More updates for oxidation, more doc pages

doc/src/compute_nbond_atom.rst

@@ -8,10 +8,17 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   compute ID group-ID nbond/atom
+   compute ID group-ID nbond/atom keyword value
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * nbond/atom = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *bond/type*
+
+  .. parsed-literal::
+
+       *bond/type* value = *btype*
+         *btype* = bond type included in count
 
 Examples
 """"""""
@@ -19,6 +26,7 @@ Examples
 .. code-block:: LAMMPS
 
    compute 1 all nbond/atom
+   compute 1 all nbond/atom bond/type 2
 
 Description
 """""""""""
@@ -31,6 +39,9 @@ the :doc:`Howto broken bonds <Howto_bpm>` page for more information.
 The number of bonds will be zero for atoms not in the specified
 compute group. This compute does not depend on Newton bond settings.
 
+If the keyword *bond/type* is specified, only bonds of *btype* are
+counted.
+
 Output info
 """""""""""
 

doc/src/fix_rheo_pressure.rst

@@ -8,12 +8,13 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID rheo/pressure style args
+   fix ID group-ID rheo/pressure type1 pstyle1 args1 ... typeN pstyleN argsN
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * rheo/pressure = style name of this fix command
+* one or more types and pressure styles must be appended
 * types = lists of types (see below)
-* style = *linear* or *taitwater* or *cubic*
+* pstyle = *linear* or *taitwater* or *cubic*
 
   .. parsed-literal::
 
@@ -32,10 +33,41 @@ Examples
 Description
 """""""""""
 
-This fix...
+This fix defines a pressure equation of state for RHEO particles. One can
+define different equations of state for different atom types, but an
+equation must be specified for every atom type.
 
-Only one instance of fix rheo/pressure can be defined and the fix group must be set to all.
+One first defines the atom *types*. A wild-card asterisk can be used in place
+of or in conjunction with the *types* argument to set the coefficients for
+multiple pairs of atom types.  This takes the form "\*" or "\*n" or "m\*"
+or "m\*n".  If :math:`N` is the number of atom types, then an asterisk with
+no numeric values means all types from 1 to :math:`N`.  A leading asterisk
+means all types from 1 to n (inclusive).  A trailing asterisk means all types
+from m to :math:`N` (inclusive).  A middle asterisk means all types from m to n
+(inclusive).
 
+The *types* definition is followed by the pressure style, *pstyle*. Current
+options *linear*, *taitwater*, and *cubic*. Style *linear* is a linear
+equation of state with a particle pressure :math:`P` calculated as
+
+.. math::
+
+   P = c (\rho - \rho_0)
+
+where :math:`c` is the speed of sound, :math:`\rho_0` is the equilibrium density,
+and :math:`\rho` is the current density of a particle. The numerical values of
+:math:`c` and :math:`\rho_0` are set in :doc:`fix rheo <fix_rheo>`. Style *cubic*
+is a cubic equation of state which has an extra argument :math:`A_3`,
+
+.. math::
+
+   P = c ((\rho - \rho_0) + A_3 (\rho - \rho_0)^3) .
+
+Style *taitwater* is Tait's equation of state:
+
+.. math::
+
+   P = \frac{c^2 \rho_0}{7} \biggl[\left(\frac{\rho}{\rho_0}\right)^{7} - 1\biggr].
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -52,7 +84,7 @@ Restrictions
 This fix must be used with an atom style that includes density
 such as atom_style rheo or rheo/thermal. This fix must be used in
 conjuction with :doc:`fix rheo <fix_rheo>`. The fix group must be
-set to all.
+set to all. Only one instance of fix rheo/pressure can be defined.
 
 This fix is part of the RHEO package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
@@ -60,8 +92,7 @@ LAMMPS was built with that package.  See the :doc:`Build package <Build_package>
 Related commands
 """"""""""""""""
 
-:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
+:doc:`fix rheo <fix_rheo>`,
-:doc:`fix rheo/thermal <fix_rheo_thermal>`,
 :doc:`pair rheo <pair_rheo>`,
 :doc:`compute rheo/property/atom <compute_rheo_property_atom>`
 

doc/src/fix_rheo_thermal.rst

@@ -48,26 +48,38 @@ Examples
 Description
 """""""""""
 
-This fix...
+This fix performs time integration of temperature evolution for atom style
+rheo/thermal. In addition, it  defines multiple thermal properties of
+particles and handles melting/solidification, if applicable. For more details
+on phase transitions in RHEO, see :doc:`the RHEO howto <Howto_rheo>`.
 
