-  forceclearflag = 1;
-
-  atom->status_flag = 1;
-  atom->conductivity_flag = 1;
-  atom->temperature_flag = 1;
-  atom->heatflow_flag = 1;
-  atom->pressure_flag = 1;
-  atom->rho_flag = 1;
-  atom->viscosity_flag = 1;
-
-  // strings with peratom variables to include in each AtomVec method
-  // strings cannot contain fields in corresponding AtomVec default strings
-  // order of fields in a string does not matter
-  // except: fields_data_atom & fields_data_vel must match data file
-
-  fields_grow = {"status", "rho", "drho", "temperature", "heatflow", "conductivity", "pressure", "viscosity"};
-  fields_copy = {"status", "rho", "drho", "temperature", "heatflow", "conductivity", "pressure", "viscosity"};
-  fields_comm = {"status", "rho", "temperature"};
-  fields_comm_vel = {"status", "rho", "temperature"};
-  fields_reverse = {"drho", "heatflow"};
-  fields_border = {"status", "rho", "temperature"};
-  fields_border_vel = {"status", "rho", "temperature"};
-  fields_exchange = {"status", "rho", "temperature"};
-  fields_restart = {"status", "rho", "temperature"};
-  fields_create = {"status", "rho", "drho", "temperature", "heatflow", "conductivity", "pressure", "viscosity"};
-  fields_data_atom = {"id", "type", "status", "rho", "temperature", "x"};
-  fields_data_vel = {"id", "v"};
-
-  setup_fields();
-}
-
-/* ----------------------------------------------------------------------
-   set local copies of all grow ptrs used by this class, except defaults
-   needed in replicate when 2 atom classes exist and it calls pack_restart()
-------------------------------------------------------------------------- */
-
-void AtomVecRHEOThermal::grow_pointers()
-{
-  status = atom->status;
-  conductivity = atom->conductivity;
-  temperature = atom->temperature;
-  heatflow = atom->heatflow;
-  pressure = atom->pressure;
-  rho = atom->rho;
-  drho = atom->drho;
-  viscosity = atom->viscosity;
-}
-
-/* ----------------------------------------------------------------------
-   clear extra forces starting at atom N
-   nbytes = # of bytes to clear for a per-atom vector
-------------------------------------------------------------------------- */
-
-void AtomVecRHEOThermal::force_clear(int n, size_t nbytes)
-{
-  memset(&drho[n], 0, nbytes);
-  memset(&heatflow[n], 0, nbytes);
-}
-
-/* ----------------------------------------------------------------------
-   modify what AtomVec::data_atom() just unpacked
-   or initialize other atom quantities
-------------------------------------------------------------------------- */
-
-void AtomVecRHEOThermal::data_atom_post(int ilocal)
-{
-  drho[ilocal] = 0.0;
-  heatflow[ilocal] = 0.0;
-  pressure[ilocal] = 0.0;
-  viscosity[ilocal] = 0.0;
-  conductivity[ilocal] = 0.0;
-}
-
-/* ----------------------------------------------------------------------
-   assign an index to named atom property and return index
-   return -1 if name is unknown to this atom style
-------------------------------------------------------------------------- */
-
-int AtomVecRHEOThermal::property_atom(const std::string &name)
-{
-  if (name == "status") return 0;
-  if (name == "rho") return 1;
-  if (name == "drho") return 2;
-  if (name == "temperature") return 3;
-  if (name == "heatflow") return 4;
-  if (name == "conductivity") return 5;
-  if (name == "pressure") return 6;
-  if (name == "viscosity") return 7;
-  return -1;
-}
-
-/* ----------------------------------------------------------------------
-   pack per-atom data into buf for ComputePropertyAtom
-   index maps to data specific to this atom style
-------------------------------------------------------------------------- */
-
-void AtomVecRHEOThermal::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
-{
-  int *mask = atom->mask;
-  int nlocal = atom->nlocal;
-  int n = 0;
-
-  if (index == 0) {
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit)
-        buf[n] = status[i];
-      else
-        buf[n] = 0.0;
-      n += nvalues;
-    }
-  } else if (index == 1) {
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit)
-        buf[n] = rho[i];
-      else
-        buf[n] = 0.0;
-      n += nvalues;
-    }
-  } else if (index == 2) {
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit)
-        buf[n] = drho[i];
-      else
-        buf[n] = 0.0;
-      n += nvalues;
-    }
-  } else if (index == 3) {
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit)
-        buf[n] = temperature[i];
-      else
-        buf[n] = 0.0;
-      n += nvalues;
-    }
-  } else if (index == 4) {
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit)
-        buf[n] = heatflow[i];
-      else
-        buf[n] = 0.0;
-      n += nvalues;
-    }
-  } else if (index == 5) {
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit)
-        buf[n] = conductivity[i];
-      else
-        buf[n] = 0.0;
-      n += nvalues;
-    }
-  } else if (index == 6) {
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit)
-        buf[n] = pressure[i];
-      else
-        buf[n] = 0.0;
-      n += nvalues;
-    }
-  } else if (index == 7) {
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit)
-        buf[n] = viscosity[i];
-      else
-        buf[n] = 0.0;
-      n += nvalues;
-    }
-  }
-}

src/atom_vec_rheo_thermal.h

@@ -1,46 +0,0 @@
-/* -*- c++ -*- ----------------------------------------------------------
-   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.
-------------------------------------------------------------------------- */
-
-#ifdef ATOM_CLASS
-// clang-format off
-AtomStyle(rheo/thermal,AtomVecRHEOThermal);
-// clang-format on
-#else
-
-#ifndef LMP_ATOM_VEC_RHEO_THERMAL_H
-#define LMP_ATOM_VEC_RHEO_THERMAL_H
-
-#include "atom_vec.h"
-
-namespace LAMMPS_NS {
-
-class AtomVecRHEOThermal : virtual public AtomVec {
- public:
-  AtomVecRHEOThermal(class LAMMPS *);
-
-  void grow_pointers() override;
-  void force_clear(int, size_t) override;
-  void data_atom_post(int) override;
-  int property_atom(const std::string &) override;
-  void pack_property_atom(int, double *, int, int) override;
-
- private:
-  int *status;
-  double *conductivity, *temperature, *heatflow;
-  double *pressure, *rho, *drho, *viscosity;
-};
-
-}    // namespace LAMMPS_NS
-
-#endif
-#endif