-Each list consists of a series of type
+For each atom type, one can define attributes for the *conductivity*,
-ranges separated by commas. The range can be specified as a
+*specific/heat*, *latent/heat*, and critical temperature (*Tfreeze*).
-single numeric value, or a wildcard asterisk can be used to specify a range
+The conductivity and specific heat must be defined for all atom types.
-of values.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  For
+The latent heat and critical temperature are optional. However, a
-example, if M = the number of atom types, then an asterisk with no numeric
+critical temperature must be defined to specify a latent heat.
-values means all types from 1 to M.  A leading asterisk means all types
-from 1 to n (inclusive).  A trailing asterisk means all types from n to M
-(inclusive).  A middle asterisk means all types from m to n (inclusive).
-Note that all atom types must be included in exactly one of the N collections.
 
-While the *Tfreeze* keyword is optional, the *conductivity* and
+For each property, one must first define a list of atom types. A wild-card
-*specific/heat* keywords are mandatory.
+asterisk can be used in place of or in conjunction with the *types* argument
+to set the coefficients for multiple pairs of atom types.  This takes the
+form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is the number of atom
+types, then an asterisk with no numeric values means all types from 1 to
+:math:`N`.  A leading asterisk means all types from 1 to n (inclusive).
+A trailing asterisk means all types from m to :math:`N` (inclusive).  A
+middle asterisk means all types from m to n (inclusive).
 
-Multiple instances of this fix may be defined to apply different
+The *types* definition for each property is followed by the style. Currently,
-properties to different groups. However, the union of fix groups
+the only option is *constant*. Style *constant* simply applies a constant value
-across all instances of fix rheo/thermal must cover all atoms.
+of respective property to each particle of the assigned type.
-If there are multiple instances of this fix, any intersections in
+
-the fix groups will lead to incorrect thermal integration.
+The *react* keyword controls whether bonds are created/deleted when particles
+transition between a fluid and solid state. This option only applies to atom
+types that have a defined value of *Tfreeze*. When a fluid particle's
+temperature drops below *Tfreeze*, bonds of type *btype* are created between
+nearby solid particles within a distance of *cut*. The particle's status also
+swaps to a solid state. When a solid particle's temperature rises above
+*Tfreeze*, all bonds of type *btype* are broken and the particle's tatus swaps
+to a fluid state.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -84,7 +96,8 @@ Restrictions
 This fix must be used with an atom style that includes temperature,
 heatflow, and conductivity such as atom_tyle rheo/thermal This fix
 must be used in conjuction with :doc:`fix rheo <fix_rheo>` with the
-*thermal* setting.
+*thermal* setting. The fix group must be set to all. Only one
+instance of fix rheo/pressure can be defined.
 
 This fix is part of the RHEO package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
@@ -93,8 +106,6 @@ Related commands
 """"""""""""""""
 
 :doc:`fix rheo <fix_rheo>`,
-:doc:`fix rheo/viscosity <fix_rheo_viscosity>`,
-:doc:`fix rheo/pressure <fix_rheo_pressure>`,
 :doc:`pair rheo <pair_rheo>`,
 :doc:`compute rheo/property/atom <compute_rheo_property_atom>`
 

doc/src/fix_rheo_viscosity.rst

@@ -8,22 +8,18 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID rheo/viscosity types style args ...
+   fix ID group-ID rheo/viscosity type1 pstyle1 args1 ... typeN pstyleN argsN
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * rheo/viscosity = style name of this fix command
+* one or more types and viscosity styles must be appended
 * types = lists of types (see below)
-* style = *constant* or *power*
+* vstyle = *constant*
 
   .. parsed-literal::
 
-       *constant* args = viscosity (mass/(length*time))
+       *constant* args = *eta*
-       *power* args = *eta* *gd0* *K* *npow* *tau0*
+         *eta* = viscosity
-         *eta* = (units)
-         *gd0* = (units)
-         *K* = (units)
-         *npow* = (units)
-         *tau0* = (units)
 
 Examples
 """"""""
@@ -31,20 +27,27 @@ Examples
 .. code-block:: LAMMPS
 
    fix 1 all rheo/viscosity * constant 1.0
-   fix 1 all rheo/viscosity 1 constant 1.0 2 power 0.1 1e-2 0.5 0.01
+   fix 1 all rheo/viscosity 1 constant 1.0 2 constant 2.0
 
 Description
 """""""""""
 
-This fix...
+This fix defines a viscosity for RHEO particles. One can define different
+viscosities for different atom types, but a viscosity must be specified for
+every atom type.
 
-Multiple instances of this fix may be defined to apply different
+One first defines the atom *types*. A wild-card asterisk can be used in place
-properties to different groups. However, the union of fix groups
+of or in conjunction with the *types* argument to set the coefficients for
-across all instances of fix rheo/viscosity must cover all atoms.
+multiple pairs of atom types.  This takes the form "\*" or "\*n" or "m\*"
-If there are multiple instances of this fix, any intersection
+or "m\*n".  If :math:`N` is the number of atom types, then an asterisk with
-between fix groups will cause the viscosity for the affected atoms
+no numeric values means all types from 1 to :math:`N`.  A leading asterisk
-to be calculated multiple times. Any such affected atoms will enabled
+means all types from 1 to n (inclusive).  A trailing asterisk means all types
-up with a viscosity calculated by the latest defined fix.
+from m to :math:`N` (inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+The *types* definition is followed by the viscosity style, *vstyle*. Currently,
+the only option is *constant*. Style *constant* simply applies a constant value
+of the viscosity *eta* to each particle of the assigned type.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -60,7 +63,8 @@ Restrictions
 
 This fix must be used with an atom style that includes viscosity
 such as atom_style rheo or rheo/thermal. This fix must be used in
-conjuction with :doc:`fix rheo <fix_rheo>`.
+conjuction with :doc:`fix rheo <fix_rheo>`. The fix group must be
+set to all. Only one instance of fix rheo/viscosity can be defined.
 
 This fix is part of the RHEO package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
@@ -69,8 +73,6 @@ Related commands
 """"""""""""""""
 
 :doc:`fix rheo <fix_rheo>`,
-:doc:`fix rheo/pressure <fix_rheo_pressure>`,
-:doc:`fix rheo/thermal <fix_rheo_thermal>`,
 :doc:`pair rheo <pair_rheo>`,
 :doc:`compute rheo/property/atom <compute_rheo_property_atom>`
 

src/BPM/compute_nbond_atom.cpp

@@ -25,7 +25,20 @@ using namespace LAMMPS_NS;
 ComputeNBondAtom::ComputeNBondAtom(LAMMPS *_lmp, int narg, char **arg) :
     Compute(_lmp, narg, arg), nbond(nullptr)
 {
-  if (narg < 3) utils::missing_cmd_args(FLERR, "compute nbond/atom", error);
+  if (narg < 4) utils::missing_cmd_args(FLERR, "compute nbond/atom", error);
+
+  btype = -1;
+
+  iarg = 3;
+  while (iarg < narg) {
+    if (strcmp(arg[iarg], "bond/type") == 0) {
+      if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "compute nbond/atom bond/type", error);
+      btype = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
+      iarg += 2;
+    } else {
+      error->all(FLERR, "Unknown compute nbond/type command {}", arg[iarg]);
+    }
+  }
 
   peratom_flag = 1;
   size_peratom_cols = 0;
@@ -78,6 +91,7 @@ void ComputeNBondAtom::compute_peratom()
   for (i = 0; i < nlocal; i++) {
     for (j = 0; j < num_bond[i]; j++) {
       if (bond_type[i][j] <= 0) continue;
+      if (btype != -1 && bond_type[i][j] != btype) continue;
 
       k = atom->map(bond_atom[i][j]);
       if (k < 0) continue;

src/BPM/compute_nbond_atom.h

@@ -35,7 +35,7 @@ class ComputeNBondAtom : public Compute {
   double memory_usage() override;
 
  private:
-  int nmax;
+  int nmax, btype;
   double *nbond;
 };
 

src/RHEO/bond_rheo_shell.cpp

@@ -20,6 +20,7 @@
 
 #include "atom.h"
 #include "comm.h"
+#include "compute_rheo_surface.h"
 #include "domain.h"
 #include "error.h"
 #include "fix_bond_history.h"
@@ -42,7 +43,7 @@ using namespace RHEO_NS;
 /* ---------------------------------------------------------------------- */
 
 BondRHEOShell::BondRHEOShell(LAMMPS *_lmp) :
-    BondBPM(_lmp), k(nullptr), ecrit(nullptr), gamma(nullptr)
+    BondBPM(_lmp), compute_surface(nullptr), k(nullptr), ecrit(nullptr), gamma(nullptr)
 {
   partial_flag = 1;
   comm_reverse = 1;
@@ -279,7 +280,7 @@ void BondRHEOShell::compute(int eflag, int vflag)
   // Communicate changes in nbond
   if (newton_bond) comm->reverse_comm(this);
 
-  for(i = 0; i < nlocal; i++) {
+  for(int i = 0; i < nlocal; i++) {
     nbond[i] += dbond[i];
 
     // If it has bonds, no shifting
@@ -341,6 +342,18 @@ void BondRHEOShell::init_style()
   if (comm->ghost_velocity == 0)
     error->all(FLERR, "Bond rheo/shell requires ghost atoms store velocity");
 
+  auto fixes = modify->get_fix_by_style("^rheo$");
+  if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use bond rheo/shell");
+  class FixRHEO *fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
+
+  if (!fix_rheo->surface_flag) error->all(FLERR,
+      "Bond rheo/shell requires surface calculation in fix rheo");
+  compute_surface = fix_rheo->compute_surface;
+
+  if (fix_rheo->oxidation_fix_defined != 1)
+    error->all(FLERR, "Need to define fix rheo/oxdiation to use bond rheo/shell");
+  // check consistency in values (copy?), swap conditions to rsurf
+
   if (!id_fix_bond_history) {
     id_fix_bond_history = utils::strdup("HISTORY_RHEO_SHELL");
     fix_bond_history = dynamic_cast<FixBondHistory *>(modify->replace_fix(

src/RHEO/bond_rheo_shell.h

@@ -49,6 +49,8 @@ class BondRHEOShell : public BondBPM {
   int index_nb, nmax_store;
   char *id_fix;
 
+  class ComputeRHEOSurface *compute_surface;
+
   void process_ineligibility(int, int);
   void allocate();
   void store_data();

src/RHEO/compute_rheo_property_atom.cpp

@@ -29,6 +29,7 @@
 #include "domain.h"
 #include "error.h"
 #include "fix_rheo.h"
+#include "fix_rheo_oxidation.h"
 #include "fix_rheo_pressure.h"
 #include "fix_rheo_thermal.h"
 #include "memory.h"
@@ -177,6 +178,11 @@ void ComputeRHEOPropertyAtom::init()
     fixes = modify->get_fix_by_style("rheo/pressure");
     fix_pressure = dynamic_cast<FixRHEOPressure *>(fixes[0]);
   }
+
+  if (shell_flag) {
+    fixes = modify->get_fix_by_style("rheo/oxidation");
+    fix_oxidation = dynamic_cast<FixRHEOOxidation *>(fixes[0]);
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -381,6 +387,21 @@ void ComputeRHEOPropertyAtom::pack_pressure(int n)
 
 /* ---------------------------------------------------------------------- */
 
+void ComputeRHEOPropertyAtom::pack_nbond_shell(int n)
+{
+  int *nbond = fix_oxidation->nbond;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+
+  for (int i = 0; i < nlocal; i++) {
+    if (mask[i] & groupbit) buf[n] = nbond[i];
+    else buf[n] = 0.0;
+    n += nvalues;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
 void ComputeRHEOPropertyAtom::pack_shift_v(int n)
 {
   double **vshift = compute_vshift->vshift;
@@ -415,7 +436,7 @@ void ComputeRHEOPropertyAtom::pack_gradv(int n)
 
 void ComputeRHEOPropertyAtom::pack_atom_style(int n)
 {
-  atom->avec->pack_property_atom(avec_index[n],&buf[n],nvalues,groupbit);
+  atom->avec->pack_property_atom(avec_index[n], &buf[n], nvalues, groupbit);
 }
 
 /* ---------------------------------------------------------------------- */

src/RHEO/compute_rheo_property_atom.h

@@ -63,6 +63,7 @@ class ComputeRHEOPropertyAtom : public Compute {
   class FixRHEO *fix_rheo;
   class FixRHEOPressure *fix_pressure;
   class FixRHEOThermal *fix_thermal;
+  class FixRHEOOxidation *fix_oxidation;
   class ComputeRHEOInterface *compute_interface;
   class ComputeRHEOKernel *compute_kernel;
   class ComputeRHEOSurface *compute_surface;

src/RHEO/fix_rheo.cpp

@@ -48,12 +48,14 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
   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;
+  oxidation_flag = 0;
 
   int i;
   int n = atom->ntypes;
@@ -252,6 +254,7 @@ void FixRHEO::setup(int /*vflag*/)
   thermal_fix_defined = 0;
   viscosity_fix_defined = 0;
   pressure_fix_defined = 0;
+  oxidation_fix_defined = 0;
 
   // Check fixes cover all atoms (may still fail if atoms are created)
   // FixRHEOPressure currently requires group all

src/RHEO/fix_rheo.h

@@ -51,6 +51,7 @@ class FixRHEO : public Fix {
   int shift_flag;
   int interface_flag;
   int surface_flag;
+  int oxidation_flag;
 
   int viscosity_fix_defined;
   int pressure_fix_defined;

src/RHEO/fix_rheo_oxidation.cpp

@@ -20,6 +20,7 @@
 
 #include "atom.h"
 #include "atom_vec.h"
+#include "compute_rheo_surface.h"
 #include "error.h"
 #include "fix_rheo.h"
 #include "force.h"
@@ -36,9 +37,9 @@ enum {NONE, CONSTANT};
 /* ---------------------------------------------------------------------- */
 
 FixRHEOOxidation::FixRHEOOxidation(LAMMPS *lmp, int narg, char **arg) :
-  Fix(lmp, narg, arg) //, fix_bond_history(nullptr)
+  Fix(lmp, narg, arg), compute_surface(nullptr), fix_rheo(nullptr)
 {
-  if (narg != 5) error->all(FLERR,"Illegal fix command");
+  if (narg != 6) error->all(FLERR,"Illegal fix command");
 
   cut = utils::numeric(FLERR, arg[3], false, lmp);
   if (cut <= 0.0) error->all(FLERR, "Illegal bond cutoff {} in fix rheo/oxidation", cut);
@@ -46,6 +47,9 @@ FixRHEOOxidation::FixRHEOOxidation(LAMMPS *lmp, int narg, char **arg) :
   btype = utils::inumeric(FLERR, arg[4], false, lmp);
   if (btype < 1 || btype > atom->nbondtypes) error->all(FLERR, "Illegal value {} for bond type in fix rheo/oxidation", btype);
 
+  rsurf = utils::numeric(FLERR, arg[5], false, lmp);
+  if (rsurf <= 0.0) error->all(FLERR, "Illegal surface distance {} in fix rheo/oxidation", cut);
+
   cutsq = cut * cut;
 }
 
@@ -72,22 +76,21 @@ void FixRHEOOxidation::init()
   auto fixes = modify->get_fix_by_style("^rheo$");
   if (fixes.size() == 0) error->all(FLERR, "Need to define fix rheo to use fix rheo/oxidation");
   fix_rheo = dynamic_cast<FixRHEO *>(fixes[0]);
-  double cut_kernel = fix_rheo->h;
 
-  if (cut > cut_kernel)
+  if (cut > fix_rheo->h)
     error->all(FLERR, "Bonding length exceeds kernel cutoff");
 
+  if (rsurf >= fix_rheo->h)
+    error->all(FLERR, "Surface distance must be less than kernel cutoff");
+
   if (!force->bond) error->all(FLERR, "Must define a bond style with fix rheo/oxidation");
   if (!atom->avec->bonds_allow) error->all(FLERR, "Fix rheo/oxidation requires atom bonds");
 
-  //// find instances of bond history to delete data
+  int tmp1, tmp2;
-  //histories = modify->get_fix_by_style("BOND_HISTORY");
+  index_nb = atom->find_custom("shell_nbond", tmp1, tmp2);
-  //for (auto &ihistory: histories)
+  if (index_nb == -1)
-  //  if (strcmp(histories[i]->id, "HISTORY_RHEO_SHELL") == 0)
+    error->all(FLERR, "Must use bond style rheo/shell to use fix rheo/oxidation");
-  //    fix_bond_history = dynamic_cast<FixBondHistory *>(ihistory);
+  nbond = atom->ivector[index_nb];
-//
-  //if (!fix_bond_history)
-  //  error->all(FLERR, "Must define bond style rheo/shell to use fix rheo/oxidation");
 
   // need a half neighbor list
   auto req = neighbor->add_request(this, NeighConst::REQ_DEFAULT);
@@ -111,13 +114,14 @@ void FixRHEOOxidation::setup_pre_force(int /*vflag*/)
 
   if (!fix_rheo->surface_flag) error->all(FLERR,
       "fix rheo/oxidation requires surface calculation in fix rheo");
+  compute_surface = fix_rheo->compute_surface;
 
   pre_force(0);
 }
 
 /* ---------------------------------------------------------------------- */
 
-void FixRHEOThermal::pre_force(int /*vflag*/)
+void FixRHEOOxidation::pre_force(int /*vflag*/)
 {
 }
 
@@ -135,9 +139,9 @@ void FixRHEOOxidation::post_integrate()
 
   tagint *tag = atom->tag;
   tagint **bond_atom = atom->bond_atom;
-  int *status = atom->status;
   int **bond_type = atom->bond_type;
   int *num_bond = atom->num_bond;
+  double *rsurface = compute_surface->rsurface;
   double **x = atom->x;
 
   inum = list->inum;
@@ -148,7 +152,7 @@ void FixRHEOOxidation::post_integrate()
   // loop over neighbors of my atoms
   for (ii = 0; ii < inum; ii++) {
     i = ilist[ii];
-    if (!(status[i] & STATUS_SURFACE)) continue;
+    if (rsurface[i] > rsurf) continue;
 
     tagi = tag[i];
     xtmp = x[i][0];
@@ -162,7 +166,7 @@ void FixRHEOOxidation::post_integrate()
       j = jlist[jj];
       j &= NEIGHMASK;
 
-      if (!(status[j] & STATUS_SURFACE)) continue;
+      if (rsurface[j] > rsurf) continue;
 
       tagj = tag[j];
       delx = xtmp - x[j][0];
@@ -208,10 +212,4 @@ void FixRHEOOxidation::post_integrate()
       }
     }
   }
-
-  //todo:
-  // allow option to create near-surface bonds
-  // extract # of bonds in property/atom
-  // check bond style shell used, get index to bonds, share with compute property atom
-  // add type option to compute nbond/atom
 }

src/RHEO/fix_rheo_oxidation.h

@@ -36,14 +36,15 @@ class FixRHEOOxidation : public Fix {
   void setup_pre_force(int) override;
   void pre_force(int) override;
   void post_integrate() override;
+  int *nbond;
 
  private:
-  int btype;
+  int btype, index_nb;
-  double cut, cutsq;
+  double rsurf, cut, cutsq;
   class NeighList *list;
 
+  class ComputeRHEOSurface *compute_surface;
   class FixRHEO *fix_rheo;
-  //class FixBondHistory *fix_bond_history;
 };
 
 }    // namespace LAMMPS_NS